Query 007642
Match_columns 595
No_of_seqs 477 out of 1705
Neff 7.3
Searched_HMMs 46136
Date Thu Mar 28 13:23:30 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/007642.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/007642hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG1815 Predicted E3 ubiquitin 100.0 1.8E-71 4E-76 604.1 28.5 437 69-529 2-441 (444)
2 KOG1812 Predicted E3 ubiquitin 100.0 6.9E-34 1.5E-38 301.9 11.0 205 140-353 145-355 (384)
3 KOG1814 Predicted E3 ubiquitin 100.0 8.2E-33 1.8E-37 282.3 9.3 196 138-337 181-405 (445)
4 KOG0006 E3 ubiquitin-protein l 99.9 1.3E-23 2.9E-28 207.3 8.9 195 137-338 217-437 (446)
5 smart00647 IBR In Between Ring 99.2 2E-11 4.3E-16 97.0 6.0 63 213-275 1-64 (64)
6 PF01485 IBR: IBR domain; Int 99.1 2E-11 4.3E-16 97.0 0.8 63 213-275 1-64 (64)
7 PF15227 zf-C3HC4_4: zinc fing 98.7 6.6E-09 1.4E-13 75.5 3.2 40 144-190 1-40 (42)
8 PF13923 zf-C3HC4_2: Zinc fing 98.3 5.9E-07 1.3E-11 64.2 2.8 31 144-176 1-32 (39)
9 KOG0320 Predicted E3 ubiquitin 98.3 5.9E-07 1.3E-11 83.8 3.2 54 138-202 128-181 (187)
10 PF00097 zf-C3HC4: Zinc finger 98.2 9.7E-07 2.1E-11 63.6 3.0 38 144-190 1-39 (41)
11 PF13639 zf-RING_2: Ring finge 98.2 7.5E-07 1.6E-11 65.3 2.1 41 143-194 2-43 (44)
12 PLN03208 E3 ubiquitin-protein 98.2 1.4E-06 3E-11 83.5 3.8 65 138-206 15-86 (193)
13 PF13445 zf-RING_UBOX: RING-ty 98.1 1.8E-06 3.9E-11 62.8 2.4 41 144-190 1-43 (43)
14 KOG4367 Predicted Zn-finger pr 97.9 5.6E-05 1.2E-09 79.1 10.7 34 140-175 3-36 (699)
15 PF13920 zf-C3HC4_3: Zinc fing 97.9 8.9E-06 1.9E-10 61.4 3.2 46 141-199 2-48 (50)
16 PF01485 IBR: IBR domain; Int 97.9 7.5E-06 1.6E-10 64.7 2.5 37 299-336 18-58 (64)
17 KOG2177 Predicted E3 ubiquitin 97.9 7.2E-06 1.6E-10 84.2 3.0 110 139-275 11-122 (386)
18 smart00647 IBR In Between Ring 97.9 1.9E-05 4.1E-10 62.4 4.4 38 298-336 17-58 (64)
19 cd00162 RING RING-finger (Real 97.8 1.9E-05 4.2E-10 57.1 3.4 43 143-197 1-44 (45)
20 PF14634 zf-RING_5: zinc-RING 97.8 1.5E-05 3.4E-10 58.4 2.9 42 143-195 1-43 (44)
21 smart00504 Ubox Modified RING 97.8 2.6E-05 5.5E-10 61.6 3.7 47 142-201 2-48 (63)
22 KOG0823 Predicted E3 ubiquitin 97.8 1.4E-05 3.1E-10 77.9 2.7 56 138-203 44-99 (230)
23 TIGR00599 rad18 DNA repair pro 97.8 2E-05 4.3E-10 84.2 4.0 66 139-217 24-90 (397)
24 KOG0317 Predicted E3 ubiquitin 97.7 3.2E-05 6.9E-10 77.7 4.5 52 139-203 237-288 (293)
25 KOG0287 Postreplication repair 97.7 2.1E-05 4.6E-10 80.0 2.4 64 140-216 22-86 (442)
26 KOG2164 Predicted E3 ubiquitin 97.6 2.9E-05 6.2E-10 83.6 2.0 60 141-208 186-245 (513)
27 smart00184 RING Ring finger. E 97.6 5.7E-05 1.2E-09 52.6 2.8 30 144-175 1-30 (39)
28 PHA02926 zinc finger-like prot 97.6 5.8E-05 1.3E-09 73.2 3.6 56 139-199 168-230 (242)
29 PHA02929 N1R/p28-like protein; 97.5 6.4E-05 1.4E-09 75.1 3.8 50 139-199 172-227 (238)
30 KOG0804 Cytoplasmic Zn-finger 97.4 0.0063 1.4E-07 64.7 16.5 116 70-199 86-222 (493)
31 PF04564 U-box: U-box domain; 97.0 0.00058 1.3E-08 55.8 3.5 50 140-201 3-52 (73)
32 KOG0978 E3 ubiquitin ligase in 97.0 0.00021 4.5E-09 80.6 0.9 54 140-205 642-695 (698)
33 TIGR00570 cdk7 CDK-activating 96.9 0.00087 1.9E-08 69.1 3.9 51 142-203 4-58 (309)
34 COG5574 PEX10 RING-finger-cont 96.6 0.0015 3.1E-08 65.2 3.3 53 140-203 214-266 (271)
35 PF14835 zf-RING_6: zf-RING of 96.5 0.00073 1.6E-08 53.0 0.4 43 141-198 7-50 (65)
36 PF11789 zf-Nse: Zinc-finger o 96.4 0.0026 5.5E-08 49.4 2.9 47 140-195 10-57 (57)
37 KOG4628 Predicted E3 ubiquitin 96.3 0.0051 1.1E-07 64.5 5.3 48 142-199 230-278 (348)
38 PF12678 zf-rbx1: RING-H2 zinc 96.2 0.0047 1E-07 50.5 3.4 43 142-195 20-73 (73)
39 COG5432 RAD18 RING-finger-cont 96.1 0.0035 7.6E-08 62.9 2.7 64 140-216 24-88 (391)
40 KOG1002 Nucleotide excision re 96.1 0.0032 6.9E-08 67.8 2.3 56 138-201 533-588 (791)
41 COG5540 RING-finger-containing 96.0 0.0039 8.5E-08 63.0 2.7 51 140-200 322-373 (374)
42 PF14555 UBA_4: UBA-like domai 95.9 0.018 3.8E-07 42.0 4.8 41 80-120 1-41 (43)
43 COG5243 HRD1 HRD ubiquitin lig 95.7 0.026 5.7E-07 58.7 7.0 50 139-199 285-345 (491)
44 PF00641 zf-RanBP: Zn-finger i 95.6 0.0048 1E-07 41.3 0.8 26 570-595 3-28 (30)
45 smart00547 ZnF_RBZ Zinc finger 95.4 0.0091 2E-07 38.4 1.5 24 571-594 2-25 (26)
46 KOG0824 Predicted E3 ubiquitin 94.6 0.018 3.9E-07 58.6 2.0 53 140-204 6-58 (324)
47 PF14570 zf-RING_4: RING/Ubox 94.6 0.032 6.9E-07 41.5 2.7 45 144-198 1-47 (48)
48 KOG2879 Predicted E3 ubiquitin 94.5 0.036 7.8E-07 55.7 3.8 52 139-200 237-288 (298)
49 KOG1814 Predicted E3 ubiquitin 94.5 0.041 8.9E-07 58.2 4.4 42 296-338 270-313 (445)
50 PF11793 FANCL_C: FANCL C-term 94.5 0.023 5.1E-07 46.0 2.0 58 141-200 2-67 (70)
51 KOG4159 Predicted E3 ubiquitin 94.2 0.051 1.1E-06 58.5 4.4 49 139-200 82-130 (398)
52 COG5152 Uncharacterized conser 94.0 0.024 5.1E-07 54.1 1.4 32 141-174 196-227 (259)
53 KOG0311 Predicted E3 ubiquitin 94.0 0.0087 1.9E-07 62.0 -1.7 48 140-198 42-89 (381)
54 KOG2660 Locus-specific chromos 93.6 0.031 6.7E-07 57.7 1.4 47 140-199 14-61 (331)
55 KOG1039 Predicted E3 ubiquitin 93.3 0.061 1.3E-06 56.8 3.0 58 137-198 157-220 (344)
56 KOG0006 E3 ubiquitin-protein l 92.5 0.24 5.2E-06 50.7 5.8 95 160-272 341-438 (446)
57 PF12861 zf-Apc11: Anaphase-pr 92.2 0.14 3.1E-06 42.8 3.2 35 157-199 48-82 (85)
58 PRK00420 hypothetical protein; 92.1 1.6 3.5E-05 38.6 9.8 27 299-335 23-49 (112)
59 KOG0802 E3 ubiquitin ligase [P 92.0 0.072 1.6E-06 60.3 1.6 47 141-198 291-340 (543)
60 KOG1645 RING-finger-containing 91.9 0.18 4E-06 53.3 4.4 50 141-199 4-56 (463)
61 KOG1812 Predicted E3 ubiquitin 91.7 0.083 1.8E-06 57.1 1.7 42 228-273 304-345 (384)
62 KOG1734 Predicted RING-contain 91.2 0.15 3.2E-06 51.2 2.6 71 121-200 204-282 (328)
63 PF04931 DNA_pol_phi: DNA poly 91.2 0.34 7.4E-06 57.4 6.2 20 96-115 764-783 (784)
64 KOG2817 Predicted E3 ubiquitin 89.8 1.2 2.7E-05 47.3 8.1 55 140-202 333-388 (394)
65 PF10571 UPF0547: Uncharacteri 89.8 0.18 4E-06 32.5 1.3 24 300-328 1-24 (26)
66 KOG4692 Predicted E3 ubiquitin 89.1 0.28 6E-06 50.9 2.7 53 135-200 416-468 (489)
67 KOG4265 Predicted E3 ubiquitin 88.8 0.35 7.5E-06 50.7 3.2 65 123-200 269-337 (349)
68 TIGR00570 cdk7 CDK-activating 87.7 6.8 0.00015 40.9 11.7 34 300-335 4-37 (309)
69 KOG0317 Predicted E3 ubiquitin 87.0 0.1 2.2E-06 53.0 -1.9 38 296-340 236-273 (293)
70 smart00744 RINGv The RING-vari 86.8 0.63 1.4E-05 34.9 2.7 43 143-194 1-48 (49)
71 KOG0826 Predicted E3 ubiquitin 86.7 1.7 3.6E-05 45.2 6.5 47 141-198 300-347 (357)
72 PF13248 zf-ribbon_3: zinc-rib 85.5 0.41 8.9E-06 30.8 1.0 11 300-310 3-13 (26)
73 PF13240 zinc_ribbon_2: zinc-r 85.5 0.4 8.6E-06 30.1 0.9 10 301-310 1-10 (23)
74 KOG1813 Predicted E3 ubiquitin 84.9 0.34 7.4E-06 49.4 0.6 45 141-198 241-285 (313)
75 PF05883 Baculo_RING: Baculovi 84.9 0.37 8E-06 43.8 0.8 34 141-174 26-66 (134)
76 KOG1001 Helicase-like transcri 84.8 0.37 8.1E-06 55.6 1.0 47 142-200 455-501 (674)
77 KOG0827 Predicted E3 ubiquitin 84.6 0.45 9.8E-06 50.1 1.3 55 141-203 4-60 (465)
78 KOG1815 Predicted E3 ubiquitin 84.4 0.64 1.4E-05 51.4 2.6 34 303-338 164-198 (444)
79 KOG1428 Inhibitor of type V ad 83.9 1.6 3.5E-05 52.9 5.4 73 141-217 3486-3561(3738)
80 KOG4739 Uncharacterized protei 83.3 0.53 1.2E-05 46.9 1.2 54 142-208 4-57 (233)
81 KOG0297 TNF receptor-associate 82.8 0.7 1.5E-05 50.2 2.0 48 138-198 18-66 (391)
82 KOG1785 Tyrosine kinase negati 82.6 0.54 1.2E-05 49.7 1.0 45 142-197 370-414 (563)
83 KOG4185 Predicted E3 ubiquitin 82.0 1.2 2.6E-05 46.3 3.3 48 141-198 3-54 (296)
84 smart00661 RPOL9 RNA polymeras 81.8 1.1 2.3E-05 33.7 2.1 27 300-327 1-29 (52)
85 PF10446 DUF2457: Protein of u 81.6 1.5 3.2E-05 47.3 3.8 11 136-146 189-199 (458)
86 KOG0828 Predicted E3 ubiquitin 81.6 0.69 1.5E-05 50.2 1.4 51 140-200 570-635 (636)
87 PF15227 zf-C3HC4_4: zinc fing 81.1 0.64 1.4E-05 33.6 0.6 32 302-340 1-32 (42)
88 KOG1952 Transcription factor N 81.0 2.1 4.6E-05 49.6 4.9 54 139-196 189-244 (950)
89 COG5222 Uncharacterized conser 79.8 1.7 3.6E-05 44.3 3.3 43 142-196 275-318 (427)
90 KOG0823 Predicted E3 ubiquitin 79.7 0.71 1.5E-05 45.6 0.6 17 324-340 65-81 (230)
91 PHA03096 p28-like protein; Pro 79.6 0.9 1.9E-05 47.0 1.3 52 142-198 179-236 (284)
92 COG5220 TFB3 Cdk activating ki 78.1 0.7 1.5E-05 45.7 0.0 49 142-198 11-63 (314)
93 PHA00626 hypothetical protein 77.2 1.8 3.8E-05 33.1 1.9 28 301-329 2-34 (59)
94 KOG4172 Predicted E3 ubiquitin 76.6 0.94 2E-05 34.4 0.3 45 142-198 8-53 (62)
95 PF14835 zf-RING_6: zf-RING of 76.5 1.4 3E-05 34.9 1.3 24 300-324 8-34 (65)
96 PRK14559 putative protein seri 76.2 1.9 4E-05 49.8 2.8 23 300-335 28-50 (645)
97 KOG2038 CAATT-binding transcri 76.2 2 4.2E-05 49.3 2.8 6 8-13 887-892 (988)
98 KOG1941 Acetylcholine receptor 75.6 4.7 0.0001 42.8 5.2 46 141-195 365-412 (518)
99 KOG0825 PHD Zn-finger protein 74.2 1.1 2.5E-05 51.1 0.4 32 143-174 125-157 (1134)
100 PF08274 PhnA_Zn_Ribbon: PhnA 73.9 2.3 4.9E-05 28.5 1.6 27 300-328 3-29 (30)
101 PF09297 zf-NADH-PPase: NADH p 73.6 3.6 7.8E-05 27.7 2.6 29 298-327 2-30 (32)
102 PF10446 DUF2457: Protein of u 72.6 3.5 7.5E-05 44.6 3.5 6 167-172 211-216 (458)
103 KOG3039 Uncharacterized conser 70.8 3.1 6.8E-05 41.4 2.5 52 140-202 220-273 (303)
104 PF14952 zf-tcix: Putative tre 70.1 3.3 7.2E-05 30.1 1.8 31 293-327 5-36 (44)
105 PF04147 Nop14: Nop14-like fam 68.9 15 0.00032 44.1 8.1 17 64-80 417-436 (840)
106 PF10367 Vps39_2: Vacuolar sor 68.5 2.2 4.9E-05 36.8 0.9 31 141-171 78-108 (109)
107 PLN03086 PRLI-interacting fact 68.2 6.1 0.00013 44.7 4.4 100 187-328 408-551 (567)
108 KOG0320 Predicted E3 ubiquitin 67.8 1.9 4.1E-05 41.0 0.3 32 253-310 147-178 (187)
109 COG5175 MOT2 Transcriptional r 67.7 3.3 7.1E-05 43.1 1.9 53 141-203 14-68 (480)
110 PF14447 Prok-RING_4: Prokaryo 67.4 2.4 5.1E-05 32.5 0.7 46 141-201 7-52 (55)
111 PF04641 Rtf2: Rtf2 RING-finge 66.7 7 0.00015 40.0 4.2 58 138-207 110-169 (260)
112 PF13719 zinc_ribbon_5: zinc-r 66.0 4.6 0.0001 28.3 1.9 29 231-261 3-35 (37)
113 PRK00432 30S ribosomal protein 65.5 2.7 5.9E-05 31.7 0.7 27 299-328 20-47 (50)
114 KOG2807 RNA polymerase II tran 65.1 2.8 6.1E-05 43.4 0.9 22 249-270 342-364 (378)
115 PRK00398 rpoP DNA-directed RNA 65.0 5.8 0.00013 29.1 2.4 30 300-330 4-33 (46)
116 COG5219 Uncharacterized conser 64.9 2.2 4.8E-05 49.8 0.2 52 139-199 1467-1523(1525)
117 PRK14559 putative protein seri 64.6 5.8 0.00013 45.8 3.5 11 300-310 42-52 (645)
118 KOG3002 Zn finger protein [Gen 64.4 5.5 0.00012 41.5 2.9 47 138-199 45-91 (299)
119 PF00643 zf-B_box: B-box zinc 64.3 4.8 0.0001 28.6 1.8 29 300-336 4-33 (42)
120 KOG3800 Predicted E3 ubiquitin 62.6 11 0.00023 38.8 4.5 49 143-201 2-53 (300)
121 KOG4445 Uncharacterized conser 62.2 4.3 9.2E-05 41.7 1.6 38 140-177 114-152 (368)
122 TIGR00622 ssl1 transcription f 61.4 7.8 0.00017 34.3 2.8 39 231-271 56-101 (112)
123 TIGR02098 MJ0042_CXXC MJ0042 f 61.1 5.4 0.00012 27.8 1.5 26 301-328 4-35 (38)
124 PLN03208 E3 ubiquitin-protein 60.0 2.7 5.9E-05 40.8 -0.2 31 300-337 19-49 (193)
125 PF00627 UBA: UBA/TS-N domain; 59.4 26 0.00056 24.3 4.8 33 80-113 3-35 (37)
126 PHA02664 hypothetical protein; 58.0 24 0.00051 36.7 6.0 9 82-90 524-532 (534)
127 PF02150 RNA_POL_M_15KD: RNA p 57.9 9.3 0.0002 26.5 2.2 27 231-260 2-29 (35)
128 KOG3579 Predicted E3 ubiquitin 57.5 7.6 0.00016 39.6 2.4 53 140-196 267-322 (352)
129 KOG2034 Vacuolar sorting prote 57.5 13 0.00028 43.7 4.5 37 141-177 817-853 (911)
130 KOG3039 Uncharacterized conser 57.3 6.8 0.00015 39.2 2.0 36 141-178 43-78 (303)
131 KOG3970 Predicted E3 ubiquitin 56.9 13 0.00027 36.7 3.7 54 142-198 51-104 (299)
132 TIGR03655 anti_R_Lar restricti 56.6 7.7 0.00017 29.4 1.8 11 300-310 2-12 (53)
133 PRK08665 ribonucleotide-diphos 56.2 6.8 0.00015 46.2 2.2 27 300-329 725-751 (752)
134 KOG2114 Vacuolar assembly/sort 56.2 8.6 0.00019 44.8 2.8 103 77-197 757-881 (933)
135 KOG4739 Uncharacterized protei 56.2 2.3E+02 0.0049 28.6 12.8 23 313-336 21-47 (233)
136 KOG2906 RNA polymerase III sub 55.9 7.4 0.00016 33.3 1.7 29 301-330 3-33 (105)
137 KOG4275 Predicted E3 ubiquitin 55.3 7.3 0.00016 39.9 1.9 29 141-171 300-329 (350)
138 KOG1991 Nuclear transport rece 55.3 9.9 0.00021 45.1 3.2 36 70-108 955-990 (1010)
139 PF07191 zinc-ribbons_6: zinc- 55.2 8.1 0.00018 31.2 1.8 49 301-352 3-56 (70)
140 KOG3161 Predicted E3 ubiquitin 53.4 4.5 9.7E-05 45.5 0.1 34 141-174 11-46 (861)
141 KOG1571 Predicted E3 ubiquitin 53.3 6 0.00013 41.7 1.0 42 141-198 305-346 (355)
142 PHA02926 zinc finger-like prot 53.2 6.2 0.00013 39.0 1.0 52 299-351 170-224 (242)
143 PF07282 OrfB_Zn_ribbon: Putat 53.1 9.7 0.00021 30.3 2.0 28 298-326 27-54 (69)
144 PF13717 zinc_ribbon_4: zinc-r 52.6 11 0.00024 26.2 1.9 29 231-261 3-35 (36)
145 PF09538 FYDLN_acid: Protein o 51.5 9.3 0.0002 33.7 1.7 26 300-328 10-36 (108)
146 COG5574 PEX10 RING-finger-cont 50.9 4.1 8.8E-05 41.2 -0.7 33 300-339 216-249 (271)
147 COG5109 Uncharacterized conser 50.7 14 0.0003 38.4 3.0 50 140-197 335-385 (396)
148 cd00194 UBA Ubiquitin Associat 50.7 45 0.00097 22.9 4.9 34 82-116 4-37 (38)
149 PF06677 Auto_anti-p27: Sjogre 50.1 13 0.00028 26.9 1.9 22 300-324 18-40 (41)
150 PF13834 DUF4193: Domain of un 49.7 6.9 0.00015 33.7 0.6 32 138-169 67-98 (99)
151 PF14803 Nudix_N_2: Nudix N-te 49.4 11 0.00024 26.0 1.4 26 300-326 1-30 (34)
152 PF14446 Prok-RING_1: Prokaryo 48.6 15 0.00032 28.2 2.2 33 141-173 5-39 (54)
153 COG5151 SSL1 RNA polymerase II 47.4 5.4 0.00012 41.0 -0.4 88 163-270 308-407 (421)
154 TIGR01384 TFS_arch transcripti 46.1 12 0.00026 32.5 1.6 24 301-327 2-25 (104)
155 smart00661 RPOL9 RNA polymeras 46.0 18 0.00039 26.9 2.3 27 232-260 2-29 (52)
156 PF03115 Astro_capsid: Astrovi 45.5 7 0.00015 45.9 0.0 15 91-105 721-736 (787)
157 COG1997 RPL43A Ribosomal prote 45.3 15 0.00032 30.9 1.9 28 300-328 36-63 (89)
158 PF08580 KAR9: Yeast cortical 45.1 3.9E+02 0.0085 31.4 14.1 12 420-431 250-261 (683)
159 COG4647 AcxC Acetone carboxyla 45.1 18 0.00038 32.6 2.4 59 251-310 69-131 (165)
160 cd00021 BBOX B-Box-type zinc f 45.0 11 0.00025 25.9 1.1 26 301-334 2-28 (39)
161 PF05290 Baculo_IE-1: Baculovi 43.9 19 0.00042 32.7 2.5 53 139-199 78-132 (140)
162 smart00165 UBA Ubiquitin assoc 43.8 60 0.0013 22.1 4.6 31 83-114 5-35 (37)
163 PF07191 zinc-ribbons_6: zinc- 43.6 5.1 0.00011 32.3 -1.0 39 142-198 2-40 (70)
164 KOG4684 Uncharacterized conser 43.6 15 0.00033 35.9 2.0 17 229-245 137-153 (275)
165 COG5236 Uncharacterized conser 43.5 17 0.00036 38.1 2.4 50 138-198 58-107 (493)
166 PRK09710 lar restriction allev 43.4 16 0.00035 29.0 1.7 14 298-311 5-18 (64)
167 KOG1940 Zn-finger protein [Gen 42.7 18 0.00039 37.2 2.5 47 139-196 156-204 (276)
168 PF10168 Nup88: Nuclear pore c 42.4 5.3E+02 0.012 30.5 14.7 24 455-478 601-624 (717)
169 COG0266 Nei Formamidopyrimidin 42.2 16 0.00036 37.5 2.1 25 300-325 246-272 (273)
170 PRK05654 acetyl-CoA carboxylas 41.7 7.9 0.00017 40.3 -0.3 28 300-328 28-56 (292)
171 COG1645 Uncharacterized Zn-fin 41.6 17 0.00037 33.1 1.8 23 300-333 29-51 (131)
172 smart00804 TAP_C C-terminal do 41.6 84 0.0018 24.9 5.6 41 76-116 9-49 (63)
173 PF08746 zf-RING-like: RING-li 41.1 28 0.00061 25.3 2.6 34 144-177 1-35 (43)
174 KOG2141 Protein involved in hi 40.9 23 0.00049 40.9 3.0 14 325-338 566-579 (822)
175 PF14445 Prok-RING_2: Prokaryo 39.7 6.4 0.00014 29.5 -0.9 33 140-172 6-39 (57)
176 PF06906 DUF1272: Protein of u 39.2 20 0.00044 27.6 1.6 45 143-200 7-53 (57)
177 COG5665 NOT5 CCR4-NOT transcri 38.7 4.4E+02 0.0095 28.4 11.7 16 374-389 10-25 (548)
178 KOG0943 Predicted ubiquitin-pr 38.6 22 0.00048 43.1 2.6 16 459-474 2419-2434(3015)
179 PF07800 DUF1644: Protein of u 37.9 58 0.0013 30.6 4.7 83 141-242 2-119 (162)
180 PHA02929 N1R/p28-like protein; 37.1 14 0.00031 37.2 0.7 39 299-339 174-215 (238)
181 PRK14811 formamidopyrimidine-D 37.1 22 0.00047 36.6 2.1 25 300-325 236-262 (269)
182 PRK12775 putative trifunctiona 36.7 5.6E+02 0.012 31.6 14.3 14 299-312 796-809 (1006)
183 PF09943 DUF2175: Uncharacteri 36.5 78 0.0017 27.5 5.0 26 453-478 74-99 (101)
184 PRK14714 DNA polymerase II lar 36.4 29 0.00064 42.6 3.2 11 300-310 710-720 (1337)
185 PF03943 TAP_C: TAP C-terminal 36.3 39 0.00084 25.5 2.8 36 81-116 2-37 (51)
186 PRK14892 putative transcriptio 36.3 23 0.0005 30.7 1.8 27 300-327 22-51 (99)
187 PF06827 zf-FPG_IleRS: Zinc fi 35.9 20 0.00044 23.6 1.1 22 300-321 2-25 (30)
188 PRK11827 hypothetical protein; 35.7 29 0.00062 27.3 2.0 25 300-325 9-33 (60)
189 KOG4362 Transcriptional regula 35.6 10 0.00022 43.5 -0.6 51 140-200 20-70 (684)
190 PF12906 RINGv: RING-variant d 35.3 29 0.00063 25.6 2.0 33 144-176 1-38 (47)
191 PF09889 DUF2116: Uncharacteri 35.1 10 0.00022 29.6 -0.5 11 300-310 4-14 (59)
192 PRK01103 formamidopyrimidine/5 35.1 25 0.00054 36.2 2.2 26 299-325 245-272 (274)
193 PF05715 zf-piccolo: Piccolo Z 35.0 17 0.00037 28.3 0.7 41 300-341 3-45 (61)
194 PHA02664 hypothetical protein; 35.0 62 0.0013 33.7 4.9 15 77-91 512-526 (534)
195 KOG1991 Nuclear transport rece 34.8 20 0.00043 42.7 1.5 25 75-99 968-993 (1010)
196 CHL00174 accD acetyl-CoA carbo 34.7 11 0.00023 39.3 -0.6 28 300-328 39-67 (296)
197 TIGR00577 fpg formamidopyrimid 34.7 26 0.00057 36.1 2.2 25 300-325 246-272 (272)
198 KOG2177 Predicted E3 ubiquitin 34.6 15 0.00032 37.1 0.4 25 301-333 88-112 (386)
199 COG4530 Uncharacterized protei 34.5 42 0.00091 29.5 3.0 13 42-54 100-112 (129)
200 TIGR00515 accD acetyl-CoA carb 34.0 12 0.00025 38.9 -0.5 28 300-328 27-55 (285)
201 COG5432 RAD18 RING-finger-cont 34.0 12 0.00026 38.3 -0.3 30 300-336 26-55 (391)
202 PRK14810 formamidopyrimidine-D 34.0 26 0.00057 36.0 2.1 26 299-325 244-271 (272)
203 KOG1701 Focal adhesion adaptor 33.7 12 0.00027 40.3 -0.4 11 300-310 428-438 (468)
204 KOG0250 DNA repair protein RAD 33.5 1E+03 0.022 29.4 17.8 26 421-446 254-279 (1074)
205 PF07975 C1_4: TFIIH C1-like d 33.4 17 0.00037 27.6 0.4 23 251-273 20-43 (51)
206 smart00336 BBOX B-Box-type zin 33.3 34 0.00074 23.8 2.0 28 300-335 4-32 (42)
207 COG1998 RPS31 Ribosomal protei 33.3 25 0.00053 26.4 1.2 10 300-309 20-29 (51)
208 PRK13945 formamidopyrimidine-D 33.1 28 0.00061 36.0 2.2 25 300-325 255-281 (282)
209 KOG0933 Structural maintenance 33.0 9.7E+02 0.021 29.4 14.4 43 426-474 222-264 (1174)
210 PF13453 zf-TFIIB: Transcripti 32.7 28 0.0006 24.8 1.5 31 301-338 1-31 (41)
211 PRK10445 endonuclease VIII; Pr 32.6 29 0.00063 35.5 2.2 25 300-325 236-262 (263)
212 PF10272 Tmpp129: Putative tra 32.2 1.5E+02 0.0032 31.9 7.4 119 62-199 207-351 (358)
213 TIGR00686 phnA alkylphosphonat 31.9 30 0.00066 30.3 1.8 21 300-321 3-23 (109)
214 PF01428 zf-AN1: AN1-like Zinc 31.7 27 0.00058 25.2 1.2 28 233-267 1-29 (43)
215 PF03119 DNA_ligase_ZBD: NAD-d 31.5 33 0.00072 22.5 1.5 21 301-321 1-21 (28)
216 KOG2164 Predicted E3 ubiquitin 31.1 21 0.00045 39.5 0.8 30 299-335 186-215 (513)
217 COG1198 PriA Primosomal protei 31.1 31 0.00067 40.5 2.2 35 300-335 445-484 (730)
218 PF04147 Nop14: Nop14-like fam 31.0 41 0.00088 40.4 3.3 11 510-520 824-834 (840)
219 KOG3053 Uncharacterized conser 30.7 38 0.00081 34.3 2.4 56 140-198 19-81 (293)
220 PF02845 CUE: CUE domain; Int 30.5 1.6E+02 0.0034 20.9 5.1 37 81-117 3-40 (42)
221 TIGR02300 FYDLN_acid conserved 30.3 34 0.00073 31.0 1.8 26 300-327 10-35 (129)
222 PF01396 zf-C4_Topoisom: Topoi 30.2 43 0.00094 23.7 2.1 11 300-310 2-12 (39)
223 KOG2932 E3 ubiquitin ligase in 30.1 15 0.00032 38.0 -0.5 52 227-315 87-139 (389)
224 PF04050 Upf2: Up-frameshift s 30.0 34 0.00075 32.6 2.1 12 73-84 63-74 (170)
225 PF01363 FYVE: FYVE zinc finge 30.0 42 0.00091 26.5 2.3 35 299-336 9-43 (69)
226 COG3809 Uncharacterized protei 29.8 32 0.0007 28.3 1.5 35 300-341 2-36 (88)
227 PF06936 Selenoprotein_S: Sele 29.6 3.2E+02 0.0069 26.6 8.6 26 457-482 76-101 (190)
228 PRK12495 hypothetical protein; 29.5 38 0.00083 33.5 2.2 17 299-315 42-58 (226)
229 cd07666 BAR_SNX7 The Bin/Amphi 29.2 6.2E+02 0.013 25.7 16.7 68 375-442 91-165 (243)
230 PRK09710 lar restriction allev 28.9 67 0.0015 25.5 3.1 33 229-262 5-38 (64)
231 KOG2906 RNA polymerase III sub 28.8 51 0.0011 28.4 2.6 29 231-261 2-31 (105)
232 COG1594 RPB9 DNA-directed RNA 28.6 37 0.00081 30.1 1.9 28 300-328 3-32 (113)
233 KOG0825 PHD Zn-finger protein 28.6 30 0.00065 40.2 1.5 53 141-198 96-153 (1134)
234 KOG1493 Anaphase-promoting com 28.6 18 0.00039 29.7 -0.1 48 143-198 22-80 (84)
235 TIGR00599 rad18 DNA repair pro 28.1 19 0.00041 39.1 -0.1 32 300-338 27-58 (397)
236 smart00659 RPOLCX RNA polymera 27.9 50 0.0011 24.2 2.1 25 301-327 4-28 (44)
237 KOG0943 Predicted ubiquitin-pr 27.7 41 0.00089 41.0 2.4 7 519-525 2476-2482(3015)
238 PF03604 DNA_RNApol_7kD: DNA d 27.4 49 0.0011 22.5 1.8 25 301-327 2-26 (32)
239 COG5194 APC11 Component of SCF 27.0 56 0.0012 27.1 2.4 28 160-198 53-80 (88)
240 KOG2979 Protein involved in DN 27.0 61 0.0013 32.9 3.2 48 141-196 176-223 (262)
241 PF08792 A2L_zn_ribbon: A2L zi 27.0 57 0.0012 22.3 2.1 11 300-310 4-14 (33)
242 PRK14714 DNA polymerase II lar 26.9 34 0.00075 42.1 1.7 30 300-336 668-702 (1337)
243 PF09788 Tmemb_55A: Transmembr 26.1 64 0.0014 32.7 3.2 19 229-247 122-140 (256)
244 KOG3268 Predicted E3 ubiquitin 25.9 53 0.0011 31.4 2.4 57 141-199 165-228 (234)
245 KOG2391 Vacuolar sorting prote 25.8 8.3E+02 0.018 26.0 11.9 20 78-97 21-40 (365)
246 COG5220 TFB3 Cdk activating ki 25.8 43 0.00093 33.5 1.9 54 187-244 11-65 (314)
247 PLN02638 cellulose synthase A 25.7 49 0.0011 40.3 2.7 55 238-318 23-78 (1079)
248 KOG2930 SCF ubiquitin ligase, 25.3 43 0.00093 29.1 1.5 17 160-176 80-96 (114)
249 PRK10220 hypothetical protein; 25.2 47 0.001 29.2 1.8 29 300-338 4-32 (111)
250 PF14149 YhfH: YhfH-like prote 25.0 7.2 0.00016 27.4 -2.6 25 299-324 13-37 (37)
251 TIGR02159 PA_CoA_Oxy4 phenylac 24.9 48 0.001 30.9 1.9 94 75-173 40-140 (146)
252 KOG1451 Oligophrenin-1 and rel 24.9 1.1E+03 0.024 27.1 14.9 30 491-520 217-246 (812)
253 COG0777 AccD Acetyl-CoA carbox 24.3 26 0.00056 35.9 0.1 28 300-328 29-57 (294)
254 PF01783 Ribosomal_L32p: Ribos 24.3 41 0.00088 25.9 1.1 22 298-325 25-46 (56)
255 PRK06568 F0F1 ATP synthase sub 24.3 6E+02 0.013 23.9 14.8 55 456-515 84-139 (154)
256 PF09026 CENP-B_dimeris: Centr 23.9 26 0.00056 30.0 0.0 6 70-75 60-65 (101)
257 PF01599 Ribosomal_S27: Riboso 23.6 46 0.001 24.8 1.3 26 300-326 19-46 (47)
258 KOG1829 Uncharacterized conser 23.6 5E+02 0.011 29.8 9.9 34 300-334 341-374 (580)
259 PF07417 Crl: Transcriptional 23.4 55 0.0012 29.5 1.9 45 439-483 66-110 (125)
260 PF07058 Myosin_HC-like: Myosi 23.4 8.8E+02 0.019 25.5 18.3 37 494-530 124-166 (351)
261 PF08271 TF_Zn_Ribbon: TFIIB z 23.3 62 0.0013 23.2 1.9 8 301-308 2-9 (43)
262 PF02318 FYVE_2: FYVE-type zin 23.3 57 0.0012 29.0 2.1 36 298-335 53-88 (118)
263 PF12861 zf-Apc11: Anaphase-pr 23.2 26 0.00056 29.5 -0.1 35 300-339 33-67 (85)
264 PF07889 DUF1664: Protein of u 23.1 5.7E+02 0.012 23.2 9.8 17 510-526 106-122 (126)
265 COG3024 Uncharacterized protei 22.8 41 0.00088 26.7 0.9 13 299-311 7-19 (65)
266 PF05605 zf-Di19: Drought indu 22.7 58 0.0013 24.6 1.7 11 141-151 2-12 (54)
267 COG4640 Predicted membrane pro 22.7 4.9E+02 0.011 28.3 8.9 16 513-528 130-145 (465)
268 PF05285 SDA1: SDA1; InterPro 22.5 1.1E+02 0.0024 32.4 4.4 8 69-76 189-196 (324)
269 PHA02325 hypothetical protein 22.5 39 0.00085 26.7 0.7 12 298-309 2-13 (72)
270 PF05320 Pox_RNA_Pol_19: Poxvi 22.1 31 0.00068 32.1 0.1 9 141-149 126-134 (167)
271 PF02724 CDC45: CDC45-like pro 22.1 1.5E+02 0.0032 34.4 5.6 6 193-198 352-357 (622)
272 PF12325 TMF_TATA_bd: TATA ele 21.9 5.9E+02 0.013 22.9 10.5 24 492-515 96-119 (120)
273 PHA02825 LAP/PHD finger-like p 21.9 96 0.0021 29.3 3.3 49 140-200 7-60 (162)
274 PF14569 zf-UDP: Zinc-binding 21.9 1.3E+02 0.0027 25.0 3.5 50 139-198 7-61 (80)
275 PF06844 DUF1244: Protein of u 21.7 50 0.0011 26.4 1.1 17 164-180 11-27 (68)
276 PRK12286 rpmF 50S ribosomal pr 21.7 55 0.0012 25.4 1.4 22 298-325 26-47 (57)
277 COG1594 RPB9 DNA-directed RNA 21.7 86 0.0019 27.8 2.9 30 230-261 2-32 (113)
278 COG2816 NPY1 NTP pyrophosphohy 21.7 78 0.0017 32.7 2.9 37 290-328 103-139 (279)
279 PRK14892 putative transcriptio 21.5 1.7E+02 0.0037 25.4 4.5 55 227-286 18-74 (99)
280 PTZ00083 40S ribosomal protein 21.5 96 0.0021 26.1 2.8 30 231-263 36-66 (85)
281 PLN02189 cellulose synthase 21.2 74 0.0016 38.6 3.0 59 232-318 36-95 (1040)
282 PF00098 zf-CCHC: Zinc knuckle 21.2 55 0.0012 19.1 1.0 16 261-276 2-17 (18)
283 cd07662 BAR_SNX6 The Bin/Amphi 20.9 8.4E+02 0.018 24.3 14.7 56 459-519 155-210 (218)
284 PRK04023 DNA polymerase II lar 20.9 53 0.0012 39.5 1.7 32 297-335 624-660 (1121)
285 TIGR01206 lysW lysine biosynth 20.8 96 0.0021 23.8 2.5 28 232-261 4-32 (54)
286 PF04803 Cor1: Cor1/Xlr/Xmr co 20.8 6.5E+02 0.014 22.9 11.0 14 376-389 46-59 (130)
287 PRK08115 ribonucleotide-diphos 20.6 50 0.0011 39.5 1.4 25 300-327 828-853 (858)
288 PRK13428 F0F1 ATP synthase sub 20.6 1.2E+03 0.025 25.9 16.0 25 456-480 85-109 (445)
289 COG1315 Uncharacterized conser 20.6 6.6E+02 0.014 28.3 9.7 38 374-411 408-445 (543)
290 PRK09521 exosome complex RNA-b 20.4 64 0.0014 31.2 1.9 26 300-327 150-175 (189)
291 KOG2932 E3 ubiquitin ligase in 20.1 40 0.00088 35.0 0.5 29 300-335 91-120 (389)
No 1
>KOG1815 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=100.00 E-value=1.8e-71 Score=604.12 Aligned_cols=437 Identities=49% Similarity=0.913 Sum_probs=399.7
Q ss_pred EeCHHHHHHHHHHHHHHHHHHhCCCHHHHHHHHHHcCCChhhhHHHhhhcHHHHHHHhCCCCCCCCCCCCCCcccccccc
Q 007642 69 VLTEADIRQRQEEDITRISTVLSISKVAASILLRFYNWSVSKVHDEWFADEERVRKAVGLLEKPAVQFPDGEEMTCGICF 148 (595)
Q Consensus 69 vl~~~~i~~~~~~~i~~v~~vl~i~~~~a~~LL~~~~W~~~~l~e~~~~~~~~~~~~~gl~~~~~~~~~~~~~~~C~IC~ 148 (595)
||+++++...|.++|..|+++|++++.+|++||.+|.|+.+++++.|+.+++.++..+|+...+ .......|+||+
T Consensus 2 vl~~~~~~~~~~~~i~~~~~~ls~~~~~~~~ll~~~~W~~~kl~~~~~~~~~~~~~~~g~~~~~----~~~~~~~c~ic~ 77 (444)
T KOG1815|consen 2 VLTPDDIAALMREDIIEVSDILSLSHAVARILLAHFCWNVEKLLEEWVEDEETGCFFVGLLLWP----KKKGDVQCGICV 77 (444)
T ss_pred CCchHhhhHHhHhhHHHHHHhhcCCHHHHHHHHHhcCcchHHHHHHHHhcCcchhhhccccccC----CCCccccCCccc
Confidence 6889999999999999999999999999999999999999999999999999999999986653 345578899999
Q ss_pred ccccCCCceecCCCCcccHhHHHHHHhccccCCCCccccccCCCcCCCccchhHHhhhcCh-HHHHHHHHHHHHHhhhhC
Q 007642 149 ENYPSDRLLAAACGHPFCSSCWTGYISTAINDGPGCLMLRCPDPSCGAAVGQDMIYLLSSD-EDKVKYNRYFIRSYVEDN 227 (595)
Q Consensus 149 e~~~~~~~~~l~CgH~fC~~C~~~yi~~~i~~g~~~~~i~CP~~~C~~~v~~~~i~~ll~~-e~~eky~~~~~~~~v~~~ 227 (595)
+.++. .+..+.|||.||..||..|+..+|..+.... |+||.+.|.+.+..+.|..++++ +..++|.++++++|++.+
T Consensus 78 ~~~~~-~~~~~~c~H~~c~~cw~~yl~~kI~~~~~~~-i~cp~~~C~a~v~~~~i~~~~s~~~~~~ky~~~i~~syve~~ 155 (444)
T KOG1815|consen 78 ESYDG-EIIGLGCGHPFCPPCWTGYLGTKIHEGEEAK-IKCPAHGCPALVGEDTVEKLVSDKEDKEKYQRYILRSYVEDN 155 (444)
T ss_pred CCCcc-hhhhcCCCcHHHHHHHHHHhhheeecccccc-ccCCCCCccccCCCceeeeecCCHHHHHHHHHHHHHHHHhcC
Confidence 98865 6888999999999999999999999886433 89999999999999999999998 599999999999999999
Q ss_pred CCcccCCCCCCCCeeeeecCCCCceeeecCCCcccccCCcccCCCCCchhHHHHHHhhhHhHHhHHHHHhcCccCCCCCc
Q 007642 228 RKTKWCPAPGCDYAVDFVVGSGNYDVTCRCSYSFCWNCTEEAHRPVDCDTVAKWVLKNSAESENMNWILANSKPCPRCKR 307 (595)
Q Consensus 228 ~~~~~CP~p~C~~~i~~~~~~~~~~v~C~C~~~fC~~C~~~~H~p~~C~~~~~~~~k~~~~~e~~~wi~~ntK~CPkC~~ 307 (595)
..++|||+|+|++++.+. ......|.|.|++.|||.|+.+||.|.+|.....|+.+..+++++.+||.+|+++||+|..
T Consensus 156 ~~lkwCP~~~C~~av~~~-~~~~~~v~C~~g~~FC~~C~~~~H~p~~C~~~~~wl~k~~~~se~~~wi~~ntk~CP~c~~ 234 (444)
T KOG1815|consen 156 VPLKWCPAPGCGLAVKFG-SLESVEVDCGCGHEFCFACGEESHSPVSCPGAKKWLKKCRDDSETINWILANTKECPKCKV 234 (444)
T ss_pred CccccCCCCCCCceeecc-CCCccceeCCCCchhHhhccccccCCCcccchHHHHHhhhhhhhhhhhhhccCccCCCccc
Confidence 999999999999999875 4456789999999999999999999999999999999999999999999999999999999
Q ss_pred ceeecCCCCcccccCC--CcceeeecccccccCCCCCCCCcccCCchhhhhhcCcchhHHHHHHHHHHHHHHHHHHHHHH
Q 007642 308 PIEKNQGCMHMTCTPP--CKFEFCWLCLGQWSDHGERTGGFYACNRYETAKQEGVYDESEKRREMAKNSLERYTHYYERW 385 (595)
Q Consensus 308 ~IEK~~GCnhmtC~~~--C~~~FCw~C~~~~~~H~~~~g~~y~C~~~~~~~~~~~~~~~e~~~~~~~~~l~ry~~y~~r~ 385 (595)
+|||++|||||+|. . |++.|||+|++.|.+|+..+ +|.|++|...+... .+++++..|.||+|||.||
T Consensus 235 ~iek~~gc~~~~~~-~~~c~~~FCw~Cl~~~~~h~~~~--~~~c~~~~~~~~~~-------~~~~a~~~l~r~~~~~~~~ 304 (444)
T KOG1815|consen 235 PIEKDGGCNHMTCK-SASCKHEFCWVCLASLSDHGSST--GYSCNRYVDGKSKS-------ARSKARRSLKRYTHYYNRW 304 (444)
T ss_pred chhccCCccccccc-cCCcCCeeceeeecccccccccc--eeeeeeeechhhhh-------HHHHHHHHHHHHHHHHhhH
Confidence 99999999999998 5 99999999999999999754 89999998654311 4678899999999999999
Q ss_pred hhhHHHHHHHHHHHHHHHHHHHHHHhhhcCCCchhHHHHHHHHHHHHHHHHHHhhhhhhhcccCccchhhHHHHHHHHHH
Q 007642 386 ATNQSSRQKALADLQQMQTVHLEKLSDVQCQPESQLKFITEAWLQIVECRRVLKWTYAYGYYLPDHEHAKRQFFEYLQGE 465 (595)
Q Consensus 386 ~~h~~s~~~~~~~l~~~~~~~~~~l~~~~~~~~~~~~~l~~a~~~l~~~r~~L~~sy~~~yy~~~~~~~~~~~fe~~Q~~ 465 (595)
++|+.+++++...+..+...+..++......++.+++|+.+++.+|.++|++|+|+|+|+||+. ...++.+||++|.+
T Consensus 305 ~~~q~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~e~r~~l~~s~~~~~~~~--~~~~~~~fe~~q~~ 382 (444)
T KOG1815|consen 305 MEHQVSLKLEGKLLSKVEEVKKPKLSDSLSLSWIDVQFLRDAGDVLVECRRTLKWTYAYAYYLS--ENNKRNLFEDNQTD 382 (444)
T ss_pred HhhhhhhhhhhhhHHHHHHHhhhhhhcccCeeeeeeeeechhHHHHHhhhhhhhhhhhhhhhhc--ccchhhhhHHHHHH
Confidence 9999999999888888877888888887777889999999999999999999999999999997 44567899999999
Q ss_pred HHHhHHHHHHHHHHHHHHHhhcCCCCCcHHHHHHHHHHHHHHHHHHHHHHHHHHHccccccccc
Q 007642 466 AESGLERLHQCAEKELQIYLNADGPSKDFNEFRTKLAGLTSVTRNYFENLVRALENGLSDVDTH 529 (595)
Q Consensus 466 le~~~E~L~~~le~e~~~~~~~~~~~~~~~~~~~~l~~lt~~~~~~~~~l~~~le~~l~~~~~~ 529 (595)
|+..+|.|+..++.++. ..+...+..++.+|.++|.+++++|+++++++++||.++...
T Consensus 383 ~~~~~e~ls~~~~~~~~-----~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~ 441 (444)
T KOG1815|consen 383 LESAVEPLSSCLEESLK-----DISSETLAEFKQKLTDLTSYVRNRFENLLKHLEEGLEDVGSE 441 (444)
T ss_pred HhhhhhhhHHHhccccc-----cCCcccHHHHHhhccccchhhhhHHHHHHHHHHhcccccccc
Confidence 99999999999998776 456688999999999999999999999999999999998543
No 2
>KOG1812 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=100.00 E-value=6.9e-34 Score=301.92 Aligned_cols=205 Identities=26% Similarity=0.687 Sum_probs=174.9
Q ss_pred CccccccccccccC-CCce-ecCCCCcccHhHHHHHHhccccCCCCccccccCCCcCCCccchhHHhhhcChHHHHHHHH
Q 007642 140 EEMTCGICFENYPS-DRLL-AAACGHPFCSSCWTGYISTAINDGPGCLMLRCPDPSCGAAVGQDMIYLLSSDEDKVKYNR 217 (595)
Q Consensus 140 ~~~~C~IC~e~~~~-~~~~-~l~CgH~fC~~C~~~yi~~~i~~g~~~~~i~CP~~~C~~~v~~~~i~~ll~~e~~eky~~ 217 (595)
...+|+||+...+. ..++ ...|+|.||.+||++|++.+...|. .++||+.+|...++.+....++++++.++|++
T Consensus 145 ~~~~C~iC~~e~~~~~~~f~~~~C~H~fC~~C~k~~iev~~~~~~---~~~C~~~~C~~~l~~~~c~~llt~kl~e~~e~ 221 (384)
T KOG1812|consen 145 PKEECGICFVEDPEAEDMFSVLKCGHRFCKDCVKQHIEVKLLSGT---VIRCPHDGCESRLTLESCRKLLTPKLREMWEQ 221 (384)
T ss_pred ccccCccCccccccHhhhHHHhcccchhhhHHhHHHhhhhhccCC---CccCCCCCCCccCCHHHHhhhcCHHHHHHHHH
Confidence 36789999954443 2444 4679999999999999999855553 89999999999999999999999999999999
Q ss_pred HHHHHhhhhCCCcccCCCCCCCCeeeeecC---CCCceeee-cCCCcccccCCcccCCCCCchhHHHHHHhhhHhHHhHH
Q 007642 218 YFIRSYVEDNRKTKWCPAPGCDYAVDFVVG---SGNYDVTC-RCSYSFCWNCTEEAHRPVDCDTVAKWVLKNSAESENMN 293 (595)
Q Consensus 218 ~~~~~~v~~~~~~~~CP~p~C~~~i~~~~~---~~~~~v~C-~C~~~fC~~C~~~~H~p~~C~~~~~~~~k~~~~~e~~~ 293 (595)
++.+.++.....+ +||.|+|...+..... .......| .|+..||..|+.+||.+.+|+.+++|......+...++
T Consensus 222 ~~~e~~i~~~~~~-ycp~~~C~~l~~~~el~~~~~~~~~~C~~C~~~fCv~C~~~wh~~~sC~eykk~~~~~~~d~~~~~ 300 (384)
T KOG1812|consen 222 RLKEEVIPSLDRV-YCPYPRCSSLMSKTELSSEVKSKRRPCVKCHELFCVKCKVPWHANLSCEEYKKLNPEEYVDDITLK 300 (384)
T ss_pred HHHHHhhhhhhcc-cCCCCCchHhhhhhhhccchhhcccccccCCCceeecCCCcCCCCCCHHHHHHhCCcccccHHHHH
Confidence 9999999888777 9999999877654321 22344578 89999999999999999999999999877667777888
Q ss_pred HHHhcCccCCCCCcceeecCCCCcccccCCCcceeeecccccccCCCCCCCCcccCCchh
Q 007642 294 WILANSKPCPRCKRPIEKNQGCMHMTCTPPCKFEFCWLCLGQWSDHGERTGGFYACNRYE 353 (595)
Q Consensus 294 wi~~ntK~CPkC~~~IEK~~GCnhmtC~~~C~~~FCw~C~~~~~~H~~~~g~~y~C~~~~ 353 (595)
|+.++++.||+|+..||+++|||||+|+ ||++|||.|+++|..|+. .+|.|.++.
T Consensus 301 ~la~~wr~CpkC~~~ie~~~GCnhm~Cr--C~~~fcy~C~~~~~~~~~---~~~~~~r~~ 355 (384)
T KOG1812|consen 301 YLAKRWRQCPKCKFMIELSEGCNHMTCR--CGHQFCYMCGGDWKTHNG---ECYECCRYK 355 (384)
T ss_pred HHHHhcCcCcccceeeeecCCcceEEee--ccccchhhcCcchhhCCc---cccCccccc
Confidence 8888999999999999999999999998 999999999999998874 456676654
No 3
>KOG1814 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=99.97 E-value=8.2e-33 Score=282.27 Aligned_cols=196 Identities=30% Similarity=0.703 Sum_probs=169.8
Q ss_pred CCCccccccccccccC-CCceecCCCCcccHhHHHHHHhccccCCCCccccccCCCcCCCccchhHHhhhcChHHHHHHH
Q 007642 138 DGEEMTCGICFENYPS-DRLLAAACGHPFCSSCWTGYISTAINDGPGCLMLRCPDPSCGAAVGQDMIYLLSSDEDKVKYN 216 (595)
Q Consensus 138 ~~~~~~C~IC~e~~~~-~~~~~l~CgH~fC~~C~~~yi~~~i~~g~~~~~i~CP~~~C~~~v~~~~i~~ll~~e~~eky~ 216 (595)
....+.|.|||+.... ..++.+||+|.||+.|++.|+...|++|. ...++||+++|+...++..++.++..+++++|+
T Consensus 181 ~~slf~C~ICf~e~~G~~c~~~lpC~Hv~Ck~C~kdY~~~~i~eg~-v~~l~Cp~~~C~~~a~~g~vKelvg~EL~arYe 259 (445)
T KOG1814|consen 181 VNSLFDCCICFEEQMGQHCFKFLPCSHVFCKSCLKDYFTIQIQEGQ-VSCLKCPDPKCGSVAPPGQVKELVGDELFARYE 259 (445)
T ss_pred HhhcccceeeehhhcCcceeeecccchHHHHHHHHHHHHHhhhcce-eeeecCCCCCCcccCCchHHHHHHHHHHHHHHH
Confidence 3457899999998765 57889999999999999999999999885 568999999999999999999999999999999
Q ss_pred HHHHHHhhhhCCCcccCCCCCCCCeeeeecCCCCceeee-cCCCcccccCCcccCCCCCchhHH--------HHH-----
Q 007642 217 RYFIRSYVEDNRKTKWCPAPGCDYAVDFVVGSGNYDVTC-RCSYSFCWNCTEEAHRPVDCDTVA--------KWV----- 282 (595)
Q Consensus 217 ~~~~~~~v~~~~~~~~CP~p~C~~~i~~~~~~~~~~v~C-~C~~~fC~~C~~~~H~p~~C~~~~--------~~~----- 282 (595)
++++++.++...++++||++.|..++.. ..+..-+.| .|.++||..|+..||...+|.... .|.
T Consensus 260 ~l~lqk~l~~msdv~yCPr~~Cq~p~~~--d~~~~l~~CskCnFaFCtlCk~t~HG~s~Ck~~~~~~~~l~~~~~~~d~a 337 (445)
T KOG1814|consen 260 KLMLQKTLELMSDVVYCPRACCQLPVKQ--DPGRALAICSKCNFAFCTLCKLTWHGVSPCKVKAEKLIELYLEYLEADEA 337 (445)
T ss_pred HHHHHHHHHhhcccccCChhhccCcccc--CchhhhhhhccCccHHHHHHHHhhcCCCcccCchHHHHHHHHHHhhcCHH
Confidence 9999999999999999999999988743 345566799 999999999999999998997541 121
Q ss_pred --------------HhhhHhHHhHHHHHhcCccCCCCCcceeecCCCCcccccCCCcceeeeccccccc
Q 007642 283 --------------LKNSAESENMNWILANSKPCPRCKRPIEKNQGCMHMTCTPPCKFEFCWLCLGQWS 337 (595)
Q Consensus 283 --------------~k~~~~~e~~~wi~~ntK~CPkC~~~IEK~~GCnhmtC~~~C~~~FCw~C~~~~~ 337 (595)
+....+..+..|+..|.|+||+|+++|||++|||||+|. .|++.|||+|.....
T Consensus 338 ~k~ele~Ryg~rvve~~vn~~lsekwl~~N~krCP~C~v~IEr~eGCnKM~C~-~c~~~fc~~c~~~l~ 405 (445)
T KOG1814|consen 338 RKRELEKRYGKRVVEELVNDFLSEKWLESNSKRCPKCKVVIERSEGCNKMHCT-KCGTYFCWICAELLY 405 (445)
T ss_pred HHHHHHHHhhHHHHHHHHHHHHHHHHHHhcCCCCCcccceeecCCCccceeec-cccccceeehhhhcC
Confidence 111233445689999999999999999999999999999 899999999987543
No 4
>KOG0006 consensus E3 ubiquitin-protein ligase (Parkin protein) [Posttranslational modification, protein turnover, chaperones]
Probab=99.89 E-value=1.3e-23 Score=207.35 Aligned_cols=195 Identities=31% Similarity=0.693 Sum_probs=147.8
Q ss_pred CCCCccccccccccccCCCceecCCC--CcccHhHHHHHHhccccCCC------CccccccCCCcCCCccchh-HHhhhc
Q 007642 137 PDGEEMTCGICFENYPSDRLLAAACG--HPFCSSCWTGYISTAINDGP------GCLMLRCPDPSCGAAVGQD-MIYLLS 207 (595)
Q Consensus 137 ~~~~~~~C~IC~e~~~~~~~~~l~Cg--H~fC~~C~~~yi~~~i~~g~------~~~~i~CP~~~C~~~v~~~-~i~~ll 207 (595)
.+....+|-.|-+.- +.+..++|. |..|.+|++.|..+.+++.. -...+.||. +|...+-.+ .--+++
T Consensus 217 ~N~~ni~C~~Ctdv~--~~vlvf~Cns~HvtC~dCFr~yc~~Rl~~rqf~~~p~~gyslpc~a-gc~~s~i~e~HHF~il 293 (446)
T KOG0006|consen 217 TNSRNITCITCTDVR--SPVLVFQCNSRHVTCLDCFRLYCVTRLNDRQFVHDPQLGYSLPCVA-GCPNSLIKELHHFRIL 293 (446)
T ss_pred cccccceeEEecCCc--cceEEEecCCceeehHHhhhhHhhhcccccccccCccccccccccC-CCchHHHHhhhhheec
Confidence 356678999998763 344557898 99999999999999886542 124678885 887766444 334678
Q ss_pred ChHHHHHHHHHHHHHhhhhCCCcccCCCCCCCCeeeeecCCCCceeee--cCCCcccccCCcccCCCCCchhHHHH----
Q 007642 208 SDEDKVKYNRYFIRSYVEDNRKTKWCPAPGCDYAVDFVVGSGNYDVTC--RCSYSFCWNCTEEAHRPVDCDTVAKW---- 281 (595)
Q Consensus 208 ~~e~~eky~~~~~~~~v~~~~~~~~CP~p~C~~~i~~~~~~~~~~v~C--~C~~~fC~~C~~~~H~p~~C~~~~~~---- 281 (595)
..+.+.+|+++..+.+|.... -+.||+|+|+..+...+ ....|+| -||+.||..|++.+|.+. |.....-
T Consensus 294 g~e~Y~rYQr~atEe~vlq~g-GVlCP~pgCG~gll~EP--D~rkvtC~~gCgf~FCR~C~e~yh~ge-C~~~~~as~t~ 369 (446)
T KOG0006|consen 294 GEEQYNRYQRYATEECVLQMG-GVLCPRPGCGAGLLPEP--DQRKVTCEGGCGFAFCRECKEAYHEGE-CSAVFEASGTT 369 (446)
T ss_pred chhHHHHHHHhhhhhheeecC-CEecCCCCCCcccccCC--CCCcccCCCCchhHhHHHHHhhhcccc-ceeeecccccc
Confidence 889999999999998887665 57999999998776654 4567999 499999999999999873 3311000
Q ss_pred -----HHhhhH-----hHHhHHHHHhcCccCCCCCcceeecCCCCcccccC-CCcceeeecccccccC
Q 007642 282 -----VLKNSA-----ESENMNWILANSKPCPRCKRPIEKNQGCMHMTCTP-PCKFEFCWLCLGQWSD 338 (595)
Q Consensus 282 -----~~k~~~-----~~e~~~wi~~ntK~CPkC~~~IEK~~GCnhmtC~~-~C~~~FCw~C~~~~~~ 338 (595)
+..+.+ +..+..-|+..|||||+|+.|.||||||+||.|.. .||.++||.|+..|..
T Consensus 370 tc~y~vde~~a~~arwd~as~~TIk~tTkpCPkChvptErnGGCmHm~Ct~~~Cg~eWCw~C~tEW~r 437 (446)
T KOG0006|consen 370 TCAYRVDERAAEQARWDAASKETIKKTTKPCPKCHVPTERNGGCMHMKCTQPQCGLEWCWNCGTEWNR 437 (446)
T ss_pred ceeeecChhhhhhhhhhhhhhhhhhhccCCCCCccCccccCCceEEeecCCCCCCceeEeccCChhhh
Confidence 001111 12233347888999999999999999999999983 6999999999999963
No 5
>smart00647 IBR In Between Ring fingers. the domains occurs between pairs og RING fingers
Probab=99.21 E-value=2e-11 Score=97.03 Aligned_cols=63 Identities=46% Similarity=1.028 Sum_probs=56.0
Q ss_pred HHHHHHHHHHhhhhCCCcccCCCCCCCCeeeeecCCCCceeee-cCCCcccccCCcccCCCCCc
Q 007642 213 VKYNRYFIRSYVEDNRKTKWCPAPGCDYAVDFVVGSGNYDVTC-RCSYSFCWNCTEEAHRPVDC 275 (595)
Q Consensus 213 eky~~~~~~~~v~~~~~~~~CP~p~C~~~i~~~~~~~~~~v~C-~C~~~fC~~C~~~~H~p~~C 275 (595)
++|.+++++++|+.++.++|||+|+|+.++......+...|.| .|++.||+.|+.+||.|.+|
T Consensus 1 ~~y~~~~~~~~i~~~~~~~~CP~~~C~~~~~~~~~~~~~~v~C~~C~~~fC~~C~~~~H~~~~C 64 (64)
T smart00647 1 EKYERLLLESYVESNPDLKWCPAPDCSAAIIVTEEEGCNRVTCPKCGFSFCFRCKVPWHSPVSC 64 (64)
T ss_pred ChHHHHHHHHHHhcCCCccCCCCCCCcceEEecCCCCCCeeECCCCCCeECCCCCCcCCCCCCC
Confidence 4789999999999989999999999999988753345678999 99999999999999999987
No 6
>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=99.09 E-value=2e-11 Score=97.01 Aligned_cols=63 Identities=35% Similarity=0.964 Sum_probs=41.8
Q ss_pred HHHHHHHHHHhhhhCCCcccCCCCCCCCeeeeecCCCCceeee-cCCCcccccCCcccCCCCCc
Q 007642 213 VKYNRYFIRSYVEDNRKTKWCPAPGCDYAVDFVVGSGNYDVTC-RCSYSFCWNCTEEAHRPVDC 275 (595)
Q Consensus 213 eky~~~~~~~~v~~~~~~~~CP~p~C~~~i~~~~~~~~~~v~C-~C~~~fC~~C~~~~H~p~~C 275 (595)
++|.+++++.+++.++.++|||+|+|+.++..........|+| .|++.||+.|+.+||.|.+|
T Consensus 1 eky~~~~~~~~~~~~~~~~~Cp~~~C~~~~~~~~~~~~~~~~C~~C~~~fC~~C~~~~H~~~~C 64 (64)
T PF01485_consen 1 EKYQKFLLKRYLESDPNIRWCPNPDCEYIIEKDDGCNSPIVTCPSCGTEFCFKCGEPWHEGVTC 64 (64)
T ss_dssp HCHHHCCCHS---S---CC--TTSST---ECS-SSTTS--CCTTSCCSEECSSSTSESCTTS-H
T ss_pred ChHHHHHHHHHHHCCCCccCCCCCCCcccEEecCCCCCCeeECCCCCCcCccccCcccCCCCCC
Confidence 4788889999998888999999999999998764444335899 69999999999999999887
No 7
>PF15227 zf-C3HC4_4: zinc finger of C3HC4-type, RING; PDB: 2EGP_A 2ECV_A 2ECJ_A 2YSL_A 2YSJ_A.
Probab=98.74 E-value=6.6e-09 Score=75.48 Aligned_cols=40 Identities=30% Similarity=0.848 Sum_probs=30.1
Q ss_pred cccccccccCCCceecCCCCcccHhHHHHHHhccccCCCCccccccC
Q 007642 144 CGICFENYPSDRLLAAACGHPFCSSCWTGYISTAINDGPGCLMLRCP 190 (595)
Q Consensus 144 C~IC~e~~~~~~~~~l~CgH~fC~~C~~~yi~~~i~~g~~~~~i~CP 190 (595)
|+||++.+ .+|++++|||+||..|+..+|...-.. .+.||
T Consensus 1 CpiC~~~~--~~Pv~l~CGH~FC~~Cl~~~~~~~~~~-----~~~CP 40 (42)
T PF15227_consen 1 CPICLDLF--KDPVSLPCGHSFCRSCLERLWKEPSGS-----GFSCP 40 (42)
T ss_dssp ETTTTSB---SSEEE-SSSSEEEHHHHHHHHCCSSSS-----T---S
T ss_pred CCccchhh--CCccccCCcCHHHHHHHHHHHHccCCc-----CCCCc
Confidence 89999998 899999999999999999999764221 37898
No 8
>PF13923 zf-C3HC4_2: Zinc finger, C3HC4 type (RING finger); PDB: 3HCU_A 2ECI_A 2JMD_A 3HCS_B 3HCT_A 3ZTG_A 2YUR_A 3L11_A.
Probab=98.27 E-value=5.9e-07 Score=64.15 Aligned_cols=31 Identities=32% Similarity=1.006 Sum_probs=26.7
Q ss_pred cccccccccCCCc-eecCCCCcccHhHHHHHHhc
Q 007642 144 CGICFENYPSDRL-LAAACGHPFCSSCWTGYIST 176 (595)
Q Consensus 144 C~IC~e~~~~~~~-~~l~CgH~fC~~C~~~yi~~ 176 (595)
|+||++.+ .++ +.++|||.||..||..|++.
T Consensus 1 C~iC~~~~--~~~~~~~~CGH~fC~~C~~~~~~~ 32 (39)
T PF13923_consen 1 CPICLDEL--RDPVVVTPCGHSFCKECIEKYLEK 32 (39)
T ss_dssp ETTTTSB---SSEEEECTTSEEEEHHHHHHHHHC
T ss_pred CCCCCCcc--cCcCEECCCCCchhHHHHHHHHHC
Confidence 89999987 556 68899999999999999876
No 9
>KOG0320 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=98.25 E-value=5.9e-07 Score=83.76 Aligned_cols=54 Identities=24% Similarity=0.709 Sum_probs=44.2
Q ss_pred CCCccccccccccccCCCceecCCCCcccHhHHHHHHhccccCCCCccccccCCCcCCCccchhH
Q 007642 138 DGEEMTCGICFENYPSDRLLAAACGHPFCSSCWTGYISTAINDGPGCLMLRCPDPSCGAAVGQDM 202 (595)
Q Consensus 138 ~~~~~~C~IC~e~~~~~~~~~l~CgH~fC~~C~~~yi~~~i~~g~~~~~i~CP~~~C~~~v~~~~ 202 (595)
+...+.||||++.+....+++..|||.||..|++.-+.. .-+|| .|+..|....
T Consensus 128 ~~~~~~CPiCl~~~sek~~vsTkCGHvFC~~Cik~alk~---------~~~CP--~C~kkIt~k~ 181 (187)
T KOG0320|consen 128 KEGTYKCPICLDSVSEKVPVSTKCGHVFCSQCIKDALKN---------TNKCP--TCRKKITHKQ 181 (187)
T ss_pred cccccCCCceecchhhccccccccchhHHHHHHHHHHHh---------CCCCC--Ccccccchhh
Confidence 455789999999998778899999999999999998765 35899 7776665543
No 10
>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=98.21 E-value=9.7e-07 Score=63.63 Aligned_cols=38 Identities=34% Similarity=1.093 Sum_probs=32.0
Q ss_pred cccccccccCCCce-ecCCCCcccHhHHHHHHhccccCCCCccccccC
Q 007642 144 CGICFENYPSDRLL-AAACGHPFCSSCWTGYISTAINDGPGCLMLRCP 190 (595)
Q Consensus 144 C~IC~e~~~~~~~~-~l~CgH~fC~~C~~~yi~~~i~~g~~~~~i~CP 190 (595)
|+||++.+ ..++ .++|||.||..||..++.. .+ .++||
T Consensus 1 C~iC~~~~--~~~~~~~~C~H~fC~~C~~~~~~~---~~----~~~CP 39 (41)
T PF00097_consen 1 CPICLEPF--EDPVILLPCGHSFCRDCLRKWLEN---SG----SVKCP 39 (41)
T ss_dssp ETTTSSBC--SSEEEETTTSEEEEHHHHHHHHHH---TS----SSBTT
T ss_pred CCcCCccc--cCCCEEecCCCcchHHHHHHHHHh---cC----CccCC
Confidence 89999987 5565 8899999999999999987 22 47898
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=98.19 E-value=7.5e-07 Score=65.35 Aligned_cols=41 Identities=32% Similarity=0.946 Sum_probs=33.5
Q ss_pred cccccccccc-CCCceecCCCCcccHhHHHHHHhccccCCCCccccccCCCcC
Q 007642 143 TCGICFENYP-SDRLLAAACGHPFCSSCWTGYISTAINDGPGCLMLRCPDPSC 194 (595)
Q Consensus 143 ~C~IC~e~~~-~~~~~~l~CgH~fC~~C~~~yi~~~i~~g~~~~~i~CP~~~C 194 (595)
.|+||++.+. ...++.++|||.||.+||..|+... .+|| .|
T Consensus 2 ~C~IC~~~~~~~~~~~~l~C~H~fh~~Ci~~~~~~~---------~~CP--~C 43 (44)
T PF13639_consen 2 ECPICLEEFEDGEKVVKLPCGHVFHRSCIKEWLKRN---------NSCP--VC 43 (44)
T ss_dssp CETTTTCBHHTTSCEEEETTSEEEEHHHHHHHHHHS---------SB-T--TT
T ss_pred CCcCCChhhcCCCeEEEccCCCeeCHHHHHHHHHhC---------CcCC--cc
Confidence 5999999985 4567889999999999999999662 3898 66
No 12
>PLN03208 E3 ubiquitin-protein ligase RMA2; Provisional
Probab=98.17 E-value=1.4e-06 Score=83.47 Aligned_cols=65 Identities=23% Similarity=0.607 Sum_probs=47.4
Q ss_pred CCCccccccccccccCCCceecCCCCcccHhHHHHHHhccccC-------CCCccccccCCCcCCCccchhHHhhh
Q 007642 138 DGEEMTCGICFENYPSDRLLAAACGHPFCSSCWTGYISTAIND-------GPGCLMLRCPDPSCGAAVGQDMIYLL 206 (595)
Q Consensus 138 ~~~~~~C~IC~e~~~~~~~~~l~CgH~fC~~C~~~yi~~~i~~-------g~~~~~i~CP~~~C~~~v~~~~i~~l 206 (595)
..+.+.|+||++.+ .+++.++|||.||..|+..|+...-.. .......+|| .|+..+....+..+
T Consensus 15 ~~~~~~CpICld~~--~dPVvT~CGH~FC~~CI~~wl~~s~~s~~~~~~~~~~k~~~~CP--vCR~~Is~~~LvPi 86 (193)
T PLN03208 15 SGGDFDCNICLDQV--RDPVVTLCGHLFCWPCIHKWTYASNNSRQRVDQYDHKREPPKCP--VCKSDVSEATLVPI 86 (193)
T ss_pred CCCccCCccCCCcC--CCcEEcCCCchhHHHHHHHHHHhccccccccccccccCCCCcCC--CCCCcCChhcEEEe
Confidence 34578999999986 788889999999999999987642110 0001257899 89999876655443
No 13
>PF13445 zf-RING_UBOX: RING-type zinc-finger; PDB: 2CT2_A.
Probab=98.10 E-value=1.8e-06 Score=62.84 Aligned_cols=41 Identities=29% Similarity=0.801 Sum_probs=23.2
Q ss_pred cccccccccC--CCceecCCCCcccHhHHHHHHhccccCCCCccccccC
Q 007642 144 CGICFENYPS--DRLLAAACGHPFCSSCWTGYISTAINDGPGCLMLRCP 190 (595)
Q Consensus 144 C~IC~e~~~~--~~~~~l~CgH~fC~~C~~~yi~~~i~~g~~~~~i~CP 190 (595)
|+||.+ +.. ..|+.|+|||.||++|+.+.+.... + ..++||
T Consensus 1 CpIc~e-~~~~~n~P~~L~CGH~~c~~cl~~l~~~~~--~---~~~kCP 43 (43)
T PF13445_consen 1 CPICKE-FSTEENPPMVLPCGHVFCKDCLQKLSKKSD--R---NRFKCP 43 (43)
T ss_dssp -TTT-----TTSS-EEE-SSS-EEEHHHHHHHHHH-S------S-B--T
T ss_pred CCcccc-ccCCCCCCEEEeCccHHHHHHHHHHHhcCC--C---CeeeCc
Confidence 899999 632 2378899999999999999998543 1 268887
No 14
>KOG4367 consensus Predicted Zn-finger protein [Function unknown]
Probab=97.94 E-value=5.6e-05 Score=79.06 Aligned_cols=34 Identities=26% Similarity=0.727 Sum_probs=29.9
Q ss_pred CccccccccccccCCCceecCCCCcccHhHHHHHHh
Q 007642 140 EEMTCGICFENYPSDRLLAAACGHPFCSSCWTGYIS 175 (595)
Q Consensus 140 ~~~~C~IC~e~~~~~~~~~l~CgH~fC~~C~~~yi~ 175 (595)
+++.|+||..-| .+|+.++|+|+.|+-|-+..+.
T Consensus 3 eelkc~vc~~f~--~epiil~c~h~lc~~ca~~~~~ 36 (699)
T KOG4367|consen 3 EELKCPVCGSFY--REPIILPCSHNLCQACARNILV 36 (699)
T ss_pred ccccCceehhhc--cCceEeecccHHHHHHHHhhcc
Confidence 467899999887 8999999999999999987654
No 15
>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=97.91 E-value=8.9e-06 Score=61.37 Aligned_cols=46 Identities=33% Similarity=0.853 Sum_probs=37.2
Q ss_pred ccccccccccccCCCceecCCCCc-ccHhHHHHHHhccccCCCCccccccCCCcCCCccc
Q 007642 141 EMTCGICFENYPSDRLLAAACGHP-FCSSCWTGYISTAINDGPGCLMLRCPDPSCGAAVG 199 (595)
Q Consensus 141 ~~~C~IC~e~~~~~~~~~l~CgH~-fC~~C~~~yi~~~i~~g~~~~~i~CP~~~C~~~v~ 199 (595)
...|.||++.. .+++.++|||. ||..|+..++.. ..+|| .|+..|.
T Consensus 2 ~~~C~iC~~~~--~~~~~~pCgH~~~C~~C~~~~~~~---------~~~CP--~Cr~~i~ 48 (50)
T PF13920_consen 2 DEECPICFENP--RDVVLLPCGHLCFCEECAERLLKR---------KKKCP--ICRQPIE 48 (50)
T ss_dssp HSB-TTTSSSB--SSEEEETTCEEEEEHHHHHHHHHT---------TSBBT--TTTBB-S
T ss_pred cCCCccCCccC--CceEEeCCCChHHHHHHhHHhccc---------CCCCC--cCChhhc
Confidence 46799999975 67889999999 999999999872 46899 8988764
No 16
>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=97.88 E-value=7.5e-06 Score=64.69 Aligned_cols=37 Identities=43% Similarity=1.092 Sum_probs=29.2
Q ss_pred CccCCC--CCcceeecCCCCc--ccccCCCcceeeecccccc
Q 007642 299 SKPCPR--CKRPIEKNQGCMH--MTCTPPCKFEFCWLCLGQW 336 (595)
Q Consensus 299 tK~CPk--C~~~IEK~~GCnh--mtC~~~C~~~FCw~C~~~~ 336 (595)
.+.||+ |...|++..|.++ |+|. .|++.|||.|+.+|
T Consensus 18 ~~~Cp~~~C~~~~~~~~~~~~~~~~C~-~C~~~fC~~C~~~~ 58 (64)
T PF01485_consen 18 IRWCPNPDCEYIIEKDDGCNSPIVTCP-SCGTEFCFKCGEPW 58 (64)
T ss_dssp CC--TTSST---ECS-SSTTS--CCTT-SCCSEECSSSTSES
T ss_pred ccCCCCCCCcccEEecCCCCCCeeECC-CCCCcCccccCccc
Confidence 479987 9999999999999 9998 89999999999999
No 17
>KOG2177 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=97.87 E-value=7.2e-06 Score=84.22 Aligned_cols=110 Identities=24% Similarity=0.483 Sum_probs=64.8
Q ss_pred CCccccccccccccCCCceecCCCCcccHhHHHHHHhccccCCCCccccccCCCcCCCccchhHHhhhcChHHHHHHHHH
Q 007642 139 GEEMTCGICFENYPSDRLLAAACGHPFCSSCWTGYISTAINDGPGCLMLRCPDPSCGAAVGQDMIYLLSSDEDKVKYNRY 218 (595)
Q Consensus 139 ~~~~~C~IC~e~~~~~~~~~l~CgH~fC~~C~~~yi~~~i~~g~~~~~i~CP~~~C~~~v~~~~i~~ll~~e~~eky~~~ 218 (595)
...+.|+||++.+ ..+..++|||.||..|+...|. + .+.|| .|+. .......+.....+.+.+...
T Consensus 11 ~~~~~C~iC~~~~--~~p~~l~C~H~~c~~C~~~~~~-----~----~~~Cp--~cr~-~~~~~~~n~~l~~~~~~~~~~ 76 (386)
T KOG2177|consen 11 QEELTCPICLEYF--REPVLLPCGHNFCRACLTRSWE-----G----PLSCP--VCRP-PSRNLRPNVLLANLVERLRQL 76 (386)
T ss_pred cccccChhhHHHh--hcCccccccchHhHHHHHHhcC-----C----CcCCc--ccCC-chhccCccHHHHHHHHHHHhc
Confidence 4578999999998 6668899999999999999998 2 58999 8984 222111111111222222211
Q ss_pred HHHHhhhhCCCcccCCCCCCCCeeeeecCCCCceeee-cCCCcccccCC-cccCCCCCc
Q 007642 219 FIRSYVEDNRKTKWCPAPGCDYAVDFVVGSGNYDVTC-RCSYSFCWNCT-EEAHRPVDC 275 (595)
Q Consensus 219 ~~~~~v~~~~~~~~CP~p~C~~~i~~~~~~~~~~v~C-~C~~~fC~~C~-~~~H~p~~C 275 (595)
..... .......|+. ......+.| .|....|..|. ...|.....
T Consensus 77 ~~~~~--~~~~~~~c~~-----------~~~~~~~~c~~~~~~~c~~c~~~~~h~~h~~ 122 (386)
T KOG2177|consen 77 RLSRP--LGSKEELCEK-----------HGEELKLFCEEDEKLLCVLCRESGEHRGHPV 122 (386)
T ss_pred CCccc--ccccchhhhh-----------cCCcceEEecccccccCCCCCCcccccCCcc
Confidence 11000 0000002331 111255789 89999999998 666766543
No 18
>smart00647 IBR In Between Ring fingers. the domains occurs between pairs og RING fingers
Probab=97.85 E-value=1.9e-05 Score=62.44 Aligned_cols=38 Identities=39% Similarity=1.046 Sum_probs=34.3
Q ss_pred cCccCC--CCCcceeecC--CCCcccccCCCcceeeecccccc
Q 007642 298 NSKPCP--RCKRPIEKNQ--GCMHMTCTPPCKFEFCWLCLGQW 336 (595)
Q Consensus 298 ntK~CP--kC~~~IEK~~--GCnhmtC~~~C~~~FCw~C~~~~ 336 (595)
+.+.|| +|+..|+... |..+|+|. .|++.|||.|+.+|
T Consensus 17 ~~~~CP~~~C~~~~~~~~~~~~~~v~C~-~C~~~fC~~C~~~~ 58 (64)
T smart00647 17 DLKWCPAPDCSAAIIVTEEEGCNRVTCP-KCGFSFCFRCKVPW 58 (64)
T ss_pred CccCCCCCCCcceEEecCCCCCCeeECC-CCCCeECCCCCCcC
Confidence 357899 9999999965 99999996 69999999999998
No 19
>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=97.80 E-value=1.9e-05 Score=57.08 Aligned_cols=43 Identities=35% Similarity=0.976 Sum_probs=33.3
Q ss_pred ccccccccccCCCcee-cCCCCcccHhHHHHHHhccccCCCCccccccCCCcCCCc
Q 007642 143 TCGICFENYPSDRLLA-AACGHPFCSSCWTGYISTAINDGPGCLMLRCPDPSCGAA 197 (595)
Q Consensus 143 ~C~IC~e~~~~~~~~~-l~CgH~fC~~C~~~yi~~~i~~g~~~~~i~CP~~~C~~~ 197 (595)
.|+||++.+ ..++. .+|||.||..|+..|+.. + ..+|| .|+..
T Consensus 1 ~C~iC~~~~--~~~~~~~~C~H~~c~~C~~~~~~~----~----~~~Cp--~C~~~ 44 (45)
T cd00162 1 ECPICLEEF--REPVVLLPCGHVFCRSCIDKWLKS----G----KNTCP--LCRTP 44 (45)
T ss_pred CCCcCchhh--hCceEecCCCChhcHHHHHHHHHh----C----cCCCC--CCCCc
Confidence 499999987 44444 459999999999999875 2 46799 78764
No 20
>PF14634 zf-RING_5: zinc-RING finger domain
Probab=97.80 E-value=1.5e-05 Score=58.41 Aligned_cols=42 Identities=40% Similarity=1.048 Sum_probs=33.9
Q ss_pred cccccccccc-CCCceecCCCCcccHhHHHHHHhccccCCCCccccccCCCcCC
Q 007642 143 TCGICFENYP-SDRLLAAACGHPFCSSCWTGYISTAINDGPGCLMLRCPDPSCG 195 (595)
Q Consensus 143 ~C~IC~e~~~-~~~~~~l~CgH~fC~~C~~~yi~~~i~~g~~~~~i~CP~~~C~ 195 (595)
.|+||++.+. ...++.++|||.||..|+.... +. .+.|| .|+
T Consensus 1 ~C~~C~~~~~~~~~~~l~~CgH~~C~~C~~~~~------~~---~~~CP--~C~ 43 (44)
T PF14634_consen 1 HCNICFEKYSEERRPRLTSCGHIFCEKCLKKLK------GK---SVKCP--ICR 43 (44)
T ss_pred CCcCcCccccCCCCeEEcccCCHHHHHHHHhhc------CC---CCCCc--CCC
Confidence 4999999983 3467888999999999999986 21 57899 675
No 21
>smart00504 Ubox Modified RING finger domain. Modified RING finger domain, without the full complement of Zn2+-binding ligands. Probable involvement in E2-dependent ubiquitination.
Probab=97.76 E-value=2.6e-05 Score=61.56 Aligned_cols=47 Identities=13% Similarity=0.265 Sum_probs=39.2
Q ss_pred cccccccccccCCCceecCCCCcccHhHHHHHHhccccCCCCccccccCCCcCCCccchh
Q 007642 142 MTCGICFENYPSDRLLAAACGHPFCSSCWTGYISTAINDGPGCLMLRCPDPSCGAAVGQD 201 (595)
Q Consensus 142 ~~C~IC~e~~~~~~~~~l~CgH~fC~~C~~~yi~~~i~~g~~~~~i~CP~~~C~~~v~~~ 201 (595)
+.|+||++.+ .+|+.++|||.||+.|+..|+.. + ..|| .|+..++..
T Consensus 2 ~~Cpi~~~~~--~~Pv~~~~G~v~~~~~i~~~~~~----~-----~~cP--~~~~~~~~~ 48 (63)
T smart00504 2 FLCPISLEVM--KDPVILPSGQTYERRAIEKWLLS----H-----GTDP--VTGQPLTHE 48 (63)
T ss_pred cCCcCCCCcC--CCCEECCCCCEEeHHHHHHHHHH----C-----CCCC--CCcCCCChh
Confidence 6799999987 77999999999999999999965 1 3688 788777543
No 22
>KOG0823 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=97.76 E-value=1.4e-05 Score=77.93 Aligned_cols=56 Identities=34% Similarity=0.754 Sum_probs=46.8
Q ss_pred CCCccccccccccccCCCceecCCCCcccHhHHHHHHhccccCCCCccccccCCCcCCCccchhHH
Q 007642 138 DGEEMTCGICFENYPSDRLLAAACGHPFCSSCWTGYISTAINDGPGCLMLRCPDPSCGAAVGQDMI 203 (595)
Q Consensus 138 ~~~~~~C~IC~e~~~~~~~~~l~CgH~fC~~C~~~yi~~~i~~g~~~~~i~CP~~~C~~~v~~~~i 203 (595)
....|.|.|||+.- .++|...|||.||-.||-+|+..... .-.|| .|+..|..+.+
T Consensus 44 ~~~~FdCNICLd~a--kdPVvTlCGHLFCWpClyqWl~~~~~------~~~cP--VCK~~Vs~~~v 99 (230)
T KOG0823|consen 44 DGGFFDCNICLDLA--KDPVVTLCGHLFCWPCLYQWLQTRPN------SKECP--VCKAEVSIDTV 99 (230)
T ss_pred CCCceeeeeecccc--CCCEEeecccceehHHHHHHHhhcCC------CeeCC--ccccccccceE
Confidence 45689999999976 89999999999999999999987643 24688 89998876644
No 23
>TIGR00599 rad18 DNA repair protein rad18. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=97.75 E-value=2e-05 Score=84.18 Aligned_cols=66 Identities=24% Similarity=0.530 Sum_probs=49.8
Q ss_pred CCccccccccccccCCCceecCCCCcccHhHHHHHHhccccCCCCccccccCCCcCCCccchh-HHhhhcChHHHHHHHH
Q 007642 139 GEEMTCGICFENYPSDRLLAAACGHPFCSSCWTGYISTAINDGPGCLMLRCPDPSCGAAVGQD-MIYLLSSDEDKVKYNR 217 (595)
Q Consensus 139 ~~~~~C~IC~e~~~~~~~~~l~CgH~fC~~C~~~yi~~~i~~g~~~~~i~CP~~~C~~~v~~~-~i~~ll~~e~~eky~~ 217 (595)
...+.|+||++.+ ..++.++|||.||..|+..|+.. ...|| .|+..+... +..+.+..++++.|..
T Consensus 24 e~~l~C~IC~d~~--~~PvitpCgH~FCs~CI~~~l~~---------~~~CP--~Cr~~~~~~~Lr~N~~L~~iVe~~~~ 90 (397)
T TIGR00599 24 DTSLRCHICKDFF--DVPVLTSCSHTFCSLCIRRCLSN---------QPKCP--LCRAEDQESKLRSNWLVSEIVESFKN 90 (397)
T ss_pred ccccCCCcCchhh--hCccCCCCCCchhHHHHHHHHhC---------CCCCC--CCCCccccccCccchHHHHHHHHHHH
Confidence 3578999999987 78888999999999999999864 13799 899988653 3334444556666653
No 24
>KOG0317 consensus Predicted E3 ubiquitin ligase, integral peroxisomal membrane protein [Posttranslational modification, protein turnover, chaperones]
Probab=97.72 E-value=3.2e-05 Score=77.68 Aligned_cols=52 Identities=31% Similarity=0.703 Sum_probs=43.3
Q ss_pred CCccccccccccccCCCceecCCCCcccHhHHHHHHhccccCCCCccccccCCCcCCCccchhHH
Q 007642 139 GEEMTCGICFENYPSDRLLAAACGHPFCSSCWTGYISTAINDGPGCLMLRCPDPSCGAAVGQDMI 203 (595)
Q Consensus 139 ~~~~~C~IC~e~~~~~~~~~l~CgH~fC~~C~~~yi~~~i~~g~~~~~i~CP~~~C~~~v~~~~i 203 (595)
.....|.+|++.. .+|..+||||.||-.||..|...+ -.|| .|+..+.+..+
T Consensus 237 ~a~~kC~LCLe~~--~~pSaTpCGHiFCWsCI~~w~~ek---------~eCP--lCR~~~~pskv 288 (293)
T KOG0317|consen 237 EATRKCSLCLENR--SNPSATPCGHIFCWSCILEWCSEK---------AECP--LCREKFQPSKV 288 (293)
T ss_pred CCCCceEEEecCC--CCCCcCcCcchHHHHHHHHHHccc---------cCCC--cccccCCCcce
Confidence 3457899999975 789999999999999999998653 2499 99999877644
No 25
>KOG0287 consensus Postreplication repair protein RAD18 [Replication, recombination and repair]
Probab=97.67 E-value=2.1e-05 Score=79.97 Aligned_cols=64 Identities=31% Similarity=0.682 Sum_probs=50.7
Q ss_pred CccccccccccccCCCceecCCCCcccHhHHHHHHhccccCCCCccccccCCCcCCCccchhHHh-hhcChHHHHHHH
Q 007642 140 EEMTCGICFENYPSDRLLAAACGHPFCSSCWTGYISTAINDGPGCLMLRCPDPSCGAAVGQDMIY-LLSSDEDKVKYN 216 (595)
Q Consensus 140 ~~~~C~IC~e~~~~~~~~~l~CgH~fC~~C~~~yi~~~i~~g~~~~~i~CP~~~C~~~v~~~~i~-~ll~~e~~eky~ 216 (595)
..+.|.||++.| .-++.+||+|.||.-||+.|+.. ...|| .|...+.+..++ +.+..++++-|.
T Consensus 22 ~lLRC~IC~eyf--~ip~itpCsHtfCSlCIR~~L~~---------~p~CP--~C~~~~~Es~Lr~n~il~Eiv~S~~ 86 (442)
T KOG0287|consen 22 DLLRCGICFEYF--NIPMITPCSHTFCSLCIRKFLSY---------KPQCP--TCCVTVTESDLRNNRILDEIVKSLN 86 (442)
T ss_pred HHHHHhHHHHHh--cCceeccccchHHHHHHHHHhcc---------CCCCC--ceecccchhhhhhhhHHHHHHHHHH
Confidence 357899999998 67888899999999999999865 35799 899999776554 455567666654
No 26
>KOG2164 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=97.57 E-value=2.9e-05 Score=83.58 Aligned_cols=60 Identities=27% Similarity=0.614 Sum_probs=46.7
Q ss_pred ccccccccccccCCCceecCCCCcccHhHHHHHHhccccCCCCccccccCCCcCCCccchhHHhhhcC
Q 007642 141 EMTCGICFENYPSDRLLAAACGHPFCSSCWTGYISTAINDGPGCLMLRCPDPSCGAAVGQDMIYLLSS 208 (595)
Q Consensus 141 ~~~C~IC~e~~~~~~~~~l~CgH~fC~~C~~~yi~~~i~~g~~~~~i~CP~~~C~~~v~~~~i~~ll~ 208 (595)
...|||||+.. .-++.+.|||.||-.||-.||......+ ..+|| -|...|.+..+..+.-
T Consensus 186 ~~~CPICL~~~--~~p~~t~CGHiFC~~CiLqy~~~s~~~~----~~~CP--iC~s~I~~kdl~pv~~ 245 (513)
T KOG2164|consen 186 DMQCPICLEPP--SVPVRTNCGHIFCGPCILQYWNYSAIKG----PCSCP--ICRSTITLKDLLPVFI 245 (513)
T ss_pred CCcCCcccCCC--CcccccccCceeeHHHHHHHHhhhcccC----CccCC--chhhhccccceeeeee
Confidence 67899999875 4456667999999999999999873333 57899 8999988766555443
No 27
>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=97.56 E-value=5.7e-05 Score=52.59 Aligned_cols=30 Identities=37% Similarity=1.009 Sum_probs=26.9
Q ss_pred cccccccccCCCceecCCCCcccHhHHHHHHh
Q 007642 144 CGICFENYPSDRLLAAACGHPFCSSCWTGYIS 175 (595)
Q Consensus 144 C~IC~e~~~~~~~~~l~CgH~fC~~C~~~yi~ 175 (595)
|+||++.. ..++.++|||.||..|+..|+.
T Consensus 1 C~iC~~~~--~~~~~~~C~H~~c~~C~~~~~~ 30 (39)
T smart00184 1 CPICLEEL--KDPVVLPCGHTFCRSCIRKWLK 30 (39)
T ss_pred CCcCccCC--CCcEEecCCChHHHHHHHHHHH
Confidence 78999873 6788899999999999999987
No 28
>PHA02926 zinc finger-like protein; Provisional
Probab=97.56 E-value=5.8e-05 Score=73.20 Aligned_cols=56 Identities=34% Similarity=0.670 Sum_probs=40.1
Q ss_pred CCccccccccccccC-----C--CceecCCCCcccHhHHHHHHhccccCCCCccccccCCCcCCCccc
Q 007642 139 GEEMTCGICFENYPS-----D--RLLAAACGHPFCSSCWTGYISTAINDGPGCLMLRCPDPSCGAAVG 199 (595)
Q Consensus 139 ~~~~~C~IC~e~~~~-----~--~~~~l~CgH~fC~~C~~~yi~~~i~~g~~~~~i~CP~~~C~~~v~ 199 (595)
+...+|+||++..-. . -.+..+|+|.||..|++.|-..+...|. .-.|| .|+..+.
T Consensus 168 SkE~eCgICmE~I~eK~~~~eRrFGIL~~CnHsFCl~CIr~Wr~~r~~~~~---~rsCP--iCR~~f~ 230 (242)
T PHA02926 168 SKEKECGICYEVVYSKRLENDRYFGLLDSCNHIFCITCINIWHRTRRETGA---SDNCP--ICRTRFR 230 (242)
T ss_pred cCCCCCccCccccccccccccccccccCCCCchHHHHHHHHHHHhccccCc---CCcCC--CCcceee
Confidence 456889999987421 1 1345579999999999999886533332 45799 8998654
No 29
>PHA02929 N1R/p28-like protein; Provisional
Probab=97.54 E-value=6.4e-05 Score=75.07 Aligned_cols=50 Identities=24% Similarity=0.615 Sum_probs=37.5
Q ss_pred CCccccccccccccCCC------ceecCCCCcccHhHHHHHHhccccCCCCccccccCCCcCCCccc
Q 007642 139 GEEMTCGICFENYPSDR------LLAAACGHPFCSSCWTGYISTAINDGPGCLMLRCPDPSCGAAVG 199 (595)
Q Consensus 139 ~~~~~C~IC~e~~~~~~------~~~l~CgH~fC~~C~~~yi~~~i~~g~~~~~i~CP~~~C~~~v~ 199 (595)
.....|+||++.+.... .+.++|||.||..|+..|+.. ...|| .|+..+.
T Consensus 172 ~~~~eC~ICle~~~~~~~~~~~~~vl~~C~H~FC~~CI~~Wl~~---------~~tCP--lCR~~~~ 227 (238)
T PHA02929 172 SKDKECAICMEKVYDKEIKNMYFGILSNCNHVFCIECIDIWKKE---------KNTCP--VCRTPFI 227 (238)
T ss_pred CCCCCCccCCcccccCccccccceecCCCCCcccHHHHHHHHhc---------CCCCC--CCCCEee
Confidence 34678999999864322 245679999999999998753 24799 8998764
No 30
>KOG0804 consensus Cytoplasmic Zn-finger protein BRAP2 (BRCA1 associated protein) [General function prediction only]
Probab=97.40 E-value=0.0063 Score=64.72 Aligned_cols=116 Identities=22% Similarity=0.335 Sum_probs=67.2
Q ss_pred eCHHHHHHHHHHHHHHHHHHhCCCHH--HHHHHHHHcCCChhhh--HHHh----hh--cHHHHHHHhCCC-----CC-CC
Q 007642 70 LTEADIRQRQEEDITRISTVLSISKV--AASILLRFYNWSVSKV--HDEW----FA--DEERVRKAVGLL-----EK-PA 133 (595)
Q Consensus 70 l~~~~i~~~~~~~i~~v~~vl~i~~~--~a~~LL~~~~W~~~~l--~e~~----~~--~~~~~~~~~gl~-----~~-~~ 133 (595)
+|..|+..-+..-+..|+.+.=|-.+ .-.++|..|+=..+.. .+.| |. +++ +...+-+. .. +.
T Consensus 86 mt~~Dll~F~~~~~~~I~~irivRd~~pnrymvLIkFr~q~da~~Fy~efNGk~Fn~le~e-~Chll~V~~ve~~~s~d~ 164 (493)
T KOG0804|consen 86 MTSHDLLRFCASFIKQISDIRIVRDGMPNRYMVLIKFRDQADADTFYEEFNGKQFNSLEPE-VCHLLYVDRVEVTESEDG 164 (493)
T ss_pred ccHHHHHHHHHHHhhhhheeEEeecCCCceEEEEEEeccchhHHHHHHHcCCCcCCCCCcc-ceeEEEEEEEEEEecccC
Confidence 78899999988888888877655321 2234455565443322 1221 10 111 11111110 00 01
Q ss_pred C---CCCCCCccccccccccccC--CCceecCCCCcccHhHHHHHHhccccCCCCccccccCCCcCCCccc
Q 007642 134 V---QFPDGEEMTCGICFENYPS--DRLLAAACGHPFCSSCWTGYISTAINDGPGCLMLRCPDPSCGAAVG 199 (595)
Q Consensus 134 ~---~~~~~~~~~C~IC~e~~~~--~~~~~l~CgH~fC~~C~~~yi~~~i~~g~~~~~i~CP~~~C~~~v~ 199 (595)
. .....+..+||||++-... +-+++..|.|.|--.|+..|+ ..+|| .|+....
T Consensus 165 as~~~~~~tELPTCpVCLERMD~s~~gi~t~~c~Hsfh~~cl~~w~-----------~~scp--vcR~~q~ 222 (493)
T KOG0804|consen 165 ASEPPTGLTELPTCPVCLERMDSSTTGILTILCNHSFHCSCLMKWW-----------DSSCP--VCRYCQS 222 (493)
T ss_pred CCCCCCCcccCCCcchhHhhcCccccceeeeecccccchHHHhhcc-----------cCcCh--hhhhhcC
Confidence 1 1112346789999997753 245778899999999999996 35798 7865444
No 31
>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=97.04 E-value=0.00058 Score=55.81 Aligned_cols=50 Identities=16% Similarity=0.208 Sum_probs=38.1
Q ss_pred CccccccccccccCCCceecCCCCcccHhHHHHHHhccccCCCCccccccCCCcCCCccchh
Q 007642 140 EEMTCGICFENYPSDRLLAAACGHPFCSSCWTGYISTAINDGPGCLMLRCPDPSCGAAVGQD 201 (595)
Q Consensus 140 ~~~~C~IC~e~~~~~~~~~l~CgH~fC~~C~~~yi~~~i~~g~~~~~i~CP~~~C~~~v~~~ 201 (595)
+.|.|+|+.+.+ .+|+.+++||.|++.||..|+.. + ...|| .|+..+...
T Consensus 3 ~~f~CpIt~~lM--~dPVi~~~G~tyer~~I~~~l~~----~----~~~~P--~t~~~l~~~ 52 (73)
T PF04564_consen 3 DEFLCPITGELM--RDPVILPSGHTYERSAIERWLEQ----N----GGTDP--FTRQPLSES 52 (73)
T ss_dssp GGGB-TTTSSB---SSEEEETTSEEEEHHHHHHHHCT----T----SSB-T--TT-SB-SGG
T ss_pred cccCCcCcCcHh--hCceeCCcCCEEcHHHHHHHHHc----C----CCCCC--CCCCcCCcc
Confidence 478999999987 89999999999999999999976 1 35798 777777654
No 32
>KOG0978 consensus E3 ubiquitin ligase involved in syntaxin degradation [Posttranslational modification, protein turnover, chaperones]
Probab=97.01 E-value=0.00021 Score=80.61 Aligned_cols=54 Identities=30% Similarity=0.741 Sum_probs=44.9
Q ss_pred CccccccccccccCCCceecCCCCcccHhHHHHHHhccccCCCCccccccCCCcCCCccchhHHhh
Q 007642 140 EEMTCGICFENYPSDRLLAAACGHPFCSSCWTGYISTAINDGPGCLMLRCPDPSCGAAVGQDMIYL 205 (595)
Q Consensus 140 ~~~~C~IC~e~~~~~~~~~l~CgH~fC~~C~~~yi~~~i~~g~~~~~i~CP~~~C~~~v~~~~i~~ 205 (595)
..++||+|..-. .+.+...|||.||..|++..+.+. .-+|| .|+..|++..|..
T Consensus 642 ~~LkCs~Cn~R~--Kd~vI~kC~H~FC~~Cvq~r~etR--------qRKCP--~Cn~aFganDv~~ 695 (698)
T KOG0978|consen 642 ELLKCSVCNTRW--KDAVITKCGHVFCEECVQTRYETR--------QRKCP--KCNAAFGANDVHR 695 (698)
T ss_pred hceeCCCccCch--hhHHHHhcchHHHHHHHHHHHHHh--------cCCCC--CCCCCCCcccccc
Confidence 467899999543 788889999999999999998774 34899 9999998877654
No 33
>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=96.87 E-value=0.00087 Score=69.07 Aligned_cols=51 Identities=24% Similarity=0.603 Sum_probs=37.1
Q ss_pred cccccccccccC-CC---ceecCCCCcccHhHHHHHHhccccCCCCccccccCCCcCCCccchhHH
Q 007642 142 MTCGICFENYPS-DR---LLAAACGHPFCSSCWTGYISTAINDGPGCLMLRCPDPSCGAAVGQDMI 203 (595)
Q Consensus 142 ~~C~IC~e~~~~-~~---~~~l~CgH~fC~~C~~~yi~~~i~~g~~~~~i~CP~~~C~~~v~~~~i 203 (595)
..||||...... .. ++. +|||.||..|+...|.. | +..|| .|+..+....+
T Consensus 4 ~~CP~Ck~~~y~np~~kl~i~-~CGH~~C~sCv~~l~~~----~----~~~CP--~C~~~lrk~~f 58 (309)
T TIGR00570 4 QGCPRCKTTKYRNPSLKLMVN-VCGHTLCESCVDLLFVR----G----SGSCP--ECDTPLRKNNF 58 (309)
T ss_pred CCCCcCCCCCccCcccccccC-CCCCcccHHHHHHHhcC----C----CCCCC--CCCCccchhhc
Confidence 579999985222 22 233 79999999999999842 3 35899 99998876543
No 34
>COG5574 PEX10 RING-finger-containing E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=96.63 E-value=0.0015 Score=65.19 Aligned_cols=53 Identities=28% Similarity=0.565 Sum_probs=42.1
Q ss_pred CccccccccccccCCCceecCCCCcccHhHHHHHHhccccCCCCccccccCCCcCCCccchhHH
Q 007642 140 EEMTCGICFENYPSDRLLAAACGHPFCSSCWTGYISTAINDGPGCLMLRCPDPSCGAAVGQDMI 203 (595)
Q Consensus 140 ~~~~C~IC~e~~~~~~~~~l~CgH~fC~~C~~~yi~~~i~~g~~~~~i~CP~~~C~~~v~~~~i 203 (595)
..+.|.||++.. ..+..++|||.||..|+-..|..+- .-.|| .|++.+.+..|
T Consensus 214 ~d~kC~lC~e~~--~~ps~t~CgHlFC~~Cl~~~~t~~k-------~~~Cp--lCRak~~pk~v 266 (271)
T COG5574 214 ADYKCFLCLEEP--EVPSCTPCGHLFCLSCLLISWTKKK-------YEFCP--LCRAKVYPKKV 266 (271)
T ss_pred cccceeeeeccc--CCcccccccchhhHHHHHHHHHhhc-------cccCc--hhhhhccchhh
Confidence 367899999975 7889999999999999999665421 23599 89998876655
No 35
>PF14835 zf-RING_6: zf-RING of BARD1-type protein; PDB: 1JM7_B.
Probab=96.53 E-value=0.00073 Score=52.98 Aligned_cols=43 Identities=35% Similarity=0.870 Sum_probs=22.3
Q ss_pred ccccccccccccCCCceec-CCCCcccHhHHHHHHhccccCCCCccccccCCCcCCCcc
Q 007642 141 EMTCGICFENYPSDRLLAA-ACGHPFCSSCWTGYISTAINDGPGCLMLRCPDPSCGAAV 198 (595)
Q Consensus 141 ~~~C~IC~e~~~~~~~~~l-~CgH~fC~~C~~~yi~~~i~~g~~~~~i~CP~~~C~~~v 198 (595)
.+.|++|.+.+ ..|+.+ .|.|.||..|++..+. ..|| .|..+-
T Consensus 7 lLrCs~C~~~l--~~pv~l~~CeH~fCs~Ci~~~~~-----------~~CP--vC~~Pa 50 (65)
T PF14835_consen 7 LLRCSICFDIL--KEPVCLGGCEHIFCSSCIRDCIG-----------SECP--VCHTPA 50 (65)
T ss_dssp TTS-SSS-S----SS-B---SSS--B-TTTGGGGTT-----------TB-S--SS--B-
T ss_pred hcCCcHHHHHh--cCCceeccCccHHHHHHhHHhcC-----------CCCC--CcCChH
Confidence 45799999987 788865 6999999999977542 3599 888654
No 36
>PF11789 zf-Nse: Zinc-finger of the MIZ type in Nse subunit; PDB: 2YU4_A 3HTK_C.
Probab=96.43 E-value=0.0026 Score=49.39 Aligned_cols=47 Identities=26% Similarity=0.603 Sum_probs=30.8
Q ss_pred CccccccccccccCCCcee-cCCCCcccHhHHHHHHhccccCCCCccccccCCCcCC
Q 007642 140 EEMTCGICFENYPSDRLLA-AACGHPFCSSCWTGYISTAINDGPGCLMLRCPDPSCG 195 (595)
Q Consensus 140 ~~~~C~IC~e~~~~~~~~~-l~CgH~fC~~C~~~yi~~~i~~g~~~~~i~CP~~~C~ 195 (595)
-.+.|||.+..+ .+|+. ..|||.|.++.+..|+. .+ ..++||..+|.
T Consensus 10 ~~~~CPiT~~~~--~~PV~s~~C~H~fek~aI~~~i~----~~---~~~~CPv~GC~ 57 (57)
T PF11789_consen 10 ISLKCPITLQPF--EDPVKSKKCGHTFEKEAILQYIQ----RN---GSKRCPVAGCN 57 (57)
T ss_dssp --SB-TTTSSB---SSEEEESSS--EEEHHHHHHHCT----TT---S-EE-SCCC-S
T ss_pred eccCCCCcCChh--hCCcCcCCCCCeecHHHHHHHHH----hc---CCCCCCCCCCC
Confidence 367899999887 77765 58999999999999992 22 26899998884
No 37
>KOG4628 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=96.33 E-value=0.0051 Score=64.51 Aligned_cols=48 Identities=29% Similarity=0.754 Sum_probs=39.0
Q ss_pred cccccccccccCC-CceecCCCCcccHhHHHHHHhccccCCCCccccccCCCcCCCccc
Q 007642 142 MTCGICFENYPSD-RLLAAACGHPFCSSCWTGYISTAINDGPGCLMLRCPDPSCGAAVG 199 (595)
Q Consensus 142 ~~C~IC~e~~~~~-~~~~l~CgH~fC~~C~~~yi~~~i~~g~~~~~i~CP~~~C~~~v~ 199 (595)
.+|.||+|.|... ....|||+|.|...|+..|+... .-.|| -|+.-+.
T Consensus 230 ~~CaIClEdY~~GdklRiLPC~H~FH~~CIDpWL~~~--------r~~CP--vCK~di~ 278 (348)
T KOG4628|consen 230 DTCAICLEDYEKGDKLRILPCSHKFHVNCIDPWLTQT--------RTFCP--VCKRDIR 278 (348)
T ss_pred ceEEEeecccccCCeeeEecCCCchhhccchhhHhhc--------CccCC--CCCCcCC
Confidence 6999999999765 46779999999999999999763 13599 7887553
No 38
>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=96.20 E-value=0.0047 Score=50.50 Aligned_cols=43 Identities=28% Similarity=0.715 Sum_probs=30.3
Q ss_pred cccccccccccC----------CC-ceecCCCCcccHhHHHHHHhccccCCCCccccccCCCcCC
Q 007642 142 MTCGICFENYPS----------DR-LLAAACGHPFCSSCWTGYISTAINDGPGCLMLRCPDPSCG 195 (595)
Q Consensus 142 ~~C~IC~e~~~~----------~~-~~~l~CgH~fC~~C~~~yi~~~i~~g~~~~~i~CP~~~C~ 195 (595)
-.|.||++.+.. .. ++..+|||.|...||..++... -.|| .|+
T Consensus 20 d~C~IC~~~l~~~~~~~~~~~~~~~i~~~~C~H~FH~~Ci~~Wl~~~---------~~CP--~CR 73 (73)
T PF12678_consen 20 DNCAICREPLEDPCPECQAPQDECPIVWGPCGHIFHFHCISQWLKQN---------NTCP--LCR 73 (73)
T ss_dssp SBETTTTSBTTSTTCCHHHCTTTS-EEEETTSEEEEHHHHHHHHTTS---------SB-T--TSS
T ss_pred CcccccChhhhChhhhhcCCccccceEecccCCCEEHHHHHHHHhcC---------CcCC--CCC
Confidence 349999998721 12 2345799999999999998552 2798 664
No 39
>COG5432 RAD18 RING-finger-containing E3 ubiquitin ligase [Signal transduction mechanisms]
Probab=96.12 E-value=0.0035 Score=62.92 Aligned_cols=64 Identities=25% Similarity=0.434 Sum_probs=45.3
Q ss_pred CccccccccccccCCCceecCCCCcccHhHHHHHHhccccCCCCccccccCCCcCCCccchhHHh-hhcChHHHHHHH
Q 007642 140 EEMTCGICFENYPSDRLLAAACGHPFCSSCWTGYISTAINDGPGCLMLRCPDPSCGAAVGQDMIY-LLSSDEDKVKYN 216 (595)
Q Consensus 140 ~~~~C~IC~e~~~~~~~~~l~CgH~fC~~C~~~yi~~~i~~g~~~~~i~CP~~~C~~~v~~~~i~-~ll~~e~~eky~ 216 (595)
....|-||-+-+ .-++..+|||.||.-||+.|+.+ ..-|| .|+.......++ ..+..++.+-|.
T Consensus 24 s~lrC~IC~~~i--~ip~~TtCgHtFCslCIR~hL~~---------qp~CP--~Cr~~~~esrlr~~s~~~ei~es~~ 88 (391)
T COG5432 24 SMLRCRICDCRI--SIPCETTCGHTFCSLCIRRHLGT---------QPFCP--VCREDPCESRLRGSSGSREINESHA 88 (391)
T ss_pred hHHHhhhhhhee--ecceecccccchhHHHHHHHhcC---------CCCCc--cccccHHhhhcccchhHHHHHHhhh
Confidence 356799998877 66788899999999999999855 34688 788766443332 233345555554
No 40
>KOG1002 consensus Nucleotide excision repair protein RAD16 [Replication, recombination and repair]
Probab=96.06 E-value=0.0032 Score=67.82 Aligned_cols=56 Identities=25% Similarity=0.797 Sum_probs=45.8
Q ss_pred CCCccccccccccccCCCceecCCCCcccHhHHHHHHhccccCCCCccccccCCCcCCCccchh
Q 007642 138 DGEEMTCGICFENYPSDRLLAAACGHPFCSSCWTGYISTAINDGPGCLMLRCPDPSCGAAVGQD 201 (595)
Q Consensus 138 ~~~~~~C~IC~e~~~~~~~~~l~CgH~fC~~C~~~yi~~~i~~g~~~~~i~CP~~~C~~~v~~~ 201 (595)
+.....|++|-+.- .+++...|.|.||+-|++.|+....... .+.|| .|...++.+
T Consensus 533 nk~~~~C~lc~d~a--ed~i~s~ChH~FCrlCi~eyv~~f~~~~----nvtCP--~C~i~LsiD 588 (791)
T KOG1002|consen 533 NKGEVECGLCHDPA--EDYIESSCHHKFCRLCIKEYVESFMENN----NVTCP--VCHIGLSID 588 (791)
T ss_pred ccCceeecccCChh--hhhHhhhhhHHHHHHHHHHHHHhhhccc----CCCCc--ccccccccc
Confidence 45678999999864 7788889999999999999998765433 48999 898877654
No 41
>COG5540 RING-finger-containing ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=96.04 E-value=0.0039 Score=63.04 Aligned_cols=51 Identities=27% Similarity=0.719 Sum_probs=41.9
Q ss_pred CccccccccccccCC-CceecCCCCcccHhHHHHHHhccccCCCCccccccCCCcCCCccch
Q 007642 140 EEMTCGICFENYPSD-RLLAAACGHPFCSSCWTGYISTAINDGPGCLMLRCPDPSCGAAVGQ 200 (595)
Q Consensus 140 ~~~~C~IC~e~~~~~-~~~~l~CgH~fC~~C~~~yi~~~i~~g~~~~~i~CP~~~C~~~v~~ 200 (595)
....|.||++.+... ..+.+||.|.|...|+.+|+.. ...+|| .|+..++|
T Consensus 322 ~GveCaICms~fiK~d~~~vlPC~H~FH~~Cv~kW~~~--------y~~~CP--vCrt~iPP 373 (374)
T COG5540 322 KGVECAICMSNFIKNDRLRVLPCDHRFHVGCVDKWLLG--------YSNKCP--VCRTAIPP 373 (374)
T ss_pred CCceEEEEhhhhcccceEEEeccCceechhHHHHHHhh--------hcccCC--ccCCCCCC
Confidence 357899999998643 4678899999999999999842 256899 99999876
No 42
>PF14555 UBA_4: UBA-like domain; PDB: 2DAL_A 3BQ3_A 2L4E_A 2L4F_A 2DZL_A 2L2D_A 2DAM_A 1V92_A 3E21_A.
Probab=95.86 E-value=0.018 Score=41.96 Aligned_cols=41 Identities=22% Similarity=0.427 Sum_probs=35.0
Q ss_pred HHHHHHHHHHhCCCHHHHHHHHHHcCCChhhhHHHhhhcHH
Q 007642 80 EEDITRISTVLSISKVAASILLRFYNWSVSKVHDEWFADEE 120 (595)
Q Consensus 80 ~~~i~~v~~vl~i~~~~a~~LL~~~~W~~~~l~e~~~~~~~ 120 (595)
++.|.+..+|.++++..|..+|...+||++..++.||.+++
T Consensus 1 ~e~i~~F~~iTg~~~~~A~~~L~~~~wdle~Av~~y~~~~~ 41 (43)
T PF14555_consen 1 DEKIAQFMSITGADEDVAIQYLEANNWDLEAAVNAYFDDGE 41 (43)
T ss_dssp HHHHHHHHHHH-SSHHHHHHHHHHTTT-HHHHHHHHHHSS-
T ss_pred CHHHHHHHHHHCcCHHHHHHHHHHcCCCHHHHHHHHHhCCC
Confidence 36789999999999999999999999999999999998653
No 43
>COG5243 HRD1 HRD ubiquitin ligase complex, ER membrane component [Posttranslational modification, protein turnover, chaperones]
Probab=95.71 E-value=0.026 Score=58.67 Aligned_cols=50 Identities=26% Similarity=0.672 Sum_probs=38.6
Q ss_pred CCcccccccccc-ccCC----------CceecCCCCcccHhHHHHHHhccccCCCCccccccCCCcCCCccc
Q 007642 139 GEEMTCGICFEN-YPSD----------RLLAAACGHPFCSSCWTGYISTAINDGPGCLMLRCPDPSCGAAVG 199 (595)
Q Consensus 139 ~~~~~C~IC~e~-~~~~----------~~~~l~CgH~fC~~C~~~yi~~~i~~g~~~~~i~CP~~~C~~~v~ 199 (595)
.+...|.||+++ +... .|..+||||.+...|++.|++.+ -.|| -|+..+-
T Consensus 285 n~D~~C~ICmde~~h~~~~~~~~~~~~~pKrLpCGHilHl~CLknW~ERq---------QTCP--ICr~p~i 345 (491)
T COG5243 285 NSDRTCTICMDEMFHPDHEPLPRGLDMTPKRLPCGHILHLHCLKNWLERQ---------QTCP--ICRRPVI 345 (491)
T ss_pred CCCCeEEEecccccCCCCccCcccccCCcccccccceeeHHHHHHHHHhc---------cCCC--cccCccc
Confidence 446689999998 3221 35789999999999999999752 4799 8998753
No 44
>PF00641 zf-RanBP: Zn-finger in Ran binding protein and others; InterPro: IPR001876 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 RanBP2 proteins. Ran is an evolutionary conserved member of the Ras superfamily that regulates all receptor-mediated transport between the nucleus and the cytoplasm. Ran binding protein 2 (RanBP2) is a 358kDa nucleoporin located on the cytoplasmic side of the nuclear pore complex which plays a role in nuclear protein import []. RanBP2 contains multiple zinc fingers which mediate binding to RanGDP []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0005622 intracellular; PDB: 2D9G_A 2EBR_A 2WX0_C 2WX1_C 2WWZ_C 3GJ6_B 2LK0_A 2LK1_A 3GJ5_B 3GJ8_B ....
Probab=95.59 E-value=0.0048 Score=41.26 Aligned_cols=26 Identities=35% Similarity=0.928 Sum_probs=20.9
Q ss_pred CccccCCCCcccCCcccccccccCCC
Q 007642 570 SHWYCDQCTYANVNSATACAMCQHSR 595 (595)
Q Consensus 570 ~~~~~~~c~~~~~~~~~~c~~c~~~~ 595 (595)
+.|.|..|||.|..+...|.||.-+|
T Consensus 3 g~W~C~~C~~~N~~~~~~C~~C~~~r 28 (30)
T PF00641_consen 3 GDWKCPSCTFMNPASRSKCVACGAPR 28 (30)
T ss_dssp SSEEETTTTEEEESSSSB-TTT--BT
T ss_pred cCccCCCCcCCchHHhhhhhCcCCCC
Confidence 46999999999999999999997654
No 45
>smart00547 ZnF_RBZ Zinc finger domain. Zinc finger domain in Ran-binding proteins (RanBPs), and other proteins. In RanBPs, this domain binds RanGDP.
Probab=95.37 E-value=0.0091 Score=38.42 Aligned_cols=24 Identities=33% Similarity=0.906 Sum_probs=22.3
Q ss_pred ccccCCCCcccCCcccccccccCC
Q 007642 571 HWYCDQCTYANVNSATACAMCQHS 594 (595)
Q Consensus 571 ~~~~~~c~~~~~~~~~~c~~c~~~ 594 (595)
.|.|..||+.|..+...|.+|..+
T Consensus 2 ~W~C~~C~~~N~~~~~~C~~C~~p 25 (26)
T smart00547 2 DWECPACTFLNFASRSKCFACGAP 25 (26)
T ss_pred cccCCCCCCcChhhhccccccCCc
Confidence 599999999999999999999765
No 46
>KOG0824 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=94.63 E-value=0.018 Score=58.56 Aligned_cols=53 Identities=21% Similarity=0.539 Sum_probs=41.2
Q ss_pred CccccccccccccCCCceecCCCCcccHhHHHHHHhccccCCCCccccccCCCcCCCccchhHHh
Q 007642 140 EEMTCGICFENYPSDRLLAAACGHPFCSSCWTGYISTAINDGPGCLMLRCPDPSCGAAVGQDMIY 204 (595)
Q Consensus 140 ~~~~C~IC~e~~~~~~~~~l~CgH~fC~~C~~~yi~~~i~~g~~~~~i~CP~~~C~~~v~~~~i~ 204 (595)
..-.|.||+..- ..|+.++|+|.||..|+++-... + ...|| .|+..|+...+.
T Consensus 6 ~~~eC~IC~nt~--n~Pv~l~C~HkFCyiCiKGsy~n----d----k~~Ca--vCR~pids~i~~ 58 (324)
T KOG0824|consen 6 KKKECLICYNTG--NCPVNLYCFHKFCYICIKGSYKN----D----KKTCA--VCRFPIDSTIDF 58 (324)
T ss_pred cCCcceeeeccC--CcCccccccchhhhhhhcchhhc----C----CCCCc--eecCCCCcchhc
Confidence 356799999875 67899999999999999976433 2 34698 899998776543
No 47
>PF14570 zf-RING_4: RING/Ubox like zinc-binding domain; PDB: 1E4U_A 1UR6_B.
Probab=94.59 E-value=0.032 Score=41.51 Aligned_cols=45 Identities=24% Similarity=0.718 Sum_probs=22.0
Q ss_pred cccccccccCC--CceecCCCCcccHhHHHHHHhccccCCCCccccccCCCcCCCcc
Q 007642 144 CGICFENYPSD--RLLAAACGHPFCSSCWTGYISTAINDGPGCLMLRCPDPSCGAAV 198 (595)
Q Consensus 144 C~IC~e~~~~~--~~~~l~CgH~fC~~C~~~yi~~~i~~g~~~~~i~CP~~~C~~~v 198 (595)
|++|.+.+... ++..-+||+.+|+.||..-... + .=+|| +|+...
T Consensus 1 cp~C~e~~d~~d~~~~PC~Cgf~IC~~C~~~i~~~----~----~g~CP--gCr~~Y 47 (48)
T PF14570_consen 1 CPLCDEELDETDKDFYPCECGFQICRFCYHDILEN----E----GGRCP--GCREPY 47 (48)
T ss_dssp -TTTS-B--CCCTT--SSTTS----HHHHHHHTTS----S-----SB-T--TT--B-
T ss_pred CCCcccccccCCCccccCcCCCcHHHHHHHHHHhc----c----CCCCC--CCCCCC
Confidence 78999887544 3455679999999999987652 2 23799 898653
No 48
>KOG2879 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=94.52 E-value=0.036 Score=55.68 Aligned_cols=52 Identities=27% Similarity=0.621 Sum_probs=37.9
Q ss_pred CCccccccccccccCCCceecCCCCcccHhHHHHHHhccccCCCCccccccCCCcCCCccch
Q 007642 139 GEEMTCGICFENYPSDRLLAAACGHPFCSSCWTGYISTAINDGPGCLMLRCPDPSCGAAVGQ 200 (595)
Q Consensus 139 ~~~~~C~IC~e~~~~~~~~~l~CgH~fC~~C~~~yi~~~i~~g~~~~~i~CP~~~C~~~v~~ 200 (595)
....+|++|-+. |....+..+|||.||--|+..-..... .+.|| .|+..+.+
T Consensus 237 t~~~~C~~Cg~~-PtiP~~~~~C~HiyCY~Ci~ts~~~~a-------sf~Cp--~Cg~~~~~ 288 (298)
T KOG2879|consen 237 TSDTECPVCGEP-PTIPHVIGKCGHIYCYYCIATSRLWDA-------SFTCP--LCGENVEP 288 (298)
T ss_pred cCCceeeccCCC-CCCCeeeccccceeehhhhhhhhcchh-------hcccC--ccCCCCcc
Confidence 346789999875 323334556999999999998765421 58999 89887653
No 49
>KOG1814 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=94.49 E-value=0.041 Score=58.20 Aligned_cols=42 Identities=33% Similarity=0.956 Sum_probs=37.2
Q ss_pred HhcCccCCC--CCcceeecCCCCcccccCCCcceeeecccccccC
Q 007642 296 LANSKPCPR--CKRPIEKNQGCMHMTCTPPCKFEFCWLCLGQWSD 338 (595)
Q Consensus 296 ~~ntK~CPk--C~~~IEK~~GCnhmtC~~~C~~~FCw~C~~~~~~ 338 (595)
.++..-||+ |..|+-...|++-..|. .|.+.||.+|...|+.
T Consensus 270 msdv~yCPr~~Cq~p~~~d~~~~l~~Cs-kCnFaFCtlCk~t~HG 313 (445)
T KOG1814|consen 270 MSDVVYCPRACCQLPVKQDPGRALAICS-KCNFAFCTLCKLTWHG 313 (445)
T ss_pred hcccccCChhhccCccccCchhhhhhhc-cCccHHHHHHHHhhcC
Confidence 356789998 99999778999999999 8999999999998853
No 50
>PF11793 FANCL_C: FANCL C-terminal domain; PDB: 3K1L_A.
Probab=94.48 E-value=0.023 Score=46.01 Aligned_cols=58 Identities=21% Similarity=0.547 Sum_probs=26.3
Q ss_pred cccccccccccc-CCC-ce-e---cCCCCcccHhHHHHHHhccccCCCCccc--cccCCCcCCCccch
Q 007642 141 EMTCGICFENYP-SDR-LL-A---AACGHPFCSSCWTGYISTAINDGPGCLM--LRCPDPSCGAAVGQ 200 (595)
Q Consensus 141 ~~~C~IC~e~~~-~~~-~~-~---l~CgH~fC~~C~~~yi~~~i~~g~~~~~--i~CP~~~C~~~v~~ 200 (595)
+..|+||+.... ... +. . ..|++.|...|+..|+...-.......+ =.|| .|+..|.-
T Consensus 2 ~~~C~IC~~~~~~~~~~p~~~C~n~~C~~~fH~~CL~~wf~~~~~~~~~~~~~~G~CP--~C~~~i~~ 67 (70)
T PF11793_consen 2 ELECGICYSYRLDDGEIPDVVCPNPSCGKKFHLLCLSEWFLSLEKSRQSFIPIFGECP--YCSSPISW 67 (70)
T ss_dssp --S-SSS--SS-TT-----B--S-TT----B-SGGGHHHHHHHHSSS-TTT--EEE-T--TT-SEEEG
T ss_pred CCCCCcCCcEecCCCCcCceEcCCcccCCHHHHHHHHHHHHHcccCCeeecccccCCc--CCCCeeeE
Confidence 467999998754 222 21 1 2589999999999999875443321112 2699 89987753
No 51
>KOG4159 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=94.18 E-value=0.051 Score=58.50 Aligned_cols=49 Identities=24% Similarity=0.682 Sum_probs=39.0
Q ss_pred CCccccccccccccCCCceecCCCCcccHhHHHHHHhccccCCCCccccccCCCcCCCccch
Q 007642 139 GEEMTCGICFENYPSDRLLAAACGHPFCSSCWTGYISTAINDGPGCLMLRCPDPSCGAAVGQ 200 (595)
Q Consensus 139 ~~~~~C~IC~e~~~~~~~~~l~CgH~fC~~C~~~yi~~~i~~g~~~~~i~CP~~~C~~~v~~ 200 (595)
..+|.|.||+..+ -.+++++|||.||..|+..-+. . ...|| .|+..+..
T Consensus 82 ~sef~c~vc~~~l--~~pv~tpcghs~c~~Cl~r~ld----~-----~~~cp--~Cr~~l~e 130 (398)
T KOG4159|consen 82 RSEFECCVCSRAL--YPPVVTPCGHSFCLECLDRSLD----Q-----ETECP--LCRDELVE 130 (398)
T ss_pred cchhhhhhhHhhc--CCCccccccccccHHHHHHHhc----c-----CCCCc--cccccccc
Confidence 5689999999887 7788889999999999777332 1 35788 79988763
No 52
>COG5152 Uncharacterized conserved protein, contains RING and CCCH-type Zn-fingers [General function prediction only]
Probab=94.05 E-value=0.024 Score=54.12 Aligned_cols=32 Identities=38% Similarity=0.943 Sum_probs=28.0
Q ss_pred ccccccccccccCCCceecCCCCcccHhHHHHHH
Q 007642 141 EMTCGICFENYPSDRLLAAACGHPFCSSCWTGYI 174 (595)
Q Consensus 141 ~~~C~IC~e~~~~~~~~~l~CgH~fC~~C~~~yi 174 (595)
.|.|.||-.+| ..|+...|||+||..|...-.
T Consensus 196 PF~C~iCKkdy--~spvvt~CGH~FC~~Cai~~y 227 (259)
T COG5152 196 PFLCGICKKDY--ESPVVTECGHSFCSLCAIRKY 227 (259)
T ss_pred ceeehhchhhc--cchhhhhcchhHHHHHHHHHh
Confidence 68999999998 789999999999999976543
No 53
>KOG0311 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=94.03 E-value=0.0087 Score=61.99 Aligned_cols=48 Identities=25% Similarity=0.662 Sum_probs=35.0
Q ss_pred CccccccccccccCCCceecCCCCcccHhHHHHHHhccccCCCCccccccCCCcCCCcc
Q 007642 140 EEMTCGICFENYPSDRLLAAACGHPFCSSCWTGYISTAINDGPGCLMLRCPDPSCGAAV 198 (595)
Q Consensus 140 ~~~~C~IC~e~~~~~~~~~l~CgH~fC~~C~~~yi~~~i~~g~~~~~i~CP~~~C~~~v 198 (595)
.++.|+||++.+. .-+.+..|+|.||.+||-.-+.. | .-.|| .|+..+
T Consensus 42 ~~v~c~icl~llk-~tmttkeClhrfc~~ci~~a~r~----g----n~ecp--tcRk~l 89 (381)
T KOG0311|consen 42 IQVICPICLSLLK-KTMTTKECLHRFCFDCIWKALRS----G----NNECP--TCRKKL 89 (381)
T ss_pred hhhccHHHHHHHH-hhcccHHHHHHHHHHHHHHHHHh----c----CCCCc--hHHhhc
Confidence 4788999999873 23445569999999999776543 3 23798 888654
No 54
>KOG2660 consensus Locus-specific chromosome binding proteins [Function unknown]
Probab=93.59 E-value=0.031 Score=57.67 Aligned_cols=47 Identities=28% Similarity=0.696 Sum_probs=36.8
Q ss_pred CccccccccccccCCCcee-cCCCCcccHhHHHHHHhccccCCCCccccccCCCcCCCccc
Q 007642 140 EEMTCGICFENYPSDRLLA-AACGHPFCSSCWTGYISTAINDGPGCLMLRCPDPSCGAAVG 199 (595)
Q Consensus 140 ~~~~C~IC~e~~~~~~~~~-l~CgH~fC~~C~~~yi~~~i~~g~~~~~i~CP~~~C~~~v~ 199 (595)
...+|.+|-..+ .+..+ ..|-|.||+.||-.|+.. ...|| .|+..+.
T Consensus 14 ~~itC~LC~GYl--iDATTI~eCLHTFCkSCivk~l~~---------~~~CP--~C~i~ih 61 (331)
T KOG2660|consen 14 PHITCRLCGGYL--IDATTITECLHTFCKSCIVKYLEE---------SKYCP--TCDIVIH 61 (331)
T ss_pred cceehhhcccee--ecchhHHHHHHHHHHHHHHHHHHH---------hccCC--ccceecc
Confidence 467899998776 44444 459999999999999987 24799 7887764
No 55
>KOG1039 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=93.27 E-value=0.061 Score=56.80 Aligned_cols=58 Identities=24% Similarity=0.562 Sum_probs=38.4
Q ss_pred CCCCccccccccccccCCC-----cee-cCCCCcccHhHHHHHHhccccCCCCccccccCCCcCCCcc
Q 007642 137 PDGEEMTCGICFENYPSDR-----LLA-AACGHPFCSSCWTGYISTAINDGPGCLMLRCPDPSCGAAV 198 (595)
Q Consensus 137 ~~~~~~~C~IC~e~~~~~~-----~~~-l~CgH~fC~~C~~~yi~~~i~~g~~~~~i~CP~~~C~~~v 198 (595)
+......|+||++...... .-. .+|.|.||..|++.|=...-. +. ...-.|| .|+...
T Consensus 157 ~~s~~k~CGICme~i~ek~~~~~rfgilpnC~H~~Cl~Cir~wr~~~q~-~~-~~sksCP--~CRv~s 220 (344)
T KOG1039|consen 157 QKSSEKECGICMETINEKAASERRFGILPNCNHSFCLNCIRKWRQATQF-ES-KTSKSCP--FCRVPS 220 (344)
T ss_pred CccccccceehhhhccccchhhhhcccCCCcchhhhhcHhHhhhhhhcc-cc-ccccCCC--cccCcc
Confidence 3466889999999864332 212 459999999999998533211 11 1245799 888653
No 56
>KOG0006 consensus E3 ubiquitin-protein ligase (Parkin protein) [Posttranslational modification, protein turnover, chaperones]
Probab=92.54 E-value=0.24 Score=50.70 Aligned_cols=95 Identities=23% Similarity=0.599 Sum_probs=56.0
Q ss_pred CCCCcccHhHHHHHHhccccCCCCccccccCCCcCCCccchhHHhhhcChHHHHHHHHHHHHHhhhhCCCcccCCCCCCC
Q 007642 160 ACGHPFCSSCWTGYISTAINDGPGCLMLRCPDPSCGAAVGQDMIYLLSSDEDKVKYNRYFIRSYVEDNRKTKWCPAPGCD 239 (595)
Q Consensus 160 ~CgH~fC~~C~~~yi~~~i~~g~~~~~i~CP~~~C~~~v~~~~i~~ll~~e~~eky~~~~~~~~v~~~~~~~~CP~p~C~ 239 (595)
.||-.||+.|+..|-.-.-..+.+.. -...|...+.+... ...+|...... .+ ....+.|| .|.
T Consensus 341 gCgf~FCR~C~e~yh~geC~~~~~as----~t~tc~y~vde~~a-------~~arwd~as~~-TI--k~tTkpCP--kCh 404 (446)
T KOG0006|consen 341 GCGFAFCRECKEAYHEGECSAVFEAS----GTTTCAYRVDERAA-------EQARWDAASKE-TI--KKTTKPCP--KCH 404 (446)
T ss_pred CchhHhHHHHHhhhccccceeeeccc----cccceeeecChhhh-------hhhhhhhhhhh-hh--hhccCCCC--Ccc
Confidence 49999999999999643322211000 01135544544322 12344432221 11 23457888 598
Q ss_pred CeeeeecCCCCceeee---cCCCcccccCCcccCCC
Q 007642 240 YAVDFVVGSGNYDVTC---RCSYSFCWNCTEEAHRP 272 (595)
Q Consensus 240 ~~i~~~~~~~~~~v~C---~C~~~fC~~C~~~~H~p 272 (595)
.+.+.. .+-..+.| .||..+||.|+-+|.+.
T Consensus 405 vptErn--GGCmHm~Ct~~~Cg~eWCw~C~tEW~r~ 438 (446)
T KOG0006|consen 405 VPTERN--GGCMHMKCTQPQCGLEWCWNCGTEWNRV 438 (446)
T ss_pred CccccC--CceEEeecCCCCCCceeEeccCChhhhh
Confidence 776653 45677889 49999999999988653
No 57
>PF12861 zf-Apc11: Anaphase-promoting complex subunit 11 RING-H2 finger
Probab=92.24 E-value=0.14 Score=42.79 Aligned_cols=35 Identities=26% Similarity=0.548 Sum_probs=26.6
Q ss_pred eecCCCCcccHhHHHHHHhccccCCCCccccccCCCcCCCccc
Q 007642 157 LAAACGHPFCSSCWTGYISTAINDGPGCLMLRCPDPSCGAAVG 199 (595)
Q Consensus 157 ~~l~CgH~fC~~C~~~yi~~~i~~g~~~~~i~CP~~~C~~~v~ 199 (595)
+.-.|+|.|...||..+++++-. .-.|| -|+..+.
T Consensus 48 v~g~C~H~FH~hCI~kWl~~~~~------~~~CP--mCR~~w~ 82 (85)
T PF12861_consen 48 VWGKCSHNFHMHCILKWLSTQSS------KGQCP--MCRQPWK 82 (85)
T ss_pred eeccCccHHHHHHHHHHHccccC------CCCCC--CcCCeee
Confidence 34469999999999999987522 23799 7987653
No 58
>PRK00420 hypothetical protein; Validated
Probab=92.09 E-value=1.6 Score=38.63 Aligned_cols=27 Identities=26% Similarity=0.294 Sum_probs=19.2
Q ss_pred CccCCCCCcceeecCCCCcccccCCCcceeeeccccc
Q 007642 299 SKPCPRCKRPIEKNQGCMHMTCTPPCKFEFCWLCLGQ 335 (595)
Q Consensus 299 tK~CPkC~~~IEK~~GCnhmtC~~~C~~~FCw~C~~~ 335 (595)
...||.|+.|+-+. .-|..||..|+..
T Consensus 23 ~~~CP~Cg~pLf~l----------k~g~~~Cp~Cg~~ 49 (112)
T PRK00420 23 SKHCPVCGLPLFEL----------KDGEVVCPVHGKV 49 (112)
T ss_pred cCCCCCCCCcceec----------CCCceECCCCCCe
Confidence 48999999998841 2456667777653
No 59
>KOG0802 consensus E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=91.97 E-value=0.072 Score=60.32 Aligned_cols=47 Identities=30% Similarity=0.711 Sum_probs=37.1
Q ss_pred ccccccccccccCC---CceecCCCCcccHhHHHHHHhccccCCCCccccccCCCcCCCcc
Q 007642 141 EMTCGICFENYPSD---RLLAAACGHPFCSSCWTGYISTAINDGPGCLMLRCPDPSCGAAV 198 (595)
Q Consensus 141 ~~~C~IC~e~~~~~---~~~~l~CgH~fC~~C~~~yi~~~i~~g~~~~~i~CP~~~C~~~v 198 (595)
...|.||.+.+... .+..++|||.||..|++.|++. .-.|| .|+..+
T Consensus 291 ~~~C~IC~e~l~~~~~~~~~rL~C~Hifh~~CL~~W~er---------~qtCP--~CR~~~ 340 (543)
T KOG0802|consen 291 DELCIICLEELHSGHNITPKRLPCGHIFHDSCLRSWFER---------QQTCP--TCRTVL 340 (543)
T ss_pred CCeeeeechhhccccccccceeecccchHHHHHHHHHHH---------hCcCC--cchhhh
Confidence 56899999987421 2678899999999999999987 24799 787733
No 60
>KOG1645 consensus RING-finger-containing E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=91.95 E-value=0.18 Score=53.34 Aligned_cols=50 Identities=30% Similarity=0.820 Sum_probs=38.9
Q ss_pred ccccccccccccC---CCceecCCCCcccHhHHHHHHhccccCCCCccccccCCCcCCCccc
Q 007642 141 EMTCGICFENYPS---DRLLAAACGHPFCSSCWTGYISTAINDGPGCLMLRCPDPSCGAAVG 199 (595)
Q Consensus 141 ~~~C~IC~e~~~~---~~~~~l~CgH~fC~~C~~~yi~~~i~~g~~~~~i~CP~~~C~~~v~ 199 (595)
..+||||++.+.. ..++++.|||.|=.+|+++|+. ++ ...+|| .|...-.
T Consensus 4 g~tcpiclds~~~~g~hr~vsl~cghlFgs~cie~wl~-k~------~~~~cp--~c~~kat 56 (463)
T KOG1645|consen 4 GTTCPICLDSYTTAGNHRIVSLQCGHLFGSQCIEKWLG-KK------TKMQCP--LCSGKAT 56 (463)
T ss_pred cccCceeeeeeeecCceEEeeecccccccHHHHHHHHh-hh------hhhhCc--ccCChhH
Confidence 4589999998643 3578899999999999999993 22 357899 7876543
No 61
>KOG1812 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=91.74 E-value=0.083 Score=57.06 Aligned_cols=42 Identities=26% Similarity=0.821 Sum_probs=33.3
Q ss_pred CCcccCCCCCCCCeeeeecCCCCceeeecCCCcccccCCcccCCCC
Q 007642 228 RKTKWCPAPGCDYAVDFVVGSGNYDVTCRCSYSFCWNCTEEAHRPV 273 (595)
Q Consensus 228 ~~~~~CP~p~C~~~i~~~~~~~~~~v~C~C~~~fC~~C~~~~H~p~ 273 (595)
...+.|| .|...|... .+-..++|.||+.||+.|+.+|+...
T Consensus 304 ~~wr~Cp--kC~~~ie~~--~GCnhm~CrC~~~fcy~C~~~~~~~~ 345 (384)
T KOG1812|consen 304 KRWRQCP--KCKFMIELS--EGCNHMTCRCGHQFCYMCGGDWKTHN 345 (384)
T ss_pred HhcCcCc--ccceeeeec--CCcceEEeeccccchhhcCcchhhCC
Confidence 4467899 499888664 45778999999999999998886543
No 62
>KOG1734 consensus Predicted RING-containing E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=91.20 E-value=0.15 Score=51.16 Aligned_cols=71 Identities=18% Similarity=0.457 Sum_probs=47.6
Q ss_pred HHHHHhCCCCCCCCCCCCCCccccccccccccCC--------CceecCCCCcccHhHHHHHHhccccCCCCccccccCCC
Q 007642 121 RVRKAVGLLEKPAVQFPDGEEMTCGICFENYPSD--------RLLAAACGHPFCSSCWTGYISTAINDGPGCLMLRCPDP 192 (595)
Q Consensus 121 ~~~~~~gl~~~~~~~~~~~~~~~C~IC~e~~~~~--------~~~~l~CgH~fC~~C~~~yi~~~i~~g~~~~~i~CP~~ 192 (595)
.+...+|.-.....+....+.-.|.||-..+..+ ++..++|+|.|...|+++|... |+ .-.||
T Consensus 204 ~mAs~iGfYs~~glPtkhl~d~vCaVCg~~~~~s~~eegvienty~LsCnHvFHEfCIrGWciv----GK---kqtCP-- 274 (328)
T KOG1734|consen 204 YMASTIGFYSPSGLPTKHLSDSVCAVCGQQIDVSVDEEGVIENTYKLSCNHVFHEFCIRGWCIV----GK---KQTCP-- 274 (328)
T ss_pred HHHHHhcccCCCCCCCCCCCcchhHhhcchheeecchhhhhhhheeeecccchHHHhhhhheee----cC---CCCCc--
Confidence 3444555543333333334566799998765432 4678999999999999999754 33 45899
Q ss_pred cCCCccch
Q 007642 193 SCGAAVGQ 200 (595)
Q Consensus 193 ~C~~~v~~ 200 (595)
-|+..+..
T Consensus 275 YCKekVdl 282 (328)
T KOG1734|consen 275 YCKEKVDL 282 (328)
T ss_pred hHHHHhhH
Confidence 79887643
No 63
>PF04931 DNA_pol_phi: DNA polymerase phi; InterPro: IPR007015 Proteins of this family are predominantly nucleolar. The majority are described as transcription factor transactivators. The family also includes the fifth essential DNA polymerase (Pol5p) of Schizosaccharomyces pombe (Fission yeast) and Saccharomyces cerevisiae (Baker's yeast) (2.7.7.7 from EC). Pol5p is localized exclusively to the nucleolus and binds near or at the enhancer region of rRNA-encoding DNA repeating units.; GO: 0003677 DNA binding, 0003887 DNA-directed DNA polymerase activity, 0006351 transcription, DNA-dependent
Probab=91.16 E-value=0.34 Score=57.38 Aligned_cols=20 Identities=10% Similarity=0.069 Sum_probs=14.2
Q ss_pred HHHHHHHHcCCChhhhHHHh
Q 007642 96 AASILLRFYNWSVSKVHDEW 115 (595)
Q Consensus 96 ~a~~LL~~~~W~~~~l~e~~ 115 (595)
.+...+.+|+-.+-.|++.|
T Consensus 764 ~~~~~~~~Fk~RvlDLleiy 783 (784)
T PF04931_consen 764 EAKENVIHFKNRVLDLLEIY 783 (784)
T ss_pred HHHHHHHHHHHHHHHHHHHh
Confidence 56677788887777776655
No 64
>KOG2817 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=89.80 E-value=1.2 Score=47.29 Aligned_cols=55 Identities=16% Similarity=0.359 Sum_probs=39.2
Q ss_pred CccccccccccccC-CCceecCCCCcccHhHHHHHHhccccCCCCccccccCCCcCCCccchhH
Q 007642 140 EEMTCGICFENYPS-DRLLAAACGHPFCSSCWTGYISTAINDGPGCLMLRCPDPSCGAAVGQDM 202 (595)
Q Consensus 140 ~~~~C~IC~e~~~~-~~~~~l~CgH~fC~~C~~~yi~~~i~~g~~~~~i~CP~~~C~~~v~~~~ 202 (595)
+.|.|||=-+.-.. +.|..+.|||..|++=+...... | ...++|| -|........
T Consensus 333 SvF~CPVlKeqtsdeNPPm~L~CGHVISkdAlnrLS~n----g--~~sfKCP--YCP~e~~~~~ 388 (394)
T KOG2817|consen 333 SVFICPVLKEQTSDENPPMMLICGHVISKDALNRLSKN----G--SQSFKCP--YCPVEQLASD 388 (394)
T ss_pred ceeecccchhhccCCCCCeeeeccceecHHHHHHHhhC----C--CeeeeCC--CCCcccCHHh
Confidence 47899995554333 45789999999999998887533 3 2368999 7876554443
No 65
>PF10571 UPF0547: Uncharacterised protein family UPF0547; InterPro: IPR018886 This domain may well be a type of zinc-finger as it carries two pairs of highly conserved cysteine residues though with no accompanying histidines. Several members are annotated as putative helicases.
Probab=89.79 E-value=0.18 Score=32.55 Aligned_cols=24 Identities=29% Similarity=0.945 Sum_probs=15.9
Q ss_pred ccCCCCCcceeecCCCCcccccCCCccee
Q 007642 300 KPCPRCKRPIEKNQGCMHMTCTPPCKFEF 328 (595)
Q Consensus 300 K~CPkC~~~IEK~~GCnhmtC~~~C~~~F 328 (595)
|.||.|+..|-.+ -..|. .||+.|
T Consensus 1 K~CP~C~~~V~~~----~~~Cp-~CG~~F 24 (26)
T PF10571_consen 1 KTCPECGAEVPES----AKFCP-HCGYDF 24 (26)
T ss_pred CcCCCCcCCchhh----cCcCC-CCCCCC
Confidence 6799999888622 24555 577665
No 66
>KOG4692 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=89.11 E-value=0.28 Score=50.95 Aligned_cols=53 Identities=30% Similarity=0.631 Sum_probs=39.2
Q ss_pred CCCCCCccccccccccccCCCceecCCCCcccHhHHHHHHhccccCCCCccccccCCCcCCCccch
Q 007642 135 QFPDGEEMTCGICFENYPSDRLLAAACGHPFCSSCWTGYISTAINDGPGCLMLRCPDPSCGAAVGQ 200 (595)
Q Consensus 135 ~~~~~~~~~C~IC~e~~~~~~~~~l~CgH~fC~~C~~~yi~~~i~~g~~~~~i~CP~~~C~~~v~~ 200 (595)
..|.++.-.|+||+-. +-..+..||+|.-|..||.+++-+ .-+|- .|+..+..
T Consensus 416 ~lp~sEd~lCpICyA~--pi~Avf~PC~H~SC~~CI~qHlmN---------~k~CF--fCktTv~~ 468 (489)
T KOG4692|consen 416 DLPDSEDNLCPICYAG--PINAVFAPCSHRSCYGCITQHLMN---------CKRCF--FCKTTVID 468 (489)
T ss_pred CCCCcccccCcceecc--cchhhccCCCCchHHHHHHHHHhc---------CCeee--Eecceeee
Confidence 3456677889999963 234567799999999999999854 23565 78887654
No 67
>KOG4265 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=88.78 E-value=0.35 Score=50.69 Aligned_cols=65 Identities=18% Similarity=0.459 Sum_probs=44.5
Q ss_pred HHHhCCCCCCCCCCC---CCCccccccccccccCCCceecCCCCc-ccHhHHHHHHhccccCCCCccccccCCCcCCCcc
Q 007642 123 RKAVGLLEKPAVQFP---DGEEMTCGICFENYPSDRLLAAACGHP-FCSSCWTGYISTAINDGPGCLMLRCPDPSCGAAV 198 (595)
Q Consensus 123 ~~~~gl~~~~~~~~~---~~~~~~C~IC~e~~~~~~~~~l~CgH~-fC~~C~~~yi~~~i~~g~~~~~i~CP~~~C~~~v 198 (595)
++..||..++....+ +.....|-||+... .+.+.+||.|. .|.+|-+..- .. .=+|| -|+..|
T Consensus 269 qEiyGien~~v~~~~~~~~~~gkeCVIClse~--rdt~vLPCRHLCLCs~Ca~~Lr---~q------~n~CP--ICRqpi 335 (349)
T KOG4265|consen 269 QEIYGIENSTVEGTDADESESGKECVICLSES--RDTVVLPCRHLCLCSGCAKSLR---YQ------TNNCP--ICRQPI 335 (349)
T ss_pred ehhhccccCCCCCCccccccCCCeeEEEecCC--cceEEecchhhehhHhHHHHHH---Hh------hcCCC--ccccch
Confidence 445576544333222 23467899999875 78999999997 8999988764 11 22699 899876
Q ss_pred ch
Q 007642 199 GQ 200 (595)
Q Consensus 199 ~~ 200 (595)
..
T Consensus 336 ~~ 337 (349)
T KOG4265|consen 336 EE 337 (349)
T ss_pred Hh
Confidence 43
No 68
>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=87.68 E-value=6.8 Score=40.89 Aligned_cols=34 Identities=29% Similarity=0.640 Sum_probs=20.4
Q ss_pred ccCCCCCcceeecCCCCcccccCCCcceeeeccccc
Q 007642 300 KPCPRCKRPIEKNQGCMHMTCTPPCKFEFCWLCLGQ 335 (595)
Q Consensus 300 K~CPkC~~~IEK~~GCnhmtC~~~C~~~FCw~C~~~ 335 (595)
..||.|+...-.+..=.-|.= .|||.||-.|+..
T Consensus 4 ~~CP~Ck~~~y~np~~kl~i~--~CGH~~C~sCv~~ 37 (309)
T TIGR00570 4 QGCPRCKTTKYRNPSLKLMVN--VCGHTLCESCVDL 37 (309)
T ss_pred CCCCcCCCCCccCcccccccC--CCCCcccHHHHHH
Confidence 579999985443322111111 3888888888765
No 69
>KOG0317 consensus Predicted E3 ubiquitin ligase, integral peroxisomal membrane protein [Posttranslational modification, protein turnover, chaperones]
Probab=87.01 E-value=0.1 Score=52.97 Aligned_cols=38 Identities=26% Similarity=0.808 Sum_probs=28.8
Q ss_pred HhcCccCCCCCcceeecCCCCcccccCCCcceeeecccccccCCC
Q 007642 296 LANSKPCPRCKRPIEKNQGCMHMTCTPPCKFEFCWLCLGQWSDHG 340 (595)
Q Consensus 296 ~~ntK~CPkC~~~IEK~~GCnhmtC~~~C~~~FCw~C~~~~~~H~ 340 (595)
..++.+|--|-...+ |-+|+ +|||-|||.|...|-.-.
T Consensus 236 ~~a~~kC~LCLe~~~------~pSaT-pCGHiFCWsCI~~w~~ek 273 (293)
T KOG0317|consen 236 PEATRKCSLCLENRS------NPSAT-PCGHIFCWSCILEWCSEK 273 (293)
T ss_pred CCCCCceEEEecCCC------CCCcC-cCcchHHHHHHHHHHccc
Confidence 345667777766665 57898 799999999999996443
No 70
>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=86.77 E-value=0.63 Score=34.89 Aligned_cols=43 Identities=21% Similarity=0.512 Sum_probs=32.0
Q ss_pred ccccccccccCCCceecCCC-----CcccHhHHHHHHhccccCCCCccccccCCCcC
Q 007642 143 TCGICFENYPSDRLLAAACG-----HPFCSSCWTGYISTAINDGPGCLMLRCPDPSC 194 (595)
Q Consensus 143 ~C~IC~e~~~~~~~~~l~Cg-----H~fC~~C~~~yi~~~i~~g~~~~~i~CP~~~C 194 (595)
.|-||++.....++...||. |.+...|+..|+..+- ..+|| .|
T Consensus 1 ~CrIC~~~~~~~~~l~~PC~C~G~~~~vH~~Cl~~W~~~~~-------~~~C~--iC 48 (49)
T smart00744 1 ICRICHDEGDEGDPLVSPCRCKGSLKYVHQECLERWINESG-------NKTCE--IC 48 (49)
T ss_pred CccCCCCCCCCCCeeEeccccCCchhHHHHHHHHHHHHHcC-------CCcCC--CC
Confidence 48999984444667777885 8899999999997642 24788 55
No 71
>KOG0826 consensus Predicted E3 ubiquitin ligase involved in peroxisome organization [Posttranslational modification, protein turnover, chaperones]
Probab=86.66 E-value=1.7 Score=45.16 Aligned_cols=47 Identities=26% Similarity=0.607 Sum_probs=34.0
Q ss_pred ccccccccccccCCCceec-CCCCcccHhHHHHHHhccccCCCCccccccCCCcCCCcc
Q 007642 141 EMTCGICFENYPSDRLLAA-ACGHPFCSSCWTGYISTAINDGPGCLMLRCPDPSCGAAV 198 (595)
Q Consensus 141 ~~~C~IC~e~~~~~~~~~l-~CgH~fC~~C~~~yi~~~i~~g~~~~~i~CP~~~C~~~v 198 (595)
.-.|+||+... .++..+ -=|-.||-.|+-.|+.+ .| .||-.+|...+
T Consensus 300 ~~~CpvClk~r--~Nptvl~vSGyVfCY~Ci~~Yv~~---~~------~CPVT~~p~~v 347 (357)
T KOG0826|consen 300 REVCPVCLKKR--QNPTVLEVSGYVFCYPCIFSYVVN---YG------HCPVTGYPASV 347 (357)
T ss_pred cccChhHHhcc--CCCceEEecceEEeHHHHHHHHHh---cC------CCCccCCcchH
Confidence 45799999764 344333 45999999999999873 23 68877776544
No 72
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=85.51 E-value=0.41 Score=30.84 Aligned_cols=11 Identities=36% Similarity=0.914 Sum_probs=9.2
Q ss_pred ccCCCCCccee
Q 007642 300 KPCPRCKRPIE 310 (595)
Q Consensus 300 K~CPkC~~~IE 310 (595)
+.||+|+..|+
T Consensus 3 ~~Cp~Cg~~~~ 13 (26)
T PF13248_consen 3 MFCPNCGAEID 13 (26)
T ss_pred CCCcccCCcCC
Confidence 68999999776
No 73
>PF13240 zinc_ribbon_2: zinc-ribbon domain
Probab=85.46 E-value=0.4 Score=30.05 Aligned_cols=10 Identities=50% Similarity=1.105 Sum_probs=8.5
Q ss_pred cCCCCCccee
Q 007642 301 PCPRCKRPIE 310 (595)
Q Consensus 301 ~CPkC~~~IE 310 (595)
.||+|+..|+
T Consensus 1 ~Cp~CG~~~~ 10 (23)
T PF13240_consen 1 YCPNCGAEIE 10 (23)
T ss_pred CCcccCCCCC
Confidence 4899999888
No 74
>KOG1813 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=84.93 E-value=0.34 Score=49.39 Aligned_cols=45 Identities=29% Similarity=0.685 Sum_probs=35.3
Q ss_pred ccccccccccccCCCceecCCCCcccHhHHHHHHhccccCCCCccccccCCCcCCCcc
Q 007642 141 EMTCGICFENYPSDRLLAAACGHPFCSSCWTGYISTAINDGPGCLMLRCPDPSCGAAV 198 (595)
Q Consensus 141 ~~~C~IC~e~~~~~~~~~l~CgH~fC~~C~~~yi~~~i~~g~~~~~i~CP~~~C~~~v 198 (595)
.|-|.||-..| ..||...|+|.||..|....+.. + -+|+ .|....
T Consensus 241 Pf~c~icr~~f--~~pVvt~c~h~fc~~ca~~~~qk----~-----~~c~--vC~~~t 285 (313)
T KOG1813|consen 241 PFKCFICRKYF--YRPVVTKCGHYFCEVCALKPYQK----G-----EKCY--VCSQQT 285 (313)
T ss_pred Ccccccccccc--ccchhhcCCceeehhhhcccccc----C-----Ccce--eccccc
Confidence 46799999988 78999999999999998776532 2 3676 777554
No 75
>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=84.85 E-value=0.37 Score=43.79 Aligned_cols=34 Identities=26% Similarity=0.701 Sum_probs=28.3
Q ss_pred ccccccccccccC-CCceecCCC------CcccHhHHHHHH
Q 007642 141 EMTCGICFENYPS-DRLLAAACG------HPFCSSCWTGYI 174 (595)
Q Consensus 141 ~~~C~IC~e~~~~-~~~~~l~Cg------H~fC~~C~~~yi 174 (595)
..+|.||++.+.. +-.+.++|| |.||.+|++.|-
T Consensus 26 ~~EC~IC~~~I~~~~GvV~vt~~g~lnLEkmfc~~C~~rw~ 66 (134)
T PF05883_consen 26 TVECQICFDRIDNNDGVVYVTDGGTLNLEKMFCADCDKRWR 66 (134)
T ss_pred CeeehhhhhhhhcCCCEEEEecCCeehHHHHHHHHHHHHHH
Confidence 6789999999876 456778887 689999999984
No 76
>KOG1001 consensus Helicase-like transcription factor HLTF/DNA helicase RAD5, DEAD-box superfamily [Transcription; Replication, recombination and repair]
Probab=84.78 E-value=0.37 Score=55.62 Aligned_cols=47 Identities=30% Similarity=0.747 Sum_probs=37.5
Q ss_pred cccccccccccCCCceecCCCCcccHhHHHHHHhccccCCCCccccccCCCcCCCccch
Q 007642 142 MTCGICFENYPSDRLLAAACGHPFCSSCWTGYISTAINDGPGCLMLRCPDPSCGAAVGQ 200 (595)
Q Consensus 142 ~~C~IC~e~~~~~~~~~l~CgH~fC~~C~~~yi~~~i~~g~~~~~i~CP~~~C~~~v~~ 200 (595)
+.|+||.+ .+.++...|||.||..||..+|...- ...|| .|+..+..
T Consensus 455 ~~c~ic~~---~~~~~it~c~h~~c~~c~~~~i~~~~-------~~~~~--~cr~~l~~ 501 (674)
T KOG1001|consen 455 HWCHICCD---LDSFFITRCGHDFCVECLKKSIQQSE-------NAPCP--LCRNVLKE 501 (674)
T ss_pred cccccccc---cccceeecccchHHHHHHHhcccccc-------CCCCc--HHHHHHHH
Confidence 79999998 47889999999999999999987532 12677 78766543
No 77
>KOG0827 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=84.56 E-value=0.45 Score=50.13 Aligned_cols=55 Identities=27% Similarity=0.683 Sum_probs=38.2
Q ss_pred ccccccccccccCC-CceecC-CCCcccHhHHHHHHhccccCCCCccccccCCCcCCCccchhHH
Q 007642 141 EMTCGICFENYPSD-RLLAAA-CGHPFCSSCWTGYISTAINDGPGCLMLRCPDPSCGAAVGQDMI 203 (595)
Q Consensus 141 ~~~C~IC~e~~~~~-~~~~l~-CgH~fC~~C~~~yi~~~i~~g~~~~~i~CP~~~C~~~v~~~~i 203 (595)
...|.||-+-+|.. +.-++. |||.|...|+..|++..-.. -.|| .|+..++...+
T Consensus 4 ~A~C~Ic~d~~p~~~~l~~i~~cGhifh~~cl~qwfe~~Ps~------R~cp--ic~ik~~~r~~ 60 (465)
T KOG0827|consen 4 MAECHICIDGRPNDHELGPIGTCGHIFHTTCLTQWFEGDPSN------RGCP--ICQIKLQERHV 60 (465)
T ss_pred cceeeEeccCCccccccccccchhhHHHHHHHHHHHccCCcc------CCCC--ceeecccceee
Confidence 34699997766643 445555 99999999999999764332 3688 77755554433
No 78
>KOG1815 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=84.45 E-value=0.64 Score=51.37 Aligned_cols=34 Identities=24% Similarity=0.672 Sum_probs=29.5
Q ss_pred CCCCcceee-cCCCCcccccCCCcceeeecccccccC
Q 007642 303 PRCKRPIEK-NQGCMHMTCTPPCKFEFCWLCLGQWSD 338 (595)
Q Consensus 303 PkC~~~IEK-~~GCnhmtC~~~C~~~FCw~C~~~~~~ 338 (595)
|.|+..+.- .+.+.-+.|. |++.|||.|+.+|+.
T Consensus 164 ~~C~~av~~~~~~~~~v~C~--~g~~FC~~C~~~~H~ 198 (444)
T KOG1815|consen 164 PGCGLAVKFGSLESVEVDCG--CGHEFCFACGEESHS 198 (444)
T ss_pred CCCCceeeccCCCccceeCC--CCchhHhhccccccC
Confidence 579999987 7888889997 999999999888753
No 79
>KOG1428 consensus Inhibitor of type V adenylyl cyclases/Neuronal presynaptic protein Highwire/PAM/RPM-1 [Signal transduction mechanisms]
Probab=83.86 E-value=1.6 Score=52.90 Aligned_cols=73 Identities=22% Similarity=0.433 Sum_probs=52.2
Q ss_pred cccccccccccc-CCCceecCCCCcccHhHHHHHHhccccCCCCc--cccccCCCcCCCccchhHHhhhcChHHHHHHHH
Q 007642 141 EMTCGICFENYP-SDRLLAAACGHPFCSSCWTGYISTAINDGPGC--LMLRCPDPSCGAAVGQDMIYLLSSDEDKVKYNR 217 (595)
Q Consensus 141 ~~~C~IC~e~~~-~~~~~~l~CgH~fC~~C~~~yi~~~i~~g~~~--~~i~CP~~~C~~~v~~~~i~~ll~~e~~eky~~ 217 (595)
.-.|.|||.+-- ....+.+.|+|.|...|.+..++..-. |+.+ ..|.|| -|+..|..-.++.|+.+ +.+.|+.
T Consensus 3486 DDmCmICFTE~L~AAP~IqL~C~HiFHlqC~R~vLE~RW~-GPRItF~FisCP--iC~n~InH~~LkDLldP-iKel~ed 3561 (3738)
T KOG1428|consen 3486 DDMCMICFTEALSAAPAIQLDCSHIFHLQCCRRVLENRWL-GPRITFGFISCP--ICKNKINHIVLKDLLDP-IKELYED 3561 (3738)
T ss_pred CceEEEEehhhhCCCcceecCCccchhHHHHHHHHHhccc-CCeeEEeeeecc--cccchhhhHHHHHHHHH-HHHHHHH
Confidence 356999997632 234477899999999999999887653 4422 258999 89999988777777763 3444443
No 80
>KOG4739 consensus Uncharacterized protein involved in synaptonemal complex formation [Cell cycle control, cell division, chromosome partitioning; General function prediction only]
Probab=83.29 E-value=0.53 Score=46.86 Aligned_cols=54 Identities=24% Similarity=0.531 Sum_probs=37.3
Q ss_pred cccccccccccCCCceecCCCCcccHhHHHHHHhccccCCCCccccccCCCcCCCccchhHHhhhcC
Q 007642 142 MTCGICFENYPSDRLLAAACGHPFCSSCWTGYISTAINDGPGCLMLRCPDPSCGAAVGQDMIYLLSS 208 (595)
Q Consensus 142 ~~C~IC~e~~~~~~~~~l~CgH~fC~~C~~~yi~~~i~~g~~~~~i~CP~~~C~~~v~~~~i~~ll~ 208 (595)
+.|..|+---+...++.+.|+|.||..|.+.-. .-.|| .|+..+....+..-++
T Consensus 4 VhCn~C~~~~~~~~f~LTaC~HvfC~~C~k~~~-----------~~~C~--lCkk~ir~i~l~~slp 57 (233)
T KOG4739|consen 4 VHCNKCFRFPSQDPFFLTACRHVFCEPCLKASS-----------PDVCP--LCKKSIRIIQLNRSLP 57 (233)
T ss_pred EEeccccccCCCCceeeeechhhhhhhhcccCC-----------ccccc--cccceeeeeecccccc
Confidence 568989876554556778899999999986531 22799 8998875444333333
No 81
>KOG0297 consensus TNF receptor-associated factor [Signal transduction mechanisms]
Probab=82.79 E-value=0.7 Score=50.16 Aligned_cols=48 Identities=29% Similarity=0.781 Sum_probs=36.7
Q ss_pred CCCccccccccccccCCCcee-cCCCCcccHhHHHHHHhccccCCCCccccccCCCcCCCcc
Q 007642 138 DGEEMTCGICFENYPSDRLLA-AACGHPFCSSCWTGYISTAINDGPGCLMLRCPDPSCGAAV 198 (595)
Q Consensus 138 ~~~~~~C~IC~e~~~~~~~~~-l~CgH~fC~~C~~~yi~~~i~~g~~~~~i~CP~~~C~~~v 198 (595)
......|++|...+ .+++. ..|||.||..|+..+... ...|| .|...+
T Consensus 18 ~~~~l~C~~C~~vl--~~p~~~~~cgh~fC~~C~~~~~~~---------~~~cp--~~~~~~ 66 (391)
T KOG0297|consen 18 LDENLLCPICMSVL--RDPVQTTTCGHRFCAGCLLESLSN---------HQKCP--VCRQEL 66 (391)
T ss_pred CcccccCccccccc--cCCCCCCCCCCcccccccchhhcc---------CcCCc--cccccc
Confidence 45578999999887 66766 599999999999998754 24687 665443
No 82
>KOG1785 consensus Tyrosine kinase negative regulator CBL [Defense mechanisms]
Probab=82.65 E-value=0.54 Score=49.65 Aligned_cols=45 Identities=33% Similarity=0.780 Sum_probs=33.2
Q ss_pred cccccccccccCCCceecCCCCcccHhHHHHHHhccccCCCCccccccCCCcCCCc
Q 007642 142 MTCGICFENYPSDRLLAAACGHPFCSSCWTGYISTAINDGPGCLMLRCPDPSCGAA 197 (595)
Q Consensus 142 ~~C~IC~e~~~~~~~~~l~CgH~fC~~C~~~yi~~~i~~g~~~~~i~CP~~~C~~~ 197 (595)
..|-||-+.- .++..-+|||..|..|+..|-.. ++ .-.|| .|+..
T Consensus 370 eLCKICaend--KdvkIEPCGHLlCt~CLa~WQ~s---d~----gq~CP--FCRcE 414 (563)
T KOG1785|consen 370 ELCKICAEND--KDVKIEPCGHLLCTSCLAAWQDS---DE----GQTCP--FCRCE 414 (563)
T ss_pred HHHHHhhccC--CCcccccccchHHHHHHHhhccc---CC----CCCCC--ceeeE
Confidence 3599999863 67788899999999999998533 32 13688 56543
No 83
>KOG4185 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=81.97 E-value=1.2 Score=46.33 Aligned_cols=48 Identities=29% Similarity=0.703 Sum_probs=37.3
Q ss_pred ccccccccccccCC----CceecCCCCcccHhHHHHHHhccccCCCCccccccCCCcCCCcc
Q 007642 141 EMTCGICFENYPSD----RLLAAACGHPFCSSCWTGYISTAINDGPGCLMLRCPDPSCGAAV 198 (595)
Q Consensus 141 ~~~C~IC~e~~~~~----~~~~l~CgH~fC~~C~~~yi~~~i~~g~~~~~i~CP~~~C~~~v 198 (595)
...|.||-++|... -|..+.|||.+|..|+...+.. ..+.|| .|+...
T Consensus 3 ~~~c~~c~~~~s~~~~~~~p~~l~c~h~~c~~c~~~l~~~--------~~i~cp--fcR~~~ 54 (296)
T KOG4185|consen 3 FPECEICNEDYSSEDGDHIPRVLKCGHTICQNCASKLLGN--------SRILCP--FCRETT 54 (296)
T ss_pred CCceeecCccccccCcccCCcccccCceehHhHHHHHhcC--------ceeecc--CCCCcc
Confidence 35799999988754 2556779999999999998743 257787 899883
No 84
>smart00661 RPOL9 RNA polymerase subunit 9.
Probab=81.81 E-value=1.1 Score=33.65 Aligned_cols=27 Identities=26% Similarity=0.719 Sum_probs=19.9
Q ss_pred ccCCCCCcceeecC--CCCcccccCCCcce
Q 007642 300 KPCPRCKRPIEKNQ--GCMHMTCTPPCKFE 327 (595)
Q Consensus 300 K~CPkC~~~IEK~~--GCnhmtC~~~C~~~ 327 (595)
+-||.|+.++.... +-++..|+ .||+.
T Consensus 1 ~FCp~Cg~~l~~~~~~~~~~~vC~-~Cg~~ 29 (52)
T smart00661 1 KFCPKCGNMLIPKEGKEKRRFVCR-KCGYE 29 (52)
T ss_pred CCCCCCCCccccccCCCCCEEECC-cCCCe
Confidence 36999999887553 34688898 78865
No 85
>PF10446 DUF2457: Protein of unknown function (DUF2457); InterPro: IPR018853 This entry represents a family of uncharacterised proteins.
Probab=81.64 E-value=1.5 Score=47.35 Aligned_cols=11 Identities=36% Similarity=1.102 Sum_probs=7.4
Q ss_pred CCCCCcccccc
Q 007642 136 FPDGEEMTCGI 146 (595)
Q Consensus 136 ~~~~~~~~C~I 146 (595)
.|.+..|.|+-
T Consensus 189 LPDSTDFVCGT 199 (458)
T PF10446_consen 189 LPDSTDFVCGT 199 (458)
T ss_pred CCCcccccCCC
Confidence 45666777775
No 86
>KOG0828 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=81.62 E-value=0.69 Score=50.16 Aligned_cols=51 Identities=24% Similarity=0.561 Sum_probs=37.1
Q ss_pred CccccccccccccCC-----C----------ceecCCCCcccHhHHHHHHhccccCCCCccccccCCCcCCCccch
Q 007642 140 EEMTCGICFENYPSD-----R----------LLAAACGHPFCSSCWTGYISTAINDGPGCLMLRCPDPSCGAAVGQ 200 (595)
Q Consensus 140 ~~~~C~IC~e~~~~~-----~----------~~~l~CgH~fC~~C~~~yi~~~i~~g~~~~~i~CP~~~C~~~v~~ 200 (595)
....|.||+...+.. . ....||.|.|...|+.+|..+ ..+.|| .|+..+++
T Consensus 570 ~t~dC~ICMt~I~l~~~~s~~~~~~~~~~~nYm~tPC~HifH~~CL~~WMd~--------ykl~CP--vCR~pLPp 635 (636)
T KOG0828|consen 570 RTNDCVICMTPIDLRSTGSDCMVASMMVRRNYMLTPCHHIFHRQCLLQWMDT--------YKLICP--VCRCPLPP 635 (636)
T ss_pred ccccceEeccccceeeccCcchhhhhhhhccccccchHHHHHHHHHHHHHhh--------hcccCC--ccCCCCCC
Confidence 356799999875431 1 113489999999999999864 247899 78877764
No 87
>PF15227 zf-C3HC4_4: zinc finger of C3HC4-type, RING; PDB: 2EGP_A 2ECV_A 2ECJ_A 2YSL_A 2YSJ_A.
Probab=81.13 E-value=0.64 Score=33.61 Aligned_cols=32 Identities=28% Similarity=0.704 Sum_probs=20.7
Q ss_pred CCCCCcceeecCCCCcccccCCCcceeeecccccccCCC
Q 007642 302 CPRCKRPIEKNQGCMHMTCTPPCKFEFCWLCLGQWSDHG 340 (595)
Q Consensus 302 CPkC~~~IEK~~GCnhmtC~~~C~~~FCw~C~~~~~~H~ 340 (595)
||-|...+. +.++= .|||.||..|+..|....
T Consensus 1 CpiC~~~~~-----~Pv~l--~CGH~FC~~Cl~~~~~~~ 32 (42)
T PF15227_consen 1 CPICLDLFK-----DPVSL--PCGHSFCRSCLERLWKEP 32 (42)
T ss_dssp ETTTTSB-S-----SEEE---SSSSEEEHHHHHHHHCCS
T ss_pred CCccchhhC-----Ccccc--CCcCHHHHHHHHHHHHcc
Confidence 566666555 23554 499999999998764433
No 88
>KOG1952 consensus Transcription factor NF-X1, contains NFX-type Zn2+-binding and R3H domains [Transcription]
Probab=80.99 E-value=2.1 Score=49.56 Aligned_cols=54 Identities=24% Similarity=0.543 Sum_probs=40.3
Q ss_pred CCccccccccccccCCCc-eec-CCCCcccHhHHHHHHhccccCCCCccccccCCCcCCC
Q 007642 139 GEEMTCGICFENYPSDRL-LAA-ACGHPFCSSCWTGYISTAINDGPGCLMLRCPDPSCGA 196 (595)
Q Consensus 139 ~~~~~C~IC~e~~~~~~~-~~l-~CgH~fC~~C~~~yi~~~i~~g~~~~~i~CP~~~C~~ 196 (595)
...+.|.||++.+....+ .+. .|-|.|...||+.|..+.-..+. ..-+|| .|..
T Consensus 189 ~~~yeCmIC~e~I~~t~~~WSC~sCYhVFHl~CI~~WArs~ek~~~--~~WrCP--~Cqs 244 (950)
T KOG1952|consen 189 NRKYECMICTERIKRTAPVWSCKSCYHVFHLNCIKKWARSSEKTGQ--DGWRCP--ACQS 244 (950)
T ss_pred cCceEEEEeeeeccccCCceecchhhhhhhHHHHHHHHHHhhhccC--ccccCC--cccc
Confidence 346889999998865544 343 49999999999999988444443 367999 7863
No 89
>COG5222 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=79.82 E-value=1.7 Score=44.34 Aligned_cols=43 Identities=26% Similarity=0.819 Sum_probs=32.4
Q ss_pred cccccccccccCCCceec-CCCCcccHhHHHHHHhccccCCCCccccccCCCcCCC
Q 007642 142 MTCGICFENYPSDRLLAA-ACGHPFCSSCWTGYISTAINDGPGCLMLRCPDPSCGA 196 (595)
Q Consensus 142 ~~C~IC~e~~~~~~~~~l-~CgH~fC~~C~~~yi~~~i~~g~~~~~i~CP~~~C~~ 196 (595)
+.|+.|-..+ .+++.. .|+|.||..||..-+... .+.|| .|..
T Consensus 275 LkCplc~~Ll--rnp~kT~cC~~~fc~eci~~al~ds--------Df~Cp--nC~r 318 (427)
T COG5222 275 LKCPLCHCLL--RNPMKTPCCGHTFCDECIGTALLDS--------DFKCP--NCSR 318 (427)
T ss_pred ccCcchhhhh--hCcccCccccchHHHHHHhhhhhhc--------cccCC--Cccc
Confidence 7899998765 555554 599999999998765431 47899 6764
No 90
>KOG0823 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=79.69 E-value=0.71 Score=45.65 Aligned_cols=17 Identities=47% Similarity=1.249 Sum_probs=14.8
Q ss_pred CcceeeecccccccCCC
Q 007642 324 CKFEFCWLCLGQWSDHG 340 (595)
Q Consensus 324 C~~~FCw~C~~~~~~H~ 340 (595)
|||-|||-|+-.|..+.
T Consensus 65 CGHLFCWpClyqWl~~~ 81 (230)
T KOG0823|consen 65 CGHLFCWPCLYQWLQTR 81 (230)
T ss_pred cccceehHHHHHHHhhc
Confidence 99999999999997554
No 91
>PHA03096 p28-like protein; Provisional
Probab=79.55 E-value=0.9 Score=46.99 Aligned_cols=52 Identities=17% Similarity=0.332 Sum_probs=34.1
Q ss_pred cccccccccccCC----C-ceec-CCCCcccHhHHHHHHhccccCCCCccccccCCCcCCCcc
Q 007642 142 MTCGICFENYPSD----R-LLAA-ACGHPFCSSCWTGYISTAINDGPGCLMLRCPDPSCGAAV 198 (595)
Q Consensus 142 ~~C~IC~e~~~~~----~-~~~l-~CgH~fC~~C~~~yi~~~i~~g~~~~~i~CP~~~C~~~v 198 (595)
..|+||++..... . .-.+ .|.|.||..|++.|........ ..-.|| .|+..+
T Consensus 179 k~c~ic~e~~~~k~~~~~~fgil~~c~h~fc~~ci~~wr~~~~~~e---~~~~c~--~~~~~~ 236 (284)
T PHA03096 179 KICGICLENIKAKYIIKKYYGILSEIKHEFNIFCIKIWMTESLYKE---TEPENR--RLNTVI 236 (284)
T ss_pred hhcccchhhhhhhccccccccccccCCcHHHHHHHHHHHHhhhhcc---cCcccc--chhhHH
Confidence 6799999875422 1 2233 5999999999999988765322 133455 555444
No 92
>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=78.09 E-value=0.7 Score=45.66 Aligned_cols=49 Identities=27% Similarity=0.626 Sum_probs=35.2
Q ss_pred cccccccccccC-CCce---ecCCCCcccHhHHHHHHhccccCCCCccccccCCCcCCCcc
Q 007642 142 MTCGICFENYPS-DRLL---AAACGHPFCSSCWTGYISTAINDGPGCLMLRCPDPSCGAAV 198 (595)
Q Consensus 142 ~~C~IC~e~~~~-~~~~---~l~CgH~fC~~C~~~yi~~~i~~g~~~~~i~CP~~~C~~~v 198 (595)
..||||-.+.-. -++. ...|-|..|-+|+...++. | +-.||.++|+.++
T Consensus 11 ~~CPvCksDrYLnPdik~linPECyHrmCESCvdRIFs~----G----pAqCP~~gC~kIL 63 (314)
T COG5220 11 RRCPVCKSDRYLNPDIKILINPECYHRMCESCVDRIFSR----G----PAQCPYKGCGKIL 63 (314)
T ss_pred ccCCccccccccCCCeEEEECHHHHHHHHHHHHHHHhcC----C----CCCCCCccHHHHH
Confidence 469999876321 2232 2239999999999998754 4 5789999997654
No 93
>PHA00626 hypothetical protein
Probab=77.21 E-value=1.8 Score=33.15 Aligned_cols=28 Identities=25% Similarity=0.692 Sum_probs=20.1
Q ss_pred cCCCCCc-ceeecCCCCc----ccccCCCcceee
Q 007642 301 PCPRCKR-PIEKNQGCMH----MTCTPPCKFEFC 329 (595)
Q Consensus 301 ~CPkC~~-~IEK~~GCnh----mtC~~~C~~~FC 329 (595)
.||+|+. -|-|.+-|+. ..|. .||+.|=
T Consensus 2 ~CP~CGS~~Ivrcg~cr~~snrYkCk-dCGY~ft 34 (59)
T PHA00626 2 SCPKCGSGNIAKEKTMRGWSDDYVCC-DCGYNDS 34 (59)
T ss_pred CCCCCCCceeeeeceecccCcceEcC-CCCCeec
Confidence 5999998 4778776654 6676 6777663
No 94
>KOG4172 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=76.59 E-value=0.94 Score=34.42 Aligned_cols=45 Identities=29% Similarity=0.611 Sum_probs=33.8
Q ss_pred cccccccccccCCCceecCCCCc-ccHhHHHHHHhccccCCCCccccccCCCcCCCcc
Q 007642 142 MTCGICFENYPSDRLLAAACGHP-FCSSCWTGYISTAINDGPGCLMLRCPDPSCGAAV 198 (595)
Q Consensus 142 ~~C~IC~e~~~~~~~~~l~CgH~-fC~~C~~~yi~~~i~~g~~~~~i~CP~~~C~~~v 198 (595)
-+|.||++.- -+.+.-.|||. .|-.|-...|.. + .=.|| -|++++
T Consensus 8 dECTICye~p--vdsVlYtCGHMCmCy~Cg~rl~~~----~----~g~CP--iCRapi 53 (62)
T KOG4172|consen 8 DECTICYEHP--VDSVLYTCGHMCMCYACGLRLKKA----L----HGCCP--ICRAPI 53 (62)
T ss_pred cceeeeccCc--chHHHHHcchHHhHHHHHHHHHHc----c----CCcCc--chhhHH
Confidence 5699999853 45666789996 899999888764 1 23688 898765
No 95
>PF14835 zf-RING_6: zf-RING of BARD1-type protein; PDB: 1JM7_B.
Probab=76.50 E-value=1.4 Score=34.91 Aligned_cols=24 Identities=29% Similarity=0.866 Sum_probs=10.7
Q ss_pred ccCCCCCcceeec---CCCCcccccCCC
Q 007642 300 KPCPRCKRPIEKN---QGCMHMTCTPPC 324 (595)
Q Consensus 300 K~CPkC~~~IEK~---~GCnhmtC~~~C 324 (595)
-+|++|...+... +||.|++|+ .|
T Consensus 8 LrCs~C~~~l~~pv~l~~CeH~fCs-~C 34 (65)
T PF14835_consen 8 LRCSICFDILKEPVCLGGCEHIFCS-SC 34 (65)
T ss_dssp TS-SSS-S--SS-B---SSS--B-T-TT
T ss_pred cCCcHHHHHhcCCceeccCccHHHH-HH
Confidence 6899999877643 677776666 44
No 96
>PRK14559 putative protein serine/threonine phosphatase; Provisional
Probab=76.22 E-value=1.9 Score=49.77 Aligned_cols=23 Identities=30% Similarity=0.768 Sum_probs=15.8
Q ss_pred ccCCCCCcceeecCCCCcccccCCCcceeeeccccc
Q 007642 300 KPCPRCKRPIEKNQGCMHMTCTPPCKFEFCWLCLGQ 335 (595)
Q Consensus 300 K~CPkC~~~IEK~~GCnhmtC~~~C~~~FCw~C~~~ 335 (595)
+.||+|+..+. =+..||..||..
T Consensus 28 ~~Cp~CG~~~~-------------~~~~fC~~CG~~ 50 (645)
T PRK14559 28 KPCPQCGTEVP-------------VDEAHCPNCGAE 50 (645)
T ss_pred CcCCCCCCCCC-------------cccccccccCCc
Confidence 56777777765 345588888764
No 97
>KOG2038 consensus CAATT-binding transcription factor/60S ribosomal subunit biogenesis protein [Translation, ribosomal structure and biogenesis; Transcription]
Probab=76.21 E-value=2 Score=49.34 Aligned_cols=6 Identities=17% Similarity=0.174 Sum_probs=2.2
Q ss_pred chhhcc
Q 007642 8 DMQDAN 13 (595)
Q Consensus 8 ~~~~~~ 13 (595)
|+.+.+
T Consensus 887 d~~s~~ 892 (988)
T KOG2038|consen 887 DENSLG 892 (988)
T ss_pred chhccc
Confidence 333333
No 98
>KOG1941 consensus Acetylcholine receptor-associated protein of the synapse (rapsyn) [Extracellular structures]
Probab=75.60 E-value=4.7 Score=42.78 Aligned_cols=46 Identities=35% Similarity=0.803 Sum_probs=37.2
Q ss_pred ccccccccccccC--CCceecCCCCcccHhHHHHHHhccccCCCCccccccCCCcCC
Q 007642 141 EMTCGICFENYPS--DRLLAAACGHPFCSSCWTGYISTAINDGPGCLMLRCPDPSCG 195 (595)
Q Consensus 141 ~~~C~IC~e~~~~--~~~~~l~CgH~fC~~C~~~yi~~~i~~g~~~~~i~CP~~~C~ 195 (595)
++.|+.|-+.+.. +....+||.|.|...|+..|+.. .+ +-+|| .|+
T Consensus 365 ~L~Cg~CGe~~Glk~e~LqALpCsHIfH~rCl~e~L~~---n~----~rsCP--~Cr 412 (518)
T KOG1941|consen 365 ELYCGLCGESIGLKNERLQALPCSHIFHLRCLQEILEN---NG----TRSCP--NCR 412 (518)
T ss_pred hhhhhhhhhhhcCCcccccccchhHHHHHHHHHHHHHh---CC----CCCCc--cHH
Confidence 6789999998764 34678999999999999999954 33 46899 787
No 99
>KOG0825 consensus PHD Zn-finger protein [General function prediction only]
Probab=74.23 E-value=1.1 Score=51.06 Aligned_cols=32 Identities=19% Similarity=0.487 Sum_probs=15.2
Q ss_pred ccccccccccCCCc-eecCCCCcccHhHHHHHH
Q 007642 143 TCGICFENYPSDRL-LAAACGHPFCSSCWTGYI 174 (595)
Q Consensus 143 ~C~IC~e~~~~~~~-~~l~CgH~fC~~C~~~yi 174 (595)
.|++|+..+..... ....|+|.||..|+..|-
T Consensus 125 ~CP~Ci~s~~DqL~~~~k~c~H~FC~~Ci~sWs 157 (1134)
T KOG0825|consen 125 QCPNCLKSCNDQLEESEKHTAHYFCEECVGSWS 157 (1134)
T ss_pred hhhHHHHHHHHHhhccccccccccHHHHhhhhh
Confidence 35555544322111 123466666666665553
No 100
>PF08274 PhnA_Zn_Ribbon: PhnA Zinc-Ribbon ; InterPro: IPR013987 The PhnA protein family includes the uncharacterised Escherichia coli protein PhnA and its homologues. The E. coli phnA gene is part of a large operon associated with alkylphosphonate uptake and carbon-phosphorus bond cleavage []. The protein is not related to the characterised phosphonoacetate hydrolase designated PhnA []. This entry represents the N-terminal domain of PhnA, which is predicted to form a zinc-ribbon.; PDB: 2AKL_A.
Probab=73.92 E-value=2.3 Score=28.53 Aligned_cols=27 Identities=26% Similarity=0.766 Sum_probs=14.2
Q ss_pred ccCCCCCcceeecCCCCcccccCCCccee
Q 007642 300 KPCPRCKRPIEKNQGCMHMTCTPPCKFEF 328 (595)
Q Consensus 300 K~CPkC~~~IEK~~GCnhmtC~~~C~~~F 328 (595)
-+||+|+....-.+|.+ |.|. .|+++|
T Consensus 3 p~Cp~C~se~~y~D~~~-~vCp-~C~~ew 29 (30)
T PF08274_consen 3 PKCPLCGSEYTYEDGEL-LVCP-ECGHEW 29 (30)
T ss_dssp ---TTT-----EE-SSS-EEET-TTTEEE
T ss_pred CCCCCCCCcceeccCCE-EeCC-cccccC
Confidence 37999998887777766 7787 788875
No 101
>PF09297 zf-NADH-PPase: NADH pyrophosphatase zinc ribbon domain; InterPro: IPR015376 This domain has a zinc ribbon structure and is often found between two NUDIX domains.; GO: 0016787 hydrolase activity, 0046872 metal ion binding; PDB: 1VK6_A 2GB5_A.
Probab=73.64 E-value=3.6 Score=27.75 Aligned_cols=29 Identities=31% Similarity=0.699 Sum_probs=17.7
Q ss_pred cCccCCCCCcceeecCCCCcccccCCCcce
Q 007642 298 NSKPCPRCKRPIEKNQGCMHMTCTPPCKFE 327 (595)
Q Consensus 298 ntK~CPkC~~~IEK~~GCnhmtC~~~C~~~ 327 (595)
+.+-||+|+.+.....+=.-|.|. .|++.
T Consensus 2 ~~rfC~~CG~~t~~~~~g~~r~C~-~Cg~~ 30 (32)
T PF09297_consen 2 NHRFCGRCGAPTKPAPGGWARRCP-SCGHE 30 (32)
T ss_dssp TTSB-TTT--BEEE-SSSS-EEES-SSS-E
T ss_pred CCcccCcCCccccCCCCcCEeECC-CCcCE
Confidence 347899999999888776668887 68764
No 102
>PF10446 DUF2457: Protein of unknown function (DUF2457); InterPro: IPR018853 This entry represents a family of uncharacterised proteins.
Probab=72.65 E-value=3.5 Score=44.64 Aligned_cols=6 Identities=33% Similarity=0.645 Sum_probs=2.7
Q ss_pred HhHHHH
Q 007642 167 SSCWTG 172 (595)
Q Consensus 167 ~~C~~~ 172 (595)
..|+..
T Consensus 211 ~Scle~ 216 (458)
T PF10446_consen 211 ISCLEA 216 (458)
T ss_pred HHHHHH
Confidence 344443
No 103
>KOG3039 consensus Uncharacterized conserved protein [Function unknown]
Probab=70.80 E-value=3.1 Score=41.45 Aligned_cols=52 Identities=12% Similarity=0.217 Sum_probs=37.7
Q ss_pred CccccccccccccCCCc--eecCCCCcccHhHHHHHHhccccCCCCccccccCCCcCCCccchhH
Q 007642 140 EEMTCGICFENYPSDRL--LAAACGHPFCSSCWTGYISTAINDGPGCLMLRCPDPSCGAAVGQDM 202 (595)
Q Consensus 140 ~~~~C~IC~e~~~~~~~--~~l~CgH~fC~~C~~~yi~~~i~~g~~~~~i~CP~~~C~~~v~~~~ 202 (595)
..+.||||-+.+...-+ +.-+|||.||.+|...+|.. ...|| .|...+....
T Consensus 220 ~ryiCpvtrd~LtNt~~ca~Lr~sg~Vv~~ecvEklir~---------D~v~p--v~d~plkdrd 273 (303)
T KOG3039|consen 220 KRYICPVTRDTLTNTTPCAVLRPSGHVVTKECVEKLIRK---------DMVDP--VTDKPLKDRD 273 (303)
T ss_pred cceecccchhhhcCccceEEeccCCcEeeHHHHHHhccc---------ccccc--CCCCcCcccc
Confidence 46889999998854332 33479999999999999754 24577 6777665543
No 104
>PF14952 zf-tcix: Putative treble-clef, zinc-finger, Zn-binding
Probab=70.15 E-value=3.3 Score=30.06 Aligned_cols=31 Identities=23% Similarity=0.540 Sum_probs=21.3
Q ss_pred HHHHhcCccCCCCCcceeecCCCCcccccC-CCcce
Q 007642 293 NWILANSKPCPRCKRPIEKNQGCMHMTCTP-PCKFE 327 (595)
Q Consensus 293 ~wi~~ntK~CPkC~~~IEK~~GCnhmtC~~-~C~~~ 327 (595)
.|.+-..|.||+|+..- |+--+.|.+ .|++.
T Consensus 5 k~TlRGirkCp~CGt~N----G~R~~~CKN~~C~~~ 36 (44)
T PF14952_consen 5 KPTLRGIRKCPKCGTYN----GTRGLSCKNKSCPQV 36 (44)
T ss_pred hhhHhccccCCcCcCcc----CcccccccCCccchh
Confidence 35556679999999865 666677763 45443
No 105
>PF04147 Nop14: Nop14-like family ; InterPro: IPR007276 Emg1 and Nop14 are novel proteins whose interaction is required for the maturation of the 18S rRNA and for 40S ribosome production [].
Probab=68.94 E-value=15 Score=44.10 Aligned_cols=17 Identities=12% Similarity=0.319 Sum_probs=9.7
Q ss_pred CcceEE---eCHHHHHHHHH
Q 007642 64 QLNYTV---LTEADIRQRQE 80 (595)
Q Consensus 64 ~~~y~v---l~~~~i~~~~~ 80 (595)
+.+|++ -|.+++...+.
T Consensus 417 elPftf~~P~s~eel~~lL~ 436 (840)
T PF04147_consen 417 ELPFTFPCPSSHEELLELLD 436 (840)
T ss_pred CCCceecCCCCHHHHHHHHh
Confidence 456765 45666655543
No 106
>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=68.51 E-value=2.2 Score=36.81 Aligned_cols=31 Identities=23% Similarity=0.562 Sum_probs=26.4
Q ss_pred ccccccccccccCCCceecCCCCcccHhHHH
Q 007642 141 EMTCGICFENYPSDRLLAAACGHPFCSSCWT 171 (595)
Q Consensus 141 ~~~C~IC~e~~~~~~~~~l~CgH~fC~~C~~ 171 (595)
...|++|...+....++..||||.|...|.+
T Consensus 78 ~~~C~vC~k~l~~~~f~~~p~~~v~H~~C~~ 108 (109)
T PF10367_consen 78 STKCSVCGKPLGNSVFVVFPCGHVVHYSCIK 108 (109)
T ss_pred CCCccCcCCcCCCceEEEeCCCeEEeccccc
Confidence 4569999999877777888999999999975
No 107
>PLN03086 PRLI-interacting factor K; Provisional
Probab=68.16 E-value=6.1 Score=44.68 Aligned_cols=100 Identities=23% Similarity=0.531 Sum_probs=0.0
Q ss_pred cccCCCcCCCccchhHHhhhcChHHHHHHHHHHHHHhhhhCCCcccCCCCCCCCeeeeecCCCCceeee-cCCCcc----
Q 007642 187 LRCPDPSCGAAVGQDMIYLLSSDEDKVKYNRYFIRSYVEDNRKTKWCPAPGCDYAVDFVVGSGNYDVTC-RCSYSF---- 261 (595)
Q Consensus 187 i~CP~~~C~~~v~~~~i~~ll~~e~~eky~~~~~~~~v~~~~~~~~CP~p~C~~~i~~~~~~~~~~v~C-~C~~~f---- 261 (595)
+.|| .|+..++...+..... .-....+.||+.+|+..+.. ......+.| .|+..|
T Consensus 408 V~C~--NC~~~i~l~~l~lHe~----------------~C~r~~V~Cp~~~Cg~v~~r--~el~~H~~C~~Cgk~f~~s~ 467 (567)
T PLN03086 408 VECR--NCKHYIPSRSIALHEA----------------YCSRHNVVCPHDGCGIVLRV--EEAKNHVHCEKCGQAFQQGE 467 (567)
T ss_pred EECC--CCCCccchhHHHHHHh----------------hCCCcceeCCcccccceeec--cccccCccCCCCCCccchHH
Q ss_pred -------------cccCCcc-------cCCCCCchhHHHHHHhhhHhHHhHHHHHhcCccCCCCCcce------------
Q 007642 262 -------------CWNCTEE-------AHRPVDCDTVAKWVLKNSAESENMNWILANSKPCPRCKRPI------------ 309 (595)
Q Consensus 262 -------------C~~C~~~-------~H~p~~C~~~~~~~~k~~~~~e~~~wi~~ntK~CPkC~~~I------------ 309 (595)
|. |+.. .|....|.... ..||.|+..+
T Consensus 468 LekH~~~~Hkpv~Cp-Cg~~~~R~~L~~H~~thCp~Kp--------------------i~C~fC~~~v~~g~~~~d~~d~ 526 (567)
T PLN03086 468 MEKHMKVFHEPLQCP-CGVVLEKEQMVQHQASTCPLRL--------------------ITCRFCGDMVQAGGSAMDVRDR 526 (567)
T ss_pred HHHHHHhcCCCccCC-CCCCcchhHHHhhhhccCCCCc--------------------eeCCCCCCccccCccccchhhh
Q ss_pred -------eecCCCCcccccCCCccee
Q 007642 310 -------EKNQGCMHMTCTPPCKFEF 328 (595)
Q Consensus 310 -------EK~~GCnhmtC~~~C~~~F 328 (595)
+..-|-.|..|. .||..|
T Consensus 527 ~s~Lt~HE~~CG~rt~~C~-~Cgk~V 551 (567)
T PLN03086 527 LRGMSEHESICGSRTAPCD-SCGRSV 551 (567)
T ss_pred hhhHHHHHHhcCCcceEcc-ccCCee
No 108
>KOG0320 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=67.78 E-value=1.9 Score=41.00 Aligned_cols=32 Identities=34% Similarity=0.977 Sum_probs=22.9
Q ss_pred eeecCCCcccccCCcccCCCCCchhHHHHHHhhhHhHHhHHHHHhcCccCCCCCccee
Q 007642 253 VTCRCSYSFCWNCTEEAHRPVDCDTVAKWVLKNSAESENMNWILANSKPCPRCKRPIE 310 (595)
Q Consensus 253 v~C~C~~~fC~~C~~~~H~p~~C~~~~~~~~k~~~~~e~~~wi~~ntK~CPkC~~~IE 310 (595)
|.=.|||.||..|.+. ...++.+||-|++-|-
T Consensus 147 vsTkCGHvFC~~Cik~--------------------------alk~~~~CP~C~kkIt 178 (187)
T KOG0320|consen 147 VSTKCGHVFCSQCIKD--------------------------ALKNTNKCPTCRKKIT 178 (187)
T ss_pred cccccchhHHHHHHHH--------------------------HHHhCCCCCCcccccc
Confidence 4458999999888643 1234589999997664
No 109
>COG5175 MOT2 Transcriptional repressor [Transcription]
Probab=67.65 E-value=3.3 Score=43.06 Aligned_cols=53 Identities=23% Similarity=0.659 Sum_probs=38.6
Q ss_pred ccccccccccccC--CCceecCCCCcccHhHHHHHHhccccCCCCccccccCCCcCCCccchhHH
Q 007642 141 EMTCGICFENYPS--DRLLAAACGHPFCSSCWTGYISTAINDGPGCLMLRCPDPSCGAAVGQDMI 203 (595)
Q Consensus 141 ~~~C~IC~e~~~~--~~~~~l~CgH~fC~~C~~~yi~~~i~~g~~~~~i~CP~~~C~~~v~~~~i 203 (595)
.-.||+|.+.... .+++..+||-..|+-||... ...+ .=+|| .|+.....+-+
T Consensus 14 ed~cplcie~mditdknf~pc~cgy~ic~fc~~~i-rq~l-------ngrcp--acrr~y~denv 68 (480)
T COG5175 14 EDYCPLCIEPMDITDKNFFPCPCGYQICQFCYNNI-RQNL-------NGRCP--ACRRKYDDENV 68 (480)
T ss_pred cccCcccccccccccCCcccCCcccHHHHHHHHHH-Hhhc-------cCCCh--Hhhhhccccce
Confidence 4459999998654 46778899999999999764 3323 23899 89987765544
No 110
>PF14447 Prok-RING_4: Prokaryotic RING finger family 4
Probab=67.38 E-value=2.4 Score=32.51 Aligned_cols=46 Identities=30% Similarity=0.680 Sum_probs=31.1
Q ss_pred ccccccccccccCCCceecCCCCcccHhHHHHHHhccccCCCCccccccCCCcCCCccchh
Q 007642 141 EMTCGICFENYPSDRLLAAACGHPFCSSCWTGYISTAINDGPGCLMLRCPDPSCGAAVGQD 201 (595)
Q Consensus 141 ~~~C~IC~e~~~~~~~~~l~CgH~fC~~C~~~yi~~~i~~g~~~~~i~CP~~~C~~~v~~~ 201 (595)
...|-.|... ....+.++|||..|..||-.- ..-.|| .|...|...
T Consensus 7 ~~~~~~~~~~--~~~~~~~pCgH~I~~~~f~~~-----------rYngCP--fC~~~~~~~ 52 (55)
T PF14447_consen 7 EQPCVFCGFV--GTKGTVLPCGHLICDNCFPGE-----------RYNGCP--FCGTPFEFD 52 (55)
T ss_pred ceeEEEcccc--ccccccccccceeeccccChh-----------hccCCC--CCCCcccCC
Confidence 3445555543 255678899999999999642 123599 898877543
No 111
>PF04641 Rtf2: Rtf2 RING-finger
Probab=66.68 E-value=7 Score=39.98 Aligned_cols=58 Identities=17% Similarity=0.461 Sum_probs=41.4
Q ss_pred CCCccccccccccccCC-Cceec-CCCCcccHhHHHHHHhccccCCCCccccccCCCcCCCccchhHHhhhc
Q 007642 138 DGEEMTCGICFENYPSD-RLLAA-ACGHPFCSSCWTGYISTAINDGPGCLMLRCPDPSCGAAVGQDMIYLLS 207 (595)
Q Consensus 138 ~~~~~~C~IC~e~~~~~-~~~~l-~CgH~fC~~C~~~yi~~~i~~g~~~~~i~CP~~~C~~~v~~~~i~~ll 207 (595)
....+.|||....+... .++.+ +|||.|+..+++..= . .-.|| .|...|....|-.|.
T Consensus 110 ~~~~~~CPvt~~~~~~~~~fv~l~~cG~V~s~~alke~k----~------~~~Cp--~c~~~f~~~DiI~Ln 169 (260)
T PF04641_consen 110 SEGRFICPVTGKEFNGKHKFVYLRPCGCVFSEKALKELK----K------SKKCP--VCGKPFTEEDIIPLN 169 (260)
T ss_pred CCceeECCCCCcccCCceeEEEEcCCCCEeeHHHHHhhc----c------ccccc--ccCCccccCCEEEec
Confidence 35679999999888532 34444 899999999999871 1 13599 899998765443333
No 112
>PF13719 zinc_ribbon_5: zinc-ribbon domain
Probab=65.96 E-value=4.6 Score=28.30 Aligned_cols=29 Identities=28% Similarity=0.670 Sum_probs=20.8
Q ss_pred ccCCCCCCCCeeeeecC---CCCceeee-cCCCcc
Q 007642 231 KWCPAPGCDYAVDFVVG---SGNYDVTC-RCSYSF 261 (595)
Q Consensus 231 ~~CP~p~C~~~i~~~~~---~~~~~v~C-~C~~~f 261 (595)
+.||+ |+..+.+... .+...|.| .|++.|
T Consensus 3 i~CP~--C~~~f~v~~~~l~~~~~~vrC~~C~~~f 35 (37)
T PF13719_consen 3 ITCPN--CQTRFRVPDDKLPAGGRKVRCPKCGHVF 35 (37)
T ss_pred EECCC--CCceEEcCHHHcccCCcEEECCCCCcEe
Confidence 57885 9988776533 34567899 899876
No 113
>PRK00432 30S ribosomal protein S27ae; Validated
Probab=65.47 E-value=2.7 Score=31.65 Aligned_cols=27 Identities=26% Similarity=0.635 Sum_probs=19.8
Q ss_pred CccCCCCCc-ceeecCCCCcccccCCCccee
Q 007642 299 SKPCPRCKR-PIEKNQGCMHMTCTPPCKFEF 328 (595)
Q Consensus 299 tK~CPkC~~-~IEK~~GCnhmtC~~~C~~~F 328 (595)
-+-||+|+. .+.... +.++|. .||+.+
T Consensus 20 ~~fCP~Cg~~~m~~~~--~r~~C~-~Cgyt~ 47 (50)
T PRK00432 20 NKFCPRCGSGFMAEHL--DRWHCG-KCGYTE 47 (50)
T ss_pred cCcCcCCCcchheccC--CcEECC-CcCCEE
Confidence 478999988 444333 689998 798865
No 114
>KOG2807 consensus RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit SSL1 [Transcription; Replication, recombination and repair]
Probab=65.09 E-value=2.8 Score=43.41 Aligned_cols=22 Identities=27% Similarity=0.714 Sum_probs=18.2
Q ss_pred CCceeee-cCCCcccccCCcccC
Q 007642 249 GNYDVTC-RCSYSFCWNCTEEAH 270 (595)
Q Consensus 249 ~~~~v~C-~C~~~fC~~C~~~~H 270 (595)
......| .|...||..|..-.|
T Consensus 342 ~~~~y~C~~Ck~~FCldCDv~iH 364 (378)
T KOG2807|consen 342 SSGRYRCESCKNVFCLDCDVFIH 364 (378)
T ss_pred CCCcEEchhccceeeccchHHHH
Confidence 4566799 999999999987666
No 115
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=65.04 E-value=5.8 Score=29.09 Aligned_cols=30 Identities=23% Similarity=0.642 Sum_probs=20.6
Q ss_pred ccCCCCCcceeecCCCCcccccCCCcceeee
Q 007642 300 KPCPRCKRPIEKNQGCMHMTCTPPCKFEFCW 330 (595)
Q Consensus 300 K~CPkC~~~IEK~~GCnhmtC~~~C~~~FCw 330 (595)
-.||+|+..++-..+=..++|. .||..+=+
T Consensus 4 y~C~~CG~~~~~~~~~~~~~Cp-~CG~~~~~ 33 (46)
T PRK00398 4 YKCARCGREVELDEYGTGVRCP-YCGYRILF 33 (46)
T ss_pred EECCCCCCEEEECCCCCceECC-CCCCeEEE
Confidence 4799999988765443367887 67765543
No 116
>COG5219 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=64.85 E-value=2.2 Score=49.82 Aligned_cols=52 Identities=19% Similarity=0.551 Sum_probs=37.0
Q ss_pred CCccccccccccccC---CCc--eecCCCCcccHhHHHHHHhccccCCCCccccccCCCcCCCccc
Q 007642 139 GEEMTCGICFENYPS---DRL--LAAACGHPFCSSCWTGYISTAINDGPGCLMLRCPDPSCGAAVG 199 (595)
Q Consensus 139 ~~~~~C~IC~e~~~~---~~~--~~l~CgH~fC~~C~~~yi~~~i~~g~~~~~i~CP~~~C~~~v~ 199 (595)
++...|+||+..+.. .-| ....|.|.|...|+-.|+.+. + .-+|| -|+..++
T Consensus 1467 sG~eECaICYsvL~~vdr~lPskrC~TCknKFH~~CLyKWf~Ss---~----~s~CP--lCRseit 1523 (1525)
T COG5219 1467 SGHEECAICYSVLDMVDRSLPSKRCATCKNKFHTRCLYKWFASS---A----RSNCP--LCRSEIT 1523 (1525)
T ss_pred CCcchhhHHHHHHHHHhccCCccccchhhhhhhHHHHHHHHHhc---C----CCCCC--ccccccc
Confidence 345679999987642 222 123499999999999999873 2 34799 8987654
No 117
>PRK14559 putative protein serine/threonine phosphatase; Provisional
Probab=64.63 E-value=5.8 Score=45.80 Aligned_cols=11 Identities=27% Similarity=0.782 Sum_probs=8.9
Q ss_pred ccCCCCCccee
Q 007642 300 KPCPRCKRPIE 310 (595)
Q Consensus 300 K~CPkC~~~IE 310 (595)
+.||+|+..+-
T Consensus 42 ~fC~~CG~~~~ 52 (645)
T PRK14559 42 AHCPNCGAETG 52 (645)
T ss_pred ccccccCCccc
Confidence 78888888766
No 118
>KOG3002 consensus Zn finger protein [General function prediction only]
Probab=64.40 E-value=5.5 Score=41.54 Aligned_cols=47 Identities=32% Similarity=0.770 Sum_probs=34.0
Q ss_pred CCCccccccccccccCCCceecCCCCcccHhHHHHHHhccccCCCCccccccCCCcCCCccc
Q 007642 138 DGEEMTCGICFENYPSDRLLAAACGHPFCSSCWTGYISTAINDGPGCLMLRCPDPSCGAAVG 199 (595)
Q Consensus 138 ~~~~~~C~IC~e~~~~~~~~~l~CgH~fC~~C~~~yi~~~i~~g~~~~~i~CP~~~C~~~v~ 199 (595)
....+.||||++.+. ..+....=||..|..|-..- .-+|| .|+..++
T Consensus 45 ~~~lleCPvC~~~l~-~Pi~QC~nGHlaCssC~~~~------------~~~CP--~Cr~~~g 91 (299)
T KOG3002|consen 45 DLDLLDCPVCFNPLS-PPIFQCDNGHLACSSCRTKV------------SNKCP--TCRLPIG 91 (299)
T ss_pred chhhccCchhhccCc-ccceecCCCcEehhhhhhhh------------cccCC--ccccccc
Confidence 345789999998862 12333445899999998732 45899 7998887
No 119
>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=64.27 E-value=4.8 Score=28.62 Aligned_cols=29 Identities=21% Similarity=0.564 Sum_probs=24.7
Q ss_pred ccCCCCCcc-eeecCCCCcccccCCCcceeeecccccc
Q 007642 300 KPCPRCKRP-IEKNQGCMHMTCTPPCKFEFCWLCLGQW 336 (595)
Q Consensus 300 K~CPkC~~~-IEK~~GCnhmtC~~~C~~~FCw~C~~~~ 336 (595)
..|+.|... +. ++|. .|+..+|..|...-
T Consensus 4 ~~C~~H~~~~~~-------~~C~-~C~~~~C~~C~~~~ 33 (42)
T PF00643_consen 4 PKCPEHPEEPLS-------LFCE-DCNEPLCSECTVSG 33 (42)
T ss_dssp SB-SSTTTSBEE-------EEET-TTTEEEEHHHHHTS
T ss_pred ccCccCCccceE-------EEec-CCCCccCccCCCCC
Confidence 689999988 88 9999 89999999998653
No 120
>KOG3800 consensus Predicted E3 ubiquitin ligase containing RING finger, subunit of transcription/repair factor TFIIH and CDK-activating kinase assembly factor [Posttranslational modification, protein turnover, chaperones]
Probab=62.59 E-value=11 Score=38.78 Aligned_cols=49 Identities=29% Similarity=0.649 Sum_probs=33.3
Q ss_pred ccccccccccC-CCce--ecCCCCcccHhHHHHHHhccccCCCCccccccCCCcCCCccchh
Q 007642 143 TCGICFENYPS-DRLL--AAACGHPFCSSCWTGYISTAINDGPGCLMLRCPDPSCGAAVGQD 201 (595)
Q Consensus 143 ~C~IC~e~~~~-~~~~--~l~CgH~fC~~C~~~yi~~~i~~g~~~~~i~CP~~~C~~~v~~~ 201 (595)
.||+|-...-. -+++ .-+|||..|.+|+-..+.. | +..|| .|..++...
T Consensus 2 ~Cp~CKt~~Y~np~lk~~in~C~H~lCEsCvd~iF~~----g----~~~Cp--eC~~iLRk~ 53 (300)
T KOG3800|consen 2 ACPKCKTDRYLNPDLKLMINECGHRLCESCVDRIFSL----G----PAQCP--ECMVILRKN 53 (300)
T ss_pred CCcccccceecCccceeeeccccchHHHHHHHHHHhc----C----CCCCC--cccchhhhc
Confidence 48888765211 1221 2279999999999988754 3 46799 999877543
No 121
>KOG4445 consensus Uncharacterized conserved protein, contains RWD domain [Function unknown]
Probab=62.21 E-value=4.3 Score=41.67 Aligned_cols=38 Identities=24% Similarity=0.591 Sum_probs=30.6
Q ss_pred CccccccccccccCCC-ceecCCCCcccHhHHHHHHhcc
Q 007642 140 EEMTCGICFENYPSDR-LLAAACGHPFCSSCWTGYISTA 177 (595)
Q Consensus 140 ~~~~C~IC~e~~~~~~-~~~l~CgH~fC~~C~~~yi~~~ 177 (595)
....|.||+--|...+ +...+|-|+|..-|+..|+...
T Consensus 114 p~gqCvICLygfa~~~~ft~T~C~Hy~H~~ClaRyl~~~ 152 (368)
T KOG4445|consen 114 PNGQCVICLYGFASSPAFTVTACDHYMHFACLARYLTEC 152 (368)
T ss_pred CCCceEEEEEeecCCCceeeehhHHHHHHHHHHHHHHHH
Confidence 4567888887776655 6678899999999999998653
No 122
>TIGR00622 ssl1 transcription factor ssl1. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=61.36 E-value=7.8 Score=34.33 Aligned_cols=39 Identities=23% Similarity=0.556 Sum_probs=25.3
Q ss_pred ccCCCCCCCCeeeeecC------CCCceeee-cCCCcccccCCcccCC
Q 007642 231 KWCPAPGCDYAVDFVVG------SGNYDVTC-RCSYSFCWNCTEEAHR 271 (595)
Q Consensus 231 ~~CP~p~C~~~i~~~~~------~~~~~v~C-~C~~~fC~~C~~~~H~ 271 (595)
..|- +|...+...+. .......| .|+..||..|..-.|.
T Consensus 56 ~~C~--~C~~~f~~~~~~~~~~~~~~~~y~C~~C~~~FC~dCD~fiHe 101 (112)
T TIGR00622 56 RFCF--GCQGPFPKPPVSPFDELKDSHRYVCAVCKNVFCVDCDVFVHE 101 (112)
T ss_pred Cccc--CcCCCCCCcccccccccccccceeCCCCCCccccccchhhhh
Confidence 4576 48765532211 11234579 9999999999887774
No 123
>TIGR02098 MJ0042_CXXC MJ0042 family finger-like domain. This domain contains a CXXCX(19)CXXC motif suggestive of both zinc fingers and thioredoxin, usually found at the N-terminus of prokaryotic proteins. One partially characterized gene, agmX, is among a large set in Myxococcus whose interruption affects adventurous gliding motility.
Probab=61.09 E-value=5.4 Score=27.85 Aligned_cols=26 Identities=27% Similarity=0.759 Sum_probs=15.9
Q ss_pred cCCCCCcceeec------CCCCcccccCCCccee
Q 007642 301 PCPRCKRPIEKN------QGCMHMTCTPPCKFEF 328 (595)
Q Consensus 301 ~CPkC~~~IEK~------~GCnhmtC~~~C~~~F 328 (595)
.||+|+..+.-. .| ..+.|. .|++.|
T Consensus 4 ~CP~C~~~~~v~~~~~~~~~-~~v~C~-~C~~~~ 35 (38)
T TIGR02098 4 QCPNCKTSFRVVDSQLGANG-GKVRCG-KCGHVW 35 (38)
T ss_pred ECCCCCCEEEeCHHHcCCCC-CEEECC-CCCCEE
Confidence 588888755422 12 267777 677655
No 124
>PLN03208 E3 ubiquitin-protein ligase RMA2; Provisional
Probab=59.95 E-value=2.7 Score=40.77 Aligned_cols=31 Identities=29% Similarity=0.922 Sum_probs=23.3
Q ss_pred ccCCCCCcceeecCCCCcccccCCCcceeeeccccccc
Q 007642 300 KPCPRCKRPIEKNQGCMHMTCTPPCKFEFCWLCLGQWS 337 (595)
Q Consensus 300 K~CPkC~~~IEK~~GCnhmtC~~~C~~~FCw~C~~~~~ 337 (595)
-.||-|...+.. .+. . .|||.|||.|+..|.
T Consensus 19 ~~CpICld~~~d-----PVv-T-~CGH~FC~~CI~~wl 49 (193)
T PLN03208 19 FDCNICLDQVRD-----PVV-T-LCGHLFCWPCIHKWT 49 (193)
T ss_pred cCCccCCCcCCC-----cEE-c-CCCchhHHHHHHHHH
Confidence 579999877641 122 4 599999999999884
No 125
>PF00627 UBA: UBA/TS-N domain; InterPro: IPR000449 UBA domains are a commonly occurring sequence motif of approximately 45 amino acid residues that are found in diverse proteins involved in the ubiquitin/proteasome pathway, DNA excision-repair, and cell signalling via protein kinases []. The human homologue of yeast Rad23A is one example of a nucleotide excision-repair protein that contains both an internal and a C-terminal UBA domain. The solution structure of human Rad23A UBA(2) showed that the domain forms a compact three-helix bundle []. Comparison of the structures of UBA(1) and UBA(2) reveals that both form very similar folds and have a conserved large hydrophobic surface patch which may be a common protein-interacting surface present in diverse UBA domains. Evidence that ubiquitin binds to UBA domains leads to the prediction that the hydrophobic surface patch of UBA domains interacts with the hydrophobic surface on the five-stranded beta-sheet of ubiquitin []. This domain is similar in sequence to the N-terminal domain of translation elongation factor EF1B (or EF-Ts) from bacteria, mitochondria and chloroplasts. More information about EF1B (EF-Ts) proteins can be found at Protein of the Month: Elongation Factors [].; GO: 0005515 protein binding; PDB: 2DAI_A 2OO9_C 2JUJ_A 1WHC_A 1YLA_A 2O25_B 3K9O_A 3K9P_A 3F92_A 3E46_A ....
Probab=59.36 E-value=26 Score=24.25 Aligned_cols=33 Identities=27% Similarity=0.339 Sum_probs=27.3
Q ss_pred HHHHHHHHHHhCCCHHHHHHHHHHcCCChhhhHH
Q 007642 80 EEDITRISTVLSISKVAASILLRFYNWSVSKVHD 113 (595)
Q Consensus 80 ~~~i~~v~~vl~i~~~~a~~LL~~~~W~~~~l~e 113 (595)
.+.|.++.+. |.++..+..-|+..+||++...+
T Consensus 3 ~~~v~~L~~m-Gf~~~~~~~AL~~~~~nve~A~~ 35 (37)
T PF00627_consen 3 EEKVQQLMEM-GFSREQAREALRACNGNVERAVD 35 (37)
T ss_dssp HHHHHHHHHH-TS-HHHHHHHHHHTTTSHHHHHH
T ss_pred HHHHHHHHHc-CCCHHHHHHHHHHcCCCHHHHHH
Confidence 3567788888 99999999999999999988664
No 126
>PHA02664 hypothetical protein; Provisional
Probab=58.00 E-value=24 Score=36.66 Aligned_cols=9 Identities=11% Similarity=0.294 Sum_probs=3.7
Q ss_pred HHHHHHHHh
Q 007642 82 DITRISTVL 90 (595)
Q Consensus 82 ~i~~v~~vl 90 (595)
.+..|.+.|
T Consensus 524 vl~ava~ml 532 (534)
T PHA02664 524 VLGAVAEML 532 (534)
T ss_pred HHHHHHHHh
Confidence 334444443
No 127
>PF02150 RNA_POL_M_15KD: RNA polymerases M/15 Kd subunit; InterPro: IPR001529 DNA-directed RNA polymerases 2.7.7.6 from EC (also known as DNA-dependent RNA polymerases) are responsible for the polymerisation of ribonucleotides into a sequence complementary to the template DNA. In eukaryotes, there are three different forms of DNA-directed RNA polymerases transcribing different sets of genes. Most RNA polymerases are multimeric enzymes and are composed of a variable number of subunits. The core RNA polymerase complex consists of five subunits (two alpha, one beta, one beta-prime and one omega) and is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. The core RNA polymerase complex forms a "crab claw"-like structure with an internal channel running along the full length []. The key functional sites of the enzyme, as defined by mutational and cross-linking analysis, are located on the inner wall of this channel. RNA synthesis follows after the attachment of RNA polymerase to a specific site, the promoter, on the template DNA strand. The RNA synthesis process continues until a termination sequence is reached. The RNA product, which is synthesised in the 5' to 3'direction, is known as the primary transcript. Eukaryotic nuclei contain three distinct types of RNA polymerases that differ in the RNA they synthesise: RNA polymerase I: located in the nucleoli, synthesises precursors of most ribosomal RNAs. RNA polymerase II: occurs in the nucleoplasm, synthesises mRNA precursors. RNA polymerase III: also occurs in the nucleoplasm, synthesises the precursors of 5S ribosomal RNA, the tRNAs, and a variety of other small nuclear and cytosolic RNAs. Eukaryotic cells are also known to contain separate mitochondrial and chloroplast RNA polymerases. Eukaryotic RNA polymerases, whose molecular masses vary in size from 500 to 700 kDa, contain two non-identical large (>100 kDa) subunits and an array of up to 12 different small (less than 50 kDa) subunits. In archaebacteria, there is generally a single form of RNA polymerase which also consist of an oligomeric assemblage of 10 to 13 polypeptides. It has recently been shown [], [] that small subunits of about 15 kDa, found in polymerase types I and II, are highly conserved. These proteins contain a probable zinc finger in their N-terminal region and a C-terminal zinc ribbon domain (see IPR001222 from INTERPRO).; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 3H0G_I 3M4O_I 3S14_I 2E2J_I 4A3J_I 3HOZ_I 1TWA_I 3S1Q_I 3S1N_I 1TWG_I ....
Probab=57.86 E-value=9.3 Score=26.49 Aligned_cols=27 Identities=22% Similarity=0.648 Sum_probs=17.2
Q ss_pred ccCCCCCCCCeeeeecCCCCceeee-cCCCc
Q 007642 231 KWCPAPGCDYAVDFVVGSGNYDVTC-RCSYS 260 (595)
Q Consensus 231 ~~CP~p~C~~~i~~~~~~~~~~v~C-~C~~~ 260 (595)
++|| .|+..+....+..... .| .|++.
T Consensus 2 ~FCp--~C~nlL~p~~~~~~~~-~C~~C~Y~ 29 (35)
T PF02150_consen 2 RFCP--ECGNLLYPKEDKEKRV-ACRTCGYE 29 (35)
T ss_dssp -BET--TTTSBEEEEEETTTTE-EESSSS-E
T ss_pred eeCC--CCCccceEcCCCccCc-CCCCCCCc
Confidence 5898 5999887764443333 78 78765
No 128
>KOG3579 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=57.49 E-value=7.6 Score=39.59 Aligned_cols=53 Identities=23% Similarity=0.575 Sum_probs=39.3
Q ss_pred CccccccccccccCCCceecC--CCCcccHhHHHHHHhccccCCCCccccccCC-CcCCC
Q 007642 140 EEMTCGICFENYPSDRLLAAA--CGHPFCSSCWTGYISTAINDGPGCLMLRCPD-PSCGA 196 (595)
Q Consensus 140 ~~~~C~IC~e~~~~~~~~~l~--CgH~fC~~C~~~yi~~~i~~g~~~~~i~CP~-~~C~~ 196 (595)
..+.|.+|-+-+....+|..+ =.|.||.-|-++.|..+-..| .+.||. ..|..
T Consensus 267 apLcCTLC~ERLEDTHFVQCPSVp~HKFCFPCSResIK~Qg~sg----evYCPSGdkCPL 322 (352)
T KOG3579|consen 267 APLCCTLCHERLEDTHFVQCPSVPSHKFCFPCSRESIKQQGASG----EVYCPSGDKCPL 322 (352)
T ss_pred CceeehhhhhhhccCceeecCCCcccceecccCHHHHHhhcCCC----ceeCCCCCcCcc
Confidence 458899999988555555544 379999999999998876555 477885 24654
No 129
>KOG2034 consensus Vacuolar sorting protein PEP3/VPS18 [Intracellular trafficking, secretion, and vesicular transport]
Probab=57.48 E-value=13 Score=43.71 Aligned_cols=37 Identities=19% Similarity=0.418 Sum_probs=30.5
Q ss_pred ccccccccccccCCCceecCCCCcccHhHHHHHHhcc
Q 007642 141 EMTCGICFENYPSDRLLAAACGHPFCSSCWTGYISTA 177 (595)
Q Consensus 141 ~~~C~IC~e~~~~~~~~~l~CgH~fC~~C~~~yi~~~ 177 (595)
.-.|.+|.-.+-...++..+|||.|..+|+...+..-
T Consensus 817 ~d~C~~C~~~ll~~pF~vf~CgH~FH~~Cl~~~v~~~ 853 (911)
T KOG2034|consen 817 QDSCDHCGRPLLIKPFYVFPCGHCFHRDCLIRHVLSL 853 (911)
T ss_pred ccchHHhcchhhcCcceeeeccchHHHHHHHHHHHcc
Confidence 5679999987766666778999999999999987543
No 130
>KOG3039 consensus Uncharacterized conserved protein [Function unknown]
Probab=57.30 E-value=6.8 Score=39.17 Aligned_cols=36 Identities=14% Similarity=0.145 Sum_probs=30.6
Q ss_pred ccccccccccccCCCceecCCCCcccHhHHHHHHhccc
Q 007642 141 EMTCGICFENYPSDRLLAAACGHPFCSSCWTGYISTAI 178 (595)
Q Consensus 141 ~~~C~IC~e~~~~~~~~~l~CgH~fC~~C~~~yi~~~i 178 (595)
.-.|+.|+..+ .+|+..+=||.||++||.+||-.+-
T Consensus 43 FdcCsLtLqPc--~dPvit~~GylfdrEaILe~ilaqK 78 (303)
T KOG3039|consen 43 FDCCSLTLQPC--RDPVITPDGYLFDREAILEYILAQK 78 (303)
T ss_pred cceeeeecccc--cCCccCCCCeeeeHHHHHHHHHHHH
Confidence 34588888766 8899999999999999999997754
No 131
>KOG3970 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=56.92 E-value=13 Score=36.74 Aligned_cols=54 Identities=19% Similarity=0.411 Sum_probs=41.2
Q ss_pred cccccccccccCCCceecCCCCcccHhHHHHHHhccccCCCCccccccCCCcCCCcc
Q 007642 142 MTCGICFENYPSDRLLAAACGHPFCSSCWTGYISTAINDGPGCLMLRCPDPSCGAAV 198 (595)
Q Consensus 142 ~~C~IC~e~~~~~~~~~l~CgH~fC~~C~~~yi~~~i~~g~~~~~i~CP~~~C~~~v 198 (595)
-.|..|--.+...+.+.+-|-|.|.-.|+...-..--.. ..-..++|| .|...|
T Consensus 51 pNC~LC~t~La~gdt~RLvCyhlfHW~ClneraA~lPan-TAPaGyqCP--~Cs~ei 104 (299)
T KOG3970|consen 51 PNCRLCNTPLASGDTTRLVCYHLFHWKCLNERAANLPAN-TAPAGYQCP--CCSQEI 104 (299)
T ss_pred CCCceeCCccccCcceeehhhhhHHHHHhhHHHhhCCCc-CCCCcccCC--CCCCcc
Confidence 459999988888899999999999999999876443222 111257999 898766
No 132
>TIGR03655 anti_R_Lar restriction alleviation protein, Lar family. Restriction alleviation proteins provide a countermeasure to host cell restriction enzyme defense against foreign DNA such as phage or plasmids. This family consists of homologs to the phage antirestriction protein Lar, and most members belong to phage genomes or prophage regions of bacterial genomes.
Probab=56.64 E-value=7.7 Score=29.43 Aligned_cols=11 Identities=45% Similarity=0.930 Sum_probs=8.8
Q ss_pred ccCCCCCccee
Q 007642 300 KPCPRCKRPIE 310 (595)
Q Consensus 300 K~CPkC~~~IE 310 (595)
||||.|+-.-+
T Consensus 2 kPCPfCGg~~~ 12 (53)
T TIGR03655 2 KPCPFCGGADV 12 (53)
T ss_pred CCCCCCCCcce
Confidence 89999986554
No 133
>PRK08665 ribonucleotide-diphosphate reductase subunit alpha; Validated
Probab=56.21 E-value=6.8 Score=46.20 Aligned_cols=27 Identities=33% Similarity=1.123 Sum_probs=23.7
Q ss_pred ccCCCCCcceeecCCCCcccccCCCcceee
Q 007642 300 KPCPRCKRPIEKNQGCMHMTCTPPCKFEFC 329 (595)
Q Consensus 300 K~CPkC~~~IEK~~GCnhmtC~~~C~~~FC 329 (595)
..||.|+..+...+||. +|. .||+.=|
T Consensus 725 ~~Cp~Cg~~l~~~~GC~--~C~-~CG~skC 751 (752)
T PRK08665 725 GACPECGSILEHEEGCV--VCH-SCGYSKC 751 (752)
T ss_pred CCCCCCCcccEECCCCC--cCC-CCCCCCC
Confidence 35999999999999997 999 8998765
No 134
>KOG2114 consensus Vacuolar assembly/sorting protein PEP5/VPS11 [Intracellular trafficking, secretion, and vesicular transport]
Probab=56.19 E-value=8.6 Score=44.84 Aligned_cols=103 Identities=19% Similarity=0.325 Sum_probs=57.1
Q ss_pred HHHHHHHHHHHHHhCCCHHHHHHHHHHcCCCh----hhhHHHhh------------------hcHHHHHHHhCCCCCCCC
Q 007642 77 QRQEEDITRISTVLSISKVAASILLRFYNWSV----SKVHDEWF------------------ADEERVRKAVGLLEKPAV 134 (595)
Q Consensus 77 ~~~~~~i~~v~~vl~i~~~~a~~LL~~~~W~~----~~l~e~~~------------------~~~~~~~~~~gl~~~~~~ 134 (595)
+...+.++.|-.--.|||-...-+|-+..=-. ...+-.|. .+-++.+..++.+...+.
T Consensus 757 ~~v~~vl~~I~~~~~ippl~VL~~Lakn~~ltls~IkD~ii~~l~~~~~~I~qd~~~Ie~yk~~i~e~r~~l~~lr~sa~ 836 (933)
T KOG2114|consen 757 EIVYKVLEAIEMQERIPPLHVLQILAKNGTLTLSVIKDYIIKWLNKYSTIIEQDEDAIEVYKKDIEEKRQELETLRTSAQ 836 (933)
T ss_pred HHHHHHHHHHHhcccCCHHHHHHHHhcCCceEEehhHHHHHHHHHhhhHHHHhhHHHHHHHHHHHHHHHHHHHHhhcccc
Confidence 34555566666667788877766664332111 11222232 222333444433322111
Q ss_pred CCCCCCccccccccccccCCCceecCCCCcccHhHHHHHHhccccCCCCccccccCCCcCCCc
Q 007642 135 QFPDGEEMTCGICFENYPSDRLLAAACGHPFCSSCWTGYISTAINDGPGCLMLRCPDPSCGAA 197 (595)
Q Consensus 135 ~~~~~~~~~C~IC~e~~~~~~~~~l~CgH~fC~~C~~~yi~~~i~~g~~~~~i~CP~~~C~~~ 197 (595)
.. ..-.|..|--.+. -.+|...|||.|...|+. ++ .-.|| .|...
T Consensus 837 i~---q~skCs~C~~~Ld-lP~VhF~CgHsyHqhC~e--------~~----~~~CP--~C~~e 881 (933)
T KOG2114|consen 837 IF---QVSKCSACEGTLD-LPFVHFLCGHSYHQHCLE--------DK----EDKCP--KCLPE 881 (933)
T ss_pred ee---eeeeecccCCccc-cceeeeecccHHHHHhhc--------cC----cccCC--ccchh
Confidence 11 1246999976652 234677899999999998 22 35899 89763
No 135
>KOG4739 consensus Uncharacterized protein involved in synaptonemal complex formation [Cell cycle control, cell division, chromosome partitioning; General function prediction only]
Probab=56.16 E-value=2.3e+02 Score=28.56 Aligned_cols=23 Identities=35% Similarity=0.905 Sum_probs=17.0
Q ss_pred CCCCcccccCCC----cceeeecccccc
Q 007642 313 QGCMHMTCTPPC----KFEFCWLCLGQW 336 (595)
Q Consensus 313 ~GCnhmtC~~~C----~~~FCw~C~~~~ 336 (595)
..|.||+|. .| ...+|.+|....
T Consensus 21 TaC~HvfC~-~C~k~~~~~~C~lCkk~i 47 (233)
T KOG4739|consen 21 TACRHVFCE-PCLKASSPDVCPLCKKSI 47 (233)
T ss_pred eechhhhhh-hhcccCCcccccccccee
Confidence 469999998 45 445899998764
No 136
>KOG2906 consensus RNA polymerase III subunit C11 [Transcription]
Probab=55.93 E-value=7.4 Score=33.35 Aligned_cols=29 Identities=24% Similarity=0.766 Sum_probs=21.6
Q ss_pred cCCCCCccee--ecCCCCcccccCCCcceeee
Q 007642 301 PCPRCKRPIE--KNQGCMHMTCTPPCKFEFCW 330 (595)
Q Consensus 301 ~CPkC~~~IE--K~~GCnhmtC~~~C~~~FCw 330 (595)
-||.|+.++. +.+-||...|+ .|.+.|=-
T Consensus 3 FCP~Cgn~Live~g~~~~rf~C~-tCpY~~~I 33 (105)
T KOG2906|consen 3 FCPTCGNMLIVESGESCNRFSCR-TCPYVFPI 33 (105)
T ss_pred ccCCCCCEEEEecCCeEeeEEcC-CCCceeeE
Confidence 5999987654 44558999998 78776643
No 137
>KOG4275 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=55.32 E-value=7.3 Score=39.88 Aligned_cols=29 Identities=28% Similarity=0.715 Sum_probs=22.9
Q ss_pred ccccccccccccCCCceecCCCCc-ccHhHHH
Q 007642 141 EMTCGICFENYPSDRLLAAACGHP-FCSSCWT 171 (595)
Q Consensus 141 ~~~C~IC~e~~~~~~~~~l~CgH~-fC~~C~~ 171 (595)
...|.||++.. .+-+.|+|||. -|..|-+
T Consensus 300 ~~LC~ICmDaP--~DCvfLeCGHmVtCt~CGk 329 (350)
T KOG4275|consen 300 RRLCAICMDAP--RDCVFLECGHMVTCTKCGK 329 (350)
T ss_pred HHHHHHHhcCC--cceEEeecCcEEeehhhcc
Confidence 56799999864 78899999994 5766643
No 138
>KOG1991 consensus Nuclear transport receptor RANBP7/RANBP8 (importin beta superfamily) [Nuclear structure; Intracellular trafficking, secretion, and vesicular transport]
Probab=55.31 E-value=9.9 Score=45.06 Aligned_cols=36 Identities=22% Similarity=0.132 Sum_probs=18.3
Q ss_pred eCHHHHHHHHHHHHHHHHHHhCCCHHHHHHHHHHcCCCh
Q 007642 70 LTEADIRQRQEEDITRISTVLSISKVAASILLRFYNWSV 108 (595)
Q Consensus 70 l~~~~i~~~~~~~i~~v~~vl~i~~~~a~~LL~~~~W~~ 108 (595)
|.+-|......+.+..++. -.+.....|+++..-..
T Consensus 955 LD~VD~f~~f~~~i~~lq~---~d~~~yq~l~~~L~~~q 990 (1010)
T KOG1991|consen 955 LDQVDPFQLFKEAITNLQS---SDAVRYQKLISTLTPEQ 990 (1010)
T ss_pred ccccchHHHHHHHHHhhhc---cChHHHHHHHhcCCHHH
Confidence 6666666666665554432 23444445555444333
No 139
>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=55.22 E-value=8.1 Score=31.20 Aligned_cols=49 Identities=27% Similarity=0.571 Sum_probs=28.1
Q ss_pred cCCCCCcceeecCCCCcccccCCCcce-----eeecccccccCCCCCCCCcccCCch
Q 007642 301 PCPRCKRPIEKNQGCMHMTCTPPCKFE-----FCWLCLGQWSDHGERTGGFYACNRY 352 (595)
Q Consensus 301 ~CPkC~~~IEK~~GCnhmtC~~~C~~~-----FCw~C~~~~~~H~~~~g~~y~C~~~ 352 (595)
.||.|+.+++.++ .+.+|. .|+.. +|.-|+.+......-..-.|.|+.-
T Consensus 3 ~CP~C~~~L~~~~--~~~~C~-~C~~~~~~~a~CPdC~~~Le~LkACGAvdYFC~~c 56 (70)
T PF07191_consen 3 TCPKCQQELEWQG--GHYHCE-ACQKDYKKEAFCPDCGQPLEVLKACGAVDYFCNHC 56 (70)
T ss_dssp B-SSS-SBEEEET--TEEEET-TT--EEEEEEE-TTT-SB-EEEEETTEEEEE-TTT
T ss_pred cCCCCCCccEEeC--CEEECc-cccccceecccCCCcccHHHHHHHhcccceeeccC
Confidence 6999999999888 688898 78754 6899987754322111135777754
No 140
>KOG3161 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=53.41 E-value=4.5 Score=45.54 Aligned_cols=34 Identities=24% Similarity=0.631 Sum_probs=27.8
Q ss_pred ccccccccccccC--CCceecCCCCcccHhHHHHHH
Q 007642 141 EMTCGICFENYPS--DRLLAAACGHPFCSSCWTGYI 174 (595)
Q Consensus 141 ~~~C~IC~e~~~~--~~~~~l~CgH~fC~~C~~~yi 174 (595)
.+.|+||+..|-. -.++++.|||..|..|.....
T Consensus 11 ~l~c~ic~n~f~~~~~~Pvsl~cghtic~~c~~~ly 46 (861)
T KOG3161|consen 11 LLLCDICLNLFVVQRLEPVSLQCGHTICGHCVQLLY 46 (861)
T ss_pred HhhchHHHHHHHHHhcCcccccccchHHHHHHHhHh
Confidence 4579999877643 468999999999999998764
No 141
>KOG1571 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=53.28 E-value=6 Score=41.75 Aligned_cols=42 Identities=24% Similarity=0.682 Sum_probs=30.4
Q ss_pred ccccccccccccCCCceecCCCCcccHhHHHHHHhccccCCCCccccccCCCcCCCcc
Q 007642 141 EMTCGICFENYPSDRLLAAACGHPFCSSCWTGYISTAINDGPGCLMLRCPDPSCGAAV 198 (595)
Q Consensus 141 ~~~C~IC~e~~~~~~~~~l~CgH~fC~~C~~~yi~~~i~~g~~~~~i~CP~~~C~~~v 198 (595)
...|.||++.. .+.+-+||||.-| |..-+-. ...|| -|+..|
T Consensus 305 p~lcVVcl~e~--~~~~fvpcGh~cc--ct~cs~~----------l~~CP--vCR~rI 346 (355)
T KOG1571|consen 305 PDLCVVCLDEP--KSAVFVPCGHVCC--CTLCSKH----------LPQCP--VCRQRI 346 (355)
T ss_pred CCceEEecCCc--cceeeecCCcEEE--chHHHhh----------CCCCc--hhHHHH
Confidence 45799999876 6688999999976 6544311 34699 887654
No 142
>PHA02926 zinc finger-like protein; Provisional
Probab=53.20 E-value=6.2 Score=39.05 Aligned_cols=52 Identities=23% Similarity=0.496 Sum_probs=31.9
Q ss_pred CccCCCCCcce-eec-CCCCccccc-CCCcceeeecccccccCCCCCCCCcccCCc
Q 007642 299 SKPCPRCKRPI-EKN-QGCMHMTCT-PPCKFEFCWLCLGQWSDHGERTGGFYACNR 351 (595)
Q Consensus 299 tK~CPkC~~~I-EK~-~GCnhmtC~-~~C~~~FCw~C~~~~~~H~~~~g~~y~C~~ 351 (595)
-+.|+-|-..+ +|. .++.. +-. +.|+|.||+.|...|......+|.-..|+-
T Consensus 170 E~eCgICmE~I~eK~~~~eRr-FGIL~~CnHsFCl~CIr~Wr~~r~~~~~~rsCPi 224 (242)
T PHA02926 170 EKECGICYEVVYSKRLENDRY-FGLLDSCNHIFCITCINIWHRTRRETGASDNCPI 224 (242)
T ss_pred CCCCccCcccccccccccccc-ccccCCCCchHHHHHHHHHHHhccccCcCCcCCC
Confidence 38899998665 432 11110 001 159999999999999764333455556773
No 143
>PF07282 OrfB_Zn_ribbon: Putative transposase DNA-binding domain; InterPro: IPR010095 This entry represents a region of a sequence similarity between a family of putative transposases of Thermoanaerobacter tengcongensis, smaller related proteins from Bacillus anthracis, putative transposes described by IPR001959 from INTERPRO, and other proteins. More information about these proteins can be found at Protein of the Month: Transposase [].
Probab=53.09 E-value=9.7 Score=30.27 Aligned_cols=28 Identities=36% Similarity=0.815 Sum_probs=18.1
Q ss_pred cCccCCCCCcceeecCCCCcccccCCCcc
Q 007642 298 NSKPCPRCKRPIEKNQGCMHMTCTPPCKF 326 (595)
Q Consensus 298 ntK~CPkC~~~IEK~~GCnhmtC~~~C~~ 326 (595)
.++.||.|+....+...=..++|. .||+
T Consensus 27 TSq~C~~CG~~~~~~~~~r~~~C~-~Cg~ 54 (69)
T PF07282_consen 27 TSQTCPRCGHRNKKRRSGRVFTCP-NCGF 54 (69)
T ss_pred CccCccCcccccccccccceEEcC-CCCC
Confidence 358999999999873333345565 4443
No 144
>PF13717 zinc_ribbon_4: zinc-ribbon domain
Probab=52.59 E-value=11 Score=26.24 Aligned_cols=29 Identities=24% Similarity=0.581 Sum_probs=19.9
Q ss_pred ccCCCCCCCCeeeeecC---CCCceeee-cCCCcc
Q 007642 231 KWCPAPGCDYAVDFVVG---SGNYDVTC-RCSYSF 261 (595)
Q Consensus 231 ~~CP~p~C~~~i~~~~~---~~~~~v~C-~C~~~f 261 (595)
+.||+ |+....+... .....|.| .|++.|
T Consensus 3 i~Cp~--C~~~y~i~d~~ip~~g~~v~C~~C~~~f 35 (36)
T PF13717_consen 3 ITCPN--CQAKYEIDDEKIPPKGRKVRCSKCGHVF 35 (36)
T ss_pred EECCC--CCCEEeCCHHHCCCCCcEEECCCCCCEe
Confidence 56884 9887766532 23457899 898876
No 145
>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=51.53 E-value=9.3 Score=33.69 Aligned_cols=26 Identities=31% Similarity=0.777 Sum_probs=17.6
Q ss_pred ccCCCCCccee-ecCCCCcccccCCCccee
Q 007642 300 KPCPRCKRPIE-KNQGCMHMTCTPPCKFEF 328 (595)
Q Consensus 300 K~CPkC~~~IE-K~~GCnhmtC~~~C~~~F 328 (595)
+.||.|++..- .|- +.++|. .||..|
T Consensus 10 R~Cp~CG~kFYDLnk--~PivCP-~CG~~~ 36 (108)
T PF09538_consen 10 RTCPSCGAKFYDLNK--DPIVCP-KCGTEF 36 (108)
T ss_pred ccCCCCcchhccCCC--CCccCC-CCCCcc
Confidence 68999987654 333 778887 565544
No 146
>COG5574 PEX10 RING-finger-containing E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=50.92 E-value=4.1 Score=41.20 Aligned_cols=33 Identities=36% Similarity=0.821 Sum_probs=26.0
Q ss_pred ccCCCCCcceeecCCCCcccccCCCcceeeeccccc-ccCC
Q 007642 300 KPCPRCKRPIEKNQGCMHMTCTPPCKFEFCWLCLGQ-WSDH 339 (595)
Q Consensus 300 K~CPkC~~~IEK~~GCnhmtC~~~C~~~FCw~C~~~-~~~H 339 (595)
.+|+-|-..++. -.|+ .|||-|||.|+-. |..-
T Consensus 216 ~kC~lC~e~~~~------ps~t-~CgHlFC~~Cl~~~~t~~ 249 (271)
T COG5574 216 YKCFLCLEEPEV------PSCT-PCGHLFCLSCLLISWTKK 249 (271)
T ss_pred cceeeeecccCC------cccc-cccchhhHHHHHHHHHhh
Confidence 679888887772 4677 7999999999986 7543
No 147
>COG5109 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=50.70 E-value=14 Score=38.35 Aligned_cols=50 Identities=20% Similarity=0.460 Sum_probs=34.3
Q ss_pred CccccccccccccC-CCceecCCCCcccHhHHHHHHhccccCCCCccccccCCCcCCCc
Q 007642 140 EEMTCGICFENYPS-DRLLAAACGHPFCSSCWTGYISTAINDGPGCLMLRCPDPSCGAA 197 (595)
Q Consensus 140 ~~~~C~IC~e~~~~-~~~~~l~CgH~fC~~C~~~yi~~~i~~g~~~~~i~CP~~~C~~~ 197 (595)
+.|+||+=-+.-.. +.|+++.|||..=+.=++..-. +| ...++|| -|...
T Consensus 335 s~FiCPVlKe~~t~ENpP~ml~CgHVIskeal~~LS~----nG--~~~FKCP--YCP~~ 385 (396)
T COG5109 335 SLFICPVLKELCTDENPPVMLECGHVISKEALSVLSQ----NG--VLSFKCP--YCPEM 385 (396)
T ss_pred ceeeccccHhhhcccCCCeeeeccceeeHHHHHHHhh----cC--cEEeeCC--CCCcc
Confidence 46899995444322 5679999999988777665422 23 4589999 78653
No 148
>cd00194 UBA Ubiquitin Associated domain. The UBA domain is a commonly occurring sequence motif in some members of the ubiquitination pathway, UV excision repair proteins, and certain protein kinases. Although its specific role is so far unknown, it has been suggested that UBA domains are involved in conferring protein target specificity. The domain, a compact three helix bundle, has a conserved GFP-loop and the proline is thought to be critical for binding. The UBA domain is distinct from the conserved three helical domain seen in the N-terminus of EF-TS and eukaryotic NAC proteins.
Probab=50.66 E-value=45 Score=22.91 Aligned_cols=34 Identities=18% Similarity=0.209 Sum_probs=26.6
Q ss_pred HHHHHHHHhCCCHHHHHHHHHHcCCChhhhHHHhh
Q 007642 82 DITRISTVLSISKVAASILLRFYNWSVSKVHDEWF 116 (595)
Q Consensus 82 ~i~~v~~vl~i~~~~a~~LL~~~~W~~~~l~e~~~ 116 (595)
.|.++.+ +|.+...+...|...+||+++..+-++
T Consensus 4 ~v~~L~~-mGf~~~~~~~AL~~~~~d~~~A~~~L~ 37 (38)
T cd00194 4 KLEQLLE-MGFSREEARKALRATNNNVERAVEWLL 37 (38)
T ss_pred HHHHHHH-cCCCHHHHHHHHHHhCCCHHHHHHHHh
Confidence 4444544 589999999999999999998876543
No 149
>PF06677 Auto_anti-p27: Sjogren's syndrome/scleroderma autoantigen 1 (Autoantigen p27); InterPro: IPR009563 The proteins in this entry are functionally uncharacterised and include several proteins that characterise Sjogren's syndrome/scleroderma autoantigen 1 (Autoantigen p27). It is thought that the potential association of anti-p27 with anti-centromere antibodies suggests that autoantigen p27 might play a role in mitosis [].
Probab=50.08 E-value=13 Score=26.87 Aligned_cols=22 Identities=32% Similarity=1.106 Sum_probs=16.3
Q ss_pred ccCCCCCcceee-cCCCCcccccCCC
Q 007642 300 KPCPRCKRPIEK-NQGCMHMTCTPPC 324 (595)
Q Consensus 300 K~CPkC~~~IEK-~~GCnhmtC~~~C 324 (595)
..||.|+.|+-+ ..| .++|. .|
T Consensus 18 ~~Cp~C~~PL~~~k~g--~~~Cv-~C 40 (41)
T PF06677_consen 18 EHCPDCGTPLMRDKDG--KIYCV-SC 40 (41)
T ss_pred CccCCCCCeeEEecCC--CEECC-CC
Confidence 789999999987 344 46666 45
No 150
>PF13834 DUF4193: Domain of unknown function (DUF4193)
Probab=49.65 E-value=6.9 Score=33.69 Aligned_cols=32 Identities=31% Similarity=0.752 Sum_probs=24.9
Q ss_pred CCCccccccccccccCCCceecCCCCcccHhH
Q 007642 138 DGEEMTCGICFENYPSDRLLAAACGHPFCSSC 169 (595)
Q Consensus 138 ~~~~~~C~IC~e~~~~~~~~~l~CgH~fC~~C 169 (595)
...+|+|.-||=....+.+....=|+.+|.+|
T Consensus 67 q~DEFTCssCFLV~HRSqLa~~~~g~~iC~DC 98 (99)
T PF13834_consen 67 QADEFTCSSCFLVHHRSQLAREKDGQPICRDC 98 (99)
T ss_pred CCCceeeeeeeeEechhhhccccCCCEecccc
Confidence 45799999999776655665555689999988
No 151
>PF14803 Nudix_N_2: Nudix N-terminal; PDB: 3CNG_C.
Probab=49.40 E-value=11 Score=26.04 Aligned_cols=26 Identities=35% Similarity=0.972 Sum_probs=12.8
Q ss_pred ccCCCCCcceeec----CCCCcccccCCCcc
Q 007642 300 KPCPRCKRPIEKN----QGCMHMTCTPPCKF 326 (595)
Q Consensus 300 K~CPkC~~~IEK~----~GCnhmtC~~~C~~ 326 (595)
|-||+|+.+++.. ++=..+.|. .||+
T Consensus 1 kfC~~CG~~l~~~ip~gd~r~R~vC~-~Cg~ 30 (34)
T PF14803_consen 1 KFCPQCGGPLERRIPEGDDRERLVCP-ACGF 30 (34)
T ss_dssp -B-TTT--B-EEE--TT-SS-EEEET-TTTE
T ss_pred CccccccChhhhhcCCCCCccceECC-CCCC
Confidence 4688898888853 344457777 6764
No 152
>PF14446 Prok-RING_1: Prokaryotic RING finger family 1
Probab=48.59 E-value=15 Score=28.21 Aligned_cols=33 Identities=24% Similarity=0.866 Sum_probs=26.3
Q ss_pred cccccccccccc-CCCceecC-CCCcccHhHHHHH
Q 007642 141 EMTCGICFENYP-SDRLLAAA-CGHPFCSSCWTGY 173 (595)
Q Consensus 141 ~~~C~IC~e~~~-~~~~~~l~-CgH~fC~~C~~~y 173 (595)
...|++|-+.+. .+++|..+ ||-.|.++||...
T Consensus 5 ~~~C~~Cg~~~~~~dDiVvCp~CgapyHR~C~~~~ 39 (54)
T PF14446_consen 5 GCKCPVCGKKFKDGDDIVVCPECGAPYHRDCWEKA 39 (54)
T ss_pred CccChhhCCcccCCCCEEECCCCCCcccHHHHhhC
Confidence 446999999885 45677765 9999999999764
No 153
>COG5151 SSL1 RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit SSL1 [Transcription / DNA replication, recombination, and repair]
Probab=47.37 E-value=5.4 Score=41.04 Aligned_cols=88 Identities=25% Similarity=0.506 Sum_probs=45.7
Q ss_pred CcccHhHHHHHHhccccCCCCccccccCCCcCCCccchhHHhhhcChHHHHHHHHHH-HHHhhhh----CCCcccCCCCC
Q 007642 163 HPFCSSCWTGYISTAINDGPGCLMLRCPDPSCGAAVGQDMIYLLSSDEDKVKYNRYF-IRSYVED----NRKTKWCPAPG 237 (595)
Q Consensus 163 H~fC~~C~~~yi~~~i~~g~~~~~i~CP~~~C~~~v~~~~i~~ll~~e~~eky~~~~-~~~~v~~----~~~~~~CP~p~ 237 (595)
-.+|..|-..-. .+++.|| .|...+ +++..+...|..+. ++.+++. ++....|-.
T Consensus 308 Gy~CP~CktkVC---------sLPi~CP--~Csl~L-------ilsthLarSyhhL~PLk~f~E~p~~~~~ks~~Cf~-- 367 (421)
T COG5151 308 GYECPVCKTKVC---------SLPISCP--ICSLQL-------ILSTHLARSYHHLYPLKPFVEKPEGTNPKSTHCFV-- 367 (421)
T ss_pred ceeCCcccceee---------cCCccCc--chhHHH-------HHHHHHHHHHHhhccCcccccccCCCCCCCcccee--
Confidence 356666654332 2467777 664332 22223334444332 3344443 233345653
Q ss_pred CCCeeeeecCC------CCceeee-cCCCcccccCCcccC
Q 007642 238 CDYAVDFVVGS------GNYDVTC-RCSYSFCWNCTEEAH 270 (595)
Q Consensus 238 C~~~i~~~~~~------~~~~v~C-~C~~~fC~~C~~~~H 270 (595)
|+..+...+.. ......| .|...||..|..-.|
T Consensus 368 CQ~~fp~~~~~~~~~~~ss~rY~Ce~CK~~FC~dCdvfiH 407 (421)
T COG5151 368 CQGPFPKPPVSPFDESTSSGRYQCELCKSTFCSDCDVFIH 407 (421)
T ss_pred ccCCCCCCCCCcccccccccceechhhhhhhhhhhHHHHH
Confidence 66544332211 2345689 899999999886666
No 154
>TIGR01384 TFS_arch transcription factor S, archaeal. There has been an apparent duplication event in the Halobacteriaceae lineage (Haloarcula, Haloferax, Haloquadratum, Halobacterium and Natromonas). There appears to be a separate duplication in Methanosphaera stadtmanae.
Probab=46.10 E-value=12 Score=32.45 Aligned_cols=24 Identities=25% Similarity=0.758 Sum_probs=17.8
Q ss_pred cCCCCCcceeecCCCCcccccCCCcce
Q 007642 301 PCPRCKRPIEKNQGCMHMTCTPPCKFE 327 (595)
Q Consensus 301 ~CPkC~~~IEK~~GCnhmtC~~~C~~~ 327 (595)
.||+|+.++...+ +.+.|. .|++.
T Consensus 2 fC~~Cg~~l~~~~--~~~~C~-~C~~~ 25 (104)
T TIGR01384 2 FCPKCGSLMTPKN--GVYVCP-SCGYE 25 (104)
T ss_pred CCcccCcccccCC--CeEECc-CCCCc
Confidence 6999999887654 378887 67654
No 155
>smart00661 RPOL9 RNA polymerase subunit 9.
Probab=46.03 E-value=18 Score=26.89 Aligned_cols=27 Identities=26% Similarity=0.747 Sum_probs=16.8
Q ss_pred cCCCCCCCCeeeeecCCCCceeee-cCCCc
Q 007642 232 WCPAPGCDYAVDFVVGSGNYDVTC-RCSYS 260 (595)
Q Consensus 232 ~CP~p~C~~~i~~~~~~~~~~v~C-~C~~~ 260 (595)
+|| .|+..+............| .||+.
T Consensus 2 FCp--~Cg~~l~~~~~~~~~~~vC~~Cg~~ 29 (52)
T smart00661 2 FCP--KCGNMLIPKEGKEKRRFVCRKCGYE 29 (52)
T ss_pred CCC--CCCCccccccCCCCCEEECCcCCCe
Confidence 688 5988776553333335678 67754
No 156
>PF03115 Astro_capsid: Astrovirus capsid protein precursor; InterPro: IPR004337 The astrovirus genome is apparently organised with nonstructural proteins encoded at the 5' end and structural proteins at the 3' end []. Proteins in this family are encoded by astrovirus ORF2, one of the three astrovirus ORFs (1a, 1b, 2). The proteins contain a viral RNA-dependent RNA polymerase motif []. The 87kDa precursor polyprotein undergoes an intracellular cleavage to form a 79kDa protein. Subsequently, extracellular trypsin cleavage yields the three proteins forming the infectious virion [].; PDB: 3QSQ_A 3TS3_D.
Probab=45.48 E-value=7 Score=45.93 Aligned_cols=15 Identities=27% Similarity=0.290 Sum_probs=0.0
Q ss_pred CCCHHHH-HHHHHHcC
Q 007642 91 SISKVAA-SILLRFYN 105 (595)
Q Consensus 91 ~i~~~~a-~~LL~~~~ 105 (595)
+|+.+.| ++-.|.|.
T Consensus 721 Gi~eerAaria~RAfP 736 (787)
T PF03115_consen 721 GIPEERAARIAKRAFP 736 (787)
T ss_dssp ----------------
T ss_pred CCCHHHHHhhhhccCC
Confidence 4444433 23334443
No 157
>COG1997 RPL43A Ribosomal protein L37AE/L43A [Translation, ribosomal structure and biogenesis]
Probab=45.31 E-value=15 Score=30.93 Aligned_cols=28 Identities=29% Similarity=0.589 Sum_probs=21.7
Q ss_pred ccCCCCCcceeecCCCCcccccCCCccee
Q 007642 300 KPCPRCKRPIEKNQGCMHMTCTPPCKFEF 328 (595)
Q Consensus 300 K~CPkC~~~IEK~~GCnhmtC~~~C~~~F 328 (595)
-.||.|++..-|..+=---.|+ .||+.|
T Consensus 36 ~~Cp~C~~~~VkR~a~GIW~C~-kCg~~f 63 (89)
T COG1997 36 HVCPFCGRTTVKRIATGIWKCR-KCGAKF 63 (89)
T ss_pred CcCCCCCCcceeeeccCeEEcC-CCCCee
Confidence 5899999998888776667777 566554
No 158
>PF08580 KAR9: Yeast cortical protein KAR9; InterPro: IPR013889 The KAR9 protein in Saccharomyces cerevisiae (Baker's yeast) is a cytoskeletal protein required for karyogamy, correct positioning of the mitotic spindle and for orientation of cytoplasmic microtubules []. KAR9 localises at the shmoo tip in mating cells and at the tip of the growing bud in anaphase [].
Probab=45.11 E-value=3.9e+02 Score=31.38 Aligned_cols=12 Identities=8% Similarity=0.036 Sum_probs=6.2
Q ss_pred hHHHHHHHHHHH
Q 007642 420 QLKFITEAWLQI 431 (595)
Q Consensus 420 ~~~~l~~a~~~l 431 (595)
.+++|...++.|
T Consensus 250 k~~~L~~e~~~L 261 (683)
T PF08580_consen 250 KWKKLEKEAESL 261 (683)
T ss_pred HHHHHHHHHHHH
Confidence 355555555444
No 159
>COG4647 AcxC Acetone carboxylase, gamma subunit [Secondary metabolites biosynthesis, transport, and catabolism]
Probab=45.07 E-value=18 Score=32.61 Aligned_cols=59 Identities=17% Similarity=0.297 Sum_probs=30.4
Q ss_pred ceeeecCCCcccccCCcccC--CCCCchhHHHHHHhh--hHhHHhHHHHHhcCccCCCCCccee
Q 007642 251 YDVTCRCSYSFCWNCTEEAH--RPVDCDTVAKWVLKN--SAESENMNWILANSKPCPRCKRPIE 310 (595)
Q Consensus 251 ~~v~C~C~~~fC~~C~~~~H--~p~~C~~~~~~~~k~--~~~~e~~~wi~~ntK~CPkC~~~IE 310 (595)
..+.|.||++||-- .+.|. ....-..-..-+... ..+...-+|+..---.||.|+.+.+
T Consensus 69 rv~rcecghsf~d~-r~nwkl~a~i~vrdtee~lreiyp~s~ipdp~wme~reficpecg~l~e 131 (165)
T COG4647 69 RVIRCECGHSFGDY-RENWKLHANIYVRDTEEKLREIYPKSDIPDPQWMEIREFICPECGILHE 131 (165)
T ss_pred cEEEEeccccccCh-hhCceeeeEEEEcchHHHHHHhCcccCCCCchHHHHHHhhCccccceee
Confidence 45689999999954 22332 211111100000000 1112234676665578999999888
No 160
>cd00021 BBOX B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction.
Probab=45.00 E-value=11 Score=25.90 Aligned_cols=26 Identities=19% Similarity=0.437 Sum_probs=23.2
Q ss_pred cCCCCCc-ceeecCCCCcccccCCCcceeeecccc
Q 007642 301 PCPRCKR-PIEKNQGCMHMTCTPPCKFEFCWLCLG 334 (595)
Q Consensus 301 ~CPkC~~-~IEK~~GCnhmtC~~~C~~~FCw~C~~ 334 (595)
.||.|+. ++. ++|. .|+...|..|..
T Consensus 2 ~C~~H~~~~~~-------~fC~-~~~~~iC~~C~~ 28 (39)
T cd00021 2 LCDEHGEEPLS-------LFCE-TDRALLCVDCDL 28 (39)
T ss_pred CCCccCCcceE-------EEeC-ccChhhhhhcCh
Confidence 5899987 889 9999 899999999964
No 161
>PF05290 Baculo_IE-1: Baculovirus immediate-early protein (IE-0); InterPro: IPR007954 This entry contains the Baculovirus immediate-early protein IE-0.
Probab=43.88 E-value=19 Score=32.75 Aligned_cols=53 Identities=26% Similarity=0.673 Sum_probs=39.0
Q ss_pred CCccccccccccccCCCceec--CCCCcccHhHHHHHHhccccCCCCccccccCCCcCCCccc
Q 007642 139 GEEMTCGICFENYPSDRLLAA--ACGHPFCSSCWTGYISTAINDGPGCLMLRCPDPSCGAAVG 199 (595)
Q Consensus 139 ~~~~~C~IC~e~~~~~~~~~l--~CgH~fC~~C~~~yi~~~i~~g~~~~~i~CP~~~C~~~v~ 199 (595)
....+|.||-|......+... -||=..|.-|....|...- ....|| .|+..+-
T Consensus 78 ~~lYeCnIC~etS~ee~FLKPneCCgY~iCn~Cya~LWK~~~------~ypvCP--vCkTSFK 132 (140)
T PF05290_consen 78 PKLYECNICKETSAEERFLKPNECCGYSICNACYANLWKFCN------LYPVCP--VCKTSFK 132 (140)
T ss_pred CCceeccCcccccchhhcCCcccccchHHHHHHHHHHHHHcc------cCCCCC--ccccccc
Confidence 367899999998643333222 2999999999999998753 256899 8987763
No 162
>smart00165 UBA Ubiquitin associated domain. Present in Rad23, SNF1-like kinases. The newly-found UBA in p62 is known to bind ubiquitin.
Probab=43.80 E-value=60 Score=22.14 Aligned_cols=31 Identities=23% Similarity=0.225 Sum_probs=24.1
Q ss_pred HHHHHHHhCCCHHHHHHHHHHcCCChhhhHHH
Q 007642 83 ITRISTVLSISKVAASILLRFYNWSVSKVHDE 114 (595)
Q Consensus 83 i~~v~~vl~i~~~~a~~LL~~~~W~~~~l~e~ 114 (595)
|.++.+ +|.++..|...|+..+||+++..+-
T Consensus 5 v~~L~~-mGf~~~~a~~aL~~~~~d~~~A~~~ 35 (37)
T smart00165 5 IDQLLE-MGFSREEALKALRAANGNVERAAEY 35 (37)
T ss_pred HHHHHH-cCCCHHHHHHHHHHhCCCHHHHHHH
Confidence 444433 3899999999999999998887653
No 163
>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=43.64 E-value=5.1 Score=32.33 Aligned_cols=39 Identities=31% Similarity=0.747 Sum_probs=21.7
Q ss_pred cccccccccccCCCceecCCCCcccHhHHHHHHhccccCCCCccccccCCCcCCCcc
Q 007642 142 MTCGICFENYPSDRLLAAACGHPFCSSCWTGYISTAINDGPGCLMLRCPDPSCGAAV 198 (595)
Q Consensus 142 ~~C~IC~e~~~~~~~~~l~CgH~fC~~C~~~yi~~~i~~g~~~~~i~CP~~~C~~~v 198 (595)
..||.|-.++... . +|.+|..|-..|.. ...|| .|...+
T Consensus 2 ~~CP~C~~~L~~~-----~-~~~~C~~C~~~~~~----------~a~CP--dC~~~L 40 (70)
T PF07191_consen 2 NTCPKCQQELEWQ-----G-GHYHCEACQKDYKK----------EAFCP--DCGQPL 40 (70)
T ss_dssp -B-SSS-SBEEEE-----T-TEEEETTT--EEEE----------EEE-T--TT-SB-
T ss_pred CcCCCCCCccEEe-----C-CEEECcccccccee----------cccCC--CcccHH
Confidence 5799998765322 2 89999999987632 45799 787654
No 164
>KOG4684 consensus Uncharacterized conserved protein, contains C4-type Zn-finger [General function prediction only]
Probab=43.57 E-value=15 Score=35.89 Aligned_cols=17 Identities=24% Similarity=0.704 Sum_probs=14.1
Q ss_pred CcccCCCCCCCCeeeee
Q 007642 229 KTKWCPAPGCDYAVDFV 245 (595)
Q Consensus 229 ~~~~CP~p~C~~~i~~~ 245 (595)
..+-||.|+|.++|...
T Consensus 137 qRIACPRpnCkRiInL~ 153 (275)
T KOG4684|consen 137 QRIACPRPNCKRIINLD 153 (275)
T ss_pred ceeccCCCCcceeeecC
Confidence 45789999999998764
No 165
>COG5236 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=43.49 E-value=17 Score=38.14 Aligned_cols=50 Identities=30% Similarity=0.628 Sum_probs=33.8
Q ss_pred CCCccccccccccccCCCceecCCCCcccHhHHHHHHhccccCCCCccccccCCCcCCCcc
Q 007642 138 DGEEMTCGICFENYPSDRLLAAACGHPFCSSCWTGYISTAINDGPGCLMLRCPDPSCGAAV 198 (595)
Q Consensus 138 ~~~~~~C~IC~e~~~~~~~~~l~CgH~fC~~C~~~yi~~~i~~g~~~~~i~CP~~~C~~~v 198 (595)
..+...|.||-..+ .-...+||+|..|.-|--..- ++-. .-.|| .|+...
T Consensus 58 DEen~~C~ICA~~~--TYs~~~PC~H~~CH~Ca~RlR--ALY~-----~K~C~--~CrTE~ 107 (493)
T COG5236 58 DEENMNCQICAGST--TYSARYPCGHQICHACAVRLR--ALYM-----QKGCP--LCRTET 107 (493)
T ss_pred ccccceeEEecCCc--eEEEeccCCchHHHHHHHHHH--HHHh-----ccCCC--cccccc
Confidence 34577899998765 334567999999999975532 1211 24688 788654
No 166
>PRK09710 lar restriction alleviation and modification protein; Reviewed
Probab=43.36 E-value=16 Score=28.96 Aligned_cols=14 Identities=50% Similarity=0.992 Sum_probs=10.9
Q ss_pred cCccCCCCCcceee
Q 007642 298 NSKPCPRCKRPIEK 311 (595)
Q Consensus 298 ntK~CPkC~~~IEK 311 (595)
+.||||.|+..+.+
T Consensus 5 ~lKPCPFCG~~~~~ 18 (64)
T PRK09710 5 NVKPCPFCGCPSVT 18 (64)
T ss_pred cccCCCCCCCceeE
Confidence 35999999977653
No 167
>KOG1940 consensus Zn-finger protein [General function prediction only]
Probab=42.69 E-value=18 Score=37.19 Aligned_cols=47 Identities=30% Similarity=0.613 Sum_probs=36.3
Q ss_pred CCccccccccccccC--CCceecCCCCcccHhHHHHHHhccccCCCCccccccCCCcCCC
Q 007642 139 GEEMTCGICFENYPS--DRLLAAACGHPFCSSCWTGYISTAINDGPGCLMLRCPDPSCGA 196 (595)
Q Consensus 139 ~~~~~C~IC~e~~~~--~~~~~l~CgH~fC~~C~~~yi~~~i~~g~~~~~i~CP~~~C~~ 196 (595)
...+.||||.+.+-. ..+..++|||.--..|++.++-. .++|| -|..
T Consensus 156 ~~~~ncPic~e~l~~s~~~~~~~~CgH~~h~~cf~e~~~~---------~y~CP--~C~~ 204 (276)
T KOG1940|consen 156 SSEFNCPICKEYLFLSFEDAGVLKCGHYMHSRCFEEMICE---------GYTCP--ICSK 204 (276)
T ss_pred cccCCCchhHHHhccccccCCccCcccchHHHHHHHHhcc---------CCCCC--cccc
Confidence 446679999987543 34567889999999999999743 37899 7877
No 168
>PF10168 Nup88: Nuclear pore component; InterPro: IPR019321 Nup88 can be divided into two structural domains; the N-terminal two-thirds of the protein have no obvious structural motifs. It is, however, where it binds to Nup98; one of the components of the nuclear pore. The C-terminal end is a predicted coiled-coil domain []. Nup88 is over expressed in tumour cells [].
Probab=42.39 E-value=5.3e+02 Score=30.52 Aligned_cols=24 Identities=13% Similarity=0.026 Sum_probs=17.0
Q ss_pred hHHHHHHHHHHHHHhHHHHHHHHH
Q 007642 455 KRQFFEYLQGEAESGLERLHQCAE 478 (595)
Q Consensus 455 ~~~~fe~~Q~~le~~~E~L~~~le 478 (595)
+.+-....|+.+...++.+.+.+.
T Consensus 601 R~e~a~d~Qe~L~~R~~~vl~~l~ 624 (717)
T PF10168_consen 601 RYEEAKDKQEKLMKRVDRVLQLLN 624 (717)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHh
Confidence 455666778888888887766553
No 169
>COG0266 Nei Formamidopyrimidine-DNA glycosylase [DNA replication, recombination, and repair]
Probab=42.15 E-value=16 Score=37.49 Aligned_cols=25 Identities=44% Similarity=0.987 Sum_probs=20.9
Q ss_pred ccCCCCCcceeec--CCCCcccccCCCc
Q 007642 300 KPCPRCKRPIEKN--QGCMHMTCTPPCK 325 (595)
Q Consensus 300 K~CPkC~~~IEK~--~GCnhmtC~~~C~ 325 (595)
++|+.|+.+|+|. +|=+-.+|. .|+
T Consensus 246 epC~~CGt~I~k~~~~gR~t~~CP-~CQ 272 (273)
T COG0266 246 EPCRRCGTPIEKIKLGGRSTFYCP-VCQ 272 (273)
T ss_pred CCCCccCCEeEEEEEcCCcCEeCC-CCC
Confidence 7999999999976 787777777 675
No 170
>PRK05654 acetyl-CoA carboxylase subunit beta; Validated
Probab=41.72 E-value=7.9 Score=40.32 Aligned_cols=28 Identities=18% Similarity=0.564 Sum_probs=21.6
Q ss_pred ccCCCCCcceee-cCCCCcccccCCCccee
Q 007642 300 KPCPRCKRPIEK-NQGCMHMTCTPPCKFEF 328 (595)
Q Consensus 300 K~CPkC~~~IEK-~~GCnhmtC~~~C~~~F 328 (595)
.+||+|+..|-+ .-.=|.+.|. .|+++|
T Consensus 28 ~~c~~c~~~~~~~~l~~~~~vc~-~c~~h~ 56 (292)
T PRK05654 28 TKCPSCGQVLYRKELEANLNVCP-KCGHHM 56 (292)
T ss_pred eECCCccchhhHHHHHhcCCCCC-CCCCCe
Confidence 889999988863 3445668898 798887
No 171
>COG1645 Uncharacterized Zn-finger containing protein [General function prediction only]
Probab=41.59 E-value=17 Score=33.10 Aligned_cols=23 Identities=35% Similarity=0.797 Sum_probs=18.9
Q ss_pred ccCCCCCcceeecCCCCcccccCCCcceeeeccc
Q 007642 300 KPCPRCKRPIEKNQGCMHMTCTPPCKFEFCWLCL 333 (595)
Q Consensus 300 K~CPkC~~~IEK~~GCnhmtC~~~C~~~FCw~C~ 333 (595)
+.||.|+.|+.+ .-|.-||.+|+
T Consensus 29 ~hCp~Cg~PLF~-----------KdG~v~CPvC~ 51 (131)
T COG1645 29 KHCPKCGTPLFR-----------KDGEVFCPVCG 51 (131)
T ss_pred hhCcccCCccee-----------eCCeEECCCCC
Confidence 799999999983 36777888886
No 172
>smart00804 TAP_C C-terminal domain of vertebrate Tap protein. The vertebrate Tap protein is a member of the NXF family of shuttling transport receptors for the nuclear export of mRNA. Its most C-terminal domain is important for binding to FG repeat-containing nuclear pore proteins (FG-nucleoporins) and is sufficient to mediate shuttling. This domain forms a compact four-helix fold related to that of a UBA domain.
Probab=41.56 E-value=84 Score=24.89 Aligned_cols=41 Identities=15% Similarity=0.245 Sum_probs=36.3
Q ss_pred HHHHHHHHHHHHHHhCCCHHHHHHHHHHcCCChhhhHHHhh
Q 007642 76 RQRQEEDITRISTVLSISKVAASILLRFYNWSVSKVHDEWF 116 (595)
Q Consensus 76 ~~~~~~~i~~v~~vl~i~~~~a~~LL~~~~W~~~~l~e~~~ 116 (595)
...+.+.|..++...+++..-+..+|...+||-+..+..|-
T Consensus 9 ~~~q~~~v~~~~~~Tgmn~~~s~~cLe~~~Wd~~~Al~~F~ 49 (63)
T smart00804 9 SPEQQEMVQAFSAQTGMNAEYSQMCLEDNNWDYERALKNFT 49 (63)
T ss_pred CHHHHHHHHHHHHHHCCCHHHHHHHHHHcCCCHHHHHHHHH
Confidence 34678889999999999999999999999999998887663
No 173
>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=41.10 E-value=28 Score=25.26 Aligned_cols=34 Identities=18% Similarity=0.465 Sum_probs=16.5
Q ss_pred cccccccccCCCce-ecCCCCcccHhHHHHHHhcc
Q 007642 144 CGICFENYPSDRLL-AAACGHPFCSSCWTGYISTA 177 (595)
Q Consensus 144 C~IC~e~~~~~~~~-~l~CgH~fC~~C~~~yi~~~ 177 (595)
|.+|-+.......- ...|+=.+...|+..||...
T Consensus 1 C~~C~~iv~~G~~C~~~~C~~r~H~~C~~~y~r~~ 35 (43)
T PF08746_consen 1 CEACKEIVTQGQRCSNRDCNVRLHDDCFKKYFRHR 35 (43)
T ss_dssp -TTT-SB-SSSEE-SS--S--EE-HHHHHHHTTT-
T ss_pred CcccchhHeeeccCCCCccCchHHHHHHHHHHhcC
Confidence 56776654222111 12477789999999999764
No 174
>KOG2141 consensus Protein involved in high osmolarity signaling pathway [Signal transduction mechanisms]
Probab=40.87 E-value=23 Score=40.86 Aligned_cols=14 Identities=21% Similarity=0.508 Sum_probs=9.2
Q ss_pred cceeeecccccccC
Q 007642 325 KFEFCWLCLGQWSD 338 (595)
Q Consensus 325 ~~~FCw~C~~~~~~ 338 (595)
+..=-|+=|..|..
T Consensus 566 ~kGrWWlVGsaw~g 579 (822)
T KOG2141|consen 566 QKGRWWLVGSAWRG 579 (822)
T ss_pred hcCceEEecchhcC
Confidence 34446788888865
No 175
>PF14445 Prok-RING_2: Prokaryotic RING finger family 2
Probab=39.71 E-value=6.4 Score=29.46 Aligned_cols=33 Identities=30% Similarity=0.838 Sum_probs=27.2
Q ss_pred CccccccccccccCCCceec-CCCCcccHhHHHH
Q 007642 140 EEMTCGICFENYPSDRLLAA-ACGHPFCSSCWTG 172 (595)
Q Consensus 140 ~~~~C~IC~e~~~~~~~~~l-~CgH~fC~~C~~~ 172 (595)
..++|..|-+.+|..+.... -||.--|..||+.
T Consensus 6 sry~CDLCn~~~p~~~LRQCvlCGRWaC~sCW~d 39 (57)
T PF14445_consen 6 SRYSCDLCNSSHPISELRQCVLCGRWACNSCWQD 39 (57)
T ss_pred hhHhHHhhcccCcHHHHHHHhhhchhhhhhhhhh
Confidence 36889999998877766554 5999999999986
No 176
>PF06906 DUF1272: Protein of unknown function (DUF1272); InterPro: IPR010696 This family consists of several hypothetical bacterial proteins of around 80 residues in length. This family contains a number of conserved cysteine residues and its function is unknown.
Probab=39.20 E-value=20 Score=27.58 Aligned_cols=45 Identities=29% Similarity=0.753 Sum_probs=31.8
Q ss_pred ccccccccccCCCceecCCCC--cccHhHHHHHHhccccCCCCccccccCCCcCCCccch
Q 007642 143 TCGICFENYPSDRLLAAACGH--PFCSSCWTGYISTAINDGPGCLMLRCPDPSCGAAVGQ 200 (595)
Q Consensus 143 ~C~IC~e~~~~~~~~~l~CgH--~fC~~C~~~yi~~~i~~g~~~~~i~CP~~~C~~~v~~ 200 (595)
.|..|-.+++.+..-..-|.+ .||.+|-...+. -.|| .|+..+..
T Consensus 7 nCE~C~~dLp~~s~~A~ICSfECTFC~~C~e~~l~-----------~~CP--NCgGelv~ 53 (57)
T PF06906_consen 7 NCECCDKDLPPDSPEAYICSFECTFCADCAETMLN-----------GVCP--NCGGELVR 53 (57)
T ss_pred CccccCCCCCCCCCcceEEeEeCcccHHHHHHHhc-----------CcCc--CCCCcccc
Confidence 488888888776655555654 699999988752 2688 78776543
No 177
>COG5665 NOT5 CCR4-NOT transcriptional regulation complex, NOT5 subunit [Transcription]
Probab=38.70 E-value=4.4e+02 Score=28.38 Aligned_cols=16 Identities=19% Similarity=0.661 Sum_probs=9.0
Q ss_pred HHHHHHHHHHHHhhhH
Q 007642 374 SLERYTHYYERWATNQ 389 (595)
Q Consensus 374 ~l~ry~~y~~r~~~h~ 389 (595)
-++-|-.-|+.|.+..
T Consensus 10 ~i~~fd~iyek~~~s~ 25 (548)
T COG5665 10 GIEDFDDIYEKFQSTD 25 (548)
T ss_pred hhhhHHHHHHHHhccC
Confidence 3455555666665554
No 178
>KOG0943 consensus Predicted ubiquitin-protein ligase/hyperplastic discs protein, HECT superfamily [Posttranslational modification, protein turnover, chaperones]
Probab=38.60 E-value=22 Score=43.11 Aligned_cols=16 Identities=25% Similarity=0.447 Sum_probs=9.6
Q ss_pred HHHHHHHHHHhHHHHH
Q 007642 459 FEYLQGEAESGLERLH 474 (595)
Q Consensus 459 fe~~Q~~le~~~E~L~ 474 (595)
||..|....+.+|+|.
T Consensus 2419 FEtKer~Fnka~EK~R 2434 (3015)
T KOG0943|consen 2419 FETKERKFNKAMEKLR 2434 (3015)
T ss_pred cchHHHHHHHHHHHHH
Confidence 5666666666666654
No 179
>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=37.88 E-value=58 Score=30.65 Aligned_cols=83 Identities=24% Similarity=0.530 Sum_probs=46.5
Q ss_pred ccccccccccccCCCceecCC-------CCccc------HhHHHHHHhccccCC----------------------CCcc
Q 007642 141 EMTCGICFENYPSDRLLAAAC-------GHPFC------SSCWTGYISTAINDG----------------------PGCL 185 (595)
Q Consensus 141 ~~~C~IC~e~~~~~~~~~l~C-------gH~fC------~~C~~~yi~~~i~~g----------------------~~~~ 185 (595)
..+||||++-- -+-|.|-| .-+.| .+|+.+|-....... ....
T Consensus 2 d~~CpICme~P--HNAVLLlCSS~~kgcRpymc~Ts~rhSNCLdqfkka~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 79 (162)
T PF07800_consen 2 DVTCPICMEHP--HNAVLLLCSSHEKGCRPYMCDTSYRHSNCLDQFKKAYGKSSSSSSQSSSSAPSDSSSSESSESQEQP 79 (162)
T ss_pred CccCceeccCC--CceEEEEeccccCCccccccCCccchhHHHHHHHHHhcCCCCccccccccCcCCCcccccccccccc
Confidence 46899999853 45555543 33334 578888875432211 1123
Q ss_pred ccccCCCcCCCccchhHHhhhcChHHHHHHHHHHHHHhhhhCCCcccCCCCCCCCee
Q 007642 186 MLRCPDPSCGAAVGQDMIYLLSSDEDKVKYNRYFIRSYVEDNRKTKWCPAPGCDYAV 242 (595)
Q Consensus 186 ~i~CP~~~C~~~v~~~~i~~ll~~e~~eky~~~~~~~~v~~~~~~~~CP~p~C~~~i 242 (595)
.+.|| .|+..|.--.+- +.. +.|+ |.+.+-|+..+|.+.-
T Consensus 80 ~L~CP--LCRG~V~GWtvv-----e~A--------R~~L--N~K~RsC~~e~C~F~G 119 (162)
T PF07800_consen 80 ELACP--LCRGEVKGWTVV-----EPA--------RRFL--NAKKRSCSQESCSFSG 119 (162)
T ss_pred cccCc--cccCceeceEEc-----hHH--------HHHh--ccCCccCccccccccc
Confidence 67899 898776433220 111 2222 2345689988887654
No 180
>PHA02929 N1R/p28-like protein; Provisional
Probab=37.13 E-value=14 Score=37.21 Aligned_cols=39 Identities=21% Similarity=0.577 Sum_probs=26.8
Q ss_pred CccCCCCCcceeecCCCCc---ccccCCCcceeeecccccccCC
Q 007642 299 SKPCPRCKRPIEKNQGCMH---MTCTPPCKFEFCWLCLGQWSDH 339 (595)
Q Consensus 299 tK~CPkC~~~IEK~~GCnh---mtC~~~C~~~FCw~C~~~~~~H 339 (595)
...||-|...+.....-+. +.- .|+|.||..|...|...
T Consensus 174 ~~eC~ICle~~~~~~~~~~~~~vl~--~C~H~FC~~CI~~Wl~~ 215 (238)
T PHA02929 174 DKECAICMEKVYDKEIKNMYFGILS--NCNHVFCIECIDIWKKE 215 (238)
T ss_pred CCCCccCCcccccCccccccceecC--CCCCcccHHHHHHHHhc
Confidence 4689999988764432211 222 49999999999999654
No 181
>PRK14811 formamidopyrimidine-DNA glycosylase; Provisional
Probab=37.05 E-value=22 Score=36.59 Aligned_cols=25 Identities=48% Similarity=1.055 Sum_probs=17.6
Q ss_pred ccCCCCCcceeec--CCCCcccccCCCc
Q 007642 300 KPCPRCKRPIEKN--QGCMHMTCTPPCK 325 (595)
Q Consensus 300 K~CPkC~~~IEK~--~GCnhmtC~~~C~ 325 (595)
++||.|+.+|+|. +|=.-.+|. .|+
T Consensus 236 ~pC~~Cg~~I~~~~~~gR~ty~Cp-~CQ 262 (269)
T PRK14811 236 QPCPRCGTPIEKIVVGGRGTHFCP-QCQ 262 (269)
T ss_pred CCCCcCCCeeEEEEECCCCcEECC-CCc
Confidence 7999999999864 664444554 443
No 182
>PRK12775 putative trifunctional 2-polyprenylphenol hydroxylase/glutamate synthase subunit beta/ferritin domain-containing protein; Provisional
Probab=36.66 E-value=5.6e+02 Score=31.63 Aligned_cols=14 Identities=43% Similarity=1.246 Sum_probs=11.6
Q ss_pred CccCCCCCcceeec
Q 007642 299 SKPCPRCKRPIEKN 312 (595)
Q Consensus 299 tK~CPkC~~~IEK~ 312 (595)
.-.||+|++|+|-+
T Consensus 796 ~~~~~~~~~~~~~~ 809 (1006)
T PRK12775 796 VATCPKCHRPLEGD 809 (1006)
T ss_pred CccCcccCCCCCCC
Confidence 36899999999944
No 183
>PF09943 DUF2175: Uncharacterized protein conserved in archaea (DUF2175); InterPro: IPR018686 This family of various hypothetical archaeal proteins has no known function.
Probab=36.45 E-value=78 Score=27.53 Aligned_cols=26 Identities=12% Similarity=0.235 Sum_probs=16.4
Q ss_pred hhhHHHHHHHHHHHHHhHHHHHHHHH
Q 007642 453 HAKRQFFEYLQGEAESGLERLHQCAE 478 (595)
Q Consensus 453 ~~~~~~fe~~Q~~le~~~E~L~~~le 478 (595)
...+++++...+++|+....|...++
T Consensus 74 ee~k~~~~q~rK~~Ek~Aa~LT~~i~ 99 (101)
T PF09943_consen 74 EEVKKVLRQVRKDLEKNAAKLTRKIE 99 (101)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 34566666667777777766665544
No 184
>PRK14714 DNA polymerase II large subunit; Provisional
Probab=36.44 E-value=29 Score=42.61 Aligned_cols=11 Identities=36% Similarity=1.023 Sum_probs=6.9
Q ss_pred ccCCCCCccee
Q 007642 300 KPCPRCKRPIE 310 (595)
Q Consensus 300 K~CPkC~~~IE 310 (595)
..||+|+.++.
T Consensus 710 ~~CP~CGtplv 720 (1337)
T PRK14714 710 VECPRCDVELT 720 (1337)
T ss_pred ccCCCCCCccc
Confidence 56777776554
No 185
>PF03943 TAP_C: TAP C-terminal domain; InterPro: IPR005637 This entry contains the NXF family of shuttling transport receptors for nuclear export of mRNA, which include: vertebrate mRNA export factor TAP or nuclear RNA export factor 1 (NXF1). Caenorhabditis elegans nuclear RNA export factor 1 (nxf-1). yeast mRNA export factor MEX67. Members of the NXF family have a modular structure. A nuclear localization sequence and a noncanonical RNA recognition motif (RRM) (see PDOC00030 from PROSITEDOC) followed by four LRR repeats are located in its N-terminal half. The C-terminal half contains a NTF2 domain (see PDOC50177 from PROSITEDOC) followed by a second domain, TAP-C. The TAP-C domain is important for binding to FG repeat-containing nuclear pore proteins (FG-nucleoporins) and is sufficient to mediate nuclear shuttling [,]. The Tap-C domain is made of four alpha helices packed against each other. The arrangement of helices 1, 2 and 3 is similar to that seen in a UBA fold. and is joined to the next module by flexible 12-residue Pro-rich linker [, ].; GO: 0051028 mRNA transport, 0005634 nucleus; PDB: 1OAI_A 1GO5_A 2KHH_A 2JP7_A.
Probab=36.32 E-value=39 Score=25.49 Aligned_cols=36 Identities=14% Similarity=0.174 Sum_probs=30.6
Q ss_pred HHHHHHHHHhCCCHHHHHHHHHHcCCChhhhHHHhh
Q 007642 81 EDITRISTVLSISKVAASILLRFYNWSVSKVHDEWF 116 (595)
Q Consensus 81 ~~i~~v~~vl~i~~~~a~~LL~~~~W~~~~l~e~~~ 116 (595)
+.|..++...++.+.-+...|...+||.++.+..|.
T Consensus 2 ~mv~~~s~~Tgmn~~~s~~CL~~n~Wd~~~A~~~F~ 37 (51)
T PF03943_consen 2 EMVQQFSQQTGMNLEWSQKCLEENNWDYERALQNFE 37 (51)
T ss_dssp HHHHHHHHHCSS-CCHHHHHHHHTTT-CCHHHHHHH
T ss_pred HHHHHHHHHHCCCHHHHHHHHHHcCCCHHHHHHHHH
Confidence 578899999999999999999999999999887764
No 186
>PRK14892 putative transcription elongation factor Elf1; Provisional
Probab=36.29 E-value=23 Score=30.72 Aligned_cols=27 Identities=26% Similarity=0.636 Sum_probs=17.1
Q ss_pred ccCCCCCcce---eecCCCCcccccCCCcce
Q 007642 300 KPCPRCKRPI---EKNQGCMHMTCTPPCKFE 327 (595)
Q Consensus 300 K~CPkC~~~I---EK~~GCnhmtC~~~C~~~ 327 (595)
-.||+|+... .+..|=-|..|. .||+.
T Consensus 22 f~CP~Cge~~v~v~~~k~~~h~~C~-~CG~y 51 (99)
T PRK14892 22 FECPRCGKVSISVKIKKNIAIITCG-NCGLY 51 (99)
T ss_pred eECCCCCCeEeeeecCCCcceEECC-CCCCc
Confidence 5799999322 233355678887 66554
No 187
>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=35.91 E-value=20 Score=23.58 Aligned_cols=22 Identities=36% Similarity=0.733 Sum_probs=11.4
Q ss_pred ccCCCCCcceeec--CCCCccccc
Q 007642 300 KPCPRCKRPIEKN--QGCMHMTCT 321 (595)
Q Consensus 300 K~CPkC~~~IEK~--~GCnhmtC~ 321 (595)
++||+|+.+|++. +|=+...|.
T Consensus 2 ~~C~rC~~~~~~~~~~~r~~~~C~ 25 (30)
T PF06827_consen 2 EKCPRCWNYIEDIGINGRSTYLCP 25 (30)
T ss_dssp SB-TTT--BBEEEEETTEEEEE-T
T ss_pred CcCccCCCcceEeEecCCCCeECc
Confidence 6899999999744 344444444
No 188
>PRK11827 hypothetical protein; Provisional
Probab=35.73 E-value=29 Score=27.28 Aligned_cols=25 Identities=24% Similarity=0.452 Sum_probs=18.1
Q ss_pred ccCCCCCcceeecCCCCcccccCCCc
Q 007642 300 KPCPRCKRPIEKNQGCMHMTCTPPCK 325 (595)
Q Consensus 300 K~CPkC~~~IEK~~GCnhmtC~~~C~ 325 (595)
-.||.|+.+++-..+=+...|. .|+
T Consensus 9 LaCP~ckg~L~~~~~~~~Lic~-~~~ 33 (60)
T PRK11827 9 IACPVCNGKLWYNQEKQELICK-LDN 33 (60)
T ss_pred eECCCCCCcCeEcCCCCeEECC-ccC
Confidence 5799999999866554567777 443
No 189
>KOG4362 consensus Transcriptional regulator BRCA1 [Replication, recombination and repair; Transcription]
Probab=35.63 E-value=10 Score=43.55 Aligned_cols=51 Identities=20% Similarity=0.499 Sum_probs=39.1
Q ss_pred CccccccccccccCCCceecCCCCcccHhHHHHHHhccccCCCCccccccCCCcCCCccch
Q 007642 140 EEMTCGICFENYPSDRLLAAACGHPFCSSCWTGYISTAINDGPGCLMLRCPDPSCGAAVGQ 200 (595)
Q Consensus 140 ~~~~C~IC~e~~~~~~~~~l~CgH~fC~~C~~~yi~~~i~~g~~~~~i~CP~~~C~~~v~~ 200 (595)
...+|+||+..+ ..++.+.|.|.||..||..-+...-. ...|| -|+..+..
T Consensus 20 k~lEc~ic~~~~--~~p~~~kc~~~~l~~~~n~~f~~~~~------~~~~~--lc~~~~eK 70 (684)
T KOG4362|consen 20 KILECPICLEHV--KEPSLLKCDHIFLKFCLNKLFESKKG------PKQCA--LCKSDIEK 70 (684)
T ss_pred hhccCCceeEEe--eccchhhhhHHHHhhhhhceeeccCc------cccch--hhhhhhhh
Confidence 356799999987 66788999999999999987765321 46787 78766543
No 190
>PF12906 RINGv: RING-variant domain; PDB: 2D8S_A 1VYX_A.
Probab=35.29 E-value=29 Score=25.64 Aligned_cols=33 Identities=30% Similarity=0.615 Sum_probs=22.8
Q ss_pred cccccccccCCCceecCCCC-----cccHhHHHHHHhc
Q 007642 144 CGICFENYPSDRLLAAACGH-----PFCSSCWTGYIST 176 (595)
Q Consensus 144 C~IC~e~~~~~~~~~l~CgH-----~fC~~C~~~yi~~ 176 (595)
|-||++....+.+...||+- .....|+..|+..
T Consensus 1 CrIC~~~~~~~~~li~pC~C~Gs~~~vH~~CL~~W~~~ 38 (47)
T PF12906_consen 1 CRICLEGEEEDEPLISPCRCKGSMKYVHRSCLERWIRE 38 (47)
T ss_dssp ETTTTEE-SSSS-EE-SSS-SSCCGSEECCHHHHHHHH
T ss_pred CeEeCCcCCCCCceecccccCCCcchhHHHHHHHHHHh
Confidence 77999886655566677653 5678899999987
No 191
>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=35.12 E-value=10 Score=29.61 Aligned_cols=11 Identities=55% Similarity=1.313 Sum_probs=10.2
Q ss_pred ccCCCCCccee
Q 007642 300 KPCPRCKRPIE 310 (595)
Q Consensus 300 K~CPkC~~~IE 310 (595)
|.||.|+.+|.
T Consensus 4 kHC~~CG~~Ip 14 (59)
T PF09889_consen 4 KHCPVCGKPIP 14 (59)
T ss_pred CcCCcCCCcCC
Confidence 78999999998
No 192
>PRK01103 formamidopyrimidine/5-formyluracil/ 5-hydroxymethyluracil DNA glycosylase; Validated
Probab=35.07 E-value=25 Score=36.22 Aligned_cols=26 Identities=42% Similarity=0.962 Sum_probs=18.6
Q ss_pred CccCCCCCcceeec--CCCCcccccCCCc
Q 007642 299 SKPCPRCKRPIEKN--QGCMHMTCTPPCK 325 (595)
Q Consensus 299 tK~CPkC~~~IEK~--~GCnhmtC~~~C~ 325 (595)
.++||.|+.+|+|. +|=.-.+|. .|+
T Consensus 245 g~pC~~Cg~~I~~~~~~gR~t~~CP-~CQ 272 (274)
T PRK01103 245 GEPCRRCGTPIEKIKQGGRSTFFCP-RCQ 272 (274)
T ss_pred CCCCCCCCCeeEEEEECCCCcEECc-CCC
Confidence 37999999999864 665555555 454
No 193
>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=35.04 E-value=17 Score=28.27 Aligned_cols=41 Identities=32% Similarity=0.515 Sum_probs=31.5
Q ss_pred ccCCCCCcceee--cCCCCcccccCCCcceeeecccccccCCCC
Q 007642 300 KPCPRCKRPIEK--NQGCMHMTCTPPCKFEFCWLCLGQWSDHGE 341 (595)
Q Consensus 300 K~CPkC~~~IEK--~~GCnhmtC~~~C~~~FCw~C~~~~~~H~~ 341 (595)
..||-|+..+-- .+-=|+-+|+ .|+...|-+||-.-.+|-.
T Consensus 3 ~~CPlCkt~~n~gsk~~pNyntCT-~Ck~~VCnlCGFNP~Phl~ 45 (61)
T PF05715_consen 3 SLCPLCKTTLNVGSKDPPNYNTCT-ECKSQVCNLCGFNPTPHLT 45 (61)
T ss_pred ccCCcccchhhcCCCCCCCccHHH-HHhhhhhcccCCCCCcccc
Confidence 579999987731 1346899999 8999999999876566653
No 194
>PHA02664 hypothetical protein; Provisional
Probab=34.97 E-value=62 Score=33.71 Aligned_cols=15 Identities=33% Similarity=0.295 Sum_probs=7.1
Q ss_pred HHHHHHHHHHHHHhC
Q 007642 77 QRQEEDITRISTVLS 91 (595)
Q Consensus 77 ~~~~~~i~~v~~vl~ 91 (595)
+.+++..++-..+|+
T Consensus 512 q~ieee~~ee~~vl~ 526 (534)
T PHA02664 512 QAIEEEEEEERAVLG 526 (534)
T ss_pred hhhhHHHHHHHHHHH
Confidence 344444444445543
No 195
>KOG1991 consensus Nuclear transport receptor RANBP7/RANBP8 (importin beta superfamily) [Nuclear structure; Intracellular trafficking, secretion, and vesicular transport]
Probab=34.83 E-value=20 Score=42.70 Aligned_cols=25 Identities=20% Similarity=0.275 Sum_probs=10.8
Q ss_pred HHHHHHHHHHHHHHHhC-CCHHHHHH
Q 007642 75 IRQRQEEDITRISTVLS-ISKVAASI 99 (595)
Q Consensus 75 i~~~~~~~i~~v~~vl~-i~~~~a~~ 99 (595)
|...|..+-..-+.+++ ++++....
T Consensus 968 i~~lq~~d~~~yq~l~~~L~~~q~~~ 993 (1010)
T KOG1991|consen 968 ITNLQSSDAVRYQKLISTLTPEQQDS 993 (1010)
T ss_pred HHhhhccChHHHHHHHhcCCHHHHHH
Confidence 44444444444444433 34444433
No 196
>CHL00174 accD acetyl-CoA carboxylase beta subunit; Reviewed
Probab=34.68 E-value=11 Score=39.28 Aligned_cols=28 Identities=18% Similarity=0.418 Sum_probs=15.7
Q ss_pred ccCCCCCcceeec-CCCCcccccCCCccee
Q 007642 300 KPCPRCKRPIEKN-QGCMHMTCTPPCKFEF 328 (595)
Q Consensus 300 K~CPkC~~~IEK~-~GCnhmtC~~~C~~~F 328 (595)
.+||+|+..|-+. -.=|...|. .|+++|
T Consensus 39 ~kc~~C~~~~~~~~l~~~~~vcp-~c~~h~ 67 (296)
T CHL00174 39 VQCENCYGLNYKKFLKSKMNICE-QCGYHL 67 (296)
T ss_pred eECCCccchhhHHHHHHcCCCCC-CCCCCc
Confidence 6677777666532 234456665 565533
No 197
>TIGR00577 fpg formamidopyrimidine-DNA glycosylase (fpg). All proteins in the FPG family with known functions are FAPY-DNA glycosylases that function in base excision repair. Homologous to endonuclease VIII (nei). This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=34.66 E-value=26 Score=36.06 Aligned_cols=25 Identities=44% Similarity=0.938 Sum_probs=18.3
Q ss_pred ccCCCCCcceeec--CCCCcccccCCCc
Q 007642 300 KPCPRCKRPIEKN--QGCMHMTCTPPCK 325 (595)
Q Consensus 300 K~CPkC~~~IEK~--~GCnhmtC~~~C~ 325 (595)
++||.|+.+|+|. +|=.-.+|. .|+
T Consensus 246 ~pC~~Cg~~I~~~~~~gR~t~~CP-~CQ 272 (272)
T TIGR00577 246 EPCRRCGTPIEKIKVGGRGTHFCP-QCQ 272 (272)
T ss_pred CCCCCCCCeeEEEEECCCCCEECC-CCC
Confidence 6999999999965 665555665 453
No 198
>KOG2177 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=34.57 E-value=15 Score=37.11 Aligned_cols=25 Identities=20% Similarity=0.533 Sum_probs=19.9
Q ss_pred cCCCCCcceeecCCCCcccccCCCcceeeeccc
Q 007642 301 PCPRCKRPIEKNQGCMHMTCTPPCKFEFCWLCL 333 (595)
Q Consensus 301 ~CPkC~~~IEK~~GCnhmtC~~~C~~~FCw~C~ 333 (595)
.|+.+... .+++|. .|+...|+.|.
T Consensus 88 ~c~~~~~~-------~~~~c~-~~~~~~c~~c~ 112 (386)
T KOG2177|consen 88 LCEKHGEE-------LKLFCE-EDEKLLCVLCR 112 (386)
T ss_pred hhhhcCCc-------ceEEec-ccccccCCCCC
Confidence 56666655 459999 89999999997
No 199
>COG4530 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=34.52 E-value=42 Score=29.46 Aligned_cols=13 Identities=31% Similarity=0.657 Sum_probs=5.9
Q ss_pred ccccccCCCCCCC
Q 007642 42 VADYEFIDNDSDD 54 (595)
Q Consensus 42 ~~d~~~~~~~~~~ 54 (595)
++|.-|.+++.|+
T Consensus 100 ddDdtFLedeedd 112 (129)
T COG4530 100 DDDDTFLEDEEDD 112 (129)
T ss_pred CCccccccccccc
Confidence 3344466543333
No 200
>TIGR00515 accD acetyl-CoA carboxylase, carboxyl transferase, beta subunit. The enzyme acetyl-CoA carboxylase contains a biotin carboxyl carrier protein or domain, a biotin carboxylase, and a carboxyl transferase. This model represents the beta chain of the carboxyl transferase for cases in which the architecture of the protein is as in E. coli, in which the carboxyltransferase portion consists of two non-identical subnits, alpha and beta.
Probab=34.03 E-value=12 Score=38.93 Aligned_cols=28 Identities=18% Similarity=0.555 Sum_probs=19.9
Q ss_pred ccCCCCCcceeec-CCCCcccccCCCccee
Q 007642 300 KPCPRCKRPIEKN-QGCMHMTCTPPCKFEF 328 (595)
Q Consensus 300 K~CPkC~~~IEK~-~GCnhmtC~~~C~~~F 328 (595)
..||+|+..|-+. -.=|.+.|. .|+++|
T Consensus 27 ~~c~~c~~~~~~~~l~~~~~vc~-~c~~h~ 55 (285)
T TIGR00515 27 TKCPKCGQVLYTKELERNLEVCP-KCDHHM 55 (285)
T ss_pred eECCCCcchhhHHHHHhhCCCCC-CCCCcC
Confidence 7899999888643 334557887 687764
No 201
>COG5432 RAD18 RING-finger-containing E3 ubiquitin ligase [Signal transduction mechanisms]
Probab=34.03 E-value=12 Score=38.26 Aligned_cols=30 Identities=30% Similarity=0.843 Sum_probs=23.5
Q ss_pred ccCCCCCcceeecCCCCcccccCCCcceeeecccccc
Q 007642 300 KPCPRCKRPIEKNQGCMHMTCTPPCKFEFCWLCLGQW 336 (595)
Q Consensus 300 K~CPkC~~~IEK~~GCnhmtC~~~C~~~FCw~C~~~~ 336 (595)
-+|--|.-.|. +-|-..|||.||++|-..+
T Consensus 26 lrC~IC~~~i~-------ip~~TtCgHtFCslCIR~h 55 (391)
T COG5432 26 LRCRICDCRIS-------IPCETTCGHTFCSLCIRRH 55 (391)
T ss_pred HHhhhhhheee-------cceecccccchhHHHHHHH
Confidence 46888887777 7775479999999998654
No 202
>PRK14810 formamidopyrimidine-DNA glycosylase; Provisional
Probab=34.03 E-value=26 Score=36.03 Aligned_cols=26 Identities=35% Similarity=0.879 Sum_probs=18.5
Q ss_pred CccCCCCCcceeec--CCCCcccccCCCc
Q 007642 299 SKPCPRCKRPIEKN--QGCMHMTCTPPCK 325 (595)
Q Consensus 299 tK~CPkC~~~IEK~--~GCnhmtC~~~C~ 325 (595)
.++||+|+.+|++. +|=.-.+|. .|+
T Consensus 244 g~pCprCG~~I~~~~~~gR~t~~CP-~CQ 271 (272)
T PRK14810 244 GEPCLNCKTPIRRVVVAGRSSHYCP-HCQ 271 (272)
T ss_pred CCcCCCCCCeeEEEEECCCccEECc-CCc
Confidence 47999999999854 665555555 454
No 203
>KOG1701 consensus Focal adhesion adaptor protein Paxillin and related LIM proteins [Signal transduction mechanisms]
Probab=33.68 E-value=12 Score=40.31 Aligned_cols=11 Identities=18% Similarity=0.513 Sum_probs=7.2
Q ss_pred ccCCCCCccee
Q 007642 300 KPCPRCKRPIE 310 (595)
Q Consensus 300 K~CPkC~~~IE 310 (595)
-.|-.|+..+-
T Consensus 428 Y~CEDCg~~LS 438 (468)
T KOG1701|consen 428 YKCEDCGLLLS 438 (468)
T ss_pred eehhhcCcccc
Confidence 46667777665
No 204
>KOG0250 consensus DNA repair protein RAD18 (SMC family protein) [Replication, recombination and repair]
Probab=33.45 E-value=1e+03 Score=29.43 Aligned_cols=26 Identities=8% Similarity=0.268 Sum_probs=18.7
Q ss_pred HHHHHHHHHHHHHHHHHHhhhhhhhc
Q 007642 421 LKFITEAWLQIVECRRVLKWTYAYGY 446 (595)
Q Consensus 421 ~~~l~~a~~~l~~~r~~L~~sy~~~y 446 (595)
+.-+......+..+..-+.|..||.+
T Consensus 254 ~~~~e~~~~~l~~Lk~k~~W~~V~~~ 279 (1074)
T KOG0250|consen 254 LEQLEDLKENLEQLKAKMAWAWVNEV 279 (1074)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 33445555667777888999999887
No 205
>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=33.41 E-value=17 Score=27.56 Aligned_cols=23 Identities=26% Similarity=0.765 Sum_probs=13.9
Q ss_pred ceeee-cCCCcccccCCcccCCCC
Q 007642 251 YDVTC-RCSYSFCWNCTEEAHRPV 273 (595)
Q Consensus 251 ~~v~C-~C~~~fC~~C~~~~H~p~ 273 (595)
....| .|+..||+.|-.-.|..+
T Consensus 20 ~~y~C~~C~~~FC~dCD~fiHE~L 43 (51)
T PF07975_consen 20 SRYRCPKCKNHFCIDCDVFIHETL 43 (51)
T ss_dssp EEE--TTTT--B-HHHHHTTTTTS
T ss_pred CeEECCCCCCccccCcChhhhccc
Confidence 55789 999999999987777543
No 206
>smart00336 BBOX B-Box-type zinc finger.
Probab=33.34 E-value=34 Score=23.83 Aligned_cols=28 Identities=25% Similarity=0.602 Sum_probs=24.7
Q ss_pred ccCCCCC-cceeecCCCCcccccCCCcceeeeccccc
Q 007642 300 KPCPRCK-RPIEKNQGCMHMTCTPPCKFEFCWLCLGQ 335 (595)
Q Consensus 300 K~CPkC~-~~IEK~~GCnhmtC~~~C~~~FCw~C~~~ 335 (595)
..|+.|. .++. ++|. .|....|..|...
T Consensus 4 ~~C~~h~~~~~~-------~~C~-~c~~~iC~~C~~~ 32 (42)
T smart00336 4 PKCDSHGDEPAE-------FFCE-ECGALLCRTCDEA 32 (42)
T ss_pred CcCCCCCCCceE-------EECC-CCCcccccccChh
Confidence 6799998 8888 9999 8999999999754
No 207
>COG1998 RPS31 Ribosomal protein S27AE [Translation, ribosomal structure and biogenesis]
Probab=33.31 E-value=25 Score=26.41 Aligned_cols=10 Identities=40% Similarity=1.122 Sum_probs=6.9
Q ss_pred ccCCCCCcce
Q 007642 300 KPCPRCKRPI 309 (595)
Q Consensus 300 K~CPkC~~~I 309 (595)
+.||+|+-.+
T Consensus 20 ~~CPrCG~gv 29 (51)
T COG1998 20 RFCPRCGPGV 29 (51)
T ss_pred ccCCCCCCcc
Confidence 6788888533
No 208
>PRK13945 formamidopyrimidine-DNA glycosylase; Provisional
Probab=33.08 E-value=28 Score=36.04 Aligned_cols=25 Identities=40% Similarity=0.943 Sum_probs=18.9
Q ss_pred ccCCCCCcceeec--CCCCcccccCCCc
Q 007642 300 KPCPRCKRPIEKN--QGCMHMTCTPPCK 325 (595)
Q Consensus 300 K~CPkC~~~IEK~--~GCnhmtC~~~C~ 325 (595)
++||.|+.+|+|. +|=.-.+|. .|+
T Consensus 255 ~pC~~Cg~~I~~~~~~gR~t~~CP-~CQ 281 (282)
T PRK13945 255 KPCRKCGTPIERIKLAGRSTHWCP-NCQ 281 (282)
T ss_pred CCCCcCCCeeEEEEECCCccEECC-CCc
Confidence 7999999999864 775556665 554
No 209
>KOG0933 consensus Structural maintenance of chromosome protein 2 (chromosome condensation complex Condensin, subunit E) [Chromatin structure and dynamics; Cell cycle control, cell division, chromosome partitioning]
Probab=32.97 E-value=9.7e+02 Score=29.42 Aligned_cols=43 Identities=19% Similarity=0.223 Sum_probs=21.1
Q ss_pred HHHHHHHHHHHHHhhhhhhhcccCccchhhHHHHHHHHHHHHHhHHHHH
Q 007642 426 EAWLQIVECRRVLKWTYAYGYYLPDHEHAKRQFFEYLQGEAESGLERLH 474 (595)
Q Consensus 426 ~a~~~l~~~r~~L~~sy~~~yy~~~~~~~~~~~fe~~Q~~le~~~E~L~ 474 (595)
....-|.+-+|++ -+|.||..+ .+.......-++.+..+..+.
T Consensus 222 ~~~~dle~l~R~~---ia~eY~~~~---~~~~~~~~~i~e~~~~i~~l~ 264 (1174)
T KOG0933|consen 222 KINRDLERLSRIC---IAYEYLQAE---EKRKNSAHEIEEMKDKIAKLD 264 (1174)
T ss_pred HHHHHHHHHHHHH---HHHHHHHHH---HHHHHHHHHHHHHHHHHHHHH
Confidence 3344555556665 578888732 233333333444444444443
No 210
>PF13453 zf-TFIIB: Transcription factor zinc-finger
Probab=32.74 E-value=28 Score=24.80 Aligned_cols=31 Identities=32% Similarity=0.743 Sum_probs=19.0
Q ss_pred cCCCCCcceeecCCCCcccccCCCcceeeecccccccC
Q 007642 301 PCPRCKRPIEKNQGCMHMTCTPPCKFEFCWLCLGQWSD 338 (595)
Q Consensus 301 ~CPkC~~~IEK~~GCnhmtC~~~C~~~FCw~C~~~~~~ 338 (595)
.||+|+..++...- . .=...-|-.|++.|-+
T Consensus 1 ~CP~C~~~l~~~~~------~-~~~id~C~~C~G~W~d 31 (41)
T PF13453_consen 1 KCPRCGTELEPVRL------G-DVEIDVCPSCGGIWFD 31 (41)
T ss_pred CcCCCCcccceEEE------C-CEEEEECCCCCeEEcc
Confidence 59999998874433 1 2233345677777754
No 211
>PRK10445 endonuclease VIII; Provisional
Probab=32.55 E-value=29 Score=35.53 Aligned_cols=25 Identities=32% Similarity=0.673 Sum_probs=18.6
Q ss_pred ccCCCCCcceeec--CCCCcccccCCCc
Q 007642 300 KPCPRCKRPIEKN--QGCMHMTCTPPCK 325 (595)
Q Consensus 300 K~CPkC~~~IEK~--~GCnhmtC~~~C~ 325 (595)
++||.|+.+|++. +|=.-.+|. .|+
T Consensus 236 ~~Cp~Cg~~I~~~~~~gR~t~~CP-~CQ 262 (263)
T PRK10445 236 EACERCGGIIEKTTLSSRPFYWCP-GCQ 262 (263)
T ss_pred CCCCCCCCEeEEEEECCCCcEECC-CCc
Confidence 8999999999854 675556665 554
No 212
>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=32.20 E-value=1.5e+02 Score=31.87 Aligned_cols=119 Identities=21% Similarity=0.433 Sum_probs=60.7
Q ss_pred cCCcceEE-eCHHHHHHHHHHHHHHHHHHhCCCHHHHHHHHHHcCCChhhhHHHhhhc-HHHHHHHhCCCCCCCCCCC--
Q 007642 62 RHQLNYTV-LTEADIRQRQEEDITRISTVLSISKVAASILLRFYNWSVSKVHDEWFAD-EERVRKAVGLLEKPAVQFP-- 137 (595)
Q Consensus 62 ~~~~~y~v-l~~~~i~~~~~~~i~~v~~vl~i~~~~a~~LL~~~~W~~~~l~e~~~~~-~~~~~~~~gl~~~~~~~~~-- 137 (595)
+.-.+|.+ |...+....+++.-.-|...-+|. .+ ..|.|+|.+. .+.|. .+|....+
T Consensus 207 ~~v~~F~Irlns~~y~~L~~kL~~PI~~~~ni~--------i~-----~tl~drF~e~F~~~V~------~Np~y~~~~~ 267 (358)
T PF10272_consen 207 PGVKPFTIRLNSSEYRDLREKLRAPIRIARNIV--------IH-----QTLSDRFVEAFKEQVE------QNPRYSYPES 267 (358)
T ss_pred CCCcceEEEEcHHHHHHHHHHhhCccccCCCce--------EC-----CCHHHHHHHHHHHHHH------hCCccccCCC
Confidence 44567888 888888887777544443333331 00 1233443322 22221 22222222
Q ss_pred CCCccccccccccccCCCce--------------------ecCCCCcccHhHHHHHHhccccCC--CCccccccCCCcCC
Q 007642 138 DGEEMTCGICFENYPSDRLL--------------------AAACGHPFCSSCWTGYISTAINDG--PGCLMLRCPDPSCG 195 (595)
Q Consensus 138 ~~~~~~C~IC~e~~~~~~~~--------------------~l~CgH~fC~~C~~~yi~~~i~~g--~~~~~i~CP~~~C~ 195 (595)
..+.-.|--|+..-+.-.+. ..-|.-..|.+|+..++.++-.+. ...+.=+||.|.|+
T Consensus 268 ~~e~e~CigC~~~~~~vkl~k~C~~~~~~g~~~~~~~~C~~C~CRPmWC~~Cm~kwFasrQd~~~~~~Wl~~~~~CPtCR 347 (358)
T PF10272_consen 268 GQELEPCIGCMQAQPNVKLVKRCADEEQEGSPLPNEPPCQQCYCRPMWCLECMGKWFASRQDQQHPETWLSGKCPCPTCR 347 (358)
T ss_pred ccccCCccccccCCCCcEEEeccCCcccCCcccccCCCCccccccchHHHHHHHHHhhhcCCCCChhhhhcCCCCCCCCc
Confidence 23345577777543221111 112445679999999997654322 12333355555999
Q ss_pred Cccc
Q 007642 196 AAVG 199 (595)
Q Consensus 196 ~~v~ 199 (595)
+.|-
T Consensus 348 a~FC 351 (358)
T PF10272_consen 348 AKFC 351 (358)
T ss_pred ccce
Confidence 8763
No 213
>TIGR00686 phnA alkylphosphonate utilization operon protein PhnA. The protein family includes an uncharacterized member designated phnA in Escherichia coli, part of a large operon associated with alkylphosphonate uptake and carbon-phosphorus bond cleavage. This protein is not related to the characterized phosphonoacetate hydrolase designated PhnA by Kulakova, et al. (2001, 1997).
Probab=31.92 E-value=30 Score=30.32 Aligned_cols=21 Identities=29% Similarity=0.928 Sum_probs=12.6
Q ss_pred ccCCCCCcceeecCCCCccccc
Q 007642 300 KPCPRCKRPIEKNQGCMHMTCT 321 (595)
Q Consensus 300 K~CPkC~~~IEK~~GCnhmtC~ 321 (595)
-+||+|+.-.--..|=+ +.|.
T Consensus 3 p~CP~C~seytY~dg~~-~iCp 23 (109)
T TIGR00686 3 PPCPKCNSEYTYHDGTQ-LICP 23 (109)
T ss_pred CcCCcCCCcceEecCCe-eECc
Confidence 57999987655444432 4454
No 214
>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=31.70 E-value=27 Score=25.22 Aligned_cols=28 Identities=32% Similarity=0.776 Sum_probs=15.0
Q ss_pred CCCCCCCCeeeeecCCCCceeee-cCCCcccccCCc
Q 007642 233 CPAPGCDYAVDFVVGSGNYDVTC-RCSYSFCWNCTE 267 (595)
Q Consensus 233 CP~p~C~~~i~~~~~~~~~~v~C-~C~~~fC~~C~~ 267 (595)
|..++|.... ...+.| .|+..||..++.
T Consensus 1 C~~~~C~~~~-------~~~~~C~~C~~~FC~~Hr~ 29 (43)
T PF01428_consen 1 CSFPGCKKKD-------FLPFKCKHCGKSFCLKHRL 29 (43)
T ss_dssp -SSTTT--BC-------TSHEE-TTTS-EE-TTTHS
T ss_pred CccCcCcCcc-------CCCeECCCCCcccCccccC
Confidence 4445676432 246799 699999998874
No 215
>PF03119 DNA_ligase_ZBD: NAD-dependent DNA ligase C4 zinc finger domain; InterPro: IPR004149 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents the zinc finger domain found in NAD-dependent DNA ligases. DNA ligases catalyse the crucial step of joining the breaks in duplex DNA during DNA replication, repair and recombination, utilizing either ATP or NAD(+) as a cofactor []. This domain is a small zinc binding motif that is presumably DNA binding. It is found only in NAD-dependent DNA ligases. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003911 DNA ligase (NAD+) activity, 0006260 DNA replication, 0006281 DNA repair; PDB: 1DGS_A 1V9P_B 2OWO_A.
Probab=31.53 E-value=33 Score=22.51 Aligned_cols=21 Identities=24% Similarity=0.833 Sum_probs=13.5
Q ss_pred cCCCCCcceeecCCCCccccc
Q 007642 301 PCPRCKRPIEKNQGCMHMTCT 321 (595)
Q Consensus 301 ~CPkC~~~IEK~~GCnhmtC~ 321 (595)
.||.|+..+.+..|=-+.+|.
T Consensus 1 ~CP~C~s~l~~~~~ev~~~C~ 21 (28)
T PF03119_consen 1 TCPVCGSKLVREEGEVDIRCP 21 (28)
T ss_dssp B-TTT--BEEE-CCTTCEEE-
T ss_pred CcCCCCCEeEcCCCCEeEECC
Confidence 499999999999887777776
No 216
>KOG2164 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=31.15 E-value=21 Score=39.53 Aligned_cols=30 Identities=30% Similarity=0.708 Sum_probs=20.1
Q ss_pred CccCCCCCcceeecCCCCcccccCCCcceeeeccccc
Q 007642 299 SKPCPRCKRPIEKNQGCMHMTCTPPCKFEFCWLCLGQ 335 (595)
Q Consensus 299 tK~CPkC~~~IEK~~GCnhmtC~~~C~~~FCw~C~~~ 335 (595)
--.||-|-.+-. .-++..|||-|||-|+-.
T Consensus 186 ~~~CPICL~~~~-------~p~~t~CGHiFC~~CiLq 215 (513)
T KOG2164|consen 186 DMQCPICLEPPS-------VPVRTNCGHIFCGPCILQ 215 (513)
T ss_pred CCcCCcccCCCC-------cccccccCceeeHHHHHH
Confidence 368999987665 333225788888888653
No 217
>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]
Probab=31.09 E-value=31 Score=40.53 Aligned_cols=35 Identities=23% Similarity=0.732 Sum_probs=28.3
Q ss_pred ccCCCCCcceeecCCCCcccccCCCcce-----eeeccccc
Q 007642 300 KPCPRCKRPIEKNQGCMHMTCTPPCKFE-----FCWLCLGQ 335 (595)
Q Consensus 300 K~CPkC~~~IEK~~GCnhmtC~~~C~~~-----FCw~C~~~ 335 (595)
-.||+|..++.-...=|.|.|. .||+. .|..|++.
T Consensus 445 ~~Cp~Cd~~lt~H~~~~~L~CH-~Cg~~~~~p~~Cp~Cgs~ 484 (730)
T COG1198 445 AECPNCDSPLTLHKATGQLRCH-YCGYQEPIPQSCPECGSE 484 (730)
T ss_pred ccCCCCCcceEEecCCCeeEeC-CCCCCCCCCCCCCCCCCC
Confidence 4788888888765555889998 89987 89999876
No 218
>PF04147 Nop14: Nop14-like family ; InterPro: IPR007276 Emg1 and Nop14 are novel proteins whose interaction is required for the maturation of the 18S rRNA and for 40S ribosome production [].
Probab=31.03 E-value=41 Score=40.42 Aligned_cols=11 Identities=9% Similarity=0.392 Sum_probs=5.5
Q ss_pred HHHHHHHHHHH
Q 007642 510 NYFENLVRALE 520 (595)
Q Consensus 510 ~~~~~l~~~le 520 (595)
....+++..|+
T Consensus 824 ~K~k~i~~~Lq 834 (840)
T PF04147_consen 824 EKMKRIMSSLQ 834 (840)
T ss_pred HHHHHHHHHHH
Confidence 34455555554
No 219
>KOG3053 consensus Uncharacterized conserved protein [Function unknown]
Probab=30.68 E-value=38 Score=34.30 Aligned_cols=56 Identities=27% Similarity=0.551 Sum_probs=38.4
Q ss_pred CccccccccccccCCCc--eecCCC-----CcccHhHHHHHHhccccCCCCccccccCCCcCCCcc
Q 007642 140 EEMTCGICFENYPSDRL--LAAACG-----HPFCSSCWTGYISTAINDGPGCLMLRCPDPSCGAAV 198 (595)
Q Consensus 140 ~~~~C~IC~e~~~~~~~--~~l~Cg-----H~fC~~C~~~yi~~~i~~g~~~~~i~CP~~~C~~~v 198 (595)
.+-.|=|||..-..+.. ..-||. |-....|+..|+..+-. |....++.|| +|....
T Consensus 19 ~eR~CWiCF~TdeDn~~a~WV~PCrCRGt~KWVHqsCL~rWiDEK~~-~n~~q~V~C~--QCqTEY 81 (293)
T KOG3053|consen 19 LERCCWICFATDEDNRLAAWVHPCRCRGTTKWVHQSCLSRWIDEKQR-GNPLQTVSCP--QCQTEY 81 (293)
T ss_pred cceeEEEEeccCcccchhhhcccccccCccHHHHHHHHHHHHhHHhc-CCCCceeech--hhcchh
Confidence 46689999986432211 123553 56889999999988765 4445689999 898753
No 220
>PF02845 CUE: CUE domain; InterPro: IPR003892 This domain may be involved in binding ubiquitin-conjugating enzymes (UBCs). CUE domains also occur in two proteins of the IL-1 signal transduction pathway, tollip and TAB2.; GO: 0005515 protein binding; PDB: 2EKF_A 1OTR_A 1P3Q_Q 1MN3_A 1WGL_A 2EJS_A 2DAE_A 2DHY_A 2DI0_A.
Probab=30.53 E-value=1.6e+02 Score=20.89 Aligned_cols=37 Identities=14% Similarity=0.236 Sum_probs=29.1
Q ss_pred HHHHHHHHHh-CCCHHHHHHHHHHcCCChhhhHHHhhh
Q 007642 81 EDITRISTVL-SISKVAASILLRFYNWSVSKVHDEWFA 117 (595)
Q Consensus 81 ~~i~~v~~vl-~i~~~~a~~LL~~~~W~~~~l~e~~~~ 117 (595)
+.|..+.+++ +++++.....|..+++|++...+....
T Consensus 3 ~~v~~L~~mFP~~~~~~I~~~L~~~~~~ve~ai~~LL~ 40 (42)
T PF02845_consen 3 EMVQQLQEMFPDLDREVIEAVLQANNGDVEAAIDALLE 40 (42)
T ss_dssp HHHHHHHHHSSSS-HHHHHHHHHHTTTTHHHHHHHHHH
T ss_pred HHHHHHHHHCCCCCHHHHHHHHHHcCCCHHHHHHHHHc
Confidence 5677777777 578889999999999999998876543
No 221
>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=30.26 E-value=34 Score=30.98 Aligned_cols=26 Identities=8% Similarity=0.033 Sum_probs=17.0
Q ss_pred ccCCCCCcceeecCCCCcccccCCCcce
Q 007642 300 KPCPRCKRPIEKNQGCMHMTCTPPCKFE 327 (595)
Q Consensus 300 K~CPkC~~~IEK~~GCnhmtC~~~C~~~ 327 (595)
+.||+|++..---.- +.++|. .||..
T Consensus 10 r~Cp~cg~kFYDLnk-~p~vcP-~cg~~ 35 (129)
T TIGR02300 10 RICPNTGSKFYDLNR-RPAVSP-YTGEQ 35 (129)
T ss_pred ccCCCcCccccccCC-CCccCC-CcCCc
Confidence 689999876642222 678887 56554
No 222
>PF01396 zf-C4_Topoisom: Topoisomerase DNA binding C4 zinc finger; InterPro: IPR013498 DNA topoisomerases regulate the number of topological links between two DNA strands (i.e. change the number of superhelical turns) by catalysing transient single- or double-strand breaks, crossing the strands through one another, then resealing the breaks []. These enzymes have several functions: to remove DNA supercoils during transcription and DNA replication; for strand breakage during recombination; for chromosome condensation; and to disentangle intertwined DNA during mitosis [, ]. DNA topoisomerases are divided into two classes: type I enzymes (5.99.1.2 from EC; topoisomerases I, III and V) break single-strand DNA, and type II enzymes (5.99.1.3 from EC; topoisomerases II, IV and VI) break double-strand DNA []. Type I topoisomerases are ATP-independent enzymes (except for reverse gyrase), and can be subdivided according to their structure and reaction mechanisms: type IA (bacterial and archaeal topoisomerase I, topoisomerase III and reverse gyrase) and type IB (eukaryotic topoisomerase I and topoisomerase V). These enzymes are primarily responsible for relaxing positively and/or negatively supercoiled DNA, except for reverse gyrase, which can introduce positive supercoils into DNA. This entry represents the zinc-finger domain found in type IA topoisomerases, including bacterial and archaeal topoisomerase I and III enzymes, and in eukaryotic topoisomerase III enzymes. Escherichia coli topoisomerase I proteins contain five copies of a zinc-ribbon-like domain at their C terminus, two of which have lost their cysteine residues and are therefore probably not able to bind zinc []. This domain is still considered to be a member of the zinc-ribbon superfamily despite not being able to bind zinc. More information about this protein can be found at Protein of the Month: DNA Topoisomerase [].; GO: 0003677 DNA binding, 0003916 DNA topoisomerase activity, 0006265 DNA topological change, 0005694 chromosome
Probab=30.17 E-value=43 Score=23.72 Aligned_cols=11 Identities=36% Similarity=1.219 Sum_probs=8.3
Q ss_pred ccCCCCCccee
Q 007642 300 KPCPRCKRPIE 310 (595)
Q Consensus 300 K~CPkC~~~IE 310 (595)
+.||.|+..+.
T Consensus 2 ~~CP~Cg~~lv 12 (39)
T PF01396_consen 2 EKCPKCGGPLV 12 (39)
T ss_pred cCCCCCCceeE
Confidence 57999986665
No 223
>KOG2932 consensus E3 ubiquitin ligase involved in ubiquitination of E-cadherin complex [Posttranslational modification, protein turnover, chaperones]
Probab=30.12 E-value=15 Score=38.03 Aligned_cols=52 Identities=23% Similarity=0.772 Sum_probs=36.1
Q ss_pred CCCcccCCCCCCCCeeeeecCCCCceeee-cCCCcccccCCcccCCCCCchhHHHHHHhhhHhHHhHHHHHhcCccCCCC
Q 007642 227 NRKTKWCPAPGCDYAVDFVVGSGNYDVTC-RCSYSFCWNCTEEAHRPVDCDTVAKWVLKNSAESENMNWILANSKPCPRC 305 (595)
Q Consensus 227 ~~~~~~CP~p~C~~~i~~~~~~~~~~v~C-~C~~~fC~~C~~~~H~p~~C~~~~~~~~k~~~~~e~~~wi~~ntK~CPkC 305 (595)
++.+-+|- .|+..|.+- + .= .|.+.||..|... |. . |.||.|
T Consensus 87 ~p~VHfCd--~Cd~PI~IY-G------RmIPCkHvFCl~CAr~-~~------------------d---------K~Cp~C 129 (389)
T KOG2932|consen 87 GPRVHFCD--RCDFPIAIY-G------RMIPCKHVFCLECARS-DS------------------D---------KICPLC 129 (389)
T ss_pred CcceEeec--ccCCcceee-e------cccccchhhhhhhhhc-Cc------------------c---------ccCcCc
Confidence 44566777 487766432 1 11 6899999999743 32 1 899999
Q ss_pred CcceeecCCC
Q 007642 306 KRPIEKNQGC 315 (595)
Q Consensus 306 ~~~IEK~~GC 315 (595)
.-.|+|.+-|
T Consensus 130 ~d~VqrIeq~ 139 (389)
T KOG2932|consen 130 DDRVQRIEQI 139 (389)
T ss_pred ccHHHHHHHh
Confidence 9999988765
No 224
>PF04050 Upf2: Up-frameshift suppressor 2 ; InterPro: IPR007193 This entry represents Up-frameshift suppressor 2 (also known as Nonsense-mediated mRNA decay protein 2). Transcripts harbouring premature signals for translation termination are recognised and rapidly degraded by eukaryotic cells through a pathway known as nonsense-mediated mRNA decay. In Saccharomyces cerevisiae, three trans-acting factors (Upf1 to Upf3) are required for nonsense-mediated mRNA decay [].; PDB: 2WJV_D.
Probab=30.04 E-value=34 Score=32.57 Aligned_cols=12 Identities=8% Similarity=0.235 Sum_probs=5.9
Q ss_pred HHHHHHHHHHHH
Q 007642 73 ADIRQRQEEDIT 84 (595)
Q Consensus 73 ~~i~~~~~~~i~ 84 (595)
+++.+.+.+.+.
T Consensus 63 ~dFeref~kmm~ 74 (170)
T PF04050_consen 63 EDFEREFQKMMA 74 (170)
T ss_dssp HHHHHHHHHHHH
T ss_pred HHHHHHHHHHHH
Confidence 355555555444
No 225
>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=29.98 E-value=42 Score=26.50 Aligned_cols=35 Identities=20% Similarity=0.399 Sum_probs=18.7
Q ss_pred CccCCCCCcceeecCCCCcccccCCCcceeeecccccc
Q 007642 299 SKPCPRCKRPIEKNQGCMHMTCTPPCKFEFCWLCLGQW 336 (595)
Q Consensus 299 tK~CPkC~~~IEK~~GCnhmtC~~~C~~~FCw~C~~~~ 336 (595)
...|+.|++..- ---..-.|+ .||.-||-.|....
T Consensus 9 ~~~C~~C~~~F~--~~~rrhhCr-~CG~~vC~~Cs~~~ 43 (69)
T PF01363_consen 9 ASNCMICGKKFS--LFRRRHHCR-NCGRVVCSSCSSQR 43 (69)
T ss_dssp -SB-TTT--B-B--SSS-EEE-T-TT--EEECCCS-EE
T ss_pred CCcCcCcCCcCC--CceeeEccC-CCCCEECCchhCCE
Confidence 478999998884 223446788 89999999998643
No 226
>COG3809 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=29.82 E-value=32 Score=28.31 Aligned_cols=35 Identities=31% Similarity=0.779 Sum_probs=25.6
Q ss_pred ccCCCCCcceeecCCCCcccccCCCcceeeecccccccCCCC
Q 007642 300 KPCPRCKRPIEKNQGCMHMTCTPPCKFEFCWLCLGQWSDHGE 341 (595)
Q Consensus 300 K~CPkC~~~IEK~~GCnhmtC~~~C~~~FCw~C~~~~~~H~~ 341 (595)
..||.|+..+. |.=+..=-...|..|.+.|-+.|.
T Consensus 2 llCP~C~v~l~-------~~~rs~vEiD~CPrCrGVWLDrGE 36 (88)
T COG3809 2 LLCPICGVELV-------MSVRSGVEIDYCPRCRGVWLDRGE 36 (88)
T ss_pred cccCcCCceee-------eeeecCceeeeCCccccEeecchh
Confidence 57999999888 554423445668899999987664
No 227
>PF06936 Selenoprotein_S: Selenoprotein S (SelS); InterPro: IPR009703 This family consists of several mammalian selenoprotein S (SelS) sequences. SelS is a plasma membrane protein and is present in a variety of tissues and cell types. These proteins are involved in the degradation process of misfolded endoplasmic reticulum (ER) luminal proteins which participate in the transfer of misfolded proteins from the ER to the cytosol, where they are destroyed by the proteasome in a ubiquitin-dependent manner []. They probably serve as a linker between DER1, which mediates the retro-translocation of misfolded proteins into the cytosol, and the ATPase complex VCP, which mediates the translocation and ubiquitination.; GO: 0008430 selenium binding, 0006886 intracellular protein transport, 0030176 integral to endoplasmic reticulum membrane; PDB: 2Q2F_A.
Probab=29.60 E-value=3.2e+02 Score=26.65 Aligned_cols=26 Identities=12% Similarity=0.130 Sum_probs=13.4
Q ss_pred HHHHHHHHHHHHhHHHHHHHHHHHHH
Q 007642 457 QFFEYLQGEAESGLERLHQCAEKELQ 482 (595)
Q Consensus 457 ~~fe~~Q~~le~~~E~L~~~le~e~~ 482 (595)
..+...|..++..-.++.+.+++...
T Consensus 76 d~v~~rqEa~eaAR~RmQEE~dakA~ 101 (190)
T PF06936_consen 76 DVVVRRQEAMEAARRRMQEELDAKAE 101 (190)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred hHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 34445555555555555555544433
No 228
>PRK12495 hypothetical protein; Provisional
Probab=29.47 E-value=38 Score=33.53 Aligned_cols=17 Identities=29% Similarity=0.733 Sum_probs=13.4
Q ss_pred CccCCCCCcceeecCCC
Q 007642 299 SKPCPRCKRPIEKNQGC 315 (595)
Q Consensus 299 tK~CPkC~~~IEK~~GC 315 (595)
.+.||.|+.||-+..||
T Consensus 42 a~hC~~CG~PIpa~pG~ 58 (226)
T PRK12495 42 NAHCDECGDPIFRHDGQ 58 (226)
T ss_pred hhhcccccCcccCCCCe
Confidence 47999999999955443
No 229
>cd07666 BAR_SNX7 The Bin/Amphiphysin/Rvs (BAR) domain of Sorting Nexin 7. BAR domains are dimerization, lipid binding and curvature sensing modules found in many different proteins with diverse functions. Sorting nexins (SNXs) are Phox homology (PX) domain containing proteins that are involved in regulating membrane traffic and protein sorting in the endosomal system. SNXs differ from each other in their lipid-binding specificity, subcellular localization and specific function in the endocytic pathway. A subset of SNXs also contain BAR domains. The PX-BAR structural unit determines the specific membrane targeting of SNXs. The specific function of SNX7 is still unknown. BAR domains form dimers that bind to membranes, induce membrane bending and curvature, and may also be involved in protein-protein interactions.
Probab=29.23 E-value=6.2e+02 Score=25.67 Aligned_cols=68 Identities=13% Similarity=0.275 Sum_probs=30.2
Q ss_pred HHHHHHHHHHHhhhHHHHHHHHHHHHHHHH-------HHHHHHhhhcCCCchhHHHHHHHHHHHHHHHHHHhhhh
Q 007642 375 LERYTHYYERWATNQSSRQKALADLQQMQT-------VHLEKLSDVQCQPESQLKFITEAWLQIVECRRVLKWTY 442 (595)
Q Consensus 375 l~ry~~y~~r~~~h~~s~~~~~~~l~~~~~-------~~~~~l~~~~~~~~~~~~~l~~a~~~l~~~r~~L~~sy 442 (595)
+..|.--|.-|.+.+..+......+..... ..+..+......+-.+.-.+.+|++.+..-|..+..+|
T Consensus 91 ~~~fgk~~~lws~~E~~L~~~L~~~a~~~d~~~~~~~~~~~~l~~~f~~~Lkeyv~y~~slK~vlk~R~~~Q~~l 165 (243)
T cd07666 91 LKEYGPIYTLWSASEEELADSLKGMASCIDRCCKATDKRMKGLSEQLLPVIHEYVLYSETLMGVIKRRDQIQAEL 165 (243)
T ss_pred HHHHHHHHHHHhccchhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 334444555666666555444444333322 11222222222222344455555555555555554444
No 230
>PRK09710 lar restriction alleviation and modification protein; Reviewed
Probab=28.91 E-value=67 Score=25.52 Aligned_cols=33 Identities=30% Similarity=0.493 Sum_probs=20.3
Q ss_pred CcccCCCCCCCCeeeeecCCCCceeee-cCCCccc
Q 007642 229 KTKWCPAPGCDYAVDFVVGSGNYDVTC-RCSYSFC 262 (595)
Q Consensus 229 ~~~~CP~p~C~~~i~~~~~~~~~~v~C-~C~~~fC 262 (595)
.++.||.-+|..+.... ..+-..+.| .|+...+
T Consensus 5 ~lKPCPFCG~~~~~v~~-~~g~~~v~C~~CgA~~~ 38 (64)
T PRK09710 5 NVKPCPFCGCPSVTVKA-ISGYYRAKCNGCESRTG 38 (64)
T ss_pred cccCCCCCCCceeEEEe-cCceEEEEcCCCCcCcc
Confidence 57899975555444333 234456788 8888643
No 231
>KOG2906 consensus RNA polymerase III subunit C11 [Transcription]
Probab=28.79 E-value=51 Score=28.39 Aligned_cols=29 Identities=28% Similarity=0.764 Sum_probs=18.6
Q ss_pred ccCCCCCCCCeeeeecCCCCceeee-cCCCcc
Q 007642 231 KWCPAPGCDYAVDFVVGSGNYDVTC-RCSYSF 261 (595)
Q Consensus 231 ~~CP~p~C~~~i~~~~~~~~~~v~C-~C~~~f 261 (595)
.+|| .|+..+.+..+.....+.| .|++.|
T Consensus 2 ~FCP--~Cgn~Live~g~~~~rf~C~tCpY~~ 31 (105)
T KOG2906|consen 2 LFCP--TCGNMLIVESGESCNRFSCRTCPYVF 31 (105)
T ss_pred cccC--CCCCEEEEecCCeEeeEEcCCCCcee
Confidence 4798 4988887765444455667 665443
No 232
>COG1594 RPB9 DNA-directed RNA polymerase, subunit M/Transcription elongation factor TFIIS [Transcription]
Probab=28.62 E-value=37 Score=30.14 Aligned_cols=28 Identities=21% Similarity=0.645 Sum_probs=18.7
Q ss_pred ccCCCCCcceee--cCCCCcccccCCCccee
Q 007642 300 KPCPRCKRPIEK--NQGCMHMTCTPPCKFEF 328 (595)
Q Consensus 300 K~CPkC~~~IEK--~~GCnhmtC~~~C~~~F 328 (595)
+-||+|+.++.- .++=+-+.|+ +||+.+
T Consensus 3 ~FCp~Cgsll~p~~~~~~~~l~C~-kCgye~ 32 (113)
T COG1594 3 RFCPKCGSLLYPKKDDEGGKLVCR-KCGYEE 32 (113)
T ss_pred cccCCccCeeEEeEcCCCcEEECC-CCCcch
Confidence 679999988874 1122277888 676653
No 233
>KOG0825 consensus PHD Zn-finger protein [General function prediction only]
Probab=28.62 E-value=30 Score=40.18 Aligned_cols=53 Identities=13% Similarity=0.170 Sum_probs=32.5
Q ss_pred ccccccccccccC--CCceecC---CCCcccHhHHHHHHhccccCCCCccccccCCCcCCCcc
Q 007642 141 EMTCGICFENYPS--DRLLAAA---CGHPFCSSCWTGYISTAINDGPGCLMLRCPDPSCGAAV 198 (595)
Q Consensus 141 ~~~C~IC~e~~~~--~~~~~l~---CgH~fC~~C~~~yi~~~i~~g~~~~~i~CP~~~C~~~v 198 (595)
..+|.||.-.+.. +-.-.++ |+|.||..||..+....+... +.|-++.|..-|
T Consensus 96 s~Ss~~C~~E~S~~~ds~~i~P~~~~~~~~CP~Ci~s~~DqL~~~~-----k~c~H~FC~~Ci 153 (1134)
T KOG0825|consen 96 SDTSPVCEKEHSPDVDSSNICPVQTHVENQCPNCLKSCNDQLEESE-----KHTAHYFCEECV 153 (1134)
T ss_pred ccccchhheecCCcccccCcCchhhhhhhhhhHHHHHHHHHhhccc-----cccccccHHHHh
Confidence 3455555544422 1123334 999999999999988766543 455555676543
No 234
>KOG1493 consensus Anaphase-promoting complex (APC), subunit 11 [Cell cycle control, cell division, chromosome partitioning; Posttranslational modification, protein turnover, chaperones]
Probab=28.56 E-value=18 Score=29.65 Aligned_cols=48 Identities=33% Similarity=0.753 Sum_probs=33.2
Q ss_pred ccccccccccC---------CC-ceec-CCCCcccHhHHHHHHhccccCCCCccccccCCCcCCCcc
Q 007642 143 TCGICFENYPS---------DR-LLAA-ACGHPFCSSCWTGYISTAINDGPGCLMLRCPDPSCGAAV 198 (595)
Q Consensus 143 ~C~IC~e~~~~---------~~-~~~l-~CgH~fC~~C~~~yi~~~i~~g~~~~~i~CP~~~C~~~v 198 (595)
+|+||.-.|.. ++ |..+ -|.|.|-.-|+..++.+.-++| .|| -|+..+
T Consensus 22 ~CGiCRm~Fdg~Cp~Ck~PgDdCPLv~G~C~h~fh~hCI~~wl~~~tsq~------~CP--mcRq~~ 80 (84)
T KOG1493|consen 22 TCGICRMPFDGCCPDCKLPGDDCPLVWGYCLHAFHAHCILKWLNTPTSQG------QCP--MCRQTW 80 (84)
T ss_pred ccceEecccCCcCCCCcCCCCCCccHHHHHHHHHHHHHHHHHhcCccccc------cCC--cchhee
Confidence 67777655432 22 2222 4999999999999998866544 588 687654
No 235
>TIGR00599 rad18 DNA repair protein rad18. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=28.13 E-value=19 Score=39.10 Aligned_cols=32 Identities=28% Similarity=0.685 Sum_probs=23.2
Q ss_pred ccCCCCCcceeecCCCCcccccCCCcceeeecccccccC
Q 007642 300 KPCPRCKRPIEKNQGCMHMTCTPPCKFEFCWLCLGQWSD 338 (595)
Q Consensus 300 K~CPkC~~~IEK~~GCnhmtC~~~C~~~FCw~C~~~~~~ 338 (595)
-.||.|...+. +.+. . .|+|.||..|...|-.
T Consensus 27 l~C~IC~d~~~-----~Pvi-t-pCgH~FCs~CI~~~l~ 58 (397)
T TIGR00599 27 LRCHICKDFFD-----VPVL-T-SCSHTFCSLCIRRCLS 58 (397)
T ss_pred cCCCcCchhhh-----CccC-C-CCCCchhHHHHHHHHh
Confidence 58999987764 2332 3 5999999999887643
No 236
>smart00659 RPOLCX RNA polymerase subunit CX. present in RNA polymerase I, II and III
Probab=27.91 E-value=50 Score=24.17 Aligned_cols=25 Identities=24% Similarity=0.587 Sum_probs=13.0
Q ss_pred cCCCCCcceeecCCCCcccccCCCcce
Q 007642 301 PCPRCKRPIEKNQGCMHMTCTPPCKFE 327 (595)
Q Consensus 301 ~CPkC~~~IEK~~GCnhmtC~~~C~~~ 327 (595)
.|..|+..++...+ .-+.|+ .||+.
T Consensus 4 ~C~~Cg~~~~~~~~-~~irC~-~CG~r 28 (44)
T smart00659 4 ICGECGRENEIKSK-DVVRCR-ECGYR 28 (44)
T ss_pred ECCCCCCEeecCCC-CceECC-CCCce
Confidence 46666665554432 335565 45543
No 237
>KOG0943 consensus Predicted ubiquitin-protein ligase/hyperplastic discs protein, HECT superfamily [Posttranslational modification, protein turnover, chaperones]
Probab=27.74 E-value=41 Score=40.99 Aligned_cols=7 Identities=43% Similarity=0.648 Sum_probs=2.9
Q ss_pred HHccccc
Q 007642 519 LENGLSD 525 (595)
Q Consensus 519 le~~l~~ 525 (595)
||.|-..
T Consensus 2476 lesghaP 2482 (3015)
T KOG0943|consen 2476 LESGHAP 2482 (3015)
T ss_pred cccCCCc
Confidence 4444433
No 238
>PF03604 DNA_RNApol_7kD: DNA directed RNA polymerase, 7 kDa subunit; InterPro: IPR006591 DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Each class of RNA polymerase is assembled from 9 to 15 different polypeptides. Rbp10 (RNA polymerase CX) is a domain found in RNA polymerase subunit 10; present in RNA polymerase I, II and III.; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 2PMZ_Z 3HKZ_X 2NVX_L 3S1Q_L 2JA6_L 3S17_L 3HOW_L 3HOV_L 3PO2_L 3HOZ_L ....
Probab=27.36 E-value=49 Score=22.51 Aligned_cols=25 Identities=24% Similarity=0.651 Sum_probs=12.5
Q ss_pred cCCCCCcceeecCCCCcccccCCCcce
Q 007642 301 PCPRCKRPIEKNQGCMHMTCTPPCKFE 327 (595)
Q Consensus 301 ~CPkC~~~IEK~~GCnhmtC~~~C~~~ 327 (595)
.|..|+..++-..+ ..+.|+ .||+.
T Consensus 2 ~C~~Cg~~~~~~~~-~~irC~-~CG~R 26 (32)
T PF03604_consen 2 ICGECGAEVELKPG-DPIRCP-ECGHR 26 (32)
T ss_dssp BESSSSSSE-BSTS-STSSBS-SSS-S
T ss_pred CCCcCCCeeEcCCC-CcEECC-cCCCe
Confidence 35666666663332 346666 56654
No 239
>COG5194 APC11 Component of SCF ubiquitin ligase and anaphase-promoting complex [Posttranslational modification, protein turnover, chaperones / Cell division and chromosome partitioning]
Probab=27.02 E-value=56 Score=27.10 Aligned_cols=28 Identities=29% Similarity=0.675 Sum_probs=21.7
Q ss_pred CCCCcccHhHHHHHHhccccCCCCccccccCCCcCCCcc
Q 007642 160 ACGHPFCSSCWTGYISTAINDGPGCLMLRCPDPSCGAAV 198 (595)
Q Consensus 160 ~CgH~fC~~C~~~yi~~~i~~g~~~~~i~CP~~~C~~~v 198 (595)
-|.|.|...||..++.+ .| .|| -++..+
T Consensus 53 ~CnHaFH~HCI~rWL~T---k~------~CP--ld~q~w 80 (88)
T COG5194 53 VCNHAFHDHCIYRWLDT---KG------VCP--LDRQTW 80 (88)
T ss_pred ecchHHHHHHHHHHHhh---CC------CCC--CCCcee
Confidence 49999999999999987 22 588 565544
No 240
>KOG2979 consensus Protein involved in DNA repair [General function prediction only]
Probab=26.97 E-value=61 Score=32.88 Aligned_cols=48 Identities=17% Similarity=0.393 Sum_probs=35.3
Q ss_pred ccccccccccccCCCceecCCCCcccHhHHHHHHhccccCCCCccccccCCCcCCC
Q 007642 141 EMTCGICFENYPSDRLLAAACGHPFCSSCWTGYISTAINDGPGCLMLRCPDPSCGA 196 (595)
Q Consensus 141 ~~~C~IC~e~~~~~~~~~l~CgH~fC~~C~~~yi~~~i~~g~~~~~i~CP~~~C~~ 196 (595)
.+.|||=+-.+ ...+++..|||.|=++=+..++... ..++||..+|..
T Consensus 176 s~rdPis~~~I-~nPviSkkC~HvydrDsI~~~l~~~-------~~i~CPv~gC~~ 223 (262)
T KOG2979|consen 176 SNRDPISKKPI-VNPVISKKCGHVYDRDSIMQILCDE-------ITIRCPVLGCEN 223 (262)
T ss_pred cccCchhhhhh-hchhhhcCcCcchhhhhHHHHhccC-------ceeecccccCCc
Confidence 35688865443 1344677899999999999887542 268999999983
No 241
>PF08792 A2L_zn_ribbon: A2L zinc ribbon domain; InterPro: IPR014900 This zinc ribbon protein is found associated with some viral A2L transcription factors [].
Probab=26.96 E-value=57 Score=22.34 Aligned_cols=11 Identities=27% Similarity=0.561 Sum_probs=8.8
Q ss_pred ccCCCCCccee
Q 007642 300 KPCPRCKRPIE 310 (595)
Q Consensus 300 K~CPkC~~~IE 310 (595)
+.|+.|+....
T Consensus 4 ~~C~~C~~~~i 14 (33)
T PF08792_consen 4 KKCSKCGGNGI 14 (33)
T ss_pred eEcCCCCCCeE
Confidence 78998887766
No 242
>PRK14714 DNA polymerase II large subunit; Provisional
Probab=26.85 E-value=34 Score=42.05 Aligned_cols=30 Identities=23% Similarity=0.608 Sum_probs=22.6
Q ss_pred ccCCCCCcceeecCCCCcccccCCCcce-----eeecccccc
Q 007642 300 KPCPRCKRPIEKNQGCMHMTCTPPCKFE-----FCWLCLGQW 336 (595)
Q Consensus 300 K~CPkC~~~IEK~~GCnhmtC~~~C~~~-----FCw~C~~~~ 336 (595)
..||+|+..+-. -+|. .||.. +|-.|+...
T Consensus 668 rkCPkCG~~t~~------~fCP-~CGs~te~vy~CPsCGaev 702 (1337)
T PRK14714 668 RRCPSCGTETYE------NRCP-DCGTHTEPVYVCPDCGAEV 702 (1337)
T ss_pred EECCCCCCcccc------ccCc-ccCCcCCCceeCccCCCcc
Confidence 789999997653 2887 78866 488888754
No 243
>PF09788 Tmemb_55A: Transmembrane protein 55A; InterPro: IPR019178 Members of this family catalyse the hydrolysis of the 4-position phosphate of phosphatidylinositol 4,5-bisphosphate, in the reaction: 1-phosphatidyl-myo-inositol 4,5-bisphosphate + H(2)O = 1-phosphatidyl-1D-myo-inositol 5-phosphate + phosphate.
Probab=26.06 E-value=64 Score=32.71 Aligned_cols=19 Identities=21% Similarity=0.599 Sum_probs=15.3
Q ss_pred CcccCCCCCCCCeeeeecC
Q 007642 229 KTKWCPAPGCDYAVDFVVG 247 (595)
Q Consensus 229 ~~~~CP~p~C~~~i~~~~~ 247 (595)
..+-||.|+|.++|...+.
T Consensus 122 ~rIaCPRp~CkRiI~L~~~ 140 (256)
T PF09788_consen 122 QRIACPRPNCKRIINLGPS 140 (256)
T ss_pred ccccCCCCCCcceEEeCCc
Confidence 4578999999999976543
No 244
>KOG3268 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=25.91 E-value=53 Score=31.37 Aligned_cols=57 Identities=23% Similarity=0.612 Sum_probs=34.6
Q ss_pred ccccccccccccC-C--C--ceecCCCCcccHhHHHHHHhccccCCCC--ccccccCCCcCCCccc
Q 007642 141 EMTCGICFENYPS-D--R--LLAAACGHPFCSSCWTGYISTAINDGPG--CLMLRCPDPSCGAAVG 199 (595)
Q Consensus 141 ~~~C~IC~e~~~~-~--~--~~~l~CgH~fC~~C~~~yi~~~i~~g~~--~~~i~CP~~~C~~~v~ 199 (595)
...|+||+-..-. . + --...||..|..-|+..|+..-+....+ +..=.|| -|...+.
T Consensus 165 ~~~cgicyayqldGTipDqtCdN~qCgkpFHqiCL~dWLRgilTsRQSFdiiFGeCP--YCS~Pia 228 (234)
T KOG3268|consen 165 LGACGICYAYQLDGTIPDQTCDNIQCGKPFHQICLTDWLRGILTSRQSFDIIFGECP--YCSDPIA 228 (234)
T ss_pred hhcccceeeeecCCccccccccccccCCcHHHHHHHHHHHHHhhccceeeeeeccCC--CCCCcce
Confidence 3457777753211 1 1 1234699999999999999876554331 1122588 6876654
No 245
>KOG2391 consensus Vacuolar sorting protein/ubiquitin receptor VPS23 [Posttranslational modification, protein turnover, chaperones; Intracellular trafficking, secretion, and vesicular transport]
Probab=25.82 E-value=8.3e+02 Score=26.04 Aligned_cols=20 Identities=10% Similarity=0.170 Sum_probs=11.2
Q ss_pred HHHHHHHHHHHHhCCCHHHH
Q 007642 78 RQEEDITRISTVLSISKVAA 97 (595)
Q Consensus 78 ~~~~~i~~v~~vl~i~~~~a 97 (595)
..++.+..|+...++.|..+
T Consensus 21 ~~~~~l~lls~~~sL~P~t~ 40 (365)
T KOG2391|consen 21 TRQDLLNLLSSFKSLRPKTD 40 (365)
T ss_pred HHHHHHHHHHhccccCcccc
Confidence 34455666666666655443
No 246
>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=25.76 E-value=43 Score=33.49 Aligned_cols=54 Identities=20% Similarity=0.321 Sum_probs=33.1
Q ss_pred cccCCCcCCCcc-chhHHhhhcChHHHHHHHHHHHHHhhhhCCCcccCCCCCCCCeeee
Q 007642 187 LRCPDPSCGAAV-GQDMIYLLSSDEDKVKYNRYFIRSYVEDNRKTKWCPAPGCDYAVDF 244 (595)
Q Consensus 187 i~CP~~~C~~~v-~~~~i~~ll~~e~~eky~~~~~~~~v~~~~~~~~CP~p~C~~~i~~ 244 (595)
-+|| .|+.-. ....++-|++++-+.+.-..-....+.. ....||.|+|+.++..
T Consensus 11 ~~CP--vCksDrYLnPdik~linPECyHrmCESCvdRIFs~--GpAqCP~~gC~kILRK 65 (314)
T COG5220 11 RRCP--VCKSDRYLNPDIKILINPECYHRMCESCVDRIFSR--GPAQCPYKGCGKILRK 65 (314)
T ss_pred ccCC--ccccccccCCCeEEEECHHHHHHHHHHHHHHHhcC--CCCCCCCccHHHHHHH
Confidence 4799 787643 2234566778776655544333333333 3468999999977653
No 247
>PLN02638 cellulose synthase A (UDP-forming), catalytic subunit
Probab=25.72 E-value=49 Score=40.25 Aligned_cols=55 Identities=25% Similarity=0.658 Sum_probs=36.3
Q ss_pred CCCeeeeecCCCCceeee-cCCCcccccCCcccCCCCCchhHHHHHHhhhHhHHhHHHHHhcCccCCCCCcceeecCCCC
Q 007642 238 CDYAVDFVVGSGNYDVTC-RCSYSFCWNCTEEAHRPVDCDTVAKWVLKNSAESENMNWILANSKPCPRCKRPIEKNQGCM 316 (595)
Q Consensus 238 C~~~i~~~~~~~~~~v~C-~C~~~fC~~C~~~~H~p~~C~~~~~~~~k~~~~~e~~~wi~~ntK~CPkC~~~IEK~~GCn 316 (595)
|+--|... ..+.+-|-| .|++-.|..|-+ +.. ...++-||+|+....+-.||.
T Consensus 23 CGD~vg~~-~~Ge~FVAC~eC~FPVCrpCYE----------YEr---------------~eG~q~CPqCktrYkr~kgsp 76 (1079)
T PLN02638 23 CGDNVGKT-VDGEPFVACDVCAFPVCRPCYE----------YER---------------KDGNQSCPQCKTKYKRHKGSP 76 (1079)
T ss_pred cccccCcC-CCCCEEEEeccCCCccccchhh----------hhh---------------hcCCccCCccCCchhhhcCCC
Confidence 66555444 346678999 899999987762 211 012278888888888666666
Q ss_pred cc
Q 007642 317 HM 318 (595)
Q Consensus 317 hm 318 (595)
.+
T Consensus 77 rv 78 (1079)
T PLN02638 77 AI 78 (1079)
T ss_pred Cc
Confidence 54
No 248
>KOG2930 consensus SCF ubiquitin ligase, Rbx1 component [Posttranslational modification, protein turnover, chaperones]
Probab=25.26 E-value=43 Score=29.13 Aligned_cols=17 Identities=29% Similarity=0.798 Sum_probs=15.7
Q ss_pred CCCCcccHhHHHHHHhc
Q 007642 160 ACGHPFCSSCWTGYIST 176 (595)
Q Consensus 160 ~CgH~fC~~C~~~yi~~ 176 (595)
.|.|.|..-||..++.+
T Consensus 80 ~CNHaFH~hCisrWlkt 96 (114)
T KOG2930|consen 80 VCNHAFHFHCISRWLKT 96 (114)
T ss_pred ecchHHHHHHHHHHHhh
Confidence 49999999999999976
No 249
>PRK10220 hypothetical protein; Provisional
Probab=25.23 E-value=47 Score=29.18 Aligned_cols=29 Identities=24% Similarity=0.701 Sum_probs=16.6
Q ss_pred ccCCCCCcceeecCCCCcccccCCCcceeeecccccccC
Q 007642 300 KPCPRCKRPIEKNQGCMHMTCTPPCKFEFCWLCLGQWSD 338 (595)
Q Consensus 300 K~CPkC~~~IEK~~GCnhmtC~~~C~~~FCw~C~~~~~~ 338 (595)
-+||+|..-.--..|= .+.| .-|+.+|..
T Consensus 4 P~CP~C~seytY~d~~-~~vC---------peC~hEW~~ 32 (111)
T PRK10220 4 PHCPKCNSEYTYEDNG-MYIC---------PECAHEWND 32 (111)
T ss_pred CcCCCCCCcceEcCCC-eEEC---------CcccCcCCc
Confidence 5899998755433332 2444 455556654
No 250
>PF14149 YhfH: YhfH-like protein
Probab=24.98 E-value=7.2 Score=27.42 Aligned_cols=25 Identities=32% Similarity=0.877 Sum_probs=19.9
Q ss_pred CccCCCCCcceeecCCCCcccccCCC
Q 007642 299 SKPCPRCKRPIEKNQGCMHMTCTPPC 324 (595)
Q Consensus 299 tK~CPkC~~~IEK~~GCnhmtC~~~C 324 (595)
.|.||.|+..|+-..-|-.+.|. .|
T Consensus 13 ~K~C~~CG~~i~EQ~E~Y~n~C~-~C 37 (37)
T PF14149_consen 13 PKKCTECGKEIEEQAECYGNECD-RC 37 (37)
T ss_pred CcccHHHHHHHHHHHHHHhCcCC-CC
Confidence 49999999999877777777776 44
No 251
>TIGR02159 PA_CoA_Oxy4 phenylacetate-CoA oxygenase, PaaJ subunit. Phenylacetate-CoA oxygenase is comprised of a five gene complex responsible for the hydroxylation of phenylacetate-CoA (PA-CoA) as the second catabolic step in phenylacetic acid (PA) degradation. Although the exact function of this enzyme has not been determined, it has been shown to be required for phenylacetic acid degradation and has been proposed to function in a multicomponent oxygenase acting on phenylacetate-CoA.
Probab=24.93 E-value=48 Score=30.90 Aligned_cols=94 Identities=13% Similarity=0.200 Sum_probs=50.4
Q ss_pred HHHHHHHHHHHHHHHhCCCHHHHHHHHHHcCCChhhhHHHhhhcHHHHHHHhCCCCCCCCCCCC----CCcccccccccc
Q 007642 75 IRQRQEEDITRISTVLSISKVAASILLRFYNWSVSKVHDEWFADEERVRKAVGLLEKPAVQFPD----GEEMTCGICFEN 150 (595)
Q Consensus 75 i~~~~~~~i~~v~~vl~i~~~~a~~LL~~~~W~~~~l~e~~~~~~~~~~~~~gl~~~~~~~~~~----~~~~~C~IC~e~ 150 (595)
+...++++|.+.-..+++..... .+-..--|+.+.+.+. ..+-+..+||-.......+. .....||-|-..
T Consensus 40 a~e~L~~~I~~aL~~~Gv~~V~V-~i~~~p~Wt~d~it~~----gr~~l~~~giapp~~~~~~~~~~~~~~~~cp~c~s~ 114 (146)
T TIGR02159 40 ALEVIRQDIRDAVRALGVEVVEV-STSLDPPWTTDWITED----AREKLREYGIAPPAGHYVVGVSPEPPSVQCPRCGSA 114 (146)
T ss_pred hHHHHHHHHHHHHHhcCCCeEEE-eEeeCCCCChHHCCHH----HHHHHHhcCccCCCccCCCcccCCCCCCcCCCCCCC
Confidence 34444444444333346543222 2345677998887764 23345567875432211111 124789999876
Q ss_pred ccC--CCceecCCC-CcccHhHHHHH
Q 007642 151 YPS--DRLLAAACG-HPFCSSCWTGY 173 (595)
Q Consensus 151 ~~~--~~~~~l~Cg-H~fC~~C~~~y 173 (595)
... +.+-+..|. ..+|.+|..-|
T Consensus 115 ~t~~~s~fg~t~cka~~~c~~c~epf 140 (146)
T TIGR02159 115 DTTITSIFGPTACKALYRCRACKEPF 140 (146)
T ss_pred CcEeecCCCChhhHHHhhhhhhCCcH
Confidence 421 334456686 56888887654
No 252
>KOG1451 consensus Oligophrenin-1 and related Rho GTPase-activating proteins [Signal transduction mechanisms]
Probab=24.85 E-value=1.1e+03 Score=27.14 Aligned_cols=30 Identities=30% Similarity=0.432 Sum_probs=22.2
Q ss_pred CCcHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 007642 491 SKDFNEFRTKLAGLTSVTRNYFENLVRALE 520 (595)
Q Consensus 491 ~~~~~~~~~~l~~lt~~~~~~~~~l~~~le 520 (595)
.++|..|+++|...-..|++.|..--...|
T Consensus 217 ~qDF~pfk~qlq~s~QnTrn~f~~Tr~E~E 246 (812)
T KOG1451|consen 217 HQDFKPFKDQLQTSVQNTRNNFNATRAEAE 246 (812)
T ss_pred HhhhhhHHHHHHHHHHHhhhcccchHHHHH
Confidence 378999999998777788888765444444
No 253
>COG0777 AccD Acetyl-CoA carboxylase beta subunit [Lipid metabolism]
Probab=24.30 E-value=26 Score=35.93 Aligned_cols=28 Identities=18% Similarity=0.548 Sum_probs=20.1
Q ss_pred ccCCCCCcceee-cCCCCcccccCCCccee
Q 007642 300 KPCPRCKRPIEK-NQGCMHMTCTPPCKFEF 328 (595)
Q Consensus 300 K~CPkC~~~IEK-~~GCnhmtC~~~C~~~F 328 (595)
-+||.|+..+-+ .-+=|...|. +|+|+|
T Consensus 29 ~KCp~c~~~~y~~eL~~n~~vcp-~c~~h~ 57 (294)
T COG0777 29 TKCPSCGEMLYRKELESNLKVCP-KCGHHM 57 (294)
T ss_pred eECCCccceeeHHHHHhhhhccc-ccCccc
Confidence 789999988864 3566677776 665544
No 254
>PF01783 Ribosomal_L32p: Ribosomal L32p protein family; InterPro: IPR002677 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. Ribosomal protein L32p is part of the 50S ribosomal subunit. This family is found in both prokaryotes and eukaryotes. Ribosomal protein L32 of yeast binds to and regulates the splicing and the translation of the transcript of its own gene [].; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0015934 large ribosomal subunit; PDB: 3PYT_2 3F1F_5 3PYV_2 3D5B_5 3MRZ_2 3D5D_5 3F1H_5 1VSP_Y 3PYR_2 3MS1_2 ....
Probab=24.30 E-value=41 Score=25.89 Aligned_cols=22 Identities=36% Similarity=0.857 Sum_probs=15.2
Q ss_pred cCccCCCCCcceeecCCCCcccccCCCc
Q 007642 298 NSKPCPRCKRPIEKNQGCMHMTCTPPCK 325 (595)
Q Consensus 298 ntK~CPkC~~~IEK~~GCnhmtC~~~C~ 325 (595)
+.-.||.|+.+.. .|..|. .||
T Consensus 25 ~l~~c~~cg~~~~-----~H~vc~-~cG 46 (56)
T PF01783_consen 25 NLVKCPNCGEPKL-----PHRVCP-SCG 46 (56)
T ss_dssp SEEESSSSSSEES-----TTSBCT-TTB
T ss_pred ceeeeccCCCEec-----ccEeeC-CCC
Confidence 3468999998777 556665 454
No 255
>PRK06568 F0F1 ATP synthase subunit B; Validated
Probab=24.25 E-value=6e+02 Score=23.85 Aligned_cols=55 Identities=16% Similarity=0.190 Sum_probs=32.5
Q ss_pred HHHHHHHHHHHHHhHHHHHHHHHHHHHHHhhcCCCCCcHHHHHHHHHHHHH-HHHHHHHHH
Q 007642 456 RQFFEYLQGEAESGLERLHQCAEKELQIYLNADGPSKDFNEFRTKLAGLTS-VTRNYFENL 515 (595)
Q Consensus 456 ~~~fe~~Q~~le~~~E~L~~~le~e~~~~~~~~~~~~~~~~~~~~l~~lt~-~~~~~~~~l 515 (595)
..+.+....+++..++++.+...+++..-.. .-+.++|..+..|.. +..+||..+
T Consensus 84 ~~~~~ea~~eA~~ea~r~~~~A~~~Ie~Ek~-----~Al~elr~eva~Lav~iAsk~~~~~ 139 (154)
T PRK06568 84 KKIIQEKTKEIEEFLEHKKSDAIQLIQNQKS-----TASKELQDEFCDEVIKLVSEYFQSV 139 (154)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-----HHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 3444445555555555555554444433222 346688888888876 778888754
No 256
>PF09026 CENP-B_dimeris: Centromere protein B dimerisation domain; InterPro: IPR015115 Centromere protein B (CENP-B) interacts with centromeric heterochromatin in chromosomes and binds to a specific subset of alphoid satellite DNA, called the CENP-B box. CENP-B may organise arrays of centromere satellite DNA into a higher order structure, which then directs centromere formation and kinetochore assembly in mammalian chromosomes. The CENP-B dimerisation domain is composed of two alpha-helices, which are folded into an antiparallel configuration. Dimerisation of CENP-B is mediated by this domain, in which monomers dimerise to form a symmetrical, antiparallel, four-helix bundle structure with a large hydrophobic patch in which 23 residues of one monomer form van der Waals contacts with the other monomer. This CENP-B dimer configuration may be suitable for capturing two distant CENP-B boxes during centromeric heterochromatin formation []. ; GO: 0003677 DNA binding, 0003682 chromatin binding, 0006355 regulation of transcription, DNA-dependent, 0000775 chromosome, centromeric region, 0005634 nucleus; PDB: 1UFI_A.
Probab=23.92 E-value=26 Score=30.03 Aligned_cols=6 Identities=50% Similarity=0.429 Sum_probs=1.5
Q ss_pred eCHHHH
Q 007642 70 LTEADI 75 (595)
Q Consensus 70 l~~~~i 75 (595)
|+.-.|
T Consensus 60 ltSf~i 65 (101)
T PF09026_consen 60 LTSFPI 65 (101)
T ss_dssp HCTS--
T ss_pred hhccch
Confidence 333333
No 257
>PF01599 Ribosomal_S27: Ribosomal protein S27a; InterPro: IPR002906 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. This family of ribosomal proteins consists mainly of the 40S ribosomal protein S27a which is synthesized as a C-terminal extension of ubiquitin (CEP) (IPR000626 from INTERPRO). The S27a domain compromises the C-terminal half of the protein. The synthesis of ribosomal proteins as extensions of ubiquitin promotes their incorporation into nascent ribosomes by a transient metabolic stabilisation and is required for efficient ribosome biogenesis []. The ribosomal extension protein S27a contains a basic region that is proposed to form a zinc finger; its fusion gene is proposed as a mechanism to maintain a fixed ratio between ubiquitin necessary for degrading proteins and ribosomes a source of proteins [].; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 2K4X_A 3U5C_f 3U5G_f 2XZN_9 2XZM_9.
Probab=23.63 E-value=46 Score=24.80 Aligned_cols=26 Identities=27% Similarity=0.634 Sum_probs=17.4
Q ss_pred ccCC--CCCcceeecCCCCcccccCCCcc
Q 007642 300 KPCP--RCKRPIEKNQGCMHMTCTPPCKF 326 (595)
Q Consensus 300 K~CP--kC~~~IEK~~GCnhmtC~~~C~~ 326 (595)
+.|| .|+.-+--..--+..+|. +|++
T Consensus 19 k~CP~~~CG~GvFMA~H~dR~~CG-KCg~ 46 (47)
T PF01599_consen 19 KECPSPRCGAGVFMAEHKDRHYCG-KCGY 46 (47)
T ss_dssp EE-TSTTTTSSSEEEE-SSEEEET-TTSS
T ss_pred hcCCCcccCCceEeeecCCCccCC-Cccc
Confidence 7899 999877544445667887 6764
No 258
>KOG1829 consensus Uncharacterized conserved protein, contains C1, PH and RUN domains [Signal transduction mechanisms]
Probab=23.57 E-value=5e+02 Score=29.83 Aligned_cols=34 Identities=21% Similarity=0.314 Sum_probs=26.5
Q ss_pred ccCCCCCcceeecCCCCcccccCCCcceeeecccc
Q 007642 300 KPCPRCKRPIEKNQGCMHMTCTPPCKFEFCWLCLG 334 (595)
Q Consensus 300 K~CPkC~~~IEK~~GCnhmtC~~~C~~~FCw~C~~ 334 (595)
-.|-.|+.+|....==..=+|. .+|..||-.|..
T Consensus 341 ~~CAgC~~~i~~~~~~~~R~C~-y~G~y~C~~Ch~ 374 (580)
T KOG1829|consen 341 FRCAGCGHTIGPDLEQRPRLCR-YLGKYFCDCCHQ 374 (580)
T ss_pred ceecccCCCcccccccchhHhh-hhhhhhCchhcc
Confidence 4899999999954333446788 899999999964
No 259
>PF07417 Crl: Transcriptional regulator Crl; InterPro: IPR009986 This family contains the bacterial transcriptional regulator Crl (approximately 130 residues long). This is a transcriptional regulator of the csgA curlin subunit gene for curli fibres that are found on the surface of certain bacteria [].These proteins bind to the sigma-S subunit of RNA polymerase, activating expression of sigma-S-regulated genes. They also stimulate RNA polymerase holoenzyme formation and may bind to several other sigma factors, such as sigma-70 and sigma-32.; GO: 0016987 sigma factor activity, 0045893 positive regulation of transcription, DNA-dependent, 0005737 cytoplasm; PDB: 3RPJ_A.
Probab=23.40 E-value=55 Score=29.47 Aligned_cols=45 Identities=22% Similarity=0.346 Sum_probs=27.9
Q ss_pred hhhhhhhcccCccchhhHHHHHHHHHHHHHhHHHHHHHHHHHHHH
Q 007642 439 KWTYAYGYYLPDHEHAKRQFFEYLQGEAESGLERLHQCAEKELQI 483 (595)
Q Consensus 439 ~~sy~~~yy~~~~~~~~~~~fe~~Q~~le~~~E~L~~~le~e~~~ 483 (595)
.|.|-+|.|-...+-....|=...|.+++..++..|+.|..-+++
T Consensus 66 ~y~Y~~Glydk~G~W~~~~i~~~~~~~v~~Tl~~Fh~kL~~~L~~ 110 (125)
T PF07417_consen 66 EYRYQFGLYDKEGNWQAEKIKKEVQEEVERTLRDFHQKLVELLEE 110 (125)
T ss_dssp EEEEEEEEE-TTS-EES----HHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred EEEEeeccccCCCCeeecCCCHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 466777778755543344444777888888888888877776665
No 260
>PF07058 Myosin_HC-like: Myosin II heavy chain-like; InterPro: IPR009768 This family represents a conserved region within a number of myosin II heavy chain-like proteins that seem to be specific to Arabidopsis thaliana.
Probab=23.37 E-value=8.8e+02 Score=25.47 Aligned_cols=37 Identities=22% Similarity=0.346 Sum_probs=24.2
Q ss_pred HHHHHHHHHHHHH------HHHHHHHHHHHHHHcccccccccc
Q 007642 494 FNEFRTKLAGLTS------VTRNYFENLVRALENGLSDVDTHA 530 (595)
Q Consensus 494 ~~~~~~~l~~lt~------~~~~~~~~l~~~le~~l~~~~~~~ 530 (595)
...+|++|+.-.+ .++..|.--++.||+||....+.+
T Consensus 124 mQ~LrDKLAiaERtAkaEaQLkeK~klRLK~LEe~Lk~~~s~~ 166 (351)
T PF07058_consen 124 MQQLRDKLAIAERTAKAEAQLKEKLKLRLKVLEEGLKGSSSNS 166 (351)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhccCCCCCC
Confidence 4455666554422 255667778899999999886543
No 261
>PF08271 TF_Zn_Ribbon: TFIIB zinc-binding; InterPro: IPR013137 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 motif found in transcription factor IIB (TFIIB). In eukaryotes the initiation of transcription of protein encoding genes by the polymerase II complexe (Pol II) is modulated by general and specific transcription factors. The general transcription factors operate through common promoters elements (such as the TATA box). At least seven different proteins associate to form the general transcription factors: TFIIA, -IIB, -IID, -IIE, -IIF, -IIG, and -IIH []. TFIIB and TFIID are responsible for promoter recognition and interaction with pol II; together with Pol II, they form a minimal initiation complex capable of transcription under certain conditions. The TATA box of a Pol II promoter is bound in the initiation complex by the TBP subunit of TFIID, which bends the DNA around the C-terminal domain of TFIIB whereas the N-terminal zinc finger of TFIIB interacts with Pol II [, ]. The TFIIB zinc finger adopts a zinc ribbon fold characterised by two beta-hairpins forming two structurally similar zinc-binding sub-sites []. The zinc finger contacts the rbp1 subunit of Pol II through its dock domain, a conserved region of about 70 amino acids located close to the polymerase active site []. In the Pol II complex this surface is located near the RNA exit groove. Interestingly this sequence is best conserved in the three polymerases that utilise a TFIIB-like general transcription factor (Pol II, Pol III, and archaeal RNA polymerase) but not in Pol I []. 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; PDB: 1VD4_A 1PFT_A 3K1F_M 3K7A_M 1RO4_A 1RLY_A 1DL6_A.
Probab=23.34 E-value=62 Score=23.22 Aligned_cols=8 Identities=38% Similarity=1.182 Sum_probs=5.5
Q ss_pred cCCCCCcc
Q 007642 301 PCPRCKRP 308 (595)
Q Consensus 301 ~CPkC~~~ 308 (595)
.||.|+..
T Consensus 2 ~Cp~Cg~~ 9 (43)
T PF08271_consen 2 KCPNCGSK 9 (43)
T ss_dssp SBTTTSSS
T ss_pred CCcCCcCC
Confidence 47777764
No 262
>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=23.33 E-value=57 Score=29.04 Aligned_cols=36 Identities=25% Similarity=0.534 Sum_probs=26.3
Q ss_pred cCccCCCCCcceeecCCCCcccccCCCcceeeeccccc
Q 007642 298 NSKPCPRCKRPIEKNQGCMHMTCTPPCKFEFCWLCLGQ 335 (595)
Q Consensus 298 ntK~CPkC~~~IEK~~GCnhmtC~~~C~~~FCw~C~~~ 335 (595)
+.+.|..|+.+.-...+.. ..|. .|++.+|-.|+..
T Consensus 53 ~~~~C~~C~~~fg~l~~~~-~~C~-~C~~~VC~~C~~~ 88 (118)
T PF02318_consen 53 GERHCARCGKPFGFLFNRG-RVCV-DCKHRVCKKCGVY 88 (118)
T ss_dssp CCSB-TTTS-BCSCTSTTC-EEET-TTTEEEETTSEEE
T ss_pred CCcchhhhCCcccccCCCC-CcCC-cCCccccCccCCc
Confidence 3478999998765555444 7888 8999999999865
No 263
>PF12861 zf-Apc11: Anaphase-promoting complex subunit 11 RING-H2 finger
Probab=23.25 E-value=26 Score=29.52 Aligned_cols=35 Identities=29% Similarity=0.737 Sum_probs=26.7
Q ss_pred ccCCCCCcceeecCCCCcccccCCCcceeeecccccccCC
Q 007642 300 KPCPRCKRPIEKNQGCMHMTCTPPCKFEFCWLCLGQWSDH 339 (595)
Q Consensus 300 K~CPkC~~~IEK~~GCnhmtC~~~C~~~FCw~C~~~~~~H 339 (595)
--||.|+.| ...|.-+.+. |++.|=..|...|-.-
T Consensus 33 g~Cp~Ck~P---gd~Cplv~g~--C~H~FH~hCI~kWl~~ 67 (85)
T PF12861_consen 33 GCCPDCKFP---GDDCPLVWGK--CSHNFHMHCILKWLST 67 (85)
T ss_pred cCCCCccCC---CCCCceeecc--CccHHHHHHHHHHHcc
Confidence 457888877 3467667775 9999999999999653
No 264
>PF07889 DUF1664: Protein of unknown function (DUF1664); InterPro: IPR012458 The members of this family are hypothetical plant proteins of unknown function. The region featured in this family is approximately 100 amino acids long.
Probab=23.06 E-value=5.7e+02 Score=23.20 Aligned_cols=17 Identities=18% Similarity=0.509 Sum_probs=10.7
Q ss_pred HHHHHHHHHHHcccccc
Q 007642 510 NYFENLVRALENGLSDV 526 (595)
Q Consensus 510 ~~~~~l~~~le~~l~~~ 526 (595)
..++.+|..||.-|..+
T Consensus 106 ~~v~~~V~~Le~ki~~i 122 (126)
T PF07889_consen 106 DSVQQMVEGLEGKIDEI 122 (126)
T ss_pred HHHHHHHHHHHHHHHHH
Confidence 34666777777666555
No 265
>COG3024 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=22.85 E-value=41 Score=26.66 Aligned_cols=13 Identities=38% Similarity=1.145 Sum_probs=11.5
Q ss_pred CccCCCCCcceee
Q 007642 299 SKPCPRCKRPIEK 311 (595)
Q Consensus 299 tK~CPkC~~~IEK 311 (595)
+.+||.|+++++.
T Consensus 7 ~v~CP~Cgkpv~w 19 (65)
T COG3024 7 TVPCPTCGKPVVW 19 (65)
T ss_pred cccCCCCCCcccc
Confidence 5899999999984
No 266
>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=22.74 E-value=58 Score=24.58 Aligned_cols=11 Identities=27% Similarity=0.803 Sum_probs=8.4
Q ss_pred ccccccccccc
Q 007642 141 EMTCGICFENY 151 (595)
Q Consensus 141 ~~~C~IC~e~~ 151 (595)
.|.||.|...+
T Consensus 2 ~f~CP~C~~~~ 12 (54)
T PF05605_consen 2 SFTCPYCGKGF 12 (54)
T ss_pred CcCCCCCCCcc
Confidence 57899998744
No 267
>COG4640 Predicted membrane protein [Function unknown]
Probab=22.74 E-value=4.9e+02 Score=28.32 Aligned_cols=16 Identities=25% Similarity=0.426 Sum_probs=10.3
Q ss_pred HHHHHHHHcccccccc
Q 007642 513 ENLVRALENGLSDVDT 528 (595)
Q Consensus 513 ~~l~~~le~~l~~~~~ 528 (595)
.+|+..|.+.-..|++
T Consensus 130 k~lf~eLndead~~as 145 (465)
T COG4640 130 KNLFHELNDEADSVAS 145 (465)
T ss_pred hhHHHHHhhhhhhhcc
Confidence 5677777766666644
No 268
>PF05285 SDA1: SDA1; InterPro: IPR007949 This domain consists of several SDA1 protein homologues. SDA1 is a Saccharomyces cerevisiae protein which is involved in the control of the actin cytoskeleton. The protein is essential for cell viability and is localised in the nucleus [].
Probab=22.54 E-value=1.1e+02 Score=32.37 Aligned_cols=8 Identities=38% Similarity=0.592 Sum_probs=3.4
Q ss_pred EeCHHHHH
Q 007642 69 VLTEADIR 76 (595)
Q Consensus 69 vl~~~~i~ 76 (595)
|||++|+.
T Consensus 189 ILT~eDF~ 196 (324)
T PF05285_consen 189 ILTPEDFA 196 (324)
T ss_pred CCCHHHHH
Confidence 34444443
No 269
>PHA02325 hypothetical protein
Probab=22.45 E-value=39 Score=26.66 Aligned_cols=12 Identities=33% Similarity=0.922 Sum_probs=9.3
Q ss_pred cCccCCCCCcce
Q 007642 298 NSKPCPRCKRPI 309 (595)
Q Consensus 298 ntK~CPkC~~~I 309 (595)
++|.||+|+..-
T Consensus 2 ~~k~CPkC~A~W 13 (72)
T PHA02325 2 DTKICPKCGARW 13 (72)
T ss_pred CccccCccCCEe
Confidence 468999998754
No 270
>PF05320 Pox_RNA_Pol_19: Poxvirus DNA-directed RNA polymerase 19 kDa subunit; InterPro: IPR007984 DNA-directed RNA polymerases 2.7.7.6 from EC (also known as DNA-dependent RNA polymerases) are responsible for the polymerisation of ribonucleotides into a sequence complementary to the template DNA. In eukaryotes, there are three different forms of DNA-directed RNA polymerases transcribing different sets of genes. Most RNA polymerases are multimeric enzymes and are composed of a variable number of subunits. The core RNA polymerase complex consists of five subunits (two alpha, one beta, one beta-prime and one omega) and is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. The core RNA polymerase complex forms a "crab claw"-like structure with an internal channel running along the full length []. The key functional sites of the enzyme, as defined by mutational and cross-linking analysis, are located on the inner wall of this channel. RNA synthesis follows after the attachment of RNA polymerase to a specific site, the promoter, on the template DNA strand. The RNA synthesis process continues until a termination sequence is reached. The RNA product, which is synthesised in the 5' to 3'direction, is known as the primary transcript. Eukaryotic nuclei contain three distinct types of RNA polymerases that differ in the RNA they synthesise: RNA polymerase I: located in the nucleoli, synthesises precursors of most ribosomal RNAs. RNA polymerase II: occurs in the nucleoplasm, synthesises mRNA precursors. RNA polymerase III: also occurs in the nucleoplasm, synthesises the precursors of 5S ribosomal RNA, the tRNAs, and a variety of other small nuclear and cytosolic RNAs. Eukaryotic cells are also known to contain separate mitochondrial and chloroplast RNA polymerases. Eukaryotic RNA polymerases, whose molecular masses vary in size from 500 to 700 kDa, contain two non-identical large (>100 kDa) subunits and an array of up to 12 different small (less than 50 kDa) subunits. The poxvirus DNA-directed RNA polymerase (2.7.7.6 from EC) catalyses the transcription of DNA into RNA. It consists of at least eight subunits, this is the 19 kDa subunit.; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent
Probab=22.14 E-value=31 Score=32.10 Aligned_cols=9 Identities=56% Similarity=0.781 Sum_probs=4.5
Q ss_pred ccccccccc
Q 007642 141 EMTCGICFE 149 (595)
Q Consensus 141 ~~~C~IC~e 149 (595)
+.+|||=-+
T Consensus 126 Eg~CPIVIe 134 (167)
T PF05320_consen 126 EGTCPIVIE 134 (167)
T ss_pred cCCCcEEEe
Confidence 445665443
No 271
>PF02724 CDC45: CDC45-like protein; InterPro: IPR003874 CDC45 is an essential gene required for initiation of DNA replication in Saccharomyces cerevisiae (cell division control protein 45), forming a complex with MCM5/CDC46. Homologs of CDC45 have been identified in human [], mouse and the smut fungus, Melampsora spp., (tsd2 protein) among others.; GO: 0006270 DNA-dependent DNA replication initiation
Probab=22.07 E-value=1.5e+02 Score=34.44 Aligned_cols=6 Identities=0% Similarity=-0.108 Sum_probs=2.4
Q ss_pred cCCCcc
Q 007642 193 SCGAAV 198 (595)
Q Consensus 193 ~C~~~v 198 (595)
.|++.+
T Consensus 352 ~~~Q~y 357 (622)
T PF02724_consen 352 QAQQKY 357 (622)
T ss_pred HHcCCc
Confidence 344433
No 272
>PF12325 TMF_TATA_bd: TATA element modulatory factor 1 TATA binding; InterPro: IPR022091 This is the C-terminal conserved coiled coil region of a family of TATA element modulatory factor 1 proteins conserved in eukaryotes []. The proteins bind to the TATA element of some RNA polymerase II promoters and repress their activity. by competing with the binding of TATA binding protein. TMF1_TATA_bd is the most conserved part of the TMFs []. TMFs are evolutionarily conserved golgins that bind Rab6, a ubiquitous ras-like GTP-binding Golgi protein, and contribute to Golgi organisation in animal [] and plant cells. The Rab6-binding domain appears to be the same region as this C-terminal family [].
Probab=21.90 E-value=5.9e+02 Score=22.88 Aligned_cols=24 Identities=21% Similarity=0.477 Sum_probs=15.3
Q ss_pred CcHHHHHHHHHHHHHHHHHHHHHH
Q 007642 492 KDFNEFRTKLAGLTSVTRNYFENL 515 (595)
Q Consensus 492 ~~~~~~~~~l~~lt~~~~~~~~~l 515 (595)
+...+++..|..+....+..+..|
T Consensus 96 E~veEL~~Dv~DlK~myr~Qi~~l 119 (120)
T PF12325_consen 96 EEVEELRADVQDLKEMYREQIDQL 119 (120)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHh
Confidence 456677788877766655555443
No 273
>PHA02825 LAP/PHD finger-like protein; Provisional
Probab=21.88 E-value=96 Score=29.26 Aligned_cols=49 Identities=20% Similarity=0.490 Sum_probs=34.0
Q ss_pred CccccccccccccCCCceecCCC--C---cccHhHHHHHHhccccCCCCccccccCCCcCCCccch
Q 007642 140 EEMTCGICFENYPSDRLLAAACG--H---PFCSSCWTGYISTAINDGPGCLMLRCPDPSCGAAVGQ 200 (595)
Q Consensus 140 ~~~~C~IC~e~~~~~~~~~l~Cg--H---~fC~~C~~~yi~~~i~~g~~~~~i~CP~~~C~~~v~~ 200 (595)
....|-||++... . ..-||. . ....+|+..|+... + ..+|| .|+..+..
T Consensus 7 ~~~~CRIC~~~~~-~--~~~PC~CkGs~k~VH~sCL~rWi~~s---~----~~~Ce--iC~~~Y~i 60 (162)
T PHA02825 7 MDKCCWICKDEYD-V--VTNYCNCKNENKIVHKECLEEWINTS---K----NKSCK--ICNGPYNI 60 (162)
T ss_pred CCCeeEecCCCCC-C--ccCCcccCCCchHHHHHHHHHHHhcC---C----CCccc--ccCCeEEE
Confidence 4567999998753 2 223554 3 45899999999853 2 57899 89887643
No 274
>PF14569 zf-UDP: Zinc-binding RING-finger; PDB: 1WEO_A.
Probab=21.88 E-value=1.3e+02 Score=24.96 Aligned_cols=50 Identities=22% Similarity=0.612 Sum_probs=19.7
Q ss_pred CCccccccccccccCC---Ccee-c-CCCCcccHhHHHHHHhccccCCCCccccccCCCcCCCcc
Q 007642 139 GEEMTCGICFENYPSD---RLLA-A-ACGHPFCSSCWTGYISTAINDGPGCLMLRCPDPSCGAAV 198 (595)
Q Consensus 139 ~~~~~C~IC~e~~~~~---~~~~-l-~CgH~fC~~C~~~yi~~~i~~g~~~~~i~CP~~~C~~~v 198 (595)
.....|.||-+.+..+ +++. . .|+-..|+.|+.--. ++|. -.|| +|+..+
T Consensus 7 ~~~qiCqiCGD~VGl~~~Ge~FVAC~eC~fPvCr~CyEYEr----keg~----q~Cp--qCkt~y 61 (80)
T PF14569_consen 7 LNGQICQICGDDVGLTENGEVFVACHECAFPVCRPCYEYER----KEGN----QVCP--QCKTRY 61 (80)
T ss_dssp -SS-B-SSS--B--B-SSSSB--S-SSS-----HHHHHHHH----HTS-----SB-T--TT--B-
T ss_pred cCCcccccccCccccCCCCCEEEEEcccCCccchhHHHHHh----hcCc----cccc--ccCCCc
Confidence 3456799999986542 3333 2 488999999987543 3453 4799 897544
No 275
>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=21.70 E-value=50 Score=26.36 Aligned_cols=17 Identities=24% Similarity=0.727 Sum_probs=11.5
Q ss_pred cccHhHHHHHHhccccC
Q 007642 164 PFCSSCWTGYISTAIND 180 (595)
Q Consensus 164 ~fC~~C~~~yi~~~i~~ 180 (595)
-||++|+..|...+-.+
T Consensus 11 gFCRNCLskWy~~aA~~ 27 (68)
T PF06844_consen 11 GFCRNCLSKWYREAAEE 27 (68)
T ss_dssp S--HHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHh
Confidence 38999999998776543
No 276
>PRK12286 rpmF 50S ribosomal protein L32; Reviewed
Probab=21.69 E-value=55 Score=25.40 Aligned_cols=22 Identities=32% Similarity=0.807 Sum_probs=14.6
Q ss_pred cCccCCCCCcceeecCCCCcccccCCCc
Q 007642 298 NSKPCPRCKRPIEKNQGCMHMTCTPPCK 325 (595)
Q Consensus 298 ntK~CPkC~~~IEK~~GCnhmtC~~~C~ 325 (595)
+.-.||.|+.+.. .|-.|. .||
T Consensus 26 ~l~~C~~CG~~~~-----~H~vC~-~CG 47 (57)
T PRK12286 26 GLVECPNCGEPKL-----PHRVCP-SCG 47 (57)
T ss_pred cceECCCCCCccC-----CeEECC-CCC
Confidence 3467999999888 355554 344
No 277
>COG1594 RPB9 DNA-directed RNA polymerase, subunit M/Transcription elongation factor TFIIS [Transcription]
Probab=21.69 E-value=86 Score=27.84 Aligned_cols=30 Identities=20% Similarity=0.586 Sum_probs=20.2
Q ss_pred cccCCCCCCCCeeeeecCCCCceeee-cCCCcc
Q 007642 230 TKWCPAPGCDYAVDFVVGSGNYDVTC-RCSYSF 261 (595)
Q Consensus 230 ~~~CP~p~C~~~i~~~~~~~~~~v~C-~C~~~f 261 (595)
+.+|| .|+.++............| .||+.+
T Consensus 2 m~FCp--~Cgsll~p~~~~~~~~l~C~kCgye~ 32 (113)
T COG1594 2 MRFCP--KCGSLLYPKKDDEGGKLVCRKCGYEE 32 (113)
T ss_pred ccccC--CccCeeEEeEcCCCcEEECCCCCcch
Confidence 56899 5999887753333346678 787664
No 278
>COG2816 NPY1 NTP pyrophosphohydrolases containing a Zn-finger, probably nucleic-acid-binding [DNA replication, recombination, and repair]
Probab=21.69 E-value=78 Score=32.70 Aligned_cols=37 Identities=22% Similarity=0.556 Sum_probs=26.2
Q ss_pred HhHHHHHhcCccCCCCCcceeecCCCCcccccCCCccee
Q 007642 290 ENMNWILANSKPCPRCKRPIEKNQGCMHMTCTPPCKFEF 328 (595)
Q Consensus 290 e~~~wi~~ntK~CPkC~~~IEK~~GCnhmtC~~~C~~~F 328 (595)
+-..|... -|-||+|+.+.+-..|=-.+.|. .|++.+
T Consensus 103 ~l~~w~~~-~RFCg~CG~~~~~~~~g~~~~C~-~cg~~~ 139 (279)
T COG2816 103 QLLEWYRS-HRFCGRCGTKTYPREGGWARVCP-KCGHEH 139 (279)
T ss_pred HHHHHHhh-CcCCCCCCCcCccccCceeeeCC-CCCCcc
Confidence 34456443 38999999999877776667777 677654
No 279
>PRK14892 putative transcription elongation factor Elf1; Provisional
Probab=21.48 E-value=1.7e+02 Score=25.41 Aligned_cols=55 Identities=16% Similarity=0.239 Sum_probs=31.9
Q ss_pred CCCcccCCCCCCCC-eeeeecCCCCceeee-cCCCcccccCCcccCCCCCchhHHHHHHhhh
Q 007642 227 NRKTKWCPAPGCDY-AVDFVVGSGNYDVTC-RCSYSFCWNCTEEAHRPVDCDTVAKWVLKNS 286 (595)
Q Consensus 227 ~~~~~~CP~p~C~~-~i~~~~~~~~~~v~C-~C~~~fC~~C~~~~H~p~~C~~~~~~~~k~~ 286 (595)
.+.+..||+ |+. .+......+...+.| .||+.+=.. -.+...+=+.|..|+....
T Consensus 18 lpt~f~CP~--Cge~~v~v~~~k~~~h~~C~~CG~y~~~~---V~~l~epIDVY~~wiD~~~ 74 (99)
T PRK14892 18 LPKIFECPR--CGKVSISVKIKKNIAIITCGNCGLYTEFE---VPSVYDEVDVYNKFIDLYL 74 (99)
T ss_pred CCcEeECCC--CCCeEeeeecCCCcceEECCCCCCccCEE---CCccccchhhHHHHHHHHH
Confidence 356788995 873 332222334566788 888775221 2233334477889987653
No 280
>PTZ00083 40S ribosomal protein S27; Provisional
Probab=21.45 E-value=96 Score=26.06 Aligned_cols=30 Identities=30% Similarity=0.691 Sum_probs=21.0
Q ss_pred ccCCCCCCCCeeeeecCCCCceeee-cCCCcccc
Q 007642 231 KWCPAPGCDYAVDFVVGSGNYDVTC-RCSYSFCW 263 (595)
Q Consensus 231 ~~CP~p~C~~~i~~~~~~~~~~v~C-~C~~~fC~ 263 (595)
+.|| +|...-.+- ......|.| .|+...|.
T Consensus 36 VkCp--~C~n~q~VF-ShA~t~V~C~~Cg~~L~~ 66 (85)
T PTZ00083 36 VKCP--GCSQITTVF-SHAQTVVLCGGCSSQLCQ 66 (85)
T ss_pred EECC--CCCCeeEEE-ecCceEEEccccCCEeec
Confidence 6898 697653332 345677899 89999884
No 281
>PLN02189 cellulose synthase
Probab=21.21 E-value=74 Score=38.64 Aligned_cols=59 Identities=24% Similarity=0.695 Sum_probs=39.1
Q ss_pred cCCCCCCCCeeeeecCCCCceeee-cCCCcccccCCcccCCCCCchhHHHHHHhhhHhHHhHHHHHhcCccCCCCCccee
Q 007642 232 WCPAPGCDYAVDFVVGSGNYDVTC-RCSYSFCWNCTEEAHRPVDCDTVAKWVLKNSAESENMNWILANSKPCPRCKRPIE 310 (595)
Q Consensus 232 ~CP~p~C~~~i~~~~~~~~~~v~C-~C~~~fC~~C~~~~H~p~~C~~~~~~~~k~~~~~e~~~wi~~ntK~CPkC~~~IE 310 (595)
-|.- |+--|... ..+..-|-| .|++-.|..|-+ +.. +..++.||+|+....
T Consensus 36 ~C~i--Cgd~vg~~-~~g~~fvaC~~C~fpvCr~Cye----------yer---------------~eg~q~CpqCkt~Y~ 87 (1040)
T PLN02189 36 VCEI--CGDEIGLT-VDGDLFVACNECGFPVCRPCYE----------YER---------------REGTQNCPQCKTRYK 87 (1040)
T ss_pred cccc--cccccCcC-CCCCEEEeeccCCCccccchhh----------hhh---------------hcCCccCcccCCchh
Confidence 4553 76655544 446677999 899999988762 110 112278999998888
Q ss_pred ecCCCCcc
Q 007642 311 KNQGCMHM 318 (595)
Q Consensus 311 K~~GCnhm 318 (595)
+-.|++.+
T Consensus 88 r~kgs~~v 95 (1040)
T PLN02189 88 RLKGSPRV 95 (1040)
T ss_pred hccCCCCc
Confidence 76677654
No 282
>PF00098 zf-CCHC: Zinc knuckle; InterPro: IPR001878 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 CysCysHisCys (CCHC) type zinc finger domains, and have the sequence: C-X2-C-X4-H-X4-C where X can be any amino acid, and number indicates the number of residues. These 18 residues CCHC zinc finger domains are mainly found in the nucleocapsid protein of retroviruses. It is required for viral genome packaging and for early infection process [, , ]. It is also found in eukaryotic proteins involved in RNA binding or single-stranded DNA binding []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003676 nucleic acid binding, 0008270 zinc ion binding; PDB: 2L44_A 1A1T_A 1WWG_A 1U6P_A 1WWD_A 1WWE_A 1A6B_B 1F6U_A 1MFS_A 1NCP_C ....
Probab=21.19 E-value=55 Score=19.13 Aligned_cols=16 Identities=44% Similarity=0.978 Sum_probs=12.8
Q ss_pred ccccCCcccCCCCCch
Q 007642 261 FCWNCTEEAHRPVDCD 276 (595)
Q Consensus 261 fC~~C~~~~H~p~~C~ 276 (595)
.|++|++.-|.-..|.
T Consensus 2 ~C~~C~~~GH~~~~Cp 17 (18)
T PF00098_consen 2 KCFNCGEPGHIARDCP 17 (18)
T ss_dssp BCTTTSCSSSCGCTSS
T ss_pred cCcCCCCcCcccccCc
Confidence 5899999999776664
No 283
>cd07662 BAR_SNX6 The Bin/Amphiphysin/Rvs (BAR) domain of Sorting Nexin 6. BAR domains are dimerization, lipid binding and curvature sensing modules found in many different proteins with diverse functions. Sorting nexins (SNXs) are Phox homology (PX) domain containing proteins that are involved in regulating membrane traffic and protein sorting in the endosomal system. SNXs differ from each other in their lipid-binding specificity, subcellular localization and specific function in the endocytic pathway. A subset of SNXs also contain BAR domains. The PX-BAR structural unit determines the specific membrane targeting of SNXs. SNX6 forms a stable complex with SNX1 and may be a component of the retromer complex, a membrane coat multimeric complex required for endosomal retrieval of lysosomal hydrolase receptors to the Golgi, acting as a mammalian equivalent of yeast Vsp17p. It interacts with the receptor serine/threonine kinases from the transforming growth factor-beta family. It also plays
Probab=20.90 E-value=8.4e+02 Score=24.33 Aligned_cols=56 Identities=20% Similarity=0.241 Sum_probs=37.8
Q ss_pred HHHHHHHHHHhHHHHHHHHHHHHHHHhhcCCCCCcHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 007642 459 FEYLQGEAESGLERLHQCAEKELQIYLNADGPSKDFNEFRTKLAGLTSVTRNYFENLVRAL 519 (595)
Q Consensus 459 fe~~Q~~le~~~E~L~~~le~e~~~~~~~~~~~~~~~~~~~~l~~lt~~~~~~~~~l~~~l 519 (595)
-|..|.+++...|.++..+.+|+..|.. .++..|+..|..+.-..-...++-+.-|
T Consensus 155 aE~~~~~a~~~Fe~IS~~aK~El~rF~~-----~Rv~~Fkk~Lv~y~E~~lkhak~~~~~~ 210 (218)
T cd07662 155 AETTQQLCCQKFEKISESAKQELIDFKT-----RRVAAFRKNLVELAELELKHAKGNLQLL 210 (218)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHH-----HHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3678889999999999999999988754 4466677666655544333333333333
No 284
>PRK04023 DNA polymerase II large subunit; Validated
Probab=20.88 E-value=53 Score=39.54 Aligned_cols=32 Identities=22% Similarity=0.507 Sum_probs=23.8
Q ss_pred hcCccCCCCCcceeecCCCCcccccCCCcc-----eeeeccccc
Q 007642 297 ANSKPCPRCKRPIEKNQGCMHMTCTPPCKF-----EFCWLCLGQ 335 (595)
Q Consensus 297 ~ntK~CPkC~~~IEK~~GCnhmtC~~~C~~-----~FCw~C~~~ 335 (595)
...+.||.|+... ....|. .||. .||..|+..
T Consensus 624 Vg~RfCpsCG~~t------~~frCP-~CG~~Te~i~fCP~CG~~ 660 (1121)
T PRK04023 624 IGRRKCPSCGKET------FYRRCP-FCGTHTEPVYRCPRCGIE 660 (1121)
T ss_pred ccCccCCCCCCcC------CcccCC-CCCCCCCcceeCccccCc
Confidence 3458999999885 347887 7985 599999653
No 285
>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=20.79 E-value=96 Score=23.82 Aligned_cols=28 Identities=21% Similarity=0.507 Sum_probs=19.4
Q ss_pred cCCCCCCCCeeeeecCCCCceeee-cCCCcc
Q 007642 232 WCPAPGCDYAVDFVVGSGNYDVTC-RCSYSF 261 (595)
Q Consensus 232 ~CP~p~C~~~i~~~~~~~~~~v~C-~C~~~f 261 (595)
-|| .|+..|.+........|.| .||..+
T Consensus 4 ~CP--~CG~~iev~~~~~GeiV~Cp~CGael 32 (54)
T TIGR01206 4 ECP--DCGAEIELENPELGELVICDECGAEL 32 (54)
T ss_pred CCC--CCCCEEecCCCccCCEEeCCCCCCEE
Confidence 587 5998887754333456788 788765
No 286
>PF04803 Cor1: Cor1/Xlr/Xmr conserved region; InterPro: IPR006888 Cor1 is a component of the chromosome core in the meiotic prophase chromosomes []. Xlr is a lymphoid cell specific protein []. Xmr is abundantly transcribed in testis in a tissue-specific and developmentally regulated manner. The protein is located in the nuclei of spermatocytes, early in the prophase of the first meiotic division, and later becomes concentrated in the XY nuclear subregion where it is in particular associated with the axes of sex chromosomes [].
Probab=20.77 E-value=6.5e+02 Score=22.95 Aligned_cols=14 Identities=7% Similarity=0.793 Sum_probs=7.5
Q ss_pred HHHHHHHHHHhhhH
Q 007642 376 ERYTHYYERWATNQ 389 (595)
Q Consensus 376 ~ry~~y~~r~~~h~ 389 (595)
..|..-|..|..-.
T Consensus 46 ~q~~~l~~qw~~D~ 59 (130)
T PF04803_consen 46 QQFSTLFQQWEADV 59 (130)
T ss_pred HHHHHHHHHHHHHH
Confidence 45555566665443
No 287
>PRK08115 ribonucleotide-diphosphate reductase subunit alpha; Validated
Probab=20.63 E-value=50 Score=39.46 Aligned_cols=25 Identities=40% Similarity=1.040 Sum_probs=20.1
Q ss_pred ccCCCCCc-ceeecCCCCcccccCCCcce
Q 007642 300 KPCPRCKR-PIEKNQGCMHMTCTPPCKFE 327 (595)
Q Consensus 300 K~CPkC~~-~IEK~~GCnhmtC~~~C~~~ 327 (595)
-.||-|+. .||..|||| ||+ .|+.+
T Consensus 828 ~~cp~c~~~~~~~~~~c~--~c~-~c~~~ 853 (858)
T PRK08115 828 NTCPVCREGTVEEIGGCN--TCT-NCGAQ 853 (858)
T ss_pred CCCCccCCCceeecCCCc--ccc-chhhh
Confidence 48999975 678999998 688 68754
No 288
>PRK13428 F0F1 ATP synthase subunit delta; Provisional
Probab=20.59 E-value=1.2e+03 Score=25.86 Aligned_cols=25 Identities=16% Similarity=-0.082 Sum_probs=10.2
Q ss_pred HHHHHHHHHHHHHhHHHHHHHHHHH
Q 007642 456 RQFFEYLQGEAESGLERLHQCAEKE 480 (595)
Q Consensus 456 ~~~fe~~Q~~le~~~E~L~~~le~e 480 (595)
.++.+..+.++++..+.-...++.+
T Consensus 85 ~~~~~~A~~ea~~i~~~a~~~Ie~e 109 (445)
T PRK13428 85 EQLRAQADAEAERIKVQGARQVQLL 109 (445)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3344444444444444433333333
No 289
>COG1315 Uncharacterized conserved protein [Function unknown]
Probab=20.57 E-value=6.6e+02 Score=28.30 Aligned_cols=38 Identities=18% Similarity=0.174 Sum_probs=27.8
Q ss_pred HHHHHHHHHHHHhhhHHHHHHHHHHHHHHHHHHHHHHh
Q 007642 374 SLERYTHYYERWATNQSSRQKALADLQQMQTVHLEKLS 411 (595)
Q Consensus 374 ~l~ry~~y~~r~~~h~~s~~~~~~~l~~~~~~~~~~l~ 411 (595)
..+|+..|-+++..|+..++++...|+.+++.+++...
T Consensus 408 ~~~~l~~lt~~~~~~ee~l~~Lt~~l~~l~~~~i~~~~ 445 (543)
T COG1315 408 IVERLKELTEEISLHEERLKKLTKLLVALVKVKIESKK 445 (543)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhc
Confidence 45677778888888998888888888777765444443
No 290
>PRK09521 exosome complex RNA-binding protein Csl4; Provisional
Probab=20.42 E-value=64 Score=31.22 Aligned_cols=26 Identities=31% Similarity=0.782 Sum_probs=20.3
Q ss_pred ccCCCCCcceeecCCCCcccccCCCcce
Q 007642 300 KPCPRCKRPIEKNQGCMHMTCTPPCKFE 327 (595)
Q Consensus 300 K~CPkC~~~IEK~~GCnhmtC~~~C~~~ 327 (595)
-.||+|+.++.+ .+.|+|.|. .|++.
T Consensus 150 a~~~~~g~~~~~-~~~~~~~c~-~~~~~ 175 (189)
T PRK09521 150 AMCSRCRTPLVK-KGENELKCP-NCGNI 175 (189)
T ss_pred EEccccCCceEE-CCCCEEECC-CCCCE
Confidence 379999999987 445999998 67654
No 291
>KOG2932 consensus E3 ubiquitin ligase involved in ubiquitination of E-cadherin complex [Posttranslational modification, protein turnover, chaperones]
Probab=20.10 E-value=40 Score=34.96 Aligned_cols=29 Identities=38% Similarity=0.844 Sum_probs=20.5
Q ss_pred ccCCCCCcceeecCCCCcccccC-CCcceeeeccccc
Q 007642 300 KPCPRCKRPIEKNQGCMHMTCTP-PCKFEFCWLCLGQ 335 (595)
Q Consensus 300 K~CPkC~~~IEK~~GCnhmtC~~-~C~~~FCw~C~~~ 335 (595)
.-|-+|..+|- ++=+- .|++.||+.|-..
T Consensus 91 HfCd~Cd~PI~-------IYGRmIPCkHvFCl~CAr~ 120 (389)
T KOG2932|consen 91 HFCDRCDFPIA-------IYGRMIPCKHVFCLECARS 120 (389)
T ss_pred EeecccCCcce-------eeecccccchhhhhhhhhc
Confidence 56999999998 44332 4777777777544
Done!