Query 008441
Match_columns 565
No_of_seqs 438 out of 1793
Neff 7.2
Searched_HMMs 46136
Date Thu Mar 28 12:11:53 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/008441.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/008441hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG1812 Predicted E3 ubiquitin 100.0 6.1E-54 1.3E-58 452.1 18.4 351 158-527 1-357 (384)
2 KOG1814 Predicted E3 ubiquitin 100.0 3.8E-32 8.2E-37 276.1 8.2 194 306-513 182-405 (445)
3 KOG1815 Predicted E3 ubiquitin 99.9 4.2E-28 9.2E-33 262.5 6.7 250 255-529 25-283 (444)
4 KOG0006 E3 ubiquitin-protein l 99.9 9E-26 2E-30 221.7 6.7 239 258-514 170-437 (446)
5 PRK07708 hypothetical protein; 99.9 4E-23 8.6E-28 202.5 13.7 134 154-294 71-209 (219)
6 PRK13907 rnhA ribonuclease H; 99.9 5E-23 1.1E-27 186.2 11.6 126 156-292 1-126 (128)
7 COG0328 RnhA Ribonuclease HI [ 99.9 5.7E-22 1.2E-26 181.9 10.1 129 155-294 2-146 (154)
8 PRK07238 bifunctional RNase H/ 99.9 1.2E-21 2.7E-26 208.3 14.2 131 156-294 2-133 (372)
9 PRK08719 ribonuclease H; Revie 99.7 2.3E-16 5E-21 145.9 12.1 126 155-292 3-146 (147)
10 cd06222 RnaseH RNase H (RNase 99.6 4.2E-15 9.1E-20 130.8 12.1 126 158-291 1-130 (130)
11 PRK06548 ribonuclease H; Provi 99.6 9.8E-15 2.1E-19 136.4 11.3 126 155-295 4-144 (161)
12 PRK00203 rnhA ribonuclease H; 99.5 5.9E-14 1.3E-18 130.5 10.7 126 156-294 3-143 (150)
13 PF13456 RVT_3: Reverse transc 99.5 8.6E-14 1.9E-18 116.1 7.2 86 206-292 1-86 (87)
14 PF00075 RNase_H: RNase H; In 99.4 2.6E-12 5.7E-17 116.0 9.8 119 156-291 3-131 (132)
15 smart00647 IBR In Between Ring 98.9 2E-09 4.4E-14 84.9 4.3 62 379-451 2-64 (64)
16 PF01485 IBR: IBR domain; Int 98.8 1.8E-09 3.8E-14 85.2 1.5 62 379-451 2-64 (64)
17 KOG3752 Ribonuclease H [Replic 98.7 3.6E-08 7.8E-13 101.6 10.0 126 157-290 213-362 (371)
18 smart00647 IBR In Between Ring 98.3 1E-06 2.2E-11 69.4 5.2 48 468-515 8-61 (64)
19 PF13639 zf-RING_2: Ring finge 98.1 7.1E-07 1.5E-11 65.1 1.1 41 310-356 2-42 (44)
20 KOG0320 Predicted E3 ubiquitin 98.1 1.3E-06 2.8E-11 81.2 2.0 55 305-368 128-182 (187)
21 PF15227 zf-C3HC4_4: zinc fing 98.1 8.5E-07 1.8E-11 64.1 0.5 41 311-356 1-41 (42)
22 PF13923 zf-C3HC4_2: Zinc fing 98.0 2.4E-06 5.1E-11 60.7 2.0 38 311-356 1-38 (39)
23 PF01485 IBR: IBR domain; Int 98.0 1.4E-06 3.1E-11 68.4 0.8 39 476-514 17-60 (64)
24 PF00097 zf-C3HC4: Zinc finger 98.0 5.7E-06 1.2E-10 59.3 3.7 40 311-356 1-40 (41)
25 PF13445 zf-RING_UBOX: RING-ty 98.0 4.1E-06 8.9E-11 60.7 2.5 43 311-355 1-43 (43)
26 PF14634 zf-RING_5: zinc-RING 97.9 8.4E-06 1.8E-10 59.5 3.2 43 310-360 1-43 (44)
27 cd00162 RING RING-finger (Real 97.8 1.8E-05 3.9E-10 56.8 3.9 44 310-362 1-44 (45)
28 PLN03208 E3 ubiquitin-protein 97.8 1.1E-05 2.3E-10 77.0 2.9 61 307-372 17-87 (193)
29 PHA02926 zinc finger-like prot 97.6 4E-05 8.6E-10 74.0 3.4 59 304-364 166-230 (242)
30 PF13920 zf-C3HC4_3: Zinc fing 97.6 6.7E-05 1.4E-09 56.3 3.3 46 308-364 2-48 (50)
31 KOG0823 Predicted E3 ubiquitin 97.5 4.6E-05 9.9E-10 74.1 2.2 59 305-371 44-102 (230)
32 KOG2177 Predicted E3 ubiquitin 97.5 7.4E-05 1.6E-09 75.9 3.5 107 307-451 12-122 (386)
33 PHA02929 N1R/p28-like protein; 97.4 8.9E-05 1.9E-09 73.6 3.1 51 306-364 172-227 (238)
34 smart00184 RING Ring finger. E 97.3 0.0002 4.2E-09 49.5 3.0 38 311-356 1-38 (39)
35 KOG2164 Predicted E3 ubiquitin 97.3 9.7E-05 2.1E-09 79.2 1.9 59 308-372 186-244 (513)
36 KOG4628 Predicted E3 ubiquitin 97.3 0.00048 1E-08 71.6 6.8 48 309-363 230-277 (348)
37 smart00504 Ubox Modified RING 97.2 0.00036 7.9E-09 54.6 4.1 50 309-369 2-51 (63)
38 KOG0287 Postreplication repair 97.1 0.00031 6.8E-09 71.3 3.3 63 308-381 23-86 (442)
39 TIGR00599 rad18 DNA repair pro 97.0 0.00062 1.4E-08 72.5 4.1 65 306-381 24-89 (397)
40 KOG0317 Predicted E3 ubiquitin 97.0 0.00035 7.6E-09 70.0 1.9 51 307-368 238-288 (293)
41 COG5540 RING-finger-containing 96.8 0.00087 1.9E-08 67.3 3.1 54 305-365 320-373 (374)
42 TIGR00570 cdk7 CDK-activating 96.7 0.0012 2.6E-08 67.7 3.6 52 309-367 4-57 (309)
43 PF11789 zf-Nse: Zinc-finger o 96.5 0.002 4.4E-08 49.7 2.5 50 305-360 8-57 (57)
44 KOG2879 Predicted E3 ubiquitin 96.3 0.0057 1.2E-07 61.0 4.9 54 303-364 234-287 (298)
45 PF12678 zf-rbx1: RING-H2 zinc 96.2 0.0027 5.8E-08 51.6 1.8 43 308-356 19-71 (73)
46 PF06524 NOA36: NOA36 protein; 96.1 0.0086 1.9E-07 59.1 5.3 52 424-490 168-222 (314)
47 PF11793 FANCL_C: FANCL C-term 96.0 0.0053 1.1E-07 49.5 2.7 57 308-366 2-68 (70)
48 PF14835 zf-RING_6: zf-RING of 96.0 0.0013 2.8E-08 51.4 -0.8 50 308-369 7-56 (65)
49 KOG1002 Nucleotide excision re 95.9 0.004 8.6E-08 66.8 2.3 59 304-368 532-590 (791)
50 KOG4367 Predicted Zn-finger pr 95.9 0.004 8.6E-08 65.3 1.9 81 423-513 172-254 (699)
51 COG5574 PEX10 RING-finger-cont 95.6 0.0095 2.1E-07 59.2 3.3 54 306-368 213-266 (271)
52 KOG0978 E3 ubiquitin ligase in 95.4 0.0049 1.1E-07 69.5 0.7 55 307-371 642-696 (698)
53 COG5432 RAD18 RING-finger-cont 95.4 0.012 2.6E-07 58.9 3.2 63 307-380 24-87 (391)
54 COG5243 HRD1 HRD ubiquitin lig 95.2 0.013 2.7E-07 60.7 2.6 53 307-367 286-348 (491)
55 PF04564 U-box: U-box domain; 94.9 0.036 7.8E-07 45.0 4.2 52 307-368 3-54 (73)
56 KOG1039 Predicted E3 ubiquitin 94.9 0.017 3.6E-07 60.6 2.8 57 306-364 159-221 (344)
57 PF12861 zf-Apc11: Anaphase-pr 92.8 0.081 1.7E-06 44.0 2.5 53 308-365 21-83 (85)
58 KOG1814 Predicted E3 ubiquitin 92.8 0.026 5.6E-07 59.4 -0.6 38 477-514 273-313 (445)
59 KOG0006 E3 ubiquitin-protein l 92.6 0.18 3.8E-06 51.4 5.0 145 272-447 290-437 (446)
60 KOG0824 Predicted E3 ubiquitin 92.5 0.074 1.6E-06 53.9 2.2 52 306-367 5-56 (324)
61 KOG1812 Predicted E3 ubiquitin 92.3 0.041 8.9E-07 59.0 0.2 104 308-450 238-346 (384)
62 KOG0802 E3 ubiquitin ligase [P 91.7 0.098 2.1E-06 58.8 2.2 47 307-361 290-338 (543)
63 KOG1428 Inhibitor of type V ad 91.7 0.23 5E-06 59.3 5.1 68 305-374 3483-3554(3738)
64 KOG0311 Predicted E3 ubiquitin 91.6 0.027 5.8E-07 58.2 -2.1 49 306-363 41-89 (381)
65 KOG4185 Predicted E3 ubiquitin 91.4 0.37 7.9E-06 49.8 6.0 56 308-370 3-63 (296)
66 KOG2660 Locus-specific chromos 91.1 0.079 1.7E-06 54.5 0.7 47 307-363 14-60 (331)
67 KOG0828 Predicted E3 ubiquitin 91.1 0.12 2.5E-06 55.6 1.9 53 305-364 568-634 (636)
68 PHA03096 p28-like protein; Pro 90.5 0.14 3E-06 52.6 1.7 53 309-363 179-236 (284)
69 KOG4739 Uncharacterized protei 89.8 0.093 2E-06 51.8 -0.1 46 309-365 4-49 (233)
70 KOG1815 Predicted E3 ubiquitin 89.5 0.14 3.1E-06 56.1 1.0 52 477-531 158-212 (444)
71 PLN03086 PRLI-interacting fact 89.4 0.42 9.1E-06 53.4 4.5 56 352-437 408-463 (567)
72 KOG1734 Predicted RING-contain 89.0 0.23 4.9E-06 49.6 1.9 56 306-368 222-285 (328)
73 KOG0825 PHD Zn-finger protein 88.9 0.19 4E-06 56.8 1.4 48 308-363 123-170 (1134)
74 KOG0297 TNF receptor-associate 88.3 0.37 7.9E-06 52.0 3.1 51 305-365 18-68 (391)
75 COG5220 TFB3 Cdk activating ki 87.8 0.14 3E-06 50.2 -0.5 51 308-363 10-63 (314)
76 PHA00626 hypothetical protein 87.0 0.44 9.6E-06 36.2 2.0 27 479-505 2-34 (59)
77 smart00744 RINGv The RING-vari 87.0 0.57 1.2E-05 34.9 2.6 42 310-356 1-47 (49)
78 PF10571 UPF0547: Uncharacteri 86.8 0.3 6.4E-06 31.5 0.8 23 478-504 1-24 (26)
79 COG5175 MOT2 Transcriptional r 86.8 0.45 9.7E-06 49.0 2.5 54 308-369 14-69 (480)
80 KOG4265 Predicted E3 ubiquitin 86.7 0.55 1.2E-05 49.0 3.1 47 307-364 289-336 (349)
81 COG5152 Uncharacterized conser 86.4 0.33 7.2E-06 46.3 1.3 46 306-362 194-239 (259)
82 PRK14559 putative protein seri 86.1 0.39 8.5E-06 54.8 1.9 13 501-513 40-52 (645)
83 PF13719 zinc_ribbon_5: zinc-r 85.8 0.61 1.3E-05 32.6 2.1 33 395-437 3-35 (37)
84 PF05883 Baculo_RING: Baculovi 85.7 0.36 7.7E-06 43.7 1.0 36 307-343 25-67 (134)
85 KOG0804 Cytoplasmic Zn-finger 85.6 0.46 1E-05 50.8 2.0 49 303-362 170-220 (493)
86 PRK05654 acetyl-CoA carboxylas 85.6 0.18 4E-06 52.0 -0.9 31 474-504 24-56 (292)
87 KOG0317 Predicted E3 ubiquitin 85.6 0.19 4.2E-06 50.8 -0.8 26 496-523 252-278 (293)
88 smart00661 RPOL9 RNA polymeras 85.4 0.55 1.2E-05 35.1 1.8 27 478-504 1-30 (52)
89 KOG4159 Predicted E3 ubiquitin 84.9 1.1 2.5E-05 48.0 4.6 48 306-364 82-129 (398)
90 KOG2817 Predicted E3 ubiquitin 84.5 0.51 1.1E-05 49.8 1.7 58 307-370 333-391 (394)
91 KOG4692 Predicted E3 ubiquitin 84.3 0.72 1.6E-05 47.8 2.6 49 305-364 419-467 (489)
92 COG0777 AccD Acetyl-CoA carbox 84.1 0.38 8.2E-06 48.5 0.5 32 474-505 25-58 (294)
93 KOG1785 Tyrosine kinase negati 84.0 0.45 9.7E-06 50.0 1.0 44 309-359 370-413 (563)
94 KOG4445 Uncharacterized conser 83.8 0.7 1.5E-05 46.9 2.3 40 306-345 113-152 (368)
95 KOG1645 RING-finger-containing 83.6 1.4 3E-05 46.8 4.3 51 308-364 4-56 (463)
96 PF15227 zf-C3HC4_4: zinc fing 83.2 0.48 1E-05 34.1 0.6 38 480-522 1-40 (42)
97 KOG0823 Predicted E3 ubiquitin 83.2 0.34 7.5E-06 47.6 -0.2 20 500-519 65-84 (230)
98 PF13717 zinc_ribbon_4: zinc-r 83.0 0.94 2E-05 31.5 2.0 33 395-437 3-35 (36)
99 PF14570 zf-RING_4: RING/Ubox 82.8 0.92 2E-05 33.7 2.0 45 311-363 1-47 (48)
100 CHL00174 accD acetyl-CoA carbo 82.8 0.28 6E-06 50.5 -1.0 30 475-504 36-67 (296)
101 PF13240 zinc_ribbon_2: zinc-r 82.7 0.56 1.2E-05 29.2 0.7 11 479-489 1-11 (23)
102 PF00097 zf-C3HC4: Zinc finger 82.5 0.22 4.7E-06 35.2 -1.4 25 499-523 16-40 (41)
103 KOG4172 Predicted E3 ubiquitin 82.4 0.42 9E-06 36.2 0.0 46 308-363 7-53 (62)
104 TIGR00515 accD acetyl-CoA carb 82.0 0.32 7E-06 50.0 -0.9 30 475-504 24-55 (285)
105 PF07975 C1_4: TFIIH C1-like d 81.8 0.49 1.1E-05 35.6 0.3 25 425-449 19-43 (51)
106 PF05290 Baculo_IE-1: Baculovi 81.8 1.3 2.8E-05 39.9 2.9 108 251-364 15-132 (140)
107 PF13248 zf-ribbon_3: zinc-rib 81.4 0.76 1.6E-05 29.5 1.0 23 478-511 3-25 (26)
108 PF13639 zf-RING_2: Ring finge 80.1 0.28 6.1E-06 35.4 -1.6 41 479-523 2-42 (44)
109 KOG0826 Predicted E3 ubiquitin 79.3 1.5 3.3E-05 45.2 2.8 50 305-362 297-346 (357)
110 KOG2807 RNA polymerase II tran 79.1 0.73 1.6E-05 47.4 0.5 26 424-449 342-367 (378)
111 PRK14559 putative protein seri 78.7 1.6 3.4E-05 50.0 3.1 12 478-489 42-53 (645)
112 KOG0827 Predicted E3 ubiquitin 78.5 1.2 2.6E-05 46.8 1.9 48 308-360 4-52 (465)
113 KOG1952 Transcription factor N 78.3 1.8 3.9E-05 49.8 3.3 52 307-360 190-243 (950)
114 PLN03208 E3 ubiquitin-protein 78.3 0.52 1.1E-05 45.4 -0.8 32 477-513 18-49 (193)
115 PF12773 DZR: Double zinc ribb 77.7 1.8 3.8E-05 32.1 2.1 12 478-489 30-41 (50)
116 PRK00432 30S ribosomal protein 77.6 1.4 3E-05 33.1 1.5 26 478-505 21-48 (50)
117 PF04641 Rtf2: Rtf2 RING-finge 77.2 2.6 5.7E-05 42.8 3.9 72 304-384 109-182 (260)
118 PRK00398 rpoP DNA-directed RNA 76.8 2.2 4.8E-05 31.1 2.4 29 478-506 4-33 (46)
119 KOG3039 Uncharacterized conser 76.8 1.5 3.2E-05 43.4 1.9 54 307-368 220-274 (303)
120 KOG1001 Helicase-like transcri 76.8 0.81 1.8E-05 52.6 0.1 49 309-367 455-503 (674)
121 PF08274 PhnA_Zn_Ribbon: PhnA 76.7 1.6 3.5E-05 29.1 1.4 26 478-504 3-29 (30)
122 KOG1813 Predicted E3 ubiquitin 75.6 1.1 2.5E-05 45.5 0.7 47 307-364 240-286 (313)
123 COG5151 SSL1 RNA polymerase II 75.4 1.2 2.5E-05 45.5 0.7 96 330-447 307-408 (421)
124 PHA02929 N1R/p28-like protein; 74.8 1.7 3.8E-05 43.4 1.8 42 478-519 175-219 (238)
125 PRK14714 DNA polymerase II lar 73.2 2.9 6.2E-05 50.5 3.3 10 478-487 710-719 (1337)
126 PRK04023 DNA polymerase II lar 72.0 3.1 6.7E-05 49.1 3.2 20 427-446 638-662 (1121)
127 TIGR02098 MJ0042_CXXC MJ0042 f 71.9 3.2 6.9E-05 28.8 2.1 33 395-437 3-35 (38)
128 PF13923 zf-C3HC4_2: Zinc fing 71.2 0.84 1.8E-05 32.0 -1.0 22 499-522 16-37 (39)
129 COG1198 PriA Primosomal protei 70.5 3.1 6.7E-05 48.2 2.8 34 478-511 445-484 (730)
130 PF10367 Vps39_2: Vacuolar sor 69.9 2 4.3E-05 36.9 0.9 31 308-339 78-108 (109)
131 PF14952 zf-tcix: Putative tre 69.2 2.3 4.9E-05 30.8 0.8 25 476-504 10-37 (44)
132 KOG3800 Predicted E3 ubiquitin 68.0 7.3 0.00016 39.7 4.4 50 310-366 2-53 (300)
133 PRK08665 ribonucleotide-diphos 67.5 2.8 6.1E-05 49.0 1.7 26 478-505 725-751 (752)
134 PF09297 zf-NADH-PPase: NADH p 67.4 5.6 0.00012 26.7 2.5 26 478-503 4-30 (32)
135 PRK14890 putative Zn-ribbon RN 67.3 5.5 0.00012 30.9 2.6 21 424-444 22-45 (59)
136 KOG2906 RNA polymerase III sub 67.2 3.8 8.3E-05 34.9 1.9 29 479-507 3-34 (105)
137 COG5432 RAD18 RING-finger-cont 66.5 1.9 4.1E-05 43.6 0.0 39 478-523 26-67 (391)
138 COG5219 Uncharacterized conser 65.4 2.1 4.6E-05 49.7 0.2 52 307-364 1468-1523(1525)
139 PF04216 FdhE: Protein involve 65.1 3.3 7.2E-05 42.7 1.5 13 435-447 197-209 (290)
140 PF10157 DUF2365: Uncharacteri 65.0 39 0.00085 31.4 8.3 34 85-121 48-81 (149)
141 PF09538 FYDLN_acid: Protein o 64.7 3.2 6.8E-05 36.4 1.0 27 478-505 10-37 (108)
142 KOG3268 Predicted E3 ubiquitin 63.7 6.8 0.00015 37.0 3.1 60 304-365 161-229 (234)
143 PF14447 Prok-RING_4: Prokaryo 63.6 3.3 7.2E-05 31.6 0.8 46 308-366 7-52 (55)
144 KOG3183 Predicted Zn-finger pr 63.5 0.99 2.1E-05 44.5 -2.6 109 322-452 22-138 (250)
145 TIGR00622 ssl1 transcription f 63.3 4.4 9.5E-05 35.7 1.6 26 424-449 78-103 (112)
146 COG1998 RPS31 Ribosomal protei 63.3 4.3 9.3E-05 30.2 1.3 26 478-503 20-46 (51)
147 COG5222 Uncharacterized conser 63.2 7.6 0.00017 39.6 3.5 45 308-361 274-318 (427)
148 PF07800 DUF1644: Protein of u 62.6 17 0.00036 34.0 5.3 36 308-345 2-49 (162)
149 PF12861 zf-Apc11: Anaphase-pr 62.2 4.1 8.9E-05 34.0 1.2 44 478-524 33-77 (85)
150 KOG3002 Zn finger protein [Gen 62.1 6.9 0.00015 40.6 3.1 47 305-364 45-91 (299)
151 PF02891 zf-MIZ: MIZ/SP-RING z 62.0 10 0.00022 28.3 3.2 47 309-361 3-49 (50)
152 KOG1701 Focal adhesion adaptor 62.0 2.9 6.3E-05 44.7 0.4 27 422-448 377-407 (468)
153 PF06524 NOA36: NOA36 protein; 61.7 5.2 0.00011 40.1 2.0 22 478-506 172-194 (314)
154 TIGR00622 ssl1 transcription f 60.0 8.4 0.00018 33.9 2.8 42 478-519 56-106 (112)
155 smart00661 RPOL9 RNA polymeras 59.6 7.7 0.00017 28.7 2.2 27 396-435 2-28 (52)
156 KOG4684 Uncharacterized conser 59.4 7.5 0.00016 37.8 2.6 54 391-445 135-199 (275)
157 TIGR00570 cdk7 CDK-activating 59.0 4.3 9.3E-05 42.1 1.0 41 478-518 4-45 (309)
158 KOG3579 Predicted E3 ubiquitin 58.7 5 0.00011 40.6 1.4 48 307-355 267-315 (352)
159 KOG2034 Vacuolar sorting prote 58.6 8.4 0.00018 44.9 3.3 39 305-344 814-852 (911)
160 PLN02638 cellulose synthase A 58.6 8.3 0.00018 46.2 3.3 56 478-534 18-75 (1079)
161 TIGR00595 priA primosomal prot 58.2 8 0.00017 43.2 3.0 34 478-511 223-262 (505)
162 PF09788 Tmemb_55A: Transmembr 57.9 9.7 0.00021 38.2 3.2 104 304-437 61-167 (256)
163 PF02150 RNA_POL_M_15KD: RNA p 57.6 6.7 0.00015 27.1 1.5 28 395-436 2-29 (35)
164 KOG2789 Putative Zn-finger pro 57.5 3.3 7.2E-05 43.7 -0.1 34 307-341 73-106 (482)
165 PLN02436 cellulose synthase A 57.1 9.5 0.00021 45.7 3.5 55 477-532 36-92 (1094)
166 COG1997 RPL43A Ribosomal prote 57.1 7.7 0.00017 32.4 2.0 28 478-505 36-64 (89)
167 PRK14873 primosome assembly pr 55.9 8.7 0.00019 44.4 2.9 34 478-511 393-431 (665)
168 PHA02926 zinc finger-like prot 55.5 6.2 0.00014 38.8 1.4 39 477-515 170-212 (242)
169 PF03854 zf-P11: P-11 zinc fin 55.4 7.3 0.00016 28.8 1.4 44 309-365 3-47 (50)
170 PLN02400 cellulose synthase 55.2 14 0.00031 44.3 4.5 57 477-534 36-94 (1085)
171 PRK14892 putative transcriptio 54.5 9.1 0.0002 33.0 2.1 28 477-504 21-52 (99)
172 KOG2164 Predicted E3 ubiquitin 54.1 3.9 8.4E-05 44.8 -0.3 41 478-523 187-230 (513)
173 PF14569 zf-UDP: Zinc-binding 53.7 5.2 0.00011 32.7 0.5 45 422-493 23-67 (80)
174 PLN02189 cellulose synthase 53.0 12 0.00026 44.8 3.4 54 478-532 35-90 (1040)
175 KOG1832 HIV-1 Vpr-binding prot 52.8 7.6 0.00017 45.2 1.7 19 519-537 1390-1408(1516)
176 PF06677 Auto_anti-p27: Sjogre 52.6 12 0.00025 26.9 2.0 22 478-501 18-41 (41)
177 PF14353 CpXC: CpXC protein 52.3 9.1 0.0002 34.3 1.9 17 477-493 38-54 (128)
178 PF14149 YhfH: YhfH-like prote 52.1 1.5 3.3E-05 30.6 -2.4 30 471-500 7-37 (37)
179 COG5574 PEX10 RING-finger-cont 52.1 4.2 9.1E-05 40.9 -0.4 37 307-343 94-132 (271)
180 PF07191 zinc-ribbons_6: zinc- 52.0 12 0.00025 30.2 2.2 33 479-513 3-41 (70)
181 COG3024 Uncharacterized protei 51.9 10 0.00023 29.7 1.8 15 476-490 6-20 (65)
182 PLN02915 cellulose synthase A 51.5 12 0.00026 44.8 3.1 55 478-533 16-72 (1044)
183 PF14835 zf-RING_6: zf-RING of 51.5 5.9 0.00013 31.3 0.4 28 478-512 8-38 (65)
184 TIGR03655 anti_R_Lar restricti 51.2 11 0.00025 28.3 2.0 29 478-506 2-38 (53)
185 KOG1941 Acetylcholine receptor 50.9 5.7 0.00012 42.0 0.3 51 305-361 362-413 (518)
186 COG2888 Predicted Zn-ribbon RN 50.6 16 0.00034 28.4 2.6 32 395-441 10-41 (61)
187 KOG0801 Predicted E3 ubiquitin 50.4 6.8 0.00015 36.4 0.7 30 306-335 175-204 (205)
188 COG1645 Uncharacterized Zn-fin 50.3 10 0.00022 34.3 1.8 24 478-510 29-52 (131)
189 PRK05580 primosome assembly pr 50.1 12 0.00027 43.4 2.9 33 479-511 392-430 (679)
190 PF08746 zf-RING-like: RING-li 49.0 11 0.00023 27.3 1.4 42 311-356 1-42 (43)
191 KOG0978 E3 ubiquitin ligase in 48.8 5.9 0.00013 45.4 0.1 12 432-443 660-671 (698)
192 PF07282 OrfB_Zn_ribbon: Putat 47.7 12 0.00025 29.6 1.6 26 478-503 29-55 (69)
193 PF01599 Ribosomal_S27: Riboso 47.6 13 0.00028 27.5 1.7 25 478-502 19-46 (47)
194 PF12906 RINGv: RING-variant d 47.1 16 0.00035 26.9 2.1 33 311-344 1-38 (47)
195 PRK04023 DNA polymerase II lar 47.1 11 0.00023 44.8 1.8 31 477-513 626-662 (1121)
196 TIGR00686 phnA alkylphosphonat 47.1 13 0.00028 32.4 1.9 24 478-502 3-27 (109)
197 PTZ00415 transmission-blocking 47.0 13 0.00028 46.3 2.4 9 525-533 147-155 (2849)
198 PF06906 DUF1272: Protein of u 46.7 14 0.00031 28.3 1.8 47 308-365 5-53 (57)
199 KOG1493 Anaphase-promoting com 46.6 3.6 7.9E-05 33.4 -1.4 52 308-364 20-81 (84)
200 TIGR01384 TFS_arch transcripti 46.6 11 0.00025 32.4 1.5 23 479-503 2-25 (104)
201 KOG1824 TATA-binding protein-i 46.3 9.6 0.00021 44.8 1.3 15 549-563 327-343 (1233)
202 PF11336 DUF3138: Protein of u 46.3 55 0.0012 35.4 6.7 59 40-102 38-96 (514)
203 KOG1940 Zn-finger protein [Gen 46.2 19 0.00042 36.8 3.3 47 307-361 157-204 (276)
204 PF14803 Nudix_N_2: Nudix N-te 46.0 13 0.00028 25.6 1.4 31 395-436 1-31 (34)
205 KOG0826 Predicted E3 ubiquitin 45.9 5.3 0.00011 41.4 -0.8 37 478-519 301-338 (357)
206 PRK00420 hypothetical protein; 45.7 14 0.0003 32.7 1.8 27 478-513 24-51 (112)
207 KOG3161 Predicted E3 ubiquitin 45.7 6.7 0.00015 44.0 -0.1 34 308-342 11-46 (861)
208 PRK14714 DNA polymerase II lar 44.5 14 0.0003 45.0 2.2 30 478-513 668-703 (1337)
209 PF03833 PolC_DP2: DNA polymer 44.1 7.5 0.00016 45.2 0.0 22 43-64 92-113 (900)
210 TIGR02443 conserved hypothetic 43.9 21 0.00046 27.7 2.4 26 478-503 10-40 (59)
211 PRK09710 lar restriction allev 43.8 19 0.00041 28.4 2.1 29 476-504 5-37 (64)
212 PLN03086 PRLI-interacting fact 43.7 32 0.0007 38.8 4.8 27 478-504 434-463 (567)
213 KOG2930 SCF ubiquitin ligase, 43.6 9.5 0.00021 32.9 0.5 30 327-364 79-108 (114)
214 KOG3895 Synaptic vesicle prote 43.6 6.6 0.00014 41.1 -0.5 83 154-247 125-213 (488)
215 PF03119 DNA_ligase_ZBD: NAD-d 43.1 23 0.0005 23.1 2.2 20 479-498 1-20 (28)
216 TIGR02300 FYDLN_acid conserved 42.1 13 0.00028 33.4 1.1 26 478-504 10-36 (129)
217 TIGR00599 rad18 DNA repair pro 41.6 9 0.00019 41.3 0.1 37 478-519 27-63 (397)
218 PF11014 DUF2852: Protein of u 40.7 66 0.0014 28.5 5.3 33 77-112 66-98 (115)
219 TIGR01206 lysW lysine biosynth 40.4 25 0.00054 26.9 2.3 27 478-504 3-32 (54)
220 PF01428 zf-AN1: AN1-like Zinc 40.0 20 0.00043 25.8 1.7 19 426-444 12-30 (43)
221 PF07975 C1_4: TFIIH C1-like d 39.9 15 0.00032 27.8 1.0 17 322-338 20-36 (51)
222 smart00531 TFIIE Transcription 39.8 63 0.0014 29.7 5.4 36 392-436 97-132 (147)
223 KOG1571 Predicted E3 ubiquitin 39.6 20 0.00043 37.7 2.3 44 306-363 303-346 (355)
224 PF09526 DUF2387: Probable met 39.6 27 0.00059 28.2 2.6 26 478-503 9-39 (71)
225 COG5109 Uncharacterized conser 39.5 23 0.0005 36.6 2.6 55 307-367 335-390 (396)
226 PRK10220 hypothetical protein; 39.3 21 0.00046 31.1 2.0 30 478-515 4-33 (111)
227 KOG2462 C2H2-type Zn-finger pr 39.0 33 0.00071 34.9 3.6 13 425-437 159-171 (279)
228 PRK14890 putative Zn-ribbon RN 38.7 19 0.00042 27.9 1.5 35 478-512 8-46 (59)
229 COG5194 APC11 Component of SCF 38.6 23 0.00049 29.2 1.9 49 308-364 31-81 (88)
230 PF15295 CCDC50_N: Coiled-coil 38.5 71 0.0015 29.0 5.2 23 30-53 22-44 (132)
231 PF14446 Prok-RING_1: Prokaryo 38.3 29 0.00062 26.5 2.3 34 307-340 4-38 (54)
232 PF12677 DUF3797: Domain of un 38.2 28 0.00061 25.9 2.2 27 477-503 13-47 (49)
233 PF09538 FYDLN_acid: Protein o 38.2 18 0.00039 31.7 1.4 9 427-435 26-34 (108)
234 KOG3970 Predicted E3 ubiquitin 38.0 26 0.00056 34.5 2.6 55 308-365 50-106 (299)
235 PF09723 Zn-ribbon_8: Zinc rib 38.0 35 0.00076 24.4 2.7 12 478-489 27-39 (42)
236 PRK03564 formate dehydrogenase 37.8 21 0.00047 37.1 2.2 14 435-448 212-225 (309)
237 KOG4275 Predicted E3 ubiquitin 37.6 6.7 0.00015 39.9 -1.5 30 308-340 300-330 (350)
238 KOG0827 Predicted E3 ubiquitin 37.6 8.8 0.00019 40.6 -0.7 131 210-366 115-247 (465)
239 KOG0825 PHD Zn-finger protein 37.3 21 0.00045 41.2 2.1 44 307-350 95-142 (1134)
240 PF05129 Elf1: Transcription e 37.0 20 0.00044 29.7 1.5 27 478-504 23-56 (81)
241 KOG3053 Uncharacterized conser 37.0 25 0.00055 35.3 2.4 58 304-363 16-81 (293)
242 PRK11827 hypothetical protein; 36.7 27 0.00058 27.3 2.0 25 478-502 9-34 (60)
243 cd01284 Riboflavin_deaminase-r 36.1 1.1E+02 0.0023 27.1 6.1 41 176-220 17-57 (115)
244 KOG2114 Vacuolar assembly/sort 35.8 28 0.0006 40.6 2.8 41 308-361 840-880 (933)
245 KOG0309 Conserved WD40 repeat- 35.8 23 0.00049 40.7 2.0 49 305-361 1025-1073(1081)
246 PF08271 TF_Zn_Ribbon: TFIIB z 35.7 34 0.00074 24.4 2.4 24 479-502 2-27 (43)
247 TIGR01562 FdhE formate dehydro 35.6 24 0.00051 36.8 2.1 14 435-448 210-223 (305)
248 COG5236 Uncharacterized conser 35.6 22 0.00048 37.1 1.8 51 304-363 57-107 (493)
249 PF14445 Prok-RING_2: Prokaryo 35.4 7.3 0.00016 29.1 -1.2 34 307-340 6-39 (57)
250 PF10122 Mu-like_Com: Mu-like 35.2 14 0.00031 27.7 0.3 25 478-502 5-32 (51)
251 KOG0824 Predicted E3 ubiquitin 35.1 15 0.00032 37.8 0.4 33 478-519 8-45 (324)
252 COG1594 RPB9 DNA-directed RNA 34.1 33 0.00071 30.3 2.5 27 478-504 3-32 (113)
253 cd01285 nucleoside_deaminase N 34.1 1.2E+02 0.0026 26.1 6.0 57 176-234 15-73 (109)
254 KOG2691 RNA polymerase II subu 33.8 36 0.00079 29.6 2.5 34 393-437 3-36 (113)
255 PF15135 UPF0515: Uncharacteri 33.8 44 0.00096 33.5 3.5 35 478-512 133-184 (278)
256 PF10083 DUF2321: Uncharacteri 33.7 15 0.00033 34.1 0.3 33 478-513 40-79 (158)
257 PLN02189 cellulose synthase 33.3 32 0.00069 41.4 2.8 46 422-494 48-93 (1040)
258 COG3357 Predicted transcriptio 33.3 17 0.00036 30.7 0.4 13 362-374 18-30 (97)
259 PLN02638 cellulose synthase A 33.2 26 0.00056 42.3 2.1 44 422-492 31-74 (1079)
260 KOG1824 TATA-binding protein-i 33.0 22 0.00047 42.0 1.4 19 538-556 325-343 (1233)
261 PF15616 TerY-C: TerY-C metal 32.8 25 0.00054 31.9 1.5 24 478-507 78-101 (131)
262 PF08792 A2L_zn_ribbon: A2L zi 32.7 38 0.00083 23.1 2.0 26 478-503 4-30 (33)
263 PRK14827 undecaprenyl pyrophos 32.4 83 0.0018 32.7 5.4 71 176-258 67-137 (296)
264 COG0450 AhpC Peroxiredoxin [Po 32.4 1.2E+02 0.0026 29.4 6.1 49 175-226 120-168 (194)
265 PF01614 IclR: Bacterial trans 32.3 1.6E+02 0.0036 25.6 6.8 46 174-221 76-122 (129)
266 PF06827 zf-FPG_IleRS: Zinc fi 31.3 34 0.00073 22.4 1.6 21 478-498 2-24 (30)
267 PF08882 Acetone_carb_G: Aceto 31.2 33 0.00072 30.1 1.9 13 494-506 23-35 (112)
268 PF01363 FYVE: FYVE zinc finge 30.9 26 0.00056 27.6 1.2 36 306-341 7-43 (69)
269 PF06844 DUF1244: Protein of u 30.4 34 0.00073 27.2 1.6 17 332-348 11-27 (68)
270 COG3813 Uncharacterized protei 30.3 34 0.00074 27.6 1.7 47 308-365 5-53 (84)
271 PHA02862 5L protein; Provision 30.1 50 0.0011 30.4 2.9 47 309-365 3-54 (156)
272 smart00659 RPOLCX RNA polymera 30.1 42 0.0009 24.4 2.0 23 479-502 4-27 (44)
273 KOG4362 Transcriptional regula 29.8 9.9 0.00021 43.4 -1.9 57 305-369 18-74 (684)
274 TIGR00373 conserved hypothetic 29.4 85 0.0018 29.3 4.6 32 391-436 106-137 (158)
275 PRK14829 undecaprenyl pyrophos 29.4 1.1E+02 0.0025 30.7 5.7 73 174-258 12-84 (243)
276 PRK06266 transcription initiat 29.3 89 0.0019 29.9 4.7 30 392-435 115-144 (178)
277 PF14354 Lar_restr_allev: Rest 29.3 38 0.00083 25.9 1.9 12 477-488 3-14 (61)
278 PLN02436 cellulose synthase A 29.3 35 0.00075 41.2 2.3 21 422-442 50-70 (1094)
279 TIGR03142 cytochro_ccmI cytoch 29.1 39 0.00086 29.8 2.1 42 81-122 35-76 (117)
280 PRK13190 putative peroxiredoxi 28.8 1E+02 0.0022 29.8 5.2 76 176-268 114-189 (202)
281 KOG0320 Predicted E3 ubiquitin 28.7 14 0.00031 35.1 -0.8 38 478-518 132-169 (187)
282 COG0590 CumB Cytosine/adenosin 28.5 1.3E+02 0.0028 27.9 5.6 43 177-221 27-71 (152)
283 COG1594 RPB9 DNA-directed RNA 28.5 39 0.00084 29.9 2.0 31 394-437 2-32 (113)
284 KOG2879 Predicted E3 ubiquitin 28.4 25 0.00054 35.7 0.8 40 478-523 240-281 (298)
285 PRK15370 E3 ubiquitin-protein 28.3 70 0.0015 37.7 4.6 51 33-105 608-658 (754)
286 COG0295 Cdd Cytidine deaminase 27.7 1.7E+02 0.0037 26.7 6.0 30 207-237 54-83 (134)
287 PRK15000 peroxidase; Provision 27.7 1.9E+02 0.0041 28.0 6.8 73 176-265 122-194 (200)
288 KOG3088 Secretory carrier memb 27.4 3.3E+02 0.0072 28.1 8.4 16 87-102 58-73 (313)
289 PF12760 Zn_Tnp_IS1595: Transp 26.9 1E+02 0.0023 22.3 3.7 25 478-502 19-45 (46)
290 PRK14830 undecaprenyl pyrophos 26.9 1.5E+02 0.0032 30.1 6.0 73 174-258 20-92 (251)
291 TIGR02300 FYDLN_acid conserved 26.7 35 0.00076 30.7 1.3 11 426-436 25-35 (129)
292 PRK14833 undecaprenyl pyrophos 26.6 1.4E+02 0.0031 29.8 5.8 73 174-258 2-74 (233)
293 PRK14831 undecaprenyl pyrophos 26.5 1.5E+02 0.0032 30.0 5.9 73 174-258 18-90 (249)
294 PLN02400 cellulose synthase 26.3 41 0.00088 40.7 2.1 44 422-492 50-93 (1085)
295 PF03833 PolC_DP2: DNA polymer 26.3 22 0.00048 41.6 0.0 33 477-515 655-693 (900)
296 PF04216 FdhE: Protein involve 26.0 37 0.0008 35.0 1.6 34 478-511 173-220 (290)
297 PRK14828 undecaprenyl pyrophos 25.9 1.5E+02 0.0032 30.2 5.8 74 174-259 24-98 (256)
298 PF07754 DUF1610: Domain of un 25.8 61 0.0013 20.5 1.9 12 424-435 13-24 (24)
299 COG1579 Zn-ribbon protein, pos 25.8 57 0.0012 32.7 2.8 60 367-435 167-229 (239)
300 PTZ00415 transmission-blocking 25.7 42 0.0009 42.3 2.1 21 478-498 94-114 (2849)
301 PF14205 Cys_rich_KTR: Cystein 25.6 44 0.00095 25.5 1.5 9 476-484 3-11 (55)
302 KOG1602 Cis-prenyltransferase 25.4 2.2E+02 0.0047 29.0 6.7 74 174-259 34-107 (271)
303 PF14471 DUF4428: Domain of un 25.3 51 0.0011 24.8 1.8 30 310-341 1-30 (51)
304 PHA02825 LAP/PHD finger-like p 25.0 73 0.0016 29.9 3.1 50 307-366 7-61 (162)
305 PRK14834 undecaprenyl pyrophos 24.7 2.1E+02 0.0045 29.0 6.6 73 174-258 12-84 (249)
306 COG2824 PhnA Uncharacterized Z 24.4 54 0.0012 28.5 2.0 23 478-502 4-28 (112)
307 smart00834 CxxC_CXXC_SSSS Puta 24.4 43 0.00093 23.2 1.2 10 479-488 7-16 (41)
308 PLN02915 cellulose synthase A 24.1 47 0.001 40.0 2.1 46 422-494 29-74 (1044)
309 COG1096 Predicted RNA-binding 24.0 52 0.0011 31.7 2.0 25 478-504 150-175 (188)
310 KOG2807 RNA polymerase II tran 23.9 39 0.00084 35.2 1.2 28 311-338 333-360 (378)
311 PRK13189 peroxiredoxin; Provis 23.9 1.1E+02 0.0024 30.2 4.5 72 180-268 127-202 (222)
312 PF03115 Astro_capsid: Astrovi 23.8 26 0.00057 41.1 0.0 20 238-258 246-269 (787)
313 PF13834 DUF4193: Domain of un 23.8 37 0.0008 29.2 0.9 33 304-337 66-98 (99)
314 PF00628 PHD: PHD-finger; Int 23.6 42 0.00091 24.5 1.1 34 310-343 1-34 (51)
315 cd03016 PRX_1cys Peroxiredoxin 23.6 1.5E+02 0.0032 28.6 5.3 43 181-226 119-161 (203)
316 PRK12286 rpmF 50S ribosomal pr 23.4 45 0.00098 25.7 1.2 21 477-502 27-48 (57)
317 PRK13191 putative peroxiredoxi 23.4 1.4E+02 0.003 29.4 5.0 43 180-225 125-167 (215)
318 PRK09521 exosome complex RNA-b 23.3 56 0.0012 31.4 2.2 26 478-504 150-176 (189)
319 TIGR03826 YvyF flagellar opero 23.1 62 0.0013 29.7 2.3 25 477-513 81-105 (137)
320 KOG2932 E3 ubiquitin ligase in 23.1 37 0.0008 35.1 0.9 32 308-341 90-121 (389)
321 PF11023 DUF2614: Protein of u 23.0 48 0.001 29.2 1.4 23 425-447 67-97 (114)
322 cd02960 AGR Anterior Gradient 23.0 1.1E+02 0.0023 27.8 3.8 47 174-224 72-125 (130)
323 COG2816 NPY1 NTP pyrophosphohy 22.9 69 0.0015 32.9 2.8 28 477-504 111-139 (279)
324 PF13382 Adenine_deam_C: Adeni 22.9 1.6E+02 0.0034 28.1 5.0 47 179-226 89-136 (171)
325 PF05715 zf-piccolo: Piccolo Z 22.9 32 0.00068 26.7 0.3 39 478-516 3-44 (61)
326 KOG1039 Predicted E3 ubiquitin 22.4 30 0.00064 36.7 0.1 39 431-490 185-223 (344)
327 PRK14835 undecaprenyl pyrophos 22.4 1.8E+02 0.0039 29.9 5.8 74 175-260 40-113 (275)
328 PRK14837 undecaprenyl pyrophos 22.4 2.1E+02 0.0045 28.7 6.0 74 175-260 5-78 (230)
329 PRK14842 undecaprenyl pyrophos 22.4 1.9E+02 0.0042 29.0 5.9 75 174-260 6-80 (241)
330 PF13453 zf-TFIIB: Transcripti 22.3 54 0.0012 23.2 1.4 10 396-407 1-10 (41)
331 PF01873 eIF-5_eIF-2B: Domain 22.2 74 0.0016 28.6 2.6 34 468-503 86-123 (125)
332 PRK13599 putative peroxiredoxi 22.0 1.5E+02 0.0033 29.1 5.0 44 180-226 120-163 (215)
333 PRK14841 undecaprenyl pyrophos 21.9 1.9E+02 0.0042 28.9 5.7 64 188-260 12-75 (233)
334 PF02318 FYVE_2: FYVE-type zin 21.9 97 0.0021 27.4 3.3 35 476-511 53-88 (118)
335 PF10272 Tmpp129: Putative tra 21.7 1.7E+02 0.0037 31.2 5.6 62 304-365 267-352 (358)
336 COG1198 PriA Primosomal protei 21.5 59 0.0013 38.0 2.3 67 372-444 405-484 (730)
337 COG4640 Predicted membrane pro 21.3 42 0.00091 35.8 0.9 8 478-485 2-9 (465)
338 TIGR00055 uppS undecaprenyl di 21.2 1.7E+02 0.0037 29.1 5.1 46 207-259 25-70 (226)
339 COG0266 Nei Formamidopyrimidin 21.2 65 0.0014 33.0 2.2 21 478-498 246-268 (273)
340 KOG0943 Predicted ubiquitin-pr 21.1 59 0.0013 39.6 2.1 10 37-46 960-969 (3015)
341 PF03604 DNA_RNApol_7kD: DNA d 21.0 38 0.00083 22.9 0.4 10 478-487 18-27 (32)
342 PF01780 Ribosomal_L37ae: Ribo 20.9 58 0.0013 27.6 1.5 28 478-505 36-64 (90)
343 PF00643 zf-B_box: B-box zinc 20.9 30 0.00065 24.3 -0.2 24 426-449 14-37 (42)
344 cd00021 BBOX B-Box-type zinc f 20.8 55 0.0012 22.2 1.2 26 425-450 10-35 (39)
345 PF10426 zf-RAG1: Recombinatio 20.8 47 0.001 22.2 0.7 22 352-373 3-24 (30)
346 KOG1991 Nuclear transport rece 20.8 56 0.0012 38.9 1.8 19 33-51 490-508 (1010)
347 PF11682 DUF3279: Protein of u 20.6 60 0.0013 29.4 1.6 13 478-490 111-123 (128)
348 COG1645 Uncharacterized Zn-fin 20.6 64 0.0014 29.3 1.8 24 395-435 29-52 (131)
349 smart00064 FYVE Protein presen 20.6 39 0.00085 26.4 0.4 37 308-344 10-47 (68)
350 PF04032 Rpr2: RNAse P Rpr2/Rp 20.4 72 0.0016 26.0 2.0 19 434-452 45-63 (85)
351 KOG0943 Predicted ubiquitin-pr 20.2 65 0.0014 39.2 2.2 13 112-124 1053-1065(3015)
352 PF02148 zf-UBP: Zn-finger in 20.2 1.1E+02 0.0024 23.7 2.9 32 311-344 1-36 (63)
353 PRK12495 hypothetical protein; 20.2 57 0.0012 32.2 1.5 29 477-514 42-70 (226)
No 1
>KOG1812 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=100.00 E-value=6.1e-54 Score=452.15 Aligned_cols=351 Identities=47% Similarity=0.924 Sum_probs=303.6
Q ss_pred EEEEccceeecccCCCCCCCceEEEEEEeC-CCCeEEEeeeeccccC-CChHHHHHHHHHHHHHHHHhcCCCeEEeecCC
Q 008441 158 KVYSKGLVIEELVNGERVSLSAIGVAICDQ-MDNLIFELKKPLIKSG-LNKSAAETKALIEGLNAALSMELDRVRVFIDC 235 (565)
Q Consensus 158 ~vyfdGa~~~~~~~~~npg~ag~Gv~i~~~-~~~~~~~~~~~~~~~~-tn~n~AEy~Ali~gL~~al~l~~~~v~v~~DS 235 (565)
++||.|.++.+.+ +. ...+|.||+|.+. +....+.+.....+.. .+.-.||++||+.||.+|+++|+.++.++.|+
T Consensus 1 ~l~~k~lv~~e~~-~~-~~~~g~~vai~d~~d~~~~f~~k~~~~~~~~~~~~~ae~~al~~~l~ea~~~~~~~~~~~~d~ 78 (384)
T KOG1812|consen 1 RLYFKGLVSEESI-ND-ILLAGFGVAICDEHDDDLLFQMKASDHDSDSITPLEAELMALKRGLTEALELGLNHIVIYCDD 78 (384)
T ss_pred CCccccchhhhhh-hh-hhcccCceeeeccccHHHHHHhhcCcccccccchhhHHHHHHhhccHHHHhhccccceEeccc
Confidence 3799999977643 22 5679999999997 4556666666664433 66689999999999999999999999999999
Q ss_pred ccchhhccCccCCcch-hhHHHHHHHHHHhhhcccccccccccc-chHHHHHHHHHhhhcccccccccccCcccccccce
Q 008441 236 FPLFQFVTGRWPAKQR-KISVLVDQVSLLEKRFSYFKPRHVARN-DMKYVYELARAAINSQMTVPAEISRGKTINETCVI 313 (565)
Q Consensus 236 ~lv~~qv~G~w~~k~~-~l~~l~~~v~~Ll~~F~~~~~~~V~R~-~n~~Ad~LA~eal~sqi~~~~~~~~~~~~~~~C~I 313 (565)
.++++.+.|+..+++. ++..+++++..+..+|......++++. +.+++.+||.+++.+.. .......+|.|
T Consensus 79 ~~~~~~v~~~~~~~~~~~~~~l~~~v~~~r~~l~~~~~i~~~~~~d~~~~~~lA~e~i~s~~-------~~~~~~~~C~i 151 (384)
T KOG1812|consen 79 ELIYESVAGREKPEQHRKIVLLVELVQRIREQLTSSEPILVPKNADIKFAYKLAREAIVSQL-------PSKLPKEECGI 151 (384)
T ss_pred HHHHHHHhhhhhHHHHHHHHHHHHHHHHHHHHhhcccceecccchhhHHHHHHHHHhhcccc-------ccccccccCcc
Confidence 9999999999999988 799999999999999999999888776 88999999999998711 23345789999
Q ss_pred ec-cccccCCceeecCCCcccchhhHHHHHHHHHhCCCCCCCCCCCCCCccchhhHHHhhhhHHHHHHHHHHHHhcCCCC
Q 008441 314 CL-EDTDVGHMFSIDGCLHRYCFLCMKKHIEEKLRQGMEPTCPHEGCKSKLEVESCRIFLTLKLFEIWNQRMKEALIPVT 392 (565)
Q Consensus 314 C~-e~~~~~~~~~l~~C~H~fC~~Cl~~~i~~~i~~g~~~kCP~~~C~~~l~~~~i~~lL~~e~~e~y~~~~~e~~i~~~ 392 (565)
|+ +......++.+..|+|.||.+|+++|++++..++..|+||..+|+..++.+.+..+|++++.++|.+++.+..++..
T Consensus 152 C~~e~~~~~~~f~~~~C~H~fC~~C~k~~iev~~~~~~~~~C~~~~C~~~l~~~~c~~llt~kl~e~~e~~~~e~~i~~~ 231 (384)
T KOG1812|consen 152 CFVEDPEAEDMFSVLKCGHRFCKDCVKQHIEVKLLSGTVIRCPHDGCESRLTLESCRKLLTPKLREMWEQRLKEEVIPSL 231 (384)
T ss_pred CccccccHhhhHHHhcccchhhhHHhHHHhhhhhccCCCccCCCCCCCccCCHHHHhhhcCHHHHHHHHHHHHHHhhhhh
Confidence 99 55455577778899999999999999999988888999999999999999999999999999999999999999877
Q ss_pred CcccccCCCCCCcccchhhhhccCCCcccccccCceeCCCCCCceecccCCCcCCCCChhhHhhhCCCCChhHHHHHHHH
Q 008441 393 EKVYCPYPKCSALMSKSEIERDASSSSFVGRRLGARKCTKCHRRFCIDCKVPWHNNMTCIYYKRLNPNPPTEDVKLKSLA 472 (565)
Q Consensus 393 ~~~~CP~p~C~~~i~~~~~~e~~~s~~~~~~~~~~~~C~~C~~~fC~~C~~~~H~g~tC~e~~~~~~~~~~ed~~l~~l~ 472 (565)
+.+|||+|+|..++...++. .........|+.|+..||.+|+.+||.+.+|++|+++.......+..++.++
T Consensus 232 ~~~ycp~~~C~~l~~~~el~--------~~~~~~~~~C~~C~~~fCv~C~~~wh~~~sC~eykk~~~~~~~d~~~~~~la 303 (384)
T KOG1812|consen 232 DRVYCPYPRCSSLMSKTELS--------SEVKSKRRPCVKCHELFCVKCKVPWHANLSCEEYKKLNPEEYVDDITLKYLA 303 (384)
T ss_pred hcccCCCCCchHhhhhhhhc--------cchhhcccccccCCCceeecCCCcCCCCCCHHHHHHhCCcccccHHHHHHHH
Confidence 77799999999999877652 1345667889999999999999999999999999999987776677777777
Q ss_pred hcCCccccCCCCceeEecCCcceEEeecCccccccccccccCCCCCc-CCCCCCCC
Q 008441 473 SSNLWRQCVKCNHLIELAEGCFHMTCRCGHEFCYNCGAEWKNKKATC-SCPLWDED 527 (565)
Q Consensus 473 ~~~~~k~CPkC~~~IEK~~GCnHMtC~Cg~~FCw~C~~~~~~~~~~c-~C~~~~~~ 527 (565)
+.||+||+|++.|++.+|||||||+||++|||.|+.+|..+.+.| .|..+++.
T Consensus 304 --~~wr~CpkC~~~ie~~~GCnhm~CrC~~~fcy~C~~~~~~~~~~~~~~~r~~~~ 357 (384)
T KOG1812|consen 304 --KRWRQCPKCKFMIELSEGCNHMTCRCGHQFCYMCGGDWKTHNGECYECCRYKES 357 (384)
T ss_pred --HhcCcCcccceeeeecCCcceEEeeccccchhhcCcchhhCCccccCccccccc
Confidence 779999999999999999999999999999999999999888765 55544444
No 2
>KOG1814 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=99.97 E-value=3.8e-32 Score=276.12 Aligned_cols=194 Identities=26% Similarity=0.584 Sum_probs=158.8
Q ss_pred ccccccceeccccccCCceeecCCCcccchhhHHHHHHHHHhCCCC--CCCCCCCCCCccchhhHHHhhhhHHHHHHHHH
Q 008441 306 TINETCVICLEDTDVGHMFSIDGCLHRYCFLCMKKHIEEKLRQGME--PTCPHEGCKSKLEVESCRIFLTLKLFEIWNQR 383 (565)
Q Consensus 306 ~~~~~C~IC~e~~~~~~~~~l~~C~H~fC~~Cl~~~i~~~i~~g~~--~kCP~~~C~~~l~~~~i~~lL~~e~~e~y~~~ 383 (565)
...+.|.||+++......+..++|+|.||+.|++.|++..|.+|.+ ++||+.+|+...+...++.+|+.+++++|...
T Consensus 182 ~slf~C~ICf~e~~G~~c~~~lpC~Hv~Ck~C~kdY~~~~i~eg~v~~l~Cp~~~C~~~a~~g~vKelvg~EL~arYe~l 261 (445)
T KOG1814|consen 182 NSLFDCCICFEEQMGQHCFKFLPCSHVFCKSCLKDYFTIQIQEGQVSCLKCPDPKCGSVAPPGQVKELVGDELFARYEKL 261 (445)
T ss_pred hhcccceeeehhhcCcceeeecccchHHHHHHHHHHHHHhhhcceeeeecCCCCCCcccCCchHHHHHHHHHHHHHHHHH
Confidence 3578999999999887888888999999999999999999999987 79999999999999999999999999999998
Q ss_pred HHHhcCC-CCCcccccCCCCCCcccchhhhhccCCCcccccccCceeCCCCCCceecccCCCcCCCCChhh--------H
Q 008441 384 MKEALIP-VTEKVYCPYPKCSALMSKSEIERDASSSSFVGRRLGARKCTKCHRRFCIDCKVPWHNNMTCIY--------Y 454 (565)
Q Consensus 384 ~~e~~i~-~~~~~~CP~p~C~~~i~~~~~~e~~~s~~~~~~~~~~~~C~~C~~~fC~~C~~~~H~g~tC~e--------~ 454 (565)
+.+..+. .++.+|||++.|+.+.. ..+....+.|.+|++.||+.|+..||+...|.- +
T Consensus 262 ~lqk~l~~msdv~yCPr~~Cq~p~~-------------~d~~~~l~~CskCnFaFCtlCk~t~HG~s~Ck~~~~~~~~l~ 328 (445)
T KOG1814|consen 262 MLQKTLELMSDVVYCPRACCQLPVK-------------QDPGRALAICSKCNFAFCTLCKLTWHGVSPCKVKAEKLIELY 328 (445)
T ss_pred HHHHHHHhhcccccCChhhccCccc-------------cCchhhhhhhccCccHHHHHHHHhhcCCCcccCchHHHHHHH
Confidence 8877764 57889999999998762 234567789999999999999999999999963 2
Q ss_pred hhhCCCCChhHH---------HHH---------HHHhcCCccccCCCCceeEecCCcceEEe-ecCcccccccccccc
Q 008441 455 KRLNPNPPTEDV---------KLK---------SLASSNLWRQCVKCNHLIELAEGCFHMTC-RCGHEFCYNCGAEWK 513 (565)
Q Consensus 455 ~~~~~~~~~ed~---------~l~---------~l~~~~~~k~CPkC~~~IEK~~GCnHMtC-~Cg~~FCw~C~~~~~ 513 (565)
..|.....+... .++ .++.. +-|+||+|+++|||++|||||+| .|++.|||+|+....
T Consensus 329 ~~~~~~d~a~k~ele~Ryg~rvve~~vn~~lsekwl~~-N~krCP~C~v~IEr~eGCnKM~C~~c~~~fc~~c~~~l~ 405 (445)
T KOG1814|consen 329 LEYLEADEARKRELEKRYGKRVVEELVNDFLSEKWLES-NSKRCPKCKVVIERSEGCNKMHCTKCGTYFCWICAELLY 405 (445)
T ss_pred HHHhhcCHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHh-cCCCCCcccceeecCCCccceeeccccccceeehhhhcC
Confidence 223222111000 011 11111 23999999999999999999999 699999999988655
No 3
>KOG1815 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=99.94 E-value=4.2e-28 Score=262.53 Aligned_cols=250 Identities=21% Similarity=0.419 Sum_probs=189.7
Q ss_pred HHHHHHHHHhhhccccccccccccchHHHHHHHHHhhhcccccccccccCcccccccceeccccccCCceeecCCCcccc
Q 008441 255 VLVDQVSLLEKRFSYFKPRHVARNDMKYVYELARAAINSQMTVPAEISRGKTINETCVICLEDTDVGHMFSIDGCLHRYC 334 (565)
Q Consensus 255 ~l~~~v~~Ll~~F~~~~~~~V~R~~n~~Ad~LA~eal~sqi~~~~~~~~~~~~~~~C~IC~e~~~~~~~~~l~~C~H~fC 334 (565)
.-......|+.+|.|...+++.+.......- ...+...... ......+|.||++..+. .++ ...|+|.||
T Consensus 25 ~~~~~~~~ll~~~~W~~~kl~~~~~~~~~~~--~~~~g~~~~~------~~~~~~~c~ic~~~~~~-~~~-~~~c~H~~c 94 (444)
T KOG1815|consen 25 LSHAVARILLAHFCWNVEKLLEEWVEDEETG--CFFVGLLLWP------KKKGDVQCGICVESYDG-EII-GLGCGHPFC 94 (444)
T ss_pred CCHHHHHHHHHhcCcchHHHHHHHHhcCcch--hhhccccccC------CCCccccCCcccCCCcc-hhh-hcCCCcHHH
Confidence 3345667788888886655543322110000 0001111110 33456899999998765 444 449999999
Q ss_pred hhhHHHHHHHHHhCCCC--CCCCCCCCCCccchhhHHHhhhh-HHHHHHHHHHHHhcCC-CCCcccccCCCCCCcccchh
Q 008441 335 FLCMKKHIEEKLRQGME--PTCPHEGCKSKLEVESCRIFLTL-KLFEIWNQRMKEALIP-VTEKVYCPYPKCSALMSKSE 410 (565)
Q Consensus 335 ~~Cl~~~i~~~i~~g~~--~kCP~~~C~~~l~~~~i~~lL~~-e~~e~y~~~~~e~~i~-~~~~~~CP~p~C~~~i~~~~ 410 (565)
..||..|+..+|..+.. ++||..+|...+..+.|..++++ ....+|.+.+...++. ....+|||.|+|+..+...
T Consensus 95 ~~cw~~yl~~kI~~~~~~~i~cp~~~C~a~v~~~~i~~~~s~~~~~~ky~~~i~~syve~~~~lkwCP~~~C~~av~~~- 173 (444)
T KOG1815|consen 95 PPCWTGYLGTKIHEGEEAKIKCPAHGCPALVGEDTVEKLVSDKEDKEKYQRYILRSYVEDNVPLKWCPAPGCGLAVKFG- 173 (444)
T ss_pred HHHHHHHhhheeeccccccccCCCCCccccCCCceeeeecCCHHHHHHHHHHHHHHHHhcCCccccCCCCCCCceeecc-
Confidence 99999999999988766 79999999999999999999888 4888898888777775 3357899999999887421
Q ss_pred hhhccCCCcccccccCceeCCCCCCceecccCCCcCCCCChhhHhhhCCCCChhHHHHHHHHhcCCccccCCCCceeEec
Q 008441 411 IERDASSSSFVGRRLGARKCTKCHRRFCIDCKVPWHNNMTCIYYKRLNPNPPTEDVKLKSLASSNLWRQCVKCNHLIELA 490 (565)
Q Consensus 411 ~~e~~~s~~~~~~~~~~~~C~~C~~~fC~~C~~~~H~g~tC~e~~~~~~~~~~ed~~l~~l~~~~~~k~CPkC~~~IEK~ 490 (565)
......+.| .|+..||+.|+.+||.|.+|.....|......+...+.++ .. .+++||+|.++|||+
T Consensus 174 -----------~~~~~~v~C-~~g~~FC~~C~~~~H~p~~C~~~~~wl~k~~~~se~~~wi-~~-ntk~CP~c~~~iek~ 239 (444)
T KOG1815|consen 174 -----------SLESVEVDC-GCGHEFCFACGEESHSPVSCPGAKKWLKKCRDDSETINWI-LA-NTKECPKCKVPIEKD 239 (444)
T ss_pred -----------CCCccceeC-CCCchhHhhccccccCCCcccchHHHHHhhhhhhhhhhhh-hc-cCccCCCcccchhcc
Confidence 335677899 5777999999999999999999999998877666555533 32 248899999999999
Q ss_pred CCcceEEee---cCccccccccccccCCCCC--cCCCCCCCCCc
Q 008441 491 EGCFHMTCR---CGHEFCYNCGAEWKNKKAT--CSCPLWDEDNI 529 (565)
Q Consensus 491 ~GCnHMtC~---Cg~~FCw~C~~~~~~~~~~--c~C~~~~~~~~ 529 (565)
+|||||+|. |+++|||.|++.|..|+.+ +.|+.|.....
T Consensus 240 ~gc~~~~~~~~~c~~~FCw~Cl~~~~~h~~~~~~~c~~~~~~~~ 283 (444)
T KOG1815|consen 240 GGCNHMTCKSASCKHEFCWVCLASLSDHGSSTGYSCNRYVDGKS 283 (444)
T ss_pred CCccccccccCCcCCeeceeeecccccccccceeeeeeeechhh
Confidence 999999994 9999999999999999764 78888866553
No 4
>KOG0006 consensus E3 ubiquitin-protein ligase (Parkin protein) [Posttranslational modification, protein turnover, chaperones]
Probab=99.92 E-value=9e-26 Score=221.66 Aligned_cols=239 Identities=21% Similarity=0.448 Sum_probs=168.0
Q ss_pred HHHHHHhhhccccccccccccchHHHHHHHHHhhh-cccccccccccCcccccccceeccccccCCceeecCCC--cccc
Q 008441 258 DQVSLLEKRFSYFKPRHVARNDMKYVYELARAAIN-SQMTVPAEISRGKTINETCVICLEDTDVGHMFSIDGCL--HRYC 334 (565)
Q Consensus 258 ~~v~~Ll~~F~~~~~~~V~R~~n~~Ad~LA~eal~-sqi~~~~~~~~~~~~~~~C~IC~e~~~~~~~~~l~~C~--H~fC 334 (565)
++|..-.+-=..++.-++|--..+|.++.+..... +....+......+.++.+|..|-+- ..++-+++|. |..|
T Consensus 170 dDVLks~Ripg~Ces~~~pg~fAEFfFKC~ah~~~~k~~aa~lhli~~N~~ni~C~~Ctdv---~~~vlvf~Cns~HvtC 246 (446)
T KOG0006|consen 170 DDVLKSKRIPGVCESCCTPGLFAEFFFKCGAHPTSDKETAAALHLIATNSRNITCITCTDV---RSPVLVFQCNSRHVTC 246 (446)
T ss_pred hhhhhcccCccccccccCCcchHhheehhccCCCccccchhHHHHhhcccccceeEEecCC---ccceEEEecCCceeeh
Confidence 34444433444556666666666666666543222 1111122223567788999999764 4455556898 9999
Q ss_pred hhhHHHHHHHHHhCC---------CCCCCCCCCCCCccchh-hHHHhhhhHHHHHHHHHHHHhcCCCCCcccccCCCCCC
Q 008441 335 FLCMKKHIEEKLRQG---------MEPTCPHEGCKSKLEVE-SCRIFLTLKLFEIWNQRMKEALIPVTEKVYCPYPKCSA 404 (565)
Q Consensus 335 ~~Cl~~~i~~~i~~g---------~~~kCP~~~C~~~l~~~-~i~~lL~~e~~e~y~~~~~e~~i~~~~~~~CP~p~C~~ 404 (565)
.+|++.|...++++. +.+.||. +|...+-.+ .-.++|+.+.+.+|+++..+..+.....+.||+|+|+.
T Consensus 247 ~dCFr~yc~~Rl~~rqf~~~p~~gyslpc~a-gc~~s~i~e~HHF~ilg~e~Y~rYQr~atEe~vlq~gGVlCP~pgCG~ 325 (446)
T KOG0006|consen 247 LDCFRLYCVTRLNDRQFVHDPQLGYSLPCVA-GCPNSLIKELHHFRILGEEQYNRYQRYATEECVLQMGGVLCPRPGCGA 325 (446)
T ss_pred HHhhhhHhhhcccccccccCccccccccccC-CCchHHHHhhhhheecchhHHHHHHHhhhhhheeecCCEecCCCCCCc
Confidence 999999999998664 3357986 788765443 23577999999999999999888877789999999998
Q ss_pred cccchhhhhccCCCcccccccCceeCCC-CCCceecccCCCcCCCCChhhHhh--------hCCCC-ChhHHHH---HHH
Q 008441 405 LMSKSEIERDASSSSFVGRRLGARKCTK-CHRRFCIDCKVPWHNNMTCIYYKR--------LNPNP-PTEDVKL---KSL 471 (565)
Q Consensus 405 ~i~~~~~~e~~~s~~~~~~~~~~~~C~~-C~~~fC~~C~~~~H~g~tC~e~~~--------~~~~~-~~ed~~l---~~l 471 (565)
.+. ..+...++.|+. |++.||..|+..||.+. |.+.-. +.... .++.... ...
T Consensus 326 gll-------------~EPD~rkvtC~~gCgf~FCR~C~e~yh~ge-C~~~~~as~t~tc~y~vde~~a~~arwd~as~~ 391 (446)
T KOG0006|consen 326 GLL-------------PEPDQRKVTCEGGCGFAFCRECKEAYHEGE-CSAVFEASGTTTCAYRVDERAAEQARWDAASKE 391 (446)
T ss_pred ccc-------------cCCCCCcccCCCCchhHhHHHHHhhhcccc-ceeeeccccccceeeecChhhhhhhhhhhhhhh
Confidence 763 345778999986 99999999999999875 431110 00010 0111111 111
Q ss_pred HhcCCccccCCCCceeEecCCcceEEe-e--cCccccccccccccC
Q 008441 472 ASSNLWRQCVKCNHLIELAEGCFHMTC-R--CGHEFCYNCGAEWKN 514 (565)
Q Consensus 472 ~~~~~~k~CPkC~~~IEK~~GCnHMtC-~--Cg~~FCw~C~~~~~~ 514 (565)
..+..+|+||+|+++.||++||+||.| + ||.+|||.|+-+|+.
T Consensus 392 TIk~tTkpCPkChvptErnGGCmHm~Ct~~~Cg~eWCw~C~tEW~r 437 (446)
T KOG0006|consen 392 TIKKTTKPCPKCHVPTERNGGCMHMKCTQPQCGLEWCWNCGTEWNR 437 (446)
T ss_pred hhhhccCCCCCccCccccCCceEEeecCCCCCCceeEeccCChhhh
Confidence 123456999999999999999999999 4 999999999999984
No 5
>PRK07708 hypothetical protein; Validated
Probab=99.89 E-value=4e-23 Score=202.52 Aligned_cols=134 Identities=17% Similarity=0.257 Sum_probs=117.0
Q ss_pred CceEEEEEccceeecccCCCCCCCceEEEEEEeCCCCeEEEee--eeccccCCChHHHHHHHHHHHHHHHHhcCCCe--E
Q 008441 154 DYFFKVYSKGLVIEELVNGERVSLSAIGVAICDQMDNLIFELK--KPLIKSGLNKSAAETKALIEGLNAALSMELDR--V 229 (565)
Q Consensus 154 ~~~~~vyfdGa~~~~~~~~~npg~ag~Gv~i~~~~~~~~~~~~--~~~~~~~tn~n~AEy~Ali~gL~~al~l~~~~--v 229 (565)
...|+|||||++ .+ |||++|+|++|+++.|...+.+. ..+ +...+||+|||.||+.||+.|+++|+++ |
T Consensus 71 p~~~~vY~DGs~-~~-----n~g~aG~GvVI~~~~g~~~~~~~~~~~l-~~~~TNN~AEy~Ali~aL~~A~e~g~~~~~V 143 (219)
T PRK07708 71 PHEILVYFDGGF-DK-----ETKLAGLGIVIYYKQGNKRYRIRRNAYI-EGIYDNNEAEYAALYYAMQELEELGVKHEPV 143 (219)
T ss_pred CCcEEEEEeecc-CC-----CCCCcEEEEEEEECCCCEEEEEEeeccc-cccccCcHHHHHHHHHHHHHHHHcCCCcceE
Confidence 346999999998 54 99999999999998777655443 455 4333448999999999999999999987 8
Q ss_pred EeecCCccchhhccCccCCcchhhHHHHHHHHHHhhhccc-cccccccccchHHHHHHHHHhhhcc
Q 008441 230 RVFIDCFPLFQFVTGRWPAKQRKISVLVDQVSLLEKRFSY-FKPRHVARNDMKYVYELARAAINSQ 294 (565)
Q Consensus 230 ~v~~DS~lv~~qv~G~w~~k~~~l~~l~~~v~~Ll~~F~~-~~~~~V~R~~n~~Ad~LA~eal~sq 294 (565)
.|++||++|++|+.|.|+.+++.+..|++.+..+.++|.. +.+.||+|..|+.||.||+.++...
T Consensus 144 ~I~~DSqlVi~qi~g~wk~~~~~l~~y~~~i~~l~~~~~l~~~~~~VpR~~N~~AD~LAk~Al~~~ 209 (219)
T PRK07708 144 TFRGDSQVVLNQLAGEWPCYDEHLNHWLDRIEQKLKQLKLTPVYEPISRKQNKEADQLATQALEGT 209 (219)
T ss_pred EEEeccHHHHHHhCCCceeCChhHHHHHHHHHHHHhhCCceEEEEECCchhhhHHHHHHHHHHhcC
Confidence 8999999999999999999999999999999999999975 6789999999999999999999854
No 6
>PRK13907 rnhA ribonuclease H; Provisional
Probab=99.89 E-value=5e-23 Score=186.19 Aligned_cols=126 Identities=25% Similarity=0.257 Sum_probs=112.3
Q ss_pred eEEEEEccceeecccCCCCCCCceEEEEEEeCCCCeEEEeeeeccccCCChHHHHHHHHHHHHHHHHhcCCCeEEeecCC
Q 008441 156 FFKVYSKGLVIEELVNGERVSLSAIGVAICDQMDNLIFELKKPLIKSGLNKSAAETKALIEGLNAALSMELDRVRVFIDC 235 (565)
Q Consensus 156 ~~~vyfdGa~~~~~~~~~npg~ag~Gv~i~~~~~~~~~~~~~~~~~~~tn~n~AEy~Ali~gL~~al~l~~~~v~v~~DS 235 (565)
|++|||||++ ++ |||++|+|++|.+..|.+. .+.+. +..|| |.|||+|++.||+.|+++|+++|.|++||
T Consensus 1 ~~~iy~DGa~-~~-----~~g~~G~G~vi~~~~~~~~--~~~~~-~~~tn-~~AE~~All~aL~~a~~~g~~~v~i~sDS 70 (128)
T PRK13907 1 MIEVYIDGAS-KG-----NPGPSGAGVFIKGVQPAVQ--LSLPL-GTMSN-HEAEYHALLAALKYCTEHNYNIVSFRTDS 70 (128)
T ss_pred CEEEEEeeCC-CC-----CCCccEEEEEEEECCeeEE--EEecc-cccCC-cHHHHHHHHHHHHHHHhCCCCEEEEEech
Confidence 6899999999 44 9999999999998766443 33444 54555 89999999999999999999999999999
Q ss_pred ccchhhccCccCCcchhhHHHHHHHHHHhhhccccccccccccchHHHHHHHHHhhh
Q 008441 236 FPLFQFVTGRWPAKQRKISVLVDQVSLLEKRFSYFKPRHVARNDMKYVYELARAAIN 292 (565)
Q Consensus 236 ~lv~~qv~G~w~~k~~~l~~l~~~v~~Ll~~F~~~~~~~V~R~~n~~Ad~LA~eal~ 292 (565)
++|++++.+.|. +++.++.|+.++..|+++|..+.++||+|+.|+.||.||+.++.
T Consensus 71 ~~vi~~~~~~~~-~~~~~~~l~~~~~~l~~~f~~~~~~~v~r~~N~~Ad~LA~~a~~ 126 (128)
T PRK13907 71 QLVERAVEKEYA-KNKMFAPLLEEALQYIKSFDLFFIKWIPSSQNKVADELARKAIL 126 (128)
T ss_pred HHHHHHHhHHHh-cChhHHHHHHHHHHHHhcCCceEEEEcCchhchhHHHHHHHHHh
Confidence 999999999996 56789999999999999999999999999999999999998875
No 7
>COG0328 RnhA Ribonuclease HI [DNA replication, recombination, and repair]
Probab=99.86 E-value=5.7e-22 Score=181.92 Aligned_cols=129 Identities=22% Similarity=0.207 Sum_probs=110.7
Q ss_pred ceEEEEEccceeecccCCCCCCCceEEEEEEeCCCCeEEEeeeeccccCCChHHHHHHHHHHHHHHHHhcCCCeEEeecC
Q 008441 155 YFFKVYSKGLVIEELVNGERVSLSAIGVAICDQMDNLIFELKKPLIKSGLNKSAAETKALIEGLNAALSMELDRVRVFID 234 (565)
Q Consensus 155 ~~~~vyfdGa~~~~~~~~~npg~ag~Gv~i~~~~~~~~~~~~~~~~~~~tn~n~AEy~Ali~gL~~al~l~~~~v~v~~D 234 (565)
..+.|||||++ .| |||++|+|++|....+. ..++..+ +.+|| |.|||+|||+||+.+.++|...|.|+||
T Consensus 2 ~~v~if~DGa~-~g-----NpG~gG~g~vl~~~~~~--~~~s~~~-~~tTN-NraEl~A~i~AL~~l~~~~~~~v~l~tD 71 (154)
T COG0328 2 KKVEIFTDGAC-LG-----NPGPGGWGAVLRYGDGE--KELSGGE-GRTTN-NRAELRALIEALEALKELGACEVTLYTD 71 (154)
T ss_pred CceEEEecCcc-CC-----CCCCceEEEEEEcCCce--EEEeeee-ecccC-hHHHHHHHHHHHHHHHhcCCceEEEEec
Confidence 35889999999 66 99999999999955443 3677777 54555 8999999999999999999999999999
Q ss_pred CccchhhccCccCCcchhhH------------HHHHHHHHHhhhcccccccccc----ccchHHHHHHHHHhhhcc
Q 008441 235 CFPLFQFVTGRWPAKQRKIS------------VLVDQVSLLEKRFSYFKPRHVA----RNDMKYVYELARAAINSQ 294 (565)
Q Consensus 235 S~lv~~qv~G~w~~k~~~l~------------~l~~~v~~Ll~~F~~~~~~~V~----R~~n~~Ad~LA~eal~sq 294 (565)
|++|+++|+ .|..+.+... .|+.++.+++++|..+.++||+ +..|+.||.||+.++...
T Consensus 72 S~yv~~~i~-~w~~~w~~~~w~~~~~~pvkn~dl~~~~~~~~~~~~~v~~~WVkgH~g~~~NeraD~LA~~~~~~~ 146 (154)
T COG0328 72 SKYVVEGIT-RWIVKWKKNGWKTADKKPVKNKDLWEELDELLKRHELVFWEWVKGHAGHPENERADQLAREAARAA 146 (154)
T ss_pred HHHHHHHHH-HHHhhccccCccccccCccccHHHHHHHHHHHhhCCeEEEEEeeCCCCChHHHHHHHHHHHHHHhh
Confidence 999999999 8865544444 4599999999999999999999 889999999999998765
No 8
>PRK07238 bifunctional RNase H/acid phosphatase; Provisional
Probab=99.86 E-value=1.2e-21 Score=208.29 Aligned_cols=131 Identities=22% Similarity=0.291 Sum_probs=120.7
Q ss_pred eEEEEEccceeecccCCCCCCCceEEEEEEeCCCC-eEEEeeeeccccCCChHHHHHHHHHHHHHHHHhcCCCeEEeecC
Q 008441 156 FFKVYSKGLVIEELVNGERVSLSAIGVAICDQMDN-LIFELKKPLIKSGLNKSAAETKALIEGLNAALSMELDRVRVFID 234 (565)
Q Consensus 156 ~~~vyfdGa~~~~~~~~~npg~ag~Gv~i~~~~~~-~~~~~~~~~~~~~tn~n~AEy~Ali~gL~~al~l~~~~v~v~~D 234 (565)
.++|||||++ ++ |||++|+|++|.++.|. ++.+.+.++ +..|| |+|||+|||.||+.|+++|+++|.|++|
T Consensus 2 ~~~i~~DGa~-~~-----n~g~aG~G~vi~~~~~~~~~~~~~~~~-~~~tn-n~AE~~All~gL~~a~~~g~~~v~i~~D 73 (372)
T PRK07238 2 KVVVEADGGS-RG-----NPGPAGYGAVVWDADRGEVLAERAEAI-GRATN-NVAEYRGLIAGLEAAAELGATEVEVRMD 73 (372)
T ss_pred eEEEEecCCC-CC-----CCCceEEEEEEEeCCCCcEEEEeeccc-CCCCc-hHHHHHHHHHHHHHHHhCCCCeEEEEeC
Confidence 3789999999 55 99999999999998765 567888888 66666 8999999999999999999999999999
Q ss_pred CccchhhccCccCCcchhhHHHHHHHHHHhhhccccccccccccchHHHHHHHHHhhhcc
Q 008441 235 CFPLFQFVTGRWPAKQRKISVLVDQVSLLEKRFSYFKPRHVARNDMKYVYELARAAINSQ 294 (565)
Q Consensus 235 S~lv~~qv~G~w~~k~~~l~~l~~~v~~Ll~~F~~~~~~~V~R~~n~~Ad~LA~eal~sq 294 (565)
|++|++++.|+|+.+++.|..|+.++..|+++|..+.++||+|.+|+.||.||+.++...
T Consensus 74 S~lvi~~i~~~~~~~~~~l~~~~~~i~~l~~~f~~~~i~~v~r~~N~~AD~LA~~a~~~~ 133 (372)
T PRK07238 74 SKLVVEQMSGRWKVKHPDMKPLAAQARELASQFGRVTYTWIPRARNAHADRLANEAMDAA 133 (372)
T ss_pred cHHHHHHhCCCCccCChHHHHHHHHHHHHHhcCCceEEEECCchhhhHHHHHHHHHHHhh
Confidence 999999999999999999999999999999999999999999999999999999998744
No 9
>PRK08719 ribonuclease H; Reviewed
Probab=99.68 E-value=2.3e-16 Score=145.88 Aligned_cols=126 Identities=21% Similarity=0.217 Sum_probs=100.0
Q ss_pred ceEEEEEccceeecccCCCCCC---CceEEEEEEeCCCCeEEEeeeeccccCCChHHHHHHHHHHHHHHHHhcCCCeEEe
Q 008441 155 YFFKVYSKGLVIEELVNGERVS---LSAIGVAICDQMDNLIFELKKPLIKSGLNKSAAETKALIEGLNAALSMELDRVRV 231 (565)
Q Consensus 155 ~~~~vyfdGa~~~~~~~~~npg---~ag~Gv~i~~~~~~~~~~~~~~~~~~~tn~n~AEy~Ali~gL~~al~l~~~~v~v 231 (565)
..++|||||++ .+ ||+ ++|+|++|.++.|..+...+.++ +..++||.||++|++.||+.+.+. ..|
T Consensus 3 ~~~~iYtDGs~-~~-----n~~~~~~~G~G~vv~~~~~~~~~~~~~~~-~~~~Tnn~aEl~A~~~aL~~~~~~----~~i 71 (147)
T PRK08719 3 ASYSIYIDGAA-PN-----NQHGCVRGGIGLVVYDEAGEIVDEQSITV-NRYTDNAELELLALIEALEYARDG----DVI 71 (147)
T ss_pred ceEEEEEeccc-CC-----CCCCCCCcEEEEEEEeCCCCeeEEEEecC-CCCccHHHHHHHHHHHHHHHcCCC----CEE
Confidence 46899999999 44 776 68999999998777666666667 444566999999999999988754 379
Q ss_pred ecCCccchhhc--------cCccCCcchhh---HHHHHHHHHHhhhccccccccccc----cchHHHHHHHHHhhh
Q 008441 232 FIDCFPLFQFV--------TGRWPAKQRKI---SVLVDQVSLLEKRFSYFKPRHVAR----NDMKYVYELARAAIN 292 (565)
Q Consensus 232 ~~DS~lv~~qv--------~G~w~~k~~~l---~~l~~~v~~Ll~~F~~~~~~~V~R----~~n~~Ad~LA~eal~ 292 (565)
++||++|++++ .+.|+...... ..|++.+..|.+ +..+.+.||+. ..|+.||+||+.+..
T Consensus 72 ~tDS~yvi~~i~~~~~~W~~~~w~~s~g~~v~n~dl~~~i~~l~~-~~~i~~~~VkgH~g~~~Ne~aD~lA~~a~~ 146 (147)
T PRK08719 72 YSDSDYCVRGFNEWLDTWKQKGWRKSDKKPVANRDLWQQVDELRA-RKYVEVEKVTAHSGIEGNEAADMLAQAAAE 146 (147)
T ss_pred EechHHHHHHHHHHHHHHHhCCcccCCCcccccHHHHHHHHHHhC-CCcEEEEEecCCCCChhHHHHHHHHHHHhh
Confidence 99999999999 67887665433 456777777766 46688899999 569999999998753
No 10
>cd06222 RnaseH RNase H (RNase HI) is an endonuclease that cleaves the RNA strand of an RNA/DNA hybrid in a not sequence-specific manner. One of the important functions of RNase H is to remove Okazaki fragments during DNA replication. RNase H knockout mice lack mitochondrial DNA replication and die as embryos. The retroviral reverse transcriptase contains an RNase H domain that plays an important role in converting a single stranded retroviral genomic RNA into a dsDNA for integration into host chromosomes. RNase H inhibitors have been explored as an anti-HIV drug target because RNase H inactivation inhibits reverse transcription.
Probab=99.62 E-value=4.2e-15 Score=130.83 Aligned_cols=126 Identities=23% Similarity=0.241 Sum_probs=110.5
Q ss_pred EEEEccceeecccCCCCCCCceEEEEEEeCCCCeEEEeeeeccccCCChHHHHHHHHHHHHHHHHhcCCCeEEeecCCcc
Q 008441 158 KVYSKGLVIEELVNGERVSLSAIGVAICDQMDNLIFELKKPLIKSGLNKSAAETKALIEGLNAALSMELDRVRVFIDCFP 237 (565)
Q Consensus 158 ~vyfdGa~~~~~~~~~npg~ag~Gv~i~~~~~~~~~~~~~~~~~~~tn~n~AEy~Ali~gL~~al~l~~~~v~v~~DS~l 237 (565)
+|||||++.. +.+.+|+|+++.++.+...+...... ...+++.+|+.|++.||+.+...+.++|.|++||+.
T Consensus 1 ~~~~Dgs~~~------~~~~~g~g~v~~~~~~~~~~~~~~~~--~~~s~~~aEl~al~~al~~~~~~~~~~i~i~~Ds~~ 72 (130)
T cd06222 1 VIYTDGSCRG------NPGPAGAGVVLRDPGGEVLLSGGLLG--GNTTNNRAELLALIEALELALELGGKKVNIYTDSQY 72 (130)
T ss_pred CEEecccCCC------CCCceEEEEEEEeCCCeEEEeccccC--CCCcHHHHHHHHHHHHHHHHHhCCCceEEEEECHHH
Confidence 4899999933 55899999999998777666655554 344558999999999999999999999999999999
Q ss_pred chhhccCccCCcchhhHHHHHHHHHHhhhccccccccccc----cchHHHHHHHHHhh
Q 008441 238 LFQFVTGRWPAKQRKISVLVDQVSLLEKRFSYFKPRHVAR----NDMKYVYELARAAI 291 (565)
Q Consensus 238 v~~qv~G~w~~k~~~l~~l~~~v~~Ll~~F~~~~~~~V~R----~~n~~Ad~LA~eal 291 (565)
+++++.+.+....+.+..+...+..+.+++..+.+.||++ ..|..||.||+.++
T Consensus 73 ~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~i~~v~~h~~~~~n~~ad~la~~~~ 130 (130)
T cd06222 73 VINALTGWYEGKPVKNVDLWQRLLALLKRFHKVRFEWVPGHSGIEGNERADALAKEAA 130 (130)
T ss_pred HHHHhhccccCCChhhHHHHHHHHHHHhCCCeEEEEEcCCCCCCcchHHHHHHHHhhC
Confidence 9999999988788899999999999998999999999999 99999999998753
No 11
>PRK06548 ribonuclease H; Provisional
Probab=99.58 E-value=9.8e-15 Score=136.42 Aligned_cols=126 Identities=14% Similarity=0.041 Sum_probs=93.7
Q ss_pred ceEEEEEccceeecccCCCCCCCceEEEEEEeCCCCeEEEeeeeccccCCChHHHHHHHHHHHHHHHHhcCCCeEEeecC
Q 008441 155 YFFKVYSKGLVIEELVNGERVSLSAIGVAICDQMDNLIFELKKPLIKSGLNKSAAETKALIEGLNAALSMELDRVRVFID 234 (565)
Q Consensus 155 ~~~~vyfdGa~~~~~~~~~npg~ag~Gv~i~~~~~~~~~~~~~~~~~~~tn~n~AEy~Ali~gL~~al~l~~~~v~v~~D 234 (565)
..+.|||||++ ++ |||++|+|++|.+. + ..+.+. + .++||.||++|+|.||+. +..+...|.|++|
T Consensus 4 ~~~~IytDGa~-~g-----npg~~G~g~~~~~~-~----~~~g~~-~-~~TNnraEl~Aii~aL~~-~~~~~~~v~I~TD 69 (161)
T PRK06548 4 NEIIAATDGSS-LA-----NPGPSGWAWYVDEN-T----WDSGGW-D-IATNNIAELTAVRELLIA-TRHTDRPILILSD 69 (161)
T ss_pred CEEEEEEeecc-CC-----CCCceEEEEEEeCC-c----EEccCC-C-CCCHHHHHHHHHHHHHHh-hhcCCceEEEEeC
Confidence 34899999999 55 99999999998642 1 223333 3 345599999999999964 4455568999999
Q ss_pred CccchhhccC--------ccCCc--chhh-HHHHHHHHHHhhhcccccccccccc----chHHHHHHHHHhhhccc
Q 008441 235 CFPLFQFVTG--------RWPAK--QRKI-SVLVDQVSLLEKRFSYFKPRHVARN----DMKYVYELARAAINSQM 295 (565)
Q Consensus 235 S~lv~~qv~G--------~w~~k--~~~l-~~l~~~v~~Ll~~F~~~~~~~V~R~----~n~~Ad~LA~eal~sqi 295 (565)
|++|++.|+. .|+.. .|.. +.|.+++..++++. .+.+.||+-. .|+.||+||+++.....
T Consensus 70 S~yvi~~i~~W~~~Wk~~gWk~s~G~pV~N~dL~~~l~~l~~~~-~v~~~wVkgHsg~~gNe~aD~LA~~aa~~~~ 144 (161)
T PRK06548 70 SKYVINSLTKWVYSWKMRKWRKADGKPVLNQEIIQEIDSLMENR-NIRMSWVNAHTGHPLNEAADSLARQAANNFS 144 (161)
T ss_pred hHHHHHHHHHHHHHHHHCCCcccCCCccccHHHHHHHHHHHhcC-ceEEEEEecCCCCHHHHHHHHHHHHHHHHhc
Confidence 9999999994 55543 3333 67788888887764 5777887654 59999999999876443
No 12
>PRK00203 rnhA ribonuclease H; Reviewed
Probab=99.52 E-value=5.9e-14 Score=130.53 Aligned_cols=126 Identities=21% Similarity=0.153 Sum_probs=93.9
Q ss_pred eEEEEEccceeecccCCCCCCCceEEEEEEeCCCCeEEEeeeeccccCCChHHHHHHHHHHHHHHHHhcCCCeEEeecCC
Q 008441 156 FFKVYSKGLVIEELVNGERVSLSAIGVAICDQMDNLIFELKKPLIKSGLNKSAAETKALIEGLNAALSMELDRVRVFIDC 235 (565)
Q Consensus 156 ~~~vyfdGa~~~~~~~~~npg~ag~Gv~i~~~~~~~~~~~~~~~~~~~tn~n~AEy~Ali~gL~~al~l~~~~v~v~~DS 235 (565)
+++||+||+++ + ||+++|+|+++.... ....+.... + .++||.||++|++.||+.+.+ ...|.|++||
T Consensus 3 ~v~iytDGs~~-~-----n~~~~g~g~v~~~~~--~~~~~~~~~-~-~~TN~~aEL~Ai~~AL~~~~~--~~~v~I~tDS 70 (150)
T PRK00203 3 QVEIYTDGACL-G-----NPGPGGWGAILRYKG--HEKELSGGE-A-LTTNNRMELMAAIEALEALKE--PCEVTLYTDS 70 (150)
T ss_pred eEEEEEEeccc-C-----CCCceEEEEEEEECC--eeEEEecCC-C-CCcHHHHHHHHHHHHHHHcCC--CCeEEEEECH
Confidence 58899999994 4 999999999998643 334455545 3 345589999999999987654 3689999999
Q ss_pred ccchhhccC--------ccCCcc--h-hhHHHHHHHHHHhhhcccccccccc----ccchHHHHHHHHHhhhcc
Q 008441 236 FPLFQFVTG--------RWPAKQ--R-KISVLVDQVSLLEKRFSYFKPRHVA----RNDMKYVYELARAAINSQ 294 (565)
Q Consensus 236 ~lv~~qv~G--------~w~~k~--~-~l~~l~~~v~~Ll~~F~~~~~~~V~----R~~n~~Ad~LA~eal~sq 294 (565)
++|++.|.+ .|.... | .-+.|.+++..++.. ..+.+.||+ +..|..||+||+.++...
T Consensus 71 ~yvi~~i~~w~~~Wk~~~~~~~~g~~v~n~dl~~~i~~l~~~-~~v~~~wV~~H~~~~~N~~AD~lA~~a~~~~ 143 (150)
T PRK00203 71 QYVRQGITEWIHGWKKNGWKTADKKPVKNVDLWQRLDAALKR-HQIKWHWVKGHAGHPENERCDELARAGAEEA 143 (150)
T ss_pred HHHHHHHHHHHHHHHHcCCcccCCCccccHHHHHHHHHHhcc-CceEEEEecCCCCCHHHHHHHHHHHHHHHHh
Confidence 999998886 343321 1 224566777777665 456778888 567999999999988743
No 13
>PF13456 RVT_3: Reverse transcriptase-like; PDB: 3ALY_A 2EHG_A 3HST_B.
Probab=99.47 E-value=8.6e-14 Score=116.14 Aligned_cols=86 Identities=24% Similarity=0.339 Sum_probs=75.7
Q ss_pred hHHHHHHHHHHHHHHHHhcCCCeEEeecCCccchhhccCccCCcchhhHHHHHHHHHHhhhccccccccccccchHHHHH
Q 008441 206 KSAAETKALIEGLNAALSMELDRVRVFIDCFPLFQFVTGRWPAKQRKISVLVDQVSLLEKRFSYFKPRHVARNDMKYVYE 285 (565)
Q Consensus 206 ~n~AEy~Ali~gL~~al~l~~~~v~v~~DS~lv~~qv~G~w~~k~~~l~~l~~~v~~Ll~~F~~~~~~~V~R~~n~~Ad~ 285 (565)
+++||+.||+.||+.|.++|+++|.|++||+.|++++.+.+..+. .+..++.++..+++.|..+.++||+|+.|..|+.
T Consensus 1 ~~~aE~~al~~al~~a~~~g~~~i~v~sDs~~vv~~i~~~~~~~~-~~~~~~~~i~~~~~~~~~~~~~~i~r~~N~~A~~ 79 (87)
T PF13456_consen 1 PLEAEALALLEALQLAWELGIRKIIVESDSQLVVDAINGRSSSRS-ELRPLIQDIRSLLDRFWNVSVSHIPREQNKVADA 79 (87)
T ss_dssp HHHHHHHHHHHHHHHHHCCT-SCEEEEES-HHHHHHHTTSS---S-CCHHHHHHHHHHHCCCSCEEEEE--GGGSHHHHH
T ss_pred CcHHHHHHHHHHHHHHHHCCCCEEEEEecCccccccccccccccc-cccccchhhhhhhccccceEEEEEChHHhHHHHH
Confidence 479999999999999999999999999999999999999999987 9999999999999999999999999999999999
Q ss_pred HHHHhhh
Q 008441 286 LARAAIN 292 (565)
Q Consensus 286 LA~eal~ 292 (565)
||+.++.
T Consensus 80 LA~~a~~ 86 (87)
T PF13456_consen 80 LAKFALS 86 (87)
T ss_dssp HHHHHHH
T ss_pred HHHHHhh
Confidence 9998763
No 14
>PF00075 RNase_H: RNase H; InterPro: IPR002156 The RNase H domain is responsible for hydrolysis of the RNA portion of RNA x DNA hybrids, and this activity requires the presence of divalent cations (Mg2+ or Mn2+) that bind its active site. This domain is a part of a large family of homologous RNase H enzymes of which the RNase HI protein from Escherichia coli is the best characterised []. Secondary structure predictions for the enzymes from E. coli, yeast, human liver and diverse retroviruses (such as Rous sarcoma virus and the Foamy viruses) supported, in every case, the five beta-strands (1 to 5) and four or five alpha-helices (A, B/C, D, E) that have been identified by crystallography in the RNase H domain of Human immunodeficiency virus 1 (HIV-1) reverse transcriptase and in E. coli RNase H []. Reverse transcriptase (RT) is a modular enzyme carrying polymerase and ribonuclease H (RNase H) activities in separable domains. Reverse transcriptase (RT) converts the single-stranded RNA genome of a retrovirus into a double-stranded DNA copy for integration into the host genome. This process requires ribonuclease H as well as RNA- and DNA-directed DNA polymerase activities. Retroviral RNase H is synthesised as part of the POL polyprotein that contains; an aspartyl protease, a reverse transcriptase, RNase H and integrase. POL polyprotein undergoes specific enzymatic cleavage to yield the mature proteins. Bacterial RNase H 3.1.26.4 from EC catalyses endonucleolytic cleavage to 5'-phosphomonoester acting on RNA-DNA hybrids. The 3D structure of the RNase H domain from diverse bacteria and retroviruses has been solved [, , ]. All have four beta strands and four to five alpha helices. The E. coli RNase H1 protein binds a single Mg2+ ion cofactor in the active site of the enzyme. The divalent cation is bound by the carboxyl groups of four acidic residues, Asp-10, Glu-48, Asp-70, and Asp-134 []. The first three acidic residues are highly conserved in all bacterial and retroviral RNase H sequences. ; GO: 0003676 nucleic acid binding, 0004523 ribonuclease H activity; PDB: 3LP3_B 2KW4_A 3P1G_A 1RIL_A 2RPI_A 4EQJ_G 4EP2_B 3OTY_P 3U3G_D 2ZQB_D ....
Probab=99.36 E-value=2.6e-12 Score=115.96 Aligned_cols=119 Identities=19% Similarity=0.222 Sum_probs=91.0
Q ss_pred eEEEEEccceeecccCCCCCCCceEEEEEEeCCCCeEEEeeeeccccCCChHHHHHHHHHHHHHHHHhcCCCeEEeecCC
Q 008441 156 FFKVYSKGLVIEELVNGERVSLSAIGVAICDQMDNLIFELKKPLIKSGLNKSAAETKALIEGLNAALSMELDRVRVFIDC 235 (565)
Q Consensus 156 ~~~vyfdGa~~~~~~~~~npg~ag~Gv~i~~~~~~~~~~~~~~~~~~~tn~n~AEy~Ali~gL~~al~l~~~~v~v~~DS 235 (565)
.+.||+||++.. +++.+|+|+++ .. | ...+..+ + ..++|.||+.|++.||+ ++ .. +.|.|++||
T Consensus 3 ~~~iytDgS~~~------~~~~~~~g~v~-~~-~---~~~~~~~-~-~~s~~~aEl~Ai~~AL~-~~-~~-~~v~I~tDS 66 (132)
T PF00075_consen 3 AIIIYTDGSCRP------NPGKGGAGYVV-WG-G---RNFSFRL-G-GQSNNRAELQAIIEALK-AL-EH-RKVTIYTDS 66 (132)
T ss_dssp SEEEEEEEEECT------TTTEEEEEEEE-ET-T---EEEEEEE-E-SECHHHHHHHHHHHHHH-TH-ST-SEEEEEES-
T ss_pred cEEEEEeCCccC------CCCceEEEEEE-EC-C---eEEEecc-c-ccchhhhheehHHHHHH-Hh-hc-ccccccccH
Confidence 478999999943 78888999955 33 3 2555666 4 55669999999999999 66 33 999999999
Q ss_pred ccchhhccC-----ccCCcchhhHHHHHHHHHHhhhcccccccccccc-----chHHHHHHHHHhh
Q 008441 236 FPLFQFVTG-----RWPAKQRKISVLVDQVSLLEKRFSYFKPRHVARN-----DMKYVYELARAAI 291 (565)
Q Consensus 236 ~lv~~qv~G-----~w~~k~~~l~~l~~~v~~Ll~~F~~~~~~~V~R~-----~n~~Ad~LA~eal 291 (565)
+.+++.+.. .|..+ ...+++..++..++.+...+.+.||+.. .|..||+||+.+.
T Consensus 67 ~~v~~~l~~~~~~~~~~~~-~~~~~i~~~i~~~~~~~~~v~~~~V~~H~~~~~~N~~aD~lAk~a~ 131 (132)
T PF00075_consen 67 QYVLNALNKWLHGNGWKKT-SNGRPIKNEIWELLSRGIKVRFRWVPGHSGVPQGNERADRLAKEAA 131 (132)
T ss_dssp HHHHHHHHTHHHHTTSBSC-TSSSBHTHHHHHHHHHSSEEEEEESSSSSSSHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHhccccccccc-cccccchhheeeccccceEEeeeeccCcCCCchhHHHHHHHHHHhc
Confidence 999998888 67654 3333555677777677777888999987 6778999999875
No 15
>smart00647 IBR In Between Ring fingers. the domains occurs between pairs og RING fingers
Probab=98.87 E-value=2e-09 Score=84.89 Aligned_cols=62 Identities=32% Similarity=0.820 Sum_probs=49.1
Q ss_pred HHHHHHHHhcCCC-CCcccccCCCCCCcccchhhhhccCCCcccccccCceeCCCCCCceecccCCCcCCCCCh
Q 008441 379 IWNQRMKEALIPV-TEKVYCPYPKCSALMSKSEIERDASSSSFVGRRLGARKCTKCHRRFCIDCKVPWHNNMTC 451 (565)
Q Consensus 379 ~y~~~~~e~~i~~-~~~~~CP~p~C~~~i~~~~~~e~~~s~~~~~~~~~~~~C~~C~~~fC~~C~~~~H~g~tC 451 (565)
+|.+++.+..+.. ++.+|||+|+|+.++...+ ......+.|+.|+..||+.|+.+||.+.+|
T Consensus 2 ~y~~~~~~~~i~~~~~~~~CP~~~C~~~~~~~~-----------~~~~~~v~C~~C~~~fC~~C~~~~H~~~~C 64 (64)
T smart00647 2 KYERLLLESYVESNPDLKWCPAPDCSAAIIVTE-----------EEGCNRVTCPKCGFSFCFRCKVPWHSPVSC 64 (64)
T ss_pred hHHHHHHHHHHhcCCCccCCCCCCCcceEEecC-----------CCCCCeeECCCCCCeECCCCCCcCCCCCCC
Confidence 4666666666543 6789999999999885321 225678999999999999999999999987
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=98.79 E-value=1.8e-09 Score=85.17 Aligned_cols=62 Identities=24% Similarity=0.711 Sum_probs=35.9
Q ss_pred HHHHHHHHhcCC-CCCcccccCCCCCCcccchhhhhccCCCcccccccCceeCCCCCCceecccCCCcCCCCCh
Q 008441 379 IWNQRMKEALIP-VTEKVYCPYPKCSALMSKSEIERDASSSSFVGRRLGARKCTKCHRRFCIDCKVPWHNNMTC 451 (565)
Q Consensus 379 ~y~~~~~e~~i~-~~~~~~CP~p~C~~~i~~~~~~e~~~s~~~~~~~~~~~~C~~C~~~fC~~C~~~~H~g~tC 451 (565)
+|.+.+.+..+. ..+++|||+|+|+.++...+. .....+.|+.|+..||+.|+.+||.|.+|
T Consensus 2 ky~~~~~~~~~~~~~~~~~Cp~~~C~~~~~~~~~-----------~~~~~~~C~~C~~~fC~~C~~~~H~~~~C 64 (64)
T PF01485_consen 2 KYQKFLLKRYLESDPNIRWCPNPDCEYIIEKDDG-----------CNSPIVTCPSCGTEFCFKCGEPWHEGVTC 64 (64)
T ss_dssp CHHHCCCHS---S---CC--TTSST---ECS-SS-----------TTS--CCTTSCCSEECSSSTSESCTTS-H
T ss_pred hHHHHHHHHHHHCCCCccCCCCCCCcccEEecCC-----------CCCCeeECCCCCCcCccccCcccCCCCCC
Confidence 344444444443 346689999999999864321 11114999999999999999999999987
No 17
>KOG3752 consensus Ribonuclease H [Replication, recombination and repair]
Probab=98.75 E-value=3.6e-08 Score=101.61 Aligned_cols=126 Identities=23% Similarity=0.265 Sum_probs=87.5
Q ss_pred EEEEEccceeecccCCCCC-CCceEEEEEEeCCCCeEEEeeeecc-ccCCChHHHHHHHHHHHHHHHHhcCCCeEEeecC
Q 008441 157 FKVYSKGLVIEELVNGERV-SLSAIGVAICDQMDNLIFELKKPLI-KSGLNKSAAETKALIEGLNAALSMELDRVRVFID 234 (565)
Q Consensus 157 ~~vyfdGa~~~~~~~~~np-g~ag~Gv~i~~~~~~~~~~~~~~~~-~~~tn~n~AEy~Ali~gL~~al~l~~~~v~v~~D 234 (565)
..||+||.+++. + .+ ..||+||.+-+. .-.-.+.+|. |..|| |.||+.|+++||+.|++.++.+|.|+||
T Consensus 213 ~vvytDGS~~~n---g-~~~~~AGyGvywg~~---~e~N~s~pv~~g~qtN-nrAEl~Av~~ALkka~~~~~~kv~I~TD 284 (371)
T KOG3752|consen 213 QVVYTDGSSSGN---G-RKSSRAGYGVYWGPG---HELNVSGPLAGGRQTN-NRAELIAAIEALKKARSKNINKVVIRTD 284 (371)
T ss_pred eEEEecCccccC---C-CCCCcceeEEeeCCC---CcccccccCCCCcccc-cHHHHHHHHHHHHHHHhcCCCcEEEEec
Confidence 679999999763 1 33 459999988543 2234467774 66777 8999999999999999999999999999
Q ss_pred Cccchhhcc--------CccCCc--chh------hHHHHHHHHHHhhhc--ccccccccccc----chHHHHHHHHHh
Q 008441 235 CFPLFQFVT--------GRWPAK--QRK------ISVLVDQVSLLEKRF--SYFKPRHVARN----DMKYVYELARAA 290 (565)
Q Consensus 235 S~lv~~qv~--------G~w~~k--~~~------l~~l~~~v~~Ll~~F--~~~~~~~V~R~----~n~~Ad~LA~ea 290 (565)
|+++++-|+ -.|+.+ .+. -...+.++..|.+.. ..+++.||+-. .|..|+.||+..
T Consensus 285 S~~~i~~l~~wv~~~k~~~~k~~~~~~~i~~~v~n~~~~~e~~~l~q~~~~~~vq~~~V~Gh~gi~gne~Ad~lARkg 362 (371)
T KOG3752|consen 285 SEYFINSLTLWVQGWKKNGWKTSNGSDRICAYVKNQDFFNELDELEQEISNKKVQQEYVGGHSGILGNEMADALARKG 362 (371)
T ss_pred hHHHHHHHHHHHhhhccCccccccCCCccceeeecchHHHHHHHHHhhhccCceEEEEecCcCCcchHHHHHHHHhhh
Confidence 999999765 223322 121 112344555555553 33444555543 578899998865
No 18
>smart00647 IBR In Between Ring fingers. the domains occurs between pairs og RING fingers
Probab=98.30 E-value=1e-06 Score=69.38 Aligned_cols=48 Identities=35% Similarity=0.925 Sum_probs=39.6
Q ss_pred HHHHHhc-CCccccC--CCCceeEecC--CcceEEe-ecCccccccccccccCC
Q 008441 468 LKSLASS-NLWRQCV--KCNHLIELAE--GCFHMTC-RCGHEFCYNCGAEWKNK 515 (565)
Q Consensus 468 l~~l~~~-~~~k~CP--kC~~~IEK~~--GCnHMtC-~Cg~~FCw~C~~~~~~~ 515 (565)
++.++.. ..++.|| +|...|+..+ |..+|+| .|++.|||.|+.+|+.+
T Consensus 8 ~~~~i~~~~~~~~CP~~~C~~~~~~~~~~~~~~v~C~~C~~~fC~~C~~~~H~~ 61 (64)
T smart00647 8 LESYVESNPDLKWCPAPDCSAAIIVTEEEGCNRVTCPKCGFSFCFRCKVPWHSP 61 (64)
T ss_pred HHHHHhcCCCccCCCCCCCcceEEecCCCCCCeeECCCCCCeECCCCCCcCCCC
Confidence 3444433 5678999 9999999975 9999999 79999999999999643
No 19
>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=98.15 E-value=7.1e-07 Score=65.15 Aligned_cols=41 Identities=29% Similarity=0.651 Sum_probs=32.4
Q ss_pred ccceeccccccCCceeecCCCcccchhhHHHHHHHHHhCCCCCCCCC
Q 008441 310 TCVICLEDTDVGHMFSIDGCLHRYCFLCMKKHIEEKLRQGMEPTCPH 356 (565)
Q Consensus 310 ~C~IC~e~~~~~~~~~l~~C~H~fC~~Cl~~~i~~~i~~g~~~kCP~ 356 (565)
+|+||++++...+.+..++|+|.||.+|+..|++.+ .+||.
T Consensus 2 ~C~IC~~~~~~~~~~~~l~C~H~fh~~Ci~~~~~~~------~~CP~ 42 (44)
T PF13639_consen 2 ECPICLEEFEDGEKVVKLPCGHVFHRSCIKEWLKRN------NSCPV 42 (44)
T ss_dssp CETTTTCBHHTTSCEEEETTSEEEEHHHHHHHHHHS------SB-TT
T ss_pred CCcCCChhhcCCCeEEEccCCCeeCHHHHHHHHHhC------CcCCc
Confidence 699999998655555555899999999999999763 27886
No 20
>KOG0320 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=98.09 E-value=1.3e-06 Score=81.19 Aligned_cols=55 Identities=27% Similarity=0.634 Sum_probs=42.4
Q ss_pred cccccccceeccccccCCceeecCCCcccchhhHHHHHHHHHhCCCCCCCCCCCCCCccchhhH
Q 008441 305 KTINETCVICLEDTDVGHMFSIDGCLHRYCFLCMKKHIEEKLRQGMEPTCPHEGCKSKLEVESC 368 (565)
Q Consensus 305 ~~~~~~C~IC~e~~~~~~~~~l~~C~H~fC~~Cl~~~i~~~i~~g~~~kCP~~~C~~~l~~~~i 368 (565)
+...+.|+||++.+....+++. .|||.||+.|++.-+... -+||. |++.|+..++
T Consensus 128 ~~~~~~CPiCl~~~sek~~vsT-kCGHvFC~~Cik~alk~~------~~CP~--C~kkIt~k~~ 182 (187)
T KOG0320|consen 128 KEGTYKCPICLDSVSEKVPVST-KCGHVFCSQCIKDALKNT------NKCPT--CRKKITHKQF 182 (187)
T ss_pred cccccCCCceecchhhcccccc-ccchhHHHHHHHHHHHhC------CCCCC--cccccchhhh
Confidence 3446899999999876655666 899999999999988543 38997 7777765443
No 21
>PF15227 zf-C3HC4_4: zinc finger of C3HC4-type, RING; PDB: 2EGP_A 2ECV_A 2ECJ_A 2YSL_A 2YSJ_A.
Probab=98.09 E-value=8.5e-07 Score=64.12 Aligned_cols=41 Identities=32% Similarity=0.719 Sum_probs=28.5
Q ss_pred cceeccccccCCceeecCCCcccchhhHHHHHHHHHhCCCCCCCCC
Q 008441 311 CVICLEDTDVGHMFSIDGCLHRYCFLCMKKHIEEKLRQGMEPTCPH 356 (565)
Q Consensus 311 C~IC~e~~~~~~~~~l~~C~H~fC~~Cl~~~i~~~i~~g~~~kCP~ 356 (565)
|+||++.+ .+++++ .|||.||+.||.++++..- +..+.||.
T Consensus 1 CpiC~~~~--~~Pv~l-~CGH~FC~~Cl~~~~~~~~--~~~~~CP~ 41 (42)
T PF15227_consen 1 CPICLDLF--KDPVSL-PCGHSFCRSCLERLWKEPS--GSGFSCPE 41 (42)
T ss_dssp ETTTTSB---SSEEE--SSSSEEEHHHHHHHHCCSS--SST---SS
T ss_pred CCccchhh--CCcccc-CCcCHHHHHHHHHHHHccC--CcCCCCcC
Confidence 89999885 577776 9999999999999986432 22257885
No 22
>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=98.04 E-value=2.4e-06 Score=60.71 Aligned_cols=38 Identities=34% Similarity=0.909 Sum_probs=29.2
Q ss_pred cceeccccccCCceeecCCCcccchhhHHHHHHHHHhCCCCCCCCC
Q 008441 311 CVICLEDTDVGHMFSIDGCLHRYCFLCMKKHIEEKLRQGMEPTCPH 356 (565)
Q Consensus 311 C~IC~e~~~~~~~~~l~~C~H~fC~~Cl~~~i~~~i~~g~~~kCP~ 356 (565)
|+||++.+ .+++.+.+|||.||.+|+.+|++.+ .+||.
T Consensus 1 C~iC~~~~--~~~~~~~~CGH~fC~~C~~~~~~~~------~~CP~ 38 (39)
T PF13923_consen 1 CPICLDEL--RDPVVVTPCGHSFCKECIEKYLEKN------PKCPV 38 (39)
T ss_dssp ETTTTSB---SSEEEECTTSEEEEHHHHHHHHHCT------SB-TT
T ss_pred CCCCCCcc--cCcCEECCCCCchhHHHHHHHHHCc------CCCcC
Confidence 89999875 4565667999999999999998642 47885
No 23
>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=98.03 E-value=1.4e-06 Score=68.43 Aligned_cols=39 Identities=44% Similarity=1.171 Sum_probs=29.4
Q ss_pred CccccCC--CCceeEecCCcce--EEee-cCccccccccccccC
Q 008441 476 LWRQCVK--CNHLIELAEGCFH--MTCR-CGHEFCYNCGAEWKN 514 (565)
Q Consensus 476 ~~k~CPk--C~~~IEK~~GCnH--MtC~-Cg~~FCw~C~~~~~~ 514 (565)
..+.||+ |...|++..|+++ |+|. |++.|||.|+.+|+.
T Consensus 17 ~~~~Cp~~~C~~~~~~~~~~~~~~~~C~~C~~~fC~~C~~~~H~ 60 (64)
T PF01485_consen 17 NIRWCPNPDCEYIIEKDDGCNSPIVTCPSCGTEFCFKCGEPWHE 60 (64)
T ss_dssp -CC--TTSST---ECS-SSTTS--CCTTSCCSEECSSSTSESCT
T ss_pred CccCCCCCCCcccEEecCCCCCCeeECCCCCCcCccccCcccCC
Confidence 4589987 9999999999999 9996 999999999999964
No 24
>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=98.01 E-value=5.7e-06 Score=59.26 Aligned_cols=40 Identities=33% Similarity=0.731 Sum_probs=31.7
Q ss_pred cceeccccccCCceeecCCCcccchhhHHHHHHHHHhCCCCCCCCC
Q 008441 311 CVICLEDTDVGHMFSIDGCLHRYCFLCMKKHIEEKLRQGMEPTCPH 356 (565)
Q Consensus 311 C~IC~e~~~~~~~~~l~~C~H~fC~~Cl~~~i~~~i~~g~~~kCP~ 356 (565)
|+||++.+. +...+++|+|.||..|+.+|++. ...++||.
T Consensus 1 C~iC~~~~~--~~~~~~~C~H~fC~~C~~~~~~~----~~~~~CP~ 40 (41)
T PF00097_consen 1 CPICLEPFE--DPVILLPCGHSFCRDCLRKWLEN----SGSVKCPL 40 (41)
T ss_dssp ETTTSSBCS--SEEEETTTSEEEEHHHHHHHHHH----TSSSBTTT
T ss_pred CCcCCcccc--CCCEEecCCCcchHHHHHHHHHh----cCCccCCc
Confidence 899998753 34446799999999999999987 44457885
No 25
>PF13445 zf-RING_UBOX: RING-type zinc-finger; PDB: 2CT2_A.
Probab=97.99 E-value=4.1e-06 Score=60.72 Aligned_cols=43 Identities=26% Similarity=0.457 Sum_probs=23.6
Q ss_pred cceeccccccCCceeecCCCcccchhhHHHHHHHHHhCCCCCCCC
Q 008441 311 CVICLEDTDVGHMFSIDGCLHRYCFLCMKKHIEEKLRQGMEPTCP 355 (565)
Q Consensus 311 C~IC~e~~~~~~~~~l~~C~H~fC~~Cl~~~i~~~i~~g~~~kCP 355 (565)
|+||.+.....++..++.|||.||++|+.+.+.... +..++||
T Consensus 1 CpIc~e~~~~~n~P~~L~CGH~~c~~cl~~l~~~~~--~~~~kCP 43 (43)
T PF13445_consen 1 CPICKEFSTEENPPMVLPCGHVFCKDCLQKLSKKSD--RNRFKCP 43 (43)
T ss_dssp -TTT----TTSS-EEE-SSS-EEEHHHHHHHHHH-S---S-B--T
T ss_pred CCccccccCCCCCCEEEeCccHHHHHHHHHHHhcCC--CCeeeCc
Confidence 899999324455556678999999999999987532 3456887
No 26
>PF14634 zf-RING_5: zinc-RING finger domain
Probab=97.92 E-value=8.4e-06 Score=59.51 Aligned_cols=43 Identities=33% Similarity=0.755 Sum_probs=35.1
Q ss_pred ccceeccccccCCceeecCCCcccchhhHHHHHHHHHhCCCCCCCCCCCCC
Q 008441 310 TCVICLEDTDVGHMFSIDGCLHRYCFLCMKKHIEEKLRQGMEPTCPHEGCK 360 (565)
Q Consensus 310 ~C~IC~e~~~~~~~~~l~~C~H~fC~~Cl~~~i~~~i~~g~~~kCP~~~C~ 360 (565)
.|+||++.+.....+.+++|||.||..|+.... +..+.||. |+
T Consensus 1 ~C~~C~~~~~~~~~~~l~~CgH~~C~~C~~~~~------~~~~~CP~--C~ 43 (44)
T PF14634_consen 1 HCNICFEKYSEERRPRLTSCGHIFCEKCLKKLK------GKSVKCPI--CR 43 (44)
T ss_pred CCcCcCccccCCCCeEEcccCCHHHHHHHHhhc------CCCCCCcC--CC
Confidence 499999998555667788999999999999877 44468997 75
No 27
>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=97.85 E-value=1.8e-05 Score=56.84 Aligned_cols=44 Identities=32% Similarity=0.770 Sum_probs=34.0
Q ss_pred ccceeccccccCCceeecCCCcccchhhHHHHHHHHHhCCCCCCCCCCCCCCc
Q 008441 310 TCVICLEDTDVGHMFSIDGCLHRYCFLCMKKHIEEKLRQGMEPTCPHEGCKSK 362 (565)
Q Consensus 310 ~C~IC~e~~~~~~~~~l~~C~H~fC~~Cl~~~i~~~i~~g~~~kCP~~~C~~~ 362 (565)
+|+||++.+ ...+.+.+|+|.||..|+..|++. ...+||. |+..
T Consensus 1 ~C~iC~~~~--~~~~~~~~C~H~~c~~C~~~~~~~-----~~~~Cp~--C~~~ 44 (45)
T cd00162 1 ECPICLEEF--REPVVLLPCGHVFCRSCIDKWLKS-----GKNTCPL--CRTP 44 (45)
T ss_pred CCCcCchhh--hCceEecCCCChhcHHHHHHHHHh-----CcCCCCC--CCCc
Confidence 599999886 455556679999999999999875 2347986 7754
No 28
>PLN03208 E3 ubiquitin-protein ligase RMA2; Provisional
Probab=97.82 E-value=1.1e-05 Score=76.99 Aligned_cols=61 Identities=25% Similarity=0.515 Sum_probs=44.6
Q ss_pred cccccceeccccccCCceeecCCCcccchhhHHHHHHHHH----------hCCCCCCCCCCCCCCccchhhHHHhh
Q 008441 307 INETCVICLEDTDVGHMFSIDGCLHRYCFLCMKKHIEEKL----------RQGMEPTCPHEGCKSKLEVESCRIFL 372 (565)
Q Consensus 307 ~~~~C~IC~e~~~~~~~~~l~~C~H~fC~~Cl~~~i~~~i----------~~g~~~kCP~~~C~~~l~~~~i~~lL 372 (565)
..++|+||++.+ .+++.+ .|||.||..|+..|+...- ..+..++||. |+..+....+..+.
T Consensus 17 ~~~~CpICld~~--~dPVvT-~CGH~FC~~CI~~wl~~s~~s~~~~~~~~~~k~~~~CPv--CR~~Is~~~LvPiy 87 (193)
T PLN03208 17 GDFDCNICLDQV--RDPVVT-LCGHLFCWPCIHKWTYASNNSRQRVDQYDHKREPPKCPV--CKSDVSEATLVPIY 87 (193)
T ss_pred CccCCccCCCcC--CCcEEc-CCCchhHHHHHHHHHHhccccccccccccccCCCCcCCC--CCCcCChhcEEEee
Confidence 468999999875 455544 8999999999999986421 0223468997 99999876655443
No 29
>PHA02926 zinc finger-like protein; Provisional
Probab=97.62 E-value=4e-05 Score=73.97 Aligned_cols=59 Identities=22% Similarity=0.579 Sum_probs=42.4
Q ss_pred Ccccccccceecccccc-----C-CceeecCCCcccchhhHHHHHHHHHhCCCCCCCCCCCCCCccc
Q 008441 304 GKTINETCVICLEDTDV-----G-HMFSIDGCLHRYCFLCMKKHIEEKLRQGMEPTCPHEGCKSKLE 364 (565)
Q Consensus 304 ~~~~~~~C~IC~e~~~~-----~-~~~~l~~C~H~fC~~Cl~~~i~~~i~~g~~~kCP~~~C~~~l~ 364 (565)
...+..+|+||++.... . .+-.+.+|+|.||..|+..|...+...+..-.||. |+..+.
T Consensus 166 ~~SkE~eCgICmE~I~eK~~~~eRrFGIL~~CnHsFCl~CIr~Wr~~r~~~~~~rsCPi--CR~~f~ 230 (242)
T PHA02926 166 RVSKEKECGICYEVVYSKRLENDRYFGLLDSCNHIFCITCINIWHRTRRETGASDNCPI--CRTRFR 230 (242)
T ss_pred hccCCCCCccCccccccccccccccccccCCCCchHHHHHHHHHHHhccccCcCCcCCC--Ccceee
Confidence 34456899999987521 1 12345699999999999999987544444457998 987654
No 30
>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=97.57 E-value=6.7e-05 Score=56.27 Aligned_cols=46 Identities=28% Similarity=0.795 Sum_probs=34.4
Q ss_pred ccccceeccccccCCceeecCCCcc-cchhhHHHHHHHHHhCCCCCCCCCCCCCCccc
Q 008441 308 NETCVICLEDTDVGHMFSIDGCLHR-YCFLCMKKHIEEKLRQGMEPTCPHEGCKSKLE 364 (565)
Q Consensus 308 ~~~C~IC~e~~~~~~~~~l~~C~H~-fC~~Cl~~~i~~~i~~g~~~kCP~~~C~~~l~ 364 (565)
...|.||++.. .++ .+.+|||. ||..|+.+++. ...+||. |+..+.
T Consensus 2 ~~~C~iC~~~~--~~~-~~~pCgH~~~C~~C~~~~~~------~~~~CP~--Cr~~i~ 48 (50)
T PF13920_consen 2 DEECPICFENP--RDV-VLLPCGHLCFCEECAERLLK------RKKKCPI--CRQPIE 48 (50)
T ss_dssp HSB-TTTSSSB--SSE-EEETTCEEEEEHHHHHHHHH------TTSBBTT--TTBB-S
T ss_pred cCCCccCCccC--Cce-EEeCCCChHHHHHHhHHhcc------cCCCCCc--CChhhc
Confidence 46899999874 334 44599999 99999999997 3348997 988764
No 31
>KOG0823 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=97.51 E-value=4.6e-05 Score=74.07 Aligned_cols=59 Identities=20% Similarity=0.529 Sum_probs=44.1
Q ss_pred cccccccceeccccccCCceeecCCCcccchhhHHHHHHHHHhCCCCCCCCCCCCCCccchhhHHHh
Q 008441 305 KTINETCVICLEDTDVGHMFSIDGCLHRYCFLCMKKHIEEKLRQGMEPTCPHEGCKSKLEVESCRIF 371 (565)
Q Consensus 305 ~~~~~~C~IC~e~~~~~~~~~l~~C~H~fC~~Cl~~~i~~~i~~g~~~kCP~~~C~~~l~~~~i~~l 371 (565)
....++|.||++.. .+++.. .|||.||-.||-+|+..+.... .||. |+..++.+.+--+
T Consensus 44 ~~~~FdCNICLd~a--kdPVvT-lCGHLFCWpClyqWl~~~~~~~---~cPV--CK~~Vs~~~vvPl 102 (230)
T KOG0823|consen 44 DGGFFDCNICLDLA--KDPVVT-LCGHLFCWPCLYQWLQTRPNSK---ECPV--CKAEVSIDTVVPL 102 (230)
T ss_pred CCCceeeeeecccc--CCCEEe-ecccceehHHHHHHHhhcCCCe---eCCc--cccccccceEEee
Confidence 34579999999873 455544 7999999999999998764333 5787 9988877655433
No 32
>KOG2177 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=97.48 E-value=7.4e-05 Score=75.93 Aligned_cols=107 Identities=21% Similarity=0.364 Sum_probs=64.3
Q ss_pred cccccceeccccccCCceeecCCCcccchhhHHHHHHHHHhCCCCCCCCCCCCCCccchhhHHHhhhhHHHHHHHHHHHH
Q 008441 307 INETCVICLEDTDVGHMFSIDGCLHRYCFLCMKKHIEEKLRQGMEPTCPHEGCKSKLEVESCRIFLTLKLFEIWNQRMKE 386 (565)
Q Consensus 307 ~~~~C~IC~e~~~~~~~~~l~~C~H~fC~~Cl~~~i~~~i~~g~~~kCP~~~C~~~l~~~~i~~lL~~e~~e~y~~~~~e 386 (565)
....|+||++.+... .+++|+|.||..|+...+. ..+.||. |+. .......+.+-.++.+.+.+
T Consensus 12 ~~~~C~iC~~~~~~p---~~l~C~H~~c~~C~~~~~~------~~~~Cp~--cr~-~~~~~~~n~~l~~~~~~~~~---- 75 (386)
T KOG2177|consen 12 EELTCPICLEYFREP---VLLPCGHNFCRACLTRSWE------GPLSCPV--CRP-PSRNLRPNVLLANLVERLRQ---- 75 (386)
T ss_pred ccccChhhHHHhhcC---ccccccchHhHHHHHHhcC------CCcCCcc--cCC-chhccCccHHHHHHHHHHHh----
Confidence 468999999997544 5669999999999999987 3368997 884 21111111222222222222
Q ss_pred hcCCCC---CcccccCCCCCCcccchhhhhccCCCcccccccCceeCCCCCCceecccC-CCcCCCCCh
Q 008441 387 ALIPVT---EKVYCPYPKCSALMSKSEIERDASSSSFVGRRLGARKCTKCHRRFCIDCK-VPWHNNMTC 451 (565)
Q Consensus 387 ~~i~~~---~~~~CP~p~C~~~i~~~~~~e~~~s~~~~~~~~~~~~C~~C~~~fC~~C~-~~~H~g~tC 451 (565)
...... ....|+ .......+.|..|...+|..|. ...|.++..
T Consensus 76 ~~~~~~~~~~~~~c~----------------------~~~~~~~~~c~~~~~~~c~~c~~~~~h~~h~~ 122 (386)
T KOG2177|consen 76 LRLSRPLGSKEELCE----------------------KHGEELKLFCEEDEKLLCVLCRESGEHRGHPV 122 (386)
T ss_pred cCCcccccccchhhh----------------------hcCCcceEEecccccccCCCCCCcccccCCcc
Confidence 111100 000222 1111267889999999999998 667776643
No 33
>PHA02929 N1R/p28-like protein; Provisional
Probab=97.42 E-value=8.9e-05 Score=73.63 Aligned_cols=51 Identities=25% Similarity=0.683 Sum_probs=37.9
Q ss_pred ccccccceeccccccCC-----ceeecCCCcccchhhHHHHHHHHHhCCCCCCCCCCCCCCccc
Q 008441 306 TINETCVICLEDTDVGH-----MFSIDGCLHRYCFLCMKKHIEEKLRQGMEPTCPHEGCKSKLE 364 (565)
Q Consensus 306 ~~~~~C~IC~e~~~~~~-----~~~l~~C~H~fC~~Cl~~~i~~~i~~g~~~kCP~~~C~~~l~ 364 (565)
....+|+||++.+.... +..+.+|+|.||..|+..|+.. ...||. |+..+.
T Consensus 172 ~~~~eC~ICle~~~~~~~~~~~~~vl~~C~H~FC~~CI~~Wl~~------~~tCPl--CR~~~~ 227 (238)
T PHA02929 172 SKDKECAICMEKVYDKEIKNMYFGILSNCNHVFCIECIDIWKKE------KNTCPV--CRTPFI 227 (238)
T ss_pred CCCCCCccCCcccccCccccccceecCCCCCcccHHHHHHHHhc------CCCCCC--CCCEee
Confidence 34689999999864322 2345689999999999999853 237997 987664
No 34
>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=97.32 E-value=0.0002 Score=49.48 Aligned_cols=38 Identities=34% Similarity=0.800 Sum_probs=27.9
Q ss_pred cceeccccccCCceeecCCCcccchhhHHHHHHHHHhCCCCCCCCC
Q 008441 311 CVICLEDTDVGHMFSIDGCLHRYCFLCMKKHIEEKLRQGMEPTCPH 356 (565)
Q Consensus 311 C~IC~e~~~~~~~~~l~~C~H~fC~~Cl~~~i~~~i~~g~~~kCP~ 356 (565)
|+||++.. ..+ .+++|+|.||..|+..|+. ....+||.
T Consensus 1 C~iC~~~~--~~~-~~~~C~H~~c~~C~~~~~~-----~~~~~CP~ 38 (39)
T smart00184 1 CPICLEEL--KDP-VVLPCGHTFCRSCIRKWLK-----SGNNTCPI 38 (39)
T ss_pred CCcCccCC--CCc-EEecCCChHHHHHHHHHHH-----hCcCCCCC
Confidence 78998872 333 4458999999999999987 12246874
No 35
>KOG2164 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=97.31 E-value=9.7e-05 Score=79.19 Aligned_cols=59 Identities=24% Similarity=0.474 Sum_probs=43.5
Q ss_pred ccccceeccccccCCceeecCCCcccchhhHHHHHHHHHhCCCCCCCCCCCCCCccchhhHHHhh
Q 008441 308 NETCVICLEDTDVGHMFSIDGCLHRYCFLCMKKHIEEKLRQGMEPTCPHEGCKSKLEVESCRIFL 372 (565)
Q Consensus 308 ~~~C~IC~e~~~~~~~~~l~~C~H~fC~~Cl~~~i~~~i~~g~~~kCP~~~C~~~l~~~~i~~lL 372 (565)
...||||++..+... +..|||.||..||.+||.... -..+-+||- |...|.+.++..+.
T Consensus 186 ~~~CPICL~~~~~p~---~t~CGHiFC~~CiLqy~~~s~-~~~~~~CPi--C~s~I~~kdl~pv~ 244 (513)
T KOG2164|consen 186 DMQCPICLEPPSVPV---RTNCGHIFCGPCILQYWNYSA-IKGPCSCPI--CRSTITLKDLLPVF 244 (513)
T ss_pred CCcCCcccCCCCccc---ccccCceeeHHHHHHHHhhhc-ccCCccCCc--hhhhccccceeeee
Confidence 679999998854332 336999999999999998761 122347997 99988876665443
No 36
>KOG4628 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=97.30 E-value=0.00048 Score=71.65 Aligned_cols=48 Identities=33% Similarity=0.814 Sum_probs=40.2
Q ss_pred cccceeccccccCCceeecCCCcccchhhHHHHHHHHHhCCCCCCCCCCCCCCcc
Q 008441 309 ETCVICLEDTDVGHMFSIDGCLHRYCFLCMKKHIEEKLRQGMEPTCPHEGCKSKL 363 (565)
Q Consensus 309 ~~C~IC~e~~~~~~~~~l~~C~H~fC~~Cl~~~i~~~i~~g~~~kCP~~~C~~~l 363 (565)
.+|.||+|++...+....++|+|.|...|+..|+... +. .||. |+..+
T Consensus 230 ~~CaIClEdY~~GdklRiLPC~H~FH~~CIDpWL~~~---r~--~CPv--CK~di 277 (348)
T KOG4628|consen 230 DTCAICLEDYEKGDKLRILPCSHKFHVNCIDPWLTQT---RT--FCPV--CKRDI 277 (348)
T ss_pred ceEEEeecccccCCeeeEecCCCchhhccchhhHhhc---Cc--cCCC--CCCcC
Confidence 6999999999888888888999999999999999654 21 4997 77644
No 37
>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=97.24 E-value=0.00036 Score=54.56 Aligned_cols=50 Identities=20% Similarity=0.107 Sum_probs=38.4
Q ss_pred cccceeccccccCCceeecCCCcccchhhHHHHHHHHHhCCCCCCCCCCCCCCccchhhHH
Q 008441 309 ETCVICLEDTDVGHMFSIDGCLHRYCFLCMKKHIEEKLRQGMEPTCPHEGCKSKLEVESCR 369 (565)
Q Consensus 309 ~~C~IC~e~~~~~~~~~l~~C~H~fC~~Cl~~~i~~~i~~g~~~kCP~~~C~~~l~~~~i~ 369 (565)
+.|+||.+.+ .+++.. +|||.||+.|+.+|+.. ..+||. |+..++..++.
T Consensus 2 ~~Cpi~~~~~--~~Pv~~-~~G~v~~~~~i~~~~~~------~~~cP~--~~~~~~~~~l~ 51 (63)
T smart00504 2 FLCPISLEVM--KDPVIL-PSGQTYERRAIEKWLLS------HGTDPV--TGQPLTHEDLI 51 (63)
T ss_pred cCCcCCCCcC--CCCEEC-CCCCEEeHHHHHHHHHH------CCCCCC--CcCCCChhhce
Confidence 5799999875 455544 89999999999999965 237997 88887665543
No 38
>KOG0287 consensus Postreplication repair protein RAD18 [Replication, recombination and repair]
Probab=97.13 E-value=0.00031 Score=71.32 Aligned_cols=63 Identities=27% Similarity=0.600 Sum_probs=46.8
Q ss_pred ccccceeccccccCCceeecCCCcccchhhHHHHHHHHHhCCCCCCCCCCCCCCccchhhHH-HhhhhHHHHHHH
Q 008441 308 NETCVICLEDTDVGHMFSIDGCLHRYCFLCMKKHIEEKLRQGMEPTCPHEGCKSKLEVESCR-IFLTLKLFEIWN 381 (565)
Q Consensus 308 ~~~C~IC~e~~~~~~~~~l~~C~H~fC~~Cl~~~i~~~i~~g~~~kCP~~~C~~~l~~~~i~-~lL~~e~~e~y~ 381 (565)
..-|.||++.+... .+.+|+|.||.-|++.|+.. .|.||. |...+....++ +++-.++++.|.
T Consensus 23 lLRC~IC~eyf~ip---~itpCsHtfCSlCIR~~L~~------~p~CP~--C~~~~~Es~Lr~n~il~Eiv~S~~ 86 (442)
T KOG0287|consen 23 LLRCGICFEYFNIP---MITPCSHTFCSLCIRKFLSY------KPQCPT--CCVTVTESDLRNNRILDEIVKSLN 86 (442)
T ss_pred HHHHhHHHHHhcCc---eeccccchHHHHHHHHHhcc------CCCCCc--eecccchhhhhhhhHHHHHHHHHH
Confidence 46899999987543 23489999999999999954 368997 88888777765 344456666553
No 39
>TIGR00599 rad18 DNA repair protein rad18. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=96.98 E-value=0.00062 Score=72.48 Aligned_cols=65 Identities=23% Similarity=0.642 Sum_probs=46.0
Q ss_pred ccccccceeccccccCCceeecCCCcccchhhHHHHHHHHHhCCCCCCCCCCCCCCccchhhH-HHhhhhHHHHHHH
Q 008441 306 TINETCVICLEDTDVGHMFSIDGCLHRYCFLCMKKHIEEKLRQGMEPTCPHEGCKSKLEVESC-RIFLTLKLFEIWN 381 (565)
Q Consensus 306 ~~~~~C~IC~e~~~~~~~~~l~~C~H~fC~~Cl~~~i~~~i~~g~~~kCP~~~C~~~l~~~~i-~~lL~~e~~e~y~ 381 (565)
...+.|+||++.+. .++ +.+|+|.||..|+..|+... ..||. |+..+....+ .+.+-.++++.|.
T Consensus 24 e~~l~C~IC~d~~~--~Pv-itpCgH~FCs~CI~~~l~~~------~~CP~--Cr~~~~~~~Lr~N~~L~~iVe~~~ 89 (397)
T TIGR00599 24 DTSLRCHICKDFFD--VPV-LTSCSHTFCSLCIRRCLSNQ------PKCPL--CRAEDQESKLRSNWLVSEIVESFK 89 (397)
T ss_pred ccccCCCcCchhhh--Ccc-CCCCCCchhHHHHHHHHhCC------CCCCC--CCCccccccCccchHHHHHHHHHH
Confidence 35689999998763 444 45999999999999998541 37996 9988765443 2344455666664
No 40
>KOG0317 consensus Predicted E3 ubiquitin ligase, integral peroxisomal membrane protein [Posttranslational modification, protein turnover, chaperones]
Probab=96.97 E-value=0.00035 Score=70.00 Aligned_cols=51 Identities=29% Similarity=0.760 Sum_probs=39.5
Q ss_pred cccccceeccccccCCceeecCCCcccchhhHHHHHHHHHhCCCCCCCCCCCCCCccchhhH
Q 008441 307 INETCVICLEDTDVGHMFSIDGCLHRYCFLCMKKHIEEKLRQGMEPTCPHEGCKSKLEVESC 368 (565)
Q Consensus 307 ~~~~C~IC~e~~~~~~~~~l~~C~H~fC~~Cl~~~i~~~i~~g~~~kCP~~~C~~~l~~~~i 368 (565)
....|.+|++.. .++ +..+|||.||-.|+..|...+- -||. |+..+.+..+
T Consensus 238 a~~kC~LCLe~~--~~p-SaTpCGHiFCWsCI~~w~~ek~------eCPl--CR~~~~pskv 288 (293)
T KOG0317|consen 238 ATRKCSLCLENR--SNP-SATPCGHIFCWSCILEWCSEKA------ECPL--CREKFQPSKV 288 (293)
T ss_pred CCCceEEEecCC--CCC-CcCcCcchHHHHHHHHHHcccc------CCCc--ccccCCCcce
Confidence 467999999875 344 3459999999999999996543 4997 9988776543
No 41
>COG5540 RING-finger-containing ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=96.80 E-value=0.00087 Score=67.32 Aligned_cols=54 Identities=22% Similarity=0.564 Sum_probs=43.5
Q ss_pred cccccccceeccccccCCceeecCCCcccchhhHHHHHHHHHhCCCCCCCCCCCCCCccch
Q 008441 305 KTINETCVICLEDTDVGHMFSIDGCLHRYCFLCMKKHIEEKLRQGMEPTCPHEGCKSKLEV 365 (565)
Q Consensus 305 ~~~~~~C~IC~e~~~~~~~~~l~~C~H~fC~~Cl~~~i~~~i~~g~~~kCP~~~C~~~l~~ 365 (565)
..+..+|.||++++...+-+.+++|.|.|...|+.+|+. +...+||. |+..+++
T Consensus 320 a~~GveCaICms~fiK~d~~~vlPC~H~FH~~Cv~kW~~-----~y~~~CPv--Crt~iPP 373 (374)
T COG5540 320 ADKGVECAICMSNFIKNDRLRVLPCDHRFHVGCVDKWLL-----GYSNKCPV--CRTAIPP 373 (374)
T ss_pred cCCCceEEEEhhhhcccceEEEeccCceechhHHHHHHh-----hhcccCCc--cCCCCCC
Confidence 334589999999986555567779999999999999994 34458997 9988864
No 42
>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=96.73 E-value=0.0012 Score=67.70 Aligned_cols=52 Identities=21% Similarity=0.567 Sum_probs=36.1
Q ss_pred cccceecccccc-CCc-eeecCCCcccchhhHHHHHHHHHhCCCCCCCCCCCCCCccchhh
Q 008441 309 ETCVICLEDTDV-GHM-FSIDGCLHRYCFLCMKKHIEEKLRQGMEPTCPHEGCKSKLEVES 367 (565)
Q Consensus 309 ~~C~IC~e~~~~-~~~-~~l~~C~H~fC~~Cl~~~i~~~i~~g~~~kCP~~~C~~~l~~~~ 367 (565)
..||+|..+... ..+ +.+..|||.||.+|+...+. .+ ...||. |+..+....
T Consensus 4 ~~CP~Ck~~~y~np~~kl~i~~CGH~~C~sCv~~l~~----~~-~~~CP~--C~~~lrk~~ 57 (309)
T TIGR00570 4 QGCPRCKTTKYRNPSLKLMVNVCGHTLCESCVDLLFV----RG-SGSCPE--CDTPLRKNN 57 (309)
T ss_pred CCCCcCCCCCccCcccccccCCCCCcccHHHHHHHhc----CC-CCCCCC--CCCccchhh
Confidence 579999986322 221 12227999999999999873 22 348995 998776654
No 43
>PF11789 zf-Nse: Zinc-finger of the MIZ type in Nse subunit; PDB: 2YU4_A 3HTK_C.
Probab=96.47 E-value=0.002 Score=49.73 Aligned_cols=50 Identities=24% Similarity=0.421 Sum_probs=33.4
Q ss_pred cccccccceeccccccCCceeecCCCcccchhhHHHHHHHHHhCCCCCCCCCCCCC
Q 008441 305 KTINETCVICLEDTDVGHMFSIDGCLHRYCFLCMKKHIEEKLRQGMEPTCPHEGCK 360 (565)
Q Consensus 305 ~~~~~~C~IC~e~~~~~~~~~l~~C~H~fC~~Cl~~~i~~~i~~g~~~kCP~~~C~ 360 (565)
....+.|+|.+..+ .+++....|+|.|.++.+.+|+ ..+...+||..||.
T Consensus 8 ~~~~~~CPiT~~~~--~~PV~s~~C~H~fek~aI~~~i----~~~~~~~CPv~GC~ 57 (57)
T PF11789_consen 8 GTISLKCPITLQPF--EDPVKSKKCGHTFEKEAILQYI----QRNGSKRCPVAGCN 57 (57)
T ss_dssp SB--SB-TTTSSB---SSEEEESSS--EEEHHHHHHHC----TTTS-EE-SCCC-S
T ss_pred cEeccCCCCcCChh--hCCcCcCCCCCeecHHHHHHHH----HhcCCCCCCCCCCC
Confidence 34578999999764 6777777999999999999999 34445699999995
No 44
>KOG2879 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=96.25 E-value=0.0057 Score=60.96 Aligned_cols=54 Identities=28% Similarity=0.549 Sum_probs=40.7
Q ss_pred cCcccccccceeccccccCCceeecCCCcccchhhHHHHHHHHHhCCCCCCCCCCCCCCccc
Q 008441 303 RGKTINETCVICLEDTDVGHMFSIDGCLHRYCFLCMKKHIEEKLRQGMEPTCPHEGCKSKLE 364 (565)
Q Consensus 303 ~~~~~~~~C~IC~e~~~~~~~~~l~~C~H~fC~~Cl~~~i~~~i~~g~~~kCP~~~C~~~l~ 364 (565)
.......+|++|.+. +..++...+|+|+||..|+..-+.. ...+.||. |+....
T Consensus 234 s~~t~~~~C~~Cg~~--PtiP~~~~~C~HiyCY~Ci~ts~~~----~asf~Cp~--Cg~~~~ 287 (298)
T KOG2879|consen 234 STGTSDTECPVCGEP--PTIPHVIGKCGHIYCYYCIATSRLW----DASFTCPL--CGENVE 287 (298)
T ss_pred ccccCCceeeccCCC--CCCCeeeccccceeehhhhhhhhcc----hhhcccCc--cCCCCc
Confidence 445567899999876 4667777789999999999976643 22358997 888765
No 45
>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=96.16 E-value=0.0027 Score=51.64 Aligned_cols=43 Identities=26% Similarity=0.648 Sum_probs=30.4
Q ss_pred ccccceecccccc----------CCceeecCCCcccchhhHHHHHHHHHhCCCCCCCCC
Q 008441 308 NETCVICLEDTDV----------GHMFSIDGCLHRYCFLCMKKHIEEKLRQGMEPTCPH 356 (565)
Q Consensus 308 ~~~C~IC~e~~~~----------~~~~~l~~C~H~fC~~Cl~~~i~~~i~~g~~~kCP~ 356 (565)
...|.||++.+.. .-.+.+..|+|.|+..||.+|++.+ ..||.
T Consensus 19 ~d~C~IC~~~l~~~~~~~~~~~~~~~i~~~~C~H~FH~~Ci~~Wl~~~------~~CP~ 71 (73)
T PF12678_consen 19 DDNCAICREPLEDPCPECQAPQDECPIVWGPCGHIFHFHCISQWLKQN------NTCPL 71 (73)
T ss_dssp CSBETTTTSBTTSTTCCHHHCTTTS-EEEETTSEEEEHHHHHHHHTTS------SB-TT
T ss_pred CCcccccChhhhChhhhhcCCccccceEecccCCCEEHHHHHHHHhcC------CcCCC
Confidence 4469999998721 2334556899999999999999432 17886
No 46
>PF06524 NOA36: NOA36 protein; InterPro: IPR010531 This family consists of several NOA36 proteins which contain 29 highly conserved cysteine residues. The function of this protein is unknown.; GO: 0008270 zinc ion binding, 0005634 nucleus
Probab=96.11 E-value=0.0086 Score=59.10 Aligned_cols=52 Identities=23% Similarity=0.410 Sum_probs=30.5
Q ss_pred ccCceeCCCCCC---ceecccCCCcCCCCChhhHhhhCCCCChhHHHHHHHHhcCCccccCCCCceeEec
Q 008441 424 RLGARKCTKCHR---RFCIDCKVPWHNNMTCIYYKRLNPNPPTEDVKLKSLASSNLWRQCVKCNHLIELA 490 (565)
Q Consensus 424 ~~~~~~C~~C~~---~fC~~C~~~~H~g~tC~e~~~~~~~~~~ed~~l~~l~~~~~~k~CPkC~~~IEK~ 490 (565)
....+.|..|+. ..|++|+.-+ |++..+.+. ....++ ...+||+|+....-.
T Consensus 168 e~E~~KC~SCNrlGq~sCLRCK~cf-----CddHvrrKg---------~ky~k~-k~~PCPKCg~et~eT 222 (314)
T PF06524_consen 168 ESETFKCQSCNRLGQYSCLRCKICF-----CDDHVRRKG---------FKYEKG-KPIPCPKCGYETQET 222 (314)
T ss_pred hcccccccccccccchhhhheeeee-----hhhhhhhcc---------cccccC-CCCCCCCCCCccccc
Confidence 345678888854 6899998754 433322211 111122 236999999987644
No 47
>PF11793 FANCL_C: FANCL C-terminal domain; PDB: 3K1L_A.
Probab=95.99 E-value=0.0053 Score=49.49 Aligned_cols=57 Identities=21% Similarity=0.483 Sum_probs=27.3
Q ss_pred ccccceeccccc-cCCc--ee--ecCCCcccchhhHHHHHHHHHhCCC--CC---CCCCCCCCCccchh
Q 008441 308 NETCVICLEDTD-VGHM--FS--IDGCLHRYCFLCMKKHIEEKLRQGM--EP---TCPHEGCKSKLEVE 366 (565)
Q Consensus 308 ~~~C~IC~e~~~-~~~~--~~--l~~C~H~fC~~Cl~~~i~~~i~~g~--~~---kCP~~~C~~~l~~~ 366 (565)
..+|+||+.... .... .. ...|++.|...||.+||...-.... .+ +||. |+.+|...
T Consensus 2 ~~~C~IC~~~~~~~~~~p~~~C~n~~C~~~fH~~CL~~wf~~~~~~~~~~~~~~G~CP~--C~~~i~~~ 68 (70)
T PF11793_consen 2 ELECGICYSYRLDDGEIPDVVCPNPSCGKKFHLLCLSEWFLSLEKSRQSFIPIFGECPY--CSSPISWS 68 (70)
T ss_dssp --S-SSS--SS-TT-----B--S-TT----B-SGGGHHHHHHHHSSS-TTT--EEE-TT--T-SEEEGG
T ss_pred CCCCCcCCcEecCCCCcCceEcCCcccCCHHHHHHHHHHHHHcccCCeeecccccCCcC--CCCeeeEe
Confidence 468999998754 2221 11 1378899999999999987554432 22 6997 99988753
No 48
>PF14835 zf-RING_6: zf-RING of BARD1-type protein; PDB: 1JM7_B.
Probab=95.98 E-value=0.0013 Score=51.36 Aligned_cols=50 Identities=24% Similarity=0.666 Sum_probs=24.1
Q ss_pred ccccceeccccccCCceeecCCCcccchhhHHHHHHHHHhCCCCCCCCCCCCCCccchhhHH
Q 008441 308 NETCVICLEDTDVGHMFSIDGCLHRYCFLCMKKHIEEKLRQGMEPTCPHEGCKSKLEVESCR 369 (565)
Q Consensus 308 ~~~C~IC~e~~~~~~~~~l~~C~H~fC~~Cl~~~i~~~i~~g~~~kCP~~~C~~~l~~~~i~ 369 (565)
..-|++|.+.+ ..++.+..|.|.||..|++..+. -.||. |..+--..+++
T Consensus 7 lLrCs~C~~~l--~~pv~l~~CeH~fCs~Ci~~~~~--------~~CPv--C~~Paw~qD~~ 56 (65)
T PF14835_consen 7 LLRCSICFDIL--KEPVCLGGCEHIFCSSCIRDCIG--------SECPV--CHTPAWIQDIQ 56 (65)
T ss_dssp TTS-SSS-S----SS-B---SSS--B-TTTGGGGTT--------TB-SS--S--B-S-SS--
T ss_pred hcCCcHHHHHh--cCCceeccCccHHHHHHhHHhcC--------CCCCC--cCChHHHHHHH
Confidence 46799999874 56777789999999999987542 25997 88776555543
No 49
>KOG1002 consensus Nucleotide excision repair protein RAD16 [Replication, recombination and repair]
Probab=95.94 E-value=0.004 Score=66.81 Aligned_cols=59 Identities=24% Similarity=0.616 Sum_probs=44.5
Q ss_pred CcccccccceeccccccCCceeecCCCcccchhhHHHHHHHHHhCCCCCCCCCCCCCCccchhhH
Q 008441 304 GKTINETCVICLEDTDVGHMFSIDGCLHRYCFLCMKKHIEEKLRQGMEPTCPHEGCKSKLEVESC 368 (565)
Q Consensus 304 ~~~~~~~C~IC~e~~~~~~~~~l~~C~H~fC~~Cl~~~i~~~i~~g~~~kCP~~~C~~~l~~~~i 368 (565)
.+.....|.+|-+.- .+.+ ...|.|.||+-|++.|+..-..+.. +.||. |...|+.+.-
T Consensus 532 enk~~~~C~lc~d~a--ed~i-~s~ChH~FCrlCi~eyv~~f~~~~n-vtCP~--C~i~LsiDls 590 (791)
T KOG1002|consen 532 ENKGEVECGLCHDPA--EDYI-ESSCHHKFCRLCIKEYVESFMENNN-VTCPV--CHIGLSIDLS 590 (791)
T ss_pred cccCceeecccCChh--hhhH-hhhhhHHHHHHHHHHHHHhhhcccC-CCCcc--cccccccccc
Confidence 455678999998763 3444 3489999999999999987654444 79997 9888776643
No 50
>KOG4367 consensus Predicted Zn-finger protein [Function unknown]
Probab=95.87 E-value=0.004 Score=65.27 Aligned_cols=81 Identities=25% Similarity=0.467 Sum_probs=45.8
Q ss_pred cccCceeCCCCCCceecccCCCcCCCCChhhHhhhCCCCChhHHHHHHHHhcCCccccCCCCceeEecCCcce-EEe-ec
Q 008441 423 RRLGARKCTKCHRRFCIDCKVPWHNNMTCIYYKRLNPNPPTEDVKLKSLASSNLWRQCVKCNHLIELAEGCFH-MTC-RC 500 (565)
Q Consensus 423 ~~~~~~~C~~C~~~fC~~C~~~~H~g~tC~e~~~~~~~~~~ed~~l~~l~~~~~~k~CPkC~~~IEK~~GCnH-MtC-~C 500 (565)
++...+.|..|...+|.-|+..-|++..=-.-.++.+-.+ -.+..-..-....+|.. -+|=|| |+| .|
T Consensus 172 ~k~a~v~ceqcdv~yc~pc~~~~hp~rgplakh~l~~~~~---grvs~~~s~r~~~~ct~-------h~~e~~smyc~~c 241 (699)
T KOG4367|consen 172 PKEATVMCEQCDVFYCDPCRLRCHPPRGPLAKHRLVPPAQ---GRVSRRLSPRKVSTCTD-------HELENHSMYCVQC 241 (699)
T ss_pred hhhhhhhHhhCceEEechHHhccCCCCCchhhcccCCccc---CceeeccchhhhhhccC-------CCCCCceEEEEec
Confidence 4566789999999999999998887642110001111111 01000000000112221 235565 999 59
Q ss_pred Ccccccccccccc
Q 008441 501 GHEFCYNCGAEWK 513 (565)
Q Consensus 501 g~~FCw~C~~~~~ 513 (565)
+.-.||.|+...+
T Consensus 242 k~pvc~~clee~k 254 (699)
T KOG4367|consen 242 KMPVCYQCLEEGK 254 (699)
T ss_pred CChHHHHHHHhhc
Confidence 9999999998855
No 51
>COG5574 PEX10 RING-finger-containing E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=95.60 E-value=0.0095 Score=59.21 Aligned_cols=54 Identities=26% Similarity=0.610 Sum_probs=38.7
Q ss_pred ccccccceeccccccCCceeecCCCcccchhhHHHHHHHHHhCCCCCCCCCCCCCCccchhhH
Q 008441 306 TINETCVICLEDTDVGHMFSIDGCLHRYCFLCMKKHIEEKLRQGMEPTCPHEGCKSKLEVESC 368 (565)
Q Consensus 306 ~~~~~C~IC~e~~~~~~~~~l~~C~H~fC~~Cl~~~i~~~i~~g~~~kCP~~~C~~~l~~~~i 368 (565)
...+.|.||++.. ..++..+|||.||..|+...++.+ .+-.||. |+....+..+
T Consensus 213 ~~d~kC~lC~e~~---~~ps~t~CgHlFC~~Cl~~~~t~~----k~~~Cpl--CRak~~pk~v 266 (271)
T COG5574 213 LADYKCFLCLEEP---EVPSCTPCGHLFCLSCLLISWTKK----KYEFCPL--CRAKVYPKKV 266 (271)
T ss_pred ccccceeeeeccc---CCcccccccchhhHHHHHHHHHhh----ccccCch--hhhhccchhh
Confidence 4578899999873 334556999999999999854322 2236997 9887776554
No 52
>KOG0978 consensus E3 ubiquitin ligase involved in syntaxin degradation [Posttranslational modification, protein turnover, chaperones]
Probab=95.44 E-value=0.0049 Score=69.48 Aligned_cols=55 Identities=20% Similarity=0.524 Sum_probs=40.9
Q ss_pred cccccceeccccccCCceeecCCCcccchhhHHHHHHHHHhCCCCCCCCCCCCCCccchhhHHHh
Q 008441 307 INETCVICLEDTDVGHMFSIDGCLHRYCFLCMKKHIEEKLRQGMEPTCPHEGCKSKLEVESCRIF 371 (565)
Q Consensus 307 ~~~~C~IC~e~~~~~~~~~l~~C~H~fC~~Cl~~~i~~~i~~g~~~kCP~~~C~~~l~~~~i~~l 371 (565)
...+|++|..- ..+.+ +..|+|.||.+|++..+..+- -+||. |+..+...++..+
T Consensus 642 ~~LkCs~Cn~R--~Kd~v-I~kC~H~FC~~Cvq~r~etRq-----RKCP~--Cn~aFganDv~~I 696 (698)
T KOG0978|consen 642 ELLKCSVCNTR--WKDAV-ITKCGHVFCEECVQTRYETRQ-----RKCPK--CNAAFGANDVHRI 696 (698)
T ss_pred hceeCCCccCc--hhhHH-HHhcchHHHHHHHHHHHHHhc-----CCCCC--CCCCCCccccccc
Confidence 35799999843 23333 458999999999999887642 27996 9999888776543
No 53
>COG5432 RAD18 RING-finger-containing E3 ubiquitin ligase [Signal transduction mechanisms]
Probab=95.40 E-value=0.012 Score=58.90 Aligned_cols=63 Identities=24% Similarity=0.482 Sum_probs=40.6
Q ss_pred cccccceeccccccCCceeecCCCcccchhhHHHHHHHHHhCCCCCCCCCCCCCCccchhhHH-HhhhhHHHHHH
Q 008441 307 INETCVICLEDTDVGHMFSIDGCLHRYCFLCMKKHIEEKLRQGMEPTCPHEGCKSKLEVESCR-IFLTLKLFEIW 380 (565)
Q Consensus 307 ~~~~C~IC~e~~~~~~~~~l~~C~H~fC~~Cl~~~i~~~i~~g~~~kCP~~~C~~~l~~~~i~-~lL~~e~~e~y 380 (565)
...-|-||-+-+.. .....|||.||.-|++.|+. .-+.||. |....-...++ ..+..++.+.|
T Consensus 24 s~lrC~IC~~~i~i---p~~TtCgHtFCslCIR~hL~------~qp~CP~--Cr~~~~esrlr~~s~~~ei~es~ 87 (391)
T COG5432 24 SMLRCRICDCRISI---PCETTCGHTFCSLCIRRHLG------TQPFCPV--CREDPCESRLRGSSGSREINESH 87 (391)
T ss_pred hHHHhhhhhheeec---ceecccccchhHHHHHHHhc------CCCCCcc--ccccHHhhhcccchhHHHHHHhh
Confidence 45789999876532 23448999999999999994 3467887 77654433322 23334444444
No 54
>COG5243 HRD1 HRD ubiquitin ligase complex, ER membrane component [Posttranslational modification, protein turnover, chaperones]
Probab=95.16 E-value=0.013 Score=60.66 Aligned_cols=53 Identities=25% Similarity=0.577 Sum_probs=38.8
Q ss_pred cccccceecccc-ccC---------CceeecCCCcccchhhHHHHHHHHHhCCCCCCCCCCCCCCccchhh
Q 008441 307 INETCVICLEDT-DVG---------HMFSIDGCLHRYCFLCMKKHIEEKLRQGMEPTCPHEGCKSKLEVES 367 (565)
Q Consensus 307 ~~~~C~IC~e~~-~~~---------~~~~l~~C~H~fC~~Cl~~~i~~~i~~g~~~kCP~~~C~~~l~~~~ 367 (565)
....|.||+++. ... .....++|||.+..+|++.|++.+- .||. |+.++-.+.
T Consensus 286 ~D~~C~ICmde~~h~~~~~~~~~~~~~pKrLpCGHilHl~CLknW~ERqQ------TCPI--Cr~p~ifd~ 348 (491)
T COG5243 286 SDRTCTICMDEMFHPDHEPLPRGLDMTPKRLPCGHILHLHCLKNWLERQQ------TCPI--CRRPVIFDQ 348 (491)
T ss_pred CCCeEEEecccccCCCCccCcccccCCcccccccceeeHHHHHHHHHhcc------CCCc--ccCcccccc
Confidence 367999999983 222 1223459999999999999997542 7997 988765443
No 55
>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=94.94 E-value=0.036 Score=44.96 Aligned_cols=52 Identities=17% Similarity=0.110 Sum_probs=36.0
Q ss_pred cccccceeccccccCCceeecCCCcccchhhHHHHHHHHHhCCCCCCCCCCCCCCccchhhH
Q 008441 307 INETCVICLEDTDVGHMFSIDGCLHRYCFLCMKKHIEEKLRQGMEPTCPHEGCKSKLEVESC 368 (565)
Q Consensus 307 ~~~~C~IC~e~~~~~~~~~l~~C~H~fC~~Cl~~~i~~~i~~g~~~kCP~~~C~~~l~~~~i 368 (565)
..+.|+|+.+-+ .+++.+ ++||.|++.|+..|+.. ....||. |+..+....+
T Consensus 3 ~~f~CpIt~~lM--~dPVi~-~~G~tyer~~I~~~l~~-----~~~~~P~--t~~~l~~~~l 54 (73)
T PF04564_consen 3 DEFLCPITGELM--RDPVIL-PSGHTYERSAIERWLEQ-----NGGTDPF--TRQPLSESDL 54 (73)
T ss_dssp GGGB-TTTSSB---SSEEEE-TTSEEEEHHHHHHHHCT-----TSSB-TT--T-SB-SGGGS
T ss_pred cccCCcCcCcHh--hCceeC-CcCCEEcHHHHHHHHHc-----CCCCCCC--CCCcCCcccc
Confidence 367999999764 567766 88999999999999954 2347997 7777776543
No 56
>KOG1039 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=94.91 E-value=0.017 Score=60.56 Aligned_cols=57 Identities=21% Similarity=0.592 Sum_probs=39.4
Q ss_pred ccccccceeccccccCC-----ceeecCCCcccchhhHHHHHHHHHhC-CCCCCCCCCCCCCccc
Q 008441 306 TINETCVICLEDTDVGH-----MFSIDGCLHRYCFLCMKKHIEEKLRQ-GMEPTCPHEGCKSKLE 364 (565)
Q Consensus 306 ~~~~~C~IC~e~~~~~~-----~~~l~~C~H~fC~~Cl~~~i~~~i~~-g~~~kCP~~~C~~~l~ 364 (565)
.+..+|+||++...... +-.+++|.|.||..|++.|-...-.+ .+...||. |+....
T Consensus 159 s~~k~CGICme~i~ek~~~~~rfgilpnC~H~~Cl~Cir~wr~~~q~~~~~sksCP~--CRv~s~ 221 (344)
T KOG1039|consen 159 SSEKECGICMETINEKAASERRFGILPNCNHSFCLNCIRKWRQATQFESKTSKSCPF--CRVPSS 221 (344)
T ss_pred cccccceehhhhccccchhhhhcccCCCcchhhhhcHhHhhhhhhccccccccCCCc--ccCccc
Confidence 45789999999864332 22346899999999999987543322 23347998 876543
No 57
>PF12861 zf-Apc11: Anaphase-promoting complex subunit 11 RING-H2 finger
Probab=92.82 E-value=0.081 Score=44.05 Aligned_cols=53 Identities=21% Similarity=0.545 Sum_probs=36.0
Q ss_pred ccccceecccccc---------CC-ceeecCCCcccchhhHHHHHHHHHhCCCCCCCCCCCCCCccch
Q 008441 308 NETCVICLEDTDV---------GH-MFSIDGCLHRYCFLCMKKHIEEKLRQGMEPTCPHEGCKSKLEV 365 (565)
Q Consensus 308 ~~~C~IC~e~~~~---------~~-~~~l~~C~H~fC~~Cl~~~i~~~i~~g~~~kCP~~~C~~~l~~ 365 (565)
...|+||...++. .+ ++..-.|+|.|...|+.+|+..+-. ...||- |++.+..
T Consensus 21 dd~CgICr~~fdg~Cp~Ck~Pgd~Cplv~g~C~H~FH~hCI~kWl~~~~~---~~~CPm--CR~~w~~ 83 (85)
T PF12861_consen 21 DDVCGICRMPFDGCCPDCKFPGDDCPLVWGKCSHNFHMHCILKWLSTQSS---KGQCPM--CRQPWKF 83 (85)
T ss_pred CCceeeEecccccCCCCccCCCCCCceeeccCccHHHHHHHHHHHccccC---CCCCCC--cCCeeee
Confidence 4567777666542 11 2334479999999999999986522 237997 8877643
No 58
>KOG1814 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=92.79 E-value=0.026 Score=59.39 Aligned_cols=38 Identities=24% Similarity=0.691 Sum_probs=34.5
Q ss_pred ccccCC--CCceeEecCCcceEEe-ecCccccccccccccC
Q 008441 477 WRQCVK--CNHLIELAEGCFHMTC-RCGHEFCYNCGAEWKN 514 (565)
Q Consensus 477 ~k~CPk--C~~~IEK~~GCnHMtC-~Cg~~FCw~C~~~~~~ 514 (565)
.+.||+ |..++-...|++-..| +|.+-||.+|...|++
T Consensus 273 v~yCPr~~Cq~p~~~d~~~~l~~CskCnFaFCtlCk~t~HG 313 (445)
T KOG1814|consen 273 VVYCPRACCQLPVKQDPGRALAICSKCNFAFCTLCKLTWHG 313 (445)
T ss_pred cccCChhhccCccccCchhhhhhhccCccHHHHHHHHhhcC
Confidence 489998 9999966779999999 6999999999999985
No 59
>KOG0006 consensus E3 ubiquitin-protein ligase (Parkin protein) [Posttranslational modification, protein turnover, chaperones]
Probab=92.57 E-value=0.18 Score=51.37 Aligned_cols=145 Identities=19% Similarity=0.307 Sum_probs=72.8
Q ss_pred cccccccchHHHHHHHHHhhhcccccccccccCcccccccceeccccccCCceee-cCCCcccchhhHHHHHHHHHhCCC
Q 008441 272 PRHVARNDMKYVYELARAAINSQMTVPAEISRGKTINETCVICLEDTDVGHMFSI-DGCLHRYCFLCMKKHIEEKLRQGM 350 (565)
Q Consensus 272 ~~~V~R~~n~~Ad~LA~eal~sqi~~~~~~~~~~~~~~~C~IC~e~~~~~~~~~l-~~C~H~fC~~Cl~~~i~~~i~~g~ 350 (565)
++++.+++.....+.|++....+..-..-+ +.-|+.=+=.-+...-++. .+|+-.||++|+..|-...-..+.
T Consensus 290 F~ilg~e~Y~rYQr~atEe~vlq~gGVlCP------~pgCG~gll~EPD~rkvtC~~gCgf~FCR~C~e~yh~geC~~~~ 363 (446)
T KOG0006|consen 290 FRILGEEQYNRYQRYATEECVLQMGGVLCP------RPGCGAGLLPEPDQRKVTCEGGCGFAFCRECKEAYHEGECSAVF 363 (446)
T ss_pred heecchhHHHHHHHhhhhhheeecCCEecC------CCCCCcccccCCCCCcccCCCCchhHhHHHHHhhhccccceeee
Confidence 456777777777777777665443211111 1122221111111111222 259999999999988643211111
Q ss_pred CCCCCCCCCCCccchhhHHHhhhhHHHHHHHHHHHHhcCCCCCcccccCCCCCCcccchhhhhccCCCcccccccCceeC
Q 008441 351 EPTCPHEGCKSKLEVESCRIFLTLKLFEIWNQRMKEALIPVTEKVYCPYPKCSALMSKSEIERDASSSSFVGRRLGARKC 430 (565)
Q Consensus 351 ~~kCP~~~C~~~l~~~~i~~lL~~e~~e~y~~~~~e~~i~~~~~~~CP~p~C~~~i~~~~~~e~~~s~~~~~~~~~~~~C 430 (565)
.- =-...|...++.... ...+|..... ..|+ ...+.|| +|..... .......+.|
T Consensus 364 ~a-s~t~tc~y~vde~~a-------~~arwd~as~-~TIk-~tTkpCP--kChvptE-------------rnGGCmHm~C 418 (446)
T KOG0006|consen 364 EA-SGTTTCAYRVDERAA-------EQARWDAASK-ETIK-KTTKPCP--KCHVPTE-------------RNGGCMHMKC 418 (446)
T ss_pred cc-ccccceeeecChhhh-------hhhhhhhhhh-hhhh-hccCCCC--CccCccc-------------cCCceEEeec
Confidence 00 001124433333221 1223333221 1121 2244566 8886542 2335567889
Q ss_pred CC--CCCceecccCCCcCC
Q 008441 431 TK--CHRRFCIDCKVPWHN 447 (565)
Q Consensus 431 ~~--C~~~fC~~C~~~~H~ 447 (565)
+. |+..+|+.|+..|..
T Consensus 419 t~~~Cg~eWCw~C~tEW~r 437 (446)
T KOG0006|consen 419 TQPQCGLEWCWNCGTEWNR 437 (446)
T ss_pred CCCCCCceeEeccCChhhh
Confidence 65 999999999999853
No 60
>KOG0824 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=92.49 E-value=0.074 Score=53.91 Aligned_cols=52 Identities=23% Similarity=0.683 Sum_probs=37.4
Q ss_pred ccccccceeccccccCCceeecCCCcccchhhHHHHHHHHHhCCCCCCCCCCCCCCccchhh
Q 008441 306 TINETCVICLEDTDVGHMFSIDGCLHRYCFLCMKKHIEEKLRQGMEPTCPHEGCKSKLEVES 367 (565)
Q Consensus 306 ~~~~~C~IC~e~~~~~~~~~l~~C~H~fC~~Cl~~~i~~~i~~g~~~kCP~~~C~~~l~~~~ 367 (565)
....+|.||+.+-. -++ .+.|+|.||.-|++.-+.. ++ ..|+. |..+|+...
T Consensus 5 ~~~~eC~IC~nt~n--~Pv-~l~C~HkFCyiCiKGsy~n----dk-~~Cav--CR~pids~i 56 (324)
T KOG0824|consen 5 TKKKECLICYNTGN--CPV-NLYCFHKFCYICIKGSYKN----DK-KTCAV--CRFPIDSTI 56 (324)
T ss_pred ccCCcceeeeccCC--cCc-cccccchhhhhhhcchhhc----CC-CCCce--ecCCCCcch
Confidence 35679999998843 333 4599999999999965532 22 25987 998887644
No 61
>KOG1812 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=92.33 E-value=0.041 Score=59.02 Aligned_cols=104 Identities=16% Similarity=0.399 Sum_probs=60.5
Q ss_pred ccccceeccccccC---Cc--eeecCCCcccchhhHHHHHHHHHhCCCCCCCCCCCCCCccchhhHHHhhhhHHHHHHHH
Q 008441 308 NETCVICLEDTDVG---HM--FSIDGCLHRYCFLCMKKHIEEKLRQGMEPTCPHEGCKSKLEVESCRIFLTLKLFEIWNQ 382 (565)
Q Consensus 308 ~~~C~IC~e~~~~~---~~--~~l~~C~H~fC~~Cl~~~i~~~i~~g~~~kCP~~~C~~~l~~~~i~~lL~~e~~e~y~~ 382 (565)
...|+.|+...... +. .....|+-.||..|-..|-.. ++-++++++.++........
T Consensus 238 ~~~C~~l~~~~el~~~~~~~~~~C~~C~~~fCv~C~~~wh~~------------------~sC~eykk~~~~~~~d~~~~ 299 (384)
T KOG1812|consen 238 YPRCSSLMSKTELSSEVKSKRRPCVKCHELFCVKCKVPWHAN------------------LSCEEYKKLNPEEYVDDITL 299 (384)
T ss_pred CCCchHhhhhhhhccchhhcccccccCCCceeecCCCcCCCC------------------CCHHHHHHhCCcccccHHHH
Confidence 34666666543321 11 223367777888886654321 22344555544332221111
Q ss_pred HHHHhcCCCCCcccccCCCCCCcccchhhhhccCCCcccccccCceeCCCCCCceecccCCCcCCCCC
Q 008441 383 RMKEALIPVTEKVYCPYPKCSALMSKSEIERDASSSSFVGRRLGARKCTKCHRRFCIDCKVPWHNNMT 450 (565)
Q Consensus 383 ~~~e~~i~~~~~~~CP~p~C~~~i~~~~~~e~~~s~~~~~~~~~~~~C~~C~~~fC~~C~~~~H~g~t 450 (565)
+.. . ...+.|| .|+..+. .....+.+.|. |++.||..|..+|+.+..
T Consensus 300 ~~l----a-~~wr~Cp--kC~~~ie-------------~~~GCnhm~Cr-C~~~fcy~C~~~~~~~~~ 346 (384)
T KOG1812|consen 300 KYL----A-KRWRQCP--KCKFMIE-------------LSEGCNHMTCR-CGHQFCYMCGGDWKTHNG 346 (384)
T ss_pred HHH----H-HhcCcCc--ccceeee-------------ecCCcceEEee-ccccchhhcCcchhhCCc
Confidence 111 1 3467898 9998773 23458899998 999999999999965443
No 62
>KOG0802 consensus E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=91.66 E-value=0.098 Score=58.84 Aligned_cols=47 Identities=32% Similarity=0.705 Sum_probs=35.2
Q ss_pred cccccceeccccccC--CceeecCCCcccchhhHHHHHHHHHhCCCCCCCCCCCCCC
Q 008441 307 INETCVICLEDTDVG--HMFSIDGCLHRYCFLCMKKHIEEKLRQGMEPTCPHEGCKS 361 (565)
Q Consensus 307 ~~~~C~IC~e~~~~~--~~~~l~~C~H~fC~~Cl~~~i~~~i~~g~~~kCP~~~C~~ 361 (565)
....|.||.+..... .....++|+|.||..|+++|++.+- .||. |+.
T Consensus 290 ~~~~C~IC~e~l~~~~~~~~~rL~C~Hifh~~CL~~W~er~q------tCP~--CR~ 338 (543)
T KOG0802|consen 290 SDELCIICLEELHSGHNITPKRLPCGHIFHDSCLRSWFERQQ------TCPT--CRT 338 (543)
T ss_pred cCCeeeeechhhccccccccceeecccchHHHHHHHHHHHhC------cCCc--chh
Confidence 367999999986432 1134569999999999999998732 6886 665
No 63
>KOG1428 consensus Inhibitor of type V adenylyl cyclases/Neuronal presynaptic protein Highwire/PAM/RPM-1 [Signal transduction mechanisms]
Probab=91.65 E-value=0.23 Score=59.27 Aligned_cols=68 Identities=19% Similarity=0.418 Sum_probs=51.1
Q ss_pred cccccccceeccccccCCceeecCCCcccchhhHHHHHHHHHhCCC----CCCCCCCCCCCccchhhHHHhhhh
Q 008441 305 KTINETCVICLEDTDVGHMFSIDGCLHRYCFLCMKKHIEEKLRQGM----EPTCPHEGCKSKLEVESCRIFLTL 374 (565)
Q Consensus 305 ~~~~~~C~IC~e~~~~~~~~~l~~C~H~fC~~Cl~~~i~~~i~~g~----~~kCP~~~C~~~l~~~~i~~lL~~ 374 (565)
+...-.|.|||.+....-+...+.|+|.|...|.+.-++.+-.... ++.||. |+++|.--.++.+|++
T Consensus 3483 QD~DDmCmICFTE~L~AAP~IqL~C~HiFHlqC~R~vLE~RW~GPRItF~FisCPi--C~n~InH~~LkDLldP 3554 (3738)
T KOG1428|consen 3483 QDADDMCMICFTEALSAAPAIQLDCSHIFHLQCCRRVLENRWLGPRITFGFISCPI--CKNKINHIVLKDLLDP 3554 (3738)
T ss_pred cccCceEEEEehhhhCCCcceecCCccchhHHHHHHHHHhcccCCeeEEeeeeccc--ccchhhhHHHHHHHHH
Confidence 3345679999987654445455699999999999988876543322 258997 9999998888888875
No 64
>KOG0311 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=91.56 E-value=0.027 Score=58.16 Aligned_cols=49 Identities=39% Similarity=0.929 Sum_probs=34.4
Q ss_pred ccccccceeccccccCCceeecCCCcccchhhHHHHHHHHHhCCCCCCCCCCCCCCcc
Q 008441 306 TINETCVICLEDTDVGHMFSIDGCLHRYCFLCMKKHIEEKLRQGMEPTCPHEGCKSKL 363 (565)
Q Consensus 306 ~~~~~C~IC~e~~~~~~~~~l~~C~H~fC~~Cl~~~i~~~i~~g~~~kCP~~~C~~~l 363 (565)
...+.|+||++-+. ...+...|.|+||.+|+-.-+.. +.- .||. |++.+
T Consensus 41 ~~~v~c~icl~llk--~tmttkeClhrfc~~ci~~a~r~----gn~-ecpt--cRk~l 89 (381)
T KOG0311|consen 41 DIQVICPICLSLLK--KTMTTKECLHRFCFDCIWKALRS----GNN-ECPT--CRKKL 89 (381)
T ss_pred hhhhccHHHHHHHH--hhcccHHHHHHHHHHHHHHHHHh----cCC-CCch--HHhhc
Confidence 35789999998754 33445689999999999776642 221 5885 77654
No 65
>KOG4185 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=91.42 E-value=0.37 Score=49.78 Aligned_cols=56 Identities=25% Similarity=0.520 Sum_probs=39.0
Q ss_pred ccccceeccccccC---CceeecCCCcccchhhHHHHHHHHHhCCCCCCCCCCCCCCc--cchhhHHH
Q 008441 308 NETCVICLEDTDVG---HMFSIDGCLHRYCFLCMKKHIEEKLRQGMEPTCPHEGCKSK--LEVESCRI 370 (565)
Q Consensus 308 ~~~C~IC~e~~~~~---~~~~l~~C~H~fC~~Cl~~~i~~~i~~g~~~kCP~~~C~~~--l~~~~i~~ 370 (565)
...|.||-+++... ....++.|||.+|..|+...+. ...+.||. |... +....++.
T Consensus 3 ~~~c~~c~~~~s~~~~~~~p~~l~c~h~~c~~c~~~l~~-----~~~i~cpf--cR~~~~~~~~~~~~ 63 (296)
T KOG4185|consen 3 FPECEICNEDYSSEDGDHIPRVLKCGHTICQNCASKLLG-----NSRILCPF--CRETTEIPDGDVKS 63 (296)
T ss_pred CCceeecCccccccCcccCCcccccCceehHhHHHHHhc-----CceeeccC--CCCcccCCchhHhh
Confidence 35899999987543 3445668999999999988763 33456776 8887 44444443
No 66
>KOG2660 consensus Locus-specific chromosome binding proteins [Function unknown]
Probab=91.10 E-value=0.079 Score=54.45 Aligned_cols=47 Identities=32% Similarity=0.668 Sum_probs=35.1
Q ss_pred cccccceeccccccCCceeecCCCcccchhhHHHHHHHHHhCCCCCCCCCCCCCCcc
Q 008441 307 INETCVICLEDTDVGHMFSIDGCLHRYCFLCMKKHIEEKLRQGMEPTCPHEGCKSKL 363 (565)
Q Consensus 307 ~~~~C~IC~e~~~~~~~~~l~~C~H~fC~~Cl~~~i~~~i~~g~~~kCP~~~C~~~l 363 (565)
...+|.+|-..+ -+..++..|-|.||+.||-.|++.. -.||. |+..+
T Consensus 14 ~~itC~LC~GYl--iDATTI~eCLHTFCkSCivk~l~~~------~~CP~--C~i~i 60 (331)
T KOG2660|consen 14 PHITCRLCGGYL--IDATTITECLHTFCKSCIVKYLEES------KYCPT--CDIVI 60 (331)
T ss_pred cceehhhcccee--ecchhHHHHHHHHHHHHHHHHHHHh------ccCCc--cceec
Confidence 367999998765 3444556899999999999999862 26886 66544
No 67
>KOG0828 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=91.06 E-value=0.12 Score=55.62 Aligned_cols=53 Identities=23% Similarity=0.626 Sum_probs=38.3
Q ss_pred cccccccceeccccccCC--------------ceeecCCCcccchhhHHHHHHHHHhCCCCCCCCCCCCCCccc
Q 008441 305 KTINETCVICLEDTDVGH--------------MFSIDGCLHRYCFLCMKKHIEEKLRQGMEPTCPHEGCKSKLE 364 (565)
Q Consensus 305 ~~~~~~C~IC~e~~~~~~--------------~~~l~~C~H~fC~~Cl~~~i~~~i~~g~~~kCP~~~C~~~l~ 364 (565)
......|.||+.+++... -+.+.+|.|.|...|+.+|+.. ..+.||. |+.+|+
T Consensus 568 ~~~t~dC~ICMt~I~l~~~~s~~~~~~~~~~~nYm~tPC~HifH~~CL~~WMd~-----ykl~CPv--CR~pLP 634 (636)
T KOG0828|consen 568 VRRTNDCVICMTPIDLRSTGSDCMVASMMVRRNYMLTPCHHIFHRQCLLQWMDT-----YKLICPV--CRCPLP 634 (636)
T ss_pred hhccccceEeccccceeeccCcchhhhhhhhccccccchHHHHHHHHHHHHHhh-----hcccCCc--cCCCCC
Confidence 345679999998875311 1224599999999999999962 2358997 877765
No 68
>PHA03096 p28-like protein; Provisional
Probab=90.49 E-value=0.14 Score=52.61 Aligned_cols=53 Identities=23% Similarity=0.518 Sum_probs=38.6
Q ss_pred cccceecccccc----CCce-eecCCCcccchhhHHHHHHHHHhCCCCCCCCCCCCCCcc
Q 008441 309 ETCVICLEDTDV----GHMF-SIDGCLHRYCFLCMKKHIEEKLRQGMEPTCPHEGCKSKL 363 (565)
Q Consensus 309 ~~C~IC~e~~~~----~~~~-~l~~C~H~fC~~Cl~~~i~~~i~~g~~~kCP~~~C~~~l 363 (565)
..|.||++.... ...| .+..|.|.||..|++.|...+......+.||. |...+
T Consensus 179 k~c~ic~e~~~~k~~~~~~fgil~~c~h~fc~~ci~~wr~~~~~~e~~~~c~~--~~~~~ 236 (284)
T PHA03096 179 KICGICLENIKAKYIIKKYYGILSEIKHEFNIFCIKIWMTESLYKETEPENRR--LNTVI 236 (284)
T ss_pred hhcccchhhhhhhccccccccccccCCcHHHHHHHHHHHHhhhhcccCccccc--hhhHH
Confidence 689999997542 2222 35689999999999999998875555566775 55443
No 69
>KOG4739 consensus Uncharacterized protein involved in synaptonemal complex formation [Cell cycle control, cell division, chromosome partitioning; General function prediction only]
Probab=89.83 E-value=0.093 Score=51.84 Aligned_cols=46 Identities=26% Similarity=0.692 Sum_probs=34.5
Q ss_pred cccceeccccccCCceeecCCCcccchhhHHHHHHHHHhCCCCCCCCCCCCCCccch
Q 008441 309 ETCVICLEDTDVGHMFSIDGCLHRYCFLCMKKHIEEKLRQGMEPTCPHEGCKSKLEV 365 (565)
Q Consensus 309 ~~C~IC~e~~~~~~~~~l~~C~H~fC~~Cl~~~i~~~i~~g~~~kCP~~~C~~~l~~ 365 (565)
..|..|+.--. ...|.+..|+|+||..|.+.-. ...||. |+..+-.
T Consensus 4 VhCn~C~~~~~-~~~f~LTaC~HvfC~~C~k~~~--------~~~C~l--Ckk~ir~ 49 (233)
T KOG4739|consen 4 VHCNKCFRFPS-QDPFFLTACRHVFCEPCLKASS--------PDVCPL--CKKSIRI 49 (233)
T ss_pred EEeccccccCC-CCceeeeechhhhhhhhcccCC--------cccccc--ccceeee
Confidence 46999987655 6677788999999999987422 127987 9987643
No 70
>KOG1815 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=89.50 E-value=0.14 Score=56.09 Aligned_cols=52 Identities=29% Similarity=0.660 Sum_probs=42.4
Q ss_pred ccccC--CCCceeEe-cCCcceEEeecCccccccccccccCCCCCcCCCCCCCCCccc
Q 008441 477 WRQCV--KCNHLIEL-AEGCFHMTCRCGHEFCYNCGAEWKNKKATCSCPLWDEDNILD 531 (565)
Q Consensus 477 ~k~CP--kC~~~IEK-~~GCnHMtC~Cg~~FCw~C~~~~~~~~~~c~C~~~~~~~~~~ 531 (565)
.|.|| .|+..+.. .+.+.-+.|.||+.|||.|+.+|+.. +.|+.+.......
T Consensus 158 lkwCP~~~C~~av~~~~~~~~~v~C~~g~~FC~~C~~~~H~p---~~C~~~~~wl~k~ 212 (444)
T KOG1815|consen 158 LKWCPAPGCGLAVKFGSLESVEVDCGCGHEFCFACGEESHSP---VSCPGAKKWLKKC 212 (444)
T ss_pred cccCCCCCCCceeeccCCCccceeCCCCchhHhhccccccCC---CcccchHHHHHhh
Confidence 57776 69999987 78899999999999999999998744 4788776665544
No 71
>PLN03086 PRLI-interacting factor K; Provisional
Probab=89.36 E-value=0.42 Score=53.43 Aligned_cols=56 Identities=23% Similarity=0.539 Sum_probs=34.7
Q ss_pred CCCCCCCCCCccchhhHHHhhhhHHHHHHHHHHHHhcCCCCCcccccCCCCCCcccchhhhhccCCCcccccccCceeCC
Q 008441 352 PTCPHEGCKSKLEVESCRIFLTLKLFEIWNQRMKEALIPVTEKVYCPYPKCSALMSKSEIERDASSSSFVGRRLGARKCT 431 (565)
Q Consensus 352 ~kCP~~~C~~~l~~~~i~~lL~~e~~e~y~~~~~e~~i~~~~~~~CP~p~C~~~i~~~~~~e~~~s~~~~~~~~~~~~C~ 431 (565)
+.||+ |+..++...+...+. + . ..+.+.||+.+|+..+.+.+. .....|+
T Consensus 408 V~C~N--C~~~i~l~~l~lHe~------~-------C--~r~~V~Cp~~~Cg~v~~r~el-------------~~H~~C~ 457 (567)
T PLN03086 408 VECRN--CKHYIPSRSIALHEA------Y-------C--SRHNVVCPHDGCGIVLRVEEA-------------KNHVHCE 457 (567)
T ss_pred EECCC--CCCccchhHHHHHHh------h-------C--CCcceeCCcccccceeecccc-------------ccCccCC
Confidence 47987 988887655443221 1 1 113567887789988854432 3345888
Q ss_pred CCCCce
Q 008441 432 KCHRRF 437 (565)
Q Consensus 432 ~C~~~f 437 (565)
.|+..|
T Consensus 458 ~Cgk~f 463 (567)
T PLN03086 458 KCGQAF 463 (567)
T ss_pred CCCCcc
Confidence 887765
No 72
>KOG1734 consensus Predicted RING-containing E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=89.01 E-value=0.23 Score=49.64 Aligned_cols=56 Identities=25% Similarity=0.680 Sum_probs=42.8
Q ss_pred ccccccceeccccccC--------CceeecCCCcccchhhHHHHHHHHHhCCCCCCCCCCCCCCccchhhH
Q 008441 306 TINETCVICLEDTDVG--------HMFSIDGCLHRYCFLCMKKHIEEKLRQGMEPTCPHEGCKSKLEVESC 368 (565)
Q Consensus 306 ~~~~~C~IC~e~~~~~--------~~~~l~~C~H~fC~~Cl~~~i~~~i~~g~~~kCP~~~C~~~l~~~~i 368 (565)
..+..|.||...+..+ +.+.+ +|+|.|.-.|++.|... |....||- |+..++....
T Consensus 222 l~d~vCaVCg~~~~~s~~eegvienty~L-sCnHvFHEfCIrGWciv----GKkqtCPY--CKekVdl~rm 285 (328)
T KOG1734|consen 222 LSDSVCAVCGQQIDVSVDEEGVIENTYKL-SCNHVFHEFCIRGWCIV----GKKQTCPY--CKEKVDLKRM 285 (328)
T ss_pred CCcchhHhhcchheeecchhhhhhhheee-ecccchHHHhhhhheee----cCCCCCch--HHHHhhHhhh
Confidence 3467899998876543 44555 99999999999999843 55678998 9988876543
No 73
>KOG0825 consensus PHD Zn-finger protein [General function prediction only]
Probab=88.89 E-value=0.19 Score=56.83 Aligned_cols=48 Identities=21% Similarity=0.389 Sum_probs=24.3
Q ss_pred ccccceeccccccCCceeecCCCcccchhhHHHHHHHHHhCCCCCCCCCCCCCCcc
Q 008441 308 NETCVICLEDTDVGHMFSIDGCLHRYCFLCMKKHIEEKLRQGMEPTCPHEGCKSKL 363 (565)
Q Consensus 308 ~~~C~IC~e~~~~~~~~~l~~C~H~fC~~Cl~~~i~~~i~~g~~~kCP~~~C~~~l 363 (565)
...|++|+..+.......-..|+|.||..|+..|-+.. -.||. |..++
T Consensus 123 ~~~CP~Ci~s~~DqL~~~~k~c~H~FC~~Ci~sWsR~a------qTCPi--DR~EF 170 (1134)
T KOG0825|consen 123 ENQCPNCLKSCNDQLEESEKHTAHYFCEECVGSWSRCA------QTCPV--DRGEF 170 (1134)
T ss_pred hhhhhHHHHHHHHHhhccccccccccHHHHhhhhhhhc------ccCch--hhhhh
Confidence 34566665544322222333566666666666665432 15665 55544
No 74
>KOG0297 consensus TNF receptor-associated factor [Signal transduction mechanisms]
Probab=88.32 E-value=0.37 Score=51.97 Aligned_cols=51 Identities=25% Similarity=0.619 Sum_probs=36.6
Q ss_pred cccccccceeccccccCCceeecCCCcccchhhHHHHHHHHHhCCCCCCCCCCCCCCccch
Q 008441 305 KTINETCVICLEDTDVGHMFSIDGCLHRYCFLCMKKHIEEKLRQGMEPTCPHEGCKSKLEV 365 (565)
Q Consensus 305 ~~~~~~C~IC~e~~~~~~~~~l~~C~H~fC~~Cl~~~i~~~i~~g~~~kCP~~~C~~~l~~ 365 (565)
...+..|++|.... .+++....|||.||..|+..+... .++||. |...+..
T Consensus 18 ~~~~l~C~~C~~vl--~~p~~~~~cgh~fC~~C~~~~~~~------~~~cp~--~~~~~~~ 68 (391)
T KOG0297|consen 18 LDENLLCPICMSVL--RDPVQTTTCGHRFCAGCLLESLSN------HQKCPV--CRQELTQ 68 (391)
T ss_pred CcccccCccccccc--cCCCCCCCCCCcccccccchhhcc------CcCCcc--cccccch
Confidence 34568999998664 444443489999999999998865 347886 6555443
No 75
>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=87.81 E-value=0.14 Score=50.24 Aligned_cols=51 Identities=25% Similarity=0.658 Sum_probs=35.9
Q ss_pred ccccceecccccc-CCc--eeecCCCcccchhhHHHHHHHHHhCCCCCCCCCCCCCCcc
Q 008441 308 NETCVICLEDTDV-GHM--FSIDGCLHRYCFLCMKKHIEEKLRQGMEPTCPHEGCKSKL 363 (565)
Q Consensus 308 ~~~C~IC~e~~~~-~~~--~~l~~C~H~fC~~Cl~~~i~~~i~~g~~~kCP~~~C~~~l 363 (565)
...||||..+.-. .++ ...+.|-|++|-+|+..-|. ..+-.||..+|+..|
T Consensus 10 d~~CPvCksDrYLnPdik~linPECyHrmCESCvdRIFs-----~GpAqCP~~gC~kIL 63 (314)
T COG5220 10 DRRCPVCKSDRYLNPDIKILINPECYHRMCESCVDRIFS-----RGPAQCPYKGCGKIL 63 (314)
T ss_pred cccCCccccccccCCCeEEEECHHHHHHHHHHHHHHHhc-----CCCCCCCCccHHHHH
Confidence 4589999887432 222 22335999999999988763 233489999999754
No 76
>PHA00626 hypothetical protein
Probab=87.04 E-value=0.44 Score=36.18 Aligned_cols=27 Identities=26% Similarity=0.492 Sum_probs=20.8
Q ss_pred ccCCCCc-eeEecCCcce----EEee-cCcccc
Q 008441 479 QCVKCNH-LIELAEGCFH----MTCR-CGHEFC 505 (565)
Q Consensus 479 ~CPkC~~-~IEK~~GCnH----MtC~-Cg~~FC 505 (565)
.||+|+. .|.|.+-|+. ..|. |||.|=
T Consensus 2 ~CP~CGS~~Ivrcg~cr~~snrYkCkdCGY~ft 34 (59)
T PHA00626 2 SCPKCGSGNIAKEKTMRGWSDDYVCCDCGYNDS 34 (59)
T ss_pred CCCCCCCceeeeeceecccCcceEcCCCCCeec
Confidence 5999999 5888887654 7784 888774
No 77
>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=86.98 E-value=0.57 Score=34.93 Aligned_cols=42 Identities=26% Similarity=0.532 Sum_probs=29.2
Q ss_pred ccceeccccccCCceeecCCC-----cccchhhHHHHHHHHHhCCCCCCCCC
Q 008441 310 TCVICLEDTDVGHMFSIDGCL-----HRYCFLCMKKHIEEKLRQGMEPTCPH 356 (565)
Q Consensus 310 ~C~IC~e~~~~~~~~~l~~C~-----H~fC~~Cl~~~i~~~i~~g~~~kCP~ 356 (565)
.|-||++.....+++. .+|. |.+...||.+|+..+-. .+||.
T Consensus 1 ~CrIC~~~~~~~~~l~-~PC~C~G~~~~vH~~Cl~~W~~~~~~----~~C~i 47 (49)
T smart00744 1 ICRICHDEGDEGDPLV-SPCRCKGSLKYVHQECLERWINESGN----KTCEI 47 (49)
T ss_pred CccCCCCCCCCCCeeE-eccccCCchhHHHHHHHHHHHHHcCC----CcCCC
Confidence 4889998433445553 4775 78999999999976432 26775
No 78
>PF10571 UPF0547: Uncharacterised protein family UPF0547; InterPro: IPR018886 This domain may well be a type of zinc-finger as it carries two pairs of highly conserved cysteine residues though with no accompanying histidines. Several members are annotated as putative helicases.
Probab=86.83 E-value=0.3 Score=31.46 Aligned_cols=23 Identities=26% Similarity=0.791 Sum_probs=15.3
Q ss_pred cccCCCCceeEecCCcceEEee-cCccc
Q 008441 478 RQCVKCNHLIELAEGCFHMTCR-CGHEF 504 (565)
Q Consensus 478 k~CPkC~~~IEK~~GCnHMtC~-Cg~~F 504 (565)
|.||.|+..|-.. -+.|. |||.|
T Consensus 1 K~CP~C~~~V~~~----~~~Cp~CG~~F 24 (26)
T PF10571_consen 1 KTCPECGAEVPES----AKFCPHCGYDF 24 (26)
T ss_pred CcCCCCcCCchhh----cCcCCCCCCCC
Confidence 5799999888543 23452 77766
No 79
>COG5175 MOT2 Transcriptional repressor [Transcription]
Probab=86.82 E-value=0.45 Score=48.96 Aligned_cols=54 Identities=31% Similarity=0.845 Sum_probs=37.9
Q ss_pred ccccceeccccccC--CceeecCCCcccchhhHHHHHHHHHhCCCCCCCCCCCCCCccchhhHH
Q 008441 308 NETCVICLEDTDVG--HMFSIDGCLHRYCFLCMKKHIEEKLRQGMEPTCPHEGCKSKLEVESCR 369 (565)
Q Consensus 308 ~~~C~IC~e~~~~~--~~~~l~~C~H~fC~~Cl~~~i~~~i~~g~~~kCP~~~C~~~l~~~~i~ 369 (565)
.-.|+.|.++++.. ++|.+ +||-++|+-||.. ++..+ +| +||. |+.....+.++
T Consensus 14 ed~cplcie~mditdknf~pc-~cgy~ic~fc~~~-irq~l-ng---rcpa--crr~y~denv~ 69 (480)
T COG5175 14 EDYCPLCIEPMDITDKNFFPC-PCGYQICQFCYNN-IRQNL-NG---RCPA--CRRKYDDENVR 69 (480)
T ss_pred cccCcccccccccccCCcccC-CcccHHHHHHHHH-HHhhc-cC---CChH--hhhhcccccee
Confidence 34599999987654 45555 8999999999974 33332 33 7998 98877665554
No 80
>KOG4265 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=86.67 E-value=0.55 Score=48.97 Aligned_cols=47 Identities=30% Similarity=0.701 Sum_probs=33.4
Q ss_pred cccccceeccccccCCceeecCCCcc-cchhhHHHHHHHHHhCCCCCCCCCCCCCCccc
Q 008441 307 INETCVICLEDTDVGHMFSIDGCLHR-YCFLCMKKHIEEKLRQGMEPTCPHEGCKSKLE 364 (565)
Q Consensus 307 ~~~~C~IC~e~~~~~~~~~l~~C~H~-fC~~Cl~~~i~~~i~~g~~~kCP~~~C~~~l~ 364 (565)
...+|.||+.+. .+ ..+++|+|. .|..|.+..- .... +||. |++.+.
T Consensus 289 ~gkeCVIClse~--rd-t~vLPCRHLCLCs~Ca~~Lr---~q~n---~CPI--CRqpi~ 336 (349)
T KOG4265|consen 289 SGKECVICLSES--RD-TVVLPCRHLCLCSGCAKSLR---YQTN---NCPI--CRQPIE 336 (349)
T ss_pred CCCeeEEEecCC--cc-eEEecchhhehhHhHHHHHH---Hhhc---CCCc--cccchH
Confidence 357999999873 33 445699998 9999988654 1112 6997 987753
No 81
>COG5152 Uncharacterized conserved protein, contains RING and CCCH-type Zn-fingers [General function prediction only]
Probab=86.40 E-value=0.33 Score=46.31 Aligned_cols=46 Identities=26% Similarity=0.602 Sum_probs=31.1
Q ss_pred ccccccceeccccccCCceeecCCCcccchhhHHHHHHHHHhCCCCCCCCCCCCCCc
Q 008441 306 TINETCVICLEDTDVGHMFSIDGCLHRYCFLCMKKHIEEKLRQGMEPTCPHEGCKSK 362 (565)
Q Consensus 306 ~~~~~C~IC~e~~~~~~~~~l~~C~H~fC~~Cl~~~i~~~i~~g~~~kCP~~~C~~~ 362 (565)
.-.+.|.||-.++. .++.. .|||.||..|...-++ . .+.|-. |+..
T Consensus 194 ~IPF~C~iCKkdy~--spvvt-~CGH~FC~~Cai~~y~----k--g~~C~~--Cgk~ 239 (259)
T COG5152 194 KIPFLCGICKKDYE--SPVVT-ECGHSFCSLCAIRKYQ----K--GDECGV--CGKA 239 (259)
T ss_pred CCceeehhchhhcc--chhhh-hcchhHHHHHHHHHhc----c--CCccee--cchh
Confidence 34689999998874 33333 8999999999765432 2 246765 6653
No 82
>PRK14559 putative protein serine/threonine phosphatase; Provisional
Probab=86.06 E-value=0.39 Score=54.82 Aligned_cols=13 Identities=46% Similarity=0.823 Sum_probs=9.7
Q ss_pred Ccccccccccccc
Q 008441 501 GHEFCYNCGAEWK 513 (565)
Q Consensus 501 g~~FCw~C~~~~~ 513 (565)
+..||-.||.+..
T Consensus 40 ~~~fC~~CG~~~~ 52 (645)
T PRK14559 40 DEAHCPNCGAETG 52 (645)
T ss_pred ccccccccCCccc
Confidence 3459999998854
No 83
>PF13719 zinc_ribbon_5: zinc-ribbon domain
Probab=85.84 E-value=0.61 Score=32.60 Aligned_cols=33 Identities=21% Similarity=0.515 Sum_probs=22.8
Q ss_pred ccccCCCCCCcccchhhhhccCCCcccccccCceeCCCCCCce
Q 008441 395 VYCPYPKCSALMSKSEIERDASSSSFVGRRLGARKCTKCHRRF 437 (565)
Q Consensus 395 ~~CP~p~C~~~i~~~~~~e~~~s~~~~~~~~~~~~C~~C~~~f 437 (565)
+.|| .|+..+..++- ........++|+.|+..|
T Consensus 3 i~CP--~C~~~f~v~~~--------~l~~~~~~vrC~~C~~~f 35 (37)
T PF13719_consen 3 ITCP--NCQTRFRVPDD--------KLPAGGRKVRCPKCGHVF 35 (37)
T ss_pred EECC--CCCceEEcCHH--------HcccCCcEEECCCCCcEe
Confidence 5687 89988765442 122456689999998865
No 84
>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=85.66 E-value=0.36 Score=43.66 Aligned_cols=36 Identities=19% Similarity=0.398 Sum_probs=27.8
Q ss_pred cccccceecccccc-CCceeecCCC------cccchhhHHHHHH
Q 008441 307 INETCVICLEDTDV-GHMFSIDGCL------HRYCFLCMKKHIE 343 (565)
Q Consensus 307 ~~~~C~IC~e~~~~-~~~~~l~~C~------H~fC~~Cl~~~i~ 343 (565)
...+|.||++.+.. ..++.+ .|+ |.||.+|+++|-.
T Consensus 25 ~~~EC~IC~~~I~~~~GvV~v-t~~g~lnLEkmfc~~C~~rw~~ 67 (134)
T PF05883_consen 25 CTVECQICFDRIDNNDGVVYV-TDGGTLNLEKMFCADCDKRWRR 67 (134)
T ss_pred cCeeehhhhhhhhcCCCEEEE-ecCCeehHHHHHHHHHHHHHHh
Confidence 36799999999876 344444 665 7899999999953
No 85
>KOG0804 consensus Cytoplasmic Zn-finger protein BRAP2 (BRCA1 associated protein) [General function prediction only]
Probab=85.59 E-value=0.46 Score=50.76 Aligned_cols=49 Identities=33% Similarity=0.695 Sum_probs=35.6
Q ss_pred cCcccccccceeccccccC--CceeecCCCcccchhhHHHHHHHHHhCCCCCCCCCCCCCCc
Q 008441 303 RGKTINETCVICLEDTDVG--HMFSIDGCLHRYCFLCMKKHIEEKLRQGMEPTCPHEGCKSK 362 (565)
Q Consensus 303 ~~~~~~~~C~IC~e~~~~~--~~~~l~~C~H~fC~~Cl~~~i~~~i~~g~~~kCP~~~C~~~ 362 (565)
.+.....+|+||++-.+.+ .+.+. .|.|.|.-.|+..|... .||. |+..
T Consensus 170 ~~~tELPTCpVCLERMD~s~~gi~t~-~c~Hsfh~~cl~~w~~~--------scpv--cR~~ 220 (493)
T KOG0804|consen 170 TGLTELPTCPVCLERMDSSTTGILTI-LCNHSFHCSCLMKWWDS--------SCPV--CRYC 220 (493)
T ss_pred CCcccCCCcchhHhhcCccccceeee-ecccccchHHHhhcccC--------cChh--hhhh
Confidence 3555678999999987543 23444 79999999999988732 6886 6543
No 86
>PRK05654 acetyl-CoA carboxylase subunit beta; Validated
Probab=85.57 E-value=0.18 Score=51.96 Aligned_cols=31 Identities=29% Similarity=0.846 Sum_probs=25.5
Q ss_pred cCCccccCCCCceeEecC-CcceEEe-ecCccc
Q 008441 474 SNLWRQCVKCNHLIELAE-GCFHMTC-RCGHEF 504 (565)
Q Consensus 474 ~~~~k~CPkC~~~IEK~~-GCnHMtC-~Cg~~F 504 (565)
+..|.+||+|+..|-+.+ .=|.+.| +|+|||
T Consensus 24 ~~~~~~c~~c~~~~~~~~l~~~~~vc~~c~~h~ 56 (292)
T PRK05654 24 EGLWTKCPSCGQVLYRKELEANLNVCPKCGHHM 56 (292)
T ss_pred CCCeeECCCccchhhHHHHHhcCCCCCCCCCCe
Confidence 346999999999988765 6677899 599987
No 87
>KOG0317 consensus Predicted E3 ubiquitin ligase, integral peroxisomal membrane protein [Posttranslational modification, protein turnover, chaperones]
Probab=85.57 E-value=0.19 Score=50.78 Aligned_cols=26 Identities=50% Similarity=1.218 Sum_probs=20.8
Q ss_pred EEe-ecCccccccccccccCCCCCcCCCC
Q 008441 496 MTC-RCGHEFCYNCGAEWKNKKATCSCPL 523 (565)
Q Consensus 496 MtC-~Cg~~FCw~C~~~~~~~~~~c~C~~ 523 (565)
-+| .|||-|||.|...|-..... ||+
T Consensus 252 pSaTpCGHiFCWsCI~~w~~ek~e--CPl 278 (293)
T KOG0317|consen 252 PSATPCGHIFCWSCILEWCSEKAE--CPL 278 (293)
T ss_pred CCcCcCcchHHHHHHHHHHccccC--CCc
Confidence 346 49999999999999977765 554
No 88
>smart00661 RPOL9 RNA polymerase subunit 9.
Probab=85.40 E-value=0.55 Score=35.07 Aligned_cols=27 Identities=33% Similarity=0.705 Sum_probs=20.6
Q ss_pred cccCCCCceeEecC--CcceEEee-cCccc
Q 008441 478 RQCVKCNHLIELAE--GCFHMTCR-CGHEF 504 (565)
Q Consensus 478 k~CPkC~~~IEK~~--GCnHMtC~-Cg~~F 504 (565)
+-||.|+.++...+ +-+++.|. ||+++
T Consensus 1 ~FCp~Cg~~l~~~~~~~~~~~vC~~Cg~~~ 30 (52)
T smart00661 1 KFCPKCGNMLIPKEGKEKRRFVCRKCGYEE 30 (52)
T ss_pred CCCCCCCCccccccCCCCCEEECCcCCCeE
Confidence 36999999987764 35689994 99763
No 89
>KOG4159 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=84.94 E-value=1.1 Score=48.01 Aligned_cols=48 Identities=23% Similarity=0.670 Sum_probs=35.6
Q ss_pred ccccccceeccccccCCceeecCCCcccchhhHHHHHHHHHhCCCCCCCCCCCCCCccc
Q 008441 306 TINETCVICLEDTDVGHMFSIDGCLHRYCFLCMKKHIEEKLRQGMEPTCPHEGCKSKLE 364 (565)
Q Consensus 306 ~~~~~C~IC~e~~~~~~~~~l~~C~H~fC~~Cl~~~i~~~i~~g~~~kCP~~~C~~~l~ 364 (565)
...+.|.||+..+ ..+++. +|||.||..|+.+-+. ....||. |+..+.
T Consensus 82 ~sef~c~vc~~~l--~~pv~t-pcghs~c~~Cl~r~ld------~~~~cp~--Cr~~l~ 129 (398)
T KOG4159|consen 82 RSEFECCVCSRAL--YPPVVT-PCGHSFCLECLDRSLD------QETECPL--CRDELV 129 (398)
T ss_pred cchhhhhhhHhhc--CCCccc-cccccccHHHHHHHhc------cCCCCcc--cccccc
Confidence 3579999998764 455655 9999999999777332 2347886 888776
No 90
>KOG2817 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=84.48 E-value=0.51 Score=49.84 Aligned_cols=58 Identities=16% Similarity=0.155 Sum_probs=43.5
Q ss_pred cccccceeccccccCCceeecCCCcccchhhHHHHHHHHHhCCC-CCCCCCCCCCCccchhhHHH
Q 008441 307 INETCVICLEDTDVGHMFSIDGCLHRYCFLCMKKHIEEKLRQGM-EPTCPHEGCKSKLEVESCRI 370 (565)
Q Consensus 307 ~~~~C~IC~e~~~~~~~~~l~~C~H~fC~~Cl~~~i~~~i~~g~-~~kCP~~~C~~~l~~~~i~~ 370 (565)
..+.|||=-+....+++...+.|||++|++=+.+..+ +|. .+|||. |.........++
T Consensus 333 SvF~CPVlKeqtsdeNPPm~L~CGHVISkdAlnrLS~----ng~~sfKCPY--CP~e~~~~~~kq 391 (394)
T KOG2817|consen 333 SVFICPVLKEQTSDENPPMMLICGHVISKDALNRLSK----NGSQSFKCPY--CPVEQLASDTKQ 391 (394)
T ss_pred ceeecccchhhccCCCCCeeeeccceecHHHHHHHhh----CCCeeeeCCC--CCcccCHHhccc
Confidence 4689999887776777777789999999998877653 232 379998 887776665544
No 91
>KOG4692 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=84.30 E-value=0.72 Score=47.76 Aligned_cols=49 Identities=27% Similarity=0.735 Sum_probs=33.7
Q ss_pred cccccccceeccccccCCceeecCCCcccchhhHHHHHHHHHhCCCCCCCCCCCCCCccc
Q 008441 305 KTINETCVICLEDTDVGHMFSIDGCLHRYCFLCMKKHIEEKLRQGMEPTCPHEGCKSKLE 364 (565)
Q Consensus 305 ~~~~~~C~IC~e~~~~~~~~~l~~C~H~fC~~Cl~~~i~~~i~~g~~~kCP~~~C~~~l~ 364 (565)
....-.|+||+-. +.+-+| .+|+|+-|..|+.+|+-+ .. .|-. |+..+.
T Consensus 419 ~sEd~lCpICyA~-pi~Avf--~PC~H~SC~~CI~qHlmN---~k---~CFf--CktTv~ 467 (489)
T KOG4692|consen 419 DSEDNLCPICYAG-PINAVF--APCSHRSCYGCITQHLMN---CK---RCFF--CKTTVI 467 (489)
T ss_pred CcccccCcceecc-cchhhc--cCCCCchHHHHHHHHHhc---CC---eeeE--ecceee
Confidence 3456789999964 333343 489999999999999843 11 4655 776554
No 92
>COG0777 AccD Acetyl-CoA carboxylase beta subunit [Lipid metabolism]
Probab=84.12 E-value=0.38 Score=48.52 Aligned_cols=32 Identities=28% Similarity=0.803 Sum_probs=27.5
Q ss_pred cCCccccCCCCceeEecC-CcceEEe-ecCcccc
Q 008441 474 SNLWRQCVKCNHLIELAE-GCFHMTC-RCGHEFC 505 (565)
Q Consensus 474 ~~~~k~CPkC~~~IEK~~-GCnHMtC-~Cg~~FC 505 (565)
...|.+||+|+.++-+.+ +=|.+.| +|+|||=
T Consensus 25 e~lw~KCp~c~~~~y~~eL~~n~~vcp~c~~h~r 58 (294)
T COG0777 25 EGLWTKCPSCGEMLYRKELESNLKVCPKCGHHMR 58 (294)
T ss_pred CCceeECCCccceeeHHHHHhhhhcccccCcccc
Confidence 567999999999999887 8888999 5999874
No 93
>KOG1785 consensus Tyrosine kinase negative regulator CBL [Defense mechanisms]
Probab=84.00 E-value=0.45 Score=49.98 Aligned_cols=44 Identities=34% Similarity=0.786 Sum_probs=31.8
Q ss_pred cccceeccccccCCceeecCCCcccchhhHHHHHHHHHhCCCCCCCCCCCC
Q 008441 309 ETCVICLEDTDVGHMFSIDGCLHRYCFLCMKKHIEEKLRQGMEPTCPHEGC 359 (565)
Q Consensus 309 ~~C~IC~e~~~~~~~~~l~~C~H~fC~~Cl~~~i~~~i~~g~~~kCP~~~C 359 (565)
..|.||-+. ++-+.+.+|||..|..|+..|-... +|. .||...|
T Consensus 370 eLCKICaen---dKdvkIEPCGHLlCt~CLa~WQ~sd--~gq--~CPFCRc 413 (563)
T KOG1785|consen 370 ELCKICAEN---DKDVKIEPCGHLLCTSCLAAWQDSD--EGQ--TCPFCRC 413 (563)
T ss_pred HHHHHhhcc---CCCcccccccchHHHHHHHhhcccC--CCC--CCCceee
Confidence 469999876 4456677999999999999886432 133 6988334
No 94
>KOG4445 consensus Uncharacterized conserved protein, contains RWD domain [Function unknown]
Probab=83.85 E-value=0.7 Score=46.94 Aligned_cols=40 Identities=30% Similarity=0.609 Sum_probs=32.9
Q ss_pred ccccccceeccccccCCceeecCCCcccchhhHHHHHHHH
Q 008441 306 TINETCVICLEDTDVGHMFSIDGCLHRYCFLCMKKHIEEK 345 (565)
Q Consensus 306 ~~~~~C~IC~e~~~~~~~~~l~~C~H~fC~~Cl~~~i~~~ 345 (565)
.....|.||+--|..+.-|+...|.|.|...||..|++.-
T Consensus 113 ~p~gqCvICLygfa~~~~ft~T~C~Hy~H~~ClaRyl~~~ 152 (368)
T KOG4445|consen 113 HPNGQCVICLYGFASSPAFTVTACDHYMHFACLARYLTEC 152 (368)
T ss_pred CCCCceEEEEEeecCCCceeeehhHHHHHHHHHHHHHHHH
Confidence 3467899998777767767778999999999999998653
No 95
>KOG1645 consensus RING-finger-containing E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=83.57 E-value=1.4 Score=46.76 Aligned_cols=51 Identities=29% Similarity=0.594 Sum_probs=36.0
Q ss_pred ccccceecccccc--CCceeecCCCcccchhhHHHHHHHHHhCCCCCCCCCCCCCCccc
Q 008441 308 NETCVICLEDTDV--GHMFSIDGCLHRYCFLCMKKHIEEKLRQGMEPTCPHEGCKSKLE 364 (565)
Q Consensus 308 ~~~C~IC~e~~~~--~~~~~l~~C~H~fC~~Cl~~~i~~~i~~g~~~kCP~~~C~~~l~ 364 (565)
..+|+||++.+.. +.....+.|+|-|=.+|++.|+- ++ ....||. |+.+-.
T Consensus 4 g~tcpiclds~~~~g~hr~vsl~cghlFgs~cie~wl~-k~---~~~~cp~--c~~kat 56 (463)
T KOG1645|consen 4 GTTCPICLDSYTTAGNHRIVSLQCGHLFGSQCIEKWLG-KK---TKMQCPL--CSGKAT 56 (463)
T ss_pred cccCceeeeeeeecCceEEeeecccccccHHHHHHHHh-hh---hhhhCcc--cCChhH
Confidence 3589999998643 22233458999999999999993 32 2347987 776543
No 96
>PF15227 zf-C3HC4_4: zinc finger of C3HC4-type, RING; PDB: 2EGP_A 2ECV_A 2ECJ_A 2YSL_A 2YSJ_A.
Probab=83.20 E-value=0.48 Score=34.07 Aligned_cols=38 Identities=32% Similarity=0.745 Sum_probs=21.9
Q ss_pred cCCCCceeEecCCcceEEeecCccccccccccccCCCCC--cCCC
Q 008441 480 CVKCNHLIELAEGCFHMTCRCGHEFCYNCGAEWKNKKAT--CSCP 522 (565)
Q Consensus 480 CPkC~~~IEK~~GCnHMtC~Cg~~FCw~C~~~~~~~~~~--c~C~ 522 (565)
||-|..... +-++=.|||.||..|...|...... ..||
T Consensus 1 CpiC~~~~~-----~Pv~l~CGH~FC~~Cl~~~~~~~~~~~~~CP 40 (42)
T PF15227_consen 1 CPICLDLFK-----DPVSLPCGHSFCRSCLERLWKEPSGSGFSCP 40 (42)
T ss_dssp ETTTTSB-S-----SEEE-SSSSEEEHHHHHHHHCCSSSST---S
T ss_pred CCccchhhC-----CccccCCcCHHHHHHHHHHHHccCCcCCCCc
Confidence 455554443 2355569999999999987655433 4666
No 97
>KOG0823 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=83.17 E-value=0.34 Score=47.55 Aligned_cols=20 Identities=35% Similarity=1.100 Sum_probs=17.7
Q ss_pred cCccccccccccccCCCCCc
Q 008441 500 CGHEFCYNCGAEWKNKKATC 519 (565)
Q Consensus 500 Cg~~FCw~C~~~~~~~~~~c 519 (565)
|||-|||-|+-+|......+
T Consensus 65 CGHLFCWpClyqWl~~~~~~ 84 (230)
T KOG0823|consen 65 CGHLFCWPCLYQWLQTRPNS 84 (230)
T ss_pred cccceehHHHHHHHhhcCCC
Confidence 99999999999999776664
No 98
>PF13717 zinc_ribbon_4: zinc-ribbon domain
Probab=83.01 E-value=0.94 Score=31.48 Aligned_cols=33 Identities=24% Similarity=0.589 Sum_probs=22.6
Q ss_pred ccccCCCCCCcccchhhhhccCCCcccccccCceeCCCCCCce
Q 008441 395 VYCPYPKCSALMSKSEIERDASSSSFVGRRLGARKCTKCHRRF 437 (565)
Q Consensus 395 ~~CP~p~C~~~i~~~~~~e~~~s~~~~~~~~~~~~C~~C~~~f 437 (565)
+.|| +|+..+..++- ........++|+.|+..|
T Consensus 3 i~Cp--~C~~~y~i~d~--------~ip~~g~~v~C~~C~~~f 35 (36)
T PF13717_consen 3 ITCP--NCQAKYEIDDE--------KIPPKGRKVRCSKCGHVF 35 (36)
T ss_pred EECC--CCCCEEeCCHH--------HCCCCCcEEECCCCCCEe
Confidence 5687 88887765442 233456689999998765
No 99
>PF14570 zf-RING_4: RING/Ubox like zinc-binding domain; PDB: 1E4U_A 1UR6_B.
Probab=82.80 E-value=0.92 Score=33.69 Aligned_cols=45 Identities=24% Similarity=0.699 Sum_probs=20.3
Q ss_pred cceeccccccC--CceeecCCCcccchhhHHHHHHHHHhCCCCCCCCCCCCCCcc
Q 008441 311 CVICLEDTDVG--HMFSIDGCLHRYCFLCMKKHIEEKLRQGMEPTCPHEGCKSKL 363 (565)
Q Consensus 311 C~IC~e~~~~~--~~~~l~~C~H~fC~~Cl~~~i~~~i~~g~~~kCP~~~C~~~l 363 (565)
|++|.++.+.. +++.. .|++.+|+.|+..-.+ ...-+||. |+...
T Consensus 1 cp~C~e~~d~~d~~~~PC-~Cgf~IC~~C~~~i~~-----~~~g~CPg--Cr~~Y 47 (48)
T PF14570_consen 1 CPLCDEELDETDKDFYPC-ECGFQICRFCYHDILE-----NEGGRCPG--CREPY 47 (48)
T ss_dssp -TTTS-B--CCCTT--SS-TTS----HHHHHHHTT-----SS-SB-TT--T--B-
T ss_pred CCCcccccccCCCccccC-cCCCcHHHHHHHHHHh-----ccCCCCCC--CCCCC
Confidence 78898887443 33333 7999999999987553 11237996 87653
No 100
>CHL00174 accD acetyl-CoA carboxylase beta subunit; Reviewed
Probab=82.78 E-value=0.28 Score=50.51 Aligned_cols=30 Identities=30% Similarity=0.603 Sum_probs=24.4
Q ss_pred CCccccCCCCceeEecC-CcceEEe-ecCccc
Q 008441 475 NLWRQCVKCNHLIELAE-GCFHMTC-RCGHEF 504 (565)
Q Consensus 475 ~~~k~CPkC~~~IEK~~-GCnHMtC-~Cg~~F 504 (565)
..|.+||+|+..+-+.. .=|.+.| +|+|||
T Consensus 36 ~lw~kc~~C~~~~~~~~l~~~~~vcp~c~~h~ 67 (296)
T CHL00174 36 HLWVQCENCYGLNYKKFLKSKMNICEQCGYHL 67 (296)
T ss_pred CCeeECCCccchhhHHHHHHcCCCCCCCCCCc
Confidence 35999999999998776 5677889 599866
No 101
>PF13240 zinc_ribbon_2: zinc-ribbon domain
Probab=82.72 E-value=0.56 Score=29.24 Aligned_cols=11 Identities=36% Similarity=0.628 Sum_probs=8.5
Q ss_pred ccCCCCceeEe
Q 008441 479 QCVKCNHLIEL 489 (565)
Q Consensus 479 ~CPkC~~~IEK 489 (565)
.||+|+..|+.
T Consensus 1 ~Cp~CG~~~~~ 11 (23)
T PF13240_consen 1 YCPNCGAEIED 11 (23)
T ss_pred CCcccCCCCCC
Confidence 48888888874
No 102
>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=82.47 E-value=0.22 Score=35.23 Aligned_cols=25 Identities=40% Similarity=1.186 Sum_probs=19.5
Q ss_pred ecCccccccccccccCCCCCcCCCC
Q 008441 499 RCGHEFCYNCGAEWKNKKATCSCPL 523 (565)
Q Consensus 499 ~Cg~~FCw~C~~~~~~~~~~c~C~~ 523 (565)
.|||.||+.|...|........||+
T Consensus 16 ~C~H~fC~~C~~~~~~~~~~~~CP~ 40 (41)
T PF00097_consen 16 PCGHSFCRDCLRKWLENSGSVKCPL 40 (41)
T ss_dssp TTSEEEEHHHHHHHHHHTSSSBTTT
T ss_pred cCCCcchHHHHHHHHHhcCCccCCc
Confidence 4999999999999887545556764
No 103
>KOG4172 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=82.40 E-value=0.42 Score=36.16 Aligned_cols=46 Identities=28% Similarity=0.799 Sum_probs=30.8
Q ss_pred ccccceeccccccCCceeecCCCcc-cchhhHHHHHHHHHhCCCCCCCCCCCCCCcc
Q 008441 308 NETCVICLEDTDVGHMFSIDGCLHR-YCFLCMKKHIEEKLRQGMEPTCPHEGCKSKL 363 (565)
Q Consensus 308 ~~~C~IC~e~~~~~~~~~l~~C~H~-fC~~Cl~~~i~~~i~~g~~~kCP~~~C~~~l 363 (565)
.-+|.||++.- .+.+ +-.|||. +|.+|-.+.++. ..| .||. |+.++
T Consensus 7 ~dECTICye~p-vdsV--lYtCGHMCmCy~Cg~rl~~~--~~g---~CPi--CRapi 53 (62)
T KOG4172|consen 7 SDECTICYEHP-VDSV--LYTCGHMCMCYACGLRLKKA--LHG---CCPI--CRAPI 53 (62)
T ss_pred ccceeeeccCc-chHH--HHHcchHHhHHHHHHHHHHc--cCC---cCcc--hhhHH
Confidence 36899999863 2222 2369998 899998776643 122 6886 76654
No 104
>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=82.00 E-value=0.32 Score=50.00 Aligned_cols=30 Identities=27% Similarity=0.792 Sum_probs=24.1
Q ss_pred CCccccCCCCceeEecC-CcceEEe-ecCccc
Q 008441 475 NLWRQCVKCNHLIELAE-GCFHMTC-RCGHEF 504 (565)
Q Consensus 475 ~~~k~CPkC~~~IEK~~-GCnHMtC-~Cg~~F 504 (565)
..|.+||+|+..|-+.+ .=|.+.| +|+|||
T Consensus 24 ~~~~~c~~c~~~~~~~~l~~~~~vc~~c~~h~ 55 (285)
T TIGR00515 24 GVWTKCPKCGQVLYTKELERNLEVCPKCDHHM 55 (285)
T ss_pred CCeeECCCCcchhhHHHHHhhCCCCCCCCCcC
Confidence 46999999999998764 4567888 599875
No 105
>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=81.85 E-value=0.49 Score=35.59 Aligned_cols=25 Identities=40% Similarity=0.980 Sum_probs=16.0
Q ss_pred cCceeCCCCCCceecccCCCcCCCC
Q 008441 425 LGARKCTKCHRRFCIDCKVPWHNNM 449 (565)
Q Consensus 425 ~~~~~C~~C~~~fC~~C~~~~H~g~ 449 (565)
.....|+.|+..||..|-.-.|..+
T Consensus 19 ~~~y~C~~C~~~FC~dCD~fiHE~L 43 (51)
T PF07975_consen 19 SSRYRCPKCKNHFCIDCDVFIHETL 43 (51)
T ss_dssp -EEE--TTTT--B-HHHHHTTTTTS
T ss_pred CCeEECCCCCCccccCcChhhhccc
Confidence 4679999999999999988778654
No 106
>PF05290 Baculo_IE-1: Baculovirus immediate-early protein (IE-0); InterPro: IPR007954 This entry contains the Baculovirus immediate-early protein IE-0.
Probab=81.82 E-value=1.3 Score=39.89 Aligned_cols=108 Identities=19% Similarity=0.267 Sum_probs=62.7
Q ss_pred hhhHHHHHHHHHHhhhccccc--cccccccchHHHHHHHHHhhhcc-----ccccc--ccccCcccccccceeccccccC
Q 008441 251 RKISVLVDQVSLLEKRFSYFK--PRHVARNDMKYVYELARAAINSQ-----MTVPA--EISRGKTINETCVICLEDTDVG 321 (565)
Q Consensus 251 ~~l~~l~~~v~~Ll~~F~~~~--~~~V~R~~n~~Ad~LA~eal~sq-----i~~~~--~~~~~~~~~~~C~IC~e~~~~~ 321 (565)
=.+-||+++++.++.-|..-. .+.|..... ..+.|-.+..... +.... -....+.+..+|.||.+.....
T Consensus 15 ~IflPYlKQL~~il~~f~nd~CC~k~v~~~~~-~l~~ll~~~~~~l~~I~~~n~r~qvmnvF~d~~lYeCnIC~etS~ee 93 (140)
T PF05290_consen 15 FIFLPYLKQLRIILKMFVNDYCCKKTVKSLQM-YLNELLSHSLKYLEKIKAINRRLQVMNVFLDPKLYECNICKETSAEE 93 (140)
T ss_pred EEehHHHHHHHHHHHHHhhhHhHHHHHHHHHH-HHHHHHHHHHHHHHHHHHHHHHHHHheeecCCCceeccCcccccchh
Confidence 467789999998888886531 123322221 1222222221100 00000 0112333688999999886544
Q ss_pred Ccee-ecCCCcccchhhHHHHHHHHHhCCCCCCCCCCCCCCccc
Q 008441 322 HMFS-IDGCLHRYCFLCMKKHIEEKLRQGMEPTCPHEGCKSKLE 364 (565)
Q Consensus 322 ~~~~-l~~C~H~fC~~Cl~~~i~~~i~~g~~~kCP~~~C~~~l~ 364 (565)
.+.. -..||=.+|.-|....|+.. ...|+||. |+..+.
T Consensus 94 ~FLKPneCCgY~iCn~Cya~LWK~~---~~ypvCPv--CkTSFK 132 (140)
T PF05290_consen 94 RFLKPNECCGYSICNACYANLWKFC---NLYPVCPV--CKTSFK 132 (140)
T ss_pred hcCCcccccchHHHHHHHHHHHHHc---ccCCCCCc--cccccc
Confidence 4432 24689999999999888754 35689998 887653
No 107
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=81.35 E-value=0.76 Score=29.47 Aligned_cols=23 Identities=39% Similarity=0.868 Sum_probs=16.2
Q ss_pred cccCCCCceeEecCCcceEEeecCcccccccccc
Q 008441 478 RQCVKCNHLIELAEGCFHMTCRCGHEFCYNCGAE 511 (565)
Q Consensus 478 k~CPkC~~~IEK~~GCnHMtC~Cg~~FCw~C~~~ 511 (565)
+.||+|+..|... ..||-.||.+
T Consensus 3 ~~Cp~Cg~~~~~~-----------~~fC~~CG~~ 25 (26)
T PF13248_consen 3 MFCPNCGAEIDPD-----------AKFCPNCGAK 25 (26)
T ss_pred CCCcccCCcCCcc-----------cccChhhCCC
Confidence 6799999976643 5677777654
No 108
>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=80.10 E-value=0.28 Score=35.37 Aligned_cols=41 Identities=34% Similarity=0.732 Sum_probs=26.9
Q ss_pred ccCCCCceeEecCCcceEEeecCccccccccccccCCCCCcCCCC
Q 008441 479 QCVKCNHLIELAEGCFHMTCRCGHEFCYNCGAEWKNKKATCSCPL 523 (565)
Q Consensus 479 ~CPkC~~~IEK~~GCnHMtC~Cg~~FCw~C~~~~~~~~~~c~C~~ 523 (565)
.||-|...++. +=.-+...|||.||+.|...|-..+. .||+
T Consensus 2 ~C~IC~~~~~~--~~~~~~l~C~H~fh~~Ci~~~~~~~~--~CP~ 42 (44)
T PF13639_consen 2 ECPICLEEFED--GEKVVKLPCGHVFHRSCIKEWLKRNN--SCPV 42 (44)
T ss_dssp CETTTTCBHHT--TSCEEEETTSEEEEHHHHHHHHHHSS--B-TT
T ss_pred CCcCCChhhcC--CCeEEEccCCCeeCHHHHHHHHHhCC--cCCc
Confidence 36666666654 22223446999999999999987654 5653
No 109
>KOG0826 consensus Predicted E3 ubiquitin ligase involved in peroxisome organization [Posttranslational modification, protein turnover, chaperones]
Probab=79.29 E-value=1.5 Score=45.18 Aligned_cols=50 Identities=20% Similarity=0.503 Sum_probs=35.2
Q ss_pred cccccccceeccccccCCceeecCCCcccchhhHHHHHHHHHhCCCCCCCCCCCCCCc
Q 008441 305 KTINETCVICLEDTDVGHMFSIDGCLHRYCFLCMKKHIEEKLRQGMEPTCPHEGCKSK 362 (565)
Q Consensus 305 ~~~~~~C~IC~e~~~~~~~~~l~~C~H~fC~~Cl~~~i~~~i~~g~~~kCP~~~C~~~ 362 (565)
......|+||+...... ..+..=|-.||..|+.+|+.. .+ +||..+|...
T Consensus 297 ~~~~~~CpvClk~r~Np--tvl~vSGyVfCY~Ci~~Yv~~---~~---~CPVT~~p~~ 346 (357)
T KOG0826|consen 297 PPDREVCPVCLKKRQNP--TVLEVSGYVFCYPCIFSYVVN---YG---HCPVTGYPAS 346 (357)
T ss_pred CCccccChhHHhccCCC--ceEEecceEEeHHHHHHHHHh---cC---CCCccCCcch
Confidence 33567899999775433 333345889999999999962 23 7998777543
No 110
>KOG2807 consensus RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit SSL1 [Transcription; Replication, recombination and repair]
Probab=79.07 E-value=0.73 Score=47.36 Aligned_cols=26 Identities=35% Similarity=0.934 Sum_probs=21.8
Q ss_pred ccCceeCCCCCCceecccCCCcCCCC
Q 008441 424 RLGARKCTKCHRRFCIDCKVPWHNNM 449 (565)
Q Consensus 424 ~~~~~~C~~C~~~fC~~C~~~~H~g~ 449 (565)
.....+|..|+..||..|..-.|...
T Consensus 342 ~~~~y~C~~Ck~~FCldCDv~iHesL 367 (378)
T KOG2807|consen 342 SSGRYRCESCKNVFCLDCDVFIHESL 367 (378)
T ss_pred CCCcEEchhccceeeccchHHHHhhh
Confidence 56779999999999999988777543
No 111
>PRK14559 putative protein serine/threonine phosphatase; Provisional
Probab=78.70 E-value=1.6 Score=50.00 Aligned_cols=12 Identities=17% Similarity=0.465 Sum_probs=8.7
Q ss_pred cccCCCCceeEe
Q 008441 478 RQCVKCNHLIEL 489 (565)
Q Consensus 478 k~CPkC~~~IEK 489 (565)
+.||+|+....+
T Consensus 42 ~fC~~CG~~~~~ 53 (645)
T PRK14559 42 AHCPNCGAETGT 53 (645)
T ss_pred ccccccCCcccc
Confidence 778888877653
No 112
>KOG0827 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=78.54 E-value=1.2 Score=46.79 Aligned_cols=48 Identities=25% Similarity=0.616 Sum_probs=33.3
Q ss_pred ccccceeccccccCC-ceeecCCCcccchhhHHHHHHHHHhCCCCCCCCCCCCC
Q 008441 308 NETCVICLEDTDVGH-MFSIDGCLHRYCFLCMKKHIEEKLRQGMEPTCPHEGCK 360 (565)
Q Consensus 308 ~~~C~IC~e~~~~~~-~~~l~~C~H~fC~~Cl~~~i~~~i~~g~~~kCP~~~C~ 360 (565)
.-.|.||-+-++... +-.+..|||.|...|+.+||+..-.+. .||. |+
T Consensus 4 ~A~C~Ic~d~~p~~~~l~~i~~cGhifh~~cl~qwfe~~Ps~R---~cpi--c~ 52 (465)
T KOG0827|consen 4 MAECHICIDGRPNDHELGPIGTCGHIFHTTCLTQWFEGDPSNR---GCPI--CQ 52 (465)
T ss_pred cceeeEeccCCccccccccccchhhHHHHHHHHHHHccCCccC---CCCc--ee
Confidence 458999966665543 334445999999999999997543332 4765 55
No 113
>KOG1952 consensus Transcription factor NF-X1, contains NFX-type Zn2+-binding and R3H domains [Transcription]
Probab=78.34 E-value=1.8 Score=49.83 Aligned_cols=52 Identities=27% Similarity=0.649 Sum_probs=40.0
Q ss_pred cccccceeccccccC-CceeecCCCcccchhhHHHHHHHHHhCCCC-CCCCCCCCC
Q 008441 307 INETCVICLEDTDVG-HMFSIDGCLHRYCFLCMKKHIEEKLRQGME-PTCPHEGCK 360 (565)
Q Consensus 307 ~~~~C~IC~e~~~~~-~~~~l~~C~H~fC~~Cl~~~i~~~i~~g~~-~kCP~~~C~ 360 (565)
..++|.||++.+... .+++...|-|+|...|++.|....-.++.. -+||. |.
T Consensus 190 ~~yeCmIC~e~I~~t~~~WSC~sCYhVFHl~CI~~WArs~ek~~~~~WrCP~--Cq 243 (950)
T KOG1952|consen 190 RKYECMICTERIKRTAPVWSCKSCYHVFHLNCIKKWARSSEKTGQDGWRCPA--CQ 243 (950)
T ss_pred CceEEEEeeeeccccCCceecchhhhhhhHHHHHHHHHHhhhccCccccCCc--cc
Confidence 368999999997654 466777899999999999999884444332 38886 66
No 114
>PLN03208 E3 ubiquitin-protein ligase RMA2; Provisional
Probab=78.30 E-value=0.52 Score=45.40 Aligned_cols=32 Identities=28% Similarity=0.733 Sum_probs=24.1
Q ss_pred ccccCCCCceeEecCCcceEEeecCcccccccccccc
Q 008441 477 WRQCVKCNHLIELAEGCFHMTCRCGHEFCYNCGAEWK 513 (565)
Q Consensus 477 ~k~CPkC~~~IEK~~GCnHMtC~Cg~~FCw~C~~~~~ 513 (565)
.-.||-|.-.+..- +.-.|||.|||.|...|.
T Consensus 18 ~~~CpICld~~~dP-----VvT~CGH~FC~~CI~~wl 49 (193)
T PLN03208 18 DFDCNICLDQVRDP-----VVTLCGHLFCWPCIHKWT 49 (193)
T ss_pred ccCCccCCCcCCCc-----EEcCCCchhHHHHHHHHH
Confidence 36899998766321 333699999999999884
No 115
>PF12773 DZR: Double zinc ribbon
Probab=77.65 E-value=1.8 Score=32.06 Aligned_cols=12 Identities=17% Similarity=0.390 Sum_probs=9.0
Q ss_pred cccCCCCceeEe
Q 008441 478 RQCVKCNHLIEL 489 (565)
Q Consensus 478 k~CPkC~~~IEK 489 (565)
+.||+|+..+..
T Consensus 30 ~~C~~Cg~~~~~ 41 (50)
T PF12773_consen 30 KICPNCGAENPP 41 (50)
T ss_pred CCCcCCcCCCcC
Confidence 678888887664
No 116
>PRK00432 30S ribosomal protein S27ae; Validated
Probab=77.61 E-value=1.4 Score=33.07 Aligned_cols=26 Identities=19% Similarity=0.544 Sum_probs=19.0
Q ss_pred cccCCCCc-eeEecCCcceEEe-ecCcccc
Q 008441 478 RQCVKCNH-LIELAEGCFHMTC-RCGHEFC 505 (565)
Q Consensus 478 k~CPkC~~-~IEK~~GCnHMtC-~Cg~~FC 505 (565)
+.||+|+. ...... +.++| +||+.+.
T Consensus 21 ~fCP~Cg~~~m~~~~--~r~~C~~Cgyt~~ 48 (50)
T PRK00432 21 KFCPRCGSGFMAEHL--DRWHCGKCGYTEF 48 (50)
T ss_pred CcCcCCCcchheccC--CcEECCCcCCEEe
Confidence 68999998 333333 78999 5998763
No 117
>PF04641 Rtf2: Rtf2 RING-finger
Probab=77.21 E-value=2.6 Score=42.81 Aligned_cols=72 Identities=14% Similarity=0.195 Sum_probs=48.8
Q ss_pred Ccccccccceecccccc-CCceeecCCCcccchhhHHHHHHHHHhCCCCCCCCCCCCCCccchhhHHHhhh-hHHHHHHH
Q 008441 304 GKTINETCVICLEDTDV-GHMFSIDGCLHRYCFLCMKKHIEEKLRQGMEPTCPHEGCKSKLEVESCRIFLT-LKLFEIWN 381 (565)
Q Consensus 304 ~~~~~~~C~IC~e~~~~-~~~~~l~~C~H~fC~~Cl~~~i~~~i~~g~~~kCP~~~C~~~l~~~~i~~lL~-~e~~e~y~ 381 (565)
.....+.|||...++.. ..++.+-+|||+|+..++++.- .. -.||. |+.++...+|-.+-+ .+.++.+.
T Consensus 109 ~~~~~~~CPvt~~~~~~~~~fv~l~~cG~V~s~~alke~k-----~~--~~Cp~--c~~~f~~~DiI~Lnp~~ee~~~l~ 179 (260)
T PF04641_consen 109 NSEGRFICPVTGKEFNGKHKFVYLRPCGCVFSEKALKELK-----KS--KKCPV--CGKPFTEEDIIPLNPPEEELEKLR 179 (260)
T ss_pred cCCceeECCCCCcccCCceeEEEEcCCCCEeeHHHHHhhc-----cc--ccccc--cCCccccCCEEEecCCccHHHHHH
Confidence 34567899999988744 3566777999999999999861 11 25997 999988766544433 23344444
Q ss_pred HHH
Q 008441 382 QRM 384 (565)
Q Consensus 382 ~~~ 384 (565)
.++
T Consensus 180 ~~~ 182 (260)
T PF04641_consen 180 ERM 182 (260)
T ss_pred HHH
Confidence 333
No 118
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=76.84 E-value=2.2 Score=31.15 Aligned_cols=29 Identities=28% Similarity=0.691 Sum_probs=21.8
Q ss_pred cccCCCCceeEecCCcceEEe-ecCccccc
Q 008441 478 RQCVKCNHLIELAEGCFHMTC-RCGHEFCY 506 (565)
Q Consensus 478 k~CPkC~~~IEK~~GCnHMtC-~Cg~~FCw 506 (565)
-.||+|+..++...+=..++| .||..+=|
T Consensus 4 y~C~~CG~~~~~~~~~~~~~Cp~CG~~~~~ 33 (46)
T PRK00398 4 YKCARCGREVELDEYGTGVRCPYCGYRILF 33 (46)
T ss_pred EECCCCCCEEEECCCCCceECCCCCCeEEE
Confidence 479999999988765447888 48876654
No 119
>KOG3039 consensus Uncharacterized conserved protein [Function unknown]
Probab=76.81 E-value=1.5 Score=43.44 Aligned_cols=54 Identities=15% Similarity=0.130 Sum_probs=39.2
Q ss_pred cccccceeccccccC-CceeecCCCcccchhhHHHHHHHHHhCCCCCCCCCCCCCCccchhhH
Q 008441 307 INETCVICLEDTDVG-HMFSIDGCLHRYCFLCMKKHIEEKLRQGMEPTCPHEGCKSKLEVESC 368 (565)
Q Consensus 307 ~~~~C~IC~e~~~~~-~~~~l~~C~H~fC~~Cl~~~i~~~i~~g~~~kCP~~~C~~~l~~~~i 368 (565)
..+.|+||-+..... ....+.+|||.||.+|....+..- + .||. |+.++...+|
T Consensus 220 ~ryiCpvtrd~LtNt~~ca~Lr~sg~Vv~~ecvEklir~D----~--v~pv--~d~plkdrdi 274 (303)
T KOG3039|consen 220 KRYICPVTRDTLTNTTPCAVLRPSGHVVTKECVEKLIRKD----M--VDPV--TDKPLKDRDI 274 (303)
T ss_pred cceecccchhhhcCccceEEeccCCcEeeHHHHHHhcccc----c--cccC--CCCcCcccce
Confidence 478999999886543 334567999999999999988532 2 5776 7777665443
No 120
>KOG1001 consensus Helicase-like transcription factor HLTF/DNA helicase RAD5, DEAD-box superfamily [Transcription; Replication, recombination and repair]
Probab=76.78 E-value=0.81 Score=52.58 Aligned_cols=49 Identities=31% Similarity=0.798 Sum_probs=35.2
Q ss_pred cccceeccccccCCceeecCCCcccchhhHHHHHHHHHhCCCCCCCCCCCCCCccchhh
Q 008441 309 ETCVICLEDTDVGHMFSIDGCLHRYCFLCMKKHIEEKLRQGMEPTCPHEGCKSKLEVES 367 (565)
Q Consensus 309 ~~C~IC~e~~~~~~~~~l~~C~H~fC~~Cl~~~i~~~i~~g~~~kCP~~~C~~~l~~~~ 367 (565)
..|.||.+ ...++.. .|+|.||.+|+..+++..-.. +||. |...+....
T Consensus 455 ~~c~ic~~---~~~~~it-~c~h~~c~~c~~~~i~~~~~~----~~~~--cr~~l~~~~ 503 (674)
T KOG1001|consen 455 HWCHICCD---LDSFFIT-RCGHDFCVECLKKSIQQSENA----PCPL--CRNVLKEKK 503 (674)
T ss_pred cccccccc---cccceee-cccchHHHHHHHhccccccCC----CCcH--HHHHHHHHH
Confidence 79999998 3445544 899999999999988543211 6775 776665443
No 121
>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=76.74 E-value=1.6 Score=29.11 Aligned_cols=26 Identities=31% Similarity=0.905 Sum_probs=13.2
Q ss_pred cccCCCCceeEecCCcceEEe-ecCccc
Q 008441 478 RQCVKCNHLIELAEGCFHMTC-RCGHEF 504 (565)
Q Consensus 478 k~CPkC~~~IEK~~GCnHMtC-~Cg~~F 504 (565)
-+||+|+....-.+|.. |.| .|+++|
T Consensus 3 p~Cp~C~se~~y~D~~~-~vCp~C~~ew 29 (30)
T PF08274_consen 3 PKCPLCGSEYTYEDGEL-LVCPECGHEW 29 (30)
T ss_dssp ---TTT-----EE-SSS-EEETTTTEEE
T ss_pred CCCCCCCCcceeccCCE-EeCCcccccC
Confidence 37999999888877765 778 488875
No 122
>KOG1813 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=75.59 E-value=1.1 Score=45.47 Aligned_cols=47 Identities=21% Similarity=0.486 Sum_probs=33.4
Q ss_pred cccccceeccccccCCceeecCCCcccchhhHHHHHHHHHhCCCCCCCCCCCCCCccc
Q 008441 307 INETCVICLEDTDVGHMFSIDGCLHRYCFLCMKKHIEEKLRQGMEPTCPHEGCKSKLE 364 (565)
Q Consensus 307 ~~~~C~IC~e~~~~~~~~~l~~C~H~fC~~Cl~~~i~~~i~~g~~~kCP~~~C~~~l~ 364 (565)
..+-|.||-.++. .++.. .|+|.||..|....++. ..+|+. |...+.
T Consensus 240 ~Pf~c~icr~~f~--~pVvt-~c~h~fc~~ca~~~~qk------~~~c~v--C~~~t~ 286 (313)
T KOG1813|consen 240 LPFKCFICRKYFY--RPVVT-KCGHYFCEVCALKPYQK------GEKCYV--CSQQTH 286 (313)
T ss_pred CCccccccccccc--cchhh-cCCceeehhhhcccccc------CCccee--cccccc
Confidence 3578999998873 44433 89999999998776632 247876 776543
No 123
>COG5151 SSL1 RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit SSL1 [Transcription / DNA replication, recombination, and repair]
Probab=75.43 E-value=1.2 Score=45.55 Aligned_cols=96 Identities=22% Similarity=0.436 Sum_probs=54.4
Q ss_pred CcccchhhHHHHHHHHHhCCCCCCCCCCCCCCccchhhHHHhhhhHHHHHHHHHHHHhc---CC---CCCcccccCCCCC
Q 008441 330 LHRYCFLCMKKHIEEKLRQGMEPTCPHEGCKSKLEVESCRIFLTLKLFEIWNQRMKEAL---IP---VTEKVYCPYPKCS 403 (565)
Q Consensus 330 ~H~fC~~Cl~~~i~~~i~~g~~~kCP~~~C~~~l~~~~i~~lL~~e~~e~y~~~~~e~~---i~---~~~~~~CP~p~C~ 403 (565)
|-.+|..|-..-. ..++.||. |.. .-+|+..+...|...+--.. ++ +.....|- .|+
T Consensus 307 gGy~CP~CktkVC------sLPi~CP~--Csl-------~LilsthLarSyhhL~PLk~f~E~p~~~~~ks~~Cf--~CQ 369 (421)
T COG5151 307 GGYECPVCKTKVC------SLPISCPI--CSL-------QLILSTHLARSYHHLYPLKPFVEKPEGTNPKSTHCF--VCQ 369 (421)
T ss_pred CceeCCcccceee------cCCccCcc--hhH-------HHHHHHHHHHHHHhhccCcccccccCCCCCCCccce--ecc
Confidence 3456776644322 12346875 643 33455555555654331111 11 11223565 788
Q ss_pred CcccchhhhhccCCCcccccccCceeCCCCCCceecccCCCcCC
Q 008441 404 ALMSKSEIERDASSSSFVGRRLGARKCTKCHRRFCIDCKVPWHN 447 (565)
Q Consensus 404 ~~i~~~~~~e~~~s~~~~~~~~~~~~C~~C~~~fC~~C~~~~H~ 447 (565)
..+++..... +.......+..|+.|+..||..|.+-.|.
T Consensus 370 ~~fp~~~~~~-----~~~~~ss~rY~Ce~CK~~FC~dCdvfiHe 408 (421)
T COG5151 370 GPFPKPPVSP-----FDESTSSGRYQCELCKSTFCSDCDVFIHE 408 (421)
T ss_pred CCCCCCCCCc-----ccccccccceechhhhhhhhhhhHHHHHH
Confidence 8777655422 23334567899999999999999887664
No 124
>PHA02929 N1R/p28-like protein; Provisional
Probab=74.79 E-value=1.7 Score=43.41 Aligned_cols=42 Identities=31% Similarity=0.682 Sum_probs=31.6
Q ss_pred cccCCCCceeEecCCcc---eEEeecCccccccccccccCCCCCc
Q 008441 478 RQCVKCNHLIELAEGCF---HMTCRCGHEFCYNCGAEWKNKKATC 519 (565)
Q Consensus 478 k~CPkC~~~IEK~~GCn---HMtC~Cg~~FCw~C~~~~~~~~~~c 519 (565)
..||-|.-.+.....-+ -+.-.|+|.||..|...|...+.+|
T Consensus 175 ~eC~ICle~~~~~~~~~~~~~vl~~C~H~FC~~CI~~Wl~~~~tC 219 (238)
T PHA02929 175 KECAICMEKVYDKEIKNMYFGILSNCNHVFCIECIDIWKKEKNTC 219 (238)
T ss_pred CCCccCCcccccCccccccceecCCCCCcccHHHHHHHHhcCCCC
Confidence 68999999876554322 2344699999999999998876654
No 125
>PRK14714 DNA polymerase II large subunit; Provisional
Probab=73.20 E-value=2.9 Score=50.54 Aligned_cols=10 Identities=20% Similarity=0.793 Sum_probs=6.3
Q ss_pred cccCCCCcee
Q 008441 478 RQCVKCNHLI 487 (565)
Q Consensus 478 k~CPkC~~~I 487 (565)
..||+|+.+.
T Consensus 710 ~~CP~CGtpl 719 (1337)
T PRK14714 710 VECPRCDVEL 719 (1337)
T ss_pred ccCCCCCCcc
Confidence 4677777554
No 126
>PRK04023 DNA polymerase II large subunit; Validated
Probab=72.00 E-value=3.1 Score=49.07 Aligned_cols=20 Identities=25% Similarity=0.630 Sum_probs=13.3
Q ss_pred ceeCCCCCC-----ceecccCCCcC
Q 008441 427 ARKCTKCHR-----RFCIDCKVPWH 446 (565)
Q Consensus 427 ~~~C~~C~~-----~fC~~C~~~~H 446 (565)
.+.|+.||. .||..|+...+
T Consensus 638 ~frCP~CG~~Te~i~fCP~CG~~~~ 662 (1121)
T PRK04023 638 YRRCPFCGTHTEPVYRCPRCGIEVE 662 (1121)
T ss_pred cccCCCCCCCCCcceeCccccCcCC
Confidence 467888874 47777766543
No 127
>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=71.90 E-value=3.2 Score=28.85 Aligned_cols=33 Identities=24% Similarity=0.656 Sum_probs=20.2
Q ss_pred ccccCCCCCCcccchhhhhccCCCcccccccCceeCCCCCCce
Q 008441 395 VYCPYPKCSALMSKSEIERDASSSSFVGRRLGARKCTKCHRRF 437 (565)
Q Consensus 395 ~~CP~p~C~~~i~~~~~~e~~~s~~~~~~~~~~~~C~~C~~~f 437 (565)
+.|| .|+..+..++- ........++|+.|+..|
T Consensus 3 ~~CP--~C~~~~~v~~~--------~~~~~~~~v~C~~C~~~~ 35 (38)
T TIGR02098 3 IQCP--NCKTSFRVVDS--------QLGANGGKVRCGKCGHVW 35 (38)
T ss_pred EECC--CCCCEEEeCHH--------HcCCCCCEEECCCCCCEE
Confidence 4577 88887654331 111233478999998765
No 128
>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=71.18 E-value=0.84 Score=32.00 Aligned_cols=22 Identities=41% Similarity=1.140 Sum_probs=17.1
Q ss_pred ecCccccccccccccCCCCCcCCC
Q 008441 499 RCGHEFCYNCGAEWKNKKATCSCP 522 (565)
Q Consensus 499 ~Cg~~FCw~C~~~~~~~~~~c~C~ 522 (565)
.|||.||+.|...|...+. .||
T Consensus 16 ~CGH~fC~~C~~~~~~~~~--~CP 37 (39)
T PF13923_consen 16 PCGHSFCKECIEKYLEKNP--KCP 37 (39)
T ss_dssp TTSEEEEHHHHHHHHHCTS--B-T
T ss_pred CCCCchhHHHHHHHHHCcC--CCc
Confidence 6999999999999876642 555
No 129
>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]
Probab=70.47 E-value=3.1 Score=48.22 Aligned_cols=34 Identities=29% Similarity=0.857 Sum_probs=30.0
Q ss_pred cccCCCCceeEecCCcceEEee-cCcc-----cccccccc
Q 008441 478 RQCVKCNHLIELAEGCFHMTCR-CGHE-----FCYNCGAE 511 (565)
Q Consensus 478 k~CPkC~~~IEK~~GCnHMtC~-Cg~~-----FCw~C~~~ 511 (565)
-+||+|..+..--..=+.|.|+ ||++ .|..||..
T Consensus 445 ~~Cp~Cd~~lt~H~~~~~L~CH~Cg~~~~~p~~Cp~Cgs~ 484 (730)
T COG1198 445 AECPNCDSPLTLHKATGQLRCHYCGYQEPIPQSCPECGSE 484 (730)
T ss_pred ccCCCCCcceEEecCCCeeEeCCCCCCCCCCCCCCCCCCC
Confidence 4799999998877766999995 9988 99999998
No 130
>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=69.93 E-value=2 Score=36.86 Aligned_cols=31 Identities=23% Similarity=0.560 Sum_probs=25.6
Q ss_pred ccccceeccccccCCceeecCCCcccchhhHH
Q 008441 308 NETCVICLEDTDVGHMFSIDGCLHRYCFLCMK 339 (565)
Q Consensus 308 ~~~C~IC~e~~~~~~~~~l~~C~H~fC~~Cl~ 339 (565)
...|.+|...+.. ..|.+.+|||.|+..|++
T Consensus 78 ~~~C~vC~k~l~~-~~f~~~p~~~v~H~~C~~ 108 (109)
T PF10367_consen 78 STKCSVCGKPLGN-SVFVVFPCGHVVHYSCIK 108 (109)
T ss_pred CCCccCcCCcCCC-ceEEEeCCCeEEeccccc
Confidence 4579999998865 566677999999999975
No 131
>PF14952 zf-tcix: Putative treble-clef, zinc-finger, Zn-binding
Probab=69.20 E-value=2.3 Score=30.78 Aligned_cols=25 Identities=32% Similarity=0.772 Sum_probs=19.0
Q ss_pred CccccCCCCceeEecCCcceEEee---cCccc
Q 008441 476 LWRQCVKCNHLIELAEGCFHMTCR---CGHEF 504 (565)
Q Consensus 476 ~~k~CPkC~~~IEK~~GCnHMtC~---Cg~~F 504 (565)
++|+||+|++.- |+--+.|+ |++.|
T Consensus 10 GirkCp~CGt~N----G~R~~~CKN~~C~~~~ 37 (44)
T PF14952_consen 10 GIRKCPKCGTYN----GTRGLSCKNKSCPQVF 37 (44)
T ss_pred ccccCCcCcCcc----CcccccccCCccchhh
Confidence 469999999875 77778883 77655
No 132
>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=67.97 E-value=7.3 Score=39.71 Aligned_cols=50 Identities=28% Similarity=0.609 Sum_probs=33.4
Q ss_pred ccceeccccc--cCCceeecCCCcccchhhHHHHHHHHHhCCCCCCCCCCCCCCccchh
Q 008441 310 TCVICLEDTD--VGHMFSIDGCLHRYCFLCMKKHIEEKLRQGMEPTCPHEGCKSKLEVE 366 (565)
Q Consensus 310 ~C~IC~e~~~--~~~~~~l~~C~H~fC~~Cl~~~i~~~i~~g~~~kCP~~~C~~~l~~~ 366 (565)
.|++|-.+.- ..-.+.+..|+|..|.+|+-.-|.. | .-.|| .|...+-..
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 5889976642 2222334589999999999887632 2 22799 599876544
No 133
>PRK08665 ribonucleotide-diphosphate reductase subunit alpha; Validated
Probab=67.48 E-value=2.8 Score=49.01 Aligned_cols=26 Identities=38% Similarity=1.113 Sum_probs=22.9
Q ss_pred cccCCCCceeEecCCcceEEee-cCcccc
Q 008441 478 RQCVKCNHLIELAEGCFHMTCR-CGHEFC 505 (565)
Q Consensus 478 k~CPkC~~~IEK~~GCnHMtC~-Cg~~FC 505 (565)
..||.|+..+...+||. +|+ |||.=|
T Consensus 725 ~~Cp~Cg~~l~~~~GC~--~C~~CG~skC 751 (752)
T PRK08665 725 GACPECGSILEHEEGCV--VCHSCGYSKC 751 (752)
T ss_pred CCCCCCCcccEECCCCC--cCCCCCCCCC
Confidence 36999999999999998 895 999766
No 134
>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=67.36 E-value=5.6 Score=26.66 Aligned_cols=26 Identities=38% Similarity=0.852 Sum_probs=17.1
Q ss_pred cccCCCCceeEecCCcceEEe-ecCcc
Q 008441 478 RQCVKCNHLIELAEGCFHMTC-RCGHE 503 (565)
Q Consensus 478 k~CPkC~~~IEK~~GCnHMtC-~Cg~~ 503 (565)
+-||+|+.+.+...+=-.|.| .||++
T Consensus 4 rfC~~CG~~t~~~~~g~~r~C~~Cg~~ 30 (32)
T PF09297_consen 4 RFCGRCGAPTKPAPGGWARRCPSCGHE 30 (32)
T ss_dssp SB-TTT--BEEE-SSSS-EEESSSS-E
T ss_pred cccCcCCccccCCCCcCEeECCCCcCE
Confidence 789999999999988788999 48875
No 135
>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional
Probab=67.30 E-value=5.5 Score=30.86 Aligned_cols=21 Identities=19% Similarity=0.572 Sum_probs=15.1
Q ss_pred ccCceeCCCCCCce---ecccCCC
Q 008441 424 RLGARKCTKCHRRF---CIDCKVP 444 (565)
Q Consensus 424 ~~~~~~C~~C~~~f---C~~C~~~ 444 (565)
....+.||.||... |.+|++.
T Consensus 22 ~~~~F~CPnCG~~~I~RC~~CRk~ 45 (59)
T PRK14890 22 KAVKFLCPNCGEVIIYRCEKCRKQ 45 (59)
T ss_pred ccCEeeCCCCCCeeEeechhHHhc
Confidence 46789999999873 5566553
No 136
>KOG2906 consensus RNA polymerase III subunit C11 [Transcription]
Probab=67.16 E-value=3.8 Score=34.89 Aligned_cols=29 Identities=31% Similarity=0.805 Sum_probs=21.6
Q ss_pred ccCCCCcee--EecCCcceEEee-cCcccccc
Q 008441 479 QCVKCNHLI--ELAEGCFHMTCR-CGHEFCYN 507 (565)
Q Consensus 479 ~CPkC~~~I--EK~~GCnHMtC~-Cg~~FCw~ 507 (565)
-||.|+.++ +..+-||...|+ |+|.|=-.
T Consensus 3 FCP~Cgn~Live~g~~~~rf~C~tCpY~~~I~ 34 (105)
T KOG2906|consen 3 FCPTCGNMLIVESGESCNRFSCRTCPYVFPIS 34 (105)
T ss_pred ccCCCCCEEEEecCCeEeeEEcCCCCceeeEe
Confidence 599999864 444569999996 99876443
No 137
>COG5432 RAD18 RING-finger-containing E3 ubiquitin ligase [Signal transduction mechanisms]
Probab=66.52 E-value=1.9 Score=43.64 Aligned_cols=39 Identities=31% Similarity=0.811 Sum_probs=28.4
Q ss_pred cccCCCCceeEecCCcceEEe--ecCccccccccccccCCCCCc-CCCC
Q 008441 478 RQCVKCNHLIELAEGCFHMTC--RCGHEFCYNCGAEWKNKKATC-SCPL 523 (565)
Q Consensus 478 k~CPkC~~~IEK~~GCnHMtC--~Cg~~FCw~C~~~~~~~~~~c-~C~~ 523 (565)
-+|--|.-.|- +-| .|||.||++|-+.+.+.+..| -|..
T Consensus 26 lrC~IC~~~i~-------ip~~TtCgHtFCslCIR~hL~~qp~CP~Cr~ 67 (391)
T COG5432 26 LRCRICDCRIS-------IPCETTCGHTFCSLCIRRHLGTQPFCPVCRE 67 (391)
T ss_pred HHhhhhhheee-------cceecccccchhHHHHHHHhcCCCCCccccc
Confidence 46776665553 567 499999999999988777765 4443
No 138
>COG5219 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=65.41 E-value=2.1 Score=49.72 Aligned_cols=52 Identities=25% Similarity=0.577 Sum_probs=36.3
Q ss_pred cccccceeccccc-cCC--c-eeecCCCcccchhhHHHHHHHHHhCCCCCCCCCCCCCCccc
Q 008441 307 INETCVICLEDTD-VGH--M-FSIDGCLHRYCFLCMKKHIEEKLRQGMEPTCPHEGCKSKLE 364 (565)
Q Consensus 307 ~~~~C~IC~e~~~-~~~--~-~~l~~C~H~fC~~Cl~~~i~~~i~~g~~~kCP~~~C~~~l~ 364 (565)
.-.+|.|||.-.. ++. + -.+..|.|.|...|+-+|+...- .-+||- |+.+++
T Consensus 1468 G~eECaICYsvL~~vdr~lPskrC~TCknKFH~~CLyKWf~Ss~----~s~CPl--CRseit 1523 (1525)
T COG5219 1468 GHEECAICYSVLDMVDRSLPSKRCATCKNKFHTRCLYKWFASSA----RSNCPL--CRSEIT 1523 (1525)
T ss_pred CcchhhHHHHHHHHHhccCCccccchhhhhhhHHHHHHHHHhcC----CCCCCc--cccccc
Confidence 4579999997543 111 1 11346999999999999997643 237997 987765
No 139
>PF04216 FdhE: Protein involved in formate dehydrogenase formation; InterPro: IPR006452 This family of sequences describe an accessory protein required for the assembly of formate dehydrogenase of certain proteobacteria although not present in the final complex []. The exact nature of the function of FdhE in the assembly of the complex is unknown, but considering the presence of selenocysteine, molybdopterin, iron-sulphur clusters and cytochrome b556, it is likely to be involved in the insertion of cofactors. ; GO: 0005737 cytoplasm; PDB: 2FIY_B.
Probab=65.09 E-value=3.3 Score=42.71 Aligned_cols=13 Identities=23% Similarity=0.595 Sum_probs=6.0
Q ss_pred CceecccCCCcCC
Q 008441 435 RRFCIDCKVPWHN 447 (565)
Q Consensus 435 ~~fC~~C~~~~H~ 447 (565)
+.+|..|...||.
T Consensus 197 ~L~Cs~C~t~W~~ 209 (290)
T PF04216_consen 197 YLHCSLCGTEWRF 209 (290)
T ss_dssp EEEETTT--EEE-
T ss_pred EEEcCCCCCeeee
Confidence 3456666666764
No 140
>PF10157 DUF2365: Uncharacterized conserved protein (DUF2365); InterPro: IPR019314 This entry is found in a highly conserved family of proteins which have no known function.
Probab=64.98 E-value=39 Score=31.38 Aligned_cols=34 Identities=15% Similarity=0.305 Sum_probs=20.7
Q ss_pred cccHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHhhh
Q 008441 85 SLQSEELMKLDRELADSRQAKLEMQKAREDLQRAIHD 121 (565)
Q Consensus 85 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 121 (565)
.|-.+-|..|| ++++..-.-...+-..|+-.++.
T Consensus 48 ~id~~~L~~LE---~~a~~ia~svd~ll~~L~~~L~~ 81 (149)
T PF10157_consen 48 PIDPAVLHDLE---RDAQAIAESVDSLLRSLRSSLHS 81 (149)
T ss_pred cccHHHHHHHH---HHHHHHHHHHHHHHHHHHHHHHH
Confidence 46677889999 45555444455555555555543
No 141
>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=64.69 E-value=3.2 Score=36.43 Aligned_cols=27 Identities=30% Similarity=0.652 Sum_probs=18.0
Q ss_pred cccCCCCceeEecCCcceEEe-ecCcccc
Q 008441 478 RQCVKCNHLIELAEGCFHMTC-RCGHEFC 505 (565)
Q Consensus 478 k~CPkC~~~IEK~~GCnHMtC-~Cg~~FC 505 (565)
|.||+|+..+---.- +-++| +||+.|=
T Consensus 10 R~Cp~CG~kFYDLnk-~PivCP~CG~~~~ 37 (108)
T PF09538_consen 10 RTCPSCGAKFYDLNK-DPIVCPKCGTEFP 37 (108)
T ss_pred ccCCCCcchhccCCC-CCccCCCCCCccC
Confidence 679999886543222 67888 5777653
No 142
>KOG3268 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=63.67 E-value=6.8 Score=36.98 Aligned_cols=60 Identities=15% Similarity=0.323 Sum_probs=40.6
Q ss_pred Ccccccccceeccccc----cCCceeecCCCcccchhhHHHHHHHHHhCCCC----C-CCCCCCCCCccch
Q 008441 304 GKTINETCVICLEDTD----VGHMFSIDGCLHRYCFLCMKKHIEEKLRQGME----P-TCPHEGCKSKLEV 365 (565)
Q Consensus 304 ~~~~~~~C~IC~e~~~----~~~~~~l~~C~H~fC~~Cl~~~i~~~i~~g~~----~-kCP~~~C~~~l~~ 365 (565)
+......|+|||.... .+...-...|+..|..-|+..|++.-+..... + .||. |..++.+
T Consensus 161 kdd~~~~cgicyayqldGTipDqtCdN~qCgkpFHqiCL~dWLRgilTsRQSFdiiFGeCPY--CS~Pial 229 (234)
T KOG3268|consen 161 KDDELGACGICYAYQLDGTIPDQTCDNIQCGKPFHQICLTDWLRGILTSRQSFDIIFGECPY--CSDPIAL 229 (234)
T ss_pred cchhhhcccceeeeecCCccccccccccccCCcHHHHHHHHHHHHHhhccceeeeeeccCCC--CCCccee
Confidence 3445678999986421 12222234799999999999999887655433 2 7997 8887764
No 143
>PF14447 Prok-RING_4: Prokaryotic RING finger family 4
Probab=63.58 E-value=3.3 Score=31.57 Aligned_cols=46 Identities=24% Similarity=0.495 Sum_probs=30.2
Q ss_pred ccccceeccccccCCceeecCCCcccchhhHHHHHHHHHhCCCCCCCCCCCCCCccchh
Q 008441 308 NETCVICLEDTDVGHMFSIDGCLHRYCFLCMKKHIEEKLRQGMEPTCPHEGCKSKLEVE 366 (565)
Q Consensus 308 ~~~C~IC~e~~~~~~~~~l~~C~H~fC~~Cl~~~i~~~i~~g~~~kCP~~~C~~~l~~~ 366 (565)
...|..|.... ..-.+++|+|.+|..||-.. ..-.||. |+..+...
T Consensus 7 ~~~~~~~~~~~---~~~~~~pCgH~I~~~~f~~~--------rYngCPf--C~~~~~~~ 52 (55)
T PF14447_consen 7 EQPCVFCGFVG---TKGTVLPCGHLICDNCFPGE--------RYNGCPF--CGTPFEFD 52 (55)
T ss_pred ceeEEEccccc---cccccccccceeeccccChh--------hccCCCC--CCCcccCC
Confidence 45677776432 22345699999999998531 1126998 98887654
No 144
>KOG3183 consensus Predicted Zn-finger protein [General function prediction only]
Probab=63.47 E-value=0.99 Score=44.52 Aligned_cols=109 Identities=22% Similarity=0.437 Sum_probs=57.4
Q ss_pred CceeecCCCcccchhhHHHHHHH---HH--hCCCCCCCCCCCCCCccchh---hHHHhhhhHHHHHHHHHHHHhcCCCCC
Q 008441 322 HMFSIDGCLHRYCFLCMKKHIEE---KL--RQGMEPTCPHEGCKSKLEVE---SCRIFLTLKLFEIWNQRMKEALIPVTE 393 (565)
Q Consensus 322 ~~~~l~~C~H~fC~~Cl~~~i~~---~i--~~g~~~kCP~~~C~~~l~~~---~i~~lL~~e~~e~y~~~~~e~~i~~~~ 393 (565)
.+|....|.+.||.+=.. |-.. .. .+..++.||. |...++.. .+...+.+. +...-++.....-....
T Consensus 22 LPf~Cd~C~~~FC~eHrs-ye~H~Cp~~~~~~~~v~icp~--cs~pv~~~~de~~~~~v~~h-~~~dC~~~~~~~~~k~~ 97 (250)
T KOG3183|consen 22 LPFKCDGCSGIFCLEHRS-YESHHCPKGLRIDVQVPICPL--CSKPVPTKKDEAPDKVVEPH-ISNDCDRHPEQKKRKVF 97 (250)
T ss_pred cceeeCCccchhhhccch-HhhcCCCcccccceeecccCC--CCCCCCCCCCcchhhhhchh-hccccccCchhhhcccc
Confidence 467788999999875221 1100 00 1123468986 88776643 122223222 11111110000001112
Q ss_pred cccccCCCCCCcccchhhhhccCCCcccccccCceeCCCCCCceecccCCCcCCCCChh
Q 008441 394 KVYCPYPKCSALMSKSEIERDASSSSFVGRRLGARKCTKCHRRFCIDCKVPWHNNMTCI 452 (565)
Q Consensus 394 ~~~CP~p~C~~~i~~~~~~e~~~s~~~~~~~~~~~~C~~C~~~fC~~C~~~~H~g~tC~ 452 (565)
...||.|.|..... -.+.+.|..|+..||.+-+.+. +++|.
T Consensus 98 t~kc~~~~c~k~~~----------------~~~~~~c~~c~~~~c~khr~~~--dhsc~ 138 (250)
T KOG3183|consen 98 TNKCPVPRCKKTLT----------------LANKITCSKCGRNFCLKHRHPL--DHSCN 138 (250)
T ss_pred cccCCchhhHHHHH----------------HHHhhhhHhhcchhhhhccCCC--Cchhh
Confidence 34688888875432 3456899999999999877653 34565
No 145
>TIGR00622 ssl1 transcription factor ssl1. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=63.29 E-value=4.4 Score=35.68 Aligned_cols=26 Identities=31% Similarity=0.754 Sum_probs=21.6
Q ss_pred ccCceeCCCCCCceecccCCCcCCCC
Q 008441 424 RLGARKCTKCHRRFCIDCKVPWHNNM 449 (565)
Q Consensus 424 ~~~~~~C~~C~~~fC~~C~~~~H~g~ 449 (565)
......|+.|+..||..|..-+|..+
T Consensus 78 ~~~~y~C~~C~~~FC~dCD~fiHe~L 103 (112)
T TIGR00622 78 DSHRYVCAVCKNVFCVDCDVFVHESL 103 (112)
T ss_pred cccceeCCCCCCccccccchhhhhhc
Confidence 34578899999999999999888643
No 146
>COG1998 RPS31 Ribosomal protein S27AE [Translation, ribosomal structure and biogenesis]
Probab=63.25 E-value=4.3 Score=30.18 Aligned_cols=26 Identities=27% Similarity=0.635 Sum_probs=17.6
Q ss_pred cccCCCCceeEecCCcceEEe-ecCcc
Q 008441 478 RQCVKCNHLIELAEGCFHMTC-RCGHE 503 (565)
Q Consensus 478 k~CPkC~~~IEK~~GCnHMtC-~Cg~~ 503 (565)
+.||+|+--+....-=+...| +||+.
T Consensus 20 ~~CPrCG~gvfmA~H~dR~~CGkCgyT 46 (51)
T COG1998 20 RFCPRCGPGVFMADHKDRWACGKCGYT 46 (51)
T ss_pred ccCCCCCCcchhhhcCceeEeccccce
Confidence 789999965544433346778 68863
No 147
>COG5222 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=63.20 E-value=7.6 Score=39.56 Aligned_cols=45 Identities=20% Similarity=0.563 Sum_probs=32.3
Q ss_pred ccccceeccccccCCceeecCCCcccchhhHHHHHHHHHhCCCCCCCCCCCCCC
Q 008441 308 NETCVICLEDTDVGHMFSIDGCLHRYCFLCMKKHIEEKLRQGMEPTCPHEGCKS 361 (565)
Q Consensus 308 ~~~C~IC~e~~~~~~~~~l~~C~H~fC~~Cl~~~i~~~i~~g~~~kCP~~~C~~ 361 (565)
...|+.|-.- ..++.....|+|.||.+|+..-+- + .-++||. |..
T Consensus 274 ~LkCplc~~L--lrnp~kT~cC~~~fc~eci~~al~----d-sDf~Cpn--C~r 318 (427)
T COG5222 274 SLKCPLCHCL--LRNPMKTPCCGHTFCDECIGTALL----D-SDFKCPN--CSR 318 (427)
T ss_pred cccCcchhhh--hhCcccCccccchHHHHHHhhhhh----h-ccccCCC--ccc
Confidence 4789999754 345555668999999999986552 2 2258997 765
No 148
>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=62.55 E-value=17 Score=34.01 Aligned_cols=36 Identities=25% Similarity=0.621 Sum_probs=22.6
Q ss_pred ccccceeccccccCCceee------cCCCcccc------hhhHHHHHHHH
Q 008441 308 NETCVICLEDTDVGHMFSI------DGCLHRYC------FLCMKKHIEEK 345 (565)
Q Consensus 308 ~~~C~IC~e~~~~~~~~~l------~~C~H~fC------~~Cl~~~i~~~ 345 (565)
..+|+||++-- -+-+-+ .+|.-.+| .+||.+|-+..
T Consensus 2 d~~CpICme~P--HNAVLLlCSS~~kgcRpymc~Ts~rhSNCLdqfkka~ 49 (162)
T PF07800_consen 2 DVTCPICMEHP--HNAVLLLCSSHEKGCRPYMCDTSYRHSNCLDQFKKAY 49 (162)
T ss_pred CccCceeccCC--CceEEEEeccccCCccccccCCccchhHHHHHHHHHh
Confidence 46899999852 232222 14555566 57999887653
No 149
>PF12861 zf-Apc11: Anaphase-promoting complex subunit 11 RING-H2 finger
Probab=62.17 E-value=4.1 Score=34.05 Aligned_cols=44 Identities=23% Similarity=0.697 Sum_probs=34.4
Q ss_pred cccCCCCceeEecCCcceEEeecCccccccccccccCCCC-CcCCCCC
Q 008441 478 RQCVKCNHLIELAEGCFHMTCRCGHEFCYNCGAEWKNKKA-TCSCPLW 524 (565)
Q Consensus 478 k~CPkC~~~IEK~~GCnHMtC~Cg~~FCw~C~~~~~~~~~-~c~C~~~ 524 (565)
..||.|+.+ ...|--+.+.|+|.|=..|...|..... .=.||+-
T Consensus 33 g~Cp~Ck~P---gd~Cplv~g~C~H~FH~hCI~kWl~~~~~~~~CPmC 77 (85)
T PF12861_consen 33 GCCPDCKFP---GDDCPLVWGKCSHNFHMHCILKWLSTQSSKGQCPMC 77 (85)
T ss_pred cCCCCccCC---CCCCceeeccCccHHHHHHHHHHHccccCCCCCCCc
Confidence 368999887 4578888889999999999999987542 2367753
No 150
>KOG3002 consensus Zn finger protein [General function prediction only]
Probab=62.06 E-value=6.9 Score=40.59 Aligned_cols=47 Identities=21% Similarity=0.458 Sum_probs=32.6
Q ss_pred cccccccceeccccccCCceeecCCCcccchhhHHHHHHHHHhCCCCCCCCCCCCCCccc
Q 008441 305 KTINETCVICLEDTDVGHMFSIDGCLHRYCFLCMKKHIEEKLRQGMEPTCPHEGCKSKLE 364 (565)
Q Consensus 305 ~~~~~~C~IC~e~~~~~~~~~l~~C~H~fC~~Cl~~~i~~~i~~g~~~kCP~~~C~~~l~ 364 (565)
...-++||||++.+.... ++. .=||..|..|-.. + .-+||. |...+.
T Consensus 45 ~~~lleCPvC~~~l~~Pi-~QC-~nGHlaCssC~~~-----~----~~~CP~--Cr~~~g 91 (299)
T KOG3002|consen 45 DLDLLDCPVCFNPLSPPI-FQC-DNGHLACSSCRTK-----V----SNKCPT--CRLPIG 91 (299)
T ss_pred chhhccCchhhccCcccc-eec-CCCcEehhhhhhh-----h----cccCCc--cccccc
Confidence 445689999998865432 222 3379999999862 1 127997 988877
No 151
>PF02891 zf-MIZ: MIZ/SP-RING zinc finger; InterPro: IPR004181 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents MIZ-type zinc finger domains. Miz1 (Msx-interacting-zinc finger) is a zinc finger-containing protein with homology to the yeast protein, Nfi-1. Miz1 is a sequence specific DNA binding protein that can function as a positive-acting transcription factor. Miz1 binds to the homeobox protein Msx2, enhancing the specific DNA-binding ability of Msx2 []. Other proteins containing this domain include the human pias family (protein inhibitor of activated STAT protein). More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 3I2D_A.
Probab=62.02 E-value=10 Score=28.33 Aligned_cols=47 Identities=21% Similarity=0.462 Sum_probs=25.7
Q ss_pred cccceeccccccCCceeecCCCcccchhhHHHHHHHHHhCCCCCCCCCCCCCC
Q 008441 309 ETCVICLEDTDVGHMFSIDGCLHRYCFLCMKKHIEEKLRQGMEPTCPHEGCKS 361 (565)
Q Consensus 309 ~~C~IC~e~~~~~~~~~l~~C~H~fC~~Cl~~~i~~~i~~g~~~kCP~~~C~~ 361 (565)
..|+|-+..+ ..+.....|.|.-|.+ +..|+......+. -+||. |++
T Consensus 3 L~CPls~~~i--~~P~Rg~~C~H~~CFD-l~~fl~~~~~~~~-W~CPi--C~~ 49 (50)
T PF02891_consen 3 LRCPLSFQRI--RIPVRGKNCKHLQCFD-LESFLESNQRTPK-WKCPI--CNK 49 (50)
T ss_dssp SB-TTTSSB---SSEEEETT--SS--EE-HHHHHHHHHHS----B-TT--T--
T ss_pred eeCCCCCCEE--EeCccCCcCcccceEC-HHHHHHHhhccCC-eECcC--CcC
Confidence 5788887654 4566667999998855 7788887766655 48997 764
No 152
>KOG1701 consensus Focal adhesion adaptor protein Paxillin and related LIM proteins [Signal transduction mechanisms]
Probab=61.96 E-value=2.9 Score=44.66 Aligned_cols=27 Identities=15% Similarity=0.207 Sum_probs=16.7
Q ss_pred ccccCceeCCCCCCc----eecccCCCcCCC
Q 008441 422 GRRLGARKCTKCHRR----FCIDCKVPWHNN 448 (565)
Q Consensus 422 ~~~~~~~~C~~C~~~----fC~~C~~~~H~g 448 (565)
.+..+.+.|..|.+. -|..|..+.-..
T Consensus 377 vd~~n~v~Cv~dfh~kfAPrCs~C~~PI~P~ 407 (468)
T KOG1701|consen 377 VDSQNNVYCVPDFHKKFAPRCSVCGNPILPR 407 (468)
T ss_pred ccCCCceeeehhhhhhcCcchhhccCCccCC
Confidence 456677888776542 377777765443
No 153
>PF06524 NOA36: NOA36 protein; InterPro: IPR010531 This family consists of several NOA36 proteins which contain 29 highly conserved cysteine residues. The function of this protein is unknown.; GO: 0008270 zinc ion binding, 0005634 nucleus
Probab=61.70 E-value=5.2 Score=40.08 Aligned_cols=22 Identities=41% Similarity=0.967 Sum_probs=12.1
Q ss_pred cccCCCCceeEecCCcceEEe-ecCccccc
Q 008441 478 RQCVKCNHLIELAEGCFHMTC-RCGHEFCY 506 (565)
Q Consensus 478 k~CPkC~~~IEK~~GCnHMtC-~Cg~~FCw 506 (565)
-+|..|+.+=+ -+| +|+.-||=
T Consensus 172 ~KC~SCNrlGq-------~sCLRCK~cfCd 194 (314)
T PF06524_consen 172 FKCQSCNRLGQ-------YSCLRCKICFCD 194 (314)
T ss_pred ccccccccccc-------hhhhheeeeehh
Confidence 35777665533 345 56665553
No 154
>TIGR00622 ssl1 transcription factor ssl1. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=59.95 E-value=8.4 Score=33.92 Aligned_cols=42 Identities=21% Similarity=0.597 Sum_probs=30.3
Q ss_pred cccCCCCceeEec--------CCcceEEe-ecCccccccccccccCCCCCc
Q 008441 478 RQCVKCNHLIELA--------EGCFHMTC-RCGHEFCYNCGAEWKNKKATC 519 (565)
Q Consensus 478 k~CPkC~~~IEK~--------~GCnHMtC-~Cg~~FCw~C~~~~~~~~~~c 519 (565)
+.|-.|...+... ..=....| +|+..||..|-.-+...-++|
T Consensus 56 ~~C~~C~~~f~~~~~~~~~~~~~~~~y~C~~C~~~FC~dCD~fiHe~Lh~C 106 (112)
T TIGR00622 56 RFCFGCQGPFPKPPVSPFDELKDSHRYVCAVCKNVFCVDCDVFVHESLHCC 106 (112)
T ss_pred CcccCcCCCCCCcccccccccccccceeCCCCCCccccccchhhhhhccCC
Confidence 5699999876532 12335679 699999999999887655554
No 155
>smart00661 RPOL9 RNA polymerase subunit 9.
Probab=59.57 E-value=7.7 Score=28.73 Aligned_cols=27 Identities=30% Similarity=0.725 Sum_probs=17.5
Q ss_pred cccCCCCCCcccchhhhhccCCCcccccccCceeCCCCCC
Q 008441 396 YCPYPKCSALMSKSEIERDASSSSFVGRRLGARKCTKCHR 435 (565)
Q Consensus 396 ~CP~p~C~~~i~~~~~~e~~~s~~~~~~~~~~~~C~~C~~ 435 (565)
+|| .|+.++.+.+. .......|+.|++
T Consensus 2 FCp--~Cg~~l~~~~~-----------~~~~~~vC~~Cg~ 28 (52)
T smart00661 2 FCP--KCGNMLIPKEG-----------KEKRRFVCRKCGY 28 (52)
T ss_pred CCC--CCCCccccccC-----------CCCCEEECCcCCC
Confidence 687 89988754321 1224678888885
No 156
>KOG4684 consensus Uncharacterized conserved protein, contains C4-type Zn-finger [General function prediction only]
Probab=59.41 E-value=7.5 Score=37.81 Aligned_cols=54 Identities=19% Similarity=0.523 Sum_probs=34.7
Q ss_pred CCCcccccCCCCCCcccchhhhhccCCCcccccccCceeCCCCCCce-----------ecccCCCc
Q 008441 391 VTEKVYCPYPKCSALMSKSEIERDASSSSFVGRRLGARKCTKCHRRF-----------CIDCKVPW 445 (565)
Q Consensus 391 ~~~~~~CP~p~C~~~i~~~~~~e~~~s~~~~~~~~~~~~C~~C~~~f-----------C~~C~~~~ 445 (565)
.++++-||.|+|+.+|......+-... -...+..-++.|.+|+..| |.+|++-.
T Consensus 135 sSqRIACPRpnCkRiInL~p~~~~p~~-P~~~P~gcRV~CgHC~~tFLfnt~tnaLArCPHCrKvS 199 (275)
T KOG4684|consen 135 SSQRIACPRPNCKRIINLDPLIEKPRD-PGTAPTGCRVKCGHCNETFLFNTLTNALARCPHCRKVS 199 (275)
T ss_pred ccceeccCCCCcceeeecCCCCCCCCC-CCCCCcceEEEecCccceeehhhHHHHHhcCCcccchh
Confidence 346788999999999876544221110 0112334578999998766 77777644
No 157
>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=58.96 E-value=4.3 Score=42.06 Aligned_cols=41 Identities=20% Similarity=0.440 Sum_probs=26.2
Q ss_pred cccCCCCceeEecCCcceEEeecCcccccccccc-ccCCCCC
Q 008441 478 RQCVKCNHLIELAEGCFHMTCRCGHEFCYNCGAE-WKNKKAT 518 (565)
Q Consensus 478 k~CPkC~~~IEK~~GCnHMtC~Cg~~FCw~C~~~-~~~~~~~ 518 (565)
..||.|+...-.+..=.-|.=.|||.||-.|... |..+...
T Consensus 4 ~~CP~Ck~~~y~np~~kl~i~~CGH~~C~sCv~~l~~~~~~~ 45 (309)
T TIGR00570 4 QGCPRCKTTKYRNPSLKLMVNVCGHTLCESCVDLLFVRGSGS 45 (309)
T ss_pred CCCCcCCCCCccCcccccccCCCCCcccHHHHHHHhcCCCCC
Confidence 4699999965554332112226999999999888 5444333
No 158
>KOG3579 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=58.71 E-value=5 Score=40.62 Aligned_cols=48 Identities=25% Similarity=0.613 Sum_probs=34.0
Q ss_pred cccccceeccccccCCceeecC-CCcccchhhHHHHHHHHHhCCCCCCCC
Q 008441 307 INETCVICLEDTDVGHMFSIDG-CLHRYCFLCMKKHIEEKLRQGMEPTCP 355 (565)
Q Consensus 307 ~~~~C~IC~e~~~~~~~~~l~~-C~H~fC~~Cl~~~i~~~i~~g~~~kCP 355 (565)
...-|.+|-+..+...++.+.. =.|.||+.|-++.|+.+-..+.+ .||
T Consensus 267 apLcCTLC~ERLEDTHFVQCPSVp~HKFCFPCSResIK~Qg~sgev-YCP 315 (352)
T KOG3579|consen 267 APLCCTLCHERLEDTHFVQCPSVPSHKFCFPCSRESIKQQGASGEV-YCP 315 (352)
T ss_pred CceeehhhhhhhccCceeecCCCcccceecccCHHHHHhhcCCCce-eCC
Confidence 3488999998876555543211 16999999999999887666643 455
No 159
>KOG2034 consensus Vacuolar sorting protein PEP3/VPS18 [Intracellular trafficking, secretion, and vesicular transport]
Probab=58.65 E-value=8.4 Score=44.93 Aligned_cols=39 Identities=18% Similarity=0.281 Sum_probs=31.5
Q ss_pred cccccccceeccccccCCceeecCCCcccchhhHHHHHHH
Q 008441 305 KTINETCVICLEDTDVGHMFSIDGCLHRYCFLCMKKHIEE 344 (565)
Q Consensus 305 ~~~~~~C~IC~e~~~~~~~~~l~~C~H~fC~~Cl~~~i~~ 344 (565)
-.....|.+|...+- .++|.+.+|||.|..+|+.+++..
T Consensus 814 ~ep~d~C~~C~~~ll-~~pF~vf~CgH~FH~~Cl~~~v~~ 852 (911)
T KOG2034|consen 814 LEPQDSCDHCGRPLL-IKPFYVFPCGHCFHRDCLIRHVLS 852 (911)
T ss_pred ecCccchHHhcchhh-cCcceeeeccchHHHHHHHHHHHc
Confidence 335679999988764 456777799999999999998854
No 160
>PLN02638 cellulose synthase A (UDP-forming), catalytic subunit
Probab=58.57 E-value=8.3 Score=46.21 Aligned_cols=56 Identities=23% Similarity=0.510 Sum_probs=39.2
Q ss_pred cccCCCCceeEecC-CcceEEee-cCccccccccccccCCCCCcCCCCCCCCCccccCC
Q 008441 478 RQCVKCNHLIELAE-GCFHMTCR-CGHEFCYNCGAEWKNKKATCSCPLWDEDNILDDDS 534 (565)
Q Consensus 478 k~CPkC~~~IEK~~-GCnHMtC~-Cg~~FCw~C~~~~~~~~~~c~C~~~~~~~~~~~~~ 534 (565)
+-|--|+=-|..+. |=-.+-|. |++--|=-|. +|....++=.||.=+-....+++.
T Consensus 18 qiCqICGD~vg~~~~Ge~FVAC~eC~FPVCrpCY-EYEr~eG~q~CPqCktrYkr~kgs 75 (1079)
T PLN02638 18 QVCQICGDNVGKTVDGEPFVACDVCAFPVCRPCY-EYERKDGNQSCPQCKTKYKRHKGS 75 (1079)
T ss_pred ceeeecccccCcCCCCCEEEEeccCCCccccchh-hhhhhcCCccCCccCCchhhhcCC
Confidence 67999999888864 87888895 9999998888 666555554555544444444443
No 161
>TIGR00595 priA primosomal protein N'. All proteins in this family for which functions are known are components of the primosome which is involved in replication, repair, and recombination.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=58.16 E-value=8 Score=43.23 Aligned_cols=34 Identities=26% Similarity=0.681 Sum_probs=22.1
Q ss_pred cccCCCCceeEecCCcceEEe-ecCcc-----cccccccc
Q 008441 478 RQCVKCNHLIELAEGCFHMTC-RCGHE-----FCYNCGAE 511 (565)
Q Consensus 478 k~CPkC~~~IEK~~GCnHMtC-~Cg~~-----FCw~C~~~ 511 (565)
-+||+|..+..--..=|.+.| .||+. .|-.|+..
T Consensus 223 ~~C~~C~~~l~~h~~~~~l~Ch~Cg~~~~~~~~Cp~C~s~ 262 (505)
T TIGR00595 223 LCCPNCDVSLTYHKKEGKLRCHYCGYQEPIPKTCPQCGSE 262 (505)
T ss_pred cCCCCCCCceEEecCCCeEEcCCCcCcCCCCCCCCCCCCC
Confidence 357777766554333457788 48766 58888774
No 162
>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=57.94 E-value=9.7 Score=38.19 Aligned_cols=104 Identities=18% Similarity=0.392 Sum_probs=54.4
Q ss_pred CcccccccceeccccccCCceeecCCCcc-cchhhHHHHH-HHHHhCCCCCCCCCCCCCCccchhhHHHhhhhHHHHHHH
Q 008441 304 GKTINETCVICLEDTDVGHMFSIDGCLHR-YCFLCMKKHI-EEKLRQGMEPTCPHEGCKSKLEVESCRIFLTLKLFEIWN 381 (565)
Q Consensus 304 ~~~~~~~C~IC~e~~~~~~~~~l~~C~H~-fC~~Cl~~~i-~~~i~~g~~~kCP~~~C~~~l~~~~i~~lL~~e~~e~y~ 381 (565)
+.....+|-+|...++.+.-. =+|. -|..|-...- +..-..+.+++|| |+-.|--
T Consensus 61 ~~~p~v~CrVCq~~I~i~gk~----~QhVVkC~~CnEATPIr~aPpGKKYVRCP---CNCLLIC---------------- 117 (256)
T PF09788_consen 61 GGAPVVTCRVCQSLIDIEGKM----HQHVVKCSVCNEATPIRNAPPGKKYVRCP---CNCLLIC---------------- 117 (256)
T ss_pred CCCceEEeecCCceecccCcc----ceeeEECCCCCccccccCCCCCCeeEecC---CceEEEe----------------
Confidence 344578999998765443211 1232 4555644221 1111112335788 5543211
Q ss_pred HHHHHhcCCCCCcccccCCCCCCcccchhhhhccCC-CcccccccCceeCCCCCCce
Q 008441 382 QRMKEALIPVTEKVYCPYPKCSALMSKSEIERDASS-SSFVGRRLGARKCTKCHRRF 437 (565)
Q Consensus 382 ~~~~e~~i~~~~~~~CP~p~C~~~i~~~~~~e~~~s-~~~~~~~~~~~~C~~C~~~f 437 (565)
-....++-||.|+|+.+|..........+ .....+...++.|.+|+..|
T Consensus 118 -------k~sS~rIaCPRp~CkRiI~L~~~~~~p~~~~~~~~p~~~rv~CghC~~~F 167 (256)
T PF09788_consen 118 -------KSSSQRIACPRPNCKRIINLGPSHQGPVTPPVPTQPGSCRVICGHCSNTF 167 (256)
T ss_pred -------ecccccccCCCCCCcceEEeCCccCCCCCCCCCCCCCceeEECCCCCCcE
Confidence 01346789999999999865433110000 00112345678999998766
No 163
>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=57.58 E-value=6.7 Score=27.06 Aligned_cols=28 Identities=25% Similarity=0.656 Sum_probs=16.8
Q ss_pred ccccCCCCCCcccchhhhhccCCCcccccccCceeCCCCCCc
Q 008441 395 VYCPYPKCSALMSKSEIERDASSSSFVGRRLGARKCTKCHRR 436 (565)
Q Consensus 395 ~~CP~p~C~~~i~~~~~~e~~~s~~~~~~~~~~~~C~~C~~~ 436 (565)
++|| .|++++.+.+- ....+.|..|++.
T Consensus 2 ~FCp--~C~nlL~p~~~------------~~~~~~C~~C~Y~ 29 (35)
T PF02150_consen 2 RFCP--ECGNLLYPKED------------KEKRVACRTCGYE 29 (35)
T ss_dssp -BET--TTTSBEEEEEE------------TTTTEEESSSS-E
T ss_pred eeCC--CCCccceEcCC------------CccCcCCCCCCCc
Confidence 5788 99999875431 2222378877764
No 164
>KOG2789 consensus Putative Zn-finger protein [General function prediction only]
Probab=57.52 E-value=3.3 Score=43.70 Aligned_cols=34 Identities=18% Similarity=0.355 Sum_probs=25.8
Q ss_pred cccccceeccccccCCceeecCCCcccchhhHHHH
Q 008441 307 INETCVICLEDTDVGHMFSIDGCLHRYCFLCMKKH 341 (565)
Q Consensus 307 ~~~~C~IC~e~~~~~~~~~l~~C~H~fC~~Cl~~~ 341 (565)
.+.+|+|||-.++...-.+. .|.-.+|..|+..+
T Consensus 73 r~~ecpicflyyps~~n~~r-cC~~~Ic~ecf~~~ 106 (482)
T KOG2789|consen 73 RKTECPICFLYYPSAKNLVR-CCSETICGECFAPF 106 (482)
T ss_pred ccccCceeeeecccccchhh-hhccchhhhheecc
Confidence 45799999987765333333 79999999999865
No 165
>PLN02436 cellulose synthase A
Probab=57.11 E-value=9.5 Score=45.66 Aligned_cols=55 Identities=24% Similarity=0.556 Sum_probs=38.9
Q ss_pred ccccCCCCceeEec-CCcceEEee-cCccccccccccccCCCCCcCCCCCCCCCcccc
Q 008441 477 WRQCVKCNHLIELA-EGCFHMTCR-CGHEFCYNCGAEWKNKKATCSCPLWDEDNILDD 532 (565)
Q Consensus 477 ~k~CPkC~~~IEK~-~GCnHMtC~-Cg~~FCw~C~~~~~~~~~~c~C~~~~~~~~~~~ 532 (565)
.+-|.-|+=-|..+ .|=-.+-|. |++..|--|. +|....++=.||.-+-....++
T Consensus 36 ~~iCqICGD~Vg~t~dGe~FVACn~C~fpvCr~Cy-eyer~eg~~~Cpqckt~Y~r~k 92 (1094)
T PLN02436 36 GQTCQICGDEIELTVDGEPFVACNECAFPVCRPCY-EYERREGNQACPQCKTRYKRIK 92 (1094)
T ss_pred CccccccccccCcCCCCCEEEeeccCCCccccchh-hhhhhcCCccCcccCCchhhcc
Confidence 36899999988775 487889995 9999999998 6665555545555444444333
No 166
>COG1997 RPL43A Ribosomal protein L37AE/L43A [Translation, ribosomal structure and biogenesis]
Probab=57.06 E-value=7.7 Score=32.43 Aligned_cols=28 Identities=21% Similarity=0.485 Sum_probs=22.7
Q ss_pred cccCCCCceeEecCCcceEEe-ecCcccc
Q 008441 478 RQCVKCNHLIELAEGCFHMTC-RCGHEFC 505 (565)
Q Consensus 478 k~CPkC~~~IEK~~GCnHMtC-~Cg~~FC 505 (565)
-.||.|+....|..+=---.| +||+.|=
T Consensus 36 ~~Cp~C~~~~VkR~a~GIW~C~kCg~~fA 64 (89)
T COG1997 36 HVCPFCGRTTVKRIATGIWKCRKCGAKFA 64 (89)
T ss_pred CcCCCCCCcceeeeccCeEEcCCCCCeec
Confidence 589999999998887777778 4887763
No 167
>PRK14873 primosome assembly protein PriA; Provisional
Probab=55.95 E-value=8.7 Score=44.37 Aligned_cols=34 Identities=26% Similarity=0.708 Sum_probs=20.2
Q ss_pred cccCCCCceeEecCCcceEEe-ecCcc----cccccccc
Q 008441 478 RQCVKCNHLIELAEGCFHMTC-RCGHE----FCYNCGAE 511 (565)
Q Consensus 478 k~CPkC~~~IEK~~GCnHMtC-~Cg~~----FCw~C~~~ 511 (565)
-+||+|..+..--.+=+.+.| .||+. .|-.|+..
T Consensus 393 ~~C~~C~~~L~~h~~~~~l~Ch~CG~~~~p~~Cp~Cgs~ 431 (665)
T PRK14873 393 ARCRHCTGPLGLPSAGGTPRCRWCGRAAPDWRCPRCGSD 431 (665)
T ss_pred eECCCCCCceeEecCCCeeECCCCcCCCcCccCCCCcCC
Confidence 356666666554444456777 37653 46777665
No 168
>PHA02926 zinc finger-like protein; Provisional
Probab=55.52 E-value=6.2 Score=38.82 Aligned_cols=39 Identities=21% Similarity=0.457 Sum_probs=26.0
Q ss_pred ccccCCCCceeEecCCcceE-Ee---ecCccccccccccccCC
Q 008441 477 WRQCVKCNHLIELAEGCFHM-TC---RCGHEFCYNCGAEWKNK 515 (565)
Q Consensus 477 ~k~CPkC~~~IEK~~GCnHM-tC---~Cg~~FCw~C~~~~~~~ 515 (565)
-+.|+=|--.+-+....+.- .- .|+|-||+.|-..|...
T Consensus 170 E~eCgICmE~I~eK~~~~eRrFGIL~~CnHsFCl~CIr~Wr~~ 212 (242)
T PHA02926 170 EKECGICYEVVYSKRLENDRYFGLLDSCNHIFCITCINIWHRT 212 (242)
T ss_pred CCCCccCccccccccccccccccccCCCCchHHHHHHHHHHHh
Confidence 37899999766332221111 11 48899999999999864
No 169
>PF03854 zf-P11: P-11 zinc finger; InterPro: IPR003224 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. The RING-finger is a specialised type of Zn-finger of 40 to 60 residues that binds two atoms of zinc, and is probably involved in mediating protein-protein interactions [, , ]. There are two different variants, the C3HC4-type and a C3H2C3-type, which is clearly related despite the different cysteine/histidine pattern. The latter type is sometimes referred to as 'RING-H2 finger'. The RING domain is a protein interaction domain which has been implicated in a range of diverse biological processes. Several 3D-structures for RING-fingers are known [, ]. The 3D structure of the zinc ligation system is unique to the RING domain and is referred to as the 'cross-brace' motif. The spacing of the cysteines in such a domain is: C-x(2)-C-x(9 to 39)-C-x(1 to 3)-H-x(2 to 3)-C-x(2)-C-x(4 to 48)-C-x(2)-C Metal ligand pairs one and three co-ordinate to bind one zinc ion, whilst pairs two and four bind the second. This entry represents RING finger protein Z, a small polypeptide found in some negative-strand RNA viruses including Lassa fever virus, which plays a crucial role in virion assembly and budding. RING finger Z has been shown to interact with several host proteins, including promyelocytic leukemia protein and the eukaryotic translation initiation factor 4E [, ]. It is sufficient in the absence of any other viral proteins to release virus-like particles from the infected cell []. This protein is also responsible for arenavirus superinfection exclusion; expression of this protein in a host cell strongly and specifically inhibits areanavirus transcription and replication []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003723 RNA binding, 0008270 zinc ion binding; PDB: 2KO5_A.
Probab=55.43 E-value=7.3 Score=28.78 Aligned_cols=44 Identities=23% Similarity=0.578 Sum_probs=22.4
Q ss_pred cccceeccccccCCceeecCC-CcccchhhHHHHHHHHHhCCCCCCCCCCCCCCccch
Q 008441 309 ETCVICLEDTDVGHMFSIDGC-LHRYCFLCMKKHIEEKLRQGMEPTCPHEGCKSKLEV 365 (565)
Q Consensus 309 ~~C~IC~e~~~~~~~~~l~~C-~H~fC~~Cl~~~i~~~i~~g~~~kCP~~~C~~~l~~ 365 (565)
+.|-.|+ |....++ .| .|..|..|+...+. ....||. |+.+++-
T Consensus 3 ~nCKsCW--f~~k~Li---~C~dHYLCl~CLt~ml~------~s~~C~i--C~~~LPt 47 (50)
T PF03854_consen 3 YNCKSCW--FANKGLI---KCSDHYLCLNCLTLMLS------RSDRCPI--CGKPLPT 47 (50)
T ss_dssp ----SS---S--SSEE---E-SS-EEEHHHHHHT-S------SSSEETT--TTEE---
T ss_pred ccChhhh--hcCCCee---eecchhHHHHHHHHHhc------cccCCCc--ccCcCcc
Confidence 5788888 4445554 34 59999999987662 2347987 8887763
No 170
>PLN02400 cellulose synthase
Probab=55.20 E-value=14 Score=44.33 Aligned_cols=57 Identities=25% Similarity=0.543 Sum_probs=39.4
Q ss_pred ccccCCCCceeEecC-CcceEEee-cCccccccccccccCCCCCcCCCCCCCCCccccCC
Q 008441 477 WRQCVKCNHLIELAE-GCFHMTCR-CGHEFCYNCGAEWKNKKATCSCPLWDEDNILDDDS 534 (565)
Q Consensus 477 ~k~CPkC~~~IEK~~-GCnHMtC~-Cg~~FCw~C~~~~~~~~~~c~C~~~~~~~~~~~~~ 534 (565)
.+-|--|+=-|..+. |=-.+-|. |++--|=-|. +|....++=.||.=+-....+++.
T Consensus 36 gqiCqICGD~VG~t~dGe~FVAC~eCaFPVCRpCY-EYERkeGnq~CPQCkTrYkR~Kgs 94 (1085)
T PLN02400 36 GQICQICGDDVGVTETGDVFVACNECAFPVCRPCY-EYERKDGTQCCPQCKTRYRRHKGS 94 (1085)
T ss_pred CceeeecccccCcCCCCCEEEEEccCCCccccchh-heecccCCccCcccCCccccccCC
Confidence 368999999888864 87888894 9999998888 666555554555544444444443
No 171
>PRK14892 putative transcription elongation factor Elf1; Provisional
Probab=54.48 E-value=9.1 Score=33.01 Aligned_cols=28 Identities=21% Similarity=0.587 Sum_probs=18.9
Q ss_pred ccccCCCCcee---EecCCcceEEe-ecCccc
Q 008441 477 WRQCVKCNHLI---ELAEGCFHMTC-RCGHEF 504 (565)
Q Consensus 477 ~k~CPkC~~~I---EK~~GCnHMtC-~Cg~~F 504 (565)
.-.||+|+... .+..|=-|++| .||+.|
T Consensus 21 ~f~CP~Cge~~v~v~~~k~~~h~~C~~CG~y~ 52 (99)
T PRK14892 21 IFECPRCGKVSISVKIKKNIAIITCGNCGLYT 52 (99)
T ss_pred EeECCCCCCeEeeeecCCCcceEECCCCCCcc
Confidence 36799999432 23446668999 588764
No 172
>KOG2164 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=54.06 E-value=3.9 Score=44.77 Aligned_cols=41 Identities=39% Similarity=0.750 Sum_probs=27.3
Q ss_pred cccCCCCceeEecCCcceEEeecCccccccccccccCC---CCCcCCCC
Q 008441 478 RQCVKCNHLIELAEGCFHMTCRCGHEFCYNCGAEWKNK---KATCSCPL 523 (565)
Q Consensus 478 k~CPkC~~~IEK~~GCnHMtC~Cg~~FCw~C~~~~~~~---~~~c~C~~ 523 (565)
.+||-|-.+-. +--|| .|||-|||-|+-.|-.. .+.|.||+
T Consensus 187 ~~CPICL~~~~----~p~~t-~CGHiFC~~CiLqy~~~s~~~~~~~CPi 230 (513)
T KOG2164|consen 187 MQCPICLEPPS----VPVRT-NCGHIFCGPCILQYWNYSAIKGPCSCPI 230 (513)
T ss_pred CcCCcccCCCC----ccccc-ccCceeeHHHHHHHHhhhcccCCccCCc
Confidence 58999876543 22222 29999999998764332 34478997
No 173
>PF14569 zf-UDP: Zinc-binding RING-finger; PDB: 1WEO_A.
Probab=53.70 E-value=5.2 Score=32.67 Aligned_cols=45 Identities=20% Similarity=0.419 Sum_probs=17.6
Q ss_pred ccccCceeCCCCCCceecccCCCcCCCCChhhHhhhCCCCChhHHHHHHHHhcCCccccCCCCceeEecCCc
Q 008441 422 GRRLGARKCTKCHRRFCIDCKVPWHNNMTCIYYKRLNPNPPTEDVKLKSLASSNLWRQCVKCNHLIELAEGC 493 (565)
Q Consensus 422 ~~~~~~~~C~~C~~~fC~~C~~~~H~g~tC~e~~~~~~~~~~ed~~l~~l~~~~~~k~CPkC~~~IEK~~GC 493 (565)
......+-|..|++..|..| .+|.+ +.+.+-||+|+....+..|+
T Consensus 23 ~~Ge~FVAC~eC~fPvCr~C----------yEYEr-----------------keg~q~CpqCkt~ykr~kgs 67 (80)
T PF14569_consen 23 ENGEVFVACHECAFPVCRPC----------YEYER-----------------KEGNQVCPQCKTRYKRHKGS 67 (80)
T ss_dssp SSSSB--S-SSS-----HHH----------HHHHH-----------------HTS-SB-TTT--B----TT-
T ss_pred CCCCEEEEEcccCCccchhH----------HHHHh-----------------hcCcccccccCCCcccccCC
Confidence 34556788999998888754 55543 23347899998777655553
No 174
>PLN02189 cellulose synthase
Probab=52.96 E-value=12 Score=44.78 Aligned_cols=54 Identities=26% Similarity=0.634 Sum_probs=37.1
Q ss_pred cccCCCCceeEec-CCcceEEee-cCccccccccccccCCCCCcCCCCCCCCCcccc
Q 008441 478 RQCVKCNHLIELA-EGCFHMTCR-CGHEFCYNCGAEWKNKKATCSCPLWDEDNILDD 532 (565)
Q Consensus 478 k~CPkC~~~IEK~-~GCnHMtC~-Cg~~FCw~C~~~~~~~~~~c~C~~~~~~~~~~~ 532 (565)
+-|.-|+=-|..+ .|=-.+-|. |++.-|--|. +|....++=.||.-+-....++
T Consensus 35 ~~C~iCgd~vg~~~~g~~fvaC~~C~fpvCr~Cy-eyer~eg~q~CpqCkt~Y~r~k 90 (1040)
T PLN02189 35 QVCEICGDEIGLTVDGDLFVACNECGFPVCRPCY-EYERREGTQNCPQCKTRYKRLK 90 (1040)
T ss_pred ccccccccccCcCCCCCEEEeeccCCCccccchh-hhhhhcCCccCcccCCchhhcc
Confidence 6799999888765 377788895 9999999998 5555555545555444443333
No 175
>KOG1832 consensus HIV-1 Vpr-binding protein [Cell cycle control, cell division, chromosome partitioning]
Probab=52.84 E-value=7.6 Score=45.24 Aligned_cols=19 Identities=21% Similarity=0.281 Sum_probs=11.6
Q ss_pred cCCCCCCCCCccccCCCCC
Q 008441 519 CSCPLWDEDNILDDDSDSS 537 (565)
Q Consensus 519 c~C~~~~~~~~~~~~~~~~ 537 (565)
-.|.+|+-......+.++|
T Consensus 1390 T~~r~yEIGR~r~~~dd~D 1408 (1516)
T KOG1832|consen 1390 TSARMYEIGRRRPTDDDSD 1408 (1516)
T ss_pred hhhhhhhhcccCCCccccC
Confidence 3788887766655444333
No 176
>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=52.65 E-value=12 Score=26.95 Aligned_cols=22 Identities=27% Similarity=0.896 Sum_probs=16.6
Q ss_pred cccCCCCceeEe-cCCcceEEe-ecC
Q 008441 478 RQCVKCNHLIEL-AEGCFHMTC-RCG 501 (565)
Q Consensus 478 k~CPkC~~~IEK-~~GCnHMtC-~Cg 501 (565)
..||.|+.+..+ ..| .+.| .|+
T Consensus 18 ~~Cp~C~~PL~~~k~g--~~~Cv~C~ 41 (41)
T PF06677_consen 18 EHCPDCGTPLMRDKDG--KIYCVSCG 41 (41)
T ss_pred CccCCCCCeeEEecCC--CEECCCCC
Confidence 689999999998 445 5677 364
No 177
>PF14353 CpXC: CpXC protein
Probab=52.32 E-value=9.1 Score=34.29 Aligned_cols=17 Identities=24% Similarity=0.368 Sum_probs=11.9
Q ss_pred ccccCCCCceeEecCCc
Q 008441 477 WRQCVKCNHLIELAEGC 493 (565)
Q Consensus 477 ~k~CPkC~~~IEK~~GC 493 (565)
.-.||+|+..+.-...+
T Consensus 38 ~~~CP~Cg~~~~~~~p~ 54 (128)
T PF14353_consen 38 SFTCPSCGHKFRLEYPL 54 (128)
T ss_pred EEECCCCCCceecCCCE
Confidence 36899998887655443
No 178
>PF14149 YhfH: YhfH-like protein
Probab=52.11 E-value=1.5 Score=30.58 Aligned_cols=30 Identities=27% Similarity=0.679 Sum_probs=23.6
Q ss_pred HHhcCCccccCCCCceeEecCCcceEEe-ec
Q 008441 471 LASSNLWRQCVKCNHLIELAEGCFHMTC-RC 500 (565)
Q Consensus 471 l~~~~~~k~CPkC~~~IEK~~GCnHMtC-~C 500 (565)
+.++-..|.|+.|+..|+-..-|..++| +|
T Consensus 7 FfrnLp~K~C~~CG~~i~EQ~E~Y~n~C~~C 37 (37)
T PF14149_consen 7 FFRNLPPKKCTECGKEIEEQAECYGNECDRC 37 (37)
T ss_pred HHHhCCCcccHHHHHHHHHHHHHHhCcCCCC
Confidence 3344455999999999998888888888 56
No 179
>COG5574 PEX10 RING-finger-containing E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=52.08 E-value=4.2 Score=40.87 Aligned_cols=37 Identities=19% Similarity=0.155 Sum_probs=25.1
Q ss_pred cccccceecc-cccc-CCceeecCCCcccchhhHHHHHH
Q 008441 307 INETCVICLE-DTDV-GHMFSIDGCLHRYCFLCMKKHIE 343 (565)
Q Consensus 307 ~~~~C~IC~e-~~~~-~~~~~l~~C~H~fC~~Cl~~~i~ 343 (565)
...++.+++. +... .+...+..|+|.||..|-.-++.
T Consensus 94 ~~~~ls~~~s~e~~~~~e~~~~y~~~~~f~i~~~~i~~~ 132 (271)
T COG5574 94 REETLSIEYSRETNIDKEGEVLYPCGIFFCIGCDYIWSI 132 (271)
T ss_pred cccccccccCcccccccccceeeecccccchhhhHHHHH
Confidence 4678889887 3221 23334457999999999776665
No 180
>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=52.02 E-value=12 Score=30.20 Aligned_cols=33 Identities=33% Similarity=0.895 Sum_probs=21.0
Q ss_pred ccCCCCceeEecCCcceEEe-ecCcc-----cccccccccc
Q 008441 479 QCVKCNHLIELAEGCFHMTC-RCGHE-----FCYNCGAEWK 513 (565)
Q Consensus 479 ~CPkC~~~IEK~~GCnHMtC-~Cg~~-----FCw~C~~~~~ 513 (565)
.||.|+..++..+ .+.+| .|+.. ||-.|+++..
T Consensus 3 ~CP~C~~~L~~~~--~~~~C~~C~~~~~~~a~CPdC~~~Le 41 (70)
T PF07191_consen 3 TCPKCQQELEWQG--GHYHCEACQKDYKKEAFCPDCGQPLE 41 (70)
T ss_dssp B-SSS-SBEEEET--TEEEETTT--EEEEEEE-TTT-SB-E
T ss_pred cCCCCCCccEEeC--CEEECccccccceecccCCCcccHHH
Confidence 6999999999888 68888 48755 5888888754
No 181
>COG3024 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=51.93 E-value=10 Score=29.74 Aligned_cols=15 Identities=13% Similarity=0.404 Sum_probs=11.9
Q ss_pred CccccCCCCceeEec
Q 008441 476 LWRQCVKCNHLIELA 490 (565)
Q Consensus 476 ~~k~CPkC~~~IEK~ 490 (565)
...+||.|+.+++..
T Consensus 6 ~~v~CP~Cgkpv~w~ 20 (65)
T COG3024 6 ITVPCPTCGKPVVWG 20 (65)
T ss_pred ccccCCCCCCccccc
Confidence 347899999999853
No 182
>PLN02915 cellulose synthase A [UDP-forming], catalytic subunit
Probab=51.45 E-value=12 Score=44.75 Aligned_cols=55 Identities=22% Similarity=0.596 Sum_probs=39.4
Q ss_pred cccCCCCceeEecC-CcceEEee-cCccccccccccccCCCCCcCCCCCCCCCccccC
Q 008441 478 RQCVKCNHLIELAE-GCFHMTCR-CGHEFCYNCGAEWKNKKATCSCPLWDEDNILDDD 533 (565)
Q Consensus 478 k~CPkC~~~IEK~~-GCnHMtC~-Cg~~FCw~C~~~~~~~~~~c~C~~~~~~~~~~~~ 533 (565)
+-|--|+--|..+. |=-.+-|. |++-.|--|. +|....++=.||.-+-....+.+
T Consensus 16 ~~c~iCGd~vg~~~~Ge~FVAC~eC~fpvCr~cy-eye~~~g~~~cp~c~t~y~~~~~ 72 (1044)
T PLN02915 16 KTCRVCGDEVGVKEDGQPFVACHVCGFPVCKPCY-EYERSEGNQCCPQCNTRYKRHKG 72 (1044)
T ss_pred chhhccccccCcCCCCCEEEEeccCCCccccchh-hhhhhcCCccCCccCCchhhhcC
Confidence 67888988888764 77888995 9999999998 66665555456665555444443
No 183
>PF14835 zf-RING_6: zf-RING of BARD1-type protein; PDB: 1JM7_B.
Probab=51.45 E-value=5.9 Score=31.27 Aligned_cols=28 Identities=29% Similarity=0.788 Sum_probs=12.3
Q ss_pred cccCCCCceeEec---CCcceEEeecCccccccccccc
Q 008441 478 RQCVKCNHLIELA---EGCFHMTCRCGHEFCYNCGAEW 512 (565)
Q Consensus 478 k~CPkC~~~IEK~---~GCnHMtC~Cg~~FCw~C~~~~ 512 (565)
-+|++|....... +| |.|-||+.|-.+.
T Consensus 8 LrCs~C~~~l~~pv~l~~-------CeH~fCs~Ci~~~ 38 (65)
T PF14835_consen 8 LRCSICFDILKEPVCLGG-------CEHIFCSSCIRDC 38 (65)
T ss_dssp TS-SSS-S--SS-B---S-------SS--B-TTTGGGG
T ss_pred cCCcHHHHHhcCCceecc-------CccHHHHHHhHHh
Confidence 4799998775432 45 5555666676654
No 184
>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=51.24 E-value=11 Score=28.34 Aligned_cols=29 Identities=21% Similarity=0.332 Sum_probs=18.0
Q ss_pred cccCCCCceeEe------cCCcceEE-e-ecCccccc
Q 008441 478 RQCVKCNHLIEL------AEGCFHMT-C-RCGHEFCY 506 (565)
Q Consensus 478 k~CPkC~~~IEK------~~GCnHMt-C-~Cg~~FCw 506 (565)
|+||.|+-.-+. +.+..++. | .||+...+
T Consensus 2 kPCPfCGg~~~~~~~~~~~~~~~~~~~C~~Cga~~~~ 38 (53)
T TIGR03655 2 KPCPFCGGADVYLRRGFDPLDLSHYFECSTCGASGPV 38 (53)
T ss_pred CCCCCCCCcceeeEeccCCCCCEEEEECCCCCCCccc
Confidence 799999986552 23555554 6 36665443
No 185
>KOG1941 consensus Acetylcholine receptor-associated protein of the synapse (rapsyn) [Extracellular structures]
Probab=50.95 E-value=5.7 Score=41.98 Aligned_cols=51 Identities=20% Similarity=0.552 Sum_probs=35.4
Q ss_pred cccccccceeccccccC-CceeecCCCcccchhhHHHHHHHHHhCCCCCCCCCCCCCC
Q 008441 305 KTINETCVICLEDTDVG-HMFSIDGCLHRYCFLCMKKHIEEKLRQGMEPTCPHEGCKS 361 (565)
Q Consensus 305 ~~~~~~C~IC~e~~~~~-~~~~l~~C~H~fC~~Cl~~~i~~~i~~g~~~kCP~~~C~~ 361 (565)
......|..|.+.+... +-..-++|.|+|...|+..|+.. ...-.||. |++
T Consensus 362 ~e~~L~Cg~CGe~~Glk~e~LqALpCsHIfH~rCl~e~L~~----n~~rsCP~--Crk 413 (518)
T KOG1941|consen 362 EETELYCGLCGESIGLKNERLQALPCSHIFHLRCLQEILEN----NGTRSCPN--CRK 413 (518)
T ss_pred HHHhhhhhhhhhhhcCCcccccccchhHHHHHHHHHHHHHh----CCCCCCcc--HHH
Confidence 34567899999876432 22334599999999999999932 22337886 763
No 186
>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]
Probab=50.60 E-value=16 Score=28.37 Aligned_cols=32 Identities=19% Similarity=0.468 Sum_probs=20.8
Q ss_pred ccccCCCCCCcccchhhhhccCCCcccccccCceeCCCCCCceeccc
Q 008441 395 VYCPYPKCSALMSKSEIERDASSSSFVGRRLGARKCTKCHRRFCIDC 441 (565)
Q Consensus 395 ~~CP~p~C~~~i~~~~~~e~~~s~~~~~~~~~~~~C~~C~~~fC~~C 441 (565)
..|. .|+..+.+ ......+.||.||...=.+|
T Consensus 10 ~~Ct--SCg~~i~p-------------~e~~v~F~CPnCGe~~I~Rc 41 (61)
T COG2888 10 PVCT--SCGREIAP-------------GETAVKFPCPNCGEVEIYRC 41 (61)
T ss_pred ceec--cCCCEecc-------------CCceeEeeCCCCCceeeehh
Confidence 4565 67776633 23567799999996654444
No 187
>KOG0801 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=50.37 E-value=6.8 Score=36.44 Aligned_cols=30 Identities=37% Similarity=0.620 Sum_probs=25.1
Q ss_pred ccccccceeccccccCCceeecCCCcccch
Q 008441 306 TINETCVICLEDTDVGHMFSIDGCLHRYCF 335 (565)
Q Consensus 306 ~~~~~C~IC~e~~~~~~~~~l~~C~H~fC~ 335 (565)
..+.+|.||+++....+.+..++|-++|.+
T Consensus 175 ddkGECvICLEdL~~GdtIARLPCLCIYHK 204 (205)
T KOG0801|consen 175 DDKGECVICLEDLEAGDTIARLPCLCIYHK 204 (205)
T ss_pred ccCCcEEEEhhhccCCCceeccceEEEeec
Confidence 346899999999988888888899888764
No 188
>COG1645 Uncharacterized Zn-finger containing protein [General function prediction only]
Probab=50.28 E-value=10 Score=34.32 Aligned_cols=24 Identities=33% Similarity=0.823 Sum_probs=18.9
Q ss_pred cccCCCCceeEecCCcceEEeecCccccccccc
Q 008441 478 RQCVKCNHLIELAEGCFHMTCRCGHEFCYNCGA 510 (565)
Q Consensus 478 k~CPkC~~~IEK~~GCnHMtC~Cg~~FCw~C~~ 510 (565)
+.||.|+.+..+.. |.-||-+|+.
T Consensus 29 ~hCp~Cg~PLF~Kd---------G~v~CPvC~~ 52 (131)
T COG1645 29 KHCPKCGTPLFRKD---------GEVFCPVCGY 52 (131)
T ss_pred hhCcccCCcceeeC---------CeEECCCCCc
Confidence 78999999988754 4677777774
No 189
>PRK05580 primosome assembly protein PriA; Validated
Probab=50.07 E-value=12 Score=43.36 Aligned_cols=33 Identities=27% Similarity=0.781 Sum_probs=18.8
Q ss_pred ccCCCCceeEecCCcceEEe-ecCcc-----cccccccc
Q 008441 479 QCVKCNHLIELAEGCFHMTC-RCGHE-----FCYNCGAE 511 (565)
Q Consensus 479 ~CPkC~~~IEK~~GCnHMtC-~Cg~~-----FCw~C~~~ 511 (565)
+||+|..+..--..=+.+.| .||+. .|..|+..
T Consensus 392 ~C~~C~~~l~~h~~~~~l~Ch~Cg~~~~~~~~Cp~Cg~~ 430 (679)
T PRK05580 392 ECPHCDASLTLHRFQRRLRCHHCGYQEPIPKACPECGST 430 (679)
T ss_pred CCCCCCCceeEECCCCeEECCCCcCCCCCCCCCCCCcCC
Confidence 56666665543223356677 37765 47777664
No 190
>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=49.01 E-value=11 Score=27.29 Aligned_cols=42 Identities=31% Similarity=0.570 Sum_probs=19.3
Q ss_pred cceeccccccCCceeecCCCcccchhhHHHHHHHHHhCCCCCCCCC
Q 008441 311 CVICLEDTDVGHMFSIDGCLHRYCFLCMKKHIEEKLRQGMEPTCPH 356 (565)
Q Consensus 311 C~IC~e~~~~~~~~~l~~C~H~fC~~Cl~~~i~~~i~~g~~~kCP~ 356 (565)
|.+|-+-......-....|+-++...|++.|++.+ ..++||.
T Consensus 1 C~~C~~iv~~G~~C~~~~C~~r~H~~C~~~y~r~~----~~~~CP~ 42 (43)
T PF08746_consen 1 CEACKEIVTQGQRCSNRDCNVRLHDDCFKKYFRHR----SNPKCPN 42 (43)
T ss_dssp -TTT-SB-SSSEE-SS--S--EE-HHHHHHHTTT-----SS-B-TT
T ss_pred CcccchhHeeeccCCCCccCchHHHHHHHHHHhcC----CCCCCcC
Confidence 56676554333222223688899999999999643 2236885
No 191
>KOG0978 consensus E3 ubiquitin ligase involved in syntaxin degradation [Posttranslational modification, protein turnover, chaperones]
Probab=48.82 E-value=5.9 Score=45.39 Aligned_cols=12 Identities=42% Similarity=1.074 Sum_probs=9.5
Q ss_pred CCCCceecccCC
Q 008441 432 KCHRRFCIDCKV 443 (565)
Q Consensus 432 ~C~~~fC~~C~~ 443 (565)
.|++.||..|-.
T Consensus 660 kC~H~FC~~Cvq 671 (698)
T KOG0978|consen 660 KCGHVFCEECVQ 671 (698)
T ss_pred hcchHHHHHHHH
Confidence 678888988855
No 192
>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=47.69 E-value=12 Score=29.61 Aligned_cols=26 Identities=31% Similarity=0.708 Sum_probs=19.8
Q ss_pred cccCCCCceeEecCCcceEEee-cCcc
Q 008441 478 RQCVKCNHLIELAEGCFHMTCR-CGHE 503 (565)
Q Consensus 478 k~CPkC~~~IEK~~GCnHMtC~-Cg~~ 503 (565)
+.||.|+....+...=-.++|. ||+.
T Consensus 29 q~C~~CG~~~~~~~~~r~~~C~~Cg~~ 55 (69)
T PF07282_consen 29 QTCPRCGHRNKKRRSGRVFTCPNCGFE 55 (69)
T ss_pred cCccCcccccccccccceEEcCCCCCE
Confidence 7899999999984444567784 8775
No 193
>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=47.61 E-value=13 Score=27.51 Aligned_cols=25 Identities=28% Similarity=0.671 Sum_probs=18.6
Q ss_pred cccC--CCCceeEecCCcceEEe-ecCc
Q 008441 478 RQCV--KCNHLIELAEGCFHMTC-RCGH 502 (565)
Q Consensus 478 k~CP--kC~~~IEK~~GCnHMtC-~Cg~ 502 (565)
+.|| .|+.-|....=-+..+| +|++
T Consensus 19 k~CP~~~CG~GvFMA~H~dR~~CGKCg~ 46 (47)
T PF01599_consen 19 KECPSPRCGAGVFMAEHKDRHYCGKCGY 46 (47)
T ss_dssp EE-TSTTTTSSSEEEE-SSEEEETTTSS
T ss_pred hcCCCcccCCceEeeecCCCccCCCccc
Confidence 8999 99997766666678889 7886
No 194
>PF12906 RINGv: RING-variant domain; PDB: 2D8S_A 1VYX_A.
Probab=47.11 E-value=16 Score=26.89 Aligned_cols=33 Identities=27% Similarity=0.551 Sum_probs=22.4
Q ss_pred cceeccccccCCceeecCCCc-----ccchhhHHHHHHH
Q 008441 311 CVICLEDTDVGHMFSIDGCLH-----RYCFLCMKKHIEE 344 (565)
Q Consensus 311 C~IC~e~~~~~~~~~l~~C~H-----~fC~~Cl~~~i~~ 344 (565)
|-||++.......+. .+|.. .....||.+|+..
T Consensus 1 CrIC~~~~~~~~~li-~pC~C~Gs~~~vH~~CL~~W~~~ 38 (47)
T PF12906_consen 1 CRICLEGEEEDEPLI-SPCRCKGSMKYVHRSCLERWIRE 38 (47)
T ss_dssp ETTTTEE-SSSS-EE--SSS-SSCCGSEECCHHHHHHHH
T ss_pred CeEeCCcCCCCCcee-cccccCCCcchhHHHHHHHHHHh
Confidence 679998866555333 36653 5789999999987
No 195
>PRK04023 DNA polymerase II large subunit; Validated
Probab=47.06 E-value=11 Score=44.84 Aligned_cols=31 Identities=35% Similarity=0.804 Sum_probs=24.9
Q ss_pred ccccCCCCceeEecCCcceEEe-ecCc-----ccccccccccc
Q 008441 477 WRQCVKCNHLIELAEGCFHMTC-RCGH-----EFCYNCGAEWK 513 (565)
Q Consensus 477 ~k~CPkC~~~IEK~~GCnHMtC-~Cg~-----~FCw~C~~~~~ 513 (565)
.+.||.|+... ....| .||. .||-.|+..-.
T Consensus 626 ~RfCpsCG~~t------~~frCP~CG~~Te~i~fCP~CG~~~~ 662 (1121)
T PRK04023 626 RRKCPSCGKET------FYRRCPFCGTHTEPVYRCPRCGIEVE 662 (1121)
T ss_pred CccCCCCCCcC------CcccCCCCCCCCCcceeCccccCcCC
Confidence 48999999985 55789 4996 49999988755
No 196
>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=47.06 E-value=13 Score=32.39 Aligned_cols=24 Identities=29% Similarity=0.645 Sum_probs=16.3
Q ss_pred cccCCCCceeEecCCcceEEee-cCc
Q 008441 478 RQCVKCNHLIELAEGCFHMTCR-CGH 502 (565)
Q Consensus 478 k~CPkC~~~IEK~~GCnHMtC~-Cg~ 502 (565)
-.||+|..-..-..|=+ +.|. |+|
T Consensus 3 p~CP~C~seytY~dg~~-~iCpeC~~ 27 (109)
T TIGR00686 3 PPCPKCNSEYTYHDGTQ-LICPSCLY 27 (109)
T ss_pred CcCCcCCCcceEecCCe-eECccccc
Confidence 47999998777666643 5553 555
No 197
>PTZ00415 transmission-blocking target antigen s230; Provisional
Probab=46.99 E-value=13 Score=46.32 Aligned_cols=9 Identities=44% Similarity=0.615 Sum_probs=3.8
Q ss_pred CCCCccccC
Q 008441 525 DEDNILDDD 533 (565)
Q Consensus 525 ~~~~~~~~~ 533 (565)
++.|.+.++
T Consensus 147 ~~~~~~~d~ 155 (2849)
T PTZ00415 147 PRDNFVIDD 155 (2849)
T ss_pred cccccccCC
Confidence 344444433
No 198
>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=46.74 E-value=14 Score=28.27 Aligned_cols=47 Identities=21% Similarity=0.513 Sum_probs=32.2
Q ss_pred ccccceeccccccCCceeecCCC--cccchhhHHHHHHHHHhCCCCCCCCCCCCCCccch
Q 008441 308 NETCVICLEDTDVGHMFSIDGCL--HRYCFLCMKKHIEEKLRQGMEPTCPHEGCKSKLEV 365 (565)
Q Consensus 308 ~~~C~IC~e~~~~~~~~~l~~C~--H~fC~~Cl~~~i~~~i~~g~~~kCP~~~C~~~l~~ 365 (565)
...|..|-.+.+....-.. -|. +.||.+|....+.. .||+ |+..|..
T Consensus 5 rpnCE~C~~dLp~~s~~A~-ICSfECTFC~~C~e~~l~~--------~CPN--CgGelv~ 53 (57)
T PF06906_consen 5 RPNCECCDKDLPPDSPEAY-ICSFECTFCADCAETMLNG--------VCPN--CGGELVR 53 (57)
T ss_pred CCCccccCCCCCCCCCcce-EEeEeCcccHHHHHHHhcC--------cCcC--CCCcccc
Confidence 4579999888766542222 354 57999999876622 6997 8887643
No 199
>KOG1493 consensus Anaphase-promoting complex (APC), subunit 11 [Cell cycle control, cell division, chromosome partitioning; Posttranslational modification, protein turnover, chaperones]
Probab=46.65 E-value=3.6 Score=33.41 Aligned_cols=52 Identities=31% Similarity=0.642 Sum_probs=34.1
Q ss_pred ccccceecccccc---------CCc-eeecCCCcccchhhHHHHHHHHHhCCCCCCCCCCCCCCccc
Q 008441 308 NETCVICLEDTDV---------GHM-FSIDGCLHRYCFLCMKKHIEEKLRQGMEPTCPHEGCKSKLE 364 (565)
Q Consensus 308 ~~~C~IC~e~~~~---------~~~-~~l~~C~H~fC~~Cl~~~i~~~i~~g~~~kCP~~~C~~~l~ 364 (565)
..+|+||--.|+. ++. ...--|.|.|...|+.+|+..+-+++ .||- |++...
T Consensus 20 ~e~CGiCRm~Fdg~Cp~Ck~PgDdCPLv~G~C~h~fh~hCI~~wl~~~tsq~---~CPm--cRq~~~ 81 (84)
T KOG1493|consen 20 DETCGICRMPFDGCCPDCKLPGDDCPLVWGYCLHAFHAHCILKWLNTPTSQG---QCPM--CRQTWQ 81 (84)
T ss_pred CCccceEecccCCcCCCCcCCCCCCccHHHHHHHHHHHHHHHHHhcCccccc---cCCc--chheeE
Confidence 3488888766543 121 11124789999999999997665554 6886 777654
No 200
>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=46.65 E-value=11 Score=32.37 Aligned_cols=23 Identities=35% Similarity=0.725 Sum_probs=17.8
Q ss_pred ccCCCCceeEecCCcceEEe-ecCcc
Q 008441 479 QCVKCNHLIELAEGCFHMTC-RCGHE 503 (565)
Q Consensus 479 ~CPkC~~~IEK~~GCnHMtC-~Cg~~ 503 (565)
-||+|+.++...+ +.+.| .|++.
T Consensus 2 fC~~Cg~~l~~~~--~~~~C~~C~~~ 25 (104)
T TIGR01384 2 FCPKCGSLMTPKN--GVYVCPSCGYE 25 (104)
T ss_pred CCcccCcccccCC--CeEECcCCCCc
Confidence 5999999997655 37888 48775
No 201
>KOG1824 consensus TATA-binding protein-interacting protein [General function prediction only]
Probab=46.29 E-value=9.6 Score=44.80 Aligned_cols=15 Identities=20% Similarity=0.494 Sum_probs=8.4
Q ss_pred ccccccc--cccCccCc
Q 008441 549 DVIDEYE--SEFESEEE 563 (565)
Q Consensus 549 ~~~~~~~--~~~~~~~~ 563 (565)
||.|||| ++|+|||.
T Consensus 327 ed~eDde~~deYsDDeD 343 (1233)
T KOG1824|consen 327 EDEEDDEQDDEYSDDED 343 (1233)
T ss_pred hccccchhccccccccc
Confidence 3334444 77777664
No 202
>PF11336 DUF3138: Protein of unknown function (DUF3138); InterPro: IPR021485 This family of proteins with unknown function appear to be restricted to Proteobacteria.
Probab=46.26 E-value=55 Score=35.40 Aligned_cols=59 Identities=19% Similarity=0.347 Sum_probs=33.8
Q ss_pred HhhHHHHHHhhccCCCCCCCCCCCCCCCCCCCCCCCCCCCchhhhcccHHHHHHHHHHHHhHH
Q 008441 40 RLQLQEAISASLAHVPSSSSTSSLPPSTSSAPPPLPHDAASPTLASLQSEELMKLDRELADSR 102 (565)
Q Consensus 40 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 102 (565)
|-||. +|+++|.++|+..++.+...+...++...| +.++-+.+..+++..+.|++...+
T Consensus 38 q~~v~-eL~~~laa~~~aa~~gA~~~~~~~a~~~aP---~~~a~~~~T~d~~~~~~qqiAn~~ 96 (514)
T PF11336_consen 38 QDQVN-ELRAKLAAKPAAAPGGAAIGPAATAAAAAP---SSDAQAGLTNDDATEMRQQIANAQ 96 (514)
T ss_pred HHHHH-HHHHHHhcCCCCCCccccccccccccccCC---CcccccccChHHHHHHHHHHHhhh
Confidence 34444 478889998886544332221101222222 222444899999999988887643
No 203
>KOG1940 consensus Zn-finger protein [General function prediction only]
Probab=46.21 E-value=19 Score=36.77 Aligned_cols=47 Identities=28% Similarity=0.428 Sum_probs=33.8
Q ss_pred cccccceecccccc-CCceeecCCCcccchhhHHHHHHHHHhCCCCCCCCCCCCCC
Q 008441 307 INETCVICLEDTDV-GHMFSIDGCLHRYCFLCMKKHIEEKLRQGMEPTCPHEGCKS 361 (565)
Q Consensus 307 ~~~~C~IC~e~~~~-~~~~~l~~C~H~fC~~Cl~~~i~~~i~~g~~~kCP~~~C~~ 361 (565)
....||||.+.... ......+.|+|..-..|++.++. .+ ..||. |..
T Consensus 157 ~~~ncPic~e~l~~s~~~~~~~~CgH~~h~~cf~e~~~----~~--y~CP~--C~~ 204 (276)
T KOG1940|consen 157 SEFNCPICKEYLFLSFEDAGVLKCGHYMHSRCFEEMIC----EG--YTCPI--CSK 204 (276)
T ss_pred ccCCCchhHHHhccccccCCccCcccchHHHHHHHHhc----cC--CCCCc--ccc
Confidence 34569999987532 33344569999999999988773 34 48997 877
No 204
>PF14803 Nudix_N_2: Nudix N-terminal; PDB: 3CNG_C.
Probab=45.97 E-value=13 Score=25.58 Aligned_cols=31 Identities=19% Similarity=0.489 Sum_probs=15.3
Q ss_pred ccccCCCCCCcccchhhhhccCCCcccccccCceeCCCCCCc
Q 008441 395 VYCPYPKCSALMSKSEIERDASSSSFVGRRLGARKCTKCHRR 436 (565)
Q Consensus 395 ~~CP~p~C~~~i~~~~~~e~~~s~~~~~~~~~~~~C~~C~~~ 436 (565)
+||| .|+..+...- ...+...+..|+.|+..
T Consensus 1 kfC~--~CG~~l~~~i---------p~gd~r~R~vC~~Cg~I 31 (34)
T PF14803_consen 1 KFCP--QCGGPLERRI---------PEGDDRERLVCPACGFI 31 (34)
T ss_dssp -B-T--TT--B-EEE-----------TT-SS-EEEETTTTEE
T ss_pred Cccc--cccChhhhhc---------CCCCCccceECCCCCCE
Confidence 4787 8988764321 22356678999999863
No 205
>KOG0826 consensus Predicted E3 ubiquitin ligase involved in peroxisome organization [Posttranslational modification, protein turnover, chaperones]
Probab=45.85 E-value=5.3 Score=41.36 Aligned_cols=37 Identities=22% Similarity=0.437 Sum_probs=30.3
Q ss_pred cccCCCCceeEecCCcceEEe-ecCccccccccccccCCCCCc
Q 008441 478 RQCVKCNHLIELAEGCFHMTC-RCGHEFCYNCGAEWKNKKATC 519 (565)
Q Consensus 478 k~CPkC~~~IEK~~GCnHMtC-~Cg~~FCw~C~~~~~~~~~~c 519 (565)
-.||-|...++ |--.| .-||-|||.|--.|-.+++.|
T Consensus 301 ~~CpvClk~r~-----Nptvl~vSGyVfCY~Ci~~Yv~~~~~C 338 (357)
T KOG0826|consen 301 EVCPVCLKKRQ-----NPTVLEVSGYVFCYPCIFSYVVNYGHC 338 (357)
T ss_pred ccChhHHhccC-----CCceEEecceEEeHHHHHHHHHhcCCC
Confidence 47999988887 55556 479999999999998877776
No 206
>PRK00420 hypothetical protein; Validated
Probab=45.68 E-value=14 Score=32.67 Aligned_cols=27 Identities=19% Similarity=0.426 Sum_probs=19.9
Q ss_pred cccCCCCceeEe-cCCcceEEeecCcccccccccccc
Q 008441 478 RQCVKCNHLIEL-AEGCFHMTCRCGHEFCYNCGAEWK 513 (565)
Q Consensus 478 k~CPkC~~~IEK-~~GCnHMtC~Cg~~FCw~C~~~~~ 513 (565)
..||.|+.+..+ .. |..||-.|+....
T Consensus 24 ~~CP~Cg~pLf~lk~---------g~~~Cp~Cg~~~~ 51 (112)
T PRK00420 24 KHCPVCGLPLFELKD---------GEVVCPVHGKVYI 51 (112)
T ss_pred CCCCCCCCcceecCC---------CceECCCCCCeee
Confidence 799999999987 43 4566777777643
No 207
>KOG3161 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=45.67 E-value=6.7 Score=43.98 Aligned_cols=34 Identities=29% Similarity=0.366 Sum_probs=25.3
Q ss_pred ccccceeccccccCC--ceeecCCCcccchhhHHHHH
Q 008441 308 NETCVICLEDTDVGH--MFSIDGCLHRYCFLCMKKHI 342 (565)
Q Consensus 308 ~~~C~IC~e~~~~~~--~~~l~~C~H~fC~~Cl~~~i 342 (565)
-..|.||+..+.... +++ +.|||.+|+.|+....
T Consensus 11 ~l~c~ic~n~f~~~~~~Pvs-l~cghtic~~c~~~ly 46 (861)
T KOG3161|consen 11 LLLCDICLNLFVVQRLEPVS-LQCGHTICGHCVQLLY 46 (861)
T ss_pred HhhchHHHHHHHHHhcCccc-ccccchHHHHHHHhHh
Confidence 457999987764433 333 4899999999998755
No 208
>PRK14714 DNA polymerase II large subunit; Provisional
Probab=44.50 E-value=14 Score=45.00 Aligned_cols=30 Identities=37% Similarity=0.854 Sum_probs=22.0
Q ss_pred cccCCCCceeEecCCcceEEe-ecCccc-----ccccccccc
Q 008441 478 RQCVKCNHLIELAEGCFHMTC-RCGHEF-----CYNCGAEWK 513 (565)
Q Consensus 478 k~CPkC~~~IEK~~GCnHMtC-~Cg~~F-----Cw~C~~~~~ 513 (565)
++||+|+..+... .| .||.+. |-.|+....
T Consensus 668 rkCPkCG~~t~~~------fCP~CGs~te~vy~CPsCGaev~ 703 (1337)
T PRK14714 668 RRCPSCGTETYEN------RCPDCGTHTEPVYVCPDCGAEVP 703 (1337)
T ss_pred EECCCCCCccccc------cCcccCCcCCCceeCccCCCccC
Confidence 7999999976432 77 488664 888888654
No 209
>PF03833 PolC_DP2: DNA polymerase II large subunit DP2; InterPro: IPR016033 DP2 is the large subunit of a two-subunit novel archaebacterial replicative DNA polymerase first characterised for Pyrococcus furiosus. The structure of DP2 appears to be organised as a ~950 residue component separated from a ~300 residue component by a ~150 residue intein. The other subunit, DP1, has sequence similarity to the eukaryotic DNA polymerase delta small subunit. This entry represents the N-terminal ~950 residue component of DP2.; GO: 0003887 DNA-directed DNA polymerase activity; PDB: 3O59_X.
Probab=44.11 E-value=7.5 Score=45.23 Aligned_cols=22 Identities=18% Similarity=0.345 Sum_probs=10.9
Q ss_pred HHHHHHhhccCCCCCCCCCCCC
Q 008441 43 LQEAISASLAHVPSSSSTSSLP 64 (565)
Q Consensus 43 ~~~~~~~~~~~~~~~~~~~~~~ 64 (565)
+.-||..+|+....--.++|..
T Consensus 92 ~d~AVRtalAilTEGVVaAPlE 113 (900)
T PF03833_consen 92 IDQAVRTALAILTEGVVAAPLE 113 (900)
T ss_dssp HHHHHHHHHHHHTTT-SSCCCC
T ss_pred HHHHHHHHHHhhcCceEecccc
Confidence 4446666666654444444433
No 210
>TIGR02443 conserved hypothetical metal-binding protein. Members of this family are small proteins, about 70 residues in length, with a basic triplet near the N-terminus and a probable metal-binding motif CPXCX(18)CXXC. Members are found in various Proteobacteria.
Probab=43.88 E-value=21 Score=27.69 Aligned_cols=26 Identities=19% Similarity=0.497 Sum_probs=19.3
Q ss_pred cccCCCCce----eEecCCcceEEe-ecCcc
Q 008441 478 RQCVKCNHL----IELAEGCFHMTC-RCGHE 503 (565)
Q Consensus 478 k~CPkC~~~----IEK~~GCnHMtC-~Cg~~ 503 (565)
-.||+|+.+ .-+..|=.++.| .|||.
T Consensus 10 A~CP~C~~~Dtl~~~~e~~~e~vECv~Cg~~ 40 (59)
T TIGR02443 10 AVCPACSAQDTLAMWKENNIELVECVECGYQ 40 (59)
T ss_pred ccCCCCcCccEEEEEEeCCceEEEeccCCCc
Confidence 469999874 334567789999 49985
No 211
>PRK09710 lar restriction alleviation and modification protein; Reviewed
Probab=43.77 E-value=19 Score=28.43 Aligned_cols=29 Identities=17% Similarity=0.430 Sum_probs=18.9
Q ss_pred CccccCCCCceeEec---CCcceEEe-ecCccc
Q 008441 476 LWRQCVKCNHLIELA---EGCFHMTC-RCGHEF 504 (565)
Q Consensus 476 ~~k~CPkC~~~IEK~---~GCnHMtC-~Cg~~F 504 (565)
..|+||.|+..+.+. +|=....| .|+..-
T Consensus 5 ~lKPCPFCG~~~~~v~~~~g~~~v~C~~CgA~~ 37 (64)
T PRK09710 5 NVKPCPFCGCPSVTVKAISGYYRAKCNGCESRT 37 (64)
T ss_pred cccCCCCCCCceeEEEecCceEEEEcCCCCcCc
Confidence 359999999866543 45445566 477653
No 212
>PLN03086 PRLI-interacting factor K; Provisional
Probab=43.70 E-value=32 Score=38.80 Aligned_cols=27 Identities=30% Similarity=0.855 Sum_probs=23.6
Q ss_pred cccCC--CCceeEecCCcceEEe-ecCccc
Q 008441 478 RQCVK--CNHLIELAEGCFHMTC-RCGHEF 504 (565)
Q Consensus 478 k~CPk--C~~~IEK~~GCnHMtC-~Cg~~F 504 (565)
..||+ |+..+.+...=+|.+| .|+..|
T Consensus 434 V~Cp~~~Cg~v~~r~el~~H~~C~~Cgk~f 463 (567)
T PLN03086 434 VVCPHDGCGIVLRVEEAKNHVHCEKCGQAF 463 (567)
T ss_pred eeCCcccccceeeccccccCccCCCCCCcc
Confidence 68995 9999999999999999 598765
No 213
>KOG2930 consensus SCF ubiquitin ligase, Rbx1 component [Posttranslational modification, protein turnover, chaperones]
Probab=43.63 E-value=9.5 Score=32.88 Aligned_cols=30 Identities=20% Similarity=0.586 Sum_probs=23.2
Q ss_pred cCCCcccchhhHHHHHHHHHhCCCCCCCCCCCCCCccc
Q 008441 327 DGCLHRYCFLCMKKHIEEKLRQGMEPTCPHEGCKSKLE 364 (565)
Q Consensus 327 ~~C~H~fC~~Cl~~~i~~~i~~g~~~kCP~~~C~~~l~ 364 (565)
-.|.|.|...|+.+|++.+. .||- |.+...
T Consensus 79 G~CNHaFH~hCisrWlktr~------vCPL--dn~eW~ 108 (114)
T KOG2930|consen 79 GVCNHAFHFHCISRWLKTRN------VCPL--DNKEWV 108 (114)
T ss_pred eecchHHHHHHHHHHHhhcC------cCCC--cCccee
Confidence 36999999999999997643 6986 555443
No 214
>KOG3895 consensus Synaptic vesicle protein Synapsin [Signal transduction mechanisms; Intracellular trafficking, secretion, and vesicular transport]
Probab=43.62 E-value=6.6 Score=41.08 Aligned_cols=83 Identities=18% Similarity=0.117 Sum_probs=46.2
Q ss_pred CceEEEEEccceeecccCCCCCCCceEEEEEEeCCCCeEEEeeeeccccCCChHHH---HHHHHHHHHHHHHh---cCCC
Q 008441 154 DYFFKVYSKGLVIEELVNGERVSLSAIGVAICDQMDNLIFELKKPLIKSGLNKSAA---ETKALIEGLNAALS---MELD 227 (565)
Q Consensus 154 ~~~~~vyfdGa~~~~~~~~~npg~ag~Gv~i~~~~~~~~~~~~~~~~~~~tn~n~A---Ey~Ali~gL~~al~---l~~~ 227 (565)
.--+.-+.+|++.-. ...-..|.||++..-.-.-|+- +.... ..| .|+.|+.||+.|-= +...
T Consensus 125 eLnl~a~~~g~~~vd----m~V~rNg~kvv~RsfkPdfVli------rqhA~-~mA~~~d~rslvig~qyagiP~vNSl~ 193 (488)
T KOG3895|consen 125 ELNLVAHAKGGCMVD----MQVLRNGTKVVVRSFKPDFVLI------RQHAF-SMALNEDYRSLVIGLQYAGIPSVNSLT 193 (488)
T ss_pred hheeeeeccCceeEE----EEEEecCcceeeeeccCCEEEE------cccch-hhccccchHHHHHHHHhcCCcccchhH
Confidence 344566778876441 1223456677766554343322 22112 144 79999999987631 2234
Q ss_pred eEEeecCCccchhhccCccC
Q 008441 228 RVRVFIDCFPLFQFVTGRWP 247 (565)
Q Consensus 228 ~v~v~~DS~lv~~qv~G~w~ 247 (565)
.+.-|+|-..|+.|+...+.
T Consensus 194 SvynFcdkpwvf~Qlvki~~ 213 (488)
T KOG3895|consen 194 SVYNFCDKPWVFAQLVKITK 213 (488)
T ss_pred HHHHhccchHHHHHHHHHHH
Confidence 45557777777777654333
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=43.14 E-value=23 Score=23.14 Aligned_cols=20 Identities=25% Similarity=0.630 Sum_probs=13.5
Q ss_pred ccCCCCceeEecCCcceEEe
Q 008441 479 QCVKCNHLIELAEGCFHMTC 498 (565)
Q Consensus 479 ~CPkC~~~IEK~~GCnHMtC 498 (565)
.||.|+..+.+.+|=-++.|
T Consensus 1 ~CP~C~s~l~~~~~ev~~~C 20 (28)
T PF03119_consen 1 TCPVCGSKLVREEGEVDIRC 20 (28)
T ss_dssp B-TTT--BEEE-CCTTCEEE
T ss_pred CcCCCCCEeEcCCCCEeEEC
Confidence 49999999999988777777
No 216
>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=42.14 E-value=13 Score=33.44 Aligned_cols=26 Identities=15% Similarity=0.161 Sum_probs=17.6
Q ss_pred cccCCCCceeEecCCcceEEe-ecCccc
Q 008441 478 RQCVKCNHLIELAEGCFHMTC-RCGHEF 504 (565)
Q Consensus 478 k~CPkC~~~IEK~~GCnHMtC-~Cg~~F 504 (565)
+.||+|+..+---.- +-++| +||+.|
T Consensus 10 r~Cp~cg~kFYDLnk-~p~vcP~cg~~~ 36 (129)
T TIGR02300 10 RICPNTGSKFYDLNR-RPAVSPYTGEQF 36 (129)
T ss_pred ccCCCcCccccccCC-CCccCCCcCCcc
Confidence 679999887543222 67888 577764
No 217
>TIGR00599 rad18 DNA repair protein rad18. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=41.65 E-value=9 Score=41.29 Aligned_cols=37 Identities=22% Similarity=0.666 Sum_probs=24.4
Q ss_pred cccCCCCceeEecCCcceEEeecCccccccccccccCCCCCc
Q 008441 478 RQCVKCNHLIELAEGCFHMTCRCGHEFCYNCGAEWKNKKATC 519 (565)
Q Consensus 478 k~CPkC~~~IEK~~GCnHMtC~Cg~~FCw~C~~~~~~~~~~c 519 (565)
-.||-|.-.+. +.++=.|||.||+.|...|......|
T Consensus 27 l~C~IC~d~~~-----~PvitpCgH~FCs~CI~~~l~~~~~C 63 (397)
T TIGR00599 27 LRCHICKDFFD-----VPVLTSCSHTFCSLCIRRCLSNQPKC 63 (397)
T ss_pred cCCCcCchhhh-----CccCCCCCCchhHHHHHHHHhCCCCC
Confidence 58999987653 22221488888888888776555433
No 218
>PF11014 DUF2852: Protein of unknown function (DUF2852); InterPro: IPR021273 This bacterial family of proteins has no known function.
Probab=40.71 E-value=66 Score=28.50 Aligned_cols=33 Identities=12% Similarity=0.274 Sum_probs=23.1
Q ss_pred CCCchhhhcccHHHHHHHHHHHHhHHHHHHHHHHHH
Q 008441 77 DAASPTLASLQSEELMKLDRELADSRQAKLEMQKAR 112 (565)
Q Consensus 77 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 112 (565)
++++.+.-+-+.++|+|||.|.+ .=+.+++++|
T Consensus 66 ~sGN~AFD~YR~~tL~RLEeEq~---eF~~Fl~rLR 98 (115)
T PF11014_consen 66 SSGNAAFDEYREDTLRRLEEEQR---EFEDFLERLR 98 (115)
T ss_pred CCcchhHHHHHHHHHHHHHHHHH---HHHHHHHHHH
Confidence 35566666899999999998877 4444444443
No 219
>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=40.40 E-value=25 Score=26.86 Aligned_cols=27 Identities=33% Similarity=0.669 Sum_probs=19.4
Q ss_pred cccCCCCceeEecCCc--ceEEee-cCccc
Q 008441 478 RQCVKCNHLIELAEGC--FHMTCR-CGHEF 504 (565)
Q Consensus 478 k~CPkC~~~IEK~~GC--nHMtC~-Cg~~F 504 (565)
..||.|+..|+....= -.+.|. ||..|
T Consensus 3 ~~CP~CG~~iev~~~~~GeiV~Cp~CGael 32 (54)
T TIGR01206 3 FECPDCGAEIELENPELGELVICDECGAEL 32 (54)
T ss_pred cCCCCCCCEEecCCCccCCEEeCCCCCCEE
Confidence 4799999999986532 367784 77765
No 220
>PF01428 zf-AN1: AN1-like Zinc finger; InterPro: IPR000058 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents the AN1-type zinc finger domain, which has a dimetal (zinc)-bound alpha/beta fold. This domain was first identified as a zinc finger at the C terminus of AN1 Q91889 from SWISSPROT, a ubiquitin-like protein in Xenopus laevis []. The AN1-type zinc finger contains six conserved cysteines and two histidines that could potentially coordinate 2 zinc atoms. Certain stress-associated proteins (SAP) contain AN1 domain, often in combination with A20 zinc finger domains (SAP8) or C2H2 domains (SAP16) []. For example, the human protein Znf216 has an A20 zinc-finger at the N terminus and an AN1 zinc-finger at the C terminus, acting to negatively regulate the NFkappaB activation pathway and to interact with components of the immune response like RIP, IKKgamma and TRAF6. The interact of Znf216 with IKK-gamma and RIP is mediated by the A20 zinc-finger domain, while its interaction with TRAF6 is mediated by the AN1 zinc-finger domain; therefore, both zinc-finger domains are involved in regulating the immune response []. The AN1 zinc finger domain is also found in proteins containing a ubiquitin-like domain, which are involved in the ubiquitination pathway []. Proteins containing an AN1-type zinc finger include: Ascidian posterior end mark 6 (pem-6) protein []. Human AWP1 protein (associated with PRK1), which is expressed during early embryogenesis []. Human immunoglobulin mu binding protein 2 (SMUBP-2), mutations in which cause muscular atrophy with respiratory distress type 1 []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 1WFP_A 1WYS_A 1WG2_A 1WFH_A 1X4W_A 1WFE_A 1WFL_A 1X4V_A.
Probab=40.01 E-value=20 Score=25.76 Aligned_cols=19 Identities=32% Similarity=0.934 Sum_probs=13.6
Q ss_pred CceeCCCCCCceecccCCC
Q 008441 426 GARKCTKCHRRFCIDCKVP 444 (565)
Q Consensus 426 ~~~~C~~C~~~fC~~C~~~ 444 (565)
..+.|+.|+..||...+.+
T Consensus 12 ~~~~C~~C~~~FC~~Hr~~ 30 (43)
T PF01428_consen 12 LPFKCKHCGKSFCLKHRLP 30 (43)
T ss_dssp SHEE-TTTS-EE-TTTHST
T ss_pred CCeECCCCCcccCccccCc
Confidence 4689999999999998875
No 221
>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=39.88 E-value=15 Score=27.75 Aligned_cols=17 Identities=18% Similarity=0.655 Sum_probs=9.4
Q ss_pred CceeecCCCcccchhhH
Q 008441 322 HMFSIDGCLHRYCFLCM 338 (565)
Q Consensus 322 ~~~~l~~C~H~fC~~Cl 338 (565)
..+....|++.||.+|=
T Consensus 20 ~~y~C~~C~~~FC~dCD 36 (51)
T PF07975_consen 20 SRYRCPKCKNHFCIDCD 36 (51)
T ss_dssp EEE--TTTT--B-HHHH
T ss_pred CeEECCCCCCccccCcC
Confidence 34667789999999994
No 222
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=39.79 E-value=63 Score=29.75 Aligned_cols=36 Identities=19% Similarity=0.449 Sum_probs=21.2
Q ss_pred CCcccccCCCCCCcccchhhhhccCCCcccccccCceeCCCCCCc
Q 008441 392 TEKVYCPYPKCSALMSKSEIERDASSSSFVGRRLGARKCTKCHRR 436 (565)
Q Consensus 392 ~~~~~CP~p~C~~~i~~~~~~e~~~s~~~~~~~~~~~~C~~C~~~ 436 (565)
.....|| .|+.-+...+.... .. ....+.||.||..
T Consensus 97 ~~~Y~Cp--~C~~~y~~~ea~~~------~d-~~~~f~Cp~Cg~~ 132 (147)
T smart00531 97 NAYYKCP--NCQSKYTFLEANQL------LD-MDGTFTCPRCGEE 132 (147)
T ss_pred CcEEECc--CCCCEeeHHHHHHh------cC-CCCcEECCCCCCE
Confidence 3456798 78877765443211 01 1345889888764
No 223
>KOG1571 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=39.61 E-value=20 Score=37.73 Aligned_cols=44 Identities=27% Similarity=0.751 Sum_probs=28.1
Q ss_pred ccccccceeccccccCCceeecCCCcccchhhHHHHHHHHHhCCCCCCCCCCCCCCcc
Q 008441 306 TINETCVICLEDTDVGHMFSIDGCLHRYCFLCMKKHIEEKLRQGMEPTCPHEGCKSKL 363 (565)
Q Consensus 306 ~~~~~C~IC~e~~~~~~~~~l~~C~H~fC~~Cl~~~i~~~i~~g~~~kCP~~~C~~~l 363 (565)
.....|.||.++.. +. ...+|||..| |..-+- ..++||. |...|
T Consensus 303 ~~p~lcVVcl~e~~--~~-~fvpcGh~cc--ct~cs~-------~l~~CPv--CR~rI 346 (355)
T KOG1571|consen 303 PQPDLCVVCLDEPK--SA-VFVPCGHVCC--CTLCSK-------HLPQCPV--CRQRI 346 (355)
T ss_pred CCCCceEEecCCcc--ce-eeecCCcEEE--chHHHh-------hCCCCch--hHHHH
Confidence 34578999998853 33 3449999966 543221 1357997 86554
No 224
>PF09526 DUF2387: Probable metal-binding protein (DUF2387); InterPro: IPR012658 Members of this family are small proteins, about 70 residues in length, with a basic triplet near the N terminus and a probable metal-binding motif CPXCX(18)CXXC. Members are found in various proteobacteria.
Probab=39.57 E-value=27 Score=28.21 Aligned_cols=26 Identities=27% Similarity=0.662 Sum_probs=19.5
Q ss_pred cccCCCCce----eEecCCcceEEe-ecCcc
Q 008441 478 RQCVKCNHL----IELAEGCFHMTC-RCGHE 503 (565)
Q Consensus 478 k~CPkC~~~----IEK~~GCnHMtC-~Cg~~ 503 (565)
-.||+|+.+ .-+..|=.++.| .|||.
T Consensus 9 a~CP~C~~~D~i~~~~e~~ve~vECV~CGy~ 39 (71)
T PF09526_consen 9 AVCPKCQAMDTIMMWRENGVEYVECVECGYT 39 (71)
T ss_pred ccCCCCcCccEEEEEEeCCceEEEecCCCCe
Confidence 369999874 334567889999 49984
No 225
>COG5109 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=39.49 E-value=23 Score=36.55 Aligned_cols=55 Identities=16% Similarity=0.156 Sum_probs=37.4
Q ss_pred cccccceeccccccCCceeecCCCcccchhhHHHHHHHHHhCCC-CCCCCCCCCCCccchhh
Q 008441 307 INETCVICLEDTDVGHMFSIDGCLHRYCFLCMKKHIEEKLRQGM-EPTCPHEGCKSKLEVES 367 (565)
Q Consensus 307 ~~~~C~IC~e~~~~~~~~~l~~C~H~fC~~Cl~~~i~~~i~~g~-~~kCP~~~C~~~l~~~~ 367 (565)
..+.||+=-+.-...++..++.|||.+=+.=+...- ++|. .++||. |...-....
T Consensus 335 s~FiCPVlKe~~t~ENpP~ml~CgHVIskeal~~LS----~nG~~~FKCPY--CP~~~~~~~ 390 (396)
T COG5109 335 SLFICPVLKELCTDENPPVMLECGHVISKEALSVLS----QNGVLSFKCPY--CPEMSKYEN 390 (396)
T ss_pred ceeeccccHhhhcccCCCeeeeccceeeHHHHHHHh----hcCcEEeeCCC--CCcchhhhh
Confidence 468999977766666777777999999777665433 3443 368887 765544433
No 226
>PRK10220 hypothetical protein; Provisional
Probab=39.27 E-value=21 Score=31.14 Aligned_cols=30 Identities=27% Similarity=0.718 Sum_probs=19.1
Q ss_pred cccCCCCceeEecCCcceEEeecCccccccccccccCC
Q 008441 478 RQCVKCNHLIELAEGCFHMTCRCGHEFCYNCGAEWKNK 515 (565)
Q Consensus 478 k~CPkC~~~IEK~~GCnHMtC~Cg~~FCw~C~~~~~~~ 515 (565)
-.||+|..-..-..|= .+.| -.|+.+|...
T Consensus 4 P~CP~C~seytY~d~~-~~vC-------peC~hEW~~~ 33 (111)
T PRK10220 4 PHCPKCNSEYTYEDNG-MYIC-------PECAHEWNDA 33 (111)
T ss_pred CcCCCCCCcceEcCCC-eEEC-------CcccCcCCcc
Confidence 5799999877766663 3555 3444466644
No 227
>KOG2462 consensus C2H2-type Zn-finger protein [Transcription]
Probab=39.01 E-value=33 Score=34.94 Aligned_cols=13 Identities=23% Similarity=0.552 Sum_probs=7.3
Q ss_pred cCceeCCCCCCce
Q 008441 425 LGARKCTKCHRRF 437 (565)
Q Consensus 425 ~~~~~C~~C~~~f 437 (565)
...+.|+.|++.+
T Consensus 159 ~ka~~C~~C~K~Y 171 (279)
T KOG2462|consen 159 KKAFSCKYCGKVY 171 (279)
T ss_pred cccccCCCCCcee
Confidence 4455666666543
No 228
>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional
Probab=38.69 E-value=19 Score=27.88 Aligned_cols=35 Identities=26% Similarity=0.643 Sum_probs=22.7
Q ss_pred cccCCCCceeEecCCcceEEe-ecCcc---ccccccccc
Q 008441 478 RQCVKCNHLIELAEGCFHMTC-RCGHE---FCYNCGAEW 512 (565)
Q Consensus 478 k~CPkC~~~IEK~~GCnHMtC-~Cg~~---FCw~C~~~~ 512 (565)
..|-.|+..|.-.+..-+..| .||.. =|..|.+.-
T Consensus 8 ~~CtSCg~~i~~~~~~~~F~CPnCG~~~I~RC~~CRk~~ 46 (59)
T PRK14890 8 PKCTSCGIEIAPREKAVKFLCPNCGEVIIYRCEKCRKQS 46 (59)
T ss_pred ccccCCCCcccCCCccCEeeCCCCCCeeEeechhHHhcC
Confidence 357777777766665677777 47766 355565553
No 229
>COG5194 APC11 Component of SCF ubiquitin ligase and anaphase-promoting complex [Posttranslational modification, protein turnover, chaperones / Cell division and chromosome partitioning]
Probab=38.60 E-value=23 Score=29.21 Aligned_cols=49 Identities=22% Similarity=0.434 Sum_probs=30.5
Q ss_pred ccccceeccccccC-C-ceeecCCCcccchhhHHHHHHHHHhCCCCCCCCCCCCCCccc
Q 008441 308 NETCVICLEDTDVG-H-MFSIDGCLHRYCFLCMKKHIEEKLRQGMEPTCPHEGCKSKLE 364 (565)
Q Consensus 308 ~~~C~IC~e~~~~~-~-~~~l~~C~H~fC~~Cl~~~i~~~i~~g~~~kCP~~~C~~~l~ 364 (565)
..+|+-|.-..... + ++.--.|.|.|...|+.+|+..+ + .||- +++...
T Consensus 31 m~~C~eCq~~~~~~~eC~v~wG~CnHaFH~HCI~rWL~Tk---~---~CPl--d~q~w~ 81 (88)
T COG5194 31 MGTCPECQFGMTPGDECPVVWGVCNHAFHDHCIYRWLDTK---G---VCPL--DRQTWV 81 (88)
T ss_pred cCcCcccccCCCCCCcceEEEEecchHHHHHHHHHHHhhC---C---CCCC--CCceeE
Confidence 45666665422222 2 22233699999999999999762 2 5886 665544
No 230
>PF15295 CCDC50_N: Coiled-coil domain-containing protein 50 N-terminus
Probab=38.47 E-value=71 Score=29.01 Aligned_cols=23 Identities=43% Similarity=0.385 Sum_probs=18.3
Q ss_pred hccccchhhHHhhHHHHHHhhccC
Q 008441 30 SVESDLDFAFRLQLQEAISASLAH 53 (565)
Q Consensus 30 ~~~~~~~~~~~~~~~~~~~~~~~~ 53 (565)
+|-.|..|||+||=+| |..=+++
T Consensus 22 ~V~EDgaLA~~LQeqE-Ie~hy~~ 44 (132)
T PF15295_consen 22 AVLEDGALAHRLQEQE-IEHHYAS 44 (132)
T ss_pred HHhhhHHHHHHHHHHH-HHHHHHh
Confidence 4557999999999999 6666654
No 231
>PF14446 Prok-RING_1: Prokaryotic RING finger family 1
Probab=38.28 E-value=29 Score=26.51 Aligned_cols=34 Identities=18% Similarity=0.301 Sum_probs=28.2
Q ss_pred cccccceeccccc-cCCceeecCCCcccchhhHHH
Q 008441 307 INETCVICLEDTD-VGHMFSIDGCLHRYCFLCMKK 340 (565)
Q Consensus 307 ~~~~C~IC~e~~~-~~~~~~l~~C~H~fC~~Cl~~ 340 (565)
....|++|-+.+. ..+++....|+-.+.++||..
T Consensus 4 ~~~~C~~Cg~~~~~~dDiVvCp~CgapyHR~C~~~ 38 (54)
T PF14446_consen 4 EGCKCPVCGKKFKDGDDIVVCPECGAPYHRDCWEK 38 (54)
T ss_pred cCccChhhCCcccCCCCEEECCCCCCcccHHHHhh
Confidence 3567999999885 567788889999999999964
No 232
>PF12677 DUF3797: Domain of unknown function (DUF3797); InterPro: IPR024256 This presumed domain is functionally uncharacterised. This domain family is found in bacteria and viruses, and is approximately 50 amino acids in length. There is a conserved CGN sequence motif.
Probab=38.20 E-value=28 Score=25.88 Aligned_cols=27 Identities=30% Similarity=0.704 Sum_probs=18.6
Q ss_pred ccccCCCCceeEecC--------CcceEEeecCcc
Q 008441 477 WRQCVKCNHLIELAE--------GCFHMTCRCGHE 503 (565)
Q Consensus 477 ~k~CPkC~~~IEK~~--------GCnHMtC~Cg~~ 503 (565)
+-.||+|+.-..-++ .=.+=+|+||..
T Consensus 13 Y~~Cp~CGN~~vGngEG~liV~edtfkRtCkCGfn 47 (49)
T PF12677_consen 13 YCKCPKCGNDKVGNGEGTLIVEEDTFKRTCKCGFN 47 (49)
T ss_pred hccCcccCCcEeecCcceEEEeccceeeeeccccc
Confidence 468999998766654 234556888764
No 233
>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=38.17 E-value=18 Score=31.72 Aligned_cols=9 Identities=33% Similarity=0.774 Sum_probs=4.8
Q ss_pred ceeCCCCCC
Q 008441 427 ARKCTKCHR 435 (565)
Q Consensus 427 ~~~C~~C~~ 435 (565)
.+.||+||.
T Consensus 26 PivCP~CG~ 34 (108)
T PF09538_consen 26 PIVCPKCGT 34 (108)
T ss_pred CccCCCCCC
Confidence 355665554
No 234
>KOG3970 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=38.00 E-value=26 Score=34.49 Aligned_cols=55 Identities=18% Similarity=0.489 Sum_probs=39.6
Q ss_pred ccccceeccccccCCceeecCCCcccchhhHHHHHHHHHhCCCC--CCCCCCCCCCccch
Q 008441 308 NETCVICLEDTDVGHMFSIDGCLHRYCFLCMKKHIEEKLRQGME--PTCPHEGCKSKLEV 365 (565)
Q Consensus 308 ~~~C~IC~e~~~~~~~~~l~~C~H~fC~~Cl~~~i~~~i~~g~~--~kCP~~~C~~~l~~ 365 (565)
...|..|-.+....+.+.+ .|-|.|.-.|+..+...--.+... ..||. |..+|-+
T Consensus 50 ~pNC~LC~t~La~gdt~RL-vCyhlfHW~ClneraA~lPanTAPaGyqCP~--Cs~eiFP 106 (299)
T KOG3970|consen 50 NPNCRLCNTPLASGDTTRL-VCYHLFHWKCLNERAANLPANTAPAGYQCPC--CSQEIFP 106 (299)
T ss_pred CCCCceeCCccccCcceee-hhhhhHHHHHhhHHHhhCCCcCCCCcccCCC--CCCccCC
Confidence 5689999888777777666 899999999999876442222211 37996 8887643
No 235
>PF09723 Zn-ribbon_8: Zinc ribbon domain; InterPro: IPR013429 This entry represents a region of about 41 amino acids found in a number of small proteins in a wide range of bacteria. The region usually begins with the initiator Met and contains two CxxC motifs separated by 17 amino acids. One protein in this entry has been noted as a putative regulatory protein, designated FmdB []. Most proteins in this entry have a C-terminal region containing highly degenerate sequence.
Probab=37.99 E-value=35 Score=24.40 Aligned_cols=12 Identities=17% Similarity=0.526 Sum_probs=7.9
Q ss_pred cccCCCCc-eeEe
Q 008441 478 RQCVKCNH-LIEL 489 (565)
Q Consensus 478 k~CPkC~~-~IEK 489 (565)
..||+|+. .++|
T Consensus 27 ~~CP~Cg~~~~~r 39 (42)
T PF09723_consen 27 VPCPECGSTEVRR 39 (42)
T ss_pred CcCCCCCCCceEE
Confidence 56888777 5554
No 236
>PRK03564 formate dehydrogenase accessory protein FdhE; Provisional
Probab=37.84 E-value=21 Score=37.14 Aligned_cols=14 Identities=29% Similarity=0.657 Sum_probs=9.7
Q ss_pred CceecccCCCcCCC
Q 008441 435 RRFCIDCKVPWHNN 448 (565)
Q Consensus 435 ~~fC~~C~~~~H~g 448 (565)
+..|..|...||..
T Consensus 212 yL~CslC~teW~~~ 225 (309)
T PRK03564 212 YLHCNLCESEWHVV 225 (309)
T ss_pred EEEcCCCCCccccc
Confidence 44667777888864
No 237
>KOG4275 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=37.63 E-value=6.7 Score=39.94 Aligned_cols=30 Identities=27% Similarity=0.648 Sum_probs=22.6
Q ss_pred ccccceeccccccCCceeecCCCcc-cchhhHHH
Q 008441 308 NETCVICLEDTDVGHMFSIDGCLHR-YCFLCMKK 340 (565)
Q Consensus 308 ~~~C~IC~e~~~~~~~~~l~~C~H~-fC~~Cl~~ 340 (565)
...|.||++- +.+.|-+ .|||. -|..|-+.
T Consensus 300 ~~LC~ICmDa--P~DCvfL-eCGHmVtCt~CGkr 330 (350)
T KOG4275|consen 300 RRLCAICMDA--PRDCVFL-ECGHMVTCTKCGKR 330 (350)
T ss_pred HHHHHHHhcC--CcceEEe-ecCcEEeehhhccc
Confidence 6789999975 3455544 99996 78888654
No 238
>KOG0827 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=37.60 E-value=8.8 Score=40.62 Aligned_cols=131 Identities=23% Similarity=0.222 Sum_probs=68.9
Q ss_pred HHHHHHHHHHHHHhcC-CCeEEeecCCccchhhccCccCCcchhhHHHHHHHHHHhhhccccccccccccchHHHHHHHH
Q 008441 210 ETKALIEGLNAALSME-LDRVRVFIDCFPLFQFVTGRWPAKQRKISVLVDQVSLLEKRFSYFKPRHVARNDMKYVYELAR 288 (565)
Q Consensus 210 Ey~Ali~gL~~al~l~-~~~v~v~~DS~lv~~qv~G~w~~k~~~l~~l~~~v~~Ll~~F~~~~~~~V~R~~n~~Ad~LA~ 288 (565)
+..|.+.|+..|+..- ...=.+.-|++.+.++ ++....+.+....|+......+. +.--..+-...+++
T Consensus 115 ~~~a~vv~~~~al~ki~~~~~~Lk~~~~~l~q~--------~~et~~lqE~~~~L~~~~~~~~~--~~lls~~~~~~~~e 184 (465)
T KOG0827|consen 115 DTIAIVVGKIGALKKIVVYSGDLKEDFQDLKQF--------DPETLELQENPSDLLISHEYIFG--AALLSIKCFFQTAE 184 (465)
T ss_pred HHHHHHHHHHHHhhhHHHhHHHHHHHHHHHHhh--------CHHHHHHHHhHHHHHHHHHHHHH--HHHHHHHHHHHHHH
Confidence 4667777777666321 1111112334444442 34444555555555444443211 11111122334555
Q ss_pred HhhhcccccccccccCcccccccceeccccccC-CceeecCCCcccchhhHHHHHHHHHhCCCCCCCCCCCCCCccchh
Q 008441 289 AAINSQMTVPAEISRGKTINETCVICLEDTDVG-HMFSIDGCLHRYCFLCMKKHIEEKLRQGMEPTCPHEGCKSKLEVE 366 (565)
Q Consensus 289 eal~sqi~~~~~~~~~~~~~~~C~IC~e~~~~~-~~~~l~~C~H~fC~~Cl~~~i~~~i~~g~~~kCP~~~C~~~l~~~ 366 (565)
.+..++. .......|.||++.+... .-..-..|||.+-.+|+.+++..+- +||. |..+++..
T Consensus 185 ~~~t~~~--------~~slv~sl~I~~~slK~~y~k~~~~~~g~~~~~~kL~k~L~~~~------kl~~--~~rel~~~ 247 (465)
T KOG0827|consen 185 HWMTSQP--------TSSLVGSLSICFESLKQNYDKISAIVCGHIYHHGKLSKWLATKR------KLPS--CRRELPKN 247 (465)
T ss_pred HHhhcCc--------hHHHHhhhHhhHHHHHHHHHHHHHHhhcccchhhHHHHHHHHHH------HhHH--HHhhhhhh
Confidence 5554443 333467899999875332 1223348999999999999997632 5653 66666544
No 239
>KOG0825 consensus PHD Zn-finger protein [General function prediction only]
Probab=37.33 E-value=21 Score=41.22 Aligned_cols=44 Identities=11% Similarity=0.289 Sum_probs=27.8
Q ss_pred cccccceecccccc----CCceeecCCCcccchhhHHHHHHHHHhCCC
Q 008441 307 INETCVICLEDTDV----GHMFSIDGCLHRYCFLCMKKHIEEKLRQGM 350 (565)
Q Consensus 307 ~~~~C~IC~e~~~~----~~~~~l~~C~H~fC~~Cl~~~i~~~i~~g~ 350 (565)
...+|.+|.-++.. .....+..|+|.+|..||+.|...-+....
T Consensus 95 ~s~Ss~~C~~E~S~~~ds~~i~P~~~~~~~~CP~Ci~s~~DqL~~~~k 142 (1134)
T KOG0825|consen 95 ESDTSPVCEKEHSPDVDSSNICPVQTHVENQCPNCLKSCNDQLEESEK 142 (1134)
T ss_pred cccccchhheecCCcccccCcCchhhhhhhhhhHHHHHHHHHhhcccc
Confidence 44566666555432 122223459999999999999876654443
No 240
>PF05129 Elf1: Transcription elongation factor Elf1 like; InterPro: IPR007808 This family of uncharacterised, mostly short, proteins contain a putative zinc binding domain with four conserved cysteines.; PDB: 1WII_A.
Probab=37.00 E-value=20 Score=29.65 Aligned_cols=27 Identities=41% Similarity=0.832 Sum_probs=14.9
Q ss_pred cccCCCC----ce--eEecCCcceEEee-cCccc
Q 008441 478 RQCVKCN----HL--IELAEGCFHMTCR-CGHEF 504 (565)
Q Consensus 478 k~CPkC~----~~--IEK~~GCnHMtC~-Cg~~F 504 (565)
-.||.|+ +. |.+..|=-+++|. ||..|
T Consensus 23 F~CPfC~~~~sV~v~idkk~~~~~~~C~~Cg~~~ 56 (81)
T PF05129_consen 23 FDCPFCNHEKSVSVKIDKKEGIGILSCRVCGESF 56 (81)
T ss_dssp ---TTT--SS-EEEEEETTTTEEEEEESSS--EE
T ss_pred EcCCcCCCCCeEEEEEEccCCEEEEEecCCCCeE
Confidence 5899999 33 4445688899994 87766
No 241
>KOG3053 consensus Uncharacterized conserved protein [Function unknown]
Probab=36.96 E-value=25 Score=35.28 Aligned_cols=58 Identities=21% Similarity=0.574 Sum_probs=38.8
Q ss_pred CcccccccceeccccccCCce-eecCCC-----cccchhhHHHHHHHHHhCC--CCCCCCCCCCCCcc
Q 008441 304 GKTINETCVICLEDTDVGHMF-SIDGCL-----HRYCFLCMKKHIEEKLRQG--MEPTCPHEGCKSKL 363 (565)
Q Consensus 304 ~~~~~~~C~IC~e~~~~~~~~-~l~~C~-----H~fC~~Cl~~~i~~~i~~g--~~~kCP~~~C~~~l 363 (565)
+......|-|||.+......- -+.+|. |.....|+..|+..+-... ..+.||+ |..+.
T Consensus 16 ~~e~eR~CWiCF~TdeDn~~a~WV~PCrCRGt~KWVHqsCL~rWiDEK~~~n~~q~V~C~Q--CqTEY 81 (293)
T KOG3053|consen 16 NQELERCCWICFATDEDNRLAAWVHPCRCRGTTKWVHQSCLSRWIDEKQRGNPLQTVSCPQ--CQTEY 81 (293)
T ss_pred ccccceeEEEEeccCcccchhhhcccccccCccHHHHHHHHHHHHhHHhcCCCCceeechh--hcchh
Confidence 344567899999875332211 133665 6799999999998876522 2358998 88754
No 242
>PRK11827 hypothetical protein; Provisional
Probab=36.73 E-value=27 Score=27.30 Aligned_cols=25 Identities=16% Similarity=0.308 Sum_probs=18.7
Q ss_pred cccCCCCceeEecCCcceEEee-cCc
Q 008441 478 RQCVKCNHLIELAEGCFHMTCR-CGH 502 (565)
Q Consensus 478 k~CPkC~~~IEK~~GCnHMtC~-Cg~ 502 (565)
-.||.|+...+-..+=+...|+ ||-
T Consensus 9 LaCP~ckg~L~~~~~~~~Lic~~~~l 34 (60)
T PRK11827 9 IACPVCNGKLWYNQEKQELICKLDNL 34 (60)
T ss_pred eECCCCCCcCeEcCCCCeEECCccCe
Confidence 5799999998877665677773 554
No 243
>cd01284 Riboflavin_deaminase-reductase Riboflavin-specific deaminase. Riboflavin biosynthesis protein RibD (Diaminohydroxyphosphoribosylaminopyrimidine deaminase) catalyzes the deamination of 2,5-diamino-6-ribosylamino-4(3H)-pyrimidinone 5'-phosphate, which is an intermediate step in the biosynthesis of riboflavin.The ribG gene of Bacillus subtilis and the ribD gene of E. coli are bifunctional and contain this deaminase domain and a reductase domain which catalyzes the subsequent reduction of the ribosyl side chain.
Probab=36.13 E-value=1.1e+02 Score=27.06 Aligned_cols=41 Identities=22% Similarity=0.189 Sum_probs=27.6
Q ss_pred CCceEEEEEEeCCCCeEEEeeeeccccCCChHHHHHHHHHHHHHH
Q 008441 176 SLSAIGVAICDQMDNLIFELKKPLIKSGLNKSAAETKALIEGLNA 220 (565)
Q Consensus 176 g~ag~Gv~i~~~~~~~~~~~~~~~~~~~tn~n~AEy~Ali~gL~~ 220 (565)
+...+|.+|++++|++|.+..... ..+ .-||..||..+.+.
T Consensus 17 ~~~pvGaviv~~~g~iv~~g~n~~--~~~--~HAE~~ai~~a~~~ 57 (115)
T cd01284 17 PNPPVGCVIVDDDGEIVGEGYHRK--AGG--PHAEVNALASAGEK 57 (115)
T ss_pred CCCCEEEEEEeCCCeEEEEecCCC--CCc--ccHHHHHHHHHhhc
Confidence 345688999987787775544444 233 46999998877653
No 244
>KOG2114 consensus Vacuolar assembly/sorting protein PEP5/VPS11 [Intracellular trafficking, secretion, and vesicular transport]
Probab=35.83 E-value=28 Score=40.63 Aligned_cols=41 Identities=29% Similarity=0.587 Sum_probs=29.3
Q ss_pred ccccceeccccccCCceeecCCCcccchhhHHHHHHHHHhCCCCCCCCCCCCCC
Q 008441 308 NETCVICLEDTDVGHMFSIDGCLHRYCFLCMKKHIEEKLRQGMEPTCPHEGCKS 361 (565)
Q Consensus 308 ~~~C~IC~e~~~~~~~~~l~~C~H~fC~~Cl~~~i~~~i~~g~~~kCP~~~C~~ 361 (565)
.-.|..|--+.+ -++.-..|+|.|...|+. + ..-+||. |.-
T Consensus 840 ~skCs~C~~~Ld--lP~VhF~CgHsyHqhC~e--------~-~~~~CP~--C~~ 880 (933)
T KOG2114|consen 840 VSKCSACEGTLD--LPFVHFLCGHSYHQHCLE--------D-KEDKCPK--CLP 880 (933)
T ss_pred eeeecccCCccc--cceeeeecccHHHHHhhc--------c-CcccCCc--cch
Confidence 468999986654 344445799999999998 2 2237986 865
No 245
>KOG0309 consensus Conserved WD40 repeat-containing protein [Function unknown]
Probab=35.75 E-value=23 Score=40.75 Aligned_cols=49 Identities=29% Similarity=0.510 Sum_probs=33.6
Q ss_pred cccccccceeccccccCCceeecCCCcccchhhHHHHHHHHHhCCCCCCCCCCCCCC
Q 008441 305 KTINETCVICLEDTDVGHMFSIDGCLHRYCFLCMKKHIEEKLRQGMEPTCPHEGCKS 361 (565)
Q Consensus 305 ~~~~~~C~IC~e~~~~~~~~~l~~C~H~fC~~Cl~~~i~~~i~~g~~~kCP~~~C~~ 361 (565)
....+.|.||.-.+...-.|.. .|+|....+|++.||+. |. .||. +|+-
T Consensus 1025 ~~~~~~C~~C~l~V~gss~~Cg-~C~Hv~H~sc~~eWf~~----gd--~Cps-GCGC 1073 (1081)
T KOG0309|consen 1025 KGFTFQCAICHLAVRGSSNFCG-TCGHVGHTSCMMEWFRT----GD--VCPS-GCGC 1073 (1081)
T ss_pred ccceeeeeeEeeEeeccchhhc-cccccccHHHHHHHHhc----CC--cCCC-CCCc
Confidence 3355668888655544444444 79999999999999964 33 6885 4543
No 246
>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=35.69 E-value=34 Score=24.44 Aligned_cols=24 Identities=25% Similarity=0.649 Sum_probs=12.7
Q ss_pred ccCCCCce-eEecCCcceEEee-cCc
Q 008441 479 QCVKCNHL-IELAEGCFHMTCR-CGH 502 (565)
Q Consensus 479 ~CPkC~~~-IEK~~GCnHMtC~-Cg~ 502 (565)
.||.|+.. +.-+..=..+.|. ||.
T Consensus 2 ~Cp~Cg~~~~~~D~~~g~~vC~~CG~ 27 (43)
T PF08271_consen 2 KCPNCGSKEIVFDPERGELVCPNCGL 27 (43)
T ss_dssp SBTTTSSSEEEEETTTTEEEETTT-B
T ss_pred CCcCCcCCceEEcCCCCeEECCCCCC
Confidence 58888875 3334333445663 553
No 247
>TIGR01562 FdhE formate dehydrogenase accessory protein FdhE. The only sequence scoring between trusted and noise is that from Aquifex aeolicus, which shows certain structural differences from the proteobacterial forms in the alignment. However it is notable that A. aeolicus also has a sequence scoring above trusted to the alpha subunit of formate dehydrogenase (TIGR01553).
Probab=35.65 E-value=24 Score=36.80 Aligned_cols=14 Identities=29% Similarity=0.622 Sum_probs=9.7
Q ss_pred CceecccCCCcCCC
Q 008441 435 RRFCIDCKVPWHNN 448 (565)
Q Consensus 435 ~~fC~~C~~~~H~g 448 (565)
+..|..|...||..
T Consensus 210 yL~CslC~teW~~~ 223 (305)
T TIGR01562 210 YLSCSLCATEWHYV 223 (305)
T ss_pred EEEcCCCCCccccc
Confidence 34567777888864
No 248
>COG5236 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=35.56 E-value=22 Score=37.12 Aligned_cols=51 Identities=25% Similarity=0.521 Sum_probs=32.5
Q ss_pred CcccccccceeccccccCCceeecCCCcccchhhHHHHHHHHHhCCCCCCCCCCCCCCcc
Q 008441 304 GKTINETCVICLEDTDVGHMFSIDGCLHRYCFLCMKKHIEEKLRQGMEPTCPHEGCKSKL 363 (565)
Q Consensus 304 ~~~~~~~C~IC~e~~~~~~~~~l~~C~H~fC~~Cl~~~i~~~i~~g~~~kCP~~~C~~~l 363 (565)
..+....|.||-+... -..+.+|+|.+|.-|--..-. +-.. -.||. |+.+.
T Consensus 57 tDEen~~C~ICA~~~T---Ys~~~PC~H~~CH~Ca~RlRA--LY~~--K~C~~--CrTE~ 107 (493)
T COG5236 57 TDEENMNCQICAGSTT---YSARYPCGHQICHACAVRLRA--LYMQ--KGCPL--CRTET 107 (493)
T ss_pred cccccceeEEecCCce---EEEeccCCchHHHHHHHHHHH--HHhc--cCCCc--ccccc
Confidence 3445788999987642 234669999999999654221 1111 14886 77654
No 249
>PF14445 Prok-RING_2: Prokaryotic RING finger family 2
Probab=35.39 E-value=7.3 Score=29.07 Aligned_cols=34 Identities=15% Similarity=0.344 Sum_probs=28.6
Q ss_pred cccccceeccccccCCceeecCCCcccchhhHHH
Q 008441 307 INETCVICLEDTDVGHMFSIDGCLHRYCFLCMKK 340 (565)
Q Consensus 307 ~~~~C~IC~e~~~~~~~~~l~~C~H~fC~~Cl~~ 340 (565)
..++|..|-...+..++-...-||..-|..||+.
T Consensus 6 sry~CDLCn~~~p~~~LRQCvlCGRWaC~sCW~d 39 (57)
T PF14445_consen 6 SRYSCDLCNSSHPISELRQCVLCGRWACNSCWQD 39 (57)
T ss_pred hhHhHHhhcccCcHHHHHHHhhhchhhhhhhhhh
Confidence 3689999999888777766667999999999985
No 250
>PF10122 Mu-like_Com: Mu-like prophage protein Com; InterPro: IPR019294 Members of this entry belong to the Com family of proteins that act as translational regulators of mom [, ].
Probab=35.19 E-value=14 Score=27.68 Aligned_cols=25 Identities=32% Similarity=0.808 Sum_probs=13.9
Q ss_pred cccCCCCceeEecCCc--ceEEe-ecCc
Q 008441 478 RQCVKCNHLIELAEGC--FHMTC-RCGH 502 (565)
Q Consensus 478 k~CPkC~~~IEK~~GC--nHMtC-~Cg~ 502 (565)
.+|++|+...-+.++= -.|.| +||+
T Consensus 5 iRC~~CnklLa~~g~~~~leIKCpRC~t 32 (51)
T PF10122_consen 5 IRCGHCNKLLAKAGEVIELEIKCPRCKT 32 (51)
T ss_pred eeccchhHHHhhhcCccEEEEECCCCCc
Confidence 3566666666664322 35666 4654
No 251
>KOG0824 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=35.07 E-value=15 Score=37.82 Aligned_cols=33 Identities=42% Similarity=1.011 Sum_probs=21.4
Q ss_pred cccCCCCceeEecCCcceEEe----ecCcccccccccc-ccCCCCCc
Q 008441 478 RQCVKCNHLIELAEGCFHMTC----RCGHEFCYNCGAE-WKNKKATC 519 (565)
Q Consensus 478 k~CPkC~~~IEK~~GCnHMtC----~Cg~~FCw~C~~~-~~~~~~~c 519 (565)
+.|+-|. |.|.| -|+|.|||+|.+- +...+.+|
T Consensus 8 ~eC~IC~---------nt~n~Pv~l~C~HkFCyiCiKGsy~ndk~~C 45 (324)
T KOG0824|consen 8 KECLICY---------NTGNCPVNLYCFHKFCYICIKGSYKNDKKTC 45 (324)
T ss_pred Ccceeee---------ccCCcCccccccchhhhhhhcchhhcCCCCC
Confidence 5677664 33445 2999999999875 33344555
No 252
>COG1594 RPB9 DNA-directed RNA polymerase, subunit M/Transcription elongation factor TFIIS [Transcription]
Probab=34.07 E-value=33 Score=30.31 Aligned_cols=27 Identities=37% Similarity=0.716 Sum_probs=19.1
Q ss_pred cccCCCCceeEec--CCcceEEee-cCccc
Q 008441 478 RQCVKCNHLIELA--EGCFHMTCR-CGHEF 504 (565)
Q Consensus 478 k~CPkC~~~IEK~--~GCnHMtC~-Cg~~F 504 (565)
+-||+|+.++.-. ++=+-+.|+ |||++
T Consensus 3 ~FCp~Cgsll~p~~~~~~~~l~C~kCgye~ 32 (113)
T COG1594 3 RFCPKCGSLLYPKKDDEGGKLVCRKCGYEE 32 (113)
T ss_pred cccCCccCeeEEeEcCCCcEEECCCCCcch
Confidence 6799999987752 123388894 88854
No 253
>cd01285 nucleoside_deaminase Nucleoside deaminases include adenosine, guanine and cytosine deaminases. These enzymes are Zn dependent and catalyze the deamination of nucleosides. The zinc ion in the active site plays a central role in the proposed catalytic mechanism, activating a water molecule to form a hydroxide ion that performs a nucleophilic attack on the substrate. The functional enzyme is a homodimer. Cytosine deaminase catalyzes the deamination of cytosine to uracil and ammonia and is a member of the pyrimidine salvage pathway. Cytosine deaminase is found in bacteria and fungi but is not present in mammals; for this reason, the enzyme is currently of interest for antimicrobial drug design and gene therapy applications against tumors. Some members of this family are tRNA-specific adenosine deaminases that generate inosine at the first position of their anticodon (position 34) of specific tRNAs; this modification is thought to enlarge the codon recognition capacity during protei
Probab=34.06 E-value=1.2e+02 Score=26.15 Aligned_cols=57 Identities=16% Similarity=0.106 Sum_probs=32.4
Q ss_pred CCceEEEEEEeCCCCeEEEeeeecc--ccCCChHHHHHHHHHHHHHHHHhcCCCeEEeecC
Q 008441 176 SLSAIGVAICDQMDNLIFELKKPLI--KSGLNKSAAETKALIEGLNAALSMELDRVRVFID 234 (565)
Q Consensus 176 g~ag~Gv~i~~~~~~~~~~~~~~~~--~~~tn~n~AEy~Ali~gL~~al~l~~~~v~v~~D 234 (565)
|...+|.+|++++|+++....-... +..+ .-||..|+..+.+.-.........+|+-
T Consensus 15 ~~~~vgaviv~~~~~ii~~g~n~~~~~~~~~--~HAE~~ai~~~~~~~~~~~~~~~~ly~t 73 (109)
T cd01285 15 GEVPFGAVIVDDDGKVIARGHNRVEQDGDPT--AHAEIVAIRNAARRLGSYLLSGCTLYTT 73 (109)
T ss_pred CCCcEEEEEEeCCCEEEEEEeCCCCCCCCCc--ccHHHHHHHHHHHHhCCCccCCeEEEEe
Confidence 4567899999987777655443331 1123 3689888877654321112444555543
No 254
>KOG2691 consensus RNA polymerase II subunit 9 [Transcription]
Probab=33.79 E-value=36 Score=29.61 Aligned_cols=34 Identities=18% Similarity=0.385 Sum_probs=20.5
Q ss_pred CcccccCCCCCCcccchhhhhccCCCcccccccCceeCCCCCCce
Q 008441 393 EKVYCPYPKCSALMSKSEIERDASSSSFVGRRLGARKCTKCHRRF 437 (565)
Q Consensus 393 ~~~~CP~p~C~~~i~~~~~~e~~~s~~~~~~~~~~~~C~~C~~~f 437 (565)
..++|+ .|++.+.+.+ ...+......|..|...+
T Consensus 3 ~~rfC~--eCNNmLYPkE---------Dked~~L~laCrnCd~ve 36 (113)
T KOG2691|consen 3 GIRFCR--ECNNMLYPKE---------DKEDRILLLACRNCDYVE 36 (113)
T ss_pred ccchhh--hhhccccccc---------cccccEEEEEecCCcceE
Confidence 356887 8988876543 222344456677766544
No 255
>PF15135 UPF0515: Uncharacterised protein UPF0515
Probab=33.76 E-value=44 Score=33.45 Aligned_cols=35 Identities=34% Similarity=0.923 Sum_probs=22.8
Q ss_pred cccCCCCceeE-----ecCCcceEEe-ecCccc-----------cccccccc
Q 008441 478 RQCVKCNHLIE-----LAEGCFHMTC-RCGHEF-----------CYNCGAEW 512 (565)
Q Consensus 478 k~CPkC~~~IE-----K~~GCnHMtC-~Cg~~F-----------Cw~C~~~~ 512 (565)
.+|-+|++.++ |..|=-..+| +|++.| ||.|+.+.
T Consensus 133 SRCr~C~~rYDPVP~dkmwG~aef~C~~C~h~F~G~~qm~v~sPCy~C~~~v 184 (278)
T PF15135_consen 133 SRCRKCRKRYDPVPCDKMWGIAEFHCPKCRHNFRGFAQMGVPSPCYGCGNPV 184 (278)
T ss_pred ccccccccccCCCccccccceeeeecccccccchhhhhcCCCCCccCCCCcc
Confidence 56777776543 3456666777 588777 77776654
No 256
>PF10083 DUF2321: Uncharacterized protein conserved in bacteria (DUF2321); InterPro: IPR016891 This entry is represented by Bacteriophage 'Lactobacillus prophage Lj928', Orf-Ljo1454. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. There is currently no experimental data for members of this group or their homologues, nor do they exhibit features indicative of any function.
Probab=33.72 E-value=15 Score=34.10 Aligned_cols=33 Identities=24% Similarity=0.670 Sum_probs=22.7
Q ss_pred cccCCCCceeEecCCcceEEeec-------Ccccccccccccc
Q 008441 478 RQCVKCNHLIELAEGCFHMTCRC-------GHEFCYNCGAEWK 513 (565)
Q Consensus 478 k~CPkC~~~IEK~~GCnHMtC~C-------g~~FCw~C~~~~~ 513 (565)
..||+|+.+|.-. .|+-=.. --.||+.||++|.
T Consensus 40 ~~Cp~C~~~IrG~---y~v~gv~~~g~~~~~PsYC~~CGkpyP 79 (158)
T PF10083_consen 40 TSCPNCSTPIRGD---YHVEGVFGLGGHYEAPSYCHNCGKPYP 79 (158)
T ss_pred HHCcCCCCCCCCc---eecCCeeeeCCCCCCChhHHhCCCCCc
Confidence 6899999999743 2211011 4578999999876
No 257
>PLN02189 cellulose synthase
Probab=33.30 E-value=32 Score=41.36 Aligned_cols=46 Identities=20% Similarity=0.346 Sum_probs=30.8
Q ss_pred ccccCceeCCCCCCceecccCCCcCCCCChhhHhhhCCCCChhHHHHHHHHhcCCccccCCCCceeEecCCcc
Q 008441 422 GRRLGARKCTKCHRRFCIDCKVPWHNNMTCIYYKRLNPNPPTEDVKLKSLASSNLWRQCVKCNHLIELAEGCF 494 (565)
Q Consensus 422 ~~~~~~~~C~~C~~~fC~~C~~~~H~g~tC~e~~~~~~~~~~ed~~l~~l~~~~~~k~CPkC~~~IEK~~GCn 494 (565)
......+-|..|++..|..|- +|.+ +.+.+.||+|+....+-.||+
T Consensus 48 ~~g~~fvaC~~C~fpvCr~Cy----------eyer-----------------~eg~q~CpqCkt~Y~r~kgs~ 93 (1040)
T PLN02189 48 VDGDLFVACNECGFPVCRPCY----------EYER-----------------REGTQNCPQCKTRYKRLKGSP 93 (1040)
T ss_pred CCCCEEEeeccCCCccccchh----------hhhh-----------------hcCCccCcccCCchhhccCCC
Confidence 345577999999999998663 4432 123378999887776544444
No 258
>COG3357 Predicted transcriptional regulator containing an HTH domain fused to a Zn-ribbon [Transcription]
Probab=33.27 E-value=17 Score=30.67 Aligned_cols=13 Identities=23% Similarity=0.054 Sum_probs=7.4
Q ss_pred ccchhhHHHhhhh
Q 008441 362 KLEVESCRIFLTL 374 (565)
Q Consensus 362 ~l~~~~i~~lL~~ 374 (565)
+++...+..+++.
T Consensus 18 plt~~ei~~~~~~ 30 (97)
T COG3357 18 PLTVAEIFELLNG 30 (97)
T ss_pred cchHHHHHHHHcC
Confidence 4555566666653
No 259
>PLN02638 cellulose synthase A (UDP-forming), catalytic subunit
Probab=33.17 E-value=26 Score=42.25 Aligned_cols=44 Identities=20% Similarity=0.421 Sum_probs=29.3
Q ss_pred ccccCceeCCCCCCceecccCCCcCCCCChhhHhhhCCCCChhHHHHHHHHhcCCccccCCCCceeEecCC
Q 008441 422 GRRLGARKCTKCHRRFCIDCKVPWHNNMTCIYYKRLNPNPPTEDVKLKSLASSNLWRQCVKCNHLIELAEG 492 (565)
Q Consensus 422 ~~~~~~~~C~~C~~~fC~~C~~~~H~g~tC~e~~~~~~~~~~ed~~l~~l~~~~~~k~CPkC~~~IEK~~G 492 (565)
......+-|..|++-.|.-| .+|.+ +.+.+-||+|++...+-.|
T Consensus 31 ~~Ge~FVAC~eC~FPVCrpC----------YEYEr-----------------~eG~q~CPqCktrYkr~kg 74 (1079)
T PLN02638 31 VDGEPFVACDVCAFPVCRPC----------YEYER-----------------KDGNQSCPQCKTKYKRHKG 74 (1079)
T ss_pred CCCCEEEEeccCCCccccch----------hhhhh-----------------hcCCccCCccCCchhhhcC
Confidence 34567789999999888865 45543 2234789998776654333
No 260
>KOG1824 consensus TATA-binding protein-interacting protein [General function prediction only]
Probab=33.02 E-value=22 Score=42.04 Aligned_cols=19 Identities=42% Similarity=0.702 Sum_probs=10.1
Q ss_pred cccccccCCCCcccccccc
Q 008441 538 FEEEEEEDDDDDVIDEYES 556 (565)
Q Consensus 538 ~~~~~~~~~~~~~~~~~~~ 556 (565)
+.|++|||+.+|+|.|||+
T Consensus 325 ~~ed~eDde~~deYsDDeD 343 (1233)
T KOG1824|consen 325 FLEDEEDDEQDDEYSDDED 343 (1233)
T ss_pred hhhccccchhccccccccc
Confidence 3443445555566666654
No 261
>PF15616 TerY-C: TerY-C metal binding domain
Probab=32.84 E-value=25 Score=31.91 Aligned_cols=24 Identities=29% Similarity=0.867 Sum_probs=16.2
Q ss_pred cccCCCCceeEecCCcceEEeecCcccccc
Q 008441 478 RQCVKCNHLIELAEGCFHMTCRCGHEFCYN 507 (565)
Q Consensus 478 k~CPkC~~~IEK~~GCnHMtC~Cg~~FCw~ 507 (565)
--||.|+... ....|.||.-|||.
T Consensus 78 PgCP~CGn~~------~fa~C~CGkl~Ci~ 101 (131)
T PF15616_consen 78 PGCPHCGNQY------AFAVCGCGKLFCID 101 (131)
T ss_pred CCCCCCcChh------cEEEecCCCEEEeC
Confidence 5799999875 24455666666653
No 262
>PF08792 A2L_zn_ribbon: A2L zinc ribbon domain; InterPro: IPR014900 This zinc ribbon protein is found associated with some viral A2L transcription factors [].
Probab=32.72 E-value=38 Score=23.05 Aligned_cols=26 Identities=23% Similarity=0.455 Sum_probs=15.0
Q ss_pred cccCCCCceeEecCCcceEEee-cCcc
Q 008441 478 RQCVKCNHLIELAEGCFHMTCR-CGHE 503 (565)
Q Consensus 478 k~CPkC~~~IEK~~GCnHMtC~-Cg~~ 503 (565)
+.|+.|+....-+.-=..+.|. ||..
T Consensus 4 ~~C~~C~~~~i~~~~~~~~~C~~Cg~~ 30 (33)
T PF08792_consen 4 KKCSKCGGNGIVNKEDDYEVCIFCGSS 30 (33)
T ss_pred eEcCCCCCCeEEEecCCeEEcccCCcE
Confidence 6788888865543322355553 5543
No 263
>PRK14827 undecaprenyl pyrophosphate synthase; Provisional
Probab=32.40 E-value=83 Score=32.65 Aligned_cols=71 Identities=10% Similarity=0.192 Sum_probs=45.2
Q ss_pred CCceEEEEEEeCCCCeEEEeeeeccccCCChHHHHHHHHHHHHHHHHhcCCCeEEeecCCccchhhccCccCCcchhhHH
Q 008441 176 SLSAIGVAICDQMDNLIFELKKPLIKSGLNKSAAETKALIEGLNAALSMELDRVRVFIDCFPLFQFVTGRWPAKQRKISV 255 (565)
Q Consensus 176 g~ag~Gv~i~~~~~~~~~~~~~~~~~~~tn~n~AEy~Ali~gL~~al~l~~~~v~v~~DS~lv~~qv~G~w~~k~~~l~~ 255 (565)
-|.=+|+++ +||.-+.-.+.+ ..... ..+=+.+++.-+++++++||+.|.||.=| ++.|+-....+..
T Consensus 67 iP~HVAiIM---DGNrRwAk~~gl-~~~~G-H~~G~~~l~~v~~~c~~lGI~~lTvYaFS-------tEN~kR~~~EV~~ 134 (296)
T PRK14827 67 LPNHVAIVM---DGNGRWATQRGL-ARTEG-HKMGEAVVIDIACGAIELGIKWLSLYAFS-------TENWKRSPEEVRF 134 (296)
T ss_pred CCCeEEEec---cCchHHHHHCCC-CHhHH-HHHHHHHHHHHHHHHHHcCCCEEEEeeec-------chhhcCCHHHHHH
Confidence 344455543 345433333334 22224 47778899999999999999999999844 4667666556555
Q ss_pred HHH
Q 008441 256 LVD 258 (565)
Q Consensus 256 l~~ 258 (565)
|++
T Consensus 135 Lm~ 137 (296)
T PRK14827 135 LMG 137 (296)
T ss_pred HHH
Confidence 444
No 264
>COG0450 AhpC Peroxiredoxin [Posttranslational modification, protein turnover, chaperones]
Probab=32.38 E-value=1.2e+02 Score=29.45 Aligned_cols=49 Identities=20% Similarity=0.207 Sum_probs=37.0
Q ss_pred CCCceEEEEEEeCCCCeEEEeeeeccccCCChHHHHHHHHHHHHHHHHhcCC
Q 008441 175 VSLSAIGVAICDQMDNLIFELKKPLIKSGLNKSAAETKALIEGLNAALSMEL 226 (565)
Q Consensus 175 pg~ag~Gv~i~~~~~~~~~~~~~~~~~~~tn~n~AEy~Ali~gL~~al~l~~ 226 (565)
.|.+-=|+.|+|++|.+.....-++ .+++|.-|...+|.||+.-.+.|.
T Consensus 120 ~g~a~R~~FIIDp~g~ir~~~v~~~---~iGRn~dEilR~idAlq~~~~hg~ 168 (194)
T COG0450 120 EGLALRGTFIIDPDGVIRHILVNPL---TIGRNVDEILRVIDALQFVAKHGE 168 (194)
T ss_pred CCcceeEEEEECCCCeEEEEEEecC---CCCcCHHHHHHHHHHHHHHHHhCC
Confidence 3557779999999886654444444 557789999999999998666663
No 265
>PF01614 IclR: Bacterial transcriptional regulator This Pfam family contains some of the members of the iclR family; InterPro: IPR014757 The many bacterial transcription regulation proteins which bind DNA through a 'helix-turn-helix' motif can be classified into subfamilies on the basis of sequence similarities. One of these subfamilies, called 'iclR', groups several proteins including: gylR, a possible activator protein for the gylABX glycerol operon in Streptomyces. iclR, the repressor of the acetate operon (also known as glyoxylate bypass operon) in Escherichia coli and Salmonella typhimurium. These proteins have a Helix-Turn-Helix motif at the N terminus that is similar to that of other DNA-binding proteins [].; PDB: 3MQ0_A 2IA2_D 3OBF_B 2G7U_C 3R4K_A 1TF1_D 1MKM_A 1YSP_A 3BJN_A 1TD5_A ....
Probab=32.32 E-value=1.6e+02 Score=25.60 Aligned_cols=46 Identities=20% Similarity=0.226 Sum_probs=30.5
Q ss_pred CCCCceEEEEEEeCCCCeEEEeeeeccccCCChHHHHHHH-HHHHHHHH
Q 008441 174 RVSLSAIGVAICDQMDNLIFELKKPLIKSGLNKSAAETKA-LIEGLNAA 221 (565)
Q Consensus 174 npg~ag~Gv~i~~~~~~~~~~~~~~~~~~~tn~n~AEy~A-li~gL~~a 221 (565)
.+|..++++.|.+..|.++.-++-.......+ ..+... ++..|..+
T Consensus 76 ~~gv~~iA~Pi~~~~g~~~~alsv~~~~~~~~--~~~~~~~~~~~l~~~ 122 (129)
T PF01614_consen 76 EPGVAAIAVPIFDPNGQVVAALSVSGPSERFD--EERLEERLAPALREA 122 (129)
T ss_dssp STTEEEEEEEEEETTSCEEEEEEEEEEGGGSH--HHHHHHHHHHHHHHH
T ss_pred ccccceEEEEEECCCCCEEEEEEEeeEhHhCC--HHHHHHHHHHHHHHH
Confidence 88999999999999899888777776333333 222222 55555543
No 266
>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=31.29 E-value=34 Score=22.40 Aligned_cols=21 Identities=29% Similarity=0.583 Sum_probs=11.4
Q ss_pred cccCCCCceeEecC--CcceEEe
Q 008441 478 RQCVKCNHLIELAE--GCFHMTC 498 (565)
Q Consensus 478 k~CPkC~~~IEK~~--GCnHMtC 498 (565)
++||.|+..|++.+ |=+...|
T Consensus 2 ~~C~rC~~~~~~~~~~~r~~~~C 24 (30)
T PF06827_consen 2 EKCPRCWNYIEDIGINGRSTYLC 24 (30)
T ss_dssp SB-TTT--BBEEEEETTEEEEE-
T ss_pred CcCccCCCcceEeEecCCCCeEC
Confidence 58999999998753 4444445
No 267
>PF08882 Acetone_carb_G: Acetone carboxylase gamma subunit; InterPro: IPR014979 Acetone carboxylase is the key enzyme of bacterial acetone metabolism, catalysing the condensation of acetone and CO2 to form acetoacetate [] according to the following reaction: CH3COCH3 + CO2 + ATP = CH3COCH2COO- + AMP + 2P(i) + H+ It has the subunit composition: (alpha(2)beta(2)gamma(2) multimers of 85kDa, 78kDa, and 20kDa subunits). It is expressed to high levels (17 to 25% of soluble protein) in cells grown with acetone as the carbon source but are not present at detectable levels in cells grown with other carbon sources []. Acetone carboxylase may enable Helicobacter pylori to survive off acetone in the stomach of humans and other mammals where it is the etiological agent of peptic ulcer disease []. This entry represents the family of gamma subunit-related acetone carboxylase proteins.
Probab=31.21 E-value=33 Score=30.06 Aligned_cols=13 Identities=54% Similarity=1.306 Sum_probs=11.1
Q ss_pred ceEEeecCccccc
Q 008441 494 FHMTCRCGHEFCY 506 (565)
Q Consensus 494 nHMtC~Cg~~FCw 506 (565)
..+.|.|||.||-
T Consensus 23 k~vkc~CGh~f~d 35 (112)
T PF08882_consen 23 KVVKCDCGHEFCD 35 (112)
T ss_pred ceeeccCCCeecC
Confidence 4788999999993
No 268
>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=30.91 E-value=26 Score=27.57 Aligned_cols=36 Identities=17% Similarity=0.421 Sum_probs=18.1
Q ss_pred ccccccceecccccc-CCceeecCCCcccchhhHHHH
Q 008441 306 TINETCVICLEDTDV-GHMFSIDGCLHRYCFLCMKKH 341 (565)
Q Consensus 306 ~~~~~C~IC~e~~~~-~~~~~l~~C~H~fC~~Cl~~~ 341 (565)
.....|.+|...|.. ..-...-.||+.||..|....
T Consensus 7 ~~~~~C~~C~~~F~~~~rrhhCr~CG~~vC~~Cs~~~ 43 (69)
T PF01363_consen 7 SEASNCMICGKKFSLFRRRHHCRNCGRVVCSSCSSQR 43 (69)
T ss_dssp GG-SB-TTT--B-BSSS-EEE-TTT--EEECCCS-EE
T ss_pred CCCCcCcCcCCcCCCceeeEccCCCCCEECCchhCCE
Confidence 346789999988743 222334589999999998643
No 269
>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=30.37 E-value=34 Score=27.16 Aligned_cols=17 Identities=24% Similarity=0.589 Sum_probs=11.9
Q ss_pred ccchhhHHHHHHHHHhC
Q 008441 332 RYCFLCMKKHIEEKLRQ 348 (565)
Q Consensus 332 ~fC~~Cl~~~i~~~i~~ 348 (565)
-||++||..|+...-..
T Consensus 11 gFCRNCLskWy~~aA~~ 27 (68)
T PF06844_consen 11 GFCRNCLSKWYREAAEE 27 (68)
T ss_dssp S--HHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHh
Confidence 39999999999876544
No 270
>COG3813 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=30.31 E-value=34 Score=27.57 Aligned_cols=47 Identities=23% Similarity=0.577 Sum_probs=30.6
Q ss_pred ccccceeccccccCCceeecCC--CcccchhhHHHHHHHHHhCCCCCCCCCCCCCCccch
Q 008441 308 NETCVICLEDTDVGHMFSIDGC--LHRYCFLCMKKHIEEKLRQGMEPTCPHEGCKSKLEV 365 (565)
Q Consensus 308 ~~~C~IC~e~~~~~~~~~l~~C--~H~fC~~Cl~~~i~~~i~~g~~~kCP~~~C~~~l~~ 365 (565)
...|..|-.+.+....-.+ -| .|.||.+|...-+ .| .||+ |+..+..
T Consensus 5 RPnCECCDrDLpp~s~dA~-ICtfEcTFCadCae~~l-----~g---~CPn--CGGelv~ 53 (84)
T COG3813 5 RPNCECCDRDLPPDSTDAR-ICTFECTFCADCAENRL-----HG---LCPN--CGGELVA 53 (84)
T ss_pred cCCCcccCCCCCCCCCcee-EEEEeeehhHhHHHHhh-----cC---cCCC--CCchhhc
Confidence 4578888777654432222 34 4889999987655 23 5987 8887654
No 271
>PHA02862 5L protein; Provisional
Probab=30.14 E-value=50 Score=30.42 Aligned_cols=47 Identities=26% Similarity=0.478 Sum_probs=33.0
Q ss_pred cccceeccccccCCceeecCCCc-----ccchhhHHHHHHHHHhCCCCCCCCCCCCCCccch
Q 008441 309 ETCVICLEDTDVGHMFSIDGCLH-----RYCFLCMKKHIEEKLRQGMEPTCPHEGCKSKLEV 365 (565)
Q Consensus 309 ~~C~IC~e~~~~~~~~~l~~C~H-----~fC~~Cl~~~i~~~i~~g~~~kCP~~~C~~~l~~ 365 (565)
..|=||+++-+.. ..+|.+ ....+||.+|+.. .....||. |+.+...
T Consensus 3 diCWIC~~~~~e~----~~PC~C~GS~K~VHq~CL~~WIn~----S~k~~CeL--CkteY~I 54 (156)
T PHA02862 3 DICWICNDVCDER----NNFCGCNEEYKVVHIKCMQLWINY----SKKKECNL--CKTKYNI 54 (156)
T ss_pred CEEEEecCcCCCC----cccccccCcchhHHHHHHHHHHhc----CCCcCccC--CCCeEEE
Confidence 5799999885322 135654 5899999999943 33348997 9887754
No 272
>smart00659 RPOLCX RNA polymerase subunit CX. present in RNA polymerase I, II and III
Probab=30.06 E-value=42 Score=24.45 Aligned_cols=23 Identities=30% Similarity=0.674 Sum_probs=11.2
Q ss_pred ccCCCCceeEecCCcceEEee-cCc
Q 008441 479 QCVKCNHLIELAEGCFHMTCR-CGH 502 (565)
Q Consensus 479 ~CPkC~~~IEK~~GCnHMtC~-Cg~ 502 (565)
.|..|+..++...+ .-|.|+ ||+
T Consensus 4 ~C~~Cg~~~~~~~~-~~irC~~CG~ 27 (44)
T smart00659 4 ICGECGRENEIKSK-DVVRCRECGY 27 (44)
T ss_pred ECCCCCCEeecCCC-CceECCCCCc
Confidence 35555555554433 345553 554
No 273
>KOG4362 consensus Transcriptional regulator BRCA1 [Replication, recombination and repair; Transcription]
Probab=29.84 E-value=9.9 Score=43.41 Aligned_cols=57 Identities=33% Similarity=0.540 Sum_probs=38.3
Q ss_pred cccccccceeccccccCCceeecCCCcccchhhHHHHHHHHHhCCCCCCCCCCCCCCccchhhHH
Q 008441 305 KTINETCVICLEDTDVGHMFSIDGCLHRYCFLCMKKHIEEKLRQGMEPTCPHEGCKSKLEVESCR 369 (565)
Q Consensus 305 ~~~~~~C~IC~e~~~~~~~~~l~~C~H~fC~~Cl~~~i~~~i~~g~~~kCP~~~C~~~l~~~~i~ 369 (565)
..+..+|+||+..+... +++.|.|.||..||..-+..+-. ...||. |+..+....++
T Consensus 18 ~~k~lEc~ic~~~~~~p---~~~kc~~~~l~~~~n~~f~~~~~---~~~~~l--c~~~~eK~s~~ 74 (684)
T KOG4362|consen 18 MQKILECPICLEHVKEP---SLLKCDHIFLKFCLNKLFESKKG---PKQCAL--CKSDIEKRSLR 74 (684)
T ss_pred HhhhccCCceeEEeecc---chhhhhHHHHhhhhhceeeccCc---cccchh--hhhhhhhhhcc
Confidence 34578999999886433 45589999999999876654321 336775 77665544433
No 274
>TIGR00373 conserved hypothetical protein TIGR00373. This family of proteins is, so far, restricted to archaeal genomes. The family appears to be distantly related to the N-terminal region of the eukaryotic transcription initiation factor IIE alpha chain.
Probab=29.45 E-value=85 Score=29.34 Aligned_cols=32 Identities=16% Similarity=0.235 Sum_probs=20.1
Q ss_pred CCCcccccCCCCCCcccchhhhhccCCCcccccccCceeCCCCCCc
Q 008441 391 VTEKVYCPYPKCSALMSKSEIERDASSSSFVGRRLGARKCTKCHRR 436 (565)
Q Consensus 391 ~~~~~~CP~p~C~~~i~~~~~~e~~~s~~~~~~~~~~~~C~~C~~~ 436 (565)
.+.+-.|| .|+.-+...+.+ ...+.||.||..
T Consensus 106 ~~~~Y~Cp--~c~~r~tf~eA~------------~~~F~Cp~Cg~~ 137 (158)
T TIGR00373 106 NNMFFICP--NMCVRFTFNEAM------------ELNFTCPRCGAM 137 (158)
T ss_pred CCCeEECC--CCCcEeeHHHHH------------HcCCcCCCCCCE
Confidence 34566797 688666544432 246888888763
No 275
>PRK14829 undecaprenyl pyrophosphate synthase; Provisional
Probab=29.42 E-value=1.1e+02 Score=30.71 Aligned_cols=73 Identities=15% Similarity=0.204 Sum_probs=47.7
Q ss_pred CCCCceEEEEEEeCCCCeEEEeeeeccccCCChHHHHHHHHHHHHHHHHhcCCCeEEeecCCccchhhccCccCCcchhh
Q 008441 174 RVSLSAIGVAICDQMDNLIFELKKPLIKSGLNKSAAETKALIEGLNAALSMELDRVRVFIDCFPLFQFVTGRWPAKQRKI 253 (565)
Q Consensus 174 npg~ag~Gv~i~~~~~~~~~~~~~~~~~~~tn~n~AEy~Ali~gL~~al~l~~~~v~v~~DS~lv~~qv~G~w~~k~~~l 253 (565)
++-|.=+|+++ +||.-+.-.+.+ -.... ..+=+.++..-++++.++||+.|.||.=| ++.|+-....+
T Consensus 12 ~~~P~HvaiIm---DGNrRwAk~~g~-~~~~G-H~~G~~~l~~iv~~c~~~gI~~vTvYaFS-------~eN~kR~~~Ev 79 (243)
T PRK14829 12 NKLPRHIAVVM---DGNGRWATQRGL-KRTEG-HKAGEPVLFDVVAGAIEAGVPYLSLYTFS-------TENWKRSPDEV 79 (243)
T ss_pred CCCCCeEEEec---CCCHHHHHHCCC-ChhHH-HHHHHHHHHHHHHHHHHcCCCEEEEeeec-------chhhCCCHHHH
Confidence 44566666654 455433333333 12224 47778899999999999999999999843 56676665555
Q ss_pred HHHHH
Q 008441 254 SVLVD 258 (565)
Q Consensus 254 ~~l~~ 258 (565)
..|++
T Consensus 80 ~~lm~ 84 (243)
T PRK14829 80 RFLMG 84 (243)
T ss_pred HHHHH
Confidence 55444
No 276
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=29.34 E-value=89 Score=29.87 Aligned_cols=30 Identities=20% Similarity=0.517 Sum_probs=18.6
Q ss_pred CCcccccCCCCCCcccchhhhhccCCCcccccccCceeCCCCCC
Q 008441 392 TEKVYCPYPKCSALMSKSEIERDASSSSFVGRRLGARKCTKCHR 435 (565)
Q Consensus 392 ~~~~~CP~p~C~~~i~~~~~~e~~~s~~~~~~~~~~~~C~~C~~ 435 (565)
..+-.|| .|+.-+...+.+ ...+.||.||.
T Consensus 115 ~~~Y~Cp--~C~~rytf~eA~------------~~~F~Cp~Cg~ 144 (178)
T PRK06266 115 NMFFFCP--NCHIRFTFDEAM------------EYGFRCPQCGE 144 (178)
T ss_pred CCEEECC--CCCcEEeHHHHh------------hcCCcCCCCCC
Confidence 3566798 588666544431 24578887775
No 277
>PF14354 Lar_restr_allev: Restriction alleviation protein Lar
Probab=29.28 E-value=38 Score=25.90 Aligned_cols=12 Identities=17% Similarity=0.362 Sum_probs=8.9
Q ss_pred ccccCCCCceeE
Q 008441 477 WRQCVKCNHLIE 488 (565)
Q Consensus 477 ~k~CPkC~~~IE 488 (565)
.|+||.|+....
T Consensus 3 LkPCPFCG~~~~ 14 (61)
T PF14354_consen 3 LKPCPFCGSADV 14 (61)
T ss_pred CcCCCCCCCcce
Confidence 389999986543
No 278
>PLN02436 cellulose synthase A
Probab=29.28 E-value=35 Score=41.16 Aligned_cols=21 Identities=19% Similarity=0.382 Sum_probs=16.4
Q ss_pred ccccCceeCCCCCCceecccC
Q 008441 422 GRRLGARKCTKCHRRFCIDCK 442 (565)
Q Consensus 422 ~~~~~~~~C~~C~~~fC~~C~ 442 (565)
.+....+-|..|++..|..|-
T Consensus 50 ~dGe~FVACn~C~fpvCr~Cy 70 (1094)
T PLN02436 50 VDGEPFVACNECAFPVCRPCY 70 (1094)
T ss_pred CCCCEEEeeccCCCccccchh
Confidence 345677899999999998664
No 279
>TIGR03142 cytochro_ccmI cytochrome c-type biogenesis protein CcmI. This TPR repeat-containing protein is the CcmI protein (also called CycH) of c-type cytochrome biogenesis. CcmI is thought to act as an apo-cytochrome c chaperone. This model describes the N-terminal region of the protein, Members of this protein family
Probab=29.13 E-value=39 Score=29.82 Aligned_cols=42 Identities=26% Similarity=0.381 Sum_probs=35.2
Q ss_pred hhhhcccHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHhhhh
Q 008441 81 PTLASLQSEELMKLDRELADSRQAKLEMQKAREDLQRAIHDH 122 (565)
Q Consensus 81 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 122 (565)
....++..+.|..||+|+..=..+..++.+++.+++|++.+.
T Consensus 35 ~~n~~iyr~qL~ELe~d~~~G~l~~~e~~~~~~El~rrLL~d 76 (117)
T TIGR03142 35 ELNLAVYRDRLAELERDLAEGLLDEAEAEAARAELQRRLLAD 76 (117)
T ss_pred HHHHHHHHHHHHHHHHHHHcCCCCHHHHHHHHHHHHHHHHHC
Confidence 344489999999999998877778999999999999997543
No 280
>PRK13190 putative peroxiredoxin; Provisional
Probab=28.82 E-value=1e+02 Score=29.84 Aligned_cols=76 Identities=16% Similarity=0.205 Sum_probs=50.2
Q ss_pred CCceEEEEEEeCCCCeEEEeeeeccccCCChHHHHHHHHHHHHHHHHhcCCCeEEeecCCccchhhccCccCCcchhhHH
Q 008441 176 SLSAIGVAICDQMDNLIFELKKPLIKSGLNKSAAETKALIEGLNAALSMELDRVRVFIDCFPLFQFVTGRWPAKQRKISV 255 (565)
Q Consensus 176 g~ag~Gv~i~~~~~~~~~~~~~~~~~~~tn~n~AEy~Ali~gL~~al~l~~~~v~v~~DS~lv~~qv~G~w~~k~~~l~~ 255 (565)
|.+-=+++|+|++|.+++....++ .+.+|..|...+|.+|+..-+.|.- .=-.|++.+..+.+
T Consensus 114 g~~~p~~fiId~~G~I~~~~~~~~---~~gr~~~ellr~l~~l~~~~~~~~~--------------~p~~w~~g~~~~~~ 176 (202)
T PRK13190 114 GATVRGVFIIDPNQIVRWMIYYPA---ETGRNIDEIIRITKALQVNWKRKVA--------------TPANWQPGQEGIVP 176 (202)
T ss_pred CcEEeEEEEECCCCEEEEEEEeCC---CCCCCHHHHHHHHHHhhhHHhcCCC--------------cCCCCCcCCceecC
Confidence 334567889999887766555555 3345799999999999887766631 11357777766666
Q ss_pred HHHHHHHHhhhcc
Q 008441 256 LVDQVSLLEKRFS 268 (565)
Q Consensus 256 l~~~v~~Ll~~F~ 268 (565)
..........+|.
T Consensus 177 ~~~~~~~~~~~~~ 189 (202)
T PRK13190 177 APSTLDEAEMRIK 189 (202)
T ss_pred CCCCHHHHHHHhc
Confidence 5555555555553
No 281
>KOG0320 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=28.68 E-value=14 Score=35.11 Aligned_cols=38 Identities=21% Similarity=0.532 Sum_probs=27.1
Q ss_pred cccCCCCceeEecCCcceEEeecCccccccccccccCCCCC
Q 008441 478 RQCVKCNHLIELAEGCFHMTCRCGHEFCYNCGAEWKNKKAT 518 (565)
Q Consensus 478 k~CPkC~~~IEK~~GCnHMtC~Cg~~FCw~C~~~~~~~~~~ 518 (565)
-.||.|-..+.+..- +.=+|||-||-.|.+.-.+....
T Consensus 132 ~~CPiCl~~~sek~~---vsTkCGHvFC~~Cik~alk~~~~ 169 (187)
T KOG0320|consen 132 YKCPICLDSVSEKVP---VSTKCGHVFCSQCIKDALKNTNK 169 (187)
T ss_pred cCCCceecchhhccc---cccccchhHHHHHHHHHHHhCCC
Confidence 479999888887643 22259999999998876655443
No 282
>COG0590 CumB Cytosine/adenosine deaminases [Nucleotide transport and metabolism / Translation, ribosomal structure and biogenesis]
Probab=28.51 E-value=1.3e+02 Score=27.89 Aligned_cols=43 Identities=16% Similarity=0.095 Sum_probs=26.9
Q ss_pred CceEEEEEEeCCCCeEEEeeeecc--ccCCChHHHHHHHHHHHHHHH
Q 008441 177 LSAIGVAICDQMDNLIFELKKPLI--KSGLNKSAAETKALIEGLNAA 221 (565)
Q Consensus 177 ~ag~Gv~i~~~~~~~~~~~~~~~~--~~~tn~n~AEy~Ali~gL~~a 221 (565)
...+|.||++++|.++.+...... +..|. -||..||-.+-+..
T Consensus 27 e~PvGaviV~~~~~ii~~~~N~~~~~~dpta--HAEi~air~a~~~~ 71 (152)
T COG0590 27 EVPVGAVIVDADGEIIARGHNRREEDNDPTA--HAEILAIRAAAETL 71 (152)
T ss_pred CCCEEEEEEcCCCCEEEEecCccccCCCccc--cHHHHHHHHHHHhh
Confidence 356899999977877766555541 12223 57877776655443
No 283
>COG1594 RPB9 DNA-directed RNA polymerase, subunit M/Transcription elongation factor TFIIS [Transcription]
Probab=28.50 E-value=39 Score=29.86 Aligned_cols=31 Identities=29% Similarity=0.604 Sum_probs=20.8
Q ss_pred cccccCCCCCCcccchhhhhccCCCcccccccCceeCCCCCCce
Q 008441 394 KVYCPYPKCSALMSKSEIERDASSSSFVGRRLGARKCTKCHRRF 437 (565)
Q Consensus 394 ~~~CP~p~C~~~i~~~~~~e~~~s~~~~~~~~~~~~C~~C~~~f 437 (565)
..+|| .|+++|.+.+. .......|++|+..+
T Consensus 2 m~FCp--~Cgsll~p~~~-----------~~~~~l~C~kCgye~ 32 (113)
T COG1594 2 MRFCP--KCGSLLYPKKD-----------DEGGKLVCRKCGYEE 32 (113)
T ss_pred ccccC--CccCeeEEeEc-----------CCCcEEECCCCCcch
Confidence 46898 99999976431 123478888887643
No 284
>KOG2879 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=28.39 E-value=25 Score=35.71 Aligned_cols=40 Identities=35% Similarity=0.803 Sum_probs=24.2
Q ss_pred cccCCCCceeE--ecCCcceEEeecCccccccccccccCCCCCcCCCC
Q 008441 478 RQCVKCNHLIE--LAEGCFHMTCRCGHEFCYNCGAEWKNKKATCSCPL 523 (565)
Q Consensus 478 k~CPkC~~~IE--K~~GCnHMtC~Cg~~FCw~C~~~~~~~~~~c~C~~ 523 (565)
+.||-|+.+=. ...| .|||-|||.|...--.-..+..||.
T Consensus 240 ~~C~~Cg~~PtiP~~~~------~C~HiyCY~Ci~ts~~~~asf~Cp~ 281 (298)
T KOG2879|consen 240 TECPVCGEPPTIPHVIG------KCGHIYCYYCIATSRLWDASFTCPL 281 (298)
T ss_pred ceeeccCCCCCCCeeec------cccceeehhhhhhhhcchhhcccCc
Confidence 78999997532 2233 3777888888776333333334554
No 285
>PRK15370 E3 ubiquitin-protein ligase SlrP; Provisional
Probab=28.34 E-value=70 Score=37.68 Aligned_cols=51 Identities=14% Similarity=0.209 Sum_probs=37.1
Q ss_pred ccchhhHHhhHHHHHHhhccCCCCCCCCCCCCCCCCCCCCCCCCCCCchhhhcccHHHHHHHHHHHHhHHHHH
Q 008441 33 SDLDFAFRLQLQEAISASLAHVPSSSSTSSLPPSTSSAPPPLPHDAASPTLASLQSEELMKLDRELADSRQAK 105 (565)
Q Consensus 33 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 105 (565)
.-.=||||.||+|++.- +. + |..-.....|.|..+||.+++.+++.+|.++
T Consensus 608 iEV~Layr~~L~~~L~L--p~-----------~---------~~~M~f~~~s~vt~~dl~~A~~~V~~~E~~~ 658 (754)
T PRK15370 608 IEVFLGFQNQLRESLSL--TT-----------M---------TQDMRFYNVSGITESDLDEAEIRIKIAENRD 658 (754)
T ss_pred eeehHHHHHHHHHhcCC--CC-----------C---------CccCeeccccCCCHHHHHHHHHHHHHHHHHH
Confidence 44558999999998753 21 1 1123355556899999999999999999874
No 286
>COG0295 Cdd Cytidine deaminase [Nucleotide transport and metabolism]
Probab=27.71 E-value=1.7e+02 Score=26.69 Aligned_cols=30 Identities=23% Similarity=0.233 Sum_probs=21.9
Q ss_pred HHHHHHHHHHHHHHHHhcCCCeEEeecCCcc
Q 008441 207 SAAETKALIEGLNAALSMELDRVRVFIDCFP 237 (565)
Q Consensus 207 n~AEy~Ali~gL~~al~l~~~~v~v~~DS~l 237 (565)
+-||-.|+..+... -...+..|.|++|+..
T Consensus 54 ~CAErsAI~~ais~-G~~~~~~v~v~~~~~~ 83 (134)
T COG0295 54 VCAERSAIFKAISE-GKRKFDAVVVVADTGK 83 (134)
T ss_pred hhHHHHHHHHHHHc-CCCcEEEEEEEcCCCC
Confidence 68999999987755 3345567788888743
No 287
>PRK15000 peroxidase; Provisional
Probab=27.69 E-value=1.9e+02 Score=27.97 Aligned_cols=73 Identities=14% Similarity=0.176 Sum_probs=49.3
Q ss_pred CCceEEEEEEeCCCCeEEEeeeeccccCCChHHHHHHHHHHHHHHHHhcCCCeEEeecCCccchhhccCccCCcchhhHH
Q 008441 176 SLSAIGVAICDQMDNLIFELKKPLIKSGLNKSAAETKALIEGLNAALSMELDRVRVFIDCFPLFQFVTGRWPAKQRKISV 255 (565)
Q Consensus 176 g~ag~Gv~i~~~~~~~~~~~~~~~~~~~tn~n~AEy~Ali~gL~~al~l~~~~v~v~~DS~lv~~qv~G~w~~k~~~l~~ 255 (565)
|.+-=+.+|+|++|.++......+ ...+|..|...++.+|+..-+.|. + .=-.|++.++.+.+
T Consensus 122 g~~~r~tfiID~~G~I~~~~~~~~---~~gr~~~eilr~l~al~~~~~~~~----~----------~p~~w~~g~~~~~~ 184 (200)
T PRK15000 122 GVALRGSFLIDANGIVRHQVVNDL---PLGRNIDEMLRMVDALQFHEEHGD----V----------CPAQWEKGKEGMNA 184 (200)
T ss_pred CcEEeEEEEECCCCEEEEEEecCC---CCCCCHHHHHHHHHHhhhHHhcCC----C----------cCCCCCCCCceecc
Confidence 345567888999998776655555 334479999999999887776663 0 11358887777777
Q ss_pred HHHHHHHHhh
Q 008441 256 LVDQVSLLEK 265 (565)
Q Consensus 256 l~~~v~~Ll~ 265 (565)
..+-+..+..
T Consensus 185 ~~~~~~~~~~ 194 (200)
T PRK15000 185 SPDGVAKYLA 194 (200)
T ss_pred CHHHHHHHHH
Confidence 6655555433
No 288
>KOG3088 consensus Secretory carrier membrane protein [Intracellular trafficking, secretion, and vesicular transport]
Probab=27.38 E-value=3.3e+02 Score=28.10 Aligned_cols=16 Identities=31% Similarity=0.437 Sum_probs=9.2
Q ss_pred cHHHHHHHHHHHHhHH
Q 008441 87 QSEELMKLDRELADSR 102 (565)
Q Consensus 87 ~~~~~~~~~~~~~~~~ 102 (565)
+..||.+.++|+..+|
T Consensus 58 ~a~~~~~kq~eL~~rq 73 (313)
T KOG3088|consen 58 QAKDLAKKQAELLKKQ 73 (313)
T ss_pred hhhHHHHHHHHHHHHH
Confidence 3556666666665544
No 289
>PF12760 Zn_Tnp_IS1595: Transposase zinc-ribbon domain; InterPro: IPR024442 This zinc binding domain is found in a range of transposase proteins such as ISSPO8, ISSOD11, ISRSSP2 etc. It may be a zinc-binding beta ribbon domain that could bind DNA.
Probab=26.93 E-value=1e+02 Score=22.29 Aligned_cols=25 Identities=16% Similarity=0.347 Sum_probs=14.4
Q ss_pred cccCCCCce-eEecCCcceEEee-cCc
Q 008441 478 RQCVKCNHL-IELAEGCFHMTCR-CGH 502 (565)
Q Consensus 478 k~CPkC~~~-IEK~~GCnHMtC~-Cg~ 502 (565)
-.||+|+.. +-+..+=....|+ |++
T Consensus 19 ~~CP~Cg~~~~~~~~~~~~~~C~~C~~ 45 (46)
T PF12760_consen 19 FVCPHCGSTKHYRLKTRGRYRCKACRK 45 (46)
T ss_pred CCCCCCCCeeeEEeCCCCeEECCCCCC
Confidence 469999984 2233333445563 665
No 290
>PRK14830 undecaprenyl pyrophosphate synthase; Provisional
Probab=26.88 E-value=1.5e+02 Score=30.09 Aligned_cols=73 Identities=14% Similarity=0.149 Sum_probs=47.1
Q ss_pred CCCCceEEEEEEeCCCCeEEEeeeeccccCCChHHHHHHHHHHHHHHHHhcCCCeEEeecCCccchhhccCccCCcchhh
Q 008441 174 RVSLSAIGVAICDQMDNLIFELKKPLIKSGLNKSAAETKALIEGLNAALSMELDRVRVFIDCFPLFQFVTGRWPAKQRKI 253 (565)
Q Consensus 174 npg~ag~Gv~i~~~~~~~~~~~~~~~~~~~tn~n~AEy~Ali~gL~~al~l~~~~v~v~~DS~lv~~qv~G~w~~k~~~l 253 (565)
.+-|.=+||++ +||.-+.-...+ ..... ..+=+.++..-++++.++|++.|.||.-| +..|+.....+
T Consensus 20 ~~~P~HVAiIm---DGNrRwAk~~gl-~~~~G-h~~G~~~l~~~l~~c~~~GI~~vTvYaFS-------~eN~~R~~~Ev 87 (251)
T PRK14830 20 GNIPKHIAIIM---DGNGRWAKKRML-PRIAG-HKAGMDTVKKITKAASELGVKVLTLYAFS-------TENWKRPKDEV 87 (251)
T ss_pred CCCCCeEEEEe---cCchHHHHHCCC-chhhh-HHHHHHHHHHHHHHHHHcCCCEEEEEEEe-------hhhcCCCHHHH
Confidence 45567777665 345333323333 11224 36667799999999999999999999843 45666666666
Q ss_pred HHHHH
Q 008441 254 SVLVD 258 (565)
Q Consensus 254 ~~l~~ 258 (565)
..|++
T Consensus 88 ~~Lm~ 92 (251)
T PRK14830 88 KFLMN 92 (251)
T ss_pred HHHHH
Confidence 66554
No 291
>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=26.71 E-value=35 Score=30.72 Aligned_cols=11 Identities=0% Similarity=-0.145 Sum_probs=6.1
Q ss_pred CceeCCCCCCc
Q 008441 426 GARKCTKCHRR 436 (565)
Q Consensus 426 ~~~~C~~C~~~ 436 (565)
..+.||+||..
T Consensus 25 ~p~vcP~cg~~ 35 (129)
T TIGR02300 25 RPAVSPYTGEQ 35 (129)
T ss_pred CCccCCCcCCc
Confidence 44566666553
No 292
>PRK14833 undecaprenyl pyrophosphate synthase; Provisional
Probab=26.59 E-value=1.4e+02 Score=29.82 Aligned_cols=73 Identities=12% Similarity=0.146 Sum_probs=48.3
Q ss_pred CCCCceEEEEEEeCCCCeEEEeeeeccccCCChHHHHHHHHHHHHHHHHhcCCCeEEeecCCccchhhccCccCCcchhh
Q 008441 174 RVSLSAIGVAICDQMDNLIFELKKPLIKSGLNKSAAETKALIEGLNAALSMELDRVRVFIDCFPLFQFVTGRWPAKQRKI 253 (565)
Q Consensus 174 npg~ag~Gv~i~~~~~~~~~~~~~~~~~~~tn~n~AEy~Ali~gL~~al~l~~~~v~v~~DS~lv~~qv~G~w~~k~~~l 253 (565)
|+-|.=+|++. +||.-+.-++.+ ..... ..+=+.+|.+-++++.++|++.|.||.=| +..|+-....+
T Consensus 2 ~~~P~HVaiIm---DGNrRwA~~~gl-~~~~G-H~~G~~~l~~~~~~c~~~gI~~lTvyaFS-------~eN~~R~~~Ev 69 (233)
T PRK14833 2 DNTLKHLAIIM---DGNGRWAKLRGK-ARAAG-HKKGVKTLREITIWCANHKLECLTLYAFS-------TENWKRPKSEV 69 (233)
T ss_pred CCCCCeEEEEc---cCCHHHHHHCCC-Chhhh-HHHHHHHHHHHHHHHHHcCCCEEEEeecc-------hhhcCcCHHHH
Confidence 34455566554 456544444444 22334 47888999999999999999999999855 34566555566
Q ss_pred HHHHH
Q 008441 254 SVLVD 258 (565)
Q Consensus 254 ~~l~~ 258 (565)
..|++
T Consensus 70 ~~Lm~ 74 (233)
T PRK14833 70 DFLMK 74 (233)
T ss_pred HHHHH
Confidence 65554
No 293
>PRK14831 undecaprenyl pyrophosphate synthase; Provisional
Probab=26.45 E-value=1.5e+02 Score=30.05 Aligned_cols=73 Identities=12% Similarity=0.167 Sum_probs=47.2
Q ss_pred CCCCceEEEEEEeCCCCeEEEeeeeccccCCChHHHHHHHHHHHHHHHHhcCCCeEEeecCCccchhhccCccCCcchhh
Q 008441 174 RVSLSAIGVAICDQMDNLIFELKKPLIKSGLNKSAAETKALIEGLNAALSMELDRVRVFIDCFPLFQFVTGRWPAKQRKI 253 (565)
Q Consensus 174 npg~ag~Gv~i~~~~~~~~~~~~~~~~~~~tn~n~AEy~Ali~gL~~al~l~~~~v~v~~DS~lv~~qv~G~w~~k~~~l 253 (565)
++-|.=+|++. +||.-+.-.+.+ ..... ..+=+.++..-++++.++|++.|.+|.=| ++.|+-....+
T Consensus 18 ~~~P~HVaiIm---DGNrRwA~~~gl-~~~~G-H~~G~~~l~~i~~~c~~~GI~~vT~yaFS-------~eN~kR~~~Ev 85 (249)
T PRK14831 18 QRLPKHVAVIM---DGNGRWAKRRGL-PRIMG-HRRGVDALKDLLRCCKDWGIGALTAYAFS-------TENWSRPLEEV 85 (249)
T ss_pred CCCCCeEEEec---CCcHHHHHHCCC-chhhh-HHHHHHHHHHHHHHHHHcCCCEEEEeecc-------hhhhCcCHHHH
Confidence 34456666654 455444444444 22335 47778899999999999999999999844 35666555555
Q ss_pred HHHHH
Q 008441 254 SVLVD 258 (565)
Q Consensus 254 ~~l~~ 258 (565)
..|++
T Consensus 86 ~~Lm~ 90 (249)
T PRK14831 86 NFLMT 90 (249)
T ss_pred HHHHH
Confidence 54443
No 294
>PLN02400 cellulose synthase
Probab=26.28 E-value=41 Score=40.67 Aligned_cols=44 Identities=20% Similarity=0.419 Sum_probs=28.7
Q ss_pred ccccCceeCCCCCCceecccCCCcCCCCChhhHhhhCCCCChhHHHHHHHHhcCCccccCCCCceeEecCC
Q 008441 422 GRRLGARKCTKCHRRFCIDCKVPWHNNMTCIYYKRLNPNPPTEDVKLKSLASSNLWRQCVKCNHLIELAEG 492 (565)
Q Consensus 422 ~~~~~~~~C~~C~~~fC~~C~~~~H~g~tC~e~~~~~~~~~~ed~~l~~l~~~~~~k~CPkC~~~IEK~~G 492 (565)
.+....+-|..|++..|.-| .+|.+ +.+.+-||+|++...+-.|
T Consensus 50 ~dGe~FVAC~eCaFPVCRpC----------YEYER-----------------keGnq~CPQCkTrYkR~Kg 93 (1085)
T PLN02400 50 ETGDVFVACNECAFPVCRPC----------YEYER-----------------KDGTQCCPQCKTRYRRHKG 93 (1085)
T ss_pred CCCCEEEEEccCCCccccch----------hheec-----------------ccCCccCcccCCccccccC
Confidence 34557788999999888865 34432 1234789998776654333
No 295
>PF03833 PolC_DP2: DNA polymerase II large subunit DP2; InterPro: IPR016033 DP2 is the large subunit of a two-subunit novel archaebacterial replicative DNA polymerase first characterised for Pyrococcus furiosus. The structure of DP2 appears to be organised as a ~950 residue component separated from a ~300 residue component by a ~150 residue intein. The other subunit, DP1, has sequence similarity to the eukaryotic DNA polymerase delta small subunit. This entry represents the N-terminal ~950 residue component of DP2.; GO: 0003887 DNA-directed DNA polymerase activity; PDB: 3O59_X.
Probab=26.27 E-value=22 Score=41.58 Aligned_cols=33 Identities=33% Similarity=0.807 Sum_probs=0.0
Q ss_pred ccccCCCCceeEecCCcceEEe-ecCcc-----ccccccccccCC
Q 008441 477 WRQCVKCNHLIELAEGCFHMTC-RCGHE-----FCYNCGAEWKNK 515 (565)
Q Consensus 477 ~k~CPkC~~~IEK~~GCnHMtC-~Cg~~-----FCw~C~~~~~~~ 515 (565)
.++||+|+...- ..+| .||.+ +|..|+......
T Consensus 655 ~r~Cp~Cg~~t~------~~~Cp~CG~~T~~~~~Cp~C~~~~~~~ 693 (900)
T PF03833_consen 655 RRRCPKCGKETF------YNRCPECGSHTEPVYVCPDCGIEVEED 693 (900)
T ss_dssp ---------------------------------------------
T ss_pred cccCcccCCcch------hhcCcccCCccccceeccccccccCcc
Confidence 388999998754 3467 48866 888888876643
No 296
>PF04216 FdhE: Protein involved in formate dehydrogenase formation; InterPro: IPR006452 This family of sequences describe an accessory protein required for the assembly of formate dehydrogenase of certain proteobacteria although not present in the final complex []. The exact nature of the function of FdhE in the assembly of the complex is unknown, but considering the presence of selenocysteine, molybdopterin, iron-sulphur clusters and cytochrome b556, it is likely to be involved in the insertion of cofactors. ; GO: 0005737 cytoplasm; PDB: 2FIY_B.
Probab=26.03 E-value=37 Score=34.95 Aligned_cols=34 Identities=32% Similarity=0.760 Sum_probs=14.0
Q ss_pred cccCCCCce-----eEecC--CcceEEe-ecCccc------ccccccc
Q 008441 478 RQCVKCNHL-----IELAE--GCFHMTC-RCGHEF------CYNCGAE 511 (565)
Q Consensus 478 k~CPkC~~~-----IEK~~--GCnHMtC-~Cg~~F------Cw~C~~~ 511 (565)
..||-|+.. |...+ |=-+++| .|+++| |-.||..
T Consensus 173 g~CPvCGs~P~~s~l~~~~~~G~R~L~Cs~C~t~W~~~R~~Cp~Cg~~ 220 (290)
T PF04216_consen 173 GYCPVCGSPPVLSVLRGGEREGKRYLHCSLCGTEWRFVRIKCPYCGNT 220 (290)
T ss_dssp SS-TTT---EEEEEEE------EEEEEETTT--EEE--TTS-TTT---
T ss_pred CcCCCCCCcCceEEEecCCCCccEEEEcCCCCCeeeecCCCCcCCCCC
Confidence 589999985 33333 7778888 477765 5555554
No 297
>PRK14828 undecaprenyl pyrophosphate synthase; Provisional
Probab=25.89 E-value=1.5e+02 Score=30.18 Aligned_cols=74 Identities=15% Similarity=0.153 Sum_probs=47.1
Q ss_pred CCCCceEEEEEEeCCCCeEEEeeeeccccC-CChHHHHHHHHHHHHHHHHhcCCCeEEeecCCccchhhccCccCCcchh
Q 008441 174 RVSLSAIGVAICDQMDNLIFELKKPLIKSG-LNKSAAETKALIEGLNAALSMELDRVRVFIDCFPLFQFVTGRWPAKQRK 252 (565)
Q Consensus 174 npg~ag~Gv~i~~~~~~~~~~~~~~~~~~~-tn~n~AEy~Ali~gL~~al~l~~~~v~v~~DS~lv~~qv~G~w~~k~~~ 252 (565)
.+-|.=+|+++ | ||.-+.-.+.+ ... .. ..+=+.++..-++++.++|++.|.||.-| +..|+.....
T Consensus 24 ~~~P~HvAiIm-D--GNrRwA~~~gl-~~~~~G-H~~G~~~l~~~~~~~~~~gIk~lTvYaFS-------~eN~~R~~~E 91 (256)
T PRK14828 24 AQVPGHVGIIV-D--GNRRWARKAGF-TDVSQG-HRAGAAKIGEFLGWCDETDVNVVTLYLLS-------TDNLGRPSEE 91 (256)
T ss_pred CCCCCEEEEEe-c--CChHHHHHcCC-CchHHH-HHHHHHHHHHHHHHHHHcCCCEEEEEEEE-------hhhcCCCHHH
Confidence 34556666654 3 44333333333 112 33 36778899999999999999999999855 3456666556
Q ss_pred hHHHHHH
Q 008441 253 ISVLVDQ 259 (565)
Q Consensus 253 l~~l~~~ 259 (565)
+..|++-
T Consensus 92 v~~Lm~L 98 (256)
T PRK14828 92 LNPLLDI 98 (256)
T ss_pred HHHHHHH
Confidence 6655543
No 298
>PF07754 DUF1610: Domain of unknown function (DUF1610); InterPro: IPR011668 This domain is found in archaeal species. It is likely to bind zinc via its four well-conserved cysteine residues.
Probab=25.82 E-value=61 Score=20.54 Aligned_cols=12 Identities=17% Similarity=0.357 Sum_probs=9.2
Q ss_pred ccCceeCCCCCC
Q 008441 424 RLGARKCTKCHR 435 (565)
Q Consensus 424 ~~~~~~C~~C~~ 435 (565)
....+.||.||.
T Consensus 13 ~~v~f~CPnCG~ 24 (24)
T PF07754_consen 13 QAVPFPCPNCGF 24 (24)
T ss_pred cCceEeCCCCCC
Confidence 366789999974
No 299
>COG1579 Zn-ribbon protein, possibly nucleic acid-binding [General function prediction only]
Probab=25.76 E-value=57 Score=32.74 Aligned_cols=60 Identities=17% Similarity=0.240 Sum_probs=37.0
Q ss_pred hHHHhhhhHHHHHHHHHHHHh-cCC--CCCcccccCCCCCCcccchhhhhccCCCcccccccCceeCCCCCC
Q 008441 367 SCRIFLTLKLFEIWNQRMKEA-LIP--VTEKVYCPYPKCSALMSKSEIERDASSSSFVGRRLGARKCTKCHR 435 (565)
Q Consensus 367 ~i~~lL~~e~~e~y~~~~~e~-~i~--~~~~~~CP~p~C~~~i~~~~~~e~~~s~~~~~~~~~~~~C~~C~~ 435 (565)
.+..-++++++..|.+..... ... .-...-|. +|...++..... ........++||.||.
T Consensus 167 ~L~~~l~~ell~~yeri~~~~kg~gvvpl~g~~C~--GC~m~l~~~~~~-------~V~~~d~iv~CP~CgR 229 (239)
T COG1579 167 ELKEKLDPELLSEYERIRKNKKGVGVVPLEGRVCG--GCHMKLPSQTLS-------KVRKKDEIVFCPYCGR 229 (239)
T ss_pred HHHHhcCHHHHHHHHHHHhcCCCceEEeecCCccc--CCeeeecHHHHH-------HHhcCCCCccCCccch
Confidence 355667889999888766544 221 12334676 888777654431 1122566789999885
No 300
>PTZ00415 transmission-blocking target antigen s230; Provisional
Probab=25.73 E-value=42 Score=42.26 Aligned_cols=21 Identities=24% Similarity=0.415 Sum_probs=9.3
Q ss_pred cccCCCCceeEecCCcceEEe
Q 008441 478 RQCVKCNHLIELAEGCFHMTC 498 (565)
Q Consensus 478 k~CPkC~~~IEK~~GCnHMtC 498 (565)
+.||--+.--.-.-|-..+||
T Consensus 94 ~~~~~~~~~~~~~~~~~~~~~ 114 (2849)
T PTZ00415 94 RTCPFHKEGSSFEMGSKNITC 114 (2849)
T ss_pred ccCccccccccccccccccce
Confidence 556643332222235555555
No 301
>PF14205 Cys_rich_KTR: Cysteine-rich KTR
Probab=25.60 E-value=44 Score=25.52 Aligned_cols=9 Identities=33% Similarity=0.995 Sum_probs=5.6
Q ss_pred CccccCCCC
Q 008441 476 LWRQCVKCN 484 (565)
Q Consensus 476 ~~k~CPkC~ 484 (565)
.|-.||.|+
T Consensus 3 ~Wi~CP~Cg 11 (55)
T PF14205_consen 3 EWILCPICG 11 (55)
T ss_pred eEEECCCCC
Confidence 356666666
No 302
>KOG1602 consensus Cis-prenyltransferase [Lipid transport and metabolism]
Probab=25.36 E-value=2.2e+02 Score=28.97 Aligned_cols=74 Identities=18% Similarity=0.181 Sum_probs=51.3
Q ss_pred CCCCceEEEEEEeCCCCeEEEeeeeccccCCChHHHHHHHHHHHHHHHHhcCCCeEEeecCCccchhhccCccCCcchhh
Q 008441 174 RVSLSAIGVAICDQMDNLIFELKKPLIKSGLNKSAAETKALIEGLNAALSMELDRVRVFIDCFPLFQFVTGRWPAKQRKI 253 (565)
Q Consensus 174 npg~ag~Gv~i~~~~~~~~~~~~~~~~~~~tn~n~AEy~Ali~gL~~al~l~~~~v~v~~DS~lv~~qv~G~w~~k~~~l 253 (565)
+|-|-=+++++ +||.-+.-++.+ ...-. ..|=+.+|++=|+...++|++.|.+|.=|- ..|+.....+
T Consensus 34 g~~P~HVaFIM---DGNRR~AKk~~L-~~~~G-H~aGf~~l~~ile~C~~lGI~~vT~fAFSi-------eNFkRs~eEV 101 (271)
T KOG1602|consen 34 GPMPRHVAFIM---DGNRRYAKKRGL-ETSEG-HEAGFEALKEILELCKELGIKEVTVFAFSI-------ENFKRSPEEV 101 (271)
T ss_pred CCCcceeEEEe---cCchHHHHhcCC-Ccccc-hHHHHHHHHHHHHHHHHcCCcEEEEEEEeh-------hhhCCCHHHH
Confidence 45556666654 467666667777 33345 599999999999999999999999998653 3344444445
Q ss_pred HHHHHH
Q 008441 254 SVLVDQ 259 (565)
Q Consensus 254 ~~l~~~ 259 (565)
.-|++=
T Consensus 102 d~LM~L 107 (271)
T KOG1602|consen 102 DGLMDL 107 (271)
T ss_pred HHHHHH
Confidence 444443
No 303
>PF14471 DUF4428: Domain of unknown function (DUF4428)
Probab=25.31 E-value=51 Score=24.77 Aligned_cols=30 Identities=30% Similarity=0.472 Sum_probs=21.2
Q ss_pred ccceeccccccCCceeecCCCcccchhhHHHH
Q 008441 310 TCVICLEDTDVGHMFSIDGCLHRYCFLCMKKH 341 (565)
Q Consensus 310 ~C~IC~e~~~~~~~~~l~~C~H~fC~~Cl~~~ 341 (565)
.|.||......-..+.+ .=| ..|.+|++..
T Consensus 1 ~C~iCg~kigl~~~~k~-~DG-~iC~~C~~Kl 30 (51)
T PF14471_consen 1 KCAICGKKIGLFKRFKI-KDG-YICKDCLKKL 30 (51)
T ss_pred CCCccccccccccceec-cCc-cchHHHHHHh
Confidence 49999988654443444 335 8999999875
No 304
>PHA02825 LAP/PHD finger-like protein; Provisional
Probab=25.04 E-value=73 Score=29.85 Aligned_cols=50 Identities=20% Similarity=0.513 Sum_probs=34.3
Q ss_pred cccccceeccccccCCceeecCCCc-----ccchhhHHHHHHHHHhCCCCCCCCCCCCCCccchh
Q 008441 307 INETCVICLEDTDVGHMFSIDGCLH-----RYCFLCMKKHIEEKLRQGMEPTCPHEGCKSKLEVE 366 (565)
Q Consensus 307 ~~~~C~IC~e~~~~~~~~~l~~C~H-----~fC~~Cl~~~i~~~i~~g~~~kCP~~~C~~~l~~~ 366 (565)
....|-||+++... . . .+|.+ ....+|++.|+..+ ....|+. |+.+....
T Consensus 7 ~~~~CRIC~~~~~~-~-~--~PC~CkGs~k~VH~sCL~rWi~~s----~~~~Cei--C~~~Y~i~ 61 (162)
T PHA02825 7 MDKCCWICKDEYDV-V-T--NYCNCKNENKIVHKECLEEWINTS----KNKSCKI--CNGPYNIK 61 (162)
T ss_pred CCCeeEecCCCCCC-c-c--CCcccCCCchHHHHHHHHHHHhcC----CCCcccc--cCCeEEEE
Confidence 45699999988532 2 1 25554 56999999999742 3457987 88776543
No 305
>PRK14834 undecaprenyl pyrophosphate synthase; Provisional
Probab=24.71 E-value=2.1e+02 Score=29.01 Aligned_cols=73 Identities=16% Similarity=0.204 Sum_probs=45.9
Q ss_pred CCCCceEEEEEEeCCCCeEEEeeeeccccCCChHHHHHHHHHHHHHHHHhcCCCeEEeecCCccchhhccCccCCcchhh
Q 008441 174 RVSLSAIGVAICDQMDNLIFELKKPLIKSGLNKSAAETKALIEGLNAALSMELDRVRVFIDCFPLFQFVTGRWPAKQRKI 253 (565)
Q Consensus 174 npg~ag~Gv~i~~~~~~~~~~~~~~~~~~~tn~n~AEy~Ali~gL~~al~l~~~~v~v~~DS~lv~~qv~G~w~~k~~~l 253 (565)
++-|.=+|+++ | ||.-+.-.+.+ ..... ..+=+..|..-++++.++|++.|.||.-| +..|+-....+
T Consensus 12 ~~~P~HVAiIm-D--GNrRwAk~~g~-~~~~G-H~~G~~~l~~i~~~c~~lgI~~lTvYaFS-------~eN~~R~~~EV 79 (249)
T PRK14834 12 MSVPRHVAIIM-D--GNGRWAKARGL-PRAAG-HRAGVEALRRVVRAAGELGIGYLTLFAFS-------SENWSRPASEV 79 (249)
T ss_pred CCCCCeEEEEe-c--CchHHHHHCCC-chhhh-HHHHHHHHHHHHHHHHHcCCCEEEEEEEe-------ccccCCCHHHH
Confidence 45566676654 4 44322222333 11224 46778889999999999999999999855 34565555555
Q ss_pred HHHHH
Q 008441 254 SVLVD 258 (565)
Q Consensus 254 ~~l~~ 258 (565)
..|++
T Consensus 80 ~~Lm~ 84 (249)
T PRK14834 80 SDLFG 84 (249)
T ss_pred HHHHH
Confidence 55544
No 306
>COG2824 PhnA Uncharacterized Zn-ribbon-containing protein involved in phosphonate metabolism [Inorganic ion transport and metabolism]
Probab=24.44 E-value=54 Score=28.54 Aligned_cols=23 Identities=35% Similarity=0.881 Sum_probs=14.8
Q ss_pred cccCCCCceeEe-cCCcceEEee-cCc
Q 008441 478 RQCVKCNHLIEL-AEGCFHMTCR-CGH 502 (565)
Q Consensus 478 k~CPkC~~~IEK-~~GCnHMtC~-Cg~ 502 (565)
..||+|..-..- +++ +|.|. |.+
T Consensus 4 p~cp~c~sEytYed~~--~~~cpec~~ 28 (112)
T COG2824 4 PPCPKCNSEYTYEDGG--QLICPECAH 28 (112)
T ss_pred CCCCccCCceEEecCc--eEeCchhcc
Confidence 579999765444 444 77764 555
No 307
>smart00834 CxxC_CXXC_SSSS Putative regulatory protein. CxxC_CXXC_SSSS represents a region of about 41 amino acids found in a number of small proteins in a wide range of bacteria. The region usually begins with the initiator Met and contains two CxxC motifs separated by 17 amino acids. One protein in this entry has been noted as a putative regulatory protein, designated FmdB. Most proteins in this entry have a C-terminal region containing highly degenerate sequence.
Probab=24.40 E-value=43 Score=23.23 Aligned_cols=10 Identities=40% Similarity=1.092 Sum_probs=4.6
Q ss_pred ccCCCCceeE
Q 008441 479 QCVKCNHLIE 488 (565)
Q Consensus 479 ~CPkC~~~IE 488 (565)
+||+|+..++
T Consensus 7 ~C~~Cg~~fe 16 (41)
T smart00834 7 RCEDCGHTFE 16 (41)
T ss_pred EcCCCCCEEE
Confidence 3444444444
No 308
>PLN02915 cellulose synthase A [UDP-forming], catalytic subunit
Probab=24.07 E-value=47 Score=40.00 Aligned_cols=46 Identities=26% Similarity=0.478 Sum_probs=30.1
Q ss_pred ccccCceeCCCCCCceecccCCCcCCCCChhhHhhhCCCCChhHHHHHHHHhcCCccccCCCCceeEecCCcc
Q 008441 422 GRRLGARKCTKCHRRFCIDCKVPWHNNMTCIYYKRLNPNPPTEDVKLKSLASSNLWRQCVKCNHLIELAEGCF 494 (565)
Q Consensus 422 ~~~~~~~~C~~C~~~fC~~C~~~~H~g~tC~e~~~~~~~~~~ed~~l~~l~~~~~~k~CPkC~~~IEK~~GCn 494 (565)
......+-|..|++..|..|- +|.+ +.+.+-||+|+....+-.|++
T Consensus 29 ~~Ge~FVAC~eC~fpvCr~cy----------eye~-----------------~~g~~~cp~c~t~y~~~~~~~ 74 (1044)
T PLN02915 29 EDGQPFVACHVCGFPVCKPCY----------EYER-----------------SEGNQCCPQCNTRYKRHKGCP 74 (1044)
T ss_pred CCCCEEEEeccCCCccccchh----------hhhh-----------------hcCCccCCccCCchhhhcCCC
Confidence 345677999999999998663 3432 123378999877766444433
No 309
>COG1096 Predicted RNA-binding protein (consists of S1 domain and a Zn-ribbon domain) [Translation, ribosomal structure and biogenesis]
Probab=24.01 E-value=52 Score=31.66 Aligned_cols=25 Identities=24% Similarity=0.733 Sum_probs=19.6
Q ss_pred cccCCCCceeEecCCcceEEe-ecCccc
Q 008441 478 RQCVKCNHLIELAEGCFHMTC-RCGHEF 504 (565)
Q Consensus 478 k~CPkC~~~IEK~~GCnHMtC-~Cg~~F 504 (565)
-.|++|+...++ .| +.|+| +||+.=
T Consensus 150 A~CsrC~~~L~~-~~-~~l~Cp~Cg~tE 175 (188)
T COG1096 150 ARCSRCRAPLVK-KG-NMLKCPNCGNTE 175 (188)
T ss_pred EEccCCCcceEE-cC-cEEECCCCCCEE
Confidence 579999999999 33 78888 588743
No 310
>KOG2807 consensus RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit SSL1 [Transcription; Replication, recombination and repair]
Probab=23.91 E-value=39 Score=35.18 Aligned_cols=28 Identities=18% Similarity=0.622 Sum_probs=17.8
Q ss_pred cceeccccccCCceeecCCCcccchhhH
Q 008441 311 CVICLEDTDVGHMFSIDGCLHRYCFLCM 338 (565)
Q Consensus 311 C~IC~e~~~~~~~~~l~~C~H~fC~~Cl 338 (565)
|-.|.++......+....|.+.||.+|=
T Consensus 333 Cf~C~~~~~~~~~y~C~~Ck~~FCldCD 360 (378)
T KOG2807|consen 333 CFACQGELLSSGRYRCESCKNVFCLDCD 360 (378)
T ss_pred eeeeccccCCCCcEEchhccceeeccch
Confidence 6666555544555666667777777773
No 311
>PRK13189 peroxiredoxin; Provisional
Probab=23.88 E-value=1.1e+02 Score=30.17 Aligned_cols=72 Identities=19% Similarity=0.256 Sum_probs=45.2
Q ss_pred EEEEEEeCCCCeEEEeeeeccccCCChHHHHHHHHHHHHHHHHhcCCCeEEeecCCccchhhccCccCCcc----hhhHH
Q 008441 180 IGVAICDQMDNLIFELKKPLIKSGLNKSAAETKALIEGLNAALSMELDRVRVFIDCFPLFQFVTGRWPAKQ----RKISV 255 (565)
Q Consensus 180 ~Gv~i~~~~~~~~~~~~~~~~~~~tn~n~AEy~Ali~gL~~al~l~~~~v~v~~DS~lv~~qv~G~w~~k~----~~l~~ 255 (565)
=+++|+|++|.+......++ ...+|..|...+|.+|+..-+.|.- .=-.|.+.+ +.+.+
T Consensus 127 r~tfIID~~G~Ir~~~~~~~---~~gr~~~eilr~l~alq~~~~~~~~--------------~p~~w~~g~~~~~~~~~~ 189 (222)
T PRK13189 127 RAVFIIDPKGIIRAILYYPQ---EVGRNMDEILRLVKALQTSDEKGVA--------------TPANWPPNDLIKDKVIVP 189 (222)
T ss_pred eEEEEECCCCeEEEEEecCC---CCCCCHHHHHHHHHHhhhHhhcCcC--------------cCCCCCCCCCCCCceeeC
Confidence 46889999887655544444 2344688999999988876666630 113476666 55655
Q ss_pred HHHHHHHHhhhcc
Q 008441 256 LVDQVSLLEKRFS 268 (565)
Q Consensus 256 l~~~v~~Ll~~F~ 268 (565)
-...+....++|+
T Consensus 190 ~~~~~~~~~~~~~ 202 (222)
T PRK13189 190 PASSVEEAKKRLE 202 (222)
T ss_pred CCCCHHHHHHhhc
Confidence 5445555555554
No 312
>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=23.84 E-value=26 Score=41.07 Aligned_cols=20 Identities=20% Similarity=0.489 Sum_probs=0.0
Q ss_pred chhhccCccCCc----chhhHHHHH
Q 008441 238 LFQFVTGRWPAK----QRKISVLVD 258 (565)
Q Consensus 238 v~~qv~G~w~~k----~~~l~~l~~ 258 (565)
++. |.+.|... +|.|..|..
T Consensus 246 lvE-~~~~w~F~~Y~~~P~L~~L~~ 269 (787)
T PF03115_consen 246 LVE-LRATWQFSNYNAKPALANLVK 269 (787)
T ss_dssp -------------------------
T ss_pred EEE-EEEEEEecCCCCCcchhhhhc
Confidence 444 55666544 355555544
No 313
>PF13834 DUF4193: Domain of unknown function (DUF4193)
Probab=23.78 E-value=37 Score=29.18 Aligned_cols=33 Identities=15% Similarity=0.230 Sum_probs=24.2
Q ss_pred CcccccccceeccccccCCceeecCCCcccchhh
Q 008441 304 GKTINETCVICLEDTDVGHMFSIDGCLHRYCFLC 337 (565)
Q Consensus 304 ~~~~~~~C~IC~e~~~~~~~~~l~~C~H~fC~~C 337 (565)
++...|+|.-||=-...+++-. ..=|+.+|.+|
T Consensus 66 ~q~DEFTCssCFLV~HRSqLa~-~~~g~~iC~DC 98 (99)
T PF13834_consen 66 KQADEFTCSSCFLVHHRSQLAR-EKDGQPICRDC 98 (99)
T ss_pred CCCCceeeeeeeeEechhhhcc-ccCCCEecccc
Confidence 4556899999996655555544 34588999998
No 314
>PF00628 PHD: PHD-finger; InterPro: IPR019787 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents the PHD (homeodomain) zinc finger domain [,], which is a C4HC3 zinc-finger-like motif found in nuclear proteins thought to be involved in chromatin-mediated transcriptional regulation. The PHD finger motif is reminiscent of, but distinct from the C3HC4 type RING finger. The function of this domain is not yet known but in analogy with the LIM domain it could be involved in protein-protein interaction and be important for the assembly or activity of multicomponent complexes involved in transcriptional activation or repression. Alternatively, the interactions could be intra-molecular and be important in maintaining the structural integrity of the protein. In similarity to the RING finger and the LIM domain, the PHD finger is thought to bind two zinc ions. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0005515 protein binding; PDB: 3ZVY_A 2LGG_A 3SOW_A 3SOU_B 3ASL_A 3ASK_A 3ZVZ_B 3T6R_A 2LGK_A 3SOX_B ....
Probab=23.61 E-value=42 Score=24.52 Aligned_cols=34 Identities=26% Similarity=0.549 Sum_probs=27.4
Q ss_pred ccceeccccccCCceeecCCCcccchhhHHHHHH
Q 008441 310 TCVICLEDTDVGHMFSIDGCLHRYCFLCMKKHIE 343 (565)
Q Consensus 310 ~C~IC~e~~~~~~~~~l~~C~H~fC~~Cl~~~i~ 343 (565)
.|.||........++....|+..|...|+.-...
T Consensus 1 ~C~vC~~~~~~~~~i~C~~C~~~~H~~C~~~~~~ 34 (51)
T PF00628_consen 1 YCPVCGQSDDDGDMIQCDSCNRWYHQECVGPPEK 34 (51)
T ss_dssp EBTTTTSSCTTSSEEEBSTTSCEEETTTSTSSHS
T ss_pred eCcCCCCcCCCCCeEEcCCCChhhCcccCCCChh
Confidence 4888988666778888889999999999886554
No 315
>cd03016 PRX_1cys Peroxiredoxin (PRX) family, 1-cys PRX subfamily; composed of PRXs containing only one conserved cysteine, which serves as the peroxidatic cysteine. They are homodimeric thiol-specific antioxidant (TSA) proteins that confer a protective role in cells by reducing and detoxifying hydrogen peroxide, peroxynitrite, and organic hydroperoxides. As with all other PRXs, a cysteine sulfenic acid intermediate is formed upon reaction of 1-cys PRX with its substrates. Having no resolving cysteine, the oxidized enzyme is resolved by an external small-molecule or protein reductant such as thioredoxin or glutaredoxin. Similar to typical 2-cys PRX, 1-cys PRX forms a functional dimeric unit with a B-type interface, as well as a decameric structure which is stabilized in the reduced form of the enzyme. Other oligomeric forms, tetramers and hexamers, have also been reported. Mammalian 1-cys PRX is localized cellularly in the cytosol and is expressed at high levels in brain, eye, testes an
Probab=23.58 E-value=1.5e+02 Score=28.64 Aligned_cols=43 Identities=16% Similarity=0.176 Sum_probs=31.2
Q ss_pred EEEEEeCCCCeEEEeeeeccccCCChHHHHHHHHHHHHHHHHhcCC
Q 008441 181 GVAICDQMDNLIFELKKPLIKSGLNKSAAETKALIEGLNAALSMEL 226 (565)
Q Consensus 181 Gv~i~~~~~~~~~~~~~~~~~~~tn~n~AEy~Ali~gL~~al~l~~ 226 (565)
+++|+|++|.+++....++ ...+|..|...+|.+|+..-+.|+
T Consensus 119 ~~fiID~~G~I~~~~~~~~---~~gr~~~ell~~l~~lq~~~~~~~ 161 (203)
T cd03016 119 AVFIIDPDKKIRLILYYPA---TTGRNFDEILRVVDALQLTDKHKV 161 (203)
T ss_pred EEEEECCCCeEEEEEecCC---CCCCCHHHHHHHHHHHhhHhhcCc
Confidence 5788899988776665555 234468999999988877666654
No 316
>PRK12286 rpmF 50S ribosomal protein L32; Reviewed
Probab=23.41 E-value=45 Score=25.71 Aligned_cols=21 Identities=29% Similarity=0.672 Sum_probs=14.9
Q ss_pred ccccCCCCceeEecCCcceEEe-ecCc
Q 008441 477 WRQCVKCNHLIELAEGCFHMTC-RCGH 502 (565)
Q Consensus 477 ~k~CPkC~~~IEK~~GCnHMtC-~Cg~ 502 (565)
...||+|+.+.. .|-.| .||+
T Consensus 27 l~~C~~CG~~~~-----~H~vC~~CG~ 48 (57)
T PRK12286 27 LVECPNCGEPKL-----PHRVCPSCGY 48 (57)
T ss_pred ceECCCCCCccC-----CeEECCCCCc
Confidence 467999999887 36666 3653
No 317
>PRK13191 putative peroxiredoxin; Provisional
Probab=23.39 E-value=1.4e+02 Score=29.38 Aligned_cols=43 Identities=19% Similarity=0.188 Sum_probs=31.6
Q ss_pred EEEEEEeCCCCeEEEeeeeccccCCChHHHHHHHHHHHHHHHHhcC
Q 008441 180 IGVAICDQMDNLIFELKKPLIKSGLNKSAAETKALIEGLNAALSME 225 (565)
Q Consensus 180 ~Gv~i~~~~~~~~~~~~~~~~~~~tn~n~AEy~Ali~gL~~al~l~ 225 (565)
=++.|+|++|.+.+....++ .+++|..|...+|.+|+..-+.|
T Consensus 125 r~tfIID~~G~Ir~~~~~~~---~~gr~~~eilr~l~alq~~~~~~ 167 (215)
T PRK13191 125 RAVFIVDDKGTVRLILYYPM---EIGRNIDEILRAIRALQLVDKAG 167 (215)
T ss_pred EEEEEECCCCEEEEEEecCC---CCCCCHHHHHHHHHHhhhhhhcC
Confidence 37789999887766555555 33457999999999988766555
No 318
>PRK09521 exosome complex RNA-binding protein Csl4; Provisional
Probab=23.31 E-value=56 Score=31.40 Aligned_cols=26 Identities=23% Similarity=0.630 Sum_probs=20.6
Q ss_pred cccCCCCceeEecCCcceEEe-ecCccc
Q 008441 478 RQCVKCNHLIELAEGCFHMTC-RCGHEF 504 (565)
Q Consensus 478 k~CPkC~~~IEK~~GCnHMtC-~Cg~~F 504 (565)
-.|++|+.+..+ .+.|+|.| .||+..
T Consensus 150 a~~~~~g~~~~~-~~~~~~~c~~~~~~e 176 (189)
T PRK09521 150 AMCSRCRTPLVK-KGENELKCPNCGNIE 176 (189)
T ss_pred EEccccCCceEE-CCCCEEECCCCCCEE
Confidence 479999999987 44599999 598753
No 319
>TIGR03826 YvyF flagellar operon protein TIGR03826. This gene is found in flagellar operons of Bacillus-related organisms. Its function has not been determined and an official gene symbol has not been assigned, although the gene is designated yvyF in B. subtilus. A tentative assignment as a regulator is suggested in the NCBI record GI:16080597.
Probab=23.13 E-value=62 Score=29.67 Aligned_cols=25 Identities=28% Similarity=0.622 Sum_probs=17.6
Q ss_pred ccccCCCCceeEecCCcceEEeecCcccccccccccc
Q 008441 477 WRQCVKCNHLIELAEGCFHMTCRCGHEFCYNCGAEWK 513 (565)
Q Consensus 477 ~k~CPkC~~~IEK~~GCnHMtC~Cg~~FCw~C~~~~~ 513 (565)
.-+|.+|+.+|.. -.||-.|.....
T Consensus 81 ~~~CE~CG~~I~~------------Gr~C~~C~~~l~ 105 (137)
T TIGR03826 81 GYPCERCGTSIRE------------GRLCDSCAGELK 105 (137)
T ss_pred cCcccccCCcCCC------------CCccHHHHHHHH
Confidence 3678888888862 267778877654
No 320
>KOG2932 consensus E3 ubiquitin ligase involved in ubiquitination of E-cadherin complex [Posttranslational modification, protein turnover, chaperones]
Probab=23.08 E-value=37 Score=35.07 Aligned_cols=32 Identities=19% Similarity=0.430 Sum_probs=21.7
Q ss_pred ccccceeccccccCCceeecCCCcccchhhHHHH
Q 008441 308 NETCVICLEDTDVGHMFSIDGCLHRYCFLCMKKH 341 (565)
Q Consensus 308 ~~~C~IC~e~~~~~~~~~l~~C~H~fC~~Cl~~~ 341 (565)
...|.-|--. ..---.+.+|.|.||.+|-+..
T Consensus 90 VHfCd~Cd~P--I~IYGRmIPCkHvFCl~CAr~~ 121 (389)
T KOG2932|consen 90 VHFCDRCDFP--IAIYGRMIPCKHVFCLECARSD 121 (389)
T ss_pred eEeecccCCc--ceeeecccccchhhhhhhhhcC
Confidence 4578888533 2222235699999999998754
No 321
>PF11023 DUF2614: Protein of unknown function (DUF2614); InterPro: IPR020912 This entry describes proteins of unknown function, which are thought to be membrane proteins.; GO: 0005887 integral to plasma membrane
Probab=22.99 E-value=48 Score=29.18 Aligned_cols=23 Identities=26% Similarity=0.720 Sum_probs=15.1
Q ss_pred cCceeCCCCCCc--------eecccCCCcCC
Q 008441 425 LGARKCTKCHRR--------FCIDCKVPWHN 447 (565)
Q Consensus 425 ~~~~~C~~C~~~--------fC~~C~~~~H~ 447 (565)
...+.||.|++. .|..|+.|-+-
T Consensus 67 av~V~CP~C~K~TKmLGr~D~CM~C~~pLTL 97 (114)
T PF11023_consen 67 AVQVECPNCGKQTKMLGRVDACMHCKEPLTL 97 (114)
T ss_pred ceeeECCCCCChHhhhchhhccCcCCCcCcc
Confidence 445667777654 48888887653
No 322
>cd02960 AGR Anterior Gradient (AGR) family; members of this family are similar to secreted proteins encoded by the cement gland-specific genes XAG-1 and XAG-2, expressed in the anterior region of dorsal ectoderm of Xenopus. They are implicated in the formation of the cement gland and the induction of forebrain fate. The human homologs, hAG-2 and hAG-3, are secreted proteins associated with estrogen-positive breast tumors. Yeast two-hybrid studies identified the metastasis-associated C4.4a protein and dystroglycan as binding partners, indicating possible roles in the development and progression of breast cancer. hAG-2 has also been implicated in prostate cancer. Its gene was cloned as an androgen-inducible gene and it was shown to be overexpressed in prostate cancer cells at the mRNA and protein levels. AGR proteins contain one conserved cysteine corresponding to the first cysteine in the CXXC motif of TRX. They show high sequence similarity to ERp19.
Probab=22.97 E-value=1.1e+02 Score=27.78 Aligned_cols=47 Identities=19% Similarity=0.219 Sum_probs=30.6
Q ss_pred CCCCceEE---EEEEeCCCCeEEEeeeeccccCCChH----HHHHHHHHHHHHHHHhc
Q 008441 174 RVSLSAIG---VAICDQMDNLIFELKKPLIKSGLNKS----AAETKALIEGLNAALSM 224 (565)
Q Consensus 174 npg~ag~G---v~i~~~~~~~~~~~~~~~~~~~tn~n----~AEy~Ali~gL~~al~l 224 (565)
|+.+.|.| +++.+++|.++.++.+.+ +|+. .++..-|+.+++.|+.|
T Consensus 72 ~~~~~g~~vPtivFld~~g~vi~~i~Gy~----~~~~~~y~~~~~~~~~~~m~~a~~~ 125 (130)
T cd02960 72 NLSPDGQYVPRIMFVDPSLTVRADITGRY----SNRLYTYEPADIPLLIENMKKALKL 125 (130)
T ss_pred CcCccCcccCeEEEECCCCCCcccccccc----cCccceeCcCcHHHHHHHHHHHHHH
Confidence 55455555 477899998886665444 4431 34555788888888765
No 323
>COG2816 NPY1 NTP pyrophosphohydrolases containing a Zn-finger, probably nucleic-acid-binding [DNA replication, recombination, and repair]
Probab=22.94 E-value=69 Score=32.89 Aligned_cols=28 Identities=36% Similarity=0.793 Sum_probs=23.7
Q ss_pred ccccCCCCceeEecCCcceEEe-ecCccc
Q 008441 477 WRQCVKCNHLIELAEGCFHMTC-RCGHEF 504 (565)
Q Consensus 477 ~k~CPkC~~~IEK~~GCnHMtC-~Cg~~F 504 (565)
.|-||+|+...+-..|=-.+.| .||+.+
T Consensus 111 ~RFCg~CG~~~~~~~~g~~~~C~~cg~~~ 139 (279)
T COG2816 111 HRFCGRCGTKTYPREGGWARVCPKCGHEH 139 (279)
T ss_pred CcCCCCCCCcCccccCceeeeCCCCCCcc
Confidence 3889999999999888888888 588765
No 324
>PF13382 Adenine_deam_C: Adenine deaminase C-terminal domain; PDB: 3T8L_B 3T81_A 3NQB_A.
Probab=22.92 E-value=1.6e+02 Score=28.09 Aligned_cols=47 Identities=23% Similarity=0.293 Sum_probs=34.2
Q ss_pred eEEEEEEeCCCCeEEEeeeeccccCCChHHHHHHHHHHHHHHHH-hcCC
Q 008441 179 AIGVAICDQMDNLIFELKKPLIKSGLNKSAAETKALIEGLNAAL-SMEL 226 (565)
Q Consensus 179 g~Gv~i~~~~~~~~~~~~~~~~~~~tn~n~AEy~Ali~gL~~al-~l~~ 226 (565)
|-|+++++ +|+++.++.-|+-|-.++....|..+-++.|+.|+ ++|.
T Consensus 89 gGG~vvv~-~g~v~a~lpLpi~GlmS~~~~eev~~~~~~l~~~~~~lG~ 136 (171)
T PF13382_consen 89 GGGIVVVD-DGEVLAELPLPIAGLMSDLPAEEVARQLEELEEALRELGC 136 (171)
T ss_dssp TSEEEEEE-TTEEEEEEE-TBTTTBBSS-HHHHHHHHHHHHHHHHTTS-
T ss_pred CCCEEEEE-CCEEEEEEeccccceecCCCHHHHHHHHHHHHHHHHHcCC
Confidence 45777777 47899999999967677766788888888888776 5674
No 325
>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=22.88 E-value=32 Score=26.73 Aligned_cols=39 Identities=21% Similarity=0.479 Sum_probs=29.6
Q ss_pred cccCCCCceeEec--CCcceEEe-ecCccccccccccccCCC
Q 008441 478 RQCVKCNHLIELA--EGCFHMTC-RCGHEFCYNCGAEWKNKK 516 (565)
Q Consensus 478 k~CPkC~~~IEK~--~GCnHMtC-~Cg~~FCw~C~~~~~~~~ 516 (565)
..||-|+...--. +-=|+=+| .|+..-|-.||-.-.+|-
T Consensus 3 ~~CPlCkt~~n~gsk~~pNyntCT~Ck~~VCnlCGFNP~Phl 44 (61)
T PF05715_consen 3 SLCPLCKTTLNVGSKDPPNYNTCTECKSQVCNLCGFNPTPHL 44 (61)
T ss_pred ccCCcccchhhcCCCCCCCccHHHHHhhhhhcccCCCCCccc
Confidence 4699999876321 24588999 599999999998766553
No 326
>KOG1039 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=22.43 E-value=30 Score=36.66 Aligned_cols=39 Identities=21% Similarity=0.657 Sum_probs=26.3
Q ss_pred CCCCCceecccCCCcCCCCChhhHhhhCCCCChhHHHHHHHHhcCCccccCCCCceeEec
Q 008441 431 TKCHRRFCIDCKVPWHNNMTCIYYKRLNPNPPTEDVKLKSLASSNLWRQCVKCNHLIELA 490 (565)
Q Consensus 431 ~~C~~~fC~~C~~~~H~g~tC~e~~~~~~~~~~ed~~l~~l~~~~~~k~CPkC~~~IEK~ 490 (565)
+.|.+.||.+|...|+.-.. . ..+..|-||-|++.....
T Consensus 185 pnC~H~~Cl~Cir~wr~~~q-----------------~----~~~~sksCP~CRv~s~~v 223 (344)
T KOG1039|consen 185 PNCNHSFCLNCIRKWRQATQ-----------------F----ESKTSKSCPFCRVPSSFV 223 (344)
T ss_pred CCcchhhhhcHhHhhhhhhc-----------------c----ccccccCCCcccCccccc
Confidence 67999999999998863210 0 223347888888876643
No 327
>PRK14835 undecaprenyl pyrophosphate synthase; Provisional
Probab=22.43 E-value=1.8e+02 Score=29.86 Aligned_cols=74 Identities=15% Similarity=0.225 Sum_probs=47.0
Q ss_pred CCCceEEEEEEeCCCCeEEEeeeeccccCCChHHHHHHHHHHHHHHHHhcCCCeEEeecCCccchhhccCccCCcchhhH
Q 008441 175 VSLSAIGVAICDQMDNLIFELKKPLIKSGLNKSAAETKALIEGLNAALSMELDRVRVFIDCFPLFQFVTGRWPAKQRKIS 254 (565)
Q Consensus 175 pg~ag~Gv~i~~~~~~~~~~~~~~~~~~~tn~n~AEy~Ali~gL~~al~l~~~~v~v~~DS~lv~~qv~G~w~~k~~~l~ 254 (565)
+-|.=+|+++ | ||..+.-.+.+ ....+ ..+=+.+|..-++++.++|++.|.||.-| +..|+-....+.
T Consensus 40 ~~P~HVAiIm-D--GNrRwAk~~g~-~~~~G-H~~G~~~l~~i~~~c~~lGIk~lTvYaFS-------~EN~~R~~~EV~ 107 (275)
T PRK14835 40 KLPRHLGLIL-D--GNRRFARALGL-QREMG-HEFGVQKAYEVLEWCLELGIPTVTIWVFS-------TDNFSRSPAEVE 107 (275)
T ss_pred CCCCEEEEEe-c--CchHHHHHCCC-CHHHH-HHHHHHHHHHHHHHHHHcCCCEEEEEEEE-------ccccCCCHHHHH
Confidence 3455566554 4 45433333333 22224 36778899999999999999999999855 355665555666
Q ss_pred HHHHHH
Q 008441 255 VLVDQV 260 (565)
Q Consensus 255 ~l~~~v 260 (565)
.|++-+
T Consensus 108 ~Lm~L~ 113 (275)
T PRK14835 108 TLMNLF 113 (275)
T ss_pred HHHHHH
Confidence 665543
No 328
>PRK14837 undecaprenyl pyrophosphate synthase; Provisional
Probab=22.35 E-value=2.1e+02 Score=28.66 Aligned_cols=74 Identities=20% Similarity=0.252 Sum_probs=47.9
Q ss_pred CCCceEEEEEEeCCCCeEEEeeeeccccCCChHHHHHHHHHHHHHHHHhcCCCeEEeecCCccchhhccCccCCcchhhH
Q 008441 175 VSLSAIGVAICDQMDNLIFELKKPLIKSGLNKSAAETKALIEGLNAALSMELDRVRVFIDCFPLFQFVTGRWPAKQRKIS 254 (565)
Q Consensus 175 pg~ag~Gv~i~~~~~~~~~~~~~~~~~~~tn~n~AEy~Ali~gL~~al~l~~~~v~v~~DS~lv~~qv~G~w~~k~~~l~ 254 (565)
+-|.=+|+++ | ||.-+.-.+.+ ..... ..+=+.++..-++++.++|++.|.+|.=| +..|+-....+.
T Consensus 5 ~~P~HVAiIm-D--GNrRwAk~~gl-~~~~G-H~~G~~~~~~i~~~c~~~GI~~lT~YaFS-------~EN~~Rp~~EV~ 72 (230)
T PRK14837 5 SLPSHVGIIM-D--GNRRWALKKGL-SFFEG-HKEGLKRAKEIVKHSLKLGIKYLSLYVFS-------TENWNRTDSEIE 72 (230)
T ss_pred CCCCeEEEEc-c--CCHHHHHHCCC-chhhh-HHHHHHHHHHHHHHHHHcCCCEEEEEEee-------hhhcCCCHHHHH
Confidence 3445555543 4 45433333444 22234 47888899999999999999999999855 356776666666
Q ss_pred HHHHHH
Q 008441 255 VLVDQV 260 (565)
Q Consensus 255 ~l~~~v 260 (565)
.|++-+
T Consensus 73 ~Lm~L~ 78 (230)
T PRK14837 73 HLMFLI 78 (230)
T ss_pred HHHHHH
Confidence 665533
No 329
>PRK14842 undecaprenyl pyrophosphate synthase; Provisional
Probab=22.35 E-value=1.9e+02 Score=29.04 Aligned_cols=75 Identities=15% Similarity=0.167 Sum_probs=48.6
Q ss_pred CCCCceEEEEEEeCCCCeEEEeeeeccccCCChHHHHHHHHHHHHHHHHhcCCCeEEeecCCccchhhccCccCCcchhh
Q 008441 174 RVSLSAIGVAICDQMDNLIFELKKPLIKSGLNKSAAETKALIEGLNAALSMELDRVRVFIDCFPLFQFVTGRWPAKQRKI 253 (565)
Q Consensus 174 npg~ag~Gv~i~~~~~~~~~~~~~~~~~~~tn~n~AEy~Ali~gL~~al~l~~~~v~v~~DS~lv~~qv~G~w~~k~~~l 253 (565)
.|-|.=+|+++ +||.-+...+.+ ..... ..+=+..+..-++++.++|++.|.||.=| +..|+-....+
T Consensus 6 ~~~P~HVaiIm---DGNrRwAk~~gl-~~~~G-H~~G~~~l~~i~~~c~~lgI~~vTvYaFS-------~eN~~R~~~EV 73 (241)
T PRK14842 6 STIPAHIAVIM---DGNGRWAESQGK-KRSEG-HREGANAIDRLMDASLEYGLKNISLYAFS-------TENWKRPITEI 73 (241)
T ss_pred CCCCCeEEEEc---CCCHHHHHHCCC-ChhHh-HHHHHHHHHHHHHHHHHcCCCEEEEEEee-------hhhcCCCHHHH
Confidence 34455666654 455433333444 22334 47788899999999999999999999855 34566665666
Q ss_pred HHHHHHH
Q 008441 254 SVLVDQV 260 (565)
Q Consensus 254 ~~l~~~v 260 (565)
..|++-+
T Consensus 74 ~~Lm~L~ 80 (241)
T PRK14842 74 RSIFGLL 80 (241)
T ss_pred HHHHHHH
Confidence 6655533
No 330
>PF13453 zf-TFIIB: Transcription factor zinc-finger
Probab=22.26 E-value=54 Score=23.17 Aligned_cols=10 Identities=30% Similarity=1.079 Sum_probs=6.8
Q ss_pred cccCCCCCCccc
Q 008441 396 YCPYPKCSALMS 407 (565)
Q Consensus 396 ~CP~p~C~~~i~ 407 (565)
.|| .|+..|.
T Consensus 1 ~CP--~C~~~l~ 10 (41)
T PF13453_consen 1 KCP--RCGTELE 10 (41)
T ss_pred CcC--CCCcccc
Confidence 366 8887664
No 331
>PF01873 eIF-5_eIF-2B: Domain found in IF2B/IF5; InterPro: IPR002735 The beta subunit of archaeal and eukaryotic translation initiation factor 2 (IF2beta) and the N-terminal domain of translation initiation factor 5 (IF5) show significant sequence homology []. Archaeal IF2beta contains two independent structural domains: an N-terminal mixed alpha/beta core domain (topological similarity to the common core of ribosomal proteins L23 and L15e), and a C-terminal domain consisting of a zinc-binding C4 finger []. Archaeal IF2beta is a ribosome-dependent GTPase that stimulates the binding of initiator Met-tRNA(i)(Met) to the ribosomes, even in the absence of other factors []. The C-terminal domain of eukaryotic IF5 is involved in the formation of the multi-factor complex (MFC), an important intermediate for the 43S pre-initiation complex assembly []. IF5 interacts directly with IF1, IF2beta and IF3c, which together with IF2-bound Met-tRNA(i)(Met) form the MFC. This entry represents both the N-terminal and zinc-binding domains of IF2, as well as a domain in IF5.; GO: 0003743 translation initiation factor activity, 0006413 translational initiation; PDB: 2DCU_B 2D74_B 2E9H_A 2G2K_A 1NEE_A 3CW2_L 2QMU_C 3V11_C 2NXU_A 2QN6_C ....
Probab=22.24 E-value=74 Score=28.64 Aligned_cols=34 Identities=18% Similarity=0.560 Sum_probs=24.9
Q ss_pred HHHHHhcCCccccCCCCce---eEecCCcceEEee-cCcc
Q 008441 468 LKSLASSNLWRQCVKCNHL---IELAEGCFHMTCR-CGHE 503 (565)
Q Consensus 468 l~~l~~~~~~k~CPkC~~~---IEK~~GCnHMtC~-Cg~~ 503 (565)
+..++.. +-.||.|+.+ +.+.++-..|.|. ||..
T Consensus 86 L~~fI~~--yVlC~~C~spdT~l~k~~r~~~l~C~aCGa~ 123 (125)
T PF01873_consen 86 LDKFIKE--YVLCPECGSPDTELIKEGRLIFLKCKACGAS 123 (125)
T ss_dssp HHHHHCH--HSSCTSTSSSSEEEEEETTCCEEEETTTSCE
T ss_pred HHHHHHH--EEEcCCCCCCccEEEEcCCEEEEEecccCCc
Confidence 4444443 3689999986 6677888999995 9974
No 332
>PRK13599 putative peroxiredoxin; Provisional
Probab=21.99 E-value=1.5e+02 Score=29.10 Aligned_cols=44 Identities=16% Similarity=0.194 Sum_probs=31.2
Q ss_pred EEEEEEeCCCCeEEEeeeeccccCCChHHHHHHHHHHHHHHHHhcCC
Q 008441 180 IGVAICDQMDNLIFELKKPLIKSGLNKSAAETKALIEGLNAALSMEL 226 (565)
Q Consensus 180 ~Gv~i~~~~~~~~~~~~~~~~~~~tn~n~AEy~Ali~gL~~al~l~~ 226 (565)
=.+.|+|++|.+++....+. .+.+|..|...+|.+|+..-+.|+
T Consensus 120 R~tfIID~dG~Ir~~~~~p~---~~gr~~~eilr~l~~lq~~~~~~~ 163 (215)
T PRK13599 120 RAVFIVDDKGTIRLIMYYPQ---EVGRNVDEILRALKALQTADQYGV 163 (215)
T ss_pred eEEEEECCCCEEEEEEEcCC---CCCCCHHHHHHHHHHhhhhhhcCC
Confidence 46688899887766554444 334579999999988877666654
No 333
>PRK14841 undecaprenyl pyrophosphate synthase; Provisional
Probab=21.91 E-value=1.9e+02 Score=28.92 Aligned_cols=64 Identities=16% Similarity=0.203 Sum_probs=43.4
Q ss_pred CCCeEEEeeeeccccCCChHHHHHHHHHHHHHHHHhcCCCeEEeecCCccchhhccCccCCcchhhHHHHHHH
Q 008441 188 MDNLIFELKKPLIKSGLNKSAAETKALIEGLNAALSMELDRVRVFIDCFPLFQFVTGRWPAKQRKISVLVDQV 260 (565)
Q Consensus 188 ~~~~~~~~~~~~~~~~tn~n~AEy~Ali~gL~~al~l~~~~v~v~~DS~lv~~qv~G~w~~k~~~l~~l~~~v 260 (565)
+||.-+...+.+ -.... ..+=+.++.+-++++.++||+.|.||.=| +..|+-....+..|++-+
T Consensus 12 DGNrRwAk~~g~-~~~~G-H~~G~~~l~~i~~~~~~lgIk~lTvYaFS-------~eN~~R~~~Ev~~Lm~L~ 75 (233)
T PRK14841 12 DGNGRWAKKRGL-PRIKG-HQRGAEVLHNTVKWSLELGIKYLTAFSFS-------TENWKRPKEEVEFLMDLF 75 (233)
T ss_pred cCCHHHHHHCCC-chhhh-HHHHHHHHHHHHHHHHHcCCCEEEEEeee-------HhhcCCCHHHHHHHHHHH
Confidence 345433333434 22334 47888999999999999999999999855 356776666666666543
No 334
>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=21.88 E-value=97 Score=27.35 Aligned_cols=35 Identities=26% Similarity=0.593 Sum_probs=26.0
Q ss_pred CccccCCCCceeEecCCcceEEee-cCcccccccccc
Q 008441 476 LWRQCVKCNHLIELAEGCFHMTCR-CGHEFCYNCGAE 511 (565)
Q Consensus 476 ~~k~CPkC~~~IEK~~GCnHMtC~-Cg~~FCw~C~~~ 511 (565)
.-+.|..|..+.-...+.. ..|. |++.+|-.|+..
T Consensus 53 ~~~~C~~C~~~fg~l~~~~-~~C~~C~~~VC~~C~~~ 88 (118)
T PF02318_consen 53 GERHCARCGKPFGFLFNRG-RVCVDCKHRVCKKCGVY 88 (118)
T ss_dssp CCSB-TTTS-BCSCTSTTC-EEETTTTEEEETTSEEE
T ss_pred CCcchhhhCCcccccCCCC-CcCCcCCccccCccCCc
Confidence 3478999998876665555 7884 999999999887
No 335
>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=21.71 E-value=1.7e+02 Score=31.20 Aligned_cols=62 Identities=21% Similarity=0.455 Sum_probs=36.9
Q ss_pred CcccccccceeccccccCCceeec--------------C-----CCcccchhhHHHHHHHHHhCCC---CC--CCCCCCC
Q 008441 304 GKTINETCVICLEDTDVGHMFSID--------------G-----CLHRYCFLCMKKHIEEKLRQGM---EP--TCPHEGC 359 (565)
Q Consensus 304 ~~~~~~~C~IC~e~~~~~~~~~l~--------------~-----C~H~fC~~Cl~~~i~~~i~~g~---~~--kCP~~~C 359 (565)
+......|.-|+...+.-++...- . |.-..|.+||.+||..+-.+.. ++ +||-+.|
T Consensus 267 ~~~e~e~CigC~~~~~~vkl~k~C~~~~~~g~~~~~~~~C~~C~CRPmWC~~Cm~kwFasrQd~~~~~~Wl~~~~~CPtC 346 (358)
T PF10272_consen 267 SGQELEPCIGCMQAQPNVKLVKRCADEEQEGSPLPNEPPCQQCYCRPMWCLECMGKWFASRQDQQHPETWLSGKCPCPTC 346 (358)
T ss_pred CccccCCccccccCCCCcEEEeccCCcccCCcccccCCCCccccccchHHHHHHHHHhhhcCCCCChhhhhcCCCCCCCC
Confidence 334567899998765443333211 2 2234699999999987653321 12 4554569
Q ss_pred CCccch
Q 008441 360 KSKLEV 365 (565)
Q Consensus 360 ~~~l~~ 365 (565)
+..+-.
T Consensus 347 Ra~FCi 352 (358)
T PF10272_consen 347 RAKFCI 352 (358)
T ss_pred ccccee
Confidence 887543
No 336
>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]
Probab=21.50 E-value=59 Score=37.99 Aligned_cols=67 Identities=16% Similarity=0.385 Sum_probs=36.7
Q ss_pred hhhHHHHHHHHHHHHhc--C---CC---CCcccccCCCCCCcccchhhhhccCCCcccccccCceeCCCCCCc-----ee
Q 008441 372 LTLKLFEIWNQRMKEAL--I---PV---TEKVYCPYPKCSALMSKSEIERDASSSSFVGRRLGARKCTKCHRR-----FC 438 (565)
Q Consensus 372 L~~e~~e~y~~~~~e~~--i---~~---~~~~~CP~p~C~~~i~~~~~~e~~~s~~~~~~~~~~~~C~~C~~~-----fC 438 (565)
|++.+++...+.+.... + +. .....|. .|++.+.-++. ..+..-+...+...|..||+. .|
T Consensus 405 lS~~Ll~~i~~~l~~geQ~llflnRRGys~~l~C~--~Cg~v~~Cp~C----d~~lt~H~~~~~L~CH~Cg~~~~~p~~C 478 (730)
T COG1198 405 LSPALLEAIRKTLERGEQVLLFLNRRGYAPLLLCR--DCGYIAECPNC----DSPLTLHKATGQLRCHYCGYQEPIPQSC 478 (730)
T ss_pred CCHHHHHHHHHHHhcCCeEEEEEccCCccceeecc--cCCCcccCCCC----CcceEEecCCCeeEeCCCCCCCCCCCCC
Confidence 66777777766654321 1 11 1223455 45444322211 111123345688999999985 79
Q ss_pred cccCCC
Q 008441 439 IDCKVP 444 (565)
Q Consensus 439 ~~C~~~ 444 (565)
..|+..
T Consensus 479 p~Cgs~ 484 (730)
T COG1198 479 PECGSE 484 (730)
T ss_pred CCCCCC
Confidence 999987
No 337
>COG4640 Predicted membrane protein [Function unknown]
Probab=21.28 E-value=42 Score=35.84 Aligned_cols=8 Identities=38% Similarity=1.028 Sum_probs=5.9
Q ss_pred cccCCCCc
Q 008441 478 RQCVKCNH 485 (565)
Q Consensus 478 k~CPkC~~ 485 (565)
+-||+|+.
T Consensus 2 ~fC~kcG~ 9 (465)
T COG4640 2 KFCPKCGS 9 (465)
T ss_pred Cccccccc
Confidence 56888883
No 338
>TIGR00055 uppS undecaprenyl diphosphate synthase. Alternate name: undecaprenyl pyrophosphate synthetase. Activity has been demonstrated experimentally for members of this family from Micrococcus luteus, E. coli, Haemophilus influenzae, and Streptococcus pneumoniae.
Probab=21.22 E-value=1.7e+02 Score=29.13 Aligned_cols=46 Identities=15% Similarity=0.286 Sum_probs=36.3
Q ss_pred HHHHHHHHHHHHHHHHhcCCCeEEeecCCccchhhccCccCCcchhhHHHHHH
Q 008441 207 SAAETKALIEGLNAALSMELDRVRVFIDCFPLFQFVTGRWPAKQRKISVLVDQ 259 (565)
Q Consensus 207 n~AEy~Ali~gL~~al~l~~~~v~v~~DS~lv~~qv~G~w~~k~~~l~~l~~~ 259 (565)
..+=+.++..-++++.++|++.|.||.=| +..|+-....+..|++-
T Consensus 25 H~~G~~~~~~v~~~c~~~GI~~lT~yaFS-------tEN~~Rp~~EV~~Lm~L 70 (226)
T TIGR00055 25 HKAGVKSLRRILRWCANLGVECLTLYAFS-------TENWKRPKEEVDFLMEL 70 (226)
T ss_pred HHHHHHHHHHHHHHHHHcCCCEEEEEEee-------hhhcCcCHHHHHHHHHH
Confidence 47778899999999999999999999855 35677666666666553
No 339
>COG0266 Nei Formamidopyrimidine-DNA glycosylase [DNA replication, recombination, and repair]
Probab=21.19 E-value=65 Score=32.99 Aligned_cols=21 Identities=29% Similarity=0.605 Sum_probs=16.3
Q ss_pred cccCCCCceeEec--CCcceEEe
Q 008441 478 RQCVKCNHLIELA--EGCFHMTC 498 (565)
Q Consensus 478 k~CPkC~~~IEK~--~GCnHMtC 498 (565)
++|+.|+.+|+|. +|=+-..|
T Consensus 246 epC~~CGt~I~k~~~~gR~t~~C 268 (273)
T COG0266 246 EPCRRCGTPIEKIKLGGRSTFYC 268 (273)
T ss_pred CCCCccCCEeEEEEEcCCcCEeC
Confidence 7999999999986 46554455
No 340
>KOG0943 consensus Predicted ubiquitin-protein ligase/hyperplastic discs protein, HECT superfamily [Posttranslational modification, protein turnover, chaperones]
Probab=21.11 E-value=59 Score=39.57 Aligned_cols=10 Identities=30% Similarity=0.464 Sum_probs=6.7
Q ss_pred hhHHhhHHHH
Q 008441 37 FAFRLQLQEA 46 (565)
Q Consensus 37 ~~~~~~~~~~ 46 (565)
+-|+|||.|-
T Consensus 960 hEf~~iM~eq 969 (3015)
T KOG0943|consen 960 HEFNLIMLEQ 969 (3015)
T ss_pred HHHHHHHHHH
Confidence 4577777764
No 341
>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=21.00 E-value=38 Score=22.92 Aligned_cols=10 Identities=40% Similarity=0.989 Sum_probs=5.2
Q ss_pred cccCCCCcee
Q 008441 478 RQCVKCNHLI 487 (565)
Q Consensus 478 k~CPkC~~~I 487 (565)
.+||.|+..|
T Consensus 18 irC~~CG~RI 27 (32)
T PF03604_consen 18 IRCPECGHRI 27 (32)
T ss_dssp SSBSSSS-SE
T ss_pred EECCcCCCeE
Confidence 4566666554
No 342
>PF01780 Ribosomal_L37ae: Ribosomal L37ae protein family; InterPro: IPR002674 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 ribosomal protein is found in archaebacteria and eukaryotes []. Ribosomal protein L37 has a single zinc finger-like motif of the C2-C2 type [].; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 4A1E_Y 4A17_Y 4A1C_Y 4A1A_Y 3O58_g 3IZS_m 3O5H_g 1S1I_9 3IZR_m 1YSH_D ....
Probab=20.91 E-value=58 Score=27.59 Aligned_cols=28 Identities=21% Similarity=0.487 Sum_probs=22.8
Q ss_pred cccCCCCceeEecCCcceEEe-ecCcccc
Q 008441 478 RQCVKCNHLIELAEGCFHMTC-RCGHEFC 505 (565)
Q Consensus 478 k~CPkC~~~IEK~~GCnHMtC-~Cg~~FC 505 (565)
-.||.|+..-.+..+----.| .|+..|=
T Consensus 36 y~Cp~Cgk~~vkR~a~GIW~C~~C~~~~A 64 (90)
T PF01780_consen 36 YTCPFCGKTSVKRVATGIWKCKKCGKKFA 64 (90)
T ss_dssp BEESSSSSSEEEEEETTEEEETTTTEEEE
T ss_pred CcCCCCCCceeEEeeeEEeecCCCCCEEe
Confidence 579999999888887777888 4887763
No 343
>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=20.90 E-value=30 Score=24.28 Aligned_cols=24 Identities=25% Similarity=0.653 Sum_probs=21.2
Q ss_pred CceeCCCCCCceecccCCCcCCCC
Q 008441 426 GARKCTKCHRRFCIDCKVPWHNNM 449 (565)
Q Consensus 426 ~~~~C~~C~~~fC~~C~~~~H~g~ 449 (565)
..+.|..|+..+|..|...-|.++
T Consensus 14 ~~~~C~~C~~~~C~~C~~~~H~~H 37 (42)
T PF00643_consen 14 LSLFCEDCNEPLCSECTVSGHKGH 37 (42)
T ss_dssp EEEEETTTTEEEEHHHHHTSTTTS
T ss_pred eEEEecCCCCccCccCCCCCCCCC
Confidence 678999999999999998778774
No 344
>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=20.82 E-value=55 Score=22.21 Aligned_cols=26 Identities=19% Similarity=0.433 Sum_probs=21.2
Q ss_pred cCceeCCCCCCceecccCCCcCCCCC
Q 008441 425 LGARKCTKCHRRFCIDCKVPWHNNMT 450 (565)
Q Consensus 425 ~~~~~C~~C~~~fC~~C~~~~H~g~t 450 (565)
...+.|..|+..+|..|....|.++.
T Consensus 10 ~~~~fC~~~~~~iC~~C~~~~H~~H~ 35 (39)
T cd00021 10 PLSLFCETDRALLCVDCDLSVHSGHR 35 (39)
T ss_pred ceEEEeCccChhhhhhcChhhcCCCC
Confidence 45789999999999999876687653
No 345
>PF10426 zf-RAG1: Recombination-activating protein 1 zinc-finger domain; InterPro: IPR019485 During lymphocyte development, the genes encoding immunoglobulins and T-cell receptors are assembled from variable (V), diversity (D), and joining (J) gene segments. This combinatorial process, known as V(D)J recombination, allows the generation of an enormous range of binding specificities from a limited amount of genetic information. The V(D)J recombination-activating proteins 1 and 2 (RAG1 and RAG2) form a complex that initiates this process by binding to the conserved recombination signal sequences (RSS) and introducing a double-strand break between the RSS and the adjacent coding segment. These breaks are generated in two steps, nicking of one strand (hydrolysis), followed by hairpin formation (transesterification). RAG1/2 has also been shown to function as a transposase in vitro, and to possess RSS-independent endonuclease activity (end processing) and hairpin opening. RAG1 alone can bind to RSS but stable, efficient binding requires RAG2. All known catalytic activities require the presence of both proteins. For more information see []. 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. C2H2-type (classical) zinc fingers (Znf) were the first class to be characterised. They contain a short beta hairpin and an alpha helix (beta/beta/alpha structure), where a single zinc atom is held in place by Cys(2)His(2) (C2H2) residues in a tetrahedral array. C2H2 Znf's can be divided into three groups based on the number and pattern of fingers: triple-C2H2 (binds single ligand), multiple-adjacent-C2H2 (binds multiple ligands), and separated paired-C2H2 []. C2H2 Znf's are the most common DNA-binding motifs found in eukaryotic transcription factors, and have also been identified in prokaryotes []. Transcription factors usually contain several Znf's (each with a conserved beta/beta/alpha structure) capable of making multiple contacts along the DNA, where the C2H2 Znf motifs recognise DNA sequences by binding to the major groove of DNA via a short alpha-helix in the Znf, the Znf spanning 3-4 bases of the DNA []. C2H2 Znf's can also bind to RNA and protein targets []. This entry represents a C2H2-type zinc-finger domain found in the RAG1 protein. The structure contains the characteristic two-stranded beta-sheet and alpha-helix of a classical zinc-finger. The domain binds one zinc and, in complex with an adjacent RING-type zinc finger domain, helps to stabilise the whole of the dimerisation region of recombination activating protein 1 (RAG1) []. The function of the whole is to bind double-stranded DNA. ; GO: 0016788 hydrolase activity, acting on ester bonds, 0016881 acid-amino acid ligase activity; PDB: 1RMD_A.
Probab=20.79 E-value=47 Score=22.20 Aligned_cols=22 Identities=18% Similarity=0.537 Sum_probs=11.9
Q ss_pred CCCCCCCCCCccchhhHHHhhh
Q 008441 352 PTCPHEGCKSKLEVESCRIFLT 373 (565)
Q Consensus 352 ~kCP~~~C~~~l~~~~i~~lL~ 373 (565)
++||..+|..++........++
T Consensus 3 vrCPvkdC~EEv~lgKY~~H~s 24 (30)
T PF10426_consen 3 VRCPVKDCDEEVSLGKYSHHLS 24 (30)
T ss_dssp EE--STT---EEEHHHHHHHHH
T ss_pred cccccccCcchhhhhhhccccc
Confidence 5899999999988766555443
No 346
>KOG1991 consensus Nuclear transport receptor RANBP7/RANBP8 (importin beta superfamily) [Nuclear structure; Intracellular trafficking, secretion, and vesicular transport]
Probab=20.79 E-value=56 Score=38.90 Aligned_cols=19 Identities=32% Similarity=0.364 Sum_probs=8.3
Q ss_pred ccchhhHHhhHHHHHHhhc
Q 008441 33 SDLDFAFRLQLQEAISASL 51 (565)
Q Consensus 33 ~~~~~~~~~~~~~~~~~~~ 51 (565)
|+.||-=+.++++|+..-+
T Consensus 490 ~~~df~d~~~l~~ale~t~ 508 (1010)
T KOG1991|consen 490 SSIDFKDPNNLSEALELTH 508 (1010)
T ss_pred HhccCCChHHHHHHHHHHH
Confidence 3444444444444444433
No 347
>PF11682 DUF3279: Protein of unknown function (DUF3279); InterPro: IPR021696 This family of proteins with unknown function appears to be restricted to Enterobacteriaceae.
Probab=20.63 E-value=60 Score=29.36 Aligned_cols=13 Identities=31% Similarity=0.501 Sum_probs=9.6
Q ss_pred cccCCCCceeEec
Q 008441 478 RQCVKCNHLIELA 490 (565)
Q Consensus 478 k~CPkC~~~IEK~ 490 (565)
|.||+|+.-|--.
T Consensus 111 K~C~~C~tGiYS~ 123 (128)
T PF11682_consen 111 KYCPKCGTGIYSI 123 (128)
T ss_pred EecCCCCCcccce
Confidence 7899998876433
No 348
>COG1645 Uncharacterized Zn-finger containing protein [General function prediction only]
Probab=20.61 E-value=64 Score=29.28 Aligned_cols=24 Identities=29% Similarity=0.688 Sum_probs=16.5
Q ss_pred ccccCCCCCCcccchhhhhccCCCcccccccCceeCCCCCC
Q 008441 395 VYCPYPKCSALMSKSEIERDASSSSFVGRRLGARKCTKCHR 435 (565)
Q Consensus 395 ~~CP~p~C~~~i~~~~~~e~~~s~~~~~~~~~~~~C~~C~~ 435 (565)
.+|| .|+..+.. ....++||.|++
T Consensus 29 ~hCp--~Cg~PLF~---------------KdG~v~CPvC~~ 52 (131)
T COG1645 29 KHCP--KCGTPLFR---------------KDGEVFCPVCGY 52 (131)
T ss_pred hhCc--ccCCccee---------------eCCeEECCCCCc
Confidence 4798 88876631 456677887775
No 349
>smart00064 FYVE Protein present in Fab1, YOTB, Vac1, and EEA1. The FYVE zinc finger is named after four proteins where it was first found: Fab1, YOTB/ZK632.12, Vac1, and EEA1. The FYVE finger has been shown to bind two Zn2+ ions. The FYVE finger has eight potential zinc coordinating cysteine positions. The FYVE finger is structurally related to the PF04032 Rpr2: RNAse P Rpr2/Rpp21/SNM1 subunit domain; InterPro: IPR007175 This family contains a ribonuclease P subunit of human and yeast. Other members of the family include the probable archaeal homologues. This subunit possibly binds the precursor tRNA [].; PDB: 2K3R_A 2KI7_B 2ZAE_B 1X0T_A.
Probab=20.40 E-value=72 Score=26.01 Aligned_cols=19 Identities=21% Similarity=0.553 Sum_probs=10.6
Q ss_pred CCceecccCCCcCCCCChh
Q 008441 434 HRRFCIDCKVPWHNNMTCI 452 (565)
Q Consensus 434 ~~~fC~~C~~~~H~g~tC~ 452 (565)
...||..|+...-+|.+|.
T Consensus 45 kr~~Ck~C~~~liPG~~~~ 63 (85)
T PF04032_consen 45 KRTICKKCGSLLIPGVNCS 63 (85)
T ss_dssp CCTB-TTT--B--CTTTEE
T ss_pred hcccccCCCCEEeCCCccE
Confidence 4567888888888888775
No 351
>KOG0943 consensus Predicted ubiquitin-protein ligase/hyperplastic discs protein, HECT superfamily [Posttranslational modification, protein turnover, chaperones]
Probab=20.22 E-value=65 Score=39.23 Aligned_cols=13 Identities=23% Similarity=0.406 Sum_probs=5.1
Q ss_pred HHHHHHHhhhhhH
Q 008441 112 REDLQRAIHDHNF 124 (565)
Q Consensus 112 ~~~~~~~~~~~~~ 124 (565)
++-++|++..+.+
T Consensus 1053 ~e~mlRS~pa~e~ 1065 (3015)
T KOG0943|consen 1053 REMMLRSLPAAEL 1065 (3015)
T ss_pred HHHHHhccchhhc
Confidence 3334444433333
No 352
>PF02148 zf-UBP: Zn-finger in ubiquitin-hydrolases and other protein; InterPro: IPR001607 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents UBP-type zinc finger domains, which display some similarity with the Zn-binding domain of the insulinase family. The UBP-type zinc finger domain is found only in a small subfamily of ubiquitin C-terminal hydrolases (deubiquitinases or UBP) [, ], All members of this subfamily are isopeptidase-T, which are known to cleave isopeptide bonds between ubiquitin moieties. Some of the proteins containing an UBP zinc finger include: Homo sapiens (Human) deubiquitinating enzyme 13 (UBPD) Human deubiquitinating enzyme 5 (UBP5) Dictyostelium discoideum (Slime mold) deubiquitinating enzyme A (UBPA) Saccharomyces cerevisiae (Baker's yeast) deubiquitinating enzyme 8 (UBP8) Yeast deubiquitinating enzyme 14 (UBP14) More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 3GV4_A 3PHD_B 3C5K_A 2UZG_A 3IHP_B 2G43_B 2G45_D 2I50_A 3MHH_A 3MHS_A ....
Probab=20.18 E-value=1.1e+02 Score=23.73 Aligned_cols=32 Identities=22% Similarity=0.320 Sum_probs=21.8
Q ss_pred cceeccccccCCceeecCCCcccchh----hHHHHHHH
Q 008441 311 CVICLEDTDVGHMFSIDGCLHRYCFL----CMKKHIEE 344 (565)
Q Consensus 311 C~IC~e~~~~~~~~~l~~C~H~fC~~----Cl~~~i~~ 344 (565)
|.+|... ..++...+.|++.+|.. ....|++.
T Consensus 1 C~~C~~~--~~~lw~CL~Cg~~~C~~~~~~Ha~~H~~~ 36 (63)
T PF02148_consen 1 CSVCGST--NSNLWLCLTCGYVGCGRYSNGHALKHYKE 36 (63)
T ss_dssp -SSSHTC--SSSEEEETTTS-EEETTTSTSHHHHHHHH
T ss_pred CCCCCCc--CCceEEeCCCCcccccCCcCcHHHHhhcc
Confidence 5667644 35677778999999986 77777763
No 353
>PRK12495 hypothetical protein; Provisional
Probab=20.16 E-value=57 Score=32.16 Aligned_cols=29 Identities=28% Similarity=0.558 Sum_probs=22.3
Q ss_pred ccccCCCCceeEecCCcceEEeecCccccccccccccC
Q 008441 477 WRQCVKCNHLIELAEGCFHMTCRCGHEFCYNCGAEWKN 514 (565)
Q Consensus 477 ~k~CPkC~~~IEK~~GCnHMtC~Cg~~FCw~C~~~~~~ 514 (565)
-+.||.|+.+|.+..|| .||-.|...+..
T Consensus 42 a~hC~~CG~PIpa~pG~---------~~Cp~CQ~~~~~ 70 (226)
T PRK12495 42 NAHCDECGDPIFRHDGQ---------EFCPTCQQPVTE 70 (226)
T ss_pred hhhcccccCcccCCCCe---------eECCCCCCcccc
Confidence 47899999999977665 477777777653
Done!