Query 006225
Match_columns 655
No_of_seqs 502 out of 2323
Neff 7.3
Searched_HMMs 46136
Date Thu Mar 28 20:12:02 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/006225.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/006225hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG1814 Predicted E3 ubiquitin 100.0 1.2E-64 2.6E-69 521.1 22.1 407 153-573 3-423 (445)
2 KOG1812 Predicted E3 ubiquitin 99.9 1.3E-25 2.8E-30 242.2 7.2 187 348-558 146-342 (384)
3 KOG1815 Predicted E3 ubiquitin 99.9 1.2E-24 2.6E-29 240.6 11.7 193 347-638 69-265 (444)
4 KOG1814 Predicted E3 ubiquitin 99.9 1.6E-23 3.4E-28 217.3 4.3 181 458-648 204-417 (445)
5 KOG0006 E3 ubiquitin-protein l 99.8 7.4E-21 1.6E-25 190.3 8.1 205 346-644 219-444 (446)
6 KOG1812 Predicted E3 ubiquitin 99.7 1E-18 2.2E-23 188.7 2.7 185 436-641 146-345 (384)
7 PF05773 RWD: RWD domain; Int 99.7 8.9E-16 1.9E-20 138.0 13.1 111 154-293 1-113 (113)
8 smart00591 RWD domain in RING 99.6 2E-15 4.3E-20 134.5 11.7 105 162-295 1-106 (107)
9 KOG4018 Uncharacterized conser 99.5 5.2E-14 1.1E-18 135.9 9.7 115 152-297 1-116 (215)
10 KOG4445 Uncharacterized conser 99.2 1E-10 2.2E-15 117.5 11.4 105 232-385 47-153 (368)
11 KOG1815 Predicted E3 ubiquitin 98.9 5.8E-10 1.3E-14 124.0 4.9 118 430-572 158-279 (444)
12 smart00647 IBR In Between Ring 98.7 8.6E-09 1.9E-13 83.0 4.1 59 419-477 1-64 (64)
13 KOG0006 E3 ubiquitin-protein l 98.6 2.8E-08 6E-13 100.7 5.2 47 512-558 388-436 (446)
14 smart00647 IBR In Between Ring 98.6 7.7E-08 1.7E-12 77.4 5.2 51 508-558 3-59 (64)
15 PF01485 IBR: IBR domain; Int 98.5 2E-08 4.3E-13 80.8 0.3 59 419-477 1-64 (64)
16 PF01485 IBR: IBR domain; Int 98.3 1.8E-07 3.9E-12 75.2 0.3 39 520-558 17-59 (64)
17 PF15227 zf-C3HC4_4: zinc fing 98.2 5.9E-07 1.3E-11 66.2 2.0 41 351-397 1-41 (42)
18 PF13639 zf-RING_2: Ring finge 98.0 2.3E-06 5E-11 63.7 2.2 40 350-397 2-42 (44)
19 PF00097 zf-C3HC4: Zinc finger 97.8 1.1E-05 2.5E-10 58.8 2.9 40 351-397 1-40 (41)
20 PF13923 zf-C3HC4_2: Zinc fing 97.8 1E-05 2.2E-10 58.6 2.5 38 351-397 1-38 (39)
21 PLN03208 E3 ubiquitin-protein 97.8 1.5E-05 3.2E-10 77.5 4.3 64 347-414 17-88 (193)
22 PF13445 zf-RING_UBOX: RING-ty 97.8 1.5E-05 3.2E-10 58.9 3.1 41 351-396 1-43 (43)
23 KOG1035 eIF-2alpha kinase GCN2 97.7 6E-06 1.3E-10 97.8 -0.9 114 152-297 3-117 (1351)
24 KOG0320 Predicted E3 ubiquitin 97.7 1.9E-05 4.2E-10 74.8 2.7 53 347-409 130-182 (187)
25 PF14634 zf-RING_5: zinc-RING 97.7 3.2E-05 6.9E-10 57.6 3.0 42 350-401 1-43 (44)
26 cd00162 RING RING-finger (Real 97.6 5.7E-05 1.2E-09 55.4 3.8 44 350-403 1-44 (45)
27 PF13920 zf-C3HC4_3: Zinc fing 97.5 8.8E-05 1.9E-09 56.7 3.2 45 349-405 3-48 (50)
28 KOG0823 Predicted E3 ubiquitin 97.4 9.5E-05 2.1E-09 73.3 3.1 60 346-414 45-104 (230)
29 KOG2177 Predicted E3 ubiquitin 97.3 8.7E-05 1.9E-09 77.4 2.1 110 346-476 11-121 (386)
30 smart00184 RING Ring finger. E 97.3 0.00023 4.9E-09 50.2 3.1 38 351-397 1-38 (39)
31 smart00504 Ubox Modified RING 97.2 0.00046 1E-08 55.1 4.3 51 349-411 2-52 (63)
32 KOG2164 Predicted E3 ubiquitin 97.1 0.00024 5.2E-09 77.7 2.5 61 348-415 186-246 (513)
33 PHA02926 zinc finger-like prot 97.1 0.00042 9.1E-09 68.3 3.3 55 347-405 169-230 (242)
34 PHA02929 N1R/p28-like protein; 97.0 0.00051 1.1E-08 69.7 3.7 49 347-405 173-227 (238)
35 TIGR00599 rad18 DNA repair pro 97.0 0.00064 1.4E-08 73.9 4.1 65 347-423 25-90 (397)
36 KOG0317 Predicted E3 ubiquitin 96.9 0.00052 1.1E-08 70.1 2.3 51 347-409 238-288 (293)
37 COG5540 RING-finger-containing 96.7 0.0012 2.5E-08 67.6 3.2 49 349-406 324-373 (374)
38 KOG1002 Nucleotide excision re 96.5 0.0012 2.7E-08 71.7 2.3 89 328-423 516-604 (791)
39 KOG0978 E3 ubiquitin ligase in 96.2 0.0018 3.8E-08 74.3 1.2 56 346-412 641-696 (698)
40 KOG0287 Postreplication repair 96.2 0.0021 4.5E-08 66.7 1.3 63 348-422 23-86 (442)
41 TIGR00570 cdk7 CDK-activating 96.1 0.0092 2E-07 62.5 6.1 55 349-412 4-61 (309)
42 KOG4628 Predicted E3 ubiquitin 96.1 0.0037 8.1E-08 66.4 3.2 48 349-405 230-278 (348)
43 PF12678 zf-rbx1: RING-H2 zinc 95.4 0.01 2.2E-07 49.3 2.3 40 350-397 21-71 (73)
44 PF11789 zf-Nse: Zinc-finger o 95.4 0.016 3.4E-07 45.7 3.1 45 349-401 12-57 (57)
45 PF14835 zf-RING_6: zf-RING of 95.1 0.0036 7.9E-08 49.8 -1.2 50 347-410 6-56 (65)
46 COG5219 Uncharacterized conser 95.0 0.049 1.1E-06 63.5 6.9 50 348-405 1469-1523(1525)
47 PF04564 U-box: U-box domain; 94.8 0.028 6E-07 46.6 3.2 51 348-409 4-54 (73)
48 KOG0309 Conserved WD40 repeat- 94.7 0.27 5.9E-06 56.3 11.7 133 126-292 394-531 (1081)
49 PF11793 FANCL_C: FANCL C-term 94.6 0.02 4.4E-07 47.1 1.9 56 349-406 3-67 (70)
50 COG5574 PEX10 RING-finger-cont 94.3 0.026 5.7E-07 57.2 2.3 51 349-409 216-266 (271)
51 COG5243 HRD1 HRD ubiquitin lig 93.3 0.073 1.6E-06 56.2 3.6 52 346-407 285-347 (491)
52 COG5432 RAD18 RING-finger-cont 92.7 0.058 1.3E-06 55.1 1.8 65 347-423 24-89 (391)
53 PF10571 UPF0547: Uncharacteri 92.7 0.042 9E-07 36.1 0.4 24 522-549 1-24 (26)
54 KOG1039 Predicted E3 ubiquitin 92.4 0.083 1.8E-06 56.6 2.6 92 347-441 160-264 (344)
55 PF10571 UPF0547: Uncharacteri 91.9 0.076 1.7E-06 34.8 1.0 24 602-629 1-24 (26)
56 KOG0824 Predicted E3 ubiquitin 91.9 0.079 1.7E-06 54.7 1.6 52 348-410 7-58 (324)
57 KOG4367 Predicted Zn-finger pr 91.6 0.048 1E-06 58.5 -0.4 35 347-383 3-37 (699)
58 KOG0828 Predicted E3 ubiquitin 91.0 0.12 2.6E-06 56.5 1.9 55 343-406 566-635 (636)
59 KOG2660 Locus-specific chromos 90.4 0.14 3.1E-06 53.6 1.8 48 347-406 14-62 (331)
60 PF09297 zf-NADH-PPase: NADH p 89.7 0.36 7.8E-06 33.2 2.8 30 520-549 2-31 (32)
61 KOG2879 Predicted E3 ubiquitin 89.7 0.3 6.5E-06 49.9 3.4 49 348-405 239-287 (298)
62 PHA00626 hypothetical protein 89.3 0.23 5E-06 38.4 1.7 28 602-629 1-33 (59)
63 KOG0825 PHD Zn-finger protein 89.0 0.2 4.4E-06 57.6 1.7 110 349-470 124-248 (1134)
64 smart00744 RINGv The RING-vari 88.6 0.48 1E-05 36.1 3.1 42 350-397 1-47 (49)
65 KOG4185 Predicted E3 ubiquitin 88.0 0.82 1.8E-05 48.2 5.6 48 348-404 3-54 (296)
66 KOG1428 Inhibitor of type V ad 87.7 0.49 1.1E-05 57.6 3.8 65 349-415 3487-3554(3738)
67 PF13719 zinc_ribbon_5: zinc-r 87.7 0.32 7E-06 34.7 1.5 28 436-463 2-35 (37)
68 KOG4739 Uncharacterized protei 87.6 0.24 5.3E-06 49.9 1.2 57 348-416 3-59 (233)
69 PF05883 Baculo_RING: Baculovi 87.6 0.27 5.7E-06 45.4 1.3 40 342-381 20-66 (134)
70 KOG0802 E3 ubiquitin ligase [P 87.6 0.31 6.7E-06 56.1 2.2 49 346-404 289-340 (543)
71 KOG1645 RING-finger-containing 87.5 0.27 5.9E-06 52.8 1.5 50 349-406 5-57 (463)
72 KOG0804 Cytoplasmic Zn-finger 87.3 0.27 5.9E-06 53.4 1.3 48 346-405 173-222 (493)
73 smart00661 RPOL9 RNA polymeras 86.7 0.45 9.7E-06 36.3 2.0 28 522-549 1-30 (52)
74 KOG4159 Predicted E3 ubiquitin 85.7 0.63 1.4E-05 51.0 3.1 49 346-406 82-130 (398)
75 KOG0823 Predicted E3 ubiquitin 85.7 0.3 6.4E-06 48.9 0.6 17 539-557 61-77 (230)
76 PF13717 zinc_ribbon_4: zinc-r 85.6 0.46 1E-05 33.7 1.4 28 436-463 2-35 (36)
77 PF13248 zf-ribbon_3: zinc-rib 85.5 0.42 9.1E-06 31.3 1.0 13 601-613 2-14 (26)
78 KOG0311 Predicted E3 ubiquitin 85.4 0.12 2.7E-06 54.4 -2.3 47 348-404 43-89 (381)
79 PF12861 zf-Apc11: Anaphase-pr 85.3 0.82 1.8E-05 38.9 3.0 32 367-405 51-82 (85)
80 COG5152 Uncharacterized conser 85.3 0.3 6.6E-06 47.4 0.4 31 348-380 196-226 (259)
81 smart00661 RPOL9 RNA polymeras 85.2 0.62 1.3E-05 35.5 2.1 27 603-629 2-30 (52)
82 KOG0978 E3 ubiquitin ligase in 84.8 0.28 6E-06 56.8 -0.1 30 435-469 642-671 (698)
83 PF14570 zf-RING_4: RING/Ubox 84.8 0.71 1.5E-05 35.0 2.1 44 351-403 1-46 (48)
84 PLN00172 ubiquitin conjugating 84.3 20 0.00042 33.9 12.3 21 232-253 50-70 (147)
85 PF14803 Nudix_N_2: Nudix N-te 84.1 0.85 1.8E-05 32.0 2.1 27 522-548 1-31 (34)
86 PF13719 zinc_ribbon_5: zinc-r 83.0 1.1 2.4E-05 31.9 2.4 28 522-549 3-35 (37)
87 PRK00398 rpoP DNA-directed RNA 82.9 1.2 2.6E-05 33.2 2.8 30 522-551 4-33 (46)
88 PLN03086 PRLI-interacting fact 82.6 1 2.2E-05 51.4 3.3 108 520-639 432-553 (567)
89 PHA00626 hypothetical protein 81.8 1.2 2.6E-05 34.6 2.3 28 523-550 2-34 (59)
90 KOG3299 Uncharacterized conser 81.5 0.71 1.5E-05 45.3 1.3 53 241-295 2-54 (206)
91 PF13240 zinc_ribbon_2: zinc-r 81.1 0.78 1.7E-05 29.2 0.9 22 603-628 1-22 (23)
92 PF12773 DZR: Double zinc ribb 80.8 0.66 1.4E-05 35.1 0.7 27 519-546 10-36 (50)
93 PRK04023 DNA polymerase II lar 80.0 1.1 2.4E-05 53.7 2.4 35 519-559 624-663 (1121)
94 PRK00432 30S ribosomal protein 79.5 1.1 2.4E-05 34.3 1.5 29 520-550 19-48 (50)
95 PTZ00390 ubiquitin-conjugating 79.4 33 0.00071 32.6 11.9 21 232-253 51-71 (152)
96 PF04641 Rtf2: Rtf2 RING-finge 79.2 3.9 8.5E-05 42.5 6.0 71 345-426 110-183 (260)
97 KOG4265 Predicted E3 ubiquitin 79.0 1.3 2.7E-05 47.3 2.2 49 346-406 288-337 (349)
98 KOG3970 Predicted E3 ubiquitin 78.8 1.7 3.8E-05 43.1 3.0 68 332-404 37-104 (299)
99 PF00179 UQ_con: Ubiquitin-con 78.6 24 0.00052 32.7 10.6 22 232-254 47-68 (140)
100 TIGR02098 MJ0042_CXXC MJ0042 f 78.5 1.6 3.5E-05 31.0 2.0 28 522-549 3-35 (38)
101 COG5175 MOT2 Transcriptional r 78.2 2.7 5.9E-05 44.2 4.3 60 350-418 16-78 (480)
102 PF13717 zinc_ribbon_4: zinc-r 77.9 2 4.2E-05 30.5 2.3 28 522-549 3-35 (36)
103 KOG1785 Tyrosine kinase negati 77.9 0.73 1.6E-05 49.3 0.1 47 347-401 368-414 (563)
104 TIGR00570 cdk7 CDK-activating 77.6 0.92 2E-05 47.8 0.7 35 522-557 4-38 (309)
105 KOG3039 Uncharacterized conser 76.9 2.1 4.6E-05 43.2 3.0 56 347-412 220-277 (303)
106 PRK00420 hypothetical protein; 76.3 4 8.6E-05 36.7 4.3 44 416-462 6-49 (112)
107 PF09538 FYDLN_acid: Protein o 76.1 1.4 3.1E-05 39.4 1.4 28 601-629 9-36 (108)
108 KOG0320 Predicted E3 ubiquitin 75.8 1 2.2E-05 43.4 0.4 31 436-469 131-161 (187)
109 PF02150 RNA_POL_M_15KD: RNA p 75.8 2.1 4.5E-05 30.2 1.9 28 522-549 2-30 (35)
110 PRK00398 rpoP DNA-directed RNA 75.7 1.9 4.1E-05 32.2 1.8 30 602-631 4-33 (46)
111 KOG1734 Predicted RING-contain 75.4 0.99 2.1E-05 46.1 0.3 53 349-409 225-285 (328)
112 TIGR02098 MJ0042_CXXC MJ0042 f 75.0 2.1 4.5E-05 30.4 1.8 27 602-629 3-35 (38)
113 KOG1952 Transcription factor N 74.3 2.7 5.8E-05 49.4 3.4 57 342-401 185-243 (950)
114 PF09297 zf-NADH-PPase: NADH p 73.4 2.5 5.4E-05 29.0 1.8 29 600-628 2-30 (32)
115 KOG0827 Predicted E3 ubiquitin 73.2 2.1 4.5E-05 46.0 2.0 51 349-406 5-57 (465)
116 PHA03096 p28-like protein; Pro 73.0 1.9 4E-05 45.3 1.6 38 349-386 179-222 (284)
117 PF07975 C1_4: TFIIH C1-like d 72.8 1.4 3E-05 33.9 0.4 40 439-478 2-47 (51)
118 PRK00432 30S ribosomal protein 72.4 2.6 5.7E-05 32.3 1.9 28 600-629 19-47 (50)
119 PF08274 PhnA_Zn_Ribbon: PhnA 72.4 1.8 3.8E-05 29.5 0.8 26 438-463 4-29 (30)
120 KOG2817 Predicted E3 ubiquitin 71.3 3.2 6.9E-05 44.9 2.9 58 347-411 333-391 (394)
121 KOG4172 Predicted E3 ubiquitin 71.1 1.1 2.3E-05 34.6 -0.5 45 349-404 8-53 (62)
122 PF10367 Vps39_2: Vacuolar sor 71.0 2.1 4.6E-05 37.6 1.3 32 347-378 77-108 (109)
123 cd00195 UBCc Ubiquitin-conjuga 70.8 24 0.00051 32.8 8.4 22 232-254 48-69 (141)
124 KOG2034 Vacuolar sorting prote 70.2 1.9 4.1E-05 50.9 1.0 38 348-385 817-854 (911)
125 KOG0826 Predicted E3 ubiquitin 70.2 3.3 7.2E-05 43.6 2.6 67 326-403 280-346 (357)
126 PF07191 zinc-ribbons_6: zinc- 70.0 3.2 7E-05 34.0 2.0 35 603-639 3-42 (70)
127 KOG0416 Ubiquitin-protein liga 69.1 20 0.00044 34.4 7.3 56 232-293 49-107 (189)
128 PF13639 zf-RING_2: Ring finge 68.3 1.6 3.5E-05 32.0 -0.0 32 438-471 2-33 (44)
129 COG2888 Predicted Zn-ribbon RN 68.3 2.4 5.2E-05 33.4 0.9 26 602-627 28-58 (61)
130 KOG1001 Helicase-like transcri 68.1 1.6 3.5E-05 51.3 -0.2 47 349-406 455-501 (674)
131 COG1645 Uncharacterized Zn-fin 67.9 7.5 0.00016 35.8 4.2 25 521-547 28-52 (131)
132 PRK14714 DNA polymerase II lar 67.8 3.4 7.3E-05 50.9 2.4 31 521-557 667-702 (1337)
133 PF08274 PhnA_Zn_Ribbon: PhnA 67.5 4.8 0.0001 27.4 2.1 27 522-549 3-29 (30)
134 PRK00420 hypothetical protein; 67.3 10 0.00022 34.2 4.7 24 521-546 23-47 (112)
135 COG1645 Uncharacterized Zn-fin 67.0 2.9 6.4E-05 38.5 1.3 25 437-462 29-53 (131)
136 COG5078 Ubiquitin-protein liga 66.6 35 0.00076 32.5 8.5 58 232-294 55-116 (153)
137 TIGR00686 phnA alkylphosphonat 66.6 2.8 6.1E-05 37.1 1.1 27 437-463 3-29 (109)
138 PF10272 Tmpp129: Putative tra 66.1 41 0.00089 36.6 10.0 40 367-408 310-354 (358)
139 PHA02926 zinc finger-like prot 65.9 4.9 0.00011 40.3 2.7 51 416-472 156-210 (242)
140 COG5220 TFB3 Cdk activating ki 65.8 1.5 3.1E-05 44.1 -0.9 49 349-404 11-63 (314)
141 PF12773 DZR: Double zinc ribb 65.7 3.2 6.9E-05 31.3 1.1 12 601-612 12-23 (50)
142 PF07282 OrfB_Zn_ribbon: Putat 65.6 4.5 9.6E-05 32.8 2.0 29 600-628 27-55 (69)
143 PRK14559 putative protein seri 65.4 2.8 6.1E-05 49.1 1.1 33 519-557 13-51 (645)
144 COG1998 RPS31 Ribosomal protei 65.1 3.4 7.5E-05 31.3 1.1 29 520-548 18-46 (51)
145 COG2888 Predicted Zn-ribbon RN 64.9 3.5 7.5E-05 32.5 1.2 26 522-547 28-58 (61)
146 PF03604 DNA_RNApol_7kD: DNA d 64.8 4.6 9.9E-05 27.9 1.6 26 438-463 2-27 (32)
147 PHA02929 N1R/p28-like protein; 64.6 4.3 9.3E-05 41.5 2.1 37 435-471 173-212 (238)
148 smart00212 UBCc Ubiquitin-conj 64.5 35 0.00076 31.8 8.2 56 232-293 48-109 (145)
149 KOG2906 RNA polymerase III sub 64.2 5.9 0.00013 34.4 2.5 31 522-552 2-34 (105)
150 PRK05654 acetyl-CoA carboxylas 63.2 2 4.2E-05 45.4 -0.6 29 601-629 27-56 (292)
151 KOG0317 Predicted E3 ubiquitin 63.1 1.2 2.7E-05 46.0 -2.0 39 595-639 233-271 (293)
152 PRK10220 hypothetical protein; 63.1 3.8 8.2E-05 36.3 1.2 28 437-464 4-31 (111)
153 PF02318 FYVE_2: FYVE-type zin 61.9 23 0.0005 32.1 6.2 36 520-556 53-88 (118)
154 PF09538 FYDLN_acid: Protein o 61.1 4.5 9.8E-05 36.2 1.4 30 437-466 10-39 (108)
155 PF07282 OrfB_Zn_ribbon: Putat 61.0 5.8 0.00013 32.1 1.9 29 520-548 27-55 (69)
156 CHL00174 accD acetyl-CoA carbo 60.8 2.2 4.8E-05 44.9 -0.7 34 601-634 38-72 (296)
157 COG0777 AccD Acetyl-CoA carbox 60.6 3.1 6.7E-05 43.0 0.3 36 520-555 27-63 (294)
158 PF14447 Prok-RING_4: Prokaryo 60.4 5.3 0.00012 31.1 1.5 46 349-408 8-53 (55)
159 PRK12495 hypothetical protein; 60.2 12 0.00026 37.5 4.2 17 601-617 42-58 (226)
160 PRK05654 acetyl-CoA carboxylas 60.0 2.4 5.1E-05 44.8 -0.7 30 521-550 27-57 (292)
161 PF14952 zf-tcix: Putative tre 59.8 4.8 0.0001 29.7 1.1 26 600-629 10-37 (44)
162 KOG1813 Predicted E3 ubiquitin 59.8 3.1 6.7E-05 43.2 0.1 45 348-404 241-285 (313)
163 KOG0297 TNF receptor-associate 59.7 4.5 9.7E-05 44.6 1.4 47 346-404 19-66 (391)
164 PF06677 Auto_anti-p27: Sjogre 59.6 4.8 0.0001 29.5 1.1 24 437-460 18-41 (41)
165 PF07975 C1_4: TFIIH C1-like d 59.6 2.6 5.5E-05 32.4 -0.4 35 524-558 2-40 (51)
166 COG1997 RPL43A Ribosomal prote 59.5 14 0.00031 31.5 4.0 31 519-549 33-63 (89)
167 PRK09710 lar restriction allev 58.9 6.9 0.00015 31.4 1.9 28 520-547 5-35 (64)
168 CHL00174 accD acetyl-CoA carbo 58.9 2.3 5.1E-05 44.7 -1.0 34 521-554 38-72 (296)
169 TIGR00515 accD acetyl-CoA carb 58.7 2.6 5.7E-05 44.3 -0.6 30 601-630 26-56 (285)
170 PRK14559 putative protein seri 58.5 4.7 0.0001 47.3 1.3 34 600-639 14-53 (645)
171 PF14835 zf-RING_6: zf-RING of 58.3 6 0.00013 31.9 1.5 36 601-636 7-49 (65)
172 PF00627 UBA: UBA/TS-N domain; 58.2 7.8 0.00017 27.4 1.9 26 110-135 2-37 (37)
173 PF06677 Auto_anti-p27: Sjogre 58.0 22 0.00047 26.1 4.2 25 521-546 17-41 (41)
174 TIGR00515 accD acetyl-CoA carb 57.7 2.6 5.7E-05 44.3 -0.8 31 521-551 26-57 (285)
175 COG2816 NPY1 NTP pyrophosphohy 57.6 12 0.00026 39.0 4.0 34 516-549 106-139 (279)
176 PF08792 A2L_zn_ribbon: A2L zi 57.0 12 0.00025 26.1 2.5 29 521-549 3-31 (33)
177 KOG3579 Predicted E3 ubiquitin 56.8 7 0.00015 40.4 2.0 52 347-401 267-321 (352)
178 KOG4692 Predicted E3 ubiquitin 56.7 6.6 0.00014 41.7 1.9 48 347-406 421-468 (489)
179 PRK00241 nudC NADH pyrophospha 56.6 16 0.00035 37.8 4.8 34 516-549 94-127 (256)
180 PF14353 CpXC: CpXC protein 56.4 8.9 0.00019 35.1 2.5 30 522-551 2-50 (128)
181 KOG0427 Ubiquitin conjugating 56.3 50 0.0011 30.3 7.1 22 232-253 63-84 (161)
182 smart00659 RPOLCX RNA polymera 56.0 7.1 0.00015 29.0 1.5 26 438-463 4-29 (44)
183 COG0777 AccD Acetyl-CoA carbox 55.9 3.9 8.5E-05 42.2 0.1 33 601-633 28-61 (294)
184 KOG3800 Predicted E3 ubiquitin 55.6 16 0.00035 38.1 4.4 51 350-409 2-55 (300)
185 PRK09710 lar restriction allev 55.4 9.7 0.00021 30.6 2.2 30 599-628 4-36 (64)
186 KOG3053 Uncharacterized conser 55.4 12 0.00026 38.3 3.4 54 349-404 21-81 (293)
187 PF07191 zinc-ribbons_6: zinc- 55.3 12 0.00027 30.7 2.8 33 523-557 3-40 (70)
188 TIGR02300 FYDLN_acid conserved 54.9 6.5 0.00014 35.9 1.3 28 601-629 9-36 (129)
189 COG1594 RPB9 DNA-directed RNA 54.6 9 0.00019 34.6 2.2 29 521-549 2-32 (113)
190 PRK12495 hypothetical protein; 54.3 13 0.00028 37.2 3.4 28 520-557 41-68 (226)
191 KOG1493 Anaphase-promoting com 54.1 3 6.6E-05 34.5 -0.8 48 350-404 22-80 (84)
192 KOG2879 Predicted E3 ubiquitin 53.7 6.9 0.00015 40.4 1.4 32 520-556 238-269 (298)
193 COG1997 RPL43A Ribosomal prote 53.5 8.8 0.00019 32.7 1.8 29 602-630 36-64 (89)
194 PF02318 FYVE_2: FYVE-type zin 52.8 26 0.00056 31.7 4.9 36 435-470 53-88 (118)
195 KOG2164 Predicted E3 ubiquitin 52.8 4.3 9.3E-05 45.3 -0.2 14 544-557 203-216 (513)
196 PRK08665 ribonucleotide-diphos 52.3 7.1 0.00015 46.7 1.5 27 522-550 725-751 (752)
197 PF06827 zf-FPG_IleRS: Zinc fi 51.6 12 0.00026 25.1 1.9 25 602-626 2-28 (30)
198 COG1198 PriA Primosomal protei 51.4 9.9 0.00021 45.1 2.5 35 522-556 445-484 (730)
199 PRK14892 putative transcriptio 51.4 10 0.00022 33.4 1.9 30 520-549 20-52 (99)
200 PRK08665 ribonucleotide-diphos 50.1 8.3 0.00018 46.2 1.6 27 602-630 725-751 (752)
201 TIGR03655 anti_R_Lar restricti 50.1 14 0.00031 28.4 2.4 30 602-631 2-38 (53)
202 PRK14892 putative transcriptio 49.9 11 0.00024 33.2 2.0 31 599-629 19-52 (99)
203 PF08792 A2L_zn_ribbon: A2L zi 49.9 12 0.00026 26.1 1.7 29 435-463 2-31 (33)
204 PF07754 DUF1610: Domain of un 49.7 11 0.00024 24.3 1.4 23 439-461 1-24 (24)
205 KOG0418 Ubiquitin-protein liga 49.6 34 0.00073 33.5 5.3 42 232-274 55-100 (200)
206 PF14570 zf-RING_4: RING/Ubox 48.8 7.3 0.00016 29.5 0.6 30 439-469 1-30 (48)
207 KOG3002 Zn finger protein [Gen 48.7 12 0.00027 39.6 2.5 46 346-405 46-91 (299)
208 TIGR01384 TFS_arch transcripti 48.7 11 0.00024 33.2 1.8 26 603-630 2-27 (104)
209 TIGR01384 TFS_arch transcripti 48.4 9.5 0.00021 33.6 1.3 26 522-549 1-26 (104)
210 PF08271 TF_Zn_Ribbon: TFIIB z 48.2 16 0.00034 26.8 2.3 25 523-547 2-27 (43)
211 TIGR00686 phnA alkylphosphonat 47.9 14 0.0003 32.9 2.2 27 522-549 3-29 (109)
212 KOG0417 Ubiquitin-protein liga 47.6 76 0.0016 30.0 7.1 21 232-253 50-70 (148)
213 KOG2906 RNA polymerase III sub 47.6 11 0.00024 32.8 1.5 30 603-632 3-34 (105)
214 COG5222 Uncharacterized conser 47.4 23 0.0005 36.9 4.0 44 349-402 275-318 (427)
215 COG5175 MOT2 Transcriptional r 47.3 11 0.00024 39.8 1.8 42 437-479 15-58 (480)
216 PF12760 Zn_Tnp_IS1595: Transp 47.3 29 0.00063 25.8 3.6 29 599-627 16-45 (46)
217 PLN03208 E3 ubiquitin-protein 46.4 7.5 0.00016 38.3 0.4 32 601-638 18-49 (193)
218 PF12861 zf-Apc11: Anaphase-pr 46.3 8.3 0.00018 32.9 0.6 31 523-557 34-64 (85)
219 TIGR01206 lysW lysine biosynth 46.3 20 0.00043 28.0 2.6 30 522-551 3-34 (54)
220 PF06113 BRE: Brain and reprod 46.2 71 0.0015 34.3 7.5 68 151-255 263-330 (333)
221 PF01363 FYVE: FYVE zinc finge 46.1 18 0.00038 29.2 2.5 36 520-557 8-43 (69)
222 PF08694 UFC1: Ubiquitin-fold 46.1 13 0.00029 34.5 1.9 21 232-253 77-97 (161)
223 PF14369 zf-RING_3: zinc-finge 45.9 18 0.00039 25.5 2.1 28 522-549 3-31 (35)
224 TIGR02300 FYDLN_acid conserved 45.6 12 0.00026 34.3 1.5 28 436-463 9-36 (129)
225 PF14569 zf-UDP: Zinc-binding 45.6 16 0.00034 30.5 2.1 35 435-469 8-44 (80)
226 KOG3799 Rab3 effector RIM1 and 45.0 7.6 0.00016 35.6 0.2 36 602-639 66-101 (169)
227 cd00194 UBA Ubiquitin Associat 45.0 18 0.00039 25.3 2.1 25 111-135 2-36 (38)
228 COG5236 Uncharacterized conser 44.9 23 0.0005 37.7 3.6 53 345-407 58-110 (493)
229 KOG0801 Predicted E3 ubiquitin 44.7 8 0.00017 36.7 0.3 38 333-374 166-204 (205)
230 PF09788 Tmemb_55A: Transmembr 44.1 17 0.00037 37.2 2.5 90 349-462 86-186 (256)
231 PF12906 RINGv: RING-variant d 44.0 20 0.00043 26.9 2.3 33 351-383 1-38 (47)
232 smart00165 UBA Ubiquitin assoc 43.8 19 0.00042 25.1 2.1 25 111-135 2-36 (37)
233 PRK14714 DNA polymerase II lar 43.7 13 0.00028 46.1 1.8 13 601-613 667-679 (1337)
234 PF13453 zf-TFIIB: Transcripti 43.5 18 0.00039 26.2 1.9 12 523-534 1-12 (41)
235 smart00531 TFIIE Transcription 42.8 12 0.00026 35.4 1.1 31 433-463 96-133 (147)
236 PRK11827 hypothetical protein; 42.6 20 0.00043 28.6 2.1 29 521-549 8-36 (60)
237 PF14353 CpXC: CpXC protein 42.2 11 0.00024 34.5 0.8 45 392-446 1-48 (128)
238 PF14354 Lar_restr_allev: Rest 41.9 20 0.00043 28.1 2.1 13 521-533 3-15 (61)
239 COG1594 RPB9 DNA-directed RNA 41.9 16 0.00035 32.9 1.8 28 602-629 3-32 (113)
240 COG0266 Nei Formamidopyrimidin 41.8 16 0.00034 38.1 1.9 28 600-627 244-273 (273)
241 KOG1701 Focal adhesion adaptor 41.6 13 0.00028 40.7 1.3 26 447-472 376-405 (468)
242 PF05715 zf-piccolo: Piccolo Z 41.6 8.9 0.00019 30.2 0.0 36 602-637 3-40 (61)
243 PF03119 DNA_ligase_ZBD: NAD-d 41.1 22 0.00047 23.7 1.9 21 523-543 1-21 (28)
244 PRK14890 putative Zn-ribbon RN 40.8 16 0.00034 28.9 1.3 37 522-558 8-47 (59)
245 PF09526 DUF2387: Probable met 40.7 22 0.00048 29.3 2.2 28 522-549 9-40 (71)
246 PRK03681 hypA hydrogenase nick 40.7 12 0.00027 33.7 0.8 29 434-462 68-96 (114)
247 PF09606 Med15: ARC105 or Med1 40.5 9.2 0.0002 45.7 0.0 25 228-253 711-736 (799)
248 TIGR00373 conserved hypothetic 40.5 16 0.00035 35.0 1.7 31 432-462 105-137 (158)
249 TIGR02443 conserved hypothetic 39.5 22 0.00049 28.1 2.0 28 522-549 10-41 (59)
250 PRK10220 hypothetical protein; 39.3 22 0.00047 31.7 2.1 28 521-549 3-30 (111)
251 PF01780 Ribosomal_L37ae: Ribo 39.3 44 0.00095 28.9 3.9 29 521-549 35-63 (90)
252 KOG2932 E3 ubiquitin ligase in 39.0 8.6 0.00019 40.2 -0.5 32 520-556 89-120 (389)
253 PRK11827 hypothetical protein; 38.7 24 0.00051 28.2 2.0 28 602-629 9-36 (60)
254 PF01599 Ribosomal_S27: Riboso 38.6 19 0.00042 27.2 1.4 27 521-547 18-46 (47)
255 PF10122 Mu-like_Com: Mu-like 38.6 17 0.00038 27.8 1.2 26 602-627 5-32 (51)
256 PRK14811 formamidopyrimidine-D 38.4 20 0.00043 37.4 2.1 29 600-628 234-264 (269)
257 KOG3268 Predicted E3 ubiquitin 38.2 32 0.0007 33.2 3.2 58 347-406 164-229 (234)
258 PRK06266 transcription initiat 37.8 16 0.00035 35.7 1.2 30 433-462 114-145 (178)
259 KOG1941 Acetylcholine receptor 36.7 12 0.00025 40.5 0.0 47 348-402 365-413 (518)
260 TIGR00595 priA primosomal prot 36.5 23 0.00051 40.4 2.4 35 522-556 223-262 (505)
261 TIGR01053 LSD1 zinc finger dom 36.1 38 0.00082 23.3 2.4 25 523-547 3-27 (31)
262 PF01363 FYVE: FYVE zinc finge 36.0 18 0.00039 29.1 1.1 34 435-469 8-41 (69)
263 TIGR00622 ssl1 transcription f 36.0 24 0.00053 31.7 1.9 42 437-478 56-107 (112)
264 PF09526 DUF2387: Probable met 35.7 24 0.00051 29.2 1.7 28 601-628 8-39 (71)
265 COG1198 PriA Primosomal protei 35.2 24 0.00052 42.0 2.2 35 602-636 445-484 (730)
266 PRK01103 formamidopyrimidine/5 35.1 24 0.00052 36.9 2.1 28 600-627 244-273 (274)
267 TIGR00577 fpg formamidopyrimid 35.0 24 0.00052 36.9 2.1 26 601-626 245-272 (272)
268 KOG4275 Predicted E3 ubiquitin 35.0 17 0.00036 37.9 0.8 31 348-380 300-331 (350)
269 PF06844 DUF1244: Protein of u 34.8 29 0.00062 28.1 1.9 17 372-388 12-28 (68)
270 PF05129 Elf1: Transcription e 34.7 22 0.00048 30.1 1.4 30 600-629 21-56 (81)
271 PRK00564 hypA hydrogenase nick 34.6 19 0.00042 32.6 1.1 29 434-462 69-97 (117)
272 PRK10445 endonuclease VIII; Pr 34.5 25 0.00054 36.6 2.1 26 601-626 235-262 (263)
273 PRK12286 rpmF 50S ribosomal pr 34.4 29 0.00063 27.4 1.9 26 598-628 24-49 (57)
274 PRK14810 formamidopyrimidine-D 34.2 24 0.00053 36.8 1.9 27 600-626 243-271 (272)
275 PF15616 TerY-C: TerY-C metal 33.1 25 0.00055 32.5 1.6 25 521-552 77-101 (131)
276 KOG0419 Ubiquitin-protein liga 33.0 1.7E+02 0.0037 27.1 6.7 20 232-252 53-72 (152)
277 COG1096 Predicted RNA-binding 33.0 29 0.00063 34.0 2.1 32 522-555 150-181 (188)
278 PRK13945 formamidopyrimidine-D 33.0 27 0.00058 36.7 2.0 27 600-626 253-281 (282)
279 KOG0422 Ubiquitin-protein liga 32.5 83 0.0018 29.4 4.7 21 232-253 51-71 (153)
280 PRK03976 rpl37ae 50S ribosomal 32.4 58 0.0013 28.2 3.5 31 520-550 35-65 (90)
281 TIGR00622 ssl1 transcription f 31.9 29 0.00063 31.2 1.7 38 521-558 55-100 (112)
282 smart00834 CxxC_CXXC_SSSS Puta 31.8 35 0.00075 24.3 1.9 26 522-547 6-34 (41)
283 KOG0421 Ubiquitin-protein liga 31.4 75 0.0016 29.6 4.3 42 232-274 78-122 (175)
284 TIGR00280 L37a ribosomal prote 31.0 59 0.0013 28.2 3.4 31 520-550 34-64 (91)
285 PTZ00255 60S ribosomal protein 30.7 64 0.0014 27.9 3.5 31 520-550 35-65 (90)
286 COG5222 Uncharacterized conser 30.7 43 0.00094 34.9 3.0 60 414-479 244-315 (427)
287 PF01396 zf-C4_Topoisom: Topoi 30.7 38 0.00083 24.4 1.9 22 602-624 2-26 (39)
288 KOG2807 RNA polymerase II tran 30.4 32 0.00068 36.5 1.9 39 435-475 329-367 (378)
289 COG5151 SSL1 RNA polymerase II 30.2 18 0.0004 37.8 0.2 87 369-472 307-407 (421)
290 PF14446 Prok-RING_1: Prokaryo 30.0 50 0.0011 25.8 2.5 32 349-380 6-39 (54)
291 COG5574 PEX10 RING-finger-cont 29.8 18 0.00038 37.3 -0.0 33 601-639 215-248 (271)
292 KOG3161 Predicted E3 ubiquitin 29.7 16 0.00034 42.0 -0.4 34 349-382 12-47 (861)
293 KOG0309 Conserved WD40 repeat- 29.6 32 0.0007 40.3 2.0 46 348-402 1028-1073(1081)
294 KOG4362 Transcriptional regula 29.2 14 0.00031 43.1 -0.9 62 341-411 14-75 (684)
295 KOG0424 Ubiquitin-protein liga 28.4 46 0.001 31.1 2.4 22 232-254 58-79 (158)
296 PF03966 Trm112p: Trm112p-like 28.3 30 0.00066 28.0 1.2 13 451-463 51-63 (68)
297 COG3478 Predicted nucleic-acid 28.3 50 0.0011 26.6 2.3 10 618-627 39-48 (68)
298 PF06943 zf-LSD1: LSD1 zinc fi 28.1 57 0.0012 21.3 2.1 24 524-547 1-24 (25)
299 PLN02189 cellulose synthase 28.0 35 0.00075 41.9 2.0 35 435-469 33-69 (1040)
300 PF01873 eIF-5_eIF-2B: Domain 28.0 83 0.0018 28.9 4.1 29 520-548 92-123 (125)
301 KOG1940 Zn-finger protein [Gen 27.8 61 0.0013 33.9 3.5 45 348-402 158-204 (276)
302 COG1656 Uncharacterized conser 27.8 44 0.00095 32.1 2.3 15 433-447 94-108 (165)
303 KOG3039 Uncharacterized conser 27.8 49 0.0011 33.8 2.7 38 347-386 42-79 (303)
304 PF05290 Baculo_IE-1: Baculovi 27.4 47 0.001 30.8 2.3 52 347-405 79-132 (140)
305 PRK05580 primosome assembly pr 27.4 40 0.00086 40.1 2.4 35 522-556 391-430 (679)
306 PRK08115 ribonucleotide-diphos 27.4 27 0.00059 42.2 1.0 25 602-628 828-853 (858)
307 TIGR01031 rpmF_bact ribosomal 27.2 43 0.00094 26.2 1.8 24 599-627 24-47 (55)
308 PRK14873 primosome assembly pr 27.1 40 0.00087 39.9 2.3 35 522-556 393-431 (665)
309 KOG0429 Ubiquitin-conjugating 26.9 1.2E+02 0.0026 30.5 5.1 62 232-296 67-134 (258)
310 PRK03824 hypA hydrogenase nick 26.8 28 0.00061 32.4 0.8 14 435-448 69-82 (135)
311 KOG2315 Predicted translation 26.1 2E+02 0.0044 32.8 7.3 91 64-167 473-565 (566)
312 COG1096 Predicted RNA-binding 25.9 40 0.00086 33.1 1.7 25 602-628 150-174 (188)
313 cd00065 FYVE FYVE domain; Zinc 25.7 37 0.0008 26.0 1.2 31 438-469 4-34 (57)
314 TIGR00595 priA primosomal prot 25.6 45 0.00097 38.1 2.3 35 602-636 223-262 (505)
315 PRK04023 DNA polymerase II lar 25.4 38 0.00081 41.3 1.7 35 598-638 623-662 (1121)
316 PF14149 YhfH: YhfH-like prote 25.4 9 0.00019 27.4 -2.1 25 601-625 13-37 (37)
317 PRK09521 exosome complex RNA-b 25.2 44 0.00095 32.9 1.9 26 603-629 151-176 (189)
318 PF14462 Prok-E2_E: Prokaryoti 25.0 83 0.0018 28.9 3.4 26 232-258 44-69 (122)
319 COG2824 PhnA Uncharacterized Z 24.6 34 0.00073 30.3 0.8 26 437-462 4-29 (112)
320 COG3677 Transposase and inacti 24.6 86 0.0019 29.0 3.5 34 433-466 27-66 (129)
321 COG2051 RPS27A Ribosomal prote 24.1 42 0.00092 27.2 1.2 29 437-465 20-50 (67)
322 KOG1571 Predicted E3 ubiquitin 23.6 37 0.00081 36.5 1.1 43 347-404 304-346 (355)
323 smart00653 eIF2B_5 domain pres 23.5 1.1E+02 0.0023 27.5 3.9 28 520-547 79-109 (110)
324 PF01783 Ribosomal_L32p: Ribos 23.4 52 0.0011 25.7 1.6 23 520-547 25-47 (56)
325 KOG0420 Ubiquitin-protein liga 23.4 1.1E+02 0.0024 29.6 4.0 19 232-251 78-96 (184)
326 smart00531 TFIIE Transcription 23.3 85 0.0018 29.5 3.4 27 521-547 99-131 (147)
327 KOG2691 RNA polymerase II subu 22.8 90 0.002 27.8 3.1 31 520-550 3-37 (113)
328 PF06906 DUF1272: Protein of u 22.7 66 0.0014 25.2 2.0 46 349-406 6-53 (57)
329 COG0266 Nei Formamidopyrimidin 22.6 64 0.0014 33.8 2.5 27 520-546 244-272 (273)
330 PF05502 Dynactin_p62: Dynacti 22.3 80 0.0017 35.9 3.5 67 434-549 3-96 (483)
331 PF03884 DUF329: Domain of unk 22.1 24 0.00052 27.8 -0.5 19 601-619 2-20 (57)
332 PF12677 DUF3797: Domain of un 22.0 68 0.0015 24.4 1.9 27 521-548 13-47 (49)
333 PHA02825 LAP/PHD finger-like p 21.9 73 0.0016 30.5 2.5 51 348-407 8-61 (162)
334 TIGR00311 aIF-2beta translatio 21.9 1.1E+02 0.0024 28.4 3.8 29 520-548 96-127 (133)
335 PLN03086 PRLI-interacting fact 21.9 44 0.00095 38.6 1.3 30 600-629 432-463 (567)
336 KOG0425 Ubiquitin-protein liga 21.8 86 0.0019 29.8 2.9 21 232-253 55-75 (171)
337 PRK05978 hypothetical protein; 21.8 43 0.00094 31.7 1.0 9 601-609 33-41 (148)
338 PF01155 HypA: Hydrogenase exp 21.4 35 0.00076 30.7 0.3 27 435-462 69-95 (113)
339 PF05743 UEV: UEV domain; Int 21.4 93 0.002 28.3 3.1 22 232-254 50-71 (121)
340 PLN02638 cellulose synthase A 21.3 53 0.0011 40.6 1.8 57 439-540 20-78 (1079)
341 PLN02436 cellulose synthase A 21.1 57 0.0012 40.2 2.0 57 439-540 39-97 (1094)
342 PRK03988 translation initiatio 21.0 1.2E+02 0.0027 28.4 3.8 29 520-548 101-132 (138)
343 PRK10445 endonuclease VIII; Pr 21.0 72 0.0016 33.2 2.6 26 521-546 235-262 (263)
344 PRK14810 formamidopyrimidine-D 21.0 71 0.0015 33.4 2.6 26 521-546 244-271 (272)
345 PRK14811 formamidopyrimidine-D 20.9 67 0.0015 33.5 2.4 26 521-546 235-262 (269)
346 KOG0895 Ubiquitin-conjugating 20.8 81 0.0018 38.7 3.2 42 232-274 900-945 (1101)
347 PRK05580 primosome assembly pr 20.8 63 0.0014 38.4 2.4 35 602-636 391-430 (679)
348 PF07800 DUF1644: Protein of u 20.7 1.3E+02 0.0029 28.7 4.0 35 349-385 3-50 (162)
349 TIGR00577 fpg formamidopyrimid 20.6 75 0.0016 33.2 2.6 26 521-546 245-272 (272)
350 KOG2932 E3 ubiquitin ligase in 20.6 48 0.001 34.9 1.1 31 348-380 90-121 (389)
351 KOG2462 C2H2-type Zn-finger pr 20.6 73 0.0016 33.2 2.4 11 521-531 161-171 (279)
352 KOG2930 SCF ubiquitin ligase, 20.5 62 0.0013 28.6 1.6 29 361-397 72-102 (114)
353 PF01927 Mut7-C: Mut7-C RNAse 20.5 88 0.0019 29.4 2.9 15 433-447 88-102 (147)
354 PLN00215 predicted protein; Pr 20.3 1.3E+02 0.0028 25.3 3.3 68 24-93 18-85 (110)
355 PRK12380 hydrogenase nickel in 20.3 45 0.00098 30.0 0.8 27 434-461 68-94 (113)
356 COG2824 PhnA Uncharacterized Z 20.3 76 0.0016 28.2 2.1 27 521-548 3-29 (112)
357 PF04606 Ogr_Delta: Ogr/Delta- 20.2 85 0.0018 23.5 2.1 10 523-532 1-10 (47)
358 COG1996 RPC10 DNA-directed RNA 20.1 60 0.0013 24.8 1.3 26 523-548 8-33 (49)
359 COG2816 NPY1 NTP pyrophosphohy 20.0 64 0.0014 33.8 1.9 31 599-629 109-139 (279)
No 1
>KOG1814 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=100.00 E-value=1.2e-64 Score=521.15 Aligned_cols=407 Identities=38% Similarity=0.679 Sum_probs=342.9
Q ss_pred hchHHHHHHHHHHHHHhcCCCeeeeccCCCCceEEEEEeeccCCCceEEeecCCCCccccCCCCCCCcccccccccCCcE
Q 006225 153 RINDQSQGDELLALESIYGDSVFILDRQRDLRSCQIHVHVETLDGLTVTAKLNSSTDLDARSESSDDFSYSFKVQYLPPI 232 (655)
Q Consensus 153 ~~n~e~Q~~EleaLeSIY~d~~~~~~~~~~~~~f~i~i~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~v~~LPpi 232 (655)
++|.++|++||+||+|||+++.+........+.|+|++.+++.-++.+..+.+...+ ++. ...+++++.+||||
T Consensus 3 ~dn~~~qedEL~AL~siy~e~~~~~~~~~~~~~~~ir~ni~v~f~~~~~~~vnie~~----s~~--~~~f~~~~~~lPpi 76 (445)
T KOG1814|consen 3 EDNRELQEDELEALESIYPENEFRKVSYWEDGEFEIRLNIEVNFEILYSPKVNIEGT----SDS--MDLFSLPLDHLPPI 76 (445)
T ss_pred chHHHHHHHHHHHHHHhccccccccccccccccceeEeeeeccceeecccccccccc----ccc--ccccccccccCCCe
Confidence 468999999999999999988776554444467888887666555544444332221 111 12378999999999
Q ss_pred EEEEEcCCCCCCCCCCeEEeecccCCHHHHHHHHHHHHHHHHhCCCchhhHHHHHHHhhccccccccccceecCCCCccc
Q 006225 233 VLTCLLPKSYPSHLPPYFTISARWLNSTKISNLCSMLESIWIDQPGQEILYQWIEWLQNSSLSYLGFNEEIVLGPYGVAC 312 (655)
Q Consensus 233 ~L~~~lP~~YPs~~pP~~~l~s~wL~~~~l~~L~~~L~~~~ee~~G~~~lf~~ie~lqe~~~~~l~~~~~~~l~~~~~~~ 312 (655)
.|.|.||++||+.+||.|.|++.||+.++++.|++. +.+|..++|+|.+||++...+++++...++|.++....
T Consensus 77 vlkf~LP~~YPs~spP~f~l~s~Wmn~~q~~~lc~~------el~~i~~~~q~m~~l~~~~~s~l~~i~~~~lki~~~~~ 150 (445)
T KOG1814|consen 77 VLKFHLPNDYPSVSPPKFELKSYWMNPDQKSALCSK------ELRLIEELNQMMDFLKESTISILNLIAPFELKIISQKE 150 (445)
T ss_pred eeeeecCCccccCCCCceeeehcccCHHHhhhccch------hhccceeHHHHHHHHHHHHHHHHHhcccceeccchhhh
Confidence 999999999999999999999999999999999887 67899999999999999999999999999998877665
Q ss_pred cCCcccccccCCCCCCchhhhccchhhhhhhccccccccccccccccCCCeE-ecCCCCcccHhhHHHHHHHHhhcCCcc
Q 006225 313 IGDRRAISESVSPDVDIPSIRSYNHERCHENFLKSFHECRICFSEFAGTDFV-RLPCHHFFCWKCMKTYLDIHISEGTVS 391 (655)
Q Consensus 313 ~~d~~~~~~~~s~~~~~~~l~~~n~~~~~~~f~~~~~~C~IC~e~~~~~~~~-~l~C~H~fC~~Cl~~yi~~~i~~g~~~ 391 (655)
..+.++.. .+++.+++.+++|++++..+.|.++.+.|.|||++..|...+ .++|+|+||+.|++.|++..|++|.+.
T Consensus 151 ~~~~~~~~--~~~~sl~~~Il~~deea~~~~F~~slf~C~ICf~e~~G~~c~~~lpC~Hv~Ck~C~kdY~~~~i~eg~v~ 228 (445)
T KOG1814|consen 151 FPALIRQG--ESIDSLKKEILQFDEEATLEKFVNSLFDCCICFEEQMGQHCFKFLPCSHVFCKSCLKDYFTIQIQEGQVS 228 (445)
T ss_pred cccccccc--cChHHHHHHHHhhhHHHHHHHHHhhcccceeeehhhcCcceeeecccchHHHHHHHHHHHHHhhhcceee
Confidence 55554443 467778899999999999999999999999999999985544 469999999999999999999999999
Q ss_pred eeccCCCCCCCCCCcccccccCChHHHHHHHHHHHHHHhhcCCCcccccC--CCCCcccc-cccccccccccceeecccc
Q 006225 392 KLQCPDAKCGGMVPPSLLKKLLGDEEFERWESLMLQKTLESMSDVAYCPR--CETPCIED-EEQHAQCSKCFYSFCTLCR 468 (655)
Q Consensus 392 ~i~CP~~~C~~~l~~~~i~~ll~~e~~ery~~~~~~~~l~~~~~~~~CP~--C~~~~~~~-~~~~~~C~~C~~~fC~~C~ 468 (655)
.++||+++|+...++..++.+|+.++++||+.+++++.++.+.|.+|||+ |+.++..+ ....+.|.+|.++||+.|+
T Consensus 229 ~l~Cp~~~C~~~a~~g~vKelvg~EL~arYe~l~lqk~l~~msdv~yCPr~~Cq~p~~~d~~~~l~~CskCnFaFCtlCk 308 (445)
T KOG1814|consen 229 CLKCPDPKCGSVAPPGQVKELVGDELFARYEKLMLQKTLELMSDVVYCPRACCQLPVKQDPGRALAICSKCNFAFCTLCK 308 (445)
T ss_pred eecCCCCCCcccCCchHHHHHHHHHHHHHHHHHHHHHHHHhhcccccCChhhccCccccCchhhhhhhccCccHHHHHHH
Confidence 99999999999999999999999999999999999999999999999998 99997544 4578999999999999999
Q ss_pred ccccCCcCCCchHHH-HHHHHHhhc--chhhhhhhhHHH----HHHHHHHHhHHHHhcccccCccccceeEEecCcCcee
Q 006225 469 ERRHVGVVCMTPEIK-LRILQERQN--SSQVKEGQKQRE----HEMINELLSVKEILRDAKQCPSCKMAISRTEGCNKIV 541 (655)
Q Consensus 469 ~~~H~~~sC~~~~~~-~~~~~e~~~--~~~~~~~~~~~e----~e~~~e~l~~~~i~~~~k~CP~C~~~iek~~Gcn~m~ 541 (655)
..||+...|...+.+ ..+..++.. .+......+++. .+++++.++++|+..|.++||.|+++|++++|||+|+
T Consensus 309 ~t~HG~s~Ck~~~~~~~~l~~~~~~~d~a~k~ele~Ryg~rvve~~vn~~lsekwl~~N~krCP~C~v~IEr~eGCnKM~ 388 (445)
T KOG1814|consen 309 LTWHGVSPCKVKAEKLIELYLEYLEADEARKRELEKRYGKRVVEELVNDFLSEKWLESNSKRCPKCKVVIERSEGCNKMH 388 (445)
T ss_pred HhhcCCCcccCchHHHHHHHHHHhhcCHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHhcCCCCCcccceeecCCCcccee
Confidence 999999999755333 222222222 222233334444 7788899999999999999999999999999999999
Q ss_pred ccccCeeeeccccccc---cCCCCCCCCCCCCChh
Q 006225 542 CNNCGQYFCYRCNKAI---DGYDHFRTGTCELFPQ 573 (655)
Q Consensus 542 C~~C~~~FC~~C~~~~---~~~~H~~~~~C~~~~~ 573 (655)
|..|++.|||.|.... +||.||+...+..|+.
T Consensus 389 C~~c~~~fc~~c~~~l~~~nPYkHF~e~~s~c~~~ 423 (445)
T KOG1814|consen 389 CTKCGTYFCWICAELLYPENPYKHFSEPGSECYGQ 423 (445)
T ss_pred eccccccceeehhhhcCCCChhhhhcCCcCccccc
Confidence 9999999999999887 5799999998877754
No 2
>KOG1812 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=99.92 E-value=1.3e-25 Score=242.15 Aligned_cols=187 Identities=30% Similarity=0.703 Sum_probs=148.8
Q ss_pred cccccccccccc-CCCeE-ecCCCCcccHhhHHHHHHHHhhcCCcceeccCCCCCCCCCCcccccccCChHHHHHHHHHH
Q 006225 348 FHECRICFSEFA-GTDFV-RLPCHHFFCWKCMKTYLDIHISEGTVSKLQCPDAKCGGMVPPSLLKKLLGDEEFERWESLM 425 (655)
Q Consensus 348 ~~~C~IC~e~~~-~~~~~-~l~C~H~fC~~Cl~~yi~~~i~~g~~~~i~CP~~~C~~~l~~~~i~~ll~~e~~ery~~~~ 425 (655)
..+|.||+.+.+ ..+++ ...|+|.||.+|+++|++.+...| ..++||..+|...++.+.+..+|++++.++|++.+
T Consensus 146 ~~~C~iC~~e~~~~~~~f~~~~C~H~fC~~C~k~~iev~~~~~--~~~~C~~~~C~~~l~~~~c~~llt~kl~e~~e~~~ 223 (384)
T KOG1812|consen 146 KEECGICFVEDPEAEDMFSVLKCGHRFCKDCVKQHIEVKLLSG--TVIRCPHDGCESRLTLESCRKLLTPKLREMWEQRL 223 (384)
T ss_pred cccCccCccccccHhhhHHHhcccchhhhHHhHHHhhhhhccC--CCccCCCCCCCccCCHHHHhhhcCHHHHHHHHHHH
Confidence 478999995544 32333 358999999999999999985444 56999999999999999999999999999999999
Q ss_pred HHHHhhcCCCcccccC--CCCCccc------ccccccccccccceeeccccccccCCcCCCchHHHHHHHHHhhcchhhh
Q 006225 426 LQKTLESMSDVAYCPR--CETPCIE------DEEQHAQCSKCFYSFCTLCRERRHVGVVCMTPEIKLRILQERQNSSQVK 497 (655)
Q Consensus 426 ~~~~l~~~~~~~~CP~--C~~~~~~------~~~~~~~C~~C~~~fC~~C~~~~H~~~sC~~~~~~~~~~~e~~~~~~~~ 497 (655)
.+.++.....+ |||. |...+.. .......|+.|+..||..|+.+||.+.+|.+++.... ..
T Consensus 224 ~e~~i~~~~~~-ycp~~~C~~l~~~~el~~~~~~~~~~C~~C~~~fCv~C~~~wh~~~sC~eykk~~~--------~~-- 292 (384)
T KOG1812|consen 224 KEEVIPSLDRV-YCPYPRCSSLMSKTELSSEVKSKRRPCVKCHELFCVKCKVPWHANLSCEEYKKLNP--------EE-- 292 (384)
T ss_pred HHHhhhhhhcc-cCCCCCchHhhhhhhhccchhhcccccccCCCceeecCCCcCCCCCCHHHHHHhCC--------cc--
Confidence 99888777666 9975 8765542 2234567999999999999999999999987643210 00
Q ss_pred hhhhHHHHHHHHHHHhHHHHhcccccCccccceeEEecCcCceeccccCeeeecccccccc
Q 006225 498 EGQKQREHEMINELLSVKEILRDAKQCPSCKMAISRTEGCNKIVCNNCGQYFCYRCNKAID 558 (655)
Q Consensus 498 ~~~~~~e~e~~~e~l~~~~i~~~~k~CP~C~~~iek~~Gcn~m~C~~C~~~FC~~C~~~~~ 558 (655)
+.+....+++..+|+.||.|+..|++..|||||+|. ||+.|||.|+..|.
T Consensus 293 ----------~~d~~~~~~la~~wr~CpkC~~~ie~~~GCnhm~Cr-C~~~fcy~C~~~~~ 342 (384)
T KOG1812|consen 293 ----------YVDDITLKYLAKRWRQCPKCKFMIELSEGCNHMTCR-CGHQFCYMCGGDWK 342 (384)
T ss_pred ----------cccHHHHHHHHHhcCcCcccceeeeecCCcceEEee-ccccchhhcCcchh
Confidence 011111223336799999999999999999999999 99999999999983
No 3
>KOG1815 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=99.91 E-value=1.2e-24 Score=240.62 Aligned_cols=193 Identities=27% Similarity=0.677 Sum_probs=156.7
Q ss_pred cccccccccccccCCCeEecCCCCcccHhhHHHHHHHHhhcCCcceeccCCCCCCCCCCcccccccCCh-HHHHHHHHHH
Q 006225 347 SFHECRICFSEFAGTDFVRLPCHHFFCWKCMKTYLDIHISEGTVSKLQCPDAKCGGMVPPSLLKKLLGD-EEFERWESLM 425 (655)
Q Consensus 347 ~~~~C~IC~e~~~~~~~~~l~C~H~fC~~Cl~~yi~~~i~~g~~~~i~CP~~~C~~~l~~~~i~~ll~~-e~~ery~~~~ 425 (655)
...+|.||++.+++ .++.+.|+|.||..||..|+..+|.++....|+||..+|...+..+.|..++++ +..++|.+++
T Consensus 69 ~~~~c~ic~~~~~~-~~~~~~c~H~~c~~cw~~yl~~kI~~~~~~~i~cp~~~C~a~v~~~~i~~~~s~~~~~~ky~~~i 147 (444)
T KOG1815|consen 69 GDVQCGICVESYDG-EIIGLGCGHPFCPPCWTGYLGTKIHEGEEAKIKCPAHGCPALVGEDTVEKLVSDKEDKEKYQRYI 147 (444)
T ss_pred ccccCCcccCCCcc-hhhhcCCCcHHHHHHHHHHhhheeeccccccccCCCCCccccCCCceeeeecCCHHHHHHHHHHH
Confidence 34789999999876 666779999999999999999999888765699999999999999999999998 4899999999
Q ss_pred HHHHhhcCCCcccccCCCCCcccccccccccccccceeeccccccccCCcCCCchHHHHHHHHHhhcchhhhhhhhHHHH
Q 006225 426 LQKTLESMSDVAYCPRCETPCIEDEEQHAQCSKCFYSFCTLCRERRHVGVVCMTPEIKLRILQERQNSSQVKEGQKQREH 505 (655)
Q Consensus 426 ~~~~l~~~~~~~~CP~C~~~~~~~~~~~~~C~~C~~~fC~~C~~~~H~~~sC~~~~~~~~~~~e~~~~~~~~~~~~~~e~ 505 (655)
+.++++....+.|||.
T Consensus 148 ~~syve~~~~lkwCP~---------------------------------------------------------------- 163 (444)
T KOG1815|consen 148 LRSYVEDNVPLKWCPA---------------------------------------------------------------- 163 (444)
T ss_pred HHHHHhcCCccccCCC----------------------------------------------------------------
Confidence 9999987766777765
Q ss_pred HHHHHHHhHHHHhcccccCccccceeEE-ecCcCceeccccCeeeeccccccccCCCCCCCCCCCCChhHHHHHHHHHHH
Q 006225 506 EMINELLSVKEILRDAKQCPSCKMAISR-TEGCNKIVCNNCGQYFCYRCNKAIDGYDHFRTGTCELFPQEMIRDWEERLN 584 (655)
Q Consensus 506 e~~~e~l~~~~i~~~~k~CP~C~~~iek-~~Gcn~m~C~~C~~~FC~~C~~~~~~~~H~~~~~C~~~~~~~~~~~~~~~~ 584 (655)
|+|+.++.. ...+..+.|. ||+.|||.|+.+| |.+.+|..+. .|.....
T Consensus 164 -------------------~~C~~av~~~~~~~~~v~C~-~g~~FC~~C~~~~-----H~p~~C~~~~-----~wl~k~~ 213 (444)
T KOG1815|consen 164 -------------------PGCGLAVKFGSLESVEVDCG-CGHEFCFACGEES-----HSPVSCPGAK-----KWLKKCR 213 (444)
T ss_pred -------------------CCCCceeeccCCCccceeCC-CCchhHhhccccc-----cCCCcccchH-----HHHHhhh
Confidence 022222222 3334567887 8889999999998 6778998773 4433322
Q ss_pred HHHHHHHHHhccccccCccCCccCccccccCCcceEEccc--cccccccccccccc
Q 006225 585 ARQVVAQIQADMFDEHGLSCPNCRQFNAKVGNNNHMFCWA--CQIHYCYLCKKIVR 638 (655)
Q Consensus 585 ~~~~~~~~~~~~~~~~~k~CP~C~~~ieK~~GCnhm~C~~--C~~~FC~~C~~~~~ 638 (655)
+... . -.|+..|+++||+|..+|+|++|||||+|.. |+++|||+|++.|.
T Consensus 214 ~~se--~--~~wi~~ntk~CP~c~~~iek~~gc~~~~~~~~~c~~~FCw~Cl~~~~ 265 (444)
T KOG1815|consen 214 DDSE--T--INWILANTKECPKCKVPIEKDGGCNHMTCKSASCKHEFCWVCLASLS 265 (444)
T ss_pred hhhh--h--hhhhhccCccCCCcccchhccCCccccccccCCcCCeeceeeecccc
Confidence 2221 1 1288899999999999999999999999987 99999999999998
No 4
>KOG1814 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=99.88 E-value=1.6e-23 Score=217.28 Aligned_cols=181 Identities=22% Similarity=0.531 Sum_probs=127.9
Q ss_pred cccceeeccccccc---------cCCcCCCchHHHHHHHHHhhcchhhhhhhhHHHHHHHHHHHhHHHH--hcccccCcc
Q 006225 458 KCFYSFCTLCRERR---------HVGVVCMTPEIKLRILQERQNSSQVKEGQKQREHEMINELLSVKEI--LRDAKQCPS 526 (655)
Q Consensus 458 ~C~~~fC~~C~~~~---------H~~~sC~~~~~~~~~~~e~~~~~~~~~~~~~~e~e~~~e~l~~~~i--~~~~k~CP~ 526 (655)
.|+|.||..|.+.| ...+.|++.+|.....+. .++........+.++.++-.+.+ +.++++||+
T Consensus 204 pC~Hv~Ck~C~kdY~~~~i~eg~v~~l~Cp~~~C~~~a~~g-----~vKelvg~EL~arYe~l~lqk~l~~msdv~yCPr 278 (445)
T KOG1814|consen 204 PCSHVFCKSCLKDYFTIQIQEGQVSCLKCPDPKCGSVAPPG-----QVKELVGDELFARYEKLMLQKTLELMSDVVYCPR 278 (445)
T ss_pred ccchHHHHHHHHHHHHHhhhcceeeeecCCCCCCcccCCch-----HHHHHHHHHHHHHHHHHHHHHHHHhhcccccCCh
Confidence 57999999999843 223568877765432221 22322223334444444444433 457899995
Q ss_pred --ccceeEEecCcCceeccccCeeeeccccccccCCCCCCCCCCCCChhHHHHHHHHH--------------HHHH---H
Q 006225 527 --CKMAISRTEGCNKIVCNNCGQYFCYRCNKAIDGYDHFRTGTCELFPQEMIRDWEER--------------LNAR---Q 587 (655)
Q Consensus 527 --C~~~iek~~Gcn~m~C~~C~~~FC~~C~~~~~~~~H~~~~~C~~~~~~~~~~~~~~--------------~~~~---~ 587 (655)
|..++..+.|+....|.+|.+.||..|+..||| ...|..-..+.+....++ -..+ .
T Consensus 279 ~~Cq~p~~~d~~~~l~~CskCnFaFCtlCk~t~HG-----~s~Ck~~~~~~~~l~~~~~~~d~a~k~ele~Ryg~rvve~ 353 (445)
T KOG1814|consen 279 ACCQLPVKQDPGRALAICSKCNFAFCTLCKLTWHG-----VSPCKVKAEKLIELYLEYLEADEARKRELEKRYGKRVVEE 353 (445)
T ss_pred hhccCccccCchhhhhhhccCccHHHHHHHHhhcC-----CCcccCchHHHHHHHHHHhhcCHHHHHHHHHHhhHHHHHH
Confidence 999997788999999999999999999999955 446877644333322211 1101 1
Q ss_pred HH-HHHHhccccccCccCCccCccccccCCcceEEccccccccccccccccccc--ccccCCCC
Q 006225 588 VV-AQIQADMFDEHGLSCPNCRQFNAKVGNNNHMFCWACQIHYCYLCKKIVRRS--TQHYGPKG 648 (655)
Q Consensus 588 ~~-~~~~~~~~~~~~k~CP~C~~~ieK~~GCnhm~C~~C~~~FC~~C~~~~~~~--~~Hf~~~~ 648 (655)
.+ +.+...|+..|.++||+|+++|||++|||||+|..|++.|||+|+..+.+. ++||+..+
T Consensus 354 ~vn~~lsekwl~~N~krCP~C~v~IEr~eGCnKM~C~~c~~~fc~~c~~~l~~~nPYkHF~e~~ 417 (445)
T KOG1814|consen 354 LVNDFLSEKWLESNSKRCPKCKVVIERSEGCNKMHCTKCGTYFCWICAELLYPENPYKHFSEPG 417 (445)
T ss_pred HHHHHHHHHHHHhcCCCCCcccceeecCCCccceeeccccccceeehhhhcCCCChhhhhcCCc
Confidence 11 222336888999999999999999999999999999999999999999976 69998533
No 5
>KOG0006 consensus E3 ubiquitin-protein ligase (Parkin protein) [Posttranslational modification, protein turnover, chaperones]
Probab=99.83 E-value=7.4e-21 Score=190.32 Aligned_cols=205 Identities=22% Similarity=0.567 Sum_probs=150.4
Q ss_pred ccccccccccccccCCCeEecCCC--CcccHhhHHHHHHHHhhcCCc-------ceeccCCCCCCCCCC-cccccccCCh
Q 006225 346 KSFHECRICFSEFAGTDFVRLPCH--HFFCWKCMKTYLDIHISEGTV-------SKLQCPDAKCGGMVP-PSLLKKLLGD 415 (655)
Q Consensus 346 ~~~~~C~IC~e~~~~~~~~~l~C~--H~fC~~Cl~~yi~~~i~~g~~-------~~i~CP~~~C~~~l~-~~~i~~ll~~ 415 (655)
....+|..|-+.- .....++|. |..|.+|++-|....+.+.++ ..+.||. +|...+- .-.-.++|+.
T Consensus 219 ~~ni~C~~Ctdv~--~~vlvf~Cns~HvtC~dCFr~yc~~Rl~~rqf~~~p~~gyslpc~a-gc~~s~i~e~HHF~ilg~ 295 (446)
T KOG0006|consen 219 SRNITCITCTDVR--SPVLVFQCNSRHVTCLDCFRLYCVTRLNDRQFVHDPQLGYSLPCVA-GCPNSLIKELHHFRILGE 295 (446)
T ss_pred cccceeEEecCCc--cceEEEecCCceeehHHhhhhHhhhcccccccccCccccccccccC-CCchHHHHhhhhheecch
Confidence 3458999997763 234556887 999999999999999977654 4688886 7776543 3344568999
Q ss_pred HHHHHHHHHHHHHHhhcCCCcccccC--CCCCcc-ccccccccccc-ccceeeccccccccCCcCCCchHHHHHHHHHhh
Q 006225 416 EEFERWESLMLQKTLESMSDVAYCPR--CETPCI-EDEEQHAQCSK-CFYSFCTLCRERRHVGVVCMTPEIKLRILQERQ 491 (655)
Q Consensus 416 e~~ery~~~~~~~~l~~~~~~~~CP~--C~~~~~-~~~~~~~~C~~-C~~~fC~~C~~~~H~~~sC~~~~~~~~~~~e~~ 491 (655)
+.|++|+++..+.++..+ +-+.||+ |+..+. ..+..++.|+. |++.||..|+..||.+. |.+.
T Consensus 296 e~Y~rYQr~atEe~vlq~-gGVlCP~pgCG~gll~EPD~rkvtC~~gCgf~FCR~C~e~yh~ge-C~~~----------- 362 (446)
T KOG0006|consen 296 EQYNRYQRYATEECVLQM-GGVLCPRPGCGAGLLPEPDQRKVTCEGGCGFAFCRECKEAYHEGE-CSAV----------- 362 (446)
T ss_pred hHHHHHHHhhhhhheeec-CCEecCCCCCCcccccCCCCCcccCCCCchhHhHHHHHhhhcccc-ceee-----------
Confidence 999999999999888665 4778986 988765 45567899986 99999999999999764 3210
Q ss_pred cchhhhhhhhHHHHHHHHHHHhHHHHhcccccCccccceeEEecCcCceeccccCeeeeccccccccCCCCCCCCCCCCC
Q 006225 492 NSSQVKEGQKQREHEMINELLSVKEILRDAKQCPSCKMAISRTEGCNKIVCNNCGQYFCYRCNKAIDGYDHFRTGTCELF 571 (655)
Q Consensus 492 ~~~~~~~~~~~~e~e~~~e~l~~~~i~~~~k~CP~C~~~iek~~Gcn~m~C~~C~~~FC~~C~~~~~~~~H~~~~~C~~~ 571 (655)
.+ . ....+|..-
T Consensus 363 ---------------------------------------~~-a----------------------------s~t~tc~y~ 374 (446)
T KOG0006|consen 363 ---------------------------------------FE-A----------------------------SGTTTCAYR 374 (446)
T ss_pred ---------------------------------------ec-c----------------------------ccccceeee
Confidence 00 0 111122211
Q ss_pred hhH---HHHHHHHHHHHHHHHHHHHhccccccCccCCccCccccccCCcceEEccc--ccccccccccccccccc--ccc
Q 006225 572 PQE---MIRDWEERLNARQVVAQIQADMFDEHGLSCPNCRQFNAKVGNNNHMFCWA--CQIHYCYLCKKIVRRST--QHY 644 (655)
Q Consensus 572 ~~~---~~~~~~~~~~~~~~~~~~~~~~~~~~~k~CP~C~~~ieK~~GCnhm~C~~--C~~~FC~~C~~~~~~~~--~Hf 644 (655)
..+ ....|+ .+..+.|...|++||+|+++.|++|||+||.|.+ ||.++||.|+-.|.+.+ +|+
T Consensus 375 vde~~a~~arwd----------~as~~TIk~tTkpCPkChvptErnGGCmHm~Ct~~~Cg~eWCw~C~tEW~r~CmgdHW 444 (446)
T KOG0006|consen 375 VDERAAEQARWD----------AASKETIKKTTKPCPKCHVPTERNGGCMHMKCTQPQCGLEWCWNCGTEWNRVCMGDHW 444 (446)
T ss_pred cChhhhhhhhhh----------hhhhhhhhhccCCCCCccCccccCCceEEeecCCCCCCceeEeccCChhhhhhccccc
Confidence 110 112332 2334566778999999999999999999999996 99999999999999755 564
No 6
>KOG1812 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=99.72 E-value=1e-18 Score=188.70 Aligned_cols=185 Identities=23% Similarity=0.465 Sum_probs=122.4
Q ss_pred cccccCCCCCcccccccccccccccceeeccccccc------cC-CcCCCchHHHHHHHHHhhcchhhhhhhhHHHHHHH
Q 006225 436 VAYCPRCETPCIEDEEQHAQCSKCFYSFCTLCRERR------HV-GVVCMTPEIKLRILQERQNSSQVKEGQKQREHEMI 508 (655)
Q Consensus 436 ~~~CP~C~~~~~~~~~~~~~C~~C~~~fC~~C~~~~------H~-~~sC~~~~~~~~~~~e~~~~~~~~~~~~~~e~e~~ 508 (655)
...|..|....+..+.... =..|+|.||..|++.+ ++ .++|+...|...+..+ .....+.....+++
T Consensus 146 ~~~C~iC~~e~~~~~~~f~-~~~C~H~fC~~C~k~~iev~~~~~~~~~C~~~~C~~~l~~~-----~c~~llt~kl~e~~ 219 (384)
T KOG1812|consen 146 KEECGICFVEDPEAEDMFS-VLKCGHRFCKDCVKQHIEVKLLSGTVIRCPHDGCESRLTLE-----SCRKLLTPKLREMW 219 (384)
T ss_pred cccCccCccccccHhhhHH-HhcccchhhhHHhHHHhhhhhccCCCccCCCCCCCccCCHH-----HHhhhcCHHHHHHH
Confidence 3467777643332212112 2378999999999832 22 3578887776544332 22333334556677
Q ss_pred HHHHhHHHHhcc-cccCc--cccceeEEec-----CcCceeccccCeeeeccccccccCCCCCCCCCCCCChhHHHHHHH
Q 006225 509 NELLSVKEILRD-AKQCP--SCKMAISRTE-----GCNKIVCNNCGQYFCYRCNKAIDGYDHFRTGTCELFPQEMIRDWE 580 (655)
Q Consensus 509 ~e~l~~~~i~~~-~k~CP--~C~~~iek~~-----Gcn~m~C~~C~~~FC~~C~~~~~~~~H~~~~~C~~~~~~~~~~~~ 580 (655)
+..+.+..+... -.+|| +|...+.+.+ .-....|..|+..||..|+.+| |.+.+|..| +.|.
T Consensus 220 e~~~~e~~i~~~~~~ycp~~~C~~l~~~~el~~~~~~~~~~C~~C~~~fCv~C~~~w-----h~~~sC~ey-----kk~~ 289 (384)
T KOG1812|consen 220 EQRLKEEVIPSLDRVYCPYPRCSSLMSKTELSSEVKSKRRPCVKCHELFCVKCKVPW-----HANLSCEEY-----KKLN 289 (384)
T ss_pred HHHHHHHhhhhhhcccCCCCCchHhhhhhhhccchhhcccccccCCCceeecCCCcC-----CCCCCHHHH-----HHhC
Confidence 777766666542 23776 8877766532 2344579999999999999999 556788755 2222
Q ss_pred HHHHHHHHHHHHHhccccccCccCCccCccccccCCcceEEcccccccccccccccccccc
Q 006225 581 ERLNARQVVAQIQADMFDEHGLSCPNCRQFNAKVGNNNHMFCWACQIHYCYLCKKIVRRST 641 (655)
Q Consensus 581 ~~~~~~~~~~~~~~~~~~~~~k~CP~C~~~ieK~~GCnhm~C~~C~~~FC~~C~~~~~~~~ 641 (655)
.....+.+...++..+++.||+|+..|++.+|||||+|+ ||++|||.|+..|..++
T Consensus 290 ----~~~~~d~~~~~~la~~wr~CpkC~~~ie~~~GCnhm~Cr-C~~~fcy~C~~~~~~~~ 345 (384)
T KOG1812|consen 290 ----PEEYVDDITLKYLAKRWRQCPKCKFMIELSEGCNHMTCR-CGHQFCYMCGGDWKTHN 345 (384)
T ss_pred ----CcccccHHHHHHHHHhcCcCcccceeeeecCCcceEEee-ccccchhhcCcchhhCC
Confidence 122222223333346789999999999999999999997 99999999999997543
No 7
>PF05773 RWD: RWD domain; InterPro: IPR006575 The RWD eukaryotic domain is found in RING finger (IPR001841 from INTERPRO) and WD repeat (IPR001680 from INTERPRO) containing proteins and DEXDc-like helicase (IPR001410 from INTERPRO) subfamily related to the ubiquitin-conjugating enzymes domain (IPR000608 from INTERPRO). ; GO: 0005515 protein binding; PDB: 2EBM_A 2EBK_A 2DAX_A 2DAW_A 2DAY_A 2DMF_A 1UKX_A 2YZ0_A.
Probab=99.66 E-value=8.9e-16 Score=137.95 Aligned_cols=111 Identities=28% Similarity=0.491 Sum_probs=81.9
Q ss_pred chHHHHHHHHHHHHHhcCCCeeeeccCCCCceEEEEEeeccCCCceEEeecCCCCccccCCCCCCCcccccccccCCcEE
Q 006225 154 INDQSQGDELLALESIYGDSVFILDRQRDLRSCQIHVHVETLDGLTVTAKLNSSTDLDARSESSDDFSYSFKVQYLPPIV 233 (655)
Q Consensus 154 ~n~e~Q~~EleaLeSIY~d~~~~~~~~~~~~~f~i~i~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~v~~LPpi~ 233 (655)
++.++|++||+||+|||++++.... ......+++.+.... ........+.+.
T Consensus 1 e~~e~~~~EieaL~sIy~~~~~~~~-~~~~~~~~~~l~~~~---------------------------~~~~~~~~~~~~ 52 (113)
T PF05773_consen 1 ECEEQQEEEIEALQSIYPDDFIEIE-SKSPPSLEVKLDESS---------------------------SSFESSSFPSVT 52 (113)
T ss_dssp HHHHHHHHHHHHHHHHSSSSESSST-SSSSEEEEEEE--CE---------------------------ECCTTTTSEEEE
T ss_pred CCHHHHHHHHHHHHHHcCCCccccc-cCCCCceeeeecccc---------------------------cccccccceeEE
Confidence 4789999999999999999883222 122245555542100 001122345699
Q ss_pred EEEEcCCCCCCCCCCeEEeecccCCH-HHHHHHHHHHHHHHHhCC-CchhhHHHHHHHhhcc
Q 006225 234 LTCLLPKSYPSHLPPYFTISARWLNS-TKISNLCSMLESIWIDQP-GQEILYQWIEWLQNSS 293 (655)
Q Consensus 234 L~~~lP~~YPs~~pP~~~l~s~wL~~-~~l~~L~~~L~~~~ee~~-G~~~lf~~ie~lqe~~ 293 (655)
|.|+||++|| ..||.|.|.+.+... .++..|.+.|.+.|+++. |++|||++++||||++
T Consensus 53 l~~~~p~~YP-~~~P~i~l~~~~~~~~~~~~~l~~~l~~~~~~~~~G~~~i~~ii~~~qe~~ 113 (113)
T PF05773_consen 53 LHFTLPPGYP-ESPPKISLESPKNSRNEQIEKLNKELEQIAEENRQGEPCIFQIIEWLQENL 113 (113)
T ss_dssp EEEEE-SSTT-SS--EEEEEEESSSHCHHHHHHHHHHHHHHHHSTTTS-CHHHHHHHHHHHH
T ss_pred EEEeCCCcCC-CcCCEEEEEcCCCCCHHHHHHHHHHHHHHHHHhCCCcCHHHHHHHHHHhhC
Confidence 9999999999 559999999999888 999999999999999998 9999999999999864
No 8
>smart00591 RWD domain in RING finger and WD repeat containing proteins and DEXDc-like helicases subfamily related to the UBCc domain.
Probab=99.63 E-value=2e-15 Score=134.48 Aligned_cols=105 Identities=24% Similarity=0.391 Sum_probs=80.4
Q ss_pred HHHHHHHhcCCCeeeeccCCCCceEEEEEeeccCCCceEEeecCCCCccccCCCCCCCcccccccccCCcEEEEEEcCCC
Q 006225 162 ELLALESIYGDSVFILDRQRDLRSCQIHVHVETLDGLTVTAKLNSSTDLDARSESSDDFSYSFKVQYLPPIVLTCLLPKS 241 (655)
Q Consensus 162 EleaLeSIY~d~~~~~~~~~~~~~f~i~i~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~v~~LPpi~L~~~lP~~ 241 (655)
|++||+|||++++..++.......|+|++..... + +. ...+.+.|.|.+|++
T Consensus 1 EieaL~sIy~~~~~~~~~~~~~~~~~i~l~~~~~------------~--------~~--------~~~~~~~l~~~~p~~ 52 (107)
T smart00591 1 ELEALESIYPEDFEVIDEDARIPEITIKLSPSSD------------E--------GE--------DQYVSLTLQVKLPEN 52 (107)
T ss_pred ChHHHHhhccceeEEecCCCCccEEEEEEecCCC------------C--------CC--------ccceEEEEEEECCCC
Confidence 7999999999988776542221245555431110 0 00 123459999999999
Q ss_pred CCCCCCCeEEee-cccCCHHHHHHHHHHHHHHHHhCCCchhhHHHHHHHhhcccc
Q 006225 242 YPSHLPPYFTIS-ARWLNSTKISNLCSMLESIWIDQPGQEILYQWIEWLQNSSLS 295 (655)
Q Consensus 242 YPs~~pP~~~l~-s~wL~~~~l~~L~~~L~~~~ee~~G~~~lf~~ie~lqe~~~~ 295 (655)
||+. +|.+.+. +.||+..++..|...|.++|+++.|++|||+|++|+|+.+.+
T Consensus 53 YP~~-~P~i~~~~~~~l~~~~~~~l~~~l~~~~~e~~g~~~if~~v~~~~e~l~~ 106 (107)
T smart00591 53 YPDE-APPISLLNSEGLSDEQLAELLKKLEEIAEENLGEVMIFELVEKLQEFLSE 106 (107)
T ss_pred CCCC-CCCeEEECCCCCCHHHHHHHHHHHHHHHHHhCCCEEhhHHHHHHHHHHhc
Confidence 9996 7777765 569999999999999999999999999999999999998764
No 9
>KOG4018 consensus Uncharacterized conserved protein, contains RWD domain [Function unknown]
Probab=99.51 E-value=5.2e-14 Score=135.91 Aligned_cols=115 Identities=17% Similarity=0.290 Sum_probs=84.2
Q ss_pred hhchHHHHHHHHHHHHHhcCCCeeeeccCCCCceEEEEEeeccCCCceEEeecCCCCccccCCCCCCCcccccccccCCc
Q 006225 152 LRINDQSQGDELLALESIYGDSVFILDRQRDLRSCQIHVHVETLDGLTVTAKLNSSTDLDARSESSDDFSYSFKVQYLPP 231 (655)
Q Consensus 152 ~~~n~e~Q~~EleaLeSIY~d~~~~~~~~~~~~~f~i~i~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~v~~LPp 231 (655)
|+.+ |+|++|+|||+|||+|++..+...+. ..|+|.|. ...... +++.. .
T Consensus 1 Ms~~-EeQe~E~EaLeSIY~de~~~i~~~~~-~~f~v~iq------------~e~~e~--------d~~~~--------~ 50 (215)
T KOG4018|consen 1 MSQY-EEQEEELEALESIYPDEFKHINSEDP-PIFEVTIQ------------YEEGEN--------DEPKG--------S 50 (215)
T ss_pred CCcH-HHHHHHHHHHHHhccchhhhhhccCC-ccceeeee------------cccccC--------CCccc--------c
Confidence 3445 89999999999999999854433222 23554432 221111 11100 2
Q ss_pred EEEEEEcCCCCCCCCCCeEEeec-ccCCHHHHHHHHHHHHHHHHhCCCchhhHHHHHHHhhcccccc
Q 006225 232 IVLTCLLPKSYPSHLPPYFTISA-RWLNSTKISNLCSMLESIWIDQPGQEILYQWIEWLQNSSLSYL 297 (655)
Q Consensus 232 i~L~~~lP~~YPs~~pP~~~l~s-~wL~~~~l~~L~~~L~~~~ee~~G~~~lf~~ie~lqe~~~~~l 297 (655)
+.|.|+|+++||++ ||.+.+.. ..+....+..|...|....++++||.|+|++++.+|+.+..++
T Consensus 51 ~~l~~s~tEnYPDe-~Pli~~~~~~~~~~~~i~~i~~~l~~~aeenLGmaMiftLvss~ke~l~e~~ 116 (215)
T KOG4018|consen 51 FILVFSLTENYPDE-APLIEAFENENLEDAEIEGILEKLQQEAEENLGMAMIFTLVSSAKEELNEIV 116 (215)
T ss_pred EEEEEEccCCCCCC-CcceeccccccccHHHHHHHHHHHHHHHHHhcchHHHHHHHHHHHHHHHHHH
Confidence 88999999999998 89888765 5677788999999999999999999999999977777666554
No 10
>KOG4445 consensus Uncharacterized conserved protein, contains RWD domain [Function unknown]
Probab=99.20 E-value=1e-10 Score=117.51 Aligned_cols=105 Identities=24% Similarity=0.482 Sum_probs=89.9
Q ss_pred EEEEEEcCCCCCCCCCCeEEee-cccCCHHHHHHHHHHHHHHHHhCCCchhhHHHHHHHhhccccccccccceecCCCCc
Q 006225 232 IVLTCLLPKSYPSHLPPYFTIS-ARWLNSTKISNLCSMLESIWIDQPGQEILYQWIEWLQNSSLSYLGFNEEIVLGPYGV 310 (655)
Q Consensus 232 i~L~~~lP~~YPs~~pP~~~l~-s~wL~~~~l~~L~~~L~~~~ee~~G~~~lf~~ie~lqe~~~~~l~~~~~~~l~~~~~ 310 (655)
|+|.++.|++||.+ .|.|+|+ ..+|++.++..|.+.+..+++++.|++|||++|+..+|.+...-
T Consensus 47 vtl~m~vs~gYP~e-sPtvtl~nPRGl~d~~~~~i~~~~~~iikq~~g~pii~~lie~~~e~LT~nn------------- 112 (368)
T KOG4445|consen 47 VTLEMTVSEGYPAE-SPTVTLSNPRGLGDPEFREIQRQIQEIIKQNSGMPIICQLIEHCSEFLTENN------------- 112 (368)
T ss_pred EEEEEecCCCCCCc-CCceEecCCCCCCcHHHHHHHHHHHHHHHhcCCCchhHHHHHHHHHHcccCC-------------
Confidence 88999999999998 8888875 58999999999999999999999999999999999998775420
Q ss_pred cccCCcccccccCCCCCCchhhhccchhhhhhhccccccccccccccccCCC-eEecCCCCcccHhhHHHHHHHHh
Q 006225 311 ACIGDRRAISESVSPDVDIPSIRSYNHERCHENFLKSFHECRICFSEFAGTD-FVRLPCHHFFCWKCMKTYLDIHI 385 (655)
Q Consensus 311 ~~~~d~~~~~~~~s~~~~~~~l~~~n~~~~~~~f~~~~~~C~IC~e~~~~~~-~~~l~C~H~fC~~Cl~~yi~~~i 385 (655)
-....|.||+--|...+ |+...|.|+|...||..|+....
T Consensus 113 -----------------------------------~p~gqCvICLygfa~~~~ft~T~C~Hy~H~~ClaRyl~~~~ 153 (368)
T KOG4445|consen 113 -----------------------------------HPNGQCVICLYGFASSPAFTVTACDHYMHFACLARYLTECL 153 (368)
T ss_pred -----------------------------------CCCCceEEEEEeecCCCceeeehhHHHHHHHHHHHHHHHHH
Confidence 01257999998888666 66679999999999999987643
No 11
>KOG1815 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=98.94 E-value=5.8e-10 Score=123.98 Aligned_cols=118 Identities=28% Similarity=0.593 Sum_probs=83.5
Q ss_pred hhcCCCcccccCCCCCcccccccccccccccceeeccccccccCCcCCCchHHHHHHHHHhhcchhhhhhhhHHHHHHHH
Q 006225 430 LESMSDVAYCPRCETPCIEDEEQHAQCSKCFYSFCTLCRERRHVGVVCMTPEIKLRILQERQNSSQVKEGQKQREHEMIN 509 (655)
Q Consensus 430 l~~~~~~~~CP~C~~~~~~~~~~~~~C~~C~~~fC~~C~~~~H~~~sC~~~~~~~~~~~e~~~~~~~~~~~~~~e~e~~~ 509 (655)
+.-.+. .-|+..-... ......+.| .|++.||+.|..+||.+.+|.....++.... .+.+++
T Consensus 158 lkwCP~-~~C~~av~~~-~~~~~~v~C-~~g~~FC~~C~~~~H~p~~C~~~~~wl~k~~--------------~~se~~- 219 (444)
T KOG1815|consen 158 LKWCPA-PGCGLAVKFG-SLESVEVDC-GCGHEFCFACGEESHSPVSCPGAKKWLKKCR--------------DDSETI- 219 (444)
T ss_pred cccCCC-CCCCceeecc-CCCccceeC-CCCchhHhhccccccCCCcccchHHHHHhhh--------------hhhhhh-
Confidence 333445 6787632221 334566788 6888999999999999999987655443211 111122
Q ss_pred HHHhHHHHhcccccCccccceeEEecCcCceeccc--cCeeeeccccccccCCCCCC--CCCCCCCh
Q 006225 510 ELLSVKEILRDAKQCPSCKMAISRTEGCNKIVCNN--CGQYFCYRCNKAIDGYDHFR--TGTCELFP 572 (655)
Q Consensus 510 e~l~~~~i~~~~k~CP~C~~~iek~~Gcn~m~C~~--C~~~FC~~C~~~~~~~~H~~--~~~C~~~~ 572 (655)
.|+..+++.||+|..+|++++|||||+|.. |++.|||.|...|.. |.. ...|..|.
T Consensus 220 -----~wi~~ntk~CP~c~~~iek~~gc~~~~~~~~~c~~~FCw~Cl~~~~~--h~~~~~~~c~~~~ 279 (444)
T KOG1815|consen 220 -----NWILANTKECPKCKVPIEKDGGCNHMTCKSASCKHEFCWVCLASLSD--HGSSTGYSCNRYV 279 (444)
T ss_pred -----hhhhccCccCCCcccchhccCCccccccccCCcCCeeceeeeccccc--ccccceeeeeeee
Confidence 267788999999999999999999999987 999999999888832 221 23565554
No 12
>smart00647 IBR In Between Ring fingers. the domains occurs between pairs og RING fingers
Probab=98.74 E-value=8.6e-09 Score=82.97 Aligned_cols=59 Identities=36% Similarity=0.793 Sum_probs=52.9
Q ss_pred HHHHHHHHHHHhhcCCCccccc--CCCCCcccc---cccccccccccceeeccccccccCCcCC
Q 006225 419 ERWESLMLQKTLESMSDVAYCP--RCETPCIED---EEQHAQCSKCFYSFCTLCRERRHVGVVC 477 (655)
Q Consensus 419 ery~~~~~~~~l~~~~~~~~CP--~C~~~~~~~---~~~~~~C~~C~~~fC~~C~~~~H~~~sC 477 (655)
++|++++.+++++.+++++||| +|+..+... ....+.|+.|++.||+.|+.+||.+++|
T Consensus 1 ~~y~~~~~~~~i~~~~~~~~CP~~~C~~~~~~~~~~~~~~v~C~~C~~~fC~~C~~~~H~~~~C 64 (64)
T smart00647 1 EKYERLLLESYVESNPDLKWCPAPDCSAAIIVTEEEGCNRVTCPKCGFSFCFRCKVPWHSPVSC 64 (64)
T ss_pred ChHHHHHHHHHHhcCCCccCCCCCCCcceEEecCCCCCCeeECCCCCCeECCCCCCcCCCCCCC
Confidence 4799999999999888999999 799888664 4578999999999999999999999987
No 13
>KOG0006 consensus E3 ubiquitin-protein ligase (Parkin protein) [Posttranslational modification, protein turnover, chaperones]
Probab=98.64 E-value=2.8e-08 Score=100.74 Aligned_cols=47 Identities=30% Similarity=0.861 Sum_probs=42.8
Q ss_pred HhHHHHhcccccCccccceeEEecCcCceeccc--cCeeeecccccccc
Q 006225 512 LSVKEILRDAKQCPSCKMAISRTEGCNKIVCNN--CGQYFCYRCNKAID 558 (655)
Q Consensus 512 l~~~~i~~~~k~CP~C~~~iek~~Gcn~m~C~~--C~~~FC~~C~~~~~ 558 (655)
++...|...+|+||+|..+.++++||.||.|+. ||..+||.|+-+|+
T Consensus 388 as~~TIk~tTkpCPkChvptErnGGCmHm~Ct~~~Cg~eWCw~C~tEW~ 436 (446)
T KOG0006|consen 388 ASKETIKKTTKPCPKCHVPTERNGGCMHMKCTQPQCGLEWCWNCGTEWN 436 (446)
T ss_pred hhhhhhhhccCCCCCccCccccCCceEEeecCCCCCCceeEeccCChhh
Confidence 455567788999999999999999999999987 99999999999994
No 14
>smart00647 IBR In Between Ring fingers. the domains occurs between pairs og RING fingers
Probab=98.58 E-value=7.7e-08 Score=77.37 Aligned_cols=51 Identities=41% Similarity=0.887 Sum_probs=41.2
Q ss_pred HHHHHhHHHHhc--ccccCc--cccceeEEec--CcCceeccccCeeeecccccccc
Q 006225 508 INELLSVKEILR--DAKQCP--SCKMAISRTE--GCNKIVCNNCGQYFCYRCNKAID 558 (655)
Q Consensus 508 ~~e~l~~~~i~~--~~k~CP--~C~~~iek~~--Gcn~m~C~~C~~~FC~~C~~~~~ 558 (655)
+++++...++.. ++++|| +|..+|+..+ +..+|+|+.|++.|||.|+.+||
T Consensus 3 y~~~~~~~~i~~~~~~~~CP~~~C~~~~~~~~~~~~~~v~C~~C~~~fC~~C~~~~H 59 (64)
T smart00647 3 YERLLLESYVESNPDLKWCPAPDCSAAIIVTEEEGCNRVTCPKCGFSFCFRCKVPWH 59 (64)
T ss_pred HHHHHHHHHHhcCCCccCCCCCCCcceEEecCCCCCCeeECCCCCCeECCCCCCcCC
Confidence 344444455544 689999 9999999964 89999998899999999999983
No 15
>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=98.52 E-value=2e-08 Score=80.76 Aligned_cols=59 Identities=34% Similarity=0.802 Sum_probs=39.5
Q ss_pred HHHHHHHHHHHhhcCCCcccccC--CCCCcccccc-cc--cccccccceeeccccccccCCcCC
Q 006225 419 ERWESLMLQKTLESMSDVAYCPR--CETPCIEDEE-QH--AQCSKCFYSFCTLCRERRHVGVVC 477 (655)
Q Consensus 419 ery~~~~~~~~l~~~~~~~~CP~--C~~~~~~~~~-~~--~~C~~C~~~fC~~C~~~~H~~~sC 477 (655)
++|++++++++++.++++.|||+ |+.++..+.. .. +.|+.|++.||+.|+.+||.+++|
T Consensus 1 eky~~~~~~~~~~~~~~~~~Cp~~~C~~~~~~~~~~~~~~~~C~~C~~~fC~~C~~~~H~~~~C 64 (64)
T PF01485_consen 1 EKYQKFLLKRYLESDPNIRWCPNPDCEYIIEKDDGCNSPIVTCPSCGTEFCFKCGEPWHEGVTC 64 (64)
T ss_dssp HCHHHCCCHS---S---CC--TTSST---ECS-SSTTS--CCTTSCCSEECSSSTSESCTTS-H
T ss_pred ChHHHHHHHHHHHCCCCccCCCCCCCcccEEecCCCCCCeeECCCCCCcCccccCcccCCCCCC
Confidence 57888889999988889999987 9998876433 33 899999999999999999999887
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=98.27 E-value=1.8e-07 Score=75.19 Aligned_cols=39 Identities=33% Similarity=1.135 Sum_probs=29.7
Q ss_pred ccccCcc--ccceeEEecCcCc--eeccccCeeeecccccccc
Q 006225 520 DAKQCPS--CKMAISRTEGCNK--IVCNNCGQYFCYRCNKAID 558 (655)
Q Consensus 520 ~~k~CP~--C~~~iek~~Gcn~--m~C~~C~~~FC~~C~~~~~ 558 (655)
+.++||+ |..++....+.+. |+|+.|++.|||.|+.+||
T Consensus 17 ~~~~Cp~~~C~~~~~~~~~~~~~~~~C~~C~~~fC~~C~~~~H 59 (64)
T PF01485_consen 17 NIRWCPNPDCEYIIEKDDGCNSPIVTCPSCGTEFCFKCGEPWH 59 (64)
T ss_dssp -CC--TTSST---ECS-SSTTS--CCTTSCCSEECSSSTSESC
T ss_pred CccCCCCCCCcccEEecCCCCCCeeECCCCCCcCccccCcccC
Confidence 5689986 9999999999998 9999999999999999983
No 17
>PF15227 zf-C3HC4_4: zinc finger of C3HC4-type, RING; PDB: 2EGP_A 2ECV_A 2ECJ_A 2YSL_A 2YSJ_A.
Probab=98.22 E-value=5.9e-07 Score=66.20 Aligned_cols=41 Identities=37% Similarity=0.909 Sum_probs=29.2
Q ss_pred cccccccccCCCeEecCCCCcccHhhHHHHHHHHhhcCCcceeccCC
Q 006225 351 CRICFSEFAGTDFVRLPCHHFFCWKCMKTYLDIHISEGTVSKLQCPD 397 (655)
Q Consensus 351 C~IC~e~~~~~~~~~l~C~H~fC~~Cl~~yi~~~i~~g~~~~i~CP~ 397 (655)
|+||++.+ .++++++|||.||..||.+++...-.. .+.||.
T Consensus 1 CpiC~~~~--~~Pv~l~CGH~FC~~Cl~~~~~~~~~~----~~~CP~ 41 (42)
T PF15227_consen 1 CPICLDLF--KDPVSLPCGHSFCRSCLERLWKEPSGS----GFSCPE 41 (42)
T ss_dssp ETTTTSB---SSEEE-SSSSEEEHHHHHHHHCCSSSS----T---SS
T ss_pred CCccchhh--CCccccCCcCHHHHHHHHHHHHccCCc----CCCCcC
Confidence 89999998 488999999999999999998643221 278986
No 18
>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=98.05 E-value=2.3e-06 Score=63.69 Aligned_cols=40 Identities=45% Similarity=1.046 Sum_probs=32.8
Q ss_pred cccccccccc-CCCeEecCCCCcccHhhHHHHHHHHhhcCCcceeccCC
Q 006225 350 ECRICFSEFA-GTDFVRLPCHHFFCWKCMKTYLDIHISEGTVSKLQCPD 397 (655)
Q Consensus 350 ~C~IC~e~~~-~~~~~~l~C~H~fC~~Cl~~yi~~~i~~g~~~~i~CP~ 397 (655)
+|+||++++. ....+.++|+|.||.+|+.+|+... .+||.
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 6999999996 4667778999999999999998752 28986
No 19
>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=97.85 E-value=1.1e-05 Score=58.83 Aligned_cols=40 Identities=35% Similarity=1.020 Sum_probs=31.6
Q ss_pred cccccccccCCCeEecCCCCcccHhhHHHHHHHHhhcCCcceeccCC
Q 006225 351 CRICFSEFAGTDFVRLPCHHFFCWKCMKTYLDIHISEGTVSKLQCPD 397 (655)
Q Consensus 351 C~IC~e~~~~~~~~~l~C~H~fC~~Cl~~yi~~~i~~g~~~~i~CP~ 397 (655)
|+||++.+... ...++|+|.||..|+.+|+.. . ..+.||.
T Consensus 1 C~iC~~~~~~~-~~~~~C~H~fC~~C~~~~~~~---~---~~~~CP~ 40 (41)
T PF00097_consen 1 CPICLEPFEDP-VILLPCGHSFCRDCLRKWLEN---S---GSVKCPL 40 (41)
T ss_dssp ETTTSSBCSSE-EEETTTSEEEEHHHHHHHHHH---T---SSSBTTT
T ss_pred CCcCCccccCC-CEEecCCCcchHHHHHHHHHh---c---CCccCCc
Confidence 89999987532 236799999999999999987 2 2577986
No 20
>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=97.85 E-value=1e-05 Score=58.59 Aligned_cols=38 Identities=39% Similarity=1.004 Sum_probs=28.5
Q ss_pred cccccccccCCCeEecCCCCcccHhhHHHHHHHHhhcCCcceeccCC
Q 006225 351 CRICFSEFAGTDFVRLPCHHFFCWKCMKTYLDIHISEGTVSKLQCPD 397 (655)
Q Consensus 351 C~IC~e~~~~~~~~~l~C~H~fC~~Cl~~yi~~~i~~g~~~~i~CP~ 397 (655)
|+||++.+.. ..+.++|||.||.+|+.+|++.. .+||.
T Consensus 1 C~iC~~~~~~-~~~~~~CGH~fC~~C~~~~~~~~--------~~CP~ 38 (39)
T PF13923_consen 1 CPICLDELRD-PVVVTPCGHSFCKECIEKYLEKN--------PKCPV 38 (39)
T ss_dssp ETTTTSB-SS-EEEECTTSEEEEHHHHHHHHHCT--------SB-TT
T ss_pred CCCCCCcccC-cCEECCCCCchhHHHHHHHHHCc--------CCCcC
Confidence 8999998753 33567999999999999997742 57885
No 21
>PLN03208 E3 ubiquitin-protein ligase RMA2; Provisional
Probab=97.84 E-value=1.5e-05 Score=77.55 Aligned_cols=64 Identities=27% Similarity=0.662 Sum_probs=48.3
Q ss_pred cccccccccccccCCCeEecCCCCcccHhhHHHHHHHHhh--------cCCcceeccCCCCCCCCCCcccccccCC
Q 006225 347 SFHECRICFSEFAGTDFVRLPCHHFFCWKCMKTYLDIHIS--------EGTVSKLQCPDAKCGGMVPPSLLKKLLG 414 (655)
Q Consensus 347 ~~~~C~IC~e~~~~~~~~~l~C~H~fC~~Cl~~yi~~~i~--------~g~~~~i~CP~~~C~~~l~~~~i~~ll~ 414 (655)
+.++|+||++.+ .+.+.+.|||.||..|+.+|+...-. .......+||. |+..++...+..+.+
T Consensus 17 ~~~~CpICld~~--~dPVvT~CGH~FC~~CI~~wl~~s~~s~~~~~~~~~~k~~~~CPv--CR~~Is~~~LvPiyg 88 (193)
T PLN03208 17 GDFDCNICLDQV--RDPVVTLCGHLFCWPCIHKWTYASNNSRQRVDQYDHKREPPKCPV--CKSDVSEATLVPIYG 88 (193)
T ss_pred CccCCccCCCcC--CCcEEcCCCchhHHHHHHHHHHhccccccccccccccCCCCcCCC--CCCcCChhcEEEeec
Confidence 357999999986 46677799999999999999764211 01123579998 999999888777654
No 22
>PF13445 zf-RING_UBOX: RING-type zinc-finger; PDB: 2CT2_A.
Probab=97.83 E-value=1.5e-05 Score=58.94 Aligned_cols=41 Identities=32% Similarity=0.823 Sum_probs=22.7
Q ss_pred cccccccccC--CCeEecCCCCcccHhhHHHHHHHHhhcCCcceeccC
Q 006225 351 CRICFSEFAG--TDFVRLPCHHFFCWKCMKTYLDIHISEGTVSKLQCP 396 (655)
Q Consensus 351 C~IC~e~~~~--~~~~~l~C~H~fC~~Cl~~yi~~~i~~g~~~~i~CP 396 (655)
|+||.+ +.. +.+..|+|||.||++|+.+++.... ...++||
T Consensus 1 CpIc~e-~~~~~n~P~~L~CGH~~c~~cl~~l~~~~~----~~~~kCP 43 (43)
T PF13445_consen 1 CPICKE-FSTEENPPMVLPCGHVFCKDCLQKLSKKSD----RNRFKCP 43 (43)
T ss_dssp -TTT-----TTSS-EEE-SSS-EEEHHHHHHHHHH-S-----S-B--T
T ss_pred CCcccc-ccCCCCCCEEEeCccHHHHHHHHHHHhcCC----CCeeeCc
Confidence 899999 643 2366789999999999999987432 2368887
No 23
>KOG1035 consensus eIF-2alpha kinase GCN2 [Translation, ribosomal structure and biogenesis]
Probab=97.71 E-value=6e-06 Score=97.82 Aligned_cols=114 Identities=20% Similarity=0.219 Sum_probs=86.9
Q ss_pred hhchHHHHHHHHHHHHHhcCCCeeeeccCCCCceEEEEEeeccCCCceEEeecCCCCccccCCCCCCCcccccccccCCc
Q 006225 152 LRINDQSQGDELLALESIYGDSVFILDRQRDLRSCQIHVHVETLDGLTVTAKLNSSTDLDARSESSDDFSYSFKVQYLPP 231 (655)
Q Consensus 152 ~~~n~e~Q~~EleaLeSIY~d~~~~~~~~~~~~~f~i~i~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~v~~LPp 231 (655)
++.+.|.|.+|+|||.|||++++..+...... . .+|.. +.+..-.. .+ .
T Consensus 3 ~e~~~eiQ~~e~ea~k~i~~~d~e~l~~r~~w-~--~~i~l-------~~l~s~~~-----------------~~----~ 51 (1351)
T KOG1035|consen 3 LELNYEIQENELEALKAIYMDDFEELKARWAW-V--CHILL-------IALRSCSL-----------------KL----S 51 (1351)
T ss_pred hHHHHHHHHHHHHhhcccccchHHHHHHHHhh-h--hhhhh-------hhhhhhhH-----------------HH----h
Confidence 45688999999999999999998876532211 1 11110 11110000 11 1
Q ss_pred EEEEEEcCCCCCCCCCCeEEe-ecccCCHHHHHHHHHHHHHHHHhCCCchhhHHHHHHHhhcccccc
Q 006225 232 IVLTCLLPKSYPSHLPPYFTI-SARWLNSTKISNLCSMLESIWIDQPGQEILYQWIEWLQNSSLSYL 297 (655)
Q Consensus 232 i~L~~~lP~~YPs~~pP~~~l-~s~wL~~~~l~~L~~~L~~~~ee~~G~~~lf~~ie~lqe~~~~~l 297 (655)
+.|++..++.||.. +|.+.+ ....+.+.++..|...|..+.+...|++|+|.+...+||.+.++-
T Consensus 52 ~~lh~~~~~~yp~~-kp~i~lk~~~~~~d~~i~~L~~~l~~~~~~~~G~~~i~eLa~~vqefl~~~~ 117 (1351)
T KOG1035|consen 52 GRLHVKCKRKYPYS-KPEIKLKDHQGVSDEDIELLSNELTALAKTLRGEVMIAELASIVQEFLKDHQ 117 (1351)
T ss_pred hHhhhhhccccCCC-CccccccccccchHHHHHHHHHHHHHhhccccccEEeeeHhhhhHHHHhccC
Confidence 78999999999998 888877 468999999999999999999999999999999999999987764
No 24
>KOG0320 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=97.71 E-value=1.9e-05 Score=74.81 Aligned_cols=53 Identities=26% Similarity=0.623 Sum_probs=41.6
Q ss_pred cccccccccccccCCCeEecCCCCcccHhhHHHHHHHHhhcCCcceeccCCCCCCCCCCcccc
Q 006225 347 SFHECRICFSEFAGTDFVRLPCHHFFCWKCMKTYLDIHISEGTVSKLQCPDAKCGGMVPPSLL 409 (655)
Q Consensus 347 ~~~~C~IC~e~~~~~~~~~l~C~H~fC~~Cl~~yi~~~i~~g~~~~i~CP~~~C~~~l~~~~i 409 (655)
..+-|+||++.+.....+...|||.||..|++.-+.. ..+||. |...|...++
T Consensus 130 ~~~~CPiCl~~~sek~~vsTkCGHvFC~~Cik~alk~--------~~~CP~--C~kkIt~k~~ 182 (187)
T KOG0320|consen 130 GTYKCPICLDSVSEKVPVSTKCGHVFCSQCIKDALKN--------TNKCPT--CRKKITHKQF 182 (187)
T ss_pred cccCCCceecchhhccccccccchhHHHHHHHHHHHh--------CCCCCC--cccccchhhh
Confidence 4588999999998666666799999999999997653 368998 7766665444
No 25
>PF14634 zf-RING_5: zinc-RING finger domain
Probab=97.68 E-value=3.2e-05 Score=57.58 Aligned_cols=42 Identities=33% Similarity=0.858 Sum_probs=33.3
Q ss_pred ccccccccccC-CCeEecCCCCcccHhhHHHHHHHHhhcCCcceeccCCCCCC
Q 006225 350 ECRICFSEFAG-TDFVRLPCHHFFCWKCMKTYLDIHISEGTVSKLQCPDAKCG 401 (655)
Q Consensus 350 ~C~IC~e~~~~-~~~~~l~C~H~fC~~Cl~~yi~~~i~~g~~~~i~CP~~~C~ 401 (655)
.|+||++.+.. ..+..++|||.||..|+.+.. ...+.||. |+
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 49999999943 346667999999999999976 23588998 65
No 26
>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=97.63 E-value=5.7e-05 Score=55.36 Aligned_cols=44 Identities=43% Similarity=0.994 Sum_probs=33.0
Q ss_pred ccccccccccCCCeEecCCCCcccHhhHHHHHHHHhhcCCcceeccCCCCCCCC
Q 006225 350 ECRICFSEFAGTDFVRLPCHHFFCWKCMKTYLDIHISEGTVSKLQCPDAKCGGM 403 (655)
Q Consensus 350 ~C~IC~e~~~~~~~~~l~C~H~fC~~Cl~~yi~~~i~~g~~~~i~CP~~~C~~~ 403 (655)
+|+||++.+. ......+|+|.||..|+..|+.. ...+||. |+..
T Consensus 1 ~C~iC~~~~~-~~~~~~~C~H~~c~~C~~~~~~~-------~~~~Cp~--C~~~ 44 (45)
T cd00162 1 ECPICLEEFR-EPVVLLPCGHVFCRSCIDKWLKS-------GKNTCPL--CRTP 44 (45)
T ss_pred CCCcCchhhh-CceEecCCCChhcHHHHHHHHHh-------CcCCCCC--CCCc
Confidence 5999999872 23333469999999999999875 2467987 7754
No 27
>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=97.49 E-value=8.8e-05 Score=56.74 Aligned_cols=45 Identities=42% Similarity=0.952 Sum_probs=35.4
Q ss_pred cccccccccccCCCeEecCCCCc-ccHhhHHHHHHHHhhcCCcceeccCCCCCCCCCC
Q 006225 349 HECRICFSEFAGTDFVRLPCHHF-FCWKCMKTYLDIHISEGTVSKLQCPDAKCGGMVP 405 (655)
Q Consensus 349 ~~C~IC~e~~~~~~~~~l~C~H~-fC~~Cl~~yi~~~i~~g~~~~i~CP~~~C~~~l~ 405 (655)
..|.||++... +.+.++|||. ||..|+.+++. ...+||. |+..+.
T Consensus 3 ~~C~iC~~~~~--~~~~~pCgH~~~C~~C~~~~~~--------~~~~CP~--Cr~~i~ 48 (50)
T PF13920_consen 3 EECPICFENPR--DVVLLPCGHLCFCEECAERLLK--------RKKKCPI--CRQPIE 48 (50)
T ss_dssp SB-TTTSSSBS--SEEEETTCEEEEEHHHHHHHHH--------TTSBBTT--TTBB-S
T ss_pred CCCccCCccCC--ceEEeCCCChHHHHHHhHHhcc--------cCCCCCc--CChhhc
Confidence 57999999853 5666799999 99999999987 2468998 887764
No 28
>KOG0823 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=97.42 E-value=9.5e-05 Score=73.27 Aligned_cols=60 Identities=32% Similarity=0.763 Sum_probs=48.0
Q ss_pred ccccccccccccccCCCeEecCCCCcccHhhHHHHHHHHhhcCCcceeccCCCCCCCCCCcccccccCC
Q 006225 346 KSFHECRICFSEFAGTDFVRLPCHHFFCWKCMKTYLDIHISEGTVSKLQCPDAKCGGMVPPSLLKKLLG 414 (655)
Q Consensus 346 ~~~~~C~IC~e~~~~~~~~~l~C~H~fC~~Cl~~yi~~~i~~g~~~~i~CP~~~C~~~l~~~~i~~ll~ 414 (655)
...|+|.||++.- .+++...|||.||..||-+|+..+.. .-.||. |+..++.+.|--|..
T Consensus 45 ~~~FdCNICLd~a--kdPVvTlCGHLFCWpClyqWl~~~~~-----~~~cPV--CK~~Vs~~~vvPlYG 104 (230)
T KOG0823|consen 45 GGFFDCNICLDLA--KDPVVTLCGHLFCWPCLYQWLQTRPN-----SKECPV--CKAEVSIDTVVPLYG 104 (230)
T ss_pred CCceeeeeecccc--CCCEEeecccceehHHHHHHHhhcCC-----CeeCCc--cccccccceEEeeec
Confidence 4568999999985 46677789999999999999987543 346888 999998887766643
No 29
>KOG2177 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=97.34 E-value=8.7e-05 Score=77.35 Aligned_cols=110 Identities=30% Similarity=0.557 Sum_probs=64.1
Q ss_pred ccccccccccccccCCCeEecCCCCcccHhhHHHHHHHHhhcCCcceeccCCCCCCCCCCcccccccCChHHHHHHHHHH
Q 006225 346 KSFHECRICFSEFAGTDFVRLPCHHFFCWKCMKTYLDIHISEGTVSKLQCPDAKCGGMVPPSLLKKLLGDEEFERWESLM 425 (655)
Q Consensus 346 ~~~~~C~IC~e~~~~~~~~~l~C~H~fC~~Cl~~yi~~~i~~g~~~~i~CP~~~C~~~l~~~~i~~ll~~e~~ery~~~~ 425 (655)
.+..+|+||++.+... ..++|+|.||..|+...+. ..+.||. |+. .........+-....+.+....
T Consensus 11 ~~~~~C~iC~~~~~~p--~~l~C~H~~c~~C~~~~~~--------~~~~Cp~--cr~-~~~~~~~n~~l~~~~~~~~~~~ 77 (386)
T KOG2177|consen 11 QEELTCPICLEYFREP--VLLPCGHNFCRACLTRSWE--------GPLSCPV--CRP-PSRNLRPNVLLANLVERLRQLR 77 (386)
T ss_pred cccccChhhHHHhhcC--ccccccchHhHHHHHHhcC--------CCcCCcc--cCC-chhccCccHHHHHHHHHHHhcC
Confidence 3558999999998643 6679999999999999987 3589998 884 2221111111112222222111
Q ss_pred HHHHhhcCCCcccccCCCCCcccccccccccccccceeecccc-ccccCCcC
Q 006225 426 LQKTLESMSDVAYCPRCETPCIEDEEQHAQCSKCFYSFCTLCR-ERRHVGVV 476 (655)
Q Consensus 426 ~~~~l~~~~~~~~CP~C~~~~~~~~~~~~~C~~C~~~fC~~C~-~~~H~~~s 476 (655)
..... ......|+.... .....|..|....|..|. ...|....
T Consensus 78 ~~~~~--~~~~~~c~~~~~------~~~~~c~~~~~~~c~~c~~~~~h~~h~ 121 (386)
T KOG2177|consen 78 LSRPL--GSKEELCEKHGE------ELKLFCEEDEKLLCVLCRESGEHRGHP 121 (386)
T ss_pred Ccccc--cccchhhhhcCC------cceEEecccccccCCCCCCcccccCCc
Confidence 11000 000113333211 156789999999999998 55665543
No 30
>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=97.28 E-value=0.00023 Score=50.19 Aligned_cols=38 Identities=45% Similarity=1.087 Sum_probs=29.8
Q ss_pred cccccccccCCCeEecCCCCcccHhhHHHHHHHHhhcCCcceeccCC
Q 006225 351 CRICFSEFAGTDFVRLPCHHFFCWKCMKTYLDIHISEGTVSKLQCPD 397 (655)
Q Consensus 351 C~IC~e~~~~~~~~~l~C~H~fC~~Cl~~yi~~~i~~g~~~~i~CP~ 397 (655)
|+||++.. ...+.++|+|.||..|+..|+. .+ ..+||.
T Consensus 1 C~iC~~~~--~~~~~~~C~H~~c~~C~~~~~~----~~---~~~CP~ 38 (39)
T smart00184 1 CPICLEEL--KDPVVLPCGHTFCRSCIRKWLK----SG---NNTCPI 38 (39)
T ss_pred CCcCccCC--CCcEEecCCChHHHHHHHHHHH----hC---cCCCCC
Confidence 78999883 4666779999999999999987 11 356875
No 31
>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=97.19 E-value=0.00046 Score=55.13 Aligned_cols=51 Identities=20% Similarity=0.217 Sum_probs=40.2
Q ss_pred cccccccccccCCCeEecCCCCcccHhhHHHHHHHHhhcCCcceeccCCCCCCCCCCcccccc
Q 006225 349 HECRICFSEFAGTDFVRLPCHHFFCWKCMKTYLDIHISEGTVSKLQCPDAKCGGMVPPSLLKK 411 (655)
Q Consensus 349 ~~C~IC~e~~~~~~~~~l~C~H~fC~~Cl~~yi~~~i~~g~~~~i~CP~~~C~~~l~~~~i~~ 411 (655)
+.|+||.+.+. +++.++|||.||+.|+.+|+.. ...||. |+..++.+.+..
T Consensus 2 ~~Cpi~~~~~~--~Pv~~~~G~v~~~~~i~~~~~~--------~~~cP~--~~~~~~~~~l~~ 52 (63)
T smart00504 2 FLCPISLEVMK--DPVILPSGQTYERRAIEKWLLS--------HGTDPV--TGQPLTHEDLIP 52 (63)
T ss_pred cCCcCCCCcCC--CCEECCCCCEEeHHHHHHHHHH--------CCCCCC--CcCCCChhhcee
Confidence 57999999874 5677899999999999999875 247998 777776555443
No 32
>KOG2164 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=97.12 E-value=0.00024 Score=77.70 Aligned_cols=61 Identities=25% Similarity=0.515 Sum_probs=47.1
Q ss_pred ccccccccccccCCCeEecCCCCcccHhhHHHHHHHHhhcCCcceeccCCCCCCCCCCcccccccCCh
Q 006225 348 FHECRICFSEFAGTDFVRLPCHHFFCWKCMKTYLDIHISEGTVSKLQCPDAKCGGMVPPSLLKKLLGD 415 (655)
Q Consensus 348 ~~~C~IC~e~~~~~~~~~l~C~H~fC~~Cl~~yi~~~i~~g~~~~i~CP~~~C~~~l~~~~i~~ll~~ 415 (655)
...|+|||+.... .....|||.||..||.+||...... ...+||. |...|...++..+.-.
T Consensus 186 ~~~CPICL~~~~~--p~~t~CGHiFC~~CiLqy~~~s~~~---~~~~CPi--C~s~I~~kdl~pv~~e 246 (513)
T KOG2164|consen 186 DMQCPICLEPPSV--PVRTNCGHIFCGPCILQYWNYSAIK---GPCSCPI--CRSTITLKDLLPVFIE 246 (513)
T ss_pred CCcCCcccCCCCc--ccccccCceeeHHHHHHHHhhhccc---CCccCCc--hhhhccccceeeeeec
Confidence 5789999998542 2334699999999999999887322 2688998 9999988777766543
No 33
>PHA02926 zinc finger-like protein; Provisional
Probab=97.06 E-value=0.00042 Score=68.27 Aligned_cols=55 Identities=27% Similarity=0.656 Sum_probs=39.0
Q ss_pred ccccccccccccc-----CC-CeEec-CCCCcccHhhHHHHHHHHhhcCCcceeccCCCCCCCCCC
Q 006225 347 SFHECRICFSEFA-----GT-DFVRL-PCHHFFCWKCMKTYLDIHISEGTVSKLQCPDAKCGGMVP 405 (655)
Q Consensus 347 ~~~~C~IC~e~~~-----~~-~~~~l-~C~H~fC~~Cl~~yi~~~i~~g~~~~i~CP~~~C~~~l~ 405 (655)
...+|+||++... .. .+-.| +|+|.||..|+.+|...+...| ..-.||. |+..+.
T Consensus 169 kE~eCgICmE~I~eK~~~~eRrFGIL~~CnHsFCl~CIr~Wr~~r~~~~--~~rsCPi--CR~~f~ 230 (242)
T PHA02926 169 KEKECGICYEVVYSKRLENDRYFGLLDSCNHIFCITCINIWHRTRRETG--ASDNCPI--CRTRFR 230 (242)
T ss_pred CCCCCccCccccccccccccccccccCCCCchHHHHHHHHHHHhccccC--cCCcCCC--Ccceee
Confidence 3479999999752 12 23334 8999999999999987653222 2467998 887654
No 34
>PHA02929 N1R/p28-like protein; Provisional
Probab=97.02 E-value=0.00051 Score=69.67 Aligned_cols=49 Identities=29% Similarity=0.678 Sum_probs=36.6
Q ss_pred cccccccccccccCCC-----eEe-cCCCCcccHhhHHHHHHHHhhcCCcceeccCCCCCCCCCC
Q 006225 347 SFHECRICFSEFAGTD-----FVR-LPCHHFFCWKCMKTYLDIHISEGTVSKLQCPDAKCGGMVP 405 (655)
Q Consensus 347 ~~~~C~IC~e~~~~~~-----~~~-l~C~H~fC~~Cl~~yi~~~i~~g~~~~i~CP~~~C~~~l~ 405 (655)
...+|+||++.+.... +.. .+|+|.||.+|+..|+.. ...||. |+..+.
T Consensus 173 ~~~eC~ICle~~~~~~~~~~~~~vl~~C~H~FC~~CI~~Wl~~--------~~tCPl--CR~~~~ 227 (238)
T PHA02929 173 KDKECAICMEKVYDKEIKNMYFGILSNCNHVFCIECIDIWKKE--------KNTCPV--CRTPFI 227 (238)
T ss_pred CCCCCccCCcccccCccccccceecCCCCCcccHHHHHHHHhc--------CCCCCC--CCCEee
Confidence 3479999999865322 223 489999999999998752 247998 987665
No 35
>TIGR00599 rad18 DNA repair protein rad18. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=96.97 E-value=0.00064 Score=73.87 Aligned_cols=65 Identities=29% Similarity=0.532 Sum_probs=47.3
Q ss_pred cccccccccccccCCCeEecCCCCcccHhhHHHHHHHHhhcCCcceeccCCCCCCCCCCccccc-ccCChHHHHHHHH
Q 006225 347 SFHECRICFSEFAGTDFVRLPCHHFFCWKCMKTYLDIHISEGTVSKLQCPDAKCGGMVPPSLLK-KLLGDEEFERWES 423 (655)
Q Consensus 347 ~~~~C~IC~e~~~~~~~~~l~C~H~fC~~Cl~~yi~~~i~~g~~~~i~CP~~~C~~~l~~~~i~-~ll~~e~~ery~~ 423 (655)
..+.|+||++.+. ..+.++|+|.||..|+..|+.. ...||. |+..+....+. ..+-.++++.|..
T Consensus 25 ~~l~C~IC~d~~~--~PvitpCgH~FCs~CI~~~l~~--------~~~CP~--Cr~~~~~~~Lr~N~~L~~iVe~~~~ 90 (397)
T TIGR00599 25 TSLRCHICKDFFD--VPVLTSCSHTFCSLCIRRCLSN--------QPKCPL--CRAEDQESKLRSNWLVSEIVESFKN 90 (397)
T ss_pred cccCCCcCchhhh--CccCCCCCCchhHHHHHHHHhC--------CCCCCC--CCCccccccCccchHHHHHHHHHHH
Confidence 4579999999874 5566799999999999999753 137997 99887765443 3334456666654
No 36
>KOG0317 consensus Predicted E3 ubiquitin ligase, integral peroxisomal membrane protein [Posttranslational modification, protein turnover, chaperones]
Probab=96.87 E-value=0.00052 Score=70.06 Aligned_cols=51 Identities=27% Similarity=0.828 Sum_probs=41.2
Q ss_pred cccccccccccccCCCeEecCCCCcccHhhHHHHHHHHhhcCCcceeccCCCCCCCCCCcccc
Q 006225 347 SFHECRICFSEFAGTDFVRLPCHHFFCWKCMKTYLDIHISEGTVSKLQCPDAKCGGMVPPSLL 409 (655)
Q Consensus 347 ~~~~C~IC~e~~~~~~~~~l~C~H~fC~~Cl~~yi~~~i~~g~~~~i~CP~~~C~~~l~~~~i 409 (655)
...-|.+|++... ++...+|||.||..|+..|...+- .||. |+..+.+..+
T Consensus 238 a~~kC~LCLe~~~--~pSaTpCGHiFCWsCI~~w~~ek~--------eCPl--CR~~~~pskv 288 (293)
T KOG0317|consen 238 ATRKCSLCLENRS--NPSATPCGHIFCWSCILEWCSEKA--------ECPL--CREKFQPSKV 288 (293)
T ss_pred CCCceEEEecCCC--CCCcCcCcchHHHHHHHHHHcccc--------CCCc--ccccCCCcce
Confidence 3478999999863 556679999999999999987542 3998 9999888765
No 37
>COG5540 RING-finger-containing ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=96.69 E-value=0.0012 Score=67.59 Aligned_cols=49 Identities=37% Similarity=0.796 Sum_probs=40.7
Q ss_pred cccccccccccC-CCeEecCCCCcccHhhHHHHHHHHhhcCCcceeccCCCCCCCCCCc
Q 006225 349 HECRICFSEFAG-TDFVRLPCHHFFCWKCMKTYLDIHISEGTVSKLQCPDAKCGGMVPP 406 (655)
Q Consensus 349 ~~C~IC~e~~~~-~~~~~l~C~H~fC~~Cl~~yi~~~i~~g~~~~i~CP~~~C~~~l~~ 406 (655)
.+|.||+++|.. +....++|.|.|...|+.+|+.. ...+||. |+..+++
T Consensus 324 veCaICms~fiK~d~~~vlPC~H~FH~~Cv~kW~~~-------y~~~CPv--Crt~iPP 373 (374)
T COG5540 324 VECAICMSNFIKNDRLRVLPCDHRFHVGCVDKWLLG-------YSNKCPV--CRTAIPP 373 (374)
T ss_pred ceEEEEhhhhcccceEEEeccCceechhHHHHHHhh-------hcccCCc--cCCCCCC
Confidence 799999999864 44556799999999999999752 3678998 9998875
No 38
>KOG1002 consensus Nucleotide excision repair protein RAD16 [Replication, recombination and repair]
Probab=96.53 E-value=0.0012 Score=71.75 Aligned_cols=89 Identities=24% Similarity=0.551 Sum_probs=58.9
Q ss_pred CchhhhccchhhhhhhccccccccccccccccCCCeEecCCCCcccHhhHHHHHHHHhhcCCcceeccCCCCCCCCCCcc
Q 006225 328 DIPSIRSYNHERCHENFLKSFHECRICFSEFAGTDFVRLPCHHFFCWKCMKTYLDIHISEGTVSKLQCPDAKCGGMVPPS 407 (655)
Q Consensus 328 ~~~~l~~~n~~~~~~~f~~~~~~C~IC~e~~~~~~~~~l~C~H~fC~~Cl~~yi~~~i~~g~~~~i~CP~~~C~~~l~~~ 407 (655)
+.|.|..|...+--..-+++..+|.+|-+.- .+.+...|.|.||+-|+++|+....... .+.||. |-..++.+
T Consensus 516 DHP~LVl~S~~~n~~~enk~~~~C~lc~d~a--ed~i~s~ChH~FCrlCi~eyv~~f~~~~---nvtCP~--C~i~LsiD 588 (791)
T KOG1002|consen 516 DHPDLVLYSANANLPDENKGEVECGLCHDPA--EDYIESSCHHKFCRLCIKEYVESFMENN---NVTCPV--CHIGLSID 588 (791)
T ss_pred cCcceeeehhhcCCCccccCceeecccCChh--hhhHhhhhhHHHHHHHHHHHHHhhhccc---CCCCcc--cccccccc
Confidence 4455555532222223345678999998764 4566669999999999999998766543 389998 99888776
Q ss_pred cccccCChHHHHHHHH
Q 006225 408 LLKKLLGDEEFERWES 423 (655)
Q Consensus 408 ~i~~ll~~e~~ery~~ 423 (655)
.-...+..-..+.|..
T Consensus 589 lse~alek~~l~~Fk~ 604 (791)
T KOG1002|consen 589 LSEPALEKTDLKGFKA 604 (791)
T ss_pred ccchhhhhcchhhhhh
Confidence 5444444434444443
No 39
>KOG0978 consensus E3 ubiquitin ligase involved in syntaxin degradation [Posttranslational modification, protein turnover, chaperones]
Probab=96.19 E-value=0.0018 Score=74.33 Aligned_cols=56 Identities=25% Similarity=0.714 Sum_probs=45.3
Q ss_pred ccccccccccccccCCCeEecCCCCcccHhhHHHHHHHHhhcCCcceeccCCCCCCCCCCccccccc
Q 006225 346 KSFHECRICFSEFAGTDFVRLPCHHFFCWKCMKTYLDIHISEGTVSKLQCPDAKCGGMVPPSLLKKL 412 (655)
Q Consensus 346 ~~~~~C~IC~e~~~~~~~~~l~C~H~fC~~Cl~~yi~~~i~~g~~~~i~CP~~~C~~~l~~~~i~~l 412 (655)
.+...|++|.... .+.+...|+|.||..|++..+... +-+||. |+..|...+|..+
T Consensus 641 K~~LkCs~Cn~R~--Kd~vI~kC~H~FC~~Cvq~r~etR-------qRKCP~--Cn~aFganDv~~I 696 (698)
T KOG0978|consen 641 KELLKCSVCNTRW--KDAVITKCGHVFCEECVQTRYETR-------QRKCPK--CNAAFGANDVHRI 696 (698)
T ss_pred HhceeCCCccCch--hhHHHHhcchHHHHHHHHHHHHHh-------cCCCCC--CCCCCCccccccc
Confidence 3568999999554 466667999999999999988754 458997 9999999888654
No 40
>KOG0287 consensus Postreplication repair protein RAD18 [Replication, recombination and repair]
Probab=96.15 E-value=0.0021 Score=66.71 Aligned_cols=63 Identities=35% Similarity=0.686 Sum_probs=47.8
Q ss_pred ccccccccccccCCCeEecCCCCcccHhhHHHHHHHHhhcCCcceeccCCCCCCCCCCcccccc-cCChHHHHHHH
Q 006225 348 FHECRICFSEFAGTDFVRLPCHHFFCWKCMKTYLDIHISEGTVSKLQCPDAKCGGMVPPSLLKK-LLGDEEFERWE 422 (655)
Q Consensus 348 ~~~C~IC~e~~~~~~~~~l~C~H~fC~~Cl~~yi~~~i~~g~~~~i~CP~~~C~~~l~~~~i~~-ll~~e~~ery~ 422 (655)
..-|.||++.|. -++..+|+|.||.-|++.|+.. +..||. |...+....++. .+-.++++-|.
T Consensus 23 lLRC~IC~eyf~--ip~itpCsHtfCSlCIR~~L~~--------~p~CP~--C~~~~~Es~Lr~n~il~Eiv~S~~ 86 (442)
T KOG0287|consen 23 LLRCGICFEYFN--IPMITPCSHTFCSLCIRKFLSY--------KPQCPT--CCVTVTESDLRNNRILDEIVKSLN 86 (442)
T ss_pred HHHHhHHHHHhc--CceeccccchHHHHHHHHHhcc--------CCCCCc--eecccchhhhhhhhHHHHHHHHHH
Confidence 467999999985 2344589999999999999764 467998 998888877765 34456666554
No 41
>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=96.14 E-value=0.0092 Score=62.52 Aligned_cols=55 Identities=18% Similarity=0.465 Sum_probs=38.5
Q ss_pred cccccccccccCC-Ce--EecCCCCcccHhhHHHHHHHHhhcCCcceeccCCCCCCCCCCccccccc
Q 006225 349 HECRICFSEFAGT-DF--VRLPCHHFFCWKCMKTYLDIHISEGTVSKLQCPDAKCGGMVPPSLLKKL 412 (655)
Q Consensus 349 ~~C~IC~e~~~~~-~~--~~l~C~H~fC~~Cl~~yi~~~i~~g~~~~i~CP~~~C~~~l~~~~i~~l 412 (655)
..|++|..+...+ ++ ....|||.||..|+...+. .| ...||. |+..+....++..
T Consensus 4 ~~CP~Ck~~~y~np~~kl~i~~CGH~~C~sCv~~l~~----~~---~~~CP~--C~~~lrk~~fr~q 61 (309)
T TIGR00570 4 QGCPRCKTTKYRNPSLKLMVNVCGHTLCESCVDLLFV----RG---SGSCPE--CDTPLRKNNFRVQ 61 (309)
T ss_pred CCCCcCCCCCccCcccccccCCCCCcccHHHHHHHhc----CC---CCCCCC--CCCccchhhcccc
Confidence 4799999864322 22 2227999999999999863 22 358996 9988877655443
No 42
>KOG4628 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=96.14 E-value=0.0037 Score=66.42 Aligned_cols=48 Identities=29% Similarity=0.767 Sum_probs=38.1
Q ss_pred cccccccccccCCC-eEecCCCCcccHhhHHHHHHHHhhcCCcceeccCCCCCCCCCC
Q 006225 349 HECRICFSEFAGTD-FVRLPCHHFFCWKCMKTYLDIHISEGTVSKLQCPDAKCGGMVP 405 (655)
Q Consensus 349 ~~C~IC~e~~~~~~-~~~l~C~H~fC~~Cl~~yi~~~i~~g~~~~i~CP~~~C~~~l~ 405 (655)
.+|.||+|+|...+ ...|+|.|.|...|+..|+... .-.||. |+..+.
T Consensus 230 ~~CaIClEdY~~GdklRiLPC~H~FH~~CIDpWL~~~-------r~~CPv--CK~di~ 278 (348)
T KOG4628|consen 230 DTCAICLEDYEKGDKLRILPCSHKFHVNCIDPWLTQT-------RTFCPV--CKRDIR 278 (348)
T ss_pred ceEEEeecccccCCeeeEecCCCchhhccchhhHhhc-------CccCCC--CCCcCC
Confidence 69999999998655 4457999999999999998753 235998 776443
No 43
>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=95.40 E-value=0.01 Score=49.27 Aligned_cols=40 Identities=28% Similarity=0.703 Sum_probs=28.2
Q ss_pred ccccccccccC---------C-CeEe-cCCCCcccHhhHHHHHHHHhhcCCcceeccCC
Q 006225 350 ECRICFSEFAG---------T-DFVR-LPCHHFFCWKCMKTYLDIHISEGTVSKLQCPD 397 (655)
Q Consensus 350 ~C~IC~e~~~~---------~-~~~~-l~C~H~fC~~Cl~~yi~~~i~~g~~~~i~CP~ 397 (655)
.|.||++.+.. + -.+. ..|+|.|+..||.+|+... -.||.
T Consensus 21 ~C~IC~~~l~~~~~~~~~~~~~~~i~~~~C~H~FH~~Ci~~Wl~~~--------~~CP~ 71 (73)
T PF12678_consen 21 NCAICREPLEDPCPECQAPQDECPIVWGPCGHIFHFHCISQWLKQN--------NTCPL 71 (73)
T ss_dssp BETTTTSBTTSTTCCHHHCTTTS-EEEETTSEEEEHHHHHHHHTTS--------SB-TT
T ss_pred cccccChhhhChhhhhcCCccccceEecccCCCEEHHHHHHHHhcC--------CcCCC
Confidence 59999999821 1 1222 3899999999999998532 27987
No 44
>PF11789 zf-Nse: Zinc-finger of the MIZ type in Nse subunit; PDB: 2YU4_A 3HTK_C.
Probab=95.36 E-value=0.016 Score=45.71 Aligned_cols=45 Identities=29% Similarity=0.589 Sum_probs=30.3
Q ss_pred cccccccccccCCCeEe-cCCCCcccHhhHHHHHHHHhhcCCcceeccCCCCCC
Q 006225 349 HECRICFSEFAGTDFVR-LPCHHFFCWKCMKTYLDIHISEGTVSKLQCPDAKCG 401 (655)
Q Consensus 349 ~~C~IC~e~~~~~~~~~-l~C~H~fC~~Cl~~yi~~~i~~g~~~~i~CP~~~C~ 401 (655)
+.|+|....+. ++++ ..|+|.|.++.+.+|+ +....++||..+|.
T Consensus 12 ~~CPiT~~~~~--~PV~s~~C~H~fek~aI~~~i------~~~~~~~CPv~GC~ 57 (57)
T PF11789_consen 12 LKCPITLQPFE--DPVKSKKCGHTFEKEAILQYI------QRNGSKRCPVAGCN 57 (57)
T ss_dssp SB-TTTSSB-S--SEEEESSS--EEEHHHHHHHC------TTTS-EE-SCCC-S
T ss_pred cCCCCcCChhh--CCcCcCCCCCeecHHHHHHHH------HhcCCCCCCCCCCC
Confidence 68999998874 5555 5899999999999998 22347999999985
No 45
>PF14835 zf-RING_6: zf-RING of BARD1-type protein; PDB: 1JM7_B.
Probab=95.10 E-value=0.0036 Score=49.84 Aligned_cols=50 Identities=28% Similarity=0.701 Sum_probs=23.6
Q ss_pred cccccccccccccCCCeEec-CCCCcccHhhHHHHHHHHhhcCCcceeccCCCCCCCCCCccccc
Q 006225 347 SFHECRICFSEFAGTDFVRL-PCHHFFCWKCMKTYLDIHISEGTVSKLQCPDAKCGGMVPPSLLK 410 (655)
Q Consensus 347 ~~~~C~IC~e~~~~~~~~~l-~C~H~fC~~Cl~~yi~~~i~~g~~~~i~CP~~~C~~~l~~~~i~ 410 (655)
+..-|++|++.+. .++.+ .|.|.||..|++..+. -.||. |..+.-..+++
T Consensus 6 ~lLrCs~C~~~l~--~pv~l~~CeH~fCs~Ci~~~~~----------~~CPv--C~~Paw~qD~~ 56 (65)
T PF14835_consen 6 ELLRCSICFDILK--EPVCLGGCEHIFCSSCIRDCIG----------SECPV--CHTPAWIQDIQ 56 (65)
T ss_dssp HTTS-SSS-S--S--S-B---SSS--B-TTTGGGGTT----------TB-SS--S--B-S-SS--
T ss_pred HhcCCcHHHHHhc--CCceeccCccHHHHHHhHHhcC----------CCCCC--cCChHHHHHHH
Confidence 3468999999864 55555 8999999999977422 24998 88776555543
No 46
>COG5219 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=94.99 E-value=0.049 Score=63.48 Aligned_cols=50 Identities=26% Similarity=0.634 Sum_probs=35.9
Q ss_pred ccccccccccccCCC---e-Eec-CCCCcccHhhHHHHHHHHhhcCCcceeccCCCCCCCCCC
Q 006225 348 FHECRICFSEFAGTD---F-VRL-PCHHFFCWKCMKTYLDIHISEGTVSKLQCPDAKCGGMVP 405 (655)
Q Consensus 348 ~~~C~IC~e~~~~~~---~-~~l-~C~H~fC~~Cl~~yi~~~i~~g~~~~i~CP~~~C~~~l~ 405 (655)
..+|+|||.-....+ + -++ .|.|.|...|+-+|+...- .-+||- |+..++
T Consensus 1469 ~eECaICYsvL~~vdr~lPskrC~TCknKFH~~CLyKWf~Ss~------~s~CPl--CRseit 1523 (1525)
T COG5219 1469 HEECAICYSVLDMVDRSLPSKRCATCKNKFHTRCLYKWFASSA------RSNCPL--CRSEIT 1523 (1525)
T ss_pred cchhhHHHHHHHHHhccCCccccchhhhhhhHHHHHHHHHhcC------CCCCCc--cccccc
Confidence 358999998764211 1 122 5999999999999998642 357998 987665
No 47
>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=94.77 E-value=0.028 Score=46.59 Aligned_cols=51 Identities=22% Similarity=0.163 Sum_probs=36.9
Q ss_pred ccccccccccccCCCeEecCCCCcccHhhHHHHHHHHhhcCCcceeccCCCCCCCCCCcccc
Q 006225 348 FHECRICFSEFAGTDFVRLPCHHFFCWKCMKTYLDIHISEGTVSKLQCPDAKCGGMVPPSLL 409 (655)
Q Consensus 348 ~~~C~IC~e~~~~~~~~~l~C~H~fC~~Cl~~yi~~~i~~g~~~~i~CP~~~C~~~l~~~~i 409 (655)
.+.|+|+.+-+ .+++.+++||.|++.++.+|+.. ....||. |+..+....+
T Consensus 4 ~f~CpIt~~lM--~dPVi~~~G~tyer~~I~~~l~~-------~~~~~P~--t~~~l~~~~l 54 (73)
T PF04564_consen 4 EFLCPITGELM--RDPVILPSGHTYERSAIERWLEQ-------NGGTDPF--TRQPLSESDL 54 (73)
T ss_dssp GGB-TTTSSB---SSEEEETTSEEEEHHHHHHHHCT-------TSSB-TT--T-SB-SGGGS
T ss_pred ccCCcCcCcHh--hCceeCCcCCEEcHHHHHHHHHc-------CCCCCCC--CCCcCCcccc
Confidence 47899999887 48888899999999999999875 2467998 6777776543
No 48
>KOG0309 consensus Conserved WD40 repeat-containing protein [Function unknown]
Probab=94.73 E-value=0.27 Score=56.31 Aligned_cols=133 Identities=23% Similarity=0.368 Sum_probs=84.1
Q ss_pred CChhhHHHHHHHHhh-cCCCCCccHHhhhchHHHHHHHHHHHHHhcCCCee-eeccCCCCceEEEEEeeccCCCceEEee
Q 006225 126 SNVNDVESILRELSS-SVEEPELEAEQLRINDQSQGDELLALESIYGDSVF-ILDRQRDLRSCQIHVHVETLDGLTVTAK 203 (655)
Q Consensus 126 ~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~n~e~Q~~EleaLeSIY~d~~~-~~~~~~~~~~f~i~i~~~~~~~~~i~~~ 203 (655)
+.++.-.+.|.+|.. ..+..+|-.+.+..|+ .+|+.++--=|+.-.+ .++..+ ++..|.++
T Consensus 394 ~k~~np~n~l~wl~gi~mgq~~~~n~~~pQnL---geE~S~Ig~k~~nV~fEkidva~--Rsctvsln------------ 456 (1081)
T KOG0309|consen 394 LKEDNPRNLLEWLKGIQMGQEDLFNETLPQNL---GEEFSLIGVKIRNVNFEKIDVAD--RSCTVSLN------------ 456 (1081)
T ss_pred cccCCCCchhhhhhccccccccccchhhhhhH---HhHHhHhhccccccceEeecccc--ceEEEEec------------
Confidence 344444566777665 3355666555554332 3678877777765333 233222 34444332
Q ss_pred cCCCCccccCCCCCCCcccccccccCCcEEEEEEcCCCCCCCCCCeEEe-ecccCCHHHHHHHHHHHHHHHHhC--CCch
Q 006225 204 LNSSTDLDARSESSDDFSYSFKVQYLPPIVLTCLLPKSYPSHLPPYFTI-SARWLNSTKISNLCSMLESIWIDQ--PGQE 280 (655)
Q Consensus 204 ~~~~~~~~~~~~~~~~~~~~~~v~~LPpi~L~~~lP~~YPs~~pP~~~l-~s~wL~~~~l~~L~~~L~~~~ee~--~G~~ 280 (655)
.+. ..+| .|.+ |.|.|.||.+||..++|.|++ .++-++.++...|...|.++..+. .|+-
T Consensus 457 --~p~-------~~~d-~y~f-------lrm~V~FP~nYPn~a~P~Fq~e~~s~~t~~~~~~~l~~L~~i~~q~v~s~~y 519 (1081)
T KOG0309|consen 457 --CPN-------HRVD-DYIF-------LRMLVKFPANYPNNAAPSFQFENPSTITSTMKAKLLKILKDIALQKVKSGQY 519 (1081)
T ss_pred --CCC-------Cccc-ccee-------EEEEEeccccCCCCCCCceEEecCccccHHHHHHHHHHHHHHHHHHhhcCch
Confidence 110 0011 1222 789999999999999999988 568999999999999999988775 6776
Q ss_pred hhHHHHHHHhhc
Q 006225 281 ILYQWIEWLQNS 292 (655)
Q Consensus 281 ~lf~~ie~lqe~ 292 (655)
+|=..+..|--+
T Consensus 520 ClepClr~l~gn 531 (1081)
T KOG0309|consen 520 CLEPCLRQLVGN 531 (1081)
T ss_pred HHHHHHHHHhcc
Confidence 666666666554
No 49
>PF11793 FANCL_C: FANCL C-terminal domain; PDB: 3K1L_A.
Probab=94.57 E-value=0.02 Score=47.08 Aligned_cols=56 Identities=20% Similarity=0.359 Sum_probs=27.0
Q ss_pred ccccccccccc-CCCe-Ee-c---CCCCcccHhhHHHHHHHHhhcCCc-c--eeccCCCCCCCCCCc
Q 006225 349 HECRICFSEFA-GTDF-VR-L---PCHHFFCWKCMKTYLDIHISEGTV-S--KLQCPDAKCGGMVPP 406 (655)
Q Consensus 349 ~~C~IC~e~~~-~~~~-~~-l---~C~H~fC~~Cl~~yi~~~i~~g~~-~--~i~CP~~~C~~~l~~ 406 (655)
.+|.||++... .... .. . .|++.|...||.+||...-..... . .=.||. |+..|..
T Consensus 3 ~~C~IC~~~~~~~~~~p~~~C~n~~C~~~fH~~CL~~wf~~~~~~~~~~~~~~G~CP~--C~~~i~~ 67 (70)
T PF11793_consen 3 LECGICYSYRLDDGEIPDVVCPNPSCGKKFHLLCLSEWFLSLEKSRQSFIPIFGECPY--CSSPISW 67 (70)
T ss_dssp -S-SSS--SS-TT-----B--S-TT----B-SGGGHHHHHHHHSSS-TTT--EEE-TT--T-SEEEG
T ss_pred CCCCcCCcEecCCCCcCceEcCCcccCCHHHHHHHHHHHHHcccCCeeecccccCCcC--CCCeeeE
Confidence 58999998865 2222 22 1 589999999999999876544322 1 247998 9887654
No 50
>COG5574 PEX10 RING-finger-containing E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=94.28 E-value=0.026 Score=57.25 Aligned_cols=51 Identities=27% Similarity=0.564 Sum_probs=38.4
Q ss_pred cccccccccccCCCeEecCCCCcccHhhHHHHHHHHhhcCCcceeccCCCCCCCCCCcccc
Q 006225 349 HECRICFSEFAGTDFVRLPCHHFFCWKCMKTYLDIHISEGTVSKLQCPDAKCGGMVPPSLL 409 (655)
Q Consensus 349 ~~C~IC~e~~~~~~~~~l~C~H~fC~~Cl~~yi~~~i~~g~~~~i~CP~~~C~~~l~~~~i 409 (655)
+.|.||++.. ..+...+|||.||..||...++.+- .-.||. |+..+.+..+
T Consensus 216 ~kC~lC~e~~--~~ps~t~CgHlFC~~Cl~~~~t~~k------~~~Cpl--CRak~~pk~v 266 (271)
T COG5574 216 YKCFLCLEEP--EVPSCTPCGHLFCLSCLLISWTKKK------YEFCPL--CRAKVYPKKV 266 (271)
T ss_pred cceeeeeccc--CCcccccccchhhHHHHHHHHHhhc------cccCch--hhhhccchhh
Confidence 6799999875 3566679999999999999543221 245998 9988777655
No 51
>COG5243 HRD1 HRD ubiquitin ligase complex, ER membrane component [Posttranslational modification, protein turnover, chaperones]
Probab=93.33 E-value=0.073 Score=56.21 Aligned_cols=52 Identities=33% Similarity=0.674 Sum_probs=38.7
Q ss_pred ccccccccccccc-cCC----------CeEecCCCCcccHhhHHHHHHHHhhcCCcceeccCCCCCCCCCCcc
Q 006225 346 KSFHECRICFSEF-AGT----------DFVRLPCHHFFCWKCMKTYLDIHISEGTVSKLQCPDAKCGGMVPPS 407 (655)
Q Consensus 346 ~~~~~C~IC~e~~-~~~----------~~~~l~C~H~fC~~Cl~~yi~~~i~~g~~~~i~CP~~~C~~~l~~~ 407 (655)
..-..|.||+++. ... .+-+|+|||.+...|++.|++.+ =.||- |+.++-.+
T Consensus 285 n~D~~C~ICmde~~h~~~~~~~~~~~~~pKrLpCGHilHl~CLknW~ERq--------QTCPI--Cr~p~ifd 347 (491)
T COG5243 285 NSDRTCTICMDEMFHPDHEPLPRGLDMTPKRLPCGHILHLHCLKNWLERQ--------QTCPI--CRRPVIFD 347 (491)
T ss_pred CCCCeEEEecccccCCCCccCcccccCCcccccccceeeHHHHHHHHHhc--------cCCCc--ccCccccc
Confidence 3447899999993 211 23568999999999999998853 36998 98875443
No 52
>COG5432 RAD18 RING-finger-containing E3 ubiquitin ligase [Signal transduction mechanisms]
Probab=92.70 E-value=0.058 Score=55.13 Aligned_cols=65 Identities=28% Similarity=0.422 Sum_probs=43.9
Q ss_pred cccccccccccccCCCeEecCCCCcccHhhHHHHHHHHhhcCCcceeccCCCCCCCCCCcccccc-cCChHHHHHHHH
Q 006225 347 SFHECRICFSEFAGTDFVRLPCHHFFCWKCMKTYLDIHISEGTVSKLQCPDAKCGGMVPPSLLKK-LLGDEEFERWES 423 (655)
Q Consensus 347 ~~~~C~IC~e~~~~~~~~~l~C~H~fC~~Cl~~yi~~~i~~g~~~~i~CP~~~C~~~l~~~~i~~-ll~~e~~ery~~ 423 (655)
...-|-||-+-+. -....+|||.||.-|++.|+.. +--||. |....-...++. .+..+..+-|..
T Consensus 24 s~lrC~IC~~~i~--ip~~TtCgHtFCslCIR~hL~~--------qp~CP~--Cr~~~~esrlr~~s~~~ei~es~~~ 89 (391)
T COG5432 24 SMLRCRICDCRIS--IPCETTCGHTFCSLCIRRHLGT--------QPFCPV--CREDPCESRLRGSSGSREINESHAR 89 (391)
T ss_pred hHHHhhhhhheee--cceecccccchhHHHHHHHhcC--------CCCCcc--ccccHHhhhcccchhHHHHHHhhhh
Confidence 4567999987764 2233489999999999999753 456987 887665554443 344455555543
No 53
>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=92.66 E-value=0.042 Score=36.07 Aligned_cols=24 Identities=33% Similarity=0.930 Sum_probs=18.4
Q ss_pred ccCccccceeEEecCcCceeccccCeee
Q 006225 522 KQCPSCKMAISRTEGCNKIVCNNCGQYF 549 (655)
Q Consensus 522 k~CP~C~~~iek~~Gcn~m~C~~C~~~F 549 (655)
|.||.|+..|.. .-..|+.||+.|
T Consensus 1 K~CP~C~~~V~~----~~~~Cp~CG~~F 24 (26)
T PF10571_consen 1 KTCPECGAEVPE----SAKFCPHCGYDF 24 (26)
T ss_pred CcCCCCcCCchh----hcCcCCCCCCCC
Confidence 579999988854 335688899887
No 54
>KOG1039 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=92.42 E-value=0.083 Score=56.59 Aligned_cols=92 Identities=25% Similarity=0.464 Sum_probs=52.6
Q ss_pred cccccccccccccCCC-----eEec-CCCCcccHhhHHHHHHHHhhcCCcceeccCCCCCCCCCC---ccc--ccc-cCC
Q 006225 347 SFHECRICFSEFAGTD-----FVRL-PCHHFFCWKCMKTYLDIHISEGTVSKLQCPDAKCGGMVP---PSL--LKK-LLG 414 (655)
Q Consensus 347 ~~~~C~IC~e~~~~~~-----~~~l-~C~H~fC~~Cl~~yi~~~i~~g~~~~i~CP~~~C~~~l~---~~~--i~~-ll~ 414 (655)
...+|.||++...... +-.+ +|.|.||..|+++|=...-. +....-.||+ |+.... +.. +.. --.
T Consensus 160 ~~k~CGICme~i~ek~~~~~rfgilpnC~H~~Cl~Cir~wr~~~q~-~~~~sksCP~--CRv~s~~v~pS~~Wv~t~~~k 236 (344)
T KOG1039|consen 160 SEKECGICMETINEKAASERRFGILPNCNHSFCLNCIRKWRQATQF-ESKTSKSCPF--CRVPSSFVNPSSFWVETKEEK 236 (344)
T ss_pred ccccceehhhhccccchhhhhcccCCCcchhhhhcHhHhhhhhhcc-ccccccCCCc--ccCccccccccceeeeecccc
Confidence 4579999999875433 3334 79999999999998533222 3333578998 886432 111 111 122
Q ss_pred hHHHHHHHHHHHHHHh-hcCCCcccccC
Q 006225 415 DEEFERWESLMLQKTL-ESMSDVAYCPR 441 (655)
Q Consensus 415 ~e~~ery~~~~~~~~l-~~~~~~~~CP~ 441 (655)
..+++.|++.+..+.. -.......||.
T Consensus 237 ~~li~e~~~~~s~~~c~yf~~~~g~cPf 264 (344)
T KOG1039|consen 237 QKLIEEYEAEMSAKDCKYFSQGLGSCPF 264 (344)
T ss_pred cccHHHHHHHhhccchhhhcCCCCCCCC
Confidence 2355666554433211 12235567875
No 55
>PF10571 UPF0547: Uncharacterised protein family UPF0547; InterPro: IPR018886 This domain may well be a type of zinc-finger as it carries two pairs of highly conserved cysteine residues though with no accompanying histidines. Several members are annotated as putative helicases.
Probab=91.90 E-value=0.076 Score=34.84 Aligned_cols=24 Identities=25% Similarity=0.719 Sum_probs=18.7
Q ss_pred ccCCccCccccccCCcceEEcccccccc
Q 006225 602 LSCPNCRQFNAKVGNNNHMFCWACQIHY 629 (655)
Q Consensus 602 k~CP~C~~~ieK~~GCnhm~C~~C~~~F 629 (655)
|.||.|+..|.. .-..|..||+.|
T Consensus 1 K~CP~C~~~V~~----~~~~Cp~CG~~F 24 (26)
T PF10571_consen 1 KTCPECGAEVPE----SAKFCPHCGYDF 24 (26)
T ss_pred CcCCCCcCCchh----hcCcCCCCCCCC
Confidence 579999988854 456888898887
No 56
>KOG0824 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=91.85 E-value=0.079 Score=54.75 Aligned_cols=52 Identities=29% Similarity=0.540 Sum_probs=39.6
Q ss_pred ccccccccccccCCCeEecCCCCcccHhhHHHHHHHHhhcCCcceeccCCCCCCCCCCccccc
Q 006225 348 FHECRICFSEFAGTDFVRLPCHHFFCWKCMKTYLDIHISEGTVSKLQCPDAKCGGMVPPSLLK 410 (655)
Q Consensus 348 ~~~C~IC~e~~~~~~~~~l~C~H~fC~~Cl~~yi~~~i~~g~~~~i~CP~~~C~~~l~~~~i~ 410 (655)
.-+|.||+.+- ..++.|.|+|.||.-|++..+.. ....|+. |...|+...+.
T Consensus 7 ~~eC~IC~nt~--n~Pv~l~C~HkFCyiCiKGsy~n-------dk~~Cav--CR~pids~i~~ 58 (324)
T KOG0824|consen 7 KKECLICYNTG--NCPVNLYCFHKFCYICIKGSYKN-------DKKTCAV--CRFPIDSTIDF 58 (324)
T ss_pred CCcceeeeccC--CcCccccccchhhhhhhcchhhc-------CCCCCce--ecCCCCcchhc
Confidence 35899999874 35578899999999999986442 1456998 99988765543
No 57
>KOG4367 consensus Predicted Zn-finger protein [Function unknown]
Probab=91.55 E-value=0.048 Score=58.45 Aligned_cols=35 Identities=29% Similarity=0.639 Sum_probs=28.7
Q ss_pred cccccccccccccCCCeEecCCCCcccHhhHHHHHHH
Q 006225 347 SFHECRICFSEFAGTDFVRLPCHHFFCWKCMKTYLDI 383 (655)
Q Consensus 347 ~~~~C~IC~e~~~~~~~~~l~C~H~fC~~Cl~~yi~~ 383 (655)
+...|+||..-| .+++.|+|+|..|+.|....+.+
T Consensus 3 eelkc~vc~~f~--~epiil~c~h~lc~~ca~~~~~~ 37 (699)
T KOG4367|consen 3 EELKCPVCGSFY--REPIILPCSHNLCQACARNILVQ 37 (699)
T ss_pred ccccCceehhhc--cCceEeecccHHHHHHHHhhccc
Confidence 346799998776 47888999999999999976654
No 58
>KOG0828 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=91.01 E-value=0.12 Score=56.52 Aligned_cols=55 Identities=36% Similarity=0.889 Sum_probs=40.3
Q ss_pred hccccccccccccccccC----CCe----------Eec-CCCCcccHhhHHHHHHHHhhcCCcceeccCCCCCCCCCCc
Q 006225 343 NFLKSFHECRICFSEFAG----TDF----------VRL-PCHHFFCWKCMKTYLDIHISEGTVSKLQCPDAKCGGMVPP 406 (655)
Q Consensus 343 ~f~~~~~~C~IC~e~~~~----~~~----------~~l-~C~H~fC~~Cl~~yi~~~i~~g~~~~i~CP~~~C~~~l~~ 406 (655)
.|...+..|.||+.+++. .+. ..+ +|.|.|.+.||.+|... .++.||. |+..+++
T Consensus 566 ~~~~~t~dC~ICMt~I~l~~~~s~~~~~~~~~~~nYm~tPC~HifH~~CL~~WMd~-------ykl~CPv--CR~pLPp 635 (636)
T KOG0828|consen 566 AFVRRTNDCVICMTPIDLRSTGSDCMVASMMVRRNYMLTPCHHIFHRQCLLQWMDT-------YKLICPV--CRCPLPP 635 (636)
T ss_pred chhhccccceEeccccceeeccCcchhhhhhhhccccccchHHHHHHHHHHHHHhh-------hcccCCc--cCCCCCC
Confidence 455667899999998652 111 112 89999999999999762 2578998 8877764
No 59
>KOG2660 consensus Locus-specific chromosome binding proteins [Function unknown]
Probab=90.45 E-value=0.14 Score=53.63 Aligned_cols=48 Identities=29% Similarity=0.728 Sum_probs=36.4
Q ss_pred cccccccccccccCCCeEec-CCCCcccHhhHHHHHHHHhhcCCcceeccCCCCCCCCCCc
Q 006225 347 SFHECRICFSEFAGTDFVRL-PCHHFFCWKCMKTYLDIHISEGTVSKLQCPDAKCGGMVPP 406 (655)
Q Consensus 347 ~~~~C~IC~e~~~~~~~~~l-~C~H~fC~~Cl~~yi~~~i~~g~~~~i~CP~~~C~~~l~~ 406 (655)
..++|.+|-..+- +..+. .|-|.||+.||-+|++. ...||. |+..+..
T Consensus 14 ~~itC~LC~GYli--DATTI~eCLHTFCkSCivk~l~~--------~~~CP~--C~i~ih~ 62 (331)
T KOG2660|consen 14 PHITCRLCGGYLI--DATTITECLHTFCKSCIVKYLEE--------SKYCPT--CDIVIHK 62 (331)
T ss_pred cceehhhccceee--cchhHHHHHHHHHHHHHHHHHHH--------hccCCc--cceeccC
Confidence 3479999987763 33443 89999999999999986 357998 7765543
No 60
>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=89.73 E-value=0.36 Score=33.20 Aligned_cols=30 Identities=20% Similarity=0.491 Sum_probs=20.3
Q ss_pred ccccCccccceeEEecCcCceeccccCeee
Q 006225 520 DAKQCPSCKMAISRTEGCNKIVCNNCGQYF 549 (655)
Q Consensus 520 ~~k~CP~C~~~iek~~Gcn~m~C~~C~~~F 549 (655)
+.++||.|+.+.....+=..+.|+.|+...
T Consensus 2 ~~rfC~~CG~~t~~~~~g~~r~C~~Cg~~~ 31 (32)
T PF09297_consen 2 NHRFCGRCGAPTKPAPGGWARRCPSCGHEH 31 (32)
T ss_dssp TTSB-TTT--BEEE-SSSS-EEESSSS-EE
T ss_pred CCcccCcCCccccCCCCcCEeECCCCcCEe
Confidence 468999999999998887889999998753
No 61
>KOG2879 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=89.68 E-value=0.3 Score=49.95 Aligned_cols=49 Identities=29% Similarity=0.619 Sum_probs=36.4
Q ss_pred ccccccccccccCCCeEecCCCCcccHhhHHHHHHHHhhcCCcceeccCCCCCCCCCC
Q 006225 348 FHECRICFSEFAGTDFVRLPCHHFFCWKCMKTYLDIHISEGTVSKLQCPDAKCGGMVP 405 (655)
Q Consensus 348 ~~~C~IC~e~~~~~~~~~l~C~H~fC~~Cl~~yi~~~i~~g~~~~i~CP~~~C~~~l~ 405 (655)
..+|++|-+. +...++...|+|.||--|+..-+... ..+.||. |+....
T Consensus 239 ~~~C~~Cg~~-PtiP~~~~~C~HiyCY~Ci~ts~~~~------asf~Cp~--Cg~~~~ 287 (298)
T KOG2879|consen 239 DTECPVCGEP-PTIPHVIGKCGHIYCYYCIATSRLWD------ASFTCPL--CGENVE 287 (298)
T ss_pred CceeeccCCC-CCCCeeeccccceeehhhhhhhhcch------hhcccCc--cCCCCc
Confidence 4799999765 33344445799999999999875532 2589998 988766
No 62
>PHA00626 hypothetical protein
Probab=89.32 E-value=0.23 Score=38.36 Aligned_cols=28 Identities=29% Similarity=0.570 Sum_probs=22.3
Q ss_pred ccCCccCc-cccccCCcce----EEcccccccc
Q 006225 602 LSCPNCRQ-FNAKVGNNNH----MFCWACQIHY 629 (655)
Q Consensus 602 k~CP~C~~-~ieK~~GCnh----m~C~~C~~~F 629 (655)
+.||+|++ -|.|.+-|+. ..|..|++.|
T Consensus 1 m~CP~CGS~~Ivrcg~cr~~snrYkCkdCGY~f 33 (59)
T PHA00626 1 MSCPKCGSGNIAKEKTMRGWSDDYVCCDCGYND 33 (59)
T ss_pred CCCCCCCCceeeeeceecccCcceEcCCCCCee
Confidence 36999998 5878887744 8898888877
No 63
>KOG0825 consensus PHD Zn-finger protein [General function prediction only]
Probab=88.99 E-value=0.2 Score=57.56 Aligned_cols=110 Identities=17% Similarity=0.310 Sum_probs=62.2
Q ss_pred cccccccccccCCCeEe-cCCCCcccHhhHHHHHHHHhhcCCcceeccCCCCCCCCCCccccccc---------CChHHH
Q 006225 349 HECRICFSEFAGTDFVR-LPCHHFFCWKCMKTYLDIHISEGTVSKLQCPDAKCGGMVPPSLLKKL---------LGDEEF 418 (655)
Q Consensus 349 ~~C~IC~e~~~~~~~~~-l~C~H~fC~~Cl~~yi~~~i~~g~~~~i~CP~~~C~~~l~~~~i~~l---------l~~e~~ 418 (655)
..|++|+..+....... ..|+|+||..|+..|.... =.||. |...+..-.+... |..++-
T Consensus 124 ~~CP~Ci~s~~DqL~~~~k~c~H~FC~~Ci~sWsR~a--------qTCPi--DR~EF~~v~V~eS~~~~~~vR~lP~EEs 193 (1134)
T KOG0825|consen 124 NQCPNCLKSCNDQLEESEKHTAHYFCEECVGSWSRCA--------QTCPV--DRGEFGEVKVLESTGIEANVRCLPSEES 193 (1134)
T ss_pred hhhhHHHHHHHHHhhccccccccccHHHHhhhhhhhc--------ccCch--hhhhhheeeeeccccccceeEecchhhh
Confidence 35889988765433222 4799999999999886532 35776 7766554333222 233332
Q ss_pred HHHHHHHHH----HHhhcCCCcccccCCCCCcccccccccccccccce-eecccccc
Q 006225 419 ERWESLMLQ----KTLESMSDVAYCPRCETPCIEDEEQHAQCSKCFYS-FCTLCRER 470 (655)
Q Consensus 419 ery~~~~~~----~~l~~~~~~~~CP~C~~~~~~~~~~~~~C~~C~~~-fC~~C~~~ 470 (655)
++-..+... .+........-|-.|... ..++..+.|..|... +=..|+.+
T Consensus 194 ~~~~e~~~d~~~d~~~~~~~E~~~C~IC~~~--DpEdVLLLCDsCN~~~YH~YCLDP 248 (1134)
T KOG0825|consen 194 ENILEKGGDEKQDQISGLSQEEVKCDICTVH--DPEDVLLLCDSCNKVYYHVYCLDP 248 (1134)
T ss_pred hhhhhhccccccccccCcccccccceeeccC--ChHHhheeecccccceeeccccCc
Confidence 222221111 111122234557777543 334578899999887 66777764
No 64
>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=88.64 E-value=0.48 Score=36.05 Aligned_cols=42 Identities=24% Similarity=0.555 Sum_probs=30.1
Q ss_pred ccccccccccCCCeEecCCC-----CcccHhhHHHHHHHHhhcCCcceeccCC
Q 006225 350 ECRICFSEFAGTDFVRLPCH-----HFFCWKCMKTYLDIHISEGTVSKLQCPD 397 (655)
Q Consensus 350 ~C~IC~e~~~~~~~~~l~C~-----H~fC~~Cl~~yi~~~i~~g~~~~i~CP~ 397 (655)
.|-||++.....+....+|. |.+...||.+|+..+- ..+||.
T Consensus 1 ~CrIC~~~~~~~~~l~~PC~C~G~~~~vH~~Cl~~W~~~~~------~~~C~i 47 (49)
T smart00744 1 ICRICHDEGDEGDPLVSPCRCKGSLKYVHQECLERWINESG------NKTCEI 47 (49)
T ss_pred CccCCCCCCCCCCeeEeccccCCchhHHHHHHHHHHHHHcC------CCcCCC
Confidence 48999984444455556774 8899999999987642 237876
No 65
>KOG4185 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=88.03 E-value=0.82 Score=48.24 Aligned_cols=48 Identities=33% Similarity=0.764 Sum_probs=36.5
Q ss_pred ccccccccccccCCC----eEecCCCCcccHhhHHHHHHHHhhcCCcceeccCCCCCCCCC
Q 006225 348 FHECRICFSEFAGTD----FVRLPCHHFFCWKCMKTYLDIHISEGTVSKLQCPDAKCGGMV 404 (655)
Q Consensus 348 ~~~C~IC~e~~~~~~----~~~l~C~H~fC~~Cl~~yi~~~i~~g~~~~i~CP~~~C~~~l 404 (655)
...|.||-++|+..+ +..|.|||.||..|+...+.. ..+.||. |+...
T Consensus 3 ~~~c~~c~~~~s~~~~~~~p~~l~c~h~~c~~c~~~l~~~-------~~i~cpf--cR~~~ 54 (296)
T KOG4185|consen 3 FPECEICNEDYSSEDGDHIPRVLKCGHTICQNCASKLLGN-------SRILCPF--CRETT 54 (296)
T ss_pred CCceeecCccccccCcccCCcccccCceehHhHHHHHhcC-------ceeeccC--CCCcc
Confidence 468999999987543 333589999999999998542 2577887 88873
No 66
>KOG1428 consensus Inhibitor of type V adenylyl cyclases/Neuronal presynaptic protein Highwire/PAM/RPM-1 [Signal transduction mechanisms]
Probab=87.66 E-value=0.49 Score=57.65 Aligned_cols=65 Identities=28% Similarity=0.601 Sum_probs=51.8
Q ss_pred ccccccccccc-CCCeEecCCCCcccHhhHHHHHHHHhhcCCc--ceeccCCCCCCCCCCcccccccCCh
Q 006225 349 HECRICFSEFA-GTDFVRLPCHHFFCWKCMKTYLDIHISEGTV--SKLQCPDAKCGGMVPPSLLKKLLGD 415 (655)
Q Consensus 349 ~~C~IC~e~~~-~~~~~~l~C~H~fC~~Cl~~yi~~~i~~g~~--~~i~CP~~~C~~~l~~~~i~~ll~~ 415 (655)
-.|.|||.+-- ....+.|.|+|.|...|.+.-++..-..-.+ .-|.||. |+.++....++.+|++
T Consensus 3487 DmCmICFTE~L~AAP~IqL~C~HiFHlqC~R~vLE~RW~GPRItF~FisCPi--C~n~InH~~LkDLldP 3554 (3738)
T KOG1428|consen 3487 DMCMICFTEALSAAPAIQLDCSHIFHLQCCRRVLENRWLGPRITFGFISCPI--CKNKINHIVLKDLLDP 3554 (3738)
T ss_pred ceEEEEehhhhCCCcceecCCccchhHHHHHHHHHhcccCCeeEEeeeeccc--ccchhhhHHHHHHHHH
Confidence 57999997643 4567789999999999999988876544332 3589998 9999999999998875
No 67
>PF13719 zinc_ribbon_5: zinc-ribbon domain
Probab=87.65 E-value=0.32 Score=34.71 Aligned_cols=28 Identities=29% Similarity=0.668 Sum_probs=21.6
Q ss_pred cccccCCCCCcccc------ccccccccccccee
Q 006225 436 VAYCPRCETPCIED------EEQHAQCSKCFYSF 463 (655)
Q Consensus 436 ~~~CP~C~~~~~~~------~~~~~~C~~C~~~f 463 (655)
.+.||.|+..+..+ ....++|+.|++.|
T Consensus 2 ~i~CP~C~~~f~v~~~~l~~~~~~vrC~~C~~~f 35 (37)
T PF13719_consen 2 IITCPNCQTRFRVPDDKLPAGGRKVRCPKCGHVF 35 (37)
T ss_pred EEECCCCCceEEcCHHHcccCCcEEECCCCCcEe
Confidence 35799999877533 34579999999987
No 68
>KOG4739 consensus Uncharacterized protein involved in synaptonemal complex formation [Cell cycle control, cell division, chromosome partitioning; General function prediction only]
Probab=87.64 E-value=0.24 Score=49.94 Aligned_cols=57 Identities=28% Similarity=0.577 Sum_probs=40.4
Q ss_pred ccccccccccccCCCeEecCCCCcccHhhHHHHHHHHhhcCCcceeccCCCCCCCCCCcccccccCChH
Q 006225 348 FHECRICFSEFAGTDFVRLPCHHFFCWKCMKTYLDIHISEGTVSKLQCPDAKCGGMVPPSLLKKLLGDE 416 (655)
Q Consensus 348 ~~~C~IC~e~~~~~~~~~l~C~H~fC~~Cl~~yi~~~i~~g~~~~i~CP~~~C~~~l~~~~i~~ll~~e 416 (655)
...|..|+---+...++...|.|+||..|.+.-. .-.||. |+..+....+..-|+..
T Consensus 3 ~VhCn~C~~~~~~~~f~LTaC~HvfC~~C~k~~~----------~~~C~l--Ckk~ir~i~l~~slp~~ 59 (233)
T KOG4739|consen 3 FVHCNKCFRFPSQDPFFLTACRHVFCEPCLKASS----------PDVCPL--CKKSIRIIQLNRSLPTD 59 (233)
T ss_pred eEEeccccccCCCCceeeeechhhhhhhhcccCC----------cccccc--ccceeeeeecccccchh
Confidence 3679999887666667777999999999987531 127987 99876654444444433
No 69
>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=87.63 E-value=0.27 Score=45.36 Aligned_cols=40 Identities=25% Similarity=0.625 Sum_probs=30.3
Q ss_pred hhccccccccccccccccCC-CeEecCCC------CcccHhhHHHHH
Q 006225 342 ENFLKSFHECRICFSEFAGT-DFVRLPCH------HFFCWKCMKTYL 381 (655)
Q Consensus 342 ~~f~~~~~~C~IC~e~~~~~-~~~~l~C~------H~fC~~Cl~~yi 381 (655)
+.+.....+|.||++.+... -.+.+.|+ |.||.+|+++|-
T Consensus 20 ~~w~~~~~EC~IC~~~I~~~~GvV~vt~~g~lnLEkmfc~~C~~rw~ 66 (134)
T PF05883_consen 20 DQWPRCTVECQICFDRIDNNDGVVYVTDGGTLNLEKMFCADCDKRWR 66 (134)
T ss_pred HHccccCeeehhhhhhhhcCCCEEEEecCCeehHHHHHHHHHHHHHH
Confidence 45566679999999998763 34445664 789999999993
No 70
>KOG0802 consensus E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=87.62 E-value=0.31 Score=56.10 Aligned_cols=49 Identities=31% Similarity=0.743 Sum_probs=37.5
Q ss_pred ccccccccccccccCC---CeEecCCCCcccHhhHHHHHHHHhhcCCcceeccCCCCCCCCC
Q 006225 346 KSFHECRICFSEFAGT---DFVRLPCHHFFCWKCMKTYLDIHISEGTVSKLQCPDAKCGGMV 404 (655)
Q Consensus 346 ~~~~~C~IC~e~~~~~---~~~~l~C~H~fC~~Cl~~yi~~~i~~g~~~~i~CP~~~C~~~l 404 (655)
.....|.||.+..... ...+++|+|.||..|++.|++. .-.||. |+..+
T Consensus 289 ~~~~~C~IC~e~l~~~~~~~~~rL~C~Hifh~~CL~~W~er--------~qtCP~--CR~~~ 340 (543)
T KOG0802|consen 289 LSDELCIICLEELHSGHNITPKRLPCGHIFHDSCLRSWFER--------QQTCPT--CRTVL 340 (543)
T ss_pred hcCCeeeeechhhccccccccceeecccchHHHHHHHHHHH--------hCcCCc--chhhh
Confidence 3457899999997532 1456799999999999999987 246998 76633
No 71
>KOG1645 consensus RING-finger-containing E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=87.52 E-value=0.27 Score=52.82 Aligned_cols=50 Identities=34% Similarity=0.893 Sum_probs=38.2
Q ss_pred ccccccccccc--CC-CeEecCCCCcccHhhHHHHHHHHhhcCCcceeccCCCCCCCCCCc
Q 006225 349 HECRICFSEFA--GT-DFVRLPCHHFFCWKCMKTYLDIHISEGTVSKLQCPDAKCGGMVPP 406 (655)
Q Consensus 349 ~~C~IC~e~~~--~~-~~~~l~C~H~fC~~Cl~~yi~~~i~~g~~~~i~CP~~~C~~~l~~ 406 (655)
.+|+||++.+. ++ .++.+.|+|.|=.+|+++|+. ......||. |.....-
T Consensus 5 ~tcpiclds~~~~g~hr~vsl~cghlFgs~cie~wl~------k~~~~~cp~--c~~katk 57 (463)
T KOG1645|consen 5 TTCPICLDSYTTAGNHRIVSLQCGHLFGSQCIEKWLG------KKTKMQCPL--CSGKATK 57 (463)
T ss_pred ccCceeeeeeeecCceEEeeecccccccHHHHHHHHh------hhhhhhCcc--cCChhHH
Confidence 58999999864 33 355679999999999999983 234678998 8765443
No 72
>KOG0804 consensus Cytoplasmic Zn-finger protein BRAP2 (BRCA1 associated protein) [General function prediction only]
Probab=87.26 E-value=0.27 Score=53.45 Aligned_cols=48 Identities=19% Similarity=0.636 Sum_probs=35.8
Q ss_pred ccccccccccccccCCC--eEecCCCCcccHhhHHHHHHHHhhcCCcceeccCCCCCCCCCC
Q 006225 346 KSFHECRICFSEFAGTD--FVRLPCHHFFCWKCMKTYLDIHISEGTVSKLQCPDAKCGGMVP 405 (655)
Q Consensus 346 ~~~~~C~IC~e~~~~~~--~~~l~C~H~fC~~Cl~~yi~~~i~~g~~~~i~CP~~~C~~~l~ 405 (655)
.+..+|+||++-.+..- ..+..|.|.|.-.|+.+|. ...||. |+....
T Consensus 173 tELPTCpVCLERMD~s~~gi~t~~c~Hsfh~~cl~~w~----------~~scpv--cR~~q~ 222 (493)
T KOG0804|consen 173 TELPTCPVCLERMDSSTTGILTILCNHSFHCSCLMKWW----------DSSCPV--CRYCQS 222 (493)
T ss_pred ccCCCcchhHhhcCccccceeeeecccccchHHHhhcc----------cCcChh--hhhhcC
Confidence 45689999999876422 3345899999999999983 468997 765444
No 73
>smart00661 RPOL9 RNA polymerase subunit 9.
Probab=86.73 E-value=0.45 Score=36.31 Aligned_cols=28 Identities=36% Similarity=0.770 Sum_probs=21.5
Q ss_pred ccCccccceeEEecC--cCceeccccCeee
Q 006225 522 KQCPSCKMAISRTEG--CNKIVCNNCGQYF 549 (655)
Q Consensus 522 k~CP~C~~~iek~~G--cn~m~C~~C~~~F 549 (655)
++||.|+.++....+ .++..|+.||+.+
T Consensus 1 ~FCp~Cg~~l~~~~~~~~~~~vC~~Cg~~~ 30 (52)
T smart00661 1 KFCPKCGNMLIPKEGKEKRRFVCRKCGYEE 30 (52)
T ss_pred CCCCCCCCccccccCCCCCEEECCcCCCeE
Confidence 479999998876543 3588899999764
No 74
>KOG4159 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=85.67 E-value=0.63 Score=51.02 Aligned_cols=49 Identities=29% Similarity=0.692 Sum_probs=36.8
Q ss_pred ccccccccccccccCCCeEecCCCCcccHhhHHHHHHHHhhcCCcceeccCCCCCCCCCCc
Q 006225 346 KSFHECRICFSEFAGTDFVRLPCHHFFCWKCMKTYLDIHISEGTVSKLQCPDAKCGGMVPP 406 (655)
Q Consensus 346 ~~~~~C~IC~e~~~~~~~~~l~C~H~fC~~Cl~~yi~~~i~~g~~~~i~CP~~~C~~~l~~ 406 (655)
...++|.||+..+. +.+.++|||.||..|+..- +. ..-.||. |+..+..
T Consensus 82 ~sef~c~vc~~~l~--~pv~tpcghs~c~~Cl~r~----ld----~~~~cp~--Cr~~l~e 130 (398)
T KOG4159|consen 82 RSEFECCVCSRALY--PPVVTPCGHSFCLECLDRS----LD----QETECPL--CRDELVE 130 (398)
T ss_pred cchhhhhhhHhhcC--CCccccccccccHHHHHHH----hc----cCCCCcc--ccccccc
Confidence 45589999988874 5677799999999997772 22 2457887 8887764
No 75
>KOG0823 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=85.67 E-value=0.3 Score=48.94 Aligned_cols=17 Identities=29% Similarity=0.888 Sum_probs=14.7
Q ss_pred ceeccccCeeeeccccccc
Q 006225 539 KIVCNNCGQYFCYRCNKAI 557 (655)
Q Consensus 539 ~m~C~~C~~~FC~~C~~~~ 557 (655)
-+|| |||-|||-|.-.|
T Consensus 61 VvTl--CGHLFCWpClyqW 77 (230)
T KOG0823|consen 61 VVTL--CGHLFCWPCLYQW 77 (230)
T ss_pred EEee--cccceehHHHHHH
Confidence 3566 9999999999988
No 76
>PF13717 zinc_ribbon_4: zinc-ribbon domain
Probab=85.62 E-value=0.46 Score=33.70 Aligned_cols=28 Identities=32% Similarity=0.749 Sum_probs=21.3
Q ss_pred cccccCCCCCcccc------ccccccccccccee
Q 006225 436 VAYCPRCETPCIED------EEQHAQCSKCFYSF 463 (655)
Q Consensus 436 ~~~CP~C~~~~~~~------~~~~~~C~~C~~~f 463 (655)
.+.||+|+..+..+ ....++|+.|++.|
T Consensus 2 ~i~Cp~C~~~y~i~d~~ip~~g~~v~C~~C~~~f 35 (36)
T PF13717_consen 2 IITCPNCQAKYEIDDEKIPPKGRKVRCSKCGHVF 35 (36)
T ss_pred EEECCCCCCEEeCCHHHCCCCCcEEECCCCCCEe
Confidence 35799999876432 34679999999986
No 77
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=85.49 E-value=0.42 Score=31.29 Aligned_cols=13 Identities=31% Similarity=0.636 Sum_probs=9.9
Q ss_pred CccCCccCccccc
Q 006225 601 GLSCPNCRQFNAK 613 (655)
Q Consensus 601 ~k~CP~C~~~ieK 613 (655)
.+.||+|+..|..
T Consensus 2 ~~~Cp~Cg~~~~~ 14 (26)
T PF13248_consen 2 EMFCPNCGAEIDP 14 (26)
T ss_pred cCCCcccCCcCCc
Confidence 3679999987754
No 78
>KOG0311 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=85.40 E-value=0.12 Score=54.41 Aligned_cols=47 Identities=30% Similarity=0.706 Sum_probs=34.1
Q ss_pred ccccccccccccCCCeEecCCCCcccHhhHHHHHHHHhhcCCcceeccCCCCCCCCC
Q 006225 348 FHECRICFSEFAGTDFVRLPCHHFFCWKCMKTYLDIHISEGTVSKLQCPDAKCGGMV 404 (655)
Q Consensus 348 ~~~C~IC~e~~~~~~~~~l~C~H~fC~~Cl~~yi~~~i~~g~~~~i~CP~~~C~~~l 404 (655)
.+.|+||++-+.. .+.+..|.|.||.+|+..-+.. |+ =.||. |+..+
T Consensus 43 ~v~c~icl~llk~-tmttkeClhrfc~~ci~~a~r~----gn---~ecpt--cRk~l 89 (381)
T KOG0311|consen 43 QVICPICLSLLKK-TMTTKECLHRFCFDCIWKALRS----GN---NECPT--CRKKL 89 (381)
T ss_pred hhccHHHHHHHHh-hcccHHHHHHHHHHHHHHHHHh----cC---CCCch--HHhhc
Confidence 3689999998764 3445689999999999886543 32 35886 77543
No 79
>PF12861 zf-Apc11: Anaphase-promoting complex subunit 11 RING-H2 finger
Probab=85.35 E-value=0.82 Score=38.89 Aligned_cols=32 Identities=34% Similarity=0.646 Sum_probs=25.1
Q ss_pred CCCCcccHhhHHHHHHHHhhcCCcceeccCCCCCCCCCC
Q 006225 367 PCHHFFCWKCMKTYLDIHISEGTVSKLQCPDAKCGGMVP 405 (655)
Q Consensus 367 ~C~H~fC~~Cl~~yi~~~i~~g~~~~i~CP~~~C~~~l~ 405 (655)
.|+|.|...|+.+++..+-. .=.||. |+..+.
T Consensus 51 ~C~H~FH~hCI~kWl~~~~~-----~~~CPm--CR~~w~ 82 (85)
T PF12861_consen 51 KCSHNFHMHCILKWLSTQSS-----KGQCPM--CRQPWK 82 (85)
T ss_pred cCccHHHHHHHHHHHccccC-----CCCCCC--cCCeee
Confidence 79999999999999986521 237998 887653
No 80
>COG5152 Uncharacterized conserved protein, contains RING and CCCH-type Zn-fingers [General function prediction only]
Probab=85.28 E-value=0.3 Score=47.41 Aligned_cols=31 Identities=29% Similarity=0.570 Sum_probs=25.3
Q ss_pred ccccccccccccCCCeEecCCCCcccHhhHHHH
Q 006225 348 FHECRICFSEFAGTDFVRLPCHHFFCWKCMKTY 380 (655)
Q Consensus 348 ~~~C~IC~e~~~~~~~~~l~C~H~fC~~Cl~~y 380 (655)
.|.|.||-.+|. .++...|||.||..|...-
T Consensus 196 PF~C~iCKkdy~--spvvt~CGH~FC~~Cai~~ 226 (259)
T COG5152 196 PFLCGICKKDYE--SPVVTECGHSFCSLCAIRK 226 (259)
T ss_pred ceeehhchhhcc--chhhhhcchhHHHHHHHHH
Confidence 478999999884 4566699999999998754
No 81
>smart00661 RPOL9 RNA polymerase subunit 9.
Probab=85.17 E-value=0.62 Score=35.52 Aligned_cols=27 Identities=19% Similarity=0.541 Sum_probs=21.0
Q ss_pred cCCccCccccccCC--cceEEcccccccc
Q 006225 603 SCPNCRQFNAKVGN--NNHMFCWACQIHY 629 (655)
Q Consensus 603 ~CP~C~~~ieK~~G--Cnhm~C~~C~~~F 629 (655)
-||.|+.++....+ .+++.|..|++.+
T Consensus 2 FCp~Cg~~l~~~~~~~~~~~vC~~Cg~~~ 30 (52)
T smart00661 2 FCPKCGNMLIPKEGKEKRRFVCRKCGYEE 30 (52)
T ss_pred CCCCCCCccccccCCCCCEEECCcCCCeE
Confidence 59999987766543 4689999999764
No 82
>KOG0978 consensus E3 ubiquitin ligase involved in syntaxin degradation [Posttranslational modification, protein turnover, chaperones]
Probab=84.80 E-value=0.28 Score=56.85 Aligned_cols=30 Identities=27% Similarity=0.616 Sum_probs=20.0
Q ss_pred CcccccCCCCCcccccccccccccccceeeccccc
Q 006225 435 DVAYCPRCETPCIEDEEQHAQCSKCFYSFCTLCRE 469 (655)
Q Consensus 435 ~~~~CP~C~~~~~~~~~~~~~C~~C~~~fC~~C~~ 469 (655)
.+..||.|+.- ..+..+ +.|+|.||..|..
T Consensus 642 ~~LkCs~Cn~R---~Kd~vI--~kC~H~FC~~Cvq 671 (698)
T KOG0978|consen 642 ELLKCSVCNTR---WKDAVI--TKCGHVFCEECVQ 671 (698)
T ss_pred hceeCCCccCc---hhhHHH--HhcchHHHHHHHH
Confidence 56789999831 122222 2789999999865
No 83
>PF14570 zf-RING_4: RING/Ubox like zinc-binding domain; PDB: 1E4U_A 1UR6_B.
Probab=84.76 E-value=0.71 Score=34.96 Aligned_cols=44 Identities=27% Similarity=0.670 Sum_probs=20.8
Q ss_pred cccccccccC--CCeEecCCCCcccHhhHHHHHHHHhhcCCcceeccCCCCCCCC
Q 006225 351 CRICFSEFAG--TDFVRLPCHHFFCWKCMKTYLDIHISEGTVSKLQCPDAKCGGM 403 (655)
Q Consensus 351 C~IC~e~~~~--~~~~~l~C~H~fC~~Cl~~yi~~~i~~g~~~~i~CP~~~C~~~ 403 (655)
|++|.++... .++...+|++.+|+.|+.+-.+ ++ .=+||. |+..
T Consensus 1 cp~C~e~~d~~d~~~~PC~Cgf~IC~~C~~~i~~----~~---~g~CPg--Cr~~ 46 (48)
T PF14570_consen 1 CPLCDEELDETDKDFYPCECGFQICRFCYHDILE----NE---GGRCPG--CREP 46 (48)
T ss_dssp -TTTS-B--CCCTT--SSTTS----HHHHHHHTT----SS----SB-TT--T--B
T ss_pred CCCcccccccCCCccccCcCCCcHHHHHHHHHHh----cc---CCCCCC--CCCC
Confidence 7889988753 3455558999999999988543 22 247986 8765
No 84
>PLN00172 ubiquitin conjugating enzyme; Provisional
Probab=84.34 E-value=20 Score=33.91 Aligned_cols=21 Identities=33% Similarity=0.760 Sum_probs=17.8
Q ss_pred EEEEEEcCCCCCCCCCCeEEee
Q 006225 232 IVLTCLLPKSYPSHLPPYFTIS 253 (655)
Q Consensus 232 i~L~~~lP~~YPs~~pP~~~l~ 253 (655)
+.|.|.||++||.. ||.+...
T Consensus 50 f~~~i~fp~~YP~~-pP~v~f~ 70 (147)
T PLN00172 50 FFLSILFPPDYPFK-PPKVQFT 70 (147)
T ss_pred EEEEEECCcccCCC-CCEEEEe
Confidence 78999999999997 9977653
No 85
>PF14803 Nudix_N_2: Nudix N-terminal; PDB: 3CNG_C.
Probab=84.12 E-value=0.85 Score=31.97 Aligned_cols=27 Identities=33% Similarity=0.865 Sum_probs=15.5
Q ss_pred ccCccccceeEEe----cCcCceeccccCee
Q 006225 522 KQCPSCKMAISRT----EGCNKIVCNNCGQY 548 (655)
Q Consensus 522 k~CP~C~~~iek~----~Gcn~m~C~~C~~~ 548 (655)
|+||.|+.+++.. ++-..+.|+.||+.
T Consensus 1 kfC~~CG~~l~~~ip~gd~r~R~vC~~Cg~I 31 (34)
T PF14803_consen 1 KFCPQCGGPLERRIPEGDDRERLVCPACGFI 31 (34)
T ss_dssp -B-TTT--B-EEE--TT-SS-EEEETTTTEE
T ss_pred CccccccChhhhhcCCCCCccceECCCCCCE
Confidence 5899999998873 34456889989864
No 86
>PF13719 zinc_ribbon_5: zinc-ribbon domain
Probab=82.97 E-value=1.1 Score=31.92 Aligned_cols=28 Identities=32% Similarity=0.917 Sum_probs=21.9
Q ss_pred ccCccccceeEEec-----CcCceeccccCeee
Q 006225 522 KQCPSCKMAISRTE-----GCNKIVCNNCGQYF 549 (655)
Q Consensus 522 k~CP~C~~~iek~~-----Gcn~m~C~~C~~~F 549 (655)
..||+|++.....+ +-..+.|++|++.|
T Consensus 3 i~CP~C~~~f~v~~~~l~~~~~~vrC~~C~~~f 35 (37)
T PF13719_consen 3 ITCPNCQTRFRVPDDKLPAGGRKVRCPKCGHVF 35 (37)
T ss_pred EECCCCCceEEcCHHHcccCCcEEECCCCCcEe
Confidence 47999998876532 34589999999987
No 87
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=82.94 E-value=1.2 Score=33.24 Aligned_cols=30 Identities=20% Similarity=0.526 Sum_probs=24.1
Q ss_pred ccCccccceeEEecCcCceeccccCeeeec
Q 006225 522 KQCPSCKMAISRTEGCNKIVCNNCGQYFCY 551 (655)
Q Consensus 522 k~CP~C~~~iek~~Gcn~m~C~~C~~~FC~ 551 (655)
-.||+|+..++.+..-..++|+.||..+-+
T Consensus 4 y~C~~CG~~~~~~~~~~~~~Cp~CG~~~~~ 33 (46)
T PRK00398 4 YKCARCGREVELDEYGTGVRCPYCGYRILF 33 (46)
T ss_pred EECCCCCCEEEECCCCCceECCCCCCeEEE
Confidence 469999999988766557899999877654
No 88
>PLN03086 PRLI-interacting factor K; Provisional
Probab=82.63 E-value=1 Score=51.42 Aligned_cols=108 Identities=19% Similarity=0.393 Sum_probs=59.1
Q ss_pred ccccCcc--ccceeEEecCcCceeccccCeeeeccccccccCCCCCCCCCCCCChhHHHHHHHHHHHHHHHHHHHHhccc
Q 006225 520 DAKQCPS--CKMAISRTEGCNKIVCNNCGQYFCYRCNKAIDGYDHFRTGTCELFPQEMIRDWEERLNARQVVAQIQADMF 597 (655)
Q Consensus 520 ~~k~CP~--C~~~iek~~Gcn~m~C~~C~~~FC~~C~~~~~~~~H~~~~~C~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 597 (655)
+...||+ |+..+.+...-+|..|..|+..| -.-...-|-..||.+..|. =+. .+. ...+.. .. ..--
T Consensus 432 ~~V~Cp~~~Cg~v~~r~el~~H~~C~~Cgk~f-~~s~LekH~~~~Hkpv~Cp-Cg~-~~~--R~~L~~-----H~-~thC 500 (567)
T PLN03086 432 HNVVCPHDGCGIVLRVEEAKNHVHCEKCGQAF-QQGEMEKHMKVFHEPLQCP-CGV-VLE--KEQMVQ-----HQ-ASTC 500 (567)
T ss_pred cceeCCcccccceeeccccccCccCCCCCCcc-chHHHHHHHHhcCCCccCC-CCC-Ccc--hhHHHh-----hh-hccC
Confidence 4577994 99999998888999999998877 2211111223344555554 110 000 000100 00 0011
Q ss_pred cccCccCCccCcccccc-----------CCcce-EEcccccccccccccccccc
Q 006225 598 DEHGLSCPNCRQFNAKV-----------GNNNH-MFCWACQIHYCYLCKKIVRR 639 (655)
Q Consensus 598 ~~~~k~CP~C~~~ieK~-----------~GCnh-m~C~~C~~~FC~~C~~~~~~ 639 (655)
......|+.|+..+.+- +=-.| .+| .-++.-|..|++.++-
T Consensus 501 p~Kpi~C~fC~~~v~~g~~~~d~~d~~s~Lt~HE~~C-G~rt~~C~~Cgk~Vrl 553 (567)
T PLN03086 501 PLRLITCRFCGDMVQAGGSAMDVRDRLRGMSEHESIC-GSRTAPCDSCGRSVML 553 (567)
T ss_pred CCCceeCCCCCCccccCccccchhhhhhhHHHHHHhc-CCcceEccccCCeeee
Confidence 22346899999877421 11134 345 3457888888887763
No 89
>PHA00626 hypothetical protein
Probab=81.75 E-value=1.2 Score=34.57 Aligned_cols=28 Identities=29% Similarity=0.758 Sum_probs=21.1
Q ss_pred cCccccce-eEEecCc----CceeccccCeeee
Q 006225 523 QCPSCKMA-ISRTEGC----NKIVCNNCGQYFC 550 (655)
Q Consensus 523 ~CP~C~~~-iek~~Gc----n~m~C~~C~~~FC 550 (655)
.||+|+.. |.+.+-| +...|+.||+.|=
T Consensus 2 ~CP~CGS~~Ivrcg~cr~~snrYkCkdCGY~ft 34 (59)
T PHA00626 2 SCPKCGSGNIAKEKTMRGWSDDYVCCDCGYNDS 34 (59)
T ss_pred CCCCCCCceeeeeceecccCcceEcCCCCCeec
Confidence 59999984 7786655 4477888888773
No 90
>KOG3299 consensus Uncharacterized conserved protein [Function unknown]
Probab=81.52 E-value=0.71 Score=45.33 Aligned_cols=53 Identities=21% Similarity=0.332 Sum_probs=44.0
Q ss_pred CCCCCCCCeEEeecccCCHHHHHHHHHHHHHHHHhCCCchhhHHHHHHHhhcccc
Q 006225 241 SYPSHLPPYFTISARWLNSTKISNLCSMLESIWIDQPGQEILYQWIEWLQNSSLS 295 (655)
Q Consensus 241 ~YPs~~pP~~~l~s~wL~~~~l~~L~~~L~~~~ee~~G~~~lf~~ie~lqe~~~~ 295 (655)
.||+++||++.+.+.|+...+-..|-..+ ..-+..|..|++.|++-+++.+..
T Consensus 2 ~yps~ap~i~e~~~v~~~~~~~~~l~~a~--~~~s~~~~~l~~~~~~~~~~~~~~ 54 (206)
T KOG3299|consen 2 DYPSSAPTIKELVGVEKELAKRKLLSNAL--VYISEIGDSLFLLWVEDPRDVLNK 54 (206)
T ss_pred CCCCCCCcHhHhhhHHHHHHHHHhhhhhh--HHHHhhhhhhhhhhhccHHHHHHH
Confidence 69999999999999999999999898888 333346778999999998876654
No 91
>PF13240 zinc_ribbon_2: zinc-ribbon domain
Probab=81.13 E-value=0.78 Score=29.19 Aligned_cols=22 Identities=32% Similarity=0.637 Sum_probs=14.5
Q ss_pred cCCccCccccccCCcceEEccccccc
Q 006225 603 SCPNCRQFNAKVGNNNHMFCWACQIH 628 (655)
Q Consensus 603 ~CP~C~~~ieK~~GCnhm~C~~C~~~ 628 (655)
.||+|+..|+.. ...|.+||+.
T Consensus 1 ~Cp~CG~~~~~~----~~fC~~CG~~ 22 (23)
T PF13240_consen 1 YCPNCGAEIEDD----AKFCPNCGTP 22 (23)
T ss_pred CCcccCCCCCCc----CcchhhhCCc
Confidence 489999888653 3356666654
No 92
>PF12773 DZR: Double zinc ribbon
Probab=80.77 E-value=0.66 Score=35.14 Aligned_cols=27 Identities=41% Similarity=0.907 Sum_probs=18.3
Q ss_pred cccccCccccceeEEecCcCceeccccC
Q 006225 519 RDAKQCPSCKMAISRTEGCNKIVCNNCG 546 (655)
Q Consensus 519 ~~~k~CP~C~~~iek~~Gcn~m~C~~C~ 546 (655)
.+.++||+|+..+.. ..-..+.|+.||
T Consensus 10 ~~~~fC~~CG~~l~~-~~~~~~~C~~Cg 36 (50)
T PF12773_consen 10 DDAKFCPHCGTPLPP-PDQSKKICPNCG 36 (50)
T ss_pred ccccCChhhcCChhh-ccCCCCCCcCCc
Confidence 457889999998872 222346677776
No 93
>PRK04023 DNA polymerase II large subunit; Validated
Probab=80.02 E-value=1.1 Score=53.66 Aligned_cols=35 Identities=31% Similarity=0.757 Sum_probs=27.2
Q ss_pred cccccCccccceeEEecCcCceeccccCe-----eeeccccccccC
Q 006225 519 RDAKQCPSCKMAISRTEGCNKIVCNNCGQ-----YFCYRCNKAIDG 559 (655)
Q Consensus 519 ~~~k~CP~C~~~iek~~Gcn~m~C~~C~~-----~FC~~C~~~~~~ 559 (655)
...+.||.|+... ....|+.||. .||-.|+....+
T Consensus 624 Vg~RfCpsCG~~t------~~frCP~CG~~Te~i~fCP~CG~~~~~ 663 (1121)
T PRK04023 624 IGRRKCPSCGKET------FYRRCPFCGTHTEPVYRCPRCGIEVEE 663 (1121)
T ss_pred ccCccCCCCCCcC------CcccCCCCCCCCCcceeCccccCcCCC
Confidence 3578999999874 4468999985 599999887543
No 94
>PRK00432 30S ribosomal protein S27ae; Validated
Probab=79.45 E-value=1.1 Score=34.29 Aligned_cols=29 Identities=24% Similarity=0.586 Sum_probs=21.2
Q ss_pred ccccCccccc-eeEEecCcCceeccccCeeee
Q 006225 520 DAKQCPSCKM-AISRTEGCNKIVCNNCGQYFC 550 (655)
Q Consensus 520 ~~k~CP~C~~-~iek~~Gcn~m~C~~C~~~FC 550 (655)
..+.||.|+. .+.... +.+.|..||+.+-
T Consensus 19 ~~~fCP~Cg~~~m~~~~--~r~~C~~Cgyt~~ 48 (50)
T PRK00432 19 KNKFCPRCGSGFMAEHL--DRWHCGKCGYTEF 48 (50)
T ss_pred ccCcCcCCCcchheccC--CcEECCCcCCEEe
Confidence 4578999998 443333 6889999998763
No 95
>PTZ00390 ubiquitin-conjugating enzyme; Provisional
Probab=79.43 E-value=33 Score=32.62 Aligned_cols=21 Identities=33% Similarity=0.656 Sum_probs=17.7
Q ss_pred EEEEEEcCCCCCCCCCCeEEee
Q 006225 232 IVLTCLLPKSYPSHLPPYFTIS 253 (655)
Q Consensus 232 i~L~~~lP~~YPs~~pP~~~l~ 253 (655)
+.|.|.||++||.. ||.+...
T Consensus 51 f~~~i~~p~~YP~~-pP~v~F~ 71 (152)
T PTZ00390 51 YKLELFLPEQYPME-PPKVRFL 71 (152)
T ss_pred EEEEEECccccCCC-CCEEEEe
Confidence 78999999999997 9877553
No 96
>PF04641 Rtf2: Rtf2 RING-finger
Probab=79.18 E-value=3.9 Score=42.47 Aligned_cols=71 Identities=30% Similarity=0.462 Sum_probs=51.3
Q ss_pred cccccccccccccccCC-CeEec-CCCCcccHhhHHHHHHHHhhcCCcceeccCCCCCCCCCCcccccccCCh-HHHHHH
Q 006225 345 LKSFHECRICFSEFAGT-DFVRL-PCHHFFCWKCMKTYLDIHISEGTVSKLQCPDAKCGGMVPPSLLKKLLGD-EEFERW 421 (655)
Q Consensus 345 ~~~~~~C~IC~e~~~~~-~~~~l-~C~H~fC~~Cl~~yi~~~i~~g~~~~i~CP~~~C~~~l~~~~i~~ll~~-e~~ery 421 (655)
....+.|+|...++.+. .++.+ +|||+|+..++++.- . .-.||. |+..+...+|-.|-+. +.++..
T Consensus 110 ~~~~~~CPvt~~~~~~~~~fv~l~~cG~V~s~~alke~k----~-----~~~Cp~--c~~~f~~~DiI~Lnp~~ee~~~l 178 (260)
T PF04641_consen 110 SEGRFICPVTGKEFNGKHKFVYLRPCGCVFSEKALKELK----K-----SKKCPV--CGKPFTEEDIIPLNPPEEELEKL 178 (260)
T ss_pred CCceeECCCCCcccCCceeEEEEcCCCCEeeHHHHHhhc----c-----cccccc--cCCccccCCEEEecCCccHHHHH
Confidence 34568999999998653 46666 999999999999971 1 234998 9999998887777543 455555
Q ss_pred HHHHH
Q 006225 422 ESLML 426 (655)
Q Consensus 422 ~~~~~ 426 (655)
...+.
T Consensus 179 ~~~~~ 183 (260)
T PF04641_consen 179 RERME 183 (260)
T ss_pred HHHHH
Confidence 54443
No 97
>KOG4265 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=78.98 E-value=1.3 Score=47.29 Aligned_cols=49 Identities=39% Similarity=0.762 Sum_probs=37.0
Q ss_pred ccccccccccccccCCCeEecCCCCc-ccHhhHHHHHHHHhhcCCcceeccCCCCCCCCCCc
Q 006225 346 KSFHECRICFSEFAGTDFVRLPCHHF-FCWKCMKTYLDIHISEGTVSKLQCPDAKCGGMVPP 406 (655)
Q Consensus 346 ~~~~~C~IC~e~~~~~~~~~l~C~H~-fC~~Cl~~yi~~~i~~g~~~~i~CP~~~C~~~l~~ 406 (655)
.+-.+|-||+++. .+.+.|+|.|. .|.+|.+..- .. .=+||. |+..+..
T Consensus 288 ~~gkeCVIClse~--rdt~vLPCRHLCLCs~Ca~~Lr---~q-----~n~CPI--CRqpi~~ 337 (349)
T KOG4265|consen 288 ESGKECVICLSES--RDTVVLPCRHLCLCSGCAKSLR---YQ-----TNNCPI--CRQPIEE 337 (349)
T ss_pred cCCCeeEEEecCC--cceEEecchhhehhHhHHHHHH---Hh-----hcCCCc--cccchHh
Confidence 3457999999985 46678899999 7999998763 11 246998 9987643
No 98
>KOG3970 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=78.82 E-value=1.7 Score=43.12 Aligned_cols=68 Identities=28% Similarity=0.614 Sum_probs=48.9
Q ss_pred hhccchhhhhhhccccccccccccccccCCCeEecCCCCcccHhhHHHHHHHHhhcCCcceeccCCCCCCCCC
Q 006225 332 IRSYNHERCHENFLKSFHECRICFSEFAGTDFVRLPCHHFFCWKCMKTYLDIHISEGTVSKLQCPDAKCGGMV 404 (655)
Q Consensus 332 l~~~n~~~~~~~f~~~~~~C~IC~e~~~~~~~~~l~C~H~fC~~Cl~~yi~~~i~~g~~~~i~CP~~~C~~~l 404 (655)
+++|-.-.+..++. -.|.+|-......+.++|.|-|.|.-+|+..+...--....-.-..||. |...|
T Consensus 37 VQSYLqWL~DsDY~---pNC~LC~t~La~gdt~RLvCyhlfHW~ClneraA~lPanTAPaGyqCP~--Cs~ei 104 (299)
T KOG3970|consen 37 VQSYLQWLQDSDYN---PNCRLCNTPLASGDTTRLVCYHLFHWKCLNERAANLPANTAPAGYQCPC--CSQEI 104 (299)
T ss_pred HHHHHHHHhhcCCC---CCCceeCCccccCcceeehhhhhHHHHHhhHHHhhCCCcCCCCcccCCC--CCCcc
Confidence 45565555555554 3699999998888999999999999999999855433322223478987 88764
No 99
>PF00179 UQ_con: Ubiquitin-conjugating enzyme; InterPro: IPR000608 The post-translational attachment of ubiquitin (IPR000626 from INTERPRO) to proteins (ubiquitinylation) alters the function, location or trafficking of a protein, or targets it to the 26S proteasome for degradation [, , ]. Ubiquitinylation is an ATP-dependent process that involves the action of at least three enzymes: a ubiquitin-activating enzyme (E1, IPR000011 from INTERPRO), a ubiquitin-conjugating enzyme (E2), and a ubiquitin ligase (E3, IPR000569 from INTERPRO, IPR003613 from INTERPRO), which work sequentially in a cascade []. The E1 enzyme mediates an ATP-dependent transfer of a thioester-linked ubiquitin molecule to a cysteine residue on the E2 enzyme. The E2 enzyme (6.3.2.19 from EC) then either transfers the ubiquitin moiety directly to a substrate, or to an E3 ligase, which can also ubiquitinylate a substrate. There are several different E2 enzymes (over 30 in humans), which are broadly grouped into four classes, all of which have a core catalytic domain (containing the active site cysteine), and some of which have short N- and C-terminal amino acid extensions: class I enzymes consist of just the catalytic core domain (UBC), class II possess a UBC and a C-terminal extension, class III possess a UBC and an N-terminal extension, and class IV possess a UBC and both N- and C-terminal extensions. These extensions appear to be important for some subfamily function, including E2 localisation and protein-protein interactions []. In addition, there are proteins with an E2-like fold that are devoid of catalytic activity, but which appear to assist in poly-ubiquitin chain formation.; GO: 0016881 acid-amino acid ligase activity; PDB: 2AAK_A 3SY2_C 1FBV_C 3SQV_C 1C4Z_D 1JAT_B 2GMI_B 2H2Y_D 2R0J_A 3E95_B ....
Probab=78.62 E-value=24 Score=32.71 Aligned_cols=22 Identities=23% Similarity=0.490 Sum_probs=17.3
Q ss_pred EEEEEEcCCCCCCCCCCeEEeec
Q 006225 232 IVLTCLLPKSYPSHLPPYFTISA 254 (655)
Q Consensus 232 i~L~~~lP~~YPs~~pP~~~l~s 254 (655)
+.+.|.||++||.+ ||.+....
T Consensus 47 f~~~i~~p~~YP~~-pP~v~f~t 68 (140)
T PF00179_consen 47 FKFRISFPPDYPFS-PPKVRFLT 68 (140)
T ss_dssp EEEEEEETTTTTTS---EEEESS
T ss_pred cccccccccccccc-cccccccc
Confidence 78999999999997 99887655
No 100
>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=78.55 E-value=1.6 Score=31.03 Aligned_cols=28 Identities=32% Similarity=0.891 Sum_probs=20.8
Q ss_pred ccCccccceeEEec-----CcCceeccccCeee
Q 006225 522 KQCPSCKMAISRTE-----GCNKIVCNNCGQYF 549 (655)
Q Consensus 522 k~CP~C~~~iek~~-----Gcn~m~C~~C~~~F 549 (655)
..||+|+..+.... +-..+.|++||..|
T Consensus 3 ~~CP~C~~~~~v~~~~~~~~~~~v~C~~C~~~~ 35 (38)
T TIGR02098 3 IQCPNCKTSFRVVDSQLGANGGKVRCGKCGHVW 35 (38)
T ss_pred EECCCCCCEEEeCHHHcCCCCCEEECCCCCCEE
Confidence 46999999876542 12378999999877
No 101
>COG5175 MOT2 Transcriptional repressor [Transcription]
Probab=78.20 E-value=2.7 Score=44.18 Aligned_cols=60 Identities=22% Similarity=0.536 Sum_probs=43.5
Q ss_pred ccccccccccC--CCeEecCCCCcccHhhHHHHHHHHhhcCCcceeccCCCCCCCCCCccccccc-CChHHH
Q 006225 350 ECRICFSEFAG--TDFVRLPCHHFFCWKCMKTYLDIHISEGTVSKLQCPDAKCGGMVPPSLLKKL-LGDEEF 418 (655)
Q Consensus 350 ~C~IC~e~~~~--~~~~~l~C~H~fC~~Cl~~yi~~~i~~g~~~~i~CP~~~C~~~l~~~~i~~l-l~~e~~ 418 (655)
.|++|+++.+. ..|+..+||-..|+-||..- ...+ .=+||. |+.....+-++-. |+++.+
T Consensus 16 ~cplcie~mditdknf~pc~cgy~ic~fc~~~i-rq~l------ngrcpa--crr~y~denv~~~~~s~ee~ 78 (480)
T COG5175 16 YCPLCIEPMDITDKNFFPCPCGYQICQFCYNNI-RQNL------NGRCPA--CRRKYDDENVRYVTLSPEEL 78 (480)
T ss_pred cCcccccccccccCCcccCCcccHHHHHHHHHH-Hhhc------cCCChH--hhhhccccceeEEecCHHHH
Confidence 49999998764 45777789999999999763 3222 237998 9998887766643 565544
No 102
>PF13717 zinc_ribbon_4: zinc-ribbon domain
Probab=77.94 E-value=2 Score=30.52 Aligned_cols=28 Identities=29% Similarity=0.827 Sum_probs=21.4
Q ss_pred ccCccccceeEEec-----CcCceeccccCeee
Q 006225 522 KQCPSCKMAISRTE-----GCNKIVCNNCGQYF 549 (655)
Q Consensus 522 k~CP~C~~~iek~~-----Gcn~m~C~~C~~~F 549 (655)
..||+|++.....+ +-..++|++|++.|
T Consensus 3 i~Cp~C~~~y~i~d~~ip~~g~~v~C~~C~~~f 35 (36)
T PF13717_consen 3 ITCPNCQAKYEIDDEKIPPKGRKVRCSKCGHVF 35 (36)
T ss_pred EECCCCCCEEeCCHHHCCCCCcEEECCCCCCEe
Confidence 46999998876532 23579999999887
No 103
>KOG1785 consensus Tyrosine kinase negative regulator CBL [Defense mechanisms]
Probab=77.88 E-value=0.73 Score=49.32 Aligned_cols=47 Identities=34% Similarity=0.856 Sum_probs=32.0
Q ss_pred cccccccccccccCCCeEecCCCCcccHhhHHHHHHHHhhcCCcceeccCCCCCC
Q 006225 347 SFHECRICFSEFAGTDFVRLPCHHFFCWKCMKTYLDIHISEGTVSKLQCPDAKCG 401 (655)
Q Consensus 347 ~~~~C~IC~e~~~~~~~~~l~C~H~fC~~Cl~~yi~~~i~~g~~~~i~CP~~~C~ 401 (655)
....|.||-+.-. +.-.-+|||..|..||..|-... +| -.||+..|.
T Consensus 368 TFeLCKICaendK--dvkIEPCGHLlCt~CLa~WQ~sd--~g----q~CPFCRcE 414 (563)
T KOG1785|consen 368 TFELCKICAENDK--DVKIEPCGHLLCTSCLAAWQDSD--EG----QTCPFCRCE 414 (563)
T ss_pred hHHHHHHhhccCC--CcccccccchHHHHHHHhhcccC--CC----CCCCceeeE
Confidence 3468999998742 33334999999999999984321 13 359994443
No 104
>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=77.64 E-value=0.92 Score=47.85 Aligned_cols=35 Identities=29% Similarity=0.702 Sum_probs=25.1
Q ss_pred ccCccccceeEEecCcCceeccccCeeeeccccccc
Q 006225 522 KQCPSCKMAISRTEGCNKIVCNNCGQYFCYRCNKAI 557 (655)
Q Consensus 522 k~CP~C~~~iek~~Gcn~m~C~~C~~~FC~~C~~~~ 557 (655)
..||.|+.-...+..-..|.= .|||.||-.|...+
T Consensus 4 ~~CP~Ck~~~y~np~~kl~i~-~CGH~~C~sCv~~l 38 (309)
T TIGR00570 4 QGCPRCKTTKYRNPSLKLMVN-VCGHTLCESCVDLL 38 (309)
T ss_pred CCCCcCCCCCccCcccccccC-CCCCcccHHHHHHH
Confidence 469999986655554444444 49999999998763
No 105
>KOG3039 consensus Uncharacterized conserved protein [Function unknown]
Probab=76.94 E-value=2.1 Score=43.20 Aligned_cols=56 Identities=14% Similarity=0.194 Sum_probs=42.3
Q ss_pred cccccccccccccCC-CeEec-CCCCcccHhhHHHHHHHHhhcCCcceeccCCCCCCCCCCccccccc
Q 006225 347 SFHECRICFSEFAGT-DFVRL-PCHHFFCWKCMKTYLDIHISEGTVSKLQCPDAKCGGMVPPSLLKKL 412 (655)
Q Consensus 347 ~~~~C~IC~e~~~~~-~~~~l-~C~H~fC~~Cl~~yi~~~i~~g~~~~i~CP~~~C~~~l~~~~i~~l 412 (655)
..+.|+||-+.+... .+..| +|||+||.+|..+++.. ...||. |+.++...+|-.|
T Consensus 220 ~ryiCpvtrd~LtNt~~ca~Lr~sg~Vv~~ecvEklir~--------D~v~pv--~d~plkdrdiI~L 277 (303)
T KOG3039|consen 220 KRYICPVTRDTLTNTTPCAVLRPSGHVVTKECVEKLIRK--------DMVDPV--TDKPLKDRDIIGL 277 (303)
T ss_pred cceecccchhhhcCccceEEeccCCcEeeHHHHHHhccc--------cccccC--CCCcCcccceEee
Confidence 347899999998754 45556 89999999999998652 356787 8888877666544
No 106
>PRK00420 hypothetical protein; Validated
Probab=76.31 E-value=4 Score=36.74 Aligned_cols=44 Identities=18% Similarity=0.277 Sum_probs=27.4
Q ss_pred HHHHHHHHHHHHHHhhcCCCcccccCCCCCcccccccccccccccce
Q 006225 416 EEFERWESLMLQKTLESMSDVAYCPRCETPCIEDEEQHAQCSKCFYS 462 (655)
Q Consensus 416 e~~ery~~~~~~~~l~~~~~~~~CP~C~~~~~~~~~~~~~C~~C~~~ 462 (655)
+...+..++++.-+-. -...||.|+.++........+||.||..
T Consensus 6 ~~~k~~a~~Ll~Ga~m---l~~~CP~Cg~pLf~lk~g~~~Cp~Cg~~ 49 (112)
T PRK00420 6 DIVKKAAELLLKGAKM---LSKHCPVCGLPLFELKDGEVVCPVHGKV 49 (112)
T ss_pred HHHHHHHHHHHhHHHH---ccCCCCCCCCcceecCCCceECCCCCCe
Confidence 3444555555543221 1268999999988766666777777664
No 107
>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=76.12 E-value=1.4 Score=39.37 Aligned_cols=28 Identities=18% Similarity=0.579 Sum_probs=23.4
Q ss_pred CccCCccCccccccCCcceEEcccccccc
Q 006225 601 GLSCPNCRQFNAKVGNNNHMFCWACQIHY 629 (655)
Q Consensus 601 ~k~CP~C~~~ieK~~GCnhm~C~~C~~~F 629 (655)
.+.||+|+....-... +-++|++||+.|
T Consensus 9 KR~Cp~CG~kFYDLnk-~PivCP~CG~~~ 36 (108)
T PF09538_consen 9 KRTCPSCGAKFYDLNK-DPIVCPKCGTEF 36 (108)
T ss_pred cccCCCCcchhccCCC-CCccCCCCCCcc
Confidence 3789999988877666 779999999877
No 108
>KOG0320 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=75.84 E-value=1 Score=43.44 Aligned_cols=31 Identities=29% Similarity=0.608 Sum_probs=21.1
Q ss_pred cccccCCCCCcccccccccccccccceeeccccc
Q 006225 436 VAYCPRCETPCIEDEEQHAQCSKCFYSFCTLCRE 469 (655)
Q Consensus 436 ~~~CP~C~~~~~~~~~~~~~C~~C~~~fC~~C~~ 469 (655)
...||.|...+..... .=.+|||.||..|.+
T Consensus 131 ~~~CPiCl~~~sek~~---vsTkCGHvFC~~Cik 161 (187)
T KOG0320|consen 131 TYKCPICLDSVSEKVP---VSTKCGHVFCSQCIK 161 (187)
T ss_pred ccCCCceecchhhccc---cccccchhHHHHHHH
Confidence 3569999876644322 223789999999855
No 109
>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=75.83 E-value=2.1 Score=30.20 Aligned_cols=28 Identities=25% Similarity=0.653 Sum_probs=17.5
Q ss_pred ccCccccceeEEec-CcCceeccccCeee
Q 006225 522 KQCPSCKMAISRTE-GCNKIVCNNCGQYF 549 (655)
Q Consensus 522 k~CP~C~~~iek~~-Gcn~m~C~~C~~~F 549 (655)
+.||.|+..+.... +-..+.|..|++.+
T Consensus 2 ~FCp~C~nlL~p~~~~~~~~~C~~C~Y~~ 30 (35)
T PF02150_consen 2 RFCPECGNLLYPKEDKEKRVACRTCGYEE 30 (35)
T ss_dssp -BETTTTSBEEEEEETTTTEEESSSS-EE
T ss_pred eeCCCCCccceEcCCCccCcCCCCCCCcc
Confidence 68999998875533 33334788888754
No 110
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=75.67 E-value=1.9 Score=32.20 Aligned_cols=30 Identities=13% Similarity=0.295 Sum_probs=22.6
Q ss_pred ccCCccCccccccCCcceEEcccccccccc
Q 006225 602 LSCPNCRQFNAKVGNNNHMFCWACQIHYCY 631 (655)
Q Consensus 602 k~CP~C~~~ieK~~GCnhm~C~~C~~~FC~ 631 (655)
..||+|+..++...+=..++|..||..+=+
T Consensus 4 y~C~~CG~~~~~~~~~~~~~Cp~CG~~~~~ 33 (46)
T PRK00398 4 YKCARCGREVELDEYGTGVRCPYCGYRILF 33 (46)
T ss_pred EECCCCCCEEEECCCCCceECCCCCCeEEE
Confidence 579999988776655447899989876643
No 111
>KOG1734 consensus Predicted RING-containing E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=75.40 E-value=0.99 Score=46.08 Aligned_cols=53 Identities=25% Similarity=0.587 Sum_probs=39.6
Q ss_pred cccccccccccCC--------CeEecCCCCcccHhhHHHHHHHHhhcCCcceeccCCCCCCCCCCcccc
Q 006225 349 HECRICFSEFAGT--------DFVRLPCHHFFCWKCMKTYLDIHISEGTVSKLQCPDAKCGGMVPPSLL 409 (655)
Q Consensus 349 ~~C~IC~e~~~~~--------~~~~l~C~H~fC~~Cl~~yi~~~i~~g~~~~i~CP~~~C~~~l~~~~i 409 (655)
..|.||-..+..+ +..+|.|+|.|...|++.|... | ..-.||- |+..++...+
T Consensus 225 ~vCaVCg~~~~~s~~eegvienty~LsCnHvFHEfCIrGWciv----G--KkqtCPY--CKekVdl~rm 285 (328)
T KOG1734|consen 225 SVCAVCGQQIDVSVDEEGVIENTYKLSCNHVFHEFCIRGWCIV----G--KKQTCPY--CKEKVDLKRM 285 (328)
T ss_pred chhHhhcchheeecchhhhhhhheeeecccchHHHhhhhheee----c--CCCCCch--HHHHhhHhhh
Confidence 5799998776532 4567899999999999999643 2 2457998 9988765443
No 112
>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=74.96 E-value=2.1 Score=30.43 Aligned_cols=27 Identities=26% Similarity=0.655 Sum_probs=18.0
Q ss_pred ccCCccCcccccc------CCcceEEcccccccc
Q 006225 602 LSCPNCRQFNAKV------GNNNHMFCWACQIHY 629 (655)
Q Consensus 602 k~CP~C~~~ieK~------~GCnhm~C~~C~~~F 629 (655)
..||+|++.+.-. .| ..+.|.+|+..|
T Consensus 3 ~~CP~C~~~~~v~~~~~~~~~-~~v~C~~C~~~~ 35 (38)
T TIGR02098 3 IQCPNCKTSFRVVDSQLGANG-GKVRCGKCGHVW 35 (38)
T ss_pred EECCCCCCEEEeCHHHcCCCC-CEEECCCCCCEE
Confidence 4699999743322 12 378999998765
No 113
>KOG1952 consensus Transcription factor NF-X1, contains NFX-type Zn2+-binding and R3H domains [Transcription]
Probab=74.32 E-value=2.7 Score=49.42 Aligned_cols=57 Identities=28% Similarity=0.569 Sum_probs=43.2
Q ss_pred hhccccccccccccccccCCCeEec--CCCCcccHhhHHHHHHHHhhcCCcceeccCCCCCC
Q 006225 342 ENFLKSFHECRICFSEFAGTDFVRL--PCHHFFCWKCMKTYLDIHISEGTVSKLQCPDAKCG 401 (655)
Q Consensus 342 ~~f~~~~~~C~IC~e~~~~~~~~~l--~C~H~fC~~Cl~~yi~~~i~~g~~~~i~CP~~~C~ 401 (655)
+......++|.||++.+.....+.- .|-|+|...|+++|....-+++. ..-+||. |.
T Consensus 185 ~~l~~~~yeCmIC~e~I~~t~~~WSC~sCYhVFHl~CI~~WArs~ek~~~-~~WrCP~--Cq 243 (950)
T KOG1952|consen 185 EQLSNRKYECMICTERIKRTAPVWSCKSCYHVFHLNCIKKWARSSEKTGQ-DGWRCPA--CQ 243 (950)
T ss_pred HHHhcCceEEEEeeeeccccCCceecchhhhhhhHHHHHHHHHHhhhccC-ccccCCc--cc
Confidence 3445667999999999887665553 79999999999999988444443 3578987 65
No 114
>PF09297 zf-NADH-PPase: NADH pyrophosphatase zinc ribbon domain; InterPro: IPR015376 This domain has a zinc ribbon structure and is often found between two NUDIX domains.; GO: 0016787 hydrolase activity, 0046872 metal ion binding; PDB: 1VK6_A 2GB5_A.
Probab=73.41 E-value=2.5 Score=29.00 Aligned_cols=29 Identities=14% Similarity=0.201 Sum_probs=19.3
Q ss_pred cCccCCccCccccccCCcceEEccccccc
Q 006225 600 HGLSCPNCRQFNAKVGNNNHMFCWACQIH 628 (655)
Q Consensus 600 ~~k~CP~C~~~ieK~~GCnhm~C~~C~~~ 628 (655)
+.+-||.|+.+.....+=-.|.|..|+.+
T Consensus 2 ~~rfC~~CG~~t~~~~~g~~r~C~~Cg~~ 30 (32)
T PF09297_consen 2 NHRFCGRCGAPTKPAPGGWARRCPSCGHE 30 (32)
T ss_dssp TTSB-TTT--BEEE-SSSS-EEESSSS-E
T ss_pred CCcccCcCCccccCCCCcCEeECCCCcCE
Confidence 45789999999888888788999999865
No 115
>KOG0827 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=73.20 E-value=2.1 Score=46.00 Aligned_cols=51 Identities=24% Similarity=0.566 Sum_probs=34.5
Q ss_pred cccccccccccCCC-eEec-CCCCcccHhhHHHHHHHHhhcCCcceeccCCCCCCCCCCc
Q 006225 349 HECRICFSEFAGTD-FVRL-PCHHFFCWKCMKTYLDIHISEGTVSKLQCPDAKCGGMVPP 406 (655)
Q Consensus 349 ~~C~IC~e~~~~~~-~~~l-~C~H~fC~~Cl~~yi~~~i~~g~~~~i~CP~~~C~~~l~~ 406 (655)
-.|.||-+-++... .-.. .|||.|...|+.+||+..-.. -.||. |+-.++.
T Consensus 5 A~C~Ic~d~~p~~~~l~~i~~cGhifh~~cl~qwfe~~Ps~-----R~cpi--c~ik~~~ 57 (465)
T KOG0827|consen 5 AECHICIDGRPNDHELGPIGTCGHIFHTTCLTQWFEGDPSN-----RGCPI--CQIKLQE 57 (465)
T ss_pred ceeeEeccCCccccccccccchhhHHHHHHHHHHHccCCcc-----CCCCc--eeecccc
Confidence 47999966555433 3334 499999999999999854432 46887 6644433
No 116
>PHA03096 p28-like protein; Provisional
Probab=73.02 E-value=1.9 Score=45.33 Aligned_cols=38 Identities=21% Similarity=0.453 Sum_probs=29.6
Q ss_pred cccccccccccC----C-CeEec-CCCCcccHhhHHHHHHHHhh
Q 006225 349 HECRICFSEFAG----T-DFVRL-PCHHFFCWKCMKTYLDIHIS 386 (655)
Q Consensus 349 ~~C~IC~e~~~~----~-~~~~l-~C~H~fC~~Cl~~yi~~~i~ 386 (655)
..|.||++.... + .+-.| .|.|.||..|++.|......
T Consensus 179 k~c~ic~e~~~~k~~~~~~fgil~~c~h~fc~~ci~~wr~~~~~ 222 (284)
T PHA03096 179 KICGICLENIKAKYIIKKYYGILSEIKHEFNIFCIKIWMTESLY 222 (284)
T ss_pred hhcccchhhhhhhccccccccccccCCcHHHHHHHHHHHHhhhh
Confidence 789999998642 2 33345 79999999999999887653
No 117
>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=72.76 E-value=1.4 Score=33.88 Aligned_cols=40 Identities=28% Similarity=0.675 Sum_probs=23.3
Q ss_pred ccCCCCCcccc-----cccccccccccceeeccccccccCCc-CCC
Q 006225 439 CPRCETPCIED-----EEQHAQCSKCFYSFCTLCRERRHVGV-VCM 478 (655)
Q Consensus 439 CP~C~~~~~~~-----~~~~~~C~~C~~~fC~~C~~~~H~~~-sC~ 478 (655)
|-.|+..+... .....+|+.|+..||..|-.-.|..+ .|+
T Consensus 2 CfgC~~~~~~~~~~~~~~~~y~C~~C~~~FC~dCD~fiHE~LH~CP 47 (51)
T PF07975_consen 2 CFGCQKPFPDGPEKKADSSRYRCPKCKNHFCIDCDVFIHETLHNCP 47 (51)
T ss_dssp ETTTTEE-TTS-------EEE--TTTT--B-HHHHHTTTTTS-SSS
T ss_pred CccCCCCCCCcccccccCCeEECCCCCCccccCcChhhhccccCCc
Confidence 55666665442 23678999999999999998777765 465
No 118
>PRK00432 30S ribosomal protein S27ae; Validated
Probab=72.45 E-value=2.6 Score=32.25 Aligned_cols=28 Identities=25% Similarity=0.522 Sum_probs=20.8
Q ss_pred cCccCCccCc-cccccCCcceEEcccccccc
Q 006225 600 HGLSCPNCRQ-FNAKVGNNNHMFCWACQIHY 629 (655)
Q Consensus 600 ~~k~CP~C~~-~ieK~~GCnhm~C~~C~~~F 629 (655)
..+-||+|+. +..... +.+.|.+|++.+
T Consensus 19 ~~~fCP~Cg~~~m~~~~--~r~~C~~Cgyt~ 47 (50)
T PRK00432 19 KNKFCPRCGSGFMAEHL--DRWHCGKCGYTE 47 (50)
T ss_pred ccCcCcCCCcchheccC--CcEECCCcCCEE
Confidence 3468999998 444433 689999999765
No 119
>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=72.37 E-value=1.8 Score=29.51 Aligned_cols=26 Identities=19% Similarity=0.583 Sum_probs=15.2
Q ss_pred cccCCCCCccccccccccccccccee
Q 006225 438 YCPRCETPCIEDEEQHAQCSKCFYSF 463 (655)
Q Consensus 438 ~CP~C~~~~~~~~~~~~~C~~C~~~f 463 (655)
.||.|+......+...+.|+.|++.+
T Consensus 4 ~Cp~C~se~~y~D~~~~vCp~C~~ew 29 (30)
T PF08274_consen 4 KCPLCGSEYTYEDGELLVCPECGHEW 29 (30)
T ss_dssp --TTT-----EE-SSSEEETTTTEEE
T ss_pred CCCCCCCcceeccCCEEeCCcccccC
Confidence 58999987777777889999999864
No 120
>KOG2817 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=71.28 E-value=3.2 Score=44.90 Aligned_cols=58 Identities=19% Similarity=0.303 Sum_probs=42.4
Q ss_pred ccccccccccccc-CCCeEecCCCCcccHhhHHHHHHHHhhcCCcceeccCCCCCCCCCCcccccc
Q 006225 347 SFHECRICFSEFA-GTDFVRLPCHHFFCWKCMKTYLDIHISEGTVSKLQCPDAKCGGMVPPSLLKK 411 (655)
Q Consensus 347 ~~~~C~IC~e~~~-~~~~~~l~C~H~fC~~Cl~~yi~~~i~~g~~~~i~CP~~~C~~~l~~~~i~~ 411 (655)
+.|.|+|=-+.-. .+.+..|.|||+.+++=+.+... +|.. .++||. |.........++
T Consensus 333 SvF~CPVlKeqtsdeNPPm~L~CGHVISkdAlnrLS~----ng~~-sfKCPY--CP~e~~~~~~kq 391 (394)
T KOG2817|consen 333 SVFICPVLKEQTSDENPPMMLICGHVISKDALNRLSK----NGSQ-SFKCPY--CPVEQLASDTKQ 391 (394)
T ss_pred ceeecccchhhccCCCCCeeeeccceecHHHHHHHhh----CCCe-eeeCCC--CCcccCHHhccc
Confidence 4589999776554 35577789999999998888643 3433 799998 987766655544
No 121
>KOG4172 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=71.10 E-value=1.1 Score=34.61 Aligned_cols=45 Identities=29% Similarity=0.685 Sum_probs=31.0
Q ss_pred cccccccccccCCCeEecCCCCc-ccHhhHHHHHHHHhhcCCcceeccCCCCCCCCC
Q 006225 349 HECRICFSEFAGTDFVRLPCHHF-FCWKCMKTYLDIHISEGTVSKLQCPDAKCGGMV 404 (655)
Q Consensus 349 ~~C~IC~e~~~~~~~~~l~C~H~-fC~~Cl~~yi~~~i~~g~~~~i~CP~~~C~~~l 404 (655)
-+|.||++.-- +-+...|||. .|.+|-.+.+.. ..=.||. |+.++
T Consensus 8 dECTICye~pv--dsVlYtCGHMCmCy~Cg~rl~~~-------~~g~CPi--CRapi 53 (62)
T KOG4172|consen 8 DECTICYEHPV--DSVLYTCGHMCMCYACGLRLKKA-------LHGCCPI--CRAPI 53 (62)
T ss_pred cceeeeccCcc--hHHHHHcchHHhHHHHHHHHHHc-------cCCcCcc--hhhHH
Confidence 47999998731 2233389998 799998887653 1236887 77654
No 122
>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=71.03 E-value=2.1 Score=37.55 Aligned_cols=32 Identities=28% Similarity=0.776 Sum_probs=27.3
Q ss_pred cccccccccccccCCCeEecCCCCcccHhhHH
Q 006225 347 SFHECRICFSEFAGTDFVRLPCHHFFCWKCMK 378 (655)
Q Consensus 347 ~~~~C~IC~e~~~~~~~~~l~C~H~fC~~Cl~ 378 (655)
+...|.+|...+....++.++|||.|+..|++
T Consensus 77 ~~~~C~vC~k~l~~~~f~~~p~~~v~H~~C~~ 108 (109)
T PF10367_consen 77 ESTKCSVCGKPLGNSVFVVFPCGHVVHYSCIK 108 (109)
T ss_pred CCCCccCcCCcCCCceEEEeCCCeEEeccccc
Confidence 34579999999987778888999999999975
No 123
>cd00195 UBCc Ubiquitin-conjugating enzyme E2, catalytic (UBCc) domain. This is part of the ubiquitin-mediated protein degradation pathway in which a thiol-ester linkage forms between a conserved cysteine and the C-terminus of ubiquitin and complexes with ubiquitin protein ligase enzymes, E3. This pathway regulates many fundamental cellular processes. There are also other E2s which form thiol-ester linkages without the use of E3s as well as several UBC homologs (TSG101, Mms2, Croc-1 and similar proteins) which lack the active site cysteine essential for ubiquitination and appear to function in DNA repair pathways which were omitted from the scope of this CD.
Probab=70.78 E-value=24 Score=32.81 Aligned_cols=22 Identities=27% Similarity=0.569 Sum_probs=18.6
Q ss_pred EEEEEEcCCCCCCCCCCeEEeec
Q 006225 232 IVLTCLLPKSYPSHLPPYFTISA 254 (655)
Q Consensus 232 i~L~~~lP~~YPs~~pP~~~l~s 254 (655)
+.+.|.||++||.+ ||.+....
T Consensus 48 ~~~~~~~p~~yP~~-pP~v~f~~ 69 (141)
T cd00195 48 FKLDIEFPEDYPFK-PPKVRFVT 69 (141)
T ss_pred EEEEEECCCccCCC-CCeEEEeC
Confidence 77899999999987 99887643
No 124
>KOG2034 consensus Vacuolar sorting protein PEP3/VPS18 [Intracellular trafficking, secretion, and vesicular transport]
Probab=70.21 E-value=1.9 Score=50.92 Aligned_cols=38 Identities=21% Similarity=0.426 Sum_probs=32.9
Q ss_pred ccccccccccccCCCeEecCCCCcccHhhHHHHHHHHh
Q 006225 348 FHECRICFSEFAGTDFVRLPCHHFFCWKCMKTYLDIHI 385 (655)
Q Consensus 348 ~~~C~IC~e~~~~~~~~~l~C~H~fC~~Cl~~yi~~~i 385 (655)
.-.|.+|.-.+-...|+.++|||.|..+|+.+.+....
T Consensus 817 ~d~C~~C~~~ll~~pF~vf~CgH~FH~~Cl~~~v~~~~ 854 (911)
T KOG2034|consen 817 QDSCDHCGRPLLIKPFYVFPCGHCFHRDCLIRHVLSLL 854 (911)
T ss_pred ccchHHhcchhhcCcceeeeccchHHHHHHHHHHHccc
Confidence 46899999988888888899999999999999876543
No 125
>KOG0826 consensus Predicted E3 ubiquitin ligase involved in peroxisome organization [Posttranslational modification, protein turnover, chaperones]
Probab=70.17 E-value=3.3 Score=43.61 Aligned_cols=67 Identities=19% Similarity=0.366 Sum_probs=40.9
Q ss_pred CCCchhhhccchhhhhhhccccccccccccccccCCCeEecCCCCcccHhhHHHHHHHHhhcCCcceeccCCCCCCCC
Q 006225 326 DVDIPSIRSYNHERCHENFLKSFHECRICFSEFAGTDFVRLPCHHFFCWKCMKTYLDIHISEGTVSKLQCPDAKCGGM 403 (655)
Q Consensus 326 ~~~~~~l~~~n~~~~~~~f~~~~~~C~IC~e~~~~~~~~~l~C~H~fC~~Cl~~yi~~~i~~g~~~~i~CP~~~C~~~ 403 (655)
+...|...+++.+-.. .....-.|+||+..... +.+..-=|=+||-.|+..|+.. . =+||..+|...
T Consensus 280 p~PpPPh~~~~se~e~--l~~~~~~CpvClk~r~N-ptvl~vSGyVfCY~Ci~~Yv~~---~-----~~CPVT~~p~~ 346 (357)
T KOG0826|consen 280 PIPPPPHKQYNSESEL--LPPDREVCPVCLKKRQN-PTVLEVSGYVFCYPCIFSYVVN---Y-----GHCPVTGYPAS 346 (357)
T ss_pred CCCcCChhhccccccc--CCCccccChhHHhccCC-CceEEecceEEeHHHHHHHHHh---c-----CCCCccCCcch
Confidence 3333444555544322 22234689999987642 2222244888999999999872 2 36998777653
No 126
>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=70.01 E-value=3.2 Score=33.96 Aligned_cols=35 Identities=34% Similarity=0.735 Sum_probs=23.5
Q ss_pred cCCccCccccccCCcceEEccccc-----ccccccccccccc
Q 006225 603 SCPNCRQFNAKVGNNNHMFCWACQ-----IHYCYLCKKIVRR 639 (655)
Q Consensus 603 ~CP~C~~~ieK~~GCnhm~C~~C~-----~~FC~~C~~~~~~ 639 (655)
.||.|++.++..+ .+.+|..|+ ..||--|++++..
T Consensus 3 ~CP~C~~~L~~~~--~~~~C~~C~~~~~~~a~CPdC~~~Le~ 42 (70)
T PF07191_consen 3 TCPKCQQELEWQG--GHYHCEACQKDYKKEAFCPDCGQPLEV 42 (70)
T ss_dssp B-SSS-SBEEEET--TEEEETTT--EEEEEEE-TTT-SB-EE
T ss_pred cCCCCCCccEEeC--CEEECccccccceecccCCCcccHHHH
Confidence 6999999988887 688898898 4568888888874
No 127
>KOG0416 consensus Ubiquitin-protein ligase [Posttranslational modification, protein turnover, chaperones]
Probab=69.13 E-value=20 Score=34.36 Aligned_cols=56 Identities=16% Similarity=0.270 Sum_probs=36.0
Q ss_pred EEEEEEcCCCCCCCCCCeEEee---cccCCHHHHHHHHHHHHHHHHhCCCchhhHHHHHHHhhcc
Q 006225 232 IVLTCLLPKSYPSHLPPYFTIS---ARWLNSTKISNLCSMLESIWIDQPGQEILYQWIEWLQNSS 293 (655)
Q Consensus 232 i~L~~~lP~~YPs~~pP~~~l~---s~wL~~~~l~~L~~~L~~~~ee~~G~~~lf~~ie~lqe~~ 293 (655)
-.++|.||.+||-.+|-+=.+. -+.+....-+.-.+.|++.|. -+|+++....-.+
T Consensus 49 Wkv~V~lPd~YP~KSPSIGFvnKIfHPNIDe~SGsVCLDViNQtWS------p~yDL~NIfetfL 107 (189)
T KOG0416|consen 49 WKVRVELPDNYPFKSPSIGFVNKIFHPNIDEASGSVCLDVINQTWS------PLYDLVNIFETFL 107 (189)
T ss_pred EEEEEECCCCCCCCCCcccceeeccCCCchhccCccHHHHHhhhhh------HHHHHHHHHHHHh
Confidence 4688999999999844322233 255555555566778888897 4566665544333
No 128
>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=68.31 E-value=1.6 Score=32.00 Aligned_cols=32 Identities=22% Similarity=0.414 Sum_probs=21.7
Q ss_pred cccCCCCCcccccccccccccccceeeccccccc
Q 006225 438 YCPRCETPCIEDEEQHAQCSKCFYSFCTLCRERR 471 (655)
Q Consensus 438 ~CP~C~~~~~~~~~~~~~C~~C~~~fC~~C~~~~ 471 (655)
.||.|...+... ...+.. .|+|.||..|...|
T Consensus 2 ~C~IC~~~~~~~-~~~~~l-~C~H~fh~~Ci~~~ 33 (44)
T PF13639_consen 2 ECPICLEEFEDG-EKVVKL-PCGHVFHRSCIKEW 33 (44)
T ss_dssp CETTTTCBHHTT-SCEEEE-TTSEEEEHHHHHHH
T ss_pred CCcCCChhhcCC-CeEEEc-cCCCeeCHHHHHHH
Confidence 378888776542 233344 38999999997755
No 129
>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]
Probab=68.30 E-value=2.4 Score=33.36 Aligned_cols=26 Identities=27% Similarity=0.571 Sum_probs=15.6
Q ss_pred ccCCccC-ccccccCCc----ceEEcccccc
Q 006225 602 LSCPNCR-QFNAKVGNN----NHMFCWACQI 627 (655)
Q Consensus 602 k~CP~C~-~~ieK~~GC----nhm~C~~C~~ 627 (655)
.+||+|+ ..|.+-..| |-.+|.+||+
T Consensus 28 F~CPnCGe~~I~Rc~~CRk~g~~Y~Cp~CGF 58 (61)
T COG2888 28 FPCPNCGEVEIYRCAKCRKLGNPYRCPKCGF 58 (61)
T ss_pred eeCCCCCceeeehhhhHHHcCCceECCCcCc
Confidence 4677777 566555555 4466666664
No 130
>KOG1001 consensus Helicase-like transcription factor HLTF/DNA helicase RAD5, DEAD-box superfamily [Transcription; Replication, recombination and repair]
Probab=68.06 E-value=1.6 Score=51.28 Aligned_cols=47 Identities=30% Similarity=0.699 Sum_probs=35.5
Q ss_pred cccccccccccCCCeEecCCCCcccHhhHHHHHHHHhhcCCcceeccCCCCCCCCCCc
Q 006225 349 HECRICFSEFAGTDFVRLPCHHFFCWKCMKTYLDIHISEGTVSKLQCPDAKCGGMVPP 406 (655)
Q Consensus 349 ~~C~IC~e~~~~~~~~~l~C~H~fC~~Cl~~yi~~~i~~g~~~~i~CP~~~C~~~l~~ 406 (655)
+.|.||.+ .+.++...|+|.||.+|+..++...- ...||. |...+..
T Consensus 455 ~~c~ic~~---~~~~~it~c~h~~c~~c~~~~i~~~~------~~~~~~--cr~~l~~ 501 (674)
T KOG1001|consen 455 HWCHICCD---LDSFFITRCGHDFCVECLKKSIQQSE------NAPCPL--CRNVLKE 501 (674)
T ss_pred cccccccc---cccceeecccchHHHHHHHhcccccc------CCCCcH--HHHHHHH
Confidence 89999999 35667779999999999999976432 126776 8765544
No 131
>COG1645 Uncharacterized Zn-finger containing protein [General function prediction only]
Probab=67.94 E-value=7.5 Score=35.85 Aligned_cols=25 Identities=40% Similarity=1.058 Sum_probs=18.5
Q ss_pred cccCccccceeEEecCcCceeccccCe
Q 006225 521 AKQCPSCKMAISRTEGCNKIVCNNCGQ 547 (655)
Q Consensus 521 ~k~CP~C~~~iek~~Gcn~m~C~~C~~ 547 (655)
...||.|++++.+-+| .+.|+.|++
T Consensus 28 ~~hCp~Cg~PLF~KdG--~v~CPvC~~ 52 (131)
T COG1645 28 AKHCPKCGTPLFRKDG--EVFCPVCGY 52 (131)
T ss_pred HhhCcccCCcceeeCC--eEECCCCCc
Confidence 4779999999988555 466666665
No 132
>PRK14714 DNA polymerase II large subunit; Provisional
Probab=67.80 E-value=3.4 Score=50.93 Aligned_cols=31 Identities=29% Similarity=0.852 Sum_probs=21.1
Q ss_pred cccCccccceeEEecCcCceeccccCee-----eeccccccc
Q 006225 521 AKQCPSCKMAISRTEGCNKIVCNNCGQY-----FCYRCNKAI 557 (655)
Q Consensus 521 ~k~CP~C~~~iek~~Gcn~m~C~~C~~~-----FC~~C~~~~ 557 (655)
.+.||+|+..+.. ..|+.||.. +|-.|+...
T Consensus 667 ~rkCPkCG~~t~~------~fCP~CGs~te~vy~CPsCGaev 702 (1337)
T PRK14714 667 RRRCPSCGTETYE------NRCPDCGTHTEPVYVCPDCGAEV 702 (1337)
T ss_pred EEECCCCCCcccc------ccCcccCCcCCCceeCccCCCcc
Confidence 4789999987633 267777755 377777654
No 133
>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=67.48 E-value=4.8 Score=27.43 Aligned_cols=27 Identities=30% Similarity=0.838 Sum_probs=14.3
Q ss_pred ccCccccceeEEecCcCceeccccCeee
Q 006225 522 KQCPSCKMAISRTEGCNKIVCNNCGQYF 549 (655)
Q Consensus 522 k~CP~C~~~iek~~Gcn~m~C~~C~~~F 549 (655)
-.||.|+....-.+|. .+.|+.|++.+
T Consensus 3 p~Cp~C~se~~y~D~~-~~vCp~C~~ew 29 (30)
T PF08274_consen 3 PKCPLCGSEYTYEDGE-LLVCPECGHEW 29 (30)
T ss_dssp ---TTT-----EE-SS-SEEETTTTEEE
T ss_pred CCCCCCCCcceeccCC-EEeCCcccccC
Confidence 4699999888777774 57799998875
No 134
>PRK00420 hypothetical protein; Validated
Probab=67.26 E-value=10 Score=34.21 Aligned_cols=24 Identities=33% Similarity=0.948 Sum_probs=15.9
Q ss_pred cccCccccceeEE-ecCcCceeccccC
Q 006225 521 AKQCPSCKMAISR-TEGCNKIVCNNCG 546 (655)
Q Consensus 521 ~k~CP~C~~~iek-~~Gcn~m~C~~C~ 546 (655)
...||.|+.++.+ ..| ...|+.||
T Consensus 23 ~~~CP~Cg~pLf~lk~g--~~~Cp~Cg 47 (112)
T PRK00420 23 SKHCPVCGLPLFELKDG--EVVCPVHG 47 (112)
T ss_pred cCCCCCCCCcceecCCC--ceECCCCC
Confidence 4889999999987 333 34444433
No 135
>COG1645 Uncharacterized Zn-finger containing protein [General function prediction only]
Probab=66.99 E-value=2.9 Score=38.47 Aligned_cols=25 Identities=32% Similarity=0.863 Sum_probs=20.1
Q ss_pred ccccCCCCCcccccccccccccccce
Q 006225 437 AYCPRCETPCIEDEEQHAQCSKCFYS 462 (655)
Q Consensus 437 ~~CP~C~~~~~~~~~~~~~C~~C~~~ 462 (655)
..||.|+.+.+. .+..++||.|++.
T Consensus 29 ~hCp~Cg~PLF~-KdG~v~CPvC~~~ 53 (131)
T COG1645 29 KHCPKCGTPLFR-KDGEVFCPVCGYR 53 (131)
T ss_pred hhCcccCCccee-eCCeEECCCCCce
Confidence 479999999887 5667788888873
No 136
>COG5078 Ubiquitin-protein ligase [Posttranslational modification, protein turnover, chaperones]
Probab=66.61 E-value=35 Score=32.53 Aligned_cols=58 Identities=24% Similarity=0.331 Sum_probs=32.7
Q ss_pred EEEEEEcCCCCCCCCCCeEEeec----ccCCHHHHHHHHHHHHHHHHhCCCchhhHHHHHHHhhccc
Q 006225 232 IVLTCLLPKSYPSHLPPYFTISA----RWLNSTKISNLCSMLESIWIDQPGQEILYQWIEWLQNSSL 294 (655)
Q Consensus 232 i~L~~~lP~~YPs~~pP~~~l~s----~wL~~~~l~~L~~~L~~~~ee~~G~~~lf~~ie~lqe~~~ 294 (655)
+.|.+.||.+||.. ||.+...+ ..+. ..-+.-.+.|.+.|. +.. .|=+++..|+..+.
T Consensus 55 f~~~l~fP~~YP~~-PPkv~F~t~i~HPNV~-~~G~vCLdIL~~~Ws--P~~-~l~sILlsl~slL~ 116 (153)
T COG5078 55 FKLTLEFPEDYPFK-PPKVRFTTKIFHPNVD-PSGNVCLDILKDRWS--PVY-TLETILLSLQSLLL 116 (153)
T ss_pred EEEEEECCCCCCCC-CCeeeeccCCcCCCcC-CCCCChhHHHhCCCC--ccc-cHHHHHHHHHHHHc
Confidence 78999999999998 99876544 2222 111122234556776 221 23445555554443
No 137
>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=66.59 E-value=2.8 Score=37.11 Aligned_cols=27 Identities=22% Similarity=0.816 Sum_probs=22.7
Q ss_pred ccccCCCCCccccccccccccccccee
Q 006225 437 AYCPRCETPCIEDEEQHAQCSKCFYSF 463 (655)
Q Consensus 437 ~~CP~C~~~~~~~~~~~~~C~~C~~~f 463 (655)
-.||.|+..+.......+.||.|+|.+
T Consensus 3 p~CP~C~seytY~dg~~~iCpeC~~EW 29 (109)
T TIGR00686 3 PPCPKCNSEYTYHDGTQLICPSCLYEW 29 (109)
T ss_pred CcCCcCCCcceEecCCeeECccccccc
Confidence 369999998887777789999999885
No 138
>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=66.13 E-value=41 Score=36.57 Aligned_cols=40 Identities=20% Similarity=0.506 Sum_probs=27.2
Q ss_pred CCCCcccHhhHHHHHHHHhhcCCc-----ceeccCCCCCCCCCCccc
Q 006225 367 PCHHFFCWKCMKTYLDIHISEGTV-----SKLQCPDAKCGGMVPPSL 408 (655)
Q Consensus 367 ~C~H~fC~~Cl~~yi~~~i~~g~~-----~~i~CP~~~C~~~l~~~~ 408 (655)
-|.-..|.+|+.+||..+-.+..- ....||. |+..+-.-+
T Consensus 310 ~CRPmWC~~Cm~kwFasrQd~~~~~~Wl~~~~~CPt--CRa~FCilD 354 (358)
T PF10272_consen 310 YCRPMWCLECMGKWFASRQDQQHPETWLSGKCPCPT--CRAKFCILD 354 (358)
T ss_pred cccchHHHHHHHHHhhhcCCCCChhhhhcCCCCCCC--Ccccceeee
Confidence 366678999999999887643321 2456665 998765443
No 139
>PHA02926 zinc finger-like protein; Provisional
Probab=65.87 E-value=4.9 Score=40.31 Aligned_cols=51 Identities=18% Similarity=0.355 Sum_probs=31.8
Q ss_pred HHHHHHHHHHHHHHhhcCCCcccccCCCCCccccc----ccccccccccceeecccccccc
Q 006225 416 EEFERWESLMLQKTLESMSDVAYCPRCETPCIEDE----EQHAQCSKCFYSFCTLCRERRH 472 (655)
Q Consensus 416 e~~ery~~~~~~~~l~~~~~~~~CP~C~~~~~~~~----~~~~~C~~C~~~fC~~C~~~~H 472 (655)
..+.+|+..... +.-..|+.|...+.... .....=+.|+|.||..|-..|.
T Consensus 156 ~il~~ye~~~~~------SkE~eCgICmE~I~eK~~~~eRrFGIL~~CnHsFCl~CIr~Wr 210 (242)
T PHA02926 156 KILDKYEDVYRV------SKEKECGICYEVVYSKRLENDRYFGLLDSCNHIFCITCINIWH 210 (242)
T ss_pred HHHHHHHHHHhc------cCCCCCccCccccccccccccccccccCCCCchHHHHHHHHHH
Confidence 456666654332 24467999988764321 1112224799999999988764
No 140
>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=65.79 E-value=1.5 Score=44.08 Aligned_cols=49 Identities=31% Similarity=0.687 Sum_probs=35.9
Q ss_pred cccccccccccCC-CeEec---CCCCcccHhhHHHHHHHHhhcCCcceeccCCCCCCCCC
Q 006225 349 HECRICFSEFAGT-DFVRL---PCHHFFCWKCMKTYLDIHISEGTVSKLQCPDAKCGGMV 404 (655)
Q Consensus 349 ~~C~IC~e~~~~~-~~~~l---~C~H~fC~~Cl~~yi~~~i~~g~~~~i~CP~~~C~~~l 404 (655)
.-|+||-.+.-.+ ++..+ .|-|.+|-.|+..-|.. | +-.||..+|+..+
T Consensus 11 ~~CPvCksDrYLnPdik~linPECyHrmCESCvdRIFs~----G---pAqCP~~gC~kIL 63 (314)
T COG5220 11 RRCPVCKSDRYLNPDIKILINPECYHRMCESCVDRIFSR----G---PAQCPYKGCGKIL 63 (314)
T ss_pred ccCCccccccccCCCeEEEECHHHHHHHHHHHHHHHhcC----C---CCCCCCccHHHHH
Confidence 3699998775432 33333 49999999999987652 3 5789999999654
No 141
>PF12773 DZR: Double zinc ribbon
Probab=65.74 E-value=3.2 Score=31.34 Aligned_cols=12 Identities=25% Similarity=0.553 Sum_probs=6.7
Q ss_pred CccCCccCcccc
Q 006225 601 GLSCPNCRQFNA 612 (655)
Q Consensus 601 ~k~CP~C~~~ie 612 (655)
.+.||+|++.+.
T Consensus 12 ~~fC~~CG~~l~ 23 (50)
T PF12773_consen 12 AKFCPHCGTPLP 23 (50)
T ss_pred ccCChhhcCChh
Confidence 455666665554
No 142
>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=65.55 E-value=4.5 Score=32.77 Aligned_cols=29 Identities=24% Similarity=0.559 Sum_probs=23.9
Q ss_pred cCccCCccCccccccCCcceEEccccccc
Q 006225 600 HGLSCPNCRQFNAKVGNNNHMFCWACQIH 628 (655)
Q Consensus 600 ~~k~CP~C~~~ieK~~GCnhm~C~~C~~~ 628 (655)
.++.||.|+....+...=-.++|..||..
T Consensus 27 TSq~C~~CG~~~~~~~~~r~~~C~~Cg~~ 55 (69)
T PF07282_consen 27 TSQTCPRCGHRNKKRRSGRVFTCPNCGFE 55 (69)
T ss_pred CccCccCcccccccccccceEEcCCCCCE
Confidence 46999999999988556667899888865
No 143
>PRK14559 putative protein serine/threonine phosphatase; Provisional
Probab=65.37 E-value=2.8 Score=49.06 Aligned_cols=33 Identities=21% Similarity=0.725 Sum_probs=26.5
Q ss_pred cccccCccccceeEEecCcCceeccccCee------eeccccccc
Q 006225 519 RDAKQCPSCKMAISRTEGCNKIVCNNCGQY------FCYRCNKAI 557 (655)
Q Consensus 519 ~~~k~CP~C~~~iek~~Gcn~m~C~~C~~~------FC~~C~~~~ 557 (655)
.+.++||.|+..+. +..|+.||+. ||-.||...
T Consensus 13 ~~akFC~~CG~~l~------~~~Cp~CG~~~~~~~~fC~~CG~~~ 51 (645)
T PRK14559 13 NNNRFCQKCGTSLT------HKPCPQCGTEVPVDEAHCPNCGAET 51 (645)
T ss_pred CCCccccccCCCCC------CCcCCCCCCCCCcccccccccCCcc
Confidence 35789999998873 3579999865 999999886
No 144
>COG1998 RPS31 Ribosomal protein S27AE [Translation, ribosomal structure and biogenesis]
Probab=65.13 E-value=3.4 Score=31.26 Aligned_cols=29 Identities=21% Similarity=0.642 Sum_probs=20.0
Q ss_pred ccccCccccceeEEecCcCceeccccCee
Q 006225 520 DAKQCPSCKMAISRTEGCNKIVCNNCGQY 548 (655)
Q Consensus 520 ~~k~CP~C~~~iek~~Gcn~m~C~~C~~~ 548 (655)
.-+.||+|+..+.-...-+...|.+||+.
T Consensus 18 k~~~CPrCG~gvfmA~H~dR~~CGkCgyT 46 (51)
T COG1998 18 KNRFCPRCGPGVFMADHKDRWACGKCGYT 46 (51)
T ss_pred ccccCCCCCCcchhhhcCceeEeccccce
Confidence 35789999975554444457788888853
No 145
>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]
Probab=64.86 E-value=3.5 Score=32.50 Aligned_cols=26 Identities=38% Similarity=0.930 Sum_probs=12.5
Q ss_pred ccCcccc-ceeEEecCc----CceeccccCe
Q 006225 522 KQCPSCK-MAISRTEGC----NKIVCNNCGQ 547 (655)
Q Consensus 522 k~CP~C~-~~iek~~Gc----n~m~C~~C~~ 547 (655)
..||+|+ ..|.+-..| |.-+|++||+
T Consensus 28 F~CPnCGe~~I~Rc~~CRk~g~~Y~Cp~CGF 58 (61)
T COG2888 28 FPCPNCGEVEIYRCAKCRKLGNPYRCPKCGF 58 (61)
T ss_pred eeCCCCCceeeehhhhHHHcCCceECCCcCc
Confidence 4466666 444443333 3344555554
No 146
>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=64.77 E-value=4.6 Score=27.94 Aligned_cols=26 Identities=15% Similarity=0.419 Sum_probs=18.8
Q ss_pred cccCCCCCccccccccccccccccee
Q 006225 438 YCPRCETPCIEDEEQHAQCSKCFYSF 463 (655)
Q Consensus 438 ~CP~C~~~~~~~~~~~~~C~~C~~~f 463 (655)
.|..|+..+.......++|+.||+..
T Consensus 2 ~C~~Cg~~~~~~~~~~irC~~CG~RI 27 (32)
T PF03604_consen 2 ICGECGAEVELKPGDPIRCPECGHRI 27 (32)
T ss_dssp BESSSSSSE-BSTSSTSSBSSSS-SE
T ss_pred CCCcCCCeeEcCCCCcEECCcCCCeE
Confidence 47888888776666778999999864
No 147
>PHA02929 N1R/p28-like protein; Provisional
Probab=64.55 E-value=4.3 Score=41.51 Aligned_cols=37 Identities=22% Similarity=0.384 Sum_probs=24.9
Q ss_pred CcccccCCCCCcccccc---cccccccccceeeccccccc
Q 006225 435 DVAYCPRCETPCIEDEE---QHAQCSKCFYSFCTLCRERR 471 (655)
Q Consensus 435 ~~~~CP~C~~~~~~~~~---~~~~C~~C~~~fC~~C~~~~ 471 (655)
....||.|...+..+.. ....=+.|+|.||..|...|
T Consensus 173 ~~~eC~ICle~~~~~~~~~~~~~vl~~C~H~FC~~CI~~W 212 (238)
T PHA02929 173 KDKECAICMEKVYDKEIKNMYFGILSNCNHVFCIECIDIW 212 (238)
T ss_pred CCCCCccCCcccccCccccccceecCCCCCcccHHHHHHH
Confidence 44689999987654321 11223479999999997755
No 148
>smart00212 UBCc Ubiquitin-conjugating enzyme E2, catalytic domain homologues. Proteins destined for proteasome-mediated degradation may be ubiquitinated. Ubiquitination follows conjugation of ubiquitin to a conserved cysteine residue of UBC homologues. This pathway functions in regulating many fundamental processes required for cell viability.TSG101 is one of several UBC homologues that lacks this active site cysteine.
Probab=64.48 E-value=35 Score=31.79 Aligned_cols=56 Identities=25% Similarity=0.422 Sum_probs=32.4
Q ss_pred EEEEEEcCCCCCCCCCCeEEeec----ccCCHHHHHHHHHH-HH-HHHHhCCCchhhHHHHHHHhhcc
Q 006225 232 IVLTCLLPKSYPSHLPPYFTISA----RWLNSTKISNLCSM-LE-SIWIDQPGQEILYQWIEWLQNSS 293 (655)
Q Consensus 232 i~L~~~lP~~YPs~~pP~~~l~s----~wL~~~~l~~L~~~-L~-~~~ee~~G~~~lf~~ie~lqe~~ 293 (655)
+.+.+.||++||.. ||.+.... ..+.. . -.++-. |. +-|. ++ ..|.+++..|+..+
T Consensus 48 f~~~l~~p~~yP~~-pP~v~f~~~i~Hp~i~~-~-G~icl~~l~~~~W~--p~-~~l~~il~~i~~~l 109 (145)
T smart00212 48 FKLTIEFPPDYPFK-PPKVKFITKIYHPNVDS-S-GEICLDILKQEKWS--PA-TTLETVLLSIQSLL 109 (145)
T ss_pred EEEEEECCcccCCC-CCEEEEeCCceEeeECC-C-CCEehhhcCCCCCC--CC-CcHHHHHHHHHHHH
Confidence 77999999999998 89776643 12221 0 112222 22 3565 33 34666666666544
No 149
>KOG2906 consensus RNA polymerase III subunit C11 [Transcription]
Probab=64.19 E-value=5.9 Score=34.41 Aligned_cols=31 Identities=29% Similarity=0.717 Sum_probs=21.9
Q ss_pred ccCccccceeEEe--cCcCceeccccCeeeecc
Q 006225 522 KQCPSCKMAISRT--EGCNKIVCNNCGQYFCYR 552 (655)
Q Consensus 522 k~CP~C~~~iek~--~Gcn~m~C~~C~~~FC~~ 552 (655)
..||.|+..+... +.|+...|..|.+.|=..
T Consensus 2 ~FCP~Cgn~Live~g~~~~rf~C~tCpY~~~I~ 34 (105)
T KOG2906|consen 2 LFCPTCGNMLIVESGESCNRFSCRTCPYVFPIS 34 (105)
T ss_pred cccCCCCCEEEEecCCeEeeEEcCCCCceeeEe
Confidence 4799999876543 347888888888766443
No 150
>PRK05654 acetyl-CoA carboxylase subunit beta; Validated
Probab=63.19 E-value=2 Score=45.43 Aligned_cols=29 Identities=28% Similarity=0.503 Sum_probs=24.6
Q ss_pred CccCCccCccccccC-CcceEEcccccccc
Q 006225 601 GLSCPNCRQFNAKVG-NNNHMFCWACQIHY 629 (655)
Q Consensus 601 ~k~CP~C~~~ieK~~-GCnhm~C~~C~~~F 629 (655)
..+||+|+..|.+.. .-|.+.|.+|+++|
T Consensus 27 ~~~c~~c~~~~~~~~l~~~~~vc~~c~~h~ 56 (292)
T PRK05654 27 WTKCPSCGQVLYRKELEANLNVCPKCGHHM 56 (292)
T ss_pred eeECCCccchhhHHHHHhcCCCCCCCCCCe
Confidence 579999999887775 45778999999998
No 151
>KOG0317 consensus Predicted E3 ubiquitin ligase, integral peroxisomal membrane protein [Posttranslational modification, protein turnover, chaperones]
Probab=63.11 E-value=1.2 Score=45.97 Aligned_cols=39 Identities=15% Similarity=0.297 Sum_probs=29.8
Q ss_pred ccccccCccCCccCccccccCCcceEEcccccccccccccccccc
Q 006225 595 DMFDEHGLSCPNCRQFNAKVGNNNHMFCWACQIHYCYLCKKIVRR 639 (655)
Q Consensus 595 ~~~~~~~k~CP~C~~~ieK~~GCnhm~C~~C~~~FC~~C~~~~~~ 639 (655)
..+..++.+|-=|-... -|-+|.-||+-|||.|...|-.
T Consensus 233 ~~i~~a~~kC~LCLe~~------~~pSaTpCGHiFCWsCI~~w~~ 271 (293)
T KOG0317|consen 233 SSIPEATRKCSLCLENR------SNPSATPCGHIFCWSCILEWCS 271 (293)
T ss_pred ccCCCCCCceEEEecCC------CCCCcCcCcchHHHHHHHHHHc
Confidence 34456677888776554 3568889999999999999975
No 152
>PRK10220 hypothetical protein; Provisional
Probab=63.08 E-value=3.8 Score=36.35 Aligned_cols=28 Identities=18% Similarity=0.613 Sum_probs=23.1
Q ss_pred ccccCCCCCcccccccccccccccceee
Q 006225 437 AYCPRCETPCIEDEEQHAQCSKCFYSFC 464 (655)
Q Consensus 437 ~~CP~C~~~~~~~~~~~~~C~~C~~~fC 464 (655)
-.||.|+..+.+.....+.||.|+|.+=
T Consensus 4 P~CP~C~seytY~d~~~~vCpeC~hEW~ 31 (111)
T PRK10220 4 PHCPKCNSEYTYEDNGMYICPECAHEWN 31 (111)
T ss_pred CcCCCCCCcceEcCCCeEECCcccCcCC
Confidence 4699999988877777899999998853
No 153
>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=61.95 E-value=23 Score=32.08 Aligned_cols=36 Identities=19% Similarity=0.547 Sum_probs=26.6
Q ss_pred ccccCccccceeEEecCcCceeccccCeeeecccccc
Q 006225 520 DAKQCPSCKMAISRTEGCNKIVCNNCGQYFCYRCNKA 556 (655)
Q Consensus 520 ~~k~CP~C~~~iek~~Gcn~m~C~~C~~~FC~~C~~~ 556 (655)
+.+.|..|..+.-...+.. ..|..|++.+|-.|+..
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 4678999998765444433 78999999999999986
No 154
>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=61.08 E-value=4.5 Score=36.21 Aligned_cols=30 Identities=23% Similarity=0.499 Sum_probs=21.7
Q ss_pred ccccCCCCCcccccccccccccccceeecc
Q 006225 437 AYCPRCETPCIEDEEQHAQCSKCFYSFCTL 466 (655)
Q Consensus 437 ~~CP~C~~~~~~~~~~~~~C~~C~~~fC~~ 466 (655)
..||.|+.-|.--+..-+.||+||..|=..
T Consensus 10 R~Cp~CG~kFYDLnk~PivCP~CG~~~~~~ 39 (108)
T PF09538_consen 10 RTCPSCGAKFYDLNKDPIVCPKCGTEFPPE 39 (108)
T ss_pred ccCCCCcchhccCCCCCccCCCCCCccCcc
Confidence 469999987754444667899998887444
No 155
>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=60.99 E-value=5.8 Score=32.09 Aligned_cols=29 Identities=24% Similarity=0.637 Sum_probs=21.9
Q ss_pred ccccCccccceeEEecCcCceeccccCee
Q 006225 520 DAKQCPSCKMAISRTEGCNKIVCNNCGQY 548 (655)
Q Consensus 520 ~~k~CP~C~~~iek~~Gcn~m~C~~C~~~ 548 (655)
..+.||.|+....+...-..++|+.||+.
T Consensus 27 TSq~C~~CG~~~~~~~~~r~~~C~~Cg~~ 55 (69)
T PF07282_consen 27 TSQTCPRCGHRNKKRRSGRVFTCPNCGFE 55 (69)
T ss_pred CccCccCcccccccccccceEEcCCCCCE
Confidence 46789999999988444456788877764
No 156
>CHL00174 accD acetyl-CoA carboxylase beta subunit; Reviewed
Probab=60.78 E-value=2.2 Score=44.91 Aligned_cols=34 Identities=24% Similarity=0.386 Sum_probs=26.8
Q ss_pred CccCCccCccccccC-CcceEEccccccccccccc
Q 006225 601 GLSCPNCRQFNAKVG-NNNHMFCWACQIHYCYLCK 634 (655)
Q Consensus 601 ~k~CP~C~~~ieK~~-GCnhm~C~~C~~~FC~~C~ 634 (655)
..+||+|+..+.+.. .=|.+.|++|+++|=-.=.
T Consensus 38 w~kc~~C~~~~~~~~l~~~~~vcp~c~~h~rltAr 72 (296)
T CHL00174 38 WVQCENCYGLNYKKFLKSKMNICEQCGYHLKMSSS 72 (296)
T ss_pred eeECCCccchhhHHHHHHcCCCCCCCCCCcCCCHH
Confidence 478999999888776 5678999999998844333
No 157
>COG0777 AccD Acetyl-CoA carboxylase beta subunit [Lipid metabolism]
Probab=60.61 E-value=3.1 Score=42.96 Aligned_cols=36 Identities=31% Similarity=0.589 Sum_probs=27.9
Q ss_pred ccccCccccceeEEec-CcCceeccccCeeeeccccc
Q 006225 520 DAKQCPSCKMAISRTE-GCNKIVCNNCGQYFCYRCNK 555 (655)
Q Consensus 520 ~~k~CP~C~~~iek~~-Gcn~m~C~~C~~~FC~~C~~ 555 (655)
-|.+||.|+..+-+.+ +-|...|++|+++|=..=..
T Consensus 27 lw~KCp~c~~~~y~~eL~~n~~vcp~c~~h~ri~A~~ 63 (294)
T COG0777 27 LWTKCPSCGEMLYRKELESNLKVCPKCGHHMRISARE 63 (294)
T ss_pred ceeECCCccceeeHHHHHhhhhcccccCcccccCHHH
Confidence 3788999999987654 67888999999988554333
No 158
>PF14447 Prok-RING_4: Prokaryotic RING finger family 4
Probab=60.43 E-value=5.3 Score=31.11 Aligned_cols=46 Identities=30% Similarity=0.558 Sum_probs=31.9
Q ss_pred cccccccccccCCCeEecCCCCcccHhhHHHHHHHHhhcCCcceeccCCCCCCCCCCccc
Q 006225 349 HECRICFSEFAGTDFVRLPCHHFFCWKCMKTYLDIHISEGTVSKLQCPDAKCGGMVPPSL 408 (655)
Q Consensus 349 ~~C~IC~e~~~~~~~~~l~C~H~fC~~Cl~~yi~~~i~~g~~~~i~CP~~~C~~~l~~~~ 408 (655)
+.|-.|... +..-+.++|+|..|..||-.. . --.||. |...+....
T Consensus 8 ~~~~~~~~~--~~~~~~~pCgH~I~~~~f~~~--------r--YngCPf--C~~~~~~~~ 53 (55)
T PF14447_consen 8 QPCVFCGFV--GTKGTVLPCGHLICDNCFPGE--------R--YNGCPF--CGTPFEFDD 53 (55)
T ss_pred eeEEEcccc--ccccccccccceeeccccChh--------h--ccCCCC--CCCcccCCC
Confidence 556666544 234566799999999998642 1 135998 998887654
No 159
>PRK12495 hypothetical protein; Provisional
Probab=60.15 E-value=12 Score=37.50 Aligned_cols=17 Identities=12% Similarity=0.298 Sum_probs=13.9
Q ss_pred CccCCccCccccccCCc
Q 006225 601 GLSCPNCRQFNAKVGNN 617 (655)
Q Consensus 601 ~k~CP~C~~~ieK~~GC 617 (655)
.+.||.|+.+|.+..|+
T Consensus 42 a~hC~~CG~PIpa~pG~ 58 (226)
T PRK12495 42 NAHCDECGDPIFRHDGQ 58 (226)
T ss_pred hhhcccccCcccCCCCe
Confidence 47899999999976554
No 160
>PRK05654 acetyl-CoA carboxylase subunit beta; Validated
Probab=60.05 E-value=2.4 Score=44.81 Aligned_cols=30 Identities=37% Similarity=0.755 Sum_probs=24.3
Q ss_pred cccCccccceeEEec-CcCceeccccCeeee
Q 006225 521 AKQCPSCKMAISRTE-GCNKIVCNNCGQYFC 550 (655)
Q Consensus 521 ~k~CP~C~~~iek~~-Gcn~m~C~~C~~~FC 550 (655)
|..||.|+..+-+.+ .-|...|+.|+++|=
T Consensus 27 ~~~c~~c~~~~~~~~l~~~~~vc~~c~~h~r 57 (292)
T PRK05654 27 WTKCPSCGQVLYRKELEANLNVCPKCGHHMR 57 (292)
T ss_pred eeECCCccchhhHHHHHhcCCCCCCCCCCee
Confidence 788999999886643 456789999999883
No 161
>PF14952 zf-tcix: Putative treble-clef, zinc-finger, Zn-binding
Probab=59.83 E-value=4.8 Score=29.70 Aligned_cols=26 Identities=23% Similarity=0.676 Sum_probs=19.0
Q ss_pred cCccCCccCccccccCCcceEEcc--cccccc
Q 006225 600 HGLSCPNCRQFNAKVGNNNHMFCW--ACQIHY 629 (655)
Q Consensus 600 ~~k~CP~C~~~ieK~~GCnhm~C~--~C~~~F 629 (655)
..+.||+|+++. |+--+.|. .|++.|
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 458999999998 77667775 365544
No 162
>KOG1813 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=59.83 E-value=3.1 Score=43.25 Aligned_cols=45 Identities=27% Similarity=0.495 Sum_probs=33.1
Q ss_pred ccccccccccccCCCeEecCCCCcccHhhHHHHHHHHhhcCCcceeccCCCCCCCCC
Q 006225 348 FHECRICFSEFAGTDFVRLPCHHFFCWKCMKTYLDIHISEGTVSKLQCPDAKCGGMV 404 (655)
Q Consensus 348 ~~~C~IC~e~~~~~~~~~l~C~H~fC~~Cl~~yi~~~i~~g~~~~i~CP~~~C~~~l 404 (655)
.+-|.||-..|. +++...|+|+||..|....++. .-+|+. |....
T Consensus 241 Pf~c~icr~~f~--~pVvt~c~h~fc~~ca~~~~qk--------~~~c~v--C~~~t 285 (313)
T KOG1813|consen 241 PFKCFICRKYFY--RPVVTKCGHYFCEVCALKPYQK--------GEKCYV--CSQQT 285 (313)
T ss_pred Cccccccccccc--cchhhcCCceeehhhhcccccc--------CCccee--ccccc
Confidence 478999998874 5677799999999998876542 245665 66543
No 163
>KOG0297 consensus TNF receptor-associated factor [Signal transduction mechanisms]
Probab=59.70 E-value=4.5 Score=44.62 Aligned_cols=47 Identities=32% Similarity=0.649 Sum_probs=34.4
Q ss_pred ccccccccccccccCCCeEe-cCCCCcccHhhHHHHHHHHhhcCCcceeccCCCCCCCCC
Q 006225 346 KSFHECRICFSEFAGTDFVR-LPCHHFFCWKCMKTYLDIHISEGTVSKLQCPDAKCGGMV 404 (655)
Q Consensus 346 ~~~~~C~IC~e~~~~~~~~~-l~C~H~fC~~Cl~~yi~~~i~~g~~~~i~CP~~~C~~~l 404 (655)
++...|++|..... +.+. ..|||.||..|+..+... ...||. |...+
T Consensus 19 ~~~l~C~~C~~vl~--~p~~~~~cgh~fC~~C~~~~~~~--------~~~cp~--~~~~~ 66 (391)
T KOG0297|consen 19 DENLLCPICMSVLR--DPVQTTTCGHRFCAGCLLESLSN--------HQKCPV--CRQEL 66 (391)
T ss_pred cccccCcccccccc--CCCCCCCCCCcccccccchhhcc--------CcCCcc--ccccc
Confidence 44578999998874 4444 589999999999998664 356776 54433
No 164
>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=59.62 E-value=4.8 Score=29.49 Aligned_cols=24 Identities=33% Similarity=0.852 Sum_probs=18.5
Q ss_pred ccccCCCCCccccccccccccccc
Q 006225 437 AYCPRCETPCIEDEEQHAQCSKCF 460 (655)
Q Consensus 437 ~~CP~C~~~~~~~~~~~~~C~~C~ 460 (655)
.+||.|+.+...+......|+.|+
T Consensus 18 ~~Cp~C~~PL~~~k~g~~~Cv~C~ 41 (41)
T PF06677_consen 18 EHCPDCGTPLMRDKDGKIYCVSCG 41 (41)
T ss_pred CccCCCCCeeEEecCCCEECCCCC
Confidence 479999998887666667777764
No 165
>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=59.62 E-value=2.6 Score=32.43 Aligned_cols=35 Identities=23% Similarity=0.695 Sum_probs=18.5
Q ss_pred CccccceeEEe----cCcCceeccccCeeeecccccccc
Q 006225 524 CPSCKMAISRT----EGCNKIVCNNCGQYFCYRCNKAID 558 (655)
Q Consensus 524 CP~C~~~iek~----~Gcn~m~C~~C~~~FC~~C~~~~~ 558 (655)
|-.|..++... .+-....|++|+..||+.|-.-+|
T Consensus 2 CfgC~~~~~~~~~~~~~~~~y~C~~C~~~FC~dCD~fiH 40 (51)
T PF07975_consen 2 CFGCQKPFPDGPEKKADSSRYRCPKCKNHFCIDCDVFIH 40 (51)
T ss_dssp ETTTTEE-TTS-------EEE--TTTT--B-HHHHHTTT
T ss_pred CccCCCCCCCcccccccCCeEECCCCCCccccCcChhhh
Confidence 55676666442 123567899999999999987654
No 166
>COG1997 RPL43A Ribosomal protein L37AE/L43A [Translation, ribosomal structure and biogenesis]
Probab=59.47 E-value=14 Score=31.49 Aligned_cols=31 Identities=26% Similarity=0.614 Sum_probs=23.9
Q ss_pred cccccCccccceeEEecCcCceeccccCeee
Q 006225 519 RDAKQCPSCKMAISRTEGCNKIVCNNCGQYF 549 (655)
Q Consensus 519 ~~~k~CP~C~~~iek~~Gcn~m~C~~C~~~F 549 (655)
.....||.|+....+..+-..-.|..||+.|
T Consensus 33 ~~~~~Cp~C~~~~VkR~a~GIW~C~kCg~~f 63 (89)
T COG1997 33 RAKHVCPFCGRTTVKRIATGIWKCRKCGAKF 63 (89)
T ss_pred hcCCcCCCCCCcceeeeccCeEEcCCCCCee
Confidence 3456799999998887776667788788776
No 167
>PRK09710 lar restriction alleviation and modification protein; Reviewed
Probab=58.89 E-value=6.9 Score=31.43 Aligned_cols=28 Identities=29% Similarity=0.708 Sum_probs=17.9
Q ss_pred ccccCccccceeEE---ecCcCceeccccCe
Q 006225 520 DAKQCPSCKMAISR---TEGCNKIVCNNCGQ 547 (655)
Q Consensus 520 ~~k~CP~C~~~iek---~~Gcn~m~C~~C~~ 547 (655)
++|+||.|+..+.. .+|--.+.|..|+.
T Consensus 5 ~lKPCPFCG~~~~~v~~~~g~~~v~C~~CgA 35 (64)
T PRK09710 5 NVKPCPFCGCPSVTVKAISGYYRAKCNGCES 35 (64)
T ss_pred cccCCCCCCCceeEEEecCceEEEEcCCCCc
Confidence 47999999876544 34444455665554
No 168
>CHL00174 accD acetyl-CoA carboxylase beta subunit; Reviewed
Probab=58.87 E-value=2.3 Score=44.74 Aligned_cols=34 Identities=18% Similarity=0.335 Sum_probs=26.2
Q ss_pred cccCccccceeEEec-CcCceeccccCeeeecccc
Q 006225 521 AKQCPSCKMAISRTE-GCNKIVCNNCGQYFCYRCN 554 (655)
Q Consensus 521 ~k~CP~C~~~iek~~-Gcn~m~C~~C~~~FC~~C~ 554 (655)
|..||+|+..+.+.. .-|...|+.|+++|=..=+
T Consensus 38 w~kc~~C~~~~~~~~l~~~~~vcp~c~~h~rltAr 72 (296)
T CHL00174 38 WVQCENCYGLNYKKFLKSKMNICEQCGYHLKMSSS 72 (296)
T ss_pred eeECCCccchhhHHHHHHcCCCCCCCCCCcCCCHH
Confidence 788999999887643 4577899999998854433
No 169
>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=58.73 E-value=2.6 Score=44.33 Aligned_cols=30 Identities=27% Similarity=0.462 Sum_probs=24.7
Q ss_pred CccCCccCccccccC-CcceEEccccccccc
Q 006225 601 GLSCPNCRQFNAKVG-NNNHMFCWACQIHYC 630 (655)
Q Consensus 601 ~k~CP~C~~~ieK~~-GCnhm~C~~C~~~FC 630 (655)
..+||+|+..+.+.+ .=|.+.|.+|+++|=
T Consensus 26 ~~~c~~c~~~~~~~~l~~~~~vc~~c~~h~r 56 (285)
T TIGR00515 26 WTKCPKCGQVLYTKELERNLEVCPKCDHHMR 56 (285)
T ss_pred eeECCCCcchhhHHHHHhhCCCCCCCCCcCc
Confidence 578999999888764 457789999999874
No 170
>PRK14559 putative protein serine/threonine phosphatase; Provisional
Probab=58.48 E-value=4.7 Score=47.25 Aligned_cols=34 Identities=21% Similarity=0.400 Sum_probs=26.1
Q ss_pred cCccCCccCccccccCCcceEEccccccc------ccccccccccc
Q 006225 600 HGLSCPNCRQFNAKVGNNNHMFCWACQIH------YCYLCKKIVRR 639 (655)
Q Consensus 600 ~~k~CP~C~~~ieK~~GCnhm~C~~C~~~------FC~~C~~~~~~ 639 (655)
+.+-||+|+..+. +..|..||+. ||-.||.+...
T Consensus 14 ~akFC~~CG~~l~------~~~Cp~CG~~~~~~~~fC~~CG~~~~~ 53 (645)
T PRK14559 14 NNRFCQKCGTSLT------HKPCPQCGTEVPVDEAHCPNCGAETGT 53 (645)
T ss_pred CCccccccCCCCC------CCcCCCCCCCCCcccccccccCCcccc
Confidence 4577888888763 3578889866 99999988763
No 171
>PF14835 zf-RING_6: zf-RING of BARD1-type protein; PDB: 1JM7_B.
Probab=58.35 E-value=6 Score=31.86 Aligned_cols=36 Identities=28% Similarity=0.671 Sum_probs=15.1
Q ss_pred CccCCccCcccccc---CCcceEEcccccccc----ccccccc
Q 006225 601 GLSCPNCRQFNAKV---GNNNHMFCWACQIHY----CYLCKKI 636 (655)
Q Consensus 601 ~k~CP~C~~~ieK~---~GCnhm~C~~C~~~F----C~~C~~~ 636 (655)
..+|++|......- +||-|+.|+.|=..+ |-.|..+
T Consensus 7 lLrCs~C~~~l~~pv~l~~CeH~fCs~Ci~~~~~~~CPvC~~P 49 (65)
T PF14835_consen 7 LLRCSICFDILKEPVCLGGCEHIFCSSCIRDCIGSECPVCHTP 49 (65)
T ss_dssp TTS-SSS-S--SS-B---SSS--B-TTTGGGGTTTB-SSS--B
T ss_pred hcCCcHHHHHhcCCceeccCccHHHHHHhHHhcCCCCCCcCCh
Confidence 36899999775443 677777777664332 5555544
No 172
>PF00627 UBA: UBA/TS-N domain; InterPro: IPR000449 UBA domains are a commonly occurring sequence motif of approximately 45 amino acid residues that are found in diverse proteins involved in the ubiquitin/proteasome pathway, DNA excision-repair, and cell signalling via protein kinases []. The human homologue of yeast Rad23A is one example of a nucleotide excision-repair protein that contains both an internal and a C-terminal UBA domain. The solution structure of human Rad23A UBA(2) showed that the domain forms a compact three-helix bundle []. Comparison of the structures of UBA(1) and UBA(2) reveals that both form very similar folds and have a conserved large hydrophobic surface patch which may be a common protein-interacting surface present in diverse UBA domains. Evidence that ubiquitin binds to UBA domains leads to the prediction that the hydrophobic surface patch of UBA domains interacts with the hydrophobic surface on the five-stranded beta-sheet of ubiquitin []. This domain is similar in sequence to the N-terminal domain of translation elongation factor EF1B (or EF-Ts) from bacteria, mitochondria and chloroplasts. More information about EF1B (EF-Ts) proteins can be found at Protein of the Month: Elongation Factors [].; GO: 0005515 protein binding; PDB: 2DAI_A 2OO9_C 2JUJ_A 1WHC_A 1YLA_A 2O25_B 3K9O_A 3K9P_A 3F92_A 3E46_A ....
Probab=58.20 E-value=7.8 Score=27.37 Aligned_cols=26 Identities=35% Similarity=0.354 Sum_probs=20.0
Q ss_pred hhhhhhhhcccCCC----------CCCChhhHHHHH
Q 006225 110 EEVKEKQDEEEGLP----------SNSNVNDVESIL 135 (655)
Q Consensus 110 ~~~~~~~~~~~~~~----------~~~~~~~~~~~~ 135 (655)
.+.++++|.+-||+ +++|++.|+..|
T Consensus 2 ~~~~v~~L~~mGf~~~~~~~AL~~~~~nve~A~~~L 37 (37)
T PF00627_consen 2 DEEKVQQLMEMGFSREQAREALRACNGNVERAVDWL 37 (37)
T ss_dssp HHHHHHHHHHHTS-HHHHHHHHHHTTTSHHHHHHHH
T ss_pred CHHHHHHHHHcCCCHHHHHHHHHHcCCCHHHHHHhC
Confidence 35778899999998 778888887755
No 173
>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=57.99 E-value=22 Score=26.11 Aligned_cols=25 Identities=36% Similarity=0.986 Sum_probs=18.0
Q ss_pred cccCccccceeEEecCcCceeccccC
Q 006225 521 AKQCPSCKMAISRTEGCNKIVCNNCG 546 (655)
Q Consensus 521 ~k~CP~C~~~iek~~Gcn~m~C~~C~ 546 (655)
...||.|+.++.++.. ..+.|+.|+
T Consensus 17 ~~~Cp~C~~PL~~~k~-g~~~Cv~C~ 41 (41)
T PF06677_consen 17 DEHCPDCGTPLMRDKD-GKIYCVSCG 41 (41)
T ss_pred cCccCCCCCeeEEecC-CCEECCCCC
Confidence 4679999999988322 357777664
No 174
>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=57.71 E-value=2.6 Score=44.32 Aligned_cols=31 Identities=26% Similarity=0.556 Sum_probs=24.7
Q ss_pred cccCccccceeEEec-CcCceeccccCeeeec
Q 006225 521 AKQCPSCKMAISRTE-GCNKIVCNNCGQYFCY 551 (655)
Q Consensus 521 ~k~CP~C~~~iek~~-Gcn~m~C~~C~~~FC~ 551 (655)
|..||+|+..+.+.+ .-|...|+.|+++|=.
T Consensus 26 ~~~c~~c~~~~~~~~l~~~~~vc~~c~~h~rl 57 (285)
T TIGR00515 26 WTKCPKCGQVLYTKELERNLEVCPKCDHHMRM 57 (285)
T ss_pred eeECCCCcchhhHHHHHhhCCCCCCCCCcCcC
Confidence 788999999987643 4567899999998743
No 175
>COG2816 NPY1 NTP pyrophosphohydrolases containing a Zn-finger, probably nucleic-acid-binding [DNA replication, recombination, and repair]
Probab=57.59 E-value=12 Score=39.00 Aligned_cols=34 Identities=29% Similarity=0.539 Sum_probs=28.1
Q ss_pred HHhcccccCccccceeEEecCcCceeccccCeee
Q 006225 516 EILRDAKQCPSCKMAISRTEGCNKIVCNNCGQYF 549 (655)
Q Consensus 516 ~i~~~~k~CP~C~~~iek~~Gcn~m~C~~C~~~F 549 (655)
......++||+|+....-..|--.+.|++||+.+
T Consensus 106 ~w~~~~RFCg~CG~~~~~~~~g~~~~C~~cg~~~ 139 (279)
T COG2816 106 EWYRSHRFCGRCGTKTYPREGGWARVCPKCGHEH 139 (279)
T ss_pred HHHhhCcCCCCCCCcCccccCceeeeCCCCCCcc
Confidence 3345689999999999988888889999998655
No 176
>PF08792 A2L_zn_ribbon: A2L zinc ribbon domain; InterPro: IPR014900 This zinc ribbon protein is found associated with some viral A2L transcription factors [].
Probab=57.05 E-value=12 Score=26.13 Aligned_cols=29 Identities=28% Similarity=0.476 Sum_probs=20.9
Q ss_pred cccCccccceeEEecCcCceeccccCeee
Q 006225 521 AKQCPSCKMAISRTEGCNKIVCNNCGQYF 549 (655)
Q Consensus 521 ~k~CP~C~~~iek~~Gcn~m~C~~C~~~F 549 (655)
.+.|+.|+........-..+.|..||..|
T Consensus 3 ~~~C~~C~~~~i~~~~~~~~~C~~Cg~~~ 31 (33)
T PF08792_consen 3 LKKCSKCGGNGIVNKEDDYEVCIFCGSSF 31 (33)
T ss_pred ceEcCCCCCCeEEEecCCeEEcccCCcEe
Confidence 46799999877664444567888787665
No 177
>KOG3579 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=56.79 E-value=7 Score=40.37 Aligned_cols=52 Identities=29% Similarity=0.724 Sum_probs=40.9
Q ss_pred cccccccccccccCCCeEecC--CCCcccHhhHHHHHHHHhhcCCcceeccCC-CCCC
Q 006225 347 SFHECRICFSEFAGTDFVRLP--CHHFFCWKCMKTYLDIHISEGTVSKLQCPD-AKCG 401 (655)
Q Consensus 347 ~~~~C~IC~e~~~~~~~~~l~--C~H~fC~~Cl~~yi~~~i~~g~~~~i~CP~-~~C~ 401 (655)
..+-|.+|-+.+....|+.++ =.|.||.-|-++.|+.+-..| .+.||. ..|.
T Consensus 267 apLcCTLC~ERLEDTHFVQCPSVp~HKFCFPCSResIK~Qg~sg---evYCPSGdkCP 321 (352)
T KOG3579|consen 267 APLCCTLCHERLEDTHFVQCPSVPSHKFCFPCSRESIKQQGASG---EVYCPSGDKCP 321 (352)
T ss_pred CceeehhhhhhhccCceeecCCCcccceecccCHHHHHhhcCCC---ceeCCCCCcCc
Confidence 458899999998877887753 489999999999998776555 578886 3554
No 178
>KOG4692 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=56.67 E-value=6.6 Score=41.67 Aligned_cols=48 Identities=27% Similarity=0.501 Sum_probs=31.9
Q ss_pred cccccccccccccCCCeEecCCCCcccHhhHHHHHHHHhhcCCcceeccCCCCCCCCCCc
Q 006225 347 SFHECRICFSEFAGTDFVRLPCHHFFCWKCMKTYLDIHISEGTVSKLQCPDAKCGGMVPP 406 (655)
Q Consensus 347 ~~~~C~IC~e~~~~~~~~~l~C~H~fC~~Cl~~yi~~~i~~g~~~~i~CP~~~C~~~l~~ 406 (655)
+...|+||+-.-. ..+--+|+|.-|.+|+.+|+-. .-.|-. |+..+..
T Consensus 421 Ed~lCpICyA~pi--~Avf~PC~H~SC~~CI~qHlmN--------~k~CFf--CktTv~~ 468 (489)
T KOG4692|consen 421 EDNLCPICYAGPI--NAVFAPCSHRSCYGCITQHLMN--------CKRCFF--CKTTVID 468 (489)
T ss_pred ccccCcceecccc--hhhccCCCCchHHHHHHHHHhc--------CCeeeE--ecceeee
Confidence 4568999986521 1222399999999999998643 234554 7766543
No 179
>PRK00241 nudC NADH pyrophosphatase; Reviewed
Probab=56.64 E-value=16 Score=37.83 Aligned_cols=34 Identities=18% Similarity=0.531 Sum_probs=26.3
Q ss_pred HHhcccccCccccceeEEecCcCceeccccCeee
Q 006225 516 EILRDAKQCPSCKMAISRTEGCNKIVCNNCGQYF 549 (655)
Q Consensus 516 ~i~~~~k~CP~C~~~iek~~Gcn~m~C~~C~~~F 549 (655)
....+.++||.|+..+....+-..+.|+.|+..+
T Consensus 94 ~w~~~~~fC~~CG~~~~~~~~~~~~~C~~c~~~~ 127 (256)
T PRK00241 94 EFYRSHRFCGYCGHPMHPSKTEWAMLCPHCRERY 127 (256)
T ss_pred HHhhcCccccccCCCCeecCCceeEECCCCCCEE
Confidence 3455689999999998776555678899998554
No 180
>PF14353 CpXC: CpXC protein
Probab=56.40 E-value=8.9 Score=35.14 Aligned_cols=30 Identities=23% Similarity=0.594 Sum_probs=21.2
Q ss_pred ccCccccceeEEe-------------------cCcCceeccccCeeeec
Q 006225 522 KQCPSCKMAISRT-------------------EGCNKIVCNNCGQYFCY 551 (655)
Q Consensus 522 k~CP~C~~~iek~-------------------~Gcn~m~C~~C~~~FC~ 551 (655)
..||+|+...... +.=+..+|+.||+.|=.
T Consensus 2 itCP~C~~~~~~~v~~~I~~~~~p~l~e~il~g~l~~~~CP~Cg~~~~~ 50 (128)
T PF14353_consen 2 ITCPHCGHEFEFEVWTSINADEDPELKEKILDGSLFSFTCPSCGHKFRL 50 (128)
T ss_pred cCCCCCCCeeEEEEEeEEcCcCCHHHHHHHHcCCcCEEECCCCCCceec
Confidence 3699999876541 22457889999988843
No 181
>KOG0427 consensus Ubiquitin conjugating enzyme [Posttranslational modification, protein turnover, chaperones]
Probab=56.33 E-value=50 Score=30.25 Aligned_cols=22 Identities=23% Similarity=0.472 Sum_probs=18.0
Q ss_pred EEEEEEcCCCCCCCCCCeEEee
Q 006225 232 IVLTCLLPKSYPSHLPPYFTIS 253 (655)
Q Consensus 232 i~L~~~lP~~YPs~~pP~~~l~ 253 (655)
+.|+|.||+.||-++|-++.+.
T Consensus 63 ~qLq~~F~~~YP~esPqVmF~~ 84 (161)
T KOG0427|consen 63 YQLQVEFPEHYPMESPQVMFVG 84 (161)
T ss_pred EEEEEecCCCCCCCCCeEEEec
Confidence 7899999999999966655554
No 182
>smart00659 RPOLCX RNA polymerase subunit CX. present in RNA polymerase I, II and III
Probab=55.96 E-value=7.1 Score=29.03 Aligned_cols=26 Identities=19% Similarity=0.542 Sum_probs=20.3
Q ss_pred cccCCCCCccccccccccccccccee
Q 006225 438 YCPRCETPCIEDEEQHAQCSKCFYSF 463 (655)
Q Consensus 438 ~CP~C~~~~~~~~~~~~~C~~C~~~f 463 (655)
.|..|+..+..+....++|+.||+..
T Consensus 4 ~C~~Cg~~~~~~~~~~irC~~CG~rI 29 (44)
T smart00659 4 ICGECGRENEIKSKDVVRCRECGYRI 29 (44)
T ss_pred ECCCCCCEeecCCCCceECCCCCceE
Confidence 48888887766666778999998864
No 183
>COG0777 AccD Acetyl-CoA carboxylase beta subunit [Lipid metabolism]
Probab=55.90 E-value=3.9 Score=42.22 Aligned_cols=33 Identities=21% Similarity=0.422 Sum_probs=27.3
Q ss_pred CccCCccCccccccC-CcceEEcccccccccccc
Q 006225 601 GLSCPNCRQFNAKVG-NNNHMFCWACQIHYCYLC 633 (655)
Q Consensus 601 ~k~CP~C~~~ieK~~-GCnhm~C~~C~~~FC~~C 633 (655)
..+||+|+..+.+.+ +=|.+.|.+|+++|=..=
T Consensus 28 w~KCp~c~~~~y~~eL~~n~~vcp~c~~h~ri~A 61 (294)
T COG0777 28 WTKCPSCGEMLYRKELESNLKVCPKCGHHMRISA 61 (294)
T ss_pred eeECCCccceeeHHHHHhhhhcccccCcccccCH
Confidence 478999999988886 778999999999984433
No 184
>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=55.55 E-value=16 Score=38.07 Aligned_cols=51 Identities=24% Similarity=0.602 Sum_probs=34.6
Q ss_pred ccccccccccCC-CeEec--CCCCcccHhhHHHHHHHHhhcCCcceeccCCCCCCCCCCcccc
Q 006225 350 ECRICFSEFAGT-DFVRL--PCHHFFCWKCMKTYLDIHISEGTVSKLQCPDAKCGGMVPPSLL 409 (655)
Q Consensus 350 ~C~IC~e~~~~~-~~~~l--~C~H~fC~~Cl~~yi~~~i~~g~~~~i~CP~~~C~~~l~~~~i 409 (655)
.|++|-.+.-.. ++..+ +|+|..|.+|+-..+.. | +-.|| .|...+--.-+
T Consensus 2 ~Cp~CKt~~Y~np~lk~~in~C~H~lCEsCvd~iF~~----g---~~~Cp--eC~~iLRk~nf 55 (300)
T KOG3800|consen 2 ACPKCKTDRYLNPDLKLMINECGHRLCESCVDRIFSL----G---PAQCP--ECMVILRKNNF 55 (300)
T ss_pred CCcccccceecCccceeeeccccchHHHHHHHHHHhc----C---CCCCC--cccchhhhccc
Confidence 589997664322 23322 89999999999987653 2 45799 59987654433
No 185
>PRK09710 lar restriction alleviation and modification protein; Reviewed
Probab=55.41 E-value=9.7 Score=30.62 Aligned_cols=30 Identities=17% Similarity=0.382 Sum_probs=20.2
Q ss_pred ccCccCCccCcc---ccccCCcceEEccccccc
Q 006225 599 EHGLSCPNCRQF---NAKVGNNNHMFCWACQIH 628 (655)
Q Consensus 599 ~~~k~CP~C~~~---ieK~~GCnhm~C~~C~~~ 628 (655)
++.|+||.|+.. ++..+|=....|.+|+..
T Consensus 4 d~lKPCPFCG~~~~~v~~~~g~~~v~C~~CgA~ 36 (64)
T PRK09710 4 DNVKPCPFCGCPSVTVKAISGYYRAKCNGCESR 36 (64)
T ss_pred ccccCCCCCCCceeEEEecCceEEEEcCCCCcC
Confidence 456999999954 333455455777777765
No 186
>KOG3053 consensus Uncharacterized conserved protein [Function unknown]
Probab=55.37 E-value=12 Score=38.26 Aligned_cols=54 Identities=20% Similarity=0.624 Sum_probs=39.7
Q ss_pred cccccccccccCCCeEe-c-CC-----CCcccHhhHHHHHHHHhhcCCcceeccCCCCCCCCC
Q 006225 349 HECRICFSEFAGTDFVR-L-PC-----HHFFCWKCMKTYLDIHISEGTVSKLQCPDAKCGGMV 404 (655)
Q Consensus 349 ~~C~IC~e~~~~~~~~~-l-~C-----~H~fC~~Cl~~yi~~~i~~g~~~~i~CP~~~C~~~l 404 (655)
..|=|||.+-..+.... . +| .|-....||..|+..+-.......+.||+ |....
T Consensus 21 R~CWiCF~TdeDn~~a~WV~PCrCRGt~KWVHqsCL~rWiDEK~~~n~~q~V~C~Q--CqTEY 81 (293)
T KOG3053|consen 21 RCCWICFATDEDNRLAAWVHPCRCRGTTKWVHQSCLSRWIDEKQRGNPLQTVSCPQ--CQTEY 81 (293)
T ss_pred eeEEEEeccCcccchhhhcccccccCccHHHHHHHHHHHHhHHhcCCCCceeechh--hcchh
Confidence 57999998755433221 2 55 35689999999999887755567899998 88653
No 187
>PF07191 zinc-ribbons_6: zinc-ribbons; InterPro: IPR010807 This family consists of several short, hypothetical bacterial proteins of around 70 residues in length. Members of this family 8 highly conserved cysteine residues. The function of the family is unknown.; PDB: 2JRP_A 2JNE_A.
Probab=55.27 E-value=12 Score=30.66 Aligned_cols=33 Identities=24% Similarity=0.846 Sum_probs=20.3
Q ss_pred cCccccceeEEecCcCceeccccC-----eeeeccccccc
Q 006225 523 QCPSCKMAISRTEGCNKIVCNNCG-----QYFCYRCNKAI 557 (655)
Q Consensus 523 ~CP~C~~~iek~~Gcn~m~C~~C~-----~~FC~~C~~~~ 557 (655)
.||.|...++..+ .+..|..|+ ..||-.|+.++
T Consensus 3 ~CP~C~~~L~~~~--~~~~C~~C~~~~~~~a~CPdC~~~L 40 (70)
T PF07191_consen 3 TCPKCQQELEWQG--GHYHCEACQKDYKKEAFCPDCGQPL 40 (70)
T ss_dssp B-SSS-SBEEEET--TEEEETTT--EEEEEEE-TTT-SB-
T ss_pred cCCCCCCccEEeC--CEEECccccccceecccCCCcccHH
Confidence 5999999988877 467788786 44577777665
No 188
>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=54.95 E-value=6.5 Score=35.95 Aligned_cols=28 Identities=11% Similarity=0.056 Sum_probs=22.4
Q ss_pred CccCCccCccccccCCcceEEcccccccc
Q 006225 601 GLSCPNCRQFNAKVGNNNHMFCWACQIHY 629 (655)
Q Consensus 601 ~k~CP~C~~~ieK~~GCnhm~C~~C~~~F 629 (655)
.+.||+|+....-... +-++|++||..|
T Consensus 9 Kr~Cp~cg~kFYDLnk-~p~vcP~cg~~~ 36 (129)
T TIGR02300 9 KRICPNTGSKFYDLNR-RPAVSPYTGEQF 36 (129)
T ss_pred cccCCCcCccccccCC-CCccCCCcCCcc
Confidence 3689999988776655 779999999775
No 189
>COG1594 RPB9 DNA-directed RNA polymerase, subunit M/Transcription elongation factor TFIIS [Transcription]
Probab=54.57 E-value=9 Score=34.60 Aligned_cols=29 Identities=28% Similarity=0.674 Sum_probs=21.5
Q ss_pred cccCccccceeEEe--cCcCceeccccCeee
Q 006225 521 AKQCPSCKMAISRT--EGCNKIVCNNCGQYF 549 (655)
Q Consensus 521 ~k~CP~C~~~iek~--~Gcn~m~C~~C~~~F 549 (655)
.++||.|+.++... ++-+.+.|++||+.+
T Consensus 2 m~FCp~Cgsll~p~~~~~~~~l~C~kCgye~ 32 (113)
T COG1594 2 MRFCPKCGSLLYPKKDDEGGKLVCRKCGYEE 32 (113)
T ss_pred ccccCCccCeeEEeEcCCCcEEECCCCCcch
Confidence 47899999988652 234578899888755
No 190
>PRK12495 hypothetical protein; Provisional
Probab=54.31 E-value=13 Score=37.24 Aligned_cols=28 Identities=32% Similarity=0.790 Sum_probs=20.2
Q ss_pred ccccCccccceeEEecCcCceeccccCeeeeccccccc
Q 006225 520 DAKQCPSCKMAISRTEGCNKIVCNNCGQYFCYRCNKAI 557 (655)
Q Consensus 520 ~~k~CP~C~~~iek~~Gcn~m~C~~C~~~FC~~C~~~~ 557 (655)
..+.|+.|+.+|.+..| ..||..|...+
T Consensus 41 sa~hC~~CG~PIpa~pG----------~~~Cp~CQ~~~ 68 (226)
T PRK12495 41 TNAHCDECGDPIFRHDG----------QEFCPTCQQPV 68 (226)
T ss_pred chhhcccccCcccCCCC----------eeECCCCCCcc
Confidence 46789999999986555 35666666664
No 191
>KOG1493 consensus Anaphase-promoting complex (APC), subunit 11 [Cell cycle control, cell division, chromosome partitioning; Posttranslational modification, protein turnover, chaperones]
Probab=54.09 E-value=3 Score=34.50 Aligned_cols=48 Identities=33% Similarity=0.648 Sum_probs=33.7
Q ss_pred cccccccccc---------CCCeEec--CCCCcccHhhHHHHHHHHhhcCCcceeccCCCCCCCCC
Q 006225 350 ECRICFSEFA---------GTDFVRL--PCHHFFCWKCMKTYLDIHISEGTVSKLQCPDAKCGGMV 404 (655)
Q Consensus 350 ~C~IC~e~~~---------~~~~~~l--~C~H~fC~~Cl~~yi~~~i~~g~~~~i~CP~~~C~~~l 404 (655)
+|.||-..|. +++...+ -|.|.|..-|+.+++...-.+ -.||. |+..+
T Consensus 22 ~CGiCRm~Fdg~Cp~Ck~PgDdCPLv~G~C~h~fh~hCI~~wl~~~tsq-----~~CPm--cRq~~ 80 (84)
T KOG1493|consen 22 TCGICRMPFDGCCPDCKLPGDDCPLVWGYCLHAFHAHCILKWLNTPTSQ-----GQCPM--CRQTW 80 (84)
T ss_pred ccceEecccCCcCCCCcCCCCCCccHHHHHHHHHHHHHHHHHhcCcccc-----ccCCc--chhee
Confidence 7888876654 3343332 589999999999998765544 36887 77654
No 192
>KOG2879 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=53.71 E-value=6.9 Score=40.36 Aligned_cols=32 Identities=28% Similarity=0.763 Sum_probs=20.7
Q ss_pred ccccCccccceeEEecCcCceeccccCeeeecccccc
Q 006225 520 DAKQCPSCKMAISRTEGCNKIVCNNCGQYFCYRCNKA 556 (655)
Q Consensus 520 ~~k~CP~C~~~iek~~Gcn~m~C~~C~~~FC~~C~~~ 556 (655)
....||-|+.+=.- -.+|- .|++.+||.|-..
T Consensus 238 ~~~~C~~Cg~~Pti---P~~~~--~C~HiyCY~Ci~t 269 (298)
T KOG2879|consen 238 SDTECPVCGEPPTI---PHVIG--KCGHIYCYYCIAT 269 (298)
T ss_pred CCceeeccCCCCCC---Ceeec--cccceeehhhhhh
Confidence 35679999854211 11222 2999999999876
No 193
>COG1997 RPL43A Ribosomal protein L37AE/L43A [Translation, ribosomal structure and biogenesis]
Probab=53.47 E-value=8.8 Score=32.74 Aligned_cols=29 Identities=21% Similarity=0.457 Sum_probs=25.2
Q ss_pred ccCCccCccccccCCcceEEccccccccc
Q 006225 602 LSCPNCRQFNAKVGNNNHMFCWACQIHYC 630 (655)
Q Consensus 602 k~CP~C~~~ieK~~GCnhm~C~~C~~~FC 630 (655)
..||.|+....|..+--.-.|.+|++.|=
T Consensus 36 ~~Cp~C~~~~VkR~a~GIW~C~kCg~~fA 64 (89)
T COG1997 36 HVCPFCGRTTVKRIATGIWKCRKCGAKFA 64 (89)
T ss_pred CcCCCCCCcceeeeccCeEEcCCCCCeec
Confidence 68999999988888888889998988773
No 194
>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=52.80 E-value=26 Score=31.74 Aligned_cols=36 Identities=22% Similarity=0.420 Sum_probs=27.1
Q ss_pred CcccccCCCCCcccccccccccccccceeecccccc
Q 006225 435 DVAYCPRCETPCIEDEEQHAQCSKCFYSFCTLCRER 470 (655)
Q Consensus 435 ~~~~CP~C~~~~~~~~~~~~~C~~C~~~fC~~C~~~ 470 (655)
+...|..|..++.........|..|++.+|..|...
T Consensus 53 ~~~~C~~C~~~fg~l~~~~~~C~~C~~~VC~~C~~~ 88 (118)
T PF02318_consen 53 GERHCARCGKPFGFLFNRGRVCVDCKHRVCKKCGVY 88 (118)
T ss_dssp CCSB-TTTS-BCSCTSTTCEEETTTTEEEETTSEEE
T ss_pred CCcchhhhCCcccccCCCCCcCCcCCccccCccCCc
Confidence 456799998876554455589999999999999875
No 195
>KOG2164 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=52.80 E-value=4.3 Score=45.31 Aligned_cols=14 Identities=43% Similarity=0.992 Sum_probs=12.2
Q ss_pred ccCeeeeccccccc
Q 006225 544 NCGQYFCYRCNKAI 557 (655)
Q Consensus 544 ~C~~~FC~~C~~~~ 557 (655)
.|||.|||-|.-.|
T Consensus 203 ~CGHiFC~~CiLqy 216 (513)
T KOG2164|consen 203 NCGHIFCGPCILQY 216 (513)
T ss_pred ccCceeeHHHHHHH
Confidence 49999999998775
No 196
>PRK08665 ribonucleotide-diphosphate reductase subunit alpha; Validated
Probab=52.31 E-value=7.1 Score=46.72 Aligned_cols=27 Identities=41% Similarity=1.096 Sum_probs=23.9
Q ss_pred ccCccccceeEEecCcCceeccccCeeee
Q 006225 522 KQCPSCKMAISRTEGCNKIVCNNCGQYFC 550 (655)
Q Consensus 522 k~CP~C~~~iek~~Gcn~m~C~~C~~~FC 550 (655)
..||.|+..++..+||. +|..||+.=|
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 46999999999999996 8999998766
No 197
>PF06827 zf-FPG_IleRS: Zinc finger found in FPG and IleRS; InterPro: IPR010663 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents a zinc finger domain found at the C-terminal in both DNA glycosylase/AP lyase enzymes and in isoleucyl tRNA synthetase. In these two types of enzymes, the C-terminal domain forms a zinc finger. Some related proteins may not bind zinc. DNA glycosylase/AP lyase enzymes are involved in base excision repair of DNA damaged by oxidation or by mutagenic agents. These enzymes have both DNA glycosylase activity (3.2.2 from EC) and AP lyase activity (4.2.99.18 from EC) []. Examples include formamidopyrimidine-DNA glycosylases (Fpg; MutM) and endonuclease VIII (Nei). Formamidopyrimidine-DNA glycosylases (Fpg, MutM) is a trifunctional DNA base excision repair enzyme that removes a wide range of oxidation-damaged bases (N-glycosylase activity; 3.2.2.23 from EC) and cleaves both the 3'- and 5'-phosphodiester bonds of the resulting apurinic/apyrimidinic site (AP lyase activity; 4.2.99.18 from EC). Fpg has a preference for oxidised purines, excising oxidized purine bases such as 7,8-dihydro-8-oxoguanine (8-oxoG). ITs AP (apurinic/apyrimidinic) lyase activity introduces nicks in the DNA strand, cleaving the DNA backbone by beta-delta elimination to generate a single-strand break at the site of the removed base with both 3'- and 5'-phosphates. Fpg is a monomer composed of 2 domains connected by a flexible hinge []. The two DNA-binding motifs (a zinc finger and the helix-two-turns-helix motifs) suggest that the oxidized base is flipped out from double-stranded DNA in the binding mode and excised by a catalytic mechanism similar to that of bifunctional base excision repair enzymes []. Fpg binds one ion of zinc at the C terminus, which contains four conserved and essential cysteines []. Endonuclease VIII (Nei) has the same enzyme activities as Fpg above, but with a preference for oxidized pyrimidines, such as thymine glycol, 5,6-dihydrouracil and 5,6-dihydrothymine [, ]. An Fpg-type zinc finger is also found at the C terminus of isoleucyl tRNA synthetase (6.1.1.5 from EC) [, ]. This enzyme catalyses the attachment of isoleucine to tRNA(Ile). As IleRS can inadvertently accommodate and process structurally similar amino acids such as valine, to avoid such errors it has two additional distinct tRNA(Ile)-dependent editing activities. One activity is designated as 'pre-transfer' editing and involves the hydrolysis of activated Val-AMP. The other activity is designated 'post-transfer' editing and involves deacylation of mischarged Val-tRNA(Ile) []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003824 catalytic activity; PDB: 1K82_C 1Q39_A 2OQ4_B 2OPF_A 1K3X_A 1K3W_A 1Q3B_A 2EA0_A 1Q3C_A 2XZF_A ....
Probab=51.62 E-value=12 Score=25.12 Aligned_cols=25 Identities=24% Similarity=0.757 Sum_probs=15.4
Q ss_pred ccCCccCcccccc--CCcceEEccccc
Q 006225 602 LSCPNCRQFNAKV--GNNNHMFCWACQ 626 (655)
Q Consensus 602 k~CP~C~~~ieK~--~GCnhm~C~~C~ 626 (655)
.+||.|+.+|++. ++=+...|.+|.
T Consensus 2 ~~C~rC~~~~~~~~~~~r~~~~C~rCq 28 (30)
T PF06827_consen 2 EKCPRCWNYIEDIGINGRSTYLCPRCQ 28 (30)
T ss_dssp SB-TTT--BBEEEEETTEEEEE-TTTC
T ss_pred CcCccCCCcceEeEecCCCCeECcCCc
Confidence 5899999998766 455667787775
No 198
>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]
Probab=51.44 E-value=9.9 Score=45.13 Aligned_cols=35 Identities=23% Similarity=0.780 Sum_probs=31.1
Q ss_pred ccCccccceeEEecCcCceeccccCee-----eecccccc
Q 006225 522 KQCPSCKMAISRTEGCNKIVCNNCGQY-----FCYRCNKA 556 (655)
Q Consensus 522 k~CP~C~~~iek~~Gcn~m~C~~C~~~-----FC~~C~~~ 556 (655)
-.||+|..++.-...-+.|.|..||++ .|..|+..
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 469999999988777799999999987 89999987
No 199
>PRK14892 putative transcription elongation factor Elf1; Provisional
Probab=51.36 E-value=10 Score=33.44 Aligned_cols=30 Identities=30% Similarity=0.668 Sum_probs=20.9
Q ss_pred ccccCccccceeE---EecCcCceeccccCeee
Q 006225 520 DAKQCPSCKMAIS---RTEGCNKIVCNNCGQYF 549 (655)
Q Consensus 520 ~~k~CP~C~~~ie---k~~Gcn~m~C~~C~~~F 549 (655)
+...||+|+.... ...|--|..|+.||+.+
T Consensus 20 t~f~CP~Cge~~v~v~~~k~~~h~~C~~CG~y~ 52 (99)
T PRK14892 20 KIFECPRCGKVSISVKIKKNIAIITCGNCGLYT 52 (99)
T ss_pred cEeECCCCCCeEeeeecCCCcceEECCCCCCcc
Confidence 4677999994332 23356688899898765
No 200
>PRK08665 ribonucleotide-diphosphate reductase subunit alpha; Validated
Probab=50.14 E-value=8.3 Score=46.19 Aligned_cols=27 Identities=22% Similarity=0.625 Sum_probs=24.4
Q ss_pred ccCCccCccccccCCcceEEccccccccc
Q 006225 602 LSCPNCRQFNAKVGNNNHMFCWACQIHYC 630 (655)
Q Consensus 602 k~CP~C~~~ieK~~GCnhm~C~~C~~~FC 630 (655)
..||.|+..+...+||. +|..||+.-|
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 46999999999999998 8999999877
No 201
>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=50.06 E-value=14 Score=28.37 Aligned_cols=30 Identities=20% Similarity=0.337 Sum_probs=18.0
Q ss_pred ccCCccCcccc------ccCCcceE-Ecccccccccc
Q 006225 602 LSCPNCRQFNA------KVGNNNHM-FCWACQIHYCY 631 (655)
Q Consensus 602 k~CP~C~~~ie------K~~GCnhm-~C~~C~~~FC~ 631 (655)
++||.|+..-+ .+.+..++ .|..|+....+
T Consensus 2 kPCPfCGg~~~~~~~~~~~~~~~~~~~C~~Cga~~~~ 38 (53)
T TIGR03655 2 KPCPFCGGADVYLRRGFDPLDLSHYFECSTCGASGPV 38 (53)
T ss_pred CCCCCCCCcceeeEeccCCCCCEEEEECCCCCCCccc
Confidence 79999995433 22234443 47777766543
No 202
>PRK14892 putative transcription elongation factor Elf1; Provisional
Probab=49.93 E-value=11 Score=33.16 Aligned_cols=31 Identities=19% Similarity=0.432 Sum_probs=21.7
Q ss_pred ccCccCCccCccc---cccCCcceEEcccccccc
Q 006225 599 EHGLSCPNCRQFN---AKVGNNNHMFCWACQIHY 629 (655)
Q Consensus 599 ~~~k~CP~C~~~i---eK~~GCnhm~C~~C~~~F 629 (655)
.+...||+|+... ....|=-|..|.+||+.|
T Consensus 19 pt~f~CP~Cge~~v~v~~~k~~~h~~C~~CG~y~ 52 (99)
T PRK14892 19 PKIFECPRCGKVSISVKIKKNIAIITCGNCGLYT 52 (99)
T ss_pred CcEeECCCCCCeEeeeecCCCcceEECCCCCCcc
Confidence 3457899999322 222366799999999875
No 203
>PF08792 A2L_zn_ribbon: A2L zinc ribbon domain; InterPro: IPR014900 This zinc ribbon protein is found associated with some viral A2L transcription factors [].
Probab=49.89 E-value=12 Score=26.09 Aligned_cols=29 Identities=28% Similarity=0.563 Sum_probs=21.3
Q ss_pred CcccccCCCCCccc-cccccccccccccee
Q 006225 435 DVAYCPRCETPCIE-DEEQHAQCSKCFYSF 463 (655)
Q Consensus 435 ~~~~CP~C~~~~~~-~~~~~~~C~~C~~~f 463 (655)
+...|+.|+...+. .......|+.|+..|
T Consensus 2 ~~~~C~~C~~~~i~~~~~~~~~C~~Cg~~~ 31 (33)
T PF08792_consen 2 NLKKCSKCGGNGIVNKEDDYEVCIFCGSSF 31 (33)
T ss_pred CceEcCCCCCCeEEEecCCeEEcccCCcEe
Confidence 34579999988766 666677888887664
No 204
>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=49.75 E-value=11 Score=24.32 Aligned_cols=23 Identities=26% Similarity=0.716 Sum_probs=14.3
Q ss_pred ccCCCCCccccc-ccccccccccc
Q 006225 439 CPRCETPCIEDE-EQHAQCSKCFY 461 (655)
Q Consensus 439 CP~C~~~~~~~~-~~~~~C~~C~~ 461 (655)
|-.|+..+...+ ...+.||.||+
T Consensus 1 C~sC~~~i~~r~~~v~f~CPnCG~ 24 (24)
T PF07754_consen 1 CTSCGRPIAPREQAVPFPCPNCGF 24 (24)
T ss_pred CccCCCcccCcccCceEeCCCCCC
Confidence 445665554433 56788888874
No 205
>KOG0418 consensus Ubiquitin-protein ligase [Posttranslational modification, protein turnover, chaperones]
Probab=49.62 E-value=34 Score=33.46 Aligned_cols=42 Identities=21% Similarity=0.400 Sum_probs=29.2
Q ss_pred EEEEEEcCCCCCCCCCCeEEeec----ccCCHHHHHHHHHHHHHHHH
Q 006225 232 IVLTCLLPKSYPSHLPPYFTISA----RWLNSTKISNLCSMLESIWI 274 (655)
Q Consensus 232 i~L~~~lP~~YPs~~pP~~~l~s----~wL~~~~l~~L~~~L~~~~e 274 (655)
+.|.+.+|++||-. ||.+.... +.++......-.+.|.+.|.
T Consensus 55 FeldI~iPe~YPF~-pPkv~F~TkIwHPnVSs~tGaICLDilkd~Wa 100 (200)
T KOG0418|consen 55 FELDIKIPENYPFK-PPKVKFITKIWHPNVSSQTGAICLDILKDQWA 100 (200)
T ss_pred EEEEEecCCCCCCC-CCceeeeeeeecCCCCcccccchhhhhhcccc
Confidence 88999999999998 88664332 33554444444566777886
No 206
>PF14570 zf-RING_4: RING/Ubox like zinc-binding domain; PDB: 1E4U_A 1UR6_B.
Probab=48.82 E-value=7.3 Score=29.55 Aligned_cols=30 Identities=27% Similarity=0.886 Sum_probs=15.5
Q ss_pred ccCCCCCcccccccccccccccceeeccccc
Q 006225 439 CPRCETPCIEDEEQHAQCSKCFYSFCTLCRE 469 (655)
Q Consensus 439 CP~C~~~~~~~~~~~~~C~~C~~~fC~~C~~ 469 (655)
||.|...+........-| .|++.+|..|+.
T Consensus 1 cp~C~e~~d~~d~~~~PC-~Cgf~IC~~C~~ 30 (48)
T PF14570_consen 1 CPLCDEELDETDKDFYPC-ECGFQICRFCYH 30 (48)
T ss_dssp -TTTS-B--CCCTT--SS-TTS----HHHHH
T ss_pred CCCcccccccCCCccccC-cCCCcHHHHHHH
Confidence 678877775555567788 799999999976
No 207
>KOG3002 consensus Zn finger protein [General function prediction only]
Probab=48.72 E-value=12 Score=39.55 Aligned_cols=46 Identities=20% Similarity=0.563 Sum_probs=33.4
Q ss_pred ccccccccccccccCCCeEecCCCCcccHhhHHHHHHHHhhcCCcceeccCCCCCCCCCC
Q 006225 346 KSFHECRICFSEFAGTDFVRLPCHHFFCWKCMKTYLDIHISEGTVSKLQCPDAKCGGMVP 405 (655)
Q Consensus 346 ~~~~~C~IC~e~~~~~~~~~l~C~H~fC~~Cl~~yi~~~i~~g~~~~i~CP~~~C~~~l~ 405 (655)
...++|+||++.+.. ..+..+=||..|..|-.+- .-+||. |...+.
T Consensus 46 ~~lleCPvC~~~l~~-Pi~QC~nGHlaCssC~~~~-----------~~~CP~--Cr~~~g 91 (299)
T KOG3002|consen 46 LDLLDCPVCFNPLSP-PIFQCDNGHLACSSCRTKV-----------SNKCPT--CRLPIG 91 (299)
T ss_pred hhhccCchhhccCcc-cceecCCCcEehhhhhhhh-----------cccCCc--cccccc
Confidence 355899999998753 2233344899999998742 468998 988877
No 208
>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=48.67 E-value=11 Score=33.17 Aligned_cols=26 Identities=19% Similarity=0.479 Sum_probs=20.2
Q ss_pred cCCccCccccccCCcceEEccccccccc
Q 006225 603 SCPNCRQFNAKVGNNNHMFCWACQIHYC 630 (655)
Q Consensus 603 ~CP~C~~~ieK~~GCnhm~C~~C~~~FC 630 (655)
-||.|+.++...+ +.+.|..|++.+=
T Consensus 2 fC~~Cg~~l~~~~--~~~~C~~C~~~~~ 27 (104)
T TIGR01384 2 FCPKCGSLMTPKN--GVYVCPSCGYEKE 27 (104)
T ss_pred CCcccCcccccCC--CeEECcCCCCccc
Confidence 5999998886654 4889999997643
No 209
>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=48.39 E-value=9.5 Score=33.58 Aligned_cols=26 Identities=31% Similarity=0.705 Sum_probs=19.4
Q ss_pred ccCccccceeEEecCcCceeccccCeee
Q 006225 522 KQCPSCKMAISRTEGCNKIVCNNCGQYF 549 (655)
Q Consensus 522 k~CP~C~~~iek~~Gcn~m~C~~C~~~F 549 (655)
+.||.|+.++...+ +.+.|+.|++.+
T Consensus 1 ~fC~~Cg~~l~~~~--~~~~C~~C~~~~ 26 (104)
T TIGR01384 1 KFCPKCGSLMTPKN--GVYVCPSCGYEK 26 (104)
T ss_pred CCCcccCcccccCC--CeEECcCCCCcc
Confidence 37999999986643 468888887653
No 210
>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=48.15 E-value=16 Score=26.80 Aligned_cols=25 Identities=36% Similarity=0.868 Sum_probs=15.0
Q ss_pred cCccccce-eEEecCcCceeccccCe
Q 006225 523 QCPSCKMA-ISRTEGCNKIVCNNCGQ 547 (655)
Q Consensus 523 ~CP~C~~~-iek~~Gcn~m~C~~C~~ 547 (655)
.||.|+.. +.-+..-..+.|+.||.
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 59999875 34444444566776654
No 211
>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=47.88 E-value=14 Score=32.90 Aligned_cols=27 Identities=22% Similarity=0.765 Sum_probs=20.4
Q ss_pred ccCccccceeEEecCcCceeccccCeee
Q 006225 522 KQCPSCKMAISRTEGCNKIVCNNCGQYF 549 (655)
Q Consensus 522 k~CP~C~~~iek~~Gcn~m~C~~C~~~F 549 (655)
-.||.|.....-.+|- .+.|+.|++.|
T Consensus 3 p~CP~C~seytY~dg~-~~iCpeC~~EW 29 (109)
T TIGR00686 3 PPCPKCNSEYTYHDGT-QLICPSCLYEW 29 (109)
T ss_pred CcCCcCCCcceEecCC-eeECccccccc
Confidence 5799999888777774 47788777654
No 212
>KOG0417 consensus Ubiquitin-protein ligase [Posttranslational modification, protein turnover, chaperones]
Probab=47.65 E-value=76 Score=29.98 Aligned_cols=21 Identities=29% Similarity=0.610 Sum_probs=18.1
Q ss_pred EEEEEEcCCCCCCCCCCeEEee
Q 006225 232 IVLTCLLPKSYPSHLPPYFTIS 253 (655)
Q Consensus 232 i~L~~~lP~~YPs~~pP~~~l~ 253 (655)
+.|.+.||+.||.. ||.+...
T Consensus 50 F~l~I~~p~~YP~~-PPkV~F~ 70 (148)
T KOG0417|consen 50 FFLEIHFPEDYPFK-PPKVRFL 70 (148)
T ss_pred EEEEEECCCCCCCC-CCceEee
Confidence 88999999999998 9977544
No 213
>KOG2906 consensus RNA polymerase III subunit C11 [Transcription]
Probab=47.63 E-value=11 Score=32.83 Aligned_cols=30 Identities=20% Similarity=0.483 Sum_probs=23.4
Q ss_pred cCCccCc--cccccCCcceEEccccccccccc
Q 006225 603 SCPNCRQ--FNAKVGNNNHMFCWACQIHYCYL 632 (655)
Q Consensus 603 ~CP~C~~--~ieK~~GCnhm~C~~C~~~FC~~ 632 (655)
-||.|+. .|++-+.||-..|..|.+.|=..
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 4999995 45666678999999999887444
No 214
>COG5222 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=47.43 E-value=23 Score=36.87 Aligned_cols=44 Identities=30% Similarity=0.754 Sum_probs=31.0
Q ss_pred cccccccccccCCCeEecCCCCcccHhhHHHHHHHHhhcCCcceeccCCCCCCC
Q 006225 349 HECRICFSEFAGTDFVRLPCHHFFCWKCMKTYLDIHISEGTVSKLQCPDAKCGG 402 (655)
Q Consensus 349 ~~C~IC~e~~~~~~~~~l~C~H~fC~~Cl~~yi~~~i~~g~~~~i~CP~~~C~~ 402 (655)
+.|++|-.-.. +.+-+-.|+|.||.+|+..-+. + ..+.||. |..
T Consensus 275 LkCplc~~Llr-np~kT~cC~~~fc~eci~~al~----d---sDf~Cpn--C~r 318 (427)
T COG5222 275 LKCPLCHCLLR-NPMKTPCCGHTFCDECIGTALL----D---SDFKCPN--CSR 318 (427)
T ss_pred ccCcchhhhhh-CcccCccccchHHHHHHhhhhh----h---ccccCCC--ccc
Confidence 67999976643 2233347999999999987543 2 2588998 765
No 215
>COG5175 MOT2 Transcriptional repressor [Transcription]
Probab=47.33 E-value=11 Score=39.82 Aligned_cols=42 Identities=26% Similarity=0.694 Sum_probs=32.3
Q ss_pred ccccCCCCCcccccccccccccccceeeccccccccC--CcCCCc
Q 006225 437 AYCPRCETPCIEDEEQHAQCSKCFYSFCTLCRERRHV--GVVCMT 479 (655)
Q Consensus 437 ~~CP~C~~~~~~~~~~~~~C~~C~~~fC~~C~~~~H~--~~sC~~ 479 (655)
-|||-|..++...+...+-| .||+..|..||..... ...|+.
T Consensus 15 d~cplcie~mditdknf~pc-~cgy~ic~fc~~~irq~lngrcpa 58 (480)
T COG5175 15 DYCPLCIEPMDITDKNFFPC-PCGYQICQFCYNNIRQNLNGRCPA 58 (480)
T ss_pred ccCcccccccccccCCcccC-CcccHHHHHHHHHHHhhccCCChH
Confidence 46999999987777788889 5999999999874322 235764
No 216
>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=47.26 E-value=29 Score=25.81 Aligned_cols=29 Identities=24% Similarity=0.671 Sum_probs=20.2
Q ss_pred ccCccCCccCcc-ccccCCcceEEcccccc
Q 006225 599 EHGLSCPNCRQF-NAKVGNNNHMFCWACQI 627 (655)
Q Consensus 599 ~~~k~CP~C~~~-ieK~~GCnhm~C~~C~~ 627 (655)
.++..||+|+.. +....+=....|..|++
T Consensus 16 ~~g~~CP~Cg~~~~~~~~~~~~~~C~~C~~ 45 (46)
T PF12760_consen 16 PDGFVCPHCGSTKHYRLKTRGRYRCKACRK 45 (46)
T ss_pred CCCCCCCCCCCeeeEEeCCCCeEECCCCCC
Confidence 456779999963 44444556788888875
No 217
>PLN03208 E3 ubiquitin-protein ligase RMA2; Provisional
Probab=46.43 E-value=7.5 Score=38.34 Aligned_cols=32 Identities=16% Similarity=0.404 Sum_probs=24.2
Q ss_pred CccCCccCccccccCCcceEEccccccccccccccccc
Q 006225 601 GLSCPNCRQFNAKVGNNNHMFCWACQIHYCYLCKKIVR 638 (655)
Q Consensus 601 ~k~CP~C~~~ieK~~GCnhm~C~~C~~~FC~~C~~~~~ 638 (655)
...||-|...+..- .+ ..||+.|||.|...|.
T Consensus 18 ~~~CpICld~~~dP----Vv--T~CGH~FC~~CI~~wl 49 (193)
T PLN03208 18 DFDCNICLDQVRDP----VV--TLCGHLFCWPCIHKWT 49 (193)
T ss_pred ccCCccCCCcCCCc----EE--cCCCchhHHHHHHHHH
Confidence 46899998765321 22 3699999999999985
No 218
>PF12861 zf-Apc11: Anaphase-promoting complex subunit 11 RING-H2 finger
Probab=46.34 E-value=8.3 Score=32.90 Aligned_cols=31 Identities=26% Similarity=0.704 Sum_probs=20.5
Q ss_pred cCccccceeEEecCcCceeccccCeeeeccccccc
Q 006225 523 QCPSCKMAISRTEGCNKIVCNNCGQYFCYRCNKAI 557 (655)
Q Consensus 523 ~CP~C~~~iek~~Gcn~m~C~~C~~~FC~~C~~~~ 557 (655)
-||.|+.+ .+.|..+.+. |++.|=..|...|
T Consensus 34 ~Cp~Ck~P---gd~Cplv~g~-C~H~FH~hCI~kW 64 (85)
T PF12861_consen 34 CCPDCKFP---GDDCPLVWGK-CSHNFHMHCILKW 64 (85)
T ss_pred CCCCccCC---CCCCceeecc-CccHHHHHHHHHH
Confidence 46777665 3456666665 8888877776666
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=46.29 E-value=20 Score=27.97 Aligned_cols=30 Identities=23% Similarity=0.651 Sum_probs=21.9
Q ss_pred ccCccccceeEEecCc--CceeccccCeeeec
Q 006225 522 KQCPSCKMAISRTEGC--NKIVCNNCGQYFCY 551 (655)
Q Consensus 522 k~CP~C~~~iek~~Gc--n~m~C~~C~~~FC~ 551 (655)
..||.|+..|+..+.- -.+.|+.||..+=.
T Consensus 3 ~~CP~CG~~iev~~~~~GeiV~Cp~CGaeleV 34 (54)
T TIGR01206 3 FECPDCGAEIELENPELGELVICDECGAELEV 34 (54)
T ss_pred cCCCCCCCEEecCCCccCCEEeCCCCCCEEEE
Confidence 4799999999875421 46789888877643
No 220
>PF06113 BRE: Brain and reproductive organ-expressed protein (BRE); InterPro: IPR010358 This family consists of several eukaryotic brain and reproductive organ-expressed (BRE) proteins. BRE is a putative stress-modulating gene, found able to down-regulate TNF-alpha-induced-NF-kappaB activation upon over expression. A total of six isoforms are produced by alternative splicing predominantly at either end of the gene. Compared to normal cells, immortalised human cell lines uniformly express higher levels of BRE. Peripheral blood monocytes respond to LPS by down-regulating the expression of all the BRE isoforms. It is thought that the function of BRE and its isoforms is to regulate peroxisomal activities [].
Probab=46.18 E-value=71 Score=34.28 Aligned_cols=68 Identities=22% Similarity=0.362 Sum_probs=43.6
Q ss_pred hhhchHHHHHHHHHHHHHhcCCCeeeeccCCCCceEEEEEeeccCCCceEEeecCCCCccccCCCCCCCcccccccccCC
Q 006225 151 QLRINDQSQGDELLALESIYGDSVFILDRQRDLRSCQIHVHVETLDGLTVTAKLNSSTDLDARSESSDDFSYSFKVQYLP 230 (655)
Q Consensus 151 ~~~~n~e~Q~~EleaLeSIY~d~~~~~~~~~~~~~f~i~i~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~v~~LP 230 (655)
+...+.+...+=|+||-+.||......+.. .|+ . +++-... +++
T Consensus 263 ~~v~~~~~RrefI~al~~~fg~~vLE~D~~----~~~---------k--~s~L~~~-----------~~F---------- 306 (333)
T PF06113_consen 263 EVVQSIKKRREFIEALLSHFGRPVLEYDAE----FFR---------K--ISFLLES-----------GDF---------- 306 (333)
T ss_pred HHHHHHHHHHHHHHHHHHhcCCcceeeccc----ccc---------h--hhHHhhc-----------CCe----------
Confidence 355677788888999999999875443321 111 0 1111000 111
Q ss_pred cEEEEEEcCCCCCCCCCCeEEeecc
Q 006225 231 PIVLTCLLPKSYPSHLPPYFTISAR 255 (655)
Q Consensus 231 pi~L~~~lP~~YPs~~pP~~~l~s~ 255 (655)
-+.++|.||..+|.+ .|.+++.|.
T Consensus 307 ~flvHi~Lp~~FP~~-qP~ltlqS~ 330 (333)
T PF06113_consen 307 TFLVHISLPIQFPKD-QPSLTLQSV 330 (333)
T ss_pred EEEEEEeccCCCCCc-CCeEEEEee
Confidence 178999999999998 999998764
No 221
>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=46.08 E-value=18 Score=29.16 Aligned_cols=36 Identities=28% Similarity=0.627 Sum_probs=19.9
Q ss_pred ccccCccccceeEEecCcCceeccccCeeeeccccccc
Q 006225 520 DAKQCPSCKMAISRTEGCNKIVCNNCGQYFCYRCNKAI 557 (655)
Q Consensus 520 ~~k~CP~C~~~iek~~Gcn~m~C~~C~~~FC~~C~~~~ 557 (655)
....|+.|+..+.. --..-.|..||..||..|....
T Consensus 8 ~~~~C~~C~~~F~~--~~rrhhCr~CG~~vC~~Cs~~~ 43 (69)
T PF01363_consen 8 EASNCMICGKKFSL--FRRRHHCRNCGRVVCSSCSSQR 43 (69)
T ss_dssp G-SB-TTT--B-BS--SS-EEE-TTT--EEECCCS-EE
T ss_pred CCCcCcCcCCcCCC--ceeeEccCCCCCEECCchhCCE
Confidence 35789999988732 3455779999999999998765
No 222
>PF08694 UFC1: Ubiquitin-fold modifier-conjugating enzyme 1; InterPro: IPR014806 Ubiquitin-like (UBL) post-translational modifiers are covalently linked to most, if not all, target protein(s) through an enzymatic cascade analogous to ubiquitylation, consisting of E1 (activating), E2 (conjugating), and E3 (ligating) enzymes. Ubiquitin-fold modifier 1 (Ufm1) a ubiquitin-like protein is activated by a novel E1-like enzyme, Uba5, by forming a high-energy thioester bond. Activated Ufm1 is then transferred to its cognate E2-like enzyme, Ufc1, in a similar thioester linkage. This family represents the E2-like enzyme [].; PDB: 2Z6P_A 2K07_A 2Z6O_A 3EVX_D 3KPA_A.
Probab=46.06 E-value=13 Score=34.51 Aligned_cols=21 Identities=24% Similarity=0.540 Sum_probs=12.4
Q ss_pred EEEEEEcCCCCCCCCCCeEEee
Q 006225 232 IVLTCLLPKSYPSHLPPYFTIS 253 (655)
Q Consensus 232 i~L~~~lP~~YPs~~pP~~~l~ 253 (655)
+.|.|.+|.+||.. ||.+.|-
T Consensus 77 F~~eFdIP~tYP~t-~pEi~lP 97 (161)
T PF08694_consen 77 FDLEFDIPVTYPTT-APEIALP 97 (161)
T ss_dssp EEEEEE--TTTTTS-----B-G
T ss_pred EeeecCCCccCCCC-Ccceecc
Confidence 88999999999998 8888763
No 223
>PF14369 zf-RING_3: zinc-finger
Probab=45.94 E-value=18 Score=25.49 Aligned_cols=28 Identities=18% Similarity=0.447 Sum_probs=18.9
Q ss_pred ccCccccceeEEec-CcCceeccccCeee
Q 006225 522 KQCPSCKMAISRTE-GCNKIVCNNCGQYF 549 (655)
Q Consensus 522 k~CP~C~~~iek~~-Gcn~m~C~~C~~~F 549 (655)
-||-.|...|.... +-..+.|+.|+-.|
T Consensus 3 ywCh~C~~~V~~~~~~~~~~~CP~C~~gF 31 (35)
T PF14369_consen 3 YWCHQCNRFVRIAPSPDSDVACPRCHGGF 31 (35)
T ss_pred EeCccCCCEeEeCcCCCCCcCCcCCCCcE
Confidence 47888988887642 33334588887766
No 224
>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=45.57 E-value=12 Score=34.27 Aligned_cols=28 Identities=14% Similarity=0.157 Sum_probs=21.3
Q ss_pred cccccCCCCCccccccccccccccccee
Q 006225 436 VAYCPRCETPCIEDEEQHAQCSKCFYSF 463 (655)
Q Consensus 436 ~~~CP~C~~~~~~~~~~~~~C~~C~~~f 463 (655)
...||.|+.-+.--+..-+.||+||..|
T Consensus 9 Kr~Cp~cg~kFYDLnk~p~vcP~cg~~~ 36 (129)
T TIGR02300 9 KRICPNTGSKFYDLNRRPAVSPYTGEQF 36 (129)
T ss_pred cccCCCcCccccccCCCCccCCCcCCcc
Confidence 3469999987765555778899988876
No 225
>PF14569 zf-UDP: Zinc-binding RING-finger; PDB: 1WEO_A.
Probab=45.57 E-value=16 Score=30.54 Aligned_cols=35 Identities=26% Similarity=0.656 Sum_probs=14.4
Q ss_pred CcccccCCCCCcc--cccccccccccccceeeccccc
Q 006225 435 DVAYCPRCETPCI--EDEEQHAQCSKCFYSFCTLCRE 469 (655)
Q Consensus 435 ~~~~CP~C~~~~~--~~~~~~~~C~~C~~~fC~~C~~ 469 (655)
+...|-.|+..+- .+....+.|..|++..|..|..
T Consensus 8 ~~qiCqiCGD~VGl~~~Ge~FVAC~eC~fPvCr~CyE 44 (80)
T PF14569_consen 8 NGQICQICGDDVGLTENGEVFVACHECAFPVCRPCYE 44 (80)
T ss_dssp SS-B-SSS--B--B-SSSSB--S-SSS-----HHHHH
T ss_pred CCcccccccCccccCCCCCEEEEEcccCCccchhHHH
Confidence 3456888887664 3456788999999999988743
No 226
>KOG3799 consensus Rab3 effector RIM1 and related proteins, contain Rab3a binding domain [Intracellular trafficking, secretion, and vesicular transport]
Probab=45.01 E-value=7.6 Score=35.65 Aligned_cols=36 Identities=25% Similarity=0.544 Sum_probs=26.8
Q ss_pred ccCCccCccccccCCcceEEcccccccccccccccccc
Q 006225 602 LSCPNCRQFNAKVGNNNHMFCWACQIHYCYLCKKIVRR 639 (655)
Q Consensus 602 k~CP~C~~~ieK~~GCnhm~C~~C~~~FC~~C~~~~~~ 639 (655)
-.|--|+..- -.+||-| .|..|...||-+||+.+.-
T Consensus 66 atC~IC~KTK-FADG~GH-~C~YCq~r~CARCGGrv~l 101 (169)
T KOG3799|consen 66 ATCGICHKTK-FADGCGH-NCSYCQTRFCARCGGRVSL 101 (169)
T ss_pred cchhhhhhcc-cccccCc-ccchhhhhHHHhcCCeeee
Confidence 3465665321 1479999 7989999999999998873
No 227
>cd00194 UBA Ubiquitin Associated domain. The UBA domain is a commonly occurring sequence motif in some members of the ubiquitination pathway, UV excision repair proteins, and certain protein kinases. Although its specific role is so far unknown, it has been suggested that UBA domains are involved in conferring protein target specificity. The domain, a compact three helix bundle, has a conserved GFP-loop and the proline is thought to be critical for binding. The UBA domain is distinct from the conserved three helical domain seen in the N-terminus of EF-TS and eukaryotic NAC proteins.
Probab=45.00 E-value=18 Score=25.34 Aligned_cols=25 Identities=36% Similarity=0.327 Sum_probs=19.1
Q ss_pred hhhhhhhcccCCC----------CCCChhhHHHHH
Q 006225 111 EVKEKQDEEEGLP----------SNSNVNDVESIL 135 (655)
Q Consensus 111 ~~~~~~~~~~~~~----------~~~~~~~~~~~~ 135 (655)
+.++.+|.+.||+ .++|.++|++.|
T Consensus 2 ~~~v~~L~~mGf~~~~~~~AL~~~~~d~~~A~~~L 36 (38)
T cd00194 2 EEKLEQLLEMGFSREEARKALRATNNNVERAVEWL 36 (38)
T ss_pred HHHHHHHHHcCCCHHHHHHHHHHhCCCHHHHHHHH
Confidence 3467788899997 777888877655
No 228
>COG5236 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=44.92 E-value=23 Score=37.66 Aligned_cols=53 Identities=23% Similarity=0.481 Sum_probs=35.1
Q ss_pred cccccccccccccccCCCeEecCCCCcccHhhHHHHHHHHhhcCCcceeccCCCCCCCCCCcc
Q 006225 345 LKSFHECRICFSEFAGTDFVRLPCHHFFCWKCMKTYLDIHISEGTVSKLQCPDAKCGGMVPPS 407 (655)
Q Consensus 345 ~~~~~~C~IC~e~~~~~~~~~l~C~H~fC~~Cl~~yi~~~i~~g~~~~i~CP~~~C~~~l~~~ 407 (655)
..+...|.||-+... -...++|+|..|.-|-...-. +- ..-.||. |+.....-
T Consensus 58 DEen~~C~ICA~~~T--Ys~~~PC~H~~CH~Ca~RlRA--LY----~~K~C~~--CrTE~e~V 110 (493)
T COG5236 58 DEENMNCQICAGSTT--YSARYPCGHQICHACAVRLRA--LY----MQKGCPL--CRTETEAV 110 (493)
T ss_pred ccccceeEEecCCce--EEEeccCCchHHHHHHHHHHH--HH----hccCCCc--cccccceE
Confidence 445678999988753 233469999999999776422 21 2346887 88754433
No 229
>KOG0801 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=44.69 E-value=8 Score=36.66 Aligned_cols=38 Identities=29% Similarity=0.631 Sum_probs=26.2
Q ss_pred hccchhhhhhhccccccccccccccccC-CCeEecCCCCcccH
Q 006225 333 RSYNHERCHENFLKSFHECRICFSEFAG-TDFVRLPCHHFFCW 374 (655)
Q Consensus 333 ~~~n~~~~~~~f~~~~~~C~IC~e~~~~-~~~~~l~C~H~fC~ 374 (655)
.+||++- .....-+|.||++++.. +.+.+|+|-.+|.+
T Consensus 166 lsYNdDV----L~ddkGECvICLEdL~~GdtIARLPCLCIYHK 204 (205)
T KOG0801|consen 166 LSYNDDV----LKDDKGECVICLEDLEAGDTIARLPCLCIYHK 204 (205)
T ss_pred cccccch----hcccCCcEEEEhhhccCCCceeccceEEEeec
Confidence 4677642 33445799999999874 44666899776653
No 230
>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=44.11 E-value=17 Score=37.24 Aligned_cols=90 Identities=19% Similarity=0.498 Sum_probs=55.8
Q ss_pred ccccccccccc------CCCeEecCCCCc-ccHhhHHHHHHHHhhcCCcceeccCCCCCCCCCCcccccc-cCChHHHHH
Q 006225 349 HECRICFSEFA------GTDFVRLPCHHF-FCWKCMKTYLDIHISEGTVSKLQCPDAKCGGMVPPSLLKK-LLGDEEFER 420 (655)
Q Consensus 349 ~~C~IC~e~~~------~~~~~~l~C~H~-fC~~Cl~~yi~~~i~~g~~~~i~CP~~~C~~~l~~~~i~~-ll~~e~~er 420 (655)
..|..|-|-.+ +...++.+|+.. .|+. ....|.||-++|+..|....... -+++...
T Consensus 86 VkC~~CnEATPIr~aPpGKKYVRCPCNCLLICk~-------------sS~rIaCPRp~CkRiI~L~~~~~~p~~~~~~-- 150 (256)
T PF09788_consen 86 VKCSVCNEATPIRNAPPGKKYVRCPCNCLLICKS-------------SSQRIACPRPNCKRIINLGPSHQGPVTPPVP-- 150 (256)
T ss_pred EECCCCCccccccCCCCCCeeEecCCceEEEeec-------------ccccccCCCCCCcceEEeCCccCCCCCCCCC--
Confidence 57999988754 456777888764 5652 22369999999999887665522 1111110
Q ss_pred HHHHHHHHHhhcCCCcccccCCCCCcccc---cccccccccccce
Q 006225 421 WESLMLQKTLESMSDVAYCPRCETPCIED---EEQHAQCSKCFYS 462 (655)
Q Consensus 421 y~~~~~~~~l~~~~~~~~CP~C~~~~~~~---~~~~~~C~~C~~~ 462 (655)
-....-.+.|+.|...+..+ +...++||.|.+.
T Consensus 151 ---------~~p~~~rv~CghC~~~Fl~~~~~~~tlARCPHCrKv 186 (256)
T PF09788_consen 151 ---------TQPGSCRVICGHCSNTFLFNTLTSNTLARCPHCRKV 186 (256)
T ss_pred ---------CCCCceeEECCCCCCcEeccCCCCCccccCCCCcee
Confidence 00112357799999877543 2356788876543
No 231
>PF12906 RINGv: RING-variant domain; PDB: 2D8S_A 1VYX_A.
Probab=43.95 E-value=20 Score=26.94 Aligned_cols=33 Identities=21% Similarity=0.652 Sum_probs=22.8
Q ss_pred cccccccccCCCeEecCC--CC---cccHhhHHHHHHH
Q 006225 351 CRICFSEFAGTDFVRLPC--HH---FFCWKCMKTYLDI 383 (655)
Q Consensus 351 C~IC~e~~~~~~~~~l~C--~H---~fC~~Cl~~yi~~ 383 (655)
|-||+++.........+| .- .....||.+|+..
T Consensus 1 CrIC~~~~~~~~~li~pC~C~Gs~~~vH~~CL~~W~~~ 38 (47)
T PF12906_consen 1 CRICLEGEEEDEPLISPCRCKGSMKYVHRSCLERWIRE 38 (47)
T ss_dssp ETTTTEE-SSSS-EE-SSS-SSCCGSEECCHHHHHHHH
T ss_pred CeEeCCcCCCCCceecccccCCCcchhHHHHHHHHHHh
Confidence 779998876555444454 33 6899999999987
No 232
>smart00165 UBA Ubiquitin associated domain. Present in Rad23, SNF1-like kinases. The newly-found UBA in p62 is known to bind ubiquitin.
Probab=43.81 E-value=19 Score=25.07 Aligned_cols=25 Identities=36% Similarity=0.347 Sum_probs=18.5
Q ss_pred hhhhhhhcccCCC----------CCCChhhHHHHH
Q 006225 111 EVKEKQDEEEGLP----------SNSNVNDVESIL 135 (655)
Q Consensus 111 ~~~~~~~~~~~~~----------~~~~~~~~~~~~ 135 (655)
+.++.+|.+-||+ +++|+++|++.|
T Consensus 2 ~~~v~~L~~mGf~~~~a~~aL~~~~~d~~~A~~~L 36 (37)
T smart00165 2 EEKIDQLLEMGFSREEALKALRAANGNVERAAEYL 36 (37)
T ss_pred HHHHHHHHHcCCCHHHHHHHHHHhCCCHHHHHHHH
Confidence 4567788888997 677888776654
No 233
>PRK14714 DNA polymerase II large subunit; Provisional
Probab=43.67 E-value=13 Score=46.13 Aligned_cols=13 Identities=23% Similarity=0.583 Sum_probs=10.1
Q ss_pred CccCCccCccccc
Q 006225 601 GLSCPNCRQFNAK 613 (655)
Q Consensus 601 ~k~CP~C~~~ieK 613 (655)
...||+|+..+..
T Consensus 667 ~rkCPkCG~~t~~ 679 (1337)
T PRK14714 667 RRRCPSCGTETYE 679 (1337)
T ss_pred EEECCCCCCcccc
Confidence 4789999987654
No 234
>PF13453 zf-TFIIB: Transcription factor zinc-finger
Probab=43.55 E-value=18 Score=26.23 Aligned_cols=12 Identities=25% Similarity=0.897 Sum_probs=9.3
Q ss_pred cCccccceeEEe
Q 006225 523 QCPSCKMAISRT 534 (655)
Q Consensus 523 ~CP~C~~~iek~ 534 (655)
.||+|+..++..
T Consensus 1 ~CP~C~~~l~~~ 12 (41)
T PF13453_consen 1 KCPRCGTELEPV 12 (41)
T ss_pred CcCCCCcccceE
Confidence 599999877654
No 235
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=42.85 E-value=12 Score=35.35 Aligned_cols=31 Identities=16% Similarity=0.378 Sum_probs=19.1
Q ss_pred CCCcccccCCCCCcccc-------ccccccccccccee
Q 006225 433 MSDVAYCPRCETPCIED-------EEQHAQCSKCFYSF 463 (655)
Q Consensus 433 ~~~~~~CP~C~~~~~~~-------~~~~~~C~~C~~~f 463 (655)
......||.|+..+... ....+.||.||...
T Consensus 96 ~~~~Y~Cp~C~~~y~~~ea~~~~d~~~~f~Cp~Cg~~l 133 (147)
T smart00531 96 NNAYYKCPNCQSKYTFLEANQLLDMDGTFTCPRCGEEL 133 (147)
T ss_pred CCcEEECcCCCCEeeHHHHHHhcCCCCcEECCCCCCEE
Confidence 44566799999765432 22237787777653
No 236
>PRK11827 hypothetical protein; Provisional
Probab=42.63 E-value=20 Score=28.61 Aligned_cols=29 Identities=17% Similarity=0.428 Sum_probs=21.3
Q ss_pred cccCccccceeEEecCcCceeccccCeee
Q 006225 521 AKQCPSCKMAISRTEGCNKIVCNNCGQYF 549 (655)
Q Consensus 521 ~k~CP~C~~~iek~~Gcn~m~C~~C~~~F 549 (655)
+-.||.|+..+.-..+-+...|..|+..|
T Consensus 8 ILaCP~ckg~L~~~~~~~~Lic~~~~laY 36 (60)
T PRK11827 8 IIACPVCNGKLWYNQEKQELICKLDNLAF 36 (60)
T ss_pred heECCCCCCcCeEcCCCCeEECCccCeec
Confidence 46799999998876665667787655443
No 237
>PF14353 CpXC: CpXC protein
Probab=42.18 E-value=11 Score=34.54 Aligned_cols=45 Identities=22% Similarity=0.443 Sum_probs=26.8
Q ss_pred eeccCCCCCCCCCCcccccccC---ChHHHHHHHHHHHHHHhhcCCCcccccCCCCCc
Q 006225 392 KLQCPDAKCGGMVPPSLLKKLL---GDEEFERWESLMLQKTLESMSDVAYCPRCETPC 446 (655)
Q Consensus 392 ~i~CP~~~C~~~l~~~~i~~ll---~~e~~ery~~~~~~~~l~~~~~~~~CP~C~~~~ 446 (655)
.|+||. |+..+..+....+- ++++.++ .+...-....||.|+..+
T Consensus 1 ~itCP~--C~~~~~~~v~~~I~~~~~p~l~e~--------il~g~l~~~~CP~Cg~~~ 48 (128)
T PF14353_consen 1 EITCPH--CGHEFEFEVWTSINADEDPELKEK--------ILDGSLFSFTCPSCGHKF 48 (128)
T ss_pred CcCCCC--CCCeeEEEEEeEEcCcCCHHHHHH--------HHcCCcCEEECCCCCCce
Confidence 378998 99888776655442 2333322 232333556788888754
No 238
>PF14354 Lar_restr_allev: Restriction alleviation protein Lar
Probab=41.89 E-value=20 Score=28.13 Aligned_cols=13 Identities=38% Similarity=0.578 Sum_probs=9.6
Q ss_pred cccCccccceeEE
Q 006225 521 AKQCPSCKMAISR 533 (655)
Q Consensus 521 ~k~CP~C~~~iek 533 (655)
.++||.|+.....
T Consensus 3 LkPCPFCG~~~~~ 15 (61)
T PF14354_consen 3 LKPCPFCGSADVL 15 (61)
T ss_pred CcCCCCCCCcceE
Confidence 5899999865443
No 239
>COG1594 RPB9 DNA-directed RNA polymerase, subunit M/Transcription elongation factor TFIIS [Transcription]
Probab=41.89 E-value=16 Score=32.94 Aligned_cols=28 Identities=18% Similarity=0.506 Sum_probs=20.3
Q ss_pred ccCCccCccccc-c-CCcceEEcccccccc
Q 006225 602 LSCPNCRQFNAK-V-GNNNHMFCWACQIHY 629 (655)
Q Consensus 602 k~CP~C~~~ieK-~-~GCnhm~C~~C~~~F 629 (655)
+-||+|+.++.- . ++-+.+.|.+|++++
T Consensus 3 ~FCp~Cgsll~p~~~~~~~~l~C~kCgye~ 32 (113)
T COG1594 3 RFCPKCGSLLYPKKDDEGGKLVCRKCGYEE 32 (113)
T ss_pred cccCCccCeeEEeEcCCCcEEECCCCCcch
Confidence 469999976544 2 234489999999875
No 240
>COG0266 Nei Formamidopyrimidine-DNA glycosylase [DNA replication, recombination, and repair]
Probab=41.76 E-value=16 Score=38.14 Aligned_cols=28 Identities=29% Similarity=0.688 Sum_probs=23.6
Q ss_pred cCccCCccCcccccc--CCcceEEcccccc
Q 006225 600 HGLSCPNCRQFNAKV--GNNNHMFCWACQI 627 (655)
Q Consensus 600 ~~k~CP~C~~~ieK~--~GCnhm~C~~C~~ 627 (655)
...+|+.|+..|+|. +|=+-..|+.|+.
T Consensus 244 ~GepC~~CGt~I~k~~~~gR~t~~CP~CQ~ 273 (273)
T COG0266 244 AGEPCRRCGTPIEKIKLGGRSTFYCPVCQK 273 (273)
T ss_pred CCCCCCccCCEeEEEEEcCCcCEeCCCCCC
Confidence 468999999999987 6878888888873
No 241
>KOG1701 consensus Focal adhesion adaptor protein Paxillin and related LIM proteins [Signal transduction mechanisms]
Probab=41.61 E-value=13 Score=40.70 Aligned_cols=26 Identities=23% Similarity=0.565 Sum_probs=14.9
Q ss_pred ccccccccccccccce-e---ecccccccc
Q 006225 447 IEDEEQHAQCSKCFYS-F---CTLCRERRH 472 (655)
Q Consensus 447 ~~~~~~~~~C~~C~~~-f---C~~C~~~~H 472 (655)
..+..+.+.|-.|.|. | |..|..+..
T Consensus 376 tvd~~n~v~Cv~dfh~kfAPrCs~C~~PI~ 405 (468)
T KOG1701|consen 376 TVDSQNNVYCVPDFHKKFAPRCSVCGNPIL 405 (468)
T ss_pred cccCCCceeeehhhhhhcCcchhhccCCcc
Confidence 4566677777666543 2 666655433
No 242
>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=41.60 E-value=8.9 Score=30.25 Aligned_cols=36 Identities=25% Similarity=0.468 Sum_probs=27.7
Q ss_pred ccCCccCcccc--ccCCcceEEcccccccccccccccc
Q 006225 602 LSCPNCRQFNA--KVGNNNHMFCWACQIHYCYLCKKIV 637 (655)
Q Consensus 602 k~CP~C~~~ie--K~~GCnhm~C~~C~~~FC~~C~~~~ 637 (655)
..||-|++..- -.+-=|+-+|..|+...|-+||=.-
T Consensus 3 ~~CPlCkt~~n~gsk~~pNyntCT~Ck~~VCnlCGFNP 40 (61)
T PF05715_consen 3 SLCPLCKTTLNVGSKDPPNYNTCTECKSQVCNLCGFNP 40 (61)
T ss_pred ccCCcccchhhcCCCCCCCccHHHHHhhhhhcccCCCC
Confidence 46999997551 2234489999999999999999544
No 243
>PF03119 DNA_ligase_ZBD: NAD-dependent DNA ligase C4 zinc finger domain; InterPro: IPR004149 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents the zinc finger domain found in NAD-dependent DNA ligases. DNA ligases catalyse the crucial step of joining the breaks in duplex DNA during DNA replication, repair and recombination, utilizing either ATP or NAD(+) as a cofactor []. This domain is a small zinc binding motif that is presumably DNA binding. It is found only in NAD-dependent DNA ligases. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003911 DNA ligase (NAD+) activity, 0006260 DNA replication, 0006281 DNA repair; PDB: 1DGS_A 1V9P_B 2OWO_A.
Probab=41.11 E-value=22 Score=23.74 Aligned_cols=21 Identities=38% Similarity=0.812 Sum_probs=12.7
Q ss_pred cCccccceeEEecCcCceecc
Q 006225 523 QCPSCKMAISRTEGCNKIVCN 543 (655)
Q Consensus 523 ~CP~C~~~iek~~Gcn~m~C~ 543 (655)
.||.|+..+.+.+|--...|.
T Consensus 1 ~CP~C~s~l~~~~~ev~~~C~ 21 (28)
T PF03119_consen 1 TCPVCGSKLVREEGEVDIRCP 21 (28)
T ss_dssp B-TTT--BEEE-CCTTCEEE-
T ss_pred CcCCCCCEeEcCCCCEeEECC
Confidence 499999999998876666665
No 244
>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional
Probab=40.82 E-value=16 Score=28.94 Aligned_cols=37 Identities=35% Similarity=0.855 Sum_probs=25.1
Q ss_pred ccCccccceeEEecCcCceeccccCee---eecccccccc
Q 006225 522 KQCPSCKMAISRTEGCNKIVCNNCGQY---FCYRCNKAID 558 (655)
Q Consensus 522 k~CP~C~~~iek~~Gcn~m~C~~C~~~---FC~~C~~~~~ 558 (655)
..|-.|+..|.-.+...++.|++||.. =|..|++.-+
T Consensus 8 ~~CtSCg~~i~~~~~~~~F~CPnCG~~~I~RC~~CRk~~~ 47 (59)
T PRK14890 8 PKCTSCGIEIAPREKAVKFLCPNCGEVIIYRCEKCRKQSN 47 (59)
T ss_pred ccccCCCCcccCCCccCEeeCCCCCCeeEeechhHHhcCC
Confidence 458888888876665677788888865 4555655543
No 245
>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=40.73 E-value=22 Score=29.35 Aligned_cols=28 Identities=29% Similarity=0.726 Sum_probs=21.0
Q ss_pred ccCccccce----eEEecCcCceeccccCeee
Q 006225 522 KQCPSCKMA----ISRTEGCNKIVCNNCGQYF 549 (655)
Q Consensus 522 k~CP~C~~~----iek~~Gcn~m~C~~C~~~F 549 (655)
-.||.|+.. +-...+-.++.|..||+..
T Consensus 9 a~CP~C~~~D~i~~~~e~~ve~vECV~CGy~e 40 (71)
T PF09526_consen 9 AVCPKCQAMDTIMMWRENGVEYVECVECGYTE 40 (71)
T ss_pred ccCCCCcCccEEEEEEeCCceEEEecCCCCee
Confidence 469999865 3346677889999998754
No 246
>PRK03681 hypA hydrogenase nickel incorporation protein; Validated
Probab=40.69 E-value=12 Score=33.72 Aligned_cols=29 Identities=14% Similarity=0.454 Sum_probs=19.4
Q ss_pred CCcccccCCCCCcccccccccccccccce
Q 006225 434 SDVAYCPRCETPCIEDEEQHAQCSKCFYS 462 (655)
Q Consensus 434 ~~~~~CP~C~~~~~~~~~~~~~C~~C~~~ 462 (655)
+...+|+.|+..+.........||.||..
T Consensus 68 p~~~~C~~Cg~~~~~~~~~~~~CP~Cgs~ 96 (114)
T PRK03681 68 EAECWCETCQQYVTLLTQRVRRCPQCHGD 96 (114)
T ss_pred CcEEEcccCCCeeecCCccCCcCcCcCCC
Confidence 45678999997665544444668888743
No 247
>PF09606 Med15: ARC105 or Med15 subunit of Mediator complex non-fungal; InterPro: IPR019087 The Mediator complex is a coactivator involved in the regulated transcription of nearly all RNA polymerase II-dependent genes. Mediator functions as a bridge to convey information from gene-specific regulatory proteins to the basal RNA polymerase II transcription machinery. The Mediator complex, having a compact conformation in its free form, is recruited to promoters by direct interactions with regulatory proteins and serves for the assembly of a functional preinitiation complex with RNA polymerase II and the general transcription factors. On recruitment the Mediator complex unfolds to an extended conformation and partially surrounds RNA polymerase II, specifically interacting with the unphosphorylated form of the C-terminal domain (CTD) of RNA polymerase II. The Mediator complex dissociates from the RNA polymerase II holoenzyme and stays at the promoter when transcriptional elongation begins. The Mediator complex is composed of at least 31 subunits: MED1, MED4, MED6, MED7, MED8, MED9, MED10, MED11, MED12, MED13, MED13L, MED14, MED15, MED16, MED17, MED18, MED19, MED20, MED21, MED22, MED23, MED24, MED25, MED26, MED27, MED29, MED30, MED31, CCNC, CDK8 and CDC2L6/CDK11. The subunits form at least three structurally distinct submodules. The head and the middle modules interact directly with RNA polymerase II, whereas the elongated tail module interacts with gene-specific regulatory proteins. Mediator containing the CDK8 module is less active than Mediator lacking this module in supporting transcriptional activation. The head module contains: MED6, MED8, MED11, SRB4/MED17, SRB5/MED18, ROX3/MED19, SRB2/MED20 and SRB6/MED22. The middle module contains: MED1, MED4, NUT1/MED5, MED7, CSE2/MED9, NUT2/MED10, SRB7/MED21 and SOH1/MED31. CSE2/MED9 interacts directly with MED4. The tail module contains: MED2, PGD1/MED3, RGR1/MED14, GAL11/MED15 and SIN4/MED16. The CDK8 module contains: MED12, MED13, CCNC and CDK8. Individual preparations of the Mediator complex lacking one or more distinct subunits have been variously termed ARC, CRSP, DRIP, PC2, SMCC and TRAP. The proteins in this entry represent subunit Med15 of the Mediator complex. They contain a single copy of the approximately 70 residue ARC105 domain. The ARC105 domain of the ARC-Mediator co-activator is a three-helix bundle with marked similarity to the KIX domain. The sterol regulatory element binding protein (SREBP) family of transcription activators use the ARC105 subunit to activate target genes in the regulation of cholesterol and fatty acid homeostasis. In addition, ARC105 is a critical transducer of gene activation signals that control early metazoan development []. ; GO: 0001104 RNA polymerase II transcription cofactor activity, 0006357 regulation of transcription from RNA polymerase II promoter, 0016592 mediator complex; PDB: 2GUT_A.
Probab=40.53 E-value=9.2 Score=45.67 Aligned_cols=25 Identities=28% Similarity=0.659 Sum_probs=0.0
Q ss_pred cCCcEE-EEEEcCCCCCCCCCCeEEee
Q 006225 228 YLPPIV-LTCLLPKSYPSHLPPYFTIS 253 (655)
Q Consensus 228 ~LPpi~-L~~~lP~~YPs~~pP~~~l~ 253 (655)
+||+|= |.+++|.+||.. +|...+.
T Consensus 711 ~LP~VPPl~l~vP~~YP~~-sp~~~~~ 736 (799)
T PF09606_consen 711 NLPSVPPLRLTVPADYPRQ-SPQCSVD 736 (799)
T ss_dssp ---------------------------
T ss_pred CCCCCCCeeEeCCCCCCcc-CCcCccc
Confidence 454443 566799999987 7765543
No 248
>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=40.50 E-value=16 Score=34.96 Aligned_cols=31 Identities=19% Similarity=0.298 Sum_probs=20.3
Q ss_pred cCCCcccccCCCCCccccc--ccccccccccce
Q 006225 432 SMSDVAYCPRCETPCIEDE--EQHAQCSKCFYS 462 (655)
Q Consensus 432 ~~~~~~~CP~C~~~~~~~~--~~~~~C~~C~~~ 462 (655)
....+..||+|..-+...+ ...+.||.||..
T Consensus 105 ~~~~~Y~Cp~c~~r~tf~eA~~~~F~Cp~Cg~~ 137 (158)
T TIGR00373 105 TNNMFFICPNMCVRFTFNEAMELNFTCPRCGAM 137 (158)
T ss_pred cCCCeEECCCCCcEeeHHHHHHcCCcCCCCCCE
Confidence 3445667999986554332 246888888766
No 249
>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=39.49 E-value=22 Score=28.11 Aligned_cols=28 Identities=21% Similarity=0.619 Sum_probs=20.6
Q ss_pred ccCccccce----eEEecCcCceeccccCeee
Q 006225 522 KQCPSCKMA----ISRTEGCNKIVCNNCGQYF 549 (655)
Q Consensus 522 k~CP~C~~~----iek~~Gcn~m~C~~C~~~F 549 (655)
-.||.|+.. +-+..+-.++.|..||+.-
T Consensus 10 A~CP~C~~~Dtl~~~~e~~~e~vECv~Cg~~~ 41 (59)
T TIGR02443 10 AVCPACSAQDTLAMWKENNIELVECVECGYQE 41 (59)
T ss_pred ccCCCCcCccEEEEEEeCCceEEEeccCCCcc
Confidence 469999864 3446677889999888753
No 250
>PRK10220 hypothetical protein; Provisional
Probab=39.34 E-value=22 Score=31.70 Aligned_cols=28 Identities=18% Similarity=0.668 Sum_probs=20.3
Q ss_pred cccCccccceeEEecCcCceeccccCeee
Q 006225 521 AKQCPSCKMAISRTEGCNKIVCNNCGQYF 549 (655)
Q Consensus 521 ~k~CP~C~~~iek~~Gcn~m~C~~C~~~F 549 (655)
.-.||.|.....-.+|- .+.|+.|++.|
T Consensus 3 lP~CP~C~seytY~d~~-~~vCpeC~hEW 30 (111)
T PRK10220 3 LPHCPKCNSEYTYEDNG-MYICPECAHEW 30 (111)
T ss_pred CCcCCCCCCcceEcCCC-eEECCcccCcC
Confidence 46799999887777774 47788666644
No 251
>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=39.33 E-value=44 Score=28.89 Aligned_cols=29 Identities=24% Similarity=0.616 Sum_probs=20.8
Q ss_pred cccCccccceeEEecCcCceeccccCeee
Q 006225 521 AKQCPSCKMAISRTEGCNKIVCNNCGQYF 549 (655)
Q Consensus 521 ~k~CP~C~~~iek~~Gcn~m~C~~C~~~F 549 (655)
...||.|+..-.+..+.-.-.|..|+..|
T Consensus 35 ky~Cp~Cgk~~vkR~a~GIW~C~~C~~~~ 63 (90)
T PF01780_consen 35 KYTCPFCGKTSVKRVATGIWKCKKCGKKF 63 (90)
T ss_dssp -BEESSSSSSEEEEEETTEEEETTTTEEE
T ss_pred CCcCCCCCCceeEEeeeEEeecCCCCCEE
Confidence 45699999887776555556777777766
No 252
>KOG2932 consensus E3 ubiquitin ligase involved in ubiquitination of E-cadherin complex [Posttranslational modification, protein turnover, chaperones]
Probab=39.04 E-value=8.6 Score=40.24 Aligned_cols=32 Identities=22% Similarity=0.733 Sum_probs=22.1
Q ss_pred ccccCccccceeEEecCcCceeccccCeeeecccccc
Q 006225 520 DAKQCPSCKMAISRTEGCNKIVCNNCGQYFCYRCNKA 556 (655)
Q Consensus 520 ~~k~CP~C~~~iek~~Gcn~m~C~~C~~~FC~~C~~~ 556 (655)
.+..|-+|..+|..-+. |. -|++.||+.|-..
T Consensus 89 ~VHfCd~Cd~PI~IYGR---mI--PCkHvFCl~CAr~ 120 (389)
T KOG2932|consen 89 RVHFCDRCDFPIAIYGR---MI--PCKHVFCLECARS 120 (389)
T ss_pred ceEeecccCCcceeeec---cc--ccchhhhhhhhhc
Confidence 36778899998854322 22 3889999988655
No 253
>PRK11827 hypothetical protein; Provisional
Probab=38.69 E-value=24 Score=28.17 Aligned_cols=28 Identities=14% Similarity=0.411 Sum_probs=21.6
Q ss_pred ccCCccCccccccCCcceEEcccccccc
Q 006225 602 LSCPNCRQFNAKVGNNNHMFCWACQIHY 629 (655)
Q Consensus 602 k~CP~C~~~ieK~~GCnhm~C~~C~~~F 629 (655)
..||.|+...+-..+=+...|..|+..|
T Consensus 9 LaCP~ckg~L~~~~~~~~Lic~~~~laY 36 (60)
T PRK11827 9 IACPVCNGKLWYNQEKQELICKLDNLAF 36 (60)
T ss_pred eECCCCCCcCeEcCCCCeEECCccCeec
Confidence 5799999887766555778898887554
No 254
>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=38.62 E-value=19 Score=27.19 Aligned_cols=27 Identities=30% Similarity=0.774 Sum_probs=19.2
Q ss_pred cccCc--cccceeEEecCcCceeccccCe
Q 006225 521 AKQCP--SCKMAISRTEGCNKIVCNNCGQ 547 (655)
Q Consensus 521 ~k~CP--~C~~~iek~~Gcn~m~C~~C~~ 547 (655)
-+.|| .|+.-|.-..--+...|.+||.
T Consensus 18 rk~CP~~~CG~GvFMA~H~dR~~CGKCg~ 46 (47)
T PF01599_consen 18 RKECPSPRCGAGVFMAEHKDRHYCGKCGY 46 (47)
T ss_dssp SEE-TSTTTTSSSEEEE-SSEEEETTTSS
T ss_pred hhcCCCcccCCceEeeecCCCccCCCccc
Confidence 47799 9998776555567788888875
No 255
>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=38.59 E-value=17 Score=27.82 Aligned_cols=26 Identities=27% Similarity=0.665 Sum_probs=17.5
Q ss_pred ccCCccCccccccCCc--ceEEcccccc
Q 006225 602 LSCPNCRQFNAKVGNN--NHMFCWACQI 627 (655)
Q Consensus 602 k~CP~C~~~ieK~~GC--nhm~C~~C~~ 627 (655)
.+|++|+..+-+.++- -.|.|++|++
T Consensus 5 iRC~~CnklLa~~g~~~~leIKCpRC~t 32 (51)
T PF10122_consen 5 IRCGHCNKLLAKAGEVIELEIKCPRCKT 32 (51)
T ss_pred eeccchhHHHhhhcCccEEEEECCCCCc
Confidence 5788888777775433 3577777774
No 256
>PRK14811 formamidopyrimidine-DNA glycosylase; Provisional
Probab=38.41 E-value=20 Score=37.44 Aligned_cols=29 Identities=34% Similarity=0.741 Sum_probs=22.1
Q ss_pred cCccCCccCcccccc--CCcceEEccccccc
Q 006225 600 HGLSCPNCRQFNAKV--GNNNHMFCWACQIH 628 (655)
Q Consensus 600 ~~k~CP~C~~~ieK~--~GCnhm~C~~C~~~ 628 (655)
..++||.|+..|.+. +|=.-..|..|+..
T Consensus 234 ~g~pC~~Cg~~I~~~~~~gR~ty~Cp~CQ~~ 264 (269)
T PRK14811 234 EGQPCPRCGTPIEKIVVGGRGTHFCPQCQPL 264 (269)
T ss_pred CcCCCCcCCCeeEEEEECCCCcEECCCCcCC
Confidence 358999999999876 57666777777743
No 257
>KOG3268 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=38.20 E-value=32 Score=33.22 Aligned_cols=58 Identities=21% Similarity=0.459 Sum_probs=39.2
Q ss_pred cccccccccccc-cCCC----eEecCCCCcccHhhHHHHHHHHhhcCCcce---eccCCCCCCCCCCc
Q 006225 347 SFHECRICFSEF-AGTD----FVRLPCHHFFCWKCMKTYLDIHISEGTVSK---LQCPDAKCGGMVPP 406 (655)
Q Consensus 347 ~~~~C~IC~e~~-~~~~----~~~l~C~H~fC~~Cl~~yi~~~i~~g~~~~---i~CP~~~C~~~l~~ 406 (655)
++..|.|||-.. .+.. +-...|+..|..-||..|+..-+...+... =.||. |..++..
T Consensus 164 ~~~~cgicyayqldGTipDqtCdN~qCgkpFHqiCL~dWLRgilTsRQSFdiiFGeCPY--CS~Pial 229 (234)
T KOG3268|consen 164 ELGACGICYAYQLDGTIPDQTCDNIQCGKPFHQICLTDWLRGILTSRQSFDIIFGECPY--CSDPIAL 229 (234)
T ss_pred hhhcccceeeeecCCccccccccccccCCcHHHHHHHHHHHHHhhccceeeeeeccCCC--CCCccee
Confidence 457899998642 2221 222479999999999999988776554333 35886 8776643
No 258
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=37.83 E-value=16 Score=35.73 Aligned_cols=30 Identities=27% Similarity=0.520 Sum_probs=19.1
Q ss_pred CCCcccccCCCCCccccc--ccccccccccce
Q 006225 433 MSDVAYCPRCETPCIEDE--EQHAQCSKCFYS 462 (655)
Q Consensus 433 ~~~~~~CP~C~~~~~~~~--~~~~~C~~C~~~ 462 (655)
...+..||+|+.-+...+ ...+.||.||..
T Consensus 114 ~~~~Y~Cp~C~~rytf~eA~~~~F~Cp~Cg~~ 145 (178)
T PRK06266 114 NNMFFFCPNCHIRFTFDEAMEYGFRCPQCGEM 145 (178)
T ss_pred CCCEEECCCCCcEEeHHHHhhcCCcCCCCCCC
Confidence 445667999987554332 245778777655
No 259
>KOG1941 consensus Acetylcholine receptor-associated protein of the synapse (rapsyn) [Extracellular structures]
Probab=36.72 E-value=12 Score=40.49 Aligned_cols=47 Identities=28% Similarity=0.750 Sum_probs=35.4
Q ss_pred cccccccccccc--CCCeEecCCCCcccHhhHHHHHHHHhhcCCcceeccCCCCCCC
Q 006225 348 FHECRICFSEFA--GTDFVRLPCHHFFCWKCMKTYLDIHISEGTVSKLQCPDAKCGG 402 (655)
Q Consensus 348 ~~~C~IC~e~~~--~~~~~~l~C~H~fC~~Cl~~yi~~~i~~g~~~~i~CP~~~C~~ 402 (655)
...|..|-+.+. .+..-.|+|.|.|...|+..|+.. .+ +-.||. |+.
T Consensus 365 ~L~Cg~CGe~~Glk~e~LqALpCsHIfH~rCl~e~L~~---n~---~rsCP~--Crk 413 (518)
T KOG1941|consen 365 ELYCGLCGESIGLKNERLQALPCSHIFHLRCLQEILEN---NG---TRSCPN--CRK 413 (518)
T ss_pred hhhhhhhhhhhcCCcccccccchhHHHHHHHHHHHHHh---CC---CCCCcc--HHH
Confidence 478999988764 334555799999999999999843 22 467997 773
No 260
>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=36.48 E-value=23 Score=40.41 Aligned_cols=35 Identities=26% Similarity=0.758 Sum_probs=28.9
Q ss_pred ccCccccceeEEecCcCceeccccCee-----eecccccc
Q 006225 522 KQCPSCKMAISRTEGCNKIVCNNCGQY-----FCYRCNKA 556 (655)
Q Consensus 522 k~CP~C~~~iek~~Gcn~m~C~~C~~~-----FC~~C~~~ 556 (655)
-.||+|..++.-...-+.+.|..||+. .|-.|+..
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 579999999887666678999999976 58888765
No 261
>TIGR01053 LSD1 zinc finger domain, LSD1 subclass. This model describes a putative zinc finger domain found in three closely spaced copies in Arabidopsis protein LSD1 and in two copies in other proteins from the same species. The motif resembles CxxCRxxLMYxxGASxVxCxxC
Probab=36.12 E-value=38 Score=23.25 Aligned_cols=25 Identities=20% Similarity=0.656 Sum_probs=22.5
Q ss_pred cCccccceeEEecCcCceeccccCe
Q 006225 523 QCPSCKMAISRTEGCNKIVCNNCGQ 547 (655)
Q Consensus 523 ~CP~C~~~iek~~Gcn~m~C~~C~~ 547 (655)
.|..|++.+.-..|-..+.|..|+.
T Consensus 3 ~C~~C~t~L~yP~gA~~vrCs~C~~ 27 (31)
T TIGR01053 3 VCGGCRTLLMYPRGASSVRCALCQT 27 (31)
T ss_pred CcCCCCcEeecCCCCCeEECCCCCe
Confidence 6999999999999999999998875
No 262
>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=36.04 E-value=18 Score=29.09 Aligned_cols=34 Identities=18% Similarity=0.502 Sum_probs=18.8
Q ss_pred CcccccCCCCCcccccccccccccccceeeccccc
Q 006225 435 DVAYCPRCETPCIEDEEQHAQCSKCFYSFCTLCRE 469 (655)
Q Consensus 435 ~~~~CP~C~~~~~~~~~~~~~C~~C~~~fC~~C~~ 469 (655)
....|..|+..+.. -.....|..||..||..|..
T Consensus 8 ~~~~C~~C~~~F~~-~~rrhhCr~CG~~vC~~Cs~ 41 (69)
T PF01363_consen 8 EASNCMICGKKFSL-FRRRHHCRNCGRVVCSSCSS 41 (69)
T ss_dssp G-SB-TTT--B-BS-SS-EEE-TTT--EEECCCS-
T ss_pred CCCcCcCcCCcCCC-ceeeEccCCCCCEECCchhC
Confidence 45679999887733 25677899999999999976
No 263
>TIGR00622 ssl1 transcription factor ssl1. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=36.00 E-value=24 Score=31.72 Aligned_cols=42 Identities=24% Similarity=0.633 Sum_probs=31.9
Q ss_pred ccccCCCCCcccc---------cccccccccccceeeccccccccCCc-CCC
Q 006225 437 AYCPRCETPCIED---------EEQHAQCSKCFYSFCTLCRERRHVGV-VCM 478 (655)
Q Consensus 437 ~~CP~C~~~~~~~---------~~~~~~C~~C~~~fC~~C~~~~H~~~-sC~ 478 (655)
..|-.|+..+... ......|+.|+..||..|..-.|..+ .|+
T Consensus 56 ~~C~~C~~~f~~~~~~~~~~~~~~~~y~C~~C~~~FC~dCD~fiHe~Lh~CP 107 (112)
T TIGR00622 56 RFCFGCQGPFPKPPVSPFDELKDSHRYVCAVCKNVFCVDCDVFVHESLHCCP 107 (112)
T ss_pred CcccCcCCCCCCcccccccccccccceeCCCCCCccccccchhhhhhccCCc
Confidence 4699999877532 23467899999999999998888765 454
No 264
>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=35.67 E-value=24 Score=29.17 Aligned_cols=28 Identities=21% Similarity=0.561 Sum_probs=21.7
Q ss_pred CccCCccCcc----ccccCCcceEEccccccc
Q 006225 601 GLSCPNCRQF----NAKVGNNNHMFCWACQIH 628 (655)
Q Consensus 601 ~k~CP~C~~~----ieK~~GCnhm~C~~C~~~ 628 (655)
+-.||+|+.+ ..+..|=.++.|..||+.
T Consensus 8 Ga~CP~C~~~D~i~~~~e~~ve~vECV~CGy~ 39 (71)
T PF09526_consen 8 GAVCPKCQAMDTIMMWRENGVEYVECVECGYT 39 (71)
T ss_pred CccCCCCcCccEEEEEEeCCceEEEecCCCCe
Confidence 3579999954 344567899999999975
No 265
>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]
Probab=35.15 E-value=24 Score=42.03 Aligned_cols=35 Identities=23% Similarity=0.518 Sum_probs=29.4
Q ss_pred ccCCccCccccccCCcceEEccccccc-----cccccccc
Q 006225 602 LSCPNCRQFNAKVGNNNHMFCWACQIH-----YCYLCKKI 636 (655)
Q Consensus 602 k~CP~C~~~ieK~~GCnhm~C~~C~~~-----FC~~C~~~ 636 (655)
-.||+|.....-...=|.|.|..||++ .|-.|+..
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 479999977666666699999999976 89999988
No 266
>PRK01103 formamidopyrimidine/5-formyluracil/ 5-hydroxymethyluracil DNA glycosylase; Validated
Probab=35.08 E-value=24 Score=36.90 Aligned_cols=28 Identities=32% Similarity=0.717 Sum_probs=21.6
Q ss_pred cCccCCccCcccccc--CCcceEEcccccc
Q 006225 600 HGLSCPNCRQFNAKV--GNNNHMFCWACQI 627 (655)
Q Consensus 600 ~~k~CP~C~~~ieK~--~GCnhm~C~~C~~ 627 (655)
..++||.|+..|.|. +|=.-..|+.|+.
T Consensus 244 ~g~pC~~Cg~~I~~~~~~gR~t~~CP~CQ~ 273 (274)
T PRK01103 244 EGEPCRRCGTPIEKIKQGGRSTFFCPRCQK 273 (274)
T ss_pred CCCCCCCCCCeeEEEEECCCCcEECcCCCC
Confidence 357999999999876 5666677777764
No 267
>TIGR00577 fpg formamidopyrimidine-DNA glycosylase (fpg). All proteins in the FPG family with known functions are FAPY-DNA glycosylases that function in base excision repair. Homologous to endonuclease VIII (nei). This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=34.99 E-value=24 Score=36.88 Aligned_cols=26 Identities=35% Similarity=0.755 Sum_probs=20.7
Q ss_pred CccCCccCcccccc--CCcceEEccccc
Q 006225 601 GLSCPNCRQFNAKV--GNNNHMFCWACQ 626 (655)
Q Consensus 601 ~k~CP~C~~~ieK~--~GCnhm~C~~C~ 626 (655)
.++||.|+..|.|. +|=.-..|+.|+
T Consensus 245 g~pC~~Cg~~I~~~~~~gR~t~~CP~CQ 272 (272)
T TIGR00577 245 GEPCRRCGTPIEKIKVGGRGTHFCPQCQ 272 (272)
T ss_pred CCCCCCCCCeeEEEEECCCCCEECCCCC
Confidence 57999999999876 576667777775
No 268
>KOG4275 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=34.95 E-value=17 Score=37.93 Aligned_cols=31 Identities=39% Similarity=0.690 Sum_probs=24.9
Q ss_pred ccccccccccccCCCeEecCCCCc-ccHhhHHHH
Q 006225 348 FHECRICFSEFAGTDFVRLPCHHF-FCWKCMKTY 380 (655)
Q Consensus 348 ~~~C~IC~e~~~~~~~~~l~C~H~-fC~~Cl~~y 380 (655)
-..|.|||+-- .+++-|.|||. -|..|=+.+
T Consensus 300 ~~LC~ICmDaP--~DCvfLeCGHmVtCt~CGkrm 331 (350)
T KOG4275|consen 300 RRLCAICMDAP--RDCVFLECGHMVTCTKCGKRM 331 (350)
T ss_pred HHHHHHHhcCC--cceEEeecCcEEeehhhcccc
Confidence 46799999873 58888999997 599996654
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=34.84 E-value=29 Score=28.07 Aligned_cols=17 Identities=24% Similarity=0.677 Sum_probs=12.6
Q ss_pred ccHhhHHHHHHHHhhcC
Q 006225 372 FCWKCMKTYLDIHISEG 388 (655)
Q Consensus 372 fC~~Cl~~yi~~~i~~g 388 (655)
||+.||.+|+...-.+.
T Consensus 12 FCRNCLskWy~~aA~~~ 28 (68)
T PF06844_consen 12 FCRNCLSKWYREAAEER 28 (68)
T ss_dssp --HHHHHHHHHHHHHHC
T ss_pred HHHHHHHHHHHHHHHhc
Confidence 99999999998876654
No 270
>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=34.74 E-value=22 Score=30.09 Aligned_cols=30 Identities=20% Similarity=0.463 Sum_probs=17.4
Q ss_pred cCccCCccCc------cccccCCcceEEcccccccc
Q 006225 600 HGLSCPNCRQ------FNAKVGNNNHMFCWACQIHY 629 (655)
Q Consensus 600 ~~k~CP~C~~------~ieK~~GCnhm~C~~C~~~F 629 (655)
..-.||.|+. .|.+..|--+++|..|+..|
T Consensus 21 ~~F~CPfC~~~~sV~v~idkk~~~~~~~C~~Cg~~~ 56 (81)
T PF05129_consen 21 KVFDCPFCNHEKSVSVKIDKKEGIGILSCRVCGESF 56 (81)
T ss_dssp S----TTT--SS-EEEEEETTTTEEEEEESSS--EE
T ss_pred ceEcCCcCCCCCeEEEEEEccCCEEEEEecCCCCeE
Confidence 4578999992 35666788889999998776
No 271
>PRK00564 hypA hydrogenase nickel incorporation protein; Provisional
Probab=34.57 E-value=19 Score=32.60 Aligned_cols=29 Identities=17% Similarity=0.344 Sum_probs=18.6
Q ss_pred CCcccccCCCCCcccccccccccccccce
Q 006225 434 SDVAYCPRCETPCIEDEEQHAQCSKCFYS 462 (655)
Q Consensus 434 ~~~~~CP~C~~~~~~~~~~~~~C~~C~~~ 462 (655)
+-..+|..|+..+..+......||.||..
T Consensus 69 p~~~~C~~Cg~~~~~~~~~~~~CP~Cgs~ 97 (117)
T PRK00564 69 KVELECKDCSHVFKPNALDYGVCEKCHSK 97 (117)
T ss_pred CCEEEhhhCCCccccCCccCCcCcCCCCC
Confidence 34578999987665544344458887753
No 272
>PRK10445 endonuclease VIII; Provisional
Probab=34.50 E-value=25 Score=36.59 Aligned_cols=26 Identities=27% Similarity=0.671 Sum_probs=21.2
Q ss_pred CccCCccCcccccc--CCcceEEccccc
Q 006225 601 GLSCPNCRQFNAKV--GNNNHMFCWACQ 626 (655)
Q Consensus 601 ~k~CP~C~~~ieK~--~GCnhm~C~~C~ 626 (655)
.++||.|+..|++. +|=.-..|.+|+
T Consensus 235 g~~Cp~Cg~~I~~~~~~gR~t~~CP~CQ 262 (263)
T PRK10445 235 GEACERCGGIIEKTTLSSRPFYWCPGCQ 262 (263)
T ss_pred CCCCCCCCCEeEEEEECCCCcEECCCCc
Confidence 57999999999876 676777888776
No 273
>PRK12286 rpmF 50S ribosomal protein L32; Reviewed
Probab=34.40 E-value=29 Score=27.36 Aligned_cols=26 Identities=27% Similarity=0.577 Sum_probs=19.5
Q ss_pred cccCccCCccCccccccCCcceEEccccccc
Q 006225 598 DEHGLSCPNCRQFNAKVGNNNHMFCWACQIH 628 (655)
Q Consensus 598 ~~~~k~CP~C~~~ieK~~GCnhm~C~~C~~~ 628 (655)
..+...||+|+.+.. .|-.|..||++
T Consensus 24 ~~~l~~C~~CG~~~~-----~H~vC~~CG~Y 49 (57)
T PRK12286 24 APGLVECPNCGEPKL-----PHRVCPSCGYY 49 (57)
T ss_pred CCcceECCCCCCccC-----CeEECCCCCcC
Confidence 345578999998875 48888888853
No 274
>PRK14810 formamidopyrimidine-DNA glycosylase; Provisional
Probab=34.17 E-value=24 Score=36.84 Aligned_cols=27 Identities=30% Similarity=0.686 Sum_probs=21.2
Q ss_pred cCccCCccCcccccc--CCcceEEccccc
Q 006225 600 HGLSCPNCRQFNAKV--GNNNHMFCWACQ 626 (655)
Q Consensus 600 ~~k~CP~C~~~ieK~--~GCnhm~C~~C~ 626 (655)
..++||.|+..|++. +|=.-..|..|+
T Consensus 243 ~g~pCprCG~~I~~~~~~gR~t~~CP~CQ 271 (272)
T PRK14810 243 TGEPCLNCKTPIRRVVVAGRSSHYCPHCQ 271 (272)
T ss_pred CCCcCCCCCCeeEEEEECCCccEECcCCc
Confidence 358999999999876 566667777776
No 275
>PF15616 TerY-C: TerY-C metal binding domain
Probab=33.05 E-value=25 Score=32.55 Aligned_cols=25 Identities=40% Similarity=0.999 Sum_probs=17.6
Q ss_pred cccCccccceeEEecCcCceeccccCeeeecc
Q 006225 521 AKQCPSCKMAISRTEGCNKIVCNNCGQYFCYR 552 (655)
Q Consensus 521 ~k~CP~C~~~iek~~Gcn~m~C~~C~~~FC~~ 552 (655)
..-||+|+... ..+.|. ||..|||.
T Consensus 77 ~PgCP~CGn~~------~fa~C~-CGkl~Ci~ 101 (131)
T PF15616_consen 77 APGCPHCGNQY------AFAVCG-CGKLFCID 101 (131)
T ss_pred CCCCCCCcChh------cEEEec-CCCEEEeC
Confidence 46699999764 345674 88888854
No 276
>KOG0419 consensus Ubiquitin-protein ligase [Posttranslational modification, protein turnover, chaperones]
Probab=33.03 E-value=1.7e+02 Score=27.07 Aligned_cols=20 Identities=30% Similarity=0.602 Sum_probs=16.9
Q ss_pred EEEEEEcCCCCCCCCCCeEEe
Q 006225 232 IVLTCLLPKSYPSHLPPYFTI 252 (655)
Q Consensus 232 i~L~~~lP~~YPs~~pP~~~l 252 (655)
+.|.++|++.||.. ||.+..
T Consensus 53 FkLtl~FteeYpnk-PP~VrF 72 (152)
T KOG0419|consen 53 FKLTLEFTEEYPNK-PPTVRF 72 (152)
T ss_pred EEEEEEcccccCCC-CCeeEe
Confidence 78999999999997 887643
No 277
>COG1096 Predicted RNA-binding protein (consists of S1 domain and a Zn-ribbon domain) [Translation, ribosomal structure and biogenesis]
Probab=33.02 E-value=29 Score=34.00 Aligned_cols=32 Identities=25% Similarity=0.613 Sum_probs=23.9
Q ss_pred ccCccccceeEEecCcCceeccccCeeeeccccc
Q 006225 522 KQCPSCKMAISRTEGCNKIVCNNCGQYFCYRCNK 555 (655)
Q Consensus 522 k~CP~C~~~iek~~Gcn~m~C~~C~~~FC~~C~~ 555 (655)
-.|++|+..+++ .-+.|.|++||+.==-.|..
T Consensus 150 A~CsrC~~~L~~--~~~~l~Cp~Cg~tEkRKia~ 181 (188)
T COG1096 150 ARCSRCRAPLVK--KGNMLKCPNCGNTEKRKIAK 181 (188)
T ss_pred EEccCCCcceEE--cCcEEECCCCCCEEeeeecc
Confidence 469999999999 34789999999754444433
No 278
>PRK13945 formamidopyrimidine-DNA glycosylase; Provisional
Probab=32.99 E-value=27 Score=36.71 Aligned_cols=27 Identities=22% Similarity=0.620 Sum_probs=21.7
Q ss_pred cCccCCccCcccccc--CCcceEEccccc
Q 006225 600 HGLSCPNCRQFNAKV--GNNNHMFCWACQ 626 (655)
Q Consensus 600 ~~k~CP~C~~~ieK~--~GCnhm~C~~C~ 626 (655)
..++||.|+..|.|. +|=.-..|..|+
T Consensus 253 ~g~pC~~Cg~~I~~~~~~gR~t~~CP~CQ 281 (282)
T PRK13945 253 TGKPCRKCGTPIERIKLAGRSTHWCPNCQ 281 (282)
T ss_pred CcCCCCcCCCeeEEEEECCCccEECCCCc
Confidence 358999999999876 677777888886
No 279
>KOG0422 consensus Ubiquitin-protein ligase [Posttranslational modification, protein turnover, chaperones]
Probab=32.46 E-value=83 Score=29.35 Aligned_cols=21 Identities=29% Similarity=0.547 Sum_probs=18.2
Q ss_pred EEEEEEcCCCCCCCCCCeEEee
Q 006225 232 IVLTCLLPKSYPSHLPPYFTIS 253 (655)
Q Consensus 232 i~L~~~lP~~YPs~~pP~~~l~ 253 (655)
+.|.+.||..||-. ||.+...
T Consensus 51 F~l~I~fp~eYPFK-PP~i~f~ 71 (153)
T KOG0422|consen 51 FRLEIDFPVEYPFK-PPKIKFK 71 (153)
T ss_pred eEEEeeCCCCCCCC-CCeeeee
Confidence 88999999999998 9977654
No 280
>PRK03976 rpl37ae 50S ribosomal protein L37Ae; Reviewed
Probab=32.43 E-value=58 Score=28.18 Aligned_cols=31 Identities=26% Similarity=0.641 Sum_probs=21.5
Q ss_pred ccccCccccceeEEecCcCceeccccCeeee
Q 006225 520 DAKQCPSCKMAISRTEGCNKIVCNNCGQYFC 550 (655)
Q Consensus 520 ~~k~CP~C~~~iek~~Gcn~m~C~~C~~~FC 550 (655)
....||.|+..-.+..+--.-.|..|+..|=
T Consensus 35 a~y~CpfCgk~~vkR~a~GIW~C~~C~~~~A 65 (90)
T PRK03976 35 AKHVCPVCGRPKVKRVGTGIWECRKCGAKFA 65 (90)
T ss_pred cCccCCCCCCCceEEEEEEEEEcCCCCCEEe
Confidence 3466999987766655555566877777663
No 281
>TIGR00622 ssl1 transcription factor ssl1. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=31.94 E-value=29 Score=31.25 Aligned_cols=38 Identities=21% Similarity=0.707 Sum_probs=27.8
Q ss_pred cccCccccceeEEe--------cCcCceeccccCeeeecccccccc
Q 006225 521 AKQCPSCKMAISRT--------EGCNKIVCNNCGQYFCYRCNKAID 558 (655)
Q Consensus 521 ~k~CP~C~~~iek~--------~Gcn~m~C~~C~~~FC~~C~~~~~ 558 (655)
.+.|-.|...+... ..-....|.+|+..||..|..-+|
T Consensus 55 ~~~C~~C~~~f~~~~~~~~~~~~~~~~y~C~~C~~~FC~dCD~fiH 100 (112)
T TIGR00622 55 SRFCFGCQGPFPKPPVSPFDELKDSHRYVCAVCKNVFCVDCDVFVH 100 (112)
T ss_pred CCcccCcCCCCCCcccccccccccccceeCCCCCCccccccchhhh
Confidence 35699999876431 123456799999999999987764
No 282
>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=31.78 E-value=35 Score=24.25 Aligned_cols=26 Identities=19% Similarity=0.522 Sum_probs=17.3
Q ss_pred ccCccccceeEEecC---cCceeccccCe
Q 006225 522 KQCPSCKMAISRTEG---CNKIVCNNCGQ 547 (655)
Q Consensus 522 k~CP~C~~~iek~~G---cn~m~C~~C~~ 547 (655)
-.||.|+..++...+ .....|+.||.
T Consensus 6 y~C~~Cg~~fe~~~~~~~~~~~~CP~Cg~ 34 (41)
T smart00834 6 YRCEDCGHTFEVLQKISDDPLATCPECGG 34 (41)
T ss_pred EEcCCCCCEEEEEEecCCCCCCCCCCCCC
Confidence 368999987765332 34567887775
No 283
>KOG0421 consensus Ubiquitin-protein ligase [Posttranslational modification, protein turnover, chaperones]
Probab=31.39 E-value=75 Score=29.62 Aligned_cols=42 Identities=19% Similarity=0.400 Sum_probs=27.2
Q ss_pred EEEEEEcCCCCCCCCCCeE-EeecccCCHHH--HHHHHHHHHHHHH
Q 006225 232 IVLTCLLPKSYPSHLPPYF-TISARWLNSTK--ISNLCSMLESIWI 274 (655)
Q Consensus 232 i~L~~~lP~~YPs~~pP~~-~l~s~wL~~~~--l~~L~~~L~~~~e 274 (655)
..|..+||.+||.. ||.+ .+++-|-..-+ -..-.+.|.+.|.
T Consensus 78 yklSl~Fp~~YPy~-pP~vkFltpc~HPNVD~~GnIcLDILkdKWS 122 (175)
T KOG0421|consen 78 YKLSLSFPNNYPYK-PPTVKFLTPCFHPNVDLSGNICLDILKDKWS 122 (175)
T ss_pred EEEEEecCCCCCCC-CCeeEeeccccCCCccccccchHHHHHHHHH
Confidence 66788999999998 7755 45554433222 2233466778886
No 284
>TIGR00280 L37a ribosomal protein L37a. This model finds eukaryotic ribosomal protein L37a and its archaeal orthologs. The nomeclature is tricky because eukaryotes have proteins called both L37 and L37a.
Probab=31.04 E-value=59 Score=28.16 Aligned_cols=31 Identities=23% Similarity=0.570 Sum_probs=21.2
Q ss_pred ccccCccccceeEEecCcCceeccccCeeee
Q 006225 520 DAKQCPSCKMAISRTEGCNKIVCNNCGQYFC 550 (655)
Q Consensus 520 ~~k~CP~C~~~iek~~Gcn~m~C~~C~~~FC 550 (655)
....||.|+..-.+..+--.-.|..|+..|=
T Consensus 34 a~y~CpfCgk~~vkR~a~GIW~C~~C~~~~A 64 (91)
T TIGR00280 34 AKYVCPFCGKKTVKRGSTGIWTCRKCGAKFA 64 (91)
T ss_pred cCccCCCCCCCceEEEeeEEEEcCCCCCEEe
Confidence 3567999987656655555566877777663
No 285
>PTZ00255 60S ribosomal protein L37a; Provisional
Probab=30.69 E-value=64 Score=27.93 Aligned_cols=31 Identities=16% Similarity=0.429 Sum_probs=21.2
Q ss_pred ccccCccccceeEEecCcCceeccccCeeee
Q 006225 520 DAKQCPSCKMAISRTEGCNKIVCNNCGQYFC 550 (655)
Q Consensus 520 ~~k~CP~C~~~iek~~Gcn~m~C~~C~~~FC 550 (655)
....||.|+..-.+..+-..-.|..|+..|=
T Consensus 35 a~y~CpfCgk~~vkR~a~GIW~C~~C~~~~A 65 (90)
T PTZ00255 35 AKYFCPFCGKHAVKRQAVGIWRCKGCKKTVA 65 (90)
T ss_pred CCccCCCCCCCceeeeeeEEEEcCCCCCEEe
Confidence 3566999987655655555566877777663
No 286
>COG5222 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=30.68 E-value=43 Score=34.93 Aligned_cols=60 Identities=17% Similarity=0.368 Sum_probs=34.0
Q ss_pred ChHHHHHHHHHHHHHHhhcCCCc----------ccccCCCCCcccccccccccccccceeecccccccc--CCcCCCc
Q 006225 414 GDEEFERWESLMLQKTLESMSDV----------AYCPRCETPCIEDEEQHAQCSKCFYSFCTLCRERRH--VGVVCMT 479 (655)
Q Consensus 414 ~~e~~ery~~~~~~~~l~~~~~~----------~~CP~C~~~~~~~~~~~~~C~~C~~~fC~~C~~~~H--~~~sC~~ 479 (655)
+...++.|++...... .+++. ..||-|....... +.-+-|++.||..|....- ....|+.
T Consensus 244 dvqsWe~Yq~r~~a~~--~~~Dqv~k~~~~~i~LkCplc~~Llrnp----~kT~cC~~~fc~eci~~al~dsDf~Cpn 315 (427)
T COG5222 244 DVQSWEKYQQRTKAVA--EIPDQVYKMQPPNISLKCPLCHCLLRNP----MKTPCCGHTFCDECIGTALLDSDFKCPN 315 (427)
T ss_pred chHHHHHHHHHHHhhh--hCchhhhccCCCCccccCcchhhhhhCc----ccCccccchHHHHHHhhhhhhccccCCC
Confidence 4446777776544332 33332 4588887654332 1114599999999987422 2344654
No 287
>PF01396 zf-C4_Topoisom: Topoisomerase DNA binding C4 zinc finger; InterPro: IPR013498 DNA topoisomerases regulate the number of topological links between two DNA strands (i.e. change the number of superhelical turns) by catalysing transient single- or double-strand breaks, crossing the strands through one another, then resealing the breaks []. These enzymes have several functions: to remove DNA supercoils during transcription and DNA replication; for strand breakage during recombination; for chromosome condensation; and to disentangle intertwined DNA during mitosis [, ]. DNA topoisomerases are divided into two classes: type I enzymes (5.99.1.2 from EC; topoisomerases I, III and V) break single-strand DNA, and type II enzymes (5.99.1.3 from EC; topoisomerases II, IV and VI) break double-strand DNA []. Type I topoisomerases are ATP-independent enzymes (except for reverse gyrase), and can be subdivided according to their structure and reaction mechanisms: type IA (bacterial and archaeal topoisomerase I, topoisomerase III and reverse gyrase) and type IB (eukaryotic topoisomerase I and topoisomerase V). These enzymes are primarily responsible for relaxing positively and/or negatively supercoiled DNA, except for reverse gyrase, which can introduce positive supercoils into DNA. This entry represents the zinc-finger domain found in type IA topoisomerases, including bacterial and archaeal topoisomerase I and III enzymes, and in eukaryotic topoisomerase III enzymes. Escherichia coli topoisomerase I proteins contain five copies of a zinc-ribbon-like domain at their C terminus, two of which have lost their cysteine residues and are therefore probably not able to bind zinc []. This domain is still considered to be a member of the zinc-ribbon superfamily despite not being able to bind zinc. More information about this protein can be found at Protein of the Month: DNA Topoisomerase [].; GO: 0003677 DNA binding, 0003916 DNA topoisomerase activity, 0006265 DNA topological change, 0005694 chromosome
Probab=30.66 E-value=38 Score=24.37 Aligned_cols=22 Identities=23% Similarity=0.594 Sum_probs=15.0
Q ss_pred ccCCccCc-cccccC--CcceEEccc
Q 006225 602 LSCPNCRQ-FNAKVG--NNNHMFCWA 624 (655)
Q Consensus 602 k~CP~C~~-~ieK~~--GCnhm~C~~ 624 (655)
..||.|+. ++.|.+ | ..+.|+.
T Consensus 2 ~~CP~Cg~~lv~r~~k~g-~F~~Cs~ 26 (39)
T PF01396_consen 2 EKCPKCGGPLVLRRGKKG-KFLGCSN 26 (39)
T ss_pred cCCCCCCceeEEEECCCC-CEEECCC
Confidence 47999995 455554 4 6677873
No 288
>KOG2807 consensus RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit SSL1 [Transcription; Replication, recombination and repair]
Probab=30.39 E-value=32 Score=36.50 Aligned_cols=39 Identities=21% Similarity=0.476 Sum_probs=28.4
Q ss_pred CcccccCCCCCcccccccccccccccceeeccccccccCCc
Q 006225 435 DVAYCPRCETPCIEDEEQHAQCSKCFYSFCTLCRERRHVGV 475 (655)
Q Consensus 435 ~~~~CP~C~~~~~~~~~~~~~C~~C~~~fC~~C~~~~H~~~ 475 (655)
+...|-.|+.. .......+|..|+..||..|..-.|..+
T Consensus 329 ~~~~Cf~C~~~--~~~~~~y~C~~Ck~~FCldCDv~iHesL 367 (378)
T KOG2807|consen 329 GSRFCFACQGE--LLSSGRYRCESCKNVFCLDCDVFIHESL 367 (378)
T ss_pred CCcceeeeccc--cCCCCcEEchhccceeeccchHHHHhhh
Confidence 44458788432 2334678999999999999998777654
No 289
>COG5151 SSL1 RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit SSL1 [Transcription / DNA replication, recombination, and repair]
Probab=30.19 E-value=18 Score=37.83 Aligned_cols=87 Identities=21% Similarity=0.423 Sum_probs=50.2
Q ss_pred CCcccHhhHHHHHHHHhhcCCcceeccCCCCCCCCCCcccccccCChHHHHHHHHHHH-HHHhh----cCCCcccccCCC
Q 006225 369 HHFFCWKCMKTYLDIHISEGTVSKLQCPDAKCGGMVPPSLLKKLLGDEEFERWESLML-QKTLE----SMSDVAYCPRCE 443 (655)
Q Consensus 369 ~H~fC~~Cl~~yi~~~i~~g~~~~i~CP~~~C~~~l~~~~i~~ll~~e~~ery~~~~~-~~~l~----~~~~~~~CP~C~ 443 (655)
|-++|..|-..-.. .++.||. |.. .-+++..+...|..+.- +.+.+ .++....|-.|+
T Consensus 307 gGy~CP~CktkVCs--------LPi~CP~--Csl-------~LilsthLarSyhhL~PLk~f~E~p~~~~~ks~~Cf~CQ 369 (421)
T COG5151 307 GGYECPVCKTKVCS--------LPISCPI--CSL-------QLILSTHLARSYHHLYPLKPFVEKPEGTNPKSTHCFVCQ 369 (421)
T ss_pred CceeCCcccceeec--------CCccCcc--hhH-------HHHHHHHHHHHHHhhccCcccccccCCCCCCCccceecc
Confidence 34566666443221 3677775 543 23444455555554432 11221 233445688899
Q ss_pred CCcccc---------cccccccccccceeecccccccc
Q 006225 444 TPCIED---------EEQHAQCSKCFYSFCTLCRERRH 472 (655)
Q Consensus 444 ~~~~~~---------~~~~~~C~~C~~~fC~~C~~~~H 472 (655)
.++... .....+|+.|...||..|..-.|
T Consensus 370 ~~fp~~~~~~~~~~~ss~rY~Ce~CK~~FC~dCdvfiH 407 (421)
T COG5151 370 GPFPKPPVSPFDESTSSGRYQCELCKSTFCSDCDVFIH 407 (421)
T ss_pred CCCCCCCCCcccccccccceechhhhhhhhhhhHHHHH
Confidence 877532 23568999999999999977554
No 290
>PF14446 Prok-RING_1: Prokaryotic RING finger family 1
Probab=30.03 E-value=50 Score=25.77 Aligned_cols=32 Identities=25% Similarity=0.597 Sum_probs=26.3
Q ss_pred ccccccccccc-CCCeEec-CCCCcccHhhHHHH
Q 006225 349 HECRICFSEFA-GTDFVRL-PCHHFFCWKCMKTY 380 (655)
Q Consensus 349 ~~C~IC~e~~~-~~~~~~l-~C~H~fC~~Cl~~y 380 (655)
--|.+|-+.+. .++.+.. .|+-.+.++||...
T Consensus 6 ~~C~~Cg~~~~~~dDiVvCp~CgapyHR~C~~~~ 39 (54)
T PF14446_consen 6 CKCPVCGKKFKDGDDIVVCPECGAPYHRDCWEKA 39 (54)
T ss_pred ccChhhCCcccCCCCEEECCCCCCcccHHHHhhC
Confidence 46999999986 5666666 79999999999763
No 291
>COG5574 PEX10 RING-finger-containing E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=29.78 E-value=18 Score=37.31 Aligned_cols=33 Identities=21% Similarity=0.451 Sum_probs=25.2
Q ss_pred CccCCccCccccccCCcceEEccccccccccccccc-ccc
Q 006225 601 GLSCPNCRQFNAKVGNNNHMFCWACQIHYCYLCKKI-VRR 639 (655)
Q Consensus 601 ~k~CP~C~~~ieK~~GCnhm~C~~C~~~FC~~C~~~-~~~ 639 (655)
-.+|+-|--..++ -.|.-||+-|||.|+-. |..
T Consensus 215 d~kC~lC~e~~~~------ps~t~CgHlFC~~Cl~~~~t~ 248 (271)
T COG5574 215 DYKCFLCLEEPEV------PSCTPCGHLFCLSCLLISWTK 248 (271)
T ss_pred ccceeeeecccCC------cccccccchhhHHHHHHHHHh
Confidence 3679999877654 46778999999999887 764
No 292
>KOG3161 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=29.69 E-value=16 Score=41.95 Aligned_cols=34 Identities=29% Similarity=0.660 Sum_probs=26.6
Q ss_pred cccccccccccCCC--eEecCCCCcccHhhHHHHHH
Q 006225 349 HECRICFSEFAGTD--FVRLPCHHFFCWKCMKTYLD 382 (655)
Q Consensus 349 ~~C~IC~e~~~~~~--~~~l~C~H~fC~~Cl~~yi~ 382 (655)
..|.||+..|.... .+.+.|||..|+.|+.....
T Consensus 12 l~c~ic~n~f~~~~~~Pvsl~cghtic~~c~~~lyn 47 (861)
T KOG3161|consen 12 LLCDICLNLFVVQRLEPVSLQCGHTICGHCVQLLYN 47 (861)
T ss_pred hhchHHHHHHHHHhcCcccccccchHHHHHHHhHhh
Confidence 57999988876443 45578999999999987643
No 293
>KOG0309 consensus Conserved WD40 repeat-containing protein [Function unknown]
Probab=29.61 E-value=32 Score=40.30 Aligned_cols=46 Identities=28% Similarity=0.636 Sum_probs=35.7
Q ss_pred ccccccccccccCCCeEecCCCCcccHhhHHHHHHHHhhcCCcceeccCCCCCCC
Q 006225 348 FHECRICFSEFAGTDFVRLPCHHFFCWKCMKTYLDIHISEGTVSKLQCPDAKCGG 402 (655)
Q Consensus 348 ~~~C~IC~e~~~~~~~~~l~C~H~fC~~Cl~~yi~~~i~~g~~~~i~CP~~~C~~ 402 (655)
.+.|.||--.+.+..++...|+|....+|++.||.. |. .||. +|+.
T Consensus 1028 ~~~C~~C~l~V~gss~~Cg~C~Hv~H~sc~~eWf~~----gd----~Cps-GCGC 1073 (1081)
T KOG0309|consen 1028 TFQCAICHLAVRGSSNFCGTCGHVGHTSCMMEWFRT----GD----VCPS-GCGC 1073 (1081)
T ss_pred eeeeeeEeeEeeccchhhccccccccHHHHHHHHhc----CC----cCCC-CCCc
Confidence 467999987777776777789999999999999975 32 6885 4443
No 294
>KOG4362 consensus Transcriptional regulator BRCA1 [Replication, recombination and repair; Transcription]
Probab=29.20 E-value=14 Score=43.06 Aligned_cols=62 Identities=23% Similarity=0.480 Sum_probs=44.6
Q ss_pred hhhccccccccccccccccCCCeEecCCCCcccHhhHHHHHHHHhhcCCcceeccCCCCCCCCCCcccccc
Q 006225 341 HENFLKSFHECRICFSEFAGTDFVRLPCHHFFCWKCMKTYLDIHISEGTVSKLQCPDAKCGGMVPPSLLKK 411 (655)
Q Consensus 341 ~~~f~~~~~~C~IC~e~~~~~~~~~l~C~H~fC~~Cl~~yi~~~i~~g~~~~i~CP~~~C~~~l~~~~i~~ 411 (655)
...+.+...+|+||+..+. +.+.+.|.|.||..|+..-+...-. ...||. |+..+.-..++.
T Consensus 14 vi~~~~k~lEc~ic~~~~~--~p~~~kc~~~~l~~~~n~~f~~~~~-----~~~~~l--c~~~~eK~s~~E 75 (684)
T KOG4362|consen 14 VINAMQKILECPICLEHVK--EPSLLKCDHIFLKFCLNKLFESKKG-----PKQCAL--CKSDIEKRSLRE 75 (684)
T ss_pred HHHHHhhhccCCceeEEee--ccchhhhhHHHHhhhhhceeeccCc-----cccchh--hhhhhhhhhccc
Confidence 3456667789999999875 3366799999999999987664321 577887 776665544444
No 295
>KOG0424 consensus Ubiquitin-protein ligase [Posttranslational modification, protein turnover, chaperones]
Probab=28.38 E-value=46 Score=31.12 Aligned_cols=22 Identities=36% Similarity=0.650 Sum_probs=17.2
Q ss_pred EEEEEEcCCCCCCCCCCeEEeec
Q 006225 232 IVLTCLLPKSYPSHLPPYFTISA 254 (655)
Q Consensus 232 i~L~~~lP~~YPs~~pP~~~l~s 254 (655)
..|.+.||++||+. ||......
T Consensus 58 y~l~v~F~~dyP~~-PPkckF~~ 79 (158)
T KOG0424|consen 58 YKLTVNFPDDYPSS-PPKCKFKP 79 (158)
T ss_pred EEEEEeCCccCCCC-CCccccCC
Confidence 56889999999998 88655443
No 296
>PF03966 Trm112p: Trm112p-like protein; InterPro: IPR005651 This family of short proteins have no known function. The bacterial members are about 60-70 amino acids in length and the eukaryotic examples are about 120 amino acids in length. The C terminus contains the strongest conservation. The function of this family is uncertain. The bacterial members are about 60-70 amino acids in length and the eukaryotic examples are about 120 amino acids in length. The C terminus contains the strongest conservation. The entry contains 2 families: Trm112, which is required for tRNA methylation in Saccharomyces cerevisiae (Baker's yeast) and is found in complexes with 2 tRNA methylases (TRM9 and TRM11) also with putative methyltransferase YDR140W []. The zinc-finger protein Ynr046w is plurifunctional and a component of the eRF1 methyltransferase in yeast []. The crystal structure of Ynr046w has been determined to 1.7 A resolution. It comprises a zinc-binding domain built from both the N- and C-terminal sequences and an inserted domain, absent from bacterial and archaeal orthologs of the protein, composed of three alpha-helices []. UPF0434, which are proteins that are functionally uncharacterised. ; PDB: 3Q87_A 2KPI_A 2K5R_A 2HF1_A 2JS4_A 2J6A_A 2JR6_A 2PK7_A 2JNY_A.
Probab=28.30 E-value=30 Score=28.00 Aligned_cols=13 Identities=23% Similarity=0.585 Sum_probs=8.8
Q ss_pred cccccccccccee
Q 006225 451 EQHAQCSKCFYSF 463 (655)
Q Consensus 451 ~~~~~C~~C~~~f 463 (655)
.....|+.|++.|
T Consensus 51 eg~L~Cp~c~r~Y 63 (68)
T PF03966_consen 51 EGELICPECGREY 63 (68)
T ss_dssp TTEEEETTTTEEE
T ss_pred CCEEEcCCCCCEE
Confidence 3456777777766
No 297
>COG3478 Predicted nucleic-acid-binding protein containing a Zn-ribbon domain [General function prediction only]
Probab=28.27 E-value=50 Score=26.61 Aligned_cols=10 Identities=20% Similarity=0.434 Sum_probs=8.0
Q ss_pred ceEEcccccc
Q 006225 618 NHMFCWACQI 627 (655)
Q Consensus 618 nhm~C~~C~~ 627 (655)
-+++|.+||+
T Consensus 39 ~~itCk~CgY 48 (68)
T COG3478 39 IVITCKNCGY 48 (68)
T ss_pred EEEEeccCCc
Confidence 4589999995
No 298
>PF06943 zf-LSD1: LSD1 zinc finger; InterPro: IPR005735 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 model describes a putative zinc finger domain found in three closely spaced copies in Arabidopsis protein LSD1 and in two copies in other proteins from the same species. The motif resembles CxxCRxxLMYxxGASxVxCxxC []. This domain may play a role in the regulation of transcription, via either repression of a prodeath pathway or activation of an antideath pathway, in response to signals emanating from cells undergoing pathogen-induced hypersensitive cell death. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].
Probab=28.11 E-value=57 Score=21.32 Aligned_cols=24 Identities=21% Similarity=0.690 Sum_probs=20.3
Q ss_pred CccccceeEEecCcCceeccccCe
Q 006225 524 CPSCKMAISRTEGCNKIVCNNCGQ 547 (655)
Q Consensus 524 CP~C~~~iek~~Gcn~m~C~~C~~ 547 (655)
|-+|++.+.-..|-..+.|..|++
T Consensus 1 C~~Cr~~L~yp~GA~sVrCa~C~~ 24 (25)
T PF06943_consen 1 CGGCRTLLMYPRGAPSVRCACCHT 24 (25)
T ss_pred CCCCCceEEcCCCCCCeECCccCc
Confidence 568999998889999999988864
No 299
>PLN02189 cellulose synthase
Probab=28.04 E-value=35 Score=41.89 Aligned_cols=35 Identities=26% Similarity=0.610 Sum_probs=27.5
Q ss_pred CcccccCCCCCcc--cccccccccccccceeeccccc
Q 006225 435 DVAYCPRCETPCI--EDEEQHAQCSKCFYSFCTLCRE 469 (655)
Q Consensus 435 ~~~~CP~C~~~~~--~~~~~~~~C~~C~~~fC~~C~~ 469 (655)
+...|..|+..+. .+....+.|..|++..|..|..
T Consensus 33 ~~~~C~iCgd~vg~~~~g~~fvaC~~C~fpvCr~Cye 69 (1040)
T PLN02189 33 DGQVCEICGDEIGLTVDGDLFVACNECGFPVCRPCYE 69 (1040)
T ss_pred cCccccccccccCcCCCCCEEEeeccCCCccccchhh
Confidence 3447999998765 3456779999999999999864
No 300
>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=28.00 E-value=83 Score=28.94 Aligned_cols=29 Identities=21% Similarity=0.565 Sum_probs=22.8
Q ss_pred ccccCccccce---eEEecCcCceeccccCee
Q 006225 520 DAKQCPSCKMA---ISRTEGCNKIVCNNCGQY 548 (655)
Q Consensus 520 ~~k~CP~C~~~---iek~~Gcn~m~C~~C~~~ 548 (655)
....||.|+.+ +.+..+--.+.|..||..
T Consensus 92 ~yVlC~~C~spdT~l~k~~r~~~l~C~aCGa~ 123 (125)
T PF01873_consen 92 EYVLCPECGSPDTELIKEGRLIFLKCKACGAS 123 (125)
T ss_dssp HHSSCTSTSSSSEEEEEETTCCEEEETTTSCE
T ss_pred HEEEcCCCCCCccEEEEcCCEEEEEecccCCc
Confidence 35789999976 666777788999989864
No 301
>KOG1940 consensus Zn-finger protein [General function prediction only]
Probab=27.84 E-value=61 Score=33.93 Aligned_cols=45 Identities=29% Similarity=0.620 Sum_probs=32.9
Q ss_pred ccccccccccccC--CCeEecCCCCcccHhhHHHHHHHHhhcCCcceeccCCCCCCC
Q 006225 348 FHECRICFSEFAG--TDFVRLPCHHFFCWKCMKTYLDIHISEGTVSKLQCPDAKCGG 402 (655)
Q Consensus 348 ~~~C~IC~e~~~~--~~~~~l~C~H~fC~~Cl~~yi~~~i~~g~~~~i~CP~~~C~~ 402 (655)
.+.|+||.+.... .....+.|+|..-..|+..++- ++ ..||. |..
T Consensus 158 ~~ncPic~e~l~~s~~~~~~~~CgH~~h~~cf~e~~~----~~----y~CP~--C~~ 204 (276)
T KOG1940|consen 158 EFNCPICKEYLFLSFEDAGVLKCGHYMHSRCFEEMIC----EG----YTCPI--CSK 204 (276)
T ss_pred cCCCchhHHHhccccccCCccCcccchHHHHHHHHhc----cC----CCCCc--ccc
Confidence 3559999987543 2334469999999999999854 22 78997 776
No 302
>COG1656 Uncharacterized conserved protein [Function unknown]
Probab=27.83 E-value=44 Score=32.14 Aligned_cols=15 Identities=20% Similarity=0.671 Sum_probs=11.6
Q ss_pred CCCcccccCCCCCcc
Q 006225 433 MSDVAYCPRCETPCI 447 (655)
Q Consensus 433 ~~~~~~CP~C~~~~~ 447 (655)
.+.+..||.|+..+.
T Consensus 94 ~~e~~RCp~CN~~L~ 108 (165)
T COG1656 94 FPEFSRCPECNGELE 108 (165)
T ss_pred ccccccCcccCCEec
Confidence 345778999998764
No 303
>KOG3039 consensus Uncharacterized conserved protein [Function unknown]
Probab=27.79 E-value=49 Score=33.78 Aligned_cols=38 Identities=18% Similarity=0.276 Sum_probs=29.8
Q ss_pred cccccccccccccCCCeEecCCCCcccHhhHHHHHHHHhh
Q 006225 347 SFHECRICFSEFAGTDFVRLPCHHFFCWKCMKTYLDIHIS 386 (655)
Q Consensus 347 ~~~~C~IC~e~~~~~~~~~l~C~H~fC~~Cl~~yi~~~i~ 386 (655)
.+.-|.+|+..+. +++..+=||.||++|+.+||..+-+
T Consensus 42 ~FdcCsLtLqPc~--dPvit~~GylfdrEaILe~ilaqKk 79 (303)
T KOG3039|consen 42 PFDCCSLTLQPCR--DPVITPDGYLFDREAILEYILAQKK 79 (303)
T ss_pred Ccceeeeeccccc--CCccCCCCeeeeHHHHHHHHHHHHH
Confidence 4457999998763 5666677999999999999876643
No 304
>PF05290 Baculo_IE-1: Baculovirus immediate-early protein (IE-0); InterPro: IPR007954 This entry contains the Baculovirus immediate-early protein IE-0.
Probab=27.44 E-value=47 Score=30.78 Aligned_cols=52 Identities=23% Similarity=0.446 Sum_probs=40.5
Q ss_pred cccccccccccccCCCeEec--CCCCcccHhhHHHHHHHHhhcCCcceeccCCCCCCCCCC
Q 006225 347 SFHECRICFSEFAGTDFVRL--PCHHFFCWKCMKTYLDIHISEGTVSKLQCPDAKCGGMVP 405 (655)
Q Consensus 347 ~~~~C~IC~e~~~~~~~~~l--~C~H~fC~~Cl~~yi~~~i~~g~~~~i~CP~~~C~~~l~ 405 (655)
...+|.||-+......|... -||=..|..|-.+.|+..- ....||. |+..+-
T Consensus 79 ~lYeCnIC~etS~ee~FLKPneCCgY~iCn~Cya~LWK~~~-----~ypvCPv--CkTSFK 132 (140)
T PF05290_consen 79 KLYECNICKETSAEERFLKPNECCGYSICNACYANLWKFCN-----LYPVCPV--CKTSFK 132 (140)
T ss_pred CceeccCcccccchhhcCCcccccchHHHHHHHHHHHHHcc-----cCCCCCc--cccccc
Confidence 45799999998776667665 3898999999999988653 2578998 887653
No 305
>PRK05580 primosome assembly protein PriA; Validated
Probab=27.42 E-value=40 Score=40.08 Aligned_cols=35 Identities=23% Similarity=0.749 Sum_probs=27.8
Q ss_pred ccCccccceeEEecCcCceeccccCee-----eecccccc
Q 006225 522 KQCPSCKMAISRTEGCNKIVCNNCGQY-----FCYRCNKA 556 (655)
Q Consensus 522 k~CP~C~~~iek~~Gcn~m~C~~C~~~-----FC~~C~~~ 556 (655)
-.||+|..++.-...-+.+.|..||+. .|-.|+..
T Consensus 391 ~~C~~C~~~l~~h~~~~~l~Ch~Cg~~~~~~~~Cp~Cg~~ 430 (679)
T PRK05580 391 AECPHCDASLTLHRFQRRLRCHHCGYQEPIPKACPECGST 430 (679)
T ss_pred cCCCCCCCceeEECCCCeEECCCCcCCCCCCCCCCCCcCC
Confidence 469999988876556678999999976 58888765
No 306
>PRK08115 ribonucleotide-diphosphate reductase subunit alpha; Validated
Probab=27.37 E-value=27 Score=42.19 Aligned_cols=25 Identities=32% Similarity=0.781 Sum_probs=21.4
Q ss_pred ccCCccCc-cccccCCcceEEccccccc
Q 006225 602 LSCPNCRQ-FNAKVGNNNHMFCWACQIH 628 (655)
Q Consensus 602 k~CP~C~~-~ieK~~GCnhm~C~~C~~~ 628 (655)
-.||-|+. .|+..|||| +|+.|+.+
T Consensus 828 ~~cp~c~~~~~~~~~~c~--~c~~c~~~ 853 (858)
T PRK08115 828 NTCPVCREGTVEEIGGCN--TCTNCGAQ 853 (858)
T ss_pred CCCCccCCCceeecCCCc--cccchhhh
Confidence 58999995 899999999 68888854
No 307
>TIGR01031 rpmF_bact ribosomal protein L32. This protein describes bacterial ribosomal protein L32. The noise cutoff is set low enough to include the equivalent protein from mitochondria and chloroplasts. No related proteins from the Archaea nor from the eukaryotic cytosol are detected by this model. This model is a fragment model; the putative L32 of some species shows similarity only toward the N-terminus.
Probab=27.22 E-value=43 Score=26.15 Aligned_cols=24 Identities=33% Similarity=0.808 Sum_probs=18.2
Q ss_pred ccCccCCccCccccccCCcceEEcccccc
Q 006225 599 EHGLSCPNCRQFNAKVGNNNHMFCWACQI 627 (655)
Q Consensus 599 ~~~k~CP~C~~~ieK~~GCnhm~C~~C~~ 627 (655)
.+...||.|+.+.. .|-.|..||+
T Consensus 24 p~l~~C~~cG~~~~-----~H~vc~~cG~ 47 (55)
T TIGR01031 24 PTLVVCPNCGEFKL-----PHRVCPSCGY 47 (55)
T ss_pred CcceECCCCCCccc-----CeeECCccCe
Confidence 44567999998764 6888888885
No 308
>PRK14873 primosome assembly protein PriA; Provisional
Probab=27.07 E-value=40 Score=39.88 Aligned_cols=35 Identities=23% Similarity=0.599 Sum_probs=25.8
Q ss_pred ccCccccceeEEecCcCceeccccCee----eecccccc
Q 006225 522 KQCPSCKMAISRTEGCNKIVCNNCGQY----FCYRCNKA 556 (655)
Q Consensus 522 k~CP~C~~~iek~~Gcn~m~C~~C~~~----FC~~C~~~ 556 (655)
-.||+|..++....+-+.+.|..||+. .|-.|+..
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 469999988877656678999999863 46666654
No 309
>KOG0429 consensus Ubiquitin-conjugating enzyme-related protein Ft1, involved in programmed cell death [Posttranslational modification, protein turnover, chaperones]
Probab=26.94 E-value=1.2e+02 Score=30.50 Aligned_cols=62 Identities=18% Similarity=0.307 Sum_probs=41.8
Q ss_pred EEEEEEcCCCCC-CCCCCeEEeecccC----CH-HHHHHHHHHHHHHHHhCCCchhhHHHHHHHhhccccc
Q 006225 232 IVLTCLLPKSYP-SHLPPYFTISARWL----NS-TKISNLCSMLESIWIDQPGQEILYQWIEWLQNSSLSY 296 (655)
Q Consensus 232 i~L~~~lP~~YP-s~~pP~~~l~s~wL----~~-~~l~~L~~~L~~~~ee~~G~~~lf~~ie~lqe~~~~~ 296 (655)
+.++|.+|++|| +.+.|.+...-+.+ .. +.--.|...+.+ |. .++--|.+++-+||-.+.+.
T Consensus 67 FRFtIliPdnfPdd~dlPrvvF~q~vfHP~icp~skeLdl~raf~e-WR--k~ehhiwqvL~ylqriF~dp 134 (258)
T KOG0429|consen 67 FRFTILIPDNFPDDSDLPRVVFEQSVFHPLICPKSKELDLNRAFPE-WR--KEEHHIWQVLVYLQRIFYDP 134 (258)
T ss_pred EEEEEEcCccCCCcCCCCeEEeeccccccccCCCccceeHhhhhhh-hh--ccccHHHHHHHHHHHHhcCc
Confidence 788999999999 55578654433221 11 222345666666 87 67778999999999666554
No 310
>PRK03824 hypA hydrogenase nickel incorporation protein; Provisional
Probab=26.81 E-value=28 Score=32.40 Aligned_cols=14 Identities=21% Similarity=0.377 Sum_probs=9.8
Q ss_pred CcccccCCCCCccc
Q 006225 435 DVAYCPRCETPCIE 448 (655)
Q Consensus 435 ~~~~CP~C~~~~~~ 448 (655)
...+|+.|+..+..
T Consensus 69 ~~~~C~~CG~~~~~ 82 (135)
T PRK03824 69 AVLKCRNCGNEWSL 82 (135)
T ss_pred eEEECCCCCCEEec
Confidence 45679999876543
No 311
>KOG2315 consensus Predicted translation initiation factor related to eIF-3a [Translation, ribosomal structure and biogenesis]
Probab=26.13 E-value=2e+02 Score=32.80 Aligned_cols=91 Identities=19% Similarity=0.057 Sum_probs=55.6
Q ss_pred CCcccCCcccccccccccccccchhhccc-cccc-cchhhhcccccchhhhhhhhhcccCCCCCCChhhHHHHHHHHhhc
Q 006225 64 IPKYQGNLRWVSRRRRARVAKPKFVKKTE-SREE-KLLNDEVGSLSIGEEVKEKQDEEEGLPSNSNVNDVESILRELSSS 141 (655)
Q Consensus 64 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 141 (655)
++.+-.+.|=.-|++...+||+..--+-- .+.+ +. +. -....|.+|+.|.. .=+|.+.|+++++.
T Consensus 473 ~~~~~~a~Kn~~~~~~k~~a~~~A~~~~~~~~a~~~~----~p-q~~~~ekKir~L~k--------kLraIe~LK~r~a~ 539 (566)
T KOG2315|consen 473 KAGSGSANKNRRRNKEKVVAKPVANQKPRRRRANKPA----TP-QPSEEEKKIRSLLK--------KLRAIEALKERMAN 539 (566)
T ss_pred ccCCccccccccccccccccchhhccCcccccCCCCC----CC-CCchHHHHHHHHHH--------HHHHHHHHHHHHhc
Confidence 44444455556666666665544322211 0111 11 00 12266777777753 44678999999998
Q ss_pred CCCCCccHHhhhchHHHHHHHHHHHH
Q 006225 142 VEEPELEAEQLRINDQSQGDELLALE 167 (655)
Q Consensus 142 ~~~~~~~~~~~~~n~e~Q~~EleaLe 167 (655)
+++-+.++-+...-+..-+.||++|.
T Consensus 540 Ge~Le~nQl~kIq~E~~~l~ELk~L~ 565 (566)
T KOG2315|consen 540 GEQLEVNQLNKIQKEPKLLSELKKLG 565 (566)
T ss_pred ccccCHHHHHHHhhhHHHHHHHHhhc
Confidence 88888888776667778889999884
No 312
>COG1096 Predicted RNA-binding protein (consists of S1 domain and a Zn-ribbon domain) [Translation, ribosomal structure and biogenesis]
Probab=25.89 E-value=40 Score=33.09 Aligned_cols=25 Identities=28% Similarity=0.535 Sum_probs=19.7
Q ss_pred ccCCccCccccccCCcceEEccccccc
Q 006225 602 LSCPNCRQFNAKVGNNNHMFCWACQIH 628 (655)
Q Consensus 602 k~CP~C~~~ieK~~GCnhm~C~~C~~~ 628 (655)
-.|++|+...++ .=+.|.|++|+..
T Consensus 150 A~CsrC~~~L~~--~~~~l~Cp~Cg~t 174 (188)
T COG1096 150 ARCSRCRAPLVK--KGNMLKCPNCGNT 174 (188)
T ss_pred EEccCCCcceEE--cCcEEECCCCCCE
Confidence 479999999988 3467889888853
No 313
>cd00065 FYVE FYVE domain; Zinc-binding domain; targets proteins to membrane lipids via interaction with phosphatidylinositol-3-phosphate, PI3P; present in Fab1, YOTB, Vac1, and EEA1;
Probab=25.67 E-value=37 Score=26.04 Aligned_cols=31 Identities=26% Similarity=0.725 Sum_probs=23.5
Q ss_pred cccCCCCCcccccccccccccccceeeccccc
Q 006225 438 YCPRCETPCIEDEEQHAQCSKCFYSFCTLCRE 469 (655)
Q Consensus 438 ~CP~C~~~~~~~~~~~~~C~~C~~~fC~~C~~ 469 (655)
.|+.|...+.. ......|..||..||..|..
T Consensus 4 ~C~~C~~~F~~-~~rk~~Cr~Cg~~~C~~C~~ 34 (57)
T cd00065 4 SCMGCGKPFTL-TRRRHHCRNCGRIFCSKCSS 34 (57)
T ss_pred cCcccCccccC-CccccccCcCcCCcChHHcC
Confidence 57778765543 23567899999999999976
No 314
>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=25.58 E-value=45 Score=38.14 Aligned_cols=35 Identities=26% Similarity=0.580 Sum_probs=27.2
Q ss_pred ccCCccCccccccCCcceEEccccccc-----cccccccc
Q 006225 602 LSCPNCRQFNAKVGNNNHMFCWACQIH-----YCYLCKKI 636 (655)
Q Consensus 602 k~CP~C~~~ieK~~GCnhm~C~~C~~~-----FC~~C~~~ 636 (655)
..||+|.....-...=|.+.|..||+. .|-.|+..
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 379999976655445568999999965 69999875
No 315
>PRK04023 DNA polymerase II large subunit; Validated
Probab=25.45 E-value=38 Score=41.30 Aligned_cols=35 Identities=23% Similarity=0.378 Sum_probs=26.1
Q ss_pred cccCccCCccCccccccCCcceEEcccccc-----ccccccccccc
Q 006225 598 DEHGLSCPNCRQFNAKVGNNNHMFCWACQI-----HYCYLCKKIVR 638 (655)
Q Consensus 598 ~~~~k~CP~C~~~ieK~~GCnhm~C~~C~~-----~FC~~C~~~~~ 638 (655)
....+.||.|+... ....|..||. .||-.|+....
T Consensus 623 EVg~RfCpsCG~~t------~~frCP~CG~~Te~i~fCP~CG~~~~ 662 (1121)
T PRK04023 623 EIGRRKCPSCGKET------FYRRCPFCGTHTEPVYRCPRCGIEVE 662 (1121)
T ss_pred cccCccCCCCCCcC------CcccCCCCCCCCCcceeCccccCcCC
Confidence 34568999999874 4568888984 58888877654
No 316
>PF14149 YhfH: YhfH-like protein
Probab=25.45 E-value=9 Score=27.37 Aligned_cols=25 Identities=16% Similarity=0.292 Sum_probs=21.3
Q ss_pred CccCCccCccccccCCcceEEcccc
Q 006225 601 GLSCPNCRQFNAKVGNNNHMFCWAC 625 (655)
Q Consensus 601 ~k~CP~C~~~ieK~~GCnhm~C~~C 625 (655)
.|.|+.|+..|+-..-|..++|-+|
T Consensus 13 ~K~C~~CG~~i~EQ~E~Y~n~C~~C 37 (37)
T PF14149_consen 13 PKKCTECGKEIEEQAECYGNECDRC 37 (37)
T ss_pred CcccHHHHHHHHHHHHHHhCcCCCC
Confidence 4899999999988888888888766
No 317
>PRK09521 exosome complex RNA-binding protein Csl4; Provisional
Probab=25.19 E-value=44 Score=32.86 Aligned_cols=26 Identities=31% Similarity=0.539 Sum_probs=20.8
Q ss_pred cCCccCccccccCCcceEEcccccccc
Q 006225 603 SCPNCRQFNAKVGNNNHMFCWACQIHY 629 (655)
Q Consensus 603 ~CP~C~~~ieK~~GCnhm~C~~C~~~F 629 (655)
.|++|+.+..+.++ |.|.|..|++..
T Consensus 151 ~~~~~g~~~~~~~~-~~~~c~~~~~~e 176 (189)
T PRK09521 151 MCSRCRTPLVKKGE-NELKCPNCGNIE 176 (189)
T ss_pred EccccCCceEECCC-CEEECCCCCCEE
Confidence 69999998877544 999999998643
No 318
>PF14462 Prok-E2_E: Prokaryotic E2 family E
Probab=25.00 E-value=83 Score=28.85 Aligned_cols=26 Identities=23% Similarity=0.381 Sum_probs=19.5
Q ss_pred EEEEEEcCCCCCCCCCCeEEeecccCC
Q 006225 232 IVLTCLLPKSYPSHLPPYFTISARWLN 258 (655)
Q Consensus 232 i~L~~~lP~~YPs~~pP~~~l~s~wL~ 258 (655)
+.|.|.+|++||...+.-|.+. .+|.
T Consensus 44 ~dili~iP~gYP~~~~DmfY~~-P~L~ 69 (122)
T PF14462_consen 44 VDILILIPPGYPDAPLDMFYVY-PPLK 69 (122)
T ss_pred eEEEEECCCCCCCCCCCcEEEC-CceE
Confidence 7899999999999866556554 4443
No 319
>COG2824 PhnA Uncharacterized Zn-ribbon-containing protein involved in phosphonate metabolism [Inorganic ion transport and metabolism]
Probab=24.59 E-value=34 Score=30.34 Aligned_cols=26 Identities=19% Similarity=0.649 Sum_probs=17.9
Q ss_pred ccccCCCCCcccccccccccccccce
Q 006225 437 AYCPRCETPCIEDEEQHAQCSKCFYS 462 (655)
Q Consensus 437 ~~CP~C~~~~~~~~~~~~~C~~C~~~ 462 (655)
-.||.|+..+...+...+.||.|.|.
T Consensus 4 p~cp~c~sEytYed~~~~~cpec~~e 29 (112)
T COG2824 4 PPCPKCNSEYTYEDGGQLICPECAHE 29 (112)
T ss_pred CCCCccCCceEEecCceEeCchhccc
Confidence 46899988776665556777666554
No 320
>COG3677 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=24.57 E-value=86 Score=29.00 Aligned_cols=34 Identities=24% Similarity=0.542 Sum_probs=22.6
Q ss_pred CCCcccccCCCCCccc------ccccccccccccceeecc
Q 006225 433 MSDVAYCPRCETPCIE------DEEQHAQCSKCFYSFCTL 466 (655)
Q Consensus 433 ~~~~~~CP~C~~~~~~------~~~~~~~C~~C~~~fC~~ 466 (655)
....+.||.|...... ...+...|+.|+..|=..
T Consensus 27 ~~~~~~cP~C~s~~~~k~g~~~~~~qRyrC~~C~~tf~~~ 66 (129)
T COG3677 27 QITKVNCPRCKSSNVVKIGGIRRGHQRYKCKSCGSTFTVE 66 (129)
T ss_pred hcccCcCCCCCccceeeECCccccccccccCCcCcceeee
Confidence 3355799999876521 235678888888777433
No 321
>COG2051 RPS27A Ribosomal protein S27E [Translation, ribosomal structure and biogenesis]
Probab=24.10 E-value=42 Score=27.20 Aligned_cols=29 Identities=17% Similarity=0.468 Sum_probs=20.6
Q ss_pred ccccCCCCCc--ccccccccccccccceeec
Q 006225 437 AYCPRCETPC--IEDEEQHAQCSKCFYSFCT 465 (655)
Q Consensus 437 ~~CP~C~~~~--~~~~~~~~~C~~C~~~fC~ 465 (655)
+.||+|++.- ..-....+.|..||...+.
T Consensus 20 VkCpdC~N~q~vFshast~V~C~~CG~~l~~ 50 (67)
T COG2051 20 VKCPDCGNEQVVFSHASTVVTCLICGTTLAE 50 (67)
T ss_pred EECCCCCCEEEEeccCceEEEecccccEEEe
Confidence 5699998742 2334567889888887764
No 322
>KOG1571 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=23.61 E-value=37 Score=36.50 Aligned_cols=43 Identities=30% Similarity=0.658 Sum_probs=28.5
Q ss_pred cccccccccccccCCCeEecCCCCcccHhhHHHHHHHHhhcCCcceeccCCCCCCCCC
Q 006225 347 SFHECRICFSEFAGTDFVRLPCHHFFCWKCMKTYLDIHISEGTVSKLQCPDAKCGGMV 404 (655)
Q Consensus 347 ~~~~C~IC~e~~~~~~~~~l~C~H~fC~~Cl~~yi~~~i~~g~~~~i~CP~~~C~~~l 404 (655)
....|.||.++.. ++.-++|||..| |..-+-. -..||. |...+
T Consensus 304 ~p~lcVVcl~e~~--~~~fvpcGh~cc--ct~cs~~---------l~~CPv--CR~rI 346 (355)
T KOG1571|consen 304 QPDLCVVCLDEPK--SAVFVPCGHVCC--CTLCSKH---------LPQCPV--CRQRI 346 (355)
T ss_pred CCCceEEecCCcc--ceeeecCCcEEE--chHHHhh---------CCCCch--hHHHH
Confidence 3468999999865 355569999966 5543311 245997 77543
No 323
>smart00653 eIF2B_5 domain present in translation initiation factor eIF2B and eIF5.
Probab=23.49 E-value=1.1e+02 Score=27.54 Aligned_cols=28 Identities=21% Similarity=0.625 Sum_probs=21.3
Q ss_pred ccccCccccce---eEEecCcCceeccccCe
Q 006225 520 DAKQCPSCKMA---ISRTEGCNKIVCNNCGQ 547 (655)
Q Consensus 520 ~~k~CP~C~~~---iek~~Gcn~m~C~~C~~ 547 (655)
....||.|+.+ +++..+-..+.|..||.
T Consensus 79 ~yVlC~~C~spdT~l~k~~r~~~l~C~aCGa 109 (110)
T smart00653 79 EYVLCPECGSPDTELIKENRLFFLKCEACGA 109 (110)
T ss_pred hcEECCCCCCCCcEEEEeCCeEEEEccccCC
Confidence 46789999976 56666666788988885
No 324
>PF01783 Ribosomal_L32p: Ribosomal L32p protein family; InterPro: IPR002677 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. Ribosomal protein L32p is part of the 50S ribosomal subunit. This family is found in both prokaryotes and eukaryotes. Ribosomal protein L32 of yeast binds to and regulates the splicing and the translation of the transcript of its own gene [].; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0015934 large ribosomal subunit; PDB: 3PYT_2 3F1F_5 3PYV_2 3D5B_5 3MRZ_2 3D5D_5 3F1H_5 1VSP_Y 3PYR_2 3MS1_2 ....
Probab=23.41 E-value=52 Score=25.72 Aligned_cols=23 Identities=30% Similarity=0.781 Sum_probs=16.1
Q ss_pred ccccCccccceeEEecCcCceeccccCe
Q 006225 520 DAKQCPSCKMAISRTEGCNKIVCNNCGQ 547 (655)
Q Consensus 520 ~~k~CP~C~~~iek~~Gcn~m~C~~C~~ 547 (655)
+...||.|+.+.. .|..|+.||+
T Consensus 25 ~l~~c~~cg~~~~-----~H~vc~~cG~ 47 (56)
T PF01783_consen 25 NLVKCPNCGEPKL-----PHRVCPSCGY 47 (56)
T ss_dssp SEEESSSSSSEES-----TTSBCTTTBB
T ss_pred ceeeeccCCCEec-----ccEeeCCCCe
Confidence 5677999986653 4667777763
No 325
>KOG0420 consensus Ubiquitin-protein ligase [Posttranslational modification, protein turnover, chaperones]
Probab=23.36 E-value=1.1e+02 Score=29.60 Aligned_cols=19 Identities=26% Similarity=0.674 Sum_probs=16.5
Q ss_pred EEEEEEcCCCCCCCCCCeEE
Q 006225 232 IVLTCLLPKSYPSHLPPYFT 251 (655)
Q Consensus 232 i~L~~~lP~~YPs~~pP~~~ 251 (655)
+.+.|..|+.||.+ ||.+.
T Consensus 78 f~F~~~v~~~Yp~~-PPKVk 96 (184)
T KOG0420|consen 78 FRFKFKVPNAYPHE-PPKVK 96 (184)
T ss_pred EEEEEECCCCCCCC-CCeee
Confidence 88999999999998 88653
No 326
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=23.28 E-value=85 Score=29.53 Aligned_cols=27 Identities=26% Similarity=0.714 Sum_probs=15.9
Q ss_pred cccCccccceeEEecC------cCceeccccCe
Q 006225 521 AKQCPSCKMAISRTEG------CNKIVCNNCGQ 547 (655)
Q Consensus 521 ~k~CP~C~~~iek~~G------cn~m~C~~C~~ 547 (655)
.-.||+|+..+.-.+. -..++|+.||.
T Consensus 99 ~Y~Cp~C~~~y~~~ea~~~~d~~~~f~Cp~Cg~ 131 (147)
T smart00531 99 YYKCPNCQSKYTFLEANQLLDMDGTFTCPRCGE 131 (147)
T ss_pred EEECcCCCCEeeHHHHHHhcCCCCcEECCCCCC
Confidence 4559999987764321 12266665553
No 327
>KOG2691 consensus RNA polymerase II subunit 9 [Transcription]
Probab=22.80 E-value=90 Score=27.81 Aligned_cols=31 Identities=16% Similarity=0.381 Sum_probs=19.5
Q ss_pred ccccCccccceeEE-ecC---cCceeccccCeeee
Q 006225 520 DAKQCPSCKMAISR-TEG---CNKIVCNNCGQYFC 550 (655)
Q Consensus 520 ~~k~CP~C~~~iek-~~G---cn~m~C~~C~~~FC 550 (655)
+.++|+.|+.++-- .+. --...|.+|.+.|=
T Consensus 3 ~~rfC~eCNNmLYPkEDked~~L~laCrnCd~ve~ 37 (113)
T KOG2691|consen 3 GIRFCRECNNMLYPKEDKEDRILLLACRNCDYVEE 37 (113)
T ss_pred ccchhhhhhccccccccccccEEEEEecCCcceEe
Confidence 46889999987643 222 22355887877663
No 328
>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=22.73 E-value=66 Score=25.25 Aligned_cols=46 Identities=28% Similarity=0.683 Sum_probs=31.3
Q ss_pred cccccccccccCCCeEecCC--CCcccHhhHHHHHHHHhhcCCcceeccCCCCCCCCCCc
Q 006225 349 HECRICFSEFAGTDFVRLPC--HHFFCWKCMKTYLDIHISEGTVSKLQCPDAKCGGMVPP 406 (655)
Q Consensus 349 ~~C~IC~e~~~~~~~~~l~C--~H~fC~~Cl~~yi~~~i~~g~~~~i~CP~~~C~~~l~~ 406 (655)
-.|..|-.+++.+..-..-| ...||.+|....+. -.||. |+..+..
T Consensus 6 pnCE~C~~dLp~~s~~A~ICSfECTFC~~C~e~~l~----------~~CPN--CgGelv~ 53 (57)
T PF06906_consen 6 PNCECCDKDLPPDSPEAYICSFECTFCADCAETMLN----------GVCPN--CGGELVR 53 (57)
T ss_pred CCccccCCCCCCCCCcceEEeEeCcccHHHHHHHhc----------CcCcC--CCCcccc
Confidence 36888988887655222234 34699999988642 35987 8887654
No 329
>COG0266 Nei Formamidopyrimidine-DNA glycosylase [DNA replication, recombination, and repair]
Probab=22.56 E-value=64 Score=33.77 Aligned_cols=27 Identities=22% Similarity=0.635 Sum_probs=20.9
Q ss_pred ccccCccccceeEEe--cCcCceeccccC
Q 006225 520 DAKQCPSCKMAISRT--EGCNKIVCNNCG 546 (655)
Q Consensus 520 ~~k~CP~C~~~iek~--~Gcn~m~C~~C~ 546 (655)
.-.+|+.|+.+|++. +|-+...|+.|.
T Consensus 244 ~GepC~~CGt~I~k~~~~gR~t~~CP~CQ 272 (273)
T COG0266 244 AGEPCRRCGTPIEKIKLGGRSTFYCPVCQ 272 (273)
T ss_pred CCCCCCccCCEeEEEEEcCCcCEeCCCCC
Confidence 357899999999984 566667777775
No 330
>PF05502 Dynactin_p62: Dynactin p62 family; InterPro: IPR008603 Dynactin is a multi-subunit complex and a required cofactor for most, or all, o f the cellular processes powered by the microtubule-based motor cytoplasmic dyn ein. p62 binds directly to the Arp1 subunit of dynactin [, ].
Probab=22.26 E-value=80 Score=35.93 Aligned_cols=67 Identities=22% Similarity=0.570 Sum_probs=0.0
Q ss_pred CCcccccCCCCCcccccccccccccc-----cceeeccccc------cccCCcCCCchHHHHHHHHHhhcchhhhhhhhH
Q 006225 434 SDVAYCPRCETPCIEDEEQHAQCSKC-----FYSFCTLCRE------RRHVGVVCMTPEIKLRILQERQNSSQVKEGQKQ 502 (655)
Q Consensus 434 ~~~~~CP~C~~~~~~~~~~~~~C~~C-----~~~fC~~C~~------~~H~~~sC~~~~~~~~~~~e~~~~~~~~~~~~~ 502 (655)
..+.||..|.. ++|+.| ...||..|.. ..-.+..|
T Consensus 3 ~~L~fC~~C~~---------irc~~c~~~Ei~~~yCp~CL~~~p~~e~~~~~nrC------------------------- 48 (483)
T PF05502_consen 3 EELYFCEHCHK---------IRCPRCVSEEIDSYYCPNCLFEVPSSEARSEKNRC------------------------- 48 (483)
T ss_pred ccceecccccc---------cCChhhcccccceeECccccccCChhhheecccee-------------------------
Q ss_pred HHHHHHHHHHhHHHHhcccccCccccceeEEe----------------cCcCceeccccCeee
Q 006225 503 REHEMINELLSVKEILRDAKQCPSCKMAISRT----------------EGCNKIVCNNCGQYF 549 (655)
Q Consensus 503 ~e~e~~~e~l~~~~i~~~~k~CP~C~~~iek~----------------~Gcn~m~C~~C~~~F 549 (655)
.++...||.|...+... .+-..+.|..|....
T Consensus 49 ---------------~r~Cf~CP~C~~~L~~~~~~~~~~~~~~~~~~~~~~~~l~C~~C~Wss 96 (483)
T PF05502_consen 49 ---------------SRNCFDCPICFSPLSVRASDTPPSPPDPSSDSGGKPYYLSCSYCRWSS 96 (483)
T ss_pred ---------------ccccccCCCCCCcceeEecccccccccccccCCCCCEEEECCCceeec
No 331
>PF03884 DUF329: Domain of unknown function (DUF329); InterPro: IPR005584 The biological function of these short proteins is unknown, but they contain four conserved cysteines, suggesting that they all bind zinc. YacG (Q5X8H6 from SWISSPROT) from Escherichia coli has been shown to bind zinc and contains the structural motifs typical of zinc-binding proteins []. The conserved four cysteine motif in these proteins (-C-X(2)-C-X(15)-C-X(3)-C-) is not found in other zinc-binding proteins with known structures.; GO: 0008270 zinc ion binding; PDB: 1LV3_A.
Probab=22.06 E-value=24 Score=27.84 Aligned_cols=19 Identities=21% Similarity=0.364 Sum_probs=9.2
Q ss_pred CccCCccCccccccCCcce
Q 006225 601 GLSCPNCRQFNAKVGNNNH 619 (655)
Q Consensus 601 ~k~CP~C~~~ieK~~GCnh 619 (655)
+.+||.|+..++-..+..+
T Consensus 2 ~v~CP~C~k~~~~~~~n~~ 20 (57)
T PF03884_consen 2 TVKCPICGKPVEWSPENPF 20 (57)
T ss_dssp EEE-TTT--EEE-SSSSS-
T ss_pred cccCCCCCCeecccCCCCc
Confidence 3579999888777554444
No 332
>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=21.98 E-value=68 Score=24.40 Aligned_cols=27 Identities=30% Similarity=0.585 Sum_probs=18.4
Q ss_pred cccCccccceeEEe--------cCcCceeccccCee
Q 006225 521 AKQCPSCKMAISRT--------EGCNKIVCNNCGQY 548 (655)
Q Consensus 521 ~k~CP~C~~~iek~--------~Gcn~m~C~~C~~~ 548 (655)
.-.||.|+.-..-+ +.-.+-+|. ||+.
T Consensus 13 Y~~Cp~CGN~~vGngEG~liV~edtfkRtCk-CGfn 47 (49)
T PF12677_consen 13 YCKCPKCGNDKVGNGEGTLIVEEDTFKRTCK-CGFN 47 (49)
T ss_pred hccCcccCCcEeecCcceEEEeccceeeeec-cccc
Confidence 56799999765543 334567786 8864
No 333
>PHA02825 LAP/PHD finger-like protein; Provisional
Probab=21.94 E-value=73 Score=30.49 Aligned_cols=51 Identities=18% Similarity=0.403 Sum_probs=34.5
Q ss_pred ccccccccccccCCCeEecCCCC---cccHhhHHHHHHHHhhcCCcceeccCCCCCCCCCCcc
Q 006225 348 FHECRICFSEFAGTDFVRLPCHH---FFCWKCMKTYLDIHISEGTVSKLQCPDAKCGGMVPPS 407 (655)
Q Consensus 348 ~~~C~IC~e~~~~~~~~~l~C~H---~fC~~Cl~~yi~~~i~~g~~~~i~CP~~~C~~~l~~~ 407 (655)
...|-||+++... ......|.. ....+|+..|+... ....|+. |.......
T Consensus 8 ~~~CRIC~~~~~~-~~~PC~CkGs~k~VH~sCL~rWi~~s------~~~~Cei--C~~~Y~i~ 61 (162)
T PHA02825 8 DKCCWICKDEYDV-VTNYCNCKNENKIVHKECLEEWINTS------KNKSCKI--CNGPYNIK 61 (162)
T ss_pred CCeeEecCCCCCC-ccCCcccCCCchHHHHHHHHHHHhcC------CCCcccc--cCCeEEEE
Confidence 4689999988532 221124544 46999999998743 2578998 98876544
No 334
>TIGR00311 aIF-2beta translation initiation factor aIF-2, beta subunit, putative.
Probab=21.94 E-value=1.1e+02 Score=28.44 Aligned_cols=29 Identities=21% Similarity=0.543 Sum_probs=21.0
Q ss_pred ccccCccccce---eEEecCcCceeccccCee
Q 006225 520 DAKQCPSCKMA---ISRTEGCNKIVCNNCGQY 548 (655)
Q Consensus 520 ~~k~CP~C~~~---iek~~Gcn~m~C~~C~~~ 548 (655)
....||.|+.+ +.+.+.-..+.|..||..
T Consensus 96 ~yVlC~~C~sPdT~l~k~~r~~~l~C~ACGa~ 127 (133)
T TIGR00311 96 KYVICRECNRPDTRIIKEGRVSLLKCEACGAK 127 (133)
T ss_pred heEECCCCCCCCcEEEEeCCeEEEecccCCCC
Confidence 46789999976 566555556788888864
No 335
>PLN03086 PRLI-interacting factor K; Provisional
Probab=21.93 E-value=44 Score=38.56 Aligned_cols=30 Identities=27% Similarity=0.664 Sum_probs=24.7
Q ss_pred cCccCCc--cCccccccCCcceEEcccccccc
Q 006225 600 HGLSCPN--CRQFNAKVGNNNHMFCWACQIHY 629 (655)
Q Consensus 600 ~~k~CP~--C~~~ieK~~GCnhm~C~~C~~~F 629 (655)
+...||+ |+..+.+...=+|..|..|+..|
T Consensus 432 ~~V~Cp~~~Cg~v~~r~el~~H~~C~~Cgk~f 463 (567)
T PLN03086 432 HNVVCPHDGCGIVLRVEEAKNHVHCEKCGQAF 463 (567)
T ss_pred cceeCCcccccceeeccccccCccCCCCCCcc
Confidence 4568995 99999999999999999897655
No 336
>KOG0425 consensus Ubiquitin-protein ligase [Posttranslational modification, protein turnover, chaperones]
Probab=21.85 E-value=86 Score=29.84 Aligned_cols=21 Identities=29% Similarity=0.668 Sum_probs=17.5
Q ss_pred EEEEEEcCCCCCCCCCCeEEee
Q 006225 232 IVLTCLLPKSYPSHLPPYFTIS 253 (655)
Q Consensus 232 i~L~~~lP~~YPs~~pP~~~l~ 253 (655)
+.-+..||.+||.. ||.|...
T Consensus 55 FkA~m~FP~dYP~s-PP~~rF~ 75 (171)
T KOG0425|consen 55 FKAHMKFPQDYPLS-PPTFRFT 75 (171)
T ss_pred eEEEEeCcccCCCC-CCceeee
Confidence 66788999999997 9988543
No 337
>PRK05978 hypothetical protein; Provisional
Probab=21.84 E-value=43 Score=31.73 Aligned_cols=9 Identities=33% Similarity=0.940 Sum_probs=7.4
Q ss_pred CccCCccCc
Q 006225 601 GLSCPNCRQ 609 (655)
Q Consensus 601 ~k~CP~C~~ 609 (655)
..+||+|+.
T Consensus 33 ~grCP~CG~ 41 (148)
T PRK05978 33 RGRCPACGE 41 (148)
T ss_pred cCcCCCCCC
Confidence 468999985
No 338
>PF01155 HypA: Hydrogenase expression/synthesis hypA family; InterPro: IPR000688 Bacterial membrane-bound nickel-dependent hydrogenases requires a number of accessory proteins which are involved in their maturation. The exact role of these proteins is not yet clear, but some seem to be required for the incorporation of the nickel ions []. One of these proteins is generally known as hypA. It is a protein of about 12 to 14 kDa that contains, in its C-terminal region, four conserved cysteines that form a zinc-finger like motif. Escherichia coli has two proteins that belong to this family, hypA and hybF. A homologue, MJ0214, has also been found in a number of archaeal species, including the genome of Methanocaldococcus jannaschii (Methanococcus jannaschii).; GO: 0016151 nickel ion binding, 0006464 protein modification process; PDB: 2KDX_A 3A44_D 3A43_B.
Probab=21.39 E-value=35 Score=30.70 Aligned_cols=27 Identities=26% Similarity=0.459 Sum_probs=14.4
Q ss_pred CcccccCCCCCcccccccccccccccce
Q 006225 435 DVAYCPRCETPCIEDEEQHAQCSKCFYS 462 (655)
Q Consensus 435 ~~~~CP~C~~~~~~~~~~~~~C~~C~~~ 462 (655)
-..+|..|+..+..+... ..||.|+..
T Consensus 69 ~~~~C~~Cg~~~~~~~~~-~~CP~Cgs~ 95 (113)
T PF01155_consen 69 ARARCRDCGHEFEPDEFD-FSCPRCGSP 95 (113)
T ss_dssp -EEEETTTS-EEECHHCC-HH-SSSSSS
T ss_pred CcEECCCCCCEEecCCCC-CCCcCCcCC
Confidence 446788887765443222 567777654
No 339
>PF05743 UEV: UEV domain; InterPro: IPR008883 The N-terminal ubiquitin E2 variant (UEV) domain is ~145 amino acid residues in length and shows significant sequence similarity to E2 ubiquitin ligases but is unable to catalyze ubiquitin transfer as it lacks the active site cysteine that forms the transient thioester bond with the C terminus of ubiquitin (Ub). Nevertheless, at least some UEVs have retained the ability to bind Ub, and appear to act either as cofactors in ubiquitylation reactions, or as ubiquitin sensors. UEV domains also frequently contain other protein recognition motifs, and may generally serve to couple protein and Ub binding functions to facilitate the formation of multiprotein complexes [, , , ]. The UEV domain consists of a twisted four-stranded antiparallel beta-sheet having a meander topology, with four alpha-helices packed against one face of the sheet. The UEV fold is generally similar to canonical E2 ligases in the hydrophobic core and 'active site' regions, but differs significantly at both its N- and C-termini [, ]. The UEV domain is found in the eukaryotic tumour susceptibility gene 101 protein (TSG101). Altered transcripts of this gene have been detected in sporadic breast cancers and many other Homo sapiens malignancies. However, the involvement of this gene in neoplastic transformation and tumourigenesis is still elusive. TSG101 is required for normal cell function of embryonic and adult tissues but this gene is not a tumour suppressor for sporadic forms of breast cancer [].; GO: 0006464 protein modification process, 0015031 protein transport; PDB: 3R3Q_A 3R42_A 1UZX_A 3OBX_A 3OBS_A 3P9H_A 2F0R_A 3P9G_A 3OBQ_A 3OBU_A ....
Probab=21.35 E-value=93 Score=28.34 Aligned_cols=22 Identities=32% Similarity=0.691 Sum_probs=17.5
Q ss_pred EEEEEEcCCCCCCCCCCeEEeec
Q 006225 232 IVLTCLLPKSYPSHLPPYFTISA 254 (655)
Q Consensus 232 i~L~~~lP~~YPs~~pP~~~l~s 254 (655)
|-+.+-+|.+||.. ||.+.+..
T Consensus 50 iPi~Iwlp~~yP~~-pP~v~v~p 71 (121)
T PF05743_consen 50 IPICIWLPENYPYS-PPIVYVRP 71 (121)
T ss_dssp EEEEEEE-TTTTTS-SSEEEE-G
T ss_pred eeEEEEEcccCCCC-CCEEEEeC
Confidence 77889999999997 99888875
No 340
>PLN02638 cellulose synthase A (UDP-forming), catalytic subunit
Probab=21.29 E-value=53 Score=40.55 Aligned_cols=57 Identities=30% Similarity=0.680 Sum_probs=0.0
Q ss_pred ccCCCCCc--ccccccccccccccceeeccccccccCCcCCCchHHHHHHHHHhhcchhhhhhhhHHHHHHHHHHHhHHH
Q 006225 439 CPRCETPC--IEDEEQHAQCSKCFYSFCTLCRERRHVGVVCMTPEIKLRILQERQNSSQVKEGQKQREHEMINELLSVKE 516 (655)
Q Consensus 439 CP~C~~~~--~~~~~~~~~C~~C~~~fC~~C~~~~H~~~sC~~~~~~~~~~~e~~~~~~~~~~~~~~e~e~~~e~l~~~~ 516 (655)
|-.|+..+ ..+.+..+.|..|++-.|.-|.. -.
T Consensus 20 CqICGD~vg~~~~Ge~FVAC~eC~FPVCrpCYE---------------------------------------------YE 54 (1079)
T PLN02638 20 CQICGDNVGKTVDGEPFVACDVCAFPVCRPCYE---------------------------------------------YE 54 (1079)
T ss_pred eeecccccCcCCCCCEEEEeccCCCccccchhh---------------------------------------------hh
Q ss_pred HhcccccCccccceeEEecCcCce
Q 006225 517 ILRDAKQCPSCKMAISRTEGCNKI 540 (655)
Q Consensus 517 i~~~~k~CP~C~~~iek~~Gcn~m 540 (655)
.....+.||.|++...+-.|+..+
T Consensus 55 r~eG~q~CPqCktrYkr~kgsprv 78 (1079)
T PLN02638 55 RKDGNQSCPQCKTKYKRHKGSPAI 78 (1079)
T ss_pred hhcCCccCCccCCchhhhcCCCCc
No 341
>PLN02436 cellulose synthase A
Probab=21.10 E-value=57 Score=40.24 Aligned_cols=57 Identities=28% Similarity=0.706 Sum_probs=0.0
Q ss_pred ccCCCCCc--ccccccccccccccceeeccccccccCCcCCCchHHHHHHHHHhhcchhhhhhhhHHHHHHHHHHHhHHH
Q 006225 439 CPRCETPC--IEDEEQHAQCSKCFYSFCTLCRERRHVGVVCMTPEIKLRILQERQNSSQVKEGQKQREHEMINELLSVKE 516 (655)
Q Consensus 439 CP~C~~~~--~~~~~~~~~C~~C~~~fC~~C~~~~H~~~sC~~~~~~~~~~~e~~~~~~~~~~~~~~e~e~~~e~l~~~~ 516 (655)
|..|+-.+ ..+.+..+.|..|++..|..|.. -.
T Consensus 39 CqICGD~Vg~t~dGe~FVACn~C~fpvCr~Cye---------------------------------------------ye 73 (1094)
T PLN02436 39 CQICGDEIELTVDGEPFVACNECAFPVCRPCYE---------------------------------------------YE 73 (1094)
T ss_pred ccccccccCcCCCCCEEEeeccCCCccccchhh---------------------------------------------hh
Q ss_pred HhcccccCccccceeEEecCcCce
Q 006225 517 ILRDAKQCPSCKMAISRTEGCNKI 540 (655)
Q Consensus 517 i~~~~k~CP~C~~~iek~~Gcn~m 540 (655)
.....+.||.|++...+-.|+..+
T Consensus 74 r~eg~~~Cpqckt~Y~r~kgs~~~ 97 (1094)
T PLN02436 74 RREGNQACPQCKTRYKRIKGSPRV 97 (1094)
T ss_pred hhcCCccCcccCCchhhccCCCCc
No 342
>PRK03988 translation initiation factor IF-2 subunit beta; Validated
Probab=21.02 E-value=1.2e+02 Score=28.36 Aligned_cols=29 Identities=21% Similarity=0.567 Sum_probs=21.4
Q ss_pred ccccCccccce---eEEecCcCceeccccCee
Q 006225 520 DAKQCPSCKMA---ISRTEGCNKIVCNNCGQY 548 (655)
Q Consensus 520 ~~k~CP~C~~~---iek~~Gcn~m~C~~C~~~ 548 (655)
....||.|+.+ +++.+.-..+.|..||..
T Consensus 101 ~yVlC~~C~spdT~l~k~~r~~~l~C~ACGa~ 132 (138)
T PRK03988 101 EYVICPECGSPDTKLIKEGRIWVLKCEACGAE 132 (138)
T ss_pred hcEECCCCCCCCcEEEEcCCeEEEEcccCCCC
Confidence 46789999976 566655556889888864
No 343
>PRK10445 endonuclease VIII; Provisional
Probab=20.98 E-value=72 Score=33.16 Aligned_cols=26 Identities=23% Similarity=0.516 Sum_probs=18.9
Q ss_pred cccCccccceeEEe--cCcCceeccccC
Q 006225 521 AKQCPSCKMAISRT--EGCNKIVCNNCG 546 (655)
Q Consensus 521 ~k~CP~C~~~iek~--~Gcn~m~C~~C~ 546 (655)
-+.||.|+..|++. +|-.-..|+.|.
T Consensus 235 g~~Cp~Cg~~I~~~~~~gR~t~~CP~CQ 262 (263)
T PRK10445 235 GEACERCGGIIEKTTLSSRPFYWCPGCQ 262 (263)
T ss_pred CCCCCCCCCEeEEEEECCCCcEECCCCc
Confidence 47899999999874 455556666664
No 344
>PRK14810 formamidopyrimidine-DNA glycosylase; Provisional
Probab=20.97 E-value=71 Score=33.37 Aligned_cols=26 Identities=31% Similarity=0.755 Sum_probs=18.8
Q ss_pred cccCccccceeEEe--cCcCceeccccC
Q 006225 521 AKQCPSCKMAISRT--EGCNKIVCNNCG 546 (655)
Q Consensus 521 ~k~CP~C~~~iek~--~Gcn~m~C~~C~ 546 (655)
.+.||.|+..|++. +|-.-..|+.|+
T Consensus 244 g~pCprCG~~I~~~~~~gR~t~~CP~CQ 271 (272)
T PRK14810 244 GEPCLNCKTPIRRVVVAGRSSHYCPHCQ 271 (272)
T ss_pred CCcCCCCCCeeEEEEECCCccEECcCCc
Confidence 57899999999874 454455566664
No 345
>PRK14811 formamidopyrimidine-DNA glycosylase; Provisional
Probab=20.94 E-value=67 Score=33.52 Aligned_cols=26 Identities=27% Similarity=0.781 Sum_probs=17.8
Q ss_pred cccCccccceeEEe--cCcCceeccccC
Q 006225 521 AKQCPSCKMAISRT--EGCNKIVCNNCG 546 (655)
Q Consensus 521 ~k~CP~C~~~iek~--~Gcn~m~C~~C~ 546 (655)
-+.||.|+..|.+. +|-.-..|+.|.
T Consensus 235 g~pC~~Cg~~I~~~~~~gR~ty~Cp~CQ 262 (269)
T PRK14811 235 GQPCPRCGTPIEKIVVGGRGTHFCPQCQ 262 (269)
T ss_pred cCCCCcCCCeeEEEEECCCCcEECCCCc
Confidence 57899999999874 454444455554
No 346
>KOG0895 consensus Ubiquitin-conjugating enzyme [Posttranslational modification, protein turnover, chaperones]
Probab=20.77 E-value=81 Score=38.68 Aligned_cols=42 Identities=24% Similarity=0.543 Sum_probs=27.7
Q ss_pred EEEEEEcCCCCCCCCCCeEEeecccC--CHH--HHHHHHHHHHHHHH
Q 006225 232 IVLTCLLPKSYPSHLPPYFTISARWL--NST--KISNLCSMLESIWI 274 (655)
Q Consensus 232 i~L~~~lP~~YPs~~pP~~~l~s~wL--~~~--~l~~L~~~L~~~~e 274 (655)
+.+.|.||.+||++ ||.....+..+ .++ .--+++-.|-..|.
T Consensus 900 f~fd~~~~~~yp~~-pp~~~~~s~~~r~npnly~~g~vc~s~l~tw~ 945 (1101)
T KOG0895|consen 900 FFFDFQFPQDYPSS-PPLVHYHSGGVRLNPNLYEDGKVCLSLLNTWH 945 (1101)
T ss_pred EEEEeecCCCCCCC-CCceEeecCceeeCcccccccceehhhhcccc
Confidence 67899999999998 99887776432 221 22344555555664
No 347
>PRK05580 primosome assembly protein PriA; Validated
Probab=20.76 E-value=63 Score=38.42 Aligned_cols=35 Identities=20% Similarity=0.499 Sum_probs=27.1
Q ss_pred ccCCccCccccccCCcceEEccccccc-----cccccccc
Q 006225 602 LSCPNCRQFNAKVGNNNHMFCWACQIH-----YCYLCKKI 636 (655)
Q Consensus 602 k~CP~C~~~ieK~~GCnhm~C~~C~~~-----FC~~C~~~ 636 (655)
..||+|.....-...=+.+.|..||+. .|-.|+..
T Consensus 391 ~~C~~C~~~l~~h~~~~~l~Ch~Cg~~~~~~~~Cp~Cg~~ 430 (679)
T PRK05580 391 AECPHCDASLTLHRFQRRLRCHHCGYQEPIPKACPECGST 430 (679)
T ss_pred cCCCCCCCceeEECCCCeEECCCCcCCCCCCCCCCCCcCC
Confidence 579999977654444578999999965 69999876
No 348
>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=20.68 E-value=1.3e+02 Score=28.74 Aligned_cols=35 Identities=23% Similarity=0.601 Sum_probs=21.5
Q ss_pred cccccccccccCCCeEec-------CCCCccc------HhhHHHHHHHHh
Q 006225 349 HECRICFSEFAGTDFVRL-------PCHHFFC------WKCMKTYLDIHI 385 (655)
Q Consensus 349 ~~C~IC~e~~~~~~~~~l-------~C~H~fC------~~Cl~~yi~~~i 385 (655)
.+|+||++-- .+.+.| +|.-++| ..||.+|-....
T Consensus 3 ~~CpICme~P--HNAVLLlCSS~~kgcRpymc~Ts~rhSNCLdqfkka~~ 50 (162)
T PF07800_consen 3 VTCPICMEHP--HNAVLLLCSSHEKGCRPYMCDTSYRHSNCLDQFKKAYG 50 (162)
T ss_pred ccCceeccCC--CceEEEEeccccCCccccccCCccchhHHHHHHHHHhc
Confidence 5799999863 233333 3544444 578888876543
No 349
>TIGR00577 fpg formamidopyrimidine-DNA glycosylase (fpg). All proteins in the FPG family with known functions are FAPY-DNA glycosylases that function in base excision repair. Homologous to endonuclease VIII (nei). This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=20.57 E-value=75 Score=33.18 Aligned_cols=26 Identities=23% Similarity=0.668 Sum_probs=18.9
Q ss_pred cccCccccceeEEe--cCcCceeccccC
Q 006225 521 AKQCPSCKMAISRT--EGCNKIVCNNCG 546 (655)
Q Consensus 521 ~k~CP~C~~~iek~--~Gcn~m~C~~C~ 546 (655)
-+.||.|+..|.+. +|-.-..|+.|.
T Consensus 245 g~pC~~Cg~~I~~~~~~gR~t~~CP~CQ 272 (272)
T TIGR00577 245 GEPCRRCGTPIEKIKVGGRGTHFCPQCQ 272 (272)
T ss_pred CCCCCCCCCeeEEEEECCCCCEECCCCC
Confidence 47899999999874 455556666663
No 350
>KOG2932 consensus E3 ubiquitin ligase involved in ubiquitination of E-cadherin complex [Posttranslational modification, protein turnover, chaperones]
Probab=20.56 E-value=48 Score=34.91 Aligned_cols=31 Identities=35% Similarity=0.866 Sum_probs=20.2
Q ss_pred ccccccccccccCCCeEe-cCCCCcccHhhHHHH
Q 006225 348 FHECRICFSEFAGTDFVR-LPCHHFFCWKCMKTY 380 (655)
Q Consensus 348 ~~~C~IC~e~~~~~~~~~-l~C~H~fC~~Cl~~y 380 (655)
.+.|.-|--.+. -.-+ ++|.|.||.+|.+..
T Consensus 90 VHfCd~Cd~PI~--IYGRmIPCkHvFCl~CAr~~ 121 (389)
T KOG2932|consen 90 VHFCDRCDFPIA--IYGRMIPCKHVFCLECARSD 121 (389)
T ss_pred eEeecccCCcce--eeecccccchhhhhhhhhcC
Confidence 366887843321 1122 499999999998753
No 351
>KOG2462 consensus C2H2-type Zn-finger protein [Transcription]
Probab=20.55 E-value=73 Score=33.16 Aligned_cols=11 Identities=27% Similarity=0.507 Sum_probs=5.3
Q ss_pred cccCcccccee
Q 006225 521 AKQCPSCKMAI 531 (655)
Q Consensus 521 ~k~CP~C~~~i 531 (655)
.+.|+.|+...
T Consensus 161 a~~C~~C~K~Y 171 (279)
T KOG2462|consen 161 AFSCKYCGKVY 171 (279)
T ss_pred cccCCCCCcee
Confidence 34455555443
No 352
>KOG2930 consensus SCF ubiquitin ligase, Rbx1 component [Posttranslational modification, protein turnover, chaperones]
Probab=20.53 E-value=62 Score=28.61 Aligned_cols=29 Identities=24% Similarity=0.646 Sum_probs=22.1
Q ss_pred CCeEec--CCCCcccHhhHHHHHHHHhhcCCcceeccCC
Q 006225 361 TDFVRL--PCHHFFCWKCMKTYLDIHISEGTVSKLQCPD 397 (655)
Q Consensus 361 ~~~~~l--~C~H~fC~~Cl~~yi~~~i~~g~~~~i~CP~ 397 (655)
.+++.. .|+|.|..-|+.+|+... -.||.
T Consensus 72 ~EC~VaWG~CNHaFH~hCisrWlktr--------~vCPL 102 (114)
T KOG2930|consen 72 EECTVAWGVCNHAFHFHCISRWLKTR--------NVCPL 102 (114)
T ss_pred CceEEEeeecchHHHHHHHHHHHhhc--------CcCCC
Confidence 344443 699999999999998752 46886
No 353
>PF01927 Mut7-C: Mut7-C RNAse domain; InterPro: IPR002782 This prokaryotic family of proteins have no known function. The proteins contain four conserved cysteines that may be involved in metal binding or disulphide bridges.
Probab=20.46 E-value=88 Score=29.40 Aligned_cols=15 Identities=27% Similarity=0.662 Sum_probs=11.0
Q ss_pred CCCcccccCCCCCcc
Q 006225 433 MSDVAYCPRCETPCI 447 (655)
Q Consensus 433 ~~~~~~CP~C~~~~~ 447 (655)
.+.+..|+.|+..+.
T Consensus 88 ~~~~sRC~~CN~~L~ 102 (147)
T PF01927_consen 88 DPIFSRCPKCNGPLR 102 (147)
T ss_pred CCCCCccCCCCcEee
Confidence 334678999998753
No 354
>PLN00215 predicted protein; Provisional
Probab=20.30 E-value=1.3e+02 Score=25.30 Aligned_cols=68 Identities=29% Similarity=0.394 Sum_probs=38.4
Q ss_pred CcccccCCCCCCCCCchhhhhhhcccCCCCCCCCCCCCCCCCcccCCcccccccccccccccchhhcccc
Q 006225 24 DLTVKPLNDAPPAAPPSQQKRHQQHSLDSPSTSDQPNNEPIPKYQGNLRWVSRRRRARVAKPKFVKKTES 93 (655)
Q Consensus 24 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 93 (655)
+++..-...+|-+.|---.--+-|-+|..|-...-|...-++ -|.-.||-|++-++--|+++--.+.+
T Consensus 18 dlttrytrpapidepnrgkgctmhlslpppmskrrsaakmip--gqggqwvlrrgtsrdckpdlpmatss 85 (110)
T PLN00215 18 DLTTRYTRPAPIDEPNRGKGCTMHLSLPPPMSKRRSAAKMIP--GQGGQWVLRRGTSRDCKPDLPMATSS 85 (110)
T ss_pred ccceecccCCCCCCCCCCCCeEEeecCCCCcchhhhhhhccC--CCCCeEEEecCcccCCCCCCcccccc
Confidence 444444445555554443333445555444333333333333 34567999999999999998655543
No 355
>PRK12380 hydrogenase nickel incorporation protein HybF; Provisional
Probab=20.28 E-value=45 Score=30.01 Aligned_cols=27 Identities=26% Similarity=0.550 Sum_probs=16.5
Q ss_pred CCcccccCCCCCcccccccccccccccc
Q 006225 434 SDVAYCPRCETPCIEDEEQHAQCSKCFY 461 (655)
Q Consensus 434 ~~~~~CP~C~~~~~~~~~~~~~C~~C~~ 461 (655)
+-..+|+.|+..+... .....||.||.
T Consensus 68 p~~~~C~~Cg~~~~~~-~~~~~CP~Cgs 94 (113)
T PRK12380 68 PAQAWCWDCSQVVEIH-QHDAQCPHCHG 94 (113)
T ss_pred CcEEEcccCCCEEecC-CcCccCcCCCC
Confidence 3457888888655433 23445877763
No 356
>COG2824 PhnA Uncharacterized Zn-ribbon-containing protein involved in phosphonate metabolism [Inorganic ion transport and metabolism]
Probab=20.27 E-value=76 Score=28.23 Aligned_cols=27 Identities=22% Similarity=0.786 Sum_probs=18.4
Q ss_pred cccCccccceeEEecCcCceeccccCee
Q 006225 521 AKQCPSCKMAISRTEGCNKIVCNNCGQY 548 (655)
Q Consensus 521 ~k~CP~C~~~iek~~Gcn~m~C~~C~~~ 548 (655)
...||+|..-..-.+|- .+.|+.|.+.
T Consensus 3 lp~cp~c~sEytYed~~-~~~cpec~~e 29 (112)
T COG2824 3 LPPCPKCNSEYTYEDGG-QLICPECAHE 29 (112)
T ss_pred CCCCCccCCceEEecCc-eEeCchhccc
Confidence 35799998766655554 7888865543
No 357
>PF04606 Ogr_Delta: Ogr/Delta-like zinc finger; InterPro: IPR007684 This entry is represented by Bacteriophage P2, Ogr. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This is a viral family of phage zinc-binding transcriptional activators, which also contains cryptic members in some bacterial genomes []. The P4 phage delta protein contains two such domains attached covalently, while the P2 phage Ogr proteins possess one domain but function as dimers. All the members of this family have the following consensus sequence: C-X(2)-C-X(3)-A-(X)2-R-X(15)-C-X(4)-C-X(3)-F [].; GO: 0006355 regulation of transcription, DNA-dependent
Probab=20.19 E-value=85 Score=23.47 Aligned_cols=10 Identities=30% Similarity=0.933 Sum_probs=7.4
Q ss_pred cCccccceeE
Q 006225 523 QCPSCKMAIS 532 (655)
Q Consensus 523 ~CP~C~~~ie 532 (655)
.||.|+....
T Consensus 1 ~CP~Cg~~a~ 10 (47)
T PF04606_consen 1 RCPHCGSKAR 10 (47)
T ss_pred CcCCCCCeeE
Confidence 5999997543
No 358
>COG1996 RPC10 DNA-directed RNA polymerase, subunit RPC10 (contains C4-type Zn-finger) [Transcription]
Probab=20.11 E-value=60 Score=24.81 Aligned_cols=26 Identities=23% Similarity=0.644 Sum_probs=16.9
Q ss_pred cCccccceeEEecCcCceeccccCee
Q 006225 523 QCPSCKMAISRTEGCNKIVCNNCGQY 548 (655)
Q Consensus 523 ~CP~C~~~iek~~Gcn~m~C~~C~~~ 548 (655)
.|-.|+..++....-.-+.|+.||+.
T Consensus 8 ~C~~Cg~~~~~~~~~~~irCp~Cg~r 33 (49)
T COG1996 8 KCARCGREVELDQETRGIRCPYCGSR 33 (49)
T ss_pred EhhhcCCeeehhhccCceeCCCCCcE
Confidence 47777777765544455677777754
No 359
>COG2816 NPY1 NTP pyrophosphohydrolases containing a Zn-finger, probably nucleic-acid-binding [DNA replication, recombination, and repair]
Probab=20.04 E-value=64 Score=33.80 Aligned_cols=31 Identities=13% Similarity=0.147 Sum_probs=26.2
Q ss_pred ccCccCCccCccccccCCcceEEcccccccc
Q 006225 599 EHGLSCPNCRQFNAKVGNNNHMFCWACQIHY 629 (655)
Q Consensus 599 ~~~k~CP~C~~~ieK~~GCnhm~C~~C~~~F 629 (655)
.+-+-||+|+...+-..|=-.+.|++|++.+
T Consensus 109 ~~~RFCg~CG~~~~~~~~g~~~~C~~cg~~~ 139 (279)
T COG2816 109 RSHRFCGRCGTKTYPREGGWARVCPKCGHEH 139 (279)
T ss_pred hhCcCCCCCCCcCccccCceeeeCCCCCCcc
Confidence 3458899999999888888999999998543
Done!