Query 007763
Match_columns 590
No_of_seqs 450 out of 1645
Neff 7.2
Searched_HMMs 46136
Date Thu Mar 28 15:00:40 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/007763.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/007763hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG1815 Predicted E3 ubiquitin 100.0 5E-72 1.1E-76 608.3 27.7 432 69-524 2-441 (444)
2 KOG1812 Predicted E3 ubiquitin 100.0 5E-33 1.1E-37 295.3 10.6 219 140-387 145-371 (384)
3 KOG1814 Predicted E3 ubiquitin 100.0 4E-31 8.6E-36 270.1 8.7 190 139-332 182-405 (445)
4 KOG0006 E3 ubiquitin-protein l 99.9 2.5E-23 5.4E-28 205.6 7.6 190 137-333 217-437 (446)
5 smart00647 IBR In Between Ring 99.3 6.4E-12 1.4E-16 99.9 6.1 63 208-270 1-64 (64)
6 PF01485 IBR: IBR domain; Int 99.1 6.9E-12 1.5E-16 99.6 0.4 63 208-270 1-64 (64)
7 PF15227 zf-C3HC4_4: zinc fing 98.6 2.6E-08 5.6E-13 72.5 3.0 40 144-185 1-40 (42)
8 KOG0320 Predicted E3 ubiquitin 98.1 1.3E-06 2.9E-11 81.5 3.1 54 138-198 128-182 (187)
9 PF13445 zf-RING_UBOX: RING-ty 98.0 1.9E-06 4.1E-11 62.8 1.3 41 144-185 1-43 (43)
10 smart00647 IBR In Between Ring 98.0 1E-05 2.2E-10 64.0 4.4 39 293-332 17-59 (64)
11 PF01485 IBR: IBR domain; Int 97.9 4.3E-06 9.4E-11 66.1 2.3 38 294-332 18-59 (64)
12 PF13923 zf-C3HC4_2: Zinc fing 97.9 6.5E-06 1.4E-10 58.8 2.3 36 144-185 1-37 (39)
13 PLN03208 E3 ubiquitin-protein 97.8 9.9E-06 2.1E-10 77.7 3.2 60 139-202 16-87 (193)
14 PF00097 zf-C3HC4: Zinc finger 97.8 8E-06 1.7E-10 58.8 1.8 38 144-185 1-39 (41)
15 PF13639 zf-RING_2: Ring finge 97.8 8.2E-06 1.8E-10 59.9 1.0 41 143-189 2-43 (44)
16 PF14634 zf-RING_5: zinc-RING 97.7 2.4E-05 5.2E-10 57.4 2.7 42 143-190 1-43 (44)
17 PF13920 zf-C3HC4_3: Zinc fing 97.6 3.4E-05 7.5E-10 58.2 2.7 46 141-194 2-48 (50)
18 KOG2177 Predicted E3 ubiquitin 97.6 2.9E-05 6.3E-10 79.5 2.8 45 139-191 11-55 (386)
19 KOG4367 Predicted Zn-finger pr 97.5 0.00069 1.5E-08 71.2 10.8 78 245-331 174-253 (699)
20 cd00162 RING RING-finger (Real 97.3 0.00018 3.8E-09 51.9 3.1 43 143-192 1-44 (45)
21 TIGR00599 rad18 DNA repair pro 97.3 0.00014 3.1E-09 77.7 3.6 66 139-212 24-90 (397)
22 KOG0804 Cytoplasmic Zn-finger 97.3 0.02 4.4E-07 61.0 19.2 116 70-194 86-222 (493)
23 KOG0823 Predicted E3 ubiquitin 97.3 0.00014 3.1E-09 71.1 2.2 57 138-199 44-100 (230)
24 smart00504 Ubox Modified RING 97.3 0.00022 4.7E-09 56.2 3.0 48 142-197 2-49 (63)
25 KOG0317 Predicted E3 ubiquitin 97.2 0.00027 5.9E-09 71.1 4.1 51 140-198 238-288 (293)
26 KOG2164 Predicted E3 ubiquitin 97.2 0.00016 3.5E-09 78.0 2.5 60 141-204 186-246 (513)
27 PHA02929 N1R/p28-like protein; 97.2 0.00026 5.7E-09 70.8 3.7 49 140-194 173-227 (238)
28 smart00184 RING Ring finger. E 97.0 0.00042 9.1E-09 48.1 2.3 37 144-185 1-37 (39)
29 KOG0287 Postreplication repair 97.0 0.00035 7.7E-09 71.3 1.9 63 140-211 22-86 (442)
30 TIGR00570 cdk7 CDK-activating 96.9 0.0014 3E-08 67.6 6.1 53 142-200 4-60 (309)
31 PHA02926 zinc finger-like prot 96.9 0.00065 1.4E-08 66.2 3.2 54 139-194 168-230 (242)
32 KOG0978 E3 ubiquitin ligase in 96.4 0.001 2.2E-08 75.3 0.4 54 140-201 642-696 (698)
33 COG5574 PEX10 RING-finger-cont 96.3 0.0029 6.4E-08 63.1 3.0 52 140-198 214-266 (271)
34 PF04564 U-box: U-box domain; 96.0 0.0049 1.1E-07 50.4 2.6 50 140-196 3-52 (73)
35 COG5540 RING-finger-containing 95.9 0.0038 8.3E-08 63.2 1.9 51 140-195 322-373 (374)
36 PF14555 UBA_4: UBA-like domai 95.9 0.017 3.8E-07 42.1 4.9 41 80-120 1-41 (43)
37 PF14835 zf-RING_6: zf-RING of 95.9 0.0034 7.4E-08 49.4 1.1 41 142-193 8-50 (65)
38 PF00641 zf-RanBP: Zn-finger i 95.8 0.0032 7E-08 42.2 0.6 26 565-590 3-28 (30)
39 KOG4628 Predicted E3 ubiquitin 95.5 0.016 3.4E-07 60.9 4.8 48 142-194 230-278 (348)
40 smart00547 ZnF_RBZ Zinc finger 95.5 0.0076 1.7E-07 38.8 1.5 24 566-589 2-25 (26)
41 PF14570 zf-RING_4: RING/Ubox 95.3 0.015 3.2E-07 43.3 2.7 44 144-192 1-46 (48)
42 KOG0824 Predicted E3 ubiquitin 95.2 0.011 2.3E-07 60.2 2.3 52 140-199 6-58 (324)
43 PF11789 zf-Nse: Zinc-finger o 95.1 0.019 4.2E-07 44.5 2.9 46 140-190 10-57 (57)
44 KOG2879 Predicted E3 ubiquitin 94.6 0.03 6.4E-07 56.3 3.6 51 139-195 237-288 (298)
45 PF12678 zf-rbx1: RING-H2 zinc 94.6 0.036 7.8E-07 45.3 3.5 44 141-190 19-73 (73)
46 KOG0311 Predicted E3 ubiquitin 94.6 0.0043 9.3E-08 64.2 -2.5 47 140-193 42-89 (381)
47 COG5152 Uncharacterized conser 94.5 0.014 3E-07 55.7 0.9 35 141-177 196-231 (259)
48 KOG4159 Predicted E3 ubiquitin 94.2 0.046 1E-06 58.8 4.1 48 139-195 82-130 (398)
49 COG5432 RAD18 RING-finger-cont 94.1 0.035 7.5E-07 56.0 2.7 62 141-211 25-88 (391)
50 COG5243 HRD1 HRD ubiquitin lig 93.9 0.16 3.5E-06 53.0 7.1 95 92-194 235-345 (491)
51 KOG1002 Nucleotide excision re 93.8 0.029 6.4E-07 60.7 1.7 57 137-197 532-589 (791)
52 KOG1814 Predicted E3 ubiquitin 93.4 0.034 7.4E-07 58.8 1.3 42 291-333 270-313 (445)
53 KOG1812 Predicted E3 ubiquitin 92.8 0.07 1.5E-06 57.6 2.6 41 223-267 304-344 (384)
54 PF04931 DNA_pol_phi: DNA poly 92.1 0.25 5.4E-06 58.5 6.3 20 96-115 764-783 (784)
55 KOG1039 Predicted E3 ubiquitin 91.7 0.11 2.4E-06 54.9 2.5 55 137-193 157-220 (344)
56 KOG0006 E3 ubiquitin-protein l 91.2 0.37 8E-06 49.4 5.5 94 160-267 341-438 (446)
57 KOG2817 Predicted E3 ubiquitin 90.9 0.87 1.9E-05 48.4 8.1 56 140-198 333-389 (394)
58 PF10571 UPF0547: Uncharacteri 90.9 0.12 2.6E-06 33.5 1.1 24 295-323 1-24 (26)
59 KOG2660 Locus-specific chromos 88.7 0.17 3.7E-06 52.4 0.8 47 140-194 14-61 (331)
60 TIGR00570 cdk7 CDK-activating 88.4 9.2 0.0002 39.9 13.1 34 295-330 4-37 (309)
61 PRK00420 hypothetical protein; 87.4 4.2 9E-05 36.1 8.6 27 294-330 23-49 (112)
62 KOG4739 Uncharacterized protei 87.3 0.29 6.4E-06 48.7 1.5 54 142-203 4-57 (233)
63 KOG0317 Predicted E3 ubiquitin 86.9 0.12 2.6E-06 52.5 -1.5 37 292-335 237-273 (293)
64 KOG4265 Predicted E3 ubiquitin 86.7 0.51 1.1E-05 49.5 2.9 65 123-195 269-337 (349)
65 KOG1785 Tyrosine kinase negati 86.6 0.28 6.1E-06 51.7 1.0 46 142-193 370-415 (563)
66 KOG1813 Predicted E3 ubiquitin 86.5 0.31 6.7E-06 49.7 1.2 44 141-193 241-285 (313)
67 COG5175 MOT2 Transcriptional r 86.1 0.35 7.6E-06 50.0 1.4 53 141-198 14-68 (480)
68 KOG1815 Predicted E3 ubiquitin 85.6 0.51 1.1E-05 52.1 2.5 35 298-334 164-199 (444)
69 PF13248 zf-ribbon_3: zinc-rib 84.3 0.52 1.1E-05 30.4 1.0 11 295-305 3-13 (26)
70 PF15227 zf-C3HC4_4: zinc fing 84.2 0.44 9.5E-06 34.5 0.8 32 297-335 1-32 (42)
71 PF13240 zinc_ribbon_2: zinc-r 84.1 0.48 1E-05 29.7 0.8 10 296-305 1-10 (23)
72 KOG4692 Predicted E3 ubiquitin 84.0 0.77 1.7E-05 47.8 2.7 51 136-195 417-468 (489)
73 COG5220 TFB3 Cdk activating ki 83.8 0.57 1.2E-05 46.3 1.6 49 142-194 11-64 (314)
74 KOG0826 Predicted E3 ubiquitin 83.8 2.6 5.6E-05 43.8 6.3 46 140-192 299-346 (357)
75 KOG0802 E3 ubiquitin ligase [P 83.6 0.42 9.1E-06 54.2 0.7 46 141-192 291-339 (543)
76 KOG1428 Inhibitor of type V ad 83.5 1.4 3.1E-05 53.4 4.8 62 141-204 3486-3554(3738)
77 COG5222 Uncharacterized conser 83.1 0.8 1.7E-05 46.6 2.3 42 142-191 275-318 (427)
78 PF11793 FANCL_C: FANCL C-term 82.7 0.86 1.9E-05 36.9 2.0 53 141-195 2-67 (70)
79 KOG1645 RING-finger-containing 81.7 1.3 2.9E-05 47.1 3.5 49 141-193 4-55 (463)
80 smart00661 RPOL9 RNA polymeras 81.3 1.2 2.6E-05 33.4 2.3 27 295-322 1-29 (52)
81 KOG0823 Predicted E3 ubiquitin 81.2 0.56 1.2E-05 46.4 0.5 20 313-335 62-81 (230)
82 KOG4185 Predicted E3 ubiquitin 79.8 1.6 3.5E-05 45.3 3.4 48 141-193 3-54 (296)
83 KOG0827 Predicted E3 ubiquitin 79.6 0.82 1.8E-05 48.3 1.1 54 142-198 5-60 (465)
84 PF08274 PhnA_Zn_Ribbon: PhnA 78.6 1.8 3.8E-05 29.1 2.1 27 295-323 3-29 (30)
85 KOG1001 Helicase-like transcri 78.3 0.98 2.1E-05 52.3 1.3 46 142-195 455-501 (674)
86 PF14447 Prok-RING_4: Prokaryo 78.0 1.1 2.3E-05 34.4 1.0 46 141-196 7-52 (55)
87 PF05883 Baculo_RING: Baculovi 77.9 0.91 2E-05 41.3 0.7 33 141-173 26-65 (134)
88 PHA00626 hypothetical protein 77.8 1.7 3.8E-05 33.3 2.1 28 296-324 2-34 (59)
89 KOG0297 TNF receptor-associate 77.3 2.6 5.7E-05 45.7 4.2 47 139-193 19-66 (391)
90 PF12861 zf-Apc11: Anaphase-pr 77.0 2.5 5.5E-05 35.5 3.1 34 157-193 48-81 (85)
91 PF14835 zf-RING_6: zf-RING of 76.9 1.3 2.9E-05 35.1 1.3 22 295-316 8-32 (65)
92 KOG1734 Predicted RING-contain 76.9 2 4.3E-05 43.4 2.8 70 121-195 204-282 (328)
93 PF10446 DUF2457: Protein of u 76.7 2.7 5.8E-05 45.5 3.9 11 136-146 189-199 (458)
94 PF09297 zf-NADH-PPase: NADH p 76.5 3.3 7.1E-05 28.0 3.0 29 293-322 2-30 (32)
95 PRK14559 putative protein seri 75.7 1.9 4.2E-05 49.7 2.7 23 295-330 28-50 (645)
96 KOG0828 Predicted E3 ubiquitin 74.9 1.4 2.9E-05 48.0 1.1 51 140-195 570-635 (636)
97 PF14952 zf-tcix: Putative tre 74.1 2.3 4.9E-05 30.9 1.8 31 288-322 5-36 (44)
98 PF04641 Rtf2: Rtf2 RING-finge 73.6 4 8.7E-05 41.7 4.2 69 138-213 110-181 (260)
99 PLN03086 PRLI-interacting fact 73.2 5.1 0.00011 45.3 5.2 57 180-256 406-463 (567)
100 KOG0825 PHD Zn-finger protein 73.1 1.1 2.4E-05 51.3 -0.1 48 142-195 124-172 (1134)
101 PF13923 zf-C3HC4_2: Zinc fing 72.8 1.3 2.8E-05 31.2 0.3 32 297-334 1-32 (39)
102 smart00744 RINGv The RING-vari 71.5 3.3 7.1E-05 31.0 2.2 43 143-189 1-48 (49)
103 PF13719 zinc_ribbon_5: zinc-r 71.4 3.1 6.6E-05 29.3 1.9 29 226-256 3-35 (37)
104 KOG4275 Predicted E3 ubiquitin 70.9 1.3 2.8E-05 45.2 -0.2 40 141-192 300-340 (350)
105 KOG4172 Predicted E3 ubiquitin 70.3 1.3 2.8E-05 33.8 -0.2 45 142-193 8-53 (62)
106 KOG1991 Nuclear transport rece 68.9 8.7 0.00019 45.5 5.9 40 70-112 955-994 (1010)
107 KOG0320 Predicted E3 ubiquitin 68.6 1.4 3E-05 41.9 -0.4 30 250-305 149-178 (187)
108 KOG3800 Predicted E3 ubiquitin 68.0 7 0.00015 40.1 4.3 50 143-197 2-54 (300)
109 PRK00432 30S ribosomal protein 66.8 2.6 5.7E-05 31.8 0.8 28 293-323 19-47 (50)
110 PF13240 zinc_ribbon_2: zinc-r 66.3 3.7 8E-05 25.8 1.3 22 568-589 1-22 (23)
111 TIGR02098 MJ0042_CXXC MJ0042 f 66.1 4.2 9E-05 28.5 1.7 26 296-323 4-35 (38)
112 KOG3002 Zn finger protein [Gen 66.1 4.2 9.2E-05 42.4 2.5 47 138-194 45-91 (299)
113 PRK00398 rpoP DNA-directed RNA 65.5 5.6 0.00012 29.2 2.4 29 295-324 4-32 (46)
114 PF00097 zf-C3HC4: Zinc finger 65.3 1.9 4.2E-05 30.5 -0.2 31 297-333 1-31 (41)
115 KOG3039 Uncharacterized conser 65.3 4.7 0.0001 40.3 2.4 53 140-198 220-274 (303)
116 KOG2807 RNA polymerase II tran 64.5 5.4 0.00012 41.5 2.8 22 244-265 342-364 (378)
117 PF00643 zf-B_box: B-box zinc 64.3 5.6 0.00012 28.3 2.2 29 295-331 4-33 (42)
118 PLN03208 E3 ubiquitin-protein 64.0 2.1 4.6E-05 41.5 -0.2 31 295-332 19-49 (193)
119 KOG2038 CAATT-binding transcri 63.2 6.3 0.00014 45.5 3.2 15 2-16 881-895 (988)
120 PF10367 Vps39_2: Vacuolar sor 62.0 4.1 8.8E-05 35.1 1.3 30 141-170 78-107 (109)
121 PF04147 Nop14: Nop14-like fam 61.7 26 0.00056 42.1 8.2 17 64-80 417-436 (840)
122 PF00627 UBA: UBA/TS-N domain; 60.5 26 0.00056 24.3 4.9 33 80-113 3-35 (37)
123 PF07191 zinc-ribbons_6: zinc- 59.4 7.4 0.00016 31.5 2.2 49 296-347 3-56 (70)
124 PF13248 zf-ribbon_3: zinc-rib 59.3 5.8 0.00012 25.5 1.3 23 567-589 3-25 (26)
125 PRK14559 putative protein seri 59.1 6.8 0.00015 45.3 2.7 12 295-306 42-53 (645)
126 KOG1941 Acetylcholine receptor 59.0 13 0.00029 39.6 4.5 46 141-191 365-413 (518)
127 PF10571 UPF0547: Uncharacteri 58.5 5.9 0.00013 25.7 1.2 23 143-165 2-24 (26)
128 PHA02664 hypothetical protein; 58.2 23 0.00051 36.7 6.0 10 81-90 523-532 (534)
129 PF07282 OrfB_Zn_ribbon: Putat 58.1 7.7 0.00017 30.9 2.1 28 293-321 27-54 (69)
130 PF13639 zf-RING_2: Ring finge 57.6 3.3 7.2E-05 29.9 -0.1 35 296-334 2-36 (44)
131 PF13717 zinc_ribbon_4: zinc-r 57.5 8.8 0.00019 26.8 2.1 29 226-256 3-35 (36)
132 COG5109 Uncharacterized conser 57.4 9.8 0.00021 39.4 3.2 50 140-192 335-385 (396)
133 KOG3759 Uncharacterized RUN do 56.8 99 0.0021 33.9 10.6 46 465-518 204-250 (621)
134 TIGR03655 anti_R_Lar restricti 56.5 8 0.00017 29.4 1.9 11 295-305 2-12 (53)
135 PRK08665 ribonucleotide-diphos 56.2 6.5 0.00014 46.4 2.0 27 295-324 725-751 (752)
136 COG5151 SSL1 RNA polymerase II 55.3 3.2 6.9E-05 42.7 -0.6 89 162-265 307-407 (421)
137 PF13834 DUF4193: Domain of un 54.7 5 0.00011 34.6 0.5 33 137-169 66-98 (99)
138 PF08580 KAR9: Yeast cortical 54.3 2.8E+02 0.006 32.6 14.7 22 450-471 270-291 (683)
139 PHA02926 zinc finger-like prot 54.3 5.3 0.00012 39.5 0.7 54 294-348 170-226 (242)
140 PF09538 FYDLN_acid: Protein o 54.0 7.6 0.00016 34.3 1.6 27 295-323 10-36 (108)
141 PF02150 RNA_POL_M_15KD: RNA p 53.9 11 0.00025 26.1 2.1 27 226-255 2-29 (35)
142 TIGR00622 ssl1 transcription f 53.1 12 0.00026 33.2 2.7 39 226-266 56-101 (112)
143 KOG2114 Vacuolar assembly/sort 53.0 9.8 0.00021 44.4 2.6 103 77-192 757-881 (933)
144 KOG3970 Predicted E3 ubiquitin 52.2 12 0.00027 36.8 2.8 50 142-193 51-104 (299)
145 PF07975 C1_4: TFIIH C1-like d 52.1 12 0.00025 28.4 2.1 25 160-190 26-50 (51)
146 cd00194 UBA Ubiquitin Associat 51.0 47 0.001 22.8 5.0 34 82-116 4-37 (38)
147 COG5236 Uncharacterized conser 50.6 10 0.00023 39.6 2.1 47 138-193 58-107 (493)
148 COG4647 AcxC Acetone carboxyla 50.0 9.8 0.00021 34.2 1.6 59 246-305 69-131 (165)
149 KOG4684 Uncharacterized conser 49.9 11 0.00024 36.9 2.0 18 224-241 137-154 (275)
150 PF10168 Nup88: Nuclear pore c 49.5 2.4E+02 0.0053 33.3 13.4 24 450-473 601-624 (717)
151 PF06677 Auto_anti-p27: Sjogre 49.4 29 0.00063 25.1 3.7 22 295-319 18-40 (41)
152 COG5574 PEX10 RING-finger-cont 49.0 4.4 9.5E-05 41.0 -0.8 33 295-334 216-249 (271)
153 KOG2141 Protein involved in hi 48.5 11 0.00024 43.3 2.1 12 322-333 568-579 (822)
154 KOG3130 Uncharacterized conser 48.5 13 0.00028 39.8 2.5 6 146-151 396-401 (514)
155 KOG3579 Predicted E3 ubiquitin 48.1 15 0.00032 37.6 2.8 52 140-191 267-322 (352)
156 PF05290 Baculo_IE-1: Baculovi 47.9 12 0.00026 34.1 1.9 52 139-193 78-131 (140)
157 smart00661 RPOL9 RNA polymeras 47.3 16 0.00034 27.2 2.2 27 227-255 2-29 (52)
158 PHA03096 p28-like protein; Pro 47.1 9.2 0.0002 39.7 1.2 32 142-173 179-216 (284)
159 COG5219 Uncharacterized conser 46.8 4.7 0.0001 47.3 -1.1 52 139-194 1467-1523(1525)
160 PRK09710 lar restriction allev 45.8 15 0.00033 29.1 1.9 14 293-306 5-18 (64)
161 TIGR01384 TFS_arch transcripti 45.7 13 0.00028 32.3 1.7 24 296-322 2-25 (104)
162 KOG2906 RNA polymerase III sub 45.2 14 0.0003 31.8 1.7 28 296-324 3-32 (105)
163 PF14803 Nudix_N_2: Nudix N-te 44.6 20 0.00043 24.8 2.1 28 226-255 1-31 (34)
164 smart00165 UBA Ubiquitin assoc 44.0 63 0.0014 22.0 4.7 32 82-114 4-35 (37)
165 PRK05654 acetyl-CoA carboxylas 43.8 6.5 0.00014 40.9 -0.5 28 295-323 28-56 (292)
166 KOG3161 Predicted E3 ubiquitin 43.7 6.1 0.00013 44.6 -0.8 35 141-175 11-47 (861)
167 KOG0825 PHD Zn-finger protein 42.4 11 0.00024 43.5 1.0 53 141-193 96-153 (1134)
168 COG1997 RPL43A Ribosomal prote 42.2 20 0.00043 30.2 2.2 28 295-323 36-63 (89)
169 KOG2034 Vacuolar sorting prote 42.0 14 0.0003 43.5 1.7 34 140-173 816-850 (911)
170 cd00021 BBOX B-Box-type zinc f 41.7 16 0.00034 25.2 1.3 27 296-330 2-29 (39)
171 KOG1571 Predicted E3 ubiquitin 41.0 14 0.00029 39.2 1.3 42 141-193 305-346 (355)
172 COG1645 Uncharacterized Zn-fin 40.9 19 0.00041 32.8 2.0 23 295-328 29-51 (131)
173 smart00804 TAP_C C-terminal do 40.9 92 0.002 24.7 5.7 40 76-115 9-48 (63)
174 PF14569 zf-UDP: Zinc-binding 40.2 32 0.00069 28.4 3.0 49 139-193 7-61 (80)
175 KOG4739 Uncharacterized protei 39.8 4.1E+02 0.0089 26.8 12.4 24 308-332 21-48 (233)
176 PRK14892 putative transcriptio 39.8 19 0.00042 31.2 1.9 27 295-322 22-51 (99)
177 KOG1952 Transcription factor N 39.0 34 0.00075 40.1 4.2 51 139-191 189-244 (950)
178 PHA02929 N1R/p28-like protein; 38.7 13 0.00028 37.5 0.7 40 294-335 174-216 (238)
179 KOG0943 Predicted ubiquitin-pr 37.5 20 0.00043 43.5 2.0 16 454-469 2419-2434(3015)
180 KOG0943 Predicted ubiquitin-pr 37.5 24 0.00051 42.9 2.6 9 513-521 2475-2483(3015)
181 KOG2177 Predicted E3 ubiquitin 37.5 13 0.00029 37.4 0.6 25 296-328 88-112 (386)
182 PRK04023 DNA polymerase II lar 37.4 26 0.00056 42.0 2.9 33 222-264 623-661 (1121)
183 COG1998 RPS31 Ribosomal protei 36.9 23 0.00049 26.6 1.5 26 295-321 20-45 (51)
184 COG5432 RAD18 RING-finger-cont 36.5 10 0.00023 38.7 -0.3 30 295-331 26-55 (391)
185 COG1198 PriA Primosomal protei 36.5 24 0.00051 41.4 2.5 35 295-330 445-484 (730)
186 PRK14714 DNA polymerase II lar 36.4 30 0.00066 42.5 3.3 11 295-305 710-720 (1337)
187 PF14446 Prok-RING_1: Prokaryo 35.9 29 0.00062 26.7 2.0 32 141-172 5-38 (54)
188 PF01428 zf-AN1: AN1-like Zinc 35.8 20 0.00043 25.9 1.1 29 228-263 1-30 (43)
189 TIGR00515 accD acetyl-CoA carb 35.7 9.8 0.00021 39.5 -0.7 28 295-323 27-55 (285)
190 CHL00174 accD acetyl-CoA carbo 35.7 9.4 0.0002 39.7 -0.8 28 295-323 39-67 (296)
191 PF03115 Astro_capsid: Astrovi 35.0 13 0.00028 43.8 0.0 15 91-105 721-736 (787)
192 COG0266 Nei Formamidopyrimidin 35.0 26 0.00057 36.1 2.2 25 295-320 246-272 (273)
193 TIGR00686 phnA alkylphosphonat 34.4 27 0.0006 30.6 1.9 26 295-322 3-28 (109)
194 PF03943 TAP_C: TAP C-terminal 33.8 41 0.00089 25.4 2.6 36 81-116 2-37 (51)
195 PF02845 CUE: CUE domain; Int 33.8 1.3E+02 0.0028 21.4 5.1 36 81-116 3-39 (42)
196 PF01363 FYVE: FYVE zinc finge 33.6 37 0.0008 26.8 2.5 35 294-331 9-43 (69)
197 PRK11827 hypothetical protein; 33.4 34 0.00074 26.9 2.1 25 295-320 9-33 (60)
198 PF03119 DNA_ligase_ZBD: NAD-d 33.1 37 0.00079 22.3 1.9 21 296-316 1-21 (28)
199 KOG2932 E3 ubiquitin ligase in 33.1 12 0.00027 38.6 -0.4 53 222-311 87-140 (389)
200 TIGR00599 rad18 DNA repair pro 32.9 13 0.00029 40.2 -0.3 32 295-333 27-58 (397)
201 COG2888 Predicted Zn-ribbon RN 32.7 18 0.0004 28.2 0.5 7 295-301 28-34 (61)
202 PF09726 Macoilin: Transmembra 32.3 9E+02 0.02 28.5 14.6 72 414-502 587-658 (697)
203 KOG2906 RNA polymerase III sub 32.3 42 0.00092 28.9 2.7 29 226-256 2-31 (105)
204 TIGR02300 FYDLN_acid conserved 32.2 28 0.0006 31.5 1.7 26 295-322 10-35 (129)
205 PF06906 DUF1272: Protein of u 32.1 33 0.00071 26.5 1.8 44 143-194 7-52 (57)
206 PF09889 DUF2116: Uncharacteri 32.0 8.8 0.00019 30.0 -1.3 11 295-305 4-14 (59)
207 COG3809 Uncharacterized protei 31.9 35 0.00075 28.2 2.0 35 295-336 2-36 (88)
208 PF05715 zf-piccolo: Piccolo Z 31.7 20 0.00043 28.0 0.6 41 295-336 3-45 (61)
209 PF09723 Zn-ribbon_8: Zinc rib 31.5 50 0.0011 23.7 2.7 12 295-306 27-39 (42)
210 COG1594 RPB9 DNA-directed RNA 31.3 33 0.00071 30.5 2.0 28 295-323 3-32 (113)
211 PF04147 Nop14: Nop14-like fam 30.9 41 0.00089 40.4 3.3 6 508-513 827-832 (840)
212 PF04050 Upf2: Up-frameshift s 30.5 33 0.00072 32.7 2.0 12 73-84 63-74 (170)
213 PRK14811 formamidopyrimidine-D 30.5 34 0.00073 35.2 2.2 22 295-316 236-259 (269)
214 PF06827 zf-FPG_IleRS: Zinc fi 30.4 32 0.00069 22.7 1.3 22 295-316 2-25 (30)
215 PRK12495 hypothetical protein; 29.5 39 0.00085 33.5 2.3 27 294-331 42-68 (226)
216 PF12861 zf-Apc11: Anaphase-pr 29.5 17 0.00037 30.6 -0.1 35 295-334 33-67 (85)
217 smart00659 RPOLCX RNA polymera 29.1 46 0.00099 24.4 2.1 25 296-322 4-28 (44)
218 PF13453 zf-TFIIB: Transcripti 29.0 38 0.00082 24.1 1.6 31 296-333 1-31 (41)
219 PRK01103 formamidopyrimidine/5 28.9 39 0.00084 34.8 2.4 26 294-320 245-272 (274)
220 PF01599 Ribosomal_S27: Riboso 28.9 36 0.00079 25.4 1.5 26 295-321 19-46 (47)
221 PF08792 A2L_zn_ribbon: A2L zi 28.6 55 0.0012 22.5 2.3 12 294-305 3-14 (33)
222 TIGR00577 fpg formamidopyrimid 28.3 41 0.00088 34.6 2.4 24 295-319 246-271 (272)
223 KOG2164 Predicted E3 ubiquitin 28.2 24 0.00052 39.1 0.7 30 294-330 186-215 (513)
224 PF14445 Prok-RING_2: Prokaryo 28.2 12 0.00025 28.2 -1.1 31 140-170 6-37 (57)
225 PF14149 YhfH: YhfH-like prote 28.1 5.9 0.00013 27.9 -2.5 25 294-319 13-37 (37)
226 PRK14714 DNA polymerase II lar 28.1 34 0.00073 42.1 1.9 30 295-331 668-702 (1337)
227 PF14569 zf-UDP: Zinc-binding 28.0 31 0.00067 28.5 1.1 54 233-312 15-69 (80)
228 PRK10220 hypothetical protein; 27.9 41 0.00089 29.6 1.9 30 295-334 4-33 (111)
229 PHA02664 hypothetical protein; 27.9 96 0.0021 32.4 4.9 13 78-90 513-525 (534)
230 smart00336 BBOX B-Box-type zin 27.6 52 0.0011 22.9 2.2 28 295-330 4-32 (42)
231 PF03615 GCM: GCM motif protei 27.4 55 0.0012 29.8 2.7 36 266-322 69-106 (143)
232 COG1315 Uncharacterized conser 27.4 4.2E+02 0.009 29.8 9.8 38 368-405 407-444 (543)
233 PF08271 TF_Zn_Ribbon: TFIIB z 27.4 57 0.0012 23.4 2.4 8 296-303 2-9 (43)
234 PF05320 Pox_RNA_Pol_19: Poxvi 27.3 22 0.00048 33.1 0.2 9 141-149 126-134 (167)
235 PRK10445 endonuclease VIII; Pr 27.2 43 0.00094 34.3 2.3 25 295-320 236-262 (263)
236 KOG2907 RNA polymerase I trans 27.1 42 0.00092 29.7 1.9 35 164-200 8-42 (116)
237 KOG1701 Focal adhesion adaptor 27.0 18 0.00038 39.2 -0.6 11 295-305 428-438 (468)
238 PRK14810 formamidopyrimidine-D 27.0 43 0.00094 34.5 2.3 26 294-320 244-271 (272)
239 PRK13945 formamidopyrimidine-D 26.8 44 0.00095 34.6 2.3 25 295-320 255-281 (282)
240 PF03604 DNA_RNApol_7kD: DNA d 26.8 45 0.00098 22.7 1.6 24 297-322 3-26 (32)
241 PF09788 Tmemb_55A: Transmembr 26.5 62 0.0014 32.8 3.2 88 140-257 64-168 (256)
242 PTZ00415 transmission-blocking 25.9 62 0.0013 41.1 3.5 9 426-434 617-625 (2849)
243 PF01783 Ribosomal_L32p: Ribos 25.8 32 0.0007 26.5 0.8 22 293-320 25-46 (56)
244 COG0777 AccD Acetyl-CoA carbox 25.7 22 0.00048 36.4 -0.1 28 295-323 29-57 (294)
245 COG2816 NPY1 NTP pyrophosphohy 25.4 59 0.0013 33.5 2.9 36 286-323 104-139 (279)
246 PF02318 FYVE_2: FYVE-type zin 25.4 57 0.0012 29.1 2.5 36 293-330 53-88 (118)
247 PF12773 DZR: Double zinc ribb 25.2 51 0.0011 24.3 1.8 24 563-586 26-49 (50)
248 KOG2932 E3 ubiquitin ligase in 24.8 30 0.00065 35.9 0.6 30 295-331 91-121 (389)
249 PRK12286 rpmF 50S ribosomal pr 24.7 44 0.00095 25.9 1.4 22 293-320 26-47 (57)
250 PRK09710 lar restriction allev 24.7 94 0.002 24.8 3.2 33 224-257 5-38 (64)
251 PF04803 Cor1: Cor1/Xlr/Xmr co 24.4 5.5E+02 0.012 23.4 11.4 11 372-382 47-57 (130)
252 PRK09521 exosome complex RNA-b 24.2 49 0.0011 32.0 2.0 25 296-322 151-175 (189)
253 COG5220 TFB3 Cdk activating ki 23.9 44 0.00095 33.5 1.6 54 182-239 11-65 (314)
254 KOG3183 Predicted Zn-finger pr 23.6 32 0.0007 34.4 0.6 57 226-306 9-67 (250)
255 PHA02325 hypothetical protein 23.6 36 0.00078 26.9 0.7 13 293-305 2-14 (72)
256 COG2824 PhnA Uncharacterized Z 23.2 51 0.0011 28.8 1.6 24 295-321 4-28 (112)
257 KOG2807 RNA polymerase II tran 23.2 48 0.0011 34.7 1.8 16 160-175 350-365 (378)
258 KOG0250 DNA repair protein RAD 23.1 1.5E+03 0.032 28.0 16.6 26 416-441 254-279 (1074)
259 PF05285 SDA1: SDA1; InterPro 23.0 1E+02 0.0022 32.7 4.2 9 69-77 189-197 (324)
260 PF05129 Elf1: Transcription e 23.0 41 0.00089 28.0 1.0 29 294-323 22-56 (81)
261 TIGR01206 lysW lysine biosynth 23.0 80 0.0017 24.3 2.5 28 227-256 4-32 (54)
262 COG1594 RPB9 DNA-directed RNA 23.0 80 0.0017 28.1 2.9 30 225-256 2-32 (113)
263 KOG4445 Uncharacterized conser 23.0 39 0.00084 35.0 1.0 33 141-173 115-149 (368)
264 KOG1940 Zn-finger protein [Gen 22.8 55 0.0012 33.7 2.1 48 138-191 155-204 (276)
265 KOG0956 PHD finger protein AF1 22.6 1.1E+02 0.0024 35.4 4.4 34 224-261 21-55 (900)
266 PLN02638 cellulose synthase A 22.5 59 0.0013 39.6 2.5 55 233-313 23-78 (1079)
267 KOG2979 Protein involved in DN 22.5 91 0.002 31.7 3.5 48 141-191 176-223 (262)
268 PRK11546 zraP zinc resistance 22.5 6.3E+02 0.014 23.5 10.1 54 448-501 46-103 (143)
269 COG5293 Predicted ATPase [Gene 22.4 1.1E+03 0.024 26.3 12.7 23 499-521 439-461 (591)
270 COG0021 TktA Transketolase [Ca 22.4 4.2E+02 0.0092 30.7 9.0 94 424-522 270-375 (663)
271 KOG4460 Nuclear pore complex, 22.1 1.2E+03 0.026 26.6 13.2 16 506-521 666-681 (741)
272 KOG1991 Nuclear transport rece 22.1 56 0.0012 39.1 2.2 24 75-98 968-992 (1010)
273 KOG4362 Transcriptional regula 22.1 28 0.00061 40.1 -0.2 50 141-195 21-70 (684)
274 TIGR01031 rpmF_bact ribosomal 22.0 58 0.0012 25.1 1.6 21 294-320 26-46 (55)
275 PRK13428 F0F1 ATP synthase sub 21.5 1.1E+03 0.024 26.0 15.6 25 451-475 85-109 (445)
276 PLN00209 ribosomal protein S27 21.5 96 0.0021 26.2 2.9 34 226-262 37-71 (86)
277 PF14354 Lar_restr_allev: Rest 21.5 94 0.002 23.8 2.8 29 224-254 2-37 (61)
278 TIGR00595 priA primosomal prot 21.4 64 0.0014 36.3 2.5 35 295-330 223-262 (505)
279 PTZ00083 40S ribosomal protein 21.2 95 0.0021 26.1 2.8 35 226-263 36-71 (85)
280 KOG2141 Protein involved in hi 21.2 1E+02 0.0022 35.8 3.9 42 73-114 313-360 (822)
281 smart00546 CUE Domain that may 21.1 2.8E+02 0.0062 19.6 5.0 38 80-117 3-41 (43)
282 KOG4198 RNA-binding Ran Zn-fin 20.8 1.6E+02 0.0035 30.5 4.9 29 562-590 136-164 (280)
283 PRK04023 DNA polymerase II lar 20.7 51 0.0011 39.7 1.5 32 292-330 624-660 (1121)
284 KOG2879 Predicted E3 ubiquitin 20.6 45 0.00097 34.2 0.9 31 294-330 239-269 (298)
285 KOG4364 Chromatin assembly fac 20.3 86 0.0019 36.0 3.1 8 7-14 517-524 (811)
286 KOG2789 Putative Zn-finger pro 20.2 46 0.001 35.7 1.0 32 139-170 72-103 (482)
287 COG5243 HRD1 HRD ubiquitin lig 20.2 70 0.0015 34.1 2.2 11 295-305 335-345 (491)
288 PF00098 zf-CCHC: Zinc knuckle 20.1 61 0.0013 19.0 1.0 16 256-271 2-17 (18)
289 PRK14892 putative transcriptio 20.1 1.1E+02 0.0023 26.7 3.0 54 222-280 18-73 (99)
290 COG3813 Uncharacterized protei 20.1 70 0.0015 26.0 1.7 43 143-193 7-51 (84)
291 TIGR02159 PA_CoA_Oxy4 phenylac 20.0 88 0.0019 29.1 2.7 92 74-170 39-137 (146)
No 1
>KOG1815 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=100.00 E-value=5e-72 Score=608.27 Aligned_cols=432 Identities=48% Similarity=0.908 Sum_probs=392.8
Q ss_pred EeCHHHHHHHHHHHHHHHHHHhCCCHHHHHHHHHhcCCChHHHHHHhhcCHHHHHHHcCCCCCCCCCCCCCCcccccccc
Q 007763 69 VLTEADIRQRQEEDITRISTVLSISKVAASILLRFYNWSVSKVHDEWFADEERVRKAVGLLEKPAVQFPDGEEMTCGICF 148 (590)
Q Consensus 69 vl~~~~i~~~~~~~i~~v~~il~i~~~~a~~LL~~~~W~~~~l~e~~~~~~~~~~~~~gl~~~~~~~~~~~~~~~C~IC~ 148 (590)
||+.+++...|.++|.+|+++|++++.+|++||.+|.|+++++++.|+.+++.++..+|+...+ .......|.||+
T Consensus 2 vl~~~~~~~~~~~~i~~~~~~ls~~~~~~~~ll~~~~W~~~kl~~~~~~~~~~~~~~~g~~~~~----~~~~~~~c~ic~ 77 (444)
T KOG1815|consen 2 VLTPDDIAALMREDIIEVSDILSLSHAVARILLAHFCWNVEKLLEEWVEDEETGCFFVGLLLWP----KKKGDVQCGICV 77 (444)
T ss_pred CCchHhhhHHhHhhHHHHHHhhcCCHHHHHHHHHhcCcchHHHHHHHHhcCcchhhhccccccC----CCCccccCCccc
Confidence 6889999999999999999999999999999999999999999999999999999999986653 334578899999
Q ss_pred cccCCCCceecCCCCccchhhH-----HHhhcCCCceecccCCCCCCCccchhHHhhcCCh-HHHHHHHHHHHHHHhhcC
Q 007763 149 ENYPSDRLLAAACGHPFCSSCW-----TAINDGPGCLMLRCPDPSCGAAVGQDMIYLLSSD-EDKVKYNRYFIRSYVEDN 222 (590)
Q Consensus 149 e~~~~~~~~~l~CgH~fC~~C~-----~~i~~g~~~~~i~CP~~~C~~~i~~~~i~~ll~~-e~~eky~~~l~~~~v~~~ 222 (590)
+.++. .++.+.|||.||..|| +.|..+.... |+||...|.+.+..+.|..++++ ++.++|.++++++|++.+
T Consensus 78 ~~~~~-~~~~~~c~H~~c~~cw~~yl~~kI~~~~~~~-i~cp~~~C~a~v~~~~i~~~~s~~~~~~ky~~~i~~syve~~ 155 (444)
T KOG1815|consen 78 ESYDG-EIIGLGCGHPFCPPCWTGYLGTKIHEGEEAK-IKCPAHGCPALVGEDTVEKLVSDKEDKEKYQRYILRSYVEDN 155 (444)
T ss_pred CCCcc-hhhhcCCCcHHHHHHHHHHhhheeecccccc-ccCCCCCccccCCCceeeeecCCHHHHHHHHHHHHHHHHhcC
Confidence 99865 6888999999999999 4555665323 99999999999999999999998 599999999999999999
Q ss_pred CCcccCCCCCCCceEeeecCCCcceeEecCCCccccccCCCcCCCCCchhHHHHHHhhhhhhhhHHHHHhcCcCCCCCCc
Q 007763 223 RKTKWCPAPGCDYAVDFVVGSGNYDVTCRCSYSFCWNCTEEAHRPVDCDTVAKWVLKNSAESENMNWILANSKPCPRCKR 302 (590)
Q Consensus 223 ~~~~~CP~p~C~~~i~~~~~~~~~~v~C~C~~~fC~~C~~~~H~p~~C~~~~~w~~k~~~e~e~~~wi~~ntK~CP~C~~ 302 (590)
..++|||+|+|++++.+. ......|.|.|++.|||.|+.+||.|++|....+|+.+..+++++.+||.+|+++||+|.+
T Consensus 156 ~~lkwCP~~~C~~av~~~-~~~~~~v~C~~g~~FC~~C~~~~H~p~~C~~~~~wl~k~~~~se~~~wi~~ntk~CP~c~~ 234 (444)
T KOG1815|consen 156 VPLKWCPAPGCGLAVKFG-SLESVEVDCGCGHEFCFACGEESHSPVSCPGAKKWLKKCRDDSETINWILANTKECPKCKV 234 (444)
T ss_pred CccccCCCCCCCceeecc-CCCccceeCCCCchhHhhccccccCCCcccchHHHHHhhhhhhhhhhhhhccCccCCCccc
Confidence 999999999999999875 4456789999999999999999999999999999999999999999999999999999999
Q ss_pred ceeeccCCCceeecCC--CcceeeecccccccCCCCCCCCcccCCchhhhhhcCcchhHHHHHHHHHHHHHHHHHHHHHH
Q 007763 303 PIEKNQGCMHMTCTPP--CKFEFCWLCLGQWSDHGERTGGFYACNRYETAKQEGVYDESEKRREMAKNSLERYTHYYERW 380 (590)
Q Consensus 303 ~IEK~~GCnhMtC~~~--C~~~FCw~C~~~w~~H~~~~g~~y~C~~~~~~~~~~~~~~~e~~~~~~~~~l~ry~~y~~r~ 380 (590)
+|||++|||||+|. . |++.|||+|++.|.+|+..+ +|.|++|...+.. . .+++++..|.||+|||.||
T Consensus 235 ~iek~~gc~~~~~~-~~~c~~~FCw~Cl~~~~~h~~~~--~~~c~~~~~~~~~------~-~~~~a~~~l~r~~~~~~~~ 304 (444)
T KOG1815|consen 235 PIEKDGGCNHMTCK-SASCKHEFCWVCLASLSDHGSST--GYSCNRYVDGKSK------S-ARSKARRSLKRYTHYYNRW 304 (444)
T ss_pred chhccCCccccccc-cCCcCCeeceeeecccccccccc--eeeeeeeechhhh------h-HHHHHHHHHHHHHHHHhhH
Confidence 99999999999998 6 99999999999999999754 8999999765421 1 4678889999999999999
Q ss_pred HhhHHHHHHHHHHHHHHHHHHHHHHhhhcCCCchhHHHHHHHHHHHHHHHHHHHhhhhhhcccCccchhHHHHHHHHHHH
Q 007763 381 ATNQSSRQKALADLQQMQTVHLEKLSDVQCQPESQLKFITEAWLQIVECRRVLKWTYAYGYYLPDHEHAKRQFFEYLQGE 460 (590)
Q Consensus 381 ~~h~~s~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~l~~a~~~l~~~R~~L~~sy~~~yyl~~~~~~~~~~fe~~Q~~ 460 (590)
++|+.+++++...+..+...+..++......++++++|+.+++.+|.+||++|+|||+|+||+. ..+++++||++|.+
T Consensus 305 ~~~q~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~e~r~~l~~s~~~~~~~~--~~~~~~~fe~~q~~ 382 (444)
T KOG1815|consen 305 MEHQVSLKLEGKLLSKVEEVKKPKLSDSLSLSWIDVQFLRDAGDVLVECRRTLKWTYAYAYYLS--ENNKRNLFEDNQTD 382 (444)
T ss_pred HhhhhhhhhhhhhHHHHHHHhhhhhhcccCeeeeeeeeechhHHHHHhhhhhhhhhhhhhhhhc--ccchhhhhHHHHHH
Confidence 9999999999888888877778888877777889999999999999999999999999999997 44677999999999
Q ss_pred HHHhHHHHHHHHHHHHHHHhhcCCCCCcHHHHHHHHHHHHHhHHHHHHHHHHHHHccccccccc
Q 007763 461 AESGLERLHQCAEKELQIYLNADGPSKDFNEFRTKLAGLTSVTRNYFENLVRALENGLSDVDTH 524 (590)
Q Consensus 461 le~~~E~L~~~le~~l~~~~~~~~~~~~~~~~~~~l~~lt~~~~~~~~~l~~~le~gl~~~~~~ 524 (590)
|++.+|.|+..+|.++. +.+...+..+|.++.++|.++++||++++.++++||.++...
T Consensus 383 ~~~~~e~ls~~~~~~~~-----~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~ 441 (444)
T KOG1815|consen 383 LESAVEPLSSCLEESLK-----DISSETLAEFKQKLTDLTSYVRNRFENLLKHLEEGLEDVGSE 441 (444)
T ss_pred HhhhhhhhHHHhccccc-----cCCcccHHHHHhhccccchhhhhHHHHHHHHHHhcccccccc
Confidence 99999999999998776 556789999999999999999999999999999999999553
No 2
>KOG1812 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=99.98 E-value=5e-33 Score=295.31 Aligned_cols=219 Identities=26% Similarity=0.654 Sum_probs=179.8
Q ss_pred CcccccccccccCC-CCce-ecCCCCccchhhH-HHhhc-CCCceecccCCCCCCCccchhHHhhcCChHHHHHHHHHHH
Q 007763 140 EEMTCGICFENYPS-DRLL-AAACGHPFCSSCW-TAIND-GPGCLMLRCPDPSCGAAVGQDMIYLLSSDEDKVKYNRYFI 215 (590)
Q Consensus 140 ~~~~C~IC~e~~~~-~~~~-~l~CgH~fC~~C~-~~i~~-g~~~~~i~CP~~~C~~~i~~~~i~~ll~~e~~eky~~~l~ 215 (590)
...+|+||+...+. +.++ ...|+|.||.+|| .+|.. +.....++||+.+|...++.+....++++++.++|.+++.
T Consensus 145 ~~~~C~iC~~e~~~~~~~f~~~~C~H~fC~~C~k~~iev~~~~~~~~~C~~~~C~~~l~~~~c~~llt~kl~e~~e~~~~ 224 (384)
T KOG1812|consen 145 PKEECGICFVEDPEAEDMFSVLKCGHRFCKDCVKQHIEVKLLSGTVIRCPHDGCESRLTLESCRKLLTPKLREMWEQRLK 224 (384)
T ss_pred ccccCccCccccccHhhhHHHhcccchhhhHHhHHHhhhhhccCCCccCCCCCCCccCCHHHHhhhcCHHHHHHHHHHHH
Confidence 36789999954443 3444 4679999999999 33321 2233689999999999999999999999999999999999
Q ss_pred HHHhhcCCCcccCCCCCCCceEeeecC---CCcceeEe-cCCCccccccCCCcCCCCCchhHHHHHHhhhhhhhhHHHHH
Q 007763 216 RSYVEDNRKTKWCPAPGCDYAVDFVVG---SGNYDVTC-RCSYSFCWNCTEEAHRPVDCDTVAKWVLKNSAESENMNWIL 291 (590)
Q Consensus 216 ~~~v~~~~~~~~CP~p~C~~~i~~~~~---~~~~~v~C-~C~~~fC~~C~~~~H~p~~C~~~~~w~~k~~~e~e~~~wi~ 291 (590)
+.++.....+ +||.|+|...+..... .......| .|+..||..|+.+||.+.+|+.+++|......+...++|+.
T Consensus 225 e~~i~~~~~~-ycp~~~C~~l~~~~el~~~~~~~~~~C~~C~~~fCv~C~~~wh~~~sC~eykk~~~~~~~d~~~~~~la 303 (384)
T KOG1812|consen 225 EEVIPSLDRV-YCPYPRCSSLMSKTELSSEVKSKRRPCVKCHELFCVKCKVPWHANLSCEEYKKLNPEEYVDDITLKYLA 303 (384)
T ss_pred HHhhhhhhcc-cCCCCCchHhhhhhhhccchhhcccccccCCCceeecCCCcCCCCCCHHHHHHhCCcccccHHHHHHHH
Confidence 9999988888 9999999877654321 22344568 99999999999999999999999999877777788888988
Q ss_pred hcCcCCCCCCcceeeccCCCceeecCCCcceeeecccccccCCCCCCCCcccCCchhhhhhcCcchhHHHHHHHHHHHHH
Q 007763 292 ANSKPCPRCKRPIEKNQGCMHMTCTPPCKFEFCWLCLGQWSDHGERTGGFYACNRYETAKQEGVYDESEKRREMAKNSLE 371 (590)
Q Consensus 292 ~ntK~CP~C~~~IEK~~GCnhMtC~~~C~~~FCw~C~~~w~~H~~~~g~~y~C~~~~~~~~~~~~~~~e~~~~~~~~~l~ 371 (590)
++++.||+|+..|++++|||||+|+ |||+|||.|+++|..|+. .+|.|.++...
T Consensus 304 ~~wr~CpkC~~~ie~~~GCnhm~Cr--C~~~fcy~C~~~~~~~~~---~~~~~~r~~~~--------------------- 357 (384)
T KOG1812|consen 304 KRWRQCPKCKFMIELSEGCNHMTCR--CGHQFCYMCGGDWKTHNG---ECYECCRYKES--------------------- 357 (384)
T ss_pred HhcCcCcccceeeeecCCcceEEee--ccccchhhcCcchhhCCc---cccCccccccc---------------------
Confidence 9999999999999999999999998 999999999999998875 46677766421
Q ss_pred HHHHHHHHHHhhHHHH
Q 007763 372 RYTHYYERWATNQSSR 387 (590)
Q Consensus 372 ry~~y~~r~~~h~~s~ 387 (590)
++||.++.+|....
T Consensus 358 --~~~~~~~~~~~~~~ 371 (384)
T KOG1812|consen 358 --THYFEDDENHDKSI 371 (384)
T ss_pred --cccccccccccccc
Confidence 56777777666554
No 3
>KOG1814 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=99.97 E-value=4e-31 Score=270.14 Aligned_cols=190 Identities=31% Similarity=0.712 Sum_probs=162.2
Q ss_pred CCcccccccccccCC-CCceecCCCCccchhhH-----HHhhcCCCceecccCCCCCCCccchhHHhhcCChHHHHHHHH
Q 007763 139 GEEMTCGICFENYPS-DRLLAAACGHPFCSSCW-----TAINDGPGCLMLRCPDPSCGAAVGQDMIYLLSSDEDKVKYNR 212 (590)
Q Consensus 139 ~~~~~C~IC~e~~~~-~~~~~l~CgH~fC~~C~-----~~i~~g~~~~~i~CP~~~C~~~i~~~~i~~ll~~e~~eky~~ 212 (590)
...+.|.|||+.... ..++.++|+|.||+.|+ ..|.+|. ...++||+++|+...++..++.++..+++++|++
T Consensus 182 ~slf~C~ICf~e~~G~~c~~~lpC~Hv~Ck~C~kdY~~~~i~eg~-v~~l~Cp~~~C~~~a~~g~vKelvg~EL~arYe~ 260 (445)
T KOG1814|consen 182 NSLFDCCICFEEQMGQHCFKFLPCSHVFCKSCLKDYFTIQIQEGQ-VSCLKCPDPKCGSVAPPGQVKELVGDELFARYEK 260 (445)
T ss_pred hhcccceeeehhhcCcceeeecccchHHHHHHHHHHHHHhhhcce-eeeecCCCCCCcccCCchHHHHHHHHHHHHHHHH
Confidence 457899999998765 57788999999999999 4556664 5789999999999999999999999999999999
Q ss_pred HHHHHHhhcCCCcccCCCCCCCceEeeecCCCcceeEe-cCCCccccccCCCcCCCCCchhHH--------HHH------
Q 007763 213 YFIRSYVEDNRKTKWCPAPGCDYAVDFVVGSGNYDVTC-RCSYSFCWNCTEEAHRPVDCDTVA--------KWV------ 277 (590)
Q Consensus 213 ~l~~~~v~~~~~~~~CP~p~C~~~i~~~~~~~~~~v~C-~C~~~fC~~C~~~~H~p~~C~~~~--------~w~------ 277 (590)
+++++.++...++++||++.|..++.. ..+..-+.| .|..+||.-|+..||...+|.... .|.
T Consensus 261 l~lqk~l~~msdv~yCPr~~Cq~p~~~--d~~~~l~~CskCnFaFCtlCk~t~HG~s~Ck~~~~~~~~l~~~~~~~d~a~ 338 (445)
T KOG1814|consen 261 LMLQKTLELMSDVVYCPRACCQLPVKQ--DPGRALAICSKCNFAFCTLCKLTWHGVSPCKVKAEKLIELYLEYLEADEAR 338 (445)
T ss_pred HHHHHHHHhhcccccCChhhccCcccc--CchhhhhhhccCccHHHHHHHHhhcCCCcccCchHHHHHHHHHHhhcCHHH
Confidence 999999999999999999999988743 345566789 999999999999999998996541 121
Q ss_pred -------------HhhhhhhhhHHHHHhcCcCCCCCCcceeeccCCCceeecCCCcceeeeccccccc
Q 007763 278 -------------LKNSAESENMNWILANSKPCPRCKRPIEKNQGCMHMTCTPPCKFEFCWLCLGQWS 332 (590)
Q Consensus 278 -------------~k~~~e~e~~~wi~~ntK~CP~C~~~IEK~~GCnhMtC~~~C~~~FCw~C~~~w~ 332 (590)
.....+-.+..|+..|.|+||+|+++|||++|||||+|. .|++.|||+|.....
T Consensus 339 k~ele~Ryg~rvve~~vn~~lsekwl~~N~krCP~C~v~IEr~eGCnKM~C~-~c~~~fc~~c~~~l~ 405 (445)
T KOG1814|consen 339 KRELEKRYGKRVVEELVNDFLSEKWLESNSKRCPKCKVVIERSEGCNKMHCT-KCGTYFCWICAELLY 405 (445)
T ss_pred HHHHHHHhhHHHHHHHHHHHHHHHHHHhcCCCCCcccceeecCCCccceeec-cccccceeehhhhcC
Confidence 111233445689999999999999999999999999999 899999999988654
No 4
>KOG0006 consensus E3 ubiquitin-protein ligase (Parkin protein) [Posttranslational modification, protein turnover, chaperones]
Probab=99.88 E-value=2.5e-23 Score=205.61 Aligned_cols=190 Identities=31% Similarity=0.720 Sum_probs=141.3
Q ss_pred CCCCcccccccccccCCCCceecCCC--CccchhhH-----HHhhcC------CCceecccCCCCCCCccchh-HHhhcC
Q 007763 137 PDGEEMTCGICFENYPSDRLLAAACG--HPFCSSCW-----TAINDG------PGCLMLRCPDPSCGAAVGQD-MIYLLS 202 (590)
Q Consensus 137 ~~~~~~~C~IC~e~~~~~~~~~l~Cg--H~fC~~C~-----~~i~~g------~~~~~i~CP~~~C~~~i~~~-~i~~ll 202 (590)
.+....+|..|-+.- +.+..++|. |..|.+|+ +.+++. .-...+.||. +|...+-.+ .--+++
T Consensus 217 ~N~~ni~C~~Ctdv~--~~vlvf~Cns~HvtC~dCFr~yc~~Rl~~rqf~~~p~~gyslpc~a-gc~~s~i~e~HHF~il 293 (446)
T KOG0006|consen 217 TNSRNITCITCTDVR--SPVLVFQCNSRHVTCLDCFRLYCVTRLNDRQFVHDPQLGYSLPCVA-GCPNSLIKELHHFRIL 293 (446)
T ss_pred cccccceeEEecCCc--cceEEEecCCceeehHHhhhhHhhhcccccccccCccccccccccC-CCchHHHHhhhhheec
Confidence 456678899998764 344567888 99999999 333332 1225688986 887766443 334678
Q ss_pred ChHHHHHHHHHHHHHHhhcCCCcccCCCCCCCceEeeecCCCcceeEe--cCCCccccccCCCcCCCCCchhHH------
Q 007763 203 SDEDKVKYNRYFIRSYVEDNRKTKWCPAPGCDYAVDFVVGSGNYDVTC--RCSYSFCWNCTEEAHRPVDCDTVA------ 274 (590)
Q Consensus 203 ~~e~~eky~~~l~~~~v~~~~~~~~CP~p~C~~~i~~~~~~~~~~v~C--~C~~~fC~~C~~~~H~p~~C~~~~------ 274 (590)
..+.+.+|+++..+.+|.... -+-||+|+|+..+...+ ....|+| .||+.||..|++.+|.+- |...-
T Consensus 294 g~e~Y~rYQr~atEe~vlq~g-GVlCP~pgCG~gll~EP--D~rkvtC~~gCgf~FCR~C~e~yh~ge-C~~~~~as~t~ 369 (446)
T KOG0006|consen 294 GEEQYNRYQRYATEECVLQMG-GVLCPRPGCGAGLLPEP--DQRKVTCEGGCGFAFCRECKEAYHEGE-CSAVFEASGTT 369 (446)
T ss_pred chhHHHHHHHhhhhhheeecC-CEecCCCCCCcccccCC--CCCcccCCCCchhHhHHHHHhhhcccc-ceeeecccccc
Confidence 899999999999999887765 56999999998776544 5678999 599999999999999862 32110
Q ss_pred --HH-HHhhhh-----hhhhHHHHHhcCcCCCCCCcceeeccCCCceeecC-CCcceeeecccccccC
Q 007763 275 --KW-VLKNSA-----ESENMNWILANSKPCPRCKRPIEKNQGCMHMTCTP-PCKFEFCWLCLGQWSD 333 (590)
Q Consensus 275 --~w-~~k~~~-----e~e~~~wi~~ntK~CP~C~~~IEK~~GCnhMtC~~-~C~~~FCw~C~~~w~~ 333 (590)
.+ +..+.+ +..+..-|+..|||||+|+.|.||||||+||.|.. .||.+|||.|+..|..
T Consensus 370 tc~y~vde~~a~~arwd~as~~TIk~tTkpCPkChvptErnGGCmHm~Ct~~~Cg~eWCw~C~tEW~r 437 (446)
T KOG0006|consen 370 TCAYRVDERAAEQARWDAASKETIKKTTKPCPKCHVPTERNGGCMHMKCTQPQCGLEWCWNCGTEWNR 437 (446)
T ss_pred ceeeecChhhhhhhhhhhhhhhhhhhccCCCCCccCccccCCceEEeecCCCCCCceeEeccCChhhh
Confidence 00 000000 22234457888999999999999999999999984 5999999999999973
No 5
>smart00647 IBR In Between Ring fingers. the domains occurs between pairs og RING fingers
Probab=99.27 E-value=6.4e-12 Score=99.88 Aligned_cols=63 Identities=46% Similarity=1.028 Sum_probs=56.4
Q ss_pred HHHHHHHHHHHhhcCCCcccCCCCCCCceEeeecCCCcceeEe-cCCCccccccCCCcCCCCCc
Q 007763 208 VKYNRYFIRSYVEDNRKTKWCPAPGCDYAVDFVVGSGNYDVTC-RCSYSFCWNCTEEAHRPVDC 270 (590)
Q Consensus 208 eky~~~l~~~~v~~~~~~~~CP~p~C~~~i~~~~~~~~~~v~C-~C~~~fC~~C~~~~H~p~~C 270 (590)
++|.+++++++|+.++.++|||+|+|+.++......+...|.| .|++.||+.|+.+||.|.+|
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 4799999999999999999999999999988753346678999 99999999999999999987
No 6
>PF01485 IBR: IBR domain; InterPro: IPR002867 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents a cysteine-rich (C6HC) zinc finger domain that is present in Triad1, and which is conserved in other proteins encoded by various eukaryotes. The C6HC consensus pattern is: C-x(4)-C-x(14-30)-C-x(1-4)-C-x(4)-C-x(2)-C-x(4)-H-x(4)-C The C6HC zinc finger motif is the fourth family member of the zinc-binding RING, LIM, and LAP/PHD fingers. Strikingly, in most of the proteins the C6HC domain is flanked by two RING finger structures IPR001841 from INTERPRO. The novel C6HC motif has been called DRIL (double RING finger linked). The strong conservation of the larger tripartite TRIAD (twoRING fingers and DRIL) structure indicates that the three subdomains are functionally linked and identifies a novel class of proteins []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 2CT7_A 1WD2_A 2JMO_A 1WIM_A.
Probab=99.15 E-value=6.9e-12 Score=99.63 Aligned_cols=63 Identities=35% Similarity=0.964 Sum_probs=42.1
Q ss_pred HHHHHHHHHHHhhcCCCcccCCCCCCCceEeeecCCCcceeEe-cCCCccccccCCCcCCCCCc
Q 007763 208 VKYNRYFIRSYVEDNRKTKWCPAPGCDYAVDFVVGSGNYDVTC-RCSYSFCWNCTEEAHRPVDC 270 (590)
Q Consensus 208 eky~~~l~~~~v~~~~~~~~CP~p~C~~~i~~~~~~~~~~v~C-~C~~~fC~~C~~~~H~p~~C 270 (590)
++|.+++++.+++.++.++|||+|+|+.++..........|+| .|++.||+.|+.+||.|++|
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 5788999999998888999999999999998765444335899 69999999999999999987
No 7
>PF15227 zf-C3HC4_4: zinc finger of C3HC4-type, RING; PDB: 2EGP_A 2ECV_A 2ECJ_A 2YSL_A 2YSJ_A.
Probab=98.61 E-value=2.6e-08 Score=72.46 Aligned_cols=40 Identities=33% Similarity=0.894 Sum_probs=28.8
Q ss_pred ccccccccCCCCceecCCCCccchhhHHHhhcCCCceecccC
Q 007763 144 CGICFENYPSDRLLAAACGHPFCSSCWTAINDGPGCLMLRCP 185 (590)
Q Consensus 144 C~IC~e~~~~~~~~~l~CgH~fC~~C~~~i~~g~~~~~i~CP 185 (590)
|+||++.+ .+|++++|||.||..|+..++.......+.||
T Consensus 1 CpiC~~~~--~~Pv~l~CGH~FC~~Cl~~~~~~~~~~~~~CP 40 (42)
T PF15227_consen 1 CPICLDLF--KDPVSLPCGHSFCRSCLERLWKEPSGSGFSCP 40 (42)
T ss_dssp ETTTTSB---SSEEE-SSSSEEEHHHHHHHHCCSSSST---S
T ss_pred CCccchhh--CCccccCCcCHHHHHHHHHHHHccCCcCCCCc
Confidence 89999998 89999999999999999666655433348999
No 8
>KOG0320 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=98.14 E-value=1.3e-06 Score=81.52 Aligned_cols=54 Identities=26% Similarity=0.754 Sum_probs=42.8
Q ss_pred CCCcccccccccccCCCCceecCCCCccchhhH-HHhhcCCCceecccCCCCCCCccchhHH
Q 007763 138 DGEEMTCGICFENYPSDRLLAAACGHPFCSSCW-TAINDGPGCLMLRCPDPSCGAAVGQDMI 198 (590)
Q Consensus 138 ~~~~~~C~IC~e~~~~~~~~~l~CgH~fC~~C~-~~i~~g~~~~~i~CP~~~C~~~i~~~~i 198 (590)
....+.||||++.+....+++..|||.||..|+ ..+..+ .+|| .|+..|....+
T Consensus 128 ~~~~~~CPiCl~~~sek~~vsTkCGHvFC~~Cik~alk~~-----~~CP--~C~kkIt~k~~ 182 (187)
T KOG0320|consen 128 KEGTYKCPICLDSVSEKVPVSTKCGHVFCSQCIKDALKNT-----NKCP--TCRKKITHKQF 182 (187)
T ss_pred cccccCCCceecchhhccccccccchhHHHHHHHHHHHhC-----CCCC--Ccccccchhhh
Confidence 445689999999998778899999999999999 666654 5899 67766655443
No 9
>PF13445 zf-RING_UBOX: RING-type zinc-finger; PDB: 2CT2_A.
Probab=98.02 E-value=1.9e-06 Score=62.81 Aligned_cols=41 Identities=29% Similarity=0.861 Sum_probs=20.9
Q ss_pred ccccccccCC--CCceecCCCCccchhhHHHhhcCCCceecccC
Q 007763 144 CGICFENYPS--DRLLAAACGHPFCSSCWTAINDGPGCLMLRCP 185 (590)
Q Consensus 144 C~IC~e~~~~--~~~~~l~CgH~fC~~C~~~i~~g~~~~~i~CP 185 (590)
|+||.+ +.. ..++.|+|||.||.+|+..+........++||
T Consensus 1 CpIc~e-~~~~~n~P~~L~CGH~~c~~cl~~l~~~~~~~~~kCP 43 (43)
T PF13445_consen 1 CPICKE-FSTEENPPMVLPCGHVFCKDCLQKLSKKSDRNRFKCP 43 (43)
T ss_dssp -TTT-----TTSS-EEE-SSS-EEEHHHHHHHHHH-S-S-B--T
T ss_pred CCcccc-ccCCCCCCEEEeCccHHHHHHHHHHHhcCCCCeeeCc
Confidence 899999 632 23688999999999999555443212468898
No 10
>smart00647 IBR In Between Ring fingers. the domains occurs between pairs og RING fingers
Probab=97.95 E-value=1e-05 Score=64.02 Aligned_cols=39 Identities=38% Similarity=1.018 Sum_probs=34.8
Q ss_pred cCcCCC--CCCcceeecc--CCCceeecCCCcceeeeccccccc
Q 007763 293 NSKPCP--RCKRPIEKNQ--GCMHMTCTPPCKFEFCWLCLGQWS 332 (590)
Q Consensus 293 ntK~CP--~C~~~IEK~~--GCnhMtC~~~C~~~FCw~C~~~w~ 332 (590)
+.+.|| +|+..|+... |.++|+|. .|++.|||.|+.+|+
T Consensus 17 ~~~~CP~~~C~~~~~~~~~~~~~~v~C~-~C~~~fC~~C~~~~H 59 (64)
T smart00647 17 DLKWCPAPDCSAAIIVTEEEGCNRVTCP-KCGFSFCFRCKVPWH 59 (64)
T ss_pred CccCCCCCCCcceEEecCCCCCCeeECC-CCCCeECCCCCCcCC
Confidence 357899 9999999964 99999996 699999999999984
No 11
>PF01485 IBR: IBR domain; InterPro: IPR002867 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents a cysteine-rich (C6HC) zinc finger domain that is present in Triad1, and which is conserved in other proteins encoded by various eukaryotes. The C6HC consensus pattern is: C-x(4)-C-x(14-30)-C-x(1-4)-C-x(4)-C-x(2)-C-x(4)-H-x(4)-C The C6HC zinc finger motif is the fourth family member of the zinc-binding RING, LIM, and LAP/PHD fingers. Strikingly, in most of the proteins the C6HC domain is flanked by two RING finger structures IPR001841 from INTERPRO. The novel C6HC motif has been called DRIL (double RING finger linked). The strong conservation of the larger tripartite TRIAD (twoRING fingers and DRIL) structure indicates that the three subdomains are functionally linked and identifies a novel class of proteins []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 2CT7_A 1WD2_A 2JMO_A 1WIM_A.
Probab=97.95 E-value=4.3e-06 Score=66.08 Aligned_cols=38 Identities=42% Similarity=1.062 Sum_probs=29.6
Q ss_pred CcCCCC--CCcceeeccCCCc--eeecCCCcceeeeccccccc
Q 007763 294 SKPCPR--CKRPIEKNQGCMH--MTCTPPCKFEFCWLCLGQWS 332 (590)
Q Consensus 294 tK~CP~--C~~~IEK~~GCnh--MtC~~~C~~~FCw~C~~~w~ 332 (590)
.+.||+ |...|++..|.++ |+|. .|++.|||.|+++|+
T Consensus 18 ~~~Cp~~~C~~~~~~~~~~~~~~~~C~-~C~~~fC~~C~~~~H 59 (64)
T PF01485_consen 18 IRWCPNPDCEYIIEKDDGCNSPIVTCP-SCGTEFCFKCGEPWH 59 (64)
T ss_dssp CC--TTSST---ECS-SSTTS--CCTT-SCCSEECSSSTSESC
T ss_pred ccCCCCCCCcccEEecCCCCCCeeECC-CCCCcCccccCcccC
Confidence 479988 9999999999999 9998 799999999999993
No 12
>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=97.91 E-value=6.5e-06 Score=58.81 Aligned_cols=36 Identities=31% Similarity=0.924 Sum_probs=26.3
Q ss_pred ccccccccCCCCc-eecCCCCccchhhHHHhhcCCCceecccC
Q 007763 144 CGICFENYPSDRL-LAAACGHPFCSSCWTAINDGPGCLMLRCP 185 (590)
Q Consensus 144 C~IC~e~~~~~~~-~~l~CgH~fC~~C~~~i~~g~~~~~i~CP 185 (590)
|+||++.+ .++ +.++|||.||..||..+.... .+||
T Consensus 1 C~iC~~~~--~~~~~~~~CGH~fC~~C~~~~~~~~----~~CP 37 (39)
T PF13923_consen 1 CPICLDEL--RDPVVVTPCGHSFCKECIEKYLEKN----PKCP 37 (39)
T ss_dssp ETTTTSB---SSEEEECTTSEEEEHHHHHHHHHCT----SB-T
T ss_pred CCCCCCcc--cCcCEECCCCCchhHHHHHHHHHCc----CCCc
Confidence 89999987 446 688999999999994443332 6888
No 13
>PLN03208 E3 ubiquitin-protein ligase RMA2; Provisional
Probab=97.85 E-value=9.9e-06 Score=77.70 Aligned_cols=60 Identities=23% Similarity=0.600 Sum_probs=44.2
Q ss_pred CCcccccccccccCCCCceecCCCCccchhhHHHhhcC------------CCceecccCCCCCCCccchhHHhhcC
Q 007763 139 GEEMTCGICFENYPSDRLLAAACGHPFCSSCWTAINDG------------PGCLMLRCPDPSCGAAVGQDMIYLLS 202 (590)
Q Consensus 139 ~~~~~C~IC~e~~~~~~~~~l~CgH~fC~~C~~~i~~g------------~~~~~i~CP~~~C~~~i~~~~i~~ll 202 (590)
.+.+.|+||++.+ .+++.++|||.||..|+..|... ......+|| .|+..+....+..+.
T Consensus 16 ~~~~~CpICld~~--~dPVvT~CGH~FC~~CI~~wl~~s~~s~~~~~~~~~~k~~~~CP--vCR~~Is~~~LvPiy 87 (193)
T PLN03208 16 GGDFDCNICLDQV--RDPVVTLCGHLFCWPCIHKWTYASNNSRQRVDQYDHKREPPKCP--VCKSDVSEATLVPIY 87 (193)
T ss_pred CCccCCccCCCcC--CCcEEcCCCchhHHHHHHHHHHhccccccccccccccCCCCcCC--CCCCcCChhcEEEee
Confidence 4578999999986 77888999999999999444211 011357999 899998776554443
No 14
>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=97.83 E-value=8e-06 Score=58.84 Aligned_cols=38 Identities=32% Similarity=0.920 Sum_probs=28.7
Q ss_pred ccccccccCCCCce-ecCCCCccchhhHHHhhcCCCceecccC
Q 007763 144 CGICFENYPSDRLL-AAACGHPFCSSCWTAINDGPGCLMLRCP 185 (590)
Q Consensus 144 C~IC~e~~~~~~~~-~l~CgH~fC~~C~~~i~~g~~~~~i~CP 185 (590)
|+||++.+ ..+. .++|||.||..||..+.... ..++||
T Consensus 1 C~iC~~~~--~~~~~~~~C~H~fC~~C~~~~~~~~--~~~~CP 39 (41)
T PF00097_consen 1 CPICLEPF--EDPVILLPCGHSFCRDCLRKWLENS--GSVKCP 39 (41)
T ss_dssp ETTTSSBC--SSEEEETTTSEEEEHHHHHHHHHHT--SSSBTT
T ss_pred CCcCCccc--cCCCEEecCCCcchHHHHHHHHHhc--CCccCC
Confidence 89999987 4555 88999999999994443322 357898
No 15
>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=97.77 E-value=8.2e-06 Score=59.85 Aligned_cols=41 Identities=32% Similarity=0.849 Sum_probs=31.1
Q ss_pred cccccccccC-CCCceecCCCCccchhhHHHhhcCCCceecccCCCCC
Q 007763 143 TCGICFENYP-SDRLLAAACGHPFCSSCWTAINDGPGCLMLRCPDPSC 189 (590)
Q Consensus 143 ~C~IC~e~~~-~~~~~~l~CgH~fC~~C~~~i~~g~~~~~i~CP~~~C 189 (590)
.|+||++.+. .+.++.++|||.||.+|+..+.... .+|| .|
T Consensus 2 ~C~IC~~~~~~~~~~~~l~C~H~fh~~Ci~~~~~~~----~~CP--~C 43 (44)
T PF13639_consen 2 ECPICLEEFEDGEKVVKLPCGHVFHRSCIKEWLKRN----NSCP--VC 43 (44)
T ss_dssp CETTTTCBHHTTSCEEEETTSEEEEHHHHHHHHHHS----SB-T--TT
T ss_pred CCcCCChhhcCCCeEEEccCCCeeCHHHHHHHHHhC----CcCC--cc
Confidence 5999999985 4567889999999999995544332 3898 56
No 16
>PF14634 zf-RING_5: zinc-RING finger domain
Probab=97.71 E-value=2.4e-05 Score=57.43 Aligned_cols=42 Identities=40% Similarity=1.087 Sum_probs=33.1
Q ss_pred cccccccccC-CCCceecCCCCccchhhHHHhhcCCCceecccCCCCCC
Q 007763 143 TCGICFENYP-SDRLLAAACGHPFCSSCWTAINDGPGCLMLRCPDPSCG 190 (590)
Q Consensus 143 ~C~IC~e~~~-~~~~~~l~CgH~fC~~C~~~i~~g~~~~~i~CP~~~C~ 190 (590)
.|+||++.+. ...++.++|||.||..|+..+. + ..+.|| .|+
T Consensus 1 ~C~~C~~~~~~~~~~~l~~CgH~~C~~C~~~~~-~---~~~~CP--~C~ 43 (44)
T PF14634_consen 1 HCNICFEKYSEERRPRLTSCGHIFCEKCLKKLK-G---KSVKCP--ICR 43 (44)
T ss_pred CCcCcCccccCCCCeEEcccCCHHHHHHHHhhc-C---CCCCCc--CCC
Confidence 4999999983 3467888999999999996555 2 358999 675
No 17
>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=97.64 E-value=3.4e-05 Score=58.19 Aligned_cols=46 Identities=33% Similarity=0.832 Sum_probs=35.1
Q ss_pred cccccccccccCCCCceecCCCCc-cchhhHHHhhcCCCceecccCCCCCCCccc
Q 007763 141 EMTCGICFENYPSDRLLAAACGHP-FCSSCWTAINDGPGCLMLRCPDPSCGAAVG 194 (590)
Q Consensus 141 ~~~C~IC~e~~~~~~~~~l~CgH~-fC~~C~~~i~~g~~~~~i~CP~~~C~~~i~ 194 (590)
...|.||++.. ..++.++|||. ||..|+..+... ..+|| .|+..|.
T Consensus 2 ~~~C~iC~~~~--~~~~~~pCgH~~~C~~C~~~~~~~----~~~CP--~Cr~~i~ 48 (50)
T PF13920_consen 2 DEECPICFENP--RDVVLLPCGHLCFCEECAERLLKR----KKKCP--ICRQPIE 48 (50)
T ss_dssp HSB-TTTSSSB--SSEEEETTCEEEEEHHHHHHHHHT----TSBBT--TTTBB-S
T ss_pred cCCCccCCccC--CceEEeCCCChHHHHHHhHHhccc----CCCCC--cCChhhc
Confidence 35799999975 66888999999 999999555443 36899 8988764
No 18
>KOG2177 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=97.62 E-value=2.9e-05 Score=79.54 Aligned_cols=45 Identities=40% Similarity=0.905 Sum_probs=37.1
Q ss_pred CCcccccccccccCCCCceecCCCCccchhhHHHhhcCCCceecccCCCCCCC
Q 007763 139 GEEMTCGICFENYPSDRLLAAACGHPFCSSCWTAINDGPGCLMLRCPDPSCGA 191 (590)
Q Consensus 139 ~~~~~C~IC~e~~~~~~~~~l~CgH~fC~~C~~~i~~g~~~~~i~CP~~~C~~ 191 (590)
...+.|+||++.+ ..+..++|||.||..|+..+.. ..+.|| .|+.
T Consensus 11 ~~~~~C~iC~~~~--~~p~~l~C~H~~c~~C~~~~~~----~~~~Cp--~cr~ 55 (386)
T KOG2177|consen 11 QEELTCPICLEYF--REPVLLPCGHNFCRACLTRSWE----GPLSCP--VCRP 55 (386)
T ss_pred cccccChhhHHHh--hcCccccccchHhHHHHHHhcC----CCcCCc--ccCC
Confidence 3578899999998 5568899999999999966655 349999 7884
No 19
>KOG4367 consensus Predicted Zn-finger protein [Function unknown]
Probab=97.50 E-value=0.00069 Score=71.15 Aligned_cols=78 Identities=22% Similarity=0.445 Sum_probs=45.8
Q ss_pred cceeEe-cCCCccccccCCCcCCCCCchhHHHHHHhhhhhhhhHHHHHhcCcCCCCCCcceeeccCCCc-eeecCCCcce
Q 007763 245 NYDVTC-RCSYSFCWNCTEEAHRPVDCDTVAKWVLKNSAESENMNWILANSKPCPRCKRPIEKNQGCMH-MTCTPPCKFE 322 (590)
Q Consensus 245 ~~~v~C-~C~~~fC~~C~~~~H~p~~C~~~~~w~~k~~~e~e~~~wi~~ntK~CP~C~~~IEK~~GCnh-MtC~~~C~~~ 322 (590)
...|.| .|...+|--|...-|.|..=-..+.++..+... -+...-....-.|..+ .|=|| |+|. .|+.-
T Consensus 174 ~a~v~ceqcdv~yc~pc~~~~hp~rgplakh~l~~~~~gr-vs~~~s~r~~~~ct~h-------~~e~~smyc~-~ck~p 244 (699)
T KOG4367|consen 174 EATVMCEQCDVFYCDPCRLRCHPPRGPLAKHRLVPPAQGR-VSRRLSPRKVSTCTDH-------ELENHSMYCV-QCKMP 244 (699)
T ss_pred hhhhhHhhCceEEechHHhccCCCCCchhhcccCCcccCc-eeeccchhhhhhccCC-------CCCCceEEEE-ecCCh
Confidence 456789 999999999998888775433333333222110 0000000011233322 22344 9999 89999
Q ss_pred eeecccccc
Q 007763 323 FCWLCLGQW 331 (590)
Q Consensus 323 FCw~C~~~w 331 (590)
.|+.|+.+-
T Consensus 245 vc~~clee~ 253 (699)
T KOG4367|consen 245 VCYQCLEEG 253 (699)
T ss_pred HHHHHHHhh
Confidence 999999764
No 20
>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=97.33 E-value=0.00018 Score=51.90 Aligned_cols=43 Identities=33% Similarity=0.790 Sum_probs=30.5
Q ss_pred cccccccccCCCCce-ecCCCCccchhhHHHhhcCCCceecccCCCCCCCc
Q 007763 143 TCGICFENYPSDRLL-AAACGHPFCSSCWTAINDGPGCLMLRCPDPSCGAA 192 (590)
Q Consensus 143 ~C~IC~e~~~~~~~~-~l~CgH~fC~~C~~~i~~g~~~~~i~CP~~~C~~~ 192 (590)
.|+||++.+ ..++ ..+|||.||..|+..+... ...+|| .|+..
T Consensus 1 ~C~iC~~~~--~~~~~~~~C~H~~c~~C~~~~~~~---~~~~Cp--~C~~~ 44 (45)
T cd00162 1 ECPICLEEF--REPVVLLPCGHVFCRSCIDKWLKS---GKNTCP--LCRTP 44 (45)
T ss_pred CCCcCchhh--hCceEecCCCChhcHHHHHHHHHh---CcCCCC--CCCCc
Confidence 499999987 3444 4459999999999444332 246899 78754
No 21
>TIGR00599 rad18 DNA repair protein rad18. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=97.33 E-value=0.00014 Score=77.73 Aligned_cols=66 Identities=23% Similarity=0.495 Sum_probs=47.3
Q ss_pred CCcccccccccccCCCCceecCCCCccchhhHHHhhcCCCceecccCCCCCCCccchh-HHhhcCChHHHHHHHH
Q 007763 139 GEEMTCGICFENYPSDRLLAAACGHPFCSSCWTAINDGPGCLMLRCPDPSCGAAVGQD-MIYLLSSDEDKVKYNR 212 (590)
Q Consensus 139 ~~~~~C~IC~e~~~~~~~~~l~CgH~fC~~C~~~i~~g~~~~~i~CP~~~C~~~i~~~-~i~~ll~~e~~eky~~ 212 (590)
...+.|+||++.+ ..++.++|||.||..|+..+.... ..|| .|+..+... +..+.+..++++.|..
T Consensus 24 e~~l~C~IC~d~~--~~PvitpCgH~FCs~CI~~~l~~~----~~CP--~Cr~~~~~~~Lr~N~~L~~iVe~~~~ 90 (397)
T TIGR00599 24 DTSLRCHICKDFF--DVPVLTSCSHTFCSLCIRRCLSNQ----PKCP--LCRAEDQESKLRSNWLVSEIVESFKN 90 (397)
T ss_pred ccccCCCcCchhh--hCccCCCCCCchhHHHHHHHHhCC----CCCC--CCCCccccccCccchHHHHHHHHHHH
Confidence 3468999999987 678889999999999995444332 3799 899988654 2233444566666653
No 22
>KOG0804 consensus Cytoplasmic Zn-finger protein BRAP2 (BRCA1 associated protein) [General function prediction only]
Probab=97.32 E-value=0.02 Score=61.02 Aligned_cols=116 Identities=23% Similarity=0.339 Sum_probs=66.4
Q ss_pred eCHHHHHHHHHHHHHHHHHHhCCCHH--HHHHHHHhcCCChHHH--HHHh----hc--CHHHHHHHcCCC-----CC-CC
Q 007763 70 LTEADIRQRQEEDITRISTVLSISKV--AASILLRFYNWSVSKV--HDEW----FA--DEERVRKAVGLL-----EK-PA 133 (590)
Q Consensus 70 l~~~~i~~~~~~~i~~v~~il~i~~~--~a~~LL~~~~W~~~~l--~e~~----~~--~~~~~~~~~gl~-----~~-~~ 133 (590)
||.-|+..-+...+.+|+.|.=|-.+ .-..+|..|+=..+.. .+.| |. +++ +...+.+. .. +.
T Consensus 86 mt~~Dll~F~~~~~~~I~~irivRd~~pnrymvLIkFr~q~da~~Fy~efNGk~Fn~le~e-~Chll~V~~ve~~~s~d~ 164 (493)
T KOG0804|consen 86 MTSHDLLRFCASFIKQISDIRIVRDGMPNRYMVLIKFRDQADADTFYEEFNGKQFNSLEPE-VCHLLYVDRVEVTESEDG 164 (493)
T ss_pred ccHHHHHHHHHHHhhhhheeEEeecCCCceEEEEEEeccchhHHHHHHHcCCCcCCCCCcc-ceeEEEEEEEEEEecccC
Confidence 78899999999888888877666422 2234455555333221 1111 11 111 21111110 00 01
Q ss_pred C---CCCCCCcccccccccccCCC--CceecCCCCccchhhHHHhhcCCCceecccCCCCCCCccc
Q 007763 134 V---QFPDGEEMTCGICFENYPSD--RLLAAACGHPFCSSCWTAINDGPGCLMLRCPDPSCGAAVG 194 (590)
Q Consensus 134 ~---~~~~~~~~~C~IC~e~~~~~--~~~~l~CgH~fC~~C~~~i~~g~~~~~i~CP~~~C~~~i~ 194 (590)
. +.......+||||++-...+ -+++..|.|.|--.|+..|++ .+|| .|+....
T Consensus 165 as~~~~~~tELPTCpVCLERMD~s~~gi~t~~c~Hsfh~~cl~~w~~------~scp--vcR~~q~ 222 (493)
T KOG0804|consen 165 ASEPPTGLTELPTCPVCLERMDSSTTGILTILCNHSFHCSCLMKWWD------SSCP--VCRYCQS 222 (493)
T ss_pred CCCCCCCcccCCCcchhHhhcCccccceeeeecccccchHHHhhccc------CcCh--hhhhhcC
Confidence 1 11123456899999987543 357788999999999988765 5798 7765443
No 23
>KOG0823 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=97.25 E-value=0.00014 Score=71.14 Aligned_cols=57 Identities=30% Similarity=0.619 Sum_probs=43.2
Q ss_pred CCCcccccccccccCCCCceecCCCCccchhhHHHhhcCCCceecccCCCCCCCccchhHHh
Q 007763 138 DGEEMTCGICFENYPSDRLLAAACGHPFCSSCWTAINDGPGCLMLRCPDPSCGAAVGQDMIY 199 (590)
Q Consensus 138 ~~~~~~C~IC~e~~~~~~~~~l~CgH~fC~~C~~~i~~g~~~~~i~CP~~~C~~~i~~~~i~ 199 (590)
....|.|.||+|.. .+++...|||.||-.|+-+|-+-.. ..-.|| .|+..|+.+.|-
T Consensus 44 ~~~~FdCNICLd~a--kdPVvTlCGHLFCWpClyqWl~~~~-~~~~cP--VCK~~Vs~~~vv 100 (230)
T KOG0823|consen 44 DGGFFDCNICLDLA--KDPVVTLCGHLFCWPCLYQWLQTRP-NSKECP--VCKAEVSIDTVV 100 (230)
T ss_pred CCCceeeeeecccc--CCCEEeecccceehHHHHHHHhhcC-CCeeCC--ccccccccceEE
Confidence 45689999999986 7899999999999999955433221 235678 899888766553
No 24
>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=97.25 E-value=0.00022 Score=56.19 Aligned_cols=48 Identities=13% Similarity=0.143 Sum_probs=36.7
Q ss_pred ccccccccccCCCCceecCCCCccchhhHHHhhcCCCceecccCCCCCCCccchhH
Q 007763 142 MTCGICFENYPSDRLLAAACGHPFCSSCWTAINDGPGCLMLRCPDPSCGAAVGQDM 197 (590)
Q Consensus 142 ~~C~IC~e~~~~~~~~~l~CgH~fC~~C~~~i~~g~~~~~i~CP~~~C~~~i~~~~ 197 (590)
+.|+||.+.+ .+++.++|||.||+.|+..+... ...|| .|+..++...
T Consensus 2 ~~Cpi~~~~~--~~Pv~~~~G~v~~~~~i~~~~~~----~~~cP--~~~~~~~~~~ 49 (63)
T smart00504 2 FLCPISLEVM--KDPVILPSGQTYERRAIEKWLLS----HGTDP--VTGQPLTHED 49 (63)
T ss_pred cCCcCCCCcC--CCCEECCCCCEEeHHHHHHHHHH----CCCCC--CCcCCCChhh
Confidence 6799999987 67899999999999999443332 24799 6887775443
No 25
>KOG0317 consensus Predicted E3 ubiquitin ligase, integral peroxisomal membrane protein [Posttranslational modification, protein turnover, chaperones]
Probab=97.23 E-value=0.00027 Score=71.15 Aligned_cols=51 Identities=29% Similarity=0.667 Sum_probs=40.8
Q ss_pred CcccccccccccCCCCceecCCCCccchhhHHHhhcCCCceecccCCCCCCCccchhHH
Q 007763 140 EEMTCGICFENYPSDRLLAAACGHPFCSSCWTAINDGPGCLMLRCPDPSCGAAVGQDMI 198 (590)
Q Consensus 140 ~~~~C~IC~e~~~~~~~~~l~CgH~fC~~C~~~i~~g~~~~~i~CP~~~C~~~i~~~~i 198 (590)
....|.+|++.. .++..+||||.||-.|+..+-... -.|| .|+..+.+..+
T Consensus 238 a~~kC~LCLe~~--~~pSaTpCGHiFCWsCI~~w~~ek----~eCP--lCR~~~~pskv 288 (293)
T KOG0317|consen 238 ATRKCSLCLENR--SNPSATPCGHIFCWSCILEWCSEK----AECP--LCREKFQPSKV 288 (293)
T ss_pred CCCceEEEecCC--CCCCcCcCcchHHHHHHHHHHccc----cCCC--cccccCCCcce
Confidence 356799999975 789999999999999996665443 3499 89999877654
No 26
>KOG2164 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=97.23 E-value=0.00016 Score=78.01 Aligned_cols=60 Identities=25% Similarity=0.511 Sum_probs=45.3
Q ss_pred cccccccccccCCCCceecCCCCccchhhH-HHhhcCCCceecccCCCCCCCccchhHHhhcCCh
Q 007763 141 EMTCGICFENYPSDRLLAAACGHPFCSSCW-TAINDGPGCLMLRCPDPSCGAAVGQDMIYLLSSD 204 (590)
Q Consensus 141 ~~~C~IC~e~~~~~~~~~l~CgH~fC~~C~-~~i~~g~~~~~i~CP~~~C~~~i~~~~i~~ll~~ 204 (590)
...|||||+.. .-++.+.|||.||-.|+ .+|+.+.-....+|| -|...|.+..+..+.-.
T Consensus 186 ~~~CPICL~~~--~~p~~t~CGHiFC~~CiLqy~~~s~~~~~~~CP--iC~s~I~~kdl~pv~~e 246 (513)
T KOG2164|consen 186 DMQCPICLEPP--SVPVRTNCGHIFCGPCILQYWNYSAIKGPCSCP--ICRSTITLKDLLPVFIE 246 (513)
T ss_pred CCcCCcccCCC--CcccccccCceeeHHHHHHHHhhhcccCCccCC--chhhhccccceeeeeec
Confidence 67899999875 44555669999999999 666655334568899 89999988766655543
No 27
>PHA02929 N1R/p28-like protein; Provisional
Probab=97.21 E-value=0.00026 Score=70.75 Aligned_cols=49 Identities=24% Similarity=0.628 Sum_probs=36.2
Q ss_pred CcccccccccccCCCC------ceecCCCCccchhhHHHhhcCCCceecccCCCCCCCccc
Q 007763 140 EEMTCGICFENYPSDR------LLAAACGHPFCSSCWTAINDGPGCLMLRCPDPSCGAAVG 194 (590)
Q Consensus 140 ~~~~C~IC~e~~~~~~------~~~l~CgH~fC~~C~~~i~~g~~~~~i~CP~~~C~~~i~ 194 (590)
....|+||++.+.... .+.++|+|.||..|+..+... ...|| .|+..+.
T Consensus 173 ~~~eC~ICle~~~~~~~~~~~~~vl~~C~H~FC~~CI~~Wl~~----~~tCP--lCR~~~~ 227 (238)
T PHA02929 173 KDKECAICMEKVYDKEIKNMYFGILSNCNHVFCIECIDIWKKE----KNTCP--VCRTPFI 227 (238)
T ss_pred CCCCCccCCcccccCccccccceecCCCCCcccHHHHHHHHhc----CCCCC--CCCCEee
Confidence 4578999999864322 245679999999999666543 25899 8998764
No 28
>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=97.03 E-value=0.00042 Score=48.07 Aligned_cols=37 Identities=35% Similarity=0.811 Sum_probs=28.4
Q ss_pred ccccccccCCCCceecCCCCccchhhHHHhhcCCCceecccC
Q 007763 144 CGICFENYPSDRLLAAACGHPFCSSCWTAINDGPGCLMLRCP 185 (590)
Q Consensus 144 C~IC~e~~~~~~~~~l~CgH~fC~~C~~~i~~g~~~~~i~CP 185 (590)
|+||++.. ..++.++|||.||..|+..+... ....||
T Consensus 1 C~iC~~~~--~~~~~~~C~H~~c~~C~~~~~~~---~~~~CP 37 (39)
T smart00184 1 CPICLEEL--KDPVVLPCGHTFCRSCIRKWLKS---GNNTCP 37 (39)
T ss_pred CCcCccCC--CCcEEecCCChHHHHHHHHHHHh---CcCCCC
Confidence 78999873 67888899999999999544432 236788
No 29
>KOG0287 consensus Postreplication repair protein RAD18 [Replication, recombination and repair]
Probab=96.96 E-value=0.00035 Score=71.33 Aligned_cols=63 Identities=30% Similarity=0.652 Sum_probs=47.6
Q ss_pred CcccccccccccCCCCceecCCCCccchhhH-HHhhcCCCceecccCCCCCCCccchhHHhh-cCChHHHHHHH
Q 007763 140 EEMTCGICFENYPSDRLLAAACGHPFCSSCW-TAINDGPGCLMLRCPDPSCGAAVGQDMIYL-LSSDEDKVKYN 211 (590)
Q Consensus 140 ~~~~C~IC~e~~~~~~~~~l~CgH~fC~~C~-~~i~~g~~~~~i~CP~~~C~~~i~~~~i~~-ll~~e~~eky~ 211 (590)
..+.|.||++.| .-++.++|+|.||.-|| ..+... ..|| .|...+....+++ .+..++++-|.
T Consensus 22 ~lLRC~IC~eyf--~ip~itpCsHtfCSlCIR~~L~~~-----p~CP--~C~~~~~Es~Lr~n~il~Eiv~S~~ 86 (442)
T KOG0287|consen 22 DLLRCGICFEYF--NIPMITPCSHTFCSLCIRKFLSYK-----PQCP--TCCVTVTESDLRNNRILDEIVKSLN 86 (442)
T ss_pred HHHHHhHHHHHh--cCceeccccchHHHHHHHHHhccC-----CCCC--ceecccchhhhhhhhHHHHHHHHHH
Confidence 356799999998 66788889999999999 565543 5799 8999987766653 44456666554
No 30
>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=96.94 E-value=0.0014 Score=67.62 Aligned_cols=53 Identities=21% Similarity=0.523 Sum_probs=36.9
Q ss_pred ccccccccccC--CCC--ceecCCCCccchhhHHHhhcCCCceecccCCCCCCCccchhHHhh
Q 007763 142 MTCGICFENYP--SDR--LLAAACGHPFCSSCWTAINDGPGCLMLRCPDPSCGAAVGQDMIYL 200 (590)
Q Consensus 142 ~~C~IC~e~~~--~~~--~~~l~CgH~fC~~C~~~i~~g~~~~~i~CP~~~C~~~i~~~~i~~ 200 (590)
..||||..... ++. ++. +|||.||.+|+..+.... ...|| .|+..+....++.
T Consensus 4 ~~CP~Ck~~~y~np~~kl~i~-~CGH~~C~sCv~~l~~~~---~~~CP--~C~~~lrk~~fr~ 60 (309)
T TIGR00570 4 QGCPRCKTTKYRNPSLKLMVN-VCGHTLCESCVDLLFVRG---SGSCP--ECDTPLRKNNFRV 60 (309)
T ss_pred CCCCcCCCCCccCcccccccC-CCCCcccHHHHHHHhcCC---CCCCC--CCCCccchhhccc
Confidence 57999998532 221 233 799999999996654332 35899 9999887665544
No 31
>PHA02926 zinc finger-like protein; Provisional
Probab=96.91 E-value=0.00065 Score=66.16 Aligned_cols=54 Identities=31% Similarity=0.618 Sum_probs=36.2
Q ss_pred CCcccccccccccCC-----C--CceecCCCCccchhhHHHhhcCC--CceecccCCCCCCCccc
Q 007763 139 GEEMTCGICFENYPS-----D--RLLAAACGHPFCSSCWTAINDGP--GCLMLRCPDPSCGAAVG 194 (590)
Q Consensus 139 ~~~~~C~IC~e~~~~-----~--~~~~l~CgH~fC~~C~~~i~~g~--~~~~i~CP~~~C~~~i~ 194 (590)
+...+|+||++..-. + -.+..+|+|.||..|+..|.... ....-.|| .|+..+.
T Consensus 168 SkE~eCgICmE~I~eK~~~~eRrFGIL~~CnHsFCl~CIr~Wr~~r~~~~~~rsCP--iCR~~f~ 230 (242)
T PHA02926 168 SKEKECGICYEVVYSKRLENDRYFGLLDSCNHIFCITCINIWHRTRRETGASDNCP--ICRTRFR 230 (242)
T ss_pred cCCCCCccCccccccccccccccccccCCCCchHHHHHHHHHHHhccccCcCCcCC--CCcceee
Confidence 456889999997521 1 12455799999999996555421 11245799 8987653
No 32
>KOG0978 consensus E3 ubiquitin ligase involved in syntaxin degradation [Posttranslational modification, protein turnover, chaperones]
Probab=96.36 E-value=0.001 Score=75.27 Aligned_cols=54 Identities=30% Similarity=0.774 Sum_probs=42.4
Q ss_pred CcccccccccccCCCCceecCCCCccchhhH-HHhhcCCCceecccCCCCCCCccchhHHhhc
Q 007763 140 EEMTCGICFENYPSDRLLAAACGHPFCSSCW-TAINDGPGCLMLRCPDPSCGAAVGQDMIYLL 201 (590)
Q Consensus 140 ~~~~C~IC~e~~~~~~~~~l~CgH~fC~~C~-~~i~~g~~~~~i~CP~~~C~~~i~~~~i~~l 201 (590)
....||+|..-. .+.+...|||.||..|+ ..+... .=+|| .|+..|++..|..+
T Consensus 642 ~~LkCs~Cn~R~--Kd~vI~kC~H~FC~~Cvq~r~etR----qRKCP--~Cn~aFganDv~~I 696 (698)
T KOG0978|consen 642 ELLKCSVCNTRW--KDAVITKCGHVFCEECVQTRYETR----QRKCP--KCNAAFGANDVHRI 696 (698)
T ss_pred hceeCCCccCch--hhHHHHhcchHHHHHHHHHHHHHh----cCCCC--CCCCCCCccccccc
Confidence 467899999543 67888899999999999 555443 35899 99999988776543
No 33
>COG5574 PEX10 RING-finger-containing E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=96.27 E-value=0.0029 Score=63.11 Aligned_cols=52 Identities=29% Similarity=0.613 Sum_probs=40.2
Q ss_pred CcccccccccccCCCCceecCCCCccchhhHHH-hhcCCCceecccCCCCCCCccchhHH
Q 007763 140 EEMTCGICFENYPSDRLLAAACGHPFCSSCWTA-INDGPGCLMLRCPDPSCGAAVGQDMI 198 (590)
Q Consensus 140 ~~~~C~IC~e~~~~~~~~~l~CgH~fC~~C~~~-i~~g~~~~~i~CP~~~C~~~i~~~~i 198 (590)
..+.|.||++.. ..+..++|||.||..|+.. +.... .-.|| -|++.+.+..|
T Consensus 214 ~d~kC~lC~e~~--~~ps~t~CgHlFC~~Cl~~~~t~~k---~~~Cp--lCRak~~pk~v 266 (271)
T COG5574 214 ADYKCFLCLEEP--EVPSCTPCGHLFCLSCLLISWTKKK---YEFCP--LCRAKVYPKKV 266 (271)
T ss_pred cccceeeeeccc--CCcccccccchhhHHHHHHHHHhhc---cccCc--hhhhhccchhh
Confidence 367899999975 7788999999999999943 44332 35699 89988766655
No 34
>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=96.00 E-value=0.0049 Score=50.40 Aligned_cols=50 Identities=16% Similarity=0.120 Sum_probs=35.2
Q ss_pred CcccccccccccCCCCceecCCCCccchhhHHHhhcCCCceecccCCCCCCCccchh
Q 007763 140 EEMTCGICFENYPSDRLLAAACGHPFCSSCWTAINDGPGCLMLRCPDPSCGAAVGQD 196 (590)
Q Consensus 140 ~~~~C~IC~e~~~~~~~~~l~CgH~fC~~C~~~i~~g~~~~~i~CP~~~C~~~i~~~ 196 (590)
..|.|+|+.+.+ .+++.+++||.|++.||..+... ....|| .|+..+...
T Consensus 3 ~~f~CpIt~~lM--~dPVi~~~G~tyer~~I~~~l~~---~~~~~P--~t~~~l~~~ 52 (73)
T PF04564_consen 3 DEFLCPITGELM--RDPVILPSGHTYERSAIERWLEQ---NGGTDP--FTRQPLSES 52 (73)
T ss_dssp GGGB-TTTSSB---SSEEEETTSEEEEHHHHHHHHCT---TSSB-T--TT-SB-SGG
T ss_pred cccCCcCcCcHh--hCceeCCcCCEEcHHHHHHHHHc---CCCCCC--CCCCcCCcc
Confidence 468999999987 88999999999999999544433 136899 677777654
No 35
>COG5540 RING-finger-containing ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=95.91 E-value=0.0038 Score=63.16 Aligned_cols=51 Identities=31% Similarity=0.701 Sum_probs=42.1
Q ss_pred CcccccccccccCC-CCceecCCCCccchhhHHHhhcCCCceecccCCCCCCCccch
Q 007763 140 EEMTCGICFENYPS-DRLLAAACGHPFCSSCWTAINDGPGCLMLRCPDPSCGAAVGQ 195 (590)
Q Consensus 140 ~~~~C~IC~e~~~~-~~~~~l~CgH~fC~~C~~~i~~g~~~~~i~CP~~~C~~~i~~ 195 (590)
....|.||++.+.. +..+.+||.|.|...|+.+|-.| ....|| .|+..++|
T Consensus 322 ~GveCaICms~fiK~d~~~vlPC~H~FH~~Cv~kW~~~---y~~~CP--vCrt~iPP 373 (374)
T COG5540 322 KGVECAICMSNFIKNDRLRVLPCDHRFHVGCVDKWLLG---YSNKCP--VCRTAIPP 373 (374)
T ss_pred CCceEEEEhhhhcccceEEEeccCceechhHHHHHHhh---hcccCC--ccCCCCCC
Confidence 45789999999864 35678999999999999887765 358999 89998875
No 36
>PF14555 UBA_4: UBA-like domain; PDB: 2DAL_A 3BQ3_A 2L4E_A 2L4F_A 2DZL_A 2L2D_A 2DAM_A 1V92_A 3E21_A.
Probab=95.89 E-value=0.017 Score=42.06 Aligned_cols=41 Identities=22% Similarity=0.427 Sum_probs=35.0
Q ss_pred HHHHHHHHHHhCCCHHHHHHHHHhcCCChHHHHHHhhcCHH
Q 007763 80 EEDITRISTVLSISKVAASILLRFYNWSVSKVHDEWFADEE 120 (590)
Q Consensus 80 ~~~i~~v~~il~i~~~~a~~LL~~~~W~~~~l~e~~~~~~~ 120 (590)
++.|.+..+|+++++..|..+|...+||++..++.||.+++
T Consensus 1 ~e~i~~F~~iTg~~~~~A~~~L~~~~wdle~Av~~y~~~~~ 41 (43)
T PF14555_consen 1 DEKIAQFMSITGADEDVAIQYLEANNWDLEAAVNAYFDDGE 41 (43)
T ss_dssp HHHHHHHHHHH-SSHHHHHHHHHHTTT-HHHHHHHHHHSS-
T ss_pred CHHHHHHHHHHCcCHHHHHHHHHHcCCCHHHHHHHHHhCCC
Confidence 36789999999999999999999999999999999998653
No 37
>PF14835 zf-RING_6: zf-RING of BARD1-type protein; PDB: 1JM7_B.
Probab=95.87 E-value=0.0034 Score=49.37 Aligned_cols=41 Identities=37% Similarity=0.944 Sum_probs=20.0
Q ss_pred ccccccccccCCCCceec-CCCCccchhhH-HHhhcCCCceecccCCCCCCCcc
Q 007763 142 MTCGICFENYPSDRLLAA-ACGHPFCSSCW-TAINDGPGCLMLRCPDPSCGAAV 193 (590)
Q Consensus 142 ~~C~IC~e~~~~~~~~~l-~CgH~fC~~C~-~~i~~g~~~~~i~CP~~~C~~~i 193 (590)
..|++|++.+ ..++.+ .|.|.||..|+ ..+. ..|| .|..+.
T Consensus 8 LrCs~C~~~l--~~pv~l~~CeH~fCs~Ci~~~~~-------~~CP--vC~~Pa 50 (65)
T PF14835_consen 8 LRCSICFDIL--KEPVCLGGCEHIFCSSCIRDCIG-------SECP--VCHTPA 50 (65)
T ss_dssp TS-SSS-S----SS-B---SSS--B-TTTGGGGTT-------TB-S--SS--B-
T ss_pred cCCcHHHHHh--cCCceeccCccHHHHHHhHHhcC-------CCCC--CcCChH
Confidence 5699999987 778765 59999999999 3322 3599 787654
No 38
>PF00641 zf-RanBP: Zn-finger in Ran binding protein and others; InterPro: IPR001876 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents the zinc finger domain found in RanBP2 proteins. Ran is an evolutionary conserved member of the Ras superfamily that regulates all receptor-mediated transport between the nucleus and the cytoplasm. Ran binding protein 2 (RanBP2) is a 358kDa nucleoporin located on the cytoplasmic side of the nuclear pore complex which plays a role in nuclear protein import []. RanBP2 contains multiple zinc fingers which mediate binding to RanGDP []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0005622 intracellular; PDB: 2D9G_A 2EBR_A 2WX0_C 2WX1_C 2WWZ_C 3GJ6_B 2LK0_A 2LK1_A 3GJ5_B 3GJ8_B ....
Probab=95.80 E-value=0.0032 Score=42.18 Aligned_cols=26 Identities=35% Similarity=0.928 Sum_probs=20.8
Q ss_pred CccccCCCCccCCCccccccccCCCC
Q 007763 565 SHWYCDQCTYANVNSATACAMCQHSR 590 (590)
Q Consensus 565 ~~~~c~~c~~~~~~~~~~c~~c~~~~ 590 (590)
+.|.|..|||.|..+...|.||.-+|
T Consensus 3 g~W~C~~C~~~N~~~~~~C~~C~~~r 28 (30)
T PF00641_consen 3 GDWKCPSCTFMNPASRSKCVACGAPR 28 (30)
T ss_dssp SSEEETTTTEEEESSSSB-TTT--BT
T ss_pred cCccCCCCcCCchHHhhhhhCcCCCC
Confidence 35999999999999999999997654
No 39
>KOG4628 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=95.54 E-value=0.016 Score=60.89 Aligned_cols=48 Identities=29% Similarity=0.665 Sum_probs=36.8
Q ss_pred ccccccccccCCC-CceecCCCCccchhhHHHhhcCCCceecccCCCCCCCccc
Q 007763 142 MTCGICFENYPSD-RLLAAACGHPFCSSCWTAINDGPGCLMLRCPDPSCGAAVG 194 (590)
Q Consensus 142 ~~C~IC~e~~~~~-~~~~l~CgH~fC~~C~~~i~~g~~~~~i~CP~~~C~~~i~ 194 (590)
.+|.||+|+|... .+..|||+|.|...|+..|-... .-.|| -|+..+.
T Consensus 230 ~~CaIClEdY~~GdklRiLPC~H~FH~~CIDpWL~~~---r~~CP--vCK~di~ 278 (348)
T KOG4628|consen 230 DTCAICLEDYEKGDKLRILPCSHKFHVNCIDPWLTQT---RTFCP--VCKRDIR 278 (348)
T ss_pred ceEEEeecccccCCeeeEecCCCchhhccchhhHhhc---CccCC--CCCCcCC
Confidence 6999999999764 55779999999999996664332 24699 7877553
No 40
>smart00547 ZnF_RBZ Zinc finger domain. Zinc finger domain in Ran-binding proteins (RanBPs), and other proteins. In RanBPs, this domain binds RanGDP.
Probab=95.51 E-value=0.0076 Score=38.83 Aligned_cols=24 Identities=33% Similarity=0.906 Sum_probs=22.3
Q ss_pred ccccCCCCccCCCccccccccCCC
Q 007763 566 HWYCDQCTYANVNSATACAMCQHS 589 (590)
Q Consensus 566 ~~~c~~c~~~~~~~~~~c~~c~~~ 589 (590)
.|.|..||+.|......|.+|..|
T Consensus 2 ~W~C~~C~~~N~~~~~~C~~C~~p 25 (26)
T smart00547 2 DWECPACTFLNFASRSKCFACGAP 25 (26)
T ss_pred cccCCCCCCcChhhhccccccCCc
Confidence 599999999999999999999865
No 41
>PF14570 zf-RING_4: RING/Ubox like zinc-binding domain; PDB: 1E4U_A 1UR6_B.
Probab=95.34 E-value=0.015 Score=43.33 Aligned_cols=44 Identities=27% Similarity=0.751 Sum_probs=21.8
Q ss_pred ccccccccCCC--CceecCCCCccchhhHHHhhcCCCceecccCCCCCCCc
Q 007763 144 CGICFENYPSD--RLLAAACGHPFCSSCWTAINDGPGCLMLRCPDPSCGAA 192 (590)
Q Consensus 144 C~IC~e~~~~~--~~~~l~CgH~fC~~C~~~i~~g~~~~~i~CP~~~C~~~ 192 (590)
|++|.+.+... ++...+||+.+|..||..|.... .=+|| +|+..
T Consensus 1 cp~C~e~~d~~d~~~~PC~Cgf~IC~~C~~~i~~~~---~g~CP--gCr~~ 46 (48)
T PF14570_consen 1 CPLCDEELDETDKDFYPCECGFQICRFCYHDILENE---GGRCP--GCREP 46 (48)
T ss_dssp -TTTS-B--CCCTT--SSTTS----HHHHHHHTTSS----SB-T--TT--B
T ss_pred CCCcccccccCCCccccCcCCCcHHHHHHHHHHhcc---CCCCC--CCCCC
Confidence 78999887543 44566799999999996665421 24899 89865
No 42
>KOG0824 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=95.24 E-value=0.011 Score=60.20 Aligned_cols=52 Identities=19% Similarity=0.539 Sum_probs=40.7
Q ss_pred CcccccccccccCCCCceecCCCCccchhhH-HHhhcCCCceecccCCCCCCCccchhHHh
Q 007763 140 EEMTCGICFENYPSDRLLAAACGHPFCSSCW-TAINDGPGCLMLRCPDPSCGAAVGQDMIY 199 (590)
Q Consensus 140 ~~~~C~IC~e~~~~~~~~~l~CgH~fC~~C~-~~i~~g~~~~~i~CP~~~C~~~i~~~~i~ 199 (590)
..-.|.||+.+. ..++.++|+|.||..|+ ..++.+. ..|| -|+..|+...+.
T Consensus 6 ~~~eC~IC~nt~--n~Pv~l~C~HkFCyiCiKGsy~ndk----~~Ca--vCR~pids~i~~ 58 (324)
T KOG0824|consen 6 KKKECLICYNTG--NCPVNLYCFHKFCYICIKGSYKNDK----KTCA--VCRFPIDSTIDF 58 (324)
T ss_pred cCCcceeeeccC--CcCccccccchhhhhhhcchhhcCC----CCCc--eecCCCCcchhc
Confidence 345799999876 66799999999999999 5555443 4698 899998776553
No 43
>PF11789 zf-Nse: Zinc-finger of the MIZ type in Nse subunit; PDB: 2YU4_A 3HTK_C.
Probab=95.08 E-value=0.019 Score=44.54 Aligned_cols=46 Identities=24% Similarity=0.564 Sum_probs=29.0
Q ss_pred CcccccccccccCCCCcee-cCCCCccchhhH-HHhhcCCCceecccCCCCCC
Q 007763 140 EEMTCGICFENYPSDRLLA-AACGHPFCSSCW-TAINDGPGCLMLRCPDPSCG 190 (590)
Q Consensus 140 ~~~~C~IC~e~~~~~~~~~-l~CgH~fC~~C~-~~i~~g~~~~~i~CP~~~C~ 190 (590)
..+.|||....+ .+|+. ..|||.|.++.+ ..|..+ ..++||..+|.
T Consensus 10 ~~~~CPiT~~~~--~~PV~s~~C~H~fek~aI~~~i~~~---~~~~CPv~GC~ 57 (57)
T PF11789_consen 10 ISLKCPITLQPF--EDPVKSKKCGHTFEKEAILQYIQRN---GSKRCPVAGCN 57 (57)
T ss_dssp --SB-TTTSSB---SSEEEESSS--EEEHHHHHHHCTTT---S-EE-SCCC-S
T ss_pred eccCCCCcCChh--hCCcCcCCCCCeecHHHHHHHHHhc---CCCCCCCCCCC
Confidence 357899999887 66755 689999999999 666332 46999999884
No 44
>KOG2879 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=94.65 E-value=0.03 Score=56.31 Aligned_cols=51 Identities=27% Similarity=0.586 Sum_probs=35.6
Q ss_pred CCcccccccccccCCCCceecCCCCccchhhH-HHhhcCCCceecccCCCCCCCccch
Q 007763 139 GEEMTCGICFENYPSDRLLAAACGHPFCSSCW-TAINDGPGCLMLRCPDPSCGAAVGQ 195 (590)
Q Consensus 139 ~~~~~C~IC~e~~~~~~~~~l~CgH~fC~~C~-~~i~~g~~~~~i~CP~~~C~~~i~~ 195 (590)
....+|++|-+.. ....+..+|||.||-.|+ +...-. ..+.|| .|+..+.+
T Consensus 237 t~~~~C~~Cg~~P-tiP~~~~~C~HiyCY~Ci~ts~~~~---asf~Cp--~Cg~~~~~ 288 (298)
T KOG2879|consen 237 TSDTECPVCGEPP-TIPHVIGKCGHIYCYYCIATSRLWD---ASFTCP--LCGENVEP 288 (298)
T ss_pred cCCceeeccCCCC-CCCeeeccccceeehhhhhhhhcch---hhcccC--ccCCCCcc
Confidence 3467899998753 333445569999999999 443322 248999 89887653
No 45
>PF12678 zf-rbx1: RING-H2 zinc finger; InterPro: IPR024766 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This domain constitutes a conserved region found in proteins that participate in diverse functions relevant to chromosome metabolism and cell cycle control [].The domain contains 8 cysteine/ histidine residues which are proposed to be the conserved residues involved in zinc binding.; PDB: 4A0C_D 4A0L_I 4A0K_B 2ECL_A 1LDK_C 3RTR_F 3DQV_Y 1U6G_B 1LDJ_B 2HYE_D ....
Probab=94.63 E-value=0.036 Score=45.31 Aligned_cols=44 Identities=27% Similarity=0.628 Sum_probs=29.7
Q ss_pred cccccccccccCC----------CC-ceecCCCCccchhhHHHhhcCCCceecccCCCCCC
Q 007763 141 EMTCGICFENYPS----------DR-LLAAACGHPFCSSCWTAINDGPGCLMLRCPDPSCG 190 (590)
Q Consensus 141 ~~~C~IC~e~~~~----------~~-~~~l~CgH~fC~~C~~~i~~g~~~~~i~CP~~~C~ 190 (590)
...|.||++.+.. .. +...+|||.|...|+..+-... -.|| .|+
T Consensus 19 ~d~C~IC~~~l~~~~~~~~~~~~~~~i~~~~C~H~FH~~Ci~~Wl~~~----~~CP--~CR 73 (73)
T PF12678_consen 19 DDNCAICREPLEDPCPECQAPQDECPIVWGPCGHIFHFHCISQWLKQN----NTCP--LCR 73 (73)
T ss_dssp CSBETTTTSBTTSTTCCHHHCTTTS-EEEETTSEEEEHHHHHHHHTTS----SB-T--TSS
T ss_pred CCcccccChhhhChhhhhcCCccccceEecccCCCEEHHHHHHHHhcC----CcCC--CCC
Confidence 3459999998821 12 2344799999999997766543 3899 564
No 46
>KOG0311 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=94.60 E-value=0.0043 Score=64.24 Aligned_cols=47 Identities=28% Similarity=0.747 Sum_probs=35.5
Q ss_pred CcccccccccccCCCCceecCCCCccchhhH-HHhhcCCCceecccCCCCCCCcc
Q 007763 140 EEMTCGICFENYPSDRLLAAACGHPFCSSCW-TAINDGPGCLMLRCPDPSCGAAV 193 (590)
Q Consensus 140 ~~~~C~IC~e~~~~~~~~~l~CgH~fC~~C~-~~i~~g~~~~~i~CP~~~C~~~i 193 (590)
..+.|+||++.+. .-+.+..|.|.||.+|| ..+..+. -.|| .|+..+
T Consensus 42 ~~v~c~icl~llk-~tmttkeClhrfc~~ci~~a~r~gn----~ecp--tcRk~l 89 (381)
T KOG0311|consen 42 IQVICPICLSLLK-KTMTTKECLHRFCFDCIWKALRSGN----NECP--TCRKKL 89 (381)
T ss_pred hhhccHHHHHHHH-hhcccHHHHHHHHHHHHHHHHHhcC----CCCc--hHHhhc
Confidence 4688999999873 23445569999999999 6766654 4798 788654
No 47
>COG5152 Uncharacterized conserved protein, contains RING and CCCH-type Zn-fingers [General function prediction only]
Probab=94.51 E-value=0.014 Score=55.68 Aligned_cols=35 Identities=37% Similarity=0.959 Sum_probs=31.0
Q ss_pred cccccccccccCCCCceecCCCCccchhhH-HHhhcCC
Q 007763 141 EMTCGICFENYPSDRLLAAACGHPFCSSCW-TAINDGP 177 (590)
Q Consensus 141 ~~~C~IC~e~~~~~~~~~l~CgH~fC~~C~-~~i~~g~ 177 (590)
.|.|.||-.++ ..|+...|||.||..|. ..+..|.
T Consensus 196 PF~C~iCKkdy--~spvvt~CGH~FC~~Cai~~y~kg~ 231 (259)
T COG5152 196 PFLCGICKKDY--ESPVVTECGHSFCSLCAIRKYQKGD 231 (259)
T ss_pred ceeehhchhhc--cchhhhhcchhHHHHHHHHHhccCC
Confidence 58999999998 77899999999999999 7777775
No 48
>KOG4159 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=94.16 E-value=0.046 Score=58.83 Aligned_cols=48 Identities=25% Similarity=0.734 Sum_probs=37.9
Q ss_pred CCcccccccccccCCCCceecCCCCccchhhH-HHhhcCCCceecccCCCCCCCccch
Q 007763 139 GEEMTCGICFENYPSDRLLAAACGHPFCSSCW-TAINDGPGCLMLRCPDPSCGAAVGQ 195 (590)
Q Consensus 139 ~~~~~C~IC~e~~~~~~~~~l~CgH~fC~~C~-~~i~~g~~~~~i~CP~~~C~~~i~~ 195 (590)
.++|.|.||+..+ -.+++++|||.||..|+ ..+.. ...|| .|+..+..
T Consensus 82 ~sef~c~vc~~~l--~~pv~tpcghs~c~~Cl~r~ld~-----~~~cp--~Cr~~l~e 130 (398)
T KOG4159|consen 82 RSEFECCVCSRAL--YPPVVTPCGHSFCLECLDRSLDQ-----ETECP--LCRDELVE 130 (398)
T ss_pred cchhhhhhhHhhc--CCCccccccccccHHHHHHHhcc-----CCCCc--cccccccc
Confidence 5689999999887 67888899999999998 43332 35788 69887753
No 49
>COG5432 RAD18 RING-finger-containing E3 ubiquitin ligase [Signal transduction mechanisms]
Probab=94.08 E-value=0.035 Score=56.03 Aligned_cols=62 Identities=24% Similarity=0.446 Sum_probs=42.5
Q ss_pred cccccccccccCCCCceecCCCCccchhhH-HHhhcCCCceecccCCCCCCCccchhHHh-hcCChHHHHHHH
Q 007763 141 EMTCGICFENYPSDRLLAAACGHPFCSSCW-TAINDGPGCLMLRCPDPSCGAAVGQDMIY-LLSSDEDKVKYN 211 (590)
Q Consensus 141 ~~~C~IC~e~~~~~~~~~l~CgH~fC~~C~-~~i~~g~~~~~i~CP~~~C~~~i~~~~i~-~ll~~e~~eky~ 211 (590)
-..|-||-+-+ .-++..+|||.||.-|| .++... .-|| .|+.......++ ..+..++.+-|.
T Consensus 25 ~lrC~IC~~~i--~ip~~TtCgHtFCslCIR~hL~~q-----p~CP--~Cr~~~~esrlr~~s~~~ei~es~~ 88 (391)
T COG5432 25 MLRCRICDCRI--SIPCETTCGHTFCSLCIRRHLGTQ-----PFCP--VCREDPCESRLRGSSGSREINESHA 88 (391)
T ss_pred HHHhhhhhhee--ecceecccccchhHHHHHHHhcCC-----CCCc--cccccHHhhhcccchhHHHHHHhhh
Confidence 45799998877 56788899999999999 676554 4688 787765444332 233345555554
No 50
>COG5243 HRD1 HRD ubiquitin ligase complex, ER membrane component [Posttranslational modification, protein turnover, chaperones]
Probab=93.86 E-value=0.16 Score=53.04 Aligned_cols=95 Identities=18% Similarity=0.251 Sum_probs=56.7
Q ss_pred CCHHHHHHHHHhcCCChHHHHHHhhc-----CHHHHHHHcCCCCCCCCCCCCCCccccccccccc-CCC----------C
Q 007763 92 ISKVAASILLRFYNWSVSKVHDEWFA-----DEERVRKAVGLLEKPAVQFPDGEEMTCGICFENY-PSD----------R 155 (590)
Q Consensus 92 i~~~~a~~LL~~~~W~~~~l~e~~~~-----~~~~~~~~~gl~~~~~~~~~~~~~~~C~IC~e~~-~~~----------~ 155 (590)
++-..-..|++.-=|....|..+..+ ...+-+++.- +.....+. ..+...|.||+|+. ... .
T Consensus 235 ~~~r~Pi~l~r~~~t~~~AL~~~i~~~~~~~r~~kdl~~~~-~t~t~eql-~n~D~~C~ICmde~~h~~~~~~~~~~~~~ 312 (491)
T COG5243 235 PYVRVPIYLIRQMYTCFYALFRRIREHARFRRATKDLNAMY-PTATEEQL-TNSDRTCTICMDEMFHPDHEPLPRGLDMT 312 (491)
T ss_pred cchhchHHHHHHHHHHHHHHHHHHHHHHHHHHHhhHHHhhc-chhhhhhh-cCCCCeEEEecccccCCCCccCcccccCC
Confidence 34445567777777777776654321 1111122111 10011112 34456899999982 221 3
Q ss_pred ceecCCCCccchhhHHHhhcCCCceecccCCCCCCCccc
Q 007763 156 LLAAACGHPFCSSCWTAINDGPGCLMLRCPDPSCGAAVG 194 (590)
Q Consensus 156 ~~~l~CgH~fC~~C~~~i~~g~~~~~i~CP~~~C~~~i~ 194 (590)
|..++|||.+...|+..|-+.+ -.|| -|+..+-
T Consensus 313 pKrLpCGHilHl~CLknW~ERq----QTCP--ICr~p~i 345 (491)
T COG5243 313 PKRLPCGHILHLHCLKNWLERQ----QTCP--ICRRPVI 345 (491)
T ss_pred cccccccceeeHHHHHHHHHhc----cCCC--cccCccc
Confidence 4678999999999998877654 4899 8998753
No 51
>KOG1002 consensus Nucleotide excision repair protein RAD16 [Replication, recombination and repair]
Probab=93.80 E-value=0.029 Score=60.71 Aligned_cols=57 Identities=23% Similarity=0.642 Sum_probs=41.6
Q ss_pred CCCCcccccccccccCCCCceecCCCCccchhhH-HHhhcCCCceecccCCCCCCCccchhH
Q 007763 137 PDGEEMTCGICFENYPSDRLLAAACGHPFCSSCW-TAINDGPGCLMLRCPDPSCGAAVGQDM 197 (590)
Q Consensus 137 ~~~~~~~C~IC~e~~~~~~~~~l~CgH~fC~~C~-~~i~~g~~~~~i~CP~~~C~~~i~~~~ 197 (590)
.+.....|++|-+.- .+.+...|.|.||+-|+ .+|..-.....+.|| .|...++.++
T Consensus 532 enk~~~~C~lc~d~a--ed~i~s~ChH~FCrlCi~eyv~~f~~~~nvtCP--~C~i~LsiDl 589 (791)
T KOG1002|consen 532 ENKGEVECGLCHDPA--EDYIESSCHHKFCRLCIKEYVESFMENNNVTCP--VCHIGLSIDL 589 (791)
T ss_pred cccCceeecccCChh--hhhHhhhhhHHHHHHHHHHHHHhhhcccCCCCc--cccccccccc
Confidence 355678999999864 67888899999999999 444321112359999 8988776553
No 52
>KOG1814 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=93.37 E-value=0.034 Score=58.82 Aligned_cols=42 Identities=33% Similarity=0.956 Sum_probs=37.4
Q ss_pred HhcCcCCCC--CCcceeeccCCCceeecCCCcceeeecccccccC
Q 007763 291 LANSKPCPR--CKRPIEKNQGCMHMTCTPPCKFEFCWLCLGQWSD 333 (590)
Q Consensus 291 ~~ntK~CP~--C~~~IEK~~GCnhMtC~~~C~~~FCw~C~~~w~~ 333 (590)
.++..-||+ |+.|+-...|++-..|. .|.+.||.+|...|+.
T Consensus 270 msdv~yCPr~~Cq~p~~~d~~~~l~~Cs-kCnFaFCtlCk~t~HG 313 (445)
T KOG1814|consen 270 MSDVVYCPRACCQLPVKQDPGRALAICS-KCNFAFCTLCKLTWHG 313 (445)
T ss_pred hcccccCChhhccCccccCchhhhhhhc-cCccHHHHHHHHhhcC
Confidence 456789998 99999778999999999 8999999999998854
No 53
>KOG1812 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=92.75 E-value=0.07 Score=57.60 Aligned_cols=41 Identities=27% Similarity=0.865 Sum_probs=33.1
Q ss_pred CCcccCCCCCCCceEeeecCCCcceeEecCCCccccccCCCcCCC
Q 007763 223 RKTKWCPAPGCDYAVDFVVGSGNYDVTCRCSYSFCWNCTEEAHRP 267 (590)
Q Consensus 223 ~~~~~CP~p~C~~~i~~~~~~~~~~v~C~C~~~fC~~C~~~~H~p 267 (590)
...+.||. |...|... .+...++|.||+.||+.|+.+|+..
T Consensus 304 ~~wr~Cpk--C~~~ie~~--~GCnhm~CrC~~~fcy~C~~~~~~~ 344 (384)
T KOG1812|consen 304 KRWRQCPK--CKFMIELS--EGCNHMTCRCGHQFCYMCGGDWKTH 344 (384)
T ss_pred HhcCcCcc--cceeeeec--CCcceEEeeccccchhhcCcchhhC
Confidence 45688995 99888654 3577899999999999999888654
No 54
>PF04931 DNA_pol_phi: DNA polymerase phi; InterPro: IPR007015 Proteins of this family are predominantly nucleolar. The majority are described as transcription factor transactivators. The family also includes the fifth essential DNA polymerase (Pol5p) of Schizosaccharomyces pombe (Fission yeast) and Saccharomyces cerevisiae (Baker's yeast) (2.7.7.7 from EC). Pol5p is localized exclusively to the nucleolus and binds near or at the enhancer region of rRNA-encoding DNA repeating units.; GO: 0003677 DNA binding, 0003887 DNA-directed DNA polymerase activity, 0006351 transcription, DNA-dependent
Probab=92.07 E-value=0.25 Score=58.50 Aligned_cols=20 Identities=10% Similarity=0.069 Sum_probs=14.7
Q ss_pred HHHHHHHhcCCChHHHHHHh
Q 007763 96 AASILLRFYNWSVSKVHDEW 115 (590)
Q Consensus 96 ~a~~LL~~~~W~~~~l~e~~ 115 (590)
.++..+.+|+-.+-.|++-|
T Consensus 764 ~~~~~~~~Fk~RvlDLleiy 783 (784)
T PF04931_consen 764 EAKENVIHFKNRVLDLLEIY 783 (784)
T ss_pred HHHHHHHHHHHHHHHHHHHh
Confidence 56778888887777777665
No 55
>KOG1039 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=91.73 E-value=0.11 Score=54.89 Aligned_cols=55 Identities=25% Similarity=0.610 Sum_probs=37.0
Q ss_pred CCCCcccccccccccCCCC-----cee-cCCCCccchhhHHHhhcC---CCceecccCCCCCCCcc
Q 007763 137 PDGEEMTCGICFENYPSDR-----LLA-AACGHPFCSSCWTAINDG---PGCLMLRCPDPSCGAAV 193 (590)
Q Consensus 137 ~~~~~~~C~IC~e~~~~~~-----~~~-l~CgH~fC~~C~~~i~~g---~~~~~i~CP~~~C~~~i 193 (590)
+......|+||++...... .-. .+|.|.||..|+..+... .....-.|| .|+...
T Consensus 157 ~~s~~k~CGICme~i~ek~~~~~rfgilpnC~H~~Cl~Cir~wr~~~q~~~~~sksCP--~CRv~s 220 (344)
T KOG1039|consen 157 QKSSEKECGICMETINEKAASERRFGILPNCNHSFCLNCIRKWRQATQFESKTSKSCP--FCRVPS 220 (344)
T ss_pred CccccccceehhhhccccchhhhhcccCCCcchhhhhcHhHhhhhhhccccccccCCC--cccCcc
Confidence 3466889999999874333 222 459999999999555422 122357899 788653
No 56
>KOG0006 consensus E3 ubiquitin-protein ligase (Parkin protein) [Posttranslational modification, protein turnover, chaperones]
Probab=91.21 E-value=0.37 Score=49.42 Aligned_cols=94 Identities=24% Similarity=0.667 Sum_probs=52.5
Q ss_pred CCCCccchhhHHHhhcCCCceecc-cCCCCCCCccchhHHhhcCChHHHHHHHHHHHHHHhhcCCCcccCCCCCCCceEe
Q 007763 160 ACGHPFCSSCWTAINDGPGCLMLR-CPDPSCGAAVGQDMIYLLSSDEDKVKYNRYFIRSYVEDNRKTKWCPAPGCDYAVD 238 (590)
Q Consensus 160 ~CgH~fC~~C~~~i~~g~~~~~i~-CP~~~C~~~i~~~~i~~ll~~e~~eky~~~l~~~~v~~~~~~~~CP~p~C~~~i~ 238 (590)
.||-.||+.|......|.-...+- =-...|...+.+... ...+|...... .| ....+.|| .|..+.+
T Consensus 341 gCgf~FCR~C~e~yh~geC~~~~~as~t~tc~y~vde~~a-------~~arwd~as~~-TI--k~tTkpCP--kChvptE 408 (446)
T KOG0006|consen 341 GCGFAFCRECKEAYHEGECSAVFEASGTTTCAYRVDERAA-------EQARWDAASKE-TI--KKTTKPCP--KCHVPTE 408 (446)
T ss_pred CchhHhHHHHHhhhccccceeeeccccccceeeecChhhh-------hhhhhhhhhhh-hh--hhccCCCC--CccCccc
Confidence 499999999996555442000000 000134444433221 12334332211 11 23457788 4987766
Q ss_pred eecCCCcceeEe-c--CCCccccccCCCcCCC
Q 007763 239 FVVGSGNYDVTC-R--CSYSFCWNCTEEAHRP 267 (590)
Q Consensus 239 ~~~~~~~~~v~C-~--C~~~fC~~C~~~~H~p 267 (590)
.. .+...+.| . ||..+||.|+-+|.+.
T Consensus 409 rn--GGCmHm~Ct~~~Cg~eWCw~C~tEW~r~ 438 (446)
T KOG0006|consen 409 RN--GGCMHMKCTQPQCGLEWCWNCGTEWNRV 438 (446)
T ss_pred cC--CceEEeecCCCCCCceeEeccCChhhhh
Confidence 43 45677889 4 9999999999998643
No 57
>KOG2817 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=90.92 E-value=0.87 Score=48.42 Aligned_cols=56 Identities=14% Similarity=0.339 Sum_probs=40.8
Q ss_pred CcccccccccccCC-CCceecCCCCccchhhHHHhhcCCCceecccCCCCCCCccchhHH
Q 007763 140 EEMTCGICFENYPS-DRLLAAACGHPFCSSCWTAINDGPGCLMLRCPDPSCGAAVGQDMI 198 (590)
Q Consensus 140 ~~~~C~IC~e~~~~-~~~~~l~CgH~fC~~C~~~i~~g~~~~~i~CP~~~C~~~i~~~~i 198 (590)
+.|.|||=-+.... +.|..+.|||..|++=+..+..|.. ..++|| -|.........
T Consensus 333 SvF~CPVlKeqtsdeNPPm~L~CGHVISkdAlnrLS~ng~-~sfKCP--YCP~e~~~~~~ 389 (394)
T KOG2817|consen 333 SVFICPVLKEQTSDENPPMMLICGHVISKDALNRLSKNGS-QSFKCP--YCPVEQLASDT 389 (394)
T ss_pred ceeecccchhhccCCCCCeeeeccceecHHHHHHHhhCCC-eeeeCC--CCCcccCHHhc
Confidence 57899996554433 4678999999999999977665542 479999 78766544433
No 58
>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=90.85 E-value=0.12 Score=33.46 Aligned_cols=24 Identities=29% Similarity=0.945 Sum_probs=16.1
Q ss_pred cCCCCCCcceeeccCCCceeecCCCccee
Q 007763 295 KPCPRCKRPIEKNQGCMHMTCTPPCKFEF 323 (590)
Q Consensus 295 K~CP~C~~~IEK~~GCnhMtC~~~C~~~F 323 (590)
|.||.|+..|-.+ -+.|. .|||.|
T Consensus 1 K~CP~C~~~V~~~----~~~Cp-~CG~~F 24 (26)
T PF10571_consen 1 KTCPECGAEVPES----AKFCP-HCGYDF 24 (26)
T ss_pred CcCCCCcCCchhh----cCcCC-CCCCCC
Confidence 6799998888522 25565 577766
No 59
>KOG2660 consensus Locus-specific chromosome binding proteins [Function unknown]
Probab=88.70 E-value=0.17 Score=52.38 Aligned_cols=47 Identities=28% Similarity=0.687 Sum_probs=34.2
Q ss_pred CcccccccccccCCCCceecCCCCccchhhH-HHhhcCCCceecccCCCCCCCccc
Q 007763 140 EEMTCGICFENYPSDRLLAAACGHPFCSSCW-TAINDGPGCLMLRCPDPSCGAAVG 194 (590)
Q Consensus 140 ~~~~C~IC~e~~~~~~~~~l~CgH~fC~~C~-~~i~~g~~~~~i~CP~~~C~~~i~ 194 (590)
...+|.+|-..+. +......|-|.||++|| .++.. ...|| .|...+.
T Consensus 14 ~~itC~LC~GYli-DATTI~eCLHTFCkSCivk~l~~-----~~~CP--~C~i~ih 61 (331)
T KOG2660|consen 14 PHITCRLCGGYLI-DATTITECLHTFCKSCIVKYLEE-----SKYCP--TCDIVIH 61 (331)
T ss_pred cceehhhccceee-cchhHHHHHHHHHHHHHHHHHHH-----hccCC--ccceecc
Confidence 4678999987662 33344569999999999 66655 25899 7887664
No 60
>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=88.35 E-value=9.2 Score=39.94 Aligned_cols=34 Identities=29% Similarity=0.640 Sum_probs=21.3
Q ss_pred cCCCCCCcceeeccCCCceeecCCCcceeeeccccc
Q 007763 295 KPCPRCKRPIEKNQGCMHMTCTPPCKFEFCWLCLGQ 330 (590)
Q Consensus 295 K~CP~C~~~IEK~~GCnhMtC~~~C~~~FCw~C~~~ 330 (590)
..||.|+...-.|..=.-|.= .|||.||-.|...
T Consensus 4 ~~CP~Ck~~~y~np~~kl~i~--~CGH~~C~sCv~~ 37 (309)
T TIGR00570 4 QGCPRCKTTKYRNPSLKLMVN--VCGHTLCESCVDL 37 (309)
T ss_pred CCCCcCCCCCccCcccccccC--CCCCcccHHHHHH
Confidence 579999995543332111221 3888888888876
No 61
>PRK00420 hypothetical protein; Validated
Probab=87.40 E-value=4.2 Score=36.10 Aligned_cols=27 Identities=26% Similarity=0.294 Sum_probs=18.9
Q ss_pred CcCCCCCCcceeeccCCCceeecCCCcceeeeccccc
Q 007763 294 SKPCPRCKRPIEKNQGCMHMTCTPPCKFEFCWLCLGQ 330 (590)
Q Consensus 294 tK~CP~C~~~IEK~~GCnhMtC~~~C~~~FCw~C~~~ 330 (590)
...||.|+.|+.+. .=|..||..|+..
T Consensus 23 ~~~CP~Cg~pLf~l----------k~g~~~Cp~Cg~~ 49 (112)
T PRK00420 23 SKHCPVCGLPLFEL----------KDGEVVCPVHGKV 49 (112)
T ss_pred cCCCCCCCCcceec----------CCCceECCCCCCe
Confidence 48999999998841 2455666677653
No 62
>KOG4739 consensus Uncharacterized protein involved in synaptonemal complex formation [Cell cycle control, cell division, chromosome partitioning; General function prediction only]
Probab=87.30 E-value=0.29 Score=48.68 Aligned_cols=54 Identities=26% Similarity=0.560 Sum_probs=37.1
Q ss_pred ccccccccccCCCCceecCCCCccchhhHHHhhcCCCceecccCCCCCCCccchhHHhhcCC
Q 007763 142 MTCGICFENYPSDRLLAAACGHPFCSSCWTAINDGPGCLMLRCPDPSCGAAVGQDMIYLLSS 203 (590)
Q Consensus 142 ~~C~IC~e~~~~~~~~~l~CgH~fC~~C~~~i~~g~~~~~i~CP~~~C~~~i~~~~i~~ll~ 203 (590)
+.|..|+--.+...++.+.|+|.||..|...-. .-.|| .|+..+....+..-++
T Consensus 4 VhCn~C~~~~~~~~f~LTaC~HvfC~~C~k~~~------~~~C~--lCkk~ir~i~l~~slp 57 (233)
T KOG4739|consen 4 VHCNKCFRFPSQDPFFLTACRHVFCEPCLKASS------PDVCP--LCKKSIRIIQLNRSLP 57 (233)
T ss_pred EEeccccccCCCCceeeeechhhhhhhhcccCC------ccccc--cccceeeeeecccccc
Confidence 468989876665666778899999999983211 11798 8998875444433333
No 63
>KOG0317 consensus Predicted E3 ubiquitin ligase, integral peroxisomal membrane protein [Posttranslational modification, protein turnover, chaperones]
Probab=86.85 E-value=0.12 Score=52.53 Aligned_cols=37 Identities=27% Similarity=0.851 Sum_probs=28.3
Q ss_pred hcCcCCCCCCcceeeccCCCceeecCCCcceeeecccccccCCC
Q 007763 292 ANSKPCPRCKRPIEKNQGCMHMTCTPPCKFEFCWLCLGQWSDHG 335 (590)
Q Consensus 292 ~ntK~CP~C~~~IEK~~GCnhMtC~~~C~~~FCw~C~~~w~~H~ 335 (590)
.++.+|-=|-...+ |-+|+ +|||-|||-|...|-.-.
T Consensus 237 ~a~~kC~LCLe~~~------~pSaT-pCGHiFCWsCI~~w~~ek 273 (293)
T KOG0317|consen 237 EATRKCSLCLENRS------NPSAT-PCGHIFCWSCILEWCSEK 273 (293)
T ss_pred CCCCceEEEecCCC------CCCcC-cCcchHHHHHHHHHHccc
Confidence 34566777766654 57899 799999999999996544
No 64
>KOG4265 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=86.66 E-value=0.51 Score=49.52 Aligned_cols=65 Identities=18% Similarity=0.468 Sum_probs=44.3
Q ss_pred HHHcCCCCCCCCCCC---CCCcccccccccccCCCCceecCCCCc-cchhhHHHhhcCCCceecccCCCCCCCccch
Q 007763 123 RKAVGLLEKPAVQFP---DGEEMTCGICFENYPSDRLLAAACGHP-FCSSCWTAINDGPGCLMLRCPDPSCGAAVGQ 195 (590)
Q Consensus 123 ~~~~gl~~~~~~~~~---~~~~~~C~IC~e~~~~~~~~~l~CgH~-fC~~C~~~i~~g~~~~~i~CP~~~C~~~i~~ 195 (590)
++.+||.+++..... +.....|-||+.+. .+.+.|||.|. .|.+|-..+.- ..=.|| -|+..|..
T Consensus 269 qEiyGien~~v~~~~~~~~~~gkeCVIClse~--rdt~vLPCRHLCLCs~Ca~~Lr~----q~n~CP--ICRqpi~~ 337 (349)
T KOG4265|consen 269 QEIYGIENSTVEGTDADESESGKECVICLSES--RDTVVLPCRHLCLCSGCAKSLRY----QTNNCP--ICRQPIEE 337 (349)
T ss_pred ehhhccccCCCCCCccccccCCCeeEEEecCC--cceEEecchhhehhHhHHHHHHH----hhcCCC--ccccchHh
Confidence 455676544333222 13467899999875 78899999996 89999955541 123699 89987643
No 65
>KOG1785 consensus Tyrosine kinase negative regulator CBL [Defense mechanisms]
Probab=86.58 E-value=0.28 Score=51.73 Aligned_cols=46 Identities=35% Similarity=0.759 Sum_probs=34.4
Q ss_pred ccccccccccCCCCceecCCCCccchhhHHHhhcCCCceecccCCCCCCCcc
Q 007763 142 MTCGICFENYPSDRLLAAACGHPFCSSCWTAINDGPGCLMLRCPDPSCGAAV 193 (590)
Q Consensus 142 ~~C~IC~e~~~~~~~~~l~CgH~fC~~C~~~i~~g~~~~~i~CP~~~C~~~i 193 (590)
..|-||-+.- .++..-+|||..|..|++.|.+..+ .-.|| .|+..|
T Consensus 370 eLCKICaend--KdvkIEPCGHLlCt~CLa~WQ~sd~--gq~CP--FCRcEI 415 (563)
T KOG1785|consen 370 ELCKICAEND--KDVKIEPCGHLLCTSCLAAWQDSDE--GQTCP--FCRCEI 415 (563)
T ss_pred HHHHHhhccC--CCcccccccchHHHHHHHhhcccCC--CCCCC--ceeeEe
Confidence 4599999864 6677789999999999988875431 35799 565443
No 66
>KOG1813 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=86.52 E-value=0.31 Score=49.70 Aligned_cols=44 Identities=30% Similarity=0.769 Sum_probs=34.5
Q ss_pred cccccccccccCCCCceecCCCCccchhhH-HHhhcCCCceecccCCCCCCCcc
Q 007763 141 EMTCGICFENYPSDRLLAAACGHPFCSSCW-TAINDGPGCLMLRCPDPSCGAAV 193 (590)
Q Consensus 141 ~~~C~IC~e~~~~~~~~~l~CgH~fC~~C~-~~i~~g~~~~~i~CP~~~C~~~i 193 (590)
.|-|.||-..+ ..++...|+|.||..|- ..+..+. +|+ .|...+
T Consensus 241 Pf~c~icr~~f--~~pVvt~c~h~fc~~ca~~~~qk~~-----~c~--vC~~~t 285 (313)
T KOG1813|consen 241 PFKCFICRKYF--YRPVVTKCGHYFCEVCALKPYQKGE-----KCY--VCSQQT 285 (313)
T ss_pred Ccccccccccc--ccchhhcCCceeehhhhccccccCC-----cce--eccccc
Confidence 56799999988 78899999999999999 6665554 565 666543
No 67
>COG5175 MOT2 Transcriptional repressor [Transcription]
Probab=86.13 E-value=0.35 Score=49.98 Aligned_cols=53 Identities=25% Similarity=0.666 Sum_probs=41.1
Q ss_pred cccccccccccCC--CCceecCCCCccchhhHHHhhcCCCceecccCCCCCCCccchhHH
Q 007763 141 EMTCGICFENYPS--DRLLAAACGHPFCSSCWTAINDGPGCLMLRCPDPSCGAAVGQDMI 198 (590)
Q Consensus 141 ~~~C~IC~e~~~~--~~~~~l~CgH~fC~~C~~~i~~g~~~~~i~CP~~~C~~~i~~~~i 198 (590)
...||+|.+.... ..++..+||-..|.-||..|.++. .=+|| -|+.....+-+
T Consensus 14 ed~cplcie~mditdknf~pc~cgy~ic~fc~~~irq~l---ngrcp--acrr~y~denv 68 (480)
T COG5175 14 EDYCPLCIEPMDITDKNFFPCPCGYQICQFCYNNIRQNL---NGRCP--ACRRKYDDENV 68 (480)
T ss_pred cccCcccccccccccCCcccCCcccHHHHHHHHHHHhhc---cCCCh--Hhhhhccccce
Confidence 4459999998654 467888999999999998887663 45899 79987655444
No 68
>KOG1815 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=85.58 E-value=0.51 Score=52.09 Aligned_cols=35 Identities=23% Similarity=0.642 Sum_probs=30.1
Q ss_pred CCCCcceee-ccCCCceeecCCCcceeeecccccccCC
Q 007763 298 PRCKRPIEK-NQGCMHMTCTPPCKFEFCWLCLGQWSDH 334 (590)
Q Consensus 298 P~C~~~IEK-~~GCnhMtC~~~C~~~FCw~C~~~w~~H 334 (590)
|.|+..+.- .+.+.-+.|. |++.|||.|+.+|+.-
T Consensus 164 ~~C~~av~~~~~~~~~v~C~--~g~~FC~~C~~~~H~p 199 (444)
T KOG1815|consen 164 PGCGLAVKFGSLESVEVDCG--CGHEFCFACGEESHSP 199 (444)
T ss_pred CCCCceeeccCCCccceeCC--CCchhHhhccccccCC
Confidence 579999987 7888889997 9999999999888643
No 69
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=84.28 E-value=0.52 Score=30.43 Aligned_cols=11 Identities=36% Similarity=0.914 Sum_probs=9.0
Q ss_pred cCCCCCCccee
Q 007763 295 KPCPRCKRPIE 305 (590)
Q Consensus 295 K~CP~C~~~IE 305 (590)
+.||+|+..|.
T Consensus 3 ~~Cp~Cg~~~~ 13 (26)
T PF13248_consen 3 MFCPNCGAEID 13 (26)
T ss_pred CCCcccCCcCC
Confidence 68999998776
No 70
>PF15227 zf-C3HC4_4: zinc finger of C3HC4-type, RING; PDB: 2EGP_A 2ECV_A 2ECJ_A 2YSL_A 2YSJ_A.
Probab=84.17 E-value=0.44 Score=34.50 Aligned_cols=32 Identities=28% Similarity=0.704 Sum_probs=21.3
Q ss_pred CCCCCcceeeccCCCceeecCCCcceeeecccccccCCC
Q 007763 297 CPRCKRPIEKNQGCMHMTCTPPCKFEFCWLCLGQWSDHG 335 (590)
Q Consensus 297 CP~C~~~IEK~~GCnhMtC~~~C~~~FCw~C~~~w~~H~ 335 (590)
||-|...+. +.++= .|||.||..|+..|....
T Consensus 1 CpiC~~~~~-----~Pv~l--~CGH~FC~~Cl~~~~~~~ 32 (42)
T PF15227_consen 1 CPICLDLFK-----DPVSL--PCGHSFCRSCLERLWKEP 32 (42)
T ss_dssp ETTTTSB-S-----SEEE---SSSSEEEHHHHHHHHCCS
T ss_pred CCccchhhC-----Ccccc--CCcCHHHHHHHHHHHHcc
Confidence 566666665 33554 499999999998765443
No 71
>PF13240 zinc_ribbon_2: zinc-ribbon domain
Probab=84.11 E-value=0.48 Score=29.73 Aligned_cols=10 Identities=50% Similarity=1.105 Sum_probs=8.2
Q ss_pred CCCCCCccee
Q 007763 296 PCPRCKRPIE 305 (590)
Q Consensus 296 ~CP~C~~~IE 305 (590)
.||+|+..|+
T Consensus 1 ~Cp~CG~~~~ 10 (23)
T PF13240_consen 1 YCPNCGAEIE 10 (23)
T ss_pred CCcccCCCCC
Confidence 3888988887
No 72
>KOG4692 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=83.95 E-value=0.77 Score=47.84 Aligned_cols=51 Identities=29% Similarity=0.625 Sum_probs=35.9
Q ss_pred CCCCCcccccccccccCCCCceecCCCCccchhhH-HHhhcCCCceecccCCCCCCCccch
Q 007763 136 FPDGEEMTCGICFENYPSDRLLAAACGHPFCSSCW-TAINDGPGCLMLRCPDPSCGAAVGQ 195 (590)
Q Consensus 136 ~~~~~~~~C~IC~e~~~~~~~~~l~CgH~fC~~C~-~~i~~g~~~~~i~CP~~~C~~~i~~ 195 (590)
.|.+....|+||+-.- -.-+..||+|.-|..|+ ..+.+. -.|- .|+..+..
T Consensus 417 lp~sEd~lCpICyA~p--i~Avf~PC~H~SC~~CI~qHlmN~-----k~CF--fCktTv~~ 468 (489)
T KOG4692|consen 417 LPDSEDNLCPICYAGP--INAVFAPCSHRSCYGCITQHLMNC-----KRCF--FCKTTVID 468 (489)
T ss_pred CCCcccccCcceeccc--chhhccCCCCchHHHHHHHHHhcC-----Ceee--Eecceeee
Confidence 4556678899999642 34566799999999999 444443 2565 68877654
No 73
>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=83.84 E-value=0.57 Score=46.28 Aligned_cols=49 Identities=27% Similarity=0.691 Sum_probs=34.2
Q ss_pred ccccccccccCCC-Cc---eecCCCCccchhhHHHh-hcCCCceecccCCCCCCCccc
Q 007763 142 MTCGICFENYPSD-RL---LAAACGHPFCSSCWTAI-NDGPGCLMLRCPDPSCGAAVG 194 (590)
Q Consensus 142 ~~C~IC~e~~~~~-~~---~~l~CgH~fC~~C~~~i-~~g~~~~~i~CP~~~C~~~i~ 194 (590)
..||||-.+.-.+ ++ +...|-|..|.+|+..| ..| +-.||-++|+.++.
T Consensus 11 ~~CPvCksDrYLnPdik~linPECyHrmCESCvdRIFs~G----pAqCP~~gC~kILR 64 (314)
T COG5220 11 RRCPVCKSDRYLNPDIKILINPECYHRMCESCVDRIFSRG----PAQCPYKGCGKILR 64 (314)
T ss_pred ccCCccccccccCCCeEEEECHHHHHHHHHHHHHHHhcCC----CCCCCCccHHHHHH
Confidence 4699998763221 22 22239999999999555 444 47899999998774
No 74
>KOG0826 consensus Predicted E3 ubiquitin ligase involved in peroxisome organization [Posttranslational modification, protein turnover, chaperones]
Probab=83.76 E-value=2.6 Score=43.81 Aligned_cols=46 Identities=20% Similarity=0.482 Sum_probs=31.6
Q ss_pred CcccccccccccCCCCceecC-CCCccchhhH-HHhhcCCCceecccCCCCCCCc
Q 007763 140 EEMTCGICFENYPSDRLLAAA-CGHPFCSSCW-TAINDGPGCLMLRCPDPSCGAA 192 (590)
Q Consensus 140 ~~~~C~IC~e~~~~~~~~~l~-CgH~fC~~C~-~~i~~g~~~~~i~CP~~~C~~~ 192 (590)
....|+||+... .++..+. =|-.||-.|+ .++..- =+||-.+|...
T Consensus 299 ~~~~CpvClk~r--~Nptvl~vSGyVfCY~Ci~~Yv~~~-----~~CPVT~~p~~ 346 (357)
T KOG0826|consen 299 DREVCPVCLKKR--QNPTVLEVSGYVFCYPCIFSYVVNY-----GHCPVTGYPAS 346 (357)
T ss_pred ccccChhHHhcc--CCCceEEecceEEeHHHHHHHHHhc-----CCCCccCCcch
Confidence 355799999765 3444443 5899999999 666533 27887777654
No 75
>KOG0802 consensus E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=83.65 E-value=0.42 Score=54.17 Aligned_cols=46 Identities=30% Similarity=0.665 Sum_probs=34.9
Q ss_pred cccccccccccCCC---CceecCCCCccchhhHHHhhcCCCceecccCCCCCCCc
Q 007763 141 EMTCGICFENYPSD---RLLAAACGHPFCSSCWTAINDGPGCLMLRCPDPSCGAA 192 (590)
Q Consensus 141 ~~~C~IC~e~~~~~---~~~~l~CgH~fC~~C~~~i~~g~~~~~i~CP~~~C~~~ 192 (590)
...|+||.+.+... .+..++|||.||..|+..|-+.. -.|| .|+..
T Consensus 291 ~~~C~IC~e~l~~~~~~~~~rL~C~Hifh~~CL~~W~er~----qtCP--~CR~~ 339 (543)
T KOG0802|consen 291 DELCIICLEELHSGHNITPKRLPCGHIFHDSCLRSWFERQ----QTCP--TCRTV 339 (543)
T ss_pred CCeeeeechhhccccccccceeecccchHHHHHHHHHHHh----CcCC--cchhh
Confidence 56899999987431 15778999999999997665543 5899 77763
No 76
>KOG1428 consensus Inhibitor of type V adenylyl cyclases/Neuronal presynaptic protein Highwire/PAM/RPM-1 [Signal transduction mechanisms]
Probab=83.47 E-value=1.4 Score=53.39 Aligned_cols=62 Identities=23% Similarity=0.498 Sum_probs=45.8
Q ss_pred ccccccccccc-CCCCceecCCCCccchhhHHHh----hcCCCc--eecccCCCCCCCccchhHHhhcCCh
Q 007763 141 EMTCGICFENY-PSDRLLAAACGHPFCSSCWTAI----NDGPGC--LMLRCPDPSCGAAVGQDMIYLLSSD 204 (590)
Q Consensus 141 ~~~C~IC~e~~-~~~~~~~l~CgH~fC~~C~~~i----~~g~~~--~~i~CP~~~C~~~i~~~~i~~ll~~ 204 (590)
...|.|||.+- .....+.+.|+|.|...|...| +.|+.+ ..|+|| -|+..|..-.++.|+.+
T Consensus 3486 DDmCmICFTE~L~AAP~IqL~C~HiFHlqC~R~vLE~RW~GPRItF~FisCP--iC~n~InH~~LkDLldP 3554 (3738)
T KOG1428|consen 3486 DDMCMICFTEALSAAPAIQLDCSHIFHLQCCRRVLENRWLGPRITFGFISCP--ICKNKINHIVLKDLLDP 3554 (3738)
T ss_pred CceEEEEehhhhCCCcceecCCccchhHHHHHHHHHhcccCCeeEEeeeecc--cccchhhhHHHHHHHHH
Confidence 45799999763 3334578899999999999333 445533 369999 89999988777777763
No 77
>COG5222 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=83.10 E-value=0.8 Score=46.62 Aligned_cols=42 Identities=33% Similarity=0.942 Sum_probs=31.8
Q ss_pred ccccccccccCCCCce-ecCCCCccchhhH-HHhhcCCCceecccCCCCCCC
Q 007763 142 MTCGICFENYPSDRLL-AAACGHPFCSSCW-TAINDGPGCLMLRCPDPSCGA 191 (590)
Q Consensus 142 ~~C~IC~e~~~~~~~~-~l~CgH~fC~~C~-~~i~~g~~~~~i~CP~~~C~~ 191 (590)
+.|+.|-..+ .+++ +..|+|.||..|+ +++.+. .+.|| .|..
T Consensus 275 LkCplc~~Ll--rnp~kT~cC~~~fc~eci~~al~ds----Df~Cp--nC~r 318 (427)
T COG5222 275 LKCPLCHCLL--RNPMKTPCCGHTFCDECIGTALLDS----DFKCP--NCSR 318 (427)
T ss_pred ccCcchhhhh--hCcccCccccchHHHHHHhhhhhhc----cccCC--Cccc
Confidence 6799998765 4444 4469999999999 666654 48999 7764
No 78
>PF11793 FANCL_C: FANCL C-terminal domain; PDB: 3K1L_A.
Probab=82.72 E-value=0.86 Score=36.89 Aligned_cols=53 Identities=23% Similarity=0.692 Sum_probs=20.1
Q ss_pred cccccccccccC-CCCc--ee---cCCCCccchhhHHH----hhcCCC---ceecccCCCCCCCccch
Q 007763 141 EMTCGICFENYP-SDRL--LA---AACGHPFCSSCWTA----INDGPG---CLMLRCPDPSCGAAVGQ 195 (590)
Q Consensus 141 ~~~C~IC~e~~~-~~~~--~~---l~CgH~fC~~C~~~----i~~g~~---~~~i~CP~~~C~~~i~~ 195 (590)
+..|+||+.... .... +. ..|++.|...|+.. ...+.. ...=.|| .|+..|.-
T Consensus 2 ~~~C~IC~~~~~~~~~~p~~~C~n~~C~~~fH~~CL~~wf~~~~~~~~~~~~~~G~CP--~C~~~i~~ 67 (70)
T PF11793_consen 2 ELECGICYSYRLDDGEIPDVVCPNPSCGKKFHLLCLSEWFLSLEKSRQSFIPIFGECP--YCSSPISW 67 (70)
T ss_dssp --S-SSS--SS-TT-----B--S-TT----B-SGGGHHHHHHHHSSS-TTT--EEE-T--TT-SEEEG
T ss_pred CCCCCcCCcEecCCCCcCceEcCCcccCCHHHHHHHHHHHHHcccCCeeecccccCCc--CCCCeeeE
Confidence 457999998754 2222 11 25889999999922 222211 1123699 89988754
No 79
>KOG1645 consensus RING-finger-containing E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=81.71 E-value=1.3 Score=47.09 Aligned_cols=49 Identities=33% Similarity=0.802 Sum_probs=37.2
Q ss_pred cccccccccccCC---CCceecCCCCccchhhHHHhhcCCCceecccCCCCCCCcc
Q 007763 141 EMTCGICFENYPS---DRLLAAACGHPFCSSCWTAINDGPGCLMLRCPDPSCGAAV 193 (590)
Q Consensus 141 ~~~C~IC~e~~~~---~~~~~l~CgH~fC~~C~~~i~~g~~~~~i~CP~~~C~~~i 193 (590)
..+||||++.+.. ..++++.|||.|=.+|+..+- + .+....|| .|...-
T Consensus 4 g~tcpiclds~~~~g~hr~vsl~cghlFgs~cie~wl-~-k~~~~~cp--~c~~ka 55 (463)
T KOG1645|consen 4 GTTCPICLDSYTTAGNHRIVSLQCGHLFGSQCIEKWL-G-KKTKMQCP--LCSGKA 55 (463)
T ss_pred cccCceeeeeeeecCceEEeeecccccccHHHHHHHH-h-hhhhhhCc--ccCChh
Confidence 4689999998642 367889999999999996554 3 34678999 787543
No 80
>smart00661 RPOL9 RNA polymerase subunit 9.
Probab=81.27 E-value=1.2 Score=33.38 Aligned_cols=27 Identities=26% Similarity=0.719 Sum_probs=20.1
Q ss_pred cCCCCCCcceeecc--CCCceeecCCCcce
Q 007763 295 KPCPRCKRPIEKNQ--GCMHMTCTPPCKFE 322 (590)
Q Consensus 295 K~CP~C~~~IEK~~--GCnhMtC~~~C~~~ 322 (590)
+-||.|+.++.... +-++..|. .||+.
T Consensus 1 ~FCp~Cg~~l~~~~~~~~~~~vC~-~Cg~~ 29 (52)
T smart00661 1 KFCPKCGNMLIPKEGKEKRRFVCR-KCGYE 29 (52)
T ss_pred CCCCCCCCccccccCCCCCEEECC-cCCCe
Confidence 36999999887543 34688898 78865
No 81
>KOG0823 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=81.24 E-value=0.56 Score=46.37 Aligned_cols=20 Identities=45% Similarity=1.105 Sum_probs=16.6
Q ss_pred eeecCCCcceeeecccccccCCC
Q 007763 313 MTCTPPCKFEFCWLCLGQWSDHG 335 (590)
Q Consensus 313 MtC~~~C~~~FCw~C~~~w~~H~ 335 (590)
+|| |||-|||-|+-.|-.+.
T Consensus 62 vTl---CGHLFCWpClyqWl~~~ 81 (230)
T KOG0823|consen 62 VTL---CGHLFCWPCLYQWLQTR 81 (230)
T ss_pred Eee---cccceehHHHHHHHhhc
Confidence 565 99999999999997554
No 82
>KOG4185 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=79.82 E-value=1.6 Score=45.30 Aligned_cols=48 Identities=29% Similarity=0.684 Sum_probs=36.0
Q ss_pred cccccccccccCCC----CceecCCCCccchhhHHHhhcCCCceecccCCCCCCCcc
Q 007763 141 EMTCGICFENYPSD----RLLAAACGHPFCSSCWTAINDGPGCLMLRCPDPSCGAAV 193 (590)
Q Consensus 141 ~~~C~IC~e~~~~~----~~~~l~CgH~fC~~C~~~i~~g~~~~~i~CP~~~C~~~i 193 (590)
...|.||-+++... -|..+.|||.+|..|...+-.. ..+.|| .|+...
T Consensus 3 ~~~c~~c~~~~s~~~~~~~p~~l~c~h~~c~~c~~~l~~~---~~i~cp--fcR~~~ 54 (296)
T KOG4185|consen 3 FPECEICNEDYSSEDGDHIPRVLKCGHTICQNCASKLLGN---SRILCP--FCRETT 54 (296)
T ss_pred CCceeecCccccccCcccCCcccccCceehHhHHHHHhcC---ceeecc--CCCCcc
Confidence 35699999988654 3456779999999999666544 247787 899883
No 83
>KOG0827 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=79.58 E-value=0.82 Score=48.28 Aligned_cols=54 Identities=30% Similarity=0.672 Sum_probs=37.9
Q ss_pred ccccccccccCCC-CceecC-CCCccchhhHHHhhcCCCceecccCCCCCCCccchhHH
Q 007763 142 MTCGICFENYPSD-RLLAAA-CGHPFCSSCWTAINDGPGCLMLRCPDPSCGAAVGQDMI 198 (590)
Q Consensus 142 ~~C~IC~e~~~~~-~~~~l~-CgH~fC~~C~~~i~~g~~~~~i~CP~~~C~~~i~~~~i 198 (590)
-.|.||-+.+|.. +..++. |||.|...|++.|.++.. ..-.|| .|+..++..++
T Consensus 5 A~C~Ic~d~~p~~~~l~~i~~cGhifh~~cl~qwfe~~P-s~R~cp--ic~ik~~~r~~ 60 (465)
T KOG0827|consen 5 AECHICIDGRPNDHELGPIGTCGHIFHTTCLTQWFEGDP-SNRGCP--ICQIKLQERHV 60 (465)
T ss_pred ceeeEeccCCccccccccccchhhHHHHHHHHHHHccCC-ccCCCC--ceeecccceee
Confidence 4699997776654 455666 999999999999988752 124788 67755444433
No 84
>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=78.64 E-value=1.8 Score=29.10 Aligned_cols=27 Identities=26% Similarity=0.766 Sum_probs=14.9
Q ss_pred cCCCCCCcceeeccCCCceeecCCCccee
Q 007763 295 KPCPRCKRPIEKNQGCMHMTCTPPCKFEF 323 (590)
Q Consensus 295 K~CP~C~~~IEK~~GCnhMtC~~~C~~~F 323 (590)
-+||+|+....-.+|.+ |.|. .|+++|
T Consensus 3 p~Cp~C~se~~y~D~~~-~vCp-~C~~ew 29 (30)
T PF08274_consen 3 PKCPLCGSEYTYEDGEL-LVCP-ECGHEW 29 (30)
T ss_dssp ---TTT-----EE-SSS-EEET-TTTEEE
T ss_pred CCCCCCCCcceeccCCE-EeCC-cccccC
Confidence 37999999888777766 8898 898876
No 85
>KOG1001 consensus Helicase-like transcription factor HLTF/DNA helicase RAD5, DEAD-box superfamily [Transcription; Replication, recombination and repair]
Probab=78.30 E-value=0.98 Score=52.27 Aligned_cols=46 Identities=30% Similarity=0.814 Sum_probs=34.6
Q ss_pred ccccccccccCCCCceecCCCCccchhhH-HHhhcCCCceecccCCCCCCCccch
Q 007763 142 MTCGICFENYPSDRLLAAACGHPFCSSCW-TAINDGPGCLMLRCPDPSCGAAVGQ 195 (590)
Q Consensus 142 ~~C~IC~e~~~~~~~~~l~CgH~fC~~C~-~~i~~g~~~~~i~CP~~~C~~~i~~ 195 (590)
+.|+||.+ .+.++...|||.||..|| ..|.... ...|| .|+..+..
T Consensus 455 ~~c~ic~~---~~~~~it~c~h~~c~~c~~~~i~~~~---~~~~~--~cr~~l~~ 501 (674)
T KOG1001|consen 455 HWCHICCD---LDSFFITRCGHDFCVECLKKSIQQSE---NAPCP--LCRNVLKE 501 (674)
T ss_pred cccccccc---cccceeecccchHHHHHHHhcccccc---CCCCc--HHHHHHHH
Confidence 78999999 378899999999999999 4444322 23777 78766543
No 86
>PF14447 Prok-RING_4: Prokaryotic RING finger family 4
Probab=78.04 E-value=1.1 Score=34.41 Aligned_cols=46 Identities=28% Similarity=0.604 Sum_probs=30.1
Q ss_pred cccccccccccCCCCceecCCCCccchhhHHHhhcCCCceecccCCCCCCCccchh
Q 007763 141 EMTCGICFENYPSDRLLAAACGHPFCSSCWTAINDGPGCLMLRCPDPSCGAAVGQD 196 (590)
Q Consensus 141 ~~~C~IC~e~~~~~~~~~l~CgH~fC~~C~~~i~~g~~~~~i~CP~~~C~~~i~~~ 196 (590)
...|-.|.... ...+.++|||..|..||.-- .--.|| .|...|...
T Consensus 7 ~~~~~~~~~~~--~~~~~~pCgH~I~~~~f~~~------rYngCP--fC~~~~~~~ 52 (55)
T PF14447_consen 7 EQPCVFCGFVG--TKGTVLPCGHLICDNCFPGE------RYNGCP--FCGTPFEFD 52 (55)
T ss_pred ceeEEEccccc--cccccccccceeeccccChh------hccCCC--CCCCcccCC
Confidence 34455555432 45678899999999999211 113588 888877543
No 87
>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=77.90 E-value=0.91 Score=41.34 Aligned_cols=33 Identities=27% Similarity=0.691 Sum_probs=27.2
Q ss_pred cccccccccccCC-CCceecCCC------CccchhhHHHh
Q 007763 141 EMTCGICFENYPS-DRLLAAACG------HPFCSSCWTAI 173 (590)
Q Consensus 141 ~~~C~IC~e~~~~-~~~~~l~Cg------H~fC~~C~~~i 173 (590)
..+|.||++.... +-.+.++|| |.||.+|+..+
T Consensus 26 ~~EC~IC~~~I~~~~GvV~vt~~g~lnLEkmfc~~C~~rw 65 (134)
T PF05883_consen 26 TVECQICFDRIDNNDGVVYVTDGGTLNLEKMFCADCDKRW 65 (134)
T ss_pred CeeehhhhhhhhcCCCEEEEecCCeehHHHHHHHHHHHHH
Confidence 5789999999876 456778886 88999999766
No 88
>PHA00626 hypothetical protein
Probab=77.85 E-value=1.7 Score=33.25 Aligned_cols=28 Identities=25% Similarity=0.692 Sum_probs=20.2
Q ss_pred CCCCCCc-ceeeccCCCc----eeecCCCcceee
Q 007763 296 PCPRCKR-PIEKNQGCMH----MTCTPPCKFEFC 324 (590)
Q Consensus 296 ~CP~C~~-~IEK~~GCnh----MtC~~~C~~~FC 324 (590)
.||+|+. -|-|++-|+. -.|. .||+.|=
T Consensus 2 ~CP~CGS~~Ivrcg~cr~~snrYkCk-dCGY~ft 34 (59)
T PHA00626 2 SCPKCGSGNIAKEKTMRGWSDDYVCC-DCGYNDS 34 (59)
T ss_pred CCCCCCCceeeeeceecccCcceEcC-CCCCeec
Confidence 5999999 4778777655 5676 6777663
No 89
>KOG0297 consensus TNF receptor-associated factor [Signal transduction mechanisms]
Probab=77.34 E-value=2.6 Score=45.73 Aligned_cols=47 Identities=28% Similarity=0.779 Sum_probs=33.3
Q ss_pred CCcccccccccccCCCCcee-cCCCCccchhhHHHhhcCCCceecccCCCCCCCcc
Q 007763 139 GEEMTCGICFENYPSDRLLA-AACGHPFCSSCWTAINDGPGCLMLRCPDPSCGAAV 193 (590)
Q Consensus 139 ~~~~~C~IC~e~~~~~~~~~-l~CgH~fC~~C~~~i~~g~~~~~i~CP~~~C~~~i 193 (590)
.....|++|...+ .+++. ..|||.||..|+..+... ...|| .|...+
T Consensus 19 ~~~l~C~~C~~vl--~~p~~~~~cgh~fC~~C~~~~~~~----~~~cp--~~~~~~ 66 (391)
T KOG0297|consen 19 DENLLCPICMSVL--RDPVQTTTCGHRFCAGCLLESLSN----HQKCP--VCRQEL 66 (391)
T ss_pred cccccCccccccc--cCCCCCCCCCCcccccccchhhcc----CcCCc--cccccc
Confidence 4568899999887 55665 699999999999444322 35777 565443
No 90
>PF12861 zf-Apc11: Anaphase-promoting complex subunit 11 RING-H2 finger
Probab=77.05 E-value=2.5 Score=35.48 Aligned_cols=34 Identities=21% Similarity=0.408 Sum_probs=23.7
Q ss_pred eecCCCCccchhhHHHhhcCCCceecccCCCCCCCcc
Q 007763 157 LAAACGHPFCSSCWTAINDGPGCLMLRCPDPSCGAAV 193 (590)
Q Consensus 157 ~~l~CgH~fC~~C~~~i~~g~~~~~i~CP~~~C~~~i 193 (590)
+.-.|+|.|..-|+..+.+.+. ..-.|| -|++.+
T Consensus 48 v~g~C~H~FH~hCI~kWl~~~~-~~~~CP--mCR~~w 81 (85)
T PF12861_consen 48 VWGKCSHNFHMHCILKWLSTQS-SKGQCP--MCRQPW 81 (85)
T ss_pred eeccCccHHHHHHHHHHHcccc-CCCCCC--CcCCee
Confidence 3345999999999966544432 235899 788765
No 91
>PF14835 zf-RING_6: zf-RING of BARD1-type protein; PDB: 1JM7_B.
Probab=76.89 E-value=1.3 Score=35.07 Aligned_cols=22 Identities=27% Similarity=0.765 Sum_probs=9.2
Q ss_pred cCCCCCCcceeec---cCCCceeec
Q 007763 295 KPCPRCKRPIEKN---QGCMHMTCT 316 (590)
Q Consensus 295 K~CP~C~~~IEK~---~GCnhMtC~ 316 (590)
-.|++|...+... +||-|++|+
T Consensus 8 LrCs~C~~~l~~pv~l~~CeH~fCs 32 (65)
T PF14835_consen 8 LRCSICFDILKEPVCLGGCEHIFCS 32 (65)
T ss_dssp TS-SSS-S--SS-B---SSS--B-T
T ss_pred cCCcHHHHHhcCCceeccCccHHHH
Confidence 6899998877643 565555555
No 92
>KOG1734 consensus Predicted RING-containing E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=76.87 E-value=2 Score=43.42 Aligned_cols=70 Identities=17% Similarity=0.398 Sum_probs=44.2
Q ss_pred HHHHHcCCCCCCCCCCCCCCcccccccccccCCC--------CceecCCCCccchhhHHHhh-cCCCceecccCCCCCCC
Q 007763 121 RVRKAVGLLEKPAVQFPDGEEMTCGICFENYPSD--------RLLAAACGHPFCSSCWTAIN-DGPGCLMLRCPDPSCGA 191 (590)
Q Consensus 121 ~~~~~~gl~~~~~~~~~~~~~~~C~IC~e~~~~~--------~~~~l~CgH~fC~~C~~~i~-~g~~~~~i~CP~~~C~~ 191 (590)
.+...+|.-.+...+....+...|.||-..+..+ ++..++|+|.|...|+.-+- -|. .-.|| -|+.
T Consensus 204 ~mAs~iGfYs~~glPtkhl~d~vCaVCg~~~~~s~~eegvienty~LsCnHvFHEfCIrGWcivGK---kqtCP--YCKe 278 (328)
T KOG1734|consen 204 YMASTIGFYSPSGLPTKHLSDSVCAVCGQQIDVSVDEEGVIENTYKLSCNHVFHEFCIRGWCIVGK---KQTCP--YCKE 278 (328)
T ss_pred HHHHHhcccCCCCCCCCCCCcchhHhhcchheeecchhhhhhhheeeecccchHHHhhhhheeecC---CCCCc--hHHH
Confidence 3444455544333333334566799998765432 56789999999999994331 232 35899 8987
Q ss_pred ccch
Q 007763 192 AVGQ 195 (590)
Q Consensus 192 ~i~~ 195 (590)
.+..
T Consensus 279 kVdl 282 (328)
T KOG1734|consen 279 KVDL 282 (328)
T ss_pred HhhH
Confidence 7643
No 93
>PF10446 DUF2457: Protein of unknown function (DUF2457); InterPro: IPR018853 This entry represents a family of uncharacterised proteins.
Probab=76.66 E-value=2.7 Score=45.47 Aligned_cols=11 Identities=36% Similarity=1.102 Sum_probs=7.5
Q ss_pred CCCCCcccccc
Q 007763 136 FPDGEEMTCGI 146 (590)
Q Consensus 136 ~~~~~~~~C~I 146 (590)
+|.+..|.|+-
T Consensus 189 LPDSTDFVCGT 199 (458)
T PF10446_consen 189 LPDSTDFVCGT 199 (458)
T ss_pred CCCcccccCCC
Confidence 45666787775
No 94
>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=76.55 E-value=3.3 Score=28.01 Aligned_cols=29 Identities=31% Similarity=0.699 Sum_probs=18.2
Q ss_pred cCcCCCCCCcceeeccCCCceeecCCCcce
Q 007763 293 NSKPCPRCKRPIEKNQGCMHMTCTPPCKFE 322 (590)
Q Consensus 293 ntK~CP~C~~~IEK~~GCnhMtC~~~C~~~ 322 (590)
+.+-||+|+.+.....+=--|.|. .|++.
T Consensus 2 ~~rfC~~CG~~t~~~~~g~~r~C~-~Cg~~ 30 (32)
T PF09297_consen 2 NHRFCGRCGAPTKPAPGGWARRCP-SCGHE 30 (32)
T ss_dssp TTSB-TTT--BEEE-SSSS-EEES-SSS-E
T ss_pred CCcccCcCCccccCCCCcCEeECC-CCcCE
Confidence 357899999999988776678897 78865
No 95
>PRK14559 putative protein serine/threonine phosphatase; Provisional
Probab=75.69 E-value=1.9 Score=49.66 Aligned_cols=23 Identities=30% Similarity=0.768 Sum_probs=16.2
Q ss_pred cCCCCCCcceeeccCCCceeecCCCcceeeeccccc
Q 007763 295 KPCPRCKRPIEKNQGCMHMTCTPPCKFEFCWLCLGQ 330 (590)
Q Consensus 295 K~CP~C~~~IEK~~GCnhMtC~~~C~~~FCw~C~~~ 330 (590)
+.||+|+..+. =+..||..||.+
T Consensus 28 ~~Cp~CG~~~~-------------~~~~fC~~CG~~ 50 (645)
T PRK14559 28 KPCPQCGTEVP-------------VDEAHCPNCGAE 50 (645)
T ss_pred CcCCCCCCCCC-------------cccccccccCCc
Confidence 56888777765 455588888765
No 96
>KOG0828 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=74.93 E-value=1.4 Score=48.04 Aligned_cols=51 Identities=24% Similarity=0.501 Sum_probs=36.8
Q ss_pred CcccccccccccCCC-----C----------ceecCCCCccchhhHHHhhcCCCceecccCCCCCCCccch
Q 007763 140 EEMTCGICFENYPSD-----R----------LLAAACGHPFCSSCWTAINDGPGCLMLRCPDPSCGAAVGQ 195 (590)
Q Consensus 140 ~~~~C~IC~e~~~~~-----~----------~~~l~CgH~fC~~C~~~i~~g~~~~~i~CP~~~C~~~i~~ 195 (590)
....|.||+.+.+.. . ....||.|.|...|+..+.++ ..+.|| .|+..+++
T Consensus 570 ~t~dC~ICMt~I~l~~~~s~~~~~~~~~~~nYm~tPC~HifH~~CL~~WMd~---ykl~CP--vCR~pLPp 635 (636)
T KOG0828|consen 570 RTNDCVICMTPIDLRSTGSDCMVASMMVRRNYMLTPCHHIFHRQCLLQWMDT---YKLICP--VCRCPLPP 635 (636)
T ss_pred ccccceEeccccceeeccCcchhhhhhhhccccccchHHHHHHHHHHHHHhh---hcccCC--ccCCCCCC
Confidence 356799999876421 1 112489999999999877775 358899 78877764
No 97
>PF14952 zf-tcix: Putative treble-clef, zinc-finger, Zn-binding
Probab=74.15 E-value=2.3 Score=30.93 Aligned_cols=31 Identities=23% Similarity=0.540 Sum_probs=21.8
Q ss_pred HHHHhcCcCCCCCCcceeeccCCCceeecC-CCcce
Q 007763 288 NWILANSKPCPRCKRPIEKNQGCMHMTCTP-PCKFE 322 (590)
Q Consensus 288 ~wi~~ntK~CP~C~~~IEK~~GCnhMtC~~-~C~~~ 322 (590)
.|++...+.||+|+..- |+--+.|.+ .|.+.
T Consensus 5 k~TlRGirkCp~CGt~N----G~R~~~CKN~~C~~~ 36 (44)
T PF14952_consen 5 KPTLRGIRKCPKCGTYN----GTRGLSCKNKSCPQV 36 (44)
T ss_pred hhhHhccccCCcCcCcc----CcccccccCCccchh
Confidence 45666779999999864 666677764 45543
No 98
>PF04641 Rtf2: Rtf2 RING-finger
Probab=73.56 E-value=4 Score=41.75 Aligned_cols=69 Identities=17% Similarity=0.446 Sum_probs=45.8
Q ss_pred CCCcccccccccccCCC-Cceec-CCCCccchhhHHHhhcCCCceecccCCCCCCCccchhHHhhcCC-hHHHHHHHHH
Q 007763 138 DGEEMTCGICFENYPSD-RLLAA-ACGHPFCSSCWTAINDGPGCLMLRCPDPSCGAAVGQDMIYLLSS-DEDKVKYNRY 213 (590)
Q Consensus 138 ~~~~~~C~IC~e~~~~~-~~~~l-~CgH~fC~~C~~~i~~g~~~~~i~CP~~~C~~~i~~~~i~~ll~-~e~~eky~~~ 213 (590)
....+.|||....+... .++.+ +|||.|+..++..+. . .-.|| .|...|....|-.|-+ .+.++.....
T Consensus 110 ~~~~~~CPvt~~~~~~~~~fv~l~~cG~V~s~~alke~k-~----~~~Cp--~c~~~f~~~DiI~Lnp~~ee~~~l~~~ 181 (260)
T PF04641_consen 110 SEGRFICPVTGKEFNGKHKFVYLRPCGCVFSEKALKELK-K----SKKCP--VCGKPFTEEDIIPLNPPEEELEKLRER 181 (260)
T ss_pred CCceeECCCCCcccCCceeEEEEcCCCCEeeHHHHHhhc-c----ccccc--ccCCccccCCEEEecCCccHHHHHHHH
Confidence 35678999999888543 34444 799999999997775 1 13599 8999987655443333 3344444433
No 99
>PLN03086 PRLI-interacting factor K; Provisional
Probab=73.25 E-value=5.1 Score=45.30 Aligned_cols=57 Identities=23% Similarity=0.510 Sum_probs=33.7
Q ss_pred eecccCCCCCCCccchhHHhhcCChHHHHHHHHHHHHHHhhcCCCcccCCCCCCCceEeeecCCCcceeEe-cCCCcc
Q 007763 180 LMLRCPDPSCGAAVGQDMIYLLSSDEDKVKYNRYFIRSYVEDNRKTKWCPAPGCDYAVDFVVGSGNYDVTC-RCSYSF 256 (590)
Q Consensus 180 ~~i~CP~~~C~~~i~~~~i~~ll~~e~~eky~~~l~~~~v~~~~~~~~CP~p~C~~~i~~~~~~~~~~v~C-~C~~~f 256 (590)
..+.|| .|+..++...+..... .-....+-||..+|+..+..... ...+.| .|+..|
T Consensus 406 ~~V~C~--NC~~~i~l~~l~lHe~----------------~C~r~~V~Cp~~~Cg~v~~r~el--~~H~~C~~Cgk~f 463 (567)
T PLN03086 406 DTVECR--NCKHYIPSRSIALHEA----------------YCSRHNVVCPHDGCGIVLRVEEA--KNHVHCEKCGQAF 463 (567)
T ss_pred CeEECC--CCCCccchhHHHHHHh----------------hCCCcceeCCcccccceeecccc--ccCccCCCCCCcc
Confidence 357899 5988876654421110 11123568998789988865422 233467 676655
No 100
>KOG0825 consensus PHD Zn-finger protein [General function prediction only]
Probab=73.06 E-value=1.1 Score=51.26 Aligned_cols=48 Identities=19% Similarity=0.425 Sum_probs=26.4
Q ss_pred ccccccccccCCCCc-eecCCCCccchhhHHHhhcCCCceecccCCCCCCCccch
Q 007763 142 MTCGICFENYPSDRL-LAAACGHPFCSSCWTAINDGPGCLMLRCPDPSCGAAVGQ 195 (590)
Q Consensus 142 ~~C~IC~e~~~~~~~-~~l~CgH~fC~~C~~~i~~g~~~~~i~CP~~~C~~~i~~ 195 (590)
-.|++|+..+..... ....|+|.||..|+..|.... -.|| .|+..|..
T Consensus 124 ~~CP~Ci~s~~DqL~~~~k~c~H~FC~~Ci~sWsR~a----qTCP--iDR~EF~~ 172 (1134)
T KOG0825|consen 124 NQCPNCLKSCNDQLEESEKHTAHYFCEECVGSWSRCA----QTCP--VDRGEFGE 172 (1134)
T ss_pred hhhhHHHHHHHHHhhccccccccccHHHHhhhhhhhc----ccCc--hhhhhhhe
Confidence 346666655432222 223577777777775554332 3576 66666543
No 101
>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=72.81 E-value=1.3 Score=31.21 Aligned_cols=32 Identities=28% Similarity=0.860 Sum_probs=21.5
Q ss_pred CCCCCcceeeccCCCceeecCCCcceeeecccccccCC
Q 007763 297 CPRCKRPIEKNQGCMHMTCTPPCKFEFCWLCLGQWSDH 334 (590)
Q Consensus 297 CP~C~~~IEK~~GCnhMtC~~~C~~~FCw~C~~~w~~H 334 (590)
||-|...+.. .+.-. +|||.||+.|...|...
T Consensus 1 C~iC~~~~~~-----~~~~~-~CGH~fC~~C~~~~~~~ 32 (39)
T PF13923_consen 1 CPICLDELRD-----PVVVT-PCGHSFCKECIEKYLEK 32 (39)
T ss_dssp ETTTTSB-SS-----EEEEC-TTSEEEEHHHHHHHHHC
T ss_pred CCCCCCcccC-----cCEEC-CCCCchhHHHHHHHHHC
Confidence 5556555542 34555 69999999999887543
No 102
>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=71.48 E-value=3.3 Score=31.04 Aligned_cols=43 Identities=19% Similarity=0.417 Sum_probs=29.0
Q ss_pred cccccccccCCCCceecCCC-----CccchhhHHHhhcCCCceecccCCCCC
Q 007763 143 TCGICFENYPSDRLLAAACG-----HPFCSSCWTAINDGPGCLMLRCPDPSC 189 (590)
Q Consensus 143 ~C~IC~e~~~~~~~~~l~Cg-----H~fC~~C~~~i~~g~~~~~i~CP~~~C 189 (590)
.|-||++.....++...||. |.+...|+..+-... ...+|| .|
T Consensus 1 ~CrIC~~~~~~~~~l~~PC~C~G~~~~vH~~Cl~~W~~~~--~~~~C~--iC 48 (49)
T smart00744 1 ICRICHDEGDEGDPLVSPCRCKGSLKYVHQECLERWINES--GNKTCE--IC 48 (49)
T ss_pred CccCCCCCCCCCCeeEeccccCCchhHHHHHHHHHHHHHc--CCCcCC--CC
Confidence 38899984444566777875 789999995554332 235888 55
No 103
>PF13719 zinc_ribbon_5: zinc-ribbon domain
Probab=71.40 E-value=3.1 Score=29.25 Aligned_cols=29 Identities=28% Similarity=0.670 Sum_probs=21.3
Q ss_pred ccCCCCCCCceEeeecC---CCcceeEe-cCCCcc
Q 007763 226 KWCPAPGCDYAVDFVVG---SGNYDVTC-RCSYSF 256 (590)
Q Consensus 226 ~~CP~p~C~~~i~~~~~---~~~~~v~C-~C~~~f 256 (590)
..||+ |+........ .+...|.| .|++.|
T Consensus 3 i~CP~--C~~~f~v~~~~l~~~~~~vrC~~C~~~f 35 (37)
T PF13719_consen 3 ITCPN--CQTRFRVPDDKLPAGGRKVRCPKCGHVF 35 (37)
T ss_pred EECCC--CCceEEcCHHHcccCCcEEECCCCCcEe
Confidence 57885 9988776543 34568899 899876
No 104
>KOG4275 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=70.94 E-value=1.3 Score=45.23 Aligned_cols=40 Identities=30% Similarity=0.781 Sum_probs=29.1
Q ss_pred cccccccccccCCCCceecCCCCc-cchhhHHHhhcCCCceecccCCCCCCCc
Q 007763 141 EMTCGICFENYPSDRLLAAACGHP-FCSSCWTAINDGPGCLMLRCPDPSCGAA 192 (590)
Q Consensus 141 ~~~C~IC~e~~~~~~~~~l~CgH~-fC~~C~~~i~~g~~~~~i~CP~~~C~~~ 192 (590)
...|.||++.. .+-+.|+|||. -|..|-+.++ .|| -|+..
T Consensus 300 ~~LC~ICmDaP--~DCvfLeCGHmVtCt~CGkrm~--------eCP--ICRqy 340 (350)
T KOG4275|consen 300 RRLCAICMDAP--RDCVFLECGHMVTCTKCGKRMN--------ECP--ICRQY 340 (350)
T ss_pred HHHHHHHhcCC--cceEEeecCcEEeehhhccccc--------cCc--hHHHH
Confidence 56799999864 67899999994 5666643332 688 67543
No 105
>KOG4172 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=70.30 E-value=1.3 Score=33.80 Aligned_cols=45 Identities=29% Similarity=0.673 Sum_probs=31.4
Q ss_pred ccccccccccCCCCceecCCCCc-cchhhHHHhhcCCCceecccCCCCCCCcc
Q 007763 142 MTCGICFENYPSDRLLAAACGHP-FCSSCWTAINDGPGCLMLRCPDPSCGAAV 193 (590)
Q Consensus 142 ~~C~IC~e~~~~~~~~~l~CgH~-fC~~C~~~i~~g~~~~~i~CP~~~C~~~i 193 (590)
-+|.||++.. -+.+.-.|||. .|..|-..++.+. .=.|| -|+.++
T Consensus 8 dECTICye~p--vdsVlYtCGHMCmCy~Cg~rl~~~~---~g~CP--iCRapi 53 (62)
T KOG4172|consen 8 DECTICYEHP--VDSVLYTCGHMCMCYACGLRLKKAL---HGCCP--ICRAPI 53 (62)
T ss_pred cceeeeccCc--chHHHHHcchHHhHHHHHHHHHHcc---CCcCc--chhhHH
Confidence 5699999863 44566679996 7888884444432 24788 788765
No 106
>KOG1991 consensus Nuclear transport receptor RANBP7/RANBP8 (importin beta superfamily) [Nuclear structure; Intracellular trafficking, secretion, and vesicular transport]
Probab=68.91 E-value=8.7 Score=45.51 Aligned_cols=40 Identities=20% Similarity=0.101 Sum_probs=21.5
Q ss_pred eCHHHHHHHHHHHHHHHHHHhCCCHHHHHHHHHhcCCChHHHH
Q 007763 70 LTEADIRQRQEEDITRISTVLSISKVAASILLRFYNWSVSKVH 112 (590)
Q Consensus 70 l~~~~i~~~~~~~i~~v~~il~i~~~~a~~LL~~~~W~~~~l~ 112 (590)
|.+-|......+.+..++. -.+.-...|+++..-...+++
T Consensus 955 LD~VD~f~~f~~~i~~lq~---~d~~~yq~l~~~L~~~q~~~l 994 (1010)
T KOG1991|consen 955 LDQVDPFQLFKEAITNLQS---SDAVRYQKLISTLTPEQQDSL 994 (1010)
T ss_pred ccccchHHHHHHHHHhhhc---cChHHHHHHHhcCCHHHHHHH
Confidence 6666666676666655543 344455555555544443333
No 107
>KOG0320 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=68.58 E-value=1.4 Score=41.94 Aligned_cols=30 Identities=37% Similarity=1.023 Sum_probs=22.0
Q ss_pred ecCCCccccccCCCcCCCCCchhHHHHHHhhhhhhhhHHHHHhcCcCCCCCCccee
Q 007763 250 CRCSYSFCWNCTEEAHRPVDCDTVAKWVLKNSAESENMNWILANSKPCPRCKRPIE 305 (590)
Q Consensus 250 C~C~~~fC~~C~~~~H~p~~C~~~~~w~~k~~~e~e~~~wi~~ntK~CP~C~~~IE 305 (590)
=.|||.||..|...+ ..++.+||-|++-|-
T Consensus 149 TkCGHvFC~~Cik~a--------------------------lk~~~~CP~C~kkIt 178 (187)
T KOG0320|consen 149 TKCGHVFCSQCIKDA--------------------------LKNTNKCPTCRKKIT 178 (187)
T ss_pred cccchhHHHHHHHHH--------------------------HHhCCCCCCcccccc
Confidence 379999999997432 234589999997664
No 108
>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=68.04 E-value=7 Score=40.09 Aligned_cols=50 Identities=26% Similarity=0.574 Sum_probs=32.2
Q ss_pred cccccccccCCC-Cc--eecCCCCccchhhHHHhhcCCCceecccCCCCCCCccchhH
Q 007763 143 TCGICFENYPSD-RL--LAAACGHPFCSSCWTAINDGPGCLMLRCPDPSCGAAVGQDM 197 (590)
Q Consensus 143 ~C~IC~e~~~~~-~~--~~l~CgH~fC~~C~~~i~~g~~~~~i~CP~~~C~~~i~~~~ 197 (590)
.||+|-...-.. .+ ..-+|+|..|.+|+..|..- .+..|| .|..++...-
T Consensus 2 ~Cp~CKt~~Y~np~lk~~in~C~H~lCEsCvd~iF~~---g~~~Cp--eC~~iLRk~n 54 (300)
T KOG3800|consen 2 ACPKCKTDRYLNPDLKLMINECGHRLCESCVDRIFSL---GPAQCP--ECMVILRKNN 54 (300)
T ss_pred CCcccccceecCccceeeeccccchHHHHHHHHHHhc---CCCCCC--cccchhhhcc
Confidence 488887652211 12 22279999999999555432 136899 8998875443
No 109
>PRK00432 30S ribosomal protein S27ae; Validated
Probab=66.79 E-value=2.6 Score=31.80 Aligned_cols=28 Identities=25% Similarity=0.622 Sum_probs=20.3
Q ss_pred cCcCCCCCCc-ceeeccCCCceeecCCCccee
Q 007763 293 NSKPCPRCKR-PIEKNQGCMHMTCTPPCKFEF 323 (590)
Q Consensus 293 ntK~CP~C~~-~IEK~~GCnhMtC~~~C~~~F 323 (590)
+-+-||+|+. .+.... +.++|. .||+.+
T Consensus 19 ~~~fCP~Cg~~~m~~~~--~r~~C~-~Cgyt~ 47 (50)
T PRK00432 19 KNKFCPRCGSGFMAEHL--DRWHCG-KCGYTE 47 (50)
T ss_pred ccCcCcCCCcchheccC--CcEECC-CcCCEE
Confidence 3479999988 444333 689999 899865
No 110
>PF13240 zinc_ribbon_2: zinc-ribbon domain
Probab=66.34 E-value=3.7 Score=25.75 Aligned_cols=22 Identities=27% Similarity=0.696 Sum_probs=19.3
Q ss_pred ccCCCCccCCCccccccccCCC
Q 007763 568 YCDQCTYANVNSATACAMCQHS 589 (590)
Q Consensus 568 ~c~~c~~~~~~~~~~c~~c~~~ 589 (590)
+|.+|...++..+.+|..|..+
T Consensus 1 ~Cp~CG~~~~~~~~fC~~CG~~ 22 (23)
T PF13240_consen 1 YCPNCGAEIEDDAKFCPNCGTP 22 (23)
T ss_pred CCcccCCCCCCcCcchhhhCCc
Confidence 5899999999999999999754
No 111
>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=66.11 E-value=4.2 Score=28.45 Aligned_cols=26 Identities=27% Similarity=0.759 Sum_probs=16.6
Q ss_pred CCCCCCcceeec------cCCCceeecCCCccee
Q 007763 296 PCPRCKRPIEKN------QGCMHMTCTPPCKFEF 323 (590)
Q Consensus 296 ~CP~C~~~IEK~------~GCnhMtC~~~C~~~F 323 (590)
.||+|+..+.-. .| ..+.|. .|++.|
T Consensus 4 ~CP~C~~~~~v~~~~~~~~~-~~v~C~-~C~~~~ 35 (38)
T TIGR02098 4 QCPNCKTSFRVVDSQLGANG-GKVRCG-KCGHVW 35 (38)
T ss_pred ECCCCCCEEEeCHHHcCCCC-CEEECC-CCCCEE
Confidence 588888855432 12 267887 687765
No 112
>KOG3002 consensus Zn finger protein [General function prediction only]
Probab=66.11 E-value=4.2 Score=42.41 Aligned_cols=47 Identities=32% Similarity=0.805 Sum_probs=34.0
Q ss_pred CCCcccccccccccCCCCceecCCCCccchhhHHHhhcCCCceecccCCCCCCCccc
Q 007763 138 DGEEMTCGICFENYPSDRLLAAACGHPFCSSCWTAINDGPGCLMLRCPDPSCGAAVG 194 (590)
Q Consensus 138 ~~~~~~C~IC~e~~~~~~~~~l~CgH~fC~~C~~~i~~g~~~~~i~CP~~~C~~~i~ 194 (590)
....+.||||++.+. ..+....=||..|.+|-..+ .-+|| .|+..++
T Consensus 45 ~~~lleCPvC~~~l~-~Pi~QC~nGHlaCssC~~~~-------~~~CP--~Cr~~~g 91 (299)
T KOG3002|consen 45 DLDLLDCPVCFNPLS-PPIFQCDNGHLACSSCRTKV-------SNKCP--TCRLPIG 91 (299)
T ss_pred chhhccCchhhccCc-ccceecCCCcEehhhhhhhh-------cccCC--ccccccc
Confidence 345688999999863 12334445899999998643 46899 6998887
No 113
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=65.47 E-value=5.6 Score=29.19 Aligned_cols=29 Identities=24% Similarity=0.623 Sum_probs=20.2
Q ss_pred cCCCCCCcceeeccCCCceeecCCCcceee
Q 007763 295 KPCPRCKRPIEKNQGCMHMTCTPPCKFEFC 324 (590)
Q Consensus 295 K~CP~C~~~IEK~~GCnhMtC~~~C~~~FC 324 (590)
-.||+|+..++-..+=..++|. .||..+=
T Consensus 4 y~C~~CG~~~~~~~~~~~~~Cp-~CG~~~~ 32 (46)
T PRK00398 4 YKCARCGREVELDEYGTGVRCP-YCGYRIL 32 (46)
T ss_pred EECCCCCCEEEECCCCCceECC-CCCCeEE
Confidence 4699999988765443368887 6776554
No 114
>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=65.34 E-value=1.9 Score=30.46 Aligned_cols=31 Identities=39% Similarity=1.023 Sum_probs=21.3
Q ss_pred CCCCCcceeeccCCCceeecCCCcceeeecccccccC
Q 007763 297 CPRCKRPIEKNQGCMHMTCTPPCKFEFCWLCLGQWSD 333 (590)
Q Consensus 297 CP~C~~~IEK~~GCnhMtC~~~C~~~FCw~C~~~w~~ 333 (590)
||-|...+.... +=. +|||.||..|+..|-.
T Consensus 1 C~iC~~~~~~~~-----~~~-~C~H~fC~~C~~~~~~ 31 (41)
T PF00097_consen 1 CPICLEPFEDPV-----ILL-PCGHSFCRDCLRKWLE 31 (41)
T ss_dssp ETTTSSBCSSEE-----EET-TTSEEEEHHHHHHHHH
T ss_pred CCcCCccccCCC-----EEe-cCCCcchHHHHHHHHH
Confidence 556666555332 334 6999999999988754
No 115
>KOG3039 consensus Uncharacterized conserved protein [Function unknown]
Probab=65.30 E-value=4.7 Score=40.30 Aligned_cols=53 Identities=11% Similarity=0.223 Sum_probs=36.9
Q ss_pred CcccccccccccCCCCc--eecCCCCccchhhHHHhhcCCCceecccCCCCCCCccchhHH
Q 007763 140 EEMTCGICFENYPSDRL--LAAACGHPFCSSCWTAINDGPGCLMLRCPDPSCGAAVGQDMI 198 (590)
Q Consensus 140 ~~~~C~IC~e~~~~~~~--~~l~CgH~fC~~C~~~i~~g~~~~~i~CP~~~C~~~i~~~~i 198 (590)
..+.|+||-+.+...-+ +.-+|||.||..|...+..+. ..|| .|...+....|
T Consensus 220 ~ryiCpvtrd~LtNt~~ca~Lr~sg~Vv~~ecvEklir~D----~v~p--v~d~plkdrdi 274 (303)
T KOG3039|consen 220 KRYICPVTRDTLTNTTPCAVLRPSGHVVTKECVEKLIRKD----MVDP--VTDKPLKDRDI 274 (303)
T ss_pred cceecccchhhhcCccceEEeccCCcEeeHHHHHHhcccc----cccc--CCCCcCcccce
Confidence 46789999998854333 334799999999996654443 5677 67776655443
No 116
>KOG2807 consensus RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit SSL1 [Transcription; Replication, recombination and repair]
Probab=64.50 E-value=5.4 Score=41.46 Aligned_cols=22 Identities=27% Similarity=0.714 Sum_probs=18.1
Q ss_pred CcceeEe-cCCCccccccCCCcC
Q 007763 244 GNYDVTC-RCSYSFCWNCTEEAH 265 (590)
Q Consensus 244 ~~~~v~C-~C~~~fC~~C~~~~H 265 (590)
....++| .|...||..|-.-.|
T Consensus 342 ~~~~y~C~~Ck~~FCldCDv~iH 364 (378)
T KOG2807|consen 342 SSGRYRCESCKNVFCLDCDVFIH 364 (378)
T ss_pred CCCcEEchhccceeeccchHHHH
Confidence 3456789 999999999987666
No 117
>PF00643 zf-B_box: B-box zinc finger; InterPro: IPR000315 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents B-box-type zinc finger domains, which are around 40 residues in length. B-box zinc fingers can be divided into two groups, where types 1 and 2 B-box domains differ in their consensus sequence and in the spacing of the 7-8 zinc-binding residues. Several proteins contain both types 1 and 2 B-boxes, suggesting some level of cooperativity between these two domains. B-box domains are found in over 1500 proteins from a variety of organisms. They are found in TRIM (tripartite motif) proteins that consist of an N-terminal RING finger (originally called an A-box), followed by 1-2 B-box domains and a coiled-coil domain (also called RBCC for Ring, B-box, Coiled-Coil). TRIM proteins contain a type 2 B-box domain, and may also contain a type 1 B-box. In proteins that do not contain RING or coiled-coil domains, the B-box domain is primarily type 2. Many type 2 B-box proteins are involved in ubiquitinylation. Proteins containing a B-box zinc finger domain include transcription factors, ribonucleoproteins and proto-oncoproteins; for example, MID1, MID2, TRIM9, TNL, TRIM36, TRIM63, TRIFIC, NCL1 and CONSTANS-like proteins []. The microtubule-associated E3 ligase MID1 (6.3.2 from EC) contains a type 1 B-box zinc finger domain. MID1 specifically binds Alpha-4, which in turn recruits the catalytic subunit of phosphatase 2A (PP2Ac). This complex is required for targeting of PP2Ac for proteasome-mediated degradation. The MID1 B-box coordinates two zinc ions and adopts a beta/beta/alpha cross-brace structure similar to that of ZZ, PHD, RING and FYVE zinc fingers [, ]. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0005622 intracellular; PDB: 3DDT_B 2D8U_A 3Q1D_A 2EGM_A 2YVR_B 2DJA_A 2DQ5_A 2JUN_A 2YRG_A 2DID_A ....
Probab=64.33 E-value=5.6 Score=28.28 Aligned_cols=29 Identities=21% Similarity=0.564 Sum_probs=24.8
Q ss_pred cCCCCCCcc-eeeccCCCceeecCCCcceeeecccccc
Q 007763 295 KPCPRCKRP-IEKNQGCMHMTCTPPCKFEFCWLCLGQW 331 (590)
Q Consensus 295 K~CP~C~~~-IEK~~GCnhMtC~~~C~~~FCw~C~~~w 331 (590)
..|+.|... +. ++|. .|+..+|..|...-
T Consensus 4 ~~C~~H~~~~~~-------~~C~-~C~~~~C~~C~~~~ 33 (42)
T PF00643_consen 4 PKCPEHPEEPLS-------LFCE-DCNEPLCSECTVSG 33 (42)
T ss_dssp SB-SSTTTSBEE-------EEET-TTTEEEEHHHHHTS
T ss_pred ccCccCCccceE-------EEec-CCCCccCccCCCCC
Confidence 689999988 88 9999 89999999998753
No 118
>PLN03208 E3 ubiquitin-protein ligase RMA2; Provisional
Probab=63.99 E-value=2.1 Score=41.54 Aligned_cols=31 Identities=29% Similarity=0.922 Sum_probs=23.5
Q ss_pred cCCCCCCcceeeccCCCceeecCCCcceeeeccccccc
Q 007763 295 KPCPRCKRPIEKNQGCMHMTCTPPCKFEFCWLCLGQWS 332 (590)
Q Consensus 295 K~CP~C~~~IEK~~GCnhMtC~~~C~~~FCw~C~~~w~ 332 (590)
-.||-|...+.. .+. . .|||.|||.|+..|.
T Consensus 19 ~~CpICld~~~d-----PVv-T-~CGH~FC~~CI~~wl 49 (193)
T PLN03208 19 FDCNICLDQVRD-----PVV-T-LCGHLFCWPCIHKWT 49 (193)
T ss_pred cCCccCCCcCCC-----cEE-c-CCCchhHHHHHHHHH
Confidence 579999887641 122 4 599999999999884
No 119
>KOG2038 consensus CAATT-binding transcription factor/60S ribosomal subunit biogenesis protein [Translation, ribosomal structure and biogenesis; Transcription]
Probab=63.24 E-value=6.3 Score=45.47 Aligned_cols=15 Identities=13% Similarity=0.302 Sum_probs=6.7
Q ss_pred CCccccchhhccCCC
Q 007763 2 ESEDEFDMQDANASA 16 (590)
Q Consensus 2 ~~~~~~d~~~~~~~~ 16 (590)
|.+||-|+.+.++++
T Consensus 881 deddd~d~~s~~~~e 895 (988)
T KOG2038|consen 881 DEDDDEDENSLGSEE 895 (988)
T ss_pred ccccccchhcccCcc
Confidence 333333555555433
No 120
>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=62.03 E-value=4.1 Score=35.14 Aligned_cols=30 Identities=23% Similarity=0.579 Sum_probs=25.6
Q ss_pred cccccccccccCCCCceecCCCCccchhhH
Q 007763 141 EMTCGICFENYPSDRLLAAACGHPFCSSCW 170 (590)
Q Consensus 141 ~~~C~IC~e~~~~~~~~~l~CgH~fC~~C~ 170 (590)
...|++|...+....++..||||.|...|.
T Consensus 78 ~~~C~vC~k~l~~~~f~~~p~~~v~H~~C~ 107 (109)
T PF10367_consen 78 STKCSVCGKPLGNSVFVVFPCGHVVHYSCI 107 (109)
T ss_pred CCCccCcCCcCCCceEEEeCCCeEEecccc
Confidence 456999999987777788899999998885
No 121
>PF04147 Nop14: Nop14-like family ; InterPro: IPR007276 Emg1 and Nop14 are novel proteins whose interaction is required for the maturation of the 18S rRNA and for 40S ribosome production [].
Probab=61.70 E-value=26 Score=42.05 Aligned_cols=17 Identities=12% Similarity=0.319 Sum_probs=9.3
Q ss_pred CCceEE---eCHHHHHHHHH
Q 007763 64 QLNYTV---LTEADIRQRQE 80 (590)
Q Consensus 64 ~~~y~v---l~~~~i~~~~~ 80 (590)
+.+|++ -|.+++...+.
T Consensus 417 elPftf~~P~s~eel~~lL~ 436 (840)
T PF04147_consen 417 ELPFTFPCPSSHEELLELLD 436 (840)
T ss_pred CCCceecCCCCHHHHHHHHh
Confidence 456765 45566655443
No 122
>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=60.46 E-value=26 Score=24.30 Aligned_cols=33 Identities=27% Similarity=0.339 Sum_probs=27.5
Q ss_pred HHHHHHHHHHhCCCHHHHHHHHHhcCCChHHHHH
Q 007763 80 EEDITRISTVLSISKVAASILLRFYNWSVSKVHD 113 (590)
Q Consensus 80 ~~~i~~v~~il~i~~~~a~~LL~~~~W~~~~l~e 113 (590)
.+.|.++.+. |.+...+...|+..+||++..++
T Consensus 3 ~~~v~~L~~m-Gf~~~~~~~AL~~~~~nve~A~~ 35 (37)
T PF00627_consen 3 EEKVQQLMEM-GFSREQAREALRACNGNVERAVD 35 (37)
T ss_dssp HHHHHHHHHH-TS-HHHHHHHHHHTTTSHHHHHH
T ss_pred HHHHHHHHHc-CCCHHHHHHHHHHcCCCHHHHHH
Confidence 3567788888 99999999999999999988765
No 123
>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=59.35 E-value=7.4 Score=31.47 Aligned_cols=49 Identities=27% Similarity=0.571 Sum_probs=28.8
Q ss_pred CCCCCCcceeeccCCCceeecCCCcce-----eeecccccccCCCCCCCCcccCCch
Q 007763 296 PCPRCKRPIEKNQGCMHMTCTPPCKFE-----FCWLCLGQWSDHGERTGGFYACNRY 347 (590)
Q Consensus 296 ~CP~C~~~IEK~~GCnhMtC~~~C~~~-----FCw~C~~~w~~H~~~~g~~y~C~~~ 347 (590)
.||.|+.+++..+ .+.+|. .|+.. +|.-|+.+......-.-..|.|+.-
T Consensus 3 ~CP~C~~~L~~~~--~~~~C~-~C~~~~~~~a~CPdC~~~Le~LkACGAvdYFC~~c 56 (70)
T PF07191_consen 3 TCPKCQQELEWQG--GHYHCE-ACQKDYKKEAFCPDCGQPLEVLKACGAVDYFCNHC 56 (70)
T ss_dssp B-SSS-SBEEEET--TEEEET-TT--EEEEEEE-TTT-SB-EEEEETTEEEEE-TTT
T ss_pred cCCCCCCccEEeC--CEEECc-cccccceecccCCCcccHHHHHHHhcccceeeccC
Confidence 6999999999888 688998 79865 5999988765332211135777754
No 124
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=59.29 E-value=5.8 Score=25.53 Aligned_cols=23 Identities=22% Similarity=0.541 Sum_probs=20.6
Q ss_pred cccCCCCccCCCccccccccCCC
Q 007763 567 WYCDQCTYANVNSATACAMCQHS 589 (590)
Q Consensus 567 ~~c~~c~~~~~~~~~~c~~c~~~ 589 (590)
..|..|...++.++++|..|..+
T Consensus 3 ~~Cp~Cg~~~~~~~~fC~~CG~~ 25 (26)
T PF13248_consen 3 MFCPNCGAEIDPDAKFCPNCGAK 25 (26)
T ss_pred CCCcccCCcCCcccccChhhCCC
Confidence 58999999999999999999754
No 125
>PRK14559 putative protein serine/threonine phosphatase; Provisional
Probab=59.07 E-value=6.8 Score=45.26 Aligned_cols=12 Identities=25% Similarity=0.720 Sum_probs=9.4
Q ss_pred cCCCCCCcceee
Q 007763 295 KPCPRCKRPIEK 306 (590)
Q Consensus 295 K~CP~C~~~IEK 306 (590)
+.||+|+..+-+
T Consensus 42 ~fC~~CG~~~~~ 53 (645)
T PRK14559 42 AHCPNCGAETGT 53 (645)
T ss_pred ccccccCCcccc
Confidence 889988887653
No 126
>KOG1941 consensus Acetylcholine receptor-associated protein of the synapse (rapsyn) [Extracellular structures]
Probab=58.96 E-value=13 Score=39.58 Aligned_cols=46 Identities=33% Similarity=0.730 Sum_probs=35.0
Q ss_pred cccccccccccCC--CCceecCCCCccchhhH-HHhhcCCCceecccCCCCCCC
Q 007763 141 EMTCGICFENYPS--DRLLAAACGHPFCSSCW-TAINDGPGCLMLRCPDPSCGA 191 (590)
Q Consensus 141 ~~~C~IC~e~~~~--~~~~~l~CgH~fC~~C~-~~i~~g~~~~~i~CP~~~C~~ 191 (590)
+..|+.|-+.+.. +....+||.|.|...|+ +.+..+ .+-+|| .|+.
T Consensus 365 ~L~Cg~CGe~~Glk~e~LqALpCsHIfH~rCl~e~L~~n---~~rsCP--~Crk 413 (518)
T KOG1941|consen 365 ELYCGLCGESIGLKNERLQALPCSHIFHLRCLQEILENN---GTRSCP--NCRK 413 (518)
T ss_pred hhhhhhhhhhhcCCcccccccchhHHHHHHHHHHHHHhC---CCCCCc--cHHH
Confidence 5779999998754 45678999999999999 444333 357899 7873
No 127
>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=58.48 E-value=5.9 Score=25.65 Aligned_cols=23 Identities=30% Similarity=0.661 Sum_probs=15.7
Q ss_pred cccccccccCCCCceecCCCCcc
Q 007763 143 TCGICFENYPSDRLLAAACGHPF 165 (590)
Q Consensus 143 ~C~IC~e~~~~~~~~~l~CgH~f 165 (590)
+||-|...++.....-..|||.|
T Consensus 2 ~CP~C~~~V~~~~~~Cp~CG~~F 24 (26)
T PF10571_consen 2 TCPECGAEVPESAKFCPHCGYDF 24 (26)
T ss_pred cCCCCcCCchhhcCcCCCCCCCC
Confidence 58888887765444444588876
No 128
>PHA02664 hypothetical protein; Provisional
Probab=58.24 E-value=23 Score=36.73 Aligned_cols=10 Identities=10% Similarity=0.265 Sum_probs=4.6
Q ss_pred HHHHHHHHHh
Q 007763 81 EDITRISTVL 90 (590)
Q Consensus 81 ~~i~~v~~il 90 (590)
+.+..|++.|
T Consensus 523 ~vl~ava~ml 532 (534)
T PHA02664 523 AVLGAVAEML 532 (534)
T ss_pred HHHHHHHHHh
Confidence 3344454444
No 129
>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=58.08 E-value=7.7 Score=30.88 Aligned_cols=28 Identities=36% Similarity=0.815 Sum_probs=19.1
Q ss_pred cCcCCCCCCcceeeccCCCceeecCCCcc
Q 007763 293 NSKPCPRCKRPIEKNQGCMHMTCTPPCKF 321 (590)
Q Consensus 293 ntK~CP~C~~~IEK~~GCnhMtC~~~C~~ 321 (590)
.++.||.|+....+...=..++|. .||+
T Consensus 27 TSq~C~~CG~~~~~~~~~r~~~C~-~Cg~ 54 (69)
T PF07282_consen 27 TSQTCPRCGHRNKKRRSGRVFTCP-NCGF 54 (69)
T ss_pred CccCccCcccccccccccceEEcC-CCCC
Confidence 368999999999874333346666 4544
No 130
>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=57.62 E-value=3.3 Score=29.86 Aligned_cols=35 Identities=26% Similarity=0.716 Sum_probs=23.8
Q ss_pred CCCCCCcceeeccCCCceeecCCCcceeeecccccccCC
Q 007763 296 PCPRCKRPIEKNQGCMHMTCTPPCKFEFCWLCLGQWSDH 334 (590)
Q Consensus 296 ~CP~C~~~IEK~~GCnhMtC~~~C~~~FCw~C~~~w~~H 334 (590)
.||-|...++.... +.-. +|+|.||+.|+..|-..
T Consensus 2 ~C~IC~~~~~~~~~---~~~l-~C~H~fh~~Ci~~~~~~ 36 (44)
T PF13639_consen 2 ECPICLEEFEDGEK---VVKL-PCGHVFHRSCIKEWLKR 36 (44)
T ss_dssp CETTTTCBHHTTSC---EEEE-TTSEEEEHHHHHHHHHH
T ss_pred CCcCCChhhcCCCe---EEEc-cCCCeeCHHHHHHHHHh
Confidence 36667766653211 3333 59999999999999754
No 131
>PF13717 zinc_ribbon_4: zinc-ribbon domain
Probab=57.46 E-value=8.8 Score=26.80 Aligned_cols=29 Identities=24% Similarity=0.581 Sum_probs=20.3
Q ss_pred ccCCCCCCCceEeeecC---CCcceeEe-cCCCcc
Q 007763 226 KWCPAPGCDYAVDFVVG---SGNYDVTC-RCSYSF 256 (590)
Q Consensus 226 ~~CP~p~C~~~i~~~~~---~~~~~v~C-~C~~~f 256 (590)
+.||+ |+....++.. .....|.| .|++.|
T Consensus 3 i~Cp~--C~~~y~i~d~~ip~~g~~v~C~~C~~~f 35 (36)
T PF13717_consen 3 ITCPN--CQAKYEIDDEKIPPKGRKVRCSKCGHVF 35 (36)
T ss_pred EECCC--CCCEEeCCHHHCCCCCcEEECCCCCCEe
Confidence 46885 9887766532 34467899 899876
No 132
>COG5109 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=57.40 E-value=9.8 Score=39.40 Aligned_cols=50 Identities=18% Similarity=0.457 Sum_probs=36.1
Q ss_pred CcccccccccccCC-CCceecCCCCccchhhHHHhhcCCCceecccCCCCCCCc
Q 007763 140 EEMTCGICFENYPS-DRLLAAACGHPFCSSCWTAINDGPGCLMLRCPDPSCGAA 192 (590)
Q Consensus 140 ~~~~C~IC~e~~~~-~~~~~l~CgH~fC~~C~~~i~~g~~~~~i~CP~~~C~~~ 192 (590)
+.|+||+=-+.... +.|+.+.|||.+=+.=+..+..+. ...++|| -|...
T Consensus 335 s~FiCPVlKe~~t~ENpP~ml~CgHVIskeal~~LS~nG-~~~FKCP--YCP~~ 385 (396)
T COG5109 335 SLFICPVLKELCTDENPPVMLECGHVISKEALSVLSQNG-VLSFKCP--YCPEM 385 (396)
T ss_pred ceeeccccHhhhcccCCCeeeeccceeeHHHHHHHhhcC-cEEeeCC--CCCcc
Confidence 46899995444322 567899999999988886665543 3689999 78653
No 133
>KOG3759 consensus Uncharacterized RUN domain protein [Signal transduction mechanisms]
Probab=56.79 E-value=99 Score=33.95 Aligned_cols=46 Identities=15% Similarity=0.359 Sum_probs=20.2
Q ss_pred HHHHHHHHHHHHHHHhhcCCCCCc-HHHHHHHHHHHHHhHHHHHHHHHHHHHccc
Q 007763 465 LERLHQCAEKELQIYLNADGPSKD-FNEFRTKLAGLTSVTRNYFENLVRALENGL 518 (590)
Q Consensus 465 ~E~L~~~le~~l~~~~~~~~~~~~-~~~~~~~l~~lt~~~~~~~~~l~~~le~gl 518 (590)
+|.|.+.+..-+.+|.+.....++ +.+++++|.. ++.+|+.|+.+-
T Consensus 204 teelr~qVD~A~~q~VnP~k~KeQLV~QLkTQItD--------LErFInFlQ~e~ 250 (621)
T KOG3759|consen 204 TEELRRQVDDALKQLVNPFKEKEQLVDQLKTQITD--------LERFINFLQDEV 250 (621)
T ss_pred HHHHHHHHHHHHHHHhChHHHHHHHHHHHHHHHHH--------HHHHHHHHHHhh
Confidence 344555555555555442222222 3344444433 345555565443
No 134
>TIGR03655 anti_R_Lar restriction alleviation protein, Lar family. Restriction alleviation proteins provide a countermeasure to host cell restriction enzyme defense against foreign DNA such as phage or plasmids. This family consists of homologs to the phage antirestriction protein Lar, and most members belong to phage genomes or prophage regions of bacterial genomes.
Probab=56.54 E-value=8 Score=29.35 Aligned_cols=11 Identities=45% Similarity=0.930 Sum_probs=9.0
Q ss_pred cCCCCCCccee
Q 007763 295 KPCPRCKRPIE 305 (590)
Q Consensus 295 K~CP~C~~~IE 305 (590)
||||.|+-.-+
T Consensus 2 kPCPfCGg~~~ 12 (53)
T TIGR03655 2 KPCPFCGGADV 12 (53)
T ss_pred CCCCCCCCcce
Confidence 89999987555
No 135
>PRK08665 ribonucleotide-diphosphate reductase subunit alpha; Validated
Probab=56.17 E-value=6.5 Score=46.37 Aligned_cols=27 Identities=33% Similarity=1.123 Sum_probs=23.7
Q ss_pred cCCCCCCcceeeccCCCceeecCCCcceee
Q 007763 295 KPCPRCKRPIEKNQGCMHMTCTPPCKFEFC 324 (590)
Q Consensus 295 K~CP~C~~~IEK~~GCnhMtC~~~C~~~FC 324 (590)
..||.|+..+...+||. +|. .||+.=|
T Consensus 725 ~~Cp~Cg~~l~~~~GC~--~C~-~CG~skC 751 (752)
T PRK08665 725 GACPECGSILEHEEGCV--VCH-SCGYSKC 751 (752)
T ss_pred CCCCCCCcccEECCCCC--cCC-CCCCCCC
Confidence 35999999999999997 999 8998765
No 136
>COG5151 SSL1 RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit SSL1 [Transcription / DNA replication, recombination, and repair]
Probab=55.30 E-value=3.2 Score=42.70 Aligned_cols=89 Identities=25% Similarity=0.539 Sum_probs=47.4
Q ss_pred CCccchhhHHHhhcCCCceecccCCCCCCCccchhHHhhcCChHHHHHHHHHH-HHHHhhc----CCCcccCCCCCCCce
Q 007763 162 GHPFCSSCWTAINDGPGCLMLRCPDPSCGAAVGQDMIYLLSSDEDKVKYNRYF-IRSYVED----NRKTKWCPAPGCDYA 236 (590)
Q Consensus 162 gH~fC~~C~~~i~~g~~~~~i~CP~~~C~~~i~~~~i~~ll~~e~~eky~~~l-~~~~v~~----~~~~~~CP~p~C~~~ 236 (590)
|-.+|..|-+++-. +++.|| .|...+ +++..+...|..+. ++.+++. +++...|-. |+..
T Consensus 307 gGy~CP~CktkVCs----LPi~CP--~Csl~L-------ilsthLarSyhhL~PLk~f~E~p~~~~~ks~~Cf~--CQ~~ 371 (421)
T COG5151 307 GGYECPVCKTKVCS----LPISCP--ICSLQL-------ILSTHLARSYHHLYPLKPFVEKPEGTNPKSTHCFV--CQGP 371 (421)
T ss_pred CceeCCcccceeec----CCccCc--chhHHH-------HHHHHHHHHHHhhccCcccccccCCCCCCCcccee--ccCC
Confidence 34567777654432 467777 664322 23333334454433 3444443 233445553 6554
Q ss_pred EeeecC------CCcceeEe-cCCCccccccCCCcC
Q 007763 237 VDFVVG------SGNYDVTC-RCSYSFCWNCTEEAH 265 (590)
Q Consensus 237 i~~~~~------~~~~~v~C-~C~~~fC~~C~~~~H 265 (590)
+...+. .......| .|...||..|..-.|
T Consensus 372 fp~~~~~~~~~~~ss~rY~Ce~CK~~FC~dCdvfiH 407 (421)
T COG5151 372 FPKPPVSPFDESTSSGRYQCELCKSTFCSDCDVFIH 407 (421)
T ss_pred CCCCCCCcccccccccceechhhhhhhhhhhHHHHH
Confidence 433221 12345689 999999999986666
No 137
>PF13834 DUF4193: Domain of unknown function (DUF4193)
Probab=54.72 E-value=5 Score=34.59 Aligned_cols=33 Identities=30% Similarity=0.723 Sum_probs=26.0
Q ss_pred CCCCcccccccccccCCCCceecCCCCccchhh
Q 007763 137 PDGEEMTCGICFENYPSDRLLAAACGHPFCSSC 169 (590)
Q Consensus 137 ~~~~~~~C~IC~e~~~~~~~~~l~CgH~fC~~C 169 (590)
....+|+|.-||=....+.+..-.=|+.+|.+|
T Consensus 66 ~q~DEFTCssCFLV~HRSqLa~~~~g~~iC~DC 98 (99)
T PF13834_consen 66 KQADEFTCSSCFLVHHRSQLAREKDGQPICRDC 98 (99)
T ss_pred CCCCceeeeeeeeEechhhhccccCCCEecccc
Confidence 346799999999877666666655689999998
No 138
>PF08580 KAR9: Yeast cortical protein KAR9; InterPro: IPR013889 The KAR9 protein in Saccharomyces cerevisiae (Baker's yeast) is a cytoskeletal protein required for karyogamy, correct positioning of the mitotic spindle and for orientation of cytoplasmic microtubules []. KAR9 localises at the shmoo tip in mating cells and at the tip of the growing bud in anaphase [].
Probab=54.34 E-value=2.8e+02 Score=32.62 Aligned_cols=22 Identities=18% Similarity=0.170 Sum_probs=11.2
Q ss_pred HHHHHHHHHHHHHHhHHHHHHH
Q 007763 450 KRQFFEYLQGEAESGLERLHQC 471 (590)
Q Consensus 450 ~~~~fe~~Q~~le~~~E~L~~~ 471 (590)
...+|.++-.++...++.|...
T Consensus 270 W~~vFr~l~~q~~~m~esver~ 291 (683)
T PF08580_consen 270 WNIVFRNLGRQAQKMCESVERS 291 (683)
T ss_pred HHHHHHHHHHHHHHHHHHHHHH
Confidence 3445555555555555544433
No 139
>PHA02926 zinc finger-like protein; Provisional
Probab=54.27 E-value=5.3 Score=39.52 Aligned_cols=54 Identities=22% Similarity=0.476 Sum_probs=33.8
Q ss_pred CcCCCCCCcce-eec-cCCCc-eeecCCCcceeeecccccccCCCCCCCCcccCCchh
Q 007763 294 SKPCPRCKRPI-EKN-QGCMH-MTCTPPCKFEFCWLCLGQWSDHGERTGGFYACNRYE 348 (590)
Q Consensus 294 tK~CP~C~~~I-EK~-~GCnh-MtC~~~C~~~FCw~C~~~w~~H~~~~g~~y~C~~~~ 348 (590)
-+.|+=|-..+ +|. .++.. -.=. +|+|-||+.|...|......+|.-..|+--+
T Consensus 170 E~eCgICmE~I~eK~~~~eRrFGIL~-~CnHsFCl~CIr~Wr~~r~~~~~~rsCPiCR 226 (242)
T PHA02926 170 EKECGICYEVVYSKRLENDRYFGLLD-SCNHIFCITCINIWHRTRRETGASDNCPICR 226 (242)
T ss_pred CCCCccCccccccccccccccccccC-CCCchHHHHHHHHHHHhccccCcCCcCCCCc
Confidence 38899998665 332 11110 0111 6999999999999986543445556787543
No 140
>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=53.96 E-value=7.6 Score=34.28 Aligned_cols=27 Identities=26% Similarity=0.673 Sum_probs=18.6
Q ss_pred cCCCCCCcceeeccCCCceeecCCCccee
Q 007763 295 KPCPRCKRPIEKNQGCMHMTCTPPCKFEF 323 (590)
Q Consensus 295 K~CP~C~~~IEK~~GCnhMtC~~~C~~~F 323 (590)
+.||+|++..-=-.- +.++|. .||..|
T Consensus 10 R~Cp~CG~kFYDLnk-~PivCP-~CG~~~ 36 (108)
T PF09538_consen 10 RTCPSCGAKFYDLNK-DPIVCP-KCGTEF 36 (108)
T ss_pred ccCCCCcchhccCCC-CCccCC-CCCCcc
Confidence 689999987763222 778887 566554
No 141
>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=53.86 E-value=11 Score=26.09 Aligned_cols=27 Identities=22% Similarity=0.648 Sum_probs=16.9
Q ss_pred ccCCCCCCCceEeeecCCCcceeEe-cCCCc
Q 007763 226 KWCPAPGCDYAVDFVVGSGNYDVTC-RCSYS 255 (590)
Q Consensus 226 ~~CP~p~C~~~i~~~~~~~~~~v~C-~C~~~ 255 (590)
++|| .|+..+....+..... .| .|++.
T Consensus 2 ~FCp--~C~nlL~p~~~~~~~~-~C~~C~Y~ 29 (35)
T PF02150_consen 2 RFCP--ECGNLLYPKEDKEKRV-ACRTCGYE 29 (35)
T ss_dssp -BET--TTTSBEEEEEETTTTE-EESSSS-E
T ss_pred eeCC--CCCccceEcCCCccCc-CCCCCCCc
Confidence 5898 5999887764433333 78 78765
No 142
>TIGR00622 ssl1 transcription factor ssl1. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=53.07 E-value=12 Score=33.17 Aligned_cols=39 Identities=23% Similarity=0.556 Sum_probs=25.0
Q ss_pred ccCCCCCCCceEeeecC------CCcceeEe-cCCCccccccCCCcCC
Q 007763 226 KWCPAPGCDYAVDFVVG------SGNYDVTC-RCSYSFCWNCTEEAHR 266 (590)
Q Consensus 226 ~~CP~p~C~~~i~~~~~------~~~~~v~C-~C~~~fC~~C~~~~H~ 266 (590)
..|- +|...+...+. .......| .|+..||..|-.-+|.
T Consensus 56 ~~C~--~C~~~f~~~~~~~~~~~~~~~~y~C~~C~~~FC~dCD~fiHe 101 (112)
T TIGR00622 56 RFCF--GCQGPFPKPPVSPFDELKDSHRYVCAVCKNVFCVDCDVFVHE 101 (112)
T ss_pred Cccc--CcCCCCCCcccccccccccccceeCCCCCCccccccchhhhh
Confidence 4576 47765532211 11234579 9999999999877774
No 143
>KOG2114 consensus Vacuolar assembly/sorting protein PEP5/VPS11 [Intracellular trafficking, secretion, and vesicular transport]
Probab=53.01 E-value=9.8 Score=44.40 Aligned_cols=103 Identities=18% Similarity=0.291 Sum_probs=57.7
Q ss_pred HHHHHHHHHHHHHhCCCHHHHHHHHHhcCCCh----H------------------HHHHHhhcCHHHHHHHcCCCCCCCC
Q 007763 77 QRQEEDITRISTVLSISKVAASILLRFYNWSV----S------------------KVHDEWFADEERVRKAVGLLEKPAV 134 (590)
Q Consensus 77 ~~~~~~i~~v~~il~i~~~~a~~LL~~~~W~~----~------------------~l~e~~~~~~~~~~~~~gl~~~~~~ 134 (590)
+...+.++.|-.--.|||-...-+|-+..=-. . +.++.|-.+-++.+..++.......
T Consensus 757 ~~v~~vl~~I~~~~~ippl~VL~~Lakn~~ltls~IkD~ii~~l~~~~~~I~qd~~~Ie~yk~~i~e~r~~l~~lr~sa~ 836 (933)
T KOG2114|consen 757 EIVYKVLEAIEMQERIPPLHVLQILAKNGTLTLSVIKDYIIKWLNKYSTIIEQDEDAIEVYKKDIEEKRQELETLRTSAQ 836 (933)
T ss_pred HHHHHHHHHHHhcccCCHHHHHHHHhcCCceEEehhHHHHHHHHHhhhHHHHhhHHHHHHHHHHHHHHHHHHHHhhcccc
Confidence 34555566666667788877776664432111 1 1122222223333444443332221
Q ss_pred CCCCCCcccccccccccCCCCceecCCCCccchhhHHHhhcCCCceecccCCCCCCCc
Q 007763 135 QFPDGEEMTCGICFENYPSDRLLAAACGHPFCSSCWTAINDGPGCLMLRCPDPSCGAA 192 (590)
Q Consensus 135 ~~~~~~~~~C~IC~e~~~~~~~~~l~CgH~fC~~C~~~i~~g~~~~~i~CP~~~C~~~ 192 (590)
+. ..-.|..|--++. -.+|...|||.|...|++ ++ .-.|| .|...
T Consensus 837 i~---q~skCs~C~~~Ld-lP~VhF~CgHsyHqhC~e---~~----~~~CP--~C~~e 881 (933)
T KOG2114|consen 837 IF---QVSKCSACEGTLD-LPFVHFLCGHSYHQHCLE---DK----EDKCP--KCLPE 881 (933)
T ss_pred ee---eeeeecccCCccc-cceeeeecccHHHHHhhc---cC----cccCC--ccchh
Confidence 11 1246999976652 234677899999999997 33 36899 88763
No 144
>KOG3970 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=52.22 E-value=12 Score=36.82 Aligned_cols=50 Identities=20% Similarity=0.479 Sum_probs=37.6
Q ss_pred ccccccccccCCCCceecCCCCccchhhHH----HhhcCCCceecccCCCCCCCcc
Q 007763 142 MTCGICFENYPSDRLLAAACGHPFCSSCWT----AINDGPGCLMLRCPDPSCGAAV 193 (590)
Q Consensus 142 ~~C~IC~e~~~~~~~~~l~CgH~fC~~C~~----~i~~g~~~~~i~CP~~~C~~~i 193 (590)
-.|..|-..+...+.+.+.|-|.|.-.|+. .+-.+..-..+.|| .|...|
T Consensus 51 pNC~LC~t~La~gdt~RLvCyhlfHW~ClneraA~lPanTAPaGyqCP--~Cs~ei 104 (299)
T KOG3970|consen 51 PNCRLCNTPLASGDTTRLVCYHLFHWKCLNERAANLPANTAPAGYQCP--CCSQEI 104 (299)
T ss_pred CCCceeCCccccCcceeehhhhhHHHHHhhHHHhhCCCcCCCCcccCC--CCCCcc
Confidence 459999988888899999999999999992 22222112358999 788765
No 145
>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=52.09 E-value=12 Score=28.45 Aligned_cols=25 Identities=32% Similarity=0.858 Sum_probs=15.7
Q ss_pred CCCCccchhhHHHhhcCCCceecccCCCCCC
Q 007763 160 ACGHPFCSSCWTAINDGPGCLMLRCPDPSCG 190 (590)
Q Consensus 160 ~CgH~fC~~C~~~i~~g~~~~~i~CP~~~C~ 190 (590)
.|++.||.+|=..|-+.. -.|| +|.
T Consensus 26 ~C~~~FC~dCD~fiHE~L----H~CP--GC~ 50 (51)
T PF07975_consen 26 KCKNHFCIDCDVFIHETL----HNCP--GCE 50 (51)
T ss_dssp TTT--B-HHHHHTTTTTS-----SSS--TT-
T ss_pred CCCCccccCcChhhhccc----cCCc--CCC
Confidence 499999999998777653 4788 774
No 146
>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=51.04 E-value=47 Score=22.82 Aligned_cols=34 Identities=18% Similarity=0.209 Sum_probs=26.9
Q ss_pred HHHHHHHHhCCCHHHHHHHHHhcCCChHHHHHHhh
Q 007763 82 DITRISTVLSISKVAASILLRFYNWSVSKVHDEWF 116 (590)
Q Consensus 82 ~i~~v~~il~i~~~~a~~LL~~~~W~~~~l~e~~~ 116 (590)
.|.++.+ +|.+...+...|...+||+++..+-++
T Consensus 4 ~v~~L~~-mGf~~~~~~~AL~~~~~d~~~A~~~L~ 37 (38)
T cd00194 4 KLEQLLE-MGFSREEARKALRATNNNVERAVEWLL 37 (38)
T ss_pred HHHHHHH-cCCCHHHHHHHHHHhCCCHHHHHHHHh
Confidence 4445544 589999999999999999999876543
No 147
>COG5236 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=50.61 E-value=10 Score=39.65 Aligned_cols=47 Identities=32% Similarity=0.690 Sum_probs=33.1
Q ss_pred CCCcccccccccccCCCCceecCCCCccchhhH---HHhhcCCCceecccCCCCCCCcc
Q 007763 138 DGEEMTCGICFENYPSDRLLAAACGHPFCSSCW---TAINDGPGCLMLRCPDPSCGAAV 193 (590)
Q Consensus 138 ~~~~~~C~IC~e~~~~~~~~~l~CgH~fC~~C~---~~i~~g~~~~~i~CP~~~C~~~i 193 (590)
......|.||.... .-...+||+|..|.-|- .++-. .-.|| .|+...
T Consensus 58 DEen~~C~ICA~~~--TYs~~~PC~H~~CH~Ca~RlRALY~-----~K~C~--~CrTE~ 107 (493)
T COG5236 58 DEENMNCQICAGST--TYSARYPCGHQICHACAVRLRALYM-----QKGCP--LCRTET 107 (493)
T ss_pred ccccceeEEecCCc--eEEEeccCCchHHHHHHHHHHHHHh-----ccCCC--cccccc
Confidence 44567899999865 33456799999999998 33322 24687 788654
No 148
>COG4647 AcxC Acetone carboxylase, gamma subunit [Secondary metabolites biosynthesis, transport, and catabolism]
Probab=49.98 E-value=9.8 Score=34.24 Aligned_cols=59 Identities=17% Similarity=0.299 Sum_probs=31.6
Q ss_pred ceeEecCCCccccccCCCcCC--CCCchhHHHHHHh--hhhhhhhHHHHHhcCcCCCCCCccee
Q 007763 246 YDVTCRCSYSFCWNCTEEAHR--PVDCDTVAKWVLK--NSAESENMNWILANSKPCPRCKRPIE 305 (590)
Q Consensus 246 ~~v~C~C~~~fC~~C~~~~H~--p~~C~~~~~w~~k--~~~e~e~~~wi~~ntK~CP~C~~~IE 305 (590)
..+.|.||++||-- .+.|.. ..--.....-+.. -..+....+|+..---.||.|+.+.+
T Consensus 69 rv~rcecghsf~d~-r~nwkl~a~i~vrdtee~lreiyp~s~ipdp~wme~reficpecg~l~e 131 (165)
T COG4647 69 RVIRCECGHSFGDY-RENWKLHANIYVRDTEEKLREIYPKSDIPDPQWMEIREFICPECGILHE 131 (165)
T ss_pred cEEEEeccccccCh-hhCceeeeEEEEcchHHHHHHhCcccCCCCchHHHHHHhhCccccceee
Confidence 34579999999965 334432 2111111100100 01122345677666678999999887
No 149
>KOG4684 consensus Uncharacterized conserved protein, contains C4-type Zn-finger [General function prediction only]
Probab=49.95 E-value=11 Score=36.94 Aligned_cols=18 Identities=22% Similarity=0.632 Sum_probs=14.4
Q ss_pred CcccCCCCCCCceEeeec
Q 007763 224 KTKWCPAPGCDYAVDFVV 241 (590)
Q Consensus 224 ~~~~CP~p~C~~~i~~~~ 241 (590)
..+-||.|+|.++|...+
T Consensus 137 qRIACPRpnCkRiInL~p 154 (275)
T KOG4684|consen 137 QRIACPRPNCKRIINLDP 154 (275)
T ss_pred ceeccCCCCcceeeecCC
Confidence 356899999999987653
No 150
>PF10168 Nup88: Nuclear pore component; InterPro: IPR019321 Nup88 can be divided into two structural domains; the N-terminal two-thirds of the protein have no obvious structural motifs. It is, however, where it binds to Nup98; one of the components of the nuclear pore. The C-terminal end is a predicted coiled-coil domain []. Nup88 is over expressed in tumour cells [].
Probab=49.55 E-value=2.4e+02 Score=33.26 Aligned_cols=24 Identities=13% Similarity=0.026 Sum_probs=17.6
Q ss_pred HHHHHHHHHHHHHHhHHHHHHHHH
Q 007763 450 KRQFFEYLQGEAESGLERLHQCAE 473 (590)
Q Consensus 450 ~~~~fe~~Q~~le~~~E~L~~~le 473 (590)
+.+-+...|+.+..+++.+.+.+.
T Consensus 601 R~e~a~d~Qe~L~~R~~~vl~~l~ 624 (717)
T PF10168_consen 601 RYEEAKDKQEKLMKRVDRVLQLLN 624 (717)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHh
Confidence 456667778888888888876553
No 151
>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=49.39 E-value=29 Score=25.08 Aligned_cols=22 Identities=32% Similarity=1.106 Sum_probs=16.4
Q ss_pred cCCCCCCcceee-ccCCCceeecCCC
Q 007763 295 KPCPRCKRPIEK-NQGCMHMTCTPPC 319 (590)
Q Consensus 295 K~CP~C~~~IEK-~~GCnhMtC~~~C 319 (590)
..||.|+.|+-+ .+| .++|. .|
T Consensus 18 ~~Cp~C~~PL~~~k~g--~~~Cv-~C 40 (41)
T PF06677_consen 18 EHCPDCGTPLMRDKDG--KIYCV-SC 40 (41)
T ss_pred CccCCCCCeeEEecCC--CEECC-CC
Confidence 789999999987 344 46676 45
No 152
>COG5574 PEX10 RING-finger-containing E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=48.97 E-value=4.4 Score=41.01 Aligned_cols=33 Identities=36% Similarity=0.821 Sum_probs=26.0
Q ss_pred cCCCCCCcceeeccCCCceeecCCCcceeeeccccc-ccCC
Q 007763 295 KPCPRCKRPIEKNQGCMHMTCTPPCKFEFCWLCLGQ-WSDH 334 (590)
Q Consensus 295 K~CP~C~~~IEK~~GCnhMtC~~~C~~~FCw~C~~~-w~~H 334 (590)
..|+=|-..++. -.|+ .|||-|||.|+-. |..-
T Consensus 216 ~kC~lC~e~~~~------ps~t-~CgHlFC~~Cl~~~~t~~ 249 (271)
T COG5574 216 YKCFLCLEEPEV------PSCT-PCGHLFCLSCLLISWTKK 249 (271)
T ss_pred cceeeeecccCC------cccc-cccchhhHHHHHHHHHhh
Confidence 678888887772 4677 7999999999987 7644
No 153
>KOG2141 consensus Protein involved in high osmolarity signaling pathway [Signal transduction mechanisms]
Probab=48.54 E-value=11 Score=43.27 Aligned_cols=12 Identities=25% Similarity=0.642 Sum_probs=8.5
Q ss_pred eeeecccccccC
Q 007763 322 EFCWLCLGQWSD 333 (590)
Q Consensus 322 ~FCw~C~~~w~~ 333 (590)
.--|+=|..|..
T Consensus 568 GrWWlVGsaw~g 579 (822)
T KOG2141|consen 568 GRWWLVGSAWRG 579 (822)
T ss_pred CceEEecchhcC
Confidence 346888888875
No 154
>KOG3130 consensus Uncharacterized conserved protein [Function unknown]
Probab=48.52 E-value=13 Score=39.78 Aligned_cols=6 Identities=33% Similarity=0.778 Sum_probs=3.4
Q ss_pred cccccc
Q 007763 146 ICFENY 151 (590)
Q Consensus 146 IC~e~~ 151 (590)
||++.-
T Consensus 396 Ic~~ts 401 (514)
T KOG3130|consen 396 ICSDTS 401 (514)
T ss_pred ccccCC
Confidence 666553
No 155
>KOG3579 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=48.13 E-value=15 Score=37.57 Aligned_cols=52 Identities=21% Similarity=0.566 Sum_probs=37.3
Q ss_pred CcccccccccccCCCCceecC--CCCccchhhH-HHhhcCCCceecccCC-CCCCC
Q 007763 140 EEMTCGICFENYPSDRLLAAA--CGHPFCSSCW-TAINDGPGCLMLRCPD-PSCGA 191 (590)
Q Consensus 140 ~~~~C~IC~e~~~~~~~~~l~--CgH~fC~~C~-~~i~~g~~~~~i~CP~-~~C~~ 191 (590)
..+.|.+|-|-+....+|..+ =.|.||.-|- ..|+.......+.||. ..|..
T Consensus 267 apLcCTLC~ERLEDTHFVQCPSVp~HKFCFPCSResIK~Qg~sgevYCPSGdkCPL 322 (352)
T KOG3579|consen 267 APLCCTLCHERLEDTHFVQCPSVPSHKFCFPCSRESIKQQGASGEVYCPSGDKCPL 322 (352)
T ss_pred CceeehhhhhhhccCceeecCCCcccceecccCHHHHHhhcCCCceeCCCCCcCcc
Confidence 458899999998555555544 3799999999 7776543335789996 35764
No 156
>PF05290 Baculo_IE-1: Baculovirus immediate-early protein (IE-0); InterPro: IPR007954 This entry contains the Baculovirus immediate-early protein IE-0.
Probab=47.93 E-value=12 Score=34.05 Aligned_cols=52 Identities=27% Similarity=0.671 Sum_probs=37.4
Q ss_pred CCcccccccccccCCCCceecC--CCCccchhhHHHhhcCCCceecccCCCCCCCcc
Q 007763 139 GEEMTCGICFENYPSDRLLAAA--CGHPFCSSCWTAINDGPGCLMLRCPDPSCGAAV 193 (590)
Q Consensus 139 ~~~~~C~IC~e~~~~~~~~~l~--CgH~fC~~C~~~i~~g~~~~~i~CP~~~C~~~i 193 (590)
.....|.||-|......+.... ||-..|.-|...+|.-.. ....|| -|+..+
T Consensus 78 ~~lYeCnIC~etS~ee~FLKPneCCgY~iCn~Cya~LWK~~~-~ypvCP--vCkTSF 131 (140)
T PF05290_consen 78 PKLYECNICKETSAEERFLKPNECCGYSICNACYANLWKFCN-LYPVCP--VCKTSF 131 (140)
T ss_pred CCceeccCcccccchhhcCCcccccchHHHHHHHHHHHHHcc-cCCCCC--cccccc
Confidence 3568899999986443333332 999999999966665432 567899 798766
No 157
>smart00661 RPOL9 RNA polymerase subunit 9.
Probab=47.28 E-value=16 Score=27.22 Aligned_cols=27 Identities=26% Similarity=0.747 Sum_probs=16.5
Q ss_pred cCCCCCCCceEeeecCCCcceeEe-cCCCc
Q 007763 227 WCPAPGCDYAVDFVVGSGNYDVTC-RCSYS 255 (590)
Q Consensus 227 ~CP~p~C~~~i~~~~~~~~~~v~C-~C~~~ 255 (590)
+|| .|+..+............| .||+.
T Consensus 2 FCp--~Cg~~l~~~~~~~~~~~vC~~Cg~~ 29 (52)
T smart00661 2 FCP--KCGNMLIPKEGKEKRRFVCRKCGYE 29 (52)
T ss_pred CCC--CCCCccccccCCCCCEEECCcCCCe
Confidence 688 4988776553323235677 67754
No 158
>PHA03096 p28-like protein; Provisional
Probab=47.06 E-value=9.2 Score=39.65 Aligned_cols=32 Identities=28% Similarity=0.508 Sum_probs=22.4
Q ss_pred ccccccccccCCC----Cc-eec-CCCCccchhhHHHh
Q 007763 142 MTCGICFENYPSD----RL-LAA-ACGHPFCSSCWTAI 173 (590)
Q Consensus 142 ~~C~IC~e~~~~~----~~-~~l-~CgH~fC~~C~~~i 173 (590)
..|+||++..-.. .. -.+ .|.|.||..|+..+
T Consensus 179 k~c~ic~e~~~~k~~~~~~fgil~~c~h~fc~~ci~~w 216 (284)
T PHA03096 179 KICGICLENIKAKYIIKKYYGILSEIKHEFNIFCIKIW 216 (284)
T ss_pred hhcccchhhhhhhccccccccccccCCcHHHHHHHHHH
Confidence 6799999875422 12 233 49999999999433
No 159
>COG5219 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=46.82 E-value=4.7 Score=47.35 Aligned_cols=52 Identities=17% Similarity=0.442 Sum_probs=34.4
Q ss_pred CCcccccccccccCC---CCc-eec-CCCCccchhhHHHhhcCCCceecccCCCCCCCccc
Q 007763 139 GEEMTCGICFENYPS---DRL-LAA-ACGHPFCSSCWTAINDGPGCLMLRCPDPSCGAAVG 194 (590)
Q Consensus 139 ~~~~~C~IC~e~~~~---~~~-~~l-~CgH~fC~~C~~~i~~g~~~~~i~CP~~~C~~~i~ 194 (590)
++..+|+||+..+.. .-| ... .|.|.|...|+-+|-... ..-+|| -|+..++
T Consensus 1467 sG~eECaICYsvL~~vdr~lPskrC~TCknKFH~~CLyKWf~Ss--~~s~CP--lCRseit 1523 (1525)
T COG5219 1467 SGHEECAICYSVLDMVDRSLPSKRCATCKNKFHTRCLYKWFASS--ARSNCP--LCRSEIT 1523 (1525)
T ss_pred CCcchhhHHHHHHHHHhccCCccccchhhhhhhHHHHHHHHHhc--CCCCCC--ccccccc
Confidence 445679999987641 222 122 399999999995554332 246899 8987654
No 160
>PRK09710 lar restriction alleviation and modification protein; Reviewed
Probab=45.76 E-value=15 Score=29.14 Aligned_cols=14 Identities=50% Similarity=0.992 Sum_probs=11.1
Q ss_pred cCcCCCCCCcceee
Q 007763 293 NSKPCPRCKRPIEK 306 (590)
Q Consensus 293 ntK~CP~C~~~IEK 306 (590)
+.||||.|+..+.+
T Consensus 5 ~lKPCPFCG~~~~~ 18 (64)
T PRK09710 5 NVKPCPFCGCPSVT 18 (64)
T ss_pred cccCCCCCCCceeE
Confidence 45999999987664
No 161
>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=45.69 E-value=13 Score=32.26 Aligned_cols=24 Identities=25% Similarity=0.758 Sum_probs=17.9
Q ss_pred CCCCCCcceeeccCCCceeecCCCcce
Q 007763 296 PCPRCKRPIEKNQGCMHMTCTPPCKFE 322 (590)
Q Consensus 296 ~CP~C~~~IEK~~GCnhMtC~~~C~~~ 322 (590)
-||+|+.++...+ +.+.|. .|++.
T Consensus 2 fC~~Cg~~l~~~~--~~~~C~-~C~~~ 25 (104)
T TIGR01384 2 FCPKCGSLMTPKN--GVYVCP-SCGYE 25 (104)
T ss_pred CCcccCcccccCC--CeEECc-CCCCc
Confidence 6999999887654 378887 67665
No 162
>KOG2906 consensus RNA polymerase III subunit C11 [Transcription]
Probab=45.22 E-value=14 Score=31.78 Aligned_cols=28 Identities=25% Similarity=0.815 Sum_probs=21.2
Q ss_pred CCCCCCccee--eccCCCceeecCCCcceee
Q 007763 296 PCPRCKRPIE--KNQGCMHMTCTPPCKFEFC 324 (590)
Q Consensus 296 ~CP~C~~~IE--K~~GCnhMtC~~~C~~~FC 324 (590)
-||.|+..+. +.+-||...|+ .|.+.|=
T Consensus 3 FCP~Cgn~Live~g~~~~rf~C~-tCpY~~~ 32 (105)
T KOG2906|consen 3 FCPTCGNMLIVESGESCNRFSCR-TCPYVFP 32 (105)
T ss_pred ccCCCCCEEEEecCCeEeeEEcC-CCCceee
Confidence 5999987654 55558999998 8877653
No 163
>PF14803 Nudix_N_2: Nudix N-terminal; PDB: 3CNG_C.
Probab=44.58 E-value=20 Score=24.80 Aligned_cols=28 Identities=25% Similarity=0.814 Sum_probs=14.1
Q ss_pred ccCCCCCCCceEeeec--CCCcceeEe-cCCCc
Q 007763 226 KWCPAPGCDYAVDFVV--GSGNYDVTC-RCSYS 255 (590)
Q Consensus 226 ~~CP~p~C~~~i~~~~--~~~~~~v~C-~C~~~ 255 (590)
++||. |+..+.... +.......| .||..
T Consensus 1 kfC~~--CG~~l~~~ip~gd~r~R~vC~~Cg~I 31 (34)
T PF14803_consen 1 KFCPQ--CGGPLERRIPEGDDRERLVCPACGFI 31 (34)
T ss_dssp -B-TT--T--B-EEE--TT-SS-EEEETTTTEE
T ss_pred Ccccc--ccChhhhhcCCCCCccceECCCCCCE
Confidence 47885 988876653 355677788 88764
No 164
>smart00165 UBA Ubiquitin associated domain. Present in Rad23, SNF1-like kinases. The newly-found UBA in p62 is known to bind ubiquitin.
Probab=44.01 E-value=63 Score=22.05 Aligned_cols=32 Identities=22% Similarity=0.224 Sum_probs=24.7
Q ss_pred HHHHHHHHhCCCHHHHHHHHHhcCCChHHHHHH
Q 007763 82 DITRISTVLSISKVAASILLRFYNWSVSKVHDE 114 (590)
Q Consensus 82 ~i~~v~~il~i~~~~a~~LL~~~~W~~~~l~e~ 114 (590)
.|.++.+ +|.+...|...|...+||+++..+-
T Consensus 4 ~v~~L~~-mGf~~~~a~~aL~~~~~d~~~A~~~ 35 (37)
T smart00165 4 KIDQLLE-MGFSREEALKALRAANGNVERAAEY 35 (37)
T ss_pred HHHHHHH-cCCCHHHHHHHHHHhCCCHHHHHHH
Confidence 3444433 3899999999999999999887653
No 165
>PRK05654 acetyl-CoA carboxylase subunit beta; Validated
Probab=43.81 E-value=6.5 Score=40.93 Aligned_cols=28 Identities=18% Similarity=0.564 Sum_probs=22.1
Q ss_pred cCCCCCCcceee-ccCCCceeecCCCccee
Q 007763 295 KPCPRCKRPIEK-NQGCMHMTCTPPCKFEF 323 (590)
Q Consensus 295 K~CP~C~~~IEK-~~GCnhMtC~~~C~~~F 323 (590)
..||+|+..|-+ .-.=|.+.|. .|+|+|
T Consensus 28 ~~c~~c~~~~~~~~l~~~~~vc~-~c~~h~ 56 (292)
T PRK05654 28 TKCPSCGQVLYRKELEANLNVCP-KCGHHM 56 (292)
T ss_pred eECCCccchhhHHHHHhcCCCCC-CCCCCe
Confidence 889999998874 3455678998 799888
No 166
>KOG3161 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=43.67 E-value=6.1 Score=44.56 Aligned_cols=35 Identities=23% Similarity=0.684 Sum_probs=27.1
Q ss_pred cccccccccccCC--CCceecCCCCccchhhHHHhhc
Q 007763 141 EMTCGICFENYPS--DRLLAAACGHPFCSSCWTAIND 175 (590)
Q Consensus 141 ~~~C~IC~e~~~~--~~~~~l~CgH~fC~~C~~~i~~ 175 (590)
...|+||+..+-. -.++++.|||..|.-|.+.+..
T Consensus 11 ~l~c~ic~n~f~~~~~~Pvsl~cghtic~~c~~~lyn 47 (861)
T KOG3161|consen 11 LLLCDICLNLFVVQRLEPVSLQCGHTICGHCVQLLYN 47 (861)
T ss_pred HhhchHHHHHHHHHhcCcccccccchHHHHHHHhHhh
Confidence 3569999877643 3678999999999999965543
No 167
>KOG0825 consensus PHD Zn-finger protein [General function prediction only]
Probab=42.43 E-value=11 Score=43.48 Aligned_cols=53 Identities=17% Similarity=0.189 Sum_probs=33.7
Q ss_pred cccccccccccCC--CCceecC---CCCccchhhHHHhhcCCCceecccCCCCCCCcc
Q 007763 141 EMTCGICFENYPS--DRLLAAA---CGHPFCSSCWTAINDGPGCLMLRCPDPSCGAAV 193 (590)
Q Consensus 141 ~~~C~IC~e~~~~--~~~~~l~---CgH~fC~~C~~~i~~g~~~~~i~CP~~~C~~~i 193 (590)
..+|.||.-++.. +-.-.++ |+|.+|-.||..+.++.....+.|-++.|..-|
T Consensus 96 s~Ss~~C~~E~S~~~ds~~i~P~~~~~~~~CP~Ci~s~~DqL~~~~k~c~H~FC~~Ci 153 (1134)
T KOG0825|consen 96 SDTSPVCEKEHSPDVDSSNICPVQTHVENQCPNCLKSCNDQLEESEKHTAHYFCEECV 153 (1134)
T ss_pred ccccchhheecCCcccccCcCchhhhhhhhhhHHHHHHHHHhhccccccccccHHHHh
Confidence 3455555544432 2233344 999999999976666654456777777887655
No 168
>COG1997 RPL43A Ribosomal protein L37AE/L43A [Translation, ribosomal structure and biogenesis]
Probab=42.18 E-value=20 Score=30.23 Aligned_cols=28 Identities=29% Similarity=0.589 Sum_probs=21.8
Q ss_pred cCCCCCCcceeeccCCCceeecCCCccee
Q 007763 295 KPCPRCKRPIEKNQGCMHMTCTPPCKFEF 323 (590)
Q Consensus 295 K~CP~C~~~IEK~~GCnhMtC~~~C~~~F 323 (590)
-.||.|++..-|-.+=--=.|+ .||+.|
T Consensus 36 ~~Cp~C~~~~VkR~a~GIW~C~-kCg~~f 63 (89)
T COG1997 36 HVCPFCGRTTVKRIATGIWKCR-KCGAKF 63 (89)
T ss_pred CcCCCCCCcceeeeccCeEEcC-CCCCee
Confidence 5899999998887776667787 676655
No 169
>KOG2034 consensus Vacuolar sorting protein PEP3/VPS18 [Intracellular trafficking, secretion, and vesicular transport]
Probab=41.97 E-value=14 Score=43.45 Aligned_cols=34 Identities=21% Similarity=0.495 Sum_probs=27.5
Q ss_pred CcccccccccccCCCCceecCCCCccchhhH-HHh
Q 007763 140 EEMTCGICFENYPSDRLLAAACGHPFCSSCW-TAI 173 (590)
Q Consensus 140 ~~~~C~IC~e~~~~~~~~~l~CgH~fC~~C~-~~i 173 (590)
+...|.+|.-.+-...++..+|||.|..+|+ ..+
T Consensus 816 p~d~C~~C~~~ll~~pF~vf~CgH~FH~~Cl~~~v 850 (911)
T KOG2034|consen 816 PQDSCDHCGRPLLIKPFYVFPCGHCFHRDCLIRHV 850 (911)
T ss_pred CccchHHhcchhhcCcceeeeccchHHHHHHHHHH
Confidence 3567999998876666777899999999999 444
No 170
>cd00021 BBOX B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction.
Probab=41.74 E-value=16 Score=25.22 Aligned_cols=27 Identities=19% Similarity=0.423 Sum_probs=23.5
Q ss_pred CCCCCCc-ceeeccCCCceeecCCCcceeeeccccc
Q 007763 296 PCPRCKR-PIEKNQGCMHMTCTPPCKFEFCWLCLGQ 330 (590)
Q Consensus 296 ~CP~C~~-~IEK~~GCnhMtC~~~C~~~FCw~C~~~ 330 (590)
.||.|.. ++. ++|. .|+...|..|...
T Consensus 2 ~C~~H~~~~~~-------~fC~-~~~~~iC~~C~~~ 29 (39)
T cd00021 2 LCDEHGEEPLS-------LFCE-TDRALLCVDCDLS 29 (39)
T ss_pred CCCccCCcceE-------EEeC-ccChhhhhhcChh
Confidence 5899977 888 9999 8999999999643
No 171
>KOG1571 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=41.02 E-value=14 Score=39.20 Aligned_cols=42 Identities=24% Similarity=0.730 Sum_probs=29.6
Q ss_pred cccccccccccCCCCceecCCCCccchhhHHHhhcCCCceecccCCCCCCCcc
Q 007763 141 EMTCGICFENYPSDRLLAAACGHPFCSSCWTAINDGPGCLMLRCPDPSCGAAV 193 (590)
Q Consensus 141 ~~~C~IC~e~~~~~~~~~l~CgH~fC~~C~~~i~~g~~~~~i~CP~~~C~~~i 193 (590)
...|.||.+.. .+.+.++|||.-| |...-.. ...|| -|+..+
T Consensus 305 p~lcVVcl~e~--~~~~fvpcGh~cc--ct~cs~~-----l~~CP--vCR~rI 346 (355)
T KOG1571|consen 305 PDLCVVCLDEP--KSAVFVPCGHVCC--CTLCSKH-----LPQCP--VCRQRI 346 (355)
T ss_pred CCceEEecCCc--cceeeecCCcEEE--chHHHhh-----CCCCc--hhHHHH
Confidence 56799999876 5688999999966 6622111 24599 787654
No 172
>COG1645 Uncharacterized Zn-finger containing protein [General function prediction only]
Probab=40.92 E-value=19 Score=32.81 Aligned_cols=23 Identities=35% Similarity=0.797 Sum_probs=18.4
Q ss_pred cCCCCCCcceeeccCCCceeecCCCcceeeeccc
Q 007763 295 KPCPRCKRPIEKNQGCMHMTCTPPCKFEFCWLCL 328 (590)
Q Consensus 295 K~CP~C~~~IEK~~GCnhMtC~~~C~~~FCw~C~ 328 (590)
+-||.|+.|+.+ .-|.-||.+|+
T Consensus 29 ~hCp~Cg~PLF~-----------KdG~v~CPvC~ 51 (131)
T COG1645 29 KHCPKCGTPLFR-----------KDGEVFCPVCG 51 (131)
T ss_pred hhCcccCCccee-----------eCCeEECCCCC
Confidence 789999999983 36677777776
No 173
>smart00804 TAP_C C-terminal domain of vertebrate Tap protein. The vertebrate Tap protein is a member of the NXF family of shuttling transport receptors for the nuclear export of mRNA. Its most C-terminal domain is important for binding to FG repeat-containing nuclear pore proteins (FG-nucleoporins) and is sufficient to mediate shuttling. This domain forms a compact four-helix fold related to that of a UBA domain.
Probab=40.88 E-value=92 Score=24.69 Aligned_cols=40 Identities=15% Similarity=0.269 Sum_probs=36.1
Q ss_pred HHHHHHHHHHHHHHhCCCHHHHHHHHHhcCCChHHHHHHh
Q 007763 76 RQRQEEDITRISTVLSISKVAASILLRFYNWSVSKVHDEW 115 (590)
Q Consensus 76 ~~~~~~~i~~v~~il~i~~~~a~~LL~~~~W~~~~l~e~~ 115 (590)
...+.+.|..++...++....+..+|...+||-+..+..|
T Consensus 9 ~~~q~~~v~~~~~~Tgmn~~~s~~cLe~~~Wd~~~Al~~F 48 (63)
T smart00804 9 SPEQQEMVQAFSAQTGMNAEYSQMCLEDNNWDYERALKNF 48 (63)
T ss_pred CHHHHHHHHHHHHHHCCCHHHHHHHHHHcCCCHHHHHHHH
Confidence 3467888999999999999999999999999999988776
No 174
>PF14569 zf-UDP: Zinc-binding RING-finger; PDB: 1WEO_A.
Probab=40.20 E-value=32 Score=28.39 Aligned_cols=49 Identities=24% Similarity=0.685 Sum_probs=19.7
Q ss_pred CCcccccccccccCCC---Cce-ec-CCCCccchhhHH-HhhcCCCceecccCCCCCCCcc
Q 007763 139 GEEMTCGICFENYPSD---RLL-AA-ACGHPFCSSCWT-AINDGPGCLMLRCPDPSCGAAV 193 (590)
Q Consensus 139 ~~~~~C~IC~e~~~~~---~~~-~l-~CgH~fC~~C~~-~i~~g~~~~~i~CP~~~C~~~i 193 (590)
.....|.||-+.+... +++ .. .|+-..|+.|+. .+++|. -.|| +|+...
T Consensus 7 ~~~qiCqiCGD~VGl~~~Ge~FVAC~eC~fPvCr~CyEYErkeg~----q~Cp--qCkt~y 61 (80)
T PF14569_consen 7 LNGQICQICGDDVGLTENGEVFVACHECAFPVCRPCYEYERKEGN----QVCP--QCKTRY 61 (80)
T ss_dssp -SS-B-SSS--B--B-SSSSB--S-SSS-----HHHHHHHHHTS-----SB-T--TT--B-
T ss_pred cCCcccccccCccccCCCCCEEEEEcccCCccchhHHHHHhhcCc----cccc--ccCCCc
Confidence 3456799999986532 333 33 388899999994 455654 4788 887543
No 175
>KOG4739 consensus Uncharacterized protein involved in synaptonemal complex formation [Cell cycle control, cell division, chromosome partitioning; General function prediction only]
Probab=39.82 E-value=4.1e+02 Score=26.79 Aligned_cols=24 Identities=33% Similarity=0.865 Sum_probs=17.9
Q ss_pred cCCCceeecCCC----cceeeeccccccc
Q 007763 308 QGCMHMTCTPPC----KFEFCWLCLGQWS 332 (590)
Q Consensus 308 ~GCnhMtC~~~C----~~~FCw~C~~~w~ 332 (590)
..|.||.|. +| ...+|.+|.....
T Consensus 21 TaC~HvfC~-~C~k~~~~~~C~lCkk~ir 48 (233)
T KOG4739|consen 21 TACRHVFCE-PCLKASSPDVCPLCKKSIR 48 (233)
T ss_pred eechhhhhh-hhcccCCccccccccceee
Confidence 569999998 45 3459999987643
No 176
>PRK14892 putative transcription elongation factor Elf1; Provisional
Probab=39.75 E-value=19 Score=31.21 Aligned_cols=27 Identities=26% Similarity=0.588 Sum_probs=17.1
Q ss_pred cCCCCCCccee---eccCCCceeecCCCcce
Q 007763 295 KPCPRCKRPIE---KNQGCMHMTCTPPCKFE 322 (590)
Q Consensus 295 K~CP~C~~~IE---K~~GCnhMtC~~~C~~~ 322 (590)
-.||+|+...- +..|=-|..|. .||+.
T Consensus 22 f~CP~Cge~~v~v~~~k~~~h~~C~-~CG~y 51 (99)
T PRK14892 22 FECPRCGKVSISVKIKKNIAIITCG-NCGLY 51 (99)
T ss_pred eECCCCCCeEeeeecCCCcceEECC-CCCCc
Confidence 57999994322 23355678887 67654
No 177
>KOG1952 consensus Transcription factor NF-X1, contains NFX-type Zn2+-binding and R3H domains [Transcription]
Probab=39.00 E-value=34 Score=40.13 Aligned_cols=51 Identities=25% Similarity=0.518 Sum_probs=33.9
Q ss_pred CCcccccccccccCCCCc-eec-CCCCccchhhHHHhhc---CCCceecccCCCCCCC
Q 007763 139 GEEMTCGICFENYPSDRL-LAA-ACGHPFCSSCWTAIND---GPGCLMLRCPDPSCGA 191 (590)
Q Consensus 139 ~~~~~C~IC~e~~~~~~~-~~l-~CgH~fC~~C~~~i~~---g~~~~~i~CP~~~C~~ 191 (590)
...+.|.||++.+....+ .+. .|-|.|-..||..|.. ..+...-+|| .|..
T Consensus 189 ~~~yeCmIC~e~I~~t~~~WSC~sCYhVFHl~CI~~WArs~ek~~~~~WrCP--~Cqs 244 (950)
T KOG1952|consen 189 NRKYECMICTERIKRTAPVWSCKSCYHVFHLNCIKKWARSSEKTGQDGWRCP--ACQS 244 (950)
T ss_pred cCceEEEEeeeeccccCCceecchhhhhhhHHHHHHHHHHhhhccCccccCC--cccc
Confidence 346789999999865443 443 4899999999943321 1112457999 7853
No 178
>PHA02929 N1R/p28-like protein; Provisional
Probab=38.73 E-value=13 Score=37.50 Aligned_cols=40 Identities=20% Similarity=0.553 Sum_probs=27.8
Q ss_pred CcCCCCCCcceeeccCCCc---eeecCCCcceeeecccccccCCC
Q 007763 294 SKPCPRCKRPIEKNQGCMH---MTCTPPCKFEFCWLCLGQWSDHG 335 (590)
Q Consensus 294 tK~CP~C~~~IEK~~GCnh---MtC~~~C~~~FCw~C~~~w~~H~ 335 (590)
...||-|...+.....-+. +.- +|+|.||..|...|....
T Consensus 174 ~~eC~ICle~~~~~~~~~~~~~vl~--~C~H~FC~~CI~~Wl~~~ 216 (238)
T PHA02929 174 DKECAICMEKVYDKEIKNMYFGILS--NCNHVFCIECIDIWKKEK 216 (238)
T ss_pred CCCCccCCcccccCccccccceecC--CCCCcccHHHHHHHHhcC
Confidence 4689999998764432211 222 499999999999997543
No 179
>KOG0943 consensus Predicted ubiquitin-protein ligase/hyperplastic discs protein, HECT superfamily [Posttranslational modification, protein turnover, chaperones]
Probab=37.52 E-value=20 Score=43.47 Aligned_cols=16 Identities=25% Similarity=0.447 Sum_probs=7.8
Q ss_pred HHHHHHHHHHhHHHHH
Q 007763 454 FEYLQGEAESGLERLH 469 (590)
Q Consensus 454 fe~~Q~~le~~~E~L~ 469 (590)
||-.|....+.+|+|.
T Consensus 2419 FEtKer~Fnka~EK~R 2434 (3015)
T KOG0943|consen 2419 FETKERKFNKAMEKLR 2434 (3015)
T ss_pred cchHHHHHHHHHHHHH
Confidence 4444444555555543
No 180
>KOG0943 consensus Predicted ubiquitin-protein ligase/hyperplastic discs protein, HECT superfamily [Posttranslational modification, protein turnover, chaperones]
Probab=37.51 E-value=24 Score=42.88 Aligned_cols=9 Identities=33% Similarity=0.612 Sum_probs=4.1
Q ss_pred HHHcccccc
Q 007763 513 ALENGLSDV 521 (590)
Q Consensus 513 ~le~gl~~~ 521 (590)
.||.|-..+
T Consensus 2475 slesghaPl 2483 (3015)
T KOG0943|consen 2475 SLESGHAPL 2483 (3015)
T ss_pred ccccCCCcc
Confidence 345554443
No 181
>KOG2177 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=37.51 E-value=13 Score=37.41 Aligned_cols=25 Identities=20% Similarity=0.533 Sum_probs=19.8
Q ss_pred CCCCCCcceeeccCCCceeecCCCcceeeeccc
Q 007763 296 PCPRCKRPIEKNQGCMHMTCTPPCKFEFCWLCL 328 (590)
Q Consensus 296 ~CP~C~~~IEK~~GCnhMtC~~~C~~~FCw~C~ 328 (590)
.|+.+... .++.|. .|....|+.|.
T Consensus 88 ~c~~~~~~-------~~~~c~-~~~~~~c~~c~ 112 (386)
T KOG2177|consen 88 LCEKHGEE-------LKLFCE-EDEKLLCVLCR 112 (386)
T ss_pred hhhhcCCc-------ceEEec-ccccccCCCCC
Confidence 56666555 559999 89999999997
No 182
>PRK04023 DNA polymerase II large subunit; Validated
Probab=37.41 E-value=26 Score=42.02 Aligned_cols=33 Identities=24% Similarity=0.582 Sum_probs=21.8
Q ss_pred CCCcccCCCCCCCceEeeecCCCcceeEe-cCCC-----ccccccCCCc
Q 007763 222 NRKTKWCPAPGCDYAVDFVVGSGNYDVTC-RCSY-----SFCWNCTEEA 264 (590)
Q Consensus 222 ~~~~~~CP~p~C~~~i~~~~~~~~~~v~C-~C~~-----~fC~~C~~~~ 264 (590)
....+.||. |+... ....| .||. .||..|+...
T Consensus 623 EVg~RfCps--CG~~t--------~~frCP~CG~~Te~i~fCP~CG~~~ 661 (1121)
T PRK04023 623 EIGRRKCPS--CGKET--------FYRRCPFCGTHTEPVYRCPRCGIEV 661 (1121)
T ss_pred cccCccCCC--CCCcC--------CcccCCCCCCCCCcceeCccccCcC
Confidence 345678995 87542 34578 7985 4888887553
No 183
>COG1998 RPS31 Ribosomal protein S27AE [Translation, ribosomal structure and biogenesis]
Probab=36.88 E-value=23 Score=26.65 Aligned_cols=26 Identities=23% Similarity=0.607 Sum_probs=13.7
Q ss_pred cCCCCCCcceeeccCCCceeecCCCcc
Q 007763 295 KPCPRCKRPIEKNQGCMHMTCTPPCKF 321 (590)
Q Consensus 295 K~CP~C~~~IEK~~GCnhMtC~~~C~~ 321 (590)
+.||+|+..+.-..-=+...|. .||+
T Consensus 20 ~~CPrCG~gvfmA~H~dR~~CG-kCgy 45 (51)
T COG1998 20 RFCPRCGPGVFMADHKDRWACG-KCGY 45 (51)
T ss_pred ccCCCCCCcchhhhcCceeEec-cccc
Confidence 7888888544322111235565 5653
No 184
>COG5432 RAD18 RING-finger-containing E3 ubiquitin ligase [Signal transduction mechanisms]
Probab=36.54 E-value=10 Score=38.74 Aligned_cols=30 Identities=30% Similarity=0.843 Sum_probs=23.7
Q ss_pred cCCCCCCcceeeccCCCceeecCCCcceeeecccccc
Q 007763 295 KPCPRCKRPIEKNQGCMHMTCTPPCKFEFCWLCLGQW 331 (590)
Q Consensus 295 K~CP~C~~~IEK~~GCnhMtC~~~C~~~FCw~C~~~w 331 (590)
-+|--|.-.|- +-|.-+|||.||++|-..+
T Consensus 26 lrC~IC~~~i~-------ip~~TtCgHtFCslCIR~h 55 (391)
T COG5432 26 LRCRICDCRIS-------IPCETTCGHTFCSLCIRRH 55 (391)
T ss_pred HHhhhhhheee-------cceecccccchhHHHHHHH
Confidence 46888887777 7775479999999998754
No 185
>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]
Probab=36.50 E-value=24 Score=41.43 Aligned_cols=35 Identities=23% Similarity=0.732 Sum_probs=28.4
Q ss_pred cCCCCCCcceeeccCCCceeecCCCcce-----eeeccccc
Q 007763 295 KPCPRCKRPIEKNQGCMHMTCTPPCKFE-----FCWLCLGQ 330 (590)
Q Consensus 295 K~CP~C~~~IEK~~GCnhMtC~~~C~~~-----FCw~C~~~ 330 (590)
-.||+|..++.-...=|.|.|. .||++ .|.-|++.
T Consensus 445 ~~Cp~Cd~~lt~H~~~~~L~CH-~Cg~~~~~p~~Cp~Cgs~ 484 (730)
T COG1198 445 AECPNCDSPLTLHKATGQLRCH-YCGYQEPIPQSCPECGSE 484 (730)
T ss_pred ccCCCCCcceEEecCCCeeEeC-CCCCCCCCCCCCCCCCCC
Confidence 4788888888765555889998 89988 89999876
No 186
>PRK14714 DNA polymerase II large subunit; Provisional
Probab=36.36 E-value=30 Score=42.50 Aligned_cols=11 Identities=36% Similarity=1.023 Sum_probs=6.1
Q ss_pred cCCCCCCccee
Q 007763 295 KPCPRCKRPIE 305 (590)
Q Consensus 295 K~CP~C~~~IE 305 (590)
..||+|+.++.
T Consensus 710 ~~CP~CGtplv 720 (1337)
T PRK14714 710 VECPRCDVELT 720 (1337)
T ss_pred ccCCCCCCccc
Confidence 45666665543
No 187
>PF14446 Prok-RING_1: Prokaryotic RING finger family 1
Probab=35.93 E-value=29 Score=26.70 Aligned_cols=32 Identities=25% Similarity=0.923 Sum_probs=25.1
Q ss_pred cccccccccccC-CCCceecC-CCCccchhhHHH
Q 007763 141 EMTCGICFENYP-SDRLLAAA-CGHPFCSSCWTA 172 (590)
Q Consensus 141 ~~~C~IC~e~~~-~~~~~~l~-CgH~fC~~C~~~ 172 (590)
...|++|-+.+. .++++..+ ||-.|.++||..
T Consensus 5 ~~~C~~Cg~~~~~~dDiVvCp~CgapyHR~C~~~ 38 (54)
T PF14446_consen 5 GCKCPVCGKKFKDGDDIVVCPECGAPYHRDCWEK 38 (54)
T ss_pred CccChhhCCcccCCCCEEECCCCCCcccHHHHhh
Confidence 346999999885 45676665 999999999943
No 188
>PF01428 zf-AN1: AN1-like Zinc finger; InterPro: IPR000058 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents the AN1-type zinc finger domain, which has a dimetal (zinc)-bound alpha/beta fold. This domain was first identified as a zinc finger at the C terminus of AN1 Q91889 from SWISSPROT, a ubiquitin-like protein in Xenopus laevis []. The AN1-type zinc finger contains six conserved cysteines and two histidines that could potentially coordinate 2 zinc atoms. Certain stress-associated proteins (SAP) contain AN1 domain, often in combination with A20 zinc finger domains (SAP8) or C2H2 domains (SAP16) []. For example, the human protein Znf216 has an A20 zinc-finger at the N terminus and an AN1 zinc-finger at the C terminus, acting to negatively regulate the NFkappaB activation pathway and to interact with components of the immune response like RIP, IKKgamma and TRAF6. The interact of Znf216 with IKK-gamma and RIP is mediated by the A20 zinc-finger domain, while its interaction with TRAF6 is mediated by the AN1 zinc-finger domain; therefore, both zinc-finger domains are involved in regulating the immune response []. The AN1 zinc finger domain is also found in proteins containing a ubiquitin-like domain, which are involved in the ubiquitination pathway []. Proteins containing an AN1-type zinc finger include: Ascidian posterior end mark 6 (pem-6) protein []. Human AWP1 protein (associated with PRK1), which is expressed during early embryogenesis []. Human immunoglobulin mu binding protein 2 (SMUBP-2), mutations in which cause muscular atrophy with respiratory distress type 1 []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 1WFP_A 1WYS_A 1WG2_A 1WFH_A 1X4W_A 1WFE_A 1WFL_A 1X4V_A.
Probab=35.76 E-value=20 Score=25.92 Aligned_cols=29 Identities=31% Similarity=0.744 Sum_probs=15.8
Q ss_pred CCCCCCCceEeeecCCCcceeEe-cCCCccccccCCC
Q 007763 228 CPAPGCDYAVDFVVGSGNYDVTC-RCSYSFCWNCTEE 263 (590)
Q Consensus 228 CP~p~C~~~i~~~~~~~~~~v~C-~C~~~fC~~C~~~ 263 (590)
|..++|.... ...+.| .|+..||..++.+
T Consensus 1 C~~~~C~~~~-------~~~~~C~~C~~~FC~~Hr~~ 30 (43)
T PF01428_consen 1 CSFPGCKKKD-------FLPFKCKHCGKSFCLKHRLP 30 (43)
T ss_dssp -SSTTT--BC-------TSHEE-TTTS-EE-TTTHST
T ss_pred CccCcCcCcc-------CCCeECCCCCcccCccccCc
Confidence 4455676432 246789 7999999998744
No 189
>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=35.72 E-value=9.8 Score=39.49 Aligned_cols=28 Identities=18% Similarity=0.555 Sum_probs=20.4
Q ss_pred cCCCCCCcceeec-cCCCceeecCCCccee
Q 007763 295 KPCPRCKRPIEKN-QGCMHMTCTPPCKFEF 323 (590)
Q Consensus 295 K~CP~C~~~IEK~-~GCnhMtC~~~C~~~F 323 (590)
..||+|+..|-+. -.=|.+.|. .|+|+|
T Consensus 27 ~~c~~c~~~~~~~~l~~~~~vc~-~c~~h~ 55 (285)
T TIGR00515 27 TKCPKCGQVLYTKELERNLEVCP-KCDHHM 55 (285)
T ss_pred eECCCCcchhhHHHHHhhCCCCC-CCCCcC
Confidence 7899999888743 345567887 788765
No 190
>CHL00174 accD acetyl-CoA carboxylase beta subunit; Reviewed
Probab=35.68 E-value=9.4 Score=39.73 Aligned_cols=28 Identities=18% Similarity=0.418 Sum_probs=16.4
Q ss_pred cCCCCCCcceeec-cCCCceeecCCCccee
Q 007763 295 KPCPRCKRPIEKN-QGCMHMTCTPPCKFEF 323 (590)
Q Consensus 295 K~CP~C~~~IEK~-~GCnhMtC~~~C~~~F 323 (590)
..||+|+..|.+. -.=|...|. .|+|+|
T Consensus 39 ~kc~~C~~~~~~~~l~~~~~vcp-~c~~h~ 67 (296)
T CHL00174 39 VQCENCYGLNYKKFLKSKMNICE-QCGYHL 67 (296)
T ss_pred eECCCccchhhHHHHHHcCCCCC-CCCCCc
Confidence 5677777766532 334556665 566643
No 191
>PF03115 Astro_capsid: Astrovirus capsid protein precursor; InterPro: IPR004337 The astrovirus genome is apparently organised with nonstructural proteins encoded at the 5' end and structural proteins at the 3' end []. Proteins in this family are encoded by astrovirus ORF2, one of the three astrovirus ORFs (1a, 1b, 2). The proteins contain a viral RNA-dependent RNA polymerase motif []. The 87kDa precursor polyprotein undergoes an intracellular cleavage to form a 79kDa protein. Subsequently, extracellular trypsin cleavage yields the three proteins forming the infectious virion [].; PDB: 3QSQ_A 3TS3_D.
Probab=35.03 E-value=13 Score=43.83 Aligned_cols=15 Identities=27% Similarity=0.290 Sum_probs=0.0
Q ss_pred CCCHHHH-HHHHHhcC
Q 007763 91 SISKVAA-SILLRFYN 105 (590)
Q Consensus 91 ~i~~~~a-~~LL~~~~ 105 (590)
+|+.+.| ++-.|.|.
T Consensus 721 Gi~eerAaria~RAfP 736 (787)
T PF03115_consen 721 GIPEERAARIAKRAFP 736 (787)
T ss_dssp ----------------
T ss_pred CCCHHHHHhhhhccCC
Confidence 4444433 23344443
No 192
>COG0266 Nei Formamidopyrimidine-DNA glycosylase [DNA replication, recombination, and repair]
Probab=34.96 E-value=26 Score=36.06 Aligned_cols=25 Identities=44% Similarity=0.987 Sum_probs=20.5
Q ss_pred cCCCCCCcceeec--cCCCceeecCCCc
Q 007763 295 KPCPRCKRPIEKN--QGCMHMTCTPPCK 320 (590)
Q Consensus 295 K~CP~C~~~IEK~--~GCnhMtC~~~C~ 320 (590)
++|+.|+.+|+|. +|=+--.|. .|+
T Consensus 246 epC~~CGt~I~k~~~~gR~t~~CP-~CQ 272 (273)
T COG0266 246 EPCRRCGTPIEKIKLGGRSTFYCP-VCQ 272 (273)
T ss_pred CCCCccCCEeEEEEEcCCcCEeCC-CCC
Confidence 7999999999975 777777776 675
No 193
>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=34.37 E-value=27 Score=30.62 Aligned_cols=26 Identities=31% Similarity=0.986 Sum_probs=15.3
Q ss_pred cCCCCCCcceeeccCCCceeecCCCcce
Q 007763 295 KPCPRCKRPIEKNQGCMHMTCTPPCKFE 322 (590)
Q Consensus 295 K~CP~C~~~IEK~~GCnhMtC~~~C~~~ 322 (590)
-+||+|+.-.--..|=+ +.|. .|+|+
T Consensus 3 p~CP~C~seytY~dg~~-~iCp-eC~~E 28 (109)
T TIGR00686 3 PPCPKCNSEYTYHDGTQ-LICP-SCLYE 28 (109)
T ss_pred CcCCcCCCcceEecCCe-eECc-ccccc
Confidence 57999987665444432 5555 44443
No 194
>PF03943 TAP_C: TAP C-terminal domain; InterPro: IPR005637 This entry contains the NXF family of shuttling transport receptors for nuclear export of mRNA, which include: vertebrate mRNA export factor TAP or nuclear RNA export factor 1 (NXF1). Caenorhabditis elegans nuclear RNA export factor 1 (nxf-1). yeast mRNA export factor MEX67. Members of the NXF family have a modular structure. A nuclear localization sequence and a noncanonical RNA recognition motif (RRM) (see PDOC00030 from PROSITEDOC) followed by four LRR repeats are located in its N-terminal half. The C-terminal half contains a NTF2 domain (see PDOC50177 from PROSITEDOC) followed by a second domain, TAP-C. The TAP-C domain is important for binding to FG repeat-containing nuclear pore proteins (FG-nucleoporins) and is sufficient to mediate nuclear shuttling [,]. The Tap-C domain is made of four alpha helices packed against each other. The arrangement of helices 1, 2 and 3 is similar to that seen in a UBA fold. and is joined to the next module by flexible 12-residue Pro-rich linker [, ].; GO: 0051028 mRNA transport, 0005634 nucleus; PDB: 1OAI_A 1GO5_A 2KHH_A 2JP7_A.
Probab=33.82 E-value=41 Score=25.39 Aligned_cols=36 Identities=14% Similarity=0.174 Sum_probs=30.6
Q ss_pred HHHHHHHHHhCCCHHHHHHHHHhcCCChHHHHHHhh
Q 007763 81 EDITRISTVLSISKVAASILLRFYNWSVSKVHDEWF 116 (590)
Q Consensus 81 ~~i~~v~~il~i~~~~a~~LL~~~~W~~~~l~e~~~ 116 (590)
+.|..++...++.+.-+...|...+||-++.+..|.
T Consensus 2 ~mv~~~s~~Tgmn~~~s~~CL~~n~Wd~~~A~~~F~ 37 (51)
T PF03943_consen 2 EMVQQFSQQTGMNLEWSQKCLEENNWDYERALQNFE 37 (51)
T ss_dssp HHHHHHHHHCSS-CCHHHHHHHHTTT-CCHHHHHHH
T ss_pred HHHHHHHHHHCCCHHHHHHHHHHcCCCHHHHHHHHH
Confidence 568899999999999999999999999999887764
No 195
>PF02845 CUE: CUE domain; InterPro: IPR003892 This domain may be involved in binding ubiquitin-conjugating enzymes (UBCs). CUE domains also occur in two proteins of the IL-1 signal transduction pathway, tollip and TAB2.; GO: 0005515 protein binding; PDB: 2EKF_A 1OTR_A 1P3Q_Q 1MN3_A 1WGL_A 2EJS_A 2DAE_A 2DHY_A 2DI0_A.
Probab=33.80 E-value=1.3e+02 Score=21.38 Aligned_cols=36 Identities=14% Similarity=0.242 Sum_probs=29.2
Q ss_pred HHHHHHHHHh-CCCHHHHHHHHHhcCCChHHHHHHhh
Q 007763 81 EDITRISTVL-SISKVAASILLRFYNWSVSKVHDEWF 116 (590)
Q Consensus 81 ~~i~~v~~il-~i~~~~a~~LL~~~~W~~~~l~e~~~ 116 (590)
+.|..+.+++ +++++.....|..+++|++..++...
T Consensus 3 ~~v~~L~~mFP~~~~~~I~~~L~~~~~~ve~ai~~LL 39 (42)
T PF02845_consen 3 EMVQQLQEMFPDLDREVIEAVLQANNGDVEAAIDALL 39 (42)
T ss_dssp HHHHHHHHHSSSS-HHHHHHHHHHTTTTHHHHHHHHH
T ss_pred HHHHHHHHHCCCCCHHHHHHHHHHcCCCHHHHHHHHH
Confidence 5677777777 57899999999999999999887764
No 196
>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=33.58 E-value=37 Score=26.83 Aligned_cols=35 Identities=20% Similarity=0.399 Sum_probs=19.0
Q ss_pred CcCCCCCCcceeeccCCCceeecCCCcceeeecccccc
Q 007763 294 SKPCPRCKRPIEKNQGCMHMTCTPPCKFEFCWLCLGQW 331 (590)
Q Consensus 294 tK~CP~C~~~IEK~~GCnhMtC~~~C~~~FCw~C~~~w 331 (590)
...|+.|++..- ---..-.|+ .||.-||-.|....
T Consensus 9 ~~~C~~C~~~F~--~~~rrhhCr-~CG~~vC~~Cs~~~ 43 (69)
T PF01363_consen 9 ASNCMICGKKFS--LFRRRHHCR-NCGRVVCSSCSSQR 43 (69)
T ss_dssp -SB-TTT--B-B--SSS-EEE-T-TT--EEECCCS-EE
T ss_pred CCcCcCcCCcCC--CceeeEccC-CCCCEECCchhCCE
Confidence 478999999884 234446798 89999999998643
No 197
>PRK11827 hypothetical protein; Provisional
Probab=33.37 E-value=34 Score=26.88 Aligned_cols=25 Identities=24% Similarity=0.452 Sum_probs=18.4
Q ss_pred cCCCCCCcceeeccCCCceeecCCCc
Q 007763 295 KPCPRCKRPIEKNQGCMHMTCTPPCK 320 (590)
Q Consensus 295 K~CP~C~~~IEK~~GCnhMtC~~~C~ 320 (590)
-.||.|+.+++-..+=+...|. .|+
T Consensus 9 LaCP~ckg~L~~~~~~~~Lic~-~~~ 33 (60)
T PRK11827 9 IACPVCNGKLWYNQEKQELICK-LDN 33 (60)
T ss_pred eECCCCCCcCeEcCCCCeEECC-ccC
Confidence 5799999999866554567777 454
No 198
>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=33.06 E-value=37 Score=22.35 Aligned_cols=21 Identities=24% Similarity=0.833 Sum_probs=13.7
Q ss_pred CCCCCCcceeeccCCCceeec
Q 007763 296 PCPRCKRPIEKNQGCMHMTCT 316 (590)
Q Consensus 296 ~CP~C~~~IEK~~GCnhMtC~ 316 (590)
.||.|+..+.+..|=-+.+|.
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 499999999998887778876
No 199
>KOG2932 consensus E3 ubiquitin ligase involved in ubiquitination of E-cadherin complex [Posttranslational modification, protein turnover, chaperones]
Probab=33.06 E-value=12 Score=38.58 Aligned_cols=53 Identities=25% Similarity=0.773 Sum_probs=37.2
Q ss_pred CCCcccCCCCCCCceEeeecCCCcceeEe-cCCCccccccCCCcCCCCCchhHHHHHHhhhhhhhhHHHHHhcCcCCCCC
Q 007763 222 NRKTKWCPAPGCDYAVDFVVGSGNYDVTC-RCSYSFCWNCTEEAHRPVDCDTVAKWVLKNSAESENMNWILANSKPCPRC 300 (590)
Q Consensus 222 ~~~~~~CP~p~C~~~i~~~~~~~~~~v~C-~C~~~fC~~C~~~~H~p~~C~~~~~w~~k~~~e~e~~~wi~~ntK~CP~C 300 (590)
++.+.+|-. |+..|.+- + .= .|.+.||..|... |. .|.||.|
T Consensus 87 ~p~VHfCd~--Cd~PI~IY-G------RmIPCkHvFCl~CAr~-~~---------------------------dK~Cp~C 129 (389)
T KOG2932|consen 87 GPRVHFCDR--CDFPIAIY-G------RMIPCKHVFCLECARS-DS---------------------------DKICPLC 129 (389)
T ss_pred CcceEeecc--cCCcceee-e------cccccchhhhhhhhhc-Cc---------------------------cccCcCc
Confidence 456677874 87766432 1 12 5899999999743 31 1999999
Q ss_pred CcceeeccCCC
Q 007763 301 KRPIEKNQGCM 311 (590)
Q Consensus 301 ~~~IEK~~GCn 311 (590)
.-.|+|.+-|+
T Consensus 130 ~d~VqrIeq~~ 140 (389)
T KOG2932|consen 130 DDRVQRIEQIM 140 (389)
T ss_pred ccHHHHHHHhc
Confidence 99999887763
No 200
>TIGR00599 rad18 DNA repair protein rad18. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=32.86 E-value=13 Score=40.24 Aligned_cols=32 Identities=28% Similarity=0.685 Sum_probs=23.9
Q ss_pred cCCCCCCcceeeccCCCceeecCCCcceeeecccccccC
Q 007763 295 KPCPRCKRPIEKNQGCMHMTCTPPCKFEFCWLCLGQWSD 333 (590)
Q Consensus 295 K~CP~C~~~IEK~~GCnhMtC~~~C~~~FCw~C~~~w~~ 333 (590)
-.||-|...+. +++. . +|+|.||..|...|-.
T Consensus 27 l~C~IC~d~~~-----~Pvi-t-pCgH~FCs~CI~~~l~ 58 (397)
T TIGR00599 27 LRCHICKDFFD-----VPVL-T-SCSHTFCSLCIRRCLS 58 (397)
T ss_pred cCCCcCchhhh-----CccC-C-CCCCchhHHHHHHHHh
Confidence 58999988764 3333 4 6999999999987653
No 201
>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]
Probab=32.66 E-value=18 Score=28.18 Aligned_cols=7 Identities=57% Similarity=1.621 Sum_probs=4.2
Q ss_pred cCCCCCC
Q 007763 295 KPCPRCK 301 (590)
Q Consensus 295 K~CP~C~ 301 (590)
-+||+|+
T Consensus 28 F~CPnCG 34 (61)
T COG2888 28 FPCPNCG 34 (61)
T ss_pred eeCCCCC
Confidence 3566666
No 202
>PF09726 Macoilin: Transmembrane protein; InterPro: IPR019130 This entry represents the multi-pass transmembrane protein Macoilin, which is highly conserved in eukaryotes. ; GO: 0016021 integral to membrane
Probab=32.29 E-value=9e+02 Score=28.53 Aligned_cols=72 Identities=24% Similarity=0.317 Sum_probs=37.9
Q ss_pred hhHHHHHHHHHHHHHHHHHHHhhhhhhcccCccchhHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHhhcCCCCCcHHHHH
Q 007763 414 SQLKFITEAWLQIVECRRVLKWTYAYGYYLPDHEHAKRQFFEYLQGEAESGLERLHQCAEKELQIYLNADGPSKDFNEFR 493 (590)
Q Consensus 414 ~~~~~l~~a~~~l~~~R~~L~~sy~~~yyl~~~~~~~~~~fe~~Q~~le~~~E~L~~~le~~l~~~~~~~~~~~~~~~~~ 493 (590)
.+...|..|+..+.+=-..|..+ |..+...|..||..+ +++.+++|.+...|-+.- +++.++|
T Consensus 587 ~~~e~L~~aL~amqdk~~~LE~s------LsaEtriKldLfsaL-g~akrq~ei~~~~~~~~d----------~ei~~lk 649 (697)
T PF09726_consen 587 KDTEVLMSALSAMQDKNQHLENS------LSAETRIKLDLFSAL-GDAKRQLEIAQGQLRKKD----------KEIEELK 649 (697)
T ss_pred hhHHHHHHHHHHHHHHHHHHHHh------hhHHHHHHHHHHHHH-HHHHHHHHHHHHHHHHHH----------HHHHHHH
Confidence 45556666666666655555221 222233466677665 666667666665543311 1233556
Q ss_pred HHHHHHHHh
Q 007763 494 TKLAGLTSV 502 (590)
Q Consensus 494 ~~l~~lt~~ 502 (590)
.+|+.+..|
T Consensus 650 ~ki~~~~av 658 (697)
T PF09726_consen 650 AKIAQLLAV 658 (697)
T ss_pred HHHHHHHhc
Confidence 666555443
No 203
>KOG2906 consensus RNA polymerase III subunit C11 [Transcription]
Probab=32.28 E-value=42 Score=28.92 Aligned_cols=29 Identities=28% Similarity=0.784 Sum_probs=18.5
Q ss_pred ccCCCCCCCceEeeecCCCcceeEe-cCCCcc
Q 007763 226 KWCPAPGCDYAVDFVVGSGNYDVTC-RCSYSF 256 (590)
Q Consensus 226 ~~CP~p~C~~~i~~~~~~~~~~v~C-~C~~~f 256 (590)
.+||. |++.+.+..+.....+.| .|++.|
T Consensus 2 ~FCP~--Cgn~Live~g~~~~rf~C~tCpY~~ 31 (105)
T KOG2906|consen 2 LFCPT--CGNMLIVESGESCNRFSCRTCPYVF 31 (105)
T ss_pred cccCC--CCCEEEEecCCeEeeEEcCCCCcee
Confidence 47985 988887765544455666 565443
No 204
>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=32.25 E-value=28 Score=31.53 Aligned_cols=26 Identities=8% Similarity=0.033 Sum_probs=17.8
Q ss_pred cCCCCCCcceeeccCCCceeecCCCcce
Q 007763 295 KPCPRCKRPIEKNQGCMHMTCTPPCKFE 322 (590)
Q Consensus 295 K~CP~C~~~IEK~~GCnhMtC~~~C~~~ 322 (590)
+.||+|++..---.- +.++|. .||..
T Consensus 10 r~Cp~cg~kFYDLnk-~p~vcP-~cg~~ 35 (129)
T TIGR02300 10 RICPNTGSKFYDLNR-RPAVSP-YTGEQ 35 (129)
T ss_pred ccCCCcCccccccCC-CCccCC-CcCCc
Confidence 689999987763222 678887 56554
No 205
>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=32.12 E-value=33 Score=26.51 Aligned_cols=44 Identities=30% Similarity=0.749 Sum_probs=30.3
Q ss_pred cccccccccCCCCceecCCC--CccchhhHHHhhcCCCceecccCCCCCCCccc
Q 007763 143 TCGICFENYPSDRLLAAACG--HPFCSSCWTAINDGPGCLMLRCPDPSCGAAVG 194 (590)
Q Consensus 143 ~C~IC~e~~~~~~~~~l~Cg--H~fC~~C~~~i~~g~~~~~i~CP~~~C~~~i~ 194 (590)
.|..|-.+++.+..-..-|. ..||.+|...+-. -.|| .|+-.+.
T Consensus 7 nCE~C~~dLp~~s~~A~ICSfECTFC~~C~e~~l~------~~CP--NCgGelv 52 (57)
T PF06906_consen 7 NCECCDKDLPPDSPEAYICSFECTFCADCAETMLN------GVCP--NCGGELV 52 (57)
T ss_pred CccccCCCCCCCCCcceEEeEeCcccHHHHHHHhc------CcCc--CCCCccc
Confidence 58888888877665555565 3799999955433 3688 7876553
No 206
>PF09889 DUF2116: Uncharacterized protein containing a Zn-ribbon (DUF2116); InterPro: IPR019216 This entry contains various hypothetical prokaryotic proteins whose functions are unknown. They contain a conserved zinc ribbon motif in the N-terminal part and a predicted transmembrane segment in the C-terminal part.
Probab=32.00 E-value=8.8 Score=30.03 Aligned_cols=11 Identities=55% Similarity=1.313 Sum_probs=9.9
Q ss_pred cCCCCCCccee
Q 007763 295 KPCPRCKRPIE 305 (590)
Q Consensus 295 K~CP~C~~~IE 305 (590)
|-||.|+.+|.
T Consensus 4 kHC~~CG~~Ip 14 (59)
T PF09889_consen 4 KHCPVCGKPIP 14 (59)
T ss_pred CcCCcCCCcCC
Confidence 78999999998
No 207
>COG3809 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=31.87 E-value=35 Score=28.19 Aligned_cols=35 Identities=31% Similarity=0.779 Sum_probs=26.1
Q ss_pred cCCCCCCcceeeccCCCceeecCCCcceeeecccccccCCCC
Q 007763 295 KPCPRCKRPIEKNQGCMHMTCTPPCKFEFCWLCLGQWSDHGE 336 (590)
Q Consensus 295 K~CP~C~~~IEK~~GCnhMtC~~~C~~~FCw~C~~~w~~H~~ 336 (590)
..||.|++.+. |.=+..=-...|-.|.+-|-+.|.
T Consensus 2 llCP~C~v~l~-------~~~rs~vEiD~CPrCrGVWLDrGE 36 (88)
T COG3809 2 LLCPICGVELV-------MSVRSGVEIDYCPRCRGVWLDRGE 36 (88)
T ss_pred cccCcCCceee-------eeeecCceeeeCCccccEeecchh
Confidence 57999999888 655523445668899999987664
No 208
>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=31.73 E-value=20 Score=27.96 Aligned_cols=41 Identities=32% Similarity=0.515 Sum_probs=31.7
Q ss_pred cCCCCCCcceee--ccCCCceeecCCCcceeeecccccccCCCC
Q 007763 295 KPCPRCKRPIEK--NQGCMHMTCTPPCKFEFCWLCLGQWSDHGE 336 (590)
Q Consensus 295 K~CP~C~~~IEK--~~GCnhMtC~~~C~~~FCw~C~~~w~~H~~ 336 (590)
..||-|+...-- .+-=|+-+|+ .|+...|-+||-.-.+|-.
T Consensus 3 ~~CPlCkt~~n~gsk~~pNyntCT-~Ck~~VCnlCGFNP~Phl~ 45 (61)
T PF05715_consen 3 SLCPLCKTTLNVGSKDPPNYNTCT-ECKSQVCNLCGFNPTPHLT 45 (61)
T ss_pred ccCCcccchhhcCCCCCCCccHHH-HHhhhhhcccCCCCCcccc
Confidence 579999987731 1346889999 8999999999876566653
No 209
>PF09723 Zn-ribbon_8: Zinc ribbon domain; InterPro: IPR013429 This entry represents a region of about 41 amino acids found in a number of small proteins in a wide range of bacteria. The region usually begins with the initiator Met and contains two CxxC motifs separated by 17 amino acids. One protein in this entry has been noted as a putative regulatory protein, designated FmdB []. Most proteins in this entry have a C-terminal region containing highly degenerate sequence.
Probab=31.54 E-value=50 Score=23.72 Aligned_cols=12 Identities=33% Similarity=1.146 Sum_probs=8.8
Q ss_pred cCCCCCCc-ceee
Q 007763 295 KPCPRCKR-PIEK 306 (590)
Q Consensus 295 K~CP~C~~-~IEK 306 (590)
..||+|+. .++|
T Consensus 27 ~~CP~Cg~~~~~r 39 (42)
T PF09723_consen 27 VPCPECGSTEVRR 39 (42)
T ss_pred CcCCCCCCCceEE
Confidence 67888887 6554
No 210
>COG1594 RPB9 DNA-directed RNA polymerase, subunit M/Transcription elongation factor TFIIS [Transcription]
Probab=31.28 E-value=33 Score=30.52 Aligned_cols=28 Identities=21% Similarity=0.645 Sum_probs=19.2
Q ss_pred cCCCCCCcceee--ccCCCceeecCCCccee
Q 007763 295 KPCPRCKRPIEK--NQGCMHMTCTPPCKFEF 323 (590)
Q Consensus 295 K~CP~C~~~IEK--~~GCnhMtC~~~C~~~F 323 (590)
+-||+|+.++.- .++=+-+.|+ +||+.+
T Consensus 3 ~FCp~Cgsll~p~~~~~~~~l~C~-kCgye~ 32 (113)
T COG1594 3 RFCPKCGSLLYPKKDDEGGKLVCR-KCGYEE 32 (113)
T ss_pred cccCCccCeeEEeEcCCCcEEECC-CCCcch
Confidence 679999998874 1122278888 677654
No 211
>PF04147 Nop14: Nop14-like family ; InterPro: IPR007276 Emg1 and Nop14 are novel proteins whose interaction is required for the maturation of the 18S rRNA and for 40S ribosome production [].
Probab=30.94 E-value=41 Score=40.37 Aligned_cols=6 Identities=0% Similarity=0.379 Sum_probs=2.2
Q ss_pred HHHHHH
Q 007763 508 ENLVRA 513 (590)
Q Consensus 508 ~~l~~~ 513 (590)
.+++..
T Consensus 827 k~i~~~ 832 (840)
T PF04147_consen 827 KRIMSS 832 (840)
T ss_pred HHHHHH
Confidence 333333
No 212
>PF04050 Upf2: Up-frameshift suppressor 2 ; InterPro: IPR007193 This entry represents Up-frameshift suppressor 2 (also known as Nonsense-mediated mRNA decay protein 2). Transcripts harbouring premature signals for translation termination are recognised and rapidly degraded by eukaryotic cells through a pathway known as nonsense-mediated mRNA decay. In Saccharomyces cerevisiae, three trans-acting factors (Upf1 to Upf3) are required for nonsense-mediated mRNA decay [].; PDB: 2WJV_D.
Probab=30.54 E-value=33 Score=32.69 Aligned_cols=12 Identities=8% Similarity=0.235 Sum_probs=5.9
Q ss_pred HHHHHHHHHHHH
Q 007763 73 ADIRQRQEEDIT 84 (590)
Q Consensus 73 ~~i~~~~~~~i~ 84 (590)
+++.+.+.+.+.
T Consensus 63 ~dFeref~kmm~ 74 (170)
T PF04050_consen 63 EDFEREFQKMMA 74 (170)
T ss_dssp HHHHHHHHHHHH
T ss_pred HHHHHHHHHHHH
Confidence 355555554444
No 213
>PRK14811 formamidopyrimidine-DNA glycosylase; Provisional
Probab=30.46 E-value=34 Score=35.19 Aligned_cols=22 Identities=50% Similarity=1.005 Sum_probs=15.8
Q ss_pred cCCCCCCcceeec--cCCCceeec
Q 007763 295 KPCPRCKRPIEKN--QGCMHMTCT 316 (590)
Q Consensus 295 K~CP~C~~~IEK~--~GCnhMtC~ 316 (590)
++||.|+.+|+|. +|=.--+|.
T Consensus 236 ~pC~~Cg~~I~~~~~~gR~ty~Cp 259 (269)
T PRK14811 236 QPCPRCGTPIEKIVVGGRGTHFCP 259 (269)
T ss_pred CCCCcCCCeeEEEEECCCCcEECC
Confidence 7999999999964 554444444
No 214
>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=30.39 E-value=32 Score=22.67 Aligned_cols=22 Identities=36% Similarity=0.733 Sum_probs=11.4
Q ss_pred cCCCCCCcceeec--cCCCceeec
Q 007763 295 KPCPRCKRPIEKN--QGCMHMTCT 316 (590)
Q Consensus 295 K~CP~C~~~IEK~--~GCnhMtC~ 316 (590)
++||+|+.+|++. +|=+...|.
T Consensus 2 ~~C~rC~~~~~~~~~~~r~~~~C~ 25 (30)
T PF06827_consen 2 EKCPRCWNYIEDIGINGRSTYLCP 25 (30)
T ss_dssp SB-TTT--BBEEEEETTEEEEE-T
T ss_pred CcCccCCCcceEeEecCCCCeECc
Confidence 6899999999753 344444554
No 215
>PRK12495 hypothetical protein; Provisional
Probab=29.54 E-value=39 Score=33.46 Aligned_cols=27 Identities=33% Similarity=0.730 Sum_probs=18.9
Q ss_pred CcCCCCCCcceeeccCCCceeecCCCcceeeecccccc
Q 007763 294 SKPCPRCKRPIEKNQGCMHMTCTPPCKFEFCWLCLGQW 331 (590)
Q Consensus 294 tK~CP~C~~~IEK~~GCnhMtC~~~C~~~FCw~C~~~w 331 (590)
.+.||.|+.||-+..| ..||-.|....
T Consensus 42 a~hC~~CG~PIpa~pG-----------~~~Cp~CQ~~~ 68 (226)
T PRK12495 42 NAHCDECGDPIFRHDG-----------QEFCPTCQQPV 68 (226)
T ss_pred hhhcccccCcccCCCC-----------eeECCCCCCcc
Confidence 4799999999995444 44566666543
No 216
>PF12861 zf-Apc11: Anaphase-promoting complex subunit 11 RING-H2 finger
Probab=29.49 E-value=17 Score=30.62 Aligned_cols=35 Identities=29% Similarity=0.737 Sum_probs=28.1
Q ss_pred cCCCCCCcceeeccCCCceeecCCCcceeeecccccccCC
Q 007763 295 KPCPRCKRPIEKNQGCMHMTCTPPCKFEFCWLCLGQWSDH 334 (590)
Q Consensus 295 K~CP~C~~~IEK~~GCnhMtC~~~C~~~FCw~C~~~w~~H 334 (590)
-.||.|+.| ...|.-+.+. |+|.|=..|...|-.-
T Consensus 33 g~Cp~Ck~P---gd~Cplv~g~--C~H~FH~hCI~kWl~~ 67 (85)
T PF12861_consen 33 GCCPDCKFP---GDDCPLVWGK--CSHNFHMHCILKWLST 67 (85)
T ss_pred cCCCCccCC---CCCCceeecc--CccHHHHHHHHHHHcc
Confidence 468888887 3577777776 9999999999999653
No 217
>smart00659 RPOLCX RNA polymerase subunit CX. present in RNA polymerase I, II and III
Probab=29.10 E-value=46 Score=24.39 Aligned_cols=25 Identities=24% Similarity=0.587 Sum_probs=12.8
Q ss_pred CCCCCCcceeeccCCCceeecCCCcce
Q 007763 296 PCPRCKRPIEKNQGCMHMTCTPPCKFE 322 (590)
Q Consensus 296 ~CP~C~~~IEK~~GCnhMtC~~~C~~~ 322 (590)
.|..|+..++...+ .-+.|. .||+.
T Consensus 4 ~C~~Cg~~~~~~~~-~~irC~-~CG~r 28 (44)
T smart00659 4 ICGECGRENEIKSK-DVVRCR-ECGYR 28 (44)
T ss_pred ECCCCCCEeecCCC-CceECC-CCCce
Confidence 45666665554422 335565 45544
No 218
>PF13453 zf-TFIIB: Transcription factor zinc-finger
Probab=29.01 E-value=38 Score=24.13 Aligned_cols=31 Identities=32% Similarity=0.717 Sum_probs=19.0
Q ss_pred CCCCCCcceeeccCCCceeecCCCcceeeecccccccC
Q 007763 296 PCPRCKRPIEKNQGCMHMTCTPPCKFEFCWLCLGQWSD 333 (590)
Q Consensus 296 ~CP~C~~~IEK~~GCnhMtC~~~C~~~FCw~C~~~w~~ 333 (590)
.||+|+..++...- . .=...-|-.|++.|-+
T Consensus 1 ~CP~C~~~l~~~~~-~------~~~id~C~~C~G~W~d 31 (41)
T PF13453_consen 1 KCPRCGTELEPVRL-G------DVEIDVCPSCGGIWFD 31 (41)
T ss_pred CcCCCCcccceEEE-C------CEEEEECCCCCeEEcc
Confidence 59999998875433 1 1223346677777754
No 219
>PRK01103 formamidopyrimidine/5-formyluracil/ 5-hydroxymethyluracil DNA glycosylase; Validated
Probab=28.90 E-value=39 Score=34.81 Aligned_cols=26 Identities=42% Similarity=0.962 Sum_probs=18.0
Q ss_pred CcCCCCCCcceeec--cCCCceeecCCCc
Q 007763 294 SKPCPRCKRPIEKN--QGCMHMTCTPPCK 320 (590)
Q Consensus 294 tK~CP~C~~~IEK~--~GCnhMtC~~~C~ 320 (590)
.++||.|+.+|+|. +|=.-.+|. .|+
T Consensus 245 g~pC~~Cg~~I~~~~~~gR~t~~CP-~CQ 272 (274)
T PRK01103 245 GEPCRRCGTPIEKIKQGGRSTFFCP-RCQ 272 (274)
T ss_pred CCCCCCCCCeeEEEEECCCCcEECc-CCC
Confidence 37999999999964 664445554 454
No 220
>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=28.88 E-value=36 Score=25.38 Aligned_cols=26 Identities=27% Similarity=0.634 Sum_probs=18.5
Q ss_pred cCCC--CCCcceeeccCCCceeecCCCcc
Q 007763 295 KPCP--RCKRPIEKNQGCMHMTCTPPCKF 321 (590)
Q Consensus 295 K~CP--~C~~~IEK~~GCnhMtC~~~C~~ 321 (590)
+.|| .|+.-+.-..--+..+|. +|+.
T Consensus 19 k~CP~~~CG~GvFMA~H~dR~~CG-KCg~ 46 (47)
T PF01599_consen 19 KECPSPRCGAGVFMAEHKDRHYCG-KCGY 46 (47)
T ss_dssp EE-TSTTTTSSSEEEE-SSEEEET-TTSS
T ss_pred hcCCCcccCCceEeeecCCCccCC-Cccc
Confidence 7899 999987655556778888 6874
No 221
>PF08792 A2L_zn_ribbon: A2L zinc ribbon domain; InterPro: IPR014900 This zinc ribbon protein is found associated with some viral A2L transcription factors [].
Probab=28.60 E-value=55 Score=22.46 Aligned_cols=12 Identities=25% Similarity=0.456 Sum_probs=9.2
Q ss_pred CcCCCCCCccee
Q 007763 294 SKPCPRCKRPIE 305 (590)
Q Consensus 294 tK~CP~C~~~IE 305 (590)
.+.|+.|+....
T Consensus 3 ~~~C~~C~~~~i 14 (33)
T PF08792_consen 3 LKKCSKCGGNGI 14 (33)
T ss_pred ceEcCCCCCCeE
Confidence 378998888776
No 222
>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=28.28 E-value=41 Score=34.63 Aligned_cols=24 Identities=46% Similarity=0.956 Sum_probs=17.4
Q ss_pred cCCCCCCcceeec--cCCCceeecCCC
Q 007763 295 KPCPRCKRPIEKN--QGCMHMTCTPPC 319 (590)
Q Consensus 295 K~CP~C~~~IEK~--~GCnhMtC~~~C 319 (590)
++||.|+.+|+|. +|=.-..|. .|
T Consensus 246 ~pC~~Cg~~I~~~~~~gR~t~~CP-~C 271 (272)
T TIGR00577 246 EPCRRCGTPIEKIKVGGRGTHFCP-QC 271 (272)
T ss_pred CCCCCCCCeeEEEEECCCCCEECC-CC
Confidence 6999999999964 664445554 44
No 223
>KOG2164 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=28.21 E-value=24 Score=39.05 Aligned_cols=30 Identities=33% Similarity=0.650 Sum_probs=20.1
Q ss_pred CcCCCCCCcceeeccCCCceeecCCCcceeeeccccc
Q 007763 294 SKPCPRCKRPIEKNQGCMHMTCTPPCKFEFCWLCLGQ 330 (590)
Q Consensus 294 tK~CP~C~~~IEK~~GCnhMtC~~~C~~~FCw~C~~~ 330 (590)
--.||-|-.+-. +..|| .|||-|||-|+-.
T Consensus 186 ~~~CPICL~~~~----~p~~t---~CGHiFC~~CiLq 215 (513)
T KOG2164|consen 186 DMQCPICLEPPS----VPVRT---NCGHIFCGPCILQ 215 (513)
T ss_pred CCcCCcccCCCC----ccccc---ccCceeeHHHHHH
Confidence 368999987665 22232 5888888888653
No 224
>PF14445 Prok-RING_2: Prokaryotic RING finger family 2
Probab=28.21 E-value=12 Score=28.17 Aligned_cols=31 Identities=32% Similarity=0.891 Sum_probs=25.7
Q ss_pred CcccccccccccCCCCceec-CCCCccchhhH
Q 007763 140 EEMTCGICFENYPSDRLLAA-ACGHPFCSSCW 170 (590)
Q Consensus 140 ~~~~C~IC~e~~~~~~~~~l-~CgH~fC~~C~ 170 (590)
..++|..|-+.+|..+.... -||..-|..||
T Consensus 6 sry~CDLCn~~~p~~~LRQCvlCGRWaC~sCW 37 (57)
T PF14445_consen 6 SRYSCDLCNSSHPISELRQCVLCGRWACNSCW 37 (57)
T ss_pred hhHhHHhhcccCcHHHHHHHhhhchhhhhhhh
Confidence 36889999998887766554 59999999999
No 225
>PF14149 YhfH: YhfH-like protein
Probab=28.12 E-value=5.9 Score=27.90 Aligned_cols=25 Identities=32% Similarity=0.877 Sum_probs=20.4
Q ss_pred CcCCCCCCcceeeccCCCceeecCCC
Q 007763 294 SKPCPRCKRPIEKNQGCMHMTCTPPC 319 (590)
Q Consensus 294 tK~CP~C~~~IEK~~GCnhMtC~~~C 319 (590)
.|.||.|+..|+-..-|..+.|. .|
T Consensus 13 ~K~C~~CG~~i~EQ~E~Y~n~C~-~C 37 (37)
T PF14149_consen 13 PKKCTECGKEIEEQAECYGNECD-RC 37 (37)
T ss_pred CcccHHHHHHHHHHHHHHhCcCC-CC
Confidence 59999999999977777777776 45
No 226
>PRK14714 DNA polymerase II large subunit; Provisional
Probab=28.06 E-value=34 Score=42.13 Aligned_cols=30 Identities=23% Similarity=0.608 Sum_probs=22.6
Q ss_pred cCCCCCCcceeeccCCCceeecCCCcce-----eeecccccc
Q 007763 295 KPCPRCKRPIEKNQGCMHMTCTPPCKFE-----FCWLCLGQW 331 (590)
Q Consensus 295 K~CP~C~~~IEK~~GCnhMtC~~~C~~~-----FCw~C~~~w 331 (590)
..||+|+..+.. -+|. .||.. +|-.|+...
T Consensus 668 rkCPkCG~~t~~------~fCP-~CGs~te~vy~CPsCGaev 702 (1337)
T PRK14714 668 RRCPSCGTETYE------NRCP-DCGTHTEPVYVCPDCGAEV 702 (1337)
T ss_pred EECCCCCCcccc------ccCc-ccCCcCCCceeCccCCCcc
Confidence 789999997653 2887 78866 488888754
No 227
>PF14569 zf-UDP: Zinc-binding RING-finger; PDB: 1WEO_A.
Probab=28.03 E-value=31 Score=28.48 Aligned_cols=54 Identities=24% Similarity=0.673 Sum_probs=18.1
Q ss_pred CCceEeeecCCCcceeEe-cCCCccccccCCCcCCCCCchhHHHHHHhhhhhhhhHHHHHhcCcCCCCCCcceeeccCCC
Q 007763 233 CDYAVDFVVGSGNYDVTC-RCSYSFCWNCTEEAHRPVDCDTVAKWVLKNSAESENMNWILANSKPCPRCKRPIEKNQGCM 311 (590)
Q Consensus 233 C~~~i~~~~~~~~~~v~C-~C~~~fC~~C~~~~H~p~~C~~~~~w~~k~~~e~e~~~wi~~ntK~CP~C~~~IEK~~GCn 311 (590)
|+--|-.. ..+...|-| .|++-.|..|. .+. ++..++-||+|+.+..+..|+.
T Consensus 15 CGD~VGl~-~~Ge~FVAC~eC~fPvCr~Cy----------EYE---------------rkeg~q~CpqCkt~ykr~kgsp 68 (80)
T PF14569_consen 15 CGDDVGLT-ENGEVFVACHECAFPVCRPCY----------EYE---------------RKEGNQVCPQCKTRYKRHKGSP 68 (80)
T ss_dssp S--B--B--SSSSB--S-SSS-----HHHH----------HHH---------------HHTS-SB-TTT--B----TT--
T ss_pred ccCccccC-CCCCEEEEEcccCCccchhHH----------HHH---------------hhcCcccccccCCCcccccCCC
Confidence 66555444 345677789 89888887765 221 1123389999999888777764
Q ss_pred c
Q 007763 312 H 312 (590)
Q Consensus 312 h 312 (590)
.
T Consensus 69 ~ 69 (80)
T PF14569_consen 69 R 69 (80)
T ss_dssp -
T ss_pred C
Confidence 4
No 228
>PRK10220 hypothetical protein; Provisional
Probab=27.94 E-value=41 Score=29.61 Aligned_cols=30 Identities=23% Similarity=0.726 Sum_probs=17.5
Q ss_pred cCCCCCCcceeeccCCCceeecCCCcceeeecccccccCC
Q 007763 295 KPCPRCKRPIEKNQGCMHMTCTPPCKFEFCWLCLGQWSDH 334 (590)
Q Consensus 295 K~CP~C~~~IEK~~GCnhMtC~~~C~~~FCw~C~~~w~~H 334 (590)
-+||+|..-.-=..|= .+.|. .|+..|...
T Consensus 4 P~CP~C~seytY~d~~-~~vCp---------eC~hEW~~~ 33 (111)
T PRK10220 4 PHCPKCNSEYTYEDNG-MYICP---------ECAHEWNDA 33 (111)
T ss_pred CcCCCCCCcceEcCCC-eEECC---------cccCcCCcc
Confidence 6899998765533332 24454 555566543
No 229
>PHA02664 hypothetical protein; Provisional
Probab=27.92 E-value=96 Score=32.39 Aligned_cols=13 Identities=31% Similarity=0.261 Sum_probs=5.3
Q ss_pred HHHHHHHHHHHHh
Q 007763 78 RQEEDITRISTVL 90 (590)
Q Consensus 78 ~~~~~i~~v~~il 90 (590)
.++++..+-..+|
T Consensus 513 ~ieee~~ee~~vl 525 (534)
T PHA02664 513 AIEEEEEEERAVL 525 (534)
T ss_pred hhhHHHHHHHHHH
Confidence 3344444444444
No 230
>smart00336 BBOX B-Box-type zinc finger.
Probab=27.63 E-value=52 Score=22.88 Aligned_cols=28 Identities=25% Similarity=0.602 Sum_probs=24.7
Q ss_pred cCCCCCC-cceeeccCCCceeecCCCcceeeeccccc
Q 007763 295 KPCPRCK-RPIEKNQGCMHMTCTPPCKFEFCWLCLGQ 330 (590)
Q Consensus 295 K~CP~C~-~~IEK~~GCnhMtC~~~C~~~FCw~C~~~ 330 (590)
..|+.|. .++. ++|. .|....|..|...
T Consensus 4 ~~C~~h~~~~~~-------~~C~-~c~~~iC~~C~~~ 32 (42)
T smart00336 4 PKCDSHGDEPAE-------FFCE-ECGALLCRTCDEA 32 (42)
T ss_pred CcCCCCCCCceE-------EECC-CCCcccccccChh
Confidence 6799998 8888 9999 8999999999854
No 231
>PF03615 GCM: GCM motif protein; InterPro: IPR003902 GCM transcription factors are a family of proteins which contain a GCM motif. The GCM motif is a domain that has been identified in proteins belonging to a family of transcriptional regulators involved in fundamental developmental processes which comprise Drosophila melanogaster GCM and its mammalian homologs [, , , ]. IN GCM transcription factors the N-terminal moiety contains a DNA-binding domain of 150 residues. Sequence conservation is highest in this GCM domain. In contrast, the C-terminal moiety contains one or two transactivating regions and is only poorly conserved. The GCM motif has been shown to be a DNA binding domain that recognises preferentially the nonpalindromic octamer 5'-ATGCGGGT-3' [, , ]. The GCM motif contains many conserved basic amino acid residues, seven cysteine residues, and four histidine residues []. The conserved cysteines are involved in shaping the overall conformation of the domain, in the process of DNA binding and in the redox regulation of DNA binding []. The GCM domain as a new class of Zn-containing DNA-binding domain with no similarity to any other DNA-binding domain []. The GCM domain consists of a large and a small domain tethered together by one of the two Zn ions present in the structure. The large and the small domains comprise five- and three-stranded beta-sheets, respectively, with three small helical segments packed against the same side of the two beta-sheets. The GCM domain exercises a novel mode of sequence-specific DNA recognition, where the five-stranded beta-pleated sheet inserts into the major groove of the DNA. Residues protruding from the edge strand of the beta-pleated sheet and the following loop and strand contact the bases and backbone of both DNA strands, providing specificity for its DNA target site. ; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 1ODH_A.
Probab=27.41 E-value=55 Score=29.80 Aligned_cols=36 Identities=39% Similarity=0.865 Sum_probs=17.2
Q ss_pred CCCCchhHHHHHHhhhhhhhhHHHHHhcCcCCCC--CCcceeeccCCCceeecCCCcce
Q 007763 266 RPVDCDTVAKWVLKNSAESENMNWILANSKPCPR--CKRPIEKNQGCMHMTCTPPCKFE 322 (590)
Q Consensus 266 ~p~~C~~~~~w~~k~~~e~e~~~wi~~ntK~CP~--C~~~IEK~~GCnhMtC~~~C~~~ 322 (590)
+|..|+.+.+- ..+ |+||+ |.-+++ ++-|+..||+-
T Consensus 69 RPAicdkAR~K----------Qq~-----k~Cpn~~C~g~L~------~~pCrGh~GYP 106 (143)
T PF03615_consen 69 RPAICDKARKK----------QQG-----KPCPNRNCKGRLE------LIPCRGHCGYP 106 (143)
T ss_dssp ---SSHHHHHH----------HHH-----SB-SS--S--BEE------EE---TBTTB-
T ss_pred chHHhHHHHHH----------hcC-----CCCCccccCCcee------EEeccCcCCCc
Confidence 57788876541 112 99999 999888 67787445543
No 232
>COG1315 Uncharacterized conserved protein [Function unknown]
Probab=27.39 E-value=4.2e+02 Score=29.80 Aligned_cols=38 Identities=18% Similarity=0.181 Sum_probs=29.2
Q ss_pred HHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHH
Q 007763 368 NSLERYTHYYERWATNQSSRQKALADLQQMQTVHLEKL 405 (590)
Q Consensus 368 ~~l~ry~~y~~r~~~h~~s~~~~~~~l~~~~~~~~~~~ 405 (590)
...+||..|-+++..|+..++++...|+.+++.+++..
T Consensus 407 e~~~~l~~lt~~~~~~ee~l~~Lt~~l~~l~~~~i~~~ 444 (543)
T COG1315 407 EIVERLKELTEEISLHEERLKKLTKLLVALVKVKIESK 444 (543)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Confidence 34567888889999999999988888888877544443
No 233
>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=27.37 E-value=57 Score=23.44 Aligned_cols=8 Identities=38% Similarity=1.182 Sum_probs=5.8
Q ss_pred CCCCCCcc
Q 007763 296 PCPRCKRP 303 (590)
Q Consensus 296 ~CP~C~~~ 303 (590)
.||.|+..
T Consensus 2 ~Cp~Cg~~ 9 (43)
T PF08271_consen 2 KCPNCGSK 9 (43)
T ss_dssp SBTTTSSS
T ss_pred CCcCCcCC
Confidence 58888775
No 234
>PF05320 Pox_RNA_Pol_19: Poxvirus DNA-directed RNA polymerase 19 kDa subunit; InterPro: IPR007984 DNA-directed RNA polymerases 2.7.7.6 from EC (also known as DNA-dependent RNA polymerases) are responsible for the polymerisation of ribonucleotides into a sequence complementary to the template DNA. In eukaryotes, there are three different forms of DNA-directed RNA polymerases transcribing different sets of genes. Most RNA polymerases are multimeric enzymes and are composed of a variable number of subunits. The core RNA polymerase complex consists of five subunits (two alpha, one beta, one beta-prime and one omega) and is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. The core RNA polymerase complex forms a "crab claw"-like structure with an internal channel running along the full length []. The key functional sites of the enzyme, as defined by mutational and cross-linking analysis, are located on the inner wall of this channel. RNA synthesis follows after the attachment of RNA polymerase to a specific site, the promoter, on the template DNA strand. The RNA synthesis process continues until a termination sequence is reached. The RNA product, which is synthesised in the 5' to 3'direction, is known as the primary transcript. Eukaryotic nuclei contain three distinct types of RNA polymerases that differ in the RNA they synthesise: RNA polymerase I: located in the nucleoli, synthesises precursors of most ribosomal RNAs. RNA polymerase II: occurs in the nucleoplasm, synthesises mRNA precursors. RNA polymerase III: also occurs in the nucleoplasm, synthesises the precursors of 5S ribosomal RNA, the tRNAs, and a variety of other small nuclear and cytosolic RNAs. Eukaryotic cells are also known to contain separate mitochondrial and chloroplast RNA polymerases. Eukaryotic RNA polymerases, whose molecular masses vary in size from 500 to 700 kDa, contain two non-identical large (>100 kDa) subunits and an array of up to 12 different small (less than 50 kDa) subunits. The poxvirus DNA-directed RNA polymerase (2.7.7.6 from EC) catalyses the transcription of DNA into RNA. It consists of at least eight subunits, this is the 19 kDa subunit.; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent
Probab=27.31 E-value=22 Score=33.08 Aligned_cols=9 Identities=56% Similarity=0.781 Sum_probs=4.2
Q ss_pred ccccccccc
Q 007763 141 EMTCGICFE 149 (590)
Q Consensus 141 ~~~C~IC~e 149 (590)
+.+|||=.+
T Consensus 126 Eg~CPIVIe 134 (167)
T PF05320_consen 126 EGTCPIVIE 134 (167)
T ss_pred cCCCcEEEe
Confidence 344555443
No 235
>PRK10445 endonuclease VIII; Provisional
Probab=27.18 E-value=43 Score=34.28 Aligned_cols=25 Identities=32% Similarity=0.673 Sum_probs=18.2
Q ss_pred cCCCCCCcceeec--cCCCceeecCCCc
Q 007763 295 KPCPRCKRPIEKN--QGCMHMTCTPPCK 320 (590)
Q Consensus 295 K~CP~C~~~IEK~--~GCnhMtC~~~C~ 320 (590)
++||.|+.+|++. +|=.-.+|. .|+
T Consensus 236 ~~Cp~Cg~~I~~~~~~gR~t~~CP-~CQ 262 (263)
T PRK10445 236 EACERCGGIIEKTTLSSRPFYWCP-GCQ 262 (263)
T ss_pred CCCCCCCCEeEEEEECCCCcEECC-CCc
Confidence 8999999999964 665555555 454
No 236
>KOG2907 consensus RNA polymerase I transcription factor TFIIS, subunit A12.2/RPA12 [Transcription]
Probab=27.09 E-value=42 Score=29.66 Aligned_cols=35 Identities=17% Similarity=0.352 Sum_probs=21.2
Q ss_pred ccchhhHHHhhcCCCceecccCCCCCCCccchhHHhh
Q 007763 164 PFCSSCWTAINDGPGCLMLRCPDPSCGAAVGQDMIYL 200 (590)
Q Consensus 164 ~fC~~C~~~i~~g~~~~~i~CP~~~C~~~i~~~~i~~ 200 (590)
.||.+|-.-+........+.|+ .|+..++...+..
T Consensus 8 ~FC~~CG~ll~~~~~~~~~~C~--~Ck~~~~v~~~~~ 42 (116)
T KOG2907|consen 8 DFCSDCGSLLEEPSAQSTVLCI--RCKIEYPVSQFSG 42 (116)
T ss_pred chhhhhhhhcccccccCceEec--cccccCCHHHhCC
Confidence 4677776444332222345688 8998887766544
No 237
>KOG1701 consensus Focal adhesion adaptor protein Paxillin and related LIM proteins [Signal transduction mechanisms]
Probab=27.03 E-value=18 Score=39.17 Aligned_cols=11 Identities=18% Similarity=0.513 Sum_probs=6.4
Q ss_pred cCCCCCCccee
Q 007763 295 KPCPRCKRPIE 305 (590)
Q Consensus 295 K~CP~C~~~IE 305 (590)
-.|-.|+..+.
T Consensus 428 Y~CEDCg~~LS 438 (468)
T KOG1701|consen 428 YKCEDCGLLLS 438 (468)
T ss_pred eehhhcCcccc
Confidence 35556666655
No 238
>PRK14810 formamidopyrimidine-DNA glycosylase; Provisional
Probab=27.02 E-value=43 Score=34.46 Aligned_cols=26 Identities=35% Similarity=0.879 Sum_probs=17.7
Q ss_pred CcCCCCCCcceeec--cCCCceeecCCCc
Q 007763 294 SKPCPRCKRPIEKN--QGCMHMTCTPPCK 320 (590)
Q Consensus 294 tK~CP~C~~~IEK~--~GCnhMtC~~~C~ 320 (590)
.++||+|+.+|++. +|=.--+|. .|+
T Consensus 244 g~pCprCG~~I~~~~~~gR~t~~CP-~CQ 271 (272)
T PRK14810 244 GEPCLNCKTPIRRVVVAGRSSHYCP-HCQ 271 (272)
T ss_pred CCcCCCCCCeeEEEEECCCccEECc-CCc
Confidence 37999999999963 664444454 443
No 239
>PRK13945 formamidopyrimidine-DNA glycosylase; Provisional
Probab=26.85 E-value=44 Score=34.60 Aligned_cols=25 Identities=40% Similarity=0.943 Sum_probs=18.4
Q ss_pred cCCCCCCcceeec--cCCCceeecCCCc
Q 007763 295 KPCPRCKRPIEKN--QGCMHMTCTPPCK 320 (590)
Q Consensus 295 K~CP~C~~~IEK~--~GCnhMtC~~~C~ 320 (590)
++||.|+.+|+|. +|=.-..|. .|+
T Consensus 255 ~pC~~Cg~~I~~~~~~gR~t~~CP-~CQ 281 (282)
T PRK13945 255 KPCRKCGTPIERIKLAGRSTHWCP-NCQ 281 (282)
T ss_pred CCCCcCCCeeEEEEECCCccEECC-CCc
Confidence 7999999999964 665555565 454
No 240
>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=26.78 E-value=45 Score=22.72 Aligned_cols=24 Identities=25% Similarity=0.714 Sum_probs=11.5
Q ss_pred CCCCCcceeeccCCCceeecCCCcce
Q 007763 297 CPRCKRPIEKNQGCMHMTCTPPCKFE 322 (590)
Q Consensus 297 CP~C~~~IEK~~GCnhMtC~~~C~~~ 322 (590)
|..|+..++-..+ ..+.|. .||+.
T Consensus 3 C~~Cg~~~~~~~~-~~irC~-~CG~R 26 (32)
T PF03604_consen 3 CGECGAEVELKPG-DPIRCP-ECGHR 26 (32)
T ss_dssp ESSSSSSE-BSTS-STSSBS-SSS-S
T ss_pred CCcCCCeeEcCCC-CcEECC-cCCCe
Confidence 5566666653322 345666 56654
No 241
>PF09788 Tmemb_55A: Transmembrane protein 55A; InterPro: IPR019178 Members of this family catalyse the hydrolysis of the 4-position phosphate of phosphatidylinositol 4,5-bisphosphate, in the reaction: 1-phosphatidyl-myo-inositol 4,5-bisphosphate + H(2)O = 1-phosphatidyl-1D-myo-inositol 5-phosphate + phosphate.
Probab=26.49 E-value=62 Score=32.80 Aligned_cols=88 Identities=28% Similarity=0.622 Sum_probs=48.4
Q ss_pred CcccccccccccCCCCceecCCCCc-cchhhH--HHhhcC-CCceecccCCCCCCCccchhHHhhcCChHHHHHHHHHHH
Q 007763 140 EEMTCGICFENYPSDRLLAAACGHP-FCSSCW--TAINDG-PGCLMLRCPDPSCGAAVGQDMIYLLSSDEDKVKYNRYFI 215 (590)
Q Consensus 140 ~~~~C~IC~e~~~~~~~~~l~CgH~-fC~~C~--~~i~~g-~~~~~i~CP~~~C~~~i~~~~i~~ll~~e~~eky~~~l~ 215 (590)
...+|-+|........- .=.|. -|..|- +-|... .+..-++|| |+..+-=
T Consensus 64 p~v~CrVCq~~I~i~gk---~~QhVVkC~~CnEATPIr~aPpGKKYVRCP---CNCLLIC-------------------- 117 (256)
T PF09788_consen 64 PVVTCRVCQSLIDIEGK---MHQHVVKCSVCNEATPIRNAPPGKKYVRCP---CNCLLIC-------------------- 117 (256)
T ss_pred ceEEeecCCceecccCc---cceeeEECCCCCccccccCCCCCCeeEecC---CceEEEe--------------------
Confidence 46789999876532211 01221 245565 445443 245678998 5432210
Q ss_pred HHHhhcCCCcccCCCCCCCceEeeecCC------------CcceeEe-cCCCccc
Q 007763 216 RSYVEDNRKTKWCPAPGCDYAVDFVVGS------------GNYDVTC-RCSYSFC 257 (590)
Q Consensus 216 ~~~v~~~~~~~~CP~p~C~~~i~~~~~~------------~~~~v~C-~C~~~fC 257 (590)
......+-||.|+|.++|...+.. +...|.| .|...|=
T Consensus 118 ----k~sS~rIaCPRp~CkRiI~L~~~~~~p~~~~~~~~p~~~rv~CghC~~~Fl 168 (256)
T PF09788_consen 118 ----KSSSQRIACPRPNCKRIINLGPSHQGPVTPPVPTQPGSCRVICGHCSNTFL 168 (256)
T ss_pred ----ecccccccCCCCCCcceEEeCCccCCCCCCCCCCCCCceeEECCCCCCcEe
Confidence 112234689999999999765431 2245666 6666653
No 242
>PTZ00415 transmission-blocking target antigen s230; Provisional
Probab=25.94 E-value=62 Score=41.11 Aligned_cols=9 Identities=44% Similarity=0.899 Sum_probs=4.5
Q ss_pred HHHHHHHHH
Q 007763 426 IVECRRVLK 434 (590)
Q Consensus 426 l~~~R~~L~ 434 (590)
++-||.-|+
T Consensus 617 v~icrk~lk 625 (2849)
T PTZ00415 617 LFICRKHLK 625 (2849)
T ss_pred EEEEhhhcc
Confidence 344555553
No 243
>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=25.80 E-value=32 Score=26.47 Aligned_cols=22 Identities=36% Similarity=0.857 Sum_probs=15.6
Q ss_pred cCcCCCCCCcceeeccCCCceeecCCCc
Q 007763 293 NSKPCPRCKRPIEKNQGCMHMTCTPPCK 320 (590)
Q Consensus 293 ntK~CP~C~~~IEK~~GCnhMtC~~~C~ 320 (590)
+.-.||+|+.+.. .|..|. .||
T Consensus 25 ~l~~c~~cg~~~~-----~H~vc~-~cG 46 (56)
T PF01783_consen 25 NLVKCPNCGEPKL-----PHRVCP-SCG 46 (56)
T ss_dssp SEEESSSSSSEES-----TTSBCT-TTB
T ss_pred ceeeeccCCCEec-----ccEeeC-CCC
Confidence 4468999998776 566666 565
No 244
>COG0777 AccD Acetyl-CoA carboxylase beta subunit [Lipid metabolism]
Probab=25.67 E-value=22 Score=36.41 Aligned_cols=28 Identities=18% Similarity=0.548 Sum_probs=21.2
Q ss_pred cCCCCCCcceee-ccCCCceeecCCCccee
Q 007763 295 KPCPRCKRPIEK-NQGCMHMTCTPPCKFEF 323 (590)
Q Consensus 295 K~CP~C~~~IEK-~~GCnhMtC~~~C~~~F 323 (590)
-.||.|+..+-+ .-+=|...|. +|+|+|
T Consensus 29 ~KCp~c~~~~y~~eL~~n~~vcp-~c~~h~ 57 (294)
T COG0777 29 TKCPSCGEMLYRKELESNLKVCP-KCGHHM 57 (294)
T ss_pred eECCCccceeeHHHHHhhhhccc-ccCccc
Confidence 789999998874 4566777887 676654
No 245
>COG2816 NPY1 NTP pyrophosphohydrolases containing a Zn-finger, probably nucleic-acid-binding [DNA replication, recombination, and repair]
Probab=25.44 E-value=59 Score=33.54 Aligned_cols=36 Identities=22% Similarity=0.569 Sum_probs=26.1
Q ss_pred hHHHHHhcCcCCCCCCcceeeccCCCceeecCCCccee
Q 007763 286 NMNWILANSKPCPRCKRPIEKNQGCMHMTCTPPCKFEF 323 (590)
Q Consensus 286 ~~~wi~~ntK~CP~C~~~IEK~~GCnhMtC~~~C~~~F 323 (590)
-..|...+ +-||+|+.+.+-..|=-.+.|. .|++.+
T Consensus 104 l~~w~~~~-RFCg~CG~~~~~~~~g~~~~C~-~cg~~~ 139 (279)
T COG2816 104 LLEWYRSH-RFCGRCGTKTYPREGGWARVCP-KCGHEH 139 (279)
T ss_pred HHHHHhhC-cCCCCCCCcCccccCceeeeCC-CCCCcc
Confidence 34554443 8999999999877776777887 677654
No 246
>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=25.40 E-value=57 Score=29.06 Aligned_cols=36 Identities=25% Similarity=0.534 Sum_probs=26.6
Q ss_pred cCcCCCCCCcceeeccCCCceeecCCCcceeeeccccc
Q 007763 293 NSKPCPRCKRPIEKNQGCMHMTCTPPCKFEFCWLCLGQ 330 (590)
Q Consensus 293 ntK~CP~C~~~IEK~~GCnhMtC~~~C~~~FCw~C~~~ 330 (590)
+.+.|..|+.+.-.-.+.. ..|. .|++.+|-.|+..
T Consensus 53 ~~~~C~~C~~~fg~l~~~~-~~C~-~C~~~VC~~C~~~ 88 (118)
T PF02318_consen 53 GERHCARCGKPFGFLFNRG-RVCV-DCKHRVCKKCGVY 88 (118)
T ss_dssp CCSB-TTTS-BCSCTSTTC-EEET-TTTEEEETTSEEE
T ss_pred CCcchhhhCCcccccCCCC-CcCC-cCCccccCccCCc
Confidence 4578999998765554444 8898 8999999999876
No 247
>PF12773 DZR: Double zinc ribbon
Probab=25.23 E-value=51 Score=24.26 Aligned_cols=24 Identities=33% Similarity=0.646 Sum_probs=20.3
Q ss_pred CCCccccCCCCccCCCcccccccc
Q 007763 563 DSSHWYCDQCTYANVNSATACAMC 586 (590)
Q Consensus 563 ~~~~~~c~~c~~~~~~~~~~c~~c 586 (590)
....++|..|...|...+++|.-|
T Consensus 26 ~~~~~~C~~Cg~~~~~~~~fC~~C 49 (50)
T PF12773_consen 26 DQSKKICPNCGAENPPNAKFCPNC 49 (50)
T ss_pred cCCCCCCcCCcCCCcCCcCccCcc
Confidence 444589999999999999999887
No 248
>KOG2932 consensus E3 ubiquitin ligase involved in ubiquitination of E-cadherin complex [Posttranslational modification, protein turnover, chaperones]
Probab=24.77 E-value=30 Score=35.88 Aligned_cols=30 Identities=37% Similarity=0.759 Sum_probs=21.6
Q ss_pred cCCCCCCcceeeccCCCceeecC-CCcceeeecccccc
Q 007763 295 KPCPRCKRPIEKNQGCMHMTCTP-PCKFEFCWLCLGQW 331 (590)
Q Consensus 295 K~CP~C~~~IEK~~GCnhMtC~~-~C~~~FCw~C~~~w 331 (590)
--|-+|..+|- ++=+. .|+|.||+.|-...
T Consensus 91 HfCd~Cd~PI~-------IYGRmIPCkHvFCl~CAr~~ 121 (389)
T KOG2932|consen 91 HFCDRCDFPIA-------IYGRMIPCKHVFCLECARSD 121 (389)
T ss_pred EeecccCCcce-------eeecccccchhhhhhhhhcC
Confidence 46999999997 43332 58888888886543
No 249
>PRK12286 rpmF 50S ribosomal protein L32; Reviewed
Probab=24.72 E-value=44 Score=25.95 Aligned_cols=22 Identities=32% Similarity=0.807 Sum_probs=15.2
Q ss_pred cCcCCCCCCcceeeccCCCceeecCCCc
Q 007763 293 NSKPCPRCKRPIEKNQGCMHMTCTPPCK 320 (590)
Q Consensus 293 ntK~CP~C~~~IEK~~GCnhMtC~~~C~ 320 (590)
+.-.||+|+.+.. .|-.|. .||
T Consensus 26 ~l~~C~~CG~~~~-----~H~vC~-~CG 47 (57)
T PRK12286 26 GLVECPNCGEPKL-----PHRVCP-SCG 47 (57)
T ss_pred cceECCCCCCccC-----CeEECC-CCC
Confidence 3467999999887 355565 454
No 250
>PRK09710 lar restriction alleviation and modification protein; Reviewed
Probab=24.69 E-value=94 Score=24.75 Aligned_cols=33 Identities=30% Similarity=0.493 Sum_probs=19.9
Q ss_pred CcccCCCCCCCceEeeecCCCcceeEe-cCCCccc
Q 007763 224 KTKWCPAPGCDYAVDFVVGSGNYDVTC-RCSYSFC 257 (590)
Q Consensus 224 ~~~~CP~p~C~~~i~~~~~~~~~~v~C-~C~~~fC 257 (590)
.++.||.-+|..+.... ..+-..|.| .|+...+
T Consensus 5 ~lKPCPFCG~~~~~v~~-~~g~~~v~C~~CgA~~~ 38 (64)
T PRK09710 5 NVKPCPFCGCPSVTVKA-ISGYYRAKCNGCESRTG 38 (64)
T ss_pred cccCCCCCCCceeEEEe-cCceEEEEcCCCCcCcc
Confidence 46889975555443332 334456788 8887633
No 251
>PF04803 Cor1: Cor1/Xlr/Xmr conserved region; InterPro: IPR006888 Cor1 is a component of the chromosome core in the meiotic prophase chromosomes []. Xlr is a lymphoid cell specific protein []. Xmr is abundantly transcribed in testis in a tissue-specific and developmentally regulated manner. The protein is located in the nuclei of spermatocytes, early in the prophase of the first meiotic division, and later becomes concentrated in the XY nuclear subregion where it is in particular associated with the axes of sex chromosomes [].
Probab=24.42 E-value=5.5e+02 Score=23.44 Aligned_cols=11 Identities=9% Similarity=0.936 Sum_probs=5.1
Q ss_pred HHHHHHHHHHh
Q 007763 372 RYTHYYERWAT 382 (590)
Q Consensus 372 ry~~y~~r~~~ 382 (590)
.|..-|..|..
T Consensus 47 q~~~l~~qw~~ 57 (130)
T PF04803_consen 47 QFSTLFQQWEA 57 (130)
T ss_pred HHHHHHHHHHH
Confidence 44444444443
No 252
>PRK09521 exosome complex RNA-binding protein Csl4; Provisional
Probab=24.21 E-value=49 Score=31.98 Aligned_cols=25 Identities=32% Similarity=0.818 Sum_probs=20.3
Q ss_pred CCCCCCcceeeccCCCceeecCCCcce
Q 007763 296 PCPRCKRPIEKNQGCMHMTCTPPCKFE 322 (590)
Q Consensus 296 ~CP~C~~~IEK~~GCnhMtC~~~C~~~ 322 (590)
.||+|+.++.+ .+.|+|.|. .|++.
T Consensus 151 ~~~~~g~~~~~-~~~~~~~c~-~~~~~ 175 (189)
T PRK09521 151 MCSRCRTPLVK-KGENELKCP-NCGNI 175 (189)
T ss_pred EccccCCceEE-CCCCEEECC-CCCCE
Confidence 69999999987 455999998 67754
No 253
>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=23.90 E-value=44 Score=33.45 Aligned_cols=54 Identities=20% Similarity=0.321 Sum_probs=32.3
Q ss_pred cccCCCCCCCcc-chhHHhhcCChHHHHHHHHHHHHHHhhcCCCcccCCCCCCCceEee
Q 007763 182 LRCPDPSCGAAV-GQDMIYLLSSDEDKVKYNRYFIRSYVEDNRKTKWCPAPGCDYAVDF 239 (590)
Q Consensus 182 i~CP~~~C~~~i-~~~~i~~ll~~e~~eky~~~l~~~~v~~~~~~~~CP~p~C~~~i~~ 239 (590)
-+|| -|+.-. ....++-|++++-+.+.-..-....... ....||.|+|+.++..
T Consensus 11 ~~CP--vCksDrYLnPdik~linPECyHrmCESCvdRIFs~--GpAqCP~~gC~kILRK 65 (314)
T COG5220 11 RRCP--VCKSDRYLNPDIKILINPECYHRMCESCVDRIFSR--GPAQCPYKGCGKILRK 65 (314)
T ss_pred ccCC--ccccccccCCCeEEEECHHHHHHHHHHHHHHHhcC--CCCCCCCccHHHHHHH
Confidence 4799 787643 2334566788776655443333222222 3468999999987653
No 254
>KOG3183 consensus Predicted Zn-finger protein [General function prediction only]
Probab=23.64 E-value=32 Score=34.43 Aligned_cols=57 Identities=30% Similarity=0.688 Sum_probs=36.8
Q ss_pred ccCCCCCCCceEeeecCCCcceeEe-cCCCccccccCC-CcCCCCCchhHHHHHHhhhhhhhhHHHHHhcCcCCCCCCcc
Q 007763 226 KWCPAPGCDYAVDFVVGSGNYDVTC-RCSYSFCWNCTE-EAHRPVDCDTVAKWVLKNSAESENMNWILANSKPCPRCKRP 303 (590)
Q Consensus 226 ~~CP~p~C~~~i~~~~~~~~~~v~C-~C~~~fC~~C~~-~~H~p~~C~~~~~w~~k~~~e~e~~~wi~~ntK~CP~C~~~ 303 (590)
+.|-.+.|... .-..++| .|+..||..+.. +.| .|..... +....+.||.|.++
T Consensus 9 kHCs~~~Ckql-------DFLPf~Cd~C~~~FC~eHrsye~H---~Cp~~~~--------------~~~~v~icp~cs~p 64 (250)
T KOG3183|consen 9 KHCSVPYCKQL-------DFLPFKCDGCSGIFCLEHRSYESH---HCPKGLR--------------IDVQVPICPLCSKP 64 (250)
T ss_pred cccCcchhhhc-------cccceeeCCccchhhhccchHhhc---CCCcccc--------------cceeecccCCCCCC
Confidence 56777777632 2345799 999999999873 344 4553221 11223889999998
Q ss_pred eee
Q 007763 304 IEK 306 (590)
Q Consensus 304 IEK 306 (590)
|.-
T Consensus 65 v~~ 67 (250)
T KOG3183|consen 65 VPT 67 (250)
T ss_pred CCC
Confidence 873
No 255
>PHA02325 hypothetical protein
Probab=23.61 E-value=36 Score=26.91 Aligned_cols=13 Identities=31% Similarity=0.779 Sum_probs=9.9
Q ss_pred cCcCCCCCCccee
Q 007763 293 NSKPCPRCKRPIE 305 (590)
Q Consensus 293 ntK~CP~C~~~IE 305 (590)
++|.||+|++.--
T Consensus 2 ~~k~CPkC~A~Wl 14 (72)
T PHA02325 2 DTKICPKCGARWL 14 (72)
T ss_pred CccccCccCCEeE
Confidence 4689999987653
No 256
>COG2824 PhnA Uncharacterized Zn-ribbon-containing protein involved in phosphonate metabolism [Inorganic ion transport and metabolism]
Probab=23.18 E-value=51 Score=28.85 Aligned_cols=24 Identities=29% Similarity=0.992 Sum_probs=15.3
Q ss_pred cCCCCCCcce-eeccCCCceeecCCCcc
Q 007763 295 KPCPRCKRPI-EKNQGCMHMTCTPPCKF 321 (590)
Q Consensus 295 K~CP~C~~~I-EK~~GCnhMtC~~~C~~ 321 (590)
-+||+|+.-. -..++ +|.|. .|.+
T Consensus 4 p~cp~c~sEytYed~~--~~~cp-ec~~ 28 (112)
T COG2824 4 PPCPKCNSEYTYEDGG--QLICP-ECAH 28 (112)
T ss_pred CCCCccCCceEEecCc--eEeCc-hhcc
Confidence 6899996544 35555 67776 4433
No 257
>KOG2807 consensus RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit SSL1 [Transcription; Replication, recombination and repair]
Probab=23.18 E-value=48 Score=34.70 Aligned_cols=16 Identities=31% Similarity=0.827 Sum_probs=10.5
Q ss_pred CCCCccchhhHHHhhc
Q 007763 160 ACGHPFCSSCWTAIND 175 (590)
Q Consensus 160 ~CgH~fC~~C~~~i~~ 175 (590)
.|.|.||.+|=..|.+
T Consensus 350 ~Ck~~FCldCDv~iHe 365 (378)
T KOG2807|consen 350 SCKNVFCLDCDVFIHE 365 (378)
T ss_pred hccceeeccchHHHHh
Confidence 3777777777755544
No 258
>KOG0250 consensus DNA repair protein RAD18 (SMC family protein) [Replication, recombination and repair]
Probab=23.11 E-value=1.5e+03 Score=28.04 Aligned_cols=26 Identities=8% Similarity=0.268 Sum_probs=18.9
Q ss_pred HHHHHHHHHHHHHHHHHHHhhhhhhc
Q 007763 416 LKFITEAWLQIVECRRVLKWTYAYGY 441 (590)
Q Consensus 416 ~~~l~~a~~~l~~~R~~L~~sy~~~y 441 (590)
+.-+......+..+..-+.|..||-+
T Consensus 254 ~~~~e~~~~~l~~Lk~k~~W~~V~~~ 279 (1074)
T KOG0250|consen 254 LEQLEDLKENLEQLKAKMAWAWVNEV 279 (1074)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 34455555677777888999999877
No 259
>PF05285 SDA1: SDA1; InterPro: IPR007949 This domain consists of several SDA1 protein homologues. SDA1 is a Saccharomyces cerevisiae protein which is involved in the control of the actin cytoskeleton. The protein is essential for cell viability and is localised in the nucleus [].
Probab=23.03 E-value=1e+02 Score=32.66 Aligned_cols=9 Identities=33% Similarity=0.582 Sum_probs=4.1
Q ss_pred EeCHHHHHH
Q 007763 69 VLTEADIRQ 77 (590)
Q Consensus 69 vl~~~~i~~ 77 (590)
|||++|+..
T Consensus 189 ILT~eDF~k 197 (324)
T PF05285_consen 189 ILTPEDFAK 197 (324)
T ss_pred CCCHHHHHH
Confidence 444444443
No 260
>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=23.03 E-value=41 Score=28.04 Aligned_cols=29 Identities=31% Similarity=0.723 Sum_probs=14.1
Q ss_pred CcCCCCCCc------ceeeccCCCceeecCCCccee
Q 007763 294 SKPCPRCKR------PIEKNQGCMHMTCTPPCKFEF 323 (590)
Q Consensus 294 tK~CP~C~~------~IEK~~GCnhMtC~~~C~~~F 323 (590)
+-.||.|+. -|.|..|=-++.|+ .||..|
T Consensus 22 ~F~CPfC~~~~sV~v~idkk~~~~~~~C~-~Cg~~~ 56 (81)
T PF05129_consen 22 VFDCPFCNHEKSVSVKIDKKEGIGILSCR-VCGESF 56 (81)
T ss_dssp ----TTT--SS-EEEEEETTTTEEEEEES-SS--EE
T ss_pred eEcCCcCCCCCeEEEEEEccCCEEEEEec-CCCCeE
Confidence 358999992 23345666678888 675555
No 261
>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=23.01 E-value=80 Score=24.26 Aligned_cols=28 Identities=21% Similarity=0.507 Sum_probs=19.6
Q ss_pred cCCCCCCCceEeeecCCCcceeEe-cCCCcc
Q 007763 227 WCPAPGCDYAVDFVVGSGNYDVTC-RCSYSF 256 (590)
Q Consensus 227 ~CP~p~C~~~i~~~~~~~~~~v~C-~C~~~f 256 (590)
-|| .|+..|..........|.| .||..+
T Consensus 4 ~CP--~CG~~iev~~~~~GeiV~Cp~CGael 32 (54)
T TIGR01206 4 ECP--DCGAEIELENPELGELVICDECGAEL 32 (54)
T ss_pred CCC--CCCCEEecCCCccCCEEeCCCCCCEE
Confidence 588 4999887754433456789 788765
No 262
>COG1594 RPB9 DNA-directed RNA polymerase, subunit M/Transcription elongation factor TFIIS [Transcription]
Probab=22.97 E-value=80 Score=28.07 Aligned_cols=30 Identities=20% Similarity=0.586 Sum_probs=20.3
Q ss_pred cccCCCCCCCceEeeecCCCcceeEe-cCCCcc
Q 007763 225 TKWCPAPGCDYAVDFVVGSGNYDVTC-RCSYSF 256 (590)
Q Consensus 225 ~~~CP~p~C~~~i~~~~~~~~~~v~C-~C~~~f 256 (590)
+++|| .|+..+..........+.| .||+.+
T Consensus 2 m~FCp--~Cgsll~p~~~~~~~~l~C~kCgye~ 32 (113)
T COG1594 2 MRFCP--KCGSLLYPKKDDEGGKLVCRKCGYEE 32 (113)
T ss_pred ccccC--CccCeeEEeEcCCCcEEECCCCCcch
Confidence 46899 5999887754333346678 787664
No 263
>KOG4445 consensus Uncharacterized conserved protein, contains RWD domain [Function unknown]
Probab=22.95 E-value=39 Score=34.97 Aligned_cols=33 Identities=24% Similarity=0.567 Sum_probs=25.1
Q ss_pred cccccccccccCCCC-ceecCCCCccchhhH-HHh
Q 007763 141 EMTCGICFENYPSDR-LLAAACGHPFCSSCW-TAI 173 (590)
Q Consensus 141 ~~~C~IC~e~~~~~~-~~~l~CgH~fC~~C~-~~i 173 (590)
...|.||+--|...+ +...+|-|+|...|+ .+|
T Consensus 115 ~gqCvICLygfa~~~~ft~T~C~Hy~H~~ClaRyl 149 (368)
T KOG4445|consen 115 NGQCVICLYGFASSPAFTVTACDHYMHFACLARYL 149 (368)
T ss_pred CCceEEEEEeecCCCceeeehhHHHHHHHHHHHHH
Confidence 456888887776555 667889999999999 444
No 264
>KOG1940 consensus Zn-finger protein [General function prediction only]
Probab=22.82 E-value=55 Score=33.74 Aligned_cols=48 Identities=27% Similarity=0.542 Sum_probs=34.2
Q ss_pred CCCcccccccccccCC--CCceecCCCCccchhhHHHhhcCCCceecccCCCCCCC
Q 007763 138 DGEEMTCGICFENYPS--DRLLAAACGHPFCSSCWTAINDGPGCLMLRCPDPSCGA 191 (590)
Q Consensus 138 ~~~~~~C~IC~e~~~~--~~~~~l~CgH~fC~~C~~~i~~g~~~~~i~CP~~~C~~ 191 (590)
....+.||||.+.+.. ..+..++|||.--..|+.....+ . ++|| -|..
T Consensus 155 ~~~~~ncPic~e~l~~s~~~~~~~~CgH~~h~~cf~e~~~~---~-y~CP--~C~~ 204 (276)
T KOG1940|consen 155 RSSEFNCPICKEYLFLSFEDAGVLKCGHYMHSRCFEEMICE---G-YTCP--ICSK 204 (276)
T ss_pred hcccCCCchhHHHhccccccCCccCcccchHHHHHHHHhcc---C-CCCC--cccc
Confidence 3446679999987643 34566789999889999443332 2 8999 7876
No 265
>KOG0956 consensus PHD finger protein AF10 [General function prediction only]
Probab=22.57 E-value=1.1e+02 Score=35.37 Aligned_cols=34 Identities=24% Similarity=0.532 Sum_probs=21.3
Q ss_pred CcccCCCCCCCceEeeecCCCcceeEe-cCCCccccccC
Q 007763 224 KTKWCPAPGCDYAVDFVVGSGNYDVTC-RCSYSFCWNCT 261 (590)
Q Consensus 224 ~~~~CP~p~C~~~i~~~~~~~~~~v~C-~C~~~fC~~C~ 261 (590)
.++||-+.+|..+|... .+-|+= .=|--||.+|-
T Consensus 21 PLVYCDG~nCsVAVHQa----CYGIvqVPtGpWfCrKCe 55 (900)
T KOG0956|consen 21 PLVYCDGHNCSVAVHQA----CYGIVQVPTGPWFCRKCE 55 (900)
T ss_pred ceeeecCCCceeeeehh----cceeEecCCCchhhhhhh
Confidence 36899999999887532 222221 34566777775
No 266
>PLN02638 cellulose synthase A (UDP-forming), catalytic subunit
Probab=22.52 E-value=59 Score=39.61 Aligned_cols=55 Identities=25% Similarity=0.654 Sum_probs=36.6
Q ss_pred CCceEeeecCCCcceeEe-cCCCccccccCCCcCCCCCchhHHHHHHhhhhhhhhHHHHHhcCcCCCCCCcceeeccCCC
Q 007763 233 CDYAVDFVVGSGNYDVTC-RCSYSFCWNCTEEAHRPVDCDTVAKWVLKNSAESENMNWILANSKPCPRCKRPIEKNQGCM 311 (590)
Q Consensus 233 C~~~i~~~~~~~~~~v~C-~C~~~fC~~C~~~~H~p~~C~~~~~w~~k~~~e~e~~~wi~~ntK~CP~C~~~IEK~~GCn 311 (590)
|+--|... ..+...|-| .|++-.|..|- ++- . ...++-||+|+....+--||+
T Consensus 23 CGD~vg~~-~~Ge~FVAC~eC~FPVCrpCY-EYE---------r---------------~eG~q~CPqCktrYkr~kgsp 76 (1079)
T PLN02638 23 CGDNVGKT-VDGEPFVACDVCAFPVCRPCY-EYE---------R---------------KDGNQSCPQCKTKYKRHKGSP 76 (1079)
T ss_pred cccccCcC-CCCCEEEEeccCCCccccchh-hhh---------h---------------hcCCccCCccCCchhhhcCCC
Confidence 66555444 346677999 99999999887 221 0 012278999988888666666
Q ss_pred ce
Q 007763 312 HM 313 (590)
Q Consensus 312 hM 313 (590)
.+
T Consensus 77 rv 78 (1079)
T PLN02638 77 AI 78 (1079)
T ss_pred Cc
Confidence 54
No 267
>KOG2979 consensus Protein involved in DNA repair [General function prediction only]
Probab=22.48 E-value=91 Score=31.71 Aligned_cols=48 Identities=19% Similarity=0.365 Sum_probs=34.0
Q ss_pred cccccccccccCCCCceecCCCCccchhhHHHhhcCCCceecccCCCCCCC
Q 007763 141 EMTCGICFENYPSDRLLAAACGHPFCSSCWTAINDGPGCLMLRCPDPSCGA 191 (590)
Q Consensus 141 ~~~C~IC~e~~~~~~~~~l~CgH~fC~~C~~~i~~g~~~~~i~CP~~~C~~ 191 (590)
...|||=+..+ ...+++-.|||.|=++=+..+-.+. ..++||..+|..
T Consensus 176 s~rdPis~~~I-~nPviSkkC~HvydrDsI~~~l~~~--~~i~CPv~gC~~ 223 (262)
T KOG2979|consen 176 SNRDPISKKPI-VNPVISKKCGHVYDRDSIMQILCDE--ITIRCPVLGCEN 223 (262)
T ss_pred cccCchhhhhh-hchhhhcCcCcchhhhhHHHHhccC--ceeecccccCCc
Confidence 35688865443 1445677899999999885444432 579999999983
No 268
>PRK11546 zraP zinc resistance protein; Provisional
Probab=22.46 E-value=6.3e+02 Score=23.48 Aligned_cols=54 Identities=15% Similarity=0.238 Sum_probs=39.0
Q ss_pred hhHHHHHHHHHHHHHHhHHHHHHHHHH---HHHHHhhcCCCCCc-HHHHHHHHHHHHH
Q 007763 448 HAKRQFFEYLQGEAESGLERLHQCAEK---ELQIYLNADGPSKD-FNEFRTKLAGLTS 501 (590)
Q Consensus 448 ~~~~~~fe~~Q~~le~~~E~L~~~le~---~l~~~~~~~~~~~~-~~~~~~~l~~lt~ 501 (590)
.++...++.+..+....++.|.+.|-. ||+.|+....|..+ +..+..+|..|..
T Consensus 46 ~EQQa~~q~I~~~f~~~t~~LRqqL~aKr~ELnALl~~~~pD~~kI~aL~kEI~~Lr~ 103 (143)
T PRK11546 46 TEQQAAWQKIHNDFYAQTSALRQQLVSKRYEYNALLTANPPDSSKINAVAKEMENLRQ 103 (143)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHHHH
Confidence 456777888888888888888877743 77777877777643 6677777776644
No 269
>COG5293 Predicted ATPase [General function prediction only]
Probab=22.45 E-value=1.1e+03 Score=26.28 Aligned_cols=23 Identities=13% Similarity=0.325 Sum_probs=17.1
Q ss_pred HHHhHHHHHHHHHHHHHcccccc
Q 007763 499 LTSVTRNYFENLVRALENGLSDV 521 (590)
Q Consensus 499 lt~~~~~~~~~l~~~le~gl~~~ 521 (590)
|.+-++.+|+++++.+-+--..+
T Consensus 439 ~~~~~~~lF~~~~r~~yd~~G~L 461 (591)
T COG5293 439 LFASIGRLFKEMIREVYDCYGSL 461 (591)
T ss_pred HHHHHHHHHHHHHHHHhcCCCeE
Confidence 34457899999999988755544
No 270
>COG0021 TktA Transketolase [Carbohydrate transport and metabolism]
Probab=22.42 E-value=4.2e+02 Score=30.69 Aligned_cols=94 Identities=20% Similarity=0.365 Sum_probs=51.6
Q ss_pred HHHHHHHHHHHhhhhhhcccCccchhHHHHHHHHH---HHHHHhHHHHHHHHH-------HHHHHHhhcCCCCCcHHHHH
Q 007763 424 LQIVECRRVLKWTYAYGYYLPDHEHAKRQFFEYLQ---GEAESGLERLHQCAE-------KELQIYLNADGPSKDFNEFR 493 (590)
Q Consensus 424 ~~l~~~R~~L~~sy~~~yyl~~~~~~~~~~fe~~Q---~~le~~~E~L~~~le-------~~l~~~~~~~~~~~~~~~~~ 493 (590)
+.+.+.|..|-|.|.- ||+++. ....|+..+ ..++..-+.+-..-+ .+++..+....|. .+..+.
T Consensus 270 ~ev~~~k~~lgw~~~~-F~vp~e---v~~~~~~~~~~g~~~~~~W~~~~~~y~~~~Pe~~~~~~r~~~~~~p~-~~~~~~ 344 (663)
T COG0021 270 EEVAAAKKALGWEPEP-FEVPEE---VYAAFRAVEERGAKAEAAWNELFAAYKKKYPELAAEFERRLNGELPA-NWAAFL 344 (663)
T ss_pred HHHHHHHHHhCCCCCc-eecCHH---HHHHHHHHhhhhhhHHHHHHHHHHHHHhhChHHHHHHHHHhcccCch-hHHHhh
Confidence 4567889999999988 998644 344444222 233333332222211 1223333333332 121111
Q ss_pred HHHH--HHHHhHHHHHHHHHHHHHccccccc
Q 007763 494 TKLA--GLTSVTRNYFENLVRALENGLSDVD 522 (590)
Q Consensus 494 ~~l~--~lt~~~~~~~~~l~~~le~gl~~~~ 522 (590)
.++. .....||++..+.+++|-.-|+++-
T Consensus 345 ~~~~~~~~~~ATR~as~~~L~~l~~~~p~l~ 375 (663)
T COG0021 345 PKFEANGKSIATRKASGKALNALAKKLPELI 375 (663)
T ss_pred hhhcccccccchHHHHHHHHHHHHhhCcccc
Confidence 1111 1224689999999999999999983
No 271
>KOG4460 consensus Nuclear pore complex, Nup88/rNup84 component [Nuclear structure; Intracellular trafficking, secretion, and vesicular transport]
Probab=22.11 E-value=1.2e+03 Score=26.59 Aligned_cols=16 Identities=25% Similarity=0.432 Sum_probs=9.0
Q ss_pred HHHHHHHHHHcccccc
Q 007763 506 YFENLVRALENGLSDV 521 (590)
Q Consensus 506 ~~~~l~~~le~gl~~~ 521 (590)
|....+++|.+|+.-+
T Consensus 666 ~~~~~~~~L~~~iET~ 681 (741)
T KOG4460|consen 666 LIPDQLRHLGNAIETV 681 (741)
T ss_pred HhHHHHHHHHHHHHHH
Confidence 4445556666666655
No 272
>KOG1991 consensus Nuclear transport receptor RANBP7/RANBP8 (importin beta superfamily) [Nuclear structure; Intracellular trafficking, secretion, and vesicular transport]
Probab=22.07 E-value=56 Score=39.08 Aligned_cols=24 Identities=21% Similarity=0.311 Sum_probs=10.1
Q ss_pred HHHHHHHHHHHHHHHhC-CCHHHHH
Q 007763 75 IRQRQEEDITRISTVLS-ISKVAAS 98 (590)
Q Consensus 75 i~~~~~~~i~~v~~il~-i~~~~a~ 98 (590)
|...|..+-...+.+++ ++++...
T Consensus 968 i~~lq~~d~~~yq~l~~~L~~~q~~ 992 (1010)
T KOG1991|consen 968 ITNLQSSDAVRYQKLISTLTPEQQD 992 (1010)
T ss_pred HHhhhccChHHHHHHHhcCCHHHHH
Confidence 33444444444444433 3444443
No 273
>KOG4362 consensus Transcriptional regulator BRCA1 [Replication, recombination and repair; Transcription]
Probab=22.05 E-value=28 Score=40.14 Aligned_cols=50 Identities=20% Similarity=0.480 Sum_probs=34.4
Q ss_pred cccccccccccCCCCceecCCCCccchhhHHHhhcCCCceecccCCCCCCCccch
Q 007763 141 EMTCGICFENYPSDRLLAAACGHPFCSSCWTAINDGPGCLMLRCPDPSCGAAVGQ 195 (590)
Q Consensus 141 ~~~C~IC~e~~~~~~~~~l~CgH~fC~~C~~~i~~g~~~~~i~CP~~~C~~~i~~ 195 (590)
..+|+||+..+ ..++.+.|.|.||..||.....-.. ....|| -|+..+..
T Consensus 21 ~lEc~ic~~~~--~~p~~~kc~~~~l~~~~n~~f~~~~-~~~~~~--lc~~~~eK 70 (684)
T KOG4362|consen 21 ILECPICLEHV--KEPSLLKCDHIFLKFCLNKLFESKK-GPKQCA--LCKSDIEK 70 (684)
T ss_pred hccCCceeEEe--eccchhhhhHHHHhhhhhceeeccC-ccccch--hhhhhhhh
Confidence 56799999987 5668889999999999932211110 146777 67755543
No 274
>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=21.97 E-value=58 Score=25.08 Aligned_cols=21 Identities=29% Similarity=0.638 Sum_probs=14.4
Q ss_pred CcCCCCCCcceeeccCCCceeecCCCc
Q 007763 294 SKPCPRCKRPIEKNQGCMHMTCTPPCK 320 (590)
Q Consensus 294 tK~CP~C~~~IEK~~GCnhMtC~~~C~ 320 (590)
.-.||+|+.+.. .|-.|. .||
T Consensus 26 l~~C~~cG~~~~-----~H~vc~-~cG 46 (55)
T TIGR01031 26 LVVCPNCGEFKL-----PHRVCP-SCG 46 (55)
T ss_pred ceECCCCCCccc-----CeeECC-ccC
Confidence 457999998887 555555 454
No 275
>PRK13428 F0F1 ATP synthase subunit delta; Provisional
Probab=21.55 E-value=1.1e+03 Score=26.00 Aligned_cols=25 Identities=16% Similarity=-0.082 Sum_probs=10.7
Q ss_pred HHHHHHHHHHHHHhHHHHHHHHHHH
Q 007763 451 RQFFEYLQGEAESGLERLHQCAEKE 475 (590)
Q Consensus 451 ~~~fe~~Q~~le~~~E~L~~~le~~ 475 (590)
.++.+..+.++++..+.-...++.+
T Consensus 85 ~~~~~~A~~ea~~i~~~a~~~Ie~e 109 (445)
T PRK13428 85 EQLRAQADAEAERIKVQGARQVQLL 109 (445)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3444444444444444444444433
No 276
>PLN00209 ribosomal protein S27; Provisional
Probab=21.52 E-value=96 Score=26.16 Aligned_cols=34 Identities=21% Similarity=0.444 Sum_probs=22.3
Q ss_pred ccCCCCCCCceEeeecCCCcceeEe-cCCCccccccCC
Q 007763 226 KWCPAPGCDYAVDFVVGSGNYDVTC-RCSYSFCWNCTE 262 (590)
Q Consensus 226 ~~CP~p~C~~~i~~~~~~~~~~v~C-~C~~~fC~~C~~ 262 (590)
+-|| +|...-..- +.....|.| .||...|.-=+.
T Consensus 37 VkCp--~C~n~q~VF-ShA~t~V~C~~Cg~~L~~PTGG 71 (86)
T PLN00209 37 VKCQ--GCFNITTVF-SHSQTVVVCGSCQTVLCQPTGG 71 (86)
T ss_pred EECC--CCCCeeEEE-ecCceEEEccccCCEeeccCCC
Confidence 6798 587653322 335567889 999988754443
No 277
>PF14354 Lar_restr_allev: Restriction alleviation protein Lar
Probab=21.46 E-value=94 Score=23.84 Aligned_cols=29 Identities=34% Similarity=0.650 Sum_probs=15.2
Q ss_pred CcccCCCCCCCceEeeecCC-Cc-----ceeEe-cCCC
Q 007763 224 KTKWCPAPGCDYAVDFVVGS-GN-----YDVTC-RCSY 254 (590)
Q Consensus 224 ~~~~CP~p~C~~~i~~~~~~-~~-----~~v~C-~C~~ 254 (590)
.++.||. |+......... .. ..|.| .||.
T Consensus 2 ~LkPCPF--CG~~~~~~~~~~~~~~~~~~~V~C~~Cga 37 (61)
T PF14354_consen 2 ELKPCPF--CGSADVLIRQDEGFDYGMYYYVECTDCGA 37 (61)
T ss_pred CCcCCCC--CCCcceEeecccCCCCCCEEEEEcCCCCC
Confidence 4678996 76443322111 11 55677 6765
No 278
>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=21.38 E-value=64 Score=36.35 Aligned_cols=35 Identities=20% Similarity=0.579 Sum_probs=22.7
Q ss_pred cCCCCCCcceeeccCCCceeecCCCcce-----eeeccccc
Q 007763 295 KPCPRCKRPIEKNQGCMHMTCTPPCKFE-----FCWLCLGQ 330 (590)
Q Consensus 295 K~CP~C~~~IEK~~GCnhMtC~~~C~~~-----FCw~C~~~ 330 (590)
-.||+|..++.--..=|.+.|. .||+. .|..|++.
T Consensus 223 ~~C~~C~~~l~~h~~~~~l~Ch-~Cg~~~~~~~~Cp~C~s~ 262 (505)
T TIGR00595 223 LCCPNCDVSLTYHKKEGKLRCH-YCGYQEPIPKTCPQCGSE 262 (505)
T ss_pred cCCCCCCCceEEecCCCeEEcC-CCcCcCCCCCCCCCCCCC
Confidence 3677777776633233467887 78776 57788763
No 279
>PTZ00083 40S ribosomal protein S27; Provisional
Probab=21.21 E-value=95 Score=26.12 Aligned_cols=35 Identities=26% Similarity=0.573 Sum_probs=23.0
Q ss_pred ccCCCCCCCceEeeecCCCcceeEe-cCCCccccccCCC
Q 007763 226 KWCPAPGCDYAVDFVVGSGNYDVTC-RCSYSFCWNCTEE 263 (590)
Q Consensus 226 ~~CP~p~C~~~i~~~~~~~~~~v~C-~C~~~fC~~C~~~ 263 (590)
+-|| +|...-..- +..+..|.| .|+...|.-=+..
T Consensus 36 VkCp--~C~n~q~VF-ShA~t~V~C~~Cg~~L~~PTGGK 71 (85)
T PTZ00083 36 VKCP--GCSQITTVF-SHAQTVVLCGGCSSQLCQPTGGK 71 (85)
T ss_pred EECC--CCCCeeEEE-ecCceEEEccccCCEeeccCCCC
Confidence 6788 597653322 335567889 9999987654433
No 280
>KOG2141 consensus Protein involved in high osmolarity signaling pathway [Signal transduction mechanisms]
Probab=21.19 E-value=1e+02 Score=35.85 Aligned_cols=42 Identities=17% Similarity=0.160 Sum_probs=20.6
Q ss_pred HHHHHHHHHHHHHHHHHhC------CCHHHHHHHHHhcCCChHHHHHH
Q 007763 73 ADIRQRQEEDITRISTVLS------ISKVAASILLRFYNWSVSKVHDE 114 (590)
Q Consensus 73 ~~i~~~~~~~i~~v~~il~------i~~~~a~~LL~~~~W~~~~l~e~ 114 (590)
.+...++...|+.+-.-|+ |..+.|.+-...-+.++..-+..
T Consensus 313 sE~l~rl~rkv~g~LNKLSdaNi~~I~~~i~~Ly~~~sr~~v~~sLtk 360 (822)
T KOG2141|consen 313 SEQLQRLRRKVNGSLNKLSDANIIKIIAGIAELYMNNSRYDVTSSLTK 360 (822)
T ss_pred hHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcchhhHHHHHHH
Confidence 3455555555554443333 33444555554555555544443
No 281
>smart00546 CUE Domain that may be involved in binding ubiquitin-conjugating enzymes (UBCs). CUE domains also occur in two protein of the IL-1 signal transduction pathway, tollip and TAB2. Ponting (Biochem. J.) "Proteins of the Endoplasmic reticulum" (in press)
Probab=21.09 E-value=2.8e+02 Score=19.59 Aligned_cols=38 Identities=11% Similarity=0.225 Sum_probs=29.7
Q ss_pred HHHHHHHHHHh-CCCHHHHHHHHHhcCCChHHHHHHhhc
Q 007763 80 EEDITRISTVL-SISKVAASILLRFYNWSVSKVHDEWFA 117 (590)
Q Consensus 80 ~~~i~~v~~il-~i~~~~a~~LL~~~~W~~~~l~e~~~~ 117 (590)
.+.+..+.+++ +++.+.+...|..++++++..++....
T Consensus 3 ~~~v~~L~~mFP~l~~~~I~~~L~~~~g~ve~~i~~LL~ 41 (43)
T smart00546 3 DEALHDLKDMFPNLDEEVIKAVLEANNGNVEATINNLLE 41 (43)
T ss_pred HHHHHHHHHHCCCCCHHHHHHHHHHcCCCHHHHHHHHHc
Confidence 34566677766 578889999999999999998876643
No 282
>KOG4198 consensus RNA-binding Ran Zn-finger protein and related proteins [General function prediction only]
Probab=20.77 E-value=1.6e+02 Score=30.48 Aligned_cols=29 Identities=28% Similarity=0.709 Sum_probs=24.7
Q ss_pred CCCCccccCCCCccCCCccccccccCCCC
Q 007763 562 DDSSHWYCDQCTYANVNSATACAMCQHSR 590 (590)
Q Consensus 562 ~~~~~~~c~~c~~~~~~~~~~c~~c~~~~ 590 (590)
-..+-|-|..|+|.|-..-..|--|..+|
T Consensus 136 ~~~GDW~Cp~C~fhNfarn~~C~rC~~~r 164 (280)
T KOG4198|consen 136 WRSGDWECPGCNFHNFARNSECFRCGAKR 164 (280)
T ss_pred ccccCcccCCCCceeccccchhhhcCCcC
Confidence 35566999999999999999999997654
No 283
>PRK04023 DNA polymerase II large subunit; Validated
Probab=20.73 E-value=51 Score=39.69 Aligned_cols=32 Identities=22% Similarity=0.507 Sum_probs=23.8
Q ss_pred hcCcCCCCCCcceeeccCCCceeecCCCcc-----eeeeccccc
Q 007763 292 ANSKPCPRCKRPIEKNQGCMHMTCTPPCKF-----EFCWLCLGQ 330 (590)
Q Consensus 292 ~ntK~CP~C~~~IEK~~GCnhMtC~~~C~~-----~FCw~C~~~ 330 (590)
...+.||.|+... ....|. .||. .||-.|+..
T Consensus 624 Vg~RfCpsCG~~t------~~frCP-~CG~~Te~i~fCP~CG~~ 660 (1121)
T PRK04023 624 IGRRKCPSCGKET------FYRRCP-FCGTHTEPVYRCPRCGIE 660 (1121)
T ss_pred ccCccCCCCCCcC------CcccCC-CCCCCCCcceeCccccCc
Confidence 3458999999884 347887 7985 599999654
No 284
>KOG2879 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=20.56 E-value=45 Score=34.16 Aligned_cols=31 Identities=23% Similarity=0.788 Sum_probs=21.4
Q ss_pred CcCCCCCCcceeeccCCCceeecCCCcceeeeccccc
Q 007763 294 SKPCPRCKRPIEKNQGCMHMTCTPPCKFEFCWLCLGQ 330 (590)
Q Consensus 294 tK~CP~C~~~IEK~~GCnhMtC~~~C~~~FCw~C~~~ 330 (590)
++.||-|+.+=- +.|+=. +|+|-+||.|...
T Consensus 239 ~~~C~~Cg~~Pt-----iP~~~~-~C~HiyCY~Ci~t 269 (298)
T KOG2879|consen 239 DTECPVCGEPPT-----IPHVIG-KCGHIYCYYCIAT 269 (298)
T ss_pred CceeeccCCCCC-----CCeeec-cccceeehhhhhh
Confidence 578999987543 122222 4999999999874
No 285
>KOG4364 consensus Chromatin assembly factor-I [Chromatin structure and dynamics]
Probab=20.29 E-value=86 Score=35.97 Aligned_cols=8 Identities=13% Similarity=0.235 Sum_probs=3.4
Q ss_pred cchhhccC
Q 007763 7 FDMQDANA 14 (590)
Q Consensus 7 ~d~~~~~~ 14 (590)
|||.=+.|
T Consensus 517 lDYEVdSD 524 (811)
T KOG4364|consen 517 LDYEVDSD 524 (811)
T ss_pred ccccccCc
Confidence 45543333
No 286
>KOG2789 consensus Putative Zn-finger protein [General function prediction only]
Probab=20.21 E-value=46 Score=35.69 Aligned_cols=32 Identities=34% Similarity=0.934 Sum_probs=26.2
Q ss_pred CCcccccccccccCCCCceecCCCCccchhhH
Q 007763 139 GEEMTCGICFENYPSDRLLAAACGHPFCSSCW 170 (590)
Q Consensus 139 ~~~~~C~IC~e~~~~~~~~~l~CgH~fC~~C~ 170 (590)
.....|+|||-.++...-.+--|.-.+|..|+
T Consensus 72 rr~~ecpicflyyps~~n~~rcC~~~Ic~ecf 103 (482)
T KOG2789|consen 72 RRKTECPICFLYYPSAKNLVRCCSETICGECF 103 (482)
T ss_pred cccccCceeeeecccccchhhhhccchhhhhe
Confidence 35678999998887655566679999999999
No 287
>COG5243 HRD1 HRD ubiquitin ligase complex, ER membrane component [Posttranslational modification, protein turnover, chaperones]
Probab=20.18 E-value=70 Score=34.13 Aligned_cols=11 Identities=45% Similarity=1.367 Sum_probs=9.5
Q ss_pred cCCCCCCccee
Q 007763 295 KPCPRCKRPIE 305 (590)
Q Consensus 295 K~CP~C~~~IE 305 (590)
+.||-|+.|+-
T Consensus 335 QTCPICr~p~i 345 (491)
T COG5243 335 QTCPICRRPVI 345 (491)
T ss_pred cCCCcccCccc
Confidence 78999999965
No 288
>PF00098 zf-CCHC: Zinc knuckle; InterPro: IPR001878 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents the CysCysHisCys (CCHC) type zinc finger domains, and have the sequence: C-X2-C-X4-H-X4-C where X can be any amino acid, and number indicates the number of residues. These 18 residues CCHC zinc finger domains are mainly found in the nucleocapsid protein of retroviruses. It is required for viral genome packaging and for early infection process [, , ]. It is also found in eukaryotic proteins involved in RNA binding or single-stranded DNA binding []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003676 nucleic acid binding, 0008270 zinc ion binding; PDB: 2L44_A 1A1T_A 1WWG_A 1U6P_A 1WWD_A 1WWE_A 1A6B_B 1F6U_A 1MFS_A 1NCP_C ....
Probab=20.08 E-value=61 Score=18.98 Aligned_cols=16 Identities=44% Similarity=0.978 Sum_probs=12.6
Q ss_pred cccccCCCcCCCCCch
Q 007763 256 FCWNCTEEAHRPVDCD 271 (590)
Q Consensus 256 fC~~C~~~~H~p~~C~ 271 (590)
.|++|++.-|.-..|.
T Consensus 2 ~C~~C~~~GH~~~~Cp 17 (18)
T PF00098_consen 2 KCFNCGEPGHIARDCP 17 (18)
T ss_dssp BCTTTSCSSSCGCTSS
T ss_pred cCcCCCCcCcccccCc
Confidence 5899999999776664
No 289
>PRK14892 putative transcription elongation factor Elf1; Provisional
Probab=20.08 E-value=1.1e+02 Score=26.71 Aligned_cols=54 Identities=17% Similarity=0.256 Sum_probs=30.6
Q ss_pred CCCcccCCCCCCCc-eEeeecCCCcceeEe-cCCCccccccCCCcCCCCCchhHHHHHHhh
Q 007763 222 NRKTKWCPAPGCDY-AVDFVVGSGNYDVTC-RCSYSFCWNCTEEAHRPVDCDTVAKWVLKN 280 (590)
Q Consensus 222 ~~~~~~CP~p~C~~-~i~~~~~~~~~~v~C-~C~~~fC~~C~~~~H~p~~C~~~~~w~~k~ 280 (590)
.+.+..||+ |+. .+......+...+.| .||+.+=.. -.+.--+=+-+.+|+...
T Consensus 18 lpt~f~CP~--Cge~~v~v~~~k~~~h~~C~~CG~y~~~~---V~~l~epIDVY~~wiD~~ 73 (99)
T PRK14892 18 LPKIFECPR--CGKVSISVKIKKNIAIITCGNCGLYTEFE---VPSVYDEVDVYNKFIDLY 73 (99)
T ss_pred CCcEeECCC--CCCeEeeeecCCCcceEECCCCCCccCEE---CCccccchhhHHHHHHHH
Confidence 356778996 873 332222334456788 888775332 122222346788898765
No 290
>COG3813 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=20.08 E-value=70 Score=26.00 Aligned_cols=43 Identities=33% Similarity=0.812 Sum_probs=29.5
Q ss_pred cccccccccCCCCceecCC--CCccchhhHHHhhcCCCceecccCCCCCCCcc
Q 007763 143 TCGICFENYPSDRLLAAAC--GHPFCSSCWTAINDGPGCLMLRCPDPSCGAAV 193 (590)
Q Consensus 143 ~C~IC~e~~~~~~~~~l~C--gH~fC~~C~~~i~~g~~~~~i~CP~~~C~~~i 193 (590)
.|..|--+++++..-.+-| .|.||.+|-+..-.| .|| .|+-.+
T Consensus 7 nCECCDrDLpp~s~dA~ICtfEcTFCadCae~~l~g------~CP--nCGGel 51 (84)
T COG3813 7 NCECCDRDLPPDSTDARICTFECTFCADCAENRLHG------LCP--NCGGEL 51 (84)
T ss_pred CCcccCCCCCCCCCceeEEEEeeehhHhHHHHhhcC------cCC--CCCchh
Confidence 4888887877765545555 478999999544344 488 787654
No 291
>TIGR02159 PA_CoA_Oxy4 phenylacetate-CoA oxygenase, PaaJ subunit. Phenylacetate-CoA oxygenase is comprised of a five gene complex responsible for the hydroxylation of phenylacetate-CoA (PA-CoA) as the second catabolic step in phenylacetic acid (PA) degradation. Although the exact function of this enzyme has not been determined, it has been shown to be required for phenylacetic acid degradation and has been proposed to function in a multicomponent oxygenase acting on phenylacetate-CoA.
Probab=20.03 E-value=88 Score=29.12 Aligned_cols=92 Identities=13% Similarity=0.190 Sum_probs=49.6
Q ss_pred HHHHHHHHHHHHHHHHhCCCHHHHHHHHHhcCCChHHHHHHhhcCHHHHHHHcCCCCCCCCCCCC----CCccccccccc
Q 007763 74 DIRQRQEEDITRISTVLSISKVAASILLRFYNWSVSKVHDEWFADEERVRKAVGLLEKPAVQFPD----GEEMTCGICFE 149 (590)
Q Consensus 74 ~i~~~~~~~i~~v~~il~i~~~~a~~LL~~~~W~~~~l~e~~~~~~~~~~~~~gl~~~~~~~~~~----~~~~~C~IC~e 149 (590)
.....++++|.+.-..+++..... .+-..--|+.+.+.+. ..+.+.++||-.......+. .....||-|-.
T Consensus 39 pa~e~L~~~I~~aL~~~Gv~~V~V-~i~~~p~Wt~d~it~~----gr~~l~~~giapp~~~~~~~~~~~~~~~~cp~c~s 113 (146)
T TIGR02159 39 PALEVIRQDIRDAVRALGVEVVEV-STSLDPPWTTDWITED----AREKLREYGIAPPAGHYVVGVSPEPPSVQCPRCGS 113 (146)
T ss_pred chHHHHHHHHHHHHHhcCCCeEEE-eEeeCCCCChHHCCHH----HHHHHHhcCccCCCccCCCcccCCCCCCcCCCCCC
Confidence 344444554544433346543222 2344677998877664 23445677885443221111 11468999987
Q ss_pred ccC--CCCceecCCC-CccchhhH
Q 007763 150 NYP--SDRLLAAACG-HPFCSSCW 170 (590)
Q Consensus 150 ~~~--~~~~~~l~Cg-H~fC~~C~ 170 (590)
... .+.+-+..|. ..+|.+|.
T Consensus 114 ~~t~~~s~fg~t~cka~~~c~~c~ 137 (146)
T TIGR02159 114 ADTTITSIFGPTACKALYRCRACK 137 (146)
T ss_pred CCcEeecCCCChhhHHHhhhhhhC
Confidence 642 1344456686 46788886
Done!