Query 019860
Match_columns 334
No_of_seqs 168 out of 696
Neff 6.6
Searched_HMMs 46136
Date Fri Mar 29 05:07:05 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/019860.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/019860hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG0826 Predicted E3 ubiquitin 100.0 6.2E-73 1.3E-77 528.4 15.4 291 1-333 64-356 (357)
2 PF04757 Pex2_Pex12: Pex2 / Pe 100.0 3.8E-31 8.2E-36 242.6 17.1 189 2-245 41-229 (229)
3 KOG0317 Predicted E3 ubiquitin 99.5 2.6E-13 5.7E-18 126.6 10.6 55 276-331 238-292 (293)
4 smart00504 Ubox Modified RING 99.4 2.5E-13 5.4E-18 100.1 4.8 53 278-331 2-54 (63)
5 PLN03208 E3 ubiquitin-protein 99.3 1.6E-12 3.5E-17 116.0 4.7 56 276-332 17-88 (193)
6 KOG0320 Predicted E3 ubiquitin 99.3 3.2E-12 6.9E-17 111.8 4.7 57 276-332 130-187 (187)
7 KOG0823 Predicted E3 ubiquitin 99.2 3.8E-12 8.3E-17 115.7 3.8 58 274-332 44-104 (230)
8 PF13923 zf-C3HC4_2: Zinc fing 99.2 8.4E-12 1.8E-16 83.9 2.7 39 280-318 1-39 (39)
9 PF04564 U-box: U-box domain; 99.1 2.2E-11 4.8E-16 93.1 2.9 54 276-330 3-57 (73)
10 PF15227 zf-C3HC4_4: zinc fing 99.0 2.9E-10 6.2E-15 77.9 2.6 38 280-318 1-42 (42)
11 PF13639 zf-RING_2: Ring finge 98.9 3.8E-10 8.3E-15 77.7 1.7 41 278-319 1-44 (44)
12 PF13920 zf-C3HC4_3: Zinc fing 98.9 8.6E-10 1.9E-14 78.0 2.9 46 277-323 2-48 (50)
13 KOG2164 Predicted E3 ubiquitin 98.9 8.5E-10 1.8E-14 110.2 3.5 55 277-332 186-245 (513)
14 PHA02929 N1R/p28-like protein; 98.9 1.4E-09 3.1E-14 100.7 4.1 48 276-323 173-227 (238)
15 TIGR00599 rad18 DNA repair pro 98.9 1.8E-09 4E-14 106.7 5.1 55 274-329 23-77 (397)
16 KOG0978 E3 ubiquitin ligase in 98.8 9.8E-10 2.1E-14 114.3 2.4 55 277-332 643-698 (698)
17 cd00162 RING RING-finger (Real 98.8 3.3E-09 7.1E-14 71.5 3.5 43 279-321 1-44 (45)
18 PF00097 zf-C3HC4: Zinc finger 98.8 5.1E-09 1.1E-13 70.7 2.9 39 280-318 1-41 (41)
19 smart00184 RING Ring finger. E 98.7 1.1E-08 2.3E-13 66.6 3.2 38 280-318 1-39 (39)
20 KOG3039 Uncharacterized conser 98.7 1.5E-08 3.2E-13 93.0 3.4 55 276-330 220-277 (303)
21 COG5574 PEX10 RING-finger-cont 98.7 1E-08 2.2E-13 95.0 2.5 51 276-327 214-266 (271)
22 PF13445 zf-RING_UBOX: RING-ty 98.6 2.4E-08 5.2E-13 68.7 2.1 35 280-316 1-43 (43)
23 PF14835 zf-RING_6: zf-RING of 98.6 1.8E-08 3.9E-13 74.4 1.1 50 277-328 7-56 (65)
24 PHA02926 zinc finger-like prot 98.5 7.2E-08 1.6E-12 87.6 3.6 48 276-323 169-230 (242)
25 KOG2879 Predicted E3 ubiquitin 98.5 1.7E-06 3.7E-11 80.8 12.7 49 275-323 237-287 (298)
26 PF11789 zf-Nse: Zinc-finger o 98.4 8.9E-08 1.9E-12 69.8 2.1 43 277-319 11-55 (57)
27 TIGR00570 cdk7 CDK-activating 98.4 2.1E-07 4.5E-12 89.0 4.6 54 276-329 2-60 (309)
28 PF14634 zf-RING_5: zinc-RING 98.4 1.9E-07 4.1E-12 64.3 3.0 42 279-320 1-44 (44)
29 COG5432 RAD18 RING-finger-cont 98.4 6.6E-08 1.4E-12 90.6 0.9 48 275-323 23-70 (391)
30 PF12678 zf-rbx1: RING-H2 zinc 98.4 2.6E-07 5.7E-12 70.6 3.1 42 278-319 20-73 (73)
31 PF04641 Rtf2: Rtf2 RING-finge 98.2 1.7E-06 3.8E-11 81.5 4.4 58 275-333 111-171 (260)
32 KOG4172 Predicted E3 ubiquitin 98.1 4.1E-07 9E-12 64.9 -0.5 53 277-332 7-61 (62)
33 KOG0287 Postreplication repair 98.1 5.1E-07 1.1E-11 86.4 -0.5 54 275-329 21-74 (442)
34 KOG0824 Predicted E3 ubiquitin 98.0 2E-06 4.4E-11 81.2 2.2 47 277-324 7-54 (324)
35 COG5243 HRD1 HRD ubiquitin lig 98.0 3E-06 6.4E-11 82.1 3.2 48 275-323 285-345 (491)
36 KOG0802 E3 ubiquitin ligase [P 98.0 2.4E-06 5.2E-11 88.5 1.9 46 276-322 290-340 (543)
37 KOG2660 Locus-specific chromos 97.9 2.7E-06 5.8E-11 81.4 1.0 48 276-323 14-61 (331)
38 KOG2177 Predicted E3 ubiquitin 97.9 3.6E-06 7.8E-11 77.5 1.7 44 275-319 11-54 (386)
39 KOG0297 TNF receptor-associate 97.8 7.6E-06 1.6E-10 81.5 2.5 54 275-328 19-72 (391)
40 PF12861 zf-Apc11: Anaphase-pr 97.7 3.7E-05 8.1E-10 60.3 3.5 49 277-325 32-84 (85)
41 KOG0311 Predicted E3 ubiquitin 97.6 7.5E-06 1.6E-10 78.9 -2.4 48 276-323 42-90 (381)
42 KOG1002 Nucleotide excision re 97.5 3.5E-05 7.7E-10 77.7 1.9 48 277-325 536-588 (791)
43 COG5222 Uncharacterized conser 97.5 5E-05 1.1E-09 71.9 2.6 44 277-320 274-318 (427)
44 COG5540 RING-finger-containing 97.5 4.4E-05 9.5E-10 72.4 1.9 45 277-322 323-371 (374)
45 KOG4628 Predicted E3 ubiquitin 97.5 0.00011 2.5E-09 71.5 4.3 44 278-322 230-277 (348)
46 KOG1813 Predicted E3 ubiquitin 97.5 4.4E-05 9.6E-10 72.1 1.4 44 278-322 242-285 (313)
47 COG5152 Uncharacterized conser 97.2 0.00017 3.6E-09 64.7 2.0 45 277-322 196-240 (259)
48 KOG1734 Predicted RING-contain 97.0 0.00089 1.9E-08 62.8 5.0 51 276-327 223-285 (328)
49 KOG1645 RING-finger-containing 97.0 0.00022 4.8E-09 70.1 0.5 58 275-332 2-65 (463)
50 COG5175 MOT2 Transcriptional r 96.9 0.00054 1.2E-08 66.0 2.8 52 276-328 13-69 (480)
51 KOG4265 Predicted E3 ubiquitin 96.9 0.00055 1.2E-08 66.4 2.2 52 277-331 290-342 (349)
52 KOG4692 Predicted E3 ubiquitin 96.8 0.00075 1.6E-08 65.4 2.8 50 273-323 417-467 (489)
53 PF14570 zf-RING_4: RING/Ubox 96.8 0.00095 2.1E-08 46.9 2.4 41 280-321 1-46 (48)
54 KOG0828 Predicted E3 ubiquitin 96.7 0.00084 1.8E-08 67.5 2.4 50 274-323 568-634 (636)
55 KOG4159 Predicted E3 ubiquitin 96.6 0.0011 2.4E-08 66.0 2.1 47 275-322 82-128 (398)
56 COG5194 APC11 Component of SCF 96.4 0.0029 6.3E-08 48.9 2.7 49 277-325 31-83 (88)
57 KOG0825 PHD Zn-finger protein 96.3 0.00082 1.8E-08 70.8 -0.7 47 276-322 122-170 (1134)
58 PF14447 Prok-RING_4: Prokaryo 96.3 0.0021 4.4E-08 46.3 1.4 49 276-327 6-54 (55)
59 KOG3039 Uncharacterized conser 96.1 0.0037 8E-08 58.0 2.8 34 276-310 42-75 (303)
60 PF11793 FANCL_C: FANCL C-term 96.1 0.0017 3.7E-08 49.2 0.4 49 277-325 2-68 (70)
61 KOG1039 Predicted E3 ubiquitin 96.1 0.0036 7.7E-08 61.3 2.6 48 276-323 160-221 (344)
62 KOG0827 Predicted E3 ubiquitin 96.0 0.003 6.5E-08 62.0 1.8 52 277-328 4-61 (465)
63 KOG2817 Predicted E3 ubiquitin 95.8 0.024 5.1E-07 56.0 6.7 97 219-331 287-393 (394)
64 KOG1001 Helicase-like transcri 95.6 0.0025 5.5E-08 67.6 -0.6 48 278-327 455-504 (674)
65 KOG0883 Cyclophilin type, U bo 95.3 0.011 2.4E-07 58.1 2.7 54 277-331 40-93 (518)
66 KOG0804 Cytoplasmic Zn-finger 95.1 0.011 2.4E-07 59.1 1.9 43 279-323 177-222 (493)
67 KOG1785 Tyrosine kinase negati 94.9 0.012 2.5E-07 58.1 1.4 45 278-323 370-416 (563)
68 PF10367 Vps39_2: Vacuolar sor 94.9 0.013 2.9E-07 46.9 1.5 30 276-306 77-108 (109)
69 smart00744 RINGv The RING-vari 94.8 0.031 6.7E-07 39.4 3.0 40 279-319 1-49 (49)
70 KOG1571 Predicted E3 ubiquitin 94.7 0.016 3.6E-07 56.4 1.9 42 277-322 305-346 (355)
71 KOG2932 E3 ubiquitin ligase in 94.7 0.012 2.6E-07 56.3 0.9 42 278-322 91-133 (389)
72 KOG3113 Uncharacterized conser 94.3 0.036 7.7E-07 51.8 3.0 55 276-332 110-167 (293)
73 KOG1493 Anaphase-promoting com 94.3 0.021 4.6E-07 43.8 1.2 48 277-324 31-82 (84)
74 KOG2930 SCF ubiquitin ligase, 94.2 0.028 6.2E-07 45.5 2.0 45 278-322 47-107 (114)
75 PF02891 zf-MIZ: MIZ/SP-RING z 93.8 0.06 1.3E-06 38.1 2.8 43 278-321 3-50 (50)
76 KOG4275 Predicted E3 ubiquitin 93.5 0.0088 1.9E-07 56.8 -2.4 41 277-322 300-341 (350)
77 KOG2979 Protein involved in DN 93.4 0.044 9.5E-07 51.3 1.9 45 277-321 176-222 (262)
78 PF10571 UPF0547: Uncharacteri 93.2 0.049 1.1E-06 33.4 1.3 22 279-300 2-24 (26)
79 PF04216 FdhE: Protein involve 93.0 0.018 4E-07 55.1 -1.2 46 276-321 171-220 (290)
80 KOG3002 Zn finger protein [Gen 92.9 0.065 1.4E-06 51.7 2.3 44 276-323 47-91 (299)
81 PF05290 Baculo_IE-1: Baculovi 92.8 0.09 1.9E-06 44.6 2.7 47 277-323 80-132 (140)
82 KOG3579 Predicted E3 ubiquitin 92.7 0.089 1.9E-06 49.9 2.9 37 276-312 267-306 (352)
83 KOG0298 DEAD box-containing he 92.5 0.027 5.8E-07 62.7 -1.0 43 277-319 1153-1195(1394)
84 COG5219 Uncharacterized conser 91.9 0.054 1.2E-06 58.7 0.4 47 277-323 1469-1523(1525)
85 COG5236 Uncharacterized conser 91.5 0.11 2.4E-06 50.6 2.1 45 276-321 60-106 (493)
86 PRK04023 DNA polymerase II lar 90.8 0.19 4.1E-06 55.2 3.2 54 273-329 622-680 (1121)
87 TIGR01562 FdhE formate dehydro 90.6 0.086 1.9E-06 51.0 0.4 46 276-321 183-233 (305)
88 PLN02189 cellulose synthase 89.2 0.25 5.5E-06 54.5 2.6 46 276-322 33-86 (1040)
89 KOG4367 Predicted Zn-finger pr 89.0 0.21 4.5E-06 50.1 1.7 35 276-311 3-37 (699)
90 KOG1941 Acetylcholine receptor 88.6 0.17 3.6E-06 50.1 0.7 42 277-319 365-412 (518)
91 PF05883 Baculo_RING: Baculovi 88.6 0.21 4.6E-06 42.5 1.2 41 277-317 26-74 (134)
92 KOG4185 Predicted E3 ubiquitin 88.3 0.28 6E-06 46.8 2.0 43 279-322 5-54 (296)
93 PLN02436 cellulose synthase A 87.9 0.34 7.5E-06 53.7 2.6 46 276-322 35-88 (1094)
94 PF14446 Prok-RING_1: Prokaryo 87.3 0.69 1.5E-05 33.3 3.0 44 276-323 4-52 (54)
95 KOG1814 Predicted E3 ubiquitin 86.7 0.41 8.9E-06 47.7 2.1 45 277-321 184-238 (445)
96 PF07191 zinc-ribbons_6: zinc- 86.5 0.069 1.5E-06 40.5 -2.6 40 278-323 2-41 (70)
97 PHA03096 p28-like protein; Pro 86.4 0.39 8.4E-06 46.1 1.8 44 278-321 179-232 (284)
98 PRK03564 formate dehydrogenase 86.2 0.34 7.4E-06 47.0 1.3 46 276-321 186-235 (309)
99 PF03854 zf-P11: P-11 zinc fin 85.7 0.32 6.9E-06 34.1 0.6 43 279-323 4-46 (50)
100 PF09538 FYDLN_acid: Protein o 85.5 0.48 1E-05 39.0 1.7 28 276-303 8-39 (108)
101 PF10235 Cript: Microtubule-as 84.9 0.69 1.5E-05 36.8 2.2 36 277-322 44-79 (90)
102 cd00350 rubredoxin_like Rubred 84.8 0.48 1E-05 30.4 1.1 11 311-321 16-26 (33)
103 PF08746 zf-RING-like: RING-li 84.2 1 2.2E-05 30.8 2.6 39 280-318 1-43 (43)
104 KOG3800 Predicted E3 ubiquitin 83.4 0.67 1.4E-05 44.3 1.9 38 295-332 22-61 (300)
105 PLN02638 cellulose synthase A 83.3 0.8 1.7E-05 50.9 2.6 45 276-321 16-68 (1079)
106 KOG3268 Predicted E3 ubiquitin 82.7 1.1 2.5E-05 39.9 2.9 48 277-325 165-230 (234)
107 KOG1812 Predicted E3 ubiquitin 82.6 0.52 1.1E-05 47.1 0.8 42 277-319 306-352 (384)
108 PRK05978 hypothetical protein; 82.3 0.87 1.9E-05 39.6 2.0 33 277-325 33-65 (148)
109 TIGR02300 FYDLN_acid conserved 81.6 0.88 1.9E-05 38.4 1.7 28 276-303 8-39 (129)
110 PLN02195 cellulose synthase A 81.4 1.3 2.8E-05 48.9 3.3 46 277-323 6-59 (977)
111 KOG1812 Predicted E3 ubiquitin 80.9 0.7 1.5E-05 46.2 1.1 53 277-330 146-210 (384)
112 PLN02915 cellulose synthase A 80.5 1.2 2.5E-05 49.6 2.6 46 276-322 14-67 (1044)
113 KOG2068 MOT2 transcription fac 80.3 2.1 4.5E-05 41.7 4.0 45 278-322 250-297 (327)
114 COG1592 Rubrerythrin [Energy p 80.1 1.1 2.3E-05 39.7 1.8 13 277-289 134-146 (166)
115 KOG3970 Predicted E3 ubiquitin 79.2 1.6 3.4E-05 40.5 2.6 44 279-322 52-104 (299)
116 PF14569 zf-UDP: Zinc-binding 79.0 2.4 5.2E-05 32.8 3.2 47 276-322 8-61 (80)
117 cd00729 rubredoxin_SM Rubredox 78.9 1.1 2.3E-05 29.1 1.1 10 313-322 19-28 (34)
118 KOG2169 Zn-finger transcriptio 78.8 1.4 3E-05 47.0 2.5 51 277-328 306-361 (636)
119 PF12773 DZR: Double zinc ribb 78.2 0.87 1.9E-05 31.6 0.5 16 273-288 8-23 (50)
120 KOG1940 Zn-finger protein [Gen 78.1 1.4 2.9E-05 42.2 2.0 44 277-321 158-205 (276)
121 TIGR00622 ssl1 transcription f 78.1 3 6.4E-05 34.6 3.7 43 277-319 55-110 (112)
122 PF07975 C1_4: TFIIH C1-like d 77.9 1.6 3.4E-05 31.1 1.8 28 291-319 22-50 (51)
123 PRK14714 DNA polymerase II lar 77.3 1.2 2.6E-05 50.2 1.6 48 278-326 668-723 (1337)
124 KOG4718 Non-SMC (structural ma 77.2 1 2.2E-05 41.3 0.8 45 276-320 180-224 (235)
125 COG0068 HypF Hydrogenase matur 76.5 1.1 2.5E-05 47.6 1.1 50 273-322 97-183 (750)
126 KOG1815 Predicted E3 ubiquitin 76.0 3.2 7E-05 42.2 4.2 55 276-330 69-133 (444)
127 KOG0309 Conserved WD40 repeat- 75.9 1.7 3.7E-05 46.5 2.1 47 277-323 1028-1076(1081)
128 COG5183 SSM4 Protein involved 75.6 2.1 4.6E-05 46.2 2.7 55 273-327 8-70 (1175)
129 PLN02400 cellulose synthase 75.5 1.6 3.4E-05 48.7 1.8 46 276-322 35-88 (1085)
130 KOG2034 Vacuolar sorting prote 75.3 1.4 3E-05 47.9 1.3 34 277-310 817-851 (911)
131 COG5109 Uncharacterized conser 75.2 1.8 3.8E-05 42.0 1.9 54 277-331 336-395 (396)
132 COG5627 MMS21 DNA repair prote 74.9 1.7 3.8E-05 40.4 1.7 41 277-317 189-231 (275)
133 COG5220 TFB3 Cdk activating ki 74.8 1.2 2.5E-05 41.6 0.6 45 277-321 10-62 (314)
134 KOG2042 Ubiquitin fusion degra 74.6 2.6 5.7E-05 46.4 3.2 54 276-329 869-922 (943)
135 KOG0825 PHD Zn-finger protein 73.7 2.2 4.7E-05 46.0 2.2 44 276-319 95-150 (1134)
136 PHA02862 5L protein; Provision 73.7 2.8 6.1E-05 36.2 2.6 47 277-323 2-53 (156)
137 PF04423 Rad50_zn_hook: Rad50 73.2 0.7 1.5E-05 32.9 -1.1 14 313-326 21-34 (54)
138 PHA02825 LAP/PHD finger-like p 73.1 3.7 8E-05 36.1 3.2 48 276-325 7-61 (162)
139 PF06750 DiS_P_DiS: Bacterial 71.1 5.3 0.00011 31.8 3.4 38 277-324 33-70 (92)
140 PF03833 PolC_DP2: DNA polymer 71.0 1.3 2.9E-05 48.0 0.0 44 277-323 655-703 (900)
141 PF09889 DUF2116: Uncharacteri 70.3 2.4 5.2E-05 31.1 1.2 16 310-325 1-16 (59)
142 KOG2114 Vacuolar assembly/sort 70.0 2.3 5E-05 46.1 1.5 40 278-320 841-880 (933)
143 PF05605 zf-Di19: Drought indu 69.3 2.8 6E-05 29.7 1.3 40 276-323 1-42 (54)
144 KOG0883 Cyclophilin type, U bo 68.0 3.3 7.2E-05 41.3 2.0 58 275-332 99-161 (518)
145 KOG1815 Predicted E3 ubiquitin 67.9 2.5 5.3E-05 43.0 1.1 18 290-308 179-196 (444)
146 KOG0269 WD40 repeat-containing 67.4 4.6 9.9E-05 43.4 3.0 50 277-326 779-831 (839)
147 PF04641 Rtf2: Rtf2 RING-finge 66.2 8.2 0.00018 36.4 4.2 54 277-330 34-91 (260)
148 PF10497 zf-4CXXC_R1: Zinc-fin 65.9 7.6 0.00017 31.7 3.5 44 277-320 7-69 (105)
149 KOG4739 Uncharacterized protei 65.8 2.9 6.2E-05 39.0 1.0 33 278-310 4-37 (233)
150 COG3357 Predicted transcriptio 65.4 2.5 5.3E-05 33.7 0.4 29 288-320 56-84 (97)
151 COG1645 Uncharacterized Zn-fin 64.4 2.4 5.2E-05 36.1 0.2 24 277-305 28-51 (131)
152 KOG1356 Putative transcription 63.5 1.9 4E-05 46.7 -0.7 45 277-321 229-280 (889)
153 PF15616 TerY-C: TerY-C metal 63.1 2.8 6.1E-05 35.7 0.4 40 279-325 79-118 (131)
154 KOG4445 Uncharacterized conser 63.0 2.1 4.7E-05 41.2 -0.3 47 277-324 115-187 (368)
155 KOG4362 Transcriptional regula 62.9 2 4.3E-05 45.7 -0.6 46 277-323 21-69 (684)
156 PF09986 DUF2225: Uncharacteri 62.4 2.3 4.9E-05 39.1 -0.3 55 275-329 3-65 (214)
157 smart00647 IBR In Between Ring 62.0 2.1 4.4E-05 30.7 -0.5 18 291-308 41-58 (64)
158 PF09723 Zn-ribbon_8: Zinc rib 61.5 2.7 5.8E-05 28.4 0.0 10 311-320 25-34 (42)
159 PF13240 zinc_ribbon_2: zinc-r 61.5 1.5 3.2E-05 26.0 -1.1 11 280-290 2-12 (23)
160 KOG0824 Predicted E3 ubiquitin 60.6 2.9 6.3E-05 40.3 0.1 47 275-321 103-149 (324)
161 PLN02248 cellulose synthase-li 60.4 6.2 0.00013 44.3 2.6 36 291-327 146-181 (1135)
162 PF06906 DUF1272: Protein of u 59.9 11 0.00024 27.3 2.9 41 279-322 7-51 (57)
163 smart00064 FYVE Protein presen 59.8 7.3 0.00016 28.6 2.1 35 277-311 10-47 (68)
164 KOG1952 Transcription factor N 59.4 5.2 0.00011 43.5 1.7 45 275-319 189-243 (950)
165 KOG3161 Predicted E3 ubiquitin 59.2 3 6.4E-05 44.0 -0.1 37 277-316 11-51 (861)
166 PRK14559 putative protein seri 59.0 3.6 7.8E-05 43.9 0.5 42 273-323 11-52 (645)
167 PF14205 Cys_rich_KTR: Cystein 58.8 3.7 8.1E-05 29.6 0.4 22 279-301 6-31 (55)
168 PRK00420 hypothetical protein; 57.9 4.5 9.8E-05 33.5 0.8 12 277-288 23-34 (112)
169 PF12906 RINGv: RING-variant d 57.7 4.8 0.0001 27.9 0.8 32 287-318 14-47 (47)
170 TIGR00143 hypF [NiFe] hydrogen 57.5 3.5 7.7E-05 44.5 0.1 51 273-323 64-151 (711)
171 KOG2113 Predicted RNA binding 57.5 7.9 0.00017 37.6 2.4 50 277-331 343-393 (394)
172 PTZ00303 phosphatidylinositol 57.1 6.7 0.00014 42.5 2.0 32 278-309 461-500 (1374)
173 PF02148 zf-UBP: Zn-finger in 56.5 6 0.00013 28.9 1.2 34 280-313 1-38 (63)
174 PF12660 zf-TFIIIC: Putative z 55.8 6.3 0.00014 31.8 1.3 43 278-322 15-65 (99)
175 PF12312 NeA_P2: Nepovirus sub 55.3 12 0.00027 34.0 3.1 31 232-262 172-208 (258)
176 cd00065 FYVE FYVE domain; Zinc 54.9 10 0.00022 26.7 2.1 34 278-311 3-39 (57)
177 PF01363 FYVE: FYVE zinc finge 54.2 3.8 8.2E-05 30.2 -0.2 34 276-309 8-44 (69)
178 KOG1729 FYVE finger containing 53.9 7.7 0.00017 37.4 1.7 46 276-321 167-223 (288)
179 cd00730 rubredoxin Rubredoxin; 53.7 6.9 0.00015 27.7 1.0 13 309-321 31-43 (50)
180 KOG1100 Predicted E3 ubiquitin 53.4 4.9 0.00011 36.8 0.3 41 279-323 160-200 (207)
181 PHA00626 hypothetical protein 53.1 10 0.00022 27.6 1.8 7 279-285 2-8 (59)
182 PF13248 zf-ribbon_3: zinc-rib 53.1 2.7 5.9E-05 25.4 -1.0 10 278-287 3-12 (26)
183 COG3813 Uncharacterized protei 52.4 10 0.00022 29.0 1.8 30 290-322 22-51 (84)
184 KOG1609 Protein involved in mR 51.2 13 0.00027 35.3 2.8 50 274-323 75-134 (323)
185 PF07800 DUF1644: Protein of u 50.6 8.2 0.00018 33.9 1.2 34 277-310 2-47 (162)
186 PF00412 LIM: LIM domain; Int 50.3 14 0.00029 25.8 2.2 32 276-307 25-56 (58)
187 COG3058 FdhE Uncharacterized p 50.2 14 0.00031 35.3 2.8 46 276-321 184-234 (308)
188 PF10272 Tmpp129: Putative tra 50.2 22 0.00049 35.3 4.3 52 276-327 270-355 (358)
189 TIGR01031 rpmF_bact ribosomal 49.0 9.2 0.0002 27.6 1.1 22 277-298 26-47 (55)
190 KOG2041 WD40 repeat protein [G 48.3 13 0.00028 40.2 2.4 52 269-323 1123-1185(1189)
191 PRK07218 replication factor A; 48.2 12 0.00026 38.0 2.2 27 278-327 298-324 (423)
192 PRK12286 rpmF 50S ribosomal pr 46.7 11 0.00025 27.3 1.3 22 277-298 27-48 (57)
193 KOG4218 Nuclear hormone recept 46.6 13 0.00029 36.6 2.1 11 277-287 15-25 (475)
194 PF08271 TF_Zn_Ribbon: TFIIB z 46.1 13 0.00028 25.1 1.4 8 279-286 2-9 (43)
195 PRK06393 rpoE DNA-directed RNA 45.4 10 0.00022 28.3 0.9 34 297-332 4-40 (64)
196 PF01783 Ribosomal_L32p: Ribos 44.8 13 0.00029 26.7 1.4 23 276-298 25-47 (56)
197 COG4068 Uncharacterized protei 44.8 12 0.00027 27.4 1.2 16 310-325 6-21 (64)
198 COG3686 Predicted membrane pro 44.4 1.3E+02 0.0027 25.4 7.2 46 126-172 48-113 (125)
199 smart00734 ZnF_Rad18 Rad18-lik 44.3 7.8 0.00017 23.5 0.1 8 315-322 4-11 (26)
200 PRK08270 anaerobic ribonucleos 44.2 13 0.00029 39.8 1.9 19 310-330 637-655 (656)
201 smart00154 ZnF_AN1 AN1-like Zi 43.5 15 0.00033 24.4 1.4 23 280-302 1-24 (39)
202 PF14803 Nudix_N_2: Nudix N-te 43.4 8.2 0.00018 25.1 0.1 22 279-300 2-32 (34)
203 TIGR00373 conserved hypothetic 43.4 7.7 0.00017 33.9 -0.0 32 276-323 108-139 (158)
204 COG1773 Rubredoxin [Energy pro 43.3 13 0.00028 26.9 1.1 15 306-320 30-44 (55)
205 KOG0006 E3 ubiquitin-protein l 43.3 15 0.00033 35.8 1.9 33 277-309 315-355 (446)
206 PRK06386 replication factor A; 43.2 15 0.00032 36.5 1.9 12 278-289 237-248 (358)
207 PF04710 Pellino: Pellino; In 43.2 7.9 0.00017 38.7 0.0 55 277-331 328-410 (416)
208 smart00661 RPOL9 RNA polymeras 42.7 15 0.00033 25.2 1.4 9 279-287 2-10 (52)
209 PRK12496 hypothetical protein; 42.4 6.3 0.00014 34.7 -0.7 30 277-325 127-156 (164)
210 KOG4642 Chaperone-dependent E3 42.0 14 0.00031 34.9 1.4 55 273-329 208-263 (284)
211 COG5113 UFD2 Ubiquitin fusion 42.0 23 0.00049 37.8 3.0 53 276-328 853-905 (929)
212 COG1997 RPL43A Ribosomal prote 41.7 16 0.00034 29.0 1.4 30 276-308 34-63 (89)
213 KOG3476 Microtubule-associated 41.0 2.5 5.5E-05 33.3 -3.0 35 278-322 55-89 (100)
214 PF01485 IBR: IBR domain; Int 40.8 9.3 0.0002 27.1 0.1 31 278-308 19-58 (64)
215 PRK00398 rpoP DNA-directed RNA 40.7 9.2 0.0002 26.1 0.0 29 278-323 4-32 (46)
216 PRK12495 hypothetical protein; 40.7 11 0.00024 34.8 0.5 25 277-306 42-66 (226)
217 KOG0396 Uncharacterized conser 40.2 16 0.00034 36.4 1.5 55 277-332 330-388 (389)
218 PF14471 DUF4428: Domain of un 38.8 25 0.00054 24.9 2.0 28 279-308 1-30 (51)
219 PRK07217 replication factor A; 38.8 22 0.00048 34.6 2.3 28 278-328 189-218 (311)
220 KOG3726 Uncharacterized conser 38.6 17 0.00038 38.7 1.6 42 278-322 655-699 (717)
221 smart00834 CxxC_CXXC_SSSS Puta 38.2 12 0.00025 24.5 0.2 31 276-320 4-34 (41)
222 PF00301 Rubredoxin: Rubredoxi 37.9 12 0.00026 26.2 0.2 13 309-321 31-43 (47)
223 PF07578 LAB_N: Lipid A Biosyn 37.9 29 0.00063 26.5 2.3 20 228-247 4-24 (72)
224 PF01428 zf-AN1: AN1-like Zinc 37.4 16 0.00036 24.6 0.9 25 280-304 1-27 (43)
225 PF01258 zf-dskA_traR: Prokary 36.8 15 0.00033 23.7 0.6 31 278-308 4-34 (36)
226 TIGR02605 CxxC_CxxC_SSSS putat 36.8 12 0.00026 26.0 0.1 9 312-320 26-34 (52)
227 PRK08351 DNA-directed RNA poly 36.5 14 0.0003 27.4 0.4 14 309-322 12-25 (61)
228 KOG3842 Adaptor protein Pellin 36.3 32 0.00069 33.6 2.9 54 277-330 341-422 (429)
229 PF07282 OrfB_Zn_ribbon: Putat 36.0 24 0.00052 25.9 1.6 14 276-289 27-40 (69)
230 PLN02720 complex II 35.7 18 0.00039 30.7 1.0 9 235-243 129-137 (140)
231 smart00132 LIM Zinc-binding do 35.5 29 0.00063 21.6 1.8 36 279-322 1-37 (39)
232 PRK11827 hypothetical protein; 34.4 23 0.0005 26.1 1.3 13 277-289 8-20 (60)
233 PF02318 FYVE_2: FYVE-type zin 33.9 22 0.00047 29.4 1.2 31 277-307 54-88 (118)
234 KOG2462 C2H2-type Zn-finger pr 33.7 41 0.00089 32.2 3.1 12 277-288 130-141 (279)
235 PF14353 CpXC: CpXC protein 32.5 32 0.0007 28.5 2.1 44 278-324 2-50 (128)
236 KOG1814 Predicted E3 ubiquitin 32.4 17 0.00038 36.5 0.5 51 275-331 271-328 (445)
237 PHA02768 hypothetical protein; 32.3 35 0.00075 24.7 1.9 42 277-330 5-50 (55)
238 TIGR02827 RNR_anaer_Bdell anae 31.5 27 0.00058 37.0 1.7 18 313-331 547-564 (586)
239 PF04088 Peroxin-13_N: Peroxin 31.4 61 0.0013 28.5 3.6 27 46-72 130-156 (158)
240 KOG1701 Focal adhesion adaptor 31.3 29 0.00063 35.2 1.8 51 278-330 361-416 (468)
241 KOG1842 FYVE finger-containing 30.9 19 0.0004 36.7 0.4 70 225-306 139-212 (505)
242 PRK06266 transcription initiat 30.7 43 0.00092 29.9 2.6 32 276-323 116-147 (178)
243 TIGR00375 conserved hypothetic 30.5 12 0.00027 37.3 -1.0 18 135-152 84-101 (374)
244 PF06827 zf-FPG_IleRS: Zinc fi 30.3 12 0.00026 23.2 -0.7 26 279-305 3-28 (30)
245 PF10013 DUF2256: Uncharacteri 30.3 28 0.00061 23.8 1.1 10 313-322 9-18 (42)
246 PRK14714 DNA polymerase II lar 30.2 23 0.0005 40.5 1.0 30 277-306 679-717 (1337)
247 COG4530 Uncharacterized protei 29.8 29 0.00063 28.7 1.3 25 276-300 8-36 (129)
248 PRK00448 polC DNA polymerase I 29.8 43 0.00094 39.2 3.1 37 277-325 908-946 (1437)
249 CHL00174 accD acetyl-CoA carbo 29.7 23 0.00051 34.2 0.9 26 277-302 38-69 (296)
250 TIGR00398 metG methionyl-tRNA 29.5 34 0.00074 35.3 2.1 47 277-328 136-182 (530)
251 COG2176 PolC DNA polymerase II 29.4 49 0.0011 37.9 3.3 37 277-325 914-952 (1444)
252 PF02202 Tachykinin: Tachykini 29.3 15 0.00032 18.1 -0.3 6 18-23 5-10 (11)
253 PF06677 Auto_anti-p27: Sjogre 29.2 19 0.00041 24.4 0.1 24 277-304 17-40 (41)
254 COG1439 Predicted nucleic acid 29.2 15 0.00032 32.9 -0.6 12 311-322 152-163 (177)
255 PRK08271 anaerobic ribonucleos 29.2 18 0.00039 38.6 -0.1 30 292-330 568-597 (623)
256 KOG2272 Focal adhesion protein 28.7 30 0.00066 32.7 1.4 39 275-319 161-199 (332)
257 smart00531 TFIIE Transcription 28.5 31 0.00067 29.6 1.3 37 276-323 98-134 (147)
258 KOG1428 Inhibitor of type V ad 28.1 20 0.00043 41.8 0.0 48 276-323 3485-3544(3738)
259 PRK01343 zinc-binding protein; 27.7 55 0.0012 23.9 2.3 35 277-317 9-48 (57)
260 PF08274 PhnA_Zn_Ribbon: PhnA 27.4 23 0.0005 22.4 0.2 21 279-299 4-28 (30)
261 KOG2807 RNA polymerase II tran 27.3 38 0.00083 33.2 1.8 42 278-319 331-374 (378)
262 PRK14892 putative transcriptio 27.0 27 0.00059 28.3 0.7 11 276-286 20-30 (99)
263 COG2093 DNA-directed RNA polym 26.9 20 0.00043 26.7 -0.1 23 297-321 3-27 (64)
264 TIGR00515 accD acetyl-CoA carb 26.7 24 0.00051 34.0 0.3 25 277-301 26-56 (285)
265 KOG2675 Adenylate cyclase-asso 26.3 47 0.001 33.8 2.3 11 222-232 201-211 (480)
266 TIGR03847 conserved hypothetic 26.2 38 0.00082 30.2 1.5 11 279-290 158-168 (177)
267 PRK02935 hypothetical protein; 26.0 41 0.00088 27.6 1.5 15 311-325 85-99 (110)
268 PF08394 Arc_trans_TRASH: Arch 25.9 65 0.0014 21.4 2.2 32 280-311 1-36 (37)
269 PRK14890 putative Zn-ribbon RN 25.6 38 0.00082 24.9 1.1 18 301-320 39-56 (59)
270 smart00746 TRASH metallochaper 25.5 77 0.0017 18.5 2.5 31 280-310 1-37 (39)
271 PF03119 DNA_ligase_ZBD: NAD-d 25.3 24 0.00052 21.8 0.0 10 314-323 1-10 (28)
272 PF04184 ST7: ST7 protein; In 25.2 15 0.00033 38.0 -1.4 19 2-20 63-81 (539)
273 PF10164 DUF2367: Uncharacteri 25.1 70 0.0015 25.9 2.7 43 277-320 49-96 (98)
274 smart00290 ZnF_UBP Ubiquitin C 25.0 42 0.00091 22.8 1.2 25 279-304 1-25 (50)
275 COG0333 RpmF Ribosomal protein 24.9 42 0.00091 24.5 1.2 22 277-298 27-48 (57)
276 PRK14873 primosome assembly pr 24.5 24 0.00053 37.9 -0.1 42 278-321 384-431 (665)
277 PRK08665 ribonucleotide-diphos 24.4 43 0.00093 36.6 1.8 25 277-301 724-751 (752)
278 COG5151 SSL1 RNA polymerase II 24.3 65 0.0014 31.5 2.7 26 296-321 394-419 (421)
279 PRK05654 acetyl-CoA carboxylas 24.2 28 0.0006 33.6 0.2 24 277-300 27-56 (292)
280 KOG4217 Nuclear receptors of t 24.0 69 0.0015 33.1 3.0 42 276-321 268-320 (605)
281 PF03966 Trm112p: Trm112p-like 24.0 31 0.00066 25.6 0.4 11 277-287 7-17 (68)
282 PF06170 DUF983: Protein of un 24.0 40 0.00086 26.5 1.1 18 307-324 3-20 (86)
283 PF13717 zinc_ribbon_4: zinc-r 23.8 40 0.00086 22.0 0.9 8 279-286 4-11 (36)
284 COG1656 Uncharacterized conser 23.7 35 0.00076 30.2 0.8 15 276-290 96-110 (165)
285 PF14354 Lar_restr_allev: Rest 23.7 30 0.00065 24.7 0.3 27 279-305 5-36 (61)
286 PRK01110 rpmF 50S ribosomal pr 23.3 38 0.00083 24.8 0.8 21 277-298 27-47 (60)
287 KOG2066 Vacuolar assembly/sort 22.9 27 0.00059 38.0 -0.1 41 277-319 784-831 (846)
288 PF06750 DiS_P_DiS: Bacterial 22.8 35 0.00076 27.1 0.5 22 310-331 31-52 (92)
289 TIGR01405 polC_Gram_pos DNA po 22.7 62 0.0013 37.3 2.7 37 277-325 683-721 (1213)
290 COG1675 TFA1 Transcription ini 22.5 39 0.00085 30.2 0.9 33 277-325 113-145 (176)
291 TIGR02098 MJ0042_CXXC MJ0042 f 22.5 37 0.00081 21.9 0.5 12 279-290 4-15 (38)
292 PRK08579 anaerobic ribonucleos 22.3 15 0.00032 39.2 -2.2 24 297-320 567-590 (625)
293 KOG3807 Predicted membrane pro 22.1 21 0.00046 35.4 -1.0 19 2-20 78-96 (556)
294 COG1198 PriA Primosomal protei 22.1 35 0.00076 37.1 0.6 44 277-321 435-484 (730)
295 PLN03086 PRLI-interacting fact 22.1 89 0.0019 33.1 3.5 46 276-322 452-514 (567)
296 PF10217 DUF2039: Uncharacteri 22.1 62 0.0013 25.9 1.8 36 277-321 55-90 (92)
297 COG1326 Uncharacterized archae 21.7 49 0.0011 30.1 1.3 7 278-284 7-13 (201)
298 PRK09710 lar restriction allev 21.6 30 0.00065 25.8 -0.1 27 279-305 8-34 (64)
299 COG4338 Uncharacterized protei 21.4 27 0.00058 24.6 -0.3 10 278-287 13-22 (54)
300 PRK13130 H/ACA RNA-protein com 21.4 20 0.00043 26.1 -1.0 12 312-323 17-28 (56)
301 PRK00418 DNA gyrase inhibitor; 21.3 48 0.001 24.6 0.9 11 313-323 7-17 (62)
302 TIGR01206 lysW lysine biosynth 21.2 38 0.00081 24.4 0.4 31 278-323 3-33 (54)
303 PF08273 Prim_Zn_Ribbon: Zinc- 21.2 33 0.00072 23.1 0.1 25 279-304 5-32 (40)
304 KOG0314 Predicted E3 ubiquitin 21.1 32 0.00069 35.2 0.0 44 276-320 218-263 (448)
305 PRK07726 DNA topoisomerase III 20.7 58 0.0013 35.0 1.8 41 277-320 610-657 (658)
306 TIGR00595 priA primosomal prot 20.7 65 0.0014 33.4 2.2 34 279-321 224-262 (505)
307 KOG4577 Transcription factor L 20.2 27 0.00059 33.6 -0.7 46 279-328 62-108 (383)
308 TIGR00627 tfb4 transcription f 20.1 1.4E+02 0.003 28.7 4.1 35 278-321 243-278 (279)
309 COG4647 AcxC Acetone carboxyla 20.0 40 0.00086 28.8 0.3 21 281-302 61-81 (165)
No 1
>KOG0826 consensus Predicted E3 ubiquitin ligase involved in peroxisome organization [Posttranslational modification, protein turnover, chaperones]
Probab=100.00 E-value=6.2e-73 Score=528.39 Aligned_cols=291 Identities=37% Similarity=0.662 Sum_probs=248.3
Q ss_pred CeeeeecccccCCCcccccccCeeeeccccccccccccccCCCCccCCCCCcchHHHHHHHHHHHHhHHHHHHHHHHHhH
Q 019860 1 MLILETHSLRNTDASFSESLYGLRRRSVRIRAKKDDTRLKSSDGIHHSGLEKRQRVLSVVFMVVLPYFKSKLHSVYNKER 80 (334)
Q Consensus 1 ~llvE~~~Lk~~~aSFaE~FYGLkR~~~~~~~~~~~~~~~~~~~~~~~~Lt~~q~~~sLl~lV~~PYlk~KLd~~ye~~~ 80 (334)
|++||+|||++|||||+||||||||...++.- .+.|+++.+|.++|+++|+++||++||+++|||++|++++
T Consensus 64 ~liLq~hyLr~~~sSF~E~fYgLqr~ss~drl--------~se~~~~~~l~krQr~~s~~~lv~lPYv~~KL~~i~~k~~ 135 (357)
T KOG0826|consen 64 DLILQWHYLRTYNSSFIESFYGLQRISSRDRL--------TSEWPQGLGLNKRQRIVSFLFLVILPYVEAKLDEIYEKLR 135 (357)
T ss_pred HHHHHHHHHhcccccHHHhhhhhhhhhccccc--------cccccCCCCcchhHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 57999999999999999999999999877542 1457778899999999999999999999999999999965
Q ss_pred HHHHhhhhcCCCCCCCCCccCCCCCCCCCccCCCCCCchhhhhhHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHhCCC
Q 019860 81 EARLQASLWGPTDERFDDVDYFGGGGNPLFSRGGTDAETSVRTSLTKKIQKIIFACYPWLHASCEGLSFTYQLLYLLDAT 160 (334)
Q Consensus 81 ~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~k~~f~~~YP~i~~~~e~~~l~~~l~YL~g~t 160 (334)
+.....+ .+.-+++.+++|..+||+|++++|+++++.++.|+.+++
T Consensus 136 e~~~~~S----------------------------------~e~~~~~~~~aF~~~~p~i~~a~els~lvq~l~yIlkrs 181 (357)
T KOG0826|consen 136 ENNEFSS----------------------------------DETENKRPKRAFLRIYPFIKMALELSKLVQQLRYILKRS 181 (357)
T ss_pred hcccccC----------------------------------chhhhhhHHHHHhhhhHHHHHHHHHHHHHHHHHHHHHhc
Confidence 4321110 011257889999999999999999999999999999999
Q ss_pred CCCCHHHHHhcceEeecccccccccchhhh--hhhhhhHhhhcChhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 019860 161 GFYSVGLHALGIHVCRATGQELMDNSSRIS--KIRSRERERLLGPLWLKKLQGALLSCAYTMLDYAQTGLIAAVFFFKMM 238 (334)
Q Consensus 161 ~y~sP~l~l~gi~l~R~~~~d~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lp~~iF~lKfL 238 (334)
..||||+|++|+.++.++++|+.+.+.... ....+.....+..++...+++.++++...+.++++++|+++||+|||+
T Consensus 182 ~~hSPll~lsgv~L~~lt~~dl~a~~~gp~e~~~~~q~~r~t~~e~i~l~~qgaL~~~~~~v~~~~stgl~~~vFflqfl 261 (357)
T KOG0826|consen 182 SHHSPLLYLSGVQLGTLTPEDLQALEHGPAELSMMDQPARKTVSEKIFLLMQGALKKAVRGVAFSLSTGLSVGVFFLQFL 261 (357)
T ss_pred ccccHHHHHhhcccccccHHHHHHhhccccccchhhhhhhhhhhhhHHHHHHhHHHHHHhhHHHHHHhhHHHHHHHHHHH
Confidence 999999999999999999999977433221 112223333334456677889999999999999999999999999999
Q ss_pred HHHhcccccccCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCcCCCCCCCcccccCCcccccHHHHHHHhhcCCCCCCC
Q 019860 239 EWWYQSAEERMSAPTVYPPPPPPPPPKVAREGIPLPPDRTICPLCSQKRANPSVVTVSGFVFCYACIFKYVSQYKRCPVT 318 (334)
Q Consensus 239 EWWyss~~~r~~~~~~lp~pppP~~~~~~~~~~~~~~~~~~CpiC~~~~~~p~~~~~~G~vfC~~Ci~~~~~~~~~CPv~ 318 (334)
||||++|+++..+.+..|+|||||....+.++...|.|+..||+|++.++||+|+.++||||||+||++|+.++++||||
T Consensus 262 dWWyssd~~~~~k~~l~~p~PpPPh~~~~se~e~l~~~~~~CpvClk~r~Nptvl~vSGyVfCY~Ci~~Yv~~~~~CPVT 341 (357)
T KOG0826|consen 262 DWWYSSDNQRKIKSTLDPPIPPPPHKQYNSESELLPPDREVCPVCLKKRQNPTVLEVSGYVFCYPCIFSYVVNYGHCPVT 341 (357)
T ss_pred HHHhcchHHHhhccCCCCCCCcCChhhcccccccCCCccccChhHHhccCCCceEEecceEEeHHHHHHHHHhcCCCCcc
Confidence 99999999887777776677777655556778888889999999999999999999999999999999999999999999
Q ss_pred CCCCCccCeeeCccC
Q 019860 319 LMPATVEQIRRLFHD 333 (334)
Q Consensus 319 ~~~~~~~~l~ri~~~ 333 (334)
+.|+.++||+|+|.+
T Consensus 342 ~~p~~v~~l~rl~~~ 356 (357)
T KOG0826|consen 342 GYPASVDHLIRLFNK 356 (357)
T ss_pred CCcchHHHHHHHhcC
Confidence 999999999999975
No 2
>PF04757 Pex2_Pex12: Pex2 / Pex12 amino terminal region; InterPro: IPR006845 This region is the N-terminal part of a number of peroxisomal biogenesis proteins, including Pex2, Pex10 and Pex12, which contain two predicted transmembrane segments. The majority of these proteins have a C-terminal ring finger domain IPR001841 from INTERPRO.; GO: 0007031 peroxisome organization, 0005778 peroxisomal membrane
Probab=99.97 E-value=3.8e-31 Score=242.61 Aligned_cols=189 Identities=30% Similarity=0.490 Sum_probs=144.6
Q ss_pred eeeeecccccCCCcccccccCeeeeccccccccccccccCCCCccCCCCCcchHHHHHHHHHHHHhHHHHHHHHHHHhHH
Q 019860 2 LILETHSLRNTDASFSESLYGLRRRSVRIRAKKDDTRLKSSDGIHHSGLEKRQRVLSVVFMVVLPYFKSKLHSVYNKERE 81 (334)
Q Consensus 2 llvE~~~Lk~~~aSFaE~FYGLkR~~~~~~~~~~~~~~~~~~~~~~~~Lt~~q~~~sLl~lV~~PYlk~KLd~~ye~~~~ 81 (334)
+++|.|+++++|+||.|+||||+|++....+. .+..++++|++.+++++|++||+++|+++++++.
T Consensus 41 ~l~~~~tl~~~~~T~gE~~~~L~r~~~~~~~~------------~~~~ls~~~r~~~l~~~vl~PYl~~Kl~~~~~~~-- 106 (229)
T PF04757_consen 41 LLYESLTLLRGNQTFGEEFYGLKRVNSRSSSR------------ERRPLSRRQRLLSLLLLVLGPYLKEKLDSLLERL-- 106 (229)
T ss_pred HHHHHHHHhcCCCcHHHHhhCeEEeecccccc------------ccCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHh--
Confidence 67899999999999999999999998543211 1457999999999999999999999999999982
Q ss_pred HHHhhhhcCCCCCCCCCccCCCCCCCCCccCCCCCCchhhhhhHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHhCCCC
Q 019860 82 ARLQASLWGPTDERFDDVDYFGGGGNPLFSRGGTDAETSVRTSLTKKIQKIIFACYPWLHASCEGLSFTYQLLYLLDATG 161 (334)
Q Consensus 82 ~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~k~~f~~~YP~i~~~~e~~~l~~~l~YL~g~t~ 161 (334)
........ ....+...+.+++..+++.|.++||++++++++++++++++||+++++
T Consensus 107 --------~~~~~~~~----------------~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Fl~~g~~ 162 (229)
T PF04757_consen 107 --------SERSAESI----------------SSRSARARRARLKSKLKRRFVKLYPYLNALYELLNLLHLLLFLLGGTP 162 (229)
T ss_pred --------cccccccc----------------cchhhhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCC
Confidence 22111100 000111123367888999999999999999999999999999999999
Q ss_pred CCCHHHHHhcceEeecccccccccchhhhhhhhhhHhhhcChhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 019860 162 FYSVGLHALGIHVCRATGQELMDNSSRISKIRSRERERLLGPLWLKKLQGALLSCAYTMLDYAQTGLIAAVFFFKMMEWW 241 (334)
Q Consensus 162 y~sP~l~l~gi~l~R~~~~d~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lp~~iF~lKfLEWW 241 (334)
|+||+++++||+++|.++.|..+.. ...++... -.+..+...+...+..+++.++|+|||+|||
T Consensus 163 y~s~~~rllgi~~~~~~~~~~~~~~---------------~~~~l~~~-l~~~~~~~~~~~~~~~l~~~~~~~~~~~eww 226 (229)
T PF04757_consen 163 YYSPSKRLLGIRYVRLSPSDLQRNP---------------SYEFLGRQ-LLWQLLSEFLLFLLPLLLPRSLFFLKFLEWW 226 (229)
T ss_pred CCCHHHHHhCcEEEECCccchhhhc---------------cHHHHHHH-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 9999999999999999888775420 00111000 0111344566677789999999999999999
Q ss_pred hccc
Q 019860 242 YQSA 245 (334)
Q Consensus 242 yss~ 245 (334)
| +|
T Consensus 227 ~-~~ 229 (229)
T PF04757_consen 227 Y-SD 229 (229)
T ss_pred C-CC
Confidence 9 75
No 3
>KOG0317 consensus Predicted E3 ubiquitin ligase, integral peroxisomal membrane protein [Posttranslational modification, protein turnover, chaperones]
Probab=99.47 E-value=2.6e-13 Score=126.59 Aligned_cols=55 Identities=29% Similarity=0.698 Sum_probs=51.0
Q ss_pred CCCCCCcCCCCCCCcccccCCcccccHHHHHHHhhcCCCCCCCCCCCCccCeeeCc
Q 019860 276 DRTICPLCSQKRANPSVVTVSGFVFCYACIFKYVSQYKRCPVTLMPATVEQIRRLF 331 (334)
Q Consensus 276 ~~~~CpiC~~~~~~p~~~~~~G~vfC~~Ci~~~~~~~~~CPv~~~~~~~~~l~ri~ 331 (334)
...+|.||++.+.||++++ |||+|||.||.+|+.+...||+|+.+.+..+++-++
T Consensus 238 a~~kC~LCLe~~~~pSaTp-CGHiFCWsCI~~w~~ek~eCPlCR~~~~pskvi~Lr 292 (293)
T KOG0317|consen 238 ATRKCSLCLENRSNPSATP-CGHIFCWSCILEWCSEKAECPLCREKFQPSKVICLR 292 (293)
T ss_pred CCCceEEEecCCCCCCcCc-CcchHHHHHHHHHHccccCCCcccccCCCcceeeec
Confidence 3568999999999999987 999999999999999999999999999999988664
No 4
>smart00504 Ubox Modified RING finger domain. Modified RING finger domain, without the full complement of Zn2+-binding ligands. Probable involvement in E2-dependent ubiquitination.
Probab=99.40 E-value=2.5e-13 Score=100.09 Aligned_cols=53 Identities=25% Similarity=0.361 Sum_probs=49.2
Q ss_pred CCCCcCCCCCCCcccccCCcccccHHHHHHHhhcCCCCCCCCCCCCccCeeeCc
Q 019860 278 TICPLCSQKRANPSVVTVSGFVFCYACIFKYVSQYKRCPVTLMPATVEQIRRLF 331 (334)
Q Consensus 278 ~~CpiC~~~~~~p~~~~~~G~vfC~~Ci~~~~~~~~~CPv~~~~~~~~~l~ri~ 331 (334)
..||||++.++||++++ ||||||+.||.+|++++++||+|+.+++.++|++..
T Consensus 2 ~~Cpi~~~~~~~Pv~~~-~G~v~~~~~i~~~~~~~~~cP~~~~~~~~~~l~~~~ 54 (63)
T smart00504 2 FLCPISLEVMKDPVILP-SGQTYERRAIEKWLLSHGTDPVTGQPLTHEDLIPNL 54 (63)
T ss_pred cCCcCCCCcCCCCEECC-CCCEEeHHHHHHHHHHCCCCCCCcCCCChhhceeCH
Confidence 47999999999998876 999999999999999999999999999999998764
No 5
>PLN03208 E3 ubiquitin-protein ligase RMA2; Provisional
Probab=99.31 E-value=1.6e-12 Score=116.02 Aligned_cols=56 Identities=23% Similarity=0.608 Sum_probs=50.3
Q ss_pred CCCCCCcCCCCCCCcccccCCcccccHHHHHHHhhc----------------CCCCCCCCCCCCccCeeeCcc
Q 019860 276 DRTICPLCSQKRANPSVVTVSGFVFCYACIFKYVSQ----------------YKRCPVTLMPATVEQIRRLFH 332 (334)
Q Consensus 276 ~~~~CpiC~~~~~~p~~~~~~G~vfC~~Ci~~~~~~----------------~~~CPv~~~~~~~~~l~ri~~ 332 (334)
+...||||++..++|++++ |||+||+.||.+|+.. ..+||+|+.+++..+|++||.
T Consensus 17 ~~~~CpICld~~~dPVvT~-CGH~FC~~CI~~wl~~s~~s~~~~~~~~~~k~~~~CPvCR~~Is~~~LvPiyg 88 (193)
T PLN03208 17 GDFDCNICLDQVRDPVVTL-CGHLFCWPCIHKWTYASNNSRQRVDQYDHKREPPKCPVCKSDVSEATLVPIYG 88 (193)
T ss_pred CccCCccCCCcCCCcEEcC-CCchhHHHHHHHHHHhccccccccccccccCCCCcCCCCCCcCChhcEEEeec
Confidence 3578999999999998876 9999999999999852 358999999999999999996
No 6
>KOG0320 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=99.27 E-value=3.2e-12 Score=111.81 Aligned_cols=57 Identities=28% Similarity=0.592 Sum_probs=50.5
Q ss_pred CCCCCCcCCCCCCCcc-cccCCcccccHHHHHHHhhcCCCCCCCCCCCCccCeeeCcc
Q 019860 276 DRTICPLCSQKRANPS-VVTVSGFVFCYACIFKYVSQYKRCPVTLMPATVEQIRRLFH 332 (334)
Q Consensus 276 ~~~~CpiC~~~~~~p~-~~~~~G~vfC~~Ci~~~~~~~~~CPv~~~~~~~~~l~ri~~ 332 (334)
..+.||||+.....-. +-+.||||||..||.+.++...+||+|+++++.+++.|||.
T Consensus 130 ~~~~CPiCl~~~sek~~vsTkCGHvFC~~Cik~alk~~~~CP~C~kkIt~k~~~rI~L 187 (187)
T KOG0320|consen 130 GTYKCPICLDSVSEKVPVSTKCGHVFCSQCIKDALKNTNKCPTCRKKITHKQFHRIYL 187 (187)
T ss_pred cccCCCceecchhhccccccccchhHHHHHHHHHHHhCCCCCCcccccchhhheeccC
Confidence 3579999999987654 32459999999999999999999999999999999999994
No 7
>KOG0823 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=99.24 E-value=3.8e-12 Score=115.70 Aligned_cols=58 Identities=22% Similarity=0.657 Sum_probs=52.1
Q ss_pred CCCCCCCCcCCCCCCCcccccCCcccccHHHHHHHhhcC---CCCCCCCCCCCccCeeeCcc
Q 019860 274 PPDRTICPLCSQKRANPSVVTVSGFVFCYACIFKYVSQY---KRCPVTLMPATVEQIRRLFH 332 (334)
Q Consensus 274 ~~~~~~CpiC~~~~~~p~~~~~~G~vfC~~Ci~~~~~~~---~~CPv~~~~~~~~~l~ri~~ 332 (334)
+.....|-||++.-++|+|.. |||.|||+||++|+.-+ +.||||+-.++.+.|+.||.
T Consensus 44 ~~~~FdCNICLd~akdPVvTl-CGHLFCWpClyqWl~~~~~~~~cPVCK~~Vs~~~vvPlYG 104 (230)
T KOG0823|consen 44 DGGFFDCNICLDLAKDPVVTL-CGHLFCWPCLYQWLQTRPNSKECPVCKAEVSIDTVVPLYG 104 (230)
T ss_pred CCCceeeeeeccccCCCEEee-cccceehHHHHHHHhhcCCCeeCCccccccccceEEeeec
Confidence 334679999999999998875 99999999999999854 67899999999999999996
No 8
>PF13923 zf-C3HC4_2: Zinc finger, C3HC4 type (RING finger); PDB: 3HCU_A 2ECI_A 2JMD_A 3HCS_B 3HCT_A 3ZTG_A 2YUR_A 3L11_A.
Probab=99.20 E-value=8.4e-12 Score=83.90 Aligned_cols=39 Identities=44% Similarity=1.005 Sum_probs=34.0
Q ss_pred CCcCCCCCCCcccccCCcccccHHHHHHHhhcCCCCCCC
Q 019860 280 CPLCSQKRANPSVVTVSGFVFCYACIFKYVSQYKRCPVT 318 (334)
Q Consensus 280 CpiC~~~~~~p~~~~~~G~vfC~~Ci~~~~~~~~~CPv~ 318 (334)
||||.+.++||+++..|||+||+.||.+|++.+.+||+|
T Consensus 1 C~iC~~~~~~~~~~~~CGH~fC~~C~~~~~~~~~~CP~C 39 (39)
T PF13923_consen 1 CPICLDELRDPVVVTPCGHSFCKECIEKYLEKNPKCPVC 39 (39)
T ss_dssp ETTTTSB-SSEEEECTTSEEEEHHHHHHHHHCTSB-TTT
T ss_pred CCCCCCcccCcCEECCCCCchhHHHHHHHHHCcCCCcCC
Confidence 899999999996555699999999999999999999997
No 9
>PF04564 U-box: U-box domain; InterPro: IPR003613 Quality control of intracellular proteins is essential for cellular homeostasis. Molecular chaperones recognise and contribute to the refolding of misfolded or unfolded proteins, whereas the ubiquitin-proteasome system mediates the degradation of such abnormal proteins. Ubiquitin-protein ligases (E3s) determine the substrate specificity for ubiquitylation and have been classified into HECT and RING-finger families. More recently, however, U-box proteins, which contain a domain (the U box) of about 70 amino acids that is conserved from yeast to humans, have been identified as a new type of E3 []. Members of the U-box family of proteins constitute a class of ubiquitin-protein ligases (E3s) distinct from the HECT-type and RING finger-containing E3 families []. Using yeast two-hybrid technology, all mammalian U-box proteins have been reported to interact with molecular chaperones or co-chaperones, including Hsp90, Hsp70, DnaJc7, EKN1, CRN, and VCP. This suggests that the function of U box-type E3s is to mediate the degradation of unfolded or misfolded proteins in conjunction with molecular chaperones as receptors that recognise such abnormal proteins [, ]. Unlike the RING finger domain, IPR001841 from INTERPRO, that is stabilised by Zn2+ ions coordinated by the cysteines and a histidine, the U-box scaffold is probably stabilised by a system of salt-bridges and hydrogen bonds. The charged and polar residues that participate in this network of bonds are more strongly conserved in the U-box proteins than in classic RING fingers, which supports their role in maintaining the stability of the U box. Thus, the U box appears to have evolved from a RING finger domain by appropriation of a new set of residues required to stabilise its structure, concomitant with the loss of the original, metal-chelating residues [].; GO: 0004842 ubiquitin-protein ligase activity, 0016567 protein ubiquitination, 0000151 ubiquitin ligase complex; PDB: 1T1H_A 2C2L_D 2C2V_V 1WGM_A 2KR4_A 3L1Z_B 3L1X_A 2KRE_A 3M63_A 2QIZ_A ....
Probab=99.14 E-value=2.2e-11 Score=93.13 Aligned_cols=54 Identities=20% Similarity=0.389 Sum_probs=44.9
Q ss_pred CCCCCCcCCCCCCCcccccCCcccccHHHHHHHhhc-CCCCCCCCCCCCccCeeeC
Q 019860 276 DRTICPLCSQKRANPSVVTVSGFVFCYACIFKYVSQ-YKRCPVTLMPATVEQIRRL 330 (334)
Q Consensus 276 ~~~~CpiC~~~~~~p~~~~~~G~vfC~~Ci~~~~~~-~~~CPv~~~~~~~~~l~ri 330 (334)
+...||||++.++||++++ |||+||..||.+|+++ ++.||+|+.+++.++|+.-
T Consensus 3 ~~f~CpIt~~lM~dPVi~~-~G~tyer~~I~~~l~~~~~~~P~t~~~l~~~~l~pn 57 (73)
T PF04564_consen 3 DEFLCPITGELMRDPVILP-SGHTYERSAIERWLEQNGGTDPFTRQPLSESDLIPN 57 (73)
T ss_dssp GGGB-TTTSSB-SSEEEET-TSEEEEHHHHHHHHCTTSSB-TTT-SB-SGGGSEE-
T ss_pred cccCCcCcCcHhhCceeCC-cCCEEcHHHHHHHHHcCCCCCCCCCCcCCcccceEC
Confidence 5789999999999999987 9999999999999999 7999999999999988763
No 10
>PF15227 zf-C3HC4_4: zinc finger of C3HC4-type, RING; PDB: 2EGP_A 2ECV_A 2ECJ_A 2YSL_A 2YSJ_A.
Probab=98.98 E-value=2.9e-10 Score=77.86 Aligned_cols=38 Identities=26% Similarity=0.719 Sum_probs=31.1
Q ss_pred CCcCCCCCCCcccccCCcccccHHHHHHHhhcC----CCCCCC
Q 019860 280 CPLCSQKRANPSVVTVSGFVFCYACIFKYVSQY----KRCPVT 318 (334)
Q Consensus 280 CpiC~~~~~~p~~~~~~G~vfC~~Ci~~~~~~~----~~CPv~ 318 (334)
||||++.++||+.++ |||+||..||.+|.++. -.||+|
T Consensus 1 CpiC~~~~~~Pv~l~-CGH~FC~~Cl~~~~~~~~~~~~~CP~C 42 (42)
T PF15227_consen 1 CPICLDLFKDPVSLP-CGHSFCRSCLERLWKEPSGSGFSCPEC 42 (42)
T ss_dssp ETTTTSB-SSEEE-S-SSSEEEHHHHHHHHCCSSSST---SSS
T ss_pred CCccchhhCCccccC-CcCHHHHHHHHHHHHccCCcCCCCcCC
Confidence 899999999999997 99999999999999875 369987
No 11
>PF13639 zf-RING_2: Ring finger domain; PDB: 2KIZ_A 4EPO_C 1IYM_A 2EP4_A 2ECT_A 2JRJ_A 2ECN_A 2ECM_A 3NG2_A 2EA6_A ....
Probab=98.92 E-value=3.8e-10 Score=77.66 Aligned_cols=41 Identities=27% Similarity=0.673 Sum_probs=34.2
Q ss_pred CCCCcCCCCCCC---cccccCCcccccHHHHHHHhhcCCCCCCCC
Q 019860 278 TICPLCSQKRAN---PSVVTVSGFVFCYACIFKYVSQYKRCPVTL 319 (334)
Q Consensus 278 ~~CpiC~~~~~~---p~~~~~~G~vfC~~Ci~~~~~~~~~CPv~~ 319 (334)
+.||||++.+.+ ...++ |||+||+.||.+|++.+++||+|+
T Consensus 1 d~C~IC~~~~~~~~~~~~l~-C~H~fh~~Ci~~~~~~~~~CP~CR 44 (44)
T PF13639_consen 1 DECPICLEEFEDGEKVVKLP-CGHVFHRSCIKEWLKRNNSCPVCR 44 (44)
T ss_dssp -CETTTTCBHHTTSCEEEET-TSEEEEHHHHHHHHHHSSB-TTTH
T ss_pred CCCcCCChhhcCCCeEEEcc-CCCeeCHHHHHHHHHhCCcCCccC
Confidence 369999999853 34565 999999999999999999999995
No 12
>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=98.90 E-value=8.6e-10 Score=78.01 Aligned_cols=46 Identities=24% Similarity=0.708 Sum_probs=40.4
Q ss_pred CCCCCcCCCCCCCcccccCCccc-ccHHHHHHHhhcCCCCCCCCCCCC
Q 019860 277 RTICPLCSQKRANPSVVTVSGFV-FCYACIFKYVSQYKRCPVTLMPAT 323 (334)
Q Consensus 277 ~~~CpiC~~~~~~p~~~~~~G~v-fC~~Ci~~~~~~~~~CPv~~~~~~ 323 (334)
+..|+||.+...++.+.+ |||+ ||..|+.+|++..++||+|+.+++
T Consensus 2 ~~~C~iC~~~~~~~~~~p-CgH~~~C~~C~~~~~~~~~~CP~Cr~~i~ 48 (50)
T PF13920_consen 2 DEECPICFENPRDVVLLP-CGHLCFCEECAERLLKRKKKCPICRQPIE 48 (50)
T ss_dssp HSB-TTTSSSBSSEEEET-TCEEEEEHHHHHHHHHTTSBBTTTTBB-S
T ss_pred cCCCccCCccCCceEEeC-CCChHHHHHHhHHhcccCCCCCcCChhhc
Confidence 357999999999988876 9999 999999999999999999998864
No 13
>KOG2164 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=98.89 E-value=8.5e-10 Score=110.19 Aligned_cols=55 Identities=25% Similarity=0.634 Sum_probs=49.8
Q ss_pred CCCCCcCCCCCCCcccccCCcccccHHHHHHHhhc-----CCCCCCCCCCCCccCeeeCcc
Q 019860 277 RTICPLCSQKRANPSVVTVSGFVFCYACIFKYVSQ-----YKRCPVTLMPATVEQIRRLFH 332 (334)
Q Consensus 277 ~~~CpiC~~~~~~p~~~~~~G~vfC~~Ci~~~~~~-----~~~CPv~~~~~~~~~l~ri~~ 332 (334)
...||||+++..-|..+. |||+||.+||++|+.. ..+||+|+..++.+||..|+.
T Consensus 186 ~~~CPICL~~~~~p~~t~-CGHiFC~~CiLqy~~~s~~~~~~~CPiC~s~I~~kdl~pv~~ 245 (513)
T KOG2164|consen 186 DMQCPICLEPPSVPVRTN-CGHIFCGPCILQYWNYSAIKGPCSCPICRSTITLKDLLPVFI 245 (513)
T ss_pred CCcCCcccCCCCcccccc-cCceeeHHHHHHHHhhhcccCCccCCchhhhccccceeeeee
Confidence 678999999999998876 9999999999999964 589999999999999998875
No 14
>PHA02929 N1R/p28-like protein; Provisional
Probab=98.87 E-value=1.4e-09 Score=100.74 Aligned_cols=48 Identities=25% Similarity=0.600 Sum_probs=40.7
Q ss_pred CCCCCCcCCCCCCCc-------ccccCCcccccHHHHHHHhhcCCCCCCCCCCCC
Q 019860 276 DRTICPLCSQKRANP-------SVVTVSGFVFCYACIFKYVSQYKRCPVTLMPAT 323 (334)
Q Consensus 276 ~~~~CpiC~~~~~~p-------~~~~~~G~vfC~~Ci~~~~~~~~~CPv~~~~~~ 323 (334)
+...||||++.+.++ .+++.|||+||..||.+|++.+..||+|+.++.
T Consensus 173 ~~~eC~ICle~~~~~~~~~~~~~vl~~C~H~FC~~CI~~Wl~~~~tCPlCR~~~~ 227 (238)
T PHA02929 173 KDKECAICMEKVYDKEIKNMYFGILSNCNHVFCIECIDIWKKEKNTCPVCRTPFI 227 (238)
T ss_pred CCCCCccCCcccccCccccccceecCCCCCcccHHHHHHHHhcCCCCCCCCCEee
Confidence 356899999987764 245569999999999999999999999998754
No 15
>TIGR00599 rad18 DNA repair protein rad18. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=98.87 E-value=1.8e-09 Score=106.68 Aligned_cols=55 Identities=20% Similarity=0.479 Sum_probs=48.3
Q ss_pred CCCCCCCCcCCCCCCCcccccCCcccccHHHHHHHhhcCCCCCCCCCCCCccCeee
Q 019860 274 PPDRTICPLCSQKRANPSVVTVSGFVFCYACIFKYVSQYKRCPVTLMPATVEQIRR 329 (334)
Q Consensus 274 ~~~~~~CpiC~~~~~~p~~~~~~G~vfC~~Ci~~~~~~~~~CPv~~~~~~~~~l~r 329 (334)
..+...|+||.+.+.+|++++ |||+||..||..|+.....||+|+.++...+|++
T Consensus 23 Le~~l~C~IC~d~~~~Pvitp-CgH~FCs~CI~~~l~~~~~CP~Cr~~~~~~~Lr~ 77 (397)
T TIGR00599 23 LDTSLRCHICKDFFDVPVLTS-CSHTFCSLCIRRCLSNQPKCPLCRAEDQESKLRS 77 (397)
T ss_pred cccccCCCcCchhhhCccCCC-CCCchhHHHHHHHHhCCCCCCCCCCccccccCcc
Confidence 346789999999999998876 9999999999999999899999999887666654
No 16
>KOG0978 consensus E3 ubiquitin ligase involved in syntaxin degradation [Posttranslational modification, protein turnover, chaperones]
Probab=98.85 E-value=9.8e-10 Score=114.26 Aligned_cols=55 Identities=18% Similarity=0.522 Sum_probs=49.5
Q ss_pred CCCCCcCCCCCCCcccccCCcccccHHHHHHHhhc-CCCCCCCCCCCCccCeeeCcc
Q 019860 277 RTICPLCSQKRANPSVVTVSGFVFCYACIFKYVSQ-YKRCPVTLMPATVEQIRRLFH 332 (334)
Q Consensus 277 ~~~CpiC~~~~~~p~~~~~~G~vfC~~Ci~~~~~~-~~~CPv~~~~~~~~~l~ri~~ 332 (334)
...||+|...+.|.++.. ||||||+.|+...++. +.+||.|+.+.+..|+++||.
T Consensus 643 ~LkCs~Cn~R~Kd~vI~k-C~H~FC~~Cvq~r~etRqRKCP~Cn~aFganDv~~I~l 698 (698)
T KOG0978|consen 643 LLKCSVCNTRWKDAVITK-CGHVFCEECVQTRYETRQRKCPKCNAAFGANDVHRIHL 698 (698)
T ss_pred ceeCCCccCchhhHHHHh-cchHHHHHHHHHHHHHhcCCCCCCCCCCCcccccccCC
Confidence 568999998888887765 9999999999999985 589999999999999999984
No 17
>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=98.82 E-value=3.3e-09 Score=71.54 Aligned_cols=43 Identities=35% Similarity=0.846 Sum_probs=38.7
Q ss_pred CCCcCCCCCCCcccccCCcccccHHHHHHHhhc-CCCCCCCCCC
Q 019860 279 ICPLCSQKRANPSVVTVSGFVFCYACIFKYVSQ-YKRCPVTLMP 321 (334)
Q Consensus 279 ~CpiC~~~~~~p~~~~~~G~vfC~~Ci~~~~~~-~~~CPv~~~~ 321 (334)
.|+||++.+.++..+..|||.||..|+.+|++. ..+||+|+..
T Consensus 1 ~C~iC~~~~~~~~~~~~C~H~~c~~C~~~~~~~~~~~Cp~C~~~ 44 (45)
T cd00162 1 ECPICLEEFREPVVLLPCGHVFCRSCIDKWLKSGKNTCPLCRTP 44 (45)
T ss_pred CCCcCchhhhCceEecCCCChhcHHHHHHHHHhCcCCCCCCCCc
Confidence 499999999888777679999999999999998 7889999875
No 18
>PF00097 zf-C3HC4: Zinc finger, C3HC4 type (RING finger); InterPro: IPR018957 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. The C3HC4 type zinc-finger (RING finger) is a cysteine-rich domain of 40 to 60 residues that coordinates two zinc ions, and has the consensus sequence: C-X2-C-X(9-39)-C-X(1-3)-H-X(2-3)-C-X2-C-X(4-48)-C-X2-C where X is any amino acid []. Many proteins containing a RING finger play a key role in the ubiquitination pathway []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; PDB: 1CHC_A 2ECW_A 2Y43_B 1V87_A 2DJB_A 2H0D_B 3RPG_C 3KNV_A 2CKL_B 1JM7_A ....
Probab=98.76 E-value=5.1e-09 Score=70.70 Aligned_cols=39 Identities=28% Similarity=0.860 Sum_probs=34.5
Q ss_pred CCcCCCCCCCcccccCCcccccHHHHHHHhh--cCCCCCCC
Q 019860 280 CPLCSQKRANPSVVTVSGFVFCYACIFKYVS--QYKRCPVT 318 (334)
Q Consensus 280 CpiC~~~~~~p~~~~~~G~vfC~~Ci~~~~~--~~~~CPv~ 318 (334)
||||.+.+.+|..+..|||.||+.|+.+|++ +..+||+|
T Consensus 1 C~iC~~~~~~~~~~~~C~H~fC~~C~~~~~~~~~~~~CP~C 41 (41)
T PF00097_consen 1 CPICLEPFEDPVILLPCGHSFCRDCLRKWLENSGSVKCPLC 41 (41)
T ss_dssp ETTTSSBCSSEEEETTTSEEEEHHHHHHHHHHTSSSBTTTT
T ss_pred CCcCCccccCCCEEecCCCcchHHHHHHHHHhcCCccCCcC
Confidence 8999999999983345999999999999999 56789987
No 19
>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=98.71 E-value=1.1e-08 Score=66.61 Aligned_cols=38 Identities=34% Similarity=0.977 Sum_probs=34.7
Q ss_pred CCcCCCCCCCcccccCCcccccHHHHHHHhh-cCCCCCCC
Q 019860 280 CPLCSQKRANPSVVTVSGFVFCYACIFKYVS-QYKRCPVT 318 (334)
Q Consensus 280 CpiC~~~~~~p~~~~~~G~vfC~~Ci~~~~~-~~~~CPv~ 318 (334)
|+||++..+++.+++ |||+||+.|+.+|++ ...+||+|
T Consensus 1 C~iC~~~~~~~~~~~-C~H~~c~~C~~~~~~~~~~~CP~C 39 (39)
T smart00184 1 CPICLEELKDPVVLP-CGHTFCRSCIRKWLKSGNNTCPIC 39 (39)
T ss_pred CCcCccCCCCcEEec-CCChHHHHHHHHHHHhCcCCCCCC
Confidence 899999988888886 999999999999998 66789987
No 20
>KOG3039 consensus Uncharacterized conserved protein [Function unknown]
Probab=98.66 E-value=1.5e-08 Score=93.02 Aligned_cols=55 Identities=31% Similarity=0.432 Sum_probs=51.5
Q ss_pred CCCCCCcCCCCCCCc---ccccCCcccccHHHHHHHhhcCCCCCCCCCCCCccCeeeC
Q 019860 276 DRTICPLCSQKRANP---SVVTVSGFVFCYACIFKYVSQYKRCPVTLMPATVEQIRRL 330 (334)
Q Consensus 276 ~~~~CpiC~~~~~~p---~~~~~~G~vfC~~Ci~~~~~~~~~CPv~~~~~~~~~l~ri 330 (334)
.+++||+|+..++|. +++.+||||+|+.|+.+.++.++.||||+.|++..|||.+
T Consensus 220 ~ryiCpvtrd~LtNt~~ca~Lr~sg~Vv~~ecvEklir~D~v~pv~d~plkdrdiI~L 277 (303)
T KOG3039|consen 220 KRYICPVTRDTLTNTTPCAVLRPSGHVVTKECVEKLIRKDMVDPVTDKPLKDRDIIGL 277 (303)
T ss_pred cceecccchhhhcCccceEEeccCCcEeeHHHHHHhccccccccCCCCcCcccceEee
Confidence 578999999999997 4788899999999999999999999999999999999976
No 21
>COG5574 PEX10 RING-finger-containing E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=98.66 E-value=1e-08 Score=95.01 Aligned_cols=51 Identities=22% Similarity=0.583 Sum_probs=45.0
Q ss_pred CCCCCCcCCCCCCCcccccCCcccccHHHHHH-HhhcC-CCCCCCCCCCCccCe
Q 019860 276 DRTICPLCSQKRANPSVVTVSGFVFCYACIFK-YVSQY-KRCPVTLMPATVEQI 327 (334)
Q Consensus 276 ~~~~CpiC~~~~~~p~~~~~~G~vfC~~Ci~~-~~~~~-~~CPv~~~~~~~~~l 327 (334)
-.++|+||.+.+.+|..++ ||||||+.||.. |-.+. ..||+|+.....+++
T Consensus 214 ~d~kC~lC~e~~~~ps~t~-CgHlFC~~Cl~~~~t~~k~~~CplCRak~~pk~v 266 (271)
T COG5574 214 ADYKCFLCLEEPEVPSCTP-CGHLFCLSCLLISWTKKKYEFCPLCRAKVYPKKV 266 (271)
T ss_pred cccceeeeecccCCccccc-ccchhhHHHHHHHHHhhccccCchhhhhccchhh
Confidence 4679999999999998876 999999999999 88776 669999998877766
No 22
>PF13445 zf-RING_UBOX: RING-type zinc-finger; PDB: 2CT2_A.
Probab=98.59 E-value=2.4e-08 Score=68.69 Aligned_cols=35 Identities=37% Similarity=0.983 Sum_probs=22.5
Q ss_pred CCcCCCCCCC----cccccCCcccccHHHHHHHhhcC----CCCC
Q 019860 280 CPLCSQKRAN----PSVVTVSGFVFCYACIFKYVSQY----KRCP 316 (334)
Q Consensus 280 CpiC~~~~~~----p~~~~~~G~vfC~~Ci~~~~~~~----~~CP 316 (334)
||||.+ ..+ |.+++ ||||||..|+.++.+.. -+||
T Consensus 1 CpIc~e-~~~~~n~P~~L~-CGH~~c~~cl~~l~~~~~~~~~kCP 43 (43)
T PF13445_consen 1 CPICKE-FSTEENPPMVLP-CGHVFCKDCLQKLSKKSDRNRFKCP 43 (43)
T ss_dssp -TTT-----TTSS-EEE-S-SS-EEEHHHHHHHHHH-S-S-B--T
T ss_pred CCcccc-ccCCCCCCEEEe-CccHHHHHHHHHHHhcCCCCeeeCc
Confidence 999999 777 88997 99999999999999854 3676
No 23
>PF14835 zf-RING_6: zf-RING of BARD1-type protein; PDB: 1JM7_B.
Probab=98.56 E-value=1.8e-08 Score=74.44 Aligned_cols=50 Identities=26% Similarity=0.615 Sum_probs=27.6
Q ss_pred CCCCCcCCCCCCCcccccCCcccccHHHHHHHhhcCCCCCCCCCCCCccCee
Q 019860 277 RTICPLCSQKRANPSVVTVSGFVFCYACIFKYVSQYKRCPVTLMPATVEQIR 328 (334)
Q Consensus 277 ~~~CpiC~~~~~~p~~~~~~G~vfC~~Ci~~~~~~~~~CPv~~~~~~~~~l~ 328 (334)
-..|++|...+++|+.+..|.|+||..||-+.+.. .||||+.|+.++|++
T Consensus 7 lLrCs~C~~~l~~pv~l~~CeH~fCs~Ci~~~~~~--~CPvC~~Paw~qD~~ 56 (65)
T PF14835_consen 7 LLRCSICFDILKEPVCLGGCEHIFCSSCIRDCIGS--ECPVCHTPAWIQDIQ 56 (65)
T ss_dssp TTS-SSS-S--SS-B---SSS--B-TTTGGGGTTT--B-SSS--B-S-SS--
T ss_pred hcCCcHHHHHhcCCceeccCccHHHHHHhHHhcCC--CCCCcCChHHHHHHH
Confidence 35799999999999877779999999999887764 599999999988875
No 24
>PHA02926 zinc finger-like protein; Provisional
Probab=98.51 E-value=7.2e-08 Score=87.62 Aligned_cols=48 Identities=17% Similarity=0.475 Sum_probs=38.9
Q ss_pred CCCCCCcCCCCCCCc--------ccccCCcccccHHHHHHHhhcC------CCCCCCCCCCC
Q 019860 276 DRTICPLCSQKRANP--------SVVTVSGFVFCYACIFKYVSQY------KRCPVTLMPAT 323 (334)
Q Consensus 276 ~~~~CpiC~~~~~~p--------~~~~~~G~vfC~~Ci~~~~~~~------~~CPv~~~~~~ 323 (334)
....|+||++.+-++ .+++.|||+||..||.+|-+.. ..||+|+....
T Consensus 169 kE~eCgICmE~I~eK~~~~eRrFGIL~~CnHsFCl~CIr~Wr~~r~~~~~~rsCPiCR~~f~ 230 (242)
T PHA02926 169 KEKECGICYEVVYSKRLENDRYFGLLDSCNHIFCITCINIWHRTRRETGASDNCPICRTRFR 230 (242)
T ss_pred CCCCCccCccccccccccccccccccCCCCchHHHHHHHHHHHhccccCcCCcCCCCcceee
Confidence 467899999986432 4677799999999999999853 35999998765
No 25
>KOG2879 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=98.50 E-value=1.7e-06 Score=80.77 Aligned_cols=49 Identities=27% Similarity=0.581 Sum_probs=42.9
Q ss_pred CCCCCCCcCCCCCCCcccccCCcccccHHHHHHHhhcC--CCCCCCCCCCC
Q 019860 275 PDRTICPLCSQKRANPSVVTVSGFVFCYACIFKYVSQY--KRCPVTLMPAT 323 (334)
Q Consensus 275 ~~~~~CpiC~~~~~~p~~~~~~G~vfC~~Ci~~~~~~~--~~CPv~~~~~~ 323 (334)
.++.+||+|++..++|-++.+|||+|||-||..-+.-+ -+||.||.++.
T Consensus 237 t~~~~C~~Cg~~PtiP~~~~~C~HiyCY~Ci~ts~~~~asf~Cp~Cg~~~~ 287 (298)
T KOG2879|consen 237 TSDTECPVCGEPPTIPHVIGKCGHIYCYYCIATSRLWDASFTCPLCGENVE 287 (298)
T ss_pred cCCceeeccCCCCCCCeeeccccceeehhhhhhhhcchhhcccCccCCCCc
Confidence 36779999999999998777799999999999888755 79999997764
No 26
>PF11789 zf-Nse: Zinc-finger of the MIZ type in Nse subunit; PDB: 2YU4_A 3HTK_C.
Probab=98.45 E-value=8.9e-08 Score=69.84 Aligned_cols=43 Identities=30% Similarity=0.566 Sum_probs=32.2
Q ss_pred CCCCCcCCCCCCCcccccCCcccccHHHHHHHhhc--CCCCCCCC
Q 019860 277 RTICPLCSQKRANPSVVTVSGFVFCYACIFKYVSQ--YKRCPVTL 319 (334)
Q Consensus 277 ~~~CpiC~~~~~~p~~~~~~G~vfC~~Ci~~~~~~--~~~CPv~~ 319 (334)
..+|||++++++||+.-..|||+|....|.+|+.+ ..+||+.|
T Consensus 11 ~~~CPiT~~~~~~PV~s~~C~H~fek~aI~~~i~~~~~~~CPv~G 55 (57)
T PF11789_consen 11 SLKCPITLQPFEDPVKSKKCGHTFEKEAILQYIQRNGSKRCPVAG 55 (57)
T ss_dssp -SB-TTTSSB-SSEEEESSS--EEEHHHHHHHCTTTS-EE-SCCC
T ss_pred ccCCCCcCChhhCCcCcCCCCCeecHHHHHHHHHhcCCCCCCCCC
Confidence 57999999999999887779999999999999944 46899965
No 27
>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=98.42 E-value=2.1e-07 Score=89.01 Aligned_cols=54 Identities=30% Similarity=0.573 Sum_probs=42.7
Q ss_pred CCCCCCcCCCC-CCCcc---cccCCcccccHHHHHHHh-hcCCCCCCCCCCCCccCeee
Q 019860 276 DRTICPLCSQK-RANPS---VVTVSGFVFCYACIFKYV-SQYKRCPVTLMPATVEQIRR 329 (334)
Q Consensus 276 ~~~~CpiC~~~-~~~p~---~~~~~G~vfC~~Ci~~~~-~~~~~CPv~~~~~~~~~l~r 329 (334)
|...||+|... ..||. .+..|||.||..|+...+ ...+.||+|+.++..++++.
T Consensus 2 d~~~CP~Ck~~~y~np~~kl~i~~CGH~~C~sCv~~l~~~~~~~CP~C~~~lrk~~fr~ 60 (309)
T TIGR00570 2 DDQGCPRCKTTKYRNPSLKLMVNVCGHTLCESCVDLLFVRGSGSCPECDTPLRKNNFRV 60 (309)
T ss_pred CCCCCCcCCCCCccCcccccccCCCCCcccHHHHHHHhcCCCCCCCCCCCccchhhccc
Confidence 45689999995 45664 344699999999999966 44579999999998877653
No 28
>PF14634 zf-RING_5: zinc-RING finger domain
Probab=98.41 E-value=1.9e-07 Score=64.32 Aligned_cols=42 Identities=26% Similarity=0.641 Sum_probs=34.3
Q ss_pred CCCcCCCCC--CCcccccCCcccccHHHHHHHhhcCCCCCCCCC
Q 019860 279 ICPLCSQKR--ANPSVVTVSGFVFCYACIFKYVSQYKRCPVTLM 320 (334)
Q Consensus 279 ~CpiC~~~~--~~p~~~~~~G~vfC~~Ci~~~~~~~~~CPv~~~ 320 (334)
.|++|.+.. +.+.++..|||+||..|+.+.......||+|++
T Consensus 1 ~C~~C~~~~~~~~~~~l~~CgH~~C~~C~~~~~~~~~~CP~C~k 44 (44)
T PF14634_consen 1 HCNICFEKYSEERRPRLTSCGHIFCEKCLKKLKGKSVKCPICRK 44 (44)
T ss_pred CCcCcCccccCCCCeEEcccCCHHHHHHHHhhcCCCCCCcCCCC
Confidence 499999998 223344459999999999999977789999984
No 29
>COG5432 RAD18 RING-finger-containing E3 ubiquitin ligase [Signal transduction mechanisms]
Probab=98.41 E-value=6.6e-08 Score=90.63 Aligned_cols=48 Identities=25% Similarity=0.506 Sum_probs=43.2
Q ss_pred CCCCCCCcCCCCCCCcccccCCcccccHHHHHHHhhcCCCCCCCCCCCC
Q 019860 275 PDRTICPLCSQKRANPSVVTVSGFVFCYACIFKYVSQYKRCPVTLMPAT 323 (334)
Q Consensus 275 ~~~~~CpiC~~~~~~p~~~~~~G~vfC~~Ci~~~~~~~~~CPv~~~~~~ 323 (334)
+....|-||...+.-|+.++ |||.||+-||-.|+.++..||+|+.+--
T Consensus 23 Ds~lrC~IC~~~i~ip~~Tt-CgHtFCslCIR~hL~~qp~CP~Cr~~~~ 70 (391)
T COG5432 23 DSMLRCRICDCRISIPCETT-CGHTFCSLCIRRHLGTQPFCPVCREDPC 70 (391)
T ss_pred hhHHHhhhhhheeecceecc-cccchhHHHHHHHhcCCCCCccccccHH
Confidence 34678999999999998876 9999999999999999999999997643
No 30
>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=98.37 E-value=2.6e-07 Score=70.63 Aligned_cols=42 Identities=26% Similarity=0.698 Sum_probs=34.5
Q ss_pred CCCCcCCCCCCCc------------ccccCCcccccHHHHHHHhhcCCCCCCCC
Q 019860 278 TICPLCSQKRANP------------SVVTVSGFVFCYACIFKYVSQYKRCPVTL 319 (334)
Q Consensus 278 ~~CpiC~~~~~~p------------~~~~~~G~vfC~~Ci~~~~~~~~~CPv~~ 319 (334)
+.|+||++++.++ .++..|||.|...||.+|++.+..||+|+
T Consensus 20 d~C~IC~~~l~~~~~~~~~~~~~~~i~~~~C~H~FH~~Ci~~Wl~~~~~CP~CR 73 (73)
T PF12678_consen 20 DNCAICREPLEDPCPECQAPQDECPIVWGPCGHIFHFHCISQWLKQNNTCPLCR 73 (73)
T ss_dssp SBETTTTSBTTSTTCCHHHCTTTS-EEEETTSEEEEHHHHHHHHTTSSB-TTSS
T ss_pred CcccccChhhhChhhhhcCCccccceEecccCCCEEHHHHHHHHhcCCcCCCCC
Confidence 3599999999443 24445999999999999999999999996
No 31
>PF04641 Rtf2: Rtf2 RING-finger
Probab=98.16 E-value=1.7e-06 Score=81.54 Aligned_cols=58 Identities=28% Similarity=0.394 Sum_probs=48.9
Q ss_pred CCCCCCCcCCCCCCCc---ccccCCcccccHHHHHHHhhcCCCCCCCCCCCCccCeeeCccC
Q 019860 275 PDRTICPLCSQKRANP---SVVTVSGFVFCYACIFKYVSQYKRCPVTLMPATVEQIRRLFHD 333 (334)
Q Consensus 275 ~~~~~CpiC~~~~~~p---~~~~~~G~vfC~~Ci~~~~~~~~~CPv~~~~~~~~~l~ri~~~ 333 (334)
.....|||++..+.+- +++.+||||||+.|+.+.- ..+.||+|+.|.+.+|||.|-.+
T Consensus 111 ~~~~~CPvt~~~~~~~~~fv~l~~cG~V~s~~alke~k-~~~~Cp~c~~~f~~~DiI~Lnp~ 171 (260)
T PF04641_consen 111 EGRFICPVTGKEFNGKHKFVYLRPCGCVFSEKALKELK-KSKKCPVCGKPFTEEDIIPLNPP 171 (260)
T ss_pred CceeECCCCCcccCCceeEEEEcCCCCEeeHHHHHhhc-ccccccccCCccccCCEEEecCC
Confidence 3478999999999553 4666799999999999883 56789999999999999998653
No 32
>KOG4172 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=98.12 E-value=4.1e-07 Score=64.89 Aligned_cols=53 Identities=21% Similarity=0.637 Sum_probs=44.0
Q ss_pred CCCCCcCCCCCCCcccccCCccc-ccHHHHHHHhh-cCCCCCCCCCCCCccCeeeCcc
Q 019860 277 RTICPLCSQKRANPSVVTVSGFV-FCYACIFKYVS-QYKRCPVTLMPATVEQIRRLFH 332 (334)
Q Consensus 277 ~~~CpiC~~~~~~p~~~~~~G~v-fC~~Ci~~~~~-~~~~CPv~~~~~~~~~l~ri~~ 332 (334)
...|.||.+...|.++-. |||+ +||.|..+-.+ .++.||+|+.| ++|++|-|.
T Consensus 7 ~dECTICye~pvdsVlYt-CGHMCmCy~Cg~rl~~~~~g~CPiCRap--i~dvIkTY~ 61 (62)
T KOG4172|consen 7 SDECTICYEHPVDSVLYT-CGHMCMCYACGLRLKKALHGCCPICRAP--IKDVIKTYR 61 (62)
T ss_pred ccceeeeccCcchHHHHH-cchHHhHHHHHHHHHHccCCcCcchhhH--HHHHHHhhc
Confidence 478999999998887765 9997 79999999888 68999999966 456776663
No 33
>KOG0287 consensus Postreplication repair protein RAD18 [Replication, recombination and repair]
Probab=98.10 E-value=5.1e-07 Score=86.36 Aligned_cols=54 Identities=26% Similarity=0.544 Sum_probs=49.6
Q ss_pred CCCCCCCcCCCCCCCcccccCCcccccHHHHHHHhhcCCCCCCCCCCCCccCeee
Q 019860 275 PDRTICPLCSQKRANPSVVTVSGFVFCYACIFKYVSQYKRCPVTLMPATVEQIRR 329 (334)
Q Consensus 275 ~~~~~CpiC~~~~~~p~~~~~~G~vfC~~Ci~~~~~~~~~CPv~~~~~~~~~l~r 329 (334)
++-..|-||.+-+.-|.+++ |||.||--||-.|+..+..||.|..+.+..+|+.
T Consensus 21 D~lLRC~IC~eyf~ip~itp-CsHtfCSlCIR~~L~~~p~CP~C~~~~~Es~Lr~ 74 (442)
T KOG0287|consen 21 DDLLRCGICFEYFNIPMITP-CSHTFCSLCIRKFLSYKPQCPTCCVTVTESDLRN 74 (442)
T ss_pred HHHHHHhHHHHHhcCceecc-ccchHHHHHHHHHhccCCCCCceecccchhhhhh
Confidence 45678999999999998887 9999999999999999999999999998888774
No 34
>KOG0824 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=98.04 E-value=2e-06 Score=81.22 Aligned_cols=47 Identities=26% Similarity=0.527 Sum_probs=41.6
Q ss_pred CCCCCcCCCCCCCcccccCCcccccHHHHHHHhhcCCC-CCCCCCCCCc
Q 019860 277 RTICPLCSQKRANPSVVTVSGFVFCYACIFKYVSQYKR-CPVTLMPATV 324 (334)
Q Consensus 277 ~~~CpiC~~~~~~p~~~~~~G~vfC~~Ci~~~~~~~~~-CPv~~~~~~~ 324 (334)
..+|+||.....-|+.+. |+|+|||-||..-....++ |+||+.|++.
T Consensus 7 ~~eC~IC~nt~n~Pv~l~-C~HkFCyiCiKGsy~ndk~~CavCR~pids 54 (324)
T KOG0824|consen 7 KKECLICYNTGNCPVNLY-CFHKFCYICIKGSYKNDKKTCAVCRFPIDS 54 (324)
T ss_pred CCcceeeeccCCcCcccc-ccchhhhhhhcchhhcCCCCCceecCCCCc
Confidence 458999999999998887 9999999999988887765 9999998763
No 35
>COG5243 HRD1 HRD ubiquitin ligase complex, ER membrane component [Posttranslational modification, protein turnover, chaperones]
Probab=98.03 E-value=3e-06 Score=82.10 Aligned_cols=48 Identities=17% Similarity=0.580 Sum_probs=41.2
Q ss_pred CCCCCCCcCCCCCCCc-------------ccccCCcccccHHHHHHHhhcCCCCCCCCCCCC
Q 019860 275 PDRTICPLCSQKRANP-------------SVVTVSGFVFCYACIFKYVSQYKRCPVTLMPAT 323 (334)
Q Consensus 275 ~~~~~CpiC~~~~~~p-------------~~~~~~G~vfC~~Ci~~~~~~~~~CPv~~~~~~ 323 (334)
.+.+.|.||++.+-.| .-++ |||.+-..|+..|+++.+.||+|+.|+-
T Consensus 285 n~D~~C~ICmde~~h~~~~~~~~~~~~~pKrLp-CGHilHl~CLknW~ERqQTCPICr~p~i 345 (491)
T COG5243 285 NSDRTCTICMDEMFHPDHEPLPRGLDMTPKRLP-CGHILHLHCLKNWLERQQTCPICRRPVI 345 (491)
T ss_pred CCCCeEEEecccccCCCCccCcccccCCccccc-ccceeeHHHHHHHHHhccCCCcccCccc
Confidence 4678999999984332 4676 9999999999999999999999999953
No 36
>KOG0802 consensus E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=97.99 E-value=2.4e-06 Score=88.50 Aligned_cols=46 Identities=17% Similarity=0.548 Sum_probs=42.3
Q ss_pred CCCCCCcCCCCCCC-----cccccCCcccccHHHHHHHhhcCCCCCCCCCCC
Q 019860 276 DRTICPLCSQKRAN-----PSVVTVSGFVFCYACIFKYVSQYKRCPVTLMPA 322 (334)
Q Consensus 276 ~~~~CpiC~~~~~~-----p~~~~~~G~vfC~~Ci~~~~~~~~~CPv~~~~~ 322 (334)
....|+||.+.+.+ |..++ |||+||-.|+.+|+++...||+|+...
T Consensus 290 ~~~~C~IC~e~l~~~~~~~~~rL~-C~Hifh~~CL~~W~er~qtCP~CR~~~ 340 (543)
T KOG0802|consen 290 SDELCIICLEELHSGHNITPKRLP-CGHIFHDSCLRSWFERQQTCPTCRTVL 340 (543)
T ss_pred cCCeeeeechhhccccccccceee-cccchHHHHHHHHHHHhCcCCcchhhh
Confidence 46799999999999 78887 999999999999999999999999844
No 37
>KOG2660 consensus Locus-specific chromosome binding proteins [Function unknown]
Probab=97.94 E-value=2.7e-06 Score=81.38 Aligned_cols=48 Identities=27% Similarity=0.583 Sum_probs=43.1
Q ss_pred CCCCCCcCCCCCCCcccccCCcccccHHHHHHHhhcCCCCCCCCCCCC
Q 019860 276 DRTICPLCSQKRANPSVVTVSGFVFCYACIFKYVSQYKRCPVTLMPAT 323 (334)
Q Consensus 276 ~~~~CpiC~~~~~~p~~~~~~G~vfC~~Ci~~~~~~~~~CPv~~~~~~ 323 (334)
...+|++|.+-+.|+|.+..|=|.||..||++|++..+.||+|+.-+.
T Consensus 14 ~~itC~LC~GYliDATTI~eCLHTFCkSCivk~l~~~~~CP~C~i~ih 61 (331)
T KOG2660|consen 14 PHITCRLCGGYLIDATTITECLHTFCKSCIVKYLEESKYCPTCDIVIH 61 (331)
T ss_pred cceehhhccceeecchhHHHHHHHHHHHHHHHHHHHhccCCccceecc
Confidence 367899999999999766669999999999999999999999996654
No 38
>KOG2177 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=97.93 E-value=3.6e-06 Score=77.47 Aligned_cols=44 Identities=27% Similarity=0.657 Sum_probs=39.8
Q ss_pred CCCCCCCcCCCCCCCcccccCCcccccHHHHHHHhhcCCCCCCCC
Q 019860 275 PDRTICPLCSQKRANPSVVTVSGFVFCYACIFKYVSQYKRCPVTL 319 (334)
Q Consensus 275 ~~~~~CpiC~~~~~~p~~~~~~G~vfC~~Ci~~~~~~~~~CPv~~ 319 (334)
.+...||||.+..++|.+++ |||.||..|+..+....-.||+|+
T Consensus 11 ~~~~~C~iC~~~~~~p~~l~-C~H~~c~~C~~~~~~~~~~Cp~cr 54 (386)
T KOG2177|consen 11 QEELTCPICLEYFREPVLLP-CGHNFCRACLTRSWEGPLSCPVCR 54 (386)
T ss_pred cccccChhhHHHhhcCcccc-ccchHhHHHHHHhcCCCcCCcccC
Confidence 35679999999999998876 999999999999999667999999
No 39
>KOG0297 consensus TNF receptor-associated factor [Signal transduction mechanisms]
Probab=97.85 E-value=7.6e-06 Score=81.54 Aligned_cols=54 Identities=26% Similarity=0.617 Sum_probs=47.2
Q ss_pred CCCCCCCcCCCCCCCcccccCCcccccHHHHHHHhhcCCCCCCCCCCCCccCee
Q 019860 275 PDRTICPLCSQKRANPSVVTVSGFVFCYACIFKYVSQYKRCPVTLMPATVEQIR 328 (334)
Q Consensus 275 ~~~~~CpiC~~~~~~p~~~~~~G~vfC~~Ci~~~~~~~~~CPv~~~~~~~~~l~ 328 (334)
+....||+|+.++.+|.-.++|||.||..|+..|+..+..||+|...++.++.+
T Consensus 19 ~~~l~C~~C~~vl~~p~~~~~cgh~fC~~C~~~~~~~~~~cp~~~~~~~~~~~~ 72 (391)
T KOG0297|consen 19 DENLLCPICMSVLRDPVQTTTCGHRFCAGCLLESLSNHQKCPVCRQELTQAEEL 72 (391)
T ss_pred cccccCccccccccCCCCCCCCCCcccccccchhhccCcCCcccccccchhhcc
Confidence 457899999999999987445999999999999999999999998887766554
No 40
>PF12861 zf-Apc11: Anaphase-promoting complex subunit 11 RING-H2 finger
Probab=97.68 E-value=3.7e-05 Score=60.28 Aligned_cols=49 Identities=27% Similarity=0.530 Sum_probs=38.5
Q ss_pred CCCCCcCCCCCCC-cccccCCcccccHHHHHHHhhc---CCCCCCCCCCCCcc
Q 019860 277 RTICPLCSQKRAN-PSVVTVSGFVFCYACIFKYVSQ---YKRCPVTLMPATVE 325 (334)
Q Consensus 277 ~~~CpiC~~~~~~-p~~~~~~G~vfC~~Ci~~~~~~---~~~CPv~~~~~~~~ 325 (334)
.+.||.|..+-.+ |.|.-.|||.|-.-||.+|++. ++.||+|+.+-..+
T Consensus 32 dg~Cp~Ck~Pgd~Cplv~g~C~H~FH~hCI~kWl~~~~~~~~CPmCR~~w~~k 84 (85)
T PF12861_consen 32 DGCCPDCKFPGDDCPLVWGKCSHNFHMHCILKWLSTQSSKGQCPMCRQPWKFK 84 (85)
T ss_pred ccCCCCccCCCCCCceeeccCccHHHHHHHHHHHccccCCCCCCCcCCeeeeC
Confidence 3567777777555 6566679999999999999986 48999999876543
No 41
>KOG0311 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=97.56 E-value=7.5e-06 Score=78.93 Aligned_cols=48 Identities=23% Similarity=0.542 Sum_probs=42.0
Q ss_pred CCCCCCcCCCCCCCcccccCCcccccHHHHHHHhhc-CCCCCCCCCCCC
Q 019860 276 DRTICPLCSQKRANPSVVTVSGFVFCYACIFKYVSQ-YKRCPVTLMPAT 323 (334)
Q Consensus 276 ~~~~CpiC~~~~~~p~~~~~~G~vfC~~Ci~~~~~~-~~~CPv~~~~~~ 323 (334)
...+||||+..+++....+.|+|-||..||..-++. ++.||.|++.+.
T Consensus 42 ~~v~c~icl~llk~tmttkeClhrfc~~ci~~a~r~gn~ecptcRk~l~ 90 (381)
T KOG0311|consen 42 IQVICPICLSLLKKTMTTKECLHRFCFDCIWKALRSGNNECPTCRKKLV 90 (381)
T ss_pred hhhccHHHHHHHHhhcccHHHHHHHHHHHHHHHHHhcCCCCchHHhhcc
Confidence 367999999999998766679999999999999976 588999998764
No 42
>KOG1002 consensus Nucleotide excision repair protein RAD16 [Replication, recombination and repair]
Probab=97.54 E-value=3.5e-05 Score=77.66 Aligned_cols=48 Identities=25% Similarity=0.554 Sum_probs=42.6
Q ss_pred CCCCCcCCCCCCCcccccCCcccccHHHHHHHhhc-----CCCCCCCCCCCCcc
Q 019860 277 RTICPLCSQKRANPSVVTVSGFVFCYACIFKYVSQ-----YKRCPVTLMPATVE 325 (334)
Q Consensus 277 ~~~CpiC~~~~~~p~~~~~~G~vfC~~Ci~~~~~~-----~~~CPv~~~~~~~~ 325 (334)
...|-+|.++-+++.+.+ |.|+||.-||.+|+.. +-.||+|..+++++
T Consensus 536 ~~~C~lc~d~aed~i~s~-ChH~FCrlCi~eyv~~f~~~~nvtCP~C~i~LsiD 588 (791)
T KOG1002|consen 536 EVECGLCHDPAEDYIESS-CHHKFCRLCIKEYVESFMENNNVTCPVCHIGLSID 588 (791)
T ss_pred ceeecccCChhhhhHhhh-hhHHHHHHHHHHHHHhhhcccCCCCcccccccccc
Confidence 458999999999998876 9999999999999974 46899999998765
No 43
>COG5222 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=97.53 E-value=5e-05 Score=71.87 Aligned_cols=44 Identities=30% Similarity=0.548 Sum_probs=39.4
Q ss_pred CCCCCcCCCCCCCcccccCCcccccHHHHHHHhhc-CCCCCCCCC
Q 019860 277 RTICPLCSQKRANPSVVTVSGFVFCYACIFKYVSQ-YKRCPVTLM 320 (334)
Q Consensus 277 ~~~CpiC~~~~~~p~~~~~~G~vfC~~Ci~~~~~~-~~~CPv~~~ 320 (334)
...||+|+..+.||+-.+.|||.||..||-..|.+ +.+||+|..
T Consensus 274 ~LkCplc~~Llrnp~kT~cC~~~fc~eci~~al~dsDf~CpnC~r 318 (427)
T COG5222 274 SLKCPLCHCLLRNPMKTPCCGHTFCDECIGTALLDSDFKCPNCSR 318 (427)
T ss_pred cccCcchhhhhhCcccCccccchHHHHHHhhhhhhccccCCCccc
Confidence 37899999999999888889999999999988766 489999985
No 44
>COG5540 RING-finger-containing ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=97.50 E-value=4.4e-05 Score=72.41 Aligned_cols=45 Identities=24% Similarity=0.569 Sum_probs=37.8
Q ss_pred CCCCCcCCCC-CCCc--ccccCCcccccHHHHHHHhhcC-CCCCCCCCCC
Q 019860 277 RTICPLCSQK-RANP--SVVTVSGFVFCYACIFKYVSQY-KRCPVTLMPA 322 (334)
Q Consensus 277 ~~~CpiC~~~-~~~p--~~~~~~G~vfC~~Ci~~~~~~~-~~CPv~~~~~ 322 (334)
...|.||+.. +++. .|++ |-|+|--.|+.+|+..+ .+||||+.++
T Consensus 323 GveCaICms~fiK~d~~~vlP-C~H~FH~~Cv~kW~~~y~~~CPvCrt~i 371 (374)
T COG5540 323 GVECAICMSNFIKNDRLRVLP-CDHRFHVGCVDKWLLGYSNKCPVCRTAI 371 (374)
T ss_pred CceEEEEhhhhcccceEEEec-cCceechhHHHHHHhhhcccCCccCCCC
Confidence 4589999996 4554 4666 99999999999999975 8999999875
No 45
>KOG4628 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=97.46 E-value=0.00011 Score=71.52 Aligned_cols=44 Identities=20% Similarity=0.520 Sum_probs=37.6
Q ss_pred CCCCcCCCCCCCc---ccccCCcccccHHHHHHHhhcCCC-CCCCCCCC
Q 019860 278 TICPLCSQKRANP---SVVTVSGFVFCYACIFKYVSQYKR-CPVTLMPA 322 (334)
Q Consensus 278 ~~CpiC~~~~~~p---~~~~~~G~vfC~~Ci~~~~~~~~~-CPv~~~~~ 322 (334)
..|.||++.-+.- .+|+ |+|.|--.||..|+.++++ ||||+...
T Consensus 230 ~~CaIClEdY~~GdklRiLP-C~H~FH~~CIDpWL~~~r~~CPvCK~di 277 (348)
T KOG4628|consen 230 DTCAICLEDYEKGDKLRILP-CSHKFHVNCIDPWLTQTRTFCPVCKRDI 277 (348)
T ss_pred ceEEEeecccccCCeeeEec-CCCchhhccchhhHhhcCccCCCCCCcC
Confidence 4999999986554 4786 9999999999999999966 99999753
No 46
>KOG1813 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=97.46 E-value=4.4e-05 Score=72.14 Aligned_cols=44 Identities=25% Similarity=0.495 Sum_probs=41.2
Q ss_pred CCCCcCCCCCCCcccccCCcccccHHHHHHHhhcCCCCCCCCCCC
Q 019860 278 TICPLCSQKRANPSVVTVSGFVFCYACIFKYVSQYKRCPVTLMPA 322 (334)
Q Consensus 278 ~~CpiC~~~~~~p~~~~~~G~vfC~~Ci~~~~~~~~~CPv~~~~~ 322 (334)
..|-||++...+|+|.. |||.||-.|...-++...+|+||++.+
T Consensus 242 f~c~icr~~f~~pVvt~-c~h~fc~~ca~~~~qk~~~c~vC~~~t 285 (313)
T KOG1813|consen 242 FKCFICRKYFYRPVVTK-CGHYFCEVCALKPYQKGEKCYVCSQQT 285 (313)
T ss_pred ccccccccccccchhhc-CCceeehhhhccccccCCcceeccccc
Confidence 57999999999999986 999999999999999999999999765
No 47
>COG5152 Uncharacterized conserved protein, contains RING and CCCH-type Zn-fingers [General function prediction only]
Probab=97.21 E-value=0.00017 Score=64.73 Aligned_cols=45 Identities=22% Similarity=0.546 Sum_probs=41.2
Q ss_pred CCCCCcCCCCCCCcccccCCcccccHHHHHHHhhcCCCCCCCCCCC
Q 019860 277 RTICPLCSQKRANPSVVTVSGFVFCYACIFKYVSQYKRCPVTLMPA 322 (334)
Q Consensus 277 ~~~CpiC~~~~~~p~~~~~~G~vfC~~Ci~~~~~~~~~CPv~~~~~ 322 (334)
...|-||.+..+.|+|.. |||.||-.|...-.+.-..|=||++..
T Consensus 196 PF~C~iCKkdy~spvvt~-CGH~FC~~Cai~~y~kg~~C~~Cgk~t 240 (259)
T COG5152 196 PFLCGICKKDYESPVVTE-CGHSFCSLCAIRKYQKGDECGVCGKAT 240 (259)
T ss_pred ceeehhchhhccchhhhh-cchhHHHHHHHHHhccCCcceecchhh
Confidence 468999999999999976 999999999999999989999999764
No 48
>KOG1734 consensus Predicted RING-containing E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=97.03 E-value=0.00089 Score=62.76 Aligned_cols=51 Identities=18% Similarity=0.447 Sum_probs=40.6
Q ss_pred CCCCCCcCCCCCCCc----------ccccCCcccccHHHHHHHhh--cCCCCCCCCCCCCccCe
Q 019860 276 DRTICPLCSQKRANP----------SVVTVSGFVFCYACIFKYVS--QYKRCPVTLMPATVEQI 327 (334)
Q Consensus 276 ~~~~CpiC~~~~~~p----------~~~~~~G~vfC~~Ci~~~~~--~~~~CPv~~~~~~~~~l 327 (334)
+.+.|.+|++.+... --++ |+|||---||-.|+- +.+.||-|+.+++.+.+
T Consensus 223 ~d~vCaVCg~~~~~s~~eegvienty~Ls-CnHvFHEfCIrGWcivGKkqtCPYCKekVdl~rm 285 (328)
T KOG1734|consen 223 SDSVCAVCGQQIDVSVDEEGVIENTYKLS-CNHVFHEFCIRGWCIVGKKQTCPYCKEKVDLKRM 285 (328)
T ss_pred CcchhHhhcchheeecchhhhhhhheeee-cccchHHHhhhhheeecCCCCCchHHHHhhHhhh
Confidence 467899999986433 2465 999999999999985 56899999988876543
No 49
>KOG1645 consensus RING-finger-containing E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=96.97 E-value=0.00022 Score=70.09 Aligned_cols=58 Identities=29% Similarity=0.521 Sum_probs=48.6
Q ss_pred CCCCCCCcCCCCCCCcc----cccCCcccccHHHHHHHhhcC--CCCCCCCCCCCccCeeeCcc
Q 019860 275 PDRTICPLCSQKRANPS----VVTVSGFVFCYACIFKYVSQY--KRCPVTLMPATVEQIRRLFH 332 (334)
Q Consensus 275 ~~~~~CpiC~~~~~~p~----~~~~~G~vfC~~Ci~~~~~~~--~~CPv~~~~~~~~~l~ri~~ 332 (334)
++..+||||+..++-|. +...|||.|=-.||.+|+-+. ++||.|.-+.+..+|+.+|.
T Consensus 2 d~g~tcpiclds~~~~g~hr~vsl~cghlFgs~cie~wl~k~~~~~cp~c~~katkr~i~~e~a 65 (463)
T KOG1645|consen 2 DCGTTCPICLDSYTTAGNHRIVSLQCGHLFGSQCIEKWLGKKTKMQCPLCSGKATKRQIRPEYA 65 (463)
T ss_pred CccccCceeeeeeeecCceEEeeecccccccHHHHHHHHhhhhhhhCcccCChhHHHHHHHHHH
Confidence 46789999999988872 444599999999999999643 78999999999888887763
No 50
>COG5175 MOT2 Transcriptional repressor [Transcription]
Probab=96.93 E-value=0.00054 Score=66.01 Aligned_cols=52 Identities=23% Similarity=0.488 Sum_probs=39.3
Q ss_pred CCCCCCcCCCCCCCc----ccccCCcccccHHHHHHHhhc-CCCCCCCCCCCCccCee
Q 019860 276 DRTICPLCSQKRANP----SVVTVSGFVFCYACIFKYVSQ-YKRCPVTLMPATVEQIR 328 (334)
Q Consensus 276 ~~~~CpiC~~~~~~p----~~~~~~G~vfC~~Ci~~~~~~-~~~CPv~~~~~~~~~l~ 328 (334)
+.+.||+|.++|... --|+ |||-.|.=|-...-+. +|+||.|+..-+.++++
T Consensus 13 eed~cplcie~mditdknf~pc~-cgy~ic~fc~~~irq~lngrcpacrr~y~denv~ 69 (480)
T COG5175 13 EEDYCPLCIEPMDITDKNFFPCP-CGYQICQFCYNNIRQNLNGRCPACRRKYDDENVR 69 (480)
T ss_pred ccccCcccccccccccCCcccCC-cccHHHHHHHHHHHhhccCCChHhhhhcccccee
Confidence 355699999986432 4676 9999999997644333 59999999888877765
No 51
>KOG4265 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=96.86 E-value=0.00055 Score=66.45 Aligned_cols=52 Identities=17% Similarity=0.512 Sum_probs=44.1
Q ss_pred CCCCCcCCCCCCCcccccCCccc-ccHHHHHHHhhcCCCCCCCCCCCCccCeeeCc
Q 019860 277 RTICPLCSQKRANPSVVTVSGFV-FCYACIFKYVSQYKRCPVTLMPATVEQIRRLF 331 (334)
Q Consensus 277 ~~~CpiC~~~~~~p~~~~~~G~v-fC~~Ci~~~~~~~~~CPv~~~~~~~~~l~ri~ 331 (334)
...|-||+...+|-+|++ |=|. .|-.|+....-++++||+|+.++. .+.+|+
T Consensus 290 gkeCVIClse~rdt~vLP-CRHLCLCs~Ca~~Lr~q~n~CPICRqpi~--~ll~i~ 342 (349)
T KOG4265|consen 290 GKECVICLSESRDTVVLP-CRHLCLCSGCAKSLRYQTNNCPICRQPIE--ELLEIY 342 (349)
T ss_pred CCeeEEEecCCcceEEec-chhhehhHhHHHHHHHhhcCCCccccchH--hhheec
Confidence 678999999999999998 9886 699999988888999999998753 344444
No 52
>KOG4692 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=96.82 E-value=0.00075 Score=65.36 Aligned_cols=50 Identities=26% Similarity=0.602 Sum_probs=42.5
Q ss_pred CC-CCCCCCCcCCCCCCCcccccCCcccccHHHHHHHhhcCCCCCCCCCCCC
Q 019860 273 LP-PDRTICPLCSQKRANPSVVTVSGFVFCYACIFKYVSQYKRCPVTLMPAT 323 (334)
Q Consensus 273 ~~-~~~~~CpiC~~~~~~p~~~~~~G~vfC~~Ci~~~~~~~~~CPv~~~~~~ 323 (334)
+| .+.+.||||--...|++..+ |||--||.||.+++-+.++|=-|+..+.
T Consensus 417 lp~sEd~lCpICyA~pi~Avf~P-C~H~SC~~CI~qHlmN~k~CFfCktTv~ 467 (489)
T KOG4692|consen 417 LPDSEDNLCPICYAGPINAVFAP-CSHRSCYGCITQHLMNCKRCFFCKTTVI 467 (489)
T ss_pred CCCcccccCcceecccchhhccC-CCCchHHHHHHHHHhcCCeeeEecceee
Confidence 44 34679999999888887765 9999999999999999999999986543
No 53
>PF14570 zf-RING_4: RING/Ubox like zinc-binding domain; PDB: 1E4U_A 1UR6_B.
Probab=96.80 E-value=0.00095 Score=46.87 Aligned_cols=41 Identities=29% Similarity=0.692 Sum_probs=23.2
Q ss_pred CCcCCCCCCC--c--ccccCCcccccHHHHHHHhh-cCCCCCCCCCC
Q 019860 280 CPLCSQKRAN--P--SVVTVSGFVFCYACIFKYVS-QYKRCPVTLMP 321 (334)
Q Consensus 280 CpiC~~~~~~--p--~~~~~~G~vfC~~Ci~~~~~-~~~~CPv~~~~ 321 (334)
||+|.+.+.. - .-++ |||-.|..|-++-++ ++++||-|+.+
T Consensus 1 cp~C~e~~d~~d~~~~PC~-Cgf~IC~~C~~~i~~~~~g~CPgCr~~ 46 (48)
T PF14570_consen 1 CPLCDEELDETDKDFYPCE-CGFQICRFCYHDILENEGGRCPGCREP 46 (48)
T ss_dssp -TTTS-B--CCCTT--SST-TS----HHHHHHHTTSS-SB-TTT--B
T ss_pred CCCcccccccCCCccccCc-CCCcHHHHHHHHHHhccCCCCCCCCCC
Confidence 8999998722 1 2455 999999999999997 58999999976
No 54
>KOG0828 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=96.73 E-value=0.00084 Score=67.48 Aligned_cols=50 Identities=22% Similarity=0.538 Sum_probs=39.3
Q ss_pred CCCCCCCCcCCCCCC-----Ccc-----------cccCCcccccHHHHHHHhhcCC-CCCCCCCCCC
Q 019860 274 PPDRTICPLCSQKRA-----NPS-----------VVTVSGFVFCYACIFKYVSQYK-RCPVTLMPAT 323 (334)
Q Consensus 274 ~~~~~~CpiC~~~~~-----~p~-----------~~~~~G~vfC~~Ci~~~~~~~~-~CPv~~~~~~ 323 (334)
..+...|+||+.++. +++ ++++|.|+|-..|+.+|.+..+ .||||+.|+.
T Consensus 568 ~~~t~dC~ICMt~I~l~~~~s~~~~~~~~~~~nYm~tPC~HifH~~CL~~WMd~ykl~CPvCR~pLP 634 (636)
T KOG0828|consen 568 VRRTNDCVICMTPIDLRSTGSDCMVASMMVRRNYMLTPCHHIFHRQCLLQWMDTYKLICPVCRCPLP 634 (636)
T ss_pred hhccccceEeccccceeeccCcchhhhhhhhccccccchHHHHHHHHHHHHHhhhcccCCccCCCCC
Confidence 346789999999863 221 2346999999999999999665 9999998863
No 55
>KOG4159 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=96.56 E-value=0.0011 Score=66.03 Aligned_cols=47 Identities=26% Similarity=0.539 Sum_probs=43.0
Q ss_pred CCCCCCCcCCCCCCCcccccCCcccccHHHHHHHhhcCCCCCCCCCCC
Q 019860 275 PDRTICPLCSQKRANPSVVTVSGFVFCYACIFKYVSQYKRCPVTLMPA 322 (334)
Q Consensus 275 ~~~~~CpiC~~~~~~p~~~~~~G~vfC~~Ci~~~~~~~~~CPv~~~~~ 322 (334)
.+...|-||...+.+|++++ |||.||..||.+-+.+...||.|+.++
T Consensus 82 ~sef~c~vc~~~l~~pv~tp-cghs~c~~Cl~r~ld~~~~cp~Cr~~l 128 (398)
T KOG4159|consen 82 RSEFECCVCSRALYPPVVTP-CGHSFCLECLDRSLDQETECPLCRDEL 128 (398)
T ss_pred cchhhhhhhHhhcCCCcccc-ccccccHHHHHHHhccCCCCccccccc
Confidence 36789999999999999986 999999999999999999999998665
No 56
>COG5194 APC11 Component of SCF ubiquitin ligase and anaphase-promoting complex [Posttranslational modification, protein turnover, chaperones / Cell division and chromosome partitioning]
Probab=96.36 E-value=0.0029 Score=48.87 Aligned_cols=49 Identities=22% Similarity=0.489 Sum_probs=38.2
Q ss_pred CCCCCcCCCCCCC----cccccCCcccccHHHHHHHhhcCCCCCCCCCCCCcc
Q 019860 277 RTICPLCSQKRAN----PSVVTVSGFVFCYACIFKYVSQYKRCPVTLMPATVE 325 (334)
Q Consensus 277 ~~~CpiC~~~~~~----p~~~~~~G~vfC~~Ci~~~~~~~~~CPv~~~~~~~~ 325 (334)
.+.||-|.-.+++ |.+--+|.|.|-.-||.+||...+.||.++++-.+.
T Consensus 31 m~~C~eCq~~~~~~~eC~v~wG~CnHaFH~HCI~rWL~Tk~~CPld~q~w~~~ 83 (88)
T COG5194 31 MGTCPECQFGMTPGDECPVVWGVCNHAFHDHCIYRWLDTKGVCPLDRQTWVLA 83 (88)
T ss_pred cCcCcccccCCCCCCcceEEEEecchHHHHHHHHHHHhhCCCCCCCCceeEEe
Confidence 4567777764432 345567999999999999999999999999876443
No 57
>KOG0825 consensus PHD Zn-finger protein [General function prediction only]
Probab=96.30 E-value=0.00082 Score=70.75 Aligned_cols=47 Identities=19% Similarity=0.388 Sum_probs=39.4
Q ss_pred CCCCCCcCCCCCCCcccc--cCCcccccHHHHHHHhhcCCCCCCCCCCC
Q 019860 276 DRTICPLCSQKRANPSVV--TVSGFVFCYACIFKYVSQYKRCPVTLMPA 322 (334)
Q Consensus 276 ~~~~CpiC~~~~~~p~~~--~~~G~vfC~~Ci~~~~~~~~~CPv~~~~~ 322 (334)
+...||+|.+...+.-+. .+|||.||..|+..|-+-.+.||+|+...
T Consensus 122 ~~~~CP~Ci~s~~DqL~~~~k~c~H~FC~~Ci~sWsR~aqTCPiDR~EF 170 (1134)
T KOG0825|consen 122 VENQCPNCLKSCNDQLEESEKHTAHYFCEECVGSWSRCAQTCPVDRGEF 170 (1134)
T ss_pred hhhhhhHHHHHHHHHhhccccccccccHHHHhhhhhhhcccCchhhhhh
Confidence 467899999988776332 24999999999999999999999999654
No 58
>PF14447 Prok-RING_4: Prokaryotic RING finger family 4
Probab=96.26 E-value=0.0021 Score=46.32 Aligned_cols=49 Identities=20% Similarity=0.508 Sum_probs=40.6
Q ss_pred CCCCCCcCCCCCCCcccccCCcccccHHHHHHHhhcCCCCCCCCCCCCccCe
Q 019860 276 DRTICPLCSQKRANPSVVTVSGFVFCYACIFKYVSQYKRCPVTLMPATVEQI 327 (334)
Q Consensus 276 ~~~~CpiC~~~~~~p~~~~~~G~vfC~~Ci~~~~~~~~~CPv~~~~~~~~~l 327 (334)
+...|-.|+..-+..++++ |||+-|..|-- +++.+-||+|+.|.+..++
T Consensus 6 ~~~~~~~~~~~~~~~~~~p-CgH~I~~~~f~--~~rYngCPfC~~~~~~~~~ 54 (55)
T PF14447_consen 6 PEQPCVFCGFVGTKGTVLP-CGHLICDNCFP--GERYNGCPFCGTPFEFDDP 54 (55)
T ss_pred cceeEEEcccccccccccc-ccceeeccccC--hhhccCCCCCCCcccCCCC
Confidence 3557889999988888987 99999999965 4566899999999887653
No 59
>KOG3039 consensus Uncharacterized conserved protein [Function unknown]
Probab=96.14 E-value=0.0037 Score=58.02 Aligned_cols=34 Identities=24% Similarity=0.511 Sum_probs=30.7
Q ss_pred CCCCCCcCCCCCCCcccccCCcccccHHHHHHHhh
Q 019860 276 DRTICPLCSQKRANPSVVTVSGFVFCYACIFKYVS 310 (334)
Q Consensus 276 ~~~~CpiC~~~~~~p~~~~~~G~vfC~~Ci~~~~~ 310 (334)
+-.-|.+|+++..||++++ .||+||..||.+|+-
T Consensus 42 ~FdcCsLtLqPc~dPvit~-~GylfdrEaILe~il 75 (303)
T KOG3039|consen 42 PFDCCSLTLQPCRDPVITP-DGYLFDREAILEYIL 75 (303)
T ss_pred CcceeeeecccccCCccCC-CCeeeeHHHHHHHHH
Confidence 3557999999999999987 999999999999984
No 60
>PF11793 FANCL_C: FANCL C-terminal domain; PDB: 3K1L_A.
Probab=96.13 E-value=0.0017 Score=49.24 Aligned_cols=49 Identities=22% Similarity=0.525 Sum_probs=25.6
Q ss_pred CCCCCcCCCCCC-C---c-cccc--CCcccccHHHHHHHhhc-----------CCCCCCCCCCCCcc
Q 019860 277 RTICPLCSQKRA-N---P-SVVT--VSGFVFCYACIFKYVSQ-----------YKRCPVTLMPATVE 325 (334)
Q Consensus 277 ~~~CpiC~~~~~-~---p-~~~~--~~G~vfC~~Ci~~~~~~-----------~~~CPv~~~~~~~~ 325 (334)
...|+||...+. + | .+++ .||.+|-..|+.+|+.. .|+||.|+.+++.+
T Consensus 2 ~~~C~IC~~~~~~~~~~p~~~C~n~~C~~~fH~~CL~~wf~~~~~~~~~~~~~~G~CP~C~~~i~~~ 68 (70)
T PF11793_consen 2 ELECGICYSYRLDDGEIPDVVCPNPSCGKKFHLLCLSEWFLSLEKSRQSFIPIFGECPYCSSPISWS 68 (70)
T ss_dssp --S-SSS--SS-TT-----B--S-TT----B-SGGGHHHHHHHHSSS-TTT--EEE-TTT-SEEEGG
T ss_pred CCCCCcCCcEecCCCCcCceEcCCcccCCHHHHHHHHHHHHHcccCCeeecccccCCcCCCCeeeEe
Confidence 357999999765 3 2 3564 69999999999999973 25799999987653
No 61
>KOG1039 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=96.09 E-value=0.0036 Score=61.33 Aligned_cols=48 Identities=25% Similarity=0.647 Sum_probs=40.3
Q ss_pred CCCCCCcCCCCCCCcc-------cccCCcccccHHHHHHHh--hc-----CCCCCCCCCCCC
Q 019860 276 DRTICPLCSQKRANPS-------VVTVSGFVFCYACIFKYV--SQ-----YKRCPVTLMPAT 323 (334)
Q Consensus 276 ~~~~CpiC~~~~~~p~-------~~~~~G~vfC~~Ci~~~~--~~-----~~~CPv~~~~~~ 323 (334)
+...|-||++.+.+.. +++.|-|.||-.||..|= .+ ...||.|+.+.+
T Consensus 160 ~~k~CGICme~i~ek~~~~~rfgilpnC~H~~Cl~Cir~wr~~~q~~~~~sksCP~CRv~s~ 221 (344)
T KOG1039|consen 160 SEKECGICMETINEKAASERRFGILPNCNHSFCLNCIRKWRQATQFESKTSKSCPFCRVPSS 221 (344)
T ss_pred ccccceehhhhccccchhhhhcccCCCcchhhhhcHhHhhhhhhccccccccCCCcccCccc
Confidence 5678999999988765 556799999999999998 45 478999997753
No 62
>KOG0827 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=96.04 E-value=0.003 Score=61.99 Aligned_cols=52 Identities=17% Similarity=0.517 Sum_probs=38.4
Q ss_pred CCCCCcCCCCCCCc---ccccCCcccccHHHHHHHhhcC---CCCCCCCCCCCccCee
Q 019860 277 RTICPLCSQKRANP---SVVTVSGFVFCYACIFKYVSQY---KRCPVTLMPATVEQIR 328 (334)
Q Consensus 277 ~~~CpiC~~~~~~p---~~~~~~G~vfC~~Ci~~~~~~~---~~CPv~~~~~~~~~l~ 328 (334)
.-+|.||.+-.-|- ..+.+|||+|--.|+.+|.+.. ..||+|+..+...++.
T Consensus 4 ~A~C~Ic~d~~p~~~~l~~i~~cGhifh~~cl~qwfe~~Ps~R~cpic~ik~~~r~~~ 61 (465)
T KOG0827|consen 4 MAECHICIDGRPNDHELGPIGTCGHIFHTTCLTQWFEGDPSNRGCPICQIKLQERHVA 61 (465)
T ss_pred cceeeEeccCCccccccccccchhhHHHHHHHHHHHccCCccCCCCceeecccceeee
Confidence 45799996654332 4556699999999999999964 4899999665544444
No 63
>KOG2817 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=95.78 E-value=0.024 Score=56.03 Aligned_cols=97 Identities=16% Similarity=0.323 Sum_probs=66.0
Q ss_pred HHHHHHHHHHHHHHHHHHHHHH----HhcccccccCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCcCCCCC--CCc-c
Q 019860 219 TMLDYAQTGLIAAVFFFKMMEW----WYQSAEERMSAPTVYPPPPPPPPPKVAREGIPLPPDRTICPLCSQKR--ANP-S 291 (334)
Q Consensus 219 ~~~~~~~~~lp~~iF~lKfLEW----Wyss~~~r~~~~~~lp~pppP~~~~~~~~~~~~~~~~~~CpiC~~~~--~~p-~ 291 (334)
.+...+.++||..+=..-+++= |++.|+ ||.+---+ .+. -.-+-..|||-.+.- .|| .
T Consensus 287 v~v~aG~~Alp~Llk~~~v~~~~~~~W~~~de--------LPveIeL~------~~~-~fHSvF~CPVlKeqtsdeNPPm 351 (394)
T KOG2817|consen 287 VLVNAGCIALPQLLKYKSVMELKHGEWNTKDE--------LPVEIELG------KEY-HFHSVFICPVLKEQTSDENPPM 351 (394)
T ss_pred HHHHhhHHHHHHHHHHHHHHHHhccCcccccc--------Cccceecc------ccc-cccceeecccchhhccCCCCCe
Confidence 4455566777777766666666 665433 44322111 000 012467999988854 565 5
Q ss_pred cccCCcccccHHHHHHHhhcCC---CCCCCCCCCCccCeeeCc
Q 019860 292 VVTVSGFVFCYACIFKYVSQYK---RCPVTLMPATVEQIRRLF 331 (334)
Q Consensus 292 ~~~~~G~vfC~~Ci~~~~~~~~---~CPv~~~~~~~~~l~ri~ 331 (334)
.+. ||||-|..-+.+--++.. +||-|-.....++.+|||
T Consensus 352 ~L~-CGHVISkdAlnrLS~ng~~sfKCPYCP~e~~~~~~kql~ 393 (394)
T KOG2817|consen 352 MLI-CGHVISKDALNRLSKNGSQSFKCPYCPVEQLASDTKQLY 393 (394)
T ss_pred eee-ccceecHHHHHHHhhCCCeeeeCCCCCcccCHHhccccc
Confidence 665 999999999998887654 899999999999999987
No 64
>KOG1001 consensus Helicase-like transcription factor HLTF/DNA helicase RAD5, DEAD-box superfamily [Transcription; Replication, recombination and repair]
Probab=95.64 E-value=0.0025 Score=67.64 Aligned_cols=48 Identities=23% Similarity=0.500 Sum_probs=37.6
Q ss_pred CCCCcCCCCCCCcccccCCcccccHHHHHHHhhcC--CCCCCCCCCCCccCe
Q 019860 278 TICPLCSQKRANPSVVTVSGFVFCYACIFKYVSQY--KRCPVTLMPATVEQI 327 (334)
Q Consensus 278 ~~CpiC~~~~~~p~~~~~~G~vfC~~Ci~~~~~~~--~~CPv~~~~~~~~~l 327 (334)
..|++|.+ ...+.+ ..|||+||+.|+.+.++.. ..||+|+..+..+++
T Consensus 455 ~~c~ic~~-~~~~~i-t~c~h~~c~~c~~~~i~~~~~~~~~~cr~~l~~~~l 504 (674)
T KOG1001|consen 455 HWCHICCD-LDSFFI-TRCGHDFCVECLKKSIQQSENAPCPLCRNVLKEKKL 504 (674)
T ss_pred cccccccc-ccccee-ecccchHHHHHHHhccccccCCCCcHHHHHHHHHHH
Confidence 79999999 444445 4599999999999999864 579999866554433
No 65
>KOG0883 consensus Cyclophilin type, U box-containing peptidyl-prolyl cis-trans isomerase [Posttranslational modification, protein turnover, chaperones]
Probab=95.35 E-value=0.011 Score=58.15 Aligned_cols=54 Identities=20% Similarity=0.269 Sum_probs=49.7
Q ss_pred CCCCCcCCCCCCCcccccCCcccccHHHHHHHhhcCCCCCCCCCCCCccCeeeCc
Q 019860 277 RTICPLCSQKRANPSVVTVSGFVFCYACIFKYVSQYKRCPVTLMPATVEQIRRLF 331 (334)
Q Consensus 277 ~~~CpiC~~~~~~p~~~~~~G~vfC~~Ci~~~~~~~~~CPv~~~~~~~~~l~ri~ 331 (334)
-+.|.+.+.+..+|+.. ..|-||-+.-|+.||+.+++=|++|.+++.+|||++-
T Consensus 40 ~~hC~lt~~Pfe~PvC~-~dg~vFd~~~Ivp~lkk~g~nP~tG~kl~~~dLIkL~ 93 (518)
T KOG0883|consen 40 FNHCSLTMLPFEDPVCT-VDGTVFDLTAIVPWLKKHGTNPITGQKLDGKDLIKLK 93 (518)
T ss_pred hhhceeccccccCcccc-cCCcEEeeehhhHHHHHcCCCCCCCCccccccceeee
Confidence 45799999999999655 5999999999999999999999999999999999874
No 66
>KOG0804 consensus Cytoplasmic Zn-finger protein BRAP2 (BRCA1 associated protein) [General function prediction only]
Probab=95.11 E-value=0.011 Score=59.14 Aligned_cols=43 Identities=21% Similarity=0.614 Sum_probs=35.7
Q ss_pred CCCcCCCCCCCcc---cccCCcccccHHHHHHHhhcCCCCCCCCCCCC
Q 019860 279 ICPLCSQKRANPS---VVTVSGFVFCYACIFKYVSQYKRCPVTLMPAT 323 (334)
Q Consensus 279 ~CpiC~~~~~~p~---~~~~~G~vfC~~Ci~~~~~~~~~CPv~~~~~~ 323 (334)
+||+|++.+...+ +...|-|.|--.|+..|- +..||||+.-.+
T Consensus 177 TCpVCLERMD~s~~gi~t~~c~Hsfh~~cl~~w~--~~scpvcR~~q~ 222 (493)
T KOG0804|consen 177 TCPVCLERMDSSTTGILTILCNHSFHCSCLMKWW--DSSCPVCRYCQS 222 (493)
T ss_pred CcchhHhhcCccccceeeeecccccchHHHhhcc--cCcChhhhhhcC
Confidence 7999999997765 444599999999999995 679999996544
No 67
>KOG1785 consensus Tyrosine kinase negative regulator CBL [Defense mechanisms]
Probab=94.86 E-value=0.012 Score=58.12 Aligned_cols=45 Identities=16% Similarity=0.604 Sum_probs=37.9
Q ss_pred CCCCcCCCCCCCcccccCCcccccHHHHHHHhhcC--CCCCCCCCCCC
Q 019860 278 TICPLCSQKRANPSVVTVSGFVFCYACIFKYVSQY--KRCPVTLMPAT 323 (334)
Q Consensus 278 ~~CpiC~~~~~~p~~~~~~G~vfC~~Ci~~~~~~~--~~CPv~~~~~~ 323 (334)
..|-||-+.=+|-.+-+ |||..|-.|+..|-..+ +.||-|+..++
T Consensus 370 eLCKICaendKdvkIEP-CGHLlCt~CLa~WQ~sd~gq~CPFCRcEIK 416 (563)
T KOG1785|consen 370 ELCKICAENDKDVKIEP-CGHLLCTSCLAAWQDSDEGQTCPFCRCEIK 416 (563)
T ss_pred HHHHHhhccCCCccccc-ccchHHHHHHHhhcccCCCCCCCceeeEec
Confidence 47999999888877755 99999999999999654 78999996654
No 68
>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=94.86 E-value=0.013 Score=46.88 Aligned_cols=30 Identities=33% Similarity=0.716 Sum_probs=24.7
Q ss_pred CCCCCCcCCCCCCCcc--cccCCcccccHHHHH
Q 019860 276 DRTICPLCSQKRANPS--VVTVSGFVFCYACIF 306 (334)
Q Consensus 276 ~~~~CpiC~~~~~~p~--~~~~~G~vfC~~Ci~ 306 (334)
+...|++|++++.|.+ +.+ |||||.+.|+.
T Consensus 77 ~~~~C~vC~k~l~~~~f~~~p-~~~v~H~~C~~ 108 (109)
T PF10367_consen 77 ESTKCSVCGKPLGNSVFVVFP-CGHVVHYSCIK 108 (109)
T ss_pred CCCCccCcCCcCCCceEEEeC-CCeEEeccccc
Confidence 3557999999999873 554 99999999974
No 69
>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=94.78 E-value=0.031 Score=39.36 Aligned_cols=40 Identities=20% Similarity=0.571 Sum_probs=29.7
Q ss_pred CCCcCCC--CCCCcccccCCc-----ccccHHHHHHHhhcC--CCCCCCC
Q 019860 279 ICPLCSQ--KRANPSVVTVSG-----FVFCYACIFKYVSQY--KRCPVTL 319 (334)
Q Consensus 279 ~CpiC~~--~~~~p~~~~~~G-----~vfC~~Ci~~~~~~~--~~CPv~~ 319 (334)
.|-||.. .-.++.+.+ |. +.+-..|+.+|+... .+||+|+
T Consensus 1 ~CrIC~~~~~~~~~l~~P-C~C~G~~~~vH~~Cl~~W~~~~~~~~C~iC~ 49 (49)
T smart00744 1 ICRICHDEGDEGDPLVSP-CRCKGSLKYVHQECLERWINESGNKTCEICK 49 (49)
T ss_pred CccCCCCCCCCCCeeEec-cccCCchhHHHHHHHHHHHHHcCCCcCCCCC
Confidence 4889986 334454443 53 888999999999765 4899996
No 70
>KOG1571 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=94.68 E-value=0.016 Score=56.45 Aligned_cols=42 Identities=24% Similarity=0.562 Sum_probs=32.4
Q ss_pred CCCCCcCCCCCCCcccccCCcccccHHHHHHHhhcCCCCCCCCCCC
Q 019860 277 RTICPLCSQKRANPSVVTVSGFVFCYACIFKYVSQYKRCPVTLMPA 322 (334)
Q Consensus 277 ~~~CpiC~~~~~~p~~~~~~G~vfC~~Ci~~~~~~~~~CPv~~~~~ 322 (334)
...|-||.....|..-++ |||+.| |+.-.-.- ..||||+...
T Consensus 305 p~lcVVcl~e~~~~~fvp-cGh~cc--ct~cs~~l-~~CPvCR~rI 346 (355)
T KOG1571|consen 305 PDLCVVCLDEPKSAVFVP-CGHVCC--CTLCSKHL-PQCPVCRQRI 346 (355)
T ss_pred CCceEEecCCccceeeec-CCcEEE--chHHHhhC-CCCchhHHHH
Confidence 457999999999977776 999999 77644332 3499999653
No 71
>KOG2932 consensus E3 ubiquitin ligase involved in ubiquitination of E-cadherin complex [Posttranslational modification, protein turnover, chaperones]
Probab=94.66 E-value=0.012 Score=56.29 Aligned_cols=42 Identities=24% Similarity=0.461 Sum_probs=34.2
Q ss_pred CCCCcCCCCCCC-cccccCCcccccHHHHHHHhhcCCCCCCCCCCC
Q 019860 278 TICPLCSQKRAN-PSVVTVSGFVFCYACIFKYVSQYKRCPVTLMPA 322 (334)
Q Consensus 278 ~~CpiC~~~~~~-p~~~~~~G~vfC~~Ci~~~~~~~~~CPv~~~~~ 322 (334)
..|--|..+|.. -.+++ |-|||||+|+.. ...+-||.|..++
T Consensus 91 HfCd~Cd~PI~IYGRmIP-CkHvFCl~CAr~--~~dK~Cp~C~d~V 133 (389)
T KOG2932|consen 91 HFCDRCDFPIAIYGRMIP-CKHVFCLECARS--DSDKICPLCDDRV 133 (389)
T ss_pred EeecccCCcceeeecccc-cchhhhhhhhhc--CccccCcCcccHH
Confidence 469999999865 46777 999999999874 3478999998765
No 72
>KOG3113 consensus Uncharacterized conserved protein [Function unknown]
Probab=94.28 E-value=0.036 Score=51.76 Aligned_cols=55 Identities=18% Similarity=0.245 Sum_probs=45.3
Q ss_pred CCCCCCcCCCCCCCc---ccccCCcccccHHHHHHHhhcCCCCCCCCCCCCccCeeeCcc
Q 019860 276 DRTICPLCSQKRANP---SVVTVSGFVFCYACIFKYVSQYKRCPVTLMPATVEQIRRLFH 332 (334)
Q Consensus 276 ~~~~CpiC~~~~~~p---~~~~~~G~vfC~~Ci~~~~~~~~~CPv~~~~~~~~~l~ri~~ 332 (334)
...+|||-+-++..- +++-.|||||-++-+.+.= ...|++|+.+.+.+|+|-|=.
T Consensus 110 a~fiCPvtgleMng~~~F~~l~~CGcV~SerAlKeik--as~C~~C~a~y~~~dvIvlNg 167 (293)
T KOG3113|consen 110 ARFICPVTGLEMNGKYRFCALRCCGCVFSERALKEIK--ASVCHVCGAAYQEDDVIVLNG 167 (293)
T ss_pred ceeecccccceecceEEEEEEeccceeccHHHHHHhh--hccccccCCcccccCeEeeCC
Confidence 367999999999775 5666799999998776553 578999999999999987743
No 73
>KOG1493 consensus Anaphase-promoting complex (APC), subunit 11 [Cell cycle control, cell division, chromosome partitioning; Posttranslational modification, protein turnover, chaperones]
Probab=94.27 E-value=0.021 Score=43.82 Aligned_cols=48 Identities=23% Similarity=0.454 Sum_probs=38.9
Q ss_pred CCCCCcCCCCCCC-cccccCCcccccHHHHHHHhhc---CCCCCCCCCCCCc
Q 019860 277 RTICPLCSQKRAN-PSVVTVSGFVFCYACIFKYVSQ---YKRCPVTLMPATV 324 (334)
Q Consensus 277 ~~~CpiC~~~~~~-p~~~~~~G~vfC~~Ci~~~~~~---~~~CPv~~~~~~~ 324 (334)
.+.||-|.-+-.| |-|+-.|-|.|-.-||.+|+.. .+.||+|++.-.+
T Consensus 31 dg~Cp~Ck~PgDdCPLv~G~C~h~fh~hCI~~wl~~~tsq~~CPmcRq~~~~ 82 (84)
T KOG1493|consen 31 DGCCPDCKLPGDDCPLVWGYCLHAFHAHCILKWLNTPTSQGQCPMCRQTWQF 82 (84)
T ss_pred CCcCCCCcCCCCCCccHHHHHHHHHHHHHHHHHhcCccccccCCcchheeEe
Confidence 4578888887766 6677679999999999999974 4899999986554
No 74
>KOG2930 consensus SCF ubiquitin ligase, Rbx1 component [Posttranslational modification, protein turnover, chaperones]
Probab=94.24 E-value=0.028 Score=45.53 Aligned_cols=45 Identities=18% Similarity=0.463 Sum_probs=35.4
Q ss_pred CCCCcCCCCCCCcc----------------cccCCcccccHHHHHHHhhcCCCCCCCCCCC
Q 019860 278 TICPLCSQKRANPS----------------VVTVSGFVFCYACIFKYVSQYKRCPVTLMPA 322 (334)
Q Consensus 278 ~~CpiC~~~~~~p~----------------~~~~~G~vfC~~Ci~~~~~~~~~CPv~~~~~ 322 (334)
+.|.||+..|-|++ +=-+|.|.|-+-||.+||++.+.||.|+++=
T Consensus 47 DnCAICRnHIMd~CieCQa~~~~~~~EC~VaWG~CNHaFH~hCisrWlktr~vCPLdn~eW 107 (114)
T KOG2930|consen 47 DNCAICRNHIMDLCIECQANQSATSEECTVAWGVCNHAFHFHCISRWLKTRNVCPLDNKEW 107 (114)
T ss_pred chhHHHHHHHHHHHHhhccCCCCCCCceEEEeeecchHHHHHHHHHHHhhcCcCCCcCcce
Confidence 46888876554331 2235999999999999999999999999764
No 75
>PF02891 zf-MIZ: MIZ/SP-RING zinc finger; InterPro: IPR004181 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents MIZ-type zinc finger domains. Miz1 (Msx-interacting-zinc finger) is a zinc finger-containing protein with homology to the yeast protein, Nfi-1. Miz1 is a sequence specific DNA binding protein that can function as a positive-acting transcription factor. Miz1 binds to the homeobox protein Msx2, enhancing the specific DNA-binding ability of Msx2 []. Other proteins containing this domain include the human pias family (protein inhibitor of activated STAT protein). More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 3I2D_A.
Probab=93.81 E-value=0.06 Score=38.06 Aligned_cols=43 Identities=21% Similarity=0.430 Sum_probs=23.5
Q ss_pred CCCCcCCCCCCCcccccCCcccccHHHHHHHhh---cC--CCCCCCCCC
Q 019860 278 TICPLCSQKRANPSVVTVSGFVFCYACIFKYVS---QY--KRCPVTLMP 321 (334)
Q Consensus 278 ~~CpiC~~~~~~p~~~~~~G~vfC~~Ci~~~~~---~~--~~CPv~~~~ 321 (334)
..|||..+.++.|+=...|-|+-|++= ..|++ +. =+||+|++|
T Consensus 3 L~CPls~~~i~~P~Rg~~C~H~~CFDl-~~fl~~~~~~~~W~CPiC~~~ 50 (50)
T PF02891_consen 3 LRCPLSFQRIRIPVRGKNCKHLQCFDL-ESFLESNQRTPKWKCPICNKP 50 (50)
T ss_dssp SB-TTTSSB-SSEEEETT--SS--EEH-HHHHHHHHHS---B-TTT---
T ss_pred eeCCCCCCEEEeCccCCcCcccceECH-HHHHHHhhccCCeECcCCcCc
Confidence 479999999999986667999988763 23443 32 369999975
No 76
>KOG4275 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=93.53 E-value=0.0088 Score=56.79 Aligned_cols=41 Identities=22% Similarity=0.569 Sum_probs=34.4
Q ss_pred CCCCCcCCCCCCCcccccCCcc-cccHHHHHHHhhcCCCCCCCCCCC
Q 019860 277 RTICPLCSQKRANPSVVTVSGF-VFCYACIFKYVSQYKRCPVTLMPA 322 (334)
Q Consensus 277 ~~~CpiC~~~~~~p~~~~~~G~-vfC~~Ci~~~~~~~~~CPv~~~~~ 322 (334)
...|.||+....|=..++ ||| |-|+.|-... +.||||++.+
T Consensus 300 ~~LC~ICmDaP~DCvfLe-CGHmVtCt~CGkrm----~eCPICRqyi 341 (350)
T KOG4275|consen 300 RRLCAICMDAPRDCVFLE-CGHMVTCTKCGKRM----NECPICRQYI 341 (350)
T ss_pred HHHHHHHhcCCcceEEee-cCcEEeehhhcccc----ccCchHHHHH
Confidence 578999999999988887 999 5799998743 4899999654
No 77
>KOG2979 consensus Protein involved in DNA repair [General function prediction only]
Probab=93.39 E-value=0.044 Score=51.33 Aligned_cols=45 Identities=22% Similarity=0.366 Sum_probs=40.7
Q ss_pred CCCCCcCCCCCCCcccccCCcccccHHHHHHHhhcC--CCCCCCCCC
Q 019860 277 RTICPLCSQKRANPSVVTVSGFVFCYACIFKYVSQY--KRCPVTLMP 321 (334)
Q Consensus 277 ~~~CpiC~~~~~~p~~~~~~G~vfC~~Ci~~~~~~~--~~CPv~~~~ 321 (334)
+..||+..+++.||.+-..|||||-..-|..++... -+|||-+..
T Consensus 176 s~rdPis~~~I~nPviSkkC~HvydrDsI~~~l~~~~~i~CPv~gC~ 222 (262)
T KOG2979|consen 176 SNRDPISKKPIVNPVISKKCGHVYDRDSIMQILCDEITIRCPVLGCE 222 (262)
T ss_pred cccCchhhhhhhchhhhcCcCcchhhhhHHHHhccCceeecccccCC
Confidence 679999999999999888899999999999999884 689998765
No 78
>PF10571 UPF0547: Uncharacterised protein family UPF0547; InterPro: IPR018886 This domain may well be a type of zinc-finger as it carries two pairs of highly conserved cysteine residues though with no accompanying histidines. Several members are annotated as putative helicases.
Probab=93.21 E-value=0.049 Score=33.35 Aligned_cols=22 Identities=23% Similarity=0.643 Sum_probs=17.1
Q ss_pred CCCcCCCCCCCc-ccccCCcccc
Q 019860 279 ICPLCSQKRANP-SVVTVSGFVF 300 (334)
Q Consensus 279 ~CpiC~~~~~~p-~~~~~~G~vf 300 (334)
.||-|++.+... ..++.|||+|
T Consensus 2 ~CP~C~~~V~~~~~~Cp~CG~~F 24 (26)
T PF10571_consen 2 TCPECGAEVPESAKFCPHCGYDF 24 (26)
T ss_pred cCCCCcCCchhhcCcCCCCCCCC
Confidence 699999987544 4677788887
No 79
>PF04216 FdhE: Protein involved in formate dehydrogenase formation; InterPro: IPR006452 This family of sequences describe an accessory protein required for the assembly of formate dehydrogenase of certain proteobacteria although not present in the final complex []. The exact nature of the function of FdhE in the assembly of the complex is unknown, but considering the presence of selenocysteine, molybdopterin, iron-sulphur clusters and cytochrome b556, it is likely to be involved in the insertion of cofactors. ; GO: 0005737 cytoplasm; PDB: 2FIY_B.
Probab=93.03 E-value=0.018 Score=55.06 Aligned_cols=46 Identities=20% Similarity=0.456 Sum_probs=24.7
Q ss_pred CCCCCCcCCCCCCCcccccCC--c--ccccHHHHHHHhhcCCCCCCCCCC
Q 019860 276 DRTICPLCSQKRANPSVVTVS--G--FVFCYACIFKYVSQYKRCPVTLMP 321 (334)
Q Consensus 276 ~~~~CpiC~~~~~~p~~~~~~--G--~vfC~~Ci~~~~~~~~~CPv~~~~ 321 (334)
.++.||+|+....-..+...- | |.+|--|-.+|--...+||.|+-.
T Consensus 171 ~~g~CPvCGs~P~~s~l~~~~~~G~R~L~Cs~C~t~W~~~R~~Cp~Cg~~ 220 (290)
T PF04216_consen 171 QRGYCPVCGSPPVLSVLRGGEREGKRYLHCSLCGTEWRFVRIKCPYCGNT 220 (290)
T ss_dssp T-SS-TTT---EEEEEEE------EEEEEETTT--EEE--TTS-TTT---
T ss_pred cCCcCCCCCCcCceEEEecCCCCccEEEEcCCCCCeeeecCCCCcCCCCC
Confidence 467999999987666555422 4 789999999999999999999953
No 80
>KOG3002 consensus Zn finger protein [General function prediction only]
Probab=92.91 E-value=0.065 Score=51.73 Aligned_cols=44 Identities=25% Similarity=0.611 Sum_probs=38.0
Q ss_pred CCCCCCcCCCCCCCccc-ccCCcccccHHHHHHHhhcCCCCCCCCCCCC
Q 019860 276 DRTICPLCSQKRANPSV-VTVSGFVFCYACIFKYVSQYKRCPVTLMPAT 323 (334)
Q Consensus 276 ~~~~CpiC~~~~~~p~~-~~~~G~vfC~~Ci~~~~~~~~~CPv~~~~~~ 323 (334)
+-..||+|...+.-|.. +. .||.-|-.|-. +-..+||.|+.+++
T Consensus 47 ~lleCPvC~~~l~~Pi~QC~-nGHlaCssC~~---~~~~~CP~Cr~~~g 91 (299)
T KOG3002|consen 47 DLLDCPVCFNPLSPPIFQCD-NGHLACSSCRT---KVSNKCPTCRLPIG 91 (299)
T ss_pred hhccCchhhccCcccceecC-CCcEehhhhhh---hhcccCCccccccc
Confidence 45689999999999964 54 89999999987 56799999999987
No 81
>PF05290 Baculo_IE-1: Baculovirus immediate-early protein (IE-0); InterPro: IPR007954 This entry contains the Baculovirus immediate-early protein IE-0.
Probab=92.76 E-value=0.09 Score=44.64 Aligned_cols=47 Identities=23% Similarity=0.537 Sum_probs=36.9
Q ss_pred CCCCCcCCCCCCCcccccC---CcccccHHHHHHHh---hcCCCCCCCCCCCC
Q 019860 277 RTICPLCSQKRANPSVVTV---SGFVFCYACIFKYV---SQYKRCPVTLMPAT 323 (334)
Q Consensus 277 ~~~CpiC~~~~~~p~~~~~---~G~vfC~~Ci~~~~---~~~~~CPv~~~~~~ 323 (334)
-+.|-||.+.-.++.-+.+ |||-.|+-|-.+.. .-+..||||+....
T Consensus 80 lYeCnIC~etS~ee~FLKPneCCgY~iCn~Cya~LWK~~~~ypvCPvCkTSFK 132 (140)
T PF05290_consen 80 LYECNICKETSAEERFLKPNECCGYSICNACYANLWKFCNLYPVCPVCKTSFK 132 (140)
T ss_pred ceeccCcccccchhhcCCcccccchHHHHHHHHHHHHHcccCCCCCccccccc
Confidence 3589999999888765544 99999999966544 46799999996543
No 82
>KOG3579 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=92.70 E-value=0.089 Score=49.94 Aligned_cols=37 Identities=22% Similarity=0.576 Sum_probs=29.9
Q ss_pred CCCCCCcCCCCCCCcc--cc-cCCcccccHHHHHHHhhcC
Q 019860 276 DRTICPLCSQKRANPS--VV-TVSGFVFCYACIFKYVSQY 312 (334)
Q Consensus 276 ~~~~CpiC~~~~~~p~--~~-~~~G~vfC~~Ci~~~~~~~ 312 (334)
....|-+|++.++|.- -| ++.+|-||++|--+.|++.
T Consensus 267 apLcCTLC~ERLEDTHFVQCPSVp~HKFCFPCSResIK~Q 306 (352)
T KOG3579|consen 267 APLCCTLCHERLEDTHFVQCPSVPSHKFCFPCSRESIKQQ 306 (352)
T ss_pred CceeehhhhhhhccCceeecCCCcccceecccCHHHHHhh
Confidence 3578999999999973 22 3479999999999999864
No 83
>KOG0298 consensus DEAD box-containing helicase-like transcription factor/DNA repair protein [Replication, recombination and repair]
Probab=92.46 E-value=0.027 Score=62.66 Aligned_cols=43 Identities=21% Similarity=0.474 Sum_probs=39.3
Q ss_pred CCCCCcCCCCCCCcccccCCcccccHHHHHHHhhcCCCCCCCC
Q 019860 277 RTICPLCSQKRANPSVVTVSGFVFCYACIFKYVSQYKRCPVTL 319 (334)
Q Consensus 277 ~~~CpiC~~~~~~p~~~~~~G~vfC~~Ci~~~~~~~~~CPv~~ 319 (334)
...|++|++.+.|-..+..|||-+|-.|..-|+..+.+||+|.
T Consensus 1153 ~~~c~ic~dil~~~~~I~~cgh~~c~~c~~~~l~~~s~~~~~k 1195 (1394)
T KOG0298|consen 1153 HFVCEICLDILRNQGGIAGCGHEPCCRCDELWLYASSRCPICK 1195 (1394)
T ss_pred ccchHHHHHHHHhcCCeeeechhHhhhHHHHHHHHhccCcchh
Confidence 5589999999998766566999999999999999999999997
No 84
>COG5219 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=91.87 E-value=0.054 Score=58.69 Aligned_cols=47 Identities=19% Similarity=0.450 Sum_probs=37.1
Q ss_pred CCCCCcCCCCCC-----Cc-ccccCCcccccHHHHHHHhhcC--CCCCCCCCCCC
Q 019860 277 RTICPLCSQKRA-----NP-SVVTVSGFVFCYACIFKYVSQY--KRCPVTLMPAT 323 (334)
Q Consensus 277 ~~~CpiC~~~~~-----~p-~~~~~~G~vfC~~Ci~~~~~~~--~~CPv~~~~~~ 323 (334)
...|+||-..+. =| .-|+||-|-|--.|+++|.+.. .+||+|+...+
T Consensus 1469 ~eECaICYsvL~~vdr~lPskrC~TCknKFH~~CLyKWf~Ss~~s~CPlCRseit 1523 (1525)
T COG5219 1469 HEECAICYSVLDMVDRSLPSKRCATCKNKFHTRCLYKWFASSARSNCPLCRSEIT 1523 (1525)
T ss_pred cchhhHHHHHHHHHhccCCccccchhhhhhhHHHHHHHHHhcCCCCCCccccccc
Confidence 468999977543 24 3567899999999999999864 78999996543
No 85
>COG5236 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=91.49 E-value=0.11 Score=50.58 Aligned_cols=45 Identities=20% Similarity=0.524 Sum_probs=38.7
Q ss_pred CCCCCCcCCCCCCCcccccCCcccccHHHHHHH--hhcCCCCCCCCCC
Q 019860 276 DRTICPLCSQKRANPSVVTVSGFVFCYACIFKY--VSQYKRCPVTLMP 321 (334)
Q Consensus 276 ~~~~CpiC~~~~~~p~~~~~~G~vfC~~Ci~~~--~~~~~~CPv~~~~ 321 (334)
+...|-||-+.++.-++++ |||-.|.-|.++- |=..+.||+|+..
T Consensus 60 en~~C~ICA~~~TYs~~~P-C~H~~CH~Ca~RlRALY~~K~C~~CrTE 106 (493)
T COG5236 60 ENMNCQICAGSTTYSARYP-CGHQICHACAVRLRALYMQKGCPLCRTE 106 (493)
T ss_pred ccceeEEecCCceEEEecc-CCchHHHHHHHHHHHHHhccCCCccccc
Confidence 4678999999999999997 9999999999864 3456889999854
No 86
>PRK04023 DNA polymerase II large subunit; Validated
Probab=90.82 E-value=0.19 Score=55.17 Aligned_cols=54 Identities=19% Similarity=0.269 Sum_probs=38.9
Q ss_pred CCCCCCCCCcCCCCCCCcccccCCcc-----cccHHHHHHHhhcCCCCCCCCCCCCccCeee
Q 019860 273 LPPDRTICPLCSQKRANPSVVTVSGF-----VFCYACIFKYVSQYKRCPVTLMPATVEQIRR 329 (334)
Q Consensus 273 ~~~~~~~CpiC~~~~~~p~~~~~~G~-----vfC~~Ci~~~~~~~~~CPv~~~~~~~~~l~r 329 (334)
++.....||-|+... ....|+.||. .||..|-. ......||-|+..++...-++
T Consensus 622 VEVg~RfCpsCG~~t-~~frCP~CG~~Te~i~fCP~CG~--~~~~y~CPKCG~El~~~s~~~ 680 (1121)
T PRK04023 622 VEIGRRKCPSCGKET-FYRRCPFCGTHTEPVYRCPRCGI--EVEEDECEKCGREPTPYSKRK 680 (1121)
T ss_pred ecccCccCCCCCCcC-CcccCCCCCCCCCcceeCccccC--cCCCCcCCCCCCCCCccceEE
Confidence 555677999999985 4457888995 59999943 333467999998876544443
No 87
>TIGR01562 FdhE formate dehydrogenase accessory protein FdhE. The only sequence scoring between trusted and noise is that from Aquifex aeolicus, which shows certain structural differences from the proteobacterial forms in the alignment. However it is notable that A. aeolicus also has a sequence scoring above trusted to the alpha subunit of formate dehydrogenase (TIGR01553).
Probab=90.64 E-value=0.086 Score=51.00 Aligned_cols=46 Identities=22% Similarity=0.512 Sum_probs=36.1
Q ss_pred CCCCCCcCCCCCCCccccc---CCc--ccccHHHHHHHhhcCCCCCCCCCC
Q 019860 276 DRTICPLCSQKRANPSVVT---VSG--FVFCYACIFKYVSQYKRCPVTLMP 321 (334)
Q Consensus 276 ~~~~CpiC~~~~~~p~~~~---~~G--~vfC~~Ci~~~~~~~~~CPv~~~~ 321 (334)
..+.||+|+....-..+.. .-| |.+|--|-.+|=-...+||.|+..
T Consensus 183 ~~~~CPvCGs~P~~s~~~~~~~~~G~RyL~CslC~teW~~~R~~C~~Cg~~ 233 (305)
T TIGR01562 183 SRTLCPACGSPPVASMVRQGGKETGLRYLSCSLCATEWHYVRVKCSHCEES 233 (305)
T ss_pred CCCcCCCCCChhhhhhhcccCCCCCceEEEcCCCCCcccccCccCCCCCCC
Confidence 4679999999865443322 134 889999999999999999999964
No 88
>PLN02189 cellulose synthase
Probab=89.19 E-value=0.25 Score=54.54 Aligned_cols=46 Identities=22% Similarity=0.562 Sum_probs=36.1
Q ss_pred CCCCCCcCCCCCCC-----c-ccccCCcccccHHHHHHHhhc--CCCCCCCCCCC
Q 019860 276 DRTICPLCSQKRAN-----P-SVVTVSGFVFCYACIFKYVSQ--YKRCPVTLMPA 322 (334)
Q Consensus 276 ~~~~CpiC~~~~~~-----p-~~~~~~G~vfC~~Ci~~~~~~--~~~CPv~~~~~ 322 (334)
...+|.||++.+-- + ++|..||+--|.+|. +|-++ ++.||-|+.+-
T Consensus 33 ~~~~C~iCgd~vg~~~~g~~fvaC~~C~fpvCr~Cy-eyer~eg~q~CpqCkt~Y 86 (1040)
T PLN02189 33 DGQVCEICGDEIGLTVDGDLFVACNECGFPVCRPCY-EYERREGTQNCPQCKTRY 86 (1040)
T ss_pred cCccccccccccCcCCCCCEEEeeccCCCccccchh-hhhhhcCCccCcccCCch
Confidence 35689999998642 2 688889999999999 66654 47899998653
No 89
>KOG4367 consensus Predicted Zn-finger protein [Function unknown]
Probab=89.05 E-value=0.21 Score=50.07 Aligned_cols=35 Identities=23% Similarity=0.593 Sum_probs=31.5
Q ss_pred CCCCCCcCCCCCCCcccccCCcccccHHHHHHHhhc
Q 019860 276 DRTICPLCSQKRANPSVVTVSGFVFCYACIFKYVSQ 311 (334)
Q Consensus 276 ~~~~CpiC~~~~~~p~~~~~~G~vfC~~Ci~~~~~~ 311 (334)
+..+||||+.-.++|.+++ |||-.|..|+..-+.+
T Consensus 3 eelkc~vc~~f~~epiil~-c~h~lc~~ca~~~~~~ 37 (699)
T KOG4367|consen 3 EELKCPVCGSFYREPIILP-CSHNLCQACARNILVQ 37 (699)
T ss_pred ccccCceehhhccCceEee-cccHHHHHHHHhhccc
Confidence 3568999999999999997 9999999999988864
No 90
>KOG1941 consensus Acetylcholine receptor-associated protein of the synapse (rapsyn) [Extracellular structures]
Probab=88.62 E-value=0.17 Score=50.13 Aligned_cols=42 Identities=19% Similarity=0.536 Sum_probs=35.6
Q ss_pred CCCCCcCCCCC--CCc--ccccCCcccccHHHHHHHhhcC--CCCCCCC
Q 019860 277 RTICPLCSQKR--ANP--SVVTVSGFVFCYACIFKYVSQY--KRCPVTL 319 (334)
Q Consensus 277 ~~~CpiC~~~~--~~p--~~~~~~G~vfC~~Ci~~~~~~~--~~CPv~~ 319 (334)
...|-.|++.+ +|. -+++ |.|+|--+|++++++++ ..||.|+
T Consensus 365 ~L~Cg~CGe~~Glk~e~LqALp-CsHIfH~rCl~e~L~~n~~rsCP~Cr 412 (518)
T KOG1941|consen 365 ELYCGLCGESIGLKNERLQALP-CSHIFHLRCLQEILENNGTRSCPNCR 412 (518)
T ss_pred hhhhhhhhhhhcCCcccccccc-hhHHHHHHHHHHHHHhCCCCCCccHH
Confidence 45799999974 554 4787 99999999999999887 5799998
No 91
>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=88.58 E-value=0.21 Score=42.52 Aligned_cols=41 Identities=24% Similarity=0.526 Sum_probs=31.8
Q ss_pred CCCCCcCCCCCCC--cccccCCc------ccccHHHHHHHhhcCCCCCC
Q 019860 277 RTICPLCSQKRAN--PSVVTVSG------FVFCYACIFKYVSQYKRCPV 317 (334)
Q Consensus 277 ~~~CpiC~~~~~~--p~~~~~~G------~vfC~~Ci~~~~~~~~~CPv 317 (334)
...|.||.+.|.+ .+|.-+|| ++||..|+.+|-+++++-|-
T Consensus 26 ~~EC~IC~~~I~~~~GvV~vt~~g~lnLEkmfc~~C~~rw~~~~~rDPf 74 (134)
T PF05883_consen 26 TVECQICFDRIDNNDGVVYVTDGGTLNLEKMFCADCDKRWRRERNRDPF 74 (134)
T ss_pred CeeehhhhhhhhcCCCEEEEecCCeehHHHHHHHHHHHHHHhhccCCCc
Confidence 5689999999988 44322366 78999999999777776664
No 92
>KOG4185 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=88.31 E-value=0.28 Score=46.80 Aligned_cols=43 Identities=23% Similarity=0.567 Sum_probs=35.4
Q ss_pred CCCcCCCCC------CCcccccCCcccccHHHHHHHhhcC-CCCCCCCCCC
Q 019860 279 ICPLCSQKR------ANPSVVTVSGFVFCYACIFKYVSQY-KRCPVTLMPA 322 (334)
Q Consensus 279 ~CpiC~~~~------~~p~~~~~~G~vfC~~Ci~~~~~~~-~~CPv~~~~~ 322 (334)
.|-||.+.. ..|.++. |||.+|..|+...+... .-||-|+.+.
T Consensus 5 ~c~~c~~~~s~~~~~~~p~~l~-c~h~~c~~c~~~l~~~~~i~cpfcR~~~ 54 (296)
T KOG4185|consen 5 ECEICNEDYSSEDGDHIPRVLK-CGHTICQNCASKLLGNSRILCPFCRETT 54 (296)
T ss_pred ceeecCccccccCcccCCcccc-cCceehHhHHHHHhcCceeeccCCCCcc
Confidence 588888764 3467887 99999999999888765 6799999884
No 93
>PLN02436 cellulose synthase A
Probab=87.91 E-value=0.34 Score=53.65 Aligned_cols=46 Identities=20% Similarity=0.528 Sum_probs=36.2
Q ss_pred CCCCCCcCCCCCCC-----c-ccccCCcccccHHHHHHHhhc--CCCCCCCCCCC
Q 019860 276 DRTICPLCSQKRAN-----P-SVVTVSGFVFCYACIFKYVSQ--YKRCPVTLMPA 322 (334)
Q Consensus 276 ~~~~CpiC~~~~~~-----p-~~~~~~G~vfC~~Ci~~~~~~--~~~CPv~~~~~ 322 (334)
...+|-||++.+-- + ++|..||+--|.+|. +|-++ ++.||-|+.+-
T Consensus 35 ~~~iCqICGD~Vg~t~dGe~FVACn~C~fpvCr~Cy-eyer~eg~~~Cpqckt~Y 88 (1094)
T PLN02436 35 SGQTCQICGDEIELTVDGEPFVACNECAFPVCRPCY-EYERREGNQACPQCKTRY 88 (1094)
T ss_pred CCccccccccccCcCCCCCEEEeeccCCCccccchh-hhhhhcCCccCcccCCch
Confidence 35689999998622 2 688899999999999 66654 47899998654
No 94
>PF14446 Prok-RING_1: Prokaryotic RING finger family 1
Probab=87.34 E-value=0.69 Score=33.33 Aligned_cols=44 Identities=18% Similarity=0.301 Sum_probs=33.3
Q ss_pred CCCCCCcCCCCCC--Cc-ccccCCcccccHHHHHHHhhcCCCCCC--CCCCCC
Q 019860 276 DRTICPLCSQKRA--NP-SVVTVSGFVFCYACIFKYVSQYKRCPV--TLMPAT 323 (334)
Q Consensus 276 ~~~~CpiC~~~~~--~p-~~~~~~G~vfC~~Ci~~~~~~~~~CPv--~~~~~~ 323 (334)
....|++|+++++ +. +|++.||-.+-..|.. ..+.|-. |+.+.+
T Consensus 4 ~~~~C~~Cg~~~~~~dDiVvCp~CgapyHR~C~~----~~g~C~~~~c~~~~~ 52 (54)
T PF14446_consen 4 EGCKCPVCGKKFKDGDDIVVCPECGAPYHRDCWE----KAGGCINYSCGTGFE 52 (54)
T ss_pred cCccChhhCCcccCCCCEEECCCCCCcccHHHHh----hCCceEeccCCCCcc
Confidence 3568999999994 44 6899999999999975 4577766 555443
No 95
>KOG1814 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=86.70 E-value=0.41 Score=47.74 Aligned_cols=45 Identities=20% Similarity=0.447 Sum_probs=33.2
Q ss_pred CCCCCcCCCCCCCc--ccccCCcccccHHHHHHHhhc--------CCCCCCCCCC
Q 019860 277 RTICPLCSQKRANP--SVVTVSGFVFCYACIFKYVSQ--------YKRCPVTLMP 321 (334)
Q Consensus 277 ~~~CpiC~~~~~~p--~~~~~~G~vfC~~Ci~~~~~~--------~~~CPv~~~~ 321 (334)
-..|-||...-.-. .+..+|+||||..|..+|..- ..+||-++-+
T Consensus 184 lf~C~ICf~e~~G~~c~~~lpC~Hv~Ck~C~kdY~~~~i~eg~v~~l~Cp~~~C~ 238 (445)
T KOG1814|consen 184 LFDCCICFEEQMGQHCFKFLPCSHVFCKSCLKDYFTIQIQEGQVSCLKCPDPKCG 238 (445)
T ss_pred cccceeeehhhcCcceeeecccchHHHHHHHHHHHHHhhhcceeeeecCCCCCCc
Confidence 57899999875442 244459999999999999862 3589866543
No 96
>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=86.54 E-value=0.069 Score=40.47 Aligned_cols=40 Identities=30% Similarity=0.558 Sum_probs=24.6
Q ss_pred CCCCcCCCCCCCcccccCCcccccHHHHHHHhhcCCCCCCCCCCCC
Q 019860 278 TICPLCSQKRANPSVVTVSGFVFCYACIFKYVSQYKRCPVTLMPAT 323 (334)
Q Consensus 278 ~~CpiC~~~~~~p~~~~~~G~vfC~~Ci~~~~~~~~~CPv~~~~~~ 323 (334)
..||.|.++++ ...|+.+|-.|-.+|. ....||-|+.++.
T Consensus 2 ~~CP~C~~~L~-----~~~~~~~C~~C~~~~~-~~a~CPdC~~~Le 41 (70)
T PF07191_consen 2 NTCPKCQQELE-----WQGGHYHCEACQKDYK-KEAFCPDCGQPLE 41 (70)
T ss_dssp -B-SSS-SBEE-----EETTEEEETTT--EEE-EEEE-TTT-SB-E
T ss_pred CcCCCCCCccE-----EeCCEEECccccccce-ecccCCCcccHHH
Confidence 47999998852 2258999999998654 4589999998875
No 97
>PHA03096 p28-like protein; Provisional
Probab=86.45 E-value=0.39 Score=46.10 Aligned_cols=44 Identities=16% Similarity=0.322 Sum_probs=33.5
Q ss_pred CCCCcCCCCCCCc-------ccccCCcccccHHHHHHHhhcC---CCCCCCCCC
Q 019860 278 TICPLCSQKRANP-------SVVTVSGFVFCYACIFKYVSQY---KRCPVTLMP 321 (334)
Q Consensus 278 ~~CpiC~~~~~~p-------~~~~~~G~vfC~~Ci~~~~~~~---~~CPv~~~~ 321 (334)
.+|-||++.+..- .+++.|-|+||-.||..|-.+. ..||.|+..
T Consensus 179 k~c~ic~e~~~~k~~~~~~fgil~~c~h~fc~~ci~~wr~~~~~~e~~~~c~~~ 232 (284)
T PHA03096 179 KICGICLENIKAKYIIKKYYGILSEIKHEFNIFCIKIWMTESLYKETEPENRRL 232 (284)
T ss_pred hhcccchhhhhhhccccccccccccCCcHHHHHHHHHHHHhhhhcccCccccch
Confidence 6899999976532 4777899999999999999753 456555543
No 98
>PRK03564 formate dehydrogenase accessory protein FdhE; Provisional
Probab=86.19 E-value=0.34 Score=46.99 Aligned_cols=46 Identities=22% Similarity=0.587 Sum_probs=35.3
Q ss_pred CCCCCCcCCCCCCCccc-c-cCCc--ccccHHHHHHHhhcCCCCCCCCCC
Q 019860 276 DRTICPLCSQKRANPSV-V-TVSG--FVFCYACIFKYVSQYKRCPVTLMP 321 (334)
Q Consensus 276 ~~~~CpiC~~~~~~p~~-~-~~~G--~vfC~~Ci~~~~~~~~~CPv~~~~ 321 (334)
.+..||+|+....-..+ . ..-| |.+|--|-.+|=-...+||.|+..
T Consensus 186 ~~~~CPvCGs~P~~s~v~~~~~~G~RyL~CslC~teW~~~R~~C~~Cg~~ 235 (309)
T PRK03564 186 QRQFCPVCGSMPVSSVVQIGTTQGLRYLHCNLCESEWHVVRVKCSNCEQS 235 (309)
T ss_pred CCCCCCCCCCcchhheeeccCCCCceEEEcCCCCCcccccCccCCCCCCC
Confidence 46899999998654322 1 1244 678999999999999999999964
No 99
>PF03854 zf-P11: P-11 zinc finger; InterPro: IPR003224 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. The RING-finger is a specialised type of Zn-finger of 40 to 60 residues that binds two atoms of zinc, and is probably involved in mediating protein-protein interactions [, , ]. There are two different variants, the C3HC4-type and a C3H2C3-type, which is clearly related despite the different cysteine/histidine pattern. The latter type is sometimes referred to as 'RING-H2 finger'. The RING domain is a protein interaction domain which has been implicated in a range of diverse biological processes. Several 3D-structures for RING-fingers are known [, ]. The 3D structure of the zinc ligation system is unique to the RING domain and is referred to as the 'cross-brace' motif. The spacing of the cysteines in such a domain is: C-x(2)-C-x(9 to 39)-C-x(1 to 3)-H-x(2 to 3)-C-x(2)-C-x(4 to 48)-C-x(2)-C Metal ligand pairs one and three co-ordinate to bind one zinc ion, whilst pairs two and four bind the second. This entry represents RING finger protein Z, a small polypeptide found in some negative-strand RNA viruses including Lassa fever virus, which plays a crucial role in virion assembly and budding. RING finger Z has been shown to interact with several host proteins, including promyelocytic leukemia protein and the eukaryotic translation initiation factor 4E [, ]. It is sufficient in the absence of any other viral proteins to release virus-like particles from the infected cell []. This protein is also responsible for arenavirus superinfection exclusion; expression of this protein in a host cell strongly and specifically inhibits areanavirus transcription and replication []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003723 RNA binding, 0008270 zinc ion binding; PDB: 2KO5_A.
Probab=85.71 E-value=0.32 Score=34.08 Aligned_cols=43 Identities=23% Similarity=0.557 Sum_probs=26.5
Q ss_pred CCCcCCCCCCCcccccCCcccccHHHHHHHhhcCCCCCCCCCCCC
Q 019860 279 ICPLCSQKRANPSVVTVSGFVFCYACIFKYVSQYKRCPVTLMPAT 323 (334)
Q Consensus 279 ~CpiC~~~~~~p~~~~~~G~vfC~~Ci~~~~~~~~~CPv~~~~~~ 323 (334)
-|--|=..-++ .+..+-|--|..|+...+.....||+|++++-
T Consensus 4 nCKsCWf~~k~--Li~C~dHYLCl~CLt~ml~~s~~C~iC~~~LP 46 (50)
T PF03854_consen 4 NCKSCWFANKG--LIKCSDHYLCLNCLTLMLSRSDRCPICGKPLP 46 (50)
T ss_dssp ---SS-S--SS--EEE-SS-EEEHHHHHHT-SSSSEETTTTEE--
T ss_pred cChhhhhcCCC--eeeecchhHHHHHHHHHhccccCCCcccCcCc
Confidence 35555444433 33447899999999999999999999998764
No 100
>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=85.50 E-value=0.48 Score=39.00 Aligned_cols=28 Identities=29% Similarity=0.517 Sum_probs=22.9
Q ss_pred CCCCCCcCCCCC----CCcccccCCcccccHH
Q 019860 276 DRTICPLCSQKR----ANPSVVTVSGFVFCYA 303 (334)
Q Consensus 276 ~~~~CpiC~~~~----~~p~~~~~~G~vfC~~ 303 (334)
.+.+||-|+..+ ++|.||+.||.+|=-.
T Consensus 8 tKR~Cp~CG~kFYDLnk~PivCP~CG~~~~~~ 39 (108)
T PF09538_consen 8 TKRTCPSCGAKFYDLNKDPIVCPKCGTEFPPE 39 (108)
T ss_pred CcccCCCCcchhccCCCCCccCCCCCCccCcc
Confidence 377999999974 6799999999988554
No 101
>PF10235 Cript: Microtubule-associated protein CRIPT; InterPro: IPR019367 The CRIPT protein is a cytoskeletal protein involved in microtubule production. This C-terminal domain is essential for binding to the PDZ3 domain of the SAP90 protein, one of a super-family of PDZ-containing proteins that play an important role in coupling the membrane ion channels with their signalling partners [].
Probab=84.89 E-value=0.69 Score=36.83 Aligned_cols=36 Identities=19% Similarity=0.570 Sum_probs=29.8
Q ss_pred CCCCCcCCCCCCCcccccCCcccccHHHHHHHhhcCCCCCCCCCCC
Q 019860 277 RTICPLCSQKRANPSVVTVSGFVFCYACIFKYVSQYKRCPVTLMPA 322 (334)
Q Consensus 277 ~~~CpiC~~~~~~p~~~~~~G~vfC~~Ci~~~~~~~~~CPv~~~~~ 322 (334)
...|-+|...+.. =|+-||-.|++ ..+.|.+||+.+
T Consensus 44 ~~~C~~CK~~v~q------~g~~YCq~CAY----kkGiCamCGKki 79 (90)
T PF10235_consen 44 SSKCKICKTKVHQ------PGAKYCQTCAY----KKGICAMCGKKI 79 (90)
T ss_pred Ccccccccccccc------CCCccChhhhc----ccCcccccCCee
Confidence 5689999876533 48999999998 679999999886
No 102
>cd00350 rubredoxin_like Rubredoxin_like; nonheme iron binding domain containing a [Fe(SCys)4] center. The family includes rubredoxins, a small electron transfer protein, and a slightly smaller modular rubredoxin domain present in rubrerythrin and nigerythrin and detected either N- or C-terminal to such proteins as flavin reductase, NAD(P)H-nitrite reductase, and ferredoxin-thioredoxin reductase. In rubredoxin, the iron atom is coordinated by four cysteine residues (Fe(S-Cys)4), but iron can also be replaced by cobalt, nickel or zinc and believed to be involved in electron transfer. Rubrerythrins and nigerythrins are small homodimeric proteins, generally consisting of 2 domains: a rubredoxin domain C-terminal to a non-sulfur, oxo-bridged diiron site in the N-terminal rubrerythrin domain. Rubrerythrins and nigerythrins have putative peroxide activity.
Probab=84.82 E-value=0.48 Score=30.44 Aligned_cols=11 Identities=36% Similarity=0.477 Sum_probs=8.6
Q ss_pred cCCCCCCCCCC
Q 019860 311 QYKRCPVTLMP 321 (334)
Q Consensus 311 ~~~~CPv~~~~ 321 (334)
...+||+|+.+
T Consensus 16 ~~~~CP~Cg~~ 26 (33)
T cd00350 16 APWVCPVCGAP 26 (33)
T ss_pred CCCcCcCCCCc
Confidence 55799999864
No 103
>PF08746 zf-RING-like: RING-like domain; InterPro: IPR014857 This is a zinc finger domain that is related to the C3HC4 RING finger domain (IPR001841 from INTERPRO). ; PDB: 3NW0_A 2CT0_A.
Probab=84.18 E-value=1 Score=30.76 Aligned_cols=39 Identities=18% Similarity=0.432 Sum_probs=24.9
Q ss_pred CCcCCCCCCCccccc--CCcccccHHHHHHHhhcCC--CCCCC
Q 019860 280 CPLCSQKRANPSVVT--VSGFVFCYACIFKYVSQYK--RCPVT 318 (334)
Q Consensus 280 CpiC~~~~~~p~~~~--~~G~vfC~~Ci~~~~~~~~--~CPv~ 318 (334)
|-+|.+.++-...++ .|+--+-..|+..|++... +||.|
T Consensus 1 C~~C~~iv~~G~~C~~~~C~~r~H~~C~~~y~r~~~~~~CP~C 43 (43)
T PF08746_consen 1 CEACKEIVTQGQRCSNRDCNVRLHDDCFKKYFRHRSNPKCPNC 43 (43)
T ss_dssp -TTT-SB-SSSEE-SS--S--EE-HHHHHHHTTT-SS-B-TTT
T ss_pred CcccchhHeeeccCCCCccCchHHHHHHHHHHhcCCCCCCcCC
Confidence 678888888877766 4888899999999998765 79987
No 104
>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=83.45 E-value=0.67 Score=44.27 Aligned_cols=38 Identities=21% Similarity=0.489 Sum_probs=30.1
Q ss_pred CCcccccHHHHHHHhhc-CCCCCCCCCCCCccCee-eCcc
Q 019860 295 VSGFVFCYACIFKYVSQ-YKRCPVTLMPATVEQIR-RLFH 332 (334)
Q Consensus 295 ~~G~vfC~~Ci~~~~~~-~~~CPv~~~~~~~~~l~-ri~~ 332 (334)
+|||-.|-.|...-... .+.||.|+..+-...++ .+|.
T Consensus 22 ~C~H~lCEsCvd~iF~~g~~~CpeC~~iLRk~nfr~q~fE 61 (300)
T KOG3800|consen 22 ECGHRLCESCVDRIFSLGPAQCPECMVILRKNNFRVQTFE 61 (300)
T ss_pred cccchHHHHHHHHHHhcCCCCCCcccchhhhcccchhhcc
Confidence 59999999999987765 58999999988666554 3443
No 105
>PLN02638 cellulose synthase A (UDP-forming), catalytic subunit
Probab=83.30 E-value=0.8 Score=50.94 Aligned_cols=45 Identities=22% Similarity=0.653 Sum_probs=35.1
Q ss_pred CCCCCCcCCCCCCC-----c-ccccCCcccccHHHHHHHhhc--CCCCCCCCCC
Q 019860 276 DRTICPLCSQKRAN-----P-SVVTVSGFVFCYACIFKYVSQ--YKRCPVTLMP 321 (334)
Q Consensus 276 ~~~~CpiC~~~~~~-----p-~~~~~~G~vfC~~Ci~~~~~~--~~~CPv~~~~ 321 (334)
...+|-||++.+-- + ++|..||+--|.+|. +|=++ ++.||-|+.+
T Consensus 16 ~~qiCqICGD~vg~~~~Ge~FVAC~eC~FPVCrpCY-EYEr~eG~q~CPqCktr 68 (1079)
T PLN02638 16 GGQVCQICGDNVGKTVDGEPFVACDVCAFPVCRPCY-EYERKDGNQSCPQCKTK 68 (1079)
T ss_pred CCceeeecccccCcCCCCCEEEEeccCCCccccchh-hhhhhcCCccCCccCCc
Confidence 35589999998532 2 588889999999998 56544 5789999854
No 106
>KOG3268 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=82.72 E-value=1.1 Score=39.91 Aligned_cols=48 Identities=17% Similarity=0.494 Sum_probs=36.8
Q ss_pred CCCCCcCC-----CCCCCccc--ccCCcccccHHHHHHHhhc-----------CCCCCCCCCCCCcc
Q 019860 277 RTICPLCS-----QKRANPSV--VTVSGFVFCYACIFKYVSQ-----------YKRCPVTLMPATVE 325 (334)
Q Consensus 277 ~~~CpiC~-----~~~~~p~~--~~~~G~vfC~~Ci~~~~~~-----------~~~CPv~~~~~~~~ 325 (334)
.+.|-||- ..+.|.+. ++ ||.-|---|+.+|++. .|.||-|..|++++
T Consensus 165 ~~~cgicyayqldGTipDqtCdN~q-CgkpFHqiCL~dWLRgilTsRQSFdiiFGeCPYCS~PialK 230 (234)
T KOG3268|consen 165 LGACGICYAYQLDGTIPDQTCDNIQ-CGKPFHQICLTDWLRGILTSRQSFDIIFGECPYCSDPIALK 230 (234)
T ss_pred hhcccceeeeecCCccccccccccc-cCCcHHHHHHHHHHHHHhhccceeeeeeccCCCCCCcceee
Confidence 45788884 45555542 34 9999999999999973 48999999998764
No 107
>KOG1812 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=82.61 E-value=0.52 Score=47.11 Aligned_cols=42 Identities=24% Similarity=0.478 Sum_probs=33.1
Q ss_pred CCCCCcCCCCCC-----CcccccCCcccccHHHHHHHhhcCCCCCCCC
Q 019860 277 RTICPLCSQKRA-----NPSVVTVSGFVFCYACIFKYVSQYKRCPVTL 319 (334)
Q Consensus 277 ~~~CpiC~~~~~-----~p~~~~~~G~vfC~~Ci~~~~~~~~~CPv~~ 319 (334)
-..||.|+..+. |...+. |||-|||.|..+|...++.|.-|.
T Consensus 306 wr~CpkC~~~ie~~~GCnhm~Cr-C~~~fcy~C~~~~~~~~~~~~~~~ 352 (384)
T KOG1812|consen 306 WRQCPKCKFMIELSEGCNHMTCR-CGHQFCYMCGGDWKTHNGECYECC 352 (384)
T ss_pred cCcCcccceeeeecCCcceEEee-ccccchhhcCcchhhCCccccCcc
Confidence 468999998764 335787 999999999999998887665443
No 108
>PRK05978 hypothetical protein; Provisional
Probab=82.34 E-value=0.87 Score=39.58 Aligned_cols=33 Identities=21% Similarity=0.437 Sum_probs=25.2
Q ss_pred CCCCCcCCCCCCCcccccCCcccccHHHHHHHhhcCCCCCCCCCCCCcc
Q 019860 277 RTICPLCSQKRANPSVVTVSGFVFCYACIFKYVSQYKRCPVTLMPATVE 325 (334)
Q Consensus 277 ~~~CpiC~~~~~~p~~~~~~G~vfC~~Ci~~~~~~~~~CPv~~~~~~~~ 325 (334)
...||-|++- +.| ..|++-+.+||+|+.+.+.+
T Consensus 33 ~grCP~CG~G-----------~LF-----~g~Lkv~~~C~~CG~~~~~~ 65 (148)
T PRK05978 33 RGRCPACGEG-----------KLF-----RAFLKPVDHCAACGEDFTHH 65 (148)
T ss_pred cCcCCCCCCC-----------ccc-----ccccccCCCccccCCccccC
Confidence 6799999973 333 16888899999999887644
No 109
>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=81.62 E-value=0.88 Score=38.43 Aligned_cols=28 Identities=29% Similarity=0.429 Sum_probs=22.8
Q ss_pred CCCCCCcCCCCC----CCcccccCCcccccHH
Q 019860 276 DRTICPLCSQKR----ANPSVVTVSGFVFCYA 303 (334)
Q Consensus 276 ~~~~CpiC~~~~----~~p~~~~~~G~vfC~~ 303 (334)
.+.+||-|+..+ ++|.+|+.||.+|=-.
T Consensus 8 tKr~Cp~cg~kFYDLnk~p~vcP~cg~~~~~~ 39 (129)
T TIGR02300 8 TKRICPNTGSKFYDLNRRPAVSPYTGEQFPPE 39 (129)
T ss_pred ccccCCCcCccccccCCCCccCCCcCCccCcc
Confidence 377999999975 6799999999997443
No 110
>PLN02195 cellulose synthase A
Probab=81.36 E-value=1.3 Score=48.94 Aligned_cols=46 Identities=22% Similarity=0.491 Sum_probs=35.9
Q ss_pred CCCCCcCCCCCC-----Cc-ccccCCcccccHHHHHHHhhc--CCCCCCCCCCCC
Q 019860 277 RTICPLCSQKRA-----NP-SVVTVSGFVFCYACIFKYVSQ--YKRCPVTLMPAT 323 (334)
Q Consensus 277 ~~~CpiC~~~~~-----~p-~~~~~~G~vfC~~Ci~~~~~~--~~~CPv~~~~~~ 323 (334)
..+|-||++.+. +| ++|..||+--|.+|. +|=++ ++.||-|+.+-+
T Consensus 6 ~~~c~~cgd~~~~~~~g~~fvaC~eC~~pvCrpCy-eyer~eg~q~CpqCkt~Yk 59 (977)
T PLN02195 6 APICATCGEEVGVDSNGEAFVACHECSYPLCKACL-EYEIKEGRKVCLRCGGPYD 59 (977)
T ss_pred CccceecccccCcCCCCCeEEEeccCCCccccchh-hhhhhcCCccCCccCCccc
Confidence 458999999653 23 678889999999998 56554 578999997654
No 111
>KOG1812 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=80.94 E-value=0.7 Score=46.20 Aligned_cols=53 Identities=28% Similarity=0.568 Sum_probs=35.4
Q ss_pred CCCCCcCC-CCCCCc---ccccCCcccccHHHHHHHhhcC------CCCC--CCCCCCCccCeeeC
Q 019860 277 RTICPLCS-QKRANP---SVVTVSGFVFCYACIFKYVSQY------KRCP--VTLMPATVEQIRRL 330 (334)
Q Consensus 277 ~~~CpiC~-~~~~~p---~~~~~~G~vfC~~Ci~~~~~~~------~~CP--v~~~~~~~~~l~ri 330 (334)
...|.||. +.+.+. .+.. |||-||..|..+|++.. .+|| -|...++.++...+
T Consensus 146 ~~~C~iC~~e~~~~~~~f~~~~-C~H~fC~~C~k~~iev~~~~~~~~~C~~~~C~~~l~~~~c~~l 210 (384)
T KOG1812|consen 146 KEECGICFVEDPEAEDMFSVLK-CGHRFCKDCVKQHIEVKLLSGTVIRCPHDGCESRLTLESCRKL 210 (384)
T ss_pred cccCccCccccccHhhhHHHhc-ccchhhhHHhHHHhhhhhccCCCccCCCCCCCccCCHHHHhhh
Confidence 45799999 333331 3554 99999999999999832 5776 35555555554433
No 112
>PLN02915 cellulose synthase A [UDP-forming], catalytic subunit
Probab=80.50 E-value=1.2 Score=49.58 Aligned_cols=46 Identities=26% Similarity=0.609 Sum_probs=35.8
Q ss_pred CCCCCCcCCCCCCC-----c-ccccCCcccccHHHHHHHhhc--CCCCCCCCCCC
Q 019860 276 DRTICPLCSQKRAN-----P-SVVTVSGFVFCYACIFKYVSQ--YKRCPVTLMPA 322 (334)
Q Consensus 276 ~~~~CpiC~~~~~~-----p-~~~~~~G~vfC~~Ci~~~~~~--~~~CPv~~~~~ 322 (334)
+..+|-||++.+-- | ++|..||+--|.+|. +|=++ ++.||-|+.+-
T Consensus 14 ~~~~c~iCGd~vg~~~~Ge~FVAC~eC~fpvCr~cy-eye~~~g~~~cp~c~t~y 67 (1044)
T PLN02915 14 DAKTCRVCGDEVGVKEDGQPFVACHVCGFPVCKPCY-EYERSEGNQCCPQCNTRY 67 (1044)
T ss_pred CcchhhccccccCcCCCCCEEEEeccCCCccccchh-hhhhhcCCccCCccCCch
Confidence 46789999998532 2 578889999999999 56544 57899998653
No 113
>KOG2068 consensus MOT2 transcription factor [Transcription]
Probab=80.28 E-value=2.1 Score=41.71 Aligned_cols=45 Identities=24% Similarity=0.584 Sum_probs=36.4
Q ss_pred CCCCcCCCCC--CCccccc-CCcccccHHHHHHHhhcCCCCCCCCCCC
Q 019860 278 TICPLCSQKR--ANPSVVT-VSGFVFCYACIFKYVSQYKRCPVTLMPA 322 (334)
Q Consensus 278 ~~CpiC~~~~--~~p~~~~-~~G~vfC~~Ci~~~~~~~~~CPv~~~~~ 322 (334)
..||+|.... ++-.+++ +||+-.|..|...-+..+++||.|+++.
T Consensus 250 ~s~p~~~~~~~~~d~~~lP~~~~~~~~l~~~~t~~~~~~~~~~~rk~~ 297 (327)
T KOG2068|consen 250 PSCPICYEDLDLTDSNFLPCPCGFRLCLFCHKTISDGDGRCPGCRKPY 297 (327)
T ss_pred CCCCCCCCcccccccccccccccccchhhhhhcccccCCCCCccCCcc
Confidence 5799999976 3333322 3999999999999999999999999764
No 114
>COG1592 Rubrerythrin [Energy production and conversion]
Probab=80.15 E-value=1.1 Score=39.75 Aligned_cols=13 Identities=23% Similarity=0.764 Sum_probs=9.7
Q ss_pred CCCCCcCCCCCCC
Q 019860 277 RTICPLCSQKRAN 289 (334)
Q Consensus 277 ~~~CpiC~~~~~~ 289 (334)
-.+||+|+-...+
T Consensus 134 ~~vC~vCGy~~~g 146 (166)
T COG1592 134 VWVCPVCGYTHEG 146 (166)
T ss_pred EEEcCCCCCcccC
Confidence 4589999877655
No 115
>KOG3970 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=79.17 E-value=1.6 Score=40.47 Aligned_cols=44 Identities=20% Similarity=0.410 Sum_probs=34.9
Q ss_pred CCCcCCCCCCCc-ccccCCcccccHHHHHHHhhc--------CCCCCCCCCCC
Q 019860 279 ICPLCSQKRANP-SVVTVSGFVFCYACIFKYVSQ--------YKRCPVTLMPA 322 (334)
Q Consensus 279 ~CpiC~~~~~~p-~~~~~~G~vfC~~Ci~~~~~~--------~~~CPv~~~~~ 322 (334)
-|.+|+.++..- ++--+|-|+|-|+|..+|..+ --.||.|..++
T Consensus 52 NC~LC~t~La~gdt~RLvCyhlfHW~ClneraA~lPanTAPaGyqCP~Cs~ei 104 (299)
T KOG3970|consen 52 NCRLCNTPLASGDTTRLVCYHLFHWKCLNERAANLPANTAPAGYQCPCCSQEI 104 (299)
T ss_pred CCceeCCccccCcceeehhhhhHHHHHhhHHHhhCCCcCCCCcccCCCCCCcc
Confidence 499999988653 443359999999999999874 24899999764
No 116
>PF14569 zf-UDP: Zinc-binding RING-finger; PDB: 1WEO_A.
Probab=79.04 E-value=2.4 Score=32.82 Aligned_cols=47 Identities=17% Similarity=0.359 Sum_probs=21.5
Q ss_pred CCCCCCcCCCCCCC-----c-ccccCCcccccHHHHHHHhhc-CCCCCCCCCCC
Q 019860 276 DRTICPLCSQKRAN-----P-SVVTVSGFVFCYACIFKYVSQ-YKRCPVTLMPA 322 (334)
Q Consensus 276 ~~~~CpiC~~~~~~-----p-~~~~~~G~vfC~~Ci~~~~~~-~~~CPv~~~~~ 322 (334)
+..+|-||++.+-- + +++..||+-.|.+|..--.++ ++.||-|+.+-
T Consensus 8 ~~qiCqiCGD~VGl~~~Ge~FVAC~eC~fPvCr~CyEYErkeg~q~CpqCkt~y 61 (80)
T PF14569_consen 8 NGQICQICGDDVGLTENGEVFVACHECAFPVCRPCYEYERKEGNQVCPQCKTRY 61 (80)
T ss_dssp SS-B-SSS--B--B-SSSSB--S-SSS-----HHHHHHHHHTS-SB-TTT--B-
T ss_pred CCcccccccCccccCCCCCEEEEEcccCCccchhHHHHHhhcCcccccccCCCc
Confidence 45689999997632 2 567779999999998655544 58899998664
No 117
>cd00729 rubredoxin_SM Rubredoxin, Small Modular nonheme iron binding domain containing a [Fe(SCys)4] center, present in rubrerythrin and nigerythrin and detected either N- or C-terminal to such proteins as flavin reductase, NAD(P)H-nitrite reductase, and ferredoxin-thioredoxin reductase. In rubredoxin, the iron atom is coordinated by four cysteine residues (Fe(S-Cys)4), and believed to be involved in electron transfer. Rubrerythrins and nigerythrins are small homodimeric proteins, generally consisting of 2 domains: a rubredoxin domain C-terminal to a non-sulfur, oxo-bridged diiron site in the N-terminal rubrerythrin domain. Rubrerythrins and nigerythrins have putative peroxide activity.
Probab=78.91 E-value=1.1 Score=29.09 Aligned_cols=10 Identities=30% Similarity=0.923 Sum_probs=7.7
Q ss_pred CCCCCCCCCC
Q 019860 313 KRCPVTLMPA 322 (334)
Q Consensus 313 ~~CPv~~~~~ 322 (334)
..||+|+.+-
T Consensus 19 ~~CP~Cg~~~ 28 (34)
T cd00729 19 EKCPICGAPK 28 (34)
T ss_pred CcCcCCCCch
Confidence 5899998753
No 118
>KOG2169 consensus Zn-finger transcription factor [Transcription]
Probab=78.79 E-value=1.4 Score=46.97 Aligned_cols=51 Identities=24% Similarity=0.449 Sum_probs=41.4
Q ss_pred CCCCCcCCCCCCCcccccCCcccccHHHHHHHhhcC-----CCCCCCCCCCCccCee
Q 019860 277 RTICPLCSQKRANPSVVTVSGFVFCYACIFKYVSQY-----KRCPVTLMPATVEQIR 328 (334)
Q Consensus 277 ~~~CpiC~~~~~~p~~~~~~G~vfC~~Ci~~~~~~~-----~~CPv~~~~~~~~~l~ 328 (334)
+..|||+...++-|+-.-.|.|.=|.+=.. |+..+ =+||||.++...++|+
T Consensus 306 SL~CPl~~~Rm~~P~r~~~CkHlQcFD~~~-~lq~n~~~pTW~CPVC~~~~~~e~l~ 361 (636)
T KOG2169|consen 306 SLNCPLSKMRMSLPARGHTCKHLQCFDALS-YLQMNEQKPTWRCPVCQKAAPFEGLI 361 (636)
T ss_pred EecCCcccceeecCCcccccccceecchhh-hHHhccCCCeeeCccCCccccccchh
Confidence 568999999999998655699999998665 55432 3799999999888775
No 119
>PF12773 DZR: Double zinc ribbon
Probab=78.16 E-value=0.87 Score=31.57 Aligned_cols=16 Identities=31% Similarity=0.744 Sum_probs=11.7
Q ss_pred CCCCCCCCCcCCCCCC
Q 019860 273 LPPDRTICPLCSQKRA 288 (334)
Q Consensus 273 ~~~~~~~CpiC~~~~~ 288 (334)
++++...||-|+..+.
T Consensus 8 ~~~~~~fC~~CG~~l~ 23 (50)
T PF12773_consen 8 NPDDAKFCPHCGTPLP 23 (50)
T ss_pred CCccccCChhhcCChh
Confidence 4456778888888777
No 120
>KOG1940 consensus Zn-finger protein [General function prediction only]
Probab=78.10 E-value=1.4 Score=42.16 Aligned_cols=44 Identities=20% Similarity=0.527 Sum_probs=37.2
Q ss_pred CCCCCcCCCCCC----CcccccCCcccccHHHHHHHhhcCCCCCCCCCC
Q 019860 277 RTICPLCSQKRA----NPSVVTVSGFVFCYACIFKYVSQYKRCPVTLMP 321 (334)
Q Consensus 277 ~~~CpiC~~~~~----~p~~~~~~G~vfC~~Ci~~~~~~~~~CPv~~~~ 321 (334)
...||||.+-+. +|.+++ |||..=++|.-++..++-+||+|.++
T Consensus 158 ~~ncPic~e~l~~s~~~~~~~~-CgH~~h~~cf~e~~~~~y~CP~C~~~ 205 (276)
T KOG1940|consen 158 EFNCPICKEYLFLSFEDAGVLK-CGHYMHSRCFEEMICEGYTCPICSKP 205 (276)
T ss_pred cCCCchhHHHhccccccCCccC-cccchHHHHHHHHhccCCCCCcccch
Confidence 344999998754 456776 99999999999999999999999983
No 121
>TIGR00622 ssl1 transcription factor ssl1. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=78.06 E-value=3 Score=34.60 Aligned_cols=43 Identities=26% Similarity=0.481 Sum_probs=33.3
Q ss_pred CCCCCcCCCCCCCcc-------------cccCCcccccHHHHHHHhhcCCCCCCCC
Q 019860 277 RTICPLCSQKRANPS-------------VVTVSGFVFCYACIFKYVSQYKRCPVTL 319 (334)
Q Consensus 277 ~~~CpiC~~~~~~p~-------------~~~~~G~vfC~~Ci~~~~~~~~~CPv~~ 319 (334)
...|--|+.++.++. .++.|+.+||.+|=.=.-+.-+.||.|.
T Consensus 55 ~~~C~~C~~~f~~~~~~~~~~~~~~~~y~C~~C~~~FC~dCD~fiHe~Lh~CPGC~ 110 (112)
T TIGR00622 55 SRFCFGCQGPFPKPPVSPFDELKDSHRYVCAVCKNVFCVDCDVFVHESLHCCPGCI 110 (112)
T ss_pred CCcccCcCCCCCCcccccccccccccceeCCCCCCccccccchhhhhhccCCcCCC
Confidence 346999988876542 3778999999999875556668899996
No 122
>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=77.87 E-value=1.6 Score=31.12 Aligned_cols=28 Identities=18% Similarity=0.417 Sum_probs=16.3
Q ss_pred ccccCCcccccHHHHHHHhhcC-CCCCCCC
Q 019860 291 SVVTVSGFVFCYACIFKYVSQY-KRCPVTL 319 (334)
Q Consensus 291 ~~~~~~G~vfC~~Ci~~~~~~~-~~CPv~~ 319 (334)
-.++.|+.+||..|=. |+-+. ..||.|.
T Consensus 22 y~C~~C~~~FC~dCD~-fiHE~LH~CPGC~ 50 (51)
T PF07975_consen 22 YRCPKCKNHFCIDCDV-FIHETLHNCPGCE 50 (51)
T ss_dssp E--TTTT--B-HHHHH-TTTTTS-SSSTT-
T ss_pred EECCCCCCccccCcCh-hhhccccCCcCCC
Confidence 4577899999999976 55554 8999884
No 123
>PRK14714 DNA polymerase II large subunit; Provisional
Probab=77.27 E-value=1.2 Score=50.20 Aligned_cols=48 Identities=21% Similarity=0.329 Sum_probs=34.8
Q ss_pred CCCCcCCCCCCCcccccCCccc-----ccHHHHHHHhhc---CCCCCCCCCCCCccC
Q 019860 278 TICPLCSQKRANPSVVTVSGFV-----FCYACIFKYVSQ---YKRCPVTLMPATVEQ 326 (334)
Q Consensus 278 ~~CpiC~~~~~~p~~~~~~G~v-----fC~~Ci~~~~~~---~~~CPv~~~~~~~~~ 326 (334)
..||-|+..... ..|+.||.. .|-.|-.+.-.. ...||-|+.++....
T Consensus 668 rkCPkCG~~t~~-~fCP~CGs~te~vy~CPsCGaev~~des~a~~CP~CGtplv~~~ 723 (1337)
T PRK14714 668 RRCPSCGTETYE-NRCPDCGTHTEPVYVCPDCGAEVPPDESGRVECPRCDVELTPYQ 723 (1337)
T ss_pred EECCCCCCcccc-ccCcccCCcCCCceeCccCCCccCCCccccccCCCCCCcccccc
Confidence 689999997543 488889966 499998865433 348999998875433
No 124
>KOG4718 consensus Non-SMC (structural maintenance of chromosomes) element 1 protein (NSE1) [Chromatin structure and dynamics]
Probab=77.21 E-value=1 Score=41.25 Aligned_cols=45 Identities=18% Similarity=0.308 Sum_probs=38.2
Q ss_pred CCCCCCcCCCCCCCcccccCCcccccHHHHHHHhhcCCCCCCCCC
Q 019860 276 DRTICPLCSQKRANPSVVTVSGFVFCYACIFKYVSQYKRCPVTLM 320 (334)
Q Consensus 276 ~~~~CpiC~~~~~~p~~~~~~G~vfC~~Ci~~~~~~~~~CPv~~~ 320 (334)
.-..|-+|+..+.--.-|..||--|--+|+..|+.+...||-|+-
T Consensus 180 nlk~Cn~Ch~LvIqg~rCg~c~i~~h~~c~qty~q~~~~cphc~d 224 (235)
T KOG4718|consen 180 NLKNCNLCHCLVIQGIRCGSCNIQYHRGCIQTYLQRRDICPHCGD 224 (235)
T ss_pred HHHHHhHhHHHhheeeccCcccchhhhHHHHHHhcccCcCCchhc
Confidence 346899999977666556679999999999999999999999973
No 125
>COG0068 HypF Hydrogenase maturation factor [Posttranslational modification, protein turnover, chaperones]
Probab=76.47 E-value=1.1 Score=47.62 Aligned_cols=50 Identities=28% Similarity=0.460 Sum_probs=39.7
Q ss_pred CCCCCCCCCcCCCCCCCc---------ccccCCcc--------------------cccHHHHHHHhh--------cCCCC
Q 019860 273 LPPDRTICPLCSQKRANP---------SVVTVSGF--------------------VFCYACIFKYVS--------QYKRC 315 (334)
Q Consensus 273 ~~~~~~~CpiC~~~~~~p---------~~~~~~G~--------------------vfC~~Ci~~~~~--------~~~~C 315 (334)
.|+|-.+|+-|++.+.|| +.|+.||- ..|-.|-.+|-. +-..|
T Consensus 97 I~pD~a~C~~Cl~Ei~dp~~rrY~YPF~~CT~CGPRfTIi~alPYDR~nTsM~~F~lC~~C~~EY~dP~nRRfHAQp~aC 176 (750)
T COG0068 97 IPPDAATCEDCLEEIFDPNSRRYLYPFINCTNCGPRFTIIEALPYDRENTSMADFPLCPFCDKEYKDPLNRRFHAQPIAC 176 (750)
T ss_pred cCCchhhhHHHHHHhcCCCCcceeccccccCCCCcceeeeccCCCCcccCccccCcCCHHHHHHhcCccccccccccccC
Confidence 455788999999999988 46777985 459999999985 34689
Q ss_pred CCCCCCC
Q 019860 316 PVTLMPA 322 (334)
Q Consensus 316 Pv~~~~~ 322 (334)
|.||-.+
T Consensus 177 p~CGP~~ 183 (750)
T COG0068 177 PKCGPHL 183 (750)
T ss_pred cccCCCe
Confidence 9999654
No 126
>KOG1815 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=76.01 E-value=3.2 Score=42.16 Aligned_cols=55 Identities=22% Similarity=0.504 Sum_probs=38.0
Q ss_pred CCCCCCcCCCCCCCcccccCCcccccHHHHHHHhhcC--------CCCCCCCCCC--CccCeeeC
Q 019860 276 DRTICPLCSQKRANPSVVTVSGFVFCYACIFKYVSQY--------KRCPVTLMPA--TVEQIRRL 330 (334)
Q Consensus 276 ~~~~CpiC~~~~~~p~~~~~~G~vfC~~Ci~~~~~~~--------~~CPv~~~~~--~~~~l~ri 330 (334)
....|.||.+...+..+...|||.||-.|...|+..+ -+||..+-++ +.+.|.++
T Consensus 69 ~~~~c~ic~~~~~~~~~~~~c~H~~c~~cw~~yl~~kI~~~~~~~i~cp~~~C~a~v~~~~i~~~ 133 (444)
T KOG1815|consen 69 GDVQCGICVESYDGEIIGLGCGHPFCPPCWTGYLGTKIHEGEEAKIKCPAHGCPALVGEDTVEKL 133 (444)
T ss_pred ccccCCcccCCCcchhhhcCCCcHHHHHHHHHHhhheeeccccccccCCCCCccccCCCceeeee
Confidence 3568999999988744333499999999999999742 2577655443 33444443
No 127
>KOG0309 consensus Conserved WD40 repeat-containing protein [Function unknown]
Probab=75.90 E-value=1.7 Score=46.53 Aligned_cols=47 Identities=17% Similarity=0.321 Sum_probs=37.7
Q ss_pred CCCCCcCCCCCCCcc-cccCCcccccHHHHHHHhhcCCCCC-CCCCCCC
Q 019860 277 RTICPLCSQKRANPS-VVTVSGFVFCYACIFKYVSQYKRCP-VTLMPAT 323 (334)
Q Consensus 277 ~~~CpiC~~~~~~p~-~~~~~G~vfC~~Ci~~~~~~~~~CP-v~~~~~~ 323 (334)
...|.+|.-.++--+ +|-+||||.--.|..+|.+....|| .||-.+.
T Consensus 1028 ~~~C~~C~l~V~gss~~Cg~C~Hv~H~sc~~eWf~~gd~CpsGCGC~C~ 1076 (1081)
T KOG0309|consen 1028 TFQCAICHLAVRGSSNFCGTCGHVGHTSCMMEWFRTGDVCPSGCGCHCL 1076 (1081)
T ss_pred eeeeeeEeeEeeccchhhccccccccHHHHHHHHhcCCcCCCCCCcCch
Confidence 456888888877764 6777999999999999999999998 5664443
No 128
>COG5183 SSM4 Protein involved in mRNA turnover and stability [RNA processing and modification]
Probab=75.59 E-value=2.1 Score=46.19 Aligned_cols=55 Identities=20% Similarity=0.544 Sum_probs=37.3
Q ss_pred CCCCCCCCCcCCCC--CCCcc--cccCCccc--ccHHHHHHHhhcC--CCCCCCCCCCCccCe
Q 019860 273 LPPDRTICPLCSQK--RANPS--VVTVSGFV--FCYACIFKYVSQY--KRCPVTLMPATVEQI 327 (334)
Q Consensus 273 ~~~~~~~CpiC~~~--~~~p~--~~~~~G~v--fC~~Ci~~~~~~~--~~CPv~~~~~~~~~l 327 (334)
.-+|+..|-||+.. ..||- -|.++|-+ .-..|+.+|++-. .+|-+|..+.+.+++
T Consensus 8 mN~d~~~CRICr~e~~~d~pLfhPCKC~GSIkYiH~eCL~eW~~~s~~~kCdiChy~~~Fk~I 70 (1175)
T COG5183 8 MNEDKRSCRICRTEDIRDDPLFHPCKCSGSIKYIHRECLMEWMECSGTKKCDICHYEYKFKDI 70 (1175)
T ss_pred CCccchhceeecCCCCCCCcCcccccccchhHHHHHHHHHHHHhcCCCcceeeecceeeeeee
Confidence 34577899999874 33342 23324432 4569999999854 689999998876554
No 129
>PLN02400 cellulose synthase
Probab=75.48 E-value=1.6 Score=48.74 Aligned_cols=46 Identities=20% Similarity=0.498 Sum_probs=35.3
Q ss_pred CCCCCCcCCCCCCC-----c-ccccCCcccccHHHHHHHhhc--CCCCCCCCCCC
Q 019860 276 DRTICPLCSQKRAN-----P-SVVTVSGFVFCYACIFKYVSQ--YKRCPVTLMPA 322 (334)
Q Consensus 276 ~~~~CpiC~~~~~~-----p-~~~~~~G~vfC~~Ci~~~~~~--~~~CPv~~~~~ 322 (334)
...+|-||++.+-- + ++|..||+--|.+|- +|=++ ++.||-|+.+-
T Consensus 35 ~gqiCqICGD~VG~t~dGe~FVAC~eCaFPVCRpCY-EYERkeGnq~CPQCkTrY 88 (1085)
T PLN02400 35 NGQICQICGDDVGVTETGDVFVACNECAFPVCRPCY-EYERKDGTQCCPQCKTRY 88 (1085)
T ss_pred CCceeeecccccCcCCCCCEEEEEccCCCccccchh-heecccCCccCcccCCcc
Confidence 35689999998532 2 578889999999998 56544 57899998553
No 130
>KOG2034 consensus Vacuolar sorting protein PEP3/VPS18 [Intracellular trafficking, secretion, and vesicular transport]
Probab=75.32 E-value=1.4 Score=47.92 Aligned_cols=34 Identities=24% Similarity=0.448 Sum_probs=28.3
Q ss_pred CCCCCcCCCCCCC-cccccCCcccccHHHHHHHhh
Q 019860 277 RTICPLCSQKRAN-PSVVTVSGFVFCYACIFKYVS 310 (334)
Q Consensus 277 ~~~CpiC~~~~~~-p~~~~~~G~vfC~~Ci~~~~~ 310 (334)
...|-+|+.++-. |-++-+|||.|-..|+.+.+.
T Consensus 817 ~d~C~~C~~~ll~~pF~vf~CgH~FH~~Cl~~~v~ 851 (911)
T KOG2034|consen 817 QDSCDHCGRPLLIKPFYVFPCGHCFHRDCLIRHVL 851 (911)
T ss_pred ccchHHhcchhhcCcceeeeccchHHHHHHHHHHH
Confidence 5689999999765 655556999999999999984
No 131
>COG5109 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=75.22 E-value=1.8 Score=42.01 Aligned_cols=54 Identities=22% Similarity=0.345 Sum_probs=40.8
Q ss_pred CCCCCcCCCCC--CCc-ccccCCcccccHHHHHHHhhc---CCCCCCCCCCCCccCeeeCc
Q 019860 277 RTICPLCSQKR--ANP-SVVTVSGFVFCYACIFKYVSQ---YKRCPVTLMPATVEQIRRLF 331 (334)
Q Consensus 277 ~~~CpiC~~~~--~~p-~~~~~~G~vfC~~Ci~~~~~~---~~~CPv~~~~~~~~~l~ri~ 331 (334)
-.+||+-.+.- +|| .++. ||||--..-+...-++ .-+||-|-.....++++|+|
T Consensus 336 ~FiCPVlKe~~t~ENpP~ml~-CgHVIskeal~~LS~nG~~~FKCPYCP~~~~~~~~~rvr 395 (396)
T COG5109 336 LFICPVLKELCTDENPPVMLE-CGHVISKEALSVLSQNGVLSFKCPYCPEMSKYENILRVR 395 (396)
T ss_pred eeeccccHhhhcccCCCeeee-ccceeeHHHHHHHhhcCcEEeeCCCCCcchhhhhhhccc
Confidence 57999987754 455 5666 9999998877654432 24899999888888888886
No 132
>COG5627 MMS21 DNA repair protein MMS21 [DNA replication, recombination, and repair]
Probab=74.89 E-value=1.7 Score=40.38 Aligned_cols=41 Identities=17% Similarity=0.223 Sum_probs=36.3
Q ss_pred CCCCCcCCCCCCCcccccCCcccccHHHHHHHhhcC--CCCCC
Q 019860 277 RTICPLCSQKRANPSVVTVSGFVFCYACIFKYVSQY--KRCPV 317 (334)
Q Consensus 277 ~~~CpiC~~~~~~p~~~~~~G~vfC~~Ci~~~~~~~--~~CPv 317 (334)
.+.|||..++...|.+-+.|.|+|-.+-|.+++... ..||+
T Consensus 189 ~nrCpitl~p~~~pils~kcnh~~e~D~I~~~lq~~~trvcp~ 231 (275)
T COG5627 189 SNRCPITLNPDFYPILSSKCNHKPEMDLINKKLQVECTRVCPR 231 (275)
T ss_pred cccCCcccCcchhHHHHhhhcccccHHHHHHHhcCCceeecch
Confidence 679999999999998877799999999999999954 67884
No 133
>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=74.82 E-value=1.2 Score=41.65 Aligned_cols=45 Identities=24% Similarity=0.527 Sum_probs=34.5
Q ss_pred CCCCCcCCCCC-CCcc----cccCCcccccHHHHHHHhhc-CCCCC--CCCCC
Q 019860 277 RTICPLCSQKR-ANPS----VVTVSGFVFCYACIFKYVSQ-YKRCP--VTLMP 321 (334)
Q Consensus 277 ~~~CpiC~~~~-~~p~----~~~~~G~vfC~~Ci~~~~~~-~~~CP--v~~~~ 321 (334)
...||+|...+ -||- +-+.|-|-+|-.|..+-+.. ...|| .|++-
T Consensus 10 d~~CPvCksDrYLnPdik~linPECyHrmCESCvdRIFs~GpAqCP~~gC~kI 62 (314)
T COG5220 10 DRRCPVCKSDRYLNPDIKILINPECYHRMCESCVDRIFSRGPAQCPYKGCGKI 62 (314)
T ss_pred cccCCccccccccCCCeEEEECHHHHHHHHHHHHHHHhcCCCCCCCCccHHHH
Confidence 45899999864 6772 33449999999999998875 47899 78643
No 134
>KOG2042 consensus Ubiquitin fusion degradation protein-2 [Posttranslational modification, protein turnover, chaperones]
Probab=74.58 E-value=2.6 Score=46.42 Aligned_cols=54 Identities=20% Similarity=0.181 Sum_probs=50.4
Q ss_pred CCCCCCcCCCCCCCcccccCCcccccHHHHHHHhhcCCCCCCCCCCCCccCeee
Q 019860 276 DRTICPLCSQKRANPSVVTVSGFVFCYACIFKYVSQYKRCPVTLMPATVEQIRR 329 (334)
Q Consensus 276 ~~~~CpiC~~~~~~p~~~~~~G~vfC~~Ci~~~~~~~~~CPv~~~~~~~~~l~r 329 (334)
|...=|+-...+.||++++.+|++.|+.=|..++-...+-|.|+.|++.+++..
T Consensus 869 def~DPlm~Tlm~dPV~LP~Srv~vDRsti~rhlLs~~tdPFNR~pLt~d~v~p 922 (943)
T KOG2042|consen 869 DEFLDPLMSTLMSDPVVLPSSRVTVDRSTIERHLLSDCTDPFNREPLTEDMVSP 922 (943)
T ss_pred hhhhCccccccCCCCccCCcccccccHHHHHHHHhcCCCCccccccCchhhcCC
Confidence 677889999999999999999999999999999999999999999999888763
No 135
>KOG0825 consensus PHD Zn-finger protein [General function prediction only]
Probab=73.72 E-value=2.2 Score=45.99 Aligned_cols=44 Identities=14% Similarity=0.190 Sum_probs=32.5
Q ss_pred CCCCCCcCCCCCCCc------ccccCCcccccHHHHHHHhhc------CCCCCCCC
Q 019860 276 DRTICPLCSQKRANP------SVVTVSGFVFCYACIFKYVSQ------YKRCPVTL 319 (334)
Q Consensus 276 ~~~~CpiC~~~~~~p------~~~~~~G~vfC~~Ci~~~~~~------~~~CPv~~ 319 (334)
+...|++|.....+| +.+..|||-+|+.||..|..+ +-.|+.|.
T Consensus 95 ~s~Ss~~C~~E~S~~~ds~~i~P~~~~~~~~CP~Ci~s~~DqL~~~~k~c~H~FC~ 150 (1134)
T KOG0825|consen 95 ESDTSPVCEKEHSPDVDSSNICPVQTHVENQCPNCLKSCNDQLEESEKHTAHYFCE 150 (1134)
T ss_pred cccccchhheecCCcccccCcCchhhhhhhhhhHHHHHHHHHhhccccccccccHH
Confidence 567788888877774 344569999999999999974 23456664
No 136
>PHA02862 5L protein; Provisional
Probab=73.71 E-value=2.8 Score=36.23 Aligned_cols=47 Identities=17% Similarity=0.256 Sum_probs=33.4
Q ss_pred CCCCCcCCCCC---CCcccccCCcccccHHHHHHHhhcC--CCCCCCCCCCC
Q 019860 277 RTICPLCSQKR---ANPSVVTVSGFVFCYACIFKYVSQY--KRCPVTLMPAT 323 (334)
Q Consensus 277 ~~~CpiC~~~~---~~p~~~~~~G~vfC~~Ci~~~~~~~--~~CPv~~~~~~ 323 (334)
..+|=||.+.- .+|+.|+-+--.--..|+.+|+..+ ..||.|+.+-.
T Consensus 2 ~diCWIC~~~~~e~~~PC~C~GS~K~VHq~CL~~WIn~S~k~~CeLCkteY~ 53 (156)
T PHA02862 2 SDICWICNDVCDERNNFCGCNEEYKVVHIKCMQLWINYSKKKECNLCKTKYN 53 (156)
T ss_pred CCEEEEecCcCCCCcccccccCcchhHHHHHHHHHHhcCCCcCccCCCCeEE
Confidence 35799998863 3455554334445579999999864 68999997754
No 137
>PF04423 Rad50_zn_hook: Rad50 zinc hook motif; InterPro: IPR007517 The Mre11 complex (Mre11 Rad50 Nbs1) is central to chromosomal maintenance and functions in homologous recombination, telomere maintenance and sister chromatid association. The Rad50 coiled-coil region contains a dimer interface at the apex of the coiled coils in which pairs of conserved Cys-X-X-Cys motifs form interlocking hooks that bind one Zn ion. This alignment includes the zinc hook motif and a short stretch of coiled-coil on either side.; GO: 0004518 nuclease activity, 0005524 ATP binding, 0008270 zinc ion binding, 0006281 DNA repair; PDB: 1L8D_B.
Probab=73.16 E-value=0.7 Score=32.89 Aligned_cols=14 Identities=29% Similarity=0.484 Sum_probs=7.3
Q ss_pred CCCCCCCCCCCccC
Q 019860 313 KRCPVTLMPATVEQ 326 (334)
Q Consensus 313 ~~CPv~~~~~~~~~ 326 (334)
+.||||+.+++.++
T Consensus 21 ~~CPlC~r~l~~e~ 34 (54)
T PF04423_consen 21 GCCPLCGRPLDEEH 34 (54)
T ss_dssp EE-TTT--EE-HHH
T ss_pred CcCCCCCCCCCHHH
Confidence 49999999887543
No 138
>PHA02825 LAP/PHD finger-like protein; Provisional
Probab=73.09 E-value=3.7 Score=36.06 Aligned_cols=48 Identities=15% Similarity=0.356 Sum_probs=33.0
Q ss_pred CCCCCCcCCCCC---CCcccccCCc--ccccHHHHHHHhhcC--CCCCCCCCCCCcc
Q 019860 276 DRTICPLCSQKR---ANPSVVTVSG--FVFCYACIFKYVSQY--KRCPVTLMPATVE 325 (334)
Q Consensus 276 ~~~~CpiC~~~~---~~p~~~~~~G--~vfC~~Ci~~~~~~~--~~CPv~~~~~~~~ 325 (334)
....|-||.+.- .+|+-| .| -.--..|+.+|+... ..|+.|+.+-...
T Consensus 7 ~~~~CRIC~~~~~~~~~PC~C--kGs~k~VH~sCL~rWi~~s~~~~CeiC~~~Y~i~ 61 (162)
T PHA02825 7 MDKCCWICKDEYDVVTNYCNC--KNENKIVHKECLEEWINTSKNKSCKICNGPYNIK 61 (162)
T ss_pred CCCeeEecCCCCCCccCCccc--CCCchHHHHHHHHHHHhcCCCCcccccCCeEEEE
Confidence 356899998864 445444 34 122469999999865 6899999775433
No 139
>PF06750 DiS_P_DiS: Bacterial Peptidase A24 N-terminal domain; InterPro: IPR010627 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Aspartic endopeptidases 3.4.23. from EC of vertebrate, fungal and retroviral origin have been characterised []. More recently, aspartic endopeptidases associated with the processing of bacterial type 4 prepilin [] and archaean preflagellin have been described [, ]. Structurally, aspartic endopeptidases are bilobal enzymes, each lobe contributing a catalytic Asp residue, with an extended active site cleft localised between the two lobes of the molecule. One lobe has probably evolved from the other through a gene duplication event in the distant past. In modern-day enzymes, although the three-dimensional structures are very similar, the amino acid sequences are more divergent, except for the catalytic site motif, which is very conserved. The presence and position of disulphide bridges are other conserved features of aspartic peptidases. All or most aspartate peptidases are endopeptidases. These enzymes have been assigned into clans (proteins which are evolutionary related), and further sub-divided into families, largely on the basis of their tertiary structure. This domain is found at the N terminus of bacterial aspartic peptidases belonging to MEROPS peptidase family A24 (clan AD), subfamily A24A (type IV prepilin peptidase, IPR000045 from INTERPRO). It's function has not been specifically determined; however some of the family have been characterised as bifunctional [], and this domain may contain the N-methylation activity. The domain consists of an intracellular region between a pair of transmembrane domains. This intracellular region contains an invariant proline and four conserved cysteines. These Cys residues are arranged in a two-pair motif, with the Cys residues of a pair separated (usually) by 2 aa and with each pair separated by 21 largely hydrophilic residues (C-X-X-C...X21...C-X-X-C); they have been shown to be essential to the overall function of the enzyme [, ]. The bifunctional enzyme prepilin peptidase (PilD) from Pseudomonas aeruginosa is a key determinant in both type-IV pilus biogenesis and extracellular protein secretion, in its roles as a leader peptidase and methyl transferase (MTase). It is responsible for endopeptidic cleavage of the unique leader peptides that characterise type-IV pilin precursors, as well as proteins with homologous leader sequences that are essential components of the general secretion pathway found in a variety of Gram-negative pathogens. Following removal of the leader peptides, the same enzyme is responsible for the second posttranslational modification that characterises the type-IV pilins and their homologues, namely N-methylation of the newly exposed N-terminal amino acid residue [].
Probab=71.14 E-value=5.3 Score=31.81 Aligned_cols=38 Identities=24% Similarity=0.460 Sum_probs=32.0
Q ss_pred CCCCCcCCCCCCCcccccCCcccccHHHHHHHhhcCCCCCCCCCCCCc
Q 019860 277 RTICPLCSQKRANPSVVTVSGFVFCYACIFKYVSQYKRCPVTLMPATV 324 (334)
Q Consensus 277 ~~~CpiC~~~~~~p~~~~~~G~vfC~~Ci~~~~~~~~~CPv~~~~~~~ 324 (334)
...|+-|++++.=--.+| |..|+-..|+|.-|+.+...
T Consensus 33 rS~C~~C~~~L~~~~lIP----------i~S~l~lrGrCr~C~~~I~~ 70 (92)
T PF06750_consen 33 RSHCPHCGHPLSWWDLIP----------ILSYLLLRGRCRYCGAPIPP 70 (92)
T ss_pred CCcCcCCCCcCcccccch----------HHHHHHhCCCCcccCCCCCh
Confidence 458999999987766667 77799999999999998764
No 140
>PF03833 PolC_DP2: DNA polymerase II large subunit DP2; InterPro: IPR016033 DP2 is the large subunit of a two-subunit novel archaebacterial replicative DNA polymerase first characterised for Pyrococcus furiosus. The structure of DP2 appears to be organised as a ~950 residue component separated from a ~300 residue component by a ~150 residue intein. The other subunit, DP1, has sequence similarity to the eukaryotic DNA polymerase delta small subunit. This entry represents the N-terminal ~950 residue component of DP2.; GO: 0003887 DNA-directed DNA polymerase activity; PDB: 3O59_X.
Probab=71.04 E-value=1.3 Score=48.00 Aligned_cols=44 Identities=23% Similarity=0.419 Sum_probs=0.0
Q ss_pred CCCCCcCCCCCCCcccccCCccc-----ccHHHHHHHhhcCCCCCCCCCCCC
Q 019860 277 RTICPLCSQKRANPSVVTVSGFV-----FCYACIFKYVSQYKRCPVTLMPAT 323 (334)
Q Consensus 277 ~~~CpiC~~~~~~p~~~~~~G~v-----fC~~Ci~~~~~~~~~CPv~~~~~~ 323 (334)
...||-|+..- .-..|+.||-. +|..|-.+.-. ..||-|+.+.+
T Consensus 655 ~r~Cp~Cg~~t-~~~~Cp~CG~~T~~~~~Cp~C~~~~~~--~~C~~C~~~~~ 703 (900)
T PF03833_consen 655 RRRCPKCGKET-FYNRCPECGSHTEPVYVCPDCGIEVEE--DECPKCGRETT 703 (900)
T ss_dssp ----------------------------------------------------
T ss_pred cccCcccCCcc-hhhcCcccCCccccceeccccccccCc--cccccccccCc
Confidence 56899999863 23456668865 89999987654 49999997754
No 141
>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=70.25 E-value=2.4 Score=31.11 Aligned_cols=16 Identities=31% Similarity=0.534 Sum_probs=11.5
Q ss_pred hcCCCCCCCCCCCCcc
Q 019860 310 SQYKRCPVTLMPATVE 325 (334)
Q Consensus 310 ~~~~~CPv~~~~~~~~ 325 (334)
+.|+.||+||.|+..+
T Consensus 1 e~HkHC~~CG~~Ip~~ 16 (59)
T PF09889_consen 1 EPHKHCPVCGKPIPPD 16 (59)
T ss_pred CCCCcCCcCCCcCCcc
Confidence 3577888888877654
No 142
>KOG2114 consensus Vacuolar assembly/sorting protein PEP5/VPS11 [Intracellular trafficking, secretion, and vesicular transport]
Probab=69.95 E-value=2.3 Score=46.11 Aligned_cols=40 Identities=23% Similarity=0.497 Sum_probs=35.8
Q ss_pred CCCCcCCCCCCCcccccCCcccccHHHHHHHhhcCCCCCCCCC
Q 019860 278 TICPLCSQKRANPSVVTVSGFVFCYACIFKYVSQYKRCPVTLM 320 (334)
Q Consensus 278 ~~CpiC~~~~~~p~~~~~~G~vfC~~Ci~~~~~~~~~CPv~~~ 320 (334)
.+|..|..++.-|+|-=.|||.|--.|.- ....+||-|.-
T Consensus 841 skCs~C~~~LdlP~VhF~CgHsyHqhC~e---~~~~~CP~C~~ 880 (933)
T KOG2114|consen 841 SKCSACEGTLDLPFVHFLCGHSYHQHCLE---DKEDKCPKCLP 880 (933)
T ss_pred eeecccCCccccceeeeecccHHHHHhhc---cCcccCCccch
Confidence 58999999999999865699999999998 66789999985
No 143
>PF05605 zf-Di19: Drought induced 19 protein (Di19), zinc-binding; InterPro: IPR008598 This entry consists of several drought induced 19 (Di19) like and RING finger 114 proteins. Di19 has been found to be strongly expressed in both the roots and leaves of Arabidopsis thaliana during progressive drought [], whilst RING finger proteins are thought to play a role in spermatogenesis. The precise function is unknown.
Probab=69.31 E-value=2.8 Score=29.74 Aligned_cols=40 Identities=28% Similarity=0.469 Sum_probs=23.4
Q ss_pred CCCCCCcCCCCCCCcccccCCcccccHHHHHHHhhc--CCCCCCCCCCCC
Q 019860 276 DRTICPLCSQKRANPSVVTVSGFVFCYACIFKYVSQ--YKRCPVTLMPAT 323 (334)
Q Consensus 276 ~~~~CpiC~~~~~~p~~~~~~G~vfC~~Ci~~~~~~--~~~CPv~~~~~~ 323 (334)
+...||.|++.+...... .=|..++-.+ ...||+|....+
T Consensus 1 ~~f~CP~C~~~~~~~~L~--------~H~~~~H~~~~~~v~CPiC~~~~~ 42 (54)
T PF05605_consen 1 DSFTCPYCGKGFSESSLV--------EHCEDEHRSESKNVVCPICSSRVT 42 (54)
T ss_pred CCcCCCCCCCccCHHHHH--------HHHHhHCcCCCCCccCCCchhhhh
Confidence 357899999954333322 2333444432 357999987543
No 144
>KOG0883 consensus Cyclophilin type, U box-containing peptidyl-prolyl cis-trans isomerase [Posttranslational modification, protein turnover, chaperones]
Probab=68.02 E-value=3.3 Score=41.28 Aligned_cols=58 Identities=17% Similarity=0.145 Sum_probs=45.6
Q ss_pred CCCCCCCcCCCCCCCc---ccccCCcccccHHHHHHHhh--cCCCCCCCCCCCCccCeeeCcc
Q 019860 275 PDRTICPLCSQKRANP---SVVTVSGFVFCYACIFKYVS--QYKRCPVTLMPATVEQIRRLFH 332 (334)
Q Consensus 275 ~~~~~CpiC~~~~~~p---~~~~~~G~vfC~~Ci~~~~~--~~~~CPv~~~~~~~~~l~ri~~ 332 (334)
.+.+.||+-.+..++- +++.++|.||||.-|.+.=- .|-+--++..|.+.+|||-|=.
T Consensus 99 ~geyhcPvlfk~FT~~sHIvAv~TTGNvy~~eai~~LNiK~knwkdLltdepFtR~DiItiQd 161 (518)
T KOG0883|consen 99 EGEYHCPVLFKVFTRFSHIVAVRTTGNVYSWEAIEELNIKTKNWKDLLTDEPFTRADIITIQD 161 (518)
T ss_pred CCcccCceeeeeecccceEEEEEecCceeeHHHHHHhCcchhhHHHhhccCCcchhceeeecC
Confidence 4578999999999886 35567999999999987543 2346678888999999987754
No 145
>KOG1815 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=67.85 E-value=2.5 Score=43.01 Aligned_cols=18 Identities=28% Similarity=0.512 Sum_probs=13.7
Q ss_pred cccccCCcccccHHHHHHH
Q 019860 290 PSVVTVSGFVFCYACIFKY 308 (334)
Q Consensus 290 p~~~~~~G~vfC~~Ci~~~ 308 (334)
++.+. |||.||+.|..+|
T Consensus 179 ~v~C~-~g~~FC~~C~~~~ 196 (444)
T KOG1815|consen 179 EVDCG-CGHEFCFACGEES 196 (444)
T ss_pred ceeCC-CCchhHhhccccc
Confidence 46676 9999999986554
No 146
>KOG0269 consensus WD40 repeat-containing protein [Function unknown]
Probab=67.38 E-value=4.6 Score=43.40 Aligned_cols=50 Identities=10% Similarity=0.094 Sum_probs=41.8
Q ss_pred CCCCCcCCCCCCCcc-cccCCcccccHHHHHHHhhcCCCCCC--CCCCCCccC
Q 019860 277 RTICPLCSQKRANPS-VVTVSGFVFCYACIFKYVSQYKRCPV--TLMPATVEQ 326 (334)
Q Consensus 277 ~~~CpiC~~~~~~p~-~~~~~G~vfC~~Ci~~~~~~~~~CPv--~~~~~~~~~ 326 (334)
...|-+|.-.++.-. -++.|||..--.|+.+|...+..||. |+.++....
T Consensus 779 ~~~CtVC~~vi~G~~~~c~~C~H~gH~sh~~sw~~~~s~ca~~~C~~~c~~~~ 831 (839)
T KOG0269|consen 779 SAKCTVCDLVIRGVDVWCQVCGHGGHDSHLKSWFFKASPCAKSICPHLCHYSS 831 (839)
T ss_pred hcCceeecceeeeeEeecccccccccHHHHHHHHhcCCCCccccCCccccccc
Confidence 458999999988864 47889999999999999999999975 887765443
No 147
>PF04641 Rtf2: Rtf2 RING-finger
Probab=66.16 E-value=8.2 Score=36.38 Aligned_cols=54 Identities=22% Similarity=0.377 Sum_probs=40.3
Q ss_pred CCCCCcCCCCCCCcccccCCcccccHHHHHHHhhcCCC---CCCCCCCC-CccCeeeC
Q 019860 277 RTICPLCSQKRANPSVVTVSGFVFCYACIFKYVSQYKR---CPVTLMPA-TVEQIRRL 330 (334)
Q Consensus 277 ~~~CpiC~~~~~~p~~~~~~G~vfC~~Ci~~~~~~~~~---CPv~~~~~-~~~~l~ri 330 (334)
=..|+|.++++..|.|+-.-|++|-+.=|++||...+. =|.....+ +++||+.|
T Consensus 34 w~~CaLS~~pL~~PiV~d~~G~LynKeaile~Ll~~~~~~~~~~~~~hI~~LKDl~~l 91 (260)
T PF04641_consen 34 WTHCALSQQPLEDPIVSDRLGRLYNKEAILEFLLDKKKNKDLPKTFSHIKSLKDLVEL 91 (260)
T ss_pred cCcccCcCCccCCCeeeCCCCeeEcHHHHHHHHHhcCcCCCCccccccccCccceeeE
Confidence 46899999999999875559999999999999987642 23333333 46666654
No 148
>PF10497 zf-4CXXC_R1: Zinc-finger domain of monoamine-oxidase A repressor R1; InterPro: IPR018866 R1 is a transcription factor repressor that inhibits monoamine oxidase A gene expression. This domain is a four-CXXC zinc finger putative DNA-binding domain found at the C-terminal end of R1. The domain carries 12 cysteines of which four pairs are of the CXXC type [].
Probab=65.89 E-value=7.6 Score=31.69 Aligned_cols=44 Identities=20% Similarity=0.409 Sum_probs=30.9
Q ss_pred CCCCCcCCCCCCCc-ccc------cCC---cccccHHHHHHHhhc---------CCCCCCCCC
Q 019860 277 RTICPLCSQKRANP-SVV------TVS---GFVFCYACIFKYVSQ---------YKRCPVTLM 320 (334)
Q Consensus 277 ~~~CpiC~~~~~~p-~~~------~~~---G~vfC~~Ci~~~~~~---------~~~CPv~~~ 320 (334)
...|..|.+.-.+. +.+ +.| .-.||+.|+.....+ +-.||.|+-
T Consensus 7 g~~CHqCrqKt~~~~~~C~~~~~~~~C~~~~~~fC~~CL~~ryge~~~ev~~~~~W~CP~Crg 69 (105)
T PF10497_consen 7 GKTCHQCRQKTLDFKTICTGHWKNSSCRGCRGKFCGGCLRNRYGENVEEVLEDPNWKCPKCRG 69 (105)
T ss_pred CCCchhhcCCCCCCceEcCCCCCCCCCccCcceehHhHHHHHHhhhHHHHhcCCceECCCCCC
Confidence 45788888865554 344 445 778999998877643 357999864
No 149
>KOG4739 consensus Uncharacterized protein involved in synaptonemal complex formation [Cell cycle control, cell division, chromosome partitioning; General function prediction only]
Probab=65.78 E-value=2.9 Score=38.98 Aligned_cols=33 Identities=24% Similarity=0.508 Sum_probs=23.4
Q ss_pred CCCCcCCCCC-CCcccccCCcccccHHHHHHHhh
Q 019860 278 TICPLCSQKR-ANPSVVTVSGFVFCYACIFKYVS 310 (334)
Q Consensus 278 ~~CpiC~~~~-~~p~~~~~~G~vfC~~Ci~~~~~ 310 (334)
..|-.|.... .+|--++-|+||||-+|.-.-..
T Consensus 4 VhCn~C~~~~~~~~f~LTaC~HvfC~~C~k~~~~ 37 (233)
T KOG4739|consen 4 VHCNKCFRFPSQDPFFLTACRHVFCEPCLKASSP 37 (233)
T ss_pred EEeccccccCCCCceeeeechhhhhhhhcccCCc
Confidence 4577777643 55655556999999999865554
No 150
>COG3357 Predicted transcriptional regulator containing an HTH domain fused to a Zn-ribbon [Transcription]
Probab=65.39 E-value=2.5 Score=33.70 Aligned_cols=29 Identities=24% Similarity=0.432 Sum_probs=16.9
Q ss_pred CCcccccCCcccccHHHHHHHhhcCCCCCCCCC
Q 019860 288 ANPSVVTVSGFVFCYACIFKYVSQYKRCPVTLM 320 (334)
Q Consensus 288 ~~p~~~~~~G~vfC~~Ci~~~~~~~~~CPv~~~ 320 (334)
..|+.|..|||+|=- +-++.-.+||.|..
T Consensus 56 v~Pa~CkkCGfef~~----~~ik~pSRCP~CKS 84 (97)
T COG3357 56 VRPARCKKCGFEFRD----DKIKKPSRCPKCKS 84 (97)
T ss_pred ecChhhcccCccccc----cccCCcccCCcchh
Confidence 335555567776643 23444568888864
No 151
>COG1645 Uncharacterized Zn-finger containing protein [General function prediction only]
Probab=64.36 E-value=2.4 Score=36.06 Aligned_cols=24 Identities=33% Similarity=0.703 Sum_probs=16.9
Q ss_pred CCCCCcCCCCCCCcccccCCcccccHHHH
Q 019860 277 RTICPLCSQKRANPSVVTVSGFVFCYACI 305 (334)
Q Consensus 277 ~~~CpiC~~~~~~p~~~~~~G~vfC~~Ci 305 (334)
...||.|+-++-. . .|-|||--|-
T Consensus 28 ~~hCp~Cg~PLF~----K-dG~v~CPvC~ 51 (131)
T COG1645 28 AKHCPKCGTPLFR----K-DGEVFCPVCG 51 (131)
T ss_pred HhhCcccCCccee----e-CCeEECCCCC
Confidence 3579999998755 3 7877764443
No 152
>KOG1356 consensus Putative transcription factor 5qNCA, contains JmjC domain [Transcription]
Probab=63.48 E-value=1.9 Score=46.73 Aligned_cols=45 Identities=22% Similarity=0.531 Sum_probs=35.3
Q ss_pred CCCCCcCCCCCCC-cccccCCcccccHHHHHHHh----hc--CCCCCCCCCC
Q 019860 277 RTICPLCSQKRAN-PSVVTVSGFVFCYACIFKYV----SQ--YKRCPVTLMP 321 (334)
Q Consensus 277 ~~~CpiC~~~~~~-p~~~~~~G~vfC~~Ci~~~~----~~--~~~CPv~~~~ 321 (334)
..+|-.|.+.+.| -=+|+.||+.+|.+|+..|- ++ -.+|+-|...
T Consensus 229 ~~mC~~C~~tlfn~hw~C~~C~~~~Cl~C~r~~~p~~~~~e~a~k~~~~~~~ 280 (889)
T KOG1356|consen 229 REMCDRCETTLFNIHWRCPRCGFGVCLDCYRKWYPRLSKEEVAEKCEFSWLK 280 (889)
T ss_pred chhhhhhcccccceeEEccccCCeeeecchhhccccchHhHhhhhhhHHHHh
Confidence 5689999999998 56899999999999999994 11 2567755443
No 153
>PF15616 TerY-C: TerY-C metal binding domain
Probab=63.12 E-value=2.8 Score=35.67 Aligned_cols=40 Identities=25% Similarity=0.444 Sum_probs=29.3
Q ss_pred CCCcCCCCCCCcccccCCcccccHHHHHHHhhcCCCCCCCCCCCCcc
Q 019860 279 ICPLCSQKRANPSVVTVSGFVFCYACIFKYVSQYKRCPVTLMPATVE 325 (334)
Q Consensus 279 ~CpiC~~~~~~p~~~~~~G~vfC~~Ci~~~~~~~~~CPv~~~~~~~~ 325 (334)
-||-|+...-= +++. ||.+||+.= .+...||-|+......
T Consensus 79 gCP~CGn~~~f-a~C~-CGkl~Ci~g-----~~~~~CPwCg~~g~~~ 118 (131)
T PF15616_consen 79 GCPHCGNQYAF-AVCG-CGKLFCIDG-----EGEVTCPWCGNEGSFG 118 (131)
T ss_pred CCCCCcChhcE-EEec-CCCEEEeCC-----CCCEECCCCCCeeeec
Confidence 69999986422 4665 999999752 3357899999876543
No 154
>KOG4445 consensus Uncharacterized conserved protein, contains RWD domain [Function unknown]
Probab=62.98 E-value=2.1 Score=41.17 Aligned_cols=47 Identities=23% Similarity=0.532 Sum_probs=35.9
Q ss_pred CCCCCcCCCCCCC-c--ccccCCcccccHHHHHHHhh-----------------------cCCCCCCCCCCCCc
Q 019860 277 RTICPLCSQKRAN-P--SVVTVSGFVFCYACIFKYVS-----------------------QYKRCPVTLMPATV 324 (334)
Q Consensus 277 ~~~CpiC~~~~~~-p--~~~~~~G~vfC~~Ci~~~~~-----------------------~~~~CPv~~~~~~~ 324 (334)
.+.|.||+--+.+ | +++. |-|-|-..|.-+||. ..-.||||+.++..
T Consensus 115 ~gqCvICLygfa~~~~ft~T~-C~Hy~H~~ClaRyl~~~~~~lrqe~q~~~~~~qh~~~~~eavcpVcre~i~~ 187 (368)
T KOG4445|consen 115 NGQCVICLYGFASSPAFTVTA-CDHYMHFACLARYLTECLTGLRQEIQDAQKERQHMKEQVEAVCPVCRERIKI 187 (368)
T ss_pred CCceEEEEEeecCCCceeeeh-hHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhHhhhhhHhhhhccc
Confidence 4579999987766 3 4554 999999999999994 12369999988753
No 155
>KOG4362 consensus Transcriptional regulator BRCA1 [Replication, recombination and repair; Transcription]
Probab=62.94 E-value=2 Score=45.73 Aligned_cols=46 Identities=22% Similarity=0.485 Sum_probs=36.8
Q ss_pred CCCCCcCCCCCCCcccccCCcccccHHHHHHHhh---cCCCCCCCCCCCC
Q 019860 277 RTICPLCSQKRANPSVVTVSGFVFCYACIFKYVS---QYKRCPVTLMPAT 323 (334)
Q Consensus 277 ~~~CpiC~~~~~~p~~~~~~G~vfC~~Ci~~~~~---~~~~CPv~~~~~~ 323 (334)
.-.||||...+..|+-+. |-|.||.-|+..-+. ....||+|+.-.+
T Consensus 21 ~lEc~ic~~~~~~p~~~k-c~~~~l~~~~n~~f~~~~~~~~~~lc~~~~e 69 (684)
T KOG4362|consen 21 ILECPICLEHVKEPSLLK-CDHIFLKFCLNKLFESKKGPKQCALCKSDIE 69 (684)
T ss_pred hccCCceeEEeeccchhh-hhHHHHhhhhhceeeccCccccchhhhhhhh
Confidence 457999999999997665 999999999876554 3578999984443
No 156
>PF09986 DUF2225: Uncharacterized protein conserved in bacteria (DUF2225); InterPro: IPR018708 This conserved bacterial family has no known function.
Probab=62.44 E-value=2.3 Score=39.07 Aligned_cols=55 Identities=20% Similarity=0.324 Sum_probs=33.3
Q ss_pred CCCCCCCcCCCCCCCcccccCCccc------ccHH--HHHHHhhcCCCCCCCCCCCCccCeee
Q 019860 275 PDRTICPLCSQKRANPSVVTVSGFV------FCYA--CIFKYVSQYKRCPVTLMPATVEQIRR 329 (334)
Q Consensus 275 ~~~~~CpiC~~~~~~p~~~~~~G~v------fC~~--Ci~~~~~~~~~CPv~~~~~~~~~l~r 329 (334)
+.+..||+|++..+...|.+..+.+ ||.. =+..++=.-..||.||.....++.-+
T Consensus 3 ~k~~~CPvC~~~F~~~~vrs~~~r~~~~d~D~~~~Y~~vnP~~Y~V~vCP~CgyA~~~~~F~~ 65 (214)
T PF09986_consen 3 DKKITCPVCGKEFKTKKVRSGKIRVIRRDSDFCPRYKGVNPLFYEVWVCPHCGYAAFEEDFEK 65 (214)
T ss_pred CCceECCCCCCeeeeeEEEcCCceEeeecCCCccccCCCCCeeeeEEECCCCCCccccccccc
Confidence 4567899999999988876533333 2221 01111112358999998877665443
No 157
>smart00647 IBR In Between Ring fingers. the domains occurs between pairs og RING fingers
Probab=62.03 E-value=2.1 Score=30.71 Aligned_cols=18 Identities=28% Similarity=0.853 Sum_probs=14.3
Q ss_pred ccccCCcccccHHHHHHH
Q 019860 291 SVVTVSGFVFCYACIFKY 308 (334)
Q Consensus 291 ~~~~~~G~vfC~~Ci~~~ 308 (334)
+.++.||+.||+.|-..|
T Consensus 41 v~C~~C~~~fC~~C~~~~ 58 (64)
T smart00647 41 VTCPKCGFSFCFRCKVPW 58 (64)
T ss_pred eECCCCCCeECCCCCCcC
Confidence 456459999999998776
No 158
>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=61.52 E-value=2.7 Score=28.42 Aligned_cols=10 Identities=20% Similarity=0.205 Sum_probs=7.5
Q ss_pred cCCCCCCCCC
Q 019860 311 QYKRCPVTLM 320 (334)
Q Consensus 311 ~~~~CPv~~~ 320 (334)
....||.|+.
T Consensus 25 ~~~~CP~Cg~ 34 (42)
T PF09723_consen 25 DPVPCPECGS 34 (42)
T ss_pred CCCcCCCCCC
Confidence 3568999985
No 159
>PF13240 zinc_ribbon_2: zinc-ribbon domain
Probab=61.46 E-value=1.5 Score=25.97 Aligned_cols=11 Identities=27% Similarity=0.851 Sum_probs=7.2
Q ss_pred CCcCCCCCCCc
Q 019860 280 CPLCSQKRANP 290 (334)
Q Consensus 280 CpiC~~~~~~p 290 (334)
||-|+..+.+.
T Consensus 2 Cp~CG~~~~~~ 12 (23)
T PF13240_consen 2 CPNCGAEIEDD 12 (23)
T ss_pred CcccCCCCCCc
Confidence 77777776554
No 160
>KOG0824 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=60.60 E-value=2.9 Score=40.27 Aligned_cols=47 Identities=26% Similarity=0.472 Sum_probs=41.3
Q ss_pred CCCCCCCcCCCCCCCcccccCCcccccHHHHHHHhhcCCCCCCCCCC
Q 019860 275 PDRTICPLCSQKRANPSVVTVSGFVFCYACIFKYVSQYKRCPVTLMP 321 (334)
Q Consensus 275 ~~~~~CpiC~~~~~~p~~~~~~G~vfC~~Ci~~~~~~~~~CPv~~~~ 321 (334)
.++++|-||.+.++-|+-..-|+|-|||-|--.|-+..+.||.|.-.
T Consensus 103 ~~~~~~~~~~g~l~vpt~~qg~w~qf~~~~p~~~~~~~~~~~d~~~~ 149 (324)
T KOG0824|consen 103 QDHDICYICYGKLTVPTRIQGCWHQFCYVCPKSNFAMGNDCPDCRGK 149 (324)
T ss_pred CCccceeeeeeeEEecccccCceeeeeecCCchhhhhhhccchhhcC
Confidence 36789999999999999877799999999999999988888887643
No 161
>PLN02248 cellulose synthase-like protein
Probab=60.42 E-value=6.2 Score=44.33 Aligned_cols=36 Identities=25% Similarity=0.449 Sum_probs=30.5
Q ss_pred ccccCCcccccHHHHHHHhhcCCCCCCCCCCCCccCe
Q 019860 291 SVVTVSGFVFCYACIFKYVSQYKRCPVTLMPATVEQI 327 (334)
Q Consensus 291 ~~~~~~G~vfC~~Ci~~~~~~~~~CPv~~~~~~~~~l 327 (334)
.-|. ||+-.|.+|-.+.++..+.||.|+.+-+..|+
T Consensus 146 ~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 181 (1135)
T PLN02248 146 LPCE-CGFKICRDCYIDAVKSGGICPGCKEPYKVTDL 181 (1135)
T ss_pred Cccc-ccchhHHhHhhhhhhcCCCCCCCccccccccc
Confidence 3465 99999999999999999999999988754443
No 162
>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=59.95 E-value=11 Score=27.34 Aligned_cols=41 Identities=17% Similarity=0.345 Sum_probs=29.5
Q ss_pred CCCcCCCCCCCc----ccccCCcccccHHHHHHHhhcCCCCCCCCCCC
Q 019860 279 ICPLCSQKRANP----SVVTVSGFVFCYACIFKYVSQYKRCPVTLMPA 322 (334)
Q Consensus 279 ~CpiC~~~~~~p----~~~~~~G~vfC~~Ci~~~~~~~~~CPv~~~~~ 322 (334)
.|--|.+.+... .+++ =--.||-+|....+ ++.||.||-.+
T Consensus 7 nCE~C~~dLp~~s~~A~ICS-fECTFC~~C~e~~l--~~~CPNCgGel 51 (57)
T PF06906_consen 7 NCECCDKDLPPDSPEAYICS-FECTFCADCAETML--NGVCPNCGGEL 51 (57)
T ss_pred CccccCCCCCCCCCcceEEe-EeCcccHHHHHHHh--cCcCcCCCCcc
Confidence 477787766433 2443 45589999999888 78999998544
No 163
>smart00064 FYVE Protein present in Fab1, YOTB, Vac1, and EEA1. The FYVE zinc finger is named after four proteins where it was first found: Fab1, YOTB/ZK632.12, Vac1, and EEA1. The FYVE finger has been shown to bind two Zn2+ ions. The FYVE finger has eight potential zinc coordinating cysteine positions. The FYVE finger is structurally related to the KOG1952 consensus Transcription factor NF-X1, contains NFX-type Zn2+-binding and R3H domains [Transcription]
Probab=59.38 E-value=5.2 Score=43.51 Aligned_cols=45 Identities=24% Similarity=0.498 Sum_probs=36.6
Q ss_pred CCCCCCCcCCCCCCC--cc-cccCCcccccHHHHHHHhhc-------CCCCCCCC
Q 019860 275 PDRTICPLCSQKRAN--PS-VVTVSGFVFCYACIFKYVSQ-------YKRCPVTL 319 (334)
Q Consensus 275 ~~~~~CpiC~~~~~~--p~-~~~~~G~vfC~~Ci~~~~~~-------~~~CPv~~ 319 (334)
.+.+.|-||-+.|.- |+ .+.+|-|||-+.||.+|.+. .-+||-|.
T Consensus 189 ~~~yeCmIC~e~I~~t~~~WSC~sCYhVFHl~CI~~WArs~ek~~~~~WrCP~Cq 243 (950)
T KOG1952|consen 189 NRKYECMICTERIKRTAPVWSCKSCYHVFHLNCIKKWARSSEKTGQDGWRCPACQ 243 (950)
T ss_pred cCceEEEEeeeeccccCCceecchhhhhhhHHHHHHHHHHhhhccCccccCCccc
Confidence 457899999998754 43 56679999999999999974 13899998
No 165
>KOG3161 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=59.17 E-value=3 Score=44.05 Aligned_cols=37 Identities=22% Similarity=0.570 Sum_probs=27.0
Q ss_pred CCCCCcCCCCCCC----cccccCCcccccHHHHHHHhhcCCCCC
Q 019860 277 RTICPLCSQKRAN----PSVVTVSGFVFCYACIFKYVSQYKRCP 316 (334)
Q Consensus 277 ~~~CpiC~~~~~~----p~~~~~~G~vfC~~Ci~~~~~~~~~CP 316 (334)
-..|+||.....+ |+-+. |||+-|..|+..-- +..||
T Consensus 11 ~l~c~ic~n~f~~~~~~Pvsl~-cghtic~~c~~~ly--n~scp 51 (861)
T KOG3161|consen 11 LLLCDICLNLFVVQRLEPVSLQ-CGHTICGHCVQLLY--NASCP 51 (861)
T ss_pred HhhchHHHHHHHHHhcCccccc-ccchHHHHHHHhHh--hccCC
Confidence 3479999766544 45554 99999999998654 45677
No 166
>PRK14559 putative protein serine/threonine phosphatase; Provisional
Probab=58.99 E-value=3.6 Score=43.92 Aligned_cols=42 Identities=14% Similarity=0.256 Sum_probs=24.4
Q ss_pred CCCCCCCCCcCCCCCCCcccccCCcccccHHHHHHHhhcCCCCCCCCCCCC
Q 019860 273 LPPDRTICPLCSQKRANPSVVTVSGFVFCYACIFKYVSQYKRCPVTLMPAT 323 (334)
Q Consensus 273 ~~~~~~~CpiC~~~~~~p~~~~~~G~vfC~~Ci~~~~~~~~~CPv~~~~~~ 323 (334)
.|++...|+-|+..+.. ..|+.||+. --.+.+.||-||.++.
T Consensus 11 n~~~akFC~~CG~~l~~-~~Cp~CG~~--------~~~~~~fC~~CG~~~~ 52 (645)
T PRK14559 11 NPNNNRFCQKCGTSLTH-KPCPQCGTE--------VPVDEAHCPNCGAETG 52 (645)
T ss_pred CCCCCccccccCCCCCC-CcCCCCCCC--------CCcccccccccCCccc
Confidence 44455667777666643 234445554 3344577888887653
No 167
>PF14205 Cys_rich_KTR: Cysteine-rich KTR
Probab=58.81 E-value=3.7 Score=29.59 Aligned_cols=22 Identities=27% Similarity=0.830 Sum_probs=14.0
Q ss_pred CCCcCCCC----CCCcccccCCccccc
Q 019860 279 ICPLCSQK----RANPSVVTVSGFVFC 301 (334)
Q Consensus 279 ~CpiC~~~----~~~p~~~~~~G~vfC 301 (334)
.||+|+.. +...|++. -=-+||
T Consensus 6 ~CP~CgnKTR~kir~DT~Lk-NfPlyC 31 (55)
T PF14205_consen 6 LCPICGNKTRLKIREDTVLK-NFPLYC 31 (55)
T ss_pred ECCCCCCccceeeecCceec-cccccC
Confidence 69999953 55567775 333343
No 168
>PRK00420 hypothetical protein; Validated
Probab=57.93 E-value=4.5 Score=33.53 Aligned_cols=12 Identities=25% Similarity=0.661 Sum_probs=9.2
Q ss_pred CCCCCcCCCCCC
Q 019860 277 RTICPLCSQKRA 288 (334)
Q Consensus 277 ~~~CpiC~~~~~ 288 (334)
...||.|+.++.
T Consensus 23 ~~~CP~Cg~pLf 34 (112)
T PRK00420 23 SKHCPVCGLPLF 34 (112)
T ss_pred cCCCCCCCCcce
Confidence 357999998764
No 169
>PF12906 RINGv: RING-variant domain; PDB: 2D8S_A 1VYX_A.
Probab=57.72 E-value=4.8 Score=27.90 Aligned_cols=32 Identities=13% Similarity=0.337 Sum_probs=17.9
Q ss_pred CCCcccccCCcccccHHHHHHHhhc--CCCCCCC
Q 019860 287 RANPSVVTVSGFVFCYACIFKYVSQ--YKRCPVT 318 (334)
Q Consensus 287 ~~~p~~~~~~G~vfC~~Ci~~~~~~--~~~CPv~ 318 (334)
+.+|.-+.-+-...-..|+.+|+.. +.+|++|
T Consensus 14 li~pC~C~Gs~~~vH~~CL~~W~~~~~~~~C~~C 47 (47)
T PF12906_consen 14 LISPCRCKGSMKYVHRSCLERWIRESGNRKCEIC 47 (47)
T ss_dssp EE-SSS-SSCCGSEECCHHHHHHHHHT-SB-TTT
T ss_pred eecccccCCCcchhHHHHHHHHHHhcCCCcCCCC
Confidence 3445444322234457899999984 4689987
No 170
>TIGR00143 hypF [NiFe] hydrogenase maturation protein HypF. A previously described regulatory effect of HypF mutatation is attributable to loss of activity of a regulatory hydrogenase. A zinc finger-like region CXXCX(18)CXXCX(24)CXXCX(18)CXXC region further supported the regulatory hypothesis. However, more recent work (PUBMED:11375153) shows the direct effect is on the activity of expressed hydrogenases with nickel/iron centers, rather than on expression.
Probab=57.50 E-value=3.5 Score=44.50 Aligned_cols=51 Identities=24% Similarity=0.459 Sum_probs=38.6
Q ss_pred CCCCCCCCCcCCCCCCCc---------ccccCCc--------------------ccccHHHHHHHhhc--------CCCC
Q 019860 273 LPPDRTICPLCSQKRANP---------SVVTVSG--------------------FVFCYACIFKYVSQ--------YKRC 315 (334)
Q Consensus 273 ~~~~~~~CpiC~~~~~~p---------~~~~~~G--------------------~vfC~~Ci~~~~~~--------~~~C 315 (334)
+|+|-.+|+-|.+.+.|| +-|+-|| ...|-.|..+|-.. -..|
T Consensus 64 ippD~a~C~~Cl~E~~dp~~Rry~YpF~nCt~CGPr~~i~~~lpydr~~t~m~~f~~C~~C~~ey~~p~~rr~h~~~~~C 143 (711)
T TIGR00143 64 IPADVATCSDCLEEMLDKNDRRYLYPFISCTHCGPRFTIIEALPYDRENTSMADFPLCPDCAKEYKDPLDRRFHAQPIAC 143 (711)
T ss_pred cCCchhhHHHHHHHhcCCCcccccCCcccccCCCCCeEEeecCCCCCCCcCCCCCcCCHHHHHHhcCCccccCCCCCccC
Confidence 466888899999888887 3455577 35699999999653 2589
Q ss_pred CCCCCCCC
Q 019860 316 PVTLMPAT 323 (334)
Q Consensus 316 Pv~~~~~~ 323 (334)
|.||-.+.
T Consensus 144 ~~Cgp~l~ 151 (711)
T TIGR00143 144 PRCGPQLN 151 (711)
T ss_pred CCCCcEEE
Confidence 99997664
No 171
>KOG2113 consensus Predicted RNA binding protein, contains KH domain [General function prediction only]
Probab=57.50 E-value=7.9 Score=37.62 Aligned_cols=50 Identities=2% Similarity=-0.257 Sum_probs=38.2
Q ss_pred CCCCCcCCCCCCCcccccCCcc-cccHHHHHHHhhcCCCCCCCCCCCCccCeeeCc
Q 019860 277 RTICPLCSQKRANPSVVTVSGF-VFCYACIFKYVSQYKRCPVTLMPATVEQIRRLF 331 (334)
Q Consensus 277 ~~~CpiC~~~~~~p~~~~~~G~-vfC~~Ci~~~~~~~~~CPv~~~~~~~~~l~ri~ 331 (334)
+.+|-.|+.-....... .||| .||..|+. +.-...||+|. -...++++|-
T Consensus 343 ~~~~~~~~~~~~st~~~-~~~~n~~~~~~a~--~s~~~~~~~c~--~~~~~~~~i~ 393 (394)
T KOG2113|consen 343 SLKGTSAGFGLLSTIWS-GGNMNLSPGSLAS--ASASPTSSTCD--HNDHTLVPIN 393 (394)
T ss_pred hcccccccCceeeeEee-cCCcccChhhhhh--cccCCcccccc--ccceeeeecC
Confidence 56899999977655444 4887 79999998 77778999998 4455666663
No 172
>PTZ00303 phosphatidylinositol kinase; Provisional
Probab=57.06 E-value=6.7 Score=42.51 Aligned_cols=32 Identities=25% Similarity=0.508 Sum_probs=25.0
Q ss_pred CCCCcCCCCCC-C-------cccccCCcccccHHHHHHHh
Q 019860 278 TICPLCSQKRA-N-------PSVVTVSGFVFCYACIFKYV 309 (334)
Q Consensus 278 ~~CpiC~~~~~-~-------p~~~~~~G~vfC~~Ci~~~~ 309 (334)
..|..|.+... + .-=|..||.|||-.|-.+..
T Consensus 461 dtC~~C~kkFfSlsK~L~~RKHHCRkCGrVFC~~CSSnRs 500 (1374)
T PTZ00303 461 DSCPSCGRAFISLSRPLGTRAHHCRSCGIRLCVFCITKRA 500 (1374)
T ss_pred CcccCcCCcccccccccccccccccCCccccCccccCCcc
Confidence 57999999884 2 22367799999999997665
No 173
>PF02148 zf-UBP: Zn-finger in ubiquitin-hydrolases and other protein; InterPro: IPR001607 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents UBP-type zinc finger domains, which display some similarity with the Zn-binding domain of the insulinase family. The UBP-type zinc finger domain is found only in a small subfamily of ubiquitin C-terminal hydrolases (deubiquitinases or UBP) [, ], All members of this subfamily are isopeptidase-T, which are known to cleave isopeptide bonds between ubiquitin moieties. Some of the proteins containing an UBP zinc finger include: Homo sapiens (Human) deubiquitinating enzyme 13 (UBPD) Human deubiquitinating enzyme 5 (UBP5) Dictyostelium discoideum (Slime mold) deubiquitinating enzyme A (UBPA) Saccharomyces cerevisiae (Baker's yeast) deubiquitinating enzyme 8 (UBP8) Yeast deubiquitinating enzyme 14 (UBP14) More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 3GV4_A 3PHD_B 3C5K_A 2UZG_A 3IHP_B 2G43_B 2G45_D 2I50_A 3MHH_A 3MHS_A ....
Probab=56.53 E-value=6 Score=28.91 Aligned_cols=34 Identities=21% Similarity=0.408 Sum_probs=23.1
Q ss_pred CCcCCCCCCCcccccCCcccccHH----HHHHHhhcCC
Q 019860 280 CPLCSQKRANPSVVTVSGFVFCYA----CIFKYVSQYK 313 (334)
Q Consensus 280 CpiC~~~~~~p~~~~~~G~vfC~~----Ci~~~~~~~~ 313 (334)
|-.|+....+.-++-+||+++|.+ .+.++.++.+
T Consensus 1 C~~C~~~~~~lw~CL~Cg~~~C~~~~~~Ha~~H~~~~~ 38 (63)
T PF02148_consen 1 CSVCGSTNSNLWLCLTCGYVGCGRYSNGHALKHYKETG 38 (63)
T ss_dssp -SSSHTCSSSEEEETTTS-EEETTTSTSHHHHHHHHHT
T ss_pred CCCCCCcCCceEEeCCCCcccccCCcCcHHHHhhcccC
Confidence 667776644555666699999997 8888887543
No 174
>PF12660 zf-TFIIIC: Putative zinc-finger of transcription factor IIIC complex; InterPro: IPR024764 This zinc-finger domain is at the very C terminus of a number of different TFIIIC subunit proteins. This domain might be involved in protein-DNA and/or protein-protein interactions [].; PDB: 2J04_C.
Probab=55.79 E-value=6.3 Score=31.78 Aligned_cols=43 Identities=23% Similarity=0.569 Sum_probs=15.7
Q ss_pred CCCCcCCCCC--CCc--ccccCCcccccHHHHHHHhhc----CCCCCCCCCCC
Q 019860 278 TICPLCSQKR--ANP--SVVTVSGFVFCYACIFKYVSQ----YKRCPVTLMPA 322 (334)
Q Consensus 278 ~~CpiC~~~~--~~p--~~~~~~G~vfC~~Ci~~~~~~----~~~CPv~~~~~ 322 (334)
..|++|.+.+ .|+ ++++ .||+| -+|...++.- ...|++|+...
T Consensus 15 E~C~~C~~~i~~~~~~~~~C~-~GH~w-~RC~lT~l~i~~~~~r~C~~C~~~~ 65 (99)
T PF12660_consen 15 EKCPICGAPIPFDDLDEAQCE-NGHVW-PRCALTFLPIQTPGVRVCPVCGRRA 65 (99)
T ss_dssp --------------SSEEE-T-TS-EE-EB-SSS-SBS-SS-EEE-TTT--EE
T ss_pred ccccccccccccCCcCEeECC-CCCEE-eeeeeeeeeeccCCeeEcCCCCCEE
Confidence 6899999976 444 4565 99997 4677777642 27899998653
No 175
>PF12312 NeA_P2: Nepovirus subgroup A polyprotein ; InterPro: IPR021081 Proteins in this entry are typically between 259 and 1110 amino acids in length. They are found in association with PF03688 from PFAM, PF03689 from PFAM and PF03391 from PFAM. This entry includes RNA2 polyprotein (Protein 2A) which is implicated in RNA2 replication.
Probab=55.31 E-value=12 Score=34.04 Aligned_cols=31 Identities=42% Similarity=1.167 Sum_probs=14.6
Q ss_pred HHHHHHHHH--Hhccccccc----CCCCCCCCCCCCC
Q 019860 232 VFFFKMMEW--WYQSAEERM----SAPTVYPPPPPPP 262 (334)
Q Consensus 232 iF~lKfLEW--Wyss~~~r~----~~~~~lp~pppP~ 262 (334)
.-++|---| ||....+|+ .+..-||+|||||
T Consensus 172 fa~lkhttwrkWYDTSDeR~l~~hpGgp~lpppPPpP 208 (258)
T PF12312_consen 172 FAMLKHTTWRKWYDTSDERLLRAHPGGPCLPPPPPPP 208 (258)
T ss_pred HHHHhhhHHHhhcccchHHHhhcCCCCCcccCCCCCC
Confidence 445565555 665433343 2233455544444
No 176
>cd00065 FYVE FYVE domain; Zinc-binding domain; targets proteins to membrane lipids via interaction with phosphatidylinositol-3-phosphate, PI3P; present in Fab1, YOTB, Vac1, and EEA1;
Probab=54.93 E-value=10 Score=26.67 Aligned_cols=34 Identities=18% Similarity=0.361 Sum_probs=25.0
Q ss_pred CCCCcCCCCCCC---cccccCCcccccHHHHHHHhhc
Q 019860 278 TICPLCSQKRAN---PSVVTVSGFVFCYACIFKYVSQ 311 (334)
Q Consensus 278 ~~CpiC~~~~~~---p~~~~~~G~vfC~~Ci~~~~~~ 311 (334)
..|.+|.+.+.- ..-+..||++||..|....+..
T Consensus 3 ~~C~~C~~~F~~~~rk~~Cr~Cg~~~C~~C~~~~~~~ 39 (57)
T cd00065 3 SSCMGCGKPFTLTRRRHHCRNCGRIFCSKCSSNRIPL 39 (57)
T ss_pred CcCcccCccccCCccccccCcCcCCcChHHcCCeeec
Confidence 469999886533 2345569999999999877653
No 177
>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=54.20 E-value=3.8 Score=30.20 Aligned_cols=34 Identities=21% Similarity=0.453 Sum_probs=18.0
Q ss_pred CCCCCCcCCCCCCC---cccccCCcccccHHHHHHHh
Q 019860 276 DRTICPLCSQKRAN---PSVVTVSGFVFCYACIFKYV 309 (334)
Q Consensus 276 ~~~~CpiC~~~~~~---p~~~~~~G~vfC~~Ci~~~~ 309 (334)
+...|.+|.+.+.- ---+..||++||..|....+
T Consensus 8 ~~~~C~~C~~~F~~~~rrhhCr~CG~~vC~~Cs~~~~ 44 (69)
T PF01363_consen 8 EASNCMICGKKFSLFRRRHHCRNCGRVVCSSCSSQRI 44 (69)
T ss_dssp G-SB-TTT--B-BSSS-EEE-TTT--EEECCCS-EEE
T ss_pred CCCcCcCcCCcCCCceeeEccCCCCCEECCchhCCEE
Confidence 35689999998622 23567799999999986544
No 178
>KOG1729 consensus FYVE finger containing protein [General function prediction only]
Probab=53.90 E-value=7.7 Score=37.36 Aligned_cols=46 Identities=15% Similarity=0.382 Sum_probs=30.6
Q ss_pred CCCCCCcCCCCCCCc----ccccCCcccccHHHHHH-Hhhc----C--CCCCCCCCC
Q 019860 276 DRTICPLCSQKRANP----SVVTVSGFVFCYACIFK-YVSQ----Y--KRCPVTLMP 321 (334)
Q Consensus 276 ~~~~CpiC~~~~~~p----~~~~~~G~vfC~~Ci~~-~~~~----~--~~CPv~~~~ 321 (334)
+...|.+|..+--+. -=|.-||++||..|=.. ++-. . ..|+.|...
T Consensus 167 ea~~C~~C~~~~Ftl~~RRHHCR~CG~ivC~~Cs~n~~~l~~~~~k~~rvC~~CF~e 223 (288)
T KOG1729|consen 167 EATECMVCGCTEFTLSERRHHCRNCGDIVCAPCSRNRFLLPNLSTKPIRVCDICFEE 223 (288)
T ss_pred cceecccCCCccccHHHHHHHHHhcchHhhhhhhcCcccccccCCCCceecHHHHHH
Confidence 578999999942222 12456999999999877 3322 1 357777543
No 179
>cd00730 rubredoxin Rubredoxin; nonheme iron binding domains containing a [Fe(SCys)4] center. Rubredoxins are small nonheme iron proteins. The iron atom is coordinated by four cysteine residues (Fe(S-Cys)4), but iron can also be replaced by cobalt, nickel or zinc. They are believed to be involved in electron transfer.
Probab=53.74 E-value=6.9 Score=27.69 Aligned_cols=13 Identities=23% Similarity=0.261 Sum_probs=9.3
Q ss_pred hhcCCCCCCCCCC
Q 019860 309 VSQYKRCPVTLMP 321 (334)
Q Consensus 309 ~~~~~~CPv~~~~ 321 (334)
|..+=+||+|+.+
T Consensus 31 Lp~~w~CP~C~a~ 43 (50)
T cd00730 31 LPDDWVCPVCGAG 43 (50)
T ss_pred CCCCCCCCCCCCc
Confidence 4556689999854
No 180
>KOG1100 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=53.37 E-value=4.9 Score=36.82 Aligned_cols=41 Identities=22% Similarity=0.547 Sum_probs=31.3
Q ss_pred CCCcCCCCCCCcccccCCcccccHHHHHHHhhcCCCCCCCCCCCC
Q 019860 279 ICPLCSQKRANPSVVTVSGFVFCYACIFKYVSQYKRCPVTLMPAT 323 (334)
Q Consensus 279 ~CpiC~~~~~~p~~~~~~G~vfC~~Ci~~~~~~~~~CPv~~~~~~ 323 (334)
.|-.|++.-..-.++|+--|+.|-.|-.. -..||+|+.+.+
T Consensus 160 ~Cr~C~~~~~~VlllPCrHl~lC~~C~~~----~~~CPiC~~~~~ 200 (207)
T KOG1100|consen 160 SCRKCGEREATVLLLPCRHLCLCGICDES----LRICPICRSPKT 200 (207)
T ss_pred cceecCcCCceEEeecccceEeccccccc----CccCCCCcChhh
Confidence 49999998777667774455789999864 356999998754
No 181
>PHA00626 hypothetical protein
Probab=53.13 E-value=10 Score=27.59 Aligned_cols=7 Identities=43% Similarity=1.298 Sum_probs=5.7
Q ss_pred CCCcCCC
Q 019860 279 ICPLCSQ 285 (334)
Q Consensus 279 ~CpiC~~ 285 (334)
.||-|+.
T Consensus 2 ~CP~CGS 8 (59)
T PHA00626 2 SCPKCGS 8 (59)
T ss_pred CCCCCCC
Confidence 5888887
No 182
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=53.11 E-value=2.7 Score=25.40 Aligned_cols=10 Identities=30% Similarity=0.899 Sum_probs=6.4
Q ss_pred CCCCcCCCCC
Q 019860 278 TICPLCSQKR 287 (334)
Q Consensus 278 ~~CpiC~~~~ 287 (334)
..||-|+..+
T Consensus 3 ~~Cp~Cg~~~ 12 (26)
T PF13248_consen 3 MFCPNCGAEI 12 (26)
T ss_pred CCCcccCCcC
Confidence 4577777743
No 183
>COG3813 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=52.44 E-value=10 Score=29.02 Aligned_cols=30 Identities=20% Similarity=0.292 Sum_probs=22.9
Q ss_pred cccccCCcccccHHHHHHHhhcCCCCCCCCCCC
Q 019860 290 PSVVTVSGFVFCYACIFKYVSQYKRCPVTLMPA 322 (334)
Q Consensus 290 p~~~~~~G~vfC~~Ci~~~~~~~~~CPv~~~~~ 322 (334)
+.+++ =-+.||-.|+..-+ ++.||.||-.+
T Consensus 22 A~ICt-fEcTFCadCae~~l--~g~CPnCGGel 51 (84)
T COG3813 22 ARICT-FECTFCADCAENRL--HGLCPNCGGEL 51 (84)
T ss_pred eeEEE-EeeehhHhHHHHhh--cCcCCCCCchh
Confidence 44554 78899999998655 68999998443
No 184
>KOG1609 consensus Protein involved in mRNA turnover and stability [RNA processing and modification]
Probab=51.18 E-value=13 Score=35.27 Aligned_cols=50 Identities=20% Similarity=0.325 Sum_probs=37.4
Q ss_pred CCCCCCCCcCCC--------CCCCcccccCCcccccHHHHHHHhh--cCCCCCCCCCCCC
Q 019860 274 PPDRTICPLCSQ--------KRANPSVVTVSGFVFCYACIFKYVS--QYKRCPVTLMPAT 323 (334)
Q Consensus 274 ~~~~~~CpiC~~--------~~~~p~~~~~~G~vfC~~Ci~~~~~--~~~~CPv~~~~~~ 323 (334)
|.+...|-||+. .+..|+.|..+....-..|+..|+. +...|.+|.....
T Consensus 75 ~~~~~~cRIc~~~~~~~~~~~l~~pC~C~g~l~~vH~~cl~~W~~~~~~~~CeiC~~~~~ 134 (323)
T KOG1609|consen 75 PSSGPICRICHEEDEESNGLLLISPCSCKGSLAYVHRSCLEKWFSIKGNITCEICKSFFI 134 (323)
T ss_pred CCCCCcEEEEecccccccccccccCccccCcHHHHHHHHHHhhhccccCeeeecccccce
Confidence 444578999998 3566777665555668999999998 5678999987543
No 185
>PF07800 DUF1644: Protein of unknown function (DUF1644); InterPro: IPR012866 This family consists of sequences found in a number of hypothetical plant proteins of unknown function. The region of interest contains nine highly conserved cysteine residues and is approximately 160 amino acids in length, which probably represent a zinc-binding domain.
Probab=50.59 E-value=8.2 Score=33.90 Aligned_cols=34 Identities=21% Similarity=0.504 Sum_probs=24.6
Q ss_pred CCCCCcCCCCCCCcccccC-CcccccH-----------HHHHHHhh
Q 019860 277 RTICPLCSQKRANPSVVTV-SGFVFCY-----------ACIFKYVS 310 (334)
Q Consensus 277 ~~~CpiC~~~~~~p~~~~~-~G~vfC~-----------~Ci~~~~~ 310 (334)
...||||++...|++.|.. +-.--|. -|+.+|-+
T Consensus 2 d~~CpICme~PHNAVLLlCSS~~kgcRpymc~Ts~rhSNCLdqfkk 47 (162)
T PF07800_consen 2 DVTCPICMEHPHNAVLLLCSSHEKGCRPYMCDTSYRHSNCLDQFKK 47 (162)
T ss_pred CccCceeccCCCceEEEEeccccCCccccccCCccchhHHHHHHHH
Confidence 4589999999999986553 3334453 58888875
No 186
>PF00412 LIM: LIM domain; InterPro: IPR001781 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents LIM-type zinc finger (Znf) domains. LIM domains coordinate one or more zinc atoms, and are named after the three proteins (LIN-11, Isl1 and MEC-3) in which they were first found. They consist of two zinc-binding motifs that resemble GATA-like Znf's, however the residues holding the zinc atom(s) are variable, involving Cys, His, Asp or Glu residues. LIM domains are involved in proteins with differing functions, including gene expression, and cytoskeleton organisation and development [, ]. Protein containing LIM Znf domains include: Caenorhabditis elegans mec-3; a protein required for the differentiation of the set of six touch receptor neurons in this nematode. C. elegans. lin-11; a protein required for the asymmetric division of vulval blast cells. Vertebrate insulin gene enhancer binding protein isl-1. Isl-1 binds to one of the two cis-acting protein-binding domains of the insulin gene. Vertebrate homeobox proteins lim-1, lim-2 (lim-5) and lim3. Vertebrate lmx-1, which acts as a transcriptional activator by binding to the FLAT element; a beta-cell-specific transcriptional enhancer found in the insulin gene. Mammalian LH-2, a transcriptional regulatory protein involved in the control of cell differentiation in developing lymphoid and neural cell types. Drosophila melanogaster (Fruit fly) protein apterous, required for the normal development of the wing and halter imaginal discs. Vertebrate protein kinases LIMK-1 and LIMK-2. Mammalian rhombotins. Rhombotin 1 (RBTN1 or TTG-1) and rhombotin-2 (RBTN2 or TTG-2) are proteins of about 160 amino acids whose genes are disrupted by chromosomal translocations in T-cell leukemia. Mammalian and avian cysteine-rich protein (CRP), a 192 amino-acid protein of unknown function. Seems to interact with zyxin. Mammalian cysteine-rich intestinal protein (CRIP), a small protein which seems to have a role in zinc absorption and may function as an intracellular zinc transport protein. Vertebrate paxillin, a cytoskeletal focal adhesion protein. Mus musculus (Mouse) testin which should not be confused with rat testin which is a thiol protease homologue (see IPR000169 from INTERPRO). Helianthus annuus (Common sunflower) pollen specific protein SF3. Chicken zyxin. Zyxin is a low-abundance adhesion plaque protein which has been shown to interact with CRP. Yeast protein LRG1 which is involved in sporulation []. Saccharomyces cerevisiae (Baker's yeast) rho-type GTPase activating protein RGA1/DBM1. C. elegans homeobox protein ceh-14. C. elegans homeobox protein unc-97. S. cerevisiae hypothetical protein YKR090w. C. elegans hypothetical proteins C28H8.6. These proteins generally contain two tandem copies of the LIM domain in their N-terminal section. Zyxin and paxillin are exceptions in that they contain respectively three and four LIM domains at their C-terminal extremity. In apterous, isl-1, LH-2, lin-11, lim-1 to lim-3, lmx-1 and ceh-14 and mec-3 there is a homeobox domain some 50 to 95 amino acids after the LIM domains. LIM domains contain seven conserved cysteine residues and a histidine. The arrangement followed by these conserved residues is: C-x(2)-C-x(16,23)-H-x(2)-[CH]-x(2)-C-x(2)-C-x(16,21)-C-x(2,3)-[CHD] LIM domains bind two zinc ions []. LIM does not bind DNA, rather it seems to act as an interface for protein-protein interaction. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 2CO8_A 2EGQ_A 2CUR_A 3IXE_B 1CTL_A 1B8T_A 1X62_A 2DFY_C 1IML_A 2CUQ_A ....
Probab=50.31 E-value=14 Score=25.83 Aligned_cols=32 Identities=19% Similarity=0.441 Sum_probs=25.3
Q ss_pred CCCCCCcCCCCCCCcccccCCcccccHHHHHH
Q 019860 276 DRTICPLCSQKRANPSVVTVSGFVFCYACIFK 307 (334)
Q Consensus 276 ~~~~CpiC~~~~~~p~~~~~~G~vfC~~Ci~~ 307 (334)
+-..|-.|.+.+.+......-|.+||..|..+
T Consensus 25 ~Cf~C~~C~~~l~~~~~~~~~~~~~C~~c~~~ 56 (58)
T PF00412_consen 25 ECFKCSKCGKPLNDGDFYEKDGKPYCKDCYQK 56 (58)
T ss_dssp TTSBETTTTCBTTTSSEEEETTEEEEHHHHHH
T ss_pred cccccCCCCCccCCCeeEeECCEEECHHHHhh
Confidence 46789999999988754445899999999764
No 187
>COG3058 FdhE Uncharacterized protein involved in formate dehydrogenase formation [Posttranslational modification, protein turnover, chaperones]
Probab=50.25 E-value=14 Score=35.34 Aligned_cols=46 Identities=20% Similarity=0.475 Sum_probs=34.9
Q ss_pred CCCCCCcCCCCCCCcccccC---Cc--ccccHHHHHHHhhcCCCCCCCCCC
Q 019860 276 DRTICPLCSQKRANPSVVTV---SG--FVFCYACIFKYVSQYKRCPVTLMP 321 (334)
Q Consensus 276 ~~~~CpiC~~~~~~p~~~~~---~G--~vfC~~Ci~~~~~~~~~CPv~~~~ 321 (334)
....||+|+....--.|.-. .| |.-|--|..+|..-.-+|-.|+..
T Consensus 184 ~~~~CPvCGS~PvaSmV~~g~~~~GlRYL~CslC~teW~~VR~KC~nC~~t 234 (308)
T COG3058 184 SRQYCPVCGSMPVASMVQIGETEQGLRYLHCSLCETEWHYVRVKCSNCEQS 234 (308)
T ss_pred ccccCCCcCCCCcceeeeecCccccchhhhhhhHHHHHHHHHHHhcccccc
Confidence 45689999998766655321 12 678999999999888889888854
No 188
>PF10272 Tmpp129: Putative transmembrane protein precursor; InterPro: IPR018801 This entry consists of proteins conserved from worms to humans. They are purported to be transmembrane protein-precursors but their function is unknown.
Probab=50.20 E-value=22 Score=35.26 Aligned_cols=52 Identities=19% Similarity=0.399 Sum_probs=33.3
Q ss_pred CCCCCCcCCCCCCCcccccCC----------------cccc-----cHHHHHHHhh-------------cCCCCCCCCCC
Q 019860 276 DRTICPLCSQKRANPSVVTVS----------------GFVF-----CYACIFKYVS-------------QYKRCPVTLMP 321 (334)
Q Consensus 276 ~~~~CpiC~~~~~~p~~~~~~----------------G~vf-----C~~Ci~~~~~-------------~~~~CPv~~~~ 321 (334)
+...|--|++...|=.+.+.| +.-| |-.|+=+|.. +.-.||.|+.+
T Consensus 270 e~e~CigC~~~~~~vkl~k~C~~~~~~g~~~~~~~~C~~C~CRPmWC~~Cm~kwFasrQd~~~~~~Wl~~~~~CPtCRa~ 349 (358)
T PF10272_consen 270 ELEPCIGCMQAQPNVKLVKRCADEEQEGSPLPNEPPCQQCYCRPMWCLECMGKWFASRQDQQHPETWLSGKCPCPTCRAK 349 (358)
T ss_pred ccCCccccccCCCCcEEEeccCCcccCCcccccCCCCccccccchHHHHHHHHHhhhcCCCCChhhhhcCCCCCCCCccc
Confidence 455677777765554333333 2333 6789988874 34589999998
Q ss_pred CCccCe
Q 019860 322 ATVEQI 327 (334)
Q Consensus 322 ~~~~~l 327 (334)
.=+-|+
T Consensus 350 FCilDV 355 (358)
T PF10272_consen 350 FCILDV 355 (358)
T ss_pred ceeeee
Confidence 766555
No 189
>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=49.01 E-value=9.2 Score=27.56 Aligned_cols=22 Identities=23% Similarity=0.620 Sum_probs=17.7
Q ss_pred CCCCCcCCCCCCCcccccCCcc
Q 019860 277 RTICPLCSQKRANPSVVTVSGF 298 (334)
Q Consensus 277 ~~~CpiC~~~~~~p~~~~~~G~ 298 (334)
-..||.|++...--.|++.||+
T Consensus 26 l~~C~~cG~~~~~H~vc~~cG~ 47 (55)
T TIGR01031 26 LVVCPNCGEFKLPHRVCPSCGY 47 (55)
T ss_pred ceECCCCCCcccCeeECCccCe
Confidence 4579999998877778877885
No 190
>KOG2041 consensus WD40 repeat protein [General function prediction only]
Probab=48.34 E-value=13 Score=40.16 Aligned_cols=52 Identities=27% Similarity=0.536 Sum_probs=32.7
Q ss_pred CCCCCCCCCCCCCcCCCCCCCcccccCCcc-------cccHHHHHHHh----hcCCCCCCCCCCCC
Q 019860 269 EGIPLPPDRTICPLCSQKRANPSVVTVSGF-------VFCYACIFKYV----SQYKRCPVTLMPAT 323 (334)
Q Consensus 269 ~~~~~~~~~~~CpiC~~~~~~p~~~~~~G~-------vfC~~Ci~~~~----~~~~~CPv~~~~~~ 323 (334)
.|.++++..-.||-|...+ |+.+. +|- -.|-.|-+... ..+..||.|..+..
T Consensus 1123 cg~~i~~~~~~c~ec~~kf--P~Cia-sG~pIt~~~fWlC~~CkH~a~~~EIs~y~~CPLCHs~~~ 1185 (1189)
T KOG2041|consen 1123 CGAKIDPYDLQCSECQTKF--PVCIA-SGRPITDNIFWLCPRCKHRAHQHEISKYNCCPLCHSMES 1185 (1189)
T ss_pred cCCcCCccCCCChhhcCcC--ceeec-cCCccccceEEEccccccccccccccccccCccccChhh
Confidence 4556777778888887655 43333 442 34666655544 35689999987653
No 191
>PRK07218 replication factor A; Provisional
Probab=48.23 E-value=12 Score=37.99 Aligned_cols=27 Identities=15% Similarity=0.370 Sum_probs=18.8
Q ss_pred CCCCcCCCCCCCcccccCCcccccHHHHHHHhhcCCCCCCCCCCCCccCe
Q 019860 278 TICPLCSQKRANPSVVTVSGFVFCYACIFKYVSQYKRCPVTLMPATVEQI 327 (334)
Q Consensus 278 ~~CpiC~~~~~~p~~~~~~G~vfC~~Ci~~~~~~~~~CPv~~~~~~~~~l 327 (334)
..||.|.+.+++ +.||.|+..-...+|
T Consensus 298 ~rCP~C~r~v~~-----------------------~~C~~hG~ve~~~dl 324 (423)
T PRK07218 298 ERCPECGRVIQK-----------------------GQCRSHGAVEGEDDL 324 (423)
T ss_pred ecCcCccccccC-----------------------CcCCCCCCcCCeeee
Confidence 479999998844 678888865444333
No 192
>PRK12286 rpmF 50S ribosomal protein L32; Reviewed
Probab=46.72 E-value=11 Score=27.32 Aligned_cols=22 Identities=23% Similarity=0.573 Sum_probs=17.4
Q ss_pred CCCCCcCCCCCCCcccccCCcc
Q 019860 277 RTICPLCSQKRANPSVVTVSGF 298 (334)
Q Consensus 277 ~~~CpiC~~~~~~p~~~~~~G~ 298 (334)
-..||-|++...--.|++.||+
T Consensus 27 l~~C~~CG~~~~~H~vC~~CG~ 48 (57)
T PRK12286 27 LVECPNCGEPKLPHRVCPSCGY 48 (57)
T ss_pred ceECCCCCCccCCeEECCCCCc
Confidence 4579999998887777776885
No 193
>KOG4218 consensus Nuclear hormone receptor betaFTZ-F1 [Transcription]
Probab=46.63 E-value=13 Score=36.60 Aligned_cols=11 Identities=36% Similarity=1.108 Sum_probs=9.0
Q ss_pred CCCCCcCCCCC
Q 019860 277 RTICPLCSQKR 287 (334)
Q Consensus 277 ~~~CpiC~~~~ 287 (334)
...||+|+..+
T Consensus 15 ~ElCPVCGDkV 25 (475)
T KOG4218|consen 15 GELCPVCGDKV 25 (475)
T ss_pred ccccccccCcc
Confidence 45899999875
No 194
>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=46.10 E-value=13 Score=25.05 Aligned_cols=8 Identities=50% Similarity=1.219 Sum_probs=6.5
Q ss_pred CCCcCCCC
Q 019860 279 ICPLCSQK 286 (334)
Q Consensus 279 ~CpiC~~~ 286 (334)
+||.|+..
T Consensus 2 ~Cp~Cg~~ 9 (43)
T PF08271_consen 2 KCPNCGSK 9 (43)
T ss_dssp SBTTTSSS
T ss_pred CCcCCcCC
Confidence 68998885
No 195
>PRK06393 rpoE DNA-directed RNA polymerase subunit E''; Validated
Probab=45.37 E-value=10 Score=28.30 Aligned_cols=34 Identities=21% Similarity=0.257 Sum_probs=20.8
Q ss_pred cccccHHHHHHHhhcCCCCCCCCCCCC---ccCeeeCcc
Q 019860 297 GFVFCYACIFKYVSQYKRCPVTLMPAT---VEQIRRLFH 332 (334)
Q Consensus 297 G~vfC~~Ci~~~~~~~~~CPv~~~~~~---~~~l~ri~~ 332 (334)
.+.-|..|- +|.+...||+|+-.-+ -+.++-|..
T Consensus 4 ~~~AC~~C~--~i~~~~~Cp~Cgs~~~S~~w~G~v~i~d 40 (64)
T PRK06393 4 QYRACKKCK--RLTPEKTCPVHGDEKTTTEWFGFLIITE 40 (64)
T ss_pred hhhhHhhCC--cccCCCcCCCCCCCcCCcCcceEEEEEC
Confidence 445566663 3446779999997642 445655554
No 196
>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=44.81 E-value=13 Score=26.67 Aligned_cols=23 Identities=22% Similarity=0.589 Sum_probs=17.0
Q ss_pred CCCCCCcCCCCCCCcccccCCcc
Q 019860 276 DRTICPLCSQKRANPSVVTVSGF 298 (334)
Q Consensus 276 ~~~~CpiC~~~~~~p~~~~~~G~ 298 (334)
.-..||.|++...--.+++.|||
T Consensus 25 ~l~~c~~cg~~~~~H~vc~~cG~ 47 (56)
T PF01783_consen 25 NLVKCPNCGEPKLPHRVCPSCGY 47 (56)
T ss_dssp SEEESSSSSSEESTTSBCTTTBB
T ss_pred ceeeeccCCCEecccEeeCCCCe
Confidence 34579999987666677776775
No 197
>COG4068 Uncharacterized protein containing a Zn-ribbon [Function unknown]
Probab=44.77 E-value=12 Score=27.40 Aligned_cols=16 Identities=13% Similarity=0.152 Sum_probs=9.5
Q ss_pred hcCCCCCCCCCCCCcc
Q 019860 310 SQYKRCPVTLMPATVE 325 (334)
Q Consensus 310 ~~~~~CPv~~~~~~~~ 325 (334)
..|.-||||+++...+
T Consensus 6 ~PH~HC~VCg~aIp~d 21 (64)
T COG4068 6 VPHRHCVVCGKAIPPD 21 (64)
T ss_pred CCCccccccCCcCCCc
Confidence 3466677777665433
No 198
>COG3686 Predicted membrane protein [Function unknown]
Probab=44.45 E-value=1.3e+02 Score=25.41 Aligned_cols=46 Identities=20% Similarity=0.302 Sum_probs=30.3
Q ss_pred HHHHHHHHHHHhhHHHHH--------------------HHHHHHHHHHHHHhCCCCCCCHHHHHhcc
Q 019860 126 TKKIQKIIFACYPWLHAS--------------------CEGLSFTYQLLYLLDATGFYSVGLHALGI 172 (334)
Q Consensus 126 ~~~~k~~f~~~YP~i~~~--------------------~e~~~l~~~l~YL~g~t~y~sP~l~l~gi 172 (334)
..+.++-|+..||.+-++ |-+..++|-..||.| -+|-+-+.|+.|+
T Consensus 48 A~~A~~N~fE~fp~FaAavl~a~l~G~~~~~~~~~A~l~i~~RllYi~~Yla~-~p~lRSlvW~~gm 113 (125)
T COG3686 48 ANRAQQNFFETFPAFAAAVLVAHLTGNPSQAANTLAILFIAARLLYIPCYLAD-IPYLRSLVWLGGM 113 (125)
T ss_pred HHHHHhhhHHhhHHHHHHHHHHHHcCChHHHHHHHHHHHHHHHHHHHHHHHcC-cHHHHHHHHHHHH
Confidence 455566688889976543 455566777888887 4555556666554
No 199
>smart00734 ZnF_Rad18 Rad18-like CCHC zinc finger. Yeast Rad18p functions with Rad5p in error-free post-replicative DNA repair. This zinc finger is likely to bind nucleic-acids.
Probab=44.35 E-value=7.8 Score=23.53 Aligned_cols=8 Identities=38% Similarity=0.912 Sum_probs=4.1
Q ss_pred CCCCCCCC
Q 019860 315 CPVTLMPA 322 (334)
Q Consensus 315 CPv~~~~~ 322 (334)
||||++.+
T Consensus 4 CPiC~~~v 11 (26)
T smart00734 4 CPVCFREV 11 (26)
T ss_pred CCCCcCcc
Confidence 55555444
No 200
>PRK08270 anaerobic ribonucleoside triphosphate reductase; Provisional
Probab=44.17 E-value=13 Score=39.79 Aligned_cols=19 Identities=21% Similarity=0.275 Sum_probs=12.8
Q ss_pred hcCCCCCCCCCCCCccCeeeC
Q 019860 310 SQYKRCPVTLMPATVEQIRRL 330 (334)
Q Consensus 310 ~~~~~CPv~~~~~~~~~l~ri 330 (334)
..+..||.||.+ .+-..||
T Consensus 637 g~~~~CP~CG~~--~~v~sRi 655 (656)
T PRK08270 637 GEHEFCPKCGEE--TEVYSRV 655 (656)
T ss_pred CCCCCCcCCcCc--cceEEee
Confidence 446799999976 4444444
No 201
>smart00154 ZnF_AN1 AN1-like Zinc finger. Zinc finger at the C-terminus of An1, a ubiquitin-like protein in Xenopus laevis.
Probab=43.50 E-value=15 Score=24.41 Aligned_cols=23 Identities=26% Similarity=0.515 Sum_probs=18.1
Q ss_pred CCcCCCCCCC-cccccCCcccccH
Q 019860 280 CPLCSQKRAN-PSVVTVSGFVFCY 302 (334)
Q Consensus 280 CpiC~~~~~~-p~~~~~~G~vfC~ 302 (334)
|-+|.+...- |-.+..||.+||.
T Consensus 1 C~~C~~~~~l~~f~C~~C~~~FC~ 24 (39)
T smart00154 1 CHFCRKKVGLTGFKCRHCGNLFCG 24 (39)
T ss_pred CcccCCcccccCeECCccCCcccc
Confidence 6778887665 8778779999985
No 202
>PF14803 Nudix_N_2: Nudix N-terminal; PDB: 3CNG_C.
Probab=43.41 E-value=8.2 Score=25.09 Aligned_cols=22 Identities=32% Similarity=0.798 Sum_probs=10.6
Q ss_pred CCCcCCCCCCC--c-------ccccCCcccc
Q 019860 279 ICPLCSQKRAN--P-------SVVTVSGFVF 300 (334)
Q Consensus 279 ~CpiC~~~~~~--p-------~~~~~~G~vf 300 (334)
.||.|+.+++. | .|++.||+|.
T Consensus 2 fC~~CG~~l~~~ip~gd~r~R~vC~~Cg~Ih 32 (34)
T PF14803_consen 2 FCPQCGGPLERRIPEGDDRERLVCPACGFIH 32 (34)
T ss_dssp B-TTT--B-EEE--TT-SS-EEEETTTTEEE
T ss_pred ccccccChhhhhcCCCCCccceECCCCCCEE
Confidence 58888887543 2 3566677663
No 203
>TIGR00373 conserved hypothetical protein TIGR00373. This family of proteins is, so far, restricted to archaeal genomes. The family appears to be distantly related to the N-terminal region of the eukaryotic transcription initiation factor IIE alpha chain.
Probab=43.39 E-value=7.7 Score=33.88 Aligned_cols=32 Identities=16% Similarity=0.093 Sum_probs=22.6
Q ss_pred CCCCCCcCCCCCCCcccccCCcccccHHHHHHHhhcCCCCCCCCCCCC
Q 019860 276 DRTICPLCSQKRANPSVVTVSGFVFCYACIFKYVSQYKRCPVTLMPAT 323 (334)
Q Consensus 276 ~~~~CpiC~~~~~~p~~~~~~G~vfC~~Ci~~~~~~~~~CPv~~~~~~ 323 (334)
..+.||.|+...+---++. ..-.||+||.++.
T Consensus 108 ~~Y~Cp~c~~r~tf~eA~~----------------~~F~Cp~Cg~~L~ 139 (158)
T TIGR00373 108 MFFICPNMCVRFTFNEAME----------------LNFTCPRCGAMLD 139 (158)
T ss_pred CeEECCCCCcEeeHHHHHH----------------cCCcCCCCCCEee
Confidence 4678999997664443433 3679999998764
No 204
>COG1773 Rubredoxin [Energy production and conversion]
Probab=43.28 E-value=13 Score=26.93 Aligned_cols=15 Identities=20% Similarity=0.315 Sum_probs=10.8
Q ss_pred HHHhhcCCCCCCCCC
Q 019860 306 FKYVSQYKRCPVTLM 320 (334)
Q Consensus 306 ~~~~~~~~~CPv~~~ 320 (334)
++-|..+=.||+|+.
T Consensus 30 fedlPd~w~CP~Cg~ 44 (55)
T COG1773 30 FEDLPDDWVCPECGV 44 (55)
T ss_pred hhhCCCccCCCCCCC
Confidence 455666778899984
No 205
>KOG0006 consensus E3 ubiquitin-protein ligase (Parkin protein) [Posttranslational modification, protein turnover, chaperones]
Probab=43.28 E-value=15 Score=35.81 Aligned_cols=33 Identities=30% Similarity=0.714 Sum_probs=21.3
Q ss_pred CCCCC--cCCCC-CCCc----ccccC-CcccccHHHHHHHh
Q 019860 277 RTICP--LCSQK-RANP----SVVTV-SGFVFCYACIFKYV 309 (334)
Q Consensus 277 ~~~Cp--iC~~~-~~~p----~~~~~-~G~vfC~~Ci~~~~ 309 (334)
...|| -|+.- +..| +.++- ||++||..|...|-
T Consensus 315 GVlCP~pgCG~gll~EPD~rkvtC~~gCgf~FCR~C~e~yh 355 (446)
T KOG0006|consen 315 GVLCPRPGCGAGLLPEPDQRKVTCEGGCGFAFCRECKEAYH 355 (446)
T ss_pred CEecCCCCCCcccccCCCCCcccCCCCchhHhHHHHHhhhc
Confidence 45674 37664 3344 23333 99999999998664
No 206
>PRK06386 replication factor A; Reviewed
Probab=43.24 E-value=15 Score=36.52 Aligned_cols=12 Identities=25% Similarity=0.714 Sum_probs=10.1
Q ss_pred CCCCcCCCCCCC
Q 019860 278 TICPLCSQKRAN 289 (334)
Q Consensus 278 ~~CpiC~~~~~~ 289 (334)
..||.|.+.+++
T Consensus 237 ~rCP~C~R~l~~ 248 (358)
T PRK06386 237 TKCSVCNKIIED 248 (358)
T ss_pred ecCcCCCeEccC
Confidence 479999998875
No 207
>PF04710 Pellino: Pellino; InterPro: IPR006800 Pellino is involved in Toll-like signalling pathways, and associates with the kinase domain of the Pelle Ser/Thr kinase [, , ].; PDB: 3EGB_B 3EGA_A.
Probab=43.20 E-value=7.9 Score=38.73 Aligned_cols=55 Identities=24% Similarity=0.420 Sum_probs=0.0
Q ss_pred CCCCCcCCCCC--------------CC---cc-cccCCcccccHHHHHHHhhc---------CCCCCCCCCCCCc-cCee
Q 019860 277 RTICPLCSQKR--------------AN---PS-VVTVSGFVFCYACIFKYVSQ---------YKRCPVTLMPATV-EQIR 328 (334)
Q Consensus 277 ~~~CpiC~~~~--------------~~---p~-~~~~~G~vfC~~Ci~~~~~~---------~~~CPv~~~~~~~-~~l~ 328 (334)
...||+|++.= .| |+ +-.+||||.--+.+.-|-+- +..||-|..+++. ...+
T Consensus 328 ~r~CPlCr~~g~~V~L~mG~E~afyvD~~~pthaF~PCGHv~SekTa~yWs~i~lPhGt~~f~a~CPFCa~~L~g~~g~v 407 (416)
T PF04710_consen 328 SRTCPLCRQVGPYVPLWMGCEPAFYVDSGPPTHAFNPCGHVCSEKTAKYWSQIPLPHGTHAFHAACPFCATPLDGEQGYV 407 (416)
T ss_dssp --------------------------------------------------------------------------------
T ss_pred cccCCCccccCCceeEeeccccceeecCCCCceeecccccccchhhhhhhhcCCCCCCcccccccCCcccCcccCCCCce
Confidence 67899999641 12 22 33459999988888888752 3589999999874 4555
Q ss_pred eCc
Q 019860 329 RLF 331 (334)
Q Consensus 329 ri~ 331 (334)
|++
T Consensus 408 rLi 410 (416)
T PF04710_consen 408 RLI 410 (416)
T ss_dssp ---
T ss_pred EEE
Confidence 554
No 208
>smart00661 RPOL9 RNA polymerase subunit 9.
Probab=42.70 E-value=15 Score=25.25 Aligned_cols=9 Identities=33% Similarity=0.999 Sum_probs=6.0
Q ss_pred CCCcCCCCC
Q 019860 279 ICPLCSQKR 287 (334)
Q Consensus 279 ~CpiC~~~~ 287 (334)
.||-|+..+
T Consensus 2 FCp~Cg~~l 10 (52)
T smart00661 2 FCPKCGNML 10 (52)
T ss_pred CCCCCCCcc
Confidence 477777754
No 209
>PRK12496 hypothetical protein; Provisional
Probab=42.43 E-value=6.3 Score=34.68 Aligned_cols=30 Identities=20% Similarity=0.421 Sum_probs=18.6
Q ss_pred CCCCCcCCCCCCCcccccCCcccccHHHHHHHhhcCCCCCCCCCCCCcc
Q 019860 277 RTICPLCSQKRANPSVVTVSGFVFCYACIFKYVSQYKRCPVTLMPATVE 325 (334)
Q Consensus 277 ~~~CpiC~~~~~~p~~~~~~G~vfC~~Ci~~~~~~~~~CPv~~~~~~~~ 325 (334)
...|+-|++.....- +...||+||.++...
T Consensus 127 ~~~C~gC~~~~~~~~-------------------~~~~C~~CG~~~~r~ 156 (164)
T PRK12496 127 RKVCKGCKKKYPEDY-------------------PDDVCEICGSPVKRK 156 (164)
T ss_pred eEECCCCCccccCCC-------------------CCCcCCCCCChhhhc
Confidence 467998887663210 124688888776543
No 210
>KOG4642 consensus Chaperone-dependent E3 ubiquitin protein ligase (contains TPR repeats) [Posttranslational modification, protein turnover, chaperones]
Probab=41.99 E-value=14 Score=34.94 Aligned_cols=55 Identities=24% Similarity=0.216 Sum_probs=47.3
Q ss_pred CCCCCCCCCcCCCCCCCcccccCCcccccHHHHHHHhhcCC-CCCCCCCCCCccCeee
Q 019860 273 LPPDRTICPLCSQKRANPSVVTVSGFVFCYACIFKYVSQYK-RCPVTLMPATVEQIRR 329 (334)
Q Consensus 273 ~~~~~~~CpiC~~~~~~p~~~~~~G~vfC~~Ci~~~~~~~~-~CPv~~~~~~~~~l~r 329 (334)
+| |-.-|.|-.+.+++|++.+ +|-.|-..=|.++++.-| --|||+.+++..+++.
T Consensus 208 vp-d~lcgkIt~el~~~pvi~p-sgIty~ra~I~Ehl~rvghfdpvtr~~Lte~q~ip 263 (284)
T KOG4642|consen 208 VP-DYLCGKITLELMREPVITP-SGITYDRADIEEHLQRVGHFDPVTRWPLTEYQLIP 263 (284)
T ss_pred cc-chhhhhhhHHhhcCCccCc-cccchhHHHHHHHHHHhccCCchhcccCCHHhhcc
Confidence 44 4556788999999999886 999999999999999875 5799999999888875
No 211
>COG5113 UFD2 Ubiquitin fusion degradation protein 2 [Posttranslational modification, protein turnover, chaperones]
Probab=41.98 E-value=23 Score=37.80 Aligned_cols=53 Identities=19% Similarity=0.204 Sum_probs=49.9
Q ss_pred CCCCCCcCCCCCCCcccccCCcccccHHHHHHHhhcCCCCCCCCCCCCccCee
Q 019860 276 DRTICPLCSQKRANPSVVTVSGFVFCYACIFKYVSQYKRCPVTLMPATVEQIR 328 (334)
Q Consensus 276 ~~~~CpiC~~~~~~p~~~~~~G~vfC~~Ci~~~~~~~~~CPv~~~~~~~~~l~ 328 (334)
|...-|+--..++||++++++|-.--..-|..++-..+.-|--++|++.+|+.
T Consensus 853 DeFlDPLmftimkdPV~Lp~S~i~IDRSTikahllsd~tDPFNRmPLtlddVt 905 (929)
T COG5113 853 DEFLDPLMFTIMKDPVKLPTSRITIDRSTIKAHLLSDGTDPFNRMPLTLDDVT 905 (929)
T ss_pred hhhhCchhhhcccCCeecccccccccHHHHHHHHhcCCCCccccCCCchhhcC
Confidence 67888999999999999999999999999999999999999999999998875
No 212
>COG1997 RPL43A Ribosomal protein L37AE/L43A [Translation, ribosomal structure and biogenesis]
Probab=41.74 E-value=16 Score=28.99 Aligned_cols=30 Identities=23% Similarity=0.764 Sum_probs=16.7
Q ss_pred CCCCCCcCCCCCCCcccccCCcccccHHHHHHH
Q 019860 276 DRTICPLCSQKRANPSVVTVSGFVFCYACIFKY 308 (334)
Q Consensus 276 ~~~~CpiC~~~~~~p~~~~~~G~vfC~~Ci~~~ 308 (334)
+...||.|+.....- +. +|---|..|-..|
T Consensus 34 ~~~~Cp~C~~~~VkR--~a-~GIW~C~kCg~~f 63 (89)
T COG1997 34 AKHVCPFCGRTTVKR--IA-TGIWKCRKCGAKF 63 (89)
T ss_pred cCCcCCCCCCcceee--ec-cCeEEcCCCCCee
Confidence 467899999984332 11 4444444444333
No 213
>KOG3476 consensus Microtubule-associated protein CRIPT [Cytoskeleton]
Probab=41.03 E-value=2.5 Score=33.29 Aligned_cols=35 Identities=23% Similarity=0.613 Sum_probs=28.1
Q ss_pred CCCCcCCCCCCCcccccCCcccccHHHHHHHhhcCCCCCCCCCCC
Q 019860 278 TICPLCSQKRANPSVVTVSGFVFCYACIFKYVSQYKRCPVTLMPA 322 (334)
Q Consensus 278 ~~CpiC~~~~~~p~~~~~~G~vfC~~Ci~~~~~~~~~CPv~~~~~ 322 (334)
..|-||.+.+..| |-.||..|++ +.+.|-+|++.+
T Consensus 55 ~kC~iCk~~vHQ~------GshYC~tCAY----~KgiCAMCGKki 89 (100)
T KOG3476|consen 55 AKCRICKQLVHQP------GSHYCQTCAY----KKGICAMCGKKI 89 (100)
T ss_pred chhHHHHHHhcCC------cchhHhHhhh----hhhHHHHhhhHh
Confidence 4799999876554 6779999998 568899999764
No 214
>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=40.80 E-value=9.3 Score=27.11 Aligned_cols=31 Identities=23% Similarity=0.540 Sum_probs=17.9
Q ss_pred CCCCc--CCCCCCCc-------ccccCCcccccHHHHHHH
Q 019860 278 TICPL--CSQKRANP-------SVVTVSGFVFCYACIFKY 308 (334)
Q Consensus 278 ~~Cpi--C~~~~~~p-------~~~~~~G~vfC~~Ci~~~ 308 (334)
..||- |...+.-. +.++.||+.||+.|-..|
T Consensus 19 ~~Cp~~~C~~~~~~~~~~~~~~~~C~~C~~~fC~~C~~~~ 58 (64)
T PF01485_consen 19 RWCPNPDCEYIIEKDDGCNSPIVTCPSCGTEFCFKCGEPW 58 (64)
T ss_dssp C--TTSST---ECS-SSTTS--CCTTSCCSEECSSSTSES
T ss_pred cCCCCCCCcccEEecCCCCCCeeECCCCCCcCccccCccc
Confidence 46876 87764322 456669999999997655
No 215
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=40.72 E-value=9.2 Score=26.13 Aligned_cols=29 Identities=21% Similarity=0.251 Sum_probs=17.8
Q ss_pred CCCCcCCCCCCCcccccCCcccccHHHHHHHhhcCCCCCCCCCCCC
Q 019860 278 TICPLCSQKRANPSVVTVSGFVFCYACIFKYVSQYKRCPVTLMPAT 323 (334)
Q Consensus 278 ~~CpiC~~~~~~p~~~~~~G~vfC~~Ci~~~~~~~~~CPv~~~~~~ 323 (334)
..|+-|+..++-..... ..+||.||.++.
T Consensus 4 y~C~~CG~~~~~~~~~~-----------------~~~Cp~CG~~~~ 32 (46)
T PRK00398 4 YKCARCGREVELDEYGT-----------------GVRCPYCGYRIL 32 (46)
T ss_pred EECCCCCCEEEECCCCC-----------------ceECCCCCCeEE
Confidence 56888888764332211 257888887653
No 216
>PRK12495 hypothetical protein; Provisional
Probab=40.69 E-value=11 Score=34.84 Aligned_cols=25 Identities=24% Similarity=0.502 Sum_probs=16.1
Q ss_pred CCCCCcCCCCCCCcccccCCcccccHHHHH
Q 019860 277 RTICPLCSQKRANPSVVTVSGFVFCYACIF 306 (334)
Q Consensus 277 ~~~CpiC~~~~~~p~~~~~~G~vfC~~Ci~ 306 (334)
...|+.|+.+|- .+ -|-+||-.|-.
T Consensus 42 a~hC~~CG~PIp--a~---pG~~~Cp~CQ~ 66 (226)
T PRK12495 42 NAHCDECGDPIF--RH---DGQEFCPTCQQ 66 (226)
T ss_pred hhhcccccCccc--CC---CCeeECCCCCC
Confidence 457999998885 22 46666655543
No 217
>KOG0396 consensus Uncharacterized conserved protein [Function unknown]
Probab=40.21 E-value=16 Score=36.37 Aligned_cols=55 Identities=15% Similarity=0.292 Sum_probs=43.5
Q ss_pred CCCCCcCCCCCC--C-cccccCCcccccHHHHHHHhhcC-CCCCCCCCCCCccCeeeCcc
Q 019860 277 RTICPLCSQKRA--N-PSVVTVSGFVFCYACIFKYVSQY-KRCPVTLMPATVEQIRRLFH 332 (334)
Q Consensus 277 ~~~CpiC~~~~~--~-p~~~~~~G~vfC~~Ci~~~~~~~-~~CPv~~~~~~~~~l~ri~~ 332 (334)
.-.|.|.++.+. | |.+.+ .|||+=+.-|..+=+.+ -.||++++-+...+++++|.
T Consensus 330 ~Lvc~isge~md~~N~P~lfp-nG~Vyg~~~L~s~~~~~~i~dP~~~k~f~~~~l~kvy~ 388 (389)
T KOG0396|consen 330 RLVCSISGELMDDDNPPHLFP-NGYVYGTKALESLNEDDGIGDPRTKKVFRYSELCKVYL 388 (389)
T ss_pred HHHhhccccccCCCCCccccc-CceeehhHHHHhhcccCCCcCCCCCccccHHHHHHHhc
Confidence 345666565543 3 35665 99999999999998888 68999999999999999885
No 218
>PF14471 DUF4428: Domain of unknown function (DUF4428)
Probab=38.82 E-value=25 Score=24.85 Aligned_cols=28 Identities=25% Similarity=0.696 Sum_probs=20.9
Q ss_pred CCCcCCCCCCC--cccccCCcccccHHHHHHH
Q 019860 279 ICPLCSQKRAN--PSVVTVSGFVFCYACIFKY 308 (334)
Q Consensus 279 ~CpiC~~~~~~--p~~~~~~G~vfC~~Ci~~~ 308 (334)
.|+||++.+-- ..-+. -|| -|..|.-+.
T Consensus 1 ~C~iCg~kigl~~~~k~~-DG~-iC~~C~~Kl 30 (51)
T PF14471_consen 1 KCAICGKKIGLFKRFKIK-DGY-ICKDCLKKL 30 (51)
T ss_pred CCCccccccccccceecc-Ccc-chHHHHHHh
Confidence 59999998633 33455 885 899999876
No 219
>PRK07217 replication factor A; Reviewed
Probab=38.80 E-value=22 Score=34.57 Aligned_cols=28 Identities=25% Similarity=0.395 Sum_probs=19.7
Q ss_pred CCCCc--CCCCCCCcccccCCcccccHHHHHHHhhcCCCCCCCCCCCCccCee
Q 019860 278 TICPL--CSQKRANPSVVTVSGFVFCYACIFKYVSQYKRCPVTLMPATVEQIR 328 (334)
Q Consensus 278 ~~Cpi--C~~~~~~p~~~~~~G~vfC~~Ci~~~~~~~~~CPv~~~~~~~~~l~ 328 (334)
..||. |.+.+ +++.||.|+..-...|||
T Consensus 189 ~rCP~~~C~Rvl-----------------------~~g~C~~HG~ve~~~DLr 218 (311)
T PRK07217 189 KRCPEEDCTRVL-----------------------QNGRCSEHGKVEGEFDLR 218 (311)
T ss_pred ecCCccccCccc-----------------------cCCCCCCCCCcCCceeeE
Confidence 47999 99877 246788888665555554
No 220
>KOG3726 consensus Uncharacterized conserved protein [Function unknown]
Probab=38.63 E-value=17 Score=38.74 Aligned_cols=42 Identities=21% Similarity=0.387 Sum_probs=29.9
Q ss_pred CCCCcCCCCCCCc-cccc--CCcccccHHHHHHHhhcCCCCCCCCCCC
Q 019860 278 TICPLCSQKRANP-SVVT--VSGFVFCYACIFKYVSQYKRCPVTLMPA 322 (334)
Q Consensus 278 ~~CpiC~~~~~~p-~~~~--~~G~vfC~~Ci~~~~~~~~~CPv~~~~~ 322 (334)
..|-+|+.+-.-. .|+. -|+-+||..|-.++ ...||||+-..
T Consensus 655 r~C~vcq~pedse~~v~rt~~C~~~~C~~c~~~~---~~~~~vC~~~~ 699 (717)
T KOG3726|consen 655 RTCKVCQLPEDSETDVCRTTFCYTPYCVACSLDY---ASISEVCGPDA 699 (717)
T ss_pred HHHHHhcCCcCccccccCccccCCcchHhhhhhh---hccCcccCchh
Confidence 4678888775422 2433 39999999997765 47899999654
No 221
>smart00834 CxxC_CXXC_SSSS Putative regulatory protein. CxxC_CXXC_SSSS represents a region of about 41 amino acids found in a number of small proteins in a wide range of bacteria. The region usually begins with the initiator Met and contains two CxxC motifs separated by 17 amino acids. One protein in this entry has been noted as a putative regulatory protein, designated FmdB. Most proteins in this entry have a C-terminal region containing highly degenerate sequence.
Probab=38.19 E-value=12 Score=24.49 Aligned_cols=31 Identities=13% Similarity=0.159 Sum_probs=18.4
Q ss_pred CCCCCCcCCCCCCCcccccCCcccccHHHHHHHhhcCCCCCCCCC
Q 019860 276 DRTICPLCSQKRANPSVVTVSGFVFCYACIFKYVSQYKRCPVTLM 320 (334)
Q Consensus 276 ~~~~CpiC~~~~~~p~~~~~~G~vfC~~Ci~~~~~~~~~CPv~~~ 320 (334)
....|+-|++.++-..... - .....||.|+.
T Consensus 4 Y~y~C~~Cg~~fe~~~~~~-------------~-~~~~~CP~Cg~ 34 (41)
T smart00834 4 YEYRCEDCGHTFEVLQKIS-------------D-DPLATCPECGG 34 (41)
T ss_pred EEEEcCCCCCEEEEEEecC-------------C-CCCCCCCCCCC
Confidence 4567888887664332211 0 23468999996
No 222
>PF00301 Rubredoxin: Rubredoxin; InterPro: IPR004039 Rubredoxin is a low molecular weight iron-containing bacterial protein involved in electron transfer [, ], sometimes replacing ferredoxin as an electron carrier []. The 3-D structures of a number of rubredoxins have been solved [, ]. The fold belongs to the alpha+beta class, with 2 alpha-helices and 2-3 beta-strands. Its active site contains an iron ion which is co-ordinated by the sulphurs of four conserved cysteine residues forming an almost regular tetrahedron. The conserved cysteines reside on two loops, which are the most conserved regions of the protein. In addition, a ring of acidic residues in the proximity of the [Fe(Cys)4] centre is also well-conserved []. ; GO: 0009055 electron carrier activity, 0046872 metal ion binding; PDB: 2RDV_C 1RDV_A 1S24_A 1T9O_B 1B2J_A 1SMW_A 2PVE_B 1BFY_A 1T9P_C 1C09_C ....
Probab=37.90 E-value=12 Score=26.16 Aligned_cols=13 Identities=31% Similarity=0.496 Sum_probs=6.0
Q ss_pred hhcCCCCCCCCCC
Q 019860 309 VSQYKRCPVTLMP 321 (334)
Q Consensus 309 ~~~~~~CPv~~~~ 321 (334)
|.++=+||+|+.+
T Consensus 31 Lp~~w~CP~C~a~ 43 (47)
T PF00301_consen 31 LPDDWVCPVCGAP 43 (47)
T ss_dssp S-TT-B-TTTSSB
T ss_pred CCCCCcCcCCCCc
Confidence 3344577777754
No 223
>PF07578 LAB_N: Lipid A Biosynthesis N-terminal domain; InterPro: IPR011499 This domain is found at the N terminus of a group of Chlamydial lipid A biosynthesis proteins. It is also found by itself in a family of proteins of unknown function.; GO: 0008915 lipid-A-disaccharide synthase activity, 0009245 lipid A biosynthetic process
Probab=37.90 E-value=29 Score=26.53 Aligned_cols=20 Identities=15% Similarity=0.486 Sum_probs=13.3
Q ss_pred HHHHHHHHHH-HHHHhccccc
Q 019860 228 LIAAVFFFKM-MEWWYQSAEE 247 (334)
Q Consensus 228 lp~~iF~lKf-LEWWyss~~~ 247 (334)
+.-.+|+.|| +|||+|+..+
T Consensus 4 ~gq~lF~~Rf~~QW~~SEk~k 24 (72)
T PF07578_consen 4 IGQLLFSSRFIVQWIYSEKAK 24 (72)
T ss_pred HHHHHHHHHHHHHHHHHHHcC
Confidence 3445677775 6999987443
No 224
>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=37.43 E-value=16 Score=24.60 Aligned_cols=25 Identities=28% Similarity=0.600 Sum_probs=15.3
Q ss_pred CCc--CCCCCCCcccccCCcccccHHH
Q 019860 280 CPL--CSQKRANPSVVTVSGFVFCYAC 304 (334)
Q Consensus 280 Cpi--C~~~~~~p~~~~~~G~vfC~~C 304 (334)
|.+ |.+....|..+..||..||-.-
T Consensus 1 C~~~~C~~~~~~~~~C~~C~~~FC~~H 27 (43)
T PF01428_consen 1 CSFPGCKKKDFLPFKCKHCGKSFCLKH 27 (43)
T ss_dssp -SSTTT--BCTSHEE-TTTS-EE-TTT
T ss_pred CccCcCcCccCCCeECCCCCcccCccc
Confidence 555 8888888988888999999653
No 225
>PF01258 zf-dskA_traR: Prokaryotic dksA/traR C4-type zinc finger; InterPro: IPR000962 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 domains identified in zinc finger-containing members of the DksA/TraR family. DksA is a critical component of the rRNA transcription initiation machinery that potentiates the regulation of rRNA promoters by ppGpp and the initiating NTP. In delta-dksA mutants, rRNA promoters are unresponsive to changes in amino acid availability, growth rate, or growth phase. In vitro, DksA binds to RNAP, reduces open complex lifetime, inhibits rRNA promoter activity, and amplifies effects of ppGpp and the initiating NTP on rRNA transcription [, ]. The dksA gene product suppresses the temperature-sensitive growth and filamentation of a dnaK deletion mutant of Escherichia coli. Gene knockout [] and deletion [] experiments have shown the gene to be non-essential, mutations causing a mild sensitivity to UV light, but not affecting DNA recombination []. In Pseudomonas aeruginosa, dksA is a novel regulator involved in the post-transcriptional control of extracellular virulence factor production []. The proteins contain a C-terminal region thought to fold into a 4-cysteine zinc finger. Other proteins found to contain a similar zinc finger domain include: the traR gene products encoded on the E. coli F and R100 plasmids [, ] the traR gene products encoded on Salmonella spp. plasmids pED208 and pSLT the dnaK suppressor hypothetical proteins from bacteria and bacteriophage FHL4, LIM proteins from Homo sapiens (Human) and Mus musculus (Mouse) [] More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 2GVI_A 2KQ9_A 2KGO_A 1TJL_I.
Probab=36.82 E-value=15 Score=23.73 Aligned_cols=31 Identities=26% Similarity=0.580 Sum_probs=21.7
Q ss_pred CCCCcCCCCCCCcccccCCcccccHHHHHHH
Q 019860 278 TICPLCSQKRANPSVVTVSGFVFCYACIFKY 308 (334)
Q Consensus 278 ~~CpiC~~~~~~p~~~~~~G~vfC~~Ci~~~ 308 (334)
+.|-.|+++|-..-....=|-.+|.+|...+
T Consensus 4 g~C~~CGe~I~~~Rl~~~p~~~~C~~C~~~~ 34 (36)
T PF01258_consen 4 GICEDCGEPIPEERLVAVPGATLCVECQERR 34 (36)
T ss_dssp SB-TTTSSBEEHHHHHHCTTECS-HHHHHHH
T ss_pred CCccccCChHHHHHHHhCCCcEECHHHhCcc
Confidence 4699999999777433346999999997653
No 226
>TIGR02605 CxxC_CxxC_SSSS putative regulatory protein, FmdB family. This model represents a region of about 50 amino acids found in a number of small proteins in a wide range of bacteria. The region begins usually with the initiator Met and contains two CxxC motifs separated by 17 amino acids. One member of this family is has been noted as a putative regulatory protein, designated FmdB (PubMed:8841393). Most members of this family have a C-terminal region containing highly degenerate sequence, such as SSTSESTKSSGSSGSSGSSESKASGSTEKSTSSTTAAAAV in Mycobacterium tuberculosis and VAVGGSAPAPSPAPRAGGGGGGCCGGGCCG in Streptomyces avermitilis. These low complexity regions, which are not included in the model, resemble low-complexity C-terminal regions of some heterocycle-containing bacteriocin precursors.
Probab=36.79 E-value=12 Score=26.01 Aligned_cols=9 Identities=22% Similarity=0.305 Sum_probs=6.7
Q ss_pred CCCCCCCCC
Q 019860 312 YKRCPVTLM 320 (334)
Q Consensus 312 ~~~CPv~~~ 320 (334)
.-.||.|+.
T Consensus 26 ~~~CP~Cg~ 34 (52)
T TIGR02605 26 LATCPECGG 34 (52)
T ss_pred CCCCCCCCC
Confidence 357999985
No 227
>PRK08351 DNA-directed RNA polymerase subunit E''; Validated
Probab=36.53 E-value=14 Score=27.38 Aligned_cols=14 Identities=29% Similarity=0.527 Sum_probs=10.0
Q ss_pred hhcCCCCCCCCCCC
Q 019860 309 VSQYKRCPVTLMPA 322 (334)
Q Consensus 309 ~~~~~~CPv~~~~~ 322 (334)
|.....||+|+...
T Consensus 12 i~~~~~CP~Cgs~~ 25 (61)
T PRK08351 12 ITTEDRCPVCGSRD 25 (61)
T ss_pred ccCCCcCCCCcCCc
Confidence 33566899999754
No 228
>KOG3842 consensus Adaptor protein Pellino [Signal transduction mechanisms]
Probab=36.29 E-value=32 Score=33.64 Aligned_cols=54 Identities=15% Similarity=0.303 Sum_probs=35.7
Q ss_pred CCCCCcCCCCC--------------CCc---c-cccCCcccccHHHHHHHhh---------cCCCCCCCCCCCC-ccCee
Q 019860 277 RTICPLCSQKR--------------ANP---S-VVTVSGFVFCYACIFKYVS---------QYKRCPVTLMPAT-VEQIR 328 (334)
Q Consensus 277 ~~~CpiC~~~~--------------~~p---~-~~~~~G~vfC~~Ci~~~~~---------~~~~CPv~~~~~~-~~~l~ 328 (334)
...||+|+..- .|+ + +..+||||.-.+-..-|-+ -+..||-|...+. ....+
T Consensus 341 ~r~CPmC~~~gp~V~L~lG~E~~f~vD~G~pthaF~PCGHv~sekt~~YWs~iplPhGT~~f~a~CPFC~~~L~ge~~~i 420 (429)
T KOG3842|consen 341 ERECPMCRVVGPYVPLWLGCEAGFYVDAGPPTHAFNPCGHVCSEKTVKYWSQIPLPHGTHAFHAACPFCATQLAGEQGYI 420 (429)
T ss_pred cCcCCeeeeecceeeeeccccceeEecCCCcccccCCcccccchhhhhHhhcCcCCCccccccccCcchhhhhccCCceE
Confidence 67999998631 121 1 3345999987777776664 2468999998875 44555
Q ss_pred eC
Q 019860 329 RL 330 (334)
Q Consensus 329 ri 330 (334)
|+
T Consensus 421 kl 422 (429)
T KOG3842|consen 421 KL 422 (429)
T ss_pred EE
Confidence 54
No 229
>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=35.99 E-value=24 Score=25.87 Aligned_cols=14 Identities=21% Similarity=0.776 Sum_probs=11.7
Q ss_pred CCCCCCcCCCCCCC
Q 019860 276 DRTICPLCSQKRAN 289 (334)
Q Consensus 276 ~~~~CpiC~~~~~~ 289 (334)
.+..||.|+.....
T Consensus 27 TSq~C~~CG~~~~~ 40 (69)
T PF07282_consen 27 TSQTCPRCGHRNKK 40 (69)
T ss_pred CccCccCccccccc
Confidence 36689999999877
No 230
>PLN02720 complex II
Probab=35.73 E-value=18 Score=30.72 Aligned_cols=9 Identities=33% Similarity=1.391 Sum_probs=7.5
Q ss_pred HHHHHHHhc
Q 019860 235 FKMMEWWYQ 243 (334)
Q Consensus 235 lKfLEWWys 243 (334)
+||||||..
T Consensus 129 ~KFl~WWE~ 137 (140)
T PLN02720 129 VKFLDWWER 137 (140)
T ss_pred hHHHHHHHh
Confidence 589999973
No 231
>smart00132 LIM Zinc-binding domain present in Lin-11, Isl-1, Mec-3. Zinc-binding domain family. Some LIM domains bind protein partners via tyrosine-containing motifs. LIM domains are found in many key regulators of developmental pathways.
Probab=35.49 E-value=29 Score=21.59 Aligned_cols=36 Identities=22% Similarity=0.389 Sum_probs=20.3
Q ss_pred CCCcCCCCCCCc-ccccCCcccccHHHHHHHhhcCCCCCCCCCCC
Q 019860 279 ICPLCSQKRANP-SVVTVSGFVFCYACIFKYVSQYKRCPVTLMPA 322 (334)
Q Consensus 279 ~CpiC~~~~~~p-~~~~~~G~vfC~~Ci~~~~~~~~~CPv~~~~~ 322 (334)
.|..|.+.|.+. .++..-|..|...| -+|..|+.++
T Consensus 1 ~C~~C~~~i~~~~~~~~~~~~~~H~~C--------f~C~~C~~~L 37 (39)
T smart00132 1 KCAGCGKPIRGGELVLRALGKVWHPEC--------FKCSKCGKPL 37 (39)
T ss_pred CccccCCcccCCcEEEEeCCccccccC--------CCCcccCCcC
Confidence 488898888774 33333444444333 2455566554
No 232
>PRK11827 hypothetical protein; Provisional
Probab=34.41 E-value=23 Score=26.09 Aligned_cols=13 Identities=31% Similarity=0.628 Sum_probs=9.8
Q ss_pred CCCCCcCCCCCCC
Q 019860 277 RTICPLCSQKRAN 289 (334)
Q Consensus 277 ~~~CpiC~~~~~~ 289 (334)
-..||+|.+++.-
T Consensus 8 ILaCP~ckg~L~~ 20 (60)
T PRK11827 8 IIACPVCNGKLWY 20 (60)
T ss_pred heECCCCCCcCeE
Confidence 3479999998753
No 233
>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=33.89 E-value=22 Score=29.39 Aligned_cols=31 Identities=19% Similarity=0.317 Sum_probs=22.8
Q ss_pred CCCCCcCCCC---CCC-cccccCCcccccHHHHHH
Q 019860 277 RTICPLCSQK---RAN-PSVVTVSGFVFCYACIFK 307 (334)
Q Consensus 277 ~~~CpiC~~~---~~~-p~~~~~~G~vfC~~Ci~~ 307 (334)
...|.+|+++ +.| ..++..|+|.+|..|-..
T Consensus 54 ~~~C~~C~~~fg~l~~~~~~C~~C~~~VC~~C~~~ 88 (118)
T PF02318_consen 54 ERHCARCGKPFGFLFNRGRVCVDCKHRVCKKCGVY 88 (118)
T ss_dssp CSB-TTTS-BCSCTSTTCEEETTTTEEEETTSEEE
T ss_pred CcchhhhCCcccccCCCCCcCCcCCccccCccCCc
Confidence 4589999886 444 467888999999999775
No 234
>KOG2462 consensus C2H2-type Zn-finger protein [Transcription]
Probab=33.70 E-value=41 Score=32.18 Aligned_cols=12 Identities=33% Similarity=0.827 Sum_probs=7.0
Q ss_pred CCCCCcCCCCCC
Q 019860 277 RTICPLCSQKRA 288 (334)
Q Consensus 277 ~~~CpiC~~~~~ 288 (334)
...|+-|++...
T Consensus 130 r~~c~eCgk~ys 141 (279)
T KOG2462|consen 130 RYKCPECGKSYS 141 (279)
T ss_pred ceeccccccccc
Confidence 556666666543
No 235
>PF14353 CpXC: CpXC protein
Probab=32.46 E-value=32 Score=28.47 Aligned_cols=44 Identities=14% Similarity=0.163 Sum_probs=21.9
Q ss_pred CCCCcCCCCCCCc--ccccCCcccccHHHHHHHhhc---CCCCCCCCCCCCc
Q 019860 278 TICPLCSQKRANP--SVVTVSGFVFCYACIFKYVSQ---YKRCPVTLMPATV 324 (334)
Q Consensus 278 ~~CpiC~~~~~~p--~~~~~~G~vfC~~Ci~~~~~~---~~~CPv~~~~~~~ 324 (334)
..||-|++...-. +.+.+.-. -.=..+-+.+ .-+||-||....+
T Consensus 2 itCP~C~~~~~~~v~~~I~~~~~---p~l~e~il~g~l~~~~CP~Cg~~~~~ 50 (128)
T PF14353_consen 2 ITCPHCGHEFEFEVWTSINADED---PELKEKILDGSLFSFTCPSCGHKFRL 50 (128)
T ss_pred cCCCCCCCeeEEEEEeEEcCcCC---HHHHHHHHcCCcCEEECCCCCCceec
Confidence 3699999876443 12211111 1111222222 2589999977543
No 236
>KOG1814 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=32.42 E-value=17 Score=36.53 Aligned_cols=51 Identities=25% Similarity=0.708 Sum_probs=36.4
Q ss_pred CCCCCCCc--CCCC-CCCc----ccccCCcccccHHHHHHHhhcCCCCCCCCCCCCccCeeeCc
Q 019860 275 PDRTICPL--CSQK-RANP----SVVTVSGFVFCYACIFKYVSQYKRCPVTLMPATVEQIRRLF 331 (334)
Q Consensus 275 ~~~~~Cpi--C~~~-~~~p----~~~~~~G~vfC~~Ci~~~~~~~~~CPv~~~~~~~~~l~ri~ 331 (334)
+|...||- |..+ .++| ++++.|.++||.-|-..|=- ..+|-+.. ++++++|
T Consensus 271 sdv~yCPr~~Cq~p~~~d~~~~l~~CskCnFaFCtlCk~t~HG-~s~Ck~~~-----~~~~~l~ 328 (445)
T KOG1814|consen 271 SDVVYCPRACCQLPVKQDPGRALAICSKCNFAFCTLCKLTWHG-VSPCKVKA-----EKLIELY 328 (445)
T ss_pred cccccCChhhccCccccCchhhhhhhccCccHHHHHHHHhhcC-CCcccCch-----HHHHHHH
Confidence 35578988 8777 5666 67888999999999998865 44554443 2555555
No 237
>PHA02768 hypothetical protein; Provisional
Probab=32.30 E-value=35 Score=24.71 Aligned_cols=42 Identities=7% Similarity=0.128 Sum_probs=28.2
Q ss_pred CCCCCcCCCCCCCcccccCCcccccHHHHHHHhhc---CCCCCCCCCCC-CccCeeeC
Q 019860 277 RTICPLCSQKRANPSVVTVSGFVFCYACIFKYVSQ---YKRCPVTLMPA-TVEQIRRL 330 (334)
Q Consensus 277 ~~~CpiC~~~~~~p~~~~~~G~vfC~~Ci~~~~~~---~~~CPv~~~~~-~~~~l~ri 330 (334)
...|+.|++.......+. + +.+. .-+|..|++-. ....++.|
T Consensus 5 ~y~C~~CGK~Fs~~~~L~--~----------H~r~H~k~~kc~~C~k~f~~~s~l~~~ 50 (55)
T PHA02768 5 GYECPICGEIYIKRKSMI--T----------HLRKHNTNLKLSNCKRISLRTGEYIEI 50 (55)
T ss_pred ccCcchhCCeeccHHHHH--H----------HHHhcCCcccCCcccceecccceeEEE
Confidence 468999999988776553 2 3333 34899998763 45566665
No 238
>TIGR02827 RNR_anaer_Bdell anaerobic ribonucleoside-triphosphate reductase. Members of this family belong to the class III anaerobic ribonucleoside-triphosphate reductases (RNR). These glycine-radical-containing enzymes are oxygen-sensitive and operate under anaerobic conditions. The genes for this family are pair with genes for an acitivating protein that creates a glycine radical. Members of this family, though related, fall outside the scope of TIGR02487, a functionally equivalent protein set; no genome has members in both familes. Identification as RNR is supported by gene pairing with the activating protein, lack of other anaerobic RNR, and presence of an upstream regulatory element strongly conserved upstream of most RNR operons.
Probab=31.50 E-value=27 Score=37.02 Aligned_cols=18 Identities=28% Similarity=0.541 Sum_probs=12.6
Q ss_pred CCCCCCCCCCCccCeeeCc
Q 019860 313 KRCPVTLMPATVEQIRRLF 331 (334)
Q Consensus 313 ~~CPv~~~~~~~~~l~ri~ 331 (334)
..||.|+.. +.+.++||-
T Consensus 547 ~~CP~CGs~-~~ev~sRv~ 564 (586)
T TIGR02827 547 HRCPVCGSA-NIDYGTRVI 564 (586)
T ss_pred CcCcCCCCc-cceEEEeec
Confidence 799999953 455666663
No 239
>PF04088 Peroxin-13_N: Peroxin 13, N-terminal region; InterPro: IPR007223 Peroxin-13 is a component of the peroxisomal translocation machinery with Peroxin-14 and Peroxin-17. Both termini of Peroxin-13 are oriented to the cytosol. It is required for peroxisomal association of peroxin-14 []. The proteins also contain an SH3 domain (IPR001452 from INTERPRO).; GO: 0016560 protein import into peroxisome matrix, docking, 0005777 peroxisome, 0016021 integral to membrane
Probab=31.36 E-value=61 Score=28.49 Aligned_cols=27 Identities=22% Similarity=0.285 Sum_probs=21.2
Q ss_pred cCCCCCcchHHHHHHHHHHHHhHHHHH
Q 019860 46 HHSGLEKRQRVLSVVFMVVLPYFKSKL 72 (334)
Q Consensus 46 ~~~~Lt~~q~~~sLl~lV~~PYlk~KL 72 (334)
...+.+.+=...=+++.+++|||-.||
T Consensus 130 ~~~~~s~~PlllF~~~v~G~PyLi~Kl 156 (158)
T PF04088_consen 130 KRPKPSSKPLLLFLAAVFGLPYLIWKL 156 (158)
T ss_pred CCCCCCcccHHHHHHHHHHHHHHHHHH
Confidence 345567777777778889999999997
No 240
>KOG1701 consensus Focal adhesion adaptor protein Paxillin and related LIM proteins [Signal transduction mechanisms]
Probab=31.34 E-value=29 Score=35.16 Aligned_cols=51 Identities=24% Similarity=0.414 Sum_probs=28.3
Q ss_pred CCCCcCCCCCCC-cccccCCcccccHHHHHHHhhcCCCCCCCCCCC----CccCeeeC
Q 019860 278 TICPLCSQKRAN-PSVVTVSGFVFCYACIFKYVSQYKRCPVTLMPA----TVEQIRRL 330 (334)
Q Consensus 278 ~~CpiC~~~~~~-p~~~~~~G~vfC~~Ci~~~~~~~~~CPv~~~~~----~~~~l~ri 330 (334)
+.|-+|.+-+.. |-.+-..+-|+|-+|-++-+ -.+|-+|+.|+ ..++.+||
T Consensus 361 F~Cv~C~r~ldgipFtvd~~n~v~Cv~dfh~kf--APrCs~C~~PI~P~~G~~etvRv 416 (468)
T KOG1701|consen 361 FTCVVCARCLDGIPFTVDSQNNVYCVPDFHKKF--APRCSVCGNPILPRDGKDETVRV 416 (468)
T ss_pred eEEEEeccccCCccccccCCCceeeehhhhhhc--CcchhhccCCccCCCCCcceEEE
Confidence 455555555443 32222355566655555433 25899999886 34456665
No 241
>KOG1842 consensus FYVE finger-containing protein [General function prediction only]
Probab=30.90 E-value=19 Score=36.69 Aligned_cols=70 Identities=13% Similarity=0.159 Sum_probs=38.9
Q ss_pred HHHHHHHHHHHHHHHHHhcccc-cccCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCcCCCCCCCc---ccccCCcccc
Q 019860 225 QTGLIAAVFFFKMMEWWYQSAE-ERMSAPTVYPPPPPPPPPKVAREGIPLPPDRTICPLCSQKRANP---SVVTVSGFVF 300 (334)
Q Consensus 225 ~~~lp~~iF~lKfLEWWyss~~-~r~~~~~~lp~pppP~~~~~~~~~~~~~~~~~~CpiC~~~~~~p---~~~~~~G~vf 300 (334)
.-.+-+.|=+-|+++-|-+... .+...... .--|+. ++ .+-..||+|.+.+.-. -=|.-||-|.
T Consensus 139 ve~nkLiiRl~rL~~~~~t~~d~~k~k~~Eq----svVpW~----DD----s~V~~CP~Ca~~F~l~rRrHHCRLCG~Vm 206 (505)
T KOG1842|consen 139 VETNKLIIRLKRLEEGLPTEKDSVKRKRLEQ----SVVPWL----DD----SSVQFCPECANSFGLTRRRHHCRLCGRVM 206 (505)
T ss_pred HHHHHHHHHHHHHHccCccccchHHHHHHHh----cccccc----CC----CcccccccccchhhhHHHhhhhhhcchHH
Confidence 3345666667788888886431 11111000 011121 11 1245899999985433 2344599999
Q ss_pred cHHHHH
Q 019860 301 CYACIF 306 (334)
Q Consensus 301 C~~Ci~ 306 (334)
|..|-.
T Consensus 207 C~~C~k 212 (505)
T KOG1842|consen 207 CRDCSK 212 (505)
T ss_pred HHHHHH
Confidence 999975
No 242
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=30.71 E-value=43 Score=29.88 Aligned_cols=32 Identities=19% Similarity=0.202 Sum_probs=22.4
Q ss_pred CCCCCCcCCCCCCCcccccCCcccccHHHHHHHhhcCCCCCCCCCCCC
Q 019860 276 DRTICPLCSQKRANPSVVTVSGFVFCYACIFKYVSQYKRCPVTLMPAT 323 (334)
Q Consensus 276 ~~~~CpiC~~~~~~p~~~~~~G~vfC~~Ci~~~~~~~~~CPv~~~~~~ 323 (334)
..+.||.|+...+---++ ...-.||+||.++.
T Consensus 116 ~~Y~Cp~C~~rytf~eA~----------------~~~F~Cp~Cg~~L~ 147 (178)
T PRK06266 116 MFFFCPNCHIRFTFDEAM----------------EYGFRCPQCGEMLE 147 (178)
T ss_pred CEEECCCCCcEEeHHHHh----------------hcCCcCCCCCCCCe
Confidence 467899999766433333 23679999998874
No 243
>TIGR00375 conserved hypothetical protein TIGR00375. The member of this family from Methanococcus jannaschii, MJ0043, is considerably longer and appears to contain an intein N-terminal to the region of homology.
Probab=30.48 E-value=12 Score=37.32 Aligned_cols=18 Identities=11% Similarity=-0.069 Sum_probs=12.9
Q ss_pred HHhhHHHHHHHHHHHHHH
Q 019860 135 ACYPWLHASCEGLSFTYQ 152 (334)
Q Consensus 135 ~~YP~i~~~~e~~~l~~~ 152 (334)
-++|-+.++.++...+..
T Consensus 84 ~~fp~l~~a~~f~~~l~~ 101 (374)
T TIGR00375 84 LFMPTLADMKQFSNWLSA 101 (374)
T ss_pred EECCCHHHHHHHHHHHHh
Confidence 356778888887777774
No 244
>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=30.31 E-value=12 Score=23.15 Aligned_cols=26 Identities=19% Similarity=0.453 Sum_probs=14.8
Q ss_pred CCCcCCCCCCCcccccCCcccccHHHH
Q 019860 279 ICPLCSQKRANPSVVTVSGFVFCYACI 305 (334)
Q Consensus 279 ~CpiC~~~~~~p~~~~~~G~vfC~~Ci 305 (334)
.||.|...+.+-.+-. =+-.||..|.
T Consensus 3 ~C~rC~~~~~~~~~~~-r~~~~C~rCq 28 (30)
T PF06827_consen 3 KCPRCWNYIEDIGING-RSTYLCPRCQ 28 (30)
T ss_dssp B-TTT--BBEEEEETT-EEEEE-TTTC
T ss_pred cCccCCCcceEeEecC-CCCeECcCCc
Confidence 6999999887765543 5566777664
No 245
>PF10013 DUF2256: Uncharacterized protein conserved in bacteria (DUF2256); InterPro: IPR017136 There is currently no experimental data for members of this group or their homologues, nor do they exhibit features indicative of any function.
Probab=30.25 E-value=28 Score=23.78 Aligned_cols=10 Identities=50% Similarity=0.733 Sum_probs=5.2
Q ss_pred CCCCCCCCCC
Q 019860 313 KRCPVTLMPA 322 (334)
Q Consensus 313 ~~CPv~~~~~ 322 (334)
+.||+|+.|+
T Consensus 9 K~C~~C~rpf 18 (42)
T PF10013_consen 9 KICPVCGRPF 18 (42)
T ss_pred CcCcccCCcc
Confidence 4455555554
No 246
>PRK14714 DNA polymerase II large subunit; Provisional
Probab=30.17 E-value=23 Score=40.51 Aligned_cols=30 Identities=23% Similarity=0.402 Sum_probs=21.5
Q ss_pred CCCCCcCCCCCCCcccccCCccc---------ccHHHHH
Q 019860 277 RTICPLCSQKRANPSVVTVSGFV---------FCYACIF 306 (334)
Q Consensus 277 ~~~CpiC~~~~~~p~~~~~~G~v---------fC~~Ci~ 306 (334)
...||.|+...+.+..|+.||.. +|..|-.
T Consensus 679 ~~fCP~CGs~te~vy~CPsCGaev~~des~a~~CP~CGt 717 (1337)
T PRK14714 679 ENRCPDCGTHTEPVYVCPDCGAEVPPDESGRVECPRCDV 717 (1337)
T ss_pred cccCcccCCcCCCceeCccCCCccCCCccccccCCCCCC
Confidence 35788888887666677778874 7877754
No 247
>COG4530 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=29.84 E-value=29 Score=28.72 Aligned_cols=25 Identities=24% Similarity=0.364 Sum_probs=21.3
Q ss_pred CCCCCCcCCCCC----CCcccccCCcccc
Q 019860 276 DRTICPLCSQKR----ANPSVVTVSGFVF 300 (334)
Q Consensus 276 ~~~~CpiC~~~~----~~p~~~~~~G~vf 300 (334)
.+.+||-|++.+ ++|.|++-||..|
T Consensus 8 tKridPetg~KFYDLNrdPiVsPytG~s~ 36 (129)
T COG4530 8 TKRIDPETGKKFYDLNRDPIVSPYTGKSY 36 (129)
T ss_pred ccccCccccchhhccCCCccccCcccccc
Confidence 367999999975 6689999999988
No 248
>PRK00448 polC DNA polymerase III PolC; Validated
Probab=29.83 E-value=43 Score=39.25 Aligned_cols=37 Identities=30% Similarity=0.509 Sum_probs=26.6
Q ss_pred CCCCCcCCCC--CCCcccccCCcccccHHHHHHHhhcCCCCCCCCCCCCcc
Q 019860 277 RTICPLCSQK--RANPSVVTVSGFVFCYACIFKYVSQYKRCPVTLMPATVE 325 (334)
Q Consensus 277 ~~~CpiC~~~--~~~p~~~~~~G~vfC~~Ci~~~~~~~~~CPv~~~~~~~~ 325 (334)
++.||-|... ++|..+ . ||+=. ..+.||.||.++..+
T Consensus 908 hy~C~~C~~~ef~~~~~~-~-sG~Dl----------pdk~Cp~Cg~~~~kd 946 (1437)
T PRK00448 908 HYVCPNCKYSEFFTDGSV-G-SGFDL----------PDKDCPKCGTKLKKD 946 (1437)
T ss_pred cccCcccccccccccccc-c-ccccC----------ccccCcccccccccc
Confidence 7899999874 455555 3 77632 568999999987543
No 249
>CHL00174 accD acetyl-CoA carboxylase beta subunit; Reviewed
Probab=29.73 E-value=23 Score=34.22 Aligned_cols=26 Identities=12% Similarity=0.241 Sum_probs=16.7
Q ss_pred CCCCCcCCCCCC------CcccccCCcccccH
Q 019860 277 RTICPLCSQKRA------NPSVVTVSGFVFCY 302 (334)
Q Consensus 277 ~~~CpiC~~~~~------~p~~~~~~G~vfC~ 302 (334)
-.+||-|++.+- |--||+.|||.|=.
T Consensus 38 w~kc~~C~~~~~~~~l~~~~~vcp~c~~h~rl 69 (296)
T CHL00174 38 WVQCENCYGLNYKKFLKSKMNICEQCGYHLKM 69 (296)
T ss_pred eeECCCccchhhHHHHHHcCCCCCCCCCCcCC
Confidence 357999988753 33466667776543
No 250
>TIGR00398 metG methionyl-tRNA synthetase. The methionyl-tRNA synthetase (metG) is a class I amino acyl-tRNA ligase. This model appears to recognize the methionyl-tRNA synthetase of every species, including eukaryotic cytosolic and mitochondrial forms. The UPGMA difference tree calculated after search and alignment according to this model shows an unusual deep split between two families of MetG. One family contains forms from the Archaea, yeast cytosol, spirochetes, and E. coli, among others. The other family includes forms from yeast mitochondrion, Synechocystis sp., Bacillus subtilis, the Mycoplasmas, Aquifex aeolicus, and Helicobacter pylori. The E. coli enzyme is homodimeric, although monomeric forms can be prepared that are fully active. Activity of this enzyme in bacteria includes aminoacylation of fMet-tRNA with Met; subsequent formylation of the Met to fMet is catalyzed by a separate enzyme. Note that the protein from Aquifex aeolicus is split into an alpha (large) and beta (sma
Probab=29.54 E-value=34 Score=35.35 Aligned_cols=47 Identities=17% Similarity=0.270 Sum_probs=30.2
Q ss_pred CCCCCcCCCCCCCcccccCCcccccHHHHHHHhhcCCCCCCCCCCCCccCee
Q 019860 277 RTICPLCSQKRANPSVVTVSGFVFCYACIFKYVSQYKRCPVTLMPATVEQIR 328 (334)
Q Consensus 277 ~~~CpiC~~~~~~p~~~~~~G~vfC~~Ci~~~~~~~~~CPv~~~~~~~~~l~ 328 (334)
.+.||.|+..-.+.-+|..||+.+ ... --...+|..|+.++......
T Consensus 136 ~g~cp~c~~~~~~g~~ce~cg~~~--~~~---~l~~p~~~~~~~~~e~~~~~ 182 (530)
T TIGR00398 136 EGTCPKCGSEDARGDHCEVCGRHL--EPT---ELINPRCKICGAKPELRDSE 182 (530)
T ss_pred cCCCCCCCCcccccchhhhccccC--CHH---HhcCCccccCCCcceEEecc
Confidence 468999988655566777788754 111 11357899999887544333
No 251
>COG2176 PolC DNA polymerase III, alpha subunit (gram-positive type) [DNA replication, recombination, and repair]
Probab=29.44 E-value=49 Score=37.87 Aligned_cols=37 Identities=32% Similarity=0.561 Sum_probs=27.0
Q ss_pred CCCCCcCCCC--CCCcccccCCcccccHHHHHHHhhcCCCCCCCCCCCCcc
Q 019860 277 RTICPLCSQK--RANPSVVTVSGFVFCYACIFKYVSQYKRCPVTLMPATVE 325 (334)
Q Consensus 277 ~~~CpiC~~~--~~~p~~~~~~G~vfC~~Ci~~~~~~~~~CPv~~~~~~~~ 325 (334)
++.||-|... ++|+.+- +|+-- .++.||.|+.|+..+
T Consensus 914 HY~Cp~Cky~Ef~~d~svg--sGfDL----------pdK~CPkCg~pl~kD 952 (1444)
T COG2176 914 HYLCPECKYSEFIDDGSVG--SGFDL----------PDKDCPKCGTPLKKD 952 (1444)
T ss_pred cccCCCCceeeeecCCCcC--CCCCC----------CCCCCCcCCCccccC
Confidence 7899999874 5666663 67532 468999999997543
No 252
>PF02202 Tachykinin: Tachykinin family; InterPro: IPR002040 This family includes peptides, which belong to the tachykinin family. Tachykinins [, , ] are a group of biologically active peptides which excite neurons, evoke behavioral responses, are potent vasodilatators and contract (directly or indirectly) many smooth muscles. Tachykinins, like most other active peptides, are synthesized as larger protein precursors that are enzymatically converted to their mature forms. Tachykinins are from ten to twelve residues long.; GO: 0007217 tachykinin receptor signaling pathway, 0007268 synaptic transmission; PDB: 1MYU_A 1N6T_A 2GFR_A.
Probab=29.27 E-value=15 Score=18.06 Aligned_cols=6 Identities=50% Similarity=1.292 Sum_probs=4.8
Q ss_pred ccccCe
Q 019860 18 ESLYGL 23 (334)
Q Consensus 18 E~FYGL 23 (334)
+.||||
T Consensus 5 d~F~GL 10 (11)
T PF02202_consen 5 DQFYGL 10 (11)
T ss_dssp HHHCCC
T ss_pred ccceec
Confidence 579997
No 253
>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=29.20 E-value=19 Score=24.43 Aligned_cols=24 Identities=25% Similarity=0.757 Sum_probs=14.6
Q ss_pred CCCCCcCCCCCCCcccccCCcccccHHH
Q 019860 277 RTICPLCSQKRANPSVVTVSGFVFCYAC 304 (334)
Q Consensus 277 ~~~CpiC~~~~~~p~~~~~~G~vfC~~C 304 (334)
...||.|+.++-. ..-|.+||-.|
T Consensus 17 ~~~Cp~C~~PL~~----~k~g~~~Cv~C 40 (41)
T PF06677_consen 17 DEHCPDCGTPLMR----DKDGKIYCVSC 40 (41)
T ss_pred cCccCCCCCeeEE----ecCCCEECCCC
Confidence 3478999765533 23677776554
No 254
>COG1439 Predicted nucleic acid-binding protein, consists of a PIN domain and a Zn-ribbon module [General function prediction only]
Probab=29.19 E-value=15 Score=32.91 Aligned_cols=12 Identities=25% Similarity=0.481 Sum_probs=8.1
Q ss_pred cCCCCCCCCCCC
Q 019860 311 QYKRCPVTLMPA 322 (334)
Q Consensus 311 ~~~~CPv~~~~~ 322 (334)
+++.||+||-++
T Consensus 152 ~~~~Cp~CG~~~ 163 (177)
T COG1439 152 PKDFCPICGSPL 163 (177)
T ss_pred CCCcCCCCCCce
Confidence 456777777663
No 255
>PRK08271 anaerobic ribonucleoside triphosphate reductase; Provisional
Probab=29.18 E-value=18 Score=38.61 Aligned_cols=30 Identities=17% Similarity=0.304 Sum_probs=16.8
Q ss_pred cccCCcccccHHHHHHHhhcCCCCCCCCCCCCccCeeeC
Q 019860 292 VVTVSGFVFCYACIFKYVSQYKRCPVTLMPATVEQIRRL 330 (334)
Q Consensus 292 ~~~~~G~vfC~~Ci~~~~~~~~~CPv~~~~~~~~~l~ri 330 (334)
+|..|||. ....+..||.|+.. +.+.++||
T Consensus 568 iC~~CG~~--------~~g~~~~CP~CGs~-~~ev~~RV 597 (623)
T PRK08271 568 ICNDCHHI--------DKRTGKRCPICGSE-NIDYYTRV 597 (623)
T ss_pred cCCCCCCc--------CCCCCcCCcCCCCc-chhHHHHH
Confidence 55556654 12346789999852 23344444
No 256
>KOG2272 consensus Focal adhesion protein PINCH-1, contains LIM domains [Signal transduction mechanisms; Cytoskeleton]
Probab=28.73 E-value=30 Score=32.73 Aligned_cols=39 Identities=21% Similarity=0.435 Sum_probs=30.5
Q ss_pred CCCCCCCcCCCCCCCcccccCCcccccHHHHHHHhhcCCCCCCCC
Q 019860 275 PDRTICPLCSQKRANPSVVTVSGFVFCYACIFKYVSQYKRCPVTL 319 (334)
Q Consensus 275 ~~~~~CpiC~~~~~~p~~~~~~G~vfC~~Ci~~~~~~~~~CPv~~ 319 (334)
++...|.-|++.++..+-. +-|-.||.+|-. ...||||+
T Consensus 161 ~yHFkCt~C~keL~sdaRe-vk~eLyClrChD-----~mgipiCg 199 (332)
T KOG2272|consen 161 PYHFKCTTCGKELTSDARE-VKGELYCLRCHD-----KMGIPICG 199 (332)
T ss_pred ccceecccccccccchhhh-hccceecccccc-----ccCCcccc
Confidence 4788999999999877653 479999999975 35677765
No 257
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=28.52 E-value=31 Score=29.59 Aligned_cols=37 Identities=16% Similarity=0.090 Sum_probs=22.2
Q ss_pred CCCCCCcCCCCCCCcccccCCcccccHHHHHHHhhcCCCCCCCCCCCC
Q 019860 276 DRTICPLCSQKRANPSVVTVSGFVFCYACIFKYVSQYKRCPVTLMPAT 323 (334)
Q Consensus 276 ~~~~CpiC~~~~~~p~~~~~~G~vfC~~Ci~~~~~~~~~CPv~~~~~~ 323 (334)
..+.||-|+...+---++. -+. -...-.||.||.++.
T Consensus 98 ~~Y~Cp~C~~~y~~~ea~~-~~d----------~~~~f~Cp~Cg~~l~ 134 (147)
T smart00531 98 AYYKCPNCQSKYTFLEANQ-LLD----------MDGTFTCPRCGEELE 134 (147)
T ss_pred cEEECcCCCCEeeHHHHHH-hcC----------CCCcEECCCCCCEEE
Confidence 4678999988765332221 110 012368999998874
No 258
>KOG1428 consensus Inhibitor of type V adenylyl cyclases/Neuronal presynaptic protein Highwire/PAM/RPM-1 [Signal transduction mechanisms]
Probab=28.12 E-value=20 Score=41.82 Aligned_cols=48 Identities=15% Similarity=0.470 Sum_probs=36.9
Q ss_pred CCCCCCcCCCCCC--CcccccCCcccccHHHHHHHhhc----------CCCCCCCCCCCC
Q 019860 276 DRTICPLCSQKRA--NPSVVTVSGFVFCYACIFKYVSQ----------YKRCPVTLMPAT 323 (334)
Q Consensus 276 ~~~~CpiC~~~~~--~p~~~~~~G~vfC~~Ci~~~~~~----------~~~CPv~~~~~~ 323 (334)
..+.|-||-...- .|++---|||+|-..|.-.-+++ ...||+|..++.
T Consensus 3485 ~DDmCmICFTE~L~AAP~IqL~C~HiFHlqC~R~vLE~RW~GPRItF~FisCPiC~n~In 3544 (3738)
T KOG1428|consen 3485 ADDMCMICFTEALSAAPAIQLDCSHIFHLQCCRRVLENRWLGPRITFGFISCPICKNKIN 3544 (3738)
T ss_pred cCceEEEEehhhhCCCcceecCCccchhHHHHHHHHHhcccCCeeEEeeeecccccchhh
Confidence 3678999988643 35553349999999999988874 358999998875
No 259
>PRK01343 zinc-binding protein; Provisional
Probab=27.66 E-value=55 Score=23.88 Aligned_cols=35 Identities=23% Similarity=0.569 Sum_probs=22.9
Q ss_pred CCCCCcCCCCCCCcccccCCcccccH-HHH----HHHhhcCCCCCC
Q 019860 277 RTICPLCSQKRANPSVVTVSGFVFCY-ACI----FKYVSQYKRCPV 317 (334)
Q Consensus 277 ~~~CpiC~~~~~~p~~~~~~G~vfC~-~Ci----~~~~~~~~~CPv 317 (334)
...||+|+++..++. +-||- +|- -+|+.+.-+=|.
T Consensus 9 ~~~CP~C~k~~~~~~------rPFCS~RC~~iDLg~W~~e~Y~Ip~ 48 (57)
T PRK01343 9 TRPCPECGKPSTREA------YPFCSERCRDIDLNRWLSGSYVIPG 48 (57)
T ss_pred CCcCCCCCCcCcCCC------CcccCHHHhhhhHHHHhCCCcccCC
Confidence 457999999877543 34664 674 467776655454
No 260
>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=27.45 E-value=23 Score=22.40 Aligned_cols=21 Identities=29% Similarity=0.602 Sum_probs=8.2
Q ss_pred CCCcCCCCCC--Cc--ccccCCccc
Q 019860 279 ICPLCSQKRA--NP--SVVTVSGFV 299 (334)
Q Consensus 279 ~CpiC~~~~~--~p--~~~~~~G~v 299 (334)
.||.|+..-+ |- -|++.|||-
T Consensus 4 ~Cp~C~se~~y~D~~~~vCp~C~~e 28 (30)
T PF08274_consen 4 KCPLCGSEYTYEDGELLVCPECGHE 28 (30)
T ss_dssp --TTT-----EE-SSSEEETTTTEE
T ss_pred CCCCCCCcceeccCCEEeCCccccc
Confidence 5888887643 22 356666663
No 261
>KOG2807 consensus RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit SSL1 [Transcription; Replication, recombination and repair]
Probab=27.27 E-value=38 Score=33.22 Aligned_cols=42 Identities=19% Similarity=0.360 Sum_probs=27.5
Q ss_pred CCCCcCCCCCCCc--ccccCCcccccHHHHHHHhhcCCCCCCCC
Q 019860 278 TICPLCSQKRANP--SVVTVSGFVFCYACIFKYVSQYKRCPVTL 319 (334)
Q Consensus 278 ~~CpiC~~~~~~p--~~~~~~G~vfC~~Ci~~~~~~~~~CPv~~ 319 (334)
..|-.|......- -.|..|-++||-+|=.=-=+.-..||-|.
T Consensus 331 ~~Cf~C~~~~~~~~~y~C~~Ck~~FCldCDv~iHesLh~CpgCe 374 (378)
T KOG2807|consen 331 RFCFACQGELLSSGRYRCESCKNVFCLDCDVFIHESLHNCPGCE 374 (378)
T ss_pred cceeeeccccCCCCcEEchhccceeeccchHHHHhhhhcCCCcC
Confidence 3477775554443 35667888999998663333347899886
No 262
>PRK14892 putative transcription elongation factor Elf1; Provisional
Probab=27.03 E-value=27 Score=28.27 Aligned_cols=11 Identities=27% Similarity=0.661 Sum_probs=8.5
Q ss_pred CCCCCCcCCCC
Q 019860 276 DRTICPLCSQK 286 (334)
Q Consensus 276 ~~~~CpiC~~~ 286 (334)
.-..||-|+..
T Consensus 20 t~f~CP~Cge~ 30 (99)
T PRK14892 20 KIFECPRCGKV 30 (99)
T ss_pred cEeECCCCCCe
Confidence 46789999953
No 263
>COG2093 DNA-directed RNA polymerase, subunit E'' [Transcription]
Probab=26.95 E-value=20 Score=26.66 Aligned_cols=23 Identities=22% Similarity=0.317 Sum_probs=14.4
Q ss_pred cccccHHHHHHHhhcC--CCCCCCCCC
Q 019860 297 GFVFCYACIFKYVSQY--KRCPVTLMP 321 (334)
Q Consensus 297 G~vfC~~Ci~~~~~~~--~~CPv~~~~ 321 (334)
++--|..|-. +-+. ..||+|+.+
T Consensus 3 ~~kAC~~Ck~--l~~~d~e~CP~Cgs~ 27 (64)
T COG2093 3 TEKACKNCKR--LTPEDTEICPVCGST 27 (64)
T ss_pred hhHHHhhccc--cCCCCCccCCCCCCc
Confidence 4455777743 3333 459999977
No 264
>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=26.72 E-value=24 Score=33.96 Aligned_cols=25 Identities=24% Similarity=0.317 Sum_probs=16.6
Q ss_pred CCCCCcCCCCCCCc------ccccCCccccc
Q 019860 277 RTICPLCSQKRANP------SVVTVSGFVFC 301 (334)
Q Consensus 277 ~~~CpiC~~~~~~p------~~~~~~G~vfC 301 (334)
=.+||-|++.+-.. -||+.|||.|=
T Consensus 26 ~~~c~~c~~~~~~~~l~~~~~vc~~c~~h~r 56 (285)
T TIGR00515 26 WTKCPKCGQVLYTKELERNLEVCPKCDHHMR 56 (285)
T ss_pred eeECCCCcchhhHHHHHhhCCCCCCCCCcCc
Confidence 45799999876433 46666777653
No 265
>KOG2675 consensus Adenylate cyclase-associated protein (CAP/Srv2p) [Cytoskeleton; Signal transduction mechanisms]
Probab=26.30 E-value=47 Score=33.80 Aligned_cols=11 Identities=9% Similarity=0.244 Sum_probs=4.7
Q ss_pred HHHHHHHHHHH
Q 019860 222 DYAQTGLIAAV 232 (334)
Q Consensus 222 ~~~~~~lp~~i 232 (334)
.+.+....+++
T Consensus 201 ~YVk~hhtTGl 211 (480)
T KOG2675|consen 201 AYVKEHHTTGL 211 (480)
T ss_pred HHHHHhccccc
Confidence 34444444444
No 266
>TIGR03847 conserved hypothetical protein. The conserved hypothetical protein described here occurs as part of the trio of uncharacterized proteins common in the Actinobacteria.
Probab=26.24 E-value=38 Score=30.24 Aligned_cols=11 Identities=45% Similarity=1.232 Sum_probs=9.2
Q ss_pred CCCcCCCCCCCc
Q 019860 279 ICPLCSQKRANP 290 (334)
Q Consensus 279 ~CpiC~~~~~~p 290 (334)
.||+|+.++ ||
T Consensus 158 ~CPlCg~Pl-dP 168 (177)
T TIGR03847 158 PCPLCGRPI-DP 168 (177)
T ss_pred CCCCCCCCC-CC
Confidence 599999998 44
No 267
>PRK02935 hypothetical protein; Provisional
Probab=26.04 E-value=41 Score=27.63 Aligned_cols=15 Identities=20% Similarity=0.363 Sum_probs=10.9
Q ss_pred cCCCCCCCCCCCCcc
Q 019860 311 QYKRCPVTLMPATVE 325 (334)
Q Consensus 311 ~~~~CPv~~~~~~~~ 325 (334)
+...|.-|+.|++.+
T Consensus 85 rvD~CM~C~~PLTLd 99 (110)
T PRK02935 85 RVDACMHCNQPLTLD 99 (110)
T ss_pred ceeecCcCCCcCCcC
Confidence 345788888888764
No 268
>PF08394 Arc_trans_TRASH: Archaeal TRASH domain; InterPro: IPR013603 This region is found in the C terminus of a number of archaeal transcriptional regulators. It is thought to function as a metal-sensing regulatory module [].
Probab=25.86 E-value=65 Score=21.41 Aligned_cols=32 Identities=22% Similarity=0.729 Sum_probs=22.2
Q ss_pred CCcCCCCCC-CcccccCCc---ccccHHHHHHHhhc
Q 019860 280 CPLCSQKRA-NPSVVTVSG---FVFCYACIFKYVSQ 311 (334)
Q Consensus 280 CpiC~~~~~-~p~~~~~~G---~vfC~~Ci~~~~~~ 311 (334)
|-.|+++|. +|.+...-| |..|-.|..++.++
T Consensus 1 Cd~CG~~I~~eP~~~k~~~~~y~fCC~tC~~~fk~k 36 (37)
T PF08394_consen 1 CDYCGGEITGEPIVVKIGNKVYYFCCPTCLSQFKKK 36 (37)
T ss_pred CCccCCcccCCEEEEEECCeEEEEECHHHHHHHHhh
Confidence 778999987 476665333 34458998887653
No 269
>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional
Probab=25.62 E-value=38 Score=24.90 Aligned_cols=18 Identities=22% Similarity=0.431 Sum_probs=10.2
Q ss_pred cHHHHHHHhhcCCCCCCCCC
Q 019860 301 CYACIFKYVSQYKRCPVTLM 320 (334)
Q Consensus 301 C~~Ci~~~~~~~~~CPv~~~ 320 (334)
|.+|-..- ..=+||.||-
T Consensus 39 C~~CRk~~--~~Y~CP~CGF 56 (59)
T PRK14890 39 CEKCRKQS--NPYTCPKCGF 56 (59)
T ss_pred chhHHhcC--CceECCCCCC
Confidence 56664421 2347888874
No 270
>smart00746 TRASH metallochaperone-like domain.
Probab=25.49 E-value=77 Score=18.48 Aligned_cols=31 Identities=35% Similarity=0.836 Sum_probs=17.6
Q ss_pred CCcCCCCCCCccc---ccCCccc--cc-HHHHHHHhh
Q 019860 280 CPLCSQKRANPSV---VTVSGFV--FC-YACIFKYVS 310 (334)
Q Consensus 280 CpiC~~~~~~p~~---~~~~G~v--fC-~~Ci~~~~~ 310 (334)
|++|+..+.++.. ...-|++ || -.|...|..
T Consensus 1 c~~C~~~~~~~~~~~~~~~~g~~~~FCs~~c~~~~~~ 37 (39)
T smart00746 1 CSFCGKDIYNPGTGIMVVNDGKVFYFCSSKCLSKFKK 37 (39)
T ss_pred CCCCCCCccCCCCceEEEECCEEEEEeCHHHHHHHHh
Confidence 8899988864421 1135544 33 366666554
No 271
>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=25.26 E-value=24 Score=21.77 Aligned_cols=10 Identities=30% Similarity=0.474 Sum_probs=5.0
Q ss_pred CCCCCCCCCC
Q 019860 314 RCPVTLMPAT 323 (334)
Q Consensus 314 ~CPv~~~~~~ 323 (334)
.||+|+.++-
T Consensus 1 ~CP~C~s~l~ 10 (28)
T PF03119_consen 1 TCPVCGSKLV 10 (28)
T ss_dssp B-TTT--BEE
T ss_pred CcCCCCCEeE
Confidence 4899997763
No 272
>PF04184 ST7: ST7 protein; InterPro: IPR007311 The ST7 (for suppression of tumorigenicity 7) protein is thought to be a tumour suppressor gene. The molecular function of this protein is uncertain.
Probab=25.21 E-value=15 Score=38.00 Aligned_cols=19 Identities=37% Similarity=0.469 Sum_probs=16.5
Q ss_pred eeeeecccccCCCcccccc
Q 019860 2 LILETHSLRNTDASFSESL 20 (334)
Q Consensus 2 llvE~~~Lk~~~aSFaE~F 20 (334)
++.||-|+|+||.||+|.-
T Consensus 63 ~ifEWwyF~kygtsfieqv 81 (539)
T PF04184_consen 63 LIFEWWYFRKYGTSFIEQV 81 (539)
T ss_pred HHHHHHHHHhccchhhhhh
Confidence 4569999999999999954
No 273
>PF10164 DUF2367: Uncharacterized conserved protein (DUF2367); InterPro: IPR019317 This is a highly conserved set of proteins which contains three pairs of cysteine residues within a length of 42 amino acids and is rich in proline residues towards the N terminus. It includes a membrane protein that has been found to be highly expressed in the mouse brain and consequently, several members have been assigned as brain protein i3 (Bri3). Their function is unknown.
Probab=25.10 E-value=70 Score=25.85 Aligned_cols=43 Identities=19% Similarity=0.330 Sum_probs=26.2
Q ss_pred CCCCCcCCCCCCCcccccCCcc---cccHHHHHHHh--hcCCCCCCCCC
Q 019860 277 RTICPLCSQKRANPSVVTVSGF---VFCYACIFKYV--SQYKRCPVTLM 320 (334)
Q Consensus 277 ~~~CpiC~~~~~~p~~~~~~G~---vfC~~Ci~~~~--~~~~~CPv~~~ 320 (334)
-+-||.|+.-..+..-. .||. +||+++-.-.+ .++++|+.|+.
T Consensus 49 vggCp~CrvG~le~~ft-~~Gi~~AI~fFPiGilcc~~~r~~rC~nCG~ 96 (98)
T PF10164_consen 49 VGGCPACRVGVLEDSFT-CCGILCAIFFFPIGILCCLAMRERRCSNCGA 96 (98)
T ss_pred ecCCCCCceeeeccccc-HHHHHHHHHHHhhHHHHhhhcCccccCCCCc
Confidence 36799999865444322 2443 45555443332 46799999985
No 274
>smart00290 ZnF_UBP Ubiquitin Carboxyl-terminal Hydrolase-like zinc finger.
Probab=24.98 E-value=42 Score=22.82 Aligned_cols=25 Identities=24% Similarity=0.386 Sum_probs=16.3
Q ss_pred CCCcCCCCCCCcccccCCcccccHHH
Q 019860 279 ICPLCSQKRANPSVVTVSGFVFCYAC 304 (334)
Q Consensus 279 ~CpiC~~~~~~p~~~~~~G~vfC~~C 304 (334)
+|..|+..- +--++-.||+++|..-
T Consensus 1 ~C~~C~~~~-~l~~CL~C~~~~c~~~ 25 (50)
T smart00290 1 RCSVCGTIE-NLWLCLTCGQVGCGRY 25 (50)
T ss_pred CcccCCCcC-CeEEecCCCCcccCCC
Confidence 478888544 3334445999999554
No 275
>COG0333 RpmF Ribosomal protein L32 [Translation, ribosomal structure and biogenesis]
Probab=24.87 E-value=42 Score=24.47 Aligned_cols=22 Identities=23% Similarity=0.629 Sum_probs=15.4
Q ss_pred CCCCCcCCCCCCCcccccCCcc
Q 019860 277 RTICPLCSQKRANPSVVTVSGF 298 (334)
Q Consensus 277 ~~~CpiC~~~~~~p~~~~~~G~ 298 (334)
-..||.|++...--.|+..||+
T Consensus 27 ~~~c~~cG~~~l~Hrvc~~cg~ 48 (57)
T COG0333 27 LSVCPNCGEYKLPHRVCLKCGY 48 (57)
T ss_pred ceeccCCCCcccCceEcCCCCC
Confidence 4578888887665566666774
No 276
>PRK14873 primosome assembly protein PriA; Provisional
Probab=24.47 E-value=24 Score=37.89 Aligned_cols=42 Identities=19% Similarity=0.237 Sum_probs=26.2
Q ss_pred CCCCcCCCCCCCcc-----cc-cCCcccccHHHHHHHhhcCCCCCCCCCC
Q 019860 278 TICPLCSQKRANPS-----VV-TVSGFVFCYACIFKYVSQYKRCPVTLMP 321 (334)
Q Consensus 278 ~~CpiC~~~~~~p~-----~~-~~~G~vfC~~Ci~~~~~~~~~CPv~~~~ 321 (334)
..|.-|+...+-|. +. ...+...|.-|-+.. ....||.|+..
T Consensus 384 l~C~~Cg~~~~C~~C~~~L~~h~~~~~l~Ch~CG~~~--~p~~Cp~Cgs~ 431 (665)
T PRK14873 384 LACARCRTPARCRHCTGPLGLPSAGGTPRCRWCGRAA--PDWRCPRCGSD 431 (665)
T ss_pred eEhhhCcCeeECCCCCCceeEecCCCeeECCCCcCCC--cCccCCCCcCC
Confidence 35666666554441 11 124567788898753 46899999865
No 277
>PRK08665 ribonucleotide-diphosphate reductase subunit alpha; Validated
Probab=24.37 E-value=43 Score=36.58 Aligned_cols=25 Identities=28% Similarity=0.651 Sum_probs=16.9
Q ss_pred CCCCCcCCCCCCCc--c-cccCCccccc
Q 019860 277 RTICPLCSQKRANP--S-VVTVSGFVFC 301 (334)
Q Consensus 277 ~~~CpiC~~~~~~p--~-~~~~~G~vfC 301 (334)
...||-|+..+... | +|..|||--|
T Consensus 724 ~~~Cp~Cg~~l~~~~GC~~C~~CG~skC 751 (752)
T PRK08665 724 RGACPECGSILEHEEGCVVCHSCGYSKC 751 (752)
T ss_pred CCCCCCCCcccEECCCCCcCCCCCCCCC
Confidence 35799999876533 3 5666777665
No 278
>COG5151 SSL1 RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit SSL1 [Transcription / DNA replication, recombination, and repair]
Probab=24.31 E-value=65 Score=31.51 Aligned_cols=26 Identities=19% Similarity=0.317 Sum_probs=16.7
Q ss_pred CcccccHHHHHHHhhcCCCCCCCCCC
Q 019860 296 SGFVFCYACIFKYVSQYKRCPVTLMP 321 (334)
Q Consensus 296 ~G~vfC~~Ci~~~~~~~~~CPv~~~~ 321 (334)
|--.||-.|-.=.=+.-..||.|..+
T Consensus 394 CK~~FC~dCdvfiHe~Lh~C~gCe~~ 419 (421)
T COG5151 394 CKSTFCSDCDVFIHETLHFCIGCELP 419 (421)
T ss_pred hhhhhhhhhHHHHHHHHhhCCCCcCC
Confidence 44567777755333445789998754
No 279
>PRK05654 acetyl-CoA carboxylase subunit beta; Validated
Probab=24.17 E-value=28 Score=33.63 Aligned_cols=24 Identities=29% Similarity=0.434 Sum_probs=16.9
Q ss_pred CCCCCcCCCCCCC------cccccCCcccc
Q 019860 277 RTICPLCSQKRAN------PSVVTVSGFVF 300 (334)
Q Consensus 277 ~~~CpiC~~~~~~------p~~~~~~G~vf 300 (334)
-.+||-|++.+-. --||+.|||.|
T Consensus 27 ~~~c~~c~~~~~~~~l~~~~~vc~~c~~h~ 56 (292)
T PRK05654 27 WTKCPSCGQVLYRKELEANLNVCPKCGHHM 56 (292)
T ss_pred eeECCCccchhhHHHHHhcCCCCCCCCCCe
Confidence 4589999987643 34777777766
No 280
>KOG4217 consensus Nuclear receptors of the nerve growth factor-induced protein B type [Transcription]
Probab=24.01 E-value=69 Score=33.05 Aligned_cols=42 Identities=24% Similarity=0.528 Sum_probs=28.1
Q ss_pred CCCCCCcCCCCCCCcccccCCcccccHHHHH---HHhh--------cCCCCCCCCCC
Q 019860 276 DRTICPLCSQKRANPSVVTVSGFVFCYACIF---KYVS--------QYKRCPVTLMP 321 (334)
Q Consensus 276 ~~~~CpiC~~~~~~p~~~~~~G~vfC~~Ci~---~~~~--------~~~~CPv~~~~ 321 (334)
..+.|.+|+.. ++|..=|---|--|-= +-|+ .++.|||.+..
T Consensus 268 ~e~~CAVCgDn----AaCqHYGvRTCEGCKGFFKRTVQKnaKYvClanKnCPVDKRr 320 (605)
T KOG4217|consen 268 AEGLCAVCGDN----AACQHYGVRTCEGCKGFFKRTVQKNAKYVCLANKNCPVDKRR 320 (605)
T ss_pred ccceeeecCCh----HHhhhcCccccccchHHHHHHHhcCCeeEeecCCCCCcchhh
Confidence 47899999863 4555677777777743 2222 36789998643
No 281
>PF03966 Trm112p: Trm112p-like protein; InterPro: IPR005651 This family of short proteins have no known function. The bacterial members are about 60-70 amino acids in length and the eukaryotic examples are about 120 amino acids in length. The C terminus contains the strongest conservation. The function of this family is uncertain. The bacterial members are about 60-70 amino acids in length and the eukaryotic examples are about 120 amino acids in length. The C terminus contains the strongest conservation. The entry contains 2 families: Trm112, which is required for tRNA methylation in Saccharomyces cerevisiae (Baker's yeast) and is found in complexes with 2 tRNA methylases (TRM9 and TRM11) also with putative methyltransferase YDR140W []. The zinc-finger protein Ynr046w is plurifunctional and a component of the eRF1 methyltransferase in yeast []. The crystal structure of Ynr046w has been determined to 1.7 A resolution. It comprises a zinc-binding domain built from both the N- and C-terminal sequences and an inserted domain, absent from bacterial and archaeal orthologs of the protein, composed of three alpha-helices []. UPF0434, which are proteins that are functionally uncharacterised. ; PDB: 3Q87_A 2KPI_A 2K5R_A 2HF1_A 2JS4_A 2J6A_A 2JR6_A 2PK7_A 2JNY_A.
Probab=24.01 E-value=31 Score=25.56 Aligned_cols=11 Identities=27% Similarity=0.733 Sum_probs=7.2
Q ss_pred CCCCCcCCCCC
Q 019860 277 RTICPLCSQKR 287 (334)
Q Consensus 277 ~~~CpiC~~~~ 287 (334)
-..||.|..++
T Consensus 7 iL~Cp~ck~pL 17 (68)
T PF03966_consen 7 ILACPVCKGPL 17 (68)
T ss_dssp TBB-TTTSSBE
T ss_pred hhcCCCCCCcc
Confidence 34688888866
No 282
>PF06170 DUF983: Protein of unknown function (DUF983); InterPro: IPR009325 This family consists of several bacterial proteins of unknown function.
Probab=23.96 E-value=40 Score=26.53 Aligned_cols=18 Identities=22% Similarity=0.383 Sum_probs=13.6
Q ss_pred HHhhcCCCCCCCCCCCCc
Q 019860 307 KYVSQYKRCPVTLMPATV 324 (334)
Q Consensus 307 ~~~~~~~~CPv~~~~~~~ 324 (334)
.|++-..+||+||...+.
T Consensus 3 g~Lk~~~~C~~CG~d~~~ 20 (86)
T PF06170_consen 3 GYLKVAPRCPHCGLDYSH 20 (86)
T ss_pred ccccCCCcccccCCcccc
Confidence 467778899999977653
No 283
>PF13717 zinc_ribbon_4: zinc-ribbon domain
Probab=23.82 E-value=40 Score=21.98 Aligned_cols=8 Identities=50% Similarity=1.256 Sum_probs=4.0
Q ss_pred CCCcCCCC
Q 019860 279 ICPLCSQK 286 (334)
Q Consensus 279 ~CpiC~~~ 286 (334)
.||-|...
T Consensus 4 ~Cp~C~~~ 11 (36)
T PF13717_consen 4 TCPNCQAK 11 (36)
T ss_pred ECCCCCCE
Confidence 35555554
No 284
>COG1656 Uncharacterized conserved protein [Function unknown]
Probab=23.73 E-value=35 Score=30.22 Aligned_cols=15 Identities=20% Similarity=0.541 Sum_probs=11.2
Q ss_pred CCCCCCcCCCCCCCc
Q 019860 276 DRTICPLCSQKRANP 290 (334)
Q Consensus 276 ~~~~CpiC~~~~~~p 290 (334)
+...||.|..++...
T Consensus 96 e~~RCp~CN~~L~~v 110 (165)
T COG1656 96 EFSRCPECNGELEKV 110 (165)
T ss_pred ccccCcccCCEeccC
Confidence 456899999887654
No 285
>PF14354 Lar_restr_allev: Restriction alleviation protein Lar
Probab=23.67 E-value=30 Score=24.72 Aligned_cols=27 Identities=22% Similarity=0.394 Sum_probs=14.5
Q ss_pred CCCcCCCCCCCccccc--CC---cccccHHHH
Q 019860 279 ICPLCSQKRANPSVVT--VS---GFVFCYACI 305 (334)
Q Consensus 279 ~CpiC~~~~~~p~~~~--~~---G~vfC~~Ci 305 (334)
-||.|+.....-.... .. -+|+|..|-
T Consensus 5 PCPFCG~~~~~~~~~~~~~~~~~~~V~C~~Cg 36 (61)
T PF14354_consen 5 PCPFCGSADVLIRQDEGFDYGMYYYVECTDCG 36 (61)
T ss_pred CCCCCCCcceEeecccCCCCCCEEEEEcCCCC
Confidence 3999976533221111 12 357787773
No 286
>PRK01110 rpmF 50S ribosomal protein L32; Validated
Probab=23.32 E-value=38 Score=24.81 Aligned_cols=21 Identities=10% Similarity=0.134 Sum_probs=16.1
Q ss_pred CCCCCcCCCCCCCcccccCCcc
Q 019860 277 RTICPLCSQKRANPSVVTVSGF 298 (334)
Q Consensus 277 ~~~CpiC~~~~~~p~~~~~~G~ 298 (334)
-..||-|++...-..++. ||+
T Consensus 27 ~~~c~~cg~~~~pH~vc~-cG~ 47 (60)
T PRK01110 27 LSVDKTTGEYHLPHHVSP-KGY 47 (60)
T ss_pred eeEcCCCCceeccceecC-Ccc
Confidence 457888988887777777 775
No 287
>KOG2066 consensus Vacuolar assembly/sorting protein VPS41 [Intracellular trafficking, secretion, and vesicular transport]
Probab=22.86 E-value=27 Score=37.96 Aligned_cols=41 Identities=15% Similarity=0.417 Sum_probs=32.4
Q ss_pred CCCCCcCCCCCC------Cc-ccccCCcccccHHHHHHHhhcCCCCCCCC
Q 019860 277 RTICPLCSQKRA------NP-SVVTVSGFVFCYACIFKYVSQYKRCPVTL 319 (334)
Q Consensus 277 ~~~CpiC~~~~~------~p-~~~~~~G~vfC~~Ci~~~~~~~~~CPv~~ 319 (334)
...|..|.+++- +- .|.. |||+|-.+|+......++ |-.|.
T Consensus 784 e~rc~~c~~~~l~~~~~~~~~~v~~-c~h~yhk~c~~~~~~~~~-~~~~~ 831 (846)
T KOG2066|consen 784 EERCSSCFEPNLPSGAAFDSVVVFH-CGHMYHKECLMMESLRNA-CNIES 831 (846)
T ss_pred hhhhhhhcccccccCcccceeeEEE-ccchhhhcccccHHHhcc-cChhh
Confidence 568999999876 33 3555 999999999999988776 65554
No 288
>PF06750 DiS_P_DiS: Bacterial Peptidase A24 N-terminal domain; InterPro: IPR010627 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Aspartic endopeptidases 3.4.23. from EC of vertebrate, fungal and retroviral origin have been characterised []. More recently, aspartic endopeptidases associated with the processing of bacterial type 4 prepilin [] and archaean preflagellin have been described [, ]. Structurally, aspartic endopeptidases are bilobal enzymes, each lobe contributing a catalytic Asp residue, with an extended active site cleft localised between the two lobes of the molecule. One lobe has probably evolved from the other through a gene duplication event in the distant past. In modern-day enzymes, although the three-dimensional structures are very similar, the amino acid sequences are more divergent, except for the catalytic site motif, which is very conserved. The presence and position of disulphide bridges are other conserved features of aspartic peptidases. All or most aspartate peptidases are endopeptidases. These enzymes have been assigned into clans (proteins which are evolutionary related), and further sub-divided into families, largely on the basis of their tertiary structure. This domain is found at the N terminus of bacterial aspartic peptidases belonging to MEROPS peptidase family A24 (clan AD), subfamily A24A (type IV prepilin peptidase, IPR000045 from INTERPRO). It's function has not been specifically determined; however some of the family have been characterised as bifunctional [], and this domain may contain the N-methylation activity. The domain consists of an intracellular region between a pair of transmembrane domains. This intracellular region contains an invariant proline and four conserved cysteines. These Cys residues are arranged in a two-pair motif, with the Cys residues of a pair separated (usually) by 2 aa and with each pair separated by 21 largely hydrophilic residues (C-X-X-C...X21...C-X-X-C); they have been shown to be essential to the overall function of the enzyme [, ]. The bifunctional enzyme prepilin peptidase (PilD) from Pseudomonas aeruginosa is a key determinant in both type-IV pilus biogenesis and extracellular protein secretion, in its roles as a leader peptidase and methyl transferase (MTase). It is responsible for endopeptidic cleavage of the unique leader peptides that characterise type-IV pilin precursors, as well as proteins with homologous leader sequences that are essential components of the general secretion pathway found in a variety of Gram-negative pathogens. Following removal of the leader peptides, the same enzyme is responsible for the second posttranslational modification that characterises the type-IV pilins and their homologues, namely N-methylation of the newly exposed N-terminal amino acid residue [].
Probab=22.77 E-value=35 Score=27.08 Aligned_cols=22 Identities=14% Similarity=0.199 Sum_probs=19.1
Q ss_pred hcCCCCCCCCCCCCccCeeeCc
Q 019860 310 SQYKRCPVTLMPATVEQIRRLF 331 (334)
Q Consensus 310 ~~~~~CPv~~~~~~~~~l~ri~ 331 (334)
.....||.|+.++..-|+++|+
T Consensus 31 ~~rS~C~~C~~~L~~~~lIPi~ 52 (92)
T PF06750_consen 31 FPRSHCPHCGHPLSWWDLIPIL 52 (92)
T ss_pred CCCCcCcCCCCcCcccccchHH
Confidence 3457999999999999999875
No 289
>TIGR01405 polC_Gram_pos DNA polymerase III, alpha chain, Gram-positive type. The N-terminal region of about 200 amino acids is rich in low-complexity sequence, poorly alignable, and not included n this model.
Probab=22.68 E-value=62 Score=37.34 Aligned_cols=37 Identities=32% Similarity=0.549 Sum_probs=26.4
Q ss_pred CCCCCcCCCC--CCCcccccCCcccccHHHHHHHhhcCCCCCCCCCCCCcc
Q 019860 277 RTICPLCSQK--RANPSVVTVSGFVFCYACIFKYVSQYKRCPVTLMPATVE 325 (334)
Q Consensus 277 ~~~CpiC~~~--~~~p~~~~~~G~vfC~~Ci~~~~~~~~~CPv~~~~~~~~ 325 (334)
++.||-|... +++..+ . |||- -.++.||.|+.++..+
T Consensus 683 hy~c~~c~~~ef~~~~~~-~-sg~d----------lp~k~cp~c~~~~~~d 721 (1213)
T TIGR01405 683 HYLCPNCKYSEFITDGSV-G-SGFD----------LPDKDCPKCGAPLKKD 721 (1213)
T ss_pred cccCcccccccccccccc-c-cccc----------CccccCcccccccccc
Confidence 7899999874 455554 2 7763 2568999999887543
No 290
>COG1675 TFA1 Transcription initiation factor IIE, alpha subunit [Transcription]
Probab=22.49 E-value=39 Score=30.22 Aligned_cols=33 Identities=18% Similarity=0.205 Sum_probs=19.7
Q ss_pred CCCCCcCCCCCCCcccccCCcccccHHHHHHHhhcCCCCCCCCCCCCcc
Q 019860 277 RTICPLCSQKRANPSVVTVSGFVFCYACIFKYVSQYKRCPVTLMPATVE 325 (334)
Q Consensus 277 ~~~CpiC~~~~~~p~~~~~~G~vfC~~Ci~~~~~~~~~CPv~~~~~~~~ 325 (334)
-+.||.|.-...=..+.. . ..+||.||..+...
T Consensus 113 ~y~C~~~~~r~sfdeA~~-~---------------~F~Cp~Cg~~L~~~ 145 (176)
T COG1675 113 YYVCPNCHVKYSFDEAME-L---------------GFTCPKCGEDLEEY 145 (176)
T ss_pred ceeCCCCCCcccHHHHHH-h---------------CCCCCCCCchhhhc
Confidence 567877776654443333 2 26788888766433
No 291
>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=22.46 E-value=37 Score=21.87 Aligned_cols=12 Identities=25% Similarity=0.503 Sum_probs=7.6
Q ss_pred CCCcCCCCCCCc
Q 019860 279 ICPLCSQKRANP 290 (334)
Q Consensus 279 ~CpiC~~~~~~p 290 (334)
.||-|+....-+
T Consensus 4 ~CP~C~~~~~v~ 15 (38)
T TIGR02098 4 QCPNCKTSFRVV 15 (38)
T ss_pred ECCCCCCEEEeC
Confidence 577777765443
No 292
>PRK08579 anaerobic ribonucleoside triphosphate reductase; Provisional
Probab=22.30 E-value=15 Score=39.20 Aligned_cols=24 Identities=25% Similarity=0.494 Sum_probs=14.7
Q ss_pred cccccHHHHHHHhhcCCCCCCCCC
Q 019860 297 GFVFCYACIFKYVSQYKRCPVTLM 320 (334)
Q Consensus 297 G~vfC~~Ci~~~~~~~~~CPv~~~ 320 (334)
+...|..|-+.+...+..||+|+.
T Consensus 567 ~~~~C~~CG~~~~g~~~~CP~CGs 590 (625)
T PRK08579 567 AITVCNKCGRSTTGLYTRCPRCGS 590 (625)
T ss_pred CCccCCCCCCccCCCCCcCcCCCC
Confidence 344455555444455678999985
No 293
>KOG3807 consensus Predicted membrane protein ST7 (tumor suppressor in humans) [General function prediction only]
Probab=22.14 E-value=21 Score=35.40 Aligned_cols=19 Identities=32% Similarity=0.426 Sum_probs=16.6
Q ss_pred eeeeecccccCCCcccccc
Q 019860 2 LILETHSLRNTDASFSESL 20 (334)
Q Consensus 2 llvE~~~Lk~~~aSFaE~F 20 (334)
|+.||.|+++||.||+|..
T Consensus 78 LIFEWWYF~k~gtsfieqv 96 (556)
T KOG3807|consen 78 LIFEWWYFHKHGTSFIEQV 96 (556)
T ss_pred HHHHhHhhhccCcchhhhh
Confidence 4569999999999999964
No 294
>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]
Probab=22.14 E-value=35 Score=37.11 Aligned_cols=44 Identities=18% Similarity=0.385 Sum_probs=30.7
Q ss_pred CCCCCcCCCCCCCc------ccccCCcccccHHHHHHHhhcCCCCCCCCCC
Q 019860 277 RTICPLCSQKRANP------SVVTVSGFVFCYACIFKYVSQYKRCPVTLMP 321 (334)
Q Consensus 277 ~~~CpiC~~~~~~p------~~~~~~G~vfC~~Ci~~~~~~~~~CPv~~~~ 321 (334)
...|.-|+...+-| +.=...|...|.-|-++ -..-..||-|+..
T Consensus 435 ~l~C~~Cg~v~~Cp~Cd~~lt~H~~~~~L~CH~Cg~~-~~~p~~Cp~Cgs~ 484 (730)
T COG1198 435 LLLCRDCGYIAECPNCDSPLTLHKATGQLRCHYCGYQ-EPIPQSCPECGSE 484 (730)
T ss_pred eeecccCCCcccCCCCCcceEEecCCCeeEeCCCCCC-CCCCCCCCCCCCC
Confidence 34677777776665 22234788999999887 3334899999966
No 295
>PLN03086 PRLI-interacting factor K; Provisional
Probab=22.12 E-value=89 Score=33.05 Aligned_cols=46 Identities=15% Similarity=0.203 Sum_probs=24.9
Q ss_pred CCCCCCcCCCCCCC------------cccccCCcccccHHHHHHHhhcC-----CCCCCCCCCC
Q 019860 276 DRTICPLCSQKRAN------------PSVVTVSGFVFCYACIFKYVSQY-----KRCPVTLMPA 322 (334)
Q Consensus 276 ~~~~CpiC~~~~~~------------p~~~~~~G~vfC~~Ci~~~~~~~-----~~CPv~~~~~ 322 (334)
++..|+.|++.+.. |..|+ ||..+-..-+..+...+ -.|+-|+..+
T Consensus 452 ~H~~C~~Cgk~f~~s~LekH~~~~Hkpv~Cp-Cg~~~~R~~L~~H~~thCp~Kpi~C~fC~~~v 514 (567)
T PLN03086 452 NHVHCEKCGQAFQQGEMEKHMKVFHEPLQCP-CGVVLEKEQMVQHQASTCPLRLITCRFCGDMV 514 (567)
T ss_pred cCccCCCCCCccchHHHHHHHHhcCCCccCC-CCCCcchhHHHhhhhccCCCCceeCCCCCCcc
Confidence 45567777665432 23455 66655444444454321 3577777655
No 296
>PF10217 DUF2039: Uncharacterized conserved protein (DUF2039); InterPro: IPR019351 This entry is a region of approximately 100 residues containing three pairs of cysteine residues. The region is conserved from plants to humans but its function is unknown.
Probab=22.10 E-value=62 Score=25.92 Aligned_cols=36 Identities=31% Similarity=0.539 Sum_probs=27.7
Q ss_pred CCCCCcCCCCCCCcccccCCcccccHHHHHHHhhcCCCCCCCCCC
Q 019860 277 RTICPLCSQKRANPSVVTVSGFVFCYACIFKYVSQYKRCPVTLMP 321 (334)
Q Consensus 277 ~~~CpiC~~~~~~p~~~~~~G~vfC~~Ci~~~~~~~~~CPv~~~~ 321 (334)
...|-.|.+. +|.. .-|+.|-+|+. +.+.|+-|+.+
T Consensus 55 p~kC~~C~qk----tVk~-AYh~iC~~Ca~----~~~vCaKC~k~ 90 (92)
T PF10217_consen 55 PKKCNKCQQK----TVKH-AYHVICDPCAK----ELKVCAKCGKP 90 (92)
T ss_pred Cccccccccc----hHHH-HHHHHHHHHHH----hhccCcccCCC
Confidence 3468888764 3544 77999999998 56899999976
No 297
>COG1326 Uncharacterized archaeal Zn-finger protein [General function prediction only]
Probab=21.70 E-value=49 Score=30.10 Aligned_cols=7 Identities=43% Similarity=1.217 Sum_probs=5.9
Q ss_pred CCCCcCC
Q 019860 278 TICPLCS 284 (334)
Q Consensus 278 ~~CpiC~ 284 (334)
..||.|+
T Consensus 7 ~~Cp~Cg 13 (201)
T COG1326 7 IECPSCG 13 (201)
T ss_pred EECCCCC
Confidence 4699999
No 298
>PRK09710 lar restriction alleviation and modification protein; Reviewed
Probab=21.55 E-value=30 Score=25.83 Aligned_cols=27 Identities=19% Similarity=0.428 Sum_probs=17.4
Q ss_pred CCCcCCCCCCCcccccCCcccccHHHH
Q 019860 279 ICPLCSQKRANPSVVTVSGFVFCYACI 305 (334)
Q Consensus 279 ~CpiC~~~~~~p~~~~~~G~vfC~~Ci 305 (334)
-||-|+...........-.+|.|..|-
T Consensus 8 PCPFCG~~~~~v~~~~g~~~v~C~~Cg 34 (64)
T PRK09710 8 PCPFCGCPSVTVKAISGYYRAKCNGCE 34 (64)
T ss_pred CCCCCCCceeEEEecCceEEEEcCCCC
Confidence 499999987766553323445666553
No 299
>COG4338 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=21.37 E-value=27 Score=24.65 Aligned_cols=10 Identities=40% Similarity=1.145 Sum_probs=5.6
Q ss_pred CCCCcCCCCC
Q 019860 278 TICPLCSQKR 287 (334)
Q Consensus 278 ~~CpiC~~~~ 287 (334)
.+||+|+.++
T Consensus 13 KICpvCqRPF 22 (54)
T COG4338 13 KICPVCQRPF 22 (54)
T ss_pred hhhhhhcCch
Confidence 4566666543
No 300
>PRK13130 H/ACA RNA-protein complex component Nop10p; Reviewed
Probab=21.36 E-value=20 Score=26.06 Aligned_cols=12 Identities=25% Similarity=0.304 Sum_probs=8.0
Q ss_pred CCCCCCCCCCCC
Q 019860 312 YKRCPVTLMPAT 323 (334)
Q Consensus 312 ~~~CPv~~~~~~ 323 (334)
...||+||.++.
T Consensus 17 k~~CP~CG~~t~ 28 (56)
T PRK13130 17 KEICPVCGGKTK 28 (56)
T ss_pred cccCcCCCCCCC
Confidence 467777776654
No 301
>PRK00418 DNA gyrase inhibitor; Reviewed
Probab=21.26 E-value=48 Score=24.61 Aligned_cols=11 Identities=27% Similarity=0.576 Sum_probs=7.8
Q ss_pred CCCCCCCCCCC
Q 019860 313 KRCPVTLMPAT 323 (334)
Q Consensus 313 ~~CPv~~~~~~ 323 (334)
.+||+|++++.
T Consensus 7 v~CP~C~k~~~ 17 (62)
T PRK00418 7 VNCPTCGKPVE 17 (62)
T ss_pred ccCCCCCCccc
Confidence 46888887753
No 302
>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=21.24 E-value=38 Score=24.39 Aligned_cols=31 Identities=16% Similarity=0.144 Sum_probs=20.7
Q ss_pred CCCCcCCCCCCCcccccCCcccccHHHHHHHhhcCCCCCCCCCCCC
Q 019860 278 TICPLCSQKRANPSVVTVSGFVFCYACIFKYVSQYKRCPVTLMPAT 323 (334)
Q Consensus 278 ~~CpiC~~~~~~p~~~~~~G~vfC~~Ci~~~~~~~~~CPv~~~~~~ 323 (334)
..||.|+..+.=|.... |- --.||.|+..+.
T Consensus 3 ~~CP~CG~~iev~~~~~--Ge-------------iV~Cp~CGaele 33 (54)
T TIGR01206 3 FECPDCGAEIELENPEL--GE-------------LVICDECGAELE 33 (54)
T ss_pred cCCCCCCCEEecCCCcc--CC-------------EEeCCCCCCEEE
Confidence 58999999886654321 32 237899987653
No 303
>PF08273 Prim_Zn_Ribbon: Zinc-binding domain of primase-helicase; InterPro: IPR013237 This entry is represented by bacteriophage T7 Gp4. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This entry represents a zinc binding domain found in the N-terminal region of the bacteriophage T7 Gp4 and P4 alpha protein. P4 is a multifunctional protein with origin recognition, helicase and primase activities [, , ].; GO: 0003896 DNA primase activity, 0004386 helicase activity, 0008270 zinc ion binding; PDB: 1NUI_B.
Probab=21.19 E-value=33 Score=23.12 Aligned_cols=25 Identities=28% Similarity=0.693 Sum_probs=12.3
Q ss_pred CCCcCCCCCCCccccc---CCcccccHHH
Q 019860 279 ICPLCSQKRANPSVVT---VSGFVFCYAC 304 (334)
Q Consensus 279 ~CpiC~~~~~~p~~~~---~~G~vfC~~C 304 (334)
-||+|+..=..- +.+ ..|+-+|..|
T Consensus 5 pCP~CGG~DrFr-i~~d~~~~G~~~C~~C 32 (40)
T PF08273_consen 5 PCPICGGKDRFR-IFDDKDGRGTWICRQC 32 (40)
T ss_dssp --TTTT-TTTEE-EETT----S-EEETTT
T ss_pred CCCCCcCccccc-cCcCcccCCCEECCCC
Confidence 599999853222 111 2599999888
No 304
>KOG0314 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=21.12 E-value=32 Score=35.15 Aligned_cols=44 Identities=23% Similarity=0.394 Sum_probs=31.8
Q ss_pred CCCCCCcC-CCCCCCcccc-cCCcccccHHHHHHHhhcCCCCCCCCC
Q 019860 276 DRTICPLC-SQKRANPSVV-TVSGFVFCYACIFKYVSQYKRCPVTLM 320 (334)
Q Consensus 276 ~~~~CpiC-~~~~~~p~~~-~~~G~vfC~~Ci~~~~~~~~~CPv~~~ 320 (334)
....|++| .+.+.+..++ ..|+-.||-.||.+.+.+ +.||+|+.
T Consensus 218 e~~~c~~~~~~~~~~~~l~~~~~~~~~~~~~i~~~l~~-~~~~~c~~ 263 (448)
T KOG0314|consen 218 EGLQCPLCGKEVMLDAALLSKCCLKSFCDKCIRDALIS-KSMCVCGA 263 (448)
T ss_pred ccccCceecchhhHHHHHhhhhhcccCCcccccccccc-ccCCcchh
Confidence 36789999 4556777665 458889999999988866 45556653
No 305
>PRK07726 DNA topoisomerase III; Provisional
Probab=20.69 E-value=58 Score=34.95 Aligned_cols=41 Identities=24% Similarity=0.331 Sum_probs=22.9
Q ss_pred CCCCCcCCCCCC-----CcccccCCcccccHHHHHHHhh--cCCCCCCCCC
Q 019860 277 RTICPLCSQKRA-----NPSVVTVSGFVFCYACIFKYVS--QYKRCPVTLM 320 (334)
Q Consensus 277 ~~~CpiC~~~~~-----~p~~~~~~G~vfC~~Ci~~~~~--~~~~CPv~~~ 320 (334)
...||.|++.+. +-...-++|+-.|+. .|+. ..++||.|+.
T Consensus 610 ~~~CP~C~~~~~~~~~~~~~f~~Cs~~~~~~~---~~~~~~~~~~~~~~~~ 657 (658)
T PRK07726 610 GPKCPDCGKPMLKVKGKNGKMLVCQDRECGKR---KNVSKKTNARCPNCKK 657 (658)
T ss_pred cccccccCccceeecccCCeeEecCCCccccc---cccccccCCCCCccCC
Confidence 367999998654 111122344443433 3333 2468999985
No 306
>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=20.66 E-value=65 Score=33.37 Aligned_cols=34 Identities=21% Similarity=0.351 Sum_probs=0.0
Q ss_pred CCCcCCCCCC-----CcccccCCcccccHHHHHHHhhcCCCCCCCCCC
Q 019860 279 ICPLCSQKRA-----NPSVVTVSGFVFCYACIFKYVSQYKRCPVTLMP 321 (334)
Q Consensus 279 ~CpiC~~~~~-----~p~~~~~~G~vfC~~Ci~~~~~~~~~CPv~~~~ 321 (334)
.||-|.-.++ |...|.-||| -..-...||.|+..
T Consensus 224 ~C~~C~~~l~~h~~~~~l~Ch~Cg~---------~~~~~~~Cp~C~s~ 262 (505)
T TIGR00595 224 CCPNCDVSLTYHKKEGKLRCHYCGY---------QEPIPKTCPQCGSE 262 (505)
T ss_pred CCCCCCCceEEecCCCeEEcCCCcC---------cCCCCCCCCCCCCC
No 307
>KOG4577 consensus Transcription factor LIM3, contains LIM and HOX domains [Transcription]
Probab=20.22 E-value=27 Score=33.63 Aligned_cols=46 Identities=17% Similarity=0.460 Sum_probs=21.7
Q ss_pred CCCcCCCCCCCcccccCCcccccHHHHHHHhhcCC-CCCCCCCCCCccCee
Q 019860 279 ICPLCSQKRANPSVVTVSGFVFCYACIFKYVSQYK-RCPVTLMPATVEQIR 328 (334)
Q Consensus 279 ~CpiC~~~~~~p~~~~~~G~vfC~~Ci~~~~~~~~-~CPv~~~~~~~~~l~ 328 (334)
.|.-|+..+.+-+-.. -|-|||.. +|.++.+ +|-.|..-+-..+++
T Consensus 62 kCs~C~~qL~drCFsR-~~s~yCke---dFfKrfGTKCsaC~~GIpPtqVV 108 (383)
T KOG4577|consen 62 KCSDCHDQLADRCFSR-EGSVYCKE---DFFKRFGTKCSACQEGIPPTQVV 108 (383)
T ss_pred chhhhhhHHHHHHhhc-CCceeehH---HHHHHhCCcchhhcCCCChHHHH
Confidence 4555555555544443 55555543 3334432 455555544444333
No 308
>TIGR00627 tfb4 transcription factor tfb4. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=20.13 E-value=1.4e+02 Score=28.72 Aligned_cols=35 Identities=20% Similarity=0.308 Sum_probs=21.9
Q ss_pred CCCCcCCCCCCC-cccccCCcccccHHHHHHHhhcCCCCCCCCCC
Q 019860 278 TICPLCSQKRAN-PSVVTVSGFVFCYACIFKYVSQYKRCPVTLMP 321 (334)
Q Consensus 278 ~~CpiC~~~~~~-p~~~~~~G~vfC~~Ci~~~~~~~~~CPv~~~~ 321 (334)
..|- |++.+.+ .-+|+.|.-+||-. ...||+|+..
T Consensus 243 a~Cf-Ch~k~v~~GyvCs~Clsi~C~~--------p~~C~~Cgt~ 278 (279)
T TIGR00627 243 ASCF-CHHQLVSIGFVCSVCLSVLCQY--------TPICKTCKTA 278 (279)
T ss_pred ceee-ecCccccceEECCCccCCcCCC--------CCCCCCCCCC
Confidence 4566 4444433 45777777777743 3689999854
No 309
>COG4647 AcxC Acetone carboxylase, gamma subunit [Secondary metabolites biosynthesis, transport, and catabolism]
Probab=20.02 E-value=40 Score=28.77 Aligned_cols=21 Identities=14% Similarity=0.224 Sum_probs=14.2
Q ss_pred CcCCCCCCCcccccCCcccccH
Q 019860 281 PLCSQKRANPSVVTVSGFVFCY 302 (334)
Q Consensus 281 piC~~~~~~p~~~~~~G~vfC~ 302 (334)
=||...-..-+-|+ |||.||-
T Consensus 61 fi~qs~~~rv~rce-cghsf~d 81 (165)
T COG4647 61 FICQSAQKRVIRCE-CGHSFGD 81 (165)
T ss_pred EEEecccccEEEEe-ccccccC
Confidence 35655554445676 9999996
Done!