Query 024073
Match_columns 273
No_of_seqs 191 out of 694
Neff 6.4
Searched_HMMs 46136
Date Fri Mar 29 08:45:31 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/024073.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/024073hhsearch_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-57 1.3E-61 410.4 13.7 238 1-272 117-356 (357)
2 PF04757 Pex2_Pex12: Pex2 / Pe 99.9 6.1E-21 1.3E-25 169.2 14.9 141 1-184 89-229 (229)
3 smart00504 Ubox Modified RING 99.4 9.9E-14 2.2E-18 99.2 4.6 53 217-270 2-54 (63)
4 PLN03208 E3 ubiquitin-protein 99.3 8E-13 1.7E-17 114.8 4.5 57 215-272 17-89 (193)
5 KOG0317 Predicted E3 ubiquitin 99.3 9.5E-13 2.1E-17 119.7 3.8 55 215-270 238-292 (293)
6 KOG0320 Predicted E3 ubiquitin 99.3 2.1E-12 4.5E-17 110.1 4.5 57 215-271 130-187 (187)
7 PF13923 zf-C3HC4_2: Zinc fing 99.2 3.6E-12 7.9E-17 83.4 2.6 39 219-257 1-39 (39)
8 KOG0823 Predicted E3 ubiquitin 99.2 3.7E-12 8E-17 112.8 3.3 58 214-272 45-105 (230)
9 PF04564 U-box: U-box domain; 99.2 1.4E-11 3E-16 91.6 2.7 53 215-268 3-56 (73)
10 PF15227 zf-C3HC4_4: zinc fing 99.0 1.1E-10 2.4E-15 77.9 2.2 38 219-257 1-42 (42)
11 PF13639 zf-RING_2: Ring finge 99.0 9.4E-11 2E-15 78.5 1.4 41 217-258 1-44 (44)
12 PF13920 zf-C3HC4_3: Zinc fing 99.0 2.9E-10 6.3E-15 78.2 2.7 46 216-262 2-48 (50)
13 KOG0978 E3 ubiquitin ligase in 98.9 2.8E-10 6E-15 114.9 2.3 56 215-271 642-698 (698)
14 TIGR00599 rad18 DNA repair pro 98.9 7.6E-10 1.6E-14 106.2 5.0 54 214-268 24-77 (397)
15 KOG2164 Predicted E3 ubiquitin 98.9 5.6E-10 1.2E-14 108.4 3.4 55 216-271 186-245 (513)
16 PHA02929 N1R/p28-like protein; 98.9 9.2E-10 2E-14 99.1 4.0 48 215-262 173-227 (238)
17 cd00162 RING RING-finger (Real 98.9 1.3E-09 2.9E-14 71.3 3.3 43 218-260 1-44 (45)
18 PF00097 zf-C3HC4: Zinc finger 98.8 1.8E-09 3.9E-14 70.9 2.8 38 219-257 1-41 (41)
19 smart00184 RING Ring finger. E 98.8 3.6E-09 7.9E-14 66.8 3.1 38 219-257 1-39 (39)
20 COG5574 PEX10 RING-finger-cont 98.8 3E-09 6.6E-14 95.9 2.8 53 213-266 212-266 (271)
21 KOG3039 Uncharacterized conser 98.7 1.2E-08 2.6E-13 91.3 3.2 55 215-269 220-277 (303)
22 PF14835 zf-RING_6: zf-RING of 98.6 1.1E-08 2.3E-13 73.9 1.4 50 216-267 7-56 (65)
23 PF13445 zf-RING_UBOX: RING-ty 98.6 1.5E-08 3.2E-13 68.0 1.9 35 219-255 1-43 (43)
24 PHA02926 zinc finger-like prot 98.5 5.7E-08 1.2E-12 86.0 3.5 48 215-262 169-230 (242)
25 KOG2879 Predicted E3 ubiquitin 98.5 1.3E-06 2.9E-11 79.4 12.3 48 215-262 238-287 (298)
26 PF11789 zf-Nse: Zinc-finger o 98.5 4.8E-08 1E-12 69.4 1.8 44 215-258 10-55 (57)
27 PF14634 zf-RING_5: zinc-RING 98.5 1E-07 2.2E-12 63.9 2.8 42 218-259 1-44 (44)
28 COG5432 RAD18 RING-finger-cont 98.4 5.5E-08 1.2E-12 88.9 1.2 47 215-262 24-70 (391)
29 PF12678 zf-rbx1: RING-H2 zinc 98.4 1.3E-07 2.8E-12 70.4 3.0 43 216-258 19-73 (73)
30 TIGR00570 cdk7 CDK-activating 98.4 1.7E-07 3.8E-12 87.1 4.4 53 215-267 2-59 (309)
31 PF04641 Rtf2: Rtf2 RING-finge 98.2 1E-06 2.2E-11 80.5 4.3 57 215-272 112-171 (260)
32 KOG0287 Postreplication repair 98.1 4.1E-07 9E-12 84.8 -0.3 53 215-268 22-74 (442)
33 KOG4172 Predicted E3 ubiquitin 98.1 3.8E-07 8.2E-12 63.7 -0.9 53 216-271 7-61 (62)
34 COG5243 HRD1 HRD ubiquitin lig 98.1 2.3E-06 5.1E-11 80.7 3.0 47 214-261 285-344 (491)
35 KOG0824 Predicted E3 ubiquitin 98.0 2E-06 4.2E-11 79.2 2.2 47 216-263 7-54 (324)
36 KOG0802 E3 ubiquitin ligase [P 98.0 1.6E-06 3.4E-11 87.0 1.7 47 215-262 290-341 (543)
37 KOG2177 Predicted E3 ubiquitin 98.0 1.6E-06 3.5E-11 76.7 1.5 43 215-258 12-54 (386)
38 KOG2660 Locus-specific chromos 98.0 1.5E-06 3.3E-11 80.8 1.1 50 215-264 14-63 (331)
39 KOG0297 TNF receptor-associate 97.9 7.3E-06 1.6E-10 79.1 2.7 54 214-267 19-72 (391)
40 PF12861 zf-Apc11: Anaphase-pr 97.8 1.7E-05 3.8E-10 60.5 3.4 48 216-263 32-83 (85)
41 KOG1002 Nucleotide excision re 97.6 3.2E-05 7E-10 76.0 1.9 49 215-264 535-588 (791)
42 KOG4628 Predicted E3 ubiquitin 97.5 3.6E-05 7.7E-10 72.9 2.0 44 217-261 230-277 (348)
43 KOG1813 Predicted E3 ubiquitin 97.5 3.3E-05 7.2E-10 71.1 1.2 44 217-261 242-285 (313)
44 KOG0311 Predicted E3 ubiquitin 97.5 8.3E-06 1.8E-10 76.6 -2.7 46 216-261 43-89 (381)
45 COG5540 RING-finger-containing 97.4 6.6E-05 1.4E-09 69.4 1.9 46 216-262 323-372 (374)
46 COG5222 Uncharacterized conser 97.4 9.6E-05 2.1E-09 68.3 2.5 44 216-259 274-318 (427)
47 COG5152 Uncharacterized conser 97.2 0.00015 3.2E-09 63.6 1.6 45 216-261 196-240 (259)
48 KOG1734 Predicted RING-contain 97.2 0.00051 1.1E-08 62.7 4.6 50 215-265 223-284 (328)
49 KOG1645 RING-finger-containing 97.1 0.00014 3E-09 69.6 0.3 57 215-271 3-65 (463)
50 KOG4692 Predicted E3 ubiquitin 97.0 0.00039 8.4E-09 65.6 2.6 48 214-262 420-467 (489)
51 PF14570 zf-RING_4: RING/Ubox 96.9 0.00069 1.5E-08 46.4 2.2 42 219-261 1-47 (48)
52 COG5175 MOT2 Transcriptional r 96.8 0.00074 1.6E-08 63.5 2.7 52 215-267 13-69 (480)
53 KOG4159 Predicted E3 ubiquitin 96.6 0.0009 1.9E-08 64.8 1.9 47 214-261 82-128 (398)
54 KOG4265 Predicted E3 ubiquitin 96.6 0.0011 2.3E-08 62.7 1.9 52 216-270 290-342 (349)
55 PF11793 FANCL_C: FANCL C-term 96.4 0.0012 2.6E-08 48.7 0.8 49 216-264 2-68 (70)
56 COG5194 APC11 Component of SCF 96.4 0.0027 6E-08 47.9 2.7 48 216-263 31-82 (88)
57 PF14447 Prok-RING_4: Prokaryo 96.3 0.002 4.4E-08 45.2 1.6 49 215-266 6-54 (55)
58 KOG0828 Predicted E3 ubiquitin 96.3 0.0021 4.6E-08 63.0 2.1 49 214-262 569-634 (636)
59 KOG3039 Uncharacterized conser 96.1 0.0035 7.6E-08 56.7 2.6 34 215-249 42-75 (303)
60 KOG0827 Predicted E3 ubiquitin 96.1 0.0025 5.5E-08 60.9 1.6 52 216-267 4-61 (465)
61 KOG1039 Predicted E3 ubiquitin 96.1 0.0036 7.7E-08 59.6 2.6 49 214-262 159-221 (344)
62 KOG1001 Helicase-like transcri 95.9 0.0015 3.3E-08 67.2 -0.9 46 217-264 455-502 (674)
63 KOG0825 PHD Zn-finger protein 95.9 0.0015 3.2E-08 67.1 -1.1 47 215-261 122-170 (1134)
64 smart00744 RINGv The RING-vari 95.5 0.015 3.2E-07 39.9 2.9 40 218-258 1-49 (49)
65 KOG0804 Cytoplasmic Zn-finger 95.3 0.007 1.5E-07 58.9 1.2 43 218-262 177-222 (493)
66 KOG0883 Cyclophilin type, U bo 95.3 0.013 2.9E-07 56.1 3.0 54 216-270 40-93 (518)
67 PF10367 Vps39_2: Vacuolar sor 95.2 0.0083 1.8E-07 46.6 1.1 29 216-245 78-108 (109)
68 KOG2932 E3 ubiquitin ligase in 95.0 0.0086 1.9E-07 55.8 0.8 43 216-261 90-133 (389)
69 PF02891 zf-MIZ: MIZ/SP-RING z 94.9 0.0094 2E-07 41.1 0.6 43 217-260 3-50 (50)
70 KOG2930 SCF ubiquitin ligase, 94.9 0.016 3.4E-07 45.9 1.9 45 217-261 47-107 (114)
71 KOG3113 Uncharacterized conser 94.7 0.028 6.1E-07 51.1 3.1 56 215-272 110-168 (293)
72 KOG1785 Tyrosine kinase negati 94.6 0.015 3.1E-07 56.1 1.2 45 217-262 370-416 (563)
73 KOG1571 Predicted E3 ubiquitin 94.5 0.015 3.3E-07 55.1 1.0 42 216-261 305-346 (355)
74 KOG2817 Predicted E3 ubiquitin 94.1 0.15 3.2E-06 49.2 6.9 99 157-271 286-394 (394)
75 KOG2979 Protein involved in DN 94.1 0.026 5.5E-07 51.4 1.7 45 216-260 176-222 (262)
76 PF05290 Baculo_IE-1: Baculovi 93.6 0.056 1.2E-06 44.7 2.5 48 216-263 80-133 (140)
77 KOG3579 Predicted E3 ubiquitin 93.4 0.062 1.3E-06 49.7 2.9 37 215-251 267-306 (352)
78 PF10571 UPF0547: Uncharacteri 93.4 0.046 9.9E-07 32.7 1.3 22 218-239 2-24 (26)
79 KOG1493 Anaphase-promoting com 93.3 0.04 8.6E-07 41.3 1.2 48 216-263 31-82 (84)
80 KOG3002 Zn finger protein [Gen 92.9 0.071 1.5E-06 49.9 2.6 45 215-262 47-91 (299)
81 KOG4275 Predicted E3 ubiquitin 92.8 0.015 3.4E-07 53.8 -1.9 41 216-261 300-341 (350)
82 KOG0298 DEAD box-containing he 92.7 0.021 4.7E-07 61.7 -1.3 44 215-258 1152-1195(1394)
83 PF04216 FdhE: Protein involve 92.5 0.027 5.8E-07 52.2 -0.9 46 215-260 171-220 (290)
84 COG5236 Uncharacterized conser 92.5 0.071 1.5E-06 50.6 1.9 45 215-260 60-106 (493)
85 PRK04023 DNA polymerase II lar 90.8 0.21 4.5E-06 53.4 3.4 55 212-269 622-681 (1121)
86 COG5219 Uncharacterized conser 90.6 0.077 1.7E-06 56.1 0.1 46 216-261 1469-1522(1525)
87 KOG4185 Predicted E3 ubiquitin 89.8 0.18 4E-06 46.4 1.8 43 218-261 5-54 (296)
88 KOG4367 Predicted Zn-finger pr 89.8 0.16 3.5E-06 49.6 1.5 35 215-250 3-37 (699)
89 KOG1941 Acetylcholine receptor 89.5 0.14 3E-06 49.4 0.8 42 216-258 365-412 (518)
90 KOG1814 Predicted E3 ubiquitin 89.0 0.24 5.1E-06 48.0 2.0 46 215-260 183-238 (445)
91 TIGR01562 FdhE formate dehydro 88.9 0.15 3.3E-06 47.8 0.7 46 215-260 183-233 (305)
92 PF05883 Baculo_RING: Baculovi 88.4 0.21 4.6E-06 41.4 1.1 43 216-258 26-76 (134)
93 PLN02189 cellulose synthase 88.3 0.34 7.4E-06 52.0 2.7 47 215-262 33-87 (1040)
94 PF14446 Prok-RING_1: Prokaryo 88.2 0.52 1.1E-05 33.1 2.8 43 215-261 4-51 (54)
95 PHA03096 p28-like protein; Pro 87.0 0.34 7.4E-06 45.1 1.7 44 217-260 179-232 (284)
96 PLN02436 cellulose synthase A 86.8 0.46 1E-05 51.2 2.7 47 215-262 35-89 (1094)
97 cd00350 rubredoxin_like Rubred 86.5 0.43 9.4E-06 29.8 1.5 22 233-260 5-26 (33)
98 PF10235 Cript: Microtubule-as 85.7 0.54 1.2E-05 36.5 1.9 36 216-261 44-79 (90)
99 KOG1812 Predicted E3 ubiquitin 85.4 0.34 7.3E-06 46.9 0.8 42 216-258 306-352 (384)
100 PF07191 zinc-ribbons_6: zinc- 84.9 0.098 2.1E-06 38.6 -2.4 40 217-262 2-41 (70)
101 PF08746 zf-RING-like: RING-li 83.8 0.99 2.1E-05 30.0 2.3 39 219-257 1-43 (43)
102 PF03854 zf-P11: P-11 zinc fin 83.8 0.39 8.5E-06 32.8 0.3 43 218-262 4-46 (50)
103 PRK03564 formate dehydrogenase 83.8 0.57 1.2E-05 44.1 1.6 46 215-260 186-235 (309)
104 KOG3800 Predicted E3 ubiquitin 82.9 0.7 1.5E-05 43.0 1.7 34 234-267 22-56 (300)
105 PRK05978 hypothetical protein; 82.9 0.81 1.8E-05 38.6 2.0 33 216-264 33-65 (148)
106 KOG1812 Predicted E3 ubiquitin 81.8 0.6 1.3E-05 45.2 0.9 52 216-268 146-209 (384)
107 PLN02195 cellulose synthase A 81.2 1.4 3E-05 47.2 3.4 46 216-262 6-59 (977)
108 PLN02638 cellulose synthase A 80.9 1.2 2.6E-05 48.2 2.8 46 215-261 16-69 (1079)
109 cd00729 rubredoxin_SM Rubredox 80.2 1.1 2.4E-05 28.2 1.5 10 252-261 19-28 (34)
110 PF14569 zf-UDP: Zinc-binding 80.1 2 4.4E-05 32.4 3.0 48 215-262 8-62 (80)
111 KOG2068 MOT2 transcription fac 80.0 1.4 3E-05 41.7 2.6 45 217-261 250-297 (327)
112 PF07975 C1_4: TFIIH C1-like d 79.9 1.1 2.5E-05 31.0 1.5 28 230-258 22-50 (51)
113 PF09538 FYDLN_acid: Protein o 79.8 1.2 2.5E-05 35.7 1.8 28 215-242 8-39 (108)
114 TIGR02300 FYDLN_acid conserved 79.7 1.1 2.5E-05 36.7 1.7 27 215-241 8-38 (129)
115 KOG2169 Zn-finger transcriptio 79.4 1.3 2.8E-05 45.7 2.4 51 216-267 306-361 (636)
116 KOG1940 Zn-finger protein [Gen 78.0 1.4 3.1E-05 40.8 2.1 43 216-259 158-204 (276)
117 PLN02915 cellulose synthase A 77.5 1.7 3.8E-05 46.9 2.7 47 215-262 14-68 (1044)
118 COG1592 Rubrerythrin [Energy p 76.2 1.7 3.7E-05 37.4 1.9 13 216-228 134-146 (166)
119 TIGR00622 ssl1 transcription f 76.0 2.7 5.9E-05 33.9 2.9 43 216-258 55-110 (112)
120 PF12773 DZR: Double zinc ribb 75.7 1.3 2.7E-05 29.8 0.8 15 213-227 9-23 (50)
121 PRK14714 DNA polymerase II lar 75.6 1.6 3.5E-05 47.9 1.9 51 216-267 667-725 (1337)
122 PF05605 zf-Di19: Drought indu 75.6 1.6 3.4E-05 30.1 1.3 40 215-262 1-42 (54)
123 PHA02862 5L protein; Provision 75.5 2.3 5E-05 35.8 2.4 47 216-262 2-53 (156)
124 KOG4739 Uncharacterized protei 75.4 1.3 2.9E-05 40.0 1.0 33 217-249 4-37 (233)
125 KOG4445 Uncharacterized conser 75.3 0.75 1.6E-05 43.1 -0.6 47 216-263 115-187 (368)
126 COG5627 MMS21 DNA repair prote 75.3 1.6 3.4E-05 39.6 1.4 48 216-263 189-240 (275)
127 KOG4718 Non-SMC (structural ma 75.0 1.1 2.4E-05 40.0 0.4 44 216-259 181-224 (235)
128 KOG1815 Predicted E3 ubiquitin 74.8 5.6 0.00012 39.1 5.4 55 215-269 69-133 (444)
129 KOG2114 Vacuolar assembly/sort 74.8 1.5 3.3E-05 46.2 1.4 40 217-259 841-880 (933)
130 KOG3268 Predicted E3 ubiquitin 74.3 2.9 6.3E-05 36.5 2.8 48 216-264 165-230 (234)
131 KOG0825 PHD Zn-finger protein 74.0 2.2 4.7E-05 44.8 2.3 45 214-258 94-150 (1134)
132 PHA02825 LAP/PHD finger-like p 73.9 3.3 7.2E-05 35.4 3.0 49 215-263 7-60 (162)
133 KOG0824 Predicted E3 ubiquitin 73.6 1.2 2.6E-05 41.6 0.4 46 215-260 104-149 (324)
134 PF09889 DUF2116: Uncharacteri 73.5 1.8 4E-05 30.9 1.2 16 249-264 1-16 (59)
135 PF04423 Rad50_zn_hook: Rad50 72.6 0.87 1.9E-05 31.5 -0.7 14 252-265 21-34 (54)
136 KOG3970 Predicted E3 ubiquitin 71.6 3.2 7E-05 37.5 2.5 44 218-261 52-104 (299)
137 PLN02400 cellulose synthase 71.4 2.4 5.3E-05 46.0 2.0 47 215-262 35-89 (1085)
138 PF06750 DiS_P_DiS: Bacterial 71.1 5.7 0.00012 30.7 3.6 38 216-263 33-70 (92)
139 COG5183 SSM4 Protein involved 71.1 3.1 6.8E-05 43.8 2.6 53 214-266 10-70 (1175)
140 KOG2042 Ubiquitin fusion degra 70.9 3.6 7.8E-05 44.1 3.1 53 215-267 869-921 (943)
141 KOG2034 Vacuolar sorting prote 70.5 2.2 4.7E-05 45.2 1.4 34 216-249 817-851 (911)
142 COG0068 HypF Hydrogenase matur 70.0 1.7 3.8E-05 45.0 0.6 50 212-261 97-183 (750)
143 smart00647 IBR In Between Ring 69.2 1.2 2.6E-05 30.9 -0.6 18 230-247 41-58 (64)
144 COG3357 Predicted transcriptio 68.9 1.8 4E-05 33.5 0.4 28 228-259 57-84 (97)
145 PF15616 TerY-C: TerY-C metal 68.7 2.2 4.8E-05 35.3 0.8 40 217-263 78-117 (131)
146 PF09723 Zn-ribbon_8: Zinc rib 68.6 2.1 4.5E-05 28.2 0.5 17 250-270 25-41 (42)
147 COG5220 TFB3 Cdk activating ki 68.5 2 4.4E-05 39.1 0.6 44 216-259 10-61 (314)
148 PF03833 PolC_DP2: DNA polymer 68.4 1.6 3.6E-05 46.0 0.0 45 215-262 654-703 (900)
149 KOG0309 Conserved WD40 repeat- 68.2 3.1 6.7E-05 43.6 1.9 46 216-261 1028-1075(1081)
150 KOG0883 Cyclophilin type, U bo 67.8 3.1 6.7E-05 40.4 1.7 57 215-271 100-161 (518)
151 PLN02248 cellulose synthase-li 67.3 3.8 8.3E-05 44.6 2.4 36 230-266 146-181 (1135)
152 PF12906 RINGv: RING-variant d 66.9 3.2 6.9E-05 28.0 1.2 32 226-257 14-47 (47)
153 COG1645 Uncharacterized Zn-fin 65.4 2.6 5.7E-05 34.9 0.6 25 216-245 28-52 (131)
154 PF10497 zf-4CXXC_R1: Zinc-fin 64.9 8.1 0.00018 30.6 3.3 44 216-259 7-69 (105)
155 PF01363 FYVE: FYVE zinc finge 63.6 2.8 6E-05 30.0 0.4 34 215-248 8-44 (69)
156 KOG4362 Transcriptional regula 62.9 1.9 4.1E-05 44.6 -0.8 45 216-261 21-68 (684)
157 smart00064 FYVE Protein presen 62.5 5.9 0.00013 28.2 2.0 35 216-250 10-47 (68)
158 PF14205 Cys_rich_KTR: Cystein 61.8 3.7 8.1E-05 28.8 0.8 26 217-243 5-34 (55)
159 cd00065 FYVE FYVE domain; Zinc 61.0 6.4 0.00014 26.8 1.9 34 217-250 3-39 (57)
160 KOG0269 WD40 repeat-containing 60.9 6.8 0.00015 41.0 2.8 48 216-263 779-829 (839)
161 PF02148 zf-UBP: Zn-finger in 60.3 5.2 0.00011 28.4 1.3 33 219-251 1-37 (63)
162 PF13240 zinc_ribbon_2: zinc-r 60.1 1.7 3.7E-05 25.0 -1.0 11 219-229 2-12 (23)
163 PRK00420 hypothetical protein; 59.3 5.1 0.00011 32.3 1.3 22 217-242 24-45 (112)
164 COG3813 Uncharacterized protei 59.0 6.7 0.00015 29.3 1.7 29 228-259 21-49 (84)
165 KOG1356 Putative transcription 58.2 3.6 7.9E-05 43.4 0.3 44 216-259 229-279 (889)
166 PF09986 DUF2225: Uncharacteri 58.2 5.9 0.00013 35.2 1.6 53 215-269 4-66 (214)
167 PF12660 zf-TFIIIC: Putative z 57.9 5.6 0.00012 31.1 1.3 43 217-261 15-65 (99)
168 PHA00626 hypothetical protein 57.7 8 0.00017 27.4 1.8 7 218-224 2-8 (59)
169 KOG1952 Transcription factor N 57.0 5 0.00011 42.5 1.1 45 214-258 189-243 (950)
170 cd00730 rubredoxin Rubredoxin; 56.5 6.9 0.00015 26.9 1.4 13 248-260 31-43 (50)
171 KOG4218 Nuclear hormone recept 56.3 7.2 0.00016 37.4 1.9 11 216-226 15-25 (475)
172 PF04641 Rtf2: Rtf2 RING-finge 56.0 16 0.00035 33.3 4.1 37 216-252 34-70 (260)
173 KOG3161 Predicted E3 ubiquitin 55.3 3.4 7.4E-05 42.5 -0.4 39 216-258 11-53 (861)
174 KOG2041 WD40 repeat protein [G 55.3 9.5 0.00021 40.0 2.7 52 208-262 1123-1185(1189)
175 COG5109 Uncharacterized conser 54.4 8.4 0.00018 36.5 2.0 54 215-270 335-395 (396)
176 PRK07218 replication factor A; 53.8 9 0.00019 37.7 2.2 12 217-228 298-309 (423)
177 PF06906 DUF1272: Protein of u 53.6 17 0.00036 25.8 2.9 41 218-261 7-51 (57)
178 KOG1428 Inhibitor of type V ad 52.8 3.8 8.1E-05 46.0 -0.6 47 216-262 3486-3544(3738)
179 PRK14559 putative protein seri 52.2 6.1 0.00013 40.9 0.8 42 212-262 11-52 (645)
180 PF00412 LIM: LIM domain; Int 51.8 11 0.00023 25.6 1.8 32 215-246 25-56 (58)
181 PF13248 zf-ribbon_3: zinc-rib 51.6 3.2 6.9E-05 24.4 -0.8 9 217-225 3-11 (26)
182 KOG2113 Predicted RNA binding 51.5 11 0.00025 35.6 2.4 50 216-270 343-393 (394)
183 TIGR00143 hypF [NiFe] hydrogen 51.5 5.3 0.00012 41.8 0.2 51 212-262 64-151 (711)
184 PTZ00303 phosphatidylinositol 51.4 10 0.00022 40.2 2.1 32 217-248 461-500 (1374)
185 PF08271 TF_Zn_Ribbon: TFIIB z 51.1 7.8 0.00017 25.3 0.9 8 218-225 2-9 (43)
186 TIGR01031 rpmF_bact ribosomal 51.0 8.4 0.00018 27.0 1.1 22 216-237 26-47 (55)
187 PF01485 IBR: IBR domain; Int 50.9 6.8 0.00015 27.0 0.6 31 217-247 19-58 (64)
188 PRK06386 replication factor A; 49.6 11 0.00023 36.4 1.9 12 217-228 237-248 (358)
189 KOG0006 E3 ubiquitin-protein l 49.6 10 0.00022 36.0 1.8 33 216-248 315-355 (446)
190 PRK12286 rpmF 50S ribosomal pr 49.5 9.9 0.00021 26.9 1.3 23 215-237 26-48 (57)
191 smart00154 ZnF_AN1 AN1-like Zi 48.9 12 0.00025 24.3 1.5 24 219-242 1-25 (39)
192 KOG1609 Protein involved in mR 47.8 15 0.00032 33.6 2.6 50 213-262 75-134 (323)
193 PF01783 Ribosomal_L32p: Ribos 47.2 12 0.00025 26.2 1.4 23 215-237 25-47 (56)
194 COG4068 Uncharacterized protei 47.2 10 0.00022 27.1 1.1 17 249-265 6-22 (64)
195 PRK08270 anaerobic ribonucleos 47.0 11 0.00024 39.1 1.8 19 249-269 637-655 (656)
196 smart00734 ZnF_Rad18 Rad18-lik 46.3 6.8 0.00015 23.2 0.0 9 253-261 3-11 (26)
197 KOG1100 Predicted E3 ubiquitin 45.8 9.5 0.00021 33.9 0.9 42 217-262 159-200 (207)
198 smart00834 CxxC_CXXC_SSSS Puta 45.4 9.5 0.00021 24.2 0.6 10 250-259 25-34 (41)
199 PLN02720 complex II 44.7 11 0.00024 31.2 1.0 9 174-182 129-137 (140)
200 PF07578 LAB_N: Lipid A Biosyn 44.5 20 0.00044 26.6 2.3 19 168-186 5-24 (72)
201 PRK07217 replication factor A; 43.8 17 0.00038 34.3 2.3 28 217-267 189-218 (311)
202 PF14803 Nudix_N_2: Nudix N-te 43.7 8 0.00017 24.5 0.1 21 218-238 2-31 (34)
203 TIGR02605 CxxC_CxxC_SSSS putat 43.2 10 0.00022 25.6 0.5 9 251-259 26-34 (52)
204 PRK06393 rpoE DNA-directed RNA 42.6 12 0.00027 27.1 0.9 34 236-271 4-40 (64)
205 KOG1729 FYVE finger containing 42.5 14 0.0003 34.6 1.5 47 215-261 167-224 (288)
206 smart00661 RPOL9 RNA polymeras 42.1 16 0.00036 24.3 1.5 9 218-226 2-10 (52)
207 KOG1815 Predicted E3 ubiquitin 42.0 9.5 0.00021 37.5 0.3 36 216-252 226-268 (444)
208 PF07800 DUF1644: Protein of u 41.5 14 0.0003 31.6 1.2 34 216-249 2-47 (162)
209 PF01428 zf-AN1: AN1-like Zinc 41.2 13 0.00029 24.3 0.8 25 219-243 1-27 (43)
210 TIGR00373 conserved hypothetic 40.9 8.4 0.00018 32.6 -0.2 32 215-262 108-139 (158)
211 PRK06266 transcription initiat 40.8 10 0.00022 32.8 0.3 32 215-262 116-147 (178)
212 KOG3726 Uncharacterized conser 40.8 14 0.0003 38.4 1.3 42 217-261 655-699 (717)
213 PRK12495 hypothetical protein; 40.7 13 0.00028 33.5 0.9 25 216-245 42-66 (226)
214 PF04710 Pellino: Pellino; In 40.5 9.3 0.0002 37.2 0.0 55 216-270 328-410 (416)
215 PF00301 Rubredoxin: Rubredoxi 39.7 12 0.00027 25.4 0.5 11 250-260 33-43 (47)
216 PF10272 Tmpp129: Putative tra 39.7 40 0.00087 32.5 4.2 53 214-266 269-355 (358)
217 COG1997 RPL43A Ribosomal prote 39.6 18 0.00039 27.9 1.5 31 215-248 34-64 (89)
218 PRK12496 hypothetical protein; 39.4 8.4 0.00018 32.9 -0.4 11 216-226 127-137 (164)
219 TIGR00375 conserved hypothetic 38.9 8.3 0.00018 37.3 -0.6 24 72-97 82-105 (374)
220 PF06827 zf-FPG_IleRS: Zinc fi 38.2 9.7 0.00021 22.9 -0.2 26 218-244 3-28 (30)
221 KOG2462 C2H2-type Zn-finger pr 37.7 35 0.00077 31.7 3.3 13 216-228 130-142 (279)
222 smart00132 LIM Zinc-binding do 37.5 25 0.00053 21.3 1.7 36 218-261 1-37 (39)
223 COG3058 FdhE Uncharacterized p 36.7 32 0.00069 32.2 2.8 46 215-260 184-234 (308)
224 PF02318 FYVE_2: FYVE-type zin 36.5 23 0.0005 28.3 1.7 31 216-246 54-88 (118)
225 PF13719 zinc_ribbon_5: zinc-r 34.9 20 0.00042 22.8 0.9 12 218-229 4-15 (37)
226 PF07282 OrfB_Zn_ribbon: Putat 34.8 27 0.00059 24.8 1.7 14 215-228 27-40 (69)
227 PHA02768 hypothetical protein; 34.8 29 0.00062 24.5 1.7 43 216-270 5-51 (55)
228 PRK14714 DNA polymerase II lar 34.1 21 0.00046 39.6 1.5 30 216-245 679-717 (1337)
229 COG5113 UFD2 Ubiquitin fusion 34.0 36 0.00077 35.4 2.9 53 215-267 853-905 (929)
230 KOG4642 Chaperone-dependent E3 33.8 21 0.00046 32.9 1.2 53 215-268 210-263 (284)
231 KOG3476 Microtubule-associated 33.6 3.4 7.3E-05 31.9 -3.3 35 217-261 55-89 (100)
232 COG1545 Predicted nucleic-acid 32.3 25 0.00053 29.2 1.3 23 231-261 31-53 (140)
233 PRK11827 hypothetical protein; 32.3 25 0.00054 25.2 1.1 14 215-228 7-20 (60)
234 PF10013 DUF2256: Uncharacteri 32.2 25 0.00055 23.4 1.1 10 252-261 9-18 (42)
235 PF06677 Auto_anti-p27: Sjogre 31.5 20 0.00043 23.6 0.5 24 216-243 17-40 (41)
236 PRK00398 rpoP DNA-directed RNA 31.3 16 0.00035 24.1 0.0 10 252-261 22-31 (46)
237 smart00290 ZnF_UBP Ubiquitin C 30.9 18 0.0004 23.9 0.3 25 218-243 1-25 (50)
238 TIGR00398 metG methionyl-tRNA 30.9 32 0.00069 34.4 2.1 47 216-267 136-182 (530)
239 PF14471 DUF4428: Domain of un 30.8 39 0.00084 23.2 1.8 28 218-247 1-30 (51)
240 PRK14890 putative Zn-ribbon RN 30.7 28 0.0006 24.9 1.1 18 240-259 39-56 (59)
241 TIGR02827 RNR_anaer_Bdell anae 30.7 28 0.00062 35.7 1.7 18 252-270 547-564 (586)
242 PRK01343 zinc-binding protein; 30.5 48 0.001 23.5 2.3 35 216-256 9-48 (57)
243 PF01258 zf-dskA_traR: Prokary 30.5 18 0.00038 22.7 0.1 30 217-246 4-33 (36)
244 PRK08271 anaerobic ribonucleos 30.5 16 0.00034 37.8 -0.2 19 250-269 579-597 (623)
245 KOG3842 Adaptor protein Pellin 30.4 45 0.00097 31.8 2.8 54 216-269 341-422 (429)
246 KOG1842 FYVE finger-containing 29.8 17 0.00036 36.0 -0.1 68 164-245 139-212 (505)
247 PRK08351 DNA-directed RNA poly 29.5 29 0.00062 25.0 1.1 12 250-261 14-25 (61)
248 KOG1701 Focal adhesion adaptor 29.3 32 0.0007 33.9 1.7 50 217-269 361-416 (468)
249 KOG0396 Uncharacterized conser 29.1 28 0.00061 33.6 1.3 41 230-271 347-388 (389)
250 PF13717 zinc_ribbon_4: zinc-r 29.0 28 0.00061 22.1 0.9 8 218-225 4-11 (36)
251 KOG1814 Predicted E3 ubiquitin 28.8 20 0.00044 35.1 0.3 50 215-270 272-328 (445)
252 PF08273 Prim_Zn_Ribbon: Zinc- 28.7 25 0.00055 23.1 0.6 26 218-243 5-32 (40)
253 CHL00174 accD acetyl-CoA carbo 28.4 26 0.00057 32.9 0.9 26 216-241 38-69 (296)
254 PRK14892 putative transcriptio 28.3 25 0.00055 27.7 0.6 11 215-225 20-30 (99)
255 PF14354 Lar_restr_allev: Rest 27.9 27 0.00058 24.2 0.7 27 218-244 5-36 (61)
256 PRK14873 primosome assembly pr 27.6 22 0.00047 37.1 0.2 24 235-260 408-431 (665)
257 KOG2807 RNA polymerase II tran 27.5 41 0.00088 32.2 2.0 42 217-258 331-374 (378)
258 PF06170 DUF983: Protein of un 26.5 30 0.00065 26.4 0.8 18 246-263 3-20 (86)
259 PF03966 Trm112p: Trm112p-like 26.5 26 0.00057 25.2 0.4 11 216-226 7-17 (68)
260 smart00531 TFIIE Transcription 26.2 36 0.00079 28.2 1.3 37 215-262 98-134 (147)
261 COG0333 RpmF Ribosomal protein 26.2 40 0.00086 23.9 1.3 22 216-237 27-48 (57)
262 TIGR00515 accD acetyl-CoA carb 26.1 25 0.00054 32.8 0.3 25 216-240 26-56 (285)
263 PF12312 NeA_P2: Nepovirus sub 26.0 40 0.00087 30.0 1.6 31 171-201 172-208 (258)
264 smart00746 TRASH metallochaper 25.6 77 0.0017 17.9 2.4 31 219-249 1-37 (39)
265 COG1439 Predicted nucleic acid 25.3 21 0.00045 31.1 -0.3 11 250-260 152-162 (177)
266 KOG2066 Vacuolar assembly/sort 25.2 25 0.00053 37.2 0.1 41 216-258 784-831 (846)
267 KOG4577 Transcription factor L 25.2 17 0.00037 34.1 -0.9 47 218-268 62-109 (383)
268 TIGR01206 lysW lysine biosynth 25.0 36 0.00078 23.8 0.9 30 217-261 3-32 (54)
269 PF05566 Pox_vIL-18BP: Orthopo 24.8 26 0.00057 28.2 0.2 20 238-257 8-28 (126)
270 COG4338 Uncharacterized protei 24.8 21 0.00045 24.6 -0.3 11 216-226 12-22 (54)
271 PF03119 DNA_ligase_ZBD: NAD-d 24.6 25 0.00055 21.1 0.0 10 253-262 1-10 (28)
272 TIGR02098 MJ0042_CXXC MJ0042 f 24.4 32 0.0007 21.5 0.5 12 218-229 4-15 (38)
273 COG4530 Uncharacterized protei 24.3 43 0.00094 27.0 1.3 25 215-239 8-36 (129)
274 PF08274 PhnA_Zn_Ribbon: PhnA 24.3 28 0.00061 21.4 0.2 20 218-237 4-27 (30)
275 KOG2272 Focal adhesion protein 24.0 35 0.00076 31.5 0.9 38 215-258 162-199 (332)
276 PRK05654 acetyl-CoA carboxylas 24.0 28 0.0006 32.6 0.2 24 216-239 27-56 (292)
277 PRK01110 rpmF 50S ribosomal pr 23.9 38 0.00081 24.1 0.8 21 216-237 27-47 (60)
278 PRK08579 anaerobic ribonucleos 23.8 13 0.00029 38.4 -2.1 24 236-259 567-590 (625)
279 PF10217 DUF2039: Uncharacteri 23.8 54 0.0012 25.5 1.7 37 216-261 55-91 (92)
280 PRK02935 hypothetical protein; 23.8 49 0.0011 26.5 1.5 15 250-264 85-99 (110)
281 TIGR03655 anti_R_Lar restricti 23.3 42 0.00091 22.9 1.0 10 218-227 3-12 (53)
282 COG2176 PolC DNA polymerase II 23.2 78 0.0017 35.4 3.3 37 216-264 914-952 (1444)
283 PF08882 Acetone_carb_G: Aceto 23.0 33 0.00071 27.6 0.4 11 230-241 25-35 (112)
284 COG1656 Uncharacterized conser 22.7 37 0.0008 29.2 0.7 15 215-229 96-110 (165)
285 COG4098 comFA Superfamily II D 22.7 31 0.00068 33.5 0.3 30 215-245 38-68 (441)
286 COG0675 Transposase and inacti 22.6 40 0.00087 30.5 1.0 25 215-240 308-333 (364)
287 smart00778 Prim_Zn_Ribbon Zinc 22.5 55 0.0012 21.1 1.3 28 216-243 3-31 (37)
288 COG4855 Uncharacterized protei 22.4 9.6 0.00021 28.0 -2.5 27 216-242 7-36 (76)
289 PLN03086 PRLI-interacting fact 22.1 32 0.00069 35.2 0.2 15 215-229 406-420 (567)
290 PRK00418 DNA gyrase inhibitor; 22.1 45 0.00098 24.1 0.9 10 252-261 7-16 (62)
291 COG4647 AcxC Acetone carboxyla 21.9 32 0.0007 28.6 0.2 21 221-242 62-82 (165)
292 PF10621 FpoO: F420H2 dehydrog 21.9 71 0.0015 25.8 2.1 14 250-263 59-72 (119)
293 PRK09710 lar restriction allev 21.8 37 0.0008 24.7 0.4 28 218-245 8-35 (64)
294 PF08394 Arc_trans_TRASH: Arch 21.7 84 0.0018 20.3 2.0 32 219-250 1-36 (37)
295 COG1198 PriA Primosomal protei 21.6 37 0.0008 35.8 0.6 44 216-260 435-484 (730)
296 PRK00432 30S ribosomal protein 21.5 61 0.0013 22.1 1.5 9 216-224 20-28 (50)
297 PRK00133 metG methionyl-tRNA s 21.4 66 0.0014 33.4 2.4 45 216-265 139-183 (673)
298 TIGR00595 priA primosomal prot 21.2 64 0.0014 32.4 2.2 25 235-260 238-262 (505)
299 PF06844 DUF1244: Protein of u 21.0 52 0.0011 24.1 1.1 13 238-250 11-23 (68)
300 KOG2906 RNA polymerase III sub 20.9 39 0.00084 26.7 0.4 23 218-240 3-32 (105)
301 PF13597 NRDD: Anaerobic ribon 20.8 23 0.0005 35.9 -1.1 29 239-269 493-521 (546)
302 PRK05452 anaerobic nitric oxid 20.6 48 0.001 33.0 1.1 13 248-260 455-467 (479)
303 PRK08665 ribonucleotide-diphos 20.3 58 0.0013 34.5 1.7 25 216-240 724-751 (752)
304 COG1675 TFA1 Transcription ini 20.1 46 0.00099 28.9 0.8 32 215-262 112-143 (176)
305 PF03660 PHF5: PHF5-like prote 20.1 43 0.00094 26.6 0.5 19 251-269 27-45 (106)
No 1
>KOG0826 consensus Predicted E3 ubiquitin ligase involved in peroxisome organization [Posttranslational modification, protein turnover, chaperones]
Probab=100.00 E-value=6.2e-57 Score=410.44 Aligned_cols=238 Identities=35% Similarity=0.666 Sum_probs=196.1
Q ss_pred CccccchhhhhHHHHHhhHHHHHhhhhcCCCCCCCCCcccCCCCCCCCCCCCCCCCchhhhhhHHHHHHHHHHHHhhHHH
Q 024073 1 MVVLPYFKSKLHSVYNKEREARLQASLWGPTDERFDDVDYFGGGGNPLFSRGGTDAETSVRTSLTKKIQKIIFACYPWLH 80 (273)
Q Consensus 1 LV~~PYlk~KLd~~y~~~~~~~~~a~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~k~~f~~~YP~i~ 80 (273)
||++||+++|||++|+++++..... .+ +.-+++.+++|..+||+|+
T Consensus 117 lv~lPYv~~KL~~i~~k~~e~~~~~----------S~------------------------e~~~~~~~~aF~~~~p~i~ 162 (357)
T KOG0826|consen 117 LVILPYVEAKLDEIYEKLRENNEFS----------SD------------------------ETENKRPKRAFLRIYPFIK 162 (357)
T ss_pred HHHHHHHHHHHHHHHHHHhhccccc----------Cc------------------------hhhhhhHHHHHhhhhHHHH
Confidence 6899999999999999955332110 00 1125788999999999999
Q ss_pred HHHHHHHHHHHHHHHhCCCCCCCHHHHHhcceeeeccccccccchhhhh--hhhhhHHhhhcChhhHHHHHHHHHHHHHH
Q 024073 81 ASCEGLSFTYQLLYLLDATGFYSVGLHALGIHVCRATGQELMDNSSRIS--KIRSRERERLLGPLWLKKLQGALLSCAYT 158 (273)
Q Consensus 81 ~~~~~~~l~~~L~YL~g~t~y~sP~l~l~gi~l~Rl~~~D~~~~~~~~~--~~~~~~~~~~~~p~~~~~~~~~l~~~~~~ 158 (273)
+++|+++++.+++||.+++..||||+|++|+.|+.++++|+.+.+.... .......+..+..++...++..+.++...
T Consensus 163 ~a~els~lvq~l~yIlkrs~~hSPll~lsgv~L~~lt~~dl~a~~~gp~e~~~~~q~~r~t~~e~i~l~~qgaL~~~~~~ 242 (357)
T KOG0826|consen 163 MALELSKLVQQLRYILKRSSHHSPLLYLSGVQLGTLTPEDLQALEHGPAELSMMDQPARKTVSEKIFLLMQGALKKAVRG 242 (357)
T ss_pred HHHHHHHHHHHHHHHHHhcccccHHHHHhhcccccccHHHHHHhhccccccchhhhhhhhhhhhhHHHHHHhHHHHHHhh
Confidence 9999999999999999999999999999999999999999987543221 11112222233334556778889999999
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHhcccccccCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCcccccccccc
Q 024073 159 MLDYAQTGLIAAVFFFKMMEWWYQSAEERMSAPTVYPPPPPPPPPKVAREGIPLPPDRTICPLCSQKRANPSVVTVSGFV 238 (273)
Q Consensus 159 l~~~l~~~Lp~~IF~lKfLEWWyss~~~~~~~~~~lp~PpPP~~~~~~~~~~~~p~~~~~CpiC~~~~~np~~l~~~G~v 238 (273)
+.++++++|+++|||||||||||++|+++..+.+..|++||||+.+.++++...|.++..||+|++.++||||+.++|||
T Consensus 243 v~~~~stgl~~~vFflqfldWWyssd~~~~~k~~l~~p~PpPPh~~~~se~e~l~~~~~~CpvClk~r~Nptvl~vSGyV 322 (357)
T KOG0826|consen 243 VAFSLSTGLSVGVFFLQFLDWWYSSDNQRKIKSTLDPPIPPPPHKQYNSESELLPPDREVCPVCLKKRQNPTVLEVSGYV 322 (357)
T ss_pred HHHHHHhhHHHHHHHHHHHHHHhcchHHHhhccCCCCCCCcCChhhcccccccCCCccccChhHHhccCCCceEEecceE
Confidence 99999999999999999999999999877666554444444445455577777888999999999999999999999999
Q ss_pred cchhhHHHHHhcCCCCCCCCCCCCcCCeeeCccC
Q 024073 239 FCYACIFKYVSQYKRCPVTLMPATVEQIRRLFHD 272 (273)
Q Consensus 239 fCy~Ci~~~~~~~~~CPv~~~~~~~~~l~ri~~~ 272 (273)
|||+||++||.++++||||+.|+.++||+|+|.+
T Consensus 323 fCY~Ci~~Yv~~~~~CPVT~~p~~v~~l~rl~~~ 356 (357)
T KOG0826|consen 323 FCYPCIFSYVVNYGHCPVTGYPASVDHLIRLFNK 356 (357)
T ss_pred EeHHHHHHHHHhcCCCCccCCcchHHHHHHHhcC
Confidence 9999999999999999999999999999999975
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=99.86 E-value=6.1e-21 Score=169.23 Aligned_cols=141 Identities=28% Similarity=0.441 Sum_probs=103.2
Q ss_pred CccccchhhhhHHHHHhhHHHHHhhhhcCCCCCCCCCcccCCCCCCCCCCCCCCCCchhhhhhHHHHHHHHHHHHhhHHH
Q 024073 1 MVVLPYFKSKLHSVYNKEREARLQASLWGPTDERFDDVDYFGGGGNPLFSRGGTDAETSVRTSLTKKIQKIIFACYPWLH 80 (273)
Q Consensus 1 LV~~PYlk~KLd~~y~~~~~~~~~a~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~k~~f~~~YP~i~ 80 (273)
+|++||+++||++++++. ......... ...+...+.++..+.++.|.++||+++
T Consensus 89 ~vl~PYl~~Kl~~~~~~~----------~~~~~~~~~----------------~~~~~~~~~~~~~~~~~~~~~~~~~~~ 142 (229)
T PF04757_consen 89 LVLGPYLKEKLDSLLERL----------SERSAESIS----------------SRSARARRARLKSKLKRRFVKLYPYLN 142 (229)
T ss_pred HHHHHHHHHHHHHHHHHh----------ccccccccc----------------chhhhhhhhHHHHHHHHHHHHHHHHHH
Confidence 489999999999999983 221111000 000111223677888999999999999
Q ss_pred HHHHHHHHHHHHHHHhCCCCCCCHHHHHhcceeeeccccccccchhhhhhhhhhHHhhhcChhhHHHHHHHHHHHHHHHH
Q 024073 81 ASCEGLSFTYQLLYLLDATGFYSVGLHALGIHVCRATGQELMDNSSRISKIRSRERERLLGPLWLKKLQGALLSCAYTML 160 (273)
Q Consensus 81 ~~~~~~~l~~~L~YL~g~t~y~sP~l~l~gi~l~Rl~~~D~~~~~~~~~~~~~~~~~~~~~p~~~~~~~~~l~~~~~~l~ 160 (273)
++++++++++.++||++.++|+||+++++||+++|.++.|..+.. ...++... -.+......+.
T Consensus 143 ~~~~~~~~~~~~~Fl~~g~~y~s~~~rllgi~~~~~~~~~~~~~~---------------~~~~l~~~-l~~~~~~~~~~ 206 (229)
T PF04757_consen 143 ALYELLNLLHLLLFLLGGTPYYSPSKRLLGIRYVRLSPSDLQRNP---------------SYEFLGRQ-LLWQLLSEFLL 206 (229)
T ss_pred HHHHHHHHHHHHHHHhCCCCCCCHHHHHhCcEEEECCccchhhhc---------------cHHHHHHH-HHHHHHHHHHH
Confidence 999999999999999999999999999999999999888875421 01111000 01123445666
Q ss_pred HHHHHHHHHHHHHHHHHHHHhccc
Q 024073 161 DYAQTGLIAAVFFFKMMEWWYQSA 184 (273)
Q Consensus 161 ~~l~~~Lp~~IF~lKfLEWWyss~ 184 (273)
..+..+++.++|+|||+|||| +|
T Consensus 207 ~~~~~l~~~~~~~~~~~eww~-~~ 229 (229)
T PF04757_consen 207 FLLPLLLPRSLFFLKFLEWWY-SD 229 (229)
T ss_pred HHHHHHHHHHHHHHHHHHHhC-CC
Confidence 777899999999999999999 75
No 3
>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=99.44 E-value=9.9e-14 Score=99.22 Aligned_cols=53 Identities=25% Similarity=0.361 Sum_probs=49.3
Q ss_pred CCCCCCCCCCCCcccccccccccchhhHHHHHhcCCCCCCCCCCCCcCCeeeCc
Q 024073 217 TICPLCSQKRANPSVVTVSGFVFCYACIFKYVSQYKRCPVTLMPATVEQIRRLF 270 (273)
Q Consensus 217 ~~CpiC~~~~~np~~l~~~G~vfCy~Ci~~~~~~~~~CPv~~~~~~~~~l~ri~ 270 (273)
..||||++.++||++++ ||||||+.||.+|++++++||+|+.+++.++|++..
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 57999999999998876 999999999999999999999999999999998754
No 4
>PLN03208 E3 ubiquitin-protein ligase RMA2; Provisional
Probab=99.34 E-value=8e-13 Score=114.83 Aligned_cols=57 Identities=23% Similarity=0.596 Sum_probs=50.9
Q ss_pred CCCCCCCCCCCCCCcccccccccccchhhHHHHHhc----------------CCCCCCCCCCCCcCCeeeCccC
Q 024073 215 DRTICPLCSQKRANPSVVTVSGFVFCYACIFKYVSQ----------------YKRCPVTLMPATVEQIRRLFHD 272 (273)
Q Consensus 215 ~~~~CpiC~~~~~np~~l~~~G~vfCy~Ci~~~~~~----------------~~~CPv~~~~~~~~~l~ri~~~ 272 (273)
+...||||++..++|++++ |||+||+.||.+|+.. ..+||+|+.+++.++|+.||..
T Consensus 17 ~~~~CpICld~~~dPVvT~-CGH~FC~~CI~~wl~~s~~s~~~~~~~~~~k~~~~CPvCR~~Is~~~LvPiygr 89 (193)
T PLN03208 17 GDFDCNICLDQVRDPVVTL-CGHLFCWPCIHKWTYASNNSRQRVDQYDHKREPPKCPVCKSDVSEATLVPIYGR 89 (193)
T ss_pred CccCCccCCCcCCCcEEcC-CCchhHHHHHHHHHHhccccccccccccccCCCCcCCCCCCcCChhcEEEeecc
Confidence 4678999999999998876 9999999999999852 3589999999999999999963
No 5
>KOG0317 consensus Predicted E3 ubiquitin ligase, integral peroxisomal membrane protein [Posttranslational modification, protein turnover, chaperones]
Probab=99.31 E-value=9.5e-13 Score=119.67 Aligned_cols=55 Identities=29% Similarity=0.698 Sum_probs=51.2
Q ss_pred CCCCCCCCCCCCCCcccccccccccchhhHHHHHhcCCCCCCCCCCCCcCCeeeCc
Q 024073 215 DRTICPLCSQKRANPSVVTVSGFVFCYACIFKYVSQYKRCPVTLMPATVEQIRRLF 270 (273)
Q Consensus 215 ~~~~CpiC~~~~~np~~l~~~G~vfCy~Ci~~~~~~~~~CPv~~~~~~~~~l~ri~ 270 (273)
...+|.||++.+.||++++ |||+|||.||..|+.+...||+|+.+.+..+++-++
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 4579999999999999988 999999999999999999999999999999988664
No 6
>KOG0320 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=99.29 E-value=2.1e-12 Score=110.14 Aligned_cols=57 Identities=28% Similarity=0.592 Sum_probs=50.5
Q ss_pred CCCCCCCCCCCCCCcc-cccccccccchhhHHHHHhcCCCCCCCCCCCCcCCeeeCcc
Q 024073 215 DRTICPLCSQKRANPS-VVTVSGFVFCYACIFKYVSQYKRCPVTLMPATVEQIRRLFH 271 (273)
Q Consensus 215 ~~~~CpiC~~~~~np~-~l~~~G~vfCy~Ci~~~~~~~~~CPv~~~~~~~~~l~ri~~ 271 (273)
..+.||||+.....-. +-+.||||||..||.+.++...+||+|+++++..++.|||.
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 4589999999876654 43459999999999999999999999999999999999994
No 7
>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=99.24 E-value=3.6e-12 Score=83.42 Aligned_cols=39 Identities=44% Similarity=1.005 Sum_probs=33.9
Q ss_pred CCCCCCCCCCcccccccccccchhhHHHHHhcCCCCCCC
Q 024073 219 CPLCSQKRANPSVVTVSGFVFCYACIFKYVSQYKRCPVT 257 (273)
Q Consensus 219 CpiC~~~~~np~~l~~~G~vfCy~Ci~~~~~~~~~CPv~ 257 (273)
||||.+.++||+++..|||+||+.||.+|++.+.+||+|
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 899999999996555599999999999999999999997
No 8
>KOG0823 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=99.24 E-value=3.7e-12 Score=112.76 Aligned_cols=58 Identities=22% Similarity=0.659 Sum_probs=52.1
Q ss_pred CCCCCCCCCCCCCCCcccccccccccchhhHHHHHhcC---CCCCCCCCCCCcCCeeeCccC
Q 024073 214 PDRTICPLCSQKRANPSVVTVSGFVFCYACIFKYVSQY---KRCPVTLMPATVEQIRRLFHD 272 (273)
Q Consensus 214 ~~~~~CpiC~~~~~np~~l~~~G~vfCy~Ci~~~~~~~---~~CPv~~~~~~~~~l~ri~~~ 272 (273)
-..+.|-||++.-++|+|+- |||.|||+||++|+.-+ +.||||+-.++.+.|+.||..
T Consensus 45 ~~~FdCNICLd~akdPVvTl-CGHLFCWpClyqWl~~~~~~~~cPVCK~~Vs~~~vvPlYGr 105 (230)
T KOG0823|consen 45 GGFFDCNICLDLAKDPVVTL-CGHLFCWPCLYQWLQTRPNSKECPVCKAEVSIDTVVPLYGR 105 (230)
T ss_pred CCceeeeeeccccCCCEEee-cccceehHHHHHHHhhcCCCeeCCccccccccceEEeeecc
Confidence 35789999999999998876 99999999999999854 578999999999999999963
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=99.16 E-value=1.4e-11 Score=91.60 Aligned_cols=53 Identities=21% Similarity=0.416 Sum_probs=44.8
Q ss_pred CCCCCCCCCCCCCCcccccccccccchhhHHHHHhc-CCCCCCCCCCCCcCCeee
Q 024073 215 DRTICPLCSQKRANPSVVTVSGFVFCYACIFKYVSQ-YKRCPVTLMPATVEQIRR 268 (273)
Q Consensus 215 ~~~~CpiC~~~~~np~~l~~~G~vfCy~Ci~~~~~~-~~~CPv~~~~~~~~~l~r 268 (273)
+...||||++.++||++++ |||+||+.||.+|+++ ++.||+|+.+++.++|+.
T Consensus 3 ~~f~CpIt~~lM~dPVi~~-~G~tyer~~I~~~l~~~~~~~P~t~~~l~~~~l~p 56 (73)
T PF04564_consen 3 DEFLCPITGELMRDPVILP-SGHTYERSAIERWLEQNGGTDPFTRQPLSESDLIP 56 (73)
T ss_dssp GGGB-TTTSSB-SSEEEET-TSEEEEHHHHHHHHCTTSSB-TTT-SB-SGGGSEE
T ss_pred cccCCcCcCcHhhCceeCC-cCCEEcHHHHHHHHHcCCCCCCCCCCcCCcccceE
Confidence 5789999999999999987 9999999999999999 799999999999988875
No 10
>PF15227 zf-C3HC4_4: zinc finger of C3HC4-type, RING; PDB: 2EGP_A 2ECV_A 2ECJ_A 2YSL_A 2YSJ_A.
Probab=99.03 E-value=1.1e-10 Score=77.90 Aligned_cols=38 Identities=26% Similarity=0.719 Sum_probs=31.1
Q ss_pred CCCCCCCCCCcccccccccccchhhHHHHHhcC----CCCCCC
Q 024073 219 CPLCSQKRANPSVVTVSGFVFCYACIFKYVSQY----KRCPVT 257 (273)
Q Consensus 219 CpiC~~~~~np~~l~~~G~vfCy~Ci~~~~~~~----~~CPv~ 257 (273)
||||++.++||+.++ |||+||..||.+|.++. -.||+|
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 899999999999998 99999999999999865 269987
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=99.01 E-value=9.4e-11 Score=78.51 Aligned_cols=41 Identities=27% Similarity=0.673 Sum_probs=34.2
Q ss_pred CCCCCCCCCCCC---cccccccccccchhhHHHHHhcCCCCCCCC
Q 024073 217 TICPLCSQKRAN---PSVVTVSGFVFCYACIFKYVSQYKRCPVTL 258 (273)
Q Consensus 217 ~~CpiC~~~~~n---p~~l~~~G~vfCy~Ci~~~~~~~~~CPv~~ 258 (273)
+.|+||.+.+.+ ...++ |||+||+.||.+|++++++||+|+
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 35666 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=98.98 E-value=2.9e-10 Score=78.23 Aligned_cols=46 Identities=24% Similarity=0.708 Sum_probs=40.5
Q ss_pred CCCCCCCCCCCCCcccccccccc-cchhhHHHHHhcCCCCCCCCCCCC
Q 024073 216 RTICPLCSQKRANPSVVTVSGFV-FCYACIFKYVSQYKRCPVTLMPAT 262 (273)
Q Consensus 216 ~~~CpiC~~~~~np~~l~~~G~v-fCy~Ci~~~~~~~~~CPv~~~~~~ 262 (273)
+..|+||.+...++.+.+ |||+ ||+.|+.+|.+..++||+|+.+++
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 458999999999988877 9999 999999999999999999998764
No 13
>KOG0978 consensus E3 ubiquitin ligase involved in syntaxin degradation [Posttranslational modification, protein turnover, chaperones]
Probab=98.94 E-value=2.8e-10 Score=114.93 Aligned_cols=56 Identities=18% Similarity=0.529 Sum_probs=50.2
Q ss_pred CCCCCCCCCCCCCCcccccccccccchhhHHHHHhc-CCCCCCCCCCCCcCCeeeCcc
Q 024073 215 DRTICPLCSQKRANPSVVTVSGFVFCYACIFKYVSQ-YKRCPVTLMPATVEQIRRLFH 271 (273)
Q Consensus 215 ~~~~CpiC~~~~~np~~l~~~G~vfCy~Ci~~~~~~-~~~CPv~~~~~~~~~l~ri~~ 271 (273)
...+||+|...+.|.++.. ||||||+.|+....+. +.+||.|+.+++..|+++||.
T Consensus 642 ~~LkCs~Cn~R~Kd~vI~k-C~H~FC~~Cvq~r~etRqRKCP~Cn~aFganDv~~I~l 698 (698)
T KOG0978|consen 642 ELLKCSVCNTRWKDAVITK-CGHVFCEECVQTRYETRQRKCPKCNAAFGANDVHRIHL 698 (698)
T ss_pred hceeCCCccCchhhHHHHh-cchHHHHHHHHHHHHHhcCCCCCCCCCCCcccccccCC
Confidence 4678999998888887765 9999999999999874 589999999999999999984
No 14
>TIGR00599 rad18 DNA repair protein rad18. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=98.94 E-value=7.6e-10 Score=106.23 Aligned_cols=54 Identities=20% Similarity=0.502 Sum_probs=48.0
Q ss_pred CCCCCCCCCCCCCCCcccccccccccchhhHHHHHhcCCCCCCCCCCCCcCCeee
Q 024073 214 PDRTICPLCSQKRANPSVVTVSGFVFCYACIFKYVSQYKRCPVTLMPATVEQIRR 268 (273)
Q Consensus 214 ~~~~~CpiC~~~~~np~~l~~~G~vfCy~Ci~~~~~~~~~CPv~~~~~~~~~l~r 268 (273)
.+...|+||.+.+.+|++++ |||+||..||..|+...+.||+|+.+....+|++
T Consensus 24 e~~l~C~IC~d~~~~Pvitp-CgH~FCs~CI~~~l~~~~~CP~Cr~~~~~~~Lr~ 77 (397)
T TIGR00599 24 DTSLRCHICKDFFDVPVLTS-CSHTFCSLCIRRCLSNQPKCPLCRAEDQESKLRS 77 (397)
T ss_pred ccccCCCcCchhhhCccCCC-CCCchhHHHHHHHHhCCCCCCCCCCccccccCcc
Confidence 35789999999999998876 9999999999999999899999999887666654
No 15
>KOG2164 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=98.92 E-value=5.6e-10 Score=108.45 Aligned_cols=55 Identities=25% Similarity=0.638 Sum_probs=49.5
Q ss_pred CCCCCCCCCCCCCcccccccccccchhhHHHHHh-----cCCCCCCCCCCCCcCCeeeCcc
Q 024073 216 RTICPLCSQKRANPSVVTVSGFVFCYACIFKYVS-----QYKRCPVTLMPATVEQIRRLFH 271 (273)
Q Consensus 216 ~~~CpiC~~~~~np~~l~~~G~vfCy~Ci~~~~~-----~~~~CPv~~~~~~~~~l~ri~~ 271 (273)
...||||+++-.-|..+. |||+||.+||++|+. +.++||+|+..++..||.-|+.
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 999999999999996 4589999999999999988774
No 16
>PHA02929 N1R/p28-like protein; Provisional
Probab=98.90 E-value=9.2e-10 Score=99.13 Aligned_cols=48 Identities=25% Similarity=0.600 Sum_probs=40.8
Q ss_pred CCCCCCCCCCCCCCc-------ccccccccccchhhHHHHHhcCCCCCCCCCCCC
Q 024073 215 DRTICPLCSQKRANP-------SVVTVSGFVFCYACIFKYVSQYKRCPVTLMPAT 262 (273)
Q Consensus 215 ~~~~CpiC~~~~~np-------~~l~~~G~vfCy~Ci~~~~~~~~~CPv~~~~~~ 262 (273)
+...||||++.+.++ .+++.|||+||..||.+|++.+..||+|+.+..
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 357899999987764 245569999999999999999999999997754
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=98.89 E-value=1.3e-09 Score=71.27 Aligned_cols=43 Identities=35% Similarity=0.846 Sum_probs=38.8
Q ss_pred CCCCCCCCCCCcccccccccccchhhHHHHHhc-CCCCCCCCCC
Q 024073 218 ICPLCSQKRANPSVVTVSGFVFCYACIFKYVSQ-YKRCPVTLMP 260 (273)
Q Consensus 218 ~CpiC~~~~~np~~l~~~G~vfCy~Ci~~~~~~-~~~CPv~~~~ 260 (273)
.|+||.+.+.++..+..|||.||+.|+..|++. +.+||+|+..
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 7889999865
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=98.84 E-value=1.8e-09 Score=70.91 Aligned_cols=38 Identities=29% Similarity=0.899 Sum_probs=34.5
Q ss_pred CCCCCCCCCCcc-cccccccccchhhHHHHHh--cCCCCCCC
Q 024073 219 CPLCSQKRANPS-VVTVSGFVFCYACIFKYVS--QYKRCPVT 257 (273)
Q Consensus 219 CpiC~~~~~np~-~l~~~G~vfCy~Ci~~~~~--~~~~CPv~ 257 (273)
|+||.+...++. +++ |||.||+.|+.+|++ +..+||+|
T Consensus 1 C~iC~~~~~~~~~~~~-C~H~fC~~C~~~~~~~~~~~~CP~C 41 (41)
T PF00097_consen 1 CPICLEPFEDPVILLP-CGHSFCRDCLRKWLENSGSVKCPLC 41 (41)
T ss_dssp ETTTSSBCSSEEEETT-TSEEEEHHHHHHHHHHTSSSBTTTT
T ss_pred CCcCCccccCCCEEec-CCCcchHHHHHHHHHhcCCccCCcC
Confidence 899999999998 555 999999999999999 55789987
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=98.81 E-value=3.6e-09 Score=66.83 Aligned_cols=38 Identities=34% Similarity=0.977 Sum_probs=34.8
Q ss_pred CCCCCCCCCCcccccccccccchhhHHHHHh-cCCCCCCC
Q 024073 219 CPLCSQKRANPSVVTVSGFVFCYACIFKYVS-QYKRCPVT 257 (273)
Q Consensus 219 CpiC~~~~~np~~l~~~G~vfCy~Ci~~~~~-~~~~CPv~ 257 (273)
|+||.+..+++.+++ |||+||+.|+.+|++ .+.+||+|
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 899999998888887 999999999999998 66789987
No 20
>COG5574 PEX10 RING-finger-containing E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=98.78 E-value=3e-09 Score=95.94 Aligned_cols=53 Identities=23% Similarity=0.594 Sum_probs=45.9
Q ss_pred CCCCCCCCCCCCCCCCcccccccccccchhhHHH-HHhcC-CCCCCCCCCCCcCCe
Q 024073 213 PPDRTICPLCSQKRANPSVVTVSGFVFCYACIFK-YVSQY-KRCPVTLMPATVEQI 266 (273)
Q Consensus 213 p~~~~~CpiC~~~~~np~~l~~~G~vfCy~Ci~~-~~~~~-~~CPv~~~~~~~~~l 266 (273)
|...++|+||.+...+|..++ ||||||+.||+. |-.+. ..||+|+.....+++
T Consensus 212 p~~d~kC~lC~e~~~~ps~t~-CgHlFC~~Cl~~~~t~~k~~~CplCRak~~pk~v 266 (271)
T COG5574 212 PLADYKCFLCLEEPEVPSCTP-CGHLFCLSCLLISWTKKKYEFCPLCRAKVYPKKV 266 (271)
T ss_pred cccccceeeeecccCCccccc-ccchhhHHHHHHHHHhhccccCchhhhhccchhh
Confidence 345789999999999999887 999999999999 87766 679999988877665
No 21
>KOG3039 consensus Uncharacterized conserved protein [Function unknown]
Probab=98.67 E-value=1.2e-08 Score=91.30 Aligned_cols=55 Identities=31% Similarity=0.435 Sum_probs=51.4
Q ss_pred CCCCCCCCCCCCCCcc---cccccccccchhhHHHHHhcCCCCCCCCCCCCcCCeeeC
Q 024073 215 DRTICPLCSQKRANPS---VVTVSGFVFCYACIFKYVSQYKRCPVTLMPATVEQIRRL 269 (273)
Q Consensus 215 ~~~~CpiC~~~~~np~---~l~~~G~vfCy~Ci~~~~~~~~~CPv~~~~~~~~~l~ri 269 (273)
..++||+|...++|.+ ++..||||||+.|+.+.++..+.||||+.|++..|||-+
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 4789999999999994 777899999999999999999999999999999999876
No 22
>PF14835 zf-RING_6: zf-RING of BARD1-type protein; PDB: 1JM7_B.
Probab=98.63 E-value=1.1e-08 Score=73.85 Aligned_cols=50 Identities=26% Similarity=0.615 Sum_probs=27.6
Q ss_pred CCCCCCCCCCCCCcccccccccccchhhHHHHHhcCCCCCCCCCCCCcCCee
Q 024073 216 RTICPLCSQKRANPSVVTVSGFVFCYACIFKYVSQYKRCPVTLMPATVEQIR 267 (273)
Q Consensus 216 ~~~CpiC~~~~~np~~l~~~G~vfCy~Ci~~~~~~~~~CPv~~~~~~~~~l~ 267 (273)
-..|++|.+.+++|..+..|.|+||..||-+.+.. .||||+.|+..+|++
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 35799999999999877779999999999887753 599999999988875
No 23
>PF13445 zf-RING_UBOX: RING-type zinc-finger; PDB: 2CT2_A.
Probab=98.63 E-value=1.5e-08 Score=68.00 Aligned_cols=35 Identities=37% Similarity=1.019 Sum_probs=22.6
Q ss_pred CCCCCCCCCC----cccccccccccchhhHHHHHhcCC----CCC
Q 024073 219 CPLCSQKRAN----PSVVTVSGFVFCYACIFKYVSQYK----RCP 255 (273)
Q Consensus 219 CpiC~~~~~n----p~~l~~~G~vfCy~Ci~~~~~~~~----~CP 255 (273)
||||.+ ..+ |.+|+ ||||||..|+.+..++.. +||
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 888 88998 999999999999998542 676
No 24
>PHA02926 zinc finger-like protein; Provisional
Probab=98.53 E-value=5.7e-08 Score=86.03 Aligned_cols=48 Identities=17% Similarity=0.475 Sum_probs=38.8
Q ss_pred CCCCCCCCCCCCCCc--------ccccccccccchhhHHHHHhcC------CCCCCCCCCCC
Q 024073 215 DRTICPLCSQKRANP--------SVVTVSGFVFCYACIFKYVSQY------KRCPVTLMPAT 262 (273)
Q Consensus 215 ~~~~CpiC~~~~~np--------~~l~~~G~vfCy~Ci~~~~~~~------~~CPv~~~~~~ 262 (273)
....|+||++.+.++ .+++.|||+||..||.+|-+.. ..||+|+....
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 468999999986442 3676799999999999999853 35999998754
No 25
>KOG2879 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=98.53 E-value=1.3e-06 Score=79.43 Aligned_cols=48 Identities=27% Similarity=0.592 Sum_probs=42.6
Q ss_pred CCCCCCCCCCCCCCcccccccccccchhhHHHHHhcC--CCCCCCCCCCC
Q 024073 215 DRTICPLCSQKRANPSVVTVSGFVFCYACIFKYVSQY--KRCPVTLMPAT 262 (273)
Q Consensus 215 ~~~~CpiC~~~~~np~~l~~~G~vfCy~Ci~~~~~~~--~~CPv~~~~~~ 262 (273)
++..||+|++.-++|-++..|||+|||-||..-+.-. -+||.||.++.
T Consensus 238 ~~~~C~~Cg~~PtiP~~~~~C~HiyCY~Ci~ts~~~~asf~Cp~Cg~~~~ 287 (298)
T KOG2879|consen 238 SDTECPVCGEPPTIPHVIGKCGHIYCYYCIATSRLWDASFTCPLCGENVE 287 (298)
T ss_pred CCceeeccCCCCCCCeeeccccceeehhhhhhhhcchhhcccCccCCCCc
Confidence 5789999999999998777799999999999988754 79999997764
No 26
>PF11789 zf-Nse: Zinc-finger of the MIZ type in Nse subunit; PDB: 2YU4_A 3HTK_C.
Probab=98.50 E-value=4.8e-08 Score=69.39 Aligned_cols=44 Identities=30% Similarity=0.524 Sum_probs=32.3
Q ss_pred CCCCCCCCCCCCCCcccccccccccchhhHHHHHhc--CCCCCCCC
Q 024073 215 DRTICPLCSQKRANPSVVTVSGFVFCYACIFKYVSQ--YKRCPVTL 258 (273)
Q Consensus 215 ~~~~CpiC~~~~~np~~l~~~G~vfCy~Ci~~~~~~--~~~CPv~~ 258 (273)
-..+|||++++++||.....|||+|....|.+|+++ ..+||+.|
T Consensus 10 ~~~~CPiT~~~~~~PV~s~~C~H~fek~aI~~~i~~~~~~~CPv~G 55 (57)
T PF11789_consen 10 ISLKCPITLQPFEDPVKSKKCGHTFEKEAILQYIQRNGSKRCPVAG 55 (57)
T ss_dssp --SB-TTTSSB-SSEEEESSS--EEEHHHHHHHCTTTS-EE-SCCC
T ss_pred eccCCCCcCChhhCCcCcCCCCCeecHHHHHHHHHhcCCCCCCCCC
Confidence 367999999999999887779999999999999944 46899965
No 27
>PF14634 zf-RING_5: zinc-RING finger domain
Probab=98.48 E-value=1e-07 Score=63.92 Aligned_cols=42 Identities=26% Similarity=0.641 Sum_probs=34.1
Q ss_pred CCCCCCCCC--CCcccccccccccchhhHHHHHhcCCCCCCCCC
Q 024073 218 ICPLCSQKR--ANPSVVTVSGFVFCYACIFKYVSQYKRCPVTLM 259 (273)
Q Consensus 218 ~CpiC~~~~--~np~~l~~~G~vfCy~Ci~~~~~~~~~CPv~~~ 259 (273)
.|++|.+.. ..+..+..|||+||..|+.+.......||+|++
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 499999988 223344449999999999999977789999984
No 28
>COG5432 RAD18 RING-finger-containing E3 ubiquitin ligase [Signal transduction mechanisms]
Probab=98.45 E-value=5.5e-08 Score=88.94 Aligned_cols=47 Identities=26% Similarity=0.521 Sum_probs=43.0
Q ss_pred CCCCCCCCCCCCCCcccccccccccchhhHHHHHhcCCCCCCCCCCCC
Q 024073 215 DRTICPLCSQKRANPSVVTVSGFVFCYACIFKYVSQYKRCPVTLMPAT 262 (273)
Q Consensus 215 ~~~~CpiC~~~~~np~~l~~~G~vfCy~Ci~~~~~~~~~CPv~~~~~~ 262 (273)
....|-||...+.-|+.++ |||.||+=||.+|+..+..||+|+.+..
T Consensus 24 s~lrC~IC~~~i~ip~~Tt-CgHtFCslCIR~hL~~qp~CP~Cr~~~~ 70 (391)
T COG5432 24 SMLRCRICDCRISIPCETT-CGHTFCSLCIRRHLGTQPFCPVCREDPC 70 (391)
T ss_pred hHHHhhhhhheeecceecc-cccchhHHHHHHHhcCCCCCccccccHH
Confidence 4678999999999998876 9999999999999999999999997653
No 29
>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=98.44 E-value=1.3e-07 Score=70.36 Aligned_cols=43 Identities=26% Similarity=0.679 Sum_probs=35.0
Q ss_pred CCCCCCCCCCCCCc------------ccccccccccchhhHHHHHhcCCCCCCCC
Q 024073 216 RTICPLCSQKRANP------------SVVTVSGFVFCYACIFKYVSQYKRCPVTL 258 (273)
Q Consensus 216 ~~~CpiC~~~~~np------------~~l~~~G~vfCy~Ci~~~~~~~~~CPv~~ 258 (273)
...|+||++++.++ .++..|||+|...||.+|++.+..||+|+
T Consensus 19 ~d~C~IC~~~l~~~~~~~~~~~~~~~i~~~~C~H~FH~~Ci~~Wl~~~~~CP~CR 73 (73)
T PF12678_consen 19 DDNCAICREPLEDPCPECQAPQDECPIVWGPCGHIFHFHCISQWLKQNNTCPLCR 73 (73)
T ss_dssp CSBETTTTSBTTSTTCCHHHCTTTS-EEEETTSEEEEHHHHHHHHTTSSB-TTSS
T ss_pred CCcccccChhhhChhhhhcCCccccceEecccCCCEEHHHHHHHHhcCCcCCCCC
Confidence 34599999999444 24445999999999999999999999996
No 30
>TIGR00570 cdk7 CDK-activating kinase assembly factor MAT1. All proteins in this family for which functions are known are cyclin dependent protein kinases that are components of TFIIH, a complex that is involved in nucleotide excision repair and transcription initiation. Also known as MAT1 (menage a trois 1). This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=98.44 E-value=1.7e-07 Score=87.07 Aligned_cols=53 Identities=30% Similarity=0.596 Sum_probs=42.0
Q ss_pred CCCCCCCCCCC-CCCcc---cccccccccchhhHHHHH-hcCCCCCCCCCCCCcCCee
Q 024073 215 DRTICPLCSQK-RANPS---VVTVSGFVFCYACIFKYV-SQYKRCPVTLMPATVEQIR 267 (273)
Q Consensus 215 ~~~~CpiC~~~-~~np~---~l~~~G~vfCy~Ci~~~~-~~~~~CPv~~~~~~~~~l~ 267 (273)
|..+||+|... ..||. .+..|||.||-.|+...+ .+.+.||+|+.++..++++
T Consensus 2 d~~~CP~Ck~~~y~np~~kl~i~~CGH~~C~sCv~~l~~~~~~~CP~C~~~lrk~~fr 59 (309)
T TIGR00570 2 DDQGCPRCKTTKYRNPSLKLMVNVCGHTLCESCVDLLFVRGSGSCPECDTPLRKNNFR 59 (309)
T ss_pred CCCCCCcCCCCCccCcccccccCCCCCcccHHHHHHHhcCCCCCCCCCCCccchhhcc
Confidence 35689999994 55664 334699999999999966 4557999999998887765
No 31
>PF04641 Rtf2: Rtf2 RING-finger
Probab=98.23 E-value=1e-06 Score=80.52 Aligned_cols=57 Identities=28% Similarity=0.403 Sum_probs=48.6
Q ss_pred CCCCCCCCCCCCCCc---ccccccccccchhhHHHHHhcCCCCCCCCCCCCcCCeeeCccC
Q 024073 215 DRTICPLCSQKRANP---SVVTVSGFVFCYACIFKYVSQYKRCPVTLMPATVEQIRRLFHD 272 (273)
Q Consensus 215 ~~~~CpiC~~~~~np---~~l~~~G~vfCy~Ci~~~~~~~~~CPv~~~~~~~~~l~ri~~~ 272 (273)
..++|||++..+++- +++.+|||||++.|+.+.- ....||+|+.+.+.+|||.|..+
T Consensus 112 ~~~~CPvt~~~~~~~~~fv~l~~cG~V~s~~alke~k-~~~~Cp~c~~~f~~~DiI~Lnp~ 171 (260)
T PF04641_consen 112 GRFICPVTGKEFNGKHKFVYLRPCGCVFSEKALKELK-KSKKCPVCGKPFTEEDIIPLNPP 171 (260)
T ss_pred ceeECCCCCcccCCceeEEEEcCCCCEeeHHHHHhhc-ccccccccCCccccCCEEEecCC
Confidence 578999999999553 4666699999999999883 56789999999999999998754
No 32
>KOG0287 consensus Postreplication repair protein RAD18 [Replication, recombination and repair]
Probab=98.14 E-value=4.1e-07 Score=84.82 Aligned_cols=53 Identities=26% Similarity=0.559 Sum_probs=49.0
Q ss_pred CCCCCCCCCCCCCCcccccccccccchhhHHHHHhcCCCCCCCCCCCCcCCeee
Q 024073 215 DRTICPLCSQKRANPSVVTVSGFVFCYACIFKYVSQYKRCPVTLMPATVEQIRR 268 (273)
Q Consensus 215 ~~~~CpiC~~~~~np~~l~~~G~vfCy~Ci~~~~~~~~~CPv~~~~~~~~~l~r 268 (273)
+-..|-||.+.+.-|.+++ |||.||-=||..|+..+..||.|..+.+..+||.
T Consensus 22 ~lLRC~IC~eyf~ip~itp-CsHtfCSlCIR~~L~~~p~CP~C~~~~~Es~Lr~ 74 (442)
T KOG0287|consen 22 DLLRCGICFEYFNIPMITP-CSHTFCSLCIRKFLSYKPQCPTCCVTVTESDLRN 74 (442)
T ss_pred HHHHHhHHHHHhcCceecc-ccchHHHHHHHHHhccCCCCCceecccchhhhhh
Confidence 4678999999999998887 9999999999999999999999999998888874
No 33
>KOG4172 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=98.11 E-value=3.8e-07 Score=63.69 Aligned_cols=53 Identities=21% Similarity=0.613 Sum_probs=43.7
Q ss_pred CCCCCCCCCCCCCcccccccccc-cchhhHHHHHh-cCCCCCCCCCCCCcCCeeeCcc
Q 024073 216 RTICPLCSQKRANPSVVTVSGFV-FCYACIFKYVS-QYKRCPVTLMPATVEQIRRLFH 271 (273)
Q Consensus 216 ~~~CpiC~~~~~np~~l~~~G~v-fCy~Ci~~~~~-~~~~CPv~~~~~~~~~l~ri~~ 271 (273)
+..|.||.+...|.++-+ |||+ +||.|..+-.+ .++.||+|+.|+ +|++|-|.
T Consensus 7 ~dECTICye~pvdsVlYt-CGHMCmCy~Cg~rl~~~~~g~CPiCRapi--~dvIkTY~ 61 (62)
T KOG4172|consen 7 SDECTICYEHPVDSVLYT-CGHMCMCYACGLRLKKALHGCCPICRAPI--KDVIKTYR 61 (62)
T ss_pred ccceeeeccCcchHHHHH-cchHHhHHHHHHHHHHccCCcCcchhhHH--HHHHHhhc
Confidence 478999999998887766 9997 79999999888 789999999664 56666553
No 34
>COG5243 HRD1 HRD ubiquitin ligase complex, ER membrane component [Posttranslational modification, protein turnover, chaperones]
Probab=98.06 E-value=2.3e-06 Score=80.73 Aligned_cols=47 Identities=17% Similarity=0.596 Sum_probs=40.8
Q ss_pred CCCCCCCCCCCCCCCc-------------ccccccccccchhhHHHHHhcCCCCCCCCCCC
Q 024073 214 PDRTICPLCSQKRANP-------------SVVTVSGFVFCYACIFKYVSQYKRCPVTLMPA 261 (273)
Q Consensus 214 ~~~~~CpiC~~~~~np-------------~~l~~~G~vfCy~Ci~~~~~~~~~CPv~~~~~ 261 (273)
.+.+.|.||++.+-.| .-++ |||++-..|+..|+++++.||+|+.|+
T Consensus 285 n~D~~C~ICmde~~h~~~~~~~~~~~~~pKrLp-CGHilHl~CLknW~ERqQTCPICr~p~ 344 (491)
T COG5243 285 NSDRTCTICMDEMFHPDHEPLPRGLDMTPKRLP-CGHILHLHCLKNWLERQQTCPICRRPV 344 (491)
T ss_pred CCCCeEEEecccccCCCCccCcccccCCccccc-ccceeeHHHHHHHHHhccCCCcccCcc
Confidence 4689999999984333 4676 999999999999999999999999985
No 35
>KOG0824 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=98.05 E-value=2e-06 Score=79.24 Aligned_cols=47 Identities=26% Similarity=0.527 Sum_probs=41.3
Q ss_pred CCCCCCCCCCCCCcccccccccccchhhHHHHHhcCCC-CCCCCCCCCc
Q 024073 216 RTICPLCSQKRANPSVVTVSGFVFCYACIFKYVSQYKR-CPVTLMPATV 263 (273)
Q Consensus 216 ~~~CpiC~~~~~np~~l~~~G~vfCy~Ci~~~~~~~~~-CPv~~~~~~~ 263 (273)
...|+||.....-|+.+. |+|+|||-||..-....++ |+||+.+++.
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 9999999999988877765 9999988753
No 36
>KOG0802 consensus E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=98.05 E-value=1.6e-06 Score=86.95 Aligned_cols=47 Identities=17% Similarity=0.523 Sum_probs=42.8
Q ss_pred CCCCCCCCCCCCCC-----cccccccccccchhhHHHHHhcCCCCCCCCCCCC
Q 024073 215 DRTICPLCSQKRAN-----PSVVTVSGFVFCYACIFKYVSQYKRCPVTLMPAT 262 (273)
Q Consensus 215 ~~~~CpiC~~~~~n-----p~~l~~~G~vfCy~Ci~~~~~~~~~CPv~~~~~~ 262 (273)
....|+||.+.+.+ |..++ |||+||-.|+.+|+++...||+|+...-
T Consensus 290 ~~~~C~IC~e~l~~~~~~~~~rL~-C~Hifh~~CL~~W~er~qtCP~CR~~~~ 341 (543)
T KOG0802|consen 290 SDELCIICLEELHSGHNITPKRLP-CGHIFHDSCLRSWFERQQTCPTCRTVLY 341 (543)
T ss_pred cCCeeeeechhhccccccccceee-cccchHHHHHHHHHHHhCcCCcchhhhh
Confidence 36899999999999 78887 9999999999999999999999998443
No 37
>KOG2177 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=98.04 E-value=1.6e-06 Score=76.70 Aligned_cols=43 Identities=28% Similarity=0.674 Sum_probs=39.5
Q ss_pred CCCCCCCCCCCCCCcccccccccccchhhHHHHHhcCCCCCCCC
Q 024073 215 DRTICPLCSQKRANPSVVTVSGFVFCYACIFKYVSQYKRCPVTL 258 (273)
Q Consensus 215 ~~~~CpiC~~~~~np~~l~~~G~vfCy~Ci~~~~~~~~~CPv~~ 258 (273)
+...||||.+..++|.+++ |||.||..|+..+....-.||+|+
T Consensus 12 ~~~~C~iC~~~~~~p~~l~-C~H~~c~~C~~~~~~~~~~Cp~cr 54 (386)
T KOG2177|consen 12 EELTCPICLEYFREPVLLP-CGHNFCRACLTRSWEGPLSCPVCR 54 (386)
T ss_pred ccccChhhHHHhhcCcccc-ccchHhHHHHHHhcCCCcCCcccC
Confidence 5789999999999998877 999999999999998557999999
No 38
>KOG2660 consensus Locus-specific chromosome binding proteins [Function unknown]
Probab=98.03 E-value=1.5e-06 Score=80.82 Aligned_cols=50 Identities=26% Similarity=0.548 Sum_probs=44.7
Q ss_pred CCCCCCCCCCCCCCcccccccccccchhhHHHHHhcCCCCCCCCCCCCcC
Q 024073 215 DRTICPLCSQKRANPSVVTVSGFVFCYACIFKYVSQYKRCPVTLMPATVE 264 (273)
Q Consensus 215 ~~~~CpiC~~~~~np~~l~~~G~vfCy~Ci~~~~~~~~~CPv~~~~~~~~ 264 (273)
...+|.+|.+-+.|+|.+..|=|.||..||.+|++.+..||.|+.-+...
T Consensus 14 ~~itC~LC~GYliDATTI~eCLHTFCkSCivk~l~~~~~CP~C~i~ih~t 63 (331)
T KOG2660|consen 14 PHITCRLCGGYLIDATTITECLHTFCKSCIVKYLEESKYCPTCDIVIHKT 63 (331)
T ss_pred cceehhhccceeecchhHHHHHHHHHHHHHHHHHHHhccCCccceeccCc
Confidence 46799999999999987777999999999999999999999999765433
No 39
>KOG0297 consensus TNF receptor-associated factor [Signal transduction mechanisms]
Probab=97.87 E-value=7.3e-06 Score=79.13 Aligned_cols=54 Identities=26% Similarity=0.617 Sum_probs=46.6
Q ss_pred CCCCCCCCCCCCCCCcccccccccccchhhHHHHHhcCCCCCCCCCCCCcCCee
Q 024073 214 PDRTICPLCSQKRANPSVVTVSGFVFCYACIFKYVSQYKRCPVTLMPATVEQIR 267 (273)
Q Consensus 214 ~~~~~CpiC~~~~~np~~l~~~G~vfCy~Ci~~~~~~~~~CPv~~~~~~~~~l~ 267 (273)
..+..||+|..++.+|.-.+.|||.||..|+..|+..+..||+|......++.+
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 356899999999999987535999999999999999999999998877665543
No 40
>PF12861 zf-Apc11: Anaphase-promoting complex subunit 11 RING-H2 finger
Probab=97.81 E-value=1.7e-05 Score=60.54 Aligned_cols=48 Identities=27% Similarity=0.533 Sum_probs=37.7
Q ss_pred CCCCCCCCCCCCC-cccccccccccchhhHHHHHhc---CCCCCCCCCCCCc
Q 024073 216 RTICPLCSQKRAN-PSVVTVSGFVFCYACIFKYVSQ---YKRCPVTLMPATV 263 (273)
Q Consensus 216 ~~~CpiC~~~~~n-p~~l~~~G~vfCy~Ci~~~~~~---~~~CPv~~~~~~~ 263 (273)
.+.||.|..+-.+ |.+.-.|||.|-..||.+|++. ++.||.|+++...
T Consensus 32 dg~Cp~Ck~Pgd~Cplv~g~C~H~FH~hCI~kWl~~~~~~~~CPmCR~~w~~ 83 (85)
T PF12861_consen 32 DGCCPDCKFPGDDCPLVWGKCSHNFHMHCILKWLSTQSSKGQCPMCRQPWKF 83 (85)
T ss_pred ccCCCCccCCCCCCceeeccCccHHHHHHHHHHHccccCCCCCCCcCCeeee
Confidence 3567777776544 5566679999999999999985 4899999987654
No 41
>KOG1002 consensus Nucleotide excision repair protein RAD16 [Replication, recombination and repair]
Probab=97.56 E-value=3.2e-05 Score=76.01 Aligned_cols=49 Identities=24% Similarity=0.543 Sum_probs=43.2
Q ss_pred CCCCCCCCCCCCCCcccccccccccchhhHHHHHhc-----CCCCCCCCCCCCcC
Q 024073 215 DRTICPLCSQKRANPSVVTVSGFVFCYACIFKYVSQ-----YKRCPVTLMPATVE 264 (273)
Q Consensus 215 ~~~~CpiC~~~~~np~~l~~~G~vfCy~Ci~~~~~~-----~~~CPv~~~~~~~~ 264 (273)
....|-+|.++-+++.+.. |.|+||.-||..|++. +-.||+|..+++.+
T Consensus 535 ~~~~C~lc~d~aed~i~s~-ChH~FCrlCi~eyv~~f~~~~nvtCP~C~i~LsiD 588 (791)
T KOG1002|consen 535 GEVECGLCHDPAEDYIESS-CHHKFCRLCIKEYVESFMENNNVTCPVCHIGLSID 588 (791)
T ss_pred CceeecccCChhhhhHhhh-hhHHHHHHHHHHHHHhhhcccCCCCcccccccccc
Confidence 4678999999999998876 9999999999999973 46999999988765
No 42
>KOG4628 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=97.55 E-value=3.6e-05 Score=72.87 Aligned_cols=44 Identities=20% Similarity=0.520 Sum_probs=38.0
Q ss_pred CCCCCCCCCCCCc---ccccccccccchhhHHHHHhcCCC-CCCCCCCC
Q 024073 217 TICPLCSQKRANP---SVVTVSGFVFCYACIFKYVSQYKR-CPVTLMPA 261 (273)
Q Consensus 217 ~~CpiC~~~~~np---~~l~~~G~vfCy~Ci~~~~~~~~~-CPv~~~~~ 261 (273)
..|.||++.-+.- .+|+ |+|.|--.||..|+.++++ ||||+...
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 4999999976555 4787 9999999999999999966 99999754
No 43
>KOG1813 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=97.51 E-value=3.3e-05 Score=71.08 Aligned_cols=44 Identities=25% Similarity=0.495 Sum_probs=41.3
Q ss_pred CCCCCCCCCCCCcccccccccccchhhHHHHHhcCCCCCCCCCCC
Q 024073 217 TICPLCSQKRANPSVVTVSGFVFCYACIFKYVSQYKRCPVTLMPA 261 (273)
Q Consensus 217 ~~CpiC~~~~~np~~l~~~G~vfCy~Ci~~~~~~~~~CPv~~~~~ 261 (273)
+.|-||.+...+|+|.. |||-||-.|...-++...+|.||++..
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 57999999999999987 999999999999999999999999764
No 44
>KOG0311 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=97.51 E-value=8.3e-06 Score=76.61 Aligned_cols=46 Identities=24% Similarity=0.593 Sum_probs=41.2
Q ss_pred CCCCCCCCCCCCCcccccccccccchhhHHHHHhc-CCCCCCCCCCC
Q 024073 216 RTICPLCSQKRANPSVVTVSGFVFCYACIFKYVSQ-YKRCPVTLMPA 261 (273)
Q Consensus 216 ~~~CpiC~~~~~np~~l~~~G~vfCy~Ci~~~~~~-~~~CPv~~~~~ 261 (273)
..+||||+.-+++....+.|+|-||..||..-++. ++.||-|++.+
T Consensus 43 ~v~c~icl~llk~tmttkeClhrfc~~ci~~a~r~gn~ecptcRk~l 89 (381)
T KOG0311|consen 43 QVICPICLSLLKKTMTTKECLHRFCFDCIWKALRSGNNECPTCRKKL 89 (381)
T ss_pred hhccHHHHHHHHhhcccHHHHHHHHHHHHHHHHHhcCCCCchHHhhc
Confidence 67999999999999777779999999999999975 57899999765
No 45
>COG5540 RING-finger-containing ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=97.41 E-value=6.6e-05 Score=69.45 Aligned_cols=46 Identities=24% Similarity=0.557 Sum_probs=38.2
Q ss_pred CCCCCCCCCC-CCCc--ccccccccccchhhHHHHHhcC-CCCCCCCCCCC
Q 024073 216 RTICPLCSQK-RANP--SVVTVSGFVFCYACIFKYVSQY-KRCPVTLMPAT 262 (273)
Q Consensus 216 ~~~CpiC~~~-~~np--~~l~~~G~vfCy~Ci~~~~~~~-~~CPv~~~~~~ 262 (273)
...|.||+.. ++|. .|++ |-|+|--.|+.+|+.++ .+||||+.++.
T Consensus 323 GveCaICms~fiK~d~~~vlP-C~H~FH~~Cv~kW~~~y~~~CPvCrt~iP 372 (374)
T COG5540 323 GVECAICMSNFIKNDRLRVLP-CDHRFHVGCVDKWLLGYSNKCPVCRTAIP 372 (374)
T ss_pred CceEEEEhhhhcccceEEEec-cCceechhHHHHHHhhhcccCCccCCCCC
Confidence 4679999995 4554 4776 99999999999999965 79999998764
No 46
>COG5222 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=97.38 E-value=9.6e-05 Score=68.27 Aligned_cols=44 Identities=30% Similarity=0.554 Sum_probs=39.5
Q ss_pred CCCCCCCCCCCCCcccccccccccchhhHHHHHhcC-CCCCCCCC
Q 024073 216 RTICPLCSQKRANPSVVTVSGFVFCYACIFKYVSQY-KRCPVTLM 259 (273)
Q Consensus 216 ~~~CpiC~~~~~np~~l~~~G~vfCy~Ci~~~~~~~-~~CPv~~~ 259 (273)
...||+|+.-+.||+-++.|||.||-.||-..|-+. -+||+|..
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 378999999999999888899999999999887654 79999985
No 47
>COG5152 Uncharacterized conserved protein, contains RING and CCCH-type Zn-fingers [General function prediction only]
Probab=97.21 E-value=0.00015 Score=63.55 Aligned_cols=45 Identities=22% Similarity=0.546 Sum_probs=41.1
Q ss_pred CCCCCCCCCCCCCcccccccccccchhhHHHHHhcCCCCCCCCCCC
Q 024073 216 RTICPLCSQKRANPSVVTVSGFVFCYACIFKYVSQYKRCPVTLMPA 261 (273)
Q Consensus 216 ~~~CpiC~~~~~np~~l~~~G~vfCy~Ci~~~~~~~~~CPv~~~~~ 261 (273)
.+.|-||.+....|.|.. |||.||-.|+.+-.+.-..|=||++..
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 468999999999999986 999999999999998889999999764
No 48
>KOG1734 consensus Predicted RING-containing E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=97.15 E-value=0.00051 Score=62.72 Aligned_cols=50 Identities=18% Similarity=0.440 Sum_probs=40.1
Q ss_pred CCCCCCCCCCCCCCc----------ccccccccccchhhHHHHHh--cCCCCCCCCCCCCcCC
Q 024073 215 DRTICPLCSQKRANP----------SVVTVSGFVFCYACIFKYVS--QYKRCPVTLMPATVEQ 265 (273)
Q Consensus 215 ~~~~CpiC~~~~~np----------~~l~~~G~vfCy~Ci~~~~~--~~~~CPv~~~~~~~~~ 265 (273)
+.+.|.+|++.+... --++ |+|||-.-||.-|+- +...||-|+++++.+.
T Consensus 223 ~d~vCaVCg~~~~~s~~eegvienty~Ls-CnHvFHEfCIrGWcivGKkqtCPYCKekVdl~r 284 (328)
T KOG1734|consen 223 SDSVCAVCGQQIDVSVDEEGVIENTYKLS-CNHVFHEFCIRGWCIVGKKQTCPYCKEKVDLKR 284 (328)
T ss_pred CcchhHhhcchheeecchhhhhhhheeee-cccchHHHhhhhheeecCCCCCchHHHHhhHhh
Confidence 567999999976543 2566 999999999999985 5579999998876543
No 49
>KOG1645 consensus RING-finger-containing E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=97.08 E-value=0.00014 Score=69.61 Aligned_cols=57 Identities=30% Similarity=0.535 Sum_probs=48.0
Q ss_pred CCCCCCCCCCCCCCcc----cccccccccchhhHHHHHhcC--CCCCCCCCCCCcCCeeeCcc
Q 024073 215 DRTICPLCSQKRANPS----VVTVSGFVFCYACIFKYVSQY--KRCPVTLMPATVEQIRRLFH 271 (273)
Q Consensus 215 ~~~~CpiC~~~~~np~----~l~~~G~vfCy~Ci~~~~~~~--~~CPv~~~~~~~~~l~ri~~ 271 (273)
+..+||||++.++-|. +...|||.|=..||.+|+-+. ++||.|.-.++..+|+.+|.
T Consensus 3 ~g~tcpiclds~~~~g~hr~vsl~cghlFgs~cie~wl~k~~~~~cp~c~~katkr~i~~e~a 65 (463)
T KOG1645|consen 3 CGTTCPICLDSYTTAGNHRIVSLQCGHLFGSQCIEKWLGKKTKMQCPLCSGKATKRQIRPEYA 65 (463)
T ss_pred ccccCceeeeeeeecCceEEeeecccccccHHHHHHHHhhhhhhhCcccCChhHHHHHHHHHH
Confidence 4679999999998882 444599999999999999643 68999999999988888763
No 50
>KOG4692 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=97.02 E-value=0.00039 Score=65.63 Aligned_cols=48 Identities=23% Similarity=0.547 Sum_probs=42.2
Q ss_pred CCCCCCCCCCCCCCCcccccccccccchhhHHHHHhcCCCCCCCCCCCC
Q 024073 214 PDRTICPLCSQKRANPSVVTVSGFVFCYACIFKYVSQYKRCPVTLMPAT 262 (273)
Q Consensus 214 ~~~~~CpiC~~~~~np~~l~~~G~vfCy~Ci~~~~~~~~~CPv~~~~~~ 262 (273)
.+.+.||||--.-.|+...+ |||--||.||.+++-+.++|=-|+....
T Consensus 420 sEd~lCpICyA~pi~Avf~P-C~H~SC~~CI~qHlmN~k~CFfCktTv~ 467 (489)
T KOG4692|consen 420 SEDNLCPICYAGPINAVFAP-CSHRSCYGCITQHLMNCKRCFFCKTTVI 467 (489)
T ss_pred cccccCcceecccchhhccC-CCCchHHHHHHHHHhcCCeeeEecceee
Confidence 35789999999988887766 9999999999999999999999996544
No 51
>PF14570 zf-RING_4: RING/Ubox like zinc-binding domain; PDB: 1E4U_A 1UR6_B.
Probab=96.89 E-value=0.00069 Score=46.42 Aligned_cols=42 Identities=29% Similarity=0.664 Sum_probs=23.1
Q ss_pred CCCCCCCCCCc----ccccccccccchhhHHHHHh-cCCCCCCCCCCC
Q 024073 219 CPLCSQKRANP----SVVTVSGFVFCYACIFKYVS-QYKRCPVTLMPA 261 (273)
Q Consensus 219 CpiC~~~~~np----~~l~~~G~vfCy~Ci~~~~~-~~~~CPv~~~~~ 261 (273)
||+|.+++..- .-++ |||..|..|-++-++ ++++||-|+++-
T Consensus 1 cp~C~e~~d~~d~~~~PC~-Cgf~IC~~C~~~i~~~~~g~CPgCr~~Y 47 (48)
T PF14570_consen 1 CPLCDEELDETDKDFYPCE-CGFQICRFCYHDILENEGGRCPGCREPY 47 (48)
T ss_dssp -TTTS-B--CCCTT--SST-TS----HHHHHHHTTSS-SB-TTT--B-
T ss_pred CCCcccccccCCCccccCc-CCCcHHHHHHHHHHhccCCCCCCCCCCC
Confidence 89999987221 2455 999999999999997 689999999764
No 52
>COG5175 MOT2 Transcriptional repressor [Transcription]
Probab=96.83 E-value=0.00074 Score=63.49 Aligned_cols=52 Identities=23% Similarity=0.473 Sum_probs=38.7
Q ss_pred CCCCCCCCCCCCCCc----ccccccccccchhhHHHHHh-cCCCCCCCCCCCCcCCee
Q 024073 215 DRTICPLCSQKRANP----SVVTVSGFVFCYACIFKYVS-QYKRCPVTLMPATVEQIR 267 (273)
Q Consensus 215 ~~~~CpiC~~~~~np----~~l~~~G~vfCy~Ci~~~~~-~~~~CPv~~~~~~~~~l~ 267 (273)
+...||+|.+++... --|+ |||..|.=|-...-+ -+|+||.|++..+.++++
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 356699999986433 4677 999988888664332 259999999888877765
No 53
>KOG4159 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=96.64 E-value=0.0009 Score=64.77 Aligned_cols=47 Identities=26% Similarity=0.539 Sum_probs=43.0
Q ss_pred CCCCCCCCCCCCCCCcccccccccccchhhHHHHHhcCCCCCCCCCCC
Q 024073 214 PDRTICPLCSQKRANPSVVTVSGFVFCYACIFKYVSQYKRCPVTLMPA 261 (273)
Q Consensus 214 ~~~~~CpiC~~~~~np~~l~~~G~vfCy~Ci~~~~~~~~~CPv~~~~~ 261 (273)
.+.+.|-||...+.+|++++ |||.||..||.+-+.+...||.|+.++
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 999999999999999999999998654
No 54
>KOG4265 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=96.57 E-value=0.0011 Score=62.71 Aligned_cols=52 Identities=17% Similarity=0.512 Sum_probs=43.9
Q ss_pred CCCCCCCCCCCCCcccccccccc-cchhhHHHHHhcCCCCCCCCCCCCcCCeeeCc
Q 024073 216 RTICPLCSQKRANPSVVTVSGFV-FCYACIFKYVSQYKRCPVTLMPATVEQIRRLF 270 (273)
Q Consensus 216 ~~~CpiC~~~~~np~~l~~~G~v-fCy~Ci~~~~~~~~~CPv~~~~~~~~~l~ri~ 270 (273)
...|-||+...+|-++++ |=|. .|-.|+....=++++||||+.+.. .+.+|+
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 9996 699999988878899999998753 344444
No 55
>PF11793 FANCL_C: FANCL C-terminal domain; PDB: 3K1L_A.
Probab=96.40 E-value=0.0012 Score=48.70 Aligned_cols=49 Identities=20% Similarity=0.463 Sum_probs=25.5
Q ss_pred CCCCCCCCCCCC-Cc----cccc--ccccccchhhHHHHHhc-----------CCCCCCCCCCCCcC
Q 024073 216 RTICPLCSQKRA-NP----SVVT--VSGFVFCYACIFKYVSQ-----------YKRCPVTLMPATVE 264 (273)
Q Consensus 216 ~~~CpiC~~~~~-np----~~l~--~~G~vfCy~Ci~~~~~~-----------~~~CPv~~~~~~~~ 264 (273)
+..|+||...+. +. .+++ .||.+|-..|+.+|+.. .|+||.|+.+++.+
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 32 3554 69999999999999973 35799999887643
No 56
>COG5194 APC11 Component of SCF ubiquitin ligase and anaphase-promoting complex [Posttranslational modification, protein turnover, chaperones / Cell division and chromosome partitioning]
Probab=96.39 E-value=0.0027 Score=47.86 Aligned_cols=48 Identities=21% Similarity=0.435 Sum_probs=37.0
Q ss_pred CCCCCCCCCCCCCc----ccccccccccchhhHHHHHhcCCCCCCCCCCCCc
Q 024073 216 RTICPLCSQKRANP----SVVTVSGFVFCYACIFKYVSQYKRCPVTLMPATV 263 (273)
Q Consensus 216 ~~~CpiC~~~~~np----~~l~~~G~vfCy~Ci~~~~~~~~~CPv~~~~~~~ 263 (273)
.+.||-|.-..++. .+--+|.|.|-.-||.+|+...+.||.++++...
T Consensus 31 m~~C~eCq~~~~~~~eC~v~wG~CnHaFH~HCI~rWL~Tk~~CPld~q~w~~ 82 (88)
T COG5194 31 MGTCPECQFGMTPGDECPVVWGVCNHAFHDHCIYRWLDTKGVCPLDRQTWVL 82 (88)
T ss_pred cCcCcccccCCCCCCcceEEEEecchHHHHHHHHHHHhhCCCCCCCCceeEE
Confidence 45677776644322 4556799999999999999999999999987543
No 57
>PF14447 Prok-RING_4: Prokaryotic RING finger family 4
Probab=96.31 E-value=0.002 Score=45.23 Aligned_cols=49 Identities=20% Similarity=0.508 Sum_probs=40.4
Q ss_pred CCCCCCCCCCCCCCcccccccccccchhhHHHHHhcCCCCCCCCCCCCcCCe
Q 024073 215 DRTICPLCSQKRANPSVVTVSGFVFCYACIFKYVSQYKRCPVTLMPATVEQI 266 (273)
Q Consensus 215 ~~~~CpiC~~~~~np~~l~~~G~vfCy~Ci~~~~~~~~~CPv~~~~~~~~~l 266 (273)
+...|-.|+..-+..++++ |||+-|+.|-- +++..-||+|+.|...+++
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 3457889999988999998 99999999964 4456899999999887653
No 58
>KOG0828 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=96.29 E-value=0.0021 Score=63.03 Aligned_cols=49 Identities=22% Similarity=0.561 Sum_probs=38.4
Q ss_pred CCCCCCCCCCCCCC-----Ccc-----------cccccccccchhhHHHHHhcCC-CCCCCCCCCC
Q 024073 214 PDRTICPLCSQKRA-----NPS-----------VVTVSGFVFCYACIFKYVSQYK-RCPVTLMPAT 262 (273)
Q Consensus 214 ~~~~~CpiC~~~~~-----np~-----------~l~~~G~vfCy~Ci~~~~~~~~-~CPv~~~~~~ 262 (273)
.+...|+||+.++. +++ ++++|.|+|-..|+.+|++.-+ .||||+.++.
T Consensus 569 ~~t~dC~ICMt~I~l~~~~s~~~~~~~~~~~nYm~tPC~HifH~~CL~~WMd~ykl~CPvCR~pLP 634 (636)
T KOG0828|consen 569 RRTNDCVICMTPIDLRSTGSDCMVASMMVRRNYMLTPCHHIFHRQCLLQWMDTYKLICPVCRCPLP 634 (636)
T ss_pred hccccceEeccccceeeccCcchhhhhhhhccccccchHHHHHHHHHHHHHhhhcccCCccCCCCC
Confidence 35678999999753 221 3345999999999999999655 9999998864
No 59
>KOG3039 consensus Uncharacterized conserved protein [Function unknown]
Probab=96.15 E-value=0.0035 Score=56.72 Aligned_cols=34 Identities=24% Similarity=0.511 Sum_probs=30.9
Q ss_pred CCCCCCCCCCCCCCcccccccccccchhhHHHHHh
Q 024073 215 DRTICPLCSQKRANPSVVTVSGFVFCYACIFKYVS 249 (273)
Q Consensus 215 ~~~~CpiC~~~~~np~~l~~~G~vfCy~Ci~~~~~ 249 (273)
+-.-|.+|+++..||++++ .||+||..||.+|+-
T Consensus 42 ~FdcCsLtLqPc~dPvit~-~GylfdrEaILe~il 75 (303)
T KOG3039|consen 42 PFDCCSLTLQPCRDPVITP-DGYLFDREAILEYIL 75 (303)
T ss_pred CcceeeeecccccCCccCC-CCeeeeHHHHHHHHH
Confidence 3568999999999999887 999999999999984
No 60
>KOG0827 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=96.11 E-value=0.0025 Score=60.86 Aligned_cols=52 Identities=17% Similarity=0.517 Sum_probs=38.5
Q ss_pred CCCCCCCCCCCCCc---ccccccccccchhhHHHHHhcC---CCCCCCCCCCCcCCee
Q 024073 216 RTICPLCSQKRANP---SVVTVSGFVFCYACIFKYVSQY---KRCPVTLMPATVEQIR 267 (273)
Q Consensus 216 ~~~CpiC~~~~~np---~~l~~~G~vfCy~Ci~~~~~~~---~~CPv~~~~~~~~~l~ 267 (273)
.-.|.||.+-.-|- ..+.+|||+|--.|+.+|.+.. ..||+|+......++.
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 34799996654333 4556699999999999999964 5899999655544444
No 61
>KOG1039 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=96.11 E-value=0.0036 Score=59.56 Aligned_cols=49 Identities=24% Similarity=0.637 Sum_probs=40.7
Q ss_pred CCCCCCCCCCCCCCCcc-------cccccccccchhhHHHHH--hc-----CCCCCCCCCCCC
Q 024073 214 PDRTICPLCSQKRANPS-------VVTVSGFVFCYACIFKYV--SQ-----YKRCPVTLMPAT 262 (273)
Q Consensus 214 ~~~~~CpiC~~~~~np~-------~l~~~G~vfCy~Ci~~~~--~~-----~~~CPv~~~~~~ 262 (273)
.....|-||++.+.... +++.|-|.||-.||..|= .+ +..||.|+.+.+
T Consensus 159 s~~k~CGICme~i~ek~~~~~rfgilpnC~H~~Cl~Cir~wr~~~q~~~~~sksCP~CRv~s~ 221 (344)
T KOG1039|consen 159 SSEKECGICMETINEKAASERRFGILPNCNHSFCLNCIRKWRQATQFESKTSKSCPFCRVPSS 221 (344)
T ss_pred cccccceehhhhccccchhhhhcccCCCcchhhhhcHhHhhhhhhccccccccCCCcccCccc
Confidence 35789999999988875 456799999999999999 45 578999997653
No 62
>KOG1001 consensus Helicase-like transcription factor HLTF/DNA helicase RAD5, DEAD-box superfamily [Transcription; Replication, recombination and repair]
Probab=95.92 E-value=0.0015 Score=67.20 Aligned_cols=46 Identities=24% Similarity=0.512 Sum_probs=36.5
Q ss_pred CCCCCCCCCCCCcccccccccccchhhHHHHHhcC--CCCCCCCCCCCcC
Q 024073 217 TICPLCSQKRANPSVVTVSGFVFCYACIFKYVSQY--KRCPVTLMPATVE 264 (273)
Q Consensus 217 ~~CpiC~~~~~np~~l~~~G~vfCy~Ci~~~~~~~--~~CPv~~~~~~~~ 264 (273)
..|++|.+ ...+ ++..|||+||+.|+...++.. ..||+|+.....+
T Consensus 455 ~~c~ic~~-~~~~-~it~c~h~~c~~c~~~~i~~~~~~~~~~cr~~l~~~ 502 (674)
T KOG1001|consen 455 HWCHICCD-LDSF-FITRCGHDFCVECLKKSIQQSENAPCPLCRNVLKEK 502 (674)
T ss_pred cccccccc-cccc-eeecccchHHHHHHHhccccccCCCCcHHHHHHHHH
Confidence 79999999 4444 555599999999999999854 5799998655433
No 63
>KOG0825 consensus PHD Zn-finger protein [General function prediction only]
Probab=95.87 E-value=0.0015 Score=67.09 Aligned_cols=47 Identities=19% Similarity=0.388 Sum_probs=39.1
Q ss_pred CCCCCCCCCCCCCCcccc--cccccccchhhHHHHHhcCCCCCCCCCCC
Q 024073 215 DRTICPLCSQKRANPSVV--TVSGFVFCYACIFKYVSQYKRCPVTLMPA 261 (273)
Q Consensus 215 ~~~~CpiC~~~~~np~~l--~~~G~vfCy~Ci~~~~~~~~~CPv~~~~~ 261 (273)
....||+|.....+--+. .+|||.||-.|+..|.+-...||+|+.-.
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 367899999987776432 24999999999999999999999999653
No 64
>smart00744 RINGv The RING-variant domain is a C4HC3 zinc-finger like motif found in a number of cellular and viral proteins. Some of these proteins have been shown both in vivo and in vitro to have ubiquitin E3 ligase activity. The RING-variant domain is reminiscent of both the RING and the PHD domains and may represent an evolutionary intermediate. To describe this domain the term PHD/LAP domain has been used in the past. Extended description: The RING-variant (RINGv) domain contains a C4HC3 zinc-finger-like motif similar to the PHD domain, while some of the spacing between the Cys/His residues follow a pattern somewhat closer to that found in the RING domain. The RINGv domain, similar to the RING, PHD and LIM domains, is thought to bind two zinc ions co-ordinated by the highly conserved Cys and His residues. RING variant domain: C-x (2) -C-x(10-45)-C-x (1) -C-x (7) -H-x(2)-C-x(11-25)-C-x(2)-C As opposed to a PHD: C-x(1-2) -C-x (7-13)-C-x(2-4)-C-x(4-5)-H-x(2)-C-x(10-21)-C-x(2)-C Class
Probab=95.47 E-value=0.015 Score=39.90 Aligned_cols=40 Identities=18% Similarity=0.536 Sum_probs=29.9
Q ss_pred CCCCCCC--CCCCcccccccc-----cccchhhHHHHHhcCC--CCCCCC
Q 024073 218 ICPLCSQ--KRANPSVVTVSG-----FVFCYACIFKYVSQYK--RCPVTL 258 (273)
Q Consensus 218 ~CpiC~~--~~~np~~l~~~G-----~vfCy~Ci~~~~~~~~--~CPv~~ 258 (273)
+|-||.. .-.++.+.+ |. +.+-..|+.+|+...+ +||+|+
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 344454444 53 8889999999997664 899996
No 65
>KOG0804 consensus Cytoplasmic Zn-finger protein BRAP2 (BRCA1 associated protein) [General function prediction only]
Probab=95.31 E-value=0.007 Score=58.86 Aligned_cols=43 Identities=21% Similarity=0.614 Sum_probs=35.9
Q ss_pred CCCCCCCCCCCcc---cccccccccchhhHHHHHhcCCCCCCCCCCCC
Q 024073 218 ICPLCSQKRANPS---VVTVSGFVFCYACIFKYVSQYKRCPVTLMPAT 262 (273)
Q Consensus 218 ~CpiC~~~~~np~---~l~~~G~vfCy~Ci~~~~~~~~~CPv~~~~~~ 262 (273)
+||+|++.+...+ +...|-|.|--.|+..|- +..||||+.-.+
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 7999999998776 445599999999999995 679999986444
No 66
>KOG0883 consensus Cyclophilin type, U box-containing peptidyl-prolyl cis-trans isomerase [Posttranslational modification, protein turnover, chaperones]
Probab=95.28 E-value=0.013 Score=56.15 Aligned_cols=54 Identities=20% Similarity=0.269 Sum_probs=49.7
Q ss_pred CCCCCCCCCCCCCcccccccccccchhhHHHHHhcCCCCCCCCCCCCcCCeeeCc
Q 024073 216 RTICPLCSQKRANPSVVTVSGFVFCYACIFKYVSQYKRCPVTLMPATVEQIRRLF 270 (273)
Q Consensus 216 ~~~CpiC~~~~~np~~l~~~G~vfCy~Ci~~~~~~~~~CPv~~~~~~~~~l~ri~ 270 (273)
-+.|.+.+.+..+|+.+ +.|-||-+.-|..||+.+|+=|++|+++..++|+++-
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 46899999999999655 5999999999999999999999999999999999874
No 67
>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=95.19 E-value=0.0083 Score=46.57 Aligned_cols=29 Identities=34% Similarity=0.709 Sum_probs=24.4
Q ss_pred CCCCCCCCCCCCCcc--cccccccccchhhHH
Q 024073 216 RTICPLCSQKRANPS--VVTVSGFVFCYACIF 245 (273)
Q Consensus 216 ~~~CpiC~~~~~np~--~l~~~G~vfCy~Ci~ 245 (273)
...|++|++++.|.+ +.+ |||||.+.|+.
T Consensus 78 ~~~C~vC~k~l~~~~f~~~p-~~~v~H~~C~~ 108 (109)
T PF10367_consen 78 STKCSVCGKPLGNSVFVVFP-CGHVVHYSCIK 108 (109)
T ss_pred CCCccCcCCcCCCceEEEeC-CCeEEeccccc
Confidence 557999999999884 445 99999999974
No 68
>KOG2932 consensus E3 ubiquitin ligase involved in ubiquitination of E-cadherin complex [Posttranslational modification, protein turnover, chaperones]
Probab=94.99 E-value=0.0086 Score=55.83 Aligned_cols=43 Identities=23% Similarity=0.423 Sum_probs=34.1
Q ss_pred CCCCCCCCCCCCCc-ccccccccccchhhHHHHHhcCCCCCCCCCCC
Q 024073 216 RTICPLCSQKRANP-SVVTVSGFVFCYACIFKYVSQYKRCPVTLMPA 261 (273)
Q Consensus 216 ~~~CpiC~~~~~np-~~l~~~G~vfCy~Ci~~~~~~~~~CPv~~~~~ 261 (273)
-..|--|..+|.-= .+++ |-|||||+|+.. ...+.||.|..++
T Consensus 90 VHfCd~Cd~PI~IYGRmIP-CkHvFCl~CAr~--~~dK~Cp~C~d~V 133 (389)
T KOG2932|consen 90 VHFCDRCDFPIAIYGRMIP-CKHVFCLECARS--DSDKICPLCDDRV 133 (389)
T ss_pred eEeecccCCcceeeecccc-cchhhhhhhhhc--CccccCcCcccHH
Confidence 35699999987544 5787 999999999974 3468999998764
No 69
>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=94.92 E-value=0.0094 Score=41.08 Aligned_cols=43 Identities=21% Similarity=0.457 Sum_probs=24.4
Q ss_pred CCCCCCCCCCCCcccccccccccchhhHHHHHhcC-----CCCCCCCCC
Q 024073 217 TICPLCSQKRANPSVVTVSGFVFCYACIFKYVSQY-----KRCPVTLMP 260 (273)
Q Consensus 217 ~~CpiC~~~~~np~~l~~~G~vfCy~Ci~~~~~~~-----~~CPv~~~~ 260 (273)
..|||....++.|+=-..|-|+-|++ +..|++.+ -+||+|+++
T Consensus 3 L~CPls~~~i~~P~Rg~~C~H~~CFD-l~~fl~~~~~~~~W~CPiC~~~ 50 (50)
T PF02891_consen 3 LRCPLSFQRIRIPVRGKNCKHLQCFD-LESFLESNQRTPKWKCPICNKP 50 (50)
T ss_dssp SB-TTTSSB-SSEEEETT--SS--EE-HHHHHHHHHHS---B-TTT---
T ss_pred eeCCCCCCEEEeCccCCcCcccceEC-HHHHHHHhhccCCeECcCCcCc
Confidence 47999999999998666799998886 44455432 369999875
No 70
>KOG2930 consensus SCF ubiquitin ligase, Rbx1 component [Posttranslational modification, protein turnover, chaperones]
Probab=94.91 E-value=0.016 Score=45.89 Aligned_cols=45 Identities=18% Similarity=0.463 Sum_probs=35.7
Q ss_pred CCCCCCCCCCCCcc----------------cccccccccchhhHHHHHhcCCCCCCCCCCC
Q 024073 217 TICPLCSQKRANPS----------------VVTVSGFVFCYACIFKYVSQYKRCPVTLMPA 261 (273)
Q Consensus 217 ~~CpiC~~~~~np~----------------~l~~~G~vfCy~Ci~~~~~~~~~CPv~~~~~ 261 (273)
..|.||+..|-|.+ +=-+|.|.|-+-||.+||+....||.|+++-
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 57888887654331 2245999999999999999999999998753
No 71
>KOG3113 consensus Uncharacterized conserved protein [Function unknown]
Probab=94.66 E-value=0.028 Score=51.11 Aligned_cols=56 Identities=18% Similarity=0.241 Sum_probs=46.1
Q ss_pred CCCCCCCCCCCCCCc---ccccccccccchhhHHHHHhcCCCCCCCCCCCCcCCeeeCccC
Q 024073 215 DRTICPLCSQKRANP---SVVTVSGFVFCYACIFKYVSQYKRCPVTLMPATVEQIRRLFHD 272 (273)
Q Consensus 215 ~~~~CpiC~~~~~np---~~l~~~G~vfCy~Ci~~~~~~~~~CPv~~~~~~~~~l~ri~~~ 272 (273)
..++|||-+-++..- +++-.|||||-++-+.+.= ...|++|+.+.+.+|+|-|-.+
T Consensus 110 a~fiCPvtgleMng~~~F~~l~~CGcV~SerAlKeik--as~C~~C~a~y~~~dvIvlNg~ 168 (293)
T KOG3113|consen 110 ARFICPVTGLEMNGKYRFCALRCCGCVFSERALKEIK--ASVCHVCGAAYQEDDVIVLNGT 168 (293)
T ss_pred ceeecccccceecceEEEEEEeccceeccHHHHHHhh--hccccccCCcccccCeEeeCCC
Confidence 468999999998776 5666699999998766543 5689999999999999987653
No 72
>KOG1785 consensus Tyrosine kinase negative regulator CBL [Defense mechanisms]
Probab=94.56 E-value=0.015 Score=56.07 Aligned_cols=45 Identities=16% Similarity=0.604 Sum_probs=37.5
Q ss_pred CCCCCCCCCCCCcccccccccccchhhHHHHHhcC--CCCCCCCCCCC
Q 024073 217 TICPLCSQKRANPSVVTVSGFVFCYACIFKYVSQY--KRCPVTLMPAT 262 (273)
Q Consensus 217 ~~CpiC~~~~~np~~l~~~G~vfCy~Ci~~~~~~~--~~CPv~~~~~~ 262 (273)
..|-||-+.=+|-.+-+ |||..|-.|+-.|-... +.||.|+..++
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 45999999888877755 99999999999999654 68999996543
No 73
>KOG1571 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=94.46 E-value=0.015 Score=55.10 Aligned_cols=42 Identities=24% Similarity=0.562 Sum_probs=32.6
Q ss_pred CCCCCCCCCCCCCcccccccccccchhhHHHHHhcCCCCCCCCCCC
Q 024073 216 RTICPLCSQKRANPSVVTVSGFVFCYACIFKYVSQYKRCPVTLMPA 261 (273)
Q Consensus 216 ~~~CpiC~~~~~np~~l~~~G~vfCy~Ci~~~~~~~~~CPv~~~~~ 261 (273)
..-|-||...-.|..-++ |||+.| |+.-.-.- ..||||+...
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 457999999999977777 999988 77644332 4599999654
No 74
>KOG2817 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=94.12 E-value=0.15 Score=49.17 Aligned_cols=99 Identities=16% Similarity=0.310 Sum_probs=66.7
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHH----HhcccccccCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC--CCCc-
Q 024073 157 YTMLDYAQTGLIAAVFFFKMMEW----WYQSAEERMSAPTVYPPPPPPPPPKVAREGIPLPPDRTICPLCSQK--RANP- 229 (273)
Q Consensus 157 ~~l~~~l~~~Lp~~IF~lKfLEW----Wyss~~~~~~~~~~lp~PpPP~~~~~~~~~~~~p~~~~~CpiC~~~--~~np- 229 (273)
..+..++..+||..+=..-+++= |.+.|+ ||.+---+ ... ---+.++|||=.+. =.||
T Consensus 286 ~v~v~aG~~Alp~Llk~~~v~~~~~~~W~~~de--------LPveIeL~------~~~-~fHSvF~CPVlKeqtsdeNPP 350 (394)
T KOG2817|consen 286 SVLVNAGCIALPQLLKYKSVMELKHGEWNTKDE--------LPVEIELG------KEY-HFHSVFICPVLKEQTSDENPP 350 (394)
T ss_pred HHHHHhhHHHHHHHHHHHHHHHHhccCcccccc--------Cccceecc------ccc-cccceeecccchhhccCCCCC
Confidence 34555666777777766666776 665543 44322110 000 01246899998774 4566
Q ss_pred ccccccccccchhhHHHHHhcCC---CCCCCCCCCCcCCeeeCcc
Q 024073 230 SVVTVSGFVFCYACIFKYVSQYK---RCPVTLMPATVEQIRRLFH 271 (273)
Q Consensus 230 ~~l~~~G~vfCy~Ci~~~~~~~~---~CPv~~~~~~~~~l~ri~~ 271 (273)
..+. ||||-|..-+.+--++.. +||=|-..-..++.+|||.
T Consensus 351 m~L~-CGHVISkdAlnrLS~ng~~sfKCPYCP~e~~~~~~kql~F 394 (394)
T KOG2817|consen 351 MMLI-CGHVISKDALNRLSKNGSQSFKCPYCPVEQLASDTKQLYF 394 (394)
T ss_pred eeee-ccceecHHHHHHHhhCCCeeeeCCCCCcccCHHhcccccC
Confidence 5665 999999999998877654 7999998888999999873
No 75
>KOG2979 consensus Protein involved in DNA repair [General function prediction only]
Probab=94.10 E-value=0.026 Score=51.44 Aligned_cols=45 Identities=22% Similarity=0.366 Sum_probs=40.8
Q ss_pred CCCCCCCCCCCCCcccccccccccchhhHHHHHhcC--CCCCCCCCC
Q 024073 216 RTICPLCSQKRANPSVVTVSGFVFCYACIFKYVSQY--KRCPVTLMP 260 (273)
Q Consensus 216 ~~~CpiC~~~~~np~~l~~~G~vfCy~Ci~~~~~~~--~~CPv~~~~ 260 (273)
+..||+-.+++.||.+-..|||||-.+-|+.++... -+|||-|..
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 689999999999999988899999999999999884 589998755
No 76
>PF05290 Baculo_IE-1: Baculovirus immediate-early protein (IE-0); InterPro: IPR007954 This entry contains the Baculovirus immediate-early protein IE-0.
Probab=93.55 E-value=0.056 Score=44.71 Aligned_cols=48 Identities=25% Similarity=0.589 Sum_probs=37.7
Q ss_pred CCCCCCCCCCCCCcccccc---cccccchhhHH---HHHhcCCCCCCCCCCCCc
Q 024073 216 RTICPLCSQKRANPSVVTV---SGFVFCYACIF---KYVSQYKRCPVTLMPATV 263 (273)
Q Consensus 216 ~~~CpiC~~~~~np~~l~~---~G~vfCy~Ci~---~~~~~~~~CPv~~~~~~~ 263 (273)
-+.|-||.+.-.+..-+.+ |||--|+-|-- ++..-+..||||+...+.
T Consensus 80 lYeCnIC~etS~ee~FLKPneCCgY~iCn~Cya~LWK~~~~ypvCPvCkTSFKs 133 (140)
T PF05290_consen 80 LYECNICKETSAEERFLKPNECCGYSICNACYANLWKFCNLYPVCPVCKTSFKS 133 (140)
T ss_pred ceeccCcccccchhhcCCcccccchHHHHHHHHHHHHHcccCCCCCcccccccc
Confidence 3589999999888876643 99999999954 455578999999976653
No 77
>KOG3579 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=93.41 E-value=0.062 Score=49.69 Aligned_cols=37 Identities=24% Similarity=0.621 Sum_probs=30.4
Q ss_pred CCCCCCCCCCCCCCcccc---cccccccchhhHHHHHhcC
Q 024073 215 DRTICPLCSQKRANPSVV---TVSGFVFCYACIFKYVSQY 251 (273)
Q Consensus 215 ~~~~CpiC~~~~~np~~l---~~~G~vfCy~Ci~~~~~~~ 251 (273)
....|.+|.+.+.|-.-. ++.+|-||++|-.+.|+++
T Consensus 267 apLcCTLC~ERLEDTHFVQCPSVp~HKFCFPCSResIK~Q 306 (352)
T KOG3579|consen 267 APLCCTLCHERLEDTHFVQCPSVPSHKFCFPCSRESIKQQ 306 (352)
T ss_pred CceeehhhhhhhccCceeecCCCcccceecccCHHHHHhh
Confidence 457899999999998422 3479999999999999864
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=93.38 E-value=0.046 Score=32.69 Aligned_cols=22 Identities=23% Similarity=0.643 Sum_probs=16.4
Q ss_pred CCCCCCCCCCCc-cccccccccc
Q 024073 218 ICPLCSQKRANP-SVVTVSGFVF 239 (273)
Q Consensus 218 ~CpiC~~~~~np-~~l~~~G~vf 239 (273)
.||-|+..+... ..++.|||+|
T Consensus 2 ~CP~C~~~V~~~~~~Cp~CG~~F 24 (26)
T PF10571_consen 2 TCPECGAEVPESAKFCPHCGYDF 24 (26)
T ss_pred cCCCCcCCchhhcCcCCCCCCCC
Confidence 699999977544 4667788877
No 79
>KOG1493 consensus Anaphase-promoting complex (APC), subunit 11 [Cell cycle control, cell division, chromosome partitioning; Posttranslational modification, protein turnover, chaperones]
Probab=93.30 E-value=0.04 Score=41.34 Aligned_cols=48 Identities=23% Similarity=0.454 Sum_probs=36.4
Q ss_pred CCCCCCCCCCCCC-cccccccccccchhhHHHHHhc---CCCCCCCCCCCCc
Q 024073 216 RTICPLCSQKRAN-PSVVTVSGFVFCYACIFKYVSQ---YKRCPVTLMPATV 263 (273)
Q Consensus 216 ~~~CpiC~~~~~n-p~~l~~~G~vfCy~Ci~~~~~~---~~~CPv~~~~~~~ 263 (273)
.+.||-|.-+-.| |-|+--|-|.|-.-||.+|+.. ++.||.|++..+.
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 4567777665443 4566679999999999999974 4899999976543
No 80
>KOG3002 consensus Zn finger protein [General function prediction only]
Probab=92.94 E-value=0.071 Score=49.94 Aligned_cols=45 Identities=24% Similarity=0.561 Sum_probs=38.0
Q ss_pred CCCCCCCCCCCCCCcccccccccccchhhHHHHHhcCCCCCCCCCCCC
Q 024073 215 DRTICPLCSQKRANPSVVTVSGFVFCYACIFKYVSQYKRCPVTLMPAT 262 (273)
Q Consensus 215 ~~~~CpiC~~~~~np~~l~~~G~vfCy~Ci~~~~~~~~~CPv~~~~~~ 262 (273)
+-..||+|.+.+.-|..=-..||.-|-.|-. +...+||.|+.+++
T Consensus 47 ~lleCPvC~~~l~~Pi~QC~nGHlaCssC~~---~~~~~CP~Cr~~~g 91 (299)
T KOG3002|consen 47 DLLDCPVCFNPLSPPIFQCDNGHLACSSCRT---KVSNKCPTCRLPIG 91 (299)
T ss_pred hhccCchhhccCcccceecCCCcEehhhhhh---hhcccCCccccccc
Confidence 4578999999999996532379999999987 56789999999887
No 81
>KOG4275 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=92.83 E-value=0.015 Score=53.78 Aligned_cols=41 Identities=22% Similarity=0.569 Sum_probs=34.4
Q ss_pred CCCCCCCCCCCCCccccccccc-ccchhhHHHHHhcCCCCCCCCCCC
Q 024073 216 RTICPLCSQKRANPSVVTVSGF-VFCYACIFKYVSQYKRCPVTLMPA 261 (273)
Q Consensus 216 ~~~CpiC~~~~~np~~l~~~G~-vfCy~Ci~~~~~~~~~CPv~~~~~ 261 (273)
...|.||.+...+=..|+ ||| |-|+.|-.+- ..||||++.+
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 567999999999988887 999 6799998743 3899999754
No 82
>KOG0298 consensus DEAD box-containing helicase-like transcription factor/DNA repair protein [Replication, recombination and repair]
Probab=92.74 E-value=0.021 Score=61.67 Aligned_cols=44 Identities=20% Similarity=0.465 Sum_probs=39.9
Q ss_pred CCCCCCCCCCCCCCcccccccccccchhhHHHHHhcCCCCCCCC
Q 024073 215 DRTICPLCSQKRANPSVVTVSGFVFCYACIFKYVSQYKRCPVTL 258 (273)
Q Consensus 215 ~~~~CpiC~~~~~np~~l~~~G~vfCy~Ci~~~~~~~~~CPv~~ 258 (273)
+...|+||++.+.|-..+..|||-+|-.|..-|+..+.+||+|+
T Consensus 1152 ~~~~c~ic~dil~~~~~I~~cgh~~c~~c~~~~l~~~s~~~~~k 1195 (1394)
T KOG0298|consen 1152 GHFVCEICLDILRNQGGIAGCGHEPCCRCDELWLYASSRCPICK 1195 (1394)
T ss_pred cccchHHHHHHHHhcCCeeeechhHhhhHHHHHHHHhccCcchh
Confidence 35689999999998876666999999999999999999999998
No 83
>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=92.46 E-value=0.027 Score=52.23 Aligned_cols=46 Identities=20% Similarity=0.456 Sum_probs=24.4
Q ss_pred CCCCCCCCCCCCCCccccccc--c--cccchhhHHHHHhcCCCCCCCCCC
Q 024073 215 DRTICPLCSQKRANPSVVTVS--G--FVFCYACIFKYVSQYKRCPVTLMP 260 (273)
Q Consensus 215 ~~~~CpiC~~~~~np~~l~~~--G--~vfCy~Ci~~~~~~~~~CPv~~~~ 260 (273)
.++.||+|+..-.-..+...- | |.+|.-|-.+|--...+||.|+..
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 357999999986656555422 4 789999999999888999999954
No 84
>COG5236 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=92.45 E-value=0.071 Score=50.62 Aligned_cols=45 Identities=20% Similarity=0.524 Sum_probs=39.0
Q ss_pred CCCCCCCCCCCCCCcccccccccccchhhHHHH--HhcCCCCCCCCCC
Q 024073 215 DRTICPLCSQKRANPSVVTVSGFVFCYACIFKY--VSQYKRCPVTLMP 260 (273)
Q Consensus 215 ~~~~CpiC~~~~~np~~l~~~G~vfCy~Ci~~~--~~~~~~CPv~~~~ 260 (273)
+...|-||-+.++-.++++ |||-.|.-|.++- +=..+.||+|+..
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 5689999999999999998 9999999999864 4466889999853
No 85
>PRK04023 DNA polymerase II large subunit; Validated
Probab=90.81 E-value=0.21 Score=53.36 Aligned_cols=55 Identities=18% Similarity=0.300 Sum_probs=40.0
Q ss_pred CCCCCCCCCCCCCCCCCccccccccc-----ccchhhHHHHHhcCCCCCCCCCCCCcCCeeeC
Q 024073 212 LPPDRTICPLCSQKRANPSVVTVSGF-----VFCYACIFKYVSQYKRCPVTLMPATVEQIRRL 269 (273)
Q Consensus 212 ~p~~~~~CpiC~~~~~np~~l~~~G~-----vfCy~Ci~~~~~~~~~CPv~~~~~~~~~l~ri 269 (273)
++.....||-|+... .-..|+.||. .||..|-.. .....||-|+...+...-++|
T Consensus 622 VEVg~RfCpsCG~~t-~~frCP~CG~~Te~i~fCP~CG~~--~~~y~CPKCG~El~~~s~~~i 681 (1121)
T PRK04023 622 VEIGRRKCPSCGKET-FYRRCPFCGTHTEPVYRCPRCGIE--VEEDECEKCGREPTPYSKRKI 681 (1121)
T ss_pred ecccCccCCCCCCcC-CcccCCCCCCCCCcceeCccccCc--CCCCcCCCCCCCCCccceEEe
Confidence 455678999999985 4467888995 599999433 334679999988776554443
No 86
>COG5219 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=90.65 E-value=0.077 Score=56.11 Aligned_cols=46 Identities=17% Similarity=0.442 Sum_probs=36.2
Q ss_pred CCCCCCCCCCCC-----Cc-ccccccccccchhhHHHHHhcC--CCCCCCCCCC
Q 024073 216 RTICPLCSQKRA-----NP-SVVTVSGFVFCYACIFKYVSQY--KRCPVTLMPA 261 (273)
Q Consensus 216 ~~~CpiC~~~~~-----np-~~l~~~G~vfCy~Ci~~~~~~~--~~CPv~~~~~ 261 (273)
...|+||-..+. =| .-|++|-|-|--+|+++|.+.. .+||+|+...
T Consensus 1469 ~eECaICYsvL~~vdr~lPskrC~TCknKFH~~CLyKWf~Ss~~s~CPlCRsei 1522 (1525)
T COG5219 1469 HEECAICYSVLDMVDRSLPSKRCATCKNKFHTRCLYKWFASSARSNCPLCRSEI 1522 (1525)
T ss_pred cchhhHHHHHHHHHhccCCccccchhhhhhhHHHHHHHHHhcCCCCCCcccccc
Confidence 468999976543 33 3566799999999999999865 6899999544
No 87
>KOG4185 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=89.79 E-value=0.18 Score=46.45 Aligned_cols=43 Identities=23% Similarity=0.567 Sum_probs=35.2
Q ss_pred CCCCCCCCC------CCcccccccccccchhhHHHHHhcC-CCCCCCCCCC
Q 024073 218 ICPLCSQKR------ANPSVVTVSGFVFCYACIFKYVSQY-KRCPVTLMPA 261 (273)
Q Consensus 218 ~CpiC~~~~------~np~~l~~~G~vfCy~Ci~~~~~~~-~~CPv~~~~~ 261 (273)
.|-||.+.. ..|.++. |||.+|.-|+...+... ..||-|+.+.
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 688888753 4568887 99999999999888765 6799999873
No 88
>KOG4367 consensus Predicted Zn-finger protein [Function unknown]
Probab=89.75 E-value=0.16 Score=49.56 Aligned_cols=35 Identities=23% Similarity=0.593 Sum_probs=31.4
Q ss_pred CCCCCCCCCCCCCCcccccccccccchhhHHHHHhc
Q 024073 215 DRTICPLCSQKRANPSVVTVSGFVFCYACIFKYVSQ 250 (273)
Q Consensus 215 ~~~~CpiC~~~~~np~~l~~~G~vfCy~Ci~~~~~~ 250 (273)
+..+||||+.-..+|.+++ |||-.|..|+..-+-+
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 4578999999999999998 9999999999987753
No 89
>KOG1941 consensus Acetylcholine receptor-associated protein of the synapse (rapsyn) [Extracellular structures]
Probab=89.52 E-value=0.14 Score=49.37 Aligned_cols=42 Identities=19% Similarity=0.538 Sum_probs=35.7
Q ss_pred CCCCCCCCCC--CCCc--ccccccccccchhhHHHHHhcC--CCCCCCC
Q 024073 216 RTICPLCSQK--RANP--SVVTVSGFVFCYACIFKYVSQY--KRCPVTL 258 (273)
Q Consensus 216 ~~~CpiC~~~--~~np--~~l~~~G~vfCy~Ci~~~~~~~--~~CPv~~ 258 (273)
...|-.|++. ++|. -+++ |.|+|--+|++.+++++ ..||-|+
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 4679999995 4444 5887 99999999999999987 5899998
No 90
>KOG1814 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=88.98 E-value=0.24 Score=48.05 Aligned_cols=46 Identities=20% Similarity=0.456 Sum_probs=34.0
Q ss_pred CCCCCCCCCCCCCCc--ccccccccccchhhHHHHHh--------cCCCCCCCCCC
Q 024073 215 DRTICPLCSQKRANP--SVVTVSGFVFCYACIFKYVS--------QYKRCPVTLMP 260 (273)
Q Consensus 215 ~~~~CpiC~~~~~np--~~l~~~G~vfCy~Ci~~~~~--------~~~~CPv~~~~ 260 (273)
....|-||.+.-... .+..+|+||||..|..+|.. +..+||-++-+
T Consensus 183 slf~C~ICf~e~~G~~c~~~lpC~Hv~Ck~C~kdY~~~~i~eg~v~~l~Cp~~~C~ 238 (445)
T KOG1814|consen 183 SLFDCCICFEEQMGQHCFKFLPCSHVFCKSCLKDYFTIQIQEGQVSCLKCPDPKCG 238 (445)
T ss_pred hcccceeeehhhcCcceeeecccchHHHHHHHHHHHHHhhhcceeeeecCCCCCCc
Confidence 357899999875442 23344999999999999986 33589876643
No 91
>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=88.93 E-value=0.15 Score=47.84 Aligned_cols=46 Identities=22% Similarity=0.512 Sum_probs=35.6
Q ss_pred CCCCCCCCCCCCCCccccc---ccc--cccchhhHHHHHhcCCCCCCCCCC
Q 024073 215 DRTICPLCSQKRANPSVVT---VSG--FVFCYACIFKYVSQYKRCPVTLMP 260 (273)
Q Consensus 215 ~~~~CpiC~~~~~np~~l~---~~G--~vfCy~Ci~~~~~~~~~CPv~~~~ 260 (273)
..+.||+|+..-.-..+.. .-| |.+|--|-.+|=-...+||.|+..
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 4679999999764443322 134 899999999999889999999964
No 92
>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=88.42 E-value=0.21 Score=41.36 Aligned_cols=43 Identities=23% Similarity=0.488 Sum_probs=33.0
Q ss_pred CCCCCCCCCCCCC--cccccccc------cccchhhHHHHHhcCCCCCCCC
Q 024073 216 RTICPLCSQKRAN--PSVVTVSG------FVFCYACIFKYVSQYKRCPVTL 258 (273)
Q Consensus 216 ~~~CpiC~~~~~n--p~~l~~~G------~vfCy~Ci~~~~~~~~~CPv~~ 258 (273)
...|.||.+.|.+ -.|.-+|| ++||-.|+.+|-+++.+-|-=+
T Consensus 26 ~~EC~IC~~~I~~~~GvV~vt~~g~lnLEkmfc~~C~~rw~~~~~rDPfnR 76 (134)
T PF05883_consen 26 TVECQICFDRIDNNDGVVYVTDGGTLNLEKMFCADCDKRWRRERNRDPFNR 76 (134)
T ss_pred CeeehhhhhhhhcCCCEEEEecCCeehHHHHHHHHHHHHHHhhccCCCccc
Confidence 5689999999998 33322365 7999999999987777777543
No 93
>PLN02189 cellulose synthase
Probab=88.27 E-value=0.34 Score=52.04 Aligned_cols=47 Identities=21% Similarity=0.568 Sum_probs=36.4
Q ss_pred CCCCCCCCCCCCCCc------ccccccccccchhhHHHHHhc--CCCCCCCCCCCC
Q 024073 215 DRTICPLCSQKRANP------SVVTVSGFVFCYACIFKYVSQ--YKRCPVTLMPAT 262 (273)
Q Consensus 215 ~~~~CpiC~~~~~np------~~l~~~G~vfCy~Ci~~~~~~--~~~CPv~~~~~~ 262 (273)
...+|.||++.+--. ++|..||+--|.+|- +|-++ ++.||-|+.+-+
T Consensus 33 ~~~~C~iCgd~vg~~~~g~~fvaC~~C~fpvCr~Cy-eyer~eg~q~CpqCkt~Y~ 87 (1040)
T PLN02189 33 DGQVCEICGDEIGLTVDGDLFVACNECGFPVCRPCY-EYERREGTQNCPQCKTRYK 87 (1040)
T ss_pred cCccccccccccCcCCCCCEEEeeccCCCccccchh-hhhhhcCCccCcccCCchh
Confidence 356899999985422 588889999999998 56654 578999996643
No 94
>PF14446 Prok-RING_1: Prokaryotic RING finger family 1
Probab=88.20 E-value=0.52 Score=33.09 Aligned_cols=43 Identities=19% Similarity=0.309 Sum_probs=32.9
Q ss_pred CCCCCCCCCCCCC--Cc-ccccccccccchhhHHHHHhcCCCCCC--CCCCC
Q 024073 215 DRTICPLCSQKRA--NP-SVVTVSGFVFCYACIFKYVSQYKRCPV--TLMPA 261 (273)
Q Consensus 215 ~~~~CpiC~~~~~--np-~~l~~~G~vfCy~Ci~~~~~~~~~CPv--~~~~~ 261 (273)
...+|++|+++++ +. ++++.||-.+-..|-. ..+.|-. |+.+.
T Consensus 4 ~~~~C~~Cg~~~~~~dDiVvCp~CgapyHR~C~~----~~g~C~~~~c~~~~ 51 (54)
T PF14446_consen 4 EGCKCPVCGKKFKDGDDIVVCPECGAPYHRDCWE----KAGGCINYSCGTGF 51 (54)
T ss_pred cCccChhhCCcccCCCCEEECCCCCCcccHHHHh----hCCceEeccCCCCc
Confidence 3568999999994 44 6889999999999965 5677776 55544
No 95
>PHA03096 p28-like protein; Provisional
Probab=86.96 E-value=0.34 Score=45.08 Aligned_cols=44 Identities=16% Similarity=0.322 Sum_probs=33.7
Q ss_pred CCCCCCCCCCCCc-------ccccccccccchhhHHHHHhcC---CCCCCCCCC
Q 024073 217 TICPLCSQKRANP-------SVVTVSGFVFCYACIFKYVSQY---KRCPVTLMP 260 (273)
Q Consensus 217 ~~CpiC~~~~~np-------~~l~~~G~vfCy~Ci~~~~~~~---~~CPv~~~~ 260 (273)
.+|-||++.+..- .+++.|-|+||-.||..|-... ..||.|+..
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 4777799999999999999753 456666543
No 96
>PLN02436 cellulose synthase A
Probab=86.82 E-value=0.46 Score=51.18 Aligned_cols=47 Identities=17% Similarity=0.465 Sum_probs=36.5
Q ss_pred CCCCCCCCCCCCCCc------ccccccccccchhhHHHHHhc--CCCCCCCCCCCC
Q 024073 215 DRTICPLCSQKRANP------SVVTVSGFVFCYACIFKYVSQ--YKRCPVTLMPAT 262 (273)
Q Consensus 215 ~~~~CpiC~~~~~np------~~l~~~G~vfCy~Ci~~~~~~--~~~CPv~~~~~~ 262 (273)
...+|-||++.+--- ++|..||+--|.+|- +|-++ ++.||-|+.+-+
T Consensus 35 ~~~iCqICGD~Vg~t~dGe~FVACn~C~fpvCr~Cy-eyer~eg~~~Cpqckt~Y~ 89 (1094)
T PLN02436 35 SGQTCQICGDEIELTVDGEPFVACNECAFPVCRPCY-EYERREGNQACPQCKTRYK 89 (1094)
T ss_pred CCccccccccccCcCCCCCEEEeeccCCCccccchh-hhhhhcCCccCcccCCchh
Confidence 355899999985322 688889999999998 66654 478999997643
No 97
>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=86.54 E-value=0.43 Score=29.82 Aligned_cols=22 Identities=27% Similarity=0.440 Sum_probs=13.7
Q ss_pred cccccccchhhHHHHHhcCCCCCCCCCC
Q 024073 233 TVSGFVFCYACIFKYVSQYKRCPVTLMP 260 (273)
Q Consensus 233 ~~~G~vfCy~Ci~~~~~~~~~CPv~~~~ 260 (273)
.+|||++=-.- ..-+||+|+.+
T Consensus 5 ~~CGy~y~~~~------~~~~CP~Cg~~ 26 (33)
T cd00350 5 PVCGYIYDGEE------APWVCPVCGAP 26 (33)
T ss_pred CCCCCEECCCc------CCCcCcCCCCc
Confidence 34666554322 55799999864
No 98
>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=85.68 E-value=0.54 Score=36.45 Aligned_cols=36 Identities=19% Similarity=0.570 Sum_probs=30.1
Q ss_pred CCCCCCCCCCCCCcccccccccccchhhHHHHHhcCCCCCCCCCCC
Q 024073 216 RTICPLCSQKRANPSVVTVSGFVFCYACIFKYVSQYKRCPVTLMPA 261 (273)
Q Consensus 216 ~~~CpiC~~~~~np~~l~~~G~vfCy~Ci~~~~~~~~~CPv~~~~~ 261 (273)
...|-+|...+.. =|+-||-.|++ +.+.|.+||+.+
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 689999999886
No 99
>KOG1812 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=85.42 E-value=0.34 Score=46.95 Aligned_cols=42 Identities=24% Similarity=0.478 Sum_probs=33.3
Q ss_pred CCCCCCCCCCCC-----CcccccccccccchhhHHHHHhcCCCCCCCC
Q 024073 216 RTICPLCSQKRA-----NPSVVTVSGFVFCYACIFKYVSQYKRCPVTL 258 (273)
Q Consensus 216 ~~~CpiC~~~~~-----np~~l~~~G~vfCy~Ci~~~~~~~~~CPv~~ 258 (273)
-..||.|.--+. |...+. |||-|||.|--+|...++.|.-|.
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 468999998654 446787 999999999999998877665544
No 100
>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=84.92 E-value=0.098 Score=38.65 Aligned_cols=40 Identities=30% Similarity=0.558 Sum_probs=24.7
Q ss_pred CCCCCCCCCCCCcccccccccccchhhHHHHHhcCCCCCCCCCCCC
Q 024073 217 TICPLCSQKRANPSVVTVSGFVFCYACIFKYVSQYKRCPVTLMPAT 262 (273)
Q Consensus 217 ~~CpiC~~~~~np~~l~~~G~vfCy~Ci~~~~~~~~~CPv~~~~~~ 262 (273)
..||.|..++. ...|+.+|-.|-.+|. ....||-|+.++.
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 47999998752 2358999999998765 4579999998864
No 101
>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=83.83 E-value=0.99 Score=30.01 Aligned_cols=39 Identities=18% Similarity=0.432 Sum_probs=24.7
Q ss_pred CCCCCCCCCCccccc--ccccccchhhHHHHHhcCC--CCCCC
Q 024073 219 CPLCSQKRANPSVVT--VSGFVFCYACIFKYVSQYK--RCPVT 257 (273)
Q Consensus 219 CpiC~~~~~np~~l~--~~G~vfCy~Ci~~~~~~~~--~CPv~ 257 (273)
|-+|.+.++-...++ .|+--+-..|+..|++... +||.|
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 678888888887776 4888899999999998765 79987
No 102
>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=83.80 E-value=0.39 Score=32.84 Aligned_cols=43 Identities=23% Similarity=0.557 Sum_probs=26.4
Q ss_pred CCCCCCCCCCCcccccccccccchhhHHHHHhcCCCCCCCCCCCC
Q 024073 218 ICPLCSQKRANPSVVTVSGFVFCYACIFKYVSQYKRCPVTLMPAT 262 (273)
Q Consensus 218 ~CpiC~~~~~np~~l~~~G~vfCy~Ci~~~~~~~~~CPv~~~~~~ 262 (273)
.|--|=-.-++ .+..+.|--|..|+..-+....+||+|++++.
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 35555444444 34447899999999999999999999998764
No 103
>PRK03564 formate dehydrogenase accessory protein FdhE; Provisional
Probab=83.78 E-value=0.57 Score=44.10 Aligned_cols=46 Identities=22% Similarity=0.587 Sum_probs=34.8
Q ss_pred CCCCCCCCCCCCCCccc-c-cccc--cccchhhHHHHHhcCCCCCCCCCC
Q 024073 215 DRTICPLCSQKRANPSV-V-TVSG--FVFCYACIFKYVSQYKRCPVTLMP 260 (273)
Q Consensus 215 ~~~~CpiC~~~~~np~~-l-~~~G--~vfCy~Ci~~~~~~~~~CPv~~~~ 260 (273)
....||+|+..-.-..+ . ..-| |.+|--|-.+|=-...+||.|+..
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 46899999997543322 1 1234 788999999999899999999963
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=82.90 E-value=0.7 Score=42.95 Aligned_cols=34 Identities=21% Similarity=0.478 Sum_probs=28.4
Q ss_pred ccccccchhhHHHHHh-cCCCCCCCCCCCCcCCee
Q 024073 234 VSGFVFCYACIFKYVS-QYKRCPVTLMPATVEQIR 267 (273)
Q Consensus 234 ~~G~vfCy~Ci~~~~~-~~~~CPv~~~~~~~~~l~ 267 (273)
+|||-.|-.|...-.. +.+.||.|++.+-...++
T Consensus 22 ~C~H~lCEsCvd~iF~~g~~~CpeC~~iLRk~nfr 56 (300)
T KOG3800|consen 22 ECGHRLCESCVDRIFSLGPAQCPECMVILRKNNFR 56 (300)
T ss_pred cccchHHHHHHHHHHhcCCCCCCcccchhhhcccc
Confidence 5999999999998776 458999999987666554
No 105
>PRK05978 hypothetical protein; Provisional
Probab=82.88 E-value=0.81 Score=38.64 Aligned_cols=33 Identities=21% Similarity=0.437 Sum_probs=25.3
Q ss_pred CCCCCCCCCCCCCcccccccccccchhhHHHHHhcCCCCCCCCCCCCcC
Q 024073 216 RTICPLCSQKRANPSVVTVSGFVFCYACIFKYVSQYKRCPVTLMPATVE 264 (273)
Q Consensus 216 ~~~CpiC~~~~~np~~l~~~G~vfCy~Ci~~~~~~~~~CPv~~~~~~~~ 264 (273)
..+||-|++. +.| ..|++-+.+||+|+.+.+.+
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 26888899999999887643
No 106
>KOG1812 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=81.78 E-value=0.6 Score=45.21 Aligned_cols=52 Identities=27% Similarity=0.556 Sum_probs=34.5
Q ss_pred CCCCCCCCCCCCCc----ccccccccccchhhHHHHHhcC------CCCC--CCCCCCCcCCeee
Q 024073 216 RTICPLCSQKRANP----SVVTVSGFVFCYACIFKYVSQY------KRCP--VTLMPATVEQIRR 268 (273)
Q Consensus 216 ~~~CpiC~~~~~np----~~l~~~G~vfCy~Ci~~~~~~~------~~CP--v~~~~~~~~~l~r 268 (273)
...|.||......+ .+.. |||-||..|..+|++.. .+|| -|...++.++...
T Consensus 146 ~~~C~iC~~e~~~~~~~f~~~~-C~H~fC~~C~k~~iev~~~~~~~~~C~~~~C~~~l~~~~c~~ 209 (384)
T KOG1812|consen 146 KEECGICFVEDPEAEDMFSVLK-CGHRFCKDCVKQHIEVKLLSGTVIRCPHDGCESRLTLESCRK 209 (384)
T ss_pred cccCccCccccccHhhhHHHhc-ccchhhhHHhHHHhhhhhccCCCccCCCCCCCccCCHHHHhh
Confidence 45899999432222 3554 99999999999999832 4676 3445555554443
No 107
>PLN02195 cellulose synthase A
Probab=81.22 E-value=1.4 Score=47.24 Aligned_cols=46 Identities=22% Similarity=0.473 Sum_probs=36.0
Q ss_pred CCCCCCCCCCCC-----Cc-ccccccccccchhhHHHHHh--cCCCCCCCCCCCC
Q 024073 216 RTICPLCSQKRA-----NP-SVVTVSGFVFCYACIFKYVS--QYKRCPVTLMPAT 262 (273)
Q Consensus 216 ~~~CpiC~~~~~-----np-~~l~~~G~vfCy~Ci~~~~~--~~~~CPv~~~~~~ 262 (273)
..+|-||++.+- +| ++|-.||+--|.+|- +|=+ +++.||-|+.+-+
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 588889999999998 5654 4578999997765
No 108
>PLN02638 cellulose synthase A (UDP-forming), catalytic subunit
Probab=80.85 E-value=1.2 Score=48.22 Aligned_cols=46 Identities=20% Similarity=0.551 Sum_probs=35.4
Q ss_pred CCCCCCCCCCCCCCc------ccccccccccchhhHHHHHh--cCCCCCCCCCCC
Q 024073 215 DRTICPLCSQKRANP------SVVTVSGFVFCYACIFKYVS--QYKRCPVTLMPA 261 (273)
Q Consensus 215 ~~~~CpiC~~~~~np------~~l~~~G~vfCy~Ci~~~~~--~~~~CPv~~~~~ 261 (273)
+..+|-||++.+--- ++|-.||+--|.+|- +|=+ +++.||-|+.+-
T Consensus 16 ~~qiCqICGD~vg~~~~Ge~FVAC~eC~FPVCrpCY-EYEr~eG~q~CPqCktrY 69 (1079)
T PLN02638 16 GGQVCQICGDNVGKTVDGEPFVACDVCAFPVCRPCY-EYERKDGNQSCPQCKTKY 69 (1079)
T ss_pred CCceeeecccccCcCCCCCEEEEeccCCCccccchh-hhhhhcCCccCCccCCch
Confidence 355899999975332 588889999999998 5554 457899999654
No 109
>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=80.21 E-value=1.1 Score=28.25 Aligned_cols=10 Identities=30% Similarity=0.923 Sum_probs=7.7
Q ss_pred CCCCCCCCCC
Q 024073 252 KRCPVTLMPA 261 (273)
Q Consensus 252 ~~CPv~~~~~ 261 (273)
..||+|+.+.
T Consensus 19 ~~CP~Cg~~~ 28 (34)
T cd00729 19 EKCPICGAPK 28 (34)
T ss_pred CcCcCCCCch
Confidence 5899999653
No 110
>PF14569 zf-UDP: Zinc-binding RING-finger; PDB: 1WEO_A.
Probab=80.14 E-value=2 Score=32.35 Aligned_cols=48 Identities=17% Similarity=0.346 Sum_probs=20.9
Q ss_pred CCCCCCCCCCCCCCc------ccccccccccchhhHHHHHh-cCCCCCCCCCCCC
Q 024073 215 DRTICPLCSQKRANP------SVVTVSGFVFCYACIFKYVS-QYKRCPVTLMPAT 262 (273)
Q Consensus 215 ~~~~CpiC~~~~~np------~~l~~~G~vfCy~Ci~~~~~-~~~~CPv~~~~~~ 262 (273)
+..+|-||++.+--- +++..||+-.|.+|-.--.+ .++.||-|+.+.+
T Consensus 8 ~~qiCqiCGD~VGl~~~Ge~FVAC~eC~fPvCr~CyEYErkeg~q~CpqCkt~yk 62 (80)
T PF14569_consen 8 NGQICQICGDDVGLTENGEVFVACHECAFPVCRPCYEYERKEGNQVCPQCKTRYK 62 (80)
T ss_dssp SS-B-SSS--B--B-SSSSB--S-SSS-----HHHHHHHHHTS-SB-TTT--B--
T ss_pred CCcccccccCccccCCCCCEEEEEcccCCccchhHHHHHhhcCcccccccCCCcc
Confidence 456899999975322 46677999999999765554 4578999996643
No 111
>KOG2068 consensus MOT2 transcription factor [Transcription]
Probab=79.99 E-value=1.4 Score=41.70 Aligned_cols=45 Identities=24% Similarity=0.584 Sum_probs=36.5
Q ss_pred CCCCCCCCCC--CCccccc-ccccccchhhHHHHHhcCCCCCCCCCCC
Q 024073 217 TICPLCSQKR--ANPSVVT-VSGFVFCYACIFKYVSQYKRCPVTLMPA 261 (273)
Q Consensus 217 ~~CpiC~~~~--~np~~l~-~~G~vfCy~Ci~~~~~~~~~CPv~~~~~ 261 (273)
..||+|..+. ++-..++ +||+--|..|...-+..+++||.|+++.
T Consensus 250 ~s~p~~~~~~~~~d~~~lP~~~~~~~~l~~~~t~~~~~~~~~~~rk~~ 297 (327)
T KOG2068|consen 250 PSCPICYEDLDLTDSNFLPCPCGFRLCLFCHKTISDGDGRCPGCRKPY 297 (327)
T ss_pred CCCCCCCCcccccccccccccccccchhhhhhcccccCCCCCccCCcc
Confidence 5799999975 3333333 3999999999999999999999999764
No 112
>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=79.94 E-value=1.1 Score=31.03 Aligned_cols=28 Identities=18% Similarity=0.417 Sum_probs=16.3
Q ss_pred ccccccccccchhhHHHHHhcC-CCCCCCC
Q 024073 230 SVVTVSGFVFCYACIFKYVSQY-KRCPVTL 258 (273)
Q Consensus 230 ~~l~~~G~vfCy~Ci~~~~~~~-~~CPv~~ 258 (273)
-.++.|+.+||.+|=. |+-+. +.||.|.
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 4667799999999976 55444 7899884
No 113
>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=79.83 E-value=1.2 Score=35.70 Aligned_cols=28 Identities=29% Similarity=0.517 Sum_probs=22.5
Q ss_pred CCCCCCCCCCCC----CCcccccccccccchh
Q 024073 215 DRTICPLCSQKR----ANPSVVTVSGFVFCYA 242 (273)
Q Consensus 215 ~~~~CpiC~~~~----~np~~l~~~G~vfCy~ 242 (273)
.+.+||-|+..+ ++|.+|+.||.+|=-.
T Consensus 8 tKR~Cp~CG~kFYDLnk~PivCP~CG~~~~~~ 39 (108)
T PF09538_consen 8 TKRTCPSCGAKFYDLNKDPIVCPKCGTEFPPE 39 (108)
T ss_pred CcccCCCCcchhccCCCCCccCCCCCCccCcc
Confidence 367899999974 5789999999988654
No 114
>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=79.72 E-value=1.1 Score=36.75 Aligned_cols=27 Identities=30% Similarity=0.445 Sum_probs=22.2
Q ss_pred CCCCCCCCCCCC----CCcccccccccccch
Q 024073 215 DRTICPLCSQKR----ANPSVVTVSGFVFCY 241 (273)
Q Consensus 215 ~~~~CpiC~~~~----~np~~l~~~G~vfCy 241 (273)
.+..||-|+..+ ++|.+|+.||.+|=-
T Consensus 8 tKr~Cp~cg~kFYDLnk~p~vcP~cg~~~~~ 38 (129)
T TIGR02300 8 TKRICPNTGSKFYDLNRRPAVSPYTGEQFPP 38 (129)
T ss_pred ccccCCCcCccccccCCCCccCCCcCCccCc
Confidence 367899999974 688999999999744
No 115
>KOG2169 consensus Zn-finger transcription factor [Transcription]
Probab=79.37 E-value=1.3 Score=45.67 Aligned_cols=51 Identities=24% Similarity=0.449 Sum_probs=41.7
Q ss_pred CCCCCCCCCCCCCcccccccccccchhhHHHHHhcC-----CCCCCCCCCCCcCCee
Q 024073 216 RTICPLCSQKRANPSVVTVSGFVFCYACIFKYVSQY-----KRCPVTLMPATVEQIR 267 (273)
Q Consensus 216 ~~~CpiC~~~~~np~~l~~~G~vfCy~Ci~~~~~~~-----~~CPv~~~~~~~~~l~ 267 (273)
+..|||+...++-|+-.-.|.|.=|.+=.. |+..+ -+||||.+.+..++|+
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 578999999999998665699999998655 66543 3899999999888775
No 116
>KOG1940 consensus Zn-finger protein [General function prediction only]
Probab=78.05 E-value=1.4 Score=40.80 Aligned_cols=43 Identities=19% Similarity=0.498 Sum_probs=36.8
Q ss_pred CCCCCCCCCCC----CCcccccccccccchhhHHHHHhcCCCCCCCCC
Q 024073 216 RTICPLCSQKR----ANPSVVTVSGFVFCYACIFKYVSQYKRCPVTLM 259 (273)
Q Consensus 216 ~~~CpiC~~~~----~np~~l~~~G~vfCy~Ci~~~~~~~~~CPv~~~ 259 (273)
+..||||.+.+ .+|.+++ |||..=++|.-.+..++-+||+|.+
T Consensus 158 ~~ncPic~e~l~~s~~~~~~~~-CgH~~h~~cf~e~~~~~y~CP~C~~ 204 (276)
T KOG1940|consen 158 EFNCPICKEYLFLSFEDAGVLK-CGHYMHSRCFEEMICEGYTCPICSK 204 (276)
T ss_pred cCCCchhHHHhccccccCCccC-cccchHHHHHHHHhccCCCCCcccc
Confidence 44599999864 4556777 9999999999999999999999998
No 117
>PLN02915 cellulose synthase A [UDP-forming], catalytic subunit
Probab=77.52 E-value=1.7 Score=46.86 Aligned_cols=47 Identities=23% Similarity=0.530 Sum_probs=36.1
Q ss_pred CCCCCCCCCCCCCCc------ccccccccccchhhHHHHHh--cCCCCCCCCCCCC
Q 024073 215 DRTICPLCSQKRANP------SVVTVSGFVFCYACIFKYVS--QYKRCPVTLMPAT 262 (273)
Q Consensus 215 ~~~~CpiC~~~~~np------~~l~~~G~vfCy~Ci~~~~~--~~~~CPv~~~~~~ 262 (273)
+..+|-||++.+--. ++|-.||+--|.+|- +|=+ +++.||-|+.+-+
T Consensus 14 ~~~~c~iCGd~vg~~~~Ge~FVAC~eC~fpvCr~cy-eye~~~g~~~cp~c~t~y~ 68 (1044)
T PLN02915 14 DAKTCRVCGDEVGVKEDGQPFVACHVCGFPVCKPCY-EYERSEGNQCCPQCNTRYK 68 (1044)
T ss_pred CcchhhccccccCcCCCCCEEEEeccCCCccccchh-hhhhhcCCccCCccCCchh
Confidence 457899999975432 588889999999998 5554 3578999996543
No 118
>COG1592 Rubrerythrin [Energy production and conversion]
Probab=76.15 E-value=1.7 Score=37.36 Aligned_cols=13 Identities=23% Similarity=0.764 Sum_probs=8.8
Q ss_pred CCCCCCCCCCCCC
Q 024073 216 RTICPLCSQKRAN 228 (273)
Q Consensus 216 ~~~CpiC~~~~~n 228 (273)
-.+||+|+-...+
T Consensus 134 ~~vC~vCGy~~~g 146 (166)
T COG1592 134 VWVCPVCGYTHEG 146 (166)
T ss_pred EEEcCCCCCcccC
Confidence 4578888765544
No 119
>TIGR00622 ssl1 transcription factor ssl1. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=75.99 E-value=2.7 Score=33.85 Aligned_cols=43 Identities=26% Similarity=0.481 Sum_probs=33.0
Q ss_pred CCCCCCCCCCCCCcc-------------cccccccccchhhHHHHHhcCCCCCCCC
Q 024073 216 RTICPLCSQKRANPS-------------VVTVSGFVFCYACIFKYVSQYKRCPVTL 258 (273)
Q Consensus 216 ~~~CpiC~~~~~np~-------------~l~~~G~vfCy~Ci~~~~~~~~~CPv~~ 258 (273)
+..|--|+.++..+. .++.|+.+||.+|=.-.-+.=+.||.|.
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 346888888776542 3778999999999875556558899996
No 120
>PF12773 DZR: Double zinc ribbon
Probab=75.65 E-value=1.3 Score=29.84 Aligned_cols=15 Identities=33% Similarity=0.860 Sum_probs=11.1
Q ss_pred CCCCCCCCCCCCCCC
Q 024073 213 PPDRTICPLCSQKRA 227 (273)
Q Consensus 213 p~~~~~CpiC~~~~~ 227 (273)
+.+...||-|+.++.
T Consensus 9 ~~~~~fC~~CG~~l~ 23 (50)
T PF12773_consen 9 PDDAKFCPHCGTPLP 23 (50)
T ss_pred CccccCChhhcCChh
Confidence 446677888888777
No 121
>PRK14714 DNA polymerase II large subunit; Provisional
Probab=75.60 E-value=1.6 Score=47.94 Aligned_cols=51 Identities=24% Similarity=0.356 Sum_probs=35.9
Q ss_pred CCCCCCCCCCCCCcccccccccc-----cchhhHHHHHhc---CCCCCCCCCCCCcCCee
Q 024073 216 RTICPLCSQKRANPSVVTVSGFV-----FCYACIFKYVSQ---YKRCPVTLMPATVEQIR 267 (273)
Q Consensus 216 ~~~CpiC~~~~~np~~l~~~G~v-----fCy~Ci~~~~~~---~~~CPv~~~~~~~~~l~ 267 (273)
...||-|+..... ..|+.||.. .|-.|-...-.. ...||-|+.++....-+
T Consensus 667 ~rkCPkCG~~t~~-~fCP~CGs~te~vy~CPsCGaev~~des~a~~CP~CGtplv~~~~~ 725 (1337)
T PRK14714 667 RRRCPSCGTETYE-NRCPDCGTHTEPVYVCPDCGAEVPPDESGRVECPRCDVELTPYQRR 725 (1337)
T ss_pred EEECCCCCCcccc-ccCcccCCcCCCceeCccCCCccCCCccccccCCCCCCcccccceE
Confidence 3789999997543 488889966 499998764433 34899999887644433
No 122
>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=75.56 E-value=1.6 Score=30.11 Aligned_cols=40 Identities=28% Similarity=0.469 Sum_probs=24.0
Q ss_pred CCCCCCCCCCCCCCcccccccccccchhhHHHHHhc--CCCCCCCCCCCC
Q 024073 215 DRTICPLCSQKRANPSVVTVSGFVFCYACIFKYVSQ--YKRCPVTLMPAT 262 (273)
Q Consensus 215 ~~~~CpiC~~~~~np~~l~~~G~vfCy~Ci~~~~~~--~~~CPv~~~~~~ 262 (273)
+.+.||.|++.+...... .-|....-.+ ...||+|....+
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 357899999954433322 2344444432 357999987544
No 123
>PHA02862 5L protein; Provisional
Probab=75.50 E-value=2.3 Score=35.83 Aligned_cols=47 Identities=19% Similarity=0.305 Sum_probs=33.7
Q ss_pred CCCCCCCCCC---CCCcccccccccccchhhHHHHHhcC--CCCCCCCCCCC
Q 024073 216 RTICPLCSQK---RANPSVVTVSGFVFCYACIFKYVSQY--KRCPVTLMPAT 262 (273)
Q Consensus 216 ~~~CpiC~~~---~~np~~l~~~G~vfCy~Ci~~~~~~~--~~CPv~~~~~~ 262 (273)
+.+|=||.+. ..+|+.+.-+--.--..|+.+|++.+ ..|+.|+.+..
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 3579999885 34566664444455678999999865 68999997653
No 124
>KOG4739 consensus Uncharacterized protein involved in synaptonemal complex formation [Cell cycle control, cell division, chromosome partitioning; General function prediction only]
Probab=75.35 E-value=1.3 Score=40.01 Aligned_cols=33 Identities=24% Similarity=0.508 Sum_probs=23.1
Q ss_pred CCCCCCCCCC-CCcccccccccccchhhHHHHHh
Q 024073 217 TICPLCSQKR-ANPSVVTVSGFVFCYACIFKYVS 249 (273)
Q Consensus 217 ~~CpiC~~~~-~np~~l~~~G~vfCy~Ci~~~~~ 249 (273)
..|-.|.... .+|--|+-|+||||-+|.-.-..
T Consensus 4 VhCn~C~~~~~~~~f~LTaC~HvfC~~C~k~~~~ 37 (233)
T KOG4739|consen 4 VHCNKCFRFPSQDPFFLTACRHVFCEPCLKASSP 37 (233)
T ss_pred EEeccccccCCCCceeeeechhhhhhhhcccCCc
Confidence 3577777632 55655556999999999876554
No 125
>KOG4445 consensus Uncharacterized conserved protein, contains RWD domain [Function unknown]
Probab=75.28 E-value=0.75 Score=43.07 Aligned_cols=47 Identities=21% Similarity=0.481 Sum_probs=36.5
Q ss_pred CCCCCCCCCCCCCc---ccccccccccchhhHHHHHh-----------------------cCCCCCCCCCCCCc
Q 024073 216 RTICPLCSQKRANP---SVVTVSGFVFCYACIFKYVS-----------------------QYKRCPVTLMPATV 263 (273)
Q Consensus 216 ~~~CpiC~~~~~np---~~l~~~G~vfCy~Ci~~~~~-----------------------~~~~CPv~~~~~~~ 263 (273)
.+.|.||+--+.+- +++. |-|-|-.-|.-+||. ...-||||+.++..
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 46899999877665 4554 999999999999995 12369999988753
No 126
>COG5627 MMS21 DNA repair protein MMS21 [DNA replication, recombination, and repair]
Probab=75.26 E-value=1.6 Score=39.63 Aligned_cols=48 Identities=17% Similarity=0.185 Sum_probs=39.2
Q ss_pred CCCCCCCCCCCCCcccccccccccchhhHHHHHhcC--CCCCC--CCCCCCc
Q 024073 216 RTICPLCSQKRANPSVVTVSGFVFCYACIFKYVSQY--KRCPV--TLMPATV 263 (273)
Q Consensus 216 ~~~CpiC~~~~~np~~l~~~G~vfCy~Ci~~~~~~~--~~CPv--~~~~~~~ 263 (273)
++.|||..++..-|.+-+.|.|+|-.+-|.++++.. .-||+ |......
T Consensus 189 ~nrCpitl~p~~~pils~kcnh~~e~D~I~~~lq~~~trvcp~~~Csq~~~~ 240 (275)
T COG5627 189 SNRCPITLNPDFYPILSSKCNHKPEMDLINKKLQVECTRVCPRLICSQKEVV 240 (275)
T ss_pred cccCCcccCcchhHHHHhhhcccccHHHHHHHhcCCceeecchhhcchheec
Confidence 689999999999998877899999999999999854 56884 4444333
No 127
>KOG4718 consensus Non-SMC (structural maintenance of chromosomes) element 1 protein (NSE1) [Chromatin structure and dynamics]
Probab=74.98 E-value=1.1 Score=39.99 Aligned_cols=44 Identities=18% Similarity=0.298 Sum_probs=37.8
Q ss_pred CCCCCCCCCCCCCcccccccccccchhhHHHHHhcCCCCCCCCC
Q 024073 216 RTICPLCSQKRANPSVVTVSGFVFCYACIFKYVSQYKRCPVTLM 259 (273)
Q Consensus 216 ~~~CpiC~~~~~np~~l~~~G~vfCy~Ci~~~~~~~~~CPv~~~ 259 (273)
-..|-+|.+-+..-.-|..||.-|-.+|+..|+.+...||-||-
T Consensus 181 lk~Cn~Ch~LvIqg~rCg~c~i~~h~~c~qty~q~~~~cphc~d 224 (235)
T KOG4718|consen 181 LKNCNLCHCLVIQGIRCGSCNIQYHRGCIQTYLQRRDICPHCGD 224 (235)
T ss_pred HHHHhHhHHHhheeeccCcccchhhhHHHHHHhcccCcCCchhc
Confidence 46899999976666666679999999999999999999999974
No 128
>KOG1815 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=74.77 E-value=5.6 Score=39.12 Aligned_cols=55 Identities=22% Similarity=0.504 Sum_probs=37.8
Q ss_pred CCCCCCCCCCCCCCcccccccccccchhhHHHHHhcC--------CCCCCCCCCC--CcCCeeeC
Q 024073 215 DRTICPLCSQKRANPSVVTVSGFVFCYACIFKYVSQY--------KRCPVTLMPA--TVEQIRRL 269 (273)
Q Consensus 215 ~~~~CpiC~~~~~np~~l~~~G~vfCy~Ci~~~~~~~--------~~CPv~~~~~--~~~~l~ri 269 (273)
....|.||.+...+..+...|||.||-.|...|+... -+||-.+-++ +.+.+.++
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 3568999999888743333499999999999999732 2577665444 33444443
No 129
>KOG2114 consensus Vacuolar assembly/sorting protein PEP5/VPS11 [Intracellular trafficking, secretion, and vesicular transport]
Probab=74.76 E-value=1.5 Score=46.16 Aligned_cols=40 Identities=23% Similarity=0.497 Sum_probs=36.4
Q ss_pred CCCCCCCCCCCCcccccccccccchhhHHHHHhcCCCCCCCCC
Q 024073 217 TICPLCSQKRANPSVVTVSGFVFCYACIFKYVSQYKRCPVTLM 259 (273)
Q Consensus 217 ~~CpiC~~~~~np~~l~~~G~vfCy~Ci~~~~~~~~~CPv~~~ 259 (273)
.+|..|...+.-|+|--.|||.|--.|.- ++..+||-|.-
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 58999999999999987799999999998 66789999985
No 130
>KOG3268 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=74.27 E-value=2.9 Score=36.49 Aligned_cols=48 Identities=17% Similarity=0.485 Sum_probs=36.1
Q ss_pred CCCCCCCCC-----CCCCcc--cccccccccchhhHHHHHhc-----------CCCCCCCCCCCCcC
Q 024073 216 RTICPLCSQ-----KRANPS--VVTVSGFVFCYACIFKYVSQ-----------YKRCPVTLMPATVE 264 (273)
Q Consensus 216 ~~~CpiC~~-----~~~np~--~l~~~G~vfCy~Ci~~~~~~-----------~~~CPv~~~~~~~~ 264 (273)
-+.|-||-- .+.|-+ -++ ||.-|---|+.+|+++ .|.||-|..|++++
T Consensus 165 ~~~cgicyayqldGTipDqtCdN~q-CgkpFHqiCL~dWLRgilTsRQSFdiiFGeCPYCS~PialK 230 (234)
T KOG3268|consen 165 LGACGICYAYQLDGTIPDQTCDNIQ-CGKPFHQICLTDWLRGILTSRQSFDIIFGECPYCSDPIALK 230 (234)
T ss_pred hhcccceeeeecCCccccccccccc-cCCcHHHHHHHHHHHHHhhccceeeeeeccCCCCCCcceee
Confidence 467888854 344443 234 9999999999999983 48999999998654
No 131
>KOG0825 consensus PHD Zn-finger protein [General function prediction only]
Probab=73.99 E-value=2.2 Score=44.80 Aligned_cols=45 Identities=13% Similarity=0.188 Sum_probs=33.5
Q ss_pred CCCCCCCCCCCCCCCc------ccccccccccchhhHHHHHhc------CCCCCCCC
Q 024073 214 PDRTICPLCSQKRANP------SVVTVSGFVFCYACIFKYVSQ------YKRCPVTL 258 (273)
Q Consensus 214 ~~~~~CpiC~~~~~np------~~l~~~G~vfCy~Ci~~~~~~------~~~CPv~~ 258 (273)
.+...|++|-....+| +.+..|||-||+-||..|..+ +-.|+.|.
T Consensus 94 a~s~Ss~~C~~E~S~~~ds~~i~P~~~~~~~~CP~Ci~s~~DqL~~~~k~c~H~FC~ 150 (1134)
T KOG0825|consen 94 AESDTSPVCEKEHSPDVDSSNICPVQTHVENQCPNCLKSCNDQLEESEKHTAHYFCE 150 (1134)
T ss_pred ccccccchhheecCCcccccCcCchhhhhhhhhhHHHHHHHHHhhccccccccccHH
Confidence 3567888888887774 344569999999999999974 34566665
No 132
>PHA02825 LAP/PHD finger-like protein; Provisional
Probab=73.88 E-value=3.3 Score=35.37 Aligned_cols=49 Identities=14% Similarity=0.326 Sum_probs=32.9
Q ss_pred CCCCCCCCCCC---CCCcccccccccccchhhHHHHHhcC--CCCCCCCCCCCc
Q 024073 215 DRTICPLCSQK---RANPSVVTVSGFVFCYACIFKYVSQY--KRCPVTLMPATV 263 (273)
Q Consensus 215 ~~~~CpiC~~~---~~np~~l~~~G~vfCy~Ci~~~~~~~--~~CPv~~~~~~~ 263 (273)
....|=||.+. ..+|+.+.-+=-.--..|+.+|+... .+|++|+.+...
T Consensus 7 ~~~~CRIC~~~~~~~~~PC~CkGs~k~VH~sCL~rWi~~s~~~~CeiC~~~Y~i 60 (162)
T PHA02825 7 MDKCCWICKDEYDVVTNYCNCKNENKIVHKECLEEWINTSKNKSCKICNGPYNI 60 (162)
T ss_pred CCCeeEecCCCCCCccCCcccCCCchHHHHHHHHHHHhcCCCCcccccCCeEEE
Confidence 35689999885 35555543111122478999999865 689999977543
No 133
>KOG0824 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=73.62 E-value=1.2 Score=41.65 Aligned_cols=46 Identities=26% Similarity=0.484 Sum_probs=41.2
Q ss_pred CCCCCCCCCCCCCCcccccccccccchhhHHHHHhcCCCCCCCCCC
Q 024073 215 DRTICPLCSQKRANPSVVTVSGFVFCYACIFKYVSQYKRCPVTLMP 260 (273)
Q Consensus 215 ~~~~CpiC~~~~~np~~l~~~G~vfCy~Ci~~~~~~~~~CPv~~~~ 260 (273)
++++|-||.+.++-|+...-|+|-|||-|--.|-+...-||.|...
T Consensus 104 ~~~~~~~~~g~l~vpt~~qg~w~qf~~~~p~~~~~~~~~~~d~~~~ 149 (324)
T KOG0824|consen 104 DHDICYICYGKLTVPTRIQGCWHQFCYVCPKSNFAMGNDCPDCRGK 149 (324)
T ss_pred CccceeeeeeeEEecccccCceeeeeecCCchhhhhhhccchhhcC
Confidence 5789999999999999988799999999999999988888887643
No 134
>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=73.52 E-value=1.8 Score=30.91 Aligned_cols=16 Identities=31% Similarity=0.534 Sum_probs=12.0
Q ss_pred hcCCCCCCCCCCCCcC
Q 024073 249 SQYKRCPVTLMPATVE 264 (273)
Q Consensus 249 ~~~~~CPv~~~~~~~~ 264 (273)
+.|+.||+||.++..+
T Consensus 1 e~HkHC~~CG~~Ip~~ 16 (59)
T PF09889_consen 1 EPHKHCPVCGKPIPPD 16 (59)
T ss_pred CCCCcCCcCCCcCCcc
Confidence 3578888888887654
No 135
>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=72.64 E-value=0.87 Score=31.48 Aligned_cols=14 Identities=29% Similarity=0.484 Sum_probs=7.4
Q ss_pred CCCCCCCCCCCcCC
Q 024073 252 KRCPVTLMPATVEQ 265 (273)
Q Consensus 252 ~~CPv~~~~~~~~~ 265 (273)
++||||+.+++.++
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 136
>KOG3970 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=71.63 E-value=3.2 Score=37.47 Aligned_cols=44 Identities=20% Similarity=0.410 Sum_probs=34.2
Q ss_pred CCCCCCCCCCCc-ccccccccccchhhHHHHHhc--------CCCCCCCCCCC
Q 024073 218 ICPLCSQKRANP-SVVTVSGFVFCYACIFKYVSQ--------YKRCPVTLMPA 261 (273)
Q Consensus 218 ~CpiC~~~~~np-~~l~~~G~vfCy~Ci~~~~~~--------~~~CPv~~~~~ 261 (273)
.|.+|+.++..- ++--+|-|+|-|.|.-.|-.+ -.+||-|..++
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 599999987655 333359999999999999863 24899999764
No 137
>PLN02400 cellulose synthase
Probab=71.38 E-value=2.4 Score=45.96 Aligned_cols=47 Identities=19% Similarity=0.482 Sum_probs=35.5
Q ss_pred CCCCCCCCCCCCCCc------ccccccccccchhhHHHHHh--cCCCCCCCCCCCC
Q 024073 215 DRTICPLCSQKRANP------SVVTVSGFVFCYACIFKYVS--QYKRCPVTLMPAT 262 (273)
Q Consensus 215 ~~~~CpiC~~~~~np------~~l~~~G~vfCy~Ci~~~~~--~~~~CPv~~~~~~ 262 (273)
...+|-||++.+--- ++|-.||+--|.+|- +|=+ +++.||-|+.+-+
T Consensus 35 ~gqiCqICGD~VG~t~dGe~FVAC~eCaFPVCRpCY-EYERkeGnq~CPQCkTrYk 89 (1085)
T PLN02400 35 NGQICQICGDDVGVTETGDVFVACNECAFPVCRPCY-EYERKDGTQCCPQCKTRYR 89 (1085)
T ss_pred CCceeeecccccCcCCCCCEEEEEccCCCccccchh-heecccCCccCcccCCccc
Confidence 356899999975332 588889999999998 5554 4578999996543
No 138
>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=71.11 E-value=5.7 Score=30.67 Aligned_cols=38 Identities=24% Similarity=0.460 Sum_probs=33.0
Q ss_pred CCCCCCCCCCCCCcccccccccccchhhHHHHHhcCCCCCCCCCCCCc
Q 024073 216 RTICPLCSQKRANPSVVTVSGFVFCYACIFKYVSQYKRCPVTLMPATV 263 (273)
Q Consensus 216 ~~~CpiC~~~~~np~~l~~~G~vfCy~Ci~~~~~~~~~CPv~~~~~~~ 263 (273)
...|+-|++++.=--.+| |..|+-..|||.-|+.+...
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 358999999998877888 78899999999999998764
No 139
>COG5183 SSM4 Protein involved in mRNA turnover and stability [RNA processing and modification]
Probab=71.07 E-value=3.1 Score=43.82 Aligned_cols=53 Identities=17% Similarity=0.394 Sum_probs=35.9
Q ss_pred CCCCCCCCCCCC------CCCcccccccccccchhhHHHHHhcC--CCCCCCCCCCCcCCe
Q 024073 214 PDRTICPLCSQK------RANPSVVTVSGFVFCYACIFKYVSQY--KRCPVTLMPATVEQI 266 (273)
Q Consensus 214 ~~~~~CpiC~~~------~~np~~l~~~G~vfCy~Ci~~~~~~~--~~CPv~~~~~~~~~l 266 (273)
.|+..|-||+.. +-+|+-|+-+=.-.-..|+.+|++-. .+|-+|+.+.+.+++
T Consensus 10 ~d~~~CRICr~e~~~d~pLfhPCKC~GSIkYiH~eCL~eW~~~s~~~kCdiChy~~~Fk~I 70 (1175)
T COG5183 10 EDKRSCRICRTEDIRDDPLFHPCKCSGSIKYIHRECLMEWMECSGTKKCDICHYEYKFKDI 70 (1175)
T ss_pred ccchhceeecCCCCCCCcCcccccccchhHHHHHHHHHHHHhcCCCcceeeecceeeeeee
Confidence 467899999863 33444443222234578999999854 689999988765543
No 140
>KOG2042 consensus Ubiquitin fusion degradation protein-2 [Posttranslational modification, protein turnover, chaperones]
Probab=70.93 E-value=3.6 Score=44.09 Aligned_cols=53 Identities=21% Similarity=0.190 Sum_probs=50.0
Q ss_pred CCCCCCCCCCCCCCcccccccccccchhhHHHHHhcCCCCCCCCCCCCcCCee
Q 024073 215 DRTICPLCSQKRANPSVVTVSGFVFCYACIFKYVSQYKRCPVTLMPATVEQIR 267 (273)
Q Consensus 215 ~~~~CpiC~~~~~np~~l~~~G~vfCy~Ci~~~~~~~~~CPv~~~~~~~~~l~ 267 (273)
|...=|+-...+.||++++.+|++.|+.=|.+++-...+-|.|+.|++.++++
T Consensus 869 def~DPlm~Tlm~dPV~LP~Srv~vDRsti~rhlLs~~tdPFNR~pLt~d~v~ 921 (943)
T KOG2042|consen 869 DEFLDPLMSTLMSDPVVLPSSRVTVDRSTIERHLLSDCTDPFNREPLTEDMVS 921 (943)
T ss_pred hhhhCccccccCCCCccCCcccccccHHHHHHHHhcCCCCccccccCchhhcC
Confidence 67888999999999999999999999999999999999999999999988775
No 141
>KOG2034 consensus Vacuolar sorting protein PEP3/VPS18 [Intracellular trafficking, secretion, and vesicular transport]
Probab=70.49 E-value=2.2 Score=45.22 Aligned_cols=34 Identities=24% Similarity=0.448 Sum_probs=27.9
Q ss_pred CCCCCCCCCCCCC-cccccccccccchhhHHHHHh
Q 024073 216 RTICPLCSQKRAN-PSVVTVSGFVFCYACIFKYVS 249 (273)
Q Consensus 216 ~~~CpiC~~~~~n-p~~l~~~G~vfCy~Ci~~~~~ 249 (273)
...|-+|..++-. |-++-.|||.|-..|+.+.+.
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 5789999998554 555555999999999999984
No 142
>COG0068 HypF Hydrogenase maturation factor [Posttranslational modification, protein turnover, chaperones]
Probab=69.97 E-value=1.7 Score=45.01 Aligned_cols=50 Identities=28% Similarity=0.460 Sum_probs=38.7
Q ss_pred CCCCCCCCCCCCCCCCCc---------cccccccc--------------------ccchhhHHHHHh--------cCCCC
Q 024073 212 LPPDRTICPLCSQKRANP---------SVVTVSGF--------------------VFCYACIFKYVS--------QYKRC 254 (273)
Q Consensus 212 ~p~~~~~CpiC~~~~~np---------~~l~~~G~--------------------vfCy~Ci~~~~~--------~~~~C 254 (273)
.|+|-.+|+-|++.+.|| +.|+.||- ..|-.|-.+|-. +--.|
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 345778899999999888 46777884 459999998875 34689
Q ss_pred CCCCCCC
Q 024073 255 PVTLMPA 261 (273)
Q Consensus 255 Pv~~~~~ 261 (273)
|.||-.+
T Consensus 177 p~CGP~~ 183 (750)
T COG0068 177 PKCGPHL 183 (750)
T ss_pred cccCCCe
Confidence 9999644
No 143
>smart00647 IBR In Between Ring fingers. the domains occurs between pairs og RING fingers
Probab=69.23 E-value=1.2 Score=30.95 Aligned_cols=18 Identities=28% Similarity=0.853 Sum_probs=14.2
Q ss_pred ccccccccccchhhHHHH
Q 024073 230 SVVTVSGFVFCYACIFKY 247 (273)
Q Consensus 230 ~~l~~~G~vfCy~Ci~~~ 247 (273)
+.++.||+.||+.|-..|
T Consensus 41 v~C~~C~~~fC~~C~~~~ 58 (64)
T smart00647 41 VTCPKCGFSFCFRCKVPW 58 (64)
T ss_pred eECCCCCCeECCCCCCcC
Confidence 455459999999997766
No 144
>COG3357 Predicted transcriptional regulator containing an HTH domain fused to a Zn-ribbon [Transcription]
Probab=68.86 E-value=1.8 Score=33.55 Aligned_cols=28 Identities=25% Similarity=0.446 Sum_probs=17.8
Q ss_pred CcccccccccccchhhHHHHHhcCCCCCCCCC
Q 024073 228 NPSVVTVSGFVFCYACIFKYVSQYKRCPVTLM 259 (273)
Q Consensus 228 np~~l~~~G~vfCy~Ci~~~~~~~~~CPv~~~ 259 (273)
.|+.|..|||+|=- .-++.-.+||.|+.
T Consensus 57 ~Pa~CkkCGfef~~----~~ik~pSRCP~CKS 84 (97)
T COG3357 57 RPARCKKCGFEFRD----DKIKKPSRCPKCKS 84 (97)
T ss_pred cChhhcccCccccc----cccCCcccCCcchh
Confidence 35556667777754 23455678888873
No 145
>PF15616 TerY-C: TerY-C metal binding domain
Probab=68.68 E-value=2.2 Score=35.33 Aligned_cols=40 Identities=25% Similarity=0.452 Sum_probs=29.3
Q ss_pred CCCCCCCCCCCCcccccccccccchhhHHHHHhcCCCCCCCCCCCCc
Q 024073 217 TICPLCSQKRANPSVVTVSGFVFCYACIFKYVSQYKRCPVTLMPATV 263 (273)
Q Consensus 217 ~~CpiC~~~~~np~~l~~~G~vfCy~Ci~~~~~~~~~CPv~~~~~~~ 263 (273)
--||-|+...-= +++. ||.+||+.= ++.-.||-|++....
T Consensus 78 PgCP~CGn~~~f-a~C~-CGkl~Ci~g-----~~~~~CPwCg~~g~~ 117 (131)
T PF15616_consen 78 PGCPHCGNQYAF-AVCG-CGKLFCIDG-----EGEVTCPWCGNEGSF 117 (131)
T ss_pred CCCCCCcChhcE-EEec-CCCEEEeCC-----CCCEECCCCCCeeee
Confidence 369999986532 4666 999999852 234689999987654
No 146
>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=68.58 E-value=2.1 Score=28.18 Aligned_cols=17 Identities=24% Similarity=0.452 Sum_probs=10.9
Q ss_pred cCCCCCCCCCCCCcCCeeeCc
Q 024073 250 QYKRCPVTLMPATVEQIRRLF 270 (273)
Q Consensus 250 ~~~~CPv~~~~~~~~~l~ri~ 270 (273)
....||.|+. .+++|++
T Consensus 25 ~~~~CP~Cg~----~~~~r~~ 41 (42)
T PF09723_consen 25 DPVPCPECGS----TEVRRVI 41 (42)
T ss_pred CCCcCCCCCC----CceEEec
Confidence 4568999985 3455554
No 147
>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=68.54 E-value=2 Score=39.12 Aligned_cols=44 Identities=23% Similarity=0.510 Sum_probs=33.8
Q ss_pred CCCCCCCCCC-CCCcc----cccccccccchhhHHHHHhc-CCCCC--CCCC
Q 024073 216 RTICPLCSQK-RANPS----VVTVSGFVFCYACIFKYVSQ-YKRCP--VTLM 259 (273)
Q Consensus 216 ~~~CpiC~~~-~~np~----~l~~~G~vfCy~Ci~~~~~~-~~~CP--v~~~ 259 (273)
..+||+|... --||- +-+.|-|-+|-.|..+-+.. ...|| .|++
T Consensus 10 d~~CPvCksDrYLnPdik~linPECyHrmCESCvdRIFs~GpAqCP~~gC~k 61 (314)
T COG5220 10 DRRCPVCKSDRYLNPDIKILINPECYHRMCESCVDRIFSRGPAQCPYKGCGK 61 (314)
T ss_pred cccCCccccccccCCCeEEEECHHHHHHHHHHHHHHHhcCCCCCCCCccHHH
Confidence 4589999875 45662 33459999999999998864 57899 7774
No 148
>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=68.35 E-value=1.6 Score=46.01 Aligned_cols=45 Identities=22% Similarity=0.420 Sum_probs=0.0
Q ss_pred CCCCCCCCCCCCCCcccccccccc-----cchhhHHHHHhcCCCCCCCCCCCC
Q 024073 215 DRTICPLCSQKRANPSVVTVSGFV-----FCYACIFKYVSQYKRCPVTLMPAT 262 (273)
Q Consensus 215 ~~~~CpiC~~~~~np~~l~~~G~v-----fCy~Ci~~~~~~~~~CPv~~~~~~ 262 (273)
....||-|+..-- -..|+.||-. +|..|-.+.-.. .||-|+...+
T Consensus 654 ~~r~Cp~Cg~~t~-~~~Cp~CG~~T~~~~~Cp~C~~~~~~~--~C~~C~~~~~ 703 (900)
T PF03833_consen 654 GRRRCPKCGKETF-YNRCPECGSHTEPVYVCPDCGIEVEED--ECPKCGRETT 703 (900)
T ss_dssp -----------------------------------------------------
T ss_pred ecccCcccCCcch-hhcCcccCCccccceeccccccccCcc--ccccccccCc
Confidence 3578999998633 3456668866 899999876544 9999997754
No 149
>KOG0309 consensus Conserved WD40 repeat-containing protein [Function unknown]
Probab=68.23 E-value=3.1 Score=43.55 Aligned_cols=46 Identities=17% Similarity=0.338 Sum_probs=36.2
Q ss_pred CCCCCCCCCCCCCcc-cccccccccchhhHHHHHhcCCCCC-CCCCCC
Q 024073 216 RTICPLCSQKRANPS-VVTVSGFVFCYACIFKYVSQYKRCP-VTLMPA 261 (273)
Q Consensus 216 ~~~CpiC~~~~~np~-~l~~~G~vfCy~Ci~~~~~~~~~CP-v~~~~~ 261 (273)
...|.+|.-.++--+ +|-.||||.--.|...|.+....|| .||-.+
T Consensus 1028 ~~~C~~C~l~V~gss~~Cg~C~Hv~H~sc~~eWf~~gd~CpsGCGC~C 1075 (1081)
T KOG0309|consen 1028 TFQCAICHLAVRGSSNFCGTCGHVGHTSCMMEWFRTGDVCPSGCGCHC 1075 (1081)
T ss_pred eeeeeeEeeEeeccchhhccccccccHHHHHHHHhcCCcCCCCCCcCc
Confidence 355888887776664 6667999999999999999988999 455433
No 150
>KOG0883 consensus Cyclophilin type, U box-containing peptidyl-prolyl cis-trans isomerase [Posttranslational modification, protein turnover, chaperones]
Probab=67.83 E-value=3.1 Score=40.45 Aligned_cols=57 Identities=19% Similarity=0.169 Sum_probs=45.3
Q ss_pred CCCCCCCCCCCCCCcc---cccccccccchhhHHHHHh--cCCCCCCCCCCCCcCCeeeCcc
Q 024073 215 DRTICPLCSQKRANPS---VVTVSGFVFCYACIFKYVS--QYKRCPVTLMPATVEQIRRLFH 271 (273)
Q Consensus 215 ~~~~CpiC~~~~~np~---~l~~~G~vfCy~Ci~~~~~--~~~~CPv~~~~~~~~~l~ri~~ 271 (273)
..+.||+-.++.++-+ ++.++|.||||.-|.+-=- +|-+-=++..|.+.+|||-|=.
T Consensus 100 geyhcPvlfk~FT~~sHIvAv~TTGNvy~~eai~~LNiK~knwkdLltdepFtR~DiItiQd 161 (518)
T KOG0883|consen 100 GEYHCPVLFKVFTRFSHIVAVRTTGNVYSWEAIEELNIKTKNWKDLLTDEPFTRADIITIQD 161 (518)
T ss_pred CcccCceeeeeecccceEEEEEecCceeeHHHHHHhCcchhhHHHhhccCCcchhceeeecC
Confidence 5789999999988873 4556999999998876432 3457788899999999987754
No 151
>PLN02248 cellulose synthase-like protein
Probab=67.28 E-value=3.8 Score=44.61 Aligned_cols=36 Identities=25% Similarity=0.449 Sum_probs=30.8
Q ss_pred ccccccccccchhhHHHHHhcCCCCCCCCCCCCcCCe
Q 024073 230 SVVTVSGFVFCYACIFKYVSQYKRCPVTLMPATVEQI 266 (273)
Q Consensus 230 ~~l~~~G~vfCy~Ci~~~~~~~~~CPv~~~~~~~~~l 266 (273)
.-|. ||+--|.+|-.+.++..+.||.|+.+.+..|+
T Consensus 146 ~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 181 (1135)
T PLN02248 146 LPCE-CGFKICRDCYIDAVKSGGICPGCKEPYKVTDL 181 (1135)
T ss_pred Cccc-ccchhHHhHhhhhhhcCCCCCCCccccccccc
Confidence 4566 99999999999999999999999988765443
No 152
>PF12906 RINGv: RING-variant domain; PDB: 2D8S_A 1VYX_A.
Probab=66.93 E-value=3.2 Score=28.01 Aligned_cols=32 Identities=13% Similarity=0.337 Sum_probs=18.3
Q ss_pred CCCcccccccccccchhhHHHHHhc--CCCCCCC
Q 024073 226 RANPSVVTVSGFVFCYACIFKYVSQ--YKRCPVT 257 (273)
Q Consensus 226 ~~np~~l~~~G~vfCy~Ci~~~~~~--~~~CPv~ 257 (273)
+.+|.-+.-+-...-..|+.+|+.. +.+|++|
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 4455544322234457899999984 4689987
No 153
>COG1645 Uncharacterized Zn-finger containing protein [General function prediction only]
Probab=65.37 E-value=2.6 Score=34.86 Aligned_cols=25 Identities=32% Similarity=0.742 Sum_probs=17.9
Q ss_pred CCCCCCCCCCCCCcccccccccccchhhHH
Q 024073 216 RTICPLCSQKRANPSVVTVSGFVFCYACIF 245 (273)
Q Consensus 216 ~~~CpiC~~~~~np~~l~~~G~vfCy~Ci~ 245 (273)
...||.|+-++-. . .|-|||--|-+
T Consensus 28 ~~hCp~Cg~PLF~----K-dG~v~CPvC~~ 52 (131)
T COG1645 28 AKHCPKCGTPLFR----K-DGEVFCPVCGY 52 (131)
T ss_pred HhhCcccCCccee----e-CCeEECCCCCc
Confidence 3579999998754 3 88888755543
No 154
>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=64.88 E-value=8.1 Score=30.61 Aligned_cols=44 Identities=20% Similarity=0.409 Sum_probs=29.4
Q ss_pred CCCCCCCCCCCCCc-ccc------ccc---ccccchhhHHHHHhc---------CCCCCCCCC
Q 024073 216 RTICPLCSQKRANP-SVV------TVS---GFVFCYACIFKYVSQ---------YKRCPVTLM 259 (273)
Q Consensus 216 ~~~CpiC~~~~~np-~~l------~~~---G~vfCy~Ci~~~~~~---------~~~CPv~~~ 259 (273)
...|-.|.+.-.+. +.+ +.| .-.||+.|+.+...+ +-.||.|+-
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 45677777755544 333 345 778999998877643 357998863
No 155
>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=63.64 E-value=2.8 Score=30.02 Aligned_cols=34 Identities=21% Similarity=0.453 Sum_probs=17.9
Q ss_pred CCCCCCCCCCCCCC---cccccccccccchhhHHHHH
Q 024073 215 DRTICPLCSQKRAN---PSVVTVSGFVFCYACIFKYV 248 (273)
Q Consensus 215 ~~~~CpiC~~~~~n---p~~l~~~G~vfCy~Ci~~~~ 248 (273)
+...|.+|.+.+.- ---+..||++||..|....+
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 23566799999999986544
No 156
>KOG4362 consensus Transcriptional regulator BRCA1 [Replication, recombination and repair; Transcription]
Probab=62.86 E-value=1.9 Score=44.58 Aligned_cols=45 Identities=22% Similarity=0.496 Sum_probs=36.5
Q ss_pred CCCCCCCCCCCCCcccccccccccchhhHHHHHh---cCCCCCCCCCCC
Q 024073 216 RTICPLCSQKRANPSVVTVSGFVFCYACIFKYVS---QYKRCPVTLMPA 261 (273)
Q Consensus 216 ~~~CpiC~~~~~np~~l~~~G~vfCy~Ci~~~~~---~~~~CPv~~~~~ 261 (273)
...||||...+..|+.+. |-|.||--|+..-+. ....||+|+.-.
T Consensus 21 ~lEc~ic~~~~~~p~~~k-c~~~~l~~~~n~~f~~~~~~~~~~lc~~~~ 68 (684)
T KOG4362|consen 21 ILECPICLEHVKEPSLLK-CDHIFLKFCLNKLFESKKGPKQCALCKSDI 68 (684)
T ss_pred hccCCceeEEeeccchhh-hhHHHHhhhhhceeeccCccccchhhhhhh
Confidence 457999999999997776 999999999876554 357899998443
No 157
>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 PF14205 Cys_rich_KTR: Cysteine-rich KTR
Probab=61.83 E-value=3.7 Score=28.85 Aligned_cols=26 Identities=27% Similarity=0.797 Sum_probs=16.1
Q ss_pred CCCCCCCCC----CCCcccccccccccchhh
Q 024073 217 TICPLCSQK----RANPSVVTVSGFVFCYAC 243 (273)
Q Consensus 217 ~~CpiC~~~----~~np~~l~~~G~vfCy~C 243 (273)
..||+|+.. +...|++. -=-+||-.|
T Consensus 5 i~CP~CgnKTR~kir~DT~Lk-NfPlyCpKC 34 (55)
T PF14205_consen 5 ILCPICGNKTRLKIREDTVLK-NFPLYCPKC 34 (55)
T ss_pred EECCCCCCccceeeecCceec-cccccCCCC
Confidence 369999954 56667776 444444443
No 159
>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=61.05 E-value=6.4 Score=26.84 Aligned_cols=34 Identities=18% Similarity=0.371 Sum_probs=24.6
Q ss_pred CCCCCCCCCCCCc---ccccccccccchhhHHHHHhc
Q 024073 217 TICPLCSQKRANP---SVVTVSGFVFCYACIFKYVSQ 250 (273)
Q Consensus 217 ~~CpiC~~~~~np---~~l~~~G~vfCy~Ci~~~~~~ 250 (273)
..|.+|.+.+.-- .-+..||++||..|....+..
T Consensus 3 ~~C~~C~~~F~~~~rk~~Cr~Cg~~~C~~C~~~~~~~ 39 (57)
T cd00065 3 SSCMGCGKPFTLTRRRHHCRNCGRIFCSKCSSNRIPL 39 (57)
T ss_pred CcCcccCccccCCccccccCcCcCCcChHHcCCeeec
Confidence 4688998864332 345569999999999877653
No 160
>KOG0269 consensus WD40 repeat-containing protein [Function unknown]
Probab=60.94 E-value=6.8 Score=40.98 Aligned_cols=48 Identities=10% Similarity=0.095 Sum_probs=40.4
Q ss_pred CCCCCCCCCCCCCcc-cccccccccchhhHHHHHhcCCCCCC--CCCCCCc
Q 024073 216 RTICPLCSQKRANPS-VVTVSGFVFCYACIFKYVSQYKRCPV--TLMPATV 263 (273)
Q Consensus 216 ~~~CpiC~~~~~np~-~l~~~G~vfCy~Ci~~~~~~~~~CPv--~~~~~~~ 263 (273)
...|.+|.-+++.-. -+++|||..--.|+.+|..++..||. |+.+..-
T Consensus 779 ~~~CtVC~~vi~G~~~~c~~C~H~gH~sh~~sw~~~~s~ca~~~C~~~c~~ 829 (839)
T KOG0269|consen 779 SAKCTVCDLVIRGVDVWCQVCGHGGHDSHLKSWFFKASPCAKSICPHLCHY 829 (839)
T ss_pred hcCceeecceeeeeEeecccccccccHHHHHHHHhcCCCCccccCCccccc
Confidence 468999999988774 56789999999999999999999986 8776543
No 161
>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=60.34 E-value=5.2 Score=28.41 Aligned_cols=33 Identities=21% Similarity=0.431 Sum_probs=22.2
Q ss_pred CCCCCCCCCCcccccccccccchh----hHHHHHhcC
Q 024073 219 CPLCSQKRANPSVVTVSGFVFCYA----CIFKYVSQY 251 (273)
Q Consensus 219 CpiC~~~~~np~~l~~~G~vfCy~----Ci~~~~~~~ 251 (273)
|-.|+....+.-++-+||+++|.+ .+..+.++.
T Consensus 1 C~~C~~~~~~lw~CL~Cg~~~C~~~~~~Ha~~H~~~~ 37 (63)
T PF02148_consen 1 CSVCGSTNSNLWLCLTCGYVGCGRYSNGHALKHYKET 37 (63)
T ss_dssp -SSSHTCSSSEEEETTTS-EEETTTSTSHHHHHHHHH
T ss_pred CCCCCCcCCceEEeCCCCcccccCCcCcHHHHhhccc
Confidence 566776544555565699999997 888877753
No 162
>PF13240 zinc_ribbon_2: zinc-ribbon domain
Probab=60.13 E-value=1.7 Score=25.02 Aligned_cols=11 Identities=27% Similarity=0.851 Sum_probs=6.9
Q ss_pred CCCCCCCCCCc
Q 024073 219 CPLCSQKRANP 229 (273)
Q Consensus 219 CpiC~~~~~np 229 (273)
||-|+..+.+-
T Consensus 2 Cp~CG~~~~~~ 12 (23)
T PF13240_consen 2 CPNCGAEIEDD 12 (23)
T ss_pred CcccCCCCCCc
Confidence 66677666544
No 163
>PRK00420 hypothetical protein; Validated
Probab=59.30 E-value=5.1 Score=32.29 Aligned_cols=22 Identities=27% Similarity=0.575 Sum_probs=13.3
Q ss_pred CCCCCCCCCCCCcccccccccccchh
Q 024073 217 TICPLCSQKRANPSVVTVSGFVFCYA 242 (273)
Q Consensus 217 ~~CpiC~~~~~np~~l~~~G~vfCy~ 242 (273)
..||.|+.++.-- . .|.+||-.
T Consensus 24 ~~CP~Cg~pLf~l---k-~g~~~Cp~ 45 (112)
T PRK00420 24 KHCPVCGLPLFEL---K-DGEVVCPV 45 (112)
T ss_pred CCCCCCCCcceec---C-CCceECCC
Confidence 5799999776432 2 55555433
No 164
>COG3813 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=58.97 E-value=6.7 Score=29.26 Aligned_cols=29 Identities=21% Similarity=0.347 Sum_probs=22.3
Q ss_pred CcccccccccccchhhHHHHHhcCCCCCCCCC
Q 024073 228 NPSVVTVSGFVFCYACIFKYVSQYKRCPVTLM 259 (273)
Q Consensus 228 np~~l~~~G~vfCy~Ci~~~~~~~~~CPv~~~ 259 (273)
++.+++ =-+.||-.|+..-+ ++.||-||-
T Consensus 21 dA~ICt-fEcTFCadCae~~l--~g~CPnCGG 49 (84)
T COG3813 21 DARICT-FECTFCADCAENRL--HGLCPNCGG 49 (84)
T ss_pred ceeEEE-EeeehhHhHHHHhh--cCcCCCCCc
Confidence 334554 77899999998765 689999983
No 165
>KOG1356 consensus Putative transcription factor 5qNCA, contains JmjC domain [Transcription]
Probab=58.22 E-value=3.6 Score=43.38 Aligned_cols=44 Identities=23% Similarity=0.548 Sum_probs=34.8
Q ss_pred CCCCCCCCCCCCC-cccccccccccchhhHHHHH----hc--CCCCCCCCC
Q 024073 216 RTICPLCSQKRAN-PSVVTVSGFVFCYACIFKYV----SQ--YKRCPVTLM 259 (273)
Q Consensus 216 ~~~CpiC~~~~~n-p~~l~~~G~vfCy~Ci~~~~----~~--~~~CPv~~~ 259 (273)
..+|-.|...+.| -=+|+.||+.+|.+|+..|- ++ -.+|+.|..
T Consensus 229 ~~mC~~C~~tlfn~hw~C~~C~~~~Cl~C~r~~~p~~~~~e~a~k~~~~~~ 279 (889)
T KOG1356|consen 229 REMCDRCETTLFNIHWRCPRCGFGVCLDCYRKWYPRLSKEEVAEKCEFSWL 279 (889)
T ss_pred chhhhhhcccccceeEEccccCCeeeecchhhccccchHhHhhhhhhHHHH
Confidence 5689999999988 56899999999999999993 11 256775543
No 166
>PF09986 DUF2225: Uncharacterized protein conserved in bacteria (DUF2225); InterPro: IPR018708 This conserved bacterial family has no known function.
Probab=58.21 E-value=5.9 Score=35.21 Aligned_cols=53 Identities=26% Similarity=0.447 Sum_probs=33.1
Q ss_pred CCCCCCCCCCCCCCcccccccccc------cchhhHHHHHh----cCCCCCCCCCCCCcCCeeeC
Q 024073 215 DRTICPLCSQKRANPSVVTVSGFV------FCYACIFKYVS----QYKRCPVTLMPATVEQIRRL 269 (273)
Q Consensus 215 ~~~~CpiC~~~~~np~~l~~~G~v------fCy~Ci~~~~~----~~~~CPv~~~~~~~~~l~ri 269 (273)
....||+|++..+...|.+..+.+ ||.. +.-+. .-..||.||.....++.-+|
T Consensus 4 k~~~CPvC~~~F~~~~vrs~~~r~~~~d~D~~~~--Y~~vnP~~Y~V~vCP~CgyA~~~~~F~~l 66 (214)
T PF09986_consen 4 KKITCPVCGKEFKTKKVRSGKIRVIRRDSDFCPR--YKGVNPLFYEVWVCPHCGYAAFEEDFEKL 66 (214)
T ss_pred CceECCCCCCeeeeeEEEcCCceEeeecCCCccc--cCCCCCeeeeEEECCCCCCcccccccccC
Confidence 467899999999988776533333 3321 01111 23589999988776655443
No 167
>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=57.95 E-value=5.6 Score=31.14 Aligned_cols=43 Identities=23% Similarity=0.576 Sum_probs=15.9
Q ss_pred CCCCCCCCCC--CCc--ccccccccccchhhHHHHHh----cCCCCCCCCCCC
Q 024073 217 TICPLCSQKR--ANP--SVVTVSGFVFCYACIFKYVS----QYKRCPVTLMPA 261 (273)
Q Consensus 217 ~~CpiC~~~~--~np--~~l~~~G~vfCy~Ci~~~~~----~~~~CPv~~~~~ 261 (273)
..|++|.+.+ .|+ +.++ .||+| -+|...++. +.+.|++|+...
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 5899999976 454 4565 89998 458777774 237899998653
No 168
>PHA00626 hypothetical protein
Probab=57.67 E-value=8 Score=27.43 Aligned_cols=7 Identities=43% Similarity=1.298 Sum_probs=5.5
Q ss_pred CCCCCCC
Q 024073 218 ICPLCSQ 224 (273)
Q Consensus 218 ~CpiC~~ 224 (273)
.||-|+.
T Consensus 2 ~CP~CGS 8 (59)
T PHA00626 2 SCPKCGS 8 (59)
T ss_pred CCCCCCC
Confidence 5888887
No 169
>KOG1952 consensus Transcription factor NF-X1, contains NFX-type Zn2+-binding and R3H domains [Transcription]
Probab=57.01 E-value=5 Score=42.46 Aligned_cols=45 Identities=22% Similarity=0.458 Sum_probs=36.2
Q ss_pred CCCCCCCCCCCCCCCcc---cccccccccchhhHHHHHhc-------CCCCCCCC
Q 024073 214 PDRTICPLCSQKRANPS---VVTVSGFVFCYACIFKYVSQ-------YKRCPVTL 258 (273)
Q Consensus 214 ~~~~~CpiC~~~~~np~---~l~~~G~vfCy~Ci~~~~~~-------~~~CPv~~ 258 (273)
.+.+.|-||.+.|+--+ .+..|-|||-+.||.+|.+. .-+||-|.
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 35789999999876543 55669999999999999963 23899998
No 170
>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=56.45 E-value=6.9 Score=26.95 Aligned_cols=13 Identities=23% Similarity=0.261 Sum_probs=9.0
Q ss_pred HhcCCCCCCCCCC
Q 024073 248 VSQYKRCPVTLMP 260 (273)
Q Consensus 248 ~~~~~~CPv~~~~ 260 (273)
|..+=+||+|+.+
T Consensus 31 Lp~~w~CP~C~a~ 43 (50)
T cd00730 31 LPDDWVCPVCGAG 43 (50)
T ss_pred CCCCCCCCCCCCc
Confidence 4455689999853
No 171
>KOG4218 consensus Nuclear hormone receptor betaFTZ-F1 [Transcription]
Probab=56.26 E-value=7.2 Score=37.40 Aligned_cols=11 Identities=36% Similarity=1.108 Sum_probs=9.1
Q ss_pred CCCCCCCCCCC
Q 024073 216 RTICPLCSQKR 226 (273)
Q Consensus 216 ~~~CpiC~~~~ 226 (273)
...||+|++.+
T Consensus 15 ~ElCPVCGDkV 25 (475)
T KOG4218|consen 15 GELCPVCGDKV 25 (475)
T ss_pred ccccccccCcc
Confidence 56899999875
No 172
>PF04641 Rtf2: Rtf2 RING-finger
Probab=56.01 E-value=16 Score=33.32 Aligned_cols=37 Identities=24% Similarity=0.379 Sum_probs=33.0
Q ss_pred CCCCCCCCCCCCCcccccccccccchhhHHHHHhcCC
Q 024073 216 RTICPLCSQKRANPSVVTVSGFVFCYACIFKYVSQYK 252 (273)
Q Consensus 216 ~~~CpiC~~~~~np~~l~~~G~vfCy~Ci~~~~~~~~ 252 (273)
-..|.|-++++..|.|+-.-|++|-..-|+.||...+
T Consensus 34 w~~CaLS~~pL~~PiV~d~~G~LynKeaile~Ll~~~ 70 (260)
T PF04641_consen 34 WTHCALSQQPLEDPIVSDRLGRLYNKEAILEFLLDKK 70 (260)
T ss_pred cCcccCcCCccCCCeeeCCCCeeEcHHHHHHHHHhcC
Confidence 4689999999999987656999999999999998764
No 173
>KOG3161 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=55.34 E-value=3.4 Score=42.49 Aligned_cols=39 Identities=23% Similarity=0.539 Sum_probs=27.8
Q ss_pred CCCCCCCCCCCCC----cccccccccccchhhHHHHHhcCCCCCCCC
Q 024073 216 RTICPLCSQKRAN----PSVVTVSGFVFCYACIFKYVSQYKRCPVTL 258 (273)
Q Consensus 216 ~~~CpiC~~~~~n----p~~l~~~G~vfCy~Ci~~~~~~~~~CPv~~ 258 (273)
-..|+||.....+ |.-+. |||+-|..|+..- .+..|| |.
T Consensus 11 ~l~c~ic~n~f~~~~~~Pvsl~-cghtic~~c~~~l--yn~scp-~~ 53 (861)
T KOG3161|consen 11 LLLCDICLNLFVVQRLEPVSLQ-CGHTICGHCVQLL--YNASCP-TK 53 (861)
T ss_pred HhhchHHHHHHHHHhcCccccc-ccchHHHHHHHhH--hhccCC-CC
Confidence 3579999776554 44554 9999999999754 345788 44
No 174
>KOG2041 consensus WD40 repeat protein [General function prediction only]
Probab=55.28 E-value=9.5 Score=40.04 Aligned_cols=52 Identities=29% Similarity=0.602 Sum_probs=31.9
Q ss_pred CCCCCCCCCCCCCCCCCCCCCcccccccc-------cccchhhHHHHH----hcCCCCCCCCCCCC
Q 024073 208 EGIPLPPDRTICPLCSQKRANPSVVTVSG-------FVFCYACIFKYV----SQYKRCPVTLMPAT 262 (273)
Q Consensus 208 ~~~~~p~~~~~CpiC~~~~~np~~l~~~G-------~vfCy~Ci~~~~----~~~~~CPv~~~~~~ 262 (273)
.|.++++....||-|...+ |+.+. +| +-.|-+|-+... ..+..||.|..+..
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 3455666777888887654 43333 33 234666655544 35689999986643
No 175
>COG5109 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=54.43 E-value=8.4 Score=36.50 Aligned_cols=54 Identities=26% Similarity=0.422 Sum_probs=40.5
Q ss_pred CCCCCCCCCCC--CCCc-ccccccccccchhhHHHHHhcCC----CCCCCCCCCCcCCeeeCc
Q 024073 215 DRTICPLCSQK--RANP-SVVTVSGFVFCYACIFKYVSQYK----RCPVTLMPATVEQIRRLF 270 (273)
Q Consensus 215 ~~~~CpiC~~~--~~np-~~l~~~G~vfCy~Ci~~~~~~~~----~CPv~~~~~~~~~l~ri~ 270 (273)
.-++||+-.+. -.|| .++. ||||---.-+. -+.++| +||-|-.....++++|++
T Consensus 335 s~FiCPVlKe~~t~ENpP~ml~-CgHVIskeal~-~LS~nG~~~FKCPYCP~~~~~~~~~rvr 395 (396)
T COG5109 335 SLFICPVLKELCTDENPPVMLE-CGHVISKEALS-VLSQNGVLSFKCPYCPEMSKYENILRVR 395 (396)
T ss_pred ceeeccccHhhhcccCCCeeee-ccceeeHHHHH-HHhhcCcEEeeCCCCCcchhhhhhhccc
Confidence 35899997664 4455 5666 99999887665 455554 899999888888888886
No 176
>PRK07218 replication factor A; Provisional
Probab=53.81 E-value=9 Score=37.72 Aligned_cols=12 Identities=25% Similarity=0.659 Sum_probs=9.7
Q ss_pred CCCCCCCCCCCC
Q 024073 217 TICPLCSQKRAN 228 (273)
Q Consensus 217 ~~CpiC~~~~~n 228 (273)
..||.|.+.+++
T Consensus 298 ~rCP~C~r~v~~ 309 (423)
T PRK07218 298 ERCPECGRVIQK 309 (423)
T ss_pred ecCcCccccccC
Confidence 679999998844
No 177
>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=53.57 E-value=17 Score=25.81 Aligned_cols=41 Identities=20% Similarity=0.378 Sum_probs=28.6
Q ss_pred CCCCCCCCCCCcc----cccccccccchhhHHHHHhcCCCCCCCCCCC
Q 024073 218 ICPLCSQKRANPS----VVTVSGFVFCYACIFKYVSQYKRCPVTLMPA 261 (273)
Q Consensus 218 ~CpiC~~~~~np~----~l~~~G~vfCy~Ci~~~~~~~~~CPv~~~~~ 261 (273)
.|--|.+.+-..+ +++ =--.||-+|....+ ++.||-||=.+
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 4777777654332 333 34479999999888 67999998443
No 178
>KOG1428 consensus Inhibitor of type V adenylyl cyclases/Neuronal presynaptic protein Highwire/PAM/RPM-1 [Signal transduction mechanisms]
Probab=52.84 E-value=3.8 Score=46.03 Aligned_cols=47 Identities=13% Similarity=0.439 Sum_probs=36.3
Q ss_pred CCCCCCCCCCCCCc--ccccccccccchhhHHHHHhc----------CCCCCCCCCCCC
Q 024073 216 RTICPLCSQKRANP--SVVTVSGFVFCYACIFKYVSQ----------YKRCPVTLMPAT 262 (273)
Q Consensus 216 ~~~CpiC~~~~~np--~~l~~~G~vfCy~Ci~~~~~~----------~~~CPv~~~~~~ 262 (273)
..+|-||....-.+ ++---|||+|-..|..+.+++ ...||+|..+..
T Consensus 3486 DDmCmICFTE~L~AAP~IqL~C~HiFHlqC~R~vLE~RW~GPRItF~FisCPiC~n~In 3544 (3738)
T KOG1428|consen 3486 DDMCMICFTEALSAAPAIQLDCSHIFHLQCCRRVLENRWLGPRITFGFISCPICKNKIN 3544 (3738)
T ss_pred CceEEEEehhhhCCCcceecCCccchhHHHHHHHHHhcccCCeeEEeeeecccccchhh
Confidence 67899998864433 332239999999999999884 358999998875
No 179
>PRK14559 putative protein serine/threonine phosphatase; Provisional
Probab=52.24 E-value=6.1 Score=40.92 Aligned_cols=42 Identities=14% Similarity=0.256 Sum_probs=23.5
Q ss_pred CCCCCCCCCCCCCCCCCcccccccccccchhhHHHHHhcCCCCCCCCCCCC
Q 024073 212 LPPDRTICPLCSQKRANPSVVTVSGFVFCYACIFKYVSQYKRCPVTLMPAT 262 (273)
Q Consensus 212 ~p~~~~~CpiC~~~~~np~~l~~~G~vfCy~Ci~~~~~~~~~CPv~~~~~~ 262 (273)
.|.+...|+-|+.++.. ..|+.||+. --.+.+.||-||.++.
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 34455567777666643 234445544 3344567888886653
No 180
>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=51.85 E-value=11 Score=25.56 Aligned_cols=32 Identities=19% Similarity=0.441 Sum_probs=25.7
Q ss_pred CCCCCCCCCCCCCCcccccccccccchhhHHH
Q 024073 215 DRTICPLCSQKRANPSVVTVSGFVFCYACIFK 246 (273)
Q Consensus 215 ~~~~CpiC~~~~~np~~l~~~G~vfCy~Ci~~ 246 (273)
+-..|-.|.+.+.+......-|.+||..|-.+
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 46789999999988865555899999998654
No 181
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=51.57 E-value=3.2 Score=24.43 Aligned_cols=9 Identities=33% Similarity=1.088 Sum_probs=5.8
Q ss_pred CCCCCCCCC
Q 024073 217 TICPLCSQK 225 (273)
Q Consensus 217 ~~CpiC~~~ 225 (273)
..||-|+..
T Consensus 3 ~~Cp~Cg~~ 11 (26)
T PF13248_consen 3 MFCPNCGAE 11 (26)
T ss_pred CCCcccCCc
Confidence 457777764
No 182
>KOG2113 consensus Predicted RNA binding protein, contains KH domain [General function prediction only]
Probab=51.52 E-value=11 Score=35.61 Aligned_cols=50 Identities=2% Similarity=-0.242 Sum_probs=38.0
Q ss_pred CCCCCCCCCCCCCccccccccc-ccchhhHHHHHhcCCCCCCCCCCCCcCCeeeCc
Q 024073 216 RTICPLCSQKRANPSVVTVSGF-VFCYACIFKYVSQYKRCPVTLMPATVEQIRRLF 270 (273)
Q Consensus 216 ~~~CpiC~~~~~np~~l~~~G~-vfCy~Ci~~~~~~~~~CPv~~~~~~~~~l~ri~ 270 (273)
+.+|-.|+.-+..-.... ||| .||..|+- +.-...||+|+ -...++++|.
T Consensus 343 ~~~~~~~~~~~~st~~~~-~~~n~~~~~~a~--~s~~~~~~~c~--~~~~~~~~i~ 393 (394)
T KOG2113|consen 343 SLKGTSAGFGLLSTIWSG-GNMNLSPGSLAS--ASASPTSSTCD--HNDHTLVPIN 393 (394)
T ss_pred hcccccccCceeeeEeec-CCcccChhhhhh--cccCCcccccc--ccceeeeecC
Confidence 678999999876655544 887 69999998 66678999998 3445666664
No 183
>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=51.48 E-value=5.3 Score=41.82 Aligned_cols=51 Identities=24% Similarity=0.477 Sum_probs=36.6
Q ss_pred CCCCCCCCCCCCCCCCCcc---------cccccc--------------------cccchhhHHHHHhc--------CCCC
Q 024073 212 LPPDRTICPLCSQKRANPS---------VVTVSG--------------------FVFCYACIFKYVSQ--------YKRC 254 (273)
Q Consensus 212 ~p~~~~~CpiC~~~~~np~---------~l~~~G--------------------~vfCy~Ci~~~~~~--------~~~C 254 (273)
+|+|..+|+-|++.+.||. -|+.|| ...|-.|..+|-.. -..|
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 4557778888888877772 444566 45799999999652 2589
Q ss_pred CCCCCCCC
Q 024073 255 PVTLMPAT 262 (273)
Q Consensus 255 Pv~~~~~~ 262 (273)
|.||-++.
T Consensus 144 ~~Cgp~l~ 151 (711)
T TIGR00143 144 PRCGPQLN 151 (711)
T ss_pred CCCCcEEE
Confidence 99996653
No 184
>PTZ00303 phosphatidylinositol kinase; Provisional
Probab=51.39 E-value=10 Score=40.22 Aligned_cols=32 Identities=25% Similarity=0.548 Sum_probs=25.0
Q ss_pred CCCCCCCCCCCC--------cccccccccccchhhHHHHH
Q 024073 217 TICPLCSQKRAN--------PSVVTVSGFVFCYACIFKYV 248 (273)
Q Consensus 217 ~~CpiC~~~~~n--------p~~l~~~G~vfCy~Ci~~~~ 248 (273)
..|..|.+.... .-=|..||.|||-.|-.+..
T Consensus 461 dtC~~C~kkFfSlsK~L~~RKHHCRkCGrVFC~~CSSnRs 500 (1374)
T PTZ00303 461 DSCPSCGRAFISLSRPLGTRAHHCRSCGIRLCVFCITKRA 500 (1374)
T ss_pred CcccCcCCcccccccccccccccccCCccccCccccCCcc
Confidence 579999998842 22366799999999987665
No 185
>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=51.09 E-value=7.8 Score=25.35 Aligned_cols=8 Identities=50% Similarity=1.219 Sum_probs=6.4
Q ss_pred CCCCCCCC
Q 024073 218 ICPLCSQK 225 (273)
Q Consensus 218 ~CpiC~~~ 225 (273)
+||.|+..
T Consensus 2 ~Cp~Cg~~ 9 (43)
T PF08271_consen 2 KCPNCGSK 9 (43)
T ss_dssp SBTTTSSS
T ss_pred CCcCCcCC
Confidence 68888885
No 186
>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=50.99 E-value=8.4 Score=26.99 Aligned_cols=22 Identities=23% Similarity=0.620 Sum_probs=17.8
Q ss_pred CCCCCCCCCCCCCccccccccc
Q 024073 216 RTICPLCSQKRANPSVVTVSGF 237 (273)
Q Consensus 216 ~~~CpiC~~~~~np~~l~~~G~ 237 (273)
-..||.|++....-.|++.||+
T Consensus 26 l~~C~~cG~~~~~H~vc~~cG~ 47 (55)
T TIGR01031 26 LVVCPNCGEFKLPHRVCPSCGY 47 (55)
T ss_pred ceECCCCCCcccCeeECCccCe
Confidence 4579999998887788877885
No 187
>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=50.88 E-value=6.8 Score=26.97 Aligned_cols=31 Identities=23% Similarity=0.540 Sum_probs=17.6
Q ss_pred CCCCC--CCCCCCCc-------ccccccccccchhhHHHH
Q 024073 217 TICPL--CSQKRANP-------SVVTVSGFVFCYACIFKY 247 (273)
Q Consensus 217 ~~Cpi--C~~~~~np-------~~l~~~G~vfCy~Ci~~~ 247 (273)
..||- |...+.-. +.++.||+.||+.|-..|
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 46766 77653322 456669999999997655
No 188
>PRK06386 replication factor A; Reviewed
Probab=49.58 E-value=11 Score=36.41 Aligned_cols=12 Identities=25% Similarity=0.714 Sum_probs=10.3
Q ss_pred CCCCCCCCCCCC
Q 024073 217 TICPLCSQKRAN 228 (273)
Q Consensus 217 ~~CpiC~~~~~n 228 (273)
..||.|.+.+++
T Consensus 237 ~rCP~C~R~l~~ 248 (358)
T PRK06386 237 TKCSVCNKIIED 248 (358)
T ss_pred ecCcCCCeEccC
Confidence 689999998875
No 189
>KOG0006 consensus E3 ubiquitin-protein ligase (Parkin protein) [Posttranslational modification, protein turnover, chaperones]
Probab=49.56 E-value=10 Score=36.02 Aligned_cols=33 Identities=30% Similarity=0.736 Sum_probs=21.1
Q ss_pred CCCCCC--CCCC-CCCc----ccccc-cccccchhhHHHHH
Q 024073 216 RTICPL--CSQK-RANP----SVVTV-SGFVFCYACIFKYV 248 (273)
Q Consensus 216 ~~~Cpi--C~~~-~~np----~~l~~-~G~vfCy~Ci~~~~ 248 (273)
...||- |+.. +-.| +.++- ||++||..|...|-
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 345643 6653 3333 33433 99999999998665
No 190
>PRK12286 rpmF 50S ribosomal protein L32; Reviewed
Probab=49.54 E-value=9.9 Score=26.87 Aligned_cols=23 Identities=22% Similarity=0.550 Sum_probs=18.0
Q ss_pred CCCCCCCCCCCCCCccccccccc
Q 024073 215 DRTICPLCSQKRANPSVVTVSGF 237 (273)
Q Consensus 215 ~~~~CpiC~~~~~np~~l~~~G~ 237 (273)
.-..||-|++....-.+++.||+
T Consensus 26 ~l~~C~~CG~~~~~H~vC~~CG~ 48 (57)
T PRK12286 26 GLVECPNCGEPKLPHRVCPSCGY 48 (57)
T ss_pred cceECCCCCCccCCeEECCCCCc
Confidence 34579999998888778877885
No 191
>smart00154 ZnF_AN1 AN1-like Zinc finger. Zinc finger at the C-terminus of An1, a ubiquitin-like protein in Xenopus laevis.
Probab=48.95 E-value=12 Score=24.32 Aligned_cols=24 Identities=25% Similarity=0.494 Sum_probs=18.7
Q ss_pred CCCCCCCCCC-cccccccccccchh
Q 024073 219 CPLCSQKRAN-PSVVTVSGFVFCYA 242 (273)
Q Consensus 219 CpiC~~~~~n-p~~l~~~G~vfCy~ 242 (273)
|-+|.+...- |-.+..||.+||..
T Consensus 1 C~~C~~~~~l~~f~C~~C~~~FC~~ 25 (39)
T smart00154 1 CHFCRKKVGLTGFKCRHCGNLFCGE 25 (39)
T ss_pred CcccCCcccccCeECCccCCccccc
Confidence 6678887666 87887799999863
No 192
>KOG1609 consensus Protein involved in mRNA turnover and stability [RNA processing and modification]
Probab=47.79 E-value=15 Score=33.58 Aligned_cols=50 Identities=20% Similarity=0.325 Sum_probs=38.0
Q ss_pred CCCCCCCCCCCC--------CCCCcccccccccccchhhHHHHHh--cCCCCCCCCCCCC
Q 024073 213 PPDRTICPLCSQ--------KRANPSVVTVSGFVFCYACIFKYVS--QYKRCPVTLMPAT 262 (273)
Q Consensus 213 p~~~~~CpiC~~--------~~~np~~l~~~G~vfCy~Ci~~~~~--~~~~CPv~~~~~~ 262 (273)
|.+...|-||.. .+..|+.|..+....-..|+.+|+. +...|.+|.....
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 4567777765666668999999998 5678999997543
No 193
>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=47.24 E-value=12 Score=26.22 Aligned_cols=23 Identities=22% Similarity=0.589 Sum_probs=17.3
Q ss_pred CCCCCCCCCCCCCCccccccccc
Q 024073 215 DRTICPLCSQKRANPSVVTVSGF 237 (273)
Q Consensus 215 ~~~~CpiC~~~~~np~~l~~~G~ 237 (273)
.-..||.|++...--.+++.|||
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 34579999987766677777885
No 194
>COG4068 Uncharacterized protein containing a Zn-ribbon [Function unknown]
Probab=47.23 E-value=10 Score=27.10 Aligned_cols=17 Identities=12% Similarity=0.176 Sum_probs=10.9
Q ss_pred hcCCCCCCCCCCCCcCC
Q 024073 249 SQYKRCPVTLMPATVEQ 265 (273)
Q Consensus 249 ~~~~~CPv~~~~~~~~~ 265 (273)
..|.-|+||+++...++
T Consensus 6 ~PH~HC~VCg~aIp~de 22 (64)
T COG4068 6 VPHRHCVVCGKAIPPDE 22 (64)
T ss_pred CCCccccccCCcCCCcc
Confidence 35667777777665443
No 195
>PRK08270 anaerobic ribonucleoside triphosphate reductase; Provisional
Probab=47.02 E-value=11 Score=39.12 Aligned_cols=19 Identities=21% Similarity=0.275 Sum_probs=13.2
Q ss_pred hcCCCCCCCCCCCCcCCeeeC
Q 024073 249 SQYKRCPVTLMPATVEQIRRL 269 (273)
Q Consensus 249 ~~~~~CPv~~~~~~~~~l~ri 269 (273)
..+-.||.||.+ .+-..||
T Consensus 637 g~~~~CP~CG~~--~~v~sRi 655 (656)
T PRK08270 637 GEHEFCPKCGEE--TEVYSRV 655 (656)
T ss_pred CCCCCCcCCcCc--cceEEee
Confidence 345799999966 5555554
No 196
>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=46.33 E-value=6.8 Score=23.17 Aligned_cols=9 Identities=33% Similarity=0.866 Sum_probs=4.7
Q ss_pred CCCCCCCCC
Q 024073 253 RCPVTLMPA 261 (273)
Q Consensus 253 ~CPv~~~~~ 261 (273)
.||||++.+
T Consensus 3 ~CPiC~~~v 11 (26)
T smart00734 3 QCPVCFREV 11 (26)
T ss_pred cCCCCcCcc
Confidence 355555544
No 197
>KOG1100 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=45.82 E-value=9.5 Score=33.89 Aligned_cols=42 Identities=21% Similarity=0.532 Sum_probs=31.4
Q ss_pred CCCCCCCCCCCCcccccccccccchhhHHHHHhcCCCCCCCCCCCC
Q 024073 217 TICPLCSQKRANPSVVTVSGFVFCYACIFKYVSQYKRCPVTLMPAT 262 (273)
Q Consensus 217 ~~CpiC~~~~~np~~l~~~G~vfCy~Ci~~~~~~~~~CPv~~~~~~ 262 (273)
..|-.|++.-..-.++|.--|+.|-.|--. -..||+|+.+.+
T Consensus 159 ~~Cr~C~~~~~~VlllPCrHl~lC~~C~~~----~~~CPiC~~~~~ 200 (207)
T KOG1100|consen 159 RSCRKCGEREATVLLLPCRHLCLCGICDES----LRICPICRSPKT 200 (207)
T ss_pred ccceecCcCCceEEeecccceEeccccccc----CccCCCCcChhh
Confidence 349999998777667773445789999864 356999997754
No 198
>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=45.40 E-value=9.5 Score=24.15 Aligned_cols=10 Identities=20% Similarity=0.268 Sum_probs=7.6
Q ss_pred cCCCCCCCCC
Q 024073 250 QYKRCPVTLM 259 (273)
Q Consensus 250 ~~~~CPv~~~ 259 (273)
....||.|+.
T Consensus 25 ~~~~CP~Cg~ 34 (41)
T smart00834 25 PLATCPECGG 34 (41)
T ss_pred CCCCCCCCCC
Confidence 3468999996
No 199
>PLN02720 complex II
Probab=44.67 E-value=11 Score=31.20 Aligned_cols=9 Identities=33% Similarity=1.391 Sum_probs=7.5
Q ss_pred HHHHHHHhc
Q 024073 174 FKMMEWWYQ 182 (273)
Q Consensus 174 lKfLEWWys 182 (273)
+||||||..
T Consensus 129 ~KFl~WWE~ 137 (140)
T PLN02720 129 VKFLDWWER 137 (140)
T ss_pred hHHHHHHHh
Confidence 589999974
No 200
>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=44.45 E-value=20 Score=26.61 Aligned_cols=19 Identities=16% Similarity=0.462 Sum_probs=13.0
Q ss_pred HHHHHHHHH-HHHHhccccc
Q 024073 168 IAAVFFFKM-MEWWYQSAEE 186 (273)
Q Consensus 168 p~~IF~lKf-LEWWyss~~~ 186 (273)
.-.+|+.|| +|||+|+..+
T Consensus 5 gq~lF~~Rf~~QW~~SEk~k 24 (72)
T PF07578_consen 5 GQLLFSSRFIVQWIYSEKAK 24 (72)
T ss_pred HHHHHHHHHHHHHHHHHHcC
Confidence 445677775 6999987543
No 201
>PRK07217 replication factor A; Reviewed
Probab=43.82 E-value=17 Score=34.30 Aligned_cols=28 Identities=25% Similarity=0.395 Sum_probs=19.8
Q ss_pred CCCCC--CCCCCCCcccccccccccchhhHHHHHhcCCCCCCCCCCCCcCCee
Q 024073 217 TICPL--CSQKRANPSVVTVSGFVFCYACIFKYVSQYKRCPVTLMPATVEQIR 267 (273)
Q Consensus 217 ~~Cpi--C~~~~~np~~l~~~G~vfCy~Ci~~~~~~~~~CPv~~~~~~~~~l~ 267 (273)
..||. |.+.+ +++.||.|+..-...|||
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 67999 99887 246788888655555554
No 202
>PF14803 Nudix_N_2: Nudix N-terminal; PDB: 3CNG_C.
Probab=43.70 E-value=8 Score=24.49 Aligned_cols=21 Identities=29% Similarity=0.703 Sum_probs=10.1
Q ss_pred CCCCCCCCCCCc---------ccccccccc
Q 024073 218 ICPLCSQKRANP---------SVVTVSGFV 238 (273)
Q Consensus 218 ~CpiC~~~~~np---------~~l~~~G~v 238 (273)
.||.|+.+++-. .+++.||+|
T Consensus 2 fC~~CG~~l~~~ip~gd~r~R~vC~~Cg~I 31 (34)
T PF14803_consen 2 FCPQCGGPLERRIPEGDDRERLVCPACGFI 31 (34)
T ss_dssp B-TTT--B-EEE--TT-SS-EEEETTTTEE
T ss_pred ccccccChhhhhcCCCCCccceECCCCCCE
Confidence 488888875432 355566665
No 203
>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=43.19 E-value=10 Score=25.59 Aligned_cols=9 Identities=22% Similarity=0.305 Sum_probs=6.7
Q ss_pred CCCCCCCCC
Q 024073 251 YKRCPVTLM 259 (273)
Q Consensus 251 ~~~CPv~~~ 259 (273)
.-.||.|+.
T Consensus 26 ~~~CP~Cg~ 34 (52)
T TIGR02605 26 LATCPECGG 34 (52)
T ss_pred CCCCCCCCC
Confidence 347999985
No 204
>PRK06393 rpoE DNA-directed RNA polymerase subunit E''; Validated
Probab=42.59 E-value=12 Score=27.13 Aligned_cols=34 Identities=21% Similarity=0.257 Sum_probs=20.0
Q ss_pred ccccchhhHHHHHhcCCCCCCCCCCCC---cCCeeeCcc
Q 024073 236 GFVFCYACIFKYVSQYKRCPVTLMPAT---VEQIRRLFH 271 (273)
Q Consensus 236 G~vfCy~Ci~~~~~~~~~CPv~~~~~~---~~~l~ri~~ 271 (273)
.+.-|..|- +|.+...||+|+-.-+ -++++-|..
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 344566663 3445679999997642 345555543
No 205
>KOG1729 consensus FYVE finger containing protein [General function prediction only]
Probab=42.50 E-value=14 Score=34.58 Aligned_cols=47 Identities=15% Similarity=0.366 Sum_probs=30.7
Q ss_pred CCCCCCCCCCCCCCc----ccccccccccchhhHHH-HHh----cC--CCCCCCCCCC
Q 024073 215 DRTICPLCSQKRANP----SVVTVSGFVFCYACIFK-YVS----QY--KRCPVTLMPA 261 (273)
Q Consensus 215 ~~~~CpiC~~~~~np----~~l~~~G~vfCy~Ci~~-~~~----~~--~~CPv~~~~~ 261 (273)
+...|.+|...--+. .=+..||++||..|=.+ ++- .. ..|+.|...+
T Consensus 167 ea~~C~~C~~~~Ftl~~RRHHCR~CG~ivC~~Cs~n~~~l~~~~~k~~rvC~~CF~el 224 (288)
T KOG1729|consen 167 EATECMVCGCTEFTLSERRHHCRNCGDIVCAPCSRNRFLLPNLSTKPIRVCDICFEEL 224 (288)
T ss_pred cceecccCCCccccHHHHHHHHHhcchHhhhhhhcCcccccccCCCCceecHHHHHHH
Confidence 578999999942222 13455999999999877 332 11 2577776443
No 206
>smart00661 RPOL9 RNA polymerase subunit 9.
Probab=42.05 E-value=16 Score=24.32 Aligned_cols=9 Identities=33% Similarity=0.999 Sum_probs=5.7
Q ss_pred CCCCCCCCC
Q 024073 218 ICPLCSQKR 226 (273)
Q Consensus 218 ~CpiC~~~~ 226 (273)
.||-|+..+
T Consensus 2 FCp~Cg~~l 10 (52)
T smart00661 2 FCPKCGNML 10 (52)
T ss_pred CCCCCCCcc
Confidence 477777644
No 207
>KOG1815 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=42.04 E-value=9.5 Score=37.54 Aligned_cols=36 Identities=19% Similarity=0.495 Sum_probs=25.0
Q ss_pred CCCCCCCCCCCCCcc-----cccc--cccccchhhHHHHHhcCC
Q 024073 216 RTICPLCSQKRANPS-----VVTV--SGFVFCYACIFKYVSQYK 252 (273)
Q Consensus 216 ~~~CpiC~~~~~np~-----~l~~--~G~vfCy~Ci~~~~~~~~ 252 (273)
...||.|..++.--. .+.. |+|+||+.| ......|+
T Consensus 226 tk~CP~c~~~iek~~gc~~~~~~~~~c~~~FCw~C-l~~~~~h~ 268 (444)
T KOG1815|consen 226 TKECPKCKVPIEKDGGCNHMTCKSASCKHEFCWVC-LASLSDHG 268 (444)
T ss_pred CccCCCcccchhccCCccccccccCCcCCeeceee-eccccccc
Confidence 445999999876553 3333 999999999 44444553
No 208
>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=41.49 E-value=14 Score=31.60 Aligned_cols=34 Identities=21% Similarity=0.504 Sum_probs=24.0
Q ss_pred CCCCCCCCCCCCCccccccc-ccccch-----------hhHHHHHh
Q 024073 216 RTICPLCSQKRANPSVVTVS-GFVFCY-----------ACIFKYVS 249 (273)
Q Consensus 216 ~~~CpiC~~~~~np~~l~~~-G~vfCy-----------~Ci~~~~~ 249 (273)
...||||++..-|+++|-.+ -.--|. -|+.+|-+
T Consensus 2 d~~CpICme~PHNAVLLlCSS~~kgcRpymc~Ts~rhSNCLdqfkk 47 (162)
T PF07800_consen 2 DVTCPICMEHPHNAVLLLCSSHEKGCRPYMCDTSYRHSNCLDQFKK 47 (162)
T ss_pred CccCceeccCCCceEEEEeccccCCccccccCCccchhHHHHHHHH
Confidence 45899999999999876533 334453 37777775
No 209
>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=41.18 E-value=13 Score=24.34 Aligned_cols=25 Identities=28% Similarity=0.600 Sum_probs=15.5
Q ss_pred CCC--CCCCCCCcccccccccccchhh
Q 024073 219 CPL--CSQKRANPSVVTVSGFVFCYAC 243 (273)
Q Consensus 219 Cpi--C~~~~~np~~l~~~G~vfCy~C 243 (273)
|.+ |.+....|..++.||..||-.-
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 8888888988988999999763
No 210
>TIGR00373 conserved hypothetical protein TIGR00373. This family of proteins is, so far, restricted to archaeal genomes. The family appears to be distantly related to the N-terminal region of the eukaryotic transcription initiation factor IIE alpha chain.
Probab=40.91 E-value=8.4 Score=32.63 Aligned_cols=32 Identities=16% Similarity=0.093 Sum_probs=22.3
Q ss_pred CCCCCCCCCCCCCCcccccccccccchhhHHHHHhcCCCCCCCCCCCC
Q 024073 215 DRTICPLCSQKRANPSVVTVSGFVFCYACIFKYVSQYKRCPVTLMPAT 262 (273)
Q Consensus 215 ~~~~CpiC~~~~~np~~l~~~G~vfCy~Ci~~~~~~~~~CPv~~~~~~ 262 (273)
..+.||.|+...+---|+. ..-.||+||.++.
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 4678999997665443433 3569999997764
No 211
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=40.81 E-value=10 Score=32.84 Aligned_cols=32 Identities=19% Similarity=0.202 Sum_probs=22.0
Q ss_pred CCCCCCCCCCCCCCcccccccccccchhhHHHHHhcCCCCCCCCCCCC
Q 024073 215 DRTICPLCSQKRANPSVVTVSGFVFCYACIFKYVSQYKRCPVTLMPAT 262 (273)
Q Consensus 215 ~~~~CpiC~~~~~np~~l~~~G~vfCy~Ci~~~~~~~~~CPv~~~~~~ 262 (273)
..+.||.|+...+---++ +..-.||+||.++.
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 467899998765433333 23579999998764
No 212
>KOG3726 consensus Uncharacterized conserved protein [Function unknown]
Probab=40.81 E-value=14 Score=38.39 Aligned_cols=42 Identities=21% Similarity=0.387 Sum_probs=29.6
Q ss_pred CCCCCCCCCCCCc-cccc--ccccccchhhHHHHHhcCCCCCCCCCCC
Q 024073 217 TICPLCSQKRANP-SVVT--VSGFVFCYACIFKYVSQYKRCPVTLMPA 261 (273)
Q Consensus 217 ~~CpiC~~~~~np-~~l~--~~G~vfCy~Ci~~~~~~~~~CPv~~~~~ 261 (273)
..|-+|..+-.-. .|+. -|+-+||..|-.++ ...||||+-.+
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 4678888875522 2433 38999999987655 46899999654
No 213
>PRK12495 hypothetical protein; Provisional
Probab=40.74 E-value=13 Score=33.48 Aligned_cols=25 Identities=24% Similarity=0.502 Sum_probs=16.3
Q ss_pred CCCCCCCCCCCCCcccccccccccchhhHH
Q 024073 216 RTICPLCSQKRANPSVVTVSGFVFCYACIF 245 (273)
Q Consensus 216 ~~~CpiC~~~~~np~~l~~~G~vfCy~Ci~ 245 (273)
...|+.|+.+|- .+ -|-+||-.|-.
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 457999999884 22 46666665543
No 214
>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=40.47 E-value=9.3 Score=37.21 Aligned_cols=55 Identities=24% Similarity=0.420 Sum_probs=0.0
Q ss_pred CCCCCCCCCCC--------------CC---cc-cccccccccchhhHHHHHhc---------CCCCCCCCCCCCc-CCee
Q 024073 216 RTICPLCSQKR--------------AN---PS-VVTVSGFVFCYACIFKYVSQ---------YKRCPVTLMPATV-EQIR 267 (273)
Q Consensus 216 ~~~CpiC~~~~--------------~n---p~-~l~~~G~vfCy~Ci~~~~~~---------~~~CPv~~~~~~~-~~l~ 267 (273)
...||+|+.+= .| |+ +-.+||||.--..+.-|-+- +..||-|..++.- ...+
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 11 22 33459999988888888762 3589999999874 4555
Q ss_pred eCc
Q 024073 268 RLF 270 (273)
Q Consensus 268 ri~ 270 (273)
|++
T Consensus 408 rLi 410 (416)
T PF04710_consen 408 RLI 410 (416)
T ss_dssp ---
T ss_pred EEE
Confidence 554
No 215
>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=39.75 E-value=12 Score=25.37 Aligned_cols=11 Identities=36% Similarity=0.519 Sum_probs=5.5
Q ss_pred cCCCCCCCCCC
Q 024073 250 QYKRCPVTLMP 260 (273)
Q Consensus 250 ~~~~CPv~~~~ 260 (273)
.+=+||+|+.+
T Consensus 33 ~~w~CP~C~a~ 43 (47)
T PF00301_consen 33 DDWVCPVCGAP 43 (47)
T ss_dssp TT-B-TTTSSB
T ss_pred CCCcCcCCCCc
Confidence 44477777743
No 216
>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=39.73 E-value=40 Score=32.51 Aligned_cols=53 Identities=19% Similarity=0.391 Sum_probs=35.6
Q ss_pred CCCCCCCCCCCCCCCccccccc----------------cccc-----chhhHHHHHh-------------cCCCCCCCCC
Q 024073 214 PDRTICPLCSQKRANPSVVTVS----------------GFVF-----CYACIFKYVS-------------QYKRCPVTLM 259 (273)
Q Consensus 214 ~~~~~CpiC~~~~~np~~l~~~----------------G~vf-----Cy~Ci~~~~~-------------~~~~CPv~~~ 259 (273)
.+...|--|+....|=.+.+.| +--| |-.|+=+|+. +...||.|+.
T Consensus 269 ~e~e~CigC~~~~~~vkl~k~C~~~~~~g~~~~~~~~C~~C~CRPmWC~~Cm~kwFasrQd~~~~~~Wl~~~~~CPtCRa 348 (358)
T PF10272_consen 269 QELEPCIGCMQAQPNVKLVKRCADEEQEGSPLPNEPPCQQCYCRPMWCLECMGKWFASRQDQQHPETWLSGKCPCPTCRA 348 (358)
T ss_pred cccCCccccccCCCCcEEEeccCCcccCCcccccCCCCccccccchHHHHHHHHHhhhcCCCCChhhhhcCCCCCCCCcc
Confidence 4567898898876655444334 2333 7789988885 4458999998
Q ss_pred CCCcCCe
Q 024073 260 PATVEQI 266 (273)
Q Consensus 260 ~~~~~~l 266 (273)
+.=+-|+
T Consensus 349 ~FCilDV 355 (358)
T PF10272_consen 349 KFCILDV 355 (358)
T ss_pred cceeeee
Confidence 8655544
No 217
>COG1997 RPL43A Ribosomal protein L37AE/L43A [Translation, ribosomal structure and biogenesis]
Probab=39.62 E-value=18 Score=27.91 Aligned_cols=31 Identities=23% Similarity=0.688 Sum_probs=18.8
Q ss_pred CCCCCCCCCCCCCCcccccccccccchhhHHHHH
Q 024073 215 DRTICPLCSQKRANPSVVTVSGFVFCYACIFKYV 248 (273)
Q Consensus 215 ~~~~CpiC~~~~~np~~l~~~G~vfCy~Ci~~~~ 248 (273)
+...||.|+.....-. . +|.=-|..|-..|-
T Consensus 34 ~~~~Cp~C~~~~VkR~--a-~GIW~C~kCg~~fA 64 (89)
T COG1997 34 AKHVCPFCGRTTVKRI--A-TGIWKCRKCGAKFA 64 (89)
T ss_pred cCCcCCCCCCcceeee--c-cCeEEcCCCCCeec
Confidence 4678999999843331 2 55555655555443
No 218
>PRK12496 hypothetical protein; Provisional
Probab=39.44 E-value=8.4 Score=32.87 Aligned_cols=11 Identities=36% Similarity=0.875 Sum_probs=8.1
Q ss_pred CCCCCCCCCCC
Q 024073 216 RTICPLCSQKR 226 (273)
Q Consensus 216 ~~~CpiC~~~~ 226 (273)
...|+-|++..
T Consensus 127 ~~~C~gC~~~~ 137 (164)
T PRK12496 127 RKVCKGCKKKY 137 (164)
T ss_pred eEECCCCCccc
Confidence 46788888765
No 219
>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=38.93 E-value=8.3 Score=37.34 Aligned_cols=24 Identities=13% Similarity=0.051 Sum_probs=17.4
Q ss_pred HHHHhhHHHHHHHHHHHHHHHHHHhC
Q 024073 72 IFACYPWLHASCEGLSFTYQLLYLLD 97 (273)
Q Consensus 72 f~~~YP~i~~~~~~~~l~~~L~YL~g 97 (273)
.+-+.|-+.++.++...+.. +|-.
T Consensus 82 ~L~~fp~l~~a~~f~~~l~~--~l~~ 105 (374)
T TIGR00375 82 VLLFMPTLADMKQFSNWLSA--RLKN 105 (374)
T ss_pred EEEECCCHHHHHHHHHHHHh--hCCC
Confidence 34467999999998888775 5543
No 220
>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=38.19 E-value=9.7 Score=22.89 Aligned_cols=26 Identities=19% Similarity=0.453 Sum_probs=15.5
Q ss_pred CCCCCCCCCCCcccccccccccchhhH
Q 024073 218 ICPLCSQKRANPSVVTVSGFVFCYACI 244 (273)
Q Consensus 218 ~CpiC~~~~~np~~l~~~G~vfCy~Ci 244 (273)
.||.|...+.+-.+-. =+-.||-+|.
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 6999999887766544 5667787774
No 221
>KOG2462 consensus C2H2-type Zn-finger protein [Transcription]
Probab=37.72 E-value=35 Score=31.69 Aligned_cols=13 Identities=31% Similarity=0.777 Sum_probs=7.3
Q ss_pred CCCCCCCCCCCCC
Q 024073 216 RTICPLCSQKRAN 228 (273)
Q Consensus 216 ~~~CpiC~~~~~n 228 (273)
...|+-|++...+
T Consensus 130 r~~c~eCgk~ysT 142 (279)
T KOG2462|consen 130 RYKCPECGKSYST 142 (279)
T ss_pred ceecccccccccc
Confidence 4566666665433
No 222
>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=37.51 E-value=25 Score=21.27 Aligned_cols=36 Identities=22% Similarity=0.389 Sum_probs=19.7
Q ss_pred CCCCCCCCCCCc-ccccccccccchhhHHHHHhcCCCCCCCCCCC
Q 024073 218 ICPLCSQKRANP-SVVTVSGFVFCYACIFKYVSQYKRCPVTLMPA 261 (273)
Q Consensus 218 ~CpiC~~~~~np-~~l~~~G~vfCy~Ci~~~~~~~~~CPv~~~~~ 261 (273)
.|..|.+.+.+. .++..-|..|...| -+|..|+.++
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 478888888774 33332444443332 2455566554
No 223
>COG3058 FdhE Uncharacterized protein involved in formate dehydrogenase formation [Posttranslational modification, protein turnover, chaperones]
Probab=36.68 E-value=32 Score=32.15 Aligned_cols=46 Identities=20% Similarity=0.475 Sum_probs=34.1
Q ss_pred CCCCCCCCCCCCCCcccccc---cc--cccchhhHHHHHhcCCCCCCCCCC
Q 024073 215 DRTICPLCSQKRANPSVVTV---SG--FVFCYACIFKYVSQYKRCPVTLMP 260 (273)
Q Consensus 215 ~~~~CpiC~~~~~np~~l~~---~G--~vfCy~Ci~~~~~~~~~CPv~~~~ 260 (273)
....||+|+....-..|.-. .| |.-|--|..+|-.-.-+|--|+..
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 45689999997665544320 12 677999999999888889888854
No 224
>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=36.49 E-value=23 Score=28.32 Aligned_cols=31 Identities=19% Similarity=0.317 Sum_probs=22.3
Q ss_pred CCCCCCCCCC---CCC-cccccccccccchhhHHH
Q 024073 216 RTICPLCSQK---RAN-PSVVTVSGFVFCYACIFK 246 (273)
Q Consensus 216 ~~~CpiC~~~---~~n-p~~l~~~G~vfCy~Ci~~ 246 (273)
...|.+|+.+ +.| ..++..|+|.+|-.|-..
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 367778999999999765
No 225
>PF13719 zinc_ribbon_5: zinc-ribbon domain
Probab=34.92 E-value=20 Score=22.85 Aligned_cols=12 Identities=33% Similarity=0.874 Sum_probs=8.0
Q ss_pred CCCCCCCCCCCc
Q 024073 218 ICPLCSQKRANP 229 (273)
Q Consensus 218 ~CpiC~~~~~np 229 (273)
.||-|.....-|
T Consensus 4 ~CP~C~~~f~v~ 15 (37)
T PF13719_consen 4 TCPNCQTRFRVP 15 (37)
T ss_pred ECCCCCceEEcC
Confidence 588888765444
No 226
>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=34.79 E-value=27 Score=24.79 Aligned_cols=14 Identities=21% Similarity=0.776 Sum_probs=11.7
Q ss_pred CCCCCCCCCCCCCC
Q 024073 215 DRTICPLCSQKRAN 228 (273)
Q Consensus 215 ~~~~CpiC~~~~~n 228 (273)
.+..||.|+.....
T Consensus 27 TSq~C~~CG~~~~~ 40 (69)
T PF07282_consen 27 TSQTCPRCGHRNKK 40 (69)
T ss_pred CccCccCccccccc
Confidence 36689999998877
No 227
>PHA02768 hypothetical protein; Provisional
Probab=34.77 E-value=29 Score=24.47 Aligned_cols=43 Identities=7% Similarity=0.100 Sum_probs=28.9
Q ss_pred CCCCCCCCCCCCCcccccccccccchhhHHHHHhc---CCCCCCCCCCC-CcCCeeeCc
Q 024073 216 RTICPLCSQKRANPSVVTVSGFVFCYACIFKYVSQ---YKRCPVTLMPA-TVEQIRRLF 270 (273)
Q Consensus 216 ~~~CpiC~~~~~np~~l~~~G~vfCy~Ci~~~~~~---~~~CPv~~~~~-~~~~l~ri~ 270 (273)
.+.|+.|++.......+. + +.+. .-+|..|++-. ....|+.|-
T Consensus 5 ~y~C~~CGK~Fs~~~~L~--~----------H~r~H~k~~kc~~C~k~f~~~s~l~~~~ 51 (55)
T PHA02768 5 GYECPICGEIYIKRKSMI--T----------HLRKHNTNLKLSNCKRISLRTGEYIEIK 51 (55)
T ss_pred ccCcchhCCeeccHHHHH--H----------HHHhcCCcccCCcccceecccceeEEEe
Confidence 468999999988776653 2 3332 34899999764 456666653
No 228
>PRK14714 DNA polymerase II large subunit; Provisional
Probab=34.13 E-value=21 Score=39.64 Aligned_cols=30 Identities=23% Similarity=0.402 Sum_probs=23.4
Q ss_pred CCCCCCCCCCCCCcccccccccc---------cchhhHH
Q 024073 216 RTICPLCSQKRANPSVVTVSGFV---------FCYACIF 245 (273)
Q Consensus 216 ~~~CpiC~~~~~np~~l~~~G~v---------fCy~Ci~ 245 (273)
...||-|+.....+..|+.||.. +|..|-.
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 45899999887767778888884 7888854
No 229
>COG5113 UFD2 Ubiquitin fusion degradation protein 2 [Posttranslational modification, protein turnover, chaperones]
Probab=34.01 E-value=36 Score=35.45 Aligned_cols=53 Identities=19% Similarity=0.204 Sum_probs=49.7
Q ss_pred CCCCCCCCCCCCCCcccccccccccchhhHHHHHhcCCCCCCCCCCCCcCCee
Q 024073 215 DRTICPLCSQKRANPSVVTVSGFVFCYACIFKYVSQYKRCPVTLMPATVEQIR 267 (273)
Q Consensus 215 ~~~~CpiC~~~~~np~~l~~~G~vfCy~Ci~~~~~~~~~CPv~~~~~~~~~l~ 267 (273)
|...=|+--..++||++++++|..--..-|..++-..+.-|--++|++.+|+.
T Consensus 853 DeFlDPLmftimkdPV~Lp~S~i~IDRSTikahllsd~tDPFNRmPLtlddVt 905 (929)
T COG5113 853 DEFLDPLMFTIMKDPVKLPTSRITIDRSTIKAHLLSDGTDPFNRMPLTLDDVT 905 (929)
T ss_pred hhhhCchhhhcccCCeecccccccccHHHHHHHHhcCCCCccccCCCchhhcC
Confidence 78889999999999999999999999999999999999999999999988764
No 230
>KOG4642 consensus Chaperone-dependent E3 ubiquitin protein ligase (contains TPR repeats) [Posttranslational modification, protein turnover, chaperones]
Probab=33.82 E-value=21 Score=32.90 Aligned_cols=53 Identities=23% Similarity=0.165 Sum_probs=46.6
Q ss_pred CCCCCCCCCCCCCCcccccccccccchhhHHHHHhcCC-CCCCCCCCCCcCCeee
Q 024073 215 DRTICPLCSQKRANPSVVTVSGFVFCYACIFKYVSQYK-RCPVTLMPATVEQIRR 268 (273)
Q Consensus 215 ~~~~CpiC~~~~~np~~l~~~G~vfCy~Ci~~~~~~~~-~CPv~~~~~~~~~l~r 268 (273)
|-..|.|-.+.+++|++.+ +|..|-..=|.++++.-| --|||+.+++..+++.
T Consensus 210 d~lcgkIt~el~~~pvi~p-sgIty~ra~I~Ehl~rvghfdpvtr~~Lte~q~ip 263 (284)
T KOG4642|consen 210 DYLCGKITLELMREPVITP-SGITYDRADIEEHLQRVGHFDPVTRWPLTEYQLIP 263 (284)
T ss_pred chhhhhhhHHhhcCCccCc-cccchhHHHHHHHHHHhccCCchhcccCCHHhhcc
Confidence 5667889999999999887 999999999999999864 6899999999888764
No 231
>KOG3476 consensus Microtubule-associated protein CRIPT [Cytoskeleton]
Probab=33.59 E-value=3.4 Score=31.85 Aligned_cols=35 Identities=23% Similarity=0.613 Sum_probs=28.0
Q ss_pred CCCCCCCCCCCCcccccccccccchhhHHHHHhcCCCCCCCCCCC
Q 024073 217 TICPLCSQKRANPSVVTVSGFVFCYACIFKYVSQYKRCPVTLMPA 261 (273)
Q Consensus 217 ~~CpiC~~~~~np~~l~~~G~vfCy~Ci~~~~~~~~~CPv~~~~~ 261 (273)
..|-||...+-.| |-.||..|++ +.+.|-.||+.+
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 4799998876544 7789999998 568999999764
No 232
>COG1545 Predicted nucleic-acid-binding protein containing a Zn-ribbon [General function prediction only]
Probab=32.31 E-value=25 Score=29.20 Aligned_cols=23 Identities=17% Similarity=0.173 Sum_probs=14.6
Q ss_pred cccccccccchhhHHHHHhcCCCCCCCCCCC
Q 024073 231 VVTVSGFVFCYACIFKYVSQYKRCPVTLMPA 261 (273)
Q Consensus 231 ~l~~~G~vfCy~Ci~~~~~~~~~CPv~~~~~ 261 (273)
-|..||++|.. .+..||-|+.+.
T Consensus 31 kC~~CG~v~~P--------Pr~~Cp~C~~~~ 53 (140)
T COG1545 31 KCKKCGRVYFP--------PRAYCPKCGSET 53 (140)
T ss_pred EcCCCCeEEcC--------CcccCCCCCCCC
Confidence 34456777665 356777777664
No 233
>PRK11827 hypothetical protein; Provisional
Probab=32.28 E-value=25 Score=25.21 Aligned_cols=14 Identities=29% Similarity=0.648 Sum_probs=10.5
Q ss_pred CCCCCCCCCCCCCC
Q 024073 215 DRTICPLCSQKRAN 228 (273)
Q Consensus 215 ~~~~CpiC~~~~~n 228 (273)
+-..||+|.+++.-
T Consensus 7 eILaCP~ckg~L~~ 20 (60)
T PRK11827 7 EIIACPVCNGKLWY 20 (60)
T ss_pred hheECCCCCCcCeE
Confidence 34579999998753
No 234
>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=32.24 E-value=25 Score=23.40 Aligned_cols=10 Identities=50% Similarity=0.733 Sum_probs=5.0
Q ss_pred CCCCCCCCCC
Q 024073 252 KRCPVTLMPA 261 (273)
Q Consensus 252 ~~CPv~~~~~ 261 (273)
+.||+|+.|+
T Consensus 9 K~C~~C~rpf 18 (42)
T PF10013_consen 9 KICPVCGRPF 18 (42)
T ss_pred CcCcccCCcc
Confidence 3455555544
No 235
>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=31.53 E-value=20 Score=23.64 Aligned_cols=24 Identities=25% Similarity=0.757 Sum_probs=14.9
Q ss_pred CCCCCCCCCCCCCcccccccccccchhh
Q 024073 216 RTICPLCSQKRANPSVVTVSGFVFCYAC 243 (273)
Q Consensus 216 ~~~CpiC~~~~~np~~l~~~G~vfCy~C 243 (273)
...||.|+.++-. ..-|.+||-.|
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 3468888765433 23677777655
No 236
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=31.34 E-value=16 Score=24.14 Aligned_cols=10 Identities=30% Similarity=0.474 Sum_probs=7.2
Q ss_pred CCCCCCCCCC
Q 024073 252 KRCPVTLMPA 261 (273)
Q Consensus 252 ~~CPv~~~~~ 261 (273)
.+||-||.++
T Consensus 22 ~~Cp~CG~~~ 31 (46)
T PRK00398 22 VRCPYCGYRI 31 (46)
T ss_pred eECCCCCCeE
Confidence 5788888664
No 237
>smart00290 ZnF_UBP Ubiquitin Carboxyl-terminal Hydrolase-like zinc finger.
Probab=30.94 E-value=18 Score=23.92 Aligned_cols=25 Identities=24% Similarity=0.386 Sum_probs=16.4
Q ss_pred CCCCCCCCCCCcccccccccccchhh
Q 024073 218 ICPLCSQKRANPSVVTVSGFVFCYAC 243 (273)
Q Consensus 218 ~CpiC~~~~~np~~l~~~G~vfCy~C 243 (273)
+|..|+..- +--++-.||+++|.+-
T Consensus 1 ~C~~C~~~~-~l~~CL~C~~~~c~~~ 25 (50)
T smart00290 1 RCSVCGTIE-NLWLCLTCGQVGCGRY 25 (50)
T ss_pred CcccCCCcC-CeEEecCCCCcccCCC
Confidence 477788543 3334445999999654
No 238
>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=30.93 E-value=32 Score=34.36 Aligned_cols=47 Identities=17% Similarity=0.256 Sum_probs=30.3
Q ss_pred CCCCCCCCCCCCCcccccccccccchhhHHHHHhcCCCCCCCCCCCCcCCee
Q 024073 216 RTICPLCSQKRANPSVVTVSGFVFCYACIFKYVSQYKRCPVTLMPATVEQIR 267 (273)
Q Consensus 216 ~~~CpiC~~~~~np~~l~~~G~vfCy~Ci~~~~~~~~~CPv~~~~~~~~~l~ 267 (273)
.+.||.|+..-.+.-+|..||+.+ .... -...+|..|+.++......
T Consensus 136 ~g~cp~c~~~~~~g~~ce~cg~~~--~~~~---l~~p~~~~~~~~~e~~~~~ 182 (530)
T TIGR00398 136 EGTCPKCGSEDARGDHCEVCGRHL--EPTE---LINPRCKICGAKPELRDSE 182 (530)
T ss_pred cCCCCCCCCcccccchhhhccccC--CHHH---hcCCccccCCCcceEEecc
Confidence 468999988766666777788764 1111 1347899998876544333
No 239
>PF14471 DUF4428: Domain of unknown function (DUF4428)
Probab=30.78 E-value=39 Score=23.23 Aligned_cols=28 Identities=25% Similarity=0.696 Sum_probs=20.3
Q ss_pred CCCCCCCCCCC--cccccccccccchhhHHHH
Q 024073 218 ICPLCSQKRAN--PSVVTVSGFVFCYACIFKY 247 (273)
Q Consensus 218 ~CpiC~~~~~n--p~~l~~~G~vfCy~Ci~~~ 247 (273)
.|+||++.+.- ..-+. -|| -|-.|..+.
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 59999997533 23444 785 899999776
No 240
>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional
Probab=30.72 E-value=28 Score=24.91 Aligned_cols=18 Identities=22% Similarity=0.431 Sum_probs=9.8
Q ss_pred chhhHHHHHhcCCCCCCCCC
Q 024073 240 CYACIFKYVSQYKRCPVTLM 259 (273)
Q Consensus 240 Cy~Ci~~~~~~~~~CPv~~~ 259 (273)
|.+|-..- ..=+||.||.
T Consensus 39 C~~CRk~~--~~Y~CP~CGF 56 (59)
T PRK14890 39 CEKCRKQS--NPYTCPKCGF 56 (59)
T ss_pred chhHHhcC--CceECCCCCC
Confidence 55554321 2247888874
No 241
>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=30.68 E-value=28 Score=35.71 Aligned_cols=18 Identities=28% Similarity=0.541 Sum_probs=12.7
Q ss_pred CCCCCCCCCCCcCCeeeCc
Q 024073 252 KRCPVTLMPATVEQIRRLF 270 (273)
Q Consensus 252 ~~CPv~~~~~~~~~l~ri~ 270 (273)
..||.|+.. ..+.++||-
T Consensus 547 ~~CP~CGs~-~~ev~sRv~ 564 (586)
T TIGR02827 547 HRCPVCGSA-NIDYGTRVI 564 (586)
T ss_pred CcCcCCCCc-cceEEEeec
Confidence 699999953 456666663
No 242
>PRK01343 zinc-binding protein; Provisional
Probab=30.50 E-value=48 Score=23.53 Aligned_cols=35 Identities=23% Similarity=0.569 Sum_probs=22.2
Q ss_pred CCCCCCCCCCCCCcccccccccccch-hhH----HHHHhcCCCCCC
Q 024073 216 RTICPLCSQKRANPSVVTVSGFVFCY-ACI----FKYVSQYKRCPV 256 (273)
Q Consensus 216 ~~~CpiC~~~~~np~~l~~~G~vfCy-~Ci----~~~~~~~~~CPv 256 (273)
...||||+++..++. +-||. +|- -+|+.+.-+=|.
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 457999999877643 24664 563 467766544443
No 243
>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=30.49 E-value=18 Score=22.74 Aligned_cols=30 Identities=27% Similarity=0.619 Sum_probs=21.0
Q ss_pred CCCCCCCCCCCCcccccccccccchhhHHH
Q 024073 217 TICPLCSQKRANPSVVTVSGFVFCYACIFK 246 (273)
Q Consensus 217 ~~CpiC~~~~~np~~l~~~G~vfCy~Ci~~ 246 (273)
++|-.|+++|-..-....=|-.+|..|...
T Consensus 4 g~C~~CGe~I~~~Rl~~~p~~~~C~~C~~~ 33 (36)
T PF01258_consen 4 GICEDCGEPIPEERLVAVPGATLCVECQER 33 (36)
T ss_dssp SB-TTTSSBEEHHHHHHCTTECS-HHHHHH
T ss_pred CCccccCChHHHHHHHhCCCcEECHHHhCc
Confidence 469999999877744334688999999764
No 244
>PRK08271 anaerobic ribonucleoside triphosphate reductase; Provisional
Probab=30.49 E-value=16 Score=37.85 Aligned_cols=19 Identities=26% Similarity=0.518 Sum_probs=11.4
Q ss_pred cCCCCCCCCCCCCcCCeeeC
Q 024073 250 QYKRCPVTLMPATVEQIRRL 269 (273)
Q Consensus 250 ~~~~CPv~~~~~~~~~l~ri 269 (273)
.+..||.||.. ..+.++||
T Consensus 579 ~~~~CP~CGs~-~~ev~~RV 597 (623)
T PRK08271 579 TGKRCPICGSE-NIDYYTRV 597 (623)
T ss_pred CCcCCcCCCCc-chhHHHHH
Confidence 45789999852 23444444
No 245
>KOG3842 consensus Adaptor protein Pellino [Signal transduction mechanisms]
Probab=30.41 E-value=45 Score=31.80 Aligned_cols=54 Identities=15% Similarity=0.293 Sum_probs=35.0
Q ss_pred CCCCCCCCCCC--------------CCc----ccccccccccchhhHHHHHh---------cCCCCCCCCCCCC-cCCee
Q 024073 216 RTICPLCSQKR--------------ANP----SVVTVSGFVFCYACIFKYVS---------QYKRCPVTLMPAT-VEQIR 267 (273)
Q Consensus 216 ~~~CpiC~~~~--------------~np----~~l~~~G~vfCy~Ci~~~~~---------~~~~CPv~~~~~~-~~~l~ 267 (273)
...||+|+..- .|+ -+-.+||||.-..-..-|-+ =|..||.|...+. ....+
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 111 13345999977777766664 1458999998764 44455
Q ss_pred eC
Q 024073 268 RL 269 (273)
Q Consensus 268 ri 269 (273)
|+
T Consensus 421 kl 422 (429)
T KOG3842|consen 421 KL 422 (429)
T ss_pred EE
Confidence 44
No 246
>KOG1842 consensus FYVE finger-containing protein [General function prediction only]
Probab=29.85 E-value=17 Score=36.03 Aligned_cols=68 Identities=15% Similarity=0.234 Sum_probs=38.7
Q ss_pred HHHHHHHHHHHHHHHHHhcccc-cccCC-C-CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCc---cccccccc
Q 024073 164 QTGLIAAVFFFKMMEWWYQSAE-ERMSA-P-TVYPPPPPPPPPKVAREGIPLPPDRTICPLCSQKRANP---SVVTVSGF 237 (273)
Q Consensus 164 ~~~Lp~~IF~lKfLEWWyss~~-~~~~~-~-~~lp~PpPP~~~~~~~~~~~~p~~~~~CpiC~~~~~np---~~l~~~G~ 237 (273)
...+-+.|=+-|+++-|-+... .+... + ++.| + . ++ .+-..||+|.+.+.-. .=|.-||-
T Consensus 139 ve~nkLiiRl~rL~~~~~t~~d~~k~k~~EqsvVp------W--~--DD----s~V~~CP~Ca~~F~l~rRrHHCRLCG~ 204 (505)
T KOG1842|consen 139 VETNKLIIRLKRLEEGLPTEKDSVKRKRLEQSVVP------W--L--DD----SSVQFCPECANSFGLTRRRHHCRLCGR 204 (505)
T ss_pred HHHHHHHHHHHHHHccCccccchHHHHHHHhcccc------c--c--CC----CcccccccccchhhhHHHhhhhhhcch
Confidence 3455566777788888875421 11111 1 1111 1 1 11 1235899999975433 23445999
Q ss_pred ccchhhHH
Q 024073 238 VFCYACIF 245 (273)
Q Consensus 238 vfCy~Ci~ 245 (273)
|.|..|-.
T Consensus 205 VmC~~C~k 212 (505)
T KOG1842|consen 205 VMCRDCSK 212 (505)
T ss_pred HHHHHHHH
Confidence 99999965
No 247
>PRK08351 DNA-directed RNA polymerase subunit E''; Validated
Probab=29.50 E-value=29 Score=24.99 Aligned_cols=12 Identities=33% Similarity=0.487 Sum_probs=8.7
Q ss_pred cCCCCCCCCCCC
Q 024073 250 QYKRCPVTLMPA 261 (273)
Q Consensus 250 ~~~~CPv~~~~~ 261 (273)
....||+|+-..
T Consensus 14 ~~~~CP~Cgs~~ 25 (61)
T PRK08351 14 TEDRCPVCGSRD 25 (61)
T ss_pred CCCcCCCCcCCc
Confidence 456899998653
No 248
>KOG1701 consensus Focal adhesion adaptor protein Paxillin and related LIM proteins [Signal transduction mechanisms]
Probab=29.25 E-value=32 Score=33.89 Aligned_cols=50 Identities=22% Similarity=0.404 Sum_probs=0.0
Q ss_pred CCCCCCCCCCCCc--ccccccccccchhhHHHHHhcCCCCCCCCCCC----CcCCeeeC
Q 024073 217 TICPLCSQKRANP--SVVTVSGFVFCYACIFKYVSQYKRCPVTLMPA----TVEQIRRL 269 (273)
Q Consensus 217 ~~CpiC~~~~~np--~~l~~~G~vfCy~Ci~~~~~~~~~CPv~~~~~----~~~~l~ri 269 (273)
++|-+|.+-+..- ||=. .+-|+|-+|-++-+.- +|-||+.|+ ..++.+||
T Consensus 361 F~Cv~C~r~ldgipFtvd~-~n~v~Cv~dfh~kfAP--rCs~C~~PI~P~~G~~etvRv 416 (468)
T KOG1701|consen 361 FTCVVCARCLDGIPFTVDS-QNNVYCVPDFHKKFAP--RCSVCGNPILPRDGKDETVRV 416 (468)
T ss_pred eEEEEeccccCCccccccC-CCceeeehhhhhhcCc--chhhccCCccCCCCCcceEEE
No 249
>KOG0396 consensus Uncharacterized conserved protein [Function unknown]
Probab=29.12 E-value=28 Score=33.64 Aligned_cols=41 Identities=10% Similarity=0.143 Sum_probs=36.3
Q ss_pred ccccccccccchhhHHHHHhcC-CCCCCCCCCCCcCCeeeCcc
Q 024073 230 SVVTVSGFVFCYACIFKYVSQY-KRCPVTLMPATVEQIRRLFH 271 (273)
Q Consensus 230 ~~l~~~G~vfCy~Ci~~~~~~~-~~CPv~~~~~~~~~l~ri~~ 271 (273)
.+.+ .||||=+.-|.++=+.+ -.||++++-...++++++|.
T Consensus 347 ~lfp-nG~Vyg~~~L~s~~~~~~i~dP~~~k~f~~~~l~kvy~ 388 (389)
T KOG0396|consen 347 HLFP-NGYVYGTKALESLNEDDGIGDPRTKKVFRYSELCKVYL 388 (389)
T ss_pred cccc-CceeehhHHHHhhcccCCCcCCCCCccccHHHHHHHhc
Confidence 4555 99999999999998888 68999999999999999885
No 250
>PF13717 zinc_ribbon_4: zinc-ribbon domain
Probab=29.03 E-value=28 Score=22.05 Aligned_cols=8 Identities=50% Similarity=1.256 Sum_probs=3.7
Q ss_pred CCCCCCCC
Q 024073 218 ICPLCSQK 225 (273)
Q Consensus 218 ~CpiC~~~ 225 (273)
.||-|...
T Consensus 4 ~Cp~C~~~ 11 (36)
T PF13717_consen 4 TCPNCQAK 11 (36)
T ss_pred ECCCCCCE
Confidence 35555443
No 251
>KOG1814 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=28.78 E-value=20 Score=35.07 Aligned_cols=50 Identities=26% Similarity=0.720 Sum_probs=35.4
Q ss_pred CCCCCCC--CCCC-CCCc----ccccccccccchhhHHHHHhcCCCCCCCCCCCCcCCeeeCc
Q 024073 215 DRTICPL--CSQK-RANP----SVVTVSGFVFCYACIFKYVSQYKRCPVTLMPATVEQIRRLF 270 (273)
Q Consensus 215 ~~~~Cpi--C~~~-~~np----~~l~~~G~vfCy~Ci~~~~~~~~~CPv~~~~~~~~~l~ri~ 270 (273)
|...||- |..+ .++| +.++.|-++||.-|-..|=- ..+|-+.. ++++++|
T Consensus 272 dv~yCPr~~Cq~p~~~d~~~~l~~CskCnFaFCtlCk~t~HG-~s~Ck~~~-----~~~~~l~ 328 (445)
T KOG1814|consen 272 DVVYCPRACCQLPVKQDPGRALAICSKCNFAFCTLCKLTWHG-VSPCKVKA-----EKLIELY 328 (445)
T ss_pred ccccCChhhccCccccCchhhhhhhccCccHHHHHHHHhhcC-CCcccCch-----HHHHHHH
Confidence 4577988 7776 5555 68888999999999999864 44554443 3555554
No 252
>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=28.68 E-value=25 Score=23.06 Aligned_cols=26 Identities=27% Similarity=0.567 Sum_probs=12.3
Q ss_pred CCCCCCCCCCCcccc--cccccccchhh
Q 024073 218 ICPLCSQKRANPSVV--TVSGFVFCYAC 243 (273)
Q Consensus 218 ~CpiC~~~~~np~~l--~~~G~vfCy~C 243 (273)
-||+|+..=..-.-. ...|+-+|..|
T Consensus 5 pCP~CGG~DrFri~~d~~~~G~~~C~~C 32 (40)
T PF08273_consen 5 PCPICGGKDRFRIFDDKDGRGTWICRQC 32 (40)
T ss_dssp --TTTT-TTTEEEETT----S-EEETTT
T ss_pred CCCCCcCccccccCcCcccCCCEECCCC
Confidence 599999853322110 12699999988
No 253
>CHL00174 accD acetyl-CoA carboxylase beta subunit; Reviewed
Probab=28.35 E-value=26 Score=32.90 Aligned_cols=26 Identities=12% Similarity=0.284 Sum_probs=16.6
Q ss_pred CCCCCCCCCCC------CCcccccccccccch
Q 024073 216 RTICPLCSQKR------ANPSVVTVSGFVFCY 241 (273)
Q Consensus 216 ~~~CpiC~~~~------~np~~l~~~G~vfCy 241 (273)
-.+||-|.+.+ .|--||+.|||.|=.
T Consensus 38 w~kc~~C~~~~~~~~l~~~~~vcp~c~~h~rl 69 (296)
T CHL00174 38 WVQCENCYGLNYKKFLKSKMNICEQCGYHLKM 69 (296)
T ss_pred eeECCCccchhhHHHHHHcCCCCCCCCCCcCC
Confidence 35799998865 333566667775543
No 254
>PRK14892 putative transcription elongation factor Elf1; Provisional
Probab=28.26 E-value=25 Score=27.67 Aligned_cols=11 Identities=27% Similarity=0.661 Sum_probs=8.5
Q ss_pred CCCCCCCCCCC
Q 024073 215 DRTICPLCSQK 225 (273)
Q Consensus 215 ~~~~CpiC~~~ 225 (273)
.-..||-|+..
T Consensus 20 t~f~CP~Cge~ 30 (99)
T PRK14892 20 KIFECPRCGKV 30 (99)
T ss_pred cEeECCCCCCe
Confidence 46789999953
No 255
>PF14354 Lar_restr_allev: Restriction alleviation protein Lar
Probab=27.94 E-value=27 Score=24.21 Aligned_cols=27 Identities=22% Similarity=0.394 Sum_probs=14.6
Q ss_pred CCCCCCCCCCCccccc--cc---ccccchhhH
Q 024073 218 ICPLCSQKRANPSVVT--VS---GFVFCYACI 244 (273)
Q Consensus 218 ~CpiC~~~~~np~~l~--~~---G~vfCy~Ci 244 (273)
-||.|+..-..-.... .. -+|+|..|-
T Consensus 5 PCPFCG~~~~~~~~~~~~~~~~~~~V~C~~Cg 36 (61)
T PF14354_consen 5 PCPFCGSADVLIRQDEGFDYGMYYYVECTDCG 36 (61)
T ss_pred CCCCCCCcceEeecccCCCCCCEEEEEcCCCC
Confidence 4999976533221111 02 467888774
No 256
>PRK14873 primosome assembly protein PriA; Provisional
Probab=27.57 E-value=22 Score=37.10 Aligned_cols=24 Identities=25% Similarity=0.216 Sum_probs=18.3
Q ss_pred cccccchhhHHHHHhcCCCCCCCCCC
Q 024073 235 SGFVFCYACIFKYVSQYKRCPVTLMP 260 (273)
Q Consensus 235 ~G~vfCy~Ci~~~~~~~~~CPv~~~~ 260 (273)
.+...|.-|-+.. ...+||.|+-.
T Consensus 408 ~~~l~Ch~CG~~~--~p~~Cp~Cgs~ 431 (665)
T PRK14873 408 GGTPRCRWCGRAA--PDWRCPRCGSD 431 (665)
T ss_pred CCeeECCCCcCCC--cCccCCCCcCC
Confidence 4567788898754 36799999854
No 257
>KOG2807 consensus RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit SSL1 [Transcription; Replication, recombination and repair]
Probab=27.47 E-value=41 Score=32.17 Aligned_cols=42 Identities=19% Similarity=0.360 Sum_probs=25.7
Q ss_pred CCCCCCCCCCCCc--ccccccccccchhhHHHHHhcCCCCCCCC
Q 024073 217 TICPLCSQKRANP--SVVTVSGFVFCYACIFKYVSQYKRCPVTL 258 (273)
Q Consensus 217 ~~CpiC~~~~~np--~~l~~~G~vfCy~Ci~~~~~~~~~CPv~~ 258 (273)
..|-.|.+..+.- -.|..|-++||-+|=.=-=+.=+.||-|.
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 3477774444333 25566888888888652223337888886
No 258
>PF06170 DUF983: Protein of unknown function (DUF983); InterPro: IPR009325 This family consists of several bacterial proteins of unknown function.
Probab=26.47 E-value=30 Score=26.45 Aligned_cols=18 Identities=22% Similarity=0.383 Sum_probs=13.7
Q ss_pred HHHhcCCCCCCCCCCCCc
Q 024073 246 KYVSQYKRCPVTLMPATV 263 (273)
Q Consensus 246 ~~~~~~~~CPv~~~~~~~ 263 (273)
.|++-..+|++||.+.+.
T Consensus 3 g~Lk~~~~C~~CG~d~~~ 20 (86)
T PF06170_consen 3 GYLKVAPRCPHCGLDYSH 20 (86)
T ss_pred ccccCCCcccccCCcccc
Confidence 367777899999987653
No 259
>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=26.46 E-value=26 Score=25.16 Aligned_cols=11 Identities=27% Similarity=0.733 Sum_probs=7.6
Q ss_pred CCCCCCCCCCC
Q 024073 216 RTICPLCSQKR 226 (273)
Q Consensus 216 ~~~CpiC~~~~ 226 (273)
-..||.|..++
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 45799998866
No 260
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=26.25 E-value=36 Score=28.21 Aligned_cols=37 Identities=16% Similarity=0.090 Sum_probs=21.8
Q ss_pred CCCCCCCCCCCCCCcccccccccccchhhHHHHHhcCCCCCCCCCCCC
Q 024073 215 DRTICPLCSQKRANPSVVTVSGFVFCYACIFKYVSQYKRCPVTLMPAT 262 (273)
Q Consensus 215 ~~~~CpiC~~~~~np~~l~~~G~vfCy~Ci~~~~~~~~~CPv~~~~~~ 262 (273)
..+.||-|+...+---+.. -+. -.++-.||.||..+.
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 4678999987665332221 110 012358999998764
No 261
>COG0333 RpmF Ribosomal protein L32 [Translation, ribosomal structure and biogenesis]
Probab=26.22 E-value=40 Score=23.94 Aligned_cols=22 Identities=23% Similarity=0.629 Sum_probs=15.9
Q ss_pred CCCCCCCCCCCCCccccccccc
Q 024073 216 RTICPLCSQKRANPSVVTVSGF 237 (273)
Q Consensus 216 ~~~CpiC~~~~~np~~l~~~G~ 237 (273)
-..|+.|++...--.++..||+
T Consensus 27 ~~~c~~cG~~~l~Hrvc~~cg~ 48 (57)
T COG0333 27 LSVCPNCGEYKLPHRVCLKCGY 48 (57)
T ss_pred ceeccCCCCcccCceEcCCCCC
Confidence 4579999987766667666775
No 262
>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=26.14 E-value=25 Score=32.81 Aligned_cols=25 Identities=24% Similarity=0.317 Sum_probs=16.7
Q ss_pred CCCCCCCCCCCCCc------ccccccccccc
Q 024073 216 RTICPLCSQKRANP------SVVTVSGFVFC 240 (273)
Q Consensus 216 ~~~CpiC~~~~~np------~~l~~~G~vfC 240 (273)
-.+||-|++.+-.. -||+.|||.|=
T Consensus 26 ~~~c~~c~~~~~~~~l~~~~~vc~~c~~h~r 56 (285)
T TIGR00515 26 WTKCPKCGQVLYTKELERNLEVCPKCDHHMR 56 (285)
T ss_pred eeECCCCcchhhHHHHHhhCCCCCCCCCcCc
Confidence 45799999875433 46666777653
No 263
>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=25.98 E-value=40 Score=30.03 Aligned_cols=31 Identities=42% Similarity=1.140 Sum_probs=14.7
Q ss_pred HHHHHHHHH--HhcccccccC----CCCCCCCCCCCC
Q 024073 171 VFFFKMMEW--WYQSAEERMS----APTVYPPPPPPP 201 (273)
Q Consensus 171 IF~lKfLEW--Wyss~~~~~~----~~~~lp~PpPP~ 201 (273)
.-++|---| ||....+|+. +...||+||||+
T Consensus 172 fa~lkhttwrkWYDTSDeR~l~~hpGgp~lpppPPpP 208 (258)
T PF12312_consen 172 FAMLKHTTWRKWYDTSDERLLRAHPGGPCLPPPPPPP 208 (258)
T ss_pred HHHHhhhHHHhhcccchHHHhhcCCCCCcccCCCCCC
Confidence 445565555 6654333332 234465555544
No 264
>smart00746 TRASH metallochaperone-like domain.
Probab=25.60 E-value=77 Score=17.85 Aligned_cols=31 Identities=35% Similarity=0.836 Sum_probs=16.8
Q ss_pred CCCCCCCCCCccc---ccccccc--cc-hhhHHHHHh
Q 024073 219 CPLCSQKRANPSV---VTVSGFV--FC-YACIFKYVS 249 (273)
Q Consensus 219 CpiC~~~~~np~~---l~~~G~v--fC-y~Ci~~~~~ 249 (273)
|++|+..+.++.. ...-|++ || -.|...|.+
T Consensus 1 c~~C~~~~~~~~~~~~~~~~g~~~~FCs~~c~~~~~~ 37 (39)
T smart00746 1 CSFCGKDIYNPGTGIMVVNDGKVFYFCSSKCLSKFKK 37 (39)
T ss_pred CCCCCCCccCCCCceEEEECCEEEEEeCHHHHHHHHh
Confidence 8889888875431 1124444 33 345555543
No 265
>COG1439 Predicted nucleic acid-binding protein, consists of a PIN domain and a Zn-ribbon module [General function prediction only]
Probab=25.26 E-value=21 Score=31.09 Aligned_cols=11 Identities=27% Similarity=0.561 Sum_probs=7.5
Q ss_pred cCCCCCCCCCC
Q 024073 250 QYKRCPVTLMP 260 (273)
Q Consensus 250 ~~~~CPv~~~~ 260 (273)
.++.||+||-+
T Consensus 152 ~~~~Cp~CG~~ 162 (177)
T COG1439 152 PKDFCPICGSP 162 (177)
T ss_pred CCCcCCCCCCc
Confidence 45677777765
No 266
>KOG2066 consensus Vacuolar assembly/sorting protein VPS41 [Intracellular trafficking, secretion, and vesicular transport]
Probab=25.21 E-value=25 Score=37.21 Aligned_cols=41 Identities=15% Similarity=0.417 Sum_probs=32.5
Q ss_pred CCCCCCCCCCCC------Cc-ccccccccccchhhHHHHHhcCCCCCCCC
Q 024073 216 RTICPLCSQKRA------NP-SVVTVSGFVFCYACIFKYVSQYKRCPVTL 258 (273)
Q Consensus 216 ~~~CpiC~~~~~------np-~~l~~~G~vfCy~Ci~~~~~~~~~CPv~~ 258 (273)
...|..|.+++- +- .+.. |||+|--+|+.....+++ |-+|.
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 999999999999998776 66664
No 267
>KOG4577 consensus Transcription factor LIM3, contains LIM and HOX domains [Transcription]
Probab=25.18 E-value=17 Score=34.08 Aligned_cols=47 Identities=19% Similarity=0.484 Sum_probs=26.9
Q ss_pred CCCCCCCCCCCcccccccccccchhhHHHHHhcCC-CCCCCCCCCCcCCeee
Q 024073 218 ICPLCSQKRANPSVVTVSGFVFCYACIFKYVSQYK-RCPVTLMPATVEQIRR 268 (273)
Q Consensus 218 ~CpiC~~~~~np~~l~~~G~vfCy~Ci~~~~~~~~-~CPv~~~~~~~~~l~r 268 (273)
+|.-|...+.+-+-.. -|-|||.. +|.++.| +|-.|.+-+-..+++|
T Consensus 62 kCs~C~~qL~drCFsR-~~s~yCke---dFfKrfGTKCsaC~~GIpPtqVVR 109 (383)
T KOG4577|consen 62 KCSDCHDQLADRCFSR-EGSVYCKE---DFFKRFGTKCSACQEGIPPTQVVR 109 (383)
T ss_pred chhhhhhHHHHHHhhc-CCceeehH---HHHHHhCCcchhhcCCCChHHHHH
Confidence 4666666666665554 66666653 4555543 5777766555555443
No 268
>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=24.97 E-value=36 Score=23.81 Aligned_cols=30 Identities=17% Similarity=0.150 Sum_probs=20.1
Q ss_pred CCCCCCCCCCCCcccccccccccchhhHHHHHhcCCCCCCCCCCC
Q 024073 217 TICPLCSQKRANPSVVTVSGFVFCYACIFKYVSQYKRCPVTLMPA 261 (273)
Q Consensus 217 ~~CpiC~~~~~np~~l~~~G~vfCy~Ci~~~~~~~~~CPv~~~~~ 261 (273)
..||.|+..+.-|.... |- --.||.||..+
T Consensus 3 ~~CP~CG~~iev~~~~~--Ge-------------iV~Cp~CGael 32 (54)
T TIGR01206 3 FECPDCGAEIELENPEL--GE-------------LVICDECGAEL 32 (54)
T ss_pred cCCCCCCCEEecCCCcc--CC-------------EEeCCCCCCEE
Confidence 58999999876664321 32 23788888654
No 269
>PF05566 Pox_vIL-18BP: Orthopoxvirus interleukin 18 binding protein; InterPro: IPR008791 Interleukin-18 (IL-18) is a proinflammatory cytokine that plays a key role in the activation of natural killer and T helper 1 cell responses principally by inducing interferon-gamma (IFN-gamma). Several poxvirus genes encode proteins with sequence similarity to IL-18BPs. It has been shown that vaccinia, ectromelia and cowpox viruses secrete from infected cells a soluble IL-18BP (vIL-18BP) that may modulate the host antiviral response. The expression of vIL-18BPs by distinct poxvirus genera that cause local or general viral dissemination, or persistent or acute infections in the host, emphasises the importance of IL-18 in response to viral infections [].; PDB: 3F62_A.
Probab=24.82 E-value=26 Score=28.21 Aligned_cols=20 Identities=30% Similarity=0.906 Sum_probs=1.4
Q ss_pred ccchhhHHHHHhcC-CCCCCC
Q 024073 238 VFCYACIFKYVSQY-KRCPVT 257 (273)
Q Consensus 238 vfCy~Ci~~~~~~~-~~CPv~ 257 (273)
.|||.|.+.|++-+ .+||-=
T Consensus 8 af~~gC~~~~~n~~e~kc~nl 28 (126)
T PF05566_consen 8 AFMFGCVHSYVNADEHKCPNL 28 (126)
T ss_dssp -------------S---S---
T ss_pred HHHhcccccccccccccCCCe
Confidence 59999999999865 688843
No 270
>COG4338 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=24.76 E-value=21 Score=24.58 Aligned_cols=11 Identities=36% Similarity=1.032 Sum_probs=6.1
Q ss_pred CCCCCCCCCCC
Q 024073 216 RTICPLCSQKR 226 (273)
Q Consensus 216 ~~~CpiC~~~~ 226 (273)
..+||+|+.++
T Consensus 12 ~KICpvCqRPF 22 (54)
T COG4338 12 DKICPVCQRPF 22 (54)
T ss_pred hhhhhhhcCch
Confidence 34666666543
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=24.55 E-value=25 Score=21.09 Aligned_cols=10 Identities=30% Similarity=0.474 Sum_probs=4.9
Q ss_pred CCCCCCCCCC
Q 024073 253 RCPVTLMPAT 262 (273)
Q Consensus 253 ~CPv~~~~~~ 262 (273)
.||+|+.++-
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 4899997653
No 272
>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=24.37 E-value=32 Score=21.51 Aligned_cols=12 Identities=25% Similarity=0.503 Sum_probs=7.0
Q ss_pred CCCCCCCCCCCc
Q 024073 218 ICPLCSQKRANP 229 (273)
Q Consensus 218 ~CpiC~~~~~np 229 (273)
.||-|+....-+
T Consensus 4 ~CP~C~~~~~v~ 15 (38)
T TIGR02098 4 QCPNCKTSFRVV 15 (38)
T ss_pred ECCCCCCEEEeC
Confidence 577777754333
No 273
>COG4530 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=24.33 E-value=43 Score=27.05 Aligned_cols=25 Identities=24% Similarity=0.364 Sum_probs=21.0
Q ss_pred CCCCCCCCCCCC----CCccccccccccc
Q 024073 215 DRTICPLCSQKR----ANPSVVTVSGFVF 239 (273)
Q Consensus 215 ~~~~CpiC~~~~----~np~~l~~~G~vf 239 (273)
.+.+||-|++.+ ++|.|++-||..|
T Consensus 8 tKridPetg~KFYDLNrdPiVsPytG~s~ 36 (129)
T COG4530 8 TKRIDPETGKKFYDLNRDPIVSPYTGKSY 36 (129)
T ss_pred ccccCccccchhhccCCCccccCcccccc
Confidence 367899999975 5789999999988
No 274
>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=24.32 E-value=28 Score=21.42 Aligned_cols=20 Identities=30% Similarity=0.604 Sum_probs=7.3
Q ss_pred CCCCCCCCCCC--c--cccccccc
Q 024073 218 ICPLCSQKRAN--P--SVVTVSGF 237 (273)
Q Consensus 218 ~CpiC~~~~~n--p--~~l~~~G~ 237 (273)
.||.|+..-+- - -|++.|||
T Consensus 4 ~Cp~C~se~~y~D~~~~vCp~C~~ 27 (30)
T PF08274_consen 4 KCPLCGSEYTYEDGELLVCPECGH 27 (30)
T ss_dssp --TTT-----EE-SSSEEETTTTE
T ss_pred CCCCCCCcceeccCCEEeCCcccc
Confidence 58888875432 2 25555665
No 275
>KOG2272 consensus Focal adhesion protein PINCH-1, contains LIM domains [Signal transduction mechanisms; Cytoskeleton]
Probab=24.05 E-value=35 Score=31.51 Aligned_cols=38 Identities=18% Similarity=0.380 Sum_probs=30.2
Q ss_pred CCCCCCCCCCCCCCcccccccccccchhhHHHHHhcCCCCCCCC
Q 024073 215 DRTICPLCSQKRANPSVVTVSGFVFCYACIFKYVSQYKRCPVTL 258 (273)
Q Consensus 215 ~~~~CpiC~~~~~np~~l~~~G~vfCy~Ci~~~~~~~~~CPv~~ 258 (273)
++..|.-|++.++..+-. +-|-.||.+|-. ...||||+
T Consensus 162 yHFkCt~C~keL~sdaRe-vk~eLyClrChD-----~mgipiCg 199 (332)
T KOG2272|consen 162 YHFKCTTCGKELTSDARE-VKGELYCLRCHD-----KMGIPICG 199 (332)
T ss_pred cceecccccccccchhhh-hccceecccccc-----ccCCcccc
Confidence 689999999999887653 489999999964 35677776
No 276
>PRK05654 acetyl-CoA carboxylase subunit beta; Validated
Probab=24.02 E-value=28 Score=32.57 Aligned_cols=24 Identities=33% Similarity=0.483 Sum_probs=17.0
Q ss_pred CCCCCCCCCCCC------Cccccccccccc
Q 024073 216 RTICPLCSQKRA------NPSVVTVSGFVF 239 (273)
Q Consensus 216 ~~~CpiC~~~~~------np~~l~~~G~vf 239 (273)
-.+||-|++.+- |--||+.|||.|
T Consensus 27 ~~~c~~c~~~~~~~~l~~~~~vc~~c~~h~ 56 (292)
T PRK05654 27 WTKCPSCGQVLYRKELEANLNVCPKCGHHM 56 (292)
T ss_pred eeECCCccchhhHHHHHhcCCCCCCCCCCe
Confidence 468999998754 334777777766
No 277
>PRK01110 rpmF 50S ribosomal protein L32; Validated
Probab=23.88 E-value=38 Score=24.15 Aligned_cols=21 Identities=10% Similarity=0.134 Sum_probs=16.0
Q ss_pred CCCCCCCCCCCCCccccccccc
Q 024073 216 RTICPLCSQKRANPSVVTVSGF 237 (273)
Q Consensus 216 ~~~CpiC~~~~~np~~l~~~G~ 237 (273)
-..||-|++...-..++. ||+
T Consensus 27 ~~~c~~cg~~~~pH~vc~-cG~ 47 (60)
T PRK01110 27 LSVDKTTGEYHLPHHVSP-KGY 47 (60)
T ss_pred eeEcCCCCceeccceecC-Ccc
Confidence 457888888887777777 774
No 278
>PRK08579 anaerobic ribonucleoside triphosphate reductase; Provisional
Probab=23.82 E-value=13 Score=38.37 Aligned_cols=24 Identities=25% Similarity=0.494 Sum_probs=14.9
Q ss_pred ccccchhhHHHHHhcCCCCCCCCC
Q 024073 236 GFVFCYACIFKYVSQYKRCPVTLM 259 (273)
Q Consensus 236 G~vfCy~Ci~~~~~~~~~CPv~~~ 259 (273)
+..+|..|-+.+...+..||+||.
T Consensus 567 ~~~~C~~CG~~~~g~~~~CP~CGs 590 (625)
T PRK08579 567 AITVCNKCGRSTTGLYTRCPRCGS 590 (625)
T ss_pred CCccCCCCCCccCCCCCcCcCCCC
Confidence 344555555444445678999985
No 279
>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=23.78 E-value=54 Score=25.54 Aligned_cols=37 Identities=30% Similarity=0.528 Sum_probs=28.4
Q ss_pred CCCCCCCCCCCCCcccccccccccchhhHHHHHhcCCCCCCCCCCC
Q 024073 216 RTICPLCSQKRANPSVVTVSGFVFCYACIFKYVSQYKRCPVTLMPA 261 (273)
Q Consensus 216 ~~~CpiC~~~~~np~~l~~~G~vfCy~Ci~~~~~~~~~CPv~~~~~ 261 (273)
...|-.|.+. +|.. .-|+.|-+|+. +.+.|+-|+++.
T Consensus 55 p~kC~~C~qk----tVk~-AYh~iC~~Ca~----~~~vCaKC~k~~ 91 (92)
T PF10217_consen 55 PKKCNKCQQK----TVKH-AYHVICDPCAK----ELKVCAKCGKPP 91 (92)
T ss_pred Cccccccccc----hHHH-HHHHHHHHHHH----hhccCcccCCCC
Confidence 3578888865 3544 78999999998 568999998763
No 280
>PRK02935 hypothetical protein; Provisional
Probab=23.77 E-value=49 Score=26.48 Aligned_cols=15 Identities=20% Similarity=0.363 Sum_probs=10.3
Q ss_pred cCCCCCCCCCCCCcC
Q 024073 250 QYKRCPVTLMPATVE 264 (273)
Q Consensus 250 ~~~~CPv~~~~~~~~ 264 (273)
+...|.-|++|++.+
T Consensus 85 rvD~CM~C~~PLTLd 99 (110)
T PRK02935 85 RVDACMHCNQPLTLD 99 (110)
T ss_pred ceeecCcCCCcCCcC
Confidence 335788888887754
No 281
>TIGR03655 anti_R_Lar restriction alleviation protein, Lar family. Restriction alleviation proteins provide a countermeasure to host cell restriction enzyme defense against foreign DNA such as phage or plasmids. This family consists of homologs to the phage antirestriction protein Lar, and most members belong to phage genomes or prophage regions of bacterial genomes.
Probab=23.33 E-value=42 Score=22.89 Aligned_cols=10 Identities=30% Similarity=0.959 Sum_probs=7.2
Q ss_pred CCCCCCCCCC
Q 024073 218 ICPLCSQKRA 227 (273)
Q Consensus 218 ~CpiC~~~~~ 227 (273)
-||-|+..-.
T Consensus 3 PCPfCGg~~~ 12 (53)
T TIGR03655 3 PCPFCGGADV 12 (53)
T ss_pred CCCCCCCcce
Confidence 3999998533
No 282
>COG2176 PolC DNA polymerase III, alpha subunit (gram-positive type) [DNA replication, recombination, and repair]
Probab=23.16 E-value=78 Score=35.38 Aligned_cols=37 Identities=32% Similarity=0.550 Sum_probs=26.9
Q ss_pred CCCCCCCCC--CCCCcccccccccccchhhHHHHHhcCCCCCCCCCCCCcC
Q 024073 216 RTICPLCSQ--KRANPSVVTVSGFVFCYACIFKYVSQYKRCPVTLMPATVE 264 (273)
Q Consensus 216 ~~~CpiC~~--~~~np~~l~~~G~vfCy~Ci~~~~~~~~~CPv~~~~~~~~ 264 (273)
++.||-|.. -++|+.+ . +||-- .++.||.||.|+..+
T Consensus 914 HY~Cp~Cky~Ef~~d~sv-g-sGfDL----------pdK~CPkCg~pl~kD 952 (1444)
T COG2176 914 HYLCPECKYSEFIDDGSV-G-SGFDL----------PDKDCPKCGTPLKKD 952 (1444)
T ss_pred cccCCCCceeeeecCCCc-C-CCCCC----------CCCCCCcCCCccccC
Confidence 789999987 3566655 3 66532 468999999987654
No 283
>PF08882 Acetone_carb_G: Acetone carboxylase gamma subunit; InterPro: IPR014979 Acetone carboxylase is the key enzyme of bacterial acetone metabolism, catalysing the condensation of acetone and CO2 to form acetoacetate [] according to the following reaction: CH3COCH3 + CO2 + ATP = CH3COCH2COO- + AMP + 2P(i) + H+ It has the subunit composition: (alpha(2)beta(2)gamma(2) multimers of 85kDa, 78kDa, and 20kDa subunits). It is expressed to high levels (17 to 25% of soluble protein) in cells grown with acetone as the carbon source but are not present at detectable levels in cells grown with other carbon sources []. Acetone carboxylase may enable Helicobacter pylori to survive off acetone in the stomach of humans and other mammals where it is the etiological agent of peptic ulcer disease []. This entry represents the family of gamma subunit-related acetone carboxylase proteins.
Probab=22.97 E-value=33 Score=27.64 Aligned_cols=11 Identities=27% Similarity=0.537 Sum_probs=8.4
Q ss_pred ccccccccccch
Q 024073 230 SVVTVSGFVFCY 241 (273)
Q Consensus 230 ~~l~~~G~vfCy 241 (273)
+.|. |||+||-
T Consensus 25 vkc~-CGh~f~d 35 (112)
T PF08882_consen 25 VKCD-CGHEFCD 35 (112)
T ss_pred eecc-CCCeecC
Confidence 4555 9999995
No 284
>COG1656 Uncharacterized conserved protein [Function unknown]
Probab=22.73 E-value=37 Score=29.21 Aligned_cols=15 Identities=20% Similarity=0.541 Sum_probs=11.5
Q ss_pred CCCCCCCCCCCCCCc
Q 024073 215 DRTICPLCSQKRANP 229 (273)
Q Consensus 215 ~~~~CpiC~~~~~np 229 (273)
+...||.|+.++...
T Consensus 96 e~~RCp~CN~~L~~v 110 (165)
T COG1656 96 EFSRCPECNGELEKV 110 (165)
T ss_pred ccccCcccCCEeccC
Confidence 456899999987655
No 285
>COG4098 comFA Superfamily II DNA/RNA helicase required for DNA uptake (late competence protein) [DNA replication, recombination, and repair]
Probab=22.67 E-value=31 Score=33.46 Aligned_cols=30 Identities=17% Similarity=0.559 Sum_probs=24.9
Q ss_pred CCCCCCCCCC-CCCCcccccccccccchhhHH
Q 024073 215 DRTICPLCSQ-KRANPSVVTVSGFVFCYACIF 245 (273)
Q Consensus 215 ~~~~CpiC~~-~~~np~~l~~~G~vfCy~Ci~ 245 (273)
.+..|--|++ .+.+-+-++ ||-.||..|+.
T Consensus 38 gk~~C~RC~~~~~~~~~~lp-~~~~YCr~Cl~ 68 (441)
T COG4098 38 GKYRCNRCGNTHIELFAKLP-CGCLYCRNCLM 68 (441)
T ss_pred CcEEehhcCCcchhhhcccc-cceEeehhhhh
Confidence 4679999994 566667777 99999999997
No 286
>COG0675 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=22.64 E-value=40 Score=30.49 Aligned_cols=25 Identities=24% Similarity=0.478 Sum_probs=14.6
Q ss_pred CCCCCCCCCCCCCCc-ccccccccccc
Q 024073 215 DRTICPLCSQKRANP-SVVTVSGFVFC 240 (273)
Q Consensus 215 ~~~~CpiC~~~~~np-~~l~~~G~vfC 240 (273)
++..||.|+. +..- -.|+.||+++.
T Consensus 308 tS~~C~~cg~-~~~r~~~C~~cg~~~~ 333 (364)
T COG0675 308 TSKTCPCCGH-LSGRLFKCPRCGFVHD 333 (364)
T ss_pred CcccccccCC-ccceeEECCCCCCeeh
Confidence 4678999999 3222 24444555543
No 287
>smart00778 Prim_Zn_Ribbon Zinc-binding domain of primase-helicase. This region represents the zinc binding domain. It is found in the N-terminal region of the bacteriophage P4 alpha protein, which is a multifunctional protein with origin recognition, helicase and primase activities.
Probab=22.45 E-value=55 Score=21.07 Aligned_cols=28 Identities=25% Similarity=0.456 Sum_probs=16.9
Q ss_pred CCCCCCCCCCCCCcc-cccccccccchhh
Q 024073 216 RTICPLCSQKRANPS-VVTVSGFVFCYAC 243 (273)
Q Consensus 216 ~~~CpiC~~~~~np~-~l~~~G~vfCy~C 243 (273)
+.-||+|+..=..-- --...|+-+|..|
T Consensus 3 ~~pCP~CGG~DrFr~~d~~g~G~~~C~~C 31 (37)
T smart00778 3 HGPCPNCGGSDRFRFDDKDGRGTWFCSVC 31 (37)
T ss_pred ccCCCCCCCccccccccCCCCcCEEeCCC
Confidence 345999988422221 0113688888887
No 288
>COG4855 Uncharacterized protein conserved in archaea [Function unknown]
Probab=22.36 E-value=9.6 Score=28.02 Aligned_cols=27 Identities=19% Similarity=0.507 Sum_probs=13.7
Q ss_pred CCCCCCCCCCCCCc---ccccccccccchh
Q 024073 216 RTICPLCSQKRANP---SVVTVSGFVFCYA 242 (273)
Q Consensus 216 ~~~CpiC~~~~~np---~~l~~~G~vfCy~ 242 (273)
..+|-+|.+.=+|. .++-+||--.|..
T Consensus 7 ~mKCY~C~eeGKDtdAV~iCIVCG~GlC~E 36 (76)
T COG4855 7 MMKCYDCAEEGKDTDAVGICIVCGMGLCME 36 (76)
T ss_pred hhHHHHHHHhCCCcccEEEEEEeCchHHHH
Confidence 34566666544333 2334466666554
No 289
>PLN03086 PRLI-interacting factor K; Provisional
Probab=22.14 E-value=32 Score=35.19 Aligned_cols=15 Identities=20% Similarity=0.401 Sum_probs=9.6
Q ss_pred CCCCCCCCCCCCCCc
Q 024073 215 DRTICPLCSQKRANP 229 (273)
Q Consensus 215 ~~~~CpiC~~~~~np 229 (273)
+...|+-|...+...
T Consensus 406 ~~V~C~NC~~~i~l~ 420 (567)
T PLN03086 406 DTVECRNCKHYIPSR 420 (567)
T ss_pred CeEECCCCCCccchh
Confidence 455688887766443
No 290
>PRK00418 DNA gyrase inhibitor; Reviewed
Probab=22.11 E-value=45 Score=24.07 Aligned_cols=10 Identities=30% Similarity=0.637 Sum_probs=7.3
Q ss_pred CCCCCCCCCC
Q 024073 252 KRCPVTLMPA 261 (273)
Q Consensus 252 ~~CPv~~~~~ 261 (273)
.+||+|++++
T Consensus 7 v~CP~C~k~~ 16 (62)
T PRK00418 7 VNCPTCGKPV 16 (62)
T ss_pred ccCCCCCCcc
Confidence 4688888775
No 291
>COG4647 AcxC Acetone carboxylase, gamma subunit [Secondary metabolites biosynthesis, transport, and catabolism]
Probab=21.93 E-value=32 Score=28.56 Aligned_cols=21 Identities=14% Similarity=0.249 Sum_probs=13.4
Q ss_pred CCCCCCCCcccccccccccchh
Q 024073 221 LCSQKRANPSVVTVSGFVFCYA 242 (273)
Q Consensus 221 iC~~~~~np~~l~~~G~vfCy~ 242 (273)
||..+-..-+-|. |||.||-.
T Consensus 62 i~qs~~~rv~rce-cghsf~d~ 82 (165)
T COG4647 62 ICQSAQKRVIRCE-CGHSFGDY 82 (165)
T ss_pred EEecccccEEEEe-ccccccCh
Confidence 4555444445666 99999953
No 292
>PF10621 FpoO: F420H2 dehydrogenase subunit FpoO ; InterPro: IPR018288 This entry represents the FpoO subunit of membrane-bound multi-subunit F420H2 dehydrogenase, which oxidises the reduced coenzyme F420H2 to coenzyme F420 and feeds the electrons via an FeS cluster into an energy-conserving electron transport chain [, ]. This enzyme plays a role in the methanogenic pathway in methanogenic archaea. Reduced coenzyme F420H2 is the major cytoplasmic electron carrier of methanogens and a reversible hydride donor, much like NADH []. F420H2 + COB-S-S-CoM = F420 + CoM-SH + CoB-SH Where CoB-S-S-CoM (the heterosulphide of 2-mercaptoethanesulphonate and 7-mercaptoheptanoylthreonine phosphate) is the terminal electron acceptor of the methanogenic pathway, and is reduced with the concomitant generation of a transmembrane proton potential and ATP synthesis. The FpoO subunit of F420H2 dehydrogenase probably participates in the reduction of methanophenazine, where it acts as a special mechanism for the reduction of the methanogenic cofactor [].
Probab=21.90 E-value=71 Score=25.78 Aligned_cols=14 Identities=7% Similarity=0.223 Sum_probs=11.0
Q ss_pred cCCCCCCCCCCCCc
Q 024073 250 QYKRCPVTLMPATV 263 (273)
Q Consensus 250 ~~~~CPv~~~~~~~ 263 (273)
..++|-.||.+..+
T Consensus 59 ~~gKC~LCG~kt~l 72 (119)
T PF10621_consen 59 RSGKCDLCGKKTQL 72 (119)
T ss_pred cccceeccCCccee
Confidence 46899999987654
No 293
>PRK09710 lar restriction alleviation and modification protein; Reviewed
Probab=21.84 E-value=37 Score=24.68 Aligned_cols=28 Identities=18% Similarity=0.380 Sum_probs=18.7
Q ss_pred CCCCCCCCCCCcccccccccccchhhHH
Q 024073 218 ICPLCSQKRANPSVVTVSGFVFCYACIF 245 (273)
Q Consensus 218 ~CpiC~~~~~np~~l~~~G~vfCy~Ci~ 245 (273)
-||-|+...........-.+|.|-.|-.
T Consensus 8 PCPFCG~~~~~v~~~~g~~~v~C~~CgA 35 (64)
T PRK09710 8 PCPFCGCPSVTVKAISGYYRAKCNGCES 35 (64)
T ss_pred CCCCCCCceeEEEecCceEEEEcCCCCc
Confidence 4999999877776543344566766643
No 294
>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=21.67 E-value=84 Score=20.31 Aligned_cols=32 Identities=22% Similarity=0.729 Sum_probs=21.2
Q ss_pred CCCCCCCCC-Ccccccccc---cccchhhHHHHHhc
Q 024073 219 CPLCSQKRA-NPSVVTVSG---FVFCYACIFKYVSQ 250 (273)
Q Consensus 219 CpiC~~~~~-np~~l~~~G---~vfCy~Ci~~~~~~ 250 (273)
|-.|+++|. +|.+...=| |.-|-.|..++.++
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 778999887 666665322 33458888877653
No 295
>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]
Probab=21.65 E-value=37 Score=35.82 Aligned_cols=44 Identities=18% Similarity=0.385 Sum_probs=30.1
Q ss_pred CCCCCCCCCCCCCc------ccccccccccchhhHHHHHhcCCCCCCCCCC
Q 024073 216 RTICPLCSQKRANP------SVVTVSGFVFCYACIFKYVSQYKRCPVTLMP 260 (273)
Q Consensus 216 ~~~CpiC~~~~~np------~~l~~~G~vfCy~Ci~~~~~~~~~CPv~~~~ 260 (273)
...|.-|+...+-| +.=...|...|.-|-++ -..-..||-|+-.
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 35577777666655 22244788999999887 3334799999965
No 296
>PRK00432 30S ribosomal protein S27ae; Validated
Probab=21.47 E-value=61 Score=22.14 Aligned_cols=9 Identities=33% Similarity=1.124 Sum_probs=7.2
Q ss_pred CCCCCCCCC
Q 024073 216 RTICPLCSQ 224 (273)
Q Consensus 216 ~~~CpiC~~ 224 (273)
...||-|+.
T Consensus 20 ~~fCP~Cg~ 28 (50)
T PRK00432 20 NKFCPRCGS 28 (50)
T ss_pred cCcCcCCCc
Confidence 458999987
No 297
>PRK00133 metG methionyl-tRNA synthetase; Reviewed
Probab=21.38 E-value=66 Score=33.37 Aligned_cols=45 Identities=11% Similarity=0.273 Sum_probs=28.5
Q ss_pred CCCCCCCCCCCCCcccccccccccchhhHHHHHhcCCCCCCCCCCCCcCC
Q 024073 216 RTICPLCSQKRANPSVVTVSGFVFCYACIFKYVSQYKRCPVTLMPATVEQ 265 (273)
Q Consensus 216 ~~~CpiC~~~~~np~~l~~~G~vfCy~Ci~~~~~~~~~CPv~~~~~~~~~ 265 (273)
.+.||.|+..-.+...|..||+.+= +.. + .+.+|.+|+.+.....
T Consensus 139 ~g~cp~C~~~d~~g~~ce~cg~~~~--~~~--l-~~~~~~~~g~~~e~~~ 183 (673)
T PRK00133 139 KGTCPKCGAEDQYGDNCEVCGATYS--PTE--L-INPKSAISGATPVLKE 183 (673)
T ss_pred ecccCCCCCcccCCchhhhccccCC--hHh--h-cCCccccCCCcceEEe
Confidence 4679999987444555666887642 111 1 3478999998765433
No 298
>TIGR00595 priA primosomal protein N'. All proteins in this family for which functions are known are components of the primosome which is involved in replication, repair, and recombination.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=21.21 E-value=64 Score=32.36 Aligned_cols=25 Identities=24% Similarity=0.362 Sum_probs=16.2
Q ss_pred cccccchhhHHHHHhcCCCCCCCCCC
Q 024073 235 SGFVFCYACIFKYVSQYKRCPVTLMP 260 (273)
Q Consensus 235 ~G~vfCy~Ci~~~~~~~~~CPv~~~~ 260 (273)
.+...|..|-+..- -...||.|+..
T Consensus 238 ~~~l~Ch~Cg~~~~-~~~~Cp~C~s~ 262 (505)
T TIGR00595 238 EGKLRCHYCGYQEP-IPKTCPQCGSE 262 (505)
T ss_pred CCeEEcCCCcCcCC-CCCCCCCCCCC
Confidence 45667777775432 23689999853
No 299
>PF06844 DUF1244: Protein of unknown function (DUF1244); InterPro: IPR009654 This family consists of several short bacterial proteins of around 100 residues in length. The function of this family is unknown.; PDB: 2O35_A 3FYB_B.
Probab=21.02 E-value=52 Score=24.11 Aligned_cols=13 Identities=31% Similarity=0.828 Sum_probs=9.2
Q ss_pred ccchhhHHHHHhc
Q 024073 238 VFCYACIFKYVSQ 250 (273)
Q Consensus 238 vfCy~Ci~~~~~~ 250 (273)
-||.-|+.+|...
T Consensus 11 gFCRNCLskWy~~ 23 (68)
T PF06844_consen 11 GFCRNCLSKWYRE 23 (68)
T ss_dssp S--HHHHHHHHHH
T ss_pred HHHHHHHHHHHHH
Confidence 3999999999863
No 300
>KOG2906 consensus RNA polymerase III subunit C11 [Transcription]
Probab=20.85 E-value=39 Score=26.71 Aligned_cols=23 Identities=22% Similarity=0.453 Sum_probs=13.3
Q ss_pred CCCCCCCCCCCc-------ccccccccccc
Q 024073 218 ICPLCSQKRANP-------SVVTVSGFVFC 240 (273)
Q Consensus 218 ~CpiC~~~~~np-------~~l~~~G~vfC 240 (273)
.||.|+.-+.-. -.+.+|+|||=
T Consensus 3 FCP~Cgn~Live~g~~~~rf~C~tCpY~~~ 32 (105)
T KOG2906|consen 3 FCPTCGNMLIVESGESCNRFSCRTCPYVFP 32 (105)
T ss_pred ccCCCCCEEEEecCCeEeeEEcCCCCceee
Confidence 588888765432 34445555553
No 301
>PF13597 NRDD: Anaerobic ribonucleoside-triphosphate reductase; PDB: 1HK8_A 1H78_A 1H7A_A 1H79_A 1H7B_A.
Probab=20.76 E-value=23 Score=35.93 Aligned_cols=29 Identities=21% Similarity=0.372 Sum_probs=11.4
Q ss_pred cchhhHHHHHhcCCCCCCCCCCCCcCCeeeC
Q 024073 239 FCYACIFKYVSQYKRCPVTLMPATVEQIRRL 269 (273)
Q Consensus 239 fCy~Ci~~~~~~~~~CPv~~~~~~~~~l~ri 269 (273)
.|..|-+.-.. +..||+||.+- .+-++||
T Consensus 493 ~C~~CG~~~~~-~~~CP~CGs~~-~~~~~Rv 521 (546)
T PF13597_consen 493 ICPDCGYIGGE-GDKCPKCGSEN-IEVYSRV 521 (546)
T ss_dssp EETTT---S---EEE-CCC-----EEEEB-S
T ss_pred cccCCCcCCCC-CCCCCCCCCcc-cceEEEe
Confidence 45555554444 67899999663 4555555
No 302
>PRK05452 anaerobic nitric oxide reductase flavorubredoxin; Provisional
Probab=20.55 E-value=48 Score=32.99 Aligned_cols=13 Identities=23% Similarity=0.350 Sum_probs=9.4
Q ss_pred HhcCCCCCCCCCC
Q 024073 248 VSQYKRCPVTLMP 260 (273)
Q Consensus 248 ~~~~~~CPv~~~~ 260 (273)
|..+=+||+|+.+
T Consensus 455 lp~~~~cp~c~~~ 467 (479)
T PRK05452 455 VPDNFLCPECSLG 467 (479)
T ss_pred CCCCCcCcCCCCc
Confidence 3345699999965
No 303
>PRK08665 ribonucleotide-diphosphate reductase subunit alpha; Validated
Probab=20.33 E-value=58 Score=34.49 Aligned_cols=25 Identities=28% Similarity=0.636 Sum_probs=15.3
Q ss_pred CCCCCCCCCCCCCc---ccccccccccc
Q 024073 216 RTICPLCSQKRANP---SVVTVSGFVFC 240 (273)
Q Consensus 216 ~~~CpiC~~~~~np---~~l~~~G~vfC 240 (273)
...||-|+..+... .+|..|||--|
T Consensus 724 ~~~Cp~Cg~~l~~~~GC~~C~~CG~skC 751 (752)
T PRK08665 724 RGACPECGSILEHEEGCVVCHSCGYSKC 751 (752)
T ss_pred CCCCCCCCcccEECCCCCcCCCCCCCCC
Confidence 35799998765432 24455666554
No 304
>COG1675 TFA1 Transcription initiation factor IIE, alpha subunit [Transcription]
Probab=20.12 E-value=46 Score=28.93 Aligned_cols=32 Identities=19% Similarity=0.287 Sum_probs=19.5
Q ss_pred CCCCCCCCCCCCCCcccccccccccchhhHHHHHhcCCCCCCCCCCCC
Q 024073 215 DRTICPLCSQKRANPSVVTVSGFVFCYACIFKYVSQYKRCPVTLMPAT 262 (273)
Q Consensus 215 ~~~~CpiC~~~~~np~~l~~~G~vfCy~Ci~~~~~~~~~CPv~~~~~~ 262 (273)
.-+.||.|.-..+--.+.. ...+||.||..+.
T Consensus 112 ~~y~C~~~~~r~sfdeA~~----------------~~F~Cp~Cg~~L~ 143 (176)
T COG1675 112 NYYVCPNCHVKYSFDEAME----------------LGFTCPKCGEDLE 143 (176)
T ss_pred CceeCCCCCCcccHHHHHH----------------hCCCCCCCCchhh
Confidence 3567877776655444433 2367888886654
No 305
>PF03660 PHF5: PHF5-like protein; InterPro: IPR005345 Phf5 is a member of a novel murine multigene family that is highly conserved during evolution and belongs to the superfamily of PHD-finger proteins. At least one example, from Mus musculus (Mouse), may act as a chromatin-associated protein []. The Schizosaccharomyces pombe (Fission yeast) ini1 gene is essential, required for splicing []. It is localised in the nucleus, but not detected in the nucleolus and can be complemented by human ini1 []. The proteins of this family contain five CXXC motifs.; PDB: 2K0A_A.
Probab=20.09 E-value=43 Score=26.64 Aligned_cols=19 Identities=16% Similarity=0.186 Sum_probs=6.4
Q ss_pred CCCCCCCCCCCCcCCeeeC
Q 024073 251 YKRCPVTLMPATVEQIRRL 269 (273)
Q Consensus 251 ~~~CPv~~~~~~~~~l~ri 269 (273)
.|+||+|...+....++||
T Consensus 27 dGkCpiCDS~Vrp~~~VrI 45 (106)
T PF03660_consen 27 DGKCPICDSYVRPCTKVRI 45 (106)
T ss_dssp TT--TTT-------EE-EE
T ss_pred CCcccccCCccCCcceEEE
Confidence 5888888876666666665
Done!