Query 029888
Match_columns 186
No_of_seqs 202 out of 1139
Neff 6.3
Searched_HMMs 46136
Date Fri Mar 29 05:14:18 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/029888.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/029888hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF11789 zf-Nse: Zinc-finger o 99.8 1E-20 2.2E-25 126.9 2.2 57 77-140 1-57 (57)
2 KOG2979 Protein involved in DN 99.6 2.7E-16 5.9E-21 132.6 3.6 75 86-164 172-248 (262)
3 PF04564 U-box: U-box domain; 99.6 4.2E-15 9.1E-20 104.0 4.5 69 90-166 4-72 (73)
4 smart00504 Ubox Modified RING 99.5 1.1E-14 2.4E-19 97.8 5.1 62 91-161 2-63 (63)
5 COG5627 MMS21 DNA repair prote 99.3 1.4E-12 3.1E-17 109.0 4.6 96 55-157 148-252 (275)
6 PF15227 zf-C3HC4_4: zinc fing 99.2 6.4E-12 1.4E-16 79.2 2.9 40 93-136 1-41 (42)
7 PLN03208 E3 ubiquitin-protein 99.2 3.1E-11 6.6E-16 98.9 5.0 56 90-151 18-86 (193)
8 KOG0320 Predicted E3 ubiquitin 99.1 5.8E-11 1.3E-15 95.7 2.8 53 90-149 131-183 (187)
9 TIGR00599 rad18 DNA repair pro 99.1 2.2E-10 4.7E-15 103.2 5.8 66 90-164 26-91 (397)
10 PF13923 zf-C3HC4_2: Zinc fing 99.0 3.8E-10 8.2E-15 69.6 3.2 38 93-136 1-38 (39)
11 PF14835 zf-RING_6: zf-RING of 98.8 8.2E-10 1.8E-14 75.4 0.6 59 90-158 7-65 (65)
12 TIGR00570 cdk7 CDK-activating 98.8 1.3E-08 2.9E-13 88.8 6.3 67 91-164 4-78 (309)
13 PF00097 zf-C3HC4: Zinc finger 98.8 7.1E-09 1.5E-13 64.1 3.3 40 93-136 1-40 (41)
14 COG5222 Uncharacterized conser 98.8 9.9E-09 2.1E-13 89.0 5.2 69 88-163 272-341 (427)
15 KOG2164 Predicted E3 ubiquitin 98.7 6.5E-09 1.4E-13 95.2 3.3 56 90-151 186-243 (513)
16 KOG0823 Predicted E3 ubiquitin 98.7 1.3E-08 2.8E-13 85.2 3.9 56 89-150 46-101 (230)
17 KOG0287 Postreplication repair 98.6 1.1E-08 2.4E-13 89.9 2.3 63 90-161 23-85 (442)
18 PF13639 zf-RING_2: Ring finge 98.6 1.7E-08 3.8E-13 63.5 1.3 43 92-140 2-44 (44)
19 PF13445 zf-RING_UBOX: RING-ty 98.6 3.2E-08 6.8E-13 62.7 2.4 38 93-135 1-43 (43)
20 cd00162 RING RING-finger (Real 98.5 1.6E-07 3.5E-12 57.4 3.6 44 92-142 1-44 (45)
21 KOG2177 Predicted E3 ubiquitin 98.5 1.4E-07 3E-12 77.4 4.2 67 90-167 13-79 (386)
22 COG5432 RAD18 RING-finger-cont 98.4 1.4E-07 3.1E-12 81.6 3.1 63 90-161 25-87 (391)
23 PHA02929 N1R/p28-like protein; 98.4 2.4E-07 5.2E-12 78.5 3.7 47 90-144 174-227 (238)
24 PF02891 zf-MIZ: MIZ/SP-RING z 98.4 2.7E-07 6E-12 60.2 2.9 47 89-141 1-49 (50)
25 PF13920 zf-C3HC4_3: Zinc fing 98.4 3.4E-07 7.3E-12 59.1 3.2 46 90-144 2-48 (50)
26 KOG0317 Predicted E3 ubiquitin 98.4 2.3E-07 5E-12 79.9 3.1 51 90-149 239-289 (293)
27 KOG0978 E3 ubiquitin ligase in 98.3 2.9E-07 6.3E-12 87.6 2.6 54 89-150 642-695 (698)
28 PF14634 zf-RING_5: zinc-RING 98.3 6.6E-07 1.4E-11 56.5 3.2 44 92-141 1-44 (44)
29 smart00184 RING Ring finger. E 98.3 8.1E-07 1.7E-11 52.4 3.4 38 93-136 1-38 (39)
30 KOG0311 Predicted E3 ubiquitin 98.1 5.5E-07 1.2E-11 79.6 -0.3 75 79-161 33-108 (381)
31 COG5574 PEX10 RING-finger-cont 98.0 2.6E-06 5.5E-11 72.8 2.4 54 88-148 213-266 (271)
32 KOG2660 Locus-specific chromos 98.0 3.1E-06 6.7E-11 74.2 2.7 64 89-160 14-81 (331)
33 PHA02926 zinc finger-like prot 98.0 7.1E-06 1.5E-10 68.8 3.8 50 90-144 170-230 (242)
34 KOG0297 TNF receptor-associate 97.9 5.8E-06 1.3E-10 74.7 3.3 65 89-161 20-85 (391)
35 KOG1813 Predicted E3 ubiquitin 97.7 1.9E-05 4.2E-10 68.5 2.7 76 77-163 229-304 (313)
36 COG5152 Uncharacterized conser 97.7 2.7E-05 5.8E-10 64.4 2.6 69 79-158 186-254 (259)
37 KOG2169 Zn-finger transcriptio 97.6 5.7E-05 1.2E-09 72.2 4.9 82 73-163 292-375 (636)
38 PF12678 zf-rbx1: RING-H2 zinc 97.4 0.00013 2.8E-09 51.0 3.1 44 92-140 21-73 (73)
39 KOG2879 Predicted E3 ubiquitin 97.4 0.00012 2.5E-09 63.1 3.2 50 88-143 237-286 (298)
40 PF04641 Rtf2: Rtf2 RING-finge 97.4 0.00018 3.9E-09 61.5 3.9 58 87-150 110-167 (260)
41 KOG1002 Nucleotide excision re 97.3 0.00017 3.7E-09 67.1 2.9 52 90-147 536-589 (791)
42 KOG0826 Predicted E3 ubiquitin 97.2 0.00019 4.1E-09 63.2 2.1 47 90-142 300-346 (357)
43 PF12861 zf-Apc11: Anaphase-pr 97.1 0.00094 2E-08 48.2 4.9 54 88-145 30-83 (85)
44 KOG3039 Uncharacterized conser 97.0 0.00055 1.2E-08 58.4 2.8 54 89-150 220-276 (303)
45 KOG0824 Predicted E3 ubiquitin 96.8 0.00069 1.5E-08 59.1 2.1 50 89-146 6-55 (324)
46 KOG0289 mRNA splicing factor [ 96.7 0.00093 2E-08 60.9 2.6 52 91-150 1-52 (506)
47 COG5220 TFB3 Cdk activating ki 96.7 0.00072 1.6E-08 57.5 1.4 68 89-160 9-84 (314)
48 KOG4159 Predicted E3 ubiquitin 96.6 0.0011 2.4E-08 60.1 2.1 47 89-144 83-129 (398)
49 KOG0802 E3 ubiquitin ligase [P 96.4 0.0015 3.2E-08 61.3 1.9 46 90-144 291-341 (543)
50 KOG3113 Uncharacterized conser 96.4 0.0022 4.8E-08 54.9 2.5 54 90-150 111-164 (293)
51 KOG4642 Chaperone-dependent E3 96.4 0.0032 7E-08 53.9 3.5 69 90-166 211-279 (284)
52 COG5540 RING-finger-containing 96.2 0.0032 6.9E-08 55.2 2.5 49 91-144 324-372 (374)
53 KOG1645 RING-finger-containing 96.2 0.0023 5.1E-08 57.9 1.6 58 91-154 5-66 (463)
54 KOG3800 Predicted E3 ubiquitin 96.2 0.0079 1.7E-07 52.3 4.7 64 92-161 2-72 (300)
55 KOG3039 Uncharacterized conser 95.9 0.0049 1.1E-07 52.7 2.4 34 90-127 43-76 (303)
56 COG5243 HRD1 HRD ubiquitin lig 95.9 0.0065 1.4E-07 54.7 3.2 46 90-143 287-344 (491)
57 KOG2817 Predicted E3 ubiquitin 95.9 0.0056 1.2E-07 55.2 2.8 52 90-145 334-386 (394)
58 KOG0828 Predicted E3 ubiquitin 95.7 0.0057 1.2E-07 56.7 2.2 50 90-144 571-634 (636)
59 KOG4628 Predicted E3 ubiquitin 95.5 0.011 2.5E-07 52.7 3.0 49 91-144 230-278 (348)
60 KOG1814 Predicted E3 ubiquitin 95.3 0.0087 1.9E-07 54.3 1.7 55 90-146 184-244 (445)
61 KOG1812 Predicted E3 ubiquitin 95.2 0.014 3E-07 52.8 2.8 58 88-148 144-207 (384)
62 KOG0804 Cytoplasmic Zn-finger 95.0 0.0072 1.6E-07 55.4 0.4 45 90-144 175-222 (493)
63 KOG1001 Helicase-like transcri 94.8 0.0054 1.2E-07 59.2 -1.2 52 91-150 455-506 (674)
64 KOG4362 Transcriptional regula 94.6 0.012 2.6E-07 56.5 0.8 69 89-163 20-88 (684)
65 KOG4367 Predicted Zn-finger pr 94.6 0.018 3.9E-07 52.9 1.8 34 90-127 4-37 (699)
66 KOG1734 Predicted RING-contain 94.6 0.0076 1.7E-07 52.1 -0.6 59 89-151 223-288 (328)
67 KOG2042 Ubiquitin fusion degra 94.4 0.074 1.6E-06 52.9 5.6 71 89-167 869-939 (943)
68 KOG0825 PHD Zn-finger protein 94.3 0.0038 8.2E-08 60.6 -3.4 50 89-146 122-173 (1134)
69 KOG1039 Predicted E3 ubiquitin 92.7 0.077 1.7E-06 47.5 2.4 49 89-142 160-219 (344)
70 PF04641 Rtf2: Rtf2 RING-finge 92.7 0.15 3.3E-06 43.5 4.1 35 90-127 34-68 (260)
71 KOG4172 Predicted E3 ubiquitin 92.5 0.057 1.2E-06 36.0 0.9 44 90-143 7-53 (62)
72 COG5109 Uncharacterized conser 92.4 0.081 1.8E-06 46.8 2.1 52 90-144 336-387 (396)
73 KOG1815 Predicted E3 ubiquitin 92.2 0.15 3.2E-06 46.9 3.6 56 89-147 69-129 (444)
74 PF11793 FANCL_C: FANCL C-term 91.9 0.041 8.8E-07 38.0 -0.3 51 90-144 2-66 (70)
75 KOG0827 Predicted E3 ubiquitin 91.9 0.12 2.7E-06 46.8 2.6 47 90-140 4-52 (465)
76 KOG1493 Anaphase-promoting com 91.6 0.077 1.7E-06 37.7 0.8 54 88-145 29-82 (84)
77 KOG4739 Uncharacterized protei 90.4 0.13 2.7E-06 43.7 1.2 52 91-151 4-55 (233)
78 KOG1941 Acetylcholine receptor 90.0 0.12 2.6E-06 47.0 0.8 50 89-141 364-413 (518)
79 smart00744 RINGv The RING-vari 89.4 0.56 1.2E-05 30.1 3.4 43 93-140 2-49 (49)
80 KOG4185 Predicted E3 ubiquitin 88.2 0.63 1.4E-05 40.0 4.0 66 91-161 4-77 (296)
81 KOG4692 Predicted E3 ubiquitin 87.9 0.36 7.9E-06 43.5 2.3 46 90-144 422-467 (489)
82 PF10571 UPF0547: Uncharacteri 87.1 0.31 6.7E-06 27.5 0.9 24 92-117 2-25 (26)
83 PHA03096 p28-like protein; Pro 86.7 0.48 1E-05 41.3 2.3 49 91-143 179-236 (284)
84 COG5194 APC11 Component of SCF 86.6 0.67 1.5E-05 33.2 2.6 52 89-145 30-82 (88)
85 PF14570 zf-RING_4: RING/Ubox 85.7 0.84 1.8E-05 29.5 2.5 46 93-143 1-47 (48)
86 COG5175 MOT2 Transcriptional r 85.2 0.73 1.6E-05 41.4 2.7 52 93-148 17-68 (480)
87 smart00064 FYVE Protein presen 84.2 0.72 1.6E-05 30.9 1.8 36 91-126 11-46 (68)
88 cd00065 FYVE FYVE domain; Zinc 82.7 0.98 2.1E-05 29.1 1.9 36 91-126 3-38 (57)
89 PF01363 FYVE: FYVE zinc finge 82.0 0.29 6.4E-06 33.0 -0.8 34 90-123 9-42 (69)
90 KOG1785 Tyrosine kinase negati 81.5 0.54 1.2E-05 43.1 0.4 46 92-144 371-416 (563)
91 PHA00626 hypothetical protein 81.5 1.1 2.4E-05 30.0 1.8 20 104-123 21-40 (59)
92 KOG3161 Predicted E3 ubiquitin 81.2 0.84 1.8E-05 44.1 1.6 38 88-126 9-47 (861)
93 KOG2930 SCF ubiquitin ligase, 80.8 1.3 2.9E-05 33.2 2.2 26 111-141 80-105 (114)
94 COG5219 Uncharacterized conser 80.5 1.3 2.8E-05 44.7 2.7 48 91-144 1470-1523(1525)
95 PF12660 zf-TFIIIC: Putative z 80.3 0.14 3E-06 37.8 -3.1 47 91-142 15-64 (99)
96 KOG2114 Vacuolar assembly/sort 80.3 1 2.3E-05 44.5 1.9 41 90-141 840-880 (933)
97 TIGR02300 FYDLN_acid conserved 79.9 1.1 2.4E-05 34.7 1.6 30 90-119 9-39 (129)
98 KOG0883 Cyclophilin type, U bo 79.0 1.6 3.5E-05 40.0 2.6 35 89-127 39-73 (518)
99 COG5113 UFD2 Ubiquitin fusion 79.0 4.2 9.1E-05 39.5 5.4 70 89-166 853-922 (929)
100 KOG3002 Zn finger protein [Gen 77.8 2.3 5E-05 37.4 3.2 56 90-161 48-105 (299)
101 COG3364 Zn-ribbon containing p 77.6 1.1 2.5E-05 33.5 1.0 32 106-144 2-33 (112)
102 KOG2462 C2H2-type Zn-finger pr 77.3 1.2 2.5E-05 38.8 1.2 53 88-144 159-226 (279)
103 KOG2979 Protein involved in DN 76.6 2.7 5.9E-05 36.2 3.2 49 88-143 211-259 (262)
104 PF10367 Vps39_2: Vacuolar sor 75.4 1.5 3.3E-05 31.4 1.2 38 77-122 71-108 (109)
105 PF09538 FYDLN_acid: Protein o 73.0 2.2 4.7E-05 32.1 1.5 30 90-119 9-39 (108)
106 PF09845 DUF2072: Zn-ribbon co 72.4 1.9 4.1E-05 33.6 1.1 29 106-141 1-29 (131)
107 PF14447 Prok-RING_4: Prokaryo 72.2 2.4 5.2E-05 28.2 1.4 35 105-147 19-53 (55)
108 KOG1940 Zn-finger protein [Gen 72.1 2.8 6.1E-05 36.5 2.2 48 89-141 157-204 (276)
109 PRK11088 rrmA 23S rRNA methylt 70.4 2 4.3E-05 36.4 0.9 27 90-119 2-30 (272)
110 KOG4445 Uncharacterized conser 69.5 1.6 3.5E-05 38.6 0.2 54 87-144 112-186 (368)
111 cd00350 rubredoxin_like Rubred 69.3 2.3 5E-05 24.9 0.8 21 110-141 5-25 (33)
112 KOG0298 DEAD box-containing he 68.9 1.3 2.9E-05 45.6 -0.5 43 90-141 1153-1196(1394)
113 PF05605 zf-Di19: Drought indu 68.7 6.3 0.00014 25.4 2.8 34 90-141 2-39 (54)
114 KOG2462 C2H2-type Zn-finger pr 68.7 3.9 8.5E-05 35.6 2.3 54 89-144 129-198 (279)
115 PF14353 CpXC: CpXC protein 68.5 3.1 6.8E-05 31.4 1.6 48 91-144 2-49 (128)
116 KOG3268 Predicted E3 ubiquitin 64.1 5.7 0.00012 32.8 2.4 36 108-145 186-229 (234)
117 PF02318 FYVE_2: FYVE-type zin 62.8 2.9 6.2E-05 31.5 0.4 48 90-141 54-102 (118)
118 PF13719 zinc_ribbon_5: zinc-r 62.6 3.9 8.5E-05 24.6 0.9 12 129-142 23-34 (37)
119 COG4530 Uncharacterized protei 62.6 6.1 0.00013 30.1 2.1 34 90-123 9-43 (129)
120 KOG4265 Predicted E3 ubiquitin 62.4 5.4 0.00012 35.8 2.1 46 90-144 290-336 (349)
121 KOG2034 Vacuolar sorting prote 61.4 4.6 9.9E-05 40.3 1.6 35 90-126 817-851 (911)
122 PF06416 DUF1076: Protein of u 59.4 7.8 0.00017 29.4 2.2 51 90-146 40-93 (113)
123 KOG4718 Non-SMC (structural ma 59.3 5.2 0.00011 33.7 1.3 43 91-141 182-224 (235)
124 KOG2932 E3 ubiquitin ligase in 58.9 5.8 0.00013 35.4 1.6 41 91-141 91-131 (389)
125 PF08746 zf-RING-like: RING-li 58.0 11 0.00023 23.5 2.3 25 111-136 18-42 (43)
126 KOG3899 Uncharacterized conser 57.9 6.7 0.00015 34.7 1.8 41 106-148 319-369 (381)
127 TIGR02605 CxxC_CxxC_SSSS putat 57.7 3.2 6.9E-05 26.3 -0.1 27 109-141 8-34 (52)
128 KOG1571 Predicted E3 ubiquitin 56.2 3.7 8.1E-05 36.9 0.0 41 91-143 306-346 (355)
129 PF07191 zinc-ribbons_6: zinc- 56.1 0.77 1.7E-05 32.0 -3.4 40 91-144 2-41 (70)
130 PF13717 zinc_ribbon_4: zinc-r 55.9 6.4 0.00014 23.6 1.0 8 91-98 3-10 (36)
131 smart00531 TFIIE Transcription 55.7 7.1 0.00015 30.4 1.5 15 130-146 122-136 (147)
132 cd00729 rubredoxin_SM Rubredox 54.7 8.9 0.00019 22.6 1.5 22 109-141 5-26 (34)
133 PRK11827 hypothetical protein; 54.0 9.3 0.0002 25.8 1.7 11 90-100 8-18 (60)
134 PRK09678 DNA-binding transcrip 53.7 7.3 0.00016 27.2 1.1 8 91-98 2-9 (72)
135 KOG4275 Predicted E3 ubiquitin 53.3 3 6.5E-05 36.8 -1.0 40 90-142 300-340 (350)
136 PF03884 DUF329: Domain of unk 52.4 7.9 0.00017 25.9 1.1 11 90-100 2-12 (57)
137 PF05290 Baculo_IE-1: Baculovi 52.3 20 0.00043 28.1 3.5 53 90-146 80-134 (140)
138 KOG3970 Predicted E3 ubiquitin 52.1 37 0.0008 29.1 5.3 54 92-149 52-111 (299)
139 KOG0825 PHD Zn-finger protein 50.8 9.2 0.0002 38.1 1.7 49 90-143 96-153 (1134)
140 PRK01343 zinc-binding protein; 49.9 8.2 0.00018 25.8 0.9 13 88-100 7-19 (57)
141 PLN02189 cellulose synthase 49.8 11 0.00025 38.4 2.2 50 91-144 35-87 (1040)
142 KOG3579 Predicted E3 ubiquitin 49.7 7.4 0.00016 34.3 0.8 63 90-164 268-342 (352)
143 cd01408 SIRT1 SIRT1: Eukaryoti 49.2 22 0.00049 29.7 3.7 33 111-146 121-153 (235)
144 PF03966 Trm112p: Trm112p-like 47.8 10 0.00022 25.6 1.1 7 91-97 8-14 (68)
145 smart00834 CxxC_CXXC_SSSS Puta 47.5 3.6 7.7E-05 24.6 -1.1 12 130-143 25-36 (41)
146 TIGR01206 lysW lysine biosynth 47.5 7.6 0.00017 25.6 0.4 11 90-100 2-12 (54)
147 COG3813 Uncharacterized protei 46.7 18 0.0004 25.5 2.3 41 113-160 28-68 (84)
148 COG3024 Uncharacterized protei 45.8 10 0.00022 26.0 0.9 14 87-100 4-17 (65)
149 TIGR02098 MJ0042_CXXC MJ0042 f 45.2 15 0.00032 21.7 1.4 11 131-143 25-35 (38)
150 PF09723 Zn-ribbon_8: Zinc rib 44.9 3.2 6.8E-05 25.7 -1.6 27 109-141 8-34 (42)
151 PF02146 SIR2: Sir2 family; I 44.5 20 0.00042 28.4 2.5 33 110-145 109-141 (178)
152 PF06676 DUF1178: Protein of u 44.0 28 0.00062 27.6 3.2 26 112-141 10-40 (148)
153 PLN03086 PRLI-interacting fact 43.8 34 0.00074 32.8 4.3 30 112-143 483-514 (567)
154 COG3357 Predicted transcriptio 43.6 11 0.00023 27.7 0.7 31 102-141 54-84 (97)
155 PRK14138 NAD-dependent deacety 43.1 30 0.00065 29.2 3.5 32 111-145 124-155 (244)
156 PHA02825 LAP/PHD finger-like p 42.8 42 0.00092 27.0 4.1 48 89-144 7-59 (162)
157 PF14471 DUF4428: Domain of un 42.8 23 0.0005 22.9 2.1 30 92-124 1-30 (51)
158 PF10272 Tmpp129: Putative tra 42.1 20 0.00044 32.4 2.4 35 112-148 311-355 (358)
159 smart00154 ZnF_AN1 AN1-like Zi 41.8 16 0.00034 22.3 1.2 25 93-119 1-25 (39)
160 smart00647 IBR In Between Ring 41.6 30 0.00065 22.1 2.6 32 115-146 2-33 (64)
161 smart00659 RPOLCX RNA polymera 41.6 20 0.00044 22.5 1.7 10 130-141 18-27 (44)
162 PRK10144 formate-dependent nit 41.6 32 0.00069 26.6 3.1 36 130-167 39-75 (126)
163 PF10497 zf-4CXXC_R1: Zinc-fin 41.4 37 0.0008 25.2 3.4 27 113-141 37-69 (105)
164 PF03854 zf-P11: P-11 zinc fin 40.1 10 0.00022 24.6 0.1 29 111-144 17-46 (50)
165 PF01530 zf-C2HC: Zinc finger, 39.5 16 0.00034 21.5 0.8 11 132-142 2-12 (31)
166 TIGR03147 cyt_nit_nrfF cytochr 39.4 34 0.00074 26.4 3.0 36 130-167 39-75 (126)
167 PHA02862 5L protein; Provision 39.3 43 0.00092 26.7 3.5 48 91-146 3-55 (156)
168 PF10426 zf-RAG1: Recombinatio 38.5 6.9 0.00015 22.8 -0.7 13 132-144 3-15 (30)
169 KOG1952 Transcription factor N 37.9 34 0.00074 34.4 3.4 50 89-141 190-244 (950)
170 PRK00418 DNA gyrase inhibitor; 37.4 23 0.00049 24.1 1.5 36 89-126 5-42 (62)
171 PF14446 Prok-RING_1: Prokaryo 36.4 27 0.00059 23.1 1.7 47 90-143 5-51 (54)
172 PF14311 DUF4379: Domain of un 35.6 24 0.00053 22.6 1.4 7 130-136 48-54 (55)
173 COG4338 Uncharacterized protei 35.3 13 0.00028 24.2 0.0 13 88-100 10-22 (54)
174 KOG0314 Predicted E3 ubiquitin 35.1 19 0.00041 33.5 1.1 69 87-163 216-286 (448)
175 PF06906 DUF1272: Protein of u 34.9 45 0.00097 22.3 2.6 28 111-145 24-53 (57)
176 KOG0309 Conserved WD40 repeat- 34.9 36 0.00078 34.0 3.0 48 87-140 1025-1072(1081)
177 PRK15202 type III secretion ch 34.6 38 0.00083 25.6 2.5 31 68-98 13-49 (117)
178 KOG1428 Inhibitor of type V ad 34.5 32 0.00069 37.2 2.6 49 93-144 3489-3544(3738)
179 cd01407 SIR2-fam SIR2 family o 34.4 48 0.001 27.2 3.3 16 129-146 131-146 (218)
180 PRK06266 transcription initiat 34.2 53 0.0012 26.5 3.5 33 130-164 135-168 (178)
181 PLN02436 cellulose synthase A 33.9 27 0.00058 36.0 2.0 50 91-144 37-89 (1094)
182 PHA00732 hypothetical protein 33.8 55 0.0012 23.0 3.1 34 109-144 4-38 (79)
183 cd01410 SIRT7 SIRT7: Eukaryoti 33.0 55 0.0012 26.8 3.5 15 130-146 119-133 (206)
184 KOG1729 FYVE finger containing 32.1 8.1 0.00018 33.9 -1.7 52 90-143 168-224 (288)
185 PF15616 TerY-C: TerY-C metal 31.6 25 0.00053 27.4 1.1 40 91-145 78-117 (131)
186 PTZ00303 phosphatidylinositol 31.3 25 0.00055 35.3 1.3 35 91-125 461-500 (1374)
187 PF04423 Rad50_zn_hook: Rad50 30.7 26 0.00057 22.4 1.0 12 133-146 22-33 (54)
188 COG5236 Uncharacterized conser 30.6 34 0.00073 31.2 1.9 45 90-141 61-105 (493)
189 KOG2682 NAD-dependent histone 30.4 46 0.001 28.9 2.6 33 111-146 158-190 (314)
190 COG3088 CcmH Uncharacterized p 29.4 51 0.0011 26.3 2.6 38 130-169 43-81 (153)
191 smart00734 ZnF_Rad18 Rad18-lik 29.1 18 0.00039 20.1 -0.0 10 132-143 2-11 (26)
192 PF01485 IBR: IBR domain; Int 29.0 12 0.00025 24.0 -1.0 27 121-147 8-34 (64)
193 cd01413 SIR2_Af2 SIR2_Af2: Arc 28.9 89 0.0019 25.8 4.1 14 130-145 135-148 (222)
194 KOG1829 Uncharacterized conser 28.8 27 0.00058 33.6 1.0 41 89-139 510-556 (580)
195 COG4640 Predicted membrane pro 28.5 29 0.00064 31.9 1.2 26 92-119 3-28 (465)
196 TIGR02159 PA_CoA_Oxy4 phenylac 28.1 19 0.00041 28.3 -0.1 35 90-124 105-140 (146)
197 PLN02638 cellulose synthase A 28.1 40 0.00087 34.7 2.2 49 92-144 19-70 (1079)
198 KOG3842 Adaptor protein Pellin 27.6 52 0.0011 29.6 2.5 32 110-144 376-414 (429)
199 TIGR01562 FdhE formate dehydro 27.4 18 0.00039 32.0 -0.4 40 91-141 185-232 (305)
200 PF07824 Chaperone_III: Type I 26.9 38 0.00082 25.5 1.3 30 68-98 12-48 (112)
201 PF05502 Dynactin_p62: Dynacti 26.6 35 0.00076 31.9 1.4 12 131-144 52-63 (483)
202 PF08265 YL1_C: YL1 nuclear pr 26.4 40 0.00087 19.5 1.1 16 92-108 2-17 (30)
203 KOG1842 FYVE finger-containing 26.2 23 0.0005 33.1 0.1 34 91-124 181-214 (505)
204 KOG0006 E3 ubiquitin-protein l 25.5 48 0.001 29.9 1.9 29 94-124 321-354 (446)
205 COG0780 Enzyme related to GTP 25.5 1.1E+02 0.0024 24.2 3.9 64 55-127 21-86 (149)
206 PF00096 zf-C2H2: Zinc finger, 25.2 26 0.00056 17.9 0.2 8 91-98 1-8 (23)
207 PF04216 FdhE: Protein involve 25.0 7.4 0.00016 33.6 -3.2 41 90-141 172-219 (290)
208 PF09889 DUF2116: Uncharacteri 24.9 1.2E+02 0.0025 20.4 3.3 21 131-153 3-23 (59)
209 PLN03086 PRLI-interacting fact 24.7 79 0.0017 30.4 3.4 36 105-143 452-487 (567)
210 PF10013 DUF2256: Uncharacteri 24.4 35 0.00076 21.4 0.7 13 88-100 6-18 (42)
211 PRK03564 formate dehydrogenase 24.1 20 0.00043 31.8 -0.7 41 90-141 187-234 (309)
212 COG1592 Rubrerythrin [Energy p 23.9 59 0.0013 26.3 2.0 24 90-114 134-157 (166)
213 KOG2684 Sirtuin 5 and related 23.8 67 0.0015 29.6 2.6 41 91-141 195-235 (412)
214 PF03918 CcmH: Cytochrome C bi 23.8 66 0.0014 25.3 2.3 37 130-168 39-76 (148)
215 COG5627 MMS21 DNA repair prote 23.6 39 0.00085 29.1 1.0 35 102-144 238-272 (275)
216 PF01428 zf-AN1: AN1-like Zinc 23.3 41 0.00089 20.6 0.8 21 96-119 6-26 (43)
217 COG1326 Uncharacterized archae 23.0 35 0.00076 28.4 0.6 10 88-97 4-13 (201)
218 PRK12495 hypothetical protein; 22.8 48 0.001 28.1 1.4 13 88-100 40-52 (226)
219 KOG3183 Predicted Zn-finger pr 22.3 52 0.0011 28.3 1.5 45 95-145 15-67 (250)
220 KOG0883 Cyclophilin type, U bo 21.6 1.2E+02 0.0025 28.2 3.7 39 87-125 98-136 (518)
221 PF13894 zf-C2H2_4: C2H2-type 21.6 41 0.00088 16.7 0.5 8 91-98 1-8 (24)
222 TIGR00373 conserved hypothetic 21.4 79 0.0017 24.9 2.3 14 131-146 128-141 (158)
223 KOG4185 Predicted E3 ubiquitin 21.2 31 0.00068 29.4 -0.0 26 112-141 239-264 (296)
224 PRK07758 hypothetical protein; 21.2 57 0.0012 24.0 1.3 27 113-150 13-40 (95)
225 COG1655 Uncharacterized protei 21.1 61 0.0013 27.8 1.7 27 118-148 8-34 (267)
226 PRK00420 hypothetical protein; 20.9 66 0.0014 24.3 1.7 15 130-146 39-53 (112)
227 PTZ00410 NAD-dependent SIR2; P 20.8 1.1E+02 0.0024 27.6 3.3 15 130-146 170-184 (349)
228 PLN02195 cellulose synthase A 20.7 1E+02 0.0023 31.5 3.4 51 92-146 8-61 (977)
229 PF04606 Ogr_Delta: Ogr/Delta- 20.4 44 0.00096 20.9 0.6 9 109-117 30-38 (47)
230 COG4098 comFA Superfamily II D 20.2 50 0.0011 30.3 1.0 31 90-123 39-69 (441)
No 1
>PF11789 zf-Nse: Zinc-finger of the MIZ type in Nse subunit; PDB: 2YU4_A 3HTK_C.
Probab=99.80 E-value=1e-20 Score=126.94 Aligned_cols=57 Identities=42% Similarity=0.964 Sum_probs=38.9
Q ss_pred cceEEeccCCccceeeccCcCCCCccccCCccccCCCccccHHHHHHHHHhcCCCCCCCCCCCC
Q 029888 77 EDIVMTSTQSNILNISCPLSGKPITELAEPVRSVECKHIYEKNAIQAYIKSKNANARCPVAGCP 140 (186)
Q Consensus 77 dDi~i~~~~~~~~~l~CPI~~~~~~~l~dPV~s~~CgH~fck~~I~~~l~~~~~~~~CPv~GC~ 140 (186)
|||+|++ ++++++||||++ .|++||+|+.|||+|++++|++||+ +++..+||++||+
T Consensus 1 ddi~i~~---~~~~~~CPiT~~---~~~~PV~s~~C~H~fek~aI~~~i~-~~~~~~CPv~GC~ 57 (57)
T PF11789_consen 1 DDIVIEG---GTISLKCPITLQ---PFEDPVKSKKCGHTFEKEAILQYIQ-RNGSKRCPVAGCN 57 (57)
T ss_dssp S-----S---SB--SB-TTTSS---B-SSEEEESSS--EEEHHHHHHHCT-TTS-EE-SCCC-S
T ss_pred CceEEec---cEeccCCCCcCC---hhhCCcCcCCCCCeecHHHHHHHHH-hcCCCCCCCCCCC
Confidence 6899984 678999999998 6799999999999999999999996 5788999999995
No 2
>KOG2979 consensus Protein involved in DNA repair [General function prediction only]
Probab=99.61 E-value=2.7e-16 Score=132.62 Aligned_cols=75 Identities=28% Similarity=0.558 Sum_probs=65.4
Q ss_pred CccceeeccCcCCCCccccCCccccCCCccccHHHHHHHHHhcCCCCCCCCCCCC--CCccCCCCccCHHHHHHHHHHHh
Q 029888 86 SNILNISCPLSGKPITELAEPVRSVECKHIYEKNAIQAYIKSKNANARCPVAGCP--RKLQVSKVVCDSLLLVDIDEMRR 163 (186)
Q Consensus 86 ~~~~~l~CPI~~~~~~~l~dPV~s~~CgH~fck~~I~~~l~~~~~~~~CPv~GC~--~~l~~~~L~~d~~L~~~I~~~r~ 163 (186)
+++++++|||+.+| +++||+|++|||+|+|++|+.++. ......||++||. ..+....|.++..|++.|++..+
T Consensus 172 ~e~fs~rdPis~~~---I~nPviSkkC~HvydrDsI~~~l~-~~~~i~CPv~gC~~~~~~~~~~l~~d~el~~kIr~~qe 247 (262)
T KOG2979|consen 172 QEVFSNRDPISKKP---IVNPVISKKCGHVYDRDSIMQILC-DEITIRCPVLGCENPYYIQPGHLDEDKELQQKIRQSQE 247 (262)
T ss_pred hhhhcccCchhhhh---hhchhhhcCcCcchhhhhHHHHhc-cCceeecccccCCccccccccccCchHHHHHHHHHhcc
Confidence 47899999999986 499999999999999999999998 4667899999998 46678889999889998887654
Q ss_pred c
Q 029888 164 T 164 (186)
Q Consensus 164 ~ 164 (186)
.
T Consensus 248 ~ 248 (262)
T KOG2979|consen 248 P 248 (262)
T ss_pred c
Confidence 3
No 3
>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=99.55 E-value=4.2e-15 Score=104.04 Aligned_cols=69 Identities=25% Similarity=0.490 Sum_probs=57.0
Q ss_pred eeeccCcCCCCccccCCccccCCCccccHHHHHHHHHhcCCCCCCCCCCCCCCccCCCCccCHHHHHHHHHHHhcCc
Q 029888 90 NISCPLSGKPITELAEPVRSVECKHIYEKNAIQAYIKSKNANARCPVAGCPRKLQVSKVVCDSLLLVDIDEMRRTSK 166 (186)
Q Consensus 90 ~l~CPI~~~~~~~l~dPV~s~~CgH~fck~~I~~~l~~~~~~~~CPv~GC~~~l~~~~L~~d~~L~~~I~~~r~~~~ 166 (186)
.|.||||+. +|++||. +.|||+|++.+|++|+.. +...||+ |+..++..+|.+|..|+..|++|+..++
T Consensus 4 ~f~CpIt~~---lM~dPVi-~~~G~tyer~~I~~~l~~--~~~~~P~--t~~~l~~~~l~pn~~Lk~~I~~~~~~~~ 72 (73)
T PF04564_consen 4 EFLCPITGE---LMRDPVI-LPSGHTYERSAIERWLEQ--NGGTDPF--TRQPLSESDLIPNRALKSAIEEWCAENK 72 (73)
T ss_dssp GGB-TTTSS---B-SSEEE-ETTSEEEEHHHHHHHHCT--TSSB-TT--T-SB-SGGGSEE-HHHHHHHHHHHHHCT
T ss_pred ccCCcCcCc---HhhCcee-CCcCCEEcHHHHHHHHHc--CCCCCCC--CCCcCCcccceECHHHHHHHHHHHHHcc
Confidence 689999997 8999999 789999999999999993 4678999 7788999999999999999999988754
No 4
>smart00504 Ubox Modified RING finger domain. Modified RING finger domain, without the full complement of Zn2+-binding ligands. Probable involvement in E2-dependent ubiquitination.
Probab=99.53 E-value=1.1e-14 Score=97.84 Aligned_cols=62 Identities=26% Similarity=0.438 Sum_probs=55.8
Q ss_pred eeccCcCCCCccccCCccccCCCccccHHHHHHHHHhcCCCCCCCCCCCCCCccCCCCccCHHHHHHHHHH
Q 029888 91 ISCPLSGKPITELAEPVRSVECKHIYEKNAIQAYIKSKNANARCPVAGCPRKLQVSKVVCDSLLLVDIDEM 161 (186)
Q Consensus 91 l~CPI~~~~~~~l~dPV~s~~CgH~fck~~I~~~l~~~~~~~~CPv~GC~~~l~~~~L~~d~~L~~~I~~~ 161 (186)
+.||||++ +|++||. +.|||+||+.||.+|+.. ...||+ |+..++..+|.++..|++.|+++
T Consensus 2 ~~Cpi~~~---~~~~Pv~-~~~G~v~~~~~i~~~~~~---~~~cP~--~~~~~~~~~l~~~~~l~~~i~~~ 63 (63)
T smart00504 2 FLCPISLE---VMKDPVI-LPSGQTYERRAIEKWLLS---HGTDPV--TGQPLTHEDLIPNLALKSAIQEW 63 (63)
T ss_pred cCCcCCCC---cCCCCEE-CCCCCEEeHHHHHHHHHH---CCCCCC--CcCCCChhhceeCHHHHHHHHhC
Confidence 68999997 7899999 789999999999999983 458999 88899999999999999998863
No 5
>COG5627 MMS21 DNA repair protein MMS21 [DNA replication, recombination, and repair]
Probab=99.32 E-value=1.4e-12 Score=109.00 Aligned_cols=96 Identities=28% Similarity=0.539 Sum_probs=78.3
Q ss_pred hhhHHHHHhhcC---CCCC-C--C-CCCC--cceEEeccCCccceeeccCcCCCCccccCCccccCCCccccHHHHHHHH
Q 029888 55 HKFREAVWNVHH---AGEL-M--P-GEEQ--EDIVMTSTQSNILNISCPLSGKPITELAEPVRSVECKHIYEKNAIQAYI 125 (186)
Q Consensus 55 ~~F~~~i~~~~~---~g~~-~--~-~d~d--dDi~i~~~~~~~~~l~CPI~~~~~~~l~dPV~s~~CgH~fck~~I~~~l 125 (186)
..|++.||.... +..+ | | ++|. |+|.|.+ ++++.+||||++|. ..|+.|++|+|.|+++.|..++
T Consensus 148 l~~~~yIw~~~~~~~~d~~~mks~npee~~~d~i~I~~---~~~~nrCpitl~p~---~~pils~kcnh~~e~D~I~~~l 221 (275)
T COG5627 148 LSMDEYIWRAEALKAADNIVMKSPNPEEGLVDKILIHQ---ELLSNRCPITLNPD---FYPILSSKCNHKPEMDLINKKL 221 (275)
T ss_pred EEeehhhhcCccccccccccccCCChhhhhhhhhhhhh---hhhcccCCcccCcc---hhHHHHhhhcccccHHHHHHHh
Confidence 789999998743 2222 1 1 1333 6788884 68999999999875 8999999999999999999999
Q ss_pred HhcCCCCCCCCCCCCCCccCCCCccCHHHHHH
Q 029888 126 KSKNANARCPVAGCPRKLQVSKVVCDSLLLVD 157 (186)
Q Consensus 126 ~~~~~~~~CPv~GC~~~l~~~~L~~d~~L~~~ 157 (186)
+ ......||++||++.+....++.|+.|.++
T Consensus 222 q-~~~trvcp~~~Csq~~~~~~~v~d~IlE~R 252 (275)
T COG5627 222 Q-VECTRVCPRLICSQKEVVDPYVCDHILEKR 252 (275)
T ss_pred c-CCceeecchhhcchheeccchhhhHHHHHH
Confidence 9 456678999999999999999999988755
No 6
>PF15227 zf-C3HC4_4: zinc finger of C3HC4-type, RING; PDB: 2EGP_A 2ECV_A 2ECJ_A 2YSL_A 2YSJ_A.
Probab=99.22 E-value=6.4e-12 Score=79.22 Aligned_cols=40 Identities=23% Similarity=0.620 Sum_probs=30.5
Q ss_pred ccCcCCCCccccCCccccCCCccccHHHHHHHHHhcCCC-CCCCC
Q 029888 93 CPLSGKPITELAEPVRSVECKHIYEKNAIQAYIKSKNAN-ARCPV 136 (186)
Q Consensus 93 CPI~~~~~~~l~dPV~s~~CgH~fck~~I~~~l~~~~~~-~~CPv 136 (186)
||||++ +|++||+ +.|||+||+.||.++++...+. ..||+
T Consensus 1 CpiC~~---~~~~Pv~-l~CGH~FC~~Cl~~~~~~~~~~~~~CP~ 41 (42)
T PF15227_consen 1 CPICLD---LFKDPVS-LPCGHSFCRSCLERLWKEPSGSGFSCPE 41 (42)
T ss_dssp ETTTTS---B-SSEEE--SSSSEEEHHHHHHHHCCSSSST---SS
T ss_pred CCccch---hhCCccc-cCCcCHHHHHHHHHHHHccCCcCCCCcC
Confidence 899997 8999999 9999999999999999853232 68998
No 7
>PLN03208 E3 ubiquitin-protein ligase RMA2; Provisional
Probab=99.17 E-value=3.1e-11 Score=98.87 Aligned_cols=56 Identities=21% Similarity=0.529 Sum_probs=47.6
Q ss_pred eeeccCcCCCCccccCCccccCCCccccHHHHHHHHHh-------------cCCCCCCCCCCCCCCccCCCCccC
Q 029888 90 NISCPLSGKPITELAEPVRSVECKHIYEKNAIQAYIKS-------------KNANARCPVAGCPRKLQVSKVVCD 151 (186)
Q Consensus 90 ~l~CPI~~~~~~~l~dPV~s~~CgH~fck~~I~~~l~~-------------~~~~~~CPv~GC~~~l~~~~L~~d 151 (186)
.+.||||++ .+++||. +.|||+||..||..|+.. ..+...||+ |+..++..+|.+-
T Consensus 18 ~~~CpICld---~~~dPVv-T~CGH~FC~~CI~~wl~~s~~s~~~~~~~~~~k~~~~CPv--CR~~Is~~~LvPi 86 (193)
T PLN03208 18 DFDCNICLD---QVRDPVV-TLCGHLFCWPCIHKWTYASNNSRQRVDQYDHKREPPKCPV--CKSDVSEATLVPI 86 (193)
T ss_pred ccCCccCCC---cCCCcEE-cCCCchhHHHHHHHHHHhccccccccccccccCCCCcCCC--CCCcCChhcEEEe
Confidence 689999997 6799999 899999999999999852 123568999 9999998888774
No 8
>KOG0320 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=99.08 E-value=5.8e-11 Score=95.73 Aligned_cols=53 Identities=23% Similarity=0.624 Sum_probs=43.5
Q ss_pred eeeccCcCCCCccccCCccccCCCccccHHHHHHHHHhcCCCCCCCCCCCCCCccCCCCc
Q 029888 90 NISCPLSGKPITELAEPVRSVECKHIYEKNAIQAYIKSKNANARCPVAGCPRKLQVSKVV 149 (186)
Q Consensus 90 ~l~CPI~~~~~~~l~dPV~s~~CgH~fck~~I~~~l~~~~~~~~CPv~GC~~~l~~~~L~ 149 (186)
-++||||+.++ -=+.||. ++|||+||+.||...++ ....||+ |++.|+...+.
T Consensus 131 ~~~CPiCl~~~-sek~~vs-TkCGHvFC~~Cik~alk---~~~~CP~--C~kkIt~k~~~ 183 (187)
T KOG0320|consen 131 TYKCPICLDSV-SEKVPVS-TKCGHVFCSQCIKDALK---NTNKCPT--CRKKITHKQFH 183 (187)
T ss_pred ccCCCceecch-hhccccc-cccchhHHHHHHHHHHH---hCCCCCC--cccccchhhhe
Confidence 48999999876 4455665 89999999999999998 4468999 98878776654
No 9
>TIGR00599 rad18 DNA repair protein rad18. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=99.05 E-value=2.2e-10 Score=103.15 Aligned_cols=66 Identities=20% Similarity=0.456 Sum_probs=58.7
Q ss_pred eeeccCcCCCCccccCCccccCCCccccHHHHHHHHHhcCCCCCCCCCCCCCCccCCCCccCHHHHHHHHHHHhc
Q 029888 90 NISCPLSGKPITELAEPVRSVECKHIYEKNAIQAYIKSKNANARCPVAGCPRKLQVSKVVCDSLLLVDIDEMRRT 164 (186)
Q Consensus 90 ~l~CPI~~~~~~~l~dPV~s~~CgH~fck~~I~~~l~~~~~~~~CPv~GC~~~l~~~~L~~d~~L~~~I~~~r~~ 164 (186)
.+.||||+. +|.+||. +.|||+||..||..|+.. ...||+ |+..+....|..|..|..+|+.++..
T Consensus 26 ~l~C~IC~d---~~~~Pvi-tpCgH~FCs~CI~~~l~~---~~~CP~--Cr~~~~~~~Lr~N~~L~~iVe~~~~~ 91 (397)
T TIGR00599 26 SLRCHICKD---FFDVPVL-TSCSHTFCSLCIRRCLSN---QPKCPL--CRAEDQESKLRSNWLVSEIVESFKNL 91 (397)
T ss_pred ccCCCcCch---hhhCccC-CCCCCchhHHHHHHHHhC---CCCCCC--CCCccccccCccchHHHHHHHHHHHh
Confidence 688999997 7899998 899999999999999983 348999 99999888999999999999988654
No 10
>PF13923 zf-C3HC4_2: Zinc finger, C3HC4 type (RING finger); PDB: 3HCU_A 2ECI_A 2JMD_A 3HCS_B 3HCT_A 3ZTG_A 2YUR_A 3L11_A.
Probab=98.99 E-value=3.8e-10 Score=69.58 Aligned_cols=38 Identities=39% Similarity=0.904 Sum_probs=31.9
Q ss_pred ccCcCCCCccccCCccccCCCccccHHHHHHHHHhcCCCCCCCC
Q 029888 93 CPLSGKPITELAEPVRSVECKHIYEKNAIQAYIKSKNANARCPV 136 (186)
Q Consensus 93 CPI~~~~~~~l~dPV~s~~CgH~fck~~I~~~l~~~~~~~~CPv 136 (186)
||||++ .+.+|+..+.|||+||+.||.+|++. ..+||+
T Consensus 1 C~iC~~---~~~~~~~~~~CGH~fC~~C~~~~~~~---~~~CP~ 38 (39)
T PF13923_consen 1 CPICLD---ELRDPVVVTPCGHSFCKECIEKYLEK---NPKCPV 38 (39)
T ss_dssp ETTTTS---B-SSEEEECTTSEEEEHHHHHHHHHC---TSB-TT
T ss_pred CCCCCC---cccCcCEECCCCCchhHHHHHHHHHC---cCCCcC
Confidence 899997 78999766899999999999999992 378998
No 11
>PF14835 zf-RING_6: zf-RING of BARD1-type protein; PDB: 1JM7_B.
Probab=98.82 E-value=8.2e-10 Score=75.39 Aligned_cols=59 Identities=27% Similarity=0.482 Sum_probs=33.1
Q ss_pred eeeccCcCCCCccccCCccccCCCccccHHHHHHHHHhcCCCCCCCCCCCCCCccCCCCccCHHHHHHH
Q 029888 90 NISCPLSGKPITELAEPVRSVECKHIYEKNAIQAYIKSKNANARCPVAGCPRKLQVSKVVCDSLLLVDI 158 (186)
Q Consensus 90 ~l~CPI~~~~~~~l~dPV~s~~CgH~fck~~I~~~l~~~~~~~~CPv~GC~~~l~~~~L~~d~~L~~~I 158 (186)
.++|++|.. +|++||.-..|.|+||+.||...+. ..||+ |+.+....|++.|+.|..+|
T Consensus 7 lLrCs~C~~---~l~~pv~l~~CeH~fCs~Ci~~~~~-----~~CPv--C~~Paw~qD~~~NrqLd~~i 65 (65)
T PF14835_consen 7 LLRCSICFD---ILKEPVCLGGCEHIFCSSCIRDCIG-----SECPV--CHTPAWIQDIQINRQLDSMI 65 (65)
T ss_dssp TTS-SSS-S-----SS-B---SSS--B-TTTGGGGTT-----TB-SS--S--B-S-SS----HHHHHHH
T ss_pred hcCCcHHHH---HhcCCceeccCccHHHHHHhHHhcC-----CCCCC--cCChHHHHHHHhhhhhhccC
Confidence 589999996 8999997689999999999988666 25999 99999999999999887765
No 12
>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=98.76 E-value=1.3e-08 Score=88.75 Aligned_cols=67 Identities=19% Similarity=0.451 Sum_probs=53.7
Q ss_pred eeccCcCCCCccccCC----ccccCCCccccHHHHHHHHHhcCCCCCCCCCCCCCCccCCC----CccCHHHHHHHHHHH
Q 029888 91 ISCPLSGKPITELAEP----VRSVECKHIYEKNAIQAYIKSKNANARCPVAGCPRKLQVSK----VVCDSLLLVDIDEMR 162 (186)
Q Consensus 91 l~CPI~~~~~~~l~dP----V~s~~CgH~fck~~I~~~l~~~~~~~~CPv~GC~~~l~~~~----L~~d~~L~~~I~~~r 162 (186)
..||+|+. ....+| +.| .|||+||+.||..+|. .+...||+ |+..+.... +.+|..+.+.|.-.|
T Consensus 4 ~~CP~Ck~--~~y~np~~kl~i~-~CGH~~C~sCv~~l~~--~~~~~CP~--C~~~lrk~~fr~q~F~D~~vekEV~iRk 76 (309)
T TIGR00570 4 QGCPRCKT--TKYRNPSLKLMVN-VCGHTLCESCVDLLFV--RGSGSCPE--CDTPLRKNNFRVQLFEDPTVEKEVDIRK 76 (309)
T ss_pred CCCCcCCC--CCccCcccccccC-CCCCcccHHHHHHHhc--CCCCCCCC--CCCccchhhccccccccHHHHHHHHHHH
Confidence 56999997 345566 343 7999999999999987 25578998 999998887 788988888887665
Q ss_pred hc
Q 029888 163 RT 164 (186)
Q Consensus 163 ~~ 164 (186)
+.
T Consensus 77 rv 78 (309)
T TIGR00570 77 RV 78 (309)
T ss_pred HH
Confidence 54
No 13
>PF00097 zf-C3HC4: Zinc finger, C3HC4 type (RING finger); InterPro: IPR018957 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. The C3HC4 type zinc-finger (RING finger) is a cysteine-rich domain of 40 to 60 residues that coordinates two zinc ions, and has the consensus sequence: C-X2-C-X(9-39)-C-X(1-3)-H-X(2-3)-C-X2-C-X(4-48)-C-X2-C where X is any amino acid []. Many proteins containing a RING finger play a key role in the ubiquitination pathway []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; PDB: 1CHC_A 2ECW_A 2Y43_B 1V87_A 2DJB_A 2H0D_B 3RPG_C 3KNV_A 2CKL_B 1JM7_A ....
Probab=98.76 E-value=7.1e-09 Score=64.07 Aligned_cols=40 Identities=20% Similarity=0.765 Sum_probs=35.5
Q ss_pred ccCcCCCCccccCCccccCCCccccHHHHHHHHHhcCCCCCCCC
Q 029888 93 CPLSGKPITELAEPVRSVECKHIYEKNAIQAYIKSKNANARCPV 136 (186)
Q Consensus 93 CPI~~~~~~~l~dPV~s~~CgH~fck~~I~~~l~~~~~~~~CPv 136 (186)
||||+. .+.+|+..+.|||+||..||.+|+.. .+...||+
T Consensus 1 C~iC~~---~~~~~~~~~~C~H~fC~~C~~~~~~~-~~~~~CP~ 40 (41)
T PF00097_consen 1 CPICLE---PFEDPVILLPCGHSFCRDCLRKWLEN-SGSVKCPL 40 (41)
T ss_dssp ETTTSS---BCSSEEEETTTSEEEEHHHHHHHHHH-TSSSBTTT
T ss_pred CCcCCc---cccCCCEEecCCCcchHHHHHHHHHh-cCCccCCc
Confidence 899997 77999944899999999999999994 67788998
No 14
>COG5222 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=98.76 E-value=9.9e-09 Score=89.03 Aligned_cols=69 Identities=19% Similarity=0.480 Sum_probs=60.2
Q ss_pred cceeeccCcCCCCccccCCccccCCCccccHHHHHHHHHhcCCCCCCCCCCCCC-CccCCCCccCHHHHHHHHHHHh
Q 029888 88 ILNISCPLSGKPITELAEPVRSVECKHIYEKNAIQAYIKSKNANARCPVAGCPR-KLQVSKVVCDSLLLVDIDEMRR 163 (186)
Q Consensus 88 ~~~l~CPI~~~~~~~l~dPV~s~~CgH~fck~~I~~~l~~~~~~~~CPv~GC~~-~l~~~~L~~d~~L~~~I~~~r~ 163 (186)
.++|+||+|+. ++++||+...|||.||++||...|-. ..+.||. |.. .+-++.|.+|...+..|+.+++
T Consensus 272 ~i~LkCplc~~---Llrnp~kT~cC~~~fc~eci~~al~d--sDf~Cpn--C~rkdvlld~l~pD~dk~~EvE~~lk 341 (427)
T COG5222 272 NISLKCPLCHC---LLRNPMKTPCCGHTFCDECIGTALLD--SDFKCPN--CSRKDVLLDGLTPDIDKKLEVEKALK 341 (427)
T ss_pred CccccCcchhh---hhhCcccCccccchHHHHHHhhhhhh--ccccCCC--cccccchhhccCccHHHHHHHHHHHH
Confidence 46699999997 89999996689999999999998873 6689999 975 6788999999999999988766
No 15
>KOG2164 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=98.73 E-value=6.5e-09 Score=95.18 Aligned_cols=56 Identities=25% Similarity=0.650 Sum_probs=47.6
Q ss_pred eeeccCcCCCCccccCCccccCCCccccHHHHHHHHHhc--CCCCCCCCCCCCCCccCCCCccC
Q 029888 90 NISCPLSGKPITELAEPVRSVECKHIYEKNAIQAYIKSK--NANARCPVAGCPRKLQVSKVVCD 151 (186)
Q Consensus 90 ~l~CPI~~~~~~~l~dPV~s~~CgH~fck~~I~~~l~~~--~~~~~CPv~GC~~~l~~~~L~~d 151 (186)
.+.||||+.| ..-|++ +.|||+||-.||.+||... .+...||+ |...+.+.+|.+=
T Consensus 186 ~~~CPICL~~---~~~p~~-t~CGHiFC~~CiLqy~~~s~~~~~~~CPi--C~s~I~~kdl~pv 243 (513)
T KOG2164|consen 186 DMQCPICLEP---PSVPVR-TNCGHIFCGPCILQYWNYSAIKGPCSCPI--CRSTITLKDLLPV 243 (513)
T ss_pred CCcCCcccCC---CCcccc-cccCceeeHHHHHHHHhhhcccCCccCCc--hhhhccccceeee
Confidence 7899999985 477888 7799999999999999842 35678999 9999999888774
No 16
>KOG0823 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=98.69 E-value=1.3e-08 Score=85.18 Aligned_cols=56 Identities=20% Similarity=0.489 Sum_probs=50.1
Q ss_pred ceeeccCcCCCCccccCCccccCCCccccHHHHHHHHHhcCCCCCCCCCCCCCCccCCCCcc
Q 029888 89 LNISCPLSGKPITELAEPVRSVECKHIYEKNAIQAYIKSKNANARCPVAGCPRKLQVSKVVC 150 (186)
Q Consensus 89 ~~l~CPI~~~~~~~l~dPV~s~~CgH~fck~~I~~~l~~~~~~~~CPv~GC~~~l~~~~L~~ 150 (186)
-.|-|.||+. .-++||. +.|||-||=.||.+|+.....+..||| |...++.+.|+|
T Consensus 46 ~~FdCNICLd---~akdPVv-TlCGHLFCWpClyqWl~~~~~~~~cPV--CK~~Vs~~~vvP 101 (230)
T KOG0823|consen 46 GFFDCNICLD---LAKDPVV-TLCGHLFCWPCLYQWLQTRPNSKECPV--CKAEVSIDTVVP 101 (230)
T ss_pred Cceeeeeecc---ccCCCEE-eecccceehHHHHHHHhhcCCCeeCCc--cccccccceEEe
Confidence 3799999998 6799999 899999999999999986667788999 999998888877
No 17
>KOG0287 consensus Postreplication repair protein RAD18 [Replication, recombination and repair]
Probab=98.65 E-value=1.1e-08 Score=89.92 Aligned_cols=63 Identities=16% Similarity=0.388 Sum_probs=57.3
Q ss_pred eeeccCcCCCCccccCCccccCCCccccHHHHHHHHHhcCCCCCCCCCCCCCCccCCCCccCHHHHHHHHHH
Q 029888 90 NISCPLSGKPITELAEPVRSVECKHIYEKNAIQAYIKSKNANARCPVAGCPRKLQVSKVVCDSLLLVDIDEM 161 (186)
Q Consensus 90 ~l~CPI~~~~~~~l~dPV~s~~CgH~fck~~I~~~l~~~~~~~~CPv~GC~~~l~~~~L~~d~~L~~~I~~~ 161 (186)
.|+|-||.. +|.-||. +.|||+||.-||..||. ....||. |...++..+|+.+..|..+|+.+
T Consensus 23 lLRC~IC~e---yf~ip~i-tpCsHtfCSlCIR~~L~---~~p~CP~--C~~~~~Es~Lr~n~il~Eiv~S~ 85 (442)
T KOG0287|consen 23 LLRCGICFE---YFNIPMI-TPCSHTFCSLCIRKFLS---YKPQCPT--CCVTVTESDLRNNRILDEIVKSL 85 (442)
T ss_pred HHHHhHHHH---HhcCcee-ccccchHHHHHHHHHhc---cCCCCCc--eecccchhhhhhhhHHHHHHHHH
Confidence 589999996 8999999 88999999999999998 3468999 99999999999999998888765
No 18
>PF13639 zf-RING_2: Ring finger domain; PDB: 2KIZ_A 4EPO_C 1IYM_A 2EP4_A 2ECT_A 2JRJ_A 2ECN_A 2ECM_A 3NG2_A 2EA6_A ....
Probab=98.59 E-value=1.7e-08 Score=63.48 Aligned_cols=43 Identities=30% Similarity=0.847 Sum_probs=32.6
Q ss_pred eccCcCCCCccccCCccccCCCccccHHHHHHHHHhcCCCCCCCCCCCC
Q 029888 92 SCPLSGKPITELAEPVRSVECKHIYEKNAIQAYIKSKNANARCPVAGCP 140 (186)
Q Consensus 92 ~CPI~~~~~~~l~dPV~s~~CgH~fck~~I~~~l~~~~~~~~CPv~GC~ 140 (186)
.||||+..|.. .+.+..+.|||+|+..||.+|++. + ..||+ |+
T Consensus 2 ~C~IC~~~~~~-~~~~~~l~C~H~fh~~Ci~~~~~~-~--~~CP~--CR 44 (44)
T PF13639_consen 2 ECPICLEEFED-GEKVVKLPCGHVFHRSCIKEWLKR-N--NSCPV--CR 44 (44)
T ss_dssp CETTTTCBHHT-TSCEEEETTSEEEEHHHHHHHHHH-S--SB-TT--TH
T ss_pred CCcCCChhhcC-CCeEEEccCCCeeCHHHHHHHHHh-C--CcCCc--cC
Confidence 49999985422 345554889999999999999994 2 48999 84
No 19
>PF13445 zf-RING_UBOX: RING-type zinc-finger; PDB: 2CT2_A.
Probab=98.58 E-value=3.2e-08 Score=62.74 Aligned_cols=38 Identities=26% Similarity=0.768 Sum_probs=23.6
Q ss_pred ccCcCCCCccccC----CccccCCCccccHHHHHHHHHhc-CCCCCCC
Q 029888 93 CPLSGKPITELAE----PVRSVECKHIYEKNAIQAYIKSK-NANARCP 135 (186)
Q Consensus 93 CPI~~~~~~~l~d----PV~s~~CgH~fck~~I~~~l~~~-~~~~~CP 135 (186)
||||.+ |.+ |+. ..|||+||++||.+++..+ ...++||
T Consensus 1 CpIc~e----~~~~~n~P~~-L~CGH~~c~~cl~~l~~~~~~~~~kCP 43 (43)
T PF13445_consen 1 CPICKE----FSTEENPPMV-LPCGHVFCKDCLQKLSKKSDRNRFKCP 43 (43)
T ss_dssp -TTT--------TTSS-EEE--SSS-EEEHHHHHHHHHH-S-S-B--T
T ss_pred CCcccc----ccCCCCCCEE-EeCccHHHHHHHHHHHhcCCCCeeeCc
Confidence 899985 577 898 7899999999999999842 2578888
No 20
>cd00162 RING RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in mediating protein-protein interactions; identified in a proteins with a wide range of functions such as viral replication, signal transduction, and development; has two variants, the C3HC4-type and a C3H2C3-type (RING-H2 finger), which have different cysteine/histidine pattern; a subset of RINGs are associated with B-Boxes (C-X2-H-X7-C-X7-C-X2-C-H-X2-H)
Probab=98.48 E-value=1.6e-07 Score=57.40 Aligned_cols=44 Identities=32% Similarity=0.831 Sum_probs=36.5
Q ss_pred eccCcCCCCccccCCccccCCCccccHHHHHHHHHhcCCCCCCCCCCCCCC
Q 029888 92 SCPLSGKPITELAEPVRSVECKHIYEKNAIQAYIKSKNANARCPVAGCPRK 142 (186)
Q Consensus 92 ~CPI~~~~~~~l~dPV~s~~CgH~fck~~I~~~l~~~~~~~~CPv~GC~~~ 142 (186)
.||||+. .+.+|+....|||.|+..|+..|+.. +...||+ |+..
T Consensus 1 ~C~iC~~---~~~~~~~~~~C~H~~c~~C~~~~~~~--~~~~Cp~--C~~~ 44 (45)
T cd00162 1 ECPICLE---EFREPVVLLPCGHVFCRSCIDKWLKS--GKNTCPL--CRTP 44 (45)
T ss_pred CCCcCch---hhhCceEecCCCChhcHHHHHHHHHh--CcCCCCC--CCCc
Confidence 4999997 45788885669999999999999983 5678999 9764
No 21
>KOG2177 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=98.47 E-value=1.4e-07 Score=77.36 Aligned_cols=67 Identities=21% Similarity=0.459 Sum_probs=56.0
Q ss_pred eeeccCcCCCCccccCCccccCCCccccHHHHHHHHHhcCCCCCCCCCCCCCCccCCCCccCHHHHHHHHHHHhcCcc
Q 029888 90 NISCPLSGKPITELAEPVRSVECKHIYEKNAIQAYIKSKNANARCPVAGCPRKLQVSKVVCDSLLLVDIDEMRRTSKE 167 (186)
Q Consensus 90 ~l~CPI~~~~~~~l~dPV~s~~CgH~fck~~I~~~l~~~~~~~~CPv~GC~~~l~~~~L~~d~~L~~~I~~~r~~~~~ 167 (186)
.+.||||+. .|.+|+. ..|||+||+.||..++. ....||. |+. ... .+.++..+...+..++.....
T Consensus 13 ~~~C~iC~~---~~~~p~~-l~C~H~~c~~C~~~~~~---~~~~Cp~--cr~-~~~-~~~~n~~l~~~~~~~~~~~~~ 79 (386)
T KOG2177|consen 13 ELTCPICLE---YFREPVL-LPCGHNFCRACLTRSWE---GPLSCPV--CRP-PSR-NLRPNVLLANLVERLRQLRLS 79 (386)
T ss_pred cccChhhHH---HhhcCcc-ccccchHhHHHHHHhcC---CCcCCcc--cCC-chh-ccCccHHHHHHHHHHHhcCCc
Confidence 688999996 8899955 88999999999999998 5589999 986 333 777999999888888776443
No 22
>COG5432 RAD18 RING-finger-containing E3 ubiquitin ligase [Signal transduction mechanisms]
Probab=98.42 E-value=1.4e-07 Score=81.56 Aligned_cols=63 Identities=17% Similarity=0.299 Sum_probs=53.2
Q ss_pred eeeccCcCCCCccccCCccccCCCccccHHHHHHHHHhcCCCCCCCCCCCCCCccCCCCccCHHHHHHHHHH
Q 029888 90 NISCPLSGKPITELAEPVRSVECKHIYEKNAIQAYIKSKNANARCPVAGCPRKLQVSKVVCDSLLLVDIDEM 161 (186)
Q Consensus 90 ~l~CPI~~~~~~~l~dPV~s~~CgH~fck~~I~~~l~~~~~~~~CPv~GC~~~l~~~~L~~d~~L~~~I~~~ 161 (186)
.++|-||.. .|+-|+. +.|||+||.-||..||. ...-||+ |+.......|..+..+...++.+
T Consensus 25 ~lrC~IC~~---~i~ip~~-TtCgHtFCslCIR~hL~---~qp~CP~--Cr~~~~esrlr~~s~~~ei~es~ 87 (391)
T COG5432 25 MLRCRICDC---RISIPCE-TTCGHTFCSLCIRRHLG---TQPFCPV--CREDPCESRLRGSSGSREINESH 87 (391)
T ss_pred HHHhhhhhh---eeeccee-cccccchhHHHHHHHhc---CCCCCcc--ccccHHhhhcccchhHHHHHHhh
Confidence 478999997 7899999 89999999999999998 3468999 99988888887777666665544
No 23
>PHA02929 N1R/p28-like protein; Provisional
Probab=98.39 E-value=2.4e-07 Score=78.47 Aligned_cols=47 Identities=19% Similarity=0.576 Sum_probs=35.8
Q ss_pred eeeccCcCCCCccccCC-------ccccCCCccccHHHHHHHHHhcCCCCCCCCCCCCCCcc
Q 029888 90 NISCPLSGKPITELAEP-------VRSVECKHIYEKNAIQAYIKSKNANARCPVAGCPRKLQ 144 (186)
Q Consensus 90 ~l~CPI~~~~~~~l~dP-------V~s~~CgH~fck~~I~~~l~~~~~~~~CPv~GC~~~l~ 144 (186)
...||||+.++ ...| +. +.|||+||+.||..|+. ....||+ |+..+.
T Consensus 174 ~~eC~ICle~~--~~~~~~~~~~~vl-~~C~H~FC~~CI~~Wl~---~~~tCPl--CR~~~~ 227 (238)
T PHA02929 174 DKECAICMEKV--YDKEIKNMYFGIL-SNCNHVFCIECIDIWKK---EKNTCPV--CRTPFI 227 (238)
T ss_pred CCCCccCCccc--ccCccccccceec-CCCCCcccHHHHHHHHh---cCCCCCC--CCCEee
Confidence 46799999832 3333 33 68999999999999988 3458999 997653
No 24
>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=98.38 E-value=2.7e-07 Score=60.16 Aligned_cols=47 Identities=28% Similarity=0.769 Sum_probs=30.5
Q ss_pred ceeeccCcCCCCccccCCccccCCCcc--ccHHHHHHHHHhcCCCCCCCCCCCCC
Q 029888 89 LNISCPLSGKPITELAEPVRSVECKHI--YEKNAIQAYIKSKNANARCPVAGCPR 141 (186)
Q Consensus 89 ~~l~CPI~~~~~~~l~dPV~s~~CgH~--fck~~I~~~l~~~~~~~~CPv~GC~~ 141 (186)
++|+|||+.. .|..|+++..|.|. |+-.....+.. ..+.+.||+ |++
T Consensus 1 vsL~CPls~~---~i~~P~Rg~~C~H~~CFDl~~fl~~~~-~~~~W~CPi--C~~ 49 (50)
T PF02891_consen 1 VSLRCPLSFQ---RIRIPVRGKNCKHLQCFDLESFLESNQ-RTPKWKCPI--CNK 49 (50)
T ss_dssp EESB-TTTSS---B-SSEEEETT--SS--EEHHHHHHHHH-HS---B-TT--T--
T ss_pred CeeeCCCCCC---EEEeCccCCcCcccceECHHHHHHHhh-ccCCeECcC--CcC
Confidence 4799999997 67999999999997 77767777666 456799999 975
No 25
>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=98.37 E-value=3.4e-07 Score=59.13 Aligned_cols=46 Identities=20% Similarity=0.652 Sum_probs=37.8
Q ss_pred eeeccCcCCCCccccCCccccCCCcc-ccHHHHHHHHHhcCCCCCCCCCCCCCCcc
Q 029888 90 NISCPLSGKPITELAEPVRSVECKHI-YEKNAIQAYIKSKNANARCPVAGCPRKLQ 144 (186)
Q Consensus 90 ~l~CPI~~~~~~~l~dPV~s~~CgH~-fck~~I~~~l~~~~~~~~CPv~GC~~~l~ 144 (186)
+..|+||+. ...+++. ..|||. ||..|+.+++. ....||+ |++.++
T Consensus 2 ~~~C~iC~~---~~~~~~~-~pCgH~~~C~~C~~~~~~---~~~~CP~--Cr~~i~ 48 (50)
T PF13920_consen 2 DEECPICFE---NPRDVVL-LPCGHLCFCEECAERLLK---RKKKCPI--CRQPIE 48 (50)
T ss_dssp HSB-TTTSS---SBSSEEE-ETTCEEEEEHHHHHHHHH---TTSBBTT--TTBB-S
T ss_pred cCCCccCCc---cCCceEE-eCCCChHHHHHHhHHhcc---cCCCCCc--CChhhc
Confidence 467999997 5688887 899999 99999999998 4578999 998764
No 26
>KOG0317 consensus Predicted E3 ubiquitin ligase, integral peroxisomal membrane protein [Posttranslational modification, protein turnover, chaperones]
Probab=98.36 E-value=2.3e-07 Score=79.91 Aligned_cols=51 Identities=31% Similarity=0.632 Sum_probs=43.5
Q ss_pred eeeccCcCCCCccccCCccccCCCccccHHHHHHHHHhcCCCCCCCCCCCCCCccCCCCc
Q 029888 90 NISCPLSGKPITELAEPVRSVECKHIYEKNAIQAYIKSKNANARCPVAGCPRKLQVSKVV 149 (186)
Q Consensus 90 ~l~CPI~~~~~~~l~dPV~s~~CgH~fck~~I~~~l~~~~~~~~CPv~GC~~~l~~~~L~ 149 (186)
+.+|-||+. ...+|-- +.|||.||-.||++|.. ....||+ |+..+++.++.
T Consensus 239 ~~kC~LCLe---~~~~pSa-TpCGHiFCWsCI~~w~~---ek~eCPl--CR~~~~pskvi 289 (293)
T KOG0317|consen 239 TRKCSLCLE---NRSNPSA-TPCGHIFCWSCILEWCS---EKAECPL--CREKFQPSKVI 289 (293)
T ss_pred CCceEEEec---CCCCCCc-CcCcchHHHHHHHHHHc---cccCCCc--ccccCCCccee
Confidence 689999997 5689966 99999999999999998 3356999 99988887664
No 27
>KOG0978 consensus E3 ubiquitin ligase involved in syntaxin degradation [Posttranslational modification, protein turnover, chaperones]
Probab=98.31 E-value=2.9e-07 Score=87.65 Aligned_cols=54 Identities=17% Similarity=0.480 Sum_probs=47.2
Q ss_pred ceeeccCcCCCCccccCCccccCCCccccHHHHHHHHHhcCCCCCCCCCCCCCCccCCCCcc
Q 029888 89 LNISCPLSGKPITELAEPVRSVECKHIYEKNAIQAYIKSKNANARCPVAGCPRKLQVSKVVC 150 (186)
Q Consensus 89 ~~l~CPI~~~~~~~l~dPV~s~~CgH~fck~~I~~~l~~~~~~~~CPv~GC~~~l~~~~L~~ 150 (186)
--++||+|.. -.++-|. ++|||.||..||...+.. +..+||. |+..|...|+.+
T Consensus 642 ~~LkCs~Cn~---R~Kd~vI-~kC~H~FC~~Cvq~r~et--RqRKCP~--Cn~aFganDv~~ 695 (698)
T KOG0978|consen 642 ELLKCSVCNT---RWKDAVI-TKCGHVFCEECVQTRYET--RQRKCPK--CNAAFGANDVHR 695 (698)
T ss_pred hceeCCCccC---chhhHHH-HhcchHHHHHHHHHHHHH--hcCCCCC--CCCCCCcccccc
Confidence 3689999995 7799999 899999999999999984 5678999 999999888754
No 28
>PF14634 zf-RING_5: zinc-RING finger domain
Probab=98.29 E-value=6.6e-07 Score=56.45 Aligned_cols=44 Identities=20% Similarity=0.604 Sum_probs=33.3
Q ss_pred eccCcCCCCccccCCccccCCCccccHHHHHHHHHhcCCCCCCCCCCCCC
Q 029888 92 SCPLSGKPITELAEPVRSVECKHIYEKNAIQAYIKSKNANARCPVAGCPR 141 (186)
Q Consensus 92 ~CPI~~~~~~~l~dPV~s~~CgH~fck~~I~~~l~~~~~~~~CPv~GC~~ 141 (186)
.||+|.+++..-..|+. +.|||+||..||.... .....||+ |++
T Consensus 1 ~C~~C~~~~~~~~~~~l-~~CgH~~C~~C~~~~~---~~~~~CP~--C~k 44 (44)
T PF14634_consen 1 HCNICFEKYSEERRPRL-TSCGHIFCEKCLKKLK---GKSVKCPI--CRK 44 (44)
T ss_pred CCcCcCccccCCCCeEE-cccCCHHHHHHHHhhc---CCCCCCcC--CCC
Confidence 49999984311234555 8999999999999987 25679999 964
No 29
>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=98.29 E-value=8.1e-07 Score=52.36 Aligned_cols=38 Identities=34% Similarity=0.904 Sum_probs=32.1
Q ss_pred ccCcCCCCccccCCccccCCCccccHHHHHHHHHhcCCCCCCCC
Q 029888 93 CPLSGKPITELAEPVRSVECKHIYEKNAIQAYIKSKNANARCPV 136 (186)
Q Consensus 93 CPI~~~~~~~l~dPV~s~~CgH~fck~~I~~~l~~~~~~~~CPv 136 (186)
||||+. ....|+. +.|||+|+..||..|+. .+...||+
T Consensus 1 C~iC~~---~~~~~~~-~~C~H~~c~~C~~~~~~--~~~~~CP~ 38 (39)
T smart00184 1 CPICLE---ELKDPVV-LPCGHTFCRSCIRKWLK--SGNNTCPI 38 (39)
T ss_pred CCcCcc---CCCCcEE-ecCCChHHHHHHHHHHH--hCcCCCCC
Confidence 899997 4677877 78999999999999998 35567998
No 30
>KOG0311 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=98.10 E-value=5.5e-07 Score=79.56 Aligned_cols=75 Identities=23% Similarity=0.415 Sum_probs=60.4
Q ss_pred eEEeccCCccceeeccCcCCCCccccCCccccCCCccccHHHHHHHHHhcCCCCCCCCCCCCCCc-cCCCCccCHHHHHH
Q 029888 79 IVMTSTQSNILNISCPLSGKPITELAEPVRSVECKHIYEKNAIQAYIKSKNANARCPVAGCPRKL-QVSKVVCDSLLLVD 157 (186)
Q Consensus 79 i~i~~~~~~~~~l~CPI~~~~~~~l~dPV~s~~CgH~fck~~I~~~l~~~~~~~~CPv~GC~~~l-~~~~L~~d~~L~~~ 157 (186)
|++. -+.....+.||||+. +|+.-++...|.|.||..||...++. +...||- |++.+ +...|..|+.+..+
T Consensus 33 i~~~-l~~~~~~v~c~icl~---llk~tmttkeClhrfc~~ci~~a~r~--gn~ecpt--cRk~l~SkrsLr~Dp~fdaL 104 (381)
T KOG0311|consen 33 IMVD-LAMFDIQVICPICLS---LLKKTMTTKECLHRFCFDCIWKALRS--GNNECPT--CRKKLVSKRSLRIDPNFDAL 104 (381)
T ss_pred heec-HHHhhhhhccHHHHH---HHHhhcccHHHHHHHHHHHHHHHHHh--cCCCCch--HHhhccccccCCCCccHHHH
Confidence 5443 223456899999996 88999987899999999999999984 5578999 99854 68889999988777
Q ss_pred HHHH
Q 029888 158 IDEM 161 (186)
Q Consensus 158 I~~~ 161 (186)
|..+
T Consensus 105 is~i 108 (381)
T KOG0311|consen 105 ISKI 108 (381)
T ss_pred HHHH
Confidence 7654
No 31
>COG5574 PEX10 RING-finger-containing E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=98.03 E-value=2.6e-06 Score=72.77 Aligned_cols=54 Identities=24% Similarity=0.437 Sum_probs=43.3
Q ss_pred cceeeccCcCCCCccccCCccccCCCccccHHHHHHHHHhcCCCCCCCCCCCCCCccCCCC
Q 029888 88 ILNISCPLSGKPITELAEPVRSVECKHIYEKNAIQAYIKSKNANARCPVAGCPRKLQVSKV 148 (186)
Q Consensus 88 ~~~l~CPI~~~~~~~l~dPV~s~~CgH~fck~~I~~~l~~~~~~~~CPv~GC~~~l~~~~L 148 (186)
..+++|+||+. ....|+. +.|||+||-.||...|. ..+.-.||. |++...++..
T Consensus 213 ~~d~kC~lC~e---~~~~ps~-t~CgHlFC~~Cl~~~~t-~~k~~~Cpl--CRak~~pk~v 266 (271)
T COG5574 213 LADYKCFLCLE---EPEVPSC-TPCGHLFCLSCLLISWT-KKKYEFCPL--CRAKVYPKKV 266 (271)
T ss_pred ccccceeeeec---ccCCccc-ccccchhhHHHHHHHHH-hhccccCch--hhhhccchhh
Confidence 34789999996 6799998 89999999999999766 244455999 9986665543
No 32
>KOG2660 consensus Locus-specific chromosome binding proteins [Function unknown]
Probab=98.01 E-value=3.1e-06 Score=74.18 Aligned_cols=64 Identities=25% Similarity=0.500 Sum_probs=52.3
Q ss_pred ceeeccCcCCCCccccCCccccCCCccccHHHHHHHHHhcCCCCCCCCCCCCCCcc----CCCCccCHHHHHHHHH
Q 029888 89 LNISCPLSGKPITELAEPVRSVECKHIYEKNAIQAYIKSKNANARCPVAGCPRKLQ----VSKVVCDSLLLVDIDE 160 (186)
Q Consensus 89 ~~l~CPI~~~~~~~l~dPV~s~~CgH~fck~~I~~~l~~~~~~~~CPv~GC~~~l~----~~~L~~d~~L~~~I~~ 160 (186)
.-+.|++|.. +|.++-+-+.|=|+|||.||..||.. ...||. |...+. ...+..|..|+-+|-.
T Consensus 14 ~~itC~LC~G---YliDATTI~eCLHTFCkSCivk~l~~---~~~CP~--C~i~ih~t~pl~ni~~DrtlqdiVyK 81 (331)
T KOG2660|consen 14 PHITCRLCGG---YLIDATTITECLHTFCKSCIVKYLEE---SKYCPT--CDIVIHKTHPLLNIRSDRTLQDIVYK 81 (331)
T ss_pred cceehhhccc---eeecchhHHHHHHHHHHHHHHHHHHH---hccCCc--cceeccCccccccCCcchHHHHHHHH
Confidence 4688999995 89999987899999999999999993 578999 876554 4568888887655543
No 33
>PHA02926 zinc finger-like protein; Provisional
Probab=97.96 E-value=7.1e-06 Score=68.78 Aligned_cols=50 Identities=18% Similarity=0.543 Sum_probs=37.0
Q ss_pred eeeccCcCCCCccccC--------CccccCCCccccHHHHHHHHHhc---CCCCCCCCCCCCCCcc
Q 029888 90 NISCPLSGKPITELAE--------PVRSVECKHIYEKNAIQAYIKSK---NANARCPVAGCPRKLQ 144 (186)
Q Consensus 90 ~l~CPI~~~~~~~l~d--------PV~s~~CgH~fck~~I~~~l~~~---~~~~~CPv~GC~~~l~ 144 (186)
+..|+||++. +++. ++. ..|+|+||..||..|.... +....||+ |+..+.
T Consensus 170 E~eCgICmE~--I~eK~~~~eRrFGIL-~~CnHsFCl~CIr~Wr~~r~~~~~~rsCPi--CR~~f~ 230 (242)
T PHA02926 170 EKECGICYEV--VYSKRLENDRYFGLL-DSCNHIFCITCINIWHRTRRETGASDNCPI--CRTRFR 230 (242)
T ss_pred CCCCccCccc--ccccccccccccccc-CCCCchHHHHHHHHHHHhccccCcCCcCCC--Ccceee
Confidence 5789999972 3332 344 5899999999999999731 23456999 997653
No 34
>KOG0297 consensus TNF receptor-associated factor [Signal transduction mechanisms]
Probab=97.95 E-value=5.8e-06 Score=74.65 Aligned_cols=65 Identities=22% Similarity=0.525 Sum_probs=51.9
Q ss_pred ceeeccCcCCCCccccCCccccCCCccccHHHHHHHHHhcCCCCCCCCCCCCCCccCCCCcc-CHHHHHHHHHH
Q 029888 89 LNISCPLSGKPITELAEPVRSVECKHIYEKNAIQAYIKSKNANARCPVAGCPRKLQVSKVVC-DSLLLVDIDEM 161 (186)
Q Consensus 89 ~~l~CPI~~~~~~~l~dPV~s~~CgH~fck~~I~~~l~~~~~~~~CPv~GC~~~l~~~~L~~-d~~L~~~I~~~ 161 (186)
-++.||+|.. ++.+|+.++.|||.||..||..++. . ...||+ |...+......+ +..+++.+..+
T Consensus 20 ~~l~C~~C~~---vl~~p~~~~~cgh~fC~~C~~~~~~-~--~~~cp~--~~~~~~~~~~~~~~~~~~~~~~~l 85 (391)
T KOG0297|consen 20 ENLLCPICMS---VLRDPVQTTTCGHRFCAGCLLESLS-N--HQKCPV--CRQELTQAEELPVPRALRRELLKL 85 (391)
T ss_pred ccccCccccc---cccCCCCCCCCCCcccccccchhhc-c--CcCCcc--cccccchhhccCchHHHHHHHHhc
Confidence 3799999996 8899999669999999999999998 2 678999 988777776666 44455555543
No 35
>KOG1813 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=97.73 E-value=1.9e-05 Score=68.45 Aligned_cols=76 Identities=18% Similarity=0.329 Sum_probs=54.7
Q ss_pred cceEEeccCCccceeeccCcCCCCccccCCccccCCCccccHHHHHHHHHhcCCCCCCCCCCCCCCccCCCCccCHHHHH
Q 029888 77 EDIVMTSTQSNILNISCPLSGKPITELAEPVRSVECKHIYEKNAIQAYIKSKNANARCPVAGCPRKLQVSKVVCDSLLLV 156 (186)
Q Consensus 77 dDi~i~~~~~~~~~l~CPI~~~~~~~l~dPV~s~~CgH~fck~~I~~~l~~~~~~~~CPv~GC~~~l~~~~L~~d~~L~~ 156 (186)
+..++... -+.+-+.|-||.+ .|.+||. +.|||.||..|-...++ +...|++ |++.+ ...+.+...|..
T Consensus 229 ~~~~~~~D-~~~~Pf~c~icr~---~f~~pVv-t~c~h~fc~~ca~~~~q---k~~~c~v--C~~~t-~g~~~~akeL~~ 297 (313)
T KOG1813|consen 229 KKRVKIED-IELLPFKCFICRK---YFYRPVV-TKCGHYFCEVCALKPYQ---KGEKCYV--CSQQT-HGSFNVAKELLV 297 (313)
T ss_pred ccceecCC-cccCCcccccccc---ccccchh-hcCCceeehhhhccccc---cCCccee--ccccc-ccccchHHHHHH
Confidence 34444432 3567889999998 6799999 89999999999888877 4568999 98754 344555566665
Q ss_pred HHHHHHh
Q 029888 157 DIDEMRR 163 (186)
Q Consensus 157 ~I~~~r~ 163 (186)
.+...+.
T Consensus 298 ~L~~kks 304 (313)
T KOG1813|consen 298 SLKLKKS 304 (313)
T ss_pred HHHhhhh
Confidence 5554443
No 36
>COG5152 Uncharacterized conserved protein, contains RING and CCCH-type Zn-fingers [General function prediction only]
Probab=97.67 E-value=2.7e-05 Score=64.41 Aligned_cols=69 Identities=19% Similarity=0.314 Sum_probs=50.3
Q ss_pred eEEeccCCccceeeccCcCCCCccccCCccccCCCccccHHHHHHHHHhcCCCCCCCCCCCCCCccCCCCccCHHHHHHH
Q 029888 79 IVMTSTQSNILNISCPLSGKPITELAEPVRSVECKHIYEKNAIQAYIKSKNANARCPVAGCPRKLQVSKVVCDSLLLVDI 158 (186)
Q Consensus 79 i~i~~~~~~~~~l~CPI~~~~~~~l~dPV~s~~CgH~fck~~I~~~l~~~~~~~~CPv~GC~~~l~~~~L~~d~~L~~~I 158 (186)
.+|+. ..+.+-|.|-||.+ .++.||. +.|||.||..|...-.+ ....|-+ |++.. ...+..+..|.+++
T Consensus 186 ~v~~~-~~e~IPF~C~iCKk---dy~spvv-t~CGH~FC~~Cai~~y~---kg~~C~~--Cgk~t-~G~f~V~~d~~kmL 254 (259)
T COG5152 186 PVISG-PGEKIPFLCGICKK---DYESPVV-TECGHSFCSLCAIRKYQ---KGDECGV--CGKAT-YGRFWVVSDLQKML 254 (259)
T ss_pred ccccC-CCCCCceeehhchh---hccchhh-hhcchhHHHHHHHHHhc---cCCccee--cchhh-ccceeHHhhHHHHH
Confidence 45554 35788999999997 8899999 89999999999776655 4468999 87633 33444444455444
No 37
>KOG2169 consensus Zn-finger transcription factor [Transcription]
Probab=97.65 E-value=5.7e-05 Score=72.15 Aligned_cols=82 Identities=26% Similarity=0.523 Sum_probs=66.0
Q ss_pred CCCCcceEEeccCCccceeeccCcCCCCccccCCccccCCCccccHHHHHHHHHh--cCCCCCCCCCCCCCCccCCCCcc
Q 029888 73 GEEQEDIVMTSTQSNILNISCPLSGKPITELAEPVRSVECKHIYEKNAIQAYIKS--KNANARCPVAGCPRKLQVSKVVC 150 (186)
Q Consensus 73 ~d~ddDi~i~~~~~~~~~l~CPI~~~~~~~l~dPV~s~~CgH~fck~~I~~~l~~--~~~~~~CPv~GC~~~l~~~~L~~ 150 (186)
+++|.||+.+. ..++|.|||++. .|.-|++...|+|.-|.++ ..|+.+ ....+.||| |.+....++|..
T Consensus 292 ~~~d~~i~tt~---~~vSL~CPl~~~---Rm~~P~r~~~CkHlQcFD~-~~~lq~n~~~pTW~CPV--C~~~~~~e~l~i 362 (636)
T KOG2169|consen 292 AGPDSEIATTS---LRVSLNCPLSKM---RMSLPARGHTCKHLQCFDA-LSYLQMNEQKPTWRCPV--CQKAAPFEGLII 362 (636)
T ss_pred cCCcccceecc---ceeEecCCcccc---eeecCCcccccccceecch-hhhHHhccCCCeeeCcc--CCccccccchhh
Confidence 45566787774 568999999996 7899999999999888775 445543 457899999 999999999999
Q ss_pred CHHHHHHHHHHHh
Q 029888 151 DSLLLVDIDEMRR 163 (186)
Q Consensus 151 d~~L~~~I~~~r~ 163 (186)
|..+...+...-.
T Consensus 363 D~~~~~iL~~~~~ 375 (636)
T KOG2169|consen 363 DGYFLNILQSCQA 375 (636)
T ss_pred hHHHHHHHhhccC
Confidence 9988877776544
No 38
>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=97.43 E-value=0.00013 Score=50.95 Aligned_cols=44 Identities=27% Similarity=0.746 Sum_probs=30.4
Q ss_pred eccCcCCCCccc---------cCCccccCCCccccHHHHHHHHHhcCCCCCCCCCCCC
Q 029888 92 SCPLSGKPITEL---------AEPVRSVECKHIYEKNAIQAYIKSKNANARCPVAGCP 140 (186)
Q Consensus 92 ~CPI~~~~~~~l---------~dPV~s~~CgH~fck~~I~~~l~~~~~~~~CPv~GC~ 140 (186)
.|+||+.+|... .-|+.-..|||.|-..||.+|+.. ...||+ |+
T Consensus 21 ~C~IC~~~l~~~~~~~~~~~~~~~i~~~~C~H~FH~~Ci~~Wl~~---~~~CP~--CR 73 (73)
T PF12678_consen 21 NCAICREPLEDPCPECQAPQDECPIVWGPCGHIFHFHCISQWLKQ---NNTCPL--CR 73 (73)
T ss_dssp BETTTTSBTTSTTCCHHHCTTTS-EEEETTSEEEEHHHHHHHHTT---SSB-TT--SS
T ss_pred cccccChhhhChhhhhcCCccccceEecccCCCEEHHHHHHHHhc---CCcCCC--CC
Confidence 499999753111 233333579999999999999983 238999 85
No 39
>KOG2879 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=97.41 E-value=0.00012 Score=63.11 Aligned_cols=50 Identities=28% Similarity=0.563 Sum_probs=40.4
Q ss_pred cceeeccCcCCCCccccCCccccCCCccccHHHHHHHHHhcCCCCCCCCCCCCCCc
Q 029888 88 ILNISCPLSGKPITELAEPVRSVECKHIYEKNAIQAYIKSKNANARCPVAGCPRKL 143 (186)
Q Consensus 88 ~~~l~CPI~~~~~~~l~dPV~s~~CgH~fck~~I~~~l~~~~~~~~CPv~GC~~~l 143 (186)
+.+..||+|+++ =..|....+|||+||..||..-.. -..+..||. |+...
T Consensus 237 t~~~~C~~Cg~~---PtiP~~~~~C~HiyCY~Ci~ts~~-~~asf~Cp~--Cg~~~ 286 (298)
T KOG2879|consen 237 TSDTECPVCGEP---PTIPHVIGKCGHIYCYYCIATSRL-WDASFTCPL--CGENV 286 (298)
T ss_pred cCCceeeccCCC---CCCCeeeccccceeehhhhhhhhc-chhhcccCc--cCCCC
Confidence 457889999985 478888667999999999998776 346789999 87643
No 40
>PF04641 Rtf2: Rtf2 RING-finger
Probab=97.37 E-value=0.00018 Score=61.51 Aligned_cols=58 Identities=19% Similarity=0.475 Sum_probs=41.4
Q ss_pred ccceeeccCcCCCCccccCCccccCCCccccHHHHHHHHHhcCCCCCCCCCCCCCCccCCCCcc
Q 029888 87 NILNISCPLSGKPITELAEPVRSVECKHIYEKNAIQAYIKSKNANARCPVAGCPRKLQVSKVVC 150 (186)
Q Consensus 87 ~~~~l~CPI~~~~~~~l~dPV~s~~CgH~fck~~I~~~l~~~~~~~~CPv~GC~~~l~~~~L~~ 150 (186)
....+.||||+..|+--..=|--..|||+|+..||.+.- ....||+ |...+...|+++
T Consensus 110 ~~~~~~CPvt~~~~~~~~~fv~l~~cG~V~s~~alke~k----~~~~Cp~--c~~~f~~~DiI~ 167 (260)
T PF04641_consen 110 SEGRFICPVTGKEFNGKHKFVYLRPCGCVFSEKALKELK----KSKKCPV--CGKPFTEEDIIP 167 (260)
T ss_pred CCceeECCCCCcccCCceeEEEEcCCCCEeeHHHHHhhc----ccccccc--cCCccccCCEEE
Confidence 345799999997432111122225899999999999982 3457999 999998887653
No 41
>KOG1002 consensus Nucleotide excision repair protein RAD16 [Replication, recombination and repair]
Probab=97.28 E-value=0.00017 Score=67.14 Aligned_cols=52 Identities=29% Similarity=0.690 Sum_probs=42.5
Q ss_pred eeeccCcCCCCccccCCccccCCCccccHHHHHHHHHh--cCCCCCCCCCCCCCCccCCC
Q 029888 90 NISCPLSGKPITELAEPVRSVECKHIYEKNAIQAYIKS--KNANARCPVAGCPRKLQVSK 147 (186)
Q Consensus 90 ~l~CPI~~~~~~~l~dPV~s~~CgH~fck~~I~~~l~~--~~~~~~CPv~GC~~~l~~~~ 147 (186)
...|-+|..| -++|+. +.|.|+||+-||.+|+.+ .+..+.||+ |...|+.+.
T Consensus 536 ~~~C~lc~d~---aed~i~-s~ChH~FCrlCi~eyv~~f~~~~nvtCP~--C~i~LsiDl 589 (791)
T KOG1002|consen 536 EVECGLCHDP---AEDYIE-SSCHHKFCRLCIKEYVESFMENNNVTCPV--CHIGLSIDL 589 (791)
T ss_pred ceeecccCCh---hhhhHh-hhhhHHHHHHHHHHHHHhhhcccCCCCcc--ccccccccc
Confidence 4669999985 599999 789999999999999875 233489999 988776553
No 42
>KOG0826 consensus Predicted E3 ubiquitin ligase involved in peroxisome organization [Posttranslational modification, protein turnover, chaperones]
Probab=97.19 E-value=0.00019 Score=63.20 Aligned_cols=47 Identities=23% Similarity=0.446 Sum_probs=38.2
Q ss_pred eeeccCcCCCCccccCCccccCCCccccHHHHHHHHHhcCCCCCCCCCCCCCC
Q 029888 90 NISCPLSGKPITELAEPVRSVECKHIYEKNAIQAYIKSKNANARCPVAGCPRK 142 (186)
Q Consensus 90 ~l~CPI~~~~~~~l~dPV~s~~CgH~fck~~I~~~l~~~~~~~~CPv~GC~~~ 142 (186)
.-.||+|.+ --.+|-.-..-|.+||..||.+|+. .-..|||+||...
T Consensus 300 ~~~CpvClk---~r~Nptvl~vSGyVfCY~Ci~~Yv~---~~~~CPVT~~p~~ 346 (357)
T KOG0826|consen 300 REVCPVCLK---KRQNPTVLEVSGYVFCYPCIFSYVV---NYGHCPVTGYPAS 346 (357)
T ss_pred cccChhHHh---ccCCCceEEecceEEeHHHHHHHHH---hcCCCCccCCcch
Confidence 567999998 4578866466799999999999999 2357999999753
No 43
>PF12861 zf-Apc11: Anaphase-promoting complex subunit 11 RING-H2 finger
Probab=97.13 E-value=0.00094 Score=48.21 Aligned_cols=54 Identities=19% Similarity=0.495 Sum_probs=41.7
Q ss_pred cceeeccCcCCCCccccCCccccCCCccccHHHHHHHHHhcCCCCCCCCCCCCCCccC
Q 029888 88 ILNISCPLSGKPITELAEPVRSVECKHIYEKNAIQAYIKSKNANARCPVAGCPRKLQV 145 (186)
Q Consensus 88 ~~~l~CPI~~~~~~~l~dPV~s~~CgH~fck~~I~~~l~~~~~~~~CPv~GC~~~l~~ 145 (186)
.++-.||.|..| --.-|+.--.|+|.|-..||++|+.+......||. |++....
T Consensus 30 ~fdg~Cp~Ck~P--gd~Cplv~g~C~H~FH~hCI~kWl~~~~~~~~CPm--CR~~w~~ 83 (85)
T PF12861_consen 30 PFDGCCPDCKFP--GDDCPLVWGKCSHNFHMHCILKWLSTQSSKGQCPM--CRQPWKF 83 (85)
T ss_pred ccccCCCCccCC--CCCCceeeccCccHHHHHHHHHHHccccCCCCCCC--cCCeeee
Confidence 467789999876 23447654689999999999999985444578999 9986543
No 44
>KOG3039 consensus Uncharacterized conserved protein [Function unknown]
Probab=96.96 E-value=0.00055 Score=58.38 Aligned_cols=54 Identities=17% Similarity=0.355 Sum_probs=44.7
Q ss_pred ceeeccCcCCCCccccCCccc---cCCCccccHHHHHHHHHhcCCCCCCCCCCCCCCccCCCCcc
Q 029888 89 LNISCPLSGKPITELAEPVRS---VECKHIYEKNAIQAYIKSKNANARCPVAGCPRKLQVSKVVC 150 (186)
Q Consensus 89 ~~l~CPI~~~~~~~l~dPV~s---~~CgH~fck~~I~~~l~~~~~~~~CPv~GC~~~l~~~~L~~ 150 (186)
..+.||+|.. .|.+-+.. ..|||+|+++|++.+|+ +...||+ |...+...++++
T Consensus 220 ~ryiCpvtrd---~LtNt~~ca~Lr~sg~Vv~~ecvEklir---~D~v~pv--~d~plkdrdiI~ 276 (303)
T KOG3039|consen 220 KRYICPVTRD---TLTNTTPCAVLRPSGHVVTKECVEKLIR---KDMVDPV--TDKPLKDRDIIG 276 (303)
T ss_pred cceecccchh---hhcCccceEEeccCCcEeeHHHHHHhcc---ccccccC--CCCcCcccceEe
Confidence 4799999997 67776543 57999999999999998 5568999 888888887765
No 45
>KOG0824 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=96.80 E-value=0.00069 Score=59.10 Aligned_cols=50 Identities=22% Similarity=0.365 Sum_probs=41.2
Q ss_pred ceeeccCcCCCCccccCCccccCCCccccHHHHHHHHHhcCCCCCCCCCCCCCCccCC
Q 029888 89 LNISCPLSGKPITELAEPVRSVECKHIYEKNAIQAYIKSKNANARCPVAGCPRKLQVS 146 (186)
Q Consensus 89 ~~l~CPI~~~~~~~l~dPV~s~~CgH~fck~~I~~~l~~~~~~~~CPv~GC~~~l~~~ 146 (186)
..-.|+||+. ...-||. ..|+|.||.-||..-.. ++...||+ |+..+...
T Consensus 6 ~~~eC~IC~n---t~n~Pv~-l~C~HkFCyiCiKGsy~--ndk~~Cav--CR~pids~ 55 (324)
T KOG0824|consen 6 KKKECLICYN---TGNCPVN-LYCFHKFCYICIKGSYK--NDKKTCAV--CRFPIDST 55 (324)
T ss_pred cCCcceeeec---cCCcCcc-ccccchhhhhhhcchhh--cCCCCCce--ecCCCCcc
Confidence 4567999995 7889977 99999999999998877 35567999 99887543
No 46
>KOG0289 consensus mRNA splicing factor [General function prediction only]
Probab=96.75 E-value=0.00093 Score=60.92 Aligned_cols=52 Identities=31% Similarity=0.576 Sum_probs=43.6
Q ss_pred eeccCcCCCCccccCCccccCCCccccHHHHHHHHHhcCCCCCCCCCCCCCCccCCCCcc
Q 029888 91 ISCPLSGKPITELAEPVRSVECKHIYEKNAIQAYIKSKNANARCPVAGCPRKLQVSKVVC 150 (186)
Q Consensus 91 l~CPI~~~~~~~l~dPV~s~~CgH~fck~~I~~~l~~~~~~~~CPv~GC~~~l~~~~L~~ 150 (186)
+.|.|+++ +=++||.|..-||+|+|.-|++||.. . ..||+ -+..++.++|++
T Consensus 1 m~CaISgE---vP~~PVvS~~Sg~vfEkrLIEqyI~e-~--G~DPI--t~~pLs~eelV~ 52 (506)
T KOG0289|consen 1 MVCAISGE---VPEEPVVSPVSGHVFEKRLIEQYIAE-T--GKDPI--TNEPLSIEELVE 52 (506)
T ss_pred CeecccCC---CCCCccccccccchHHHHHHHHHHHH-c--CCCCC--CCCcCCHHHeee
Confidence 46999997 77999999999999999999999994 3 37999 557787776654
No 47
>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=96.68 E-value=0.00072 Score=57.52 Aligned_cols=68 Identities=22% Similarity=0.425 Sum_probs=49.7
Q ss_pred ceeeccCcCCCCccccCCc----cccCCCccccHHHHHHHHHhcCCCCCCCCCCCCCCccCCC----CccCHHHHHHHHH
Q 029888 89 LNISCPLSGKPITELAEPV----RSVECKHIYEKNAIQAYIKSKNANARCPVAGCPRKLQVSK----VVCDSLLLVDIDE 160 (186)
Q Consensus 89 ~~l~CPI~~~~~~~l~dPV----~s~~CgH~fck~~I~~~l~~~~~~~~CPv~GC~~~l~~~~----L~~d~~L~~~I~~ 160 (186)
.+-+||||.. -.+.+|= .|..|=|.-|.+|+...+. .|..+||..||++.|.... ...|..+.+.+.-
T Consensus 9 ~d~~CPvCks--DrYLnPdik~linPECyHrmCESCvdRIFs--~GpAqCP~~gC~kILRK~kf~~qtFeD~~vEkEvdv 84 (314)
T COG5220 9 EDRRCPVCKS--DRYLNPDIKILINPECYHRMCESCVDRIFS--RGPAQCPYKGCGKILRKIKFIKQTFEDITVEKEVDV 84 (314)
T ss_pred hcccCCcccc--ccccCCCeEEEECHHHHHHHHHHHHHHHhc--CCCCCCCCccHHHHHHHhcccccccchhhhhhhhhH
Confidence 3568999996 3556662 3456999999999999998 4789999999998876443 3445555544443
No 48
>KOG4159 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=96.60 E-value=0.0011 Score=60.14 Aligned_cols=47 Identities=21% Similarity=0.570 Sum_probs=40.4
Q ss_pred ceeeccCcCCCCccccCCccccCCCccccHHHHHHHHHhcCCCCCCCCCCCCCCcc
Q 029888 89 LNISCPLSGKPITELAEPVRSVECKHIYEKNAIQAYIKSKNANARCPVAGCPRKLQ 144 (186)
Q Consensus 89 ~~l~CPI~~~~~~~l~dPV~s~~CgH~fck~~I~~~l~~~~~~~~CPv~GC~~~l~ 144 (186)
..|-|-||.. .|..||+ +.|||+||..||.+.+. ....||. |+..+.
T Consensus 83 sef~c~vc~~---~l~~pv~-tpcghs~c~~Cl~r~ld---~~~~cp~--Cr~~l~ 129 (398)
T KOG4159|consen 83 SEFECCVCSR---ALYPPVV-TPCGHSFCLECLDRSLD---QETECPL--CRDELV 129 (398)
T ss_pred chhhhhhhHh---hcCCCcc-ccccccccHHHHHHHhc---cCCCCcc--cccccc
Confidence 4799999996 8899999 79999999999999666 5578999 987665
No 49
>KOG0802 consensus E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=96.44 E-value=0.0015 Score=61.32 Aligned_cols=46 Identities=26% Similarity=0.686 Sum_probs=37.3
Q ss_pred eeeccCcCCCCccccC-----CccccCCCccccHHHHHHHHHhcCCCCCCCCCCCCCCcc
Q 029888 90 NISCPLSGKPITELAE-----PVRSVECKHIYEKNAIQAYIKSKNANARCPVAGCPRKLQ 144 (186)
Q Consensus 90 ~l~CPI~~~~~~~l~d-----PV~s~~CgH~fck~~I~~~l~~~~~~~~CPv~GC~~~l~ 144 (186)
...|+||.+ .|.. |-+ ..|||+|...|+..|++. ...||. |+..+.
T Consensus 291 ~~~C~IC~e---~l~~~~~~~~~r-L~C~Hifh~~CL~~W~er---~qtCP~--CR~~~~ 341 (543)
T KOG0802|consen 291 DELCIICLE---ELHSGHNITPKR-LPCGHIFHDSCLRSWFER---QQTCPT--CRTVLY 341 (543)
T ss_pred CCeeeeech---hhccccccccce-eecccchHHHHHHHHHHH---hCcCCc--chhhhh
Confidence 456999998 5666 556 789999999999999993 468999 987443
No 50
>KOG3113 consensus Uncharacterized conserved protein [Function unknown]
Probab=96.39 E-value=0.0022 Score=54.87 Aligned_cols=54 Identities=19% Similarity=0.405 Sum_probs=39.1
Q ss_pred eeeccCcCCCCccccCCccccCCCccccHHHHHHHHHhcCCCCCCCCCCCCCCccCCCCcc
Q 029888 90 NISCPLSGKPITELAEPVRSVECKHIYEKNAIQAYIKSKNANARCPVAGCPRKLQVSKVVC 150 (186)
Q Consensus 90 ~l~CPI~~~~~~~l~dPV~s~~CgH~fck~~I~~~l~~~~~~~~CPv~GC~~~l~~~~L~~ 150 (186)
.|.|||++-+|+--..=+-...|||+|+..++.++- ...|++ |+..+...+.++
T Consensus 111 ~fiCPvtgleMng~~~F~~l~~CGcV~SerAlKeik-----as~C~~--C~a~y~~~dvIv 164 (293)
T KOG3113|consen 111 RFICPVTGLEMNGKYRFCALRCCGCVFSERALKEIK-----ASVCHV--CGAAYQEDDVIV 164 (293)
T ss_pred eeecccccceecceEEEEEEeccceeccHHHHHHhh-----hccccc--cCCcccccCeEe
Confidence 699999996432222222236899999999988864 357999 999888777543
No 51
>KOG4642 consensus Chaperone-dependent E3 ubiquitin protein ligase (contains TPR repeats) [Posttranslational modification, protein turnover, chaperones]
Probab=96.38 E-value=0.0032 Score=53.90 Aligned_cols=69 Identities=14% Similarity=0.172 Sum_probs=59.7
Q ss_pred eeeccCcCCCCccccCCccccCCCccccHHHHHHHHHhcCCCCCCCCCCCCCCccCCCCccCHHHHHHHHHHHhcCc
Q 029888 90 NISCPLSGKPITELAEPVRSVECKHIYEKNAIQAYIKSKNANARCPVAGCPRKLQVSKVVCDSLLLVDIDEMRRTSK 166 (186)
Q Consensus 90 ~l~CPI~~~~~~~l~dPV~s~~CgH~fck~~I~~~l~~~~~~~~CPv~GC~~~l~~~~L~~d~~L~~~I~~~r~~~~ 166 (186)
-++|.|+.. +|.+||+ +.-|-+|++..|.++++. .+. -=|+ .+..|+...+.||..|+..|..+++..+
T Consensus 211 ~lcgkIt~e---l~~~pvi-~psgIty~ra~I~Ehl~r-vgh-fdpv--tr~~Lte~q~ipN~alkevIa~fl~~n~ 279 (284)
T KOG4642|consen 211 YLCGKITLE---LMREPVI-TPSGITYDRADIEEHLQR-VGH-FDPV--TRWPLTEYQLIPNLALKEVIAAFLKENE 279 (284)
T ss_pred hhhhhhhHH---hhcCCcc-CccccchhHHHHHHHHHH-hcc-CCch--hcccCCHHhhccchHHHHHHHHHHHhcc
Confidence 367899996 8999999 899999999999999993 443 4599 6688999999999999999999998643
No 52
>COG5540 RING-finger-containing ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=96.19 E-value=0.0032 Score=55.25 Aligned_cols=49 Identities=16% Similarity=0.569 Sum_probs=38.7
Q ss_pred eeccCcCCCCccccCCccccCCCccccHHHHHHHHHhcCCCCCCCCCCCCCCcc
Q 029888 91 ISCPLSGKPITELAEPVRSVECKHIYEKNAIQAYIKSKNANARCPVAGCPRKLQ 144 (186)
Q Consensus 91 l~CPI~~~~~~~l~dPV~s~~CgH~fck~~I~~~l~~~~~~~~CPv~GC~~~l~ 144 (186)
.-|-||+.-| +=.+-++-+.|.|.|-..||..|+.. -+.+||+ |+..+.
T Consensus 324 veCaICms~f-iK~d~~~vlPC~H~FH~~Cv~kW~~~--y~~~CPv--Crt~iP 372 (374)
T COG5540 324 VECAICMSNF-IKNDRLRVLPCDHRFHVGCVDKWLLG--YSNKCPV--CRTAIP 372 (374)
T ss_pred ceEEEEhhhh-cccceEEEeccCceechhHHHHHHhh--hcccCCc--cCCCCC
Confidence 6799999744 23345555899999999999999983 5578999 988764
No 53
>KOG1645 consensus RING-finger-containing E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=96.17 E-value=0.0023 Score=57.93 Aligned_cols=58 Identities=21% Similarity=0.561 Sum_probs=44.9
Q ss_pred eeccCcCCCCccccCCc----cccCCCccccHHHHHHHHHhcCCCCCCCCCCCCCCccCCCCccCHHH
Q 029888 91 ISCPLSGKPITELAEPV----RSVECKHIYEKNAIQAYIKSKNANARCPVAGCPRKLQVSKVVCDSLL 154 (186)
Q Consensus 91 l~CPI~~~~~~~l~dPV----~s~~CgH~fck~~I~~~l~~~~~~~~CPv~GC~~~l~~~~L~~d~~L 154 (186)
.+||||+. -+.-|+ .+..|||-|-..||+.||. .....+||. |...-+..+|.+-..+
T Consensus 5 ~tcpicld---s~~~~g~hr~vsl~cghlFgs~cie~wl~-k~~~~~cp~--c~~katkr~i~~e~al 66 (463)
T KOG1645|consen 5 TTCPICLD---SYTTAGNHRIVSLQCGHLFGSQCIEKWLG-KKTKMQCPL--CSGKATKRQIRPEYAL 66 (463)
T ss_pred ccCceeee---eeeecCceEEeeecccccccHHHHHHHHh-hhhhhhCcc--cCChhHHHHHHHHHHH
Confidence 56999997 445564 3578999999999999997 456678999 9877777777664433
No 54
>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=96.16 E-value=0.0079 Score=52.29 Aligned_cols=64 Identities=20% Similarity=0.368 Sum_probs=47.0
Q ss_pred eccCcCCCCccccCCcc---ccCCCccccHHHHHHHHHhcCCCCCCCCCCCCCCccCCC----CccCHHHHHHHHHH
Q 029888 92 SCPLSGKPITELAEPVR---SVECKHIYEKNAIQAYIKSKNANARCPVAGCPRKLQVSK----VVCDSLLLVDIDEM 161 (186)
Q Consensus 92 ~CPI~~~~~~~l~dPV~---s~~CgH~fck~~I~~~l~~~~~~~~CPv~GC~~~l~~~~----L~~d~~L~~~I~~~ 161 (186)
.||+|.- ..+.+|-. +..|||.-|.+|+-..+. .+...|| ||...|.... +..|+.+...+.-.
T Consensus 2 ~Cp~CKt--~~Y~np~lk~~in~C~H~lCEsCvd~iF~--~g~~~Cp--eC~~iLRk~nfr~q~fED~~vekEv~iR 72 (300)
T KOG3800|consen 2 ACPKCKT--DRYLNPDLKLMINECGHRLCESCVDRIFS--LGPAQCP--ECMVILRKNNFRVQTFEDPTVEKEVDIR 72 (300)
T ss_pred CCccccc--ceecCccceeeeccccchHHHHHHHHHHh--cCCCCCC--cccchhhhcccchhhcchhHHHHHHHHH
Confidence 4999987 56777731 238999999999999888 4778999 4999887554 45677665554443
No 55
>KOG3039 consensus Uncharacterized conserved protein [Function unknown]
Probab=95.95 E-value=0.0049 Score=52.71 Aligned_cols=34 Identities=26% Similarity=0.469 Sum_probs=29.6
Q ss_pred eeeccCcCCCCccccCCccccCCCccccHHHHHHHHHh
Q 029888 90 NISCPLSGKPITELAEPVRSVECKHIYEKNAIQAYIKS 127 (186)
Q Consensus 90 ~l~CPI~~~~~~~l~dPV~s~~CgH~fck~~I~~~l~~ 127 (186)
--.|.+|++|+ .+||. +.=||.||++||++||-.
T Consensus 43 FdcCsLtLqPc---~dPvi-t~~GylfdrEaILe~ila 76 (303)
T KOG3039|consen 43 FDCCSLTLQPC---RDPVI-TPDGYLFDREAILEYILA 76 (303)
T ss_pred cceeeeecccc---cCCcc-CCCCeeeeHHHHHHHHHH
Confidence 34799999965 99999 788999999999999863
No 56
>COG5243 HRD1 HRD ubiquitin ligase complex, ER membrane component [Posttranslational modification, protein turnover, chaperones]
Probab=95.92 E-value=0.0065 Score=54.71 Aligned_cols=46 Identities=20% Similarity=0.623 Sum_probs=36.8
Q ss_pred eeeccCcCCCCccccCC------------ccccCCCccccHHHHHHHHHhcCCCCCCCCCCCCCCc
Q 029888 90 NISCPLSGKPITELAEP------------VRSVECKHIYEKNAIQAYIKSKNANARCPVAGCPRKL 143 (186)
Q Consensus 90 ~l~CPI~~~~~~~l~dP------------V~s~~CgH~fck~~I~~~l~~~~~~~~CPv~GC~~~l 143 (186)
+-.|-||++ ++|.-| -+ ..|||.+--.|+..|+. +...||+ |+.++
T Consensus 287 D~~C~ICmd--e~~h~~~~~~~~~~~~~pKr-LpCGHilHl~CLknW~E---RqQTCPI--Cr~p~ 344 (491)
T COG5243 287 DRTCTICMD--EMFHPDHEPLPRGLDMTPKR-LPCGHILHLHCLKNWLE---RQQTCPI--CRRPV 344 (491)
T ss_pred CCeEEEecc--cccCCCCccCcccccCCccc-ccccceeeHHHHHHHHH---hccCCCc--ccCcc
Confidence 678999998 334444 45 78999999999999998 4568999 98764
No 57
>KOG2817 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=95.92 E-value=0.0056 Score=55.20 Aligned_cols=52 Identities=25% Similarity=0.565 Sum_probs=38.0
Q ss_pred eeeccCcCCCCccccC-CccccCCCccccHHHHHHHHHhcCCCCCCCCCCCCCCccC
Q 029888 90 NISCPLSGKPITELAE-PVRSVECKHIYEKNAIQAYIKSKNANARCPVAGCPRKLQV 145 (186)
Q Consensus 90 ~l~CPI~~~~~~~l~d-PV~s~~CgH~fck~~I~~~l~~~~~~~~CPv~GC~~~l~~ 145 (186)
.|.|||..+. ..=.+ |++ ..|||+-++++|..+.++...+++||. |+.....
T Consensus 334 vF~CPVlKeq-tsdeNPPm~-L~CGHVISkdAlnrLS~ng~~sfKCPY--CP~e~~~ 386 (394)
T KOG2817|consen 334 VFICPVLKEQ-TSDENPPMM-LICGHVISKDALNRLSKNGSQSFKCPY--CPVEQLA 386 (394)
T ss_pred eeecccchhh-ccCCCCCee-eeccceecHHHHHHHhhCCCeeeeCCC--CCcccCH
Confidence 5899998752 12233 556 899999999999999884223499999 9865433
No 58
>KOG0828 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=95.74 E-value=0.0057 Score=56.74 Aligned_cols=50 Identities=24% Similarity=0.596 Sum_probs=36.4
Q ss_pred eeeccCcCCCCccccC---C-----------ccccCCCccccHHHHHHHHHhcCCCCCCCCCCCCCCcc
Q 029888 90 NISCPLSGKPITELAE---P-----------VRSVECKHIYEKNAIQAYIKSKNANARCPVAGCPRKLQ 144 (186)
Q Consensus 90 ~l~CPI~~~~~~~l~d---P-----------V~s~~CgH~fck~~I~~~l~~~~~~~~CPv~GC~~~l~ 144 (186)
..-|+||+.++ .+.. | +.-+.|.|+|-+.|+++|+.. .+..||+ |+..|.
T Consensus 571 t~dC~ICMt~I-~l~~~~s~~~~~~~~~~~nYm~tPC~HifH~~CL~~WMd~--ykl~CPv--CR~pLP 634 (636)
T KOG0828|consen 571 TNDCVICMTPI-DLRSTGSDCMVASMMVRRNYMLTPCHHIFHRQCLLQWMDT--YKLICPV--CRCPLP 634 (636)
T ss_pred cccceEecccc-ceeeccCcchhhhhhhhccccccchHHHHHHHHHHHHHhh--hcccCCc--cCCCCC
Confidence 45699999876 2221 1 111589999999999999983 4578999 987664
No 59
>KOG4628 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=95.47 E-value=0.011 Score=52.72 Aligned_cols=49 Identities=24% Similarity=0.647 Sum_probs=39.0
Q ss_pred eeccCcCCCCccccCCccccCCCccccHHHHHHHHHhcCCCCCCCCCCCCCCcc
Q 029888 91 ISCPLSGKPITELAEPVRSVECKHIYEKNAIQAYIKSKNANARCPVAGCPRKLQ 144 (186)
Q Consensus 91 l~CPI~~~~~~~l~dPV~s~~CgH~fck~~I~~~l~~~~~~~~CPv~GC~~~l~ 144 (186)
..|-||++-+ .--+=++-..|+|.|=..||-.||.+ . ...||+ |...+.
T Consensus 230 ~~CaIClEdY-~~GdklRiLPC~H~FH~~CIDpWL~~-~-r~~CPv--CK~di~ 278 (348)
T KOG4628|consen 230 DTCAICLEDY-EKGDKLRILPCSHKFHVNCIDPWLTQ-T-RTFCPV--CKRDIR 278 (348)
T ss_pred ceEEEeeccc-ccCCeeeEecCCCchhhccchhhHhh-c-CccCCC--CCCcCC
Confidence 5699999855 44566776899999999999999994 3 356999 987554
No 60
>KOG1814 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=95.30 E-value=0.0087 Score=54.34 Aligned_cols=55 Identities=15% Similarity=0.414 Sum_probs=40.2
Q ss_pred eeeccCcCCCCcccc-CCccccCCCccccHHHHHHHHHh-----cCCCCCCCCCCCCCCccCC
Q 029888 90 NISCPLSGKPITELA-EPVRSVECKHIYEKNAIQAYIKS-----KNANARCPVAGCPRKLQVS 146 (186)
Q Consensus 90 ~l~CPI~~~~~~~l~-dPV~s~~CgH~fck~~I~~~l~~-----~~~~~~CPv~GC~~~l~~~ 146 (186)
.+.|-||... .+- .=+.=+.|+|+||+.|+..|... .....+||..||.......
T Consensus 184 lf~C~ICf~e--~~G~~c~~~lpC~Hv~Ck~C~kdY~~~~i~eg~v~~l~Cp~~~C~~~a~~g 244 (445)
T KOG1814|consen 184 LFDCCICFEE--QMGQHCFKFLPCSHVFCKSCLKDYFTIQIQEGQVSCLKCPDPKCGSVAPPG 244 (445)
T ss_pred cccceeeehh--hcCcceeeecccchHHHHHHHHHHHHHhhhcceeeeecCCCCCCcccCCch
Confidence 6899999862 121 23333789999999999999863 2356789999998765554
No 61
>KOG1812 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=95.21 E-value=0.014 Score=52.79 Aligned_cols=58 Identities=22% Similarity=0.487 Sum_probs=42.5
Q ss_pred cceeeccCcCCCCccccCC---ccccCCCccccHHHHHHHHHh---cCCCCCCCCCCCCCCccCCCC
Q 029888 88 ILNISCPLSGKPITELAEP---VRSVECKHIYEKNAIQAYIKS---KNANARCPVAGCPRKLQVSKV 148 (186)
Q Consensus 88 ~~~l~CPI~~~~~~~l~dP---V~s~~CgH~fck~~I~~~l~~---~~~~~~CPv~GC~~~l~~~~L 148 (186)
.....|+||.. ....+ .....|+|.||+.|+.+|+.. .+...+||..||...++...+
T Consensus 144 ~~~~~C~iC~~---e~~~~~~~f~~~~C~H~fC~~C~k~~iev~~~~~~~~~C~~~~C~~~l~~~~c 207 (384)
T KOG1812|consen 144 LPKEECGICFV---EDPEAEDMFSVLKCGHRFCKDCVKQHIEVKLLSGTVIRCPHDGCESRLTLESC 207 (384)
T ss_pred cccccCccCcc---ccccHhhhHHHhcccchhhhHHhHHHhhhhhccCCCccCCCCCCCccCCHHHH
Confidence 44678999983 11111 123579999999999999974 356788999999988876554
No 62
>KOG0804 consensus Cytoplasmic Zn-finger protein BRAP2 (BRCA1 associated protein) [General function prediction only]
Probab=95.03 E-value=0.0072 Score=55.37 Aligned_cols=45 Identities=18% Similarity=0.516 Sum_probs=35.4
Q ss_pred eeeccCcCCCCccccCCc---cccCCCccccHHHHHHHHHhcCCCCCCCCCCCCCCcc
Q 029888 90 NISCPLSGKPITELAEPV---RSVECKHIYEKNAIQAYIKSKNANARCPVAGCPRKLQ 144 (186)
Q Consensus 90 ~l~CPI~~~~~~~l~dPV---~s~~CgH~fck~~I~~~l~~~~~~~~CPv~GC~~~l~ 144 (186)
--+||+|++ .|-.-+ ..+.|.|+|--.|++.|+- ..||| |+-..+
T Consensus 175 LPTCpVCLE---RMD~s~~gi~t~~c~Hsfh~~cl~~w~~-----~scpv--cR~~q~ 222 (493)
T KOG0804|consen 175 LPTCPVCLE---RMDSSTTGILTILCNHSFHCSCLMKWWD-----SSCPV--CRYCQS 222 (493)
T ss_pred CCCcchhHh---hcCccccceeeeecccccchHHHhhccc-----CcChh--hhhhcC
Confidence 358999997 555555 5578999999999999977 36999 976444
No 63
>KOG1001 consensus Helicase-like transcription factor HLTF/DNA helicase RAD5, DEAD-box superfamily [Transcription; Replication, recombination and repair]
Probab=94.75 E-value=0.0054 Score=59.16 Aligned_cols=52 Identities=23% Similarity=0.472 Sum_probs=42.2
Q ss_pred eeccCcCCCCccccCCccccCCCccccHHHHHHHHHhcCCCCCCCCCCCCCCccCCCCcc
Q 029888 91 ISCPLSGKPITELAEPVRSVECKHIYEKNAIQAYIKSKNANARCPVAGCPRKLQVSKVVC 150 (186)
Q Consensus 91 l~CPI~~~~~~~l~dPV~s~~CgH~fck~~I~~~l~~~~~~~~CPv~GC~~~l~~~~L~~ 150 (186)
+.|++|.. ...|+. +.|||.||.+|+...|.. .....||. |+..+....|..
T Consensus 455 ~~c~ic~~----~~~~~i-t~c~h~~c~~c~~~~i~~-~~~~~~~~--cr~~l~~~~l~s 506 (674)
T KOG1001|consen 455 HWCHICCD----LDSFFI-TRCGHDFCVECLKKSIQQ-SENAPCPL--CRNVLKEKKLLS 506 (674)
T ss_pred cccccccc----ccccee-ecccchHHHHHHHhcccc-ccCCCCcH--HHHHHHHHHHhh
Confidence 79999995 577887 899999999999999984 44458999 988776555544
No 64
>KOG4362 consensus Transcriptional regulator BRCA1 [Replication, recombination and repair; Transcription]
Probab=94.63 E-value=0.012 Score=56.52 Aligned_cols=69 Identities=19% Similarity=0.415 Sum_probs=54.0
Q ss_pred ceeeccCcCCCCccccCCccccCCCccccHHHHHHHHHhcCCCCCCCCCCCCCCccCCCCccCHHHHHHHHHHHh
Q 029888 89 LNISCPLSGKPITELAEPVRSVECKHIYEKNAIQAYIKSKNANARCPVAGCPRKLQVSKVVCDSLLLVDIDEMRR 163 (186)
Q Consensus 89 ~~l~CPI~~~~~~~l~dPV~s~~CgH~fck~~I~~~l~~~~~~~~CPv~GC~~~l~~~~L~~d~~L~~~I~~~r~ 163 (186)
..+.||||.. ...+|+. ++|-|.||+.|+-..+...+....||+ |...+....+..-+...+.++++..
T Consensus 20 k~lEc~ic~~---~~~~p~~-~kc~~~~l~~~~n~~f~~~~~~~~~~l--c~~~~eK~s~~Es~r~sq~vqe~lk 88 (684)
T KOG4362|consen 20 KILECPICLE---HVKEPSL-LKCDHIFLKFCLNKLFESKKGPKQCAL--CKSDIEKRSLRESPRFSQLSKESLK 88 (684)
T ss_pred hhccCCceeE---Eeeccch-hhhhHHHHhhhhhceeeccCccccchh--hhhhhhhhhccccchHHHHHHHhcC
Confidence 4688999997 5589976 899999999999887764455889999 9988887777775555566665443
No 65
>KOG4367 consensus Predicted Zn-finger protein [Function unknown]
Probab=94.61 E-value=0.018 Score=52.95 Aligned_cols=34 Identities=21% Similarity=0.537 Sum_probs=30.7
Q ss_pred eeeccCcCCCCccccCCccccCCCccccHHHHHHHHHh
Q 029888 90 NISCPLSGKPITELAEPVRSVECKHIYEKNAIQAYIKS 127 (186)
Q Consensus 90 ~l~CPI~~~~~~~l~dPV~s~~CgH~fck~~I~~~l~~ 127 (186)
.++||||+. .|++|+. ..|||+.|+.|-...+.+
T Consensus 4 elkc~vc~~---f~~epii-l~c~h~lc~~ca~~~~~~ 37 (699)
T KOG4367|consen 4 ELKCPVCGS---FYREPII-LPCSHNLCQACARNILVQ 37 (699)
T ss_pred cccCceehh---hccCceE-eecccHHHHHHHHhhccc
Confidence 689999997 8999999 899999999999987763
No 66
>KOG1734 consensus Predicted RING-containing E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=94.60 E-value=0.0076 Score=52.14 Aligned_cols=59 Identities=17% Similarity=0.584 Sum_probs=42.1
Q ss_pred ceeeccCcCCCCc-------cccCCccccCCCccccHHHHHHHHHhcCCCCCCCCCCCCCCccCCCCccC
Q 029888 89 LNISCPLSGKPIT-------ELAEPVRSVECKHIYEKNAIQAYIKSKNANARCPVAGCPRKLQVSKVVCD 151 (186)
Q Consensus 89 ~~l~CPI~~~~~~-------~l~dPV~s~~CgH~fck~~I~~~l~~~~~~~~CPv~GC~~~l~~~~L~~d 151 (186)
.+-.|-+|++-+- ++++-.+ ..|+|+|-..||..|.- -++...||- |.+.+..+.+..|
T Consensus 223 ~d~vCaVCg~~~~~s~~eegvienty~-LsCnHvFHEfCIrGWci-vGKkqtCPY--CKekVdl~rmfsn 288 (328)
T KOG1734|consen 223 SDSVCAVCGQQIDVSVDEEGVIENTYK-LSCNHVFHEFCIRGWCI-VGKKQTCPY--CKEKVDLKRMFSN 288 (328)
T ss_pred CcchhHhhcchheeecchhhhhhhhee-eecccchHHHhhhhhee-ecCCCCCch--HHHHhhHhhhccC
Confidence 3445778876321 1224455 78999999999999976 357788999 9887776666555
No 67
>KOG2042 consensus Ubiquitin fusion degradation protein-2 [Posttranslational modification, protein turnover, chaperones]
Probab=94.38 E-value=0.074 Score=52.92 Aligned_cols=71 Identities=15% Similarity=0.170 Sum_probs=61.5
Q ss_pred ceeeccCcCCCCccccCCccccCCCccccHHHHHHHHHhcCCCCCCCCCCCCCCccCCCCccCHHHHHHHHHHHhcCcc
Q 029888 89 LNISCPLSGKPITELAEPVRSVECKHIYEKNAIQAYIKSKNANARCPVAGCPRKLQVSKVVCDSLLLVDIDEMRRTSKE 167 (186)
Q Consensus 89 ~~l~CPI~~~~~~~l~dPV~s~~CgH~fck~~I~~~l~~~~~~~~CPv~GC~~~l~~~~L~~d~~L~~~I~~~r~~~~~ 167 (186)
..+..||.. ++|.+||.-..-|++-+|..|..++. ....=|. |+..|+.+.+.+|..|+.+|+.|.+.++.
T Consensus 869 def~DPlm~---Tlm~dPV~LP~Srv~vDRsti~rhlL---s~~tdPF--NR~pLt~d~v~pn~eLK~kI~~~~~ek~~ 939 (943)
T KOG2042|consen 869 DEFLDPLMS---TLMSDPVVLPSSRVTVDRSTIERHLL---SDCTDPF--NREPLTEDMVSPNEELKAKIRCWIKEKRN 939 (943)
T ss_pred hhhhCcccc---ccCCCCccCCcccccccHHHHHHHHh---cCCCCcc--ccccCchhhcCCCHHHHHHHHHHHHHhhh
Confidence 378899998 48999999445899999999999998 3356799 99999999999999999999999876444
No 68
>KOG0825 consensus PHD Zn-finger protein [General function prediction only]
Probab=94.29 E-value=0.0038 Score=60.65 Aligned_cols=50 Identities=14% Similarity=0.341 Sum_probs=36.5
Q ss_pred ceeeccCcCCCCccccCCccc--cCCCccccHHHHHHHHHhcCCCCCCCCCCCCCCccCC
Q 029888 89 LNISCPLSGKPITELAEPVRS--VECKHIYEKNAIQAYIKSKNANARCPVAGCPRKLQVS 146 (186)
Q Consensus 89 ~~l~CPI~~~~~~~l~dPV~s--~~CgH~fck~~I~~~l~~~~~~~~CPv~GC~~~l~~~ 146 (186)
..-.||+|+. -+.+-... ..|+|.||..||..|-+ -.-.||+ |+..+..-
T Consensus 122 ~~~~CP~Ci~---s~~DqL~~~~k~c~H~FC~~Ci~sWsR---~aqTCPi--DR~EF~~v 173 (1134)
T KOG0825|consen 122 VENQCPNCLK---SCNDQLEESEKHTAHYFCEECVGSWSR---CAQTCPV--DRGEFGEV 173 (1134)
T ss_pred hhhhhhHHHH---HHHHHhhccccccccccHHHHhhhhhh---hcccCch--hhhhhhee
Confidence 4567999985 34444432 46999999999999987 3357999 98766543
No 69
>KOG1039 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=92.72 E-value=0.077 Score=47.46 Aligned_cols=49 Identities=18% Similarity=0.408 Sum_probs=35.8
Q ss_pred ceeeccCcCCCCccccCC-----cc-ccCCCccccHHHHHHHHHhcCC-----CCCCCCCCCCCC
Q 029888 89 LNISCPLSGKPITELAEP-----VR-SVECKHIYEKNAIQAYIKSKNA-----NARCPVAGCPRK 142 (186)
Q Consensus 89 ~~l~CPI~~~~~~~l~dP-----V~-s~~CgH~fck~~I~~~l~~~~~-----~~~CPv~GC~~~ 142 (186)
....|=||+. ++..-+ .. ...|.|+||..||..|-.. .. ...||. |+..
T Consensus 160 ~~k~CGICme--~i~ek~~~~~rfgilpnC~H~~Cl~Cir~wr~~-~q~~~~~sksCP~--CRv~ 219 (344)
T KOG1039|consen 160 SEKECGICME--TINEKAASERRFGILPNCNHSFCLNCIRKWRQA-TQFESKTSKSCPF--CRVP 219 (344)
T ss_pred ccccceehhh--hccccchhhhhcccCCCcchhhhhcHhHhhhhh-hccccccccCCCc--ccCc
Confidence 3678999998 345444 21 1469999999999999852 23 578999 9764
No 70
>PF04641 Rtf2: Rtf2 RING-finger
Probab=92.68 E-value=0.15 Score=43.55 Aligned_cols=35 Identities=31% Similarity=0.586 Sum_probs=30.8
Q ss_pred eeeccCcCCCCccccCCccccCCCccccHHHHHHHHHh
Q 029888 90 NISCPLSGKPITELAEPVRSVECKHIYEKNAIQAYIKS 127 (186)
Q Consensus 90 ~l~CPI~~~~~~~l~dPV~s~~CgH~fck~~I~~~l~~ 127 (186)
=..|+|+++| |..||.+...|+.|.+++|..||..
T Consensus 34 w~~CaLS~~p---L~~PiV~d~~G~LynKeaile~Ll~ 68 (260)
T PF04641_consen 34 WTHCALSQQP---LEDPIVSDRLGRLYNKEAILEFLLD 68 (260)
T ss_pred cCcccCcCCc---cCCCeeeCCCCeeEcHHHHHHHHHh
Confidence 5679999986 5899986778999999999999974
No 71
>KOG4172 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=92.49 E-value=0.057 Score=36.04 Aligned_cols=44 Identities=23% Similarity=0.470 Sum_probs=33.8
Q ss_pred eeeccCcCCCCccccCCccc--cCCCcc-ccHHHHHHHHHhcCCCCCCCCCCCCCCc
Q 029888 90 NISCPLSGKPITELAEPVRS--VECKHI-YEKNAIQAYIKSKNANARCPVAGCPRKL 143 (186)
Q Consensus 90 ~l~CPI~~~~~~~l~dPV~s--~~CgH~-fck~~I~~~l~~~~~~~~CPv~GC~~~l 143 (186)
+--|-||. +.||-| -.|||. .|.+|-.+.++. ....||+ |+..+
T Consensus 7 ~dECTICy------e~pvdsVlYtCGHMCmCy~Cg~rl~~~--~~g~CPi--CRapi 53 (62)
T KOG4172|consen 7 SDECTICY------EHPVDSVLYTCGHMCMCYACGLRLKKA--LHGCCPI--CRAPI 53 (62)
T ss_pred ccceeeec------cCcchHHHHHcchHHhHHHHHHHHHHc--cCCcCcc--hhhHH
Confidence 46799997 577765 369996 688888888873 5578999 98754
No 72
>COG5109 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=92.44 E-value=0.081 Score=46.84 Aligned_cols=52 Identities=23% Similarity=0.503 Sum_probs=37.7
Q ss_pred eeeccCcCCCCccccCCccccCCCccccHHHHHHHHHhcCCCCCCCCCCCCCCcc
Q 029888 90 NISCPLSGKPITELAEPVRSVECKHIYEKNAIQAYIKSKNANARCPVAGCPRKLQ 144 (186)
Q Consensus 90 ~l~CPI~~~~~~~l~dPV~s~~CgH~fck~~I~~~l~~~~~~~~CPv~GC~~~l~ 144 (186)
-|+||+.... ..=++|=.+..|||+..++++...-+.+.-.++||. |+..-.
T Consensus 336 ~FiCPVlKe~-~t~ENpP~ml~CgHVIskeal~~LS~nG~~~FKCPY--CP~~~~ 387 (396)
T COG5109 336 LFICPVLKEL-CTDENPPVMLECGHVISKEALSVLSQNGVLSFKCPY--CPEMSK 387 (396)
T ss_pred eeeccccHhh-hcccCCCeeeeccceeeHHHHHHHhhcCcEEeeCCC--CCcchh
Confidence 4899998753 233455444899999999999988774344788999 976443
No 73
>KOG1815 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=92.22 E-value=0.15 Score=46.87 Aligned_cols=56 Identities=16% Similarity=0.492 Sum_probs=40.6
Q ss_pred ceeeccCcCCCCccccCCccccCCCccccHHHHHHHHHh---cCC--CCCCCCCCCCCCccCCC
Q 029888 89 LNISCPLSGKPITELAEPVRSVECKHIYEKNAIQAYIKS---KNA--NARCPVAGCPRKLQVSK 147 (186)
Q Consensus 89 ~~l~CPI~~~~~~~l~dPV~s~~CgH~fck~~I~~~l~~---~~~--~~~CPv~GC~~~l~~~~ 147 (186)
....|.||... +...+....|||.||..|...||.. .+. ...||..||...+....
T Consensus 69 ~~~~c~ic~~~---~~~~~~~~~c~H~~c~~cw~~yl~~kI~~~~~~~i~cp~~~C~a~v~~~~ 129 (444)
T KOG1815|consen 69 GDVQCGICVES---YDGEIIGLGCGHPFCPPCWTGYLGTKIHEGEEAKIKCPAHGCPALVGEDT 129 (444)
T ss_pred ccccCCcccCC---CcchhhhcCCCcHHHHHHHHHHhhheeeccccccccCCCCCccccCCCce
Confidence 35789999862 3323444799999999999999985 112 26899999988665443
No 74
>PF11793 FANCL_C: FANCL C-terminal domain; PDB: 3K1L_A.
Probab=91.93 E-value=0.041 Score=38.03 Aligned_cols=51 Identities=18% Similarity=0.425 Sum_probs=23.0
Q ss_pred eeeccCcCCCCccc---cCCcc---ccCCCccccHHHHHHHHHh--cCC------CCCCCCCCCCCCcc
Q 029888 90 NISCPLSGKPITEL---AEPVR---SVECKHIYEKNAIQAYIKS--KNA------NARCPVAGCPRKLQ 144 (186)
Q Consensus 90 ~l~CPI~~~~~~~l---~dPV~---s~~CgH~fck~~I~~~l~~--~~~------~~~CPv~GC~~~l~ 144 (186)
++.|+||... ++ ..|+. +..|+++|=..||.+|+.. ..+ ...||. |.+.|+
T Consensus 2 ~~~C~IC~~~--~~~~~~~p~~~C~n~~C~~~fH~~CL~~wf~~~~~~~~~~~~~~G~CP~--C~~~i~ 66 (70)
T PF11793_consen 2 ELECGICYSY--RLDDGEIPDVVCPNPSCGKKFHLLCLSEWFLSLEKSRQSFIPIFGECPY--CSSPIS 66 (70)
T ss_dssp --S-SSS--S--S-TT-----B--S-TT----B-SGGGHHHHHHHHSSS-TTT--EEE-TT--T-SEEE
T ss_pred CCCCCcCCcE--ecCCCCcCceEcCCcccCCHHHHHHHHHHHHHcccCCeeecccccCCcC--CCCeee
Confidence 5679999973 33 22432 2478999999999999974 111 135999 988765
No 75
>KOG0827 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=91.89 E-value=0.12 Score=46.84 Aligned_cols=47 Identities=15% Similarity=0.528 Sum_probs=31.2
Q ss_pred eeeccCcCCCCccccCCcccc-CCCccccHHHHHHHHHhcCCC-CCCCCCCCC
Q 029888 90 NISCPLSGKPITELAEPVRSV-ECKHIYEKNAIQAYIKSKNAN-ARCPVAGCP 140 (186)
Q Consensus 90 ~l~CPI~~~~~~~l~dPV~s~-~CgH~fck~~I~~~l~~~~~~-~~CPv~GC~ 140 (186)
...|.||-.-+ .-..-+.++ .|||+|--.|+.+|+.. ..+ ..||+ |+
T Consensus 4 ~A~C~Ic~d~~-p~~~~l~~i~~cGhifh~~cl~qwfe~-~Ps~R~cpi--c~ 52 (465)
T KOG0827|consen 4 MAECHICIDGR-PNDHELGPIGTCGHIFHTTCLTQWFEG-DPSNRGCPI--CQ 52 (465)
T ss_pred cceeeEeccCC-ccccccccccchhhHHHHHHHHHHHcc-CCccCCCCc--ee
Confidence 56788986411 111112223 49999999999999983 343 57999 87
No 76
>KOG1493 consensus Anaphase-promoting complex (APC), subunit 11 [Cell cycle control, cell division, chromosome partitioning; Posttranslational modification, protein turnover, chaperones]
Probab=91.59 E-value=0.077 Score=37.70 Aligned_cols=54 Identities=20% Similarity=0.483 Sum_probs=40.0
Q ss_pred cceeeccCcCCCCccccCCccccCCCccccHHHHHHHHHhcCCCCCCCCCCCCCCccC
Q 029888 88 ILNISCPLSGKPITELAEPVRSVECKHIYEKNAIQAYIKSKNANARCPVAGCPRKLQV 145 (186)
Q Consensus 88 ~~~l~CPI~~~~~~~l~dPV~s~~CgH~fck~~I~~~l~~~~~~~~CPv~GC~~~l~~ 145 (186)
-.+-.||-|.-| -=.-|+.--.|.|.|-.-||.+|+........||. |++....
T Consensus 29 ~Fdg~Cp~Ck~P--gDdCPLv~G~C~h~fh~hCI~~wl~~~tsq~~CPm--cRq~~~~ 82 (84)
T KOG1493|consen 29 PFDGCCPDCKLP--GDDCPLVWGYCLHAFHAHCILKWLNTPTSQGQCPM--CRQTWQF 82 (84)
T ss_pred ccCCcCCCCcCC--CCCCccHHHHHHHHHHHHHHHHHhcCccccccCCc--chheeEe
Confidence 356679999765 22346554579999999999999985445578999 9986543
No 77
>KOG4739 consensus Uncharacterized protein involved in synaptonemal complex formation [Cell cycle control, cell division, chromosome partitioning; General function prediction only]
Probab=90.44 E-value=0.13 Score=43.74 Aligned_cols=52 Identities=15% Similarity=0.471 Sum_probs=35.3
Q ss_pred eeccCcCCCCccccCCccccCCCccccHHHHHHHHHhcCCCCCCCCCCCCCCccCCCCccC
Q 029888 91 ISCPLSGKPITELAEPVRSVECKHIYEKNAIQAYIKSKNANARCPVAGCPRKLQVSKVVCD 151 (186)
Q Consensus 91 l~CPI~~~~~~~l~dPV~s~~CgH~fck~~I~~~l~~~~~~~~CPv~GC~~~l~~~~L~~d 151 (186)
..|--|+.- -=.+|+--+.|+|+||..|...-.. ..||. |++.+..-.|..+
T Consensus 4 VhCn~C~~~--~~~~~f~LTaC~HvfC~~C~k~~~~-----~~C~l--Ckk~ir~i~l~~s 55 (233)
T KOG4739|consen 4 VHCNKCFRF--PSQDPFFLTACRHVFCEPCLKASSP-----DVCPL--CKKSIRIIQLNRS 55 (233)
T ss_pred EEecccccc--CCCCceeeeechhhhhhhhcccCCc-----ccccc--ccceeeeeecccc
Confidence 457777652 1266776689999999999654322 28999 9988765555443
No 78
>KOG1941 consensus Acetylcholine receptor-associated protein of the synapse (rapsyn) [Extracellular structures]
Probab=90.05 E-value=0.12 Score=46.99 Aligned_cols=50 Identities=26% Similarity=0.656 Sum_probs=41.1
Q ss_pred ceeeccCcCCCCccccCCccccCCCccccHHHHHHHHHhcCCCCCCCCCCCCC
Q 029888 89 LNISCPLSGKPITELAEPVRSVECKHIYEKNAIQAYIKSKNANARCPVAGCPR 141 (186)
Q Consensus 89 ~~l~CPI~~~~~~~l~dPV~s~~CgH~fck~~I~~~l~~~~~~~~CPv~GC~~ 141 (186)
..+.|-.|++.+++=-+-.....|.|+|--.|+..++. +++...||. |++
T Consensus 364 ~~L~Cg~CGe~~Glk~e~LqALpCsHIfH~rCl~e~L~-~n~~rsCP~--Crk 413 (518)
T KOG1941|consen 364 TELYCGLCGESIGLKNERLQALPCSHIFHLRCLQEILE-NNGTRSCPN--CRK 413 (518)
T ss_pred HhhhhhhhhhhhcCCcccccccchhHHHHHHHHHHHHH-hCCCCCCcc--HHH
Confidence 46899999986644444555578999999999999998 578889999 985
No 79
>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=89.41 E-value=0.56 Score=30.13 Aligned_cols=43 Identities=16% Similarity=0.603 Sum_probs=29.8
Q ss_pred ccCcCCCCccccCCccccCCC-----ccccHHHHHHHHHhcCCCCCCCCCCCC
Q 029888 93 CPLSGKPITELAEPVRSVECK-----HIYEKNAIQAYIKSKNANARCPVAGCP 140 (186)
Q Consensus 93 CPI~~~~~~~l~dPV~s~~Cg-----H~fck~~I~~~l~~~~~~~~CPv~GC~ 140 (186)
|-||+. ...-.+|+. ..|. |.+=..|+..|+. ..+...||+ |.
T Consensus 2 CrIC~~-~~~~~~~l~-~PC~C~G~~~~vH~~Cl~~W~~-~~~~~~C~i--C~ 49 (49)
T smart00744 2 CRICHD-EGDEGDPLV-SPCRCKGSLKYVHQECLERWIN-ESGNKTCEI--CK 49 (49)
T ss_pred ccCCCC-CCCCCCeeE-eccccCCchhHHHHHHHHHHHH-HcCCCcCCC--CC
Confidence 667764 112356665 4553 7899999999998 355678999 84
No 80
>KOG4185 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=88.25 E-value=0.63 Score=39.98 Aligned_cols=66 Identities=21% Similarity=0.432 Sum_probs=46.6
Q ss_pred eeccCcCCCCccc---cCCccccCCCccccHHHHHHHHHhcCCCCCCCCCCCCCC--cc---CCCCccCHHHHHHHHHH
Q 029888 91 ISCPLSGKPITEL---AEPVRSVECKHIYEKNAIQAYIKSKNANARCPVAGCPRK--LQ---VSKVVCDSLLLVDIDEM 161 (186)
Q Consensus 91 l~CPI~~~~~~~l---~dPV~s~~CgH~fck~~I~~~l~~~~~~~~CPv~GC~~~--l~---~~~L~~d~~L~~~I~~~ 161 (186)
+.|-||..+|..- .-|- ..+|||++|..|+...+. +....||. |+.. +. ...|..+..|...++..
T Consensus 4 ~~c~~c~~~~s~~~~~~~p~-~l~c~h~~c~~c~~~l~~--~~~i~cpf--cR~~~~~~~~~~~~l~kNf~ll~~~~~~ 77 (296)
T KOG4185|consen 4 PECEICNEDYSSEDGDHIPR-VLKCGHTICQNCASKLLG--NSRILCPF--CRETTEIPDGDVKSLQKNFALLQAIEHM 77 (296)
T ss_pred CceeecCccccccCcccCCc-ccccCceehHhHHHHHhc--CceeeccC--CCCcccCCchhHhhhhhhHHHHHHHHHH
Confidence 4566776543211 2342 367999999999999998 46678999 9886 22 45677788888777775
No 81
>KOG4692 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=87.86 E-value=0.36 Score=43.51 Aligned_cols=46 Identities=20% Similarity=0.320 Sum_probs=33.4
Q ss_pred eeeccCcCCCCccccCCccccCCCccccHHHHHHHHHhcCCCCCCCCCCCCCCcc
Q 029888 90 NISCPLSGKPITELAEPVRSVECKHIYEKNAIQAYIKSKNANARCPVAGCPRKLQ 144 (186)
Q Consensus 90 ~l~CPI~~~~~~~l~dPV~s~~CgH~fck~~I~~~l~~~~~~~~CPv~GC~~~l~ 144 (186)
+-.||||-.- =...|- ..|+|.-|+.||.+++- .+..|=. |...+.
T Consensus 422 d~lCpICyA~---pi~Avf-~PC~H~SC~~CI~qHlm---N~k~CFf--CktTv~ 467 (489)
T KOG4692|consen 422 DNLCPICYAG---PINAVF-APCSHRSCYGCITQHLM---NCKRCFF--CKTTVI 467 (489)
T ss_pred cccCcceecc---cchhhc-cCCCCchHHHHHHHHHh---cCCeeeE--ecceee
Confidence 4569999751 123444 68999999999999998 3457888 866543
No 82
>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=87.08 E-value=0.31 Score=27.48 Aligned_cols=24 Identities=21% Similarity=0.373 Sum_probs=13.8
Q ss_pred eccCcCCCCccccCCccccCCCcccc
Q 029888 92 SCPLSGKPITELAEPVRSVECKHIYE 117 (186)
Q Consensus 92 ~CPI~~~~~~~l~dPV~s~~CgH~fc 117 (186)
+||-|... +-..-.....|||.|.
T Consensus 2 ~CP~C~~~--V~~~~~~Cp~CG~~F~ 25 (26)
T PF10571_consen 2 TCPECGAE--VPESAKFCPHCGYDFE 25 (26)
T ss_pred cCCCCcCC--chhhcCcCCCCCCCCc
Confidence 59999873 2222223345788874
No 83
>PHA03096 p28-like protein; Provisional
Probab=86.66 E-value=0.48 Score=41.34 Aligned_cols=49 Identities=12% Similarity=0.142 Sum_probs=33.8
Q ss_pred eeccCcCCCCccccCCccc------cCCCccccHHHHHHHHHhc---CCCCCCCCCCCCCCc
Q 029888 91 ISCPLSGKPITELAEPVRS------VECKHIYEKNAIQAYIKSK---NANARCPVAGCPRKL 143 (186)
Q Consensus 91 l~CPI~~~~~~~l~dPV~s------~~CgH~fck~~I~~~l~~~---~~~~~CPv~GC~~~l 143 (186)
-.|-||++ .++..|+.. ..|.|.||..||..|.... .....||+ |+..+
T Consensus 179 k~c~ic~e--~~~~k~~~~~~fgil~~c~h~fc~~ci~~wr~~~~~~e~~~~c~~--~~~~~ 236 (284)
T PHA03096 179 KICGICLE--NIKAKYIIKKYYGILSEIKHEFNIFCIKIWMTESLYKETEPENRR--LNTVI 236 (284)
T ss_pred hhcccchh--hhhhhccccccccccccCCcHHHHHHHHHHHHhhhhcccCccccc--hhhHH
Confidence 57999998 456565432 4799999999999998742 23444565 55433
No 84
>COG5194 APC11 Component of SCF ubiquitin ligase and anaphase-promoting complex [Posttranslational modification, protein turnover, chaperones / Cell division and chromosome partitioning]
Probab=86.62 E-value=0.67 Score=33.22 Aligned_cols=52 Identities=17% Similarity=0.363 Sum_probs=35.2
Q ss_pred ceeeccCcCCCC-ccccCCccccCCCccccHHHHHHHHHhcCCCCCCCCCCCCCCccC
Q 029888 89 LNISCPLSGKPI-TELAEPVRSVECKHIYEKNAIQAYIKSKNANARCPVAGCPRKLQV 145 (186)
Q Consensus 89 ~~l~CPI~~~~~-~~l~dPV~s~~CgH~fck~~I~~~l~~~~~~~~CPv~GC~~~l~~ 145 (186)
+.-.||-|+--. .-=+-||.=-.|.|.|--.||.+||.. ...||. +++....
T Consensus 30 im~~C~eCq~~~~~~~eC~v~wG~CnHaFH~HCI~rWL~T---k~~CPl--d~q~w~~ 82 (88)
T COG5194 30 IMGTCPECQFGMTPGDECPVVWGVCNHAFHDHCIYRWLDT---KGVCPL--DRQTWVL 82 (88)
T ss_pred ccCcCcccccCCCCCCcceEEEEecchHHHHHHHHHHHhh---CCCCCC--CCceeEE
Confidence 445688776300 011335554579999999999999993 357999 9886543
No 85
>PF14570 zf-RING_4: RING/Ubox like zinc-binding domain; PDB: 1E4U_A 1UR6_B.
Probab=85.66 E-value=0.84 Score=29.52 Aligned_cols=46 Identities=22% Similarity=0.548 Sum_probs=21.2
Q ss_pred ccCcCCCCccccC-CccccCCCccccHHHHHHHHHhcCCCCCCCCCCCCCCc
Q 029888 93 CPLSGKPITELAE-PVRSVECKHIYEKNAIQAYIKSKNANARCPVAGCPRKL 143 (186)
Q Consensus 93 CPI~~~~~~~l~d-PV~s~~CgH~fck~~I~~~l~~~~~~~~CPv~GC~~~l 143 (186)
||+|..++ ...+ =+..=.||+-.|+.|....+. .....||- |+...
T Consensus 1 cp~C~e~~-d~~d~~~~PC~Cgf~IC~~C~~~i~~--~~~g~CPg--Cr~~Y 47 (48)
T PF14570_consen 1 CPLCDEEL-DETDKDFYPCECGFQICRFCYHDILE--NEGGRCPG--CREPY 47 (48)
T ss_dssp -TTTS-B---CCCTT--SSTTS----HHHHHHHTT--SS-SB-TT--T--B-
T ss_pred CCCccccc-ccCCCccccCcCCCcHHHHHHHHHHh--ccCCCCCC--CCCCC
Confidence 78888643 2333 111125899999999888876 24568998 98643
No 86
>COG5175 MOT2 Transcriptional repressor [Transcription]
Probab=85.21 E-value=0.73 Score=41.42 Aligned_cols=52 Identities=27% Similarity=0.476 Sum_probs=32.6
Q ss_pred ccCcCCCCccccCCccccCCCccccHHHHHHHHHhcCCCCCCCCCCCCCCccCCCC
Q 029888 93 CPLSGKPITELAEPVRSVECKHIYEKNAIQAYIKSKNANARCPVAGCPRKLQVSKV 148 (186)
Q Consensus 93 CPI~~~~~~~l~dPV~s~~CgH~fck~~I~~~l~~~~~~~~CPv~GC~~~l~~~~L 148 (186)
||+|.+|+-+--.-+..-.||...|+-|--..-+ +-..+||. |+.....+.+
T Consensus 17 cplcie~mditdknf~pc~cgy~ic~fc~~~irq--~lngrcpa--crr~y~denv 68 (480)
T COG5175 17 CPLCIEPMDITDKNFFPCPCGYQICQFCYNNIRQ--NLNGRCPA--CRRKYDDENV 68 (480)
T ss_pred CcccccccccccCCcccCCcccHHHHHHHHHHHh--hccCCChH--hhhhccccce
Confidence 9999987632222233245898877777554433 24458999 9876554443
No 87
>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 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=82.71 E-value=0.98 Score=29.07 Aligned_cols=36 Identities=25% Similarity=0.341 Sum_probs=29.1
Q ss_pred eeccCcCCCCccccCCccccCCCccccHHHHHHHHH
Q 029888 91 ISCPLSGKPITELAEPVRSVECKHIYEKNAIQAYIK 126 (186)
Q Consensus 91 l~CPI~~~~~~~l~dPV~s~~CgH~fck~~I~~~l~ 126 (186)
-.|++|.+.|+.+.....-..||++||..|......
T Consensus 3 ~~C~~C~~~F~~~~rk~~Cr~Cg~~~C~~C~~~~~~ 38 (57)
T cd00065 3 SSCMGCGKPFTLTRRRHHCRNCGRIFCSKCSSNRIP 38 (57)
T ss_pred CcCcccCccccCCccccccCcCcCCcChHHcCCeee
Confidence 359999998888776666678999999999776644
No 89
>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=81.97 E-value=0.29 Score=32.98 Aligned_cols=34 Identities=12% Similarity=0.275 Sum_probs=19.5
Q ss_pred eeeccCcCCCCccccCCccccCCCccccHHHHHH
Q 029888 90 NISCPLSGKPITELAEPVRSVECKHIYEKNAIQA 123 (186)
Q Consensus 90 ~l~CPI~~~~~~~l~dPV~s~~CgH~fck~~I~~ 123 (186)
.-.|++|.++|++|..-.--..||++||..|...
T Consensus 9 ~~~C~~C~~~F~~~~rrhhCr~CG~~vC~~Cs~~ 42 (69)
T PF01363_consen 9 ASNCMICGKKFSLFRRRHHCRNCGRVVCSSCSSQ 42 (69)
T ss_dssp -SB-TTT--B-BSSS-EEE-TTT--EEECCCS-E
T ss_pred CCcCcCcCCcCCCceeeEccCCCCCEECCchhCC
Confidence 4569999999988877777778999999877543
No 90
>KOG1785 consensus Tyrosine kinase negative regulator CBL [Defense mechanisms]
Probab=81.48 E-value=0.54 Score=43.06 Aligned_cols=46 Identities=20% Similarity=0.547 Sum_probs=35.3
Q ss_pred eccCcCCCCccccCCccccCCCccccHHHHHHHHHhcCCCCCCCCCCCCCCcc
Q 029888 92 SCPLSGKPITELAEPVRSVECKHIYEKNAIQAYIKSKNANARCPVAGCPRKLQ 144 (186)
Q Consensus 92 ~CPI~~~~~~~l~dPV~s~~CgH~fck~~I~~~l~~~~~~~~CPv~GC~~~l~ 144 (186)
.|-||-+ =..=|+-..|||-.|-.|+..|..+ .....||. |+-.|.
T Consensus 371 LCKICae----ndKdvkIEPCGHLlCt~CLa~WQ~s-d~gq~CPF--CRcEIK 416 (563)
T KOG1785|consen 371 LCKICAE----NDKDVKIEPCGHLLCTSCLAAWQDS-DEGQTCPF--CRCEIK 416 (563)
T ss_pred HHHHhhc----cCCCcccccccchHHHHHHHhhccc-CCCCCCCc--eeeEec
Confidence 5888975 2345665789999999999999863 44678999 987665
No 91
>PHA00626 hypothetical protein
Probab=81.46 E-value=1.1 Score=29.99 Aligned_cols=20 Identities=15% Similarity=0.225 Sum_probs=15.5
Q ss_pred cCCccccCCCccccHHHHHH
Q 029888 104 AEPVRSVECKHIYEKNAIQA 123 (186)
Q Consensus 104 ~dPV~s~~CgH~fck~~I~~ 123 (186)
.+.+....|||.|.++++-+
T Consensus 21 snrYkCkdCGY~ft~~~~~~ 40 (59)
T PHA00626 21 SDDYVCCDCGYNDSKDAFGE 40 (59)
T ss_pred CcceEcCCCCCeechhhhhh
Confidence 56777778999999988654
No 92
>KOG3161 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=81.22 E-value=0.84 Score=44.07 Aligned_cols=38 Identities=21% Similarity=0.415 Sum_probs=27.9
Q ss_pred cceeeccCcCCCC-ccccCCccccCCCccccHHHHHHHHH
Q 029888 88 ILNISCPLSGKPI-TELAEPVRSVECKHIYEKNAIQAYIK 126 (186)
Q Consensus 88 ~~~l~CPI~~~~~-~~l~dPV~s~~CgH~fck~~I~~~l~ 126 (186)
+.-+.|+||+..| ..=..||. ..|||+-|+.|++....
T Consensus 9 ~~~l~c~ic~n~f~~~~~~Pvs-l~cghtic~~c~~~lyn 47 (861)
T KOG3161|consen 9 VLLLLCDICLNLFVVQRLEPVS-LQCGHTICGHCVQLLYN 47 (861)
T ss_pred HHHhhchHHHHHHHHHhcCccc-ccccchHHHHHHHhHhh
Confidence 3457899995311 11247988 99999999999988766
No 93
>KOG2930 consensus SCF ubiquitin ligase, Rbx1 component [Posttranslational modification, protein turnover, chaperones]
Probab=80.85 E-value=1.3 Score=33.20 Aligned_cols=26 Identities=23% Similarity=0.669 Sum_probs=22.4
Q ss_pred CCCccccHHHHHHHHHhcCCCCCCCCCCCCC
Q 029888 111 ECKHIYEKNAIQAYIKSKNANARCPVAGCPR 141 (186)
Q Consensus 111 ~CgH~fck~~I~~~l~~~~~~~~CPv~GC~~ 141 (186)
.|+|.|-.-||.+||++ ...||. |++
T Consensus 80 ~CNHaFH~hCisrWlkt---r~vCPL--dn~ 105 (114)
T KOG2930|consen 80 VCNHAFHFHCISRWLKT---RNVCPL--DNK 105 (114)
T ss_pred ecchHHHHHHHHHHHhh---cCcCCC--cCc
Confidence 59999999999999994 357999 876
No 94
>COG5219 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=80.52 E-value=1.3 Score=44.67 Aligned_cols=48 Identities=23% Similarity=0.603 Sum_probs=35.6
Q ss_pred eeccCcCCCCcccc-----CCc-cccCCCccccHHHHHHHHHhcCCCCCCCCCCCCCCcc
Q 029888 91 ISCPLSGKPITELA-----EPV-RSVECKHIYEKNAIQAYIKSKNANARCPVAGCPRKLQ 144 (186)
Q Consensus 91 l~CPI~~~~~~~l~-----dPV-~s~~CgH~fck~~I~~~l~~~~~~~~CPv~GC~~~l~ 144 (186)
--|+||-- ++- -|- +...|.|-|--.|+..|+++ .+...||. |+..++
T Consensus 1470 eECaICYs---vL~~vdr~lPskrC~TCknKFH~~CLyKWf~S-s~~s~CPl--CRseit 1523 (1525)
T COG5219 1470 EECAICYS---VLDMVDRSLPSKRCATCKNKFHTRCLYKWFAS-SARSNCPL--CRSEIT 1523 (1525)
T ss_pred chhhHHHH---HHHHHhccCCccccchhhhhhhHHHHHHHHHh-cCCCCCCc--cccccc
Confidence 35999974 332 232 22458899999999999994 67789999 997664
No 95
>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=80.30 E-value=0.14 Score=37.77 Aligned_cols=47 Identities=26% Similarity=0.743 Sum_probs=15.0
Q ss_pred eeccCcCCCCccccCCccccCC--CccccHHHHHHHHH-hcCCCCCCCCCCCCCC
Q 029888 91 ISCPLSGKPITELAEPVRSVEC--KHIYEKNAIQAYIK-SKNANARCPVAGCPRK 142 (186)
Q Consensus 91 l~CPI~~~~~~~l~dPV~s~~C--gH~fck~~I~~~l~-~~~~~~~CPv~GC~~~ 142 (186)
-+||+|..++ .+.++.. ..| ||+|.| |...++. +..+...|++ |...
T Consensus 15 E~C~~C~~~i-~~~~~~~-~~C~~GH~w~R-C~lT~l~i~~~~~r~C~~--C~~~ 64 (99)
T PF12660_consen 15 EKCPICGAPI-PFDDLDE-AQCENGHVWPR-CALTFLPIQTPGVRVCPV--CGRR 64 (99)
T ss_dssp ---------------SSE-EE-TTS-EEEB--SSS-SBS-SS-EEE-TT--T--E
T ss_pred cccccccccc-ccCCcCE-eECCCCCEEee-eeeeeeeeccCCeeEcCC--CCCE
Confidence 5799999976 6778766 557 899975 4444442 1234478999 7663
No 96
>KOG2114 consensus Vacuolar assembly/sorting protein PEP5/VPS11 [Intracellular trafficking, secretion, and vesicular transport]
Probab=80.27 E-value=1 Score=44.54 Aligned_cols=41 Identities=22% Similarity=0.569 Sum_probs=34.7
Q ss_pred eeeccCcCCCCccccCCccccCCCccccHHHHHHHHHhcCCCCCCCCCCCCC
Q 029888 90 NISCPLSGKPITELAEPVRSVECKHIYEKNAIQAYIKSKNANARCPVAGCPR 141 (186)
Q Consensus 90 ~l~CPI~~~~~~~l~dPV~s~~CgH~fck~~I~~~l~~~~~~~~CPv~GC~~ 141 (186)
--+|..|.- .|.-|+..-.|||+|=+.|+. .+...||. |..
T Consensus 840 ~skCs~C~~---~LdlP~VhF~CgHsyHqhC~e------~~~~~CP~--C~~ 880 (933)
T KOG2114|consen 840 VSKCSACEG---TLDLPFVHFLCGHSYHQHCLE------DKEDKCPK--CLP 880 (933)
T ss_pred eeeecccCC---ccccceeeeecccHHHHHhhc------cCcccCCc--cch
Confidence 358999995 789999988999999999988 26678999 964
No 97
>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=79.90 E-value=1.1 Score=34.68 Aligned_cols=30 Identities=20% Similarity=0.347 Sum_probs=24.4
Q ss_pred eeeccCcCCCCccc-cCCccccCCCccccHH
Q 029888 90 NISCPLSGKPITEL-AEPVRSVECKHIYEKN 119 (186)
Q Consensus 90 ~l~CPI~~~~~~~l-~dPV~s~~CgH~fck~ 119 (186)
...||-|++.|--| ++|+.+.+||.+|...
T Consensus 9 Kr~Cp~cg~kFYDLnk~p~vcP~cg~~~~~~ 39 (129)
T TIGR02300 9 KRICPNTGSKFYDLNRRPAVSPYTGEQFPPE 39 (129)
T ss_pred cccCCCcCccccccCCCCccCCCcCCccCcc
Confidence 46799999865444 7899999999999776
No 98
>KOG0883 consensus Cyclophilin type, U box-containing peptidyl-prolyl cis-trans isomerase [Posttranslational modification, protein turnover, chaperones]
Probab=78.99 E-value=1.6 Score=39.96 Aligned_cols=35 Identities=23% Similarity=0.408 Sum_probs=30.3
Q ss_pred ceeeccCcCCCCccccCCccccCCCccccHHHHHHHHHh
Q 029888 89 LNISCPLSGKPITELAEPVRSVECKHIYEKNAIQAYIKS 127 (186)
Q Consensus 89 ~~l~CPI~~~~~~~l~dPV~s~~CgH~fck~~I~~~l~~ 127 (186)
.-..|.+++.| |.+||- +.=|-+|+..+|..||+.
T Consensus 39 P~~hC~lt~~P---fe~PvC-~~dg~vFd~~~Ivp~lkk 73 (518)
T KOG0883|consen 39 PFNHCSLTMLP---FEDPVC-TVDGTVFDLTAIVPWLKK 73 (518)
T ss_pred Chhhceecccc---ccCccc-ccCCcEEeeehhhHHHHH
Confidence 34579999986 599998 788999999999999984
No 99
>COG5113 UFD2 Ubiquitin fusion degradation protein 2 [Posttranslational modification, protein turnover, chaperones]
Probab=78.98 E-value=4.2 Score=39.54 Aligned_cols=70 Identities=19% Similarity=0.214 Sum_probs=59.0
Q ss_pred ceeeccCcCCCCccccCCccccCCCccccHHHHHHHHHhcCCCCCCCCCCCCCCccCCCCccCHHHHHHHHHHHhcCc
Q 029888 89 LNISCPLSGKPITELAEPVRSVECKHIYEKNAIQAYIKSKNANARCPVAGCPRKLQVSKVVCDSLLLVDIDEMRRTSK 166 (186)
Q Consensus 89 ~~l~CPI~~~~~~~l~dPV~s~~CgH~fck~~I~~~l~~~~~~~~CPv~GC~~~l~~~~L~~d~~L~~~I~~~r~~~~ 166 (186)
..+..|+.. ++|++||.-..-+-+.+|+.|..++-+ . ..-|. =+.+|+.+++.||..|+.+|..+.+..+
T Consensus 853 DeFlDPLmf---timkdPV~Lp~S~i~IDRSTikahlls-d--~tDPF--NRmPLtlddVtpn~eLrekIn~f~k~k~ 922 (929)
T COG5113 853 DEFLDPLMF---TIMKDPVKLPTSRITIDRSTIKAHLLS-D--GTDPF--NRMPLTLDDVTPNAELREKINRFYKCKG 922 (929)
T ss_pred hhhhCchhh---hcccCCeecccccccccHHHHHHHHhc-C--CCCcc--ccCCCchhhcCCCHHHHHHHHHHHhccc
Confidence 468899998 589999996678899999999999983 2 35688 6678999999999999999999877543
No 100
>KOG3002 consensus Zn finger protein [General function prediction only]
Probab=77.80 E-value=2.3 Score=37.39 Aligned_cols=56 Identities=16% Similarity=0.431 Sum_probs=40.7
Q ss_pred eeeccCcCCCCccccCCccccCC--CccccHHHHHHHHHhcCCCCCCCCCCCCCCccCCCCccCHHHHHHHHHH
Q 029888 90 NISCPLSGKPITELAEPVRSVEC--KHIYEKNAIQAYIKSKNANARCPVAGCPRKLQVSKVVCDSLLLVDIDEM 161 (186)
Q Consensus 90 ~l~CPI~~~~~~~l~dPV~s~~C--gH~fck~~I~~~l~~~~~~~~CPv~GC~~~l~~~~L~~d~~L~~~I~~~ 161 (186)
-+-||+|.. .|.-|+. +| ||.-|..|=. +...+||. |+..+. +. ...+|.+.++..
T Consensus 48 lleCPvC~~---~l~~Pi~--QC~nGHlaCssC~~------~~~~~CP~--Cr~~~g--~~-R~~amEkV~e~~ 105 (299)
T KOG3002|consen 48 LLDCPVCFN---PLSPPIF--QCDNGHLACSSCRT------KVSNKCPT--CRLPIG--NI-RCRAMEKVAEAV 105 (299)
T ss_pred hccCchhhc---cCcccce--ecCCCcEehhhhhh------hhcccCCc--cccccc--cH-HHHHHHHHHHhc
Confidence 477999996 6788987 56 8999998843 24568999 997776 33 445666666654
No 101
>COG3364 Zn-ribbon containing protein [General function prediction only]
Probab=77.58 E-value=1.1 Score=33.47 Aligned_cols=32 Identities=22% Similarity=0.709 Sum_probs=21.8
Q ss_pred CccccCCCccccHHHHHHHHHhcCCCCCCCCCCCCCCcc
Q 029888 106 PVRSVECKHIYEKNAIQAYIKSKNANARCPVAGCPRKLQ 144 (186)
Q Consensus 106 PV~s~~CgH~fck~~I~~~l~~~~~~~~CPv~GC~~~l~ 144 (186)
|-+.+.|||+|... =+.++. -||.-||++.+.
T Consensus 2 pH~CtrCG~vf~~g-~~~il~------GCp~CG~nkF~y 33 (112)
T COG3364 2 PHQCTRCGEVFDDG-SEEILS------GCPKCGCNKFLY 33 (112)
T ss_pred Cceecccccccccc-cHHHHc------cCccccchheEe
Confidence 44568999999986 223333 399988887543
No 102
>KOG2462 consensus C2H2-type Zn-finger protein [Transcription]
Probab=77.28 E-value=1.2 Score=38.78 Aligned_cols=53 Identities=19% Similarity=0.415 Sum_probs=33.2
Q ss_pred cceeeccCcCCCCccccC------------CccccCCCccccHHHHHH-HHHh--cCCCCCCCCCCCCCCcc
Q 029888 88 ILNISCPLSGKPITELAE------------PVRSVECKHIYEKNAIQA-YIKS--KNANARCPVAGCPRKLQ 144 (186)
Q Consensus 88 ~~~l~CPI~~~~~~~l~d------------PV~s~~CgH~fck~~I~~-~l~~--~~~~~~CPv~GC~~~l~ 144 (186)
...+.|+.|.+. +..- |.....||..|.+--+++ +|+. ..+.+.||. |++.|.
T Consensus 159 ~ka~~C~~C~K~--YvSmpALkMHirTH~l~c~C~iCGKaFSRPWLLQGHiRTHTGEKPF~C~h--C~kAFA 226 (279)
T KOG2462|consen 159 KKAFSCKYCGKV--YVSMPALKMHIRTHTLPCECGICGKAFSRPWLLQGHIRTHTGEKPFSCPH--CGKAFA 226 (279)
T ss_pred cccccCCCCCce--eeehHHHhhHhhccCCCcccccccccccchHHhhcccccccCCCCccCCc--ccchhc
Confidence 557888888873 3332 444456777777765544 3432 446788888 887663
No 103
>KOG2979 consensus Protein involved in DNA repair [General function prediction only]
Probab=76.64 E-value=2.7 Score=36.21 Aligned_cols=49 Identities=20% Similarity=0.392 Sum_probs=41.0
Q ss_pred cceeeccCcCCCCccccCCccccCCCccccHHHHHHHHHhcCCCCCCCCCCCCCCc
Q 029888 88 ILNISCPLSGKPITELAEPVRSVECKHIYEKNAIQAYIKSKNANARCPVAGCPRKL 143 (186)
Q Consensus 88 ~~~l~CPI~~~~~~~l~dPV~s~~CgH~fck~~I~~~l~~~~~~~~CPv~GC~~~l 143 (186)
.+.++||+-+. .+|+. ..|+|.-...-++.+|+ +.....||.-||+..+
T Consensus 211 ~~~i~CPv~gC-----~~~~~-~~~~~l~~d~el~~kIr-~~qe~~~~~~~~s~~~ 259 (262)
T KOG2979|consen 211 EITIRCPVLGC-----ENPYY-IQPGHLDEDKELQQKIR-QSQEPAIPDETSSEED 259 (262)
T ss_pred CceeecccccC-----Ccccc-ccccccCchHHHHHHHH-Hhccccccccccchhh
Confidence 34689999997 58988 89999999999999998 4567889999987654
No 104
>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=75.43 E-value=1.5 Score=31.39 Aligned_cols=38 Identities=24% Similarity=0.536 Sum_probs=26.8
Q ss_pred cceEEeccCCccceeeccCcCCCCccccCCccccCCCccccHHHHH
Q 029888 77 EDIVMTSTQSNILNISCPLSGKPITELAEPVRSVECKHIYEKNAIQ 122 (186)
Q Consensus 77 dDi~i~~~~~~~~~l~CPI~~~~~~~l~dPV~s~~CgH~fck~~I~ 122 (186)
.-+.|+. +-.|++|+++| ...++.--.|||+|-..|+.
T Consensus 71 ~~v~i~~------~~~C~vC~k~l--~~~~f~~~p~~~v~H~~C~~ 108 (109)
T PF10367_consen 71 RSVVITE------STKCSVCGKPL--GNSVFVVFPCGHVVHYSCIK 108 (109)
T ss_pred ceEEECC------CCCccCcCCcC--CCceEEEeCCCeEEeccccc
Confidence 3466664 45599999964 44666546899999888863
No 105
>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=72.96 E-value=2.2 Score=32.08 Aligned_cols=30 Identities=17% Similarity=0.492 Sum_probs=16.7
Q ss_pred eeeccCcCCCCcc-ccCCccccCCCccccHH
Q 029888 90 NISCPLSGKPITE-LAEPVRSVECKHIYEKN 119 (186)
Q Consensus 90 ~l~CPI~~~~~~~-l~dPV~s~~CgH~fck~ 119 (186)
...||-|+..|=- -++|+++.+||..|...
T Consensus 9 KR~Cp~CG~kFYDLnk~PivCP~CG~~~~~~ 39 (108)
T PF09538_consen 9 KRTCPSCGAKFYDLNKDPIVCPKCGTEFPPE 39 (108)
T ss_pred cccCCCCcchhccCCCCCccCCCCCCccCcc
Confidence 3567777763311 14566666666666544
No 106
>PF09845 DUF2072: Zn-ribbon containing protein (DUF2072); InterPro: IPR018645 This archaeal Zinc-ribbon containing proteins have no known function.
Probab=72.41 E-value=1.9 Score=33.56 Aligned_cols=29 Identities=21% Similarity=0.668 Sum_probs=21.1
Q ss_pred CccccCCCccccHHHHHHHHHhcCCCCCCCCCCCCC
Q 029888 106 PVRSVECKHIYEKNAIQAYIKSKNANARCPVAGCPR 141 (186)
Q Consensus 106 PV~s~~CgH~fck~~I~~~l~~~~~~~~CPv~GC~~ 141 (186)
|-+.+.||++|...... +|. -||.-|+++
T Consensus 1 PH~Ct~Cg~~f~dgs~e-il~------GCP~CGg~k 29 (131)
T PF09845_consen 1 PHQCTKCGRVFEDGSKE-ILS------GCPECGGNK 29 (131)
T ss_pred CcccCcCCCCcCCCcHH-HHc------cCcccCCcc
Confidence 44568999999977655 444 399977766
No 107
>PF14447 Prok-RING_4: Prokaryotic RING finger family 4
Probab=72.20 E-value=2.4 Score=28.19 Aligned_cols=35 Identities=17% Similarity=0.488 Sum_probs=25.1
Q ss_pred CCccccCCCccccHHHHHHHHHhcCCCCCCCCCCCCCCccCCC
Q 029888 105 EPVRSVECKHIYEKNAIQAYIKSKNANARCPVAGCPRKLQVSK 147 (186)
Q Consensus 105 dPV~s~~CgH~fck~~I~~~l~~~~~~~~CPv~GC~~~l~~~~ 147 (186)
..+. ..|||.-|+.|.-- .+-.-||. |...+..++
T Consensus 19 ~~~~-~pCgH~I~~~~f~~-----~rYngCPf--C~~~~~~~~ 53 (55)
T PF14447_consen 19 KGTV-LPCGHLICDNCFPG-----ERYNGCPF--CGTPFEFDD 53 (55)
T ss_pred cccc-ccccceeeccccCh-----hhccCCCC--CCCcccCCC
Confidence 3445 58999999988433 24456999 998887654
No 108
>KOG1940 consensus Zn-finger protein [General function prediction only]
Probab=72.14 E-value=2.8 Score=36.52 Aligned_cols=48 Identities=19% Similarity=0.506 Sum_probs=36.7
Q ss_pred ceeeccCcCCCCccccCCccccCCCccccHHHHHHHHHhcCCCCCCCCCCCCC
Q 029888 89 LNISCPLSGKPITELAEPVRSVECKHIYEKNAIQAYIKSKNANARCPVAGCPR 141 (186)
Q Consensus 89 ~~l~CPI~~~~~~~l~dPV~s~~CgH~fck~~I~~~l~~~~~~~~CPv~GC~~ 141 (186)
..+.||||..-+......+....|||.--..|+..++.. + -.||+ |.+
T Consensus 157 ~~~ncPic~e~l~~s~~~~~~~~CgH~~h~~cf~e~~~~--~-y~CP~--C~~ 204 (276)
T KOG1940|consen 157 SEFNCPICKEYLFLSFEDAGVLKCGHYMHSRCFEEMICE--G-YTCPI--CSK 204 (276)
T ss_pred ccCCCchhHHHhccccccCCccCcccchHHHHHHHHhcc--C-CCCCc--ccc
Confidence 356699998754444455555799999888999999982 4 89999 976
No 109
>PRK11088 rrmA 23S rRNA methyltransferase A; Provisional
Probab=70.37 E-value=2 Score=36.39 Aligned_cols=27 Identities=33% Similarity=0.739 Sum_probs=17.6
Q ss_pred eeeccCcCCCCccccCCccccCC--CccccHH
Q 029888 90 NISCPLSGKPITELAEPVRSVEC--KHIYEKN 119 (186)
Q Consensus 90 ~l~CPI~~~~~~~l~dPV~s~~C--gH~fck~ 119 (186)
.|.||+|+.|+ .+.. .+..| ||+|+..
T Consensus 2 ~~~CP~C~~~l-~~~~--~~~~C~~~h~fd~a 30 (272)
T PRK11088 2 SYQCPLCHQPL-TLEE--NSWICPQNHQFDCA 30 (272)
T ss_pred cccCCCCCcch-hcCC--CEEEcCCCCCCccc
Confidence 47899999976 2222 23445 8999654
No 110
>KOG4445 consensus Uncharacterized conserved protein, contains RWD domain [Function unknown]
Probab=69.52 E-value=1.6 Score=38.57 Aligned_cols=54 Identities=22% Similarity=0.480 Sum_probs=39.2
Q ss_pred ccceeeccCcCCCCccccCC-ccccCCCccccHHHHHHHHHh--------------------cCCCCCCCCCCCCCCcc
Q 029888 87 NILNISCPLSGKPITELAEP-VRSVECKHIYEKNAIQAYIKS--------------------KNANARCPVAGCPRKLQ 144 (186)
Q Consensus 87 ~~~~l~CPI~~~~~~~l~dP-V~s~~CgH~fck~~I~~~l~~--------------------~~~~~~CPv~GC~~~l~ 144 (186)
...+..|-||+- ++-..| ++-+.|-|-|-..|+-.||.. ......||| |+..|.
T Consensus 112 n~p~gqCvICLy--gfa~~~~ft~T~C~Hy~H~~ClaRyl~~~~~~lrqe~q~~~~~~qh~~~~~eavcpV--cre~i~ 186 (368)
T KOG4445|consen 112 NHPNGQCVICLY--GFASSPAFTVTACDHYMHFACLARYLTECLTGLRQEIQDAQKERQHMKEQVEAVCPV--CRERIK 186 (368)
T ss_pred CCCCCceEEEEE--eecCCCceeeehhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhHhhhhhH--hhhhcc
Confidence 456778999986 445566 665899999999999999863 112356999 987554
No 111
>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=69.31 E-value=2.3 Score=24.90 Aligned_cols=21 Identities=38% Similarity=0.752 Sum_probs=14.3
Q ss_pred cCCCccccHHHHHHHHHhcCCCCCCCCCCCCC
Q 029888 110 VECKHIYEKNAIQAYIKSKNANARCPVAGCPR 141 (186)
Q Consensus 110 ~~CgH~fck~~I~~~l~~~~~~~~CPv~GC~~ 141 (186)
..|||+|.-. .....||+ |+.
T Consensus 5 ~~CGy~y~~~---------~~~~~CP~--Cg~ 25 (33)
T cd00350 5 PVCGYIYDGE---------EAPWVCPV--CGA 25 (33)
T ss_pred CCCCCEECCC---------cCCCcCcC--CCC
Confidence 4677777543 25578999 875
No 112
>KOG0298 consensus DEAD box-containing helicase-like transcription factor/DNA repair protein [Replication, recombination and repair]
Probab=68.90 E-value=1.3 Score=45.64 Aligned_cols=43 Identities=21% Similarity=0.425 Sum_probs=34.9
Q ss_pred eeeccCcCCCCcccc-CCccccCCCccccHHHHHHHHHhcCCCCCCCCCCCCC
Q 029888 90 NISCPLSGKPITELA-EPVRSVECKHIYEKNAIQAYIKSKNANARCPVAGCPR 141 (186)
Q Consensus 90 ~l~CPI~~~~~~~l~-dPV~s~~CgH~fck~~I~~~l~~~~~~~~CPv~GC~~ 141 (186)
.+.|+||++ +++ .=.. ..|||-||..|+..|+. ....||. |..
T Consensus 1153 ~~~c~ic~d---il~~~~~I-~~cgh~~c~~c~~~~l~---~~s~~~~--~ks 1196 (1394)
T KOG0298|consen 1153 HFVCEICLD---ILRNQGGI-AGCGHEPCCRCDELWLY---ASSRCPI--CKS 1196 (1394)
T ss_pred ccchHHHHH---HHHhcCCe-eeechhHhhhHHHHHHH---HhccCcc--hhh
Confidence 568999997 666 3444 68999999999999998 3468999 864
No 113
>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=68.68 E-value=6.3 Score=25.37 Aligned_cols=34 Identities=24% Similarity=0.722 Sum_probs=20.6
Q ss_pred eeeccCcCCCCccccCCccccCCCccccHHHHHHHHHh----cCCCCCCCCCCCCC
Q 029888 90 NISCPLSGKPITELAEPVRSVECKHIYEKNAIQAYIKS----KNANARCPVAGCPR 141 (186)
Q Consensus 90 ~l~CPI~~~~~~~l~dPV~s~~CgH~fck~~I~~~l~~----~~~~~~CPv~GC~~ 141 (186)
+|.||.|++ .|....+...+.. ..+...||+ |..
T Consensus 2 ~f~CP~C~~----------------~~~~~~L~~H~~~~H~~~~~~v~CPi--C~~ 39 (54)
T PF05605_consen 2 SFTCPYCGK----------------GFSESSLVEHCEDEHRSESKNVVCPI--CSS 39 (54)
T ss_pred CcCCCCCCC----------------ccCHHHHHHHHHhHCcCCCCCccCCC--chh
Confidence 467888874 1333445555442 235688999 975
No 114
>KOG2462 consensus C2H2-type Zn-finger protein [Transcription]
Probab=68.68 E-value=3.9 Score=35.60 Aligned_cols=54 Identities=17% Similarity=0.437 Sum_probs=30.5
Q ss_pred ceeeccCcCCCCcccc--------------CCc-cccCCCccccHHHHHHH-HHhcCCCCCCCCCCCCCCcc
Q 029888 89 LNISCPLSGKPITELA--------------EPV-RSVECKHIYEKNAIQAY-IKSKNANARCPVAGCPRKLQ 144 (186)
Q Consensus 89 ~~l~CPI~~~~~~~l~--------------dPV-~s~~CgH~fck~~I~~~-l~~~~~~~~CPv~GC~~~l~ 144 (186)
.-++||-|++.+.... .++ ....||.+|-.--.+.+ |+...-...|++ |++.|.
T Consensus 129 ~r~~c~eCgk~ysT~snLsrHkQ~H~~~~s~ka~~C~~C~K~YvSmpALkMHirTH~l~c~C~i--CGKaFS 198 (279)
T KOG2462|consen 129 PRYKCPECGKSYSTSSNLSRHKQTHRSLDSKKAFSCKYCGKVYVSMPALKMHIRTHTLPCECGI--CGKAFS 198 (279)
T ss_pred CceeccccccccccccccchhhcccccccccccccCCCCCceeeehHHHhhHhhccCCCccccc--cccccc
Confidence 3577888877554444 232 22356777765444443 343334667888 777664
No 115
>PF14353 CpXC: CpXC protein
Probab=68.55 E-value=3.1 Score=31.37 Aligned_cols=48 Identities=19% Similarity=0.369 Sum_probs=28.6
Q ss_pred eeccCcCCCCccccCCccccCCCccccHHHHHHHHHhcCCCCCCCCCCCCCCcc
Q 029888 91 ISCPLSGKPITELAEPVRSVECKHIYEKNAIQAYIKSKNANARCPVAGCPRKLQ 144 (186)
Q Consensus 91 l~CPI~~~~~~~l~dPV~s~~CgH~fck~~I~~~l~~~~~~~~CPv~GC~~~l~ 144 (186)
++||-|+.+| .-.+- +.-.-.-..+..++.+...-....||. |+..+.
T Consensus 2 itCP~C~~~~---~~~v~-~~I~~~~~p~l~e~il~g~l~~~~CP~--Cg~~~~ 49 (128)
T PF14353_consen 2 ITCPHCGHEF---EFEVW-TSINADEDPELKEKILDGSLFSFTCPS--CGHKFR 49 (128)
T ss_pred cCCCCCCCee---EEEEE-eEEcCcCCHHHHHHHHcCCcCEEECCC--CCCcee
Confidence 5799999743 44443 233334455556666653334678999 877543
No 116
>KOG3268 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=64.12 E-value=5.7 Score=32.77 Aligned_cols=36 Identities=11% Similarity=0.573 Sum_probs=27.6
Q ss_pred cccCCCccccHHHHHHHHHh---cC-----CCCCCCCCCCCCCccC
Q 029888 108 RSVECKHIYEKNAIQAYIKS---KN-----ANARCPVAGCPRKLQV 145 (186)
Q Consensus 108 ~s~~CgH~fck~~I~~~l~~---~~-----~~~~CPv~GC~~~l~~ 145 (186)
-|..||..|-.-|+..||+. .. --..||. |+.++..
T Consensus 186 dN~qCgkpFHqiCL~dWLRgilTsRQSFdiiFGeCPY--CS~Pial 229 (234)
T KOG3268|consen 186 DNIQCGKPFHQICLTDWLRGILTSRQSFDIIFGECPY--CSDPIAL 229 (234)
T ss_pred cccccCCcHHHHHHHHHHHHHhhccceeeeeeccCCC--CCCccee
Confidence 45789999999999999985 11 1246999 9987754
No 117
>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=62.82 E-value=2.9 Score=31.46 Aligned_cols=48 Identities=29% Similarity=0.414 Sum_probs=31.2
Q ss_pred eeeccCcCCCCccccC-CccccCCCccccHHHHHHHHHhcCCCCCCCCCCCCC
Q 029888 90 NISCPLSGKPITELAE-PVRSVECKHIYEKNAIQAYIKSKNANARCPVAGCPR 141 (186)
Q Consensus 90 ~l~CPI~~~~~~~l~d-PV~s~~CgH~fck~~I~~~l~~~~~~~~CPv~GC~~ 141 (186)
.-.|.+|+.||+.+.+ ......|+|.+|+.|=.. ..+...+.|-+ |.+
T Consensus 54 ~~~C~~C~~~fg~l~~~~~~C~~C~~~VC~~C~~~--~~~~~~WlC~v--C~k 102 (118)
T PF02318_consen 54 ERHCARCGKPFGFLFNRGRVCVDCKHRVCKKCGVY--SKKEPIWLCKV--CQK 102 (118)
T ss_dssp CSB-TTTS-BCSCTSTTCEEETTTTEEEETTSEEE--TSSSCCEEEHH--HHH
T ss_pred CcchhhhCCcccccCCCCCcCCcCCccccCccCCc--CCCCCCEEChh--hHH
Confidence 4479999998877754 555678999999987433 11345567777 753
No 118
>PF13719 zinc_ribbon_5: zinc-ribbon domain
Probab=62.62 E-value=3.9 Score=24.57 Aligned_cols=12 Identities=33% Similarity=0.877 Sum_probs=6.9
Q ss_pred CCCCCCCCCCCCCC
Q 029888 129 NANARCPVAGCPRK 142 (186)
Q Consensus 129 ~~~~~CPv~GC~~~ 142 (186)
++.++||. |++.
T Consensus 23 ~~~vrC~~--C~~~ 34 (37)
T PF13719_consen 23 GRKVRCPK--CGHV 34 (37)
T ss_pred CcEEECCC--CCcE
Confidence 44566666 6554
No 119
>COG4530 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=62.57 E-value=6.1 Score=30.06 Aligned_cols=34 Identities=18% Similarity=0.245 Sum_probs=24.6
Q ss_pred eeeccCcCCCCcc-ccCCccccCCCccccHHHHHH
Q 029888 90 NISCPLSGKPITE-LAEPVRSVECKHIYEKNAIQA 123 (186)
Q Consensus 90 ~l~CPI~~~~~~~-l~dPV~s~~CgH~fck~~I~~ 123 (186)
.-+||-|++-|-- =++|+.|..||.+|-++.+.+
T Consensus 9 KridPetg~KFYDLNrdPiVsPytG~s~P~s~fe~ 43 (129)
T COG4530 9 KRIDPETGKKFYDLNRDPIVSPYTGKSYPRSYFEE 43 (129)
T ss_pred cccCccccchhhccCCCccccCcccccchHHHHHh
Confidence 4579999974422 268999999999996665544
No 120
>KOG4265 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=62.44 E-value=5.4 Score=35.84 Aligned_cols=46 Identities=17% Similarity=0.508 Sum_probs=34.3
Q ss_pred eeeccCcCCCCccccCCccccCCCcc-ccHHHHHHHHHhcCCCCCCCCCCCCCCcc
Q 029888 90 NISCPLSGKPITELAEPVRSVECKHI-YEKNAIQAYIKSKNANARCPVAGCPRKLQ 144 (186)
Q Consensus 90 ~l~CPI~~~~~~~l~dPV~s~~CgH~-fck~~I~~~l~~~~~~~~CPv~GC~~~l~ 144 (186)
.-.|=||+. .-++-+. ..|.|. -|..|-....= ....||+ |++.+.
T Consensus 290 gkeCVICls---e~rdt~v-LPCRHLCLCs~Ca~~Lr~---q~n~CPI--CRqpi~ 336 (349)
T KOG4265|consen 290 GKECVICLS---ESRDTVV-LPCRHLCLCSGCAKSLRY---QTNNCPI--CRQPIE 336 (349)
T ss_pred CCeeEEEec---CCcceEE-ecchhhehhHhHHHHHHH---hhcCCCc--cccchH
Confidence 456999995 6677777 799996 78888777542 2247999 998663
No 121
>KOG2034 consensus Vacuolar sorting protein PEP3/VPS18 [Intracellular trafficking, secretion, and vesicular transport]
Probab=61.39 E-value=4.6 Score=40.32 Aligned_cols=35 Identities=23% Similarity=0.538 Sum_probs=29.8
Q ss_pred eeeccCcCCCCccccCCccccCCCccccHHHHHHHHH
Q 029888 90 NISCPLSGKPITELAEPVRSVECKHIYEKNAIQAYIK 126 (186)
Q Consensus 90 ~l~CPI~~~~~~~l~dPV~s~~CgH~fck~~I~~~l~ 126 (186)
+-.|-+|+.| ++..|.---.|||.|=+.||.....
T Consensus 817 ~d~C~~C~~~--ll~~pF~vf~CgH~FH~~Cl~~~v~ 851 (911)
T KOG2034|consen 817 QDSCDHCGRP--LLIKPFYVFPCGHCFHRDCLIRHVL 851 (911)
T ss_pred ccchHHhcch--hhcCcceeeeccchHHHHHHHHHHH
Confidence 4579999997 5777887579999999999999876
No 122
>PF06416 DUF1076: Protein of unknown function (DUF1076); InterPro: IPR010489 This entry is represented by Bacteriophage 2851, Orf74 (EP2851_74). The characteristics of the protein distribution suggest prophage matches in addition to the phage matches.; PDB: 2KKX_A 2KKY_A.
Probab=59.45 E-value=7.8 Score=29.37 Aligned_cols=51 Identities=20% Similarity=0.409 Sum_probs=26.0
Q ss_pred eeeccCcCCCC---ccccCCccccCCCccccHHHHHHHHHhcCCCCCCCCCCCCCCccCC
Q 029888 90 NISCPLSGKPI---TELAEPVRSVECKHIYEKNAIQAYIKSKNANARCPVAGCPRKLQVS 146 (186)
Q Consensus 90 ~l~CPI~~~~~---~~l~dPV~s~~CgH~fck~~I~~~l~~~~~~~~CPv~GC~~~l~~~ 146 (186)
.++||||+.-- ..+++-..|..| .-|++.|+.+.+.. + ..-|. -+..++.+
T Consensus 40 ~L~CPITL~iPe~GVFvkNs~~S~VC-~LyD~~Al~~Lv~~-~--~~HPL--SREpit~s 93 (113)
T PF06416_consen 40 HLTCPITLCIPENGVFVKNSSGSDVC-SLYDKEALSRLVRE-G--APHPL--SREPITPS 93 (113)
T ss_dssp HH-BTTTTC--SCEEEEECTTTSSEE-EEEEHHHHHHHHHC-T-----TT--T-----TT
T ss_pred HcCCCeEEeecCCceEEecCCCCccc-eecCHHHHHHHHHc-C--CCCCC--ccCCCChh
Confidence 68999998510 012333334455 56999999999983 2 34455 44445443
No 123
>KOG4718 consensus Non-SMC (structural maintenance of chromosomes) element 1 protein (NSE1) [Chromatin structure and dynamics]
Probab=59.29 E-value=5.2 Score=33.73 Aligned_cols=43 Identities=26% Similarity=0.589 Sum_probs=33.9
Q ss_pred eeccCcCCCCccccCCccccCCCccccHHHHHHHHHhcCCCCCCCCCCCCC
Q 029888 91 ISCPLSGKPITELAEPVRSVECKHIYEKNAIQAYIKSKNANARCPVAGCPR 141 (186)
Q Consensus 91 l~CPI~~~~~~~l~dPV~s~~CgH~fck~~I~~~l~~~~~~~~CPv~GC~~ 141 (186)
..|.+|.. +...=++.-.||-.|-..||..|++. ...||. |+.
T Consensus 182 k~Cn~Ch~---LvIqg~rCg~c~i~~h~~c~qty~q~---~~~cph--c~d 224 (235)
T KOG4718|consen 182 KNCNLCHC---LVIQGIRCGSCNIQYHRGCIQTYLQR---RDICPH--CGD 224 (235)
T ss_pred HHHhHhHH---HhheeeccCcccchhhhHHHHHHhcc---cCcCCc--hhc
Confidence 36999997 44555666778888999999999992 568999 853
No 124
>KOG2932 consensus E3 ubiquitin ligase involved in ubiquitination of E-cadherin complex [Posttranslational modification, protein turnover, chaperones]
Probab=58.93 E-value=5.8 Score=35.36 Aligned_cols=41 Identities=24% Similarity=0.590 Sum_probs=27.2
Q ss_pred eeccCcCCCCccccCCccccCCCccccHHHHHHHHHhcCCCCCCCCCCCCC
Q 029888 91 ISCPLSGKPITELAEPVRSVECKHIYEKNAIQAYIKSKNANARCPVAGCPR 141 (186)
Q Consensus 91 l~CPI~~~~~~~l~dPV~s~~CgH~fck~~I~~~l~~~~~~~~CPv~GC~~ 141 (186)
-.|=-|..||.++- +...|+|+||.+|-... ..+.||. |.-
T Consensus 91 HfCd~Cd~PI~IYG---RmIPCkHvFCl~CAr~~-----~dK~Cp~--C~d 131 (389)
T KOG2932|consen 91 HFCDRCDFPIAIYG---RMIPCKHVFCLECARSD-----SDKICPL--CDD 131 (389)
T ss_pred EeecccCCcceeee---cccccchhhhhhhhhcC-----ccccCcC--ccc
Confidence 45888888763332 23579999999995442 2356887 754
No 125
>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=58.03 E-value=11 Score=23.49 Aligned_cols=25 Identities=20% Similarity=0.703 Sum_probs=14.2
Q ss_pred CCCccccHHHHHHHHHhcCCCCCCCC
Q 029888 111 ECKHIYEKNAIQAYIKSKNANARCPV 136 (186)
Q Consensus 111 ~CgH~fck~~I~~~l~~~~~~~~CPv 136 (186)
.|+-.+=..|+..|++. .....||.
T Consensus 18 ~C~~r~H~~C~~~y~r~-~~~~~CP~ 42 (43)
T PF08746_consen 18 DCNVRLHDDCFKKYFRH-RSNPKCPN 42 (43)
T ss_dssp -S--EE-HHHHHHHTTT--SS-B-TT
T ss_pred ccCchHHHHHHHHHHhc-CCCCCCcC
Confidence 57767778889999984 34447998
No 126
>KOG3899 consensus Uncharacterized conserved protein [Function unknown]
Probab=57.93 E-value=6.7 Score=34.71 Aligned_cols=41 Identities=17% Similarity=0.603 Sum_probs=29.7
Q ss_pred CccccCCCccccHHHHHHHHHh----------cCCCCCCCCCCCCCCccCCCC
Q 029888 106 PVRSVECKHIYEKNAIQAYIKS----------KNANARCPVAGCPRKLQVSKV 148 (186)
Q Consensus 106 PV~s~~CgH~fck~~I~~~l~~----------~~~~~~CPv~GC~~~l~~~~L 148 (186)
|..|--|.-..|++|+.+|+.. ..++..||. |++.+...|+
T Consensus 319 ~c~nc~crp~wc~~cla~~f~~rq~~v~r~~~~~~~~~cp~--cr~~fci~dv 369 (381)
T KOG3899|consen 319 PCENCICRPLWCRSCLAQIFIGRQDNVYRYEYHRGSAQCPT--CRKNFCIRDV 369 (381)
T ss_pred cccccccccHHHHHHHHHHHhhcccchhHHHHHhcCCCCcc--hhhceEEeee
Confidence 3334456667899999999863 247889999 9998765543
No 127
>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=57.71 E-value=3.2 Score=26.34 Aligned_cols=27 Identities=26% Similarity=0.577 Sum_probs=16.4
Q ss_pred ccCCCccccHHHHHHHHHhcCCCCCCCCCCCCC
Q 029888 109 SVECKHIYEKNAIQAYIKSKNANARCPVAGCPR 141 (186)
Q Consensus 109 s~~CgH~fck~~I~~~l~~~~~~~~CPv~GC~~ 141 (186)
...|||.|+.. ..+. ......||. |+.
T Consensus 8 C~~Cg~~fe~~---~~~~-~~~~~~CP~--Cg~ 34 (52)
T TIGR02605 8 CTACGHRFEVL---QKMS-DDPLATCPE--CGG 34 (52)
T ss_pred eCCCCCEeEEE---EecC-CCCCCCCCC--CCC
Confidence 35788888742 1122 134568999 875
No 128
>KOG1571 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=56.22 E-value=3.7 Score=36.90 Aligned_cols=41 Identities=24% Similarity=0.461 Sum_probs=27.2
Q ss_pred eeccCcCCCCccccCCccccCCCccccHHHHHHHHHhcCCCCCCCCCCCCCCc
Q 029888 91 ISCPLSGKPITELAEPVRSVECKHIYEKNAIQAYIKSKNANARCPVAGCPRKL 143 (186)
Q Consensus 91 l~CPI~~~~~~~l~dPV~s~~CgH~fck~~I~~~l~~~~~~~~CPv~GC~~~l 143 (186)
..|-||.. ...+-+- ..|||+-| |+.-+.. ..+||+ |+..+
T Consensus 306 ~lcVVcl~---e~~~~~f-vpcGh~cc--ct~cs~~----l~~CPv--CR~rI 346 (355)
T KOG1571|consen 306 DLCVVCLD---EPKSAVF-VPCGHVCC--CTLCSKH----LPQCPV--CRQRI 346 (355)
T ss_pred CceEEecC---Cccceee-ecCCcEEE--chHHHhh----CCCCch--hHHHH
Confidence 45777774 3455555 68999988 6555443 235999 98654
No 129
>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=56.07 E-value=0.77 Score=32.00 Aligned_cols=40 Identities=25% Similarity=0.449 Sum_probs=20.8
Q ss_pred eeccCcCCCCccccCCccccCCCccccHHHHHHHHHhcCCCCCCCCCCCCCCcc
Q 029888 91 ISCPLSGKPITELAEPVRSVECKHIYEKNAIQAYIKSKNANARCPVAGCPRKLQ 144 (186)
Q Consensus 91 l~CPI~~~~~~~l~dPV~s~~CgH~fck~~I~~~l~~~~~~~~CPv~GC~~~l~ 144 (186)
+.||.|.. |+.... ||.+|..|-..|.. ...||- |.+.|.
T Consensus 2 ~~CP~C~~-------~L~~~~-~~~~C~~C~~~~~~----~a~CPd--C~~~Le 41 (70)
T PF07191_consen 2 NTCPKCQQ-------ELEWQG-GHYHCEACQKDYKK----EAFCPD--CGQPLE 41 (70)
T ss_dssp -B-SSS-S-------BEEEET-TEEEETTT--EEEE----EEE-TT--T-SB-E
T ss_pred CcCCCCCC-------ccEEeC-CEEECcccccccee----cccCCC--cccHHH
Confidence 57999986 343222 78888877666544 257999 887654
No 130
>PF13717 zinc_ribbon_4: zinc-ribbon domain
Probab=55.90 E-value=6.4 Score=23.57 Aligned_cols=8 Identities=38% Similarity=0.845 Sum_probs=3.8
Q ss_pred eeccCcCC
Q 029888 91 ISCPLSGK 98 (186)
Q Consensus 91 l~CPI~~~ 98 (186)
+.||-|..
T Consensus 3 i~Cp~C~~ 10 (36)
T PF13717_consen 3 ITCPNCQA 10 (36)
T ss_pred EECCCCCC
Confidence 34555554
No 131
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=55.74 E-value=7.1 Score=30.41 Aligned_cols=15 Identities=27% Similarity=0.698 Sum_probs=11.5
Q ss_pred CCCCCCCCCCCCCccCC
Q 029888 130 ANARCPVAGCPRKLQVS 146 (186)
Q Consensus 130 ~~~~CPv~GC~~~l~~~ 146 (186)
+.+.||. |+..|...
T Consensus 122 ~~f~Cp~--Cg~~l~~~ 136 (147)
T smart00531 122 GTFTCPR--CGEELEED 136 (147)
T ss_pred CcEECCC--CCCEEEEc
Confidence 5589999 99877544
No 132
>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=54.70 E-value=8.9 Score=22.65 Aligned_cols=22 Identities=32% Similarity=0.703 Sum_probs=14.1
Q ss_pred ccCCCccccHHHHHHHHHhcCCCCCCCCCCCCC
Q 029888 109 SVECKHIYEKNAIQAYIKSKNANARCPVAGCPR 141 (186)
Q Consensus 109 s~~CgH~fck~~I~~~l~~~~~~~~CPv~GC~~ 141 (186)
...|||+|... .....||+ |++
T Consensus 5 C~~CG~i~~g~---------~~p~~CP~--Cg~ 26 (34)
T cd00729 5 CPVCGYIHEGE---------EAPEKCPI--CGA 26 (34)
T ss_pred CCCCCCEeECC---------cCCCcCcC--CCC
Confidence 35688877542 23458999 865
No 133
>PRK11827 hypothetical protein; Provisional
Probab=54.03 E-value=9.3 Score=25.77 Aligned_cols=11 Identities=27% Similarity=0.751 Sum_probs=8.1
Q ss_pred eeeccCcCCCC
Q 029888 90 NISCPLSGKPI 100 (186)
Q Consensus 90 ~l~CPI~~~~~ 100 (186)
-+.||+|+.++
T Consensus 8 ILaCP~ckg~L 18 (60)
T PRK11827 8 IIACPVCNGKL 18 (60)
T ss_pred heECCCCCCcC
Confidence 36799998754
No 134
>PRK09678 DNA-binding transcriptional regulator; Provisional
Probab=53.70 E-value=7.3 Score=27.21 Aligned_cols=8 Identities=38% Similarity=0.982 Sum_probs=5.7
Q ss_pred eeccCcCC
Q 029888 91 ISCPLSGK 98 (186)
Q Consensus 91 l~CPI~~~ 98 (186)
+.||.|+.
T Consensus 2 m~CP~Cg~ 9 (72)
T PRK09678 2 FHCPLCQH 9 (72)
T ss_pred ccCCCCCC
Confidence 46888875
No 135
>KOG4275 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=53.35 E-value=3 Score=36.80 Aligned_cols=40 Identities=20% Similarity=0.454 Sum_probs=28.1
Q ss_pred eeeccCcCCCCccccCCccccCCCcc-ccHHHHHHHHHhcCCCCCCCCCCCCCC
Q 029888 90 NISCPLSGKPITELAEPVRSVECKHI-YEKNAIQAYIKSKNANARCPVAGCPRK 142 (186)
Q Consensus 90 ~l~CPI~~~~~~~l~dPV~s~~CgH~-fck~~I~~~l~~~~~~~~CPv~GC~~~ 142 (186)
...|-||+. .-.+=|- ..|||. -|-.| .+....||+ |++.
T Consensus 300 ~~LC~ICmD---aP~DCvf-LeCGHmVtCt~C-------Gkrm~eCPI--CRqy 340 (350)
T KOG4275|consen 300 RRLCAICMD---APRDCVF-LECGHMVTCTKC-------GKRMNECPI--CRQY 340 (350)
T ss_pred HHHHHHHhc---CCcceEE-eecCcEEeehhh-------ccccccCch--HHHH
Confidence 567999997 3355556 789995 46565 445568999 9763
No 136
>PF03884 DUF329: Domain of unknown function (DUF329); InterPro: IPR005584 The biological function of these short proteins is unknown, but they contain four conserved cysteines, suggesting that they all bind zinc. YacG (Q5X8H6 from SWISSPROT) from Escherichia coli has been shown to bind zinc and contains the structural motifs typical of zinc-binding proteins []. The conserved four cysteine motif in these proteins (-C-X(2)-C-X(15)-C-X(3)-C-) is not found in other zinc-binding proteins with known structures.; GO: 0008270 zinc ion binding; PDB: 1LV3_A.
Probab=52.37 E-value=7.9 Score=25.85 Aligned_cols=11 Identities=45% Similarity=1.398 Sum_probs=6.0
Q ss_pred eeeccCcCCCC
Q 029888 90 NISCPLSGKPI 100 (186)
Q Consensus 90 ~l~CPI~~~~~ 100 (186)
...||+|++++
T Consensus 2 ~v~CP~C~k~~ 12 (57)
T PF03884_consen 2 TVKCPICGKPV 12 (57)
T ss_dssp EEE-TTT--EE
T ss_pred cccCCCCCCee
Confidence 46899999864
No 137
>PF05290 Baculo_IE-1: Baculovirus immediate-early protein (IE-0); InterPro: IPR007954 This entry contains the Baculovirus immediate-early protein IE-0.
Probab=52.29 E-value=20 Score=28.13 Aligned_cols=53 Identities=19% Similarity=0.316 Sum_probs=38.9
Q ss_pred eeeccCcCCCC--ccccCCccccCCCccccHHHHHHHHHhcCCCCCCCCCCCCCCccCC
Q 029888 90 NISCPLSGKPI--TELAEPVRSVECKHIYEKNAIQAYIKSKNANARCPVAGCPRKLQVS 146 (186)
Q Consensus 90 ~l~CPI~~~~~--~~l~dPV~s~~CgH~fck~~I~~~l~~~~~~~~CPv~GC~~~l~~~ 146 (186)
-+.|-||++.- ..|-.| +.-||..-|..|-...|+--.--+.||+ |...+..+
T Consensus 80 lYeCnIC~etS~ee~FLKP--neCCgY~iCn~Cya~LWK~~~~ypvCPv--CkTSFKss 134 (140)
T PF05290_consen 80 LYECNICKETSAEERFLKP--NECCGYSICNACYANLWKFCNLYPVCPV--CKTSFKSS 134 (140)
T ss_pred ceeccCcccccchhhcCCc--ccccchHHHHHHHHHHHHHcccCCCCCc--cccccccc
Confidence 57799998621 123445 3479999999999999986456688999 98766544
No 138
>KOG3970 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=52.13 E-value=37 Score=29.14 Aligned_cols=54 Identities=20% Similarity=0.585 Sum_probs=38.1
Q ss_pred eccCcCCCCccccCCccccCCCccccHHHHHHHHHh-----cCCCCCCCCCCCCCCc-cCCCCc
Q 029888 92 SCPLSGKPITELAEPVRSVECKHIYEKNAIQAYIKS-----KNANARCPVAGCPRKL-QVSKVV 149 (186)
Q Consensus 92 ~CPI~~~~~~~l~dPV~s~~CgH~fck~~I~~~l~~-----~~~~~~CPv~GC~~~l-~~~~L~ 149 (186)
.|-+|.-|+ --.+-++ ..|=|.|--.|+-++-.+ ....-+||. |+..| ...+|+
T Consensus 52 NC~LC~t~L-a~gdt~R-LvCyhlfHW~ClneraA~lPanTAPaGyqCP~--Cs~eiFPp~Nlv 111 (299)
T KOG3970|consen 52 NCRLCNTPL-ASGDTTR-LVCYHLFHWKCLNERAANLPANTAPAGYQCPC--CSQEIFPPINLV 111 (299)
T ss_pred CCceeCCcc-ccCccee-ehhhhhHHHHHhhHHHhhCCCcCCCCcccCCC--CCCccCCCcccc
Confidence 377777543 4456777 889999999999998764 124568999 98854 455554
No 139
>KOG0825 consensus PHD Zn-finger protein [General function prediction only]
Probab=50.80 E-value=9.2 Score=38.10 Aligned_cols=49 Identities=14% Similarity=0.139 Sum_probs=33.7
Q ss_pred eeeccCcCCCCccccCCccc------cCCCccccHHHHHHHHHh---cCCCCCCCCCCCCCCc
Q 029888 90 NISCPLSGKPITELAEPVRS------VECKHIYEKNAIQAYIKS---KNANARCPVAGCPRKL 143 (186)
Q Consensus 90 ~l~CPI~~~~~~~l~dPV~s------~~CgH~fck~~I~~~l~~---~~~~~~CPv~GC~~~l 143 (186)
+-+|++|.. .|.+|+-+ ..|+|.||-.||..|..+ ......|+. |..-|
T Consensus 96 s~Ss~~C~~---E~S~~~ds~~i~P~~~~~~~~CP~Ci~s~~DqL~~~~k~c~H~F--C~~Ci 153 (1134)
T KOG0825|consen 96 SDTSPVCEK---EHSPDVDSSNICPVQTHVENQCPNCLKSCNDQLEESEKHTAHYF--CEECV 153 (1134)
T ss_pred ccccchhhe---ecCCcccccCcCchhhhhhhhhhHHHHHHHHHhhcccccccccc--HHHHh
Confidence 456888874 56665532 248999999999999875 334556777 76533
No 140
>PRK01343 zinc-binding protein; Provisional
Probab=49.93 E-value=8.2 Score=25.81 Aligned_cols=13 Identities=38% Similarity=0.662 Sum_probs=10.1
Q ss_pred cceeeccCcCCCC
Q 029888 88 ILNISCPLSGKPI 100 (186)
Q Consensus 88 ~~~l~CPI~~~~~ 100 (186)
....+||+|++++
T Consensus 7 ~p~~~CP~C~k~~ 19 (57)
T PRK01343 7 RPTRPCPECGKPS 19 (57)
T ss_pred CCCCcCCCCCCcC
Confidence 3467899999864
No 141
>PLN02189 cellulose synthase
Probab=49.78 E-value=11 Score=38.38 Aligned_cols=50 Identities=18% Similarity=0.436 Sum_probs=34.4
Q ss_pred eeccCcCCCCc--cccCCcc-ccCCCccccHHHHHHHHHhcCCCCCCCCCCCCCCcc
Q 029888 91 ISCPLSGKPIT--ELAEPVR-SVECKHIYEKNAIQAYIKSKNANARCPVAGCPRKLQ 144 (186)
Q Consensus 91 l~CPI~~~~~~--~l~dPV~-s~~CgH~fck~~I~~~l~~~~~~~~CPv~GC~~~l~ 144 (186)
-.|.||+.-++ .--+|+. ...|+.--|+.|. +|-+ ..++..||+ |+....
T Consensus 35 ~~C~iCgd~vg~~~~g~~fvaC~~C~fpvCr~Cy-eyer-~eg~q~Cpq--Ckt~Y~ 87 (1040)
T PLN02189 35 QVCEICGDEIGLTVDGDLFVACNECGFPVCRPCY-EYER-REGTQNCPQ--CKTRYK 87 (1040)
T ss_pred ccccccccccCcCCCCCEEEeeccCCCccccchh-hhhh-hcCCccCcc--cCCchh
Confidence 47999997443 1112443 3468888999998 6766 467889999 977554
No 142
>KOG3579 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=49.74 E-value=7.4 Score=34.29 Aligned_cols=63 Identities=21% Similarity=0.412 Sum_probs=41.4
Q ss_pred eeeccCcCCCCccccCCccccCC----CccccHHHHHHHHHhcC--CCC------CCCCCCCCCCccCCCCccCHHHHHH
Q 029888 90 NISCPLSGKPITELAEPVRSVEC----KHIYEKNAIQAYIKSKN--ANA------RCPVAGCPRKLQVSKVVCDSLLLVD 157 (186)
Q Consensus 90 ~l~CPI~~~~~~~l~dPV~s~~C----gH~fck~~I~~~l~~~~--~~~------~CPv~GC~~~l~~~~L~~d~~L~~~ 157 (186)
-|+|-||.+ .|+|--- ..| .|-||.-|-.+.|++.+ +.+ +||.+|-. +|=..|+-+
T Consensus 268 pLcCTLC~E---RLEDTHF-VQCPSVp~HKFCFPCSResIK~Qg~sgevYCPSGdkCPLvgS~--------vPWAFMQGE 335 (352)
T KOG3579|consen 268 PLCCTLCHE---RLEDTHF-VQCPSVPSHKFCFPCSRESIKQQGASGEVYCPSGDKCPLVGSN--------VPWAFMQGE 335 (352)
T ss_pred ceeehhhhh---hhccCce-eecCCCcccceecccCHHHHHhhcCCCceeCCCCCcCcccCCc--------ccHHHhhhh
Confidence 499999997 6787655 566 59999999999998522 233 45554422 233345666
Q ss_pred HHHHHhc
Q 029888 158 IDEMRRT 164 (186)
Q Consensus 158 I~~~r~~ 164 (186)
|..++..
T Consensus 336 IatILag 342 (352)
T KOG3579|consen 336 IATILAG 342 (352)
T ss_pred HHHHhcc
Confidence 6666544
No 143
>cd01408 SIRT1 SIRT1: Eukaryotic group (class1) which includes human sirtuins SIRT1-3 and yeast Hst1-4; and are members of the SIR2 family of proteins, silent information regulator 2 (Sir2) enzymes which catalyze NAD+-dependent protein/histone deacetylation. Sir2 proteins have been shown to regulate gene silencing, DNA repair, and life span. The most-studied function, gene silencing, involves the inactivation of chromosome domains containing key regulatory genes by packaging them into a specialized chromatin structure that is inaccessible to DNA-binding proteins. The nuclear SIRT1 has been shown to target the p53 tumor suppressor protein for deacetylation to suppress DNA damage, and the cytoplasmic SIRT2 homolog has been shown to target alpha-tubulin for deacetylation for the maintenance of cell integrity.
Probab=49.22 E-value=22 Score=29.74 Aligned_cols=33 Identities=24% Similarity=0.553 Sum_probs=20.1
Q ss_pred CCCccccHHHHHHHHHhcCCCCCCCCCCCCCCccCC
Q 029888 111 ECKHIYEKNAIQAYIKSKNANARCPVAGCPRKLQVS 146 (186)
Q Consensus 111 ~CgH~fck~~I~~~l~~~~~~~~CPv~GC~~~l~~~ 146 (186)
.|++.|....+...+. ......||. |+..+.+.
T Consensus 121 ~C~~~~~~~~~~~~~~-~~~~p~C~~--Cgg~lrP~ 153 (235)
T cd01408 121 KCKHKYPGDWMREDIF-NQEVPKCPR--CGGLVKPD 153 (235)
T ss_pred cCCCcCCHHHHHHHHh-CCCCccCCC--CCCCccCc
Confidence 4666666655555554 233578999 97766543
No 144
>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=47.82 E-value=10 Score=25.63 Aligned_cols=7 Identities=29% Similarity=1.132 Sum_probs=3.1
Q ss_pred eeccCcC
Q 029888 91 ISCPLSG 97 (186)
Q Consensus 91 l~CPI~~ 97 (186)
+.||.|.
T Consensus 8 L~Cp~ck 14 (68)
T PF03966_consen 8 LACPVCK 14 (68)
T ss_dssp BB-TTTS
T ss_pred hcCCCCC
Confidence 4455554
No 145
>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=47.48 E-value=3.6 Score=24.56 Aligned_cols=12 Identities=33% Similarity=0.775 Sum_probs=8.6
Q ss_pred CCCCCCCCCCCCCc
Q 029888 130 ANARCPVAGCPRKL 143 (186)
Q Consensus 130 ~~~~CPv~GC~~~l 143 (186)
....||. |+..+
T Consensus 25 ~~~~CP~--Cg~~~ 36 (41)
T smart00834 25 PLATCPE--CGGDV 36 (41)
T ss_pred CCCCCCC--CCCcc
Confidence 5578999 87643
No 146
>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=47.46 E-value=7.6 Score=25.60 Aligned_cols=11 Identities=36% Similarity=0.812 Sum_probs=8.3
Q ss_pred eeeccCcCCCC
Q 029888 90 NISCPLSGKPI 100 (186)
Q Consensus 90 ~l~CPI~~~~~ 100 (186)
.++||.|+..|
T Consensus 2 ~~~CP~CG~~i 12 (54)
T TIGR01206 2 QFECPDCGAEI 12 (54)
T ss_pred ccCCCCCCCEE
Confidence 36899999754
No 147
>COG3813 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=46.73 E-value=18 Score=25.49 Aligned_cols=41 Identities=12% Similarity=0.205 Sum_probs=31.0
Q ss_pred CccccHHHHHHHHHhcCCCCCCCCCCCCCCccCCCCccCHHHHHHHHH
Q 029888 113 KHIYEKNAIQAYIKSKNANARCPVAGCPRKLQVSKVVCDSLLLVDIDE 160 (186)
Q Consensus 113 gH~fck~~I~~~l~~~~~~~~CPv~GC~~~l~~~~L~~d~~L~~~I~~ 160 (186)
.|+||.+|.+.-|. ..||- |+..|...-+.|...|.+--..
T Consensus 28 EcTFCadCae~~l~-----g~CPn--CGGelv~RP~RPaa~L~r~PAS 68 (84)
T COG3813 28 ECTFCADCAENRLH-----GLCPN--CGGELVARPIRPAAKLARYPAS 68 (84)
T ss_pred eeehhHhHHHHhhc-----CcCCC--CCchhhcCcCChHHHHhhCchh
Confidence 47999999998777 37999 9888888878777655543333
No 148
>COG3024 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=45.75 E-value=10 Score=25.95 Aligned_cols=14 Identities=36% Similarity=0.947 Sum_probs=10.9
Q ss_pred ccceeeccCcCCCC
Q 029888 87 NILNISCPLSGKPI 100 (186)
Q Consensus 87 ~~~~l~CPI~~~~~ 100 (186)
..+...||+|++|+
T Consensus 4 ~~~~v~CP~Cgkpv 17 (65)
T COG3024 4 LRITVPCPTCGKPV 17 (65)
T ss_pred ccccccCCCCCCcc
Confidence 35678899999864
No 149
>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=45.19 E-value=15 Score=21.69 Aligned_cols=11 Identities=27% Similarity=0.664 Sum_probs=6.5
Q ss_pred CCCCCCCCCCCCc
Q 029888 131 NARCPVAGCPRKL 143 (186)
Q Consensus 131 ~~~CPv~GC~~~l 143 (186)
.+.||. |+..+
T Consensus 25 ~v~C~~--C~~~~ 35 (38)
T TIGR02098 25 KVRCGK--CGHVW 35 (38)
T ss_pred EEECCC--CCCEE
Confidence 456777 66543
No 150
>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=44.94 E-value=3.2 Score=25.66 Aligned_cols=27 Identities=30% Similarity=0.652 Sum_probs=17.1
Q ss_pred ccCCCccccHHHHHHHHHhcCCCCCCCCCCCCC
Q 029888 109 SVECKHIYEKNAIQAYIKSKNANARCPVAGCPR 141 (186)
Q Consensus 109 s~~CgH~fck~~I~~~l~~~~~~~~CPv~GC~~ 141 (186)
...|||.|+.-. . +. ......||. |+.
T Consensus 8 C~~Cg~~fe~~~--~-~~-~~~~~~CP~--Cg~ 34 (42)
T PF09723_consen 8 CEECGHEFEVLQ--S-IS-EDDPVPCPE--CGS 34 (42)
T ss_pred eCCCCCEEEEEE--E-cC-CCCCCcCCC--CCC
Confidence 457888887532 2 22 135678999 876
No 151
>PF02146 SIR2: Sir2 family; InterPro: IPR003000 These sequences represent the Sirtuin (Sir2-related) family of NAD+-dependent deacetylases. This family of enzymes is broadly conserved from bacteria to humans. In yeast, Sir2 proteins form complexes with other proteins to silence chromatin by accessing histones and deacetylating them. Sir2 proteins have been proposed to play a role in silencing, chromosome stability and ageing []. The bacterial enzyme CobB, an homologue of Sir2, is a phosphoribosyltransferase []. An in vitro ADP ribosyltransferase activity has also been associated with human members of this family []. Sir2-like enzymes employ NAD+ as a cosubstrate in deacetylation reactions [] and catalyse a reaction in which the cleavage of NAD(+)and histone and/or protein deacetylation are coupled to the formation of O-acetyl-ADP-ribose, a novel metabolite. The dependence of the reaction on both NAD(+) and the generation of this potential second messenger offers new clues to understanding the function and regulation of nuclear, cytoplasmic and mitochondrial Sir2-like enzymes []. Silent Information Regulator protein of Saccharomyces cerevisiae (Sir2) is one of several factors critical for silencing at least three loci. Among them, it is unique because it silences the rDNA as well as the mating type loci and telomeres []. Sir2 interacts in a complex with itself and with Sir3 and Sir4, two proteins that are able to interact with nucleosomes. In addition Sir2 also interacts with ubiquitination factors and/or complexes []. Homologues of Sir2 share a core domain including the GAG and NID motifs and a putative C4 Zinc finger. The regions containing these three conserved motifs are individually essential for Sir2 silencing function, as are the four cysteins []. In addition, the conserved residues HG next to the putative Zn finger have been shown to be essential for the ADP ribosyltransferase activity []. ; GO: 0008270 zinc ion binding, 0070403 NAD+ binding, 0006476 protein deacetylation; PDB: 1S5P_A 3PKI_E 3PKJ_F 3K35_A 1ICI_A 1M2K_A 1M2G_A 1M2N_B 1M2H_A 1M2J_A ....
Probab=44.55 E-value=20 Score=28.43 Aligned_cols=33 Identities=27% Similarity=0.619 Sum_probs=21.5
Q ss_pred cCCCccccHHHHHHHHHhcCCCCCCCCCCCCCCccC
Q 029888 110 VECKHIYEKNAIQAYIKSKNANARCPVAGCPRKLQV 145 (186)
Q Consensus 110 ~~CgH~fck~~I~~~l~~~~~~~~CPv~GC~~~l~~ 145 (186)
..|++.|...-+...+. ......||. |+..+.+
T Consensus 109 ~~C~~~~~~~~~~~~~~-~~~~~~C~~--C~~~lrp 141 (178)
T PF02146_consen 109 SKCGKEYDREDIVDSID-EEEPPRCPK--CGGLLRP 141 (178)
T ss_dssp TTTSBEEEGHHHHHHHH-TTSSCBCTT--TSCBEEE
T ss_pred cCCCccccchhhccccc-ccccccccc--cCccCCC
Confidence 34666666665665555 345678999 9886654
No 152
>PF06676 DUF1178: Protein of unknown function (DUF1178); InterPro: IPR009562 This family consists of several hypothetical bacterial proteins of around 150 residues in length. The function of this family is unknown.
Probab=43.99 E-value=28 Score=27.57 Aligned_cols=26 Identities=27% Similarity=0.479 Sum_probs=15.9
Q ss_pred CCccccH-----HHHHHHHHhcCCCCCCCCCCCCC
Q 029888 112 CKHIYEK-----NAIQAYIKSKNANARCPVAGCPR 141 (186)
Q Consensus 112 CgH~fck-----~~I~~~l~~~~~~~~CPv~GC~~ 141 (186)
|||.|+. ..+..-. ..+-+.||+ |+.
T Consensus 10 ~gH~FEgWF~ss~~fd~Q~--~~glv~CP~--Cgs 40 (148)
T PF06676_consen 10 NGHEFEGWFRSSAAFDRQQ--ARGLVSCPV--CGS 40 (148)
T ss_pred CCCccceecCCHHHHHHHH--HcCCccCCC--CCC
Confidence 5899863 2222222 357789999 754
No 153
>PLN03086 PRLI-interacting factor K; Provisional
Probab=43.77 E-value=34 Score=32.82 Aligned_cols=30 Identities=20% Similarity=0.335 Sum_probs=13.1
Q ss_pred CCccccHHHHHHHHHh--cCCCCCCCCCCCCCCc
Q 029888 112 CKHIYEKNAIQAYIKS--KNANARCPVAGCPRKL 143 (186)
Q Consensus 112 CgH~fck~~I~~~l~~--~~~~~~CPv~GC~~~l 143 (186)
||..+.+..+..++.. ..+...|+. |...+
T Consensus 483 Cg~~~~R~~L~~H~~thCp~Kpi~C~f--C~~~v 514 (567)
T PLN03086 483 CGVVLEKEQMVQHQASTCPLRLITCRF--CGDMV 514 (567)
T ss_pred CCCCcchhHHHhhhhccCCCCceeCCC--CCCcc
Confidence 4444444444444331 123344555 55444
No 154
>COG3357 Predicted transcriptional regulator containing an HTH domain fused to a Zn-ribbon [Transcription]
Probab=43.58 E-value=11 Score=27.72 Aligned_cols=31 Identities=26% Similarity=0.650 Sum_probs=22.3
Q ss_pred cccCCccccCCCccccHHHHHHHHHhcCCCCCCCCCCCCC
Q 029888 102 ELAEPVRSVECKHIYEKNAIQAYIKSKNANARCPVAGCPR 141 (186)
Q Consensus 102 ~l~dPV~s~~CgH~fck~~I~~~l~~~~~~~~CPv~GC~~ 141 (186)
++..|-+..+||..|-..- -+...+||. |..
T Consensus 54 Llv~Pa~CkkCGfef~~~~-------ik~pSRCP~--CKS 84 (97)
T COG3357 54 LLVRPARCKKCGFEFRDDK-------IKKPSRCPK--CKS 84 (97)
T ss_pred EEecChhhcccCccccccc-------cCCcccCCc--chh
Confidence 4567777789999997632 134678999 964
No 155
>PRK14138 NAD-dependent deacetylase; Provisional
Probab=43.10 E-value=30 Score=29.20 Aligned_cols=32 Identities=19% Similarity=0.465 Sum_probs=19.5
Q ss_pred CCCccccHHHHHHHHHhcCCCCCCCCCCCCCCccC
Q 029888 111 ECKHIYEKNAIQAYIKSKNANARCPVAGCPRKLQV 145 (186)
Q Consensus 111 ~CgH~fck~~I~~~l~~~~~~~~CPv~GC~~~l~~ 145 (186)
.|++.|...-+...+. ......||. |+..+.+
T Consensus 124 ~C~~~~~~~~~~~~~~-~~~~p~Cp~--Cgg~lrP 155 (244)
T PRK14138 124 RCGKRYTVEDVIEKLE-KSDVPRCDD--CSGLIRP 155 (244)
T ss_pred CCCCcccHHHHHHHHh-cCCCCCCCC--CCCeECC
Confidence 3555565555555544 234578999 9876654
No 156
>PHA02825 LAP/PHD finger-like protein; Provisional
Probab=42.76 E-value=42 Score=27.03 Aligned_cols=48 Identities=19% Similarity=0.472 Sum_probs=32.1
Q ss_pred ceeeccCcCCCCccccCCccccCC--Ccc---ccHHHHHHHHHhcCCCCCCCCCCCCCCcc
Q 029888 89 LNISCPLSGKPITELAEPVRSVEC--KHI---YEKNAIQAYIKSKNANARCPVAGCPRKLQ 144 (186)
Q Consensus 89 ~~l~CPI~~~~~~~l~dPV~s~~C--gH~---fck~~I~~~l~~~~~~~~CPv~GC~~~l~ 144 (186)
..-.|=||...- ++.. ..| ..+ -=++|++.|+. ..+...||+ |+..+.
T Consensus 7 ~~~~CRIC~~~~----~~~~-~PC~CkGs~k~VH~sCL~rWi~-~s~~~~Cei--C~~~Y~ 59 (162)
T PHA02825 7 MDKCCWICKDEY----DVVT-NYCNCKNENKIVHKECLEEWIN-TSKNKSCKI--CNGPYN 59 (162)
T ss_pred CCCeeEecCCCC----CCcc-CCcccCCCchHHHHHHHHHHHh-cCCCCcccc--cCCeEE
Confidence 456788888732 2333 234 332 35899999999 467889999 977543
No 157
>PF14471 DUF4428: Domain of unknown function (DUF4428)
Probab=42.75 E-value=23 Score=22.87 Aligned_cols=30 Identities=17% Similarity=0.382 Sum_probs=21.9
Q ss_pred eccCcCCCCccccCCccccCCCccccHHHHHHH
Q 029888 92 SCPLSGKPITELAEPVRSVECKHIYEKNAIQAY 124 (186)
Q Consensus 92 ~CPI~~~~~~~l~dPV~s~~CgH~fck~~I~~~ 124 (186)
+|+||++.+++|.. +. ..=| .-|++|+...
T Consensus 1 ~C~iCg~kigl~~~-~k-~~DG-~iC~~C~~Kl 30 (51)
T PF14471_consen 1 KCAICGKKIGLFKR-FK-IKDG-YICKDCLKKL 30 (51)
T ss_pred CCCccccccccccc-ee-ccCc-cchHHHHHHh
Confidence 49999998766654 55 5566 5888887665
No 158
>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=42.15 E-value=20 Score=32.38 Aligned_cols=35 Identities=20% Similarity=0.577 Sum_probs=26.3
Q ss_pred CCccccHHHHHHHHHh----------cCCCCCCCCCCCCCCccCCCC
Q 029888 112 CKHIYEKNAIQAYIKS----------KNANARCPVAGCPRKLQVSKV 148 (186)
Q Consensus 112 CgH~fck~~I~~~l~~----------~~~~~~CPv~GC~~~l~~~~L 148 (186)
|.=..|-+||-+|+.+ -.+...||. |++.+..-|+
T Consensus 311 CRPmWC~~Cm~kwFasrQd~~~~~~Wl~~~~~CPt--CRa~FCilDV 355 (358)
T PF10272_consen 311 CRPMWCLECMGKWFASRQDQQHPETWLSGKCPCPT--CRAKFCILDV 355 (358)
T ss_pred ccchHHHHHHHHHhhhcCCCCChhhhhcCCCCCCC--Ccccceeeee
Confidence 4445788999999974 136788999 9998876654
No 159
>smart00154 ZnF_AN1 AN1-like Zinc finger. Zinc finger at the C-terminus of An1, a ubiquitin-like protein in Xenopus laevis.
Probab=41.77 E-value=16 Score=22.27 Aligned_cols=25 Identities=12% Similarity=0.301 Sum_probs=16.7
Q ss_pred ccCcCCCCccccCCccccCCCccccHH
Q 029888 93 CPLSGKPITELAEPVRSVECKHIYEKN 119 (186)
Q Consensus 93 CPI~~~~~~~l~dPV~s~~CgH~fck~ 119 (186)
|-+|.+. .+.-|+.-..|+.+||..
T Consensus 1 C~~C~~~--~~l~~f~C~~C~~~FC~~ 25 (39)
T smart00154 1 CHFCRKK--VGLTGFKCRHCGNLFCGE 25 (39)
T ss_pred CcccCCc--ccccCeECCccCCccccc
Confidence 4556662 333488877799999864
No 160
>smart00647 IBR In Between Ring fingers. the domains occurs between pairs og RING fingers
Probab=41.64 E-value=30 Score=22.09 Aligned_cols=32 Identities=25% Similarity=0.611 Sum_probs=22.0
Q ss_pred cccHHHHHHHHHhcCCCCCCCCCCCCCCccCC
Q 029888 115 IYEKNAIQAYIKSKNANARCPVAGCPRKLQVS 146 (186)
Q Consensus 115 ~fck~~I~~~l~~~~~~~~CPv~GC~~~l~~~ 146 (186)
.|.+..+..+|..+....-||-.||...+...
T Consensus 2 ~y~~~~~~~~i~~~~~~~~CP~~~C~~~~~~~ 33 (64)
T smart00647 2 KYERLLLESYVESNPDLKWCPAPDCSAAIIVT 33 (64)
T ss_pred hHHHHHHHHHHhcCCCccCCCCCCCcceEEec
Confidence 36677778888743455669988898765543
No 161
>smart00659 RPOLCX RNA polymerase subunit CX. present in RNA polymerase I, II and III
Probab=41.63 E-value=20 Score=22.45 Aligned_cols=10 Identities=30% Similarity=0.637 Sum_probs=5.7
Q ss_pred CCCCCCCCCCCC
Q 029888 130 ANARCPVAGCPR 141 (186)
Q Consensus 130 ~~~~CPv~GC~~ 141 (186)
...+||- |+.
T Consensus 18 ~~irC~~--CG~ 27 (44)
T smart00659 18 DVVRCRE--CGY 27 (44)
T ss_pred CceECCC--CCc
Confidence 4466666 544
No 162
>PRK10144 formate-dependent nitrite reductase complex subunit NrfF; Provisional
Probab=41.63 E-value=32 Score=26.58 Aligned_cols=36 Identities=22% Similarity=0.363 Sum_probs=25.2
Q ss_pred CCCCCCCCCCCC-CccCCCCccCHHHHHHHHHHHhcCcc
Q 029888 130 ANARCPVAGCPR-KLQVSKVVCDSLLLVDIDEMRRTSKE 167 (186)
Q Consensus 130 ~~~~CPv~GC~~-~l~~~~L~~d~~L~~~I~~~r~~~~~ 167 (186)
...+||+ |.+ .+..++-.-...|+.+|++....+..
T Consensus 39 ~~LRC~v--CqnqsiadSna~iA~dmR~~Vr~~i~~G~s 75 (126)
T PRK10144 39 SQLRCPQ--CQNQNLLESNAPVAVSMRHQVYSMVAEGKS 75 (126)
T ss_pred HcCCCCC--CCCCChhhcCCHHHHHHHHHHHHHHHcCCC
Confidence 5689999 976 56555555556688888887766544
No 163
>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=41.36 E-value=37 Score=25.16 Aligned_cols=27 Identities=15% Similarity=0.437 Sum_probs=20.9
Q ss_pred CccccHHHHHHHHHh------cCCCCCCCCCCCCC
Q 029888 113 KHIYEKNAIQAYIKS------KNANARCPVAGCPR 141 (186)
Q Consensus 113 gH~fck~~I~~~l~~------~~~~~~CPv~GC~~ 141 (186)
.-.||..||...... ....+.||. |+.
T Consensus 37 ~~~fC~~CL~~ryge~~~ev~~~~~W~CP~--Crg 69 (105)
T PF10497_consen 37 RGKFCGGCLRNRYGENVEEVLEDPNWKCPK--CRG 69 (105)
T ss_pred cceehHhHHHHHHhhhHHHHhcCCceECCC--CCC
Confidence 678999998876642 246789999 976
No 164
>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=40.07 E-value=10 Score=24.62 Aligned_cols=29 Identities=28% Similarity=0.744 Sum_probs=20.4
Q ss_pred CC-CccccHHHHHHHHHhcCCCCCCCCCCCCCCcc
Q 029888 111 EC-KHIYEKNAIQAYIKSKNANARCPVAGCPRKLQ 144 (186)
Q Consensus 111 ~C-gH~fck~~I~~~l~~~~~~~~CPv~GC~~~l~ 144 (186)
.| .|-.|..|+..++. .+..||+ |...|.
T Consensus 17 ~C~dHYLCl~CLt~ml~---~s~~C~i--C~~~LP 46 (50)
T PF03854_consen 17 KCSDHYLCLNCLTLMLS---RSDRCPI--CGKPLP 46 (50)
T ss_dssp E-SS-EEEHHHHHHT-S---SSSEETT--TTEE--
T ss_pred eecchhHHHHHHHHHhc---cccCCCc--ccCcCc
Confidence 57 59999999999988 5578999 987664
No 165
>PF01530 zf-C2HC: Zinc finger, C2HC type; InterPro: IPR002515 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents the CysCysHisCys (C2HC) type zinc finger domain found in eukaryotes. Proteins containing these domains include: MYST family histone acetyltransferases [, [] Myelin transcription factor Myt1 [] Suppressor of tumourigenicity protein 18 (ST18) [] More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0008270 zinc ion binding, 0006355 regulation of transcription, DNA-dependent, 0005634 nucleus; PDB: 2CS8_A 1PXE_A 2JX1_A 2JYD_A.
Probab=39.47 E-value=16 Score=21.52 Aligned_cols=11 Identities=36% Similarity=1.132 Sum_probs=7.1
Q ss_pred CCCCCCCCCCC
Q 029888 132 ARCPVAGCPRK 142 (186)
Q Consensus 132 ~~CPv~GC~~~ 142 (186)
.+||..||...
T Consensus 2 ~~CPtpGCdg~ 12 (31)
T PF01530_consen 2 LKCPTPGCDGS 12 (31)
T ss_dssp TSSSSTT--SC
T ss_pred CcCCCCCCCcc
Confidence 47999999753
No 166
>TIGR03147 cyt_nit_nrfF cytochrome c nitrite reductase, accessory protein NrfF.
Probab=39.37 E-value=34 Score=26.41 Aligned_cols=36 Identities=25% Similarity=0.342 Sum_probs=24.9
Q ss_pred CCCCCCCCCCCC-CccCCCCccCHHHHHHHHHHHhcCcc
Q 029888 130 ANARCPVAGCPR-KLQVSKVVCDSLLLVDIDEMRRTSKE 167 (186)
Q Consensus 130 ~~~~CPv~GC~~-~l~~~~L~~d~~L~~~I~~~r~~~~~ 167 (186)
...+||+ |.+ .+..++-.-...|+.+|++....+..
T Consensus 39 ~~LRC~v--CqnqsiadS~a~iA~dmR~~Vr~~i~~G~S 75 (126)
T TIGR03147 39 KSLRCPQ--CQNQNLVESNSPIAYDLRHEVYSMVNEGKS 75 (126)
T ss_pred HhCCCCC--CCCCChhhcCCHHHHHHHHHHHHHHHcCCC
Confidence 5689999 976 56555555556688888887766444
No 167
>PHA02862 5L protein; Provisional
Probab=39.30 E-value=43 Score=26.72 Aligned_cols=48 Identities=17% Similarity=0.341 Sum_probs=31.6
Q ss_pred eeccCcCCCCccccCCccccCCCc-----cccHHHHHHHHHhcCCCCCCCCCCCCCCccCC
Q 029888 91 ISCPLSGKPITELAEPVRSVECKH-----IYEKNAIQAYIKSKNANARCPVAGCPRKLQVS 146 (186)
Q Consensus 91 l~CPI~~~~~~~l~dPV~s~~CgH-----~fck~~I~~~l~~~~~~~~CPv~GC~~~l~~~ 146 (186)
-.|=||...- .+.+ ..|.. .--++|+++|+. ..+...||+ |+......
T Consensus 3 diCWIC~~~~---~e~~--~PC~C~GS~K~VHq~CL~~WIn-~S~k~~CeL--CkteY~Ik 55 (156)
T PHA02862 3 DICWICNDVC---DERN--NFCGCNEEYKVVHIKCMQLWIN-YSKKKECNL--CKTKYNIK 55 (156)
T ss_pred CEEEEecCcC---CCCc--ccccccCcchhHHHHHHHHHHh-cCCCcCccC--CCCeEEEE
Confidence 3577887631 2222 24432 345899999998 467789999 98866543
No 168
>PF10426 zf-RAG1: Recombination-activating protein 1 zinc-finger domain; InterPro: IPR019485 During lymphocyte development, the genes encoding immunoglobulins and T-cell receptors are assembled from variable (V), diversity (D), and joining (J) gene segments. This combinatorial process, known as V(D)J recombination, allows the generation of an enormous range of binding specificities from a limited amount of genetic information. The V(D)J recombination-activating proteins 1 and 2 (RAG1 and RAG2) form a complex that initiates this process by binding to the conserved recombination signal sequences (RSS) and introducing a double-strand break between the RSS and the adjacent coding segment. These breaks are generated in two steps, nicking of one strand (hydrolysis), followed by hairpin formation (transesterification). RAG1/2 has also been shown to function as a transposase in vitro, and to possess RSS-independent endonuclease activity (end processing) and hairpin opening. RAG1 alone can bind to RSS but stable, efficient binding requires RAG2. All known catalytic activities require the presence of both proteins. For more information see []. Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. C2H2-type (classical) zinc fingers (Znf) were the first class to be characterised. They contain a short beta hairpin and an alpha helix (beta/beta/alpha structure), where a single zinc atom is held in place by Cys(2)His(2) (C2H2) residues in a tetrahedral array. C2H2 Znf's can be divided into three groups based on the number and pattern of fingers: triple-C2H2 (binds single ligand), multiple-adjacent-C2H2 (binds multiple ligands), and separated paired-C2H2 []. C2H2 Znf's are the most common DNA-binding motifs found in eukaryotic transcription factors, and have also been identified in prokaryotes []. Transcription factors usually contain several Znf's (each with a conserved beta/beta/alpha structure) capable of making multiple contacts along the DNA, where the C2H2 Znf motifs recognise DNA sequences by binding to the major groove of DNA via a short alpha-helix in the Znf, the Znf spanning 3-4 bases of the DNA []. C2H2 Znf's can also bind to RNA and protein targets []. This entry represents a C2H2-type zinc-finger domain found in the RAG1 protein. The structure contains the characteristic two-stranded beta-sheet and alpha-helix of a classical zinc-finger. The domain binds one zinc and, in complex with an adjacent RING-type zinc finger domain, helps to stabilise the whole of the dimerisation region of recombination activating protein 1 (RAG1) []. The function of the whole is to bind double-stranded DNA. ; GO: 0016788 hydrolase activity, acting on ester bonds, 0016881 acid-amino acid ligase activity; PDB: 1RMD_A.
Probab=38.48 E-value=6.9 Score=22.83 Aligned_cols=13 Identities=38% Similarity=1.060 Sum_probs=5.7
Q ss_pred CCCCCCCCCCCcc
Q 029888 132 ARCPVAGCPRKLQ 144 (186)
Q Consensus 132 ~~CPv~GC~~~l~ 144 (186)
.+||+.+|...+.
T Consensus 3 vrCPvkdC~EEv~ 15 (30)
T PF10426_consen 3 VRCPVKDCDEEVS 15 (30)
T ss_dssp EE--STT---EEE
T ss_pred cccccccCcchhh
Confidence 4799999987654
No 169
>KOG1952 consensus Transcription factor NF-X1, contains NFX-type Zn2+-binding and R3H domains [Transcription]
Probab=37.86 E-value=34 Score=34.36 Aligned_cols=50 Identities=26% Similarity=0.610 Sum_probs=39.0
Q ss_pred ceeeccCcCCCCccccCCcc-ccCCCccccHHHHHHHHHh----cCCCCCCCCCCCCC
Q 029888 89 LNISCPLSGKPITELAEPVR-SVECKHIYEKNAIQAYIKS----KNANARCPVAGCPR 141 (186)
Q Consensus 89 ~~l~CPI~~~~~~~l~dPV~-s~~CgH~fck~~I~~~l~~----~~~~~~CPv~GC~~ 141 (186)
..+-|-||...| --..||= .+.|=|+|--.||..|-++ +...|+||. |..
T Consensus 190 ~~yeCmIC~e~I-~~t~~~WSC~sCYhVFHl~CI~~WArs~ek~~~~~WrCP~--Cqs 244 (950)
T KOG1952|consen 190 RKYECMICTERI-KRTAPVWSCKSCYHVFHLNCIKKWARSSEKTGQDGWRCPA--CQS 244 (950)
T ss_pred CceEEEEeeeec-cccCCceecchhhhhhhHHHHHHHHHHhhhccCccccCCc--ccc
Confidence 478999999865 5566764 3568899999999999875 335799999 974
No 170
>PRK00418 DNA gyrase inhibitor; Reviewed
Probab=37.44 E-value=23 Score=24.10 Aligned_cols=36 Identities=25% Similarity=0.604 Sum_probs=19.3
Q ss_pred ceeeccCcCCCCccc--cCCccccCCCccccHHHHHHHHH
Q 029888 89 LNISCPLSGKPITEL--AEPVRSVECKHIYEKNAIQAYIK 126 (186)
Q Consensus 89 ~~l~CPI~~~~~~~l--~dPV~s~~CgH~fck~~I~~~l~ 126 (186)
....||+|++++ .+ .+|++ .-|...--.-=|-+|+.
T Consensus 5 ~~v~CP~C~k~~-~w~~~~~~r-PFCS~RCk~IDLg~W~~ 42 (62)
T PRK00418 5 ITVNCPTCGKPV-EWGEISPFR-PFCSKRCQLIDLGEWAA 42 (62)
T ss_pred ccccCCCCCCcc-cccCCCCcC-CcccHHHHhhhHHHHHc
Confidence 357899999964 22 34555 44543322223445554
No 171
>PF14446 Prok-RING_1: Prokaryotic RING finger family 1
Probab=36.38 E-value=27 Score=23.06 Aligned_cols=47 Identities=21% Similarity=0.475 Sum_probs=30.8
Q ss_pred eeeccCcCCCCccccCCccccCCCccccHHHHHHHHHhcCCCCCCCCCCCCCCc
Q 029888 90 NISCPLSGKPITELAEPVRSVECKHIYEKNAIQAYIKSKNANARCPVAGCPRKL 143 (186)
Q Consensus 90 ~l~CPI~~~~~~~l~dPV~s~~CgH~fck~~I~~~l~~~~~~~~CPv~GC~~~l 143 (186)
..+|++|+++|..=.+=|....||-.|=|.|-.. ...|-..||...+
T Consensus 5 ~~~C~~Cg~~~~~~dDiVvCp~CgapyHR~C~~~-------~g~C~~~~c~~~~ 51 (54)
T PF14446_consen 5 GCKCPVCGKKFKDGDDIVVCPECGAPYHRDCWEK-------AGGCINYSCGTGF 51 (54)
T ss_pred CccChhhCCcccCCCCEEECCCCCCcccHHHHhh-------CCceEeccCCCCc
Confidence 4679999986422234456678999999988332 2357777776543
No 172
>PF14311 DUF4379: Domain of unknown function (DUF4379)
Probab=35.60 E-value=24 Score=22.62 Aligned_cols=7 Identities=29% Similarity=0.781 Sum_probs=4.6
Q ss_pred CCCCCCC
Q 029888 130 ANARCPV 136 (186)
Q Consensus 130 ~~~~CPv 136 (186)
+...||.
T Consensus 48 ~~~~CP~ 54 (55)
T PF14311_consen 48 RGKGCPY 54 (55)
T ss_pred CCCCCCC
Confidence 4457887
No 173
>COG4338 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=35.31 E-value=13 Score=24.22 Aligned_cols=13 Identities=23% Similarity=0.772 Sum_probs=10.1
Q ss_pred cceeeccCcCCCC
Q 029888 88 ILNISCPLSGKPI 100 (186)
Q Consensus 88 ~~~l~CPI~~~~~ 100 (186)
+..-+||+|++||
T Consensus 10 lp~KICpvCqRPF 22 (54)
T COG4338 10 LPDKICPVCQRPF 22 (54)
T ss_pred cchhhhhhhcCch
Confidence 4456899999876
No 174
>KOG0314 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=35.13 E-value=19 Score=33.52 Aligned_cols=69 Identities=19% Similarity=0.282 Sum_probs=43.9
Q ss_pred ccceeeccCcCCCCccccCCcc-ccCCCccccHHHHHHHHHhcCCCCCCCCCCCCCC-ccCCCCccCHHHHHHHHHHHh
Q 029888 87 NILNISCPLSGKPITELAEPVR-SVECKHIYEKNAIQAYIKSKNANARCPVAGCPRK-LQVSKVVCDSLLLVDIDEMRR 163 (186)
Q Consensus 87 ~~~~l~CPI~~~~~~~l~dPV~-s~~CgH~fck~~I~~~l~~~~~~~~CPv~GC~~~-l~~~~L~~d~~L~~~I~~~r~ 163 (186)
....+.||+|.++ .|.+-+. ...|.-+||..||...+.. + .||. |.+. ..-.+|.+...++..+.+..+
T Consensus 216 ~~e~~~c~~~~~~--~~~~~~l~~~~~~~~~~~~~i~~~l~~-~---~~~~--c~~~~~~~~~~~~p~~~r~~~n~~~a 286 (448)
T KOG0314|consen 216 LPEGLQCPLCGKE--VMLDAALLSKCCLKSFCDKCIRDALIS-K---SMCV--CGASNVLADDLLPPKTLRDTINRILA 286 (448)
T ss_pred CCccccCceecch--hhHHHHHhhhhhcccCCcccccccccc-c---cCCc--chhhcccccccCCchhhHHHHHHHHh
Confidence 3456899999764 5666654 3578999999999998873 3 3444 5442 334445555556655555443
No 175
>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=34.94 E-value=45 Score=22.29 Aligned_cols=28 Identities=18% Similarity=0.504 Sum_probs=21.9
Q ss_pred CCC--ccccHHHHHHHHHhcCCCCCCCCCCCCCCccC
Q 029888 111 ECK--HIYEKNAIQAYIKSKNANARCPVAGCPRKLQV 145 (186)
Q Consensus 111 ~Cg--H~fck~~I~~~l~~~~~~~~CPv~GC~~~l~~ 145 (186)
.|. .+||..|....|. ..||- |+..|..
T Consensus 24 ICSfECTFC~~C~e~~l~-----~~CPN--CgGelv~ 53 (57)
T PF06906_consen 24 ICSFECTFCADCAETMLN-----GVCPN--CGGELVR 53 (57)
T ss_pred EEeEeCcccHHHHHHHhc-----CcCcC--CCCcccc
Confidence 465 5899999999987 36999 9876644
No 176
>KOG0309 consensus Conserved WD40 repeat-containing protein [Function unknown]
Probab=34.93 E-value=36 Score=34.01 Aligned_cols=48 Identities=15% Similarity=0.423 Sum_probs=32.1
Q ss_pred ccceeeccCcCCCCccccCCccccCCCccccHHHHHHHHHhcCCCCCCCCCCCC
Q 029888 87 NILNISCPLSGKPITELAEPVRSVECKHIYEKNAIQAYIKSKNANARCPVAGCP 140 (186)
Q Consensus 87 ~~~~l~CPI~~~~~~~l~dPV~s~~CgH~fck~~I~~~l~~~~~~~~CPv~GC~ 140 (186)
....+.|.+|.-. +=.--.....|||+--.+|.+.|++. + -.||- ||+
T Consensus 1025 ~~~~~~C~~C~l~--V~gss~~Cg~C~Hv~H~sc~~eWf~~-g--d~Cps-GCG 1072 (1081)
T KOG0309|consen 1025 KGFTFQCAICHLA--VRGSSNFCGTCGHVGHTSCMMEWFRT-G--DVCPS-GCG 1072 (1081)
T ss_pred ccceeeeeeEeeE--eeccchhhccccccccHHHHHHHHhc-C--CcCCC-CCC
Confidence 3456778888742 11122223568999999999999993 2 37995 775
No 177
>PRK15202 type III secretion chaperone protein SigE; Provisional
Probab=34.63 E-value=38 Score=25.61 Aligned_cols=31 Identities=26% Similarity=0.530 Sum_probs=20.0
Q ss_pred CCCCCCCC-----CcceEEe-ccCCccceeeccCcCC
Q 029888 68 GELMPGEE-----QEDIVMT-STQSNILNISCPLSGK 98 (186)
Q Consensus 68 g~~~~~d~-----ddDi~i~-~~~~~~~~l~CPI~~~ 98 (186)
|-+.|+|| ||||.|- ......+++.||.|--
T Consensus 13 Gld~~~depaliidddi~IYfnes~~~lem~CPf~~L 49 (117)
T PRK15202 13 GLDAPEDEPALIIDDDIQIYFNESDHTLEMCCPFMPL 49 (117)
T ss_pred CCCCCCCCceEEecCCeEEEEccCCcchhccCCcccC
Confidence 45555554 6777762 1124678999999964
No 178
>KOG1428 consensus Inhibitor of type V adenylyl cyclases/Neuronal presynaptic protein Highwire/PAM/RPM-1 [Signal transduction mechanisms]
Probab=34.50 E-value=32 Score=37.23 Aligned_cols=49 Identities=20% Similarity=0.562 Sum_probs=33.4
Q ss_pred ccCcCCCCccccCCccccCCCccccHHHHHHHHHhc--C-----CCCCCCCCCCCCCcc
Q 029888 93 CPLSGKPITELAEPVRSVECKHIYEKNAIQAYIKSK--N-----ANARCPVAGCPRKLQ 144 (186)
Q Consensus 93 CPI~~~~~~~l~dPV~s~~CgH~fck~~I~~~l~~~--~-----~~~~CPv~GC~~~l~ 144 (186)
|=||.-.- +-..|..-..|+|+|-..|....|..+ + +-..||+ |.+.+.
T Consensus 3489 CmICFTE~-L~AAP~IqL~C~HiFHlqC~R~vLE~RW~GPRItF~FisCPi--C~n~In 3544 (3738)
T KOG1428|consen 3489 CMICFTEA-LSAAPAIQLDCSHIFHLQCCRRVLENRWLGPRITFGFISCPI--CKNKIN 3544 (3738)
T ss_pred EEEEehhh-hCCCcceecCCccchhHHHHHHHHHhcccCCeeEEeeeeccc--ccchhh
Confidence 55554321 234576668999999999988887641 1 4567999 987665
No 179
>cd01407 SIR2-fam SIR2 family of proteins includes silent information regulator 2 (Sir2) enzymes which catalyze NAD+-dependent protein/histone deacetylation, where the acetyl group from the lysine epsilon-amino group is transferred to the ADP-ribose moiety of NAD+, producing nicotinamide and the novel metabolite O-acetyl-ADP-ribose. Sir2 proteins, also known as sirtuins, are found in all eukaryotes and many archaea and prokaryotes and have been shown to regulate gene silencing, DNA repair, metabolic enzymes, and life span. The most-studied function, gene silencing, involves the inactivation of chromosome domains containing key regulatory genes by packaging them into a specialized chromatin structure that is inaccessible to DNA-binding proteins. The oligomerization state of Sir2 appears to be organism-dependent, sometimes occurring as a monomer and sometimes as a multimer.
Probab=34.38 E-value=48 Score=27.20 Aligned_cols=16 Identities=31% Similarity=0.669 Sum_probs=11.3
Q ss_pred CCCCCCCCCCCCCCccCC
Q 029888 129 NANARCPVAGCPRKLQVS 146 (186)
Q Consensus 129 ~~~~~CPv~GC~~~l~~~ 146 (186)
.....||. |+..+.+.
T Consensus 131 ~~~p~C~~--Cg~~lrP~ 146 (218)
T cd01407 131 EEVPRCPK--CGGLLRPD 146 (218)
T ss_pred CCCCcCCC--CCCccCCC
Confidence 34578999 98766543
No 180
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=34.21 E-value=53 Score=26.54 Aligned_cols=33 Identities=24% Similarity=0.304 Sum_probs=20.1
Q ss_pred CCCCCCCCCCCCCccCCCC-ccCHHHHHHHHHHHhc
Q 029888 130 ANARCPVAGCPRKLQVSKV-VCDSLLLVDIDEMRRT 164 (186)
Q Consensus 130 ~~~~CPv~GC~~~l~~~~L-~~d~~L~~~I~~~r~~ 164 (186)
..+.||. |+..|...+= ..-..|+.+|..+...
T Consensus 135 ~~F~Cp~--Cg~~L~~~dn~~~~~~l~~~I~~l~~~ 168 (178)
T PRK06266 135 YGFRCPQ--CGEMLEEYDNSELIKELKEQIKELEEE 168 (178)
T ss_pred cCCcCCC--CCCCCeecccHHHHHHHHHHHHHHHHH
Confidence 3589999 9987765321 1123456666666543
No 181
>PLN02436 cellulose synthase A
Probab=33.91 E-value=27 Score=35.96 Aligned_cols=50 Identities=24% Similarity=0.563 Sum_probs=34.4
Q ss_pred eeccCcCCCCcccc--CCcc-ccCCCccccHHHHHHHHHhcCCCCCCCCCCCCCCcc
Q 029888 91 ISCPLSGKPITELA--EPVR-SVECKHIYEKNAIQAYIKSKNANARCPVAGCPRKLQ 144 (186)
Q Consensus 91 l~CPI~~~~~~~l~--dPV~-s~~CgH~fck~~I~~~l~~~~~~~~CPv~GC~~~l~ 144 (186)
-.|.||+.-+++-. +|+. ...|+.--|+.|. +|-+ ..+...||+ |.....
T Consensus 37 ~iCqICGD~Vg~t~dGe~FVACn~C~fpvCr~Cy-eyer-~eg~~~Cpq--ckt~Y~ 89 (1094)
T PLN02436 37 QTCQICGDEIELTVDGEPFVACNECAFPVCRPCY-EYER-REGNQACPQ--CKTRYK 89 (1094)
T ss_pred ccccccccccCcCCCCCEEEeeccCCCccccchh-hhhh-hcCCccCcc--cCCchh
Confidence 47999997442211 2433 3468888999998 6766 467889999 977554
No 182
>PHA00732 hypothetical protein
Probab=33.79 E-value=55 Score=22.96 Aligned_cols=34 Identities=18% Similarity=0.419 Sum_probs=18.9
Q ss_pred ccCCCcccc-HHHHHHHHHhcCCCCCCCCCCCCCCcc
Q 029888 109 SVECKHIYE-KNAIQAYIKSKNANARCPVAGCPRKLQ 144 (186)
Q Consensus 109 s~~CgH~fc-k~~I~~~l~~~~~~~~CPv~GC~~~l~ 144 (186)
...||..|- ...+...++.......|+. |++.+.
T Consensus 4 C~~Cgk~F~s~s~Lk~H~r~~H~~~~C~~--CgKsF~ 38 (79)
T PHA00732 4 CPICGFTTVTLFALKQHARRNHTLTKCPV--CNKSYR 38 (79)
T ss_pred CCCCCCccCCHHHHHHHhhcccCCCccCC--CCCEeC
Confidence 345665553 3445555541123357999 988664
No 183
>cd01410 SIRT7 SIRT7: Eukaryotic and prokaryotic group (class4) which includes human sirtuin SIRT6, SIRT7, and several bacterial homologs; and are members of the SIR2 family of proteins, silent information regulator 2 (Sir2) enzymes which catalyze NAD+-dependent protein/histone deacetylation. Sir2 proteins have been shown to regulate gene silencing, DNA repair, metabolic enzymes, and life span.
Probab=32.96 E-value=55 Score=26.83 Aligned_cols=15 Identities=27% Similarity=0.589 Sum_probs=10.3
Q ss_pred CCCCCCCCCCCCCccCC
Q 029888 130 ANARCPVAGCPRKLQVS 146 (186)
Q Consensus 130 ~~~~CPv~GC~~~l~~~ 146 (186)
....||. |+..+.+.
T Consensus 119 ~~p~C~~--Cgg~lrP~ 133 (206)
T cd01410 119 TGRRCHA--CGGILKDT 133 (206)
T ss_pred CCCcCCC--CcCccCCc
Confidence 4578999 98765543
No 184
>KOG1729 consensus FYVE finger containing protein [General function prediction only]
Probab=32.09 E-value=8.1 Score=33.85 Aligned_cols=52 Identities=15% Similarity=0.308 Sum_probs=33.0
Q ss_pred eeeccCcCC-CCccccCCccccCCCccccHHHHHH-HHHh---cCCCCCCCCCCCCCCc
Q 029888 90 NISCPLSGK-PITELAEPVRSVECKHIYEKNAIQA-YIKS---KNANARCPVAGCPRKL 143 (186)
Q Consensus 90 ~l~CPI~~~-~~~~l~dPV~s~~CgH~fck~~I~~-~l~~---~~~~~~CPv~GC~~~l 143 (186)
...|+.|.+ +|+++..==-...||++||..|=.. |+-. .+....|+. |-..+
T Consensus 168 a~~C~~C~~~~Ftl~~RRHHCR~CG~ivC~~Cs~n~~~l~~~~~k~~rvC~~--CF~el 224 (288)
T KOG1729|consen 168 ATECMVCGCTEFTLSERRHHCRNCGDIVCAPCSRNRFLLPNLSTKPIRVCDI--CFEEL 224 (288)
T ss_pred ceecccCCCccccHHHHHHHHHhcchHhhhhhhcCcccccccCCCCceecHH--HHHHH
Confidence 355999998 6655544444567999999988766 3221 223336888 85444
No 185
>PF15616 TerY-C: TerY-C metal binding domain
Probab=31.61 E-value=25 Score=27.39 Aligned_cols=40 Identities=18% Similarity=0.488 Sum_probs=27.8
Q ss_pred eeccCcCCCCccccCCccccCCCccccHHHHHHHHHhcCCCCCCCCCCCCCCccC
Q 029888 91 ISCPLSGKPITELAEPVRSVECKHIYEKNAIQAYIKSKNANARCPVAGCPRKLQV 145 (186)
Q Consensus 91 l~CPI~~~~~~~l~dPV~s~~CgH~fck~~I~~~l~~~~~~~~CPv~GC~~~l~~ 145 (186)
--||-|+.. --+..=.||++||-. ....+.||- |.+....
T Consensus 78 PgCP~CGn~-----~~fa~C~CGkl~Ci~--------g~~~~~CPw--Cg~~g~~ 117 (131)
T PF15616_consen 78 PGCPHCGNQ-----YAFAVCGCGKLFCID--------GEGEVTCPW--CGNEGSF 117 (131)
T ss_pred CCCCCCcCh-----hcEEEecCCCEEEeC--------CCCCEECCC--CCCeeee
Confidence 569999962 123223799999965 346789999 9876543
No 186
>PTZ00303 phosphatidylinositol kinase; Provisional
Probab=31.33 E-value=25 Score=35.29 Aligned_cols=35 Identities=23% Similarity=0.357 Sum_probs=24.2
Q ss_pred eeccCcCCCCccccCCcc-----ccCCCccccHHHHHHHH
Q 029888 91 ISCPLSGKPITELAEPVR-----SVECKHIYEKNAIQAYI 125 (186)
Q Consensus 91 l~CPI~~~~~~~l~dPV~-----s~~CgH~fck~~I~~~l 125 (186)
-.|..|.++|..+..++. ...||.+||..|-...+
T Consensus 461 dtC~~C~kkFfSlsK~L~~RKHHCRkCGrVFC~~CSSnRs 500 (1374)
T PTZ00303 461 DSCPSCGRAFISLSRPLGTRAHHCRSCGIRLCVFCITKRA 500 (1374)
T ss_pred CcccCcCCcccccccccccccccccCCccccCccccCCcc
Confidence 469999997644322222 35799999999976554
No 187
>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=30.72 E-value=26 Score=22.41 Aligned_cols=12 Identities=42% Similarity=0.996 Sum_probs=6.3
Q ss_pred CCCCCCCCCCccCC
Q 029888 133 RCPVAGCPRKLQVS 146 (186)
Q Consensus 133 ~CPv~GC~~~l~~~ 146 (186)
.||+ |...|...
T Consensus 22 ~CPl--C~r~l~~e 33 (54)
T PF04423_consen 22 CCPL--CGRPLDEE 33 (54)
T ss_dssp E-TT--T--EE-HH
T ss_pred cCCC--CCCCCCHH
Confidence 8999 98877654
No 188
>COG5236 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=30.63 E-value=34 Score=31.18 Aligned_cols=45 Identities=18% Similarity=0.399 Sum_probs=30.6
Q ss_pred eeeccCcCCCCccccCCccccCCCccccHHHHHHHHHhcCCCCCCCCCCCCC
Q 029888 90 NISCPLSGKPITELAEPVRSVECKHIYEKNAIQAYIKSKNANARCPVAGCPR 141 (186)
Q Consensus 90 ~l~CPI~~~~~~~l~dPV~s~~CgH~fck~~I~~~l~~~~~~~~CPv~GC~~ 141 (186)
+..|-||..- +.--.. +.|+|.-|..|-...-. --....||+ |+.
T Consensus 61 n~~C~ICA~~---~TYs~~-~PC~H~~CH~Ca~RlRA-LY~~K~C~~--CrT 105 (493)
T COG5236 61 NMNCQICAGS---TTYSAR-YPCGHQICHACAVRLRA-LYMQKGCPL--CRT 105 (493)
T ss_pred cceeEEecCC---ceEEEe-ccCCchHHHHHHHHHHH-HHhccCCCc--ccc
Confidence 4458888862 233334 68999999999776543 234467999 975
No 189
>KOG2682 consensus NAD-dependent histone deacetylases and class I sirtuins (SIR2 family) [Chromatin structure and dynamics; Transcription]
Probab=30.36 E-value=46 Score=28.91 Aligned_cols=33 Identities=24% Similarity=0.542 Sum_probs=25.9
Q ss_pred CCCccccHHHHHHHHHhcCCCCCCCCCCCCCCccCC
Q 029888 111 ECKHIYEKNAIQAYIKSKNANARCPVAGCPRKLQVS 146 (186)
Q Consensus 111 ~CgH~fck~~I~~~l~~~~~~~~CPv~GC~~~l~~~ 146 (186)
.|+|.|.-+-+.+.+- .....+|++ |...+.+.
T Consensus 158 ~C~~~yp~e~~ka~i~-~~~vpkC~v--C~~lVKP~ 190 (314)
T KOG2682|consen 158 SCRHEYPLEWMKAKIM-SEVVPKCEV--CQGLVKPD 190 (314)
T ss_pred hhcCcCCHHHHHHHHH-hccCCCCch--hhcccccc
Confidence 6999999888888887 367789999 97766544
No 190
>COG3088 CcmH Uncharacterized protein involved in biosynthesis of c-type cytochromes [Posttranslational modification, protein turnover, chaperones]
Probab=29.38 E-value=51 Score=26.31 Aligned_cols=38 Identities=21% Similarity=0.346 Sum_probs=26.7
Q ss_pred CCCCCCCCCCCC-CccCCCCccCHHHHHHHHHHHhcCcccc
Q 029888 130 ANARCPVAGCPR-KLQVSKVVCDSLLLVDIDEMRRTSKETA 169 (186)
Q Consensus 130 ~~~~CPv~GC~~-~l~~~~L~~d~~L~~~I~~~r~~~~~~~ 169 (186)
...+||+ |.+ .|-.++-.....|+.+|.+..+.+++..
T Consensus 43 ~~LRCp~--CQNqsIadSnA~IA~DlR~~V~e~l~eGkS~~ 81 (153)
T COG3088 43 EELRCPQ--CQNQSIADSNAPIARDLRHQVYELLQEGKSDQ 81 (153)
T ss_pred HhcCCCc--CCCCChhhhccHHHHHHHHHHHHHHHcCCcHH
Confidence 5578999 976 5655555555668888888877765543
No 191
>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=29.10 E-value=18 Score=20.05 Aligned_cols=10 Identities=50% Similarity=1.315 Sum_probs=8.0
Q ss_pred CCCCCCCCCCCc
Q 029888 132 ARCPVAGCPRKL 143 (186)
Q Consensus 132 ~~CPv~GC~~~l 143 (186)
+.||+ |.+.+
T Consensus 2 v~CPi--C~~~v 11 (26)
T smart00734 2 VQCPV--CFREV 11 (26)
T ss_pred CcCCC--CcCcc
Confidence 57999 98766
No 192
>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=29.00 E-value=12 Score=24.05 Aligned_cols=27 Identities=19% Similarity=0.497 Sum_probs=7.9
Q ss_pred HHHHHHhcCCCCCCCCCCCCCCccCCC
Q 029888 121 IQAYIKSKNANARCPVAGCPRKLQVSK 147 (186)
Q Consensus 121 I~~~l~~~~~~~~CPv~GC~~~l~~~~ 147 (186)
+..++........||.+||...+...+
T Consensus 8 ~~~~~~~~~~~~~Cp~~~C~~~~~~~~ 34 (64)
T PF01485_consen 8 LKRYLESDPNIRWCPNPDCEYIIEKDD 34 (64)
T ss_dssp CHS---S---CC--TTSST---ECS-S
T ss_pred HHHHHHCCCCccCCCCCCCcccEEecC
Confidence 344443222334677777766555443
No 193
>cd01413 SIR2_Af2 SIR2_Af2: Archaeal and prokaryotic group which includes Archaeoglobus fulgidus Sir2-Af2, Sulfolobus solfataricus ssSir2, and several bacterial homologs; and are members of the SIR2 family of proteins, silent information regulator 2 (Sir2) enzymes which catalyze NAD+-dependent protein/histone deacetylation. Sir2 proteins have been shown to regulate gene silencing, DNA repair, metabolic enzymes, and life span. The Sir2 homolog from the archaea Sulfolobus solftaricus deacetylates the non-specific DNA protein Alba to mediate transcription repression.
Probab=28.89 E-value=89 Score=25.81 Aligned_cols=14 Identities=29% Similarity=0.702 Sum_probs=10.1
Q ss_pred CCCCCCCCCCCCCccC
Q 029888 130 ANARCPVAGCPRKLQV 145 (186)
Q Consensus 130 ~~~~CPv~GC~~~l~~ 145 (186)
....||. |+..+.+
T Consensus 135 ~~p~C~~--Cgg~lrP 148 (222)
T cd01413 135 EVPRCPK--CGGIIRP 148 (222)
T ss_pred CCCcCCC--CCCccCC
Confidence 4578999 9776554
No 194
>KOG1829 consensus Uncharacterized conserved protein, contains C1, PH and RUN domains [Signal transduction mechanisms]
Probab=28.83 E-value=27 Score=33.62 Aligned_cols=41 Identities=22% Similarity=0.640 Sum_probs=28.5
Q ss_pred ceeeccCcCCCCccccCCc------cccCCCccccHHHHHHHHHhcCCCCCCCCCCC
Q 029888 89 LNISCPLSGKPITELAEPV------RSVECKHIYEKNAIQAYIKSKNANARCPVAGC 139 (186)
Q Consensus 89 ~~l~CPI~~~~~~~l~dPV------~s~~CgH~fck~~I~~~l~~~~~~~~CPv~GC 139 (186)
.-+.|++|.. +.+.-|. +...||++|=+.|+.. ++..||. |
T Consensus 510 ~gfiCe~Cq~--~~iiyPF~~~~~~rC~~C~avfH~~C~~r------~s~~CPr--C 556 (580)
T KOG1829|consen 510 KGFICELCQH--NDIIYPFETRNTRRCSTCLAVFHKKCLRR------KSPCCPR--C 556 (580)
T ss_pred CeeeeeeccC--CCcccccccccceeHHHHHHHHHHHHHhc------cCCCCCc--h
Confidence 3578999976 4666677 3346899998877433 3445998 8
No 195
>COG4640 Predicted membrane protein [Function unknown]
Probab=28.49 E-value=29 Score=31.95 Aligned_cols=26 Identities=23% Similarity=0.634 Sum_probs=20.4
Q ss_pred eccCcCCCCccccCCccccCCCccccHH
Q 029888 92 SCPLSGKPITELAEPVRSVECKHIYEKN 119 (186)
Q Consensus 92 ~CPI~~~~~~~l~dPV~s~~CgH~fck~ 119 (186)
.||-|+. .-.++-|.+++|||.|-..
T Consensus 3 fC~kcG~--qk~Ed~~qC~qCG~~~t~~ 28 (465)
T COG4640 3 FCPKCGS--QKAEDDVQCTQCGHKFTSR 28 (465)
T ss_pred ccccccc--ccccccccccccCCcCCch
Confidence 5999994 3678888889999987543
No 196
>TIGR02159 PA_CoA_Oxy4 phenylacetate-CoA oxygenase, PaaJ subunit. Phenylacetate-CoA oxygenase is comprised of a five gene complex responsible for the hydroxylation of phenylacetate-CoA (PA-CoA) as the second catabolic step in phenylacetic acid (PA) degradation. Although the exact function of this enzyme has not been determined, it has been shown to be required for phenylacetic acid degradation and has been proposed to function in a multicomponent oxygenase acting on phenylacetate-CoA.
Probab=28.07 E-value=19 Score=28.32 Aligned_cols=35 Identities=17% Similarity=0.406 Sum_probs=27.6
Q ss_pred eeeccCcCCCCccccCCccccCCC-ccccHHHHHHH
Q 029888 90 NISCPLSGKPITELAEPVRSVECK-HIYEKNAIQAY 124 (186)
Q Consensus 90 ~l~CPI~~~~~~~l~dPV~s~~Cg-H~fck~~I~~~ 124 (186)
...||-|+..-+.+...+-|+.|+ ..+|++|.+-|
T Consensus 105 ~~~cp~c~s~~t~~~s~fg~t~cka~~~c~~c~epf 140 (146)
T TIGR02159 105 SVQCPRCGSADTTITSIFGPTACKALYRCRACKEPF 140 (146)
T ss_pred CCcCCCCCCCCcEeecCCCChhhHHHhhhhhhCCcH
Confidence 478999998777788888889996 56788886543
No 197
>PLN02638 cellulose synthase A (UDP-forming), catalytic subunit
Probab=28.06 E-value=40 Score=34.71 Aligned_cols=49 Identities=24% Similarity=0.568 Sum_probs=30.9
Q ss_pred eccCcCCCCcccc--CCc-cccCCCccccHHHHHHHHHhcCCCCCCCCCCCCCCcc
Q 029888 92 SCPLSGKPITELA--EPV-RSVECKHIYEKNAIQAYIKSKNANARCPVAGCPRKLQ 144 (186)
Q Consensus 92 ~CPI~~~~~~~l~--dPV-~s~~CgH~fck~~I~~~l~~~~~~~~CPv~GC~~~l~ 144 (186)
.|-||+.-+++-. +|+ -...||.--||.|- +|=+ +.++..||+ |.....
T Consensus 19 iCqICGD~vg~~~~Ge~FVAC~eC~FPVCrpCY-EYEr-~eG~q~CPq--CktrYk 70 (1079)
T PLN02638 19 VCQICGDNVGKTVDGEPFVACDVCAFPVCRPCY-EYER-KDGNQSCPQ--CKTKYK 70 (1079)
T ss_pred eeeecccccCcCCCCCEEEEeccCCCccccchh-hhhh-hcCCccCCc--cCCchh
Confidence 5777776332211 132 33467777888887 6655 468889999 976554
No 198
>KOG3842 consensus Adaptor protein Pellino [Signal transduction mechanisms]
Probab=27.57 E-value=52 Score=29.61 Aligned_cols=32 Identities=25% Similarity=0.632 Sum_probs=20.7
Q ss_pred cCCCccccHHHHHHHHHh-------cCCCCCCCCCCCCCCcc
Q 029888 110 VECKHIYEKNAIQAYIKS-------KNANARCPVAGCPRKLQ 144 (186)
Q Consensus 110 ~~CgH~fck~~I~~~l~~-------~~~~~~CPv~GC~~~l~ 144 (186)
..|||+-.+.. ..||.+ ..-...||. |...|.
T Consensus 376 ~PCGHv~sekt-~~YWs~iplPhGT~~f~a~CPF--C~~~L~ 414 (429)
T KOG3842|consen 376 NPCGHVCSEKT-VKYWSQIPLPHGTHAFHAACPF--CATQLA 414 (429)
T ss_pred CCcccccchhh-hhHhhcCcCCCccccccccCcc--hhhhhc
Confidence 36999876664 456653 123467999 977664
No 199
>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=27.41 E-value=18 Score=31.96 Aligned_cols=40 Identities=23% Similarity=0.455 Sum_probs=23.9
Q ss_pred eeccCcCCCCccccCCcccc------CCC--ccccHHHHHHHHHhcCCCCCCCCCCCCC
Q 029888 91 ISCPLSGKPITELAEPVRSV------ECK--HIYEKNAIQAYIKSKNANARCPVAGCPR 141 (186)
Q Consensus 91 l~CPI~~~~~~~l~dPV~s~------~Cg--H~fck~~I~~~l~~~~~~~~CPv~GC~~ 141 (186)
-.||+|+. .|+.|. .=| |-+|.-|=.+|-- ....||. |.+
T Consensus 185 ~~CPvCGs------~P~~s~~~~~~~~~G~RyL~CslC~teW~~---~R~~C~~--Cg~ 232 (305)
T TIGR01562 185 TLCPACGS------PPVASMVRQGGKETGLRYLSCSLCATEWHY---VRVKCSH--CEE 232 (305)
T ss_pred CcCCCCCC------hhhhhhhcccCCCCCceEEEcCCCCCcccc---cCccCCC--CCC
Confidence 47999994 575431 123 3456666555532 4567888 765
No 200
>PF07824 Chaperone_III: Type III secretion chaperone domain; InterPro: IPR013095 Type III secretion chaperones are involved in delivering virulence effector proteins from bacterial pathogens directly into eukaryotic cells. The chaperones may prevent aggregation and degradation of their substrates, may target the effector to the secretion apparatus, and may ensure a secretion-component unfolded conformation of their specific substrate. One member of this family, SigE (O30917 from SWISSPROT) forms homodimers in crystal. The monomers have a novel fold with an alpha-beta(3)-alpha-beta(2)-alpha topology []. ; PDB: 1K3S_B.
Probab=26.88 E-value=38 Score=25.47 Aligned_cols=30 Identities=23% Similarity=0.602 Sum_probs=15.4
Q ss_pred CCCCCCCC-----CcceEE--eccCCccceeeccCcCC
Q 029888 68 GELMPGEE-----QEDIVM--TSTQSNILNISCPLSGK 98 (186)
Q Consensus 68 g~~~~~d~-----ddDi~i--~~~~~~~~~l~CPI~~~ 98 (186)
|-+.|.|| ||||.| ..+ ...+++.||.|--
T Consensus 12 Gl~i~~depal~iddd~~IYf~e~-~~~lem~CPf~~L 48 (112)
T PF07824_consen 12 GLDIPEDEPALIIDDDLQIYFNES-DDSLEMCCPFMPL 48 (112)
T ss_dssp T---------EEECTTEEEEEEE--TTEEEEEEEEEE-
T ss_pred CCCCCCCCceEEecCCeEEEEecC-CcceeeecCcccC
Confidence 44455554 677766 222 4678999999964
No 201
>PF05502 Dynactin_p62: Dynactin p62 family; InterPro: IPR008603 Dynactin is a multi-subunit complex and a required cofactor for most, or all, o f the cellular processes powered by the microtubule-based motor cytoplasmic dyn ein. p62 binds directly to the Arp1 subunit of dynactin [, ].
Probab=26.65 E-value=35 Score=31.94 Aligned_cols=12 Identities=33% Similarity=0.802 Sum_probs=6.7
Q ss_pred CCCCCCCCCCCCcc
Q 029888 131 NARCPVAGCPRKLQ 144 (186)
Q Consensus 131 ~~~CPv~GC~~~l~ 144 (186)
.+.||+ |...|.
T Consensus 52 Cf~CP~--C~~~L~ 63 (483)
T PF05502_consen 52 CFDCPI--CFSPLS 63 (483)
T ss_pred cccCCC--CCCcce
Confidence 455666 655443
No 202
>PF08265 YL1_C: YL1 nuclear protein C-terminal domain; InterPro: IPR013272 This domain is found at the C terminus in proteins of the YL1 family []. These proteins have been shown to be DNA-binding and may be transcription factors []. This domain is also found in proteins that do not belong to the YL1 family.
Probab=26.41 E-value=40 Score=19.51 Aligned_cols=16 Identities=25% Similarity=0.710 Sum_probs=12.6
Q ss_pred eccCcCCCCccccCCcc
Q 029888 92 SCPLSGKPITELAEPVR 108 (186)
Q Consensus 92 ~CPI~~~~~~~l~dPV~ 108 (186)
.|+||+.| ..+.||.+
T Consensus 2 ~C~iTglp-A~Y~DP~T 17 (30)
T PF08265_consen 2 YCDITGLP-ARYRDPKT 17 (30)
T ss_pred cccccCCC-ccccCCCC
Confidence 48999987 47888876
No 203
>KOG1842 consensus FYVE finger-containing protein [General function prediction only]
Probab=26.19 E-value=23 Score=33.06 Aligned_cols=34 Identities=9% Similarity=0.149 Sum_probs=26.2
Q ss_pred eeccCcCCCCccccCCccccCCCccccHHHHHHH
Q 029888 91 ISCPLSGKPITELAEPVRSVECKHIYEKNAIQAY 124 (186)
Q Consensus 91 l~CPI~~~~~~~l~dPV~s~~CgH~fck~~I~~~ 124 (186)
..||+|..+|++...---...||-+-|+.|....
T Consensus 181 ~~CP~Ca~~F~l~rRrHHCRLCG~VmC~~C~k~i 214 (505)
T KOG1842|consen 181 QFCPECANSFGLTRRRHHCRLCGRVMCRDCSKFI 214 (505)
T ss_pred cccccccchhhhHHHhhhhhhcchHHHHHHHHhc
Confidence 5699999988666555445679999999997653
No 204
>KOG0006 consensus E3 ubiquitin-protein ligase (Parkin protein) [Posttranslational modification, protein turnover, chaperones]
Probab=25.54 E-value=48 Score=29.88 Aligned_cols=29 Identities=31% Similarity=0.543 Sum_probs=0.0
Q ss_pred cCcCCCCccccCC----ccccC-CCccccHHHHHHH
Q 029888 94 PLSGKPITELAEP----VRSVE-CKHIYEKNAIQAY 124 (186)
Q Consensus 94 PI~~~~~~~l~dP----V~s~~-CgH~fck~~I~~~ 124 (186)
|-|+. ++|-+| |+... ||.+||+.|.+.|
T Consensus 321 pgCG~--gll~EPD~rkvtC~~gCgf~FCR~C~e~y 354 (446)
T KOG0006|consen 321 PGCGA--GLLPEPDQRKVTCEGGCGFAFCRECKEAY 354 (446)
T ss_pred CCCCc--ccccCCCCCcccCCCCchhHhHHHHHhhh
No 205
>COG0780 Enzyme related to GTP cyclohydrolase I [General function prediction only]
Probab=25.50 E-value=1.1e+02 Score=24.23 Aligned_cols=64 Identities=20% Similarity=0.358 Sum_probs=39.3
Q ss_pred hhhHHHHHhhcCCCCCCCCCCCcceEEeccCCccceeeccCcCCCCccccCCccccCCCcc--ccHHHHHHHHHh
Q 029888 55 HKFREAVWNVHHAGELMPGEEQEDIVMTSTQSNILNISCPLSGKPITELAEPVRSVECKHI--YEKNAIQAYIKS 127 (186)
Q Consensus 55 ~~F~~~i~~~~~~g~~~~~d~ddDi~i~~~~~~~~~l~CPI~~~~~~~l~dPV~s~~CgH~--fck~~I~~~l~~ 127 (186)
.+|..++|... +.|-++ .+-++.+++ -.+.-.||+|++| .|-.=+. .-.+.. -+..++..||.+
T Consensus 21 ~~~~~~~l~~~--~~~~~~-~~~~~~l~~---~ef~S~CpiTgqP--D~~ti~I-~Y~p~~~~ve~ksLk~yl~S 86 (149)
T COG0780 21 YEFTNAILEAF--PNPHPG-RDVLVKLVS---PEFKSLCPITGQP--DFATIYI-EYIPDKACVESKSLKLYLFS 86 (149)
T ss_pred cccChhhhhcc--CCCCCC-CcEEEEEec---ccceecCCCcCCC--CeEEEEE-EEcCchhhhhhHHHHHHHHH
Confidence 67777777652 122223 344455554 3467889999997 4544444 455555 777888888864
No 206
>PF00096 zf-C2H2: Zinc finger, C2H2 type; InterPro: IPR007087 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 C2H2 zinc finger is the classical zinc finger domain. The two conserved cysteines and histidines co-ordinate a zinc ion. The following pattern describes the zinc finger: #-X-C-X(1-5)-C-X3-#-X5-#-X2-H-X(3-6)-[H/C], where X can be any amino acid, and numbers in brackets indicate the number of residues. The positions marked # are those that are important for the stable fold of the zinc finger. The final position can be either his or cys. The C2H2 zinc finger is composed of two short beta strands followed by an alpha helix. The amino terminal part of the helix binds the major groove in DNA binding zinc fingers. The accepted consensus binding sequence for Sp1 is usually defined by the asymmetric hexanucleotide core GGGCGG but this sequence does not include, among others, the GAG (=CTC) repeat that constitutes a high-affinity site for Sp1 binding to the wt1 promoter []. This entry represents the classical C2H2 zinc finger domain. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0005622 intracellular; PDB: 2D9H_A 2EPC_A 1SP1_A 1VA3_A 2WBT_B 2ELR_A 2YTP_A 2YTT_A 1VA1_A 2ELO_A ....
Probab=25.20 E-value=26 Score=17.90 Aligned_cols=8 Identities=50% Similarity=1.298 Sum_probs=5.7
Q ss_pred eeccCcCC
Q 029888 91 ISCPLSGK 98 (186)
Q Consensus 91 l~CPI~~~ 98 (186)
+.||+|.+
T Consensus 1 y~C~~C~~ 8 (23)
T PF00096_consen 1 YKCPICGK 8 (23)
T ss_dssp EEETTTTE
T ss_pred CCCCCCCC
Confidence 46888876
No 207
>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=24.96 E-value=7.4 Score=33.58 Aligned_cols=41 Identities=24% Similarity=0.412 Sum_probs=16.3
Q ss_pred eeeccCcCCCCccccCCccccCC-------CccccHHHHHHHHHhcCCCCCCCCCCCCC
Q 029888 90 NISCPLSGKPITELAEPVRSVEC-------KHIYEKNAIQAYIKSKNANARCPVAGCPR 141 (186)
Q Consensus 90 ~l~CPI~~~~~~~l~dPV~s~~C-------gH~fck~~I~~~l~~~~~~~~CPv~GC~~ 141 (186)
.-.||+|+. .|+.+..- .|-+|.-|=.+|-- ....||. |++
T Consensus 172 ~g~CPvCGs------~P~~s~l~~~~~~G~R~L~Cs~C~t~W~~---~R~~Cp~--Cg~ 219 (290)
T PF04216_consen 172 RGYCPVCGS------PPVLSVLRGGEREGKRYLHCSLCGTEWRF---VRIKCPY--CGN 219 (290)
T ss_dssp -SS-TTT---------EEEEEEE------EEEEEETTT--EEE-----TTS-TT--T--
T ss_pred CCcCCCCCC------cCceEEEecCCCCccEEEEcCCCCCeeee---cCCCCcC--CCC
Confidence 456999984 46544211 23456655555522 3457888 754
No 208
>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=24.87 E-value=1.2e+02 Score=20.38 Aligned_cols=21 Identities=24% Similarity=0.759 Sum_probs=16.2
Q ss_pred CCCCCCCCCCCCccCCCCccCHH
Q 029888 131 NARCPVAGCPRKLQVSKVVCDSL 153 (186)
Q Consensus 131 ~~~CPv~GC~~~l~~~~L~~d~~ 153 (186)
...||+ |++.+..+....+..
T Consensus 3 HkHC~~--CG~~Ip~~~~fCS~~ 23 (59)
T PF09889_consen 3 HKHCPV--CGKPIPPDESFCSPK 23 (59)
T ss_pred CCcCCc--CCCcCCcchhhhCHH
Confidence 357999 999998877777653
No 209
>PLN03086 PRLI-interacting factor K; Provisional
Probab=24.71 E-value=79 Score=30.38 Aligned_cols=36 Identities=19% Similarity=0.516 Sum_probs=20.0
Q ss_pred CCccccCCCccccHHHHHHHHHhcCCCCCCCCCCCCCCc
Q 029888 105 EPVRSVECKHIYEKNAIQAYIKSKNANARCPVAGCPRKL 143 (186)
Q Consensus 105 dPV~s~~CgH~fck~~I~~~l~~~~~~~~CPv~GC~~~l 143 (186)
+++....||..|-+..+..+.........|| |+..+
T Consensus 452 ~H~~C~~Cgk~f~~s~LekH~~~~Hkpv~Cp---Cg~~~ 487 (567)
T PLN03086 452 NHVHCEKCGQAFQQGEMEKHMKVFHEPLQCP---CGVVL 487 (567)
T ss_pred cCccCCCCCCccchHHHHHHHHhcCCCccCC---CCCCc
Confidence 3444455666666666666655323456677 65433
No 210
>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=24.43 E-value=35 Score=21.42 Aligned_cols=13 Identities=31% Similarity=0.933 Sum_probs=9.9
Q ss_pred cceeeccCcCCCC
Q 029888 88 ILNISCPLSGKPI 100 (186)
Q Consensus 88 ~~~l~CPI~~~~~ 100 (186)
..+-.||+|++||
T Consensus 6 lp~K~C~~C~rpf 18 (42)
T PF10013_consen 6 LPSKICPVCGRPF 18 (42)
T ss_pred CCCCcCcccCCcc
Confidence 4456799999865
No 211
>PRK03564 formate dehydrogenase accessory protein FdhE; Provisional
Probab=24.14 E-value=20 Score=31.79 Aligned_cols=41 Identities=22% Similarity=0.415 Sum_probs=21.9
Q ss_pred eeeccCcCCCCccccCCcccc-----CCC--ccccHHHHHHHHHhcCCCCCCCCCCCCC
Q 029888 90 NISCPLSGKPITELAEPVRSV-----ECK--HIYEKNAIQAYIKSKNANARCPVAGCPR 141 (186)
Q Consensus 90 ~l~CPI~~~~~~~l~dPV~s~-----~Cg--H~fck~~I~~~l~~~~~~~~CPv~GC~~ 141 (186)
.-.||+|+. .||.|. .=| |-+|.-|=.+|-- ....||. |..
T Consensus 187 ~~~CPvCGs------~P~~s~v~~~~~~G~RyL~CslC~teW~~---~R~~C~~--Cg~ 234 (309)
T PRK03564 187 RQFCPVCGS------MPVSSVVQIGTTQGLRYLHCNLCESEWHV---VRVKCSN--CEQ 234 (309)
T ss_pred CCCCCCCCC------cchhheeeccCCCCceEEEcCCCCCcccc---cCccCCC--CCC
Confidence 456888884 465431 123 3345555445422 3467888 765
No 212
>COG1592 Rubrerythrin [Energy production and conversion]
Probab=23.93 E-value=59 Score=26.28 Aligned_cols=24 Identities=25% Similarity=0.369 Sum_probs=12.2
Q ss_pred eeeccCcCCCCccccCCccccCCCc
Q 029888 90 NISCPLSGKPITELAEPVRSVECKH 114 (186)
Q Consensus 90 ~l~CPI~~~~~~~l~dPV~s~~CgH 114 (186)
-..||+|+-.+ .-..|=....|||
T Consensus 134 ~~vC~vCGy~~-~ge~P~~CPiCga 157 (166)
T COG1592 134 VWVCPVCGYTH-EGEAPEVCPICGA 157 (166)
T ss_pred EEEcCCCCCcc-cCCCCCcCCCCCC
Confidence 46688887533 2233444444444
No 213
>KOG2684 consensus Sirtuin 5 and related class III sirtuins (SIR2 family) [Chromatin structure and dynamics; Transcription]
Probab=23.84 E-value=67 Score=29.59 Aligned_cols=41 Identities=20% Similarity=0.358 Sum_probs=31.0
Q ss_pred eeccCcCCCCccccCCccccCCCccccHHHHHHHHHhcCCCCCCCCCCCCC
Q 029888 91 ISCPLSGKPITELAEPVRSVECKHIYEKNAIQAYIKSKNANARCPVAGCPR 141 (186)
Q Consensus 91 l~CPI~~~~~~~l~dPV~s~~CgH~fck~~I~~~l~~~~~~~~CPv~GC~~ 141 (186)
..|-=+++ -++.+.||+.+..++|..-+. +.....||. |..
T Consensus 195 Vq~HGSf~-------t~sCt~C~~k~~~~~~~~~~~-~~~vp~CP~--C~~ 235 (412)
T KOG2684|consen 195 VQCHGSFK-------TASCTKCGYKKPFEELREDIR-NQEVPVCPD--CEG 235 (412)
T ss_pred EEeccccc-------eeeecccccccChHHHHHHHh-cCcCccCcc--ccc
Confidence 44555543 345688999999999998887 678889999 954
No 214
>PF03918 CcmH: Cytochrome C biogenesis protein; InterPro: IPR005616 Members of this family include NrfF, CcmH, CycL, Ccl2.; PDB: 2KW0_A 2HL7_A.
Probab=23.80 E-value=66 Score=25.32 Aligned_cols=37 Identities=27% Similarity=0.428 Sum_probs=22.4
Q ss_pred CCCCCCCCCCCC-CccCCCCccCHHHHHHHHHHHhcCccc
Q 029888 130 ANARCPVAGCPR-KLQVSKVVCDSLLLVDIDEMRRTSKET 168 (186)
Q Consensus 130 ~~~~CPv~GC~~-~l~~~~L~~d~~L~~~I~~~r~~~~~~ 168 (186)
...+||+ |.. .+...+-.....|+..|.+....++..
T Consensus 39 ~~LrCp~--Cq~qsi~~s~a~~A~dmR~~I~~~l~~G~s~ 76 (148)
T PF03918_consen 39 KELRCPV--CQNQSIADSNAPIARDMRREIREMLAEGKSD 76 (148)
T ss_dssp HCCE-TT--TTS-CTTT--SHHHHHHHHHHHHHHHHT--H
T ss_pred hcccCCC--CCCCchhhcCcHHHHHHHHHHHHHHHcCCCH
Confidence 4578999 854 666665555567888888887765443
No 215
>COG5627 MMS21 DNA repair protein MMS21 [DNA replication, recombination, and repair]
Probab=23.65 E-value=39 Score=29.08 Aligned_cols=35 Identities=34% Similarity=0.757 Sum_probs=26.7
Q ss_pred cccCCccccCCCccccHHHHHHHHHhcCCCCCCCCCCCCCCcc
Q 029888 102 ELAEPVRSVECKHIYEKNAIQAYIKSKNANARCPVAGCPRKLQ 144 (186)
Q Consensus 102 ~l~dPV~s~~CgH~fck~~I~~~l~~~~~~~~CPv~GC~~~l~ 144 (186)
+-.+|+. |+|+.++.|-+.|++. .. |+.||++.+.
T Consensus 238 ~~~~~~v---~d~IlE~R~~~~~ir~-sq----eq~~~~~~~~ 272 (275)
T COG5627 238 EVVDPYV---CDHILEKREAMKYIRN-SQ----EQIGCNKRLT 272 (275)
T ss_pred eeccchh---hhHHHHHHHHHHHHHh-hh----hhhchhhhhh
Confidence 4456655 9999999999999993 22 8889987554
No 216
>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=23.25 E-value=41 Score=20.59 Aligned_cols=21 Identities=14% Similarity=0.362 Sum_probs=10.9
Q ss_pred cCCCCccccCCccccCCCccccHH
Q 029888 96 SGKPITELAEPVRSVECKHIYEKN 119 (186)
Q Consensus 96 ~~~~~~~l~dPV~s~~CgH~fck~ 119 (186)
|.+. .+ -|+.-..|+.+||..
T Consensus 6 C~~~--~~-~~~~C~~C~~~FC~~ 26 (43)
T PF01428_consen 6 CKKK--DF-LPFKCKHCGKSFCLK 26 (43)
T ss_dssp T--B--CT-SHEE-TTTS-EE-TT
T ss_pred CcCc--cC-CCeECCCCCcccCcc
Confidence 6652 33 688877799999854
No 217
>COG1326 Uncharacterized archaeal Zn-finger protein [General function prediction only]
Probab=23.05 E-value=35 Score=28.37 Aligned_cols=10 Identities=40% Similarity=0.886 Sum_probs=7.7
Q ss_pred cceeeccCcC
Q 029888 88 ILNISCPLSG 97 (186)
Q Consensus 88 ~~~l~CPI~~ 97 (186)
.+.+.||.|+
T Consensus 4 ~iy~~Cp~Cg 13 (201)
T COG1326 4 EIYIECPSCG 13 (201)
T ss_pred eEEEECCCCC
Confidence 3567899888
No 218
>PRK12495 hypothetical protein; Provisional
Probab=22.85 E-value=48 Score=28.10 Aligned_cols=13 Identities=38% Similarity=0.790 Sum_probs=10.4
Q ss_pred cceeeccCcCCCC
Q 029888 88 ILNISCPLSGKPI 100 (186)
Q Consensus 88 ~~~l~CPI~~~~~ 100 (186)
...+.||.|+.||
T Consensus 40 msa~hC~~CG~PI 52 (226)
T PRK12495 40 MTNAHCDECGDPI 52 (226)
T ss_pred cchhhcccccCcc
Confidence 3478899999874
No 219
>KOG3183 consensus Predicted Zn-finger protein [General function prediction only]
Probab=22.35 E-value=52 Score=28.25 Aligned_cols=45 Identities=16% Similarity=0.410 Sum_probs=29.7
Q ss_pred CcCCCCccccCCccccCCCccccHHHHHHHHHh--------cCCCCCCCCCCCCCCccC
Q 029888 95 LSGKPITELAEPVRSVECKHIYEKNAIQAYIKS--------KNANARCPVAGCPRKLQV 145 (186)
Q Consensus 95 I~~~~~~~l~dPV~s~~CgH~fck~~I~~~l~~--------~~~~~~CPv~GC~~~l~~ 145 (186)
-|.+. .| -|++...|+++||.+-. .|-.. ......||. |+..+..
T Consensus 15 ~Ckql--DF-LPf~Cd~C~~~FC~eHr-sye~H~Cp~~~~~~~~v~icp~--cs~pv~~ 67 (250)
T KOG3183|consen 15 YCKQL--DF-LPFKCDGCSGIFCLEHR-SYESHHCPKGLRIDVQVPICPL--CSKPVPT 67 (250)
T ss_pred hhhhc--cc-cceeeCCccchhhhccc-hHhhcCCCcccccceeecccCC--CCCCCCC
Confidence 77761 33 59998999999998732 22221 234577999 9886653
No 220
>KOG0883 consensus Cyclophilin type, U box-containing peptidyl-prolyl cis-trans isomerase [Posttranslational modification, protein turnover, chaperones]
Probab=21.64 E-value=1.2e+02 Score=28.22 Aligned_cols=39 Identities=21% Similarity=0.230 Sum_probs=31.1
Q ss_pred ccceeeccCcCCCCccccCCccccCCCccccHHHHHHHH
Q 029888 87 NILNISCPLSGKPITELAEPVRSVECKHIYEKNAIQAYI 125 (186)
Q Consensus 87 ~~~~l~CPI~~~~~~~l~dPV~s~~CgH~fck~~I~~~l 125 (186)
+--.+.||+..++|..+..=|--..-|.+||-++|++.-
T Consensus 98 s~geyhcPvlfk~FT~~sHIvAv~TTGNvy~~eai~~LN 136 (518)
T KOG0883|consen 98 SEGEYHCPVLFKVFTRFSHIVAVRTTGNVYSWEAIEELN 136 (518)
T ss_pred CCCcccCceeeeeecccceEEEEEecCceeeHHHHHHhC
Confidence 345799999999887777666545679999999999873
No 221
>PF13894 zf-C2H2_4: C2H2-type zinc finger; PDB: 2ELX_A 2EPP_A 2DLK_A 1X6H_A 2EOU_A 2EMB_A 2GQJ_A 2CSH_A 2WBT_B 2ELM_A ....
Probab=21.63 E-value=41 Score=16.70 Aligned_cols=8 Identities=50% Similarity=1.373 Sum_probs=4.0
Q ss_pred eeccCcCC
Q 029888 91 ISCPLSGK 98 (186)
Q Consensus 91 l~CPI~~~ 98 (186)
+.||+|..
T Consensus 1 ~~C~~C~~ 8 (24)
T PF13894_consen 1 FQCPICGK 8 (24)
T ss_dssp EE-SSTS-
T ss_pred CCCcCCCC
Confidence 35777775
No 222
>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=21.39 E-value=79 Score=24.94 Aligned_cols=14 Identities=36% Similarity=0.667 Sum_probs=10.9
Q ss_pred CCCCCCCCCCCCccCC
Q 029888 131 NARCPVAGCPRKLQVS 146 (186)
Q Consensus 131 ~~~CPv~GC~~~l~~~ 146 (186)
.+.||. |+..|...
T Consensus 128 ~F~Cp~--Cg~~L~~~ 141 (158)
T TIGR00373 128 NFTCPR--CGAMLDYL 141 (158)
T ss_pred CCcCCC--CCCEeeec
Confidence 489999 99877544
No 223
>KOG4185 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=21.21 E-value=31 Score=29.42 Aligned_cols=26 Identities=23% Similarity=0.512 Sum_probs=22.5
Q ss_pred CCccccHHHHHHHHHhcCCCCCCCCCCCCC
Q 029888 112 CKHIYEKNAIQAYIKSKNANARCPVAGCPR 141 (186)
Q Consensus 112 CgH~fck~~I~~~l~~~~~~~~CPv~GC~~ 141 (186)
|||+.|..|+...+.+ .+ ..||. |..
T Consensus 239 c~htlc~~c~~~~l~~-~~-~~cp~--~~~ 264 (296)
T KOG4185|consen 239 EGHTLCKECIDTILLQ-AG-IKCPF--CTW 264 (296)
T ss_pred HHHHHHhcchHHHHHH-hh-hcCCc--ccc
Confidence 9999999999999884 33 89999 875
No 224
>PRK07758 hypothetical protein; Provisional
Probab=21.16 E-value=57 Score=24.04 Aligned_cols=27 Identities=22% Similarity=0.530 Sum_probs=17.6
Q ss_pred CccccHHHHHHHHHhcCCCCCCCCCCCCCCccC-CCCcc
Q 029888 113 KHIYEKNAIQAYIKSKNANARCPVAGCPRKLQV-SKVVC 150 (186)
Q Consensus 113 gH~fck~~I~~~l~~~~~~~~CPv~GC~~~l~~-~~L~~ 150 (186)
||.|-++ .....||. |.+...+ .++-+
T Consensus 13 ~~~~~~~---------~~~~~~~~--~~~~~~~~~~~~~ 40 (95)
T PRK07758 13 GHEYYKS---------SDCPTCPT--CEKERKPKEGFLS 40 (95)
T ss_pred ccceecc---------CCCCCCcc--cccccCCCCCCCc
Confidence 8888764 36678888 8775543 44444
No 225
>COG1655 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=21.11 E-value=61 Score=27.85 Aligned_cols=27 Identities=30% Similarity=0.651 Sum_probs=18.8
Q ss_pred HHHHHHHHHhcCCCCCCCCCCCCCCccCCCC
Q 029888 118 KNAIQAYIKSKNANARCPVAGCPRKLQVSKV 148 (186)
Q Consensus 118 k~~I~~~l~~~~~~~~CPv~GC~~~l~~~~L 148 (186)
+.+|.+++- ...+.||| |+..+....+
T Consensus 8 K~s~~s~f~--kk~ieCPv--C~tkFkkeev 34 (267)
T COG1655 8 KTSINSLFY--KKTIECPV--CNTKFKKEEV 34 (267)
T ss_pred hhhHHHHHh--hceeccCc--ccchhhhhhe
Confidence 456777776 36789999 9876665444
No 226
>PRK00420 hypothetical protein; Validated
Probab=20.90 E-value=66 Score=24.34 Aligned_cols=15 Identities=27% Similarity=0.483 Sum_probs=10.2
Q ss_pred CCCCCCCCCCCCCccCC
Q 029888 130 ANARCPVAGCPRKLQVS 146 (186)
Q Consensus 130 ~~~~CPv~GC~~~l~~~ 146 (186)
+...||. |+..+...
T Consensus 39 g~~~Cp~--Cg~~~~v~ 53 (112)
T PRK00420 39 GEVVCPV--HGKVYIVK 53 (112)
T ss_pred CceECCC--CCCeeeec
Confidence 5567999 88765543
No 227
>PTZ00410 NAD-dependent SIR2; Provisional
Probab=20.77 E-value=1.1e+02 Score=27.62 Aligned_cols=15 Identities=13% Similarity=0.423 Sum_probs=10.3
Q ss_pred CCCCCCCCCCCCCccCC
Q 029888 130 ANARCPVAGCPRKLQVS 146 (186)
Q Consensus 130 ~~~~CPv~GC~~~l~~~ 146 (186)
....||. |+..+.+.
T Consensus 170 ~vP~C~~--CgG~lRPd 184 (349)
T PTZ00410 170 KVPHCST--CGGIVKPD 184 (349)
T ss_pred CCCCCCC--CCCccCCc
Confidence 4578999 97765543
No 228
>PLN02195 cellulose synthase A
Probab=20.67 E-value=1e+02 Score=31.52 Aligned_cols=51 Identities=20% Similarity=0.328 Sum_probs=33.4
Q ss_pred eccCcCCCCccc--cCCc-cccCCCccccHHHHHHHHHhcCCCCCCCCCCCCCCccCC
Q 029888 92 SCPLSGKPITEL--AEPV-RSVECKHIYEKNAIQAYIKSKNANARCPVAGCPRKLQVS 146 (186)
Q Consensus 92 ~CPI~~~~~~~l--~dPV-~s~~CgH~fck~~I~~~l~~~~~~~~CPv~GC~~~l~~~ 146 (186)
.|-||+.-+++= -+|+ -...|+.--||.|- +|=+ +.++..||+ |......+
T Consensus 8 ~c~~cgd~~~~~~~g~~fvaC~eC~~pvCrpCy-eyer-~eg~q~Cpq--Ckt~Yk~~ 61 (977)
T PLN02195 8 ICATCGEEVGVDSNGEAFVACHECSYPLCKACL-EYEI-KEGRKVCLR--CGGPYDAE 61 (977)
T ss_pred cceecccccCcCCCCCeEEEeccCCCccccchh-hhhh-hcCCccCCc--cCCccccc
Confidence 588888632111 1343 23467888888887 6655 467889999 98877633
No 229
>PF04606 Ogr_Delta: Ogr/Delta-like zinc finger; InterPro: IPR007684 This entry is represented by Bacteriophage P2, Ogr. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This is a viral family of phage zinc-binding transcriptional activators, which also contains cryptic members in some bacterial genomes []. The P4 phage delta protein contains two such domains attached covalently, while the P2 phage Ogr proteins possess one domain but function as dimers. All the members of this family have the following consensus sequence: C-X(2)-C-X(3)-A-(X)2-R-X(15)-C-X(4)-C-X(3)-F [].; GO: 0006355 regulation of transcription, DNA-dependent
Probab=20.45 E-value=44 Score=20.89 Aligned_cols=9 Identities=33% Similarity=0.803 Sum_probs=6.6
Q ss_pred ccCCCcccc
Q 029888 109 SVECKHIYE 117 (186)
Q Consensus 109 s~~CgH~fc 117 (186)
|..|||+|-
T Consensus 30 N~~Cg~tfv 38 (47)
T PF04606_consen 30 NPECGHTFV 38 (47)
T ss_pred CCcCCCEEE
Confidence 456999883
No 230
>COG4098 comFA Superfamily II DNA/RNA helicase required for DNA uptake (late competence protein) [DNA replication, recombination, and repair]
Probab=20.17 E-value=50 Score=30.25 Aligned_cols=31 Identities=19% Similarity=0.472 Sum_probs=23.3
Q ss_pred eeeccCcCCCCccccCCccccCCCccccHHHHHH
Q 029888 90 NISCPLSGKPITELAEPVRSVECKHIYEKNAIQA 123 (186)
Q Consensus 90 ~l~CPI~~~~~~~l~dPV~s~~CgH~fck~~I~~ 123 (186)
.++|-=|+. .....=.+ ..||..||+.||+-
T Consensus 39 k~~C~RC~~--~~~~~~~~-lp~~~~YCr~Cl~m 69 (441)
T COG4098 39 KYRCNRCGN--THIELFAK-LPCGCLYCRNCLMM 69 (441)
T ss_pred cEEehhcCC--cchhhhcc-cccceEeehhhhhc
Confidence 688999985 23444455 68999999999863
Done!