Query 025507
Match_columns 251
No_of_seqs 274 out of 1532
Neff 5.9
Searched_HMMs 46136
Date Fri Mar 29 06:33:36 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/025507.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/025507hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG1940 Zn-finger protein [Gen 100.0 2.8E-65 6E-70 461.0 7.5 237 2-250 31-267 (276)
2 PF14599 zinc_ribbon_6: Zinc-r 99.9 8.9E-28 1.9E-32 172.3 0.2 61 188-248 1-61 (61)
3 PF05495 zf-CHY: CHY zinc fing 99.9 2.1E-24 4.6E-29 159.6 3.7 70 6-89 1-71 (71)
4 COG4357 Zinc finger domain con 99.4 2.1E-14 4.6E-19 110.9 0.8 68 3-79 12-92 (105)
5 PF13639 zf-RING_2: Ring finge 99.3 4.4E-13 9.6E-18 89.6 1.3 44 140-185 1-44 (44)
6 PF12861 zf-Apc11: Anaphase-pr 99.2 5.8E-12 1.3E-16 96.0 4.0 51 137-189 30-82 (85)
7 PF12678 zf-rbx1: RING-H2 zinc 99.0 1.2E-10 2.7E-15 86.3 3.4 47 138-185 18-73 (73)
8 KOG4628 Predicted E3 ubiquitin 99.0 2E-10 4.3E-15 107.6 3.1 50 140-190 230-279 (348)
9 cd00162 RING RING-finger (Real 99.0 7.3E-10 1.6E-14 71.9 4.0 45 141-188 1-45 (45)
10 PF13923 zf-C3HC4_2: Zinc fing 98.9 8.8E-10 1.9E-14 71.9 2.7 39 142-184 1-39 (39)
11 PHA02929 N1R/p28-like protein; 98.9 1.8E-09 4E-14 96.8 4.4 54 136-190 171-228 (238)
12 PF15227 zf-C3HC4_4: zinc fing 98.8 2.1E-09 4.5E-14 71.7 3.1 39 142-184 1-42 (42)
13 PF13920 zf-C3HC4_3: Zinc fing 98.8 2.7E-09 5.8E-14 73.1 2.3 47 139-190 2-49 (50)
14 COG5243 HRD1 HRD ubiquitin lig 98.8 2E-09 4.4E-14 101.0 2.2 55 136-191 284-348 (491)
15 KOG1493 Anaphase-promoting com 98.8 1.2E-09 2.5E-14 81.6 -0.1 51 137-189 29-81 (84)
16 PF00097 zf-C3HC4: Zinc finger 98.7 6.4E-09 1.4E-13 68.0 2.9 40 142-184 1-41 (41)
17 COG5194 APC11 Component of SCF 98.7 6.9E-09 1.5E-13 78.1 3.0 50 139-189 31-81 (88)
18 smart00184 RING Ring finger. E 98.7 1.6E-08 3.5E-13 63.2 3.0 39 142-184 1-39 (39)
19 COG5540 RING-finger-containing 98.7 1.3E-08 2.8E-13 93.5 3.6 56 134-190 318-373 (374)
20 PF14634 zf-RING_5: zinc-RING 98.6 2.6E-08 5.7E-13 66.7 3.4 44 141-186 1-44 (44)
21 PF13445 zf-RING_UBOX: RING-ty 98.6 2E-08 4.4E-13 67.4 2.6 40 142-182 1-43 (43)
22 PLN03208 E3 ubiquitin-protein 98.6 5E-08 1.1E-12 84.9 4.6 56 131-190 10-80 (193)
23 KOG0804 Cytoplasmic Zn-finger 98.5 9.1E-08 2E-12 91.7 2.9 80 140-247 176-257 (493)
24 PHA02926 zinc finger-like prot 98.4 1.4E-07 3.1E-12 83.5 3.5 56 135-190 166-231 (242)
25 smart00504 Ubox Modified RING 98.2 1.3E-06 2.8E-11 61.6 4.0 45 140-189 2-46 (63)
26 KOG0802 E3 ubiquitin ligase [P 98.1 6.7E-07 1.4E-11 88.7 1.3 54 135-189 287-341 (543)
27 KOG0320 Predicted E3 ubiquitin 98.1 2.4E-06 5.1E-11 73.4 2.9 48 139-189 131-178 (187)
28 KOG0317 Predicted E3 ubiquitin 98.1 1.9E-06 4.1E-11 78.8 2.2 47 139-190 239-285 (293)
29 KOG2177 Predicted E3 ubiquitin 98.0 1.4E-05 3.1E-10 69.1 6.0 44 138-186 12-55 (386)
30 smart00744 RINGv The RING-vari 97.9 6.9E-06 1.5E-10 56.5 3.0 43 141-185 1-49 (49)
31 TIGR00599 rad18 DNA repair pro 97.9 1E-05 2.2E-10 77.6 4.8 46 139-189 26-71 (397)
32 KOG2930 SCF ubiquitin ligase, 97.9 2.8E-06 6E-11 67.0 0.1 33 156-189 76-108 (114)
33 KOG0823 Predicted E3 ubiquitin 97.9 8.6E-06 1.9E-10 72.5 3.0 50 137-190 45-96 (230)
34 TIGR00570 cdk7 CDK-activating 97.8 1.6E-05 3.4E-10 73.9 4.2 51 139-189 3-54 (309)
35 PF11793 FANCL_C: FANCL C-term 97.7 9.2E-06 2E-10 59.8 -0.1 51 139-189 2-66 (70)
36 PF04564 U-box: U-box domain; 97.6 0.0001 2.2E-09 54.4 4.8 48 139-190 4-51 (73)
37 KOG2164 Predicted E3 ubiquitin 97.5 5.6E-05 1.2E-09 73.9 2.9 48 138-189 185-236 (513)
38 KOG0828 Predicted E3 ubiquitin 97.5 4.5E-05 9.8E-10 74.3 1.7 51 139-189 571-634 (636)
39 KOG0287 Postreplication repair 97.5 9.5E-05 2.1E-09 69.3 3.4 46 140-190 24-69 (442)
40 KOG4172 Predicted E3 ubiquitin 97.4 3E-05 6.5E-10 54.7 -0.1 53 138-194 6-59 (62)
41 KOG0827 Predicted E3 ubiquitin 97.3 0.00013 2.8E-09 69.5 1.9 46 139-185 4-52 (465)
42 COG5574 PEX10 RING-finger-cont 97.2 0.00015 3.2E-09 65.8 2.1 47 139-189 215-262 (271)
43 PF14835 zf-RING_6: zf-RING of 97.0 0.00034 7.3E-09 50.9 1.5 55 140-201 8-64 (65)
44 KOG1039 Predicted E3 ubiquitin 96.9 0.00025 5.4E-09 67.0 0.2 80 136-217 158-249 (344)
45 PF14570 zf-RING_4: RING/Ubox 96.8 0.00074 1.6E-08 46.4 2.2 47 142-188 1-47 (48)
46 COG5432 RAD18 RING-finger-cont 96.8 0.0007 1.5E-08 62.5 2.6 46 139-189 25-70 (391)
47 KOG4265 Predicted E3 ubiquitin 96.7 0.001 2.2E-08 62.7 2.8 49 137-190 288-337 (349)
48 KOG1734 Predicted RING-contain 96.7 0.00048 1E-08 62.9 0.2 52 138-189 223-281 (328)
49 KOG0311 Predicted E3 ubiquitin 96.7 0.00048 1E-08 64.9 0.1 48 139-189 43-90 (381)
50 KOG0978 E3 ubiquitin ligase in 96.5 0.00072 1.6E-08 68.8 0.6 47 140-190 644-690 (698)
51 PF11789 zf-Nse: Zinc-finger o 96.3 0.0028 6E-08 45.0 2.5 44 137-183 9-53 (57)
52 KOG1941 Acetylcholine receptor 96.2 0.0013 2.8E-08 62.9 0.2 56 131-187 358-414 (518)
53 KOG0824 Predicted E3 ubiquitin 96.2 0.0027 5.9E-08 58.8 2.1 50 136-189 4-53 (324)
54 KOG2879 Predicted E3 ubiquitin 96.0 0.0056 1.2E-07 56.1 3.1 53 137-192 237-290 (298)
55 KOG1785 Tyrosine kinase negati 96.0 0.0022 4.7E-08 61.6 0.5 54 132-189 362-416 (563)
56 COG5219 Uncharacterized conser 95.9 0.0042 9.1E-08 65.0 2.0 53 137-189 1467-1523(1525)
57 PF12906 RINGv: RING-variant d 95.6 0.0066 1.4E-07 41.3 1.6 41 142-184 1-47 (47)
58 PRK14890 putative Zn-ribbon RN 95.5 0.012 2.6E-07 42.1 2.6 47 52-104 5-56 (59)
59 KOG0825 PHD Zn-finger protein 95.3 0.006 1.3E-07 62.7 0.9 50 138-189 122-171 (1134)
60 KOG1645 RING-finger-containing 95.1 0.024 5.2E-07 54.6 4.2 50 139-188 4-55 (463)
61 KOG1428 Inhibitor of type V ad 94.7 0.031 6.8E-07 61.0 4.1 74 108-189 3462-3544(3738)
62 KOG4159 Predicted E3 ubiquitin 94.6 0.037 8.1E-07 53.4 4.0 49 137-190 82-130 (398)
63 KOG4185 Predicted E3 ubiquitin 94.5 0.035 7.5E-07 50.7 3.5 49 140-188 4-54 (296)
64 COG5175 MOT2 Transcriptional r 94.4 0.013 2.8E-07 55.4 0.4 57 139-195 14-70 (480)
65 PF10367 Vps39_2: Vacuolar sor 94.4 0.019 4.1E-07 44.0 1.3 33 137-171 76-108 (109)
66 PF14447 Prok-RING_4: Prokaryo 94.2 0.02 4.3E-07 40.5 1.0 33 155-190 19-51 (55)
67 KOG0297 TNF receptor-associate 94.0 0.034 7.3E-07 53.5 2.3 49 138-190 20-68 (391)
68 KOG3800 Predicted E3 ubiquitin 93.8 0.049 1.1E-06 50.3 2.9 49 141-189 2-51 (300)
69 PF05883 Baculo_RING: Baculovi 93.7 0.033 7.2E-07 46.1 1.5 35 139-174 26-66 (134)
70 KOG1571 Predicted E3 ubiquitin 93.7 0.039 8.5E-07 52.3 2.1 48 135-190 301-348 (355)
71 KOG4445 Uncharacterized conser 93.7 0.023 5E-07 52.9 0.5 52 137-189 113-186 (368)
72 KOG4275 Predicted E3 ubiquitin 93.3 0.013 2.7E-07 54.4 -1.8 55 128-191 286-344 (350)
73 KOG3970 Predicted E3 ubiquitin 93.0 0.14 3.1E-06 46.1 4.4 50 138-189 49-105 (299)
74 KOG3268 Predicted E3 ubiquitin 93.0 0.058 1.3E-06 46.9 1.9 31 159-189 188-228 (234)
75 KOG3002 Zn finger protein [Gen 92.4 0.16 3.6E-06 47.3 4.3 60 139-209 48-109 (299)
76 KOG1814 Predicted E3 ubiquitin 92.3 0.17 3.6E-06 49.0 4.3 46 139-185 184-236 (445)
77 PF12773 DZR: Double zinc ribb 92.0 0.16 3.5E-06 34.2 2.8 22 57-78 1-23 (50)
78 TIGR00100 hypA hydrogenase nic 91.4 0.14 3.1E-06 41.0 2.3 35 215-251 68-102 (115)
79 KOG1813 Predicted E3 ubiquitin 91.4 0.13 2.9E-06 47.7 2.3 65 137-206 239-303 (313)
80 COG2888 Predicted Zn-ribbon RN 91.3 0.13 2.8E-06 36.9 1.7 45 54-104 9-58 (61)
81 PF04641 Rtf2: Rtf2 RING-finge 91.2 0.21 4.5E-06 45.3 3.5 51 136-189 110-161 (260)
82 PF07800 DUF1644: Protein of u 91.1 0.24 5.1E-06 42.2 3.4 33 139-175 2-47 (162)
83 COG5152 Uncharacterized conser 90.9 0.14 3E-06 45.3 2.0 59 139-202 196-254 (259)
84 PHA02862 5L protein; Provision 90.2 0.2 4.3E-06 42.2 2.2 46 139-189 2-53 (156)
85 PRK00564 hypA hydrogenase nick 90.0 0.22 4.8E-06 40.0 2.3 35 215-251 69-104 (117)
86 PRK03824 hypA hydrogenase nick 89.9 0.25 5.4E-06 40.7 2.5 37 215-251 68-123 (135)
87 PHA02825 LAP/PHD finger-like p 89.9 0.3 6.5E-06 41.6 3.0 47 138-189 7-59 (162)
88 KOG2817 Predicted E3 ubiquitin 89.8 0.27 5.8E-06 47.3 3.0 47 140-187 335-383 (394)
89 COG5236 Uncharacterized conser 89.8 0.38 8.3E-06 45.9 3.9 66 120-189 42-108 (493)
90 PF13248 zf-ribbon_3: zinc-rib 89.5 0.17 3.7E-06 30.1 0.9 24 54-77 2-26 (26)
91 PRK12380 hydrogenase nickel in 89.3 0.27 5.8E-06 39.4 2.2 35 215-251 68-102 (113)
92 KOG2660 Locus-specific chromos 89.3 0.095 2.1E-06 49.2 -0.4 49 137-189 13-61 (331)
93 PF08746 zf-RING-like: RING-li 88.8 0.31 6.7E-06 32.5 1.9 42 142-184 1-43 (43)
94 PRK03681 hypA hydrogenase nick 88.8 0.32 6.9E-06 39.0 2.3 36 215-251 68-103 (114)
95 KOG1002 Nucleotide excision re 88.4 0.2 4.3E-06 50.1 1.0 52 134-189 531-586 (791)
96 PF10571 UPF0547: Uncharacteri 88.0 0.34 7.3E-06 29.1 1.5 23 56-78 2-25 (26)
97 KOG2114 Vacuolar assembly/sort 88.0 0.36 7.8E-06 50.5 2.6 43 140-189 841-883 (933)
98 KOG3039 Uncharacterized conser 87.9 0.57 1.2E-05 42.8 3.5 56 134-191 216-272 (303)
99 PF13240 zinc_ribbon_2: zinc-r 87.1 0.33 7.1E-06 28.2 1.0 21 57-77 2-23 (23)
100 PF07191 zinc-ribbons_6: zinc- 86.5 0.35 7.7E-06 35.8 1.2 36 53-88 16-59 (70)
101 PF01155 HypA: Hydrogenase exp 86.4 0.22 4.9E-06 39.7 0.1 35 215-251 68-102 (113)
102 KOG4739 Uncharacterized protei 86.3 0.3 6.5E-06 44.0 0.9 37 150-189 12-48 (233)
103 KOG4692 Predicted E3 ubiquitin 86.0 0.49 1.1E-05 45.2 2.1 53 133-190 416-468 (489)
104 PRK04023 DNA polymerase II lar 85.8 0.69 1.5E-05 49.4 3.3 31 69-103 628-658 (1121)
105 KOG3161 Predicted E3 ubiquitin 85.0 0.42 9.1E-06 48.8 1.2 42 140-185 12-53 (861)
106 PF03854 zf-P11: P-11 zinc fin 84.8 0.34 7.4E-06 33.4 0.4 32 158-190 15-47 (50)
107 PF07191 zinc-ribbons_6: zinc- 84.6 0.17 3.6E-06 37.5 -1.3 64 140-232 2-68 (70)
108 PRK00762 hypA hydrogenase nick 84.1 0.77 1.7E-05 37.3 2.3 36 215-251 68-108 (124)
109 COG5220 TFB3 Cdk activating ki 83.6 0.36 7.7E-06 43.9 0.1 50 139-188 10-63 (314)
110 KOG0309 Conserved WD40 repeat- 83.5 0.72 1.6E-05 47.9 2.2 44 137-183 1026-1069(1081)
111 PF09538 FYDLN_acid: Protein o 83.3 0.74 1.6E-05 36.8 1.8 26 67-104 9-34 (108)
112 COG0375 HybF Zn finger protein 82.5 1 2.2E-05 36.4 2.3 36 214-251 67-102 (115)
113 KOG1952 Transcription factor N 82.1 0.6 1.3E-05 48.9 1.1 48 139-189 191-247 (950)
114 KOG2034 Vacuolar sorting prote 81.8 0.66 1.4E-05 48.8 1.2 36 138-175 816-851 (911)
115 PF05290 Baculo_IE-1: Baculovi 81.8 0.99 2.2E-05 37.5 2.0 48 140-191 81-134 (140)
116 KOG1001 Helicase-like transcri 81.6 1.2 2.7E-05 45.8 3.1 44 140-188 455-499 (674)
117 PF12773 DZR: Double zinc ribb 81.1 1.4 3E-05 29.5 2.3 23 54-76 12-38 (50)
118 PRK14559 putative protein seri 81.0 1.1 2.4E-05 45.9 2.6 46 55-103 2-48 (645)
119 KOG3053 Uncharacterized conser 80.9 0.96 2.1E-05 41.5 1.8 54 136-189 17-82 (293)
120 COG5222 Uncharacterized conser 80.3 1.2 2.7E-05 41.7 2.4 44 140-186 275-318 (427)
121 PHA03096 p28-like protein; Pro 78.6 1.3 2.7E-05 41.2 1.9 47 140-186 179-231 (284)
122 TIGR00595 priA primosomal prot 76.7 2.4 5.1E-05 42.1 3.3 50 14-76 213-262 (505)
123 PRK14714 DNA polymerase II lar 75.3 2.9 6.3E-05 45.8 3.7 48 54-103 667-716 (1337)
124 PF14446 Prok-RING_1: Prokaryo 75.3 3.2 7E-05 29.2 2.8 36 138-173 4-39 (54)
125 PF02891 zf-MIZ: MIZ/SP-RING z 73.3 3.8 8.2E-05 28.0 2.7 44 141-187 4-50 (50)
126 PHA00626 hypothetical protein 73.2 3.3 7.1E-05 29.5 2.3 7 69-75 2-8 (59)
127 PF06524 NOA36: NOA36 protein; 72.3 1.7 3.6E-05 40.0 0.9 51 21-87 140-190 (314)
128 COG1198 PriA Primosomal protei 72.0 4 8.7E-05 42.6 3.7 55 14-81 435-489 (730)
129 KOG1812 Predicted E3 ubiquitin 70.5 2 4.4E-05 41.3 1.1 50 139-188 146-202 (384)
130 COG5109 Uncharacterized conser 69.7 3.5 7.7E-05 39.0 2.5 45 140-185 337-383 (396)
131 TIGR02300 FYDLN_acid conserved 69.0 3.2 7E-05 34.2 1.8 27 67-105 9-35 (129)
132 KOG4367 Predicted Zn-finger pr 67.8 3 6.5E-05 41.1 1.6 33 139-175 4-36 (699)
133 PF07282 OrfB_Zn_ribbon: Putat 67.5 4.4 9.6E-05 28.8 2.1 27 67-104 28-54 (69)
134 KOG2068 MOT2 transcription fac 65.5 5.1 0.00011 37.9 2.6 53 137-190 247-299 (327)
135 PF03107 C1_2: C1 domain; Int 65.3 4.9 0.00011 24.5 1.7 20 101-120 2-22 (30)
136 PRK04023 DNA polymerase II lar 65.2 5.4 0.00012 42.9 3.0 50 52-107 624-674 (1121)
137 PRK14873 primosome assembly pr 63.4 6.6 0.00014 40.5 3.2 49 14-76 383-431 (665)
138 PRK05580 primosome assembly pr 63.1 6.6 0.00014 40.4 3.2 51 14-77 381-431 (679)
139 PF05191 ADK_lid: Adenylate ki 63.0 1.9 4.2E-05 27.7 -0.4 27 69-104 3-29 (36)
140 KOG2272 Focal adhesion protein 62.6 1.2 2.6E-05 40.9 -2.1 123 24-190 100-233 (332)
141 PRK14714 DNA polymerase II lar 61.3 7.5 0.00016 42.8 3.3 33 68-104 668-700 (1337)
142 TIGR02605 CxxC_CxxC_SSSS putat 61.0 6.9 0.00015 26.4 2.0 33 217-249 5-41 (52)
143 KOG0827 Predicted E3 ubiquitin 60.6 0.98 2.1E-05 43.6 -3.1 52 137-189 194-245 (465)
144 PRK00398 rpoP DNA-directed RNA 60.6 6.2 0.00014 26.2 1.7 30 217-246 3-32 (46)
145 PRK14890 putative Zn-ribbon RN 60.5 6.4 0.00014 28.2 1.8 34 53-88 24-57 (59)
146 COG1656 Uncharacterized conser 60.3 6.1 0.00013 33.9 2.0 51 178-234 97-147 (165)
147 KOG1044 Actin-binding LIM Zn-f 59.3 11 0.00024 38.4 3.8 137 91-243 11-168 (670)
148 PF08271 TF_Zn_Ribbon: TFIIB z 59.0 8.8 0.00019 25.1 2.2 7 70-76 3-9 (43)
149 PF14353 CpXC: CpXC protein 58.8 1.9 4E-05 34.7 -1.3 56 179-236 2-57 (128)
150 PF14569 zf-UDP: Zinc-binding 58.6 10 0.00023 28.7 2.7 53 137-189 7-62 (80)
151 KOG0801 Predicted E3 ubiquitin 58.4 3.5 7.6E-05 35.5 0.2 29 138-167 176-204 (205)
152 smart00249 PHD PHD zinc finger 57.8 4.1 8.9E-05 25.7 0.4 41 142-184 2-47 (47)
153 KOG2907 RNA polymerase I trans 57.3 3.9 8.5E-05 33.0 0.3 19 233-251 72-94 (116)
154 PRK14559 putative protein seri 54.1 8.3 0.00018 39.7 2.1 34 54-88 15-50 (645)
155 KOG0298 DEAD box-containing he 53.3 5.4 0.00012 43.8 0.6 51 137-191 1151-1201(1394)
156 PF04216 FdhE: Protein involve 52.7 9.4 0.0002 35.0 2.1 30 52-81 195-225 (290)
157 PF01599 Ribosomal_S27: Riboso 52.7 9.1 0.0002 26.2 1.5 22 66-87 17-46 (47)
158 KOG2462 C2H2-type Zn-finger pr 52.3 15 0.00033 34.0 3.3 86 51-147 158-272 (279)
159 PRK12286 rpmF 50S ribosomal pr 52.3 16 0.00034 25.9 2.7 29 216-249 26-54 (57)
160 PF13453 zf-TFIIB: Transcripti 52.3 12 0.00025 24.3 1.9 25 70-103 2-26 (41)
161 KOG1100 Predicted E3 ubiquitin 51.4 7 0.00015 34.6 0.9 40 141-189 160-200 (207)
162 KOG2066 Vacuolar assembly/sort 51.2 5.8 0.00013 41.5 0.5 45 139-185 784-831 (846)
163 PF02701 zf-Dof: Dof domain, z 51.2 8.1 0.00018 28.0 1.1 14 235-248 5-18 (63)
164 KOG1940 Zn-finger protein [Gen 50.9 2.9 6.3E-05 38.7 -1.6 73 2-76 176-261 (276)
165 COG5183 SSM4 Protein involved 50.5 5.4 0.00012 42.1 0.1 51 137-189 10-66 (1175)
166 PF01096 TFIIS_C: Transcriptio 49.1 12 0.00026 24.2 1.6 33 69-103 2-35 (39)
167 KOG1609 Protein involved in mR 48.8 9.7 0.00021 34.4 1.5 51 139-189 78-134 (323)
168 TIGR02159 PA_CoA_Oxy4 phenylac 47.4 9.5 0.00021 31.9 1.1 16 235-250 105-120 (146)
169 KOG2932 E3 ubiquitin ligase in 47.3 7.7 0.00017 36.7 0.6 30 157-189 105-134 (389)
170 smart00734 ZnF_Rad18 Rad18-lik 47.2 19 0.00041 21.3 2.1 20 179-199 2-21 (26)
171 PF13894 zf-C2H2_4: C2H2-type 46.8 12 0.00026 20.1 1.2 17 179-195 1-17 (24)
172 cd00350 rubredoxin_like Rubred 46.6 16 0.00035 22.6 1.8 24 80-104 2-25 (33)
173 smart00659 RPOLCX RNA polymera 44.4 17 0.00036 24.3 1.7 26 217-243 2-27 (44)
174 KOG0826 Predicted E3 ubiquitin 44.0 20 0.00043 34.2 2.7 48 138-189 299-346 (357)
175 KOG2462 C2H2-type Zn-finger pr 43.7 24 0.00052 32.7 3.2 119 74-227 125-253 (279)
176 PF07649 C1_3: C1-like domain; 43.5 14 0.0003 22.3 1.1 21 102-122 3-24 (30)
177 PLN02189 cellulose synthase 43.2 20 0.00043 38.9 2.9 56 134-189 29-87 (1040)
178 COG1996 RPC10 DNA-directed RNA 42.9 18 0.00039 25.0 1.7 28 77-104 4-32 (49)
179 TIGR01562 FdhE formate dehydro 42.6 29 0.00064 32.5 3.7 24 216-243 209-232 (305)
180 COG1198 PriA Primosomal protei 42.6 28 0.00061 36.5 3.8 49 48-104 428-483 (730)
181 TIGR01384 TFS_arch transcripti 42.4 47 0.001 25.5 4.3 35 67-103 62-97 (104)
182 KOG0269 WD40 repeat-containing 42.3 25 0.00054 36.9 3.3 50 140-192 780-836 (839)
183 PF12172 DUF35_N: Rubredoxin-l 41.9 12 0.00025 23.6 0.6 23 53-75 10-33 (37)
184 TIGR01031 rpmF_bact ribosomal 41.9 23 0.00051 24.8 2.2 29 216-249 25-53 (55)
185 PF01529 zf-DHHC: DHHC palmito 41.3 21 0.00045 29.4 2.2 49 72-126 41-89 (174)
186 PRK03564 formate dehydrogenase 41.0 34 0.00073 32.2 3.8 24 216-243 211-234 (309)
187 PF08274 PhnA_Zn_Ribbon: PhnA 40.9 15 0.00033 22.7 1.0 23 69-103 4-26 (30)
188 PF04438 zf-HIT: HIT zinc fing 40.8 14 0.0003 22.7 0.8 16 70-86 5-20 (30)
189 PF15616 TerY-C: TerY-C metal 40.2 27 0.0006 28.8 2.7 34 67-103 77-112 (131)
190 PHA00626 hypothetical protein 39.7 20 0.00044 25.6 1.6 34 55-90 1-34 (59)
191 PF03604 DNA_RNApol_7kD: DNA d 39.2 20 0.00044 22.5 1.4 11 93-103 14-24 (32)
192 PF06906 DUF1272: Protein of u 38.4 48 0.0011 23.6 3.3 48 138-190 4-53 (57)
193 cd00729 rubredoxin_SM Rubredox 38.0 24 0.00052 22.2 1.6 22 55-76 3-27 (34)
194 PLN02436 cellulose synthase A 37.5 27 0.00059 38.1 2.9 56 134-189 31-89 (1094)
195 PF14952 zf-tcix: Putative tre 37.3 16 0.00036 24.6 0.8 12 236-247 12-23 (44)
196 PF10272 Tmpp129: Putative tra 36.9 40 0.00086 32.4 3.6 25 165-189 315-351 (358)
197 KOG1312 DHHC-type Zn-finger pr 36.8 9.4 0.0002 35.8 -0.5 32 100-134 149-180 (341)
198 KOG4185 Predicted E3 ubiquitin 36.4 7.3 0.00016 35.4 -1.3 48 140-187 208-265 (296)
199 COG3809 Uncharacterized protei 36.1 27 0.00058 26.6 1.9 30 179-212 22-53 (88)
200 PF10058 DUF2296: Predicted in 35.4 43 0.00092 23.4 2.7 47 196-245 4-54 (54)
201 cd01675 RNR_III Class III ribo 35.3 32 0.00069 34.7 2.9 32 213-249 515-546 (555)
202 COG2888 Predicted Zn-ribbon RN 35.0 24 0.00052 25.4 1.4 34 52-87 25-58 (61)
203 smart00661 RPOL9 RNA polymeras 34.8 34 0.00073 22.7 2.1 9 95-103 19-27 (52)
204 PF00096 zf-C2H2: Zinc finger, 34.4 19 0.0004 19.8 0.6 15 179-193 1-15 (23)
205 PF04710 Pellino: Pellino; In 34.0 14 0.0003 35.9 0.1 49 136-187 274-337 (416)
206 PF00643 zf-B_box: B-box zinc 33.8 34 0.00074 21.7 1.9 21 68-88 4-24 (42)
207 PF13717 zinc_ribbon_4: zinc-r 33.6 29 0.00063 22.0 1.5 10 15-24 3-12 (36)
208 KOG0006 E3 ubiquitin-protein l 33.2 41 0.00088 32.1 3.0 89 79-174 149-254 (446)
209 KOG1815 Predicted E3 ubiquitin 33.1 27 0.00058 34.1 1.9 38 136-176 67-104 (444)
210 PRK00366 ispG 4-hydroxy-3-meth 32.9 66 0.0014 31.0 4.4 53 179-235 269-323 (360)
211 PRK00432 30S ribosomal protein 32.7 30 0.00066 23.7 1.6 11 94-104 35-45 (50)
212 PF03833 PolC_DP2: DNA polymer 32.5 15 0.00032 39.0 0.0 46 68-122 656-701 (900)
213 KOG4317 Predicted Zn-finger pr 32.3 20 0.00044 34.0 0.9 21 68-88 8-28 (383)
214 cd02337 ZZ_CBP Zinc finger, ZZ 31.9 33 0.00072 22.5 1.6 20 97-120 1-20 (41)
215 PF05605 zf-Di19: Drought indu 31.7 54 0.0012 22.3 2.7 15 178-193 2-16 (54)
216 TIGR00595 priA primosomal prot 31.5 51 0.0011 32.8 3.6 46 52-105 211-262 (505)
217 PF13719 zinc_ribbon_5: zinc-r 31.5 32 0.0007 21.9 1.5 8 54-61 25-32 (37)
218 PF06937 EURL: EURL protein; 31.4 38 0.00083 31.4 2.4 43 137-182 28-74 (285)
219 PF12760 Zn_Tnp_IS1595: Transp 31.1 65 0.0014 21.3 3.0 9 68-76 19-27 (46)
220 PRK00464 nrdR transcriptional 31.0 30 0.00065 29.3 1.6 12 69-80 30-41 (154)
221 cd02249 ZZ Zinc finger, ZZ typ 30.6 35 0.00076 22.5 1.6 21 97-120 1-21 (46)
222 COG1998 RPS31 Ribosomal protei 30.2 34 0.00075 23.8 1.5 9 67-75 19-27 (51)
223 smart00132 LIM Zinc-binding do 30.0 30 0.00064 20.8 1.1 37 142-189 2-38 (39)
224 PRK00415 rps27e 30S ribosomal 29.9 30 0.00066 24.8 1.2 36 53-88 10-51 (59)
225 TIGR00244 transcriptional regu 29.4 34 0.00073 28.9 1.6 14 68-81 29-42 (147)
226 PF04423 Rad50_zn_hook: Rad50 29.0 28 0.00061 23.7 0.9 13 179-191 21-33 (54)
227 PF09723 Zn-ribbon_8: Zinc rib 28.8 44 0.00095 21.8 1.8 31 217-247 5-38 (42)
228 KOG3113 Uncharacterized conser 28.6 88 0.0019 28.9 4.3 49 138-189 110-158 (293)
229 PF01529 zf-DHHC: DHHC palmito 28.5 33 0.00072 28.2 1.5 39 90-134 42-80 (174)
230 smart00451 ZnF_U1 U1-like zinc 28.5 27 0.00059 21.0 0.7 11 78-88 2-12 (35)
231 KOG1701 Focal adhesion adaptor 28.4 34 0.00074 33.7 1.7 14 162-175 451-464 (468)
232 TIGR02098 MJ0042_CXXC MJ0042 f 28.2 47 0.001 20.7 1.8 10 54-63 25-34 (38)
233 PF01783 Ribosomal_L32p: Ribos 28.0 46 0.00099 23.2 1.9 29 216-249 25-53 (56)
234 KOG3842 Adaptor protein Pellin 27.8 27 0.00057 33.3 0.8 46 136-186 287-349 (429)
235 PRK04136 rpl40e 50S ribosomal 27.4 39 0.00084 23.3 1.3 23 53-75 13-36 (48)
236 PF14803 Nudix_N_2: Nudix N-te 27.4 52 0.0011 20.9 1.8 28 69-103 2-29 (34)
237 PF03966 Trm112p: Trm112p-like 27.4 29 0.00064 24.8 0.8 12 14-25 53-64 (68)
238 PLN02638 cellulose synthase A 27.4 50 0.0011 36.1 2.8 56 134-189 12-70 (1079)
239 PRK00420 hypothetical protein; 27.1 45 0.00098 26.8 1.9 20 67-86 23-47 (112)
240 PRK03564 formate dehydrogenase 26.8 67 0.0015 30.3 3.3 26 51-76 209-235 (309)
241 PF13913 zf-C2HC_2: zinc-finge 26.5 31 0.00068 20.1 0.7 12 68-79 3-14 (25)
242 PF06220 zf-U1: U1 zinc finger 26.4 26 0.00056 22.6 0.4 13 77-89 1-13 (38)
243 PF15353 HECA: Headcase protei 26.2 39 0.00085 27.0 1.4 16 160-175 39-54 (107)
244 PF03833 PolC_DP2: DNA polymer 24.8 24 0.00053 37.5 0.0 48 51-104 652-700 (900)
245 PF00130 C1_1: Phorbol esters/ 24.6 63 0.0014 21.4 2.0 13 92-104 24-36 (53)
246 COG1327 Predicted transcriptio 24.5 38 0.00082 28.8 1.1 12 69-80 30-41 (156)
247 KOG1311 DHHC-type Zn-finger pr 24.4 62 0.0013 29.5 2.6 46 74-125 108-153 (299)
248 PRK08351 DNA-directed RNA poly 24.4 45 0.00098 24.0 1.3 20 56-76 5-24 (61)
249 PF13597 NRDD: Anaerobic ribon 23.9 44 0.00096 33.7 1.6 29 216-249 490-518 (546)
250 KOG3362 Predicted BBOX Zn-fing 23.9 24 0.00051 29.9 -0.3 25 78-108 117-143 (156)
251 smart00834 CxxC_CXXC_SSSS Puta 23.1 71 0.0015 19.9 2.0 26 218-243 6-34 (41)
252 cd07973 Spt4 Transcription elo 23.0 45 0.00098 26.2 1.2 20 56-75 5-28 (98)
253 KOG4362 Transcriptional regula 22.9 36 0.00078 35.4 0.8 47 139-189 21-69 (684)
254 COG5273 Uncharacterized protei 22.9 40 0.00087 31.5 1.0 37 68-107 98-134 (309)
255 KOG4399 C2HC-type Zn-finger pr 22.7 16 0.00035 33.8 -1.6 73 72-147 197-269 (325)
256 COG1545 Predicted nucleic-acid 22.7 53 0.0011 27.1 1.6 31 47-77 22-53 (140)
257 PF12675 DUF3795: Protein of u 22.6 48 0.001 24.4 1.2 36 67-102 34-69 (78)
258 smart00647 IBR In Between Ring 21.9 35 0.00076 23.2 0.3 18 156-173 40-58 (64)
259 PF06677 Auto_anti-p27: Sjogre 21.9 67 0.0015 21.2 1.7 12 67-78 17-28 (41)
260 PF10122 Mu-like_Com: Mu-like 21.8 52 0.0011 23.0 1.1 32 217-248 4-37 (51)
261 COG5595 Zn-ribbon-containing, 21.5 67 0.0014 28.7 2.1 38 179-234 219-256 (256)
262 cd02345 ZZ_dah Zinc finger, ZZ 21.4 65 0.0014 21.8 1.6 26 218-246 1-26 (49)
263 PF09986 DUF2225: Uncharacteri 21.3 21 0.00045 31.5 -1.1 14 177-190 4-17 (214)
264 PF09297 zf-NADH-PPase: NADH p 21.2 37 0.0008 20.7 0.3 21 56-76 5-30 (32)
265 smart00440 ZnF_C2C2 C2C2 Zinc 21.1 1E+02 0.0022 19.9 2.4 33 69-103 2-35 (40)
266 PF07754 DUF1610: Domain of un 20.6 76 0.0016 18.7 1.5 9 95-103 15-23 (24)
267 PRK06266 transcription initiat 20.5 62 0.0013 27.8 1.7 11 139-149 136-146 (178)
268 smart00531 TFIIE Transcription 20.4 37 0.00081 28.0 0.3 10 69-78 101-110 (147)
269 PRK14873 primosome assembly pr 20.4 98 0.0021 32.1 3.3 28 48-79 376-404 (665)
270 PLN02400 cellulose synthase 20.3 58 0.0012 35.7 1.7 56 134-189 31-89 (1085)
No 1
>KOG1940 consensus Zn-finger protein [General function prediction only]
Probab=100.00 E-value=2.8e-65 Score=461.04 Aligned_cols=237 Identities=53% Similarity=1.090 Sum_probs=231.0
Q ss_pred CccCCccccccceeecCcCCCeecCcchhhhhccCcCcCcCCCCCCCCcccceeecCCCCccccccccCcCCCCccceEe
Q 025507 2 ITCRCQHYRRRCRIRAPCCNEIFDCRHCHNEAMNNINVDQKLRHDIPRHEVNQVICSLCGTEQKVQQVCVNCGVCMGEYF 81 (251)
Q Consensus 2 ~~~gC~HY~r~c~i~~pcC~~~y~Cr~CHde~~~~~~~~~~~~H~~~r~~~~~v~C~~C~~~q~~~~~C~~Cg~~f~~y~ 81 (251)
..+||+||+|++++++|+|.+||+||+||+++ ++|+++|+.|.+|+|+.|+++|+++++|.+|+..+|+||
T Consensus 31 ~~~~c~hy~r~~~~~a~ccd~~~~C~hCH~~s---------~~h~~~r~~v~~~~C~~C~~~q~~~~~c~~c~~~~g~~~ 101 (276)
T KOG1940|consen 31 FPYGCPHYRRNCKSRAPCCDREITCRHCHNES---------EDHDLDRKTVYELLCMKCRKIQPVGQICSNCHVELGEYY 101 (276)
T ss_pred cccCCchhhhccccccccccceeeeEEecChh---------hhcccchhhhhhhhhhhHHhhhhhhhccccchhhhhhhc
Confidence 35799999999999999999999999999997 599999999999999999999999999999999999999
Q ss_pred cCccccccCCCCCCeeecCCCCcceecCCcceeeccCCCcceeccccccccccCCCCCCCCcchhhhcccCCceeEEcCC
Q 025507 82 CESCKLFDDDTSKKQYHCDGCGICRIGGCDNFFHCNKCRCCYSMLLKNSHPCVEGAMHHDCPVCCEYLFETRQDVIVLPC 161 (251)
Q Consensus 82 C~~C~~~d~~~~k~~~HC~~CgiCR~g~~~~~fHC~~C~~c~~~~l~~~H~C~e~~~~~~CpICle~lf~s~~~~~~lpC 161 (251)
|.+|+||||+++ .||||+.|||||+|++++||||++|+.|+++.+.++|+|+|++++.+||||.|++|++...+..|+|
T Consensus 102 c~~C~l~dd~~~-~~~hC~~C~icr~g~~~~~fhc~~c~~c~~~~~~~~H~c~e~~~~~ncPic~e~l~~s~~~~~~~~C 180 (276)
T KOG1940|consen 102 CLICKLFDDDPS-KQYHCDLCGICREGLGLDFFHCKKCKACLSAYLSNWHKCVERSSEFNCPICKEYLFLSFEDAGVLKC 180 (276)
T ss_pred Cccccccccccc-ceeccccccccccccccchhHHhhhHhHHhhhcccccchhhhcccCCCchhHHHhccccccCCccCc
Confidence 999999999989 9999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CCcccHHHHHHHHhcCCCCCCCCCcCccchhHHHHHHHHHHhcCCCCHhhhcCceeEEcCCCCCCccccceeeeccCCCC
Q 025507 162 GHTIHKNCLKEMREHHQYACPICSKSVCDMSKVWEKYDREIAATPMPEAYLNKKVWILCNDCGKTSNVQFHVLAQKCPNC 241 (251)
Q Consensus 162 gH~fH~~Ci~~wl~~~~~~CP~Cr~~~~~~~~~~~~ld~~i~~~p~P~e~~~~~~~IlCndC~~~s~~~~h~lg~kC~~C 241 (251)
||.+|..|++++...+ |+||+|.+ +.||+.+|+.+|.+|+++|||++|++++++|+||||+..++++||||++||+.|
T Consensus 181 gH~~h~~cf~e~~~~~-y~CP~C~~-~~d~~~~~~~~d~~l~~~~~p~~y~~~~~~i~cndC~~~~~~k~~~l~~kc~~c 258 (276)
T KOG1940|consen 181 GHYMHSRCFEEMICEG-YTCPICSK-PGDMSHYFRKLDKELAGSPMPEEYKNKTQDILCNDCGSGTNVKYHILYHKCGKC 258 (276)
T ss_pred ccchHHHHHHHHhccC-CCCCcccc-hHHHHHHHHHHHHHHhcCCCCchhhchhheeeccCCCCCCccceehhhhhCCCc
Confidence 9999999999998866 99999999 999999999999999999999999999999999999999999999999999999
Q ss_pred CCccccccC
Q 025507 242 KSYNTRLTR 250 (251)
Q Consensus 242 ~SyNT~~~~ 250 (251)
+|||||+++
T Consensus 259 ~~~~~r~~~ 267 (276)
T KOG1940|consen 259 GSYNTRMIS 267 (276)
T ss_pred ccceeeecc
Confidence 999999985
No 2
>PF14599 zinc_ribbon_6: Zinc-ribbon; PDB: 2K2D_A.
Probab=99.93 E-value=8.9e-28 Score=172.32 Aligned_cols=61 Identities=66% Similarity=1.160 Sum_probs=22.5
Q ss_pred ccchhHHHHHHHHHHhcCCCCHhhhcCceeEEcCCCCCCccccceeeeccCCCCCCccccc
Q 025507 188 VCDMSKVWEKYDREIAATPMPEAYLNKKVWILCNDCGKTSNVQFHVLAQKCPNCKSYNTRL 248 (251)
Q Consensus 188 ~~~~~~~~~~ld~~i~~~p~P~e~~~~~~~IlCndC~~~s~~~~h~lg~kC~~C~SyNT~~ 248 (251)
+.||+..|+.||++|+++|||++|++++++|+||||+++|+++||||||||++|+||||+|
T Consensus 1 v~dM~~~w~~LD~~i~~~pmP~~Y~~~~v~IlCNDC~~~s~v~fH~lg~KC~~C~SYNT~q 61 (61)
T PF14599_consen 1 VVDMSAYWRMLDAEIAATPMPEEYRNKKVWILCNDCNAKSEVPFHFLGHKCSHCGSYNTRQ 61 (61)
T ss_dssp ---------------------------EEEEEESSS--EEEEE--TT----TTTS---EEE
T ss_pred CCCHHHHHHHHHHHHHhCCCCHHHhCCEEEEECCCCCCccceeeeHhhhcCCCCCCcccCC
Confidence 4689999999999999999999999999999999999999999999999999999999996
No 3
>PF05495 zf-CHY: CHY zinc finger; InterPro: IPR008913 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. Pirh2 is an eukaryotic ubiquitin protein ligase, which has been shown to promote p53 degradation in mammals. Pirh2 physically interacts with p53 and promotes ubiquitination of p53 independently of MDM2. Like MDM2, Pirh2 is thought to participate in an autoregulatory feedback loop that controls p53 function. Pirh2 proteins contain three distinct zinc fingers, the CHY-type, the CTCHY-type which is C-terminal to the CHY-type zinc finger and a RING finger. The CHY-type zinc finger has no currently known function []. As well as Pirh2, the CHY-type zinc finger is also found in the following proteins: Yeast helper of Tim protein 13. Hot13 may have a role in the assembly and recycling of the small Tims, a complex of the mitochondrial intermembrane space that participates in the TIM22 import pathway for assembly of the inner membrane [] Several plant hypothetical proteins that also contain haemerythrin cation binding domains Several protozoan hypothetical proteins that also contain a Myb domain The solution structure of this zinc finger has been solved and binds 3 zinc atoms as shown in the following schematic representation: ++---------+-----+ || | | CXHYxxxxxxxxxCCxxxxxCxxCHxxxxxHxxxxxxxxxxxCxxCxxxxxxxxxCxxC | | | | | | | | +-+-----------------+--+ +--+---------+--+ 'C': conserved cysteine involved in the binding of one zinc atom. 'H': conserved histidine involved in the binding of one zinc atom. More information about these proteins can be found at Protein of the Month: Zinc Fingers []; GO: 0008270 zinc ion binding; PDB: 2DKT_A 2K2C_A.
Probab=99.89 E-value=2.1e-24 Score=159.56 Aligned_cols=70 Identities=46% Similarity=1.125 Sum_probs=53.4
Q ss_pred Ccccccc-ceeecCcCCCeecCcchhhhhccCcCcCcCCCCCCCCcccceeecCCCCccccccccCcCCCCccceEecCc
Q 025507 6 CQHYRRR-CRIRAPCCNEIFDCRHCHNEAMNNINVDQKLRHDIPRHEVNQVICSLCGTEQKVQQVCVNCGVCMGEYFCES 84 (251)
Q Consensus 6 C~HY~r~-c~i~~pcC~~~y~Cr~CHde~~~~~~~~~~~~H~~~r~~~~~v~C~~C~~~q~~~~~C~~Cg~~f~~y~C~~ 84 (251)
|+||+|+ |+|+||||++|||||+||||+ ++|+++|.++++|+||.|+++|++++. +|+ |.|+|++
T Consensus 1 C~HY~~~~~~~~~~cC~~~y~C~~CHde~---------~~H~~~~~~~~~v~Cg~C~~~~~~~~~--~c~---~~~~C~~ 66 (71)
T PF05495_consen 1 CKHYHRSLCAIRFPCCGKYYPCRFCHDEL---------EDHPFDRWPVKRVICGKCRTEQPIDEY--SCG---ADYFCPI 66 (71)
T ss_dssp -SS---S-EEEEETTTTEEESSHHHHHHC---------SSS---TTT--EEEETTT--EEES-SB--TT-----SEEETT
T ss_pred CCCCCCCcEEEECCcccCeecHHHHHHHh---------ccCccccccccCeECCCCCCccChhhh--hcC---CCccCcC
Confidence 8999999 999999999999999999998 599999999999999999999999877 777 9999999
Q ss_pred ccccc
Q 025507 85 CKLFD 89 (251)
Q Consensus 85 C~~~d 89 (251)
|++||
T Consensus 67 C~~~~ 71 (71)
T PF05495_consen 67 CGLYF 71 (71)
T ss_dssp TTEEE
T ss_pred cCCCC
Confidence 99986
No 4
>COG4357 Zinc finger domain containing protein (CHY type) [Function unknown]
Probab=99.43 E-value=2.1e-14 Score=110.88 Aligned_cols=68 Identities=25% Similarity=0.668 Sum_probs=59.0
Q ss_pred ccCCccccc---cceeecCcCCCeecCcchhhhhccCcCcCcCCCCCC-----CCcccceeecCCCCccccc-----ccc
Q 025507 3 TCRCQHYRR---RCRIRAPCCNEIFDCRHCHNEAMNNINVDQKLRHDI-----PRHEVNQVICSLCGTEQKV-----QQV 69 (251)
Q Consensus 3 ~~gC~HY~r---~c~i~~pcC~~~y~Cr~CHde~~~~~~~~~~~~H~~-----~r~~~~~v~C~~C~~~q~~-----~~~ 69 (251)
+.||.||+. +++|+|.+|++||+|.+||||+ ++||+ +....+.|+||+|.+++.. ...
T Consensus 12 etRC~Hyht~~Diialkc~~C~kyYaCy~CHdel---------~~Hpf~p~~~~~~~~~~iiCGvC~~~LT~~EY~~~~~ 82 (105)
T COG4357 12 ETRCLHYHTPLDIIALKCKCCQKYYACYHCHDEL---------EDHPFEPWGLQEFNPKAIICGVCRKLLTRAEYGMCGS 82 (105)
T ss_pred cceeeEecCccceEeeeechhhhhhhHHHHHhHH---------hcCCCccCChhhcCCccEEhhhhhhhhhHHHHhhcCC
Confidence 579999999 6999999999999999999999 58886 4445678999999999864 467
Q ss_pred CcCCCCccce
Q 025507 70 CVNCGVCMGE 79 (251)
Q Consensus 70 C~~Cg~~f~~ 79 (251)
||+|..+||.
T Consensus 83 Cp~C~spFNp 92 (105)
T COG4357 83 CPYCQSPFNP 92 (105)
T ss_pred CCCcCCCCCc
Confidence 9999999984
No 5
>PF13639 zf-RING_2: Ring finger domain; PDB: 2KIZ_A 4EPO_C 1IYM_A 2EP4_A 2ECT_A 2JRJ_A 2ECN_A 2ECM_A 3NG2_A 2EA6_A ....
Probab=99.32 E-value=4.4e-13 Score=89.58 Aligned_cols=44 Identities=39% Similarity=1.081 Sum_probs=36.7
Q ss_pred CCCcchhhhcccCCceeEEcCCCCcccHHHHHHHHhcCCCCCCCCC
Q 025507 140 HDCPVCCEYLFETRQDVIVLPCGHTIHKNCLKEMREHHQYACPICS 185 (251)
Q Consensus 140 ~~CpICle~lf~s~~~~~~lpCgH~fH~~Ci~~wl~~~~~~CP~Cr 185 (251)
++||||+|.+.. ++.++.|+|||.||.+||.+|++. +.+||+||
T Consensus 1 d~C~IC~~~~~~-~~~~~~l~C~H~fh~~Ci~~~~~~-~~~CP~CR 44 (44)
T PF13639_consen 1 DECPICLEEFED-GEKVVKLPCGHVFHRSCIKEWLKR-NNSCPVCR 44 (44)
T ss_dssp -CETTTTCBHHT-TSCEEEETTSEEEEHHHHHHHHHH-SSB-TTTH
T ss_pred CCCcCCChhhcC-CCeEEEccCCCeeCHHHHHHHHHh-CCcCCccC
Confidence 479999997544 567888999999999999999996 58999997
No 6
>PF12861 zf-Apc11: Anaphase-promoting complex subunit 11 RING-H2 finger
Probab=99.24 E-value=5.8e-12 Score=95.98 Aligned_cols=51 Identities=20% Similarity=0.466 Sum_probs=40.9
Q ss_pred CCCCCCcchhhhcccCCceeEEcCCCCcccHHHHHHHHhcC--CCCCCCCCcCcc
Q 025507 137 AMHHDCPVCCEYLFETRQDVIVLPCGHTIHKNCLKEMREHH--QYACPICSKSVC 189 (251)
Q Consensus 137 ~~~~~CpICle~lf~s~~~~~~lpCgH~fH~~Ci~~wl~~~--~~~CP~Cr~~~~ 189 (251)
++++.||.|.. ..+.-+++...|+|.||.+||.+||++. +.+||+||.++.
T Consensus 30 ~fdg~Cp~Ck~--Pgd~Cplv~g~C~H~FH~hCI~kWl~~~~~~~~CPmCR~~w~ 82 (85)
T PF12861_consen 30 PFDGCCPDCKF--PGDDCPLVWGKCSHNFHMHCILKWLSTQSSKGQCPMCRQPWK 82 (85)
T ss_pred ccccCCCCccC--CCCCCceeeccCccHHHHHHHHHHHccccCCCCCCCcCCeee
Confidence 55778999984 4444566777999999999999999863 568999998765
No 7
>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=99.05 E-value=1.2e-10 Score=86.31 Aligned_cols=47 Identities=28% Similarity=0.786 Sum_probs=35.7
Q ss_pred CCCCCcchhhhcccC---------CceeEEcCCCCcccHHHHHHHHhcCCCCCCCCC
Q 025507 138 MHHDCPVCCEYLFET---------RQDVIVLPCGHTIHKNCLKEMREHHQYACPICS 185 (251)
Q Consensus 138 ~~~~CpICle~lf~s---------~~~~~~lpCgH~fH~~Ci~~wl~~~~~~CP~Cr 185 (251)
.+++|+||++.|.+. ...++.++|||.||..||.+||+. +.+||+||
T Consensus 18 ~~d~C~IC~~~l~~~~~~~~~~~~~~~i~~~~C~H~FH~~Ci~~Wl~~-~~~CP~CR 73 (73)
T PF12678_consen 18 ADDNCAICREPLEDPCPECQAPQDECPIVWGPCGHIFHFHCISQWLKQ-NNTCPLCR 73 (73)
T ss_dssp CCSBETTTTSBTTSTTCCHHHCTTTS-EEEETTSEEEEHHHHHHHHTT-SSB-TTSS
T ss_pred cCCcccccChhhhChhhhhcCCccccceEecccCCCEEHHHHHHHHhc-CCcCCCCC
Confidence 356799999977332 234566799999999999999985 46999998
No 8
>KOG4628 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=98.99 E-value=2e-10 Score=107.59 Aligned_cols=50 Identities=28% Similarity=0.824 Sum_probs=44.4
Q ss_pred CCCcchhhhcccCCceeEEcCCCCcccHHHHHHHHhcCCCCCCCCCcCccc
Q 025507 140 HDCPVCCEYLFETRQDVIVLPCGHTIHKNCLKEMREHHQYACPICSKSVCD 190 (251)
Q Consensus 140 ~~CpICle~lf~s~~~~~~lpCgH~fH~~Ci~~wl~~~~~~CP~Cr~~~~~ 190 (251)
..|+||||+ |..++.++.|||+|.||..||++||......||+|+.++..
T Consensus 230 ~~CaIClEd-Y~~GdklRiLPC~H~FH~~CIDpWL~~~r~~CPvCK~di~~ 279 (348)
T KOG4628|consen 230 DTCAICLED-YEKGDKLRILPCSHKFHVNCIDPWLTQTRTFCPVCKRDIRT 279 (348)
T ss_pred ceEEEeecc-cccCCeeeEecCCCchhhccchhhHhhcCccCCCCCCcCCC
Confidence 699999996 77788999999999999999999998655669999998764
No 9
>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=98.96 E-value=7.3e-10 Score=71.88 Aligned_cols=45 Identities=33% Similarity=1.041 Sum_probs=36.9
Q ss_pred CCcchhhhcccCCceeEEcCCCCcccHHHHHHHHhcCCCCCCCCCcCc
Q 025507 141 DCPVCCEYLFETRQDVIVLPCGHTIHKNCLKEMREHHQYACPICSKSV 188 (251)
Q Consensus 141 ~CpICle~lf~s~~~~~~lpCgH~fH~~Ci~~wl~~~~~~CP~Cr~~~ 188 (251)
.|+||++.+ ..++.+++|||.||..|+..|++..+.+||+|+..+
T Consensus 1 ~C~iC~~~~---~~~~~~~~C~H~~c~~C~~~~~~~~~~~Cp~C~~~~ 45 (45)
T cd00162 1 ECPICLEEF---REPVVLLPCGHVFCRSCIDKWLKSGKNTCPLCRTPI 45 (45)
T ss_pred CCCcCchhh---hCceEecCCCChhcHHHHHHHHHhCcCCCCCCCCcC
Confidence 599999965 235566679999999999999986568899999764
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=98.90 E-value=8.8e-10 Score=71.89 Aligned_cols=39 Identities=41% Similarity=1.110 Sum_probs=32.4
Q ss_pred CcchhhhcccCCceeEEcCCCCcccHHHHHHHHhcCCCCCCCC
Q 025507 142 CPVCCEYLFETRQDVIVLPCGHTIHKNCLKEMREHHQYACPIC 184 (251)
Q Consensus 142 CpICle~lf~s~~~~~~lpCgH~fH~~Ci~~wl~~~~~~CP~C 184 (251)
||||++.+.+ ++++++|||+|+.+|+.+|++. +.+||+|
T Consensus 1 C~iC~~~~~~---~~~~~~CGH~fC~~C~~~~~~~-~~~CP~C 39 (39)
T PF13923_consen 1 CPICLDELRD---PVVVTPCGHSFCKECIEKYLEK-NPKCPVC 39 (39)
T ss_dssp ETTTTSB-SS---EEEECTTSEEEEHHHHHHHHHC-TSB-TTT
T ss_pred CCCCCCcccC---cCEECCCCCchhHHHHHHHHHC-cCCCcCC
Confidence 7999985433 6678999999999999999996 6899997
No 11
>PHA02929 N1R/p28-like protein; Provisional
Probab=98.86 E-value=1.8e-09 Score=96.77 Aligned_cols=54 Identities=19% Similarity=0.609 Sum_probs=42.1
Q ss_pred CCCCCCCcchhhhcccCCc----eeEEcCCCCcccHHHHHHHHhcCCCCCCCCCcCccc
Q 025507 136 GAMHHDCPVCCEYLFETRQ----DVIVLPCGHTIHKNCLKEMREHHQYACPICSKSVCD 190 (251)
Q Consensus 136 ~~~~~~CpICle~lf~s~~----~~~~lpCgH~fH~~Ci~~wl~~~~~~CP~Cr~~~~~ 190 (251)
.+.+.+||||+|.+.+... -.++++|||.||.+||.+|++. +.+||+||.++..
T Consensus 171 ~~~~~eC~ICle~~~~~~~~~~~~~vl~~C~H~FC~~CI~~Wl~~-~~tCPlCR~~~~~ 228 (238)
T PHA02929 171 RSKDKECAICMEKVYDKEIKNMYFGILSNCNHVFCIECIDIWKKE-KNTCPVCRTPFIS 228 (238)
T ss_pred CCCCCCCccCCcccccCccccccceecCCCCCcccHHHHHHHHhc-CCCCCCCCCEeeE
Confidence 4556899999997654321 1245689999999999999984 6899999988764
No 12
>PF15227 zf-C3HC4_4: zinc finger of C3HC4-type, RING; PDB: 2EGP_A 2ECV_A 2ECJ_A 2YSL_A 2YSJ_A.
Probab=98.85 E-value=2.1e-09 Score=71.72 Aligned_cols=39 Identities=41% Similarity=1.233 Sum_probs=28.7
Q ss_pred CcchhhhcccCCceeEEcCCCCcccHHHHHHHHhcC---CCCCCCC
Q 025507 142 CPVCCEYLFETRQDVIVLPCGHTIHKNCLKEMREHH---QYACPIC 184 (251)
Q Consensus 142 CpICle~lf~s~~~~~~lpCgH~fH~~Ci~~wl~~~---~~~CP~C 184 (251)
||||++ +|. +++.|+|||+|+..||..|++.. .+.||+|
T Consensus 1 CpiC~~-~~~---~Pv~l~CGH~FC~~Cl~~~~~~~~~~~~~CP~C 42 (42)
T PF15227_consen 1 CPICLD-LFK---DPVSLPCGHSFCRSCLERLWKEPSGSGFSCPEC 42 (42)
T ss_dssp ETTTTS-B-S---SEEE-SSSSEEEHHHHHHHHCCSSSST---SSS
T ss_pred CCccch-hhC---CccccCCcCHHHHHHHHHHHHccCCcCCCCcCC
Confidence 899999 455 47789999999999999988753 2579987
No 13
>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=98.79 E-value=2.7e-09 Score=73.10 Aligned_cols=47 Identities=34% Similarity=0.982 Sum_probs=37.9
Q ss_pred CCCCcchhhhcccCCceeEEcCCCCc-ccHHHHHHHHhcCCCCCCCCCcCccc
Q 025507 139 HHDCPVCCEYLFETRQDVIVLPCGHT-IHKNCLKEMREHHQYACPICSKSVCD 190 (251)
Q Consensus 139 ~~~CpICle~lf~s~~~~~~lpCgH~-fH~~Ci~~wl~~~~~~CP~Cr~~~~~ 190 (251)
+..|+||++. ...++++||||. |+..|+..|++ ...+||+||+++.+
T Consensus 2 ~~~C~iC~~~----~~~~~~~pCgH~~~C~~C~~~~~~-~~~~CP~Cr~~i~~ 49 (50)
T PF13920_consen 2 DEECPICFEN----PRDVVLLPCGHLCFCEECAERLLK-RKKKCPICRQPIES 49 (50)
T ss_dssp HSB-TTTSSS----BSSEEEETTCEEEEEHHHHHHHHH-TTSBBTTTTBB-SE
T ss_pred cCCCccCCcc----CCceEEeCCCChHHHHHHhHHhcc-cCCCCCcCChhhcC
Confidence 3579999984 235778899999 99999999998 56899999998764
No 14
>COG5243 HRD1 HRD ubiquitin ligase complex, ER membrane component [Posttranslational modification, protein turnover, chaperones]
Probab=98.79 E-value=2e-09 Score=100.99 Aligned_cols=55 Identities=36% Similarity=0.821 Sum_probs=46.5
Q ss_pred CCCCCCCcchhhhcccCC---------ceeEEcCCCCcccHHHHHHHHhcCCCCCCCCCcCc-cch
Q 025507 136 GAMHHDCPVCCEYLFETR---------QDVIVLPCGHTIHKNCLKEMREHHQYACPICSKSV-CDM 191 (251)
Q Consensus 136 ~~~~~~CpICle~lf~s~---------~~~~~lpCgH~fH~~Ci~~wl~~~~~~CP~Cr~~~-~~~ 191 (251)
.+.+..|.||+|.|+.++ ..+..|||||.+|.+|++.|+++ +.+||+||.++ .|+
T Consensus 284 ~n~D~~C~ICmde~~h~~~~~~~~~~~~~pKrLpCGHilHl~CLknW~ER-qQTCPICr~p~ifd~ 348 (491)
T COG5243 284 TNSDRTCTICMDEMFHPDHEPLPRGLDMTPKRLPCGHILHLHCLKNWLER-QQTCPICRRPVIFDQ 348 (491)
T ss_pred cCCCCeEEEecccccCCCCccCcccccCCcccccccceeeHHHHHHHHHh-ccCCCcccCcccccc
Confidence 567889999999988766 34578999999999999999995 58999999994 454
No 15
>KOG1493 consensus Anaphase-promoting complex (APC), subunit 11 [Cell cycle control, cell division, chromosome partitioning; Posttranslational modification, protein turnover, chaperones]
Probab=98.77 E-value=1.2e-09 Score=81.56 Aligned_cols=51 Identities=24% Similarity=0.484 Sum_probs=39.6
Q ss_pred CCCCCCcchhhhcccCCceeEEcCCCCcccHHHHHHHHhcC--CCCCCCCCcCcc
Q 025507 137 AMHHDCPVCCEYLFETRQDVIVLPCGHTIHKNCLKEMREHH--QYACPICSKSVC 189 (251)
Q Consensus 137 ~~~~~CpICle~lf~s~~~~~~lpCgH~fH~~Ci~~wl~~~--~~~CP~Cr~~~~ 189 (251)
++++.||-|. +..+.-++++-.|.|.||..||.+|+... +..||+||.++.
T Consensus 29 ~Fdg~Cp~Ck--~PgDdCPLv~G~C~h~fh~hCI~~wl~~~tsq~~CPmcRq~~~ 81 (84)
T KOG1493|consen 29 PFDGCCPDCK--LPGDDCPLVWGYCLHAFHAHCILKWLNTPTSQGQCPMCRQTWQ 81 (84)
T ss_pred ccCCcCCCCc--CCCCCCccHHHHHHHHHHHHHHHHHhcCccccccCCcchheeE
Confidence 5678899998 45555555555899999999999999753 456999998764
No 16
>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=98.74 E-value=6.4e-09 Score=68.00 Aligned_cols=40 Identities=43% Similarity=1.116 Sum_probs=33.1
Q ss_pred CcchhhhcccCCceeEEcCCCCcccHHHHHHHHh-cCCCCCCCC
Q 025507 142 CPVCCEYLFETRQDVIVLPCGHTIHKNCLKEMRE-HHQYACPIC 184 (251)
Q Consensus 142 CpICle~lf~s~~~~~~lpCgH~fH~~Ci~~wl~-~~~~~CP~C 184 (251)
||||++.+.+ +..+++|||.|+..|+.+|++ .....||+|
T Consensus 1 C~iC~~~~~~---~~~~~~C~H~fC~~C~~~~~~~~~~~~CP~C 41 (41)
T PF00097_consen 1 CPICLEPFED---PVILLPCGHSFCRDCLRKWLENSGSVKCPLC 41 (41)
T ss_dssp ETTTSSBCSS---EEEETTTSEEEEHHHHHHHHHHTSSSBTTTT
T ss_pred CCcCCccccC---CCEEecCCCcchHHHHHHHHHhcCCccCCcC
Confidence 7999985332 446899999999999999998 566889998
No 17
>COG5194 APC11 Component of SCF ubiquitin ligase and anaphase-promoting complex [Posttranslational modification, protein turnover, chaperones / Cell division and chromosome partitioning]
Probab=98.73 E-value=6.9e-09 Score=78.06 Aligned_cols=50 Identities=20% Similarity=0.458 Sum_probs=38.3
Q ss_pred CCCCcchhhhcccCCc-eeEEcCCCCcccHHHHHHHHhcCCCCCCCCCcCcc
Q 025507 139 HHDCPVCCEYLFETRQ-DVIVLPCGHTIHKNCLKEMREHHQYACPICSKSVC 189 (251)
Q Consensus 139 ~~~CpICle~lf~s~~-~~~~lpCgH~fH~~Ci~~wl~~~~~~CP~Cr~~~~ 189 (251)
.+.||-|+-.+..+.+ +++.-.|.|.||.+||..||.+ +..||++|+++.
T Consensus 31 m~~C~eCq~~~~~~~eC~v~wG~CnHaFH~HCI~rWL~T-k~~CPld~q~w~ 81 (88)
T COG5194 31 MGTCPECQFGMTPGDECPVVWGVCNHAFHDHCIYRWLDT-KGVCPLDRQTWV 81 (88)
T ss_pred cCcCcccccCCCCCCcceEEEEecchHHHHHHHHHHHhh-CCCCCCCCceeE
Confidence 5678888754433333 3444589999999999999995 689999998875
No 18
>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=98.67 E-value=1.6e-08 Score=63.22 Aligned_cols=39 Identities=44% Similarity=1.130 Sum_probs=32.9
Q ss_pred CcchhhhcccCCceeEEcCCCCcccHHHHHHHHhcCCCCCCCC
Q 025507 142 CPVCCEYLFETRQDVIVLPCGHTIHKNCLKEMREHHQYACPIC 184 (251)
Q Consensus 142 CpICle~lf~s~~~~~~lpCgH~fH~~Ci~~wl~~~~~~CP~C 184 (251)
|+||++. ...++.++|||.||.+|++.|++....+||+|
T Consensus 1 C~iC~~~----~~~~~~~~C~H~~c~~C~~~~~~~~~~~CP~C 39 (39)
T smart00184 1 CPICLEE----LKDPVVLPCGHTFCRSCIRKWLKSGNNTCPIC 39 (39)
T ss_pred CCcCccC----CCCcEEecCCChHHHHHHHHHHHhCcCCCCCC
Confidence 7899985 34677889999999999999998556789987
No 19
>COG5540 RING-finger-containing ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=98.67 E-value=1.3e-08 Score=93.50 Aligned_cols=56 Identities=27% Similarity=0.655 Sum_probs=46.2
Q ss_pred cCCCCCCCCcchhhhcccCCceeEEcCCCCcccHHHHHHHHhcCCCCCCCCCcCccc
Q 025507 134 VEGAMHHDCPVCCEYLFETRQDVIVLPCGHTIHKNCLKEMREHHQYACPICSKSVCD 190 (251)
Q Consensus 134 ~e~~~~~~CpICle~lf~s~~~~~~lpCgH~fH~~Ci~~wl~~~~~~CP~Cr~~~~~ 190 (251)
+|.....+|+|||++ |...+.+++|||.|.||..|+++|+...+.+||+||.++..
T Consensus 318 ~ea~~GveCaICms~-fiK~d~~~vlPC~H~FH~~Cv~kW~~~y~~~CPvCrt~iPP 373 (374)
T COG5540 318 VEADKGVECAICMSN-FIKNDRLRVLPCDHRFHVGCVDKWLLGYSNKCPVCRTAIPP 373 (374)
T ss_pred HhcCCCceEEEEhhh-hcccceEEEeccCceechhHHHHHHhhhcccCCccCCCCCC
Confidence 344556799999997 45566799999999999999999998556789999987653
No 20
>PF14634 zf-RING_5: zinc-RING finger domain
Probab=98.64 E-value=2.6e-08 Score=66.65 Aligned_cols=44 Identities=32% Similarity=0.839 Sum_probs=36.8
Q ss_pred CCcchhhhcccCCceeEEcCCCCcccHHHHHHHHhcCCCCCCCCCc
Q 025507 141 DCPVCCEYLFETRQDVIVLPCGHTIHKNCLKEMREHHQYACPICSK 186 (251)
Q Consensus 141 ~CpICle~lf~s~~~~~~lpCgH~fH~~Ci~~wl~~~~~~CP~Cr~ 186 (251)
.|+||++.+ ++...+++++|||+|+.+|+..+. .....||+||+
T Consensus 1 ~C~~C~~~~-~~~~~~~l~~CgH~~C~~C~~~~~-~~~~~CP~C~k 44 (44)
T PF14634_consen 1 HCNICFEKY-SEERRPRLTSCGHIFCEKCLKKLK-GKSVKCPICRK 44 (44)
T ss_pred CCcCcCccc-cCCCCeEEcccCCHHHHHHHHhhc-CCCCCCcCCCC
Confidence 489999965 555568889999999999999998 34578999985
No 21
>PF13445 zf-RING_UBOX: RING-type zinc-finger; PDB: 2CT2_A.
Probab=98.63 E-value=2e-08 Score=67.44 Aligned_cols=40 Identities=38% Similarity=1.053 Sum_probs=24.5
Q ss_pred CcchhhhcccCCceeEEcCCCCcccHHHHHHHHhcC---CCCCC
Q 025507 142 CPVCCEYLFETRQDVIVLPCGHTIHKNCLKEMREHH---QYACP 182 (251)
Q Consensus 142 CpICle~lf~s~~~~~~lpCgH~fH~~Ci~~wl~~~---~~~CP 182 (251)
||||+| +.+...++++|+|||+|..+|++.+++.+ .++||
T Consensus 1 CpIc~e-~~~~~n~P~~L~CGH~~c~~cl~~l~~~~~~~~~kCP 43 (43)
T PF13445_consen 1 CPICKE-FSTEENPPMVLPCGHVFCKDCLQKLSKKSDRNRFKCP 43 (43)
T ss_dssp -TTT-----TTSS-EEE-SSS-EEEHHHHHHHHHH-S-S-B--T
T ss_pred CCcccc-ccCCCCCCEEEeCccHHHHHHHHHHHhcCCCCeeeCc
Confidence 899999 55656678899999999999999998853 45677
No 22
>PLN03208 E3 ubiquitin-protein ligase RMA2; Provisional
Probab=98.58 E-value=5e-08 Score=84.87 Aligned_cols=56 Identities=25% Similarity=0.623 Sum_probs=42.5
Q ss_pred ccccCCCCCCCCcchhhhcccCCceeEEcCCCCcccHHHHHHHHhc---------------CCCCCCCCCcCccc
Q 025507 131 HPCVEGAMHHDCPVCCEYLFETRQDVIVLPCGHTIHKNCLKEMREH---------------HQYACPICSKSVCD 190 (251)
Q Consensus 131 H~C~e~~~~~~CpICle~lf~s~~~~~~lpCgH~fH~~Ci~~wl~~---------------~~~~CP~Cr~~~~~ 190 (251)
-+-++...+..||||+|. +. ++++++|||.|+..||..|+.. ...+||+||..+..
T Consensus 10 ~~~~~~~~~~~CpICld~-~~---dPVvT~CGH~FC~~CI~~wl~~s~~s~~~~~~~~~~k~~~~CPvCR~~Is~ 80 (193)
T PLN03208 10 TTLVDSGGDFDCNICLDQ-VR---DPVVTLCGHLFCWPCIHKWTYASNNSRQRVDQYDHKREPPKCPVCKSDVSE 80 (193)
T ss_pred ceeccCCCccCCccCCCc-CC---CcEEcCCCchhHHHHHHHHHHhccccccccccccccCCCCcCCCCCCcCCh
Confidence 344444567899999995 33 3567899999999999999852 23579999998863
No 23
>KOG0804 consensus Cytoplasmic Zn-finger protein BRAP2 (BRCA1 associated protein) [General function prediction only]
Probab=98.45 E-value=9.1e-08 Score=91.72 Aligned_cols=80 Identities=28% Similarity=0.681 Sum_probs=65.3
Q ss_pred CCCcchhhhcccCCceeEEcCCCCcccHHHHHHHHhcCCCCCCCCCcCccchhHHHHHHHHHHhcCCCCHhhhcCceeEE
Q 025507 140 HDCPVCCEYLFETRQDVIVLPCGHTIHKNCLKEMREHHQYACPICSKSVCDMSKVWEKYDREIAATPMPEAYLNKKVWIL 219 (251)
Q Consensus 140 ~~CpICle~lf~s~~~~~~lpCgH~fH~~Ci~~wl~~~~~~CP~Cr~~~~~~~~~~~~ld~~i~~~p~P~e~~~~~~~Il 219 (251)
-.||||||.|-.+...++...|.|+||-.|+..|.. .+||+||.... |.+. ..-+
T Consensus 176 PTCpVCLERMD~s~~gi~t~~c~Hsfh~~cl~~w~~---~scpvcR~~q~----------------p~~v------e~~~ 230 (493)
T KOG0804|consen 176 PTCPVCLERMDSSTTGILTILCNHSFHCSCLMKWWD---SSCPVCRYCQS----------------PSVV------ESSL 230 (493)
T ss_pred CCcchhHhhcCccccceeeeecccccchHHHhhccc---CcChhhhhhcC----------------cchh------hhhh
Confidence 589999999999988889999999999999999954 68999994332 1111 2346
Q ss_pred cCCCCCCccccceeeeccCC--CCCCcccc
Q 025507 220 CNDCGKTSNVQFHVLAQKCP--NCKSYNTR 247 (251)
Q Consensus 220 CndC~~~s~~~~h~lg~kC~--~C~SyNT~ 247 (251)
|..|+...++ |+-+.|+ +||.|+-.
T Consensus 231 c~~c~~~~~L---wicliCg~vgcgrY~eg 257 (493)
T KOG0804|consen 231 CLACGCTEDL---WICLICGNVGCGRYKEG 257 (493)
T ss_pred hhhhcccccE---EEEEEccceecccccch
Confidence 9999999888 9999998 59999864
No 24
>PHA02926 zinc finger-like protein; Provisional
Probab=98.43 E-value=1.4e-07 Score=83.52 Aligned_cols=56 Identities=20% Similarity=0.536 Sum_probs=41.8
Q ss_pred CCCCCCCCcchhhhcccC-----CceeEEcCCCCcccHHHHHHHHhcC-----CCCCCCCCcCccc
Q 025507 135 EGAMHHDCPVCCEYLFET-----RQDVIVLPCGHTIHKNCLKEMREHH-----QYACPICSKSVCD 190 (251)
Q Consensus 135 e~~~~~~CpICle~lf~s-----~~~~~~lpCgH~fH~~Ci~~wl~~~-----~~~CP~Cr~~~~~ 190 (251)
..+.+..|+||||.+++. +...++.+|+|.||..||..|.+.. ..+||+||..+..
T Consensus 166 ~~SkE~eCgICmE~I~eK~~~~eRrFGIL~~CnHsFCl~CIr~Wr~~r~~~~~~rsCPiCR~~f~~ 231 (242)
T PHA02926 166 RVSKEKECGICYEVVYSKRLENDRYFGLLDSCNHIFCITCINIWHRTRRETGASDNCPICRTRFRN 231 (242)
T ss_pred hccCCCCCccCccccccccccccccccccCCCCchHHHHHHHHHHHhccccCcCCcCCCCcceeee
Confidence 356688999999976542 1223455999999999999998742 2459999987753
No 25
>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=98.24 E-value=1.3e-06 Score=61.64 Aligned_cols=45 Identities=18% Similarity=0.438 Sum_probs=37.9
Q ss_pred CCCcchhhhcccCCceeEEcCCCCcccHHHHHHHHhcCCCCCCCCCcCcc
Q 025507 140 HDCPVCCEYLFETRQDVIVLPCGHTIHKNCLKEMREHHQYACPICSKSVC 189 (251)
Q Consensus 140 ~~CpICle~lf~s~~~~~~lpCgH~fH~~Ci~~wl~~~~~~CP~Cr~~~~ 189 (251)
..||||++. ++. +++++|||+|.++||.+|++. +.+||+|++++.
T Consensus 2 ~~Cpi~~~~-~~~---Pv~~~~G~v~~~~~i~~~~~~-~~~cP~~~~~~~ 46 (63)
T smart00504 2 FLCPISLEV-MKD---PVILPSGQTYERRAIEKWLLS-HGTDPVTGQPLT 46 (63)
T ss_pred cCCcCCCCc-CCC---CEECCCCCEEeHHHHHHHHHH-CCCCCCCcCCCC
Confidence 469999994 442 467899999999999999985 678999998874
No 26
>KOG0802 consensus E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=98.15 E-value=6.7e-07 Score=88.74 Aligned_cols=54 Identities=31% Similarity=0.660 Sum_probs=43.8
Q ss_pred CCCCCCCCcchhhhcccCCc-eeEEcCCCCcccHHHHHHHHhcCCCCCCCCCcCcc
Q 025507 135 EGAMHHDCPVCCEYLFETRQ-DVIVLPCGHTIHKNCLKEMREHHQYACPICSKSVC 189 (251)
Q Consensus 135 e~~~~~~CpICle~lf~s~~-~~~~lpCgH~fH~~Ci~~wl~~~~~~CP~Cr~~~~ 189 (251)
+...+..|+||+|.|..+.. .+..|||||.||.+|+..|++. ..+||+||..+.
T Consensus 287 ~~~~~~~C~IC~e~l~~~~~~~~~rL~C~Hifh~~CL~~W~er-~qtCP~CR~~~~ 341 (543)
T KOG0802|consen 287 LALSDELCIICLEELHSGHNITPKRLPCGHIFHDSCLRSWFER-QQTCPTCRTVLY 341 (543)
T ss_pred hhhcCCeeeeechhhccccccccceeecccchHHHHHHHHHHH-hCcCCcchhhhh
Confidence 34568899999998877432 2457899999999999999996 689999998443
No 27
>KOG0320 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=98.07 E-value=2.4e-06 Score=73.42 Aligned_cols=48 Identities=25% Similarity=0.754 Sum_probs=38.3
Q ss_pred CCCCcchhhhcccCCceeEEcCCCCcccHHHHHHHHhcCCCCCCCCCcCcc
Q 025507 139 HHDCPVCCEYLFETRQDVIVLPCGHTIHKNCLKEMREHHQYACPICSKSVC 189 (251)
Q Consensus 139 ~~~CpICle~lf~s~~~~~~lpCgH~fH~~Ci~~wl~~~~~~CP~Cr~~~~ 189 (251)
-..|||||+.. . .+.++...|||.|+.+||+..++. ...||+|++-+.
T Consensus 131 ~~~CPiCl~~~-s-ek~~vsTkCGHvFC~~Cik~alk~-~~~CP~C~kkIt 178 (187)
T KOG0320|consen 131 TYKCPICLDSV-S-EKVPVSTKCGHVFCSQCIKDALKN-TNKCPTCRKKIT 178 (187)
T ss_pred ccCCCceecch-h-hccccccccchhHHHHHHHHHHHh-CCCCCCcccccc
Confidence 37899999963 2 233356799999999999999985 579999998654
No 28
>KOG0317 consensus Predicted E3 ubiquitin ligase, integral peroxisomal membrane protein [Posttranslational modification, protein turnover, chaperones]
Probab=98.05 E-value=1.9e-06 Score=78.82 Aligned_cols=47 Identities=28% Similarity=0.718 Sum_probs=38.6
Q ss_pred CCCCcchhhhcccCCceeEEcCCCCcccHHHHHHHHhcCCCCCCCCCcCccc
Q 025507 139 HHDCPVCCEYLFETRQDVIVLPCGHTIHKNCLKEMREHHQYACPICSKSVCD 190 (251)
Q Consensus 139 ~~~CpICle~lf~s~~~~~~lpCgH~fH~~Ci~~wl~~~~~~CP~Cr~~~~~ 190 (251)
...|.+|||. +..+...||||.|+..||.+|... ..-||+||..+..
T Consensus 239 ~~kC~LCLe~----~~~pSaTpCGHiFCWsCI~~w~~e-k~eCPlCR~~~~p 285 (293)
T KOG0317|consen 239 TRKCSLCLEN----RSNPSATPCGHIFCWSCILEWCSE-KAECPLCREKFQP 285 (293)
T ss_pred CCceEEEecC----CCCCCcCcCcchHHHHHHHHHHcc-ccCCCcccccCCC
Confidence 3579999994 334568899999999999999985 4679999987754
No 29
>KOG2177 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=97.96 E-value=1.4e-05 Score=69.10 Aligned_cols=44 Identities=39% Similarity=1.050 Sum_probs=37.2
Q ss_pred CCCCCcchhhhcccCCceeEEcCCCCcccHHHHHHHHhcCCCCCCCCCc
Q 025507 138 MHHDCPVCCEYLFETRQDVIVLPCGHTIHKNCLKEMREHHQYACPICSK 186 (251)
Q Consensus 138 ~~~~CpICle~lf~s~~~~~~lpCgH~fH~~Ci~~wl~~~~~~CP~Cr~ 186 (251)
....||||+++ |..+ ++|||||+|+..|+..++. ....||.||.
T Consensus 12 ~~~~C~iC~~~-~~~p---~~l~C~H~~c~~C~~~~~~-~~~~Cp~cr~ 55 (386)
T KOG2177|consen 12 EELTCPICLEY-FREP---VLLPCGHNFCRACLTRSWE-GPLSCPVCRP 55 (386)
T ss_pred ccccChhhHHH-hhcC---ccccccchHhHHHHHHhcC-CCcCCcccCC
Confidence 46789999996 4433 7899999999999999887 5688999994
No 30
>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=97.95 E-value=6.9e-06 Score=56.49 Aligned_cols=43 Identities=28% Similarity=0.724 Sum_probs=33.5
Q ss_pred CCcchhhhcccCCceeEEcCCC-----CcccHHHHHHHHhcC-CCCCCCCC
Q 025507 141 DCPVCCEYLFETRQDVIVLPCG-----HTIHKNCLKEMREHH-QYACPICS 185 (251)
Q Consensus 141 ~CpICle~lf~s~~~~~~lpCg-----H~fH~~Ci~~wl~~~-~~~CP~Cr 185 (251)
.|-||++ +.+...+.+.||. |.+|..|+.+|+... +.+||+|+
T Consensus 1 ~CrIC~~--~~~~~~~l~~PC~C~G~~~~vH~~Cl~~W~~~~~~~~C~iC~ 49 (49)
T smart00744 1 ICRICHD--EGDEGDPLVSPCRCKGSLKYVHQECLERWINESGNKTCEICK 49 (49)
T ss_pred CccCCCC--CCCCCCeeEeccccCCchhHHHHHHHHHHHHHcCCCcCCCCC
Confidence 3789997 3344566788995 999999999999753 45799995
No 31
>TIGR00599 rad18 DNA repair protein rad18. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=97.93 E-value=1e-05 Score=77.61 Aligned_cols=46 Identities=24% Similarity=0.699 Sum_probs=38.3
Q ss_pred CCCCcchhhhcccCCceeEEcCCCCcccHHHHHHHHhcCCCCCCCCCcCcc
Q 025507 139 HHDCPVCCEYLFETRQDVIVLPCGHTIHKNCLKEMREHHQYACPICSKSVC 189 (251)
Q Consensus 139 ~~~CpICle~lf~s~~~~~~lpCgH~fH~~Ci~~wl~~~~~~CP~Cr~~~~ 189 (251)
...|+||++. +. .+++++|||.|+..||..|+.. ...||+|+..+.
T Consensus 26 ~l~C~IC~d~-~~---~PvitpCgH~FCs~CI~~~l~~-~~~CP~Cr~~~~ 71 (397)
T TIGR00599 26 SLRCHICKDF-FD---VPVLTSCSHTFCSLCIRRCLSN-QPKCPLCRAEDQ 71 (397)
T ss_pred ccCCCcCchh-hh---CccCCCCCCchhHHHHHHHHhC-CCCCCCCCCccc
Confidence 5699999995 44 2457899999999999999985 468999998875
No 32
>KOG2930 consensus SCF ubiquitin ligase, Rbx1 component [Posttranslational modification, protein turnover, chaperones]
Probab=97.89 E-value=2.8e-06 Score=67.01 Aligned_cols=33 Identities=24% Similarity=0.509 Sum_probs=28.2
Q ss_pred eEEcCCCCcccHHHHHHHHhcCCCCCCCCCcCcc
Q 025507 156 VIVLPCGHTIHKNCLKEMREHHQYACPICSKSVC 189 (251)
Q Consensus 156 ~~~lpCgH~fH~~Ci~~wl~~~~~~CP~Cr~~~~ 189 (251)
+..--|.|+||..||..||++ +..||++.++..
T Consensus 76 VaWG~CNHaFH~hCisrWlkt-r~vCPLdn~eW~ 108 (114)
T KOG2930|consen 76 VAWGVCNHAFHFHCISRWLKT-RNVCPLDNKEWV 108 (114)
T ss_pred EEeeecchHHHHHHHHHHHhh-cCcCCCcCccee
Confidence 344589999999999999995 689999998765
No 33
>KOG0823 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=97.87 E-value=8.6e-06 Score=72.48 Aligned_cols=50 Identities=28% Similarity=0.650 Sum_probs=38.0
Q ss_pred CCCCCCcchhhhcccCCceeEEcCCCCcccHHHHHHHHhcC--CCCCCCCCcCccc
Q 025507 137 AMHHDCPVCCEYLFETRQDVIVLPCGHTIHKNCLKEMREHH--QYACPICSKSVCD 190 (251)
Q Consensus 137 ~~~~~CpICle~lf~s~~~~~~lpCgH~fH~~Ci~~wl~~~--~~~CP~Cr~~~~~ 190 (251)
...-+|-||||. . . ++++..|||.|+.-||-+||... ...||+|+..+..
T Consensus 45 ~~~FdCNICLd~-a--k-dPVvTlCGHLFCWpClyqWl~~~~~~~~cPVCK~~Vs~ 96 (230)
T KOG0823|consen 45 GGFFDCNICLDL-A--K-DPVVTLCGHLFCWPCLYQWLQTRPNSKECPVCKAEVSI 96 (230)
T ss_pred CCceeeeeeccc-c--C-CCEEeecccceehHHHHHHHhhcCCCeeCCcccccccc
Confidence 445799999983 2 2 34555699999999999999863 3458999987763
No 34
>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=97.83 E-value=1.6e-05 Score=73.88 Aligned_cols=51 Identities=24% Similarity=0.576 Sum_probs=39.0
Q ss_pred CCCCcchhhhcccCCcee-EEcCCCCcccHHHHHHHHhcCCCCCCCCCcCcc
Q 025507 139 HHDCPVCCEYLFETRQDV-IVLPCGHTIHKNCLKEMREHHQYACPICSKSVC 189 (251)
Q Consensus 139 ~~~CpICle~lf~s~~~~-~~lpCgH~fH~~Ci~~wl~~~~~~CP~Cr~~~~ 189 (251)
+..||||+.+...++.-. ++-+|||.|+..|++.++..+...||+|++++.
T Consensus 3 ~~~CP~Ck~~~y~np~~kl~i~~CGH~~C~sCv~~l~~~~~~~CP~C~~~lr 54 (309)
T TIGR00570 3 DQGCPRCKTTKYRNPSLKLMVNVCGHTLCESCVDLLFVRGSGSCPECDTPLR 54 (309)
T ss_pred CCCCCcCCCCCccCcccccccCCCCCcccHHHHHHHhcCCCCCCCCCCCccc
Confidence 357999998655554422 233799999999999977666678999998775
No 35
>PF11793 FANCL_C: FANCL C-terminal domain; PDB: 3K1L_A.
Probab=97.67 E-value=9.2e-06 Score=59.82 Aligned_cols=51 Identities=27% Similarity=0.653 Sum_probs=23.3
Q ss_pred CCCCcchhhhcccCC-ceeEEc---CCCCcccHHHHHHHHhc--CC--------CCCCCCCcCcc
Q 025507 139 HHDCPVCCEYLFETR-QDVIVL---PCGHTIHKNCLKEMREH--HQ--------YACPICSKSVC 189 (251)
Q Consensus 139 ~~~CpICle~lf~s~-~~~~~l---pCgH~fH~~Ci~~wl~~--~~--------~~CP~Cr~~~~ 189 (251)
+.+|+||.+++.+.+ .+.++- .|+..||..||.+|+.. ++ -.||.|++++.
T Consensus 2 ~~~C~IC~~~~~~~~~~p~~~C~n~~C~~~fH~~CL~~wf~~~~~~~~~~~~~~G~CP~C~~~i~ 66 (70)
T PF11793_consen 2 ELECGICYSYRLDDGEIPDVVCPNPSCGKKFHLLCLSEWFLSLEKSRQSFIPIFGECPYCSSPIS 66 (70)
T ss_dssp --S-SSS--SS-TT-----B--S-TT----B-SGGGHHHHHHHHSSS-TTT--EEE-TTT-SEEE
T ss_pred CCCCCcCCcEecCCCCcCceEcCCcccCCHHHHHHHHHHHHHcccCCeeecccccCCcCCCCeee
Confidence 458999998765333 233332 69999999999999864 11 14999998774
No 36
>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=97.61 E-value=0.0001 Score=54.41 Aligned_cols=48 Identities=25% Similarity=0.551 Sum_probs=36.3
Q ss_pred CCCCcchhhhcccCCceeEEcCCCCcccHHHHHHHHhcCCCCCCCCCcCccc
Q 025507 139 HHDCPVCCEYLFETRQDVIVLPCGHTIHKNCLKEMREHHQYACPICSKSVCD 190 (251)
Q Consensus 139 ~~~CpICle~lf~s~~~~~~lpCgH~fH~~Ci~~wl~~~~~~CP~Cr~~~~~ 190 (251)
+..|||..+ ++. +++++|+||+|-+.+|..|+.....+||+++..+..
T Consensus 4 ~f~CpIt~~-lM~---dPVi~~~G~tyer~~I~~~l~~~~~~~P~t~~~l~~ 51 (73)
T PF04564_consen 4 EFLCPITGE-LMR---DPVILPSGHTYERSAIERWLEQNGGTDPFTRQPLSE 51 (73)
T ss_dssp GGB-TTTSS-B-S---SEEEETTSEEEEHHHHHHHHCTTSSB-TTT-SB-SG
T ss_pred ccCCcCcCc-Hhh---CceeCCcCCEEcHHHHHHHHHcCCCCCCCCCCcCCc
Confidence 357999998 454 467889999999999999999757899999988764
No 37
>KOG2164 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=97.52 E-value=5.6e-05 Score=73.88 Aligned_cols=48 Identities=25% Similarity=0.650 Sum_probs=36.3
Q ss_pred CCCCCcchhhhcccCCceeEEcCCCCcccHHHHHHHHhcC----CCCCCCCCcCcc
Q 025507 138 MHHDCPVCCEYLFETRQDVIVLPCGHTIHKNCLKEMREHH----QYACPICSKSVC 189 (251)
Q Consensus 138 ~~~~CpICle~lf~s~~~~~~lpCgH~fH~~Ci~~wl~~~----~~~CP~Cr~~~~ 189 (251)
++..|||||++ +. -++.+.|||.|+..||..+|..+ --.||+|+..+.
T Consensus 185 t~~~CPICL~~-~~---~p~~t~CGHiFC~~CiLqy~~~s~~~~~~~CPiC~s~I~ 236 (513)
T KOG2164|consen 185 TDMQCPICLEP-PS---VPVRTNCGHIFCGPCILQYWNYSAIKGPCSCPICRSTIT 236 (513)
T ss_pred cCCcCCcccCC-CC---cccccccCceeeHHHHHHHHhhhcccCCccCCchhhhcc
Confidence 37899999985 22 23344599999999999977643 246999998775
No 38
>KOG0828 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=97.48 E-value=4.5e-05 Score=74.35 Aligned_cols=51 Identities=25% Similarity=0.717 Sum_probs=38.4
Q ss_pred CCCCcchhhhccc----C---------CceeEEcCCCCcccHHHHHHHHhcCCCCCCCCCcCcc
Q 025507 139 HHDCPVCCEYLFE----T---------RQDVIVLPCGHTIHKNCLKEMREHHQYACPICSKSVC 189 (251)
Q Consensus 139 ~~~CpICle~lf~----s---------~~~~~~lpCgH~fH~~Ci~~wl~~~~~~CP~Cr~~~~ 189 (251)
..+|+|||.++.- + .+..++.||.|.||..|++.|+......||+||.++.
T Consensus 571 t~dC~ICMt~I~l~~~~s~~~~~~~~~~~nYm~tPC~HifH~~CL~~WMd~ykl~CPvCR~pLP 634 (636)
T KOG0828|consen 571 TNDCVICMTPIDLRSTGSDCMVASMMVRRNYMLTPCHHIFHRQCLLQWMDTYKLICPVCRCPLP 634 (636)
T ss_pred cccceEeccccceeeccCcchhhhhhhhccccccchHHHHHHHHHHHHHhhhcccCCccCCCCC
Confidence 3589999975411 0 1235566999999999999999855568999998765
No 39
>KOG0287 consensus Postreplication repair protein RAD18 [Replication, recombination and repair]
Probab=97.45 E-value=9.5e-05 Score=69.34 Aligned_cols=46 Identities=30% Similarity=0.823 Sum_probs=39.3
Q ss_pred CCCcchhhhcccCCceeEEcCCCCcccHHHHHHHHhcCCCCCCCCCcCccc
Q 025507 140 HDCPVCCEYLFETRQDVIVLPCGHTIHKNCLKEMREHHQYACPICSKSVCD 190 (251)
Q Consensus 140 ~~CpICle~lf~s~~~~~~lpCgH~fH~~Ci~~wl~~~~~~CP~Cr~~~~~ 190 (251)
..|-||.|+ |. .+++.||||+|+.-||..+|.. +..||.|+.++..
T Consensus 24 LRC~IC~ey-f~---ip~itpCsHtfCSlCIR~~L~~-~p~CP~C~~~~~E 69 (442)
T KOG0287|consen 24 LRCGICFEY-FN---IPMITPCSHTFCSLCIRKFLSY-KPQCPTCCVTVTE 69 (442)
T ss_pred HHHhHHHHH-hc---CceeccccchHHHHHHHHHhcc-CCCCCceecccch
Confidence 479999996 54 4678899999999999999984 6899999988863
No 40
>KOG4172 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=97.42 E-value=3e-05 Score=54.67 Aligned_cols=53 Identities=26% Similarity=0.674 Sum_probs=40.4
Q ss_pred CCCCCcchhhhcccCCceeEEcCCCCc-ccHHHHHHHHhcCCCCCCCCCcCccchhHH
Q 025507 138 MHHDCPVCCEYLFETRQDVIVLPCGHT-IHKNCLKEMREHHQYACPICSKSVCDMSKV 194 (251)
Q Consensus 138 ~~~~CpICle~lf~s~~~~~~lpCgH~-fH~~Ci~~wl~~~~~~CP~Cr~~~~~~~~~ 194 (251)
...+|.||+|. +.+.++.-|||. ++-+|-.+.++...-.||+||.++.++-..
T Consensus 6 ~~dECTICye~----pvdsVlYtCGHMCmCy~Cg~rl~~~~~g~CPiCRapi~dvIkT 59 (62)
T KOG4172|consen 6 WSDECTICYEH----PVDSVLYTCGHMCMCYACGLRLKKALHGCCPICRAPIKDVIKT 59 (62)
T ss_pred cccceeeeccC----cchHHHHHcchHHhHHHHHHHHHHccCCcCcchhhHHHHHHHh
Confidence 34799999984 223455689998 899998887665678999999988775433
No 41
>KOG0827 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=97.26 E-value=0.00013 Score=69.46 Aligned_cols=46 Identities=28% Similarity=0.692 Sum_probs=37.6
Q ss_pred CCCCcchhhhcccCCceeEEc-CCCCcccHHHHHHHHhcC--CCCCCCCC
Q 025507 139 HHDCPVCCEYLFETRQDVIVL-PCGHTIHKNCLKEMREHH--QYACPICS 185 (251)
Q Consensus 139 ~~~CpICle~lf~s~~~~~~l-pCgH~fH~~Ci~~wl~~~--~~~CP~Cr 185 (251)
...|.|| ++++.....+..+ .|||.||..|+.+|+... +..||+|+
T Consensus 4 ~A~C~Ic-~d~~p~~~~l~~i~~cGhifh~~cl~qwfe~~Ps~R~cpic~ 52 (465)
T KOG0827|consen 4 MAECHIC-IDGRPNDHELGPIGTCGHIFHTTCLTQWFEGDPSNRGCPICQ 52 (465)
T ss_pred cceeeEe-ccCCccccccccccchhhHHHHHHHHHHHccCCccCCCCcee
Confidence 4579999 5578777777666 499999999999999863 35799999
No 42
>COG5574 PEX10 RING-finger-containing E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=97.24 E-value=0.00015 Score=65.84 Aligned_cols=47 Identities=28% Similarity=0.582 Sum_probs=36.7
Q ss_pred CCCCcchhhhcccCCceeEEcCCCCcccHHHHHH-HHhcCCCCCCCCCcCcc
Q 025507 139 HHDCPVCCEYLFETRQDVIVLPCGHTIHKNCLKE-MREHHQYACPICSKSVC 189 (251)
Q Consensus 139 ~~~CpICle~lf~s~~~~~~lpCgH~fH~~Ci~~-wl~~~~~~CP~Cr~~~~ 189 (251)
+..|+||+|. ...+...+|||.|+..||.. |-......||+||.-+.
T Consensus 215 d~kC~lC~e~----~~~ps~t~CgHlFC~~Cl~~~~t~~k~~~CplCRak~~ 262 (271)
T COG5574 215 DYKCFLCLEE----PEVPSCTPCGHLFCLSCLLISWTKKKYEFCPLCRAKVY 262 (271)
T ss_pred ccceeeeecc----cCCcccccccchhhHHHHHHHHHhhccccCchhhhhcc
Confidence 5579999984 33466789999999999999 87644344999996554
No 43
>PF14835 zf-RING_6: zf-RING of BARD1-type protein; PDB: 1JM7_B.
Probab=97.00 E-value=0.00034 Score=50.91 Aligned_cols=55 Identities=24% Similarity=0.619 Sum_probs=26.4
Q ss_pred CCCcchhhhcccCCceeEEcCCCCcccHHHHHHHHhcCCCCCCCCCcCcc--chhHHHHHHHHH
Q 025507 140 HDCPVCCEYLFETRQDVIVLPCGHTIHKNCLKEMREHHQYACPICSKSVC--DMSKVWEKYDRE 201 (251)
Q Consensus 140 ~~CpICle~lf~s~~~~~~lpCgH~fH~~Ci~~wl~~~~~~CP~Cr~~~~--~~~~~~~~ld~~ 201 (251)
..|++|.+.|.. ++.+..|.|.|+..|+.+-+. ..||+|+.+.- |+. ..+.+|..
T Consensus 8 LrCs~C~~~l~~---pv~l~~CeH~fCs~Ci~~~~~---~~CPvC~~Paw~qD~~-~NrqLd~~ 64 (65)
T PF14835_consen 8 LRCSICFDILKE---PVCLGGCEHIFCSSCIRDCIG---SECPVCHTPAWIQDIQ-INRQLDSM 64 (65)
T ss_dssp TS-SSS-S--SS----B---SSS--B-TTTGGGGTT---TB-SSS--B-S-SS-----HHHHHH
T ss_pred cCCcHHHHHhcC---CceeccCccHHHHHHhHHhcC---CCCCCcCChHHHHHHH-hhhhhhcc
Confidence 479999986433 566779999999999998765 45999998873 432 23445544
No 44
>KOG1039 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=96.90 E-value=0.00025 Score=66.99 Aligned_cols=80 Identities=20% Similarity=0.474 Sum_probs=51.3
Q ss_pred CCCCCCCcchhhhcccCC---ceeEE-cCCCCcccHHHHHHHHhcC------CCCCCCCCcCccch--hHHHHHHHHHHh
Q 025507 136 GAMHHDCPVCCEYLFETR---QDVIV-LPCGHTIHKNCLKEMREHH------QYACPICSKSVCDM--SKVWEKYDREIA 203 (251)
Q Consensus 136 ~~~~~~CpICle~lf~s~---~~~~~-lpCgH~fH~~Ci~~wl~~~------~~~CP~Cr~~~~~~--~~~~~~ld~~i~ 203 (251)
++.+..|.||||.+.+.. ....+ ++|.|.|+..||..|.+.. ...||+||...... +..|-.-.+ +
T Consensus 158 ~s~~k~CGICme~i~ek~~~~~rfgilpnC~H~~Cl~Cir~wr~~~q~~~~~sksCP~CRv~s~~v~pS~~Wv~t~~--~ 235 (344)
T KOG1039|consen 158 KSSEKECGICMETINEKAASERRFGILPNCNHSFCLNCIRKWRQATQFESKTSKSCPFCRVPSSFVNPSSFWVETKE--E 235 (344)
T ss_pred ccccccceehhhhccccchhhhhcccCCCcchhhhhcHhHhhhhhhccccccccCCCcccCccccccccceeeeecc--c
Confidence 356789999999765533 11223 4699999999999998543 36799999776532 223432211 4
Q ss_pred cCCCCHhhhcCcee
Q 025507 204 ATPMPEAYLNKKVW 217 (251)
Q Consensus 204 ~~p~P~e~~~~~~~ 217 (251)
.++++++|...+..
T Consensus 236 k~~li~e~~~~~s~ 249 (344)
T KOG1039|consen 236 KQKLIEEYEAEMSA 249 (344)
T ss_pred ccccHHHHHHHhhc
Confidence 55566666655443
No 45
>PF14570 zf-RING_4: RING/Ubox like zinc-binding domain; PDB: 1E4U_A 1UR6_B.
Probab=96.85 E-value=0.00074 Score=46.43 Aligned_cols=47 Identities=34% Similarity=0.699 Sum_probs=25.0
Q ss_pred CcchhhhcccCCceeEEcCCCCcccHHHHHHHHhcCCCCCCCCCcCc
Q 025507 142 CPVCCEYLFETRQDVIVLPCGHTIHKNCLKEMREHHQYACPICSKSV 188 (251)
Q Consensus 142 CpICle~lf~s~~~~~~lpCgH~fH~~Ci~~wl~~~~~~CP~Cr~~~ 188 (251)
||+|.|.|..++.....=+||+.+++.|+..-++..+.+||-||++.
T Consensus 1 cp~C~e~~d~~d~~~~PC~Cgf~IC~~C~~~i~~~~~g~CPgCr~~Y 47 (48)
T PF14570_consen 1 CPLCDEELDETDKDFYPCECGFQICRFCYHDILENEGGRCPGCREPY 47 (48)
T ss_dssp -TTTS-B--CCCTT--SSTTS----HHHHHHHTTSS-SB-TTT--B-
T ss_pred CCCcccccccCCCccccCcCCCcHHHHHHHHHHhccCCCCCCCCCCC
Confidence 79999988444443333367999999999999875578999999864
No 46
>COG5432 RAD18 RING-finger-containing E3 ubiquitin ligase [Signal transduction mechanisms]
Probab=96.84 E-value=0.0007 Score=62.53 Aligned_cols=46 Identities=26% Similarity=0.618 Sum_probs=37.9
Q ss_pred CCCCcchhhhcccCCceeEEcCCCCcccHHHHHHHHhcCCCCCCCCCcCcc
Q 025507 139 HHDCPVCCEYLFETRQDVIVLPCGHTIHKNCLKEMREHHQYACPICSKSVC 189 (251)
Q Consensus 139 ~~~CpICle~lf~s~~~~~~lpCgH~fH~~Ci~~wl~~~~~~CP~Cr~~~~ 189 (251)
...|-||-+++ . .+...+|||+|+.-||..+|. .+..||+||.+..
T Consensus 25 ~lrC~IC~~~i-~---ip~~TtCgHtFCslCIR~hL~-~qp~CP~Cr~~~~ 70 (391)
T COG5432 25 MLRCRICDCRI-S---IPCETTCGHTFCSLCIRRHLG-TQPFCPVCREDPC 70 (391)
T ss_pred HHHhhhhhhee-e---cceecccccchhHHHHHHHhc-CCCCCccccccHH
Confidence 35799999853 3 356779999999999999998 4689999997764
No 47
>KOG4265 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=96.73 E-value=0.001 Score=62.72 Aligned_cols=49 Identities=31% Similarity=0.811 Sum_probs=39.2
Q ss_pred CCCCCCcchhhhcccCCceeEEcCCCCc-ccHHHHHHHHhcCCCCCCCCCcCccc
Q 025507 137 AMHHDCPVCCEYLFETRQDVIVLPCGHT-IHKNCLKEMREHHQYACPICSKSVCD 190 (251)
Q Consensus 137 ~~~~~CpICle~lf~s~~~~~~lpCgH~-fH~~Ci~~wl~~~~~~CP~Cr~~~~~ 190 (251)
....+|.|||.. .++.++|||-|. ++..|.+...- ....|||||.++..
T Consensus 288 ~~gkeCVIClse----~rdt~vLPCRHLCLCs~Ca~~Lr~-q~n~CPICRqpi~~ 337 (349)
T KOG4265|consen 288 ESGKECVICLSE----SRDTVVLPCRHLCLCSGCAKSLRY-QTNNCPICRQPIEE 337 (349)
T ss_pred cCCCeeEEEecC----CcceEEecchhhehhHhHHHHHHH-hhcCCCccccchHh
Confidence 335699999974 446889999998 99999999753 34689999988764
No 48
>KOG1734 consensus Predicted RING-containing E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=96.66 E-value=0.00048 Score=62.92 Aligned_cols=52 Identities=23% Similarity=0.557 Sum_probs=40.2
Q ss_pred CCCCCcchhhhcccCC------ceeEEcCCCCcccHHHHHHHHh-cCCCCCCCCCcCcc
Q 025507 138 MHHDCPVCCEYLFETR------QDVIVLPCGHTIHKNCLKEMRE-HHQYACPICSKSVC 189 (251)
Q Consensus 138 ~~~~CpICle~lf~s~------~~~~~lpCgH~fH~~Ci~~wl~-~~~~~CP~Cr~~~~ 189 (251)
.++.|+||...+..+. +..-.|.|+|.||.-||.-|-- ....+||-|++.+.
T Consensus 223 ~d~vCaVCg~~~~~s~~eegvienty~LsCnHvFHEfCIrGWcivGKkqtCPYCKekVd 281 (328)
T KOG1734|consen 223 SDSVCAVCGQQIDVSVDEEGVIENTYKLSCNHVFHEFCIRGWCIVGKKQTCPYCKEKVD 281 (328)
T ss_pred CcchhHhhcchheeecchhhhhhhheeeecccchHHHhhhhheeecCCCCCchHHHHhh
Confidence 4578999998765544 2445789999999999999943 35688999997654
No 49
>KOG0311 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=96.65 E-value=0.00048 Score=64.91 Aligned_cols=48 Identities=23% Similarity=0.568 Sum_probs=40.1
Q ss_pred CCCCcchhhhcccCCceeEEcCCCCcccHHHHHHHHhcCCCCCCCCCcCcc
Q 025507 139 HHDCPVCCEYLFETRQDVIVLPCGHTIHKNCLKEMREHHQYACPICSKSVC 189 (251)
Q Consensus 139 ~~~CpICle~lf~s~~~~~~lpCgH~fH~~Ci~~wl~~~~~~CP~Cr~~~~ 189 (251)
+..|||||+-|.. ...+.-|+|.|+.+||..-++.++..||.||+.+.
T Consensus 43 ~v~c~icl~llk~---tmttkeClhrfc~~ci~~a~r~gn~ecptcRk~l~ 90 (381)
T KOG0311|consen 43 QVICPICLSLLKK---TMTTKECLHRFCFDCIWKALRSGNNECPTCRKKLV 90 (381)
T ss_pred hhccHHHHHHHHh---hcccHHHHHHHHHHHHHHHHHhcCCCCchHHhhcc
Confidence 5689999994433 34567899999999999988888899999999876
No 50
>KOG0978 consensus E3 ubiquitin ligase involved in syntaxin degradation [Posttranslational modification, protein turnover, chaperones]
Probab=96.54 E-value=0.00072 Score=68.83 Aligned_cols=47 Identities=28% Similarity=0.721 Sum_probs=40.5
Q ss_pred CCCcchhhhcccCCceeEEcCCCCcccHHHHHHHHhcCCCCCCCCCcCccc
Q 025507 140 HDCPVCCEYLFETRQDVIVLPCGHTIHKNCLKEMREHHQYACPICSKSVCD 190 (251)
Q Consensus 140 ~~CpICle~lf~s~~~~~~lpCgH~fH~~Ci~~wl~~~~~~CP~Cr~~~~~ 190 (251)
..||+|-. ...+.++..|||.|+.+|+++.+.....+||.|..+|+.
T Consensus 644 LkCs~Cn~----R~Kd~vI~kC~H~FC~~Cvq~r~etRqRKCP~Cn~aFga 690 (698)
T KOG0978|consen 644 LKCSVCNT----RWKDAVITKCGHVFCEECVQTRYETRQRKCPKCNAAFGA 690 (698)
T ss_pred eeCCCccC----chhhHHHHhcchHHHHHHHHHHHHHhcCCCCCCCCCCCc
Confidence 57999985 445677889999999999999988778899999999974
No 51
>PF11789 zf-Nse: Zinc-finger of the MIZ type in Nse subunit; PDB: 2YU4_A 3HTK_C.
Probab=96.35 E-value=0.0028 Score=44.95 Aligned_cols=44 Identities=27% Similarity=0.619 Sum_probs=29.1
Q ss_pred CCCCCCcchhhhcccCCceeEEcCCCCcccHHHHHHHHhc-CCCCCCC
Q 025507 137 AMHHDCPVCCEYLFETRQDVIVLPCGHTIHKNCLKEMREH-HQYACPI 183 (251)
Q Consensus 137 ~~~~~CpICle~lf~s~~~~~~lpCgH~fH~~Ci~~wl~~-~~~~CP~ 183 (251)
.....|||-+.. +. +++....|||+|-++.|.+||+. ....||+
T Consensus 9 ~~~~~CPiT~~~-~~--~PV~s~~C~H~fek~aI~~~i~~~~~~~CPv 53 (57)
T PF11789_consen 9 TISLKCPITLQP-FE--DPVKSKKCGHTFEKEAILQYIQRNGSKRCPV 53 (57)
T ss_dssp B--SB-TTTSSB--S--SEEEESSS--EEEHHHHHHHCTTTS-EE-SC
T ss_pred EeccCCCCcCCh-hh--CCcCcCCCCCeecHHHHHHHHHhcCCCCCCC
Confidence 345789999985 43 36777899999999999999943 4567998
No 52
>KOG1941 consensus Acetylcholine receptor-associated protein of the synapse (rapsyn) [Extracellular structures]
Probab=96.21 E-value=0.0013 Score=62.90 Aligned_cols=56 Identities=36% Similarity=0.744 Sum_probs=45.7
Q ss_pred ccccCCCCCCCCcchhhhcccCCceeEEcCCCCcccHHHHHHHHhc-CCCCCCCCCcC
Q 025507 131 HPCVEGAMHHDCPVCCEYLFETRQDVIVLPCGHTIHKNCLKEMREH-HQYACPICSKS 187 (251)
Q Consensus 131 H~C~e~~~~~~CpICle~lf~s~~~~~~lpCgH~fH~~Ci~~wl~~-~~~~CP~Cr~~ 187 (251)
|.|++ +++-.|-.|.|.+-..++....|||.|.||..|+.++|.. ...+||-||+-
T Consensus 358 ~~~~~-e~~L~Cg~CGe~~Glk~e~LqALpCsHIfH~rCl~e~L~~n~~rsCP~Crkl 414 (518)
T KOG1941|consen 358 HECVE-ETELYCGLCGESIGLKNERLQALPCSHIFHLRCLQEILENNGTRSCPNCRKL 414 (518)
T ss_pred HHHHH-HHhhhhhhhhhhhcCCcccccccchhHHHHHHHHHHHHHhCCCCCCccHHHH
Confidence 56664 4678999999987777777888999999999999998764 44679999943
No 53
>KOG0824 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=96.17 E-value=0.0027 Score=58.80 Aligned_cols=50 Identities=18% Similarity=0.429 Sum_probs=39.7
Q ss_pred CCCCCCCcchhhhcccCCceeEEcCCCCcccHHHHHHHHhcCCCCCCCCCcCcc
Q 025507 136 GAMHHDCPVCCEYLFETRQDVIVLPCGHTIHKNCLKEMREHHQYACPICSKSVC 189 (251)
Q Consensus 136 ~~~~~~CpICle~lf~s~~~~~~lpCgH~fH~~Ci~~wl~~~~~~CP~Cr~~~~ 189 (251)
+.+..+|+||+... .-++.|+|+|.|+..||+--.+.+...||+||.++.
T Consensus 4 ~~~~~eC~IC~nt~----n~Pv~l~C~HkFCyiCiKGsy~ndk~~CavCR~pid 53 (324)
T KOG0824|consen 4 RTKKKECLICYNTG----NCPVNLYCFHKFCYICIKGSYKNDKKTCAVCRFPID 53 (324)
T ss_pred cccCCcceeeeccC----CcCccccccchhhhhhhcchhhcCCCCCceecCCCC
Confidence 34577999999742 234789999999999999855545677999999886
No 54
>KOG2879 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=95.98 E-value=0.0056 Score=56.12 Aligned_cols=53 Identities=26% Similarity=0.668 Sum_probs=41.1
Q ss_pred CCCCCCcchhhhcccCCceeEEcCCCCcccHHHHHHHHhc-CCCCCCCCCcCccchh
Q 025507 137 AMHHDCPVCCEYLFETRQDVIVLPCGHTIHKNCLKEMREH-HQYACPICSKSVCDMS 192 (251)
Q Consensus 137 ~~~~~CpICle~lf~s~~~~~~lpCgH~fH~~Ci~~wl~~-~~~~CP~Cr~~~~~~~ 192 (251)
+.+.+||+|.|+ +..|.+..+|||.++--|+..-... ..++||.|+.++..+.
T Consensus 237 t~~~~C~~Cg~~---PtiP~~~~~C~HiyCY~Ci~ts~~~~asf~Cp~Cg~~~~~lq 290 (298)
T KOG2879|consen 237 TSDTECPVCGEP---PTIPHVIGKCGHIYCYYCIATSRLWDASFTCPLCGENVEPLQ 290 (298)
T ss_pred cCCceeeccCCC---CCCCeeeccccceeehhhhhhhhcchhhcccCccCCCCcchh
Confidence 456799999985 4456677799999999999984332 3589999998877653
No 55
>KOG1785 consensus Tyrosine kinase negative regulator CBL [Defense mechanisms]
Probab=95.97 E-value=0.0022 Score=61.57 Aligned_cols=54 Identities=30% Similarity=0.765 Sum_probs=42.9
Q ss_pred cccCCCCCCCCcchhhhcccCCceeEEcCCCCcccHHHHHHHHhcC-CCCCCCCCcCcc
Q 025507 132 PCVEGAMHHDCPVCCEYLFETRQDVIVLPCGHTIHKNCLKEMREHH-QYACPICSKSVC 189 (251)
Q Consensus 132 ~C~e~~~~~~CpICle~lf~s~~~~~~lpCgH~fH~~Ci~~wl~~~-~~~CP~Cr~~~~ 189 (251)
.|.-+++-..|-||-| +.+++.+=||||.++..|+..|-.++ ...||.||-.+.
T Consensus 362 YceMgsTFeLCKICae----ndKdvkIEPCGHLlCt~CLa~WQ~sd~gq~CPFCRcEIK 416 (563)
T KOG1785|consen 362 YCEMGSTFELCKICAE----NDKDVKIEPCGHLLCTSCLAAWQDSDEGQTCPFCRCEIK 416 (563)
T ss_pred HHHccchHHHHHHhhc----cCCCcccccccchHHHHHHHhhcccCCCCCCCceeeEec
Confidence 3555667788999998 45567788999999999999996443 578999996653
No 56
>COG5219 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=95.86 E-value=0.0042 Score=65.01 Aligned_cols=53 Identities=21% Similarity=0.570 Sum_probs=37.7
Q ss_pred CCCCCCcchhhhcc--cCCcee-EEcCCCCcccHHHHHHHHhc-CCCCCCCCCcCcc
Q 025507 137 AMHHDCPVCCEYLF--ETRQDV-IVLPCGHTIHKNCLKEMREH-HQYACPICSKSVC 189 (251)
Q Consensus 137 ~~~~~CpICle~lf--~s~~~~-~~lpCgH~fH~~Ci~~wl~~-~~~~CP~Cr~~~~ 189 (251)
+...+||||..-|. +..-|. +-..|.|.||..|+-+|+++ ++.+||+||.++.
T Consensus 1467 sG~eECaICYsvL~~vdr~lPskrC~TCknKFH~~CLyKWf~Ss~~s~CPlCRseit 1523 (1525)
T COG5219 1467 SGHEECAICYSVLDMVDRSLPSKRCATCKNKFHTRCLYKWFASSARSNCPLCRSEIT 1523 (1525)
T ss_pred CCcchhhHHHHHHHHHhccCCccccchhhhhhhHHHHHHHHHhcCCCCCCccccccc
Confidence 55789999986432 111111 12358899999999999876 4678999997764
No 57
>PF12906 RINGv: RING-variant domain; PDB: 2D8S_A 1VYX_A.
Probab=95.62 E-value=0.0066 Score=41.30 Aligned_cols=41 Identities=29% Similarity=0.752 Sum_probs=26.3
Q ss_pred CcchhhhcccCCceeEEcCCC-----CcccHHHHHHHHhc-CCCCCCCC
Q 025507 142 CPVCCEYLFETRQDVIVLPCG-----HTIHKNCLKEMREH-HQYACPIC 184 (251)
Q Consensus 142 CpICle~lf~s~~~~~~lpCg-----H~fH~~Ci~~wl~~-~~~~CP~C 184 (251)
|-||++...++ +..+.||+ -..|.+||..|+.. ++.+|++|
T Consensus 1 CrIC~~~~~~~--~~li~pC~C~Gs~~~vH~~CL~~W~~~~~~~~C~~C 47 (47)
T PF12906_consen 1 CRICLEGEEED--EPLISPCRCKGSMKYVHRSCLERWIRESGNRKCEIC 47 (47)
T ss_dssp ETTTTEE-SSS--S-EE-SSS-SSCCGSEECCHHHHHHHHHT-SB-TTT
T ss_pred CeEeCCcCCCC--CceecccccCCCcchhHHHHHHHHHHhcCCCcCCCC
Confidence 45888753332 35667885 46899999999875 45679987
No 58
>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional
Probab=95.49 E-value=0.012 Score=42.13 Aligned_cols=47 Identities=36% Similarity=0.861 Sum_probs=33.6
Q ss_pred cceeecCCCCcccc-----ccccCcCCCCccceEecCccccccCCCCCCeeecCCCCc
Q 025507 52 VNQVICSLCGTEQK-----VQQVCVNCGVCMGEYFCESCKLFDDDTSKKQYHCDGCGI 104 (251)
Q Consensus 52 ~~~v~C~~C~~~q~-----~~~~C~~Cg~~f~~y~C~~C~~~d~~~~k~~~HC~~Cgi 104 (251)
.....|..|+.+.. +.-.|||||.. -=|-|.+|+-+. ..|.|++||+
T Consensus 5 ~~~~~CtSCg~~i~~~~~~~~F~CPnCG~~-~I~RC~~CRk~~-----~~Y~CP~CGF 56 (59)
T PRK14890 5 MEPPKCTSCGIEIAPREKAVKFLCPNCGEV-IIYRCEKCRKQS-----NPYTCPKCGF 56 (59)
T ss_pred ccCccccCCCCcccCCCccCEeeCCCCCCe-eEeechhHHhcC-----CceECCCCCC
Confidence 34567889987764 23479999985 124489998765 4799999985
No 59
>KOG0825 consensus PHD Zn-finger protein [General function prediction only]
Probab=95.34 E-value=0.006 Score=62.73 Aligned_cols=50 Identities=14% Similarity=0.369 Sum_probs=39.5
Q ss_pred CCCCCcchhhhcccCCceeEEcCCCCcccHHHHHHHHhcCCCCCCCCCcCcc
Q 025507 138 MHHDCPVCCEYLFETRQDVIVLPCGHTIHKNCLKEMREHHQYACPICSKSVC 189 (251)
Q Consensus 138 ~~~~CpICle~lf~s~~~~~~lpCgH~fH~~Ci~~wl~~~~~~CP~Cr~~~~ 189 (251)
....||+|+.. +.........+|+|.||.+||..|-+. ..+||++|+.|.
T Consensus 122 ~~~~CP~Ci~s-~~DqL~~~~k~c~H~FC~~Ci~sWsR~-aqTCPiDR~EF~ 171 (1134)
T KOG0825|consen 122 VENQCPNCLKS-CNDQLEESEKHTAHYFCEECVGSWSRC-AQTCPVDRGEFG 171 (1134)
T ss_pred hhhhhhHHHHH-HHHHhhccccccccccHHHHhhhhhhh-cccCchhhhhhh
Confidence 35689999974 443433445689999999999999874 479999999886
No 60
>KOG1645 consensus RING-finger-containing E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=95.14 E-value=0.024 Score=54.64 Aligned_cols=50 Identities=24% Similarity=0.737 Sum_probs=38.2
Q ss_pred CCCCcchhhhcccCC-ceeEEcCCCCcccHHHHHHHHhc-CCCCCCCCCcCc
Q 025507 139 HHDCPVCCEYLFETR-QDVIVLPCGHTIHKNCLKEMREH-HQYACPICSKSV 188 (251)
Q Consensus 139 ~~~CpICle~lf~s~-~~~~~lpCgH~fH~~Ci~~wl~~-~~~~CP~Cr~~~ 188 (251)
...|||||+..-.++ ...+.|.|||.|=..||+.||.. ...+||.|....
T Consensus 4 g~tcpiclds~~~~g~hr~vsl~cghlFgs~cie~wl~k~~~~~cp~c~~ka 55 (463)
T KOG1645|consen 4 GTTCPICLDSYTTAGNHRIVSLQCGHLFGSQCIEKWLGKKTKMQCPLCSGKA 55 (463)
T ss_pred cccCceeeeeeeecCceEEeeecccccccHHHHHHHHhhhhhhhCcccCChh
Confidence 358999998765444 34567899999999999999952 235699999554
No 61
>KOG1428 consensus Inhibitor of type V adenylyl cyclases/Neuronal presynaptic protein Highwire/PAM/RPM-1 [Signal transduction mechanisms]
Probab=94.71 E-value=0.031 Score=61.02 Aligned_cols=74 Identities=27% Similarity=0.577 Sum_probs=53.5
Q ss_pred cCCcceeeccCCCcceeccccccccccCCCCCCCCcchhhhcccCCceeEEcCCCCcccHHHHHHHHhc---------CC
Q 025507 108 GGCDNFFHCNKCRCCYSMLLKNSHPCVEGAMHHDCPVCCEYLFETRQDVIVLPCGHTIHKNCLKEMREH---------HQ 178 (251)
Q Consensus 108 g~~~~~fHC~~C~~c~~~~l~~~H~C~e~~~~~~CpICle~lf~s~~~~~~lpCgH~fH~~Ci~~wl~~---------~~ 178 (251)
||.+|-.||.-|-.|-.-.. ....++.|.||+-+ ..+..+...|.|||.||.+|....|.. +-
T Consensus 3462 GGvkNEE~CLPCl~Cdks~t-------kQD~DDmCmICFTE-~L~AAP~IqL~C~HiFHlqC~R~vLE~RW~GPRItF~F 3533 (3738)
T KOG1428|consen 3462 GGVKNEEHCLPCLHCDKSAT-------KQDADDMCMICFTE-ALSAAPAIQLDCSHIFHLQCCRRVLENRWLGPRITFGF 3533 (3738)
T ss_pred cCccchhhcccccccChhhh-------hcccCceEEEEehh-hhCCCcceecCCccchhHHHHHHHHHhcccCCeeEEee
Confidence 56678888888877754322 22457789999964 334557788999999999999876653 12
Q ss_pred CCCCCCCcCcc
Q 025507 179 YACPICSKSVC 189 (251)
Q Consensus 179 ~~CP~Cr~~~~ 189 (251)
.+||+|...+.
T Consensus 3534 isCPiC~n~In 3544 (3738)
T KOG1428|consen 3534 ISCPICKNKIN 3544 (3738)
T ss_pred eecccccchhh
Confidence 46999998765
No 62
>KOG4159 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=94.60 E-value=0.037 Score=53.44 Aligned_cols=49 Identities=27% Similarity=0.756 Sum_probs=39.1
Q ss_pred CCCCCCcchhhhcccCCceeEEcCCCCcccHHHHHHHHhcCCCCCCCCCcCccc
Q 025507 137 AMHHDCPVCCEYLFETRQDVIVLPCGHTIHKNCLKEMREHHQYACPICSKSVCD 190 (251)
Q Consensus 137 ~~~~~CpICle~lf~s~~~~~~lpCgH~fH~~Ci~~wl~~~~~~CP~Cr~~~~~ 190 (251)
..+..|.||+.- +- +++++||||+|+..||..-+. ...-||+||..+..
T Consensus 82 ~sef~c~vc~~~-l~---~pv~tpcghs~c~~Cl~r~ld-~~~~cp~Cr~~l~e 130 (398)
T KOG4159|consen 82 RSEFECCVCSRA-LY---PPVVTPCGHSFCLECLDRSLD-QETECPLCRDELVE 130 (398)
T ss_pred cchhhhhhhHhh-cC---CCccccccccccHHHHHHHhc-cCCCCccccccccc
Confidence 557799999984 43 355669999999999999766 45779999988874
No 63
>KOG4185 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=94.51 E-value=0.035 Score=50.70 Aligned_cols=49 Identities=31% Similarity=0.707 Sum_probs=38.2
Q ss_pred CCCcchhhhcccC--CceeEEcCCCCcccHHHHHHHHhcCCCCCCCCCcCc
Q 025507 140 HDCPVCCEYLFET--RQDVIVLPCGHTIHKNCLKEMREHHQYACPICSKSV 188 (251)
Q Consensus 140 ~~CpICle~lf~s--~~~~~~lpCgH~fH~~Ci~~wl~~~~~~CP~Cr~~~ 188 (251)
..|-||-+++... ...+..|.|||+|...|+...+......||.||.+.
T Consensus 4 ~~c~~c~~~~s~~~~~~~p~~l~c~h~~c~~c~~~l~~~~~i~cpfcR~~~ 54 (296)
T KOG4185|consen 4 PECEICNEDYSSEDGDHIPRVLKCGHTICQNCASKLLGNSRILCPFCRETT 54 (296)
T ss_pred CceeecCccccccCcccCCcccccCceehHhHHHHHhcCceeeccCCCCcc
Confidence 3577888764332 234567899999999999999987777799999985
No 64
>COG5175 MOT2 Transcriptional repressor [Transcription]
Probab=94.39 E-value=0.013 Score=55.35 Aligned_cols=57 Identities=26% Similarity=0.604 Sum_probs=44.3
Q ss_pred CCCCcchhhhcccCCceeEEcCCCCcccHHHHHHHHhcCCCCCCCCCcCccchhHHH
Q 025507 139 HHDCPVCCEYLFETRQDVIVLPCGHTIHKNCLKEMREHHQYACPICSKSVCDMSKVW 195 (251)
Q Consensus 139 ~~~CpICle~lf~s~~~~~~lpCgH~fH~~Ci~~wl~~~~~~CP~Cr~~~~~~~~~~ 195 (251)
++-||.|+|+|-.+......-|||-.+++-|+....+.-+-+||-||+...+-+..|
T Consensus 14 ed~cplcie~mditdknf~pc~cgy~ic~fc~~~irq~lngrcpacrr~y~denv~~ 70 (480)
T COG5175 14 EDYCPLCIEPMDITDKNFFPCPCGYQICQFCYNNIRQNLNGRCPACRRKYDDENVRY 70 (480)
T ss_pred cccCcccccccccccCCcccCCcccHHHHHHHHHHHhhccCCChHhhhhccccceeE
Confidence 345999999987776666666899999999988876655678999999887644333
No 65
>PF10367 Vps39_2: Vacuolar sorting protein 39 domain 2; InterPro: IPR019453 This entry represents a domain found in the vacuolar sorting protein Vps39 and transforming growth factor beta receptor-associated protein Trap1. Vps39, a component of the C-Vps complex, is thought to be required for the fusion of endosomes and other types of transport intermediates with the vacuole [, ]. In Saccharomyces cerevisiae (Baker's yeast), Vps39 has been shown to stimulate nucleotide exchange []. Trap1 plays a role in the TGF-beta/activin signaling pathway. It associates with inactive heteromeric TGF-beta and activin receptor complexes, mainly through the type II receptor, and is released upon activation of signaling [, ]. The precise function of this domain has not been characterised In Vps39 this domain is involved in localisation and in mediating the interactions with Vps11 [].
Probab=94.38 E-value=0.019 Score=44.05 Aligned_cols=33 Identities=36% Similarity=0.850 Sum_probs=27.2
Q ss_pred CCCCCCcchhhhcccCCceeEEcCCCCcccHHHHH
Q 025507 137 AMHHDCPVCCEYLFETRQDVIVLPCGHTIHKNCLK 171 (251)
Q Consensus 137 ~~~~~CpICle~lf~s~~~~~~lpCgH~fH~~Ci~ 171 (251)
..+..|+||...|.. ....+.||||.||..|++
T Consensus 76 ~~~~~C~vC~k~l~~--~~f~~~p~~~v~H~~C~~ 108 (109)
T PF10367_consen 76 TESTKCSVCGKPLGN--SVFVVFPCGHVVHYSCIK 108 (109)
T ss_pred CCCCCccCcCCcCCC--ceEEEeCCCeEEeccccc
Confidence 446789999998766 367788999999999975
No 66
>PF14447 Prok-RING_4: Prokaryotic RING finger family 4
Probab=94.23 E-value=0.02 Score=40.45 Aligned_cols=33 Identities=39% Similarity=0.785 Sum_probs=26.5
Q ss_pred eeEEcCCCCcccHHHHHHHHhcCCCCCCCCCcCccc
Q 025507 155 DVIVLPCGHTIHKNCLKEMREHHQYACPICSKSVCD 190 (251)
Q Consensus 155 ~~~~lpCgH~fH~~Ci~~wl~~~~~~CP~Cr~~~~~ 190 (251)
.-.++||||.+...|+.-+-- .-||+|.+++..
T Consensus 19 ~~~~~pCgH~I~~~~f~~~rY---ngCPfC~~~~~~ 51 (55)
T PF14447_consen 19 KGTVLPCGHLICDNCFPGERY---NGCPFCGTPFEF 51 (55)
T ss_pred ccccccccceeeccccChhhc---cCCCCCCCcccC
Confidence 456889999999999887732 359999998864
No 67
>KOG0297 consensus TNF receptor-associated factor [Signal transduction mechanisms]
Probab=93.96 E-value=0.034 Score=53.49 Aligned_cols=49 Identities=29% Similarity=0.702 Sum_probs=39.0
Q ss_pred CCCCCcchhhhcccCCceeEEcCCCCcccHHHHHHHHhcCCCCCCCCCcCccc
Q 025507 138 MHHDCPVCCEYLFETRQDVIVLPCGHTIHKNCLKEMREHHQYACPICSKSVCD 190 (251)
Q Consensus 138 ~~~~CpICle~lf~s~~~~~~lpCgH~fH~~Ci~~wl~~~~~~CP~Cr~~~~~ 190 (251)
.+..||+|..-+.+ ++....|||.|+..|+..|+.. +..||.|+..+..
T Consensus 20 ~~l~C~~C~~vl~~---p~~~~~cgh~fC~~C~~~~~~~-~~~cp~~~~~~~~ 68 (391)
T KOG0297|consen 20 ENLLCPICMSVLRD---PVQTTTCGHRFCAGCLLESLSN-HQKCPVCRQELTQ 68 (391)
T ss_pred ccccCccccccccC---CCCCCCCCCcccccccchhhcc-CcCCcccccccch
Confidence 35789999975333 3444689999999999999986 7899999987764
No 68
>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=93.79 E-value=0.049 Score=50.33 Aligned_cols=49 Identities=20% Similarity=0.522 Sum_probs=39.1
Q ss_pred CCcchhhhcccCCceeEE-cCCCCcccHHHHHHHHhcCCCCCCCCCcCcc
Q 025507 141 DCPVCCEYLFETRQDVIV-LPCGHTIHKNCLKEMREHHQYACPICSKSVC 189 (251)
Q Consensus 141 ~CpICle~lf~s~~~~~~-lpCgH~fH~~Ci~~wl~~~~~~CP~Cr~~~~ 189 (251)
.||+|.-+...+++-... =+|||.++.+|++..+..+.+.||.|.+.+.
T Consensus 2 ~Cp~CKt~~Y~np~lk~~in~C~H~lCEsCvd~iF~~g~~~CpeC~~iLR 51 (300)
T KOG3800|consen 2 ACPKCKTDRYLNPDLKLMINECGHRLCESCVDRIFSLGPAQCPECMVILR 51 (300)
T ss_pred CCcccccceecCccceeeeccccchHHHHHHHHHHhcCCCCCCcccchhh
Confidence 589998766666543322 2999999999999998888899999997765
No 69
>PF05883 Baculo_RING: Baculovirus U-box/Ring-like domain; InterPro: IPR008573 This family consists of several Baculovirus proteins of around 130 residues in length. The function of this family is unknown, but it appears to be related to the U-box and ring finger domain by profile-profile comparison.
Probab=93.69 E-value=0.033 Score=46.09 Aligned_cols=35 Identities=20% Similarity=0.514 Sum_probs=29.8
Q ss_pred CCCCcchhhhcccCCceeEEcCCC------CcccHHHHHHHH
Q 025507 139 HHDCPVCCEYLFETRQDVIVLPCG------HTIHKNCLKEMR 174 (251)
Q Consensus 139 ~~~CpICle~lf~s~~~~~~lpCg------H~fH~~Ci~~wl 174 (251)
..+|.||++.+-+ ...++.+++| |.||.+|++.|-
T Consensus 26 ~~EC~IC~~~I~~-~~GvV~vt~~g~lnLEkmfc~~C~~rw~ 66 (134)
T PF05883_consen 26 TVECQICFDRIDN-NDGVVYVTDGGTLNLEKMFCADCDKRWR 66 (134)
T ss_pred Ceeehhhhhhhhc-CCCEEEEecCCeehHHHHHHHHHHHHHH
Confidence 4689999998766 5678888997 889999999993
No 70
>KOG1571 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=93.67 E-value=0.039 Score=52.28 Aligned_cols=48 Identities=25% Similarity=0.598 Sum_probs=34.9
Q ss_pred CCCCCCCCcchhhhcccCCceeEEcCCCCcccHHHHHHHHhcCCCCCCCCCcCccc
Q 025507 135 EGAMHHDCPVCCEYLFETRQDVIVLPCGHTIHKNCLKEMREHHQYACPICSKSVCD 190 (251)
Q Consensus 135 e~~~~~~CpICle~lf~s~~~~~~lpCgH~fH~~Ci~~wl~~~~~~CP~Cr~~~~~ 190 (251)
|.+....|.||++. +...+.+||||.-+ |..-... ..+||+||..+.-
T Consensus 301 ~~~~p~lcVVcl~e----~~~~~fvpcGh~cc--ct~cs~~--l~~CPvCR~rI~~ 348 (355)
T KOG1571|consen 301 ELPQPDLCVVCLDE----PKSAVFVPCGHVCC--CTLCSKH--LPQCPVCRQRIRL 348 (355)
T ss_pred ccCCCCceEEecCC----ccceeeecCCcEEE--chHHHhh--CCCCchhHHHHHH
Confidence 45667899999984 33477999999966 6555433 3569999976653
No 71
>KOG4445 consensus Uncharacterized conserved protein, contains RWD domain [Function unknown]
Probab=93.65 E-value=0.023 Score=52.87 Aligned_cols=52 Identities=23% Similarity=0.573 Sum_probs=40.3
Q ss_pred CCCCCCcchhhhcccCCceeEEcCCCCcccHHHHHHHHhc----------------------CCCCCCCCCcCcc
Q 025507 137 AMHHDCPVCCEYLFETRQDVIVLPCGHTIHKNCLKEMREH----------------------HQYACPICSKSVC 189 (251)
Q Consensus 137 ~~~~~CpICle~lf~s~~~~~~lpCgH~fH~~Ci~~wl~~----------------------~~~~CP~Cr~~~~ 189 (251)
--.+.|.|||- =|.+.....+.+|-|+||..||..+|.. ....||+||..+.
T Consensus 113 ~p~gqCvICLy-gfa~~~~ft~T~C~Hy~H~~ClaRyl~~~~~~lrqe~q~~~~~~qh~~~~~eavcpVcre~i~ 186 (368)
T KOG4445|consen 113 HPNGQCVICLY-GFASSPAFTVTACDHYMHFACLARYLTECLTGLRQEIQDAQKERQHMKEQVEAVCPVCRERIK 186 (368)
T ss_pred CCCCceEEEEE-eecCCCceeeehhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhHhhhhhHhhhhcc
Confidence 34679999995 4666666888899999999999988751 1235999997775
No 72
>KOG4275 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=93.26 E-value=0.013 Score=54.37 Aligned_cols=55 Identities=27% Similarity=0.690 Sum_probs=37.3
Q ss_pred cccccccCCCC---CCCCcchhhhcccCCceeEEcCCCCcc-cHHHHHHHHhcCCCCCCCCCcCccch
Q 025507 128 KNSHPCVEGAM---HHDCPVCCEYLFETRQDVIVLPCGHTI-HKNCLKEMREHHQYACPICSKSVCDM 191 (251)
Q Consensus 128 ~~~H~C~e~~~---~~~CpICle~lf~s~~~~~~lpCgH~f-H~~Ci~~wl~~~~~~CP~Cr~~~~~~ 191 (251)
+++|.+-.... +..|.||++ .+.+-+.|+|||.. +.+|-+.+ ..|||||+-+...
T Consensus 286 k~~~g~~~~~s~~~~~LC~ICmD----aP~DCvfLeCGHmVtCt~CGkrm-----~eCPICRqyi~rv 344 (350)
T KOG4275|consen 286 KGNDGEQHSRSLATRRLCAICMD----APRDCVFLECGHMVTCTKCGKRM-----NECPICRQYIVRV 344 (350)
T ss_pred hcccccccccchhHHHHHHHHhc----CCcceEEeecCcEEeehhhcccc-----ccCchHHHHHHHH
Confidence 34444443333 778999997 46678999999973 55565544 2699999765543
No 73
>KOG3970 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=93.01 E-value=0.14 Score=46.08 Aligned_cols=50 Identities=32% Similarity=0.687 Sum_probs=39.6
Q ss_pred CCCCCcchhhhcccCCceeEEcCCCCcccHHHHHHHHhc-------CCCCCCCCCcCcc
Q 025507 138 MHHDCPVCCEYLFETRQDVIVLPCGHTIHKNCLKEMREH-------HQYACPICSKSVC 189 (251)
Q Consensus 138 ~~~~CpICle~lf~s~~~~~~lpCgH~fH~~Ci~~wl~~-------~~~~CP~Cr~~~~ 189 (251)
-..+|..|.-.|.. + +.+.|.|=|.||..|+++|... ..|+||-|..++.
T Consensus 49 Y~pNC~LC~t~La~-g-dt~RLvCyhlfHW~ClneraA~lPanTAPaGyqCP~Cs~eiF 105 (299)
T KOG3970|consen 49 YNPNCRLCNTPLAS-G-DTTRLVCYHLFHWKCLNERAANLPANTAPAGYQCPCCSQEIF 105 (299)
T ss_pred CCCCCceeCCcccc-C-cceeehhhhhHHHHHhhHHHhhCCCcCCCCcccCCCCCCccC
Confidence 46799999976544 4 3456789999999999999653 2589999998875
No 74
>KOG3268 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=92.98 E-value=0.058 Score=46.93 Aligned_cols=31 Identities=29% Similarity=0.808 Sum_probs=25.0
Q ss_pred cCCCCcccHHHHHHHHhc-----CC-----CCCCCCCcCcc
Q 025507 159 LPCGHTIHKNCLKEMREH-----HQ-----YACPICSKSVC 189 (251)
Q Consensus 159 lpCgH~fH~~Ci~~wl~~-----~~-----~~CP~Cr~~~~ 189 (251)
..||-.||.-|+..||+. .+ -.||.|.+++.
T Consensus 188 ~qCgkpFHqiCL~dWLRgilTsRQSFdiiFGeCPYCS~Pia 228 (234)
T KOG3268|consen 188 IQCGKPFHQICLTDWLRGILTSRQSFDIIFGECPYCSDPIA 228 (234)
T ss_pred cccCCcHHHHHHHHHHHHHhhccceeeeeeccCCCCCCcce
Confidence 479999999999999974 11 24999999874
No 75
>KOG3002 consensus Zn finger protein [General function prediction only]
Probab=92.45 E-value=0.16 Score=47.29 Aligned_cols=60 Identities=25% Similarity=0.605 Sum_probs=44.0
Q ss_pred CCCCcchhhhcccCCceeEEcCC--CCcccHHHHHHHHhcCCCCCCCCCcCccchhHHHHHHHHHHhcCCCCH
Q 025507 139 HHDCPVCCEYLFETRQDVIVLPC--GHTIHKNCLKEMREHHQYACPICSKSVCDMSKVWEKYDREIAATPMPE 209 (251)
Q Consensus 139 ~~~CpICle~lf~s~~~~~~lpC--gH~fH~~Ci~~wl~~~~~~CP~Cr~~~~~~~~~~~~ld~~i~~~p~P~ 209 (251)
-.+||||.++|.. + ++.| ||..+..|-.+. ...||.||.++++... +.|+..+++...|=
T Consensus 48 lleCPvC~~~l~~---P--i~QC~nGHlaCssC~~~~----~~~CP~Cr~~~g~~R~--~amEkV~e~~~vpC 109 (299)
T KOG3002|consen 48 LLDCPVCFNPLSP---P--IFQCDNGHLACSSCRTKV----SNKCPTCRLPIGNIRC--RAMEKVAEAVLVPC 109 (299)
T ss_pred hccCchhhccCcc---c--ceecCCCcEehhhhhhhh----cccCCccccccccHHH--HHHHHHHHhceecc
Confidence 4689999997644 2 4456 899999998754 3679999999997533 34666677666653
No 76
>KOG1814 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=92.34 E-value=0.17 Score=48.97 Aligned_cols=46 Identities=30% Similarity=0.551 Sum_probs=36.5
Q ss_pred CCCCcchhhhcccCCceeEEcCCCCcccHHHHHHHHhc-------CCCCCCCCC
Q 025507 139 HHDCPVCCEYLFETRQDVIVLPCGHTIHKNCLKEMREH-------HQYACPICS 185 (251)
Q Consensus 139 ~~~CpICle~lf~s~~~~~~lpCgH~fH~~Ci~~wl~~-------~~~~CP~Cr 185 (251)
-..|-||++ .+.+......|||+|.|++.|+..|... ...+||-+.
T Consensus 184 lf~C~ICf~-e~~G~~c~~~lpC~Hv~Ck~C~kdY~~~~i~eg~v~~l~Cp~~~ 236 (445)
T KOG1814|consen 184 LFDCCICFE-EQMGQHCFKFLPCSHVFCKSCLKDYFTIQIQEGQVSCLKCPDPK 236 (445)
T ss_pred cccceeeeh-hhcCcceeeecccchHHHHHHHHHHHHHhhhcceeeeecCCCCC
Confidence 468999998 4666667888999999999999998642 245798766
No 77
>PF12773 DZR: Double zinc ribbon
Probab=91.99 E-value=0.16 Score=34.22 Aligned_cols=22 Identities=32% Similarity=0.845 Sum_probs=14.6
Q ss_pred cCCCCccccc-cccCcCCCCccc
Q 025507 57 CSLCGTEQKV-QQVCVNCGVCMG 78 (251)
Q Consensus 57 C~~C~~~q~~-~~~C~~Cg~~f~ 78 (251)
|..|+++.+. +..|++||+.+.
T Consensus 1 Cp~Cg~~~~~~~~fC~~CG~~l~ 23 (50)
T PF12773_consen 1 CPHCGTPNPDDAKFCPHCGTPLP 23 (50)
T ss_pred CCCcCCcCCccccCChhhcCChh
Confidence 4566666654 567777777776
No 78
>TIGR00100 hypA hydrogenase nickel insertion protein HypA. In Hpylori, hypA mutant abolished hydrogenase activity and decrease in urease activity. Nickel supplementation in media restored urease activity and partial hydrogenase activity. HypA probably involved in inserting Ni in enzymes.
Probab=91.40 E-value=0.14 Score=41.02 Aligned_cols=35 Identities=23% Similarity=0.601 Sum_probs=28.2
Q ss_pred ceeEEcCCCCCCccccceeeeccCCCCCCccccccCC
Q 025507 215 KVWILCNDCGKTSNVQFHVLAQKCPNCKSYNTRLTRG 251 (251)
Q Consensus 215 ~~~IlCndC~~~s~~~~h~lg~kC~~C~SyNT~~~~~ 251 (251)
.+...|++|+.......+ ...||.|+|+++++++|
T Consensus 68 p~~~~C~~Cg~~~~~~~~--~~~CP~Cgs~~~~i~~G 102 (115)
T TIGR00100 68 PVECECEDCSEEVSPEID--LYRCPKCHGIMLQVRAG 102 (115)
T ss_pred CcEEEcccCCCEEecCCc--CccCcCCcCCCcEEecC
Confidence 567899999987766533 35799999999998876
No 79
>KOG1813 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=91.40 E-value=0.13 Score=47.74 Aligned_cols=65 Identities=20% Similarity=0.414 Sum_probs=45.1
Q ss_pred CCCCCCcchhhhcccCCceeEEcCCCCcccHHHHHHHHhcCCCCCCCCCcCccchhHHHHHHHHHHhcCC
Q 025507 137 AMHHDCPVCCEYLFETRQDVIVLPCGHTIHKNCLKEMREHHQYACPICSKSVCDMSKVWEKYDREIAATP 206 (251)
Q Consensus 137 ~~~~~CpICle~lf~s~~~~~~lpCgH~fH~~Ci~~wl~~~~~~CP~Cr~~~~~~~~~~~~ld~~i~~~p 206 (251)
.....|-||.++ |. .+++..|||.|+..|...-++. ...|++|.+.+-.....-..|...+...+
T Consensus 239 ~~Pf~c~icr~~-f~---~pVvt~c~h~fc~~ca~~~~qk-~~~c~vC~~~t~g~~~~akeL~~~L~~kk 303 (313)
T KOG1813|consen 239 LLPFKCFICRKY-FY---RPVVTKCGHYFCEVCALKPYQK-GEKCYVCSQQTHGSFNVAKELLVSLKLKK 303 (313)
T ss_pred cCCccccccccc-cc---cchhhcCCceeehhhhcccccc-CCcceecccccccccchHHHHHHHHHhhh
Confidence 345679999996 43 3567789999999999987773 57899999987643322233444444333
No 80
>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]
Probab=91.26 E-value=0.13 Score=36.95 Aligned_cols=45 Identities=36% Similarity=0.935 Sum_probs=34.1
Q ss_pred eeecCCCCcccc-----ccccCcCCCCccceEecCccccccCCCCCCeeecCCCCc
Q 025507 54 QVICSLCGTEQK-----VQQVCVNCGVCMGEYFCESCKLFDDDTSKKQYHCDGCGI 104 (251)
Q Consensus 54 ~v~C~~C~~~q~-----~~~~C~~Cg~~f~~y~C~~C~~~d~~~~k~~~HC~~Cgi 104 (251)
...|..|+.+.. +.-.|||||... =|-|.+|+...+ +|.|++||+
T Consensus 9 ~~~CtSCg~~i~p~e~~v~F~CPnCGe~~-I~Rc~~CRk~g~-----~Y~Cp~CGF 58 (61)
T COG2888 9 PPVCTSCGREIAPGETAVKFPCPNCGEVE-IYRCAKCRKLGN-----PYRCPKCGF 58 (61)
T ss_pred CceeccCCCEeccCCceeEeeCCCCCcee-eehhhhHHHcCC-----ceECCCcCc
Confidence 568999998873 245799999543 366888987754 799999985
No 81
>PF04641 Rtf2: Rtf2 RING-finger
Probab=91.24 E-value=0.21 Score=45.33 Aligned_cols=51 Identities=25% Similarity=0.640 Sum_probs=39.5
Q ss_pred CCCCCCCcchhhhcccCCceeEE-cCCCCcccHHHHHHHHhcCCCCCCCCCcCcc
Q 025507 136 GAMHHDCPVCCEYLFETRQDVIV-LPCGHTIHKNCLKEMREHHQYACPICSKSVC 189 (251)
Q Consensus 136 ~~~~~~CpICle~lf~s~~~~~~-lpCgH~fH~~Ci~~wl~~~~~~CP~Cr~~~~ 189 (251)
....-.|||-...| ++....+. .||||.|-...|.+.- ....||+|.+++.
T Consensus 110 ~~~~~~CPvt~~~~-~~~~~fv~l~~cG~V~s~~alke~k--~~~~Cp~c~~~f~ 161 (260)
T PF04641_consen 110 SEGRFICPVTGKEF-NGKHKFVYLRPCGCVFSEKALKELK--KSKKCPVCGKPFT 161 (260)
T ss_pred CCceeECCCCCccc-CCceeEEEEcCCCCEeeHHHHHhhc--ccccccccCCccc
Confidence 34567899999865 44445554 5999999999999983 3467999999976
No 82
>PF07800 DUF1644: Protein of unknown function (DUF1644); InterPro: IPR012866 This family consists of sequences found in a number of hypothetical plant proteins of unknown function. The region of interest contains nine highly conserved cysteine residues and is approximately 160 amino acids in length, which probably represent a zinc-binding domain.
Probab=91.05 E-value=0.24 Score=42.23 Aligned_cols=33 Identities=33% Similarity=0.879 Sum_probs=22.9
Q ss_pred CCCCcchhhhcccCCceeEEcCCC-C------------cccHHHHHHHHh
Q 025507 139 HHDCPVCCEYLFETRQDVIVLPCG-H------------TIHKNCLKEMRE 175 (251)
Q Consensus 139 ~~~CpICle~lf~s~~~~~~lpCg-H------------~fH~~Ci~~wl~ 175 (251)
+..||||||.- -..|+|-|. | .-|..||+++-+
T Consensus 2 d~~CpICme~P----HNAVLLlCSS~~kgcRpymc~Ts~rhSNCLdqfkk 47 (162)
T PF07800_consen 2 DVTCPICMEHP----HNAVLLLCSSHEKGCRPYMCDTSYRHSNCLDQFKK 47 (162)
T ss_pred CccCceeccCC----CceEEEEeccccCCccccccCCccchhHHHHHHHH
Confidence 46899999952 235566663 2 268999999854
No 83
>COG5152 Uncharacterized conserved protein, contains RING and CCCH-type Zn-fingers [General function prediction only]
Probab=90.95 E-value=0.14 Score=45.28 Aligned_cols=59 Identities=20% Similarity=0.459 Sum_probs=41.9
Q ss_pred CCCCcchhhhcccCCceeEEcCCCCcccHHHHHHHHhcCCCCCCCCCcCccchhHHHHHHHHHH
Q 025507 139 HHDCPVCCEYLFETRQDVIVLPCGHTIHKNCLKEMREHHQYACPICSKSVCDMSKVWEKYDREI 202 (251)
Q Consensus 139 ~~~CpICle~lf~s~~~~~~lpCgH~fH~~Ci~~wl~~~~~~CP~Cr~~~~~~~~~~~~ld~~i 202 (251)
...|.||.++ +.+ +++..|||.|+..|+..-.+ ....|-+|.+...-....-..++..+
T Consensus 196 PF~C~iCKkd-y~s---pvvt~CGH~FC~~Cai~~y~-kg~~C~~Cgk~t~G~f~V~~d~~kmL 254 (259)
T COG5152 196 PFLCGICKKD-YES---PVVTECGHSFCSLCAIRKYQ-KGDECGVCGKATYGRFWVVSDLQKML 254 (259)
T ss_pred ceeehhchhh-ccc---hhhhhcchhHHHHHHHHHhc-cCCcceecchhhccceeHHhhHHHHH
Confidence 4589999986 443 45778999999999888655 34789999987754333334455544
No 84
>PHA02862 5L protein; Provisional
Probab=90.24 E-value=0.2 Score=42.16 Aligned_cols=46 Identities=17% Similarity=0.455 Sum_probs=33.4
Q ss_pred CCCCcchhhhcccCCceeEEcCCC-----CcccHHHHHHHHhcC-CCCCCCCCcCcc
Q 025507 139 HHDCPVCCEYLFETRQDVIVLPCG-----HTIHKNCLKEMREHH-QYACPICSKSVC 189 (251)
Q Consensus 139 ~~~CpICle~lf~s~~~~~~lpCg-----H~fH~~Ci~~wl~~~-~~~CP~Cr~~~~ 189 (251)
...|=||.+. + .+. .-||. -..|++|+++|+... +..||+|+.++.
T Consensus 2 ~diCWIC~~~--~-~e~--~~PC~C~GS~K~VHq~CL~~WIn~S~k~~CeLCkteY~ 53 (156)
T PHA02862 2 SDICWICNDV--C-DER--NNFCGCNEEYKVVHIKCMQLWINYSKKKECNLCKTKYN 53 (156)
T ss_pred CCEEEEecCc--C-CCC--cccccccCcchhHHHHHHHHHHhcCCCcCccCCCCeEE
Confidence 4678899874 1 122 34774 469999999999863 456999998875
No 85
>PRK00564 hypA hydrogenase nickel incorporation protein; Provisional
Probab=90.02 E-value=0.22 Score=40.05 Aligned_cols=35 Identities=31% Similarity=0.630 Sum_probs=28.0
Q ss_pred ceeEEcCCCCCCcccc-ceeeeccCCCCCCccccccCC
Q 025507 215 KVWILCNDCGKTSNVQ-FHVLAQKCPNCKSYNTRLTRG 251 (251)
Q Consensus 215 ~~~IlCndC~~~s~~~-~h~lg~kC~~C~SyNT~~~~~ 251 (251)
.+.+.|++|+..+... +++ .+||.|||++..+++|
T Consensus 69 p~~~~C~~Cg~~~~~~~~~~--~~CP~Cgs~~~~i~~G 104 (117)
T PRK00564 69 KVELECKDCSHVFKPNALDY--GVCEKCHSKNVIITQG 104 (117)
T ss_pred CCEEEhhhCCCccccCCccC--CcCcCCCCCceEEecC
Confidence 5678999999877665 333 4799999999998776
No 86
>PRK03824 hypA hydrogenase nickel incorporation protein; Provisional
Probab=89.91 E-value=0.25 Score=40.74 Aligned_cols=37 Identities=27% Similarity=0.734 Sum_probs=27.5
Q ss_pred ceeEEcCCCCCCcccc-------------cee------eeccCCCCCCccccccCC
Q 025507 215 KVWILCNDCGKTSNVQ-------------FHV------LAQKCPNCKSYNTRLTRG 251 (251)
Q Consensus 215 ~~~IlCndC~~~s~~~-------------~h~------lg~kC~~C~SyNT~~~~~ 251 (251)
.....|.+|+...... +|+ ...+||.|||++..+++|
T Consensus 68 p~~~~C~~CG~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~CP~Cgs~~~~i~~G 123 (135)
T PRK03824 68 EAVLKCRNCGNEWSLKEVKESLDEEIREAIHFIPEVVHAFLKCPKCGSRDFEIVKG 123 (135)
T ss_pred ceEEECCCCCCEEecccccccccccccccccccccccccCcCCcCCCCCCcEEecC
Confidence 3678999999766443 222 336899999999988776
No 87
>PHA02825 LAP/PHD finger-like protein; Provisional
Probab=89.86 E-value=0.3 Score=41.63 Aligned_cols=47 Identities=28% Similarity=0.599 Sum_probs=33.7
Q ss_pred CCCCCcchhhhcccCCceeEEcCCCC-----cccHHHHHHHHhcC-CCCCCCCCcCcc
Q 025507 138 MHHDCPVCCEYLFETRQDVIVLPCGH-----TIHKNCLKEMREHH-QYACPICSKSVC 189 (251)
Q Consensus 138 ~~~~CpICle~lf~s~~~~~~lpCgH-----~fH~~Ci~~wl~~~-~~~CP~Cr~~~~ 189 (251)
++..|=||.+.. + ...-||.- ..|.+|++.|+..+ ..+||+|+..+.
T Consensus 7 ~~~~CRIC~~~~---~--~~~~PC~CkGs~k~VH~sCL~rWi~~s~~~~CeiC~~~Y~ 59 (162)
T PHA02825 7 MDKCCWICKDEY---D--VVTNYCNCKNENKIVHKECLEEWINTSKNKSCKICNGPYN 59 (162)
T ss_pred CCCeeEecCCCC---C--CccCCcccCCCchHHHHHHHHHHHhcCCCCcccccCCeEE
Confidence 456899998752 1 12347753 56999999999863 467999997764
No 88
>KOG2817 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=89.79 E-value=0.27 Score=47.28 Aligned_cols=47 Identities=30% Similarity=0.672 Sum_probs=39.9
Q ss_pred CCCcchhhhcccCCceeEEcCCCCcccHHHHHHHHhcCC--CCCCCCCcC
Q 025507 140 HDCPVCCEYLFETRQDVIVLPCGHTIHKNCLKEMREHHQ--YACPICSKS 187 (251)
Q Consensus 140 ~~CpICle~lf~s~~~~~~lpCgH~fH~~Ci~~wl~~~~--~~CP~Cr~~ 187 (251)
..|||=.| .-+...+++.|.|||.+-++-++...+.+. +.||-|-..
T Consensus 335 F~CPVlKe-qtsdeNPPm~L~CGHVISkdAlnrLS~ng~~sfKCPYCP~e 383 (394)
T KOG2817|consen 335 FICPVLKE-QTSDENPPMMLICGHVISKDALNRLSKNGSQSFKCPYCPVE 383 (394)
T ss_pred eecccchh-hccCCCCCeeeeccceecHHHHHHHhhCCCeeeeCCCCCcc
Confidence 47999888 456667899999999999999999988766 789999753
No 89
>COG5236 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=89.78 E-value=0.38 Score=45.85 Aligned_cols=66 Identities=23% Similarity=0.450 Sum_probs=44.5
Q ss_pred CcceeccccccccccCCCCCCCCcchhhhcccCCceeEEcCCCCcccHHHHHHHHhc-CCCCCCCCCcCcc
Q 025507 120 RCCYSMLLKNSHPCVEGAMHHDCPVCCEYLFETRQDVIVLPCGHTIHKNCLKEMREH-HQYACPICSKSVC 189 (251)
Q Consensus 120 ~~c~~~~l~~~H~C~e~~~~~~CpICle~lf~s~~~~~~lpCgH~fH~~Ci~~wl~~-~~~~CP~Cr~~~~ 189 (251)
+.|...+|.++.+=..+..+..|.||.+. ...+.++||||.++-.|......- ..-.||+||....
T Consensus 42 nlsaEPnlttsSaddtDEen~~C~ICA~~----~TYs~~~PC~H~~CH~Ca~RlRALY~~K~C~~CrTE~e 108 (493)
T COG5236 42 NLSAEPNLTTSSADDTDEENMNCQICAGS----TTYSARYPCGHQICHACAVRLRALYMQKGCPLCRTETE 108 (493)
T ss_pred ccccCCccccccccccccccceeEEecCC----ceEEEeccCCchHHHHHHHHHHHHHhccCCCccccccc
Confidence 45555555444332334456799999983 345668899999999998875321 3456999997754
No 90
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=89.50 E-value=0.17 Score=30.07 Aligned_cols=24 Identities=33% Similarity=0.908 Sum_probs=18.5
Q ss_pred eeecCCCCccccc-cccCcCCCCcc
Q 025507 54 QVICSLCGTEQKV-QQVCVNCGVCM 77 (251)
Q Consensus 54 ~v~C~~C~~~q~~-~~~C~~Cg~~f 77 (251)
.+.|..|+++-+. +..|++||+.+
T Consensus 2 ~~~Cp~Cg~~~~~~~~fC~~CG~~L 26 (26)
T PF13248_consen 2 EMFCPNCGAEIDPDAKFCPNCGAKL 26 (26)
T ss_pred cCCCcccCCcCCcccccChhhCCCC
Confidence 4678899987554 67899999864
No 91
>PRK12380 hydrogenase nickel incorporation protein HybF; Provisional
Probab=89.30 E-value=0.27 Score=39.37 Aligned_cols=35 Identities=26% Similarity=0.685 Sum_probs=27.5
Q ss_pred ceeEEcCCCCCCccccceeeeccCCCCCCccccccCC
Q 025507 215 KVWILCNDCGKTSNVQFHVLAQKCPNCKSYNTRLTRG 251 (251)
Q Consensus 215 ~~~IlCndC~~~s~~~~h~lg~kC~~C~SyNT~~~~~ 251 (251)
...+.|++|+........ ...||.|||++..+++|
T Consensus 68 p~~~~C~~Cg~~~~~~~~--~~~CP~Cgs~~~~i~~G 102 (113)
T PRK12380 68 PAQAWCWDCSQVVEIHQH--DAQCPHCHGERLRVDTG 102 (113)
T ss_pred CcEEEcccCCCEEecCCc--CccCcCCCCCCcEEccC
Confidence 467899999987766532 23599999999998876
No 92
>KOG2660 consensus Locus-specific chromosome binding proteins [Function unknown]
Probab=89.29 E-value=0.095 Score=49.22 Aligned_cols=49 Identities=29% Similarity=0.673 Sum_probs=39.5
Q ss_pred CCCCCCcchhhhcccCCceeEEcCCCCcccHHHHHHHHhcCCCCCCCCCcCcc
Q 025507 137 AMHHDCPVCCEYLFETRQDVIVLPCGHTIHKNCLKEMREHHQYACPICSKSVC 189 (251)
Q Consensus 137 ~~~~~CpICle~lf~s~~~~~~lpCgH~fH~~Ci~~wl~~~~~~CP~Cr~~~~ 189 (251)
.....|.+|..+|-+. ..+.-|=|+|++.||..+|.. +..||.|...+.
T Consensus 13 n~~itC~LC~GYliDA---TTI~eCLHTFCkSCivk~l~~-~~~CP~C~i~ih 61 (331)
T KOG2660|consen 13 NPHITCRLCGGYLIDA---TTITECLHTFCKSCIVKYLEE-SKYCPTCDIVIH 61 (331)
T ss_pred ccceehhhccceeecc---hhHHHHHHHHHHHHHHHHHHH-hccCCccceecc
Confidence 3456899999987663 335679999999999999986 689999996654
No 93
>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=88.83 E-value=0.31 Score=32.50 Aligned_cols=42 Identities=29% Similarity=0.698 Sum_probs=20.1
Q ss_pred CcchhhhcccCCceeEEcCCCCcccHHHHHHHHhcCC-CCCCCC
Q 025507 142 CPVCCEYLFETRQDVIVLPCGHTIHKNCLKEMREHHQ-YACPIC 184 (251)
Q Consensus 142 CpICle~lf~s~~~~~~lpCgH~fH~~Ci~~wl~~~~-~~CP~C 184 (251)
|.+|.| +..-+..-....|+=.+|..|+..|+++.+ .+||.|
T Consensus 1 C~~C~~-iv~~G~~C~~~~C~~r~H~~C~~~y~r~~~~~~CP~C 43 (43)
T PF08746_consen 1 CEACKE-IVTQGQRCSNRDCNVRLHDDCFKKYFRHRSNPKCPNC 43 (43)
T ss_dssp -TTT-S-B-SSSEE-SS--S--EE-HHHHHHHTTT-SS-B-TTT
T ss_pred Ccccch-hHeeeccCCCCccCchHHHHHHHHHHhcCCCCCCcCC
Confidence 456666 433222111224777899999999988633 369987
No 94
>PRK03681 hypA hydrogenase nickel incorporation protein; Validated
Probab=88.77 E-value=0.32 Score=39.00 Aligned_cols=36 Identities=17% Similarity=0.480 Sum_probs=27.8
Q ss_pred ceeEEcCCCCCCccccceeeeccCCCCCCccccccCC
Q 025507 215 KVWILCNDCGKTSNVQFHVLAQKCPNCKSYNTRLTRG 251 (251)
Q Consensus 215 ~~~IlCndC~~~s~~~~h~lg~kC~~C~SyNT~~~~~ 251 (251)
.....|++|+......-+. ...||.|||+++.+++|
T Consensus 68 p~~~~C~~Cg~~~~~~~~~-~~~CP~Cgs~~~~i~~G 103 (114)
T PRK03681 68 EAECWCETCQQYVTLLTQR-VRRCPQCHGDMLRIVAD 103 (114)
T ss_pred CcEEEcccCCCeeecCCcc-CCcCcCcCCCCcEEccC
Confidence 5678999999877664332 14699999999998876
No 95
>KOG1002 consensus Nucleotide excision repair protein RAD16 [Replication, recombination and repair]
Probab=88.41 E-value=0.2 Score=50.08 Aligned_cols=52 Identities=27% Similarity=0.628 Sum_probs=41.1
Q ss_pred cCCCCCCCCcchhhhcccCCceeEEcCCCCcccHHHHHHHHhc----CCCCCCCCCcCcc
Q 025507 134 VEGAMHHDCPVCCEYLFETRQDVIVLPCGHTIHKNCLKEMREH----HQYACPICSKSVC 189 (251)
Q Consensus 134 ~e~~~~~~CpICle~lf~s~~~~~~lpCgH~fH~~Ci~~wl~~----~~~~CP~Cr~~~~ 189 (251)
.|+..+..|-+|-|+ .+++..-.|.|.|++.|+.+|+.. .+.+||+|...+.
T Consensus 531 ~enk~~~~C~lc~d~----aed~i~s~ChH~FCrlCi~eyv~~f~~~~nvtCP~C~i~Ls 586 (791)
T KOG1002|consen 531 DENKGEVECGLCHDP----AEDYIESSCHHKFCRLCIKEYVESFMENNNVTCPVCHIGLS 586 (791)
T ss_pred ccccCceeecccCCh----hhhhHhhhhhHHHHHHHHHHHHHhhhcccCCCCcccccccc
Confidence 466778899999984 234667789999999999998753 4578999998764
No 96
>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=88.03 E-value=0.34 Score=29.08 Aligned_cols=23 Identities=30% Similarity=0.778 Sum_probs=18.9
Q ss_pred ecCCCCccccc-cccCcCCCCccc
Q 025507 56 ICSLCGTEQKV-QQVCVNCGVCMG 78 (251)
Q Consensus 56 ~C~~C~~~q~~-~~~C~~Cg~~f~ 78 (251)
.|..|+.+-+. +..|++||..|.
T Consensus 2 ~CP~C~~~V~~~~~~Cp~CG~~F~ 25 (26)
T PF10571_consen 2 TCPECGAEVPESAKFCPHCGYDFE 25 (26)
T ss_pred cCCCCcCCchhhcCcCCCCCCCCc
Confidence 37788888774 689999999986
No 97
>KOG2114 consensus Vacuolar assembly/sorting protein PEP5/VPS11 [Intracellular trafficking, secretion, and vesicular transport]
Probab=88.00 E-value=0.36 Score=50.47 Aligned_cols=43 Identities=28% Similarity=0.760 Sum_probs=31.6
Q ss_pred CCCcchhhhcccCCceeEEcCCCCcccHHHHHHHHhcCCCCCCCCCcCcc
Q 025507 140 HDCPVCCEYLFETRQDVIVLPCGHTIHKNCLKEMREHHQYACPICSKSVC 189 (251)
Q Consensus 140 ~~CpICle~lf~s~~~~~~lpCgH~fH~~Ci~~wl~~~~~~CP~Cr~~~~ 189 (251)
..|..|--.| .-|.|...|||+||++|+. . +...||-|+-.+.
T Consensus 841 skCs~C~~~L---dlP~VhF~CgHsyHqhC~e---~-~~~~CP~C~~e~~ 883 (933)
T KOG2114|consen 841 SKCSACEGTL---DLPFVHFLCGHSYHQHCLE---D-KEDKCPKCLPELR 883 (933)
T ss_pred eeecccCCcc---ccceeeeecccHHHHHhhc---c-CcccCCccchhhh
Confidence 3677776433 2366777899999999999 2 4578999997443
No 98
>KOG3039 consensus Uncharacterized conserved protein [Function unknown]
Probab=87.92 E-value=0.57 Score=42.78 Aligned_cols=56 Identities=25% Similarity=0.507 Sum_probs=44.2
Q ss_pred cCCCCCCCCcchhhhcccCCceeEEc-CCCCcccHHHHHHHHhcCCCCCCCCCcCccch
Q 025507 134 VEGAMHHDCPVCCEYLFETRQDVIVL-PCGHTIHKNCLKEMREHHQYACPICSKSVCDM 191 (251)
Q Consensus 134 ~e~~~~~~CpICle~lf~s~~~~~~l-pCgH~fH~~Ci~~wl~~~~~~CP~Cr~~~~~~ 191 (251)
+..+....|||+.+.|.. ..+..+| |+||.+..+|...++.. ...+|++.+++.+.
T Consensus 216 ~a~s~ryiCpvtrd~LtN-t~~ca~Lr~sg~Vv~~ecvEklir~-D~v~pv~d~plkdr 272 (303)
T KOG3039|consen 216 IAASKRYICPVTRDTLTN-TTPCAVLRPSGHVVTKECVEKLIRK-DMVDPVTDKPLKDR 272 (303)
T ss_pred hhhccceecccchhhhcC-ccceEEeccCCcEeeHHHHHHhccc-cccccCCCCcCccc
Confidence 333456789999996654 4455565 99999999999999984 58899999998763
No 99
>PF13240 zinc_ribbon_2: zinc-ribbon domain
Probab=87.07 E-value=0.33 Score=28.24 Aligned_cols=21 Identities=38% Similarity=0.956 Sum_probs=16.2
Q ss_pred cCCCCccccc-cccCcCCCCcc
Q 025507 57 CSLCGTEQKV-QQVCVNCGVCM 77 (251)
Q Consensus 57 C~~C~~~q~~-~~~C~~Cg~~f 77 (251)
|..|+++.+. ++.|++||+.+
T Consensus 2 Cp~CG~~~~~~~~fC~~CG~~l 23 (23)
T PF13240_consen 2 CPNCGAEIEDDAKFCPNCGTPL 23 (23)
T ss_pred CcccCCCCCCcCcchhhhCCcC
Confidence 7788887764 67899999864
No 100
>PF07191 zinc-ribbons_6: zinc-ribbons; InterPro: IPR010807 This family consists of several short, hypothetical bacterial proteins of around 70 residues in length. Members of this family 8 highly conserved cysteine residues. The function of the family is unknown.; PDB: 2JRP_A 2JNE_A.
Probab=86.46 E-value=0.35 Score=35.80 Aligned_cols=36 Identities=28% Similarity=0.780 Sum_probs=22.4
Q ss_pred ceeecCCCCccccccccCcCCCCc--------cceEecCccccc
Q 025507 53 NQVICSLCGTEQKVQQVCVNCGVC--------MGEYFCESCKLF 88 (251)
Q Consensus 53 ~~v~C~~C~~~q~~~~~C~~Cg~~--------f~~y~C~~C~~~ 88 (251)
....|..|+..-.....||.|+.. -+.|||..|+=.
T Consensus 16 ~~~~C~~C~~~~~~~a~CPdC~~~Le~LkACGAvdYFC~~c~gL 59 (70)
T PF07191_consen 16 GHYHCEACQKDYKKEAFCPDCGQPLEVLKACGAVDYFCNHCHGL 59 (70)
T ss_dssp TEEEETTT--EEEEEEE-TTT-SB-EEEEETTEEEEE-TTTT-E
T ss_pred CEEECccccccceecccCCCcccHHHHHHHhcccceeeccCCce
Confidence 477788888776667778887776 368999998744
No 101
>PF01155 HypA: Hydrogenase expression/synthesis hypA family; InterPro: IPR000688 Bacterial membrane-bound nickel-dependent hydrogenases requires a number of accessory proteins which are involved in their maturation. The exact role of these proteins is not yet clear, but some seem to be required for the incorporation of the nickel ions []. One of these proteins is generally known as hypA. It is a protein of about 12 to 14 kDa that contains, in its C-terminal region, four conserved cysteines that form a zinc-finger like motif. Escherichia coli has two proteins that belong to this family, hypA and hybF. A homologue, MJ0214, has also been found in a number of archaeal species, including the genome of Methanocaldococcus jannaschii (Methanococcus jannaschii).; GO: 0016151 nickel ion binding, 0006464 protein modification process; PDB: 2KDX_A 3A44_D 3A43_B.
Probab=86.35 E-value=0.22 Score=39.69 Aligned_cols=35 Identities=26% Similarity=0.552 Sum_probs=24.7
Q ss_pred ceeEEcCCCCCCccccceeeeccCCCCCCccccccCC
Q 025507 215 KVWILCNDCGKTSNVQFHVLAQKCPNCKSYNTRLTRG 251 (251)
Q Consensus 215 ~~~IlCndC~~~s~~~~h~lg~kC~~C~SyNT~~~~~ 251 (251)
.....|++|+..+.+..+. ..||.|+|++..+++|
T Consensus 68 p~~~~C~~Cg~~~~~~~~~--~~CP~Cgs~~~~i~~G 102 (113)
T PF01155_consen 68 PARARCRDCGHEFEPDEFD--FSCPRCGSPDVEIISG 102 (113)
T ss_dssp --EEEETTTS-EEECHHCC--HH-SSSSSS-EEEEES
T ss_pred CCcEECCCCCCEEecCCCC--CCCcCCcCCCcEEccC
Confidence 5678999999998776553 5799999999888765
No 102
>KOG4739 consensus Uncharacterized protein involved in synaptonemal complex formation [Cell cycle control, cell division, chromosome partitioning; General function prediction only]
Probab=86.26 E-value=0.3 Score=44.01 Aligned_cols=37 Identities=30% Similarity=0.737 Sum_probs=27.9
Q ss_pred ccCCceeEEcCCCCcccHHHHHHHHhcCCCCCCCCCcCcc
Q 025507 150 FETRQDVIVLPCGHTIHKNCLKEMREHHQYACPICSKSVC 189 (251)
Q Consensus 150 f~s~~~~~~lpCgH~fH~~Ci~~wl~~~~~~CP~Cr~~~~ 189 (251)
+.+..+..++.|+|.|+..|...-.. ..||+|++++.
T Consensus 12 ~~~~~~f~LTaC~HvfC~~C~k~~~~---~~C~lCkk~ir 48 (233)
T KOG4739|consen 12 FPSQDPFFLTACRHVFCEPCLKASSP---DVCPLCKKSIR 48 (233)
T ss_pred cCCCCceeeeechhhhhhhhcccCCc---cccccccceee
Confidence 44444566779999999999876432 38999999964
No 103
>KOG4692 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=85.99 E-value=0.49 Score=45.24 Aligned_cols=53 Identities=21% Similarity=0.533 Sum_probs=42.5
Q ss_pred ccCCCCCCCCcchhhhcccCCceeEEcCCCCcccHHHHHHHHhcCCCCCCCCCcCccc
Q 025507 133 CVEGAMHHDCPVCCEYLFETRQDVIVLPCGHTIHKNCLKEMREHHQYACPICSKSVCD 190 (251)
Q Consensus 133 C~e~~~~~~CpICle~lf~s~~~~~~lpCgH~fH~~Ci~~wl~~~~~~CP~Cr~~~~~ 190 (251)
-..++.++.||||.. .+...+.-||||.-+..||.+.|. ....|=.|+.++.+
T Consensus 416 ~lp~sEd~lCpICyA----~pi~Avf~PC~H~SC~~CI~qHlm-N~k~CFfCktTv~~ 468 (489)
T KOG4692|consen 416 DLPDSEDNLCPICYA----GPINAVFAPCSHRSCYGCITQHLM-NCKRCFFCKTTVID 468 (489)
T ss_pred CCCCcccccCcceec----ccchhhccCCCCchHHHHHHHHHh-cCCeeeEecceeee
Confidence 344577889999985 334566789999999999999887 45789999988876
No 104
>PRK04023 DNA polymerase II large subunit; Validated
Probab=85.82 E-value=0.69 Score=49.41 Aligned_cols=31 Identities=29% Similarity=0.676 Sum_probs=14.4
Q ss_pred cCcCCCCccceEecCccccccCCCCCCeeecCCCC
Q 025507 69 VCVNCGVCMGEYFCESCKLFDDDTSKKQYHCDGCG 103 (251)
Q Consensus 69 ~C~~Cg~~f~~y~C~~C~~~d~~~~k~~~HC~~Cg 103 (251)
.|++||+.....+|+.|.-. ...+|.|++||
T Consensus 628 fCpsCG~~t~~frCP~CG~~----Te~i~fCP~CG 658 (1121)
T PRK04023 628 KCPSCGKETFYRRCPFCGTH----TEPVYRCPRCG 658 (1121)
T ss_pred cCCCCCCcCCcccCCCCCCC----CCcceeCcccc
Confidence 44455444444444444322 34455555553
No 105
>KOG3161 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=84.97 E-value=0.42 Score=48.76 Aligned_cols=42 Identities=29% Similarity=0.712 Sum_probs=35.3
Q ss_pred CCCcchhhhcccCCceeEEcCCCCcccHHHHHHHHhcCCCCCCCCC
Q 025507 140 HDCPVCCEYLFETRQDVIVLPCGHTIHKNCLKEMREHHQYACPICS 185 (251)
Q Consensus 140 ~~CpICle~lf~s~~~~~~lpCgH~fH~~Ci~~wl~~~~~~CP~Cr 185 (251)
..|+||+..++.++..++.|-|||++++.|++... +.+|| |.
T Consensus 12 l~c~ic~n~f~~~~~~Pvsl~cghtic~~c~~~ly---n~scp-~~ 53 (861)
T KOG3161|consen 12 LLCDICLNLFVVQRLEPVSLQCGHTICGHCVQLLY---NASCP-TK 53 (861)
T ss_pred hhchHHHHHHHHHhcCcccccccchHHHHHHHhHh---hccCC-CC
Confidence 47999988778888888999999999999999874 35788 55
No 106
>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=84.77 E-value=0.34 Score=33.36 Aligned_cols=32 Identities=34% Similarity=0.760 Sum_probs=22.4
Q ss_pred EcCCC-CcccHHHHHHHHhcCCCCCCCCCcCccc
Q 025507 158 VLPCG-HTIHKNCLKEMREHHQYACPICSKSVCD 190 (251)
Q Consensus 158 ~lpCg-H~fH~~Ci~~wl~~~~~~CP~Cr~~~~~ 190 (251)
.+.|. |..+..|++.+|+. +..||+|.+++..
T Consensus 15 Li~C~dHYLCl~CLt~ml~~-s~~C~iC~~~LPt 47 (50)
T PF03854_consen 15 LIKCSDHYLCLNCLTLMLSR-SDRCPICGKPLPT 47 (50)
T ss_dssp EEE-SS-EEEHHHHHHT-SS-SSEETTTTEE---
T ss_pred eeeecchhHHHHHHHHHhcc-ccCCCcccCcCcc
Confidence 55685 99999999999985 5899999987753
No 107
>PF07191 zinc-ribbons_6: zinc-ribbons; InterPro: IPR010807 This family consists of several short, hypothetical bacterial proteins of around 70 residues in length. Members of this family 8 highly conserved cysteine residues. The function of the family is unknown.; PDB: 2JRP_A 2JNE_A.
Probab=84.55 E-value=0.17 Score=37.52 Aligned_cols=64 Identities=27% Similarity=0.550 Sum_probs=36.9
Q ss_pred CCCcchhhhcccCCceeEEcCCCCcccHHHHHHHHhcCCCCCCCCCcCccchhHHHHHHHHHHhcCCCCHhhhcCceeEE
Q 025507 140 HDCPVCCEYLFETRQDVIVLPCGHTIHKNCLKEMREHHQYACPICSKSVCDMSKVWEKYDREIAATPMPEAYLNKKVWIL 219 (251)
Q Consensus 140 ~~CpICle~lf~s~~~~~~lpCgH~fH~~Ci~~wl~~~~~~CP~Cr~~~~~~~~~~~~ld~~i~~~p~P~e~~~~~~~Il 219 (251)
..||.|..+|.... |+..+..|-..+... ..||.|..++..+. +=..++.+
T Consensus 2 ~~CP~C~~~L~~~~--------~~~~C~~C~~~~~~~--a~CPdC~~~Le~Lk-------------------ACGAvdYF 52 (70)
T PF07191_consen 2 NTCPKCQQELEWQG--------GHYHCEACQKDYKKE--AFCPDCGQPLEVLK-------------------ACGAVDYF 52 (70)
T ss_dssp -B-SSS-SBEEEET--------TEEEETTT--EEEEE--EE-TTT-SB-EEEE-------------------ETTEEEEE
T ss_pred CcCCCCCCccEEeC--------CEEECccccccceec--ccCCCcccHHHHHH-------------------Hhccccee
Confidence 47999998643321 788889998887653 67999998776532 22347899
Q ss_pred cCCCCC---Cccccce
Q 025507 220 CNDCGK---TSNVQFH 232 (251)
Q Consensus 220 CndC~~---~s~~~~h 232 (251)
||.|.+ ++-|.|.
T Consensus 53 C~~c~gLiSKkrV~f~ 68 (70)
T PF07191_consen 53 CNHCHGLISKKRVRFE 68 (70)
T ss_dssp -TTTT-EE-TTTSEEE
T ss_pred eccCCceeecceEEEE
Confidence 999985 5555554
No 108
>PRK00762 hypA hydrogenase nickel incorporation protein; Provisional
Probab=84.11 E-value=0.77 Score=37.29 Aligned_cols=36 Identities=31% Similarity=0.608 Sum_probs=26.1
Q ss_pred ceeEEcCCCCCCcccc-c---ee-eeccCCCCCCccccccCC
Q 025507 215 KVWILCNDCGKTSNVQ-F---HV-LAQKCPNCKSYNTRLTRG 251 (251)
Q Consensus 215 ~~~IlCndC~~~s~~~-~---h~-lg~kC~~C~SyNT~~~~~ 251 (251)
.....| +|+..+... + |+ ....||.|||++..+++|
T Consensus 68 p~~~~C-~Cg~~~~~~~~~~~~~~~~~~CP~Cgs~~~~i~~G 108 (124)
T PRK00762 68 PVEIEC-ECGYEGVVDEDEIDHYAAVIECPVCGNKRAHILGG 108 (124)
T ss_pred CeeEEe-eCcCcccccccchhccccCCcCcCCCCCCCEEecC
Confidence 567899 999875432 1 11 235799999999998876
No 109
>COG5220 TFB3 Cdk activating kinase (CAK)/RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit TFB3 [Cell division and chromosome partitioning / Transcription / DNA replication, recombination, and repair]
Probab=83.56 E-value=0.36 Score=43.93 Aligned_cols=50 Identities=26% Similarity=0.648 Sum_probs=40.0
Q ss_pred CCCCcchhhhcccCCceeEEc-C-CCCcccHHHHHHHHhcCCCCCC--CCCcCc
Q 025507 139 HHDCPVCCEYLFETRQDVIVL-P-CGHTIHKNCLKEMREHHQYACP--ICSKSV 188 (251)
Q Consensus 139 ~~~CpICle~lf~s~~~~~~l-p-CgH~fH~~Ci~~wl~~~~~~CP--~Cr~~~ 188 (251)
+..||||..+.+.+++-..++ | |=|.++..|.+..++.+...|| -|.+.+
T Consensus 10 d~~CPvCksDrYLnPdik~linPECyHrmCESCvdRIFs~GpAqCP~~gC~kIL 63 (314)
T COG5220 10 DRRCPVCKSDRYLNPDIKILINPECYHRMCESCVDRIFSRGPAQCPYKGCGKIL 63 (314)
T ss_pred cccCCccccccccCCCeEEEECHHHHHHHHHHHHHHHhcCCCCCCCCccHHHHH
Confidence 458999998877777533333 6 9999999999999888878899 887654
No 110
>KOG0309 consensus Conserved WD40 repeat-containing protein [Function unknown]
Probab=83.54 E-value=0.72 Score=47.91 Aligned_cols=44 Identities=23% Similarity=0.508 Sum_probs=31.5
Q ss_pred CCCCCCcchhhhcccCCceeEEcCCCCcccHHHHHHHHhcCCCCCCC
Q 025507 137 AMHHDCPVCCEYLFETRQDVIVLPCGHTIHKNCLKEMREHHQYACPI 183 (251)
Q Consensus 137 ~~~~~CpICle~lf~s~~~~~~lpCgH~fH~~Ci~~wl~~~~~~CP~ 183 (251)
.....|.||-- .-.+...+-+.|||.+|..|+.+|++.+ -.||.
T Consensus 1026 ~~~~~C~~C~l--~V~gss~~Cg~C~Hv~H~sc~~eWf~~g-d~Cps 1069 (1081)
T KOG0309|consen 1026 GFTFQCAICHL--AVRGSSNFCGTCGHVGHTSCMMEWFRTG-DVCPS 1069 (1081)
T ss_pred cceeeeeeEee--EeeccchhhccccccccHHHHHHHHhcC-CcCCC
Confidence 33445888873 3333445567899999999999999864 57873
No 111
>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=83.25 E-value=0.74 Score=36.76 Aligned_cols=26 Identities=35% Similarity=0.953 Sum_probs=20.3
Q ss_pred cccCcCCCCccceEecCccccccCCCCCCeeecCCCCc
Q 025507 67 QQVCVNCGVCMGEYFCESCKLFDDDTSKKQYHCDGCGI 104 (251)
Q Consensus 67 ~~~C~~Cg~~f~~y~C~~C~~~d~~~~k~~~HC~~Cgi 104 (251)
...|++||+ ||| +.+|.+-.|++||.
T Consensus 9 KR~Cp~CG~----------kFY--DLnk~PivCP~CG~ 34 (108)
T PF09538_consen 9 KRTCPSCGA----------KFY--DLNKDPIVCPKCGT 34 (108)
T ss_pred cccCCCCcc----------hhc--cCCCCCccCCCCCC
Confidence 468999999 456 45688999999884
No 112
>COG0375 HybF Zn finger protein HypA/HybF (possibly regulating hydrogenase expression) [General function prediction only]
Probab=82.53 E-value=1 Score=36.44 Aligned_cols=36 Identities=31% Similarity=0.632 Sum_probs=29.1
Q ss_pred CceeEEcCCCCCCccccceeeeccCCCCCCccccccCC
Q 025507 214 KKVWILCNDCGKTSNVQFHVLAQKCPNCKSYNTRLTRG 251 (251)
Q Consensus 214 ~~~~IlCndC~~~s~~~~h~lg~kC~~C~SyNT~~~~~ 251 (251)
..+.+.|.+|+.....--|.+. ||.|+|-|.++++|
T Consensus 67 ~p~~~~C~~C~~~~~~e~~~~~--CP~C~s~~~~i~~G 102 (115)
T COG0375 67 EPAECWCLDCGQEVELEELDYR--CPKCGSINLRIIGG 102 (115)
T ss_pred eccEEEeccCCCeecchhheeE--CCCCCCCceEEecC
Confidence 3578899999887766665554 99999999999876
No 113
>KOG1952 consensus Transcription factor NF-X1, contains NFX-type Zn2+-binding and R3H domains [Transcription]
Probab=82.11 E-value=0.6 Score=48.90 Aligned_cols=48 Identities=29% Similarity=0.668 Sum_probs=34.6
Q ss_pred CCCCcchhhhcccCCceeEEcCC---CCcccHHHHHHHHhc------CCCCCCCCCcCcc
Q 025507 139 HHDCPVCCEYLFETRQDVIVLPC---GHTIHKNCLKEMREH------HQYACPICSKSVC 189 (251)
Q Consensus 139 ~~~CpICle~lf~s~~~~~~lpC---gH~fH~~Ci~~wl~~------~~~~CP~Cr~~~~ 189 (251)
..+|.||.|.+..+. -+|.| =|.||..||..|... ..-+||-|+....
T Consensus 191 ~yeCmIC~e~I~~t~---~~WSC~sCYhVFHl~CI~~WArs~ek~~~~~WrCP~Cqsv~~ 247 (950)
T KOG1952|consen 191 KYECMICTERIKRTA---PVWSCKSCYHVFHLNCIKKWARSSEKTGQDGWRCPACQSVSK 247 (950)
T ss_pred ceEEEEeeeeccccC---CceecchhhhhhhHHHHHHHHHHhhhccCccccCCcccchhc
Confidence 468999999765432 24445 599999999999764 2357999994443
No 114
>KOG2034 consensus Vacuolar sorting protein PEP3/VPS18 [Intracellular trafficking, secretion, and vesicular transport]
Probab=81.81 E-value=0.66 Score=48.76 Aligned_cols=36 Identities=31% Similarity=0.694 Sum_probs=29.0
Q ss_pred CCCCCcchhhhcccCCceeEEcCCCCcccHHHHHHHHh
Q 025507 138 MHHDCPVCCEYLFETRQDVIVLPCGHTIHKNCLKEMRE 175 (251)
Q Consensus 138 ~~~~CpICle~lf~s~~~~~~lpCgH~fH~~Ci~~wl~ 175 (251)
....|.+|.-+|+. ++..+.||||.||..|+..-..
T Consensus 816 p~d~C~~C~~~ll~--~pF~vf~CgH~FH~~Cl~~~v~ 851 (911)
T KOG2034|consen 816 PQDSCDHCGRPLLI--KPFYVFPCGHCFHRDCLIRHVL 851 (911)
T ss_pred CccchHHhcchhhc--CcceeeeccchHHHHHHHHHHH
Confidence 35789999976554 4677889999999999998654
No 115
>PF05290 Baculo_IE-1: Baculovirus immediate-early protein (IE-0); InterPro: IPR007954 This entry contains the Baculovirus immediate-early protein IE-0.
Probab=81.80 E-value=0.99 Score=37.50 Aligned_cols=48 Identities=27% Similarity=0.641 Sum_probs=34.5
Q ss_pred CCCcchhhhcccCCceeEEc-C---CCCcccHHHHHHHHhcC--CCCCCCCCcCccch
Q 025507 140 HDCPVCCEYLFETRQDVIVL-P---CGHTIHKNCLKEMREHH--QYACPICSKSVCDM 191 (251)
Q Consensus 140 ~~CpICle~lf~s~~~~~~l-p---CgH~fH~~Ci~~wl~~~--~~~CP~Cr~~~~~~ 191 (251)
-+|-||.|. .. + ...| | ||-.++..|....|+.. ...||+|+.|+-..
T Consensus 81 YeCnIC~et-S~--e-e~FLKPneCCgY~iCn~Cya~LWK~~~~ypvCPvCkTSFKss 134 (140)
T PF05290_consen 81 YECNICKET-SA--E-ERFLKPNECCGYSICNACYANLWKFCNLYPVCPVCKTSFKSS 134 (140)
T ss_pred eeccCcccc-cc--h-hhcCCcccccchHHHHHHHHHHHHHcccCCCCCccccccccc
Confidence 478888873 22 2 2233 2 89999999999966652 46799999998653
No 116
>KOG1001 consensus Helicase-like transcription factor HLTF/DNA helicase RAD5, DEAD-box superfamily [Transcription; Replication, recombination and repair]
Probab=81.58 E-value=1.2 Score=45.84 Aligned_cols=44 Identities=30% Similarity=0.896 Sum_probs=34.8
Q ss_pred CCCcchhhhcccCCceeEEcCCCCcccHHHHHHHHhcCCC-CCCCCCcCc
Q 025507 140 HDCPVCCEYLFETRQDVIVLPCGHTIHKNCLKEMREHHQY-ACPICSKSV 188 (251)
Q Consensus 140 ~~CpICle~lf~s~~~~~~lpCgH~fH~~Ci~~wl~~~~~-~CP~Cr~~~ 188 (251)
..|+||++ .+..+..+|||.|+.+|+...+..... .||+||..+
T Consensus 455 ~~c~ic~~-----~~~~~it~c~h~~c~~c~~~~i~~~~~~~~~~cr~~l 499 (674)
T KOG1001|consen 455 HWCHICCD-----LDSFFITRCGHDFCVECLKKSIQQSENAPCPLCRNVL 499 (674)
T ss_pred cccccccc-----cccceeecccchHHHHHHHhccccccCCCCcHHHHHH
Confidence 68999998 235667899999999999998775433 599999443
No 117
>PF12773 DZR: Double zinc ribbon
Probab=81.07 E-value=1.4 Score=29.53 Aligned_cols=23 Identities=35% Similarity=0.853 Sum_probs=13.6
Q ss_pred eeecCCCCcccc--c--cccCcCCCCc
Q 025507 54 QVICSLCGTEQK--V--QQVCVNCGVC 76 (251)
Q Consensus 54 ~v~C~~C~~~q~--~--~~~C~~Cg~~ 76 (251)
...|..|++.++ . ...|++||..
T Consensus 12 ~~fC~~CG~~l~~~~~~~~~C~~Cg~~ 38 (50)
T PF12773_consen 12 AKFCPHCGTPLPPPDQSKKICPNCGAE 38 (50)
T ss_pred ccCChhhcCChhhccCCCCCCcCCcCC
Confidence 556666766655 2 2457777664
No 118
>PRK14559 putative protein serine/threonine phosphatase; Provisional
Probab=81.02 E-value=1.1 Score=45.93 Aligned_cols=46 Identities=28% Similarity=0.723 Sum_probs=26.4
Q ss_pred eecCCCCccccc-cccCcCCCCccceEecCccccccCCCCCCeeecCCCC
Q 025507 55 VICSLCGTEQKV-QQVCVNCGVCMGEYFCESCKLFDDDTSKKQYHCDGCG 103 (251)
Q Consensus 55 v~C~~C~~~q~~-~~~C~~Cg~~f~~y~C~~C~~~d~~~~k~~~HC~~Cg 103 (251)
++|..|+++-+. +..|++||..+..-.|+.|.---. .+.-.|+.||
T Consensus 2 ~~Cp~Cg~~n~~~akFC~~CG~~l~~~~Cp~CG~~~~---~~~~fC~~CG 48 (645)
T PRK14559 2 LICPQCQFENPNNNRFCQKCGTSLTHKPCPQCGTEVP---VDEAHCPNCG 48 (645)
T ss_pred CcCCCCCCcCCCCCccccccCCCCCCCcCCCCCCCCC---cccccccccC
Confidence 467777777553 556777777776555666643311 2223455555
No 119
>KOG3053 consensus Uncharacterized conserved protein [Function unknown]
Probab=80.87 E-value=0.96 Score=41.47 Aligned_cols=54 Identities=22% Similarity=0.530 Sum_probs=37.5
Q ss_pred CCCCCCCcchhhhcccCCceeEEcCC-----CCcccHHHHHHHHhcC-------CCCCCCCCcCcc
Q 025507 136 GAMHHDCPVCCEYLFETRQDVIVLPC-----GHTIHKNCLKEMREHH-------QYACPICSKSVC 189 (251)
Q Consensus 136 ~~~~~~CpICle~lf~s~~~~~~lpC-----gH~fH~~Ci~~wl~~~-------~~~CP~Cr~~~~ 189 (251)
...+-.|=||++.-.+.+...-+=|| -|..|..|+..|+... .-+||.|+....
T Consensus 17 ~e~eR~CWiCF~TdeDn~~a~WV~PCrCRGt~KWVHqsCL~rWiDEK~~~n~~q~V~C~QCqTEYi 82 (293)
T KOG3053|consen 17 QELERCCWICFATDEDNRLAAWVHPCRCRGTTKWVHQSCLSRWIDEKQRGNPLQTVSCPQCQTEYI 82 (293)
T ss_pred cccceeEEEEeccCcccchhhhcccccccCccHHHHHHHHHHHHhHHhcCCCCceeechhhcchhe
Confidence 45577899999743333333234488 3889999999998752 235999997754
No 120
>COG5222 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=80.30 E-value=1.2 Score=41.71 Aligned_cols=44 Identities=30% Similarity=0.763 Sum_probs=34.1
Q ss_pred CCCcchhhhcccCCceeEEcCCCCcccHHHHHHHHhcCCCCCCCCCc
Q 025507 140 HDCPVCCEYLFETRQDVIVLPCGHTIHKNCLKEMREHHQYACPICSK 186 (251)
Q Consensus 140 ~~CpICle~lf~s~~~~~~lpCgH~fH~~Ci~~wl~~~~~~CP~Cr~ 186 (251)
..||.|.- |.. .+..+.-|||.|+.+||..-|....+.||.|.+
T Consensus 275 LkCplc~~-Llr--np~kT~cC~~~fc~eci~~al~dsDf~CpnC~r 318 (427)
T COG5222 275 LKCPLCHC-LLR--NPMKTPCCGHTFCDECIGTALLDSDFKCPNCSR 318 (427)
T ss_pred ccCcchhh-hhh--CcccCccccchHHHHHHhhhhhhccccCCCccc
Confidence 67999987 433 244455689999999999866556799999986
No 121
>PHA03096 p28-like protein; Provisional
Probab=78.63 E-value=1.3 Score=41.16 Aligned_cols=47 Identities=17% Similarity=0.277 Sum_probs=32.1
Q ss_pred CCCcchhhhcccC---CceeEEc-CCCCcccHHHHHHHHhcC--CCCCCCCCc
Q 025507 140 HDCPVCCEYLFET---RQDVIVL-PCGHTIHKNCLKEMREHH--QYACPICSK 186 (251)
Q Consensus 140 ~~CpICle~lf~s---~~~~~~l-pCgH~fH~~Ci~~wl~~~--~~~CP~Cr~ 186 (251)
-.|.||+|..... ......| .|.|.|+..|+..|.... ..+||.||.
T Consensus 179 k~c~ic~e~~~~k~~~~~~fgil~~c~h~fc~~ci~~wr~~~~~~e~~~~c~~ 231 (284)
T PHA03096 179 KICGICLENIKAKYIIKKYYGILSEIKHEFNIFCIKIWMTESLYKETEPENRR 231 (284)
T ss_pred hhcccchhhhhhhccccccccccccCCcHHHHHHHHHHHHhhhhcccCccccc
Confidence 5799999876542 1222345 699999999999998653 234666653
No 122
>TIGR00595 priA primosomal protein N'. All proteins in this family for which functions are known are components of the primosome which is involved in replication, repair, and recombination.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=76.74 E-value=2.4 Score=42.14 Aligned_cols=50 Identities=22% Similarity=0.647 Sum_probs=41.7
Q ss_pred eeecCcCCCeecCcchhhhhccCcCcCcCCCCCCCCcccceeecCCCCccccccccCcCCCCc
Q 025507 14 RIRAPCCNEIFDCRHCHNEAMNNINVDQKLRHDIPRHEVNQVICSLCGTEQKVQQVCVNCGVC 76 (251)
Q Consensus 14 ~i~~pcC~~~y~Cr~CHde~~~~~~~~~~~~H~~~r~~~~~v~C~~C~~~q~~~~~C~~Cg~~ 76 (251)
.+.|.-||....|..|.-.++ -|. ....+.|-.|+..+++...||+||..
T Consensus 213 ~~~C~~Cg~~~~C~~C~~~l~---------~h~----~~~~l~Ch~Cg~~~~~~~~Cp~C~s~ 262 (505)
T TIGR00595 213 NLLCRSCGYILCCPNCDVSLT---------YHK----KEGKLRCHYCGYQEPIPKTCPQCGSE 262 (505)
T ss_pred eeEhhhCcCccCCCCCCCceE---------Eec----CCCeEEcCCCcCcCCCCCCCCCCCCC
Confidence 378999999999999987763 342 23589999999999999999999875
No 123
>PRK14714 DNA polymerase II large subunit; Provisional
Probab=75.29 E-value=2.9 Score=45.84 Aligned_cols=48 Identities=31% Similarity=0.715 Sum_probs=26.6
Q ss_pred eeecCCCCccccccccCcCCCCcc-ceEecCcccccc-CCCCCCeeecCCCC
Q 025507 54 QVICSLCGTEQKVQQVCVNCGVCM-GEYFCESCKLFD-DDTSKKQYHCDGCG 103 (251)
Q Consensus 54 ~v~C~~C~~~q~~~~~C~~Cg~~f-~~y~C~~C~~~d-~~~~k~~~HC~~Cg 103 (251)
...|..|+++-+ ...|++||... ..|+|+.|..-- .++.. ...|+.||
T Consensus 667 ~rkCPkCG~~t~-~~fCP~CGs~te~vy~CPsCGaev~~des~-a~~CP~CG 716 (1337)
T PRK14714 667 RRRCPSCGTETY-ENRCPDCGTHTEPVYVCPDCGAEVPPDESG-RVECPRCD 716 (1337)
T ss_pred EEECCCCCCccc-cccCcccCCcCCCceeCccCCCccCCCccc-cccCCCCC
Confidence 467777777633 34777777665 345566665531 11122 44566666
No 124
>PF14446 Prok-RING_1: Prokaryotic RING finger family 1
Probab=75.28 E-value=3.2 Score=29.22 Aligned_cols=36 Identities=25% Similarity=0.628 Sum_probs=26.6
Q ss_pred CCCCCcchhhhcccCCceeEEcCCCCcccHHHHHHH
Q 025507 138 MHHDCPVCCEYLFETRQDVIVLPCGHTIHKNCLKEM 173 (251)
Q Consensus 138 ~~~~CpICle~lf~s~~~~~~lpCgH~fH~~Ci~~w 173 (251)
+...|++|.+.+.+..+.++-..||=.+|+.|....
T Consensus 4 ~~~~C~~Cg~~~~~~dDiVvCp~CgapyHR~C~~~~ 39 (54)
T PF14446_consen 4 EGCKCPVCGKKFKDGDDIVVCPECGAPYHRDCWEKA 39 (54)
T ss_pred cCccChhhCCcccCCCCEEECCCCCCcccHHHHhhC
Confidence 456899999976555544444579999999997653
No 125
>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=73.34 E-value=3.8 Score=28.03 Aligned_cols=44 Identities=25% Similarity=0.554 Sum_probs=19.4
Q ss_pred CCcchhhhcccCCceeEEcCCCCc--ccHHHHHHH-HhcCCCCCCCCCcC
Q 025507 141 DCPVCCEYLFETRQDVIVLPCGHT--IHKNCLKEM-REHHQYACPICSKS 187 (251)
Q Consensus 141 ~CpICle~lf~s~~~~~~lpCgH~--fH~~Ci~~w-l~~~~~~CP~Cr~~ 187 (251)
.|||-...+.. +++...|.|. |-.+=+... .+.+...||+|+++
T Consensus 4 ~CPls~~~i~~---P~Rg~~C~H~~CFDl~~fl~~~~~~~~W~CPiC~~~ 50 (50)
T PF02891_consen 4 RCPLSFQRIRI---PVRGKNCKHLQCFDLESFLESNQRTPKWKCPICNKP 50 (50)
T ss_dssp B-TTTSSB-SS---EEEETT--SS--EEHHHHHHHHHHS---B-TTT---
T ss_pred eCCCCCCEEEe---CccCCcCcccceECHHHHHHHhhccCCeECcCCcCc
Confidence 68888875533 7778889987 333222222 12245689999864
No 126
>PHA00626 hypothetical protein
Probab=73.18 E-value=3.3 Score=29.52 Aligned_cols=7 Identities=43% Similarity=1.265 Sum_probs=3.9
Q ss_pred cCcCCCC
Q 025507 69 VCVNCGV 75 (251)
Q Consensus 69 ~C~~Cg~ 75 (251)
.||+||.
T Consensus 2 ~CP~CGS 8 (59)
T PHA00626 2 SCPKCGS 8 (59)
T ss_pred CCCCCCC
Confidence 3566655
No 127
>PF06524 NOA36: NOA36 protein; InterPro: IPR010531 This family consists of several NOA36 proteins which contain 29 highly conserved cysteine residues. The function of this protein is unknown.; GO: 0008270 zinc ion binding, 0005634 nucleus
Probab=72.29 E-value=1.7 Score=40.04 Aligned_cols=51 Identities=25% Similarity=0.647 Sum_probs=33.6
Q ss_pred CCeecCcchhhhhccCcCcCcCCCCCCCCcccceeecCCCCccccccccCcCCCCccceEecCcccc
Q 025507 21 NEIFDCRHCHNEAMNNINVDQKLRHDIPRHEVNQVICSLCGTEQKVQQVCVNCGVCMGEYFCESCKL 87 (251)
Q Consensus 21 ~~~y~Cr~CHde~~~~~~~~~~~~H~~~r~~~~~v~C~~C~~~q~~~~~C~~Cg~~f~~y~C~~C~~ 87 (251)
|++|.|-+|++-+- +|-++.-.+. |+....-.-.|.+|+. +|.|.|..||.
T Consensus 140 Grif~CsfC~~flC--------EDDQFEHQAs-------CQvLe~E~~KC~SCNr-lGq~sCLRCK~ 190 (314)
T PF06524_consen 140 GRIFKCSFCDNFLC--------EDDQFEHQAS-------CQVLESETFKCQSCNR-LGQYSCLRCKI 190 (314)
T ss_pred CeEEEeecCCCeee--------ccchhhhhhh-------hhhhhccccccccccc-ccchhhhheee
Confidence 66899999988764 3333333221 4444444567888875 78999999984
No 128
>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]
Probab=72.03 E-value=4 Score=42.56 Aligned_cols=55 Identities=24% Similarity=0.544 Sum_probs=43.1
Q ss_pred eeecCcCCCeecCcchhhhhccCcCcCcCCCCCCCCcccceeecCCCCccccccccCcCCCCccceEe
Q 025507 14 RIRAPCCNEIFDCRHCHNEAMNNINVDQKLRHDIPRHEVNQVICSLCGTEQKVQQVCVNCGVCMGEYF 81 (251)
Q Consensus 14 ~i~~pcC~~~y~Cr~CHde~~~~~~~~~~~~H~~~r~~~~~v~C~~C~~~q~~~~~C~~Cg~~f~~y~ 81 (251)
.+.|.-||..+.|.+|=.-++ -|. .+..+.|-.|+.++++...||+||...=+|+
T Consensus 435 ~l~C~~Cg~v~~Cp~Cd~~lt---------~H~----~~~~L~CH~Cg~~~~~p~~Cp~Cgs~~L~~~ 489 (730)
T COG1198 435 LLLCRDCGYIAECPNCDSPLT---------LHK----ATGQLRCHYCGYQEPIPQSCPECGSEHLRAV 489 (730)
T ss_pred eeecccCCCcccCCCCCcceE---------Eec----CCCeeEeCCCCCCCCCCCCCCCCCCCeeEEe
Confidence 478999999999999976553 221 2368999999999999999999998854444
No 129
>KOG1812 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=70.47 E-value=2 Score=41.31 Aligned_cols=50 Identities=30% Similarity=0.618 Sum_probs=33.7
Q ss_pred CCCCcchhhhcccCCceeEEcCCCCcccHHHHHHHHhc-----CCCCCC--CCCcCc
Q 025507 139 HHDCPVCCEYLFETRQDVIVLPCGHTIHKNCLKEMREH-----HQYACP--ICSKSV 188 (251)
Q Consensus 139 ~~~CpICle~lf~s~~~~~~lpCgH~fH~~Ci~~wl~~-----~~~~CP--~Cr~~~ 188 (251)
...|.||............++.|+|.|+.+|+.++++. ...+|| .|...+
T Consensus 146 ~~~C~iC~~e~~~~~~~f~~~~C~H~fC~~C~k~~iev~~~~~~~~~C~~~~C~~~l 202 (384)
T KOG1812|consen 146 KEECGICFVEDPEAEDMFSVLKCGHRFCKDCVKQHIEVKLLSGTVIRCPHDGCESRL 202 (384)
T ss_pred cccCccCccccccHhhhHHHhcccchhhhHHhHHHhhhhhccCCCccCCCCCCCccC
Confidence 56899999333333333336789999999999998873 245676 344443
No 130
>COG5109 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=69.70 E-value=3.5 Score=38.97 Aligned_cols=45 Identities=33% Similarity=0.754 Sum_probs=37.7
Q ss_pred CCCcchhhhcccCCceeEEcCCCCcccHHHHHHHHhcC--CCCCCCCC
Q 025507 140 HDCPVCCEYLFETRQDVIVLPCGHTIHKNCLKEMREHH--QYACPICS 185 (251)
Q Consensus 140 ~~CpICle~lf~s~~~~~~lpCgH~fH~~Ci~~wl~~~--~~~CP~Cr 185 (251)
..|||=.| +-+...+++.|.|||.+=.+-+...-+.+ ++.||-|-
T Consensus 337 FiCPVlKe-~~t~ENpP~ml~CgHVIskeal~~LS~nG~~~FKCPYCP 383 (396)
T COG5109 337 FICPVLKE-LCTDENPPVMLECGHVISKEALSVLSQNGVLSFKCPYCP 383 (396)
T ss_pred eeccccHh-hhcccCCCeeeeccceeeHHHHHHHhhcCcEEeeCCCCC
Confidence 47999887 56667789999999999999999987654 46799997
No 131
>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=68.97 E-value=3.2 Score=34.20 Aligned_cols=27 Identities=19% Similarity=0.380 Sum_probs=20.6
Q ss_pred cccCcCCCCccceEecCccccccCCCCCCeeecCCCCcc
Q 025507 67 QQVCVNCGVCMGEYFCESCKLFDDDTSKKQYHCDGCGIC 105 (251)
Q Consensus 67 ~~~C~~Cg~~f~~y~C~~C~~~d~~~~k~~~HC~~CgiC 105 (251)
...|++||++ || +.+|.+-.|++||.=
T Consensus 9 Kr~Cp~cg~k----------FY--DLnk~p~vcP~cg~~ 35 (129)
T TIGR02300 9 KRICPNTGSK----------FY--DLNRRPAVSPYTGEQ 35 (129)
T ss_pred cccCCCcCcc----------cc--ccCCCCccCCCcCCc
Confidence 4679999984 56 456899999988853
No 132
>KOG4367 consensus Predicted Zn-finger protein [Function unknown]
Probab=67.77 E-value=3 Score=41.07 Aligned_cols=33 Identities=30% Similarity=0.926 Sum_probs=27.4
Q ss_pred CCCCcchhhhcccCCceeEEcCCCCcccHHHHHHHHh
Q 025507 139 HHDCPVCCEYLFETRQDVIVLPCGHTIHKNCLKEMRE 175 (251)
Q Consensus 139 ~~~CpICle~lf~s~~~~~~lpCgH~fH~~Ci~~wl~ 175 (251)
+..||||.. +|. ++.+|||||.+++.|...-+.
T Consensus 4 elkc~vc~~-f~~---epiil~c~h~lc~~ca~~~~~ 36 (699)
T KOG4367|consen 4 ELKCPVCGS-FYR---EPIILPCSHNLCQACARNILV 36 (699)
T ss_pred cccCceehh-hcc---CceEeecccHHHHHHHHhhcc
Confidence 568999997 565 467999999999999998654
No 133
>PF07282 OrfB_Zn_ribbon: Putative transposase DNA-binding domain; InterPro: IPR010095 This entry represents a region of a sequence similarity between a family of putative transposases of Thermoanaerobacter tengcongensis, smaller related proteins from Bacillus anthracis, putative transposes described by IPR001959 from INTERPRO, and other proteins. More information about these proteins can be found at Protein of the Month: Transposase [].
Probab=67.45 E-value=4.4 Score=28.83 Aligned_cols=27 Identities=30% Similarity=0.760 Sum_probs=17.1
Q ss_pred cccCcCCCCccceEecCccccccCCCCCCeeecCCCCc
Q 025507 67 QQVCVNCGVCMGEYFCESCKLFDDDTSKKQYHCDGCGI 104 (251)
Q Consensus 67 ~~~C~~Cg~~f~~y~C~~C~~~d~~~~k~~~HC~~Cgi 104 (251)
++.|+.||..... ......|.|+.||.
T Consensus 28 Sq~C~~CG~~~~~-----------~~~~r~~~C~~Cg~ 54 (69)
T PF07282_consen 28 SQTCPRCGHRNKK-----------RRSGRVFTCPNCGF 54 (69)
T ss_pred ccCccCccccccc-----------ccccceEEcCCCCC
Confidence 5778888877655 23445666666664
No 134
>KOG2068 consensus MOT2 transcription factor [Transcription]
Probab=65.54 E-value=5.1 Score=37.89 Aligned_cols=53 Identities=28% Similarity=0.600 Sum_probs=39.8
Q ss_pred CCCCCCcchhhhcccCCceeEEcCCCCcccHHHHHHHHhcCCCCCCCCCcCccc
Q 025507 137 AMHHDCPVCCEYLFETRQDVIVLPCGHTIHKNCLKEMREHHQYACPICSKSVCD 190 (251)
Q Consensus 137 ~~~~~CpICle~lf~s~~~~~~lpCgH~fH~~Ci~~wl~~~~~~CP~Cr~~~~~ 190 (251)
+-...||||-+++..........|||+.++..|+..-.. .+.+||.||++...
T Consensus 247 ~v~~s~p~~~~~~~~~d~~~lP~~~~~~~~l~~~~t~~~-~~~~~~~~rk~~~~ 299 (327)
T KOG2068|consen 247 SVPPSCPICYEDLDLTDSNFLPCPCGFRLCLFCHKTISD-GDGRCPGCRKPYER 299 (327)
T ss_pred ccCCCCCCCCCcccccccccccccccccchhhhhhcccc-cCCCCCccCCcccc
Confidence 445789999997644444444457899999999998876 46899999987653
No 135
>PF03107 C1_2: C1 domain; InterPro: IPR004146 This short domain is rich in cysteines and histidines. The pattern of conservation is similar to that found in DAG_PE-bind (IPR002219 from INTERPRO), therefore we have termed this domain DC1 for divergent C1 domain. This domain probably also binds to two zinc ions. The function of proteins with this domain is uncertain, however this domain may bind to molecules such as diacylglycerol. This family are found in plant proteins.
Probab=65.29 E-value=4.9 Score=24.46 Aligned_cols=20 Identities=35% Similarity=0.894 Sum_probs=14.0
Q ss_pred CCCcceecCCcc-eeeccCCC
Q 025507 101 GCGICRIGGCDN-FFHCNKCR 120 (251)
Q Consensus 101 ~CgiCR~g~~~~-~fHC~~C~ 120 (251)
.|++|+.-.... +|+|+.|+
T Consensus 2 ~C~~C~~~~~~~~~Y~C~~c~ 22 (30)
T PF03107_consen 2 WCDVCRRKIDGFYFYHCSECC 22 (30)
T ss_pred CCCCCCCCcCCCEeEEeCCCC
Confidence 467776655444 88888887
No 136
>PRK04023 DNA polymerase II large subunit; Validated
Probab=65.16 E-value=5.4 Score=42.93 Aligned_cols=50 Identities=26% Similarity=0.641 Sum_probs=37.5
Q ss_pred cceeecCCCCccccccccCcCCCCc-cceEecCccccccCCCCCCeeecCCCCccee
Q 025507 52 VNQVICSLCGTEQKVQQVCVNCGVC-MGEYFCESCKLFDDDTSKKQYHCDGCGICRI 107 (251)
Q Consensus 52 ~~~v~C~~C~~~q~~~~~C~~Cg~~-f~~y~C~~C~~~d~~~~k~~~HC~~CgiCR~ 107 (251)
+..-.|..|+++. +...|++||.. ..-|||+.|.-- -..|.|++||.=..
T Consensus 624 Vg~RfCpsCG~~t-~~frCP~CG~~Te~i~fCP~CG~~-----~~~y~CPKCG~El~ 674 (1121)
T PRK04023 624 IGRRKCPSCGKET-FYRRCPFCGTHTEPVYRCPRCGIE-----VEEDECEKCGREPT 674 (1121)
T ss_pred ccCccCCCCCCcC-CcccCCCCCCCCCcceeCccccCc-----CCCCcCCCCCCCCC
Confidence 3455899999985 66799999974 677899999332 33478999996443
No 137
>PRK14873 primosome assembly protein PriA; Provisional
Probab=63.39 E-value=6.6 Score=40.52 Aligned_cols=49 Identities=22% Similarity=0.493 Sum_probs=39.2
Q ss_pred eeecCcCCCeecCcchhhhhccCcCcCcCCCCCCCCcccceeecCCCCccccccccCcCCCCc
Q 025507 14 RIRAPCCNEIFDCRHCHNEAMNNINVDQKLRHDIPRHEVNQVICSLCGTEQKVQQVCVNCGVC 76 (251)
Q Consensus 14 ~i~~pcC~~~y~Cr~CHde~~~~~~~~~~~~H~~~r~~~~~v~C~~C~~~q~~~~~C~~Cg~~ 76 (251)
.+.|..||....|.+|.-.++ -|. ....+.|-.|+..+ ....|++||..
T Consensus 383 ~l~C~~Cg~~~~C~~C~~~L~---------~h~----~~~~l~Ch~CG~~~-~p~~Cp~Cgs~ 431 (665)
T PRK14873 383 SLACARCRTPARCRHCTGPLG---------LPS----AGGTPRCRWCGRAA-PDWRCPRCGSD 431 (665)
T ss_pred eeEhhhCcCeeECCCCCCcee---------Eec----CCCeeECCCCcCCC-cCccCCCCcCC
Confidence 478999999999999998764 232 23588999999876 57799999886
No 138
>PRK05580 primosome assembly protein PriA; Validated
Probab=63.06 E-value=6.6 Score=40.42 Aligned_cols=51 Identities=22% Similarity=0.575 Sum_probs=41.6
Q ss_pred eeecCcCCCeecCcchhhhhccCcCcCcCCCCCCCCcccceeecCCCCccccccccCcCCCCcc
Q 025507 14 RIRAPCCNEIFDCRHCHNEAMNNINVDQKLRHDIPRHEVNQVICSLCGTEQKVQQVCVNCGVCM 77 (251)
Q Consensus 14 ~i~~pcC~~~y~Cr~CHde~~~~~~~~~~~~H~~~r~~~~~v~C~~C~~~q~~~~~C~~Cg~~f 77 (251)
.+.|.-||....|..|.-.++ -|. ....+.|-.|+..++....||+||...
T Consensus 381 ~~~C~~Cg~~~~C~~C~~~l~---------~h~----~~~~l~Ch~Cg~~~~~~~~Cp~Cg~~~ 431 (679)
T PRK05580 381 FLLCRDCGWVAECPHCDASLT---------LHR----FQRRLRCHHCGYQEPIPKACPECGSTD 431 (679)
T ss_pred ceEhhhCcCccCCCCCCCcee---------EEC----CCCeEECCCCcCCCCCCCCCCCCcCCe
Confidence 478999999999999987663 332 236899999999999889999998863
No 139
>PF05191 ADK_lid: Adenylate kinase, active site lid; InterPro: IPR007862 Adenylate kinases (ADK; 2.7.4.3 from EC) are phosphotransferases that catalyse the Mg-dependent reversible conversion of ATP and AMP to two molecules of ADP, an essential reaction for many processes in living cells. In large variants of adenylate kinase, the AMP and ATP substrates are buried in a domain that undergoes conformational changes from an open to a closed state when bound to substrate; the ligand is then contained within a highly specific environment required for catalysis. Adenylate kinase is a 3-domain protein consisting of a large central CORE domain flanked by a LID domain on one side and the AMP-binding NMPbind domain on the other []. The LID domain binds ATP and covers the phosphates at the active site. The substrates first bind the CORE domain, followed by closure of the active site by the LID and NMPbind domains. Comparisons of adenylate kinases have revealed a particular divergence in the active site lid. In some organisms, particularly the Gram-positive bacteria, residues in the lid domain have been mutated to cysteines and these cysteine residues (two CX(n)C motifs) are responsible for the binding of a zinc ion. The bound zinc ion in the lid domain is clearly structurally homologous to Zinc-finger domains. However, it is unclear whether the adenylate kinase lid is a novel zinc-finger DNA/RNA binding domain, or that the lid bound zinc serves a purely structural function [].; GO: 0004017 adenylate kinase activity; PDB: 3BE4_A 2OSB_B 2ORI_A 2EU8_A 3DL0_A 1P3J_A 2QAJ_A 2OO7_A 2P3S_A 3DKV_A ....
Probab=63.00 E-value=1.9 Score=27.68 Aligned_cols=27 Identities=33% Similarity=0.725 Sum_probs=15.3
Q ss_pred cCcCCCCccceEecCccccccCCCCCCeeecCCCCc
Q 025507 69 VCVNCGVCMGEYFCESCKLFDDDTSKKQYHCDGCGI 104 (251)
Q Consensus 69 ~C~~Cg~~f~~y~C~~C~~~d~~~~k~~~HC~~Cgi 104 (251)
.|++||+.++.+| ++.|..--||.||-
T Consensus 3 ~C~~Cg~~Yh~~~---------~pP~~~~~Cd~cg~ 29 (36)
T PF05191_consen 3 ICPKCGRIYHIEF---------NPPKVEGVCDNCGG 29 (36)
T ss_dssp EETTTTEEEETTT---------B--SSTTBCTTTTE
T ss_pred CcCCCCCcccccc---------CCCCCCCccCCCCC
Confidence 4666776666554 34555566777764
No 140
>KOG2272 consensus Focal adhesion protein PINCH-1, contains LIM domains [Signal transduction mechanisms; Cytoskeleton]
Probab=62.58 E-value=1.2 Score=40.91 Aligned_cols=123 Identities=21% Similarity=0.576 Sum_probs=66.3
Q ss_pred ecCcchhhhhccCcCcCcCCCCCCCCcccceeecCCCCccccccccCcCCCCccceEecCccccc-cCCC---CCCeeec
Q 025507 24 FDCRHCHNEAMNNINVDQKLRHDIPRHEVNQVICSLCGTEQKVQQVCVNCGVCMGEYFCESCKLF-DDDT---SKKQYHC 99 (251)
Q Consensus 24 y~Cr~CHde~~~~~~~~~~~~H~~~r~~~~~v~C~~C~~~q~~~~~C~~Cg~~f~~y~C~~C~~~-d~~~---~k~~~HC 99 (251)
|.|.+|-..++ |--+-|.+ ..++|-.|+..-.+ +.-|+|-|.+|+-. |+++ .-++||
T Consensus 100 F~Cd~Cn~~La---------d~gf~rnq-gr~LC~~Cn~k~Ka--------~~~g~YvC~KCh~~iD~~~l~fr~d~yH- 160 (332)
T KOG2272|consen 100 FRCDLCNKHLA---------DQGFYRNQ-GRALCRECNQKEKA--------KGRGRYVCQKCHAHIDEQPLTFRGDPYH- 160 (332)
T ss_pred chhHHHHHHHh---------hhhhHhhc-chHHhhhhhhhhcc--------cccceeehhhhhhhcccccccccCCCCC-
Confidence 56666666553 22234443 46677777655333 23689999999754 5543 225555
Q ss_pred CCCCcceecCCcceeeccCCCcceec---cccccccccCCCCCCCCcchhhhcccCCceeEEcCCCCcccHHHHH----H
Q 025507 100 DGCGICRIGGCDNFFHCNKCRCCYSM---LLKNSHPCVEGAMHHDCPVCCEYLFETRQDVIVLPCGHTIHKNCLK----E 172 (251)
Q Consensus 100 ~~CgiCR~g~~~~~fHC~~C~~c~~~---~l~~~H~C~e~~~~~~CpICle~lf~s~~~~~~lpCgH~fH~~Ci~----~ 172 (251)
-.-|.|.+||.=+.. ++++.=-|..=-...-+|||.. |.-.+-..=|. .
T Consensus 161 -----------~yHFkCt~C~keL~sdaRevk~eLyClrChD~mgipiCga-------------C~rpIeervi~amgKh 216 (332)
T KOG2272|consen 161 -----------PYHFKCTTCGKELTSDAREVKGELYCLRCHDKMGIPICGA-------------CRRPIEERVIFAMGKH 216 (332)
T ss_pred -----------ccceecccccccccchhhhhccceeccccccccCCccccc-------------ccCchHHHHHHHhccc
Confidence 256889999877644 3333333332222234445443 11111111121 1
Q ss_pred HHhcCCCCCCCCCcCccc
Q 025507 173 MREHHQYACPICSKSVCD 190 (251)
Q Consensus 173 wl~~~~~~CP~Cr~~~~~ 190 (251)
|-. .++.|..|-+++..
T Consensus 217 WHv-eHFvCa~CekPFlG 233 (332)
T KOG2272|consen 217 WHV-EHFVCAKCEKPFLG 233 (332)
T ss_pred cch-hheeehhcCCcccc
Confidence 422 56889999988875
No 141
>PRK14714 DNA polymerase II large subunit; Provisional
Probab=61.34 E-value=7.5 Score=42.82 Aligned_cols=33 Identities=30% Similarity=0.754 Sum_probs=26.0
Q ss_pred ccCcCCCCccceEecCccccccCCCCCCeeecCCCCc
Q 025507 68 QVCVNCGVCMGEYFCESCKLFDDDTSKKQYHCDGCGI 104 (251)
Q Consensus 68 ~~C~~Cg~~f~~y~C~~C~~~d~~~~k~~~HC~~Cgi 104 (251)
-.||+||..-...||+.|.-. .+.+|+|+.||.
T Consensus 668 rkCPkCG~~t~~~fCP~CGs~----te~vy~CPsCGa 700 (1337)
T PRK14714 668 RRCPSCGTETYENRCPDCGTH----TEPVYVCPDCGA 700 (1337)
T ss_pred EECCCCCCccccccCcccCCc----CCCceeCccCCC
Confidence 579999997767799999644 345788888887
No 142
>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=61.03 E-value=6.9 Score=26.35 Aligned_cols=33 Identities=27% Similarity=0.545 Sum_probs=20.6
Q ss_pred eEEcCCCCCCcccccee---eeccCCCCCCccc-ccc
Q 025507 217 WILCNDCGKTSNVQFHV---LAQKCPNCKSYNT-RLT 249 (251)
Q Consensus 217 ~IlCndC~~~s~~~~h~---lg~kC~~C~SyNT-~~~ 249 (251)
...|.+|+...++-..+ -...|+.|||-+. +++
T Consensus 5 ey~C~~Cg~~fe~~~~~~~~~~~~CP~Cg~~~~~r~~ 41 (52)
T TIGR02605 5 EYRCTACGHRFEVLQKMSDDPLATCPECGGEKLRRLL 41 (52)
T ss_pred EEEeCCCCCEeEEEEecCCCCCCCCCCCCCCceeEEe
Confidence 35688888766553221 1237999998776 444
No 143
>KOG0827 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=60.64 E-value=0.98 Score=43.65 Aligned_cols=52 Identities=19% Similarity=0.422 Sum_probs=43.7
Q ss_pred CCCCCCcchhhhcccCCceeEEcCCCCcccHHHHHHHHhcCCCCCCCCCcCcc
Q 025507 137 AMHHDCPVCCEYLFETRQDVIVLPCGHTIHKNCLKEMREHHQYACPICSKSVC 189 (251)
Q Consensus 137 ~~~~~CpICle~lf~s~~~~~~lpCgH~fH~~Ci~~wl~~~~~~CP~Cr~~~~ 189 (251)
+....++||.+.+...-+....+-|||..|.++|.+||.. ...+|.|++.+.
T Consensus 194 slv~sl~I~~~slK~~y~k~~~~~~g~~~~~~kL~k~L~~-~~kl~~~~rel~ 245 (465)
T KOG0827|consen 194 SLVGSLSICFESLKQNYDKISAIVCGHIYHHGKLSKWLAT-KRKLPSCRRELP 245 (465)
T ss_pred HHHhhhHhhHHHHHHHHHHHHHHhhcccchhhHHHHHHHH-HHHhHHHHhhhh
Confidence 3456899999988776556677889999999999999985 578999998886
No 144
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=60.64 E-value=6.2 Score=26.17 Aligned_cols=30 Identities=20% Similarity=0.428 Sum_probs=19.3
Q ss_pred eEEcCCCCCCccccceeeeccCCCCCCccc
Q 025507 217 WILCNDCGKTSNVQFHVLAQKCPNCKSYNT 246 (251)
Q Consensus 217 ~IlCndC~~~s~~~~h~lg~kC~~C~SyNT 246 (251)
...|.+|++.....-.....+|+.||+.-.
T Consensus 3 ~y~C~~CG~~~~~~~~~~~~~Cp~CG~~~~ 32 (46)
T PRK00398 3 EYKCARCGREVELDEYGTGVRCPYCGYRIL 32 (46)
T ss_pred EEECCCCCCEEEECCCCCceECCCCCCeEE
Confidence 467888887654433333578888887543
No 145
>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional
Probab=60.54 E-value=6.4 Score=28.24 Aligned_cols=34 Identities=24% Similarity=0.591 Sum_probs=26.6
Q ss_pred ceeecCCCCccccccccCcCCCCccceEecCccccc
Q 025507 53 NQVICSLCGTEQKVQQVCVNCGVCMGEYFCESCKLF 88 (251)
Q Consensus 53 ~~v~C~~C~~~q~~~~~C~~Cg~~f~~y~C~~C~~~ 88 (251)
....|..|+++. -..|..|....+.|-|++|-|-
T Consensus 24 ~~F~CPnCG~~~--I~RC~~CRk~~~~Y~CP~CGF~ 57 (59)
T PRK14890 24 VKFLCPNCGEVI--IYRCEKCRKQSNPYTCPKCGFE 57 (59)
T ss_pred CEeeCCCCCCee--EeechhHHhcCCceECCCCCCc
Confidence 578899998752 2368889999999999998763
No 146
>COG1656 Uncharacterized conserved protein [Function unknown]
Probab=60.26 E-value=6.1 Score=33.91 Aligned_cols=51 Identities=24% Similarity=0.402 Sum_probs=34.9
Q ss_pred CCCCCCCCcCccchhHHHHHHHHHHhcCCCCHhhhcCceeEEcCCCCCCccccceee
Q 025507 178 QYACPICSKSVCDMSKVWEKYDREIAATPMPEAYLNKKVWILCNDCGKTSNVQFHVL 234 (251)
Q Consensus 178 ~~~CP~Cr~~~~~~~~~~~~ld~~i~~~p~P~e~~~~~~~IlCndC~~~s~~~~h~l 234 (251)
-.+||.|+.++...+. +++.+.-.|..|.+......|..|++..+..-||=
T Consensus 97 ~~RCp~CN~~L~~vs~------eev~~~Vp~~~~~~~~~f~~C~~CgkiYW~GsHw~ 147 (165)
T COG1656 97 FSRCPECNGELEKVSR------EEVKEKVPEKVYRNYEEFYRCPKCGKIYWKGSHWR 147 (165)
T ss_pred cccCcccCCEeccCcH------HHHhhccchhhhhcccceeECCCCcccccCchHHH
Confidence 4679999998876432 22222222345666666777999999998888873
No 147
>KOG1044 consensus Actin-binding LIM Zn-finger protein Limatin involved in axon guidance [Signal transduction mechanisms; Cytoskeleton]
Probab=59.33 E-value=11 Score=38.40 Aligned_cols=137 Identities=24% Similarity=0.439 Sum_probs=71.2
Q ss_pred CCCCCeeecCCCCc---ceecC-Ccceee-----ccCCCcceeccccccccccCCCCCCCCcchhhhcccCCceeEEcCC
Q 025507 91 DTSKKQYHCDGCGI---CRIGG-CDNFFH-----CNKCRCCYSMLLKNSHPCVEGAMHHDCPVCCEYLFETRQDVIVLPC 161 (251)
Q Consensus 91 ~~~k~~~HC~~Cgi---CR~g~-~~~~fH-----C~~C~~c~~~~l~~~H~C~e~~~~~~CpICle~lf~s~~~~~~lpC 161 (251)
...+..-||+.|+- +-|+. .+++|| |+.|+.=+.-..+. ++.-|+-.. . .-|.+. .. ..++..=
T Consensus 11 ~~~~~~i~c~~c~~kc~gevlrv~d~~fhi~cf~c~~cg~~la~~gff-~k~~~~~yg-t-~~c~~~--~~--gevvsa~ 83 (670)
T KOG1044|consen 11 QTGKQGIKCDKCRKKCSGEVLRVNDNHFHINCFQCKKCGRNLAEGGFF-TKPENRLYG-T-DDCRAF--VE--GEVVSTL 83 (670)
T ss_pred cccccceehhhhCCccccceeEeeccccceeeeeccccCCCcccccce-ecccceeec-c-cchhhh--cc--ceeEecc
Confidence 34667788888872 22221 345554 66666555544333 344442211 1 334442 21 2334445
Q ss_pred CCcccHHHHHHHHhcCCCCCCCCCcCccchhH-HH--HHHHHHHhcCCCCHhhhcCceeEEcCCCCCCc---------cc
Q 025507 162 GHTIHKNCLKEMREHHQYACPICSKSVCDMSK-VW--EKYDREIAATPMPEAYLNKKVWILCNDCGKTS---------NV 229 (251)
Q Consensus 162 gH~fH~~Ci~~wl~~~~~~CP~Cr~~~~~~~~-~~--~~ld~~i~~~p~P~e~~~~~~~IlCndC~~~s---------~~ 229 (251)
|-+||..| +.|-+|+.++..-.. .+ +...-+.-+++||-.-......-.|--|++.- ..
T Consensus 84 gktyh~~c---------f~cs~ck~pf~~g~~vt~~gk~~~c~~c~~~~~~~p~~~~~ps~cagc~~~lk~gq~llald~ 154 (670)
T KOG1044|consen 84 GKTYHPKC---------FSCSTCKSPFKSGDKVTFSGKECLCQTCSQPMPVSPAESYGPSTCAGCGEELKNGQALLALDK 154 (670)
T ss_pred cceecccc---------ceecccCCCCCCCCeeeecchhhhhhhhcCcccCCcccccCCccccchhhhhhccceeeeecc
Confidence 88888765 467788888752111 01 12222333455543211222344577777532 56
Q ss_pred cceeeeccCCCCCC
Q 025507 230 QFHVLAQKCPNCKS 243 (251)
Q Consensus 230 ~~h~lg~kC~~C~S 243 (251)
++|+..-||..|+-
T Consensus 155 qwhv~cfkc~~c~~ 168 (670)
T KOG1044|consen 155 QWHVSCFKCKSCSA 168 (670)
T ss_pred ceeeeeeehhhhcc
Confidence 89999999998864
No 148
>PF08271 TF_Zn_Ribbon: TFIIB zinc-binding; InterPro: IPR013137 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents a zinc finger motif found in transcription factor IIB (TFIIB). In eukaryotes the initiation of transcription of protein encoding genes by the polymerase II complexe (Pol II) is modulated by general and specific transcription factors. The general transcription factors operate through common promoters elements (such as the TATA box). At least seven different proteins associate to form the general transcription factors: TFIIA, -IIB, -IID, -IIE, -IIF, -IIG, and -IIH []. TFIIB and TFIID are responsible for promoter recognition and interaction with pol II; together with Pol II, they form a minimal initiation complex capable of transcription under certain conditions. The TATA box of a Pol II promoter is bound in the initiation complex by the TBP subunit of TFIID, which bends the DNA around the C-terminal domain of TFIIB whereas the N-terminal zinc finger of TFIIB interacts with Pol II [, ]. The TFIIB zinc finger adopts a zinc ribbon fold characterised by two beta-hairpins forming two structurally similar zinc-binding sub-sites []. The zinc finger contacts the rbp1 subunit of Pol II through its dock domain, a conserved region of about 70 amino acids located close to the polymerase active site []. In the Pol II complex this surface is located near the RNA exit groove. Interestingly this sequence is best conserved in the three polymerases that utilise a TFIIB-like general transcription factor (Pol II, Pol III, and archaeal RNA polymerase) but not in Pol I []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0006355 regulation of transcription, DNA-dependent; PDB: 1VD4_A 1PFT_A 3K1F_M 3K7A_M 1RO4_A 1RLY_A 1DL6_A.
Probab=58.98 E-value=8.8 Score=25.09 Aligned_cols=7 Identities=57% Similarity=1.322 Sum_probs=3.7
Q ss_pred CcCCCCc
Q 025507 70 CVNCGVC 76 (251)
Q Consensus 70 C~~Cg~~ 76 (251)
||+||..
T Consensus 3 Cp~Cg~~ 9 (43)
T PF08271_consen 3 CPNCGSK 9 (43)
T ss_dssp BTTTSSS
T ss_pred CcCCcCC
Confidence 5555554
No 149
>PF14353 CpXC: CpXC protein
Probab=58.84 E-value=1.9 Score=34.65 Aligned_cols=56 Identities=16% Similarity=0.390 Sum_probs=29.7
Q ss_pred CCCCCCCcCccchhHHHHHHHHHHhcCCCCHhhhcCceeEEcCCCCCCccccceeeec
Q 025507 179 YACPICSKSVCDMSKVWEKYDREIAATPMPEAYLNKKVWILCNDCGKTSNVQFHVLAQ 236 (251)
Q Consensus 179 ~~CP~Cr~~~~~~~~~~~~ld~~i~~~p~P~e~~~~~~~IlCndC~~~s~~~~h~lg~ 236 (251)
.+||.|+.++... .|..++......-...-..+..-.+.|..|+.+..+.+=+|++
T Consensus 2 itCP~C~~~~~~~--v~~~I~~~~~p~l~e~il~g~l~~~~CP~Cg~~~~~~~p~lY~ 57 (128)
T PF14353_consen 2 ITCPHCGHEFEFE--VWTSINADEDPELKEKILDGSLFSFTCPSCGHKFRLEYPLLYH 57 (128)
T ss_pred cCCCCCCCeeEEE--EEeEEcCcCCHHHHHHHHcCCcCEEECCCCCCceecCCCEEEE
Confidence 5799999887521 1211111000000001123344578899999998777666654
No 150
>PF14569 zf-UDP: Zinc-binding RING-finger; PDB: 1WEO_A.
Probab=58.59 E-value=10 Score=28.69 Aligned_cols=53 Identities=17% Similarity=0.434 Sum_probs=24.1
Q ss_pred CCCCCCcchhhhcccCCceeEEc---CCCCcccHHHHHHHHhcCCCCCCCCCcCcc
Q 025507 137 AMHHDCPVCCEYLFETRQDVIVL---PCGHTIHKNCLKEMREHHQYACPICSKSVC 189 (251)
Q Consensus 137 ~~~~~CpICle~lf~s~~~~~~l---pCgH~fH~~Ci~~wl~~~~~~CP~Cr~~~~ 189 (251)
.....|.||.|++-.....-+.. -|+--.++.|+.--.+.++..||.|+..+.
T Consensus 7 ~~~qiCqiCGD~VGl~~~Ge~FVAC~eC~fPvCr~CyEYErkeg~q~CpqCkt~yk 62 (80)
T PF14569_consen 7 LNGQICQICGDDVGLTENGEVFVACHECAFPVCRPCYEYERKEGNQVCPQCKTRYK 62 (80)
T ss_dssp -SS-B-SSS--B--B-SSSSB--S-SSS-----HHHHHHHHHTS-SB-TTT--B--
T ss_pred cCCcccccccCccccCCCCCEEEEEcccCCccchhHHHHHhhcCcccccccCCCcc
Confidence 34568999998764433332333 578889999999988878889999996554
No 151
>KOG0801 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=58.41 E-value=3.5 Score=35.54 Aligned_cols=29 Identities=31% Similarity=0.553 Sum_probs=23.5
Q ss_pred CCCCCcchhhhcccCCceeEEcCCCCcccH
Q 025507 138 MHHDCPVCCEYLFETRQDVIVLPCGHTIHK 167 (251)
Q Consensus 138 ~~~~CpICle~lf~s~~~~~~lpCgH~fH~ 167 (251)
...+|.||||+|.. .+.+..|||=-.+|+
T Consensus 176 dkGECvICLEdL~~-GdtIARLPCLCIYHK 204 (205)
T KOG0801|consen 176 DKGECVICLEDLEA-GDTIARLPCLCIYHK 204 (205)
T ss_pred cCCcEEEEhhhccC-CCceeccceEEEeec
Confidence 36799999998765 557888999888875
No 152
>smart00249 PHD PHD zinc finger. The plant homeodomain (PHD) finger is a C4HC3 zinc-finger-like motif found in nuclear proteins thought to be involved in epigenetics and chromatin-mediated transcriptional regulation. The PHD finger binds two zinc ions using the so-called 'cross-brace' motif and is thus structurally related to the KOG2907 consensus RNA polymerase I transcription factor TFIIS, subunit A12.2/RPA12 [Transcription]
Probab=57.32 E-value=3.9 Score=33.02 Aligned_cols=19 Identities=47% Similarity=0.950 Sum_probs=15.9
Q ss_pred eeeccCCCCC----CccccccCC
Q 025507 233 VLAQKCPNCK----SYNTRLTRG 251 (251)
Q Consensus 233 ~lg~kC~~C~----SyNT~~~~~ 251 (251)
.|-+||+.|| ||+|+|+|.
T Consensus 72 ~I~~kCpkCghe~m~Y~T~QlRS 94 (116)
T KOG2907|consen 72 VIKHKCPKCGHEEMSYHTLQLRS 94 (116)
T ss_pred chhccCcccCCchhhhhhhhccc
Confidence 4678999997 899999974
No 154
>PRK14559 putative protein serine/threonine phosphatase; Provisional
Probab=54.11 E-value=8.3 Score=39.73 Aligned_cols=34 Identities=29% Similarity=0.706 Sum_probs=18.6
Q ss_pred eeecCCCCccccccccCcCCCCc--cceEecCccccc
Q 025507 54 QVICSLCGTEQKVQQVCVNCGVC--MGEYFCESCKLF 88 (251)
Q Consensus 54 ~v~C~~C~~~q~~~~~C~~Cg~~--f~~y~C~~C~~~ 88 (251)
.-.|..|++.+.. ..|++||+. .+.-||+.|-..
T Consensus 15 akFC~~CG~~l~~-~~Cp~CG~~~~~~~~fC~~CG~~ 50 (645)
T PRK14559 15 NRFCQKCGTSLTH-KPCPQCGTEVPVDEAHCPNCGAE 50 (645)
T ss_pred CccccccCCCCCC-CcCCCCCCCCCcccccccccCCc
Confidence 4456666665432 356666654 455566666544
No 155
>KOG0298 consensus DEAD box-containing helicase-like transcription factor/DNA repair protein [Replication, recombination and repair]
Probab=53.28 E-value=5.4 Score=43.83 Aligned_cols=51 Identities=25% Similarity=0.471 Sum_probs=39.3
Q ss_pred CCCCCCcchhhhcccCCceeEEcCCCCcccHHHHHHHHhcCCCCCCCCCcCccch
Q 025507 137 AMHHDCPVCCEYLFETRQDVIVLPCGHTIHKNCLKEMREHHQYACPICSKSVCDM 191 (251)
Q Consensus 137 ~~~~~CpICle~lf~s~~~~~~lpCgH~fH~~Ci~~wl~~~~~~CP~Cr~~~~~~ 191 (251)
+....|+||++-+-. .-.+..|||.+...|+..|+.. +..||+|.....+.
T Consensus 1151 ~~~~~c~ic~dil~~---~~~I~~cgh~~c~~c~~~~l~~-~s~~~~~ksi~~df 1201 (1394)
T KOG0298|consen 1151 SGHFVCEICLDILRN---QGGIAGCGHEPCCRCDELWLYA-SSRCPICKSIKGDF 1201 (1394)
T ss_pred hcccchHHHHHHHHh---cCCeeeechhHhhhHHHHHHHH-hccCcchhhhhhhh
Confidence 445699999996543 1235569999999999999985 58999999666553
No 156
>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=52.67 E-value=9.4 Score=34.97 Aligned_cols=30 Identities=37% Similarity=0.658 Sum_probs=16.8
Q ss_pred cceeecCCCCccccc-cccCcCCCCccceEe
Q 025507 52 VNQVICSLCGTEQKV-QQVCVNCGVCMGEYF 81 (251)
Q Consensus 52 ~~~v~C~~C~~~q~~-~~~C~~Cg~~f~~y~ 81 (251)
.+-..|+.|+++=.. -..|++||..-..-+
T Consensus 195 ~R~L~Cs~C~t~W~~~R~~Cp~Cg~~~~~~l 225 (290)
T PF04216_consen 195 KRYLHCSLCGTEWRFVRIKCPYCGNTDHEKL 225 (290)
T ss_dssp EEEEEETTT--EEE--TTS-TTT---SS-EE
T ss_pred cEEEEcCCCCCeeeecCCCCcCCCCCCCcce
Confidence 367899999999774 568999988766544
No 157
>PF01599 Ribosomal_S27: Ribosomal protein S27a; InterPro: IPR002906 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. This family of ribosomal proteins consists mainly of the 40S ribosomal protein S27a which is synthesized as a C-terminal extension of ubiquitin (CEP) (IPR000626 from INTERPRO). The S27a domain compromises the C-terminal half of the protein. The synthesis of ribosomal proteins as extensions of ubiquitin promotes their incorporation into nascent ribosomes by a transient metabolic stabilisation and is required for efficient ribosome biogenesis []. The ribosomal extension protein S27a contains a basic region that is proposed to form a zinc finger; its fusion gene is proposed as a mechanism to maintain a fixed ratio between ubiquitin necessary for degrading proteins and ribosomes a source of proteins [].; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 2K4X_A 3U5C_f 3U5G_f 2XZN_9 2XZM_9.
Probab=52.66 E-value=9.1 Score=26.22 Aligned_cols=22 Identities=23% Similarity=0.792 Sum_probs=14.1
Q ss_pred ccccCc--CCCCc------cceEecCcccc
Q 025507 66 VQQVCV--NCGVC------MGEYFCESCKL 87 (251)
Q Consensus 66 ~~~~C~--~Cg~~------f~~y~C~~C~~ 87 (251)
....|| .||.. +++++|++|.+
T Consensus 17 ~rk~CP~~~CG~GvFMA~H~dR~~CGKCg~ 46 (47)
T PF01599_consen 17 LRKECPSPRCGAGVFMAEHKDRHYCGKCGY 46 (47)
T ss_dssp SSEE-TSTTTTSSSEEEE-SSEEEETTTSS
T ss_pred hhhcCCCcccCCceEeeecCCCccCCCccc
Confidence 456788 78774 56777777754
No 158
>KOG2462 consensus C2H2-type Zn-finger protein [Transcription]
Probab=52.34 E-value=15 Score=33.99 Aligned_cols=86 Identities=21% Similarity=0.492 Sum_probs=50.4
Q ss_pred ccceeecCCCCcccc-------------ccccCcCCCCccceEecCccccccC----CCCCCeeecCCCCcc-------e
Q 025507 51 EVNQVICSLCGTEQK-------------VQQVCVNCGVCMGEYFCESCKLFDD----DTSKKQYHCDGCGIC-------R 106 (251)
Q Consensus 51 ~~~~v~C~~C~~~q~-------------~~~~C~~Cg~~f~~y~C~~C~~~d~----~~~k~~~HC~~CgiC-------R 106 (251)
+.+.-.|-.|++++. ..=.|.-||+.|.+-- |+-. -...+||-|+.||== |
T Consensus 158 s~ka~~C~~C~K~YvSmpALkMHirTH~l~c~C~iCGKaFSRPW-----LLQGHiRTHTGEKPF~C~hC~kAFADRSNLR 232 (279)
T KOG2462|consen 158 SKKAFSCKYCGKVYVSMPALKMHIRTHTLPCECGICGKAFSRPW-----LLQGHIRTHTGEKPFSCPHCGKAFADRSNLR 232 (279)
T ss_pred ccccccCCCCCceeeehHHHhhHhhccCCCcccccccccccchH-----HhhcccccccCCCCccCCcccchhcchHHHH
Confidence 467889999998862 1236888999987531 2221 234567777765521 1
Q ss_pred e----cCCcceeeccCCCcceec-cccccccccCCCCCCCCcchhh
Q 025507 107 I----GGCDNFFHCNKCRCCYSM-LLKNSHPCVEGAMHHDCPVCCE 147 (251)
Q Consensus 107 ~----g~~~~~fHC~~C~~c~~~-~l~~~H~C~e~~~~~~CpICle 147 (251)
. -..++-|.|.+|+-=.+. ++-.+|- +..|.+.+.
T Consensus 233 AHmQTHS~~K~~qC~~C~KsFsl~SyLnKH~------ES~C~~~~~ 272 (279)
T KOG2462|consen 233 AHMQTHSDVKKHQCPRCGKSFALKSYLNKHS------ESACLKYLA 272 (279)
T ss_pred HHHHhhcCCccccCcchhhHHHHHHHHHHhh------hhccccccc
Confidence 1 123456788888876665 4444443 455655543
No 159
>PRK12286 rpmF 50S ribosomal protein L32; Reviewed
Probab=52.34 E-value=16 Score=25.89 Aligned_cols=29 Identities=31% Similarity=0.769 Sum_probs=22.3
Q ss_pred eeEEcCCCCCCccccceeeeccCCCCCCcccccc
Q 025507 216 VWILCNDCGKTSNVQFHVLAQKCPNCKSYNTRLT 249 (251)
Q Consensus 216 ~~IlCndC~~~s~~~~h~lg~kC~~C~SyNT~~~ 249 (251)
..+.|..|++.. .-| +-|+.||.|+-+++
T Consensus 26 ~l~~C~~CG~~~--~~H---~vC~~CG~Y~gr~v 54 (57)
T PRK12286 26 GLVECPNCGEPK--LPH---RVCPSCGYYKGREV 54 (57)
T ss_pred cceECCCCCCcc--CCe---EECCCCCcCCCEEe
Confidence 457899999763 345 45999999999885
No 160
>PF13453 zf-TFIIB: Transcription factor zinc-finger
Probab=52.30 E-value=12 Score=24.27 Aligned_cols=25 Identities=28% Similarity=0.638 Sum_probs=13.9
Q ss_pred CcCCCCccceEecCccccccCCCCCCeeecCCCC
Q 025507 70 CVNCGVCMGEYFCESCKLFDDDTSKKQYHCDGCG 103 (251)
Q Consensus 70 C~~Cg~~f~~y~C~~C~~~d~~~~k~~~HC~~Cg 103 (251)
||.|+..+..+. + .+-.++.|+.||
T Consensus 2 CP~C~~~l~~~~-----~----~~~~id~C~~C~ 26 (41)
T PF13453_consen 2 CPRCGTELEPVR-----L----GDVEIDVCPSCG 26 (41)
T ss_pred cCCCCcccceEE-----E----CCEEEEECCCCC
Confidence 666666665442 1 224566666665
No 161
>KOG1100 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=51.41 E-value=7 Score=34.58 Aligned_cols=40 Identities=33% Similarity=0.751 Sum_probs=29.1
Q ss_pred CCcchhhhcccCCceeEEcCCCCc-ccHHHHHHHHhcCCCCCCCCCcCcc
Q 025507 141 DCPVCCEYLFETRQDVIVLPCGHT-IHKNCLKEMREHHQYACPICSKSVC 189 (251)
Q Consensus 141 ~CpICle~lf~s~~~~~~lpCgH~-fH~~Ci~~wl~~~~~~CP~Cr~~~~ 189 (251)
.|-.|.+. ...+++|||-|. ++..|-.. + ..||+|+.+..
T Consensus 160 ~Cr~C~~~----~~~VlllPCrHl~lC~~C~~~-~----~~CPiC~~~~~ 200 (207)
T KOG1100|consen 160 SCRKCGER----EATVLLLPCRHLCLCGICDES-L----RICPICRSPKT 200 (207)
T ss_pred cceecCcC----CceEEeecccceEeccccccc-C----ccCCCCcChhh
Confidence 39999873 345888999876 77778665 2 45999996543
No 162
>KOG2066 consensus Vacuolar assembly/sorting protein VPS41 [Intracellular trafficking, secretion, and vesicular transport]
Probab=51.22 E-value=5.8 Score=41.54 Aligned_cols=45 Identities=36% Similarity=0.680 Sum_probs=31.6
Q ss_pred CCCCcchhhhcccCC---ceeEEcCCCCcccHHHHHHHHhcCCCCCCCCC
Q 025507 139 HHDCPVCCEYLFETR---QDVIVLPCGHTIHKNCLKEMREHHQYACPICS 185 (251)
Q Consensus 139 ~~~CpICle~lf~s~---~~~~~lpCgH~fH~~Ci~~wl~~~~~~CP~Cr 185 (251)
++.|..|.+....+. ..++++.|||.||.+|+...+... .|-+|.
T Consensus 784 e~rc~~c~~~~l~~~~~~~~~~v~~c~h~yhk~c~~~~~~~~--~~~~~~ 831 (846)
T KOG2066|consen 784 EERCSSCFEPNLPSGAAFDSVVVFHCGHMYHKECLMMESLRN--ACNIES 831 (846)
T ss_pred hhhhhhhcccccccCcccceeeEEEccchhhhcccccHHHhc--ccChhh
Confidence 446777777655444 467889999999999999875533 254444
No 163
>PF02701 zf-Dof: Dof domain, zinc finger; InterPro: IPR003851 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 consists of proteins containing a Dof domain, which is a zinc finger DNA-binding domain that shows resemblance to the Cys2 zinc finger, although it has a longer putative loop where an extra Cys residue is conserved []. AOBP, a DNA-binding protein in pumpkin (Cucurbita maxima), contains a 52 amino acid Dof domain, which is highly conserved in several DNA-binding proteins of higher plants. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003677 DNA binding, 0008270 zinc ion binding, 0006355 regulation of transcription, DNA-dependent
Probab=51.22 E-value=8.1 Score=28.01 Aligned_cols=14 Identities=43% Similarity=0.971 Sum_probs=12.2
Q ss_pred eccCCCCCCccccc
Q 025507 235 AQKCPNCKSYNTRL 248 (251)
Q Consensus 235 g~kC~~C~SyNT~~ 248 (251)
.++|+.|.|.||+.
T Consensus 5 ~~~CPRC~S~nTKF 18 (63)
T PF02701_consen 5 PLPCPRCDSTNTKF 18 (63)
T ss_pred CCCCCCcCCCCCEE
Confidence 36999999999975
No 164
>KOG1940 consensus Zn-finger protein [General function prediction only]
Probab=50.88 E-value=2.9 Score=38.68 Aligned_cols=73 Identities=18% Similarity=0.476 Sum_probs=45.2
Q ss_pred CccCCccccccceeecCcCCCeecCcchhhhhccCcCc-----CcCCCCC---CCCcccceeecCCCCccccc-----cc
Q 025507 2 ITCRCQHYRRRCRIRAPCCNEIFDCRHCHNEAMNNINV-----DQKLRHD---IPRHEVNQVICSLCGTEQKV-----QQ 68 (251)
Q Consensus 2 ~~~gC~HY~r~c~i~~pcC~~~y~Cr~CHde~~~~~~~-----~~~~~H~---~~r~~~~~v~C~~C~~~q~~-----~~ 68 (251)
..+.|.||...=.++.++|.. |+|..||+ ..+.... ...+.-| .....+..|+|-.|+.-+.+ ..
T Consensus 176 ~~~~CgH~~h~~cf~e~~~~~-y~CP~C~~-~~d~~~~~~~~d~~l~~~~~p~~y~~~~~~i~cndC~~~~~~k~~~l~~ 253 (276)
T KOG1940|consen 176 GVLKCGHYMHSRCFEEMICEG-YTCPICSK-PGDMSHYFRKLDKELAGSPMPEEYKNKTQDILCNDCGSGTNVKYHILYH 253 (276)
T ss_pred CccCcccchHHHHHHHHhccC-CCCCcccc-hHHHHHHHHHHHHHHhcCCCCchhhchhheeeccCCCCCCccceehhhh
Confidence 357899999866789999999 99999999 3222100 0001111 23344456788888766542 35
Q ss_pred cCcCCCCc
Q 025507 69 VCVNCGVC 76 (251)
Q Consensus 69 ~C~~Cg~~ 76 (251)
.|..|+..
T Consensus 254 kc~~c~~~ 261 (276)
T KOG1940|consen 254 KCGKCGSY 261 (276)
T ss_pred hCCCcccc
Confidence 56666554
No 165
>COG5183 SSM4 Protein involved in mRNA turnover and stability [RNA processing and modification]
Probab=50.50 E-value=5.4 Score=42.10 Aligned_cols=51 Identities=29% Similarity=0.626 Sum_probs=36.5
Q ss_pred CCCCCCcchhhhcccCCceeEEcCCC-----CcccHHHHHHHHhcC-CCCCCCCCcCcc
Q 025507 137 AMHHDCPVCCEYLFETRQDVIVLPCG-----HTIHKNCLKEMREHH-QYACPICSKSVC 189 (251)
Q Consensus 137 ~~~~~CpICle~lf~s~~~~~~lpCg-----H~fH~~Ci~~wl~~~-~~~CP~Cr~~~~ 189 (251)
+.+..|-||.-. +-++++..-||. -.+|++|+.+|+..+ ...|-+|..++.
T Consensus 10 ~d~~~CRICr~e--~~~d~pLfhPCKC~GSIkYiH~eCL~eW~~~s~~~kCdiChy~~~ 66 (1175)
T COG5183 10 EDKRSCRICRTE--DIRDDPLFHPCKCSGSIKYIHRECLMEWMECSGTKKCDICHYEYK 66 (1175)
T ss_pred ccchhceeecCC--CCCCCcCcccccccchhHHHHHHHHHHHHhcCCCcceeeecceee
Confidence 445789999852 233345556885 359999999999863 456999997765
No 166
>PF01096 TFIIS_C: Transcription factor S-II (TFIIS); InterPro: IPR001222 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents a zinc finger motif found in transcription factor IIs (TFIIS). In eukaryotes the initiation of transcription of protein encoding genes by polymerase II (Pol II) is modulated by general and specific transcription factors. The general transcription factors operate through common promoters elements (such as the TATA box). At least eight different proteins associate to form the general transcription factors: TFIIA, -IIB, -IID, -IIE, -IIF, -IIG, -IIH and -IIS []. During mRNA elongation, Pol II can encounter DNA sequences that cause reverse movement of the enzyme. Such backtracking involves extrusion of the RNA 3'-end into the pore, and can lead to transcriptional arrest. Escape from arrest requires cleavage of the extruded RNA with the help of TFIIS, which induces mRNA cleavage by enhancing the intrinsic nuclease activity of RNA polymerase (Pol) II, past template-encoded pause sites []. TFIIS extends from the polymerase surface via a pore to the internal active site. Two essential and invariant acidic residues in a TFIIS loop complement the Pol II active site and could position a metal ion and a water molecule for hydrolytic RNA cleavage. TFIIS also induces extensive structural changes in Pol II that would realign nucleic acids in the active centre. TFIIS is a protein of about 300 amino acids. It contains three regions: a variable N-terminal domain not required for TFIIS activity; a conserved central domain required for Pol II binding; and a conserved C-terminal C4-type zinc finger essential for RNA cleavage. The zinc finger folds in a conformation termed a zinc ribbon [] characterised by a three-stranded antiparallel beta-sheet and two beta-hairpins. A backbone model for Pol II-TFIIS complex was obtained from X-ray analysis. It shows that a beta hairpin protrudes from the zinc finger and complements the pol II active site []. Some viral proteins also contain the TFIIS zinc ribbon C-terminal domain. The Vaccinia virus protein, unlike its eukaryotic homologue, is an integral RNA polymerase subunit rather than a readily separable transcription factor []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003676 nucleic acid binding, 0008270 zinc ion binding, 0006351 transcription, DNA-dependent; PDB: 3M4O_I 3S14_I 2E2J_I 4A3J_I 3HOZ_I 1TWA_I 3S1Q_I 3S1N_I 1TWG_I 3I4M_I ....
Probab=49.09 E-value=12 Score=24.20 Aligned_cols=33 Identities=27% Similarity=0.632 Sum_probs=17.0
Q ss_pred cCcCCCCccceEecCccccc-cCCCCCCeeecCCCC
Q 025507 69 VCVNCGVCMGEYFCESCKLF-DDDTSKKQYHCDGCG 103 (251)
Q Consensus 69 ~C~~Cg~~f~~y~C~~C~~~-d~~~~k~~~HC~~Cg 103 (251)
.||+||+.-+.|| .+ ..- -|++..-.|.|-+||
T Consensus 2 ~Cp~Cg~~~a~~~-~~-Q~rsaDE~~T~fy~C~~C~ 35 (39)
T PF01096_consen 2 KCPKCGHNEAVFF-QI-QTRSADEPMTLFYVCCNCG 35 (39)
T ss_dssp --SSS-SSEEEEE-EE-SSSSSSSSSEEEEEESSST
T ss_pred CCcCCCCCeEEEE-Ee-eccCCCCCCeEEEEeCCCC
Confidence 5888888877776 00 011 233455667776665
No 167
>KOG1609 consensus Protein involved in mRNA turnover and stability [RNA processing and modification]
Probab=48.83 E-value=9.7 Score=34.40 Aligned_cols=51 Identities=24% Similarity=0.523 Sum_probs=37.0
Q ss_pred CCCCcchhhhcccCCceeEEcCCC-----CcccHHHHHHHHhc-CCCCCCCCCcCcc
Q 025507 139 HHDCPVCCEYLFETRQDVIVLPCG-----HTIHKNCLKEMREH-HQYACPICSKSVC 189 (251)
Q Consensus 139 ~~~CpICle~lf~s~~~~~~lpCg-----H~fH~~Ci~~wl~~-~~~~CP~Cr~~~~ 189 (251)
+..|=||.+..+.+.......||. ...|+.|++.|+.. ++..|.+|...+.
T Consensus 78 ~~~cRIc~~~~~~~~~~~l~~pC~C~g~l~~vH~~cl~~W~~~~~~~~CeiC~~~~~ 134 (323)
T KOG1609|consen 78 GPICRICHEEDEESNGLLLISPCSCKGSLAYVHRSCLEKWFSIKGNITCEICKSFFI 134 (323)
T ss_pred CCcEEEEecccccccccccccCccccCcHHHHHHHHHHhhhccccCeeeecccccce
Confidence 367999998655432224566883 67899999999874 3567999997654
No 168
>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=47.41 E-value=9.5 Score=31.92 Aligned_cols=16 Identities=38% Similarity=0.843 Sum_probs=14.1
Q ss_pred eccCCCCCCccccccC
Q 025507 235 AQKCPNCKSYNTRLTR 250 (251)
Q Consensus 235 g~kC~~C~SyNT~~~~ 250 (251)
...|+.|||-||++++
T Consensus 105 ~~~cp~c~s~~t~~~s 120 (146)
T TIGR02159 105 SVQCPRCGSADTTITS 120 (146)
T ss_pred CCcCCCCCCCCcEeec
Confidence 4699999999999875
No 169
>KOG2932 consensus E3 ubiquitin ligase involved in ubiquitination of E-cadherin complex [Posttranslational modification, protein turnover, chaperones]
Probab=47.31 E-value=7.7 Score=36.71 Aligned_cols=30 Identities=27% Similarity=0.752 Sum_probs=23.4
Q ss_pred EEcCCCCcccHHHHHHHHhcCCCCCCCCCcCcc
Q 025507 157 IVLPCGHTIHKNCLKEMREHHQYACPICSKSVC 189 (251)
Q Consensus 157 ~~lpCgH~fH~~Ci~~wl~~~~~~CP~Cr~~~~ 189 (251)
+.+||.|.|+.+|...- ....||.|.-.+.
T Consensus 105 RmIPCkHvFCl~CAr~~---~dK~Cp~C~d~Vq 134 (389)
T KOG2932|consen 105 RMIPCKHVFCLECARSD---SDKICPLCDDRVQ 134 (389)
T ss_pred cccccchhhhhhhhhcC---ccccCcCcccHHH
Confidence 46799999999998653 2357999986665
No 170
>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=47.18 E-value=19 Score=21.34 Aligned_cols=20 Identities=25% Similarity=0.617 Sum_probs=12.5
Q ss_pred CCCCCCCcCccchhHHHHHHH
Q 025507 179 YACPICSKSVCDMSKVWEKYD 199 (251)
Q Consensus 179 ~~CP~Cr~~~~~~~~~~~~ld 199 (251)
..||+|.+.+ ......+-+|
T Consensus 2 v~CPiC~~~v-~~~~in~HLD 21 (26)
T smart00734 2 VQCPVCFREV-PENLINSHLD 21 (26)
T ss_pred CcCCCCcCcc-cHHHHHHHHH
Confidence 3699999887 3333344455
No 171
>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=46.75 E-value=12 Score=20.09 Aligned_cols=17 Identities=41% Similarity=0.899 Sum_probs=10.7
Q ss_pred CCCCCCCcCccchhHHH
Q 025507 179 YACPICSKSVCDMSKVW 195 (251)
Q Consensus 179 ~~CP~Cr~~~~~~~~~~ 195 (251)
+.||+|.+.+......+
T Consensus 1 ~~C~~C~~~~~~~~~l~ 17 (24)
T PF13894_consen 1 FQCPICGKSFRSKSELR 17 (24)
T ss_dssp EE-SSTS-EESSHHHHH
T ss_pred CCCcCCCCcCCcHHHHH
Confidence 36999999888765543
No 172
>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=46.57 E-value=16 Score=22.63 Aligned_cols=24 Identities=29% Similarity=0.803 Sum_probs=15.9
Q ss_pred EecCccccccCCCCCCeeecCCCCc
Q 025507 80 YFCESCKLFDDDTSKKQYHCDGCGI 104 (251)
Q Consensus 80 y~C~~C~~~d~~~~k~~~HC~~Cgi 104 (251)
|-|.+|-+.-+ +.+.++.|+.||.
T Consensus 2 ~~C~~CGy~y~-~~~~~~~CP~Cg~ 25 (33)
T cd00350 2 YVCPVCGYIYD-GEEAPWVCPVCGA 25 (33)
T ss_pred EECCCCCCEEC-CCcCCCcCcCCCC
Confidence 66777765533 3457888888875
No 173
>smart00659 RPOLCX RNA polymerase subunit CX. present in RNA polymerase I, II and III
Probab=44.43 E-value=17 Score=24.34 Aligned_cols=26 Identities=19% Similarity=0.703 Sum_probs=16.1
Q ss_pred eEEcCCCCCCccccceeeeccCCCCCC
Q 025507 217 WILCNDCGKTSNVQFHVLAQKCPNCKS 243 (251)
Q Consensus 217 ~IlCndC~~~s~~~~h~lg~kC~~C~S 243 (251)
...|.+|+...+... --+.+|+.||+
T Consensus 2 ~Y~C~~Cg~~~~~~~-~~~irC~~CG~ 27 (44)
T smart00659 2 IYICGECGRENEIKS-KDVVRCRECGY 27 (44)
T ss_pred EEECCCCCCEeecCC-CCceECCCCCc
Confidence 356777777655542 34567777776
No 174
>KOG0826 consensus Predicted E3 ubiquitin ligase involved in peroxisome organization [Posttranslational modification, protein turnover, chaperones]
Probab=44.02 E-value=20 Score=34.15 Aligned_cols=48 Identities=17% Similarity=0.348 Sum_probs=34.7
Q ss_pred CCCCCcchhhhcccCCceeEEcCCCCcccHHHHHHHHhcCCCCCCCCCcCcc
Q 025507 138 MHHDCPVCCEYLFETRQDVIVLPCGHTIHKNCLKEMREHHQYACPICSKSVC 189 (251)
Q Consensus 138 ~~~~CpICle~lf~s~~~~~~lpCgH~fH~~Ci~~wl~~~~~~CP~Cr~~~~ 189 (251)
+...||||+... ..+.+.--=|-.|+-.|+..++. ...+||+=..++.
T Consensus 299 ~~~~CpvClk~r---~Nptvl~vSGyVfCY~Ci~~Yv~-~~~~CPVT~~p~~ 346 (357)
T KOG0826|consen 299 DREVCPVCLKKR---QNPTVLEVSGYVFCYPCIFSYVV-NYGHCPVTGYPAS 346 (357)
T ss_pred ccccChhHHhcc---CCCceEEecceEEeHHHHHHHHH-hcCCCCccCCcch
Confidence 457899999632 12233334599999999999998 4578998776654
No 175
>KOG2462 consensus C2H2-type Zn-finger protein [Transcription]
Probab=43.67 E-value=24 Score=32.73 Aligned_cols=119 Identities=27% Similarity=0.561 Sum_probs=66.6
Q ss_pred CCccceEecCcc-ccccCCC---CCCeeecCCCCcceecCCcceeeccCCCccee-c-cc---cccccccCCCCCCCCcc
Q 025507 74 GVCMGEYFCESC-KLFDDDT---SKKQYHCDGCGICRIGGCDNFFHCNKCRCCYS-M-LL---KNSHPCVEGAMHHDCPV 144 (251)
Q Consensus 74 g~~f~~y~C~~C-~~~d~~~---~k~~~HC~~CgiCR~g~~~~~fHC~~C~~c~~-~-~l---~~~H~C~e~~~~~~CpI 144 (251)
.+.-++|-|+.| |-|.... .-+|+||+- .-..-|+|..|+-=|. + .| ..+|+ +...|+|
T Consensus 125 ~~~~~r~~c~eCgk~ysT~snLsrHkQ~H~~~-------~s~ka~~C~~C~K~YvSmpALkMHirTH~-----l~c~C~i 192 (279)
T KOG2462|consen 125 AAKHPRYKCPECGKSYSTSSNLSRHKQTHRSL-------DSKKAFSCKYCGKVYVSMPALKMHIRTHT-----LPCECGI 192 (279)
T ss_pred cccCCceeccccccccccccccchhhcccccc-------cccccccCCCCCceeeehHHHhhHhhccC-----CCccccc
Confidence 445677888888 5664432 237888853 2257889999998773 3 22 13444 4567889
Q ss_pred hhhhcccCCceeEEcCCCCc-ccHHHHHHHHhcCCCCCCCCCcCccchhHHHHHHHHHHhcCCCCHhhhcCceeEEcCCC
Q 025507 145 CCEYLFETRQDVIVLPCGHT-IHKNCLKEMREHHQYACPICSKSVCDMSKVWEKYDREIAATPMPEAYLNKKVWILCNDC 223 (251)
Q Consensus 145 Cle~lf~s~~~~~~lpCgH~-fH~~Ci~~wl~~~~~~CP~Cr~~~~~~~~~~~~ld~~i~~~p~P~e~~~~~~~IlCndC 223 (251)
|.- .|..+ +|-=||. .|. -..-+.||.|+|.|.|.+ +|.+-++.-. +.+ ...|.-|
T Consensus 193 CGK-aFSRP----WLLQGHiRTHT-------GEKPF~C~hC~kAFADRS----NLRAHmQTHS------~~K-~~qC~~C 249 (279)
T KOG2462|consen 193 CGK-AFSRP----WLLQGHIRTHT-------GEKPFSCPHCGKAFADRS----NLRAHMQTHS------DVK-KHQCPRC 249 (279)
T ss_pred ccc-cccch----HHhhccccccc-------CCCCccCCcccchhcchH----HHHHHHHhhc------CCc-cccCcch
Confidence 886 46521 1100221 000 012478999999999854 3444433211 111 3457777
Q ss_pred CCCc
Q 025507 224 GKTS 227 (251)
Q Consensus 224 ~~~s 227 (251)
++++
T Consensus 250 ~KsF 253 (279)
T KOG2462|consen 250 GKSF 253 (279)
T ss_pred hhHH
Confidence 6543
No 176
>PF07649 C1_3: C1-like domain; InterPro: IPR011424 This short domain is rich in cysteines and histidines. The pattern of conservation is similar to that found in IPR002219 from INTERPRO. C1 domains are protein kinase C-like zinc finger structures. Diacylglycerol (DAG) kinases (DGKs) have a two or three commonly conserved cysteine-rich C1 domains []. DGKs modulate the balance between the two signaling lipids, DAG and phosphatidic acid (PA), by phosphorylating DAG to yield PA []. The PKD (protein kinase D) family are novel DAG receptors. They have twin C1 domains, designated C1a and C1b, which bind DAG or phorbol esters. Individual C1 domains differ in ligand-binding activity and selectivity []. ; GO: 0047134 protein-disulfide reductase activity, 0055114 oxidation-reduction process; PDB: 1V5N_A.
Probab=43.50 E-value=14 Score=22.29 Aligned_cols=21 Identities=24% Similarity=0.634 Sum_probs=6.6
Q ss_pred CCcceecCCc-ceeeccCCCcc
Q 025507 102 CGICRIGGCD-NFFHCNKCRCC 122 (251)
Q Consensus 102 CgiCR~g~~~-~~fHC~~C~~c 122 (251)
|.+|+..+.. .+|+|..|+.-
T Consensus 3 C~~C~~~~~~~~~Y~C~~Cdf~ 24 (30)
T PF07649_consen 3 CDACGKPIDGGWFYRCSECDFD 24 (30)
T ss_dssp -TTTS----S--EEE-TTT---
T ss_pred CCcCCCcCCCCceEECccCCCc
Confidence 4455544433 66777777653
No 177
>PLN02189 cellulose synthase
Probab=43.22 E-value=20 Score=38.94 Aligned_cols=56 Identities=16% Similarity=0.403 Sum_probs=39.5
Q ss_pred cCCCCCCCCcchhhhccc--CCceeEEc-CCCCcccHHHHHHHHhcCCCCCCCCCcCcc
Q 025507 134 VEGAMHHDCPVCCEYLFE--TRQDVIVL-PCGHTIHKNCLKEMREHHQYACPICSKSVC 189 (251)
Q Consensus 134 ~e~~~~~~CpICle~lf~--s~~~~~~l-pCgH~fH~~Ci~~wl~~~~~~CP~Cr~~~~ 189 (251)
+++.....|.||.|++-. +++..+.- -||--.++.|++-=.+.++..||.|+..+.
T Consensus 29 ~~~~~~~~C~iCgd~vg~~~~g~~fvaC~~C~fpvCr~Cyeyer~eg~q~CpqCkt~Y~ 87 (1040)
T PLN02189 29 LRNLDGQVCEICGDEIGLTVDGDLFVACNECGFPVCRPCYEYERREGTQNCPQCKTRYK 87 (1040)
T ss_pred cccccCccccccccccCcCCCCCEEEeeccCCCccccchhhhhhhcCCccCcccCCchh
Confidence 344556799999998653 33333332 377889999996656667889999997664
No 178
>COG1996 RPC10 DNA-directed RNA polymerase, subunit RPC10 (contains C4-type Zn-finger) [Transcription]
Probab=42.94 E-value=18 Score=24.99 Aligned_cols=28 Identities=32% Similarity=0.716 Sum_probs=16.1
Q ss_pred cceEecCcc-ccccCCCCCCeeecCCCCc
Q 025507 77 MGEYFCESC-KLFDDDTSKKQYHCDGCGI 104 (251)
Q Consensus 77 f~~y~C~~C-~~~d~~~~k~~~HC~~Cgi 104 (251)
+..|-|..| +.++.+..+.-.-|+.||.
T Consensus 4 ~~~Y~C~~Cg~~~~~~~~~~~irCp~Cg~ 32 (49)
T COG1996 4 MMEYKCARCGREVELDQETRGIRCPYCGS 32 (49)
T ss_pred eEEEEhhhcCCeeehhhccCceeCCCCCc
Confidence 344555555 3445455666677777774
No 179
>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=42.58 E-value=29 Score=32.53 Aligned_cols=24 Identities=25% Similarity=0.865 Sum_probs=15.9
Q ss_pred eeEEcCCCCCCccccceeeeccCCCCCC
Q 025507 216 VWILCNDCGKTSNVQFHVLAQKCPNCKS 243 (251)
Q Consensus 216 ~~IlCndC~~~s~~~~h~lg~kC~~C~S 243 (251)
....|.-|+ ..+|++-.||++|++
T Consensus 209 RyL~CslC~----teW~~~R~~C~~Cg~ 232 (305)
T TIGR01562 209 RYLSCSLCA----TEWHYVRVKCSHCEE 232 (305)
T ss_pred eEEEcCCCC----CcccccCccCCCCCC
Confidence 456677776 556666677777774
No 180
>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]
Probab=42.57 E-value=28 Score=36.48 Aligned_cols=49 Identities=24% Similarity=0.598 Sum_probs=34.5
Q ss_pred CCcc-cceeecCCCCccccccccCcCCCCccc------eEecCccccccCCCCCCeeecCCCCc
Q 025507 48 PRHE-VNQVICSLCGTEQKVQQVCVNCGVCMG------EYFCESCKLFDDDTSKKQYHCDGCGI 104 (251)
Q Consensus 48 ~r~~-~~~v~C~~C~~~q~~~~~C~~Cg~~f~------~y~C~~C~~~d~~~~k~~~HC~~Cgi 104 (251)
+|+. .+.++|..|+.. -.||||+..+. ...|--|.. .++.+.+|+.||-
T Consensus 428 nRRGys~~l~C~~Cg~v----~~Cp~Cd~~lt~H~~~~~L~CH~Cg~----~~~~p~~Cp~Cgs 483 (730)
T COG1198 428 NRRGYAPLLLCRDCGYI----AECPNCDSPLTLHKATGQLRCHYCGY----QEPIPQSCPECGS 483 (730)
T ss_pred ccCCccceeecccCCCc----ccCCCCCcceEEecCCCeeEeCCCCC----CCCCCCCCCCCCC
Confidence 4543 358999999987 47999988754 555665543 3567788888884
No 181
>TIGR01384 TFS_arch transcription factor S, archaeal. There has been an apparent duplication event in the Halobacteriaceae lineage (Haloarcula, Haloferax, Haloquadratum, Halobacterium and Natromonas). There appears to be a separate duplication in Methanosphaera stadtmanae.
Probab=42.38 E-value=47 Score=25.48 Aligned_cols=35 Identities=26% Similarity=0.638 Sum_probs=22.3
Q ss_pred cccCcCCCCccceEecCccccc-cCCCCCCeeecCCCC
Q 025507 67 QQVCVNCGVCMGEYFCESCKLF-DDDTSKKQYHCDGCG 103 (251)
Q Consensus 67 ~~~C~~Cg~~f~~y~C~~C~~~-d~~~~k~~~HC~~Cg 103 (251)
...|++||+.-+.|+= . .+- -|++..-.|.|..||
T Consensus 62 ~~~Cp~Cg~~~a~f~~-~-Q~RsadE~~T~fy~C~~C~ 97 (104)
T TIGR01384 62 RVECPKCGHKEAYYWL-L-QTRRADEPETRFYKCTKCG 97 (104)
T ss_pred cCCCCCCCCCeeEEEE-e-ccCCCCCCcEEEEEeCCCC
Confidence 5689999998887761 0 122 233455677777666
No 182
>KOG0269 consensus WD40 repeat-containing protein [Function unknown]
Probab=42.31 E-value=25 Score=36.94 Aligned_cols=50 Identities=30% Similarity=0.426 Sum_probs=31.8
Q ss_pred CCCcchhhhcccCCceeEEcCCCCcccHHHHHHHHhcCCCCCCC--C-----CcCccchh
Q 025507 140 HDCPVCCEYLFETRQDVIVLPCGHTIHKNCLKEMREHHQYACPI--C-----SKSVCDMS 192 (251)
Q Consensus 140 ~~CpICle~lf~s~~~~~~lpCgH~fH~~Ci~~wl~~~~~~CP~--C-----r~~~~~~~ 192 (251)
..|.+|-..+. +..+.---|||-.|.+++.+|+.. +.-||. | +.++.|+.
T Consensus 780 ~~CtVC~~vi~--G~~~~c~~C~H~gH~sh~~sw~~~-~s~ca~~~C~~~c~~~~~~D~~ 836 (839)
T KOG0269|consen 780 AKCTVCDLVIR--GVDVWCQVCGHGGHDSHLKSWFFK-ASPCAKSICPHLCHYSSFIDTF 836 (839)
T ss_pred cCceeecceee--eeEeecccccccccHHHHHHHHhc-CCCCccccCCccccccccchhh
Confidence 36889875322 222222369999999999999874 455665 4 45555543
No 183
>PF12172 DUF35_N: Rubredoxin-like zinc ribbon domain (DUF35_N); InterPro: IPR022002 This domain has no known function and is found in conserved hypothetical archaeal and bacterial proteins. The domain is duplicated in O53566 from SWISSPROT. The structure of a DUF35 representative reveals two long N-terminal helices followed by a rubredoxin-like zinc ribbon domain represented in this family and a C-terminal OB fold domain. Zinc is chelated by the four conserved cysteines in the alignment. ; PDB: 3IRB_A.
Probab=41.94 E-value=12 Score=23.63 Aligned_cols=23 Identities=35% Similarity=0.702 Sum_probs=12.7
Q ss_pred ceeecCCCCccc-cccccCcCCCC
Q 025507 53 NQVICSLCGTEQ-KVQQVCVNCGV 75 (251)
Q Consensus 53 ~~v~C~~C~~~q-~~~~~C~~Cg~ 75 (251)
..-.|..|++.+ |+...|++||.
T Consensus 10 ~~~rC~~Cg~~~~pPr~~Cp~C~s 33 (37)
T PF12172_consen 10 LGQRCRDCGRVQFPPRPVCPHCGS 33 (37)
T ss_dssp EEEE-TTT--EEES--SEETTTT-
T ss_pred EEEEcCCCCCEecCCCcCCCCcCc
Confidence 456788888876 56778888874
No 184
>TIGR01031 rpmF_bact ribosomal protein L32. This protein describes bacterial ribosomal protein L32. The noise cutoff is set low enough to include the equivalent protein from mitochondria and chloroplasts. No related proteins from the Archaea nor from the eukaryotic cytosol are detected by this model. This model is a fragment model; the putative L32 of some species shows similarity only toward the N-terminus.
Probab=41.85 E-value=23 Score=24.75 Aligned_cols=29 Identities=31% Similarity=0.826 Sum_probs=22.2
Q ss_pred eeEEcCCCCCCccccceeeeccCCCCCCcccccc
Q 025507 216 VWILCNDCGKTSNVQFHVLAQKCPNCKSYNTRLT 249 (251)
Q Consensus 216 ~~IlCndC~~~s~~~~h~lg~kC~~C~SyNT~~~ 249 (251)
..+.|..|++. ...| +-|+.||.|+-+++
T Consensus 25 ~l~~C~~cG~~--~~~H---~vc~~cG~Y~gr~v 53 (55)
T TIGR01031 25 TLVVCPNCGEF--KLPH---RVCPSCGYYKGRQV 53 (55)
T ss_pred cceECCCCCCc--ccCe---eECCccCeECCEEc
Confidence 45779999974 3445 45999999999886
No 185
>PF01529 zf-DHHC: DHHC palmitoyltransferase; InterPro: IPR001594 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 DHHC-type zinc finger domain, which is also known as NEW1 []. The DHHC Zn-finger was first isolated in the Drosophila putative transcription factor DNZ1 and was named after a conserved sequence motif []. This domain has palmitoyltransferase activity; this post-translational modification attaches the C16 saturated fatty acid palmitate via a thioester linkage, predominantly to cysteine residues []. This domain is found in the DHHC proteins which are palmitoyl transferases []; the DHHC motif is found within a cysteine-rich domain which is thought to contain the catalytic site. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding
Probab=41.29 E-value=21 Score=29.41 Aligned_cols=49 Identities=20% Similarity=0.441 Sum_probs=36.6
Q ss_pred CCCCccceEecCccccccCCCCCCeeecCCCCcceecCCcceeeccCCCcceecc
Q 025507 72 NCGVCMGEYFCESCKLFDDDTSKKQYHCDGCGICRIGGCDNFFHCNKCRCCYSML 126 (251)
Q Consensus 72 ~Cg~~f~~y~C~~C~~~d~~~~k~~~HC~~CgiCR~g~~~~~fHC~~C~~c~~~~ 126 (251)
.-+......+|..|+.+-- ....||..||.|..+ --.||.-=|.|++..
T Consensus 41 ~~~~~~~~~~C~~C~~~kp---~Rs~HC~~C~~CV~~---~DHHC~w~~~cIG~~ 89 (174)
T PF01529_consen 41 EDDENGELKYCSTCKIIKP---PRSHHCRVCNRCVLR---FDHHCPWLGNCIGRR 89 (174)
T ss_pred ccccCCCCEECcccCCcCC---Ccceecccccccccc---ccccchhhccccccc
Confidence 3457777889999998833 358899999999884 446888888887743
No 186
>PRK03564 formate dehydrogenase accessory protein FdhE; Provisional
Probab=41.05 E-value=34 Score=32.22 Aligned_cols=24 Identities=38% Similarity=0.974 Sum_probs=17.1
Q ss_pred eeEEcCCCCCCccccceeeeccCCCCCC
Q 025507 216 VWILCNDCGKTSNVQFHVLAQKCPNCKS 243 (251)
Q Consensus 216 ~~IlCndC~~~s~~~~h~lg~kC~~C~S 243 (251)
....|.-|+ +.+|+.-.||++|++
T Consensus 211 RyL~CslC~----teW~~~R~~C~~Cg~ 234 (309)
T PRK03564 211 RYLHCNLCE----SEWHVVRVKCSNCEQ 234 (309)
T ss_pred eEEEcCCCC----CcccccCccCCCCCC
Confidence 456777777 567777777777774
No 187
>PF08274 PhnA_Zn_Ribbon: PhnA Zinc-Ribbon ; InterPro: IPR013987 The PhnA protein family includes the uncharacterised Escherichia coli protein PhnA and its homologues. The E. coli phnA gene is part of a large operon associated with alkylphosphonate uptake and carbon-phosphorus bond cleavage []. The protein is not related to the characterised phosphonoacetate hydrolase designated PhnA []. This entry represents the N-terminal domain of PhnA, which is predicted to form a zinc-ribbon.; PDB: 2AKL_A.
Probab=40.93 E-value=15 Score=22.72 Aligned_cols=23 Identities=26% Similarity=0.582 Sum_probs=10.3
Q ss_pred cCcCCCCccceEecCccccccCCCCCCeeecCCCC
Q 025507 69 VCVNCGVCMGEYFCESCKLFDDDTSKKQYHCDGCG 103 (251)
Q Consensus 69 ~C~~Cg~~f~~y~C~~C~~~d~~~~k~~~HC~~Cg 103 (251)
.|+.|+..++- .+..+|-|+.||
T Consensus 4 ~Cp~C~se~~y------------~D~~~~vCp~C~ 26 (30)
T PF08274_consen 4 KCPLCGSEYTY------------EDGELLVCPECG 26 (30)
T ss_dssp --TTT-----E------------E-SSSEEETTTT
T ss_pred CCCCCCCccee------------ccCCEEeCCccc
Confidence 57777776654 234678888876
No 188
>PF04438 zf-HIT: HIT zinc finger; InterPro: IPR007529 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 HIT-type zinc finger, which contains 7 conserved cysteines and one histidine that can potentially coordinate two zinc atoms. It has been named after the first protein that originally defined the domain: the yeast HIT1 protein (P46973 from SWISSPROT) []. The HIT-type zinc finger displays some sequence similarities to the MYND-type zinc finger. The function of this domain is unknown but it is mainly found in nuclear proteins involved in gene regulation and chromatin remodeling. This domain is also found in the thyroid receptor interacting protein 3 (TRIP-3) Q15649 from SWISSPROT, that specifically interacts with the ligand binding domain of the thyroid receptor. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; PDB: 2YQP_A 2YQQ_A 1X4S_A.
Probab=40.79 E-value=14 Score=22.72 Aligned_cols=16 Identities=38% Similarity=1.026 Sum_probs=7.5
Q ss_pred CcCCCCccceEecCccc
Q 025507 70 CVNCGVCMGEYFCESCK 86 (251)
Q Consensus 70 C~~Cg~~f~~y~C~~C~ 86 (251)
|.-||. .++|-|+.|.
T Consensus 5 C~vC~~-~~kY~Cp~C~ 20 (30)
T PF04438_consen 5 CSVCGN-PAKYRCPRCG 20 (30)
T ss_dssp ETSSSS-EESEE-TTT-
T ss_pred CccCcC-CCEEECCCcC
Confidence 444555 5555555554
No 189
>PF15616 TerY-C: TerY-C metal binding domain
Probab=40.17 E-value=27 Score=28.85 Aligned_cols=34 Identities=35% Similarity=0.767 Sum_probs=23.3
Q ss_pred cccCcCCCCccceEecCcc-cccc-CCCCCCeeecCCCC
Q 025507 67 QQVCVNCGVCMGEYFCESC-KLFD-DDTSKKQYHCDGCG 103 (251)
Q Consensus 67 ~~~C~~Cg~~f~~y~C~~C-~~~d-~~~~k~~~HC~~Cg 103 (251)
+..||.||..+|.--| .| ||+- +++ ...+|+-||
T Consensus 77 ~PgCP~CGn~~~fa~C-~CGkl~Ci~g~--~~~~CPwCg 112 (131)
T PF15616_consen 77 APGCPHCGNQYAFAVC-GCGKLFCIDGE--GEVTCPWCG 112 (131)
T ss_pred CCCCCCCcChhcEEEe-cCCCEEEeCCC--CCEECCCCC
Confidence 3679999999999999 58 5553 221 255666665
No 190
>PHA00626 hypothetical protein
Probab=39.69 E-value=20 Score=25.56 Aligned_cols=34 Identities=21% Similarity=0.450 Sum_probs=20.6
Q ss_pred eecCCCCccccccccCcCCCCccceEecCccccccC
Q 025507 55 VICSLCGTEQKVQQVCVNCGVCMGEYFCESCKLFDD 90 (251)
Q Consensus 55 v~C~~C~~~q~~~~~C~~Cg~~f~~y~C~~C~~~d~ 90 (251)
|.|..|+..+-+ .|.-|...-++|-|..|.+.+.
T Consensus 1 m~CP~CGS~~Iv--rcg~cr~~snrYkCkdCGY~ft 34 (59)
T PHA00626 1 MSCPKCGSGNIA--KEKTMRGWSDDYVCCDCGYNDS 34 (59)
T ss_pred CCCCCCCCceee--eeceecccCcceEcCCCCCeec
Confidence 456667765443 4445555566777777776643
No 191
>PF03604 DNA_RNApol_7kD: DNA directed RNA polymerase, 7 kDa subunit; InterPro: IPR006591 DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Each class of RNA polymerase is assembled from 9 to 15 different polypeptides. Rbp10 (RNA polymerase CX) is a domain found in RNA polymerase subunit 10; present in RNA polymerase I, II and III.; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 2PMZ_Z 3HKZ_X 2NVX_L 3S1Q_L 2JA6_L 3S17_L 3HOW_L 3HOV_L 3PO2_L 3HOZ_L ....
Probab=39.24 E-value=20 Score=22.45 Aligned_cols=11 Identities=27% Similarity=0.836 Sum_probs=5.9
Q ss_pred CCCeeecCCCC
Q 025507 93 SKKQYHCDGCG 103 (251)
Q Consensus 93 ~k~~~HC~~Cg 103 (251)
..++-.|..||
T Consensus 14 ~~~~irC~~CG 24 (32)
T PF03604_consen 14 PGDPIRCPECG 24 (32)
T ss_dssp TSSTSSBSSSS
T ss_pred CCCcEECCcCC
Confidence 34445566665
No 192
>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=38.40 E-value=48 Score=23.59 Aligned_cols=48 Identities=21% Similarity=0.521 Sum_probs=33.6
Q ss_pred CCCCCcchhhhcccCCceeEEcCCC--CcccHHHHHHHHhcCCCCCCCCCcCccc
Q 025507 138 MHHDCPVCCEYLFETRQDVIVLPCG--HTIHKNCLKEMREHHQYACPICSKSVCD 190 (251)
Q Consensus 138 ~~~~CpICle~lf~s~~~~~~lpCg--H~fH~~Ci~~wl~~~~~~CP~Cr~~~~~ 190 (251)
+..+|-.|-.+|..+..+.. =|. -+|+..|.+..|. ..||-|+..+..
T Consensus 4 lrpnCE~C~~dLp~~s~~A~--ICSfECTFC~~C~e~~l~---~~CPNCgGelv~ 53 (57)
T PF06906_consen 4 LRPNCECCDKDLPPDSPEAY--ICSFECTFCADCAETMLN---GVCPNCGGELVR 53 (57)
T ss_pred cCCCccccCCCCCCCCCcce--EEeEeCcccHHHHHHHhc---CcCcCCCCcccc
Confidence 34577778777655442222 243 6799999999985 579999987764
No 193
>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=38.01 E-value=24 Score=22.15 Aligned_cols=22 Identities=27% Similarity=0.788 Sum_probs=14.2
Q ss_pred eecCCCCcccc---ccccCcCCCCc
Q 025507 55 VICSLCGTEQK---VQQVCVNCGVC 76 (251)
Q Consensus 55 v~C~~C~~~q~---~~~~C~~Cg~~ 76 (251)
-+|..|+.+.. +-+.||.||+.
T Consensus 3 ~~C~~CG~i~~g~~~p~~CP~Cg~~ 27 (34)
T cd00729 3 WVCPVCGYIHEGEEAPEKCPICGAP 27 (34)
T ss_pred EECCCCCCEeECCcCCCcCcCCCCc
Confidence 46777776643 23578888875
No 194
>PLN02436 cellulose synthase A
Probab=37.53 E-value=27 Score=38.06 Aligned_cols=56 Identities=20% Similarity=0.440 Sum_probs=39.3
Q ss_pred cCCCCCCCCcchhhhcccCCceeEEc---CCCCcccHHHHHHHHhcCCCCCCCCCcCcc
Q 025507 134 VEGAMHHDCPVCCEYLFETRQDVIVL---PCGHTIHKNCLKEMREHHQYACPICSKSVC 189 (251)
Q Consensus 134 ~e~~~~~~CpICle~lf~s~~~~~~l---pCgH~fH~~Ci~~wl~~~~~~CP~Cr~~~~ 189 (251)
+.......|.||.|++-...+.-... -||--.++.|++-=.+.++..||.|+..+.
T Consensus 31 ~~~~~~~iCqICGD~Vg~t~dGe~FVACn~C~fpvCr~Cyeyer~eg~~~Cpqckt~Y~ 89 (1094)
T PLN02436 31 VQELSGQTCQICGDEIELTVDGEPFVACNECAFPVCRPCYEYERREGNQACPQCKTRYK 89 (1094)
T ss_pred ccccCCccccccccccCcCCCCCEEEeeccCCCccccchhhhhhhcCCccCcccCCchh
Confidence 34445679999999864333332333 467779999996656667889999997654
No 195
>PF14952 zf-tcix: Putative treble-clef, zinc-finger, Zn-binding
Probab=37.30 E-value=16 Score=24.64 Aligned_cols=12 Identities=50% Similarity=1.298 Sum_probs=10.1
Q ss_pred ccCCCCCCcccc
Q 025507 236 QKCPNCKSYNTR 247 (251)
Q Consensus 236 ~kC~~C~SyNT~ 247 (251)
-||+.||.||-.
T Consensus 12 rkCp~CGt~NG~ 23 (44)
T PF14952_consen 12 RKCPKCGTYNGT 23 (44)
T ss_pred ccCCcCcCccCc
Confidence 389999999954
No 196
>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=36.89 E-value=40 Score=32.43 Aligned_cols=25 Identities=20% Similarity=0.623 Sum_probs=17.5
Q ss_pred ccHHHHHHHHhc------------CCCCCCCCCcCcc
Q 025507 165 IHKNCLKEMREH------------HQYACPICSKSVC 189 (251)
Q Consensus 165 fH~~Ci~~wl~~------------~~~~CP~Cr~~~~ 189 (251)
.+.+|+.+|+.+ ++-.||+||+.+-
T Consensus 315 WC~~Cm~kwFasrQd~~~~~~Wl~~~~~CPtCRa~FC 351 (358)
T PF10272_consen 315 WCLECMGKWFASRQDQQHPETWLSGKCPCPTCRAKFC 351 (358)
T ss_pred HHHHHHHHHhhhcCCCCChhhhhcCCCCCCCCcccce
Confidence 467777777642 3467999998864
No 197
>KOG1312 consensus DHHC-type Zn-finger proteins [General function prediction only]
Probab=36.85 E-value=9.4 Score=35.78 Aligned_cols=32 Identities=28% Similarity=0.682 Sum_probs=27.2
Q ss_pred CCCCcceecCCcceeeccCCCcceecccccccccc
Q 025507 100 DGCGICRIGGCDNFFHCNKCRCCYSMLLKNSHPCV 134 (251)
Q Consensus 100 ~~CgiCR~g~~~~~fHC~~C~~c~~~~l~~~H~C~ 134 (251)
-+|..|++.+.-...||..||.|+.. ..|.|+
T Consensus 149 ~kCSTCki~KPARSKHCsiCNrCV~r---fDHHCi 180 (341)
T KOG1312|consen 149 VKCSTCKIRKPARSKHCSICNRCVHR---FDHHCI 180 (341)
T ss_pred CccccccCCCccccccchHHHHHHHH---hccceE
Confidence 57888999888899999999999864 468887
No 198
>KOG4185 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=36.42 E-value=7.3 Score=35.42 Aligned_cols=48 Identities=27% Similarity=0.614 Sum_probs=36.6
Q ss_pred CCCcchhhhcc--cCCceeEEcC--------CCCcccHHHHHHHHhcCCCCCCCCCcC
Q 025507 140 HDCPVCCEYLF--ETRQDVIVLP--------CGHTIHKNCLKEMREHHQYACPICSKS 187 (251)
Q Consensus 140 ~~CpICle~lf--~s~~~~~~lp--------CgH~fH~~Ci~~wl~~~~~~CP~Cr~~ 187 (251)
..|.||..... +....+.++. |||+...+|++..+......||.|+..
T Consensus 208 ~~c~ic~~~~~~n~~~~~p~vl~~~~~~~~~c~htlc~~c~~~~l~~~~~~cp~~~~~ 265 (296)
T KOG4185|consen 208 KLCEICERIYSENDEKLAPLVLSLSRLKEKIEGHTLCKECIDTILLQAGIKCPFCTWS 265 (296)
T ss_pred HHHHHHHHHhhccccccchhHHHHHHHHHHHHHHHHHhcchHHHHHHhhhcCCcccce
Confidence 46999987544 2334455667 999999999999877555789999975
No 199
>COG3809 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=36.08 E-value=27 Score=26.65 Aligned_cols=30 Identities=30% Similarity=0.565 Sum_probs=18.9
Q ss_pred CCCCCCCcCccchhHHHHHHHHHHhcC--CCCHhhh
Q 025507 179 YACPICSKSVCDMSKVWEKYDREIAAT--PMPEAYL 212 (251)
Q Consensus 179 ~~CP~Cr~~~~~~~~~~~~ld~~i~~~--p~P~e~~ 212 (251)
-.||-||..++|.. .||.+|+.+ |.|.+|+
T Consensus 22 D~CPrCrGVWLDrG----ELdKli~r~r~pqpa~ys 53 (88)
T COG3809 22 DYCPRCRGVWLDRG----ELDKLIERSRYPQPAEYS 53 (88)
T ss_pred eeCCccccEeecch----hHHHHHHHhcCCCCcccC
Confidence 46999999999854 355555433 4444443
No 200
>PF10058 DUF2296: Predicted integral membrane metal-binding protein (DUF2296); InterPro: IPR019273 This domain, found mainly in the eukaryotic lunapark proteins, has no known function [].
Probab=35.40 E-value=43 Score=23.37 Aligned_cols=47 Identities=21% Similarity=0.568 Sum_probs=29.4
Q ss_pred HHHHHHHhcCCCCHhhhcCceeEEcCCCCCCc----cccceeeeccCCCCCCcc
Q 025507 196 EKYDREIAATPMPEAYLNKKVWILCNDCGKTS----NVQFHVLAQKCPNCKSYN 245 (251)
Q Consensus 196 ~~ld~~i~~~p~P~e~~~~~~~IlCndC~~~s----~~~~h~lg~kC~~C~SyN 245 (251)
+.+|-++...|+.++ + +-.+.|.-|.... ...|-.|--+|+.|+..|
T Consensus 4 ki~d~L~G~d~~~~~--~-r~aLIC~~C~~hNGla~~~~~~~i~y~C~~Cg~~N 54 (54)
T PF10058_consen 4 KILDVLLGDDPTSPS--N-RYALICSKCFSHNGLAPKEEFEEIQYRCPYCGALN 54 (54)
T ss_pred HHHHHHhCCCCcccc--C-ceeEECcccchhhcccccccCCceEEEcCCCCCcC
Confidence 346666666663322 2 2345599998643 233555677999999987
No 201
>cd01675 RNR_III Class III ribonucleotide reductase. Ribonucleotide reductase (RNR) catalyzes the reductive synthesis of deoxyribonucleotides from their corresponding ribonucleotides. It provides the precursors necessary for DNA synthesis. RNRs are separated into three classes based on their metallocofactor usage. Class I RNRs, found in eukaryotes, bacteria, and bacteriophage, use a diiron-tyrosyl radical. Class II RNRs, found in bacteria, bacteriophage, algae and archaea, use coenzyme B12 (adenosylcobalamin, AdoCbl). Class III RNRs, found in strict or facultative anaerobic bacteria, bacteriophage, and archaea, use an FeS cluster and S-adenosylmethionine to generate a glycyl radical. Many organisms have more than one class of RNR present in their genomes. All three RNRs have a ten-stranded alpha-beta barrel domain that is structurally similar to the domain of PFL (pyruvate formate lyase). The class III enzyme from phage T4 consists of two subunits, this model covers the larger subunit w
Probab=35.31 E-value=32 Score=34.71 Aligned_cols=32 Identities=34% Similarity=0.722 Sum_probs=23.1
Q ss_pred cCceeEEcCCCCCCccccceeeeccCCCCCCcccccc
Q 025507 213 NKKVWILCNDCGKTSNVQFHVLAQKCPNCKSYNTRLT 249 (251)
Q Consensus 213 ~~~~~IlCndC~~~s~~~~h~lg~kC~~C~SyNT~~~ 249 (251)
+.... .|++|+.... -++.+||.|||-|+.++
T Consensus 515 ~~p~~-~C~~CG~~~~----~~~~~CP~CGs~~~~~~ 546 (555)
T cd01675 515 NTPID-ICNDCGYIGE----GEGFKCPKCGSEDVEVI 546 (555)
T ss_pred ecCCc-cCCCCCCCCc----CCCCCCcCCCCcCceEE
Confidence 44445 8999997553 34579999999886554
No 202
>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]
Probab=35.00 E-value=24 Score=25.45 Aligned_cols=34 Identities=24% Similarity=0.614 Sum_probs=23.1
Q ss_pred cceeecCCCCccccccccCcCCCCccceEecCcccc
Q 025507 52 VNQVICSLCGTEQKVQQVCVNCGVCMGEYFCESCKL 87 (251)
Q Consensus 52 ~~~v~C~~C~~~q~~~~~C~~Cg~~f~~y~C~~C~~ 87 (251)
-....|..|+.++-. .|..|...-+.|-|++|-|
T Consensus 25 ~v~F~CPnCGe~~I~--Rc~~CRk~g~~Y~Cp~CGF 58 (61)
T COG2888 25 AVKFPCPNCGEVEIY--RCAKCRKLGNPYRCPKCGF 58 (61)
T ss_pred eeEeeCCCCCceeee--hhhhHHHcCCceECCCcCc
Confidence 346777777765433 6677777777777777765
No 203
>smart00661 RPOL9 RNA polymerase subunit 9.
Probab=34.82 E-value=34 Score=22.69 Aligned_cols=9 Identities=33% Similarity=1.313 Sum_probs=5.4
Q ss_pred CeeecCCCC
Q 025507 95 KQYHCDGCG 103 (251)
Q Consensus 95 ~~~HC~~Cg 103 (251)
..|-|+.||
T Consensus 19 ~~~vC~~Cg 27 (52)
T smart00661 19 RRFVCRKCG 27 (52)
T ss_pred CEEECCcCC
Confidence 356666666
No 204
>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=34.36 E-value=19 Score=19.77 Aligned_cols=15 Identities=53% Similarity=1.112 Sum_probs=11.1
Q ss_pred CCCCCCCcCccchhH
Q 025507 179 YACPICSKSVCDMSK 193 (251)
Q Consensus 179 ~~CP~Cr~~~~~~~~ 193 (251)
+.||.|.+.+.....
T Consensus 1 y~C~~C~~~f~~~~~ 15 (23)
T PF00096_consen 1 YKCPICGKSFSSKSN 15 (23)
T ss_dssp EEETTTTEEESSHHH
T ss_pred CCCCCCCCccCCHHH
Confidence 468999988887543
No 205
>PF04710 Pellino: Pellino; InterPro: IPR006800 Pellino is involved in Toll-like signalling pathways, and associates with the kinase domain of the Pelle Ser/Thr kinase [, , ].; PDB: 3EGB_B 3EGA_A.
Probab=34.01 E-value=14 Score=35.95 Aligned_cols=49 Identities=29% Similarity=0.565 Sum_probs=0.4
Q ss_pred CCCCCCCcchhhhc----------ccCCceeEEcCCCCcccHHHHHHHHhc-----CCCCCCCCCcC
Q 025507 136 GAMHHDCPVCCEYL----------FETRQDVIVLPCGHTIHKNCLKEMREH-----HQYACPICSKS 187 (251)
Q Consensus 136 ~~~~~~CpICle~l----------f~s~~~~~~lpCgH~fH~~Ci~~wl~~-----~~~~CP~Cr~~ 187 (251)
+++.-.|||=|..| .+..++.+.|.|||.+=. -.|-.. ....||+||..
T Consensus 274 Na~rpQCPVglnTL~fp~~~~~~~~~~~qP~VYl~CGHVhG~---h~Wg~~~~~~~~~r~CPlCr~~ 337 (416)
T PF04710_consen 274 NAGRPQCPVGLNTLVFPSKSRKDVPDERQPWVYLNCGHVHGY---HNWGQDSDRDPRSRTCPLCRQV 337 (416)
T ss_dssp S------------------------------------------------------------------
T ss_pred hhcCCCCCcCCCccccccccccccccccCceeeccccceeee---cccccccccccccccCCCcccc
Confidence 46677899987544 344567889999986422 246431 24679999954
No 206
>PF00643 zf-B_box: B-box zinc finger; InterPro: IPR000315 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents B-box-type zinc finger domains, which are around 40 residues in length. B-box zinc fingers can be divided into two groups, where types 1 and 2 B-box domains differ in their consensus sequence and in the spacing of the 7-8 zinc-binding residues. Several proteins contain both types 1 and 2 B-boxes, suggesting some level of cooperativity between these two domains. B-box domains are found in over 1500 proteins from a variety of organisms. They are found in TRIM (tripartite motif) proteins that consist of an N-terminal RING finger (originally called an A-box), followed by 1-2 B-box domains and a coiled-coil domain (also called RBCC for Ring, B-box, Coiled-Coil). TRIM proteins contain a type 2 B-box domain, and may also contain a type 1 B-box. In proteins that do not contain RING or coiled-coil domains, the B-box domain is primarily type 2. Many type 2 B-box proteins are involved in ubiquitinylation. Proteins containing a B-box zinc finger domain include transcription factors, ribonucleoproteins and proto-oncoproteins; for example, MID1, MID2, TRIM9, TNL, TRIM36, TRIM63, TRIFIC, NCL1 and CONSTANS-like proteins []. The microtubule-associated E3 ligase MID1 (6.3.2 from EC) contains a type 1 B-box zinc finger domain. MID1 specifically binds Alpha-4, which in turn recruits the catalytic subunit of phosphatase 2A (PP2Ac). This complex is required for targeting of PP2Ac for proteasome-mediated degradation. The MID1 B-box coordinates two zinc ions and adopts a beta/beta/alpha cross-brace structure similar to that of ZZ, PHD, RING and FYVE zinc fingers [, ]. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0005622 intracellular; PDB: 3DDT_B 2D8U_A 3Q1D_A 2EGM_A 2YVR_B 2DJA_A 2DQ5_A 2JUN_A 2YRG_A 2DID_A ....
Probab=33.82 E-value=34 Score=21.66 Aligned_cols=21 Identities=24% Similarity=0.360 Sum_probs=14.3
Q ss_pred ccCcCCCCccceEecCccccc
Q 025507 68 QVCVNCGVCMGEYFCESCKLF 88 (251)
Q Consensus 68 ~~C~~Cg~~f~~y~C~~C~~~ 88 (251)
..|..++...+.|||..|+.+
T Consensus 4 ~~C~~H~~~~~~~~C~~C~~~ 24 (42)
T PF00643_consen 4 PKCPEHPEEPLSLFCEDCNEP 24 (42)
T ss_dssp SB-SSTTTSBEEEEETTTTEE
T ss_pred ccCccCCccceEEEecCCCCc
Confidence 467777777788888877643
No 207
>PF13717 zinc_ribbon_4: zinc-ribbon domain
Probab=33.63 E-value=29 Score=22.04 Aligned_cols=10 Identities=30% Similarity=0.843 Sum_probs=5.2
Q ss_pred eecCcCCCee
Q 025507 15 IRAPCCNEIF 24 (251)
Q Consensus 15 i~~pcC~~~y 24 (251)
|.||.|+.-|
T Consensus 3 i~Cp~C~~~y 12 (36)
T PF13717_consen 3 ITCPNCQAKY 12 (36)
T ss_pred EECCCCCCEE
Confidence 4455555554
No 208
>KOG0006 consensus E3 ubiquitin-protein ligase (Parkin protein) [Posttranslational modification, protein turnover, chaperones]
Probab=33.23 E-value=41 Score=32.14 Aligned_cols=89 Identities=22% Similarity=0.575 Sum_probs=54.1
Q ss_pred eEecCccc-----------cccCC--CCCCeeecCCCCcceecC-CcceeeccCCCcceeccc-cccccccCCCCCCCCc
Q 025507 79 EYFCESCK-----------LFDDD--TSKKQYHCDGCGICRIGG-CDNFFHCNKCRCCYSMLL-KNSHPCVEGAMHHDCP 143 (251)
Q Consensus 79 ~y~C~~C~-----------~~d~~--~~k~~~HC~~CgiCR~g~-~~~~fHC~~C~~c~~~~l-~~~H~C~e~~~~~~Cp 143 (251)
+-+|.+|+ -|||- +.+-+-||+.| |--|. .|=||.|..+..= .+.. -..|-=..++-...|-
T Consensus 149 RV~C~~C~~~s~tv~~~P~cWdDVLks~Ripg~Ces~--~~pg~fAEFfFKC~ah~~~-~k~~aa~lhli~~N~~ni~C~ 225 (446)
T KOG0006|consen 149 RVYCQKCSSTSVTVKSEPQCWDDVLKSKRIPGVCESC--CTPGLFAEFFFKCGAHPTS-DKETAAALHLIATNSRNITCI 225 (446)
T ss_pred EEEeecccCceEEEecCccchhhhhhcccCccccccc--cCCcchHhheehhccCCCc-cccchhHHHHhhcccccceeE
Confidence 45677776 47773 46678888875 33444 4667765544332 1110 0112222344566899
Q ss_pred chhhhcccCCceeEEcCCC--CcccHHHHHHHH
Q 025507 144 VCCEYLFETRQDVIVLPCG--HTIHKNCLKEMR 174 (251)
Q Consensus 144 ICle~lf~s~~~~~~lpCg--H~fH~~Ci~~wl 174 (251)
.|.+ ..+++.+++|. |..+..|+.-|-
T Consensus 226 ~Ctd----v~~~vlvf~Cns~HvtC~dCFr~yc 254 (446)
T KOG0006|consen 226 TCTD----VRSPVLVFQCNSRHVTCLDCFRLYC 254 (446)
T ss_pred EecC----CccceEEEecCCceeehHHhhhhHh
Confidence 9986 34478889998 999999998663
No 209
>KOG1815 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=33.13 E-value=27 Score=34.13 Aligned_cols=38 Identities=24% Similarity=0.572 Sum_probs=29.9
Q ss_pred CCCCCCCcchhhhcccCCceeEEcCCCCcccHHHHHHHHhc
Q 025507 136 GAMHHDCPVCCEYLFETRQDVIVLPCGHTIHKNCLKEMREH 176 (251)
Q Consensus 136 ~~~~~~CpICle~lf~s~~~~~~lpCgH~fH~~Ci~~wl~~ 176 (251)
......|.||.+. ... ....+.|||.|+..|...++..
T Consensus 67 ~~~~~~c~ic~~~-~~~--~~~~~~c~H~~c~~cw~~yl~~ 104 (444)
T KOG1815|consen 67 KKGDVQCGICVES-YDG--EIIGLGCGHPFCPPCWTGYLGT 104 (444)
T ss_pred CCccccCCcccCC-Ccc--hhhhcCCCcHHHHHHHHHHhhh
Confidence 3556899999984 322 4667899999999999999874
No 210
>PRK00366 ispG 4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase; Reviewed
Probab=32.91 E-value=66 Score=30.97 Aligned_cols=53 Identities=19% Similarity=0.453 Sum_probs=41.9
Q ss_pred CCCCCCCcCccchhHHHHHHHHHHhcCCCCHhhhcCceeEEc--CCCCCCccccceeee
Q 025507 179 YACPICSKSVCDMSKVWEKYDREIAATPMPEAYLNKKVWILC--NDCGKTSNVQFHVLA 235 (251)
Q Consensus 179 ~~CP~Cr~~~~~~~~~~~~ld~~i~~~p~P~e~~~~~~~IlC--ndC~~~s~~~~h~lg 235 (251)
..||-|++...|....-..+++.+...++| -+.+..-| |.|++.....+=+.|
T Consensus 269 isCPgCgR~~~D~~~la~~vee~~~~~~~P----lkIAVmGC~VNgpGEa~~aDIGIaG 323 (360)
T PRK00366 269 ISCPTCGRTEFDVIQELAEVEQRLEHIKMP----LKVAVMGCVVNGPGEAKEADIGIAG 323 (360)
T ss_pred EECCCCCCCcccHHHHHHHHHHHhcCCCCC----cEEEEeCCCCCCCCchhhCcEeEec
Confidence 359999999999888888899999988888 34566678 888887776665544
No 211
>PRK00432 30S ribosomal protein S27ae; Validated
Probab=32.73 E-value=30 Score=23.70 Aligned_cols=11 Identities=36% Similarity=1.147 Sum_probs=7.1
Q ss_pred CCeeecCCCCc
Q 025507 94 KKQYHCDGCGI 104 (251)
Q Consensus 94 k~~~HC~~Cgi 104 (251)
++.|+|..||.
T Consensus 35 ~~r~~C~~Cgy 45 (50)
T PRK00432 35 LDRWHCGKCGY 45 (50)
T ss_pred CCcEECCCcCC
Confidence 35677777763
No 212
>PF03833 PolC_DP2: DNA polymerase II large subunit DP2; InterPro: IPR016033 DP2 is the large subunit of a two-subunit novel archaebacterial replicative DNA polymerase first characterised for Pyrococcus furiosus. The structure of DP2 appears to be organised as a ~950 residue component separated from a ~300 residue component by a ~150 residue intein. The other subunit, DP1, has sequence similarity to the eukaryotic DNA polymerase delta small subunit. This entry represents the N-terminal ~950 residue component of DP2.; GO: 0003887 DNA-directed DNA polymerase activity; PDB: 3O59_X.
Probab=32.50 E-value=15 Score=39.04 Aligned_cols=46 Identities=28% Similarity=0.601 Sum_probs=0.0
Q ss_pred ccCcCCCCccceEecCccccccCCCCCCeeecCCCCcceecCCcceeeccCCCcc
Q 025507 68 QVCVNCGVCMGEYFCESCKLFDDDTSKKQYHCDGCGICRIGGCDNFFHCNKCRCC 122 (251)
Q Consensus 68 ~~C~~Cg~~f~~y~C~~C~~~d~~~~k~~~HC~~CgiCR~g~~~~~fHC~~C~~c 122 (251)
-.|++||..--.-.|+.|.-. ..+.|.|+.||+ ++. -.+|.+|+.=
T Consensus 656 r~Cp~Cg~~t~~~~Cp~CG~~----T~~~~~Cp~C~~-~~~----~~~C~~C~~~ 701 (900)
T PF03833_consen 656 RRCPKCGKETFYNRCPECGSH----TEPVYVCPDCGI-EVE----EDECPKCGRE 701 (900)
T ss_dssp -------------------------------------------------------
T ss_pred ccCcccCCcchhhcCcccCCc----cccceecccccc-ccC----cccccccccc
Confidence 356666666555566666543 335677777766 221 1166666643
No 213
>KOG4317 consensus Predicted Zn-finger protein [Function unknown]
Probab=32.33 E-value=20 Score=33.97 Aligned_cols=21 Identities=43% Similarity=0.934 Sum_probs=17.0
Q ss_pred ccCcCCCCccceEecCccccc
Q 025507 68 QVCVNCGVCMGEYFCESCKLF 88 (251)
Q Consensus 68 ~~C~~Cg~~f~~y~C~~C~~~ 88 (251)
..|+-||+.+++|.|+-|+|.
T Consensus 8 ~~C~ic~vq~~~YtCPRCn~~ 28 (383)
T KOG4317|consen 8 LACGICGVQKREYTCPRCNLL 28 (383)
T ss_pred eeccccccccccccCCCCCcc
Confidence 467788888999999998864
No 214
>cd02337 ZZ_CBP Zinc finger, ZZ type. Zinc finger present in CBP/p300 and related proteins. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding. CREB-binding protein (CBP) is a large multidomain protein that provides binding sites for transcriptional coactivators, the role of the ZZ domain in CBP/p300 is unclear.
Probab=31.95 E-value=33 Score=22.49 Aligned_cols=20 Identities=30% Similarity=0.856 Sum_probs=11.6
Q ss_pred eecCCCCcceecCCcceeeccCCC
Q 025507 97 YHCDGCGICRIGGCDNFFHCNKCR 120 (251)
Q Consensus 97 ~HC~~CgiCR~g~~~~~fHC~~C~ 120 (251)
|+|+.|+. +++ ..|||..|.
T Consensus 1 y~C~~C~~--~~~--~r~~C~~C~ 20 (41)
T cd02337 1 YTCNECKH--HVE--TRWHCTVCE 20 (41)
T ss_pred CcCCCCCC--cCC--CceECCCCc
Confidence 56666655 322 567777663
No 215
>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=31.73 E-value=54 Score=22.26 Aligned_cols=15 Identities=33% Similarity=0.802 Sum_probs=10.1
Q ss_pred CCCCCCCCcCccchhH
Q 025507 178 QYACPICSKSVCDMSK 193 (251)
Q Consensus 178 ~~~CP~Cr~~~~~~~~ 193 (251)
.++||.|.+ -.+..+
T Consensus 2 ~f~CP~C~~-~~~~~~ 16 (54)
T PF05605_consen 2 SFTCPYCGK-GFSESS 16 (54)
T ss_pred CcCCCCCCC-ccCHHH
Confidence 478999998 444333
No 216
>TIGR00595 priA primosomal protein N'. All proteins in this family for which functions are known are components of the primosome which is involved in replication, repair, and recombination.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=31.52 E-value=51 Score=32.76 Aligned_cols=46 Identities=26% Similarity=0.645 Sum_probs=31.0
Q ss_pred cceeecCCCCccccccccCcCCCCccce------EecCccccccCCCCCCeeecCCCCcc
Q 025507 52 VNQVICSLCGTEQKVQQVCVNCGVCMGE------YFCESCKLFDDDTSKKQYHCDGCGIC 105 (251)
Q Consensus 52 ~~~v~C~~C~~~q~~~~~C~~Cg~~f~~------y~C~~C~~~d~~~~k~~~HC~~CgiC 105 (251)
.+.++|..|+.. ..|++|+..+.- -.|.-|.+ ....+..|+.||-=
T Consensus 211 a~~~~C~~Cg~~----~~C~~C~~~l~~h~~~~~l~Ch~Cg~----~~~~~~~Cp~C~s~ 262 (505)
T TIGR00595 211 SKNLLCRSCGYI----LCCPNCDVSLTYHKKEGKLRCHYCGY----QEPIPKTCPQCGSE 262 (505)
T ss_pred CCeeEhhhCcCc----cCCCCCCCceEEecCCCeEEcCCCcC----cCCCCCCCCCCCCC
Confidence 367899999876 479999977653 44666653 23445677777753
No 217
>PF13719 zinc_ribbon_5: zinc-ribbon domain
Probab=31.51 E-value=32 Score=21.85 Aligned_cols=8 Identities=50% Similarity=1.265 Sum_probs=3.6
Q ss_pred eeecCCCC
Q 025507 54 QVICSLCG 61 (251)
Q Consensus 54 ~v~C~~C~ 61 (251)
.|.|+.|+
T Consensus 25 ~vrC~~C~ 32 (37)
T PF13719_consen 25 KVRCPKCG 32 (37)
T ss_pred EEECCCCC
Confidence 44444444
No 218
>PF06937 EURL: EURL protein; InterPro: IPR009704 This family consists of several animal EURL proteins. EURL is preferentially expressed in chick retinal precursor cells as well as in the anterior epithelial cells of the lens at early stages of development. EURL transcripts are found primarily in the peripheral dorsal retina, i.e., the most undifferentiated part of the dorsal retina. EURL transcripts are also detected in the lens at stage 18 and remain abundant in the proliferating epithelial cells of the lens until at least day 11. The distribution pattern of EURL in the developing retina and lens suggest a role before the events leading to cell determination and differentiation [].
Probab=31.40 E-value=38 Score=31.39 Aligned_cols=43 Identities=26% Similarity=0.411 Sum_probs=27.0
Q ss_pred CCCCCCcchhhhcccCCceeEEcCCCCc----ccHHHHHHHHhcCCCCCC
Q 025507 137 AMHHDCPVCCEYLFETRQDVIVLPCGHT----IHKNCLKEMREHHQYACP 182 (251)
Q Consensus 137 ~~~~~CpICle~lf~s~~~~~~lpCgH~----fH~~Ci~~wl~~~~~~CP 182 (251)
.+-..|+||+| |...+.+-.-| -|+ =|++|+.+|---.+..||
T Consensus 28 ~tLsfChiCfE-l~iegvpks~l--lHtkSlRGHrdCFEK~HlIanQ~~p 74 (285)
T PF06937_consen 28 ETLSFCHICFE-LSIEGVPKSNL--LHTKSLRGHRDCFEKYHLIANQDCP 74 (285)
T ss_pred cceeecceeec-cccccCccccc--cccccccchHHHHHHHHHHHcCCCC
Confidence 34568999998 55444333222 132 589999998433467788
No 219
>PF12760 Zn_Tnp_IS1595: Transposase zinc-ribbon domain; InterPro: IPR024442 This zinc binding domain is found in a range of transposase proteins such as ISSPO8, ISSOD11, ISRSSP2 etc. It may be a zinc-binding beta ribbon domain that could bind DNA.
Probab=31.09 E-value=65 Score=21.25 Aligned_cols=9 Identities=44% Similarity=1.047 Sum_probs=5.6
Q ss_pred ccCcCCCCc
Q 025507 68 QVCVNCGVC 76 (251)
Q Consensus 68 ~~C~~Cg~~ 76 (251)
..||.||..
T Consensus 19 ~~CP~Cg~~ 27 (46)
T PF12760_consen 19 FVCPHCGST 27 (46)
T ss_pred CCCCCCCCe
Confidence 456666665
No 220
>PRK00464 nrdR transcriptional regulator NrdR; Validated
Probab=30.95 E-value=30 Score=29.29 Aligned_cols=12 Identities=25% Similarity=0.855 Sum_probs=7.6
Q ss_pred cCcCCCCccceE
Q 025507 69 VCVNCGVCMGEY 80 (251)
Q Consensus 69 ~C~~Cg~~f~~y 80 (251)
.|++||..|+.|
T Consensus 30 ~c~~c~~~f~~~ 41 (154)
T PRK00464 30 ECLACGKRFTTF 41 (154)
T ss_pred eccccCCcceEe
Confidence 466666666666
No 221
>cd02249 ZZ Zinc finger, ZZ type. Zinc finger present in dystrophin, CBP/p300 and many other proteins. The ZZ motif coordinates one or two zinc ions and most likely participates in ligand binding or molecular scaffolding. Many proteins containing ZZ motifs have other zinc-binding motifs as well, and the majority serve as scaffolds in pathways involving acetyltransferase, protein kinase, or ubiqitin-related activity. ZZ proteins can be grouped into the following functional classes: chromatin modifying, cytoskeletal scaffolding, ubiquitin binding or conjugating, and membrane receptor or ion-channel modifying proteins.
Probab=30.58 E-value=35 Score=22.52 Aligned_cols=21 Identities=43% Similarity=0.999 Sum_probs=11.8
Q ss_pred eecCCCCcceecCCcceeeccCCC
Q 025507 97 YHCDGCGICRIGGCDNFFHCNKCR 120 (251)
Q Consensus 97 ~HC~~CgiCR~g~~~~~fHC~~C~ 120 (251)
|.|+.|+. -+ ....|||..|.
T Consensus 1 ~~C~~C~~-~i--~g~r~~C~~C~ 21 (46)
T cd02249 1 YSCDGCLK-PI--VGVRYHCLVCE 21 (46)
T ss_pred CCCcCCCC-CC--cCCEEECCCCC
Confidence 45666665 22 22567777665
No 222
>COG1998 RPS31 Ribosomal protein S27AE [Translation, ribosomal structure and biogenesis]
Probab=30.16 E-value=34 Score=23.77 Aligned_cols=9 Identities=33% Similarity=1.058 Sum_probs=6.5
Q ss_pred cccCcCCCC
Q 025507 67 QQVCVNCGV 75 (251)
Q Consensus 67 ~~~C~~Cg~ 75 (251)
...||+||.
T Consensus 19 ~~~CPrCG~ 27 (51)
T COG1998 19 NRFCPRCGP 27 (51)
T ss_pred cccCCCCCC
Confidence 457888883
No 223
>smart00132 LIM Zinc-binding domain present in Lin-11, Isl-1, Mec-3. Zinc-binding domain family. Some LIM domains bind protein partners via tyrosine-containing motifs. LIM domains are found in many key regulators of developmental pathways.
Probab=29.99 E-value=30 Score=20.80 Aligned_cols=37 Identities=22% Similarity=0.547 Sum_probs=21.1
Q ss_pred CcchhhhcccCCceeEEcCCCCcccHHHHHHHHhcCCCCCCCCCcCcc
Q 025507 142 CPVCCEYLFETRQDVIVLPCGHTIHKNCLKEMREHHQYACPICSKSVC 189 (251)
Q Consensus 142 CpICle~lf~s~~~~~~lpCgH~fH~~Ci~~wl~~~~~~CP~Cr~~~~ 189 (251)
|+.|.+.+.++...+.. =|..||.+| ++|..|++++.
T Consensus 2 C~~C~~~i~~~~~~~~~--~~~~~H~~C---------f~C~~C~~~L~ 38 (39)
T smart00132 2 CAGCGKPIRGGELVLRA--LGKVWHPEC---------FKCSKCGKPLG 38 (39)
T ss_pred ccccCCcccCCcEEEEe--CCccccccC---------CCCcccCCcCc
Confidence 67777765443122222 267777765 45777776653
No 224
>PRK00415 rps27e 30S ribosomal protein S27e; Reviewed
Probab=29.93 E-value=30 Score=24.80 Aligned_cols=36 Identities=33% Similarity=0.541 Sum_probs=26.0
Q ss_pred ceeecCCCCccccc------cccCcCCCCccceEecCccccc
Q 025507 53 NQVICSLCGTEQKV------QQVCVNCGVCMGEYFCESCKLF 88 (251)
Q Consensus 53 ~~v~C~~C~~~q~~------~~~C~~Cg~~f~~y~C~~C~~~ 88 (251)
-.|.|..|+.+|.+ .-.|..||...++-.=++-+|.
T Consensus 10 ~~VkCp~C~n~q~vFsha~t~V~C~~Cg~~L~~PtGGKa~i~ 51 (59)
T PRK00415 10 LKVKCPDCGNEQVVFSHASTVVRCLVCGKTLAEPTGGKAKIK 51 (59)
T ss_pred EEEECCCCCCeEEEEecCCcEEECcccCCCcccCCCcceeee
Confidence 47899999999853 2469999988877655555543
No 225
>TIGR00244 transcriptional regulator NrdR. Members of this almost entirely bacterial family contain an ATP cone domain (PFAM:PF03477). There is never more than one member per genome. Common gene symbols given include nrdR, ybaD, ribX and ytcG. The member from Streptomyces coelicolor is found upstream in the operon of the class II oxygen-independent ribonucleotide reductase gene nrdJ and was shown to repress nrdJ expression. Many members of this family are found near genes for riboflavin biosynthesis in Gram-negative bacteria, suggesting a role in that pathway. However, a phylogenetic profiling study associates members of this family with the presence of a palindromic signal with consensus acaCwAtATaTwGtgt, termed the NrdR-box, an upstream element for most operons for ribonucleotide reductase of all three classes in bacterial genomes.
Probab=29.42 E-value=34 Score=28.91 Aligned_cols=14 Identities=14% Similarity=0.510 Sum_probs=11.9
Q ss_pred ccCcCCCCccceEe
Q 025507 68 QVCVNCGVCMGEYF 81 (251)
Q Consensus 68 ~~C~~Cg~~f~~y~ 81 (251)
-.|++||..|..|=
T Consensus 29 ReC~~C~~RFTTyE 42 (147)
T TIGR00244 29 RECLECHERFTTFE 42 (147)
T ss_pred ccCCccCCccceee
Confidence 35999999999993
No 226
>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=29.03 E-value=28 Score=23.74 Aligned_cols=13 Identities=23% Similarity=0.838 Sum_probs=7.0
Q ss_pred CCCCCCCcCccch
Q 025507 179 YACPICSKSVCDM 191 (251)
Q Consensus 179 ~~CP~Cr~~~~~~ 191 (251)
..||+|.++|..-
T Consensus 21 ~~CPlC~r~l~~e 33 (54)
T PF04423_consen 21 GCCPLCGRPLDEE 33 (54)
T ss_dssp EE-TTT--EE-HH
T ss_pred CcCCCCCCCCCHH
Confidence 3899999999853
No 227
>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=28.80 E-value=44 Score=21.79 Aligned_cols=31 Identities=29% Similarity=0.616 Sum_probs=18.5
Q ss_pred eEEcCCCCCCcccccee---eeccCCCCCCcccc
Q 025507 217 WILCNDCGKTSNVQFHV---LAQKCPNCKSYNTR 247 (251)
Q Consensus 217 ~IlCndC~~~s~~~~h~---lg~kC~~C~SyNT~ 247 (251)
...|.+|+...++...+ ....|+.||+-+.+
T Consensus 5 ey~C~~Cg~~fe~~~~~~~~~~~~CP~Cg~~~~~ 38 (42)
T PF09723_consen 5 EYRCEECGHEFEVLQSISEDDPVPCPECGSTEVR 38 (42)
T ss_pred EEEeCCCCCEEEEEEEcCCCCCCcCCCCCCCceE
Confidence 35677888655443222 34678888884443
No 228
>KOG3113 consensus Uncharacterized conserved protein [Function unknown]
Probab=28.61 E-value=88 Score=28.94 Aligned_cols=49 Identities=20% Similarity=0.386 Sum_probs=34.5
Q ss_pred CCCCCcchhhhcccCCceeEEcCCCCcccHHHHHHHHhcCCCCCCCCCcCcc
Q 025507 138 MHHDCPVCCEYLFETRQDVIVLPCGHTIHKNCLKEMREHHQYACPICSKSVC 189 (251)
Q Consensus 138 ~~~~CpICle~lf~s~~~~~~lpCgH~fH~~Ci~~wl~~~~~~CP~Cr~~~~ 189 (251)
....|||=.-.|...-+-...++|||.|-..-+.+.- ...|++|...+.
T Consensus 110 a~fiCPvtgleMng~~~F~~l~~CGcV~SerAlKeik---as~C~~C~a~y~ 158 (293)
T KOG3113|consen 110 ARFICPVTGLEMNGKYRFCALRCCGCVFSERALKEIK---ASVCHVCGAAYQ 158 (293)
T ss_pred ceeecccccceecceEEEEEEeccceeccHHHHHHhh---hccccccCCccc
Confidence 4567998765443322223445999999999888873 468999998775
No 229
>PF01529 zf-DHHC: DHHC palmitoyltransferase; InterPro: IPR001594 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 DHHC-type zinc finger domain, which is also known as NEW1 []. The DHHC Zn-finger was first isolated in the Drosophila putative transcription factor DNZ1 and was named after a conserved sequence motif []. This domain has palmitoyltransferase activity; this post-translational modification attaches the C16 saturated fatty acid palmitate via a thioester linkage, predominantly to cysteine residues []. This domain is found in the DHHC proteins which are palmitoyl transferases []; the DHHC motif is found within a cysteine-rich domain which is thought to contain the catalytic site. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding
Probab=28.52 E-value=33 Score=28.17 Aligned_cols=39 Identities=28% Similarity=0.606 Sum_probs=25.8
Q ss_pred CCCCCCeeecCCCCcceecCCcceeeccCCCcceecccccccccc
Q 025507 90 DDTSKKQYHCDGCGICRIGGCDNFFHCNKCRCCYSMLLKNSHPCV 134 (251)
Q Consensus 90 ~~~~k~~~HC~~CgiCR~g~~~~~fHC~~C~~c~~~~l~~~H~C~ 134 (251)
++.....-.|.. |++-....-.||..||.|+..- .|-|.
T Consensus 42 ~~~~~~~~~C~~---C~~~kp~Rs~HC~~C~~CV~~~---DHHC~ 80 (174)
T PF01529_consen 42 DDENGELKYCST---CKIIKPPRSHHCRVCNRCVLRF---DHHCP 80 (174)
T ss_pred cccCCCCEECcc---cCCcCCCcceeccccccccccc---cccch
Confidence 334445555655 5555567899999999998643 46654
No 230
>smart00451 ZnF_U1 U1-like zinc finger. Family of C2H2-type zinc fingers, present in matrin, U1 small nuclear ribonucleoprotein C and other RNA-binding proteins.
Probab=28.49 E-value=27 Score=21.03 Aligned_cols=11 Identities=27% Similarity=1.165 Sum_probs=7.6
Q ss_pred ceEecCccccc
Q 025507 78 GEYFCESCKLF 88 (251)
Q Consensus 78 ~~y~C~~C~~~ 88 (251)
+.|||++|+.+
T Consensus 2 ~~~~C~~C~~~ 12 (35)
T smart00451 2 GGFYCKLCNVT 12 (35)
T ss_pred cCeEccccCCc
Confidence 56778888654
No 231
>KOG1701 consensus Focal adhesion adaptor protein Paxillin and related LIM proteins [Signal transduction mechanisms]
Probab=28.40 E-value=34 Score=33.67 Aligned_cols=14 Identities=29% Similarity=0.548 Sum_probs=10.0
Q ss_pred CCcccHHHHHHHHh
Q 025507 162 GHTIHKNCLKEMRE 175 (251)
Q Consensus 162 gH~fH~~Ci~~wl~ 175 (251)
||.|++.|-..-|+
T Consensus 451 ~HllCk~Ch~~Rl~ 464 (468)
T KOG1701|consen 451 GHLLCKTCHLKRLQ 464 (468)
T ss_pred Cceeechhhhhhhc
Confidence 78888888766544
No 232
>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=28.20 E-value=47 Score=20.74 Aligned_cols=10 Identities=40% Similarity=0.939 Sum_probs=5.4
Q ss_pred eeecCCCCcc
Q 025507 54 QVICSLCGTE 63 (251)
Q Consensus 54 ~v~C~~C~~~ 63 (251)
.|.|+.|++.
T Consensus 25 ~v~C~~C~~~ 34 (38)
T TIGR02098 25 KVRCGKCGHV 34 (38)
T ss_pred EEECCCCCCE
Confidence 5555555543
No 233
>PF01783 Ribosomal_L32p: Ribosomal L32p protein family; InterPro: IPR002677 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. Ribosomal protein L32p is part of the 50S ribosomal subunit. This family is found in both prokaryotes and eukaryotes. Ribosomal protein L32 of yeast binds to and regulates the splicing and the translation of the transcript of its own gene [].; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0015934 large ribosomal subunit; PDB: 3PYT_2 3F1F_5 3PYV_2 3D5B_5 3MRZ_2 3D5D_5 3F1H_5 1VSP_Y 3PYR_2 3MS1_2 ....
Probab=27.95 E-value=46 Score=23.18 Aligned_cols=29 Identities=31% Similarity=0.803 Sum_probs=22.0
Q ss_pred eeEEcCCCCCCccccceeeeccCCCCCCcccccc
Q 025507 216 VWILCNDCGKTSNVQFHVLAQKCPNCKSYNTRLT 249 (251)
Q Consensus 216 ~~IlCndC~~~s~~~~h~lg~kC~~C~SyNT~~~ 249 (251)
..+.|..|++.. ..| .-|+.||-|+.+++
T Consensus 25 ~l~~c~~cg~~~--~~H---~vc~~cG~y~~r~v 53 (56)
T PF01783_consen 25 NLVKCPNCGEPK--LPH---RVCPSCGYYKGRQV 53 (56)
T ss_dssp SEEESSSSSSEE--STT---SBCTTTBBSSSSSS
T ss_pred ceeeeccCCCEe--ccc---EeeCCCCeECCEEE
Confidence 467899999643 334 46899999999885
No 234
>KOG3842 consensus Adaptor protein Pellino [Signal transduction mechanisms]
Probab=27.81 E-value=27 Score=33.32 Aligned_cols=46 Identities=30% Similarity=0.675 Sum_probs=31.2
Q ss_pred CCCCCCCcchhhhc----------ccCCceeEEcCCCCc--ccHHHHHHHHhc-----CCCCCCCCCc
Q 025507 136 GAMHHDCPVCCEYL----------FETRQDVIVLPCGHT--IHKNCLKEMREH-----HQYACPICSK 186 (251)
Q Consensus 136 ~~~~~~CpICle~l----------f~s~~~~~~lpCgH~--fH~~Ci~~wl~~-----~~~~CP~Cr~ 186 (251)
++..-.|||=|..| .+..++.+.|.|||. +| .|=.. ....||+||.
T Consensus 287 NA~RPQCPVglnTL~~P~~~~~~~~~~~QP~vYl~CGHV~G~H-----~WG~~e~~g~~~r~CPmC~~ 349 (429)
T KOG3842|consen 287 NAARPQCPVGLNTLAFPSKRRKRVVDEKQPWVYLNCGHVHGYH-----NWGVRENTGQRERECPMCRV 349 (429)
T ss_pred hccCCCCCcccceeecccccccccccccCCeEEEecccccccc-----ccccccccCcccCcCCeeee
Confidence 45677899998755 233467899999976 44 46322 2356999994
No 235
>PRK04136 rpl40e 50S ribosomal protein L40e; Provisional
Probab=27.43 E-value=39 Score=23.29 Aligned_cols=23 Identities=30% Similarity=0.743 Sum_probs=19.5
Q ss_pred ceeecCCCCccccc-cccCcCCCC
Q 025507 53 NQVICSLCGTEQKV-QQVCVNCGV 75 (251)
Q Consensus 53 ~~v~C~~C~~~q~~-~~~C~~Cg~ 75 (251)
..++|+.|+...|+ +..|-.||.
T Consensus 13 ~k~ICrkC~ARnp~~A~~CRKCg~ 36 (48)
T PRK04136 13 NKKICMRCNARNPWRATKCRKCGY 36 (48)
T ss_pred cccchhcccCCCCccccccccCCC
Confidence 57899999999886 678988886
No 236
>PF14803 Nudix_N_2: Nudix N-terminal; PDB: 3CNG_C.
Probab=27.40 E-value=52 Score=20.86 Aligned_cols=28 Identities=21% Similarity=0.743 Sum_probs=10.5
Q ss_pred cCcCCCCccceEecCccccccCCCCCCeeecCCCC
Q 025507 69 VCVNCGVCMGEYFCESCKLFDDDTSKKQYHCDGCG 103 (251)
Q Consensus 69 ~C~~Cg~~f~~y~C~~C~~~d~~~~k~~~HC~~Cg 103 (251)
.|++||..+.. ++-++ .++.-+-|+.||
T Consensus 2 fC~~CG~~l~~------~ip~g-d~r~R~vC~~Cg 29 (34)
T PF14803_consen 2 FCPQCGGPLER------RIPEG-DDRERLVCPACG 29 (34)
T ss_dssp B-TTT--B-EE------E--TT--SS-EEEETTTT
T ss_pred ccccccChhhh------hcCCC-CCccceECCCCC
Confidence 45666665432 22222 255666666665
No 237
>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=27.38 E-value=29 Score=24.81 Aligned_cols=12 Identities=17% Similarity=0.553 Sum_probs=10.9
Q ss_pred eeecCcCCCeec
Q 025507 14 RIRAPCCNEIFD 25 (251)
Q Consensus 14 ~i~~pcC~~~y~ 25 (251)
.++||-|+++||
T Consensus 53 ~L~Cp~c~r~YP 64 (68)
T PF03966_consen 53 ELICPECGREYP 64 (68)
T ss_dssp EEEETTTTEEEE
T ss_pred EEEcCCCCCEEe
Confidence 589999999997
No 238
>PLN02638 cellulose synthase A (UDP-forming), catalytic subunit
Probab=27.37 E-value=50 Score=36.11 Aligned_cols=56 Identities=16% Similarity=0.412 Sum_probs=38.7
Q ss_pred cCCCCCCCCcchhhhcccCCceeEEc---CCCCcccHHHHHHHHhcCCCCCCCCCcCcc
Q 025507 134 VEGAMHHDCPVCCEYLFETRQDVIVL---PCGHTIHKNCLKEMREHHQYACPICSKSVC 189 (251)
Q Consensus 134 ~e~~~~~~CpICle~lf~s~~~~~~l---pCgH~fH~~Ci~~wl~~~~~~CP~Cr~~~~ 189 (251)
++......|.||.|++-...+.-... -||--.++.|++-=.+.++..||.|+..+.
T Consensus 12 ~~~~~~qiCqICGD~vg~~~~Ge~FVAC~eC~FPVCrpCYEYEr~eG~q~CPqCktrYk 70 (1079)
T PLN02638 12 MKHGGGQVCQICGDNVGKTVDGEPFVACDVCAFPVCRPCYEYERKDGNQSCPQCKTKYK 70 (1079)
T ss_pred ccccCCceeeecccccCcCCCCCEEEEeccCCCccccchhhhhhhcCCccCCccCCchh
Confidence 33445668999999764433332333 467779999996656667889999996554
No 239
>PRK00420 hypothetical protein; Validated
Probab=27.08 E-value=45 Score=26.85 Aligned_cols=20 Identities=25% Similarity=0.531 Sum_probs=12.0
Q ss_pred cccCcCCCCccce-----EecCccc
Q 025507 67 QQVCVNCGVCMGE-----YFCESCK 86 (251)
Q Consensus 67 ~~~C~~Cg~~f~~-----y~C~~C~ 86 (251)
+..||.||.++-+ .||+.|.
T Consensus 23 ~~~CP~Cg~pLf~lk~g~~~Cp~Cg 47 (112)
T PRK00420 23 SKHCPVCGLPLFELKDGEVVCPVHG 47 (112)
T ss_pred cCCCCCCCCcceecCCCceECCCCC
Confidence 4678888876543 4555553
No 240
>PRK03564 formate dehydrogenase accessory protein FdhE; Provisional
Probab=26.84 E-value=67 Score=30.25 Aligned_cols=26 Identities=31% Similarity=0.700 Sum_probs=20.4
Q ss_pred ccceeecCCCCcccc-ccccCcCCCCc
Q 025507 51 EVNQVICSLCGTEQK-VQQVCVNCGVC 76 (251)
Q Consensus 51 ~~~~v~C~~C~~~q~-~~~~C~~Cg~~ 76 (251)
..+-..|+.|+++=. +-..|++||..
T Consensus 209 G~RyL~CslC~teW~~~R~~C~~Cg~~ 235 (309)
T PRK03564 209 GLRYLHCNLCESEWHVVRVKCSNCEQS 235 (309)
T ss_pred CceEEEcCCCCCcccccCccCCCCCCC
Confidence 346788999999987 45789999864
No 241
>PF13913 zf-C2HC_2: zinc-finger of a C2HC-type
Probab=26.49 E-value=31 Score=20.08 Aligned_cols=12 Identities=25% Similarity=0.512 Sum_probs=9.2
Q ss_pred ccCcCCCCccce
Q 025507 68 QVCVNCGVCMGE 79 (251)
Q Consensus 68 ~~C~~Cg~~f~~ 79 (251)
..|+.||..|+.
T Consensus 3 ~~C~~CgR~F~~ 14 (25)
T PF13913_consen 3 VPCPICGRKFNP 14 (25)
T ss_pred CcCCCCCCEECH
Confidence 368899998864
No 242
>PF06220 zf-U1: U1 zinc finger; InterPro: IPR013085 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 motif found in several U1 small nuclear ribonucleoprotein C (U1-C) proteins. Some proteins contain multiple copies of this motif. The U1 small nuclear ribonucleoprotein (U1 snRNP) binds to the pre-mRNA 5' splice site at early stages of spliceosome assembly. Recruitment of U1 to a class of weak 5' splice site is promoted by binding of the protein TIA-1 to uridine-rich sequences immediately downstream from the 5' splice site. Binding of TIA-1 in the vicinity of a 5' splice site helps to stabilise U1 snRNP recruitment, at least in part, via a direct interaction with U1-C, thus providing one molecular mechanism for the function of this splicing regulator []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 2VRD_A.
Probab=26.43 E-value=26 Score=22.63 Aligned_cols=13 Identities=38% Similarity=1.076 Sum_probs=5.5
Q ss_pred cceEecCcccccc
Q 025507 77 MGEYFCESCKLFD 89 (251)
Q Consensus 77 f~~y~C~~C~~~d 89 (251)
|-+|||+-|+.|-
T Consensus 1 m~ryyCdyC~~~~ 13 (38)
T PF06220_consen 1 MPRYYCDYCKKYL 13 (38)
T ss_dssp --S-B-TTT--B-
T ss_pred CcCeeccccccee
Confidence 4589999998775
No 243
>PF15353 HECA: Headcase protein family homologue
Probab=26.15 E-value=39 Score=27.03 Aligned_cols=16 Identities=25% Similarity=0.891 Sum_probs=13.6
Q ss_pred CCCCcccHHHHHHHHh
Q 025507 160 PCGHTIHKNCLKEMRE 175 (251)
Q Consensus 160 pCgH~fH~~Ci~~wl~ 175 (251)
|-|+.||.+|++.|-.
T Consensus 39 p~~~~MH~~CF~~wE~ 54 (107)
T PF15353_consen 39 PFGQYMHRECFEKWED 54 (107)
T ss_pred CCCCchHHHHHHHHHH
Confidence 4489999999999954
No 244
>PF03833 PolC_DP2: DNA polymerase II large subunit DP2; InterPro: IPR016033 DP2 is the large subunit of a two-subunit novel archaebacterial replicative DNA polymerase first characterised for Pyrococcus furiosus. The structure of DP2 appears to be organised as a ~950 residue component separated from a ~300 residue component by a ~150 residue intein. The other subunit, DP1, has sequence similarity to the eukaryotic DNA polymerase delta small subunit. This entry represents the N-terminal ~950 residue component of DP2.; GO: 0003887 DNA-directed DNA polymerase activity; PDB: 3O59_X.
Probab=24.78 E-value=24 Score=37.48 Aligned_cols=48 Identities=29% Similarity=0.770 Sum_probs=0.0
Q ss_pred ccceeecCCCCccccccccCcCCCCc-cceEecCccccccCCCCCCeeecCCCCc
Q 025507 51 EVNQVICSLCGTEQKVQQVCVNCGVC-MGEYFCESCKLFDDDTSKKQYHCDGCGI 104 (251)
Q Consensus 51 ~~~~v~C~~C~~~q~~~~~C~~Cg~~-f~~y~C~~C~~~d~~~~k~~~HC~~Cgi 104 (251)
++-.-.|..|+++ .....|+.||.. .-.|+|+.|+.--++. +|+.||.
T Consensus 652 ei~~r~Cp~Cg~~-t~~~~Cp~CG~~T~~~~~Cp~C~~~~~~~-----~C~~C~~ 700 (900)
T PF03833_consen 652 EIGRRRCPKCGKE-TFYNRCPECGSHTEPVYVCPDCGIEVEED-----ECPKCGR 700 (900)
T ss_dssp -------------------------------------------------------
T ss_pred eeecccCcccCCc-chhhcCcccCCccccceeccccccccCcc-----ccccccc
Confidence 3446679999988 566789999876 4578899997643321 8888884
No 245
>PF00130 C1_1: Phorbol esters/diacylglycerol binding domain (C1 domain); InterPro: IPR002219 Diacylglycerol (DAG) is an important second messenger. Phorbol esters (PE) are analogues of DAG and potent tumour promoters that cause a variety of physiological changes when administered to both cells and tissues. DAG activates a family of serine/threonine protein kinases, collectively known as protein kinase C (PKC) []. Phorbol esters can directly stimulate PKC. The N-terminal region of PKC, known as C1, has been shown [] to bind PE and DAG in a phospholipid and zinc-dependent fashion. The C1 region contains one or two copies (depending on the isozyme of PKC) of a cysteine-rich domain, which is about 50 amino-acid residues long, and which is essential for DAG/PE-binding. The DAG/PE-binding domain binds two zinc ions; the ligands of these metal ions are probably the six cysteines and two histidines that are conserved in this domain.; GO: 0035556 intracellular signal transduction; PDB: 1RFH_A 2FNF_X 3PFQ_A 1PTQ_A 1PTR_A 2VRW_B 1XA6_A 2ENN_A 1TBN_A 1TBO_A ....
Probab=24.64 E-value=63 Score=21.41 Aligned_cols=13 Identities=38% Similarity=1.027 Sum_probs=6.0
Q ss_pred CCCCeeecCCCCc
Q 025507 92 TSKKQYHCDGCGI 104 (251)
Q Consensus 92 ~~k~~~HC~~Cgi 104 (251)
..++-|+|..|++
T Consensus 24 ~~~~g~~C~~C~~ 36 (53)
T PF00130_consen 24 LGKQGYRCSWCGL 36 (53)
T ss_dssp SSSCEEEETTTT-
T ss_pred CCCCeEEECCCCC
Confidence 3445555555543
No 246
>COG1327 Predicted transcriptional regulator, consists of a Zn-ribbon and ATP-cone domains [Transcription]
Probab=24.52 E-value=38 Score=28.82 Aligned_cols=12 Identities=25% Similarity=0.883 Sum_probs=10.9
Q ss_pred cCcCCCCccceE
Q 025507 69 VCVNCGVCMGEY 80 (251)
Q Consensus 69 ~C~~Cg~~f~~y 80 (251)
.|++||..|..|
T Consensus 30 eC~~C~~RFTTf 41 (156)
T COG1327 30 ECLECGERFTTF 41 (156)
T ss_pred cccccccccchh
Confidence 599999999887
No 247
>KOG1311 consensus DHHC-type Zn-finger proteins [General function prediction only]
Probab=24.42 E-value=62 Score=29.51 Aligned_cols=46 Identities=24% Similarity=0.666 Sum_probs=34.1
Q ss_pred CCccceEecCccccccCCCCCCeeecCCCCcceecCCcceeeccCCCcceec
Q 025507 74 GVCMGEYFCESCKLFDDDTSKKQYHCDGCGICRIGGCDNFFHCNKCRCCYSM 125 (251)
Q Consensus 74 g~~f~~y~C~~C~~~d~~~~k~~~HC~~CgiCR~g~~~~~fHC~~C~~c~~~ 125 (251)
|......||+.|+++ ..+...||.-||.|-.+ ---||.==|.|+..
T Consensus 108 ~~~~~~~~C~~C~~~---rPpRs~HCsvC~~CV~r---fDHHC~WvnnCVG~ 153 (299)
T KOG1311|consen 108 GIQVEWKYCDTCQLY---RPPRSSHCSVCNNCVLR---FDHHCPWLNNCIGE 153 (299)
T ss_pred CcccceEEcCcCccc---CCCCcccchhhcccccc---cCCCCCCccceECC
Confidence 455667899999999 33567899999888773 33678777777764
No 248
>PRK08351 DNA-directed RNA polymerase subunit E''; Validated
Probab=24.39 E-value=45 Score=24.02 Aligned_cols=20 Identities=25% Similarity=0.620 Sum_probs=13.7
Q ss_pred ecCCCCccccccccCcCCCCc
Q 025507 56 ICSLCGTEQKVQQVCVNCGVC 76 (251)
Q Consensus 56 ~C~~C~~~q~~~~~C~~Cg~~ 76 (251)
.|..|...++ .+.||+||..
T Consensus 5 AC~~C~~i~~-~~~CP~Cgs~ 24 (61)
T PRK08351 5 ACRHCHYITT-EDRCPVCGSR 24 (61)
T ss_pred hhhhCCcccC-CCcCCCCcCC
Confidence 5777777663 3468888874
No 249
>PF13597 NRDD: Anaerobic ribonucleoside-triphosphate reductase; PDB: 1HK8_A 1H78_A 1H7A_A 1H79_A 1H7B_A.
Probab=23.89 E-value=44 Score=33.67 Aligned_cols=29 Identities=34% Similarity=0.723 Sum_probs=13.9
Q ss_pred eeEEcCCCCCCccccceeeeccCCCCCCcccccc
Q 025507 216 VWILCNDCGKTSNVQFHVLAQKCPNCKSYNTRLT 249 (251)
Q Consensus 216 ~~IlCndC~~~s~~~~h~lg~kC~~C~SyNT~~~ 249 (251)
..-.|++|+..... +.+||.|||-|+.++
T Consensus 490 ~~~~C~~CG~~~~~-----~~~CP~CGs~~~~~~ 518 (546)
T PF13597_consen 490 PIDICPDCGYIGGE-----GDKCPKCGSENIEVY 518 (546)
T ss_dssp -EEEETTT---S-------EEE-CCC----EEEE
T ss_pred CcccccCCCcCCCC-----CCCCCCCCCcccceE
Confidence 34569999987653 568999999997665
No 250
>KOG3362 consensus Predicted BBOX Zn-finger protein [General function prediction only]
Probab=23.87 E-value=24 Score=29.86 Aligned_cols=25 Identities=32% Similarity=0.883 Sum_probs=17.4
Q ss_pred ceEecCccccccCCCCCCeeecCCCC--cceec
Q 025507 78 GEYFCESCKLFDDDTSKKQYHCDGCG--ICRIG 108 (251)
Q Consensus 78 ~~y~C~~C~~~d~~~~k~~~HC~~Cg--iCR~g 108 (251)
.+-||++|-+| ++|-|-.|| +|-|+
T Consensus 117 ~r~fCaVCG~~------S~ysC~~CG~kyCsv~ 143 (156)
T KOG3362|consen 117 LRKFCAVCGYD------SKYSCVNCGTKYCSVR 143 (156)
T ss_pred cchhhhhcCCC------chhHHHhcCCceeech
Confidence 45677888744 467888887 66665
No 251
>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=23.09 E-value=71 Score=19.91 Aligned_cols=26 Identities=35% Similarity=0.738 Sum_probs=13.9
Q ss_pred EEcCCCCCCccccce---eeeccCCCCCC
Q 025507 218 ILCNDCGKTSNVQFH---VLAQKCPNCKS 243 (251)
Q Consensus 218 IlCndC~~~s~~~~h---~lg~kC~~C~S 243 (251)
..|.+|+...++..- -....|+.||+
T Consensus 6 y~C~~Cg~~fe~~~~~~~~~~~~CP~Cg~ 34 (41)
T smart00834 6 YRCEDCGHTFEVLQKISDDPLATCPECGG 34 (41)
T ss_pred EEcCCCCCEEEEEEecCCCCCCCCCCCCC
Confidence 456666664433221 12356777777
No 252
>cd07973 Spt4 Transcription elongation factor Spt4. Spt4 is a transcription elongation factor. Three transcription-elongation factors Spt4, Spt5, and Spt6, are conserved among eukaryotes and are essential for transcription via the modulation of chromatin structure. It is known that Spt4, Spt5, and Spt6 are general transcription-elongation factors, controlling transcription both positively and negatively in important regulatory and developmental roles. Spt4 functions entirely in the context of the Spt4-Spt5 heterodimer and it has been found only as a complex to Spt5 in Yeast and Human. Spt4 is a small protein that has zinc finger at the N-terminus. Spt5 is a large protein that has several interesting structural features of an acidic N-terminus, a single NGN domain, five or six KOW domains, and a set of simple C-termianl repeats. Spt4 binds to Spt5 NGN domain. Unlike Spt5, Spt4 is not essential for viability in yeast, however Spt4 is critical for normal function of the Spt4-Spt5 compl
Probab=22.98 E-value=45 Score=26.17 Aligned_cols=20 Identities=30% Similarity=0.660 Sum_probs=14.6
Q ss_pred ecCCCCcccccc----ccCcCCCC
Q 025507 56 ICSLCGTEQKVQ----QVCVNCGV 75 (251)
Q Consensus 56 ~C~~C~~~q~~~----~~C~~Cg~ 75 (251)
.|+.|+..++.. +.||||+.
T Consensus 5 AC~~C~~I~~~~qf~~~gCpnC~~ 28 (98)
T cd07973 5 ACLLCSLIKTEDQFERDGCPNCEG 28 (98)
T ss_pred hhccCCcccccccccCCCCCCCcc
Confidence 688888887643 57888863
No 253
>KOG4362 consensus Transcriptional regulator BRCA1 [Replication, recombination and repair; Transcription]
Probab=22.95 E-value=36 Score=35.37 Aligned_cols=47 Identities=30% Similarity=0.692 Sum_probs=36.5
Q ss_pred CCCCcchhhhcccCCceeEEcCCCCcccHHHHHHHHhc--CCCCCCCCCcCcc
Q 025507 139 HHDCPVCCEYLFETRQDVIVLPCGHTIHKNCLKEMREH--HQYACPICSKSVC 189 (251)
Q Consensus 139 ~~~CpICle~lf~s~~~~~~lpCgH~fH~~Ci~~wl~~--~~~~CP~Cr~~~~ 189 (251)
..+||||++..++. ..+.|-|.|...|+...+.. ....||+|+..+.
T Consensus 21 ~lEc~ic~~~~~~p----~~~kc~~~~l~~~~n~~f~~~~~~~~~~lc~~~~e 69 (684)
T KOG4362|consen 21 ILECPICLEHVKEP----SLLKCDHIFLKFCLNKLFESKKGPKQCALCKSDIE 69 (684)
T ss_pred hccCCceeEEeecc----chhhhhHHHHhhhhhceeeccCccccchhhhhhhh
Confidence 56899999976663 57899999999999985443 2357999996654
No 254
>COG5273 Uncharacterized protein containing DHHC-type Zn finger [General function prediction only]
Probab=22.93 E-value=40 Score=31.52 Aligned_cols=37 Identities=24% Similarity=0.673 Sum_probs=24.5
Q ss_pred ccCcCCCCccceEecCccccccCCCCCCeeecCCCCccee
Q 025507 68 QVCVNCGVCMGEYFCESCKLFDDDTSKKQYHCDGCGICRI 107 (251)
Q Consensus 68 ~~C~~Cg~~f~~y~C~~C~~~d~~~~k~~~HC~~CgiCR~ 107 (251)
..+...|....+-||.+|+.|--+ ...||..||.|-.
T Consensus 98 ~~~~~~~~~~~~~~C~~C~~~KP~---RS~HC~~Cn~CV~ 134 (309)
T COG5273 98 SRLLDDGKFGTENFCSTCNIYKPP---RSHHCSICNRCVL 134 (309)
T ss_pred hhhhhcCccccceeccccccccCC---CCccchhhcchhh
Confidence 556677888888899999999433 2345555555544
No 255
>KOG4399 consensus C2HC-type Zn-finger protein [General function prediction only]
Probab=22.72 E-value=16 Score=33.81 Aligned_cols=73 Identities=26% Similarity=0.597 Sum_probs=51.8
Q ss_pred CCCCccceEecCccccccCCCCCCeeecCCCCcceecCCcceeeccCCCcceeccccccccccCCCCCCCCcchhh
Q 025507 72 NCGVCMGEYFCESCKLFDDDTSKKQYHCDGCGICRIGGCDNFFHCNKCRCCYSMLLKNSHPCVEGAMHHDCPVCCE 147 (251)
Q Consensus 72 ~Cg~~f~~y~C~~C~~~d~~~~k~~~HC~~CgiCR~g~~~~~fHC~~C~~c~~~~l~~~H~C~e~~~~~~CpICle 147 (251)
.=|..-+-.||+.|..| ..+-.-||+.|+.|..-.++.|-||..|-.|+-.++..-..|..-+...-|-||-+
T Consensus 197 ~~~~EE~~~~~~~~~~Y---v~~~~~H~~~~~S~~~~~~~~~~H~~~~~~~~~~~~i~C~~~~~~A~~~~C~iC~~ 269 (325)
T KOG4399|consen 197 ILPTEEGYRFCSPCQRY---VSLENQHCEHCNSCTSKDGRKWNHCFLCKKCVKPSWIHCSICNHCAVKHGCFICGE 269 (325)
T ss_pred ecccccceEEEeehHHH---HHHHhhhchhhcccccchhHHHhHhHHhhhhcccceeeeecccchhhhcceeeccc
Confidence 34566677789999988 44677899999999777777899999999998877643222222233445667766
No 256
>COG1545 Predicted nucleic-acid-binding protein containing a Zn-ribbon [General function prediction only]
Probab=22.68 E-value=53 Score=27.11 Aligned_cols=31 Identities=19% Similarity=0.471 Sum_probs=24.9
Q ss_pred CCCcccceeecCCCCccc-cccccCcCCCCcc
Q 025507 47 IPRHEVNQVICSLCGTEQ-KVQQVCVNCGVCM 77 (251)
Q Consensus 47 ~~r~~~~~v~C~~C~~~q-~~~~~C~~Cg~~f 77 (251)
+.+.......|..|++.. |+...|++||..-
T Consensus 22 l~~~kl~g~kC~~CG~v~~PPr~~Cp~C~~~~ 53 (140)
T COG1545 22 LKEGKLLGTKCKKCGRVYFPPRAYCPKCGSET 53 (140)
T ss_pred hhhCcEEEEEcCCCCeEEcCCcccCCCCCCCC
Confidence 344556688999999887 7789999999874
No 257
>PF12675 DUF3795: Protein of unknown function (DUF3795); InterPro: IPR024227 This family of proteins is functionally uncharacterised and is found in bacteria and archaea. Proteins in this family are typically between 99 and 171 amino acids in length. These proteins are likely to be zinc binding given the conserved cysteines.
Probab=22.59 E-value=48 Score=24.44 Aligned_cols=36 Identities=28% Similarity=0.603 Sum_probs=23.2
Q ss_pred cccCcCCCCccceEecCccccccCCCCCCeeecCCC
Q 025507 67 QQVCVNCGVCMGEYFCESCKLFDDDTSKKQYHCDGC 102 (251)
Q Consensus 67 ~~~C~~Cg~~f~~y~C~~C~~~d~~~~k~~~HC~~C 102 (251)
...|+.|...=....+..|.+.+=-.+|.+-||-+|
T Consensus 34 ~~~C~GCr~~~~~~~~~~C~i~~C~~ekgv~~C~eC 69 (78)
T PF12675_consen 34 KIRCPGCRSGGGKCCCKSCKIRQCAKEKGVDFCGEC 69 (78)
T ss_pred CCcCcCCcCCCCCcCCCCCCcCcHHhhCCCCeeecC
Confidence 345777765544466777777766566777776555
No 258
>smart00647 IBR In Between Ring fingers. the domains occurs between pairs og RING fingers
Probab=21.91 E-value=35 Score=23.17 Aligned_cols=18 Identities=17% Similarity=0.397 Sum_probs=14.3
Q ss_pred eEEc-CCCCcccHHHHHHH
Q 025507 156 VIVL-PCGHTIHKNCLKEM 173 (251)
Q Consensus 156 ~~~l-pCgH~fH~~Ci~~w 173 (251)
.+.- .||+.|+..|..+|
T Consensus 40 ~v~C~~C~~~fC~~C~~~~ 58 (64)
T smart00647 40 RVTCPKCGFSFCFRCKVPW 58 (64)
T ss_pred eeECCCCCCeECCCCCCcC
Confidence 3444 68999999999888
No 259
>PF06677 Auto_anti-p27: Sjogren's syndrome/scleroderma autoantigen 1 (Autoantigen p27); InterPro: IPR009563 The proteins in this entry are functionally uncharacterised and include several proteins that characterise Sjogren's syndrome/scleroderma autoantigen 1 (Autoantigen p27). It is thought that the potential association of anti-p27 with anti-centromere antibodies suggests that autoantigen p27 might play a role in mitosis [].
Probab=21.86 E-value=67 Score=21.20 Aligned_cols=12 Identities=25% Similarity=0.744 Sum_probs=7.3
Q ss_pred cccCcCCCCccc
Q 025507 67 QQVCVNCGVCMG 78 (251)
Q Consensus 67 ~~~C~~Cg~~f~ 78 (251)
+..|+.||.++-
T Consensus 17 ~~~Cp~C~~PL~ 28 (41)
T PF06677_consen 17 DEHCPDCGTPLM 28 (41)
T ss_pred cCccCCCCCeeE
Confidence 456777766543
No 260
>PF10122 Mu-like_Com: Mu-like prophage protein Com; InterPro: IPR019294 Members of this entry belong to the Com family of proteins that act as translational regulators of mom [, ].
Probab=21.83 E-value=52 Score=22.96 Aligned_cols=32 Identities=34% Similarity=0.591 Sum_probs=20.1
Q ss_pred eEEcCCCCCCccc--cceeeeccCCCCCCccccc
Q 025507 217 WILCNDCGKTSNV--QFHVLAQKCPNCKSYNTRL 248 (251)
Q Consensus 217 ~IlCndC~~~s~~--~~h~lg~kC~~C~SyNT~~ 248 (251)
.|.|-.|++.--. .+-.|-.||+.|+..|...
T Consensus 4 eiRC~~CnklLa~~g~~~~leIKCpRC~tiN~~~ 37 (51)
T PF10122_consen 4 EIRCGHCNKLLAKAGEVIELEIKCPRCKTINHVR 37 (51)
T ss_pred ceeccchhHHHhhhcCccEEEEECCCCCccceEe
Confidence 4666667643211 2445778999999888643
No 261
>COG5595 Zn-ribbon-containing, possibly nucleic-acid-binding protein [General function prediction only]
Probab=21.51 E-value=67 Score=28.72 Aligned_cols=38 Identities=24% Similarity=0.599 Sum_probs=26.4
Q ss_pred CCCCCCCcCccchhHHHHHHHHHHhcCCCCHhhhcCceeEEcCCCCCCccccceee
Q 025507 179 YACPICSKSVCDMSKVWEKYDREIAATPMPEAYLNKKVWILCNDCGKTSNVQFHVL 234 (251)
Q Consensus 179 ~~CP~Cr~~~~~~~~~~~~ld~~i~~~p~P~e~~~~~~~IlCndC~~~s~~~~h~l 234 (251)
..||.|++.+.-.+..+. .-.-.|++|.-.|+..+|||
T Consensus 219 r~CPsC~k~Wqlk~~i~d------------------~fhfkcd~crlvsnlsw~~l 256 (256)
T COG5595 219 RCCPSCGKDWQLKNPIFD------------------TFHFKCDTCRLVSNLSWNFL 256 (256)
T ss_pred CCCCcccccceeccchhh------------------heeeecccceeecccccccC
Confidence 459999987654222111 12467999999999999986
No 262
>cd02345 ZZ_dah Zinc finger, ZZ type. Zinc finger present in Drosophila dah and related proteins. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding. Dah (discontinuous actin hexagon) is a membrane associated protein essential for cortical furrow formation in Drosophila.
Probab=21.42 E-value=65 Score=21.76 Aligned_cols=26 Identities=23% Similarity=0.664 Sum_probs=15.9
Q ss_pred EEcCCCCCCccccceeeeccCCCCCCccc
Q 025507 218 ILCNDCGKTSNVQFHVLAQKCPNCKSYNT 246 (251)
Q Consensus 218 IlCndC~~~s~~~~h~lg~kC~~C~SyNT 246 (251)
|.|+.|.+..-+.++ .+|..|..|+-
T Consensus 1 ~~C~~C~~~~i~g~R---~~C~~C~dydL 26 (49)
T cd02345 1 LSCSACRKQDISGIR---FPCQVCRDYSL 26 (49)
T ss_pred CcCCCCCCCCceEee---EECCCCCCcCc
Confidence 468888875444444 36777766663
No 263
>PF09986 DUF2225: Uncharacterized protein conserved in bacteria (DUF2225); InterPro: IPR018708 This conserved bacterial family has no known function.
Probab=21.30 E-value=21 Score=31.49 Aligned_cols=14 Identities=29% Similarity=0.876 Sum_probs=11.1
Q ss_pred CCCCCCCCCcCccc
Q 025507 177 HQYACPICSKSVCD 190 (251)
Q Consensus 177 ~~~~CP~Cr~~~~~ 190 (251)
...+||+|++++..
T Consensus 4 k~~~CPvC~~~F~~ 17 (214)
T PF09986_consen 4 KKITCPVCGKEFKT 17 (214)
T ss_pred CceECCCCCCeeee
Confidence 35789999998863
No 264
>PF09297 zf-NADH-PPase: NADH pyrophosphatase zinc ribbon domain; InterPro: IPR015376 This domain has a zinc ribbon structure and is often found between two NUDIX domains.; GO: 0016787 hydrolase activity, 0046872 metal ion binding; PDB: 1VK6_A 2GB5_A.
Probab=21.19 E-value=37 Score=20.71 Aligned_cols=21 Identities=33% Similarity=0.846 Sum_probs=10.6
Q ss_pred ecCCCCccccc-----cccCcCCCCc
Q 025507 56 ICSLCGTEQKV-----QQVCVNCGVC 76 (251)
Q Consensus 56 ~C~~C~~~q~~-----~~~C~~Cg~~ 76 (251)
.|+.|+.+... +..|++||..
T Consensus 5 fC~~CG~~t~~~~~g~~r~C~~Cg~~ 30 (32)
T PF09297_consen 5 FCGRCGAPTKPAPGGWARRCPSCGHE 30 (32)
T ss_dssp B-TTT--BEEE-SSSS-EEESSSS-E
T ss_pred ccCcCCccccCCCCcCEeECCCCcCE
Confidence 57888876542 3468888764
No 265
>smart00440 ZnF_C2C2 C2C2 Zinc finger. Nucleic-acid-binding motif in transcriptional elongation factor TFIIS and RNA polymerases.
Probab=21.08 E-value=1e+02 Score=19.90 Aligned_cols=33 Identities=27% Similarity=0.661 Sum_probs=19.0
Q ss_pred cCcCCCCccceEecCccccc-cCCCCCCeeecCCCC
Q 025507 69 VCVNCGVCMGEYFCESCKLF-DDDTSKKQYHCDGCG 103 (251)
Q Consensus 69 ~C~~Cg~~f~~y~C~~C~~~-d~~~~k~~~HC~~Cg 103 (251)
.|++||..-+.|| .. ..- -|++..-.|-|.+||
T Consensus 2 ~Cp~C~~~~a~~~-q~-Q~RsaDE~mT~fy~C~~C~ 35 (40)
T smart00440 2 PCPKCGNREATFF-QL-QTRSADEPMTVFYVCTKCG 35 (40)
T ss_pred cCCCCCCCeEEEE-EE-cccCCCCCCeEEEEeCCCC
Confidence 5888888777776 10 122 223445566776665
No 266
>PF07754 DUF1610: Domain of unknown function (DUF1610); InterPro: IPR011668 This domain is found in archaeal species. It is likely to bind zinc via its four well-conserved cysteine residues.
Probab=20.60 E-value=76 Score=18.70 Aligned_cols=9 Identities=33% Similarity=1.162 Sum_probs=4.0
Q ss_pred CeeecCCCC
Q 025507 95 KQYHCDGCG 103 (251)
Q Consensus 95 ~~~HC~~Cg 103 (251)
-.|.|+.||
T Consensus 15 v~f~CPnCG 23 (24)
T PF07754_consen 15 VPFPCPNCG 23 (24)
T ss_pred ceEeCCCCC
Confidence 344444444
No 267
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=20.50 E-value=62 Score=27.82 Aligned_cols=11 Identities=45% Similarity=0.990 Sum_probs=7.6
Q ss_pred CCCCcchhhhc
Q 025507 139 HHDCPVCCEYL 149 (251)
Q Consensus 139 ~~~CpICle~l 149 (251)
...||+|.+.|
T Consensus 136 ~F~Cp~Cg~~L 146 (178)
T PRK06266 136 GFRCPQCGEML 146 (178)
T ss_pred CCcCCCCCCCC
Confidence 56788887654
No 268
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=20.44 E-value=37 Score=28.00 Aligned_cols=10 Identities=30% Similarity=0.574 Sum_probs=5.4
Q ss_pred cCcCCCCccc
Q 025507 69 VCVNCGVCMG 78 (251)
Q Consensus 69 ~C~~Cg~~f~ 78 (251)
.||+||..|.
T Consensus 101 ~Cp~C~~~y~ 110 (147)
T smart00531 101 KCPNCQSKYT 110 (147)
T ss_pred ECcCCCCEee
Confidence 4666665443
No 269
>PRK14873 primosome assembly protein PriA; Provisional
Probab=20.38 E-value=98 Score=32.11 Aligned_cols=28 Identities=29% Similarity=0.635 Sum_probs=20.5
Q ss_pred CCccc-ceeecCCCCccccccccCcCCCCccce
Q 025507 48 PRHEV-NQVICSLCGTEQKVQQVCVNCGVCMGE 79 (251)
Q Consensus 48 ~r~~~-~~v~C~~C~~~q~~~~~C~~Cg~~f~~ 79 (251)
+|+.- +.++|..|+.. -.|++|+..+.-
T Consensus 376 nRrGyap~l~C~~Cg~~----~~C~~C~~~L~~ 404 (665)
T PRK14873 376 PRRGYVPSLACARCRTP----ARCRHCTGPLGL 404 (665)
T ss_pred cCCCCCCeeEhhhCcCe----eECCCCCCceeE
Confidence 55543 57799999876 479999887764
No 270
>PLN02400 cellulose synthase
Probab=20.25 E-value=58 Score=35.69 Aligned_cols=56 Identities=16% Similarity=0.428 Sum_probs=38.9
Q ss_pred cCCCCCCCCcchhhhcccCCceeEEc---CCCCcccHHHHHHHHhcCCCCCCCCCcCcc
Q 025507 134 VEGAMHHDCPVCCEYLFETRQDVIVL---PCGHTIHKNCLKEMREHHQYACPICSKSVC 189 (251)
Q Consensus 134 ~e~~~~~~CpICle~lf~s~~~~~~l---pCgH~fH~~Ci~~wl~~~~~~CP~Cr~~~~ 189 (251)
+++.....|.||-|++-...+.-... -||=-.++.|++-=.+.++..||.|+..+.
T Consensus 31 ~~~~~gqiCqICGD~VG~t~dGe~FVAC~eCaFPVCRpCYEYERkeGnq~CPQCkTrYk 89 (1085)
T PLN02400 31 LKNLNGQICQICGDDVGVTETGDVFVACNECAFPVCRPCYEYERKDGTQCCPQCKTRYR 89 (1085)
T ss_pred ccccCCceeeecccccCcCCCCCEEEEEccCCCccccchhheecccCCccCcccCCccc
Confidence 44455679999999864433322233 567779999996555667888999997654
Done!