Query 021022
Match_columns 318
No_of_seqs 276 out of 1384
Neff 4.9
Searched_HMMs 46136
Date Fri Mar 29 06:59:33 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/021022.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/021022hhsearch_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 5.2E-67 1.1E-71 492.4 6.6 249 57-317 19-267 (276)
2 PF14599 zinc_ribbon_6: Zinc-r 99.9 1.1E-27 2.5E-32 180.1 0.2 61 255-315 1-61 (61)
3 PF05495 zf-CHY: CHY zinc fing 99.9 1E-23 2.3E-28 162.7 4.1 70 73-156 1-71 (71)
4 COG4357 Zinc finger domain con 99.3 2E-13 4.4E-18 111.0 1.4 67 71-146 13-92 (105)
5 PF13639 zf-RING_2: Ring finge 99.3 1.4E-12 3E-17 90.9 1.5 44 207-252 1-44 (44)
6 PF12861 zf-Apc11: Anaphase-pr 99.1 5.7E-11 1.2E-15 95.1 4.1 51 204-256 30-82 (85)
7 PF12678 zf-rbx1: RING-H2 zinc 98.9 7.6E-10 1.6E-14 85.7 3.7 46 206-252 19-73 (73)
8 KOG4628 Predicted E3 ubiquitin 98.9 5.7E-10 1.2E-14 109.2 3.2 50 207-257 230-279 (348)
9 cd00162 RING RING-finger (Real 98.9 2E-09 4.3E-14 72.3 3.8 45 208-255 1-45 (45)
10 PF13923 zf-C3HC4_2: Zinc fing 98.8 3.9E-09 8.4E-14 72.0 2.9 39 209-251 1-39 (39)
11 PHA02929 N1R/p28-like protein; 98.7 1.3E-08 2.7E-13 95.5 4.5 54 203-257 171-228 (238)
12 PF15227 zf-C3HC4_4: zinc fing 98.7 1.3E-08 2.9E-13 71.1 3.2 39 209-251 1-42 (42)
13 COG5243 HRD1 HRD ubiquitin lig 98.7 8E-09 1.7E-13 101.6 2.3 56 203-259 284-349 (491)
14 PF13920 zf-C3HC4_3: Zinc fing 98.6 1.7E-08 3.8E-13 72.1 3.0 47 206-257 2-49 (50)
15 PF00097 zf-C3HC4: Zinc finger 98.6 2.3E-08 4.9E-13 68.2 3.1 40 209-251 1-41 (41)
16 smart00184 RING Ring finger. E 98.6 4.3E-08 9.4E-13 63.5 3.1 39 209-251 1-39 (39)
17 COG5540 RING-finger-containing 98.6 3.3E-08 7.3E-13 95.1 3.5 55 201-256 318-372 (374)
18 KOG1493 Anaphase-promoting com 98.5 1.4E-08 3E-13 79.9 0.1 51 204-256 29-81 (84)
19 PF13445 zf-RING_UBOX: RING-ty 98.5 5.6E-08 1.2E-12 68.6 2.5 40 209-249 1-43 (43)
20 PF14634 zf-RING_5: zinc-RING 98.5 9.7E-08 2.1E-12 66.8 3.5 44 208-253 1-44 (44)
21 KOG0804 Cytoplasmic Zn-finger 98.5 7.5E-08 1.6E-12 96.5 2.6 81 207-315 176-258 (493)
22 PLN03208 E3 ubiquitin-protein 98.4 2.5E-07 5.4E-12 84.3 4.5 56 198-257 10-80 (193)
23 COG5194 APC11 Component of SCF 98.4 2.3E-07 5E-12 73.7 3.0 51 206-257 31-82 (88)
24 PHA02926 zinc finger-like prot 98.2 7.2E-07 1.6E-11 82.9 3.5 56 202-257 166-231 (242)
25 smart00504 Ubox Modified RING 98.1 2.9E-06 6.3E-11 62.2 4.0 45 207-256 2-46 (63)
26 KOG0802 E3 ubiquitin ligase [P 98.0 1.6E-06 3.5E-11 89.4 1.5 54 202-256 287-341 (543)
27 KOG0320 Predicted E3 ubiquitin 97.9 7E-06 1.5E-10 74.0 3.0 48 206-256 131-178 (187)
28 KOG0317 Predicted E3 ubiquitin 97.8 1.2E-05 2.6E-10 77.1 2.4 47 206-257 239-285 (293)
29 smart00744 RINGv The RING-vari 97.8 2.1E-05 4.6E-10 56.8 3.0 43 208-252 1-49 (49)
30 KOG0823 Predicted E3 ubiquitin 97.7 2E-05 4.3E-10 73.5 3.0 50 204-257 45-96 (230)
31 TIGR00599 rad18 DNA repair pro 97.7 2.2E-05 4.8E-10 78.6 3.5 48 205-257 25-72 (397)
32 KOG2177 Predicted E3 ubiquitin 97.7 1.6E-05 3.4E-10 70.5 2.2 44 205-253 12-55 (386)
33 TIGR00570 cdk7 CDK-activating 97.7 3.3E-05 7.2E-10 75.0 4.2 52 206-257 3-55 (309)
34 KOG2930 SCF ubiquitin ligase, 97.6 1.7E-05 3.7E-10 65.9 -0.0 34 222-256 75-108 (114)
35 PF04564 U-box: U-box domain; 97.5 0.00019 4.2E-09 55.3 5.1 48 206-257 4-51 (73)
36 PF11793 FANCL_C: FANCL C-term 97.5 2.3E-05 5E-10 60.4 -0.1 51 206-256 2-66 (70)
37 KOG0287 Postreplication repair 97.4 9.1E-05 2E-09 72.8 3.2 46 207-257 24-69 (442)
38 KOG0828 Predicted E3 ubiquitin 97.4 6.7E-05 1.4E-09 76.6 1.6 51 206-256 571-634 (636)
39 KOG2164 Predicted E3 ubiquitin 97.4 0.0001 2.2E-09 75.4 2.9 50 204-257 184-237 (513)
40 KOG0827 Predicted E3 ubiquitin 97.2 0.00014 3E-09 72.4 2.0 49 206-255 4-55 (465)
41 COG5574 PEX10 RING-finger-cont 96.9 0.00043 9.4E-09 65.9 2.2 48 206-257 215-263 (271)
42 PF14835 zf-RING_6: zf-RING of 96.9 0.0004 8.7E-09 53.3 1.5 55 207-268 8-64 (65)
43 KOG4172 Predicted E3 ubiquitin 96.8 0.00034 7.3E-09 52.3 -0.0 52 204-259 5-57 (62)
44 KOG4265 Predicted E3 ubiquitin 96.6 0.0015 3.4E-08 64.4 2.9 49 204-257 288-337 (349)
45 KOG1734 Predicted RING-contain 96.5 0.00069 1.5E-08 64.9 0.5 52 205-256 223-281 (328)
46 PF14570 zf-RING_4: RING/Ubox 96.4 0.0026 5.6E-08 46.2 2.4 47 209-255 1-47 (48)
47 KOG1039 Predicted E3 ubiquitin 96.4 0.0011 2.5E-08 65.4 0.7 79 204-284 159-249 (344)
48 KOG0978 E3 ubiquitin ligase in 96.4 0.0011 2.3E-08 70.7 0.5 47 207-257 644-690 (698)
49 KOG1941 Acetylcholine receptor 96.3 0.00077 1.7E-08 67.5 -1.0 59 197-256 357-416 (518)
50 COG5432 RAD18 RING-finger-cont 96.2 0.0027 5.9E-08 61.6 2.4 46 206-256 25-70 (391)
51 KOG0311 Predicted E3 ubiquitin 96.1 0.0014 3E-08 64.8 -0.2 48 206-256 43-90 (381)
52 KOG1785 Tyrosine kinase negati 96.0 0.0021 4.6E-08 64.6 0.5 54 199-256 362-416 (563)
53 PF11789 zf-Nse: Zinc-finger o 95.9 0.0064 1.4E-07 45.3 2.6 44 204-250 9-53 (57)
54 COG5219 Uncharacterized conser 95.8 0.0044 9.6E-08 67.8 2.0 53 204-256 1467-1523(1525)
55 KOG2879 Predicted E3 ubiquitin 95.2 0.015 3.3E-07 55.9 3.2 53 204-259 237-290 (298)
56 KOG0824 Predicted E3 ubiquitin 94.9 0.015 3.3E-07 56.6 2.2 49 204-256 5-53 (324)
57 PRK14890 putative Zn-ribbon RN 94.8 0.022 4.8E-07 43.1 2.4 46 119-171 5-56 (59)
58 KOG1645 RING-finger-containing 94.7 0.032 7E-07 56.3 4.1 50 207-256 5-56 (463)
59 PF12906 RINGv: RING-variant d 94.7 0.019 4.2E-07 41.0 1.8 41 209-251 1-47 (47)
60 KOG0825 PHD Zn-finger protein 94.6 0.012 2.5E-07 63.5 0.8 50 206-257 123-172 (1134)
61 KOG3800 Predicted E3 ubiquitin 94.3 0.034 7.3E-07 53.9 3.0 49 208-256 2-51 (300)
62 PF10367 Vps39_2: Vacuolar sor 94.3 0.023 4.9E-07 45.4 1.5 33 204-238 76-108 (109)
63 KOG1428 Inhibitor of type V ad 94.2 0.039 8.5E-07 62.9 3.7 74 175-256 3462-3544(3738)
64 PF14447 Prok-RING_4: Prokaryo 93.9 0.023 4.9E-07 42.4 0.8 33 222-257 19-51 (55)
65 KOG4185 Predicted E3 ubiquitin 93.1 0.092 2E-06 49.8 3.6 49 207-256 4-55 (296)
66 KOG4739 Uncharacterized protei 92.7 0.051 1.1E-06 51.3 1.3 37 217-256 12-48 (233)
67 KOG1571 Predicted E3 ubiquitin 92.7 0.069 1.5E-06 53.0 2.2 47 202-256 301-347 (355)
68 KOG3268 Predicted E3 ubiquitin 92.6 0.073 1.6E-06 48.8 2.1 32 225-256 187-228 (234)
69 KOG0297 TNF receptor-associate 92.6 0.073 1.6E-06 53.4 2.3 49 205-257 20-68 (391)
70 COG5175 MOT2 Transcriptional r 92.6 0.045 9.9E-07 54.3 0.8 57 206-262 14-70 (480)
71 PF05883 Baculo_RING: Baculovi 92.2 0.071 1.5E-06 46.4 1.5 35 206-241 26-66 (134)
72 KOG4159 Predicted E3 ubiquitin 91.8 0.16 3.6E-06 51.3 3.7 49 204-257 82-130 (398)
73 PF07191 zinc-ribbons_6: zinc- 91.8 0.098 2.1E-06 40.9 1.6 36 120-155 16-59 (70)
74 KOG4275 Predicted E3 ubiquitin 91.5 0.031 6.6E-07 54.4 -1.7 54 195-257 286-343 (350)
75 KOG3002 Zn finger protein [Gen 91.5 0.22 4.8E-06 48.6 4.1 62 206-278 48-111 (299)
76 PF04641 Rtf2: Rtf2 RING-finge 91.4 0.19 4.2E-06 47.5 3.5 51 203-256 110-161 (260)
77 KOG1814 Predicted E3 ubiquitin 91.0 0.14 3E-06 51.9 2.3 53 198-252 177-236 (445)
78 COG2888 Predicted Zn-ribbon RN 90.8 0.17 3.6E-06 38.5 2.0 45 121-171 9-58 (61)
79 PF12773 DZR: Double zinc ribb 90.8 0.22 4.9E-06 35.1 2.6 22 124-145 1-23 (50)
80 KOG3970 Predicted E3 ubiquitin 90.7 0.35 7.5E-06 45.9 4.4 52 204-257 48-106 (299)
81 TIGR00100 hypA hydrogenase nic 90.7 0.18 3.8E-06 42.4 2.3 36 281-318 67-102 (115)
82 KOG4445 Uncharacterized conser 90.7 0.078 1.7E-06 51.9 0.1 37 205-242 114-150 (368)
83 PF07800 DUF1644: Protein of u 90.6 0.26 5.7E-06 44.1 3.4 33 206-242 2-47 (162)
84 KOG2817 Predicted E3 ubiquitin 90.2 0.22 4.8E-06 50.1 2.9 48 207-255 335-384 (394)
85 PRK00564 hypA hydrogenase nick 89.7 0.24 5.2E-06 41.8 2.3 37 280-318 67-104 (117)
86 PRK03824 hypA hydrogenase nick 89.3 0.28 6.1E-06 42.4 2.5 37 282-318 68-123 (135)
87 PF07191 zinc-ribbons_6: zinc- 88.8 0.087 1.9E-06 41.2 -0.9 65 207-300 2-69 (70)
88 COG5152 Uncharacterized conser 88.6 0.26 5.6E-06 45.9 1.9 59 206-269 196-254 (259)
89 PHA02862 5L protein; Provision 88.5 0.33 7.1E-06 43.0 2.4 46 206-256 2-53 (156)
90 KOG1813 Predicted E3 ubiquitin 88.4 0.29 6.4E-06 47.7 2.2 65 204-273 239-303 (313)
91 PRK12380 hydrogenase nickel in 88.4 0.32 7E-06 40.7 2.2 35 282-318 68-102 (113)
92 COG5236 Uncharacterized conser 88.0 0.5 1.1E-05 47.3 3.5 66 187-256 42-108 (493)
93 PRK03681 hypA hydrogenase nick 88.0 0.36 7.9E-06 40.5 2.2 36 282-318 68-103 (114)
94 KOG3039 Uncharacterized conser 87.9 0.54 1.2E-05 45.1 3.6 54 203-258 218-272 (303)
95 PHA02825 LAP/PHD finger-like p 87.5 0.54 1.2E-05 42.2 3.1 47 205-256 7-59 (162)
96 PF08746 zf-RING-like: RING-li 86.9 0.44 9.5E-06 33.5 1.8 42 209-251 1-43 (43)
97 KOG1002 Nucleotide excision re 86.0 0.33 7.1E-06 50.9 1.1 53 200-256 530-586 (791)
98 PF13248 zf-ribbon_3: zinc-rib 86.0 0.36 7.8E-06 30.3 0.9 24 121-144 2-26 (26)
99 PF01155 HypA: Hydrogenase exp 85.8 0.27 5.9E-06 41.1 0.4 36 281-318 67-102 (113)
100 KOG2660 Locus-specific chromos 85.8 0.22 4.7E-06 49.1 -0.3 49 204-256 13-61 (331)
101 KOG2114 Vacuolar assembly/sort 85.4 0.61 1.3E-05 51.1 2.8 42 208-256 842-883 (933)
102 PF03854 zf-P11: P-11 zinc fin 85.4 0.4 8.6E-06 35.0 1.0 32 225-257 15-47 (50)
103 KOG3161 Predicted E3 ubiquitin 84.8 0.38 8.2E-06 51.4 0.9 44 207-254 12-55 (861)
104 PRK04023 DNA polymerase II lar 84.7 0.78 1.7E-05 51.2 3.3 44 136-188 628-671 (1121)
105 PRK00762 hypA hydrogenase nick 83.1 0.83 1.8E-05 38.9 2.1 37 281-318 67-108 (124)
106 PF09538 FYDLN_acid: Protein o 81.4 0.98 2.1E-05 37.9 1.9 26 134-171 9-34 (108)
107 COG0375 HybF Zn finger protein 81.0 1.3 2.7E-05 37.8 2.4 36 281-318 67-102 (115)
108 COG5220 TFB3 Cdk activating ki 80.1 0.61 1.3E-05 44.6 0.3 51 206-256 10-64 (314)
109 PHA03096 p28-like protein; Pro 80.0 1 2.2E-05 43.8 1.7 47 207-253 179-231 (284)
110 KOG0309 Conserved WD40 repeat- 79.8 1.1 2.5E-05 48.7 2.2 44 204-250 1026-1069(1081)
111 PF13240 zinc_ribbon_2: zinc-r 79.8 0.91 2E-05 28.0 0.9 21 124-144 2-23 (23)
112 PRK14559 putative protein seri 79.7 1.2 2.7E-05 47.7 2.5 46 122-170 2-48 (645)
113 COG5222 Uncharacterized conser 79.5 1.2 2.7E-05 43.8 2.2 44 207-253 275-318 (427)
114 PF10571 UPF0547: Uncharacteri 78.9 1.3 2.9E-05 28.1 1.5 23 123-145 2-25 (26)
115 KOG4692 Predicted E3 ubiquitin 77.4 1.6 3.6E-05 43.9 2.4 51 202-257 418-468 (489)
116 KOG2034 Vacuolar sorting prote 77.1 1.1 2.5E-05 49.2 1.3 43 198-242 809-851 (911)
117 PHA00626 hypothetical protein 76.9 1.9 4.1E-05 32.6 2.0 7 136-142 2-8 (59)
118 PRK14714 DNA polymerase II lar 76.0 2.5 5.3E-05 48.5 3.5 32 122-154 668-700 (1337)
119 PF12773 DZR: Double zinc ribb 73.6 2.5 5.3E-05 29.8 1.9 32 121-152 12-49 (50)
120 TIGR00595 priA primosomal prot 73.1 2.6 5.6E-05 43.7 2.7 49 82-143 214-262 (505)
121 KOG1001 Helicase-like transcri 72.0 2 4.3E-05 46.4 1.5 45 207-256 455-500 (674)
122 KOG2272 Focal adhesion protein 71.4 3.7 8.1E-05 39.7 3.1 128 91-259 100-235 (332)
123 PF02891 zf-MIZ: MIZ/SP-RING z 70.7 2.9 6.4E-05 30.2 1.7 42 207-254 3-50 (50)
124 KOG1952 Transcription factor N 70.0 2.5 5.5E-05 46.5 1.8 48 206-256 191-247 (950)
125 PF05290 Baculo_IE-1: Baculovi 69.3 3.2 7E-05 36.4 2.0 48 207-258 81-134 (140)
126 KOG4367 Predicted Zn-finger pr 68.9 2.7 5.7E-05 43.5 1.6 33 206-242 4-36 (699)
127 PF14446 Prok-RING_1: Prokaryo 68.1 5.6 0.00012 29.7 2.8 35 205-240 4-39 (54)
128 KOG3053 Uncharacterized conser 67.7 3.5 7.5E-05 39.9 2.0 71 201-271 15-104 (293)
129 COG5109 Uncharacterized conser 67.1 4 8.7E-05 40.6 2.3 46 207-253 337-384 (396)
130 PRK04023 DNA polymerase II lar 66.4 4.6 9.9E-05 45.5 2.9 49 121-175 626-675 (1121)
131 TIGR02300 FYDLN_acid conserved 65.5 3.8 8.3E-05 35.6 1.7 27 134-172 9-35 (129)
132 COG1198 PriA Primosomal protei 64.2 5.8 0.00013 43.3 3.1 54 82-148 436-489 (730)
133 PRK14714 DNA polymerase II lar 63.7 5.9 0.00013 45.5 3.1 33 135-171 668-700 (1337)
134 KOG1812 Predicted E3 ubiquitin 62.0 3.7 8E-05 41.4 1.1 51 206-256 146-203 (384)
135 PRK14559 putative protein seri 61.8 4.2 9.1E-05 43.7 1.5 34 121-155 15-50 (645)
136 PF14569 zf-UDP: Zinc-binding 61.6 8.2 0.00018 31.0 2.7 53 204-256 7-62 (80)
137 PRK14873 primosome assembly pr 60.6 6.3 0.00014 42.5 2.6 49 82-144 384-432 (665)
138 PF07282 OrfB_Zn_ribbon: Putat 60.3 6.8 0.00015 29.2 2.0 27 134-171 28-54 (69)
139 PRK05580 primosome assembly pr 60.0 6.4 0.00014 42.3 2.5 50 82-144 382-431 (679)
140 PF04216 FdhE: Protein involve 59.8 5.9 0.00013 37.9 2.0 48 119-170 195-245 (290)
141 KOG2462 C2H2-type Zn-finger pr 58.9 9 0.00019 37.3 3.1 119 141-294 125-253 (279)
142 PRK14890 putative Zn-ribbon RN 58.5 7.3 0.00016 29.6 1.9 34 119-154 23-56 (59)
143 PF06524 NOA36: NOA36 protein; 56.5 4.3 9.2E-05 39.4 0.4 51 88-154 140-190 (314)
144 PF03107 C1_2: C1 domain; Int 56.2 7.9 0.00017 24.9 1.5 20 168-187 2-22 (30)
145 KOG0827 Predicted E3 ubiquitin 55.4 1.1 2.5E-05 45.3 -3.7 52 205-257 195-246 (465)
146 KOG2068 MOT2 transcription fac 55.3 9.3 0.0002 38.0 2.6 53 204-257 247-299 (327)
147 COG3809 Uncharacterized protei 54.6 9.4 0.0002 30.8 2.0 31 246-280 22-54 (88)
148 PRK00398 rpoP DNA-directed RNA 54.3 12 0.00026 26.1 2.4 8 163-170 21-28 (46)
149 PF14353 CpXC: CpXC protein 52.0 3.1 6.8E-05 34.9 -1.1 56 246-303 2-57 (128)
150 KOG1100 Predicted E3 ubiquitin 51.4 7.2 0.00016 36.2 1.0 39 209-256 161-200 (207)
151 smart00249 PHD PHD zinc finger 51.2 6.3 0.00014 25.9 0.5 42 209-251 2-47 (47)
152 PF13894 zf-C2H2_4: C2H2-type 51.0 10 0.00022 21.6 1.3 18 246-263 1-18 (24)
153 PF08271 TF_Zn_Ribbon: TFIIB z 50.8 14 0.0003 25.5 2.2 7 137-143 3-9 (43)
154 TIGR02605 CxxC_CxxC_SSSS putat 50.8 12 0.00026 26.5 1.9 30 284-313 5-37 (52)
155 PRK00398 rpoP DNA-directed RNA 50.3 13 0.00027 26.0 1.9 31 283-313 2-32 (46)
156 COG1656 Uncharacterized conser 49.5 12 0.00027 33.7 2.2 51 245-301 97-147 (165)
157 KOG2066 Vacuolar assembly/sort 49.0 6.5 0.00014 43.1 0.4 45 206-252 784-831 (846)
158 COG1198 PriA Primosomal protei 48.9 16 0.00035 39.9 3.4 48 115-170 428-482 (730)
159 PF13453 zf-TFIIB: Transcripti 48.3 14 0.0003 25.2 1.9 26 136-170 1-26 (41)
160 KOG2907 RNA polymerase I trans 47.5 7 0.00015 33.4 0.3 19 300-318 72-94 (116)
161 KOG1609 Protein involved in mR 46.9 12 0.00026 35.2 1.8 51 206-256 78-134 (323)
162 PRK12286 rpmF 50S ribosomal pr 46.1 21 0.00046 26.7 2.7 29 283-316 26-54 (57)
163 PF05191 ADK_lid: Adenylate ki 45.1 6 0.00013 26.9 -0.4 27 136-171 3-29 (36)
164 COG5183 SSM4 Protein involved 44.9 8.7 0.00019 42.5 0.6 53 203-257 9-67 (1175)
165 PF05605 zf-Di19: Drought indu 44.6 22 0.00048 25.5 2.6 8 246-253 3-10 (54)
166 KOG0269 WD40 repeat-containing 44.4 21 0.00045 39.3 3.3 70 161-250 751-820 (839)
167 smart00132 LIM Zinc-binding do 44.2 21 0.00046 22.6 2.2 37 209-256 2-38 (39)
168 PRK00420 hypothetical protein; 44.0 14 0.00031 31.3 1.7 21 135-155 24-49 (112)
169 smart00734 ZnF_Rad18 Rad18-lik 43.2 21 0.00046 22.5 1.9 19 247-266 3-21 (26)
170 PLN03086 PRLI-interacting fact 43.0 12 0.00025 39.9 1.2 84 117-215 403-513 (567)
171 PF06677 Auto_anti-p27: Sjogre 42.5 16 0.00034 25.7 1.4 13 134-146 17-29 (41)
172 PLN02189 cellulose synthase 42.2 21 0.00045 40.5 3.0 56 201-256 29-87 (1040)
173 PF01529 zf-DHHC: DHHC palmito 41.2 21 0.00045 30.7 2.3 48 139-192 41-88 (174)
174 smart00659 RPOLCX RNA polymera 40.8 19 0.00042 25.4 1.7 26 284-310 2-27 (44)
175 PF02701 zf-Dof: Dof domain, z 40.6 14 0.00031 28.4 1.0 14 302-315 5-18 (63)
176 COG1996 RPC10 DNA-directed RNA 40.4 20 0.00043 26.3 1.7 29 144-172 4-33 (49)
177 KOG1940 Zn-finger protein [Gen 39.9 4.9 0.00011 39.0 -2.0 31 67-98 174-204 (276)
178 PHA00626 hypothetical protein 39.9 20 0.00044 27.1 1.7 34 122-157 1-34 (59)
179 PF04438 zf-HIT: HIT zinc fing 39.9 15 0.00033 24.0 0.9 16 137-153 5-20 (30)
180 COG2888 Predicted Zn-ribbon RN 39.6 18 0.00039 27.6 1.4 34 119-154 25-58 (61)
181 KOG0298 DEAD box-containing he 38.9 11 0.00024 43.5 0.3 53 203-259 1150-1202(1394)
182 PLN02436 cellulose synthase A 38.3 26 0.00057 39.9 3.0 56 201-256 31-89 (1094)
183 PF00096 zf-C2H2: Zinc finger, 38.0 17 0.00037 21.1 0.9 15 246-260 1-15 (23)
184 KOG2932 E3 ubiquitin ligase in 37.7 14 0.00029 36.9 0.6 30 224-256 105-134 (389)
185 TIGR02159 PA_CoA_Oxy4 phenylac 37.0 17 0.00037 32.0 1.1 16 302-317 105-120 (146)
186 cd00350 rubredoxin_like Rubred 36.7 27 0.00058 22.9 1.8 25 146-171 1-25 (33)
187 COG1645 Uncharacterized Zn-fin 36.2 21 0.00045 31.2 1.5 19 135-153 29-51 (131)
188 KOG0006 E3 ubiquitin-protein l 36.1 33 0.00072 34.4 3.0 79 154-241 168-254 (446)
189 PRK00415 rps27e 30S ribosomal 36.0 23 0.00051 26.9 1.5 36 120-155 10-51 (59)
190 KOG0801 Predicted E3 ubiquitin 35.9 14 0.00029 33.8 0.3 29 205-234 176-204 (205)
191 TIGR01031 rpmF_bact ribosomal 35.7 32 0.0007 25.4 2.3 29 283-316 25-53 (55)
192 smart00661 RPOL9 RNA polymeras 34.7 32 0.00069 24.0 2.1 9 162-170 19-27 (52)
193 PF01096 TFIIS_C: Transcriptio 34.2 28 0.0006 23.8 1.6 31 136-170 2-35 (39)
194 PF15616 TerY-C: TerY-C metal 33.4 38 0.00083 29.5 2.7 33 135-170 78-112 (131)
195 PRK00366 ispG 4-hydroxy-3-meth 33.2 56 0.0012 33.0 4.1 53 246-302 269-323 (360)
196 PRK00432 30S ribosomal protein 33.0 27 0.00059 25.3 1.5 10 162-171 36-45 (50)
197 PF00643 zf-B_box: B-box zinc 32.8 33 0.00072 22.9 1.8 21 135-155 4-24 (42)
198 PF06827 zf-FPG_IleRS: Zinc fi 32.2 32 0.00069 21.8 1.5 18 135-152 2-27 (30)
199 KOG4185 Predicted E3 ubiquitin 32.2 8.3 0.00018 36.6 -1.8 50 206-255 207-266 (296)
200 PF03833 PolC_DP2: DNA polymer 32.0 15 0.00033 40.8 0.0 46 135-189 656-701 (900)
201 KOG4317 Predicted Zn-finger pr 31.4 21 0.00046 35.6 0.9 21 135-155 8-28 (383)
202 PF07649 C1_3: C1-like domain; 31.3 24 0.00052 22.4 0.9 20 169-188 3-23 (30)
203 TIGR01562 FdhE formate dehydro 30.9 49 0.0011 32.6 3.3 44 245-310 184-232 (305)
204 PF06906 DUF1272: Protein of u 30.8 74 0.0016 24.1 3.4 50 205-257 4-53 (57)
205 PF03604 DNA_RNApol_7kD: DNA d 30.8 32 0.00069 22.9 1.4 11 160-170 14-24 (32)
206 KOG0826 Predicted E3 ubiquitin 30.5 42 0.00091 33.7 2.7 49 204-256 298-346 (357)
207 KOG2462 C2H2-type Zn-finger pr 30.3 44 0.00096 32.6 2.8 108 135-260 131-258 (279)
208 PRK14810 formamidopyrimidine-D 30.3 28 0.0006 33.3 1.5 20 134-153 244-271 (272)
209 PF03833 PolC_DP2: DNA polymer 29.8 18 0.00038 40.3 0.0 43 122-170 656-699 (900)
210 PRK10445 endonuclease VIII; Pr 29.7 30 0.00064 32.9 1.5 20 134-153 235-262 (263)
211 PRK14811 formamidopyrimidine-D 29.7 29 0.00064 33.1 1.5 21 134-154 235-263 (269)
212 PF13717 zinc_ribbon_4: zinc-r 29.4 34 0.00074 23.0 1.4 10 82-91 3-12 (36)
213 PF13695 zf-3CxxC: Zinc-bindin 29.2 48 0.001 26.9 2.5 47 245-315 5-51 (98)
214 PRK03564 formate dehydrogenase 29.1 53 0.0011 32.4 3.2 25 119-143 210-235 (309)
215 cd01675 RNR_III Class III ribo 28.8 45 0.00098 35.2 2.8 30 282-316 517-546 (555)
216 cd02337 ZZ_CBP Zinc finger, ZZ 28.6 37 0.0008 23.6 1.4 19 164-186 1-19 (41)
217 PF01599 Ribosomal_S27: Riboso 28.6 40 0.00087 24.5 1.7 23 132-154 16-46 (47)
218 PF04423 Rad50_zn_hook: Rad50 28.5 44 0.00095 24.0 1.9 12 247-258 22-33 (54)
219 PF01529 zf-DHHC: DHHC palmito 28.4 32 0.00068 29.5 1.3 39 157-201 42-80 (174)
220 PLN02638 cellulose synthase A 28.1 48 0.001 37.9 3.0 56 201-256 12-70 (1079)
221 cd02249 ZZ Zinc finger, ZZ typ 28.0 38 0.00083 23.6 1.5 21 164-187 1-21 (46)
222 PF14952 zf-tcix: Putative tre 28.0 28 0.00061 25.0 0.8 12 303-314 12-23 (44)
223 COG1998 RPS31 Ribosomal protei 27.4 38 0.00082 25.1 1.4 19 135-153 20-44 (51)
224 cd00729 rubredoxin_SM Rubredox 27.3 42 0.00092 22.3 1.5 22 122-143 3-27 (34)
225 PRK06266 transcription initiat 27.0 40 0.00086 30.5 1.8 10 206-215 136-145 (178)
226 PRK01103 formamidopyrimidine/5 26.9 35 0.00077 32.5 1.5 20 134-153 245-272 (274)
227 PF09723 Zn-ribbon_8: Zinc rib 26.8 50 0.0011 22.8 1.9 31 284-314 5-38 (42)
228 PF06220 zf-U1: U1 zinc finger 26.7 26 0.00056 24.0 0.4 13 144-156 1-13 (38)
229 PF13719 zinc_ribbon_5: zinc-r 26.6 40 0.00086 22.7 1.3 9 121-129 25-33 (37)
230 TIGR00373 conserved hypothetic 26.5 37 0.0008 29.9 1.5 8 180-187 128-135 (158)
231 KOG1312 DHHC-type Zn-finger pr 26.3 18 0.00039 35.7 -0.6 32 167-201 149-180 (341)
232 PF04710 Pellino: Pellino; In 26.2 23 0.0005 36.2 0.1 51 203-256 274-339 (416)
233 PRK03564 formate dehydrogenase 25.8 72 0.0016 31.5 3.4 24 283-310 211-234 (309)
234 KOG3362 Predicted BBOX Zn-fing 25.7 23 0.00051 31.5 0.1 25 145-175 117-143 (156)
235 PF05502 Dynactin_p62: Dynacti 25.2 55 0.0012 34.1 2.6 18 137-154 16-34 (483)
236 TIGR00577 fpg formamidopyrimid 25.0 40 0.00087 32.1 1.5 20 134-153 245-272 (272)
237 smart00451 ZnF_U1 U1-like zinc 24.8 34 0.00075 21.7 0.7 11 145-155 2-12 (35)
238 KOG1815 Predicted E3 ubiquitin 24.7 46 0.00099 34.0 1.9 37 204-243 68-104 (444)
239 KOG1044 Actin-binding LIM Zn-f 24.6 99 0.0022 33.3 4.4 136 158-310 11-168 (670)
240 PF12760 Zn_Tnp_IS1595: Transp 24.4 87 0.0019 21.8 2.8 9 135-143 19-27 (46)
241 TIGR02098 MJ0042_CXXC MJ0042 f 24.3 55 0.0012 21.6 1.7 9 121-129 25-33 (38)
242 PF10272 Tmpp129: Putative tra 24.2 86 0.0019 31.6 3.7 26 232-257 315-352 (358)
243 PF15353 HECA: Headcase protei 24.2 45 0.00097 28.2 1.4 16 227-242 39-54 (107)
244 KOG3113 Uncharacterized conser 24.2 67 0.0015 31.3 2.8 50 204-256 109-158 (293)
245 PRK00464 nrdR transcriptional 24.1 47 0.001 29.6 1.6 11 137-147 31-41 (154)
246 KOG3842 Adaptor protein Pellin 24.0 37 0.0008 34.0 1.1 47 203-254 287-350 (429)
247 PF14803 Nudix_N_2: Nudix N-te 24.0 49 0.0011 22.3 1.4 28 136-170 2-29 (34)
248 PF08274 PhnA_Zn_Ribbon: PhnA 24.0 42 0.00091 22.1 1.0 23 136-170 4-26 (30)
249 PRK13945 formamidopyrimidine-D 24.0 44 0.00095 32.1 1.6 20 134-153 254-281 (282)
250 smart00778 Prim_Zn_Ribbon Zinc 23.7 73 0.0016 21.9 2.2 30 135-171 4-33 (37)
251 COG2051 RPS27A Ribosomal prote 23.0 47 0.001 25.9 1.2 28 120-147 18-51 (67)
252 TIGR00595 priA primosomal prot 23.0 84 0.0018 32.7 3.5 46 119-172 211-262 (505)
253 PF01667 Ribosomal_S27e: Ribos 22.6 53 0.0012 24.6 1.4 34 121-154 7-46 (55)
254 PF12172 DUF35_N: Rubredoxin-l 22.5 40 0.00087 22.3 0.7 23 120-142 10-33 (37)
255 PF07754 DUF1610: Domain of un 22.3 60 0.0013 20.4 1.4 9 162-170 15-23 (24)
256 smart00531 TFIIE Transcription 22.2 32 0.0007 29.8 0.2 10 136-145 101-110 (147)
257 PF05502 Dynactin_p62: Dynacti 22.0 51 0.0011 34.3 1.7 10 89-98 4-13 (483)
258 PF11023 DUF2614: Protein of u 21.9 56 0.0012 27.9 1.6 28 117-144 65-95 (114)
259 KOG0269 WD40 repeat-containing 21.4 47 0.001 36.7 1.3 49 136-193 755-806 (839)
260 PRK04136 rpl40e 50S ribosomal 21.4 52 0.0011 24.1 1.1 24 119-142 12-36 (48)
261 cd02345 ZZ_dah Zinc finger, ZZ 21.3 65 0.0014 23.0 1.6 26 285-313 1-26 (49)
262 cd07973 Spt4 Transcription elo 21.0 50 0.0011 27.4 1.1 20 123-142 5-28 (98)
263 PF06937 EURL: EURL protein; 20.9 77 0.0017 31.0 2.5 43 204-249 28-74 (285)
264 PLN02400 cellulose synthase 20.8 57 0.0012 37.4 1.8 56 201-256 31-89 (1085)
265 PF00130 C1_1: Phorbol esters/ 20.7 79 0.0017 22.0 2.0 13 159-171 24-36 (53)
266 KOG4399 C2HC-type Zn-finger pr 20.7 21 0.00045 34.8 -1.3 73 140-215 198-270 (325)
267 KOG1311 DHHC-type Zn-finger pr 20.7 80 0.0017 30.1 2.6 45 141-191 108-152 (299)
268 PF00628 PHD: PHD-finger; Int 20.7 1.2E+02 0.0026 20.9 2.9 20 148-169 1-20 (51)
269 PRK14892 putative transcriptio 20.6 89 0.0019 25.9 2.5 32 178-215 19-51 (99)
270 KOG4362 Transcriptional regula 20.1 49 0.0011 36.1 1.1 48 206-257 21-70 (684)
No 1
>KOG1940 consensus Zn-finger protein [General function prediction only]
Probab=100.00 E-value=5.2e-67 Score=492.39 Aligned_cols=249 Identities=51% Similarity=1.047 Sum_probs=241.0
Q ss_pred cCCCchhhccCCCccCCccccccceeEcCCCCCeecCcchHhhhhcCCCcCccCCCCCCCccCceeecCCCCcccccccc
Q 021022 57 HNGSTELLRKGFMEYGCQHYRRRCRIRAPCCNEIFDCRHCHNEAMNNINVDQKLRHDIPRHEVNQVICSLCGTEQKVQQV 136 (318)
Q Consensus 57 ~~~~~~~~~~~~~~~gC~HY~R~c~i~~pCC~~~y~Cr~CHde~~~~~~~~~~~~H~ldR~~v~~v~C~~C~~eQ~v~~~ 136 (318)
+..+.+++|++.+++||+||+|++++++|+|++||+||+||+++. +|+++|+.|.+|+|+.|.++|+++++
T Consensus 19 ~~~~~~~~d~~~~~~~c~hy~r~~~~~a~ccd~~~~C~hCH~~s~---------~h~~~r~~v~~~~C~~C~~~q~~~~~ 89 (276)
T KOG1940|consen 19 SSIHSDAEDEIAFPYGCPHYRRNCKSRAPCCDREITCRHCHNESE---------DHDLDRKTVYELLCMKCRKIQPVGQI 89 (276)
T ss_pred hhcccccccccccccCCchhhhccccccccccceeeeEEecChhh---------hcccchhhhhhhhhhhHHhhhhhhhc
Confidence 333457889999999999999999999999999999999999975 89999999999999999999999999
Q ss_pred CcCCCCccceEecCccccccCCCCCCeeecCCCCceeecCCcceeeccCccceeeccccccccccCCCCCCCCccccccc
Q 021022 137 CVNCGVCMGEYFCESCKLFDDDTSKKQYHCDGCGICRIGGCDNFFHCNKCRCCYSMLLKNSHPCVEGAMHHDCPVCCEYL 216 (318)
Q Consensus 137 C~~Cg~~f~~YfC~~Ckl~ddd~~k~~yHC~~CgiCR~G~~~~ffHC~~C~~C~s~~l~~~H~Cie~~~~~~CpIClE~l 216 (318)
|.+|+..||+|||.+|+||||+++ +||||++|||||+|++++||||++|+.|++..+.+.|+|+|++++.+||||.|+|
T Consensus 90 c~~c~~~~g~~~c~~C~l~dd~~~-~~~hC~~C~icr~g~~~~~fhc~~c~~c~~~~~~~~H~c~e~~~~~ncPic~e~l 168 (276)
T KOG1940|consen 90 CSNCHVELGEYYCLICKLFDDDPS-KQYHCDLCGICREGLGLDFFHCKKCKACLSAYLSNWHKCVERSSEFNCPICKEYL 168 (276)
T ss_pred cccchhhhhhhcCccccccccccc-ceeccccccccccccccchhHHhhhHhHHhhhcccccchhhhcccCCCchhHHHh
Confidence 999999999999999999999998 9999999999999999999999999999999999999999999999999999999
Q ss_pred ccCCceeEEcCCCCccchHHHHHHHhcCCCCCCCCCcccCchhHHHHHhHHHHHcCCCChhhhcCcceEEcCCCCCCccc
Q 021022 217 FETRQDVIVLPCGHTIHKNCLKEMREHHQYACPICSKSVCDMSKVWEKYDREIAATPMPEAYLNKKVWILCNDCGKTSNV 296 (318)
Q Consensus 217 f~s~~~v~~LpCGH~fH~~Cl~~wl~~~~~~CPiCrks~~d~~~~~~~lD~~i~~~pmPeey~~~~v~IlCnDC~~~s~v 296 (318)
|++...+..|+|||++|..|++++...+ |+||+|.+ +.||..+|+++|.+|+++|||++|.+++++|+||||+..+++
T Consensus 169 ~~s~~~~~~~~CgH~~h~~cf~e~~~~~-y~CP~C~~-~~d~~~~~~~~d~~l~~~~~p~~y~~~~~~i~cndC~~~~~~ 246 (276)
T KOG1940|consen 169 FLSFEDAGVLKCGHYMHSRCFEEMICEG-YTCPICSK-PGDMSHYFRKLDKELAGSPMPEEYKNKTQDILCNDCGSGTNV 246 (276)
T ss_pred ccccccCCccCcccchHHHHHHHHhccC-CCCCcccc-hHHHHHHHHHHHHHHhcCCCCchhhchhheeeccCCCCCCcc
Confidence 9999999999999999999999998866 99999999 999999999999999999999999999999999999999999
Q ss_pred cceeeeccCCCCCCccccccC
Q 021022 297 QFHVLAQKCPNCKSYNTRLTR 317 (318)
Q Consensus 297 ~~H~lg~KC~~C~SyNT~~~~ 317 (318)
+||||++||+.|+|||||+++
T Consensus 247 k~~~l~~kc~~c~~~~~r~~~ 267 (276)
T KOG1940|consen 247 KYHILYHKCGKCGSYNTRMIS 267 (276)
T ss_pred ceehhhhhCCCcccceeeecc
Confidence 999999999999999999985
No 2
>PF14599 zinc_ribbon_6: Zinc-ribbon; PDB: 2K2D_A.
Probab=99.93 E-value=1.1e-27 Score=180.11 Aligned_cols=61 Identities=66% Similarity=1.160 Sum_probs=22.6
Q ss_pred cCchhHHHHHhHHHHHcCCCChhhhcCcceEEcCCCCCCccccceeeeccCCCCCCccccc
Q 021022 255 VCDMSKVWEKYDREIAATPMPEAYLNKKVWILCNDCGKTSNVQFHVLAQKCPNCKSYNTRL 315 (318)
Q Consensus 255 ~~d~~~~~~~lD~~i~~~pmPeey~~~~v~IlCnDC~~~s~v~~H~lg~KC~~C~SyNT~~ 315 (318)
+.||+.+|+.||++|+++|||++|++++++|+||||+++|+|+||||||||++|+||||||
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 4689999999999999999999999999999999999999999999999999999999997
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=99.88 E-value=1e-23 Score=162.72 Aligned_cols=70 Identities=46% Similarity=1.129 Sum_probs=53.6
Q ss_pred Ccccccc-ceeEcCCCCCeecCcchHhhhhcCCCcCccCCCCCCCccCceeecCCCCccccccccCcCCCCccceEecCc
Q 021022 73 CQHYRRR-CRIRAPCCNEIFDCRHCHNEAMNNINVDQKLRHDIPRHEVNQVICSLCGTEQKVQQVCVNCGVCMGEYFCES 151 (318)
Q Consensus 73 C~HY~R~-c~i~~pCC~~~y~Cr~CHde~~~~~~~~~~~~H~ldR~~v~~v~C~~C~~eQ~v~~~C~~Cg~~f~~YfC~~ 151 (318)
|+||+|+ |+|+||||++|||||+||||++ +|+++|+++++|+||.|+++|+++++ +|+ |+|+|++
T Consensus 1 C~HY~~~~~~~~~~cC~~~y~C~~CHde~~---------~H~~~~~~~~~v~Cg~C~~~~~~~~~--~c~---~~~~C~~ 66 (71)
T PF05495_consen 1 CKHYHRSLCAIRFPCCGKYYPCRFCHDELE---------DHPFDRWPVKRVICGKCRTEQPIDEY--SCG---ADYFCPI 66 (71)
T ss_dssp -SS---S-EEEEETTTTEEESSHHHHHHCS---------SS---TTT--EEEETTT--EEES-SB--TT-----SEEETT
T ss_pred CCCCCCCcEEEECCcccCeecHHHHHHHhc---------cCccccccccCeECCCCCCccChhhh--hcC---CCccCcC
Confidence 8999999 9999999999999999999975 79999999999999999999999988 888 9999999
Q ss_pred ccccc
Q 021022 152 CKLFD 156 (318)
Q Consensus 152 Ckl~d 156 (318)
|++||
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=99.35 E-value=2e-13 Score=110.95 Aligned_cols=67 Identities=24% Similarity=0.647 Sum_probs=57.3
Q ss_pred cCCccccc---cceeEcCCCCCeecCcchHhhhhcCCCcCccCCCCCCCc-----cCceeecCCCCcccccc-----ccC
Q 021022 71 YGCQHYRR---RCRIRAPCCNEIFDCRHCHNEAMNNINVDQKLRHDIPRH-----EVNQVICSLCGTEQKVQ-----QVC 137 (318)
Q Consensus 71 ~gC~HY~R---~c~i~~pCC~~~y~Cr~CHde~~~~~~~~~~~~H~ldR~-----~v~~v~C~~C~~eQ~v~-----~~C 137 (318)
.+|.||++ .++|||.+|++||+|++||||++ +||+.++ ..+.|+||+|.++..++ ..|
T Consensus 13 tRC~Hyht~~Diialkc~~C~kyYaCy~CHdel~---------~Hpf~p~~~~~~~~~~iiCGvC~~~LT~~EY~~~~~C 83 (105)
T COG4357 13 TRCLHYHTPLDIIALKCKCCQKYYACYHCHDELE---------DHPFEPWGLQEFNPKAIICGVCRKLLTRAEYGMCGSC 83 (105)
T ss_pred ceeeEecCccceEeeeechhhhhhhHHHHHhHHh---------cCCCccCChhhcCCccEEhhhhhhhhhHHHHhhcCCC
Confidence 58999999 68999999999999999999987 5776544 45669999999998775 459
Q ss_pred cCCCCccce
Q 021022 138 VNCGVCMGE 146 (318)
Q Consensus 138 ~~Cg~~f~~ 146 (318)
++|..+|+.
T Consensus 84 p~C~spFNp 92 (105)
T COG4357 84 PYCQSPFNP 92 (105)
T ss_pred CCcCCCCCc
Confidence 999999973
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=99.26 E-value=1.4e-12 Score=90.91 Aligned_cols=44 Identities=39% Similarity=1.061 Sum_probs=36.9
Q ss_pred CCCcccccccccCCceeEEcCCCCccchHHHHHHHhcCCCCCCCCC
Q 021022 207 HDCPVCCEYLFETRQDVIVLPCGHTIHKNCLKEMREHHQYACPICS 252 (318)
Q Consensus 207 ~~CpIClE~lf~s~~~v~~LpCGH~fH~~Cl~~wl~~~~~~CPiCr 252 (318)
++||||++.+. ..+.++.|+|||.||.+|+.+|++. +.+||+||
T Consensus 1 d~C~IC~~~~~-~~~~~~~l~C~H~fh~~Ci~~~~~~-~~~CP~CR 44 (44)
T PF13639_consen 1 DECPICLEEFE-DGEKVVKLPCGHVFHRSCIKEWLKR-NNSCPVCR 44 (44)
T ss_dssp -CETTTTCBHH-TTSCEEEETTSEEEEHHHHHHHHHH-SSB-TTTH
T ss_pred CCCcCCChhhc-CCCeEEEccCCCeeCHHHHHHHHHh-CCcCCccC
Confidence 47999999754 4677889999999999999999986 58999997
No 6
>PF12861 zf-Apc11: Anaphase-promoting complex subunit 11 RING-H2 finger
Probab=99.11 E-value=5.7e-11 Score=95.06 Aligned_cols=51 Identities=20% Similarity=0.457 Sum_probs=41.1
Q ss_pred CCCCCCcccccccccCCceeEEcCCCCccchHHHHHHHhc--CCCCCCCCCcccC
Q 021022 204 AMHHDCPVCCEYLFETRQDVIVLPCGHTIHKNCLKEMREH--HQYACPICSKSVC 256 (318)
Q Consensus 204 ~~~~~CpIClE~lf~s~~~v~~LpCGH~fH~~Cl~~wl~~--~~~~CPiCrks~~ 256 (318)
+++..||.|.. ....-+++...|+|.||.+||.+||+. .+.+||+||.++.
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 55678999984 344457778899999999999999985 3468999999875
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=98.93 E-value=7.6e-10 Score=85.75 Aligned_cols=46 Identities=28% Similarity=0.808 Sum_probs=35.7
Q ss_pred CCCCcccccccccC---------CceeEEcCCCCccchHHHHHHHhcCCCCCCCCC
Q 021022 206 HHDCPVCCEYLFET---------RQDVIVLPCGHTIHKNCLKEMREHHQYACPICS 252 (318)
Q Consensus 206 ~~~CpIClE~lf~s---------~~~v~~LpCGH~fH~~Cl~~wl~~~~~~CPiCr 252 (318)
+++|+||++.|.+. ..+++.++|||.||..||.+||+. +.+||+||
T Consensus 19 ~d~C~IC~~~l~~~~~~~~~~~~~~~i~~~~C~H~FH~~Ci~~Wl~~-~~~CP~CR 73 (73)
T PF12678_consen 19 DDNCAICREPLEDPCPECQAPQDECPIVWGPCGHIFHFHCISQWLKQ-NNTCPLCR 73 (73)
T ss_dssp CSBETTTTSBTTSTTCCHHHCTTTS-EEEETTSEEEEHHHHHHHHTT-SSB-TTSS
T ss_pred CCcccccChhhhChhhhhcCCccccceEecccCCCEEHHHHHHHHhc-CCcCCCCC
Confidence 56799999987332 245577799999999999999985 46999997
No 8
>KOG4628 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=98.91 E-value=5.7e-10 Score=109.19 Aligned_cols=50 Identities=28% Similarity=0.824 Sum_probs=45.2
Q ss_pred CCCcccccccccCCceeEEcCCCCccchHHHHHHHhcCCCCCCCCCcccCc
Q 021022 207 HDCPVCCEYLFETRQDVIVLPCGHTIHKNCLKEMREHHQYACPICSKSVCD 257 (318)
Q Consensus 207 ~~CpIClE~lf~s~~~v~~LpCGH~fH~~Cl~~wl~~~~~~CPiCrks~~d 257 (318)
..|+||||+ |..++.++.|||+|.||..|+++||...+..||+|+.++..
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 88899999999999999999999998665669999998874
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=98.87 E-value=2e-09 Score=72.33 Aligned_cols=45 Identities=33% Similarity=1.041 Sum_probs=37.1
Q ss_pred CCcccccccccCCceeEEcCCCCccchHHHHHHHhcCCCCCCCCCccc
Q 021022 208 DCPVCCEYLFETRQDVIVLPCGHTIHKNCLKEMREHHQYACPICSKSV 255 (318)
Q Consensus 208 ~CpIClE~lf~s~~~v~~LpCGH~fH~~Cl~~wl~~~~~~CPiCrks~ 255 (318)
.|+||++.+ ..++.+++|||.||..|+..|++..+.+||+|++.+
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 499999974 345667779999999999999986568899999764
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=98.78 E-value=3.9e-09 Score=71.97 Aligned_cols=39 Identities=41% Similarity=1.110 Sum_probs=32.6
Q ss_pred CcccccccccCCceeEEcCCCCccchHHHHHHHhcCCCCCCCC
Q 021022 209 CPVCCEYLFETRQDVIVLPCGHTIHKNCLKEMREHHQYACPIC 251 (318)
Q Consensus 209 CpIClE~lf~s~~~v~~LpCGH~fH~~Cl~~wl~~~~~~CPiC 251 (318)
||||++.+.+ ++++++|||+|+.+|+.+|++. +.+||+|
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 7999986433 6689999999999999999986 6899998
No 11
>PHA02929 N1R/p28-like protein; Provisional
Probab=98.70 E-value=1.3e-08 Score=95.47 Aligned_cols=54 Identities=19% Similarity=0.609 Sum_probs=41.9
Q ss_pred CCCCCCCcccccccccCCc----eeEEcCCCCccchHHHHHHHhcCCCCCCCCCcccCc
Q 021022 203 GAMHHDCPVCCEYLFETRQ----DVIVLPCGHTIHKNCLKEMREHHQYACPICSKSVCD 257 (318)
Q Consensus 203 ~~~~~~CpIClE~lf~s~~----~v~~LpCGH~fH~~Cl~~wl~~~~~~CPiCrks~~d 257 (318)
.+.+..||||+|.+.+... -.++++|||.||..|+.+|++. +.+||+||..+..
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 3456899999997654321 1245689999999999999984 6799999998863
No 12
>PF15227 zf-C3HC4_4: zinc finger of C3HC4-type, RING; PDB: 2EGP_A 2ECV_A 2ECJ_A 2YSL_A 2YSJ_A.
Probab=98.69 E-value=1.3e-08 Score=71.06 Aligned_cols=39 Identities=38% Similarity=1.199 Sum_probs=28.7
Q ss_pred CcccccccccCCceeEEcCCCCccchHHHHHHHhcC---CCCCCCC
Q 021022 209 CPVCCEYLFETRQDVIVLPCGHTIHKNCLKEMREHH---QYACPIC 251 (318)
Q Consensus 209 CpIClE~lf~s~~~v~~LpCGH~fH~~Cl~~wl~~~---~~~CPiC 251 (318)
||||++. |+ +++.|+|||+|+..||.+|++.. .+.||+|
T Consensus 1 CpiC~~~-~~---~Pv~l~CGH~FC~~Cl~~~~~~~~~~~~~CP~C 42 (42)
T PF15227_consen 1 CPICLDL-FK---DPVSLPCGHSFCRSCLERLWKEPSGSGFSCPEC 42 (42)
T ss_dssp ETTTTSB--S---SEEE-SSSSEEEHHHHHHHHCCSSSST---SSS
T ss_pred CCccchh-hC---CccccCCcCHHHHHHHHHHHHccCCcCCCCcCC
Confidence 8999995 55 47889999999999999998652 2579998
No 13
>COG5243 HRD1 HRD ubiquitin ligase complex, ER membrane component [Posttranslational modification, protein turnover, chaperones]
Probab=98.67 E-value=8e-09 Score=101.57 Aligned_cols=56 Identities=38% Similarity=0.820 Sum_probs=47.4
Q ss_pred CCCCCCCcccccccccCC---------ceeEEcCCCCccchHHHHHHHhcCCCCCCCCCccc-Cchh
Q 021022 203 GAMHHDCPVCCEYLFETR---------QDVIVLPCGHTIHKNCLKEMREHHQYACPICSKSV-CDMS 259 (318)
Q Consensus 203 ~~~~~~CpIClE~lf~s~---------~~v~~LpCGH~fH~~Cl~~wl~~~~~~CPiCrks~-~d~~ 259 (318)
.+.+..|.||+|.|+.++ ..+..|||||.+|.+|++.|+++ +.+|||||.++ .|+.
T Consensus 284 ~n~D~~C~ICmde~~h~~~~~~~~~~~~~pKrLpCGHilHl~CLknW~ER-qQTCPICr~p~ifd~~ 349 (491)
T COG5243 284 TNSDRTCTICMDEMFHPDHEPLPRGLDMTPKRLPCGHILHLHCLKNWLER-QQTCPICRRPVIFDQS 349 (491)
T ss_pred cCCCCeEEEecccccCCCCccCcccccCCcccccccceeeHHHHHHHHHh-ccCCCcccCccccccC
Confidence 567889999999988876 33578999999999999999985 58999999995 4554
No 14
>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=98.65 E-value=1.7e-08 Score=72.10 Aligned_cols=47 Identities=34% Similarity=0.982 Sum_probs=38.0
Q ss_pred CCCCcccccccccCCceeEEcCCCCc-cchHHHHHHHhcCCCCCCCCCcccCc
Q 021022 206 HHDCPVCCEYLFETRQDVIVLPCGHT-IHKNCLKEMREHHQYACPICSKSVCD 257 (318)
Q Consensus 206 ~~~CpIClE~lf~s~~~v~~LpCGH~-fH~~Cl~~wl~~~~~~CPiCrks~~d 257 (318)
+..|+||++. ...++++||||. |+..|+.+|++ ...+||+||+++..
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 3579999985 335789999999 99999999998 56899999998753
No 15
>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=98.63 E-value=2.3e-08 Score=68.20 Aligned_cols=40 Identities=48% Similarity=1.205 Sum_probs=33.4
Q ss_pred CcccccccccCCceeEEcCCCCccchHHHHHHHh-cCCCCCCCC
Q 021022 209 CPVCCEYLFETRQDVIVLPCGHTIHKNCLKEMRE-HHQYACPIC 251 (318)
Q Consensus 209 CpIClE~lf~s~~~v~~LpCGH~fH~~Cl~~wl~-~~~~~CPiC 251 (318)
||||++. +. .++.+++|||.|+..|+.+|++ .....||+|
T Consensus 1 C~iC~~~-~~--~~~~~~~C~H~fC~~C~~~~~~~~~~~~CP~C 41 (41)
T PF00097_consen 1 CPICLEP-FE--DPVILLPCGHSFCRDCLRKWLENSGSVKCPLC 41 (41)
T ss_dssp ETTTSSB-CS--SEEEETTTSEEEEHHHHHHHHHHTSSSBTTTT
T ss_pred CCcCCcc-cc--CCCEEecCCCcchHHHHHHHHHhcCCccCCcC
Confidence 7999996 33 2446999999999999999998 566889998
No 16
>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=98.58 E-value=4.3e-08 Score=63.48 Aligned_cols=39 Identities=44% Similarity=1.130 Sum_probs=33.2
Q ss_pred CcccccccccCCceeEEcCCCCccchHHHHHHHhcCCCCCCCC
Q 021022 209 CPVCCEYLFETRQDVIVLPCGHTIHKNCLKEMREHHQYACPIC 251 (318)
Q Consensus 209 CpIClE~lf~s~~~v~~LpCGH~fH~~Cl~~wl~~~~~~CPiC 251 (318)
|+||++. ...++.++|||.||..|+..|++....+||+|
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 34678899999999999999997556789987
No 17
>COG5540 RING-finger-containing ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=98.57 E-value=3.3e-08 Score=95.12 Aligned_cols=55 Identities=27% Similarity=0.671 Sum_probs=46.3
Q ss_pred cCCCCCCCCcccccccccCCceeEEcCCCCccchHHHHHHHhcCCCCCCCCCcccC
Q 021022 201 VEGAMHHDCPVCCEYLFETRQDVIVLPCGHTIHKNCLKEMREHHQYACPICSKSVC 256 (318)
Q Consensus 201 ie~~~~~~CpIClE~lf~s~~~v~~LpCGH~fH~~Cl~~wl~~~~~~CPiCrks~~ 256 (318)
+|.....+|+|||++ |...+.+++|||.|.||..|+++|+...+.+||+||..+.
T Consensus 318 ~ea~~GveCaICms~-fiK~d~~~vlPC~H~FH~~Cv~kW~~~y~~~CPvCrt~iP 372 (374)
T COG5540 318 VEADKGVECAICMSN-FIKNDRLRVLPCDHRFHVGCVDKWLLGYSNKCPVCRTAIP 372 (374)
T ss_pred HhcCCCceEEEEhhh-hcccceEEEeccCceechhHHHHHHhhhcccCCccCCCCC
Confidence 344556799999998 5667789999999999999999999755678999998765
No 18
>KOG1493 consensus Anaphase-promoting complex (APC), subunit 11 [Cell cycle control, cell division, chromosome partitioning; Posttranslational modification, protein turnover, chaperones]
Probab=98.55 E-value=1.4e-08 Score=79.95 Aligned_cols=51 Identities=24% Similarity=0.490 Sum_probs=40.3
Q ss_pred CCCCCCcccccccccCCceeEEcCCCCccchHHHHHHHhc--CCCCCCCCCcccC
Q 021022 204 AMHHDCPVCCEYLFETRQDVIVLPCGHTIHKNCLKEMREH--HQYACPICSKSVC 256 (318)
Q Consensus 204 ~~~~~CpIClE~lf~s~~~v~~LpCGH~fH~~Cl~~wl~~--~~~~CPiCrks~~ 256 (318)
++++.||-|. +....-++++..|.|.||..|+.+|+.. .+-.||+||.++.
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 4555556666689999999999999864 3456999998774
No 19
>PF13445 zf-RING_UBOX: RING-type zinc-finger; PDB: 2CT2_A.
Probab=98.51 E-value=5.6e-08 Score=68.60 Aligned_cols=40 Identities=38% Similarity=1.053 Sum_probs=24.3
Q ss_pred CcccccccccCCceeEEcCCCCccchHHHHHHHhcC---CCCCC
Q 021022 209 CPVCCEYLFETRQDVIVLPCGHTIHKNCLKEMREHH---QYACP 249 (318)
Q Consensus 209 CpIClE~lf~s~~~v~~LpCGH~fH~~Cl~~wl~~~---~~~CP 249 (318)
||||+| +-+...++++|+|||+|.++|++++++.+ .++||
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 55556678899999999999999998743 46687
No 20
>PF14634 zf-RING_5: zinc-RING finger domain
Probab=98.51 E-value=9.7e-08 Score=66.84 Aligned_cols=44 Identities=32% Similarity=0.839 Sum_probs=36.9
Q ss_pred CCcccccccccCCceeEEcCCCCccchHHHHHHHhcCCCCCCCCCc
Q 021022 208 DCPVCCEYLFETRQDVIVLPCGHTIHKNCLKEMREHHQYACPICSK 253 (318)
Q Consensus 208 ~CpIClE~lf~s~~~v~~LpCGH~fH~~Cl~~wl~~~~~~CPiCrk 253 (318)
.|+||++.+ .......+++|||+|+..|+..+. .....||+||+
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 489999964 555678899999999999999998 34578999986
No 21
>KOG0804 consensus Cytoplasmic Zn-finger protein BRAP2 (BRCA1 associated protein) [General function prediction only]
Probab=98.45 E-value=7.5e-08 Score=96.50 Aligned_cols=81 Identities=27% Similarity=0.673 Sum_probs=66.3
Q ss_pred CCCcccccccccCCceeEEcCCCCccchHHHHHHHhcCCCCCCCCCcccCchhHHHHHhHHHHHcCCCChhhhcCcceEE
Q 021022 207 HDCPVCCEYLFETRQDVIVLPCGHTIHKNCLKEMREHHQYACPICSKSVCDMSKVWEKYDREIAATPMPEAYLNKKVWIL 286 (318)
Q Consensus 207 ~~CpIClE~lf~s~~~v~~LpCGH~fH~~Cl~~wl~~~~~~CPiCrks~~d~~~~~~~lD~~i~~~pmPeey~~~~v~Il 286 (318)
-.||||||.|..+...++...|.|+||..|+..|. ..+||+||.... |+. -..-+
T Consensus 176 PTCpVCLERMD~s~~gi~t~~c~Hsfh~~cl~~w~---~~scpvcR~~q~------------------p~~----ve~~~ 230 (493)
T KOG0804|consen 176 PTCPVCLERMDSSTTGILTILCNHSFHCSCLMKWW---DSSCPVCRYCQS------------------PSV----VESSL 230 (493)
T ss_pred CCcchhHhhcCccccceeeeecccccchHHHhhcc---cCcChhhhhhcC------------------cch----hhhhh
Confidence 47999999999999999999999999999999995 367999996443 111 12456
Q ss_pred cCCCCCCccccceeeeccCC--CCCCccccc
Q 021022 287 CNDCGKTSNVQFHVLAQKCP--NCKSYNTRL 315 (318)
Q Consensus 287 CnDC~~~s~v~~H~lg~KC~--~C~SyNT~~ 315 (318)
|..|+...+. |+-+.|+ +||.|+-..
T Consensus 231 c~~c~~~~~L---wicliCg~vgcgrY~egh 258 (493)
T KOG0804|consen 231 CLACGCTEDL---WICLICGNVGCGRYKEGH 258 (493)
T ss_pred hhhhcccccE---EEEEEccceecccccchh
Confidence 9999988887 9999998 599998653
No 22
>PLN03208 E3 ubiquitin-protein ligase RMA2; Provisional
Probab=98.41 E-value=2.5e-07 Score=84.28 Aligned_cols=56 Identities=25% Similarity=0.623 Sum_probs=42.8
Q ss_pred ccccCCCCCCCCcccccccccCCceeEEcCCCCccchHHHHHHHhc---------------CCCCCCCCCcccCc
Q 021022 198 HPCVEGAMHHDCPVCCEYLFETRQDVIVLPCGHTIHKNCLKEMREH---------------HQYACPICSKSVCD 257 (318)
Q Consensus 198 H~Cie~~~~~~CpIClE~lf~s~~~v~~LpCGH~fH~~Cl~~wl~~---------------~~~~CPiCrks~~d 257 (318)
-+-++...+..||||++. +. ++++++|||.|+..||.+|+.. ...+||+||..+..
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 4567899999999999999842 23579999999964
No 23
>COG5194 APC11 Component of SCF ubiquitin ligase and anaphase-promoting complex [Posttranslational modification, protein turnover, chaperones / Cell division and chromosome partitioning]
Probab=98.37 E-value=2.3e-07 Score=73.68 Aligned_cols=51 Identities=20% Similarity=0.397 Sum_probs=38.2
Q ss_pred CCCCcccccccccCC-ceeEEcCCCCccchHHHHHHHhcCCCCCCCCCcccCc
Q 021022 206 HHDCPVCCEYLFETR-QDVIVLPCGHTIHKNCLKEMREHHQYACPICSKSVCD 257 (318)
Q Consensus 206 ~~~CpIClE~lf~s~-~~v~~LpCGH~fH~~Cl~~wl~~~~~~CPiCrks~~d 257 (318)
.+.||-|.-.+-... -+++...|.|.||.+||..||.. +..||++|+++..
T Consensus 31 m~~C~eCq~~~~~~~eC~v~wG~CnHaFH~HCI~rWL~T-k~~CPld~q~w~~ 82 (88)
T COG5194 31 MGTCPECQFGMTPGDECPVVWGVCNHAFHDHCIYRWLDT-KGVCPLDRQTWVL 82 (88)
T ss_pred cCcCcccccCCCCCCcceEEEEecchHHHHHHHHHHHhh-CCCCCCCCceeEE
Confidence 456777765332222 34566789999999999999985 6899999998863
No 24
>PHA02926 zinc finger-like protein; Provisional
Probab=98.24 E-value=7.2e-07 Score=82.94 Aligned_cols=56 Identities=20% Similarity=0.536 Sum_probs=42.2
Q ss_pred CCCCCCCCcccccccccCC-----ceeEEcCCCCccchHHHHHHHhcC-----CCCCCCCCcccCc
Q 021022 202 EGAMHHDCPVCCEYLFETR-----QDVIVLPCGHTIHKNCLKEMREHH-----QYACPICSKSVCD 257 (318)
Q Consensus 202 e~~~~~~CpIClE~lf~s~-----~~v~~LpCGH~fH~~Cl~~wl~~~-----~~~CPiCrks~~d 257 (318)
+.+.+..|+||||.+++.+ ...++.+|+|.||..|+.+|.+.. ..+||+||..+..
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 4566889999999765421 223556999999999999998742 2459999998763
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=98.12 E-value=2.9e-06 Score=62.25 Aligned_cols=45 Identities=20% Similarity=0.473 Sum_probs=37.9
Q ss_pred CCCcccccccccCCceeEEcCCCCccchHHHHHHHhcCCCCCCCCCcccC
Q 021022 207 HDCPVCCEYLFETRQDVIVLPCGHTIHKNCLKEMREHHQYACPICSKSVC 256 (318)
Q Consensus 207 ~~CpIClE~lf~s~~~v~~LpCGH~fH~~Cl~~wl~~~~~~CPiCrks~~ 256 (318)
..||||++. ++ .+++++|||+|.+.|+.+|++. +.+||+|++.+.
T Consensus 2 ~~Cpi~~~~-~~---~Pv~~~~G~v~~~~~i~~~~~~-~~~cP~~~~~~~ 46 (63)
T smart00504 2 FLCPISLEV-MK---DPVILPSGQTYERRAIEKWLLS-HGTDPVTGQPLT 46 (63)
T ss_pred cCCcCCCCc-CC---CCEECCCCCEEeHHHHHHHHHH-CCCCCCCcCCCC
Confidence 469999995 44 2467899999999999999985 678999999884
No 26
>KOG0802 consensus E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=98.03 E-value=1.6e-06 Score=89.42 Aligned_cols=54 Identities=31% Similarity=0.660 Sum_probs=43.9
Q ss_pred CCCCCCCCcccccccccCCc-eeEEcCCCCccchHHHHHHHhcCCCCCCCCCcccC
Q 021022 202 EGAMHHDCPVCCEYLFETRQ-DVIVLPCGHTIHKNCLKEMREHHQYACPICSKSVC 256 (318)
Q Consensus 202 e~~~~~~CpIClE~lf~s~~-~v~~LpCGH~fH~~Cl~~wl~~~~~~CPiCrks~~ 256 (318)
....+..|+||+|.|..+.. .+..|||||.||..|+.+|++. ..+||+||..+.
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 34568899999998876421 2568999999999999999986 689999999443
No 27
>KOG0320 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=97.90 E-value=7e-06 Score=74.04 Aligned_cols=48 Identities=25% Similarity=0.742 Sum_probs=38.2
Q ss_pred CCCCcccccccccCCceeEEcCCCCccchHHHHHHHhcCCCCCCCCCcccC
Q 021022 206 HHDCPVCCEYLFETRQDVIVLPCGHTIHKNCLKEMREHHQYACPICSKSVC 256 (318)
Q Consensus 206 ~~~CpIClE~lf~s~~~v~~LpCGH~fH~~Cl~~wl~~~~~~CPiCrks~~ 256 (318)
-..|||||+. +. .+.++...|||.|+++||...++. ...||+|+|.+.
T Consensus 131 ~~~CPiCl~~-~s-ek~~vsTkCGHvFC~~Cik~alk~-~~~CP~C~kkIt 178 (187)
T KOG0320|consen 131 TYKCPICLDS-VS-EKVPVSTKCGHVFCSQCIKDALKN-TNKCPTCRKKIT 178 (187)
T ss_pred ccCCCceecc-hh-hccccccccchhHHHHHHHHHHHh-CCCCCCcccccc
Confidence 3789999996 33 222355799999999999999985 588999999664
No 28
>KOG0317 consensus Predicted E3 ubiquitin ligase, integral peroxisomal membrane protein [Posttranslational modification, protein turnover, chaperones]
Probab=97.77 E-value=1.2e-05 Score=77.07 Aligned_cols=47 Identities=28% Similarity=0.718 Sum_probs=39.0
Q ss_pred CCCCcccccccccCCceeEEcCCCCccchHHHHHHHhcCCCCCCCCCcccCc
Q 021022 206 HHDCPVCCEYLFETRQDVIVLPCGHTIHKNCLKEMREHHQYACPICSKSVCD 257 (318)
Q Consensus 206 ~~~CpIClE~lf~s~~~v~~LpCGH~fH~~Cl~~wl~~~~~~CPiCrks~~d 257 (318)
...|.+|||. +..+...||||.|+-.||.+|... ..-||+||..+..
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 345678999999999999999975 4669999988764
No 29
>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=97.77 E-value=2.1e-05 Score=56.77 Aligned_cols=43 Identities=28% Similarity=0.724 Sum_probs=33.4
Q ss_pred CCcccccccccCCceeEEcCCC-----CccchHHHHHHHhcC-CCCCCCCC
Q 021022 208 DCPVCCEYLFETRQDVIVLPCG-----HTIHKNCLKEMREHH-QYACPICS 252 (318)
Q Consensus 208 ~CpIClE~lf~s~~~v~~LpCG-----H~fH~~Cl~~wl~~~-~~~CPiCr 252 (318)
.|-||++ +.+.....+.||. |.+|..|+.+|+... +.+||+|+
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 3889997 3344566788994 999999999999653 45799995
No 30
>KOG0823 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=97.73 E-value=2e-05 Score=73.54 Aligned_cols=50 Identities=28% Similarity=0.662 Sum_probs=38.4
Q ss_pred CCCCCCcccccccccCCceeEEcCCCCccchHHHHHHHhcC--CCCCCCCCcccCc
Q 021022 204 AMHHDCPVCCEYLFETRQDVIVLPCGHTIHKNCLKEMREHH--QYACPICSKSVCD 257 (318)
Q Consensus 204 ~~~~~CpIClE~lf~s~~~v~~LpCGH~fH~~Cl~~wl~~~--~~~CPiCrks~~d 257 (318)
....+|-||||- . +++++-.|||.|+--||-+||... ...||+|+..+..
T Consensus 45 ~~~FdCNICLd~---a-kdPVvTlCGHLFCWpClyqWl~~~~~~~~cPVCK~~Vs~ 96 (230)
T KOG0823|consen 45 GGFFDCNICLDL---A-KDPVVTLCGHLFCWPCLYQWLQTRPNSKECPVCKAEVSI 96 (230)
T ss_pred CCceeeeeeccc---c-CCCEEeecccceehHHHHHHHhhcCCCeeCCcccccccc
Confidence 446799999983 2 344555599999999999999753 3348999998874
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=97.72 E-value=2.2e-05 Score=78.63 Aligned_cols=48 Identities=23% Similarity=0.684 Sum_probs=39.4
Q ss_pred CCCCCcccccccccCCceeEEcCCCCccchHHHHHHHhcCCCCCCCCCcccCc
Q 021022 205 MHHDCPVCCEYLFETRQDVIVLPCGHTIHKNCLKEMREHHQYACPICSKSVCD 257 (318)
Q Consensus 205 ~~~~CpIClE~lf~s~~~v~~LpCGH~fH~~Cl~~wl~~~~~~CPiCrks~~d 257 (318)
....|+||++. +. .+++++|||.|+..|+..|+.. ...||+|+..+..
T Consensus 25 ~~l~C~IC~d~-~~---~PvitpCgH~FCs~CI~~~l~~-~~~CP~Cr~~~~~ 72 (397)
T TIGR00599 25 TSLRCHICKDF-FD---VPVLTSCSHTFCSLCIRRCLSN-QPKCPLCRAEDQE 72 (397)
T ss_pred cccCCCcCchh-hh---CccCCCCCCchhHHHHHHHHhC-CCCCCCCCCcccc
Confidence 35799999995 44 2457899999999999999975 4689999998863
No 32
>KOG2177 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=97.72 E-value=1.6e-05 Score=70.52 Aligned_cols=44 Identities=39% Similarity=1.050 Sum_probs=37.4
Q ss_pred CCCCCcccccccccCCceeEEcCCCCccchHHHHHHHhcCCCCCCCCCc
Q 021022 205 MHHDCPVCCEYLFETRQDVIVLPCGHTIHKNCLKEMREHHQYACPICSK 253 (318)
Q Consensus 205 ~~~~CpIClE~lf~s~~~v~~LpCGH~fH~~Cl~~wl~~~~~~CPiCrk 253 (318)
....||||+++ |..+ ++|||||+|+..|+..++. ....||.||.
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 4432 8999999999999999987 5688999994
No 33
>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=97.70 E-value=3.3e-05 Score=75.04 Aligned_cols=52 Identities=23% Similarity=0.590 Sum_probs=39.8
Q ss_pred CCCCcccccccccCCce-eEEcCCCCccchHHHHHHHhcCCCCCCCCCcccCc
Q 021022 206 HHDCPVCCEYLFETRQD-VIVLPCGHTIHKNCLKEMREHHQYACPICSKSVCD 257 (318)
Q Consensus 206 ~~~CpIClE~lf~s~~~-v~~LpCGH~fH~~Cl~~wl~~~~~~CPiCrks~~d 257 (318)
+..||||+...+.+..- ..+-+|||.|+..|++.++..+...||+|++++..
T Consensus 3 ~~~CP~Ck~~~y~np~~kl~i~~CGH~~C~sCv~~l~~~~~~~CP~C~~~lrk 55 (309)
T TIGR00570 3 DQGCPRCKTTKYRNPSLKLMVNVCGHTLCESCVDLLFVRGSGSCPECDTPLRK 55 (309)
T ss_pred CCCCCcCCCCCccCcccccccCCCCCcccHHHHHHHhcCCCCCCCCCCCccch
Confidence 45799999865555432 22337999999999999776666789999998763
No 34
>KOG2930 consensus SCF ubiquitin ligase, Rbx1 component [Posttranslational modification, protein turnover, chaperones]
Probab=97.56 E-value=1.7e-05 Score=65.95 Aligned_cols=34 Identities=24% Similarity=0.494 Sum_probs=29.5
Q ss_pred eeEEcCCCCccchHHHHHHHhcCCCCCCCCCcccC
Q 021022 222 DVIVLPCGHTIHKNCLKEMREHHQYACPICSKSVC 256 (318)
Q Consensus 222 ~v~~LpCGH~fH~~Cl~~wl~~~~~~CPiCrks~~ 256 (318)
.+...-|.|+||..|+..||+. +..||++.+.+.
T Consensus 75 ~VaWG~CNHaFH~hCisrWlkt-r~vCPLdn~eW~ 108 (114)
T KOG2930|consen 75 TVAWGVCNHAFHFHCISRWLKT-RNVCPLDNKEWV 108 (114)
T ss_pred EEEeeecchHHHHHHHHHHHhh-cCcCCCcCccee
Confidence 3556689999999999999985 689999999875
No 35
>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=97.49 E-value=0.00019 Score=55.28 Aligned_cols=48 Identities=23% Similarity=0.524 Sum_probs=36.5
Q ss_pred CCCCcccccccccCCceeEEcCCCCccchHHHHHHHhcCCCCCCCCCcccCc
Q 021022 206 HHDCPVCCEYLFETRQDVIVLPCGHTIHKNCLKEMREHHQYACPICSKSVCD 257 (318)
Q Consensus 206 ~~~CpIClE~lf~s~~~v~~LpCGH~fH~~Cl~~wl~~~~~~CPiCrks~~d 257 (318)
+..|||+++- +. +++++|+||+|-+.++.+|+.....+||+++..+..
T Consensus 4 ~f~CpIt~~l-M~---dPVi~~~G~tyer~~I~~~l~~~~~~~P~t~~~l~~ 51 (73)
T PF04564_consen 4 EFLCPITGEL-MR---DPVILPSGHTYERSAIERWLEQNGGTDPFTRQPLSE 51 (73)
T ss_dssp GGB-TTTSSB--S---SEEEETTSEEEEHHHHHHHHCTTSSB-TTT-SB-SG
T ss_pred ccCCcCcCcH-hh---CceeCCcCCEEcHHHHHHHHHcCCCCCCCCCCcCCc
Confidence 4579999984 44 467899999999999999998757899999988874
No 36
>PF11793 FANCL_C: FANCL C-terminal domain; PDB: 3K1L_A.
Probab=97.49 E-value=2.3e-05 Score=60.41 Aligned_cols=51 Identities=27% Similarity=0.656 Sum_probs=23.2
Q ss_pred CCCCcccccccccCC-ceeEEc---CCCCccchHHHHHHHhc---CC-------CCCCCCCcccC
Q 021022 206 HHDCPVCCEYLFETR-QDVIVL---PCGHTIHKNCLKEMREH---HQ-------YACPICSKSVC 256 (318)
Q Consensus 206 ~~~CpIClE~lf~s~-~~v~~L---pCGH~fH~~Cl~~wl~~---~~-------~~CPiCrks~~ 256 (318)
+.+|+||.+++.+.. .+..+- .|+..||..||.+||.. .+ -+||.|++.+.
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 467999998765232 233332 69999999999999863 11 14999998874
No 37
>KOG0287 consensus Postreplication repair protein RAD18 [Replication, recombination and repair]
Probab=97.44 E-value=9.1e-05 Score=72.79 Aligned_cols=46 Identities=30% Similarity=0.823 Sum_probs=39.4
Q ss_pred CCCcccccccccCCceeEEcCCCCccchHHHHHHHhcCCCCCCCCCcccCc
Q 021022 207 HDCPVCCEYLFETRQDVIVLPCGHTIHKNCLKEMREHHQYACPICSKSVCD 257 (318)
Q Consensus 207 ~~CpIClE~lf~s~~~v~~LpCGH~fH~~Cl~~wl~~~~~~CPiCrks~~d 257 (318)
..|-||.|| |. -+++.||||+|+.-||..+|. .+..||.|+.++..
T Consensus 24 LRC~IC~ey-f~---ip~itpCsHtfCSlCIR~~L~-~~p~CP~C~~~~~E 69 (442)
T KOG0287|consen 24 LRCGICFEY-FN---IPMITPCSHTFCSLCIRKFLS-YKPQCPTCCVTVTE 69 (442)
T ss_pred HHHhHHHHH-hc---CceeccccchHHHHHHHHHhc-cCCCCCceecccch
Confidence 479999996 54 367889999999999999998 46899999999874
No 38
>KOG0828 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=97.38 E-value=6.7e-05 Score=76.59 Aligned_cols=51 Identities=25% Similarity=0.706 Sum_probs=38.7
Q ss_pred CCCCcccccccccC-------------CceeEEcCCCCccchHHHHHHHhcCCCCCCCCCcccC
Q 021022 206 HHDCPVCCEYLFET-------------RQDVIVLPCGHTIHKNCLKEMREHHQYACPICSKSVC 256 (318)
Q Consensus 206 ~~~CpIClE~lf~s-------------~~~v~~LpCGH~fH~~Cl~~wl~~~~~~CPiCrks~~ 256 (318)
..+|+|||.++..- ++..++.||.|.||++|+.+|+......||+||..+.
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 46899999765211 1235566999999999999999754467999998775
No 39
>KOG2164 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=97.37 E-value=0.0001 Score=75.36 Aligned_cols=50 Identities=26% Similarity=0.629 Sum_probs=37.6
Q ss_pred CCCCCCcccccccccCCceeEEcCCCCccchHHHHHHHhcC----CCCCCCCCcccCc
Q 021022 204 AMHHDCPVCCEYLFETRQDVIVLPCGHTIHKNCLKEMREHH----QYACPICSKSVCD 257 (318)
Q Consensus 204 ~~~~~CpIClE~lf~s~~~v~~LpCGH~fH~~Cl~~wl~~~----~~~CPiCrks~~d 257 (318)
+++..|||||++ +. -++++ .|||.|+..||.+|+... --.||||+..+..
T Consensus 184 ~t~~~CPICL~~-~~--~p~~t-~CGHiFC~~CiLqy~~~s~~~~~~~CPiC~s~I~~ 237 (513)
T KOG2164|consen 184 STDMQCPICLEP-PS--VPVRT-NCGHIFCGPCILQYWNYSAIKGPCSCPICRSTITL 237 (513)
T ss_pred CcCCcCCcccCC-CC--ccccc-ccCceeeHHHHHHHHhhhcccCCccCCchhhhccc
Confidence 447899999986 22 23444 499999999999987643 2359999998864
No 40
>KOG0827 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=97.23 E-value=0.00014 Score=72.45 Aligned_cols=49 Identities=27% Similarity=0.637 Sum_probs=38.6
Q ss_pred CCCCcccccccccCCceeEEcC-CCCccchHHHHHHHhcC--CCCCCCCCccc
Q 021022 206 HHDCPVCCEYLFETRQDVIVLP-CGHTIHKNCLKEMREHH--QYACPICSKSV 255 (318)
Q Consensus 206 ~~~CpIClE~lf~s~~~v~~Lp-CGH~fH~~Cl~~wl~~~--~~~CPiCrks~ 255 (318)
...|.|| ++++....++..+. |||+||..|+.+|+... +..||+|+-.+
T Consensus 4 ~A~C~Ic-~d~~p~~~~l~~i~~cGhifh~~cl~qwfe~~Ps~R~cpic~ik~ 55 (465)
T KOG0827|consen 4 MAECHIC-IDGRPNDHELGPIGTCGHIFHTTCLTQWFEGDPSNRGCPICQIKL 55 (465)
T ss_pred cceeeEe-ccCCccccccccccchhhHHHHHHHHHHHccCCccCCCCceeecc
Confidence 3579999 55787777777665 99999999999999863 24799999333
No 41
>COG5574 PEX10 RING-finger-containing E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=96.94 E-value=0.00043 Score=65.91 Aligned_cols=48 Identities=27% Similarity=0.565 Sum_probs=37.6
Q ss_pred CCCCcccccccccCCceeEEcCCCCccchHHHHH-HHhcCCCCCCCCCcccCc
Q 021022 206 HHDCPVCCEYLFETRQDVIVLPCGHTIHKNCLKE-MREHHQYACPICSKSVCD 257 (318)
Q Consensus 206 ~~~CpIClE~lf~s~~~v~~LpCGH~fH~~Cl~~-wl~~~~~~CPiCrks~~d 257 (318)
+..|+||+|. .......+|||.|+..||.. |.+...-.||+||.-...
T Consensus 215 d~kC~lC~e~----~~~ps~t~CgHlFC~~Cl~~~~t~~k~~~CplCRak~~p 263 (271)
T COG5574 215 DYKCFLCLEE----PEVPSCTPCGHLFCLSCLLISWTKKKYEFCPLCRAKVYP 263 (271)
T ss_pred ccceeeeecc----cCCcccccccchhhHHHHHHHHHhhccccCchhhhhccc
Confidence 5679999985 33467889999999999999 876443349999976643
No 42
>PF14835 zf-RING_6: zf-RING of BARD1-type protein; PDB: 1JM7_B.
Probab=96.92 E-value=0.0004 Score=53.27 Aligned_cols=55 Identities=24% Similarity=0.619 Sum_probs=27.1
Q ss_pred CCCcccccccccCCceeEEcCCCCccchHHHHHHHhcCCCCCCCCCcccC--chhHHHHHhHHH
Q 021022 207 HDCPVCCEYLFETRQDVIVLPCGHTIHKNCLKEMREHHQYACPICSKSVC--DMSKVWEKYDRE 268 (318)
Q Consensus 207 ~~CpIClE~lf~s~~~v~~LpCGH~fH~~Cl~~wl~~~~~~CPiCrks~~--d~~~~~~~lD~~ 268 (318)
..|++|.+.|.. ++.+..|.|.|+..|+.+.+. ..||+|+.+.- |+. ..+.||..
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 677789999999999999775 45999999884 432 23456654
No 43
>KOG4172 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=96.77 E-value=0.00034 Score=52.32 Aligned_cols=52 Identities=25% Similarity=0.665 Sum_probs=39.5
Q ss_pred CCCCCCcccccccccCCceeEEcCCCCc-cchHHHHHHHhcCCCCCCCCCcccCchh
Q 021022 204 AMHHDCPVCCEYLFETRQDVIVLPCGHT-IHKNCLKEMREHHQYACPICSKSVCDMS 259 (318)
Q Consensus 204 ~~~~~CpIClE~lf~s~~~v~~LpCGH~-fH~~Cl~~wl~~~~~~CPiCrks~~d~~ 259 (318)
+...+|.||+|. ..+.++.-|||. ++-+|-...++...-.||+||.++.+.-
T Consensus 5 ~~~dECTICye~----pvdsVlYtCGHMCmCy~Cg~rl~~~~~g~CPiCRapi~dvI 57 (62)
T KOG4172|consen 5 QWSDECTICYEH----PVDSVLYTCGHMCMCYACGLRLKKALHGCCPICRAPIKDVI 57 (62)
T ss_pred ccccceeeeccC----cchHHHHHcchHHhHHHHHHHHHHccCCcCcchhhHHHHHH
Confidence 345889999985 233456689998 8899988866656688999999887643
No 44
>KOG4265 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=96.55 E-value=0.0015 Score=64.36 Aligned_cols=49 Identities=31% Similarity=0.811 Sum_probs=39.7
Q ss_pred CCCCCCcccccccccCCceeEEcCCCCc-cchHHHHHHHhcCCCCCCCCCcccCc
Q 021022 204 AMHHDCPVCCEYLFETRQDVIVLPCGHT-IHKNCLKEMREHHQYACPICSKSVCD 257 (318)
Q Consensus 204 ~~~~~CpIClE~lf~s~~~v~~LpCGH~-fH~~Cl~~wl~~~~~~CPiCrks~~d 257 (318)
....+|.|||.. .++.++|||-|. ++..|.+...- ....|||||..+..
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 345789999974 457899999998 99999999752 35789999998763
No 45
>KOG1734 consensus Predicted RING-containing E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=96.55 E-value=0.00069 Score=64.94 Aligned_cols=52 Identities=23% Similarity=0.562 Sum_probs=41.2
Q ss_pred CCCCCcccccccccCC------ceeEEcCCCCccchHHHHHHH-hcCCCCCCCCCcccC
Q 021022 205 MHHDCPVCCEYLFETR------QDVIVLPCGHTIHKNCLKEMR-EHHQYACPICSKSVC 256 (318)
Q Consensus 205 ~~~~CpIClE~lf~s~------~~v~~LpCGH~fH~~Cl~~wl-~~~~~~CPiCrks~~ 256 (318)
.++.|+||...++.+. +..-.|.|+|+||.-|++-|- -.+..+||-|++.+.
T Consensus 223 ~d~vCaVCg~~~~~s~~eegvienty~LsCnHvFHEfCIrGWcivGKkqtCPYCKekVd 281 (328)
T KOG1734|consen 223 SDSVCAVCGQQIDVSVDEEGVIENTYKLSCNHVFHEFCIRGWCIVGKKQTCPYCKEKVD 281 (328)
T ss_pred CcchhHhhcchheeecchhhhhhhheeeecccchHHHhhhhheeecCCCCCchHHHHhh
Confidence 3578999988766654 245679999999999999994 345678999998775
No 46
>PF14570 zf-RING_4: RING/Ubox like zinc-binding domain; PDB: 1E4U_A 1UR6_B.
Probab=96.36 E-value=0.0026 Score=46.19 Aligned_cols=47 Identities=34% Similarity=0.699 Sum_probs=25.3
Q ss_pred CcccccccccCCceeEEcCCCCccchHHHHHHHhcCCCCCCCCCccc
Q 021022 209 CPVCCEYLFETRQDVIVLPCGHTIHKNCLKEMREHHQYACPICSKSV 255 (318)
Q Consensus 209 CpIClE~lf~s~~~v~~LpCGH~fH~~Cl~~wl~~~~~~CPiCrks~ 255 (318)
||+|.|.|..++.....=+||+-+++.|+...+...+.+||-||++.
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 79999988555444444467999999999999875578999999864
No 47
>KOG1039 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=96.36 E-value=0.0011 Score=65.42 Aligned_cols=79 Identities=22% Similarity=0.495 Sum_probs=52.3
Q ss_pred CCCCCCcccccccccCC---ceeEE-cCCCCccchHHHHHHHhcCC------CCCCCCCcccCch--hHHHHHhHHHHHc
Q 021022 204 AMHHDCPVCCEYLFETR---QDVIV-LPCGHTIHKNCLKEMREHHQ------YACPICSKSVCDM--SKVWEKYDREIAA 271 (318)
Q Consensus 204 ~~~~~CpIClE~lf~s~---~~v~~-LpCGH~fH~~Cl~~wl~~~~------~~CPiCrks~~d~--~~~~~~lD~~i~~ 271 (318)
+.+..|-||+|.+.+.. ....+ ++|.|+|+..|+..|.+..+ ..||+||...... +..|-.-.+ +.
T Consensus 159 s~~k~CGICme~i~ek~~~~~rfgilpnC~H~~Cl~Cir~wr~~~q~~~~~sksCP~CRv~s~~v~pS~~Wv~t~~--~k 236 (344)
T KOG1039|consen 159 SSEKECGICMETINEKAASERRFGILPNCNHSFCLNCIRKWRQATQFESKTSKSCPFCRVPSSFVNPSSFWVETKE--EK 236 (344)
T ss_pred cccccceehhhhccccchhhhhcccCCCcchhhhhcHhHhhhhhhccccccccCCCcccCccccccccceeeeecc--cc
Confidence 55789999999765533 11223 46999999999999985433 5799999887642 223532222 56
Q ss_pred CCCChhhhcCcce
Q 021022 272 TPMPEAYLNKKVW 284 (318)
Q Consensus 272 ~pmPeey~~~~v~ 284 (318)
++++++|...+..
T Consensus 237 ~~li~e~~~~~s~ 249 (344)
T KOG1039|consen 237 QKLIEEYEAEMSA 249 (344)
T ss_pred cccHHHHHHHhhc
Confidence 6677777665443
No 48
>KOG0978 consensus E3 ubiquitin ligase involved in syntaxin degradation [Posttranslational modification, protein turnover, chaperones]
Probab=96.36 E-value=0.0011 Score=70.68 Aligned_cols=47 Identities=28% Similarity=0.721 Sum_probs=40.9
Q ss_pred CCCcccccccccCCceeEEcCCCCccchHHHHHHHhcCCCCCCCCCcccCc
Q 021022 207 HDCPVCCEYLFETRQDVIVLPCGHTIHKNCLKEMREHHQYACPICSKSVCD 257 (318)
Q Consensus 207 ~~CpIClE~lf~s~~~v~~LpCGH~fH~~Cl~~wl~~~~~~CPiCrks~~d 257 (318)
..||+|-. ..+++++..|||.|+..|++..+...+.+||.|+.+|+.
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 345678889999999999999988778899999999984
No 49
>KOG1941 consensus Acetylcholine receptor-associated protein of the synapse (rapsyn) [Extracellular structures]
Probab=96.27 E-value=0.00077 Score=67.45 Aligned_cols=59 Identities=34% Similarity=0.702 Sum_probs=48.9
Q ss_pred cccccCCCCCCCCcccccccccCCceeEEcCCCCccchHHHHHHHhc-CCCCCCCCCcccC
Q 021022 197 SHPCVEGAMHHDCPVCCEYLFETRQDVIVLPCGHTIHKNCLKEMREH-HQYACPICSKSVC 256 (318)
Q Consensus 197 ~H~Cie~~~~~~CpIClE~lf~s~~~v~~LpCGH~fH~~Cl~~wl~~-~~~~CPiCrks~~ 256 (318)
.|.|++ +++..|-.|.|.+-...+....|||.|.||..|+.++|.. ...+||-||+-..
T Consensus 357 a~~~~~-e~~L~Cg~CGe~~Glk~e~LqALpCsHIfH~rCl~e~L~~n~~rsCP~CrklrS 416 (518)
T KOG1941|consen 357 AHECVE-ETELYCGLCGESIGLKNERLQALPCSHIFHLRCLQEILENNGTRSCPNCRKLRS 416 (518)
T ss_pred HHHHHH-HHhhhhhhhhhhhcCCcccccccchhHHHHHHHHHHHHHhCCCCCCccHHHHHh
Confidence 478886 6789999999988777777889999999999999999854 4467999995433
No 50
>COG5432 RAD18 RING-finger-containing E3 ubiquitin ligase [Signal transduction mechanisms]
Probab=96.21 E-value=0.0027 Score=61.58 Aligned_cols=46 Identities=26% Similarity=0.618 Sum_probs=38.0
Q ss_pred CCCCcccccccccCCceeEEcCCCCccchHHHHHHHhcCCCCCCCCCcccC
Q 021022 206 HHDCPVCCEYLFETRQDVIVLPCGHTIHKNCLKEMREHHQYACPICSKSVC 256 (318)
Q Consensus 206 ~~~CpIClE~lf~s~~~v~~LpCGH~fH~~Cl~~wl~~~~~~CPiCrks~~ 256 (318)
-..|-||-+++ . .....+|||+|+.-||..+|. .+..||+||.+..
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 35799999863 2 245679999999999999997 5799999998775
No 51
>KOG0311 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=96.10 E-value=0.0014 Score=64.82 Aligned_cols=48 Identities=23% Similarity=0.568 Sum_probs=40.2
Q ss_pred CCCCcccccccccCCceeEEcCCCCccchHHHHHHHhcCCCCCCCCCcccC
Q 021022 206 HHDCPVCCEYLFETRQDVIVLPCGHTIHKNCLKEMREHHQYACPICSKSVC 256 (318)
Q Consensus 206 ~~~CpIClE~lf~s~~~v~~LpCGH~fH~~Cl~~wl~~~~~~CPiCrks~~ 256 (318)
+..|||||+-|.. ...+.-|+|.|+.+||..-+..++..||.||+.+.
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 4689999995433 34567899999999999988888889999999987
No 52
>KOG1785 consensus Tyrosine kinase negative regulator CBL [Defense mechanisms]
Probab=95.98 E-value=0.0021 Score=64.56 Aligned_cols=54 Identities=30% Similarity=0.765 Sum_probs=45.1
Q ss_pred cccCCCCCCCCcccccccccCCceeEEcCCCCccchHHHHHHHhc-CCCCCCCCCcccC
Q 021022 199 PCVEGAMHHDCPVCCEYLFETRQDVIVLPCGHTIHKNCLKEMREH-HQYACPICSKSVC 256 (318)
Q Consensus 199 ~Cie~~~~~~CpIClE~lf~s~~~v~~LpCGH~fH~~Cl~~wl~~-~~~~CPiCrks~~ 256 (318)
.|.-+++-..|-||.| +.+++.+=||||.++..|+..|-.. +...||.||-.+.
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 4666788889999998 4567889999999999999999743 3578999998774
No 53
>PF11789 zf-Nse: Zinc-finger of the MIZ type in Nse subunit; PDB: 2YU4_A 3HTK_C.
Probab=95.90 E-value=0.0064 Score=45.29 Aligned_cols=44 Identities=27% Similarity=0.619 Sum_probs=29.5
Q ss_pred CCCCCCcccccccccCCceeEEcCCCCccchHHHHHHHhc-CCCCCCC
Q 021022 204 AMHHDCPVCCEYLFETRQDVIVLPCGHTIHKNCLKEMREH-HQYACPI 250 (318)
Q Consensus 204 ~~~~~CpIClE~lf~s~~~v~~LpCGH~fH~~Cl~~wl~~-~~~~CPi 250 (318)
.....|||-+.. +. ++++...|||+|-++.|.+|++. ....||+
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 44 47888899999999999999943 4567998
No 54
>COG5219 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=95.80 E-value=0.0044 Score=67.75 Aligned_cols=53 Identities=21% Similarity=0.570 Sum_probs=37.7
Q ss_pred CCCCCCcccccccc--cCCcee-EEcCCCCccchHHHHHHHhc-CCCCCCCCCcccC
Q 021022 204 AMHHDCPVCCEYLF--ETRQDV-IVLPCGHTIHKNCLKEMREH-HQYACPICSKSVC 256 (318)
Q Consensus 204 ~~~~~CpIClE~lf--~s~~~v-~~LpCGH~fH~~Cl~~wl~~-~~~~CPiCrks~~ 256 (318)
+...+||||..-|. +..-|. +-.-|.|-||..|+-+|+++ ++.+||+||.++.
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 55789999986443 111122 22348899999999999865 5678999997764
No 55
>KOG2879 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=95.22 E-value=0.015 Score=55.92 Aligned_cols=53 Identities=26% Similarity=0.668 Sum_probs=42.0
Q ss_pred CCCCCCcccccccccCCceeEEcCCCCccchHHHHHHHhc-CCCCCCCCCcccCchh
Q 021022 204 AMHHDCPVCCEYLFETRQDVIVLPCGHTIHKNCLKEMREH-HQYACPICSKSVCDMS 259 (318)
Q Consensus 204 ~~~~~CpIClE~lf~s~~~v~~LpCGH~fH~~Cl~~wl~~-~~~~CPiCrks~~d~~ 259 (318)
.....||+|.++ +.-|.+..+|||.|+--|+..-+.. ..++||.|+.+...+.
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 4557778899999999999985432 3589999999887653
No 56
>KOG0824 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=94.87 E-value=0.015 Score=56.55 Aligned_cols=49 Identities=18% Similarity=0.442 Sum_probs=39.3
Q ss_pred CCCCCCcccccccccCCceeEEcCCCCccchHHHHHHHhcCCCCCCCCCcccC
Q 021022 204 AMHHDCPVCCEYLFETRQDVIVLPCGHTIHKNCLKEMREHHQYACPICSKSVC 256 (318)
Q Consensus 204 ~~~~~CpIClE~lf~s~~~v~~LpCGH~fH~~Cl~~wl~~~~~~CPiCrks~~ 256 (318)
.+..+|+||+... . -++.|+|+|.|+-.|++--.+.+..+||+||.++.
T Consensus 5 ~~~~eC~IC~nt~---n-~Pv~l~C~HkFCyiCiKGsy~ndk~~CavCR~pid 53 (324)
T KOG0824|consen 5 TKKKECLICYNTG---N-CPVNLYCFHKFCYICIKGSYKNDKKTCAVCRFPID 53 (324)
T ss_pred ccCCcceeeeccC---C-cCccccccchhhhhhhcchhhcCCCCCceecCCCC
Confidence 4578999999742 2 24789999999999999855555577999999986
No 57
>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional
Probab=94.81 E-value=0.022 Score=43.06 Aligned_cols=46 Identities=33% Similarity=0.853 Sum_probs=33.3
Q ss_pred CceeecCCCCccccc-----cccCcCCCCc-cceEecCccccccCCCCCCeeecCCCCc
Q 021022 119 VNQVICSLCGTEQKV-----QQVCVNCGVC-MGEYFCESCKLFDDDTSKKQYHCDGCGI 171 (318)
Q Consensus 119 v~~v~C~~C~~eQ~v-----~~~C~~Cg~~-f~~YfC~~Ckl~ddd~~k~~yHC~~Cgi 171 (318)
.....|..|+.+... .-.|||||.. ..| |.+|+-+. ..|.|++||+
T Consensus 5 ~~~~~CtSCg~~i~~~~~~~~F~CPnCG~~~I~R--C~~CRk~~-----~~Y~CP~CGF 56 (59)
T PRK14890 5 MEPPKCTSCGIEIAPREKAVKFLCPNCGEVIIYR--CEKCRKQS-----NPYTCPKCGF 56 (59)
T ss_pred ccCccccCCCCcccCCCccCEeeCCCCCCeeEee--chhHHhcC-----CceECCCCCC
Confidence 445678889876543 3469999986 544 88997764 4799999985
No 58
>KOG1645 consensus RING-finger-containing E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=94.73 E-value=0.032 Score=56.32 Aligned_cols=50 Identities=24% Similarity=0.739 Sum_probs=38.3
Q ss_pred CCCcccccccccCCc-eeEEcCCCCccchHHHHHHHhc-CCCCCCCCCcccC
Q 021022 207 HDCPVCCEYLFETRQ-DVIVLPCGHTIHKNCLKEMREH-HQYACPICSKSVC 256 (318)
Q Consensus 207 ~~CpIClE~lf~s~~-~v~~LpCGH~fH~~Cl~~wl~~-~~~~CPiCrks~~ 256 (318)
..||||++..-.+++ ..+.|.|||.|=.+|++.||-. ....||.|.....
T Consensus 5 ~tcpiclds~~~~g~hr~vsl~cghlFgs~cie~wl~k~~~~~cp~c~~kat 56 (463)
T KOG1645|consen 5 TTCPICLDSYTTAGNHRIVSLQCGHLFGSQCIEKWLGKKTKMQCPLCSGKAT 56 (463)
T ss_pred ccCceeeeeeeecCceEEeeecccccccHHHHHHHHhhhhhhhCcccCChhH
Confidence 579999987655443 4567899999999999999942 1235999987654
No 59
>PF12906 RINGv: RING-variant domain; PDB: 2D8S_A 1VYX_A.
Probab=94.71 E-value=0.019 Score=41.00 Aligned_cols=41 Identities=29% Similarity=0.759 Sum_probs=26.3
Q ss_pred CcccccccccCCceeEEcCCC-----CccchHHHHHHHhc-CCCCCCCC
Q 021022 209 CPVCCEYLFETRQDVIVLPCG-----HTIHKNCLKEMREH-HQYACPIC 251 (318)
Q Consensus 209 CpIClE~lf~s~~~v~~LpCG-----H~fH~~Cl~~wl~~-~~~~CPiC 251 (318)
|-||++...+ ++..+.||+ -..|.+||.+|+.. ++.+|++|
T Consensus 1 CrIC~~~~~~--~~~li~pC~C~Gs~~~vH~~CL~~W~~~~~~~~C~~C 47 (47)
T PF12906_consen 1 CRICLEGEEE--DEPLISPCRCKGSMKYVHRSCLERWIRESGNRKCEIC 47 (47)
T ss_dssp ETTTTEE-SS--SS-EE-SSS-SSCCGSEECCHHHHHHHHHT-SB-TTT
T ss_pred CeEeCCcCCC--CCceecccccCCCcchhHHHHHHHHHHhcCCCcCCCC
Confidence 5688875333 235667884 47899999999864 45679987
No 60
>KOG0825 consensus PHD Zn-finger protein [General function prediction only]
Probab=94.65 E-value=0.012 Score=63.50 Aligned_cols=50 Identities=14% Similarity=0.376 Sum_probs=39.7
Q ss_pred CCCCcccccccccCCceeEEcCCCCccchHHHHHHHhcCCCCCCCCCcccCc
Q 021022 206 HHDCPVCCEYLFETRQDVIVLPCGHTIHKNCLKEMREHHQYACPICSKSVCD 257 (318)
Q Consensus 206 ~~~CpIClE~lf~s~~~v~~LpCGH~fH~~Cl~~wl~~~~~~CPiCrks~~d 257 (318)
+..||+|+.. +.........+|+|.||.+||..|-.. ..+||+||+.|..
T Consensus 123 ~~~CP~Ci~s-~~DqL~~~~k~c~H~FC~~Ci~sWsR~-aqTCPiDR~EF~~ 172 (1134)
T KOG0825|consen 123 ENQCPNCLKS-CNDQLEESEKHTAHYFCEECVGSWSRC-AQTCPVDRGEFGE 172 (1134)
T ss_pred hhhhhHHHHH-HHHHhhccccccccccHHHHhhhhhhh-cccCchhhhhhhe
Confidence 5679999974 443444456789999999999999764 4789999999873
No 61
>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=94.30 E-value=0.034 Score=53.90 Aligned_cols=49 Identities=20% Similarity=0.532 Sum_probs=40.1
Q ss_pred CCcccccccccCCceeE-EcCCCCccchHHHHHHHhcCCCCCCCCCcccC
Q 021022 208 DCPVCCEYLFETRQDVI-VLPCGHTIHKNCLKEMREHHQYACPICSKSVC 256 (318)
Q Consensus 208 ~CpIClE~lf~s~~~v~-~LpCGH~fH~~Cl~~wl~~~~~~CPiCrks~~ 256 (318)
.||+|..+.+.+..-.. +=+|||.++.+|+...+..+.+.||.|.+.+.
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 59999877776654332 23999999999999999888899999998875
No 62
>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=94.26 E-value=0.023 Score=45.37 Aligned_cols=33 Identities=36% Similarity=0.850 Sum_probs=27.6
Q ss_pred CCCCCCcccccccccCCceeEEcCCCCccchHHHH
Q 021022 204 AMHHDCPVCCEYLFETRQDVIVLPCGHTIHKNCLK 238 (318)
Q Consensus 204 ~~~~~CpIClE~lf~s~~~v~~LpCGH~fH~~Cl~ 238 (318)
.....|+||...|.. ....+.||||.+|..|++
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 467888999999999975
No 63
>KOG1428 consensus Inhibitor of type V adenylyl cyclases/Neuronal presynaptic protein Highwire/PAM/RPM-1 [Signal transduction mechanisms]
Probab=94.23 E-value=0.039 Score=62.95 Aligned_cols=74 Identities=27% Similarity=0.577 Sum_probs=54.4
Q ss_pred cCCcceeeccCccceeeccccccccccCCCCCCCCcccccccccCCceeEEcCCCCccchHHHHHHHhc---------CC
Q 021022 175 GGCDNFFHCNKCRCCYSMLLKNSHPCVEGAMHHDCPVCCEYLFETRQDVIVLPCGHTIHKNCLKEMREH---------HQ 245 (318)
Q Consensus 175 G~~~~ffHC~~C~~C~s~~l~~~H~Cie~~~~~~CpIClE~lf~s~~~v~~LpCGH~fH~~Cl~~wl~~---------~~ 245 (318)
||.+|--||.-|--|-.-.. .+..++.|.||+.+ ..+-.+...|.|||.||.+|....|.. +-
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 55677788888877643322 23447889999864 455678899999999999999886653 12
Q ss_pred CCCCCCCcccC
Q 021022 246 YACPICSKSVC 256 (318)
Q Consensus 246 ~~CPiCrks~~ 256 (318)
..||+|...+.
T Consensus 3534 isCPiC~n~In 3544 (3738)
T KOG1428|consen 3534 ISCPICKNKIN 3544 (3738)
T ss_pred eecccccchhh
Confidence 36999998875
No 64
>PF14447 Prok-RING_4: Prokaryotic RING finger family 4
Probab=93.93 E-value=0.023 Score=42.44 Aligned_cols=33 Identities=39% Similarity=0.785 Sum_probs=26.5
Q ss_pred eeEEcCCCCccchHHHHHHHhcCCCCCCCCCcccCc
Q 021022 222 DVIVLPCGHTIHKNCLKEMREHHQYACPICSKSVCD 257 (318)
Q Consensus 222 ~v~~LpCGH~fH~~Cl~~wl~~~~~~CPiCrks~~d 257 (318)
.-.++||||.+...|+.-+-- .-||+|.+.+..
T Consensus 19 ~~~~~pCgH~I~~~~f~~~rY---ngCPfC~~~~~~ 51 (55)
T PF14447_consen 19 KGTVLPCGHLICDNCFPGERY---NGCPFCGTPFEF 51 (55)
T ss_pred ccccccccceeeccccChhhc---cCCCCCCCcccC
Confidence 456899999999999887632 349999998864
No 65
>KOG4185 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=93.07 E-value=0.092 Score=49.83 Aligned_cols=49 Identities=31% Similarity=0.756 Sum_probs=38.5
Q ss_pred CCCcccccccccCC---ceeEEcCCCCccchHHHHHHHhcCCCCCCCCCcccC
Q 021022 207 HDCPVCCEYLFETR---QDVIVLPCGHTIHKNCLKEMREHHQYACPICSKSVC 256 (318)
Q Consensus 207 ~~CpIClE~lf~s~---~~v~~LpCGH~fH~~Cl~~wl~~~~~~CPiCrks~~ 256 (318)
..|-||-++ |.+. .-++.|.|||++...|+...+......||.||.+..
T Consensus 4 ~~c~~c~~~-~s~~~~~~~p~~l~c~h~~c~~c~~~l~~~~~i~cpfcR~~~~ 55 (296)
T KOG4185|consen 4 PECEICNED-YSSEDGDHIPRVLKCGHTICQNCASKLLGNSRILCPFCRETTE 55 (296)
T ss_pred CceeecCcc-ccccCcccCCcccccCceehHhHHHHHhcCceeeccCCCCccc
Confidence 457788776 4443 335788999999999999999876677999999963
No 66
>KOG4739 consensus Uncharacterized protein involved in synaptonemal complex formation [Cell cycle control, cell division, chromosome partitioning; General function prediction only]
Probab=92.73 E-value=0.051 Score=51.28 Aligned_cols=37 Identities=30% Similarity=0.737 Sum_probs=28.3
Q ss_pred ccCCceeEEcCCCCccchHHHHHHHhcCCCCCCCCCcccC
Q 021022 217 FETRQDVIVLPCGHTIHKNCLKEMREHHQYACPICSKSVC 256 (318)
Q Consensus 217 f~s~~~v~~LpCGH~fH~~Cl~~wl~~~~~~CPiCrks~~ 256 (318)
+.+..+..+..|+|+|+..|...-.. ..||+|++++-
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 44445566779999999999887532 37999999974
No 67
>KOG1571 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=92.69 E-value=0.069 Score=53.04 Aligned_cols=47 Identities=26% Similarity=0.639 Sum_probs=35.1
Q ss_pred CCCCCCCCcccccccccCCceeEEcCCCCccchHHHHHHHhcCCCCCCCCCcccC
Q 021022 202 EGAMHHDCPVCCEYLFETRQDVIVLPCGHTIHKNCLKEMREHHQYACPICSKSVC 256 (318)
Q Consensus 202 e~~~~~~CpIClE~lf~s~~~v~~LpCGH~fH~~Cl~~wl~~~~~~CPiCrks~~ 256 (318)
|.+...+|.||++. ....+.+||||+-+ |..-... ..+||+||.++.
T Consensus 301 ~~~~p~lcVVcl~e----~~~~~fvpcGh~cc--ct~cs~~--l~~CPvCR~rI~ 347 (355)
T KOG1571|consen 301 ELPQPDLCVVCLDE----PKSAVFVPCGHVCC--CTLCSKH--LPQCPVCRQRIR 347 (355)
T ss_pred ccCCCCceEEecCC----ccceeeecCCcEEE--chHHHhh--CCCCchhHHHHH
Confidence 45678999999984 33578999999966 5555432 356999998764
No 68
>KOG3268 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=92.58 E-value=0.073 Score=48.75 Aligned_cols=32 Identities=28% Similarity=0.760 Sum_probs=25.6
Q ss_pred EcCCCCccchHHHHHHHhc-----CC-----CCCCCCCcccC
Q 021022 225 VLPCGHTIHKNCLKEMREH-----HQ-----YACPICSKSVC 256 (318)
Q Consensus 225 ~LpCGH~fH~~Cl~~wl~~-----~~-----~~CPiCrks~~ 256 (318)
-..||..||.-|+.+||.. .+ -.||.|++++.
T Consensus 187 N~qCgkpFHqiCL~dWLRgilTsRQSFdiiFGeCPYCS~Pia 228 (234)
T KOG3268|consen 187 NIQCGKPFHQICLTDWLRGILTSRQSFDIIFGECPYCSDPIA 228 (234)
T ss_pred ccccCCcHHHHHHHHHHHHHhhccceeeeeeccCCCCCCcce
Confidence 4579999999999999863 11 14999999885
No 69
>KOG0297 consensus TNF receptor-associated factor [Signal transduction mechanisms]
Probab=92.57 E-value=0.073 Score=53.39 Aligned_cols=49 Identities=29% Similarity=0.690 Sum_probs=39.5
Q ss_pred CCCCCcccccccccCCceeEEcCCCCccchHHHHHHHhcCCCCCCCCCcccCc
Q 021022 205 MHHDCPVCCEYLFETRQDVIVLPCGHTIHKNCLKEMREHHQYACPICSKSVCD 257 (318)
Q Consensus 205 ~~~~CpIClE~lf~s~~~v~~LpCGH~fH~~Cl~~wl~~~~~~CPiCrks~~d 257 (318)
.+..||+|..-+- +++....|||.|+..|+.+|+.. +..||.|+..+..
T Consensus 20 ~~l~C~~C~~vl~---~p~~~~~cgh~fC~~C~~~~~~~-~~~cp~~~~~~~~ 68 (391)
T KOG0297|consen 20 ENLLCPICMSVLR---DPVQTTTCGHRFCAGCLLESLSN-HQKCPVCRQELTQ 68 (391)
T ss_pred ccccCcccccccc---CCCCCCCCCCcccccccchhhcc-CcCCcccccccch
Confidence 3578999997532 24444789999999999999986 6899999988764
No 70
>COG5175 MOT2 Transcriptional repressor [Transcription]
Probab=92.57 E-value=0.045 Score=54.33 Aligned_cols=57 Identities=26% Similarity=0.604 Sum_probs=45.6
Q ss_pred CCCCcccccccccCCceeEEcCCCCccchHHHHHHHhcCCCCCCCCCcccCchhHHH
Q 021022 206 HHDCPVCCEYLFETRQDVIVLPCGHTIHKNCLKEMREHHQYACPICSKSVCDMSKVW 262 (318)
Q Consensus 206 ~~~CpIClE~lf~s~~~v~~LpCGH~fH~~Cl~~wl~~~~~~CPiCrks~~d~~~~~ 262 (318)
++.||.|+|+|.-+.+....-|||--+++-|+....+.-+-+||-||+...+-...|
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 456999999988777666667899999999998876655678999999988755444
No 71
>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=92.20 E-value=0.071 Score=46.41 Aligned_cols=35 Identities=20% Similarity=0.514 Sum_probs=30.2
Q ss_pred CCCCcccccccccCCceeEEcCCC------CccchHHHHHHH
Q 021022 206 HHDCPVCCEYLFETRQDVIVLPCG------HTIHKNCLKEMR 241 (318)
Q Consensus 206 ~~~CpIClE~lf~s~~~v~~LpCG------H~fH~~Cl~~wl 241 (318)
..+|.||++.+.. .+.++.+++| |.||.+|+..|-
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 4689999998776 6689999997 779999999993
No 72
>KOG4159 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=91.80 E-value=0.16 Score=51.30 Aligned_cols=49 Identities=29% Similarity=0.824 Sum_probs=38.9
Q ss_pred CCCCCCcccccccccCCceeEEcCCCCccchHHHHHHHhcCCCCCCCCCcccCc
Q 021022 204 AMHHDCPVCCEYLFETRQDVIVLPCGHTIHKNCLKEMREHHQYACPICSKSVCD 257 (318)
Q Consensus 204 ~~~~~CpIClE~lf~s~~~v~~LpCGH~fH~~Cl~~wl~~~~~~CPiCrks~~d 257 (318)
..+..|-||+.-++. ++++||||+|+..|+..-+. ...-||+||-.+..
T Consensus 82 ~sef~c~vc~~~l~~----pv~tpcghs~c~~Cl~r~ld-~~~~cp~Cr~~l~e 130 (398)
T KOG4159|consen 82 RSEFECCVCSRALYP----PVVTPCGHSFCLECLDRSLD-QETECPLCRDELVE 130 (398)
T ss_pred cchhhhhhhHhhcCC----CccccccccccHHHHHHHhc-cCCCCccccccccc
Confidence 457789999874433 55669999999999999766 34679999999874
No 73
>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=91.78 E-value=0.098 Score=40.87 Aligned_cols=36 Identities=28% Similarity=0.813 Sum_probs=24.3
Q ss_pred ceeecCCCCccccccccCcCCCCcc--------ceEecCccccc
Q 021022 120 NQVICSLCGTEQKVQQVCVNCGVCM--------GEYFCESCKLF 155 (318)
Q Consensus 120 ~~v~C~~C~~eQ~v~~~C~~Cg~~f--------~~YfC~~Ckl~ 155 (318)
....|..|+..-.....||.||.++ +.|||..|+=.
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 5788999998877788899998887 68999999744
No 74
>KOG4275 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=91.53 E-value=0.031 Score=54.45 Aligned_cols=54 Identities=28% Similarity=0.680 Sum_probs=37.5
Q ss_pred cccccccCCCC---CCCCcccccccccCCceeEEcCCCCc-cchHHHHHHHhcCCCCCCCCCcccCc
Q 021022 195 KNSHPCVEGAM---HHDCPVCCEYLFETRQDVIVLPCGHT-IHKNCLKEMREHHQYACPICSKSVCD 257 (318)
Q Consensus 195 ~~~H~Cie~~~---~~~CpIClE~lf~s~~~v~~LpCGH~-fH~~Cl~~wl~~~~~~CPiCrks~~d 257 (318)
++.|-+-.... +..|.||++ .+.+-++|+|||. -+.+|-..+- .|||||+-+..
T Consensus 286 k~~~g~~~~~s~~~~~LC~ICmD----aP~DCvfLeCGHmVtCt~CGkrm~-----eCPICRqyi~r 343 (350)
T KOG4275|consen 286 KGNDGEQHSRSLATRRLCAICMD----APRDCVFLECGHMVTCTKCGKRMN-----ECPICRQYIVR 343 (350)
T ss_pred hcccccccccchhHHHHHHHHhc----CCcceEEeecCcEEeehhhccccc-----cCchHHHHHHH
Confidence 34444443333 789999998 4667899999997 4556655542 59999986643
No 75
>KOG3002 consensus Zn finger protein [General function prediction only]
Probab=91.45 E-value=0.22 Score=48.59 Aligned_cols=62 Identities=24% Similarity=0.576 Sum_probs=45.8
Q ss_pred CCCCcccccccccCCceeEEcCC--CCccchHHHHHHHhcCCCCCCCCCcccCchhHHHHHhHHHHHcCCCChhh
Q 021022 206 HHDCPVCCEYLFETRQDVIVLPC--GHTIHKNCLKEMREHHQYACPICSKSVCDMSKVWEKYDREIAATPMPEAY 278 (318)
Q Consensus 206 ~~~CpIClE~lf~s~~~v~~LpC--GH~fH~~Cl~~wl~~~~~~CPiCrks~~d~~~~~~~lD~~i~~~pmPeey 278 (318)
-.+||||.++|.. + ++.| ||..+..|-.+. ...||.||.++++... +.++..+++...|=.|
T Consensus 48 lleCPvC~~~l~~---P--i~QC~nGHlaCssC~~~~----~~~CP~Cr~~~g~~R~--~amEkV~e~~~vpC~~ 111 (299)
T KOG3002|consen 48 LLDCPVCFNPLSP---P--IFQCDNGHLACSSCRTKV----SNKCPTCRLPIGNIRC--RAMEKVAEAVLVPCKN 111 (299)
T ss_pred hccCchhhccCcc---c--ceecCCCcEehhhhhhhh----cccCCccccccccHHH--HHHHHHHHhceecccc
Confidence 4689999997543 2 5566 899999999865 3679999999996533 4567777777665443
No 76
>PF04641 Rtf2: Rtf2 RING-finger
Probab=91.36 E-value=0.19 Score=47.51 Aligned_cols=51 Identities=25% Similarity=0.658 Sum_probs=39.6
Q ss_pred CCCCCCCcccccccccCCceeE-EcCCCCccchHHHHHHHhcCCCCCCCCCcccC
Q 021022 203 GAMHHDCPVCCEYLFETRQDVI-VLPCGHTIHKNCLKEMREHHQYACPICSKSVC 256 (318)
Q Consensus 203 ~~~~~~CpIClE~lf~s~~~v~-~LpCGH~fH~~Cl~~wl~~~~~~CPiCrks~~ 256 (318)
......|||....| .+....+ +.||||+|-..++.+.- ....||+|.+++.
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 35567899999865 4444444 45999999999999984 3467999999986
No 77
>KOG1814 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=90.99 E-value=0.14 Score=51.89 Aligned_cols=53 Identities=26% Similarity=0.429 Sum_probs=38.9
Q ss_pred ccccCCCCCCCCcccccccccCCceeEEcCCCCccchHHHHHHHhc-------CCCCCCCCC
Q 021022 198 HPCVEGAMHHDCPVCCEYLFETRQDVIVLPCGHTIHKNCLKEMREH-------HQYACPICS 252 (318)
Q Consensus 198 H~Cie~~~~~~CpIClE~lf~s~~~v~~LpCGH~fH~~Cl~~wl~~-------~~~~CPiCr 252 (318)
+.+.-+ +-.+|-||++. +........|||+|+|++.|+..|+.. ...+||-+.
T Consensus 177 ~~~F~~-slf~C~ICf~e-~~G~~c~~~lpC~Hv~Ck~C~kdY~~~~i~eg~v~~l~Cp~~~ 236 (445)
T KOG1814|consen 177 LEKFVN-SLFDCCICFEE-QMGQHCFKFLPCSHVFCKSCLKDYFTIQIQEGQVSCLKCPDPK 236 (445)
T ss_pred HHHHHh-hcccceeeehh-hcCcceeeecccchHHHHHHHHHHHHHhhhcceeeeecCCCCC
Confidence 444433 35789999984 665567889999999999999998642 245687554
No 78
>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]
Probab=90.79 E-value=0.17 Score=38.50 Aligned_cols=45 Identities=33% Similarity=0.878 Sum_probs=33.3
Q ss_pred eeecCCCCcccccc-----ccCcCCCCccceEecCccccccCCCCCCeeecCCCCc
Q 021022 121 QVICSLCGTEQKVQ-----QVCVNCGVCMGEYFCESCKLFDDDTSKKQYHCDGCGI 171 (318)
Q Consensus 121 ~v~C~~C~~eQ~v~-----~~C~~Cg~~f~~YfC~~Ckl~ddd~~k~~yHC~~Cgi 171 (318)
...|..|+.+..+. -.|||||..+ =|-|.+|+.+.+ +|.|++||+
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 56899999887443 3599999443 366888887744 799999985
No 79
>PF12773 DZR: Double zinc ribbon
Probab=90.78 E-value=0.22 Score=35.14 Aligned_cols=22 Identities=32% Similarity=0.845 Sum_probs=15.2
Q ss_pred cCCCCccccc-cccCcCCCCccc
Q 021022 124 CSLCGTEQKV-QQVCVNCGVCMG 145 (318)
Q Consensus 124 C~~C~~eQ~v-~~~C~~Cg~~f~ 145 (318)
|..|+++.+. +..|++||..+.
T Consensus 1 Cp~Cg~~~~~~~~fC~~CG~~l~ 23 (50)
T PF12773_consen 1 CPHCGTPNPDDAKFCPHCGTPLP 23 (50)
T ss_pred CCCcCCcCCccccCChhhcCChh
Confidence 5567776554 567888888776
No 80
>KOG3970 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=90.72 E-value=0.35 Score=45.88 Aligned_cols=52 Identities=31% Similarity=0.654 Sum_probs=40.7
Q ss_pred CCCCCCcccccccccCCceeEEcCCCCccchHHHHHHHhc-------CCCCCCCCCcccCc
Q 021022 204 AMHHDCPVCCEYLFETRQDVIVLPCGHTIHKNCLKEMREH-------HQYACPICSKSVCD 257 (318)
Q Consensus 204 ~~~~~CpIClE~lf~s~~~v~~LpCGH~fH~~Cl~~wl~~-------~~~~CPiCrks~~d 257 (318)
-...+|..|.-.|-. + +.+.|.|=|.||-.|+++|... ..|+||-|+..+..
T Consensus 48 DY~pNC~LC~t~La~-g-dt~RLvCyhlfHW~ClneraA~lPanTAPaGyqCP~Cs~eiFP 106 (299)
T KOG3970|consen 48 DYNPNCRLCNTPLAS-G-DTTRLVCYHLFHWKCLNERAANLPANTAPAGYQCPCCSQEIFP 106 (299)
T ss_pred CCCCCCceeCCcccc-C-cceeehhhhhHHHHHhhHHHhhCCCcCCCCcccCCCCCCccCC
Confidence 346789999876443 3 4567889999999999999652 35899999999863
No 81
>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=90.70 E-value=0.18 Score=42.42 Aligned_cols=36 Identities=22% Similarity=0.595 Sum_probs=28.5
Q ss_pred CcceEEcCCCCCCccccceeeeccCCCCCCccccccCC
Q 021022 281 KKVWILCNDCGKTSNVQFHVLAQKCPNCKSYNTRLTRG 318 (318)
Q Consensus 281 ~~v~IlCnDC~~~s~v~~H~lg~KC~~C~SyNT~~~~~ 318 (318)
..+...|++|+.......+ ...||.|||++++.++|
T Consensus 67 ~p~~~~C~~Cg~~~~~~~~--~~~CP~Cgs~~~~i~~G 102 (115)
T TIGR00100 67 EPVECECEDCSEEVSPEID--LYRCPKCHGIMLQVRAG 102 (115)
T ss_pred eCcEEEcccCCCEEecCCc--CccCcCCcCCCcEEecC
Confidence 3567899999987766432 35799999999998876
No 82
>KOG4445 consensus Uncharacterized conserved protein, contains RWD domain [Function unknown]
Probab=90.66 E-value=0.078 Score=51.91 Aligned_cols=37 Identities=24% Similarity=0.517 Sum_probs=31.1
Q ss_pred CCCCCcccccccccCCceeEEcCCCCccchHHHHHHHh
Q 021022 205 MHHDCPVCCEYLFETRQDVIVLPCGHTIHKNCLKEMRE 242 (318)
Q Consensus 205 ~~~~CpIClE~lf~s~~~v~~LpCGH~fH~~Cl~~wl~ 242 (318)
-.+.|.|||= =|.+.....+.+|-|+||..||..||.
T Consensus 114 p~gqCvICLy-gfa~~~~ft~T~C~Hy~H~~ClaRyl~ 150 (368)
T KOG4445|consen 114 PNGQCVICLY-GFASSPAFTVTACDHYMHFACLARYLT 150 (368)
T ss_pred CCCceEEEEE-eecCCCceeeehhHHHHHHHHHHHHHH
Confidence 3679999995 466666788889999999999998875
No 83
>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=90.59 E-value=0.26 Score=44.12 Aligned_cols=33 Identities=33% Similarity=0.893 Sum_probs=23.8
Q ss_pred CCCCcccccccccCCceeEEcCCC-C------------ccchHHHHHHHh
Q 021022 206 HHDCPVCCEYLFETRQDVIVLPCG-H------------TIHKNCLKEMRE 242 (318)
Q Consensus 206 ~~~CpIClE~lf~s~~~v~~LpCG-H------------~fH~~Cl~~wl~ 242 (318)
+..||||||. +-..++|-|. | .-|..||+++-+
T Consensus 2 d~~CpICme~----PHNAVLLlCSS~~kgcRpymc~Ts~rhSNCLdqfkk 47 (162)
T PF07800_consen 2 DVTCPICMEH----PHNAVLLLCSSHEKGCRPYMCDTSYRHSNCLDQFKK 47 (162)
T ss_pred CccCceeccC----CCceEEEEeccccCCccccccCCccchhHHHHHHHH
Confidence 4679999995 3346677773 3 268999999865
No 84
>KOG2817 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=90.19 E-value=0.22 Score=50.11 Aligned_cols=48 Identities=29% Similarity=0.647 Sum_probs=40.2
Q ss_pred CCCcccccccccCCceeEEcCCCCccchHHHHHHHhcCC--CCCCCCCccc
Q 021022 207 HDCPVCCEYLFETRQDVIVLPCGHTIHKNCLKEMREHHQ--YACPICSKSV 255 (318)
Q Consensus 207 ~~CpIClE~lf~s~~~v~~LpCGH~fH~~Cl~~wl~~~~--~~CPiCrks~ 255 (318)
..|||=.|. -+...|++.|.|||++-++-++.+.+.+. ++||-|-...
T Consensus 335 F~CPVlKeq-tsdeNPPm~L~CGHVISkdAlnrLS~ng~~sfKCPYCP~e~ 384 (394)
T KOG2817|consen 335 FICPVLKEQ-TSDENPPMMLICGHVISKDALNRLSKNGSQSFKCPYCPVEQ 384 (394)
T ss_pred eecccchhh-ccCCCCCeeeeccceecHHHHHHHhhCCCeeeeCCCCCccc
Confidence 579998884 55567899999999999999999988766 8899997543
No 85
>PRK00564 hypA hydrogenase nickel incorporation protein; Provisional
Probab=89.67 E-value=0.24 Score=41.80 Aligned_cols=37 Identities=30% Similarity=0.627 Sum_probs=28.9
Q ss_pred cCcceEEcCCCCCCcccc-ceeeeccCCCCCCccccccCC
Q 021022 280 NKKVWILCNDCGKTSNVQ-FHVLAQKCPNCKSYNTRLTRG 318 (318)
Q Consensus 280 ~~~v~IlCnDC~~~s~v~-~H~lg~KC~~C~SyNT~~~~~ 318 (318)
...+...|++|+...... +++ .+||.|||++...++|
T Consensus 67 ~vp~~~~C~~Cg~~~~~~~~~~--~~CP~Cgs~~~~i~~G 104 (117)
T PRK00564 67 DEKVELECKDCSHVFKPNALDY--GVCEKCHSKNVIITQG 104 (117)
T ss_pred ecCCEEEhhhCCCccccCCccC--CcCcCCCCCceEEecC
Confidence 335778999999877664 333 4799999999998876
No 86
>PRK03824 hypA hydrogenase nickel incorporation protein; Provisional
Probab=89.27 E-value=0.28 Score=42.35 Aligned_cols=37 Identities=27% Similarity=0.734 Sum_probs=27.5
Q ss_pred cceEEcCCCCCCcccc-------------cee------eeccCCCCCCccccccCC
Q 021022 282 KVWILCNDCGKTSNVQ-------------FHV------LAQKCPNCKSYNTRLTRG 318 (318)
Q Consensus 282 ~v~IlCnDC~~~s~v~-------------~H~------lg~KC~~C~SyNT~~~~~ 318 (318)
.....|.+|+...... +|+ ...+||.|||++.+.++|
T Consensus 68 p~~~~C~~CG~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~CP~Cgs~~~~i~~G 123 (135)
T PRK03824 68 EAVLKCRNCGNEWSLKEVKESLDEEIREAIHFIPEVVHAFLKCPKCGSRDFEIVKG 123 (135)
T ss_pred ceEEECCCCCCEEecccccccccccccccccccccccccCcCCcCCCCCCcEEecC
Confidence 4678899999766443 222 336899999999998876
No 87
>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=88.81 E-value=0.087 Score=41.16 Aligned_cols=65 Identities=26% Similarity=0.548 Sum_probs=39.1
Q ss_pred CCCcccccccccCCceeEEcCCCCccchHHHHHHHhcCCCCCCCCCcccCchhHHHHHhHHHHHcCCCChhhhcCcceEE
Q 021022 207 HDCPVCCEYLFETRQDVIVLPCGHTIHKNCLKEMREHHQYACPICSKSVCDMSKVWEKYDREIAATPMPEAYLNKKVWIL 286 (318)
Q Consensus 207 ~~CpIClE~lf~s~~~v~~LpCGH~fH~~Cl~~wl~~~~~~CPiCrks~~d~~~~~~~lD~~i~~~pmPeey~~~~v~Il 286 (318)
..||.|...|-... ||+.+..|-..+.. ...||-|..++..+. +-..++.+
T Consensus 2 ~~CP~C~~~L~~~~--------~~~~C~~C~~~~~~--~a~CPdC~~~Le~Lk-------------------ACGAvdYF 52 (70)
T PF07191_consen 2 NTCPKCQQELEWQG--------GHYHCEACQKDYKK--EAFCPDCGQPLEVLK-------------------ACGAVDYF 52 (70)
T ss_dssp -B-SSS-SBEEEET--------TEEEETTT--EEEE--EEE-TTT-SB-EEEE-------------------ETTEEEEE
T ss_pred CcCCCCCCccEEeC--------CEEECcccccccee--cccCCCcccHHHHHH-------------------Hhccccee
Confidence 57999998643321 88999999998865 367999999886543 23357899
Q ss_pred cCCCCC---Ccccccee
Q 021022 287 CNDCGK---TSNVQFHV 300 (318)
Q Consensus 287 CnDC~~---~s~v~~H~ 300 (318)
||.|++ ++.|.|.+
T Consensus 53 C~~c~gLiSKkrV~f~~ 69 (70)
T PF07191_consen 53 CNHCHGLISKKRVRFEF 69 (70)
T ss_dssp -TTTT-EE-TTTSEEEE
T ss_pred eccCCceeecceEEEEe
Confidence 999995 66666654
No 88
>COG5152 Uncharacterized conserved protein, contains RING and CCCH-type Zn-fingers [General function prediction only]
Probab=88.62 E-value=0.26 Score=45.93 Aligned_cols=59 Identities=20% Similarity=0.459 Sum_probs=41.9
Q ss_pred CCCCcccccccccCCceeEEcCCCCccchHHHHHHHhcCCCCCCCCCcccCchhHHHHHhHHHH
Q 021022 206 HHDCPVCCEYLFETRQDVIVLPCGHTIHKNCLKEMREHHQYACPICSKSVCDMSKVWEKYDREI 269 (318)
Q Consensus 206 ~~~CpIClE~lf~s~~~v~~LpCGH~fH~~Cl~~wl~~~~~~CPiCrks~~d~~~~~~~lD~~i 269 (318)
...|.||.++ +.| +++..|||.|+..|+-.-.+ ....|-+|.+..--....-..++..+
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 553 45778999999999887655 34789999998754333334455543
No 89
>PHA02862 5L protein; Provisional
Probab=88.52 E-value=0.33 Score=43.04 Aligned_cols=46 Identities=17% Similarity=0.471 Sum_probs=33.6
Q ss_pred CCCCcccccccccCCceeEEcCCC-----CccchHHHHHHHhcC-CCCCCCCCcccC
Q 021022 206 HHDCPVCCEYLFETRQDVIVLPCG-----HTIHKNCLKEMREHH-QYACPICSKSVC 256 (318)
Q Consensus 206 ~~~CpIClE~lf~s~~~v~~LpCG-----H~fH~~Cl~~wl~~~-~~~CPiCrks~~ 256 (318)
...|=||.+. . .++ .-||. -..|++|+++|++.. ...||+|+..+.
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 35764 569999999999753 456999999886
No 90
>KOG1813 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=88.38 E-value=0.29 Score=47.71 Aligned_cols=65 Identities=20% Similarity=0.414 Sum_probs=45.1
Q ss_pred CCCCCCcccccccccCCceeEEcCCCCccchHHHHHHHhcCCCCCCCCCcccCchhHHHHHhHHHHHcCC
Q 021022 204 AMHHDCPVCCEYLFETRQDVIVLPCGHTIHKNCLKEMREHHQYACPICSKSVCDMSKVWEKYDREIAATP 273 (318)
Q Consensus 204 ~~~~~CpIClE~lf~s~~~v~~LpCGH~fH~~Cl~~wl~~~~~~CPiCrks~~d~~~~~~~lD~~i~~~p 273 (318)
.....|-||.++ |. ..++-.|||+|+..|...-++. ...|+||.+.+--....-..|...+...+
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 345679999997 43 3567789999999999987763 47899999988643222233444444433
No 91
>PRK12380 hydrogenase nickel incorporation protein HybF; Provisional
Probab=88.36 E-value=0.32 Score=40.74 Aligned_cols=35 Identities=26% Similarity=0.685 Sum_probs=27.3
Q ss_pred cceEEcCCCCCCccccceeeeccCCCCCCccccccCC
Q 021022 282 KVWILCNDCGKTSNVQFHVLAQKCPNCKSYNTRLTRG 318 (318)
Q Consensus 282 ~v~IlCnDC~~~s~v~~H~lg~KC~~C~SyNT~~~~~ 318 (318)
.....|++|+........ ...||.|||++...++|
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 467889999987766422 23599999999998876
No 92
>COG5236 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=87.99 E-value=0.5 Score=47.33 Aligned_cols=66 Identities=23% Similarity=0.450 Sum_probs=45.5
Q ss_pred cceeeccccccccccCCCCCCCCcccccccccCCceeEEcCCCCccchHHHHHHHhc-CCCCCCCCCcccC
Q 021022 187 RCCYSMLLKNSHPCVEGAMHHDCPVCCEYLFETRQDVIVLPCGHTIHKNCLKEMREH-HQYACPICSKSVC 256 (318)
Q Consensus 187 ~~C~s~~l~~~H~Cie~~~~~~CpIClE~lf~s~~~v~~LpCGH~fH~~Cl~~wl~~-~~~~CPiCrks~~ 256 (318)
+.|....|-++-+=........|.||.+. ..-+.++||||-++-.|......- ..-.||+||..+.
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 45555555444333334556799999984 345778999999999998775321 2356999998875
No 93
>PRK03681 hypA hydrogenase nickel incorporation protein; Validated
Probab=87.97 E-value=0.36 Score=40.50 Aligned_cols=36 Identities=17% Similarity=0.480 Sum_probs=27.6
Q ss_pred cceEEcCCCCCCccccceeeeccCCCCCCccccccCC
Q 021022 282 KVWILCNDCGKTSNVQFHVLAQKCPNCKSYNTRLTRG 318 (318)
Q Consensus 282 ~v~IlCnDC~~~s~v~~H~lg~KC~~C~SyNT~~~~~ 318 (318)
.+...|++|+.......+. ...||.|||++++.++|
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 5678899999876554222 14699999999999876
No 94
>KOG3039 consensus Uncharacterized conserved protein [Function unknown]
Probab=87.91 E-value=0.54 Score=45.10 Aligned_cols=54 Identities=26% Similarity=0.507 Sum_probs=43.5
Q ss_pred CCCCCCCcccccccccCCceeEEc-CCCCccchHHHHHHHhcCCCCCCCCCcccCch
Q 021022 203 GAMHHDCPVCCEYLFETRQDVIVL-PCGHTIHKNCLKEMREHHQYACPICSKSVCDM 258 (318)
Q Consensus 203 ~~~~~~CpIClE~lf~s~~~v~~L-pCGH~fH~~Cl~~wl~~~~~~CPiCrks~~d~ 258 (318)
.+....||||.+.|-. ..+..+| ||||++..+|..+++.. ...+|++.+++.+.
T Consensus 218 ~s~ryiCpvtrd~LtN-t~~ca~Lr~sg~Vv~~ecvEklir~-D~v~pv~d~plkdr 272 (303)
T KOG3039|consen 218 ASKRYICPVTRDTLTN-TTPCAVLRPSGHVVTKECVEKLIRK-DMVDPVTDKPLKDR 272 (303)
T ss_pred hccceecccchhhhcC-ccceEEeccCCcEeeHHHHHHhccc-cccccCCCCcCccc
Confidence 3456789999996544 5556665 99999999999999974 58899999999864
No 95
>PHA02825 LAP/PHD finger-like protein; Provisional
Probab=87.48 E-value=0.54 Score=42.17 Aligned_cols=47 Identities=26% Similarity=0.582 Sum_probs=34.0
Q ss_pred CCCCCcccccccccCCceeEEcCCC--C---ccchHHHHHHHhcC-CCCCCCCCcccC
Q 021022 205 MHHDCPVCCEYLFETRQDVIVLPCG--H---TIHKNCLKEMREHH-QYACPICSKSVC 256 (318)
Q Consensus 205 ~~~~CpIClE~lf~s~~~v~~LpCG--H---~fH~~Cl~~wl~~~-~~~CPiCrks~~ 256 (318)
++..|-||.+.- +. ..-||. . ..|++|++.|+..+ ..+||+|+..+.
T Consensus 7 ~~~~CRIC~~~~---~~--~~~PC~CkGs~k~VH~sCL~rWi~~s~~~~CeiC~~~Y~ 59 (162)
T PHA02825 7 MDKCCWICKDEY---DV--VTNYCNCKNENKIVHKECLEEWINTSKNKSCKICNGPYN 59 (162)
T ss_pred CCCeeEecCCCC---CC--ccCCcccCCCchHHHHHHHHHHHhcCCCCcccccCCeEE
Confidence 467899998751 11 234764 3 56999999999753 456999998875
No 96
>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=86.91 E-value=0.44 Score=33.51 Aligned_cols=42 Identities=29% Similarity=0.698 Sum_probs=20.2
Q ss_pred CcccccccccCCceeEEcCCCCccchHHHHHHHhcCC-CCCCCC
Q 021022 209 CPVCCEYLFETRQDVIVLPCGHTIHKNCLKEMREHHQ-YACPIC 251 (318)
Q Consensus 209 CpIClE~lf~s~~~v~~LpCGH~fH~~Cl~~wl~~~~-~~CPiC 251 (318)
|.+|.+ +.+.+..-....|+=.+|..|+..|++..+ .+||.|
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 556776 333222212224777899999999987643 369987
No 97
>KOG1002 consensus Nucleotide excision repair protein RAD16 [Replication, recombination and repair]
Probab=85.99 E-value=0.33 Score=50.91 Aligned_cols=53 Identities=26% Similarity=0.597 Sum_probs=42.6
Q ss_pred ccCCCCCCCCcccccccccCCceeEEcCCCCccchHHHHHHHhc----CCCCCCCCCcccC
Q 021022 200 CVEGAMHHDCPVCCEYLFETRQDVIVLPCGHTIHKNCLKEMREH----HQYACPICSKSVC 256 (318)
Q Consensus 200 Cie~~~~~~CpIClE~lf~s~~~v~~LpCGH~fH~~Cl~~wl~~----~~~~CPiCrks~~ 256 (318)
=+|+..+..|-+|-+. .+++..-.|.|.|++.|+.+|+.. .+.+||+|...+.
T Consensus 530 ~~enk~~~~C~lc~d~----aed~i~s~ChH~FCrlCi~eyv~~f~~~~nvtCP~C~i~Ls 586 (791)
T KOG1002|consen 530 PDENKGEVECGLCHDP----AEDYIESSCHHKFCRLCIKEYVESFMENNNVTCPVCHIGLS 586 (791)
T ss_pred CccccCceeecccCCh----hhhhHhhhhhHHHHHHHHHHHHHhhhcccCCCCcccccccc
Confidence 3467778899999984 345677889999999999998753 4578999998875
No 98
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=85.98 E-value=0.36 Score=30.32 Aligned_cols=24 Identities=33% Similarity=0.908 Sum_probs=18.1
Q ss_pred eeecCCCCccccc-cccCcCCCCcc
Q 021022 121 QVICSLCGTEQKV-QQVCVNCGVCM 144 (318)
Q Consensus 121 ~v~C~~C~~eQ~v-~~~C~~Cg~~f 144 (318)
++.|..|+++-+. +..|++||+.+
T Consensus 2 ~~~Cp~Cg~~~~~~~~fC~~CG~~L 26 (26)
T PF13248_consen 2 EMFCPNCGAEIDPDAKFCPNCGAKL 26 (26)
T ss_pred cCCCcccCCcCCcccccChhhCCCC
Confidence 4678899987444 57899999864
No 99
>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=85.85 E-value=0.27 Score=41.07 Aligned_cols=36 Identities=25% Similarity=0.521 Sum_probs=25.2
Q ss_pred CcceEEcCCCCCCccccceeeeccCCCCCCccccccCC
Q 021022 281 KKVWILCNDCGKTSNVQFHVLAQKCPNCKSYNTRLTRG 318 (318)
Q Consensus 281 ~~v~IlCnDC~~~s~v~~H~lg~KC~~C~SyNT~~~~~ 318 (318)
..+...|++|+....+..+. ..||.|+|++.+.++|
T Consensus 67 ~p~~~~C~~Cg~~~~~~~~~--~~CP~Cgs~~~~i~~G 102 (113)
T PF01155_consen 67 VPARARCRDCGHEFEPDEFD--FSCPRCGSPDVEIISG 102 (113)
T ss_dssp E--EEEETTTS-EEECHHCC--HH-SSSSSS-EEEEES
T ss_pred cCCcEECCCCCCEEecCCCC--CCCcCCcCCCcEEccC
Confidence 35678899999988776554 5799999999888776
No 100
>KOG2660 consensus Locus-specific chromosome binding proteins [Function unknown]
Probab=85.76 E-value=0.22 Score=49.13 Aligned_cols=49 Identities=29% Similarity=0.673 Sum_probs=40.3
Q ss_pred CCCCCCcccccccccCCceeEEcCCCCccchHHHHHHHhcCCCCCCCCCcccC
Q 021022 204 AMHHDCPVCCEYLFETRQDVIVLPCGHTIHKNCLKEMREHHQYACPICSKSVC 256 (318)
Q Consensus 204 ~~~~~CpIClE~lf~s~~~v~~LpCGH~fH~~Cl~~wl~~~~~~CPiCrks~~ 256 (318)
..+..|++|..||-+. ..+.-|=|+|++.||.++|.. ...||.|.-.+.
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 4467899999987663 335569999999999999985 688999998876
No 101
>KOG2114 consensus Vacuolar assembly/sorting protein PEP5/VPS11 [Intracellular trafficking, secretion, and vesicular transport]
Probab=85.37 E-value=0.61 Score=51.09 Aligned_cols=42 Identities=29% Similarity=0.728 Sum_probs=31.3
Q ss_pred CCcccccccccCCceeEEcCCCCccchHHHHHHHhcCCCCCCCCCcccC
Q 021022 208 DCPVCCEYLFETRQDVIVLPCGHTIHKNCLKEMREHHQYACPICSKSVC 256 (318)
Q Consensus 208 ~CpIClE~lf~s~~~v~~LpCGH~fH~~Cl~~wl~~~~~~CPiCrks~~ 256 (318)
.|..|--.|- -|.+-..|||.||+.|+. .+...||-|+-.+.
T Consensus 842 kCs~C~~~Ld---lP~VhF~CgHsyHqhC~e----~~~~~CP~C~~e~~ 883 (933)
T KOG2114|consen 842 KCSACEGTLD---LPFVHFLCGHSYHQHCLE----DKEDKCPKCLPELR 883 (933)
T ss_pred eecccCCccc---cceeeeecccHHHHHhhc----cCcccCCccchhhh
Confidence 6777764332 267777899999999999 23477999998543
No 102
>PF03854 zf-P11: P-11 zinc finger; InterPro: IPR003224 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. The RING-finger is a specialised type of Zn-finger of 40 to 60 residues that binds two atoms of zinc, and is probably involved in mediating protein-protein interactions [, , ]. There are two different variants, the C3HC4-type and a C3H2C3-type, which is clearly related despite the different cysteine/histidine pattern. The latter type is sometimes referred to as 'RING-H2 finger'. The RING domain is a protein interaction domain which has been implicated in a range of diverse biological processes. Several 3D-structures for RING-fingers are known [, ]. The 3D structure of the zinc ligation system is unique to the RING domain and is referred to as the 'cross-brace' motif. The spacing of the cysteines in such a domain is: C-x(2)-C-x(9 to 39)-C-x(1 to 3)-H-x(2 to 3)-C-x(2)-C-x(4 to 48)-C-x(2)-C Metal ligand pairs one and three co-ordinate to bind one zinc ion, whilst pairs two and four bind the second. This entry represents RING finger protein Z, a small polypeptide found in some negative-strand RNA viruses including Lassa fever virus, which plays a crucial role in virion assembly and budding. RING finger Z has been shown to interact with several host proteins, including promyelocytic leukemia protein and the eukaryotic translation initiation factor 4E [, ]. It is sufficient in the absence of any other viral proteins to release virus-like particles from the infected cell []. This protein is also responsible for arenavirus superinfection exclusion; expression of this protein in a host cell strongly and specifically inhibits areanavirus transcription and replication []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003723 RNA binding, 0008270 zinc ion binding; PDB: 2KO5_A.
Probab=85.35 E-value=0.4 Score=35.03 Aligned_cols=32 Identities=34% Similarity=0.760 Sum_probs=22.8
Q ss_pred EcCCC-CccchHHHHHHHhcCCCCCCCCCcccCc
Q 021022 225 VLPCG-HTIHKNCLKEMREHHQYACPICSKSVCD 257 (318)
Q Consensus 225 ~LpCG-H~fH~~Cl~~wl~~~~~~CPiCrks~~d 257 (318)
.+.|. |.++..|++.+++. +..||||.+++..
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 66785 99999999999985 5889999998764
No 103
>KOG3161 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=84.77 E-value=0.38 Score=51.38 Aligned_cols=44 Identities=27% Similarity=0.704 Sum_probs=36.2
Q ss_pred CCCcccccccccCCceeEEcCCCCccchHHHHHHHhcCCCCCCCCCcc
Q 021022 207 HDCPVCCEYLFETRQDVIVLPCGHTIHKNCLKEMREHHQYACPICSKS 254 (318)
Q Consensus 207 ~~CpIClE~lf~s~~~v~~LpCGH~fH~~Cl~~wl~~~~~~CPiCrks 254 (318)
..|+||+..++.++...+.|-|||++++.|++... +.+|| |..+
T Consensus 12 l~c~ic~n~f~~~~~~Pvsl~cghtic~~c~~~ly---n~scp-~~~D 55 (861)
T KOG3161|consen 12 LLCDICLNLFVVQRLEPVSLQCGHTICGHCVQLLY---NASCP-TKRD 55 (861)
T ss_pred hhchHHHHHHHHHhcCcccccccchHHHHHHHhHh---hccCC-CCcc
Confidence 47999987778888888999999999999999874 36788 5543
No 104
>PRK04023 DNA polymerase II large subunit; Validated
Probab=84.69 E-value=0.78 Score=51.24 Aligned_cols=44 Identities=30% Similarity=0.569 Sum_probs=21.6
Q ss_pred cCcCCCCccceEecCccccccCCCCCCeeecCCCCceeecCCcceeeccCccc
Q 021022 136 VCVNCGVCMGEYFCESCKLFDDDTSKKQYHCDGCGICRIGGCDNFFHCNKCRC 188 (318)
Q Consensus 136 ~C~~Cg~~f~~YfC~~Ckl~ddd~~k~~yHC~~CgiCR~G~~~~ffHC~~C~~ 188 (318)
.|+.||......+|+.|.-. ...+|.|+.||.--. -..|.+||.
T Consensus 628 fCpsCG~~t~~frCP~CG~~----Te~i~fCP~CG~~~~-----~y~CPKCG~ 671 (1121)
T PRK04023 628 KCPSCGKETFYRRCPFCGTH----TEPVYRCPRCGIEVE-----EDECEKCGR 671 (1121)
T ss_pred cCCCCCCcCCcccCCCCCCC----CCcceeCccccCcCC-----CCcCCCCCC
Confidence 45555555555555555322 345556666643322 133555554
No 105
>PRK00762 hypA hydrogenase nickel incorporation protein; Provisional
Probab=83.06 E-value=0.83 Score=38.90 Aligned_cols=37 Identities=30% Similarity=0.573 Sum_probs=26.4
Q ss_pred CcceEEcCCCCCCcccc-c---ee-eeccCCCCCCccccccCC
Q 021022 281 KKVWILCNDCGKTSNVQ-F---HV-LAQKCPNCKSYNTRLTRG 318 (318)
Q Consensus 281 ~~v~IlCnDC~~~s~v~-~---H~-lg~KC~~C~SyNT~~~~~ 318 (318)
..+...| +|+...... + |+ ....||.|||++...++|
T Consensus 67 vp~~~~C-~Cg~~~~~~~~~~~~~~~~~~CP~Cgs~~~~i~~G 108 (124)
T PRK00762 67 IPVEIEC-ECGYEGVVDEDEIDHYAAVIECPVCGNKRAHILGG 108 (124)
T ss_pred cCeeEEe-eCcCcccccccchhccccCCcCcCCCCCCCEEecC
Confidence 3567889 999875432 1 11 235799999999998876
No 106
>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=81.36 E-value=0.98 Score=37.92 Aligned_cols=26 Identities=35% Similarity=0.953 Sum_probs=20.1
Q ss_pred cccCcCCCCccceEecCccccccCCCCCCeeecCCCCc
Q 021022 134 QQVCVNCGVCMGEYFCESCKLFDDDTSKKQYHCDGCGI 171 (318)
Q Consensus 134 ~~~C~~Cg~~f~~YfC~~Ckl~ddd~~k~~yHC~~Cgi 171 (318)
...|++||+ ||| |.+|.+-.|++||.
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 467999998 557 45688999999974
No 107
>COG0375 HybF Zn finger protein HypA/HybF (possibly regulating hydrogenase expression) [General function prediction only]
Probab=81.04 E-value=1.3 Score=37.83 Aligned_cols=36 Identities=31% Similarity=0.632 Sum_probs=29.1
Q ss_pred CcceEEcCCCCCCccccceeeeccCCCCCCccccccCC
Q 021022 281 KKVWILCNDCGKTSNVQFHVLAQKCPNCKSYNTRLTRG 318 (318)
Q Consensus 281 ~~v~IlCnDC~~~s~v~~H~lg~KC~~C~SyNT~~~~~ 318 (318)
.++.+.|-+|+......-|.+. ||.|+|-|.++++|
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 3578899999887766655554 99999999999876
No 108
>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=80.07 E-value=0.61 Score=44.61 Aligned_cols=51 Identities=25% Similarity=0.621 Sum_probs=41.0
Q ss_pred CCCCcccccccccCCceeEEc-C-CCCccchHHHHHHHhcCCCCCC--CCCcccC
Q 021022 206 HHDCPVCCEYLFETRQDVIVL-P-CGHTIHKNCLKEMREHHQYACP--ICSKSVC 256 (318)
Q Consensus 206 ~~~CpIClE~lf~s~~~v~~L-p-CGH~fH~~Cl~~wl~~~~~~CP--iCrks~~ 256 (318)
+..||||..+.+.+++-..++ | |=|.++.+|.+..++.+.-.|| -|.+-+.
T Consensus 10 d~~CPvCksDrYLnPdik~linPECyHrmCESCvdRIFs~GpAqCP~~gC~kILR 64 (314)
T COG5220 10 DRRCPVCKSDRYLNPDIKILINPECYHRMCESCVDRIFSRGPAQCPYKGCGKILR 64 (314)
T ss_pred cccCCccccccccCCCeEEEECHHHHHHHHHHHHHHHhcCCCCCCCCccHHHHHH
Confidence 458999998888876533333 6 9999999999999988878899 8887654
No 109
>PHA03096 p28-like protein; Provisional
Probab=80.00 E-value=1 Score=43.78 Aligned_cols=47 Identities=17% Similarity=0.277 Sum_probs=31.8
Q ss_pred CCCcccccccccC---CceeEEc-CCCCccchHHHHHHHhcC--CCCCCCCCc
Q 021022 207 HDCPVCCEYLFET---RQDVIVL-PCGHTIHKNCLKEMREHH--QYACPICSK 253 (318)
Q Consensus 207 ~~CpIClE~lf~s---~~~v~~L-pCGH~fH~~Cl~~wl~~~--~~~CPiCrk 253 (318)
-.|.||+|..... ......| .|.|.|+..|+..|.... ..+||.|+.
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 5699999876543 1223345 599999999999998643 234555554
No 110
>KOG0309 consensus Conserved WD40 repeat-containing protein [Function unknown]
Probab=79.82 E-value=1.1 Score=48.70 Aligned_cols=44 Identities=23% Similarity=0.514 Sum_probs=30.9
Q ss_pred CCCCCCcccccccccCCceeEEcCCCCccchHHHHHHHhcCCCCCCC
Q 021022 204 AMHHDCPVCCEYLFETRQDVIVLPCGHTIHKNCLKEMREHHQYACPI 250 (318)
Q Consensus 204 ~~~~~CpIClE~lf~s~~~v~~LpCGH~fH~~Cl~~wl~~~~~~CPi 250 (318)
.....|.||--.+. +....-+.|||.+|..|+.+|+..+ -.||.
T Consensus 1026 ~~~~~C~~C~l~V~--gss~~Cg~C~Hv~H~sc~~eWf~~g-d~Cps 1069 (1081)
T KOG0309|consen 1026 GFTFQCAICHLAVR--GSSNFCGTCGHVGHTSCMMEWFRTG-DVCPS 1069 (1081)
T ss_pred cceeeeeeEeeEee--ccchhhccccccccHHHHHHHHhcC-CcCCC
Confidence 33445888864332 2344566899999999999999864 57873
No 111
>PF13240 zinc_ribbon_2: zinc-ribbon domain
Probab=79.80 E-value=0.91 Score=27.96 Aligned_cols=21 Identities=38% Similarity=0.956 Sum_probs=15.1
Q ss_pred cCCCCccccc-cccCcCCCCcc
Q 021022 124 CSLCGTEQKV-QQVCVNCGVCM 144 (318)
Q Consensus 124 C~~C~~eQ~v-~~~C~~Cg~~f 144 (318)
|..|+.+.+. +..|++||.++
T Consensus 2 Cp~CG~~~~~~~~fC~~CG~~l 23 (23)
T PF13240_consen 2 CPNCGAEIEDDAKFCPNCGTPL 23 (23)
T ss_pred CcccCCCCCCcCcchhhhCCcC
Confidence 6778777544 67788888764
No 112
>PRK14559 putative protein serine/threonine phosphatase; Provisional
Probab=79.68 E-value=1.2 Score=47.65 Aligned_cols=46 Identities=28% Similarity=0.723 Sum_probs=27.2
Q ss_pred eecCCCCccccc-cccCcCCCCccceEecCccccccCCCCCCeeecCCCC
Q 021022 122 VICSLCGTEQKV-QQVCVNCGVCMGEYFCESCKLFDDDTSKKQYHCDGCG 170 (318)
Q Consensus 122 v~C~~C~~eQ~v-~~~C~~Cg~~f~~YfC~~Ckl~ddd~~k~~yHC~~Cg 170 (318)
++|..|+.+-+. +..|++||..+..-.|+.|.---. ...-.|+.||
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 467777777554 466788877776556666644311 2233455555
No 113
>COG5222 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=79.51 E-value=1.2 Score=43.84 Aligned_cols=44 Identities=27% Similarity=0.733 Sum_probs=34.9
Q ss_pred CCCcccccccccCCceeEEcCCCCccchHHHHHHHhcCCCCCCCCCc
Q 021022 207 HDCPVCCEYLFETRQDVIVLPCGHTIHKNCLKEMREHHQYACPICSK 253 (318)
Q Consensus 207 ~~CpIClE~lf~s~~~v~~LpCGH~fH~~Cl~~wl~~~~~~CPiCrk 253 (318)
..||.|.-- .. .++.+--|||.|+.+||..-|....+.||.|.+
T Consensus 275 LkCplc~~L-lr--np~kT~cC~~~fc~eci~~al~dsDf~CpnC~r 318 (427)
T COG5222 275 LKCPLCHCL-LR--NPMKTPCCGHTFCDECIGTALLDSDFKCPNCSR 318 (427)
T ss_pred ccCcchhhh-hh--CcccCccccchHHHHHHhhhhhhccccCCCccc
Confidence 679999863 32 356665689999999999876656799999987
No 114
>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=78.91 E-value=1.3 Score=28.12 Aligned_cols=23 Identities=30% Similarity=0.778 Sum_probs=18.4
Q ss_pred ecCCCCccccc-cccCcCCCCccc
Q 021022 123 ICSLCGTEQKV-QQVCVNCGVCMG 145 (318)
Q Consensus 123 ~C~~C~~eQ~v-~~~C~~Cg~~f~ 145 (318)
.|..|+.+-+. +..|++||..|.
T Consensus 2 ~CP~C~~~V~~~~~~Cp~CG~~F~ 25 (26)
T PF10571_consen 2 TCPECGAEVPESAKFCPHCGYDFE 25 (26)
T ss_pred cCCCCcCCchhhcCcCCCCCCCCc
Confidence 37788888766 578999999986
No 115
>KOG4692 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=77.37 E-value=1.6 Score=43.86 Aligned_cols=51 Identities=22% Similarity=0.544 Sum_probs=41.1
Q ss_pred CCCCCCCCcccccccccCCceeEEcCCCCccchHHHHHHHhcCCCCCCCCCcccCc
Q 021022 202 EGAMHHDCPVCCEYLFETRQDVIVLPCGHTIHKNCLKEMREHHQYACPICSKSVCD 257 (318)
Q Consensus 202 e~~~~~~CpIClE~lf~s~~~v~~LpCGH~fH~~Cl~~wl~~~~~~CPiCrks~~d 257 (318)
..+.+..||||.-. ....+.-||||.=+..||.+.+. ....|=.|+.++.+
T Consensus 418 p~sEd~lCpICyA~----pi~Avf~PC~H~SC~~CI~qHlm-N~k~CFfCktTv~~ 468 (489)
T KOG4692|consen 418 PDSEDNLCPICYAG----PINAVFAPCSHRSCYGCITQHLM-NCKRCFFCKTTVID 468 (489)
T ss_pred CCcccccCcceecc----cchhhccCCCCchHHHHHHHHHh-cCCeeeEecceeee
Confidence 34667899999852 33457789999999999999987 45789999998875
No 116
>KOG2034 consensus Vacuolar sorting protein PEP3/VPS18 [Intracellular trafficking, secretion, and vesicular transport]
Probab=77.13 E-value=1.1 Score=49.22 Aligned_cols=43 Identities=26% Similarity=0.516 Sum_probs=31.9
Q ss_pred ccccCCCCCCCCcccccccccCCceeEEcCCCCccchHHHHHHHh
Q 021022 198 HPCVEGAMHHDCPVCCEYLFETRQDVIVLPCGHTIHKNCLKEMRE 242 (318)
Q Consensus 198 H~Cie~~~~~~CpIClE~lf~s~~~v~~LpCGH~fH~~Cl~~wl~ 242 (318)
+.+.--.-...|.+|.-.|+. ++-.+.||||.||++|+.+-..
T Consensus 809 ~ry~v~ep~d~C~~C~~~ll~--~pF~vf~CgH~FH~~Cl~~~v~ 851 (911)
T KOG2034|consen 809 QRYRVLEPQDSCDHCGRPLLI--KPFYVFPCGHCFHRDCLIRHVL 851 (911)
T ss_pred cceEEecCccchHHhcchhhc--CcceeeeccchHHHHHHHHHHH
Confidence 344333346789999976544 5778889999999999998654
No 117
>PHA00626 hypothetical protein
Probab=76.92 E-value=1.9 Score=32.59 Aligned_cols=7 Identities=43% Similarity=1.265 Sum_probs=4.0
Q ss_pred cCcCCCC
Q 021022 136 VCVNCGV 142 (318)
Q Consensus 136 ~C~~Cg~ 142 (318)
.||+||.
T Consensus 2 ~CP~CGS 8 (59)
T PHA00626 2 SCPKCGS 8 (59)
T ss_pred CCCCCCC
Confidence 3566665
No 118
>PRK14714 DNA polymerase II large subunit; Provisional
Probab=76.03 E-value=2.5 Score=48.46 Aligned_cols=32 Identities=34% Similarity=0.844 Sum_probs=17.5
Q ss_pred eecCCCCccccccccCcCCCCcc-ceEecCcccc
Q 021022 122 VICSLCGTEQKVQQVCVNCGVCM-GEYFCESCKL 154 (318)
Q Consensus 122 v~C~~C~~eQ~v~~~C~~Cg~~f-~~YfC~~Ckl 154 (318)
..|..|+++-+ ...|+.||... ..|+|+.|..
T Consensus 668 rkCPkCG~~t~-~~fCP~CGs~te~vy~CPsCGa 700 (1337)
T PRK14714 668 RRCPSCGTETY-ENRCPDCGTHTEPVYVCPDCGA 700 (1337)
T ss_pred EECCCCCCccc-cccCcccCCcCCCceeCccCCC
Confidence 55666666532 23666666655 3445666654
No 119
>PF12773 DZR: Double zinc ribbon
Probab=73.58 E-value=2.5 Score=29.75 Aligned_cols=32 Identities=34% Similarity=0.889 Sum_probs=17.4
Q ss_pred eeecCCCCcccc--c--cccCcCCCCcc--ceEecCcc
Q 021022 121 QVICSLCGTEQK--V--QQVCVNCGVCM--GEYFCESC 152 (318)
Q Consensus 121 ~v~C~~C~~eQ~--v--~~~C~~Cg~~f--~~YfC~~C 152 (318)
.-.|..|++..+ . ...|++||... +..||..|
T Consensus 12 ~~fC~~CG~~l~~~~~~~~~C~~Cg~~~~~~~~fC~~C 49 (50)
T PF12773_consen 12 AKFCPHCGTPLPPPDQSKKICPNCGAENPPNAKFCPNC 49 (50)
T ss_pred ccCChhhcCChhhccCCCCCCcCCcCCCcCCcCccCcc
Confidence 456777766655 2 24577776654 23444443
No 120
>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=73.15 E-value=2.6 Score=43.68 Aligned_cols=49 Identities=22% Similarity=0.658 Sum_probs=41.6
Q ss_pred eEcCCCCCeecCcchHhhhhcCCCcCccCCCCCCCccCceeecCCCCccccccccCcCCCCc
Q 021022 82 IRAPCCNEIFDCRHCHNEAMNNINVDQKLRHDIPRHEVNQVICSLCGTEQKVQQVCVNCGVC 143 (318)
Q Consensus 82 i~~pCC~~~y~Cr~CHde~~~~~~~~~~~~H~ldR~~v~~v~C~~C~~eQ~v~~~C~~Cg~~ 143 (318)
+.|.-||....|.+|.-.+. -|. ....+.|-.|+..+++...|++||..
T Consensus 214 ~~C~~Cg~~~~C~~C~~~l~---------~h~----~~~~l~Ch~Cg~~~~~~~~Cp~C~s~ 262 (505)
T TIGR00595 214 LLCRSCGYILCCPNCDVSLT---------YHK----KEGKLRCHYCGYQEPIPKTCPQCGSE 262 (505)
T ss_pred eEhhhCcCccCCCCCCCceE---------Eec----CCCeEEcCCCcCcCCCCCCCCCCCCC
Confidence 78999999999999986654 343 24589999999999999999999885
No 121
>KOG1001 consensus Helicase-like transcription factor HLTF/DNA helicase RAD5, DEAD-box superfamily [Transcription; Replication, recombination and repair]
Probab=72.00 E-value=2 Score=46.37 Aligned_cols=45 Identities=29% Similarity=0.856 Sum_probs=36.0
Q ss_pred CCCcccccccccCCceeEEcCCCCccchHHHHHHHhcCCC-CCCCCCcccC
Q 021022 207 HDCPVCCEYLFETRQDVIVLPCGHTIHKNCLKEMREHHQY-ACPICSKSVC 256 (318)
Q Consensus 207 ~~CpIClE~lf~s~~~v~~LpCGH~fH~~Cl~~wl~~~~~-~CPiCrks~~ 256 (318)
..|+||++ .+...+.+|||.|+.+|+.+.+..... .||+||..+.
T Consensus 455 ~~c~ic~~-----~~~~~it~c~h~~c~~c~~~~i~~~~~~~~~~cr~~l~ 500 (674)
T KOG1001|consen 455 HWCHICCD-----LDSFFITRCGHDFCVECLKKSIQQSENAPCPLCRNVLK 500 (674)
T ss_pred cccccccc-----cccceeecccchHHHHHHHhccccccCCCCcHHHHHHH
Confidence 78999998 235678899999999999998765434 4999996553
No 122
>KOG2272 consensus Focal adhesion protein PINCH-1, contains LIM domains [Signal transduction mechanisms; Cytoskeleton]
Probab=71.36 E-value=3.7 Score=39.68 Aligned_cols=128 Identities=20% Similarity=0.487 Sum_probs=65.8
Q ss_pred ecCcchHhhhhcCCCcCccCCCCCCCccCceeecCCCCccccccccCcCCCCccceEecCccccc-cCCC---CCCeeec
Q 021022 91 FDCRHCHNEAMNNINVDQKLRHDIPRHEVNQVICSLCGTEQKVQQVCVNCGVCMGEYFCESCKLF-DDDT---SKKQYHC 166 (318)
Q Consensus 91 y~Cr~CHde~~~~~~~~~~~~H~ldR~~v~~v~C~~C~~eQ~v~~~C~~Cg~~f~~YfC~~Ckl~-ddd~---~k~~yHC 166 (318)
|.|..|-..+. +-.+.|.+ .+++|-.|+....+ ..-|+|-|.+|+-. |+++ .-.+||
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 45666665554 22234433 46777777655443 34589999999744 5543 224454
Q ss_pred CCCCceeecCCcceeeccCccceeeccccccccccCCCCCCCCcccccccccCCceeEEcCCCCccchHHHHH----HHh
Q 021022 167 DGCGICRIGGCDNFFHCNKCRCCYSMLLKNSHPCVEGAMHHDCPVCCEYLFETRQDVIVLPCGHTIHKNCLKE----MRE 242 (318)
Q Consensus 167 ~~CgiCR~G~~~~ffHC~~C~~C~s~~l~~~H~Cie~~~~~~CpIClE~lf~s~~~v~~LpCGH~fH~~Cl~~----wl~ 242 (318)
-.-|.|.+||-=+....+ |-..+.-|+-|.+.|-- ++-..|.-.+-..=+.. |-
T Consensus 161 -----------~yHFkCt~C~keL~sdaR------evk~eLyClrChD~mgi----piCgaC~rpIeervi~amgKhWH- 218 (332)
T KOG2272|consen 161 -----------PYHFKCTTCGKELTSDAR------EVKGELYCLRCHDKMGI----PICGACRRPIEERVIFAMGKHWH- 218 (332)
T ss_pred -----------ccceecccccccccchhh------hhccceeccccccccCC----cccccccCchHHHHHHHhccccc-
Confidence 256888888876644221 11224444444442211 01111222222222221 32
Q ss_pred cCCCCCCCCCcccCchh
Q 021022 243 HHQYACPICSKSVCDMS 259 (318)
Q Consensus 243 ~~~~~CPiCrks~~d~~ 259 (318)
..++.|..|-|++.-..
T Consensus 219 veHFvCa~CekPFlGHr 235 (332)
T KOG2272|consen 219 VEHFVCAKCEKPFLGHR 235 (332)
T ss_pred hhheeehhcCCcccchh
Confidence 25688888888887543
No 123
>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=70.71 E-value=2.9 Score=30.15 Aligned_cols=42 Identities=29% Similarity=0.672 Sum_probs=19.6
Q ss_pred CCCcccccccccCCceeEEcCCCCccchHHHH--HHHh----cCCCCCCCCCcc
Q 021022 207 HDCPVCCEYLFETRQDVIVLPCGHTIHKNCLK--EMRE----HHQYACPICSKS 254 (318)
Q Consensus 207 ~~CpIClE~lf~s~~~v~~LpCGH~fH~~Cl~--~wl~----~~~~~CPiCrks 254 (318)
..|||-...|.. +++...|.|. +|++ .||+ .....||+|+++
T Consensus 3 L~CPls~~~i~~---P~Rg~~C~H~---~CFDl~~fl~~~~~~~~W~CPiC~~~ 50 (50)
T PF02891_consen 3 LRCPLSFQRIRI---PVRGKNCKHL---QCFDLESFLESNQRTPKWKCPICNKP 50 (50)
T ss_dssp SB-TTTSSB-SS---EEEETT--SS-----EEHHHHHHHHHHS---B-TTT---
T ss_pred eeCCCCCCEEEe---CccCCcCccc---ceECHHHHHHHhhccCCeECcCCcCc
Confidence 368888876533 7888899987 3433 3443 345679999874
No 124
>KOG1952 consensus Transcription factor NF-X1, contains NFX-type Zn2+-binding and R3H domains [Transcription]
Probab=69.95 E-value=2.5 Score=46.54 Aligned_cols=48 Identities=29% Similarity=0.668 Sum_probs=34.8
Q ss_pred CCCCcccccccccCCceeEEcCC---CCccchHHHHHHHhc------CCCCCCCCCcccC
Q 021022 206 HHDCPVCCEYLFETRQDVIVLPC---GHTIHKNCLKEMREH------HQYACPICSKSVC 256 (318)
Q Consensus 206 ~~~CpIClE~lf~s~~~v~~LpC---GH~fH~~Cl~~wl~~------~~~~CPiCrks~~ 256 (318)
...|.||.|.+..+. -++.| =|+||..||.+|... ...+||-|.....
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 568999999765432 24555 599999999999753 2356999995444
No 125
>PF05290 Baculo_IE-1: Baculovirus immediate-early protein (IE-0); InterPro: IPR007954 This entry contains the Baculovirus immediate-early protein IE-0.
Probab=69.30 E-value=3.2 Score=36.38 Aligned_cols=48 Identities=27% Similarity=0.670 Sum_probs=34.2
Q ss_pred CCCcccccccccCCceeEEc-C---CCCccchHHHHHHHhc--CCCCCCCCCcccCch
Q 021022 207 HDCPVCCEYLFETRQDVIVL-P---CGHTIHKNCLKEMREH--HQYACPICSKSVCDM 258 (318)
Q Consensus 207 ~~CpIClE~lf~s~~~v~~L-p---CGH~fH~~Cl~~wl~~--~~~~CPiCrks~~d~ 258 (318)
-.|-||.|- |. +.+.| | ||-.++..|....++. -...||+|+.|+-..
T Consensus 81 YeCnIC~et---S~-ee~FLKPneCCgY~iCn~Cya~LWK~~~~ypvCPvCkTSFKss 134 (140)
T PF05290_consen 81 YECNICKET---SA-EERFLKPNECCGYSICNACYANLWKFCNLYPVCPVCKTSFKSS 134 (140)
T ss_pred eeccCcccc---cc-hhhcCCcccccchHHHHHHHHHHHHHcccCCCCCccccccccc
Confidence 467888873 22 23344 2 8999999999997664 245799999998643
No 126
>KOG4367 consensus Predicted Zn-finger protein [Function unknown]
Probab=68.86 E-value=2.7 Score=43.48 Aligned_cols=33 Identities=30% Similarity=0.926 Sum_probs=27.7
Q ss_pred CCCCcccccccccCCceeEEcCCCCccchHHHHHHHh
Q 021022 206 HHDCPVCCEYLFETRQDVIVLPCGHTIHKNCLKEMRE 242 (318)
Q Consensus 206 ~~~CpIClE~lf~s~~~v~~LpCGH~fH~~Cl~~wl~ 242 (318)
+..||||.. +|. ++++|||||.+++.|....+.
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 455 578999999999999998764
No 127
>PF14446 Prok-RING_1: Prokaryotic RING finger family 1
Probab=68.11 E-value=5.6 Score=29.68 Aligned_cols=35 Identities=29% Similarity=0.759 Sum_probs=26.0
Q ss_pred CCCCCcccccccccCCceeEE-cCCCCccchHHHHHH
Q 021022 205 MHHDCPVCCEYLFETRQDVIV-LPCGHTIHKNCLKEM 240 (318)
Q Consensus 205 ~~~~CpIClE~lf~s~~~v~~-LpCGH~fH~~Cl~~w 240 (318)
+...|++|.+.+... +++++ .-||=.+|+.|....
T Consensus 4 ~~~~C~~Cg~~~~~~-dDiVvCp~CgapyHR~C~~~~ 39 (54)
T PF14446_consen 4 EGCKCPVCGKKFKDG-DDIVVCPECGAPYHRDCWEKA 39 (54)
T ss_pred cCccChhhCCcccCC-CCEEECCCCCCcccHHHHhhC
Confidence 456899999975544 44555 469999999997664
No 128
>KOG3053 consensus Uncharacterized conserved protein [Function unknown]
Probab=67.69 E-value=3.5 Score=39.87 Aligned_cols=71 Identities=24% Similarity=0.480 Sum_probs=44.9
Q ss_pred cCCCCCCCCcccccccccCCceeEEcCC---C--CccchHHHHHHHhcC-------CCCCCCCCcccCc-------hhHH
Q 021022 201 VEGAMHHDCPVCCEYLFETRQDVIVLPC---G--HTIHKNCLKEMREHH-------QYACPICSKSVCD-------MSKV 261 (318)
Q Consensus 201 ie~~~~~~CpIClE~lf~s~~~v~~LpC---G--H~fH~~Cl~~wl~~~-------~~~CPiCrks~~d-------~~~~ 261 (318)
.+...+..|=||+..-.+.+...-+=|| | |..|.+|+..|+..+ .-+||.|+....- .+..
T Consensus 15 ~~~e~eR~CWiCF~TdeDn~~a~WV~PCrCRGt~KWVHqsCL~rWiDEK~~~n~~q~V~C~QCqTEYiiv~P~l~~~~~~ 94 (293)
T KOG3053|consen 15 DNQELERCCWICFATDEDNRLAAWVHPCRCRGTTKWVHQSCLSRWIDEKQRGNPLQTVSCPQCQTEYIIVFPQLGPFDRV 94 (293)
T ss_pred CccccceeEEEEeccCcccchhhhcccccccCccHHHHHHHHHHHHhHHhcCCCCceeechhhcchheeeccccChHHHH
Confidence 3456678899999742222222233477 3 889999999998642 2359999988752 2334
Q ss_pred HHHhHHHHHc
Q 021022 262 WEKYDREIAA 271 (318)
Q Consensus 262 ~~~lD~~i~~ 271 (318)
.+.+|..+..
T Consensus 95 Le~~d~~i~r 104 (293)
T KOG3053|consen 95 LERLDILIFR 104 (293)
T ss_pred HHHhhhHHhh
Confidence 4555555543
No 129
>COG5109 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=67.08 E-value=4 Score=40.58 Aligned_cols=46 Identities=33% Similarity=0.746 Sum_probs=37.7
Q ss_pred CCCcccccccccCCceeEEcCCCCccchHHHHHHHhcC--CCCCCCCCc
Q 021022 207 HDCPVCCEYLFETRQDVIVLPCGHTIHKNCLKEMREHH--QYACPICSK 253 (318)
Q Consensus 207 ~~CpIClE~lf~s~~~v~~LpCGH~fH~~Cl~~wl~~~--~~~CPiCrk 253 (318)
..|||=.| +-+...+++.|.|||.+=.+-++..-+.+ +++||.|-.
T Consensus 337 FiCPVlKe-~~t~ENpP~ml~CgHVIskeal~~LS~nG~~~FKCPYCP~ 384 (396)
T COG5109 337 FICPVLKE-LCTDENPPVMLECGHVISKEALSVLSQNGVLSFKCPYCPE 384 (396)
T ss_pred eeccccHh-hhcccCCCeeeeccceeeHHHHHHHhhcCcEEeeCCCCCc
Confidence 47999887 56667789999999999999999986543 477999963
No 130
>PRK04023 DNA polymerase II large subunit; Validated
Probab=66.43 E-value=4.6 Score=45.47 Aligned_cols=49 Identities=27% Similarity=0.619 Sum_probs=36.7
Q ss_pred eeecCCCCccccccccCcCCCCc-cceEecCccccccCCCCCCeeecCCCCceeec
Q 021022 121 QVICSLCGTEQKVQQVCVNCGVC-MGEYFCESCKLFDDDTSKKQYHCDGCGICRIG 175 (318)
Q Consensus 121 ~v~C~~C~~eQ~v~~~C~~Cg~~-f~~YfC~~Ckl~ddd~~k~~yHC~~CgiCR~G 175 (318)
.-.|..|+++. +...|++||.. -.-|||+.|.-- -..|.|+.||.=...
T Consensus 626 ~RfCpsCG~~t-~~frCP~CG~~Te~i~fCP~CG~~-----~~~y~CPKCG~El~~ 675 (1121)
T PRK04023 626 RRKCPSCGKET-FYRRCPFCGTHTEPVYRCPRCGIE-----VEEDECEKCGREPTP 675 (1121)
T ss_pred CccCCCCCCcC-CcccCCCCCCCCCcceeCccccCc-----CCCCcCCCCCCCCCc
Confidence 45899999985 66799999974 577899999332 335889999964443
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=65.51 E-value=3.8 Score=35.57 Aligned_cols=27 Identities=22% Similarity=0.454 Sum_probs=20.2
Q ss_pred cccCcCCCCccceEecCccccccCCCCCCeeecCCCCce
Q 021022 134 QQVCVNCGVCMGEYFCESCKLFDDDTSKKQYHCDGCGIC 172 (318)
Q Consensus 134 ~~~C~~Cg~~f~~YfC~~Ckl~ddd~~k~~yHC~~CgiC 172 (318)
...|++||. ||| |.+|.+-.|++||.=
T Consensus 9 Kr~Cp~cg~----------kFY--DLnk~p~vcP~cg~~ 35 (129)
T TIGR02300 9 KRICPNTGS----------KFY--DLNRRPAVSPYTGEQ 35 (129)
T ss_pred cccCCCcCc----------ccc--ccCCCCccCCCcCCc
Confidence 457888888 556 456899999998753
No 132
>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]
Probab=64.15 E-value=5.8 Score=43.30 Aligned_cols=54 Identities=24% Similarity=0.568 Sum_probs=43.9
Q ss_pred eEcCCCCCeecCcchHhhhhcCCCcCccCCCCCCCccCceeecCCCCccccccccCcCCCCccceEe
Q 021022 82 IRAPCCNEIFDCRHCHNEAMNNINVDQKLRHDIPRHEVNQVICSLCGTEQKVQQVCVNCGVCMGEYF 148 (318)
Q Consensus 82 i~~pCC~~~y~Cr~CHde~~~~~~~~~~~~H~ldR~~v~~v~C~~C~~eQ~v~~~C~~Cg~~f~~Yf 148 (318)
+.|.-||..+.|++|=--+. -|. ....+.|-.|+..+++-..|++||...=+|+
T Consensus 436 l~C~~Cg~v~~Cp~Cd~~lt---------~H~----~~~~L~CH~Cg~~~~~p~~Cp~Cgs~~L~~~ 489 (730)
T COG1198 436 LLCRDCGYIAECPNCDSPLT---------LHK----ATGQLRCHYCGYQEPIPQSCPECGSEHLRAV 489 (730)
T ss_pred eecccCCCcccCCCCCcceE---------Eec----CCCeeEeCCCCCCCCCCCCCCCCCCCeeEEe
Confidence 88999999999999965543 232 2478999999999999999999999854444
No 133
>PRK14714 DNA polymerase II large subunit; Provisional
Probab=63.65 E-value=5.9 Score=45.54 Aligned_cols=33 Identities=30% Similarity=0.754 Sum_probs=25.6
Q ss_pred ccCcCCCCccceEecCccccccCCCCCCeeecCCCCc
Q 021022 135 QVCVNCGVCMGEYFCESCKLFDDDTSKKQYHCDGCGI 171 (318)
Q Consensus 135 ~~C~~Cg~~f~~YfC~~Ckl~ddd~~k~~yHC~~Cgi 171 (318)
-.|++||..-...||+.|.-. .+.+|+|+.||.
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 469999987777799999654 245788888876
No 134
>KOG1812 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=61.96 E-value=3.7 Score=41.35 Aligned_cols=51 Identities=29% Similarity=0.602 Sum_probs=33.9
Q ss_pred CCCCcccccccccCCceeEEcCCCCccchHHHHHHHhc-----CCCCCC--CCCcccC
Q 021022 206 HHDCPVCCEYLFETRQDVIVLPCGHTIHKNCLKEMREH-----HQYACP--ICSKSVC 256 (318)
Q Consensus 206 ~~~CpIClE~lf~s~~~v~~LpCGH~fH~~Cl~~wl~~-----~~~~CP--iCrks~~ 256 (318)
...|.||+...........++.|+|.|+.+|+.++++. ...+|| .|...+.
T Consensus 146 ~~~C~iC~~e~~~~~~~f~~~~C~H~fC~~C~k~~iev~~~~~~~~~C~~~~C~~~l~ 203 (384)
T KOG1812|consen 146 KEECGICFVEDPEAEDMFSVLKCGHRFCKDCVKQHIEVKLLSGTVIRCPHDGCESRLT 203 (384)
T ss_pred cccCccCccccccHhhhHHHhcccchhhhHHhHHHhhhhhccCCCccCCCCCCCccCC
Confidence 56899999333333233337789999999999999873 345575 3444443
No 135
>PRK14559 putative protein serine/threonine phosphatase; Provisional
Probab=61.75 E-value=4.2 Score=43.73 Aligned_cols=34 Identities=29% Similarity=0.706 Sum_probs=18.7
Q ss_pred eeecCCCCccccccccCcCCCCcc--ceEecCccccc
Q 021022 121 QVICSLCGTEQKVQQVCVNCGVCM--GEYFCESCKLF 155 (318)
Q Consensus 121 ~v~C~~C~~eQ~v~~~C~~Cg~~f--~~YfC~~Ckl~ 155 (318)
.-.|..|++.... ..|++||+.. +.-||+.|-..
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 3456666665432 3566666543 55566666543
No 136
>PF14569 zf-UDP: Zinc-binding RING-finger; PDB: 1WEO_A.
Probab=61.55 E-value=8.2 Score=30.96 Aligned_cols=53 Identities=17% Similarity=0.434 Sum_probs=24.6
Q ss_pred CCCCCCcccccccccCCceeEEc---CCCCccchHHHHHHHhcCCCCCCCCCcccC
Q 021022 204 AMHHDCPVCCEYLFETRQDVIVL---PCGHTIHKNCLKEMREHHQYACPICSKSVC 256 (318)
Q Consensus 204 ~~~~~CpIClE~lf~s~~~v~~L---pCGH~fH~~Cl~~wl~~~~~~CPiCrks~~ 256 (318)
.....|.||.|.+-.....-.+. -|+--.++.|+.--.+.++..||.|+..+.
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 34578999999875554443343 568889999999888888889999996654
No 137
>PRK14873 primosome assembly protein PriA; Provisional
Probab=60.59 E-value=6.3 Score=42.46 Aligned_cols=49 Identities=22% Similarity=0.483 Sum_probs=39.9
Q ss_pred eEcCCCCCeecCcchHhhhhcCCCcCccCCCCCCCccCceeecCCCCccccccccCcCCCCcc
Q 021022 82 IRAPCCNEIFDCRHCHNEAMNNINVDQKLRHDIPRHEVNQVICSLCGTEQKVQQVCVNCGVCM 144 (318)
Q Consensus 82 i~~pCC~~~y~Cr~CHde~~~~~~~~~~~~H~ldR~~v~~v~C~~C~~eQ~v~~~C~~Cg~~f 144 (318)
+.|.-|+....|.+|.--+. -|. ....+.|-.|+..+ ....|++||...
T Consensus 384 l~C~~Cg~~~~C~~C~~~L~---------~h~----~~~~l~Ch~CG~~~-~p~~Cp~Cgs~~ 432 (665)
T PRK14873 384 LACARCRTPARCRHCTGPLG---------LPS----AGGTPRCRWCGRAA-PDWRCPRCGSDR 432 (665)
T ss_pred eEhhhCcCeeECCCCCCcee---------Eec----CCCeeECCCCcCCC-cCccCCCCcCCc
Confidence 89999999999999997665 242 23578999999976 578999999863
No 138
>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=60.33 E-value=6.8 Score=29.24 Aligned_cols=27 Identities=30% Similarity=0.760 Sum_probs=17.2
Q ss_pred cccCcCCCCccceEecCccccccCCCCCCeeecCCCCc
Q 021022 134 QQVCVNCGVCMGEYFCESCKLFDDDTSKKQYHCDGCGI 171 (318)
Q Consensus 134 ~~~C~~Cg~~f~~YfC~~Ckl~ddd~~k~~yHC~~Cgi 171 (318)
++.|+.||..... ......|.|+.||.
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 5678888877655 23445666666664
No 139
>PRK05580 primosome assembly protein PriA; Validated
Probab=60.02 E-value=6.4 Score=42.29 Aligned_cols=50 Identities=22% Similarity=0.608 Sum_probs=42.0
Q ss_pred eEcCCCCCeecCcchHhhhhcCCCcCccCCCCCCCccCceeecCCCCccccccccCcCCCCcc
Q 021022 82 IRAPCCNEIFDCRHCHNEAMNNINVDQKLRHDIPRHEVNQVICSLCGTEQKVQQVCVNCGVCM 144 (318)
Q Consensus 82 i~~pCC~~~y~Cr~CHde~~~~~~~~~~~~H~ldR~~v~~v~C~~C~~eQ~v~~~C~~Cg~~f 144 (318)
+.|.-|+....|.+|.-.+. -|. ....+.|-.|+..+++...|++||...
T Consensus 382 ~~C~~Cg~~~~C~~C~~~l~---------~h~----~~~~l~Ch~Cg~~~~~~~~Cp~Cg~~~ 431 (679)
T PRK05580 382 LLCRDCGWVAECPHCDASLT---------LHR----FQRRLRCHHCGYQEPIPKACPECGSTD 431 (679)
T ss_pred eEhhhCcCccCCCCCCCcee---------EEC----CCCeEECCCCcCCCCCCCCCCCCcCCe
Confidence 88999999999999987654 242 246799999999999999999998874
No 140
>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=59.80 E-value=5.9 Score=37.91 Aligned_cols=48 Identities=31% Similarity=0.682 Sum_probs=22.8
Q ss_pred CceeecCCCCcccccc-ccCcCCCCccceEecCccccc--cCCCCCCeeecCCCC
Q 021022 119 VNQVICSLCGTEQKVQ-QVCVNCGVCMGEYFCESCKLF--DDDTSKKQYHCDGCG 170 (318)
Q Consensus 119 v~~v~C~~C~~eQ~v~-~~C~~Cg~~f~~YfC~~Ckl~--ddd~~k~~yHC~~Cg 170 (318)
.+-..|+.|+++-.+. ..|++||..-..-+ .+| ++++.-.++.|+.||
T Consensus 195 ~R~L~Cs~C~t~W~~~R~~Cp~Cg~~~~~~l----~~~~~e~~~~~rve~C~~C~ 245 (290)
T PF04216_consen 195 KRYLHCSLCGTEWRFVRIKCPYCGNTDHEKL----EYFTVEGEPAYRVEVCESCG 245 (290)
T ss_dssp EEEEEETTT--EEE--TTS-TTT---SS-EE----E--------SEEEEEETTTT
T ss_pred cEEEEcCCCCCeeeecCCCCcCCCCCCCcce----eeEecCCCCcEEEEECCccc
Confidence 4679999999998874 67999998876654 444 333344455555543
No 141
>KOG2462 consensus C2H2-type Zn-finger protein [Transcription]
Probab=58.89 E-value=9 Score=37.26 Aligned_cols=119 Identities=27% Similarity=0.554 Sum_probs=68.6
Q ss_pred CCccceEecCcc-ccccCCC---CCCeeecCCCCceeecCCcceeeccCccceeec-c-cc---ccccccCCCCCCCCcc
Q 021022 141 GVCMGEYFCESC-KLFDDDT---SKKQYHCDGCGICRIGGCDNFFHCNKCRCCYSM-L-LK---NSHPCVEGAMHHDCPV 211 (318)
Q Consensus 141 g~~f~~YfC~~C-kl~ddd~---~k~~yHC~~CgiCR~G~~~~ffHC~~C~~C~s~-~-l~---~~H~Cie~~~~~~CpI 211 (318)
...-++|-|+.| |-|.... .-+|+||+- .-..-|+|..|+-=|.. - |+ -+|. +...|+|
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 344578889999 6775543 237899842 12578999999988743 1 21 3444 4567999
Q ss_pred cccccccCCceeEEcCCCCc-cchHHHHHHHhcCCCCCCCCCcccCchhHHHHHhHHHHHcCCCChhhhcCcceEEcCCC
Q 021022 212 CCEYLFETRQDVIVLPCGHT-IHKNCLKEMREHHQYACPICSKSVCDMSKVWEKYDREIAATPMPEAYLNKKVWILCNDC 290 (318)
Q Consensus 212 ClE~lf~s~~~v~~LpCGH~-fH~~Cl~~wl~~~~~~CPiCrks~~d~~~~~~~lD~~i~~~pmPeey~~~~v~IlCnDC 290 (318)
|... |... +|-=||. .|. -..-|.||.|+|.|.|.+. |..-++.-. +.+ ...|..|
T Consensus 193 CGKa-FSRP----WLLQGHiRTHT-------GEKPF~C~hC~kAFADRSN----LRAHmQTHS------~~K-~~qC~~C 249 (279)
T KOG2462|consen 193 CGKA-FSRP----WLLQGHIRTHT-------GEKPFSCPHCGKAFADRSN----LRAHMQTHS------DVK-KHQCPRC 249 (279)
T ss_pred cccc-ccch----HHhhccccccc-------CCCCccCCcccchhcchHH----HHHHHHhhc------CCc-cccCcch
Confidence 9873 5421 1111221 110 0134789999999999753 444333221 222 4557777
Q ss_pred CCCc
Q 021022 291 GKTS 294 (318)
Q Consensus 291 ~~~s 294 (318)
+++.
T Consensus 250 ~KsF 253 (279)
T KOG2462|consen 250 GKSF 253 (279)
T ss_pred hhHH
Confidence 7643
No 142
>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional
Probab=58.51 E-value=7.3 Score=29.61 Aligned_cols=34 Identities=24% Similarity=0.628 Sum_probs=24.8
Q ss_pred CceeecCCCCccccccccCcCCCCccceEecCcccc
Q 021022 119 VNQVICSLCGTEQKVQQVCVNCGVCMGEYFCESCKL 154 (318)
Q Consensus 119 v~~v~C~~C~~eQ~v~~~C~~Cg~~f~~YfC~~Ckl 154 (318)
.....|..|+.+-- ..|..|....+.|-|++|-|
T Consensus 23 ~~~F~CPnCG~~~I--~RC~~CRk~~~~Y~CP~CGF 56 (59)
T PRK14890 23 AVKFLCPNCGEVII--YRCEKCRKQSNPYTCPKCGF 56 (59)
T ss_pred cCEeeCCCCCCeeE--eechhHHhcCCceECCCCCC
Confidence 45777888876422 35888888888888888876
No 143
>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=56.51 E-value=4.3 Score=39.40 Aligned_cols=51 Identities=25% Similarity=0.664 Sum_probs=29.8
Q ss_pred CCeecCcchHhhhhcCCCcCccCCCCCCCccCceeecCCCCccccccccCcCCCCccceEecCcccc
Q 021022 88 NEIFDCRHCHNEAMNNINVDQKLRHDIPRHEVNQVICSLCGTEQKVQQVCVNCGVCMGEYFCESCKL 154 (318)
Q Consensus 88 ~~~y~Cr~CHde~~~~~~~~~~~~H~ldR~~v~~v~C~~C~~eQ~v~~~C~~Cg~~f~~YfC~~Ckl 154 (318)
|++|.|-+|++-+-. +..+.-.+ .|+....-.-.|.+|+. +|.|.|..||.
T Consensus 140 Grif~CsfC~~flCE--------DDQFEHQA-------sCQvLe~E~~KC~SCNr-lGq~sCLRCK~ 190 (314)
T PF06524_consen 140 GRIFKCSFCDNFLCE--------DDQFEHQA-------SCQVLESETFKCQSCNR-LGQYSCLRCKI 190 (314)
T ss_pred CeEEEeecCCCeeec--------cchhhhhh-------hhhhhhccccccccccc-ccchhhhheee
Confidence 568888888876642 22222111 14444444455777764 78888888874
No 144
>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=56.25 E-value=7.9 Score=24.93 Aligned_cols=20 Identities=35% Similarity=0.894 Sum_probs=13.7
Q ss_pred CCCceeecCCcc-eeeccCcc
Q 021022 168 GCGICRIGGCDN-FFHCNKCR 187 (318)
Q Consensus 168 ~CgiCR~G~~~~-ffHC~~C~ 187 (318)
.|++||.-.... +|+|..|+
T Consensus 2 ~C~~C~~~~~~~~~Y~C~~c~ 22 (30)
T PF03107_consen 2 WCDVCRRKIDGFYFYHCSECC 22 (30)
T ss_pred CCCCCCCCcCCCEeEEeCCCC
Confidence 467776654444 88888887
No 145
>KOG0827 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=55.42 E-value=1.1 Score=45.35 Aligned_cols=52 Identities=19% Similarity=0.418 Sum_probs=43.5
Q ss_pred CCCCCcccccccccCCceeEEcCCCCccchHHHHHHHhcCCCCCCCCCcccCc
Q 021022 205 MHHDCPVCCEYLFETRQDVIVLPCGHTIHKNCLKEMREHHQYACPICSKSVCD 257 (318)
Q Consensus 205 ~~~~CpIClE~lf~s~~~v~~LpCGH~fH~~Cl~~wl~~~~~~CPiCrks~~d 257 (318)
.-..+.||.+.+...-+....+.|||.+|..+|.+||.. ...+|.|++.+..
T Consensus 195 lv~sl~I~~~slK~~y~k~~~~~~g~~~~~~kL~k~L~~-~~kl~~~~rel~~ 246 (465)
T KOG0827|consen 195 LVGSLSICFESLKQNYDKISAIVCGHIYHHGKLSKWLAT-KRKLPSCRRELPK 246 (465)
T ss_pred HHhhhHhhHHHHHHHHHHHHHHhhcccchhhHHHHHHHH-HHHhHHHHhhhhh
Confidence 345799999887665566778899999999999999975 5789999999874
No 146
>KOG2068 consensus MOT2 transcription factor [Transcription]
Probab=55.33 E-value=9.3 Score=37.97 Aligned_cols=53 Identities=28% Similarity=0.600 Sum_probs=40.3
Q ss_pred CCCCCCcccccccccCCceeEEcCCCCccchHHHHHHHhcCCCCCCCCCcccCc
Q 021022 204 AMHHDCPVCCEYLFETRQDVIVLPCGHTIHKNCLKEMREHHQYACPICSKSVCD 257 (318)
Q Consensus 204 ~~~~~CpIClE~lf~s~~~v~~LpCGH~fH~~Cl~~wl~~~~~~CPiCrks~~d 257 (318)
+-...||||-+++..........|||+.++..|+..-.. .+.+||.||++...
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 335789999997655444445557899999999998876 46899999987753
No 147
>COG3809 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=54.63 E-value=9.4 Score=30.80 Aligned_cols=31 Identities=29% Similarity=0.518 Sum_probs=20.7
Q ss_pred CCCCCCCcccCchhHHHHHhHHHHHc--CCCChhhhc
Q 021022 246 YACPICSKSVCDMSKVWEKYDREIAA--TPMPEAYLN 280 (318)
Q Consensus 246 ~~CPiCrks~~d~~~~~~~lD~~i~~--~pmPeey~~ 280 (318)
-.||-||..++|... ||.+|+. .|.|.+|+.
T Consensus 22 D~CPrCrGVWLDrGE----LdKli~r~r~pqpa~ys~ 54 (88)
T COG3809 22 DYCPRCRGVWLDRGE----LDKLIERSRYPQPAEYSQ 54 (88)
T ss_pred eeCCccccEeecchh----HHHHHHHhcCCCCcccCC
Confidence 359999999999754 5555553 345555543
No 148
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=54.29 E-value=12 Score=26.14 Aligned_cols=8 Identities=38% Similarity=0.974 Sum_probs=4.9
Q ss_pred eeecCCCC
Q 021022 163 QYHCDGCG 170 (318)
Q Consensus 163 ~yHC~~Cg 170 (318)
..+|+.||
T Consensus 21 ~~~Cp~CG 28 (46)
T PRK00398 21 GVRCPYCG 28 (46)
T ss_pred ceECCCCC
Confidence 55666665
No 149
>PF14353 CpXC: CpXC protein
Probab=51.99 E-value=3.1 Score=34.85 Aligned_cols=56 Identities=16% Similarity=0.390 Sum_probs=30.0
Q ss_pred CCCCCCCcccCchhHHHHHhHHHHHcCCCChhhhcCcceEEcCCCCCCccccceeeec
Q 021022 246 YACPICSKSVCDMSKVWEKYDREIAATPMPEAYLNKKVWILCNDCGKTSNVQFHVLAQ 303 (318)
Q Consensus 246 ~~CPiCrks~~d~~~~~~~lD~~i~~~pmPeey~~~~v~IlCnDC~~~s~v~~H~lg~ 303 (318)
.+||.|++.+... .|..++......-...-..+..-.+.|..|+.+..+.|=+|++
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 5799999988631 1222211000000001123334578899999988777666654
No 150
>KOG1100 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=51.39 E-value=7.2 Score=36.16 Aligned_cols=39 Identities=33% Similarity=0.766 Sum_probs=29.0
Q ss_pred CcccccccccCCceeEEcCCCCc-cchHHHHHHHhcCCCCCCCCCcccC
Q 021022 209 CPVCCEYLFETRQDVIVLPCGHT-IHKNCLKEMREHHQYACPICSKSVC 256 (318)
Q Consensus 209 CpIClE~lf~s~~~v~~LpCGH~-fH~~Cl~~wl~~~~~~CPiCrks~~ 256 (318)
|-.|.+. ...|.+|||-|. ++..|-.. + ..||+|+....
T Consensus 161 Cr~C~~~----~~~VlllPCrHl~lC~~C~~~-~----~~CPiC~~~~~ 200 (207)
T KOG1100|consen 161 CRKCGER----EATVLLLPCRHLCLCGICDES-L----RICPICRSPKT 200 (207)
T ss_pred ceecCcC----CceEEeecccceEeccccccc-C----ccCCCCcChhh
Confidence 9999873 345889999876 77778765 2 34999997653
No 151
>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 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=50.96 E-value=10 Score=21.58 Aligned_cols=18 Identities=39% Similarity=0.881 Sum_probs=11.7
Q ss_pred CCCCCCCcccCchhHHHH
Q 021022 246 YACPICSKSVCDMSKVWE 263 (318)
Q Consensus 246 ~~CPiCrks~~d~~~~~~ 263 (318)
+.||+|.+.+......++
T Consensus 1 ~~C~~C~~~~~~~~~l~~ 18 (24)
T PF13894_consen 1 FQCPICGKSFRSKSELRQ 18 (24)
T ss_dssp EE-SSTS-EESSHHHHHH
T ss_pred CCCcCCCCcCCcHHHHHH
Confidence 469999999988765443
No 153
>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=50.83 E-value=14 Score=25.49 Aligned_cols=7 Identities=57% Similarity=1.322 Sum_probs=3.7
Q ss_pred CcCCCCc
Q 021022 137 CVNCGVC 143 (318)
Q Consensus 137 C~~Cg~~ 143 (318)
||+||..
T Consensus 3 Cp~Cg~~ 9 (43)
T PF08271_consen 3 CPNCGSK 9 (43)
T ss_dssp BTTTSSS
T ss_pred CcCCcCC
Confidence 5555553
No 154
>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=50.77 E-value=12 Score=26.49 Aligned_cols=30 Identities=23% Similarity=0.518 Sum_probs=19.1
Q ss_pred eEEcCCCCCCcccccee---eeccCCCCCCccc
Q 021022 284 WILCNDCGKTSNVQFHV---LAQKCPNCKSYNT 313 (318)
Q Consensus 284 ~IlCnDC~~~s~v~~H~---lg~KC~~C~SyNT 313 (318)
...|.+|+...++-..+ ....|+.|||-+.
T Consensus 5 ey~C~~Cg~~fe~~~~~~~~~~~~CP~Cg~~~~ 37 (52)
T TIGR02605 5 EYRCTACGHRFEVLQKMSDDPLATCPECGGEKL 37 (52)
T ss_pred EEEeCCCCCEeEEEEecCCCCCCCCCCCCCCce
Confidence 45688888766553221 1236999998776
No 155
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=50.32 E-value=13 Score=26.03 Aligned_cols=31 Identities=19% Similarity=0.415 Sum_probs=19.4
Q ss_pred ceEEcCCCCCCccccceeeeccCCCCCCccc
Q 021022 283 VWILCNDCGKTSNVQFHVLAQKCPNCKSYNT 313 (318)
Q Consensus 283 v~IlCnDC~~~s~v~~H~lg~KC~~C~SyNT 313 (318)
....|.+|++.....-.....+|+.||+.-.
T Consensus 2 ~~y~C~~CG~~~~~~~~~~~~~Cp~CG~~~~ 32 (46)
T PRK00398 2 AEYKCARCGREVELDEYGTGVRCPYCGYRIL 32 (46)
T ss_pred CEEECCCCCCEEEECCCCCceECCCCCCeEE
Confidence 3567888887653333333678888887543
No 156
>COG1656 Uncharacterized conserved protein [Function unknown]
Probab=49.52 E-value=12 Score=33.74 Aligned_cols=51 Identities=24% Similarity=0.402 Sum_probs=35.1
Q ss_pred CCCCCCCCcccCchhHHHHHhHHHHHcCCCChhhhcCcceEEcCCCCCCccccceee
Q 021022 245 QYACPICSKSVCDMSKVWEKYDREIAATPMPEAYLNKKVWILCNDCGKTSNVQFHVL 301 (318)
Q Consensus 245 ~~~CPiCrks~~d~~~~~~~lD~~i~~~pmPeey~~~~v~IlCnDC~~~s~v~~H~l 301 (318)
-.+||.|+..+...+. +++.+.-.|..|.+......|..|++.-+..-||=
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 3579999998876432 22223322445666667788999999988888874
No 157
>KOG2066 consensus Vacuolar assembly/sorting protein VPS41 [Intracellular trafficking, secretion, and vesicular transport]
Probab=48.97 E-value=6.5 Score=43.13 Aligned_cols=45 Identities=36% Similarity=0.680 Sum_probs=31.8
Q ss_pred CCCCcccccccccCC---ceeEEcCCCCccchHHHHHHHhcCCCCCCCCC
Q 021022 206 HHDCPVCCEYLFETR---QDVIVLPCGHTIHKNCLKEMREHHQYACPICS 252 (318)
Q Consensus 206 ~~~CpIClE~lf~s~---~~v~~LpCGH~fH~~Cl~~wl~~~~~~CPiCr 252 (318)
+..|.-|.+....+. ..++++.|||.||..|+....... .|-+|.
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 346777777655444 567899999999999999876532 255554
No 158
>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]
Probab=48.93 E-value=16 Score=39.92 Aligned_cols=48 Identities=27% Similarity=0.658 Sum_probs=32.6
Q ss_pred CCcc-CceeecCCCCccccccccCcCCCCcc------ceEecCccccccCCCCCCeeecCCCC
Q 021022 115 PRHE-VNQVICSLCGTEQKVQQVCVNCGVCM------GEYFCESCKLFDDDTSKKQYHCDGCG 170 (318)
Q Consensus 115 dR~~-v~~v~C~~C~~eQ~v~~~C~~Cg~~f------~~YfC~~Ckl~ddd~~k~~yHC~~Cg 170 (318)
+|.. ...++|..|+.. ..|+||...| +...|--|..= ++.+.+|+.||
T Consensus 428 nRRGys~~l~C~~Cg~v----~~Cp~Cd~~lt~H~~~~~L~CH~Cg~~----~~~p~~Cp~Cg 482 (730)
T COG1198 428 NRRGYAPLLLCRDCGYI----AECPNCDSPLTLHKATGQLRCHYCGYQ----EPIPQSCPECG 482 (730)
T ss_pred ccCCccceeecccCCCc----ccCCCCCcceEEecCCCeeEeCCCCCC----CCCCCCCCCCC
Confidence 4443 346899999875 3689998887 45566666443 45677777777
No 159
>PF13453 zf-TFIIB: Transcription factor zinc-finger
Probab=48.26 E-value=14 Score=25.25 Aligned_cols=26 Identities=27% Similarity=0.591 Sum_probs=16.1
Q ss_pred cCcCCCCccceEecCccccccCCCCCCeeecCCCC
Q 021022 136 VCVNCGVCMGEYFCESCKLFDDDTSKKQYHCDGCG 170 (318)
Q Consensus 136 ~C~~Cg~~f~~YfC~~Ckl~ddd~~k~~yHC~~Cg 170 (318)
.||.|+..|..+. + .+-.+++|+.||
T Consensus 1 ~CP~C~~~l~~~~-----~----~~~~id~C~~C~ 26 (41)
T PF13453_consen 1 KCPRCGTELEPVR-----L----GDVEIDVCPSCG 26 (41)
T ss_pred CcCCCCcccceEE-----E----CCEEEEECCCCC
Confidence 3777777776553 1 225677777775
No 160
>KOG2907 consensus RNA polymerase I transcription factor TFIIS, subunit A12.2/RPA12 [Transcription]
Probab=47.51 E-value=7 Score=33.36 Aligned_cols=19 Identities=47% Similarity=0.950 Sum_probs=16.0
Q ss_pred eeeccCCCCC----CccccccCC
Q 021022 300 VLAQKCPNCK----SYNTRLTRG 318 (318)
Q Consensus 300 ~lg~KC~~C~----SyNT~~~~~ 318 (318)
.|-+||+.|| +|+|+|+|.
T Consensus 72 ~I~~kCpkCghe~m~Y~T~QlRS 94 (116)
T KOG2907|consen 72 VIKHKCPKCGHEEMSYHTLQLRS 94 (116)
T ss_pred chhccCcccCCchhhhhhhhccc
Confidence 4678999997 899999973
No 161
>KOG1609 consensus Protein involved in mRNA turnover and stability [RNA processing and modification]
Probab=46.93 E-value=12 Score=35.16 Aligned_cols=51 Identities=24% Similarity=0.523 Sum_probs=37.1
Q ss_pred CCCCcccccccccCCceeEEcCCC-----CccchHHHHHHHhc-CCCCCCCCCcccC
Q 021022 206 HHDCPVCCEYLFETRQDVIVLPCG-----HTIHKNCLKEMREH-HQYACPICSKSVC 256 (318)
Q Consensus 206 ~~~CpIClE~lf~s~~~v~~LpCG-----H~fH~~Cl~~wl~~-~~~~CPiCrks~~ 256 (318)
...|-||.+....+.......||. ...|+.|+..|+.. ++..|.+|...+.
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 367999998655432224566773 66899999999864 3567999998665
No 162
>PRK12286 rpmF 50S ribosomal protein L32; Reviewed
Probab=46.06 E-value=21 Score=26.65 Aligned_cols=29 Identities=31% Similarity=0.748 Sum_probs=22.4
Q ss_pred ceEEcCCCCCCccccceeeeccCCCCCCcccccc
Q 021022 283 VWILCNDCGKTSNVQFHVLAQKCPNCKSYNTRLT 316 (318)
Q Consensus 283 v~IlCnDC~~~s~v~~H~lg~KC~~C~SyNT~~~ 316 (318)
..+.|..|++. ...| +-|+.||.|+-+++
T Consensus 26 ~l~~C~~CG~~--~~~H---~vC~~CG~Y~gr~v 54 (57)
T PRK12286 26 GLVECPNCGEP--KLPH---RVCPSCGYYKGREV 54 (57)
T ss_pred cceECCCCCCc--cCCe---EECCCCCcCCCEEe
Confidence 45789999976 3346 45999999999885
No 163
>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=45.06 E-value=6 Score=26.90 Aligned_cols=27 Identities=33% Similarity=0.725 Sum_probs=14.7
Q ss_pred cCcCCCCccceEecCccccccCCCCCCeeecCCCCc
Q 021022 136 VCVNCGVCMGEYFCESCKLFDDDTSKKQYHCDGCGI 171 (318)
Q Consensus 136 ~C~~Cg~~f~~YfC~~Ckl~ddd~~k~~yHC~~Cgi 171 (318)
.|++||+.++.+| ++.|..=-||.||-
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 3566666665444 34555566777764
No 164
>COG5183 SSM4 Protein involved in mRNA turnover and stability [RNA processing and modification]
Probab=44.86 E-value=8.7 Score=42.53 Aligned_cols=53 Identities=28% Similarity=0.577 Sum_probs=37.3
Q ss_pred CCCCCCCcccccccccCCceeEEcCCC-----CccchHHHHHHHhcC-CCCCCCCCcccCc
Q 021022 203 GAMHHDCPVCCEYLFETRQDVIVLPCG-----HTIHKNCLKEMREHH-QYACPICSKSVCD 257 (318)
Q Consensus 203 ~~~~~~CpIClE~lf~s~~~v~~LpCG-----H~fH~~Cl~~wl~~~-~~~CPiCrks~~d 257 (318)
++.+..|-||.-. +.++++..=||. -.+|++|+.+|+..+ ...|-+|...+..
T Consensus 9 N~d~~~CRICr~e--~~~d~pLfhPCKC~GSIkYiH~eCL~eW~~~s~~~kCdiChy~~~F 67 (1175)
T COG5183 9 NEDKRSCRICRTE--DIRDDPLFHPCKCSGSIKYIHRECLMEWMECSGTKKCDICHYEYKF 67 (1175)
T ss_pred CccchhceeecCC--CCCCCcCcccccccchhHHHHHHHHHHHHhcCCCcceeeecceeee
Confidence 3445789999742 223345555775 459999999999753 4569999988863
No 165
>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=44.58 E-value=22 Score=25.52 Aligned_cols=8 Identities=50% Similarity=1.630 Sum_probs=4.4
Q ss_pred CCCCCCCc
Q 021022 246 YACPICSK 253 (318)
Q Consensus 246 ~~CPiCrk 253 (318)
|+||.|.+
T Consensus 3 f~CP~C~~ 10 (54)
T PF05605_consen 3 FTCPYCGK 10 (54)
T ss_pred cCCCCCCC
Confidence 45555555
No 166
>KOG0269 consensus WD40 repeat-containing protein [Function unknown]
Probab=44.40 E-value=21 Score=39.31 Aligned_cols=70 Identities=26% Similarity=0.453 Sum_probs=42.2
Q ss_pred CCeeecCCCCceeecCCcceeeccCccceeeccccccccccCCCCCCCCcccccccccCCceeEEcCCCCccchHHHHHH
Q 021022 161 KKQYHCDGCGICRIGGCDNFFHCNKCRCCYSMLLKNSHPCVEGAMHHDCPVCCEYLFETRQDVIVLPCGHTIHKNCLKEM 240 (318)
Q Consensus 161 k~~yHC~~CgiCR~G~~~~ffHC~~C~~C~s~~l~~~H~Cie~~~~~~CpIClE~lf~s~~~v~~LpCGH~fH~~Cl~~w 240 (318)
.-+|-|+.|+-=-+++++ --|++| -+.+ ...|.+|-..+.. ..+.---|||-.|.+++.+|
T Consensus 751 ~i~~~~~nc~a~~~~~~~--~~c~rc---~s~a------------~~~CtVC~~vi~G--~~~~c~~C~H~gH~sh~~sw 811 (839)
T KOG0269|consen 751 TIHYACPNCDAPMVLTKL--WQCDRC---ESRA------------SAKCTVCDLVIRG--VDVWCQVCGHGGHDSHLKSW 811 (839)
T ss_pred eeeccccccCCccccccc--eeechH---HHHh------------hcCceeecceeee--eEeecccccccccHHHHHHH
Confidence 357888888754444433 334433 3322 2468999753322 22222359999999999999
Q ss_pred HhcCCCCCCC
Q 021022 241 REHHQYACPI 250 (318)
Q Consensus 241 l~~~~~~CPi 250 (318)
+.. ..-||.
T Consensus 812 ~~~-~s~ca~ 820 (839)
T KOG0269|consen 812 FFK-ASPCAK 820 (839)
T ss_pred Hhc-CCCCcc
Confidence 874 455654
No 167
>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=44.23 E-value=21 Score=22.59 Aligned_cols=37 Identities=22% Similarity=0.605 Sum_probs=21.9
Q ss_pred CcccccccccCCceeEEcCCCCccchHHHHHHHhcCCCCCCCCCcccC
Q 021022 209 CPVCCEYLFETRQDVIVLPCGHTIHKNCLKEMREHHQYACPICSKSVC 256 (318)
Q Consensus 209 CpIClE~lf~s~~~v~~LpCGH~fH~~Cl~~wl~~~~~~CPiCrks~~ 256 (318)
|+.|.+.+..... .+..=|..||.+| ++|..|++++.
T Consensus 2 C~~C~~~i~~~~~--~~~~~~~~~H~~C---------f~C~~C~~~L~ 38 (39)
T smart00132 2 CAGCGKPIRGGEL--VLRALGKVWHPEC---------FKCSKCGKPLG 38 (39)
T ss_pred ccccCCcccCCcE--EEEeCCccccccC---------CCCcccCCcCc
Confidence 6778776554312 2222377888765 45777777664
No 168
>PRK00420 hypothetical protein; Validated
Probab=43.96 E-value=14 Score=31.28 Aligned_cols=21 Identities=24% Similarity=0.471 Sum_probs=14.1
Q ss_pred ccCcCCCCccc-----eEecCccccc
Q 021022 135 QVCVNCGVCMG-----EYFCESCKLF 155 (318)
Q Consensus 135 ~~C~~Cg~~f~-----~YfC~~Ckl~ 155 (318)
..||.||.+|. ..||+.|.-.
T Consensus 24 ~~CP~Cg~pLf~lk~g~~~Cp~Cg~~ 49 (112)
T PRK00420 24 KHCPVCGLPLFELKDGEVVCPVHGKV 49 (112)
T ss_pred CCCCCCCCcceecCCCceECCCCCCe
Confidence 57888888774 3666666543
No 169
>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=43.20 E-value=21 Score=22.46 Aligned_cols=19 Identities=26% Similarity=0.669 Sum_probs=12.5
Q ss_pred CCCCCCcccCchhHHHHHhH
Q 021022 247 ACPICSKSVCDMSKVWEKYD 266 (318)
Q Consensus 247 ~CPiCrks~~d~~~~~~~lD 266 (318)
.||+|.+.+ .+....+-+|
T Consensus 3 ~CPiC~~~v-~~~~in~HLD 21 (26)
T smart00734 3 QCPVCFREV-PENLINSHLD 21 (26)
T ss_pred cCCCCcCcc-cHHHHHHHHH
Confidence 599999988 3333444455
No 170
>PLN03086 PRLI-interacting factor K; Provisional
Probab=43.02 E-value=12 Score=39.90 Aligned_cols=84 Identities=23% Similarity=0.527 Sum_probs=46.2
Q ss_pred ccCceeecCCCCcccccc-------------ccCcC--CCCccceEecCccccccCCCCCCeeecCCCCceeecCC----
Q 021022 117 HEVNQVICSLCGTEQKVQ-------------QVCVN--CGVCMGEYFCESCKLFDDDTSKKQYHCDGCGICRIGGC---- 177 (318)
Q Consensus 117 ~~v~~v~C~~C~~eQ~v~-------------~~C~~--Cg~~f~~YfC~~Ckl~ddd~~k~~yHC~~CgiCR~G~~---- 177 (318)
.++..|.|..|....+.. ..|++ ||..|.+- .-+..+||+.||- ..+..
T Consensus 403 ~~~~~V~C~NC~~~i~l~~l~lHe~~C~r~~V~Cp~~~Cg~v~~r~-----------el~~H~~C~~Cgk-~f~~s~Lek 470 (567)
T PLN03086 403 MDVDTVECRNCKHYIPSRSIALHEAYCSRHNVVCPHDGCGIVLRVE-----------EAKNHVHCEKCGQ-AFQQGEMEK 470 (567)
T ss_pred CCCCeEECCCCCCccchhHHHHHHhhCCCcceeCCcccccceeecc-----------ccccCccCCCCCC-ccchHHHHH
Confidence 346788999998775542 23553 77665321 2244578888864 22211
Q ss_pred -----cceeeccCccceeecccccccc---ccCCCCCCCCcccccc
Q 021022 178 -----DNFFHCNKCRCCYSMLLKNSHP---CVEGAMHHDCPVCCEY 215 (318)
Q Consensus 178 -----~~ffHC~~C~~C~s~~l~~~H~---Cie~~~~~~CpIClE~ 215 (318)
..-+-|. ||.-+.......|. |-++ ...|+.|...
T Consensus 471 H~~~~Hkpv~Cp-Cg~~~~R~~L~~H~~thCp~K--pi~C~fC~~~ 513 (567)
T PLN03086 471 HMKVFHEPLQCP-CGVVLEKEQMVQHQASTCPLR--LITCRFCGDM 513 (567)
T ss_pred HHHhcCCCccCC-CCCCcchhHHHhhhhccCCCC--ceeCCCCCCc
Confidence 1124466 66544443334563 5443 4678888753
No 171
>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=42.48 E-value=16 Score=25.65 Aligned_cols=13 Identities=23% Similarity=0.697 Sum_probs=8.6
Q ss_pred cccCcCCCCccce
Q 021022 134 QQVCVNCGVCMGE 146 (318)
Q Consensus 134 ~~~C~~Cg~~f~~ 146 (318)
++.|+.||.++-+
T Consensus 17 ~~~Cp~C~~PL~~ 29 (41)
T PF06677_consen 17 DEHCPDCGTPLMR 29 (41)
T ss_pred cCccCCCCCeeEE
Confidence 3568888777643
No 172
>PLN02189 cellulose synthase
Probab=42.24 E-value=21 Score=40.53 Aligned_cols=56 Identities=18% Similarity=0.441 Sum_probs=39.9
Q ss_pred cCCCCCCCCcccccccccCCceeEEcC---CCCccchHHHHHHHhcCCCCCCCCCcccC
Q 021022 201 VEGAMHHDCPVCCEYLFETRQDVIVLP---CGHTIHKNCLKEMREHHQYACPICSKSVC 256 (318)
Q Consensus 201 ie~~~~~~CpIClE~lf~s~~~v~~Lp---CGH~fH~~Cl~~wl~~~~~~CPiCrks~~ 256 (318)
.++.....|.||.|++-.....-.... ||--.++.|++-=.+.++..||.|+..+.
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 344456799999998754333323333 67779999996556667888999998775
No 173
>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=41.22 E-value=21 Score=30.69 Aligned_cols=48 Identities=21% Similarity=0.465 Sum_probs=35.6
Q ss_pred CCCCccceEecCccccccCCCCCCeeecCCCCceeecCCcceeeccCccceeec
Q 021022 139 NCGVCMGEYFCESCKLFDDDTSKKQYHCDGCGICRIGGCDNFFHCNKCRCCYSM 192 (318)
Q Consensus 139 ~Cg~~f~~YfC~~Ckl~ddd~~k~~yHC~~CgiCR~G~~~~ffHC~~C~~C~s~ 192 (318)
..+......+|.+|+.+-- ....||..||.|..+ -..||.-=|.|+..
T Consensus 41 ~~~~~~~~~~C~~C~~~kp---~Rs~HC~~C~~CV~~---~DHHC~w~~~cIG~ 88 (174)
T PF01529_consen 41 EDDENGELKYCSTCKIIKP---PRSHHCRVCNRCVLR---FDHHCPWLGNCIGR 88 (174)
T ss_pred ccccCCCCEECcccCCcCC---Ccceecccccccccc---ccccchhhcccccc
Confidence 3457778889999998832 358899999999884 34688877777664
No 174
>smart00659 RPOLCX RNA polymerase subunit CX. present in RNA polymerase I, II and III
Probab=40.78 E-value=19 Score=25.45 Aligned_cols=26 Identities=19% Similarity=0.736 Sum_probs=16.2
Q ss_pred eEEcCCCCCCccccceeeeccCCCCCC
Q 021022 284 WILCNDCGKTSNVQFHVLAQKCPNCKS 310 (318)
Q Consensus 284 ~IlCnDC~~~s~v~~H~lg~KC~~C~S 310 (318)
...|.+|+...+.. ---+.+|+.||+
T Consensus 2 ~Y~C~~Cg~~~~~~-~~~~irC~~CG~ 27 (44)
T smart00659 2 IYICGECGRENEIK-SKDVVRCRECGY 27 (44)
T ss_pred EEECCCCCCEeecC-CCCceECCCCCc
Confidence 35677777755444 234567777776
No 175
>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=40.58 E-value=14 Score=28.39 Aligned_cols=14 Identities=43% Similarity=0.971 Sum_probs=12.1
Q ss_pred eccCCCCCCccccc
Q 021022 302 AQKCPNCKSYNTRL 315 (318)
Q Consensus 302 g~KC~~C~SyNT~~ 315 (318)
.++|+.|.|.||+.
T Consensus 5 ~~~CPRC~S~nTKF 18 (63)
T PF02701_consen 5 PLPCPRCDSTNTKF 18 (63)
T ss_pred CCCCCCcCCCCCEE
Confidence 36999999999975
No 176
>COG1996 RPC10 DNA-directed RNA polymerase, subunit RPC10 (contains C4-type Zn-finger) [Transcription]
Probab=40.42 E-value=20 Score=26.31 Aligned_cols=29 Identities=31% Similarity=0.666 Sum_probs=17.7
Q ss_pred cceEecCcc-ccccCCCCCCeeecCCCCce
Q 021022 144 MGEYFCESC-KLFDDDTSKKQYHCDGCGIC 172 (318)
Q Consensus 144 f~~YfC~~C-kl~ddd~~k~~yHC~~CgiC 172 (318)
+..|-|..| +.|+.+..+.-.-|+.||.=
T Consensus 4 ~~~Y~C~~Cg~~~~~~~~~~~irCp~Cg~r 33 (49)
T COG1996 4 MMEYKCARCGREVELDQETRGIRCPYCGSR 33 (49)
T ss_pred eEEEEhhhcCCeeehhhccCceeCCCCCcE
Confidence 345556666 34455556677778777753
No 177
>KOG1940 consensus Zn-finger protein [General function prediction only]
Probab=39.92 E-value=4.9 Score=39.01 Aligned_cols=31 Identities=19% Similarity=0.485 Sum_probs=26.1
Q ss_pred CCCccCCccccccceeEcCCCCCeecCcchHh
Q 021022 67 GFMEYGCQHYRRRCRIRAPCCNEIFDCRHCHN 98 (318)
Q Consensus 67 ~~~~~gC~HY~R~c~i~~pCC~~~y~Cr~CHd 98 (318)
....+.|.||...=-++.++|.. |+|..||+
T Consensus 174 ~~~~~~CgH~~h~~cf~e~~~~~-y~CP~C~~ 204 (276)
T KOG1940|consen 174 DAGVLKCGHYMHSRCFEEMICEG-YTCPICSK 204 (276)
T ss_pred cCCccCcccchHHHHHHHHhccC-CCCCcccc
Confidence 33446899999855589999999 99999999
No 178
>PHA00626 hypothetical protein
Probab=39.91 E-value=20 Score=27.14 Aligned_cols=34 Identities=21% Similarity=0.450 Sum_probs=21.7
Q ss_pred eecCCCCccccccccCcCCCCccceEecCccccccC
Q 021022 122 VICSLCGTEQKVQQVCVNCGVCMGEYFCESCKLFDD 157 (318)
Q Consensus 122 v~C~~C~~eQ~v~~~C~~Cg~~f~~YfC~~Ckl~dd 157 (318)
|.|..|+..+-+ .|.-|...-++|-|..|.+++.
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 457777776555 5555666666777777766643
No 179
>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=39.87 E-value=15 Score=23.97 Aligned_cols=16 Identities=38% Similarity=1.026 Sum_probs=7.9
Q ss_pred CcCCCCccceEecCccc
Q 021022 137 CVNCGVCMGEYFCESCK 153 (318)
Q Consensus 137 C~~Cg~~f~~YfC~~Ck 153 (318)
|.-||. .++|.|+.|.
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 5566666554
No 180
>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]
Probab=39.62 E-value=18 Score=27.63 Aligned_cols=34 Identities=24% Similarity=0.614 Sum_probs=21.0
Q ss_pred CceeecCCCCccccccccCcCCCCccceEecCcccc
Q 021022 119 VNQVICSLCGTEQKVQQVCVNCGVCMGEYFCESCKL 154 (318)
Q Consensus 119 v~~v~C~~C~~eQ~v~~~C~~Cg~~f~~YfC~~Ckl 154 (318)
.....|..|+.++-+ .|..|...=+.|-|++|-|
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 445666666655544 5666666666666666655
No 181
>KOG0298 consensus DEAD box-containing helicase-like transcription factor/DNA repair protein [Replication, recombination and repair]
Probab=38.90 E-value=11 Score=43.47 Aligned_cols=53 Identities=25% Similarity=0.428 Sum_probs=40.8
Q ss_pred CCCCCCCcccccccccCCceeEEcCCCCccchHHHHHHHhcCCCCCCCCCcccCchh
Q 021022 203 GAMHHDCPVCCEYLFETRQDVIVLPCGHTIHKNCLKEMREHHQYACPICSKSVCDMS 259 (318)
Q Consensus 203 ~~~~~~CpIClE~lf~s~~~v~~LpCGH~fH~~Cl~~wl~~~~~~CPiCrks~~d~~ 259 (318)
...+..|+||++.+-. .-.+.-|||.++..|+..|+.. +..||+|....++..
T Consensus 1150 ~~~~~~c~ic~dil~~---~~~I~~cgh~~c~~c~~~~l~~-~s~~~~~ksi~~dfg 1202 (1394)
T KOG0298|consen 1150 LSGHFVCEICLDILRN---QGGIAGCGHEPCCRCDELWLYA-SSRCPICKSIKGDFG 1202 (1394)
T ss_pred hhcccchHHHHHHHHh---cCCeeeechhHhhhHHHHHHHH-hccCcchhhhhhhhc
Confidence 3445689999996543 2245669999999999999985 588999997777644
No 182
>PLN02436 cellulose synthase A
Probab=38.26 E-value=26 Score=39.95 Aligned_cols=56 Identities=20% Similarity=0.445 Sum_probs=40.5
Q ss_pred cCCCCCCCCcccccccccCCceeEEcC---CCCccchHHHHHHHhcCCCCCCCCCcccC
Q 021022 201 VEGAMHHDCPVCCEYLFETRQDVIVLP---CGHTIHKNCLKEMREHHQYACPICSKSVC 256 (318)
Q Consensus 201 ie~~~~~~CpIClE~lf~s~~~v~~Lp---CGH~fH~~Cl~~wl~~~~~~CPiCrks~~ 256 (318)
++......|.||.|++-.+.+.-.... ||--.++.|++-=.+.++..||.|+....
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 444456799999998755444334443 67779999996556667888999998775
No 183
>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=38.05 E-value=17 Score=21.11 Aligned_cols=15 Identities=53% Similarity=1.112 Sum_probs=11.7
Q ss_pred CCCCCCCcccCchhH
Q 021022 246 YACPICSKSVCDMSK 260 (318)
Q Consensus 246 ~~CPiCrks~~d~~~ 260 (318)
|.||.|.+.+.....
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 469999999987554
No 184
>KOG2932 consensus E3 ubiquitin ligase involved in ubiquitination of E-cadherin complex [Posttranslational modification, protein turnover, chaperones]
Probab=37.68 E-value=14 Score=36.90 Aligned_cols=30 Identities=27% Similarity=0.752 Sum_probs=23.8
Q ss_pred EEcCCCCccchHHHHHHHhcCCCCCCCCCcccC
Q 021022 224 IVLPCGHTIHKNCLKEMREHHQYACPICSKSVC 256 (318)
Q Consensus 224 ~~LpCGH~fH~~Cl~~wl~~~~~~CPiCrks~~ 256 (318)
+.+||.|+|+.+|...- ....||.|.-.+.
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 47899999999998764 2357999987665
No 185
>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=37.04 E-value=17 Score=31.95 Aligned_cols=16 Identities=38% Similarity=0.843 Sum_probs=14.1
Q ss_pred eccCCCCCCccccccC
Q 021022 302 AQKCPNCKSYNTRLTR 317 (318)
Q Consensus 302 g~KC~~C~SyNT~~~~ 317 (318)
...|+.|||-||++++
T Consensus 105 ~~~cp~c~s~~t~~~s 120 (146)
T TIGR02159 105 SVQCPRCGSADTTITS 120 (146)
T ss_pred CCcCCCCCCCCcEeec
Confidence 4699999999999875
No 186
>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=36.72 E-value=27 Score=22.91 Aligned_cols=25 Identities=28% Similarity=0.787 Sum_probs=16.3
Q ss_pred eEecCccccccCCCCCCeeecCCCCc
Q 021022 146 EYFCESCKLFDDDTSKKQYHCDGCGI 171 (318)
Q Consensus 146 ~YfC~~Ckl~ddd~~k~~yHC~~Cgi 171 (318)
+|-|.+|-+.-+ +.+.++.|+.||.
T Consensus 1 ~~~C~~CGy~y~-~~~~~~~CP~Cg~ 25 (33)
T cd00350 1 KYVCPVCGYIYD-GEEAPWVCPVCGA 25 (33)
T ss_pred CEECCCCCCEEC-CCcCCCcCcCCCC
Confidence 366777765533 3457888888864
No 187
>COG1645 Uncharacterized Zn-finger containing protein [General function prediction only]
Probab=36.23 E-value=21 Score=31.20 Aligned_cols=19 Identities=42% Similarity=1.127 Sum_probs=14.2
Q ss_pred ccCcCCCCcc----ceEecCccc
Q 021022 135 QVCVNCGVCM----GEYFCESCK 153 (318)
Q Consensus 135 ~~C~~Cg~~f----~~YfC~~Ck 153 (318)
..|+.||.++ |+-||++|-
T Consensus 29 ~hCp~Cg~PLF~KdG~v~CPvC~ 51 (131)
T COG1645 29 KHCPKCGTPLFRKDGEVFCPVCG 51 (131)
T ss_pred hhCcccCCcceeeCCeEECCCCC
Confidence 5689998887 556777775
No 188
>KOG0006 consensus E3 ubiquitin-protein ligase (Parkin protein) [Posttranslational modification, protein turnover, chaperones]
Probab=36.10 E-value=33 Score=34.43 Aligned_cols=79 Identities=23% Similarity=0.529 Sum_probs=50.1
Q ss_pred cccC--CCCCCeeecCCCCceeecC-CcceeeccCccceeecc---ccccccccCCCCCCCCcccccccccCCceeEEcC
Q 021022 154 LFDD--DTSKKQYHCDGCGICRIGG-CDNFFHCNKCRCCYSML---LKNSHPCVEGAMHHDCPVCCEYLFETRQDVIVLP 227 (318)
Q Consensus 154 l~dd--d~~k~~yHC~~CgiCR~G~-~~~ffHC~~C~~C~s~~---l~~~H~Cie~~~~~~CpIClE~lf~s~~~v~~Lp 227 (318)
-||| .+.+-+-||+.| |--|. .|=||. |+++.+.. .-..|.=..+.-...|-.|-+ -++++.+++
T Consensus 168 cWdDVLks~Ripg~Ces~--~~pg~fAEFfFK---C~ah~~~~k~~aa~lhli~~N~~ni~C~~Ctd----v~~~vlvf~ 238 (446)
T KOG0006|consen 168 CWDDVLKSKRIPGVCESC--CTPGLFAEFFFK---CGAHPTSDKETAAALHLIATNSRNITCITCTD----VRSPVLVFQ 238 (446)
T ss_pred chhhhhhcccCccccccc--cCCcchHhheeh---hccCCCccccchhHHHHhhcccccceeEEecC----CccceEEEe
Confidence 3777 245678888887 44444 356665 45554431 011233233455678999987 245788999
Q ss_pred CC--CccchHHHHHHH
Q 021022 228 CG--HTIHKNCLKEMR 241 (318)
Q Consensus 228 CG--H~fH~~Cl~~wl 241 (318)
|. |..+..|+.-|-
T Consensus 239 Cns~HvtC~dCFr~yc 254 (446)
T KOG0006|consen 239 CNSRHVTCLDCFRLYC 254 (446)
T ss_pred cCCceeehHHhhhhHh
Confidence 98 999999999663
No 189
>PRK00415 rps27e 30S ribosomal protein S27e; Reviewed
Probab=35.99 E-value=23 Score=26.89 Aligned_cols=36 Identities=33% Similarity=0.541 Sum_probs=27.1
Q ss_pred ceeecCCCCccccc------cccCcCCCCccceEecCccccc
Q 021022 120 NQVICSLCGTEQKV------QQVCVNCGVCMGEYFCESCKLF 155 (318)
Q Consensus 120 ~~v~C~~C~~eQ~v------~~~C~~Cg~~f~~YfC~~Ckl~ 155 (318)
-.|.|..|+.+|.+ .-.|..||..+++-.=++-+|.
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 47999999999975 2469999999887665555544
No 190
>KOG0801 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=35.87 E-value=14 Score=33.79 Aligned_cols=29 Identities=31% Similarity=0.553 Sum_probs=23.7
Q ss_pred CCCCCcccccccccCCceeEEcCCCCccch
Q 021022 205 MHHDCPVCCEYLFETRQDVIVLPCGHTIHK 234 (318)
Q Consensus 205 ~~~~CpIClE~lf~s~~~v~~LpCGH~fH~ 234 (318)
...+|.||||+|.. .+.+..|||=-.||+
T Consensus 176 dkGECvICLEdL~~-GdtIARLPCLCIYHK 204 (205)
T KOG0801|consen 176 DKGECVICLEDLEA-GDTIARLPCLCIYHK 204 (205)
T ss_pred cCCcEEEEhhhccC-CCceeccceEEEeec
Confidence 36899999998654 678899999888875
No 191
>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=35.73 E-value=32 Score=25.42 Aligned_cols=29 Identities=31% Similarity=0.826 Sum_probs=22.3
Q ss_pred ceEEcCCCCCCccccceeeeccCCCCCCcccccc
Q 021022 283 VWILCNDCGKTSNVQFHVLAQKCPNCKSYNTRLT 316 (318)
Q Consensus 283 v~IlCnDC~~~s~v~~H~lg~KC~~C~SyNT~~~ 316 (318)
..+.|..|++. ...| +-|+.||.|+-+++
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 4445 45999999999886
No 192
>smart00661 RPOL9 RNA polymerase subunit 9.
Probab=34.74 E-value=32 Score=24.00 Aligned_cols=9 Identities=33% Similarity=1.313 Sum_probs=5.9
Q ss_pred CeeecCCCC
Q 021022 162 KQYHCDGCG 170 (318)
Q Consensus 162 ~~yHC~~Cg 170 (318)
..|-|+.||
T Consensus 19 ~~~vC~~Cg 27 (52)
T smart00661 19 RRFVCRKCG 27 (52)
T ss_pred CEEECCcCC
Confidence 366677666
No 193
>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=34.18 E-value=28 Score=23.82 Aligned_cols=31 Identities=29% Similarity=0.724 Sum_probs=16.5
Q ss_pred cCcCCCCccceEecCccccc---cCCCCCCeeecCCCC
Q 021022 136 VCVNCGVCMGEYFCESCKLF---DDDTSKKQYHCDGCG 170 (318)
Q Consensus 136 ~C~~Cg~~f~~YfC~~Ckl~---ddd~~k~~yHC~~Cg 170 (318)
.|++||+.-+.|| ..= -|++..-.|.|-+||
T Consensus 2 ~Cp~Cg~~~a~~~----~~Q~rsaDE~~T~fy~C~~C~ 35 (39)
T PF01096_consen 2 KCPKCGHNEAVFF----QIQTRSADEPMTLFYVCCNCG 35 (39)
T ss_dssp --SSS-SSEEEEE----EESSSSSSSSSEEEEEESSST
T ss_pred CCcCCCCCeEEEE----EeeccCCCCCCeEEEEeCCCC
Confidence 4788888777665 111 233455666776665
No 194
>PF15616 TerY-C: TerY-C metal binding domain
Probab=33.45 E-value=38 Score=29.50 Aligned_cols=33 Identities=36% Similarity=0.792 Sum_probs=23.5
Q ss_pred ccCcCCCCccceEecCcc-cccc-CCCCCCeeecCCCC
Q 021022 135 QVCVNCGVCMGEYFCESC-KLFD-DDTSKKQYHCDGCG 170 (318)
Q Consensus 135 ~~C~~Cg~~f~~YfC~~C-kl~d-dd~~k~~yHC~~Cg 170 (318)
.-||.||..+|---| .| ||+- +++ ...+|+-||
T Consensus 78 PgCP~CGn~~~fa~C-~CGkl~Ci~g~--~~~~CPwCg 112 (131)
T PF15616_consen 78 PGCPHCGNQYAFAVC-GCGKLFCIDGE--GEVTCPWCG 112 (131)
T ss_pred CCCCCCcChhcEEEe-cCCCEEEeCCC--CCEECCCCC
Confidence 579999999999988 58 5663 222 256666665
No 195
>PRK00366 ispG 4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase; Reviewed
Probab=33.22 E-value=56 Score=33.03 Aligned_cols=53 Identities=19% Similarity=0.453 Sum_probs=42.7
Q ss_pred CCCCCCCcccCchhHHHHHhHHHHHcCCCChhhhcCcceEEc--CCCCCCccccceeee
Q 021022 246 YACPICSKSVCDMSKVWEKYDREIAATPMPEAYLNKKVWILC--NDCGKTSNVQFHVLA 302 (318)
Q Consensus 246 ~~CPiCrks~~d~~~~~~~lD~~i~~~pmPeey~~~~v~IlC--nDC~~~s~v~~H~lg 302 (318)
.+||-|++...|.-..-.++++.+...++| -+.+..-| |.|++.....+=+.|
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 359999999999888888899999998888 33456779 899988777665554
No 196
>PRK00432 30S ribosomal protein S27ae; Validated
Probab=32.96 E-value=27 Score=25.32 Aligned_cols=10 Identities=40% Similarity=1.331 Sum_probs=6.3
Q ss_pred CeeecCCCCc
Q 021022 162 KQYHCDGCGI 171 (318)
Q Consensus 162 ~~yHC~~Cgi 171 (318)
+.|+|..||.
T Consensus 36 ~r~~C~~Cgy 45 (50)
T PRK00432 36 DRWHCGKCGY 45 (50)
T ss_pred CcEECCCcCC
Confidence 5666766663
No 197
>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=32.83 E-value=33 Score=22.93 Aligned_cols=21 Identities=24% Similarity=0.360 Sum_probs=14.1
Q ss_pred ccCcCCCCccceEecCccccc
Q 021022 135 QVCVNCGVCMGEYFCESCKLF 155 (318)
Q Consensus 135 ~~C~~Cg~~f~~YfC~~Ckl~ 155 (318)
..|..++...+.|||..|+.+
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 357777777778888777643
No 198
>PF06827 zf-FPG_IleRS: Zinc finger found in FPG and IleRS; InterPro: IPR010663 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents a zinc finger domain found at the C-terminal in both DNA glycosylase/AP lyase enzymes and in isoleucyl tRNA synthetase. In these two types of enzymes, the C-terminal domain forms a zinc finger. Some related proteins may not bind zinc. DNA glycosylase/AP lyase enzymes are involved in base excision repair of DNA damaged by oxidation or by mutagenic agents. These enzymes have both DNA glycosylase activity (3.2.2 from EC) and AP lyase activity (4.2.99.18 from EC) []. Examples include formamidopyrimidine-DNA glycosylases (Fpg; MutM) and endonuclease VIII (Nei). Formamidopyrimidine-DNA glycosylases (Fpg, MutM) is a trifunctional DNA base excision repair enzyme that removes a wide range of oxidation-damaged bases (N-glycosylase activity; 3.2.2.23 from EC) and cleaves both the 3'- and 5'-phosphodiester bonds of the resulting apurinic/apyrimidinic site (AP lyase activity; 4.2.99.18 from EC). Fpg has a preference for oxidised purines, excising oxidized purine bases such as 7,8-dihydro-8-oxoguanine (8-oxoG). ITs AP (apurinic/apyrimidinic) lyase activity introduces nicks in the DNA strand, cleaving the DNA backbone by beta-delta elimination to generate a single-strand break at the site of the removed base with both 3'- and 5'-phosphates. Fpg is a monomer composed of 2 domains connected by a flexible hinge []. The two DNA-binding motifs (a zinc finger and the helix-two-turns-helix motifs) suggest that the oxidized base is flipped out from double-stranded DNA in the binding mode and excised by a catalytic mechanism similar to that of bifunctional base excision repair enzymes []. Fpg binds one ion of zinc at the C terminus, which contains four conserved and essential cysteines []. Endonuclease VIII (Nei) has the same enzyme activities as Fpg above, but with a preference for oxidized pyrimidines, such as thymine glycol, 5,6-dihydrouracil and 5,6-dihydrothymine [, ]. An Fpg-type zinc finger is also found at the C terminus of isoleucyl tRNA synthetase (6.1.1.5 from EC) [, ]. This enzyme catalyses the attachment of isoleucine to tRNA(Ile). As IleRS can inadvertently accommodate and process structurally similar amino acids such as valine, to avoid such errors it has two additional distinct tRNA(Ile)-dependent editing activities. One activity is designated as 'pre-transfer' editing and involves the hydrolysis of activated Val-AMP. The other activity is designated 'post-transfer' editing and involves deacylation of mischarged Val-tRNA(Ile) []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003824 catalytic activity; PDB: 1K82_C 1Q39_A 2OQ4_B 2OPF_A 1K3X_A 1K3W_A 1Q3B_A 2EA0_A 1Q3C_A 2XZF_A ....
Probab=32.24 E-value=32 Score=21.84 Aligned_cols=18 Identities=28% Similarity=0.920 Sum_probs=7.8
Q ss_pred ccCcCCCCcc--------ceEecCcc
Q 021022 135 QVCVNCGVCM--------GEYFCESC 152 (318)
Q Consensus 135 ~~C~~Cg~~f--------~~YfC~~C 152 (318)
+.|+.|+..+ +.|||+.|
T Consensus 2 ~~C~rC~~~~~~~~~~~r~~~~C~rC 27 (30)
T PF06827_consen 2 EKCPRCWNYIEDIGINGRSTYLCPRC 27 (30)
T ss_dssp SB-TTT--BBEEEEETTEEEEE-TTT
T ss_pred CcCccCCCcceEeEecCCCCeECcCC
Confidence 4566666554 34666665
No 199
>KOG4185 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=32.23 E-value=8.3 Score=36.57 Aligned_cols=50 Identities=28% Similarity=0.585 Sum_probs=36.6
Q ss_pred CCCCccccccccc--CCceeEEcC--------CCCccchHHHHHHHhcCCCCCCCCCccc
Q 021022 206 HHDCPVCCEYLFE--TRQDVIVLP--------CGHTIHKNCLKEMREHHQYACPICSKSV 255 (318)
Q Consensus 206 ~~~CpIClE~lf~--s~~~v~~Lp--------CGH~fH~~Cl~~wl~~~~~~CPiCrks~ 255 (318)
...|.||...... ......++. |||++...|++..+......||.|+...
T Consensus 207 ~~~c~ic~~~~~~n~~~~~p~vl~~~~~~~~~c~htlc~~c~~~~l~~~~~~cp~~~~~~ 266 (296)
T KOG4185|consen 207 EKLCEICERIYSENDEKLAPLVLSLSRLKEKIEGHTLCKECIDTILLQAGIKCPFCTWSH 266 (296)
T ss_pred HHHHHHHHHHhhccccccchhHHHHHHHHHHHHHHHHHhcchHHHHHHhhhcCCccccee
Confidence 3568888765431 223445666 9999999999998775557899999853
No 200
>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=31.97 E-value=15 Score=40.76 Aligned_cols=46 Identities=28% Similarity=0.601 Sum_probs=0.0
Q ss_pred ccCcCCCCccceEecCccccccCCCCCCeeecCCCCceeecCCcceeeccCccce
Q 021022 135 QVCVNCGVCMGEYFCESCKLFDDDTSKKQYHCDGCGICRIGGCDNFFHCNKCRCC 189 (318)
Q Consensus 135 ~~C~~Cg~~f~~YfC~~Ckl~ddd~~k~~yHC~~CgiCR~G~~~~ffHC~~C~~C 189 (318)
-.|++||..--.-.|+.|.-. ....|.|+.||+ ++. -.+|.+|+.=
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 358888888777778888655 346888888887 222 1278888754
No 201
>KOG4317 consensus Predicted Zn-finger protein [Function unknown]
Probab=31.45 E-value=21 Score=35.61 Aligned_cols=21 Identities=43% Similarity=0.934 Sum_probs=17.0
Q ss_pred ccCcCCCCccceEecCccccc
Q 021022 135 QVCVNCGVCMGEYFCESCKLF 155 (318)
Q Consensus 135 ~~C~~Cg~~f~~YfC~~Ckl~ 155 (318)
..|.-||+.+++|.|+-|+|.
T Consensus 8 ~~C~ic~vq~~~YtCPRCn~~ 28 (383)
T KOG4317|consen 8 LACGICGVQKREYTCPRCNLL 28 (383)
T ss_pred eeccccccccccccCCCCCcc
Confidence 357788888999989988865
No 202
>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=31.34 E-value=24 Score=22.44 Aligned_cols=20 Identities=25% Similarity=0.718 Sum_probs=5.8
Q ss_pred CCceeecCCc-ceeeccCccc
Q 021022 169 CGICRIGGCD-NFFHCNKCRC 188 (318)
Q Consensus 169 CgiCR~G~~~-~ffHC~~C~~ 188 (318)
|.+|+..+.. .+|+|..|+.
T Consensus 3 C~~C~~~~~~~~~Y~C~~Cdf 23 (30)
T PF07649_consen 3 CDACGKPIDGGWFYRCSECDF 23 (30)
T ss_dssp -TTTS----S--EEE-TTT--
T ss_pred CCcCCCcCCCCceEECccCCC
Confidence 3444444322 5666666654
No 203
>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=30.93 E-value=49 Score=32.61 Aligned_cols=44 Identities=23% Similarity=0.716 Sum_probs=0.0
Q ss_pred CCCCCCCCcccCchhHHHHHhHHHHHcCCCChhh-----hcCcceEEcCCCCCCccccceeeeccCCCCCC
Q 021022 245 QYACPICSKSVCDMSKVWEKYDREIAATPMPEAY-----LNKKVWILCNDCGKTSNVQFHVLAQKCPNCKS 310 (318)
Q Consensus 245 ~~~CPiCrks~~d~~~~~~~lD~~i~~~pmPeey-----~~~~v~IlCnDC~~~s~v~~H~lg~KC~~C~S 310 (318)
...||+|+ ..|.-... .+....-.|.-|+ ..+|+.-.||++|++
T Consensus 184 ~~~CPvCG------------------s~P~~s~~~~~~~~~G~RyL~CslC~----teW~~~R~~C~~Cg~ 232 (305)
T TIGR01562 184 RTLCPACG------------------SPPVASMVRQGGKETGLRYLSCSLCA----TEWHYVRVKCSHCEE 232 (305)
T ss_pred CCcCCCCC------------------ChhhhhhhcccCCCCCceEEEcCCCC----CcccccCccCCCCCC
No 204
>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=30.78 E-value=74 Score=24.08 Aligned_cols=50 Identities=18% Similarity=0.441 Sum_probs=33.9
Q ss_pred CCCCCcccccccccCCceeEEcCCCCccchHHHHHHHhcCCCCCCCCCcccCc
Q 021022 205 MHHDCPVCCEYLFETRQDVIVLPCGHTIHKNCLKEMREHHQYACPICSKSVCD 257 (318)
Q Consensus 205 ~~~~CpIClE~lf~s~~~v~~LpCGH~fH~~Cl~~wl~~~~~~CPiCrks~~d 257 (318)
+.-+|-.|-.+|..+..+..+-.=--+|+..|.+..|. ..||-|+..+..
T Consensus 4 lrpnCE~C~~dLp~~s~~A~ICSfECTFC~~C~e~~l~---~~CPNCgGelv~ 53 (57)
T PF06906_consen 4 LRPNCECCDKDLPPDSPEAYICSFECTFCADCAETMLN---GVCPNCGGELVR 53 (57)
T ss_pred cCCCccccCCCCCCCCCcceEEeEeCcccHHHHHHHhc---CcCcCCCCcccc
Confidence 45577778776655432222222136799999999984 679999988764
No 205
>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=30.76 E-value=32 Score=22.90 Aligned_cols=11 Identities=27% Similarity=0.836 Sum_probs=6.3
Q ss_pred CCCeeecCCCC
Q 021022 160 SKKQYHCDGCG 170 (318)
Q Consensus 160 ~k~~yHC~~Cg 170 (318)
..++-.|..||
T Consensus 14 ~~~~irC~~CG 24 (32)
T PF03604_consen 14 PGDPIRCPECG 24 (32)
T ss_dssp TSSTSSBSSSS
T ss_pred CCCcEECCcCC
Confidence 34455666666
No 206
>KOG0826 consensus Predicted E3 ubiquitin ligase involved in peroxisome organization [Posttranslational modification, protein turnover, chaperones]
Probab=30.51 E-value=42 Score=33.67 Aligned_cols=49 Identities=16% Similarity=0.343 Sum_probs=34.9
Q ss_pred CCCCCCcccccccccCCceeEEcCCCCccchHHHHHHHhcCCCCCCCCCcccC
Q 021022 204 AMHHDCPVCCEYLFETRQDVIVLPCGHTIHKNCLKEMREHHQYACPICSKSVC 256 (318)
Q Consensus 204 ~~~~~CpIClE~lf~s~~~v~~LpCGH~fH~~Cl~~wl~~~~~~CPiCrks~~ 256 (318)
.....||||+... ..+.+.--=|-+|+-.|+.+|+. ....||+=..++.
T Consensus 298 ~~~~~CpvClk~r---~Nptvl~vSGyVfCY~Ci~~Yv~-~~~~CPVT~~p~~ 346 (357)
T KOG0826|consen 298 PDREVCPVCLKKR---QNPTVLEVSGYVFCYPCIFSYVV-NYGHCPVTGYPAS 346 (357)
T ss_pred CccccChhHHhcc---CCCceEEecceEEeHHHHHHHHH-hcCCCCccCCcch
Confidence 4467899999632 12223333499999999999997 4578999777664
No 207
>KOG2462 consensus C2H2-type Zn-finger protein [Transcription]
Probab=30.31 E-value=44 Score=32.59 Aligned_cols=108 Identities=26% Similarity=0.458 Sum_probs=64.2
Q ss_pred ccCcCCCCccceEec-Cccccc-cCCCCCCeeecCCCCceeecCC---------cceeeccCccceeecc--cc---ccc
Q 021022 135 QVCVNCGVCMGEYFC-ESCKLF-DDDTSKKQYHCDGCGICRIGGC---------DNFFHCNKCRCCYSML--LK---NSH 198 (318)
Q Consensus 135 ~~C~~Cg~~f~~YfC-~~Ckl~-ddd~~k~~yHC~~CgiCR~G~~---------~~ffHC~~C~~C~s~~--l~---~~H 198 (318)
-.|..||...+.+-= +.=|-| -+-.+++.+.|..||.=.|--+ .--+-|..||-=.|.- |+ .+|
T Consensus 131 ~~c~eCgk~ysT~snLsrHkQ~H~~~~s~ka~~C~~C~K~YvSmpALkMHirTH~l~c~C~iCGKaFSRPWLLQGHiRTH 210 (279)
T KOG2462|consen 131 YKCPECGKSYSTSSNLSRHKQTHRSLDSKKAFSCKYCGKVYVSMPALKMHIRTHTLPCECGICGKAFSRPWLLQGHIRTH 210 (279)
T ss_pred eeccccccccccccccchhhcccccccccccccCCCCCceeeehHHHhhHhhccCCCcccccccccccchHHhhcccccc
Confidence 357777777766540 000111 1122488999999997765421 2356788888877741 22 234
Q ss_pred cccCCCCCCCCcccccccccCCceeEEcCCCCccchHHHHHHHh----cCCCCCCCCCcccCchhH
Q 021022 199 PCVEGAMHHDCPVCCEYLFETRQDVIVLPCGHTIHKNCLKEMRE----HHQYACPICSKSVCDMSK 260 (318)
Q Consensus 199 ~Cie~~~~~~CpIClE~lf~s~~~v~~LpCGH~fH~~Cl~~wl~----~~~~~CPiCrks~~d~~~ 260 (318)
. +.-...||.|--- |.++.. |+..++ .+.|.|+.|.|+|.-|+-
T Consensus 211 T---GEKPF~C~hC~kA-FADRSN--------------LRAHmQTHS~~K~~qC~~C~KsFsl~Sy 258 (279)
T KOG2462|consen 211 T---GEKPFSCPHCGKA-FADRSN--------------LRAHMQTHSDVKKHQCPRCGKSFALKSY 258 (279)
T ss_pred c---CCCCccCCcccch-hcchHH--------------HHHHHHhhcCCccccCcchhhHHHHHHH
Confidence 3 3335789999874 554432 222222 257999999999987754
No 208
>PRK14810 formamidopyrimidine-DNA glycosylase; Provisional
Probab=30.30 E-value=28 Score=33.26 Aligned_cols=20 Identities=25% Similarity=0.884 Sum_probs=16.3
Q ss_pred cccCcCCCCcc--------ceEecCccc
Q 021022 134 QQVCVNCGVCM--------GEYFCESCK 153 (318)
Q Consensus 134 ~~~C~~Cg~~f--------~~YfC~~Ck 153 (318)
++.|+.||... +.|||+.|.
T Consensus 244 g~pCprCG~~I~~~~~~gR~t~~CP~CQ 271 (272)
T PRK14810 244 GEPCLNCKTPIRRVVVAGRSSHYCPHCQ 271 (272)
T ss_pred CCcCCCCCCeeEEEEECCCccEECcCCc
Confidence 46799999888 678998885
No 209
>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=29.76 E-value=18 Score=40.32 Aligned_cols=43 Identities=30% Similarity=0.811 Sum_probs=0.0
Q ss_pred eecCCCCccccccccCcCCCCc-cceEecCccccccCCCCCCeeecCCCC
Q 021022 122 VICSLCGTEQKVQQVCVNCGVC-MGEYFCESCKLFDDDTSKKQYHCDGCG 170 (318)
Q Consensus 122 v~C~~C~~eQ~v~~~C~~Cg~~-f~~YfC~~Ckl~ddd~~k~~yHC~~Cg 170 (318)
-.|..|+++ .+...|+.||.. .-.|+|+.|+.--++. +|+.||
T Consensus 656 r~Cp~Cg~~-t~~~~Cp~CG~~T~~~~~Cp~C~~~~~~~-----~C~~C~ 699 (900)
T PF03833_consen 656 RRCPKCGKE-TFYNRCPECGSHTEPVYVCPDCGIEVEED-----ECPKCG 699 (900)
T ss_dssp --------------------------------------------------
T ss_pred ccCcccCCc-chhhcCcccCCccccceeccccccccCcc-----cccccc
Confidence 456666655 334556666654 3455666665432211 566665
No 210
>PRK10445 endonuclease VIII; Provisional
Probab=29.72 E-value=30 Score=32.93 Aligned_cols=20 Identities=30% Similarity=0.953 Sum_probs=16.1
Q ss_pred cccCcCCCCcc--------ceEecCccc
Q 021022 134 QQVCVNCGVCM--------GEYFCESCK 153 (318)
Q Consensus 134 ~~~C~~Cg~~f--------~~YfC~~Ck 153 (318)
++.|+.||... +.|||+.|.
T Consensus 235 g~~Cp~Cg~~I~~~~~~gR~t~~CP~CQ 262 (263)
T PRK10445 235 GEACERCGGIIEKTTLSSRPFYWCPGCQ 262 (263)
T ss_pred CCCCCCCCCEeEEEEECCCCcEECCCCc
Confidence 47799999888 568888875
No 211
>PRK14811 formamidopyrimidine-DNA glycosylase; Provisional
Probab=29.71 E-value=29 Score=33.09 Aligned_cols=21 Identities=38% Similarity=0.961 Sum_probs=16.8
Q ss_pred cccCcCCCCcc--------ceEecCcccc
Q 021022 134 QQVCVNCGVCM--------GEYFCESCKL 154 (318)
Q Consensus 134 ~~~C~~Cg~~f--------~~YfC~~Ckl 154 (318)
++.|+.||..+ +.|||+.|.-
T Consensus 235 g~pC~~Cg~~I~~~~~~gR~ty~Cp~CQ~ 263 (269)
T PRK14811 235 GQPCPRCGTPIEKIVVGGRGTHFCPQCQP 263 (269)
T ss_pred cCCCCcCCCeeEEEEECCCCcEECCCCcC
Confidence 35799999888 6799999863
No 212
>PF13717 zinc_ribbon_4: zinc-ribbon domain
Probab=29.40 E-value=34 Score=23.02 Aligned_cols=10 Identities=30% Similarity=0.843 Sum_probs=5.5
Q ss_pred eEcCCCCCee
Q 021022 82 IRAPCCNEIF 91 (318)
Q Consensus 82 i~~pCC~~~y 91 (318)
|.||.|+.-|
T Consensus 3 i~Cp~C~~~y 12 (36)
T PF13717_consen 3 ITCPNCQAKY 12 (36)
T ss_pred EECCCCCCEE
Confidence 4555555555
No 213
>PF13695 zf-3CxxC: Zinc-binding domain
Probab=29.25 E-value=48 Score=26.88 Aligned_cols=47 Identities=28% Similarity=0.709 Sum_probs=32.0
Q ss_pred CCCCCCCCcccCchhHHHHHhHHHHHcCCCChhhhcCcceEEcCCCCCCccccceeeeccCCCCCCccccc
Q 021022 245 QYACPICSKSVCDMSKVWEKYDREIAATPMPEAYLNKKVWILCNDCGKTSNVQFHVLAQKCPNCKSYNTRL 315 (318)
Q Consensus 245 ~~~CPiCrks~~d~~~~~~~lD~~i~~~pmPeey~~~~v~IlCnDC~~~s~v~~H~lg~KC~~C~SyNT~~ 315 (318)
.+.|+.|++.+..+ .++|+-.-- ..+.+.+.++|++|..|+.+..-.
T Consensus 5 rF~C~~C~~~W~S~-----------------------~v~i~f~~~-~~g~v~~rv~~Q~C~~C~~~~~P~ 51 (98)
T PF13695_consen 5 RFQCSKCSRGWTSA-----------------------KVWILFHMY-RGGQVNMRVFGQRCKKCNPLERPY 51 (98)
T ss_pred EEECCCCCCCCccC-----------------------EEEEEEEEc-CCCeEEEEEECCCCCCCCCCCCcc
Confidence 47799998877643 233433333 346788899999999997766543
No 214
>PRK03564 formate dehydrogenase accessory protein FdhE; Provisional
Probab=29.11 E-value=53 Score=32.45 Aligned_cols=25 Identities=32% Similarity=0.739 Sum_probs=21.0
Q ss_pred CceeecCCCCccccc-cccCcCCCCc
Q 021022 119 VNQVICSLCGTEQKV-QQVCVNCGVC 143 (318)
Q Consensus 119 v~~v~C~~C~~eQ~v-~~~C~~Cg~~ 143 (318)
.+-..|+.|+++-.+ -..|++||..
T Consensus 210 ~RyL~CslC~teW~~~R~~C~~Cg~~ 235 (309)
T PRK03564 210 LRYLHCNLCESEWHVVRVKCSNCEQS 235 (309)
T ss_pred ceEEEcCCCCCcccccCccCCCCCCC
Confidence 467999999999887 4679999974
No 215
>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=28.76 E-value=45 Score=35.17 Aligned_cols=30 Identities=33% Similarity=0.727 Sum_probs=22.3
Q ss_pred cceEEcCCCCCCccccceeeeccCCCCCCcccccc
Q 021022 282 KVWILCNDCGKTSNVQFHVLAQKCPNCKSYNTRLT 316 (318)
Q Consensus 282 ~v~IlCnDC~~~s~v~~H~lg~KC~~C~SyNT~~~ 316 (318)
.+. .|++|+.... -.+.+|+.|||-|+.++
T Consensus 517 p~~-~C~~CG~~~~----~~~~~CP~CGs~~~~~~ 546 (555)
T cd01675 517 PID-ICNDCGYIGE----GEGFKCPKCGSEDVEVI 546 (555)
T ss_pred CCc-cCCCCCCCCc----CCCCCCcCCCCcCceEE
Confidence 344 8999997554 35589999999886554
No 216
>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=28.61 E-value=37 Score=23.61 Aligned_cols=19 Identities=32% Similarity=0.894 Sum_probs=10.1
Q ss_pred eecCCCCceeecCCcceeeccCc
Q 021022 164 YHCDGCGICRIGGCDNFFHCNKC 186 (318)
Q Consensus 164 yHC~~CgiCR~G~~~~ffHC~~C 186 (318)
|+|+.|+- +++ ..|||..|
T Consensus 1 y~C~~C~~--~~~--~r~~C~~C 19 (41)
T cd02337 1 YTCNECKH--HVE--TRWHCTVC 19 (41)
T ss_pred CcCCCCCC--cCC--CceECCCC
Confidence 45666654 222 55666655
No 217
>PF01599 Ribosomal_S27: Ribosomal protein S27a; InterPro: IPR002906 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. This family of ribosomal proteins consists mainly of the 40S ribosomal protein S27a which is synthesized as a C-terminal extension of ubiquitin (CEP) (IPR000626 from INTERPRO). The S27a domain compromises the C-terminal half of the protein. The synthesis of ribosomal proteins as extensions of ubiquitin promotes their incorporation into nascent ribosomes by a transient metabolic stabilisation and is required for efficient ribosome biogenesis []. The ribosomal extension protein S27a contains a basic region that is proposed to form a zinc finger; its fusion gene is proposed as a mechanism to maintain a fixed ratio between ubiquitin necessary for degrading proteins and ribosomes a source of proteins [].; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 2K4X_A 3U5C_f 3U5G_f 2XZN_9 2XZM_9.
Probab=28.57 E-value=40 Score=24.47 Aligned_cols=23 Identities=22% Similarity=0.797 Sum_probs=14.0
Q ss_pred cccccCc--CCCCc------cceEecCcccc
Q 021022 132 KVQQVCV--NCGVC------MGEYFCESCKL 154 (318)
Q Consensus 132 ~v~~~C~--~Cg~~------f~~YfC~~Ckl 154 (318)
.....|| .||.- +.|++|.+|.+
T Consensus 16 r~rk~CP~~~CG~GvFMA~H~dR~~CGKCg~ 46 (47)
T PF01599_consen 16 RLRKECPSPRCGAGVFMAEHKDRHYCGKCGY 46 (47)
T ss_dssp ESSEE-TSTTTTSSSEEEE-SSEEEETTTSS
T ss_pred EhhhcCCCcccCCceEeeecCCCccCCCccc
Confidence 3456788 78774 26677777754
No 218
>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=28.53 E-value=44 Score=24.03 Aligned_cols=12 Identities=25% Similarity=1.018 Sum_probs=6.7
Q ss_pred CCCCCCcccCch
Q 021022 247 ACPICSKSVCDM 258 (318)
Q Consensus 247 ~CPiCrks~~d~ 258 (318)
.||+|.+++..-
T Consensus 22 ~CPlC~r~l~~e 33 (54)
T PF04423_consen 22 CCPLCGRPLDEE 33 (54)
T ss_dssp E-TTT--EE-HH
T ss_pred cCCCCCCCCCHH
Confidence 899999999853
No 219
>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=28.37 E-value=32 Score=29.53 Aligned_cols=39 Identities=28% Similarity=0.606 Sum_probs=25.9
Q ss_pred CCCCCCeeecCCCCceeecCCcceeeccCccceeecccccccccc
Q 021022 157 DDTSKKQYHCDGCGICRIGGCDNFFHCNKCRCCYSMLLKNSHPCV 201 (318)
Q Consensus 157 dd~~k~~yHC~~CgiCR~G~~~~ffHC~~C~~C~s~~l~~~H~Ci 201 (318)
++.....-.|.. |++-....-.||..||.|+-.- .|.|.
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 4555667899999999998743 46665
No 220
>PLN02638 cellulose synthase A (UDP-forming), catalytic subunit
Probab=28.10 E-value=48 Score=37.94 Aligned_cols=56 Identities=16% Similarity=0.412 Sum_probs=39.8
Q ss_pred cCCCCCCCCcccccccccCCceeEEc---CCCCccchHHHHHHHhcCCCCCCCCCcccC
Q 021022 201 VEGAMHHDCPVCCEYLFETRQDVIVL---PCGHTIHKNCLKEMREHHQYACPICSKSVC 256 (318)
Q Consensus 201 ie~~~~~~CpIClE~lf~s~~~v~~L---pCGH~fH~~Cl~~wl~~~~~~CPiCrks~~ 256 (318)
.+......|.||.|++-.+.+.-... -||--.++.|++-=.+.++..||.|+..+.
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 34445679999999865544443444 466779999995556667788999998765
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=28.01 E-value=38 Score=23.61 Aligned_cols=21 Identities=43% Similarity=0.947 Sum_probs=9.8
Q ss_pred eecCCCCceeecCCcceeeccCcc
Q 021022 164 YHCDGCGICRIGGCDNFFHCNKCR 187 (318)
Q Consensus 164 yHC~~CgiCR~G~~~~ffHC~~C~ 187 (318)
|.|+.|+. -+- ...|||..|.
T Consensus 1 ~~C~~C~~-~i~--g~r~~C~~C~ 21 (46)
T cd02249 1 YSCDGCLK-PIV--GVRYHCLVCE 21 (46)
T ss_pred CCCcCCCC-CCc--CCEEECCCCC
Confidence 34555554 221 2456665553
No 222
>PF14952 zf-tcix: Putative treble-clef, zinc-finger, Zn-binding
Probab=27.98 E-value=28 Score=25.00 Aligned_cols=12 Identities=50% Similarity=1.298 Sum_probs=10.0
Q ss_pred ccCCCCCCcccc
Q 021022 303 QKCPNCKSYNTR 314 (318)
Q Consensus 303 ~KC~~C~SyNT~ 314 (318)
-||+.||-||-.
T Consensus 12 rkCp~CGt~NG~ 23 (44)
T PF14952_consen 12 RKCPKCGTYNGT 23 (44)
T ss_pred ccCCcCcCccCc
Confidence 389999999954
No 223
>COG1998 RPS31 Ribosomal protein S27AE [Translation, ribosomal structure and biogenesis]
Probab=27.36 E-value=38 Score=25.06 Aligned_cols=19 Identities=32% Similarity=0.962 Sum_probs=10.7
Q ss_pred ccCcCCCC--cc----ceEecCccc
Q 021022 135 QVCVNCGV--CM----GEYFCESCK 153 (318)
Q Consensus 135 ~~C~~Cg~--~f----~~YfC~~Ck 153 (318)
..||+||. -| .||.|.+|.
T Consensus 20 ~~CPrCG~gvfmA~H~dR~~CGkCg 44 (51)
T COG1998 20 RFCPRCGPGVFMADHKDRWACGKCG 44 (51)
T ss_pred ccCCCCCCcchhhhcCceeEecccc
Confidence 46888883 33 345555553
No 224
>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=27.32 E-value=42 Score=22.31 Aligned_cols=22 Identities=27% Similarity=0.788 Sum_probs=12.6
Q ss_pred eecCCCCcccc---ccccCcCCCCc
Q 021022 122 VICSLCGTEQK---VQQVCVNCGVC 143 (318)
Q Consensus 122 v~C~~C~~eQ~---v~~~C~~Cg~~ 143 (318)
-+|..|+..-. .-+.||.||+.
T Consensus 3 ~~C~~CG~i~~g~~~p~~CP~Cg~~ 27 (34)
T cd00729 3 WVCPVCGYIHEGEEAPEKCPICGAP 27 (34)
T ss_pred EECCCCCCEeECCcCCCcCcCCCCc
Confidence 35666765522 23567777764
No 225
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=26.99 E-value=40 Score=30.46 Aligned_cols=10 Identities=40% Similarity=0.956 Sum_probs=5.5
Q ss_pred CCCCcccccc
Q 021022 206 HHDCPVCCEY 215 (318)
Q Consensus 206 ~~~CpIClE~ 215 (318)
...||+|.+.
T Consensus 136 ~F~Cp~Cg~~ 145 (178)
T PRK06266 136 GFRCPQCGEM 145 (178)
T ss_pred CCcCCCCCCC
Confidence 3556666553
No 226
>PRK01103 formamidopyrimidine/5-formyluracil/ 5-hydroxymethyluracil DNA glycosylase; Validated
Probab=26.95 E-value=35 Score=32.46 Aligned_cols=20 Identities=30% Similarity=1.039 Sum_probs=15.7
Q ss_pred cccCcCCCCcc--------ceEecCccc
Q 021022 134 QQVCVNCGVCM--------GEYFCESCK 153 (318)
Q Consensus 134 ~~~C~~Cg~~f--------~~YfC~~Ck 153 (318)
++.|+.||... +.|||+.|.
T Consensus 245 g~pC~~Cg~~I~~~~~~gR~t~~CP~CQ 272 (274)
T PRK01103 245 GEPCRRCGTPIEKIKQGGRSTFFCPRCQ 272 (274)
T ss_pred CCCCCCCCCeeEEEEECCCCcEECcCCC
Confidence 35699999887 568888885
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=26.75 E-value=50 Score=22.78 Aligned_cols=31 Identities=29% Similarity=0.616 Sum_probs=18.4
Q ss_pred eEEcCCCCCCcccccee---eeccCCCCCCcccc
Q 021022 284 WILCNDCGKTSNVQFHV---LAQKCPNCKSYNTR 314 (318)
Q Consensus 284 ~IlCnDC~~~s~v~~H~---lg~KC~~C~SyNT~ 314 (318)
...|.+|+...++...+ ....|+.||+-+.+
T Consensus 5 ey~C~~Cg~~fe~~~~~~~~~~~~CP~Cg~~~~~ 38 (42)
T PF09723_consen 5 EYRCEECGHEFEVLQSISEDDPVPCPECGSTEVR 38 (42)
T ss_pred EEEeCCCCCEEEEEEEcCCCCCCcCCCCCCCceE
Confidence 35677887655443222 34678888884443
No 228
>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=26.66 E-value=26 Score=24.01 Aligned_cols=13 Identities=38% Similarity=1.076 Sum_probs=5.5
Q ss_pred cceEecCcccccc
Q 021022 144 MGEYFCESCKLFD 156 (318)
Q Consensus 144 f~~YfC~~Ckl~d 156 (318)
|-+|||+-|+.|=
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 4689999998775
No 229
>PF13719 zinc_ribbon_5: zinc-ribbon domain
Probab=26.61 E-value=40 Score=22.73 Aligned_cols=9 Identities=44% Similarity=1.113 Sum_probs=4.5
Q ss_pred eeecCCCCc
Q 021022 121 QVICSLCGT 129 (318)
Q Consensus 121 ~v~C~~C~~ 129 (318)
.|.|+.|++
T Consensus 25 ~vrC~~C~~ 33 (37)
T PF13719_consen 25 KVRCPKCGH 33 (37)
T ss_pred EEECCCCCc
Confidence 455555544
No 230
>TIGR00373 conserved hypothetical protein TIGR00373. This family of proteins is, so far, restricted to archaeal genomes. The family appears to be distantly related to the N-terminal region of the eukaryotic transcription initiation factor IIE alpha chain.
Probab=26.49 E-value=37 Score=29.95 Aligned_cols=8 Identities=38% Similarity=1.140 Sum_probs=3.6
Q ss_pred eeeccCcc
Q 021022 180 FFHCNKCR 187 (318)
Q Consensus 180 ffHC~~C~ 187 (318)
.|+|..||
T Consensus 128 ~F~Cp~Cg 135 (158)
T TIGR00373 128 NFTCPRCG 135 (158)
T ss_pred CCcCCCCC
Confidence 34444444
No 231
>KOG1312 consensus DHHC-type Zn-finger proteins [General function prediction only]
Probab=26.31 E-value=18 Score=35.71 Aligned_cols=32 Identities=28% Similarity=0.682 Sum_probs=26.9
Q ss_pred CCCCceeecCCcceeeccCccceeecccccccccc
Q 021022 167 DGCGICRIGGCDNFFHCNKCRCCYSMLLKNSHPCV 201 (318)
Q Consensus 167 ~~CgiCR~G~~~~ffHC~~C~~C~s~~l~~~H~Ci 201 (318)
-+|..|++.+.-...||-.||.|... ..|.|+
T Consensus 149 ~kCSTCki~KPARSKHCsiCNrCV~r---fDHHCi 180 (341)
T KOG1312|consen 149 VKCSTCKIRKPARSKHCSICNRCVHR---FDHHCI 180 (341)
T ss_pred CccccccCCCccccccchHHHHHHHH---hccceE
Confidence 57888899888889999999999864 368887
No 232
>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=26.22 E-value=23 Score=36.24 Aligned_cols=51 Identities=27% Similarity=0.515 Sum_probs=0.5
Q ss_pred CCCCCCCccccccc----------ccCCceeEEcCCCCccchHHHHHHHhc-----CCCCCCCCCcccC
Q 021022 203 GAMHHDCPVCCEYL----------FETRQDVIVLPCGHTIHKNCLKEMREH-----HQYACPICSKSVC 256 (318)
Q Consensus 203 ~~~~~~CpIClE~l----------f~s~~~v~~LpCGH~fH~~Cl~~wl~~-----~~~~CPiCrks~~ 256 (318)
+++.-.|||=|..| .+...+.++|.|||++= +-.|-.. ....||+|+..=.
T Consensus 274 Na~rpQCPVglnTL~fp~~~~~~~~~~~qP~VYl~CGHVhG---~h~Wg~~~~~~~~~r~CPlCr~~g~ 339 (416)
T PF04710_consen 274 NAGRPQCPVGLNTLVFPSKSRKDVPDERQPWVYLNCGHVHG---YHNWGQDSDRDPRSRTCPLCRQVGP 339 (416)
T ss_dssp S--------------------------------------------------------------------
T ss_pred hhcCCCCCcCCCccccccccccccccccCceeeccccceee---ecccccccccccccccCCCccccCC
Confidence 56778899987544 33456789999998642 2246321 2467999996543
No 233
>PRK03564 formate dehydrogenase accessory protein FdhE; Provisional
Probab=25.81 E-value=72 Score=31.53 Aligned_cols=24 Identities=38% Similarity=0.974 Sum_probs=16.5
Q ss_pred ceEEcCCCCCCccccceeeeccCCCCCC
Q 021022 283 VWILCNDCGKTSNVQFHVLAQKCPNCKS 310 (318)
Q Consensus 283 v~IlCnDC~~~s~v~~H~lg~KC~~C~S 310 (318)
..-.|.-|+ ..+|+.-.||++|++
T Consensus 211 RyL~CslC~----teW~~~R~~C~~Cg~ 234 (309)
T PRK03564 211 RYLHCNLCE----SEWHVVRVKCSNCEQ 234 (309)
T ss_pred eEEEcCCCC----CcccccCccCCCCCC
Confidence 456677776 556777777777774
No 234
>KOG3362 consensus Predicted BBOX Zn-finger protein [General function prediction only]
Probab=25.71 E-value=23 Score=31.53 Aligned_cols=25 Identities=32% Similarity=0.883 Sum_probs=15.4
Q ss_pred ceEecCccccccCCCCCCeeecCCCC--ceeec
Q 021022 145 GEYFCESCKLFDDDTSKKQYHCDGCG--ICRIG 175 (318)
Q Consensus 145 ~~YfC~~Ckl~ddd~~k~~yHC~~Cg--iCR~G 175 (318)
.+-||++|-+| ++|-|-.|| +|-++
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 35566677644 457777777 56654
No 235
>PF05502 Dynactin_p62: Dynactin p62 family; InterPro: IPR008603 Dynactin is a multi-subunit complex and a required cofactor for most, or all, o f the cellular processes powered by the microtubule-based motor cytoplasmic dyn ein. p62 binds directly to the Arp1 subunit of dynactin [, ].
Probab=25.17 E-value=55 Score=34.09 Aligned_cols=18 Identities=28% Similarity=1.036 Sum_probs=11.4
Q ss_pred CcCC-CCccceEecCcccc
Q 021022 137 CVNC-GVCMGEYFCESCKL 154 (318)
Q Consensus 137 C~~C-g~~f~~YfC~~Ckl 154 (318)
|+.| ...+-.|||+.|-+
T Consensus 16 c~~c~~~Ei~~~yCp~CL~ 34 (483)
T PF05502_consen 16 CPRCVSEEIDSYYCPNCLF 34 (483)
T ss_pred ChhhcccccceeECccccc
Confidence 4444 56667777777754
No 236
>TIGR00577 fpg formamidopyrimidine-DNA glycosylase (fpg). All proteins in the FPG family with known functions are FAPY-DNA glycosylases that function in base excision repair. Homologous to endonuclease VIII (nei). This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=25.00 E-value=40 Score=32.13 Aligned_cols=20 Identities=35% Similarity=1.027 Sum_probs=15.1
Q ss_pred cccCcCCCCcc--------ceEecCccc
Q 021022 134 QQVCVNCGVCM--------GEYFCESCK 153 (318)
Q Consensus 134 ~~~C~~Cg~~f--------~~YfC~~Ck 153 (318)
++.|+.||... +.|||+.|.
T Consensus 245 g~pC~~Cg~~I~~~~~~gR~t~~CP~CQ 272 (272)
T TIGR00577 245 GEPCRRCGTPIEKIKVGGRGTHFCPQCQ 272 (272)
T ss_pred CCCCCCCCCeeEEEEECCCCCEECCCCC
Confidence 35799999887 567887774
No 237
>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=24.79 E-value=34 Score=21.72 Aligned_cols=11 Identities=27% Similarity=1.165 Sum_probs=7.8
Q ss_pred ceEecCccccc
Q 021022 145 GEYFCESCKLF 155 (318)
Q Consensus 145 ~~YfC~~Ckl~ 155 (318)
+.|||+.|+.+
T Consensus 2 ~~~~C~~C~~~ 12 (35)
T smart00451 2 GGFYCKLCNVT 12 (35)
T ss_pred cCeEccccCCc
Confidence 56788888654
No 238
>KOG1815 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=24.73 E-value=46 Score=33.97 Aligned_cols=37 Identities=24% Similarity=0.597 Sum_probs=29.6
Q ss_pred CCCCCCcccccccccCCceeEEcCCCCccchHHHHHHHhc
Q 021022 204 AMHHDCPVCCEYLFETRQDVIVLPCGHTIHKNCLKEMREH 243 (318)
Q Consensus 204 ~~~~~CpIClE~lf~s~~~v~~LpCGH~fH~~Cl~~wl~~ 243 (318)
.....|.||.+. ... ....+.|||.|+..|...++..
T Consensus 68 ~~~~~c~ic~~~-~~~--~~~~~~c~H~~c~~cw~~yl~~ 104 (444)
T KOG1815|consen 68 KGDVQCGICVES-YDG--EIIGLGCGHPFCPPCWTGYLGT 104 (444)
T ss_pred CccccCCcccCC-Ccc--hhhhcCCCcHHHHHHHHHHhhh
Confidence 456889999984 321 4677899999999999999864
No 239
>KOG1044 consensus Actin-binding LIM Zn-finger protein Limatin involved in axon guidance [Signal transduction mechanisms; Cytoskeleton]
Probab=24.64 E-value=99 Score=33.34 Aligned_cols=136 Identities=24% Similarity=0.438 Sum_probs=71.9
Q ss_pred CCCCCeeecCCCCc---eeecC-Ccceee-----ccCccceeeccccccccccCCCCCCCC-cccccccccCCceeEEcC
Q 021022 158 DTSKKQYHCDGCGI---CRIGG-CDNFFH-----CNKCRCCYSMLLKNSHPCVEGAMHHDC-PVCCEYLFETRQDVIVLP 227 (318)
Q Consensus 158 d~~k~~yHC~~Cgi---CR~G~-~~~ffH-----C~~C~~C~s~~l~~~H~Cie~~~~~~C-pIClE~lf~s~~~v~~Lp 227 (318)
...+..-||+.|+- +-|+. .+++|| |++||.=+....+ -+++-|+ ..+ .-|.+. . +..++..
T Consensus 11 ~~~~~~i~c~~c~~kc~gevlrv~d~~fhi~cf~c~~cg~~la~~gf-f~k~~~~---~ygt~~c~~~--~--~gevvsa 82 (670)
T KOG1044|consen 11 QTGKQGIKCDKCRKKCSGEVLRVNDNHFHINCFQCKKCGRNLAEGGF-FTKPENR---LYGTDDCRAF--V--EGEVVST 82 (670)
T ss_pred cccccceehhhhCCccccceeEeeccccceeeeeccccCCCcccccc-eecccce---eecccchhhh--c--cceeEec
Confidence 34677788888872 22222 345555 5555554444332 2455542 222 334432 1 1234444
Q ss_pred CCCccchHHHHHHHhcCCCCCCCCCcccCchhH-HH--HHhHHHHHcCCCChhhhcCcceEEcCCCCCCc---------c
Q 021022 228 CGHTIHKNCLKEMREHHQYACPICSKSVCDMSK-VW--EKYDREIAATPMPEAYLNKKVWILCNDCGKTS---------N 295 (318)
Q Consensus 228 CGH~fH~~Cl~~wl~~~~~~CPiCrks~~d~~~-~~--~~lD~~i~~~pmPeey~~~~v~IlCnDC~~~s---------~ 295 (318)
=|-+||..| +.|-+|+.++..-+. .+ +..--+.-.|+||-.=.......-|--|++.- .
T Consensus 83 ~gktyh~~c---------f~cs~ck~pf~~g~~vt~~gk~~~c~~c~~~~~~~p~~~~~ps~cagc~~~lk~gq~llald 153 (670)
T KOG1044|consen 83 LGKTYHPKC---------FSCSTCKSPFKSGDKVTFSGKECLCQTCSQPMPVSPAESYGPSTCAGCGEELKNGQALLALD 153 (670)
T ss_pred ccceecccc---------ceecccCCCCCCCCeeeecchhhhhhhhcCcccCCcccccCCccccchhhhhhccceeeeec
Confidence 588888776 457788888753111 01 11222333455543312223345577777532 5
Q ss_pred ccceeeeccCCCCCC
Q 021022 296 VQFHVLAQKCPNCKS 310 (318)
Q Consensus 296 v~~H~lg~KC~~C~S 310 (318)
-++|+.+-||..|.-
T Consensus 154 ~qwhv~cfkc~~c~~ 168 (670)
T KOG1044|consen 154 KQWHVSCFKCKSCSA 168 (670)
T ss_pred cceeeeeeehhhhcc
Confidence 689999999998864
No 240
>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=24.41 E-value=87 Score=21.82 Aligned_cols=9 Identities=44% Similarity=1.047 Sum_probs=5.1
Q ss_pred ccCcCCCCc
Q 021022 135 QVCVNCGVC 143 (318)
Q Consensus 135 ~~C~~Cg~~ 143 (318)
.+||.||..
T Consensus 19 ~~CP~Cg~~ 27 (46)
T PF12760_consen 19 FVCPHCGST 27 (46)
T ss_pred CCCCCCCCe
Confidence 346666654
No 241
>TIGR02098 MJ0042_CXXC MJ0042 family finger-like domain. This domain contains a CXXCX(19)CXXC motif suggestive of both zinc fingers and thioredoxin, usually found at the N-terminus of prokaryotic proteins. One partially characterized gene, agmX, is among a large set in Myxococcus whose interruption affects adventurous gliding motility.
Probab=24.25 E-value=55 Score=21.59 Aligned_cols=9 Identities=44% Similarity=1.113 Sum_probs=4.5
Q ss_pred eeecCCCCc
Q 021022 121 QVICSLCGT 129 (318)
Q Consensus 121 ~v~C~~C~~ 129 (318)
.+.|+.|++
T Consensus 25 ~v~C~~C~~ 33 (38)
T TIGR02098 25 KVRCGKCGH 33 (38)
T ss_pred EEECCCCCC
Confidence 455555544
No 242
>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=24.16 E-value=86 Score=31.65 Aligned_cols=26 Identities=19% Similarity=0.551 Sum_probs=18.2
Q ss_pred cchHHHHHHHhc------------CCCCCCCCCcccCc
Q 021022 232 IHKNCLKEMREH------------HQYACPICSKSVCD 257 (318)
Q Consensus 232 fH~~Cl~~wl~~------------~~~~CPiCrks~~d 257 (318)
-+.+|+-+|+.. ++-.||.||+.+.-
T Consensus 315 WC~~Cm~kwFasrQd~~~~~~Wl~~~~~CPtCRa~FCi 352 (358)
T PF10272_consen 315 WCLECMGKWFASRQDQQHPETWLSGKCPCPTCRAKFCI 352 (358)
T ss_pred HHHHHHHHHhhhcCCCCChhhhhcCCCCCCCCccccee
Confidence 466777777642 34579999998753
No 243
>PF15353 HECA: Headcase protein family homologue
Probab=24.16 E-value=45 Score=28.23 Aligned_cols=16 Identities=25% Similarity=0.891 Sum_probs=13.7
Q ss_pred CCCCccchHHHHHHHh
Q 021022 227 PCGHTIHKNCLKEMRE 242 (318)
Q Consensus 227 pCGH~fH~~Cl~~wl~ 242 (318)
|-|+.||.+||++|-.
T Consensus 39 p~~~~MH~~CF~~wE~ 54 (107)
T PF15353_consen 39 PFGQYMHRECFEKWED 54 (107)
T ss_pred CCCCchHHHHHHHHHH
Confidence 4489999999999954
No 244
>KOG3113 consensus Uncharacterized conserved protein [Function unknown]
Probab=24.16 E-value=67 Score=31.27 Aligned_cols=50 Identities=20% Similarity=0.375 Sum_probs=36.7
Q ss_pred CCCCCCcccccccccCCceeEEcCCCCccchHHHHHHHhcCCCCCCCCCcccC
Q 021022 204 AMHHDCPVCCEYLFETRQDVIVLPCGHTIHKNCLKEMREHHQYACPICSKSVC 256 (318)
Q Consensus 204 ~~~~~CpIClE~lf~s~~~v~~LpCGH~fH~~Cl~~wl~~~~~~CPiCrks~~ 256 (318)
.....|||=.-.|...-+=....+|||+|-..-+.+.- ...|++|...+.
T Consensus 109 ~a~fiCPvtgleMng~~~F~~l~~CGcV~SerAlKeik---as~C~~C~a~y~ 158 (293)
T KOG3113|consen 109 RARFICPVTGLEMNGKYRFCALRCCGCVFSERALKEIK---ASVCHVCGAAYQ 158 (293)
T ss_pred cceeecccccceecceEEEEEEeccceeccHHHHHHhh---hccccccCCccc
Confidence 34568999865554433334556999999999988874 367999999886
No 245
>PRK00464 nrdR transcriptional regulator NrdR; Validated
Probab=24.12 E-value=47 Score=29.56 Aligned_cols=11 Identities=27% Similarity=0.990 Sum_probs=5.5
Q ss_pred CcCCCCccceE
Q 021022 137 CVNCGVCMGEY 147 (318)
Q Consensus 137 C~~Cg~~f~~Y 147 (318)
|++||..|+.|
T Consensus 31 c~~c~~~f~~~ 41 (154)
T PRK00464 31 CLACGKRFTTF 41 (154)
T ss_pred ccccCCcceEe
Confidence 44555555444
No 246
>KOG3842 consensus Adaptor protein Pellino [Signal transduction mechanisms]
Probab=24.04 E-value=37 Score=34.05 Aligned_cols=47 Identities=30% Similarity=0.654 Sum_probs=31.6
Q ss_pred CCCCCCCccccccc----------ccCCceeEEcCCCCc--cchHHHHHHHhc-----CCCCCCCCCcc
Q 021022 203 GAMHHDCPVCCEYL----------FETRQDVIVLPCGHT--IHKNCLKEMREH-----HQYACPICSKS 254 (318)
Q Consensus 203 ~~~~~~CpIClE~l----------f~s~~~v~~LpCGH~--fH~~Cl~~wl~~-----~~~~CPiCrks 254 (318)
++..-.|||=|..| .+..++.++|.|||+ +| .|=.. ....||+|+..
T Consensus 287 NA~RPQCPVglnTL~~P~~~~~~~~~~~QP~vYl~CGHV~G~H-----~WG~~e~~g~~~r~CPmC~~~ 350 (429)
T KOG3842|consen 287 NAARPQCPVGLNTLAFPSKRRKRVVDEKQPWVYLNCGHVHGYH-----NWGVRENTGQRERECPMCRVV 350 (429)
T ss_pred hccCCCCCcccceeecccccccccccccCCeEEEecccccccc-----ccccccccCcccCcCCeeeee
Confidence 45677899988655 223467899999976 44 46321 23569999954
No 247
>PF14803 Nudix_N_2: Nudix N-terminal; PDB: 3CNG_C.
Probab=24.03 E-value=49 Score=22.27 Aligned_cols=28 Identities=25% Similarity=0.799 Sum_probs=11.4
Q ss_pred cCcCCCCccceEecCccccccCCCCCCeeecCCCC
Q 021022 136 VCVNCGVCMGEYFCESCKLFDDDTSKKQYHCDGCG 170 (318)
Q Consensus 136 ~C~~Cg~~f~~YfC~~Ckl~ddd~~k~~yHC~~Cg 170 (318)
.|++||.++.. ++-++| ++.-+-|+.||
T Consensus 2 fC~~CG~~l~~------~ip~gd-~r~R~vC~~Cg 29 (34)
T PF14803_consen 2 FCPQCGGPLER------RIPEGD-DRERLVCPACG 29 (34)
T ss_dssp B-TTT--B-EE------E--TT--SS-EEEETTTT
T ss_pred ccccccChhhh------hcCCCC-CccceECCCCC
Confidence 46777766533 223332 46666677766
No 248
>PF08274 PhnA_Zn_Ribbon: PhnA Zinc-Ribbon ; InterPro: IPR013987 The PhnA protein family includes the uncharacterised Escherichia coli protein PhnA and its homologues. The E. coli phnA gene is part of a large operon associated with alkylphosphonate uptake and carbon-phosphorus bond cleavage []. The protein is not related to the characterised phosphonoacetate hydrolase designated PhnA []. This entry represents the N-terminal domain of PhnA, which is predicted to form a zinc-ribbon.; PDB: 2AKL_A.
Probab=24.01 E-value=42 Score=22.08 Aligned_cols=23 Identities=26% Similarity=0.582 Sum_probs=9.4
Q ss_pred cCcCCCCccceEecCccccccCCCCCCeeecCCCC
Q 021022 136 VCVNCGVCMGEYFCESCKLFDDDTSKKQYHCDGCG 170 (318)
Q Consensus 136 ~C~~Cg~~f~~YfC~~Ckl~ddd~~k~~yHC~~Cg 170 (318)
.|+.|+..++- .+..+|-|+.||
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 46666665543 234577777776
No 249
>PRK13945 formamidopyrimidine-DNA glycosylase; Provisional
Probab=23.99 E-value=44 Score=32.06 Aligned_cols=20 Identities=25% Similarity=0.884 Sum_probs=15.5
Q ss_pred cccCcCCCCcc--------ceEecCccc
Q 021022 134 QQVCVNCGVCM--------GEYFCESCK 153 (318)
Q Consensus 134 ~~~C~~Cg~~f--------~~YfC~~Ck 153 (318)
++.|+.||... +.|||+.|.
T Consensus 254 g~pC~~Cg~~I~~~~~~gR~t~~CP~CQ 281 (282)
T PRK13945 254 GKPCRKCGTPIERIKLAGRSTHWCPNCQ 281 (282)
T ss_pred cCCCCcCCCeeEEEEECCCccEECCCCc
Confidence 46799999887 567887774
No 250
>smart00778 Prim_Zn_Ribbon Zinc-binding domain of primase-helicase. This region represents the zinc binding domain. It is found in the N-terminal region of the bacteriophage P4 alpha protein, which is a multifunctional protein with origin recognition, helicase and primase activities.
Probab=23.71 E-value=73 Score=21.89 Aligned_cols=30 Identities=33% Similarity=0.770 Sum_probs=19.3
Q ss_pred ccCcCCCCccceEecCccccccCCCCCCeeecCCCCc
Q 021022 135 QVCVNCGVCMGEYFCESCKLFDDDTSKKQYHCDGCGI 171 (318)
Q Consensus 135 ~~C~~Cg~~f~~YfC~~Ckl~ddd~~k~~yHC~~Cgi 171 (318)
..||.||-.=.. + |+|...+.-|+|..||.
T Consensus 4 ~pCP~CGG~DrF------r-~~d~~g~G~~~C~~Cg~ 33 (37)
T smart00778 4 GPCPNCGGSDRF------R-FDDKDGRGTWFCSVCGA 33 (37)
T ss_pred cCCCCCCCcccc------c-cccCCCCcCEEeCCCCC
Confidence 458888762211 2 46666678888888864
No 251
>COG2051 RPS27A Ribosomal protein S27E [Translation, ribosomal structure and biogenesis]
Probab=22.99 E-value=47 Score=25.90 Aligned_cols=28 Identities=39% Similarity=0.739 Sum_probs=21.8
Q ss_pred ceeecCCCCcccccc------ccCcCCCCccceE
Q 021022 120 NQVICSLCGTEQKVQ------QVCVNCGVCMGEY 147 (318)
Q Consensus 120 ~~v~C~~C~~eQ~v~------~~C~~Cg~~f~~Y 147 (318)
-.|.|.-|+.+|-+= -.|..||..+++-
T Consensus 18 l~VkCpdC~N~q~vFshast~V~C~~CG~~l~~P 51 (67)
T COG2051 18 LRVKCPDCGNEQVVFSHASTVVTCLICGTTLAEP 51 (67)
T ss_pred EEEECCCCCCEEEEeccCceEEEecccccEEEec
Confidence 369999999999861 4599999887654
No 252
>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=22.96 E-value=84 Score=32.70 Aligned_cols=46 Identities=26% Similarity=0.655 Sum_probs=29.2
Q ss_pred CceeecCCCCccccccccCcCCCCccc------eEecCccccccCCCCCCeeecCCCCce
Q 021022 119 VNQVICSLCGTEQKVQQVCVNCGVCMG------EYFCESCKLFDDDTSKKQYHCDGCGIC 172 (318)
Q Consensus 119 v~~v~C~~C~~eQ~v~~~C~~Cg~~f~------~YfC~~Ckl~ddd~~k~~yHC~~CgiC 172 (318)
...++|..|+.. ..|++|+..+. .-.|.-|.+- .+.+..|+.||-=
T Consensus 211 a~~~~C~~Cg~~----~~C~~C~~~l~~h~~~~~l~Ch~Cg~~----~~~~~~Cp~C~s~ 262 (505)
T TIGR00595 211 SKNLLCRSCGYI----LCCPNCDVSLTYHKKEGKLRCHYCGYQ----EPIPKTCPQCGSE 262 (505)
T ss_pred CCeeEhhhCcCc----cCCCCCCCceEEecCCCeEEcCCCcCc----CCCCCCCCCCCCC
Confidence 346788888864 36899988774 3346655532 3345567777643
No 253
>PF01667 Ribosomal_S27e: Ribosomal protein S27; InterPro: IPR000592 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 [, ]. A number of eukaryotic and archaeal ribosomal proteins can be grouped on the basis of sequence similarities. One of these families include mammalian, yeast, Chlamydomonas reinhardtii and Entamoeba histolytica S27, and Methanocaldococcus jannaschii (Methanococcus jannaschii) MJ0250 []. These proteins have from 62 to 87 amino acids. They contain, in their central section, a putative zinc-finger region of the type C-x(2)-C-x(14)-C-x(2)-C.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 1QXF_A 3IZ6_X 2XZN_6 2XZM_6 3U5G_b 3IZB_X 3U5C_b.
Probab=22.58 E-value=53 Score=24.56 Aligned_cols=34 Identities=29% Similarity=0.518 Sum_probs=20.6
Q ss_pred eeecCCCCccccc---c---ccCcCCCCccceEecCcccc
Q 021022 121 QVICSLCGTEQKV---Q---QVCVNCGVCMGEYFCESCKL 154 (318)
Q Consensus 121 ~v~C~~C~~eQ~v---~---~~C~~Cg~~f~~YfC~~Ckl 154 (318)
.|.|..|..+|.+ + -.|..||..+++-.=++-+|
T Consensus 7 ~VkCp~C~~~q~vFSha~t~V~C~~Cg~~L~~PtGGKa~l 46 (55)
T PF01667_consen 7 DVKCPGCYNIQTVFSHAQTVVKCVVCGTVLAQPTGGKARL 46 (55)
T ss_dssp EEE-TTT-SEEEEETT-SS-EE-SSSTSEEEEE-SSSEEE
T ss_pred EEECCCCCCeeEEEecCCeEEEcccCCCEecCCCCcCeEE
Confidence 6788888888876 1 35888888887765554444
No 254
>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=22.52 E-value=40 Score=22.33 Aligned_cols=23 Identities=35% Similarity=0.702 Sum_probs=11.2
Q ss_pred ceeecCCCCccc-cccccCcCCCC
Q 021022 120 NQVICSLCGTEQ-KVQQVCVNCGV 142 (318)
Q Consensus 120 ~~v~C~~C~~eQ-~v~~~C~~Cg~ 142 (318)
.--.|..|++.+ |+...|++||.
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 345677777774 45677777764
No 255
>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=22.33 E-value=60 Score=20.43 Aligned_cols=9 Identities=33% Similarity=1.162 Sum_probs=4.1
Q ss_pred CeeecCCCC
Q 021022 162 KQYHCDGCG 170 (318)
Q Consensus 162 ~~yHC~~Cg 170 (318)
-.|.|+.||
T Consensus 15 v~f~CPnCG 23 (24)
T PF07754_consen 15 VPFPCPNCG 23 (24)
T ss_pred ceEeCCCCC
Confidence 344444444
No 256
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=22.22 E-value=32 Score=29.76 Aligned_cols=10 Identities=30% Similarity=0.574 Sum_probs=6.2
Q ss_pred cCcCCCCccc
Q 021022 136 VCVNCGVCMG 145 (318)
Q Consensus 136 ~C~~Cg~~f~ 145 (318)
.||+||..|.
T Consensus 101 ~Cp~C~~~y~ 110 (147)
T smart00531 101 KCPNCQSKYT 110 (147)
T ss_pred ECcCCCCEee
Confidence 4777776553
No 257
>PF05502 Dynactin_p62: Dynactin p62 family; InterPro: IPR008603 Dynactin is a multi-subunit complex and a required cofactor for most, or all, o f the cellular processes powered by the microtubule-based motor cytoplasmic dyn ein. p62 binds directly to the Arp1 subunit of dynactin [, ].
Probab=21.98 E-value=51 Score=34.31 Aligned_cols=10 Identities=50% Similarity=1.437 Sum_probs=6.5
Q ss_pred CeecCcchHh
Q 021022 89 EIFDCRHCHN 98 (318)
Q Consensus 89 ~~y~Cr~CHd 98 (318)
+.|-|+.||.
T Consensus 4 ~L~fC~~C~~ 13 (483)
T PF05502_consen 4 ELYFCEHCHK 13 (483)
T ss_pred cceecccccc
Confidence 4567777773
No 258
>PF11023 DUF2614: Protein of unknown function (DUF2614); InterPro: IPR020912 This entry describes proteins of unknown function, which are thought to be membrane proteins.; GO: 0005887 integral to plasma membrane
Probab=21.91 E-value=56 Score=27.93 Aligned_cols=28 Identities=29% Similarity=0.688 Sum_probs=20.6
Q ss_pred ccCceeecCCCCccccc---cccCcCCCCcc
Q 021022 117 HEVNQVICSLCGTEQKV---QQVCVNCGVCM 144 (318)
Q Consensus 117 ~~v~~v~C~~C~~eQ~v---~~~C~~Cg~~f 144 (318)
.++..|.|..|+++-.. .+.|.+|+.++
T Consensus 65 tkav~V~CP~C~K~TKmLGr~D~CM~C~~pL 95 (114)
T PF11023_consen 65 TKAVQVECPNCGKQTKMLGRVDACMHCKEPL 95 (114)
T ss_pred ccceeeECCCCCChHhhhchhhccCcCCCcC
Confidence 34567889999887543 46899998876
No 259
>KOG0269 consensus WD40 repeat-containing protein [Function unknown]
Probab=21.43 E-value=47 Score=36.66 Aligned_cols=49 Identities=20% Similarity=0.373 Sum_probs=39.6
Q ss_pred cCcCCCCccceE---ecCccccccCCCCCCeeecCCCCceeecCCcceeeccCccceeecc
Q 021022 136 VCVNCGVCMGEY---FCESCKLFDDDTSKKQYHCDGCGICRIGGCDNFFHCNKCRCCYSML 193 (318)
Q Consensus 136 ~C~~Cg~~f~~Y---fC~~Ckl~ddd~~k~~yHC~~CgiCR~G~~~~ffHC~~C~~C~s~~ 193 (318)
.|++|+++++.- +|..|.--.- .+|-+|+.+-++-+++|..|+-+.-.+
T Consensus 755 ~~~nc~a~~~~~~~~~c~rc~s~a~---------~~CtVC~~vi~G~~~~c~~C~H~gH~s 806 (839)
T KOG0269|consen 755 ACPNCDAPMVLTKLWQCDRCESRAS---------AKCTVCDLVIRGVDVWCQVCGHGGHDS 806 (839)
T ss_pred cccccCCccccccceeechHHHHhh---------cCceeecceeeeeEeecccccccccHH
Confidence 499999999765 8888876532 268899999999999999999887543
No 260
>PRK04136 rpl40e 50S ribosomal protein L40e; Provisional
Probab=21.42 E-value=52 Score=24.08 Aligned_cols=24 Identities=29% Similarity=0.714 Sum_probs=19.8
Q ss_pred CceeecCCCCccccc-cccCcCCCC
Q 021022 119 VNQVICSLCGTEQKV-QQVCVNCGV 142 (318)
Q Consensus 119 v~~v~C~~C~~eQ~v-~~~C~~Cg~ 142 (318)
...+||+.|+...++ +..|-.||.
T Consensus 12 ~~k~ICrkC~ARnp~~A~~CRKCg~ 36 (48)
T PRK04136 12 FNKKICMRCNARNPWRATKCRKCGY 36 (48)
T ss_pred hcccchhcccCCCCccccccccCCC
Confidence 356899999999887 578988886
No 261
>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=21.27 E-value=65 Score=23.03 Aligned_cols=26 Identities=23% Similarity=0.664 Sum_probs=16.8
Q ss_pred EEcCCCCCCccccceeeeccCCCCCCccc
Q 021022 285 ILCNDCGKTSNVQFHVLAQKCPNCKSYNT 313 (318)
Q Consensus 285 IlCnDC~~~s~v~~H~lg~KC~~C~SyNT 313 (318)
|.|+.|.+..-+.++ .+|..|..|+-
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 47777777764
No 262
>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=20.95 E-value=50 Score=27.36 Aligned_cols=20 Identities=30% Similarity=0.660 Sum_probs=14.5
Q ss_pred ecCCCCcccccc----ccCcCCCC
Q 021022 123 ICSLCGTEQKVQ----QVCVNCGV 142 (318)
Q Consensus 123 ~C~~C~~eQ~v~----~~C~~Cg~ 142 (318)
.|+.|+..++.. +.|+||+.
T Consensus 5 AC~~C~~I~~~~qf~~~gCpnC~~ 28 (98)
T cd07973 5 ACLLCSLIKTEDQFERDGCPNCEG 28 (98)
T ss_pred hhccCCcccccccccCCCCCCCcc
Confidence 688888887754 46888863
No 263
>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=20.86 E-value=77 Score=30.99 Aligned_cols=43 Identities=26% Similarity=0.427 Sum_probs=26.1
Q ss_pred CCCCCCcccccccccCCceeEEcCCCCc----cchHHHHHHHhcCCCCCC
Q 021022 204 AMHHDCPVCCEYLFETRQDVIVLPCGHT----IHKNCLKEMREHHQYACP 249 (318)
Q Consensus 204 ~~~~~CpIClE~lf~s~~~v~~LpCGH~----fH~~Cl~~wl~~~~~~CP 249 (318)
.+-.-|+||+| |...+.+-.-|. |+ =|++||.+|-.-.+..||
T Consensus 28 ~tLsfChiCfE-l~iegvpks~ll--HtkSlRGHrdCFEK~HlIanQ~~p 74 (285)
T PF06937_consen 28 ETLSFCHICFE-LSIEGVPKSNLL--HTKSLRGHRDCFEKYHLIANQDCP 74 (285)
T ss_pred cceeecceeec-cccccCcccccc--ccccccchHHHHHHHHHHHcCCCC
Confidence 34567888888 444443333221 32 489999999333456788
No 264
>PLN02400 cellulose synthase
Probab=20.78 E-value=57 Score=37.39 Aligned_cols=56 Identities=16% Similarity=0.428 Sum_probs=40.0
Q ss_pred cCCCCCCCCcccccccccCCceeEEc---CCCCccchHHHHHHHhcCCCCCCCCCcccC
Q 021022 201 VEGAMHHDCPVCCEYLFETRQDVIVL---PCGHTIHKNCLKEMREHHQYACPICSKSVC 256 (318)
Q Consensus 201 ie~~~~~~CpIClE~lf~s~~~v~~L---pCGH~fH~~Cl~~wl~~~~~~CPiCrks~~ 256 (318)
.+......|.||.|++-...+.-... -||--.++.|++-=.+.++..||.|+....
T Consensus 31 ~~~~~gqiCqICGD~VG~t~dGe~FVAC~eCaFPVCRpCYEYERkeGnq~CPQCkTrYk 89 (1085)
T PLN02400 31 LKNLNGQICQICGDDVGVTETGDVFVACNECAFPVCRPCYEYERKDGTQCCPQCKTRYR 89 (1085)
T ss_pred ccccCCceeeecccccCcCCCCCEEEEEccCCCccccchhheecccCCccCcccCCccc
Confidence 34445679999999875544433333 467779999995445667788999998775
No 265
>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=20.73 E-value=79 Score=22.04 Aligned_cols=13 Identities=38% Similarity=1.027 Sum_probs=6.8
Q ss_pred CCCCeeecCCCCc
Q 021022 159 TSKKQYHCDGCGI 171 (318)
Q Consensus 159 ~~k~~yHC~~Cgi 171 (318)
..++-|+|..|++
T Consensus 24 ~~~~g~~C~~C~~ 36 (53)
T PF00130_consen 24 LGKQGYRCSWCGL 36 (53)
T ss_dssp SSSCEEEETTTT-
T ss_pred CCCCeEEECCCCC
Confidence 3455666665553
No 266
>KOG4399 consensus C2HC-type Zn-finger protein [General function prediction only]
Probab=20.72 E-value=21 Score=34.84 Aligned_cols=73 Identities=26% Similarity=0.610 Sum_probs=52.7
Q ss_pred CCCccceEecCccccccCCCCCCeeecCCCCceeecCCcceeeccCccceeeccccccccccCCCCCCCCcccccc
Q 021022 140 CGVCMGEYFCESCKLFDDDTSKKQYHCDGCGICRIGGCDNFFHCNKCRCCYSMLLKNSHPCVEGAMHHDCPVCCEY 215 (318)
Q Consensus 140 Cg~~f~~YfC~~Ckl~ddd~~k~~yHC~~CgiCR~G~~~~ffHC~~C~~C~s~~l~~~H~Cie~~~~~~CpIClE~ 215 (318)
=|..=+-.||..|..| ..+-.-||+.|+.|..-.++.|-||.+|-.|+-.++..--.|..-+...-|-||.++
T Consensus 198 ~~~EE~~~~~~~~~~Y---v~~~~~H~~~~~S~~~~~~~~~~H~~~~~~~~~~~~i~C~~~~~~A~~~~C~iC~~~ 270 (325)
T KOG4399|consen 198 LPTEEGYRFCSPCQRY---VSLENQHCEHCNSCTSKDGRKWNHCFLCKKCVKPSWIHCSICNHCAVKHGCFICGEL 270 (325)
T ss_pred cccccceEEEeehHHH---HHHHhhhchhhcccccchhHHHhHhHHhhhhcccceeeeecccchhhhcceeecccc
Confidence 3455567789999988 457788999999998777789999999999998877432222222334557777763
No 267
>KOG1311 consensus DHHC-type Zn-finger proteins [General function prediction only]
Probab=20.71 E-value=80 Score=30.08 Aligned_cols=45 Identities=24% Similarity=0.696 Sum_probs=31.8
Q ss_pred CCccceEecCccccccCCCCCCeeecCCCCceeecCCcceeeccCccceee
Q 021022 141 GVCMGEYFCESCKLFDDDTSKKQYHCDGCGICRIGGCDNFFHCNKCRCCYS 191 (318)
Q Consensus 141 g~~f~~YfC~~Ckl~ddd~~k~~yHC~~CgiCR~G~~~~ffHC~~C~~C~s 191 (318)
|....-.||..|+++ ..+.-.||.-||.|-.+ ---||.==|.|+.
T Consensus 108 ~~~~~~~~C~~C~~~---rPpRs~HCsvC~~CV~r---fDHHC~WvnnCVG 152 (299)
T KOG1311|consen 108 GIQVEWKYCDTCQLY---RPPRSSHCSVCNNCVLR---FDHHCPWLNNCIG 152 (299)
T ss_pred CcccceEEcCcCccc---CCCCcccchhhcccccc---cCCCCCCccceEC
Confidence 445567899999999 33567788888888763 2357776666664
No 268
>PF00628 PHD: PHD-finger; InterPro: IPR019787 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 PHD (homeodomain) zinc finger domain [,], which is a C4HC3 zinc-finger-like motif found in nuclear proteins thought to be involved in chromatin-mediated transcriptional regulation. The PHD finger motif is reminiscent of, but distinct from the C3HC4 type RING finger. The function of this domain is not yet known but in analogy with the LIM domain it could be involved in protein-protein interaction and be important for the assembly or activity of multicomponent complexes involved in transcriptional activation or repression. Alternatively, the interactions could be intra-molecular and be important in maintaining the structural integrity of the protein. In similarity to the RING finger and the LIM domain, the PHD finger is thought to bind two zinc ions. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0005515 protein binding; PDB: 3ZVY_A 2LGG_A 3SOW_A 3SOU_B 3ASL_A 3ASK_A 3ZVZ_B 3T6R_A 2LGK_A 3SOX_B ....
Probab=20.67 E-value=1.2e+02 Score=20.87 Aligned_cols=20 Identities=30% Similarity=0.888 Sum_probs=9.4
Q ss_pred ecCccccccCCCCCCeeecCCC
Q 021022 148 FCESCKLFDDDTSKKQYHCDGC 169 (318)
Q Consensus 148 fC~~Ckl~ddd~~k~~yHC~~C 169 (318)
||.+|+-. +......-|+.|
T Consensus 1 ~C~vC~~~--~~~~~~i~C~~C 20 (51)
T PF00628_consen 1 YCPVCGQS--DDDGDMIQCDSC 20 (51)
T ss_dssp EBTTTTSS--CTTSSEEEBSTT
T ss_pred eCcCCCCc--CCCCCeEEcCCC
Confidence 45555552 223444555554
No 269
>PRK14892 putative transcription elongation factor Elf1; Provisional
Probab=20.62 E-value=89 Score=25.92 Aligned_cols=32 Identities=22% Similarity=0.559 Sum_probs=20.6
Q ss_pred cceeeccCcc-ceeeccccccccccCCCCCCCCcccccc
Q 021022 178 DNFFHCNKCR-CCYSMLLKNSHPCVEGAMHHDCPVCCEY 215 (318)
Q Consensus 178 ~~ffHC~~C~-~C~s~~l~~~H~Cie~~~~~~CpIClE~ 215 (318)
.++|+|..|| ..+++.+ .+ +..+..|++|..+
T Consensus 19 pt~f~CP~Cge~~v~v~~--~k----~~~h~~C~~CG~y 51 (99)
T PRK14892 19 PKIFECPRCGKVSISVKI--KK----NIAIITCGNCGLY 51 (99)
T ss_pred CcEeECCCCCCeEeeeec--CC----CcceEECCCCCCc
Confidence 4678888888 3333333 22 3567899999975
No 270
>KOG4362 consensus Transcriptional regulator BRCA1 [Replication, recombination and repair; Transcription]
Probab=20.09 E-value=49 Score=36.08 Aligned_cols=48 Identities=29% Similarity=0.695 Sum_probs=37.5
Q ss_pred CCCCcccccccccCCceeEEcCCCCccchHHHHHHHhcC--CCCCCCCCcccCc
Q 021022 206 HHDCPVCCEYLFETRQDVIVLPCGHTIHKNCLKEMREHH--QYACPICSKSVCD 257 (318)
Q Consensus 206 ~~~CpIClE~lf~s~~~v~~LpCGH~fH~~Cl~~wl~~~--~~~CPiCrks~~d 257 (318)
...||||++..++. ..+.|-|.|...|+..-+... .-.||+|+..+..
T Consensus 21 ~lEc~ic~~~~~~p----~~~kc~~~~l~~~~n~~f~~~~~~~~~~lc~~~~eK 70 (684)
T KOG4362|consen 21 ILECPICLEHVKEP----SLLKCDHIFLKFCLNKLFESKKGPKQCALCKSDIEK 70 (684)
T ss_pred hccCCceeEEeecc----chhhhhHHHHhhhhhceeeccCccccchhhhhhhhh
Confidence 56899999977763 678999999999999865432 3469999977653
Done!