Query 024483
Match_columns 267
No_of_seqs 222 out of 693
Neff 5.4
Searched_HMMs 46136
Date Fri Mar 29 04:56:42 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/024483.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/024483hhsearch_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 8.1E-71 1.8E-75 504.3 8.1 252 4-266 21-272 (276)
2 PF14599 zinc_ribbon_6: Zinc-r 100.0 1.8E-31 3.8E-36 194.9 0.8 61 199-259 1-61 (61)
3 PF05495 zf-CHY: CHY zinc fing 99.9 4.7E-24 1E-28 160.2 3.4 70 18-100 1-71 (71)
4 COG4357 Zinc finger domain con 99.6 4.9E-16 1.1E-20 122.3 2.0 73 15-90 12-92 (105)
5 PF13639 zf-RING_2: Ring finge 99.4 8.9E-14 1.9E-18 94.3 1.0 44 151-196 1-44 (44)
6 PF12678 zf-rbx1: RING-H2 zinc 99.0 1.5E-10 3.1E-15 87.3 3.2 48 148-196 17-73 (73)
7 COG5243 HRD1 HRD ubiquitin lig 99.0 1E-10 2.2E-15 111.5 1.5 57 147-204 284-350 (491)
8 cd00162 RING RING-finger (Real 99.0 4.3E-10 9.2E-15 73.8 3.3 45 152-199 1-45 (45)
9 KOG4628 Predicted E3 ubiquitin 98.9 5.4E-10 1.2E-14 106.3 2.2 50 151-201 230-279 (348)
10 PF13923 zf-C3HC4_2: Zinc fing 98.8 1.4E-09 3.1E-14 72.0 1.8 39 153-195 1-39 (39)
11 PHA02929 N1R/p28-like protein; 98.8 3.2E-09 6.8E-14 96.7 3.9 54 146-200 170-227 (238)
12 PF13920 zf-C3HC4_3: Zinc fing 98.7 8.7E-09 1.9E-13 71.6 1.9 46 151-201 3-49 (50)
13 smart00184 RING Ring finger. E 98.7 1.4E-08 3E-13 64.2 2.4 39 153-195 1-39 (39)
14 PF00097 zf-C3HC4: Zinc finger 98.6 1.4E-08 2.9E-13 67.4 1.8 40 153-195 1-41 (41)
15 PF14634 zf-RING_5: zinc-RING 98.6 2.6E-08 5.7E-13 67.7 2.9 44 152-197 1-44 (44)
16 COG5540 RING-finger-containing 98.6 2.9E-08 6.3E-13 92.8 2.8 53 146-199 319-371 (374)
17 KOG0804 Cytoplasmic Zn-finger 98.5 6.8E-08 1.5E-12 94.1 3.5 82 151-260 176-259 (493)
18 PF15227 zf-C3HC4_4: zinc fing 98.5 9.6E-08 2.1E-12 64.8 2.6 39 153-195 1-42 (42)
19 PF13445 zf-RING_UBOX: RING-ty 98.4 8.2E-08 1.8E-12 65.7 1.4 40 153-193 1-43 (43)
20 PF12861 zf-Apc11: Anaphase-pr 98.4 2E-07 4.2E-12 72.6 3.1 47 152-200 34-82 (85)
21 KOG0802 E3 ubiquitin ligase [P 98.4 1E-07 2.2E-12 95.7 1.0 54 146-200 287-341 (543)
22 PLN03208 E3 ubiquitin-protein 98.3 3.6E-07 7.8E-12 80.9 3.9 55 143-201 11-80 (193)
23 PHA02926 zinc finger-like prot 98.2 5.2E-07 1.1E-11 81.4 2.0 74 133-206 153-238 (242)
24 smart00504 Ubox Modified RING 98.0 3.8E-06 8.2E-11 60.0 3.1 45 151-200 2-46 (63)
25 KOG0320 Predicted E3 ubiquitin 98.0 2.8E-06 6.1E-11 74.3 1.7 46 151-200 132-178 (187)
26 smart00744 RINGv The RING-vari 97.9 5.9E-06 1.3E-10 57.9 2.2 43 152-196 1-49 (49)
27 PF11793 FANCL_C: FANCL C-term 97.9 3.5E-06 7.5E-11 63.1 0.8 51 150-200 2-66 (70)
28 KOG2177 Predicted E3 ubiquitin 97.8 4.3E-05 9.3E-10 66.4 6.1 44 149-197 12-55 (386)
29 TIGR00599 rad18 DNA repair pro 97.7 2.3E-05 5.1E-10 76.3 4.0 46 150-200 26-71 (397)
30 COG5194 APC11 Component of SCF 97.7 3.2E-05 7E-10 59.6 2.8 29 171-200 53-81 (88)
31 TIGR00570 cdk7 CDK-activating 97.5 7E-05 1.5E-09 70.8 3.7 50 150-200 3-54 (309)
32 KOG0827 Predicted E3 ubiquitin 97.5 3.4E-05 7.3E-10 74.5 1.5 46 150-196 4-52 (465)
33 KOG0317 Predicted E3 ubiquitin 97.5 4E-05 8.6E-10 71.4 1.2 45 151-200 240-284 (293)
34 KOG0287 Postreplication repair 97.3 0.00025 5.5E-09 67.7 3.8 58 151-213 24-82 (442)
35 KOG0828 Predicted E3 ubiquitin 97.2 0.00012 2.5E-09 72.7 1.0 51 150-200 571-634 (636)
36 PF04564 U-box: U-box domain; 97.2 0.00042 9.2E-09 51.8 3.8 47 151-201 5-51 (73)
37 KOG0823 Predicted E3 ubiquitin 97.2 0.00021 4.5E-09 64.9 2.4 50 148-201 45-96 (230)
38 KOG2164 Predicted E3 ubiquitin 97.0 0.00033 7.1E-09 69.7 2.1 50 148-201 184-237 (513)
39 KOG1493 Anaphase-promoting com 96.9 0.00031 6.7E-09 53.9 0.8 30 171-200 50-81 (84)
40 PF14835 zf-RING_6: zf-RING of 96.8 0.00055 1.2E-08 50.8 1.3 56 151-213 8-65 (65)
41 KOG1941 Acetylcholine receptor 96.7 0.00041 8.9E-09 67.4 -0.1 62 141-203 357-419 (518)
42 KOG1734 Predicted RING-contain 96.6 0.00065 1.4E-08 63.2 0.8 52 149-200 223-281 (328)
43 COG5574 PEX10 RING-finger-cont 96.4 0.0014 3E-08 60.7 1.5 47 150-200 215-262 (271)
44 KOG4265 Predicted E3 ubiquitin 96.4 0.0018 3.8E-08 62.1 2.2 49 148-201 288-337 (349)
45 KOG1039 Predicted E3 ubiquitin 96.3 0.00085 1.8E-08 64.4 -0.5 82 148-231 159-252 (344)
46 PF14570 zf-RING_4: RING/Ubox 96.3 0.0033 7.1E-08 44.2 2.4 44 153-198 1-46 (48)
47 KOG0825 PHD Zn-finger protein 96.1 0.002 4.3E-08 67.2 1.1 75 124-200 96-171 (1134)
48 KOG2930 SCF ubiquitin ligase, 96.1 0.0024 5.1E-08 51.7 1.1 28 171-199 80-107 (114)
49 COG5219 Uncharacterized conser 96.1 0.0033 7.2E-08 66.8 2.4 53 148-200 1467-1523(1525)
50 KOG4172 Predicted E3 ubiquitin 95.9 0.0023 5.1E-08 46.3 0.3 53 148-204 5-58 (62)
51 KOG3002 Zn finger protein [Gen 95.8 0.0075 1.6E-07 57.0 3.4 64 150-224 48-113 (299)
52 KOG1785 Tyrosine kinase negati 95.7 0.0036 7.7E-08 61.2 0.6 54 144-201 363-417 (563)
53 PF11789 zf-Nse: Zinc-finger o 95.5 0.0069 1.5E-07 43.7 1.6 44 148-194 9-53 (57)
54 PF10367 Vps39_2: Vacuolar sor 95.5 0.0051 1.1E-07 47.9 0.9 38 143-182 71-108 (109)
55 KOG0311 Predicted E3 ubiquitin 95.4 0.0046 1E-07 59.4 0.2 49 150-201 43-91 (381)
56 PRK14890 putative Zn-ribbon RN 95.3 0.015 3.2E-07 42.5 2.6 46 63-115 5-56 (59)
57 KOG1645 RING-finger-containing 95.3 0.019 4.1E-07 56.2 4.1 50 150-199 4-55 (463)
58 KOG0978 E3 ubiquitin ligase in 95.3 0.0046 1E-07 64.1 -0.2 46 151-200 644-689 (698)
59 COG5432 RAD18 RING-finger-cont 95.2 0.011 2.4E-07 55.8 2.1 46 150-200 25-70 (391)
60 PF12906 RINGv: RING-variant d 95.1 0.0089 1.9E-07 41.4 0.9 41 153-195 1-47 (47)
61 KOG1428 Inhibitor of type V ad 95.1 0.02 4.4E-07 63.3 3.8 74 119-200 3462-3544(3738)
62 KOG3970 Predicted E3 ubiquitin 94.8 0.032 7E-07 51.1 3.8 51 148-200 48-105 (299)
63 KOG2879 Predicted E3 ubiquitin 94.6 0.026 5.7E-07 52.8 2.8 53 148-203 237-290 (298)
64 KOG4275 Predicted E3 ubiquitin 93.5 0.012 2.6E-07 55.4 -1.6 62 138-207 285-349 (350)
65 KOG3800 Predicted E3 ubiquitin 93.4 0.051 1.1E-06 51.1 2.4 48 152-200 2-51 (300)
66 PF14447 Prok-RING_4: Prokaryo 93.4 0.032 6.9E-07 40.3 0.8 32 166-200 19-50 (55)
67 KOG0824 Predicted E3 ubiquitin 93.0 0.045 9.8E-07 51.8 1.4 50 147-200 4-53 (324)
68 KOG4445 Uncharacterized conser 93.0 0.024 5.2E-07 53.7 -0.4 54 147-201 112-187 (368)
69 PF05883 Baculo_RING: Baculovi 92.7 0.053 1.1E-06 45.8 1.2 36 150-186 26-67 (134)
70 KOG3268 Predicted E3 ubiquitin 92.1 0.068 1.5E-06 47.4 1.3 35 169-203 187-232 (234)
71 COG2888 Predicted Zn-ribbon RN 92.1 0.11 2.3E-06 38.2 2.0 45 65-115 9-58 (61)
72 TIGR00100 hypA hydrogenase nic 92.0 0.099 2.2E-06 42.6 2.0 38 224-263 66-103 (115)
73 PRK00564 hypA hydrogenase nick 91.7 0.1 2.3E-06 42.7 1.8 39 223-263 66-105 (117)
74 PRK03824 hypA hydrogenase nick 91.7 0.21 4.6E-06 41.8 3.7 38 226-263 68-124 (135)
75 KOG4739 Uncharacterized protei 91.6 0.089 1.9E-06 48.2 1.4 37 161-200 12-48 (233)
76 PF12773 DZR: Double zinc ribb 91.5 0.19 4.2E-06 34.4 2.8 22 68-89 1-23 (50)
77 KOG1571 Predicted E3 ubiquitin 91.1 0.13 2.7E-06 49.8 2.0 48 146-201 301-348 (355)
78 PRK03681 hypA hydrogenase nick 90.6 0.17 3.7E-06 41.2 2.1 38 225-263 67-104 (114)
79 KOG4185 Predicted E3 ubiquitin 90.5 0.2 4.3E-06 46.3 2.7 49 150-199 3-54 (296)
80 PRK12380 hydrogenase nickel in 90.2 0.18 3.9E-06 41.0 1.9 37 225-263 67-103 (113)
81 PF04641 Rtf2: Rtf2 RING-finge 89.5 0.25 5.4E-06 45.4 2.4 50 148-200 111-161 (260)
82 PF07191 zinc-ribbons_6: zinc- 89.4 0.16 3.5E-06 38.4 0.9 36 64-99 16-59 (70)
83 KOG0297 TNF receptor-associate 89.3 0.29 6.3E-06 47.8 2.9 53 149-205 20-72 (391)
84 COG5175 MOT2 Transcriptional r 88.9 0.11 2.3E-06 50.3 -0.4 57 150-206 14-70 (480)
85 KOG1814 Predicted E3 ubiquitin 88.9 0.2 4.4E-06 49.3 1.4 46 150-196 184-236 (445)
86 KOG2660 Locus-specific chromos 88.7 0.1 2.2E-06 49.8 -0.7 50 148-201 13-62 (331)
87 PF01155 HypA: Hydrogenase exp 88.6 0.15 3.3E-06 41.3 0.4 37 225-263 67-103 (113)
88 PHA02862 5L protein; Provision 87.7 0.32 6.8E-06 41.8 1.7 57 149-211 1-63 (156)
89 PF13248 zf-ribbon_3: zinc-rib 87.1 0.31 6.7E-06 29.6 1.0 24 65-88 2-26 (26)
90 KOG2817 Predicted E3 ubiquitin 87.0 0.55 1.2E-05 45.9 3.2 47 152-199 336-384 (394)
91 COG5152 Uncharacterized conser 86.9 0.35 7.6E-06 43.7 1.6 58 152-214 198-255 (259)
92 KOG2114 Vacuolar assembly/sort 86.8 0.41 8.8E-06 50.9 2.3 42 151-199 841-882 (933)
93 KOG0309 Conserved WD40 repeat- 86.8 0.34 7.4E-06 51.1 1.7 42 150-194 1028-1069(1081)
94 PF07800 DUF1644: Protein of u 86.5 0.69 1.5E-05 40.2 3.1 33 150-186 2-47 (162)
95 PF03854 zf-P11: P-11 zinc fin 86.1 0.38 8.3E-06 33.9 1.1 32 168-200 14-46 (50)
96 KOG1813 Predicted E3 ubiquitin 85.8 0.42 9.1E-06 45.3 1.6 67 151-222 242-308 (313)
97 KOG3161 Predicted E3 ubiquitin 85.6 0.45 9.7E-06 49.4 1.8 42 151-196 12-53 (861)
98 KOG4159 Predicted E3 ubiquitin 85.5 0.97 2.1E-05 44.5 4.0 49 148-201 82-130 (398)
99 PHA02825 LAP/PHD finger-like p 85.2 0.63 1.4E-05 40.5 2.3 48 148-200 6-59 (162)
100 PRK00762 hypA hydrogenase nick 84.9 0.63 1.4E-05 38.4 2.1 39 224-263 66-109 (124)
101 KOG3039 Uncharacterized conser 84.7 0.8 1.7E-05 42.6 2.9 55 147-203 218-273 (303)
102 KOG2034 Vacuolar sorting prote 84.4 0.51 1.1E-05 50.3 1.7 43 142-186 809-851 (911)
103 KOG1002 Nucleotide excision re 84.3 0.36 7.9E-06 49.1 0.5 52 145-200 531-586 (791)
104 PF09538 FYDLN_acid: Protein o 83.1 0.83 1.8E-05 37.2 2.0 29 75-115 6-34 (108)
105 PF10571 UPF0547: Uncharacteri 83.1 0.82 1.8E-05 28.0 1.5 23 67-89 2-25 (26)
106 PF07191 zinc-ribbons_6: zinc- 83.1 0.33 7.1E-06 36.7 -0.3 65 151-244 2-69 (70)
107 PF13240 zinc_ribbon_2: zinc-r 82.9 0.69 1.5E-05 27.5 1.1 21 68-88 2-23 (23)
108 PRK04023 DNA polymerase II lar 82.7 1.1 2.4E-05 48.7 3.3 31 80-114 628-658 (1121)
109 COG0375 HybF Zn finger protein 81.9 1.1 2.4E-05 36.9 2.4 40 223-264 65-104 (115)
110 KOG1952 Transcription factor N 80.2 0.81 1.8E-05 48.7 1.3 51 149-200 190-247 (950)
111 PF08746 zf-RING-like: RING-li 79.7 1.1 2.4E-05 30.4 1.4 25 171-195 18-43 (43)
112 COG5236 Uncharacterized conser 79.2 1.4 3E-05 43.0 2.3 65 131-199 42-107 (493)
113 TIGR02605 CxxC_CxxC_SSSS putat 78.6 2 4.4E-05 29.5 2.5 36 228-263 5-44 (52)
114 PF14353 CpXC: CpXC protein 78.4 0.44 9.6E-06 38.9 -1.1 56 190-247 2-57 (128)
115 COG5220 TFB3 Cdk activating ki 78.3 0.77 1.7E-05 42.6 0.4 51 149-200 9-64 (314)
116 PF14446 Prok-RING_1: Prokaryo 77.1 2 4.3E-05 30.9 2.1 35 149-184 4-39 (54)
117 TIGR00595 priA primosomal prot 77.0 2.1 4.5E-05 43.1 3.1 49 27-87 214-262 (505)
118 PHA00626 hypothetical protein 76.0 2.2 4.8E-05 31.1 2.1 7 80-86 2-8 (59)
119 PRK14559 putative protein seri 75.8 2 4.3E-05 44.8 2.6 31 67-97 3-34 (645)
120 KOG0801 Predicted E3 ubiquitin 75.5 1.1 2.5E-05 39.3 0.6 31 147-178 174-204 (205)
121 KOG2462 C2H2-type Zn-finger pr 75.4 2.3 5.1E-05 39.9 2.7 112 88-238 128-253 (279)
122 PRK14714 DNA polymerase II lar 73.7 3.3 7.1E-05 46.2 3.6 48 65-114 667-716 (1337)
123 PLN03086 PRLI-interacting fact 73.0 1.7 3.7E-05 44.6 1.3 85 61-160 403-514 (567)
124 KOG4692 Predicted E3 ubiquitin 73.0 2 4.4E-05 41.9 1.7 50 147-201 419-468 (489)
125 PRK00398 rpoP DNA-directed RNA 72.7 3 6.4E-05 28.3 2.0 35 227-261 2-36 (46)
126 PF13894 zf-C2H2_4: C2H2-type 72.4 2.5 5.5E-05 23.4 1.4 20 190-209 1-20 (24)
127 PF02891 zf-MIZ: MIZ/SP-RING z 72.2 2.4 5.3E-05 29.6 1.6 42 151-198 3-50 (50)
128 COG1198 PriA Primosomal protei 71.7 3.9 8.5E-05 43.3 3.6 54 26-91 435-488 (730)
129 smart00734 ZnF_Rad18 Rad18-lik 71.4 3.4 7.4E-05 25.1 1.9 21 190-211 2-22 (26)
130 KOG0827 Predicted E3 ubiquitin 71.1 0.45 9.6E-06 46.7 -3.2 51 149-200 195-245 (465)
131 smart00132 LIM Zinc-binding do 69.8 2.2 4.9E-05 26.5 0.9 37 153-200 2-38 (39)
132 KOG2272 Focal adhesion protein 69.8 3.6 7.8E-05 38.6 2.5 128 36-206 100-238 (332)
133 KOG1701 Focal adhesion adaptor 69.7 1.5 3.4E-05 43.5 0.1 30 218-253 405-434 (468)
134 KOG0269 WD40 repeat-containing 69.4 3.9 8.4E-05 43.3 2.9 79 105-203 751-836 (839)
135 KOG1940 Zn-finger protein [Gen 67.9 1 2.2E-05 42.4 -1.5 71 14-86 176-260 (276)
136 COG5222 Uncharacterized conser 66.4 4 8.8E-05 39.1 2.2 44 151-197 275-318 (427)
137 TIGR02300 FYDLN_acid conserved 66.2 4 8.6E-05 34.3 1.9 29 76-116 7-35 (129)
138 PRK05580 primosome assembly pr 66.0 4.9 0.00011 41.9 2.9 51 26-88 381-431 (679)
139 smart00249 PHD PHD zinc finger 65.7 2 4.3E-05 27.6 -0.0 41 153-195 2-47 (47)
140 PRK04023 DNA polymerase II lar 65.4 5 0.00011 43.9 2.8 50 63-118 624-674 (1121)
141 COG5109 Uncharacterized conser 64.6 5.7 0.00012 38.3 2.8 44 152-196 338-383 (396)
142 KOG2068 MOT2 transcription fac 64.6 4.9 0.00011 38.7 2.4 52 148-200 247-298 (327)
143 COG1996 RPC10 DNA-directed RNA 63.7 5.4 0.00012 28.2 1.8 30 226-255 4-33 (49)
144 PF07754 DUF1610: Domain of un 63.3 6.3 0.00014 23.9 1.9 9 106-114 15-23 (24)
145 PRK14873 primosome assembly pr 62.9 5.9 0.00013 41.5 2.8 49 26-87 383-431 (665)
146 PRK14714 DNA polymerase II lar 62.9 6.1 0.00013 44.1 3.0 33 79-115 668-700 (1337)
147 smart00659 RPOLCX RNA polymera 62.4 5.4 0.00012 27.3 1.6 26 228-254 2-27 (44)
148 PF07282 OrfB_Zn_ribbon: Putat 62.3 6.3 0.00014 28.5 2.1 27 78-115 28-54 (69)
149 COG1198 PriA Primosomal protei 62.2 7.3 0.00016 41.3 3.3 44 63-114 433-482 (730)
150 PF05605 zf-Di19: Drought indu 62.0 7.7 0.00017 27.1 2.4 22 189-211 2-23 (54)
151 PF03107 C1_2: C1 domain; Int 61.1 6.4 0.00014 24.4 1.7 20 112-131 2-22 (30)
152 PRK14559 putative protein seri 60.4 4.8 0.0001 42.0 1.6 34 65-99 15-50 (645)
153 KOG1001 Helicase-like transcri 60.2 4.2 9.2E-05 42.7 1.2 45 151-200 455-500 (674)
154 KOG4367 Predicted Zn-finger pr 60.0 4.2 9.1E-05 40.8 1.1 33 150-186 4-36 (699)
155 KOG3053 Uncharacterized conser 60.0 2.9 6.3E-05 39.1 -0.0 54 147-200 17-82 (293)
156 PF06524 NOA36: NOA36 protein; 59.5 3.3 7.1E-05 38.9 0.2 51 33-98 140-190 (314)
157 PRK12286 rpmF 50S ribosomal pr 58.3 9.7 0.00021 27.5 2.5 29 227-260 26-54 (57)
158 KOG2066 Vacuolar assembly/sort 57.7 3.7 7.9E-05 43.7 0.2 44 151-196 785-831 (846)
159 KOG1311 DHHC-type Zn-finger pr 55.6 7.9 0.00017 35.9 2.0 33 84-119 107-139 (299)
160 PF00096 zf-C2H2: Zinc finger, 54.6 7.8 0.00017 21.8 1.2 16 190-205 1-16 (23)
161 PF05502 Dynactin_p62: Dynacti 54.3 6.5 0.00014 39.6 1.4 58 91-163 6-65 (483)
162 PHA03096 p28-like protein; Pro 54.0 7.1 0.00015 36.8 1.5 47 151-197 179-231 (284)
163 PF13597 NRDD: Anaerobic ribon 53.1 10 0.00022 38.7 2.6 57 201-263 465-521 (546)
164 PRK00415 rps27e 30S ribosomal 51.5 8 0.00017 28.3 1.1 35 65-99 11-51 (59)
165 KOG1812 Predicted E3 ubiquitin 50.6 7.6 0.00016 38.0 1.1 36 150-186 146-182 (384)
166 PRK14890 putative Zn-ribbon RN 50.2 10 0.00022 27.8 1.5 34 63-98 23-56 (59)
167 PF10058 DUF2296: Predicted in 49.9 21 0.00046 25.4 3.1 47 207-256 4-54 (54)
168 KOG1609 Protein involved in mR 48.7 7 0.00015 35.7 0.6 51 150-200 78-134 (323)
169 PHA00626 hypothetical protein 47.5 12 0.00026 27.4 1.4 34 66-101 1-34 (59)
170 PF04216 FdhE: Protein involve 46.7 14 0.00031 34.2 2.3 48 63-114 195-245 (290)
171 KOG0298 DEAD box-containing he 46.7 13 0.00028 41.7 2.2 53 148-204 1151-1203(1394)
172 cd01675 RNR_III Class III ribo 46.3 15 0.00032 37.6 2.5 56 201-262 493-548 (555)
173 TIGR01031 rpmF_bact ribosomal 45.4 18 0.00038 25.9 2.1 29 227-260 25-53 (55)
174 PF15353 HECA: Headcase protei 45.3 10 0.00022 30.9 1.0 16 171-186 39-54 (107)
175 PF14569 zf-UDP: Zinc-binding 44.7 21 0.00045 27.7 2.5 52 148-199 7-61 (80)
176 KOG1312 DHHC-type Zn-finger pr 44.4 7.4 0.00016 37.1 -0.0 32 111-145 149-180 (341)
177 PF01096 TFIIS_C: Transcriptio 44.1 20 0.00044 23.6 2.1 34 80-114 2-35 (39)
178 PF02701 zf-Dof: Dof domain, z 44.0 11 0.00025 27.9 0.9 13 247-259 6-18 (63)
179 PF04423 Rad50_zn_hook: Rad50 43.6 19 0.00041 25.1 2.0 12 190-201 21-32 (54)
180 PF10122 Mu-like_Com: Mu-like 43.5 20 0.00044 25.5 2.1 35 228-262 4-40 (51)
181 COG1656 Uncharacterized conser 43.4 17 0.00036 31.9 2.0 49 189-244 97-146 (165)
182 PRK03564 formate dehydrogenase 43.2 23 0.00049 33.9 3.1 23 228-254 212-234 (309)
183 PF09723 Zn-ribbon_8: Zinc rib 43.2 20 0.00044 23.9 2.0 31 228-258 5-38 (42)
184 COG3809 Uncharacterized protei 43.1 18 0.0004 28.1 2.0 51 152-225 3-55 (88)
185 PF05191 ADK_lid: Adenylate ki 42.0 6.7 0.00014 25.7 -0.5 27 80-115 3-29 (36)
186 PF01529 zf-DHHC: DHHC palmito 42.0 14 0.00031 30.8 1.4 48 84-137 42-89 (174)
187 PRK00432 30S ribosomal protein 41.9 19 0.0004 25.3 1.7 9 106-114 36-44 (50)
188 COG1996 RPC10 DNA-directed RNA 41.6 18 0.00039 25.6 1.6 29 88-116 4-33 (49)
189 PF13453 zf-TFIIB: Transcripti 41.1 23 0.0005 23.3 2.0 26 80-114 1-26 (41)
190 PF07649 C1_3: C1-like domain; 40.8 15 0.00034 22.5 1.1 20 113-132 3-23 (30)
191 COG2051 RPS27A Ribosomal prote 40.5 12 0.00027 28.0 0.7 28 64-91 18-51 (67)
192 cd00350 rubredoxin_like Rubred 40.1 21 0.00046 22.6 1.6 24 91-115 2-25 (33)
193 PF08271 TF_Zn_Ribbon: TFIIB z 39.9 26 0.00056 23.3 2.1 8 80-87 2-9 (43)
194 PRK00366 ispG 4-hydroxy-3-meth 38.3 44 0.00095 32.7 4.2 54 189-246 268-323 (360)
195 cd02249 ZZ Zinc finger, ZZ typ 37.9 26 0.00056 23.6 1.9 21 108-131 1-21 (46)
196 PF13717 zinc_ribbon_4: zinc-r 37.8 19 0.00042 23.4 1.2 10 64-73 24-33 (36)
197 TIGR02159 PA_CoA_Oxy4 phenylac 37.5 17 0.00037 30.9 1.1 16 246-261 105-120 (146)
198 PF04438 zf-HIT: HIT zinc fing 36.9 17 0.00037 22.9 0.8 16 81-97 5-20 (30)
199 PF05290 Baculo_IE-1: Baculovi 35.9 18 0.00038 30.8 1.0 47 151-201 81-133 (140)
200 KOG2907 RNA polymerase I trans 35.7 13 0.00029 30.6 0.2 19 244-262 72-94 (116)
201 PF13719 zinc_ribbon_5: zinc-r 35.2 22 0.00048 23.1 1.2 9 65-73 25-33 (37)
202 PF01667 Ribosomal_S27e: Ribos 35.2 19 0.00041 26.0 0.9 34 65-98 7-46 (55)
203 PF08274 PhnA_Zn_Ribbon: PhnA 34.9 22 0.00048 22.5 1.1 23 80-114 4-26 (30)
204 PF06937 EURL: EURL protein; 34.3 48 0.001 31.3 3.6 47 146-193 26-74 (285)
205 TIGR01562 FdhE formate dehydro 34.3 42 0.0009 32.1 3.3 23 228-254 210-232 (305)
206 PF03833 PolC_DP2: DNA polymer 34.2 13 0.00029 40.0 0.0 46 79-133 656-701 (900)
207 KOG4185 Predicted E3 ubiquitin 33.9 8.6 0.00019 35.4 -1.3 50 150-199 207-266 (296)
208 PRK00420 hypothetical protein; 33.7 24 0.00051 29.0 1.4 29 150-200 23-51 (112)
209 PF04216 FdhE: Protein involve 33.4 14 0.0003 34.4 -0.1 30 227-260 196-225 (290)
210 cd02337 ZZ_CBP Zinc finger, ZZ 33.0 31 0.00068 23.1 1.7 20 108-131 1-20 (41)
211 PF03604 DNA_RNApol_7kD: DNA d 32.4 27 0.00058 22.4 1.2 10 105-114 15-24 (32)
212 PF14952 zf-tcix: Putative tre 32.1 22 0.00048 24.6 0.8 13 247-259 12-24 (44)
213 PF01907 Ribosomal_L37e: Ribos 32.0 19 0.0004 26.1 0.4 28 223-253 10-37 (55)
214 PLN02189 cellulose synthase 32.0 39 0.00086 37.3 3.1 56 145-200 29-87 (1040)
215 PF00643 zf-B_box: B-box zinc 31.9 36 0.00078 22.0 1.8 21 79-99 4-24 (42)
216 smart00661 RPOL9 RNA polymeras 31.5 38 0.00083 22.8 2.0 8 107-114 20-27 (52)
217 PF01599 Ribosomal_S27: Riboso 31.4 28 0.0006 24.4 1.2 22 77-98 17-46 (47)
218 PF06827 zf-FPG_IleRS: Zinc fi 30.8 35 0.00076 20.8 1.5 10 79-88 2-11 (30)
219 PF12874 zf-met: Zinc-finger o 30.7 26 0.00056 20.0 0.9 16 190-205 1-16 (25)
220 TIGR00595 priA primosomal prot 30.7 49 0.0011 33.4 3.3 47 62-116 210-262 (505)
221 cd00729 rubredoxin_SM Rubredox 30.7 35 0.00076 21.9 1.5 22 66-87 3-27 (34)
222 PF00412 LIM: LIM domain; Int 30.1 19 0.0004 24.6 0.2 40 153-203 1-40 (58)
223 PF01529 zf-DHHC: DHHC palmito 29.9 41 0.00088 28.0 2.3 30 113-145 51-80 (174)
224 PF15616 TerY-C: TerY-C metal 29.8 48 0.001 28.0 2.6 34 78-114 77-112 (131)
225 PF13824 zf-Mss51: Zinc-finger 29.7 43 0.00094 24.2 2.0 21 188-208 13-33 (55)
226 PRK03564 formate dehydrogenase 29.6 59 0.0013 31.1 3.5 26 62-87 209-235 (309)
227 COG1645 Uncharacterized Zn-fin 29.6 29 0.00062 29.3 1.2 20 78-97 28-51 (131)
228 COG3024 Uncharacterized protei 29.3 28 0.00061 26.0 1.0 26 76-101 5-38 (65)
229 COG2888 Predicted Zn-ribbon RN 29.2 31 0.00068 25.4 1.2 34 63-98 25-58 (61)
230 KOG0802 E3 ubiquitin ligase [P 29.1 37 0.00081 34.5 2.2 44 148-200 477-520 (543)
231 smart00834 CxxC_CXXC_SSSS Puta 29.1 56 0.0012 20.8 2.4 27 228-254 5-34 (41)
232 KOG4317 Predicted Zn-finger pr 28.9 24 0.00053 34.1 0.8 21 79-99 8-28 (383)
233 PRK14873 primosome assembly pr 28.7 58 0.0013 34.2 3.6 24 63-90 381-404 (665)
234 COG5183 SSM4 Protein involved 28.6 29 0.00063 37.6 1.3 51 148-200 10-66 (1175)
235 PF03833 PolC_DP2: DNA polymer 28.5 19 0.00041 38.9 0.0 46 64-115 654-700 (900)
236 cd02341 ZZ_ZZZ3 Zinc finger, Z 28.4 41 0.00089 23.4 1.7 22 108-131 1-22 (48)
237 KOG4399 C2HC-type Zn-finger pr 28.3 11 0.00025 35.4 -1.5 72 85-159 199-270 (325)
238 PF11023 DUF2614: Protein of u 27.7 36 0.00078 28.1 1.5 27 62-88 66-95 (114)
239 PLN02436 cellulose synthase A 27.5 52 0.0011 36.6 3.0 56 145-200 31-89 (1094)
240 PF05129 Elf1: Transcription e 27.3 31 0.00067 26.5 1.0 38 188-243 21-61 (81)
241 PF05458 Siva: Cd27 binding pr 27.3 46 0.001 29.2 2.2 36 66-101 112-158 (175)
242 COG1998 RPS31 Ribosomal protei 27.2 36 0.00077 24.3 1.2 20 78-97 19-44 (51)
243 smart00355 ZnF_C2H2 zinc finge 26.7 60 0.0013 17.6 2.0 16 190-205 1-16 (26)
244 PRK06266 transcription initiat 26.7 80 0.0017 27.6 3.6 27 188-214 135-163 (178)
245 PLN00209 ribosomal protein S27 26.7 38 0.00083 26.6 1.4 37 64-100 35-77 (86)
246 TIGR01206 lysW lysine biosynth 26.4 52 0.0011 23.5 1.9 31 190-239 3-33 (54)
247 PF12171 zf-C2H2_jaz: Zinc-fin 26.3 47 0.001 19.6 1.5 15 190-204 2-16 (27)
248 TIGR02098 MJ0042_CXXC MJ0042 f 26.2 47 0.001 21.2 1.6 10 65-74 25-34 (38)
249 TIGR00373 conserved hypothetic 26.2 79 0.0017 27.0 3.4 28 188-215 127-156 (158)
250 KOG4443 Putative transcription 25.9 80 0.0017 33.3 3.9 80 143-227 138-227 (694)
251 PRK14892 putative transcriptio 25.8 62 0.0013 26.0 2.5 32 122-159 19-51 (99)
252 KOG3362 Predicted BBOX Zn-fing 25.7 21 0.00046 30.7 -0.2 25 89-119 117-143 (156)
253 PRK14810 formamidopyrimidine-D 25.7 38 0.00083 31.4 1.5 20 78-97 244-271 (272)
254 COG5273 Uncharacterized protei 25.6 32 0.0007 32.6 1.0 44 79-145 98-141 (309)
255 PRK00464 nrdR transcriptional 25.0 43 0.00094 28.8 1.5 12 80-91 30-41 (154)
256 PRK04136 rpl40e 50S ribosomal 24.5 46 0.00099 23.5 1.3 24 63-86 12-36 (48)
257 PF11781 RRN7: RNA polymerase 24.3 42 0.00091 21.9 1.0 24 153-176 11-35 (36)
258 PRK14811 formamidopyrimidine-D 24.1 43 0.00093 31.0 1.5 20 78-97 235-262 (269)
259 TIGR02487 NrdD anaerobic ribon 23.9 68 0.0015 33.1 3.0 31 228-262 524-554 (579)
260 PRK10445 endonuclease VIII; Pr 23.8 44 0.00096 30.8 1.5 20 78-97 235-262 (263)
261 cd00112 LDLa Low Density Lipop 23.7 57 0.0012 20.8 1.6 30 123-153 4-35 (35)
262 PF01363 FYVE: FYVE zinc finge 23.6 48 0.001 23.7 1.4 25 78-115 9-33 (69)
263 PF06677 Auto_anti-p27: Sjogre 23.1 56 0.0012 22.1 1.5 13 78-90 17-29 (41)
264 PF12675 DUF3795: Protein of u 22.7 45 0.00098 25.0 1.1 37 78-114 34-70 (78)
265 PRK07111 anaerobic ribonucleos 22.6 91 0.002 33.3 3.7 44 213-262 666-709 (735)
266 PRK01103 formamidopyrimidine/5 22.5 49 0.0011 30.6 1.5 20 78-97 245-272 (274)
267 PRK01110 rpmF 50S ribosomal pr 22.5 72 0.0015 23.2 2.1 30 228-263 27-56 (60)
268 TIGR00244 transcriptional regu 22.4 56 0.0012 28.1 1.7 13 79-91 29-41 (147)
269 COG1144 Pyruvate:ferredoxin ox 22.3 41 0.00088 26.8 0.8 15 122-136 63-77 (91)
270 cd07973 Spt4 Transcription elo 22.3 47 0.001 26.6 1.2 20 67-86 5-28 (98)
271 cd02345 ZZ_dah Zinc finger, ZZ 22.2 67 0.0014 22.2 1.8 28 229-259 1-28 (49)
272 PTZ00083 40S ribosomal protein 22.2 53 0.0011 25.8 1.4 37 64-100 34-76 (85)
273 PF00130 C1_1: Phorbol esters/ 22.2 70 0.0015 21.6 1.9 11 104-114 25-35 (53)
274 PF01927 Mut7-C: Mut7-C RNAse 21.7 64 0.0014 27.0 1.9 49 189-244 91-140 (147)
275 PF09297 zf-NADH-PPase: NADH p 21.7 31 0.00067 21.5 0.0 21 67-87 5-30 (32)
276 PRK05580 primosome assembly pr 21.6 1.1E+02 0.0023 32.2 3.9 25 62-90 378-402 (679)
277 PF13913 zf-C2HC_2: zinc-finge 21.4 45 0.00098 19.9 0.7 12 79-90 3-14 (25)
278 KOG4399 C2HC-type Zn-finger pr 21.4 24 0.00052 33.3 -0.7 52 80-135 251-302 (325)
279 PF14354 Lar_restr_allev: Rest 21.3 59 0.0013 22.8 1.4 10 227-236 28-37 (61)
280 KOG1100 Predicted E3 ubiquitin 21.1 40 0.00086 30.3 0.6 39 153-200 161-200 (207)
281 PF08792 A2L_zn_ribbon: A2L zi 21.0 59 0.0013 20.9 1.2 10 66-75 4-13 (33)
282 PF06220 zf-U1: U1 zinc finger 21.0 37 0.00081 22.4 0.3 13 88-100 1-13 (38)
283 PF14445 Prok-RING_2: Prokaryo 20.6 6.8 0.00015 28.1 -3.5 46 86-136 3-53 (57)
284 smart00451 ZnF_U1 U1-like zinc 20.6 68 0.0015 19.6 1.5 18 188-205 2-19 (35)
285 PRK13945 formamidopyrimidine-D 20.3 58 0.0013 30.3 1.5 19 78-96 254-280 (282)
286 TIGR00577 fpg formamidopyrimid 20.3 58 0.0012 30.1 1.5 19 78-96 245-271 (272)
287 PRK08351 DNA-directed RNA poly 20.0 62 0.0013 23.8 1.3 20 67-87 5-24 (61)
No 1
>KOG1940 consensus Zn-finger protein [General function prediction only]
Probab=100.00 E-value=8.1e-71 Score=504.35 Aligned_cols=252 Identities=49% Similarity=1.040 Sum_probs=243.5
Q ss_pred CccccccCCCCccCccccccCcceEcCCCCCcccCcchHHhhhcCCCCCCCCccccccccceeeeCCCCccccccccCCc
Q 024483 4 SANERITFGKMGYGCKHYRRRCRIRAPCCNEIFDCRHCHNEAASMLRNPYDRHELVRQDVKQVICSVCDTEQPVAQVCTN 83 (267)
Q Consensus 4 ~~~~~~~~~~~~~gC~HY~r~c~i~~pcC~~~y~Cr~CHde~~~~~~~~~~~H~~~r~~~~~v~C~~C~~~q~v~~~C~~ 83 (267)
..++++|++.++++|+||+|++.+++|+|+++|+|++||+++. +|.++|+.+.+|+|+.|.++|+++++|.+
T Consensus 21 ~~~~~~d~~~~~~~c~hy~r~~~~~a~ccd~~~~C~hCH~~s~--------~h~~~r~~v~~~~C~~C~~~q~~~~~c~~ 92 (276)
T KOG1940|consen 21 IHSDAEDEIAFPYGCPHYRRNCKSRAPCCDREITCRHCHNESE--------DHDLDRKTVYELLCMKCRKIQPVGQICSN 92 (276)
T ss_pred cccccccccccccCCchhhhccccccccccceeeeEEecChhh--------hcccchhhhhhhhhhhHHhhhhhhhcccc
Confidence 3566889999999999999999999999999999999999874 89999999999999999999999999999
Q ss_pred CCCccceeeccccccccCCCCcCeeecCCCCcccccCccceeecCccCccccccccCcceeecCCCCCCCchhhhhhccc
Q 024483 84 CGVNMGEYFCDICKFYDDDIEKGQFHCDDCGICRIGGRENYFHCKRCGSCYSTSLRNNHLCIENSMHHHCPICYEYLFDS 163 (267)
Q Consensus 84 Cg~~f~~y~C~~C~l~dd~~~k~~yHC~~CgiCR~G~~~~~fHC~~C~~C~s~~l~~~H~C~e~~~~~~CpICle~lf~s 163 (267)
|+..+|+|||++|+||||+++ +||||+.|||||+|++++||||++|+.|++..+.+.|+|+|++++.|||||.|+||++
T Consensus 93 c~~~~g~~~c~~C~l~dd~~~-~~~hC~~C~icr~g~~~~~fhc~~c~~c~~~~~~~~H~c~e~~~~~ncPic~e~l~~s 171 (276)
T KOG1940|consen 93 CHVELGEYYCLICKLFDDDPS-KQYHCDLCGICREGLGLDFFHCKKCKACLSAYLSNWHKCVERSSEFNCPICKEYLFLS 171 (276)
T ss_pred chhhhhhhcCccccccccccc-ceeccccccccccccccchhHHhhhHhHHhhhcccccchhhhcccCCCchhHHHhccc
Confidence 999999999999999999988 9999999999999999999999999999999999999999999999999999999999
Q ss_pred CCccEEeccCCccChhhHHHHhcCCCCCCCCCCccccchhHHhHHhHHHHHhcCCChhhhcCeeEEEcCCCCCcccccee
Q 024483 164 LRNTTVMKCGHTMHCECYHEMIKRDKYCCPICSKSVIDMSRTWKRIDEEIEATVMPEDYRHKKVWILCNDCNDTTEVYFH 243 (267)
Q Consensus 164 ~~~v~~LpCGH~~H~~C~~~~~~~~~~~CPiCrks~~dm~~~~~~lD~~i~~~pmP~~y~~~~v~I~CnDC~~~s~~~fH 243 (267)
...+.+|+|||.+|..||.++...+ |+||+|.| +.||+.+|+++|.+|+++|||++|++++++|+||||+..++++||
T Consensus 172 ~~~~~~~~CgH~~h~~cf~e~~~~~-y~CP~C~~-~~d~~~~~~~~d~~l~~~~~p~~y~~~~~~i~cndC~~~~~~k~~ 249 (276)
T KOG1940|consen 172 FEDAGVLKCGHYMHSRCFEEMICEG-YTCPICSK-PGDMSHYFRKLDKELAGSPMPEEYKNKTQDILCNDCGSGTNVKYH 249 (276)
T ss_pred cccCCccCcccchHHHHHHHHhccC-CCCCcccc-hHHHHHHHHHHHHHHhcCCCCchhhchhheeeccCCCCCCcccee
Confidence 9999999999999999999999865 99999999 999999999999999999999999999999999999999999999
Q ss_pred EeeecCCCCCCccccccCCCCCC
Q 024483 244 IIGQKCSHCKSYNTRSIAPPVLP 266 (267)
Q Consensus 244 ~lg~kC~~C~SyNT~~~~~~~~~ 266 (267)
||++||+.|+|||||+++.|..+
T Consensus 250 ~l~~kc~~c~~~~~r~~~~~~~~ 272 (276)
T KOG1940|consen 250 ILYHKCGKCGSYNTRMISDPSKY 272 (276)
T ss_pred hhhhhCCCcccceeeeccCCCcc
Confidence 99999999999999999866543
No 2
>PF14599 zinc_ribbon_6: Zinc-ribbon; PDB: 2K2D_A.
Probab=99.96 E-value=1.8e-31 Score=194.89 Aligned_cols=61 Identities=67% Similarity=1.267 Sum_probs=22.6
Q ss_pred ccchhHHhHHhHHHHHhcCCChhhhcCeeEEEcCCCCCccccceeEeeecCCCCCCccccc
Q 024483 199 VIDMSRTWKRIDEEIEATVMPEDYRHKKVWILCNDCNDTTEVYFHIIGQKCSHCKSYNTRS 259 (267)
Q Consensus 199 ~~dm~~~~~~lD~~i~~~pmP~~y~~~~v~I~CnDC~~~s~~~fH~lg~kC~~C~SyNT~~ 259 (267)
|+||+++|++||++|+++|||++|++++|+|+||||+++|+|+||||||||++|+||||+|
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 5799999999999999999999999999999999999999999999999999999999997
No 3
>PF05495 zf-CHY: CHY zinc finger; InterPro: IPR008913 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. Pirh2 is an eukaryotic ubiquitin protein ligase, which has been shown to promote p53 degradation in mammals. Pirh2 physically interacts with p53 and promotes ubiquitination of p53 independently of MDM2. Like MDM2, Pirh2 is thought to participate in an autoregulatory feedback loop that controls p53 function. Pirh2 proteins contain three distinct zinc fingers, the CHY-type, the CTCHY-type which is C-terminal to the CHY-type zinc finger and a RING finger. The CHY-type zinc finger has no currently known function []. As well as Pirh2, the CHY-type zinc finger is also found in the following proteins: Yeast helper of Tim protein 13. Hot13 may have a role in the assembly and recycling of the small Tims, a complex of the mitochondrial intermembrane space that participates in the TIM22 import pathway for assembly of the inner membrane [] Several plant hypothetical proteins that also contain haemerythrin cation binding domains Several protozoan hypothetical proteins that also contain a Myb domain The solution structure of this zinc finger has been solved and binds 3 zinc atoms as shown in the following schematic representation: ++---------+-----+ || | | CXHYxxxxxxxxxCCxxxxxCxxCHxxxxxHxxxxxxxxxxxCxxCxxxxxxxxxCxxC | | | | | | | | +-+-----------------+--+ +--+---------+--+ 'C': conserved cysteine involved in the binding of one zinc atom. 'H': conserved histidine involved in the binding of one zinc atom. More information about these proteins can be found at Protein of the Month: Zinc Fingers []; GO: 0008270 zinc ion binding; PDB: 2DKT_A 2K2C_A.
Probab=99.89 E-value=4.7e-24 Score=160.17 Aligned_cols=70 Identities=51% Similarity=1.212 Sum_probs=53.2
Q ss_pred ccccccC-cceEcCCCCCcccCcchHHhhhcCCCCCCCCccccccccceeeeCCCCccccccccCCcCCCccceeecccc
Q 024483 18 CKHYRRR-CRIRAPCCNEIFDCRHCHNEAASMLRNPYDRHELVRQDVKQVICSVCDTEQPVAQVCTNCGVNMGEYFCDIC 96 (267)
Q Consensus 18 C~HY~r~-c~i~~pcC~~~y~Cr~CHde~~~~~~~~~~~H~~~r~~~~~v~C~~C~~~q~v~~~C~~Cg~~f~~y~C~~C 96 (267)
|+||+|+ |+|+||||++|||||+||||++ +|+++|+.+++|+||.|+++|++++. +|+ |+|+|++|
T Consensus 1 C~HY~~~~~~~~~~cC~~~y~C~~CHde~~--------~H~~~~~~~~~v~Cg~C~~~~~~~~~--~c~---~~~~C~~C 67 (71)
T PF05495_consen 1 CKHYHRSLCAIRFPCCGKYYPCRFCHDELE--------DHPFDRWPVKRVICGKCRTEQPIDEY--SCG---ADYFCPIC 67 (71)
T ss_dssp -SS---S-EEEEETTTTEEESSHHHHHHCS--------SS---TTT--EEEETTT--EEES-SB--TT-----SEEETTT
T ss_pred CCCCCCCcEEEECCcccCeecHHHHHHHhc--------cCccccccccCeECCCCCCccChhhh--hcC---CCccCcCc
Confidence 8999999 9999999999999999999974 79999999999999999999999888 777 99999999
Q ss_pred cccc
Q 024483 97 KFYD 100 (267)
Q Consensus 97 ~l~d 100 (267)
++||
T Consensus 68 ~~~~ 71 (71)
T PF05495_consen 68 GLYF 71 (71)
T ss_dssp TEEE
T ss_pred CCCC
Confidence 9986
No 4
>COG4357 Zinc finger domain containing protein (CHY type) [Function unknown]
Probab=99.58 E-value=4.9e-16 Score=122.28 Aligned_cols=73 Identities=26% Similarity=0.618 Sum_probs=65.8
Q ss_pred ccCccccccC---cceEcCCCCCcccCcchHHhhhcCCCCCCCCccccccccceeeeCCCCcccccc-----ccCCcCCC
Q 024483 15 GYGCKHYRRR---CRIRAPCCNEIFDCRHCHNEAASMLRNPYDRHELVRQDVKQVICSVCDTEQPVA-----QVCTNCGV 86 (267)
Q Consensus 15 ~~gC~HY~r~---c~i~~pcC~~~y~Cr~CHde~~~~~~~~~~~H~~~r~~~~~v~C~~C~~~q~v~-----~~C~~Cg~ 86 (267)
++||.||++. ++|||.+|+|||+|++||||+++|++ +.|+++.+..+.|+||+|..+++++ ..|++|..
T Consensus 12 etRC~Hyht~~Diialkc~~C~kyYaCy~CHdel~~Hpf---~p~~~~~~~~~~iiCGvC~~~LT~~EY~~~~~Cp~C~s 88 (105)
T COG4357 12 ETRCLHYHTPLDIIALKCKCCQKYYACYHCHDELEDHPF---EPWGLQEFNPKAIICGVCRKLLTRAEYGMCGSCPYCQS 88 (105)
T ss_pred cceeeEecCccceEeeeechhhhhhhHHHHHhHHhcCCC---ccCChhhcCCccEEhhhhhhhhhHHHHhhcCCCCCcCC
Confidence 4699999996 79999999999999999999998887 6777788888999999999999884 58999999
Q ss_pred ccce
Q 024483 87 NMGE 90 (267)
Q Consensus 87 ~f~~ 90 (267)
+||.
T Consensus 89 pFNp 92 (105)
T COG4357 89 PFNP 92 (105)
T ss_pred CCCc
Confidence 9984
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=99.38 E-value=8.9e-14 Score=94.34 Aligned_cols=44 Identities=39% Similarity=0.937 Sum_probs=37.4
Q ss_pred CCCchhhhhhcccCCccEEeccCCccChhhHHHHhcCCCCCCCCCC
Q 024483 151 HHCPICYEYLFDSLRNTTVMKCGHTMHCECYHEMIKRDKYCCPICS 196 (267)
Q Consensus 151 ~~CpICle~lf~s~~~v~~LpCGH~~H~~C~~~~~~~~~~~CPiCr 196 (267)
++||||++++.+ .+.++.|+|||.||.+|+.+|++. +.+||+||
T Consensus 1 d~C~IC~~~~~~-~~~~~~l~C~H~fh~~Ci~~~~~~-~~~CP~CR 44 (44)
T PF13639_consen 1 DECPICLEEFED-GEKVVKLPCGHVFHRSCIKEWLKR-NNSCPVCR 44 (44)
T ss_dssp -CETTTTCBHHT-TSCEEEETTSEEEEHHHHHHHHHH-SSB-TTTH
T ss_pred CCCcCCChhhcC-CCeEEEccCCCeeCHHHHHHHHHh-CCcCCccC
Confidence 479999999654 578889999999999999999984 68999996
No 6
>PF12678 zf-rbx1: RING-H2 zinc finger; InterPro: IPR024766 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This domain constitutes a conserved region found in proteins that participate in diverse functions relevant to chromosome metabolism and cell cycle control [].The domain contains 8 cysteine/ histidine residues which are proposed to be the conserved residues involved in zinc binding.; PDB: 4A0C_D 4A0L_I 4A0K_B 2ECL_A 1LDK_C 3RTR_F 3DQV_Y 1U6G_B 1LDJ_B 2HYE_D ....
Probab=99.03 E-value=1.5e-10 Score=87.26 Aligned_cols=48 Identities=31% Similarity=0.688 Sum_probs=36.7
Q ss_pred CCCCCCchhhhhhccc---------CCccEEeccCCccChhhHHHHhcCCCCCCCCCC
Q 024483 148 SMHHHCPICYEYLFDS---------LRNTTVMKCGHTMHCECYHEMIKRDKYCCPICS 196 (267)
Q Consensus 148 ~~~~~CpICle~lf~s---------~~~v~~LpCGH~~H~~C~~~~~~~~~~~CPiCr 196 (267)
..+++|+||++.|.+. .-++...+|||.||..||.+||+. +.+||+||
T Consensus 17 ~~~d~C~IC~~~l~~~~~~~~~~~~~~~i~~~~C~H~FH~~Ci~~Wl~~-~~~CP~CR 73 (73)
T PF12678_consen 17 IADDNCAICREPLEDPCPECQAPQDECPIVWGPCGHIFHFHCISQWLKQ-NNTCPLCR 73 (73)
T ss_dssp SCCSBETTTTSBTTSTTCCHHHCTTTS-EEEETTSEEEEHHHHHHHHTT-SSB-TTSS
T ss_pred CcCCcccccChhhhChhhhhcCCccccceEecccCCCEEHHHHHHHHhc-CCcCCCCC
Confidence 3456799999997443 244556799999999999999984 56999997
No 7
>COG5243 HRD1 HRD ubiquitin ligase complex, ER membrane component [Posttranslational modification, protein turnover, chaperones]
Probab=99.00 E-value=1e-10 Score=111.54 Aligned_cols=57 Identities=26% Similarity=0.742 Sum_probs=49.3
Q ss_pred CCCCCCCchhhhhhcccC---------CccEEeccCCccChhhHHHHhcCCCCCCCCCCcc-ccchhH
Q 024483 147 NSMHHHCPICYEYLFDSL---------RNTTVMKCGHTMHCECYHEMIKRDKYCCPICSKS-VIDMSR 204 (267)
Q Consensus 147 ~~~~~~CpICle~lf~s~---------~~v~~LpCGH~~H~~C~~~~~~~~~~~CPiCrks-~~dm~~ 204 (267)
.+.+..|.||+|+||.+. ...+.|||||.+|.+|++.|++ ++.+|||||.+ +.||++
T Consensus 284 ~n~D~~C~ICmde~~h~~~~~~~~~~~~~pKrLpCGHilHl~CLknW~E-RqQTCPICr~p~ifd~~~ 350 (491)
T COG5243 284 TNSDRTCTICMDEMFHPDHEPLPRGLDMTPKRLPCGHILHLHCLKNWLE-RQQTCPICRRPVIFDQSS 350 (491)
T ss_pred cCCCCeEEEecccccCCCCccCcccccCCcccccccceeeHHHHHHHHH-hccCCCcccCccccccCC
Confidence 677888999999998875 2347899999999999999998 57899999999 468875
No 8
>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=98.97 E-value=4.3e-10 Score=73.79 Aligned_cols=45 Identities=31% Similarity=0.866 Sum_probs=37.9
Q ss_pred CCchhhhhhcccCCccEEeccCCccChhhHHHHhcCCCCCCCCCCccc
Q 024483 152 HCPICYEYLFDSLRNTTVMKCGHTMHCECYHEMIKRDKYCCPICSKSV 199 (267)
Q Consensus 152 ~CpICle~lf~s~~~v~~LpCGH~~H~~C~~~~~~~~~~~CPiCrks~ 199 (267)
.|+||++.+ ..++..++|||.||..|++.|++....+||+|++.+
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 599999986 346667789999999999999985578899999764
No 9
>KOG4628 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=98.89 E-value=5.4e-10 Score=106.31 Aligned_cols=50 Identities=22% Similarity=0.762 Sum_probs=44.4
Q ss_pred CCCchhhhhhcccCCccEEeccCCccChhhHHHHhcCCCCCCCCCCccccc
Q 024483 151 HHCPICYEYLFDSLRNTTVMKCGHTMHCECYHEMIKRDKYCCPICSKSVID 201 (267)
Q Consensus 151 ~~CpICle~lf~s~~~v~~LpCGH~~H~~C~~~~~~~~~~~CPiCrks~~d 201 (267)
..|.||||+ |..++.+++|||+|.||..|++.||......||+|+..+..
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 489999998 78889999999999999999999998554459999998863
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=98.83 E-value=1.4e-09 Score=71.98 Aligned_cols=39 Identities=36% Similarity=0.944 Sum_probs=33.2
Q ss_pred CchhhhhhcccCCccEEeccCCccChhhHHHHhcCCCCCCCCC
Q 024483 153 CPICYEYLFDSLRNTTVMKCGHTMHCECYHEMIKRDKYCCPIC 195 (267)
Q Consensus 153 CpICle~lf~s~~~v~~LpCGH~~H~~C~~~~~~~~~~~CPiC 195 (267)
||||++.+. +++++++|||+|...|+.+|++. +.+||+|
T Consensus 1 C~iC~~~~~---~~~~~~~CGH~fC~~C~~~~~~~-~~~CP~C 39 (39)
T PF13923_consen 1 CPICLDELR---DPVVVTPCGHSFCKECIEKYLEK-NPKCPVC 39 (39)
T ss_dssp ETTTTSB-S---SEEEECTTSEEEEHHHHHHHHHC-TSB-TTT
T ss_pred CCCCCCccc---CcCEECCCCCchhHHHHHHHHHC-cCCCcCC
Confidence 899999754 37789999999999999999996 7899997
No 11
>PHA02929 N1R/p28-like protein; Provisional
Probab=98.81 E-value=3.2e-09 Score=96.72 Aligned_cols=54 Identities=30% Similarity=0.656 Sum_probs=42.6
Q ss_pred cCCCCCCCchhhhhhcccCC----ccEEeccCCccChhhHHHHhcCCCCCCCCCCcccc
Q 024483 146 ENSMHHHCPICYEYLFDSLR----NTTVMKCGHTMHCECYHEMIKRDKYCCPICSKSVI 200 (267)
Q Consensus 146 e~~~~~~CpICle~lf~s~~----~v~~LpCGH~~H~~C~~~~~~~~~~~CPiCrks~~ 200 (267)
+.+.+..||||+|.+.+... -.++++|||.||..|+.+|++ .+.+||+||+.+.
T Consensus 170 ~~~~~~eC~ICle~~~~~~~~~~~~~vl~~C~H~FC~~CI~~Wl~-~~~tCPlCR~~~~ 227 (238)
T PHA02929 170 NRSKDKECAICMEKVYDKEIKNMYFGILSNCNHVFCIECIDIWKK-EKNTCPVCRTPFI 227 (238)
T ss_pred cCCCCCCCccCCcccccCccccccceecCCCCCcccHHHHHHHHh-cCCCCCCCCCEee
Confidence 34557899999998765321 124458999999999999998 5679999999886
No 12
>PF13920 zf-C3HC4_3: Zinc finger, C3HC4 type (RING finger); PDB: 2YHN_B 2YHO_G 3T6P_A 2CSY_A 2VJE_B 2VJF_B 2HDP_B 2EA5_A 2ECG_A 3EB5_A ....
Probab=98.67 E-value=8.7e-09 Score=71.62 Aligned_cols=46 Identities=37% Similarity=0.935 Sum_probs=38.4
Q ss_pred CCCchhhhhhcccCCccEEeccCCc-cChhhHHHHhcCCCCCCCCCCccccc
Q 024483 151 HHCPICYEYLFDSLRNTTVMKCGHT-MHCECYHEMIKRDKYCCPICSKSVID 201 (267)
Q Consensus 151 ~~CpICle~lf~s~~~v~~LpCGH~-~H~~C~~~~~~~~~~~CPiCrks~~d 201 (267)
..|+||++.. ..+.++||||. |...|+.+|++ ...+||+||+.|.+
T Consensus 3 ~~C~iC~~~~----~~~~~~pCgH~~~C~~C~~~~~~-~~~~CP~Cr~~i~~ 49 (50)
T PF13920_consen 3 EECPICFENP----RDVVLLPCGHLCFCEECAERLLK-RKKKCPICRQPIES 49 (50)
T ss_dssp SB-TTTSSSB----SSEEEETTCEEEEEHHHHHHHHH-TTSBBTTTTBB-SE
T ss_pred CCCccCCccC----CceEEeCCCChHHHHHHhHHhcc-cCCCCCcCChhhcC
Confidence 5799999963 45788999999 99999999998 67899999998864
No 13
>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=98.66 E-value=1.4e-08 Score=64.22 Aligned_cols=39 Identities=44% Similarity=1.076 Sum_probs=33.7
Q ss_pred CchhhhhhcccCCccEEeccCCccChhhHHHHhcCCCCCCCCC
Q 024483 153 CPICYEYLFDSLRNTTVMKCGHTMHCECYHEMIKRDKYCCPIC 195 (267)
Q Consensus 153 CpICle~lf~s~~~v~~LpCGH~~H~~C~~~~~~~~~~~CPiC 195 (267)
|+||++. .....+++|||.||..|++.|++....+||+|
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 7899987 25788899999999999999997556789987
No 14
>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=1.4e-08 Score=67.40 Aligned_cols=40 Identities=30% Similarity=0.896 Sum_probs=34.5
Q ss_pred CchhhhhhcccCCccEEeccCCccChhhHHHHhc-CCCCCCCCC
Q 024483 153 CPICYEYLFDSLRNTTVMKCGHTMHCECYHEMIK-RDKYCCPIC 195 (267)
Q Consensus 153 CpICle~lf~s~~~v~~LpCGH~~H~~C~~~~~~-~~~~~CPiC 195 (267)
||||++.+. +++.+++|||.|+..|+.+|++ ....+||+|
T Consensus 1 C~iC~~~~~---~~~~~~~C~H~fC~~C~~~~~~~~~~~~CP~C 41 (41)
T PF00097_consen 1 CPICLEPFE---DPVILLPCGHSFCRDCLRKWLENSGSVKCPLC 41 (41)
T ss_dssp ETTTSSBCS---SEEEETTTSEEEEHHHHHHHHHHTSSSBTTTT
T ss_pred CCcCCcccc---CCCEEecCCCcchHHHHHHHHHhcCCccCCcC
Confidence 899999743 3457899999999999999998 667899998
No 15
>PF14634 zf-RING_5: zinc-RING finger domain
Probab=98.61 E-value=2.6e-08 Score=67.73 Aligned_cols=44 Identities=34% Similarity=0.848 Sum_probs=38.0
Q ss_pred CCchhhhhhcccCCccEEeccCCccChhhHHHHhcCCCCCCCCCCc
Q 024483 152 HCPICYEYLFDSLRNTTVMKCGHTMHCECYHEMIKRDKYCCPICSK 197 (267)
Q Consensus 152 ~CpICle~lf~s~~~v~~LpCGH~~H~~C~~~~~~~~~~~CPiCrk 197 (267)
.|+||++.+ +...+..+|+|||+|...|+..+.. ....||+|+|
T Consensus 1 ~C~~C~~~~-~~~~~~~l~~CgH~~C~~C~~~~~~-~~~~CP~C~k 44 (44)
T PF14634_consen 1 HCNICFEKY-SEERRPRLTSCGHIFCEKCLKKLKG-KSVKCPICRK 44 (44)
T ss_pred CCcCcCccc-cCCCCeEEcccCCHHHHHHHHhhcC-CCCCCcCCCC
Confidence 489999985 5556788899999999999999983 5789999986
No 16
>COG5540 RING-finger-containing ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=98.57 E-value=2.9e-08 Score=92.81 Aligned_cols=53 Identities=25% Similarity=0.601 Sum_probs=45.7
Q ss_pred cCCCCCCCchhhhhhcccCCccEEeccCCccChhhHHHHhcCCCCCCCCCCccc
Q 024483 146 ENSMHHHCPICYEYLFDSLRNTTVMKCGHTMHCECYHEMIKRDKYCCPICSKSV 199 (267)
Q Consensus 146 e~~~~~~CpICle~lf~s~~~v~~LpCGH~~H~~C~~~~~~~~~~~CPiCrks~ 199 (267)
|....-+|.|||++ |...+.+++|||.|.||..|+++|+.....+||+||..+
T Consensus 319 ea~~GveCaICms~-fiK~d~~~vlPC~H~FH~~Cv~kW~~~y~~~CPvCrt~i 371 (374)
T COG5540 319 EADKGVECAICMSN-FIKNDRLRVLPCDHRFHVGCVDKWLLGYSNKCPVCRTAI 371 (374)
T ss_pred hcCCCceEEEEhhh-hcccceEEEeccCceechhHHHHHHhhhcccCCccCCCC
Confidence 44445789999999 677788999999999999999999986678999999765
No 17
>KOG0804 consensus Cytoplasmic Zn-finger protein BRAP2 (BRCA1 associated protein) [General function prediction only]
Probab=98.50 E-value=6.8e-08 Score=94.08 Aligned_cols=82 Identities=27% Similarity=0.638 Sum_probs=66.0
Q ss_pred CCCchhhhhhcccCCccEEeccCCccChhhHHHHhcCCCCCCCCCCccccchhHHhHHhHHHHHhcCCChhhhcCeeEEE
Q 024483 151 HHCPICYEYLFDSLRNTTVMKCGHTMHCECYHEMIKRDKYCCPICSKSVIDMSRTWKRIDEEIEATVMPEDYRHKKVWIL 230 (267)
Q Consensus 151 ~~CpICle~lf~s~~~v~~LpCGH~~H~~C~~~~~~~~~~~CPiCrks~~dm~~~~~~lD~~i~~~pmP~~y~~~~v~I~ 230 (267)
..||||||.|-++++.+....|.|.||..|+..|- ..+||+||.... |+. ...-+
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 47999999999998888889999999999999994 579999994333 111 12457
Q ss_pred cCCCCCccccceeEeeecCCC--CCCcccccc
Q 024483 231 CNDCNDTTEVYFHIIGQKCSH--CKSYNTRSI 260 (267)
Q Consensus 231 CnDC~~~s~~~fH~lg~kC~~--C~SyNT~~~ 260 (267)
|.+|+...++ |+-+.|.+ ||-|+-...
T Consensus 231 c~~c~~~~~L---wicliCg~vgcgrY~eghA 259 (493)
T KOG0804|consen 231 CLACGCTEDL---WICLICGNVGCGRYKEGHA 259 (493)
T ss_pred hhhhcccccE---EEEEEccceecccccchhH
Confidence 9999988776 89999987 999987643
No 18
>PF15227 zf-C3HC4_4: zinc finger of C3HC4-type, RING; PDB: 2EGP_A 2ECV_A 2ECJ_A 2YSL_A 2YSJ_A.
Probab=98.47 E-value=9.6e-08 Score=64.76 Aligned_cols=39 Identities=31% Similarity=0.985 Sum_probs=28.2
Q ss_pred CchhhhhhcccCCccEEeccCCccChhhHHHHhcCC---CCCCCCC
Q 024483 153 CPICYEYLFDSLRNTTVMKCGHTMHCECYHEMIKRD---KYCCPIC 195 (267)
Q Consensus 153 CpICle~lf~s~~~v~~LpCGH~~H~~C~~~~~~~~---~~~CPiC 195 (267)
||||++.| + ..+.|+|||+|-..|+.+|.+.. .+.||+|
T Consensus 1 CpiC~~~~-~---~Pv~l~CGH~FC~~Cl~~~~~~~~~~~~~CP~C 42 (42)
T PF15227_consen 1 CPICLDLF-K---DPVSLPCGHSFCRSCLERLWKEPSGSGFSCPEC 42 (42)
T ss_dssp ETTTTSB--S---SEEE-SSSSEEEHHHHHHHHCCSSSST---SSS
T ss_pred CCccchhh-C---CccccCCcCHHHHHHHHHHHHccCCcCCCCcCC
Confidence 89999975 3 35679999999999999998753 2679987
No 19
>PF13445 zf-RING_UBOX: RING-type zinc-finger; PDB: 2CT2_A.
Probab=98.43 E-value=8.2e-08 Score=65.70 Aligned_cols=40 Identities=33% Similarity=0.904 Sum_probs=24.2
Q ss_pred CchhhhhhcccCCccEEeccCCccChhhHHHHhcC---CCCCCC
Q 024483 153 CPICYEYLFDSLRNTTVMKCGHTMHCECYHEMIKR---DKYCCP 193 (267)
Q Consensus 153 CpICle~lf~s~~~v~~LpCGH~~H~~C~~~~~~~---~~~~CP 193 (267)
||||.| +-+...+.++|+|||+|-+.|+++|+++ ..++||
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 4454556678999999999999999974 357787
No 20
>PF12861 zf-Apc11: Anaphase-promoting complex subunit 11 RING-H2 finger
Probab=98.40 E-value=2e-07 Score=72.60 Aligned_cols=47 Identities=26% Similarity=0.433 Sum_probs=33.1
Q ss_pred CCchhhhhhcccCCccEEeccCCccChhhHHHHhcC--CCCCCCCCCcccc
Q 024483 152 HCPICYEYLFDSLRNTTVMKCGHTMHCECYHEMIKR--DKYCCPICSKSVI 200 (267)
Q Consensus 152 ~CpICle~lf~s~~~v~~LpCGH~~H~~C~~~~~~~--~~~~CPiCrks~~ 200 (267)
.||.|..+-- .-+++.-.|+|.||.+||.+|+.. ++.+||+||+...
T Consensus 34 ~Cp~Ck~Pgd--~Cplv~g~C~H~FH~hCI~kWl~~~~~~~~CPmCR~~w~ 82 (85)
T PF12861_consen 34 CCPDCKFPGD--DCPLVWGKCSHNFHMHCILKWLSTQSSKGQCPMCRQPWK 82 (85)
T ss_pred CCCCccCCCC--CCceeeccCccHHHHHHHHHHHccccCCCCCCCcCCeee
Confidence 4555554421 124445579999999999999984 3578999998753
No 21
>KOG0802 consensus E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=98.37 E-value=1e-07 Score=95.68 Aligned_cols=54 Identities=24% Similarity=0.554 Sum_probs=44.5
Q ss_pred cCCCCCCCchhhhhhcccC-CccEEeccCCccChhhHHHHhcCCCCCCCCCCcccc
Q 024483 146 ENSMHHHCPICYEYLFDSL-RNTTVMKCGHTMHCECYHEMIKRDKYCCPICSKSVI 200 (267)
Q Consensus 146 e~~~~~~CpICle~lf~s~-~~v~~LpCGH~~H~~C~~~~~~~~~~~CPiCrks~~ 200 (267)
+......|+||+|.|+++. ..+++|||||.||..|+..|++ ...+||+||..+.
T Consensus 287 ~~~~~~~C~IC~e~l~~~~~~~~~rL~C~Hifh~~CL~~W~e-r~qtCP~CR~~~~ 341 (543)
T KOG0802|consen 287 LALSDELCIICLEELHSGHNITPKRLPCGHIFHDSCLRSWFE-RQQTCPTCRTVLY 341 (543)
T ss_pred hhhcCCeeeeechhhccccccccceeecccchHHHHHHHHHH-HhCcCCcchhhhh
Confidence 4456788999999997742 2267899999999999999998 5789999999443
No 22
>PLN03208 E3 ubiquitin-protein ligase RMA2; Provisional
Probab=98.35 E-value=3.6e-07 Score=80.86 Aligned_cols=55 Identities=25% Similarity=0.657 Sum_probs=42.1
Q ss_pred eeecCCCCCCCchhhhhhcccCCccEEeccCCccChhhHHHHhcC---------------CCCCCCCCCccccc
Q 024483 143 LCIENSMHHHCPICYEYLFDSLRNTTVMKCGHTMHCECYHEMIKR---------------DKYCCPICSKSVID 201 (267)
Q Consensus 143 ~C~e~~~~~~CpICle~lf~s~~~v~~LpCGH~~H~~C~~~~~~~---------------~~~~CPiCrks~~d 201 (267)
+=++......||||++.+ +..++++|||.|+..|+.+|+.. +..+||+|+..+..
T Consensus 11 ~~~~~~~~~~CpICld~~----~dPVvT~CGH~FC~~CI~~wl~~s~~s~~~~~~~~~~k~~~~CPvCR~~Is~ 80 (193)
T PLN03208 11 TLVDSGGDFDCNICLDQV----RDPVVTLCGHLFCWPCIHKWTYASNNSRQRVDQYDHKREPPKCPVCKSDVSE 80 (193)
T ss_pred eeccCCCccCCccCCCcC----CCcEEcCCCchhHHHHHHHHHHhccccccccccccccCCCCcCCCCCCcCCh
Confidence 334445567899999974 23456899999999999999842 23689999999864
No 23
>PHA02926 zinc finger-like protein; Provisional
Probab=98.22 E-value=5.2e-07 Score=81.41 Aligned_cols=74 Identities=22% Similarity=0.396 Sum_probs=49.8
Q ss_pred cccccccCcceeecCCCCCCCchhhhhhcccC-----CccEEeccCCccChhhHHHHhcCC-----CCCCCCCCcccc--
Q 024483 133 CYSTSLRNNHLCIENSMHHHCPICYEYLFDSL-----RNTTVMKCGHTMHCECYHEMIKRD-----KYCCPICSKSVI-- 200 (267)
Q Consensus 133 C~s~~l~~~H~C~e~~~~~~CpICle~lf~s~-----~~v~~LpCGH~~H~~C~~~~~~~~-----~~~CPiCrks~~-- 200 (267)
+++.-|.+-..=...+.+..|+||+|.+++.+ ......+|+|.|+..|+.+|.+.. ..+||+||..+.
T Consensus 153 ~i~~il~~ye~~~~~SkE~eCgICmE~I~eK~~~~eRrFGIL~~CnHsFCl~CIr~Wr~~r~~~~~~rsCPiCR~~f~~I 232 (242)
T PHA02926 153 DIIKILDKYEDVYRVSKEKECGICYEVVYSKRLENDRYFGLLDSCNHIFCITCINIWHRTRRETGASDNCPICRTRFRNI 232 (242)
T ss_pred chhHHHHHHHHHHhccCCCCCccCccccccccccccccccccCCCCchHHHHHHHHHHHhccccCcCCcCCCCcceeeee
Confidence 34433333333334577889999999876531 123455999999999999999732 345999999875
Q ss_pred chhHHh
Q 024483 201 DMSRTW 206 (267)
Q Consensus 201 dm~~~~ 206 (267)
.++.+|
T Consensus 233 ~pSrf~ 238 (242)
T PHA02926 233 TMSKFY 238 (242)
T ss_pred ccccce
Confidence 344444
No 24
>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=98.04 E-value=3.8e-06 Score=60.00 Aligned_cols=45 Identities=18% Similarity=0.361 Sum_probs=37.8
Q ss_pred CCCchhhhhhcccCCccEEeccCCccChhhHHHHhcCCCCCCCCCCcccc
Q 024483 151 HHCPICYEYLFDSLRNTTVMKCGHTMHCECYHEMIKRDKYCCPICSKSVI 200 (267)
Q Consensus 151 ~~CpICle~lf~s~~~v~~LpCGH~~H~~C~~~~~~~~~~~CPiCrks~~ 200 (267)
-.||||++.|-+ + ++++|||+|-+.|+.+|++. +.+||+|++.+.
T Consensus 2 ~~Cpi~~~~~~~---P-v~~~~G~v~~~~~i~~~~~~-~~~cP~~~~~~~ 46 (63)
T smart00504 2 FLCPISLEVMKD---P-VILPSGQTYERRAIEKWLLS-HGTDPVTGQPLT 46 (63)
T ss_pred cCCcCCCCcCCC---C-EECCCCCEEeHHHHHHHHHH-CCCCCCCcCCCC
Confidence 469999997532 4 56799999999999999985 679999999884
No 25
>KOG0320 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=97.97 E-value=2.8e-06 Score=74.27 Aligned_cols=46 Identities=30% Similarity=0.855 Sum_probs=37.9
Q ss_pred CCCchhhhhhcccCCcc-EEeccCCccChhhHHHHhcCCCCCCCCCCcccc
Q 024483 151 HHCPICYEYLFDSLRNT-TVMKCGHTMHCECYHEMIKRDKYCCPICSKSVI 200 (267)
Q Consensus 151 ~~CpICle~lf~s~~~v-~~LpCGH~~H~~C~~~~~~~~~~~CPiCrks~~ 200 (267)
-.|||||+.. +. .+ +...|||+|.++|+.+.++ ...+||+|+|-|.
T Consensus 132 ~~CPiCl~~~-se--k~~vsTkCGHvFC~~Cik~alk-~~~~CP~C~kkIt 178 (187)
T KOG0320|consen 132 YKCPICLDSV-SE--KVPVSTKCGHVFCSQCIKDALK-NTNKCPTCRKKIT 178 (187)
T ss_pred cCCCceecch-hh--ccccccccchhHHHHHHHHHHH-hCCCCCCcccccc
Confidence 6899999983 32 33 4479999999999999998 4679999999665
No 26
>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=97.92 E-value=5.9e-06 Score=57.85 Aligned_cols=43 Identities=28% Similarity=0.617 Sum_probs=33.6
Q ss_pred CCchhhhhhcccCCccEEeccC-----CccChhhHHHHhcCC-CCCCCCCC
Q 024483 152 HCPICYEYLFDSLRNTTVMKCG-----HTMHCECYHEMIKRD-KYCCPICS 196 (267)
Q Consensus 152 ~CpICle~lf~s~~~v~~LpCG-----H~~H~~C~~~~~~~~-~~~CPiCr 196 (267)
.|-||++ +.+.+...++||. |++|..|+.+|+..+ ..+||+|+
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 3889998 3344566688994 999999999999643 56899995
No 27
>PF11793 FANCL_C: FANCL C-terminal domain; PDB: 3K1L_A.
Probab=97.89 E-value=3.5e-06 Score=63.08 Aligned_cols=51 Identities=31% Similarity=0.656 Sum_probs=24.0
Q ss_pred CCCCchhhhhhc-ccCCccEEe---ccCCccChhhHHHHhcC---C-------CCCCCCCCcccc
Q 024483 150 HHHCPICYEYLF-DSLRNTTVM---KCGHTMHCECYHEMIKR---D-------KYCCPICSKSVI 200 (267)
Q Consensus 150 ~~~CpICle~lf-~s~~~v~~L---pCGH~~H~~C~~~~~~~---~-------~~~CPiCrks~~ 200 (267)
+.+|+||.+++. +...++.+- .|+..||..||.+|+.. + .-+||.|++.|.
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 457999999866 333444443 69999999999999962 1 136999999885
No 28
>KOG2177 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=97.80 E-value=4.3e-05 Score=66.38 Aligned_cols=44 Identities=30% Similarity=0.848 Sum_probs=37.8
Q ss_pred CCCCCchhhhhhcccCCccEEeccCCccChhhHHHHhcCCCCCCCCCCc
Q 024483 149 MHHHCPICYEYLFDSLRNTTVMKCGHTMHCECYHEMIKRDKYCCPICSK 197 (267)
Q Consensus 149 ~~~~CpICle~lf~s~~~v~~LpCGH~~H~~C~~~~~~~~~~~CPiCrk 197 (267)
....||||++++ .. + ++|||||+|-..|+..+.. ....||.||.
T Consensus 12 ~~~~C~iC~~~~-~~--p-~~l~C~H~~c~~C~~~~~~-~~~~Cp~cr~ 55 (386)
T KOG2177|consen 12 EELTCPICLEYF-RE--P-VLLPCGHNFCRACLTRSWE-GPLSCPVCRP 55 (386)
T ss_pred ccccChhhHHHh-hc--C-ccccccchHhHHHHHHhcC-CCcCCcccCC
Confidence 456899999985 43 3 8999999999999999987 6789999995
No 29
>TIGR00599 rad18 DNA repair protein rad18. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=97.75 E-value=2.3e-05 Score=76.29 Aligned_cols=46 Identities=24% Similarity=0.660 Sum_probs=38.4
Q ss_pred CCCCchhhhhhcccCCccEEeccCCccChhhHHHHhcCCCCCCCCCCcccc
Q 024483 150 HHHCPICYEYLFDSLRNTTVMKCGHTMHCECYHEMIKRDKYCCPICSKSVI 200 (267)
Q Consensus 150 ~~~CpICle~lf~s~~~v~~LpCGH~~H~~C~~~~~~~~~~~CPiCrks~~ 200 (267)
...||||++.+ . .++ +++|||.|+..|+..|+.. ...||+|+..+.
T Consensus 26 ~l~C~IC~d~~-~--~Pv-itpCgH~FCs~CI~~~l~~-~~~CP~Cr~~~~ 71 (397)
T TIGR00599 26 SLRCHICKDFF-D--VPV-LTSCSHTFCSLCIRRCLSN-QPKCPLCRAEDQ 71 (397)
T ss_pred ccCCCcCchhh-h--Ccc-CCCCCCchhHHHHHHHHhC-CCCCCCCCCccc
Confidence 46899999975 3 233 6899999999999999974 568999999886
No 30
>COG5194 APC11 Component of SCF ubiquitin ligase and anaphase-promoting complex [Posttranslational modification, protein turnover, chaperones / Cell division and chromosome partitioning]
Probab=97.66 E-value=3.2e-05 Score=59.64 Aligned_cols=29 Identities=24% Similarity=0.622 Sum_probs=26.3
Q ss_pred ccCCccChhhHHHHhcCCCCCCCCCCcccc
Q 024483 171 KCGHTMHCECYHEMIKRDKYCCPICSKSVI 200 (267)
Q Consensus 171 pCGH~~H~~C~~~~~~~~~~~CPiCrks~~ 200 (267)
-|.|.||.+|+..||. +...||+++++..
T Consensus 53 ~CnHaFH~HCI~rWL~-Tk~~CPld~q~w~ 81 (88)
T COG5194 53 VCNHAFHDHCIYRWLD-TKGVCPLDRQTWV 81 (88)
T ss_pred ecchHHHHHHHHHHHh-hCCCCCCCCceeE
Confidence 6999999999999998 4679999999875
No 31
>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=97.53 E-value=7e-05 Score=70.75 Aligned_cols=50 Identities=26% Similarity=0.622 Sum_probs=39.0
Q ss_pred CCCCchhhhhhcccCCccEEe--ccCCccChhhHHHHhcCCCCCCCCCCcccc
Q 024483 150 HHHCPICYEYLFDSLRNTTVM--KCGHTMHCECYHEMIKRDKYCCPICSKSVI 200 (267)
Q Consensus 150 ~~~CpICle~lf~s~~~v~~L--pCGH~~H~~C~~~~~~~~~~~CPiCrks~~ 200 (267)
+..||||+.+.+.+.. .++| +|||.|..+|++.++..+...||+|++++-
T Consensus 3 ~~~CP~Ck~~~y~np~-~kl~i~~CGH~~C~sCv~~l~~~~~~~CP~C~~~lr 54 (309)
T TIGR00570 3 DQGCPRCKTTKYRNPS-LKLMVNVCGHTLCESCVDLLFVRGSGSCPECDTPLR 54 (309)
T ss_pred CCCCCcCCCCCccCcc-cccccCCCCCcccHHHHHHHhcCCCCCCCCCCCccc
Confidence 4579999997555533 2222 899999999999977656789999999876
No 32
>KOG0827 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=97.52 E-value=3.4e-05 Score=74.54 Aligned_cols=46 Identities=26% Similarity=0.594 Sum_probs=38.9
Q ss_pred CCCCchhhhhhcccCCccEEec-cCCccChhhHHHHhcC--CCCCCCCCC
Q 024483 150 HHHCPICYEYLFDSLRNTTVMK-CGHTMHCECYHEMIKR--DKYCCPICS 196 (267)
Q Consensus 150 ~~~CpICle~lf~s~~~v~~Lp-CGH~~H~~C~~~~~~~--~~~~CPiCr 196 (267)
...|.|| +++|....++..+. |||+||..|+.+|++. ++.+||+|+
T Consensus 4 ~A~C~Ic-~d~~p~~~~l~~i~~cGhifh~~cl~qwfe~~Ps~R~cpic~ 52 (465)
T KOG0827|consen 4 MAECHIC-IDGRPNDHELGPIGTCGHIFHTTCLTQWFEGDPSNRGCPICQ 52 (465)
T ss_pred cceeeEe-ccCCccccccccccchhhHHHHHHHHHHHccCCccCCCCcee
Confidence 4579999 77888777777776 9999999999999985 246899999
No 33
>KOG0317 consensus Predicted E3 ubiquitin ligase, integral peroxisomal membrane protein [Posttranslational modification, protein turnover, chaperones]
Probab=97.47 E-value=4e-05 Score=71.45 Aligned_cols=45 Identities=29% Similarity=0.712 Sum_probs=37.7
Q ss_pred CCCchhhhhhcccCCccEEeccCCccChhhHHHHhcCCCCCCCCCCcccc
Q 024483 151 HHCPICYEYLFDSLRNTTVMKCGHTMHCECYHEMIKRDKYCCPICSKSVI 200 (267)
Q Consensus 151 ~~CpICle~lf~s~~~v~~LpCGH~~H~~C~~~~~~~~~~~CPiCrks~~ 200 (267)
..|.+|||.. ......||||.|.-.|+.+|... ...||+||..+-
T Consensus 240 ~kC~LCLe~~----~~pSaTpCGHiFCWsCI~~w~~e-k~eCPlCR~~~~ 284 (293)
T KOG0317|consen 240 RKCSLCLENR----SNPSATPCGHIFCWSCILEWCSE-KAECPLCREKFQ 284 (293)
T ss_pred CceEEEecCC----CCCCcCcCcchHHHHHHHHHHcc-ccCCCcccccCC
Confidence 4699999975 34557899999999999999984 567999997764
No 34
>KOG0287 consensus Postreplication repair protein RAD18 [Replication, recombination and repair]
Probab=97.25 E-value=0.00025 Score=67.73 Aligned_cols=58 Identities=29% Similarity=0.682 Sum_probs=43.8
Q ss_pred CCCchhhhhhcccCCccEEeccCCccChhhHHHHhcCCCCCCCCCCccccch-hHHhHHhHHHH
Q 024483 151 HHCPICYEYLFDSLRNTTVMKCGHTMHCECYHEMIKRDKYCCPICSKSVIDM-SRTWKRIDEEI 213 (267)
Q Consensus 151 ~~CpICle~lf~s~~~v~~LpCGH~~H~~C~~~~~~~~~~~CPiCrks~~dm-~~~~~~lD~~i 213 (267)
..|-||.|++ . ...+.||||+|...||..+|. .+-.||.|..++..- -.--+.||++|
T Consensus 24 LRC~IC~eyf-~---ip~itpCsHtfCSlCIR~~L~-~~p~CP~C~~~~~Es~Lr~n~il~Eiv 82 (442)
T KOG0287|consen 24 LRCGICFEYF-N---IPMITPCSHTFCSLCIRKFLS-YKPQCPTCCVTVTESDLRNNRILDEIV 82 (442)
T ss_pred HHHhHHHHHh-c---CceeccccchHHHHHHHHHhc-cCCCCCceecccchhhhhhhhHHHHHH
Confidence 3699999985 2 345679999999999999997 578999999998631 12234566655
No 35
>KOG0828 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=97.19 E-value=0.00012 Score=72.75 Aligned_cols=51 Identities=25% Similarity=0.595 Sum_probs=37.2
Q ss_pred CCCCchhhhhhc--ccC-----------CccEEeccCCccChhhHHHHhcCCCCCCCCCCcccc
Q 024483 150 HHHCPICYEYLF--DSL-----------RNTTVMKCGHTMHCECYHEMIKRDKYCCPICSKSVI 200 (267)
Q Consensus 150 ~~~CpICle~lf--~s~-----------~~v~~LpCGH~~H~~C~~~~~~~~~~~CPiCrks~~ 200 (267)
..+|+||+.++- ..+ ....+.||-|.||+.|+.+|+......||+||..+-
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 457899987631 111 123345999999999999999855678999998763
No 36
>PF04564 U-box: U-box domain; InterPro: IPR003613 Quality control of intracellular proteins is essential for cellular homeostasis. Molecular chaperones recognise and contribute to the refolding of misfolded or unfolded proteins, whereas the ubiquitin-proteasome system mediates the degradation of such abnormal proteins. Ubiquitin-protein ligases (E3s) determine the substrate specificity for ubiquitylation and have been classified into HECT and RING-finger families. More recently, however, U-box proteins, which contain a domain (the U box) of about 70 amino acids that is conserved from yeast to humans, have been identified as a new type of E3 []. Members of the U-box family of proteins constitute a class of ubiquitin-protein ligases (E3s) distinct from the HECT-type and RING finger-containing E3 families []. Using yeast two-hybrid technology, all mammalian U-box proteins have been reported to interact with molecular chaperones or co-chaperones, including Hsp90, Hsp70, DnaJc7, EKN1, CRN, and VCP. This suggests that the function of U box-type E3s is to mediate the degradation of unfolded or misfolded proteins in conjunction with molecular chaperones as receptors that recognise such abnormal proteins [, ]. Unlike the RING finger domain, IPR001841 from INTERPRO, that is stabilised by Zn2+ ions coordinated by the cysteines and a histidine, the U-box scaffold is probably stabilised by a system of salt-bridges and hydrogen bonds. The charged and polar residues that participate in this network of bonds are more strongly conserved in the U-box proteins than in classic RING fingers, which supports their role in maintaining the stability of the U box. Thus, the U box appears to have evolved from a RING finger domain by appropriation of a new set of residues required to stabilise its structure, concomitant with the loss of the original, metal-chelating residues [].; GO: 0004842 ubiquitin-protein ligase activity, 0016567 protein ubiquitination, 0000151 ubiquitin ligase complex; PDB: 1T1H_A 2C2L_D 2C2V_V 1WGM_A 2KR4_A 3L1Z_B 3L1X_A 2KRE_A 3M63_A 2QIZ_A ....
Probab=97.19 E-value=0.00042 Score=51.85 Aligned_cols=47 Identities=17% Similarity=0.369 Sum_probs=35.4
Q ss_pred CCCchhhhhhcccCCccEEeccCCccChhhHHHHhcCCCCCCCCCCccccc
Q 024483 151 HHCPICYEYLFDSLRNTTVMKCGHTMHCECYHEMIKRDKYCCPICSKSVID 201 (267)
Q Consensus 151 ~~CpICle~lf~s~~~v~~LpCGH~~H~~C~~~~~~~~~~~CPiCrks~~d 201 (267)
-.|||+++-|. +.+++|+||+|=+.++.+|+..+..+||+++..+..
T Consensus 5 f~CpIt~~lM~----dPVi~~~G~tyer~~I~~~l~~~~~~~P~t~~~l~~ 51 (73)
T PF04564_consen 5 FLCPITGELMR----DPVILPSGHTYERSAIERWLEQNGGTDPFTRQPLSE 51 (73)
T ss_dssp GB-TTTSSB-S----SEEEETTSEEEEHHHHHHHHCTTSSB-TTT-SB-SG
T ss_pred cCCcCcCcHhh----CceeCCcCCEEcHHHHHHHHHcCCCCCCCCCCcCCc
Confidence 46999999653 345789999999999999998668999999988863
No 37
>KOG0823 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=97.19 E-value=0.00021 Score=64.89 Aligned_cols=50 Identities=24% Similarity=0.647 Sum_probs=39.1
Q ss_pred CCCCCCchhhhhhcccCCccEEeccCCccChhhHHHHhcC--CCCCCCCCCccccc
Q 024483 148 SMHHHCPICYEYLFDSLRNTTVMKCGHTMHCECYHEMIKR--DKYCCPICSKSVID 201 (267)
Q Consensus 148 ~~~~~CpICle~lf~s~~~v~~LpCGH~~H~~C~~~~~~~--~~~~CPiCrks~~d 201 (267)
...-+|-||||. . ++.++..|||.|.-.||.+||.. +...||+|+-.|.+
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 445689999985 2 45567789999999999999974 24558999987764
No 38
>KOG2164 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=97.01 E-value=0.00033 Score=69.74 Aligned_cols=50 Identities=28% Similarity=0.614 Sum_probs=38.3
Q ss_pred CCCCCCchhhhhhcccCCccEEeccCCccChhhHHHHhcCC----CCCCCCCCccccc
Q 024483 148 SMHHHCPICYEYLFDSLRNTTVMKCGHTMHCECYHEMIKRD----KYCCPICSKSVID 201 (267)
Q Consensus 148 ~~~~~CpICle~lf~s~~~v~~LpCGH~~H~~C~~~~~~~~----~~~CPiCrks~~d 201 (267)
++...|||||++ . .-...+.|||+|.-.||-+|+..+ ...||||+.+|.-
T Consensus 184 ~t~~~CPICL~~-~---~~p~~t~CGHiFC~~CiLqy~~~s~~~~~~~CPiC~s~I~~ 237 (513)
T KOG2164|consen 184 STDMQCPICLEP-P---SVPVRTNCGHIFCGPCILQYWNYSAIKGPCSCPICRSTITL 237 (513)
T ss_pred CcCCcCCcccCC-C---CcccccccCceeeHHHHHHHHhhhcccCCccCCchhhhccc
Confidence 447899999997 2 123345699999999999987532 4679999999863
No 39
>KOG1493 consensus Anaphase-promoting complex (APC), subunit 11 [Cell cycle control, cell division, chromosome partitioning; Posttranslational modification, protein turnover, chaperones]
Probab=96.91 E-value=0.00031 Score=53.89 Aligned_cols=30 Identities=23% Similarity=0.662 Sum_probs=25.2
Q ss_pred ccCCccChhhHHHHhcC--CCCCCCCCCcccc
Q 024483 171 KCGHTMHCECYHEMIKR--DKYCCPICSKSVI 200 (267)
Q Consensus 171 pCGH~~H~~C~~~~~~~--~~~~CPiCrks~~ 200 (267)
-|-|.||..|+.+|+.. ++-.||+||++..
T Consensus 50 ~C~h~fh~hCI~~wl~~~tsq~~CPmcRq~~~ 81 (84)
T KOG1493|consen 50 YCLHAFHAHCILKWLNTPTSQGQCPMCRQTWQ 81 (84)
T ss_pred HHHHHHHHHHHHHHhcCccccccCCcchheeE
Confidence 59999999999999963 4577999998753
No 40
>PF14835 zf-RING_6: zf-RING of BARD1-type protein; PDB: 1JM7_B.
Probab=96.80 E-value=0.00055 Score=50.82 Aligned_cols=56 Identities=25% Similarity=0.640 Sum_probs=28.9
Q ss_pred CCCchhhhhhcccCCccEEeccCCccChhhHHHHhcCCCCCCCCCCcccc--chhHHhHHhHHHH
Q 024483 151 HHCPICYEYLFDSLRNTTVMKCGHTMHCECYHEMIKRDKYCCPICSKSVI--DMSRTWKRIDEEI 213 (267)
Q Consensus 151 ~~CpICle~lf~s~~~v~~LpCGH~~H~~C~~~~~~~~~~~CPiCrks~~--dm~~~~~~lD~~i 213 (267)
..|++|.+.|. +||..-.|.|+|.+.|+.+-+. ..||+|+.+.. |+. .-+.||..|
T Consensus 8 LrCs~C~~~l~---~pv~l~~CeH~fCs~Ci~~~~~---~~CPvC~~Paw~qD~~-~NrqLd~~i 65 (65)
T PF14835_consen 8 LRCSICFDILK---EPVCLGGCEHIFCSSCIRDCIG---SECPVCHTPAWIQDIQ-INRQLDSMI 65 (65)
T ss_dssp TS-SSS-S--S---S-B---SSS--B-TTTGGGGTT---TB-SSS--B-S-SS-----HHHHHHH
T ss_pred cCCcHHHHHhc---CCceeccCccHHHHHHhHHhcC---CCCCCcCChHHHHHHH-hhhhhhccC
Confidence 46999999763 4677789999999999998764 46999999986 443 346777754
No 41
>KOG1941 consensus Acetylcholine receptor-associated protein of the synapse (rapsyn) [Extracellular structures]
Probab=96.69 E-value=0.00041 Score=67.39 Aligned_cols=62 Identities=26% Similarity=0.573 Sum_probs=50.8
Q ss_pred cceeecCCCCCCCchhhhhhcccCCccEEeccCCccChhhHHHHhcC-CCCCCCCCCccccchh
Q 024483 141 NHLCIENSMHHHCPICYEYLFDSLRNTTVMKCGHTMHCECYHEMIKR-DKYCCPICSKSVIDMS 203 (267)
Q Consensus 141 ~H~C~e~~~~~~CpICle~lf~s~~~v~~LpCGH~~H~~C~~~~~~~-~~~~CPiCrks~~dm~ 203 (267)
-|.|++ .++.+|-.|.|.+-...+....|||.|+||..|+.+++.+ ...+||-|||....|.
T Consensus 357 a~~~~~-e~~L~Cg~CGe~~Glk~e~LqALpCsHIfH~rCl~e~L~~n~~rsCP~CrklrSs~~ 419 (518)
T KOG1941|consen 357 AHECVE-ETELYCGLCGESIGLKNERLQALPCSHIFHLRCLQEILENNGTRSCPNCRKLRSSMK 419 (518)
T ss_pred HHHHHH-HHhhhhhhhhhhhcCCcccccccchhHHHHHHHHHHHHHhCCCCCCccHHHHHhhcc
Confidence 466664 4678999999998777777888999999999999999964 4578999997776665
No 42
>KOG1734 consensus Predicted RING-containing E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=96.62 E-value=0.00065 Score=63.22 Aligned_cols=52 Identities=27% Similarity=0.520 Sum_probs=42.2
Q ss_pred CCCCCchhhhhhcccC------CccEEeccCCccChhhHHHHhc-CCCCCCCCCCcccc
Q 024483 149 MHHHCPICYEYLFDSL------RNTTVMKCGHTMHCECYHEMIK-RDKYCCPICSKSVI 200 (267)
Q Consensus 149 ~~~~CpICle~lf~s~------~~v~~LpCGH~~H~~C~~~~~~-~~~~~CPiCrks~~ 200 (267)
.++.|.||...++.+. +..-.|.|+|.||.-|+.-|-- ....+||.|++.+.
T Consensus 223 ~d~vCaVCg~~~~~s~~eegvienty~LsCnHvFHEfCIrGWcivGKkqtCPYCKekVd 281 (328)
T KOG1734|consen 223 SDSVCAVCGQQIDVSVDEEGVIENTYKLSCNHVFHEFCIRGWCIVGKKQTCPYCKEKVD 281 (328)
T ss_pred CcchhHhhcchheeecchhhhhhhheeeecccchHHHhhhhheeecCCCCCchHHHHhh
Confidence 4567999999887764 2556799999999999999974 34689999998875
No 43
>COG5574 PEX10 RING-finger-containing E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=96.41 E-value=0.0014 Score=60.71 Aligned_cols=47 Identities=26% Similarity=0.578 Sum_probs=37.5
Q ss_pred CCCCchhhhhhcccCCccEEeccCCccChhhHHH-HhcCCCCCCCCCCcccc
Q 024483 150 HHHCPICYEYLFDSLRNTTVMKCGHTMHCECYHE-MIKRDKYCCPICSKSVI 200 (267)
Q Consensus 150 ~~~CpICle~lf~s~~~v~~LpCGH~~H~~C~~~-~~~~~~~~CPiCrks~~ 200 (267)
+-.|+||+|.+ .....++|||.|...|+.. |.......||+||.-+.
T Consensus 215 d~kC~lC~e~~----~~ps~t~CgHlFC~~Cl~~~~t~~k~~~CplCRak~~ 262 (271)
T COG5574 215 DYKCFLCLEEP----EVPSCTPCGHLFCLSCLLISWTKKKYEFCPLCRAKVY 262 (271)
T ss_pred ccceeeeeccc----CCcccccccchhhHHHHHHHHHhhccccCchhhhhcc
Confidence 44699999975 3456789999999999999 88744444999997665
No 44
>KOG4265 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=96.41 E-value=0.0018 Score=62.14 Aligned_cols=49 Identities=27% Similarity=0.651 Sum_probs=40.5
Q ss_pred CCCCCCchhhhhhcccCCccEEeccCCc-cChhhHHHHhcCCCCCCCCCCccccc
Q 024483 148 SMHHHCPICYEYLFDSLRNTTVMKCGHT-MHCECYHEMIKRDKYCCPICSKSVID 201 (267)
Q Consensus 148 ~~~~~CpICle~lf~s~~~v~~LpCGH~-~H~~C~~~~~~~~~~~CPiCrks~~d 201 (267)
....+|.|||.+. .++.+|||-|+ |.+.|.+.+.- .+.+|||||..|..
T Consensus 288 ~~gkeCVIClse~----rdt~vLPCRHLCLCs~Ca~~Lr~-q~n~CPICRqpi~~ 337 (349)
T KOG4265|consen 288 ESGKECVICLSES----RDTVVLPCRHLCLCSGCAKSLRY-QTNNCPICRQPIEE 337 (349)
T ss_pred cCCCeeEEEecCC----cceEEecchhhehhHhHHHHHHH-hhcCCCccccchHh
Confidence 4467899999862 67899999996 89999999874 46789999998863
No 45
>KOG1039 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=96.30 E-value=0.00085 Score=64.43 Aligned_cols=82 Identities=23% Similarity=0.489 Sum_probs=57.6
Q ss_pred CCCCCCchhhhhhcccC---CccEE-eccCCccChhhHHHHhcCC------CCCCCCCCcccc--chhHHhHHhHHHHHh
Q 024483 148 SMHHHCPICYEYLFDSL---RNTTV-MKCGHTMHCECYHEMIKRD------KYCCPICSKSVI--DMSRTWKRIDEEIEA 215 (267)
Q Consensus 148 ~~~~~CpICle~lf~s~---~~v~~-LpCGH~~H~~C~~~~~~~~------~~~CPiCrks~~--dm~~~~~~lD~~i~~ 215 (267)
+.+..|-||+|.+.+.. ..-.+ ++|.|.|-..|+..|.... ...||+||...- .-+.+|..-.+ +.
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 56778999999976653 11223 4699999999999998432 478999998874 45556754333 56
Q ss_pred cCCChhhhcCeeEEEc
Q 024483 216 TVMPEDYRHKKVWILC 231 (267)
Q Consensus 216 ~pmP~~y~~~~v~I~C 231 (267)
++.+++|...+....|
T Consensus 237 ~~li~e~~~~~s~~~c 252 (344)
T KOG1039|consen 237 QKLIEEYEAEMSAKDC 252 (344)
T ss_pred cccHHHHHHHhhccch
Confidence 6777887776655433
No 46
>PF14570 zf-RING_4: RING/Ubox like zinc-binding domain; PDB: 1E4U_A 1UR6_B.
Probab=96.26 E-value=0.0033 Score=44.17 Aligned_cols=44 Identities=30% Similarity=0.828 Sum_probs=24.3
Q ss_pred CchhhhhhcccCCccEEe--ccCCccChhhHHHHhcCCCCCCCCCCcc
Q 024483 153 CPICYEYLFDSLRNTTVM--KCGHTMHCECYHEMIKRDKYCCPICSKS 198 (267)
Q Consensus 153 CpICle~lf~s~~~v~~L--pCGH~~H~~C~~~~~~~~~~~CPiCrks 198 (267)
||+|.|+|..+ ...++ +||.-|-+-|+...+++.+.+||-||+.
T Consensus 1 cp~C~e~~d~~--d~~~~PC~Cgf~IC~~C~~~i~~~~~g~CPgCr~~ 46 (48)
T PF14570_consen 1 CPLCDEELDET--DKDFYPCECGFQICRFCYHDILENEGGRCPGCREP 46 (48)
T ss_dssp -TTTS-B--CC--CTT--SSTTS----HHHHHHHTTSS-SB-TTT--B
T ss_pred CCCcccccccC--CCccccCcCCCcHHHHHHHHHHhccCCCCCCCCCC
Confidence 79999998443 44555 5699999999999997667899999975
No 47
>KOG0825 consensus PHD Zn-finger protein [General function prediction only]
Probab=96.12 E-value=0.002 Score=67.19 Aligned_cols=75 Identities=15% Similarity=0.305 Sum_probs=53.6
Q ss_pred eeecCccCccccccccCcceee-cCCCCCCCchhhhhhcccCCccEEeccCCccChhhHHHHhcCCCCCCCCCCcccc
Q 024483 124 YFHCKRCGSCYSTSLRNNHLCI-ENSMHHHCPICYEYLFDSLRNTTVMKCGHTMHCECYHEMIKRDKYCCPICSKSVI 200 (267)
Q Consensus 124 ~fHC~~C~~C~s~~l~~~H~C~-e~~~~~~CpICle~lf~s~~~v~~LpCGH~~H~~C~~~~~~~~~~~CPiCrks~~ 200 (267)
--.|..|=.+.|...-..-.|+ .+-....||+||.. |.........+|+|.||..||..|-+ ...+||+||+.+.
T Consensus 96 s~Ss~~C~~E~S~~~ds~~i~P~~~~~~~~CP~Ci~s-~~DqL~~~~k~c~H~FC~~Ci~sWsR-~aqTCPiDR~EF~ 171 (1134)
T KOG0825|consen 96 SDTSPVCEKEHSPDVDSSNICPVQTHVENQCPNCLKS-CNDQLEESEKHTAHYFCEECVGSWSR-CAQTCPVDRGEFG 171 (1134)
T ss_pred ccccchhheecCCcccccCcCchhhhhhhhhhHHHHH-HHHHhhccccccccccHHHHhhhhhh-hcccCchhhhhhh
Confidence 4456666666666333344444 23445679999987 44434455679999999999999997 5789999999876
No 48
>KOG2930 consensus SCF ubiquitin ligase, Rbx1 component [Posttranslational modification, protein turnover, chaperones]
Probab=96.10 E-value=0.0024 Score=51.69 Aligned_cols=28 Identities=29% Similarity=0.734 Sum_probs=25.1
Q ss_pred ccCCccChhhHHHHhcCCCCCCCCCCccc
Q 024483 171 KCGHTMHCECYHEMIKRDKYCCPICSKSV 199 (267)
Q Consensus 171 pCGH~~H~~C~~~~~~~~~~~CPiCrks~ 199 (267)
-|.|.||..|+..||+ ....||++.+.-
T Consensus 80 ~CNHaFH~hCisrWlk-tr~vCPLdn~eW 107 (114)
T KOG2930|consen 80 VCNHAFHFHCISRWLK-TRNVCPLDNKEW 107 (114)
T ss_pred ecchHHHHHHHHHHHh-hcCcCCCcCcce
Confidence 6999999999999998 568999998764
No 49
>COG5219 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=96.08 E-value=0.0033 Score=66.81 Aligned_cols=53 Identities=26% Similarity=0.637 Sum_probs=39.1
Q ss_pred CCCCCCchhhhhhc--ccCCccEE-eccCCccChhhHHHHhcC-CCCCCCCCCcccc
Q 024483 148 SMHHHCPICYEYLF--DSLRNTTV-MKCGHTMHCECYHEMIKR-DKYCCPICSKSVI 200 (267)
Q Consensus 148 ~~~~~CpICle~lf--~s~~~v~~-LpCGH~~H~~C~~~~~~~-~~~~CPiCrks~~ 200 (267)
+...+|+||.--|. +..-|.+. -.|.|-||..|+.+|++. ++.+||+||.++.
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 55779999988764 22223333 247899999999999975 4688999997653
No 50
>KOG4172 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=95.91 E-value=0.0023 Score=46.25 Aligned_cols=53 Identities=34% Similarity=0.778 Sum_probs=37.3
Q ss_pred CCCCCCchhhhhhcccCCccEEeccCCc-cChhhHHHHhcCCCCCCCCCCccccchhH
Q 024483 148 SMHHHCPICYEYLFDSLRNTTVMKCGHT-MHCECYHEMIKRDKYCCPICSKSVIDMSR 204 (267)
Q Consensus 148 ~~~~~CpICle~lf~s~~~v~~LpCGH~-~H~~C~~~~~~~~~~~CPiCrks~~dm~~ 204 (267)
+...+|.||+|.-.+ .++.-|||+ |.-.|-.+..+..+-.|||||..|-|.-.
T Consensus 5 ~~~dECTICye~pvd----sVlYtCGHMCmCy~Cg~rl~~~~~g~CPiCRapi~dvIk 58 (62)
T KOG4172|consen 5 QWSDECTICYEHPVD----SVLYTCGHMCMCYACGLRLKKALHGCCPICRAPIKDVIK 58 (62)
T ss_pred ccccceeeeccCcch----HHHHHcchHHhHHHHHHHHHHccCCcCcchhhHHHHHHH
Confidence 345789999997333 234589997 55666655555467899999999876543
No 51
>KOG3002 consensus Zn finger protein [General function prediction only]
Probab=95.83 E-value=0.0075 Score=56.96 Aligned_cols=64 Identities=22% Similarity=0.610 Sum_probs=49.3
Q ss_pred CCCCchhhhhhcccCCccEEecc--CCccChhhHHHHhcCCCCCCCCCCccccchhHHhHHhHHHHHhcCCChhhhc
Q 024483 150 HHHCPICYEYLFDSLRNTTVMKC--GHTMHCECYHEMIKRDKYCCPICSKSVIDMSRTWKRIDEEIEATVMPEDYRH 224 (267)
Q Consensus 150 ~~~CpICle~lf~s~~~v~~LpC--GH~~H~~C~~~~~~~~~~~CPiCrks~~dm~~~~~~lD~~i~~~pmP~~y~~ 224 (267)
-.+||||.++|.- -++.| ||+....|-.+. ..+||.|+.+|++... +.++..+++...|=.|.+
T Consensus 48 lleCPvC~~~l~~-----Pi~QC~nGHlaCssC~~~~----~~~CP~Cr~~~g~~R~--~amEkV~e~~~vpC~~~~ 113 (299)
T KOG3002|consen 48 LLDCPVCFNPLSP-----PIFQCDNGHLACSSCRTKV----SNKCPTCRLPIGNIRC--RAMEKVAEAVLVPCKNAK 113 (299)
T ss_pred hccCchhhccCcc-----cceecCCCcEehhhhhhhh----cccCCccccccccHHH--HHHHHHHHhceecccccc
Confidence 4589999999732 35667 899999999754 4699999999997644 567777888877766544
No 52
>KOG1785 consensus Tyrosine kinase negative regulator CBL [Defense mechanisms]
Probab=95.66 E-value=0.0036 Score=61.19 Aligned_cols=54 Identities=26% Similarity=0.608 Sum_probs=45.2
Q ss_pred eecCCCCCCCchhhhhhcccCCccEEeccCCccChhhHHHHhcCC-CCCCCCCCccccc
Q 024483 144 CIENSMHHHCPICYEYLFDSLRNTTVMKCGHTMHCECYHEMIKRD-KYCCPICSKSVID 201 (267)
Q Consensus 144 C~e~~~~~~CpICle~lf~s~~~v~~LpCGH~~H~~C~~~~~~~~-~~~CPiCrks~~d 201 (267)
|.-+++-+.|-||-|. .++|++=||||.+...|+..|-... ..+||.||-.|-.
T Consensus 363 ceMgsTFeLCKICaen----dKdvkIEPCGHLlCt~CLa~WQ~sd~gq~CPFCRcEIKG 417 (563)
T KOG1785|consen 363 CEMGSTFELCKICAEN----DKDVKIEPCGHLLCTSCLAAWQDSDEGQTCPFCRCEIKG 417 (563)
T ss_pred HHccchHHHHHHhhcc----CCCcccccccchHHHHHHHhhcccCCCCCCCceeeEecc
Confidence 4456788899999985 3689999999999999999998543 6899999988753
No 53
>PF11789 zf-Nse: Zinc-finger of the MIZ type in Nse subunit; PDB: 2YU4_A 3HTK_C.
Probab=95.55 E-value=0.0069 Score=43.71 Aligned_cols=44 Identities=27% Similarity=0.613 Sum_probs=30.6
Q ss_pred CCCCCCchhhhhhcccCCccEEeccCCccChhhHHHHhc-CCCCCCCC
Q 024483 148 SMHHHCPICYEYLFDSLRNTTVMKCGHTMHCECYHEMIK-RDKYCCPI 194 (267)
Q Consensus 148 ~~~~~CpICle~lf~s~~~v~~LpCGH~~H~~C~~~~~~-~~~~~CPi 194 (267)
.....|||-+..| . +||+...|||+|=+.-+.+|+. ++..+||+
T Consensus 9 ~~~~~CPiT~~~~-~--~PV~s~~C~H~fek~aI~~~i~~~~~~~CPv 53 (57)
T PF11789_consen 9 TISLKCPITLQPF-E--DPVKSKKCGHTFEKEAILQYIQRNGSKRCPV 53 (57)
T ss_dssp B--SB-TTTSSB--S--SEEEESSS--EEEHHHHHHHCTTTS-EE-SC
T ss_pred EeccCCCCcCChh-h--CCcCcCCCCCeecHHHHHHHHHhcCCCCCCC
Confidence 3456799999974 3 5899999999999999999993 35688998
No 54
>PF10367 Vps39_2: Vacuolar sorting protein 39 domain 2; InterPro: IPR019453 This entry represents a domain found in the vacuolar sorting protein Vps39 and transforming growth factor beta receptor-associated protein Trap1. Vps39, a component of the C-Vps complex, is thought to be required for the fusion of endosomes and other types of transport intermediates with the vacuole [, ]. In Saccharomyces cerevisiae (Baker's yeast), Vps39 has been shown to stimulate nucleotide exchange []. Trap1 plays a role in the TGF-beta/activin signaling pathway. It associates with inactive heteromeric TGF-beta and activin receptor complexes, mainly through the type II receptor, and is released upon activation of signaling [, ]. The precise function of this domain has not been characterised In Vps39 this domain is involved in localisation and in mediating the interactions with Vps11 [].
Probab=95.54 E-value=0.0051 Score=47.86 Aligned_cols=38 Identities=24% Similarity=0.528 Sum_probs=30.4
Q ss_pred eeecCCCCCCCchhhhhhcccCCccEEeccCCccChhhHH
Q 024483 143 LCIENSMHHHCPICYEYLFDSLRNTTVMKCGHTMHCECYH 182 (267)
Q Consensus 143 ~C~e~~~~~~CpICle~lf~s~~~v~~LpCGH~~H~~C~~ 182 (267)
..+.-.....|+||...|++ ....+.||||.+|..|++
T Consensus 71 ~~v~i~~~~~C~vC~k~l~~--~~f~~~p~~~v~H~~C~~ 108 (109)
T PF10367_consen 71 RSVVITESTKCSVCGKPLGN--SVFVVFPCGHVVHYSCIK 108 (109)
T ss_pred ceEEECCCCCccCcCCcCCC--ceEEEeCCCeEEeccccc
Confidence 34444556789999999877 478889999999999975
No 55
>KOG0311 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=95.37 E-value=0.0046 Score=59.39 Aligned_cols=49 Identities=27% Similarity=0.688 Sum_probs=41.1
Q ss_pred CCCCchhhhhhcccCCccEEeccCCccChhhHHHHhcCCCCCCCCCCccccc
Q 024483 150 HHHCPICYEYLFDSLRNTTVMKCGHTMHCECYHEMIKRDKYCCPICSKSVID 201 (267)
Q Consensus 150 ~~~CpICle~lf~s~~~v~~LpCGH~~H~~C~~~~~~~~~~~CPiCrks~~d 201 (267)
+..|||||+-|-. ......|+|-|...||..-+..++..||.|||.++.
T Consensus 43 ~v~c~icl~llk~---tmttkeClhrfc~~ci~~a~r~gn~ecptcRk~l~S 91 (381)
T KOG0311|consen 43 QVICPICLSLLKK---TMTTKECLHRFCFDCIWKALRSGNNECPTCRKKLVS 91 (381)
T ss_pred hhccHHHHHHHHh---hcccHHHHHHHHHHHHHHHHHhcCCCCchHHhhccc
Confidence 4479999996532 456778999999999998887788999999999984
No 56
>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional
Probab=95.32 E-value=0.015 Score=42.52 Aligned_cols=46 Identities=26% Similarity=0.768 Sum_probs=34.2
Q ss_pred cceeeeCCCCcccccc-----ccCCcCCCc-cceeeccccccccCCCCcCeeecCCCCc
Q 024483 63 VKQVICSVCDTEQPVA-----QVCTNCGVN-MGEYFCDICKFYDDDIEKGQFHCDDCGI 115 (267)
Q Consensus 63 ~~~v~C~~C~~~q~v~-----~~C~~Cg~~-f~~y~C~~C~l~dd~~~k~~yHC~~Cgi 115 (267)
.+...|..|+.+.... -.||+||.. ..| |.+|+-+. ..|.|++||+
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 3456788898766542 379999986 544 99998775 4799999985
No 57
>KOG1645 consensus RING-finger-containing E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=95.28 E-value=0.019 Score=56.23 Aligned_cols=50 Identities=26% Similarity=0.720 Sum_probs=38.7
Q ss_pred CCCCchhhhhhcccCCc-cEEeccCCccChhhHHHHhcC-CCCCCCCCCccc
Q 024483 150 HHHCPICYEYLFDSLRN-TTVMKCGHTMHCECYHEMIKR-DKYCCPICSKSV 199 (267)
Q Consensus 150 ~~~CpICle~lf~s~~~-v~~LpCGH~~H~~C~~~~~~~-~~~~CPiCrks~ 199 (267)
...|||||+.+-++.+. +..|.|||.|=+.|++.||.. ...+||.|.-..
T Consensus 4 g~tcpiclds~~~~g~hr~vsl~cghlFgs~cie~wl~k~~~~~cp~c~~ka 55 (463)
T KOG1645|consen 4 GTTCPICLDSYTTAGNHRIVSLQCGHLFGSQCIEKWLGKKTKMQCPLCSGKA 55 (463)
T ss_pred cccCceeeeeeeecCceEEeeecccccccHHHHHHHHhhhhhhhCcccCChh
Confidence 45799999987555444 455899999999999999952 346799997544
No 58
>KOG0978 consensus E3 ubiquitin ligase involved in syntaxin degradation [Posttranslational modification, protein turnover, chaperones]
Probab=95.26 E-value=0.0046 Score=64.10 Aligned_cols=46 Identities=24% Similarity=0.651 Sum_probs=40.8
Q ss_pred CCCchhhhhhcccCCccEEeccCCccChhhHHHHhcCCCCCCCCCCcccc
Q 024483 151 HHCPICYEYLFDSLRNTTVMKCGHTMHCECYHEMIKRDKYCCPICSKSVI 200 (267)
Q Consensus 151 ~~CpICle~lf~s~~~v~~LpCGH~~H~~C~~~~~~~~~~~CPiCrks~~ 200 (267)
..||+|-.. ..++++..|||.|...|+...+.....+||.|+.+++
T Consensus 644 LkCs~Cn~R----~Kd~vI~kC~H~FC~~Cvq~r~etRqRKCP~Cn~aFg 689 (698)
T KOG0978|consen 644 LKCSVCNTR----WKDAVITKCGHVFCEECVQTRYETRQRKCPKCNAAFG 689 (698)
T ss_pred eeCCCccCc----hhhHHHHhcchHHHHHHHHHHHHHhcCCCCCCCCCCC
Confidence 469999854 3578888999999999999999888999999999997
No 59
>COG5432 RAD18 RING-finger-containing E3 ubiquitin ligase [Signal transduction mechanisms]
Probab=95.20 E-value=0.011 Score=55.80 Aligned_cols=46 Identities=24% Similarity=0.574 Sum_probs=37.4
Q ss_pred CCCCchhhhhhcccCCccEEeccCCccChhhHHHHhcCCCCCCCCCCcccc
Q 024483 150 HHHCPICYEYLFDSLRNTTVMKCGHTMHCECYHEMIKRDKYCCPICSKSVI 200 (267)
Q Consensus 150 ~~~CpICle~lf~s~~~v~~LpCGH~~H~~C~~~~~~~~~~~CPiCrks~~ 200 (267)
...|-||-+++ ......+|||+|...||..+|. .+-.||+|+-...
T Consensus 25 ~lrC~IC~~~i----~ip~~TtCgHtFCslCIR~hL~-~qp~CP~Cr~~~~ 70 (391)
T COG5432 25 MLRCRICDCRI----SIPCETTCGHTFCSLCIRRHLG-TQPFCPVCREDPC 70 (391)
T ss_pred HHHhhhhhhee----ecceecccccchhHHHHHHHhc-CCCCCccccccHH
Confidence 34699999985 2334569999999999999997 5889999997654
No 60
>PF12906 RINGv: RING-variant domain; PDB: 2D8S_A 1VYX_A.
Probab=95.08 E-value=0.0089 Score=41.40 Aligned_cols=41 Identities=29% Similarity=0.704 Sum_probs=27.0
Q ss_pred CchhhhhhcccCCccEEecc---C--CccChhhHHHHhcC-CCCCCCCC
Q 024483 153 CPICYEYLFDSLRNTTVMKC---G--HTMHCECYHEMIKR-DKYCCPIC 195 (267)
Q Consensus 153 CpICle~lf~s~~~v~~LpC---G--H~~H~~C~~~~~~~-~~~~CPiC 195 (267)
|-||++.-.++ +..+.|| | -..|..|+.+|+.. ++.+|++|
T Consensus 1 CrIC~~~~~~~--~~li~pC~C~Gs~~~vH~~CL~~W~~~~~~~~C~~C 47 (47)
T PF12906_consen 1 CRICLEGEEED--EPLISPCRCKGSMKYVHRSCLERWIRESGNRKCEIC 47 (47)
T ss_dssp ETTTTEE-SSS--S-EE-SSS-SSCCGSEECCHHHHHHHHHT-SB-TTT
T ss_pred CeEeCCcCCCC--CceecccccCCCcchhHHHHHHHHHHhcCCCcCCCC
Confidence 56898874333 3456687 3 68999999999973 45789987
No 61
>KOG1428 consensus Inhibitor of type V adenylyl cyclases/Neuronal presynaptic protein Highwire/PAM/RPM-1 [Signal transduction mechanisms]
Probab=95.05 E-value=0.02 Score=63.34 Aligned_cols=74 Identities=26% Similarity=0.626 Sum_probs=55.6
Q ss_pred cCccceeecCccCccccccccCcceeecCCCCCCCchhhhhhcccCCccEEeccCCccChhhHHHHhcCC---------C
Q 024483 119 GGRENYFHCKRCGSCYSTSLRNNHLCIENSMHHHCPICYEYLFDSLRNTTVMKCGHTMHCECYHEMIKRD---------K 189 (267)
Q Consensus 119 G~~~~~fHC~~C~~C~s~~l~~~H~C~e~~~~~~CpICle~lf~s~~~v~~LpCGH~~H~~C~~~~~~~~---------~ 189 (267)
||.+|-.||--|-.|-.-.. ....++.|.||..+ .-+-.|.++|.|||+||.+|....|++. -
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 56678888888877643321 23446779999987 3455799999999999999998877632 3
Q ss_pred CCCCCCCcccc
Q 024483 190 YCCPICSKSVI 200 (267)
Q Consensus 190 ~~CPiCrks~~ 200 (267)
..||||...|.
T Consensus 3534 isCPiC~n~In 3544 (3738)
T KOG1428|consen 3534 ISCPICKNKIN 3544 (3738)
T ss_pred eecccccchhh
Confidence 57999998875
No 62
>KOG3970 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=94.77 E-value=0.032 Score=51.05 Aligned_cols=51 Identities=29% Similarity=0.693 Sum_probs=43.3
Q ss_pred CCCCCCchhhhhhcccCCccEEeccCCccChhhHHHHhcC-------CCCCCCCCCcccc
Q 024483 148 SMHHHCPICYEYLFDSLRNTTVMKCGHTMHCECYHEMIKR-------DKYCCPICSKSVI 200 (267)
Q Consensus 148 ~~~~~CpICle~lf~s~~~v~~LpCGH~~H~~C~~~~~~~-------~~~~CPiCrks~~ 200 (267)
....||..|...|... +.+.|-|=|.||-.|+++|... ..|+||-|+..|.
T Consensus 48 DY~pNC~LC~t~La~g--dt~RLvCyhlfHW~ClneraA~lPanTAPaGyqCP~Cs~eiF 105 (299)
T KOG3970|consen 48 DYNPNCRLCNTPLASG--DTTRLVCYHLFHWKCLNERAANLPANTAPAGYQCPCCSQEIF 105 (299)
T ss_pred CCCCCCceeCCccccC--cceeehhhhhHHHHHhhHHHhhCCCcCCCCcccCCCCCCccC
Confidence 4578999999997553 6778999999999999999862 3699999999986
No 63
>KOG2879 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=94.57 E-value=0.026 Score=52.76 Aligned_cols=53 Identities=25% Similarity=0.589 Sum_probs=43.1
Q ss_pred CCCCCCchhhhhhcccCCccEEeccCCccChhhHHHHhcC-CCCCCCCCCccccchh
Q 024483 148 SMHHHCPICYEYLFDSLRNTTVMKCGHTMHCECYHEMIKR-DKYCCPICSKSVIDMS 203 (267)
Q Consensus 148 ~~~~~CpICle~lf~s~~~v~~LpCGH~~H~~C~~~~~~~-~~~~CPiCrks~~dm~ 203 (267)
....+||+|.|+ ++.|.+..+|||.+.=-|+..=... .+++||.|+.++..|.
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 456789999997 6678888999999999999875542 3589999998887664
No 64
>KOG4275 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=93.45 E-value=0.012 Score=55.44 Aligned_cols=62 Identities=23% Similarity=0.561 Sum_probs=42.4
Q ss_pred ccCcceeecCCC---CCCCchhhhhhcccCCccEEeccCCccChhhHHHHhcCCCCCCCCCCccccchhHHhH
Q 024483 138 LRNNHLCIENSM---HHHCPICYEYLFDSLRNTTVMKCGHTMHCECYHEMIKRDKYCCPICSKSVIDMSRTWK 207 (267)
Q Consensus 138 l~~~H~C~e~~~---~~~CpICle~lf~s~~~v~~LpCGH~~H~~C~~~~~~~~~~~CPiCrks~~dm~~~~~ 207 (267)
++++|.+.-... +..|.||++- ..+-.+|+|||.. +|+.-=. .-..|||||+-|...-.+|+
T Consensus 285 ~k~~~g~~~~~s~~~~~LC~ICmDa----P~DCvfLeCGHmV--tCt~CGk--rm~eCPICRqyi~rvvrif~ 349 (350)
T KOG4275|consen 285 YKGNDGEQHSRSLATRRLCAICMDA----PRDCVFLECGHMV--TCTKCGK--RMNECPICRQYIVRVVRIFR 349 (350)
T ss_pred HhcccccccccchhHHHHHHHHhcC----CcceEEeecCcEE--eehhhcc--ccccCchHHHHHHHHHhhhc
Confidence 456666655444 7789999974 4678899999986 3443221 12389999999886655553
No 65
>KOG3800 consensus Predicted E3 ubiquitin ligase containing RING finger, subunit of transcription/repair factor TFIIH and CDK-activating kinase assembly factor [Posttranslational modification, protein turnover, chaperones]
Probab=93.40 E-value=0.051 Score=51.10 Aligned_cols=48 Identities=23% Similarity=0.563 Sum_probs=39.7
Q ss_pred CCchhhhhhcccCCccEEe--ccCCccChhhHHHHhcCCCCCCCCCCcccc
Q 024483 152 HCPICYEYLFDSLRNTTVM--KCGHTMHCECYHEMIKRDKYCCPICSKSVI 200 (267)
Q Consensus 152 ~CpICle~lf~s~~~v~~L--pCGH~~H~~C~~~~~~~~~~~CPiCrks~~ 200 (267)
.||+|..+.+... .++.| +|||.+..+|++..+..+.+.||.|.+.+.
T Consensus 2 ~Cp~CKt~~Y~np-~lk~~in~C~H~lCEsCvd~iF~~g~~~CpeC~~iLR 51 (300)
T KOG3800|consen 2 ACPKCKTDRYLNP-DLKLMINECGHRLCESCVDRIFSLGPAQCPECMVILR 51 (300)
T ss_pred CCcccccceecCc-cceeeeccccchHHHHHHHHHHhcCCCCCCcccchhh
Confidence 5999998876653 33333 999999999999999888999999998875
No 66
>PF14447 Prok-RING_4: Prokaryotic RING finger family 4
Probab=93.39 E-value=0.032 Score=40.26 Aligned_cols=32 Identities=28% Similarity=0.669 Sum_probs=26.3
Q ss_pred ccEEeccCCccChhhHHHHhcCCCCCCCCCCcccc
Q 024483 166 NTTVMKCGHTMHCECYHEMIKRDKYCCPICSKSVI 200 (267)
Q Consensus 166 ~v~~LpCGH~~H~~C~~~~~~~~~~~CPiCrks~~ 200 (267)
.-.+|||||++-..|++-+. -.-||+|.+.+.
T Consensus 19 ~~~~~pCgH~I~~~~f~~~r---YngCPfC~~~~~ 50 (55)
T PF14447_consen 19 KGTVLPCGHLICDNCFPGER---YNGCPFCGTPFE 50 (55)
T ss_pred ccccccccceeeccccChhh---ccCCCCCCCccc
Confidence 45679999999999998763 347999999875
No 67
>KOG0824 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=93.00 E-value=0.045 Score=51.78 Aligned_cols=50 Identities=24% Similarity=0.473 Sum_probs=40.4
Q ss_pred CCCCCCCchhhhhhcccCCccEEeccCCccChhhHHHHhcCCCCCCCCCCcccc
Q 024483 147 NSMHHHCPICYEYLFDSLRNTTVMKCGHTMHCECYHEMIKRDKYCCPICSKSVI 200 (267)
Q Consensus 147 ~~~~~~CpICle~lf~s~~~v~~LpCGH~~H~~C~~~~~~~~~~~CPiCrks~~ 200 (267)
+.+..+|+||+.... -| +.|+|+|.|.-.|++--..+...+||+||..|-
T Consensus 4 ~~~~~eC~IC~nt~n---~P-v~l~C~HkFCyiCiKGsy~ndk~~CavCR~pid 53 (324)
T KOG0824|consen 4 RTKKKECLICYNTGN---CP-VNLYCFHKFCYICIKGSYKNDKKTCAVCRFPID 53 (324)
T ss_pred cccCCcceeeeccCC---cC-ccccccchhhhhhhcchhhcCCCCCceecCCCC
Confidence 345679999998753 34 789999999999998766656678999999886
No 68
>KOG4445 consensus Uncharacterized conserved protein, contains RWD domain [Function unknown]
Probab=92.98 E-value=0.024 Score=53.69 Aligned_cols=54 Identities=30% Similarity=0.594 Sum_probs=41.9
Q ss_pred CCCCCCCchhhhhhcccCCccEEeccCCccChhhHHHHhcC----------------------CCCCCCCCCccccc
Q 024483 147 NSMHHHCPICYEYLFDSLRNTTVMKCGHTMHCECYHEMIKR----------------------DKYCCPICSKSVID 201 (267)
Q Consensus 147 ~~~~~~CpICle~lf~s~~~v~~LpCGH~~H~~C~~~~~~~----------------------~~~~CPiCrks~~d 201 (267)
+-..+.|.|||-- |.+.....+.+|-|+||..||..+|.. ..--|||||-.|.+
T Consensus 112 n~p~gqCvICLyg-fa~~~~ft~T~C~Hy~H~~ClaRyl~~~~~~lrqe~q~~~~~~qh~~~~~eavcpVcre~i~~ 187 (368)
T KOG4445|consen 112 NHPNGQCVICLYG-FASSPAFTVTACDHYMHFACLARYLTECLTGLRQEIQDAQKERQHMKEQVEAVCPVCRERIKI 187 (368)
T ss_pred CCCCCceEEEEEe-ecCCCceeeehhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhHhhhhhHhhhhccc
Confidence 3456789999987 556566888999999999999988761 12349999988763
No 69
>PF05883 Baculo_RING: Baculovirus U-box/Ring-like domain; InterPro: IPR008573 This family consists of several Baculovirus proteins of around 130 residues in length. The function of this family is unknown, but it appears to be related to the U-box and ring finger domain by profile-profile comparison.
Probab=92.65 E-value=0.053 Score=45.75 Aligned_cols=36 Identities=14% Similarity=0.418 Sum_probs=31.4
Q ss_pred CCCCchhhhhhcccCCccEEeccC------CccChhhHHHHhc
Q 024483 150 HHHCPICYEYLFDSLRNTTVMKCG------HTMHCECYHEMIK 186 (267)
Q Consensus 150 ~~~CpICle~lf~s~~~v~~LpCG------H~~H~~C~~~~~~ 186 (267)
..+|.||++.+-+ ...|+.+++| |+||..|+..|..
T Consensus 26 ~~EC~IC~~~I~~-~~GvV~vt~~g~lnLEkmfc~~C~~rw~~ 67 (134)
T PF05883_consen 26 TVECQICFDRIDN-NDGVVYVTDGGTLNLEKMFCADCDKRWRR 67 (134)
T ss_pred Ceeehhhhhhhhc-CCCEEEEecCCeehHHHHHHHHHHHHHHh
Confidence 4689999999877 5789999997 9999999999943
No 70
>KOG3268 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=92.13 E-value=0.068 Score=47.40 Aligned_cols=35 Identities=29% Similarity=0.731 Sum_probs=28.0
Q ss_pred EeccCCccChhhHHHHhcC-----CC-----CCCCCCCcccc-chh
Q 024483 169 VMKCGHTMHCECYHEMIKR-----DK-----YCCPICSKSVI-DMS 203 (267)
Q Consensus 169 ~LpCGH~~H~~C~~~~~~~-----~~-----~~CPiCrks~~-dm~ 203 (267)
...||-.||+-|+.+||+. .+ -.||.|+++|. .|+
T Consensus 187 N~qCgkpFHqiCL~dWLRgilTsRQSFdiiFGeCPYCS~PialKmS 232 (234)
T KOG3268|consen 187 NIQCGKPFHQICLTDWLRGILTSRQSFDIIFGECPYCSDPIALKMS 232 (234)
T ss_pred ccccCCcHHHHHHHHHHHHHhhccceeeeeeccCCCCCCcceeecc
Confidence 4689999999999999973 11 36999999985 564
No 71
>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]
Probab=92.06 E-value=0.11 Score=38.20 Aligned_cols=45 Identities=29% Similarity=0.782 Sum_probs=34.0
Q ss_pred eeeeCCCCccccc-----cccCCcCCCccceeeccccccccCCCCcCeeecCCCCc
Q 024483 65 QVICSVCDTEQPV-----AQVCTNCGVNMGEYFCDICKFYDDDIEKGQFHCDDCGI 115 (267)
Q Consensus 65 ~v~C~~C~~~q~v-----~~~C~~Cg~~f~~y~C~~C~l~dd~~~k~~yHC~~Cgi 115 (267)
...|..|+.+..+ .-.|||||... =|-|.+|+.+. .+|-|++||+
T Consensus 9 ~~~CtSCg~~i~p~e~~v~F~CPnCGe~~-I~Rc~~CRk~g-----~~Y~Cp~CGF 58 (61)
T COG2888 9 PPVCTSCGREIAPGETAVKFPCPNCGEVE-IYRCAKCRKLG-----NPYRCPKCGF 58 (61)
T ss_pred CceeccCCCEeccCCceeEeeCCCCCcee-eehhhhHHHcC-----CceECCCcCc
Confidence 5689999988754 34799999443 35688998775 4799999985
No 72
>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=92.00 E-value=0.099 Score=42.61 Aligned_cols=38 Identities=18% Similarity=0.362 Sum_probs=29.5
Q ss_pred cCeeEEEcCCCCCccccceeEeeecCCCCCCccccccCCC
Q 024483 224 HKKVWILCNDCNDTTEVYFHIIGQKCSHCKSYNTRSIAPP 263 (267)
Q Consensus 224 ~~~v~I~CnDC~~~s~~~fH~lg~kC~~C~SyNT~~~~~~ 263 (267)
...+...|++|+.......+ ...||.|||++++.++|.
T Consensus 66 ~~p~~~~C~~Cg~~~~~~~~--~~~CP~Cgs~~~~i~~G~ 103 (115)
T TIGR00100 66 DEPVECECEDCSEEVSPEID--LYRCPKCHGIMLQVRAGK 103 (115)
T ss_pred eeCcEEEcccCCCEEecCCc--CccCcCCcCCCcEEecCC
Confidence 34567899999987766432 357999999999998874
No 73
>PRK00564 hypA hydrogenase nickel incorporation protein; Provisional
Probab=91.68 E-value=0.1 Score=42.65 Aligned_cols=39 Identities=23% Similarity=0.405 Sum_probs=29.9
Q ss_pred hcCeeEEEcCCCCCccccc-eeEeeecCCCCCCccccccCCC
Q 024483 223 RHKKVWILCNDCNDTTEVY-FHIIGQKCSHCKSYNTRSIAPP 263 (267)
Q Consensus 223 ~~~~v~I~CnDC~~~s~~~-fH~lg~kC~~C~SyNT~~~~~~ 263 (267)
....+.+.|++|+..+... +++ .+|+.|||++...++|.
T Consensus 66 e~vp~~~~C~~Cg~~~~~~~~~~--~~CP~Cgs~~~~i~~G~ 105 (117)
T PRK00564 66 VDEKVELECKDCSHVFKPNALDY--GVCEKCHSKNVIITQGN 105 (117)
T ss_pred EecCCEEEhhhCCCccccCCccC--CcCcCCCCCceEEecCC
Confidence 3345678999999887665 333 47999999999988764
No 74
>PRK03824 hypA hydrogenase nickel incorporation protein; Provisional
Probab=91.66 E-value=0.21 Score=41.85 Aligned_cols=38 Identities=18% Similarity=0.435 Sum_probs=28.5
Q ss_pred eeEEEcCCCCCccccc-------------eeE------eeecCCCCCCccccccCCC
Q 024483 226 KVWILCNDCNDTTEVY-------------FHI------IGQKCSHCKSYNTRSIAPP 263 (267)
Q Consensus 226 ~v~I~CnDC~~~s~~~-------------fH~------lg~kC~~C~SyNT~~~~~~ 263 (267)
.+...|++||...... +|+ ...+|+.|||++.+.++|.
T Consensus 68 p~~~~C~~CG~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~CP~Cgs~~~~i~~G~ 124 (135)
T PRK03824 68 EAVLKCRNCGNEWSLKEVKESLDEEIREAIHFIPEVVHAFLKCPKCGSRDFEIVKGR 124 (135)
T ss_pred ceEEECCCCCCEEecccccccccccccccccccccccccCcCCcCCCCCCcEEecCc
Confidence 4678999999776543 222 3368999999999988774
No 75
>KOG4739 consensus Uncharacterized protein involved in synaptonemal complex formation [Cell cycle control, cell division, chromosome partitioning; General function prediction only]
Probab=91.57 E-value=0.089 Score=48.18 Aligned_cols=37 Identities=27% Similarity=0.546 Sum_probs=28.2
Q ss_pred cccCCccEEeccCCccChhhHHHHhcCCCCCCCCCCcccc
Q 024483 161 FDSLRNTTVMKCGHTMHCECYHEMIKRDKYCCPICSKSVI 200 (267)
Q Consensus 161 f~s~~~v~~LpCGH~~H~~C~~~~~~~~~~~CPiCrks~~ 200 (267)
|.+..+-.++.|+|+|...|...-. ...||+|+|+|-
T Consensus 12 ~~~~~~f~LTaC~HvfC~~C~k~~~---~~~C~lCkk~ir 48 (233)
T KOG4739|consen 12 FPSQDPFFLTACRHVFCEPCLKASS---PDVCPLCKKSIR 48 (233)
T ss_pred cCCCCceeeeechhhhhhhhcccCC---ccccccccceee
Confidence 4454566677999999999996532 238999999974
No 76
>PF12773 DZR: Double zinc ribbon
Probab=91.49 E-value=0.19 Score=34.39 Aligned_cols=22 Identities=36% Similarity=0.970 Sum_probs=13.0
Q ss_pred eCCCCccccc-cccCCcCCCccc
Q 024483 68 CSVCDTEQPV-AQVCTNCGVNMG 89 (267)
Q Consensus 68 C~~C~~~q~v-~~~C~~Cg~~f~ 89 (267)
|..|+++.+. +..|++||+.+.
T Consensus 1 Cp~Cg~~~~~~~~fC~~CG~~l~ 23 (50)
T PF12773_consen 1 CPHCGTPNPDDAKFCPHCGTPLP 23 (50)
T ss_pred CCCcCCcCCccccCChhhcCChh
Confidence 4456665544 456677766665
No 77
>KOG1571 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=91.08 E-value=0.13 Score=49.76 Aligned_cols=48 Identities=21% Similarity=0.492 Sum_probs=35.9
Q ss_pred cCCCCCCCchhhhhhcccCCccEEeccCCccChhhHHHHhcCCCCCCCCCCccccc
Q 024483 146 ENSMHHHCPICYEYLFDSLRNTTVMKCGHTMHCECYHEMIKRDKYCCPICSKSVID 201 (267)
Q Consensus 146 e~~~~~~CpICle~lf~s~~~v~~LpCGH~~H~~C~~~~~~~~~~~CPiCrks~~d 201 (267)
|.+..++|.||++. + .+.+.+||||+-- |...... ..+||+||.+|.-
T Consensus 301 ~~~~p~lcVVcl~e-~---~~~~fvpcGh~cc--ct~cs~~--l~~CPvCR~rI~~ 348 (355)
T KOG1571|consen 301 ELPQPDLCVVCLDE-P---KSAVFVPCGHVCC--CTLCSKH--LPQCPVCRQRIRL 348 (355)
T ss_pred ccCCCCceEEecCC-c---cceeeecCCcEEE--chHHHhh--CCCCchhHHHHHH
Confidence 45678899999997 2 4578999999954 5555433 4569999988863
No 78
>PRK03681 hypA hydrogenase nickel incorporation protein; Validated
Probab=90.58 E-value=0.17 Score=41.21 Aligned_cols=38 Identities=16% Similarity=0.403 Sum_probs=28.7
Q ss_pred CeeEEEcCCCCCccccceeEeeecCCCCCCccccccCCC
Q 024483 225 KKVWILCNDCNDTTEVYFHIIGQKCSHCKSYNTRSIAPP 263 (267)
Q Consensus 225 ~~v~I~CnDC~~~s~~~fH~lg~kC~~C~SyNT~~~~~~ 263 (267)
..+...|++|+......-+. ...||.|||++++.++|.
T Consensus 67 ~p~~~~C~~Cg~~~~~~~~~-~~~CP~Cgs~~~~i~~G~ 104 (114)
T PRK03681 67 QEAECWCETCQQYVTLLTQR-VRRCPQCHGDMLRIVADD 104 (114)
T ss_pred eCcEEEcccCCCeeecCCcc-CCcCcCcCCCCcEEccCC
Confidence 34578999999876654222 146999999999998874
No 79
>KOG4185 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=90.48 E-value=0.2 Score=46.27 Aligned_cols=49 Identities=31% Similarity=0.773 Sum_probs=39.9
Q ss_pred CCCCchhhhhhcccC---CccEEeccCCccChhhHHHHhcCCCCCCCCCCccc
Q 024483 150 HHHCPICYEYLFDSL---RNTTVMKCGHTMHCECYHEMIKRDKYCCPICSKSV 199 (267)
Q Consensus 150 ~~~CpICle~lf~s~---~~v~~LpCGH~~H~~C~~~~~~~~~~~CPiCrks~ 199 (267)
-..|-||-++ |++. ...++|.|||+|-..|+...+.++...||.||...
T Consensus 3 ~~~c~~c~~~-~s~~~~~~~p~~l~c~h~~c~~c~~~l~~~~~i~cpfcR~~~ 54 (296)
T KOG4185|consen 3 FPECEICNED-YSSEDGDHIPRVLKCGHTICQNCASKLLGNSRILCPFCRETT 54 (296)
T ss_pred CCceeecCcc-ccccCcccCCcccccCceehHhHHHHHhcCceeeccCCCCcc
Confidence 3568899998 4443 33467899999999999999988778899999994
No 80
>PRK12380 hydrogenase nickel incorporation protein HybF; Provisional
Probab=90.22 E-value=0.18 Score=40.99 Aligned_cols=37 Identities=27% Similarity=0.529 Sum_probs=28.4
Q ss_pred CeeEEEcCCCCCccccceeEeeecCCCCCCccccccCCC
Q 024483 225 KKVWILCNDCNDTTEVYFHIIGQKCSHCKSYNTRSIAPP 263 (267)
Q Consensus 225 ~~v~I~CnDC~~~s~~~fH~lg~kC~~C~SyNT~~~~~~ 263 (267)
..+.+.|++|+........ ...|+.|||++...++|.
T Consensus 67 vp~~~~C~~Cg~~~~~~~~--~~~CP~Cgs~~~~i~~G~ 103 (113)
T PRK12380 67 KPAQAWCWDCSQVVEIHQH--DAQCPHCHGERLRVDTGD 103 (113)
T ss_pred eCcEEEcccCCCEEecCCc--CccCcCCCCCCcEEccCC
Confidence 3457899999987766422 235999999999998874
No 81
>PF04641 Rtf2: Rtf2 RING-finger
Probab=89.46 E-value=0.25 Score=45.45 Aligned_cols=50 Identities=18% Similarity=0.459 Sum_probs=39.3
Q ss_pred CCCCCCchhhhhhcccCCccEEe-ccCCccChhhHHHHhcCCCCCCCCCCcccc
Q 024483 148 SMHHHCPICYEYLFDSLRNTTVM-KCGHTMHCECYHEMIKRDKYCCPICSKSVI 200 (267)
Q Consensus 148 ~~~~~CpICle~lf~s~~~v~~L-pCGH~~H~~C~~~~~~~~~~~CPiCrks~~ 200 (267)
...-.|||-...| ++....+.| ||||+|=...+.+.- ....||+|.+.+.
T Consensus 111 ~~~~~CPvt~~~~-~~~~~fv~l~~cG~V~s~~alke~k--~~~~Cp~c~~~f~ 161 (260)
T PF04641_consen 111 EGRFICPVTGKEF-NGKHKFVYLRPCGCVFSEKALKELK--KSKKCPVCGKPFT 161 (260)
T ss_pred CceeECCCCCccc-CCceeEEEEcCCCCEeeHHHHHhhc--ccccccccCCccc
Confidence 4456799999986 444455555 999999999999994 3568999999965
No 82
>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=89.44 E-value=0.16 Score=38.38 Aligned_cols=36 Identities=25% Similarity=0.783 Sum_probs=23.2
Q ss_pred ceeeeCCCCccccccccCCcCCCcc--------ceeeccccccc
Q 024483 64 KQVICSVCDTEQPVAQVCTNCGVNM--------GEYFCDICKFY 99 (267)
Q Consensus 64 ~~v~C~~C~~~q~v~~~C~~Cg~~f--------~~y~C~~C~l~ 99 (267)
....|..|+..-.....||.||..+ +.|||..|+=.
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 5788888888777777888888877 68999988743
No 83
>KOG0297 consensus TNF receptor-associated factor [Signal transduction mechanisms]
Probab=89.32 E-value=0.29 Score=47.76 Aligned_cols=53 Identities=25% Similarity=0.622 Sum_probs=42.0
Q ss_pred CCCCCchhhhhhcccCCccEEeccCCccChhhHHHHhcCCCCCCCCCCccccchhHH
Q 024483 149 MHHHCPICYEYLFDSLRNTTVMKCGHTMHCECYHEMIKRDKYCCPICSKSVIDMSRT 205 (267)
Q Consensus 149 ~~~~CpICle~lf~s~~~v~~LpCGH~~H~~C~~~~~~~~~~~CPiCrks~~dm~~~ 205 (267)
.+..||||...|- +++....|||.|-..|+.+|+.. +..||.|+..+..-..+
T Consensus 20 ~~l~C~~C~~vl~---~p~~~~~cgh~fC~~C~~~~~~~-~~~cp~~~~~~~~~~~~ 72 (391)
T KOG0297|consen 20 ENLLCPICMSVLR---DPVQTTTCGHRFCAGCLLESLSN-HQKCPVCRQELTQAEEL 72 (391)
T ss_pred ccccCcccccccc---CCCCCCCCCCcccccccchhhcc-CcCCcccccccchhhcc
Confidence 3467999998753 34444799999999999999985 78999999888754433
No 84
>COG5175 MOT2 Transcriptional repressor [Transcription]
Probab=88.92 E-value=0.11 Score=50.29 Aligned_cols=57 Identities=23% Similarity=0.470 Sum_probs=44.8
Q ss_pred CCCCchhhhhhcccCCccEEeccCCccChhhHHHHhcCCCCCCCCCCccccchhHHh
Q 024483 150 HHHCPICYEYLFDSLRNTTVMKCGHTMHCECYHEMIKRDKYCCPICSKSVIDMSRTW 206 (267)
Q Consensus 150 ~~~CpICle~lf~s~~~v~~LpCGH~~H~~C~~~~~~~~~~~CPiCrks~~dm~~~~ 206 (267)
++-||.|+|+|--+...-..-|||=-+.+-|+....+.-+-+||-||+...|-...|
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 345999999986665555556789999999999887766789999999887654445
No 85
>KOG1814 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=88.87 E-value=0.2 Score=49.28 Aligned_cols=46 Identities=20% Similarity=0.411 Sum_probs=36.8
Q ss_pred CCCCchhhhhhcccCCccEEeccCCccChhhHHHHhcC-------CCCCCCCCC
Q 024483 150 HHHCPICYEYLFDSLRNTTVMKCGHTMHCECYHEMIKR-------DKYCCPICS 196 (267)
Q Consensus 150 ~~~CpICle~lf~s~~~v~~LpCGH~~H~~C~~~~~~~-------~~~~CPiCr 196 (267)
--.|-||++. +....-.+.|||+|+|.++|+..|... +..+||-+.
T Consensus 184 lf~C~ICf~e-~~G~~c~~~lpC~Hv~Ck~C~kdY~~~~i~eg~v~~l~Cp~~~ 236 (445)
T KOG1814|consen 184 LFDCCICFEE-QMGQHCFKFLPCSHVFCKSCLKDYFTIQIQEGQVSCLKCPDPK 236 (445)
T ss_pred cccceeeehh-hcCcceeeecccchHHHHHHHHHHHHHhhhcceeeeecCCCCC
Confidence 4579999997 666577888999999999999998751 357887654
No 86
>KOG2660 consensus Locus-specific chromosome binding proteins [Function unknown]
Probab=88.74 E-value=0.1 Score=49.85 Aligned_cols=50 Identities=28% Similarity=0.663 Sum_probs=41.7
Q ss_pred CCCCCCchhhhhhcccCCccEEeccCCccChhhHHHHhcCCCCCCCCCCccccc
Q 024483 148 SMHHHCPICYEYLFDSLRNTTVMKCGHTMHCECYHEMIKRDKYCCPICSKSVID 201 (267)
Q Consensus 148 ~~~~~CpICle~lf~s~~~v~~LpCGH~~H~~C~~~~~~~~~~~CPiCrks~~d 201 (267)
.....|++|..+|-+.+ .+.-|=|+|.++||.++++. +.+||.|...|..
T Consensus 13 n~~itC~LC~GYliDAT---TI~eCLHTFCkSCivk~l~~-~~~CP~C~i~ih~ 62 (331)
T KOG2660|consen 13 NPHITCRLCGGYLIDAT---TITECLHTFCKSCIVKYLEE-SKYCPTCDIVIHK 62 (331)
T ss_pred ccceehhhccceeecch---hHHHHHHHHHHHHHHHHHHH-hccCCccceeccC
Confidence 44568999999987654 46689999999999999985 7899999988863
No 87
>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=88.60 E-value=0.15 Score=41.29 Aligned_cols=37 Identities=22% Similarity=0.306 Sum_probs=25.6
Q ss_pred CeeEEEcCCCCCccccceeEeeecCCCCCCccccccCCC
Q 024483 225 KKVWILCNDCNDTTEVYFHIIGQKCSHCKSYNTRSIAPP 263 (267)
Q Consensus 225 ~~v~I~CnDC~~~s~~~fH~lg~kC~~C~SyNT~~~~~~ 263 (267)
..+...|++|+..+.+..+. ..|+.|+|++.+.++|.
T Consensus 67 ~p~~~~C~~Cg~~~~~~~~~--~~CP~Cgs~~~~i~~G~ 103 (113)
T PF01155_consen 67 VPARARCRDCGHEFEPDEFD--FSCPRCGSPDVEIISGR 103 (113)
T ss_dssp E--EEEETTTS-EEECHHCC--HH-SSSSSS-EEEEESS
T ss_pred cCCcEECCCCCCEEecCCCC--CCCcCCcCCCcEEccCC
Confidence 35578999999988766543 57999999999888764
No 88
>PHA02862 5L protein; Provisional
Probab=87.74 E-value=0.32 Score=41.78 Aligned_cols=57 Identities=21% Similarity=0.457 Sum_probs=38.6
Q ss_pred CCCCCchhhhhhcccCCccEEecc---C--CccChhhHHHHhcCC-CCCCCCCCccccchhHHhHHhHH
Q 024483 149 MHHHCPICYEYLFDSLRNTTVMKC---G--HTMHCECYHEMIKRD-KYCCPICSKSVIDMSRTWKRIDE 211 (267)
Q Consensus 149 ~~~~CpICle~lf~s~~~v~~LpC---G--H~~H~~C~~~~~~~~-~~~CPiCrks~~dm~~~~~~lD~ 211 (267)
|.+.|=||.+.- .+.+ -|| | -..|+.|+.+|+..+ ..+||+|+.... +...|+.+.+
T Consensus 1 ~~diCWIC~~~~---~e~~--~PC~C~GS~K~VHq~CL~~WIn~S~k~~CeLCkteY~-Ik~~yKpf~k 63 (156)
T PHA02862 1 MSDICWICNDVC---DERN--NFCGCNEEYKVVHIKCMQLWINYSKKKECNLCKTKYN-IKKTYVSFKK 63 (156)
T ss_pred CCCEEEEecCcC---CCCc--ccccccCcchhHHHHHHHHHHhcCCCcCccCCCCeEE-EEEccccHHH
Confidence 346789999862 2233 455 2 789999999999753 567999998875 3334443333
No 89
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=87.07 E-value=0.31 Score=29.56 Aligned_cols=24 Identities=33% Similarity=0.924 Sum_probs=18.0
Q ss_pred eeeeCCCCccccc-cccCCcCCCcc
Q 024483 65 QVICSVCDTEQPV-AQVCTNCGVNM 88 (267)
Q Consensus 65 ~v~C~~C~~~q~v-~~~C~~Cg~~f 88 (267)
.+.|..|+++.+. +..|++||+.+
T Consensus 2 ~~~Cp~Cg~~~~~~~~fC~~CG~~L 26 (26)
T PF13248_consen 2 EMFCPNCGAEIDPDAKFCPNCGAKL 26 (26)
T ss_pred cCCCcccCCcCCcccccChhhCCCC
Confidence 4678889886544 56899999864
No 90
>KOG2817 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=87.03 E-value=0.55 Score=45.95 Aligned_cols=47 Identities=21% Similarity=0.555 Sum_probs=39.5
Q ss_pred CCchhhhhhcccCCccEEeccCCccChhhHHHHhcCCC--CCCCCCCccc
Q 024483 152 HCPICYEYLFDSLRNTTVMKCGHTMHCECYHEMIKRDK--YCCPICSKSV 199 (267)
Q Consensus 152 ~CpICle~lf~s~~~v~~LpCGH~~H~~C~~~~~~~~~--~~CPiCrks~ 199 (267)
.|||=-|. -+...|...|.|||+|-+.=++.+.+++. ++||.|-...
T Consensus 336 ~CPVlKeq-tsdeNPPm~L~CGHVISkdAlnrLS~ng~~sfKCPYCP~e~ 384 (394)
T KOG2817|consen 336 ICPVLKEQ-TSDENPPMMLICGHVISKDALNRLSKNGSQSFKCPYCPVEQ 384 (394)
T ss_pred ecccchhh-ccCCCCCeeeeccceecHHHHHHHhhCCCeeeeCCCCCccc
Confidence 69997776 45557888999999999999999998776 9999997544
No 91
>COG5152 Uncharacterized conserved protein, contains RING and CCCH-type Zn-fingers [General function prediction only]
Probab=86.92 E-value=0.35 Score=43.66 Aligned_cols=58 Identities=21% Similarity=0.483 Sum_probs=42.2
Q ss_pred CCchhhhhhcccCCccEEeccCCccChhhHHHHhcCCCCCCCCCCccccchhHHhHHhHHHHH
Q 024483 152 HCPICYEYLFDSLRNTTVMKCGHTMHCECYHEMIKRDKYCCPICSKSVIDMSRTWKRIDEEIE 214 (267)
Q Consensus 152 ~CpICle~lf~s~~~v~~LpCGH~~H~~C~~~~~~~~~~~CPiCrks~~dm~~~~~~lD~~i~ 214 (267)
.|-||.++ |.| .++..|||.|...|+..=.+ ...+|-+|.+..-..-.+-..|+.++.
T Consensus 198 ~C~iCKkd-y~s---pvvt~CGH~FC~~Cai~~y~-kg~~C~~Cgk~t~G~f~V~~d~~kmL~ 255 (259)
T COG5152 198 LCGICKKD-YES---PVVTECGHSFCSLCAIRKYQ-KGDECGVCGKATYGRFWVVSDLQKMLN 255 (259)
T ss_pred eehhchhh-ccc---hhhhhcchhHHHHHHHHHhc-cCCcceecchhhccceeHHhhHHHHHh
Confidence 69999998 443 45778999999999987666 457999999988644322235555543
No 92
>KOG2114 consensus Vacuolar assembly/sorting protein PEP5/VPS11 [Intracellular trafficking, secretion, and vesicular transport]
Probab=86.81 E-value=0.41 Score=50.90 Aligned_cols=42 Identities=26% Similarity=0.593 Sum_probs=32.9
Q ss_pred CCCchhhhhhcccCCccEEeccCCccChhhHHHHhcCCCCCCCCCCccc
Q 024483 151 HHCPICYEYLFDSLRNTTVMKCGHTMHCECYHEMIKRDKYCCPICSKSV 199 (267)
Q Consensus 151 ~~CpICle~lf~s~~~v~~LpCGH~~H~~C~~~~~~~~~~~CPiCrks~ 199 (267)
+.|..|--.| .-|++-..|||.||..|+. .+...||-|+-.+
T Consensus 841 skCs~C~~~L---dlP~VhF~CgHsyHqhC~e----~~~~~CP~C~~e~ 882 (933)
T KOG2114|consen 841 SKCSACEGTL---DLPFVHFLCGHSYHQHCLE----DKEDKCPKCLPEL 882 (933)
T ss_pred eeecccCCcc---ccceeeeecccHHHHHhhc----cCcccCCccchhh
Confidence 3577777655 2478888999999999998 3578999999833
No 93
>KOG0309 consensus Conserved WD40 repeat-containing protein [Function unknown]
Probab=86.77 E-value=0.34 Score=51.06 Aligned_cols=42 Identities=29% Similarity=0.583 Sum_probs=30.8
Q ss_pred CCCCchhhhhhcccCCccEEeccCCccChhhHHHHhcCCCCCCCC
Q 024483 150 HHHCPICYEYLFDSLRNTTVMKCGHTMHCECYHEMIKRDKYCCPI 194 (267)
Q Consensus 150 ~~~CpICle~lf~s~~~v~~LpCGH~~H~~C~~~~~~~~~~~CPi 194 (267)
...|.||--.+..+ ...-+.|||.+|..|+.+|++. ...||.
T Consensus 1028 ~~~C~~C~l~V~gs--s~~Cg~C~Hv~H~sc~~eWf~~-gd~Cps 1069 (1081)
T KOG0309|consen 1028 TFQCAICHLAVRGS--SNFCGTCGHVGHTSCMMEWFRT-GDVCPS 1069 (1081)
T ss_pred eeeeeeEeeEeecc--chhhccccccccHHHHHHHHhc-CCcCCC
Confidence 34488887654333 4455789999999999999984 568884
No 94
>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=86.47 E-value=0.69 Score=40.18 Aligned_cols=33 Identities=33% Similarity=0.775 Sum_probs=24.9
Q ss_pred CCCCchhhhhhcccCCccEEeccC-C------------ccChhhHHHHhc
Q 024483 150 HHHCPICYEYLFDSLRNTTVMKCG-H------------TMHCECYHEMIK 186 (267)
Q Consensus 150 ~~~CpICle~lf~s~~~v~~LpCG-H------------~~H~~C~~~~~~ 186 (267)
+..||||||. ..+.++|-|. | .-|+.||+++.+
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 3579999996 2567778773 3 469999999975
No 95
>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=86.07 E-value=0.38 Score=33.89 Aligned_cols=32 Identities=31% Similarity=0.745 Sum_probs=23.5
Q ss_pred EEeccC-CccChhhHHHHhcCCCCCCCCCCcccc
Q 024483 168 TVMKCG-HTMHCECYHEMIKRDKYCCPICSKSVI 200 (267)
Q Consensus 168 ~~LpCG-H~~H~~C~~~~~~~~~~~CPiCrks~~ 200 (267)
..+.|. |.+...|+..++. .+..||||.+++-
T Consensus 14 ~Li~C~dHYLCl~CLt~ml~-~s~~C~iC~~~LP 46 (50)
T PF03854_consen 14 GLIKCSDHYLCLNCLTLMLS-RSDRCPICGKPLP 46 (50)
T ss_dssp SEEE-SS-EEEHHHHHHT-S-SSSEETTTTEE--
T ss_pred CeeeecchhHHHHHHHHHhc-cccCCCcccCcCc
Confidence 366895 9999999999998 5789999998874
No 96
>KOG1813 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=85.75 E-value=0.42 Score=45.28 Aligned_cols=67 Identities=22% Similarity=0.413 Sum_probs=46.7
Q ss_pred CCCchhhhhhcccCCccEEeccCCccChhhHHHHhcCCCCCCCCCCccccchhHHhHHhHHHHHhcCCChhh
Q 024483 151 HHCPICYEYLFDSLRNTTVMKCGHTMHCECYHEMIKRDKYCCPICSKSVIDMSRTWKRIDEEIEATVMPEDY 222 (267)
Q Consensus 151 ~~CpICle~lf~s~~~v~~LpCGH~~H~~C~~~~~~~~~~~CPiCrks~~dm~~~~~~lD~~i~~~pmP~~y 222 (267)
..|-||.+++ - ..++..|||.|...|...-++ ...+|+||.+.+-.....=..|...+...++-.||
T Consensus 242 f~c~icr~~f-~---~pVvt~c~h~fc~~ca~~~~q-k~~~c~vC~~~t~g~~~~akeL~~~L~~kks~~E~ 308 (313)
T KOG1813|consen 242 FKCFICRKYF-Y---RPVVTKCGHYFCEVCALKPYQ-KGEKCYVCSQQTHGSFNVAKELLVSLKLKKSDSEY 308 (313)
T ss_pred cccccccccc-c---cchhhcCCceeehhhhccccc-cCCcceecccccccccchHHHHHHHHHhhhhhccc
Confidence 4599999984 3 345779999999999988776 45799999998864332223455555555544443
No 97
>KOG3161 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=85.57 E-value=0.45 Score=49.39 Aligned_cols=42 Identities=24% Similarity=0.613 Sum_probs=35.2
Q ss_pred CCCchhhhhhcccCCccEEeccCCccChhhHHHHhcCCCCCCCCCC
Q 024483 151 HHCPICYEYLFDSLRNTTVMKCGHTMHCECYHEMIKRDKYCCPICS 196 (267)
Q Consensus 151 ~~CpICle~lf~s~~~v~~LpCGH~~H~~C~~~~~~~~~~~CPiCr 196 (267)
..|+||+..+|.++-..+.|-|||++..+|+.... +.+|| |.
T Consensus 12 l~c~ic~n~f~~~~~~Pvsl~cghtic~~c~~~ly---n~scp-~~ 53 (861)
T KOG3161|consen 12 LLCDICLNLFVVQRLEPVSLQCGHTICGHCVQLLY---NASCP-TK 53 (861)
T ss_pred hhchHHHHHHHHHhcCcccccccchHHHHHHHhHh---hccCC-CC
Confidence 47999988888888888889999999999998763 46888 54
No 98
>KOG4159 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=85.50 E-value=0.97 Score=44.51 Aligned_cols=49 Identities=24% Similarity=0.747 Sum_probs=39.1
Q ss_pred CCCCCCchhhhhhcccCCccEEeccCCccChhhHHHHhcCCCCCCCCCCccccc
Q 024483 148 SMHHHCPICYEYLFDSLRNTTVMKCGHTMHCECYHEMIKRDKYCCPICSKSVID 201 (267)
Q Consensus 148 ~~~~~CpICle~lf~s~~~v~~LpCGH~~H~~C~~~~~~~~~~~CPiCrks~~d 201 (267)
..+-.|-||+.-|+ +.+.+||||.|-..|++.-+. ....||+||-.+..
T Consensus 82 ~sef~c~vc~~~l~----~pv~tpcghs~c~~Cl~r~ld-~~~~cp~Cr~~l~e 130 (398)
T KOG4159|consen 82 RSEFECCVCSRALY----PPVVTPCGHSFCLECLDRSLD-QETECPLCRDELVE 130 (398)
T ss_pred cchhhhhhhHhhcC----CCccccccccccHHHHHHHhc-cCCCCccccccccc
Confidence 55678999988653 344559999999999999665 56789999998874
No 99
>PHA02825 LAP/PHD finger-like protein; Provisional
Probab=85.17 E-value=0.63 Score=40.46 Aligned_cols=48 Identities=27% Similarity=0.532 Sum_probs=34.6
Q ss_pred CCCCCCchhhhhhcccCCccEEecc--CC---ccChhhHHHHhcC-CCCCCCCCCcccc
Q 024483 148 SMHHHCPICYEYLFDSLRNTTVMKC--GH---TMHCECYHEMIKR-DKYCCPICSKSVI 200 (267)
Q Consensus 148 ~~~~~CpICle~lf~s~~~v~~LpC--GH---~~H~~C~~~~~~~-~~~~CPiCrks~~ 200 (267)
.++..|=||.+.- . . ..-|| .. ..|++|++.|+.. +..+||+|+....
T Consensus 6 ~~~~~CRIC~~~~--~-~--~~~PC~CkGs~k~VH~sCL~rWi~~s~~~~CeiC~~~Y~ 59 (162)
T PHA02825 6 LMDKCCWICKDEY--D-V--VTNYCNCKNENKIVHKECLEEWINTSKNKSCKICNGPYN 59 (162)
T ss_pred CCCCeeEecCCCC--C-C--ccCCcccCCCchHHHHHHHHHHHhcCCCCcccccCCeEE
Confidence 3466799998872 1 1 23466 34 6799999999975 3578999998774
No 100
>PRK00762 hypA hydrogenase nickel incorporation protein; Provisional
Probab=84.95 E-value=0.63 Score=38.44 Aligned_cols=39 Identities=21% Similarity=0.281 Sum_probs=27.5
Q ss_pred cCeeEEEcCCCCCccccc-e---eE-eeecCCCCCCccccccCCC
Q 024483 224 HKKVWILCNDCNDTTEVY-F---HI-IGQKCSHCKSYNTRSIAPP 263 (267)
Q Consensus 224 ~~~v~I~CnDC~~~s~~~-f---H~-lg~kC~~C~SyNT~~~~~~ 263 (267)
.......| +|+..+... + |+ ....||.|||++...++|.
T Consensus 66 ~vp~~~~C-~Cg~~~~~~~~~~~~~~~~~~CP~Cgs~~~~i~~G~ 109 (124)
T PRK00762 66 MIPVEIEC-ECGYEGVVDEDEIDHYAAVIECPVCGNKRAHILGGR 109 (124)
T ss_pred ecCeeEEe-eCcCcccccccchhccccCCcCcCCCCCCCEEecCC
Confidence 34567899 999875432 1 11 2357999999999998774
No 101
>KOG3039 consensus Uncharacterized conserved protein [Function unknown]
Probab=84.70 E-value=0.8 Score=42.61 Aligned_cols=55 Identities=24% Similarity=0.479 Sum_probs=45.4
Q ss_pred CCCCCCCchhhhhhcccCCccEEe-ccCCccChhhHHHHhcCCCCCCCCCCccccchh
Q 024483 147 NSMHHHCPICYEYLFDSLRNTTVM-KCGHTMHCECYHEMIKRDKYCCPICSKSVIDMS 203 (267)
Q Consensus 147 ~~~~~~CpICle~lf~s~~~v~~L-pCGH~~H~~C~~~~~~~~~~~CPiCrks~~dm~ 203 (267)
.+..-.|||+.+.|-.. .+..+| |+||++-..|.+.++. ...-+||+.+.+-|..
T Consensus 218 ~s~ryiCpvtrd~LtNt-~~ca~Lr~sg~Vv~~ecvEklir-~D~v~pv~d~plkdrd 273 (303)
T KOG3039|consen 218 ASKRYICPVTRDTLTNT-TPCAVLRPSGHVVTKECVEKLIR-KDMVDPVTDKPLKDRD 273 (303)
T ss_pred hccceecccchhhhcCc-cceEEeccCCcEeeHHHHHHhcc-ccccccCCCCcCcccc
Confidence 34566899999997554 566666 9999999999999998 5788999999998653
No 102
>KOG2034 consensus Vacuolar sorting protein PEP3/VPS18 [Intracellular trafficking, secretion, and vesicular transport]
Probab=84.39 E-value=0.51 Score=50.32 Aligned_cols=43 Identities=21% Similarity=0.382 Sum_probs=33.9
Q ss_pred ceeecCCCCCCCchhhhhhcccCCccEEeccCCccChhhHHHHhc
Q 024483 142 HLCIENSMHHHCPICYEYLFDSLRNTTVMKCGHTMHCECYHEMIK 186 (267)
Q Consensus 142 H~C~e~~~~~~CpICle~lf~s~~~v~~LpCGH~~H~~C~~~~~~ 186 (267)
+.+.--.....|-+|.-.|+. ++-.+.||||.||+.|+.+-..
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 444444556789999998765 5888899999999999988765
No 103
>KOG1002 consensus Nucleotide excision repair protein RAD16 [Replication, recombination and repair]
Probab=84.29 E-value=0.36 Score=49.10 Aligned_cols=52 Identities=21% Similarity=0.516 Sum_probs=43.0
Q ss_pred ecCCCCCCCchhhhhhcccCCccEEeccCCccChhhHHHHhc----CCCCCCCCCCcccc
Q 024483 145 IENSMHHHCPICYEYLFDSLRNTTVMKCGHTMHCECYHEMIK----RDKYCCPICSKSVI 200 (267)
Q Consensus 145 ~e~~~~~~CpICle~lf~s~~~v~~LpCGH~~H~~C~~~~~~----~~~~~CPiCrks~~ 200 (267)
.|+..+..|-+|-++- ++.+.-.|-|.|.+.|+.+|+. +.+.+||+|.+.+.
T Consensus 531 ~enk~~~~C~lc~d~a----ed~i~s~ChH~FCrlCi~eyv~~f~~~~nvtCP~C~i~Ls 586 (791)
T KOG1002|consen 531 DENKGEVECGLCHDPA----EDYIESSCHHKFCRLCIKEYVESFMENNNVTCPVCHIGLS 586 (791)
T ss_pred ccccCceeecccCChh----hhhHhhhhhHHHHHHHHHHHHHhhhcccCCCCcccccccc
Confidence 4677788999999873 4667789999999999988875 34689999999874
No 104
>PF09538 FYDLN_acid: Protein of unknown function (FYDLN_acid); InterPro: IPR012644 Members of this family are bacterial proteins with a conserved motif [KR]FYDLN, sometimes flanked by a pair of CXXC motifs, followed by a long region of low complexity sequence in which roughly half the residues are Asp and Glu, including multiple runs of five or more acidic residues. The function of members of this family is unknown.
Probab=83.14 E-value=0.83 Score=37.15 Aligned_cols=29 Identities=31% Similarity=0.897 Sum_probs=21.7
Q ss_pred ccccccCCcCCCccceeeccccccccCCCCcCeeecCCCCc
Q 024483 75 QPVAQVCTNCGVNMGEYFCDICKFYDDDIEKGQFHCDDCGI 115 (267)
Q Consensus 75 q~v~~~C~~Cg~~f~~y~C~~C~l~dd~~~k~~yHC~~Cgi 115 (267)
+....+|++||+.| || .+|.+-.|++||.
T Consensus 6 lGtKR~Cp~CG~kF----------YD--Lnk~PivCP~CG~ 34 (108)
T PF09538_consen 6 LGTKRTCPSCGAKF----------YD--LNKDPIVCPKCGT 34 (108)
T ss_pred cCCcccCCCCcchh----------cc--CCCCCccCCCCCC
Confidence 34456899999854 66 5688889999884
No 105
>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=83.09 E-value=0.82 Score=28.03 Aligned_cols=23 Identities=35% Similarity=0.959 Sum_probs=18.1
Q ss_pred eeCCCCccccc-cccCCcCCCccc
Q 024483 67 ICSVCDTEQPV-AQVCTNCGVNMG 89 (267)
Q Consensus 67 ~C~~C~~~q~v-~~~C~~Cg~~f~ 89 (267)
.|..|+.+-+. +..|++||..|.
T Consensus 2 ~CP~C~~~V~~~~~~Cp~CG~~F~ 25 (26)
T PF10571_consen 2 TCPECGAEVPESAKFCPHCGYDFE 25 (26)
T ss_pred cCCCCcCCchhhcCcCCCCCCCCc
Confidence 37778877666 568999999986
No 106
>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=83.07 E-value=0.33 Score=36.71 Aligned_cols=65 Identities=26% Similarity=0.504 Sum_probs=38.1
Q ss_pred CCCchhhhhhcccCCccEEeccCCccChhhHHHHhcCCCCCCCCCCccccchhHHhHHhHHHHHhcCCChhhhcCeeEEE
Q 024483 151 HHCPICYEYLFDSLRNTTVMKCGHTMHCECYHEMIKRDKYCCPICSKSVIDMSRTWKRIDEEIEATVMPEDYRHKKVWIL 230 (267)
Q Consensus 151 ~~CpICle~lf~s~~~v~~LpCGH~~H~~C~~~~~~~~~~~CPiCrks~~dm~~~~~~lD~~i~~~pmP~~y~~~~v~I~ 230 (267)
..||+|..+|-... ||+.-..|-..+.. ...||-|.+.+.-+.+ =--|+++
T Consensus 2 ~~CP~C~~~L~~~~--------~~~~C~~C~~~~~~--~a~CPdC~~~Le~LkA-------------------CGAvdYF 52 (70)
T PF07191_consen 2 NTCPKCQQELEWQG--------GHYHCEACQKDYKK--EAFCPDCGQPLEVLKA-------------------CGAVDYF 52 (70)
T ss_dssp -B-SSS-SBEEEET--------TEEEETTT--EEEE--EEE-TTT-SB-EEEEE-------------------TTEEEEE
T ss_pred CcCCCCCCccEEeC--------CEEECcccccccee--cccCCCcccHHHHHHH-------------------hccccee
Confidence 46999999874321 77778888887765 4689999988864321 1147899
Q ss_pred cCCCCC---ccccceeE
Q 024483 231 CNDCND---TTEVYFHI 244 (267)
Q Consensus 231 CnDC~~---~s~~~fH~ 244 (267)
||.|++ |+-|.|.+
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 999994 55666654
No 107
>PF13240 zinc_ribbon_2: zinc-ribbon domain
Probab=82.87 E-value=0.69 Score=27.48 Aligned_cols=21 Identities=38% Similarity=0.945 Sum_probs=15.0
Q ss_pred eCCCCccccc-cccCCcCCCcc
Q 024483 68 CSVCDTEQPV-AQVCTNCGVNM 88 (267)
Q Consensus 68 C~~C~~~q~v-~~~C~~Cg~~f 88 (267)
|..|+.+.+. +..|++||+.|
T Consensus 2 Cp~CG~~~~~~~~fC~~CG~~l 23 (23)
T PF13240_consen 2 CPNCGAEIEDDAKFCPNCGTPL 23 (23)
T ss_pred CcccCCCCCCcCcchhhhCCcC
Confidence 6778777655 56788888764
No 108
>PRK04023 DNA polymerase II large subunit; Validated
Probab=82.73 E-value=1.1 Score=48.72 Aligned_cols=31 Identities=26% Similarity=0.696 Sum_probs=14.1
Q ss_pred cCCcCCCccceeeccccccccCCCCcCeeecCCCC
Q 024483 80 VCTNCGVNMGEYFCDICKFYDDDIEKGQFHCDDCG 114 (267)
Q Consensus 80 ~C~~Cg~~f~~y~C~~C~l~dd~~~k~~yHC~~Cg 114 (267)
.|+.||......+|+.|.-. ...+|.|+.||
T Consensus 628 fCpsCG~~t~~frCP~CG~~----Te~i~fCP~CG 658 (1121)
T PRK04023 628 KCPSCGKETFYRRCPFCGTH----TEPVYRCPRCG 658 (1121)
T ss_pred cCCCCCCcCCcccCCCCCCC----CCcceeCcccc
Confidence 44444444444444444322 34455555553
No 109
>COG0375 HybF Zn finger protein HypA/HybF (possibly regulating hydrogenase expression) [General function prediction only]
Probab=81.87 E-value=1.1 Score=36.90 Aligned_cols=40 Identities=25% Similarity=0.358 Sum_probs=30.8
Q ss_pred hcCeeEEEcCCCCCccccceeEeeecCCCCCCccccccCCCC
Q 024483 223 RHKKVWILCNDCNDTTEVYFHIIGQKCSHCKSYNTRSIAPPV 264 (267)
Q Consensus 223 ~~~~v~I~CnDC~~~s~~~fH~lg~kC~~C~SyNT~~~~~~~ 264 (267)
....+.+.|.||+......-|.+. ||.|+|-|.++++|..
T Consensus 65 e~~p~~~~C~~C~~~~~~e~~~~~--CP~C~s~~~~i~~G~e 104 (115)
T COG0375 65 EEEPAECWCLDCGQEVELEELDYR--CPKCGSINLRIIGGDE 104 (115)
T ss_pred EEeccEEEeccCCCeecchhheeE--CCCCCCCceEEecCCe
Confidence 344677999999887655555443 9999999999998753
No 110
>KOG1952 consensus Transcription factor NF-X1, contains NFX-type Zn2+-binding and R3H domains [Transcription]
Probab=80.21 E-value=0.81 Score=48.75 Aligned_cols=51 Identities=24% Similarity=0.525 Sum_probs=37.5
Q ss_pred CCCCCchhhhhhcccCCccEE-eccCCccChhhHHHHhcC------CCCCCCCCCcccc
Q 024483 149 MHHHCPICYEYLFDSLRNTTV-MKCGHTMHCECYHEMIKR------DKYCCPICSKSVI 200 (267)
Q Consensus 149 ~~~~CpICle~lf~s~~~v~~-LpCGH~~H~~C~~~~~~~------~~~~CPiCrks~~ 200 (267)
..-+|.||.|.|-.+ .++.. -.|=|+||..||.+|... ...+||-|.-...
T Consensus 190 ~~yeCmIC~e~I~~t-~~~WSC~sCYhVFHl~CI~~WArs~ek~~~~~WrCP~Cqsv~~ 247 (950)
T KOG1952|consen 190 RKYECMICTERIKRT-APVWSCKSCYHVFHLNCIKKWARSSEKTGQDGWRCPACQSVSK 247 (950)
T ss_pred CceEEEEeeeecccc-CCceecchhhhhhhHHHHHHHHHHhhhccCccccCCcccchhc
Confidence 345899999987554 34433 357799999999999863 3578999984433
No 111
>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=79.67 E-value=1.1 Score=30.41 Aligned_cols=25 Identities=24% Similarity=0.858 Sum_probs=15.6
Q ss_pred ccCCccChhhHHHHhcCCCC-CCCCC
Q 024483 171 KCGHTMHCECYHEMIKRDKY-CCPIC 195 (267)
Q Consensus 171 pCGH~~H~~C~~~~~~~~~~-~CPiC 195 (267)
.|+=-||..|++.|+++... +||.|
T Consensus 18 ~C~~r~H~~C~~~y~r~~~~~~CP~C 43 (43)
T PF08746_consen 18 DCNVRLHDDCFKKYFRHRSNPKCPNC 43 (43)
T ss_dssp -S--EE-HHHHHHHTTT-SS-B-TTT
T ss_pred ccCchHHHHHHHHHHhcCCCCCCcCC
Confidence 37667999999999985433 69987
No 112
>COG5236 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=79.24 E-value=1.4 Score=42.99 Aligned_cols=65 Identities=17% Similarity=0.369 Sum_probs=46.4
Q ss_pred CccccccccCcceeecCCCCCCCchhhhhhcccCCccEEeccCCccChhhHHHHhc-CCCCCCCCCCccc
Q 024483 131 GSCYSTSLRNNHLCIENSMHHHCPICYEYLFDSLRNTTVMKCGHTMHCECYHEMIK-RDKYCCPICSKSV 199 (267)
Q Consensus 131 ~~C~s~~l~~~H~C~e~~~~~~CpICle~lf~s~~~v~~LpCGH~~H~~C~~~~~~-~~~~~CPiCrks~ 199 (267)
+.|....|-++-+=......++|-||.+.+ +-+.++||||-|.-.|.-.... .....||+||..-
T Consensus 42 nlsaEPnlttsSaddtDEen~~C~ICA~~~----TYs~~~PC~H~~CH~Ca~RlRALY~~K~C~~CrTE~ 107 (493)
T COG5236 42 NLSAEPNLTTSSADDTDEENMNCQICAGST----TYSARYPCGHQICHACAVRLRALYMQKGCPLCRTET 107 (493)
T ss_pred ccccCCccccccccccccccceeEEecCCc----eEEEeccCCchHHHHHHHHHHHHHhccCCCcccccc
Confidence 556666665555544456677899999975 5677899999999999765432 1356799999753
No 113
>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=78.59 E-value=2 Score=29.52 Aligned_cols=36 Identities=19% Similarity=0.369 Sum_probs=24.7
Q ss_pred EEEcCCCCCccccceeE---eeecCCCCCCccc-cccCCC
Q 024483 228 WILCNDCNDTTEVYFHI---IGQKCSHCKSYNT-RSIAPP 263 (267)
Q Consensus 228 ~I~CnDC~~~s~~~fH~---lg~kC~~C~SyNT-~~~~~~ 263 (267)
...|++|+...++-..+ -...|+.|||-+. |++.+|
T Consensus 5 ey~C~~Cg~~fe~~~~~~~~~~~~CP~Cg~~~~~r~~s~~ 44 (52)
T TIGR02605 5 EYRCTACGHRFEVLQKMSDDPLATCPECGGEKLRRLLSAV 44 (52)
T ss_pred EEEeCCCCCEeEEEEecCCCCCCCCCCCCCCceeEEeccc
Confidence 46899999877654221 1247999999886 566654
No 114
>PF14353 CpXC: CpXC protein
Probab=78.36 E-value=0.44 Score=38.86 Aligned_cols=56 Identities=13% Similarity=0.384 Sum_probs=33.8
Q ss_pred CCCCCCCccccchhHHhHHhHHHHHhcCCChhhhcCeeEEEcCCCCCccccceeEeee
Q 024483 190 YCCPICSKSVIDMSRTWKRIDEEIEATVMPEDYRHKKVWILCNDCNDTTEVYFHIIGQ 247 (267)
Q Consensus 190 ~~CPiCrks~~dm~~~~~~lD~~i~~~pmP~~y~~~~v~I~CnDC~~~s~~~fH~lg~ 247 (267)
.+||.|++.+. ...|..++......-...-..+..-.+.|..||++..+.+=+|++
T Consensus 2 itCP~C~~~~~--~~v~~~I~~~~~p~l~e~il~g~l~~~~CP~Cg~~~~~~~p~lY~ 57 (128)
T PF14353_consen 2 ITCPHCGHEFE--FEVWTSINADEDPELKEKILDGSLFSFTCPSCGHKFRLEYPLLYH 57 (128)
T ss_pred cCCCCCCCeeE--EEEEeEEcCcCCHHHHHHHHcCCcCEEECCCCCCceecCCCEEEE
Confidence 58999999886 224544442111111112234556679999999988777666654
No 115
>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=78.35 E-value=0.77 Score=42.62 Aligned_cols=51 Identities=24% Similarity=0.578 Sum_probs=41.8
Q ss_pred CCCCCchhhhhhcccCCccEEe--c-cCCccChhhHHHHhcCCCCCCC--CCCcccc
Q 024483 149 MHHHCPICYEYLFDSLRNTTVM--K-CGHTMHCECYHEMIKRDKYCCP--ICSKSVI 200 (267)
Q Consensus 149 ~~~~CpICle~lf~s~~~v~~L--p-CGH~~H~~C~~~~~~~~~~~CP--iCrks~~ 200 (267)
.+..||||..+.+-++ ++++| | |=|-|..+|.+..+..+.-.|| -|.|.+-
T Consensus 9 ~d~~CPvCksDrYLnP-dik~linPECyHrmCESCvdRIFs~GpAqCP~~gC~kILR 64 (314)
T COG5220 9 EDRRCPVCKSDRYLNP-DIKILINPECYHRMCESCVDRIFSRGPAQCPYKGCGKILR 64 (314)
T ss_pred hcccCCccccccccCC-CeEEEECHHHHHHHHHHHHHHHhcCCCCCCCCccHHHHHH
Confidence 3457999999988775 45554 6 9999999999999988888999 8887764
No 116
>PF14446 Prok-RING_1: Prokaryotic RING finger family 1
Probab=77.13 E-value=2 Score=30.95 Aligned_cols=35 Identities=26% Similarity=0.688 Sum_probs=27.0
Q ss_pred CCCCCchhhhhhcccCCccEE-eccCCccChhhHHHH
Q 024483 149 MHHHCPICYEYLFDSLRNTTV-MKCGHTMHCECYHEM 184 (267)
Q Consensus 149 ~~~~CpICle~lf~s~~~v~~-LpCGH~~H~~C~~~~ 184 (267)
+...|++|.+.|.+. +++++ --||=.+|+.|++..
T Consensus 4 ~~~~C~~Cg~~~~~~-dDiVvCp~CgapyHR~C~~~~ 39 (54)
T PF14446_consen 4 EGCKCPVCGKKFKDG-DDIVVCPECGAPYHRDCWEKA 39 (54)
T ss_pred cCccChhhCCcccCC-CCEEECCCCCCcccHHHHhhC
Confidence 456899999996555 45555 569999999998654
No 117
>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=77.01 E-value=2.1 Score=43.11 Aligned_cols=49 Identities=20% Similarity=0.653 Sum_probs=41.3
Q ss_pred eEcCCCCCcccCcchHHhhhcCCCCCCCCccccccccceeeeCCCCccccccccCCcCCCc
Q 024483 27 IRAPCCNEIFDCRHCHNEAASMLRNPYDRHELVRQDVKQVICSVCDTEQPVAQVCTNCGVN 87 (267)
Q Consensus 27 i~~pcC~~~y~Cr~CHde~~~~~~~~~~~H~~~r~~~~~v~C~~C~~~q~v~~~C~~Cg~~ 87 (267)
+.|.-||....|..|.-.++-| . ....+.|-.|+..+++...||+||..
T Consensus 214 ~~C~~Cg~~~~C~~C~~~l~~h--------~----~~~~l~Ch~Cg~~~~~~~~Cp~C~s~ 262 (505)
T TIGR00595 214 LLCRSCGYILCCPNCDVSLTYH--------K----KEGKLRCHYCGYQEPIPKTCPQCGSE 262 (505)
T ss_pred eEhhhCcCccCCCCCCCceEEe--------c----CCCeEEcCCCcCcCCCCCCCCCCCCC
Confidence 7899999999999998766532 1 24579999999999999999999875
No 118
>PHA00626 hypothetical protein
Probab=75.99 E-value=2.2 Score=31.09 Aligned_cols=7 Identities=43% Similarity=1.355 Sum_probs=3.6
Q ss_pred cCCcCCC
Q 024483 80 VCTNCGV 86 (267)
Q Consensus 80 ~C~~Cg~ 86 (267)
.||+||.
T Consensus 2 ~CP~CGS 8 (59)
T PHA00626 2 SCPKCGS 8 (59)
T ss_pred CCCCCCC
Confidence 3555555
No 119
>PRK14559 putative protein serine/threonine phosphatase; Provisional
Probab=75.76 E-value=2 Score=44.81 Aligned_cols=31 Identities=32% Similarity=0.885 Sum_probs=15.4
Q ss_pred eeCCCCccccc-cccCCcCCCccceeeccccc
Q 024483 67 ICSVCDTEQPV-AQVCTNCGVNMGEYFCDICK 97 (267)
Q Consensus 67 ~C~~C~~~q~v-~~~C~~Cg~~f~~y~C~~C~ 97 (267)
+|..|+.+-+. +..|++||..+..-.|+.|.
T Consensus 3 ~Cp~Cg~~n~~~akFC~~CG~~l~~~~Cp~CG 34 (645)
T PRK14559 3 ICPQCQFENPNNNRFCQKCGTSLTHKPCPQCG 34 (645)
T ss_pred cCCCCCCcCCCCCccccccCCCCCCCcCCCCC
Confidence 45555555433 33455555555443444443
No 120
>KOG0801 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=75.54 E-value=1.1 Score=39.25 Aligned_cols=31 Identities=23% Similarity=0.301 Sum_probs=25.1
Q ss_pred CCCCCCCchhhhhhcccCCccEEeccCCccCh
Q 024483 147 NSMHHHCPICYEYLFDSLRNTTVMKCGHTMHC 178 (267)
Q Consensus 147 ~~~~~~CpICle~lf~s~~~v~~LpCGH~~H~ 178 (267)
.....+|.||||+|.. .+.+..|||==++|+
T Consensus 174 ~ddkGECvICLEdL~~-GdtIARLPCLCIYHK 204 (205)
T KOG0801|consen 174 KDDKGECVICLEDLEA-GDTIARLPCLCIYHK 204 (205)
T ss_pred cccCCcEEEEhhhccC-CCceeccceEEEeec
Confidence 3557899999999865 478889999877775
No 121
>KOG2462 consensus C2H2-type Zn-finger protein [Transcription]
Probab=75.38 E-value=2.3 Score=39.91 Aligned_cols=112 Identities=24% Similarity=0.519 Sum_probs=62.2
Q ss_pred cceeecccc-ccccCCC---CcCeeecCCCCcccccCccceeecCccCcccccc-ccCcceeecCCCCCCCchhhhhhcc
Q 024483 88 MGEYFCDIC-KFYDDDI---EKGQFHCDDCGICRIGGRENYFHCKRCGSCYSTS-LRNNHLCIENSMHHHCPICYEYLFD 162 (267)
Q Consensus 88 f~~y~C~~C-~l~dd~~---~k~~yHC~~CgiCR~G~~~~~fHC~~C~~C~s~~-l~~~H~C~e~~~~~~CpICle~lf~ 162 (267)
-++|-|+.| |-|.... .-+|+||+- .-..-|.|..||-=|..- ...-|.=. -...-.|+||.-. |+
T Consensus 128 ~~r~~c~eCgk~ysT~snLsrHkQ~H~~~-------~s~ka~~C~~C~K~YvSmpALkMHirT-H~l~c~C~iCGKa-FS 198 (279)
T KOG2462|consen 128 HPRYKCPECGKSYSTSSNLSRHKQTHRSL-------DSKKAFSCKYCGKVYVSMPALKMHIRT-HTLPCECGICGKA-FS 198 (279)
T ss_pred CCceeccccccccccccccchhhcccccc-------cccccccCCCCCceeeehHHHhhHhhc-cCCCccccccccc-cc
Confidence 355556666 4443322 236777742 124577788887665421 11111111 1135578888875 54
Q ss_pred cCCccEEeccCCccChhhHHHHhcC---------CCCCCCCCCccccchhHHhHHhHHHHHhcCCChhhhcCeeEEEcCC
Q 024483 163 SLRNTTVMKCGHTMHCECYHEMIKR---------DKYCCPICSKSVIDMSRTWKRIDEEIEATVMPEDYRHKKVWILCND 233 (267)
Q Consensus 163 s~~~v~~LpCGH~~H~~C~~~~~~~---------~~~~CPiCrks~~dm~~~~~~lD~~i~~~pmP~~y~~~~v~I~CnD 233 (267)
- .||.. .-|.||.|+|.+.|++. |.+-++.. .+.+ ...|--
T Consensus 199 R-------------------PWLLQGHiRTHTGEKPF~C~hC~kAFADRSN----LRAHmQTH------S~~K-~~qC~~ 248 (279)
T KOG2462|consen 199 R-------------------PWLLQGHIRTHTGEKPFSCPHCGKAFADRSN----LRAHMQTH------SDVK-KHQCPR 248 (279)
T ss_pred c-------------------hHHhhcccccccCCCCccCCcccchhcchHH----HHHHHHhh------cCCc-cccCcc
Confidence 2 26642 24889999999999864 44444332 2333 567888
Q ss_pred CCCcc
Q 024483 234 CNDTT 238 (267)
Q Consensus 234 C~~~s 238 (267)
|++.+
T Consensus 249 C~KsF 253 (279)
T KOG2462|consen 249 CGKSF 253 (279)
T ss_pred hhhHH
Confidence 88754
No 122
>PRK14714 DNA polymerase II large subunit; Provisional
Probab=73.70 E-value=3.3 Score=46.17 Aligned_cols=48 Identities=27% Similarity=0.654 Sum_probs=26.2
Q ss_pred eeeeCCCCccccccccCCcCCCcc-ceeecccccccc-CCCCcCeeecCCCC
Q 024483 65 QVICSVCDTEQPVAQVCTNCGVNM-GEYFCDICKFYD-DDIEKGQFHCDDCG 114 (267)
Q Consensus 65 ~v~C~~C~~~q~v~~~C~~Cg~~f-~~y~C~~C~l~d-d~~~k~~yHC~~Cg 114 (267)
...|..|+++- ....|+.||... ..|+|+.|..-- .+++. ...|+.||
T Consensus 667 ~rkCPkCG~~t-~~~fCP~CGs~te~vy~CPsCGaev~~des~-a~~CP~CG 716 (1337)
T PRK14714 667 RRRCPSCGTET-YENRCPDCGTHTEPVYVCPDCGAEVPPDESG-RVECPRCD 716 (1337)
T ss_pred EEECCCCCCcc-ccccCcccCCcCCCceeCccCCCccCCCccc-cccCCCCC
Confidence 46677777753 334777777765 345566665431 11122 44566666
No 123
>PLN03086 PRLI-interacting factor K; Provisional
Probab=73.02 E-value=1.7 Score=44.63 Aligned_cols=85 Identities=26% Similarity=0.600 Sum_probs=49.1
Q ss_pred cccceeeeCCCCcccccc-------------ccCCc--CCCccceeeccccccccCCCCcCeeecCCCCcccccCc----
Q 024483 61 QDVKQVICSVCDTEQPVA-------------QVCTN--CGVNMGEYFCDICKFYDDDIEKGQFHCDDCGICRIGGR---- 121 (267)
Q Consensus 61 ~~~~~v~C~~C~~~q~v~-------------~~C~~--Cg~~f~~y~C~~C~l~dd~~~k~~yHC~~CgiCR~G~~---- 121 (267)
..+..|.|..|....+.. ..|++ ||..|.+- .-+..+||+.||- ..+..
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 356688999998765542 35664 77766332 2345678888864 22211
Q ss_pred -----cceeecCccCccccccccCcce---eecCCCCCCCchhhhhh
Q 024483 122 -----ENYFHCKRCGSCYSTSLRNNHL---CIENSMHHHCPICYEYL 160 (267)
Q Consensus 122 -----~~~fHC~~C~~C~s~~l~~~H~---C~e~~~~~~CpICle~l 160 (267)
..-+-|. ||.-+.......|. |.++ .-.|+.|...+
T Consensus 471 H~~~~Hkpv~Cp-Cg~~~~R~~L~~H~~thCp~K--pi~C~fC~~~v 514 (567)
T PLN03086 471 HMKVFHEPLQCP-CGVVLEKEQMVQHQASTCPLR--LITCRFCGDMV 514 (567)
T ss_pred HHHhcCCCccCC-CCCCcchhHHHhhhhccCCCC--ceeCCCCCCcc
Confidence 1124576 77655544445663 4443 35788887653
No 124
>KOG4692 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=72.96 E-value=2 Score=41.94 Aligned_cols=50 Identities=30% Similarity=0.628 Sum_probs=41.6
Q ss_pred CCCCCCCchhhhhhcccCCccEEeccCCccChhhHHHHhcCCCCCCCCCCccccc
Q 024483 147 NSMHHHCPICYEYLFDSLRNTTVMKCGHTMHCECYHEMIKRDKYCCPICSKSVID 201 (267)
Q Consensus 147 ~~~~~~CpICle~lf~s~~~v~~LpCGH~~H~~C~~~~~~~~~~~CPiCrks~~d 201 (267)
.+.+..||||... ....++-||||--...|+.+.+. ++..|=.|+.++.+
T Consensus 419 ~sEd~lCpICyA~----pi~Avf~PC~H~SC~~CI~qHlm-N~k~CFfCktTv~~ 468 (489)
T KOG4692|consen 419 DSEDNLCPICYAG----PINAVFAPCSHRSCYGCITQHLM-NCKRCFFCKTTVID 468 (489)
T ss_pred CcccccCcceecc----cchhhccCCCCchHHHHHHHHHh-cCCeeeEecceeee
Confidence 4667789999864 34566779999999999999998 56899999999986
No 125
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=72.66 E-value=3 Score=28.29 Aligned_cols=35 Identities=17% Similarity=0.197 Sum_probs=23.3
Q ss_pred eEEEcCCCCCccccceeEeeecCCCCCCccccccC
Q 024483 227 VWILCNDCNDTTEVYFHIIGQKCSHCKSYNTRSIA 261 (267)
Q Consensus 227 v~I~CnDC~~~s~~~fH~lg~kC~~C~SyNT~~~~ 261 (267)
..+.|.+||+.....-.....+|+.||+.-....+
T Consensus 2 ~~y~C~~CG~~~~~~~~~~~~~Cp~CG~~~~~~~~ 36 (46)
T PRK00398 2 AEYKCARCGREVELDEYGTGVRCPYCGYRILFKER 36 (46)
T ss_pred CEEECCCCCCEEEECCCCCceECCCCCCeEEEccC
Confidence 45789999986543333336799999986654433
No 126
>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=72.36 E-value=2.5 Score=23.44 Aligned_cols=20 Identities=35% Similarity=0.737 Sum_probs=13.9
Q ss_pred CCCCCCCccccchhHHhHHh
Q 024483 190 YCCPICSKSVIDMSRTWKRI 209 (267)
Q Consensus 190 ~~CPiCrks~~dm~~~~~~l 209 (267)
|.||+|.+++.+...+++-+
T Consensus 1 ~~C~~C~~~~~~~~~l~~H~ 20 (24)
T PF13894_consen 1 FQCPICGKSFRSKSELRQHM 20 (24)
T ss_dssp EE-SSTS-EESSHHHHHHHH
T ss_pred CCCcCCCCcCCcHHHHHHHH
Confidence 57999999999887766544
No 127
>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=72.21 E-value=2.4 Score=29.56 Aligned_cols=42 Identities=26% Similarity=0.795 Sum_probs=20.3
Q ss_pred CCCchhhhhhcccCCccEEeccCCccChhhHH--HHhc----CCCCCCCCCCcc
Q 024483 151 HHCPICYEYLFDSLRNTTVMKCGHTMHCECYH--EMIK----RDKYCCPICSKS 198 (267)
Q Consensus 151 ~~CpICle~lf~s~~~v~~LpCGH~~H~~C~~--~~~~----~~~~~CPiCrks 198 (267)
..|||-...|. .|++-..|.|. +||+ .||. ....+||+|+++
T Consensus 3 L~CPls~~~i~---~P~Rg~~C~H~---~CFDl~~fl~~~~~~~~W~CPiC~~~ 50 (50)
T PF02891_consen 3 LRCPLSFQRIR---IPVRGKNCKHL---QCFDLESFLESNQRTPKWKCPICNKP 50 (50)
T ss_dssp SB-TTTSSB-S---SEEEETT--SS-----EEHHHHHHHHHHS---B-TTT---
T ss_pred eeCCCCCCEEE---eCccCCcCccc---ceECHHHHHHHhhccCCeECcCCcCc
Confidence 35888887763 48888889976 4654 3553 345789999874
No 128
>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]
Probab=71.70 E-value=3.9 Score=43.30 Aligned_cols=54 Identities=22% Similarity=0.532 Sum_probs=42.8
Q ss_pred ceEcCCCCCcccCcchHHhhhcCCCCCCCCccccccccceeeeCCCCccccccccCCcCCCcccee
Q 024483 26 RIRAPCCNEIFDCRHCHNEAASMLRNPYDRHELVRQDVKQVICSVCDTEQPVAQVCTNCGVNMGEY 91 (267)
Q Consensus 26 ~i~~pcC~~~y~Cr~CHde~~~~~~~~~~~H~~~r~~~~~v~C~~C~~~q~v~~~C~~Cg~~f~~y 91 (267)
.+.|.-||-.+.|++|=.-.+-|. .+..+.|-.|+..+++...|++||...=+|
T Consensus 435 ~l~C~~Cg~v~~Cp~Cd~~lt~H~------------~~~~L~CH~Cg~~~~~p~~Cp~Cgs~~L~~ 488 (730)
T COG1198 435 LLLCRDCGYIAECPNCDSPLTLHK------------ATGQLRCHYCGYQEPIPQSCPECGSEHLRA 488 (730)
T ss_pred eeecccCCCcccCCCCCcceEEec------------CCCeeEeCCCCCCCCCCCCCCCCCCCeeEE
Confidence 388999999999999976554321 246899999999999999999999884333
No 129
>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=71.40 E-value=3.4 Score=25.13 Aligned_cols=21 Identities=24% Similarity=0.539 Sum_probs=15.5
Q ss_pred CCCCCCCccccchhHHhHHhHH
Q 024483 190 YCCPICSKSVIDMSRTWKRIDE 211 (267)
Q Consensus 190 ~~CPiCrks~~dm~~~~~~lD~ 211 (267)
..||||.+.+ .+....+.||.
T Consensus 2 v~CPiC~~~v-~~~~in~HLD~ 22 (26)
T smart00734 2 VQCPVCFREV-PENLINSHLDS 22 (26)
T ss_pred CcCCCCcCcc-cHHHHHHHHHH
Confidence 3699999998 55556667773
No 130
>KOG0827 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=71.08 E-value=0.45 Score=46.73 Aligned_cols=51 Identities=22% Similarity=0.446 Sum_probs=43.8
Q ss_pred CCCCCchhhhhhcccCCccEEeccCCccChhhHHHHhcCCCCCCCCCCcccc
Q 024483 149 MHHHCPICYEYLFDSLRNTTVMKCGHTMHCECYHEMIKRDKYCCPICSKSVI 200 (267)
Q Consensus 149 ~~~~CpICle~lf~s~~~v~~LpCGH~~H~~C~~~~~~~~~~~CPiCrks~~ 200 (267)
.-..+.||.+.|...-.....+.|||..|..++.+||.. ..++|.|+..+-
T Consensus 195 lv~sl~I~~~slK~~y~k~~~~~~g~~~~~~kL~k~L~~-~~kl~~~~rel~ 245 (465)
T KOG0827|consen 195 LVGSLSICFESLKQNYDKISAIVCGHIYHHGKLSKWLAT-KRKLPSCRRELP 245 (465)
T ss_pred HHhhhHhhHHHHHHHHHHHHHHhhcccchhhHHHHHHHH-HHHhHHHHhhhh
Confidence 345799999998766567788999999999999999984 689999999885
No 131
>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=69.80 E-value=2.2 Score=26.48 Aligned_cols=37 Identities=24% Similarity=0.507 Sum_probs=22.8
Q ss_pred CchhhhhhcccCCccEEeccCCccChhhHHHHhcCCCCCCCCCCcccc
Q 024483 153 CPICYEYLFDSLRNTTVMKCGHTMHCECYHEMIKRDKYCCPICSKSVI 200 (267)
Q Consensus 153 CpICle~lf~s~~~v~~LpCGH~~H~~C~~~~~~~~~~~CPiCrks~~ 200 (267)
|+.|.+.+.... ..+..=|..||..|| +|..|+++|.
T Consensus 2 C~~C~~~i~~~~--~~~~~~~~~~H~~Cf---------~C~~C~~~L~ 38 (39)
T smart00132 2 CAGCGKPIRGGE--LVLRALGKVWHPECF---------KCSKCGKPLG 38 (39)
T ss_pred ccccCCcccCCc--EEEEeCCccccccCC---------CCcccCCcCc
Confidence 677887765431 122222778887765 6777887764
No 132
>KOG2272 consensus Focal adhesion protein PINCH-1, contains LIM domains [Signal transduction mechanisms; Cytoskeleton]
Probab=69.80 E-value=3.6 Score=38.57 Aligned_cols=128 Identities=19% Similarity=0.517 Sum_probs=73.1
Q ss_pred ccCcchHHhhhcCCCCCCCCccccccccceeeeCCCCccccccccCCcCCCccceeeccccccc-cCCC---CcCeeecC
Q 024483 36 FDCRHCHNEAASMLRNPYDRHELVRQDVKQVICSVCDTEQPVAQVCTNCGVNMGEYFCDICKFY-DDDI---EKGQFHCD 111 (267)
Q Consensus 36 y~Cr~CHde~~~~~~~~~~~H~~~r~~~~~v~C~~C~~~q~v~~~C~~Cg~~f~~y~C~~C~l~-dd~~---~k~~yHC~ 111 (267)
|.|.+|-..+.+ --+-|. .-+++|-.|+..-.+ +.-|+|-|.+|+-. |+++ .-++||
T Consensus 100 F~Cd~Cn~~Lad--------~gf~rn-qgr~LC~~Cn~k~Ka--------~~~g~YvC~KCh~~iD~~~l~fr~d~yH-- 160 (332)
T KOG2272|consen 100 FRCDLCNKHLAD--------QGFYRN-QGRALCRECNQKEKA--------KGRGRYVCQKCHAHIDEQPLTFRGDPYH-- 160 (332)
T ss_pred chhHHHHHHHhh--------hhhHhh-cchHHhhhhhhhhcc--------cccceeehhhhhhhcccccccccCCCCC--
Confidence 566677666542 223343 346777777654332 23589999999754 5543 224554
Q ss_pred CCCcccccCccceeecCccCccccc---cccCcceeecCCCCCCCchhhhhhcccCCccEEeccCCccChhhH----HHH
Q 024483 112 DCGICRIGGRENYFHCKRCGSCYST---SLRNNHLCIENSMHHHCPICYEYLFDSLRNTTVMKCGHTMHCECY----HEM 184 (267)
Q Consensus 112 ~CgiCR~G~~~~~fHC~~C~~C~s~---~l~~~H~C~e~~~~~~CpICle~lf~s~~~v~~LpCGH~~H~~C~----~~~ 184 (267)
-.-|.|.+||-=+.. ++++.--|..--...-+|||..= --.|-..=+ ..|
T Consensus 161 ----------~yHFkCt~C~keL~sdaRevk~eLyClrChD~mgipiCgaC-------------~rpIeervi~amgKhW 217 (332)
T KOG2272|consen 161 ----------PYHFKCTTCGKELTSDAREVKGELYCLRCHDKMGIPICGAC-------------RRPIEERVIFAMGKHW 217 (332)
T ss_pred ----------ccceecccccccccchhhhhccceeccccccccCCcccccc-------------cCchHHHHHHHhcccc
Confidence 257889999876654 34455555554444556666542 111111222 224
Q ss_pred hcCCCCCCCCCCccccchhHHh
Q 024483 185 IKRDKYCCPICSKSVIDMSRTW 206 (267)
Q Consensus 185 ~~~~~~~CPiCrks~~dm~~~~ 206 (267)
-. .++.|..|-|+++.-+.|.
T Consensus 218 Hv-eHFvCa~CekPFlGHrHYE 238 (332)
T KOG2272|consen 218 HV-EHFVCAKCEKPFLGHRHYE 238 (332)
T ss_pred ch-hheeehhcCCcccchhhhh
Confidence 33 4788989999888655443
No 133
>KOG1701 consensus Focal adhesion adaptor protein Paxillin and related LIM proteins [Signal transduction mechanisms]
Probab=69.70 E-value=1.5 Score=43.45 Aligned_cols=30 Identities=30% Similarity=0.622 Sum_probs=14.9
Q ss_pred CChhhhcCeeEEEcCCCCCccccceeEeeecCCCCC
Q 024483 218 MPEDYRHKKVWILCNDCNDTTEVYFHIIGQKCSHCK 253 (267)
Q Consensus 218 mP~~y~~~~v~I~CnDC~~~s~~~fH~lg~kC~~C~ 253 (267)
||++=++..|.|.+.|= .||+=-.||..|+
T Consensus 405 ~P~~G~~etvRvvamdr------~fHv~CY~CEDCg 434 (468)
T KOG1701|consen 405 LPRDGKDETVRVVAMDR------DFHVNCYKCEDCG 434 (468)
T ss_pred cCCCCCcceEEEEEccc------cccccceehhhcC
Confidence 45555555555554442 2555555554444
No 134
>KOG0269 consensus WD40 repeat-containing protein [Function unknown]
Probab=69.43 E-value=3.9 Score=43.35 Aligned_cols=79 Identities=19% Similarity=0.377 Sum_probs=48.9
Q ss_pred cCeeecCCCCcccccCccceeecCccCccccccccCcceeecCCCCCCCchhhhhhcccCCccEEeccCCccChhhHHHH
Q 024483 105 KGQFHCDDCGICRIGGRENYFHCKRCGSCYSTSLRNNHLCIENSMHHHCPICYEYLFDSLRNTTVMKCGHTMHCECYHEM 184 (267)
Q Consensus 105 k~~yHC~~CgiCR~G~~~~~fHC~~C~~C~s~~l~~~H~C~e~~~~~~CpICle~lf~s~~~v~~LpCGH~~H~~C~~~~ 184 (267)
.-+|-|+.|+-=-+++++ - +|+.|-+.. ...|.||-..+-. ..+.---|||..|..++.+|
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--W---QCDRCESRA------------SAKCTVCDLVIRG--VDVWCQVCGHGGHDSHLKSW 811 (839)
T ss_pred eeeccccccCCccccccc--e---eechHHHHh------------hcCceeecceeee--eEeecccccccccHHHHHHH
Confidence 356777777754444443 3 344444433 2358888876532 23333469999999999999
Q ss_pred hcCCCCCCCC-------CCccccchh
Q 024483 185 IKRDKYCCPI-------CSKSVIDMS 203 (267)
Q Consensus 185 ~~~~~~~CPi-------Crks~~dm~ 203 (267)
+.. +..||. +++++.||.
T Consensus 812 ~~~-~s~ca~~~C~~~c~~~~~~D~~ 836 (839)
T KOG0269|consen 812 FFK-ASPCAKSICPHLCHYSSFIDTF 836 (839)
T ss_pred Hhc-CCCCccccCCccccccccchhh
Confidence 984 556765 445555654
No 135
>KOG1940 consensus Zn-finger protein [General function prediction only]
Probab=67.92 E-value=1 Score=42.38 Aligned_cols=71 Identities=18% Similarity=0.470 Sum_probs=43.5
Q ss_pred CccCccccccCcceEcCCCCCcccCcchHHhhhcCCC-CCC-----CCcc---ccccccceeeeCCCCccccc-----cc
Q 024483 14 MGYGCKHYRRRCRIRAPCCNEIFDCRHCHNEAASMLR-NPY-----DRHE---LVRQDVKQVICSVCDTEQPV-----AQ 79 (267)
Q Consensus 14 ~~~gC~HY~r~c~i~~pcC~~~y~Cr~CHde~~~~~~-~~~-----~~H~---~~r~~~~~v~C~~C~~~q~v-----~~ 79 (267)
..+.|.||...=.++.++|.. |+|..||+ ..+... |.+ +.-| .....+..|+|-.|+.-+.+ ..
T Consensus 176 ~~~~CgH~~h~~cf~e~~~~~-y~CP~C~~-~~d~~~~~~~~d~~l~~~~~p~~y~~~~~~i~cndC~~~~~~k~~~l~~ 253 (276)
T KOG1940|consen 176 GVLKCGHYMHSRCFEEMICEG-YTCPICSK-PGDMSHYFRKLDKELAGSPMPEEYKNKTQDILCNDCGSGTNVKYHILYH 253 (276)
T ss_pred CccCcccchHHHHHHHHhccC-CCCCcccc-hHHHHHHHHHHHHHHhcCCCCchhhchhheeeccCCCCCCccceehhhh
Confidence 346899999866699999999 99999999 433211 100 1111 12234455777777765544 23
Q ss_pred cCCcCCC
Q 024483 80 VCTNCGV 86 (267)
Q Consensus 80 ~C~~Cg~ 86 (267)
.|..|+.
T Consensus 254 kc~~c~~ 260 (276)
T KOG1940|consen 254 KCGKCGS 260 (276)
T ss_pred hCCCccc
Confidence 5555554
No 136
>COG5222 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=66.40 E-value=4 Score=39.10 Aligned_cols=44 Identities=32% Similarity=0.717 Sum_probs=36.1
Q ss_pred CCCchhhhhhcccCCccEEeccCCccChhhHHHHhcCCCCCCCCCCc
Q 024483 151 HHCPICYEYLFDSLRNTTVMKCGHTMHCECYHEMIKRDKYCCPICSK 197 (267)
Q Consensus 151 ~~CpICle~lf~s~~~v~~LpCGH~~H~~C~~~~~~~~~~~CPiCrk 197 (267)
..||.|.--| +.+++.--|||.|...||..-|..+.+.||.|..
T Consensus 275 LkCplc~~Ll---rnp~kT~cC~~~fc~eci~~al~dsDf~CpnC~r 318 (427)
T COG5222 275 LKCPLCHCLL---RNPMKTPCCGHTFCDECIGTALLDSDFKCPNCSR 318 (427)
T ss_pred ccCcchhhhh---hCcccCccccchHHHHHHhhhhhhccccCCCccc
Confidence 5799998754 3466665689999999999877668899999987
No 137
>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=66.24 E-value=4 Score=34.32 Aligned_cols=29 Identities=21% Similarity=0.421 Sum_probs=21.3
Q ss_pred cccccCCcCCCccceeeccccccccCCCCcCeeecCCCCcc
Q 024483 76 PVAQVCTNCGVNMGEYFCDICKFYDDDIEKGQFHCDDCGIC 116 (267)
Q Consensus 76 ~v~~~C~~Cg~~f~~y~C~~C~l~dd~~~k~~yHC~~CgiC 116 (267)
.....|++||+.| || .+|.+-.|++||.=
T Consensus 7 GtKr~Cp~cg~kF----------YD--Lnk~p~vcP~cg~~ 35 (129)
T TIGR02300 7 GTKRICPNTGSKF----------YD--LNRRPAVSPYTGEQ 35 (129)
T ss_pred CccccCCCcCccc----------cc--cCCCCccCCCcCCc
Confidence 3456788888854 65 56888899888853
No 138
>PRK05580 primosome assembly protein PriA; Validated
Probab=66.05 E-value=4.9 Score=41.93 Aligned_cols=51 Identities=22% Similarity=0.632 Sum_probs=41.9
Q ss_pred ceEcCCCCCcccCcchHHhhhcCCCCCCCCccccccccceeeeCCCCccccccccCCcCCCcc
Q 024483 26 RIRAPCCNEIFDCRHCHNEAASMLRNPYDRHELVRQDVKQVICSVCDTEQPVAQVCTNCGVNM 88 (267)
Q Consensus 26 ~i~~pcC~~~y~Cr~CHde~~~~~~~~~~~H~~~r~~~~~v~C~~C~~~q~v~~~C~~Cg~~f 88 (267)
.+.|.-||....|..|...+.- |. ....+.|-.|+..+++...|++||...
T Consensus 381 ~~~C~~Cg~~~~C~~C~~~l~~--------h~----~~~~l~Ch~Cg~~~~~~~~Cp~Cg~~~ 431 (679)
T PRK05580 381 FLLCRDCGWVAECPHCDASLTL--------HR----FQRRLRCHHCGYQEPIPKACPECGSTD 431 (679)
T ss_pred ceEhhhCcCccCCCCCCCceeE--------EC----CCCeEECCCCcCCCCCCCCCCCCcCCe
Confidence 3889999999999999876542 21 245799999999999999999998863
No 139
>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 PRK04023 DNA polymerase II large subunit; Validated
Probab=65.37 E-value=5 Score=43.88 Aligned_cols=50 Identities=24% Similarity=0.587 Sum_probs=37.0
Q ss_pred cceeeeCCCCccccccccCCcCCCc-cceeeccccccccCCCCcCeeecCCCCcccc
Q 024483 63 VKQVICSVCDTEQPVAQVCTNCGVN-MGEYFCDICKFYDDDIEKGQFHCDDCGICRI 118 (267)
Q Consensus 63 ~~~v~C~~C~~~q~v~~~C~~Cg~~-f~~y~C~~C~l~dd~~~k~~yHC~~CgiCR~ 118 (267)
+..-.|..|+++. +...|++||.. -..|||+.|.-- -..|.|+.||.=..
T Consensus 624 Vg~RfCpsCG~~t-~~frCP~CG~~Te~i~fCP~CG~~-----~~~y~CPKCG~El~ 674 (1121)
T PRK04023 624 IGRRKCPSCGKET-FYRRCPFCGTHTEPVYRCPRCGIE-----VEEDECEKCGREPT 674 (1121)
T ss_pred ccCccCCCCCCcC-CcccCCCCCCCCCcceeCccccCc-----CCCCcCCCCCCCCC
Confidence 3455899999984 66799999975 677899999432 23478999986433
No 141
>COG5109 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=64.64 E-value=5.7 Score=38.33 Aligned_cols=44 Identities=23% Similarity=0.631 Sum_probs=36.7
Q ss_pred CCchhhhhhcccCCccEEeccCCccChhhHHHHhcCC--CCCCCCCC
Q 024483 152 HCPICYEYLFDSLRNTTVMKCGHTMHCECYHEMIKRD--KYCCPICS 196 (267)
Q Consensus 152 ~CpICle~lf~s~~~v~~LpCGH~~H~~C~~~~~~~~--~~~CPiCr 196 (267)
.|||=.|. -+...|...|.|||++=..=++.+-+++ .++||.|-
T Consensus 338 iCPVlKe~-~t~ENpP~ml~CgHVIskeal~~LS~nG~~~FKCPYCP 383 (396)
T COG5109 338 ICPVLKEL-CTDENPPVMLECGHVISKEALSVLSQNGVLSFKCPYCP 383 (396)
T ss_pred eccccHhh-hcccCCCeeeeccceeeHHHHHHHhhcCcEEeeCCCCC
Confidence 68887764 6666788899999999999999988765 58899996
No 142
>KOG2068 consensus MOT2 transcription factor [Transcription]
Probab=64.64 E-value=4.9 Score=38.67 Aligned_cols=52 Identities=31% Similarity=0.510 Sum_probs=39.6
Q ss_pred CCCCCCchhhhhhcccCCccEEeccCCccChhhHHHHhcCCCCCCCCCCcccc
Q 024483 148 SMHHHCPICYEYLFDSLRNTTVMKCGHTMHCECYHEMIKRDKYCCPICSKSVI 200 (267)
Q Consensus 148 ~~~~~CpICle~lf~s~~~v~~LpCGH~~H~~C~~~~~~~~~~~CPiCrks~~ 200 (267)
+....||||-+++-....+..--|||+-++..|+..-.. ++.+||.|++...
T Consensus 247 ~v~~s~p~~~~~~~~~d~~~lP~~~~~~~~l~~~~t~~~-~~~~~~~~rk~~~ 298 (327)
T KOG2068|consen 247 SVPPSCPICYEDLDLTDSNFLPCPCGFRLCLFCHKTISD-GDGRCPGCRKPYE 298 (327)
T ss_pred ccCCCCCCCCCcccccccccccccccccchhhhhhcccc-cCCCCCccCCccc
Confidence 445789999998744434444457799999999988877 5789999997765
No 143
>COG1996 RPC10 DNA-directed RNA polymerase, subunit RPC10 (contains C4-type Zn-finger) [Transcription]
Probab=63.70 E-value=5.4 Score=28.19 Aligned_cols=30 Identities=23% Similarity=0.454 Sum_probs=22.9
Q ss_pred eeEEEcCCCCCccccceeEeeecCCCCCCc
Q 024483 226 KVWILCNDCNDTTEVYFHIIGQKCSHCKSY 255 (267)
Q Consensus 226 ~v~I~CnDC~~~s~~~fH~lg~kC~~C~Sy 255 (267)
+..+.|.+|++.-+...---+.+|+.|||-
T Consensus 4 ~~~Y~C~~Cg~~~~~~~~~~~irCp~Cg~r 33 (49)
T COG1996 4 MMEYKCARCGREVELDQETRGIRCPYCGSR 33 (49)
T ss_pred eEEEEhhhcCCeeehhhccCceeCCCCCcE
Confidence 456889999988764545678899999873
No 144
>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=63.33 E-value=6.3 Score=23.85 Aligned_cols=9 Identities=44% Similarity=1.239 Sum_probs=4.7
Q ss_pred CeeecCCCC
Q 024483 106 GQFHCDDCG 114 (267)
Q Consensus 106 ~~yHC~~Cg 114 (267)
-.|.|++||
T Consensus 15 v~f~CPnCG 23 (24)
T PF07754_consen 15 VPFPCPNCG 23 (24)
T ss_pred ceEeCCCCC
Confidence 445555555
No 145
>PRK14873 primosome assembly protein PriA; Provisional
Probab=62.90 E-value=5.9 Score=41.46 Aligned_cols=49 Identities=20% Similarity=0.491 Sum_probs=39.2
Q ss_pred ceEcCCCCCcccCcchHHhhhcCCCCCCCCccccccccceeeeCCCCccccccccCCcCCCc
Q 024483 26 RIRAPCCNEIFDCRHCHNEAASMLRNPYDRHELVRQDVKQVICSVCDTEQPVAQVCTNCGVN 87 (267)
Q Consensus 26 ~i~~pcC~~~y~Cr~CHde~~~~~~~~~~~H~~~r~~~~~v~C~~C~~~q~v~~~C~~Cg~~ 87 (267)
.+.|.-||....|..|...++- |. ....+.|-.|+..+ +...|++||..
T Consensus 383 ~l~C~~Cg~~~~C~~C~~~L~~--------h~----~~~~l~Ch~CG~~~-~p~~Cp~Cgs~ 431 (665)
T PRK14873 383 SLACARCRTPARCRHCTGPLGL--------PS----AGGTPRCRWCGRAA-PDWRCPRCGSD 431 (665)
T ss_pred eeEhhhCcCeeECCCCCCceeE--------ec----CCCeeECCCCcCCC-cCccCCCCcCC
Confidence 3899999999999999976642 21 23578999999876 57899999886
No 146
>PRK14714 DNA polymerase II large subunit; Provisional
Probab=62.87 E-value=6.1 Score=44.13 Aligned_cols=33 Identities=30% Similarity=0.731 Sum_probs=25.2
Q ss_pred ccCCcCCCccceeeccccccccCCCCcCeeecCCCCc
Q 024483 79 QVCTNCGVNMGEYFCDICKFYDDDIEKGQFHCDDCGI 115 (267)
Q Consensus 79 ~~C~~Cg~~f~~y~C~~C~l~dd~~~k~~yHC~~Cgi 115 (267)
..|++||......||+.|.-.. +.+|+|+.||.
T Consensus 668 rkCPkCG~~t~~~fCP~CGs~t----e~vy~CPsCGa 700 (1337)
T PRK14714 668 RRCPSCGTETYENRCPDCGTHT----EPVYVCPDCGA 700 (1337)
T ss_pred EECCCCCCccccccCcccCCcC----CCceeCccCCC
Confidence 4899999987677999996542 45778887776
No 147
>smart00659 RPOLCX RNA polymerase subunit CX. present in RNA polymerase I, II and III
Probab=62.35 E-value=5.4 Score=27.30 Aligned_cols=26 Identities=19% Similarity=0.525 Sum_probs=17.9
Q ss_pred EEEcCCCCCccccceeEeeecCCCCCC
Q 024483 228 WILCNDCNDTTEVYFHIIGQKCSHCKS 254 (267)
Q Consensus 228 ~I~CnDC~~~s~~~fH~lg~kC~~C~S 254 (267)
...|.+||+..+... --..+|+.||+
T Consensus 2 ~Y~C~~Cg~~~~~~~-~~~irC~~CG~ 27 (44)
T smart00659 2 IYICGECGRENEIKS-KDVVRCRECGY 27 (44)
T ss_pred EEECCCCCCEeecCC-CCceECCCCCc
Confidence 467888887655442 34578888887
No 148
>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=62.30 E-value=6.3 Score=28.49 Aligned_cols=27 Identities=30% Similarity=0.774 Sum_probs=16.6
Q ss_pred cccCCcCCCccceeeccccccccCCCCcCeeecCCCCc
Q 024483 78 AQVCTNCGVNMGEYFCDICKFYDDDIEKGQFHCDDCGI 115 (267)
Q Consensus 78 ~~~C~~Cg~~f~~y~C~~C~l~dd~~~k~~yHC~~Cgi 115 (267)
++.|+.||....+ ......|.|+.||.
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 23445666666654
No 149
>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]
Probab=62.23 E-value=7.3 Score=41.31 Aligned_cols=44 Identities=25% Similarity=0.706 Sum_probs=28.4
Q ss_pred cceeeeCCCCccccccccCCcCCCccc------eeeccccccccCCCCcCeeecCCCC
Q 024483 63 VKQVICSVCDTEQPVAQVCTNCGVNMG------EYFCDICKFYDDDIEKGQFHCDDCG 114 (267)
Q Consensus 63 ~~~v~C~~C~~~q~v~~~C~~Cg~~f~------~y~C~~C~l~dd~~~k~~yHC~~Cg 114 (267)
.+.++|..|+.. ..|++|+..|. ...|--|..= ++.+.+|+.||
T Consensus 433 s~~l~C~~Cg~v----~~Cp~Cd~~lt~H~~~~~L~CH~Cg~~----~~~p~~Cp~Cg 482 (730)
T COG1198 433 APLLLCRDCGYI----AECPNCDSPLTLHKATGQLRCHYCGYQ----EPIPQSCPECG 482 (730)
T ss_pred cceeecccCCCc----ccCCCCCcceEEecCCCeeEeCCCCCC----CCCCCCCCCCC
Confidence 458999999975 47999998874 4444444332 34455555555
No 150
>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=61.96 E-value=7.7 Score=27.05 Aligned_cols=22 Identities=23% Similarity=0.585 Sum_probs=15.0
Q ss_pred CCCCCCCCccccchhHHhHHhHH
Q 024483 189 KYCCPICSKSVIDMSRTWKRIDE 211 (267)
Q Consensus 189 ~~~CPiCrks~~dm~~~~~~lD~ 211 (267)
.|+||.|++ -.+..++++-+++
T Consensus 2 ~f~CP~C~~-~~~~~~L~~H~~~ 23 (54)
T PF05605_consen 2 SFTCPYCGK-GFSESSLVEHCED 23 (54)
T ss_pred CcCCCCCCC-ccCHHHHHHHHHh
Confidence 588999999 5666666655443
No 151
>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=61.08 E-value=6.4 Score=24.44 Aligned_cols=20 Identities=30% Similarity=0.853 Sum_probs=13.7
Q ss_pred CCCcccccCccc-eeecCccC
Q 024483 112 DCGICRIGGREN-YFHCKRCG 131 (267)
Q Consensus 112 ~CgiCR~G~~~~-~fHC~~C~ 131 (267)
.|++|+.-.... +++|..|+
T Consensus 2 ~C~~C~~~~~~~~~Y~C~~c~ 22 (30)
T PF03107_consen 2 WCDVCRRKIDGFYFYHCSECC 22 (30)
T ss_pred CCCCCCCCcCCCEeEEeCCCC
Confidence 467776654334 88888887
No 152
>PRK14559 putative protein serine/threonine phosphatase; Provisional
Probab=60.39 E-value=4.8 Score=42.04 Aligned_cols=34 Identities=26% Similarity=0.666 Sum_probs=22.4
Q ss_pred eeeeCCCCccccccccCCcCCCcc--ceeeccccccc
Q 024483 65 QVICSVCDTEQPVAQVCTNCGVNM--GEYFCDICKFY 99 (267)
Q Consensus 65 ~v~C~~C~~~q~v~~~C~~Cg~~f--~~y~C~~C~l~ 99 (267)
.-.|..|++.++. ..|++||+.. +.-||+.|-..
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 4577778776643 4688887763 56677777544
No 153
>KOG1001 consensus Helicase-like transcription factor HLTF/DNA helicase RAD5, DEAD-box superfamily [Transcription; Replication, recombination and repair]
Probab=60.16 E-value=4.2 Score=42.65 Aligned_cols=45 Identities=31% Similarity=0.855 Sum_probs=36.6
Q ss_pred CCCchhhhhhcccCCccEEeccCCccChhhHHHHhcCCCC-CCCCCCcccc
Q 024483 151 HHCPICYEYLFDSLRNTTVMKCGHTMHCECYHEMIKRDKY-CCPICSKSVI 200 (267)
Q Consensus 151 ~~CpICle~lf~s~~~v~~LpCGH~~H~~C~~~~~~~~~~-~CPiCrks~~ 200 (267)
..|+||++ .+...+.+|||.|-..|+.+.+..... .||+|+-.+.
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 68999999 256778899999999999998875433 5999996554
No 154
>KOG4367 consensus Predicted Zn-finger protein [Function unknown]
Probab=59.99 E-value=4.2 Score=40.83 Aligned_cols=33 Identities=21% Similarity=0.823 Sum_probs=27.3
Q ss_pred CCCCchhhhhhcccCCccEEeccCCccChhhHHHHhc
Q 024483 150 HHHCPICYEYLFDSLRNTTVMKCGHTMHCECYHEMIK 186 (267)
Q Consensus 150 ~~~CpICle~lf~s~~~v~~LpCGH~~H~~C~~~~~~ 186 (267)
+..||||... | ++.++|||||.+.+.|...-+.
T Consensus 4 elkc~vc~~f-~---~epiil~c~h~lc~~ca~~~~~ 36 (699)
T KOG4367|consen 4 ELKCPVCGSF-Y---REPIILPCSHNLCQACARNILV 36 (699)
T ss_pred cccCceehhh-c---cCceEeecccHHHHHHHHhhcc
Confidence 4579999986 4 3567999999999999987764
No 155
>KOG3053 consensus Uncharacterized conserved protein [Function unknown]
Probab=59.98 E-value=2.9 Score=39.12 Aligned_cols=54 Identities=24% Similarity=0.497 Sum_probs=37.7
Q ss_pred CCCCCCCchhhhhhcccCCccEEecc-----CCccChhhHHHHhcCC-------CCCCCCCCcccc
Q 024483 147 NSMHHHCPICYEYLFDSLRNTTVMKC-----GHTMHCECYHEMIKRD-------KYCCPICSKSVI 200 (267)
Q Consensus 147 ~~~~~~CpICle~lf~s~~~v~~LpC-----GH~~H~~C~~~~~~~~-------~~~CPiCrks~~ 200 (267)
...+.-|=||++.=.+.+...-+=|| .|..|..|+..|+.+. .-+||.|+....
T Consensus 17 ~e~eR~CWiCF~TdeDn~~a~WV~PCrCRGt~KWVHqsCL~rWiDEK~~~n~~q~V~C~QCqTEYi 82 (293)
T KOG3053|consen 17 QELERCCWICFATDEDNRLAAWVHPCRCRGTTKWVHQSCLSRWIDEKQRGNPLQTVSCPQCQTEYI 82 (293)
T ss_pred cccceeEEEEeccCcccchhhhcccccccCccHHHHHHHHHHHHhHHhcCCCCceeechhhcchhe
Confidence 34566799999863333333234577 3999999999999642 347999997654
No 156
>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=59.48 E-value=3.3 Score=38.91 Aligned_cols=51 Identities=27% Similarity=0.696 Sum_probs=32.5
Q ss_pred CCcccCcchHHhhhcCCCCCCCCccccccccceeeeCCCCccccccccCCcCCCccceeecccccc
Q 024483 33 NEIFDCRHCHNEAASMLRNPYDRHELVRQDVKQVICSVCDTEQPVAQVCTNCGVNMGEYFCDICKF 98 (267)
Q Consensus 33 ~~~y~Cr~CHde~~~~~~~~~~~H~~~r~~~~~v~C~~C~~~q~v~~~C~~Cg~~f~~y~C~~C~l 98 (267)
|++|.|-+|.+-+- ++-.+.-.+ .|+....-+-.|.+|+. +|.|.|..||.
T Consensus 140 Grif~CsfC~~flC-------EDDQFEHQA-------sCQvLe~E~~KC~SCNr-lGq~sCLRCK~ 190 (314)
T PF06524_consen 140 GRIFKCSFCDNFLC-------EDDQFEHQA-------SCQVLESETFKCQSCNR-LGQYSCLRCKI 190 (314)
T ss_pred CeEEEeecCCCeee-------ccchhhhhh-------hhhhhhccccccccccc-ccchhhhheee
Confidence 56888888887654 222222212 15555555667888875 78888988884
No 157
>PRK12286 rpmF 50S ribosomal protein L32; Reviewed
Probab=58.30 E-value=9.7 Score=27.50 Aligned_cols=29 Identities=24% Similarity=0.688 Sum_probs=22.5
Q ss_pred eEEEcCCCCCccccceeEeeecCCCCCCcccccc
Q 024483 227 VWILCNDCNDTTEVYFHIIGQKCSHCKSYNTRSI 260 (267)
Q Consensus 227 v~I~CnDC~~~s~~~fH~lg~kC~~C~SyNT~~~ 260 (267)
..+.|..||+. ..-| +-|++||.|+-+++
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 45789999974 4446 45999999999886
No 158
>KOG2066 consensus Vacuolar assembly/sorting protein VPS41 [Intracellular trafficking, secretion, and vesicular transport]
Probab=57.68 E-value=3.7 Score=43.67 Aligned_cols=44 Identities=34% Similarity=0.631 Sum_probs=30.3
Q ss_pred CCCchhhhhhcccC---CccEEeccCCccChhhHHHHhcCCCCCCCCCC
Q 024483 151 HHCPICYEYLFDSL---RNTTVMKCGHTMHCECYHEMIKRDKYCCPICS 196 (267)
Q Consensus 151 ~~CpICle~lf~s~---~~v~~LpCGH~~H~~C~~~~~~~~~~~CPiCr 196 (267)
+.|.-|.+..-.+. ..++++.|||+||..|+.....+++ |-+|.
T Consensus 785 ~rc~~c~~~~l~~~~~~~~~~v~~c~h~yhk~c~~~~~~~~~--~~~~~ 831 (846)
T KOG2066|consen 785 ERCSSCFEPNLPSGAAFDSVVVFHCGHMYHKECLMMESLRNA--CNIES 831 (846)
T ss_pred hhhhhhcccccccCcccceeeEEEccchhhhcccccHHHhcc--cChhh
Confidence 35666666654343 5688999999999999987665332 54443
No 159
>KOG1311 consensus DHHC-type Zn-finger proteins [General function prediction only]
Probab=55.56 E-value=7.9 Score=35.90 Aligned_cols=33 Identities=27% Similarity=0.776 Sum_probs=20.2
Q ss_pred CCCccceeeccccccccCCCCcCeeecCCCCccccc
Q 024483 84 CGVNMGEYFCDICKFYDDDIEKGQFHCDDCGICRIG 119 (267)
Q Consensus 84 Cg~~f~~y~C~~C~l~dd~~~k~~yHC~~CgiCR~G 119 (267)
=|......||+.|+++-- +...||.-||.|-.+
T Consensus 107 ~~~~~~~~~C~~C~~~rP---pRs~HCsvC~~CV~r 139 (299)
T KOG1311|consen 107 NGIQVEWKYCDTCQLYRP---PRSSHCSVCNNCVLR 139 (299)
T ss_pred CCcccceEEcCcCcccCC---CCcccchhhcccccc
Confidence 355666789999999832 334455555555443
No 160
>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=54.62 E-value=7.8 Score=21.83 Aligned_cols=16 Identities=50% Similarity=0.916 Sum_probs=12.4
Q ss_pred CCCCCCCccccchhHH
Q 024483 190 YCCPICSKSVIDMSRT 205 (267)
Q Consensus 190 ~~CPiCrks~~dm~~~ 205 (267)
|+||+|++++.+.+.+
T Consensus 1 y~C~~C~~~f~~~~~l 16 (23)
T PF00096_consen 1 YKCPICGKSFSSKSNL 16 (23)
T ss_dssp EEETTTTEEESSHHHH
T ss_pred CCCCCCCCccCCHHHH
Confidence 5799999999866543
No 161
>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=54.34 E-value=6.5 Score=39.61 Aligned_cols=58 Identities=28% Similarity=0.643 Sum_probs=30.0
Q ss_pred eeccccccccCCCCcCeeecCCCCcccccCccceeecCccCccccccc--cCcceeecCCCCCCCchhhhhhccc
Q 024483 91 YFCDICKFYDDDIEKGQFHCDDCGICRIGGRENYFHCKRCGSCYSTSL--RNNHLCIENSMHHHCPICYEYLFDS 163 (267)
Q Consensus 91 y~C~~C~l~dd~~~k~~yHC~~CgiCR~G~~~~~fHC~~C~~C~s~~l--~~~H~C~e~~~~~~CpICle~lf~s 163 (267)
|||..|.-.- |+-|-....+ .+=|..|-.=++.+. .++.+|..+- -+||+|.-.|...
T Consensus 6 ~fC~~C~~ir------------c~~c~~~Ei~-~~yCp~CL~~~p~~e~~~~~nrC~r~C--f~CP~C~~~L~~~ 65 (483)
T PF05502_consen 6 YFCEHCHKIR------------CPRCVSEEID-SYYCPNCLFEVPSSEARSEKNRCSRNC--FDCPICFSPLSVR 65 (483)
T ss_pred eecccccccC------------Chhhcccccc-eeECccccccCChhhheeccceecccc--ccCCCCCCcceeE
Confidence 7788776552 2233333322 344555544444332 2456666443 2688887776443
No 162
>PHA03096 p28-like protein; Provisional
Probab=54.03 E-value=7.1 Score=36.84 Aligned_cols=47 Identities=17% Similarity=0.328 Sum_probs=31.6
Q ss_pred CCCchhhhhhcccC---CccEEe-ccCCccChhhHHHHhcCC--CCCCCCCCc
Q 024483 151 HHCPICYEYLFDSL---RNTTVM-KCGHTMHCECYHEMIKRD--KYCCPICSK 197 (267)
Q Consensus 151 ~~CpICle~lf~s~---~~v~~L-pCGH~~H~~C~~~~~~~~--~~~CPiCrk 197 (267)
-.|-||+|...... ..--.| .|-|.|-..|+..|.... ..+||.|+.
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 46899998866432 111234 699999999999999643 334555554
No 163
>PF13597 NRDD: Anaerobic ribonucleoside-triphosphate reductase; PDB: 1HK8_A 1H78_A 1H7A_A 1H79_A 1H7B_A.
Probab=53.07 E-value=10 Score=38.68 Aligned_cols=57 Identities=23% Similarity=0.282 Sum_probs=25.4
Q ss_pred chhHHhHHhHHHHHhcCCChhhhcCeeEEEcCCCCCccccceeEeeecCCCCCCccccccCCC
Q 024483 201 DMSRTWKRIDEEIEATVMPEDYRHKKVWILCNDCNDTTEVYFHIIGQKCSHCKSYNTRSIAPP 263 (267)
Q Consensus 201 dm~~~~~~lD~~i~~~pmP~~y~~~~v~I~CnDC~~~s~~~fH~lg~kC~~C~SyNT~~~~~~ 263 (267)
+.++.+..++.......+|----+ ...-.|++||..... +.+|+.|||-|+.++++.
T Consensus 465 n~~al~~lv~~~~~~~~i~Y~~in-~~~~~C~~CG~~~~~-----~~~CP~CGs~~~~~~~Rv 521 (546)
T PF13597_consen 465 NPEALEKLVRYAMENTGIPYFTIN-PPIDICPDCGYIGGE-----GDKCPKCGSENIEVYSRV 521 (546)
T ss_dssp -HHHHHHHHHHHHH--H-SEEEEE---EEEETTT---S-------EEE-CCC----EEEEB-S
T ss_pred CHHHHHHHHHHHHHhCCCCeEEEe-cCcccccCCCcCCCC-----CCCCCCCCCcccceEEEe
Confidence 445555555655554555533222 234679999987653 568999999998887653
No 164
>PRK00415 rps27e 30S ribosomal protein S27e; Reviewed
Probab=51.46 E-value=8 Score=28.35 Aligned_cols=35 Identities=31% Similarity=0.510 Sum_probs=25.6
Q ss_pred eeeeCCCCccccc------cccCCcCCCccceeeccccccc
Q 024483 65 QVICSVCDTEQPV------AQVCTNCGVNMGEYFCDICKFY 99 (267)
Q Consensus 65 ~v~C~~C~~~q~v------~~~C~~Cg~~f~~y~C~~C~l~ 99 (267)
.|.|..|+.+|.+ ...|..||..+++-.=.+-+|.
T Consensus 11 ~VkCp~C~n~q~vFsha~t~V~C~~Cg~~L~~PtGGKa~i~ 51 (59)
T PRK00415 11 KVKCPDCGNEQVVFSHASTVVRCLVCGKTLAEPTGGKAKIK 51 (59)
T ss_pred EEECCCCCCeEEEEecCCcEEECcccCCCcccCCCcceeee
Confidence 6889999999876 2479999988877655544443
No 165
>KOG1812 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=50.58 E-value=7.6 Score=37.99 Aligned_cols=36 Identities=31% Similarity=0.664 Sum_probs=27.4
Q ss_pred CCCCchhh-hhhcccCCccEEeccCCccChhhHHHHhc
Q 024483 150 HHHCPICY-EYLFDSLRNTTVMKCGHTMHCECYHEMIK 186 (267)
Q Consensus 150 ~~~CpICl-e~lf~s~~~v~~LpCGH~~H~~C~~~~~~ 186 (267)
...|+||. |+.+ ......++.|||.|...|..++++
T Consensus 146 ~~~C~iC~~e~~~-~~~~f~~~~C~H~fC~~C~k~~ie 182 (384)
T KOG1812|consen 146 KEECGICFVEDPE-AEDMFSVLKCGHRFCKDCVKQHIE 182 (384)
T ss_pred cccCccCcccccc-HhhhHHHhcccchhhhHHhHHHhh
Confidence 56899999 5433 323333789999999999999987
No 166
>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional
Probab=50.23 E-value=10 Score=27.84 Aligned_cols=34 Identities=24% Similarity=0.663 Sum_probs=25.2
Q ss_pred cceeeeCCCCccccccccCCcCCCccceeecccccc
Q 024483 63 VKQVICSVCDTEQPVAQVCTNCGVNMGEYFCDICKF 98 (267)
Q Consensus 63 ~~~v~C~~C~~~q~v~~~C~~Cg~~f~~y~C~~C~l 98 (267)
..+-.|..|+.+. -..|..|....+.|-|++|.|
T Consensus 23 ~~~F~CPnCG~~~--I~RC~~CRk~~~~Y~CP~CGF 56 (59)
T PRK14890 23 AVKFLCPNCGEVI--IYRCEKCRKQSNPYTCPKCGF 56 (59)
T ss_pred cCEeeCCCCCCee--EeechhHHhcCCceECCCCCC
Confidence 4577888887642 236888888888888888876
No 167
>PF10058 DUF2296: Predicted integral membrane metal-binding protein (DUF2296); InterPro: IPR019273 This domain, found mainly in the eukaryotic lunapark proteins, has no known function [].
Probab=49.88 E-value=21 Score=25.41 Aligned_cols=47 Identities=19% Similarity=0.427 Sum_probs=31.0
Q ss_pred HHhHHHHHhcCCChhhhcCeeEEEcCCCCCcc----ccceeEeeecCCCCCCcc
Q 024483 207 KRIDEEIEATVMPEDYRHKKVWILCNDCNDTT----EVYFHIIGQKCSHCKSYN 256 (267)
Q Consensus 207 ~~lD~~i~~~pmP~~y~~~~v~I~CnDC~~~s----~~~fH~lg~kC~~C~SyN 256 (267)
+.||.++.+-|+.++ .+--+.|.-|.... ...|-.|--+|+.|+..|
T Consensus 4 ki~d~L~G~d~~~~~---~r~aLIC~~C~~hNGla~~~~~~~i~y~C~~Cg~~N 54 (54)
T PF10058_consen 4 KILDVLLGDDPTSPS---NRYALICSKCFSHNGLAPKEEFEEIQYRCPYCGALN 54 (54)
T ss_pred HHHHHHhCCCCcccc---CceeEECcccchhhcccccccCCceEEEcCCCCCcC
Confidence 457777777774433 23346699998653 233445677999999987
No 168
>KOG1609 consensus Protein involved in mRNA turnover and stability [RNA processing and modification]
Probab=48.67 E-value=7 Score=35.70 Aligned_cols=51 Identities=24% Similarity=0.374 Sum_probs=38.5
Q ss_pred CCCCchhhhhhcccCCccEEecc-----CCccChhhHHHHhcC-CCCCCCCCCcccc
Q 024483 150 HHHCPICYEYLFDSLRNTTVMKC-----GHTMHCECYHEMIKR-DKYCCPICSKSVI 200 (267)
Q Consensus 150 ~~~CpICle~lf~s~~~v~~LpC-----GH~~H~~C~~~~~~~-~~~~CPiCrks~~ 200 (267)
+..|=||.+..+.+.......|| ....|+.|++.|+.. +..+|.+|.....
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 36799999987655333455677 288899999999973 4678999998664
No 169
>PHA00626 hypothetical protein
Probab=47.52 E-value=12 Score=27.36 Aligned_cols=34 Identities=18% Similarity=0.400 Sum_probs=23.3
Q ss_pred eeeCCCCccccccccCCcCCCccceeeccccccccC
Q 024483 66 VICSVCDTEQPVAQVCTNCGVNMGEYFCDICKFYDD 101 (267)
Q Consensus 66 v~C~~C~~~q~v~~~C~~Cg~~f~~y~C~~C~l~dd 101 (267)
|.|..|+..+-+ .|..|...-++|-|..|.+++.
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 467777765444 5666666777888888877754
No 170
>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=46.72 E-value=14 Score=34.25 Aligned_cols=48 Identities=25% Similarity=0.607 Sum_probs=22.0
Q ss_pred cceeeeCCCCcccccc-ccCCcCCCccceeeccccccc--cCCCCcCeeecCCCC
Q 024483 63 VKQVICSVCDTEQPVA-QVCTNCGVNMGEYFCDICKFY--DDDIEKGQFHCDDCG 114 (267)
Q Consensus 63 ~~~v~C~~C~~~q~v~-~~C~~Cg~~f~~y~C~~C~l~--dd~~~k~~yHC~~Cg 114 (267)
.+-+.|+.|+++-.+. ..|++||..-..-+ .+| ++++.-.++-|+.||
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 3678999999998774 68999998765433 223 333444555555554
No 171
>KOG0298 consensus DEAD box-containing helicase-like transcription factor/DNA repair protein [Replication, recombination and repair]
Probab=46.67 E-value=13 Score=41.71 Aligned_cols=53 Identities=30% Similarity=0.636 Sum_probs=42.1
Q ss_pred CCCCCCchhhhhhcccCCccEEeccCCccChhhHHHHhcCCCCCCCCCCccccchhH
Q 024483 148 SMHHHCPICYEYLFDSLRNTTVMKCGHTMHCECYHEMIKRDKYCCPICSKSVIDMSR 204 (267)
Q Consensus 148 ~~~~~CpICle~lf~s~~~v~~LpCGH~~H~~C~~~~~~~~~~~CPiCrks~~dm~~ 204 (267)
+....|+||++-|-. .-.+..|||.+-..|+..|+. .+..||+|.....|...
T Consensus 1151 ~~~~~c~ic~dil~~---~~~I~~cgh~~c~~c~~~~l~-~~s~~~~~ksi~~dfg~ 1203 (1394)
T KOG0298|consen 1151 SGHFVCEICLDILRN---QGGIAGCGHEPCCRCDELWLY-ASSRCPICKSIKGDFGT 1203 (1394)
T ss_pred hcccchHHHHHHHHh---cCCeeeechhHhhhHHHHHHH-HhccCcchhhhhhhhcc
Confidence 445589999998743 234678999999999999998 57899999977666543
No 172
>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=46.26 E-value=15 Score=37.57 Aligned_cols=56 Identities=21% Similarity=0.310 Sum_probs=34.8
Q ss_pred chhHHhHHhHHHHHhcCCChhhhcCeeEEEcCCCCCccccceeEeeecCCCCCCccccccCC
Q 024483 201 DMSRTWKRIDEEIEATVMPEDYRHKKVWILCNDCNDTTEVYFHIIGQKCSHCKSYNTRSIAP 262 (267)
Q Consensus 201 dm~~~~~~lD~~i~~~pmP~~y~~~~v~I~CnDC~~~s~~~fH~lg~kC~~C~SyNT~~~~~ 262 (267)
+-++++..++.......++-. -+..+. .|++||.... -++.+|+.|||-|+.++++
T Consensus 493 n~~al~~lv~~a~~~~~~y~~-~~~p~~-~C~~CG~~~~----~~~~~CP~CGs~~~~~~~R 548 (555)
T cd01675 493 NPEALEALVKKAAKRGVIYFG-INTPID-ICNDCGYIGE----GEGFKCPKCGSEDVEVISR 548 (555)
T ss_pred CHHHHHHHHHHHHHcCCceEE-EecCCc-cCCCCCCCCc----CCCCCCcCCCCcCceEEEe
Confidence 344455555554443344433 334455 9999997553 3457999999998776654
No 173
>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=45.42 E-value=18 Score=25.91 Aligned_cols=29 Identities=24% Similarity=0.752 Sum_probs=22.2
Q ss_pred eEEEcCCCCCccccceeEeeecCCCCCCcccccc
Q 024483 227 VWILCNDCNDTTEVYFHIIGQKCSHCKSYNTRSI 260 (267)
Q Consensus 227 v~I~CnDC~~~s~~~fH~lg~kC~~C~SyNT~~~ 260 (267)
..+.|..||+. ...| +-|+.||.|+-+++
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 45789999973 4456 45999999998875
No 174
>PF15353 HECA: Headcase protein family homologue
Probab=45.28 E-value=10 Score=30.89 Aligned_cols=16 Identities=31% Similarity=0.650 Sum_probs=13.8
Q ss_pred ccCCccChhhHHHHhc
Q 024483 171 KCGHTMHCECYHEMIK 186 (267)
Q Consensus 171 pCGH~~H~~C~~~~~~ 186 (267)
|-|+.||+.||++|-.
T Consensus 39 p~~~~MH~~CF~~wE~ 54 (107)
T PF15353_consen 39 PFGQYMHRECFEKWED 54 (107)
T ss_pred CCCCchHHHHHHHHHH
Confidence 3499999999999965
No 175
>PF14569 zf-UDP: Zinc-binding RING-finger; PDB: 1WEO_A.
Probab=44.65 E-value=21 Score=27.71 Aligned_cols=52 Identities=19% Similarity=0.389 Sum_probs=24.6
Q ss_pred CCCCCCchhhhhhcccCCccEE---eccCCccChhhHHHHhcCCCCCCCCCCccc
Q 024483 148 SMHHHCPICYEYLFDSLRNTTV---MKCGHTMHCECYHEMIKRDKYCCPICSKSV 199 (267)
Q Consensus 148 ~~~~~CpICle~lf~s~~~v~~---LpCGH~~H~~C~~~~~~~~~~~CPiCrks~ 199 (267)
...+.|-||.|++-...+.-.+ .-|+-.+.+.||+--++.++..||.|+...
T Consensus 7 ~~~qiCqiCGD~VGl~~~Ge~FVAC~eC~fPvCr~CyEYErkeg~q~CpqCkt~y 61 (80)
T PF14569_consen 7 LNGQICQICGDDVGLTENGEVFVACHECAFPVCRPCYEYERKEGNQVCPQCKTRY 61 (80)
T ss_dssp -SS-B-SSS--B--B-SSSSB--S-SSS-----HHHHHHHHHTS-SB-TTT--B-
T ss_pred cCCcccccccCccccCCCCCEEEEEcccCCccchhHHHHHhhcCcccccccCCCc
Confidence 4567899999987433332222 368999999999988887889999999443
No 176
>KOG1312 consensus DHHC-type Zn-finger proteins [General function prediction only]
Probab=44.35 E-value=7.4 Score=37.14 Aligned_cols=32 Identities=31% Similarity=0.782 Sum_probs=28.2
Q ss_pred CCCCcccccCccceeecCccCccccccccCcceee
Q 024483 111 DDCGICRIGGRENYFHCKRCGSCYSTSLRNNHLCI 145 (267)
Q Consensus 111 ~~CgiCR~G~~~~~fHC~~C~~C~s~~l~~~H~C~ 145 (267)
.+|..|++.+.-...||..||.|+.+- +|.|+
T Consensus 149 ~kCSTCki~KPARSKHCsiCNrCV~rf---DHHCi 180 (341)
T KOG1312|consen 149 VKCSTCKIRKPARSKHCSICNRCVHRF---DHHCI 180 (341)
T ss_pred CccccccCCCccccccchHHHHHHHHh---ccceE
Confidence 679999999988899999999999864 78886
No 177
>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=44.06 E-value=20 Score=23.61 Aligned_cols=34 Identities=29% Similarity=0.629 Sum_probs=16.5
Q ss_pred cCCcCCCccceeeccccccccCCCCcCeeecCCCC
Q 024483 80 VCTNCGVNMGEYFCDICKFYDDDIEKGQFHCDDCG 114 (267)
Q Consensus 80 ~C~~Cg~~f~~y~C~~C~l~dd~~~k~~yHC~~Cg 114 (267)
.|++||+.-+.|+ .+=--=-|++..-.|.|-+||
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 5788888776665 100000234555666666665
No 178
>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=44.03 E-value=11 Score=27.87 Aligned_cols=13 Identities=38% Similarity=0.738 Sum_probs=11.9
Q ss_pred ecCCCCCCccccc
Q 024483 247 QKCSHCKSYNTRS 259 (267)
Q Consensus 247 ~kC~~C~SyNT~~ 259 (267)
++|+.|.|.||+.
T Consensus 6 ~~CPRC~S~nTKF 18 (63)
T PF02701_consen 6 LPCPRCDSTNTKF 18 (63)
T ss_pred CCCCCcCCCCCEE
Confidence 6999999999986
No 179
>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=43.64 E-value=19 Score=25.09 Aligned_cols=12 Identities=33% Similarity=1.251 Sum_probs=6.7
Q ss_pred CCCCCCCccccc
Q 024483 190 YCCPICSKSVID 201 (267)
Q Consensus 190 ~~CPiCrks~~d 201 (267)
..||+|.+++.+
T Consensus 21 ~~CPlC~r~l~~ 32 (54)
T PF04423_consen 21 GCCPLCGRPLDE 32 (54)
T ss_dssp EE-TTT--EE-H
T ss_pred CcCCCCCCCCCH
Confidence 389999999984
No 180
>PF10122 Mu-like_Com: Mu-like prophage protein Com; InterPro: IPR019294 Members of this entry belong to the Com family of proteins that act as translational regulators of mom [, ].
Probab=43.54 E-value=20 Score=25.51 Aligned_cols=35 Identities=26% Similarity=0.430 Sum_probs=21.7
Q ss_pred EEEcCCCCCccc--cceeEeeecCCCCCCccccccCC
Q 024483 228 WILCNDCNDTTE--VYFHIIGQKCSHCKSYNTRSIAP 262 (267)
Q Consensus 228 ~I~CnDC~~~s~--~~fH~lg~kC~~C~SyNT~~~~~ 262 (267)
.|.|-.|++.-. ..|-.|-.||+.|+..|......
T Consensus 4 eiRC~~CnklLa~~g~~~~leIKCpRC~tiN~~~a~~ 40 (51)
T PF10122_consen 4 EIRCGHCNKLLAKAGEVIELEIKCPRCKTINHVRATS 40 (51)
T ss_pred ceeccchhHHHhhhcCccEEEEECCCCCccceEeccC
Confidence 356666664321 12335778999999998776543
No 181
>COG1656 Uncharacterized conserved protein [Function unknown]
Probab=43.42 E-value=17 Score=31.86 Aligned_cols=49 Identities=24% Similarity=0.388 Sum_probs=34.7
Q ss_pred CCCCCCCCccccchhHHhHHhHHHHHhcCCC-hhhhcCeeEEEcCCCCCccccceeE
Q 024483 189 KYCCPICSKSVIDMSRTWKRIDEEIEATVMP-EDYRHKKVWILCNDCNDTTEVYFHI 244 (267)
Q Consensus 189 ~~~CPiCrks~~dm~~~~~~lD~~i~~~pmP-~~y~~~~v~I~CnDC~~~s~~~fH~ 244 (267)
-.+||.|+-.+...+. +.....+| ..|.+......|--|++.-+..-||
T Consensus 97 ~~RCp~CN~~L~~vs~-------eev~~~Vp~~~~~~~~~f~~C~~CgkiYW~GsHw 146 (165)
T COG1656 97 FSRCPECNGELEKVSR-------EEVKEKVPEKVYRNYEEFYRCPKCGKIYWKGSHW 146 (165)
T ss_pred cccCcccCCEeccCcH-------HHHhhccchhhhhcccceeECCCCcccccCchHH
Confidence 4689999999986543 23333344 4477767778899999988777776
No 182
>PRK03564 formate dehydrogenase accessory protein FdhE; Provisional
Probab=43.20 E-value=23 Score=33.92 Aligned_cols=23 Identities=35% Similarity=1.003 Sum_probs=17.2
Q ss_pred EEEcCCCCCccccceeEeeecCCCCCC
Q 024483 228 WILCNDCNDTTEVYFHIIGQKCSHCKS 254 (267)
Q Consensus 228 ~I~CnDC~~~s~~~fH~lg~kC~~C~S 254 (267)
...|+-|+ ..+|+.-.||++||+
T Consensus 212 yL~CslC~----teW~~~R~~C~~Cg~ 234 (309)
T PRK03564 212 YLHCNLCE----SEWHVVRVKCSNCEQ 234 (309)
T ss_pred EEEcCCCC----CcccccCccCCCCCC
Confidence 57788777 567777788888884
No 183
>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=43.17 E-value=20 Score=23.88 Aligned_cols=31 Identities=29% Similarity=0.508 Sum_probs=20.1
Q ss_pred EEEcCCCCCccccceeE---eeecCCCCCCcccc
Q 024483 228 WILCNDCNDTTEVYFHI---IGQKCSHCKSYNTR 258 (267)
Q Consensus 228 ~I~CnDC~~~s~~~fH~---lg~kC~~C~SyNT~ 258 (267)
...|.+||...++-..+ ....|+.||+-+.+
T Consensus 5 ey~C~~Cg~~fe~~~~~~~~~~~~CP~Cg~~~~~ 38 (42)
T PF09723_consen 5 EYRCEECGHEFEVLQSISEDDPVPCPECGSTEVR 38 (42)
T ss_pred EEEeCCCCCEEEEEEEcCCCCCCcCCCCCCCceE
Confidence 46788888766544322 34689999985543
No 184
>COG3809 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=43.10 E-value=18 Score=28.15 Aligned_cols=51 Identities=31% Similarity=0.585 Sum_probs=32.6
Q ss_pred CCchhhhhhcccCCccEEeccCCccChhhHHHHhcCCCCCCCCCCccccchhHHhHHhHHHHHhc--CCChhhhcC
Q 024483 152 HCPICYEYLFDSLRNTTVMKCGHTMHCECYHEMIKRDKYCCPICSKSVIDMSRTWKRIDEEIEAT--VMPEDYRHK 225 (267)
Q Consensus 152 ~CpICle~lf~s~~~v~~LpCGH~~H~~C~~~~~~~~~~~CPiCrks~~dm~~~~~~lD~~i~~~--pmP~~y~~~ 225 (267)
.||||.-.|-.+...-+ .-..||-||-.-+|. ..||.+|+.. |-|.+|+..
T Consensus 3 lCP~C~v~l~~~~rs~v-------------------EiD~CPrCrGVWLDr----GELdKli~r~r~pqpa~ys~~ 55 (88)
T COG3809 3 LCPICGVELVMSVRSGV-------------------EIDYCPRCRGVWLDR----GELDKLIERSRYPQPAEYSQP 55 (88)
T ss_pred ccCcCCceeeeeeecCc-------------------eeeeCCccccEeecc----hhHHHHHHHhcCCCCcccCCc
Confidence 58999888765432111 125799999766665 4577777654 566667654
No 185
>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=42.02 E-value=6.7 Score=25.74 Aligned_cols=27 Identities=33% Similarity=0.671 Sum_probs=13.2
Q ss_pred cCCcCCCccceeeccccccccCCCCcCeeecCCCCc
Q 024483 80 VCTNCGVNMGEYFCDICKFYDDDIEKGQFHCDDCGI 115 (267)
Q Consensus 80 ~C~~Cg~~f~~y~C~~C~l~dd~~~k~~yHC~~Cgi 115 (267)
.|++||+.++.+| ++.|..--||.||-
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 3555666555443 23454555666653
No 186
>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=41.98 E-value=14 Score=30.75 Aligned_cols=48 Identities=25% Similarity=0.546 Sum_probs=34.9
Q ss_pred CCCccceeeccccccccCCCCcCeeecCCCCcccccCccceeecCccCcccccc
Q 024483 84 CGVNMGEYFCDICKFYDDDIEKGQFHCDDCGICRIGGRENYFHCKRCGSCYSTS 137 (267)
Q Consensus 84 Cg~~f~~y~C~~C~l~dd~~~k~~yHC~~CgiCR~G~~~~~fHC~~C~~C~s~~ 137 (267)
-+......+|..|+.+-- ....||..||.|..+- -.||.-=|.|+...
T Consensus 42 ~~~~~~~~~C~~C~~~kp---~Rs~HC~~C~~CV~~~---DHHC~w~~~cIG~~ 89 (174)
T PF01529_consen 42 DDENGELKYCSTCKIIKP---PRSHHCRVCNRCVLRF---DHHCPWLGNCIGRR 89 (174)
T ss_pred cccCCCCEECcccCCcCC---Ccceeccccccccccc---cccchhhccccccc
Confidence 456778889999998843 3477888888887763 45777777777653
No 187
>PRK00432 30S ribosomal protein S27ae; Validated
Probab=41.94 E-value=19 Score=25.28 Aligned_cols=9 Identities=44% Similarity=1.531 Sum_probs=5.0
Q ss_pred CeeecCCCC
Q 024483 106 GQFHCDDCG 114 (267)
Q Consensus 106 ~~yHC~~Cg 114 (267)
+.|+|..||
T Consensus 36 ~r~~C~~Cg 44 (50)
T PRK00432 36 DRWHCGKCG 44 (50)
T ss_pred CcEECCCcC
Confidence 455555555
No 188
>COG1996 RPC10 DNA-directed RNA polymerase, subunit RPC10 (contains C4-type Zn-finger) [Transcription]
Probab=41.61 E-value=18 Score=25.57 Aligned_cols=29 Identities=34% Similarity=0.619 Sum_probs=19.7
Q ss_pred cceeecccc-ccccCCCCcCeeecCCCCcc
Q 024483 88 MGEYFCDIC-KFYDDDIEKGQFHCDDCGIC 116 (267)
Q Consensus 88 f~~y~C~~C-~l~dd~~~k~~yHC~~CgiC 116 (267)
+..|-|..| +.++.+....-.-|+.||.=
T Consensus 4 ~~~Y~C~~Cg~~~~~~~~~~~irCp~Cg~r 33 (49)
T COG1996 4 MMEYKCARCGREVELDQETRGIRCPYCGSR 33 (49)
T ss_pred eEEEEhhhcCCeeehhhccCceeCCCCCcE
Confidence 445666666 34565667788889998853
No 189
>PF13453 zf-TFIIB: Transcription factor zinc-finger
Probab=41.15 E-value=23 Score=23.33 Aligned_cols=26 Identities=23% Similarity=0.579 Sum_probs=14.3
Q ss_pred cCCcCCCccceeeccccccccCCCCcCeeecCCCC
Q 024483 80 VCTNCGVNMGEYFCDICKFYDDDIEKGQFHCDDCG 114 (267)
Q Consensus 80 ~C~~Cg~~f~~y~C~~C~l~dd~~~k~~yHC~~Cg 114 (267)
.||.|+..|..+. + .+-.++.|+.||
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 3667766665442 1 124566666665
No 190
>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=40.82 E-value=15 Score=22.53 Aligned_cols=20 Identities=20% Similarity=0.667 Sum_probs=6.2
Q ss_pred CCcccccCc-cceeecCccCc
Q 024483 113 CGICRIGGR-ENYFHCKRCGS 132 (267)
Q Consensus 113 CgiCR~G~~-~~~fHC~~C~~ 132 (267)
|.+|+..+. ..+++|..|+.
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 445554433 25677776664
No 191
>COG2051 RPS27A Ribosomal protein S27E [Translation, ribosomal structure and biogenesis]
Probab=40.53 E-value=12 Score=28.03 Aligned_cols=28 Identities=36% Similarity=0.692 Sum_probs=21.8
Q ss_pred ceeeeCCCCccccc------cccCCcCCCcccee
Q 024483 64 KQVICSVCDTEQPV------AQVCTNCGVNMGEY 91 (267)
Q Consensus 64 ~~v~C~~C~~~q~v------~~~C~~Cg~~f~~y 91 (267)
-.|.|.-|+.+|.+ ...|..||..+++-
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 36899999999987 24799998887653
No 192
>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=40.12 E-value=21 Score=22.58 Aligned_cols=24 Identities=33% Similarity=0.915 Sum_probs=15.7
Q ss_pred eeccccccccCCCCcCeeecCCCCc
Q 024483 91 YFCDICKFYDDDIEKGQFHCDDCGI 115 (267)
Q Consensus 91 y~C~~C~l~dd~~~k~~yHC~~Cgi 115 (267)
|-|.+|-+.-+ +.+.++.|+.||.
T Consensus 2 ~~C~~CGy~y~-~~~~~~~CP~Cg~ 25 (33)
T cd00350 2 YVCPVCGYIYD-GEEAPWVCPVCGA 25 (33)
T ss_pred EECCCCCCEEC-CCcCCCcCcCCCC
Confidence 66777765532 3457788888875
No 193
>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=39.94 E-value=26 Score=23.27 Aligned_cols=8 Identities=50% Similarity=1.315 Sum_probs=4.2
Q ss_pred cCCcCCCc
Q 024483 80 VCTNCGVN 87 (267)
Q Consensus 80 ~C~~Cg~~ 87 (267)
.||+||..
T Consensus 2 ~Cp~Cg~~ 9 (43)
T PF08271_consen 2 KCPNCGSK 9 (43)
T ss_dssp SBTTTSSS
T ss_pred CCcCCcCC
Confidence 35555554
No 194
>PRK00366 ispG 4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase; Reviewed
Probab=38.31 E-value=44 Score=32.71 Aligned_cols=54 Identities=24% Similarity=0.503 Sum_probs=42.9
Q ss_pred CCCCCCCCccccchhHHhHHhHHHHHhcCCChhhhcCeeEEEc--CCCCCccccceeEee
Q 024483 189 KYCCPICSKSVIDMSRTWKRIDEEIEATVMPEDYRHKKVWILC--NDCNDTTEVYFHIIG 246 (267)
Q Consensus 189 ~~~CPiCrks~~dm~~~~~~lD~~i~~~pmP~~y~~~~v~I~C--nDC~~~s~~~fH~lg 246 (267)
-..||-|++...|+-..=..+|+.+...++| -+....=| |.|++.....+=+.|
T Consensus 268 IisCPgCgR~~~D~~~la~~vee~~~~~~~P----lkIAVmGC~VNgpGEa~~aDIGIaG 323 (360)
T PRK00366 268 VISCPTCGRTEFDVIQELAEVEQRLEHIKMP----LKVAVMGCVVNGPGEAKEADIGIAG 323 (360)
T ss_pred EEECCCCCCCcccHHHHHHHHHHHhcCCCCC----cEEEEeCCCCCCCCchhhCcEeEec
Confidence 3579999999999988888999999999988 24456779 999987766654443
No 195
>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=37.85 E-value=26 Score=23.65 Aligned_cols=21 Identities=38% Similarity=0.917 Sum_probs=9.9
Q ss_pred eecCCCCcccccCccceeecCccC
Q 024483 108 FHCDDCGICRIGGRENYFHCKRCG 131 (267)
Q Consensus 108 yHC~~CgiCR~G~~~~~fHC~~C~ 131 (267)
|.|+.|+. -+-| ..|||.+|.
T Consensus 1 ~~C~~C~~-~i~g--~r~~C~~C~ 21 (46)
T cd02249 1 YSCDGCLK-PIVG--VRYHCLVCE 21 (46)
T ss_pred CCCcCCCC-CCcC--CEEECCCCC
Confidence 34555554 2222 466666554
No 196
>PF13717 zinc_ribbon_4: zinc-ribbon domain
Probab=37.85 E-value=19 Score=23.37 Aligned_cols=10 Identities=40% Similarity=0.949 Sum_probs=5.4
Q ss_pred ceeeeCCCCc
Q 024483 64 KQVICSVCDT 73 (267)
Q Consensus 64 ~~v~C~~C~~ 73 (267)
..|.|+.|++
T Consensus 24 ~~v~C~~C~~ 33 (36)
T PF13717_consen 24 RKVRCSKCGH 33 (36)
T ss_pred cEEECCCCCC
Confidence 3555555554
No 197
>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=37.45 E-value=17 Score=30.94 Aligned_cols=16 Identities=25% Similarity=0.553 Sum_probs=14.4
Q ss_pred eecCCCCCCccccccC
Q 024483 246 GQKCSHCKSYNTRSIA 261 (267)
Q Consensus 246 g~kC~~C~SyNT~~~~ 261 (267)
...|+.|||-||+++.
T Consensus 105 ~~~cp~c~s~~t~~~s 120 (146)
T TIGR02159 105 SVQCPRCGSADTTITS 120 (146)
T ss_pred CCcCCCCCCCCcEeec
Confidence 3699999999999986
No 198
>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=36.95 E-value=17 Score=22.87 Aligned_cols=16 Identities=38% Similarity=1.028 Sum_probs=6.9
Q ss_pred CCcCCCccceeeccccc
Q 024483 81 CTNCGVNMGEYFCDICK 97 (267)
Q Consensus 81 C~~Cg~~f~~y~C~~C~ 97 (267)
|..||. .++|-|+.|.
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 344444 5555555553
No 199
>PF05290 Baculo_IE-1: Baculovirus immediate-early protein (IE-0); InterPro: IPR007954 This entry contains the Baculovirus immediate-early protein IE-0.
Probab=35.88 E-value=18 Score=30.84 Aligned_cols=47 Identities=30% Similarity=0.646 Sum_probs=33.4
Q ss_pred CCCchhhhhhcccCCccEEe-c---cCCccChhhHHHHhcC--CCCCCCCCCccccc
Q 024483 151 HHCPICYEYLFDSLRNTTVM-K---CGHTMHCECYHEMIKR--DKYCCPICSKSVID 201 (267)
Q Consensus 151 ~~CpICle~lf~s~~~v~~L-p---CGH~~H~~C~~~~~~~--~~~~CPiCrks~~d 201 (267)
-+|-||.|. | .+.+.| | ||=.+...|+.++-+. ..-.||+|+.|+-.
T Consensus 81 YeCnIC~et---S-~ee~FLKPneCCgY~iCn~Cya~LWK~~~~ypvCPvCkTSFKs 133 (140)
T PF05290_consen 81 YECNICKET---S-AEERFLKPNECCGYSICNACYANLWKFCNLYPVCPVCKTSFKS 133 (140)
T ss_pred eeccCcccc---c-chhhcCCcccccchHHHHHHHHHHHHHcccCCCCCcccccccc
Confidence 368888875 3 234455 3 8999999999884442 25679999999864
No 200
>KOG2907 consensus RNA polymerase I transcription factor TFIIS, subunit A12.2/RPA12 [Transcription]
Probab=35.67 E-value=13 Score=30.65 Aligned_cols=19 Identities=37% Similarity=0.835 Sum_probs=15.7
Q ss_pred EeeecCCCCC----CccccccCC
Q 024483 244 IIGQKCSHCK----SYNTRSIAP 262 (267)
Q Consensus 244 ~lg~kC~~C~----SyNT~~~~~ 262 (267)
.|-+||+.|| ||+|+|++-
T Consensus 72 ~I~~kCpkCghe~m~Y~T~QlRS 94 (116)
T KOG2907|consen 72 VIKHKCPKCGHEEMSYHTLQLRS 94 (116)
T ss_pred chhccCcccCCchhhhhhhhccc
Confidence 4668999986 899999974
No 201
>PF13719 zinc_ribbon_5: zinc-ribbon domain
Probab=35.24 E-value=22 Score=23.12 Aligned_cols=9 Identities=33% Similarity=0.888 Sum_probs=4.6
Q ss_pred eeeeCCCCc
Q 024483 65 QVICSVCDT 73 (267)
Q Consensus 65 ~v~C~~C~~ 73 (267)
.|.|+.|++
T Consensus 25 ~vrC~~C~~ 33 (37)
T PF13719_consen 25 KVRCPKCGH 33 (37)
T ss_pred EEECCCCCc
Confidence 555555544
No 202
>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=35.19 E-value=19 Score=26.00 Aligned_cols=34 Identities=24% Similarity=0.457 Sum_probs=19.6
Q ss_pred eeeeCCCCccccc------cccCCcCCCccceeecccccc
Q 024483 65 QVICSVCDTEQPV------AQVCTNCGVNMGEYFCDICKF 98 (267)
Q Consensus 65 ~v~C~~C~~~q~v------~~~C~~Cg~~f~~y~C~~C~l 98 (267)
.|.|..|..+|.+ ...|..||..+++-.=.+-+|
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 5778888888776 236888888777655444444
No 203
>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=34.89 E-value=22 Score=22.52 Aligned_cols=23 Identities=26% Similarity=0.710 Sum_probs=10.4
Q ss_pred cCCcCCCccceeeccccccccCCCCcCeeecCCCC
Q 024483 80 VCTNCGVNMGEYFCDICKFYDDDIEKGQFHCDDCG 114 (267)
Q Consensus 80 ~C~~Cg~~f~~y~C~~C~l~dd~~~k~~yHC~~Cg 114 (267)
.|+.|+..++- .+..+|-|+.||
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 57777776653 234678888876
No 204
>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=34.31 E-value=48 Score=31.33 Aligned_cols=47 Identities=19% Similarity=0.357 Sum_probs=28.3
Q ss_pred cCCCCCCCchhhhhhcccCCccEEeccC--CccChhhHHHHhcCCCCCCC
Q 024483 146 ENSMHHHCPICYEYLFDSLRNTTVMKCG--HTMHCECYHEMIKRDKYCCP 193 (267)
Q Consensus 146 e~~~~~~CpICle~lf~s~~~v~~LpCG--H~~H~~C~~~~~~~~~~~CP 193 (267)
+..+-..|+||+| |...+.+...|.=. =-=|+.||+.|-.-.+..||
T Consensus 26 d~~tLsfChiCfE-l~iegvpks~llHtkSlRGHrdCFEK~HlIanQ~~p 74 (285)
T PF06937_consen 26 DTETLSFCHICFE-LSIEGVPKSNLLHTKSLRGHRDCFEKYHLIANQDCP 74 (285)
T ss_pred cccceeecceeec-cccccCccccccccccccchHHHHHHHHHHHcCCCC
Confidence 3455567899988 44444444333210 01389999998654567898
No 205
>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=34.28 E-value=42 Score=32.07 Aligned_cols=23 Identities=35% Similarity=0.970 Sum_probs=17.1
Q ss_pred EEEcCCCCCccccceeEeeecCCCCCC
Q 024483 228 WILCNDCNDTTEVYFHIIGQKCSHCKS 254 (267)
Q Consensus 228 ~I~CnDC~~~s~~~fH~lg~kC~~C~S 254 (267)
...|+-|+ ..+|+.-.||++|++
T Consensus 210 yL~CslC~----teW~~~R~~C~~Cg~ 232 (305)
T TIGR01562 210 YLSCSLCA----TEWHYVRVKCSHCEE 232 (305)
T ss_pred EEEcCCCC----CcccccCccCCCCCC
Confidence 56787777 567777788888875
No 206
>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=34.23 E-value=13 Score=40.00 Aligned_cols=46 Identities=28% Similarity=0.686 Sum_probs=0.0
Q ss_pred ccCCcCCCccceeeccccccccCCCCcCeeecCCCCcccccCccceeecCccCcc
Q 024483 79 QVCTNCGVNMGEYFCDICKFYDDDIEKGQFHCDDCGICRIGGRENYFHCKRCGSC 133 (267)
Q Consensus 79 ~~C~~Cg~~f~~y~C~~C~l~dd~~~k~~yHC~~CgiCR~G~~~~~fHC~~C~~C 133 (267)
-.|++||..--.-.|+.|.-. ....|.|+.||+ ++.. .+|.+|+.=
T Consensus 656 r~Cp~Cg~~t~~~~Cp~CG~~----T~~~~~Cp~C~~-~~~~----~~C~~C~~~ 701 (900)
T PF03833_consen 656 RRCPKCGKETFYNRCPECGSH----TEPVYVCPDCGI-EVEE----DECPKCGRE 701 (900)
T ss_dssp -------------------------------------------------------
T ss_pred ccCcccCCcchhhcCcccCCc----cccceecccccc-ccCc----ccccccccc
Confidence 357777776666667766544 346777777776 2221 177777653
No 207
>KOG4185 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=33.92 E-value=8.6 Score=35.42 Aligned_cols=50 Identities=28% Similarity=0.536 Sum_probs=38.1
Q ss_pred CCCCchhhhhhc--ccCCccEEec--------cCCccChhhHHHHhcCCCCCCCCCCccc
Q 024483 150 HHHCPICYEYLF--DSLRNTTVMK--------CGHTMHCECYHEMIKRDKYCCPICSKSV 199 (267)
Q Consensus 150 ~~~CpICle~lf--~s~~~v~~Lp--------CGH~~H~~C~~~~~~~~~~~CPiCrks~ 199 (267)
...|.||...+. +......++. |||.+-..|.+..+.....+||.|++..
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 356999998755 2333334566 9999999999999875568999999864
No 208
>PRK00420 hypothetical protein; Validated
Probab=33.74 E-value=24 Score=29.00 Aligned_cols=29 Identities=38% Similarity=0.819 Sum_probs=22.2
Q ss_pred CCCCchhhhhhcccCCccEEeccCCccChhhHHHHhcCCCCCCCCCCcccc
Q 024483 150 HHHCPICYEYLFDSLRNTTVMKCGHTMHCECYHEMIKRDKYCCPICSKSVI 200 (267)
Q Consensus 150 ~~~CpICle~lf~s~~~v~~LpCGH~~H~~C~~~~~~~~~~~CPiCrks~~ 200 (267)
...||+|.-+||.. ..+...||.|+..+.
T Consensus 23 ~~~CP~Cg~pLf~l----------------------k~g~~~Cp~Cg~~~~ 51 (112)
T PRK00420 23 SKHCPVCGLPLFEL----------------------KDGEVVCPVHGKVYI 51 (112)
T ss_pred cCCCCCCCCcceec----------------------CCCceECCCCCCeee
Confidence 46799999998863 135778999998775
No 209
>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=33.43 E-value=14 Score=34.39 Aligned_cols=30 Identities=17% Similarity=0.595 Sum_probs=16.8
Q ss_pred eEEEcCCCCCccccceeEeeecCCCCCCcccccc
Q 024483 227 VWILCNDCNDTTEVYFHIIGQKCSHCKSYNTRSI 260 (267)
Q Consensus 227 v~I~CnDC~~~s~~~fH~lg~kC~~C~SyNT~~~ 260 (267)
-...|.-|+ ..+|+.-.+|++||+-+-..+
T Consensus 196 R~L~Cs~C~----t~W~~~R~~Cp~Cg~~~~~~l 225 (290)
T PF04216_consen 196 RYLHCSLCG----TEWRFVRIKCPYCGNTDHEKL 225 (290)
T ss_dssp EEEEETTT------EEE--TTS-TTT---SS-EE
T ss_pred EEEEcCCCC----CeeeecCCCCcCCCCCCCcce
Confidence 368899998 678888899999998776654
No 210
>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=32.96 E-value=31 Score=23.09 Aligned_cols=20 Identities=25% Similarity=0.861 Sum_probs=11.4
Q ss_pred eecCCCCcccccCccceeecCccC
Q 024483 108 FHCDDCGICRIGGRENYFHCKRCG 131 (267)
Q Consensus 108 yHC~~CgiCR~G~~~~~fHC~~C~ 131 (267)
|+|+.|+. +++ ..|||..|.
T Consensus 1 y~C~~C~~--~~~--~r~~C~~C~ 20 (41)
T cd02337 1 YTCNECKH--HVE--TRWHCTVCE 20 (41)
T ss_pred CcCCCCCC--cCC--CceECCCCc
Confidence 56666655 332 566776663
No 211
>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=32.35 E-value=27 Score=22.39 Aligned_cols=10 Identities=30% Similarity=1.066 Sum_probs=5.3
Q ss_pred cCeeecCCCC
Q 024483 105 KGQFHCDDCG 114 (267)
Q Consensus 105 k~~yHC~~Cg 114 (267)
.++-.|..||
T Consensus 15 ~~~irC~~CG 24 (32)
T PF03604_consen 15 GDPIRCPECG 24 (32)
T ss_dssp SSTSSBSSSS
T ss_pred CCcEECCcCC
Confidence 3444565555
No 212
>PF14952 zf-tcix: Putative treble-clef, zinc-finger, Zn-binding
Probab=32.08 E-value=22 Score=24.61 Aligned_cols=13 Identities=38% Similarity=1.004 Sum_probs=10.6
Q ss_pred ecCCCCCCccccc
Q 024483 247 QKCSHCKSYNTRS 259 (267)
Q Consensus 247 ~kC~~C~SyNT~~ 259 (267)
-||+.||.||-..
T Consensus 12 rkCp~CGt~NG~R 24 (44)
T PF14952_consen 12 RKCPKCGTYNGTR 24 (44)
T ss_pred ccCCcCcCccCcc
Confidence 3899999999544
No 213
>PF01907 Ribosomal_L37e: Ribosomal protein L37e; InterPro: IPR001569 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 consists of proteins of 56 to 96 amino-acid residues that share a highly conserved region located in the N-terminal part.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 4A19_A 4A1D_A 4A18_A 4A1B_A 1S1I_Y 3O5H_d 3IZS_l 3O58_d 2ZKR_2 3IZR_l ....
Probab=32.02 E-value=19 Score=26.11 Aligned_cols=28 Identities=36% Similarity=0.890 Sum_probs=20.6
Q ss_pred hcCeeEEEcCCCCCccccceeEeeecCCCCC
Q 024483 223 RHKKVWILCNDCNDTTEVYFHIIGQKCSHCK 253 (267)
Q Consensus 223 ~~~~v~I~CnDC~~~s~~~fH~lg~kC~~C~ 253 (267)
++.+..|+|.-||.+ .||+--..|..||
T Consensus 10 r~~ktH~~CrRCG~~---syH~qK~~CasCG 37 (55)
T PF01907_consen 10 RHNKTHTLCRRCGRR---SYHIQKKTCASCG 37 (55)
T ss_dssp S-S-SEEE-TTTSSE---EEETTTTEETTTB
T ss_pred cCCccEeeecccCCe---eeecCCCcccccC
Confidence 345689999999974 5787778899998
No 214
>PLN02189 cellulose synthase
Probab=31.99 E-value=39 Score=37.31 Aligned_cols=56 Identities=20% Similarity=0.444 Sum_probs=40.3
Q ss_pred ecCCCCCCCchhhhhhcccCCccEEe---ccCCccChhhHHHHhcCCCCCCCCCCcccc
Q 024483 145 IENSMHHHCPICYEYLFDSLRNTTVM---KCGHTMHCECYHEMIKRDKYCCPICSKSVI 200 (267)
Q Consensus 145 ~e~~~~~~CpICle~lf~s~~~v~~L---pCGH~~H~~C~~~~~~~~~~~CPiCrks~~ 200 (267)
+++...+.|.||.|++-...+.-... -||=-+.+.||+-=.++++..||-|+...-
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 45556779999999975332222333 378889999996666667889999997654
No 215
>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=31.94 E-value=36 Score=21.98 Aligned_cols=21 Identities=19% Similarity=0.363 Sum_probs=14.5
Q ss_pred ccCCcCCCccceeeccccccc
Q 024483 79 QVCTNCGVNMGEYFCDICKFY 99 (267)
Q Consensus 79 ~~C~~Cg~~f~~y~C~~C~l~ 99 (267)
..|..++...++|||..|+.+
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 467777777788888877654
No 216
>smart00661 RPOL9 RNA polymerase subunit 9.
Probab=31.53 E-value=38 Score=22.81 Aligned_cols=8 Identities=50% Similarity=1.510 Sum_probs=4.0
Q ss_pred eeecCCCC
Q 024483 107 QFHCDDCG 114 (267)
Q Consensus 107 ~yHC~~Cg 114 (267)
.|-|+.||
T Consensus 20 ~~vC~~Cg 27 (52)
T smart00661 20 RFVCRKCG 27 (52)
T ss_pred EEECCcCC
Confidence 44555544
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=31.38 E-value=28 Score=24.40 Aligned_cols=22 Identities=23% Similarity=0.883 Sum_probs=13.6
Q ss_pred ccccCC--cCCCc------cceeecccccc
Q 024483 77 VAQVCT--NCGVN------MGEYFCDICKF 98 (267)
Q Consensus 77 v~~~C~--~Cg~~------f~~y~C~~C~l 98 (267)
....|| .||.. ++|+||.+|.+
T Consensus 17 ~rk~CP~~~CG~GvFMA~H~dR~~CGKCg~ 46 (47)
T PF01599_consen 17 LRKECPSPRCGAGVFMAEHKDRHYCGKCGY 46 (47)
T ss_dssp SSEE-TSTTTTSSSEEEE-SSEEEETTTSS
T ss_pred hhhcCCCcccCCceEeeecCCCccCCCccc
Confidence 345788 78774 36777777754
No 218
>PF06827 zf-FPG_IleRS: Zinc finger found in FPG and IleRS; InterPro: IPR010663 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents a zinc finger domain found at the C-terminal in both DNA glycosylase/AP lyase enzymes and in isoleucyl tRNA synthetase. In these two types of enzymes, the C-terminal domain forms a zinc finger. Some related proteins may not bind zinc. DNA glycosylase/AP lyase enzymes are involved in base excision repair of DNA damaged by oxidation or by mutagenic agents. These enzymes have both DNA glycosylase activity (3.2.2 from EC) and AP lyase activity (4.2.99.18 from EC) []. Examples include formamidopyrimidine-DNA glycosylases (Fpg; MutM) and endonuclease VIII (Nei). Formamidopyrimidine-DNA glycosylases (Fpg, MutM) is a trifunctional DNA base excision repair enzyme that removes a wide range of oxidation-damaged bases (N-glycosylase activity; 3.2.2.23 from EC) and cleaves both the 3'- and 5'-phosphodiester bonds of the resulting apurinic/apyrimidinic site (AP lyase activity; 4.2.99.18 from EC). Fpg has a preference for oxidised purines, excising oxidized purine bases such as 7,8-dihydro-8-oxoguanine (8-oxoG). ITs AP (apurinic/apyrimidinic) lyase activity introduces nicks in the DNA strand, cleaving the DNA backbone by beta-delta elimination to generate a single-strand break at the site of the removed base with both 3'- and 5'-phosphates. Fpg is a monomer composed of 2 domains connected by a flexible hinge []. The two DNA-binding motifs (a zinc finger and the helix-two-turns-helix motifs) suggest that the oxidized base is flipped out from double-stranded DNA in the binding mode and excised by a catalytic mechanism similar to that of bifunctional base excision repair enzymes []. Fpg binds one ion of zinc at the C terminus, which contains four conserved and essential cysteines []. Endonuclease VIII (Nei) has the same enzyme activities as Fpg above, but with a preference for oxidized pyrimidines, such as thymine glycol, 5,6-dihydrouracil and 5,6-dihydrothymine [, ]. An Fpg-type zinc finger is also found at the C terminus of isoleucyl tRNA synthetase (6.1.1.5 from EC) [, ]. This enzyme catalyses the attachment of isoleucine to tRNA(Ile). As IleRS can inadvertently accommodate and process structurally similar amino acids such as valine, to avoid such errors it has two additional distinct tRNA(Ile)-dependent editing activities. One activity is designated as 'pre-transfer' editing and involves the hydrolysis of activated Val-AMP. The other activity is designated 'post-transfer' editing and involves deacylation of mischarged Val-tRNA(Ile) []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003824 catalytic activity; PDB: 1K82_C 1Q39_A 2OQ4_B 2OPF_A 1K3X_A 1K3W_A 1Q3B_A 2EA0_A 1Q3C_A 2XZF_A ....
Probab=30.83 E-value=35 Score=20.84 Aligned_cols=10 Identities=20% Similarity=0.610 Sum_probs=3.7
Q ss_pred ccCCcCCCcc
Q 024483 79 QVCTNCGVNM 88 (267)
Q Consensus 79 ~~C~~Cg~~f 88 (267)
+.|+.|+..+
T Consensus 2 ~~C~rC~~~~ 11 (30)
T PF06827_consen 2 EKCPRCWNYI 11 (30)
T ss_dssp SB-TTT--BB
T ss_pred CcCccCCCcc
Confidence 3566665544
No 219
>PF12874 zf-met: Zinc-finger of C2H2 type; PDB: 1ZU1_A 2KVG_A.
Probab=30.68 E-value=26 Score=20.00 Aligned_cols=16 Identities=31% Similarity=0.696 Sum_probs=12.2
Q ss_pred CCCCCCCccccchhHH
Q 024483 190 YCCPICSKSVIDMSRT 205 (267)
Q Consensus 190 ~~CPiCrks~~dm~~~ 205 (267)
|.|.+|.+++.+...+
T Consensus 1 ~~C~~C~~~f~s~~~~ 16 (25)
T PF12874_consen 1 FYCDICNKSFSSENSL 16 (25)
T ss_dssp EEETTTTEEESSHHHH
T ss_pred CCCCCCCCCcCCHHHH
Confidence 4799999999876543
No 220
>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=30.67 E-value=49 Score=33.37 Aligned_cols=47 Identities=28% Similarity=0.654 Sum_probs=29.5
Q ss_pred ccceeeeCCCCccccccccCCcCCCccce------eeccccccccCCCCcCeeecCCCCcc
Q 024483 62 DVKQVICSVCDTEQPVAQVCTNCGVNMGE------YFCDICKFYDDDIEKGQFHCDDCGIC 116 (267)
Q Consensus 62 ~~~~v~C~~C~~~q~v~~~C~~Cg~~f~~------y~C~~C~l~dd~~~k~~yHC~~CgiC 116 (267)
-.+.++|..|+.. ..|++|+..+.- -.|.-|.+- .+.+..|+.||-=
T Consensus 210 ya~~~~C~~Cg~~----~~C~~C~~~l~~h~~~~~l~Ch~Cg~~----~~~~~~Cp~C~s~ 262 (505)
T TIGR00595 210 YSKNLLCRSCGYI----LCCPNCDVSLTYHKKEGKLRCHYCGYQ----EPIPKTCPQCGSE 262 (505)
T ss_pred CCCeeEhhhCcCc----cCCCCCCCceEEecCCCeEEcCCCcCc----CCCCCCCCCCCCC
Confidence 3467889999865 479999988743 345555432 2344566666643
No 221
>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=30.67 E-value=35 Score=21.89 Aligned_cols=22 Identities=27% Similarity=0.757 Sum_probs=12.9
Q ss_pred eeeCCCCcccc---ccccCCcCCCc
Q 024483 66 VICSVCDTEQP---VAQVCTNCGVN 87 (267)
Q Consensus 66 v~C~~C~~~q~---v~~~C~~Cg~~ 87 (267)
-+|..|+.+.. .-..||.||+.
T Consensus 3 ~~C~~CG~i~~g~~~p~~CP~Cg~~ 27 (34)
T cd00729 3 WVCPVCGYIHEGEEAPEKCPICGAP 27 (34)
T ss_pred EECCCCCCEeECCcCCCcCcCCCCc
Confidence 46777775422 23577777764
No 222
>PF00412 LIM: LIM domain; InterPro: IPR001781 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents LIM-type zinc finger (Znf) domains. LIM domains coordinate one or more zinc atoms, and are named after the three proteins (LIN-11, Isl1 and MEC-3) in which they were first found. They consist of two zinc-binding motifs that resemble GATA-like Znf's, however the residues holding the zinc atom(s) are variable, involving Cys, His, Asp or Glu residues. LIM domains are involved in proteins with differing functions, including gene expression, and cytoskeleton organisation and development [, ]. Protein containing LIM Znf domains include: Caenorhabditis elegans mec-3; a protein required for the differentiation of the set of six touch receptor neurons in this nematode. C. elegans. lin-11; a protein required for the asymmetric division of vulval blast cells. Vertebrate insulin gene enhancer binding protein isl-1. Isl-1 binds to one of the two cis-acting protein-binding domains of the insulin gene. Vertebrate homeobox proteins lim-1, lim-2 (lim-5) and lim3. Vertebrate lmx-1, which acts as a transcriptional activator by binding to the FLAT element; a beta-cell-specific transcriptional enhancer found in the insulin gene. Mammalian LH-2, a transcriptional regulatory protein involved in the control of cell differentiation in developing lymphoid and neural cell types. Drosophila melanogaster (Fruit fly) protein apterous, required for the normal development of the wing and halter imaginal discs. Vertebrate protein kinases LIMK-1 and LIMK-2. Mammalian rhombotins. Rhombotin 1 (RBTN1 or TTG-1) and rhombotin-2 (RBTN2 or TTG-2) are proteins of about 160 amino acids whose genes are disrupted by chromosomal translocations in T-cell leukemia. Mammalian and avian cysteine-rich protein (CRP), a 192 amino-acid protein of unknown function. Seems to interact with zyxin. Mammalian cysteine-rich intestinal protein (CRIP), a small protein which seems to have a role in zinc absorption and may function as an intracellular zinc transport protein. Vertebrate paxillin, a cytoskeletal focal adhesion protein. Mus musculus (Mouse) testin which should not be confused with rat testin which is a thiol protease homologue (see IPR000169 from INTERPRO). Helianthus annuus (Common sunflower) pollen specific protein SF3. Chicken zyxin. Zyxin is a low-abundance adhesion plaque protein which has been shown to interact with CRP. Yeast protein LRG1 which is involved in sporulation []. Saccharomyces cerevisiae (Baker's yeast) rho-type GTPase activating protein RGA1/DBM1. C. elegans homeobox protein ceh-14. C. elegans homeobox protein unc-97. S. cerevisiae hypothetical protein YKR090w. C. elegans hypothetical proteins C28H8.6. These proteins generally contain two tandem copies of the LIM domain in their N-terminal section. Zyxin and paxillin are exceptions in that they contain respectively three and four LIM domains at their C-terminal extremity. In apterous, isl-1, LH-2, lin-11, lim-1 to lim-3, lmx-1 and ceh-14 and mec-3 there is a homeobox domain some 50 to 95 amino acids after the LIM domains. LIM domains contain seven conserved cysteine residues and a histidine. The arrangement followed by these conserved residues is: C-x(2)-C-x(16,23)-H-x(2)-[CH]-x(2)-C-x(2)-C-x(16,21)-C-x(2,3)-[CHD] LIM domains bind two zinc ions []. LIM does not bind DNA, rather it seems to act as an interface for protein-protein interaction. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 2CO8_A 2EGQ_A 2CUR_A 3IXE_B 1CTL_A 1B8T_A 1X62_A 2DFY_C 1IML_A 2CUQ_A ....
Probab=30.07 E-value=19 Score=24.58 Aligned_cols=40 Identities=25% Similarity=0.615 Sum_probs=27.2
Q ss_pred CchhhhhhcccCCccEEeccCCccChhhHHHHhcCCCCCCCCCCccccchh
Q 024483 153 CPICYEYLFDSLRNTTVMKCGHTMHCECYHEMIKRDKYCCPICSKSVIDMS 203 (267)
Q Consensus 153 CpICle~lf~s~~~v~~LpCGH~~H~~C~~~~~~~~~~~CPiCrks~~dm~ 203 (267)
|+.|.+.+.. ..+.+..=|..+|..| ++|-.|+++|.+..
T Consensus 1 C~~C~~~I~~--~~~~~~~~~~~~H~~C---------f~C~~C~~~l~~~~ 40 (58)
T PF00412_consen 1 CARCGKPIYG--TEIVIKAMGKFWHPEC---------FKCSKCGKPLNDGD 40 (58)
T ss_dssp BTTTSSBESS--SSEEEEETTEEEETTT---------SBETTTTCBTTTSS
T ss_pred CCCCCCCccC--cEEEEEeCCcEEEccc---------cccCCCCCccCCCe
Confidence 6677777653 2333345688899765 48889999987544
No 223
>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=29.85 E-value=41 Score=27.99 Aligned_cols=30 Identities=30% Similarity=0.791 Sum_probs=21.6
Q ss_pred CCcccccCccceeecCccCccccccccCcceee
Q 024483 113 CGICRIGGRENYFHCKRCGSCYSTSLRNNHLCI 145 (267)
Q Consensus 113 CgiCR~G~~~~~fHC~~C~~C~s~~l~~~H~C~ 145 (267)
|-.|++-....-.||..||.|+-.- +|-|.
T Consensus 51 C~~C~~~kp~Rs~HC~~C~~CV~~~---DHHC~ 80 (174)
T PF01529_consen 51 CSTCKIIKPPRSHHCRVCNRCVLRF---DHHCP 80 (174)
T ss_pred CcccCCcCCCcceeccccccccccc---cccch
Confidence 4445555666789999999998764 67765
No 224
>PF15616 TerY-C: TerY-C metal binding domain
Probab=29.85 E-value=48 Score=27.96 Aligned_cols=34 Identities=35% Similarity=0.843 Sum_probs=22.5
Q ss_pred cccCCcCCCccceeecccc-cccc-CCCCcCeeecCCCC
Q 024483 78 AQVCTNCGVNMGEYFCDIC-KFYD-DDIEKGQFHCDDCG 114 (267)
Q Consensus 78 ~~~C~~Cg~~f~~y~C~~C-~l~d-d~~~k~~yHC~~Cg 114 (267)
...||.||..+|---| .| ||+- +. -....|+-||
T Consensus 77 ~PgCP~CGn~~~fa~C-~CGkl~Ci~g--~~~~~CPwCg 112 (131)
T PF15616_consen 77 APGCPHCGNQYAFAVC-GCGKLFCIDG--EGEVTCPWCG 112 (131)
T ss_pred CCCCCCCcChhcEEEe-cCCCEEEeCC--CCCEECCCCC
Confidence 3689999999998888 57 5553 21 1245555555
No 225
>PF13824 zf-Mss51: Zinc-finger of mitochondrial splicing suppressor 51
Probab=29.67 E-value=43 Score=24.20 Aligned_cols=21 Identities=19% Similarity=0.542 Sum_probs=16.8
Q ss_pred CCCCCCCCCccccchhHHhHH
Q 024483 188 DKYCCPICSKSVIDMSRTWKR 208 (267)
Q Consensus 188 ~~~~CPiCrks~~dm~~~~~~ 208 (267)
..|.||.|+-++--....|+.
T Consensus 13 v~~~Cp~cGipthcS~ehw~~ 33 (55)
T PF13824_consen 13 VNFECPDCGIPTHCSEEHWED 33 (55)
T ss_pred cCCcCCCCCCcCccCHHHHHH
Confidence 579999999999766667753
No 226
>PRK03564 formate dehydrogenase accessory protein FdhE; Provisional
Probab=29.60 E-value=59 Score=31.13 Aligned_cols=26 Identities=27% Similarity=0.753 Sum_probs=21.0
Q ss_pred ccceeeeCCCCccccc-cccCCcCCCc
Q 024483 62 DVKQVICSVCDTEQPV-AQVCTNCGVN 87 (267)
Q Consensus 62 ~~~~v~C~~C~~~q~v-~~~C~~Cg~~ 87 (267)
..+-..|+.|+++..+ -..|++||..
T Consensus 209 G~RyL~CslC~teW~~~R~~C~~Cg~~ 235 (309)
T PRK03564 209 GLRYLHCNLCESEWHVVRVKCSNCEQS 235 (309)
T ss_pred CceEEEcCCCCCcccccCccCCCCCCC
Confidence 3467899999999877 4689999964
No 227
>COG1645 Uncharacterized Zn-finger containing protein [General function prediction only]
Probab=29.59 E-value=29 Score=29.35 Aligned_cols=20 Identities=45% Similarity=1.243 Sum_probs=14.1
Q ss_pred cccCCcCCCcc----ceeeccccc
Q 024483 78 AQVCTNCGVNM----GEYFCDICK 97 (267)
Q Consensus 78 ~~~C~~Cg~~f----~~y~C~~C~ 97 (267)
+..|+.||.++ |+-||++|-
T Consensus 28 ~~hCp~Cg~PLF~KdG~v~CPvC~ 51 (131)
T COG1645 28 AKHCPKCGTPLFRKDGEVFCPVCG 51 (131)
T ss_pred HhhCcccCCcceeeCCeEECCCCC
Confidence 35788888886 555677774
No 228
>COG3024 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=29.34 E-value=28 Score=25.99 Aligned_cols=26 Identities=31% Similarity=0.662 Sum_probs=17.8
Q ss_pred cccccCCcCCCccce-------eeccc-cccccC
Q 024483 76 PVAQVCTNCGVNMGE-------YFCDI-CKFYDD 101 (267)
Q Consensus 76 ~v~~~C~~Cg~~f~~-------y~C~~-C~l~dd 101 (267)
..+..|+-||+...+ -||++ |+|.|-
T Consensus 5 ~~~v~CP~Cgkpv~w~~~s~frPFCSkRCklIDL 38 (65)
T COG3024 5 RITVPCPTCGKPVVWGEESPFRPFCSKRCKLIDL 38 (65)
T ss_pred cccccCCCCCCcccccccCCcCcchhHhhhhcch
Confidence 445678888887644 56654 888874
No 229
>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]
Probab=29.25 E-value=31 Score=25.43 Aligned_cols=34 Identities=24% Similarity=0.574 Sum_probs=20.9
Q ss_pred cceeeeCCCCccccccccCCcCCCccceeecccccc
Q 024483 63 VKQVICSVCDTEQPVAQVCTNCGVNMGEYFCDICKF 98 (267)
Q Consensus 63 ~~~v~C~~C~~~q~v~~~C~~Cg~~f~~y~C~~C~l 98 (267)
...-.|..|+.++-. .|..|...=+.|-|++|-|
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 345667777654332 5666666667777777655
No 230
>KOG0802 consensus E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=29.12 E-value=37 Score=34.49 Aligned_cols=44 Identities=23% Similarity=0.704 Sum_probs=34.7
Q ss_pred CCCCCCchhhhhhcccCCccEEeccCCccChhhHHHHhcCCCCCCCCCCcccc
Q 024483 148 SMHHHCPICYEYLFDSLRNTTVMKCGHTMHCECYHEMIKRDKYCCPICSKSVI 200 (267)
Q Consensus 148 ~~~~~CpICle~lf~s~~~v~~LpCGH~~H~~C~~~~~~~~~~~CPiCrks~~ 200 (267)
..+++|.||++.+ ..++-+|- |..|+.+|+. ....||+|++.+.
T Consensus 477 ~~~~~~~~~~~~~-----~~~~~~~~---~~~~l~~~~~-~~~~~pl~~~~~~ 520 (543)
T KOG0802|consen 477 EPNDVCAICYQEM-----SARITPCS---HALCLRKWLY-VQEVCPLCHTYMK 520 (543)
T ss_pred cccCcchHHHHHH-----Hhcccccc---chhHHHhhhh-hccccCCCchhhh
Confidence 4578999999997 23344555 9999999997 4678999998876
No 231
>smart00834 CxxC_CXXC_SSSS Putative regulatory protein. CxxC_CXXC_SSSS represents a region of about 41 amino acids found in a number of small proteins in a wide range of bacteria. The region usually begins with the initiator Met and contains two CxxC motifs separated by 17 amino acids. One protein in this entry has been noted as a putative regulatory protein, designated FmdB. Most proteins in this entry have a C-terminal region containing highly degenerate sequence.
Probab=29.08 E-value=56 Score=20.79 Aligned_cols=27 Identities=33% Similarity=0.587 Sum_probs=16.3
Q ss_pred EEEcCCCCCccccceeE---eeecCCCCCC
Q 024483 228 WILCNDCNDTTEVYFHI---IGQKCSHCKS 254 (267)
Q Consensus 228 ~I~CnDC~~~s~~~fH~---lg~kC~~C~S 254 (267)
...|.+|+...++..-+ ....|+.||+
T Consensus 5 ~y~C~~Cg~~fe~~~~~~~~~~~~CP~Cg~ 34 (41)
T smart00834 5 EYRCEDCGHTFEVLQKISDDPLATCPECGG 34 (41)
T ss_pred EEEcCCCCCEEEEEEecCCCCCCCCCCCCC
Confidence 35677777755443221 2357888887
No 232
>KOG4317 consensus Predicted Zn-finger protein [Function unknown]
Probab=28.90 E-value=24 Score=34.08 Aligned_cols=21 Identities=38% Similarity=0.917 Sum_probs=16.4
Q ss_pred ccCCcCCCccceeeccccccc
Q 024483 79 QVCTNCGVNMGEYFCDICKFY 99 (267)
Q Consensus 79 ~~C~~Cg~~f~~y~C~~C~l~ 99 (267)
..|+-||+.+++|.|+-|+|.
T Consensus 8 ~~C~ic~vq~~~YtCPRCn~~ 28 (383)
T KOG4317|consen 8 LACGICGVQKREYTCPRCNLL 28 (383)
T ss_pred eeccccccccccccCCCCCcc
Confidence 357778888888888888864
No 233
>PRK14873 primosome assembly protein PriA; Provisional
Probab=28.67 E-value=58 Score=34.22 Aligned_cols=24 Identities=29% Similarity=0.707 Sum_probs=18.4
Q ss_pred cceeeeCCCCccccccccCCcCCCccce
Q 024483 63 VKQVICSVCDTEQPVAQVCTNCGVNMGE 90 (267)
Q Consensus 63 ~~~v~C~~C~~~q~v~~~C~~Cg~~f~~ 90 (267)
...++|..|+.. ..|++|+..+.-
T Consensus 381 ap~l~C~~Cg~~----~~C~~C~~~L~~ 404 (665)
T PRK14873 381 VPSLACARCRTP----ARCRHCTGPLGL 404 (665)
T ss_pred CCeeEhhhCcCe----eECCCCCCceeE
Confidence 367889999865 479999888753
No 234
>COG5183 SSM4 Protein involved in mRNA turnover and stability [RNA processing and modification]
Probab=28.57 E-value=29 Score=37.58 Aligned_cols=51 Identities=24% Similarity=0.447 Sum_probs=34.6
Q ss_pred CCCCCCchhhhhhcccCCccEEecc---C--CccChhhHHHHhcCC-CCCCCCCCcccc
Q 024483 148 SMHHHCPICYEYLFDSLRNTTVMKC---G--HTMHCECYHEMIKRD-KYCCPICSKSVI 200 (267)
Q Consensus 148 ~~~~~CpICle~lf~s~~~v~~LpC---G--H~~H~~C~~~~~~~~-~~~CPiCrks~~ 200 (267)
..+..|-||.-+= .+++.-.=|| | -.+|++|+.+|+..+ ..+|-+|...+.
T Consensus 10 ~d~~~CRICr~e~--~~d~pLfhPCKC~GSIkYiH~eCL~eW~~~s~~~kCdiChy~~~ 66 (1175)
T COG5183 10 EDKRSCRICRTED--IRDDPLFHPCKCSGSIKYIHRECLMEWMECSGTKKCDICHYEYK 66 (1175)
T ss_pred ccchhceeecCCC--CCCCcCcccccccchhHHHHHHHHHHHHhcCCCcceeeecceee
Confidence 3456788997651 1122223366 3 679999999999864 467999987664
No 235
>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=28.54 E-value=19 Score=38.89 Aligned_cols=46 Identities=26% Similarity=0.676 Sum_probs=0.0
Q ss_pred ceeeeCCCCccccccccCCcCCCc-cceeeccccccccCCCCcCeeecCCCCc
Q 024483 64 KQVICSVCDTEQPVAQVCTNCGVN-MGEYFCDICKFYDDDIEKGQFHCDDCGI 115 (267)
Q Consensus 64 ~~v~C~~C~~~q~v~~~C~~Cg~~-f~~y~C~~C~l~dd~~~k~~yHC~~Cgi 115 (267)
-.-.|..|+++ ++...|+.||.. .-.|+|+.|+.--++. +|+.||.
T Consensus 654 ~~r~Cp~Cg~~-t~~~~Cp~CG~~T~~~~~Cp~C~~~~~~~-----~C~~C~~ 700 (900)
T PF03833_consen 654 GRRRCPKCGKE-TFYNRCPECGSHTEPVYVCPDCGIEVEED-----ECPKCGR 700 (900)
T ss_dssp -----------------------------------------------------
T ss_pred ecccCcccCCc-chhhcCcccCCccccceeccccccccCcc-----ccccccc
Confidence 34567777766 566677777765 4566677776543221 6777763
No 236
>cd02341 ZZ_ZZZ3 Zinc finger, ZZ type. Zinc finger present in ZZZ3 (ZZ finger containing 3) and related proteins. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding.
Probab=28.39 E-value=41 Score=23.37 Aligned_cols=22 Identities=50% Similarity=1.284 Sum_probs=9.6
Q ss_pred eecCCCCcccccCccceeecCccC
Q 024483 108 FHCDDCGICRIGGRENYFHCKRCG 131 (267)
Q Consensus 108 yHC~~CgiCR~G~~~~~fHC~~C~ 131 (267)
|.|+.|+.--+-| --|||..|.
T Consensus 1 y~Cd~C~~~pI~G--~R~~C~~C~ 22 (48)
T cd02341 1 FKCDSCGIEPIPG--TRYHCSECD 22 (48)
T ss_pred CCCCCCCCCcccc--ceEECCCCC
Confidence 4455555433322 245555443
No 237
>KOG4399 consensus C2HC-type Zn-finger protein [General function prediction only]
Probab=28.29 E-value=11 Score=35.41 Aligned_cols=72 Identities=28% Similarity=0.642 Sum_probs=53.2
Q ss_pred CCccceeeccccccccCCCCcCeeecCCCCcccccCccceeecCccCccccccccCcceeecCCCCCCCchhhhh
Q 024483 85 GVNMGEYFCDICKFYDDDIEKGQFHCDDCGICRIGGRENYFHCKRCGSCYSTSLRNNHLCIENSMHHHCPICYEY 159 (267)
Q Consensus 85 g~~f~~y~C~~C~l~dd~~~k~~yHC~~CgiCR~G~~~~~fHC~~C~~C~s~~l~~~H~C~e~~~~~~CpICle~ 159 (267)
|..=+-.||+.|-.|- .+-.-||+.|+.|..-.++.|-||..|-.|+-.++-.--.|-.-+..--|-||.++
T Consensus 199 ~~EE~~~~~~~~~~Yv---~~~~~H~~~~~S~~~~~~~~~~H~~~~~~~~~~~~i~C~~~~~~A~~~~C~iC~~~ 270 (325)
T KOG4399|consen 199 PTEEGYRFCSPCQRYV---SLENQHCEHCNSCTSKDGRKWNHCFLCKKCVKPSWIHCSICNHCAVKHGCFICGEL 270 (325)
T ss_pred ccccceEEEeehHHHH---HHHhhhchhhcccccchhHHHhHhHHhhhhcccceeeeecccchhhhcceeecccc
Confidence 4444667899999884 47788999999998777778999999999998887433333333445567788775
No 238
>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=27.70 E-value=36 Score=28.10 Aligned_cols=27 Identities=22% Similarity=0.618 Sum_probs=18.4
Q ss_pred ccceeeeCCCCccccc---cccCCcCCCcc
Q 024483 62 DVKQVICSVCDTEQPV---AQVCTNCGVNM 88 (267)
Q Consensus 62 ~~~~v~C~~C~~~q~v---~~~C~~Cg~~f 88 (267)
++..|.|..|+++-.. .+.|++|+.++
T Consensus 66 kav~V~CP~C~K~TKmLGr~D~CM~C~~pL 95 (114)
T PF11023_consen 66 KAVQVECPNCGKQTKMLGRVDACMHCKEPL 95 (114)
T ss_pred cceeeECCCCCChHhhhchhhccCcCCCcC
Confidence 4567788888766433 46788887765
No 239
>PLN02436 cellulose synthase A
Probab=27.53 E-value=52 Score=36.55 Aligned_cols=56 Identities=16% Similarity=0.454 Sum_probs=40.2
Q ss_pred ecCCCCCCCchhhhhhcccCCccEEe---ccCCccChhhHHHHhcCCCCCCCCCCcccc
Q 024483 145 IENSMHHHCPICYEYLFDSLRNTTVM---KCGHTMHCECYHEMIKRDKYCCPICSKSVI 200 (267)
Q Consensus 145 ~e~~~~~~CpICle~lf~s~~~v~~L---pCGH~~H~~C~~~~~~~~~~~CPiCrks~~ 200 (267)
+.....+.|.||.|++-.+.+.-... -||=-+.+.||+-=.+.++..||-|+...-
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 44556679999999974433333333 367789999996666667889999997654
No 240
>PF05129 Elf1: Transcription elongation factor Elf1 like; InterPro: IPR007808 This family of uncharacterised, mostly short, proteins contain a putative zinc binding domain with four conserved cysteines.; PDB: 1WII_A.
Probab=27.33 E-value=31 Score=26.51 Aligned_cols=38 Identities=18% Similarity=0.561 Sum_probs=17.8
Q ss_pred CCCCCCCCCc--ccc-chhHHhHHhHHHHHhcCCChhhhcCeeEEEcCCCCCcccccee
Q 024483 188 DKYCCPICSK--SVI-DMSRTWKRIDEEIEATVMPEDYRHKKVWILCNDCNDTTEVYFH 243 (267)
Q Consensus 188 ~~~~CPiCrk--s~~-dm~~~~~~lD~~i~~~pmP~~y~~~~v~I~CnDC~~~s~~~fH 243 (267)
..++||.|+. +|. .|.. ......|.|..|+.......+
T Consensus 21 ~~F~CPfC~~~~sV~v~idk------------------k~~~~~~~C~~Cg~~~~~~i~ 61 (81)
T PF05129_consen 21 KVFDCPFCNHEKSVSVKIDK------------------KEGIGILSCRVCGESFQTKIN 61 (81)
T ss_dssp S----TTT--SS-EEEEEET------------------TTTEEEEEESSS--EEEEE--
T ss_pred ceEcCCcCCCCCeEEEEEEc------------------cCCEEEEEecCCCCeEEEccC
Confidence 4699999993 232 3322 245678999999987665544
No 241
>PF05458 Siva: Cd27 binding protein (Siva); InterPro: IPR022773 Siva binds to the CD27 cytoplasmic tail. It has a DD homology region, a box-B-like ring finger, and a zinc finger-like domain. Overexpression of Siva in various cell lines induces apoptosis, suggesting an important role for Siva in the CD27-transduced apoptotic pathway []. Siva-1 binds to and inhibits BCL-X(L)-mediated protection against UV radiation-induced apoptosis. Indeed, the unique amphipathic helical region (SAH) present in Siva-1 is required for its binding to BCL-X(L) and sensitising cells to UV radiation. Natural complexes of Siva-1/BCL-X(L) are detected in HUT78 and murine thymocyte, suggesting a potential role for Siva-1 in regulating T cell homeostasis []. This family contains both Siva-1 and the shorter Siva-2 lacking the sequence coded by exon 2. It has been suggested that Siva-2 could regulate the function of Siva-1 [].
Probab=27.31 E-value=46 Score=29.18 Aligned_cols=36 Identities=33% Similarity=0.858 Sum_probs=23.0
Q ss_pred eeeCCCCccccccccCCcCCCcc-----------ceeeccccccccC
Q 024483 66 VICSVCDTEQPVAQVCTNCGVNM-----------GEYFCDICKFYDD 101 (267)
Q Consensus 66 v~C~~C~~~q~v~~~C~~Cg~~f-----------~~y~C~~C~l~dd 101 (267)
..|..|...+.+...|.+|...+ +.+||+.|-+.|-
T Consensus 112 ~aCs~C~r~~~~~~~C~~Cdr~lC~~C~~~C~~C~~~~Cs~Cs~~~y 158 (175)
T PF05458_consen 112 RACSVCQRTQRIKSVCSQCDRALCESCIRSCSSCSEVFCSLCSTVNY 158 (175)
T ss_pred ccCcCCcCCCCCCccccccCcHHHHHHHhhhhchhhhhhcCcccccc
Confidence 35777876666777777776655 4556666655543
No 242
>COG1998 RPS31 Ribosomal protein S27AE [Translation, ribosomal structure and biogenesis]
Probab=27.21 E-value=36 Score=24.26 Aligned_cols=20 Identities=30% Similarity=0.881 Sum_probs=11.5
Q ss_pred cccCCcCCC--cc----ceeeccccc
Q 024483 78 AQVCTNCGV--NM----GEYFCDICK 97 (267)
Q Consensus 78 ~~~C~~Cg~--~f----~~y~C~~C~ 97 (267)
...||+||. -| .||+|.+|.
T Consensus 19 ~~~CPrCG~gvfmA~H~dR~~CGkCg 44 (51)
T COG1998 19 NRFCPRCGPGVFMADHKDRWACGKCG 44 (51)
T ss_pred cccCCCCCCcchhhhcCceeEecccc
Confidence 357888883 33 355555553
No 243
>smart00355 ZnF_C2H2 zinc finger.
Probab=26.74 E-value=60 Score=17.58 Aligned_cols=16 Identities=38% Similarity=0.698 Sum_probs=11.9
Q ss_pred CCCCCCCccccchhHH
Q 024483 190 YCCPICSKSVIDMSRT 205 (267)
Q Consensus 190 ~~CPiCrks~~dm~~~ 205 (267)
+.|+.|.+++...+.+
T Consensus 1 ~~C~~C~~~f~~~~~l 16 (26)
T smart00355 1 YRCPECGKVFKSKSAL 16 (26)
T ss_pred CCCCCCcchhCCHHHH
Confidence 5799999988765443
No 244
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=26.72 E-value=80 Score=27.59 Aligned_cols=27 Identities=26% Similarity=0.573 Sum_probs=17.8
Q ss_pred CCCCCCCCCccccch--hHHhHHhHHHHH
Q 024483 188 DKYCCPICSKSVIDM--SRTWKRIDEEIE 214 (267)
Q Consensus 188 ~~~~CPiCrks~~dm--~~~~~~lD~~i~ 214 (267)
..|+||.|+-.+..+ +.....|+..|+
T Consensus 135 ~~F~Cp~Cg~~L~~~dn~~~~~~l~~~I~ 163 (178)
T PRK06266 135 YGFRCPQCGEMLEEYDNSELIKELKEQIK 163 (178)
T ss_pred cCCcCCCCCCCCeecccHHHHHHHHHHHH
Confidence 479999999999743 334445554443
No 245
>PLN00209 ribosomal protein S27; Provisional
Probab=26.71 E-value=38 Score=26.62 Aligned_cols=37 Identities=19% Similarity=0.346 Sum_probs=28.5
Q ss_pred ceeeeCCCCccccc------cccCCcCCCccceeecccccccc
Q 024483 64 KQVICSVCDTEQPV------AQVCTNCGVNMGEYFCDICKFYD 100 (267)
Q Consensus 64 ~~v~C~~C~~~q~v------~~~C~~Cg~~f~~y~C~~C~l~d 100 (267)
-.|.|..|..+|.| ...|..||..+++-.=.+.+|-+
T Consensus 35 m~VkCp~C~n~q~VFShA~t~V~C~~Cg~~L~~PTGGKa~l~~ 77 (86)
T PLN00209 35 MDVKCQGCFNITTVFSHSQTVVVCGSCQTVLCQPTGGKARLTE 77 (86)
T ss_pred EEEECCCCCCeeEEEecCceEEEccccCCEeeccCCCCeEecC
Confidence 36899999999887 24799999998877666666554
No 246
>TIGR01206 lysW lysine biosynthesis protein LysW. This very small, poorly characterized protein has been shown essential in Thermus thermophilus for an unusual pathway of Lys biosynthesis from aspartate by way of alpha-aminoadipate (AAA) rather than diaminopimelate. It is found also in Deinococcus radiodurans and Pyrococcus horikoshii, which appear to share the AAA pathway.
Probab=26.35 E-value=52 Score=23.53 Aligned_cols=31 Identities=19% Similarity=0.670 Sum_probs=20.9
Q ss_pred CCCCCCCccccchhHHhHHhHHHHHhcCCChhhhcCeeEEEcCCCCCccc
Q 024483 190 YCCPICSKSVIDMSRTWKRIDEEIEATVMPEDYRHKKVWILCNDCNDTTE 239 (267)
Q Consensus 190 ~~CPiCrks~~dm~~~~~~lD~~i~~~pmP~~y~~~~v~I~CnDC~~~s~ 239 (267)
++||.|..+|. +|....+. .+-|-+||+.-.
T Consensus 3 ~~CP~CG~~ie-----------------v~~~~~Ge--iV~Cp~CGaele 33 (54)
T TIGR01206 3 FECPDCGAEIE-----------------LENPELGE--LVICDECGAELE 33 (54)
T ss_pred cCCCCCCCEEe-----------------cCCCccCC--EEeCCCCCCEEE
Confidence 68999998773 23333333 578999997543
No 247
>PF12171 zf-C2H2_jaz: Zinc-finger double-stranded RNA-binding; InterPro: IPR022755 This zinc finger is found in archaea and eukaryotes, and is approximately 30 amino acids in length. The mammalian members of this group occur multiple times along the protein, joined by flexible linkers, and are referred to as JAZ - dsRNA-binding ZF protein - zinc-fingers. The JAZ proteins are expressed in all tissues tested and localise in the nucleus, particularly the nucleolus []. JAZ preferentially binds to double-stranded (ds) RNA or RNA/DNA hybrids rather than DNA. In addition to binding double-stranded RNA, these zinc-fingers are required for nucleolar localisation. This entry represents the multiple-adjacent-C2H2 zinc finger, JAZ. ; PDB: 4DGW_A 1ZR9_A.
Probab=26.30 E-value=47 Score=19.60 Aligned_cols=15 Identities=20% Similarity=0.603 Sum_probs=12.3
Q ss_pred CCCCCCCccccchhH
Q 024483 190 YCCPICSKSVIDMSR 204 (267)
Q Consensus 190 ~~CPiCrks~~dm~~ 204 (267)
+.|++|.+.+.+...
T Consensus 2 ~~C~~C~k~f~~~~~ 16 (27)
T PF12171_consen 2 FYCDACDKYFSSENQ 16 (27)
T ss_dssp CBBTTTTBBBSSHHH
T ss_pred CCcccCCCCcCCHHH
Confidence 689999999987643
No 248
>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=26.22 E-value=47 Score=21.18 Aligned_cols=10 Identities=30% Similarity=0.737 Sum_probs=5.5
Q ss_pred eeeeCCCCcc
Q 024483 65 QVICSVCDTE 74 (267)
Q Consensus 65 ~v~C~~C~~~ 74 (267)
.|.|+.|++.
T Consensus 25 ~v~C~~C~~~ 34 (38)
T TIGR02098 25 KVRCGKCGHV 34 (38)
T ss_pred EEECCCCCCE
Confidence 4556555543
No 249
>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=26.19 E-value=79 Score=27.00 Aligned_cols=28 Identities=21% Similarity=0.539 Sum_probs=19.8
Q ss_pred CCCCCCCCCccccch--hHHhHHhHHHHHh
Q 024483 188 DKYCCPICSKSVIDM--SRTWKRIDEEIEA 215 (267)
Q Consensus 188 ~~~~CPiCrks~~dm--~~~~~~lD~~i~~ 215 (267)
..++||.|+..+..+ +..-..|++.|+.
T Consensus 127 ~~F~Cp~Cg~~L~~~dn~~~i~~l~~~i~~ 156 (158)
T TIGR00373 127 LNFTCPRCGAMLDYLDNSEAIEKLEEQIKF 156 (158)
T ss_pred cCCcCCCCCCEeeeccCHHHHHHHHHHHHh
Confidence 479999999999743 3345666666654
No 250
>KOG4443 consensus Putative transcription factor HALR/MLL3, involved in embryonic development [General function prediction only]
Probab=25.94 E-value=80 Score=33.33 Aligned_cols=80 Identities=23% Similarity=0.392 Sum_probs=48.8
Q ss_pred eeecCCCCCCCchhhhhhcccCCccEEec---cCCccChhhHHHH----hc---CCCCCCCCCCccccchhHHhHHhHHH
Q 024483 143 LCIENSMHHHCPICYEYLFDSLRNTTVMK---CGHTMHCECYHEM----IK---RDKYCCPICSKSVIDMSRTWKRIDEE 212 (267)
Q Consensus 143 ~C~e~~~~~~CpICle~lf~s~~~v~~Lp---CGH~~H~~C~~~~----~~---~~~~~CPiCrks~~dm~~~~~~lD~~ 212 (267)
.|...+.-..||||+-..-++ +....+. |.=..|..|..-. .+ ...|+|-+|| .-+.+-..|...
T Consensus 138 ~~~~c~s~~~cPvc~~~Y~~~-e~~~~~~c~~c~rwsh~~c~~~sdd~~~q~~vD~~~~CS~CR----~es~qvKdi~~~ 212 (694)
T KOG4443|consen 138 QCAPCASLSYCPVCLIVYQDS-ESLPMVCCSICQRWSHGGCDGISDDKYMQAQVDLQYKCSTCR----GESYQVKDISDA 212 (694)
T ss_pred ccccccccccCchHHHhhhhc-cchhhHHHHHhcccccCCCCccchHHHHHHhhhhhcccceee----hhhhhhhhHHHH
Confidence 344444467899999865554 3333333 5567888885322 11 1269999999 222233566666
Q ss_pred HHhcCCChhhhcCee
Q 024483 213 IEATVMPEDYRHKKV 227 (267)
Q Consensus 213 i~~~pmP~~y~~~~v 227 (267)
+..+=||..+.+...
T Consensus 213 vqe~~~~k~~~~~~~ 227 (694)
T KOG4443|consen 213 LQETWKAKDKPDKIL 227 (694)
T ss_pred HHhhcchhhccccce
Confidence 777778888776543
No 251
>PRK14892 putative transcription elongation factor Elf1; Provisional
Probab=25.78 E-value=62 Score=25.95 Aligned_cols=32 Identities=31% Similarity=0.664 Sum_probs=22.8
Q ss_pred cceeecCccC-ccccccccCcceeecCCCCCCCchhhhh
Q 024483 122 ENYFHCKRCG-SCYSTSLRNNHLCIENSMHHHCPICYEY 159 (267)
Q Consensus 122 ~~~fHC~~C~-~C~s~~l~~~H~C~e~~~~~~CpICle~ 159 (267)
..+|+|..|| .-+++.+. + +..+..||+|..+
T Consensus 19 pt~f~CP~Cge~~v~v~~~--k----~~~h~~C~~CG~y 51 (99)
T PRK14892 19 PKIFECPRCGKVSISVKIK--K----NIAIITCGNCGLY 51 (99)
T ss_pred CcEeECCCCCCeEeeeecC--C----CcceEECCCCCCc
Confidence 5789999999 33333332 2 5678899999987
No 252
>KOG3362 consensus Predicted BBOX Zn-finger protein [General function prediction only]
Probab=25.67 E-value=21 Score=30.72 Aligned_cols=25 Identities=28% Similarity=1.016 Sum_probs=17.5
Q ss_pred ceeeccccccccCCCCcCeeecCCCC--ccccc
Q 024483 89 GEYFCDICKFYDDDIEKGQFHCDDCG--ICRIG 119 (267)
Q Consensus 89 ~~y~C~~C~l~dd~~~k~~yHC~~Cg--iCR~G 119 (267)
.+-||++|-+| ++|-|..|| +|-|+
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 46678888744 468888888 66665
No 253
>PRK14810 formamidopyrimidine-DNA glycosylase; Provisional
Probab=25.67 E-value=38 Score=31.37 Aligned_cols=20 Identities=25% Similarity=0.858 Sum_probs=15.6
Q ss_pred cccCCcCCCcc--------ceeeccccc
Q 024483 78 AQVCTNCGVNM--------GEYFCDICK 97 (267)
Q Consensus 78 ~~~C~~Cg~~f--------~~y~C~~C~ 97 (267)
++.|+.||..+ +.|||+.|.
T Consensus 244 g~pCprCG~~I~~~~~~gR~t~~CP~CQ 271 (272)
T PRK14810 244 GEPCLNCKTPIRRVVVAGRSSHYCPHCQ 271 (272)
T ss_pred CCcCCCCCCeeEEEEECCCccEECcCCc
Confidence 46899999887 578888874
No 254
>COG5273 Uncharacterized protein containing DHHC-type Zn finger [General function prediction only]
Probab=25.61 E-value=32 Score=32.65 Aligned_cols=44 Identities=27% Similarity=0.596 Sum_probs=30.9
Q ss_pred ccCCcCCCccceeeccccccccCCCCcCeeecCCCCcccccCccceeecCccCccccccccCcceee
Q 024483 79 QVCTNCGVNMGEYFCDICKFYDDDIEKGQFHCDDCGICRIGGRENYFHCKRCGSCYSTSLRNNHLCI 145 (267)
Q Consensus 79 ~~C~~Cg~~f~~y~C~~C~l~dd~~~k~~yHC~~CgiCR~G~~~~~fHC~~C~~C~s~~l~~~H~C~ 145 (267)
..+...|....+-||.+|+.|-- +-.-||..||.|+-+- +|.|+
T Consensus 98 ~~~~~~~~~~~~~~C~~C~~~KP--------------------~RS~HC~~Cn~CV~k~---DHHC~ 141 (309)
T COG5273 98 SRLLDDGKFGTENFCSTCNIYKP--------------------PRSHHCSICNRCVLKF---DHHCP 141 (309)
T ss_pred hhhhhcCccccceeccccccccC--------------------CCCccchhhcchhhcc---CccCc
Confidence 45666778888889999988843 2366777777777653 56664
No 255
>PRK00464 nrdR transcriptional regulator NrdR; Validated
Probab=24.97 E-value=43 Score=28.83 Aligned_cols=12 Identities=25% Similarity=0.839 Sum_probs=5.7
Q ss_pred cCCcCCCcccee
Q 024483 80 VCTNCGVNMGEY 91 (267)
Q Consensus 80 ~C~~Cg~~f~~y 91 (267)
.|++||..|+.|
T Consensus 30 ~c~~c~~~f~~~ 41 (154)
T PRK00464 30 ECLACGKRFTTF 41 (154)
T ss_pred eccccCCcceEe
Confidence 344455544444
No 256
>PRK04136 rpl40e 50S ribosomal protein L40e; Provisional
Probab=24.48 E-value=46 Score=23.48 Aligned_cols=24 Identities=33% Similarity=0.875 Sum_probs=19.8
Q ss_pred cceeeeCCCCccccc-cccCCcCCC
Q 024483 63 VKQVICSVCDTEQPV-AQVCTNCGV 86 (267)
Q Consensus 63 ~~~v~C~~C~~~q~v-~~~C~~Cg~ 86 (267)
...++|+.|+...++ +..|..||.
T Consensus 12 ~~k~ICrkC~ARnp~~A~~CRKCg~ 36 (48)
T PRK04136 12 FNKKICMRCNARNPWRATKCRKCGY 36 (48)
T ss_pred hcccchhcccCCCCccccccccCCC
Confidence 357899999998887 568988886
No 257
>PF11781 RRN7: RNA polymerase I-specific transcription initiation factor Rrn7; InterPro: IPR021752 Rrn7 is a transcription binding factor that associates strongly with both Rrn6 and Rrn11 to form a complex which itself binds the TATA-binding protein and is required for transcription by the core domain of the RNA PolI promoter [],[].
Probab=24.32 E-value=42 Score=21.93 Aligned_cols=24 Identities=33% Similarity=0.683 Sum_probs=18.1
Q ss_pred CchhhhhhcccCCccEEe-ccCCcc
Q 024483 153 CPICYEYLFDSLRNTTVM-KCGHTM 176 (267)
Q Consensus 153 CpICle~lf~s~~~v~~L-pCGH~~ 176 (267)
|++|...+|.+.+....- .|||.+
T Consensus 11 C~~C~~~~~~~~dG~~yC~~cG~~~ 35 (36)
T PF11781_consen 11 CPVCGSRWFYSDDGFYYCDRCGHQS 35 (36)
T ss_pred CCCCCCeEeEccCCEEEhhhCceEc
Confidence 999999877776666665 788864
No 258
>PRK14811 formamidopyrimidine-DNA glycosylase; Provisional
Probab=24.14 E-value=43 Score=31.01 Aligned_cols=20 Identities=40% Similarity=1.102 Sum_probs=15.6
Q ss_pred cccCCcCCCcc--------ceeeccccc
Q 024483 78 AQVCTNCGVNM--------GEYFCDICK 97 (267)
Q Consensus 78 ~~~C~~Cg~~f--------~~y~C~~C~ 97 (267)
++.|+.||..+ +.|||+.|.
T Consensus 235 g~pC~~Cg~~I~~~~~~gR~ty~Cp~CQ 262 (269)
T PRK14811 235 GQPCPRCGTPIEKIVVGGRGTHFCPQCQ 262 (269)
T ss_pred cCCCCcCCCeeEEEEECCCCcEECCCCc
Confidence 46799998887 578888885
No 259
>TIGR02487 NrdD anaerobic ribonucleoside-triphosphate reductase. This model represents the oxygen-sensitive (anaerobic, class III) ribonucleotide reductase. The mechanism of the enzyme involves a glycine-centered radical, a C-terminal zinc binding site, and a set of conserved active site cysteines and asparagines. This enzyme requires an activating component, NrdG, a radical-SAM domain containing enzyme (TIGR02491). Together the two form an alpha-2/beta-2 heterodimer.
Probab=23.89 E-value=68 Score=33.07 Aligned_cols=31 Identities=32% Similarity=0.632 Sum_probs=21.6
Q ss_pred EEEcCCCCCccccceeEeeecCCCCCCccccccCC
Q 024483 228 WILCNDCNDTTEVYFHIIGQKCSHCKSYNTRSIAP 262 (267)
Q Consensus 228 ~I~CnDC~~~s~~~fH~lg~kC~~C~SyNT~~~~~ 262 (267)
.-.|++||..... +.-+|+.|||-|..++++
T Consensus 524 ~~~C~~CG~~g~~----~~~~CP~Cgs~~~~~~~R 554 (579)
T TIGR02487 524 VDVCEDCGYTGEG----LNDKCPKCGSHDIEVISR 554 (579)
T ss_pred CccCCCCCCCCCC----CCCcCcCCCCccceehhh
Confidence 4569999974432 235899999988665543
No 260
>PRK10445 endonuclease VIII; Provisional
Probab=23.84 E-value=44 Score=30.79 Aligned_cols=20 Identities=30% Similarity=0.894 Sum_probs=15.2
Q ss_pred cccCCcCCCcc--------ceeeccccc
Q 024483 78 AQVCTNCGVNM--------GEYFCDICK 97 (267)
Q Consensus 78 ~~~C~~Cg~~f--------~~y~C~~C~ 97 (267)
++.|+.||... +.|||+.|.
T Consensus 235 g~~Cp~Cg~~I~~~~~~gR~t~~CP~CQ 262 (263)
T PRK10445 235 GEACERCGGIIEKTTLSSRPFYWCPGCQ 262 (263)
T ss_pred CCCCCCCCCEeEEEEECCCCcEECCCCc
Confidence 57899999887 567777763
No 261
>cd00112 LDLa Low Density Lipoprotein Receptor Class A domain, a cysteine-rich repeat that plays a central role in mammalian cholesterol metabolism; the receptor protein binds LDL and transports it into cells by endocytosis; 7 successive cysteine-rich repeats of about 40 amino acids are present in the N-terminal of this multidomain membrane protein; other homologous domains occur in related receptors, including the very low-density lipoprotein receptor and the LDL receptor-related protein/alpha 2-macroglobulin receptor, and in proteins which are functionally unrelated, such as the C9 component of complement; the binding of calcium is required for in vitro formation of the native disulfide isomer and is necessary in establishing and maintaining the modular structure
Probab=23.73 E-value=57 Score=20.76 Aligned_cols=30 Identities=30% Similarity=0.658 Sum_probs=19.5
Q ss_pred ceeecCccCcccccccc--CcceeecCCCCCCC
Q 024483 123 NYFHCKRCGSCYSTSLR--NNHLCIENSMHHHC 153 (267)
Q Consensus 123 ~~fHC~~C~~C~s~~l~--~~H~C~e~~~~~~C 153 (267)
+.|.|.. +.|++..+. +.--|..++.+.+|
T Consensus 4 ~~f~C~~-~~Ci~~~~~CDg~~DC~dgsDE~~C 35 (35)
T cd00112 4 NEFRCAN-GRCIPSSWVCDGEDDCGDGSDEENC 35 (35)
T ss_pred CeEEcCC-CCeeCHHHcCCCccCCCCCcccccC
Confidence 5788888 899888754 34445555555443
No 262
>PF01363 FYVE: FYVE zinc finger; InterPro: IPR000306 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. The FYVE zinc finger is named after four proteins that it has been found in: Fab1, YOTB/ZK632.12, Vac1, and EEA1. The FYVE finger has been shown to bind two zinc ions []. The FYVE finger has eight potential zinc coordinating cysteine positions. Many members of this family also include two histidines in a motif R+HHC+XCG, where + represents a charged residue and X any residue. FYVE-type domains are divided into two known classes: FYVE domains that specifically bind to phosphatidylinositol 3-phosphate in lipid bilayers and FYVE-related domains of undetermined function []. Those that bind to phosphatidylinositol 3-phosphate are often found in proteins targeted to lipid membranes that are involved in regulating membrane traffic [, , ]. Most FYVE domains target proteins to endosomes by binding specifically to phosphatidylinositol-3-phosphate at the membrane surface. By contrast, the CARP2 FYVE-like domain is not optimized to bind to phosphoinositides or insert into lipid bilayers. FYVE domains are distinguished from other zinc fingers by three signature sequences: an N-terminal WxxD motif, a basic R(R/K)HHCR patch, and a C-terminal RVC motif. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0046872 metal ion binding; PDB: 1HYI_A 1JOC_B 1HYJ_A 1DVP_A 3ZYQ_A 4AVX_A 1VFY_A 3T7L_A 1X4U_A 1WFK_A ....
Probab=23.61 E-value=48 Score=23.70 Aligned_cols=25 Identities=32% Similarity=0.789 Sum_probs=10.8
Q ss_pred cccCCcCCCccceeeccccccccCCCCcCeeecCCCCc
Q 024483 78 AQVCTNCGVNMGEYFCDICKFYDDDIEKGQFHCDDCGI 115 (267)
Q Consensus 78 ~~~C~~Cg~~f~~y~C~~C~l~dd~~~k~~yHC~~Cgi 115 (267)
+..|..|+..|+- -+..+||..||.
T Consensus 9 ~~~C~~C~~~F~~-------------~~rrhhCr~CG~ 33 (69)
T PF01363_consen 9 ASNCMICGKKFSL-------------FRRRHHCRNCGR 33 (69)
T ss_dssp -SB-TTT--B-BS-------------SS-EEE-TTT--
T ss_pred CCcCcCcCCcCCC-------------ceeeEccCCCCC
Confidence 4567778787752 256788888874
No 263
>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=23.10 E-value=56 Score=22.08 Aligned_cols=13 Identities=23% Similarity=0.772 Sum_probs=8.0
Q ss_pred cccCCcCCCccce
Q 024483 78 AQVCTNCGVNMGE 90 (267)
Q Consensus 78 ~~~C~~Cg~~f~~ 90 (267)
+..|+.||.++-+
T Consensus 17 ~~~Cp~C~~PL~~ 29 (41)
T PF06677_consen 17 DEHCPDCGTPLMR 29 (41)
T ss_pred cCccCCCCCeeEE
Confidence 3567777776533
No 264
>PF12675 DUF3795: Protein of unknown function (DUF3795); InterPro: IPR024227 This family of proteins is functionally uncharacterised and is found in bacteria and archaea. Proteins in this family are typically between 99 and 171 amino acids in length. These proteins are likely to be zinc binding given the conserved cysteines.
Probab=22.67 E-value=45 Score=25.03 Aligned_cols=37 Identities=30% Similarity=0.644 Sum_probs=24.5
Q ss_pred cccCCcCCCccceeeccccccccCCCCcCeeecCCCC
Q 024483 78 AQVCTNCGVNMGEYFCDICKFYDDDIEKGQFHCDDCG 114 (267)
Q Consensus 78 ~~~C~~Cg~~f~~y~C~~C~l~dd~~~k~~yHC~~Cg 114 (267)
...|+.|...=....+..|.+.+=-.+|.+-||-.|.
T Consensus 34 ~~~C~GCr~~~~~~~~~~C~i~~C~~ekgv~~C~eC~ 70 (78)
T PF12675_consen 34 KIRCPGCRSGGGKCCCKSCKIRQCAKEKGVDFCGECP 70 (78)
T ss_pred CCcCcCCcCCCCCcCCCCCCcCcHHhhCCCCeeecCC
Confidence 4468877655444777778777665667777776663
No 265
>PRK07111 anaerobic ribonucleoside triphosphate reductase; Provisional
Probab=22.58 E-value=91 Score=33.25 Aligned_cols=44 Identities=20% Similarity=0.293 Sum_probs=27.7
Q ss_pred HHhcCCChhhhcCeeEEEcCCCCCccccceeEeeecCCCCCCccccccCC
Q 024483 213 IEATVMPEDYRHKKVWILCNDCNDTTEVYFHIIGQKCSHCKSYNTRSIAP 262 (267)
Q Consensus 213 i~~~pmP~~y~~~~v~I~CnDC~~~s~~~fH~lg~kC~~C~SyNT~~~~~ 262 (267)
+..+.+|-.--+.. .-.|++||.... +| .+|+.|||-|+.++++
T Consensus 666 ~~~~~i~Y~sin~~-~~~C~~CG~~~~--~~---~~CP~CG~~~~~~~~R 709 (735)
T PRK07111 666 MKNTNIGYGSINHP-VDRCPVCGYLGV--IE---DKCPKCGSTNIQRIRR 709 (735)
T ss_pred HHhCCCceEEeCCC-CeecCCCCCCCC--cC---ccCcCCCCccceeeeh
Confidence 44455655433333 456999996443 23 6999999977666543
No 266
>PRK01103 formamidopyrimidine/5-formyluracil/ 5-hydroxymethyluracil DNA glycosylase; Validated
Probab=22.52 E-value=49 Score=30.58 Aligned_cols=20 Identities=30% Similarity=1.090 Sum_probs=15.0
Q ss_pred cccCCcCCCcc--------ceeeccccc
Q 024483 78 AQVCTNCGVNM--------GEYFCDICK 97 (267)
Q Consensus 78 ~~~C~~Cg~~f--------~~y~C~~C~ 97 (267)
++.|+.||... +.|||+.|.
T Consensus 245 g~pC~~Cg~~I~~~~~~gR~t~~CP~CQ 272 (274)
T PRK01103 245 GEPCRRCGTPIEKIKQGGRSTFFCPRCQ 272 (274)
T ss_pred CCCCCCCCCeeEEEEECCCCcEECcCCC
Confidence 46799999887 567777773
No 267
>PRK01110 rpmF 50S ribosomal protein L32; Validated
Probab=22.50 E-value=72 Score=23.20 Aligned_cols=30 Identities=10% Similarity=0.073 Sum_probs=22.0
Q ss_pred EEEcCCCCCccccceeEeeecCCCCCCccccccCCC
Q 024483 228 WILCNDCNDTTEVYFHIIGQKCSHCKSYNTRSIAPP 263 (267)
Q Consensus 228 ~I~CnDC~~~s~~~fH~lg~kC~~C~SyNT~~~~~~ 263 (267)
.+.|..||.. ...|-+ |. ||.|+.+++-.+
T Consensus 27 ~~~c~~cg~~--~~pH~v---c~-cG~Y~gr~v~~~ 56 (60)
T PRK01110 27 LSVDKTTGEY--HLPHHV---SP-KGYYKGRKVLKK 56 (60)
T ss_pred eeEcCCCCce--ecccee---cC-CcccCCeEeecc
Confidence 5789999964 334544 88 999999997543
No 268
>TIGR00244 transcriptional regulator NrdR. Members of this almost entirely bacterial family contain an ATP cone domain (PFAM:PF03477). There is never more than one member per genome. Common gene symbols given include nrdR, ybaD, ribX and ytcG. The member from Streptomyces coelicolor is found upstream in the operon of the class II oxygen-independent ribonucleotide reductase gene nrdJ and was shown to repress nrdJ expression. Many members of this family are found near genes for riboflavin biosynthesis in Gram-negative bacteria, suggesting a role in that pathway. However, a phylogenetic profiling study associates members of this family with the presence of a palindromic signal with consensus acaCwAtATaTwGtgt, termed the NrdR-box, an upstream element for most operons for ribonucleotide reductase of all three classes in bacterial genomes.
Probab=22.36 E-value=56 Score=28.12 Aligned_cols=13 Identities=15% Similarity=0.634 Sum_probs=11.5
Q ss_pred ccCCcCCCcccee
Q 024483 79 QVCTNCGVNMGEY 91 (267)
Q Consensus 79 ~~C~~Cg~~f~~y 91 (267)
-.|++||..|..|
T Consensus 29 ReC~~C~~RFTTy 41 (147)
T TIGR00244 29 RECLECHERFTTF 41 (147)
T ss_pred ccCCccCCcccee
Confidence 3799999999998
No 269
>COG1144 Pyruvate:ferredoxin oxidoreductase and related 2-oxoacid:ferredoxin oxidoreductases, delta subunit [Energy production and conversion]
Probab=22.35 E-value=41 Score=26.76 Aligned_cols=15 Identities=40% Similarity=0.906 Sum_probs=12.4
Q ss_pred cceeecCccCccccc
Q 024483 122 ENYFHCKRCGSCYST 136 (267)
Q Consensus 122 ~~~fHC~~C~~C~s~ 136 (267)
.||-+|+.||.|.+.
T Consensus 63 idYdyCKGCGICa~v 77 (91)
T COG1144 63 IDYDYCKGCGICANV 77 (91)
T ss_pred eEcccccCceechhh
Confidence 488899999999764
No 270
>cd07973 Spt4 Transcription elongation factor Spt4. Spt4 is a transcription elongation factor. Three transcription-elongation factors Spt4, Spt5, and Spt6, are conserved among eukaryotes and are essential for transcription via the modulation of chromatin structure. It is known that Spt4, Spt5, and Spt6 are general transcription-elongation factors, controlling transcription both positively and negatively in important regulatory and developmental roles. Spt4 functions entirely in the context of the Spt4-Spt5 heterodimer and it has been found only as a complex to Spt5 in Yeast and Human. Spt4 is a small protein that has zinc finger at the N-terminus. Spt5 is a large protein that has several interesting structural features of an acidic N-terminus, a single NGN domain, five or six KOW domains, and a set of simple C-termianl repeats. Spt4 binds to Spt5 NGN domain. Unlike Spt5, Spt4 is not essential for viability in yeast, however Spt4 is critical for normal function of the Spt4-Spt5 compl
Probab=22.34 E-value=47 Score=26.61 Aligned_cols=20 Identities=25% Similarity=0.637 Sum_probs=14.3
Q ss_pred eeCCCCcccccc----ccCCcCCC
Q 024483 67 ICSVCDTEQPVA----QVCTNCGV 86 (267)
Q Consensus 67 ~C~~C~~~q~v~----~~C~~Cg~ 86 (267)
-|+.|+..++.. +.|+||+.
T Consensus 5 AC~~C~~I~~~~qf~~~gCpnC~~ 28 (98)
T cd07973 5 ACLLCSLIKTEDQFERDGCPNCEG 28 (98)
T ss_pred hhccCCcccccccccCCCCCCCcc
Confidence 588888777654 47888863
No 271
>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=22.23 E-value=67 Score=22.16 Aligned_cols=28 Identities=18% Similarity=0.516 Sum_probs=17.5
Q ss_pred EEcCCCCCccccceeEeeecCCCCCCccccc
Q 024483 229 ILCNDCNDTTEVYFHIIGQKCSHCKSYNTRS 259 (267)
Q Consensus 229 I~CnDC~~~s~~~fH~lg~kC~~C~SyNT~~ 259 (267)
|.|+-|.+..-+.++ .+|..|..|+.-+
T Consensus 1 ~~C~~C~~~~i~g~R---~~C~~C~dydLC~ 28 (49)
T cd02345 1 LSCSACRKQDISGIR---FPCQVCRDYSLCL 28 (49)
T ss_pred CcCCCCCCCCceEee---EECCCCCCcCchH
Confidence 468888875444333 4777777776543
No 272
>PTZ00083 40S ribosomal protein S27; Provisional
Probab=22.22 E-value=53 Score=25.80 Aligned_cols=37 Identities=19% Similarity=0.404 Sum_probs=27.6
Q ss_pred ceeeeCCCCccccc------cccCCcCCCccceeecccccccc
Q 024483 64 KQVICSVCDTEQPV------AQVCTNCGVNMGEYFCDICKFYD 100 (267)
Q Consensus 64 ~~v~C~~C~~~q~v------~~~C~~Cg~~f~~y~C~~C~l~d 100 (267)
-.|.|..|..+|.| ...|..||..+++-.=.+.+|-+
T Consensus 34 m~VkCp~C~n~q~VFShA~t~V~C~~Cg~~L~~PTGGKa~l~~ 76 (85)
T PTZ00083 34 MDVKCPGCSQITTVFSHAQTVVLCGGCSSQLCQPTGGKAKLTE 76 (85)
T ss_pred EEEECCCCCCeeEEEecCceEEEccccCCEeeccCCCCeEecC
Confidence 36889999999887 24799999888776666655544
No 273
>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=22.22 E-value=70 Score=21.56 Aligned_cols=11 Identities=36% Similarity=0.939 Sum_probs=5.0
Q ss_pred CcCeeecCCCC
Q 024483 104 EKGQFHCDDCG 114 (267)
Q Consensus 104 ~k~~yHC~~Cg 114 (267)
.++-|+|..|+
T Consensus 25 ~~~g~~C~~C~ 35 (53)
T PF00130_consen 25 GKQGYRCSWCG 35 (53)
T ss_dssp SSCEEEETTTT
T ss_pred CCCeEEECCCC
Confidence 34444444444
No 274
>PF01927 Mut7-C: Mut7-C RNAse domain; InterPro: IPR002782 This prokaryotic family of proteins have no known function. The proteins contain four conserved cysteines that may be involved in metal binding or disulphide bridges.
Probab=21.69 E-value=64 Score=27.00 Aligned_cols=49 Identities=22% Similarity=0.392 Sum_probs=29.8
Q ss_pred CCCCCCCCccccchhHHhHHhHHHHHhcCCChh-hhcCeeEEEcCCCCCccccceeE
Q 024483 189 KYCCPICSKSVIDMSRTWKRIDEEIEATVMPED-YRHKKVWILCNDCNDTTEVYFHI 244 (267)
Q Consensus 189 ~~~CPiCrks~~dm~~~~~~lD~~i~~~pmP~~-y~~~~v~I~CnDC~~~s~~~fH~ 244 (267)
-.+||.|+..+...++ +++.. .+|+. ++....--.|..|++.-+..-||
T Consensus 91 ~sRC~~CN~~L~~v~~------~~v~~-~vp~~v~~~~~~f~~C~~C~kiyW~GsH~ 140 (147)
T PF01927_consen 91 FSRCPKCNGPLRPVSK------EEVKD-RVPPYVYETYDEFWRCPGCGKIYWEGSHW 140 (147)
T ss_pred CCccCCCCcEeeechh------hcccc-ccCccccccCCeEEECCCCCCEecccccH
Confidence 3689999998775433 11222 24444 44434457799999876666554
No 275
>PF09297 zf-NADH-PPase: NADH pyrophosphatase zinc ribbon domain; InterPro: IPR015376 This domain has a zinc ribbon structure and is often found between two NUDIX domains.; GO: 0016787 hydrolase activity, 0046872 metal ion binding; PDB: 1VK6_A 2GB5_A.
Probab=21.69 E-value=31 Score=21.52 Aligned_cols=21 Identities=29% Similarity=0.819 Sum_probs=9.4
Q ss_pred eeCCCCccccc-----cccCCcCCCc
Q 024483 67 ICSVCDTEQPV-----AQVCTNCGVN 87 (267)
Q Consensus 67 ~C~~C~~~q~v-----~~~C~~Cg~~ 87 (267)
.|+.|+.+..+ +..|+.||..
T Consensus 5 fC~~CG~~t~~~~~g~~r~C~~Cg~~ 30 (32)
T PF09297_consen 5 FCGRCGAPTKPAPGGWARRCPSCGHE 30 (32)
T ss_dssp B-TTT--BEEE-SSSS-EEESSSS-E
T ss_pred ccCcCCccccCCCCcCEeECCCCcCE
Confidence 46777765433 2367777653
No 276
>PRK05580 primosome assembly protein PriA; Validated
Probab=21.55 E-value=1.1e+02 Score=32.17 Aligned_cols=25 Identities=16% Similarity=0.474 Sum_probs=18.8
Q ss_pred ccceeeeCCCCccccccccCCcCCCccce
Q 024483 62 DVKQVICSVCDTEQPVAQVCTNCGVNMGE 90 (267)
Q Consensus 62 ~~~~v~C~~C~~~q~v~~~C~~Cg~~f~~ 90 (267)
-...++|..|+.. ..|++|+..+.-
T Consensus 378 y~~~~~C~~Cg~~----~~C~~C~~~l~~ 402 (679)
T PRK05580 378 YAPFLLCRDCGWV----AECPHCDASLTL 402 (679)
T ss_pred CCCceEhhhCcCc----cCCCCCCCceeE
Confidence 3457889999865 479999988743
No 277
>PF13913 zf-C2HC_2: zinc-finger of a C2HC-type
Probab=21.44 E-value=45 Score=19.86 Aligned_cols=12 Identities=25% Similarity=0.664 Sum_probs=9.1
Q ss_pred ccCCcCCCccce
Q 024483 79 QVCTNCGVNMGE 90 (267)
Q Consensus 79 ~~C~~Cg~~f~~ 90 (267)
..|+.||..|+.
T Consensus 3 ~~C~~CgR~F~~ 14 (25)
T PF13913_consen 3 VPCPICGRKFNP 14 (25)
T ss_pred CcCCCCCCEECH
Confidence 368889988863
No 278
>KOG4399 consensus C2HC-type Zn-finger protein [General function prediction only]
Probab=21.39 E-value=24 Score=33.30 Aligned_cols=52 Identities=17% Similarity=0.180 Sum_probs=39.3
Q ss_pred cCCcCCCccceeeccccccccCCCCcCeeecCCCCcccccCccceeecCccCcccc
Q 024483 80 VCTNCGVNMGEYFCDICKFYDDDIEKGQFHCDDCGICRIGGRENYFHCKRCGSCYS 135 (267)
Q Consensus 80 ~C~~Cg~~f~~y~C~~C~l~dd~~~k~~yHC~~CgiCR~G~~~~~fHC~~C~~C~s 135 (267)
.|+-|...-+.-||.||-=+|.. .-|||.|.-||--..-.+-||+.|..|..
T Consensus 251 ~C~~~~~~A~~~~C~iC~~~~~~----R~~C~~~kA~~~~~Q~K~N~~~~~~~~~q 302 (325)
T KOG4399|consen 251 HCSICNHCAVKHGCFICGELDHK----RSTCPNIKAVRKQKQRKSNKMKMETTKGQ 302 (325)
T ss_pred eeecccchhhhcceeeccccccc----cccCccHHHHHHHHhcccchhhhhhhhhh
Confidence 56666677778889999888752 27899998888876556778888877765
No 279
>PF14354 Lar_restr_allev: Restriction alleviation protein Lar
Probab=21.27 E-value=59 Score=22.75 Aligned_cols=10 Identities=30% Similarity=1.052 Sum_probs=8.8
Q ss_pred eEEEcCCCCC
Q 024483 227 VWILCNDCND 236 (267)
Q Consensus 227 v~I~CnDC~~ 236 (267)
..|.|.+|++
T Consensus 28 ~~V~C~~Cga 37 (61)
T PF14354_consen 28 YYVECTDCGA 37 (61)
T ss_pred EEEEcCCCCC
Confidence 6799999997
No 280
>KOG1100 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=21.11 E-value=40 Score=30.32 Aligned_cols=39 Identities=26% Similarity=0.532 Sum_probs=27.9
Q ss_pred CchhhhhhcccCCccEEeccCCccC-hhhHHHHhcCCCCCCCCCCcccc
Q 024483 153 CPICYEYLFDSLRNTTVMKCGHTMH-CECYHEMIKRDKYCCPICSKSVI 200 (267)
Q Consensus 153 CpICle~lf~s~~~v~~LpCGH~~H-~~C~~~~~~~~~~~CPiCrks~~ 200 (267)
|-+|.+. ...|..|||.|..+ ..|-.. -.+||+|+....
T Consensus 161 Cr~C~~~----~~~VlllPCrHl~lC~~C~~~-----~~~CPiC~~~~~ 200 (207)
T KOG1100|consen 161 CRKCGER----EATVLLLPCRHLCLCGICDES-----LRICPICRSPKT 200 (207)
T ss_pred ceecCcC----CceEEeecccceEeccccccc-----CccCCCCcChhh
Confidence 9999885 24588899997654 455532 356999997664
No 281
>PF08792 A2L_zn_ribbon: A2L zinc ribbon domain; InterPro: IPR014900 This zinc ribbon protein is found associated with some viral A2L transcription factors [].
Probab=21.02 E-value=59 Score=20.87 Aligned_cols=10 Identities=30% Similarity=0.620 Sum_probs=4.5
Q ss_pred eeeCCCCccc
Q 024483 66 VICSVCDTEQ 75 (267)
Q Consensus 66 v~C~~C~~~q 75 (267)
.+|..|+...
T Consensus 4 ~~C~~C~~~~ 13 (33)
T PF08792_consen 4 KKCSKCGGNG 13 (33)
T ss_pred eEcCCCCCCe
Confidence 3444454443
No 282
>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=21.01 E-value=37 Score=22.39 Aligned_cols=13 Identities=54% Similarity=1.196 Sum_probs=5.5
Q ss_pred cceeecccccccc
Q 024483 88 MGEYFCDICKFYD 100 (267)
Q Consensus 88 f~~y~C~~C~l~d 100 (267)
|-+|||+-|+.|-
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 4589999998774
No 283
>PF14445 Prok-RING_2: Prokaryotic RING finger family 2
Probab=20.60 E-value=6.8 Score=28.09 Aligned_cols=46 Identities=22% Similarity=0.592 Sum_probs=26.0
Q ss_pred CccceeeccccccccCCCCcCeeecCCCCcccccC-----ccceeecCccCccccc
Q 024483 86 VNMGEYFCDICKFYDDDIEKGQFHCDDCGICRIGG-----RENYFHCKRCGSCYST 136 (267)
Q Consensus 86 ~~f~~y~C~~C~l~dd~~~k~~yHC~~CgiCR~G~-----~~~~fHC~~C~~C~s~ 136 (267)
+.|++|.|+.|+--- +.+.--.| -||-..+ .+.|+-|+.||.=+.+
T Consensus 3 ~SFsry~CDLCn~~~--p~~~LRQC---vlCGRWaC~sCW~deYY~CksC~Gii~l 53 (57)
T PF14445_consen 3 HSFSRYSCDLCNSSH--PISELRQC---VLCGRWACNSCWQDEYYTCKSCNGIINL 53 (57)
T ss_pred hHHhhHhHHhhcccC--cHHHHHHH---hhhchhhhhhhhhhhHhHHHhhhchhhh
Confidence 467788888776322 22222223 3333332 5778888888765544
No 284
>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=20.56 E-value=68 Score=19.57 Aligned_cols=18 Identities=17% Similarity=0.551 Sum_probs=13.7
Q ss_pred CCCCCCCCCccccchhHH
Q 024483 188 DKYCCPICSKSVIDMSRT 205 (267)
Q Consensus 188 ~~~~CPiCrks~~dm~~~ 205 (267)
+.+.|.+|.+++.+...+
T Consensus 2 ~~~~C~~C~~~~~~~~~~ 19 (35)
T smart00451 2 GGFYCKLCNVTFTDEISV 19 (35)
T ss_pred cCeEccccCCccCCHHHH
Confidence 357899999999865443
No 285
>PRK13945 formamidopyrimidine-DNA glycosylase; Provisional
Probab=20.29 E-value=58 Score=30.29 Aligned_cols=19 Identities=26% Similarity=0.933 Sum_probs=14.2
Q ss_pred cccCCcCCCcc--------ceeecccc
Q 024483 78 AQVCTNCGVNM--------GEYFCDIC 96 (267)
Q Consensus 78 ~~~C~~Cg~~f--------~~y~C~~C 96 (267)
++.|+.||... +.|||+.|
T Consensus 254 g~pC~~Cg~~I~~~~~~gR~t~~CP~C 280 (282)
T PRK13945 254 GKPCRKCGTPIERIKLAGRSTHWCPNC 280 (282)
T ss_pred cCCCCcCCCeeEEEEECCCccEECCCC
Confidence 46899998887 55777766
No 286
>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=20.26 E-value=58 Score=30.14 Aligned_cols=19 Identities=37% Similarity=1.111 Sum_probs=14.1
Q ss_pred cccCCcCCCcc--------ceeecccc
Q 024483 78 AQVCTNCGVNM--------GEYFCDIC 96 (267)
Q Consensus 78 ~~~C~~Cg~~f--------~~y~C~~C 96 (267)
++.|+.||... +.|||+.|
T Consensus 245 g~pC~~Cg~~I~~~~~~gR~t~~CP~C 271 (272)
T TIGR00577 245 GEPCRRCGTPIEKIKVGGRGTHFCPQC 271 (272)
T ss_pred CCCCCCCCCeeEEEEECCCCCEECCCC
Confidence 46899998877 55777766
No 287
>PRK08351 DNA-directed RNA polymerase subunit E''; Validated
Probab=20.02 E-value=62 Score=23.83 Aligned_cols=20 Identities=25% Similarity=0.693 Sum_probs=12.9
Q ss_pred eeCCCCccccccccCCcCCCc
Q 024483 67 ICSVCDTEQPVAQVCTNCGVN 87 (267)
Q Consensus 67 ~C~~C~~~q~v~~~C~~Cg~~ 87 (267)
-|..|...++ .+.||+||..
T Consensus 5 AC~~C~~i~~-~~~CP~Cgs~ 24 (61)
T PRK08351 5 ACRHCHYITT-EDRCPVCGSR 24 (61)
T ss_pred hhhhCCcccC-CCcCCCCcCC
Confidence 5666766653 3468888764
Done!