Query 024406
Match_columns 268
No_of_seqs 222 out of 681
Neff 5.4
Searched_HMMs 46136
Date Fri Mar 29 04:20:32 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/024406.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/024406hhsearch_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 1.5E-71 3.2E-76 509.7 8.5 252 4-267 21-272 (276)
2 PF14599 zinc_ribbon_6: Zinc-r 100.0 1.1E-31 2.3E-36 196.3 0.7 61 200-260 1-61 (61)
3 PF05495 zf-CHY: CHY zinc fing 99.9 5E-24 1.1E-28 160.1 3.3 70 18-100 1-71 (71)
4 COG4357 Zinc finger domain con 99.6 5.3E-16 1.1E-20 122.3 2.1 73 15-90 12-92 (105)
5 PF13639 zf-RING_2: Ring finge 99.4 1.1E-13 2.4E-18 93.9 1.8 44 151-197 1-44 (44)
6 PF12678 zf-rbx1: RING-H2 zinc 99.0 1.7E-10 3.7E-15 87.0 3.0 48 148-197 17-73 (73)
7 cd00162 RING RING-finger (Real 99.0 5.8E-10 1.3E-14 73.2 3.7 45 152-200 1-45 (45)
8 COG5243 HRD1 HRD ubiquitin lig 98.9 2.9E-10 6.4E-15 108.5 1.9 57 147-205 284-350 (491)
9 KOG4628 Predicted E3 ubiquitin 98.9 8.8E-10 1.9E-14 105.0 2.4 50 151-202 230-279 (348)
10 PF13923 zf-C3HC4_2: Zinc fing 98.8 1.6E-09 3.6E-14 71.8 2.0 39 153-196 1-39 (39)
11 PHA02929 N1R/p28-like protein; 98.8 3.9E-09 8.4E-14 96.2 4.0 54 147-202 171-228 (238)
12 PF00097 zf-C3HC4: Zinc finger 98.7 9.3E-09 2E-13 68.3 1.9 41 153-196 1-41 (41)
13 PF13920 zf-C3HC4_3: Zinc fing 98.7 1.1E-08 2.4E-13 71.1 2.2 47 150-202 2-49 (50)
14 smart00184 RING Ring finger. E 98.6 2.5E-08 5.4E-13 63.1 2.9 39 153-196 1-39 (39)
15 PF14634 zf-RING_5: zinc-RING 98.6 2.9E-08 6.3E-13 67.6 2.4 44 152-198 1-44 (44)
16 COG5540 RING-finger-containing 98.5 6.3E-08 1.4E-12 90.7 3.1 53 146-200 319-371 (374)
17 PF13445 zf-RING_UBOX: RING-ty 98.5 7.5E-08 1.6E-12 66.0 2.6 41 153-194 1-43 (43)
18 PF15227 zf-C3HC4_4: zinc fing 98.4 1.2E-07 2.5E-12 64.5 2.3 40 153-196 1-42 (42)
19 PF12861 zf-Apc11: Anaphase-pr 98.4 1.9E-07 4.1E-12 72.7 3.1 48 152-201 34-82 (85)
20 KOG0804 Cytoplasmic Zn-finger 98.4 1.8E-07 4E-12 91.3 3.1 82 151-261 176-259 (493)
21 KOG0802 E3 ubiquitin ligase [P 98.4 1.2E-07 2.7E-12 95.1 1.6 53 146-200 287-340 (543)
22 PLN03208 E3 ubiquitin-protein 98.3 6.5E-07 1.4E-11 79.4 4.1 56 143-202 11-80 (193)
23 PHA02926 zinc finger-like prot 98.1 1.9E-06 4.2E-11 77.9 3.0 69 133-201 153-230 (242)
24 smart00744 RINGv The RING-vari 98.1 2.4E-06 5.1E-11 59.9 2.8 44 152-197 1-49 (49)
25 KOG0320 Predicted E3 ubiquitin 98.1 1.8E-06 3.8E-11 75.6 1.9 46 151-201 132-178 (187)
26 PF11793 FANCL_C: FANCL C-term 98.0 1.4E-06 3.1E-11 65.3 0.7 52 150-201 2-66 (70)
27 smart00504 Ubox Modified RING 98.0 5.5E-06 1.2E-10 59.2 3.5 45 151-201 2-46 (63)
28 KOG2177 Predicted E3 ubiquitin 97.8 2E-05 4.3E-10 68.5 3.6 44 149-198 12-55 (386)
29 TIGR00599 rad18 DNA repair pro 97.7 2.5E-05 5.4E-10 76.2 4.2 46 150-201 26-71 (397)
30 COG5194 APC11 Component of SCF 97.7 3.2E-05 6.9E-10 59.8 2.7 29 171-201 53-81 (88)
31 TIGR00570 cdk7 CDK-activating 97.5 9.6E-05 2.1E-09 69.9 3.6 50 150-201 3-54 (309)
32 KOG0317 Predicted E3 ubiquitin 97.4 5.5E-05 1.2E-09 70.6 1.4 45 151-201 240-284 (293)
33 KOG0823 Predicted E3 ubiquitin 97.3 0.00014 3.1E-09 66.0 2.7 51 148-202 45-96 (230)
34 KOG0827 Predicted E3 ubiquitin 97.3 0.0001 2.2E-09 71.4 1.6 47 150-197 4-52 (465)
35 KOG0287 Postreplication repair 97.2 0.00036 7.8E-09 66.8 4.0 58 151-214 24-82 (442)
36 KOG2164 Predicted E3 ubiquitin 97.1 0.00028 6E-09 70.3 2.7 51 148-202 184-237 (513)
37 KOG1941 Acetylcholine receptor 97.1 0.00017 3.6E-09 70.1 0.6 63 141-204 357-419 (518)
38 COG5219 Uncharacterized conser 97.0 0.00047 1E-08 73.0 2.9 55 147-201 1466-1523(1525)
39 PF04564 U-box: U-box domain; 96.9 0.001 2.3E-08 49.8 3.4 48 150-202 4-51 (73)
40 KOG0828 Predicted E3 ubiquitin 96.8 0.00034 7.4E-09 69.6 0.7 51 150-201 571-634 (636)
41 KOG1734 Predicted RING-contain 96.8 0.00035 7.6E-09 65.0 0.4 53 149-201 223-281 (328)
42 PF14835 zf-RING_6: zf-RING of 96.8 0.00047 1E-08 51.2 0.7 56 151-214 8-65 (65)
43 KOG1493 Anaphase-promoting com 96.7 0.00046 9.9E-09 53.0 0.5 30 171-200 50-80 (84)
44 KOG4265 Predicted E3 ubiquitin 96.6 0.0015 3.3E-08 62.7 2.9 51 146-202 286-337 (349)
45 COG5574 PEX10 RING-finger-cont 96.3 0.0016 3.6E-08 60.3 1.6 47 150-201 215-262 (271)
46 KOG2930 SCF ubiquitin ligase, 96.3 0.0024 5.2E-08 51.7 2.2 28 171-200 80-107 (114)
47 KOG1039 Predicted E3 ubiquitin 96.3 0.00095 2.1E-08 64.1 -0.4 84 147-232 158-252 (344)
48 KOG0825 PHD Zn-finger protein 96.2 0.002 4.4E-08 67.2 1.4 75 124-201 96-171 (1134)
49 PF14570 zf-RING_4: RING/Ubox 96.1 0.0033 7.2E-08 44.2 1.9 46 153-199 1-46 (48)
50 PF12906 RINGv: RING-variant d 96.1 0.0025 5.4E-08 44.2 1.1 42 153-196 1-47 (47)
51 KOG3002 Zn finger protein [Gen 96.1 0.0052 1.1E-07 58.1 3.4 64 150-225 48-113 (299)
52 PF11789 zf-Nse: Zinc-finger o 96.0 0.003 6.5E-08 45.6 1.0 45 148-195 9-53 (57)
53 KOG0311 Predicted E3 ubiquitin 95.9 0.0025 5.5E-08 61.2 0.4 49 150-202 43-91 (381)
54 KOG1785 Tyrosine kinase negati 95.8 0.0027 5.8E-08 62.1 0.4 55 144-202 363-417 (563)
55 KOG1645 RING-finger-containing 95.7 0.013 2.8E-07 57.4 4.4 51 150-200 4-55 (463)
56 KOG2879 Predicted E3 ubiquitin 95.6 0.008 1.7E-07 56.2 2.6 54 148-204 237-290 (298)
57 PF10367 Vps39_2: Vacuolar sor 95.5 0.0049 1.1E-07 48.0 0.8 37 144-182 72-108 (109)
58 KOG0978 E3 ubiquitin ligase in 95.3 0.005 1.1E-07 63.9 0.3 47 150-201 643-689 (698)
59 KOG4172 Predicted E3 ubiquitin 95.1 0.007 1.5E-07 43.9 0.4 52 148-204 5-57 (62)
60 KOG1428 Inhibitor of type V ad 95.1 0.025 5.5E-07 62.7 4.6 75 119-201 3462-3544(3738)
61 PRK14890 putative Zn-ribbon RN 95.1 0.02 4.3E-07 41.9 2.6 46 63-115 5-56 (59)
62 KOG3970 Predicted E3 ubiquitin 95.0 0.029 6.2E-07 51.4 4.2 52 148-201 48-105 (299)
63 COG5432 RAD18 RING-finger-cont 94.8 0.016 3.4E-07 54.9 2.0 46 150-201 25-70 (391)
64 PF14447 Prok-RING_4: Prokaryo 93.9 0.019 4.1E-07 41.5 0.4 32 166-201 19-50 (55)
65 KOG3268 Predicted E3 ubiquitin 93.9 0.034 7.5E-07 49.3 2.0 35 170-204 188-232 (234)
66 KOG4445 Uncharacterized conser 93.6 0.02 4.3E-07 54.4 -0.0 55 147-202 112-187 (368)
67 PF05883 Baculo_RING: Baculovi 93.5 0.033 7.2E-07 47.0 1.2 37 150-187 26-68 (134)
68 KOG2034 Vacuolar sorting prote 93.4 0.054 1.2E-06 57.5 2.8 45 142-188 809-853 (911)
69 KOG1571 Predicted E3 ubiquitin 92.8 0.052 1.1E-06 52.4 1.5 47 146-201 301-347 (355)
70 KOG3800 Predicted E3 ubiquitin 92.6 0.085 1.8E-06 49.7 2.6 48 152-201 2-51 (300)
71 PHA02862 5L protein; Provision 92.4 0.08 1.7E-06 45.4 1.9 60 149-212 1-63 (156)
72 TIGR00100 hypA hydrogenase nic 91.8 0.11 2.3E-06 42.4 2.0 38 225-264 66-103 (115)
73 KOG0824 Predicted E3 ubiquitin 91.8 0.085 1.8E-06 50.1 1.5 49 148-201 5-53 (324)
74 KOG4739 Uncharacterized protei 91.4 0.11 2.3E-06 47.7 1.8 37 161-201 12-48 (233)
75 PF12773 DZR: Double zinc ribb 91.4 0.2 4.4E-06 34.3 2.8 22 68-89 1-23 (50)
76 PHA02825 LAP/PHD finger-like p 91.2 0.16 3.4E-06 44.2 2.5 49 148-201 6-59 (162)
77 PRK03824 hypA hydrogenase nick 91.2 0.25 5.5E-06 41.4 3.7 38 227-264 68-124 (135)
78 COG2888 Predicted Zn-ribbon RN 91.1 0.15 3.2E-06 37.5 1.9 45 65-115 9-58 (61)
79 PRK00564 hypA hydrogenase nick 90.6 0.16 3.4E-06 41.7 1.9 38 225-264 67-105 (117)
80 KOG0309 Conserved WD40 repeat- 90.2 0.16 3.4E-06 53.5 1.9 43 149-195 1027-1069(1081)
81 PF04641 Rtf2: Rtf2 RING-finge 89.9 0.21 4.6E-06 46.0 2.3 51 147-201 110-161 (260)
82 PRK12380 hydrogenase nickel in 89.8 0.2 4.4E-06 40.7 1.9 37 226-264 67-103 (113)
83 KOG1814 Predicted E3 ubiquitin 89.8 0.18 3.8E-06 49.7 1.7 48 149-197 183-236 (445)
84 KOG0297 TNF receptor-associate 89.7 0.2 4.4E-06 48.9 2.2 52 148-204 19-70 (391)
85 KOG4185 Predicted E3 ubiquitin 89.7 0.21 4.6E-06 46.1 2.2 48 151-200 4-54 (296)
86 KOG4275 Predicted E3 ubiquitin 89.6 0.076 1.6E-06 50.3 -0.9 61 138-207 285-348 (350)
87 PRK03681 hypA hydrogenase nick 89.6 0.23 4.9E-06 40.5 2.0 38 226-264 67-104 (114)
88 PF07191 zinc-ribbons_6: zinc- 89.0 0.18 3.9E-06 38.2 1.0 36 64-99 16-59 (70)
89 COG5175 MOT2 Transcriptional r 88.5 0.11 2.5E-06 50.1 -0.5 57 150-207 14-70 (480)
90 PF03854 zf-P11: P-11 zinc fin 88.3 0.18 4E-06 35.5 0.5 32 168-201 14-46 (50)
91 PF01155 HypA: Hydrogenase exp 88.0 0.17 3.7E-06 41.0 0.3 37 226-264 67-103 (113)
92 COG5152 Uncharacterized conser 86.7 0.37 8.1E-06 43.6 1.7 59 151-215 197-255 (259)
93 COG5236 Uncharacterized conser 86.7 0.53 1.2E-05 45.8 2.8 66 131-200 42-107 (493)
94 PF13248 zf-ribbon_3: zinc-rib 86.5 0.35 7.6E-06 29.4 1.0 24 65-88 2-26 (26)
95 PF08746 zf-RING-like: RING-li 86.2 0.32 7E-06 33.1 0.8 26 171-196 18-43 (43)
96 PF07800 DUF1644: Protein of u 86.0 0.8 1.7E-05 39.8 3.3 34 150-187 2-48 (162)
97 KOG2817 Predicted E3 ubiquitin 85.9 0.73 1.6E-05 45.2 3.3 49 151-200 335-384 (394)
98 KOG3039 Uncharacterized conser 85.7 0.62 1.3E-05 43.4 2.6 56 146-204 217-273 (303)
99 KOG1813 Predicted E3 ubiquitin 85.6 0.39 8.5E-06 45.5 1.3 68 150-223 241-308 (313)
100 KOG4159 Predicted E3 ubiquitin 84.8 1.1 2.3E-05 44.3 3.9 49 148-202 82-130 (398)
101 PRK00762 hypA hydrogenase nick 84.0 0.72 1.6E-05 38.1 2.1 38 226-264 67-109 (124)
102 KOG2114 Vacuolar assembly/sort 84.0 0.65 1.4E-05 49.5 2.2 41 151-199 841-881 (933)
103 KOG2660 Locus-specific chromos 84.0 0.3 6.4E-06 46.8 -0.3 50 148-202 13-62 (331)
104 COG0375 HybF Zn finger protein 83.4 0.9 1.9E-05 37.5 2.4 39 224-264 65-103 (115)
105 PRK04023 DNA polymerase II lar 83.2 1 2.2E-05 49.0 3.3 32 80-115 628-659 (1121)
106 PF07191 zinc-ribbons_6: zinc- 83.0 0.14 3.1E-06 38.7 -2.3 65 151-245 2-69 (70)
107 KOG1002 Nucleotide excision re 83.0 0.43 9.3E-06 48.7 0.4 54 144-201 530-586 (791)
108 PF13240 zinc_ribbon_2: zinc-r 82.2 0.76 1.7E-05 27.3 1.1 21 68-88 2-23 (23)
109 KOG1952 Transcription factor N 81.7 0.69 1.5E-05 49.3 1.4 54 148-202 189-248 (950)
110 PF09538 FYDLN_acid: Protein o 81.5 1 2.3E-05 36.6 2.0 28 76-115 7-34 (108)
111 PF10571 UPF0547: Uncharacteri 81.4 1 2.3E-05 27.6 1.6 23 67-89 2-25 (26)
112 PF02891 zf-MIZ: MIZ/SP-RING z 80.9 1.2 2.6E-05 31.2 1.9 43 151-199 3-50 (50)
113 TIGR02605 CxxC_CxxC_SSSS putat 80.5 1.6 3.4E-05 30.1 2.4 37 229-265 5-45 (52)
114 KOG0827 Predicted E3 ubiquitin 79.7 0.25 5.4E-06 48.5 -2.5 50 150-201 196-245 (465)
115 TIGR00595 priA primosomal prot 77.9 1.9 4.1E-05 43.4 3.1 49 27-87 214-262 (505)
116 PF14446 Prok-RING_1: Prokaryo 76.7 2.1 4.6E-05 30.8 2.2 35 148-183 3-38 (54)
117 PRK14559 putative protein seri 75.7 2 4.4E-05 44.8 2.6 31 67-97 3-34 (645)
118 PF14353 CpXC: CpXC protein 75.3 0.46 1E-05 38.8 -1.8 56 191-248 2-57 (128)
119 PF13894 zf-C2H2_4: C2H2-type 75.3 1.9 4.2E-05 24.0 1.4 20 191-210 1-20 (24)
120 KOG4692 Predicted E3 ubiquitin 75.0 1.7 3.7E-05 42.5 1.7 50 147-202 419-468 (489)
121 COG5220 TFB3 Cdk activating ki 74.4 1.1 2.3E-05 41.7 0.2 51 149-201 9-64 (314)
122 PHA00626 hypothetical protein 73.8 2.7 5.8E-05 30.7 2.1 12 88-99 21-32 (59)
123 PRK14714 DNA polymerase II lar 73.7 3.3 7.1E-05 46.2 3.7 33 65-98 667-700 (1337)
124 smart00132 LIM Zinc-binding do 73.6 1.5 3.3E-05 27.3 0.7 37 153-201 2-38 (39)
125 smart00734 ZnF_Rad18 Rad18-lik 72.9 2.9 6.3E-05 25.5 1.8 21 191-212 2-22 (26)
126 COG1198 PriA Primosomal protei 72.6 3.5 7.7E-05 43.7 3.5 54 26-91 435-488 (730)
127 PRK00398 rpoP DNA-directed RNA 71.9 3.2 7E-05 28.1 2.1 36 228-263 2-37 (46)
128 KOG0801 Predicted E3 ubiquitin 71.6 1.5 3.3E-05 38.5 0.5 31 147-178 174-204 (205)
129 KOG3161 Predicted E3 ubiquitin 69.8 3.1 6.7E-05 43.5 2.2 40 151-194 12-51 (861)
130 COG5109 Uncharacterized conser 69.1 4.1 8.9E-05 39.3 2.8 46 151-197 337-383 (396)
131 PRK05580 primosome assembly pr 67.2 4.5 9.8E-05 42.2 2.9 51 26-88 381-431 (679)
132 PLN03086 PRLI-interacting fact 67.1 2.5 5.5E-05 43.5 1.1 85 61-160 403-514 (567)
133 KOG0269 WD40 repeat-containing 66.1 4.9 0.00011 42.7 2.9 79 105-204 751-836 (839)
134 COG1198 PriA Primosomal protei 65.2 6.1 0.00013 41.9 3.4 44 63-114 433-482 (730)
135 KOG1609 Protein involved in mR 64.4 3 6.5E-05 38.2 0.9 52 150-201 78-134 (323)
136 PRK14873 primosome assembly pr 63.8 5.6 0.00012 41.7 2.8 50 26-88 383-432 (665)
137 PRK04023 DNA polymerase II lar 63.8 5.6 0.00012 43.6 2.8 50 63-118 624-674 (1121)
138 KOG2272 Focal adhesion protein 63.5 4.2 9.1E-05 38.2 1.7 128 36-207 100-238 (332)
139 TIGR02300 FYDLN_acid conserved 63.3 4.9 0.00011 33.8 1.9 28 77-116 8-35 (129)
140 KOG2462 C2H2-type Zn-finger pr 63.2 7.4 0.00016 36.7 3.2 113 88-239 128-253 (279)
141 PF05605 zf-Di19: Drought indu 62.9 7.3 0.00016 27.2 2.5 22 190-212 2-23 (54)
142 PF07282 OrfB_Zn_ribbon: Putat 62.2 6.3 0.00014 28.5 2.1 27 78-115 28-54 (69)
143 KOG2068 MOT2 transcription fac 62.0 5.1 0.00011 38.6 2.0 52 148-201 247-298 (327)
144 KOG1940 Zn-finger protein [Gen 62.0 1.5 3.3E-05 41.2 -1.5 29 14-43 176-204 (276)
145 PRK14714 DNA polymerase II lar 62.0 6.5 0.00014 44.0 3.0 33 79-115 668-700 (1337)
146 COG1996 RPC10 DNA-directed RNA 61.9 5.9 0.00013 28.0 1.8 30 227-256 4-33 (49)
147 PF03107 C1_2: C1 domain; Int 61.8 6.1 0.00013 24.6 1.7 20 112-131 2-22 (30)
148 PF07754 DUF1610: Domain of un 61.3 7.2 0.00016 23.6 1.9 9 106-114 15-23 (24)
149 PHA03096 p28-like protein; Pro 60.8 5.6 0.00012 37.5 2.0 48 151-198 179-231 (284)
150 smart00659 RPOLCX RNA polymera 59.6 6.5 0.00014 26.9 1.7 26 229-255 2-27 (44)
151 KOG0298 DEAD box-containing he 59.5 6.9 0.00015 43.8 2.7 53 148-205 1151-1203(1394)
152 PF13597 NRDD: Anaerobic ribon 58.3 7.3 0.00016 39.8 2.5 57 202-264 465-521 (546)
153 PRK14559 putative protein seri 57.9 5.6 0.00012 41.6 1.6 34 65-99 15-50 (645)
154 PF00096 zf-C2H2: Zinc finger, 57.8 6.4 0.00014 22.2 1.2 16 191-206 1-16 (23)
155 KOG1001 Helicase-like transcri 56.5 4.8 0.0001 42.3 0.9 46 151-201 455-500 (674)
156 PF05502 Dynactin_p62: Dynacti 56.4 5.5 0.00012 40.2 1.2 58 91-163 6-65 (483)
157 KOG2066 Vacuolar assembly/sort 56.4 4.4 9.4E-05 43.2 0.5 38 151-188 785-825 (846)
158 PF06524 NOA36: NOA36 protein; 54.9 4.4 9.5E-05 38.1 0.2 51 33-98 140-190 (314)
159 KOG1812 Predicted E3 ubiquitin 54.1 6.1 0.00013 38.7 1.1 36 150-186 146-182 (384)
160 PRK12286 rpmF 50S ribosomal pr 54.0 12 0.00027 27.0 2.4 29 228-261 26-54 (57)
161 KOG4367 Predicted Zn-finger pr 53.7 6.2 0.00013 39.7 1.1 34 150-187 4-37 (699)
162 cd01675 RNR_III Class III ribo 51.1 11 0.00025 38.4 2.6 57 202-264 493-549 (555)
163 PRK14890 putative Zn-ribbon RN 50.9 9.9 0.00021 27.9 1.5 34 63-98 23-56 (59)
164 COG1656 Uncharacterized conser 50.7 11 0.00024 33.0 2.0 48 191-245 98-146 (165)
165 COG5222 Uncharacterized conser 49.4 12 0.00026 36.1 2.2 44 151-198 275-318 (427)
166 PRK00415 rps27e 30S ribosomal 49.3 9.2 0.0002 28.1 1.1 34 65-98 11-50 (59)
167 smart00249 PHD PHD zinc finger 48.7 4.9 0.00011 25.7 -0.4 30 153-184 2-32 (47)
168 PF10058 DUF2296: Predicted in 48.1 23 0.0005 25.3 3.0 47 208-257 4-54 (54)
169 KOG3053 Uncharacterized conser 47.8 6.4 0.00014 37.0 0.1 70 147-216 17-104 (293)
170 PF05290 Baculo_IE-1: Baculovi 46.9 12 0.00025 31.9 1.5 49 151-203 81-134 (140)
171 PF15353 HECA: Headcase protei 46.5 10 0.00022 31.0 1.1 17 171-187 39-55 (107)
172 PHA00626 hypothetical protein 46.4 13 0.00027 27.3 1.4 29 80-115 2-31 (59)
173 PF04216 FdhE: Protein involve 46.4 14 0.00031 34.3 2.2 48 63-114 195-245 (290)
174 PF03833 PolC_DP2: DNA polymer 46.4 6.6 0.00014 42.3 0.0 44 80-132 657-700 (900)
175 PF09723 Zn-ribbon_8: Zinc rib 44.3 19 0.0004 24.1 2.0 32 229-260 5-39 (42)
176 COG3809 Uncharacterized protei 44.2 16 0.00034 28.6 1.7 52 151-226 2-55 (88)
177 PF02701 zf-Dof: Dof domain, z 43.4 12 0.00025 27.9 0.9 13 248-260 6-18 (63)
178 PF05191 ADK_lid: Adenylate ki 43.2 6.2 0.00013 25.9 -0.5 27 80-115 3-29 (36)
179 PF08271 TF_Zn_Ribbon: TFIIB z 42.7 22 0.00048 23.7 2.1 8 80-87 2-9 (43)
180 KOG1312 DHHC-type Zn-finger pr 42.4 8.3 0.00018 36.9 0.0 32 111-145 149-180 (341)
181 PF13453 zf-TFIIB: Transcripti 42.1 22 0.00047 23.5 2.0 26 80-114 1-26 (41)
182 TIGR01031 rpmF_bact ribosomal 41.6 22 0.00047 25.5 2.0 29 228-261 25-53 (55)
183 PRK03564 formate dehydrogenase 41.6 26 0.00057 33.5 3.2 23 229-255 212-234 (309)
184 PF10122 Mu-like_Com: Mu-like 41.5 23 0.0005 25.3 2.1 35 229-263 4-40 (51)
185 KOG2907 RNA polymerase I trans 41.3 9.6 0.00021 31.5 0.2 19 245-263 72-94 (116)
186 PRK00432 30S ribosomal protein 41.2 19 0.00042 25.2 1.7 9 106-114 36-44 (50)
187 PF07649 C1_3: C1-like domain; 41.2 15 0.00033 22.6 1.1 20 113-132 3-23 (30)
188 PF04423 Rad50_zn_hook: Rad50 41.1 17 0.00038 25.3 1.5 12 191-202 21-32 (54)
189 PF01096 TFIIS_C: Transcriptio 40.9 25 0.00053 23.3 2.1 34 80-114 2-35 (39)
190 PF01529 zf-DHHC: DHHC palmito 40.9 15 0.00033 30.6 1.4 48 84-137 42-89 (174)
191 cd00350 rubredoxin_like Rubred 40.5 20 0.00044 22.7 1.6 25 90-115 1-25 (33)
192 TIGR02159 PA_CoA_Oxy4 phenylac 40.0 15 0.00031 31.4 1.1 16 247-262 105-120 (146)
193 COG2051 RPS27A Ribosomal prote 39.5 13 0.00029 27.9 0.7 28 64-91 18-51 (67)
194 PRK00420 hypothetical protein; 39.3 19 0.00041 29.6 1.6 21 78-98 23-48 (112)
195 KOG2462 C2H2-type Zn-finger pr 39.1 55 0.0012 31.0 4.8 115 79-208 131-261 (279)
196 PF00412 LIM: LIM domain; Int 36.8 11 0.00024 25.7 -0.1 40 153-204 1-40 (58)
197 PF13717 zinc_ribbon_4: zinc-r 35.7 22 0.00049 23.1 1.3 10 64-73 24-33 (36)
198 KOG1311 DHHC-type Zn-finger pr 35.6 23 0.00049 32.9 1.8 35 82-119 105-139 (299)
199 cd02337 ZZ_CBP Zinc finger, ZZ 35.5 27 0.00059 23.4 1.7 20 108-131 1-20 (41)
200 COG5183 SSM4 Protein involved 34.7 20 0.00044 38.7 1.4 50 150-201 12-66 (1175)
201 PRK00366 ispG 4-hydroxy-3-meth 34.3 54 0.0012 32.1 4.1 54 190-247 268-323 (360)
202 PF08274 PhnA_Zn_Ribbon: PhnA 34.2 23 0.0005 22.5 1.1 23 80-114 4-26 (30)
203 PF04438 zf-HIT: HIT zinc fing 33.9 20 0.00044 22.6 0.8 16 81-97 5-20 (30)
204 PF06677 Auto_anti-p27: Sjogre 33.7 26 0.00056 23.7 1.4 13 78-90 17-29 (41)
205 PF01667 Ribosomal_S27e: Ribos 33.7 21 0.00045 25.8 0.9 34 65-98 7-46 (55)
206 COG1645 Uncharacterized Zn-fin 33.5 22 0.00049 30.0 1.2 20 78-97 28-51 (131)
207 KOG0802 E3 ubiquitin ligase [P 33.4 32 0.00068 35.0 2.5 44 148-201 477-520 (543)
208 TIGR00595 priA primosomal prot 33.0 43 0.00094 33.8 3.4 46 63-116 211-262 (505)
209 PF03833 PolC_DP2: DNA polymer 33.0 14 0.00031 39.8 0.0 47 63-115 653-700 (900)
210 smart00661 RPOL9 RNA polymeras 32.5 36 0.00078 23.0 2.0 8 107-114 20-27 (52)
211 PF01907 Ribosomal_L37e: Ribos 32.4 18 0.00039 26.2 0.4 28 224-254 10-37 (55)
212 PF12874 zf-met: Zinc-finger o 32.3 23 0.00051 20.2 0.8 16 191-206 1-16 (25)
213 PF14952 zf-tcix: Putative tre 32.2 22 0.00047 24.7 0.8 12 249-260 13-24 (44)
214 PF13719 zinc_ribbon_5: zinc-r 31.9 27 0.0006 22.7 1.2 11 64-74 24-34 (37)
215 cd02249 ZZ Zinc finger, ZZ typ 31.3 34 0.00074 23.1 1.7 21 108-131 1-21 (46)
216 TIGR01562 FdhE formate dehydro 30.7 46 0.00099 31.8 2.9 42 192-255 186-232 (305)
217 PRK03564 formate dehydrogenase 30.3 57 0.0012 31.3 3.5 26 62-87 209-235 (309)
218 smart00355 ZnF_C2H2 zinc finge 30.3 50 0.0011 18.0 2.0 15 191-205 1-15 (26)
219 KOG4185 Predicted E3 ubiquitin 30.0 11 0.00023 34.8 -1.4 50 150-200 207-266 (296)
220 COG2888 Predicted Zn-ribbon RN 29.9 32 0.00069 25.4 1.4 34 63-98 25-58 (61)
221 cd02341 ZZ_ZZZ3 Zinc finger, Z 29.9 37 0.00081 23.6 1.7 22 108-131 1-22 (48)
222 smart00834 CxxC_CXXC_SSSS Puta 29.9 53 0.0011 21.0 2.3 27 229-255 5-34 (41)
223 PRK04136 rpl40e 50S ribosomal 29.8 34 0.00073 24.2 1.4 24 63-86 12-36 (48)
224 PF14569 zf-UDP: Zinc-binding 29.6 61 0.0013 25.2 2.9 52 148-200 7-61 (80)
225 PF06827 zf-FPG_IleRS: Zinc fi 29.5 38 0.00083 20.7 1.5 10 79-88 2-11 (30)
226 PRK14873 primosome assembly pr 29.4 57 0.0012 34.4 3.6 28 59-90 376-404 (665)
227 PF04216 FdhE: Protein involve 29.3 16 0.00035 33.9 -0.3 30 228-261 196-225 (290)
228 cd00729 rubredoxin_SM Rubredox 29.1 40 0.00086 21.7 1.6 22 66-87 3-27 (34)
229 KOG4317 Predicted Zn-finger pr 29.1 24 0.00052 34.2 0.8 21 79-99 8-28 (383)
230 PF01529 zf-DHHC: DHHC palmito 29.0 43 0.00094 27.8 2.3 30 113-145 51-80 (174)
231 PF03604 DNA_RNApol_7kD: DNA d 29.0 33 0.00071 22.0 1.2 10 105-114 15-24 (32)
232 PRK03988 translation initiatio 27.9 54 0.0012 27.8 2.6 10 246-255 122-131 (138)
233 PF00643 zf-B_box: B-box zinc 27.9 46 0.001 21.5 1.8 21 79-99 4-24 (42)
234 COG1998 RPS31 Ribosomal protei 27.6 35 0.00075 24.4 1.2 20 78-97 19-44 (51)
235 PF15616 TerY-C: TerY-C metal 27.3 56 0.0012 27.6 2.6 34 78-114 77-112 (131)
236 PRK07111 anaerobic ribonucleos 27.2 66 0.0014 34.3 3.7 53 204-263 657-709 (735)
237 TIGR02098 MJ0042_CXXC MJ0042 f 27.2 44 0.00095 21.3 1.6 10 65-74 25-34 (38)
238 KOG3579 Predicted E3 ubiquitin 27.1 60 0.0013 31.2 3.0 61 149-218 267-340 (352)
239 PRK00464 nrdR transcriptional 26.7 38 0.00083 29.2 1.6 12 80-91 30-41 (154)
240 KOG4399 C2HC-type Zn-finger pr 26.5 13 0.00028 35.1 -1.5 72 85-159 199-270 (325)
241 KOG3362 Predicted BBOX Zn-fing 26.4 19 0.00041 31.1 -0.4 25 89-119 117-143 (156)
242 PF11781 RRN7: RNA polymerase 26.4 35 0.00076 22.3 1.0 25 152-176 10-35 (36)
243 KOG1100 Predicted E3 ubiquitin 26.0 25 0.00055 31.6 0.3 39 153-201 161-200 (207)
244 PF12171 zf-C2H2_jaz: Zinc-fin 25.8 44 0.00095 19.8 1.3 14 191-204 2-15 (27)
245 COG5273 Uncharacterized protei 25.7 32 0.00069 32.7 1.0 44 79-145 98-141 (309)
246 PRK14810 formamidopyrimidine-D 25.6 38 0.00083 31.4 1.5 20 78-97 244-271 (272)
247 PF01599 Ribosomal_S27: Riboso 25.5 41 0.00089 23.6 1.2 22 77-98 17-46 (47)
248 PLN02189 cellulose synthase 25.4 62 0.0013 35.9 3.2 56 145-201 29-87 (1040)
249 PF12172 DUF35_N: Rubredoxin-l 25.2 31 0.00068 22.1 0.6 23 64-86 10-33 (37)
250 PF06220 zf-U1: U1 zinc finger 24.9 28 0.00061 23.0 0.3 13 88-100 1-13 (38)
251 PRK14892 putative transcriptio 24.9 66 0.0014 25.8 2.5 32 122-159 19-51 (99)
252 PRK08271 anaerobic ribonucleos 24.9 48 0.001 34.7 2.1 55 202-262 541-595 (623)
253 PLN00209 ribosomal protein S27 24.7 45 0.00097 26.3 1.4 36 65-100 36-77 (86)
254 PF06937 EURL: EURL protein; 24.5 1.3E+02 0.0028 28.6 4.7 46 147-194 27-74 (285)
255 PTZ00083 40S ribosomal protein 24.4 39 0.00085 26.6 1.1 36 65-100 35-76 (85)
256 TIGR00311 aIF-2beta translatio 24.3 62 0.0014 27.2 2.3 12 230-241 119-130 (133)
257 TIGR02487 NrdD anaerobic ribon 24.2 71 0.0015 33.0 3.2 54 204-263 501-554 (579)
258 PF05129 Elf1: Transcription e 24.2 33 0.00071 26.4 0.6 37 190-244 22-61 (81)
259 PRK14811 formamidopyrimidine-D 24.0 43 0.00094 31.0 1.5 20 78-97 235-262 (269)
260 KOG4399 C2HC-type Zn-finger pr 24.0 20 0.00043 33.9 -0.7 53 79-135 250-302 (325)
261 PRK10445 endonuclease VIII; Pr 23.8 44 0.00096 30.8 1.5 20 78-97 235-262 (263)
262 TIGR00373 conserved hypothetic 23.7 1E+02 0.0022 26.4 3.6 26 191-216 129-156 (158)
263 PF11023 DUF2614: Protein of u 23.6 48 0.001 27.4 1.5 27 62-88 66-95 (114)
264 PRK06266 transcription initiat 23.5 1E+02 0.0022 26.9 3.7 26 190-215 136-163 (178)
265 smart00451 ZnF_U1 U1-like zinc 23.4 56 0.0012 20.0 1.5 16 190-205 3-18 (35)
266 PF00130 C1_1: Phorbol esters/ 23.2 65 0.0014 21.8 1.9 11 104-114 25-35 (53)
267 COG3024 Uncharacterized protei 22.9 43 0.00094 25.0 1.0 26 76-101 5-38 (65)
268 PRK01103 formamidopyrimidine/5 22.8 48 0.001 30.7 1.5 20 78-97 245-272 (274)
269 cd07973 Spt4 Transcription elo 22.6 47 0.001 26.6 1.2 19 67-85 5-27 (98)
270 PF12760 Zn_Tnp_IS1595: Transp 22.4 1.1E+02 0.0024 20.6 2.9 9 79-87 19-27 (46)
271 PRK05580 primosome assembly pr 22.4 1E+02 0.0022 32.3 4.0 24 63-90 379-402 (679)
272 KOG0269 WD40 repeat-containing 22.3 64 0.0014 34.6 2.5 51 78-137 753-806 (839)
273 PF01363 FYVE: FYVE zinc finge 22.2 54 0.0012 23.5 1.4 25 78-115 9-33 (69)
274 TIGR00244 transcriptional regu 22.2 57 0.0012 28.1 1.7 13 79-91 29-41 (147)
275 PF12675 DUF3795: Protein of u 22.1 48 0.001 24.9 1.1 37 78-114 34-70 (78)
276 TIGR01206 lysW lysine biosynth 22.1 63 0.0014 23.1 1.7 32 191-241 3-34 (54)
277 PRK08351 DNA-directed RNA poly 21.8 55 0.0012 24.1 1.4 20 67-87 5-24 (61)
278 PF05458 Siva: Cd27 binding pr 21.5 70 0.0015 28.1 2.2 36 66-101 112-158 (175)
279 PF09297 zf-NADH-PPase: NADH p 21.3 31 0.00068 21.5 -0.0 21 67-87 5-30 (32)
280 PF01927 Mut7-C: Mut7-C RNAse 20.7 61 0.0013 27.1 1.6 48 191-245 92-140 (147)
281 KOG3005 GIY-YIG type nuclease 20.6 1.3E+02 0.0027 28.6 3.8 66 150-222 182-259 (276)
282 PRK01110 rpmF 50S ribosomal pr 20.5 1E+02 0.0022 22.4 2.5 30 229-264 27-56 (60)
283 PRK13945 formamidopyrimidine-D 20.4 58 0.0013 30.3 1.5 19 78-96 254-280 (282)
284 KOG4275 Predicted E3 ubiquitin 20.4 32 0.0007 33.0 -0.1 20 79-100 322-341 (350)
285 PLN02436 cellulose synthase A 20.2 88 0.0019 34.9 3.0 56 145-201 31-89 (1094)
286 TIGR00577 fpg formamidopyrimid 20.1 58 0.0013 30.1 1.5 19 78-96 245-271 (272)
287 PF13913 zf-C2HC_2: zinc-finge 20.0 50 0.0011 19.7 0.7 12 79-90 3-14 (25)
No 1
>KOG1940 consensus Zn-finger protein [General function prediction only]
Probab=100.00 E-value=1.5e-71 Score=509.70 Aligned_cols=252 Identities=49% Similarity=1.040 Sum_probs=244.2
Q ss_pred CccccccCCCCccCccccccCcceEcCCCCCcccCcchHHhhhcCCCCCCCCccccccccceeecCCCCccccccccCCc
Q 024406 4 SANERITFGKMGYGCKHYRRRCRIRAPCCNEIFDCRHCHNEAASMLRNPYDRHELVRQDVKQVICSVCDTEQPVAQVCTN 83 (268)
Q Consensus 4 ~~~~~~~~~~~~~gC~HY~r~c~l~~pcC~~~y~Cr~CHde~~~~~~~~~~~H~~~r~~~~~v~C~~C~~~q~v~~~C~~ 83 (268)
..+++.|++.+.+||+||+|++.+++|+|+++|+|++||+++. +|.++|+.|.+|+|+.|.++|+++++|.+
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 3566889999999999999999999999999999999999974 89999999999999999999999999999
Q ss_pred CCCccceeeccccccccCCCCcCeeecCCCCcccccCccceeecCccCccccccccCcceeecCCCCCCCchhhhhhccc
Q 024406 84 CGVNMGEYFCDICKFYDDDIEKGQFHCDDCGICRIGGRENYFHCKRCGSCYSTSLRNNHLCIENSMHHHCPICYEYLFDS 163 (268)
Q Consensus 84 Cg~~f~~y~C~~C~l~d~~~~k~~yHC~~CgiCR~G~~~~ffHC~~C~~C~s~~l~~~H~C~e~~~~~~CpICle~lf~s 163 (268)
|+..||+|||.+|+||||+++ +||||+.|||||+|++++||||++|+.|++..+.+.|+|+|++++.+||||.|+||++
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 999999999999999999999 9999999999999999999999999999999999999999999999999999999999
Q ss_pred CCcceEeccCCccChHHHHHHHHcCCCcCCCCCCcchhhhhHHHHHHHHHHHhcCCChhhhcCeeEEEccCCCCccccce
Q 024406 164 LRNTTVMKCGHTMHCECYHEMIKRDNRYCCPICSKSVIDMSRTWKRIDEEIEATVMPEDYRHKKVWILCNDCNDTTEVYF 243 (268)
Q Consensus 164 ~~~v~~LpCGH~~H~~C~~~~~~~~~~~~CPiCrksi~~m~~~~~~lD~~i~~~pmP~~y~~~~v~I~CnDC~~~s~~~~ 243 (268)
...+.+|+|||.+|..||.+++..+ |+||+|.| ++||+.+|+++|.+|+++|||++|++++++|+||||+..++++|
T Consensus 172 ~~~~~~~~CgH~~h~~cf~e~~~~~--y~CP~C~~-~~d~~~~~~~~d~~l~~~~~p~~y~~~~~~i~cndC~~~~~~k~ 248 (276)
T KOG1940|consen 172 FEDAGVLKCGHYMHSRCFEEMICEG--YTCPICSK-PGDMSHYFRKLDKELAGSPMPEEYKNKTQDILCNDCGSGTNVKY 248 (276)
T ss_pred cccCCccCcccchHHHHHHHHhccC--CCCCcccc-hHHHHHHHHHHHHHHhcCCCCchhhchhheeeccCCCCCCccce
Confidence 9999999999999999999999887 99999999 99999999999999999999999999999999999999999999
Q ss_pred eEeeecCCCCCCccccccCCCCCC
Q 024406 244 HIIGQKCSHCKSYNTRSIAPPVLP 267 (268)
Q Consensus 244 H~lg~kC~~C~SyNT~~~~~~~~~ 267 (268)
|||++||+.|+|||||+++.|..+
T Consensus 249 ~~l~~kc~~c~~~~~r~~~~~~~~ 272 (276)
T KOG1940|consen 249 HILYHKCGKCGSYNTRMISDPSKY 272 (276)
T ss_pred ehhhhhCCCcccceeeeccCCCcc
Confidence 999999999999999999876653
No 2
>PF14599 zinc_ribbon_6: Zinc-ribbon; PDB: 2K2D_A.
Probab=99.96 E-value=1.1e-31 Score=196.29 Aligned_cols=61 Identities=67% Similarity=1.267 Sum_probs=22.5
Q ss_pred hhhhhHHHHHHHHHHHhcCCChhhhcCeeEEEccCCCCccccceeEeeecCCCCCCccccc
Q 024406 200 VIDMSRTWKRIDEEIEATVMPEDYRHKKVWILCNDCNDTTEVYFHIIGQKCSHCKSYNTRS 260 (268)
Q Consensus 200 i~~m~~~~~~lD~~i~~~pmP~~y~~~~v~I~CnDC~~~s~~~~H~lg~kC~~C~SyNT~~ 260 (268)
|+||+++|++||++|+++|||++|++++|+|+||||+++|+|+||||||||++|+||||||
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 5799999999999999999999999999999999999999999999999999999999996
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=5e-24 Score=160.15 Aligned_cols=70 Identities=51% Similarity=1.212 Sum_probs=53.3
Q ss_pred ccccccC-cceEcCCCCCcccCcchHHhhhcCCCCCCCCccccccccceeecCCCCccccccccCCcCCCccceeecccc
Q 024406 18 CKHYRRR-CRIRAPCCNEIFDCRHCHNEAASMLRNPYDRHELVRQDVKQVICSVCDTEQPVAQVCTNCGVNMGEYFCDIC 96 (268)
Q Consensus 18 C~HY~r~-c~l~~pcC~~~y~Cr~CHde~~~~~~~~~~~H~~~r~~~~~v~C~~C~~~q~v~~~C~~Cg~~f~~y~C~~C 96 (268)
|+||+|+ ++|+||||++|||||+||||++ +|+++|+.+++|+||.|+++|++++. +|+ ++|+|++|
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 024406 97 KFYD 100 (268)
Q Consensus 97 ~l~d 100 (268)
++||
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=5.3e-16 Score=122.27 Aligned_cols=73 Identities=26% Similarity=0.618 Sum_probs=65.7
Q ss_pred ccCccccccC---cceEcCCCCCcccCcchHHhhhcCCCCCCCCccccccccceeecCCCCcccccc-----ccCCcCCC
Q 024406 15 GYGCKHYRRR---CRIRAPCCNEIFDCRHCHNEAASMLRNPYDRHELVRQDVKQVICSVCDTEQPVA-----QVCTNCGV 86 (268)
Q Consensus 15 ~~gC~HY~r~---c~l~~pcC~~~y~Cr~CHde~~~~~~~~~~~H~~~r~~~~~v~C~~C~~~q~v~-----~~C~~Cg~ 86 (268)
++||.||++. ++|||.+|++||+|++||||+++|++ +.++++.+..+.||||.|..+++++ ..||+|.+
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 4799999997 78999999999999999999998887 6777788888999999999999884 57999999
Q ss_pred ccce
Q 024406 87 NMGE 90 (268)
Q Consensus 87 ~f~~ 90 (268)
+||.
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=99.39 E-value=1.1e-13 Score=93.94 Aligned_cols=44 Identities=39% Similarity=0.948 Sum_probs=37.9
Q ss_pred CCCchhhhhhcccCCcceEeccCCccChHHHHHHHHcCCCcCCCCCC
Q 024406 151 HHCPICYEYLFDSLRNTTVMKCGHTMHCECYHEMIKRDNRYCCPICS 197 (268)
Q Consensus 151 ~~CpICle~lf~s~~~v~~LpCGH~~H~~C~~~~~~~~~~~~CPiCr 197 (268)
.+||||+|++.+ .+.++.|+|||.||.+|+.+|++.+ .+||+||
T Consensus 1 d~C~IC~~~~~~-~~~~~~l~C~H~fh~~Ci~~~~~~~--~~CP~CR 44 (44)
T PF13639_consen 1 DECPICLEEFED-GEKVVKLPCGHVFHRSCIKEWLKRN--NSCPVCR 44 (44)
T ss_dssp -CETTTTCBHHT-TSCEEEETTSEEEEHHHHHHHHHHS--SB-TTTH
T ss_pred CCCcCCChhhcC-CCeEEEccCCCeeCHHHHHHHHHhC--CcCCccC
Confidence 379999999655 4788899999999999999999987 7999996
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=99.01 E-value=1.7e-10 Score=86.99 Aligned_cols=48 Identities=31% Similarity=0.698 Sum_probs=37.2
Q ss_pred CCCCCCchhhhhhccc---------CCcceEeccCCccChHHHHHHHHcCCCcCCCCCC
Q 024406 148 SMHHHCPICYEYLFDS---------LRNTTVMKCGHTMHCECYHEMIKRDNRYCCPICS 197 (268)
Q Consensus 148 ~~~~~CpICle~lf~s---------~~~v~~LpCGH~~H~~C~~~~~~~~~~~~CPiCr 197 (268)
..+.+|+||++.|.+. .-++..++|||.||..||.+||+.+ .+||+||
T Consensus 17 ~~~d~C~IC~~~l~~~~~~~~~~~~~~~i~~~~C~H~FH~~Ci~~Wl~~~--~~CP~CR 73 (73)
T PF12678_consen 17 IADDNCAICREPLEDPCPECQAPQDECPIVWGPCGHIFHFHCISQWLKQN--NTCPLCR 73 (73)
T ss_dssp SCCSBETTTTSBTTSTTCCHHHCTTTS-EEEETTSEEEEHHHHHHHHTTS--SB-TTSS
T ss_pred CcCCcccccChhhhChhhhhcCCccccceEecccCCCEEHHHHHHHHhcC--CcCCCCC
Confidence 3456799999998443 2345567999999999999999887 7999997
No 7
>cd00162 RING RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in mediating protein-protein interactions; identified in a proteins with a wide range of functions such as viral replication, signal transduction, and development; has two variants, the C3HC4-type and a C3H2C3-type (RING-H2 finger), which have different cysteine/histidine pattern; a subset of RINGs are associated with B-Boxes (C-X2-H-X7-C-X7-C-X2-C-H-X2-H)
Probab=98.96 E-value=5.8e-10 Score=73.17 Aligned_cols=45 Identities=29% Similarity=0.862 Sum_probs=37.8
Q ss_pred CCchhhhhhcccCCcceEeccCCccChHHHHHHHHcCCCcCCCCCCcch
Q 024406 152 HCPICYEYLFDSLRNTTVMKCGHTMHCECYHEMIKRDNRYCCPICSKSV 200 (268)
Q Consensus 152 ~CpICle~lf~s~~~v~~LpCGH~~H~~C~~~~~~~~~~~~CPiCrksi 200 (268)
.|+||++.+ ..++..++|||.||..|++.|++.. ..+||+|++.+
T Consensus 1 ~C~iC~~~~---~~~~~~~~C~H~~c~~C~~~~~~~~-~~~Cp~C~~~~ 45 (45)
T cd00162 1 ECPICLEEF---REPVVLLPCGHVFCRSCIDKWLKSG-KNTCPLCRTPI 45 (45)
T ss_pred CCCcCchhh---hCceEecCCCChhcHHHHHHHHHhC-cCCCCCCCCcC
Confidence 599999986 3466677899999999999999874 48899999764
No 8
>COG5243 HRD1 HRD ubiquitin ligase complex, ER membrane component [Posttranslational modification, protein turnover, chaperones]
Probab=98.93 E-value=2.9e-10 Score=108.49 Aligned_cols=57 Identities=28% Similarity=0.768 Sum_probs=49.4
Q ss_pred CCCCCCCchhhhhhcccC---------CcceEeccCCccChHHHHHHHHcCCCcCCCCCCcc-hhhhhH
Q 024406 147 NSMHHHCPICYEYLFDSL---------RNTTVMKCGHTMHCECYHEMIKRDNRYCCPICSKS-VIDMSR 205 (268)
Q Consensus 147 ~~~~~~CpICle~lf~s~---------~~v~~LpCGH~~H~~C~~~~~~~~~~~~CPiCrks-i~~m~~ 205 (268)
.+.+..|.||+|+||.+. ...+.|||||.+|.+|++.|+++. .+|||||.+ +.||++
T Consensus 284 ~n~D~~C~ICmde~~h~~~~~~~~~~~~~pKrLpCGHilHl~CLknW~ERq--QTCPICr~p~ifd~~~ 350 (491)
T COG5243 284 TNSDRTCTICMDEMFHPDHEPLPRGLDMTPKRLPCGHILHLHCLKNWLERQ--QTCPICRRPVIFDQSS 350 (491)
T ss_pred cCCCCeEEEecccccCCCCccCcccccCCcccccccceeeHHHHHHHHHhc--cCCCcccCccccccCC
Confidence 567889999999998865 234789999999999999999997 799999999 568775
No 9
>KOG4628 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=98.86 E-value=8.8e-10 Score=105.00 Aligned_cols=50 Identities=24% Similarity=0.775 Sum_probs=44.7
Q ss_pred CCCchhhhhhcccCCcceEeccCCccChHHHHHHHHcCCCcCCCCCCcchhh
Q 024406 151 HHCPICYEYLFDSLRNTTVMKCGHTMHCECYHEMIKRDNRYCCPICSKSVID 202 (268)
Q Consensus 151 ~~CpICle~lf~s~~~v~~LpCGH~~H~~C~~~~~~~~~~~~CPiCrksi~~ 202 (268)
..|.||||+ |..++.+++|||+|.||..|++.||... ...||+|+..+..
T Consensus 230 ~~CaIClEd-Y~~GdklRiLPC~H~FH~~CIDpWL~~~-r~~CPvCK~di~~ 279 (348)
T KOG4628|consen 230 DTCAICLED-YEKGDKLRILPCSHKFHVNCIDPWLTQT-RTFCPVCKRDIRT 279 (348)
T ss_pred ceEEEeecc-cccCCeeeEecCCCchhhccchhhHhhc-CccCCCCCCcCCC
Confidence 589999998 7788999999999999999999999876 4559999998864
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=98.82 E-value=1.6e-09 Score=71.80 Aligned_cols=39 Identities=38% Similarity=0.999 Sum_probs=33.3
Q ss_pred CchhhhhhcccCCcceEeccCCccChHHHHHHHHcCCCcCCCCC
Q 024406 153 CPICYEYLFDSLRNTTVMKCGHTMHCECYHEMIKRDNRYCCPIC 196 (268)
Q Consensus 153 CpICle~lf~s~~~v~~LpCGH~~H~~C~~~~~~~~~~~~CPiC 196 (268)
||||++.+.+ ++++++|||+|+..|+.+|++.+ .+||+|
T Consensus 1 C~iC~~~~~~---~~~~~~CGH~fC~~C~~~~~~~~--~~CP~C 39 (39)
T PF13923_consen 1 CPICLDELRD---PVVVTPCGHSFCKECIEKYLEKN--PKCPVC 39 (39)
T ss_dssp ETTTTSB-SS---EEEECTTSEEEEHHHHHHHHHCT--SB-TTT
T ss_pred CCCCCCcccC---cCEECCCCCchhHHHHHHHHHCc--CCCcCC
Confidence 8999997543 77899999999999999999885 899997
No 11
>PHA02929 N1R/p28-like protein; Provisional
Probab=98.79 E-value=3.9e-09 Score=96.21 Aligned_cols=54 Identities=28% Similarity=0.634 Sum_probs=42.8
Q ss_pred CCCCCCCchhhhhhcccCC---c-ceEeccCCccChHHHHHHHHcCCCcCCCCCCcchhh
Q 024406 147 NSMHHHCPICYEYLFDSLR---N-TTVMKCGHTMHCECYHEMIKRDNRYCCPICSKSVID 202 (268)
Q Consensus 147 ~~~~~~CpICle~lf~s~~---~-v~~LpCGH~~H~~C~~~~~~~~~~~~CPiCrksi~~ 202 (268)
.+.+..||||+|.+.+... . .++++|||.||..|+.+|++.. .+||+||+.+..
T Consensus 171 ~~~~~eC~ICle~~~~~~~~~~~~~vl~~C~H~FC~~CI~~Wl~~~--~tCPlCR~~~~~ 228 (238)
T PHA02929 171 RSKDKECAICMEKVYDKEIKNMYFGILSNCNHVFCIECIDIWKKEK--NTCPVCRTPFIS 228 (238)
T ss_pred CCCCCCCccCCcccccCccccccceecCCCCCcccHHHHHHHHhcC--CCCCCCCCEeeE
Confidence 4557899999998765321 1 2345899999999999999876 799999998863
No 12
>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=98.67 E-value=9.3e-09 Score=68.26 Aligned_cols=41 Identities=29% Similarity=0.882 Sum_probs=34.2
Q ss_pred CchhhhhhcccCCcceEeccCCccChHHHHHHHHcCCCcCCCCC
Q 024406 153 CPICYEYLFDSLRNTTVMKCGHTMHCECYHEMIKRDNRYCCPIC 196 (268)
Q Consensus 153 CpICle~lf~s~~~v~~LpCGH~~H~~C~~~~~~~~~~~~CPiC 196 (268)
||||++.+. +++.+++|||.|+..|+.+|++..+..+||+|
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 35578999999999999999983336899998
No 13
>PF13920 zf-C3HC4_3: Zinc finger, C3HC4 type (RING finger); PDB: 2YHN_B 2YHO_G 3T6P_A 2CSY_A 2VJE_B 2VJF_B 2HDP_B 2EA5_A 2ECG_A 3EB5_A ....
Probab=98.66 E-value=1.1e-08 Score=71.14 Aligned_cols=47 Identities=36% Similarity=0.934 Sum_probs=38.5
Q ss_pred CCCCchhhhhhcccCCcceEeccCCc-cChHHHHHHHHcCCCcCCCCCCcchhh
Q 024406 150 HHHCPICYEYLFDSLRNTTVMKCGHT-MHCECYHEMIKRDNRYCCPICSKSVID 202 (268)
Q Consensus 150 ~~~CpICle~lf~s~~~v~~LpCGH~-~H~~C~~~~~~~~~~~~CPiCrksi~~ 202 (268)
+..|+||++.. ..+.++||||. |...|+.+|++.. .+||+||++|.+
T Consensus 2 ~~~C~iC~~~~----~~~~~~pCgH~~~C~~C~~~~~~~~--~~CP~Cr~~i~~ 49 (50)
T PF13920_consen 2 DEECPICFENP----RDVVLLPCGHLCFCEECAERLLKRK--KKCPICRQPIES 49 (50)
T ss_dssp HSB-TTTSSSB----SSEEEETTCEEEEEHHHHHHHHHTT--SBBTTTTBB-SE
T ss_pred cCCCccCCccC----CceEEeCCCChHHHHHHhHHhcccC--CCCCcCChhhcC
Confidence 35799999962 35788999999 9999999999865 899999998863
No 14
>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=98.63 E-value=2.5e-08 Score=63.07 Aligned_cols=39 Identities=44% Similarity=1.071 Sum_probs=33.3
Q ss_pred CchhhhhhcccCCcceEeccCCccChHHHHHHHHcCCCcCCCCC
Q 024406 153 CPICYEYLFDSLRNTTVMKCGHTMHCECYHEMIKRDNRYCCPIC 196 (268)
Q Consensus 153 CpICle~lf~s~~~v~~LpCGH~~H~~C~~~~~~~~~~~~CPiC 196 (268)
|+||++. .+...+++|||.||..|++.|++.. ..+||+|
T Consensus 1 C~iC~~~----~~~~~~~~C~H~~c~~C~~~~~~~~-~~~CP~C 39 (39)
T smart00184 1 CPICLEE----LKDPVVLPCGHTFCRSCIRKWLKSG-NNTCPIC 39 (39)
T ss_pred CCcCccC----CCCcEEecCCChHHHHHHHHHHHhC-cCCCCCC
Confidence 7999987 2467889999999999999999844 4789987
No 15
>PF14634 zf-RING_5: zinc-RING finger domain
Probab=98.58 E-value=2.9e-08 Score=67.58 Aligned_cols=44 Identities=34% Similarity=0.862 Sum_probs=37.4
Q ss_pred CCchhhhhhcccCCcceEeccCCccChHHHHHHHHcCCCcCCCCCCc
Q 024406 152 HCPICYEYLFDSLRNTTVMKCGHTMHCECYHEMIKRDNRYCCPICSK 198 (268)
Q Consensus 152 ~CpICle~lf~s~~~v~~LpCGH~~H~~C~~~~~~~~~~~~CPiCrk 198 (268)
.|+||++.+ +...+..+|+|||+|...|+..+... ...||+|+|
T Consensus 1 ~C~~C~~~~-~~~~~~~l~~CgH~~C~~C~~~~~~~--~~~CP~C~k 44 (44)
T PF14634_consen 1 HCNICFEKY-SEERRPRLTSCGHIFCEKCLKKLKGK--SVKCPICRK 44 (44)
T ss_pred CCcCcCccc-cCCCCeEEcccCCHHHHHHHHhhcCC--CCCCcCCCC
Confidence 489999986 55567888999999999999999933 489999986
No 16
>COG5540 RING-finger-containing ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=98.50 E-value=6.3e-08 Score=90.72 Aligned_cols=53 Identities=25% Similarity=0.599 Sum_probs=45.2
Q ss_pred cCCCCCCCchhhhhhcccCCcceEeccCCccChHHHHHHHHcCCCcCCCCCCcch
Q 024406 146 ENSMHHHCPICYEYLFDSLRNTTVMKCGHTMHCECYHEMIKRDNRYCCPICSKSV 200 (268)
Q Consensus 146 e~~~~~~CpICle~lf~s~~~v~~LpCGH~~H~~C~~~~~~~~~~~~CPiCrksi 200 (268)
|....-+|.|||++ |...+.+++|||.|-||..|+++|+-.. ..+||+||..+
T Consensus 319 ea~~GveCaICms~-fiK~d~~~vlPC~H~FH~~Cv~kW~~~y-~~~CPvCrt~i 371 (374)
T COG5540 319 EADKGVECAICMSN-FIKNDRLRVLPCDHRFHVGCVDKWLLGY-SNKCPVCRTAI 371 (374)
T ss_pred hcCCCceEEEEhhh-hcccceEEEeccCceechhHHHHHHhhh-cccCCccCCCC
Confidence 34456799999999 6778889999999999999999999744 48999999765
No 17
>PF13445 zf-RING_UBOX: RING-type zinc-finger; PDB: 2CT2_A.
Probab=98.49 E-value=7.5e-08 Score=65.98 Aligned_cols=41 Identities=37% Similarity=0.916 Sum_probs=24.2
Q ss_pred CchhhhhhcccCCcceEeccCCccChHHHHHHHHcC--CCcCCC
Q 024406 153 CPICYEYLFDSLRNTTVMKCGHTMHCECYHEMIKRD--NRYCCP 194 (268)
Q Consensus 153 CpICle~lf~s~~~v~~LpCGH~~H~~C~~~~~~~~--~~~~CP 194 (268)
||||+| +-+...+.++|+|||+|-++|+++|++.+ ..++||
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 44444556789999999999999999854 357887
No 18
>PF15227 zf-C3HC4_4: zinc finger of C3HC4-type, RING; PDB: 2EGP_A 2ECV_A 2ECJ_A 2YSL_A 2YSJ_A.
Probab=98.43 E-value=1.2e-07 Score=64.45 Aligned_cols=40 Identities=30% Similarity=0.969 Sum_probs=28.6
Q ss_pred CchhhhhhcccCCcceEeccCCccChHHHHHHHHcCC--CcCCCCC
Q 024406 153 CPICYEYLFDSLRNTTVMKCGHTMHCECYHEMIKRDN--RYCCPIC 196 (268)
Q Consensus 153 CpICle~lf~s~~~v~~LpCGH~~H~~C~~~~~~~~~--~~~CPiC 196 (268)
||||++.| + .-+.|+|||+|-..|+..|.+..+ .+.||+|
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 89999964 3 345699999999999999987542 2689987
No 19
>PF12861 zf-Apc11: Anaphase-promoting complex subunit 11 RING-H2 finger
Probab=98.40 E-value=1.9e-07 Score=72.75 Aligned_cols=48 Identities=25% Similarity=0.490 Sum_probs=33.3
Q ss_pred CCchhhhhhcccCCcceEeccCCccChHHHHHHHHcC-CCcCCCCCCcchh
Q 024406 152 HCPICYEYLFDSLRNTTVMKCGHTMHCECYHEMIKRD-NRYCCPICSKSVI 201 (268)
Q Consensus 152 ~CpICle~lf~s~~~v~~LpCGH~~H~~C~~~~~~~~-~~~~CPiCrksi~ 201 (268)
.||.|..+--+ -+++.-.|||.||..||.+|+++. ++.+||+||....
T Consensus 34 ~Cp~Ck~Pgd~--Cplv~g~C~H~FH~hCI~kWl~~~~~~~~CPmCR~~w~ 82 (85)
T PF12861_consen 34 CCPDCKFPGDD--CPLVWGKCSHNFHMHCILKWLSTQSSKGQCPMCRQPWK 82 (85)
T ss_pred CCCCccCCCCC--CceeeccCccHHHHHHHHHHHccccCCCCCCCcCCeee
Confidence 45555544211 234445799999999999999853 2579999998653
No 20
>KOG0804 consensus Cytoplasmic Zn-finger protein BRAP2 (BRCA1 associated protein) [General function prediction only]
Probab=98.38 E-value=1.8e-07 Score=91.25 Aligned_cols=82 Identities=27% Similarity=0.628 Sum_probs=67.0
Q ss_pred CCCchhhhhhcccCCcceEeccCCccChHHHHHHHHcCCCcCCCCCCcchhhhhHHHHHHHHHHHhcCCChhhhcCeeEE
Q 024406 151 HHCPICYEYLFDSLRNTTVMKCGHTMHCECYHEMIKRDNRYCCPICSKSVIDMSRTWKRIDEEIEATVMPEDYRHKKVWI 230 (268)
Q Consensus 151 ~~CpICle~lf~s~~~v~~LpCGH~~H~~C~~~~~~~~~~~~CPiCrksi~~m~~~~~~lD~~i~~~pmP~~y~~~~v~I 230 (268)
..||||||-|-+|+..+....|.|.||..|+..|-. .+||+||.... |+. ...-
T Consensus 176 PTCpVCLERMD~s~~gi~t~~c~Hsfh~~cl~~w~~----~scpvcR~~q~------------------p~~----ve~~ 229 (493)
T KOG0804|consen 176 PTCPVCLERMDSSTTGILTILCNHSFHCSCLMKWWD----SSCPVCRYCQS------------------PSV----VESS 229 (493)
T ss_pred CCcchhHhhcCccccceeeeecccccchHHHhhccc----CcChhhhhhcC------------------cch----hhhh
Confidence 479999999999988888899999999999999972 68999994433 111 1246
Q ss_pred EccCCCCccccceeEeeecCC--CCCCcccccc
Q 024406 231 LCNDCNDTTEVYFHIIGQKCS--HCKSYNTRSI 261 (268)
Q Consensus 231 ~CnDC~~~s~~~~H~lg~kC~--~C~SyNT~~~ 261 (268)
+|.+|+...++ |+-+.|+ +||-|+-...
T Consensus 230 ~c~~c~~~~~L---wicliCg~vgcgrY~eghA 259 (493)
T KOG0804|consen 230 LCLACGCTEDL---WICLICGNVGCGRYKEGHA 259 (493)
T ss_pred hhhhhcccccE---EEEEEccceecccccchhH
Confidence 79999998888 9999998 5999987653
No 21
>KOG0802 consensus E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=98.37 E-value=1.2e-07 Score=95.11 Aligned_cols=53 Identities=26% Similarity=0.596 Sum_probs=44.4
Q ss_pred cCCCCCCCchhhhhhcccC-CcceEeccCCccChHHHHHHHHcCCCcCCCCCCcch
Q 024406 146 ENSMHHHCPICYEYLFDSL-RNTTVMKCGHTMHCECYHEMIKRDNRYCCPICSKSV 200 (268)
Q Consensus 146 e~~~~~~CpICle~lf~s~-~~v~~LpCGH~~H~~C~~~~~~~~~~~~CPiCrksi 200 (268)
+......|+||+|.|+.+. ....+|+|||.||..|+..|++.. .+||+||..+
T Consensus 287 ~~~~~~~C~IC~e~l~~~~~~~~~rL~C~Hifh~~CL~~W~er~--qtCP~CR~~~ 340 (543)
T KOG0802|consen 287 LALSDELCIICLEELHSGHNITPKRLPCGHIFHDSCLRSWFERQ--QTCPTCRTVL 340 (543)
T ss_pred hhhcCCeeeeechhhccccccccceeecccchHHHHHHHHHHHh--CcCCcchhhh
Confidence 3455789999999998742 226789999999999999999986 8999999943
No 22
>PLN03208 E3 ubiquitin-protein ligase RMA2; Provisional
Probab=98.29 E-value=6.5e-07 Score=79.35 Aligned_cols=56 Identities=23% Similarity=0.606 Sum_probs=42.4
Q ss_pred eeecCCCCCCCchhhhhhcccCCcceEeccCCccChHHHHHHHHcC--------------CCcCCCCCCcchhh
Q 024406 143 LCIENSMHHHCPICYEYLFDSLRNTTVMKCGHTMHCECYHEMIKRD--------------NRYCCPICSKSVID 202 (268)
Q Consensus 143 ~C~e~~~~~~CpICle~lf~s~~~v~~LpCGH~~H~~C~~~~~~~~--------------~~~~CPiCrksi~~ 202 (268)
+=++...+..||||++.+ . ..++++|||.|+..|+.+|+... ...+||+|+..+..
T Consensus 11 ~~~~~~~~~~CpICld~~-~---dPVvT~CGH~FC~~CI~~wl~~s~~s~~~~~~~~~~k~~~~CPvCR~~Is~ 80 (193)
T PLN03208 11 TLVDSGGDFDCNICLDQV-R---DPVVTLCGHLFCWPCIHKWTYASNNSRQRVDQYDHKREPPKCPVCKSDVSE 80 (193)
T ss_pred eeccCCCccCCccCCCcC-C---CcEEcCCCchhHHHHHHHHHHhccccccccccccccCCCCcCCCCCCcCCh
Confidence 334445678999999974 2 34568999999999999998531 13689999999864
No 23
>PHA02926 zinc finger-like protein; Provisional
Probab=98.09 E-value=1.9e-06 Score=77.90 Aligned_cols=69 Identities=20% Similarity=0.368 Sum_probs=48.0
Q ss_pred cccccccCcceeecCCCCCCCchhhhhhcccC-----CcceEeccCCccChHHHHHHHHcC----CCcCCCCCCcchh
Q 024406 133 CYSTSLRNNHLCIENSMHHHCPICYEYLFDSL-----RNTTVMKCGHTMHCECYHEMIKRD----NRYCCPICSKSVI 201 (268)
Q Consensus 133 C~s~~l~~~H~C~e~~~~~~CpICle~lf~s~-----~~v~~LpCGH~~H~~C~~~~~~~~----~~~~CPiCrksi~ 201 (268)
++..-|.+-..=.+.+.+..|+||||.+++.+ ......+|+|.|+..|+.+|.+.. ...+||+||..+.
T Consensus 153 ~i~~il~~ye~~~~~SkE~eCgICmE~I~eK~~~~eRrFGIL~~CnHsFCl~CIr~Wr~~r~~~~~~rsCPiCR~~f~ 230 (242)
T PHA02926 153 DIIKILDKYEDVYRVSKEKECGICYEVVYSKRLENDRYFGLLDSCNHIFCITCINIWHRTRRETGASDNCPICRTRFR 230 (242)
T ss_pred chhHHHHHHHHHHhccCCCCCccCccccccccccccccccccCCCCchHHHHHHHHHHHhccccCcCCcCCCCcceee
Confidence 44444433333334577899999999887532 123455999999999999999753 1346999998875
No 24
>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=98.09 E-value=2.4e-06 Score=59.93 Aligned_cols=44 Identities=27% Similarity=0.602 Sum_probs=34.8
Q ss_pred CCchhhhhhcccCCcceEeccC-----CccChHHHHHHHHcCCCcCCCCCC
Q 024406 152 HCPICYEYLFDSLRNTTVMKCG-----HTMHCECYHEMIKRDNRYCCPICS 197 (268)
Q Consensus 152 ~CpICle~lf~s~~~v~~LpCG-----H~~H~~C~~~~~~~~~~~~CPiCr 197 (268)
.|-||++ +++.+...++||. |++|..|+.+|+..+...+||+|+
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 999999999999766456899995
No 25
>KOG0320 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=98.05 E-value=1.8e-06 Score=75.60 Aligned_cols=46 Identities=30% Similarity=0.840 Sum_probs=38.5
Q ss_pred CCCchhhhhhcccCCcc-eEeccCCccChHHHHHHHHcCCCcCCCCCCcchh
Q 024406 151 HHCPICYEYLFDSLRNT-TVMKCGHTMHCECYHEMIKRDNRYCCPICSKSVI 201 (268)
Q Consensus 151 ~~CpICle~lf~s~~~v-~~LpCGH~~H~~C~~~~~~~~~~~~CPiCrksi~ 201 (268)
-.|||||+.. +. .+ +.-.|||.|.++|++.-++.. .+||+|+|.|.
T Consensus 132 ~~CPiCl~~~-se--k~~vsTkCGHvFC~~Cik~alk~~--~~CP~C~kkIt 178 (187)
T KOG0320|consen 132 YKCPICLDSV-SE--KVPVSTKCGHVFCSQCIKDALKNT--NKCPTCRKKIT 178 (187)
T ss_pred cCCCceecch-hh--ccccccccchhHHHHHHHHHHHhC--CCCCCcccccc
Confidence 6899999984 32 34 347999999999999999886 89999999765
No 26
>PF11793 FANCL_C: FANCL C-terminal domain; PDB: 3K1L_A.
Probab=98.03 E-value=1.4e-06 Score=65.27 Aligned_cols=52 Identities=31% Similarity=0.621 Sum_probs=24.3
Q ss_pred CCCCchhhhhhc-ccCCcceEe---ccCCccChHHHHHHHHcC--C-------CcCCCCCCcchh
Q 024406 150 HHHCPICYEYLF-DSLRNTTVM---KCGHTMHCECYHEMIKRD--N-------RYCCPICSKSVI 201 (268)
Q Consensus 150 ~~~CpICle~lf-~s~~~v~~L---pCGH~~H~~C~~~~~~~~--~-------~~~CPiCrksi~ 201 (268)
+.+|+||.+++. +...++.+- .|+..||..||.+|++.. + .-+||.|++.|.
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 468999999876 333444443 699999999999998742 0 125999999884
No 27
>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=98.01 E-value=5.5e-06 Score=59.18 Aligned_cols=45 Identities=18% Similarity=0.360 Sum_probs=38.0
Q ss_pred CCCchhhhhhcccCCcceEeccCCccChHHHHHHHHcCCCcCCCCCCcchh
Q 024406 151 HHCPICYEYLFDSLRNTTVMKCGHTMHCECYHEMIKRDNRYCCPICSKSVI 201 (268)
Q Consensus 151 ~~CpICle~lf~s~~~v~~LpCGH~~H~~C~~~~~~~~~~~~CPiCrksi~ 201 (268)
..||||++.|-+ + ++++|||.|-+.|+.+|++.+ .+||+|++.+.
T Consensus 2 ~~Cpi~~~~~~~---P-v~~~~G~v~~~~~i~~~~~~~--~~cP~~~~~~~ 46 (63)
T smart00504 2 FLCPISLEVMKD---P-VILPSGQTYERRAIEKWLLSH--GTDPVTGQPLT 46 (63)
T ss_pred cCCcCCCCcCCC---C-EECCCCCEEeHHHHHHHHHHC--CCCCCCcCCCC
Confidence 469999997532 4 567999999999999999875 79999999884
No 28
>KOG2177 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=97.77 E-value=2e-05 Score=68.47 Aligned_cols=44 Identities=30% Similarity=0.846 Sum_probs=37.5
Q ss_pred CCCCCchhhhhhcccCCcceEeccCCccChHHHHHHHHcCCCcCCCCCCc
Q 024406 149 MHHHCPICYEYLFDSLRNTTVMKCGHTMHCECYHEMIKRDNRYCCPICSK 198 (268)
Q Consensus 149 ~~~~CpICle~lf~s~~~v~~LpCGH~~H~~C~~~~~~~~~~~~CPiCrk 198 (268)
....||||++++ .. + ++|||||+|...|+..+.. . ...||.|+.
T Consensus 12 ~~~~C~iC~~~~-~~--p-~~l~C~H~~c~~C~~~~~~-~-~~~Cp~cr~ 55 (386)
T KOG2177|consen 12 EELTCPICLEYF-RE--P-VLLPCGHNFCRACLTRSWE-G-PLSCPVCRP 55 (386)
T ss_pred ccccChhhHHHh-hc--C-ccccccchHhHHHHHHhcC-C-CcCCcccCC
Confidence 467899999984 43 3 8899999999999999988 3 599999995
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=2.5e-05 Score=76.17 Aligned_cols=46 Identities=22% Similarity=0.583 Sum_probs=38.8
Q ss_pred CCCCchhhhhhcccCCcceEeccCCccChHHHHHHHHcCCCcCCCCCCcchh
Q 024406 150 HHHCPICYEYLFDSLRNTTVMKCGHTMHCECYHEMIKRDNRYCCPICSKSVI 201 (268)
Q Consensus 150 ~~~CpICle~lf~s~~~v~~LpCGH~~H~~C~~~~~~~~~~~~CPiCrksi~ 201 (268)
...||||++.+.. ++ +++|||.|+..|+..|+... ..||+|+..+.
T Consensus 26 ~l~C~IC~d~~~~---Pv-itpCgH~FCs~CI~~~l~~~--~~CP~Cr~~~~ 71 (397)
T TIGR00599 26 SLRCHICKDFFDV---PV-LTSCSHTFCSLCIRRCLSNQ--PKCPLCRAEDQ 71 (397)
T ss_pred ccCCCcCchhhhC---cc-CCCCCCchhHHHHHHHHhCC--CCCCCCCCccc
Confidence 5689999997532 44 68999999999999999875 68999999876
No 30
>COG5194 APC11 Component of SCF ubiquitin ligase and anaphase-promoting complex [Posttranslational modification, protein turnover, chaperones / Cell division and chromosome partitioning]
Probab=97.65 E-value=3.2e-05 Score=59.76 Aligned_cols=29 Identities=21% Similarity=0.589 Sum_probs=26.5
Q ss_pred ccCCccChHHHHHHHHcCCCcCCCCCCcchh
Q 024406 171 KCGHTMHCECYHEMIKRDNRYCCPICSKSVI 201 (268)
Q Consensus 171 pCGH~~H~~C~~~~~~~~~~~~CPiCrksi~ 201 (268)
-|.|+||..|+..||.+. ..||++++...
T Consensus 53 ~CnHaFH~HCI~rWL~Tk--~~CPld~q~w~ 81 (88)
T COG5194 53 VCNHAFHDHCIYRWLDTK--GVCPLDRQTWV 81 (88)
T ss_pred ecchHHHHHHHHHHHhhC--CCCCCCCceeE
Confidence 699999999999999886 89999998764
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=97.46 E-value=9.6e-05 Score=69.88 Aligned_cols=50 Identities=26% Similarity=0.620 Sum_probs=38.7
Q ss_pred CCCCchhhhhhcccCCcceEe--ccCCccChHHHHHHHHcCCCcCCCCCCcchh
Q 024406 150 HHHCPICYEYLFDSLRNTTVM--KCGHTMHCECYHEMIKRDNRYCCPICSKSVI 201 (268)
Q Consensus 150 ~~~CpICle~lf~s~~~v~~L--pCGH~~H~~C~~~~~~~~~~~~CPiCrksi~ 201 (268)
+..||||+.+.+.+.. .++| +|||.|..+|++.++..+ ...||+|++++-
T Consensus 3 ~~~CP~Ck~~~y~np~-~kl~i~~CGH~~C~sCv~~l~~~~-~~~CP~C~~~lr 54 (309)
T TIGR00570 3 DQGCPRCKTTKYRNPS-LKLMVNVCGHTLCESCVDLLFVRG-SGSCPECDTPLR 54 (309)
T ss_pred CCCCCcCCCCCccCcc-cccccCCCCCcccHHHHHHHhcCC-CCCCCCCCCccc
Confidence 3579999997555532 2222 899999999999987665 579999999875
No 32
>KOG0317 consensus Predicted E3 ubiquitin ligase, integral peroxisomal membrane protein [Posttranslational modification, protein turnover, chaperones]
Probab=97.42 E-value=5.5e-05 Score=70.61 Aligned_cols=45 Identities=27% Similarity=0.673 Sum_probs=38.2
Q ss_pred CCCchhhhhhcccCCcceEeccCCccChHHHHHHHHcCCCcCCCCCCcchh
Q 024406 151 HHCPICYEYLFDSLRNTTVMKCGHTMHCECYHEMIKRDNRYCCPICSKSVI 201 (268)
Q Consensus 151 ~~CpICle~lf~s~~~v~~LpCGH~~H~~C~~~~~~~~~~~~CPiCrksi~ 201 (268)
..|.+|||... .....||||.|.-.|+.+|.... ..||+||..+-
T Consensus 240 ~kC~LCLe~~~----~pSaTpCGHiFCWsCI~~w~~ek--~eCPlCR~~~~ 284 (293)
T KOG0317|consen 240 RKCSLCLENRS----NPSATPCGHIFCWSCILEWCSEK--AECPLCREKFQ 284 (293)
T ss_pred CceEEEecCCC----CCCcCcCcchHHHHHHHHHHccc--cCCCcccccCC
Confidence 57999999753 34578999999999999999876 67999997765
No 33
>KOG0823 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=97.30 E-value=0.00014 Score=65.97 Aligned_cols=51 Identities=24% Similarity=0.610 Sum_probs=39.5
Q ss_pred CCCCCCchhhhhhcccCCcceEeccCCccChHHHHHHHHcCC-CcCCCCCCcchhh
Q 024406 148 SMHHHCPICYEYLFDSLRNTTVMKCGHTMHCECYHEMIKRDN-RYCCPICSKSVID 202 (268)
Q Consensus 148 ~~~~~CpICle~lf~s~~~v~~LpCGH~~H~~C~~~~~~~~~-~~~CPiCrksi~~ 202 (268)
...-+|-||||- . ++.++-.|||+|.-.||.+||.... ...||+|+-.|..
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 456789999984 2 3456667999999999999998652 3457999987764
No 34
>KOG0827 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=97.29 E-value=0.0001 Score=71.44 Aligned_cols=47 Identities=28% Similarity=0.601 Sum_probs=39.9
Q ss_pred CCCCchhhhhhcccCCcceEec-cCCccChHHHHHHHHcCC-CcCCCCCC
Q 024406 150 HHHCPICYEYLFDSLRNTTVMK-CGHTMHCECYHEMIKRDN-RYCCPICS 197 (268)
Q Consensus 150 ~~~CpICle~lf~s~~~v~~Lp-CGH~~H~~C~~~~~~~~~-~~~CPiCr 197 (268)
...|.|| +++|.....+.... |||+||..|+.+|++... +..||+|+
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 77898877887776 999999999999998653 36899999
No 35
>KOG0287 consensus Postreplication repair protein RAD18 [Replication, recombination and repair]
Probab=97.18 E-value=0.00036 Score=66.80 Aligned_cols=58 Identities=28% Similarity=0.687 Sum_probs=44.0
Q ss_pred CCCchhhhhhcccCCcceEeccCCccChHHHHHHHHcCCCcCCCCCCcchhhhh-HHHHHHHHHH
Q 024406 151 HHCPICYEYLFDSLRNTTVMKCGHTMHCECYHEMIKRDNRYCCPICSKSVIDMS-RTWKRIDEEI 214 (268)
Q Consensus 151 ~~CpICle~lf~s~~~v~~LpCGH~~H~~C~~~~~~~~~~~~CPiCrksi~~m~-~~~~~lD~~i 214 (268)
..|-||.|++ . -..+.||||+|.+-||..+|... ..||.|...+..-. ...+.||++|
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---IPMITPCSHTFCSLCIRKFLSYK--PQCPTCCVTVTESDLRNNRILDEIV 82 (442)
T ss_pred HHHhHHHHHh-c---CceeccccchHHHHHHHHHhccC--CCCCceecccchhhhhhhhHHHHHH
Confidence 4699999984 2 34566899999999999999876 89999999986322 1234566655
No 36
>KOG2164 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=97.11 E-value=0.00028 Score=70.34 Aligned_cols=51 Identities=27% Similarity=0.607 Sum_probs=38.9
Q ss_pred CCCCCCchhhhhhcccCCcceEeccCCccChHHHHHHHHcC---CCcCCCCCCcchhh
Q 024406 148 SMHHHCPICYEYLFDSLRNTTVMKCGHTMHCECYHEMIKRD---NRYCCPICSKSVID 202 (268)
Q Consensus 148 ~~~~~CpICle~lf~s~~~v~~LpCGH~~H~~C~~~~~~~~---~~~~CPiCrksi~~ 202 (268)
++...|||||++ .. -...+.|||.|.-.||-+|+..+ .--.||||+..|.-
T Consensus 184 ~t~~~CPICL~~-~~---~p~~t~CGHiFC~~CiLqy~~~s~~~~~~~CPiC~s~I~~ 237 (513)
T KOG2164|consen 184 STDMQCPICLEP-PS---VPVRTNCGHIFCGPCILQYWNYSAIKGPCSCPICRSTITL 237 (513)
T ss_pred CcCCcCCcccCC-CC---cccccccCceeeHHHHHHHHhhhcccCCccCCchhhhccc
Confidence 448899999997 21 23345699999999999987643 24579999999864
No 37
>KOG1941 consensus Acetylcholine receptor-associated protein of the synapse (rapsyn) [Extracellular structures]
Probab=97.06 E-value=0.00017 Score=70.08 Aligned_cols=63 Identities=25% Similarity=0.576 Sum_probs=53.0
Q ss_pred cceeecCCCCCCCchhhhhhcccCCcceEeccCCccChHHHHHHHHcCCCcCCCCCCcchhhhh
Q 024406 141 NHLCIENSMHHHCPICYEYLFDSLRNTTVMKCGHTMHCECYHEMIKRDNRYCCPICSKSVIDMS 204 (268)
Q Consensus 141 ~H~C~e~~~~~~CpICle~lf~s~~~v~~LpCGH~~H~~C~~~~~~~~~~~~CPiCrksi~~m~ 204 (268)
.|.|++ .++..|-.|.|-+-...+....|||.|+||..|+.+++..+...+||-|||....|+
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 456664 468899999998877777788899999999999999998776788999997777665
No 38
>COG5219 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=96.97 E-value=0.00047 Score=73.03 Aligned_cols=55 Identities=27% Similarity=0.611 Sum_probs=42.0
Q ss_pred CCCCCCCchhhhhhc--ccCCcceE-eccCCccChHHHHHHHHcCCCcCCCCCCcchh
Q 024406 147 NSMHHHCPICYEYLF--DSLRNTTV-MKCGHTMHCECYHEMIKRDNRYCCPICSKSVI 201 (268)
Q Consensus 147 ~~~~~~CpICle~lf--~s~~~v~~-LpCGH~~H~~C~~~~~~~~~~~~CPiCrksi~ 201 (268)
-+...+||||..-|. +..-|... -.|.|-||..|+.+|++++++.+||+||.++.
T Consensus 1466 fsG~eECaICYsvL~~vdr~lPskrC~TCknKFH~~CLyKWf~Ss~~s~CPlCRseit 1523 (1525)
T COG5219 1466 FSGHEECAICYSVLDMVDRSLPSKRCATCKNKFHTRCLYKWFASSARSNCPLCRSEIT 1523 (1525)
T ss_pred cCCcchhhHHHHHHHHHhccCCccccchhhhhhhHHHHHHHHHhcCCCCCCccccccc
Confidence 356789999997654 33333333 24789999999999999887899999997653
No 39
>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=96.87 E-value=0.001 Score=49.78 Aligned_cols=48 Identities=17% Similarity=0.364 Sum_probs=35.4
Q ss_pred CCCCchhhhhhcccCCcceEeccCCccChHHHHHHHHcCCCcCCCCCCcchhh
Q 024406 150 HHHCPICYEYLFDSLRNTTVMKCGHTMHCECYHEMIKRDNRYCCPICSKSVID 202 (268)
Q Consensus 150 ~~~CpICle~lf~s~~~v~~LpCGH~~H~~C~~~~~~~~~~~~CPiCrksi~~ 202 (268)
+..|||+++-|. .-+++|+||+|-+.++.+|++.+ ..+||+++..+..
T Consensus 4 ~f~CpIt~~lM~----dPVi~~~G~tyer~~I~~~l~~~-~~~~P~t~~~l~~ 51 (73)
T PF04564_consen 4 EFLCPITGELMR----DPVILPSGHTYERSAIERWLEQN-GGTDPFTRQPLSE 51 (73)
T ss_dssp GGB-TTTSSB-S----SEEEETTSEEEEHHHHHHHHCTT-SSB-TTT-SB-SG
T ss_pred ccCCcCcCcHhh----CceeCCcCCEEcHHHHHHHHHcC-CCCCCCCCCcCCc
Confidence 346999999653 24478999999999999999984 4899999988864
No 40
>KOG0828 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=96.84 E-value=0.00034 Score=69.60 Aligned_cols=51 Identities=22% Similarity=0.530 Sum_probs=36.4
Q ss_pred CCCCchhhhhhcc--cCC-----------cceEeccCCccChHHHHHHHHcCCCcCCCCCCcchh
Q 024406 150 HHHCPICYEYLFD--SLR-----------NTTVMKCGHTMHCECYHEMIKRDNRYCCPICSKSVI 201 (268)
Q Consensus 150 ~~~CpICle~lf~--s~~-----------~v~~LpCGH~~H~~C~~~~~~~~~~~~CPiCrksi~ 201 (268)
..+|+||+.++-- ... ...+-||-|.||+.|+.+|+... ...||+||..+-
T Consensus 571 t~dC~ICMt~I~l~~~~s~~~~~~~~~~~nYm~tPC~HifH~~CL~~WMd~y-kl~CPvCR~pLP 634 (636)
T KOG0828|consen 571 TNDCVICMTPIDLRSTGSDCMVASMMVRRNYMLTPCHHIFHRQCLLQWMDTY-KLICPVCRCPLP 634 (636)
T ss_pred cccceEeccccceeeccCcchhhhhhhhccccccchHHHHHHHHHHHHHhhh-cccCCccCCCCC
Confidence 3578888876421 111 23344999999999999999854 378999997763
No 41
>KOG1734 consensus Predicted RING-containing E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=96.80 E-value=0.00035 Score=65.03 Aligned_cols=53 Identities=25% Similarity=0.499 Sum_probs=43.3
Q ss_pred CCCCCchhhhhhcccCC------cceEeccCCccChHHHHHHHHcCCCcCCCCCCcchh
Q 024406 149 MHHHCPICYEYLFDSLR------NTTVMKCGHTMHCECYHEMIKRDNRYCCPICSKSVI 201 (268)
Q Consensus 149 ~~~~CpICle~lf~s~~------~v~~LpCGH~~H~~C~~~~~~~~~~~~CPiCrksi~ 201 (268)
+++.|.||...++.+.+ ....|.|+|.||.-|++-|---++..+||.|++.+.
T Consensus 223 ~d~vCaVCg~~~~~s~~eegvienty~LsCnHvFHEfCIrGWcivGKkqtCPYCKekVd 281 (328)
T KOG1734|consen 223 SDSVCAVCGQQIDVSVDEEGVIENTYKLSCNHVFHEFCIRGWCIVGKKQTCPYCKEKVD 281 (328)
T ss_pred CcchhHhhcchheeecchhhhhhhheeeecccchHHHhhhhheeecCCCCCchHHHHhh
Confidence 45789999999877652 467799999999999999965444689999998875
No 42
>PF14835 zf-RING_6: zf-RING of BARD1-type protein; PDB: 1JM7_B.
Probab=96.75 E-value=0.00047 Score=51.24 Aligned_cols=56 Identities=25% Similarity=0.640 Sum_probs=28.5
Q ss_pred CCCchhhhhhcccCCcceEeccCCccChHHHHHHHHcCCCcCCCCCCcchh--hhhHHHHHHHHHH
Q 024406 151 HHCPICYEYLFDSLRNTTVMKCGHTMHCECYHEMIKRDNRYCCPICSKSVI--DMSRTWKRIDEEI 214 (268)
Q Consensus 151 ~~CpICle~lf~s~~~v~~LpCGH~~H~~C~~~~~~~~~~~~CPiCrksi~--~m~~~~~~lD~~i 214 (268)
..|++|.+.|. +||..-.|.|.|.+.|+.+-+. ..||+|+.+.. |+. .-+.||..|
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 46999999754 3677789999999999988552 57999999985 443 346777765
No 43
>KOG1493 consensus Anaphase-promoting complex (APC), subunit 11 [Cell cycle control, cell division, chromosome partitioning; Posttranslational modification, protein turnover, chaperones]
Probab=96.74 E-value=0.00046 Score=53.04 Aligned_cols=30 Identities=23% Similarity=0.680 Sum_probs=24.9
Q ss_pred ccCCccChHHHHHHHHcC-CCcCCCCCCcch
Q 024406 171 KCGHTMHCECYHEMIKRD-NRYCCPICSKSV 200 (268)
Q Consensus 171 pCGH~~H~~C~~~~~~~~-~~~~CPiCrksi 200 (268)
-|-|.||..|+.+|+... ++-.||+||...
T Consensus 50 ~C~h~fh~hCI~~wl~~~tsq~~CPmcRq~~ 80 (84)
T KOG1493|consen 50 YCLHAFHAHCILKWLNTPTSQGQCPMCRQTW 80 (84)
T ss_pred HHHHHHHHHHHHHHhcCccccccCCcchhee
Confidence 599999999999999643 257899999764
No 44
>KOG4265 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=96.57 E-value=0.0015 Score=62.66 Aligned_cols=51 Identities=29% Similarity=0.686 Sum_probs=41.4
Q ss_pred cCCCCCCCchhhhhhcccCCcceEeccCCc-cChHHHHHHHHcCCCcCCCCCCcchhh
Q 024406 146 ENSMHHHCPICYEYLFDSLRNTTVMKCGHT-MHCECYHEMIKRDNRYCCPICSKSVID 202 (268)
Q Consensus 146 e~~~~~~CpICle~lf~s~~~v~~LpCGH~-~H~~C~~~~~~~~~~~~CPiCrksi~~ 202 (268)
++....+|.|||.+ + +++.+|||-|+ |.+.|.+.+.-.. .+|||||..|..
T Consensus 286 ~~~~gkeCVIClse---~-rdt~vLPCRHLCLCs~Ca~~Lr~q~--n~CPICRqpi~~ 337 (349)
T KOG4265|consen 286 ESESGKECVICLSE---S-RDTVVLPCRHLCLCSGCAKSLRYQT--NNCPICRQPIEE 337 (349)
T ss_pred cccCCCeeEEEecC---C-cceEEecchhhehhHhHHHHHHHhh--cCCCccccchHh
Confidence 44557799999986 3 57899999997 8999999987443 799999998863
No 45
>COG5574 PEX10 RING-finger-containing E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=96.34 E-value=0.0016 Score=60.26 Aligned_cols=47 Identities=26% Similarity=0.550 Sum_probs=37.3
Q ss_pred CCCCchhhhhhcccCCcceEeccCCccChHHHHH-HHHcCCCcCCCCCCcchh
Q 024406 150 HHHCPICYEYLFDSLRNTTVMKCGHTMHCECYHE-MIKRDNRYCCPICSKSVI 201 (268)
Q Consensus 150 ~~~CpICle~lf~s~~~v~~LpCGH~~H~~C~~~-~~~~~~~~~CPiCrksi~ 201 (268)
+-.|+||+|.+. .....+|||.|...|+-. |.... ...||+||.-+.
T Consensus 215 d~kC~lC~e~~~----~ps~t~CgHlFC~~Cl~~~~t~~k-~~~CplCRak~~ 262 (271)
T COG5574 215 DYKCFLCLEEPE----VPSCTPCGHLFCLSCLLISWTKKK-YEFCPLCRAKVY 262 (271)
T ss_pred ccceeeeecccC----CcccccccchhhHHHHHHHHHhhc-cccCchhhhhcc
Confidence 456999999753 356789999999999999 88765 234999997664
No 46
>KOG2930 consensus SCF ubiquitin ligase, Rbx1 component [Posttranslational modification, protein turnover, chaperones]
Probab=96.31 E-value=0.0024 Score=51.72 Aligned_cols=28 Identities=29% Similarity=0.697 Sum_probs=25.4
Q ss_pred ccCCccChHHHHHHHHcCCCcCCCCCCcch
Q 024406 171 KCGHTMHCECYHEMIKRDNRYCCPICSKSV 200 (268)
Q Consensus 171 pCGH~~H~~C~~~~~~~~~~~~CPiCrksi 200 (268)
-|.|+||..|+..||++. ..|||+.|.-
T Consensus 80 ~CNHaFH~hCisrWlktr--~vCPLdn~eW 107 (114)
T KOG2930|consen 80 VCNHAFHFHCISRWLKTR--NVCPLDNKEW 107 (114)
T ss_pred ecchHHHHHHHHHHHhhc--CcCCCcCcce
Confidence 699999999999999987 8999998753
No 47
>KOG1039 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=96.26 E-value=0.00095 Score=64.15 Aligned_cols=84 Identities=23% Similarity=0.483 Sum_probs=59.4
Q ss_pred CCCCCCCchhhhhhcccC---CcceE-eccCCccChHHHHHHHHcCC-----CcCCCCCCcchh--hhhHHHHHHHHHHH
Q 024406 147 NSMHHHCPICYEYLFDSL---RNTTV-MKCGHTMHCECYHEMIKRDN-----RYCCPICSKSVI--DMSRTWKRIDEEIE 215 (268)
Q Consensus 147 ~~~~~~CpICle~lf~s~---~~v~~-LpCGH~~H~~C~~~~~~~~~-----~~~CPiCrksi~--~m~~~~~~lD~~i~ 215 (268)
++.+..|-||+|.+.+.. ....+ ++|-|+|...|+..|....+ ...||+||-... .-+.+|-.-.+ +
T Consensus 158 ~s~~k~CGICme~i~ek~~~~~rfgilpnC~H~~Cl~Cir~wr~~~q~~~~~sksCP~CRv~s~~v~pS~~Wv~t~~--~ 235 (344)
T KOG1039|consen 158 KSSEKECGICMETINEKAASERRFGILPNCNHSFCLNCIRKWRQATQFESKTSKSCPFCRVPSSFVNPSSFWVETKE--E 235 (344)
T ss_pred ccccccceehhhhccccchhhhhcccCCCcchhhhhcHhHhhhhhhccccccccCCCcccCccccccccceeeeecc--c
Confidence 366789999999887653 11223 46999999999999995542 368999998874 45556753322 6
Q ss_pred hcCCChhhhcCeeEEEc
Q 024406 216 ATVMPEDYRHKKVWILC 232 (268)
Q Consensus 216 ~~pmP~~y~~~~v~I~C 232 (268)
.++.+++|+..+....|
T Consensus 236 k~~li~e~~~~~s~~~c 252 (344)
T KOG1039|consen 236 KQKLIEEYEAEMSAKDC 252 (344)
T ss_pred ccccHHHHHHHhhccch
Confidence 66778888777665544
No 48
>KOG0825 consensus PHD Zn-finger protein [General function prediction only]
Probab=96.17 E-value=0.002 Score=67.20 Aligned_cols=75 Identities=16% Similarity=0.302 Sum_probs=53.3
Q ss_pred eeecCccCccccccccCcceee-cCCCCCCCchhhhhhcccCCcceEeccCCccChHHHHHHHHcCCCcCCCCCCcchh
Q 024406 124 YFHCKRCGSCYSTSLRNNHLCI-ENSMHHHCPICYEYLFDSLRNTTVMKCGHTMHCECYHEMIKRDNRYCCPICSKSVI 201 (268)
Q Consensus 124 ffHC~~C~~C~s~~l~~~H~C~-e~~~~~~CpICle~lf~s~~~v~~LpCGH~~H~~C~~~~~~~~~~~~CPiCrksi~ 201 (268)
--.|..|-.+.|...-..-.|+ .+-.+..||+|+....+ .......+|+|.||..||..|.+.. .+|||||+.+.
T Consensus 96 s~Ss~~C~~E~S~~~ds~~i~P~~~~~~~~CP~Ci~s~~D-qL~~~~k~c~H~FC~~Ci~sWsR~a--qTCPiDR~EF~ 171 (1134)
T KOG0825|consen 96 SDTSPVCEKEHSPDVDSSNICPVQTHVENQCPNCLKSCND-QLEESEKHTAHYFCEECVGSWSRCA--QTCPVDRGEFG 171 (1134)
T ss_pred ccccchhheecCCcccccCcCchhhhhhhhhhHHHHHHHH-HhhccccccccccHHHHhhhhhhhc--ccCchhhhhhh
Confidence 3455566666665333334444 23345689999987443 3445567999999999999999876 89999999886
No 49
>PF14570 zf-RING_4: RING/Ubox like zinc-binding domain; PDB: 1E4U_A 1UR6_B.
Probab=96.12 E-value=0.0033 Score=44.19 Aligned_cols=46 Identities=28% Similarity=0.735 Sum_probs=24.4
Q ss_pred CchhhhhhcccCCcceEeccCCccChHHHHHHHHcCCCcCCCCCCcc
Q 024406 153 CPICYEYLFDSLRNTTVMKCGHTMHCECYHEMIKRDNRYCCPICSKS 199 (268)
Q Consensus 153 CpICle~lf~s~~~v~~LpCGH~~H~~C~~~~~~~~~~~~CPiCrks 199 (268)
||+|.|+|..+.....--+||.-|.+.|+...++.. +.+||-||+.
T Consensus 1 cp~C~e~~d~~d~~~~PC~Cgf~IC~~C~~~i~~~~-~g~CPgCr~~ 46 (48)
T PF14570_consen 1 CPLCDEELDETDKDFYPCECGFQICRFCYHDILENE-GGRCPGCREP 46 (48)
T ss_dssp -TTTS-B--CCCTT--SSTTS----HHHHHHHTTSS--SB-TTT--B
T ss_pred CCCcccccccCCCccccCcCCCcHHHHHHHHHHhcc-CCCCCCCCCC
Confidence 799999984443333333579999999999998754 4899999975
No 50
>PF12906 RINGv: RING-variant domain; PDB: 2D8S_A 1VYX_A.
Probab=96.09 E-value=0.0025 Score=44.21 Aligned_cols=42 Identities=26% Similarity=0.630 Sum_probs=28.0
Q ss_pred CchhhhhhcccCCcceEeccC-----CccChHHHHHHHHcCCCcCCCCC
Q 024406 153 CPICYEYLFDSLRNTTVMKCG-----HTMHCECYHEMIKRDNRYCCPIC 196 (268)
Q Consensus 153 CpICle~lf~s~~~v~~LpCG-----H~~H~~C~~~~~~~~~~~~CPiC 196 (268)
|-||++.-.++ +..+.||+ -..|.+|+.+|+...++.+|++|
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 56899874433 34566873 68999999999986546889987
No 51
>KOG3002 consensus Zn finger protein [General function prediction only]
Probab=96.05 E-value=0.0052 Score=58.11 Aligned_cols=64 Identities=22% Similarity=0.600 Sum_probs=49.0
Q ss_pred CCCCchhhhhhcccCCcceEecc--CCccChHHHHHHHHcCCCcCCCCCCcchhhhhHHHHHHHHHHHhcCCChhhhc
Q 024406 150 HHHCPICYEYLFDSLRNTTVMKC--GHTMHCECYHEMIKRDNRYCCPICSKSVIDMSRTWKRIDEEIEATVMPEDYRH 225 (268)
Q Consensus 150 ~~~CpICle~lf~s~~~v~~LpC--GH~~H~~C~~~~~~~~~~~~CPiCrksi~~m~~~~~~lD~~i~~~pmP~~y~~ 225 (268)
=.+||||.++|.. -++.| ||+....|-.+.. .+||.|+.+|++.+. +.++..+++...|=.|.+
T Consensus 48 lleCPvC~~~l~~-----Pi~QC~nGHlaCssC~~~~~-----~~CP~Cr~~~g~~R~--~amEkV~e~~~vpC~~~~ 113 (299)
T KOG3002|consen 48 LLDCPVCFNPLSP-----PIFQCDNGHLACSSCRTKVS-----NKCPTCRLPIGNIRC--RAMEKVAEAVLVPCKNAK 113 (299)
T ss_pred hccCchhhccCcc-----cceecCCCcEehhhhhhhhc-----ccCCccccccccHHH--HHHHHHHHhceecccccc
Confidence 3589999998743 35566 8999999987543 799999999997643 577788888877766544
No 52
>PF11789 zf-Nse: Zinc-finger of the MIZ type in Nse subunit; PDB: 2YU4_A 3HTK_C.
Probab=95.95 E-value=0.003 Score=45.65 Aligned_cols=45 Identities=31% Similarity=0.685 Sum_probs=31.5
Q ss_pred CCCCCCchhhhhhcccCCcceEeccCCccChHHHHHHHHcCCCcCCCC
Q 024406 148 SMHHHCPICYEYLFDSLRNTTVMKCGHTMHCECYHEMIKRDNRYCCPI 195 (268)
Q Consensus 148 ~~~~~CpICle~lf~s~~~v~~LpCGH~~H~~C~~~~~~~~~~~~CPi 195 (268)
.....|||-+.. |. +||+-..|||+|=++-+.+|++.++..+||+
T Consensus 9 ~~~~~CPiT~~~-~~--~PV~s~~C~H~fek~aI~~~i~~~~~~~CPv 53 (57)
T PF11789_consen 9 TISLKCPITLQP-FE--DPVKSKKCGHTFEKEAILQYIQRNGSKRCPV 53 (57)
T ss_dssp B--SB-TTTSSB--S--SEEEESSS--EEEHHHHHHHCTTTS-EE-SC
T ss_pred EeccCCCCcCCh-hh--CCcCcCCCCCeecHHHHHHHHHhcCCCCCCC
Confidence 446789999997 44 4899999999999999999995544688998
No 53
>KOG0311 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=95.87 E-value=0.0025 Score=61.24 Aligned_cols=49 Identities=27% Similarity=0.684 Sum_probs=41.3
Q ss_pred CCCCchhhhhhcccCCcceEeccCCccChHHHHHHHHcCCCcCCCCCCcchhh
Q 024406 150 HHHCPICYEYLFDSLRNTTVMKCGHTMHCECYHEMIKRDNRYCCPICSKSVID 202 (268)
Q Consensus 150 ~~~CpICle~lf~s~~~v~~LpCGH~~H~~C~~~~~~~~~~~~CPiCrksi~~ 202 (268)
+..|||||+=|-. .+..+.|+|-|...||..-++.+ +..||.|||.++.
T Consensus 43 ~v~c~icl~llk~---tmttkeClhrfc~~ci~~a~r~g-n~ecptcRk~l~S 91 (381)
T KOG0311|consen 43 QVICPICLSLLKK---TMTTKECLHRFCFDCIWKALRSG-NNECPTCRKKLVS 91 (381)
T ss_pred hhccHHHHHHHHh---hcccHHHHHHHHHHHHHHHHHhc-CCCCchHHhhccc
Confidence 4589999995433 46678999999999998888877 6899999999984
No 54
>KOG1785 consensus Tyrosine kinase negative regulator CBL [Defense mechanisms]
Probab=95.82 E-value=0.0027 Score=62.10 Aligned_cols=55 Identities=25% Similarity=0.604 Sum_probs=45.5
Q ss_pred eecCCCCCCCchhhhhhcccCCcceEeccCCccChHHHHHHHHcCCCcCCCCCCcchhh
Q 024406 144 CIENSMHHHCPICYEYLFDSLRNTTVMKCGHTMHCECYHEMIKRDNRYCCPICSKSVID 202 (268)
Q Consensus 144 C~e~~~~~~CpICle~lf~s~~~v~~LpCGH~~H~~C~~~~~~~~~~~~CPiCrksi~~ 202 (268)
|.-+++-+.|-||-|. .++|++=||||.+...|+..|..+....+||.||-.|-.
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 4446888899999984 468999999999999999999865435899999988753
No 55
>KOG1645 consensus RING-finger-containing E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=95.67 E-value=0.013 Score=57.42 Aligned_cols=51 Identities=24% Similarity=0.709 Sum_probs=39.2
Q ss_pred CCCCchhhhhhcccCCc-ceEeccCCccChHHHHHHHHcCCCcCCCCCCcch
Q 024406 150 HHHCPICYEYLFDSLRN-TTVMKCGHTMHCECYHEMIKRDNRYCCPICSKSV 200 (268)
Q Consensus 150 ~~~CpICle~lf~s~~~-v~~LpCGH~~H~~C~~~~~~~~~~~~CPiCrksi 200 (268)
...|||||+..-.+.+. +..|.|||.|=++|++.||......+||.|.-..
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 4558999999999999999533246799997543
No 56
>KOG2879 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=95.61 E-value=0.008 Score=56.17 Aligned_cols=54 Identities=26% Similarity=0.605 Sum_probs=44.7
Q ss_pred CCCCCCchhhhhhcccCCcceEeccCCccChHHHHHHHHcCCCcCCCCCCcchhhhh
Q 024406 148 SMHHHCPICYEYLFDSLRNTTVMKCGHTMHCECYHEMIKRDNRYCCPICSKSVIDMS 204 (268)
Q Consensus 148 ~~~~~CpICle~lf~s~~~v~~LpCGH~~H~~C~~~~~~~~~~~~CPiCrksi~~m~ 204 (268)
.....||+|.|+ ++.|.+..+|||.+.--|+..=+...+.++||.|+.++..|.
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 456799999997 667888899999999999988765444589999999888664
No 57
>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=0.0049 Score=47.96 Aligned_cols=37 Identities=27% Similarity=0.583 Sum_probs=30.0
Q ss_pred eecCCCCCCCchhhhhhcccCCcceEeccCCccChHHHH
Q 024406 144 CIENSMHHHCPICYEYLFDSLRNTTVMKCGHTMHCECYH 182 (268)
Q Consensus 144 C~e~~~~~~CpICle~lf~s~~~v~~LpCGH~~H~~C~~ 182 (268)
.+.=..+..|+||...|+++ ...+.||||.+|..|++
T Consensus 72 ~v~i~~~~~C~vC~k~l~~~--~f~~~p~~~v~H~~C~~ 108 (109)
T PF10367_consen 72 SVVITESTKCSVCGKPLGNS--VFVVFPCGHVVHYSCIK 108 (109)
T ss_pred eEEECCCCCccCcCCcCCCc--eEEEeCCCeEEeccccc
Confidence 33335567899999998874 78889999999999975
No 58
>KOG0978 consensus E3 ubiquitin ligase involved in syntaxin degradation [Posttranslational modification, protein turnover, chaperones]
Probab=95.33 E-value=0.005 Score=63.92 Aligned_cols=47 Identities=23% Similarity=0.624 Sum_probs=40.7
Q ss_pred CCCCchhhhhhcccCCcceEeccCCccChHHHHHHHHcCCCcCCCCCCcchh
Q 024406 150 HHHCPICYEYLFDSLRNTTVMKCGHTMHCECYHEMIKRDNRYCCPICSKSVI 201 (268)
Q Consensus 150 ~~~CpICle~lf~s~~~v~~LpCGH~~H~~C~~~~~~~~~~~~CPiCrksi~ 201 (268)
-..||+|-.. ..++++..|||.|...|+...+... +.+||.|+.+++
T Consensus 643 ~LkCs~Cn~R----~Kd~vI~kC~H~FC~~Cvq~r~etR-qRKCP~Cn~aFg 689 (698)
T KOG0978|consen 643 LLKCSVCNTR----WKDAVITKCGHVFCEECVQTRYETR-QRKCPKCNAAFG 689 (698)
T ss_pred ceeCCCccCc----hhhHHHHhcchHHHHHHHHHHHHHh-cCCCCCCCCCCC
Confidence 3579999853 4578888999999999999999877 689999999997
No 59
>KOG4172 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=95.12 E-value=0.007 Score=43.91 Aligned_cols=52 Identities=35% Similarity=0.776 Sum_probs=36.6
Q ss_pred CCCCCCchhhhhhcccCCcceEeccCCc-cChHHHHHHHHcCCCcCCCCCCcchhhhh
Q 024406 148 SMHHHCPICYEYLFDSLRNTTVMKCGHT-MHCECYHEMIKRDNRYCCPICSKSVIDMS 204 (268)
Q Consensus 148 ~~~~~CpICle~lf~s~~~v~~LpCGH~-~H~~C~~~~~~~~~~~~CPiCrksi~~m~ 204 (268)
+...+|.||+|.--+ .++--|||+ |.-.|-.+..+.. .-.|||||.+|-|.-
T Consensus 5 ~~~dECTICye~pvd----sVlYtCGHMCmCy~Cg~rl~~~~-~g~CPiCRapi~dvI 57 (62)
T KOG4172|consen 5 QWSDECTICYEHPVD----SVLYTCGHMCMCYACGLRLKKAL-HGCCPICRAPIKDVI 57 (62)
T ss_pred ccccceeeeccCcch----HHHHHcchHHhHHHHHHHHHHcc-CCcCcchhhHHHHHH
Confidence 445799999996333 234589997 5567766655533 479999999998753
No 60
>KOG1428 consensus Inhibitor of type V adenylyl cyclases/Neuronal presynaptic protein Highwire/PAM/RPM-1 [Signal transduction mechanisms]
Probab=95.08 E-value=0.025 Score=62.72 Aligned_cols=75 Identities=25% Similarity=0.651 Sum_probs=56.5
Q ss_pred cCccceeecCccCccccccccCcceeecCCCCCCCchhhhhhcccCCcceEeccCCccChHHHHHHHHcC--------CC
Q 024406 119 GGRENYFHCKRCGSCYSTSLRNNHLCIENSMHHHCPICYEYLFDSLRNTTVMKCGHTMHCECYHEMIKRD--------NR 190 (268)
Q Consensus 119 G~~~~ffHC~~C~~C~s~~l~~~H~C~e~~~~~~CpICle~lf~s~~~v~~LpCGH~~H~~C~~~~~~~~--------~~ 190 (268)
||.+|-.||--|-.|-.-.. ....+..|.||..+-. +--|.+.|.|||+||.+|....|++. .-
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-------KQDADDMCMICFTEAL-SAAPAIQLDCSHIFHLQCCRRVLENRWLGPRITFGF 3533 (3738)
T ss_pred cCccchhhcccccccChhhh-------hcccCceEEEEehhhh-CCCcceecCCccchhHHHHHHHHHhcccCCeeEEee
Confidence 56778888888877643221 2345678999998744 55789999999999999999888742 13
Q ss_pred cCCCCCCcchh
Q 024406 191 YCCPICSKSVI 201 (268)
Q Consensus 191 ~~CPiCrksi~ 201 (268)
..||||...|.
T Consensus 3534 isCPiC~n~In 3544 (3738)
T KOG1428|consen 3534 ISCPICKNKIN 3544 (3738)
T ss_pred eecccccchhh
Confidence 57999998875
No 61
>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional
Probab=95.06 E-value=0.02 Score=41.93 Aligned_cols=46 Identities=26% Similarity=0.769 Sum_probs=33.8
Q ss_pred cceeecCCCCccccc-----cccCCcCCCc-cceeeccccccccCCCCcCeeecCCCCc
Q 024406 63 VKQVICSVCDTEQPV-----AQVCTNCGVN-MGEYFCDICKFYDDDIEKGQFHCDDCGI 115 (268)
Q Consensus 63 ~~~v~C~~C~~~q~v-----~~~C~~Cg~~-f~~y~C~~C~l~d~~~~k~~yHC~~Cgi 115 (268)
+....|..|+.+... .-.||+||.. ..| |.+|+-+. ..|.|++||+
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 345678888876543 3479999986 544 99998775 4799999985
No 62
>KOG3970 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=95.03 E-value=0.029 Score=51.44 Aligned_cols=52 Identities=29% Similarity=0.655 Sum_probs=43.7
Q ss_pred CCCCCCchhhhhhcccCCcceEeccCCccChHHHHHHHHcC------CCcCCCCCCcchh
Q 024406 148 SMHHHCPICYEYLFDSLRNTTVMKCGHTMHCECYHEMIKRD------NRYCCPICSKSVI 201 (268)
Q Consensus 148 ~~~~~CpICle~lf~s~~~v~~LpCGH~~H~~C~~~~~~~~------~~~~CPiCrksi~ 201 (268)
.-..+|..|.-.|-+. +.+.|-|=|.||-+|+++|...- ..|+||-|+..|.
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 4577999999987654 67889999999999999998631 3599999999986
No 63
>COG5432 RAD18 RING-finger-containing E3 ubiquitin ligase [Signal transduction mechanisms]
Probab=94.81 E-value=0.016 Score=54.89 Aligned_cols=46 Identities=24% Similarity=0.550 Sum_probs=37.5
Q ss_pred CCCCchhhhhhcccCCcceEeccCCccChHHHHHHHHcCCCcCCCCCCcchh
Q 024406 150 HHHCPICYEYLFDSLRNTTVMKCGHTMHCECYHEMIKRDNRYCCPICSKSVI 201 (268)
Q Consensus 150 ~~~CpICle~lf~s~~~v~~LpCGH~~H~~C~~~~~~~~~~~~CPiCrksi~ 201 (268)
...|-||-+++. .....+|||+|..-||..+|... .-||+|+....
T Consensus 25 ~lrC~IC~~~i~----ip~~TtCgHtFCslCIR~hL~~q--p~CP~Cr~~~~ 70 (391)
T COG5432 25 MLRCRICDCRIS----IPCETTCGHTFCSLCIRRHLGTQ--PFCPVCREDPC 70 (391)
T ss_pred HHHhhhhhheee----cceecccccchhHHHHHHHhcCC--CCCccccccHH
Confidence 457999999742 23456999999999999999876 89999997664
No 64
>PF14447 Prok-RING_4: Prokaryotic RING finger family 4
Probab=93.94 E-value=0.019 Score=41.48 Aligned_cols=32 Identities=28% Similarity=0.669 Sum_probs=26.1
Q ss_pred cceEeccCCccChHHHHHHHHcCCCcCCCCCCcchh
Q 024406 166 NTTVMKCGHTMHCECYHEMIKRDNRYCCPICSKSVI 201 (268)
Q Consensus 166 ~v~~LpCGH~~H~~C~~~~~~~~~~~~CPiCrksi~ 201 (268)
.-.+|||||++-..|++-+.. .-||+|.+.+.
T Consensus 19 ~~~~~pCgH~I~~~~f~~~rY----ngCPfC~~~~~ 50 (55)
T PF14447_consen 19 KGTVLPCGHLICDNCFPGERY----NGCPFCGTPFE 50 (55)
T ss_pred ccccccccceeeccccChhhc----cCCCCCCCccc
Confidence 456799999999999977652 46999999875
No 65
>KOG3268 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=93.87 E-value=0.034 Score=49.32 Aligned_cols=35 Identities=29% Similarity=0.683 Sum_probs=27.8
Q ss_pred eccCCccChHHHHHHHHcC----C-----CcCCCCCCcchh-hhh
Q 024406 170 MKCGHTMHCECYHEMIKRD----N-----RYCCPICSKSVI-DMS 204 (268)
Q Consensus 170 LpCGH~~H~~C~~~~~~~~----~-----~~~CPiCrksi~-~m~ 204 (268)
..||-.||.-|+.+||+.- + --.||.|+++|. .|+
T Consensus 188 ~qCgkpFHqiCL~dWLRgilTsRQSFdiiFGeCPYCS~PialKmS 232 (234)
T KOG3268|consen 188 IQCGKPFHQICLTDWLRGILTSRQSFDIIFGECPYCSDPIALKMS 232 (234)
T ss_pred cccCCcHHHHHHHHHHHHHhhccceeeeeeccCCCCCCcceeecc
Confidence 5799999999999999731 1 136999999985 564
No 66
>KOG4445 consensus Uncharacterized conserved protein, contains RWD domain [Function unknown]
Probab=93.60 E-value=0.02 Score=54.35 Aligned_cols=55 Identities=29% Similarity=0.588 Sum_probs=42.6
Q ss_pred CCCCCCCchhhhhhcccCCcceEeccCCccChHHHHHHHHc---------------------CCCcCCCCCCcchhh
Q 024406 147 NSMHHHCPICYEYLFDSLRNTTVMKCGHTMHCECYHEMIKR---------------------DNRYCCPICSKSVID 202 (268)
Q Consensus 147 ~~~~~~CpICle~lf~s~~~v~~LpCGH~~H~~C~~~~~~~---------------------~~~~~CPiCrksi~~ 202 (268)
+-...+|.|||-- |.+.....+.+|-|+||..||..+|.. ...--|||||-.|.+
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 4557899999987 556567889999999999999988753 011349999988864
No 67
>PF05883 Baculo_RING: Baculovirus U-box/Ring-like domain; InterPro: IPR008573 This family consists of several Baculovirus proteins of around 130 residues in length. The function of this family is unknown, but it appears to be related to the U-box and ring finger domain by profile-profile comparison.
Probab=93.51 E-value=0.033 Score=47.00 Aligned_cols=37 Identities=14% Similarity=0.410 Sum_probs=32.4
Q ss_pred CCCCchhhhhhcccCCcceEeccC------CccChHHHHHHHHc
Q 024406 150 HHHCPICYEYLFDSLRNTTVMKCG------HTMHCECYHEMIKR 187 (268)
Q Consensus 150 ~~~CpICle~lf~s~~~v~~LpCG------H~~H~~C~~~~~~~ 187 (268)
..+|.||++.+-+ .+.|+.+++| |+||..|+..|.+.
T Consensus 26 ~~EC~IC~~~I~~-~~GvV~vt~~g~lnLEkmfc~~C~~rw~~~ 68 (134)
T PF05883_consen 26 TVECQICFDRIDN-NDGVVYVTDGGTLNLEKMFCADCDKRWRRE 68 (134)
T ss_pred Ceeehhhhhhhhc-CCCEEEEecCCeehHHHHHHHHHHHHHHhh
Confidence 5689999999887 6789999997 99999999999543
No 68
>KOG2034 consensus Vacuolar sorting protein PEP3/VPS18 [Intracellular trafficking, secretion, and vesicular transport]
Probab=93.40 E-value=0.054 Score=57.47 Aligned_cols=45 Identities=20% Similarity=0.335 Sum_probs=35.0
Q ss_pred ceeecCCCCCCCchhhhhhcccCCcceEeccCCccChHHHHHHHHcC
Q 024406 142 HLCIENSMHHHCPICYEYLFDSLRNTTVMKCGHTMHCECYHEMIKRD 188 (268)
Q Consensus 142 H~C~e~~~~~~CpICle~lf~s~~~v~~LpCGH~~H~~C~~~~~~~~ 188 (268)
+.+.--.....|-+|.-.|+. ++-.+.||||.||+.|+.+-....
T Consensus 809 ~ry~v~ep~d~C~~C~~~ll~--~pF~vf~CgH~FH~~Cl~~~v~~~ 853 (911)
T KOG2034|consen 809 QRYRVLEPQDSCDHCGRPLLI--KPFYVFPCGHCFHRDCLIRHVLSL 853 (911)
T ss_pred cceEEecCccchHHhcchhhc--CcceeeeccchHHHHHHHHHHHcc
Confidence 444433456789999998775 588899999999999998876543
No 69
>KOG1571 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=92.79 E-value=0.052 Score=52.40 Aligned_cols=47 Identities=21% Similarity=0.529 Sum_probs=34.9
Q ss_pred cCCCCCCCchhhhhhcccCCcceEeccCCccChHHHHHHHHcCCCcCCCCCCcchh
Q 024406 146 ENSMHHHCPICYEYLFDSLRNTTVMKCGHTMHCECYHEMIKRDNRYCCPICSKSVI 201 (268)
Q Consensus 146 e~~~~~~CpICle~lf~s~~~v~~LpCGH~~H~~C~~~~~~~~~~~~CPiCrksi~ 201 (268)
|.+...+|.||+++ + .....+||||+-- |..... . ..+||+||.+|.
T Consensus 301 ~~~~p~lcVVcl~e-~---~~~~fvpcGh~cc--ct~cs~--~-l~~CPvCR~rI~ 347 (355)
T KOG1571|consen 301 ELPQPDLCVVCLDE-P---KSAVFVPCGHVCC--CTLCSK--H-LPQCPVCRQRIR 347 (355)
T ss_pred ccCCCCceEEecCC-c---cceeeecCCcEEE--chHHHh--h-CCCCchhHHHHH
Confidence 45667899999996 3 3478999999944 444433 2 367999998885
No 70
>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=92.59 E-value=0.085 Score=49.73 Aligned_cols=48 Identities=23% Similarity=0.561 Sum_probs=39.6
Q ss_pred CCchhhhhhcccCCcceEe--ccCCccChHHHHHHHHcCCCcCCCCCCcchh
Q 024406 152 HCPICYEYLFDSLRNTTVM--KCGHTMHCECYHEMIKRDNRYCCPICSKSVI 201 (268)
Q Consensus 152 ~CpICle~lf~s~~~v~~L--pCGH~~H~~C~~~~~~~~~~~~CPiCrksi~ 201 (268)
.||+|.-+.+.+. .++.| +|||.+..+|++..+..+ .+.||.|.+.+.
T Consensus 2 ~Cp~CKt~~Y~np-~lk~~in~C~H~lCEsCvd~iF~~g-~~~CpeC~~iLR 51 (300)
T KOG3800|consen 2 ACPKCKTDRYLNP-DLKLMINECGHRLCESCVDRIFSLG-PAQCPECMVILR 51 (300)
T ss_pred CCcccccceecCc-cceeeeccccchHHHHHHHHHHhcC-CCCCCcccchhh
Confidence 5999998877663 33333 899999999999999887 699999999885
No 71
>PHA02862 5L protein; Provisional
Probab=92.37 E-value=0.08 Score=45.42 Aligned_cols=60 Identities=18% Similarity=0.468 Sum_probs=40.6
Q ss_pred CCCCCchhhhhhcccCCcceEecc-C--CccChHHHHHHHHcCCCcCCCCCCcchhhhhHHHHHHHH
Q 024406 149 MHHHCPICYEYLFDSLRNTTVMKC-G--HTMHCECYHEMIKRDNRYCCPICSKSVIDMSRTWKRIDE 212 (268)
Q Consensus 149 ~~~~CpICle~lf~s~~~v~~LpC-G--H~~H~~C~~~~~~~~~~~~CPiCrksi~~m~~~~~~lD~ 212 (268)
|...|=||++. ..+.+..-.| | -..|++|+.+|+..++.-.||+|+.... +...|+.+.+
T Consensus 1 ~~diCWIC~~~---~~e~~~PC~C~GS~K~VHq~CL~~WIn~S~k~~CeLCkteY~-Ik~~yKpf~k 63 (156)
T PHA02862 1 MSDICWICNDV---CDERNNFCGCNEEYKVVHIKCMQLWINYSKKKECNLCKTKYN-IKKTYVSFKK 63 (156)
T ss_pred CCCEEEEecCc---CCCCcccccccCcchhHHHHHHHHHHhcCCCcCccCCCCeEE-EEEccccHHH
Confidence 35678999986 2223332334 2 7899999999998776788999998875 3334443333
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=91.78 E-value=0.11 Score=42.44 Aligned_cols=38 Identities=18% Similarity=0.362 Sum_probs=29.5
Q ss_pred cCeeEEEccCCCCccccceeEeeecCCCCCCccccccCCC
Q 024406 225 HKKVWILCNDCNDTTEVYFHIIGQKCSHCKSYNTRSIAPP 264 (268)
Q Consensus 225 ~~~v~I~CnDC~~~s~~~~H~lg~kC~~C~SyNT~~~~~~ 264 (268)
...+...|++|+.......+ ...||.|||++++.++|.
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 34567899999987766532 357999999999998764
No 73
>KOG0824 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=91.78 E-value=0.085 Score=50.05 Aligned_cols=49 Identities=22% Similarity=0.477 Sum_probs=39.9
Q ss_pred CCCCCCchhhhhhcccCCcceEeccCCccChHHHHHHHHcCCCcCCCCCCcchh
Q 024406 148 SMHHHCPICYEYLFDSLRNTTVMKCGHTMHCECYHEMIKRDNRYCCPICSKSVI 201 (268)
Q Consensus 148 ~~~~~CpICle~lf~s~~~v~~LpCGH~~H~~C~~~~~~~~~~~~CPiCrksi~ 201 (268)
.+..+|+||+..+. -| +.|+|+|.|.--|++--.... ..+||+||..|-
T Consensus 5 ~~~~eC~IC~nt~n---~P-v~l~C~HkFCyiCiKGsy~nd-k~~CavCR~pid 53 (324)
T KOG0824|consen 5 TKKKECLICYNTGN---CP-VNLYCFHKFCYICIKGSYKND-KKTCAVCRFPID 53 (324)
T ss_pred ccCCcceeeeccCC---cC-ccccccchhhhhhhcchhhcC-CCCCceecCCCC
Confidence 45679999998753 34 689999999999998876665 467999999885
No 74
>KOG4739 consensus Uncharacterized protein involved in synaptonemal complex formation [Cell cycle control, cell division, chromosome partitioning; General function prediction only]
Probab=91.45 E-value=0.11 Score=47.73 Aligned_cols=37 Identities=27% Similarity=0.543 Sum_probs=28.1
Q ss_pred cccCCcceEeccCCccChHHHHHHHHcCCCcCCCCCCcchh
Q 024406 161 FDSLRNTTVMKCGHTMHCECYHEMIKRDNRYCCPICSKSVI 201 (268)
Q Consensus 161 f~s~~~v~~LpCGH~~H~~C~~~~~~~~~~~~CPiCrksi~ 201 (268)
|.+..+..+..|+|.|...|...-. ...||+|+|+|-
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 4454566678999999999985422 258999999974
No 75
>PF12773 DZR: Double zinc ribbon
Probab=91.36 E-value=0.2 Score=34.31 Aligned_cols=22 Identities=36% Similarity=0.970 Sum_probs=13.4
Q ss_pred cCCCCccccc-cccCCcCCCccc
Q 024406 68 CSVCDTEQPV-AQVCTNCGVNMG 89 (268)
Q Consensus 68 C~~C~~~q~v-~~~C~~Cg~~f~ 89 (268)
|..|+++.+. +..|++||..+.
T Consensus 1 Cp~Cg~~~~~~~~fC~~CG~~l~ 23 (50)
T PF12773_consen 1 CPHCGTPNPDDAKFCPHCGTPLP 23 (50)
T ss_pred CCCcCCcCCccccCChhhcCChh
Confidence 4556666544 456777777665
No 76
>PHA02825 LAP/PHD finger-like protein; Provisional
Probab=91.21 E-value=0.16 Score=44.21 Aligned_cols=49 Identities=27% Similarity=0.478 Sum_probs=36.2
Q ss_pred CCCCCCchhhhhhcccCCcceEecc--CC---ccChHHHHHHHHcCCCcCCCCCCcchh
Q 024406 148 SMHHHCPICYEYLFDSLRNTTVMKC--GH---TMHCECYHEMIKRDNRYCCPICSKSVI 201 (268)
Q Consensus 148 ~~~~~CpICle~lf~s~~~v~~LpC--GH---~~H~~C~~~~~~~~~~~~CPiCrksi~ 201 (268)
.++..|=||.++- ... .-|| -. ..|.+|++.|+..++..+||+|+....
T Consensus 6 ~~~~~CRIC~~~~---~~~--~~PC~CkGs~k~VH~sCL~rWi~~s~~~~CeiC~~~Y~ 59 (162)
T PHA02825 6 LMDKCCWICKDEY---DVV--TNYCNCKNENKIVHKECLEEWINTSKNKSCKICNGPYN 59 (162)
T ss_pred CCCCeeEecCCCC---CCc--cCCcccCCCchHHHHHHHHHHHhcCCCCcccccCCeEE
Confidence 3467899998872 122 2465 34 679999999998776788999998774
No 77
>PRK03824 hypA hydrogenase nickel incorporation protein; Provisional
Probab=91.19 E-value=0.25 Score=41.41 Aligned_cols=38 Identities=18% Similarity=0.435 Sum_probs=28.3
Q ss_pred eeEEEccCCCCccccc-------------eeE------eeecCCCCCCccccccCCC
Q 024406 227 KVWILCNDCNDTTEVY-------------FHI------IGQKCSHCKSYNTRSIAPP 264 (268)
Q Consensus 227 ~v~I~CnDC~~~s~~~-------------~H~------lg~kC~~C~SyNT~~~~~~ 264 (268)
.+...|++||....+. +|+ ...+|+.|||++.+.++|.
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 3368999999999988764
No 78
>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]
Probab=91.12 E-value=0.15 Score=37.47 Aligned_cols=45 Identities=29% Similarity=0.795 Sum_probs=33.9
Q ss_pred eeecCCCCccccc-----cccCCcCCCccceeeccccccccCCCCcCeeecCCCCc
Q 024406 65 QVICSVCDTEQPV-----AQVCTNCGVNMGEYFCDICKFYDDDIEKGQFHCDDCGI 115 (268)
Q Consensus 65 ~v~C~~C~~~q~v-----~~~C~~Cg~~f~~y~C~~C~l~d~~~~k~~yHC~~Cgi 115 (268)
...|..|+.+..+ .-.|||||..+ =|-|.+|+.+.+ +|-|++||+
T Consensus 9 ~~~CtSCg~~i~p~e~~v~F~CPnCGe~~-I~Rc~~CRk~g~-----~Y~Cp~CGF 58 (61)
T COG2888 9 PPVCTSCGREIAPGETAVKFPCPNCGEVE-IYRCAKCRKLGN-----PYRCPKCGF 58 (61)
T ss_pred CceeccCCCEeccCCceeEeeCCCCCcee-eehhhhHHHcCC-----ceECCCcCc
Confidence 5689999988744 35899999443 356889987754 799999985
No 79
>PRK00564 hypA hydrogenase nickel incorporation protein; Provisional
Probab=90.64 E-value=0.16 Score=41.67 Aligned_cols=38 Identities=24% Similarity=0.434 Sum_probs=29.4
Q ss_pred cCeeEEEccCCCCccccc-eeEeeecCCCCCCccccccCCC
Q 024406 225 HKKVWILCNDCNDTTEVY-FHIIGQKCSHCKSYNTRSIAPP 264 (268)
Q Consensus 225 ~~~v~I~CnDC~~~s~~~-~H~lg~kC~~C~SyNT~~~~~~ 264 (268)
...+.+.|++|+..+... +++ .+||.|||++...++|.
T Consensus 67 ~vp~~~~C~~Cg~~~~~~~~~~--~~CP~Cgs~~~~i~~G~ 105 (117)
T PRK00564 67 DEKVELECKDCSHVFKPNALDY--GVCEKCHSKNVIITQGN 105 (117)
T ss_pred ecCCEEEhhhCCCccccCCccC--CcCcCCCCCceEEecCC
Confidence 345678999999887765 333 37999999999988763
No 80
>KOG0309 consensus Conserved WD40 repeat-containing protein [Function unknown]
Probab=90.18 E-value=0.16 Score=53.50 Aligned_cols=43 Identities=28% Similarity=0.591 Sum_probs=32.5
Q ss_pred CCCCCchhhhhhcccCCcceEeccCCccChHHHHHHHHcCCCcCCCC
Q 024406 149 MHHHCPICYEYLFDSLRNTTVMKCGHTMHCECYHEMIKRDNRYCCPI 195 (268)
Q Consensus 149 ~~~~CpICle~lf~s~~~v~~LpCGH~~H~~C~~~~~~~~~~~~CPi 195 (268)
....|.||---+..| ...-+.|||.+|..|+.+|++.+ ..||.
T Consensus 1027 ~~~~C~~C~l~V~gs--s~~Cg~C~Hv~H~sc~~eWf~~g--d~Cps 1069 (1081)
T KOG0309|consen 1027 FTFQCAICHLAVRGS--SNFCGTCGHVGHTSCMMEWFRTG--DVCPS 1069 (1081)
T ss_pred ceeeeeeEeeEeecc--chhhccccccccHHHHHHHHhcC--CcCCC
Confidence 334588887654433 45567899999999999999987 78884
No 81
>PF04641 Rtf2: Rtf2 RING-finger
Probab=89.88 E-value=0.21 Score=45.96 Aligned_cols=51 Identities=18% Similarity=0.421 Sum_probs=39.6
Q ss_pred CCCCCCCchhhhhhcccCCcceE-eccCCccChHHHHHHHHcCCCcCCCCCCcchh
Q 024406 147 NSMHHHCPICYEYLFDSLRNTTV-MKCGHTMHCECYHEMIKRDNRYCCPICSKSVI 201 (268)
Q Consensus 147 ~~~~~~CpICle~lf~s~~~v~~-LpCGH~~H~~C~~~~~~~~~~~~CPiCrksi~ 201 (268)
....-.|||-...|... ...+. .||||.|=...+.+.- .. ..||+|.+++.
T Consensus 110 ~~~~~~CPvt~~~~~~~-~~fv~l~~cG~V~s~~alke~k-~~--~~Cp~c~~~f~ 161 (260)
T PF04641_consen 110 SEGRFICPVTGKEFNGK-HKFVYLRPCGCVFSEKALKELK-KS--KKCPVCGKPFT 161 (260)
T ss_pred CCceeECCCCCcccCCc-eeEEEEcCCCCEeeHHHHHhhc-cc--ccccccCCccc
Confidence 35567899999987444 44444 4999999999999995 23 68999999965
No 82
>PRK12380 hydrogenase nickel incorporation protein HybF; Provisional
Probab=89.83 E-value=0.2 Score=40.74 Aligned_cols=37 Identities=27% Similarity=0.529 Sum_probs=28.4
Q ss_pred CeeEEEccCCCCccccceeEeeecCCCCCCccccccCCC
Q 024406 226 KKVWILCNDCNDTTEVYFHIIGQKCSHCKSYNTRSIAPP 264 (268)
Q Consensus 226 ~~v~I~CnDC~~~s~~~~H~lg~kC~~C~SyNT~~~~~~ 264 (268)
..+.+.|++|+........ ...||.|||++...++|.
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 3457899999987766522 235999999999998764
No 83
>KOG1814 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=89.78 E-value=0.18 Score=49.75 Aligned_cols=48 Identities=19% Similarity=0.398 Sum_probs=37.6
Q ss_pred CCCCCchhhhhhcccCCcceEeccCCccChHHHHHHHHcC------CCcCCCCCC
Q 024406 149 MHHHCPICYEYLFDSLRNTTVMKCGHTMHCECYHEMIKRD------NRYCCPICS 197 (268)
Q Consensus 149 ~~~~CpICle~lf~s~~~v~~LpCGH~~H~~C~~~~~~~~------~~~~CPiCr 197 (268)
+--+|-||++. +....-.+.|||+|.|.++|+..|.... +..+||-+.
T Consensus 183 slf~C~ICf~e-~~G~~c~~~lpC~Hv~Ck~C~kdY~~~~i~eg~v~~l~Cp~~~ 236 (445)
T KOG1814|consen 183 SLFDCCICFEE-QMGQHCFKFLPCSHVFCKSCLKDYFTIQIQEGQVSCLKCPDPK 236 (445)
T ss_pred hcccceeeehh-hcCcceeeecccchHHHHHHHHHHHHHhhhcceeeeecCCCCC
Confidence 34689999996 6565778889999999999999997531 357887654
No 84
>KOG0297 consensus TNF receptor-associated factor [Signal transduction mechanisms]
Probab=89.71 E-value=0.2 Score=48.87 Aligned_cols=52 Identities=27% Similarity=0.674 Sum_probs=41.9
Q ss_pred CCCCCCchhhhhhcccCCcceEeccCCccChHHHHHHHHcCCCcCCCCCCcchhhhh
Q 024406 148 SMHHHCPICYEYLFDSLRNTTVMKCGHTMHCECYHEMIKRDNRYCCPICSKSVIDMS 204 (268)
Q Consensus 148 ~~~~~CpICle~lf~s~~~v~~LpCGH~~H~~C~~~~~~~~~~~~CPiCrksi~~m~ 204 (268)
..+..||||..-|-+ ++....|||.|...|+.+|+..+ ..||.|+..+..-.
T Consensus 19 ~~~l~C~~C~~vl~~---p~~~~~cgh~fC~~C~~~~~~~~--~~cp~~~~~~~~~~ 70 (391)
T KOG0297|consen 19 DENLLCPICMSVLRD---PVQTTTCGHRFCAGCLLESLSNH--QKCPVCRQELTQAE 70 (391)
T ss_pred cccccCccccccccC---CCCCCCCCCcccccccchhhccC--cCCcccccccchhh
Confidence 345789999987543 55557999999999999999875 89999998887433
No 85
>KOG4185 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=89.65 E-value=0.21 Score=46.10 Aligned_cols=48 Identities=33% Similarity=0.820 Sum_probs=38.8
Q ss_pred CCCchhhhhhcccCCc---ceEeccCCccChHHHHHHHHcCCCcCCCCCCcch
Q 024406 151 HHCPICYEYLFDSLRN---TTVMKCGHTMHCECYHEMIKRDNRYCCPICSKSV 200 (268)
Q Consensus 151 ~~CpICle~lf~s~~~---v~~LpCGH~~H~~C~~~~~~~~~~~~CPiCrksi 200 (268)
..|-||-++ |++.+. .++|.|||++-..|+...+.++ ...||.||...
T Consensus 4 ~~c~~c~~~-~s~~~~~~~p~~l~c~h~~c~~c~~~l~~~~-~i~cpfcR~~~ 54 (296)
T KOG4185|consen 4 PECEICNED-YSSEDGDHIPRVLKCGHTICQNCASKLLGNS-RILCPFCRETT 54 (296)
T ss_pred CceeecCcc-ccccCcccCCcccccCceehHhHHHHHhcCc-eeeccCCCCcc
Confidence 468899998 444433 3578999999999999999877 57789999995
No 86
>KOG4275 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=89.61 E-value=0.076 Score=50.30 Aligned_cols=61 Identities=23% Similarity=0.587 Sum_probs=40.9
Q ss_pred ccCcceeecCCC---CCCCchhhhhhcccCCcceEeccCCccChHHHHHHHHcCCCcCCCCCCcchhhhhHHH
Q 024406 138 LRNNHLCIENSM---HHHCPICYEYLFDSLRNTTVMKCGHTMHCECYHEMIKRDNRYCCPICSKSVIDMSRTW 207 (268)
Q Consensus 138 l~~~H~C~e~~~---~~~CpICle~lf~s~~~v~~LpCGH~~H~~C~~~~~~~~~~~~CPiCrksi~~m~~~~ 207 (268)
+++.|.+--..+ +..|.||++ ...+-.+|+|||..= |++-=.+ ...|||||+-|...-.+|
T Consensus 285 ~k~~~g~~~~~s~~~~~LC~ICmD----aP~DCvfLeCGHmVt--Ct~CGkr---m~eCPICRqyi~rvvrif 348 (350)
T KOG4275|consen 285 YKGNDGEQHSRSLATRRLCAICMD----APRDCVFLECGHMVT--CTKCGKR---MNECPICRQYIVRVVRIF 348 (350)
T ss_pred HhcccccccccchhHHHHHHHHhc----CCcceEEeecCcEEe--ehhhccc---cccCchHHHHHHHHHhhh
Confidence 345555544444 789999998 346789999999863 4432221 137999999888655544
No 87
>PRK03681 hypA hydrogenase nickel incorporation protein; Validated
Probab=89.59 E-value=0.23 Score=40.54 Aligned_cols=38 Identities=16% Similarity=0.459 Sum_probs=28.7
Q ss_pred CeeEEEccCCCCccccceeEeeecCCCCCCccccccCCC
Q 024406 226 KKVWILCNDCNDTTEVYFHIIGQKCSHCKSYNTRSIAPP 264 (268)
Q Consensus 226 ~~v~I~CnDC~~~s~~~~H~lg~kC~~C~SyNT~~~~~~ 264 (268)
..+...|++|+.......+.+ ..||.|||++++.++|.
T Consensus 67 ~p~~~~C~~Cg~~~~~~~~~~-~~CP~Cgs~~~~i~~G~ 104 (114)
T PRK03681 67 QEAECWCETCQQYVTLLTQRV-RRCPQCHGDMLRIVADD 104 (114)
T ss_pred eCcEEEcccCCCeeecCCccC-CcCcCcCCCCcEEccCC
Confidence 345789999998776643321 46999999999998874
No 88
>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=89.03 E-value=0.18 Score=38.17 Aligned_cols=36 Identities=25% Similarity=0.783 Sum_probs=22.8
Q ss_pred ceeecCCCCccccccccCCcCCCcc--------ceeeccccccc
Q 024406 64 KQVICSVCDTEQPVAQVCTNCGVNM--------GEYFCDICKFY 99 (268)
Q Consensus 64 ~~v~C~~C~~~q~v~~~C~~Cg~~f--------~~y~C~~C~l~ 99 (268)
....|..|+..-.....||.|+..+ +.|||.-|+=.
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 5778888888777777888888877 58999888743
No 89
>COG5175 MOT2 Transcriptional repressor [Transcription]
Probab=88.50 E-value=0.11 Score=50.13 Aligned_cols=57 Identities=23% Similarity=0.467 Sum_probs=45.1
Q ss_pred CCCCchhhhhhcccCCcceEeccCCccChHHHHHHHHcCCCcCCCCCCcchhhhhHHH
Q 024406 150 HHHCPICYEYLFDSLRNTTVMKCGHTMHCECYHEMIKRDNRYCCPICSKSVIDMSRTW 207 (268)
Q Consensus 150 ~~~CpICle~lf~s~~~v~~LpCGH~~H~~C~~~~~~~~~~~~CPiCrksi~~m~~~~ 207 (268)
+.-||.|+|+|--+......-|||=-+.+-|+....+.- +-+||-||+...+-...|
T Consensus 14 ed~cplcie~mditdknf~pc~cgy~ic~fc~~~irq~l-ngrcpacrr~y~denv~~ 70 (480)
T COG5175 14 EDYCPLCIEPMDITDKNFFPCPCGYQICQFCYNNIRQNL-NGRCPACRRKYDDENVRY 70 (480)
T ss_pred cccCcccccccccccCCcccCCcccHHHHHHHHHHHhhc-cCCChHhhhhccccceeE
Confidence 456999999997776666667899999999998877664 689999999887544344
No 90
>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=88.30 E-value=0.18 Score=35.53 Aligned_cols=32 Identities=34% Similarity=0.801 Sum_probs=24.0
Q ss_pred eEeccC-CccChHHHHHHHHcCCCcCCCCCCcchh
Q 024406 168 TVMKCG-HTMHCECYHEMIKRDNRYCCPICSKSVI 201 (268)
Q Consensus 168 ~~LpCG-H~~H~~C~~~~~~~~~~~~CPiCrksi~ 201 (268)
..+.|. |.+...|+..++..+ ..||||.+++-
T Consensus 14 ~Li~C~dHYLCl~CLt~ml~~s--~~C~iC~~~LP 46 (50)
T PF03854_consen 14 GLIKCSDHYLCLNCLTLMLSRS--DRCPICGKPLP 46 (50)
T ss_dssp SEEE-SS-EEEHHHHHHT-SSS--SEETTTTEE--
T ss_pred CeeeecchhHHHHHHHHHhccc--cCCCcccCcCc
Confidence 456896 999999999999887 89999998874
No 91
>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=88.02 E-value=0.17 Score=41.04 Aligned_cols=37 Identities=22% Similarity=0.306 Sum_probs=25.7
Q ss_pred CeeEEEccCCCCccccceeEeeecCCCCCCccccccCCC
Q 024406 226 KKVWILCNDCNDTTEVYFHIIGQKCSHCKSYNTRSIAPP 264 (268)
Q Consensus 226 ~~v~I~CnDC~~~s~~~~H~lg~kC~~C~SyNT~~~~~~ 264 (268)
..+...|++|+..+.+..+. ..||.|+|++.+.++|.
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 35578999999988776544 57999999999888764
No 92
>COG5152 Uncharacterized conserved protein, contains RING and CCCH-type Zn-fingers [General function prediction only]
Probab=86.71 E-value=0.37 Score=43.55 Aligned_cols=59 Identities=20% Similarity=0.494 Sum_probs=42.8
Q ss_pred CCCchhhhhhcccCCcceEeccCCccChHHHHHHHHcCCCcCCCCCCcchhhhhHHHHHHHHHHH
Q 024406 151 HHCPICYEYLFDSLRNTTVMKCGHTMHCECYHEMIKRDNRYCCPICSKSVIDMSRTWKRIDEEIE 215 (268)
Q Consensus 151 ~~CpICle~lf~s~~~v~~LpCGH~~H~~C~~~~~~~~~~~~CPiCrksi~~m~~~~~~lD~~i~ 215 (268)
-.|-||.++ |.| .++..|||.|...|+-.=.+.+ .+|-+|.|..-..-.+-..||..+.
T Consensus 197 F~C~iCKkd-y~s---pvvt~CGH~FC~~Cai~~y~kg--~~C~~Cgk~t~G~f~V~~d~~kmL~ 255 (259)
T COG5152 197 FLCGICKKD-YES---PVVTECGHSFCSLCAIRKYQKG--DECGVCGKATYGRFWVVSDLQKMLN 255 (259)
T ss_pred eeehhchhh-ccc---hhhhhcchhHHHHHHHHHhccC--CcceecchhhccceeHHhhHHHHHh
Confidence 379999998 443 4567899999999997766665 8999999988643222245555543
No 93
>COG5236 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=86.71 E-value=0.53 Score=45.77 Aligned_cols=66 Identities=17% Similarity=0.351 Sum_probs=48.1
Q ss_pred CccccccccCcceeecCCCCCCCchhhhhhcccCCcceEeccCCccChHHHHHHHHcCCCcCCCCCCcch
Q 024406 131 GSCYSTSLRNNHLCIENSMHHHCPICYEYLFDSLRNTTVMKCGHTMHCECYHEMIKRDNRYCCPICSKSV 200 (268)
Q Consensus 131 ~~C~s~~l~~~H~C~e~~~~~~CpICle~lf~s~~~v~~LpCGH~~H~~C~~~~~~~~~~~~CPiCrksi 200 (268)
+.|....+.++..=.....+++|-||.+.+ +-+.++||||-|.--|.-....-...-.||+|+..-
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 556666666555555556678999999964 457789999999999987765432246899999653
No 94
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=86.52 E-value=0.35 Score=29.37 Aligned_cols=24 Identities=33% Similarity=0.924 Sum_probs=17.9
Q ss_pred eeecCCCCccccc-cccCCcCCCcc
Q 024406 65 QVICSVCDTEQPV-AQVCTNCGVNM 88 (268)
Q Consensus 65 ~v~C~~C~~~q~v-~~~C~~Cg~~f 88 (268)
++.|..|+++.+. +..|++||+.+
T Consensus 2 ~~~Cp~Cg~~~~~~~~fC~~CG~~L 26 (26)
T PF13248_consen 2 EMFCPNCGAEIDPDAKFCPNCGAKL 26 (26)
T ss_pred cCCCcccCCcCCcccccChhhCCCC
Confidence 4678889887544 56899999864
No 95
>PF08746 zf-RING-like: RING-like domain; InterPro: IPR014857 This is a zinc finger domain that is related to the C3HC4 RING finger domain (IPR001841 from INTERPRO). ; PDB: 3NW0_A 2CT0_A.
Probab=86.21 E-value=0.32 Score=33.08 Aligned_cols=26 Identities=23% Similarity=0.818 Sum_probs=15.9
Q ss_pred ccCCccChHHHHHHHHcCCCcCCCCC
Q 024406 171 KCGHTMHCECYHEMIKRDNRYCCPIC 196 (268)
Q Consensus 171 pCGH~~H~~C~~~~~~~~~~~~CPiC 196 (268)
.|+=.||..|++.|+++.+..+||.|
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 37778999999999987633479987
No 96
>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=86.01 E-value=0.8 Score=39.85 Aligned_cols=34 Identities=32% Similarity=0.746 Sum_probs=24.6
Q ss_pred CCCCchhhhhhcccCCcceEeccC-C------------ccChHHHHHHHHc
Q 024406 150 HHHCPICYEYLFDSLRNTTVMKCG-H------------TMHCECYHEMIKR 187 (268)
Q Consensus 150 ~~~CpICle~lf~s~~~v~~LpCG-H------------~~H~~C~~~~~~~ 187 (268)
+..||||||.= -..++|-|. | .-|+.||+++.+.
T Consensus 2 d~~CpICme~P----HNAVLLlCSS~~kgcRpymc~Ts~rhSNCLdqfkka 48 (162)
T PF07800_consen 2 DVTCPICMEHP----HNAVLLLCSSHEKGCRPYMCDTSYRHSNCLDQFKKA 48 (162)
T ss_pred CccCceeccCC----CceEEEEeccccCCccccccCCccchhHHHHHHHHH
Confidence 45799999952 346677763 2 4599999999763
No 97
>KOG2817 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=85.92 E-value=0.73 Score=45.20 Aligned_cols=49 Identities=20% Similarity=0.535 Sum_probs=39.2
Q ss_pred CCCchhhhhhcccCCcceEeccCCccChHHHHHHHHcC-CCcCCCCCCcch
Q 024406 151 HHCPICYEYLFDSLRNTTVMKCGHTMHCECYHEMIKRD-NRYCCPICSKSV 200 (268)
Q Consensus 151 ~~CpICle~lf~s~~~v~~LpCGH~~H~~C~~~~~~~~-~~~~CPiCrksi 200 (268)
-.|||=.|. -+...|...|.|||.|-++=++.+.+++ +.++||.|-...
T Consensus 335 F~CPVlKeq-tsdeNPPm~L~CGHVISkdAlnrLS~ng~~sfKCPYCP~e~ 384 (394)
T KOG2817|consen 335 FICPVLKEQ-TSDENPPMMLICGHVISKDALNRLSKNGSQSFKCPYCPVEQ 384 (394)
T ss_pred eecccchhh-ccCCCCCeeeeccceecHHHHHHHhhCCCeeeeCCCCCccc
Confidence 479998876 4444678899999999999999999876 138999997544
No 98
>KOG3039 consensus Uncharacterized conserved protein [Function unknown]
Probab=85.72 E-value=0.62 Score=43.41 Aligned_cols=56 Identities=25% Similarity=0.508 Sum_probs=46.2
Q ss_pred cCCCCCCCchhhhhhcccCCcceEe-ccCCccChHHHHHHHHcCCCcCCCCCCcchhhhh
Q 024406 146 ENSMHHHCPICYEYLFDSLRNTTVM-KCGHTMHCECYHEMIKRDNRYCCPICSKSVIDMS 204 (268)
Q Consensus 146 e~~~~~~CpICle~lf~s~~~v~~L-pCGH~~H~~C~~~~~~~~~~~~CPiCrksi~~m~ 204 (268)
..+..-.|||+.+.|... .+..+| |+||.+-.+|.+.+++.. --+||+.+.+.+..
T Consensus 217 a~s~ryiCpvtrd~LtNt-~~ca~Lr~sg~Vv~~ecvEklir~D--~v~pv~d~plkdrd 273 (303)
T KOG3039|consen 217 AASKRYICPVTRDTLTNT-TPCAVLRPSGHVVTKECVEKLIRKD--MVDPVTDKPLKDRD 273 (303)
T ss_pred hhccceecccchhhhcCc-cceEEeccCCcEeeHHHHHHhcccc--ccccCCCCcCcccc
Confidence 344567899999987654 566666 899999999999999876 78999999998654
No 99
>KOG1813 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=85.60 E-value=0.39 Score=45.51 Aligned_cols=68 Identities=24% Similarity=0.440 Sum_probs=48.4
Q ss_pred CCCCchhhhhhcccCCcceEeccCCccChHHHHHHHHcCCCcCCCCCCcchhhhhHHHHHHHHHHHhcCCChhh
Q 024406 150 HHHCPICYEYLFDSLRNTTVMKCGHTMHCECYHEMIKRDNRYCCPICSKSVIDMSRTWKRIDEEIEATVMPEDY 223 (268)
Q Consensus 150 ~~~CpICle~lf~s~~~v~~LpCGH~~H~~C~~~~~~~~~~~~CPiCrksi~~m~~~~~~lD~~i~~~pmP~~y 223 (268)
...|-||.++ |.+ .++-.|||+|...|...-++.+ .+|+||.+.+......=..|...++..++-.||
T Consensus 241 Pf~c~icr~~-f~~---pVvt~c~h~fc~~ca~~~~qk~--~~c~vC~~~t~g~~~~akeL~~~L~~kks~~E~ 308 (313)
T KOG1813|consen 241 PFKCFICRKY-FYR---PVVTKCGHYFCEVCALKPYQKG--EKCYVCSQQTHGSFNVAKELLVSLKLKKSDSEY 308 (313)
T ss_pred Cccccccccc-ccc---chhhcCCceeehhhhccccccC--CcceecccccccccchHHHHHHHHHhhhhhccc
Confidence 3459999998 432 4567999999999998877776 899999999864332223455556555554444
No 100
>KOG4159 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=84.77 E-value=1.1 Score=44.26 Aligned_cols=49 Identities=24% Similarity=0.761 Sum_probs=38.8
Q ss_pred CCCCCCchhhhhhcccCCcceEeccCCccChHHHHHHHHcCCCcCCCCCCcchhh
Q 024406 148 SMHHHCPICYEYLFDSLRNTTVMKCGHTMHCECYHEMIKRDNRYCCPICSKSVID 202 (268)
Q Consensus 148 ~~~~~CpICle~lf~s~~~v~~LpCGH~~H~~C~~~~~~~~~~~~CPiCrksi~~ 202 (268)
..+-.|-||+.-|+ +.+.+||||+|...|+..-+... ..||+||-.+..
T Consensus 82 ~sef~c~vc~~~l~----~pv~tpcghs~c~~Cl~r~ld~~--~~cp~Cr~~l~e 130 (398)
T KOG4159|consen 82 RSEFECCVCSRALY----PPVVTPCGHSFCLECLDRSLDQE--TECPLCRDELVE 130 (398)
T ss_pred cchhhhhhhHhhcC----CCccccccccccHHHHHHHhccC--CCCccccccccc
Confidence 56778999988544 34455999999999999866544 789999998874
No 101
>PRK00762 hypA hydrogenase nickel incorporation protein; Provisional
Probab=84.00 E-value=0.72 Score=38.14 Aligned_cols=38 Identities=21% Similarity=0.300 Sum_probs=27.0
Q ss_pred CeeEEEccCCCCccccc-e---eE-eeecCCCCCCccccccCCC
Q 024406 226 KKVWILCNDCNDTTEVY-F---HI-IGQKCSHCKSYNTRSIAPP 264 (268)
Q Consensus 226 ~~v~I~CnDC~~~s~~~-~---H~-lg~kC~~C~SyNT~~~~~~ 264 (268)
..+...| +|+..+... + |+ ....||.|||++...++|.
T Consensus 67 vp~~~~C-~Cg~~~~~~~~~~~~~~~~~~CP~Cgs~~~~i~~G~ 109 (124)
T PRK00762 67 IPVEIEC-ECGYEGVVDEDEIDHYAAVIECPVCGNKRAHILGGR 109 (124)
T ss_pred cCeeEEe-eCcCcccccccchhccccCCcCcCCCCCCCEEecCC
Confidence 3567899 999875432 1 11 2357999999999988763
No 102
>KOG2114 consensus Vacuolar assembly/sorting protein PEP5/VPS11 [Intracellular trafficking, secretion, and vesicular transport]
Probab=84.00 E-value=0.65 Score=49.46 Aligned_cols=41 Identities=27% Similarity=0.607 Sum_probs=31.7
Q ss_pred CCCchhhhhhcccCCcceEeccCCccChHHHHHHHHcCCCcCCCCCCcc
Q 024406 151 HHCPICYEYLFDSLRNTTVMKCGHTMHCECYHEMIKRDNRYCCPICSKS 199 (268)
Q Consensus 151 ~~CpICle~lf~s~~~v~~LpCGH~~H~~C~~~~~~~~~~~~CPiCrks 199 (268)
+.|..|--.|- -|++-..|||.||..|+. +. -..||-|+-.
T Consensus 841 skCs~C~~~Ld---lP~VhF~CgHsyHqhC~e---~~--~~~CP~C~~e 881 (933)
T KOG2114|consen 841 SKCSACEGTLD---LPFVHFLCGHSYHQHCLE---DK--EDKCPKCLPE 881 (933)
T ss_pred eeecccCCccc---cceeeeecccHHHHHhhc---cC--cccCCccchh
Confidence 35777766543 478888999999999998 33 3899999983
No 103
>KOG2660 consensus Locus-specific chromosome binding proteins [Function unknown]
Probab=83.97 E-value=0.3 Score=46.82 Aligned_cols=50 Identities=30% Similarity=0.691 Sum_probs=41.9
Q ss_pred CCCCCCchhhhhhcccCCcceEeccCCccChHHHHHHHHcCCCcCCCCCCcchhh
Q 024406 148 SMHHHCPICYEYLFDSLRNTTVMKCGHTMHCECYHEMIKRDNRYCCPICSKSVID 202 (268)
Q Consensus 148 ~~~~~CpICle~lf~s~~~v~~LpCGH~~H~~C~~~~~~~~~~~~CPiCrksi~~ 202 (268)
.....|++|..+|-+. ..+.-|=|+|.++||.+++..+ ..||.|...|..
T Consensus 13 n~~itC~LC~GYliDA---TTI~eCLHTFCkSCivk~l~~~--~~CP~C~i~ih~ 62 (331)
T KOG2660|consen 13 NPHITCRLCGGYLIDA---TTITECLHTFCKSCIVKYLEES--KYCPTCDIVIHK 62 (331)
T ss_pred ccceehhhccceeecc---hhHHHHHHHHHHHHHHHHHHHh--ccCCccceeccC
Confidence 3456899999998765 3466799999999999999886 899999988863
No 104
>COG0375 HybF Zn finger protein HypA/HybF (possibly regulating hydrogenase expression) [General function prediction only]
Probab=83.39 E-value=0.9 Score=37.52 Aligned_cols=39 Identities=26% Similarity=0.383 Sum_probs=30.6
Q ss_pred hcCeeEEEccCCCCccccceeEeeecCCCCCCccccccCCC
Q 024406 224 RHKKVWILCNDCNDTTEVYFHIIGQKCSHCKSYNTRSIAPP 264 (268)
Q Consensus 224 ~~~~v~I~CnDC~~~s~~~~H~lg~kC~~C~SyNT~~~~~~ 264 (268)
....+.+.|.||+......-|.+. ||.|+|-|.++++|.
T Consensus 65 e~~p~~~~C~~C~~~~~~e~~~~~--CP~C~s~~~~i~~G~ 103 (115)
T COG0375 65 EEEPAECWCLDCGQEVELEELDYR--CPKCGSINLRIIGGD 103 (115)
T ss_pred EEeccEEEeccCCCeecchhheeE--CCCCCCCceEEecCC
Confidence 344677999999887766655553 999999999999874
No 105
>PRK04023 DNA polymerase II large subunit; Validated
Probab=83.21 E-value=1 Score=48.97 Aligned_cols=32 Identities=28% Similarity=0.716 Sum_probs=14.4
Q ss_pred cCCcCCCccceeeccccccccCCCCcCeeecCCCCc
Q 024406 80 VCTNCGVNMGEYFCDICKFYDDDIEKGQFHCDDCGI 115 (268)
Q Consensus 80 ~C~~Cg~~f~~y~C~~C~l~d~~~~k~~yHC~~Cgi 115 (268)
.|++||......+|+.|.-. .+.+|.|+.||.
T Consensus 628 fCpsCG~~t~~frCP~CG~~----Te~i~fCP~CG~ 659 (1121)
T PRK04023 628 KCPSCGKETFYRRCPFCGTH----TEPVYRCPRCGI 659 (1121)
T ss_pred cCCCCCCcCCcccCCCCCCC----CCcceeCccccC
Confidence 34444444444444444322 244555555543
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=83.05 E-value=0.14 Score=38.72 Aligned_cols=65 Identities=26% Similarity=0.500 Sum_probs=37.8
Q ss_pred CCCchhhhhhcccCCcceEeccCCccChHHHHHHHHcCCCcCCCCCCcchhhhhHHHHHHHHHHHhcCCChhhhcCeeEE
Q 024406 151 HHCPICYEYLFDSLRNTTVMKCGHTMHCECYHEMIKRDNRYCCPICSKSVIDMSRTWKRIDEEIEATVMPEDYRHKKVWI 230 (268)
Q Consensus 151 ~~CpICle~lf~s~~~v~~LpCGH~~H~~C~~~~~~~~~~~~CPiCrksi~~m~~~~~~lD~~i~~~pmP~~y~~~~v~I 230 (268)
..||+|..+|-... ||+....|-..+... ..||-|.+.+.-+.+ =--|+.
T Consensus 2 ~~CP~C~~~L~~~~--------~~~~C~~C~~~~~~~---a~CPdC~~~Le~LkA-------------------CGAvdY 51 (70)
T PF07191_consen 2 NTCPKCQQELEWQG--------GHYHCEACQKDYKKE---AFCPDCGQPLEVLKA-------------------CGAVDY 51 (70)
T ss_dssp -B-SSS-SBEEEET--------TEEEETTT--EEEEE---EE-TTT-SB-EEEEE-------------------TTEEEE
T ss_pred CcCCCCCCccEEeC--------CEEECccccccceec---ccCCCcccHHHHHHH-------------------hcccce
Confidence 47999999875432 777777888776644 589999988864422 124789
Q ss_pred EccCCCC---ccccceeE
Q 024406 231 LCNDCND---TTEVYFHI 245 (268)
Q Consensus 231 ~CnDC~~---~s~~~~H~ 245 (268)
+||.|+. |+-|.|.+
T Consensus 52 FC~~c~gLiSKkrV~f~~ 69 (70)
T PF07191_consen 52 FCNHCHGLISKKRVRFEF 69 (70)
T ss_dssp E-TTTT-EE-TTTSEEEE
T ss_pred eeccCCceeecceEEEEe
Confidence 9999994 55666653
No 107
>KOG1002 consensus Nucleotide excision repair protein RAD16 [Replication, recombination and repair]
Probab=83.05 E-value=0.43 Score=48.67 Aligned_cols=54 Identities=22% Similarity=0.495 Sum_probs=43.6
Q ss_pred eecCCCCCCCchhhhhhcccCCcceEeccCCccChHHHHHHHHc---CCCcCCCCCCcchh
Q 024406 144 CIENSMHHHCPICYEYLFDSLRNTTVMKCGHTMHCECYHEMIKR---DNRYCCPICSKSVI 201 (268)
Q Consensus 144 C~e~~~~~~CpICle~lf~s~~~v~~LpCGH~~H~~C~~~~~~~---~~~~~CPiCrksi~ 201 (268)
=.|+..+..|-+|-|+- ++.++-.|-|.|.+.|+.+|+.. +.+.+||+|.+.+.
T Consensus 530 ~~enk~~~~C~lc~d~a----ed~i~s~ChH~FCrlCi~eyv~~f~~~~nvtCP~C~i~Ls 586 (791)
T KOG1002|consen 530 PDENKGEVECGLCHDPA----EDYIESSCHHKFCRLCIKEYVESFMENNNVTCPVCHIGLS 586 (791)
T ss_pred CccccCceeecccCChh----hhhHhhhhhHHHHHHHHHHHHHhhhcccCCCCcccccccc
Confidence 35778889999999862 35677899999999999999753 23689999998874
No 108
>PF13240 zinc_ribbon_2: zinc-ribbon domain
Probab=82.18 E-value=0.76 Score=27.33 Aligned_cols=21 Identities=38% Similarity=0.945 Sum_probs=15.1
Q ss_pred cCCCCccccc-cccCCcCCCcc
Q 024406 68 CSVCDTEQPV-AQVCTNCGVNM 88 (268)
Q Consensus 68 C~~C~~~q~v-~~~C~~Cg~~f 88 (268)
|..|+.+.+. +..|++||+.+
T Consensus 2 Cp~CG~~~~~~~~fC~~CG~~l 23 (23)
T PF13240_consen 2 CPNCGAEIEDDAKFCPNCGTPL 23 (23)
T ss_pred CcccCCCCCCcCcchhhhCCcC
Confidence 6778877654 56788888764
No 109
>KOG1952 consensus Transcription factor NF-X1, contains NFX-type Zn2+-binding and R3H domains [Transcription]
Probab=81.72 E-value=0.69 Score=49.29 Aligned_cols=54 Identities=20% Similarity=0.490 Sum_probs=39.5
Q ss_pred CCCCCCchhhhhhcccCCcceE-eccCCccChHHHHHHHHcC-----CCcCCCCCCcchhh
Q 024406 148 SMHHHCPICYEYLFDSLRNTTV-MKCGHTMHCECYHEMIKRD-----NRYCCPICSKSVID 202 (268)
Q Consensus 148 ~~~~~CpICle~lf~s~~~v~~-LpCGH~~H~~C~~~~~~~~-----~~~~CPiCrksi~~ 202 (268)
...-.|.||+|.|-.+ .++.. -.|=|+||..||.+|.++. ...+||-|......
T Consensus 189 ~~~yeCmIC~e~I~~t-~~~WSC~sCYhVFHl~CI~~WArs~ek~~~~~WrCP~Cqsv~~~ 248 (950)
T KOG1952|consen 189 NRKYECMICTERIKRT-APVWSCKSCYHVFHLNCIKKWARSSEKTGQDGWRCPACQSVSKT 248 (950)
T ss_pred cCceEEEEeeeecccc-CCceecchhhhhhhHHHHHHHHHHhhhccCccccCCcccchhcc
Confidence 3456899999987655 44443 3678999999999998642 25789999844443
No 110
>PF09538 FYDLN_acid: Protein of unknown function (FYDLN_acid); InterPro: IPR012644 Members of this family are bacterial proteins with a conserved motif [KR]FYDLN, sometimes flanked by a pair of CXXC motifs, followed by a long region of low complexity sequence in which roughly half the residues are Asp and Glu, including multiple runs of five or more acidic residues. The function of members of this family is unknown.
Probab=81.46 E-value=1 Score=36.61 Aligned_cols=28 Identities=32% Similarity=0.948 Sum_probs=21.0
Q ss_pred cccccCCcCCCccceeeccccccccCCCCcCeeecCCCCc
Q 024406 76 PVAQVCTNCGVNMGEYFCDICKFYDDDIEKGQFHCDDCGI 115 (268)
Q Consensus 76 ~v~~~C~~Cg~~f~~y~C~~C~l~d~~~~k~~yHC~~Cgi 115 (268)
....+|++||+.| || .+|.+-.|+.||.
T Consensus 7 GtKR~Cp~CG~kF----------YD--Lnk~PivCP~CG~ 34 (108)
T PF09538_consen 7 GTKRTCPSCGAKF----------YD--LNKDPIVCPKCGT 34 (108)
T ss_pred CCcccCCCCcchh----------cc--CCCCCccCCCCCC
Confidence 3456899999854 66 5688888988884
No 111
>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=81.39 E-value=1 Score=27.61 Aligned_cols=23 Identities=35% Similarity=0.959 Sum_probs=18.2
Q ss_pred ecCCCCccccc-cccCCcCCCccc
Q 024406 67 ICSVCDTEQPV-AQVCTNCGVNMG 89 (268)
Q Consensus 67 ~C~~C~~~q~v-~~~C~~Cg~~f~ 89 (268)
.|..|+.+-+. +..|+.||..|.
T Consensus 2 ~CP~C~~~V~~~~~~Cp~CG~~F~ 25 (26)
T PF10571_consen 2 TCPECGAEVPESAKFCPHCGYDFE 25 (26)
T ss_pred cCCCCcCCchhhcCcCCCCCCCCc
Confidence 37778887766 568999999986
No 112
>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=80.88 E-value=1.2 Score=31.19 Aligned_cols=43 Identities=23% Similarity=0.748 Sum_probs=20.9
Q ss_pred CCCchhhhhhcccCCcceEeccCCccChHHHHH--HHHc---CCCcCCCCCCcc
Q 024406 151 HHCPICYEYLFDSLRNTTVMKCGHTMHCECYHE--MIKR---DNRYCCPICSKS 199 (268)
Q Consensus 151 ~~CpICle~lf~s~~~v~~LpCGH~~H~~C~~~--~~~~---~~~~~CPiCrks 199 (268)
..|||-...|. .|++-..|.|. +||+. ||.. ....+||+|+++
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 46888887764 48888899977 46543 5543 235789999874
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=80.54 E-value=1.6 Score=30.13 Aligned_cols=37 Identities=19% Similarity=0.329 Sum_probs=25.6
Q ss_pred EEEccCCCCccccceeE---eeecCCCCCCccc-cccCCCC
Q 024406 229 WILCNDCNDTTEVYFHI---IGQKCSHCKSYNT-RSIAPPV 265 (268)
Q Consensus 229 ~I~CnDC~~~s~~~~H~---lg~kC~~C~SyNT-~~~~~~~ 265 (268)
...|++|+...++-..+ -...|+.|||-+. |++++|.
T Consensus 5 ey~C~~Cg~~fe~~~~~~~~~~~~CP~Cg~~~~~r~~s~~~ 45 (52)
T TIGR02605 5 EYRCTACGHRFEVLQKMSDDPLATCPECGGEKLRRLLSAVG 45 (52)
T ss_pred EEEeCCCCCEeEEEEecCCCCCCCCCCCCCCceeEEecccc
Confidence 46899999877664321 1247999999886 6666553
No 114
>KOG0827 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=79.75 E-value=0.25 Score=48.51 Aligned_cols=50 Identities=20% Similarity=0.418 Sum_probs=43.9
Q ss_pred CCCCchhhhhhcccCCcceEeccCCccChHHHHHHHHcCCCcCCCCCCcchh
Q 024406 150 HHHCPICYEYLFDSLRNTTVMKCGHTMHCECYHEMIKRDNRYCCPICSKSVI 201 (268)
Q Consensus 150 ~~~CpICle~lf~s~~~v~~LpCGH~~H~~C~~~~~~~~~~~~CPiCrksi~ 201 (268)
-..+.||.+.|...-+....+.|||..|..++.+||... .++|.|+..+-
T Consensus 196 v~sl~I~~~slK~~y~k~~~~~~g~~~~~~kL~k~L~~~--~kl~~~~rel~ 245 (465)
T KOG0827|consen 196 VGSLSICFESLKQNYDKISAIVCGHIYHHGKLSKWLATK--RKLPSCRRELP 245 (465)
T ss_pred HhhhHhhHHHHHHHHHHHHHHhhcccchhhHHHHHHHHH--HHhHHHHhhhh
Confidence 457999999988766678889999999999999999885 89999998885
No 115
>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=77.94 E-value=1.9 Score=43.44 Aligned_cols=49 Identities=22% Similarity=0.702 Sum_probs=41.4
Q ss_pred eEcCCCCCcccCcchHHhhhcCCCCCCCCccccccccceeecCCCCccccccccCCcCCCc
Q 024406 27 IRAPCCNEIFDCRHCHNEAASMLRNPYDRHELVRQDVKQVICSVCDTEQPVAQVCTNCGVN 87 (268)
Q Consensus 27 l~~pcC~~~y~Cr~CHde~~~~~~~~~~~H~~~r~~~~~v~C~~C~~~q~v~~~C~~Cg~~ 87 (268)
+.|.-||....|..|.-.++- |. ....+.|-.|+..+++...||+||..
T Consensus 214 ~~C~~Cg~~~~C~~C~~~l~~--------h~----~~~~l~Ch~Cg~~~~~~~~Cp~C~s~ 262 (505)
T TIGR00595 214 LLCRSCGYILCCPNCDVSLTY--------HK----KEGKLRCHYCGYQEPIPKTCPQCGSE 262 (505)
T ss_pred eEhhhCcCccCCCCCCCceEE--------ec----CCCeEEcCCCcCcCCCCCCCCCCCCC
Confidence 789999999999999876653 22 24589999999999999999999885
No 116
>PF14446 Prok-RING_1: Prokaryotic RING finger family 1
Probab=76.69 E-value=2.1 Score=30.84 Aligned_cols=35 Identities=26% Similarity=0.676 Sum_probs=27.1
Q ss_pred CCCCCCchhhhhhcccCCcceE-eccCCccChHHHHH
Q 024406 148 SMHHHCPICYEYLFDSLRNTTV-MKCGHTMHCECYHE 183 (268)
Q Consensus 148 ~~~~~CpICle~lf~s~~~v~~-LpCGH~~H~~C~~~ 183 (268)
-+...|++|.+.|.+. +++++ --||=.+|+.|++.
T Consensus 3 ~~~~~C~~Cg~~~~~~-dDiVvCp~CgapyHR~C~~~ 38 (54)
T PF14446_consen 3 YEGCKCPVCGKKFKDG-DDIVVCPECGAPYHRDCWEK 38 (54)
T ss_pred ccCccChhhCCcccCC-CCEEECCCCCCcccHHHHhh
Confidence 3467899999996655 45555 56999999999865
No 117
>PRK14559 putative protein serine/threonine phosphatase; Provisional
Probab=75.69 E-value=2 Score=44.80 Aligned_cols=31 Identities=32% Similarity=0.885 Sum_probs=16.4
Q ss_pred ecCCCCccccc-cccCCcCCCccceeeccccc
Q 024406 67 ICSVCDTEQPV-AQVCTNCGVNMGEYFCDICK 97 (268)
Q Consensus 67 ~C~~C~~~q~v-~~~C~~Cg~~f~~y~C~~C~ 97 (268)
+|..|+++-+. +..|++||..+..-.|+.|.
T Consensus 3 ~Cp~Cg~~n~~~akFC~~CG~~l~~~~Cp~CG 34 (645)
T PRK14559 3 ICPQCQFENPNNNRFCQKCGTSLTHKPCPQCG 34 (645)
T ss_pred cCCCCCCcCCCCCccccccCCCCCCCcCCCCC
Confidence 45666655443 34466666665544444443
No 118
>PF14353 CpXC: CpXC protein
Probab=75.35 E-value=0.46 Score=38.80 Aligned_cols=56 Identities=13% Similarity=0.384 Sum_probs=34.2
Q ss_pred cCCCCCCcchhhhhHHHHHHHHHHHhcCCChhhhcCeeEEEccCCCCccccceeEeee
Q 024406 191 YCCPICSKSVIDMSRTWKRIDEEIEATVMPEDYRHKKVWILCNDCNDTTEVYFHIIGQ 248 (268)
Q Consensus 191 ~~CPiCrksi~~m~~~~~~lD~~i~~~pmP~~y~~~~v~I~CnDC~~~s~~~~H~lg~ 248 (268)
.+||.|++++. ...|..+|......-...-..+..-.+.|..||++..+.+=+|++
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 68999999886 224554442111111112234555679999999988777666654
No 119
>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=75.27 E-value=1.9 Score=23.97 Aligned_cols=20 Identities=35% Similarity=0.737 Sum_probs=13.9
Q ss_pred cCCCCCCcchhhhhHHHHHH
Q 024406 191 YCCPICSKSVIDMSRTWKRI 210 (268)
Q Consensus 191 ~~CPiCrksi~~m~~~~~~l 210 (268)
|.||+|++.+.+...+++-+
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 120
>KOG4692 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=75.01 E-value=1.7 Score=42.49 Aligned_cols=50 Identities=30% Similarity=0.612 Sum_probs=41.8
Q ss_pred CCCCCCCchhhhhhcccCCcceEeccCCccChHHHHHHHHcCCCcCCCCCCcchhh
Q 024406 147 NSMHHHCPICYEYLFDSLRNTTVMKCGHTMHCECYHEMIKRDNRYCCPICSKSVID 202 (268)
Q Consensus 147 ~~~~~~CpICle~lf~s~~~v~~LpCGH~~H~~C~~~~~~~~~~~~CPiCrksi~~ 202 (268)
.+.+..||||... ....++-||||--...|+.+.+.++ .+|=.|+.++.+
T Consensus 419 ~sEd~lCpICyA~----pi~Avf~PC~H~SC~~CI~qHlmN~--k~CFfCktTv~~ 468 (489)
T KOG4692|consen 419 DSEDNLCPICYAG----PINAVFAPCSHRSCYGCITQHLMNC--KRCFFCKTTVID 468 (489)
T ss_pred CcccccCcceecc----cchhhccCCCCchHHHHHHHHHhcC--CeeeEecceeee
Confidence 4677899999874 2345667999999999999999887 799999999886
No 121
>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=74.45 E-value=1.1 Score=41.72 Aligned_cols=51 Identities=24% Similarity=0.576 Sum_probs=41.7
Q ss_pred CCCCCchhhhhhcccCCcceEe--c-cCCccChHHHHHHHHcCCCcCCC--CCCcchh
Q 024406 149 MHHHCPICYEYLFDSLRNTTVM--K-CGHTMHCECYHEMIKRDNRYCCP--ICSKSVI 201 (268)
Q Consensus 149 ~~~~CpICle~lf~s~~~v~~L--p-CGH~~H~~C~~~~~~~~~~~~CP--iCrksi~ 201 (268)
.+..||||..+.+-+. .+++| | |=|-|..+|.+..+..+ .-.|| -|.|.+-
T Consensus 9 ~d~~CPvCksDrYLnP-dik~linPECyHrmCESCvdRIFs~G-pAqCP~~gC~kILR 64 (314)
T COG5220 9 EDRRCPVCKSDRYLNP-DIKILINPECYHRMCESCVDRIFSRG-PAQCPYKGCGKILR 64 (314)
T ss_pred hcccCCccccccccCC-CeEEEECHHHHHHHHHHHHHHHhcCC-CCCCCCccHHHHHH
Confidence 3558999999988875 45554 6 99999999999999888 57899 8988775
No 122
>PHA00626 hypothetical protein
Probab=73.80 E-value=2.7 Score=30.69 Aligned_cols=12 Identities=25% Similarity=0.775 Sum_probs=5.4
Q ss_pred cceeeccccccc
Q 024406 88 MGEYFCDICKFY 99 (268)
Q Consensus 88 f~~y~C~~C~l~ 99 (268)
-++|-|..|.++
T Consensus 21 snrYkCkdCGY~ 32 (59)
T PHA00626 21 SDDYVCCDCGYN 32 (59)
T ss_pred CcceEcCCCCCe
Confidence 344444444444
No 123
>PRK14714 DNA polymerase II large subunit; Provisional
Probab=73.72 E-value=3.3 Score=46.20 Aligned_cols=33 Identities=30% Similarity=0.740 Sum_probs=19.9
Q ss_pred eeecCCCCccccccccCCcCCCcc-ceeecccccc
Q 024406 65 QVICSVCDTEQPVAQVCTNCGVNM-GEYFCDICKF 98 (268)
Q Consensus 65 ~v~C~~C~~~q~v~~~C~~Cg~~f-~~y~C~~C~l 98 (268)
...|..|+++-+ ...|+.||... ..|+|+.|..
T Consensus 667 ~rkCPkCG~~t~-~~fCP~CGs~te~vy~CPsCGa 700 (1337)
T PRK14714 667 RRRCPSCGTETY-ENRCPDCGTHTEPVYVCPDCGA 700 (1337)
T ss_pred EEECCCCCCccc-cccCcccCCcCCCceeCccCCC
Confidence 466777776533 34777777665 3445666654
No 124
>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=73.57 E-value=1.5 Score=27.33 Aligned_cols=37 Identities=24% Similarity=0.507 Sum_probs=23.7
Q ss_pred CchhhhhhcccCCcceEeccCCccChHHHHHHHHcCCCcCCCCCCcchh
Q 024406 153 CPICYEYLFDSLRNTTVMKCGHTMHCECYHEMIKRDNRYCCPICSKSVI 201 (268)
Q Consensus 153 CpICle~lf~s~~~v~~LpCGH~~H~~C~~~~~~~~~~~~CPiCrksi~ 201 (268)
|+.|.+.+.++. ..+..=|..+|..|| +|..|+++|.
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 677888765541 222222788888764 7888887764
No 125
>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=72.87 E-value=2.9 Score=25.48 Aligned_cols=21 Identities=24% Similarity=0.539 Sum_probs=15.8
Q ss_pred cCCCCCCcchhhhhHHHHHHHH
Q 024406 191 YCCPICSKSVIDMSRTWKRIDE 212 (268)
Q Consensus 191 ~~CPiCrksi~~m~~~~~~lD~ 212 (268)
..||||.+.+ .+....+.||.
T Consensus 2 v~CPiC~~~v-~~~~in~HLD~ 22 (26)
T smart00734 2 VQCPVCFREV-PENLINSHLDS 22 (26)
T ss_pred CcCCCCcCcc-cHHHHHHHHHH
Confidence 4799999998 55556677773
No 126
>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]
Probab=72.60 E-value=3.5 Score=43.65 Aligned_cols=54 Identities=22% Similarity=0.532 Sum_probs=43.1
Q ss_pred ceEcCCCCCcccCcchHHhhhcCCCCCCCCccccccccceeecCCCCccccccccCCcCCCcccee
Q 024406 26 RIRAPCCNEIFDCRHCHNEAASMLRNPYDRHELVRQDVKQVICSVCDTEQPVAQVCTNCGVNMGEY 91 (268)
Q Consensus 26 ~l~~pcC~~~y~Cr~CHde~~~~~~~~~~~H~~~r~~~~~v~C~~C~~~q~v~~~C~~Cg~~f~~y 91 (268)
.+.|.-||-.+.|.+|=.-++-|. .+..+.|-+|+..+++...|++||...=+|
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 236899999999999999999999985444
No 127
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=71.87 E-value=3.2 Score=28.15 Aligned_cols=36 Identities=19% Similarity=0.262 Sum_probs=24.3
Q ss_pred eEEEccCCCCccccceeEeeecCCCCCCccccccCC
Q 024406 228 VWILCNDCNDTTEVYFHIIGQKCSHCKSYNTRSIAP 263 (268)
Q Consensus 228 v~I~CnDC~~~s~~~~H~lg~kC~~C~SyNT~~~~~ 263 (268)
..+.|.+||+.....-.....+|+.||+.-....++
T Consensus 2 ~~y~C~~CG~~~~~~~~~~~~~Cp~CG~~~~~~~~~ 37 (46)
T PRK00398 2 AEYKCARCGREVELDEYGTGVRCPYCGYRILFKERP 37 (46)
T ss_pred CEEECCCCCCEEEECCCCCceECCCCCCeEEEccCC
Confidence 457899999866444333367999999866544443
No 128
>KOG0801 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=71.63 E-value=1.5 Score=38.54 Aligned_cols=31 Identities=23% Similarity=0.353 Sum_probs=25.1
Q ss_pred CCCCCCCchhhhhhcccCCcceEeccCCccCh
Q 024406 147 NSMHHHCPICYEYLFDSLRNTTVMKCGHTMHC 178 (268)
Q Consensus 147 ~~~~~~CpICle~lf~s~~~v~~LpCGH~~H~ 178 (268)
.....+|.||||+|... +.+..|||==++|+
T Consensus 174 ~ddkGECvICLEdL~~G-dtIARLPCLCIYHK 204 (205)
T KOG0801|consen 174 KDDKGECVICLEDLEAG-DTIARLPCLCIYHK 204 (205)
T ss_pred cccCCcEEEEhhhccCC-CceeccceEEEeec
Confidence 34568999999998765 77899999877775
No 129
>KOG3161 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=69.76 E-value=3.1 Score=43.53 Aligned_cols=40 Identities=25% Similarity=0.647 Sum_probs=33.9
Q ss_pred CCCchhhhhhcccCCcceEeccCCccChHHHHHHHHcCCCcCCC
Q 024406 151 HHCPICYEYLFDSLRNTTVMKCGHTMHCECYHEMIKRDNRYCCP 194 (268)
Q Consensus 151 ~~CpICle~lf~s~~~v~~LpCGH~~H~~C~~~~~~~~~~~~CP 194 (268)
..|+||+..+|.++..-+.|-|||++...|+...-. .+||
T Consensus 12 l~c~ic~n~f~~~~~~Pvsl~cghtic~~c~~~lyn----~scp 51 (861)
T KOG3161|consen 12 LLCDICLNLFVVQRLEPVSLQCGHTICGHCVQLLYN----ASCP 51 (861)
T ss_pred hhchHHHHHHHHHhcCcccccccchHHHHHHHhHhh----ccCC
Confidence 479999988888888888999999999999987652 5677
No 130
>COG5109 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=69.13 E-value=4.1 Score=39.30 Aligned_cols=46 Identities=22% Similarity=0.579 Sum_probs=37.5
Q ss_pred CCCchhhhhhcccCCcceEeccCCccChHHHHHHHHcC-CCcCCCCCC
Q 024406 151 HHCPICYEYLFDSLRNTTVMKCGHTMHCECYHEMIKRD-NRYCCPICS 197 (268)
Q Consensus 151 ~~CpICle~lf~s~~~v~~LpCGH~~H~~C~~~~~~~~-~~~~CPiCr 197 (268)
-.|||=.|. -+...|...|.|||.+=++=++.+-+++ ..++||.|-
T Consensus 337 FiCPVlKe~-~t~ENpP~ml~CgHVIskeal~~LS~nG~~~FKCPYCP 383 (396)
T COG5109 337 FICPVLKEL-CTDENPPVMLECGHVISKEALSVLSQNGVLSFKCPYCP 383 (396)
T ss_pred eeccccHhh-hcccCCCeeeeccceeeHHHHHHHhhcCcEEeeCCCCC
Confidence 379997774 5555778889999999999999988765 368999996
No 131
>PRK05580 primosome assembly protein PriA; Validated
Probab=67.22 E-value=4.5 Score=42.22 Aligned_cols=51 Identities=22% Similarity=0.632 Sum_probs=42.0
Q ss_pred ceEcCCCCCcccCcchHHhhhcCCCCCCCCccccccccceeecCCCCccccccccCCcCCCcc
Q 024406 26 RIRAPCCNEIFDCRHCHNEAASMLRNPYDRHELVRQDVKQVICSVCDTEQPVAQVCTNCGVNM 88 (268)
Q Consensus 26 ~l~~pcC~~~y~Cr~CHde~~~~~~~~~~~H~~~r~~~~~v~C~~C~~~q~v~~~C~~Cg~~f 88 (268)
.+.|.-||....|..|.-.+.- |. ....+.|-.|+..+++...|++||...
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 3889999999999999876642 22 245899999999999999999998874
No 132
>PLN03086 PRLI-interacting factor K; Provisional
Probab=67.12 E-value=2.5 Score=43.46 Aligned_cols=85 Identities=26% Similarity=0.600 Sum_probs=49.3
Q ss_pred cccceeecCCCCcccccc-------------ccCCc--CCCccceeeccccccccCCCCcCeeecCCCCcccccCc----
Q 024406 61 QDVKQVICSVCDTEQPVA-------------QVCTN--CGVNMGEYFCDICKFYDDDIEKGQFHCDDCGICRIGGR---- 121 (268)
Q Consensus 61 ~~~~~v~C~~C~~~q~v~-------------~~C~~--Cg~~f~~y~C~~C~l~d~~~~k~~yHC~~CgiCR~G~~---- 121 (268)
..+..|.|..|....+.. ..|++ ||..|.+- .-+..+||+.||- ..+..
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 356788999998766542 35664 77766332 2345578888864 22211
Q ss_pred -----cceeecCccCccccccccCcce---eecCCCCCCCchhhhhh
Q 024406 122 -----ENYFHCKRCGSCYSTSLRNNHL---CIENSMHHHCPICYEYL 160 (268)
Q Consensus 122 -----~~ffHC~~C~~C~s~~l~~~H~---C~e~~~~~~CpICle~l 160 (268)
..-+-|. ||.-+.......|. |.++ ...|+.|...+
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 77655554445663 4433 46788887653
No 133
>KOG0269 consensus WD40 repeat-containing protein [Function unknown]
Probab=66.15 E-value=4.9 Score=42.68 Aligned_cols=79 Identities=19% Similarity=0.377 Sum_probs=48.2
Q ss_pred cCeeecCCCCcccccCccceeecCccCccccccccCcceeecCCCCCCCchhhhhhcccCCcceEeccCCccChHHHHHH
Q 024406 105 KGQFHCDDCGICRIGGRENYFHCKRCGSCYSTSLRNNHLCIENSMHHHCPICYEYLFDSLRNTTVMKCGHTMHCECYHEM 184 (268)
Q Consensus 105 k~~yHC~~CgiCR~G~~~~ffHC~~C~~C~s~~l~~~H~C~e~~~~~~CpICle~lf~s~~~v~~LpCGH~~H~~C~~~~ 184 (268)
.-+|-|+.|+-=-++++. - +|+.|-+.+ ...|.||-..+-. ..+.---|||..|.+++.+|
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 356777777755454443 3 344443333 1358888765432 23333469999999999999
Q ss_pred HHcCCCcCCCC-------CCcchhhhh
Q 024406 185 IKRDNRYCCPI-------CSKSVIDMS 204 (268)
Q Consensus 185 ~~~~~~~~CPi-------Crksi~~m~ 204 (268)
+... ..||. +++++.||.
T Consensus 812 ~~~~--s~ca~~~C~~~c~~~~~~D~~ 836 (839)
T KOG0269|consen 812 FFKA--SPCAKSICPHLCHYSSFIDTF 836 (839)
T ss_pred HhcC--CCCccccCCccccccccchhh
Confidence 9865 55654 445555653
No 134
>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]
Probab=65.20 E-value=6.1 Score=41.93 Aligned_cols=44 Identities=25% Similarity=0.706 Sum_probs=29.4
Q ss_pred cceeecCCCCccccccccCCcCCCccc------eeeccccccccCCCCcCeeecCCCC
Q 024406 63 VKQVICSVCDTEQPVAQVCTNCGVNMG------EYFCDICKFYDDDIEKGQFHCDDCG 114 (268)
Q Consensus 63 ~~~v~C~~C~~~q~v~~~C~~Cg~~f~------~y~C~~C~l~d~~~~k~~yHC~~Cg 114 (268)
.+.++|..|+.. ..|++|...|. ...|--|..= ++.+.+|+.||
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 468999999976 57999998884 4445444332 34555555555
No 135
>KOG1609 consensus Protein involved in mRNA turnover and stability [RNA processing and modification]
Probab=64.37 E-value=3 Score=38.16 Aligned_cols=52 Identities=23% Similarity=0.400 Sum_probs=39.9
Q ss_pred CCCCchhhhhhcccCCcceEeccC-----CccChHHHHHHHHcCCCcCCCCCCcchh
Q 024406 150 HHHCPICYEYLFDSLRNTTVMKCG-----HTMHCECYHEMIKRDNRYCCPICSKSVI 201 (268)
Q Consensus 150 ~~~CpICle~lf~s~~~v~~LpCG-----H~~H~~C~~~~~~~~~~~~CPiCrksi~ 201 (268)
+..|=||.++.+.+.......||. ...|+.|+..|+...++..|.+|.....
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 368999999877653334556772 8889999999998554689999998664
No 136
>PRK14873 primosome assembly protein PriA; Provisional
Probab=63.82 E-value=5.6 Score=41.68 Aligned_cols=50 Identities=20% Similarity=0.470 Sum_probs=39.8
Q ss_pred ceEcCCCCCcccCcchHHhhhcCCCCCCCCccccccccceeecCCCCccccccccCCcCCCcc
Q 024406 26 RIRAPCCNEIFDCRHCHNEAASMLRNPYDRHELVRQDVKQVICSVCDTEQPVAQVCTNCGVNM 88 (268)
Q Consensus 26 ~l~~pcC~~~y~Cr~CHde~~~~~~~~~~~H~~~r~~~~~v~C~~C~~~q~v~~~C~~Cg~~f 88 (268)
.+.|.-||....|..|.--++- |. ....+.|-+|+... +...|++||...
T Consensus 383 ~l~C~~Cg~~~~C~~C~~~L~~--------h~----~~~~l~Ch~CG~~~-~p~~Cp~Cgs~~ 432 (665)
T PRK14873 383 SLACARCRTPARCRHCTGPLGL--------PS----AGGTPRCRWCGRAA-PDWRCPRCGSDR 432 (665)
T ss_pred eeEhhhCcCeeECCCCCCceeE--------ec----CCCeeECCCCcCCC-cCccCCCCcCCc
Confidence 3899999999999999977652 21 23578999999876 578999999863
No 137
>PRK04023 DNA polymerase II large subunit; Validated
Probab=63.76 E-value=5.6 Score=43.58 Aligned_cols=50 Identities=24% Similarity=0.587 Sum_probs=36.9
Q ss_pred cceeecCCCCccccccccCCcCCCc-cceeeccccccccCCCCcCeeecCCCCcccc
Q 024406 63 VKQVICSVCDTEQPVAQVCTNCGVN-MGEYFCDICKFYDDDIEKGQFHCDDCGICRI 118 (268)
Q Consensus 63 ~~~v~C~~C~~~q~v~~~C~~Cg~~-f~~y~C~~C~l~d~~~~k~~yHC~~CgiCR~ 118 (268)
+..-.|..|+++. +...|++||.. -..|||+.|.-- -..|.|+.||.=..
T Consensus 624 Vg~RfCpsCG~~t-~~frCP~CG~~Te~i~fCP~CG~~-----~~~y~CPKCG~El~ 674 (1121)
T PRK04023 624 IGRRKCPSCGKET-FYRRCPFCGTHTEPVYRCPRCGIE-----VEEDECEKCGREPT 674 (1121)
T ss_pred ccCccCCCCCCcC-CcccCCCCCCCCCcceeCccccCc-----CCCCcCCCCCCCCC
Confidence 3455899999985 66899999974 677899999433 23477999986433
No 138
>KOG2272 consensus Focal adhesion protein PINCH-1, contains LIM domains [Signal transduction mechanisms; Cytoskeleton]
Probab=63.51 E-value=4.2 Score=38.18 Aligned_cols=128 Identities=19% Similarity=0.511 Sum_probs=71.9
Q ss_pred ccCcchHHhhhcCCCCCCCCccccccccceeecCCCCccccccccCCcCCCccceeeccccccc-cCCC---CcCeeecC
Q 024406 36 FDCRHCHNEAASMLRNPYDRHELVRQDVKQVICSVCDTEQPVAQVCTNCGVNMGEYFCDICKFY-DDDI---EKGQFHCD 111 (268)
Q Consensus 36 y~Cr~CHde~~~~~~~~~~~H~~~r~~~~~v~C~~C~~~q~v~~~C~~Cg~~f~~y~C~~C~l~-d~~~---~k~~yHC~ 111 (268)
|.|.+|-..+++ --+.|. .-+++|-.|+..-.+ ..-|+|-|.+|+-. |+++ .-.+||
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 567777766652 233443 347788888755333 34589999999744 5544 224554
Q ss_pred CCCcccccCccceeecCccCccccc---cccCcceeecCCCCCCCchhhhhhcccCCcceEeccCCccChHHH----HHH
Q 024406 112 DCGICRIGGRENYFHCKRCGSCYST---SLRNNHLCIENSMHHHCPICYEYLFDSLRNTTVMKCGHTMHCECY----HEM 184 (268)
Q Consensus 112 ~CgiCR~G~~~~ffHC~~C~~C~s~---~l~~~H~C~e~~~~~~CpICle~lf~s~~~v~~LpCGH~~H~~C~----~~~ 184 (268)
-.-|.|.+||-=+.. ++++.-.|..=-...-+|||..= --.|-..=+ +.|
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 357889999876654 34444444443333445555432 111111112 124
Q ss_pred HHcCCCcCCCCCCcchhhhhHHH
Q 024406 185 IKRDNRYCCPICSKSVIDMSRTW 207 (268)
Q Consensus 185 ~~~~~~~~CPiCrksi~~m~~~~ 207 (268)
-..+ +.|..|-|+++.-+.|.
T Consensus 218 HveH--FvCa~CekPFlGHrHYE 238 (332)
T KOG2272|consen 218 HVEH--FVCAKCEKPFLGHRHYE 238 (332)
T ss_pred chhh--eeehhcCCcccchhhhh
Confidence 3334 88888888888655443
No 139
>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=63.30 E-value=4.9 Score=33.84 Aligned_cols=28 Identities=21% Similarity=0.455 Sum_probs=20.7
Q ss_pred ccccCCcCCCccceeeccccccccCCCCcCeeecCCCCcc
Q 024406 77 VAQVCTNCGVNMGEYFCDICKFYDDDIEKGQFHCDDCGIC 116 (268)
Q Consensus 77 v~~~C~~Cg~~f~~y~C~~C~l~d~~~~k~~yHC~~CgiC 116 (268)
...+|++||+.| || .+|.+-.|++||.=
T Consensus 8 tKr~Cp~cg~kF----------YD--Lnk~p~vcP~cg~~ 35 (129)
T TIGR02300 8 TKRICPNTGSKF----------YD--LNRRPAVSPYTGEQ 35 (129)
T ss_pred ccccCCCcCccc----------cc--cCCCCccCCCcCCc
Confidence 456788998854 65 56888888888853
No 140
>KOG2462 consensus C2H2-type Zn-finger protein [Transcription]
Probab=63.22 E-value=7.4 Score=36.68 Aligned_cols=113 Identities=24% Similarity=0.512 Sum_probs=63.4
Q ss_pred cceeecccc-ccccCCC---CcCeeecCCCCcccccCccceeecCccCcccccc-ccCcceeecCCCCCCCchhhhhhcc
Q 024406 88 MGEYFCDIC-KFYDDDI---EKGQFHCDDCGICRIGGRENYFHCKRCGSCYSTS-LRNNHLCIENSMHHHCPICYEYLFD 162 (268)
Q Consensus 88 f~~y~C~~C-~l~d~~~---~k~~yHC~~CgiCR~G~~~~ffHC~~C~~C~s~~-l~~~H~C~e~~~~~~CpICle~lf~ 162 (268)
-++|-|+.| |-|.... .-+|+||+- .-..-|.|..||-=|..- ...-|.=.- ...-.|+||.-. |+
T Consensus 128 ~~r~~c~eCgk~ysT~snLsrHkQ~H~~~-------~s~ka~~C~~C~K~YvSmpALkMHirTH-~l~c~C~iCGKa-FS 198 (279)
T KOG2462|consen 128 HPRYKCPECGKSYSTSSNLSRHKQTHRSL-------DSKKAFSCKYCGKVYVSMPALKMHIRTH-TLPCECGICGKA-FS 198 (279)
T ss_pred CCceeccccccccccccccchhhcccccc-------cccccccCCCCCceeeehHHHhhHhhcc-CCCccccccccc-cc
Confidence 355566666 4453322 236777743 124577888887665431 112222221 145678888874 64
Q ss_pred cCCcceEeccCCccChHHHHHHHHcC--------CCcCCCCCCcchhhhhHHHHHHHHHHHhcCCChhhhcCeeEEEccC
Q 024406 163 SLRNTTVMKCGHTMHCECYHEMIKRD--------NRYCCPICSKSVIDMSRTWKRIDEEIEATVMPEDYRHKKVWILCND 234 (268)
Q Consensus 163 s~~~v~~LpCGH~~H~~C~~~~~~~~--------~~~~CPiCrksi~~m~~~~~~lD~~i~~~pmP~~y~~~~v~I~CnD 234 (268)
- .||-.+ +-|.||.|+|.+.|++ +|.+-+... .+.+ ..-|--
T Consensus 199 R-------------------PWLLQGHiRTHTGEKPF~C~hC~kAFADRS----NLRAHmQTH------S~~K-~~qC~~ 248 (279)
T KOG2462|consen 199 R-------------------PWLLQGHIRTHTGEKPFSCPHCGKAFADRS----NLRAHMQTH------SDVK-KHQCPR 248 (279)
T ss_pred c-------------------hHHhhcccccccCCCCccCCcccchhcchH----HHHHHHHhh------cCCc-cccCcc
Confidence 2 365321 2588999999999875 455555442 2333 466778
Q ss_pred CCCcc
Q 024406 235 CNDTT 239 (268)
Q Consensus 235 C~~~s 239 (268)
|++++
T Consensus 249 C~KsF 253 (279)
T KOG2462|consen 249 CGKSF 253 (279)
T ss_pred hhhHH
Confidence 88754
No 141
>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=62.90 E-value=7.3 Score=27.19 Aligned_cols=22 Identities=23% Similarity=0.581 Sum_probs=15.5
Q ss_pred CcCCCCCCcchhhhhHHHHHHHH
Q 024406 190 RYCCPICSKSVIDMSRTWKRIDE 212 (268)
Q Consensus 190 ~~~CPiCrksi~~m~~~~~~lD~ 212 (268)
.|+||.|++ -.+..+.++-++.
T Consensus 2 ~f~CP~C~~-~~~~~~L~~H~~~ 23 (54)
T PF05605_consen 2 SFTCPYCGK-GFSESSLVEHCED 23 (54)
T ss_pred CcCCCCCCC-ccCHHHHHHHHHh
Confidence 489999999 5666666555443
No 142
>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=62.20 E-value=6.3 Score=28.51 Aligned_cols=27 Identities=30% Similarity=0.774 Sum_probs=16.9
Q ss_pred cccCCcCCCccceeeccccccccCCCCcCeeecCCCCc
Q 024406 78 AQVCTNCGVNMGEYFCDICKFYDDDIEKGQFHCDDCGI 115 (268)
Q Consensus 78 ~~~C~~Cg~~f~~y~C~~C~l~d~~~~k~~yHC~~Cgi 115 (268)
++.|+.||..... ......|.|+.||.
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 143
>KOG2068 consensus MOT2 transcription factor [Transcription]
Probab=61.99 E-value=5.1 Score=38.57 Aligned_cols=52 Identities=33% Similarity=0.529 Sum_probs=40.0
Q ss_pred CCCCCCchhhhhhcccCCcceEeccCCccChHHHHHHHHcCCCcCCCCCCcchh
Q 024406 148 SMHHHCPICYEYLFDSLRNTTVMKCGHTMHCECYHEMIKRDNRYCCPICSKSVI 201 (268)
Q Consensus 148 ~~~~~CpICle~lf~s~~~v~~LpCGH~~H~~C~~~~~~~~~~~~CPiCrksi~ 201 (268)
+....||||.+++-.......--|||+.++..|+..-...+ .+||.|+|...
T Consensus 247 ~v~~s~p~~~~~~~~~d~~~lP~~~~~~~~l~~~~t~~~~~--~~~~~~rk~~~ 298 (327)
T KOG2068|consen 247 SVPPSCPICYEDLDLTDSNFLPCPCGFRLCLFCHKTISDGD--GRCPGCRKPYE 298 (327)
T ss_pred ccCCCCCCCCCcccccccccccccccccchhhhhhcccccC--CCCCccCCccc
Confidence 34478999999875544444455789999999988887766 89999997765
No 144
>KOG1940 consensus Zn-finger protein [General function prediction only]
Probab=61.98 E-value=1.5 Score=41.25 Aligned_cols=29 Identities=21% Similarity=0.526 Sum_probs=25.7
Q ss_pred CccCccccccCcceEcCCCCCcccCcchHH
Q 024406 14 MGYGCKHYRRRCRIRAPCCNEIFDCRHCHN 43 (268)
Q Consensus 14 ~~~gC~HY~r~c~l~~pcC~~~y~Cr~CHd 43 (268)
..+.|.||...=.++.++|.. |+|..||+
T Consensus 176 ~~~~CgH~~h~~cf~e~~~~~-y~CP~C~~ 204 (276)
T KOG1940|consen 176 GVLKCGHYMHSRCFEEMICEG-YTCPICSK 204 (276)
T ss_pred CccCcccchHHHHHHHHhccC-CCCCcccc
Confidence 346899999866699999999 99999999
No 145
>PRK14714 DNA polymerase II large subunit; Provisional
Probab=61.98 E-value=6.5 Score=43.97 Aligned_cols=33 Identities=30% Similarity=0.731 Sum_probs=25.2
Q ss_pred ccCCcCCCccceeeccccccccCCCCcCeeecCCCCc
Q 024406 79 QVCTNCGVNMGEYFCDICKFYDDDIEKGQFHCDDCGI 115 (268)
Q Consensus 79 ~~C~~Cg~~f~~y~C~~C~l~d~~~~k~~yHC~~Cgi 115 (268)
..|++||......||+.|.-.. +.+|+|+.||.
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 4899999877777999996543 45678887776
No 146
>COG1996 RPC10 DNA-directed RNA polymerase, subunit RPC10 (contains C4-type Zn-finger) [Transcription]
Probab=61.94 E-value=5.9 Score=28.02 Aligned_cols=30 Identities=23% Similarity=0.454 Sum_probs=23.4
Q ss_pred eeEEEccCCCCccccceeEeeecCCCCCCc
Q 024406 227 KVWILCNDCNDTTEVYFHIIGQKCSHCKSY 256 (268)
Q Consensus 227 ~v~I~CnDC~~~s~~~~H~lg~kC~~C~Sy 256 (268)
+....|.+|++..+...-.-|.+|+.|||-
T Consensus 4 ~~~Y~C~~Cg~~~~~~~~~~~irCp~Cg~r 33 (49)
T COG1996 4 MMEYKCARCGREVELDQETRGIRCPYCGSR 33 (49)
T ss_pred eEEEEhhhcCCeeehhhccCceeCCCCCcE
Confidence 456889999988765555678899999973
No 147
>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=61.84 E-value=6.1 Score=24.58 Aligned_cols=20 Identities=30% Similarity=0.853 Sum_probs=13.7
Q ss_pred CCCcccccCccc-eeecCccC
Q 024406 112 DCGICRIGGREN-YFHCKRCG 131 (268)
Q Consensus 112 ~CgiCR~G~~~~-ffHC~~C~ 131 (268)
.|++|+.-.... +++|..|+
T Consensus 2 ~C~~C~~~~~~~~~Y~C~~c~ 22 (30)
T PF03107_consen 2 WCDVCRRKIDGFYFYHCSECC 22 (30)
T ss_pred CCCCCCCCcCCCEeEEeCCCC
Confidence 467776654444 88888887
No 148
>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=61.28 E-value=7.2 Score=23.64 Aligned_cols=9 Identities=44% Similarity=1.239 Sum_probs=4.5
Q ss_pred CeeecCCCC
Q 024406 106 GQFHCDDCG 114 (268)
Q Consensus 106 ~~yHC~~Cg 114 (268)
-.|.|+.||
T Consensus 15 v~f~CPnCG 23 (24)
T PF07754_consen 15 VPFPCPNCG 23 (24)
T ss_pred ceEeCCCCC
Confidence 345555554
No 149
>PHA03096 p28-like protein; Provisional
Probab=60.81 E-value=5.6 Score=37.55 Aligned_cols=48 Identities=15% Similarity=0.308 Sum_probs=32.3
Q ss_pred CCCchhhhhhcccC---CcceEe-ccCCccChHHHHHHHHcC-CCcCCCCCCc
Q 024406 151 HHCPICYEYLFDSL---RNTTVM-KCGHTMHCECYHEMIKRD-NRYCCPICSK 198 (268)
Q Consensus 151 ~~CpICle~lf~s~---~~v~~L-pCGH~~H~~C~~~~~~~~-~~~~CPiCrk 198 (268)
-.|-||+|...... ..-..| .|-|.|...|+..|.... ...+||.|+.
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 57999999876542 112235 699999999999998643 1344555554
No 150
>smart00659 RPOLCX RNA polymerase subunit CX. present in RNA polymerase I, II and III
Probab=59.60 E-value=6.5 Score=26.94 Aligned_cols=26 Identities=19% Similarity=0.525 Sum_probs=17.9
Q ss_pred EEEccCCCCccccceeEeeecCCCCCC
Q 024406 229 WILCNDCNDTTEVYFHIIGQKCSHCKS 255 (268)
Q Consensus 229 ~I~CnDC~~~s~~~~H~lg~kC~~C~S 255 (268)
...|.+||+..+... --..+|+.||+
T Consensus 2 ~Y~C~~Cg~~~~~~~-~~~irC~~CG~ 27 (44)
T smart00659 2 IYICGECGRENEIKS-KDVVRCRECGY 27 (44)
T ss_pred EEECCCCCCEeecCC-CCceECCCCCc
Confidence 467888887665542 34578888886
No 151
>KOG0298 consensus DEAD box-containing helicase-like transcription factor/DNA repair protein [Replication, recombination and repair]
Probab=59.53 E-value=6.9 Score=43.79 Aligned_cols=53 Identities=30% Similarity=0.637 Sum_probs=42.8
Q ss_pred CCCCCCchhhhhhcccCCcceEeccCCccChHHHHHHHHcCCCcCCCCCCcchhhhhH
Q 024406 148 SMHHHCPICYEYLFDSLRNTTVMKCGHTMHCECYHEMIKRDNRYCCPICSKSVIDMSR 205 (268)
Q Consensus 148 ~~~~~CpICle~lf~s~~~v~~LpCGH~~H~~C~~~~~~~~~~~~CPiCrksi~~m~~ 205 (268)
+....|+||++-|-. .-.+..|||.+-..|+..|+..+ ..||+|.....|-..
T Consensus 1151 ~~~~~c~ic~dil~~---~~~I~~cgh~~c~~c~~~~l~~~--s~~~~~ksi~~dfg~ 1203 (1394)
T KOG0298|consen 1151 SGHFVCEICLDILRN---QGGIAGCGHEPCCRCDELWLYAS--SRCPICKSIKGDFGT 1203 (1394)
T ss_pred hcccchHHHHHHHHh---cCCeeeechhHhhhHHHHHHHHh--ccCcchhhhhhhhcc
Confidence 344589999998753 23467899999999999999987 899999977776543
No 152
>PF13597 NRDD: Anaerobic ribonucleoside-triphosphate reductase; PDB: 1HK8_A 1H78_A 1H7A_A 1H79_A 1H7B_A.
Probab=58.32 E-value=7.3 Score=39.78 Aligned_cols=57 Identities=23% Similarity=0.282 Sum_probs=25.9
Q ss_pred hhhHHHHHHHHHHHhcCCChhhhcCeeEEEccCCCCccccceeEeeecCCCCCCccccccCCC
Q 024406 202 DMSRTWKRIDEEIEATVMPEDYRHKKVWILCNDCNDTTEVYFHIIGQKCSHCKSYNTRSIAPP 264 (268)
Q Consensus 202 ~m~~~~~~lD~~i~~~pmP~~y~~~~v~I~CnDC~~~s~~~~H~lg~kC~~C~SyNT~~~~~~ 264 (268)
+.++.++.++.......+|-.--+ ...-.|++||..... +.+||.|||-|+.++++.
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 445555666665554555533112 234679999986653 468999999998887753
No 153
>PRK14559 putative protein serine/threonine phosphatase; Provisional
Probab=57.92 E-value=5.6 Score=41.58 Aligned_cols=34 Identities=26% Similarity=0.666 Sum_probs=21.4
Q ss_pred eeecCCCCccccccccCCcCCCcc--ceeeccccccc
Q 024406 65 QVICSVCDTEQPVAQVCTNCGVNM--GEYFCDICKFY 99 (268)
Q Consensus 65 ~v~C~~C~~~q~v~~~C~~Cg~~f--~~y~C~~C~l~ 99 (268)
.-.|..|++.++. ..|++||+.. +.-||+.|-..
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 4467777776543 4677777654 55667776543
No 154
>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=57.77 E-value=6.4 Score=22.23 Aligned_cols=16 Identities=50% Similarity=0.916 Sum_probs=12.4
Q ss_pred cCCCCCCcchhhhhHH
Q 024406 191 YCCPICSKSVIDMSRT 206 (268)
Q Consensus 191 ~~CPiCrksi~~m~~~ 206 (268)
|+||+|++++.+.+.+
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 5799999999865543
No 155
>KOG1001 consensus Helicase-like transcription factor HLTF/DNA helicase RAD5, DEAD-box superfamily [Transcription; Replication, recombination and repair]
Probab=56.50 E-value=4.8 Score=42.28 Aligned_cols=46 Identities=30% Similarity=0.831 Sum_probs=37.0
Q ss_pred CCCchhhhhhcccCCcceEeccCCccChHHHHHHHHcCCCcCCCCCCcchh
Q 024406 151 HHCPICYEYLFDSLRNTTVMKCGHTMHCECYHEMIKRDNRYCCPICSKSVI 201 (268)
Q Consensus 151 ~~CpICle~lf~s~~~v~~LpCGH~~H~~C~~~~~~~~~~~~CPiCrksi~ 201 (268)
..|+||++ .+...+-+|||.|-..|+.+.+.....-.||+|+-.+.
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 78999999 25677889999999999999887552346999996554
No 156
>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=56.40 E-value=5.5 Score=40.15 Aligned_cols=58 Identities=28% Similarity=0.643 Sum_probs=30.9
Q ss_pred eeccccccccCCCCcCeeecCCCCcccccCccceeecCccCccccccc--cCcceeecCCCCCCCchhhhhhccc
Q 024406 91 YFCDICKFYDDDIEKGQFHCDDCGICRIGGRENYFHCKRCGSCYSTSL--RNNHLCIENSMHHHCPICYEYLFDS 163 (268)
Q Consensus 91 y~C~~C~l~d~~~~k~~yHC~~CgiCR~G~~~~ffHC~~C~~C~s~~l--~~~H~C~e~~~~~~CpICle~lf~s 163 (268)
|||..|.-.- |+-|-....+ .+=|..|-.=++.+. .+..+|..+- -+||+|.-.|...
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 7788876552 2333333333 344555554444432 2456666443 3688887776544
No 157
>KOG2066 consensus Vacuolar assembly/sorting protein VPS41 [Intracellular trafficking, secretion, and vesicular transport]
Probab=56.36 E-value=4.4 Score=43.17 Aligned_cols=38 Identities=32% Similarity=0.613 Sum_probs=28.4
Q ss_pred CCCchhhhhhcccC---CcceEeccCCccChHHHHHHHHcC
Q 024406 151 HHCPICYEYLFDSL---RNTTVMKCGHTMHCECYHEMIKRD 188 (268)
Q Consensus 151 ~~CpICle~lf~s~---~~v~~LpCGH~~H~~C~~~~~~~~ 188 (268)
+.|.-|.+..-.+. ..+.++.|||+||+.|+.....++
T Consensus 785 ~rc~~c~~~~l~~~~~~~~~~v~~c~h~yhk~c~~~~~~~~ 825 (846)
T KOG2066|consen 785 ERCSSCFEPNLPSGAAFDSVVVFHCGHMYHKECLMMESLRN 825 (846)
T ss_pred hhhhhhcccccccCcccceeeEEEccchhhhcccccHHHhc
Confidence 35666666655444 568999999999999998776554
No 158
>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=54.86 E-value=4.4 Score=38.15 Aligned_cols=51 Identities=27% Similarity=0.680 Sum_probs=32.2
Q ss_pred CCcccCcchHHhhhcCCCCCCCCccccccccceeecCCCCccccccccCCcCCCccceeecccccc
Q 024406 33 NEIFDCRHCHNEAASMLRNPYDRHELVRQDVKQVICSVCDTEQPVAQVCTNCGVNMGEYFCDICKF 98 (268)
Q Consensus 33 ~~~y~Cr~CHde~~~~~~~~~~~H~~~r~~~~~v~C~~C~~~q~v~~~C~~Cg~~f~~y~C~~C~l 98 (268)
|++|.|-+|.+-+.. +-.+.-.+. |+....-.-.|.+|+. +|.|.|..||.
T Consensus 140 Grif~CsfC~~flCE-------DDQFEHQAs-------CQvLe~E~~KC~SCNr-lGq~sCLRCK~ 190 (314)
T PF06524_consen 140 GRIFKCSFCDNFLCE-------DDQFEHQAS-------CQVLESETFKCQSCNR-LGQYSCLRCKI 190 (314)
T ss_pred CeEEEeecCCCeeec-------cchhhhhhh-------hhhhhccccccccccc-ccchhhhheee
Confidence 568888888876642 222222221 4444445567888875 78888988884
No 159
>KOG1812 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=54.06 E-value=6.1 Score=38.65 Aligned_cols=36 Identities=31% Similarity=0.679 Sum_probs=27.6
Q ss_pred CCCCchhh-hhhcccCCcceEeccCCccChHHHHHHHH
Q 024406 150 HHHCPICY-EYLFDSLRNTTVMKCGHTMHCECYHEMIK 186 (268)
Q Consensus 150 ~~~CpICl-e~lf~s~~~v~~LpCGH~~H~~C~~~~~~ 186 (268)
...|+||. |+++.. ....++.|||.|...|..++++
T Consensus 146 ~~~C~iC~~e~~~~~-~~f~~~~C~H~fC~~C~k~~ie 182 (384)
T KOG1812|consen 146 KEECGICFVEDPEAE-DMFSVLKCGHRFCKDCVKQHIE 182 (384)
T ss_pred cccCccCccccccHh-hhHHHhcccchhhhHHhHHHhh
Confidence 56899999 554332 2333789999999999999987
No 160
>PRK12286 rpmF 50S ribosomal protein L32; Reviewed
Probab=53.96 E-value=12 Score=26.98 Aligned_cols=29 Identities=24% Similarity=0.688 Sum_probs=22.5
Q ss_pred eEEEccCCCCccccceeEeeecCCCCCCcccccc
Q 024406 228 VWILCNDCNDTTEVYFHIIGQKCSHCKSYNTRSI 261 (268)
Q Consensus 228 v~I~CnDC~~~s~~~~H~lg~kC~~C~SyNT~~~ 261 (268)
..+.|..||+. ..-| +-|+.||.|+-+++
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 35789999974 4456 45999999999886
No 161
>KOG4367 consensus Predicted Zn-finger protein [Function unknown]
Probab=53.71 E-value=6.2 Score=39.71 Aligned_cols=34 Identities=18% Similarity=0.765 Sum_probs=27.7
Q ss_pred CCCCchhhhhhcccCCcceEeccCCccChHHHHHHHHc
Q 024406 150 HHHCPICYEYLFDSLRNTTVMKCGHTMHCECYHEMIKR 187 (268)
Q Consensus 150 ~~~CpICle~lf~s~~~v~~LpCGH~~H~~C~~~~~~~ 187 (268)
+..||||... |. +.++|||||.+.+.|....+..
T Consensus 4 elkc~vc~~f-~~---epiil~c~h~lc~~ca~~~~~~ 37 (699)
T KOG4367|consen 4 ELKCPVCGSF-YR---EPIILPCSHNLCQACARNILVQ 37 (699)
T ss_pred cccCceehhh-cc---CceEeecccHHHHHHHHhhccc
Confidence 5689999985 53 5679999999999999876643
No 162
>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=51.11 E-value=11 Score=38.44 Aligned_cols=57 Identities=21% Similarity=0.290 Sum_probs=36.1
Q ss_pred hhhHHHHHHHHHHHhcCCChhhhcCeeEEEccCCCCccccceeEeeecCCCCCCccccccCCC
Q 024406 202 DMSRTWKRIDEEIEATVMPEDYRHKKVWILCNDCNDTTEVYFHIIGQKCSHCKSYNTRSIAPP 264 (268)
Q Consensus 202 ~m~~~~~~lD~~i~~~pmP~~y~~~~v~I~CnDC~~~s~~~~H~lg~kC~~C~SyNT~~~~~~ 264 (268)
+.++.+..++.......++-. -+..+. .|++||.... -++.+|+.|||-|+.++++.
T Consensus 493 n~~al~~lv~~a~~~~~~y~~-~~~p~~-~C~~CG~~~~----~~~~~CP~CGs~~~~~~~Rv 549 (555)
T cd01675 493 NPEALEALVKKAAKRGVIYFG-INTPID-ICNDCGYIGE----GEGFKCPKCGSEDVEVISRI 549 (555)
T ss_pred CHHHHHHHHHHHHHcCCceEE-EecCCc-cCCCCCCCCc----CCCCCCcCCCCcCceEEEee
Confidence 444555555554444344433 344455 9999997553 34579999999997776653
No 163
>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional
Probab=50.91 E-value=9.9 Score=27.93 Aligned_cols=34 Identities=24% Similarity=0.663 Sum_probs=25.9
Q ss_pred cceeecCCCCccccccccCCcCCCccceeecccccc
Q 024406 63 VKQVICSVCDTEQPVAQVCTNCGVNMGEYFCDICKF 98 (268)
Q Consensus 63 ~~~v~C~~C~~~q~v~~~C~~Cg~~f~~y~C~~C~l 98 (268)
.....|..|+.+. -..|..|....+.|-|++|.|
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 3578888887642 236888888888999988876
No 164
>COG1656 Uncharacterized conserved protein [Function unknown]
Probab=50.72 E-value=11 Score=33.04 Aligned_cols=48 Identities=27% Similarity=0.436 Sum_probs=34.3
Q ss_pred cCCCCCCcchhhhhHHHHHHHHHHHhcCCCh-hhhcCeeEEEccCCCCccccceeE
Q 024406 191 YCCPICSKSVIDMSRTWKRIDEEIEATVMPE-DYRHKKVWILCNDCNDTTEVYFHI 245 (268)
Q Consensus 191 ~~CPiCrksi~~m~~~~~~lD~~i~~~pmP~-~y~~~~v~I~CnDC~~~s~~~~H~ 245 (268)
.+||.|+-.+...++ +.....+|| .|.+......|--|++.-+..-||
T Consensus 98 ~RCp~CN~~L~~vs~-------eev~~~Vp~~~~~~~~~f~~C~~CgkiYW~GsHw 146 (165)
T COG1656 98 SRCPECNGELEKVSR-------EEVKEKVPEKVYRNYEEFYRCPKCGKIYWKGSHW 146 (165)
T ss_pred ccCcccCCEeccCcH-------HHHhhccchhhhhcccceeECCCCcccccCchHH
Confidence 689999999986543 233334444 477767778899999988777776
No 165
>COG5222 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=49.39 E-value=12 Score=36.05 Aligned_cols=44 Identities=32% Similarity=0.704 Sum_probs=34.3
Q ss_pred CCCchhhhhhcccCCcceEeccCCccChHHHHHHHHcCCCcCCCCCCc
Q 024406 151 HHCPICYEYLFDSLRNTTVMKCGHTMHCECYHEMIKRDNRYCCPICSK 198 (268)
Q Consensus 151 ~~CpICle~lf~s~~~v~~LpCGH~~H~~C~~~~~~~~~~~~CPiCrk 198 (268)
..||.|.--|- .+++.--|||.|..+||..-|-.+ .+.||.|..
T Consensus 275 LkCplc~~Llr---np~kT~cC~~~fc~eci~~al~ds-Df~CpnC~r 318 (427)
T COG5222 275 LKCPLCHCLLR---NPMKTPCCGHTFCDECIGTALLDS-DFKCPNCSR 318 (427)
T ss_pred ccCcchhhhhh---CcccCccccchHHHHHHhhhhhhc-cccCCCccc
Confidence 67999987543 366666689999999999755444 499999987
No 166
>PRK00415 rps27e 30S ribosomal protein S27e; Reviewed
Probab=49.29 E-value=9.2 Score=28.07 Aligned_cols=34 Identities=32% Similarity=0.546 Sum_probs=24.7
Q ss_pred eeecCCCCccccc------cccCCcCCCccceeecccccc
Q 024406 65 QVICSVCDTEQPV------AQVCTNCGVNMGEYFCDICKF 98 (268)
Q Consensus 65 ~v~C~~C~~~q~v------~~~C~~Cg~~f~~y~C~~C~l 98 (268)
.|.|..|..+|.+ ...|..||..+++-.=.+-+|
T Consensus 11 ~VkCp~C~n~q~vFsha~t~V~C~~Cg~~L~~PtGGKa~i 50 (59)
T PRK00415 11 KVKCPDCGNEQVVFSHASTVVRCLVCGKTLAEPTGGKAKI 50 (59)
T ss_pred EEECCCCCCeEEEEecCCcEEECcccCCCcccCCCcceee
Confidence 6889999988866 247889988887655444444
No 167
>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 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=48.12 E-value=23 Score=25.25 Aligned_cols=47 Identities=19% Similarity=0.429 Sum_probs=31.2
Q ss_pred HHHHHHHHhcCCChhhhcCeeEEEccCCCCcc----ccceeEeeecCCCCCCcc
Q 024406 208 KRIDEEIEATVMPEDYRHKKVWILCNDCNDTT----EVYFHIIGQKCSHCKSYN 257 (268)
Q Consensus 208 ~~lD~~i~~~pmP~~y~~~~v~I~CnDC~~~s----~~~~H~lg~kC~~C~SyN 257 (268)
+.||.++..-|+.++ + +--+.|.-|.... ...|-.|--+|+.|+..|
T Consensus 4 ki~d~L~G~d~~~~~--~-r~aLIC~~C~~hNGla~~~~~~~i~y~C~~Cg~~N 54 (54)
T PF10058_consen 4 KILDVLLGDDPTSPS--N-RYALICSKCFSHNGLAPKEEFEEIQYRCPYCGALN 54 (54)
T ss_pred HHHHHHhCCCCcccc--C-ceeEECcccchhhcccccccCCceEEEcCCCCCcC
Confidence 467777777774443 2 3345699998644 233445577999999987
No 169
>KOG3053 consensus Uncharacterized conserved protein [Function unknown]
Probab=47.84 E-value=6.4 Score=36.97 Aligned_cols=70 Identities=26% Similarity=0.496 Sum_probs=45.1
Q ss_pred CCCCCCCchhhhhhcccCCcceEecc---C--CccChHHHHHHHHcC------CCcCCCCCCcchh----hhh---HHHH
Q 024406 147 NSMHHHCPICYEYLFDSLRNTTVMKC---G--HTMHCECYHEMIKRD------NRYCCPICSKSVI----DMS---RTWK 208 (268)
Q Consensus 147 ~~~~~~CpICle~lf~s~~~v~~LpC---G--H~~H~~C~~~~~~~~------~~~~CPiCrksi~----~m~---~~~~ 208 (268)
...+.-|=||++.=.+.+...-+=|| | |..|..|+..|+... +.-.||.|+.... .|. ..-+
T Consensus 17 ~e~eR~CWiCF~TdeDn~~a~WV~PCrCRGt~KWVHqsCL~rWiDEK~~~n~~q~V~C~QCqTEYiiv~P~l~~~~~~Le 96 (293)
T KOG3053|consen 17 QELERCCWICFATDEDNRLAAWVHPCRCRGTTKWVHQSCLSRWIDEKQRGNPLQTVSCPQCQTEYIIVFPQLGPFDRVLE 96 (293)
T ss_pred cccceeEEEEeccCcccchhhhcccccccCccHHHHHHHHHHHHhHHhcCCCCceeechhhcchheeeccccChHHHHHH
Confidence 34567899999853333333344566 3 999999999999653 3457999997653 222 2335
Q ss_pred HHHHHHHh
Q 024406 209 RIDEEIEA 216 (268)
Q Consensus 209 ~lD~~i~~ 216 (268)
++|..|..
T Consensus 97 ~~d~~i~r 104 (293)
T KOG3053|consen 97 RLDILIFR 104 (293)
T ss_pred HhhhHHhh
Confidence 66666554
No 170
>PF05290 Baculo_IE-1: Baculovirus immediate-early protein (IE-0); InterPro: IPR007954 This entry contains the Baculovirus immediate-early protein IE-0.
Probab=46.92 E-value=12 Score=31.94 Aligned_cols=49 Identities=29% Similarity=0.593 Sum_probs=34.4
Q ss_pred CCCchhhhhhcccCCcceEe-c---cCCccChHHHHHHHHcC-CCcCCCCCCcchhhh
Q 024406 151 HHCPICYEYLFDSLRNTTVM-K---CGHTMHCECYHEMIKRD-NRYCCPICSKSVIDM 203 (268)
Q Consensus 151 ~~CpICle~lf~s~~~v~~L-p---CGH~~H~~C~~~~~~~~-~~~~CPiCrksi~~m 203 (268)
-+|-||.|- |. +.+.| | ||=.+...|+..+-+.. -...||+|+.|+-..
T Consensus 81 YeCnIC~et---S~-ee~FLKPneCCgY~iCn~Cya~LWK~~~~ypvCPvCkTSFKss 134 (140)
T PF05290_consen 81 YECNICKET---SA-EERFLKPNECCGYSICNACYANLWKFCNLYPVCPVCKTSFKSS 134 (140)
T ss_pred eeccCcccc---cc-hhhcCCcccccchHHHHHHHHHHHHHcccCCCCCccccccccc
Confidence 468888874 32 34555 3 89999999998854432 236799999998643
No 171
>PF15353 HECA: Headcase protein family homologue
Probab=46.49 E-value=10 Score=31.00 Aligned_cols=17 Identities=29% Similarity=0.608 Sum_probs=14.4
Q ss_pred ccCCccChHHHHHHHHc
Q 024406 171 KCGHTMHCECYHEMIKR 187 (268)
Q Consensus 171 pCGH~~H~~C~~~~~~~ 187 (268)
|-|+.||+.||++|-.+
T Consensus 39 p~~~~MH~~CF~~wE~~ 55 (107)
T PF15353_consen 39 PFGQYMHRECFEKWEDS 55 (107)
T ss_pred CCCCchHHHHHHHHHHH
Confidence 44999999999999754
No 172
>PHA00626 hypothetical protein
Probab=46.45 E-value=13 Score=27.26 Aligned_cols=29 Identities=24% Similarity=0.673 Sum_probs=19.7
Q ss_pred cCCcCCCc-cceeeccccccccCCCCcCeeecCCCCc
Q 024406 80 VCTNCGVN-MGEYFCDICKFYDDDIEKGQFHCDDCGI 115 (268)
Q Consensus 80 ~C~~Cg~~-f~~y~C~~C~l~d~~~~k~~yHC~~Cgi 115 (268)
.||+||.. . +-|.+|+.+. +.|-|++||.
T Consensus 2 ~CP~CGS~~I--vrcg~cr~~s-----nrYkCkdCGY 31 (59)
T PHA00626 2 SCPKCGSGNI--AKEKTMRGWS-----DDYVCCDCGY 31 (59)
T ss_pred CCCCCCCcee--eeeceecccC-----cceEcCCCCC
Confidence 58888873 3 2677777664 4577887775
No 173
>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=46.44 E-value=14 Score=34.32 Aligned_cols=48 Identities=25% Similarity=0.603 Sum_probs=22.8
Q ss_pred cceeecCCCCccccc-cccCCcCCCccceeeccccccc--cCCCCcCeeecCCCC
Q 024406 63 VKQVICSVCDTEQPV-AQVCTNCGVNMGEYFCDICKFY--DDDIEKGQFHCDDCG 114 (268)
Q Consensus 63 ~~~v~C~~C~~~q~v-~~~C~~Cg~~f~~y~C~~C~l~--d~~~~k~~yHC~~Cg 114 (268)
.+-..|+.|+++-.+ -..|++||..-..-+ .+| ++++.-.++-|+.||
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 368999999999876 468999998765533 223 333444555555554
No 174
>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=46.39 E-value=6.6 Score=42.26 Aligned_cols=44 Identities=30% Similarity=0.729 Sum_probs=0.0
Q ss_pred cCCcCCCccceeeccccccccCCCCcCeeecCCCCcccccCccceeecCccCc
Q 024406 80 VCTNCGVNMGEYFCDICKFYDDDIEKGQFHCDDCGICRIGGRENYFHCKRCGS 132 (268)
Q Consensus 80 ~C~~Cg~~f~~y~C~~C~l~d~~~~k~~yHC~~CgiCR~G~~~~ffHC~~C~~ 132 (268)
.|++||..--.-.|+.|.-.. ...|.|+.||+ ++.. .+|.+||.
T Consensus 657 ~Cp~Cg~~t~~~~Cp~CG~~T----~~~~~Cp~C~~-~~~~----~~C~~C~~ 700 (900)
T PF03833_consen 657 RCPKCGKETFYNRCPECGSHT----EPVYVCPDCGI-EVEE----DECPKCGR 700 (900)
T ss_dssp -----------------------------------------------------
T ss_pred cCcccCCcchhhcCcccCCcc----ccceecccccc-ccCc----cccccccc
Confidence 577777776666677775543 46778887776 2221 16777764
No 175
>PF09723 Zn-ribbon_8: Zinc ribbon domain; InterPro: IPR013429 This entry represents a region of about 41 amino acids found in a number of small proteins in a wide range of bacteria. The region usually begins with the initiator Met and contains two CxxC motifs separated by 17 amino acids. One protein in this entry has been noted as a putative regulatory protein, designated FmdB []. Most proteins in this entry have a C-terminal region containing highly degenerate sequence.
Probab=44.32 E-value=19 Score=24.12 Aligned_cols=32 Identities=28% Similarity=0.491 Sum_probs=21.3
Q ss_pred EEEccCCCCccccceeE---eeecCCCCCCccccc
Q 024406 229 WILCNDCNDTTEVYFHI---IGQKCSHCKSYNTRS 260 (268)
Q Consensus 229 ~I~CnDC~~~s~~~~H~---lg~kC~~C~SyNT~~ 260 (268)
...|.+||...++-..+ ....|+.||+-+.++
T Consensus 5 ey~C~~Cg~~fe~~~~~~~~~~~~CP~Cg~~~~~r 39 (42)
T PF09723_consen 5 EYRCEECGHEFEVLQSISEDDPVPCPECGSTEVRR 39 (42)
T ss_pred EEEeCCCCCEEEEEEEcCCCCCCcCCCCCCCceEE
Confidence 46799999766554332 346899999955443
No 176
>COG3809 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=44.19 E-value=16 Score=28.58 Aligned_cols=52 Identities=31% Similarity=0.540 Sum_probs=33.6
Q ss_pred CCCchhhhhhcccCCcceEeccCCccChHHHHHHHHcCCCcCCCCCCcchhhhhHHHHHHHHHHHhc--CCChhhhcC
Q 024406 151 HHCPICYEYLFDSLRNTTVMKCGHTMHCECYHEMIKRDNRYCCPICSKSVIDMSRTWKRIDEEIEAT--VMPEDYRHK 226 (268)
Q Consensus 151 ~~CpICle~lf~s~~~v~~LpCGH~~H~~C~~~~~~~~~~~~CPiCrksi~~m~~~~~~lD~~i~~~--pmP~~y~~~ 226 (268)
..||||--+|-.+...-+. -..||-||-.-+|.. .||.+|+.. |-|.+|+..
T Consensus 2 llCP~C~v~l~~~~rs~vE--------------------iD~CPrCrGVWLDrG----ELdKli~r~r~pqpa~ys~~ 55 (88)
T COG3809 2 LLCPICGVELVMSVRSGVE--------------------IDYCPRCRGVWLDRG----ELDKLIERSRYPQPAEYSQP 55 (88)
T ss_pred cccCcCCceeeeeeecCce--------------------eeeCCccccEeecch----hHHHHHHHhcCCCCcccCCc
Confidence 3699998887665332211 267999998777763 577777665 556666543
No 177
>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=43.42 E-value=12 Score=27.85 Aligned_cols=13 Identities=38% Similarity=0.738 Sum_probs=11.9
Q ss_pred ecCCCCCCccccc
Q 024406 248 QKCSHCKSYNTRS 260 (268)
Q Consensus 248 ~kC~~C~SyNT~~ 260 (268)
++|+.|.|.||+.
T Consensus 6 ~~CPRC~S~nTKF 18 (63)
T PF02701_consen 6 LPCPRCDSTNTKF 18 (63)
T ss_pred CCCCCcCCCCCEE
Confidence 6999999999986
No 178
>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=43.19 E-value=6.2 Score=25.92 Aligned_cols=27 Identities=33% Similarity=0.671 Sum_probs=13.7
Q ss_pred cCCcCCCccceeeccccccccCCCCcCeeecCCCCc
Q 024406 80 VCTNCGVNMGEYFCDICKFYDDDIEKGQFHCDDCGI 115 (268)
Q Consensus 80 ~C~~Cg~~f~~y~C~~C~l~d~~~~k~~yHC~~Cgi 115 (268)
.|++||+.++.+| ++.|..=-||.||-
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 3566666665443 23454555666654
No 179
>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=42.73 E-value=22 Score=23.65 Aligned_cols=8 Identities=50% Similarity=1.315 Sum_probs=4.1
Q ss_pred cCCcCCCc
Q 024406 80 VCTNCGVN 87 (268)
Q Consensus 80 ~C~~Cg~~ 87 (268)
.||+||..
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 180
>KOG1312 consensus DHHC-type Zn-finger proteins [General function prediction only]
Probab=42.44 E-value=8.3 Score=36.85 Aligned_cols=32 Identities=31% Similarity=0.782 Sum_probs=28.2
Q ss_pred CCCCcccccCccceeecCccCccccccccCcceee
Q 024406 111 DDCGICRIGGRENYFHCKRCGSCYSTSLRNNHLCI 145 (268)
Q Consensus 111 ~~CgiCR~G~~~~ffHC~~C~~C~s~~l~~~H~C~ 145 (268)
.+|..|++.+.-...||..||.|+.+- .|.|+
T Consensus 149 ~kCSTCki~KPARSKHCsiCNrCV~rf---DHHCi 180 (341)
T KOG1312|consen 149 VKCSTCKIRKPARSKHCSICNRCVHRF---DHHCI 180 (341)
T ss_pred CccccccCCCccccccchHHHHHHHHh---ccceE
Confidence 579999999988899999999999864 78886
No 181
>PF13453 zf-TFIIB: Transcription factor zinc-finger
Probab=42.06 E-value=22 Score=23.47 Aligned_cols=26 Identities=23% Similarity=0.579 Sum_probs=14.6
Q ss_pred cCCcCCCccceeeccccccccCCCCcCeeecCCCC
Q 024406 80 VCTNCGVNMGEYFCDICKFYDDDIEKGQFHCDDCG 114 (268)
Q Consensus 80 ~C~~Cg~~f~~y~C~~C~l~d~~~~k~~yHC~~Cg 114 (268)
.||.|+..|..+. + .+-.++.|+.||
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 3677776665442 1 124566666665
No 182
>TIGR01031 rpmF_bact ribosomal protein L32. This protein describes bacterial ribosomal protein L32. The noise cutoff is set low enough to include the equivalent protein from mitochondria and chloroplasts. No related proteins from the Archaea nor from the eukaryotic cytosol are detected by this model. This model is a fragment model; the putative L32 of some species shows similarity only toward the N-terminus.
Probab=41.61 E-value=22 Score=25.49 Aligned_cols=29 Identities=24% Similarity=0.752 Sum_probs=22.1
Q ss_pred eEEEccCCCCccccceeEeeecCCCCCCcccccc
Q 024406 228 VWILCNDCNDTTEVYFHIIGQKCSHCKSYNTRSI 261 (268)
Q Consensus 228 v~I~CnDC~~~s~~~~H~lg~kC~~C~SyNT~~~ 261 (268)
..+.|..||+. ...| +-|+.||.|+-+++
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 35779999973 4455 45999999998875
No 183
>PRK03564 formate dehydrogenase accessory protein FdhE; Provisional
Probab=41.58 E-value=26 Score=33.54 Aligned_cols=23 Identities=35% Similarity=1.003 Sum_probs=16.9
Q ss_pred EEEccCCCCccccceeEeeecCCCCCC
Q 024406 229 WILCNDCNDTTEVYFHIIGQKCSHCKS 255 (268)
Q Consensus 229 ~I~CnDC~~~s~~~~H~lg~kC~~C~S 255 (268)
...|+-|+ ..+|+.-.||++||+
T Consensus 212 yL~CslC~----teW~~~R~~C~~Cg~ 234 (309)
T PRK03564 212 YLHCNLCE----SEWHVVRVKCSNCEQ 234 (309)
T ss_pred EEEcCCCC----CcccccCccCCCCCC
Confidence 57787777 567777778888874
No 184
>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=41.51 E-value=23 Score=25.31 Aligned_cols=35 Identities=26% Similarity=0.445 Sum_probs=21.3
Q ss_pred EEEccCCCCcccc--ceeEeeecCCCCCCccccccCC
Q 024406 229 WILCNDCNDTTEV--YFHIIGQKCSHCKSYNTRSIAP 263 (268)
Q Consensus 229 ~I~CnDC~~~s~~--~~H~lg~kC~~C~SyNT~~~~~ 263 (268)
.|.|-.|++.-.. .+-.|-.||+.|+..|.-....
T Consensus 4 eiRC~~CnklLa~~g~~~~leIKCpRC~tiN~~~a~~ 40 (51)
T PF10122_consen 4 EIRCGHCNKLLAKAGEVIELEIKCPRCKTINHVRATS 40 (51)
T ss_pred ceeccchhHHHhhhcCccEEEEECCCCCccceEeccC
Confidence 3556666642211 2335677999999988766543
No 185
>KOG2907 consensus RNA polymerase I transcription factor TFIIS, subunit A12.2/RPA12 [Transcription]
Probab=41.26 E-value=9.6 Score=31.51 Aligned_cols=19 Identities=37% Similarity=0.835 Sum_probs=16.0
Q ss_pred EeeecCCCCC----CccccccCC
Q 024406 245 IIGQKCSHCK----SYNTRSIAP 263 (268)
Q Consensus 245 ~lg~kC~~C~----SyNT~~~~~ 263 (268)
.|-+||+.|| ||+|+|++-
T Consensus 72 ~I~~kCpkCghe~m~Y~T~QlRS 94 (116)
T KOG2907|consen 72 VIKHKCPKCGHEEMSYHTLQLRS 94 (116)
T ss_pred chhccCcccCCchhhhhhhhccc
Confidence 5678999997 899999974
No 186
>PRK00432 30S ribosomal protein S27ae; Validated
Probab=41.21 E-value=19 Score=25.22 Aligned_cols=9 Identities=44% Similarity=1.531 Sum_probs=5.1
Q ss_pred CeeecCCCC
Q 024406 106 GQFHCDDCG 114 (268)
Q Consensus 106 ~~yHC~~Cg 114 (268)
+.|+|..||
T Consensus 36 ~r~~C~~Cg 44 (50)
T PRK00432 36 DRWHCGKCG 44 (50)
T ss_pred CcEECCCcC
Confidence 455565555
No 187
>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=41.18 E-value=15 Score=22.60 Aligned_cols=20 Identities=20% Similarity=0.667 Sum_probs=6.1
Q ss_pred CCcccccCc-cceeecCccCc
Q 024406 113 CGICRIGGR-ENYFHCKRCGS 132 (268)
Q Consensus 113 CgiCR~G~~-~~ffHC~~C~~ 132 (268)
|.+|+..+. ..+++|..|+.
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 444544433 25666666664
No 188
>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=41.10 E-value=17 Score=25.29 Aligned_cols=12 Identities=33% Similarity=1.251 Sum_probs=6.7
Q ss_pred cCCCCCCcchhh
Q 024406 191 YCCPICSKSVID 202 (268)
Q Consensus 191 ~~CPiCrksi~~ 202 (268)
..||||.+++.+
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 189
>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=40.94 E-value=25 Score=23.25 Aligned_cols=34 Identities=29% Similarity=0.629 Sum_probs=16.2
Q ss_pred cCCcCCCccceeeccccccccCCCCcCeeecCCCC
Q 024406 80 VCTNCGVNMGEYFCDICKFYDDDIEKGQFHCDDCG 114 (268)
Q Consensus 80 ~C~~Cg~~f~~y~C~~C~l~d~~~~k~~yHC~~Cg 114 (268)
.|++||+.-+.|| .+=--=-|++..-.|.|-+||
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 100000234455666666665
No 190
>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=40.88 E-value=15 Score=30.62 Aligned_cols=48 Identities=25% Similarity=0.546 Sum_probs=34.6
Q ss_pred CCCccceeeccccccccCCCCcCeeecCCCCcccccCccceeecCccCcccccc
Q 024406 84 CGVNMGEYFCDICKFYDDDIEKGQFHCDDCGICRIGGRENYFHCKRCGSCYSTS 137 (268)
Q Consensus 84 Cg~~f~~y~C~~C~l~d~~~~k~~yHC~~CgiCR~G~~~~ffHC~~C~~C~s~~ 137 (268)
-+......+|..|+.+-- ....||..||.|..+- -.||.==|.|+...
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 3477888888887762 35777777777643
No 191
>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=40.51 E-value=20 Score=22.69 Aligned_cols=25 Identities=32% Similarity=0.894 Sum_probs=16.2
Q ss_pred eeeccccccccCCCCcCeeecCCCCc
Q 024406 90 EYFCDICKFYDDDIEKGQFHCDDCGI 115 (268)
Q Consensus 90 ~y~C~~C~l~d~~~~k~~yHC~~Cgi 115 (268)
.|-|.+|-+.=+ +.+.++.|+.||.
T Consensus 1 ~~~C~~CGy~y~-~~~~~~~CP~Cg~ 25 (33)
T cd00350 1 KYVCPVCGYIYD-GEEAPWVCPVCGA 25 (33)
T ss_pred CEECCCCCCEEC-CCcCCCcCcCCCC
Confidence 366777765532 3457888888875
No 192
>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=39.98 E-value=15 Score=31.38 Aligned_cols=16 Identities=25% Similarity=0.553 Sum_probs=14.4
Q ss_pred eecCCCCCCccccccC
Q 024406 247 GQKCSHCKSYNTRSIA 262 (268)
Q Consensus 247 g~kC~~C~SyNT~~~~ 262 (268)
...|+.|||-||++++
T Consensus 105 ~~~cp~c~s~~t~~~s 120 (146)
T TIGR02159 105 SVQCPRCGSADTTITS 120 (146)
T ss_pred CCcCCCCCCCCcEeec
Confidence 3699999999999986
No 193
>COG2051 RPS27A Ribosomal protein S27E [Translation, ribosomal structure and biogenesis]
Probab=39.46 E-value=13 Score=27.89 Aligned_cols=28 Identities=36% Similarity=0.692 Sum_probs=21.6
Q ss_pred ceeecCCCCccccc------cccCCcCCCcccee
Q 024406 64 KQVICSVCDTEQPV------AQVCTNCGVNMGEY 91 (268)
Q Consensus 64 ~~v~C~~C~~~q~v------~~~C~~Cg~~f~~y 91 (268)
-.|.|.-|+.+|.+ ...|..||..+++-
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 37889999999987 24799998877653
No 194
>PRK00420 hypothetical protein; Validated
Probab=39.26 E-value=19 Score=29.60 Aligned_cols=21 Identities=24% Similarity=0.594 Sum_probs=13.0
Q ss_pred cccCCcCCCccce-----eecccccc
Q 024406 78 AQVCTNCGVNMGE-----YFCDICKF 98 (268)
Q Consensus 78 ~~~C~~Cg~~f~~-----y~C~~C~l 98 (268)
+..||.||.+|.+ .||+.|.-
T Consensus 23 ~~~CP~Cg~pLf~lk~g~~~Cp~Cg~ 48 (112)
T PRK00420 23 SKHCPVCGLPLFELKDGEVVCPVHGK 48 (112)
T ss_pred cCCCCCCCCcceecCCCceECCCCCC
Confidence 3578888887643 55555543
No 195
>KOG2462 consensus C2H2-type Zn-finger protein [Transcription]
Probab=39.10 E-value=55 Score=31.02 Aligned_cols=115 Identities=24% Similarity=0.409 Sum_probs=68.1
Q ss_pred ccCCcCCCccceeec-cccccc-cCCCCcCeeecCCCCcccccC-------c--cceeecCccCcccccc-ccCcceeec
Q 024406 79 QVCTNCGVNMGEYFC-DICKFY-DDDIEKGQFHCDDCGICRIGG-------R--ENYFHCKRCGSCYSTS-LRNNHLCIE 146 (268)
Q Consensus 79 ~~C~~Cg~~f~~y~C-~~C~l~-d~~~~k~~yHC~~CgiCR~G~-------~--~~ffHC~~C~~C~s~~-l~~~H~C~e 146 (268)
-.|..||...+.+-= ++=|-+ -+-.+++.+.|..||.=.|-- + .--+-|..||-=.|.- |...|.=.-
T Consensus 131 ~~c~eCgk~ysT~snLsrHkQ~H~~~~s~ka~~C~~C~K~YvSmpALkMHirTH~l~c~C~iCGKaFSRPWLLQGHiRTH 210 (279)
T KOG2462|consen 131 YKCPECGKSYSTSSNLSRHKQTHRSLDSKKAFSCKYCGKVYVSMPALKMHIRTHTLPCECGICGKAFSRPWLLQGHIRTH 210 (279)
T ss_pred eeccccccccccccccchhhcccccccccccccCCCCCceeeehHHHhhHhhccCCCcccccccccccchHHhhcccccc
Confidence 467778887766540 000111 111348899999999876632 1 2356788888887753 333443322
Q ss_pred -CCCCCCCchhhhhhcccCCcceEeccCCccChHHHHHHHHcC---CCcCCCCCCcchhhhhHHHH
Q 024406 147 -NSMHHHCPICYEYLFDSLRNTTVMKCGHTMHCECYHEMIKRD---NRYCCPICSKSVIDMSRTWK 208 (268)
Q Consensus 147 -~~~~~~CpICle~lf~s~~~v~~LpCGH~~H~~C~~~~~~~~---~~~~CPiCrksi~~m~~~~~ 208 (268)
+.---.||+|--- |..+.. |..-++++ +.|.|+.|.|++.-|+-.-+
T Consensus 211 TGEKPF~C~hC~kA-FADRSN--------------LRAHmQTHS~~K~~qC~~C~KsFsl~SyLnK 261 (279)
T KOG2462|consen 211 TGEKPFSCPHCGKA-FADRSN--------------LRAHMQTHSDVKKHQCPRCGKSFALKSYLNK 261 (279)
T ss_pred cCCCCccCCcccch-hcchHH--------------HHHHHHhhcCCccccCcchhhHHHHHHHHHH
Confidence 1223478888876 544322 34444432 47999999999998875443
No 196
>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=36.80 E-value=11 Score=25.74 Aligned_cols=40 Identities=25% Similarity=0.629 Sum_probs=28.0
Q ss_pred CchhhhhhcccCCcceEeccCCccChHHHHHHHHcCCCcCCCCCCcchhhhh
Q 024406 153 CPICYEYLFDSLRNTTVMKCGHTMHCECYHEMIKRDNRYCCPICSKSVIDMS 204 (268)
Q Consensus 153 CpICle~lf~s~~~v~~LpCGH~~H~~C~~~~~~~~~~~~CPiCrksi~~m~ 204 (268)
|+.|.+.+... .+.+..=|..+|..| ++|-.|+++|.+.+
T Consensus 1 C~~C~~~I~~~--~~~~~~~~~~~H~~C----------f~C~~C~~~l~~~~ 40 (58)
T PF00412_consen 1 CARCGKPIYGT--EIVIKAMGKFWHPEC----------FKCSKCGKPLNDGD 40 (58)
T ss_dssp BTTTSSBESSS--SEEEEETTEEEETTT----------SBETTTTCBTTTSS
T ss_pred CCCCCCCccCc--EEEEEeCCcEEEccc----------cccCCCCCccCCCe
Confidence 66777776532 333346688999876 58999999987543
No 197
>PF13717 zinc_ribbon_4: zinc-ribbon domain
Probab=35.66 E-value=22 Score=23.10 Aligned_cols=10 Identities=40% Similarity=0.949 Sum_probs=5.6
Q ss_pred ceeecCCCCc
Q 024406 64 KQVICSVCDT 73 (268)
Q Consensus 64 ~~v~C~~C~~ 73 (268)
..|.|+.|++
T Consensus 24 ~~v~C~~C~~ 33 (36)
T PF13717_consen 24 RKVRCSKCGH 33 (36)
T ss_pred cEEECCCCCC
Confidence 4566665554
No 198
>KOG1311 consensus DHHC-type Zn-finger proteins [General function prediction only]
Probab=35.58 E-value=23 Score=32.87 Aligned_cols=35 Identities=26% Similarity=0.711 Sum_probs=21.4
Q ss_pred CcCCCccceeeccccccccCCCCcCeeecCCCCccccc
Q 024406 82 TNCGVNMGEYFCDICKFYDDDIEKGQFHCDDCGICRIG 119 (268)
Q Consensus 82 ~~Cg~~f~~y~C~~C~l~d~~~~k~~yHC~~CgiCR~G 119 (268)
..=|....-.||+.|+++-- +...||.-||.|-.+
T Consensus 105 ~~~~~~~~~~~C~~C~~~rP---pRs~HCsvC~~CV~r 139 (299)
T KOG1311|consen 105 DVNGIQVEWKYCDTCQLYRP---PRSSHCSVCNNCVLR 139 (299)
T ss_pred ccCCcccceEEcCcCcccCC---CCcccchhhcccccc
Confidence 33455667789999999832 344555555555443
No 199
>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=35.47 E-value=27 Score=23.44 Aligned_cols=20 Identities=25% Similarity=0.861 Sum_probs=11.7
Q ss_pred eecCCCCcccccCccceeecCccC
Q 024406 108 FHCDDCGICRIGGRENYFHCKRCG 131 (268)
Q Consensus 108 yHC~~CgiCR~G~~~~ffHC~~C~ 131 (268)
|+|+.|+. +++ ..+||..|.
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 567776663
No 200
>COG5183 SSM4 Protein involved in mRNA turnover and stability [RNA processing and modification]
Probab=34.73 E-value=20 Score=38.70 Aligned_cols=50 Identities=24% Similarity=0.507 Sum_probs=33.7
Q ss_pred CCCCchhhhhhcccCCcceEecc---C--CccChHHHHHHHHcCCCcCCCCCCcchh
Q 024406 150 HHHCPICYEYLFDSLRNTTVMKC---G--HTMHCECYHEMIKRDNRYCCPICSKSVI 201 (268)
Q Consensus 150 ~~~CpICle~lf~s~~~v~~LpC---G--H~~H~~C~~~~~~~~~~~~CPiCrksi~ 201 (268)
...|-||.-+=- . +..-.=|| | -.+|++|+.+|+..++.-+|-+|...+.
T Consensus 12 ~~~CRICr~e~~-~-d~pLfhPCKC~GSIkYiH~eCL~eW~~~s~~~kCdiChy~~~ 66 (1175)
T COG5183 12 KRSCRICRTEDI-R-DDPLFHPCKCSGSIKYIHRECLMEWMECSGTKKCDICHYEYK 66 (1175)
T ss_pred chhceeecCCCC-C-CCcCcccccccchhHHHHHHHHHHHHhcCCCcceeeecceee
Confidence 456777765411 1 11222244 3 6799999999999876788999987653
No 201
>PRK00366 ispG 4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase; Reviewed
Probab=34.32 E-value=54 Score=32.13 Aligned_cols=54 Identities=24% Similarity=0.501 Sum_probs=43.2
Q ss_pred CcCCCCCCcchhhhhHHHHHHHHHHHhcCCChhhhcCeeEEEc--cCCCCccccceeEee
Q 024406 190 RYCCPICSKSVIDMSRTWKRIDEEIEATVMPEDYRHKKVWILC--NDCNDTTEVYFHIIG 247 (268)
Q Consensus 190 ~~~CPiCrksi~~m~~~~~~lD~~i~~~pmP~~y~~~~v~I~C--nDC~~~s~~~~H~lg 247 (268)
--.||-|++...|+-..=..+|+.+...++| -+....=| |.|++.....+=+.|
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 3579999999999888778999999999998 34556779 999987777655544
No 202
>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=34.21 E-value=23 Score=22.48 Aligned_cols=23 Identities=26% Similarity=0.710 Sum_probs=10.4
Q ss_pred cCCcCCCccceeeccccccccCCCCcCeeecCCCC
Q 024406 80 VCTNCGVNMGEYFCDICKFYDDDIEKGQFHCDDCG 114 (268)
Q Consensus 80 ~C~~Cg~~f~~y~C~~C~l~d~~~~k~~yHC~~Cg 114 (268)
.|+.|+..++- .+..+|-|+.||
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 203
>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=33.92 E-value=20 Score=22.55 Aligned_cols=16 Identities=38% Similarity=1.028 Sum_probs=7.1
Q ss_pred CCcCCCccceeeccccc
Q 024406 81 CTNCGVNMGEYFCDICK 97 (268)
Q Consensus 81 C~~Cg~~f~~y~C~~C~ 97 (268)
|.-||. .++|-|+.|.
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 444444 5555555554
No 204
>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=33.72 E-value=26 Score=23.73 Aligned_cols=13 Identities=23% Similarity=0.772 Sum_probs=7.9
Q ss_pred cccCCcCCCccce
Q 024406 78 AQVCTNCGVNMGE 90 (268)
Q Consensus 78 ~~~C~~Cg~~f~~ 90 (268)
+..|+.||.++-+
T Consensus 17 ~~~Cp~C~~PL~~ 29 (41)
T PF06677_consen 17 DEHCPDCGTPLMR 29 (41)
T ss_pred cCccCCCCCeeEE
Confidence 3567777766643
No 205
>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=33.71 E-value=21 Score=25.81 Aligned_cols=34 Identities=24% Similarity=0.457 Sum_probs=18.7
Q ss_pred eeecCCCCccccc------cccCCcCCCccceeecccccc
Q 024406 65 QVICSVCDTEQPV------AQVCTNCGVNMGEYFCDICKF 98 (268)
Q Consensus 65 ~v~C~~C~~~q~v------~~~C~~Cg~~f~~y~C~~C~l 98 (268)
.|.|..|..+|.+ ...|..||..+++-.=.+-+|
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 5777777777776 236777777776654444333
No 206
>COG1645 Uncharacterized Zn-finger containing protein [General function prediction only]
Probab=33.51 E-value=22 Score=30.02 Aligned_cols=20 Identities=45% Similarity=1.243 Sum_probs=13.9
Q ss_pred cccCCcCCCcc----ceeeccccc
Q 024406 78 AQVCTNCGVNM----GEYFCDICK 97 (268)
Q Consensus 78 ~~~C~~Cg~~f----~~y~C~~C~ 97 (268)
+..|+.||.++ |+-||++|-
T Consensus 28 ~~hCp~Cg~PLF~KdG~v~CPvC~ 51 (131)
T COG1645 28 AKHCPKCGTPLFRKDGEVFCPVCG 51 (131)
T ss_pred HhhCcccCCcceeeCCeEECCCCC
Confidence 35788888887 555677764
No 207
>KOG0802 consensus E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=33.39 E-value=32 Score=35.03 Aligned_cols=44 Identities=23% Similarity=0.703 Sum_probs=34.9
Q ss_pred CCCCCCchhhhhhcccCCcceEeccCCccChHHHHHHHHcCCCcCCCCCCcchh
Q 024406 148 SMHHHCPICYEYLFDSLRNTTVMKCGHTMHCECYHEMIKRDNRYCCPICSKSVI 201 (268)
Q Consensus 148 ~~~~~CpICle~lf~s~~~v~~LpCGH~~H~~C~~~~~~~~~~~~CPiCrksi~ 201 (268)
..+.+|.||++.+ . .++-+|- |..|+.+|+... ..||+|++.+.
T Consensus 477 ~~~~~~~~~~~~~-~----~~~~~~~---~~~~l~~~~~~~--~~~pl~~~~~~ 520 (543)
T KOG0802|consen 477 EPNDVCAICYQEM-S----ARITPCS---HALCLRKWLYVQ--EVCPLCHTYMK 520 (543)
T ss_pred cccCcchHHHHHH-H----hcccccc---chhHHHhhhhhc--cccCCCchhhh
Confidence 4578999999998 2 3334454 999999999875 89999998875
No 208
>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=33.03 E-value=43 Score=33.79 Aligned_cols=46 Identities=28% Similarity=0.717 Sum_probs=29.7
Q ss_pred cceeecCCCCccccccccCCcCCCccc------eeeccccccccCCCCcCeeecCCCCcc
Q 024406 63 VKQVICSVCDTEQPVAQVCTNCGVNMG------EYFCDICKFYDDDIEKGQFHCDDCGIC 116 (268)
Q Consensus 63 ~~~v~C~~C~~~q~v~~~C~~Cg~~f~------~y~C~~C~l~d~~~~k~~yHC~~CgiC 116 (268)
.+.++|..|+.. ..|++|++.+. .-.|.-|.+- .+.+..|+.||-=
T Consensus 211 a~~~~C~~Cg~~----~~C~~C~~~l~~h~~~~~l~Ch~Cg~~----~~~~~~Cp~C~s~ 262 (505)
T TIGR00595 211 SKNLLCRSCGYI----LCCPNCDVSLTYHKKEGKLRCHYCGYQ----EPIPKTCPQCGSE 262 (505)
T ss_pred CCeeEhhhCcCc----cCCCCCCCceEEecCCCeEEcCCCcCc----CCCCCCCCCCCCC
Confidence 467889999865 57999998874 3345555432 2344566666643
No 209
>PF03833 PolC_DP2: DNA polymerase II large subunit DP2; InterPro: IPR016033 DP2 is the large subunit of a two-subunit novel archaebacterial replicative DNA polymerase first characterised for Pyrococcus furiosus. The structure of DP2 appears to be organised as a ~950 residue component separated from a ~300 residue component by a ~150 residue intein. The other subunit, DP1, has sequence similarity to the eukaryotic DNA polymerase delta small subunit. This entry represents the N-terminal ~950 residue component of DP2.; GO: 0003887 DNA-directed DNA polymerase activity; PDB: 3O59_X.
Probab=33.00 E-value=14 Score=39.81 Aligned_cols=47 Identities=26% Similarity=0.683 Sum_probs=0.0
Q ss_pred cceeecCCCCccccccccCCcCCCc-cceeeccccccccCCCCcCeeecCCCCc
Q 024406 63 VKQVICSVCDTEQPVAQVCTNCGVN-MGEYFCDICKFYDDDIEKGQFHCDDCGI 115 (268)
Q Consensus 63 ~~~v~C~~C~~~q~v~~~C~~Cg~~-f~~y~C~~C~l~d~~~~k~~yHC~~Cgi 115 (268)
+-.-.|..|+++ +....|+.||.. .-.|+|+.|+.--++. +|+.||.
T Consensus 653 i~~r~Cp~Cg~~-t~~~~Cp~CG~~T~~~~~Cp~C~~~~~~~-----~C~~C~~ 700 (900)
T PF03833_consen 653 IGRRRCPKCGKE-TFYNRCPECGSHTEPVYVCPDCGIEVEED-----ECPKCGR 700 (900)
T ss_dssp ------------------------------------------------------
T ss_pred eecccCcccCCc-chhhcCcccCCccccceeccccccccCcc-----ccccccc
Confidence 445679999987 777889999876 4578899997643321 7888884
No 210
>smart00661 RPOL9 RNA polymerase subunit 9.
Probab=32.53 E-value=36 Score=22.97 Aligned_cols=8 Identities=50% Similarity=1.510 Sum_probs=4.0
Q ss_pred eeecCCCC
Q 024406 107 QFHCDDCG 114 (268)
Q Consensus 107 ~yHC~~Cg 114 (268)
.|-|+.||
T Consensus 20 ~~vC~~Cg 27 (52)
T smart00661 20 RFVCRKCG 27 (52)
T ss_pred EEECCcCC
Confidence 44455544
No 211
>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=32.38 E-value=18 Score=26.24 Aligned_cols=28 Identities=36% Similarity=0.869 Sum_probs=20.6
Q ss_pred hcCeeEEEccCCCCccccceeEeeecCCCCC
Q 024406 224 RHKKVWILCNDCNDTTEVYFHIIGQKCSHCK 254 (268)
Q Consensus 224 ~~~~v~I~CnDC~~~s~~~~H~lg~kC~~C~ 254 (268)
++.+..|+|.-||. ..||+--..|..||
T Consensus 10 r~~ktH~~CrRCG~---~syH~qK~~CasCG 37 (55)
T PF01907_consen 10 RHNKTHTLCRRCGR---RSYHIQKKTCASCG 37 (55)
T ss_dssp S-S-SEEE-TTTSS---EEEETTTTEETTTB
T ss_pred cCCccEeeecccCC---eeeecCCCcccccC
Confidence 34568999999997 45787778899998
No 212
>PF12874 zf-met: Zinc-finger of C2H2 type; PDB: 1ZU1_A 2KVG_A.
Probab=32.27 E-value=23 Score=20.23 Aligned_cols=16 Identities=31% Similarity=0.696 Sum_probs=12.2
Q ss_pred cCCCCCCcchhhhhHH
Q 024406 191 YCCPICSKSVIDMSRT 206 (268)
Q Consensus 191 ~~CPiCrksi~~m~~~ 206 (268)
|.|.+|.+++.+...+
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 4699999999876543
No 213
>PF14952 zf-tcix: Putative treble-clef, zinc-finger, Zn-binding
Probab=32.19 E-value=22 Score=24.67 Aligned_cols=12 Identities=42% Similarity=1.046 Sum_probs=10.3
Q ss_pred cCCCCCCccccc
Q 024406 249 KCSHCKSYNTRS 260 (268)
Q Consensus 249 kC~~C~SyNT~~ 260 (268)
||+.||.||-.+
T Consensus 13 kCp~CGt~NG~R 24 (44)
T PF14952_consen 13 KCPKCGTYNGTR 24 (44)
T ss_pred cCCcCcCccCcc
Confidence 899999999654
No 214
>PF13719 zinc_ribbon_5: zinc-ribbon domain
Probab=31.85 E-value=27 Score=22.70 Aligned_cols=11 Identities=27% Similarity=0.751 Sum_probs=5.7
Q ss_pred ceeecCCCCcc
Q 024406 64 KQVICSVCDTE 74 (268)
Q Consensus 64 ~~v~C~~C~~~ 74 (268)
..|.|+.|++.
T Consensus 24 ~~vrC~~C~~~ 34 (37)
T PF13719_consen 24 RKVRCPKCGHV 34 (37)
T ss_pred cEEECCCCCcE
Confidence 35555555543
No 215
>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=31.32 E-value=34 Score=23.06 Aligned_cols=21 Identities=38% Similarity=0.917 Sum_probs=10.2
Q ss_pred eecCCCCcccccCccceeecCccC
Q 024406 108 FHCDDCGICRIGGRENYFHCKRCG 131 (268)
Q Consensus 108 yHC~~CgiCR~G~~~~ffHC~~C~ 131 (268)
|.|+.|+. -+-| ..|||.+|.
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 34555555 2222 466666554
No 216
>TIGR01562 FdhE formate dehydrogenase accessory protein FdhE. The only sequence scoring between trusted and noise is that from Aquifex aeolicus, which shows certain structural differences from the proteobacterial forms in the alignment. However it is notable that A. aeolicus also has a sequence scoring above trusted to the alpha subunit of formate dehydrogenase (TIGR01553).
Probab=30.66 E-value=46 Score=31.82 Aligned_cols=42 Identities=26% Similarity=0.698 Sum_probs=0.0
Q ss_pred CCCCCCcchhhhhHHHHHHHHHHHhcCCChhh-----hcCeeEEEccCCCCccccceeEeeecCCCCCC
Q 024406 192 CCPICSKSVIDMSRTWKRIDEEIEATVMPEDY-----RHKKVWILCNDCNDTTEVYFHIIGQKCSHCKS 255 (268)
Q Consensus 192 ~CPiCrksi~~m~~~~~~lD~~i~~~pmP~~y-----~~~~v~I~CnDC~~~s~~~~H~lg~kC~~C~S 255 (268)
.||+|+ ..|+=... .+..-...|+-|+ ..+|+.-.||++|++
T Consensus 186 ~CPvCG------------------s~P~~s~~~~~~~~~G~RyL~CslC~----teW~~~R~~C~~Cg~ 232 (305)
T TIGR01562 186 LCPACG------------------SPPVASMVRQGGKETGLRYLSCSLCA----TEWHYVRVKCSHCEE 232 (305)
T ss_pred cCCCCC------------------ChhhhhhhcccCCCCCceEEEcCCCC----CcccccCccCCCCCC
No 217
>PRK03564 formate dehydrogenase accessory protein FdhE; Provisional
Probab=30.32 E-value=57 Score=31.28 Aligned_cols=26 Identities=27% Similarity=0.753 Sum_probs=21.3
Q ss_pred ccceeecCCCCccccc-cccCCcCCCc
Q 024406 62 DVKQVICSVCDTEQPV-AQVCTNCGVN 87 (268)
Q Consensus 62 ~~~~v~C~~C~~~q~v-~~~C~~Cg~~ 87 (268)
..+-..|+.|+++-.+ -..|++||..
T Consensus 209 G~RyL~CslC~teW~~~R~~C~~Cg~~ 235 (309)
T PRK03564 209 GLRYLHCNLCESEWHVVRVKCSNCEQS 235 (309)
T ss_pred CceEEEcCCCCCcccccCccCCCCCCC
Confidence 3468999999999876 4689999964
No 218
>smart00355 ZnF_C2H2 zinc finger.
Probab=30.29 E-value=50 Score=17.95 Aligned_cols=15 Identities=40% Similarity=0.773 Sum_probs=11.6
Q ss_pred cCCCCCCcchhhhhH
Q 024406 191 YCCPICSKSVIDMSR 205 (268)
Q Consensus 191 ~~CPiCrksi~~m~~ 205 (268)
+.|+.|.+++...+.
T Consensus 1 ~~C~~C~~~f~~~~~ 15 (26)
T smart00355 1 YRCPECGKVFKSKSA 15 (26)
T ss_pred CCCCCCcchhCCHHH
Confidence 579999999876544
No 219
>KOG4185 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=30.00 E-value=11 Score=34.80 Aligned_cols=50 Identities=26% Similarity=0.523 Sum_probs=37.9
Q ss_pred CCCCchhhhhhcc--cCCcceEec--------cCCccChHHHHHHHHcCCCcCCCCCCcch
Q 024406 150 HHHCPICYEYLFD--SLRNTTVMK--------CGHTMHCECYHEMIKRDNRYCCPICSKSV 200 (268)
Q Consensus 150 ~~~CpICle~lf~--s~~~v~~Lp--------CGH~~H~~C~~~~~~~~~~~~CPiCrksi 200 (268)
+..|.||...+.. ....-.+|. |||++-..|.+..+... ..+||.|++..
T Consensus 207 ~~~c~ic~~~~~~n~~~~~p~vl~~~~~~~~~c~htlc~~c~~~~l~~~-~~~cp~~~~~~ 266 (296)
T KOG4185|consen 207 EKLCEICERIYSENDEKLAPLVLSLSRLKEKIEGHTLCKECIDTILLQA-GIKCPFCTWSH 266 (296)
T ss_pred HHHHHHHHHHhhccccccchhHHHHHHHHHHHHHHHHHhcchHHHHHHh-hhcCCccccee
Confidence 3569999987652 222334566 99999999999998766 48999999864
No 220
>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]
Probab=29.94 E-value=32 Score=25.44 Aligned_cols=34 Identities=24% Similarity=0.574 Sum_probs=21.6
Q ss_pred cceeecCCCCccccccccCCcCCCccceeecccccc
Q 024406 63 VKQVICSVCDTEQPVAQVCTNCGVNMGEYFCDICKF 98 (268)
Q Consensus 63 ~~~v~C~~C~~~q~v~~~C~~Cg~~f~~y~C~~C~l 98 (268)
.....|..|+.++-. .|..|...=+.|-|++|-|
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 346667777754332 5666777777777777765
No 221
>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=29.86 E-value=37 Score=23.62 Aligned_cols=22 Identities=50% Similarity=1.284 Sum_probs=9.5
Q ss_pred eecCCCCcccccCccceeecCccC
Q 024406 108 FHCDDCGICRIGGRENYFHCKRCG 131 (268)
Q Consensus 108 yHC~~CgiCR~G~~~~ffHC~~C~ 131 (268)
|.|+.||.--+-| --|||..|.
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 3455555433322 235555443
No 222
>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=29.86 E-value=53 Score=20.96 Aligned_cols=27 Identities=33% Similarity=0.587 Sum_probs=18.0
Q ss_pred EEEccCCCCccccceeE---eeecCCCCCC
Q 024406 229 WILCNDCNDTTEVYFHI---IGQKCSHCKS 255 (268)
Q Consensus 229 ~I~CnDC~~~s~~~~H~---lg~kC~~C~S 255 (268)
...|.+|+...++..-+ ....|+.||+
T Consensus 5 ~y~C~~Cg~~fe~~~~~~~~~~~~CP~Cg~ 34 (41)
T smart00834 5 EYRCEDCGHTFEVLQKISDDPLATCPECGG 34 (41)
T ss_pred EEEcCCCCCEEEEEEecCCCCCCCCCCCCC
Confidence 46788888866544322 2467999998
No 223
>PRK04136 rpl40e 50S ribosomal protein L40e; Provisional
Probab=29.81 E-value=34 Score=24.16 Aligned_cols=24 Identities=33% Similarity=0.875 Sum_probs=20.0
Q ss_pred cceeecCCCCccccc-cccCCcCCC
Q 024406 63 VKQVICSVCDTEQPV-AQVCTNCGV 86 (268)
Q Consensus 63 ~~~v~C~~C~~~q~v-~~~C~~Cg~ 86 (268)
...+||+.|+...|+ +..|..||.
T Consensus 12 ~~k~ICrkC~ARnp~~A~~CRKCg~ 36 (48)
T PRK04136 12 FNKKICMRCNARNPWRATKCRKCGY 36 (48)
T ss_pred hcccchhcccCCCCccccccccCCC
Confidence 357899999999887 578999986
No 224
>PF14569 zf-UDP: Zinc-binding RING-finger; PDB: 1WEO_A.
Probab=29.59 E-value=61 Score=25.18 Aligned_cols=52 Identities=19% Similarity=0.385 Sum_probs=24.4
Q ss_pred CCCCCCchhhhhhcccCCcce---EeccCCccChHHHHHHHHcCCCcCCCCCCcch
Q 024406 148 SMHHHCPICYEYLFDSLRNTT---VMKCGHTMHCECYHEMIKRDNRYCCPICSKSV 200 (268)
Q Consensus 148 ~~~~~CpICle~lf~s~~~v~---~LpCGH~~H~~C~~~~~~~~~~~~CPiCrksi 200 (268)
...+.|-||.|++=...+.-. -.-|+-.+.+.||+--++.+ +..||.|+...
T Consensus 7 ~~~qiCqiCGD~VGl~~~Ge~FVAC~eC~fPvCr~CyEYErkeg-~q~CpqCkt~y 61 (80)
T PF14569_consen 7 LNGQICQICGDDVGLTENGEVFVACHECAFPVCRPCYEYERKEG-NQVCPQCKTRY 61 (80)
T ss_dssp -SS-B-SSS--B--B-SSSSB--S-SSS-----HHHHHHHHHTS--SB-TTT--B-
T ss_pred cCCcccccccCccccCCCCCEEEEEcccCCccchhHHHHHhhcC-cccccccCCCc
Confidence 456789999998744333322 24689999999998888877 68899999443
No 225
>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=29.54 E-value=38 Score=20.71 Aligned_cols=10 Identities=20% Similarity=0.610 Sum_probs=3.6
Q ss_pred ccCCcCCCcc
Q 024406 79 QVCTNCGVNM 88 (268)
Q Consensus 79 ~~C~~Cg~~f 88 (268)
+.|+.|+..+
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 3455565544
No 226
>PRK14873 primosome assembly protein PriA; Provisional
Probab=29.40 E-value=57 Score=34.35 Aligned_cols=28 Identities=29% Similarity=0.660 Sum_probs=20.5
Q ss_pred cccc-cceeecCCCCccccccccCCcCCCccce
Q 024406 59 VRQD-VKQVICSVCDTEQPVAQVCTNCGVNMGE 90 (268)
Q Consensus 59 ~r~~-~~~v~C~~C~~~q~v~~~C~~Cg~~f~~ 90 (268)
+|.. ...++|..|+.. ..|++|+..+.-
T Consensus 376 nRrGyap~l~C~~Cg~~----~~C~~C~~~L~~ 404 (665)
T PRK14873 376 PRRGYVPSLACARCRTP----ARCRHCTGPLGL 404 (665)
T ss_pred cCCCCCCeeEhhhCcCe----eECCCCCCceeE
Confidence 4442 467899999865 579999988863
No 227
>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=29.29 E-value=16 Score=33.91 Aligned_cols=30 Identities=17% Similarity=0.595 Sum_probs=16.7
Q ss_pred eEEEccCCCCccccceeEeeecCCCCCCcccccc
Q 024406 228 VWILCNDCNDTTEVYFHIIGQKCSHCKSYNTRSI 261 (268)
Q Consensus 228 v~I~CnDC~~~s~~~~H~lg~kC~~C~SyNT~~~ 261 (268)
-...|.-|+ ..+|+.-.+|++||+-+-..+
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 678888899999998776554
No 228
>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=29.10 E-value=40 Score=21.67 Aligned_cols=22 Identities=27% Similarity=0.757 Sum_probs=12.5
Q ss_pred eecCCCCcccc---ccccCCcCCCc
Q 024406 66 VICSVCDTEQP---VAQVCTNCGVN 87 (268)
Q Consensus 66 v~C~~C~~~q~---v~~~C~~Cg~~ 87 (268)
-+|..|+.... .-..||.||+.
T Consensus 3 ~~C~~CG~i~~g~~~p~~CP~Cg~~ 27 (34)
T cd00729 3 WVCPVCGYIHEGEEAPEKCPICGAP 27 (34)
T ss_pred EECCCCCCEeECCcCCCcCcCCCCc
Confidence 45667765422 22567777764
No 229
>KOG4317 consensus Predicted Zn-finger protein [Function unknown]
Probab=29.09 E-value=24 Score=34.16 Aligned_cols=21 Identities=38% Similarity=0.917 Sum_probs=16.4
Q ss_pred ccCCcCCCccceeeccccccc
Q 024406 79 QVCTNCGVNMGEYFCDICKFY 99 (268)
Q Consensus 79 ~~C~~Cg~~f~~y~C~~C~l~ 99 (268)
..|.-||+.+.+|.|+-|+|.
T Consensus 8 ~~C~ic~vq~~~YtCPRCn~~ 28 (383)
T KOG4317|consen 8 LACGICGVQKREYTCPRCNLL 28 (383)
T ss_pred eeccccccccccccCCCCCcc
Confidence 357778888888888888764
No 230
>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=29.05 E-value=43 Score=27.84 Aligned_cols=30 Identities=30% Similarity=0.791 Sum_probs=21.6
Q ss_pred CCcccccCccceeecCccCccccccccCcceee
Q 024406 113 CGICRIGGRENYFHCKRCGSCYSTSLRNNHLCI 145 (268)
Q Consensus 113 CgiCR~G~~~~ffHC~~C~~C~s~~l~~~H~C~ 145 (268)
|-.|++-....-.||..||.|+-.- +|.|.
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 3445555666789999999998764 67775
No 231
>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=29.02 E-value=33 Score=22.03 Aligned_cols=10 Identities=30% Similarity=1.066 Sum_probs=5.1
Q ss_pred cCeeecCCCC
Q 024406 105 KGQFHCDDCG 114 (268)
Q Consensus 105 k~~yHC~~Cg 114 (268)
.++-.|..||
T Consensus 15 ~~~irC~~CG 24 (32)
T PF03604_consen 15 GDPIRCPECG 24 (32)
T ss_dssp SSTSSBSSSS
T ss_pred CCcEECCcCC
Confidence 3444555555
No 232
>PRK03988 translation initiation factor IF-2 subunit beta; Validated
Probab=27.94 E-value=54 Score=27.76 Aligned_cols=10 Identities=30% Similarity=0.630 Sum_probs=4.8
Q ss_pred eeecCCCCCC
Q 024406 246 IGQKCSHCKS 255 (268)
Q Consensus 246 lg~kC~~C~S 255 (268)
+-++|..||+
T Consensus 122 ~~l~C~ACGa 131 (138)
T PRK03988 122 WVLKCEACGA 131 (138)
T ss_pred EEEEcccCCC
Confidence 3345555554
No 233
>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=27.86 E-value=46 Score=21.46 Aligned_cols=21 Identities=19% Similarity=0.363 Sum_probs=14.3
Q ss_pred ccCCcCCCccceeeccccccc
Q 024406 79 QVCTNCGVNMGEYFCDICKFY 99 (268)
Q Consensus 79 ~~C~~Cg~~f~~y~C~~C~l~ 99 (268)
..|..++....+|||.-|+.+
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 457777777788888877654
No 234
>COG1998 RPS31 Ribosomal protein S27AE [Translation, ribosomal structure and biogenesis]
Probab=27.63 E-value=35 Score=24.37 Aligned_cols=20 Identities=35% Similarity=0.968 Sum_probs=11.1
Q ss_pred cccCCcCC--Ccc----ceeeccccc
Q 024406 78 AQVCTNCG--VNM----GEYFCDICK 97 (268)
Q Consensus 78 ~~~C~~Cg--~~f----~~y~C~~C~ 97 (268)
...||+|| +-| .+|.|.+|.
T Consensus 19 ~~~CPrCG~gvfmA~H~dR~~CGkCg 44 (51)
T COG1998 19 NRFCPRCGPGVFMADHKDRWACGKCG 44 (51)
T ss_pred cccCCCCCCcchhhhcCceeEecccc
Confidence 35788888 333 345555543
No 235
>PF15616 TerY-C: TerY-C metal binding domain
Probab=27.28 E-value=56 Score=27.59 Aligned_cols=34 Identities=35% Similarity=0.805 Sum_probs=22.6
Q ss_pred cccCCcCCCccceeecccc-cccc-CCCCcCeeecCCCC
Q 024406 78 AQVCTNCGVNMGEYFCDIC-KFYD-DDIEKGQFHCDDCG 114 (268)
Q Consensus 78 ~~~C~~Cg~~f~~y~C~~C-~l~d-~~~~k~~yHC~~Cg 114 (268)
+.-||.||..+|---| -| ||+- +++ ....|+-||
T Consensus 77 ~PgCP~CGn~~~fa~C-~CGkl~Ci~g~--~~~~CPwCg 112 (131)
T PF15616_consen 77 APGCPHCGNQYAFAVC-GCGKLFCIDGE--GEVTCPWCG 112 (131)
T ss_pred CCCCCCCcChhcEEEe-cCCCEEEeCCC--CCEECCCCC
Confidence 3689999999998888 57 5553 211 245555555
No 236
>PRK07111 anaerobic ribonucleoside triphosphate reductase; Provisional
Probab=27.20 E-value=66 Score=34.32 Aligned_cols=53 Identities=17% Similarity=0.195 Sum_probs=31.7
Q ss_pred hHHHHHHHHHHHhcCCChhhhcCeeEEEccCCCCccccceeEeeecCCCCCCccccccCC
Q 024406 204 SRTWKRIDEEIEATVMPEDYRHKKVWILCNDCNDTTEVYFHIIGQKCSHCKSYNTRSIAP 263 (268)
Q Consensus 204 ~~~~~~lD~~i~~~pmP~~y~~~~v~I~CnDC~~~s~~~~H~lg~kC~~C~SyNT~~~~~ 263 (268)
++.+..++. +..+.+|-.--+.. .-.|++||.... +| .+||.|||-|+.++++
T Consensus 657 eal~~lvk~-~~~~~i~Y~sin~~-~~~C~~CG~~~~--~~---~~CP~CG~~~~~~~~R 709 (735)
T PRK07111 657 EAFEIIVKA-MKNTNIGYGSINHP-VDRCPVCGYLGV--IE---DKCPKCGSTNIQRIRR 709 (735)
T ss_pred HHHHHHHHH-HHhCCCceEEeCCC-CeecCCCCCCCC--cC---ccCcCCCCccceeeeh
Confidence 333333443 44555665422333 456999996443 23 6999999987766654
No 237
>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=27.18 E-value=44 Score=21.33 Aligned_cols=10 Identities=30% Similarity=0.737 Sum_probs=5.5
Q ss_pred eeecCCCCcc
Q 024406 65 QVICSVCDTE 74 (268)
Q Consensus 65 ~v~C~~C~~~ 74 (268)
.|.|+.|+++
T Consensus 25 ~v~C~~C~~~ 34 (38)
T TIGR02098 25 KVRCGKCGHV 34 (38)
T ss_pred EEECCCCCCE
Confidence 4556555544
No 238
>KOG3579 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=27.06 E-value=60 Score=31.18 Aligned_cols=61 Identities=28% Similarity=0.606 Sum_probs=45.2
Q ss_pred CCCCCchhhhhhcccCCcceEecc----CCccChHHHHHHHHcC---------CCcCCCCCCcchhhhhHHHHHHHHHHH
Q 024406 149 MHHHCPICYEYLFDSLRNTTVMKC----GHTMHCECYHEMIKRD---------NRYCCPICSKSVIDMSRTWKRIDEEIE 215 (268)
Q Consensus 149 ~~~~CpICle~lf~s~~~v~~LpC----GH~~H~~C~~~~~~~~---------~~~~CPiCrksi~~m~~~~~~lD~~i~ 215 (268)
...-|.+|.|.|- +.++..| +|-|.--|-.+-++.. +..+|||=...| -|..|.-||+
T Consensus 267 apLcCTLC~ERLE----DTHFVQCPSVp~HKFCFPCSResIK~Qg~sgevYCPSGdkCPLvgS~v-----PWAFMQGEIa 337 (352)
T KOG3579|consen 267 APLCCTLCHERLE----DTHFVQCPSVPSHKFCFPCSRESIKQQGASGEVYCPSGDKCPLVGSNV-----PWAFMQGEIA 337 (352)
T ss_pred Cceeehhhhhhhc----cCceeecCCCcccceecccCHHHHHhhcCCCceeCCCCCcCcccCCcc-----cHHHhhhhHH
Confidence 3468999999874 4577788 7999999999998742 246777654333 4999998998
Q ss_pred hcC
Q 024406 216 ATV 218 (268)
Q Consensus 216 ~~p 218 (268)
++-
T Consensus 338 tIL 340 (352)
T KOG3579|consen 338 TIL 340 (352)
T ss_pred HHh
Confidence 753
No 239
>PRK00464 nrdR transcriptional regulator NrdR; Validated
Probab=26.70 E-value=38 Score=29.16 Aligned_cols=12 Identities=25% Similarity=0.839 Sum_probs=6.1
Q ss_pred cCCcCCCcccee
Q 024406 80 VCTNCGVNMGEY 91 (268)
Q Consensus 80 ~C~~Cg~~f~~y 91 (268)
.|++||..|+.|
T Consensus 30 ~c~~c~~~f~~~ 41 (154)
T PRK00464 30 ECLACGKRFTTF 41 (154)
T ss_pred eccccCCcceEe
Confidence 355555555544
No 240
>KOG4399 consensus C2HC-type Zn-finger protein [General function prediction only]
Probab=26.47 E-value=13 Score=35.14 Aligned_cols=72 Identities=28% Similarity=0.669 Sum_probs=53.7
Q ss_pred CCccceeeccccccccCCCCcCeeecCCCCcccccCccceeecCccCccccccccCcceeecCCCCCCCchhhhh
Q 024406 85 GVNMGEYFCDICKFYDDDIEKGQFHCDDCGICRIGGRENYFHCKRCGSCYSTSLRNNHLCIENSMHHHCPICYEY 159 (268)
Q Consensus 85 g~~f~~y~C~~C~l~d~~~~k~~yHC~~CgiCR~G~~~~ffHC~~C~~C~s~~l~~~H~C~e~~~~~~CpICle~ 159 (268)
|..=+-.||+.|-.| ..+..-||+.|+.|..-.++.|-||.+|-.|+-.++-.--.|-.-+...-|-||.|+
T Consensus 199 ~~EE~~~~~~~~~~Y---v~~~~~H~~~~~S~~~~~~~~~~H~~~~~~~~~~~~i~C~~~~~~A~~~~C~iC~~~ 270 (325)
T KOG4399|consen 199 PTEEGYRFCSPCQRY---VSLENQHCEHCNSCTSKDGRKWNHCFLCKKCVKPSWIHCSICNHCAVKHGCFICGEL 270 (325)
T ss_pred ccccceEEEeehHHH---HHHHhhhchhhcccccchhHHHhHhHHhhhhcccceeeeecccchhhhcceeecccc
Confidence 444466789999988 457788999999998777778999999999998887432233333555678888875
No 241
>KOG3362 consensus Predicted BBOX Zn-finger protein [General function prediction only]
Probab=26.38 E-value=19 Score=31.12 Aligned_cols=25 Identities=28% Similarity=1.016 Sum_probs=18.4
Q ss_pred ceeeccccccccCCCCcCeeecCCCC--ccccc
Q 024406 89 GEYFCDICKFYDDDIEKGQFHCDDCG--ICRIG 119 (268)
Q Consensus 89 ~~y~C~~C~l~d~~~~k~~yHC~~Cg--iCR~G 119 (268)
.+-||.+|-+| ++|-|..|| +|-|+
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 46688888844 478888888 67666
No 242
>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=26.37 E-value=35 Score=22.34 Aligned_cols=25 Identities=32% Similarity=0.642 Sum_probs=19.6
Q ss_pred CCchhhhhhcccCCcceEe-ccCCcc
Q 024406 152 HCPICYEYLFDSLRNTTVM-KCGHTM 176 (268)
Q Consensus 152 ~CpICle~lf~s~~~v~~L-pCGH~~ 176 (268)
.|++|.+.+|.+.+...+- .|||.+
T Consensus 10 ~C~~C~~~~~~~~dG~~yC~~cG~~~ 35 (36)
T PF11781_consen 10 PCPVCGSRWFYSDDGFYYCDRCGHQS 35 (36)
T ss_pred cCCCCCCeEeEccCCEEEhhhCceEc
Confidence 3999999988877766665 889864
No 243
>KOG1100 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=26.03 E-value=25 Score=31.59 Aligned_cols=39 Identities=26% Similarity=0.531 Sum_probs=28.1
Q ss_pred CchhhhhhcccCCcceEeccCCccC-hHHHHHHHHcCCCcCCCCCCcchh
Q 024406 153 CPICYEYLFDSLRNTTVMKCGHTMH-CECYHEMIKRDNRYCCPICSKSVI 201 (268)
Q Consensus 153 CpICle~lf~s~~~v~~LpCGH~~H-~~C~~~~~~~~~~~~CPiCrksi~ 201 (268)
|-+|.+. ...|..|||-|..+ ..|-.. ...||+|+....
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 23588899998765 355432 267999997765
No 244
>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=25.81 E-value=44 Score=19.77 Aligned_cols=14 Identities=21% Similarity=0.610 Sum_probs=11.9
Q ss_pred cCCCCCCcchhhhh
Q 024406 191 YCCPICSKSVIDMS 204 (268)
Q Consensus 191 ~~CPiCrksi~~m~ 204 (268)
+.|++|.+.+.+..
T Consensus 2 ~~C~~C~k~f~~~~ 15 (27)
T PF12171_consen 2 FYCDACDKYFSSEN 15 (27)
T ss_dssp CBBTTTTBBBSSHH
T ss_pred CCcccCCCCcCCHH
Confidence 78999999998754
No 245
>COG5273 Uncharacterized protein containing DHHC-type Zn finger [General function prediction only]
Probab=25.68 E-value=32 Score=32.72 Aligned_cols=44 Identities=27% Similarity=0.596 Sum_probs=31.3
Q ss_pred ccCCcCCCccceeeccccccccCCCCcCeeecCCCCcccccCccceeecCccCccccccccCcceee
Q 024406 79 QVCTNCGVNMGEYFCDICKFYDDDIEKGQFHCDDCGICRIGGRENYFHCKRCGSCYSTSLRNNHLCI 145 (268)
Q Consensus 79 ~~C~~Cg~~f~~y~C~~C~l~d~~~~k~~yHC~~CgiCR~G~~~~ffHC~~C~~C~s~~l~~~H~C~ 145 (268)
..+...|....+-||.+|+.|-- +-.-||..||.|+-+- +|.|+
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 2366777788877653 67664
No 246
>PRK14810 formamidopyrimidine-DNA glycosylase; Provisional
Probab=25.63 E-value=38 Score=31.39 Aligned_cols=20 Identities=25% Similarity=0.858 Sum_probs=15.7
Q ss_pred cccCCcCCCcc--------ceeeccccc
Q 024406 78 AQVCTNCGVNM--------GEYFCDICK 97 (268)
Q Consensus 78 ~~~C~~Cg~~f--------~~y~C~~C~ 97 (268)
++.|+.||..+ +.|||+.|.
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 247
>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=25.52 E-value=41 Score=23.58 Aligned_cols=22 Identities=23% Similarity=0.883 Sum_probs=13.1
Q ss_pred ccccCC--cCCCc------cceeecccccc
Q 024406 77 VAQVCT--NCGVN------MGEYFCDICKF 98 (268)
Q Consensus 77 v~~~C~--~Cg~~------f~~y~C~~C~l 98 (268)
....|| .||.- ++|++|.+|.+
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 78773 26677777654
No 248
>PLN02189 cellulose synthase
Probab=25.44 E-value=62 Score=35.88 Aligned_cols=56 Identities=20% Similarity=0.422 Sum_probs=39.1
Q ss_pred ecCCCCCCCchhhhhhcccCCc--ceEe-ccCCccChHHHHHHHHcCCCcCCCCCCcchh
Q 024406 145 IENSMHHHCPICYEYLFDSLRN--TTVM-KCGHTMHCECYHEMIKRDNRYCCPICSKSVI 201 (268)
Q Consensus 145 ~e~~~~~~CpICle~lf~s~~~--v~~L-pCGH~~H~~C~~~~~~~~~~~~CPiCrksi~ 201 (268)
+++...+.|.||.|++-...+. -+.- -||=-+.+.||+-=.+.+ +..||-|+...-
T Consensus 29 ~~~~~~~~C~iCgd~vg~~~~g~~fvaC~~C~fpvCr~Cyeyer~eg-~q~CpqCkt~Y~ 87 (1040)
T PLN02189 29 LRNLDGQVCEICGDEIGLTVDGDLFVACNECGFPVCRPCYEYERREG-TQNCPQCKTRYK 87 (1040)
T ss_pred cccccCccccccccccCcCCCCCEEEeeccCCCccccchhhhhhhcC-CccCcccCCchh
Confidence 4555677999999997533222 2223 388889999994445555 789999997664
No 249
>PF12172 DUF35_N: Rubredoxin-like zinc ribbon domain (DUF35_N); InterPro: IPR022002 This domain has no known function and is found in conserved hypothetical archaeal and bacterial proteins. The domain is duplicated in O53566 from SWISSPROT. The structure of a DUF35 representative reveals two long N-terminal helices followed by a rubredoxin-like zinc ribbon domain represented in this family and a C-terminal OB fold domain. Zinc is chelated by the four conserved cysteines in the alignment. ; PDB: 3IRB_A.
Probab=25.16 E-value=31 Score=22.10 Aligned_cols=23 Identities=35% Similarity=0.752 Sum_probs=11.9
Q ss_pred ceeecCCCCccc-cccccCCcCCC
Q 024406 64 KQVICSVCDTEQ-PVAQVCTNCGV 86 (268)
Q Consensus 64 ~~v~C~~C~~~q-~v~~~C~~Cg~ 86 (268)
..-.|..|++.+ |+...|++||.
T Consensus 10 ~~~rC~~Cg~~~~pPr~~Cp~C~s 33 (37)
T PF12172_consen 10 LGQRCRDCGRVQFPPRPVCPHCGS 33 (37)
T ss_dssp EEEE-TTT--EEES--SEETTTT-
T ss_pred EEEEcCCCCCEecCCCcCCCCcCc
Confidence 355688888764 55677888864
No 250
>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=24.91 E-value=28 Score=23.02 Aligned_cols=13 Identities=54% Similarity=1.196 Sum_probs=5.5
Q ss_pred cceeecccccccc
Q 024406 88 MGEYFCDICKFYD 100 (268)
Q Consensus 88 f~~y~C~~C~l~d 100 (268)
|-+|||+-|+.|-
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 251
>PRK14892 putative transcription elongation factor Elf1; Provisional
Probab=24.88 E-value=66 Score=25.84 Aligned_cols=32 Identities=31% Similarity=0.664 Sum_probs=22.5
Q ss_pred cceeecCccC-ccccccccCcceeecCCCCCCCchhhhh
Q 024406 122 ENYFHCKRCG-SCYSTSLRNNHLCIENSMHHHCPICYEY 159 (268)
Q Consensus 122 ~~ffHC~~C~-~C~s~~l~~~H~C~e~~~~~~CpICle~ 159 (268)
..+|+|..|| .-+++.+. + +..+..||+|..+
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
>PRK08271 anaerobic ribonucleoside triphosphate reductase; Provisional
Probab=24.86 E-value=48 Score=34.73 Aligned_cols=55 Identities=20% Similarity=0.259 Sum_probs=32.2
Q ss_pred hhhHHHHHHHHHHHhcCCChhhhcCeeEEEccCCCCccccceeEeeecCCCCCCccccccC
Q 024406 202 DMSRTWKRIDEEIEATVMPEDYRHKKVWILCNDCNDTTEVYFHIIGQKCSHCKSYNTRSIA 262 (268)
Q Consensus 202 ~m~~~~~~lD~~i~~~pmP~~y~~~~v~I~CnDC~~~s~~~~H~lg~kC~~C~SyNT~~~~ 262 (268)
+.++.++.++.. ..+.+|-.--+ ...-.|++||..... .+..||.|||-|+.+++
T Consensus 541 n~eal~~lv~~~-~~~~i~Yf~in-~~~~iC~~CG~~~~g----~~~~CP~CGs~~~ev~~ 595 (623)
T PRK08271 541 SEEGYRKLLNIA-AKTGCNYFAFN-VKITICNDCHHIDKR----TGKRCPICGSENIDYYT 595 (623)
T ss_pred CHHHHHHHHHHH-HHcCCceEEeC-CCCccCCCCCCcCCC----CCcCCcCCCCcchhHHH
Confidence 444444444443 33555544222 234569999975322 45799999998866553
No 253
>PLN00209 ribosomal protein S27; Provisional
Probab=24.70 E-value=45 Score=26.30 Aligned_cols=36 Identities=19% Similarity=0.369 Sum_probs=27.4
Q ss_pred eeecCCCCccccc------cccCCcCCCccceeecccccccc
Q 024406 65 QVICSVCDTEQPV------AQVCTNCGVNMGEYFCDICKFYD 100 (268)
Q Consensus 65 ~v~C~~C~~~q~v------~~~C~~Cg~~f~~y~C~~C~l~d 100 (268)
.|.|..|..+|.| ...|..||..+++-.=.+.+|-+
T Consensus 36 ~VkCp~C~n~q~VFShA~t~V~C~~Cg~~L~~PTGGKa~l~~ 77 (86)
T PLN00209 36 DVKCQGCFNITTVFSHSQTVVVCGSCQTVLCQPTGGKARLTE 77 (86)
T ss_pred EEECCCCCCeeEEEecCceEEEccccCCEeeccCCCCeEecC
Confidence 7889999999887 24799999988776666665544
No 254
>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=24.55 E-value=1.3e+02 Score=28.56 Aligned_cols=46 Identities=20% Similarity=0.358 Sum_probs=26.1
Q ss_pred CCCCCCCchhhhhhcccCCcceEec-c-CCccChHHHHHHHHcCCCcCCC
Q 024406 147 NSMHHHCPICYEYLFDSLRNTTVMK-C-GHTMHCECYHEMIKRDNRYCCP 194 (268)
Q Consensus 147 ~~~~~~CpICle~lf~s~~~v~~Lp-C-GH~~H~~C~~~~~~~~~~~~CP 194 (268)
..+-..|+||+| |...+.+..-|. = .=-=|+.||++|--.- +-.||
T Consensus 27 ~~tLsfChiCfE-l~iegvpks~llHtkSlRGHrdCFEK~HlIa-nQ~~p 74 (285)
T PF06937_consen 27 TETLSFCHICFE-LSIEGVPKSNLLHTKSLRGHRDCFEKYHLIA-NQDCP 74 (285)
T ss_pred ccceeecceeec-cccccCccccccccccccchHHHHHHHHHHH-cCCCC
Confidence 344567888888 454433333221 1 0013899999994332 36888
No 255
>PTZ00083 40S ribosomal protein S27; Provisional
Probab=24.40 E-value=39 Score=26.56 Aligned_cols=36 Identities=19% Similarity=0.428 Sum_probs=26.4
Q ss_pred eeecCCCCccccc------cccCCcCCCccceeecccccccc
Q 024406 65 QVICSVCDTEQPV------AQVCTNCGVNMGEYFCDICKFYD 100 (268)
Q Consensus 65 ~v~C~~C~~~q~v------~~~C~~Cg~~f~~y~C~~C~l~d 100 (268)
.|.|..|..+|.| ...|..||..+++-.=.+.+|-+
T Consensus 35 ~VkCp~C~n~q~VFShA~t~V~C~~Cg~~L~~PTGGKa~l~~ 76 (85)
T PTZ00083 35 DVKCPGCSQITTVFSHAQTVVLCGGCSSQLCQPTGGKAKLTE 76 (85)
T ss_pred EEECCCCCCeeEEEecCceEEEccccCCEeeccCCCCeEecC
Confidence 7889999988887 24788898888776555555543
No 256
>TIGR00311 aIF-2beta translation initiation factor aIF-2, beta subunit, putative.
Probab=24.25 E-value=62 Score=27.21 Aligned_cols=12 Identities=17% Similarity=0.733 Sum_probs=5.6
Q ss_pred EEccCCCCcccc
Q 024406 230 ILCNDCNDTTEV 241 (268)
Q Consensus 230 I~CnDC~~~s~~ 241 (268)
+.|+.||+++.|
T Consensus 119 l~C~ACGa~~~v 130 (133)
T TIGR00311 119 LKCEACGAKAPL 130 (133)
T ss_pred EecccCCCCCcc
Confidence 345555544443
No 257
>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=24.24 E-value=71 Score=32.96 Aligned_cols=54 Identities=19% Similarity=0.255 Sum_probs=30.5
Q ss_pred hHHHHHHHHHHHhcCCChhhhcCeeEEEccCCCCccccceeEeeecCCCCCCccccccCC
Q 024406 204 SRTWKRIDEEIEATVMPEDYRHKKVWILCNDCNDTTEVYFHIIGQKCSHCKSYNTRSIAP 263 (268)
Q Consensus 204 ~~~~~~lD~~i~~~pmP~~y~~~~v~I~CnDC~~~s~~~~H~lg~kC~~C~SyNT~~~~~ 263 (268)
++.+..++...... ++-.--+ ...-.|++||..... +.-+|+.|||-|..++++
T Consensus 501 eal~~lv~~a~~~~-i~Y~~~n-~~~~~C~~CG~~g~~----~~~~CP~Cgs~~~~~~~R 554 (579)
T TIGR02487 501 EALKDITKKAMKNG-IGYFGIN-PPVDVCEDCGYTGEG----LNDKCPKCGSHDIEVISR 554 (579)
T ss_pred HHHHHHHHHHHhcC-CceEEec-cCCccCCCCCCCCCC----CCCcCcCCCCccceehhh
Confidence 33444444433332 4443222 234569999974332 235899999988766654
No 258
>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=24.22 E-value=33 Score=26.40 Aligned_cols=37 Identities=16% Similarity=0.551 Sum_probs=17.8
Q ss_pred CcCCCCCCcc--hh-hhhHHHHHHHHHHHhcCCChhhhcCeeEEEccCCCCcccccee
Q 024406 190 RYCCPICSKS--VI-DMSRTWKRIDEEIEATVMPEDYRHKKVWILCNDCNDTTEVYFH 244 (268)
Q Consensus 190 ~~~CPiCrks--i~-~m~~~~~~lD~~i~~~pmP~~y~~~~v~I~CnDC~~~s~~~~H 244 (268)
.+.||.|+.. |. .|.. ......|.|..|+...+...+
T Consensus 22 ~F~CPfC~~~~sV~v~idk------------------k~~~~~~~C~~Cg~~~~~~i~ 61 (81)
T PF05129_consen 22 VFDCPFCNHEKSVSVKIDK------------------KEGIGILSCRVCGESFQTKIN 61 (81)
T ss_dssp ----TTT--SS-EEEEEET------------------TTTEEEEEESSS--EEEEE--
T ss_pred eEcCCcCCCCCeEEEEEEc------------------cCCEEEEEecCCCCeEEEccC
Confidence 4899999932 32 3422 245678999999987766544
No 259
>PRK14811 formamidopyrimidine-DNA glycosylase; Provisional
Probab=24.00 E-value=43 Score=31.01 Aligned_cols=20 Identities=40% Similarity=1.102 Sum_probs=15.8
Q ss_pred cccCCcCCCcc--------ceeeccccc
Q 024406 78 AQVCTNCGVNM--------GEYFCDICK 97 (268)
Q Consensus 78 ~~~C~~Cg~~f--------~~y~C~~C~ 97 (268)
++.|+.||..+ +.|||+.|.
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 678888885
No 260
>KOG4399 consensus C2HC-type Zn-finger protein [General function prediction only]
Probab=23.99 E-value=20 Score=33.88 Aligned_cols=53 Identities=17% Similarity=0.165 Sum_probs=40.4
Q ss_pred ccCCcCCCccceeeccccccccCCCCcCeeecCCCCcccccCccceeecCccCcccc
Q 024406 79 QVCTNCGVNMGEYFCDICKFYDDDIEKGQFHCDDCGICRIGGRENYFHCKRCGSCYS 135 (268)
Q Consensus 79 ~~C~~Cg~~f~~y~C~~C~l~d~~~~k~~yHC~~CgiCR~G~~~~ffHC~~C~~C~s 135 (268)
..|+-|...-+.-||.||-=+|.. .-|||.|.-||--..-.+-||++|..|..
T Consensus 250 i~C~~~~~~A~~~~C~iC~~~~~~----R~~C~~~kA~~~~~Q~K~N~~~~~~~~~q 302 (325)
T KOG4399|consen 250 IHCSICNHCAVKHGCFICGELDHK----RSTCPNIKAVRKQKQRKSNKMKMETTKGQ 302 (325)
T ss_pred eeeecccchhhhcceeeccccccc----cccCccHHHHHHHHhcccchhhhhhhhhh
Confidence 356667777778899999888752 27899999888877666778888877765
No 261
>PRK10445 endonuclease VIII; Provisional
Probab=23.80 E-value=44 Score=30.81 Aligned_cols=20 Identities=30% Similarity=0.894 Sum_probs=15.3
Q ss_pred cccCCcCCCcc--------ceeeccccc
Q 024406 78 AQVCTNCGVNM--------GEYFCDICK 97 (268)
Q Consensus 78 ~~~C~~Cg~~f--------~~y~C~~C~ 97 (268)
++.|+.||... +.|||+.|.
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 567777773
No 262
>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=23.72 E-value=1e+02 Score=26.40 Aligned_cols=26 Identities=19% Similarity=0.599 Sum_probs=18.6
Q ss_pred cCCCCCCcchhhhh--HHHHHHHHHHHh
Q 024406 191 YCCPICSKSVIDMS--RTWKRIDEEIEA 216 (268)
Q Consensus 191 ~~CPiCrksi~~m~--~~~~~lD~~i~~ 216 (268)
++||.|+..+..+. ..-+.|...|+.
T Consensus 129 F~Cp~Cg~~L~~~dn~~~i~~l~~~i~~ 156 (158)
T TIGR00373 129 FTCPRCGAMLDYLDNSEAIEKLEEQIKF 156 (158)
T ss_pred CcCCCCCCEeeeccCHHHHHHHHHHHHh
Confidence 99999999997443 344566666654
No 263
>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=23.59 E-value=48 Score=27.41 Aligned_cols=27 Identities=22% Similarity=0.618 Sum_probs=17.9
Q ss_pred ccceeecCCCCccccc---cccCCcCCCcc
Q 024406 62 DVKQVICSVCDTEQPV---AQVCTNCGVNM 88 (268)
Q Consensus 62 ~~~~v~C~~C~~~q~v---~~~C~~Cg~~f 88 (268)
.+..|.|..|+++-.. .+.|++|+.++
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 4467778888766433 46788887765
No 264
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=23.54 E-value=1e+02 Score=26.94 Aligned_cols=26 Identities=27% Similarity=0.632 Sum_probs=17.1
Q ss_pred CcCCCCCCcchhhh--hHHHHHHHHHHH
Q 024406 190 RYCCPICSKSVIDM--SRTWKRIDEEIE 215 (268)
Q Consensus 190 ~~~CPiCrksi~~m--~~~~~~lD~~i~ 215 (268)
.++||.|+..+..+ +...+.|+..|+
T Consensus 136 ~F~Cp~Cg~~L~~~dn~~~~~~l~~~I~ 163 (178)
T PRK06266 136 GFRCPQCGEMLEEYDNSELIKELKEQIK 163 (178)
T ss_pred CCcCCCCCCCCeecccHHHHHHHHHHHH
Confidence 39999999999743 334455555443
No 265
>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=23.35 E-value=56 Score=20.00 Aligned_cols=16 Identities=19% Similarity=0.619 Sum_probs=12.8
Q ss_pred CcCCCCCCcchhhhhH
Q 024406 190 RYCCPICSKSVIDMSR 205 (268)
Q Consensus 190 ~~~CPiCrksi~~m~~ 205 (268)
.+.|.+|.+.+.+...
T Consensus 3 ~~~C~~C~~~~~~~~~ 18 (35)
T smart00451 3 GFYCKLCNVTFTDEIS 18 (35)
T ss_pred CeEccccCCccCCHHH
Confidence 4889999999986544
No 266
>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=23.17 E-value=65 Score=21.77 Aligned_cols=11 Identities=36% Similarity=0.939 Sum_probs=5.3
Q ss_pred CcCeeecCCCC
Q 024406 104 EKGQFHCDDCG 114 (268)
Q Consensus 104 ~k~~yHC~~Cg 114 (268)
.++-|+|..|+
T Consensus 25 ~~~g~~C~~C~ 35 (53)
T PF00130_consen 25 GKQGYRCSWCG 35 (53)
T ss_dssp SSCEEEETTTT
T ss_pred CCCeEEECCCC
Confidence 34445554444
No 267
>COG3024 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=22.89 E-value=43 Score=25.04 Aligned_cols=26 Identities=31% Similarity=0.658 Sum_probs=17.3
Q ss_pred cccccCCcCCCccce-------eecc-ccccccC
Q 024406 76 PVAQVCTNCGVNMGE-------YFCD-ICKFYDD 101 (268)
Q Consensus 76 ~v~~~C~~Cg~~f~~-------y~C~-~C~l~d~ 101 (268)
..+..|+-||+.... -||+ -|++.|-
T Consensus 5 ~~~v~CP~Cgkpv~w~~~s~frPFCSkRCklIDL 38 (65)
T COG3024 5 RITVPCPTCGKPVVWGEESPFRPFCSKRCKLIDL 38 (65)
T ss_pred cccccCCCCCCcccccccCCcCcchhHhhhhcch
Confidence 345578888877643 5665 4888874
No 268
>PRK01103 formamidopyrimidine/5-formyluracil/ 5-hydroxymethyluracil DNA glycosylase; Validated
Probab=22.78 E-value=48 Score=30.66 Aligned_cols=20 Identities=30% Similarity=1.090 Sum_probs=15.1
Q ss_pred cccCCcCCCcc--------ceeeccccc
Q 024406 78 AQVCTNCGVNM--------GEYFCDICK 97 (268)
Q Consensus 78 ~~~C~~Cg~~f--------~~y~C~~C~ 97 (268)
++.|+.||... +.|||+.|.
T Consensus 245 g~pC~~Cg~~I~~~~~~gR~t~~CP~CQ 272 (274)
T PRK01103 245 GEPCRRCGTPIEKIKQGGRSTFFCPRCQ 272 (274)
T ss_pred CCCCCCCCCeeEEEEECCCCcEECcCCC
Confidence 46899999887 567777773
No 269
>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=22.56 E-value=47 Score=26.64 Aligned_cols=19 Identities=26% Similarity=0.728 Sum_probs=14.1
Q ss_pred ecCCCCcccccc----ccCCcCC
Q 024406 67 ICSVCDTEQPVA----QVCTNCG 85 (268)
Q Consensus 67 ~C~~C~~~q~v~----~~C~~Cg 85 (268)
-|+.|+..++.. +.|+||+
T Consensus 5 AC~~C~~I~~~~qf~~~gCpnC~ 27 (98)
T cd07973 5 ACLLCSLIKTEDQFERDGCPNCE 27 (98)
T ss_pred hhccCCcccccccccCCCCCCCc
Confidence 588888777654 4788886
No 270
>PF12760 Zn_Tnp_IS1595: Transposase zinc-ribbon domain; InterPro: IPR024442 This zinc binding domain is found in a range of transposase proteins such as ISSPO8, ISSOD11, ISRSSP2 etc. It may be a zinc-binding beta ribbon domain that could bind DNA.
Probab=22.44 E-value=1.1e+02 Score=20.58 Aligned_cols=9 Identities=44% Similarity=1.154 Sum_probs=5.3
Q ss_pred ccCCcCCCc
Q 024406 79 QVCTNCGVN 87 (268)
Q Consensus 79 ~~C~~Cg~~ 87 (268)
.+||.||..
T Consensus 19 ~~CP~Cg~~ 27 (46)
T PF12760_consen 19 FVCPHCGST 27 (46)
T ss_pred CCCCCCCCe
Confidence 456666654
No 271
>PRK05580 primosome assembly protein PriA; Validated
Probab=22.39 E-value=1e+02 Score=32.32 Aligned_cols=24 Identities=17% Similarity=0.533 Sum_probs=18.8
Q ss_pred cceeecCCCCccccccccCCcCCCccce
Q 024406 63 VKQVICSVCDTEQPVAQVCTNCGVNMGE 90 (268)
Q Consensus 63 ~~~v~C~~C~~~q~v~~~C~~Cg~~f~~ 90 (268)
...+.|..|+.. ..|++|+..+.-
T Consensus 379 ~~~~~C~~Cg~~----~~C~~C~~~l~~ 402 (679)
T PRK05580 379 APFLLCRDCGWV----AECPHCDASLTL 402 (679)
T ss_pred CCceEhhhCcCc----cCCCCCCCceeE
Confidence 467889999866 479999988743
No 272
>KOG0269 consensus WD40 repeat-containing protein [Function unknown]
Probab=22.30 E-value=64 Score=34.64 Aligned_cols=51 Identities=27% Similarity=0.541 Sum_probs=41.4
Q ss_pred cccCCcCCCcccee---eccccccccCCCCcCeeecCCCCcccccCccceeecCccCcccccc
Q 024406 78 AQVCTNCGVNMGEY---FCDICKFYDDDIEKGQFHCDDCGICRIGGRENYFHCKRCGSCYSTS 137 (268)
Q Consensus 78 ~~~C~~Cg~~f~~y---~C~~C~l~d~~~~k~~yHC~~CgiCR~G~~~~ffHC~~C~~C~s~~ 137 (268)
.-.|++|++.++.- +|++|.--.- .+|-+|+.+-+.-+++|..|+-+.-.+
T Consensus 753 ~~~~~nc~a~~~~~~~~~c~rc~s~a~---------~~CtVC~~vi~G~~~~c~~C~H~gH~s 806 (839)
T KOG0269|consen 753 HYACPNCDAPMVLTKLWQCDRCESRAS---------AKCTVCDLVIRGVDVWCQVCGHGGHDS 806 (839)
T ss_pred eccccccCCccccccceeechHHHHhh---------cCceeecceeeeeEeecccccccccHH
Confidence 45899999999765 8998876543 268899999988999999999886654
No 273
>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=22.19 E-value=54 Score=23.49 Aligned_cols=25 Identities=32% Similarity=0.789 Sum_probs=11.1
Q ss_pred cccCCcCCCccceeeccccccccCCCCcCeeecCCCCc
Q 024406 78 AQVCTNCGVNMGEYFCDICKFYDDDIEKGQFHCDDCGI 115 (268)
Q Consensus 78 ~~~C~~Cg~~f~~y~C~~C~l~d~~~~k~~yHC~~Cgi 115 (268)
+..|..|++.|+- -+..+||-.||.
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 4567778888852 256788888874
No 274
>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=22.16 E-value=57 Score=28.11 Aligned_cols=13 Identities=15% Similarity=0.634 Sum_probs=11.5
Q ss_pred ccCCcCCCcccee
Q 024406 79 QVCTNCGVNMGEY 91 (268)
Q Consensus 79 ~~C~~Cg~~f~~y 91 (268)
-.|++||..|..|
T Consensus 29 ReC~~C~~RFTTy 41 (147)
T TIGR00244 29 RECLECHERFTTF 41 (147)
T ss_pred ccCCccCCcccee
Confidence 3799999999998
No 275
>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=22.06 E-value=48 Score=24.94 Aligned_cols=37 Identities=30% Similarity=0.644 Sum_probs=24.5
Q ss_pred cccCCcCCCccceeeccccccccCCCCcCeeecCCCC
Q 024406 78 AQVCTNCGVNMGEYFCDICKFYDDDIEKGQFHCDDCG 114 (268)
Q Consensus 78 ~~~C~~Cg~~f~~y~C~~C~l~d~~~~k~~yHC~~Cg 114 (268)
...|+.|...=....+..|.+.+=-.+|++-||-.|.
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 4567777655444677777777665667777776663
No 276
>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=22.06 E-value=63 Score=23.15 Aligned_cols=32 Identities=22% Similarity=0.652 Sum_probs=21.4
Q ss_pred cCCCCCCcchhhhhHHHHHHHHHHHhcCCChhhhcCeeEEEccCCCCcccc
Q 024406 191 YCCPICSKSVIDMSRTWKRIDEEIEATVMPEDYRHKKVWILCNDCNDTTEV 241 (268)
Q Consensus 191 ~~CPiCrksi~~m~~~~~~lD~~i~~~pmP~~y~~~~v~I~CnDC~~~s~~ 241 (268)
++||.|..+|. +|....+ ..+-|-+||+.-.|
T Consensus 3 ~~CP~CG~~ie-----------------v~~~~~G--eiV~Cp~CGaeleV 34 (54)
T TIGR01206 3 FECPDCGAEIE-----------------LENPELG--ELVICDECGAELEV 34 (54)
T ss_pred cCCCCCCCEEe-----------------cCCCccC--CEEeCCCCCCEEEE
Confidence 68999998774 2333333 35789999975443
No 277
>PRK08351 DNA-directed RNA polymerase subunit E''; Validated
Probab=21.83 E-value=55 Score=24.13 Aligned_cols=20 Identities=25% Similarity=0.693 Sum_probs=13.1
Q ss_pred ecCCCCccccccccCCcCCCc
Q 024406 67 ICSVCDTEQPVAQVCTNCGVN 87 (268)
Q Consensus 67 ~C~~C~~~q~v~~~C~~Cg~~ 87 (268)
.|..|...++ .+.||+||..
T Consensus 5 AC~~C~~i~~-~~~CP~Cgs~ 24 (61)
T PRK08351 5 ACRHCHYITT-EDRCPVCGSR 24 (61)
T ss_pred hhhhCCcccC-CCcCCCCcCC
Confidence 5667776653 3468888764
No 278
>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=21.46 E-value=70 Score=28.08 Aligned_cols=36 Identities=33% Similarity=0.858 Sum_probs=22.1
Q ss_pred eecCCCCccccccccCCcCCCcc-----------ceeeccccccccC
Q 024406 66 VICSVCDTEQPVAQVCTNCGVNM-----------GEYFCDICKFYDD 101 (268)
Q Consensus 66 v~C~~C~~~q~v~~~C~~Cg~~f-----------~~y~C~~C~l~d~ 101 (268)
..|..|...+.+...|.+|...+ +.+||..|-+.|=
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 34777766666666777766554 4556666655543
No 279
>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=21.32 E-value=31 Score=21.53 Aligned_cols=21 Identities=29% Similarity=0.819 Sum_probs=9.7
Q ss_pred ecCCCCccccc-----cccCCcCCCc
Q 024406 67 ICSVCDTEQPV-----AQVCTNCGVN 87 (268)
Q Consensus 67 ~C~~C~~~q~v-----~~~C~~Cg~~ 87 (268)
.|+.|+.+... +..|+.||..
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 47777765443 2467777753
No 280
>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=20.72 E-value=61 Score=27.14 Aligned_cols=48 Identities=21% Similarity=0.335 Sum_probs=29.1
Q ss_pred cCCCCCCcchhhhhHHHHHHHHHHHhcCCChh-hhcCeeEEEccCCCCccccceeE
Q 024406 191 YCCPICSKSVIDMSRTWKRIDEEIEATVMPED-YRHKKVWILCNDCNDTTEVYFHI 245 (268)
Q Consensus 191 ~~CPiCrksi~~m~~~~~~lD~~i~~~pmP~~-y~~~~v~I~CnDC~~~s~~~~H~ 245 (268)
.+||.|+..+...++ +-....+|+. |+....--.|..|++.-+..-||
T Consensus 92 sRC~~CN~~L~~v~~-------~~v~~~vp~~v~~~~~~f~~C~~C~kiyW~GsH~ 140 (147)
T PF01927_consen 92 SRCPKCNGPLRPVSK-------EEVKDRVPPYVYETYDEFWRCPGCGKIYWEGSHW 140 (147)
T ss_pred CccCCCCcEeeechh-------hccccccCccccccCCeEEECCCCCCEecccccH
Confidence 689999987765432 1112224444 44434456799999877666554
No 281
>KOG3005 consensus GIY-YIG type nuclease [General function prediction only]
Probab=20.57 E-value=1.3e+02 Score=28.57 Aligned_cols=66 Identities=18% Similarity=0.408 Sum_probs=41.8
Q ss_pred CCCCchhhhhhcccCCcceEe-----ccCCccChHHHHHHH-HcC------CCcCCCCCCcchhhhhHHHHHHHHHHHhc
Q 024406 150 HHHCPICYEYLFDSLRNTTVM-----KCGHTMHCECYHEMI-KRD------NRYCCPICSKSVIDMSRTWKRIDEEIEAT 217 (268)
Q Consensus 150 ~~~CpICle~lf~s~~~v~~L-----pCGH~~H~~C~~~~~-~~~------~~~~CPiCrksi~~m~~~~~~lD~~i~~~ 217 (268)
...|-+|.+++.+. ...++ -|+=..|..||.+.+ ... -.-.||.|+|.+. |..|=.++-.+
T Consensus 182 ~~~celc~~ei~e~--~~~~a~c~~~~c~~~~h~~CLa~~~~~~e~g~~~p~eg~cp~C~~~~~-----w~~lv~~~~~t 254 (276)
T KOG3005|consen 182 NVECELCEKEILET--DWSRATCPNPDCDSLNHLTCLAEELLEVEPGQLIPLEGMCPKCEKFLS-----WTTLVDLDFMT 254 (276)
T ss_pred chhhHHHHHHhccc--cceeccCCCCCCCchhhhhhhhHHHhccCCCceeccCCCCCchhceee-----HHHHHHHHhcC
Confidence 35899999987543 23333 377889999999943 221 0257999999665 55433344455
Q ss_pred CCChh
Q 024406 218 VMPED 222 (268)
Q Consensus 218 pmP~~ 222 (268)
|++.+
T Consensus 255 ~~e~~ 259 (276)
T KOG3005|consen 255 PTELA 259 (276)
T ss_pred chhhh
Confidence 55544
No 282
>PRK01110 rpmF 50S ribosomal protein L32; Validated
Probab=20.46 E-value=1e+02 Score=22.44 Aligned_cols=30 Identities=10% Similarity=0.073 Sum_probs=22.0
Q ss_pred EEEccCCCCccccceeEeeecCCCCCCccccccCCC
Q 024406 229 WILCNDCNDTTEVYFHIIGQKCSHCKSYNTRSIAPP 264 (268)
Q Consensus 229 ~I~CnDC~~~s~~~~H~lg~kC~~C~SyNT~~~~~~ 264 (268)
.+.|..|+.. ...|-+ |. ||.|+.+++-.+
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 5789999864 344534 88 999999997543
No 283
>PRK13945 formamidopyrimidine-DNA glycosylase; Provisional
Probab=20.36 E-value=58 Score=30.33 Aligned_cols=19 Identities=26% Similarity=0.933 Sum_probs=14.3
Q ss_pred cccCCcCCCcc--------ceeecccc
Q 024406 78 AQVCTNCGVNM--------GEYFCDIC 96 (268)
Q Consensus 78 ~~~C~~Cg~~f--------~~y~C~~C 96 (268)
++.|+.||... +.|||+.|
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 284
>KOG4275 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=20.35 E-value=32 Score=33.03 Aligned_cols=20 Identities=45% Similarity=1.019 Sum_probs=17.2
Q ss_pred ccCCcCCCccceeecccccccc
Q 024406 79 QVCTNCGVNMGEYFCDICKFYD 100 (268)
Q Consensus 79 ~~C~~Cg~~f~~y~C~~C~l~d 100 (268)
..|..||..|+ +|+||+-|-
T Consensus 322 VtCt~CGkrm~--eCPICRqyi 341 (350)
T KOG4275|consen 322 VTCTKCGKRMN--ECPICRQYI 341 (350)
T ss_pred Eeehhhccccc--cCchHHHHH
Confidence 47999999999 999998663
No 285
>PLN02436 cellulose synthase A
Probab=20.23 E-value=88 Score=34.91 Aligned_cols=56 Identities=16% Similarity=0.452 Sum_probs=39.0
Q ss_pred ecCCCCCCCchhhhhhcccCCcceEe---ccCCccChHHHHHHHHcCCCcCCCCCCcchh
Q 024406 145 IENSMHHHCPICYEYLFDSLRNTTVM---KCGHTMHCECYHEMIKRDNRYCCPICSKSVI 201 (268)
Q Consensus 145 ~e~~~~~~CpICle~lf~s~~~v~~L---pCGH~~H~~C~~~~~~~~~~~~CPiCrksi~ 201 (268)
+.....+.|.||.|++-.+.+.-... -||=-+.+.||+-=.+.+ +..||-|+...-
T Consensus 31 ~~~~~~~iCqICGD~Vg~t~dGe~FVACn~C~fpvCr~Cyeyer~eg-~~~Cpqckt~Y~ 89 (1094)
T PLN02436 31 VQELSGQTCQICGDEIELTVDGEPFVACNECAFPVCRPCYEYERREG-NQACPQCKTRYK 89 (1094)
T ss_pred ccccCCccccccccccCcCCCCCEEEeeccCCCccccchhhhhhhcC-CccCcccCCchh
Confidence 34456679999999974433333333 378889999994445555 789999997654
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=20.12 E-value=58 Score=30.14 Aligned_cols=19 Identities=37% Similarity=1.111 Sum_probs=14.2
Q ss_pred cccCCcCCCcc--------ceeecccc
Q 024406 78 AQVCTNCGVNM--------GEYFCDIC 96 (268)
Q Consensus 78 ~~~C~~Cg~~f--------~~y~C~~C 96 (268)
++.|+.||... +.|||+.|
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 56777766
No 287
>PF13913 zf-C2HC_2: zinc-finger of a C2HC-type
Probab=20.04 E-value=50 Score=19.68 Aligned_cols=12 Identities=25% Similarity=0.664 Sum_probs=9.0
Q ss_pred ccCCcCCCccce
Q 024406 79 QVCTNCGVNMGE 90 (268)
Q Consensus 79 ~~C~~Cg~~f~~ 90 (268)
..|+.||..|+.
T Consensus 3 ~~C~~CgR~F~~ 14 (25)
T PF13913_consen 3 VPCPICGRKFNP 14 (25)
T ss_pred CcCCCCCCEECH
Confidence 368888888863
Done!