Query 031240
Match_columns 163
No_of_seqs 266 out of 1634
Neff 7.0
Searched_HMMs 46136
Date Fri Mar 29 11:17:19 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/031240.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/031240hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG1940 Zn-finger protein [Gen 100.0 5.8E-29 1.3E-33 203.6 7.5 126 1-128 146-271 (276)
2 PF14599 zinc_ribbon_6: Zinc-r 99.9 9.9E-26 2.1E-30 146.2 -0.5 61 62-122 1-61 (61)
3 KOG0804 Cytoplasmic Zn-finger 99.8 4.2E-21 9.1E-26 164.3 1.5 112 13-152 175-288 (493)
4 PF13639 zf-RING_2: Ring finge 99.4 7.9E-14 1.7E-18 84.7 1.5 43 15-59 2-44 (44)
5 PF15227 zf-C3HC4_4: zinc fing 99.2 1.2E-11 2.5E-16 74.7 3.2 39 16-58 1-42 (42)
6 PF13923 zf-C3HC4_2: Zinc fing 99.1 3.1E-11 6.6E-16 71.5 2.5 39 16-58 1-39 (39)
7 PF12678 zf-rbx1: RING-H2 zinc 99.1 5E-11 1.1E-15 80.1 3.8 47 12-59 18-73 (73)
8 PF13920 zf-C3HC4_3: Zinc fing 99.1 6E-11 1.3E-15 73.8 2.9 46 13-63 2-48 (50)
9 cd00162 RING RING-finger (Real 99.1 1.3E-10 2.7E-15 69.1 3.8 45 15-62 1-45 (45)
10 PHA02929 N1R/p28-like protein; 99.1 1.1E-10 2.5E-15 94.5 4.1 54 10-64 171-228 (238)
11 PLN03208 E3 ubiquitin-protein 99.0 2.4E-10 5.1E-15 89.7 5.1 55 6-64 11-80 (193)
12 PF13445 zf-RING_UBOX: RING-ty 99.0 9.2E-11 2E-15 71.2 2.2 40 16-56 1-43 (43)
13 PF14634 zf-RING_5: zinc-RING 99.0 2.2E-10 4.8E-15 69.6 3.8 44 15-60 1-44 (44)
14 COG5243 HRD1 HRD ubiquitin lig 99.0 9.3E-11 2E-15 99.4 2.2 55 10-65 284-348 (491)
15 PF00097 zf-C3HC4: Zinc finger 99.0 3.3E-10 7E-15 67.4 2.8 39 16-58 1-41 (41)
16 KOG4628 Predicted E3 ubiquitin 99.0 2.8E-10 6E-15 96.4 3.3 49 14-63 230-278 (348)
17 smart00184 RING Ring finger. E 98.9 1.3E-09 2.8E-14 62.5 4.0 39 16-58 1-39 (39)
18 PHA02926 zinc finger-like prot 98.9 1.6E-09 3.4E-14 86.6 3.9 54 10-63 167-230 (242)
19 KOG0320 Predicted E3 ubiquitin 98.8 2.1E-09 4.5E-14 83.0 3.4 49 12-63 130-178 (187)
20 KOG0823 Predicted E3 ubiquitin 98.8 3.2E-09 6.9E-14 85.0 3.4 50 10-63 44-95 (230)
21 KOG0317 Predicted E3 ubiquitin 98.7 4.7E-09 1E-13 86.4 2.8 47 13-64 239-285 (293)
22 smart00504 Ubox Modified RING 98.7 1E-08 2.2E-13 66.0 3.9 44 14-62 2-45 (63)
23 PF12861 zf-Apc11: Anaphase-pr 98.7 2.1E-08 4.6E-13 69.0 4.4 34 29-62 46-81 (85)
24 COG5540 RING-finger-containing 98.7 1.2E-08 2.6E-13 84.7 3.3 51 12-63 322-372 (374)
25 KOG2177 Predicted E3 ubiquitin 98.6 9.2E-08 2E-12 76.2 5.2 45 11-60 11-55 (386)
26 TIGR00599 rad18 DNA repair pro 98.5 7.2E-08 1.6E-12 83.4 3.2 47 12-63 25-71 (397)
27 KOG2164 Predicted E3 ubiquitin 98.4 8.9E-08 1.9E-12 84.1 2.5 49 11-63 184-236 (513)
28 KOG0287 Postreplication repair 98.4 1.3E-07 2.9E-12 79.6 3.3 46 13-63 23-68 (442)
29 KOG0802 E3 ubiquitin ligase [P 98.4 1.3E-07 2.8E-12 84.9 2.4 52 10-62 288-340 (543)
30 TIGR00570 cdk7 CDK-activating 98.3 4.3E-07 9.4E-12 76.1 4.1 50 13-62 3-53 (309)
31 PF04564 U-box: U-box domain; 98.3 7.3E-07 1.6E-11 59.7 2.9 49 12-64 3-51 (73)
32 COG5574 PEX10 RING-finger-cont 98.2 8E-07 1.7E-11 72.6 2.7 48 12-63 214-262 (271)
33 PF11793 FANCL_C: FANCL C-term 98.2 3.4E-07 7.5E-12 61.0 -0.4 50 13-62 2-65 (70)
34 smart00744 RINGv The RING-vari 98.1 3.1E-06 6.6E-11 52.6 3.8 43 15-59 1-49 (49)
35 COG5194 APC11 Component of SCF 98.1 6.1E-06 1.3E-10 56.1 4.2 51 11-62 29-80 (88)
36 COG5432 RAD18 RING-finger-cont 98.0 3.2E-06 6.8E-11 70.2 2.7 45 13-62 25-69 (391)
37 KOG4172 Predicted E3 ubiquitin 98.0 1.8E-06 3.9E-11 54.6 0.6 53 12-68 6-59 (62)
38 KOG1039 Predicted E3 ubiquitin 98.0 1.6E-06 3.4E-11 73.9 0.1 83 10-94 158-252 (344)
39 KOG0827 Predicted E3 ubiquitin 97.9 6.9E-06 1.5E-10 70.4 2.8 50 12-62 3-55 (465)
40 KOG0978 E3 ubiquitin ligase in 97.9 4.1E-06 8.9E-11 76.7 1.1 48 13-64 643-690 (698)
41 PF14835 zf-RING_6: zf-RING of 97.9 4.2E-06 9.2E-11 54.6 0.7 43 13-62 7-50 (65)
42 KOG0828 Predicted E3 ubiquitin 97.8 1.2E-05 2.6E-10 70.9 2.2 51 13-63 571-634 (636)
43 KOG0311 Predicted E3 ubiquitin 97.8 4.7E-06 1E-10 70.6 -0.4 47 13-62 43-89 (381)
44 KOG1493 Anaphase-promoting com 97.7 8.4E-06 1.8E-10 54.9 0.6 48 12-62 30-80 (84)
45 KOG0824 Predicted E3 ubiquitin 97.7 1.6E-05 3.4E-10 66.2 2.3 50 10-63 4-53 (324)
46 KOG1734 Predicted RING-contain 97.7 1.3E-05 2.8E-10 66.0 0.7 51 12-62 223-280 (328)
47 KOG4265 Predicted E3 ubiquitin 97.6 5E-05 1.1E-09 64.5 3.3 48 11-63 288-336 (349)
48 PF14570 zf-RING_4: RING/Ubox 97.5 7.4E-05 1.6E-09 46.2 2.1 47 16-62 1-47 (48)
49 KOG1785 Tyrosine kinase negati 97.4 4.9E-05 1.1E-09 65.6 1.1 50 9-62 365-415 (563)
50 KOG2879 Predicted E3 ubiquitin 97.3 0.00018 3.8E-09 59.4 3.4 52 11-65 237-289 (298)
51 KOG0825 PHD Zn-finger protein 97.3 4.1E-05 9E-10 70.7 -0.3 51 11-63 121-171 (1134)
52 KOG3970 Predicted E3 ubiquitin 97.3 0.00038 8.3E-09 56.1 5.2 51 11-63 48-105 (299)
53 KOG1941 Acetylcholine receptor 97.3 8.2E-05 1.8E-09 64.1 1.1 57 5-62 358-415 (518)
54 PF11789 zf-Nse: Zinc-finger o 97.3 0.00015 3.1E-09 46.5 1.9 44 11-57 9-53 (57)
55 COG5219 Uncharacterized conser 97.1 0.00018 3.8E-09 67.9 1.5 52 11-62 1467-1522(1525)
56 KOG0297 TNF receptor-associate 97.1 0.00022 4.8E-09 61.9 1.8 108 11-134 19-141 (391)
57 KOG4185 Predicted E3 ubiquitin 97.1 0.0005 1.1E-08 57.0 3.6 50 13-62 3-54 (296)
58 KOG2930 SCF ubiquitin ligase, 97.0 0.00065 1.4E-08 48.4 3.3 30 31-61 77-106 (114)
59 KOG1645 RING-finger-containing 97.0 0.00073 1.6E-08 58.5 4.0 50 13-62 4-55 (463)
60 KOG4159 Predicted E3 ubiquitin 97.0 0.00053 1.2E-08 59.6 3.2 49 11-64 82-130 (398)
61 KOG4275 Predicted E3 ubiquitin 96.9 0.00011 2.3E-09 61.2 -1.7 54 3-65 287-344 (350)
62 COG5152 Uncharacterized conser 96.7 0.001 2.2E-08 52.8 2.3 46 13-63 196-241 (259)
63 KOG1813 Predicted E3 ubiquitin 96.5 0.0011 2.4E-08 55.3 1.5 60 13-77 241-300 (313)
64 KOG1428 Inhibitor of type V ad 96.5 0.0037 8.1E-08 61.6 5.0 51 11-62 3484-3543(3738)
65 PF14447 Prok-RING_4: Prokaryo 96.4 0.0011 2.4E-08 42.0 0.7 33 28-63 18-50 (55)
66 COG5175 MOT2 Transcriptional r 96.4 0.0013 2.7E-08 56.1 1.2 51 14-64 15-65 (480)
67 KOG2660 Locus-specific chromos 96.3 0.00094 2E-08 56.3 0.0 47 12-62 14-60 (331)
68 KOG1002 Nucleotide excision re 96.3 0.0019 4.2E-08 57.8 1.9 51 8-62 531-585 (791)
69 PF10367 Vps39_2: Vacuolar sor 96.2 0.0016 3.5E-08 45.6 0.6 38 6-45 71-108 (109)
70 PF12906 RINGv: RING-variant d 96.1 0.0031 6.7E-08 38.7 1.6 41 16-58 1-47 (47)
71 PF04641 Rtf2: Rtf2 RING-finge 96.1 0.0053 1.1E-07 50.4 3.2 52 10-63 110-161 (260)
72 KOG3800 Predicted E3 ubiquitin 96.1 0.0059 1.3E-07 50.8 3.4 48 15-62 2-50 (300)
73 KOG1814 Predicted E3 ubiquitin 96.0 0.005 1.1E-07 53.5 2.8 47 13-60 184-237 (445)
74 KOG1571 Predicted E3 ubiquitin 95.7 0.0053 1.1E-07 52.4 1.8 47 9-63 301-347 (355)
75 KOG4445 Uncharacterized conser 95.7 0.0041 8.9E-08 52.1 0.9 51 12-63 114-186 (368)
76 KOG3002 Zn finger protein [Gen 95.6 0.015 3.3E-07 48.9 4.0 62 13-85 48-111 (299)
77 KOG4692 Predicted E3 ubiquitin 95.4 0.011 2.3E-07 50.8 2.5 52 8-64 417-468 (489)
78 KOG1952 Transcription factor N 95.4 0.011 2.5E-07 55.4 2.8 48 12-61 190-245 (950)
79 COG5222 Uncharacterized conser 95.4 0.012 2.6E-07 49.5 2.7 46 13-61 274-319 (427)
80 KOG3268 Predicted E3 ubiquitin 95.4 0.014 3E-07 45.7 2.8 50 13-62 165-227 (234)
81 KOG3039 Uncharacterized conser 95.3 0.014 3.1E-07 47.8 2.9 54 10-64 218-271 (303)
82 KOG2817 Predicted E3 ubiquitin 95.3 0.015 3.2E-07 50.3 3.0 47 14-61 335-383 (394)
83 KOG4739 Uncharacterized protei 95.3 0.0094 2E-07 48.4 1.6 43 15-62 5-47 (233)
84 PF05883 Baculo_RING: Baculovi 95.2 0.011 2.4E-07 44.0 1.8 35 13-48 26-66 (134)
85 KOG3161 Predicted E3 ubiquitin 95.2 0.0081 1.8E-07 54.9 1.2 44 14-61 12-55 (861)
86 PF07800 DUF1644: Protein of u 94.8 0.035 7.5E-07 42.5 3.5 33 13-49 2-47 (162)
87 PHA02862 5L protein; Provision 94.8 0.035 7.5E-07 42.0 3.4 46 12-62 1-52 (156)
88 PHA02825 LAP/PHD finger-like p 94.7 0.038 8.2E-07 42.4 3.5 47 11-62 6-58 (162)
89 PF02148 zf-UBP: Zn-finger in 94.6 0.0041 8.8E-08 40.2 -1.7 57 94-152 1-59 (63)
90 KOG2114 Vacuolar assembly/sort 94.6 0.036 7.8E-07 52.1 3.8 43 14-63 841-883 (933)
91 COG5236 Uncharacterized conser 94.2 0.046 1E-06 46.9 3.3 48 11-62 59-107 (493)
92 PHA03096 p28-like protein; Pro 94.1 0.022 4.7E-07 47.7 1.1 47 14-60 179-231 (284)
93 PF03854 zf-P11: P-11 zinc fin 93.6 0.019 4.1E-07 35.3 -0.0 43 14-63 3-46 (50)
94 PF02891 zf-MIZ: MIZ/SP-RING z 93.6 0.034 7.5E-07 34.4 1.1 44 14-61 3-50 (50)
95 PF05290 Baculo_IE-1: Baculovi 93.0 0.1 2.2E-06 39.0 3.0 49 12-64 79-133 (140)
96 KOG1001 Helicase-like transcri 92.2 0.083 1.8E-06 49.1 2.0 44 14-62 455-499 (674)
97 KOG4367 Predicted Zn-finger pr 92.2 0.11 2.3E-06 46.0 2.5 34 12-49 3-36 (699)
98 COG5220 TFB3 Cdk activating ki 92.2 0.07 1.5E-06 43.7 1.3 48 13-61 10-62 (314)
99 KOG1812 Predicted E3 ubiquitin 91.2 0.11 2.4E-06 45.1 1.6 50 13-62 146-202 (384)
100 KOG2034 Vacuolar sorting prote 90.3 0.18 4E-06 47.7 2.2 42 6-49 810-851 (911)
101 TIGR00100 hypA hydrogenase nic 90.2 0.18 3.8E-06 36.6 1.7 36 87-124 66-101 (115)
102 PF08746 zf-RING-like: RING-li 90.1 0.3 6.6E-06 29.2 2.4 40 16-58 1-43 (43)
103 KOG0298 DEAD box-containing he 89.1 0.14 3E-06 50.4 0.5 51 12-66 1152-1202(1394)
104 PRK12380 hydrogenase nickel in 89.0 0.3 6.5E-06 35.2 2.1 36 88-125 67-102 (113)
105 PRK00564 hypA hydrogenase nick 88.4 0.35 7.6E-06 35.1 2.1 37 87-124 67-103 (117)
106 PF14446 Prok-RING_1: Prokaryo 88.3 0.43 9.4E-06 30.1 2.2 36 11-46 3-38 (54)
107 smart00290 ZnF_UBP Ubiquitin C 88.0 0.28 6.1E-06 29.7 1.2 43 93-138 1-45 (50)
108 PRK03681 hypA hydrogenase nick 88.0 0.38 8.3E-06 34.8 2.1 37 88-125 67-103 (114)
109 KOG0309 Conserved WD40 repeat- 87.5 0.37 8.1E-06 45.2 2.2 47 8-57 1023-1069(1081)
110 COG5109 Uncharacterized conser 87.3 0.44 9.6E-06 40.5 2.3 46 14-60 337-384 (396)
111 COG1066 Sms Predicted ATP-depe 87.0 0.48 1E-05 41.8 2.4 30 90-123 6-35 (456)
112 KOG0826 Predicted E3 ubiquitin 86.3 0.55 1.2E-05 40.0 2.4 48 11-62 298-345 (357)
113 PRK03824 hypA hydrogenase nick 85.6 0.51 1.1E-05 35.1 1.7 36 89-124 68-122 (135)
114 PF10272 Tmpp129: Putative tra 85.3 0.97 2.1E-05 39.1 3.5 27 37-63 313-351 (358)
115 PF01155 HypA: Hydrogenase exp 85.0 0.27 5.9E-06 35.4 -0.0 35 88-124 67-101 (113)
116 KOG2932 E3 ubiquitin ligase in 84.3 0.53 1.1E-05 40.0 1.4 29 31-62 105-133 (389)
117 PRK12286 rpmF 50S ribosomal pr 83.9 1.1 2.3E-05 28.6 2.4 29 90-123 26-54 (57)
118 PRK00398 rpoP DNA-directed RNA 83.4 0.85 1.8E-05 27.4 1.7 31 90-120 2-32 (46)
119 KOG2068 MOT2 transcription fac 83.2 0.91 2E-05 38.6 2.4 49 13-62 249-297 (327)
120 KOG1100 Predicted E3 ubiquitin 81.8 0.82 1.8E-05 36.5 1.5 39 15-62 160-199 (207)
121 COG0375 HybF Zn finger protein 81.1 1.2 2.6E-05 32.4 2.0 37 87-125 66-102 (115)
122 PF14569 zf-UDP: Zinc-binding 79.9 2.4 5.2E-05 28.8 3.0 52 11-62 7-61 (80)
123 KOG4185 Predicted E3 ubiquitin 79.8 0.37 8E-06 39.9 -1.1 50 12-61 206-265 (296)
124 PRK00762 hypA hydrogenase nick 79.7 1.3 2.8E-05 32.5 1.9 36 88-124 67-107 (124)
125 TIGR01031 rpmF_bact ribosomal 79.2 1.6 3.4E-05 27.6 1.9 29 90-123 25-53 (55)
126 PF14353 CpXC: CpXC protein 78.9 0.32 6.9E-06 35.4 -1.6 21 89-109 36-56 (128)
127 KOG0827 Predicted E3 ubiquitin 78.8 0.19 4.2E-06 43.7 -3.1 52 12-64 195-246 (465)
128 smart00659 RPOLCX RNA polymera 77.5 1.8 3.9E-05 26.0 1.7 26 91-117 2-27 (44)
129 KOG1815 Predicted E3 ubiquitin 76.1 2.1 4.6E-05 37.7 2.5 37 11-50 68-104 (444)
130 KOG3113 Uncharacterized conser 75.9 2.5 5.4E-05 35.0 2.6 48 12-62 110-157 (293)
131 COG5183 SSM4 Protein involved 75.7 2.7 5.8E-05 40.1 3.1 51 10-62 9-65 (1175)
132 TIGR02605 CxxC_CxxC_SSSS putat 71.7 2.9 6.3E-05 25.4 1.7 32 91-122 5-39 (52)
133 PF04710 Pellino: Pellino; In 71.3 1.4 3E-05 38.6 0.1 49 10-61 274-337 (416)
134 TIGR00416 sms DNA repair prote 71.1 3.5 7.6E-05 36.6 2.7 31 89-123 5-35 (454)
135 PLN02189 cellulose synthase 70.5 4 8.7E-05 39.8 3.0 54 9-62 30-86 (1040)
136 cd01121 Sms Sms (bacterial rad 69.6 2.9 6.2E-05 36.2 1.7 27 93-123 2-28 (372)
137 PRK11823 DNA repair protein Ra 69.3 4.1 8.9E-05 36.0 2.7 31 89-123 5-35 (446)
138 smart00249 PHD PHD zinc finger 69.0 1.7 3.7E-05 24.9 0.1 40 16-58 2-47 (47)
139 PLN02436 cellulose synthase A 67.7 5 0.00011 39.3 3.0 54 9-62 32-88 (1094)
140 smart00734 ZnF_Rad18 Rad18-lik 67.2 5.5 0.00012 21.1 1.9 19 54-73 3-21 (26)
141 KOG3053 Uncharacterized conser 66.8 5.4 0.00012 33.1 2.7 51 10-62 17-81 (293)
142 KOG4362 Transcriptional regula 66.7 1.7 3.7E-05 40.5 -0.3 47 12-62 20-68 (684)
143 PF01783 Ribosomal_L32p: Ribos 65.3 5.4 0.00012 25.1 1.9 29 90-123 25-53 (56)
144 COG1996 RPC10 DNA-directed RNA 65.2 3.8 8.3E-05 25.3 1.2 29 89-117 4-32 (49)
145 PF14205 Cys_rich_KTR: Cystein 64.6 6.4 0.00014 24.9 2.1 28 90-117 3-36 (55)
146 PF00628 PHD: PHD-finger; Int 64.5 0.57 1.2E-05 28.3 -2.7 42 15-59 1-49 (51)
147 PF07191 zinc-ribbons_6: zinc- 64.2 0.41 8.9E-06 31.8 -3.5 40 13-62 1-40 (70)
148 COG1198 PriA Primosomal protei 64.1 6.3 0.00014 37.2 2.9 30 88-122 459-488 (730)
149 KOG2066 Vacuolar assembly/sort 64.0 3.1 6.8E-05 39.3 0.9 46 12-59 783-831 (846)
150 KOG3899 Uncharacterized conser 62.5 6 0.00013 33.5 2.2 28 35-62 325-364 (381)
151 KOG1609 Protein involved in mR 62.2 5.7 0.00012 32.6 2.1 50 13-62 78-133 (323)
152 PF06906 DUF1272: Protein of u 61.5 16 0.00035 23.2 3.5 49 11-62 3-51 (57)
153 KOG3579 Predicted E3 ubiquitin 60.4 7.8 0.00017 32.7 2.5 58 11-77 266-337 (352)
154 smart00064 FYVE Protein presen 59.4 7.6 0.00016 24.8 1.9 38 11-48 8-45 (68)
155 PLN02638 cellulose synthase A 58.0 10 0.00022 37.4 3.1 54 9-62 13-69 (1079)
156 PRK00366 ispG 4-hydroxy-3-meth 57.9 17 0.00036 31.5 4.2 52 53-108 269-322 (360)
157 KOG4443 Putative transcription 56.8 11 0.00025 35.0 3.2 48 13-62 18-72 (694)
158 TIGR01562 FdhE formate dehydro 56.7 11 0.00023 32.0 2.9 24 90-117 209-232 (305)
159 PF13894 zf-C2H2_4: C2H2-type 56.6 6.3 0.00014 19.1 0.9 15 54-68 2-16 (24)
160 KOG2907 RNA polymerase I trans 56.2 3.9 8.5E-05 29.7 0.1 22 107-128 72-97 (116)
161 TIGR00595 priA primosomal prot 55.0 12 0.00026 33.7 3.0 26 89-119 238-263 (505)
162 PF13248 zf-ribbon_3: zinc-rib 54.7 7.2 0.00016 20.5 1.0 22 92-117 3-24 (26)
163 smart00132 LIM Zinc-binding do 54.6 11 0.00025 20.4 1.9 36 16-62 2-37 (39)
164 COG5132 BUD31 Cell cycle contr 53.9 7 0.00015 28.8 1.1 22 39-61 101-122 (146)
165 cd02339 ZZ_Mind_bomb Zinc fing 53.5 11 0.00023 22.7 1.7 28 92-122 1-28 (45)
166 PF10122 Mu-like_Com: Mu-like 53.3 9.8 0.00021 23.7 1.5 34 91-124 4-39 (51)
167 PF09723 Zn-ribbon_8: Zinc rib 53.2 10 0.00022 22.3 1.6 29 91-119 5-36 (42)
168 PF10571 UPF0547: Uncharacteri 52.1 10 0.00022 20.2 1.3 7 110-116 15-21 (26)
169 KOG4718 Non-SMC (structural ma 52.1 8.4 0.00018 31.1 1.4 43 14-60 182-224 (235)
170 PF04423 Rad50_zn_hook: Rad50 51.5 12 0.00027 22.9 1.9 11 54-64 22-32 (54)
171 cd02345 ZZ_dah Zinc finger, ZZ 50.2 15 0.00031 22.4 2.0 28 92-122 1-28 (49)
172 PF10058 DUF2296: Predicted in 50.2 26 0.00056 21.9 3.1 32 88-119 19-54 (54)
173 PF01363 FYVE: FYVE zinc finge 49.0 4.1 8.9E-05 26.1 -0.7 38 9-46 5-42 (69)
174 cd00065 FYVE FYVE domain; Zinc 48.6 11 0.00023 23.0 1.2 34 14-47 3-36 (57)
175 PF00096 zf-C2H2: Zinc finger, 48.2 8 0.00017 19.0 0.5 14 53-66 1-14 (23)
176 PRK05580 primosome assembly pr 48.1 17 0.00038 33.9 3.0 25 90-119 407-431 (679)
177 PLN02400 cellulose synthase 47.2 13 0.00027 36.7 2.0 53 10-62 33-88 (1085)
178 COG1656 Uncharacterized conser 46.7 17 0.00036 28.2 2.2 42 52-100 97-139 (165)
179 PF12773 DZR: Double zinc ribb 45.9 18 0.00039 21.5 1.9 11 90-100 28-38 (50)
180 KOG1812 Predicted E3 ubiquitin 45.6 13 0.00028 32.4 1.7 44 14-58 307-351 (384)
181 PRK01110 rpmF 50S ribosomal pr 45.6 18 0.00038 23.2 1.9 29 91-125 27-55 (60)
182 smart00834 CxxC_CXXC_SSSS Puta 45.3 19 0.00041 20.3 1.9 27 91-117 5-34 (41)
183 PLN02195 cellulose synthase A 44.6 27 0.00058 34.1 3.7 53 11-63 4-59 (977)
184 PF09986 DUF2225: Uncharacteri 44.6 4.8 0.0001 32.1 -1.1 12 52-63 5-16 (214)
185 TIGR02098 MJ0042_CXXC MJ0042 f 44.3 13 0.00028 21.0 1.0 12 90-101 24-35 (38)
186 KOG1873 Ubiquitin-specific pro 44.2 10 0.00022 36.0 0.8 63 90-152 65-145 (877)
187 PRK14892 putative transcriptio 43.9 30 0.00065 24.5 3.0 35 90-124 20-57 (99)
188 PF03604 DNA_RNApol_7kD: DNA d 43.8 13 0.00028 20.8 1.0 23 93-116 2-24 (32)
189 PLN02915 cellulose synthase A 43.6 22 0.00047 35.0 2.9 51 12-62 14-67 (1044)
190 PRK03564 formate dehydrogenase 43.3 29 0.00063 29.5 3.4 24 90-117 211-234 (309)
191 PF01907 Ribosomal_L37e: Ribos 42.5 14 0.00031 23.4 1.1 27 87-116 11-37 (55)
192 PF14952 zf-tcix: Putative tre 42.3 13 0.00027 22.5 0.8 14 110-123 12-25 (44)
193 PF13240 zinc_ribbon_2: zinc-r 42.3 15 0.00032 18.9 1.0 19 94-116 2-20 (23)
194 PF08792 A2L_zn_ribbon: A2L zi 42.3 21 0.00044 20.1 1.6 27 91-117 3-29 (33)
195 COG0333 RpmF Ribosomal protein 42.1 18 0.0004 23.0 1.6 28 91-123 27-54 (57)
196 KOG1829 Uncharacterized conser 41.4 11 0.00024 34.6 0.7 43 13-59 511-557 (580)
197 smart00647 IBR In Between Ring 41.2 7.3 0.00016 24.1 -0.4 15 34-48 45-59 (64)
198 PF05605 zf-Di19: Drought indu 41.1 34 0.00075 20.8 2.7 10 52-61 2-11 (54)
199 KOG3842 Adaptor protein Pellin 40.3 28 0.0006 29.9 2.8 56 7-62 333-413 (429)
200 PF07754 DUF1610: Domain of un 39.7 25 0.00053 18.5 1.6 6 111-116 18-23 (24)
201 cd02338 ZZ_PCMF_like Zinc fing 39.3 25 0.00055 21.3 1.9 28 92-122 1-28 (49)
202 PRK14873 primosome assembly pr 39.2 27 0.00059 32.7 2.8 28 90-123 409-436 (665)
203 cd02344 ZZ_HERC2 Zinc finger, 38.9 26 0.00055 21.1 1.8 28 92-122 1-28 (45)
204 PF10497 zf-4CXXC_R1: Zinc-fin 38.8 32 0.00069 24.4 2.6 25 36-60 37-69 (105)
205 PF13719 zinc_ribbon_5: zinc-r 38.1 28 0.0006 19.8 1.8 13 88-100 22-34 (37)
206 KOG0269 WD40 repeat-containing 37.6 33 0.00072 32.6 3.1 41 14-57 780-820 (839)
207 PF11023 DUF2614: Protein of u 37.2 27 0.00059 25.3 2.0 26 53-86 86-111 (114)
208 TIGR02159 PA_CoA_Oxy4 phenylac 36.5 19 0.0004 27.2 1.1 18 110-127 106-123 (146)
209 PRK00420 hypothetical protein; 35.9 34 0.00073 24.8 2.3 9 53-61 24-32 (112)
210 PF00412 LIM: LIM domain; Int 35.8 17 0.00036 22.0 0.6 37 16-63 1-37 (58)
211 PF13901 DUF4206: Domain of un 35.7 28 0.00061 27.4 2.1 42 13-60 152-197 (202)
212 PF09297 zf-NADH-PPase: NADH p 35.7 14 0.0003 20.3 0.2 24 93-116 5-28 (32)
213 KOG3842 Adaptor protein Pellin 35.3 16 0.00035 31.3 0.7 49 10-61 287-350 (429)
214 PRK00415 rps27e 30S ribosomal 34.9 26 0.00057 22.5 1.4 35 88-122 8-43 (59)
215 PF02701 zf-Dof: Dof domain, z 34.2 22 0.00048 23.1 1.0 14 110-123 6-19 (63)
216 KOG3005 GIY-YIG type nuclease 33.8 45 0.00098 27.8 3.0 47 14-62 183-242 (276)
217 smart00653 eIF2B_5 domain pres 33.6 36 0.00079 24.4 2.2 27 91-117 80-109 (110)
218 KOG3039 Uncharacterized conser 33.3 27 0.00059 29.0 1.6 33 14-50 44-76 (303)
219 PRK11788 tetratricopeptide rep 32.7 33 0.00072 28.4 2.2 29 91-123 354-382 (389)
220 cd02340 ZZ_NBR1_like Zinc fing 32.6 32 0.0007 20.3 1.5 27 92-122 1-27 (43)
221 PF15353 HECA: Headcase protei 32.3 32 0.0007 24.7 1.7 17 34-50 39-55 (107)
222 PF04981 NMD3: NMD3 family ; 31.9 27 0.00058 28.1 1.4 29 93-121 15-47 (236)
223 cd02342 ZZ_UBA_plant Zinc fing 31.7 35 0.00077 20.5 1.5 28 92-122 1-28 (43)
224 COG2051 RPS27A Ribosomal prote 31.6 28 0.0006 22.9 1.2 34 86-119 14-48 (67)
225 cd02334 ZZ_dystrophin Zinc fin 30.9 45 0.00099 20.3 2.0 28 92-122 1-28 (49)
226 COG3813 Uncharacterized protei 30.8 76 0.0016 21.4 3.2 48 12-62 4-51 (84)
227 PRK01343 zinc-binding protein; 30.8 29 0.00063 22.1 1.1 11 52-62 9-19 (57)
228 KOG3507 DNA-directed RNA polym 30.4 35 0.00075 22.0 1.4 28 88-116 17-44 (62)
229 PF06844 DUF1244: Protein of u 30.4 34 0.00073 22.5 1.4 13 38-50 11-23 (68)
230 PRK00418 DNA gyrase inhibitor; 29.8 29 0.00062 22.5 1.0 10 53-62 7-16 (62)
231 PF13790 DUF4182: Domain of un 29.8 81 0.0018 18.4 2.8 28 89-116 1-32 (38)
232 cd01675 RNR_III Class III ribo 29.2 63 0.0014 29.5 3.5 28 92-123 519-546 (555)
233 PF09779 Ima1_N: Ima1 N-termin 29.1 36 0.00078 25.0 1.6 32 93-124 2-35 (131)
234 COG3058 FdhE Uncharacterized p 29.0 14 0.0003 31.1 -0.7 29 91-119 225-262 (308)
235 KOG0825 PHD Zn-finger protein 28.5 30 0.00065 33.3 1.3 50 13-62 96-153 (1134)
236 KOG2462 C2H2-type Zn-finger pr 28.2 33 0.00071 28.7 1.3 56 12-68 160-231 (279)
237 PF13717 zinc_ribbon_4: zinc-r 27.9 51 0.0011 18.6 1.7 10 53-62 3-12 (36)
238 PRK12336 translation initiatio 27.8 1.1E+02 0.0023 24.2 4.1 34 91-124 98-134 (201)
239 smart00355 ZnF_C2H2 zinc finge 27.7 69 0.0015 15.1 2.1 14 53-66 1-14 (26)
240 COG2126 RPL37A Ribosomal prote 27.0 36 0.00079 21.8 1.1 29 87-118 12-40 (61)
241 cd02669 Peptidase_C19M A subfa 26.9 49 0.0011 29.1 2.3 57 93-152 18-76 (440)
242 PRK14714 DNA polymerase II lar 26.9 46 0.00099 33.6 2.2 9 53-61 668-676 (1337)
243 TIGR01562 FdhE formate dehydro 26.6 50 0.0011 28.0 2.2 22 38-60 211-232 (305)
244 TIGR01206 lysW lysine biosynth 26.6 55 0.0012 20.5 1.9 10 53-62 3-12 (54)
245 PF09567 RE_MamI: MamI restric 26.4 31 0.00067 28.7 0.9 28 91-122 82-109 (314)
246 PF01485 IBR: IBR domain; Int 25.9 4.1 8.9E-05 25.2 -3.5 34 14-47 19-58 (64)
247 PF14354 Lar_restr_allev: Rest 25.4 53 0.0012 20.3 1.7 10 90-99 28-37 (61)
248 PRK00432 30S ribosomal protein 25.3 41 0.00089 20.6 1.1 23 93-116 22-44 (50)
249 smart00291 ZnF_ZZ Zinc-binding 24.8 74 0.0016 18.6 2.1 28 91-122 4-31 (44)
250 PRK03988 translation initiatio 24.8 68 0.0015 23.9 2.4 29 91-119 102-133 (138)
251 PF12171 zf-C2H2_jaz: Zinc-fin 24.7 54 0.0012 16.8 1.4 14 53-66 2-15 (27)
252 TIGR00311 aIF-2beta translatio 24.7 69 0.0015 23.8 2.4 28 91-118 97-127 (133)
253 PF09082 DUF1922: Domain of un 24.2 27 0.0006 23.0 0.2 32 91-124 3-35 (68)
254 PF01927 Mut7-C: Mut7-C RNAse 24.1 63 0.0014 24.0 2.1 12 53-64 92-103 (147)
255 PRK14890 putative Zn-ribbon RN 23.6 1E+02 0.0022 19.8 2.7 10 51-60 47-56 (59)
256 COG4311 SoxD Sarcosine oxidase 23.5 51 0.0011 23.2 1.4 20 90-109 2-21 (97)
257 KOG2593 Transcription initiati 23.0 73 0.0016 28.4 2.6 14 52-65 128-141 (436)
258 PF14369 zf-RING_3: zinc-finge 22.8 62 0.0013 18.3 1.4 6 112-117 24-29 (35)
259 COG3809 Uncharacterized protei 22.7 76 0.0017 21.7 2.1 13 53-65 22-34 (88)
260 cd02343 ZZ_EF Zinc finger, ZZ 22.7 65 0.0014 19.7 1.6 27 92-122 1-27 (48)
261 KOG4118 Uncharacterized conser 22.7 26 0.00057 23.1 -0.2 35 52-86 38-72 (74)
262 KOG2079 Vacuolar assembly/sort 22.4 59 0.0013 32.3 2.0 40 13-56 1133-1172(1206)
263 COG1545 Predicted nucleic-acid 22.4 41 0.00088 25.0 0.8 10 90-99 28-37 (140)
264 PRK12496 hypothetical protein; 22.3 73 0.0016 24.3 2.2 28 92-121 128-155 (164)
265 PF01422 zf-NF-X1: NF-X1 type 22.3 60 0.0013 16.3 1.1 18 3-20 2-19 (20)
266 PF12088 DUF3565: Protein of u 21.8 45 0.00098 21.5 0.8 14 29-42 11-24 (61)
267 PF12756 zf-C2H2_2: C2H2 type 21.5 52 0.0011 21.6 1.1 17 53-69 51-67 (100)
268 PHA00616 hypothetical protein 21.5 50 0.0011 19.9 0.9 17 53-69 2-18 (44)
269 PF12874 zf-met: Zinc-finger o 21.4 34 0.00074 17.0 0.1 13 54-66 2-14 (25)
270 KOG2231 Predicted E3 ubiquitin 21.1 68 0.0015 30.2 2.1 44 15-62 2-51 (669)
271 PRK06393 rpoE DNA-directed RNA 21.1 57 0.0012 21.3 1.2 26 91-122 5-30 (64)
272 PF09237 GAGA: GAGA factor; I 21.0 54 0.0012 20.6 1.0 12 53-64 25-36 (54)
273 smart00531 TFIIE Transcription 20.9 65 0.0014 23.9 1.6 10 53-62 100-109 (147)
274 TIGR03830 CxxCG_CxxCG_HTH puta 20.8 64 0.0014 22.7 1.5 43 16-65 1-44 (127)
275 PRK11088 rrmA 23S rRNA methylt 20.6 67 0.0015 26.0 1.8 26 13-39 2-27 (272)
276 PF12172 DUF35_N: Rubredoxin-l 20.5 47 0.001 18.6 0.6 12 107-118 9-20 (37)
277 cd00730 rubredoxin Rubredoxin; 20.5 59 0.0013 20.0 1.1 11 51-61 33-43 (50)
278 COG1571 Predicted DNA-binding 20.4 59 0.0013 28.9 1.5 34 90-124 349-383 (421)
279 PRK00464 nrdR transcriptional 20.4 36 0.00078 25.9 0.2 10 53-62 1-10 (154)
280 PRK04179 rpl37e 50S ribosomal 20.4 54 0.0012 21.2 0.9 26 89-117 15-40 (62)
281 cd00350 rubredoxin_like Rubred 20.4 55 0.0012 18.0 0.9 10 52-61 17-26 (33)
282 PF11781 RRN7: RNA polymerase 20.3 62 0.0013 18.4 1.1 24 15-38 10-34 (36)
283 PF01873 eIF-5_eIF-2B: Domain 20.2 50 0.0011 24.2 0.9 27 91-117 93-122 (125)
No 1
>KOG1940 consensus Zn-finger protein [General function prediction only]
Probab=99.95 E-value=5.8e-29 Score=203.61 Aligned_cols=126 Identities=48% Similarity=0.970 Sum_probs=119.9
Q ss_pred CCCCcceecCCCccccccccccccCcCCccEEecCCChhhHHHHHHHHhcCCCCCCCCCCCccchhHHHHhHHHHHhcCC
Q 031240 1 MKDKHRCVERAMHHNCPICFEFIFDTMKDITVLRCGHTIHLECLKEMEKHYRYTCPVCSKSLWDMSKLWSKIDQEIASTP 80 (163)
Q Consensus 1 ~~~~H~c~e~s~~~~CpIC~e~l~~s~~~~~~L~CGH~fh~~Cl~~~~~~~~~~CPiCr~~~~~~~~~~~~l~~~~~~~~ 80 (163)
+.++|+|+|++++.+||||.|.||++...+..++|||++|.+|++++...+ |+||+|.+ +.+|+.+|++++.+++.++
T Consensus 146 ~~~~H~c~e~~~~~ncPic~e~l~~s~~~~~~~~CgH~~h~~cf~e~~~~~-y~CP~C~~-~~d~~~~~~~~d~~l~~~~ 223 (276)
T KOG1940|consen 146 LSNWHKCVERSSEFNCPICKEYLFLSFEDAGVLKCGHYMHSRCFEEMICEG-YTCPICSK-PGDMSHYFRKLDKELAGSP 223 (276)
T ss_pred cccccchhhhcccCCCchhHHHhccccccCCccCcccchHHHHHHHHhccC-CCCCcccc-hHHHHHHHHHHHHHHhcCC
Confidence 356799999999999999999999999999999999999999999998866 99999999 9999999999999999999
Q ss_pred CChhhhcCcceeeCCCCCCCCcccceeeeccCCCCCCCccccccCCCC
Q 031240 81 MPAMYQNKMVWILCNDCGANSHVQFHVIAHKCLSCKSYNTRQTRGDTA 128 (163)
Q Consensus 81 ~p~e~~~~~~~i~C~dC~~~~~~~~h~~~~kC~~C~synt~~~~~~~~ 128 (163)
||++|++++++|+||||+..++++||++++||+.|+|||||.++.+..
T Consensus 224 ~p~~y~~~~~~i~cndC~~~~~~k~~~l~~kc~~c~~~~~r~~~~~~~ 271 (276)
T KOG1940|consen 224 MPEEYKNKTQDILCNDCGSGTNVKYHILYHKCGKCGSYNTRMISDPSK 271 (276)
T ss_pred CCchhhchhheeeccCCCCCCccceehhhhhCCCcccceeeeccCCCc
Confidence 999999999999999999999999999999999999999999985554
No 2
>PF14599 zinc_ribbon_6: Zinc-ribbon; PDB: 2K2D_A.
Probab=99.90 E-value=9.9e-26 Score=146.19 Aligned_cols=61 Identities=62% Similarity=1.153 Sum_probs=22.3
Q ss_pred ccchhHHHHhHHHHHhcCCCChhhhcCcceeeCCCCCCCCcccceeeeccCCCCCCCcccc
Q 031240 62 LWDMSKLWSKIDQEIASTPMPAMYQNKMVWILCNDCGANSHVQFHVIAHKCLSCKSYNTRQ 122 (163)
Q Consensus 62 ~~~~~~~~~~l~~~~~~~~~p~e~~~~~~~i~C~dC~~~~~~~~h~~~~kC~~C~synt~~ 122 (163)
+.||+..|+.||++++.+|||++|++++++|+||||++++.++|||+|+||.+|+||||++
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 3578999999999999999999999999999999999999999999999999999999985
No 3
>KOG0804 consensus Cytoplasmic Zn-finger protein BRAP2 (BRCA1 associated protein) [General function prediction only]
Probab=99.81 E-value=4.2e-21 Score=164.30 Aligned_cols=112 Identities=26% Similarity=0.519 Sum_probs=97.9
Q ss_pred ccccccccccccCcCCccEEecCCChhhHHHHHHHHhcCCCCCCCCCCCccchhHHHHhHHHHHhcCCCChhhhcCccee
Q 031240 13 HHNCPICFEFIFDTMKDITVLRCGHTIHLECLKEMEKHYRYTCPVCSKSLWDMSKLWSKIDQEIASTPMPAMYQNKMVWI 92 (163)
Q Consensus 13 ~~~CpIC~e~l~~s~~~~~~L~CGH~fh~~Cl~~~~~~~~~~CPiCr~~~~~~~~~~~~l~~~~~~~~~p~e~~~~~~~i 92 (163)
-..||||+|.|.++...++.+.|.|+||..|+..|.. .+||+||.... |+. ...-
T Consensus 175 LPTCpVCLERMD~s~~gi~t~~c~Hsfh~~cl~~w~~---~scpvcR~~q~------------------p~~----ve~~ 229 (493)
T KOG0804|consen 175 LPTCPVCLERMDSSTTGILTILCNHSFHCSCLMKWWD---SSCPVCRYCQS------------------PSV----VESS 229 (493)
T ss_pred CCCcchhHhhcCccccceeeeecccccchHHHhhccc---CcChhhhhhcC------------------cch----hhhh
Confidence 4689999999998888889999999999999999976 57999997531 111 1123
Q ss_pred eCCCCCCCCcccceeeeccCCC--CCCCccccccCCCCCCCccccccccccceecccccccc
Q 031240 93 LCNDCGANSHVQFHVIAHKCLS--CKSYNTRQTRGDTATTCSSGDELTILSHHWDYQQHASV 152 (163)
Q Consensus 93 ~C~dC~~~~~~~~h~~~~kC~~--C~synt~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 152 (163)
.|..|+...++ |+++.|++ ||+|+..|++.|++++.|+++++|.++++|||.||.||
T Consensus 230 ~c~~c~~~~~L---wicliCg~vgcgrY~eghA~rHweet~H~yalel~tqrVWDYAGDnYV 288 (493)
T KOG0804|consen 230 LCLACGCTEDL---WICLICGNVGCGRYKEGHARRHWEETGHCYALELETQRVWDYAGDNYV 288 (493)
T ss_pred hhhhhcccccE---EEEEEccceecccccchhHHHHHHhhcceEEEeecceeeeecccchhh
Confidence 59999987776 99999998 99999999999999999999999999999999999999
No 4
>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=99.40 E-value=7.9e-14 Score=84.69 Aligned_cols=43 Identities=44% Similarity=0.977 Sum_probs=36.8
Q ss_pred ccccccccccCcCCccEEecCCChhhHHHHHHHHhcCCCCCCCCC
Q 031240 15 NCPICFEFIFDTMKDITVLRCGHTIHLECLKEMEKHYRYTCPVCS 59 (163)
Q Consensus 15 ~CpIC~e~l~~s~~~~~~L~CGH~fh~~Cl~~~~~~~~~~CPiCr 59 (163)
+|+||++.+.+ ...++.++|||.||.+||.+|++. +.+||+||
T Consensus 2 ~C~IC~~~~~~-~~~~~~l~C~H~fh~~Ci~~~~~~-~~~CP~CR 44 (44)
T PF13639_consen 2 ECPICLEEFED-GEKVVKLPCGHVFHRSCIKEWLKR-NNSCPVCR 44 (44)
T ss_dssp CETTTTCBHHT-TSCEEEETTSEEEEHHHHHHHHHH-SSB-TTTH
T ss_pred CCcCCChhhcC-CCeEEEccCCCeeCHHHHHHHHHh-CCcCCccC
Confidence 79999999644 577788999999999999999986 57999996
No 5
>PF15227 zf-C3HC4_4: zinc finger of C3HC4-type, RING; PDB: 2EGP_A 2ECV_A 2ECJ_A 2YSL_A 2YSJ_A.
Probab=99.20 E-value=1.2e-11 Score=74.72 Aligned_cols=39 Identities=41% Similarity=1.059 Sum_probs=30.1
Q ss_pred cccccccccCcCCccEEecCCChhhHHHHHHHHhcC---CCCCCCC
Q 031240 16 CPICFEFIFDTMKDITVLRCGHTIHLECLKEMEKHY---RYTCPVC 58 (163)
Q Consensus 16 CpIC~e~l~~s~~~~~~L~CGH~fh~~Cl~~~~~~~---~~~CPiC 58 (163)
||||++. .++|++|+|||+||..||.+|++.. .+.||+|
T Consensus 1 CpiC~~~----~~~Pv~l~CGH~FC~~Cl~~~~~~~~~~~~~CP~C 42 (42)
T PF15227_consen 1 CPICLDL----FKDPVSLPCGHSFCRSCLERLWKEPSGSGFSCPEC 42 (42)
T ss_dssp ETTTTSB-----SSEEE-SSSSEEEHHHHHHHHCCSSSST---SSS
T ss_pred CCccchh----hCCccccCCcCHHHHHHHHHHHHccCCcCCCCcCC
Confidence 8999987 5788999999999999999998753 2579988
No 6
>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=99.13 E-value=3.1e-11 Score=71.49 Aligned_cols=39 Identities=36% Similarity=0.962 Sum_probs=31.8
Q ss_pred cccccccccCcCCccEEecCCChhhHHHHHHHHhcCCCCCCCC
Q 031240 16 CPICFEFIFDTMKDITVLRCGHTIHLECLKEMEKHYRYTCPVC 58 (163)
Q Consensus 16 CpIC~e~l~~s~~~~~~L~CGH~fh~~Cl~~~~~~~~~~CPiC 58 (163)
|+||++.+. ++.+.++|||+||.+|+.+|++. +.+||+|
T Consensus 1 C~iC~~~~~---~~~~~~~CGH~fC~~C~~~~~~~-~~~CP~C 39 (39)
T PF13923_consen 1 CPICLDELR---DPVVVTPCGHSFCKECIEKYLEK-NPKCPVC 39 (39)
T ss_dssp ETTTTSB-S---SEEEECTTSEEEEHHHHHHHHHC-TSB-TTT
T ss_pred CCCCCCccc---CcCEECCCCCchhHHHHHHHHHC-cCCCcCC
Confidence 899998742 33368899999999999999996 6899998
No 7
>PF12678 zf-rbx1: RING-H2 zinc finger; InterPro: IPR024766 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This domain constitutes a conserved region found in proteins that participate in diverse functions relevant to chromosome metabolism and cell cycle control [].The domain contains 8 cysteine/ histidine residues which are proposed to be the conserved residues involved in zinc binding.; PDB: 4A0C_D 4A0L_I 4A0K_B 2ECL_A 1LDK_C 3RTR_F 3DQV_Y 1U6G_B 1LDJ_B 2HYE_D ....
Probab=99.13 E-value=5e-11 Score=80.12 Aligned_cols=47 Identities=36% Similarity=0.747 Sum_probs=35.9
Q ss_pred CccccccccccccCc---------CCccEEecCCChhhHHHHHHHHhcCCCCCCCCC
Q 031240 12 MHHNCPICFEFIFDT---------MKDITVLRCGHTIHLECLKEMEKHYRYTCPVCS 59 (163)
Q Consensus 12 ~~~~CpIC~e~l~~s---------~~~~~~L~CGH~fh~~Cl~~~~~~~~~~CPiCr 59 (163)
.+.+|+||++.|.+. ...++..+|||.||..||.+|++. +.+||+||
T Consensus 18 ~~d~C~IC~~~l~~~~~~~~~~~~~~~i~~~~C~H~FH~~Ci~~Wl~~-~~~CP~CR 73 (73)
T PF12678_consen 18 ADDNCAICREPLEDPCPECQAPQDECPIVWGPCGHIFHFHCISQWLKQ-NNTCPLCR 73 (73)
T ss_dssp CCSBETTTTSBTTSTTCCHHHCTTTS-EEEETTSEEEEHHHHHHHHTT-SSB-TTSS
T ss_pred cCCcccccChhhhChhhhhcCCccccceEecccCCCEEHHHHHHHHhc-CCcCCCCC
Confidence 456799999997333 234456699999999999999985 46999997
No 8
>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=99.09 E-value=6e-11 Score=73.85 Aligned_cols=46 Identities=37% Similarity=0.927 Sum_probs=38.6
Q ss_pred ccccccccccccCcCCccEEecCCCh-hhHHHHHHHHhcCCCCCCCCCCCcc
Q 031240 13 HHNCPICFEFIFDTMKDITVLRCGHT-IHLECLKEMEKHYRYTCPVCSKSLW 63 (163)
Q Consensus 13 ~~~CpIC~e~l~~s~~~~~~L~CGH~-fh~~Cl~~~~~~~~~~CPiCr~~~~ 63 (163)
+..|+||++. ...++++||||. ||..|+.+|+. ...+||+||+++.
T Consensus 2 ~~~C~iC~~~----~~~~~~~pCgH~~~C~~C~~~~~~-~~~~CP~Cr~~i~ 48 (50)
T PF13920_consen 2 DEECPICFEN----PRDVVLLPCGHLCFCEECAERLLK-RKKKCPICRQPIE 48 (50)
T ss_dssp HSB-TTTSSS----BSSEEEETTCEEEEEHHHHHHHHH-TTSBBTTTTBB-S
T ss_pred cCCCccCCcc----CCceEEeCCCChHHHHHHhHHhcc-cCCCCCcCChhhc
Confidence 5789999986 566788999999 99999999988 5689999999874
No 9
>cd00162 RING RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in mediating protein-protein interactions; identified in a proteins with a wide range of functions such as viral replication, signal transduction, and development; has two variants, the C3HC4-type and a C3H2C3-type (RING-H2 finger), which have different cysteine/histidine pattern; a subset of RINGs are associated with B-Boxes (C-X2-H-X7-C-X7-C-X2-C-H-X2-H)
Probab=99.08 E-value=1.3e-10 Score=69.05 Aligned_cols=45 Identities=33% Similarity=0.868 Sum_probs=36.1
Q ss_pred ccccccccccCcCCccEEecCCChhhHHHHHHHHhcCCCCCCCCCCCc
Q 031240 15 NCPICFEFIFDTMKDITVLRCGHTIHLECLKEMEKHYRYTCPVCSKSL 62 (163)
Q Consensus 15 ~CpIC~e~l~~s~~~~~~L~CGH~fh~~Cl~~~~~~~~~~CPiCr~~~ 62 (163)
.|+||++.+ .....+++|||.||..|+..|++....+||+|++.+
T Consensus 1 ~C~iC~~~~---~~~~~~~~C~H~~c~~C~~~~~~~~~~~Cp~C~~~~ 45 (45)
T cd00162 1 ECPICLEEF---REPVVLLPCGHVFCRSCIDKWLKSGKNTCPLCRTPI 45 (45)
T ss_pred CCCcCchhh---hCceEecCCCChhcHHHHHHHHHhCcCCCCCCCCcC
Confidence 599999874 234445569999999999999986568899999753
No 10
>PHA02929 N1R/p28-like protein; Provisional
Probab=99.06 E-value=1.1e-10 Score=94.52 Aligned_cols=54 Identities=30% Similarity=0.682 Sum_probs=41.9
Q ss_pred CCCccccccccccccCcCC----ccEEecCCChhhHHHHHHHHhcCCCCCCCCCCCccc
Q 031240 10 RAMHHNCPICFEFIFDTMK----DITVLRCGHTIHLECLKEMEKHYRYTCPVCSKSLWD 64 (163)
Q Consensus 10 ~s~~~~CpIC~e~l~~s~~----~~~~L~CGH~fh~~Cl~~~~~~~~~~CPiCr~~~~~ 64 (163)
.+.+.+||||+|.+.+... -+++++|||.||..||.+|+. ...+||+||..+..
T Consensus 171 ~~~~~eC~ICle~~~~~~~~~~~~~vl~~C~H~FC~~CI~~Wl~-~~~tCPlCR~~~~~ 228 (238)
T PHA02929 171 RSKDKECAICMEKVYDKEIKNMYFGILSNCNHVFCIECIDIWKK-EKNTCPVCRTPFIS 228 (238)
T ss_pred CCCCCCCccCCcccccCccccccceecCCCCCcccHHHHHHHHh-cCCCCCCCCCEeeE
Confidence 3557899999998654321 134568999999999999998 45799999998743
No 11
>PLN03208 E3 ubiquitin-protein ligase RMA2; Provisional
Probab=99.05 E-value=2.4e-10 Score=89.72 Aligned_cols=55 Identities=25% Similarity=0.612 Sum_probs=43.8
Q ss_pred ceecCCCccccccccccccCcCCccEEecCCChhhHHHHHHHHhc---------------CCCCCCCCCCCccc
Q 031240 6 RCVERAMHHNCPICFEFIFDTMKDITVLRCGHTIHLECLKEMEKH---------------YRYTCPVCSKSLWD 64 (163)
Q Consensus 6 ~c~e~s~~~~CpIC~e~l~~s~~~~~~L~CGH~fh~~Cl~~~~~~---------------~~~~CPiCr~~~~~ 64 (163)
+=++...+..|+||++. .+++++++|||.||..||.+|+.. ...+||+||..+..
T Consensus 11 ~~~~~~~~~~CpICld~----~~dPVvT~CGH~FC~~CI~~wl~~s~~s~~~~~~~~~~k~~~~CPvCR~~Is~ 80 (193)
T PLN03208 11 TLVDSGGDFDCNICLDQ----VRDPVVTLCGHLFCWPCIHKWTYASNNSRQRVDQYDHKREPPKCPVCKSDVSE 80 (193)
T ss_pred eeccCCCccCCccCCCc----CCCcEEcCCCchhHHHHHHHHHHhccccccccccccccCCCCcCCCCCCcCCh
Confidence 33445567899999986 467788999999999999999742 23579999999843
No 12
>PF13445 zf-RING_UBOX: RING-type zinc-finger; PDB: 2CT2_A.
Probab=99.05 E-value=9.2e-11 Score=71.15 Aligned_cols=40 Identities=40% Similarity=0.924 Sum_probs=25.1
Q ss_pred cccccccccCcCCccEEecCCChhhHHHHHHHHhcC---CCCCC
Q 031240 16 CPICFEFIFDTMKDITVLRCGHTIHLECLKEMEKHY---RYTCP 56 (163)
Q Consensus 16 CpIC~e~l~~s~~~~~~L~CGH~fh~~Cl~~~~~~~---~~~CP 56 (163)
||||.| +.+....|++|+|||+|+.+|++++.+.+ .++||
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 66667889999999999999999998753 56777
No 13
>PF14634 zf-RING_5: zinc-RING finger domain
Probab=99.04 E-value=2.2e-10 Score=69.58 Aligned_cols=44 Identities=34% Similarity=0.831 Sum_probs=37.5
Q ss_pred ccccccccccCcCCccEEecCCChhhHHHHHHHHhcCCCCCCCCCC
Q 031240 15 NCPICFEFIFDTMKDITVLRCGHTIHLECLKEMEKHYRYTCPVCSK 60 (163)
Q Consensus 15 ~CpIC~e~l~~s~~~~~~L~CGH~fh~~Cl~~~~~~~~~~CPiCr~ 60 (163)
.|+||++.+ +....+.+++|||+||..|+..+. .....||+||+
T Consensus 1 ~C~~C~~~~-~~~~~~~l~~CgH~~C~~C~~~~~-~~~~~CP~C~k 44 (44)
T PF14634_consen 1 HCNICFEKY-SEERRPRLTSCGHIFCEKCLKKLK-GKSVKCPICRK 44 (44)
T ss_pred CCcCcCccc-cCCCCeEEcccCCHHHHHHHHhhc-CCCCCCcCCCC
Confidence 489999986 555678899999999999999998 34678999985
No 14
>COG5243 HRD1 HRD ubiquitin ligase complex, ER membrane component [Posttranslational modification, protein turnover, chaperones]
Probab=99.03 E-value=9.3e-11 Score=99.42 Aligned_cols=55 Identities=33% Similarity=0.809 Sum_probs=46.5
Q ss_pred CCCccccccccccccCcC---------CccEEecCCChhhHHHHHHHHhcCCCCCCCCCCCc-cch
Q 031240 10 RAMHHNCPICFEFIFDTM---------KDITVLRCGHTIHLECLKEMEKHYRYTCPVCSKSL-WDM 65 (163)
Q Consensus 10 ~s~~~~CpIC~e~l~~s~---------~~~~~L~CGH~fh~~Cl~~~~~~~~~~CPiCr~~~-~~~ 65 (163)
...|..|.||+|+|+.+. ..|+.|||||.+|.+|++.|++. +-+||+||.++ .|+
T Consensus 284 ~n~D~~C~ICmde~~h~~~~~~~~~~~~~pKrLpCGHilHl~CLknW~ER-qQTCPICr~p~ifd~ 348 (491)
T COG5243 284 TNSDRTCTICMDEMFHPDHEPLPRGLDMTPKRLPCGHILHLHCLKNWLER-QQTCPICRRPVIFDQ 348 (491)
T ss_pred cCCCCeEEEecccccCCCCccCcccccCCcccccccceeeHHHHHHHHHh-ccCCCcccCcccccc
Confidence 567899999999987665 35688999999999999999995 57999999994 444
No 15
>PF00097 zf-C3HC4: Zinc finger, C3HC4 type (RING finger); InterPro: IPR018957 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. The C3HC4 type zinc-finger (RING finger) is a cysteine-rich domain of 40 to 60 residues that coordinates two zinc ions, and has the consensus sequence: C-X2-C-X(9-39)-C-X(1-3)-H-X(2-3)-C-X2-C-X(4-48)-C-X2-C where X is any amino acid []. Many proteins containing a RING finger play a key role in the ubiquitination pathway []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; PDB: 1CHC_A 2ECW_A 2Y43_B 1V87_A 2DJB_A 2H0D_B 3RPG_C 3KNV_A 2CKL_B 1JM7_A ....
Probab=98.99 E-value=3.3e-10 Score=67.41 Aligned_cols=39 Identities=38% Similarity=0.979 Sum_probs=33.0
Q ss_pred cccccccccCcCCcc-EEecCCChhhHHHHHHHHh-cCCCCCCCC
Q 031240 16 CPICFEFIFDTMKDI-TVLRCGHTIHLECLKEMEK-HYRYTCPVC 58 (163)
Q Consensus 16 CpIC~e~l~~s~~~~-~~L~CGH~fh~~Cl~~~~~-~~~~~CPiC 58 (163)
|+||++.+ ..+ .+++|||+||..|+.+|++ .....||+|
T Consensus 1 C~iC~~~~----~~~~~~~~C~H~fC~~C~~~~~~~~~~~~CP~C 41 (41)
T PF00097_consen 1 CPICLEPF----EDPVILLPCGHSFCRDCLRKWLENSGSVKCPLC 41 (41)
T ss_dssp ETTTSSBC----SSEEEETTTSEEEEHHHHHHHHHHTSSSBTTTT
T ss_pred CCcCCccc----cCCCEEecCCCcchHHHHHHHHHhcCCccCCcC
Confidence 89999874 333 4889999999999999998 567889998
No 16
>KOG4628 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=98.98 E-value=2.8e-10 Score=96.42 Aligned_cols=49 Identities=29% Similarity=0.778 Sum_probs=42.5
Q ss_pred cccccccccccCcCCccEEecCCChhhHHHHHHHHhcCCCCCCCCCCCcc
Q 031240 14 HNCPICFEFIFDTMKDITVLRCGHTIHLECLKEMEKHYRYTCPVCSKSLW 63 (163)
Q Consensus 14 ~~CpIC~e~l~~s~~~~~~L~CGH~fh~~Cl~~~~~~~~~~CPiCr~~~~ 63 (163)
..|.||+|++ ......++|||+|.||..||+.|+......||+|+..+.
T Consensus 230 ~~CaIClEdY-~~GdklRiLPC~H~FH~~CIDpWL~~~r~~CPvCK~di~ 278 (348)
T KOG4628|consen 230 DTCAICLEDY-EKGDKLRILPCSHKFHVNCIDPWLTQTRTFCPVCKRDIR 278 (348)
T ss_pred ceEEEeeccc-ccCCeeeEecCCCchhhccchhhHhhcCccCCCCCCcCC
Confidence 4899999995 556778899999999999999999866566999999874
No 17
>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=98.93 E-value=1.3e-09 Score=62.46 Aligned_cols=39 Identities=49% Similarity=1.056 Sum_probs=33.9
Q ss_pred cccccccccCcCCccEEecCCChhhHHHHHHHHhcCCCCCCCC
Q 031240 16 CPICFEFIFDTMKDITVLRCGHTIHLECLKEMEKHYRYTCPVC 58 (163)
Q Consensus 16 CpIC~e~l~~s~~~~~~L~CGH~fh~~Cl~~~~~~~~~~CPiC 58 (163)
|+||++. .+.++.++|||.||..|++.|+.....+||+|
T Consensus 1 C~iC~~~----~~~~~~~~C~H~~c~~C~~~~~~~~~~~CP~C 39 (39)
T smart00184 1 CPICLEE----LKDPVVLPCGHTFCRSCIRKWLKSGNNTCPIC 39 (39)
T ss_pred CCcCccC----CCCcEEecCCChHHHHHHHHHHHhCcCCCCCC
Confidence 7899976 56778899999999999999988556789987
No 18
>PHA02926 zinc finger-like protein; Provisional
Probab=98.88 E-value=1.6e-09 Score=86.56 Aligned_cols=54 Identities=19% Similarity=0.553 Sum_probs=41.6
Q ss_pred CCCccccccccccccCcC-----CccEEecCCChhhHHHHHHHHhcC-----CCCCCCCCCCcc
Q 031240 10 RAMHHNCPICFEFIFDTM-----KDITVLRCGHTIHLECLKEMEKHY-----RYTCPVCSKSLW 63 (163)
Q Consensus 10 ~s~~~~CpIC~e~l~~s~-----~~~~~L~CGH~fh~~Cl~~~~~~~-----~~~CPiCr~~~~ 63 (163)
.+.+..|+||+|.+++.. +.....+|+|.||..||..|.... ...||+||..+.
T Consensus 167 ~SkE~eCgICmE~I~eK~~~~eRrFGIL~~CnHsFCl~CIr~Wr~~r~~~~~~rsCPiCR~~f~ 230 (242)
T PHA02926 167 VSKEKECGICYEVVYSKRLENDRYFGLLDSCNHIFCITCINIWHRTRRETGASDNCPICRTRFR 230 (242)
T ss_pred ccCCCCCccCccccccccccccccccccCCCCchHHHHHHHHHHHhccccCcCCcCCCCcceee
Confidence 466899999999865431 224556999999999999999742 345999999864
No 19
>KOG0320 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=98.84 E-value=2.1e-09 Score=83.02 Aligned_cols=49 Identities=31% Similarity=0.735 Sum_probs=40.2
Q ss_pred CccccccccccccCcCCccEEecCCChhhHHHHHHHHhcCCCCCCCCCCCcc
Q 031240 12 MHHNCPICFEFIFDTMKDITVLRCGHTIHLECLKEMEKHYRYTCPVCSKSLW 63 (163)
Q Consensus 12 ~~~~CpIC~e~l~~s~~~~~~L~CGH~fh~~Cl~~~~~~~~~~CPiCr~~~~ 63 (163)
.-..|||||+.+ +.+-++...|||.||..||+..+.. ...||+|++.+.
T Consensus 130 ~~~~CPiCl~~~--sek~~vsTkCGHvFC~~Cik~alk~-~~~CP~C~kkIt 178 (187)
T KOG0320|consen 130 GTYKCPICLDSV--SEKVPVSTKCGHVFCSQCIKDALKN-TNKCPTCRKKIT 178 (187)
T ss_pred cccCCCceecch--hhccccccccchhHHHHHHHHHHHh-CCCCCCcccccc
Confidence 348999999973 3455577899999999999999884 578999998763
No 20
>KOG0823 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=98.80 E-value=3.2e-09 Score=85.00 Aligned_cols=50 Identities=30% Similarity=0.654 Sum_probs=42.2
Q ss_pred CCCccccccccccccCcCCccEEecCCChhhHHHHHHHHhcC--CCCCCCCCCCcc
Q 031240 10 RAMHHNCPICFEFIFDTMKDITVLRCGHTIHLECLKEMEKHY--RYTCPVCSKSLW 63 (163)
Q Consensus 10 ~s~~~~CpIC~e~l~~s~~~~~~L~CGH~fh~~Cl~~~~~~~--~~~CPiCr~~~~ 63 (163)
.+...+|.||+|. .++|++..|||.||+.||.+|+... ...||+|+..+.
T Consensus 44 ~~~~FdCNICLd~----akdPVvTlCGHLFCWpClyqWl~~~~~~~~cPVCK~~Vs 95 (230)
T KOG0823|consen 44 DGGFFDCNICLDL----AKDPVVTLCGHLFCWPCLYQWLQTRPNSKECPVCKAEVS 95 (230)
T ss_pred CCCceeeeeeccc----cCCCEEeecccceehHHHHHHHhhcCCCeeCCccccccc
Confidence 3556799999975 6889999999999999999999753 456899998874
No 21
>KOG0317 consensus Predicted E3 ubiquitin ligase, integral peroxisomal membrane protein [Posttranslational modification, protein turnover, chaperones]
Probab=98.75 E-value=4.7e-09 Score=86.42 Aligned_cols=47 Identities=23% Similarity=0.672 Sum_probs=40.1
Q ss_pred ccccccccccccCcCCccEEecCCChhhHHHHHHHHhcCCCCCCCCCCCccc
Q 031240 13 HHNCPICFEFIFDTMKDITVLRCGHTIHLECLKEMEKHYRYTCPVCSKSLWD 64 (163)
Q Consensus 13 ~~~CpIC~e~l~~s~~~~~~L~CGH~fh~~Cl~~~~~~~~~~CPiCr~~~~~ 64 (163)
...|.+|+|. ...|..+||||.||+.||.+|... ...||+||..+..
T Consensus 239 ~~kC~LCLe~----~~~pSaTpCGHiFCWsCI~~w~~e-k~eCPlCR~~~~p 285 (293)
T KOG0317|consen 239 TRKCSLCLEN----RSNPSATPCGHIFCWSCILEWCSE-KAECPLCREKFQP 285 (293)
T ss_pred CCceEEEecC----CCCCCcCcCcchHHHHHHHHHHcc-ccCCCcccccCCC
Confidence 4679999986 567889999999999999999974 4669999988643
No 22
>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=98.75 E-value=1e-08 Score=66.00 Aligned_cols=44 Identities=30% Similarity=0.458 Sum_probs=38.8
Q ss_pred cccccccccccCcCCccEEecCCChhhHHHHHHHHhcCCCCCCCCCCCc
Q 031240 14 HNCPICFEFIFDTMKDITVLRCGHTIHLECLKEMEKHYRYTCPVCSKSL 62 (163)
Q Consensus 14 ~~CpIC~e~l~~s~~~~~~L~CGH~fh~~Cl~~~~~~~~~~CPiCr~~~ 62 (163)
..||||++.| ++|++++|||+|+..||.+|+.. ..+||+|++.+
T Consensus 2 ~~Cpi~~~~~----~~Pv~~~~G~v~~~~~i~~~~~~-~~~cP~~~~~~ 45 (63)
T smart00504 2 FLCPISLEVM----KDPVILPSGQTYERRAIEKWLLS-HGTDPVTGQPL 45 (63)
T ss_pred cCCcCCCCcC----CCCEECCCCCEEeHHHHHHHHHH-CCCCCCCcCCC
Confidence 5799999974 55788999999999999999985 67899999987
No 23
>PF12861 zf-Apc11: Anaphase-promoting complex subunit 11 RING-H2 finger
Probab=98.70 E-value=2.1e-08 Score=69.03 Aligned_cols=34 Identities=21% Similarity=0.645 Sum_probs=28.2
Q ss_pred ccEEecCCChhhHHHHHHHHhc--CCCCCCCCCCCc
Q 031240 29 DITVLRCGHTIHLECLKEMEKH--YRYTCPVCSKSL 62 (163)
Q Consensus 29 ~~~~L~CGH~fh~~Cl~~~~~~--~~~~CPiCr~~~ 62 (163)
+++.-.|+|.||..||.+|+++ ++..||+||...
T Consensus 46 plv~g~C~H~FH~hCI~kWl~~~~~~~~CPmCR~~w 81 (85)
T PF12861_consen 46 PLVWGKCSHNFHMHCILKWLSTQSSKGQCPMCRQPW 81 (85)
T ss_pred ceeeccCccHHHHHHHHHHHccccCCCCCCCcCCee
Confidence 3445599999999999999985 357899999875
No 24
>COG5540 RING-finger-containing ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=98.68 E-value=1.2e-08 Score=84.71 Aligned_cols=51 Identities=27% Similarity=0.645 Sum_probs=42.8
Q ss_pred CccccccccccccCcCCccEEecCCChhhHHHHHHHHhcCCCCCCCCCCCcc
Q 031240 12 MHHNCPICFEFIFDTMKDITVLRCGHTIHLECLKEMEKHYRYTCPVCSKSLW 63 (163)
Q Consensus 12 ~~~~CpIC~e~l~~s~~~~~~L~CGH~fh~~Cl~~~~~~~~~~CPiCr~~~~ 63 (163)
..-+|.|||+.+ ......++|||.|.||..|+.+|+......||+||..+.
T Consensus 322 ~GveCaICms~f-iK~d~~~vlPC~H~FH~~Cv~kW~~~y~~~CPvCrt~iP 372 (374)
T COG5540 322 KGVECAICMSNF-IKNDRLRVLPCDHRFHVGCVDKWLLGYSNKCPVCRTAIP 372 (374)
T ss_pred CCceEEEEhhhh-cccceEEEeccCceechhHHHHHHhhhcccCCccCCCCC
Confidence 346899999995 455668899999999999999999755578999998764
No 25
>KOG2177 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=98.56 E-value=9.2e-08 Score=76.21 Aligned_cols=45 Identities=33% Similarity=0.846 Sum_probs=38.4
Q ss_pred CCccccccccccccCcCCccEEecCCChhhHHHHHHHHhcCCCCCCCCCC
Q 031240 11 AMHHNCPICFEFIFDTMKDITVLRCGHTIHLECLKEMEKHYRYTCPVCSK 60 (163)
Q Consensus 11 s~~~~CpIC~e~l~~s~~~~~~L~CGH~fh~~Cl~~~~~~~~~~CPiCr~ 60 (163)
.....||||++++ +.+++++|||+||..|+..++. ....||.||.
T Consensus 11 ~~~~~C~iC~~~~----~~p~~l~C~H~~c~~C~~~~~~-~~~~Cp~cr~ 55 (386)
T KOG2177|consen 11 QEELTCPICLEYF----REPVLLPCGHNFCRACLTRSWE-GPLSCPVCRP 55 (386)
T ss_pred cccccChhhHHHh----hcCccccccchHhHHHHHHhcC-CCcCCcccCC
Confidence 3578999999984 4448899999999999999987 6688999994
No 26
>TIGR00599 rad18 DNA repair protein rad18. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=98.50 E-value=7.2e-08 Score=83.41 Aligned_cols=47 Identities=23% Similarity=0.569 Sum_probs=39.8
Q ss_pred CccccccccccccCcCCccEEecCCChhhHHHHHHHHhcCCCCCCCCCCCcc
Q 031240 12 MHHNCPICFEFIFDTMKDITVLRCGHTIHLECLKEMEKHYRYTCPVCSKSLW 63 (163)
Q Consensus 12 ~~~~CpIC~e~l~~s~~~~~~L~CGH~fh~~Cl~~~~~~~~~~CPiCr~~~~ 63 (163)
....|+||++.+ ..|++++|||+||..||..|+.. ...||+|+..+.
T Consensus 25 ~~l~C~IC~d~~----~~PvitpCgH~FCs~CI~~~l~~-~~~CP~Cr~~~~ 71 (397)
T TIGR00599 25 TSLRCHICKDFF----DVPVLTSCSHTFCSLCIRRCLSN-QPKCPLCRAEDQ 71 (397)
T ss_pred cccCCCcCchhh----hCccCCCCCCchhHHHHHHHHhC-CCCCCCCCCccc
Confidence 467999999874 55678999999999999999974 458999999873
No 27
>KOG2164 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=98.45 E-value=8.9e-08 Score=84.14 Aligned_cols=49 Identities=24% Similarity=0.577 Sum_probs=39.4
Q ss_pred CCccccccccccccCcCCccEEecCCChhhHHHHHHHHhcC----CCCCCCCCCCcc
Q 031240 11 AMHHNCPICFEFIFDTMKDITVLRCGHTIHLECLKEMEKHY----RYTCPVCSKSLW 63 (163)
Q Consensus 11 s~~~~CpIC~e~l~~s~~~~~~L~CGH~fh~~Cl~~~~~~~----~~~CPiCr~~~~ 63 (163)
+.+..||||+++ ..-+..+.|||.||..||-+++..+ ...||+|+..+.
T Consensus 184 ~t~~~CPICL~~----~~~p~~t~CGHiFC~~CiLqy~~~s~~~~~~~CPiC~s~I~ 236 (513)
T KOG2164|consen 184 STDMQCPICLEP----PSVPVRTNCGHIFCGPCILQYWNYSAIKGPCSCPICRSTIT 236 (513)
T ss_pred CcCCcCCcccCC----CCcccccccCceeeHHHHHHHHhhhcccCCccCCchhhhcc
Confidence 348999999987 4445666799999999999987653 457999999874
No 28
>KOG0287 consensus Postreplication repair protein RAD18 [Replication, recombination and repair]
Probab=98.44 E-value=1.3e-07 Score=79.61 Aligned_cols=46 Identities=28% Similarity=0.742 Sum_probs=40.8
Q ss_pred ccccccccccccCcCCccEEecCCChhhHHHHHHHHhcCCCCCCCCCCCcc
Q 031240 13 HHNCPICFEFIFDTMKDITVLRCGHTIHLECLKEMEKHYRYTCPVCSKSLW 63 (163)
Q Consensus 13 ~~~CpIC~e~l~~s~~~~~~L~CGH~fh~~Cl~~~~~~~~~~CPiCr~~~~ 63 (163)
-..|.||.|+ ++.|+++||||+||.-||+.++. .+..||.|+.++.
T Consensus 23 lLRC~IC~ey----f~ip~itpCsHtfCSlCIR~~L~-~~p~CP~C~~~~~ 68 (442)
T KOG0287|consen 23 LLRCGICFEY----FNIPMITPCSHTFCSLCIRKFLS-YKPQCPTCCVTVT 68 (442)
T ss_pred HHHHhHHHHH----hcCceeccccchHHHHHHHHHhc-cCCCCCceecccc
Confidence 3589999998 57889999999999999999997 5688999999984
No 29
>KOG0802 consensus E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=98.40 E-value=1.3e-07 Score=84.92 Aligned_cols=52 Identities=31% Similarity=0.614 Sum_probs=42.8
Q ss_pred CCCccccccccccccCcC-CccEEecCCChhhHHHHHHHHhcCCCCCCCCCCCc
Q 031240 10 RAMHHNCPICFEFIFDTM-KDITVLRCGHTIHLECLKEMEKHYRYTCPVCSKSL 62 (163)
Q Consensus 10 ~s~~~~CpIC~e~l~~s~-~~~~~L~CGH~fh~~Cl~~~~~~~~~~CPiCr~~~ 62 (163)
...+..|+||.|.|..+. ..+..|+|||.||..|++.|++. ..+||+||..+
T Consensus 288 ~~~~~~C~IC~e~l~~~~~~~~~rL~C~Hifh~~CL~~W~er-~qtCP~CR~~~ 340 (543)
T KOG0802|consen 288 ALSDELCIICLEELHSGHNITPKRLPCGHIFHDSCLRSWFER-QQTCPTCRTVL 340 (543)
T ss_pred hhcCCeeeeechhhccccccccceeecccchHHHHHHHHHHH-hCcCCcchhhh
Confidence 345889999999986532 23678999999999999999995 68999999954
No 30
>TIGR00570 cdk7 CDK-activating kinase assembly factor MAT1. All proteins in this family for which functions are known are cyclin dependent protein kinases that are components of TFIIH, a complex that is involved in nucleotide excision repair and transcription initiation. Also known as MAT1 (menage a trois 1). This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=98.34 E-value=4.3e-07 Score=76.07 Aligned_cols=50 Identities=26% Similarity=0.586 Sum_probs=36.9
Q ss_pred ccccccccccccCcCC-ccEEecCCChhhHHHHHHHHhcCCCCCCCCCCCc
Q 031240 13 HHNCPICFEFIFDTMK-DITVLRCGHTIHLECLKEMEKHYRYTCPVCSKSL 62 (163)
Q Consensus 13 ~~~CpIC~e~l~~s~~-~~~~L~CGH~fh~~Cl~~~~~~~~~~CPiCr~~~ 62 (163)
+..||||......+.. ...+.+|||.||..|+..++..+...||.|++++
T Consensus 3 ~~~CP~Ck~~~y~np~~kl~i~~CGH~~C~sCv~~l~~~~~~~CP~C~~~l 53 (309)
T TIGR00570 3 DQGCPRCKTTKYRNPSLKLMVNVCGHTLCESCVDLLFVRGSGSCPECDTPL 53 (309)
T ss_pred CCCCCcCCCCCccCcccccccCCCCCcccHHHHHHHhcCCCCCCCCCCCcc
Confidence 4689999984322222 1222279999999999998766677899999876
No 31
>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=98.26 E-value=7.3e-07 Score=59.69 Aligned_cols=49 Identities=27% Similarity=0.370 Sum_probs=38.8
Q ss_pred CccccccccccccCcCCccEEecCCChhhHHHHHHHHhcCCCCCCCCCCCccc
Q 031240 12 MHHNCPICFEFIFDTMKDITVLRCGHTIHLECLKEMEKHYRYTCPVCSKSLWD 64 (163)
Q Consensus 12 ~~~~CpIC~e~l~~s~~~~~~L~CGH~fh~~Cl~~~~~~~~~~CPiCr~~~~~ 64 (163)
.+..|||+.+. .++|+++++||+|...+|.+|+.....+||+++..+..
T Consensus 3 ~~f~CpIt~~l----M~dPVi~~~G~tyer~~I~~~l~~~~~~~P~t~~~l~~ 51 (73)
T PF04564_consen 3 DEFLCPITGEL----MRDPVILPSGHTYERSAIERWLEQNGGTDPFTRQPLSE 51 (73)
T ss_dssp GGGB-TTTSSB-----SSEEEETTSEEEEHHHHHHHHCTTSSB-TTT-SB-SG
T ss_pred cccCCcCcCcH----hhCceeCCcCCEEcHHHHHHHHHcCCCCCCCCCCcCCc
Confidence 35789999987 57889999999999999999999767899999988743
No 32
>COG5574 PEX10 RING-finger-containing E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=98.20 E-value=8e-07 Score=72.58 Aligned_cols=48 Identities=27% Similarity=0.582 Sum_probs=38.8
Q ss_pred CccccccccccccCcCCccEEecCCChhhHHHHHH-HHhcCCCCCCCCCCCcc
Q 031240 12 MHHNCPICFEFIFDTMKDITVLRCGHTIHLECLKE-MEKHYRYTCPVCSKSLW 63 (163)
Q Consensus 12 ~~~~CpIC~e~l~~s~~~~~~L~CGH~fh~~Cl~~-~~~~~~~~CPiCr~~~~ 63 (163)
.+..|+||+|. ...+..++|||.||..||.. |-....-.||+||..+.
T Consensus 214 ~d~kC~lC~e~----~~~ps~t~CgHlFC~~Cl~~~~t~~k~~~CplCRak~~ 262 (271)
T COG5574 214 ADYKCFLCLEE----PEVPSCTPCGHLFCLSCLLISWTKKKYEFCPLCRAKVY 262 (271)
T ss_pred cccceeeeecc----cCCcccccccchhhHHHHHHHHHhhccccCchhhhhcc
Confidence 36789999987 56778899999999999999 66543334999998763
No 33
>PF11793 FANCL_C: FANCL C-terminal domain; PDB: 3K1L_A.
Probab=98.15 E-value=3.4e-07 Score=60.99 Aligned_cols=50 Identities=32% Similarity=0.683 Sum_probs=23.3
Q ss_pred ccccccccccccCcCCccEEe----cCCChhhHHHHHHHHhcC----------CCCCCCCCCCc
Q 031240 13 HHNCPICFEFIFDTMKDITVL----RCGHTIHLECLKEMEKHY----------RYTCPVCSKSL 62 (163)
Q Consensus 13 ~~~CpIC~e~l~~s~~~~~~L----~CGH~fh~~Cl~~~~~~~----------~~~CPiCr~~~ 62 (163)
+.+|+||++++.+....+... .|+..||..||.+|+... ..+||.|++++
T Consensus 2 ~~~C~IC~~~~~~~~~~p~~~C~n~~C~~~fH~~CL~~wf~~~~~~~~~~~~~~G~CP~C~~~i 65 (70)
T PF11793_consen 2 ELECGICYSYRLDDGEIPDVVCPNPSCGKKFHLLCLSEWFLSLEKSRQSFIPIFGECPYCSSPI 65 (70)
T ss_dssp --S-SSS--SS-TT-----B--S-TT----B-SGGGHHHHHHHHSSS-TTT--EEE-TTT-SEE
T ss_pred CCCCCcCCcEecCCCCcCceEcCCcccCCHHHHHHHHHHHHHcccCCeeecccccCCcCCCCee
Confidence 468999999865333333322 899999999999998641 12499999876
No 34
>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=98.15 E-value=3.1e-06 Score=52.62 Aligned_cols=43 Identities=30% Similarity=0.617 Sum_probs=34.0
Q ss_pred ccccccccccCcCCccEEecCC-----ChhhHHHHHHHHhcC-CCCCCCCC
Q 031240 15 NCPICFEFIFDTMKDITVLRCG-----HTIHLECLKEMEKHY-RYTCPVCS 59 (163)
Q Consensus 15 ~CpIC~e~l~~s~~~~~~L~CG-----H~fh~~Cl~~~~~~~-~~~CPiCr 59 (163)
.|-||++. +....+.+.||. |.+|..|+.+|+... ..+||+|+
T Consensus 1 ~CrIC~~~--~~~~~~l~~PC~C~G~~~~vH~~Cl~~W~~~~~~~~C~iC~ 49 (49)
T smart00744 1 ICRICHDE--GDEGDPLVSPCRCKGSLKYVHQECLERWINESGNKTCEICK 49 (49)
T ss_pred CccCCCCC--CCCCCeeEeccccCCchhHHHHHHHHHHHHHcCCCcCCCCC
Confidence 48899982 345667788995 899999999999653 56899995
No 35
>COG5194 APC11 Component of SCF ubiquitin ligase and anaphase-promoting complex [Posttranslational modification, protein turnover, chaperones / Cell division and chromosome partitioning]
Probab=98.06 E-value=6.1e-06 Score=56.05 Aligned_cols=51 Identities=18% Similarity=0.309 Sum_probs=36.8
Q ss_pred CCccccccccccccCcCCcc-EEecCCChhhHHHHHHHHhcCCCCCCCCCCCc
Q 031240 11 AMHHNCPICFEFIFDTMKDI-TVLRCGHTIHLECLKEMEKHYRYTCPVCSKSL 62 (163)
Q Consensus 11 s~~~~CpIC~e~l~~s~~~~-~~L~CGH~fh~~Cl~~~~~~~~~~CPiCr~~~ 62 (163)
.....||-|...+.....-+ +.-.|.|.||..||.+|+.. ...||++|++.
T Consensus 29 him~~C~eCq~~~~~~~eC~v~wG~CnHaFH~HCI~rWL~T-k~~CPld~q~w 80 (88)
T COG5194 29 HIMGTCPECQFGMTPGDECPVVWGVCNHAFHDHCIYRWLDT-KGVCPLDRQTW 80 (88)
T ss_pred cccCcCcccccCCCCCCcceEEEEecchHHHHHHHHHHHhh-CCCCCCCCcee
Confidence 34456666765443333333 44499999999999999985 67899999985
No 36
>COG5432 RAD18 RING-finger-containing E3 ubiquitin ligase [Signal transduction mechanisms]
Probab=98.02 E-value=3.2e-06 Score=70.22 Aligned_cols=45 Identities=27% Similarity=0.489 Sum_probs=39.5
Q ss_pred ccccccccccccCcCCccEEecCCChhhHHHHHHHHhcCCCCCCCCCCCc
Q 031240 13 HHNCPICFEFIFDTMKDITVLRCGHTIHLECLKEMEKHYRYTCPVCSKSL 62 (163)
Q Consensus 13 ~~~CpIC~e~l~~s~~~~~~L~CGH~fh~~Cl~~~~~~~~~~CPiCr~~~ 62 (163)
-..|-||-++ .+.|...+|||+||.-||+.++. .+..||+||...
T Consensus 25 ~lrC~IC~~~----i~ip~~TtCgHtFCslCIR~hL~-~qp~CP~Cr~~~ 69 (391)
T COG5432 25 MLRCRICDCR----ISIPCETTCGHTFCSLCIRRHLG-TQPFCPVCREDP 69 (391)
T ss_pred HHHhhhhhhe----eecceecccccchhHHHHHHHhc-CCCCCccccccH
Confidence 3579999987 47778899999999999999997 568899999986
No 37
>KOG4172 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=97.99 E-value=1.8e-06 Score=54.61 Aligned_cols=53 Identities=28% Similarity=0.680 Sum_probs=40.6
Q ss_pred CccccccccccccCcCCccEEecCCC-hhhHHHHHHHHhcCCCCCCCCCCCccchhHH
Q 031240 12 MHHNCPICFEFIFDTMKDITVLRCGH-TIHLECLKEMEKHYRYTCPVCSKSLWDMSKL 68 (163)
Q Consensus 12 ~~~~CpIC~e~l~~s~~~~~~L~CGH-~fh~~Cl~~~~~~~~~~CPiCr~~~~~~~~~ 68 (163)
-+.+|.||+|. .-+.++..||| -+|..|-.+.++..+-.||+||.++.++-+.
T Consensus 6 ~~dECTICye~----pvdsVlYtCGHMCmCy~Cg~rl~~~~~g~CPiCRapi~dvIkT 59 (62)
T KOG4172|consen 6 WSDECTICYEH----PVDSVLYTCGHMCMCYACGLRLKKALHGCCPICRAPIKDVIKT 59 (62)
T ss_pred cccceeeeccC----cchHHHHHcchHHhHHHHHHHHHHccCCcCcchhhHHHHHHHh
Confidence 34799999986 34446669999 6899998776665678899999998665443
No 38
>KOG1039 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=97.97 E-value=1.6e-06 Score=73.92 Aligned_cols=83 Identities=19% Similarity=0.521 Sum_probs=53.6
Q ss_pred CCCccccccccccccCcC---CccEE-ecCCChhhHHHHHHHHhcC------CCCCCCCCCCccchhH--HHHhHHHHHh
Q 031240 10 RAMHHNCPICFEFIFDTM---KDITV-LRCGHTIHLECLKEMEKHY------RYTCPVCSKSLWDMSK--LWSKIDQEIA 77 (163)
Q Consensus 10 ~s~~~~CpIC~e~l~~s~---~~~~~-L~CGH~fh~~Cl~~~~~~~------~~~CPiCr~~~~~~~~--~~~~l~~~~~ 77 (163)
++.+..|.||+|.+.+.. +.-.+ ++|.|+||..||..|.... ...||.||.....+.. .|. ....+
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 KSSEKECGICMETINEKAASERRFGILPNCNHSFCLNCIRKWRQATQFESKTSKSCPFCRVPSSFVNPSSFWV--ETKEE 235 (344)
T ss_pred ccccccceehhhhccccchhhhhcccCCCcchhhhhcHhHhhhhhhccccccccCCCcccCccccccccceee--eeccc
Confidence 366889999999865433 11122 5799999999999998443 3679999998643222 232 22224
Q ss_pred cCCCChhhhcCcceeeC
Q 031240 78 STPMPAMYQNKMVWILC 94 (163)
Q Consensus 78 ~~~~p~e~~~~~~~i~C 94 (163)
...++++|...+....|
T Consensus 236 k~~li~e~~~~~s~~~c 252 (344)
T KOG1039|consen 236 KQKLIEEYEAEMSAKDC 252 (344)
T ss_pred ccccHHHHHHHhhccch
Confidence 55667777766554433
No 39
>KOG0827 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=97.90 E-value=6.9e-06 Score=70.42 Aligned_cols=50 Identities=26% Similarity=0.573 Sum_probs=39.2
Q ss_pred CccccccccccccCcCCccEEec-CCChhhHHHHHHHHhcC--CCCCCCCCCCc
Q 031240 12 MHHNCPICFEFIFDTMKDITVLR-CGHTIHLECLKEMEKHY--RYTCPVCSKSL 62 (163)
Q Consensus 12 ~~~~CpIC~e~l~~s~~~~~~L~-CGH~fh~~Cl~~~~~~~--~~~CPiCr~~~ 62 (163)
....|.|| +++++...+...+. |||+||..|+.+|++.. +..||+|+-.+
T Consensus 3 i~A~C~Ic-~d~~p~~~~l~~i~~cGhifh~~cl~qwfe~~Ps~R~cpic~ik~ 55 (465)
T KOG0827|consen 3 IMAECHIC-IDGRPNDHELGPIGTCGHIFHTTCLTQWFEGDPSNRGCPICQIKL 55 (465)
T ss_pred ccceeeEe-ccCCccccccccccchhhHHHHHHHHHHHccCCccCCCCceeecc
Confidence 35689999 55677777777675 99999999999999863 35799999443
No 40
>KOG0978 consensus E3 ubiquitin ligase involved in syntaxin degradation [Posttranslational modification, protein turnover, chaperones]
Probab=97.88 E-value=4.1e-06 Score=76.67 Aligned_cols=48 Identities=25% Similarity=0.623 Sum_probs=41.7
Q ss_pred ccccccccccccCcCCccEEecCCChhhHHHHHHHHhcCCCCCCCCCCCccc
Q 031240 13 HHNCPICFEFIFDTMKDITVLRCGHTIHLECLKEMEKHYRYTCPVCSKSLWD 64 (163)
Q Consensus 13 ~~~CpIC~e~l~~s~~~~~~L~CGH~fh~~Cl~~~~~~~~~~CPiCr~~~~~ 64 (163)
-..||+|-.. .++.+++.|||.||..|++........+||.|+.+|+.
T Consensus 643 ~LkCs~Cn~R----~Kd~vI~kC~H~FC~~Cvq~r~etRqRKCP~Cn~aFga 690 (698)
T KOG0978|consen 643 LLKCSVCNTR----WKDAVITKCGHVFCEECVQTRYETRQRKCPKCNAAFGA 690 (698)
T ss_pred ceeCCCccCc----hhhHHHHhcchHHHHHHHHHHHHHhcCCCCCCCCCCCc
Confidence 3679999954 67788889999999999999988778899999999853
No 41
>PF14835 zf-RING_6: zf-RING of BARD1-type protein; PDB: 1JM7_B.
Probab=97.87 E-value=4.2e-06 Score=54.65 Aligned_cols=43 Identities=28% Similarity=0.753 Sum_probs=23.1
Q ss_pred ccccccccccccCcCCccE-EecCCChhhHHHHHHHHhcCCCCCCCCCCCc
Q 031240 13 HHNCPICFEFIFDTMKDIT-VLRCGHTIHLECLKEMEKHYRYTCPVCSKSL 62 (163)
Q Consensus 13 ~~~CpIC~e~l~~s~~~~~-~L~CGH~fh~~Cl~~~~~~~~~~CPiCr~~~ 62 (163)
-..|++|.+.| +.|+ +-.|.|.||+.|+.+-+. ..||+|+.+.
T Consensus 7 lLrCs~C~~~l----~~pv~l~~CeH~fCs~Ci~~~~~---~~CPvC~~Pa 50 (65)
T PF14835_consen 7 LLRCSICFDIL----KEPVCLGGCEHIFCSSCIRDCIG---SECPVCHTPA 50 (65)
T ss_dssp TTS-SSS-S------SS-B---SSS--B-TTTGGGGTT---TB-SSS--B-
T ss_pred hcCCcHHHHHh----cCCceeccCccHHHHHHhHHhcC---CCCCCcCChH
Confidence 35799999874 4454 569999999999988654 4599999987
No 42
>KOG0828 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=97.78 E-value=1.2e-05 Score=70.88 Aligned_cols=51 Identities=29% Similarity=0.637 Sum_probs=38.4
Q ss_pred ccccccccccccCc-------------CCccEEecCCChhhHHHHHHHHhcCCCCCCCCCCCcc
Q 031240 13 HHNCPICFEFIFDT-------------MKDITVLRCGHTIHLECLKEMEKHYRYTCPVCSKSLW 63 (163)
Q Consensus 13 ~~~CpIC~e~l~~s-------------~~~~~~L~CGH~fh~~Cl~~~~~~~~~~CPiCr~~~~ 63 (163)
..+|+|||..+.-. .+..+..||.|.||..|+++|.+..+..||+||..+.
T Consensus 571 t~dC~ICMt~I~l~~~~s~~~~~~~~~~~nYm~tPC~HifH~~CL~~WMd~ykl~CPvCR~pLP 634 (636)
T KOG0828|consen 571 TNDCVICMTPIDLRSTGSDCMVASMMVRRNYMLTPCHHIFHRQCLLQWMDTYKLICPVCRCPLP 634 (636)
T ss_pred cccceEeccccceeeccCcchhhhhhhhccccccchHHHHHHHHHHHHHhhhcccCCccCCCCC
Confidence 46899999864110 1123456999999999999999855568999998764
No 43
>KOG0311 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=97.77 E-value=4.7e-06 Score=70.62 Aligned_cols=47 Identities=30% Similarity=0.723 Sum_probs=39.7
Q ss_pred ccccccccccccCcCCccEEecCCChhhHHHHHHHHhcCCCCCCCCCCCc
Q 031240 13 HHNCPICFEFIFDTMKDITVLRCGHTIHLECLKEMEKHYRYTCPVCSKSL 62 (163)
Q Consensus 13 ~~~CpIC~e~l~~s~~~~~~L~CGH~fh~~Cl~~~~~~~~~~CPiCr~~~ 62 (163)
+..||||++.|. ....+..|+|.||..||..-+..++..||.||+.+
T Consensus 43 ~v~c~icl~llk---~tmttkeClhrfc~~ci~~a~r~gn~ecptcRk~l 89 (381)
T KOG0311|consen 43 QVICPICLSLLK---KTMTTKECLHRFCFDCIWKALRSGNNECPTCRKKL 89 (381)
T ss_pred hhccHHHHHHHH---hhcccHHHHHHHHHHHHHHHHHhcCCCCchHHhhc
Confidence 568999999763 22355699999999999998888889999999987
No 44
>KOG1493 consensus Anaphase-promoting complex (APC), subunit 11 [Cell cycle control, cell division, chromosome partitioning; Posttranslational modification, protein turnover, chaperones]
Probab=97.74 E-value=8.4e-06 Score=54.91 Aligned_cols=48 Identities=23% Similarity=0.479 Sum_probs=33.1
Q ss_pred CccccccccccccCcCCccEEe-cCCChhhHHHHHHHHhc--CCCCCCCCCCCc
Q 031240 12 MHHNCPICFEFIFDTMKDITVL-RCGHTIHLECLKEMEKH--YRYTCPVCSKSL 62 (163)
Q Consensus 12 ~~~~CpIC~e~l~~s~~~~~~L-~CGH~fh~~Cl~~~~~~--~~~~CPiCr~~~ 62 (163)
.+..||-|.- ....-|.++ .|.|.||..||.+|+.. ++-.||+||...
T Consensus 30 Fdg~Cp~Ck~---PgDdCPLv~G~C~h~fh~hCI~~wl~~~tsq~~CPmcRq~~ 80 (84)
T KOG1493|consen 30 FDGCCPDCKL---PGDDCPLVWGYCLHAFHAHCILKWLNTPTSQGQCPMCRQTW 80 (84)
T ss_pred cCCcCCCCcC---CCCCCccHHHHHHHHHHHHHHHHHhcCccccccCCcchhee
Confidence 3444555542 223334444 89999999999999865 356799999875
No 45
>KOG0824 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=97.74 E-value=1.6e-05 Score=66.21 Aligned_cols=50 Identities=28% Similarity=0.493 Sum_probs=41.5
Q ss_pred CCCccccccccccccCcCCccEEecCCChhhHHHHHHHHhcCCCCCCCCCCCcc
Q 031240 10 RAMHHNCPICFEFIFDTMKDITVLRCGHTIHLECLKEMEKHYRYTCPVCSKSLW 63 (163)
Q Consensus 10 ~s~~~~CpIC~e~l~~s~~~~~~L~CGH~fh~~Cl~~~~~~~~~~CPiCr~~~~ 63 (163)
..+..+|+||+.. ..-|+.|+|+|.||.-||+.....+..+|++||.++.
T Consensus 4 ~~~~~eC~IC~nt----~n~Pv~l~C~HkFCyiCiKGsy~ndk~~CavCR~pid 53 (324)
T KOG0824|consen 4 RTKKKECLICYNT----GNCPVNLYCFHKFCYICIKGSYKNDKKTCAVCRFPID 53 (324)
T ss_pred cccCCcceeeecc----CCcCccccccchhhhhhhcchhhcCCCCCceecCCCC
Confidence 4567899999975 4556899999999999999866656678999999983
No 46
>KOG1734 consensus Predicted RING-containing E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=97.66 E-value=1.3e-05 Score=65.97 Aligned_cols=51 Identities=24% Similarity=0.507 Sum_probs=40.7
Q ss_pred CccccccccccccCcCC------ccEEecCCChhhHHHHHHHHhcC-CCCCCCCCCCc
Q 031240 12 MHHNCPICFEFIFDTMK------DITVLRCGHTIHLECLKEMEKHY-RYTCPVCSKSL 62 (163)
Q Consensus 12 ~~~~CpIC~e~l~~s~~------~~~~L~CGH~fh~~Cl~~~~~~~-~~~CPiCr~~~ 62 (163)
.++.|.||...++.+.+ ..-.|.|+|+||..||+.|.--+ ..+||-|++.+
T Consensus 223 ~d~vCaVCg~~~~~s~~eegvienty~LsCnHvFHEfCIrGWcivGKkqtCPYCKekV 280 (328)
T KOG1734|consen 223 SDSVCAVCGQQIDVSVDEEGVIENTYKLSCNHVFHEFCIRGWCIVGKKQTCPYCKEKV 280 (328)
T ss_pred CcchhHhhcchheeecchhhhhhhheeeecccchHHHhhhhheeecCCCCCchHHHHh
Confidence 46899999988765542 34568999999999999997543 46899999886
No 47
>KOG4265 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=97.59 E-value=5e-05 Score=64.47 Aligned_cols=48 Identities=27% Similarity=0.657 Sum_probs=39.6
Q ss_pred CCccccccccccccCcCCccEEecCCC-hhhHHHHHHHHhcCCCCCCCCCCCcc
Q 031240 11 AMHHNCPICFEFIFDTMKDITVLRCGH-TIHLECLKEMEKHYRYTCPVCSKSLW 63 (163)
Q Consensus 11 s~~~~CpIC~e~l~~s~~~~~~L~CGH-~fh~~Cl~~~~~~~~~~CPiCr~~~~ 63 (163)
....+|.||+.. .++.++|||.| -+|..|.+.+.- ....||+||..+.
T Consensus 288 ~~gkeCVIClse----~rdt~vLPCRHLCLCs~Ca~~Lr~-q~n~CPICRqpi~ 336 (349)
T KOG4265|consen 288 ESGKECVICLSE----SRDTVVLPCRHLCLCSGCAKSLRY-QTNNCPICRQPIE 336 (349)
T ss_pred cCCCeeEEEecC----CcceEEecchhhehhHhHHHHHHH-hhcCCCccccchH
Confidence 346799999975 68889999999 589999998763 3467999999874
No 48
>PF14570 zf-RING_4: RING/Ubox like zinc-binding domain; PDB: 1E4U_A 1UR6_B.
Probab=97.48 E-value=7.4e-05 Score=46.18 Aligned_cols=47 Identities=30% Similarity=0.607 Sum_probs=24.7
Q ss_pred cccccccccCcCCccEEecCCChhhHHHHHHHHhcCCCCCCCCCCCc
Q 031240 16 CPICFEFIFDTMKDITVLRCGHTIHLECLKEMEKHYRYTCPVCSKSL 62 (163)
Q Consensus 16 CpIC~e~l~~s~~~~~~L~CGH~fh~~Cl~~~~~~~~~~CPiCr~~~ 62 (163)
||+|.|.|..+.....-=+||..+|..|+...++....+||-||+++
T Consensus 1 cp~C~e~~d~~d~~~~PC~Cgf~IC~~C~~~i~~~~~g~CPgCr~~Y 47 (48)
T PF14570_consen 1 CPLCDEELDETDKDFYPCECGFQICRFCYHDILENEGGRCPGCREPY 47 (48)
T ss_dssp -TTTS-B--CCCTT--SSTTS----HHHHHHHTTSS-SB-TTT--B-
T ss_pred CCCcccccccCCCccccCcCCCcHHHHHHHHHHhccCCCCCCCCCCC
Confidence 79999998433333222388999999999998876678999999864
No 49
>KOG1785 consensus Tyrosine kinase negative regulator CBL [Defense mechanisms]
Probab=97.42 E-value=4.9e-05 Score=65.65 Aligned_cols=50 Identities=30% Similarity=0.626 Sum_probs=42.5
Q ss_pred cCCCccccccccccccCcCCccEEecCCChhhHHHHHHHHhcC-CCCCCCCCCCc
Q 031240 9 ERAMHHNCPICFEFIFDTMKDITVLRCGHTIHLECLKEMEKHY-RYTCPVCSKSL 62 (163)
Q Consensus 9 e~s~~~~CpIC~e~l~~s~~~~~~L~CGH~fh~~Cl~~~~~~~-~~~CPiCr~~~ 62 (163)
-.+.-..|-||-|. .+++.+-||||.+|..|+..|..+. +.+||.||-.+
T Consensus 365 MgsTFeLCKICaen----dKdvkIEPCGHLlCt~CLa~WQ~sd~gq~CPFCRcEI 415 (563)
T KOG1785|consen 365 MGSTFELCKICAEN----DKDVKIEPCGHLLCTSCLAAWQDSDEGQTCPFCRCEI 415 (563)
T ss_pred ccchHHHHHHhhcc----CCCcccccccchHHHHHHHhhcccCCCCCCCceeeEe
Confidence 34566789999986 7888888999999999999998654 67899999876
No 50
>KOG2879 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=97.34 E-value=0.00018 Score=59.38 Aligned_cols=52 Identities=23% Similarity=0.595 Sum_probs=39.3
Q ss_pred CCccccccccccccCcCCccEEecCCChhhHHHHHHHHhc-CCCCCCCCCCCccch
Q 031240 11 AMHHNCPICFEFIFDTMKDITVLRCGHTIHLECLKEMEKH-YRYTCPVCSKSLWDM 65 (163)
Q Consensus 11 s~~~~CpIC~e~l~~s~~~~~~L~CGH~fh~~Cl~~~~~~-~~~~CPiCr~~~~~~ 65 (163)
+.+.+||+|.+. +..+-+..+|||.+|..|+..-... ..++||.|..++..+
T Consensus 237 t~~~~C~~Cg~~---PtiP~~~~~C~HiyCY~Ci~ts~~~~asf~Cp~Cg~~~~~l 289 (298)
T KOG2879|consen 237 TSDTECPVCGEP---PTIPHVIGKCGHIYCYYCIATSRLWDASFTCPLCGENVEPL 289 (298)
T ss_pred cCCceeeccCCC---CCCCeeeccccceeehhhhhhhhcchhhcccCccCCCCcch
Confidence 457899999986 3344444579999999999986543 357999999887543
No 51
>KOG0825 consensus PHD Zn-finger protein [General function prediction only]
Probab=97.34 E-value=4.1e-05 Score=70.67 Aligned_cols=51 Identities=22% Similarity=0.410 Sum_probs=37.7
Q ss_pred CCccccccccccccCcCCccEEecCCChhhHHHHHHHHhcCCCCCCCCCCCcc
Q 031240 11 AMHHNCPICFEFIFDTMKDITVLRCGHTIHLECLKEMEKHYRYTCPVCSKSLW 63 (163)
Q Consensus 11 s~~~~CpIC~e~l~~s~~~~~~L~CGH~fh~~Cl~~~~~~~~~~CPiCr~~~~ 63 (163)
.....||+|+....+. -...-.+|+|.||..||..|-. ...+||+||+.|.
T Consensus 121 ~~~~~CP~Ci~s~~Dq-L~~~~k~c~H~FC~~Ci~sWsR-~aqTCPiDR~EF~ 171 (1134)
T KOG0825|consen 121 HVENQCPNCLKSCNDQ-LEESEKHTAHYFCEECVGSWSR-CAQTCPVDRGEFG 171 (1134)
T ss_pred hhhhhhhHHHHHHHHH-hhccccccccccHHHHhhhhhh-hcccCchhhhhhh
Confidence 4456799998653221 2223459999999999999977 4578999999874
No 52
>KOG3970 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=97.34 E-value=0.00038 Score=56.13 Aligned_cols=51 Identities=33% Similarity=0.720 Sum_probs=42.2
Q ss_pred CCccccccccccccCcCCccEEecCCChhhHHHHHHHHhc-------CCCCCCCCCCCcc
Q 031240 11 AMHHNCPICFEFIFDTMKDITVLRCGHTIHLECLKEMEKH-------YRYTCPVCSKSLW 63 (163)
Q Consensus 11 s~~~~CpIC~e~l~~s~~~~~~L~CGH~fh~~Cl~~~~~~-------~~~~CPiCr~~~~ 63 (163)
.+..+|..|.-.|- ..+.+.|.|-|.||+.|+.+|... .++.||-|...+.
T Consensus 48 DY~pNC~LC~t~La--~gdt~RLvCyhlfHW~ClneraA~lPanTAPaGyqCP~Cs~eiF 105 (299)
T KOG3970|consen 48 DYNPNCRLCNTPLA--SGDTTRLVCYHLFHWKCLNERAANLPANTAPAGYQCPCCSQEIF 105 (299)
T ss_pred CCCCCCceeCCccc--cCcceeehhhhhHHHHHhhHHHhhCCCcCCCCcccCCCCCCccC
Confidence 46789999987764 355688999999999999999754 2689999999984
No 53
>KOG1941 consensus Acetylcholine receptor-associated protein of the synapse (rapsyn) [Extracellular structures]
Probab=97.30 E-value=8.2e-05 Score=64.12 Aligned_cols=57 Identities=35% Similarity=0.672 Sum_probs=44.6
Q ss_pred cceecCCCccccccccccccCcCCccEEecCCChhhHHHHHHHHhc-CCCCCCCCCCCc
Q 031240 5 HRCVERAMHHNCPICFEFIFDTMKDITVLRCGHTIHLECLKEMEKH-YRYTCPVCSKSL 62 (163)
Q Consensus 5 H~c~e~s~~~~CpIC~e~l~~s~~~~~~L~CGH~fh~~Cl~~~~~~-~~~~CPiCr~~~ 62 (163)
|.|++ +++..|..|.|.+-........|||.|.||.+|+.++++. +..+||-||+-.
T Consensus 358 ~~~~~-e~~L~Cg~CGe~~Glk~e~LqALpCsHIfH~rCl~e~L~~n~~rsCP~Crklr 415 (518)
T KOG1941|consen 358 HECVE-ETELYCGLCGESIGLKNERLQALPCSHIFHLRCLQEILENNGTRSCPNCRKLR 415 (518)
T ss_pred HHHHH-HHhhhhhhhhhhhcCCcccccccchhHHHHHHHHHHHHHhCCCCCCccHHHHH
Confidence 44554 4678999999987555555677899999999999998865 456899999543
No 54
>PF11789 zf-Nse: Zinc-finger of the MIZ type in Nse subunit; PDB: 2YU4_A 3HTK_C.
Probab=97.29 E-value=0.00015 Score=46.48 Aligned_cols=44 Identities=25% Similarity=0.562 Sum_probs=28.7
Q ss_pred CCccccccccccccCcCCccEEecCCChhhHHHHHHHHh-cCCCCCCC
Q 031240 11 AMHHNCPICFEFIFDTMKDITVLRCGHTIHLECLKEMEK-HYRYTCPV 57 (163)
Q Consensus 11 s~~~~CpIC~e~l~~s~~~~~~L~CGH~fh~~Cl~~~~~-~~~~~CPi 57 (163)
.....|||.+..| ..+++...|||+|-.+.|.+|+. .+...||+
T Consensus 9 ~~~~~CPiT~~~~---~~PV~s~~C~H~fek~aI~~~i~~~~~~~CPv 53 (57)
T PF11789_consen 9 TISLKCPITLQPF---EDPVKSKKCGHTFEKEAILQYIQRNGSKRCPV 53 (57)
T ss_dssp B--SB-TTTSSB----SSEEEESSS--EEEHHHHHHHCTTTS-EE-SC
T ss_pred EeccCCCCcCChh---hCCcCcCCCCCeecHHHHHHHHHhcCCCCCCC
Confidence 4567999999874 34455679999999999999993 24578998
No 55
>COG5219 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=97.13 E-value=0.00018 Score=67.87 Aligned_cols=52 Identities=25% Similarity=0.616 Sum_probs=38.2
Q ss_pred CCcccccccccccc--CcCCcc-EEecCCChhhHHHHHHHHhc-CCCCCCCCCCCc
Q 031240 11 AMHHNCPICFEFIF--DTMKDI-TVLRCGHTIHLECLKEMEKH-YRYTCPVCSKSL 62 (163)
Q Consensus 11 s~~~~CpIC~e~l~--~s~~~~-~~L~CGH~fh~~Cl~~~~~~-~~~~CPiCr~~~ 62 (163)
+...+|+||+..|. ++.-+. +-..|.|.||.+|+.+|..+ ++.+||+||..+
T Consensus 1467 sG~eECaICYsvL~~vdr~lPskrC~TCknKFH~~CLyKWf~Ss~~s~CPlCRsei 1522 (1525)
T COG5219 1467 SGHEECAICYSVLDMVDRSLPSKRCATCKNKFHTRCLYKWFASSARSNCPLCRSEI 1522 (1525)
T ss_pred CCcchhhHHHHHHHHHhccCCccccchhhhhhhHHHHHHHHHhcCCCCCCcccccc
Confidence 44679999997653 111111 23478899999999999976 467899999765
No 56
>KOG0297 consensus TNF receptor-associated factor [Signal transduction mechanisms]
Probab=97.11 E-value=0.00022 Score=61.91 Aligned_cols=108 Identities=26% Similarity=0.539 Sum_probs=65.3
Q ss_pred CCccccccccccccCcCCccEE-ecCCChhhHHHHHHHHhcCCCCCCCCCCCccchhHHH--HhHHHHHhcCCCChhhhc
Q 031240 11 AMHHNCPICFEFIFDTMKDITV-LRCGHTIHLECLKEMEKHYRYTCPVCSKSLWDMSKLW--SKIDQEIASTPMPAMYQN 87 (163)
Q Consensus 11 s~~~~CpIC~e~l~~s~~~~~~-L~CGH~fh~~Cl~~~~~~~~~~CPiCr~~~~~~~~~~--~~l~~~~~~~~~p~e~~~ 87 (163)
..+..||+|...+ .+|.. ..|||.||..|+..|+.. +..||.|+........+. ..+...+..
T Consensus 19 ~~~l~C~~C~~vl----~~p~~~~~cgh~fC~~C~~~~~~~-~~~cp~~~~~~~~~~~~~~~~~~~~~~~~--------- 84 (391)
T KOG0297|consen 19 DENLLCPICMSVL----RDPVQTTTCGHRFCAGCLLESLSN-HQKCPVCRQELTQAEELPVPRALRRELLK--------- 84 (391)
T ss_pred cccccCccccccc----cCCCCCCCCCCcccccccchhhcc-CcCCcccccccchhhccCchHHHHHHHHh---------
Confidence 4468999999874 44444 699999999999999985 688999988764322211 111122221
Q ss_pred CcceeeC----CCCCCC---Ccccceee---eccCCC-CC-CCccccccCCCCCCCccc
Q 031240 88 KMVWILC----NDCGAN---SHVQFHVI---AHKCLS-CK-SYNTRQTRGDTATTCSSG 134 (163)
Q Consensus 88 ~~~~i~C----~dC~~~---~~~~~h~~---~~kC~~-C~-synt~~~~~~~~~~~~~~ 134 (163)
..|.| .+|... ...+-|.. ..+|.+ |+ .+..+.+..|.+.++...
T Consensus 85 --l~i~c~~~~~GC~~~~~l~~~~~Hl~~c~~~~C~~~C~~~~~~~d~~~hl~~~C~~~ 141 (391)
T KOG0297|consen 85 --LPIRCIFASRGCRADLELEALQGHLSTCDPLKCPHRCGVQVPRDDLEDHLEAECPRR 141 (391)
T ss_pred --cccccccCCCCccccccHHHHHhHhccCCcccCccccccccchHHHHHHHhcccccc
Confidence 12333 344432 23333432 257887 88 777777766665445443
No 57
>KOG4185 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=97.09 E-value=0.0005 Score=56.99 Aligned_cols=50 Identities=32% Similarity=0.622 Sum_probs=41.9
Q ss_pred ccccccccccccCc--CCccEEecCCChhhHHHHHHHHhcCCCCCCCCCCCc
Q 031240 13 HHNCPICFEFIFDT--MKDITVLRCGHTIHLECLKEMEKHYRYTCPVCSKSL 62 (163)
Q Consensus 13 ~~~CpIC~e~l~~s--~~~~~~L~CGH~fh~~Cl~~~~~~~~~~CPiCr~~~ 62 (163)
-..|-||-+++-.. ...|.+|.|||++|..|+...+..+...||.||...
T Consensus 3 ~~~c~~c~~~~s~~~~~~~p~~l~c~h~~c~~c~~~l~~~~~i~cpfcR~~~ 54 (296)
T KOG4185|consen 3 FPECEICNEDYSSEDGDHIPRVLKCGHTICQNCASKLLGNSRILCPFCRETT 54 (296)
T ss_pred CCceeecCccccccCcccCCcccccCceehHhHHHHHhcCceeeccCCCCcc
Confidence 36799998885332 456889999999999999999988778899999995
No 58
>KOG2930 consensus SCF ubiquitin ligase, Rbx1 component [Posttranslational modification, protein turnover, chaperones]
Probab=97.04 E-value=0.00065 Score=48.37 Aligned_cols=30 Identities=30% Similarity=0.635 Sum_probs=26.0
Q ss_pred EEecCCChhhHHHHHHHHhcCCCCCCCCCCC
Q 031240 31 TVLRCGHTIHLECLKEMEKHYRYTCPVCSKS 61 (163)
Q Consensus 31 ~~L~CGH~fh~~Cl~~~~~~~~~~CPiCr~~ 61 (163)
+.-.|.|.||..||.+|++ ....||++.+.
T Consensus 77 aWG~CNHaFH~hCisrWlk-tr~vCPLdn~e 106 (114)
T KOG2930|consen 77 AWGVCNHAFHFHCISRWLK-TRNVCPLDNKE 106 (114)
T ss_pred EeeecchHHHHHHHHHHHh-hcCcCCCcCcc
Confidence 4448999999999999998 45789999876
No 59
>KOG1645 consensus RING-finger-containing E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=97.02 E-value=0.00073 Score=58.55 Aligned_cols=50 Identities=28% Similarity=0.702 Sum_probs=39.0
Q ss_pred ccccccccccccC-cCCccEEecCCChhhHHHHHHHHhc-CCCCCCCCCCCc
Q 031240 13 HHNCPICFEFIFD-TMKDITVLRCGHTIHLECLKEMEKH-YRYTCPVCSKSL 62 (163)
Q Consensus 13 ~~~CpIC~e~l~~-s~~~~~~L~CGH~fh~~Cl~~~~~~-~~~~CPiCr~~~ 62 (163)
...||||++.+.. ...-.+.|.|||.|-..|+++|+.. ....||.|....
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 4689999987533 3344577899999999999999953 356799998765
No 60
>KOG4159 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=97.01 E-value=0.00053 Score=59.65 Aligned_cols=49 Identities=29% Similarity=0.649 Sum_probs=40.3
Q ss_pred CCccccccccccccCcCCccEEecCCChhhHHHHHHHHhcCCCCCCCCCCCccc
Q 031240 11 AMHHNCPICFEFIFDTMKDITVLRCGHTIHLECLKEMEKHYRYTCPVCSKSLWD 64 (163)
Q Consensus 11 s~~~~CpIC~e~l~~s~~~~~~L~CGH~fh~~Cl~~~~~~~~~~CPiCr~~~~~ 64 (163)
..+..|.||+.. ..+|+++||||+||..||.+.+. ....||+||..+..
T Consensus 82 ~sef~c~vc~~~----l~~pv~tpcghs~c~~Cl~r~ld-~~~~cp~Cr~~l~e 130 (398)
T KOG4159|consen 82 RSEFECCVCSRA----LYPPVVTPCGHSFCLECLDRSLD-QETECPLCRDELVE 130 (398)
T ss_pred cchhhhhhhHhh----cCCCccccccccccHHHHHHHhc-cCCCCccccccccc
Confidence 457899999876 35667889999999999999666 45789999999853
No 61
>KOG4275 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=96.93 E-value=0.00011 Score=61.22 Aligned_cols=54 Identities=26% Similarity=0.632 Sum_probs=39.6
Q ss_pred CCcceecCCC---ccccccccccccCcCCccEEecCCC-hhhHHHHHHHHhcCCCCCCCCCCCccch
Q 031240 3 DKHRCVERAM---HHNCPICFEFIFDTMKDITVLRCGH-TIHLECLKEMEKHYRYTCPVCSKSLWDM 65 (163)
Q Consensus 3 ~~H~c~e~s~---~~~CpIC~e~l~~s~~~~~~L~CGH-~fh~~Cl~~~~~~~~~~CPiCr~~~~~~ 65 (163)
++|.+.-... +..|.||++. .++-+.|+||| .-|.+|=+++. .|||||+-+..+
T Consensus 287 ~~~g~~~~~s~~~~~LC~ICmDa----P~DCvfLeCGHmVtCt~CGkrm~-----eCPICRqyi~rv 344 (350)
T KOG4275|consen 287 GNDGEQHSRSLATRRLCAICMDA----PRDCVFLECGHMVTCTKCGKRMN-----ECPICRQYIVRV 344 (350)
T ss_pred cccccccccchhHHHHHHHHhcC----CcceEEeecCcEEeehhhccccc-----cCchHHHHHHHH
Confidence 3444444433 7899999964 78889999999 56888866654 599999876443
No 62
>COG5152 Uncharacterized conserved protein, contains RING and CCCH-type Zn-fingers [General function prediction only]
Probab=96.71 E-value=0.001 Score=52.78 Aligned_cols=46 Identities=26% Similarity=0.499 Sum_probs=36.9
Q ss_pred ccccccccccccCcCCccEEecCCChhhHHHHHHHHhcCCCCCCCCCCCcc
Q 031240 13 HHNCPICFEFIFDTMKDITVLRCGHTIHLECLKEMEKHYRYTCPVCSKSLW 63 (163)
Q Consensus 13 ~~~CpIC~e~l~~s~~~~~~L~CGH~fh~~Cl~~~~~~~~~~CPiCr~~~~ 63 (163)
...|.||.+. .+.|++..|||.||..|.-.-.. ....|-+|.+...
T Consensus 196 PF~C~iCKkd----y~spvvt~CGH~FC~~Cai~~y~-kg~~C~~Cgk~t~ 241 (259)
T COG5152 196 PFLCGICKKD----YESPVVTECGHSFCSLCAIRKYQ-KGDECGVCGKATY 241 (259)
T ss_pred ceeehhchhh----ccchhhhhcchhHHHHHHHHHhc-cCCcceecchhhc
Confidence 3579999987 46778999999999999766444 3478999998863
No 63
>KOG1813 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=96.54 E-value=0.0011 Score=55.27 Aligned_cols=60 Identities=20% Similarity=0.367 Sum_probs=42.7
Q ss_pred ccccccccccccCcCCccEEecCCChhhHHHHHHHHhcCCCCCCCCCCCccchhHHHHhHHHHHh
Q 031240 13 HHNCPICFEFIFDTMKDITVLRCGHTIHLECLKEMEKHYRYTCPVCSKSLWDMSKLWSKIDQEIA 77 (163)
Q Consensus 13 ~~~CpIC~e~l~~s~~~~~~L~CGH~fh~~Cl~~~~~~~~~~CPiCr~~~~~~~~~~~~l~~~~~ 77 (163)
...|-||.++ +..|++..|||+||..|...-+. ....|++|.+.+-........|...+.
T Consensus 241 Pf~c~icr~~----f~~pVvt~c~h~fc~~ca~~~~q-k~~~c~vC~~~t~g~~~~akeL~~~L~ 300 (313)
T KOG1813|consen 241 PFKCFICRKY----FYRPVVTKCGHYFCEVCALKPYQ-KGEKCYVCSQQTHGSFNVAKELLVSLK 300 (313)
T ss_pred Cccccccccc----cccchhhcCCceeehhhhccccc-cCCcceecccccccccchHHHHHHHHH
Confidence 3469999987 56678999999999999776555 347899999987443333333444443
No 64
>KOG1428 consensus Inhibitor of type V adenylyl cyclases/Neuronal presynaptic protein Highwire/PAM/RPM-1 [Signal transduction mechanisms]
Probab=96.51 E-value=0.0037 Score=61.61 Aligned_cols=51 Identities=25% Similarity=0.644 Sum_probs=39.2
Q ss_pred CCccccccccccccCcCCccEEecCCChhhHHHHHHHHhcC---------CCCCCCCCCCc
Q 031240 11 AMHHNCPICFEFIFDTMKDITVLRCGHTIHLECLKEMEKHY---------RYTCPVCSKSL 62 (163)
Q Consensus 11 s~~~~CpIC~e~l~~s~~~~~~L~CGH~fh~~Cl~~~~~~~---------~~~CPiCr~~~ 62 (163)
..+..|-||+-+- -+-.+...|.|||.||..|.+..++.. -..||+|...+
T Consensus 3484 D~DDmCmICFTE~-L~AAP~IqL~C~HiFHlqC~R~vLE~RW~GPRItF~FisCPiC~n~I 3543 (3738)
T KOG1428|consen 3484 DADDMCMICFTEA-LSAAPAIQLDCSHIFHLQCCRRVLENRWLGPRITFGFISCPICKNKI 3543 (3738)
T ss_pred ccCceEEEEehhh-hCCCcceecCCccchhHHHHHHHHHhcccCCeeEEeeeecccccchh
Confidence 3467899998652 234566789999999999999877652 35699999987
No 65
>PF14447 Prok-RING_4: Prokaryotic RING finger family 4
Probab=96.42 E-value=0.0011 Score=41.99 Aligned_cols=33 Identities=33% Similarity=0.634 Sum_probs=26.4
Q ss_pred CccEEecCCChhhHHHHHHHHhcCCCCCCCCCCCcc
Q 031240 28 KDITVLRCGHTIHLECLKEMEKHYRYTCPVCSKSLW 63 (163)
Q Consensus 28 ~~~~~L~CGH~fh~~Cl~~~~~~~~~~CPiCr~~~~ 63 (163)
....+++|||..+..|+.-+.- ..||+|.+++.
T Consensus 18 ~~~~~~pCgH~I~~~~f~~~rY---ngCPfC~~~~~ 50 (55)
T PF14447_consen 18 TKGTVLPCGHLICDNCFPGERY---NGCPFCGTPFE 50 (55)
T ss_pred cccccccccceeeccccChhhc---cCCCCCCCccc
Confidence 4457789999999999887654 34999999874
No 66
>COG5175 MOT2 Transcriptional repressor [Transcription]
Probab=96.41 E-value=0.0013 Score=56.07 Aligned_cols=51 Identities=27% Similarity=0.574 Sum_probs=40.3
Q ss_pred cccccccccccCcCCccEEecCCChhhHHHHHHHHhcCCCCCCCCCCCccc
Q 031240 14 HNCPICFEFIFDTMKDITVLRCGHTIHLECLKEMEKHYRYTCPVCSKSLWD 64 (163)
Q Consensus 14 ~~CpIC~e~l~~s~~~~~~L~CGH~fh~~Cl~~~~~~~~~~CPiCr~~~~~ 64 (163)
.-||.|+|.|.-+.+.-.--+||-.+|.-|+....+.-+.+||-||+.+.+
T Consensus 15 d~cplcie~mditdknf~pc~cgy~ic~fc~~~irq~lngrcpacrr~y~d 65 (480)
T COG5175 15 DYCPLCIEPMDITDKNFFPCPCGYQICQFCYNNIRQNLNGRCPACRRKYDD 65 (480)
T ss_pred ccCcccccccccccCCcccCCcccHHHHHHHHHHHhhccCCChHhhhhccc
Confidence 349999999865555444459999999999888776556799999998854
No 67
>KOG2660 consensus Locus-specific chromosome binding proteins [Function unknown]
Probab=96.34 E-value=0.00094 Score=56.32 Aligned_cols=47 Identities=26% Similarity=0.649 Sum_probs=39.4
Q ss_pred CccccccccccccCcCCccEEecCCChhhHHHHHHHHhcCCCCCCCCCCCc
Q 031240 12 MHHNCPICFEFIFDTMKDITVLRCGHTIHLECLKEMEKHYRYTCPVCSKSL 62 (163)
Q Consensus 12 ~~~~CpIC~e~l~~s~~~~~~L~CGH~fh~~Cl~~~~~~~~~~CPiCr~~~ 62 (163)
....|.+|..+|.|.+ .+.-|-|+||.+||-++++. ...||.|+..+
T Consensus 14 ~~itC~LC~GYliDAT---TI~eCLHTFCkSCivk~l~~-~~~CP~C~i~i 60 (331)
T KOG2660|consen 14 PHITCRLCGGYLIDAT---TITECLHTFCKSCIVKYLEE-SKYCPTCDIVI 60 (331)
T ss_pred cceehhhccceeecch---hHHHHHHHHHHHHHHHHHHH-hccCCccceec
Confidence 4568999999975543 46699999999999999985 68899999887
No 68
>KOG1002 consensus Nucleotide excision repair protein RAD16 [Replication, recombination and repair]
Probab=96.33 E-value=0.0019 Score=57.81 Aligned_cols=51 Identities=29% Similarity=0.565 Sum_probs=42.8
Q ss_pred ecCCCccccccccccccCcCCccEEecCCChhhHHHHHHHHhc----CCCCCCCCCCCc
Q 031240 8 VERAMHHNCPICFEFIFDTMKDITVLRCGHTIHLECLKEMEKH----YRYTCPVCSKSL 62 (163)
Q Consensus 8 ~e~s~~~~CpIC~e~l~~s~~~~~~L~CGH~fh~~Cl~~~~~~----~~~~CPiCr~~~ 62 (163)
.|+..+..|.+|-+. ..++....|.|.||+-|+.++... .+.+||+|...+
T Consensus 531 ~enk~~~~C~lc~d~----aed~i~s~ChH~FCrlCi~eyv~~f~~~~nvtCP~C~i~L 585 (791)
T KOG1002|consen 531 DENKGEVECGLCHDP----AEDYIESSCHHKFCRLCIKEYVESFMENNNVTCPVCHIGL 585 (791)
T ss_pred ccccCceeecccCCh----hhhhHhhhhhHHHHHHHHHHHHHhhhcccCCCCccccccc
Confidence 456778899999976 577788999999999999998764 368899999876
No 69
>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=96.19 E-value=0.0016 Score=45.59 Aligned_cols=38 Identities=29% Similarity=0.657 Sum_probs=30.1
Q ss_pred ceecCCCccccccccccccCcCCccEEecCCChhhHHHHH
Q 031240 6 RCVERAMHHNCPICFEFIFDTMKDITVLRCGHTIHLECLK 45 (163)
Q Consensus 6 ~c~e~s~~~~CpIC~e~l~~s~~~~~~L~CGH~fh~~Cl~ 45 (163)
..+.-+.+..|+||...|.+ ....+.||||.||..|++
T Consensus 71 ~~v~i~~~~~C~vC~k~l~~--~~f~~~p~~~v~H~~C~~ 108 (109)
T PF10367_consen 71 RSVVITESTKCSVCGKPLGN--SVFVVFPCGHVVHYSCIK 108 (109)
T ss_pred ceEEECCCCCccCcCCcCCC--ceEEEeCCCeEEeccccc
Confidence 44555667889999999764 455677999999999975
No 70
>PF12906 RINGv: RING-variant domain; PDB: 2D8S_A 1VYX_A.
Probab=96.15 E-value=0.0031 Score=38.68 Aligned_cols=41 Identities=24% Similarity=0.587 Sum_probs=26.6
Q ss_pred cccccccccCcCCccEEecCCC-----hhhHHHHHHHHhc-CCCCCCCC
Q 031240 16 CPICFEFIFDTMKDITVLRCGH-----TIHLECLKEMEKH-YRYTCPVC 58 (163)
Q Consensus 16 CpIC~e~l~~s~~~~~~L~CGH-----~fh~~Cl~~~~~~-~~~~CPiC 58 (163)
|-||++.- ....+.+.||+- ..|..|+.+|+.. +..+|++|
T Consensus 1 CrIC~~~~--~~~~~li~pC~C~Gs~~~vH~~CL~~W~~~~~~~~C~~C 47 (47)
T PF12906_consen 1 CRICLEGE--EEDEPLISPCRCKGSMKYVHRSCLERWIRESGNRKCEIC 47 (47)
T ss_dssp ETTTTEE---SSSS-EE-SSS-SSCCGSEECCHHHHHHHHHT-SB-TTT
T ss_pred CeEeCCcC--CCCCceecccccCCCcchhHHHHHHHHHHhcCCCcCCCC
Confidence 66899863 233356778863 6799999999975 45679987
No 71
>PF04641 Rtf2: Rtf2 RING-finger
Probab=96.08 E-value=0.0053 Score=50.44 Aligned_cols=52 Identities=25% Similarity=0.429 Sum_probs=40.5
Q ss_pred CCCccccccccccccCcCCccEEecCCChhhHHHHHHHHhcCCCCCCCCCCCcc
Q 031240 10 RAMHHNCPICFEFIFDTMKDITVLRCGHTIHLECLKEMEKHYRYTCPVCSKSLW 63 (163)
Q Consensus 10 ~s~~~~CpIC~e~l~~s~~~~~~L~CGH~fh~~Cl~~~~~~~~~~CPiCr~~~~ 63 (163)
......|||....|....+-+.+.+|||+|...++++.. ....||+|.+++.
T Consensus 110 ~~~~~~CPvt~~~~~~~~~fv~l~~cG~V~s~~alke~k--~~~~Cp~c~~~f~ 161 (260)
T PF04641_consen 110 SEGRFICPVTGKEFNGKHKFVYLRPCGCVFSEKALKELK--KSKKCPVCGKPFT 161 (260)
T ss_pred CCceeECCCCCcccCCceeEEEEcCCCCEeeHHHHHhhc--ccccccccCCccc
Confidence 355779999999874444444555999999999999984 3467999999973
No 72
>KOG3800 consensus Predicted E3 ubiquitin ligase containing RING finger, subunit of transcription/repair factor TFIIH and CDK-activating kinase assembly factor [Posttranslational modification, protein turnover, chaperones]
Probab=96.08 E-value=0.0059 Score=50.82 Aligned_cols=48 Identities=23% Similarity=0.501 Sum_probs=35.8
Q ss_pred ccccccccccCc-CCccEEecCCChhhHHHHHHHHhcCCCCCCCCCCCc
Q 031240 15 NCPICFEFIFDT-MKDITVLRCGHTIHLECLKEMEKHYRYTCPVCSKSL 62 (163)
Q Consensus 15 ~CpIC~e~l~~s-~~~~~~L~CGH~fh~~Cl~~~~~~~~~~CPiCr~~~ 62 (163)
.||+|.-..... .-...+-+|||.+|.+|+...+..+...||.|.+.+
T Consensus 2 ~Cp~CKt~~Y~np~lk~~in~C~H~lCEsCvd~iF~~g~~~CpeC~~iL 50 (300)
T KOG3800|consen 2 ACPKCKTDRYLNPDLKLMINECGHRLCESCVDRIFSLGPAQCPECMVIL 50 (300)
T ss_pred CCcccccceecCccceeeeccccchHHHHHHHHHHhcCCCCCCcccchh
Confidence 589997543211 111222399999999999999988889999999875
No 73
>KOG1814 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=96.01 E-value=0.005 Score=53.51 Aligned_cols=47 Identities=28% Similarity=0.441 Sum_probs=35.6
Q ss_pred ccccccccccccCcCCccEEecCCChhhHHHHHHHHhc-------CCCCCCCCCC
Q 031240 13 HHNCPICFEFIFDTMKDITVLRCGHTIHLECLKEMEKH-------YRYTCPVCSK 60 (163)
Q Consensus 13 ~~~CpIC~e~l~~s~~~~~~L~CGH~fh~~Cl~~~~~~-------~~~~CPiCr~ 60 (163)
...|.||++. +.+......+||+|+||..|+..+... +..+||-+.-
T Consensus 184 lf~C~ICf~e-~~G~~c~~~lpC~Hv~Ck~C~kdY~~~~i~eg~v~~l~Cp~~~C 237 (445)
T KOG1814|consen 184 LFDCCICFEE-QMGQHCFKFLPCSHVFCKSCLKDYFTIQIQEGQVSCLKCPDPKC 237 (445)
T ss_pred cccceeeehh-hcCcceeeecccchHHHHHHHHHHHHHhhhcceeeeecCCCCCC
Confidence 4689999987 344455678899999999999998754 2457886543
No 74
>KOG1571 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=95.74 E-value=0.0053 Score=52.44 Aligned_cols=47 Identities=26% Similarity=0.581 Sum_probs=35.2
Q ss_pred cCCCccccccccccccCcCCccEEecCCChhhHHHHHHHHhcCCCCCCCCCCCcc
Q 031240 9 ERAMHHNCPICFEFIFDTMKDITVLRCGHTIHLECLKEMEKHYRYTCPVCSKSLW 63 (163)
Q Consensus 9 e~s~~~~CpIC~e~l~~s~~~~~~L~CGH~fh~~Cl~~~~~~~~~~CPiCr~~~~ 63 (163)
+.+....|.||++. ....+.+||||.-| |..-... ...||+||..+.
T Consensus 301 ~~~~p~lcVVcl~e----~~~~~fvpcGh~cc--ct~cs~~--l~~CPvCR~rI~ 347 (355)
T KOG1571|consen 301 ELPQPDLCVVCLDE----PKSAVFVPCGHVCC--CTLCSKH--LPQCPVCRQRIR 347 (355)
T ss_pred ccCCCCceEEecCC----ccceeeecCCcEEE--chHHHhh--CCCCchhHHHHH
Confidence 44667899999976 45578999999976 6555433 346999998863
No 75
>KOG4445 consensus Uncharacterized conserved protein, contains RWD domain [Function unknown]
Probab=95.68 E-value=0.0041 Score=52.15 Aligned_cols=51 Identities=27% Similarity=0.610 Sum_probs=39.1
Q ss_pred CccccccccccccCcCCccEEecCCChhhHHHHHHHHhcC----------------------CCCCCCCCCCcc
Q 031240 12 MHHNCPICFEFIFDTMKDITVLRCGHTIHLECLKEMEKHY----------------------RYTCPVCSKSLW 63 (163)
Q Consensus 12 ~~~~CpIC~e~l~~s~~~~~~L~CGH~fh~~Cl~~~~~~~----------------------~~~CPiCr~~~~ 63 (163)
....|.||+--| .+.......+|-|.||..|+.+++..- ...||+||..+.
T Consensus 114 p~gqCvICLygf-a~~~~ft~T~C~Hy~H~~ClaRyl~~~~~~lrqe~q~~~~~~qh~~~~~eavcpVcre~i~ 186 (368)
T KOG4445|consen 114 PNGQCVICLYGF-ASSPAFTVTACDHYMHFACLARYLTECLTGLRQEIQDAQKERQHMKEQVEAVCPVCRERIK 186 (368)
T ss_pred CCCceEEEEEee-cCCCceeeehhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhHhhhhhHhhhhcc
Confidence 467899999764 444556778999999999999987530 235999999873
No 76
>KOG3002 consensus Zn finger protein [General function prediction only]
Probab=95.61 E-value=0.015 Score=48.93 Aligned_cols=62 Identities=19% Similarity=0.595 Sum_probs=43.3
Q ss_pred ccccccccccccCcCCccEEecC--CChhhHHHHHHHHhcCCCCCCCCCCCccchhHHHHhHHHHHhcCCCChhh
Q 031240 13 HHNCPICFEFIFDTMKDITVLRC--GHTIHLECLKEMEKHYRYTCPVCSKSLWDMSKLWSKIDQEIASTPMPAMY 85 (163)
Q Consensus 13 ~~~CpIC~e~l~~s~~~~~~L~C--GH~fh~~Cl~~~~~~~~~~CPiCr~~~~~~~~~~~~l~~~~~~~~~p~e~ 85 (163)
-.+||||.+.| .+| +..| ||..|..|-.+.. .+||.||.++++... ..++..++...+|=.+
T Consensus 48 lleCPvC~~~l----~~P-i~QC~nGHlaCssC~~~~~----~~CP~Cr~~~g~~R~--~amEkV~e~~~vpC~~ 111 (299)
T KOG3002|consen 48 LLDCPVCFNPL----SPP-IFQCDNGHLACSSCRTKVS----NKCPTCRLPIGNIRC--RAMEKVAEAVLVPCKN 111 (299)
T ss_pred hccCchhhccC----ccc-ceecCCCcEehhhhhhhhc----ccCCccccccccHHH--HHHHHHHHhceecccc
Confidence 46899999985 222 4566 8999999987543 579999999986532 3555666665555443
No 77
>KOG4692 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=95.43 E-value=0.011 Score=50.84 Aligned_cols=52 Identities=19% Similarity=0.464 Sum_probs=41.8
Q ss_pred ecCCCccccccccccccCcCCccEEecCCChhhHHHHHHHHhcCCCCCCCCCCCccc
Q 031240 8 VERAMHHNCPICFEFIFDTMKDITVLRCGHTIHLECLKEMEKHYRYTCPVCSKSLWD 64 (163)
Q Consensus 8 ~e~s~~~~CpIC~e~l~~s~~~~~~L~CGH~fh~~Cl~~~~~~~~~~CPiCr~~~~~ 64 (163)
...+.+..||||+.. ....+..||||.-|..||.+.+- +...|=.|+.++.+
T Consensus 417 lp~sEd~lCpICyA~----pi~Avf~PC~H~SC~~CI~qHlm-N~k~CFfCktTv~~ 468 (489)
T KOG4692|consen 417 LPDSEDNLCPICYAG----PINAVFAPCSHRSCYGCITQHLM-NCKRCFFCKTTVID 468 (489)
T ss_pred CCCcccccCcceecc----cchhhccCCCCchHHHHHHHHHh-cCCeeeEecceeee
Confidence 345778999999953 44456779999999999999876 45789999988754
No 78
>KOG1952 consensus Transcription factor NF-X1, contains NFX-type Zn2+-binding and R3H domains [Transcription]
Probab=95.41 E-value=0.011 Score=55.36 Aligned_cols=48 Identities=29% Similarity=0.607 Sum_probs=36.8
Q ss_pred CccccccccccccCcCCccEEe--cCCChhhHHHHHHHHhc------CCCCCCCCCCC
Q 031240 12 MHHNCPICFEFIFDTMKDITVL--RCGHTIHLECLKEMEKH------YRYTCPVCSKS 61 (163)
Q Consensus 12 ~~~~CpIC~e~l~~s~~~~~~L--~CGH~fh~~Cl~~~~~~------~~~~CPiCr~~ 61 (163)
...+|.||.|.+. ...+++- .|-|+||..||++|..+ ..++||-|...
T Consensus 190 ~~yeCmIC~e~I~--~t~~~WSC~sCYhVFHl~CI~~WArs~ek~~~~~WrCP~Cqsv 245 (950)
T KOG1952|consen 190 RKYECMICTERIK--RTAPVWSCKSCYHVFHLNCIKKWARSSEKTGQDGWRCPACQSV 245 (950)
T ss_pred CceEEEEeeeecc--ccCCceecchhhhhhhHHHHHHHHHHhhhccCccccCCcccch
Confidence 4579999999864 3444443 77899999999999865 25889999843
No 79
>COG5222 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=95.40 E-value=0.012 Score=49.47 Aligned_cols=46 Identities=28% Similarity=0.728 Sum_probs=36.0
Q ss_pred ccccccccccccCcCCccEEecCCChhhHHHHHHHHhcCCCCCCCCCCC
Q 031240 13 HHNCPICFEFIFDTMKDITVLRCGHTIHLECLKEMEKHYRYTCPVCSKS 61 (163)
Q Consensus 13 ~~~CpIC~e~l~~s~~~~~~L~CGH~fh~~Cl~~~~~~~~~~CPiCr~~ 61 (163)
.+-||.|...| ..+....-|||+||.+||..-+..+.+.||.|...
T Consensus 274 ~LkCplc~~Ll---rnp~kT~cC~~~fc~eci~~al~dsDf~CpnC~rk 319 (427)
T COG5222 274 SLKCPLCHCLL---RNPMKTPCCGHTFCDECIGTALLDSDFKCPNCSRK 319 (427)
T ss_pred cccCcchhhhh---hCcccCccccchHHHHHHhhhhhhccccCCCcccc
Confidence 47899998765 34444457899999999998766567999999874
No 80
>KOG3268 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=95.37 E-value=0.014 Score=45.71 Aligned_cols=50 Identities=26% Similarity=0.636 Sum_probs=37.5
Q ss_pred ccccccccccccCcCCccE---EecCCChhhHHHHHHHHhcC----------CCCCCCCCCCc
Q 031240 13 HHNCPICFEFIFDTMKDIT---VLRCGHTIHLECLKEMEKHY----------RYTCPVCSKSL 62 (163)
Q Consensus 13 ~~~CpIC~e~l~~s~~~~~---~L~CGH~fh~~Cl~~~~~~~----------~~~CPiCr~~~ 62 (163)
-..|.||+.+-.+++.+-. .+.||-.||.-|+..|+..- --.||.|.+++
T Consensus 165 ~~~cgicyayqldGTipDqtCdN~qCgkpFHqiCL~dWLRgilTsRQSFdiiFGeCPYCS~Pi 227 (234)
T KOG3268|consen 165 LGACGICYAYQLDGTIPDQTCDNIQCGKPFHQICLTDWLRGILTSRQSFDIIFGECPYCSDPI 227 (234)
T ss_pred hhcccceeeeecCCccccccccccccCCcHHHHHHHHHHHHHhhccceeeeeeccCCCCCCcc
Confidence 4679999887655544332 36999999999999998641 12599999987
No 81
>KOG3039 consensus Uncharacterized conserved protein [Function unknown]
Probab=95.34 E-value=0.014 Score=47.77 Aligned_cols=54 Identities=22% Similarity=0.384 Sum_probs=42.9
Q ss_pred CCCccccccccccccCcCCccEEecCCChhhHHHHHHHHhcCCCCCCCCCCCccc
Q 031240 10 RAMHHNCPICFEFIFDTMKDITVLRCGHTIHLECLKEMEKHYRYTCPVCSKSLWD 64 (163)
Q Consensus 10 ~s~~~~CpIC~e~l~~s~~~~~~L~CGH~fh~~Cl~~~~~~~~~~CPiCr~~~~~ 64 (163)
.+....||||.+.|.+...-.+.-+|||+|+.+|.++++. ....||+|.+++.+
T Consensus 218 ~s~ryiCpvtrd~LtNt~~ca~Lr~sg~Vv~~ecvEklir-~D~v~pv~d~plkd 271 (303)
T KOG3039|consen 218 ASKRYICPVTRDTLTNTTPCAVLRPSGHVVTKECVEKLIR-KDMVDPVTDKPLKD 271 (303)
T ss_pred hccceecccchhhhcCccceEEeccCCcEeeHHHHHHhcc-ccccccCCCCcCcc
Confidence 3457899999999865544444449999999999999987 45789999998754
No 82
>KOG2817 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=95.28 E-value=0.015 Score=50.30 Aligned_cols=47 Identities=28% Similarity=0.588 Sum_probs=39.5
Q ss_pred cccccccccccCcCCccEEecCCChhhHHHHHHHHhcCC--CCCCCCCCC
Q 031240 14 HNCPICFEFIFDTMKDITVLRCGHTIHLECLKEMEKHYR--YTCPVCSKS 61 (163)
Q Consensus 14 ~~CpIC~e~l~~s~~~~~~L~CGH~fh~~Cl~~~~~~~~--~~CPiCr~~ 61 (163)
..|||=.|. .+...+|+.|.|||++..+-+.++...+. ++||-|-..
T Consensus 335 F~CPVlKeq-tsdeNPPm~L~CGHVISkdAlnrLS~ng~~sfKCPYCP~e 383 (394)
T KOG2817|consen 335 FICPVLKEQ-TSDENPPMMLICGHVISKDALNRLSKNGSQSFKCPYCPVE 383 (394)
T ss_pred eecccchhh-ccCCCCCeeeeccceecHHHHHHHhhCCCeeeeCCCCCcc
Confidence 478988775 45568999999999999999999988766 899999654
No 83
>KOG4739 consensus Uncharacterized protein involved in synaptonemal complex formation [Cell cycle control, cell division, chromosome partitioning; General function prediction only]
Probab=95.26 E-value=0.0094 Score=48.36 Aligned_cols=43 Identities=33% Similarity=0.785 Sum_probs=31.2
Q ss_pred ccccccccccCcCCccEEecCCChhhHHHHHHHHhcCCCCCCCCCCCc
Q 031240 15 NCPICFEFIFDTMKDITVLRCGHTIHLECLKEMEKHYRYTCPVCSKSL 62 (163)
Q Consensus 15 ~CpIC~e~l~~s~~~~~~L~CGH~fh~~Cl~~~~~~~~~~CPiCr~~~ 62 (163)
.|-.|.- +.+..+--++.|+|.||..|...-. ...||+|++++
T Consensus 5 hCn~C~~--~~~~~~f~LTaC~HvfC~~C~k~~~---~~~C~lCkk~i 47 (233)
T KOG4739|consen 5 HCNKCFR--FPSQDPFFLTACRHVFCEPCLKASS---PDVCPLCKKSI 47 (233)
T ss_pred Eeccccc--cCCCCceeeeechhhhhhhhcccCC---cccccccccee
Confidence 4666763 4554444566999999999987533 23899999996
No 84
>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=95.23 E-value=0.011 Score=44.03 Aligned_cols=35 Identities=23% Similarity=0.484 Sum_probs=30.0
Q ss_pred ccccccccccccCcCCccEEecCC------ChhhHHHHHHHH
Q 031240 13 HHNCPICFEFIFDTMKDITVLRCG------HTIHLECLKEME 48 (163)
Q Consensus 13 ~~~CpIC~e~l~~s~~~~~~L~CG------H~fh~~Cl~~~~ 48 (163)
..+|.||++.+.+ ...++.++|| |.||..|+++|.
T Consensus 26 ~~EC~IC~~~I~~-~~GvV~vt~~g~lnLEkmfc~~C~~rw~ 66 (134)
T PF05883_consen 26 TVECQICFDRIDN-NDGVVYVTDGGTLNLEKMFCADCDKRWR 66 (134)
T ss_pred Ceeehhhhhhhhc-CCCEEEEecCCeehHHHHHHHHHHHHHH
Confidence 5789999999765 5678888998 789999999994
No 85
>KOG3161 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=95.19 E-value=0.0081 Score=54.92 Aligned_cols=44 Identities=27% Similarity=0.642 Sum_probs=37.4
Q ss_pred cccccccccccCcCCccEEecCCChhhHHHHHHHHhcCCCCCCCCCCC
Q 031240 14 HNCPICFEFIFDTMKDITVLRCGHTIHLECLKEMEKHYRYTCPVCSKS 61 (163)
Q Consensus 14 ~~CpIC~e~l~~s~~~~~~L~CGH~fh~~Cl~~~~~~~~~~CPiCr~~ 61 (163)
..|+||+..++.....|+.|.|||++|..|++..-. .+|| |+..
T Consensus 12 l~c~ic~n~f~~~~~~Pvsl~cghtic~~c~~~lyn---~scp-~~~D 55 (861)
T KOG3161|consen 12 LLCDICLNLFVVQRLEPVSLQCGHTICGHCVQLLYN---ASCP-TKRD 55 (861)
T ss_pred hhchHHHHHHHHHhcCcccccccchHHHHHHHhHhh---ccCC-CCcc
Confidence 589999988888889999999999999999998654 4688 6544
No 86
>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=94.81 E-value=0.035 Score=42.55 Aligned_cols=33 Identities=36% Similarity=0.847 Sum_probs=23.7
Q ss_pred ccccccccccccCcCCccEEecCC-C------------hhhHHHHHHHHh
Q 031240 13 HHNCPICFEFIFDTMKDITVLRCG-H------------TIHLECLKEMEK 49 (163)
Q Consensus 13 ~~~CpIC~e~l~~s~~~~~~L~CG-H------------~fh~~Cl~~~~~ 49 (163)
+..||||||. .-..++|.|. | .-|..||+++.+
T Consensus 2 d~~CpICme~----PHNAVLLlCSS~~kgcRpymc~Ts~rhSNCLdqfkk 47 (162)
T PF07800_consen 2 DVTCPICMEH----PHNAVLLLCSSHEKGCRPYMCDTSYRHSNCLDQFKK 47 (162)
T ss_pred CccCceeccC----CCceEEEEeccccCCccccccCCccchhHHHHHHHH
Confidence 5789999986 4555666653 2 348899999865
No 87
>PHA02862 5L protein; Provisional
Probab=94.79 E-value=0.035 Score=42.00 Aligned_cols=46 Identities=22% Similarity=0.546 Sum_probs=34.4
Q ss_pred CccccccccccccCcCCccEEecCC-----ChhhHHHHHHHHhcC-CCCCCCCCCCc
Q 031240 12 MHHNCPICFEFIFDTMKDITVLRCG-----HTIHLECLKEMEKHY-RYTCPVCSKSL 62 (163)
Q Consensus 12 ~~~~CpIC~e~l~~s~~~~~~L~CG-----H~fh~~Cl~~~~~~~-~~~CPiCr~~~ 62 (163)
|...|=||.+. +. . ..-||. -..|.+|+++|+..+ ...||+|+..+
T Consensus 1 ~~diCWIC~~~--~~-e--~~~PC~C~GS~K~VHq~CL~~WIn~S~k~~CeLCkteY 52 (156)
T PHA02862 1 MSDICWICNDV--CD-E--RNNFCGCNEEYKVVHIKCMQLWINYSKKKECNLCKTKY 52 (156)
T ss_pred CCCEEEEecCc--CC-C--CcccccccCcchhHHHHHHHHHHhcCCCcCccCCCCeE
Confidence 45789999986 11 1 135665 478999999999763 56799999987
No 88
>PHA02825 LAP/PHD finger-like protein; Provisional
Probab=94.69 E-value=0.038 Score=42.37 Aligned_cols=47 Identities=26% Similarity=0.562 Sum_probs=34.9
Q ss_pred CCccccccccccccCcCCccEEecCCC-----hhhHHHHHHHHhcC-CCCCCCCCCCc
Q 031240 11 AMHHNCPICFEFIFDTMKDITVLRCGH-----TIHLECLKEMEKHY-RYTCPVCSKSL 62 (163)
Q Consensus 11 s~~~~CpIC~e~l~~s~~~~~~L~CGH-----~fh~~Cl~~~~~~~-~~~CPiCr~~~ 62 (163)
.++..|=||.+.- . ...-||.- ..|.+|+++|+..+ ..+|++|+..+
T Consensus 6 ~~~~~CRIC~~~~----~-~~~~PC~CkGs~k~VH~sCL~rWi~~s~~~~CeiC~~~Y 58 (162)
T PHA02825 6 LMDKCCWICKDEY----D-VVTNYCNCKNENKIVHKECLEEWINTSKNKSCKICNGPY 58 (162)
T ss_pred CCCCeeEecCCCC----C-CccCCcccCCCchHHHHHHHHHHHhcCCCCcccccCCeE
Confidence 3578999999862 1 12346654 56999999999763 57899999986
No 89
>PF02148 zf-UBP: Zn-finger in ubiquitin-hydrolases and other protein; InterPro: IPR001607 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 UBP-type zinc finger domains, which display some similarity with the Zn-binding domain of the insulinase family. The UBP-type zinc finger domain is found only in a small subfamily of ubiquitin C-terminal hydrolases (deubiquitinases or UBP) [, ], All members of this subfamily are isopeptidase-T, which are known to cleave isopeptide bonds between ubiquitin moieties. Some of the proteins containing an UBP zinc finger include: Homo sapiens (Human) deubiquitinating enzyme 13 (UBPD) Human deubiquitinating enzyme 5 (UBP5) Dictyostelium discoideum (Slime mold) deubiquitinating enzyme A (UBPA) Saccharomyces cerevisiae (Baker's yeast) deubiquitinating enzyme 8 (UBP8) Yeast deubiquitinating enzyme 14 (UBP14) More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 3GV4_A 3PHD_B 3C5K_A 2UZG_A 3IHP_B 2G43_B 2G45_D 2I50_A 3MHH_A 3MHS_A ....
Probab=94.65 E-value=0.0041 Score=40.24 Aligned_cols=57 Identities=18% Similarity=0.281 Sum_probs=43.2
Q ss_pred CCCCCCCCcccceeeeccCCC--CCCCccccccCCCCCCCccccccccccceecccccccc
Q 031240 94 CNDCGANSHVQFHVIAHKCLS--CKSYNTRQTRGDTATTCSSGDELTILSHHWDYQQHASV 152 (163)
Q Consensus 94 C~dC~~~~~~~~h~~~~kC~~--C~synt~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 152 (163)
|..|+... .--|+.+.|+. |+++-..++..|.+.+.|..+..+.+..+|-|+.+.+|
T Consensus 1 C~~C~~~~--~~lw~CL~Cg~~~C~~~~~~Ha~~H~~~~~H~l~v~~~~~~i~C~~C~~~v 59 (63)
T PF02148_consen 1 CSVCGSTN--SNLWLCLTCGYVGCGRYSNGHALKHYKETGHPLAVSLSTGSIWCYACDDYV 59 (63)
T ss_dssp -SSSHTCS--SSEEEETTTS-EEETTTSTSHHHHHHHHHT--EEEETTTTCEEETTTTEEE
T ss_pred CCCCCCcC--CceEEeCCCCcccccCCcCcHHHHhhcccCCeEEEECCCCeEEEcCCCcEE
Confidence 66777551 12389999997 88877788889999889999999988889999988877
No 90
>KOG2114 consensus Vacuolar assembly/sorting protein PEP5/VPS11 [Intracellular trafficking, secretion, and vesicular transport]
Probab=94.61 E-value=0.036 Score=52.15 Aligned_cols=43 Identities=28% Similarity=0.646 Sum_probs=33.5
Q ss_pred cccccccccccCcCCccEEecCCChhhHHHHHHHHhcCCCCCCCCCCCcc
Q 031240 14 HNCPICFEFIFDTMKDITVLRCGHTIHLECLKEMEKHYRYTCPVCSKSLW 63 (163)
Q Consensus 14 ~~CpIC~e~l~~s~~~~~~L~CGH~fh~~Cl~~~~~~~~~~CPiCr~~~~ 63 (163)
..|..|--.| .-+.+...|||.||.+|++ .+...||-|+....
T Consensus 841 skCs~C~~~L---dlP~VhF~CgHsyHqhC~e----~~~~~CP~C~~e~~ 883 (933)
T KOG2114|consen 841 SKCSACEGTL---DLPFVHFLCGHSYHQHCLE----DKEDKCPKCLPELR 883 (933)
T ss_pred eeecccCCcc---ccceeeeecccHHHHHhhc----cCcccCCccchhhh
Confidence 5789998654 4556777999999999998 24578999998553
No 91
>COG5236 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=94.24 E-value=0.046 Score=46.92 Aligned_cols=48 Identities=25% Similarity=0.551 Sum_probs=36.8
Q ss_pred CCccccccccccccCcCCccEEecCCChhhHHHHHHHHhc-CCCCCCCCCCCc
Q 031240 11 AMHHNCPICFEFIFDTMKDITVLRCGHTIHLECLKEMEKH-YRYTCPVCSKSL 62 (163)
Q Consensus 11 s~~~~CpIC~e~l~~s~~~~~~L~CGH~fh~~Cl~~~~~~-~~~~CPiCr~~~ 62 (163)
..+..|-||-+.+ .-..++||||.+|.-|.-+...- ....||+||..-
T Consensus 59 Een~~C~ICA~~~----TYs~~~PC~H~~CH~Ca~RlRALY~~K~C~~CrTE~ 107 (493)
T COG5236 59 EENMNCQICAGST----TYSARYPCGHQICHACAVRLRALYMQKGCPLCRTET 107 (493)
T ss_pred cccceeEEecCCc----eEEEeccCCchHHHHHHHHHHHHHhccCCCcccccc
Confidence 4467899999863 44578899999999998775432 346799999863
No 92
>PHA03096 p28-like protein; Provisional
Probab=94.12 E-value=0.022 Score=47.66 Aligned_cols=47 Identities=23% Similarity=0.303 Sum_probs=31.5
Q ss_pred cccccccccccCcC---Cc-cEEecCCChhhHHHHHHHHhcC--CCCCCCCCC
Q 031240 14 HNCPICFEFIFDTM---KD-ITVLRCGHTIHLECLKEMEKHY--RYTCPVCSK 60 (163)
Q Consensus 14 ~~CpIC~e~l~~s~---~~-~~~L~CGH~fh~~Cl~~~~~~~--~~~CPiCr~ 60 (163)
-.|.||+|...... +. -..-.|.|.||..|+..|.... ...||.||.
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 57999999754321 11 1234999999999999998642 234555554
No 93
>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=93.64 E-value=0.019 Score=35.35 Aligned_cols=43 Identities=33% Similarity=0.746 Sum_probs=25.1
Q ss_pred cccccccccccCcCCccEEecCC-ChhhHHHHHHHHhcCCCCCCCCCCCcc
Q 031240 14 HNCPICFEFIFDTMKDITVLRCG-HTIHLECLKEMEKHYRYTCPVCSKSLW 63 (163)
Q Consensus 14 ~~CpIC~e~l~~s~~~~~~L~CG-H~fh~~Cl~~~~~~~~~~CPiCr~~~~ 63 (163)
.+|--|.- ..-..+.|. |..|..|+..++. .+..||+|.+++.
T Consensus 3 ~nCKsCWf------~~k~Li~C~dHYLCl~CLt~ml~-~s~~C~iC~~~LP 46 (50)
T PF03854_consen 3 YNCKSCWF------ANKGLIKCSDHYLCLNCLTLMLS-RSDRCPICGKPLP 46 (50)
T ss_dssp ----SS-S--------SSEEE-SS-EEEHHHHHHT-S-SSSEETTTTEE--
T ss_pred ccChhhhh------cCCCeeeecchhHHHHHHHHHhc-cccCCCcccCcCc
Confidence 46777772 222467887 9999999999987 4578999998763
No 94
>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=93.63 E-value=0.034 Score=34.43 Aligned_cols=44 Identities=25% Similarity=0.659 Sum_probs=21.0
Q ss_pred cccccccccccCcCCccEEecCCChhhHHHHHHHHh----cCCCCCCCCCCC
Q 031240 14 HNCPICFEFIFDTMKDITVLRCGHTIHLECLKEMEK----HYRYTCPVCSKS 61 (163)
Q Consensus 14 ~~CpIC~e~l~~s~~~~~~L~CGH~fh~~Cl~~~~~----~~~~~CPiCr~~ 61 (163)
..|||-...| ..+++...|.|.-|.+ ++.|++ ...+.||+|+++
T Consensus 3 L~CPls~~~i---~~P~Rg~~C~H~~CFD-l~~fl~~~~~~~~W~CPiC~~~ 50 (50)
T PF02891_consen 3 LRCPLSFQRI---RIPVRGKNCKHLQCFD-LESFLESNQRTPKWKCPICNKP 50 (50)
T ss_dssp SB-TTTSSB----SSEEEETT--SS--EE-HHHHHHHHHHS---B-TTT---
T ss_pred eeCCCCCCEE---EeCccCCcCcccceEC-HHHHHHHhhccCCeECcCCcCc
Confidence 5799998775 4566677999985543 344443 246889999864
No 95
>PF05290 Baculo_IE-1: Baculovirus immediate-early protein (IE-0); InterPro: IPR007954 This entry contains the Baculovirus immediate-early protein IE-0.
Probab=93.02 E-value=0.1 Score=38.95 Aligned_cols=49 Identities=31% Similarity=0.546 Sum_probs=37.2
Q ss_pred CccccccccccccCcCCccEEe----cCCChhhHHHHHHHHhcC--CCCCCCCCCCccc
Q 031240 12 MHHNCPICFEFIFDTMKDITVL----RCGHTIHLECLKEMEKHY--RYTCPVCSKSLWD 64 (163)
Q Consensus 12 ~~~~CpIC~e~l~~s~~~~~~L----~CGH~fh~~Cl~~~~~~~--~~~CPiCr~~~~~ 64 (163)
.-.+|.||.|. ..+...| =||-.+|..|...+|++. ...||+|+.++..
T Consensus 79 ~lYeCnIC~et----S~ee~FLKPneCCgY~iCn~Cya~LWK~~~~ypvCPvCkTSFKs 133 (140)
T PF05290_consen 79 KLYECNICKET----SAEERFLKPNECCGYSICNACYANLWKFCNLYPVCPVCKTSFKS 133 (140)
T ss_pred CceeccCcccc----cchhhcCCcccccchHHHHHHHHHHHHHcccCCCCCcccccccc
Confidence 45789999985 2333444 489999999999977653 4679999998743
No 96
>KOG1001 consensus Helicase-like transcription factor HLTF/DNA helicase RAD5, DEAD-box superfamily [Transcription; Replication, recombination and repair]
Probab=92.24 E-value=0.083 Score=49.08 Aligned_cols=44 Identities=36% Similarity=0.904 Sum_probs=36.1
Q ss_pred cccccccccccCcCCccEEecCCChhhHHHHHHHHhcCC-CCCCCCCCCc
Q 031240 14 HNCPICFEFIFDTMKDITVLRCGHTIHLECLKEMEKHYR-YTCPVCSKSL 62 (163)
Q Consensus 14 ~~CpIC~e~l~~s~~~~~~L~CGH~fh~~Cl~~~~~~~~-~~CPiCr~~~ 62 (163)
..|+||++ ...+.+.+|||.||..|+...++... ..||+||..+
T Consensus 455 ~~c~ic~~-----~~~~~it~c~h~~c~~c~~~~i~~~~~~~~~~cr~~l 499 (674)
T KOG1001|consen 455 HWCHICCD-----LDSFFITRCGHDFCVECLKKSIQQSENAPCPLCRNVL 499 (674)
T ss_pred cccccccc-----cccceeecccchHHHHHHHhccccccCCCCcHHHHHH
Confidence 78999997 35667889999999999999876543 3699998765
No 97
>KOG4367 consensus Predicted Zn-finger protein [Function unknown]
Probab=92.21 E-value=0.11 Score=46.03 Aligned_cols=34 Identities=24% Similarity=0.700 Sum_probs=29.3
Q ss_pred CccccccccccccCcCCccEEecCCChhhHHHHHHHHh
Q 031240 12 MHHNCPICFEFIFDTMKDITVLRCGHTIHLECLKEMEK 49 (163)
Q Consensus 12 ~~~~CpIC~e~l~~s~~~~~~L~CGH~fh~~Cl~~~~~ 49 (163)
.+..||||... .++|.+|+|||..|..|....+.
T Consensus 3 eelkc~vc~~f----~~epiil~c~h~lc~~ca~~~~~ 36 (699)
T KOG4367|consen 3 EELKCPVCGSF----YREPIILPCSHNLCQACARNILV 36 (699)
T ss_pred ccccCceehhh----ccCceEeecccHHHHHHHHhhcc
Confidence 46889999975 58889999999999999887654
No 98
>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=92.16 E-value=0.07 Score=43.68 Aligned_cols=48 Identities=27% Similarity=0.602 Sum_probs=36.0
Q ss_pred ccccccccccccCcCCccEEe--c-CCChhhHHHHHHHHhcCCCCCC--CCCCC
Q 031240 13 HHNCPICFEFIFDTMKDITVL--R-CGHTIHLECLKEMEKHYRYTCP--VCSKS 61 (163)
Q Consensus 13 ~~~CpIC~e~l~~s~~~~~~L--~-CGH~fh~~Cl~~~~~~~~~~CP--iCr~~ 61 (163)
+..||||..+-+-+. +.++| | |-|.+|.+|..+.+..+...|| -|.+-
T Consensus 10 d~~CPvCksDrYLnP-dik~linPECyHrmCESCvdRIFs~GpAqCP~~gC~kI 62 (314)
T COG5220 10 DRRCPVCKSDRYLNP-DIKILINPECYHRMCESCVDRIFSRGPAQCPYKGCGKI 62 (314)
T ss_pred cccCCccccccccCC-CeEEEECHHHHHHHHHHHHHHHhcCCCCCCCCccHHHH
Confidence 458999987543222 22333 5 9999999999999988888999 78664
No 99
>KOG1812 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=91.25 E-value=0.11 Score=45.13 Aligned_cols=50 Identities=30% Similarity=0.644 Sum_probs=33.6
Q ss_pred ccccccccccccCcCCccEEecCCChhhHHHHHHHHhc-----CCCCCC--CCCCCc
Q 031240 13 HHNCPICFEFIFDTMKDITVLRCGHTIHLECLKEMEKH-----YRYTCP--VCSKSL 62 (163)
Q Consensus 13 ~~~CpIC~e~l~~s~~~~~~L~CGH~fh~~Cl~~~~~~-----~~~~CP--iCr~~~ 62 (163)
...|.||+...........++.|||.||..|+.++++. ...+|| .|...+
T Consensus 146 ~~~C~iC~~e~~~~~~~f~~~~C~H~fC~~C~k~~iev~~~~~~~~~C~~~~C~~~l 202 (384)
T KOG1812|consen 146 KEECGICFVEDPEAEDMFSVLKCGHRFCKDCVKQHIEVKLLSGTVIRCPHDGCESRL 202 (384)
T ss_pred cccCccCccccccHhhhHHHhcccchhhhHHhHHHhhhhhccCCCccCCCCCCCccC
Confidence 56899999332223222336799999999999998763 245676 355554
No 100
>KOG2034 consensus Vacuolar sorting protein PEP3/VPS18 [Intracellular trafficking, secretion, and vesicular transport]
Probab=90.28 E-value=0.18 Score=47.71 Aligned_cols=42 Identities=26% Similarity=0.498 Sum_probs=31.5
Q ss_pred ceecCCCccccccccccccCcCCccEEecCCChhhHHHHHHHHh
Q 031240 6 RCVERAMHHNCPICFEFIFDTMKDITVLRCGHTIHLECLKEMEK 49 (163)
Q Consensus 6 ~c~e~s~~~~CpIC~e~l~~s~~~~~~L~CGH~fh~~Cl~~~~~ 49 (163)
++.--.....|.+|.-.|+ .++-.+.+|||.||..|+.+-..
T Consensus 810 ry~v~ep~d~C~~C~~~ll--~~pF~vf~CgH~FH~~Cl~~~v~ 851 (911)
T KOG2034|consen 810 RYRVLEPQDSCDHCGRPLL--IKPFYVFPCGHCFHRDCLIRHVL 851 (911)
T ss_pred ceEEecCccchHHhcchhh--cCcceeeeccchHHHHHHHHHHH
Confidence 3333345678999998765 45556779999999999998765
No 101
>TIGR00100 hypA hydrogenase nickel insertion protein HypA. In Hpylori, hypA mutant abolished hydrogenase activity and decrease in urease activity. Nickel supplementation in media restored urease activity and partial hydrogenase activity. HypA probably involved in inserting Ni in enzymes.
Probab=90.20 E-value=0.18 Score=36.55 Aligned_cols=36 Identities=17% Similarity=0.354 Sum_probs=26.4
Q ss_pred cCcceeeCCCCCCCCcccceeeeccCCCCCCCcccccc
Q 031240 87 NKMVWILCNDCGANSHVQFHVIAHKCLSCKSYNTRQTR 124 (163)
Q Consensus 87 ~~~~~i~C~dC~~~~~~~~h~~~~kC~~C~synt~~~~ 124 (163)
.......|++|+....... ....|+.|||++.+.+.
T Consensus 66 ~~p~~~~C~~Cg~~~~~~~--~~~~CP~Cgs~~~~i~~ 101 (115)
T TIGR00100 66 DEPVECECEDCSEEVSPEI--DLYRCPKCHGIMLQVRA 101 (115)
T ss_pred eeCcEEEcccCCCEEecCC--cCccCcCCcCCCcEEec
Confidence 3456889999997665432 24579999999987754
No 102
>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=90.08 E-value=0.3 Score=29.21 Aligned_cols=40 Identities=28% Similarity=0.701 Sum_probs=20.6
Q ss_pred cccccccccCcCCccEEe--cCCChhhHHHHHHHHhcCC-CCCCCC
Q 031240 16 CPICFEFIFDTMKDITVL--RCGHTIHLECLKEMEKHYR-YTCPVC 58 (163)
Q Consensus 16 CpIC~e~l~~s~~~~~~L--~CGH~fh~~Cl~~~~~~~~-~~CPiC 58 (163)
|.+|.+.++ ....-. .|+=.+|..|++.++.... .+||.|
T Consensus 1 C~~C~~iv~---~G~~C~~~~C~~r~H~~C~~~y~r~~~~~~CP~C 43 (43)
T PF08746_consen 1 CEACKEIVT---QGQRCSNRDCNVRLHDDCFKKYFRHRSNPKCPNC 43 (43)
T ss_dssp -TTT-SB-S---SSEE-SS--S--EE-HHHHHHHTTT-SS-B-TTT
T ss_pred CcccchhHe---eeccCCCCccCchHHHHHHHHHHhcCCCCCCcCC
Confidence 567777543 222222 5888999999999987643 369987
No 103
>KOG0298 consensus DEAD box-containing helicase-like transcription factor/DNA repair protein [Replication, recombination and repair]
Probab=89.12 E-value=0.14 Score=50.35 Aligned_cols=51 Identities=24% Similarity=0.508 Sum_probs=39.9
Q ss_pred CccccccccccccCcCCccEEecCCChhhHHHHHHHHhcCCCCCCCCCCCccchh
Q 031240 12 MHHNCPICFEFIFDTMKDITVLRCGHTIHLECLKEMEKHYRYTCPVCSKSLWDMS 66 (163)
Q Consensus 12 ~~~~CpIC~e~l~~s~~~~~~L~CGH~fh~~Cl~~~~~~~~~~CPiCr~~~~~~~ 66 (163)
....|+||.+.+- +.-.+..|||.+|..|+..|+.. +..||+|+....+..
T Consensus 1152 ~~~~c~ic~dil~---~~~~I~~cgh~~c~~c~~~~l~~-~s~~~~~ksi~~dfg 1202 (1394)
T KOG0298|consen 1152 GHFVCEICLDILR---NQGGIAGCGHEPCCRCDELWLYA-SSRCPICKSIKGDFG 1202 (1394)
T ss_pred cccchHHHHHHHH---hcCCeeeechhHhhhHHHHHHHH-hccCcchhhhhhhhc
Confidence 3558999998763 23467799999999999999984 578999987665433
No 104
>PRK12380 hydrogenase nickel incorporation protein HybF; Provisional
Probab=88.99 E-value=0.3 Score=35.24 Aligned_cols=36 Identities=22% Similarity=0.422 Sum_probs=25.8
Q ss_pred CcceeeCCCCCCCCcccceeeeccCCCCCCCccccccC
Q 031240 88 KMVWILCNDCGANSHVQFHVIAHKCLSCKSYNTRQTRG 125 (163)
Q Consensus 88 ~~~~i~C~dC~~~~~~~~h~~~~kC~~C~synt~~~~~ 125 (163)
......|++|+....... ....|+.|||++...+++
T Consensus 67 vp~~~~C~~Cg~~~~~~~--~~~~CP~Cgs~~~~i~~G 102 (113)
T PRK12380 67 KPAQAWCWDCSQVVEIHQ--HDAQCPHCHGERLRVDTG 102 (113)
T ss_pred eCcEEEcccCCCEEecCC--cCccCcCCCCCCcEEccC
Confidence 356889999997665432 233599999998776543
No 105
>PRK00564 hypA hydrogenase nickel incorporation protein; Provisional
Probab=88.38 E-value=0.35 Score=35.12 Aligned_cols=37 Identities=24% Similarity=0.349 Sum_probs=26.1
Q ss_pred cCcceeeCCCCCCCCcccceeeeccCCCCCCCcccccc
Q 031240 87 NKMVWILCNDCGANSHVQFHVIAHKCLSCKSYNTRQTR 124 (163)
Q Consensus 87 ~~~~~i~C~dC~~~~~~~~h~~~~kC~~C~synt~~~~ 124 (163)
.....+.|++|+....... ....+|+.|||++...++
T Consensus 67 ~vp~~~~C~~Cg~~~~~~~-~~~~~CP~Cgs~~~~i~~ 103 (117)
T PRK00564 67 DEKVELECKDCSHVFKPNA-LDYGVCEKCHSKNVIITQ 103 (117)
T ss_pred ecCCEEEhhhCCCccccCC-ccCCcCcCCCCCceEEec
Confidence 3456889999997765432 122369999999877654
No 106
>PF14446 Prok-RING_1: Prokaryotic RING finger family 1
Probab=88.31 E-value=0.43 Score=30.15 Aligned_cols=36 Identities=22% Similarity=0.491 Sum_probs=28.3
Q ss_pred CCccccccccccccCcCCccEEecCCChhhHHHHHH
Q 031240 11 AMHHNCPICFEFIFDTMKDITVLRCGHTIHLECLKE 46 (163)
Q Consensus 11 s~~~~CpIC~e~l~~s~~~~~~L~CGH~fh~~Cl~~ 46 (163)
-+...|++|.+.|.+....++-..||=.+|+.|..+
T Consensus 3 ~~~~~C~~Cg~~~~~~dDiVvCp~CgapyHR~C~~~ 38 (54)
T PF14446_consen 3 YEGCKCPVCGKKFKDGDDIVVCPECGAPYHRDCWEK 38 (54)
T ss_pred ccCccChhhCCcccCCCCEEECCCCCCcccHHHHhh
Confidence 356789999999766655555569999999999654
No 107
>smart00290 ZnF_UBP Ubiquitin Carboxyl-terminal Hydrolase-like zinc finger.
Probab=88.00 E-value=0.28 Score=29.66 Aligned_cols=43 Identities=16% Similarity=0.237 Sum_probs=30.0
Q ss_pred eCCCCCCCCcccceeeeccCCC--CCCCccccccCCCCCCCccccccc
Q 031240 93 LCNDCGANSHVQFHVIAHKCLS--CKSYNTRQTRGDTATTCSSGDELT 138 (163)
Q Consensus 93 ~C~dC~~~~~~~~h~~~~kC~~--C~synt~~~~~~~~~~~~~~~~~~ 138 (163)
.|.+|+.... -|+.+.|+. |+.+.-.++..|+..+.+..+..+
T Consensus 1 ~C~~C~~~~~---l~~CL~C~~~~c~~~~~~h~~~H~~~t~H~~~~~~ 45 (50)
T smart00290 1 RCSVCGTIEN---LWLCLTCGQVGCGRYQLGHALEHFEETGHPLVVKL 45 (50)
T ss_pred CcccCCCcCC---eEEecCCCCcccCCCCCcHHHHHhhhhCCCEEEEc
Confidence 4889987665 379999986 777655677778877766544433
No 108
>PRK03681 hypA hydrogenase nickel incorporation protein; Validated
Probab=87.95 E-value=0.38 Score=34.76 Aligned_cols=37 Identities=14% Similarity=0.286 Sum_probs=25.9
Q ss_pred CcceeeCCCCCCCCcccceeeeccCCCCCCCccccccC
Q 031240 88 KMVWILCNDCGANSHVQFHVIAHKCLSCKSYNTRQTRG 125 (163)
Q Consensus 88 ~~~~i~C~dC~~~~~~~~h~~~~kC~~C~synt~~~~~ 125 (163)
......|++|+.......+ ....|+.|||++...+++
T Consensus 67 ~p~~~~C~~Cg~~~~~~~~-~~~~CP~Cgs~~~~i~~G 103 (114)
T PRK03681 67 QEAECWCETCQQYVTLLTQ-RVRRCPQCHGDMLRIVAD 103 (114)
T ss_pred eCcEEEcccCCCeeecCCc-cCCcCcCcCCCCcEEccC
Confidence 3568899999976554321 124699999999877643
No 109
>KOG0309 consensus Conserved WD40 repeat-containing protein [Function unknown]
Probab=87.54 E-value=0.37 Score=45.25 Aligned_cols=47 Identities=23% Similarity=0.458 Sum_probs=30.2
Q ss_pred ecCCCccccccccccccCcCCccEEecCCChhhHHHHHHHHhcCCCCCCC
Q 031240 8 VERAMHHNCPICFEFIFDTMKDITVLRCGHTIHLECLKEMEKHYRYTCPV 57 (163)
Q Consensus 8 ~e~s~~~~CpIC~e~l~~s~~~~~~L~CGH~fh~~Cl~~~~~~~~~~CPi 57 (163)
+-......|.||-=.+. .....-..|||.+|.+|..+|++.+ ..||.
T Consensus 1023 ~~~~~~~~C~~C~l~V~--gss~~Cg~C~Hv~H~sc~~eWf~~g-d~Cps 1069 (1081)
T KOG0309|consen 1023 ICKGFTFQCAICHLAVR--GSSNFCGTCGHVGHTSCMMEWFRTG-DVCPS 1069 (1081)
T ss_pred ccccceeeeeeEeeEee--ccchhhccccccccHHHHHHHHhcC-CcCCC
Confidence 33344455777653221 1223446999999999999999854 57773
No 110
>COG5109 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=87.31 E-value=0.44 Score=40.49 Aligned_cols=46 Identities=28% Similarity=0.657 Sum_probs=37.2
Q ss_pred cccccccccccCcCCccEEecCCChhhHHHHHHHHhcC--CCCCCCCCC
Q 031240 14 HNCPICFEFIFDTMKDITVLRCGHTIHLECLKEMEKHY--RYTCPVCSK 60 (163)
Q Consensus 14 ~~CpIC~e~l~~s~~~~~~L~CGH~fh~~Cl~~~~~~~--~~~CPiCr~ 60 (163)
..|||=.|. -+...+|+.|.|||.+=.+-+.+.-+.+ .+.||.|-.
T Consensus 337 FiCPVlKe~-~t~ENpP~ml~CgHVIskeal~~LS~nG~~~FKCPYCP~ 384 (396)
T COG5109 337 FICPVLKEL-CTDENPPVMLECGHVISKEALSVLSQNGVLSFKCPYCPE 384 (396)
T ss_pred eeccccHhh-hcccCCCeeeeccceeeHHHHHHHhhcCcEEeeCCCCCc
Confidence 468887765 4557899999999999999999987654 578999954
No 111
>COG1066 Sms Predicted ATP-dependent serine protease [Posttranslational modification, protein turnover, chaperones]
Probab=86.95 E-value=0.48 Score=41.81 Aligned_cols=30 Identities=30% Similarity=0.687 Sum_probs=25.0
Q ss_pred ceeeCCCCCCCCcccceeeeccCCCCCCCccccc
Q 031240 90 VWILCNDCGANSHVQFHVIAHKCLSCKSYNTRQT 123 (163)
Q Consensus 90 ~~i~C~dC~~~~~~~~h~~~~kC~~C~synt~~~ 123 (163)
....|+.||..+. .|+| ||..||.+||-.-
T Consensus 6 t~f~C~~CG~~s~---KW~G-kCp~Cg~Wns~vE 35 (456)
T COG1066 6 TAFVCQECGYVSP---KWLG-KCPACGAWNTLVE 35 (456)
T ss_pred cEEEcccCCCCCc---cccc-cCCCCCCccceEE
Confidence 5678999998764 3888 9999999999764
No 112
>KOG0826 consensus Predicted E3 ubiquitin ligase involved in peroxisome organization [Posttranslational modification, protein turnover, chaperones]
Probab=86.26 E-value=0.55 Score=40.00 Aligned_cols=48 Identities=17% Similarity=0.335 Sum_probs=36.5
Q ss_pred CCccccccccccccCcCCccEEecCCChhhHHHHHHHHhcCCCCCCCCCCCc
Q 031240 11 AMHHNCPICFEFIFDTMKDITVLRCGHTIHLECLKEMEKHYRYTCPVCSKSL 62 (163)
Q Consensus 11 s~~~~CpIC~e~l~~s~~~~~~L~CGH~fh~~Cl~~~~~~~~~~CPiCr~~~ 62 (163)
.+...||||+.. ...+.+.---|-+||..|+-.++. ...+||+=..++
T Consensus 298 ~~~~~CpvClk~---r~Nptvl~vSGyVfCY~Ci~~Yv~-~~~~CPVT~~p~ 345 (357)
T KOG0826|consen 298 PDREVCPVCLKK---RQNPTVLEVSGYVFCYPCIFSYVV-NYGHCPVTGYPA 345 (357)
T ss_pred CccccChhHHhc---cCCCceEEecceEEeHHHHHHHHH-hcCCCCccCCcc
Confidence 356799999964 234444457799999999999988 557899876664
No 113
>PRK03824 hypA hydrogenase nickel incorporation protein; Provisional
Probab=85.63 E-value=0.51 Score=35.11 Aligned_cols=36 Identities=22% Similarity=0.493 Sum_probs=25.0
Q ss_pred cceeeCCCCCCCCccc-------------ce------eeeccCCCCCCCcccccc
Q 031240 89 MVWILCNDCGANSHVQ-------------FH------VIAHKCLSCKSYNTRQTR 124 (163)
Q Consensus 89 ~~~i~C~dC~~~~~~~-------------~h------~~~~kC~~C~synt~~~~ 124 (163)
.....|++||...... +| ....+|+.|||++.+.++
T Consensus 68 p~~~~C~~CG~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~CP~Cgs~~~~i~~ 122 (135)
T PRK03824 68 EAVLKCRNCGNEWSLKEVKESLDEEIREAIHFIPEVVHAFLKCPKCGSRDFEIVK 122 (135)
T ss_pred ceEEECCCCCCEEecccccccccccccccccccccccccCcCCcCCCCCCcEEec
Confidence 4678999999765432 11 133679999999877654
No 114
>PF10272 Tmpp129: Putative transmembrane protein precursor; InterPro: IPR018801 This entry consists of proteins conserved from worms to humans. They are purported to be transmembrane protein-precursors but their function is unknown.
Probab=85.30 E-value=0.97 Score=39.06 Aligned_cols=27 Identities=22% Similarity=0.535 Sum_probs=20.8
Q ss_pred ChhhHHHHHHHHhcC------------CCCCCCCCCCcc
Q 031240 37 HTIHLECLKEMEKHY------------RYTCPVCSKSLW 63 (163)
Q Consensus 37 H~fh~~Cl~~~~~~~------------~~~CPiCr~~~~ 63 (163)
=..|.+|+.+|+.+. .-.||+||+.+.
T Consensus 313 PmWC~~Cm~kwFasrQd~~~~~~Wl~~~~~CPtCRa~FC 351 (358)
T PF10272_consen 313 PMWCLECMGKWFASRQDQQHPETWLSGKCPCPTCRAKFC 351 (358)
T ss_pred chHHHHHHHHHhhhcCCCCChhhhhcCCCCCCCCcccce
Confidence 456999999998652 346999999863
No 115
>PF01155 HypA: Hydrogenase expression/synthesis hypA family; InterPro: IPR000688 Bacterial membrane-bound nickel-dependent hydrogenases requires a number of accessory proteins which are involved in their maturation. The exact role of these proteins is not yet clear, but some seem to be required for the incorporation of the nickel ions []. One of these proteins is generally known as hypA. It is a protein of about 12 to 14 kDa that contains, in its C-terminal region, four conserved cysteines that form a zinc-finger like motif. Escherichia coli has two proteins that belong to this family, hypA and hybF. A homologue, MJ0214, has also been found in a number of archaeal species, including the genome of Methanocaldococcus jannaschii (Methanococcus jannaschii).; GO: 0016151 nickel ion binding, 0006464 protein modification process; PDB: 2KDX_A 3A44_D 3A43_B.
Probab=85.02 E-value=0.27 Score=35.39 Aligned_cols=35 Identities=20% Similarity=0.328 Sum_probs=22.4
Q ss_pred CcceeeCCCCCCCCcccceeeeccCCCCCCCcccccc
Q 031240 88 KMVWILCNDCGANSHVQFHVIAHKCLSCKSYNTRQTR 124 (163)
Q Consensus 88 ~~~~i~C~dC~~~~~~~~h~~~~kC~~C~synt~~~~ 124 (163)
......|++|+.......+. ..|+.|||++...++
T Consensus 67 ~p~~~~C~~Cg~~~~~~~~~--~~CP~Cgs~~~~i~~ 101 (113)
T PF01155_consen 67 VPARARCRDCGHEFEPDEFD--FSCPRCGSPDVEIIS 101 (113)
T ss_dssp E--EEEETTTS-EEECHHCC--HH-SSSSSS-EEEEE
T ss_pred cCCcEECCCCCCEEecCCCC--CCCcCCcCCCcEEcc
Confidence 35688999999987655432 579999999876554
No 116
>KOG2932 consensus E3 ubiquitin ligase involved in ubiquitination of E-cadherin complex [Posttranslational modification, protein turnover, chaperones]
Probab=84.33 E-value=0.53 Score=39.98 Aligned_cols=29 Identities=28% Similarity=0.773 Sum_probs=22.9
Q ss_pred EEecCCChhhHHHHHHHHhcCCCCCCCCCCCc
Q 031240 31 TVLRCGHTIHLECLKEMEKHYRYTCPVCSKSL 62 (163)
Q Consensus 31 ~~L~CGH~fh~~Cl~~~~~~~~~~CPiCr~~~ 62 (163)
++++|.|+||.+|...- ....||.|...+
T Consensus 105 RmIPCkHvFCl~CAr~~---~dK~Cp~C~d~V 133 (389)
T KOG2932|consen 105 RMIPCKHVFCLECARSD---SDKICPLCDDRV 133 (389)
T ss_pred cccccchhhhhhhhhcC---ccccCcCcccHH
Confidence 46799999999997642 346799998776
No 117
>PRK12286 rpmF 50S ribosomal protein L32; Reviewed
Probab=83.89 E-value=1.1 Score=28.61 Aligned_cols=29 Identities=31% Similarity=0.712 Sum_probs=22.0
Q ss_pred ceeeCCCCCCCCcccceeeeccCCCCCCCccccc
Q 031240 90 VWILCNDCGANSHVQFHVIAHKCLSCKSYNTRQT 123 (163)
Q Consensus 90 ~~i~C~dC~~~~~~~~h~~~~kC~~C~synt~~~ 123 (163)
..+.|..||+.. ..|.+ |.+||.|+.+++
T Consensus 26 ~l~~C~~CG~~~--~~H~v---C~~CG~Y~gr~v 54 (57)
T PRK12286 26 GLVECPNCGEPK--LPHRV---CPSCGYYKGREV 54 (57)
T ss_pred cceECCCCCCcc--CCeEE---CCCCCcCCCEEe
Confidence 456799999754 33544 999999999875
No 118
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=83.42 E-value=0.85 Score=27.37 Aligned_cols=31 Identities=16% Similarity=0.276 Sum_probs=19.6
Q ss_pred ceeeCCCCCCCCcccceeeeccCCCCCCCcc
Q 031240 90 VWILCNDCGANSHVQFHVIAHKCLSCKSYNT 120 (163)
Q Consensus 90 ~~i~C~dC~~~~~~~~h~~~~kC~~C~synt 120 (163)
....|.+||......-.....+|+.||+.-.
T Consensus 2 ~~y~C~~CG~~~~~~~~~~~~~Cp~CG~~~~ 32 (46)
T PRK00398 2 AEYKCARCGREVELDEYGTGVRCPYCGYRIL 32 (46)
T ss_pred CEEECCCCCCEEEECCCCCceECCCCCCeEE
Confidence 4567888887653332223568999986544
No 119
>KOG2068 consensus MOT2 transcription factor [Transcription]
Probab=83.24 E-value=0.91 Score=38.63 Aligned_cols=49 Identities=31% Similarity=0.590 Sum_probs=36.5
Q ss_pred ccccccccccccCcCCccEEecCCChhhHHHHHHHHhcCCCCCCCCCCCc
Q 031240 13 HHNCPICFEFIFDTMKDITVLRCGHTIHLECLKEMEKHYRYTCPVCSKSL 62 (163)
Q Consensus 13 ~~~CpIC~e~l~~s~~~~~~L~CGH~fh~~Cl~~~~~~~~~~CPiCr~~~ 62 (163)
...||||.+.+........-.+||+..|..|+..... +..+||.||+++
T Consensus 249 ~~s~p~~~~~~~~~d~~~lP~~~~~~~~l~~~~t~~~-~~~~~~~~rk~~ 297 (327)
T KOG2068|consen 249 PPSCPICYEDLDLTDSNFLPCPCGFRLCLFCHKTISD-GDGRCPGCRKPY 297 (327)
T ss_pred CCCCCCCCCcccccccccccccccccchhhhhhcccc-cCCCCCccCCcc
Confidence 4789999998643333333348899999999888766 468999999876
No 120
>KOG1100 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=81.79 E-value=0.82 Score=36.51 Aligned_cols=39 Identities=26% Similarity=0.573 Sum_probs=29.0
Q ss_pred ccccccccccCcCCccEEecCCC-hhhHHHHHHHHhcCCCCCCCCCCCc
Q 031240 15 NCPICFEFIFDTMKDITVLRCGH-TIHLECLKEMEKHYRYTCPVCSKSL 62 (163)
Q Consensus 15 ~CpIC~e~l~~s~~~~~~L~CGH-~fh~~Cl~~~~~~~~~~CPiCr~~~ 62 (163)
.|-+|.+. ...+.++||.| .+|..|-.. -..||+|+...
T Consensus 160 ~Cr~C~~~----~~~VlllPCrHl~lC~~C~~~-----~~~CPiC~~~~ 199 (207)
T KOG1100|consen 160 SCRKCGER----EATVLLLPCRHLCLCGICDES-----LRICPICRSPK 199 (207)
T ss_pred cceecCcC----CceEEeecccceEeccccccc-----CccCCCCcChh
Confidence 39999875 45577889996 788888554 24599998764
No 121
>COG0375 HybF Zn finger protein HypA/HybF (possibly regulating hydrogenase expression) [General function prediction only]
Probab=81.08 E-value=1.2 Score=32.44 Aligned_cols=37 Identities=27% Similarity=0.452 Sum_probs=27.7
Q ss_pred cCcceeeCCCCCCCCcccceeeeccCCCCCCCccccccC
Q 031240 87 NKMVWILCNDCGANSHVQFHVIAHKCLSCKSYNTRQTRG 125 (163)
Q Consensus 87 ~~~~~i~C~dC~~~~~~~~h~~~~kC~~C~synt~~~~~ 125 (163)
.....+.|.+|+......-|.+. |+.|||-+.+...+
T Consensus 66 ~~p~~~~C~~C~~~~~~e~~~~~--CP~C~s~~~~i~~G 102 (115)
T COG0375 66 EEPAECWCLDCGQEVELEELDYR--CPKCGSINLRIIGG 102 (115)
T ss_pred EeccEEEeccCCCeecchhheeE--CCCCCCCceEEecC
Confidence 44578999999877655544443 99999999887653
No 122
>PF14569 zf-UDP: Zinc-binding RING-finger; PDB: 1WEO_A.
Probab=79.93 E-value=2.4 Score=28.78 Aligned_cols=52 Identities=19% Similarity=0.388 Sum_probs=23.7
Q ss_pred CCccccccccccccCcCC-cc--EEecCCChhhHHHHHHHHhcCCCCCCCCCCCc
Q 031240 11 AMHHNCPICFEFIFDTMK-DI--TVLRCGHTIHLECLKEMEKHYRYTCPVCSKSL 62 (163)
Q Consensus 11 s~~~~CpIC~e~l~~s~~-~~--~~L~CGH~fh~~Cl~~~~~~~~~~CPiCr~~~ 62 (163)
.....|.||.+.+-.... .+ ...-|+--.|+.|++-=.+.+...||.|+..+
T Consensus 7 ~~~qiCqiCGD~VGl~~~Ge~FVAC~eC~fPvCr~CyEYErkeg~q~CpqCkt~y 61 (80)
T PF14569_consen 7 LNGQICQICGDDVGLTENGEVFVACHECAFPVCRPCYEYERKEGNQVCPQCKTRY 61 (80)
T ss_dssp -SS-B-SSS--B--B-SSSSB--S-SSS-----HHHHHHHHHTS-SB-TTT--B-
T ss_pred cCCcccccccCccccCCCCCEEEEEcccCCccchhHHHHHhhcCcccccccCCCc
Confidence 345789999987632222 22 22378889999999977666788999999765
No 123
>KOG4185 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=79.78 E-value=0.37 Score=39.86 Aligned_cols=50 Identities=30% Similarity=0.539 Sum_probs=38.8
Q ss_pred Ccccccccccccc--CcCCccEEec--------CCChhhHHHHHHHHhcCCCCCCCCCCC
Q 031240 12 MHHNCPICFEFIF--DTMKDITVLR--------CGHTIHLECLKEMEKHYRYTCPVCSKS 61 (163)
Q Consensus 12 ~~~~CpIC~e~l~--~s~~~~~~L~--------CGH~fh~~Cl~~~~~~~~~~CPiCr~~ 61 (163)
.+..|.||...+. +....|.++. |||+.|..|+...+......||.|++.
T Consensus 206 ~~~~c~ic~~~~~~n~~~~~p~vl~~~~~~~~~c~htlc~~c~~~~l~~~~~~cp~~~~~ 265 (296)
T KOG4185|consen 206 IEKLCEICERIYSENDEKLAPLVLSLSRLKEKIEGHTLCKECIDTILLQAGIKCPFCTWS 265 (296)
T ss_pred HHHHHHHHHHHhhccccccchhHHHHHHHHHHHHHHHHHhcchHHHHHHhhhcCCcccce
Confidence 3467999977654 3445667777 999999999999876555889999975
No 124
>PRK00762 hypA hydrogenase nickel incorporation protein; Provisional
Probab=79.66 E-value=1.3 Score=32.45 Aligned_cols=36 Identities=25% Similarity=0.398 Sum_probs=24.0
Q ss_pred CcceeeCCCCCCCCccc-c---ee-eeccCCCCCCCcccccc
Q 031240 88 KMVWILCNDCGANSHVQ-F---HV-IAHKCLSCKSYNTRQTR 124 (163)
Q Consensus 88 ~~~~i~C~dC~~~~~~~-~---h~-~~~kC~~C~synt~~~~ 124 (163)
......| +|+...... + |+ ....|+.|||++...++
T Consensus 67 vp~~~~C-~Cg~~~~~~~~~~~~~~~~~~CP~Cgs~~~~i~~ 107 (124)
T PRK00762 67 IPVEIEC-ECGYEGVVDEDEIDHYAAVIECPVCGNKRAHILG 107 (124)
T ss_pred cCeeEEe-eCcCcccccccchhccccCCcCcCCCCCCCEEec
Confidence 3568899 999774321 1 11 12469999999987754
No 125
>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=79.19 E-value=1.6 Score=27.57 Aligned_cols=29 Identities=34% Similarity=0.788 Sum_probs=21.5
Q ss_pred ceeeCCCCCCCCcccceeeeccCCCCCCCccccc
Q 031240 90 VWILCNDCGANSHVQFHVIAHKCLSCKSYNTRQT 123 (163)
Q Consensus 90 ~~i~C~dC~~~~~~~~h~~~~kC~~C~synt~~~ 123 (163)
..+.|..||+.. ..|.+ |.+||-|+.+++
T Consensus 25 ~l~~C~~cG~~~--~~H~v---c~~cG~Y~gr~v 53 (55)
T TIGR01031 25 TLVVCPNCGEFK--LPHRV---CPSCGYYKGRQV 53 (55)
T ss_pred cceECCCCCCcc--cCeeE---CCccCeECCEEc
Confidence 456799998743 34544 999999998875
No 126
>PF14353 CpXC: CpXC protein
Probab=78.91 E-value=0.32 Score=35.44 Aligned_cols=21 Identities=14% Similarity=0.575 Sum_probs=14.3
Q ss_pred cceeeCCCCCCCCcccceeee
Q 031240 89 MVWILCNDCGANSHVQFHVIA 109 (163)
Q Consensus 89 ~~~i~C~dC~~~~~~~~h~~~ 109 (163)
.-.+.|..||.+..+.+-+++
T Consensus 36 l~~~~CP~Cg~~~~~~~p~lY 56 (128)
T PF14353_consen 36 LFSFTCPSCGHKFRLEYPLLY 56 (128)
T ss_pred cCEEECCCCCCceecCCCEEE
Confidence 356779999887766554444
No 127
>KOG0827 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=78.80 E-value=0.19 Score=43.69 Aligned_cols=52 Identities=25% Similarity=0.478 Sum_probs=42.1
Q ss_pred CccccccccccccCcCCccEEecCCChhhHHHHHHHHhcCCCCCCCCCCCccc
Q 031240 12 MHHNCPICFEFIFDTMKDITVLRCGHTIHLECLKEMEKHYRYTCPVCSKSLWD 64 (163)
Q Consensus 12 ~~~~CpIC~e~l~~s~~~~~~L~CGH~fh~~Cl~~~~~~~~~~CPiCr~~~~~ 64 (163)
.-..|.||.+.|.........+.|||..|..+|.+|+.. ...||.|+..+..
T Consensus 195 lv~sl~I~~~slK~~y~k~~~~~~g~~~~~~kL~k~L~~-~~kl~~~~rel~~ 246 (465)
T KOG0827|consen 195 LVGSLSICFESLKQNYDKISAIVCGHIYHHGKLSKWLAT-KRKLPSCRRELPK 246 (465)
T ss_pred HHhhhHhhHHHHHHHHHHHHHHhhcccchhhHHHHHHHH-HHHhHHHHhhhhh
Confidence 345789999887655556677899999999999999985 5789999988743
No 128
>smart00659 RPOLCX RNA polymerase subunit CX. present in RNA polymerase I, II and III
Probab=77.47 E-value=1.8 Score=26.03 Aligned_cols=26 Identities=19% Similarity=0.638 Sum_probs=16.3
Q ss_pred eeeCCCCCCCCcccceeeeccCCCCCC
Q 031240 91 WILCNDCGANSHVQFHVIAHKCLSCKS 117 (163)
Q Consensus 91 ~i~C~dC~~~~~~~~h~~~~kC~~C~s 117 (163)
...|.+||....... .-..+|.+||+
T Consensus 2 ~Y~C~~Cg~~~~~~~-~~~irC~~CG~ 27 (44)
T smart00659 2 IYICGECGRENEIKS-KDVVRCRECGY 27 (44)
T ss_pred EEECCCCCCEeecCC-CCceECCCCCc
Confidence 456888887654431 24567888875
No 129
>KOG1815 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=76.14 E-value=2.1 Score=37.75 Aligned_cols=37 Identities=27% Similarity=0.442 Sum_probs=29.7
Q ss_pred CCccccccccccccCcCCccEEecCCChhhHHHHHHHHhc
Q 031240 11 AMHHNCPICFEFIFDTMKDITVLRCGHTIHLECLKEMEKH 50 (163)
Q Consensus 11 s~~~~CpIC~e~l~~s~~~~~~L~CGH~fh~~Cl~~~~~~ 50 (163)
.....|.||.+.+.. ....+.|||.||..|...++..
T Consensus 68 ~~~~~c~ic~~~~~~---~~~~~~c~H~~c~~cw~~yl~~ 104 (444)
T KOG1815|consen 68 KGDVQCGICVESYDG---EIIGLGCGHPFCPPCWTGYLGT 104 (444)
T ss_pred CccccCCcccCCCcc---hhhhcCCCcHHHHHHHHHHhhh
Confidence 456899999986321 4677899999999999999865
No 130
>KOG3113 consensus Uncharacterized conserved protein [Function unknown]
Probab=75.86 E-value=2.5 Score=34.99 Aligned_cols=48 Identities=21% Similarity=0.387 Sum_probs=38.3
Q ss_pred CccccccccccccCcCCccEEecCCChhhHHHHHHHHhcCCCCCCCCCCCc
Q 031240 12 MHHNCPICFEFIFDTMKDITVLRCGHTIHLECLKEMEKHYRYTCPVCSKSL 62 (163)
Q Consensus 12 ~~~~CpIC~e~l~~s~~~~~~L~CGH~fh~~Cl~~~~~~~~~~CPiCr~~~ 62 (163)
....|||=.=+|....+-....+|||+|=.+-+++... ..|++|...+
T Consensus 110 a~fiCPvtgleMng~~~F~~l~~CGcV~SerAlKeika---s~C~~C~a~y 157 (293)
T KOG3113|consen 110 ARFICPVTGLEMNGKYRFCALRCCGCVFSERALKEIKA---SVCHVCGAAY 157 (293)
T ss_pred ceeecccccceecceEEEEEEeccceeccHHHHHHhhh---ccccccCCcc
Confidence 45689998777655555566679999999999998764 5799999987
No 131
>COG5183 SSM4 Protein involved in mRNA turnover and stability [RNA processing and modification]
Probab=75.73 E-value=2.7 Score=40.10 Aligned_cols=51 Identities=27% Similarity=0.470 Sum_probs=39.7
Q ss_pred CCCccccccccccccCcCCccEEecCCC-----hhhHHHHHHHHhcC-CCCCCCCCCCc
Q 031240 10 RAMHHNCPICFEFIFDTMKDITVLRCGH-----TIHLECLKEMEKHY-RYTCPVCSKSL 62 (163)
Q Consensus 10 ~s~~~~CpIC~e~l~~s~~~~~~L~CGH-----~fh~~Cl~~~~~~~-~~~CPiCr~~~ 62 (163)
|+.+..|-||..+ +...+|..-||.. .+|.+|+.+|++.+ ..+|-+|...+
T Consensus 9 N~d~~~CRICr~e--~~~d~pLfhPCKC~GSIkYiH~eCL~eW~~~s~~~kCdiChy~~ 65 (1175)
T COG5183 9 NEDKRSCRICRTE--DIRDDPLFHPCKCSGSIKYIHRECLMEWMECSGTKKCDICHYEY 65 (1175)
T ss_pred CccchhceeecCC--CCCCCcCcccccccchhHHHHHHHHHHHHhcCCCcceeeeccee
Confidence 4556899999865 4456666668864 69999999999874 56799999886
No 132
>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=71.66 E-value=2.9 Score=25.41 Aligned_cols=32 Identities=22% Similarity=0.416 Sum_probs=19.9
Q ss_pred eeeCCCCCCCCccccee---eeccCCCCCCCcccc
Q 031240 91 WILCNDCGANSHVQFHV---IAHKCLSCKSYNTRQ 122 (163)
Q Consensus 91 ~i~C~dC~~~~~~~~h~---~~~kC~~C~synt~~ 122 (163)
...|.+|+...++...+ ....|+.||+-+.+.
T Consensus 5 ey~C~~Cg~~fe~~~~~~~~~~~~CP~Cg~~~~~r 39 (52)
T TIGR02605 5 EYRCTACGHRFEVLQKMSDDPLATCPECGGEKLRR 39 (52)
T ss_pred EEEeCCCCCEeEEEEecCCCCCCCCCCCCCCceeE
Confidence 56799998766543211 123699999866533
No 133
>PF04710 Pellino: Pellino; InterPro: IPR006800 Pellino is involved in Toll-like signalling pathways, and associates with the kinase domain of the Pelle Ser/Thr kinase [, , ].; PDB: 3EGB_B 3EGA_A.
Probab=71.30 E-value=1.4 Score=38.56 Aligned_cols=49 Identities=27% Similarity=0.602 Sum_probs=0.5
Q ss_pred CCCccccccccccc-c---------CcCCccEEecCCChhhHHHHHHHHhc-----CCCCCCCCCCC
Q 031240 10 RAMHHNCPICFEFI-F---------DTMKDITVLRCGHTIHLECLKEMEKH-----YRYTCPVCSKS 61 (163)
Q Consensus 10 ~s~~~~CpIC~e~l-~---------~s~~~~~~L~CGH~fh~~Cl~~~~~~-----~~~~CPiCr~~ 61 (163)
|++...|||=+..| | +...+-+.|.|||++-.. .|... ...+||+||..
T Consensus 274 Na~rpQCPVglnTL~fp~~~~~~~~~~~qP~VYl~CGHVhG~h---~Wg~~~~~~~~~r~CPlCr~~ 337 (416)
T PF04710_consen 274 NAGRPQCPVGLNTLVFPSKSRKDVPDERQPWVYLNCGHVHGYH---NWGQDSDRDPRSRTCPLCRQV 337 (416)
T ss_dssp S------------------------------------------------------------------
T ss_pred hhcCCCCCcCCCccccccccccccccccCceeeccccceeeec---ccccccccccccccCCCcccc
Confidence 56677888877654 1 122445778999987644 34321 25689999875
No 134
>TIGR00416 sms DNA repair protein RadA. The gene protuct codes for a probable ATP-dependent protease involved in both DNA repair and degradation of proteins, peptides, glycopeptides. Also known as sms. Residues 11-28 of the SEED alignment contain a putative Zn binding domain. Residues 110-117 of the seed contain a putative ATP binding site both documented in Haemophilus and in Listeria monocytogenes. for E.coli see ( J. BACTERIOL. 178:5045-5048(1996)).
Probab=71.14 E-value=3.5 Score=36.57 Aligned_cols=31 Identities=32% Similarity=0.669 Sum_probs=24.9
Q ss_pred cceeeCCCCCCCCcccceeeeccCCCCCCCccccc
Q 031240 89 MVWILCNDCGANSHVQFHVIAHKCLSCKSYNTRQT 123 (163)
Q Consensus 89 ~~~i~C~dC~~~~~~~~h~~~~kC~~C~synt~~~ 123 (163)
+....|..||..+.. |.| +|+.|++.||-.-
T Consensus 5 ~~~y~C~~Cg~~~~~---~~g-~Cp~C~~w~t~~~ 35 (454)
T TIGR00416 5 KSKFVCQHCGADSPK---WQG-KCPACHAWNTITE 35 (454)
T ss_pred CCeEECCcCCCCCcc---ccE-ECcCCCCccccch
Confidence 456789999987754 455 8999999999875
No 135
>PLN02189 cellulose synthase
Probab=70.53 E-value=4 Score=39.81 Aligned_cols=54 Identities=20% Similarity=0.392 Sum_probs=37.6
Q ss_pred cCCCccccccccccccCcCCccEEe---cCCChhhHHHHHHHHhcCCCCCCCCCCCc
Q 031240 9 ERAMHHNCPICFEFIFDTMKDITVL---RCGHTIHLECLKEMEKHYRYTCPVCSKSL 62 (163)
Q Consensus 9 e~s~~~~CpIC~e~l~~s~~~~~~L---~CGH~fh~~Cl~~~~~~~~~~CPiCr~~~ 62 (163)
++.....|.||.+.+-.....-... -||--.|..|++.=.+.++..||.|+..+
T Consensus 30 ~~~~~~~C~iCgd~vg~~~~g~~fvaC~~C~fpvCr~Cyeyer~eg~q~CpqCkt~Y 86 (1040)
T PLN02189 30 RNLDGQVCEICGDEIGLTVDGDLFVACNECGFPVCRPCYEYERREGTQNCPQCKTRY 86 (1040)
T ss_pred ccccCccccccccccCcCCCCCEEEeeccCCCccccchhhhhhhcCCccCcccCCch
Confidence 3344569999999864222222222 57788999999665555778999999887
No 136
>cd01121 Sms Sms (bacterial radA) DNA repair protein. This protein is not related to archael radA any more than is to other RecA-like NTPases. Sms has a role in recombination and recombinational repair and is responsible for the stabilization or processing of branched DNA molecules.
Probab=69.58 E-value=2.9 Score=36.20 Aligned_cols=27 Identities=33% Similarity=0.747 Sum_probs=22.1
Q ss_pred eCCCCCCCCcccceeeeccCCCCCCCccccc
Q 031240 93 LCNDCGANSHVQFHVIAHKCLSCKSYNTRQT 123 (163)
Q Consensus 93 ~C~dC~~~~~~~~h~~~~kC~~C~synt~~~ 123 (163)
.|..||..+.. |+| +|+.|+..||-..
T Consensus 2 ~c~~cg~~~~~---~~g-~cp~c~~w~~~~e 28 (372)
T cd01121 2 VCSECGYVSPK---WLG-KCPECGEWNTLVE 28 (372)
T ss_pred CCCCCCCCCCC---ccE-ECcCCCCceeeee
Confidence 59999987653 666 8999999999775
No 137
>PRK11823 DNA repair protein RadA; Provisional
Probab=69.33 E-value=4.1 Score=36.02 Aligned_cols=31 Identities=29% Similarity=0.674 Sum_probs=24.7
Q ss_pred cceeeCCCCCCCCcccceeeeccCCCCCCCccccc
Q 031240 89 MVWILCNDCGANSHVQFHVIAHKCLSCKSYNTRQT 123 (163)
Q Consensus 89 ~~~i~C~dC~~~~~~~~h~~~~kC~~C~synt~~~ 123 (163)
+....|..||..+.. |.| +|+.|++.||-.-
T Consensus 5 ~~~y~C~~Cg~~~~~---~~g-~Cp~C~~w~t~~e 35 (446)
T PRK11823 5 KTAYVCQECGAESPK---WLG-RCPECGAWNTLVE 35 (446)
T ss_pred CCeEECCcCCCCCcc---cCe-eCcCCCCccceee
Confidence 456789999987654 555 8999999999865
No 138
>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 PLN02436 cellulose synthase A
Probab=67.74 E-value=5 Score=39.34 Aligned_cols=54 Identities=19% Similarity=0.418 Sum_probs=37.7
Q ss_pred cCCCccccccccccccCcCCccEEe---cCCChhhHHHHHHHHhcCCCCCCCCCCCc
Q 031240 9 ERAMHHNCPICFEFIFDTMKDITVL---RCGHTIHLECLKEMEKHYRYTCPVCSKSL 62 (163)
Q Consensus 9 e~s~~~~CpIC~e~l~~s~~~~~~L---~CGH~fh~~Cl~~~~~~~~~~CPiCr~~~ 62 (163)
.......|.||.+++-.....-... -||--.|..|++.=.+.++..||.|+..+
T Consensus 32 ~~~~~~iCqICGD~Vg~t~dGe~FVACn~C~fpvCr~Cyeyer~eg~~~Cpqckt~Y 88 (1094)
T PLN02436 32 QELSGQTCQICGDEIELTVDGEPFVACNECAFPVCRPCYEYERREGNQACPQCKTRY 88 (1094)
T ss_pred cccCCccccccccccCcCCCCCEEEeeccCCCccccchhhhhhhcCCccCcccCCch
Confidence 3334569999999863322222223 57778999999665555778999999887
No 140
>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=67.21 E-value=5.5 Score=21.11 Aligned_cols=19 Identities=32% Similarity=0.728 Sum_probs=11.5
Q ss_pred CCCCCCCCccchhHHHHhHH
Q 031240 54 TCPVCSKSLWDMSKLWSKID 73 (163)
Q Consensus 54 ~CPiCr~~~~~~~~~~~~l~ 73 (163)
.||+|.+.+ ....+.+.+|
T Consensus 3 ~CPiC~~~v-~~~~in~HLD 21 (26)
T smart00734 3 QCPVCFREV-PENLINSHLD 21 (26)
T ss_pred cCCCCcCcc-cHHHHHHHHH
Confidence 599998887 3333333443
No 141
>KOG3053 consensus Uncharacterized conserved protein [Function unknown]
Probab=66.83 E-value=5.4 Score=33.09 Aligned_cols=51 Identities=25% Similarity=0.606 Sum_probs=35.5
Q ss_pred CCCccccccccccccCcCCccE--EecCC-----ChhhHHHHHHHHhcC-------CCCCCCCCCCc
Q 031240 10 RAMHHNCPICFEFIFDTMKDIT--VLRCG-----HTIHLECLKEMEKHY-------RYTCPVCSKSL 62 (163)
Q Consensus 10 ~s~~~~CpIC~e~l~~s~~~~~--~L~CG-----H~fh~~Cl~~~~~~~-------~~~CPiCr~~~ 62 (163)
...+-.|=||++. +++.... +-||. |-.|..|+..|+... ...||.|+..+
T Consensus 17 ~e~eR~CWiCF~T--deDn~~a~WV~PCrCRGt~KWVHqsCL~rWiDEK~~~n~~q~V~C~QCqTEY 81 (293)
T KOG3053|consen 17 QELERCCWICFAT--DEDNRLAAWVHPCRCRGTTKWVHQSCLSRWIDEKQRGNPLQTVSCPQCQTEY 81 (293)
T ss_pred cccceeEEEEecc--CcccchhhhcccccccCccHHHHHHHHHHHHhHHhcCCCCceeechhhcchh
Confidence 3457789999985 3322222 23663 779999999998642 24699999885
No 142
>KOG4362 consensus Transcriptional regulator BRCA1 [Replication, recombination and repair; Transcription]
Probab=66.66 E-value=1.7 Score=40.47 Aligned_cols=47 Identities=26% Similarity=0.670 Sum_probs=36.9
Q ss_pred CccccccccccccCcCCccEEecCCChhhHHHHHHHHhc--CCCCCCCCCCCc
Q 031240 12 MHHNCPICFEFIFDTMKDITVLRCGHTIHLECLKEMEKH--YRYTCPVCSKSL 62 (163)
Q Consensus 12 ~~~~CpIC~e~l~~s~~~~~~L~CGH~fh~~Cl~~~~~~--~~~~CPiCr~~~ 62 (163)
...+||||.+.+++ +..+.|-|.|+..|+...+.. +...||+|+..+
T Consensus 20 k~lEc~ic~~~~~~----p~~~kc~~~~l~~~~n~~f~~~~~~~~~~lc~~~~ 68 (684)
T KOG4362|consen 20 KILECPICLEHVKE----PSLLKCDHIFLKFCLNKLFESKKGPKQCALCKSDI 68 (684)
T ss_pred hhccCCceeEEeec----cchhhhhHHHHhhhhhceeeccCccccchhhhhhh
Confidence 46899999988653 377899999999998875543 346799998665
No 143
>PF01783 Ribosomal_L32p: Ribosomal L32p protein family; InterPro: IPR002677 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. Ribosomal protein L32p is part of the 50S ribosomal subunit. This family is found in both prokaryotes and eukaryotes. Ribosomal protein L32 of yeast binds to and regulates the splicing and the translation of the transcript of its own gene [].; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0015934 large ribosomal subunit; PDB: 3PYT_2 3F1F_5 3PYV_2 3D5B_5 3MRZ_2 3D5D_5 3F1H_5 1VSP_Y 3PYR_2 3MS1_2 ....
Probab=65.33 E-value=5.4 Score=25.07 Aligned_cols=29 Identities=34% Similarity=0.718 Sum_probs=21.4
Q ss_pred ceeeCCCCCCCCcccceeeeccCCCCCCCccccc
Q 031240 90 VWILCNDCGANSHVQFHVIAHKCLSCKSYNTRQT 123 (163)
Q Consensus 90 ~~i~C~dC~~~~~~~~h~~~~kC~~C~synt~~~ 123 (163)
....|..||+.. ..| ..|.+||-|+.+++
T Consensus 25 ~l~~c~~cg~~~--~~H---~vc~~cG~y~~r~v 53 (56)
T PF01783_consen 25 NLVKCPNCGEPK--LPH---RVCPSCGYYKGRQV 53 (56)
T ss_dssp SEEESSSSSSEE--STT---SBCTTTBBSSSSSS
T ss_pred ceeeeccCCCEe--ccc---EeeCCCCeECCEEE
Confidence 457899999643 234 35899999999875
No 144
>COG1996 RPC10 DNA-directed RNA polymerase, subunit RPC10 (contains C4-type Zn-finger) [Transcription]
Probab=65.24 E-value=3.8 Score=25.34 Aligned_cols=29 Identities=24% Similarity=0.535 Sum_probs=18.9
Q ss_pred cceeeCCCCCCCCcccceeeeccCCCCCC
Q 031240 89 MVWILCNDCGANSHVQFHVIAHKCLSCKS 117 (163)
Q Consensus 89 ~~~i~C~dC~~~~~~~~h~~~~kC~~C~s 117 (163)
+....|..|++......-.-+..|..||+
T Consensus 4 ~~~Y~C~~Cg~~~~~~~~~~~irCp~Cg~ 32 (49)
T COG1996 4 MMEYKCARCGREVELDQETRGIRCPYCGS 32 (49)
T ss_pred eEEEEhhhcCCeeehhhccCceeCCCCCc
Confidence 35667888887665333345667888875
No 145
>PF14205 Cys_rich_KTR: Cysteine-rich KTR
Probab=64.57 E-value=6.4 Score=24.88 Aligned_cols=28 Identities=32% Similarity=0.809 Sum_probs=15.0
Q ss_pred ceeeCCCCCCCC------cccceeeeccCCCCCC
Q 031240 90 VWILCNDCGANS------HVQFHVIAHKCLSCKS 117 (163)
Q Consensus 90 ~~i~C~dC~~~~------~~~~h~~~~kC~~C~s 117 (163)
.||+|.-||.+. +....-+-++|+.|..
T Consensus 3 ~Wi~CP~CgnKTR~kir~DT~LkNfPlyCpKCK~ 36 (55)
T PF14205_consen 3 EWILCPICGNKTRLKIREDTVLKNFPLYCPKCKQ 36 (55)
T ss_pred eEEECCCCCCccceeeecCceeccccccCCCCCc
Confidence 456666666433 2333445566666653
No 146
>PF00628 PHD: PHD-finger; InterPro: IPR019787 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents the PHD (homeodomain) zinc finger domain [,], which is a C4HC3 zinc-finger-like motif found in nuclear proteins thought to be involved in chromatin-mediated transcriptional regulation. The PHD finger motif is reminiscent of, but distinct from the C3HC4 type RING finger. The function of this domain is not yet known but in analogy with the LIM domain it could be involved in protein-protein interaction and be important for the assembly or activity of multicomponent complexes involved in transcriptional activation or repression. Alternatively, the interactions could be intra-molecular and be important in maintaining the structural integrity of the protein. In similarity to the RING finger and the LIM domain, the PHD finger is thought to bind two zinc ions. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0005515 protein binding; PDB: 3ZVY_A 2LGG_A 3SOW_A 3SOU_B 3ASL_A 3ASK_A 3ZVZ_B 3T6R_A 2LGK_A 3SOX_B ....
Probab=64.47 E-value=0.57 Score=28.31 Aligned_cols=42 Identities=31% Similarity=0.658 Sum_probs=27.4
Q ss_pred ccccccccccCcCCccEEe--cCCChhhHHHHHHHHhc-----CCCCCCCCC
Q 031240 15 NCPICFEFIFDTMKDITVL--RCGHTIHLECLKEMEKH-----YRYTCPVCS 59 (163)
Q Consensus 15 ~CpIC~e~l~~s~~~~~~L--~CGH~fh~~Cl~~~~~~-----~~~~CPiCr 59 (163)
.|+||... + ....++. .|+-.||..|+..-... ..+.||.|+
T Consensus 1 ~C~vC~~~--~-~~~~~i~C~~C~~~~H~~C~~~~~~~~~~~~~~w~C~~C~ 49 (51)
T PF00628_consen 1 YCPVCGQS--D-DDGDMIQCDSCNRWYHQECVGPPEKAEEIPSGDWYCPNCR 49 (51)
T ss_dssp EBTTTTSS--C-TTSSEEEBSTTSCEEETTTSTSSHSHHSHHSSSBSSHHHH
T ss_pred eCcCCCCc--C-CCCCeEEcCCCChhhCcccCCCChhhccCCCCcEECcCCc
Confidence 37899873 1 2223333 88999999998764331 257788774
No 147
>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=64.23 E-value=0.41 Score=31.84 Aligned_cols=40 Identities=30% Similarity=0.616 Sum_probs=21.7
Q ss_pred ccccccccccccCcCCccEEecCCChhhHHHHHHHHhcCCCCCCCCCCCc
Q 031240 13 HHNCPICFEFIFDTMKDITVLRCGHTIHLECLKEMEKHYRYTCPVCSKSL 62 (163)
Q Consensus 13 ~~~CpIC~e~l~~s~~~~~~L~CGH~fh~~Cl~~~~~~~~~~CPiCr~~~ 62 (163)
+..||.|..+|. ... |+..|..|-..+.. ...||-|..++
T Consensus 1 e~~CP~C~~~L~-------~~~-~~~~C~~C~~~~~~--~a~CPdC~~~L 40 (70)
T PF07191_consen 1 ENTCPKCQQELE-------WQG-GHYHCEACQKDYKK--EAFCPDCGQPL 40 (70)
T ss_dssp --B-SSS-SBEE-------EET-TEEEETTT--EEEE--EEE-TTT-SB-
T ss_pred CCcCCCCCCccE-------EeC-CEEECcccccccee--cccCCCcccHH
Confidence 468999998752 112 88888888777654 25699998775
No 148
>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]
Probab=64.11 E-value=6.3 Score=37.22 Aligned_cols=30 Identities=23% Similarity=0.524 Sum_probs=22.7
Q ss_pred CcceeeCCCCCCCCcccceeeeccCCCCCCCcccc
Q 031240 88 KMVWILCNDCGANSHVQFHVIAHKCLSCKSYNTRQ 122 (163)
Q Consensus 88 ~~~~i~C~dC~~~~~~~~h~~~~kC~~C~synt~~ 122 (163)
......|+.||.....+ ..|++|||-.-+.
T Consensus 459 ~~~~L~CH~Cg~~~~~p-----~~Cp~Cgs~~L~~ 488 (730)
T COG1198 459 ATGQLRCHYCGYQEPIP-----QSCPECGSEHLRA 488 (730)
T ss_pred CCCeeEeCCCCCCCCCC-----CCCCCCCCCeeEE
Confidence 34678899999886554 5899999985444
No 149
>KOG2066 consensus Vacuolar assembly/sorting protein VPS41 [Intracellular trafficking, secretion, and vesicular transport]
Probab=63.99 E-value=3.1 Score=39.32 Aligned_cols=46 Identities=30% Similarity=0.636 Sum_probs=32.6
Q ss_pred CccccccccccccCcC---CccEEecCCChhhHHHHHHHHhcCCCCCCCCC
Q 031240 12 MHHNCPICFEFIFDTM---KDITVLRCGHTIHLECLKEMEKHYRYTCPVCS 59 (163)
Q Consensus 12 ~~~~CpIC~e~l~~s~---~~~~~L~CGH~fh~~Cl~~~~~~~~~~CPiCr 59 (163)
-+..|.-|.+....+. ...+++.|||.||..|+.....+.. |-.|.
T Consensus 783 ~e~rc~~c~~~~l~~~~~~~~~~v~~c~h~yhk~c~~~~~~~~~--~~~~~ 831 (846)
T KOG2066|consen 783 VEERCSSCFEPNLPSGAAFDSVVVFHCGHMYHKECLMMESLRNA--CNIES 831 (846)
T ss_pred ehhhhhhhcccccccCcccceeeEEEccchhhhcccccHHHhcc--cChhh
Confidence 3568999988754333 5568899999999999987655332 55553
No 150
>KOG3899 consensus Uncharacterized conserved protein [Function unknown]
Probab=62.50 E-value=6 Score=33.49 Aligned_cols=28 Identities=25% Similarity=0.536 Sum_probs=21.7
Q ss_pred CCChhhHHHHHHHHhc------------CCCCCCCCCCCc
Q 031240 35 CGHTIHLECLKEMEKH------------YRYTCPVCSKSL 62 (163)
Q Consensus 35 CGH~fh~~Cl~~~~~~------------~~~~CPiCr~~~ 62 (163)
|.-..|.+|+.+|... ++-+||+||+.+
T Consensus 325 crp~wc~~cla~~f~~rq~~v~r~~~~~~~~~cp~cr~~f 364 (381)
T KOG3899|consen 325 CRPLWCRSCLAQIFIGRQDNVYRYEYHRGSAQCPTCRKNF 364 (381)
T ss_pred cccHHHHHHHHHHHhhcccchhHHHHHhcCCCCcchhhce
Confidence 4567899999999742 245799999987
No 151
>KOG1609 consensus Protein involved in mRNA turnover and stability [RNA processing and modification]
Probab=62.23 E-value=5.7 Score=32.59 Aligned_cols=50 Identities=22% Similarity=0.411 Sum_probs=36.4
Q ss_pred ccccccccccccCcCCccEEecCC-----ChhhHHHHHHHHhc-CCCCCCCCCCCc
Q 031240 13 HHNCPICFEFIFDTMKDITVLRCG-----HTIHLECLKEMEKH-YRYTCPVCSKSL 62 (163)
Q Consensus 13 ~~~CpIC~e~l~~s~~~~~~L~CG-----H~fh~~Cl~~~~~~-~~~~CPiCr~~~ 62 (163)
+..|-||.+..+.....+...||. ...|..|++.|... +...|.+|...+
T Consensus 78 ~~~cRIc~~~~~~~~~~~l~~pC~C~g~l~~vH~~cl~~W~~~~~~~~CeiC~~~~ 133 (323)
T KOG1609|consen 78 GPICRICHEEDEESNGLLLISPCSCKGSLAYVHRSCLEKWFSIKGNITCEICKSFF 133 (323)
T ss_pred CCcEEEEecccccccccccccCccccCcHHHHHHHHHHhhhccccCeeeecccccc
Confidence 367999998754332224566774 57899999999864 467899998875
No 152
>PF06906 DUF1272: Protein of unknown function (DUF1272); InterPro: IPR010696 This family consists of several hypothetical bacterial proteins of around 80 residues in length. This family contains a number of conserved cysteine residues and its function is unknown.
Probab=61.46 E-value=16 Score=23.22 Aligned_cols=49 Identities=20% Similarity=0.408 Sum_probs=33.1
Q ss_pred CCccccccccccccCcCCccEEecCCChhhHHHHHHHHhcCCCCCCCCCCCc
Q 031240 11 AMHHNCPICFEFIFDTMKDITVLRCGHTIHLECLKEMEKHYRYTCPVCSKSL 62 (163)
Q Consensus 11 s~~~~CpIC~e~l~~s~~~~~~L~CGH~fh~~Cl~~~~~~~~~~CPiCr~~~ 62 (163)
.+..+|-.|-..|-....+..+-.=-.+||..|.+..+. ..||-|.-.+
T Consensus 3 elrpnCE~C~~dLp~~s~~A~ICSfECTFC~~C~e~~l~---~~CPNCgGel 51 (57)
T PF06906_consen 3 ELRPNCECCDKDLPPDSPEAYICSFECTFCADCAETMLN---GVCPNCGGEL 51 (57)
T ss_pred ccCCCccccCCCCCCCCCcceEEeEeCcccHHHHHHHhc---CcCcCCCCcc
Confidence 356788888877643332332222225999999999875 5799998765
No 153
>KOG3579 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=60.43 E-value=7.8 Score=32.70 Aligned_cols=58 Identities=26% Similarity=0.598 Sum_probs=39.7
Q ss_pred CCccccccccccccCcCCccEEecC----CChhhHHHHHHHHhcC----------CCCCCCCCCCccchhHHHHhHHHHH
Q 031240 11 AMHHNCPICFEFIFDTMKDITVLRC----GHTIHLECLKEMEKHY----------RYTCPVCSKSLWDMSKLWSKIDQEI 76 (163)
Q Consensus 11 s~~~~CpIC~e~l~~s~~~~~~L~C----GH~fh~~Cl~~~~~~~----------~~~CPiCr~~~~~~~~~~~~l~~~~ 76 (163)
+....|.+|.|.|.| .....| .|.||.-|-++.++.. ..+||+=...+ -|.-+..+|
T Consensus 266 ~apLcCTLC~ERLED----THFVQCPSVp~HKFCFPCSResIK~Qg~sgevYCPSGdkCPLvgS~v-----PWAFMQGEI 336 (352)
T KOG3579|consen 266 SAPLCCTLCHERLED----THFVQCPSVPSHKFCFPCSRESIKQQGASGEVYCPSGDKCPLVGSNV-----PWAFMQGEI 336 (352)
T ss_pred CCceeehhhhhhhcc----CceeecCCCcccceecccCHHHHHhhcCCCceeCCCCCcCcccCCcc-----cHHHhhhhH
Confidence 345789999998643 356677 6999999999987652 34677765554 355455555
Q ss_pred h
Q 031240 77 A 77 (163)
Q Consensus 77 ~ 77 (163)
.
T Consensus 337 a 337 (352)
T KOG3579|consen 337 A 337 (352)
T ss_pred H
Confidence 4
No 154
>smart00064 FYVE Protein present in Fab1, YOTB, Vac1, and EEA1. The FYVE zinc finger is named after four proteins where it was first found: Fab1, YOTB/ZK632.12, Vac1, and EEA1. The FYVE finger has been shown to bind two Zn2+ ions. The FYVE finger has eight potential zinc coordinating cysteine positions. The FYVE finger is structurally related to the PLN02638 cellulose synthase A (UDP-forming), catalytic subunit
Probab=57.95 E-value=10 Score=37.35 Aligned_cols=54 Identities=19% Similarity=0.379 Sum_probs=37.2
Q ss_pred cCCCccccccccccccCcCCcc---EEecCCChhhHHHHHHHHhcCCCCCCCCCCCc
Q 031240 9 ERAMHHNCPICFEFIFDTMKDI---TVLRCGHTIHLECLKEMEKHYRYTCPVCSKSL 62 (163)
Q Consensus 9 e~s~~~~CpIC~e~l~~s~~~~---~~L~CGH~fh~~Cl~~~~~~~~~~CPiCr~~~ 62 (163)
++.....|.||.+++--....- +---||=-.|+.|++-=.+.++..||.|+..+
T Consensus 13 ~~~~~qiCqICGD~vg~~~~Ge~FVAC~eC~FPVCrpCYEYEr~eG~q~CPqCktrY 69 (1079)
T PLN02638 13 KHGGGQVCQICGDNVGKTVDGEPFVACDVCAFPVCRPCYEYERKDGNQSCPQCKTKY 69 (1079)
T ss_pred cccCCceeeecccccCcCCCCCEEEEeccCCCccccchhhhhhhcCCccCCccCCch
Confidence 3445569999999853222222 22367778999999654454678899999886
No 156
>PRK00366 ispG 4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase; Reviewed
Probab=57.92 E-value=17 Score=31.53 Aligned_cols=52 Identities=21% Similarity=0.534 Sum_probs=39.3
Q ss_pred CCCCCCCCCccchhHHHHhHHHHHhcCCCChhhhcCcceeeC--CCCCCCCcccceee
Q 031240 53 YTCPVCSKSLWDMSKLWSKIDQEIASTPMPAMYQNKMVWILC--NDCGANSHVQFHVI 108 (163)
Q Consensus 53 ~~CPiCr~~~~~~~~~~~~l~~~~~~~~~p~e~~~~~~~i~C--~dC~~~~~~~~h~~ 108 (163)
..||.|+....|...+...+++.+...++| -+....=| |.|++.....+-++
T Consensus 269 isCPgCgR~~~D~~~la~~vee~~~~~~~P----lkIAVmGC~VNgpGEa~~aDIGIa 322 (360)
T PRK00366 269 ISCPTCGRTEFDVIQELAEVEQRLEHIKMP----LKVAVMGCVVNGPGEAKEADIGIA 322 (360)
T ss_pred EECCCCCCCcccHHHHHHHHHHHhcCCCCC----cEEEEeCCCCCCCCchhhCcEeEe
Confidence 469999999999888888888888777766 33455568 88988877765444
No 157
>KOG4443 consensus Putative transcription factor HALR/MLL3, involved in embryonic development [General function prediction only]
Probab=56.75 E-value=11 Score=34.99 Aligned_cols=48 Identities=23% Similarity=0.533 Sum_probs=32.9
Q ss_pred ccccccccccccCcCCcc---EEecCCChhhHHHHHHHHhc----CCCCCCCCCCCc
Q 031240 13 HHNCPICFEFIFDTMKDI---TVLRCGHTIHLECLKEMEKH----YRYTCPVCSKSL 62 (163)
Q Consensus 13 ~~~CpIC~e~l~~s~~~~---~~L~CGH~fh~~Cl~~~~~~----~~~~CPiCr~~~ 62 (163)
..-|+||--. ...+.- ..-.||-.+|..|...|+.+ +.++||-||+..
T Consensus 18 ~~mc~l~~s~--G~~~ag~m~ac~~c~~~yH~~cvt~~~~~~~l~~gWrC~~crvCe 72 (694)
T KOG4443|consen 18 CLMCPLCGSS--GKGRAGRLLACSDCGQKYHPYCVTSWAQHAVLSGGWRCPSCRVCE 72 (694)
T ss_pred hhhhhhhccc--cccccCcchhhhhhcccCCcchhhHHHhHHHhcCCcccCCceeee
Confidence 4567777532 222222 22388999999999999865 468899998764
No 158
>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=56.75 E-value=11 Score=31.97 Aligned_cols=24 Identities=25% Similarity=0.822 Sum_probs=13.9
Q ss_pred ceeeCCCCCCCCcccceeeeccCCCCCC
Q 031240 90 VWILCNDCGANSHVQFHVIAHKCLSCKS 117 (163)
Q Consensus 90 ~~i~C~dC~~~~~~~~h~~~~kC~~C~s 117 (163)
....|+-|+ ..+|+.-.+|.+||+
T Consensus 209 RyL~CslC~----teW~~~R~~C~~Cg~ 232 (305)
T TIGR01562 209 RYLSCSLCA----TEWHYVRVKCSHCEE 232 (305)
T ss_pred eEEEcCCCC----CcccccCccCCCCCC
Confidence 345566665 345555666666664
No 159
>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=56.57 E-value=6.3 Score=19.07 Aligned_cols=15 Identities=47% Similarity=1.030 Sum_probs=8.8
Q ss_pred CCCCCCCCccchhHH
Q 031240 54 TCPVCSKSLWDMSKL 68 (163)
Q Consensus 54 ~CPiCr~~~~~~~~~ 68 (163)
.||+|.+.+.....+
T Consensus 2 ~C~~C~~~~~~~~~l 16 (24)
T PF13894_consen 2 QCPICGKSFRSKSEL 16 (24)
T ss_dssp E-SSTS-EESSHHHH
T ss_pred CCcCCCCcCCcHHHH
Confidence 588998887665443
No 160
>KOG2907 consensus RNA polymerase I transcription factor TFIIS, subunit A12.2/RPA12 [Transcription]
Probab=56.22 E-value=3.9 Score=29.65 Aligned_cols=22 Identities=50% Similarity=0.812 Sum_probs=17.2
Q ss_pred eeeccCCCCC----CCccccccCCCC
Q 031240 107 VIAHKCLSCK----SYNTRQTRGDTA 128 (163)
Q Consensus 107 ~~~~kC~~C~----synt~~~~~~~~ 128 (163)
.|-+||+.|| +|+|+|+|-.-+
T Consensus 72 ~I~~kCpkCghe~m~Y~T~QlRSADE 97 (116)
T KOG2907|consen 72 VIKHKCPKCGHEEMSYHTLQLRSADE 97 (116)
T ss_pred chhccCcccCCchhhhhhhhcccccC
Confidence 4678899998 899999984443
No 161
>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=55.01 E-value=12 Score=33.68 Aligned_cols=26 Identities=23% Similarity=0.546 Sum_probs=19.7
Q ss_pred cceeeCCCCCCCCcccceeeeccCCCCCCCc
Q 031240 89 MVWILCNDCGANSHVQFHVIAHKCLSCKSYN 119 (163)
Q Consensus 89 ~~~i~C~dC~~~~~~~~h~~~~kC~~C~syn 119 (163)
.....|+.||.+...+ ..|++|||-.
T Consensus 238 ~~~l~Ch~Cg~~~~~~-----~~Cp~C~s~~ 263 (505)
T TIGR00595 238 EGKLRCHYCGYQEPIP-----KTCPQCGSED 263 (505)
T ss_pred CCeEEcCCCcCcCCCC-----CCCCCCCCCe
Confidence 3467899999876543 4899999864
No 162
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=54.75 E-value=7.2 Score=20.50 Aligned_cols=22 Identities=32% Similarity=0.874 Sum_probs=12.0
Q ss_pred eeCCCCCCCCcccceeeeccCCCCCC
Q 031240 92 ILCNDCGANSHVQFHVIAHKCLSCKS 117 (163)
Q Consensus 92 i~C~dC~~~~~~~~h~~~~kC~~C~s 117 (163)
+.|..|+..-... ...|.+||.
T Consensus 3 ~~Cp~Cg~~~~~~----~~fC~~CG~ 24 (26)
T PF13248_consen 3 MFCPNCGAEIDPD----AKFCPNCGA 24 (26)
T ss_pred CCCcccCCcCCcc----cccChhhCC
Confidence 4577777642221 235777764
No 163
>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=54.59 E-value=11 Score=20.43 Aligned_cols=36 Identities=31% Similarity=0.675 Sum_probs=22.6
Q ss_pred cccccccccCcCCccEEecCCChhhHHHHHHHHhcCCCCCCCCCCCc
Q 031240 16 CPICFEFIFDTMKDITVLRCGHTIHLECLKEMEKHYRYTCPVCSKSL 62 (163)
Q Consensus 16 CpIC~e~l~~s~~~~~~L~CGH~fh~~Cl~~~~~~~~~~CPiCr~~~ 62 (163)
|+.|.+.+.+. ...+..=|..||..| ++|..|+.++
T Consensus 2 C~~C~~~i~~~--~~~~~~~~~~~H~~C---------f~C~~C~~~L 37 (39)
T smart00132 2 CAGCGKPIRGG--ELVLRALGKVWHPEC---------FKCSKCGKPL 37 (39)
T ss_pred ccccCCcccCC--cEEEEeCCccccccC---------CCCcccCCcC
Confidence 77787765432 123334477888887 4588887765
No 164
>COG5132 BUD31 Cell cycle control protein, G10 family [Transcription / Cell division and chromosome partitioning]
Probab=53.93 E-value=7 Score=28.79 Aligned_cols=22 Identities=27% Similarity=0.699 Sum_probs=13.9
Q ss_pred hhHHHHHHHHhcCCCCCCCCCCC
Q 031240 39 IHLECLKEMEKHYRYTCPVCSKS 61 (163)
Q Consensus 39 fh~~Cl~~~~~~~~~~CPiCr~~ 61 (163)
-|.+||+.--.....+| +||.+
T Consensus 101 CCLRCIQ~~esk~GstC-ICRVP 122 (146)
T COG5132 101 CCLRCIQPIESKHGSTC-ICRVP 122 (146)
T ss_pred hhHhhcCcccccCCCEE-EEeCc
Confidence 46677776554445667 77765
No 165
>cd02339 ZZ_Mind_bomb Zinc finger, ZZ type. Zinc finger present in Drosophila Mind bomb (D-mib) and related proteins. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding. Mind bomb is an E3 ubiqitin ligase that has been shown to regulate signaling by the Notch ligand Delta in Drosophila melanogaster.
Probab=53.48 E-value=11 Score=22.70 Aligned_cols=28 Identities=29% Similarity=0.788 Sum_probs=17.1
Q ss_pred eeCCCCCCCCcccceeeeccCCCCCCCcccc
Q 031240 92 ILCNDCGANSHVQFHVIAHKCLSCKSYNTRQ 122 (163)
Q Consensus 92 i~C~dC~~~~~~~~h~~~~kC~~C~synt~~ 122 (163)
|.|+.|++....- +-.||..|..|+--+
T Consensus 1 i~Cd~C~~~~i~G---~RykC~~C~dyDLC~ 28 (45)
T cd02339 1 IICDTCRKQGIIG---IRWKCAECPNYDLCT 28 (45)
T ss_pred CCCCCCCCCCccc---CeEECCCCCCccchH
Confidence 5688898654432 334677776666544
No 166
>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=53.31 E-value=9.8 Score=23.71 Aligned_cols=34 Identities=24% Similarity=0.422 Sum_probs=22.1
Q ss_pred eeeCCCCCCCC-c-ccceeeeccCCCCCCCcccccc
Q 031240 91 WILCNDCGANS-H-VQFHVIAHKCLSCKSYNTRQTR 124 (163)
Q Consensus 91 ~i~C~dC~~~~-~-~~~h~~~~kC~~C~synt~~~~ 124 (163)
.|.|..|++.- . ..+-.+-.||+.|+..|.-...
T Consensus 4 eiRC~~CnklLa~~g~~~~leIKCpRC~tiN~~~a~ 39 (51)
T PF10122_consen 4 EIRCGHCNKLLAKAGEVIELEIKCPRCKTINHVRAT 39 (51)
T ss_pred ceeccchhHHHhhhcCccEEEEECCCCCccceEecc
Confidence 56788887521 1 1222477799999999876654
No 167
>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=53.22 E-value=10 Score=22.27 Aligned_cols=29 Identities=24% Similarity=0.400 Sum_probs=15.4
Q ss_pred eeeCCCCCCCCcccce---eeeccCCCCCCCc
Q 031240 91 WILCNDCGANSHVQFH---VIAHKCLSCKSYN 119 (163)
Q Consensus 91 ~i~C~dC~~~~~~~~h---~~~~kC~~C~syn 119 (163)
...|.+||...++... .....|+.||+-+
T Consensus 5 ey~C~~Cg~~fe~~~~~~~~~~~~CP~Cg~~~ 36 (42)
T PF09723_consen 5 EYRCEECGHEFEVLQSISEDDPVPCPECGSTE 36 (42)
T ss_pred EEEeCCCCCEEEEEEEcCCCCCCcCCCCCCCc
Confidence 4567777754432211 1234677887733
No 168
>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=52.12 E-value=10 Score=20.16 Aligned_cols=7 Identities=29% Similarity=0.795 Sum_probs=3.7
Q ss_pred ccCCCCC
Q 031240 110 HKCLSCK 116 (163)
Q Consensus 110 ~kC~~C~ 116 (163)
.+|.+||
T Consensus 15 ~~Cp~CG 21 (26)
T PF10571_consen 15 KFCPHCG 21 (26)
T ss_pred CcCCCCC
Confidence 3555555
No 169
>KOG4718 consensus Non-SMC (structural maintenance of chromosomes) element 1 protein (NSE1) [Chromatin structure and dynamics]
Probab=52.06 E-value=8.4 Score=31.10 Aligned_cols=43 Identities=26% Similarity=0.703 Sum_probs=32.1
Q ss_pred cccccccccccCcCCccEEecCCChhhHHHHHHHHhcCCCCCCCCCC
Q 031240 14 HNCPICFEFIFDTMKDITVLRCGHTIHLECLKEMEKHYRYTCPVCSK 60 (163)
Q Consensus 14 ~~CpIC~e~l~~s~~~~~~L~CGH~fh~~Cl~~~~~~~~~~CPiCr~ 60 (163)
.+|.+|-..+. ....--.||=.+|..|+..++.. ...||.|.-
T Consensus 182 k~Cn~Ch~LvI---qg~rCg~c~i~~h~~c~qty~q~-~~~cphc~d 224 (235)
T KOG4718|consen 182 KNCNLCHCLVI---QGIRCGSCNIQYHRGCIQTYLQR-RDICPHCGD 224 (235)
T ss_pred HHHhHhHHHhh---eeeccCcccchhhhHHHHHHhcc-cCcCCchhc
Confidence 57999987642 22333467778999999999985 688999953
No 170
>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=51.53 E-value=12 Score=22.94 Aligned_cols=11 Identities=36% Similarity=1.117 Sum_probs=6.1
Q ss_pred CCCCCCCCccc
Q 031240 54 TCPVCSKSLWD 64 (163)
Q Consensus 54 ~CPiCr~~~~~ 64 (163)
.||+|..++..
T Consensus 22 ~CPlC~r~l~~ 32 (54)
T PF04423_consen 22 CCPLCGRPLDE 32 (54)
T ss_dssp E-TTT--EE-H
T ss_pred cCCCCCCCCCH
Confidence 89999999864
No 171
>cd02345 ZZ_dah Zinc finger, ZZ type. Zinc finger present in Drosophila dah and related proteins. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding. Dah (discontinuous actin hexagon) is a membrane associated protein essential for cortical furrow formation in Drosophila.
Probab=50.23 E-value=15 Score=22.41 Aligned_cols=28 Identities=21% Similarity=0.593 Sum_probs=17.4
Q ss_pred eeCCCCCCCCcccceeeeccCCCCCCCcccc
Q 031240 92 ILCNDCGANSHVQFHVIAHKCLSCKSYNTRQ 122 (163)
Q Consensus 92 i~C~dC~~~~~~~~h~~~~kC~~C~synt~~ 122 (163)
|.|+.|.+....- +-.+|..|..|+--.
T Consensus 1 ~~C~~C~~~~i~g---~R~~C~~C~dydLC~ 28 (49)
T cd02345 1 LSCSACRKQDISG---IRFPCQVCRDYSLCL 28 (49)
T ss_pred CcCCCCCCCCceE---eeEECCCCCCcCchH
Confidence 4688887754333 334677777776554
No 172
>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=50.22 E-value=26 Score=21.92 Aligned_cols=32 Identities=22% Similarity=0.575 Sum_probs=20.5
Q ss_pred CcceeeCCCCCCCC----cccceeeeccCCCCCCCc
Q 031240 88 KMVWILCNDCGANS----HVQFHVIAHKCLSCKSYN 119 (163)
Q Consensus 88 ~~~~i~C~dC~~~~----~~~~h~~~~kC~~C~syn 119 (163)
.+..++|..|.... ...+.-+-.+|..||..|
T Consensus 19 ~r~aLIC~~C~~hNGla~~~~~~~i~y~C~~Cg~~N 54 (54)
T PF10058_consen 19 NRYALICSKCFSHNGLAPKEEFEEIQYRCPYCGALN 54 (54)
T ss_pred CceeEECcccchhhcccccccCCceEEEcCCCCCcC
Confidence 44567799997532 122334566899998876
No 173
>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=48.96 E-value=4.1 Score=26.11 Aligned_cols=38 Identities=18% Similarity=0.322 Sum_probs=17.6
Q ss_pred cCCCccccccccccccCcCCccEEecCCChhhHHHHHH
Q 031240 9 ERAMHHNCPICFEFIFDTMKDITVLRCGHTIHLECLKE 46 (163)
Q Consensus 9 e~s~~~~CpIC~e~l~~s~~~~~~L~CGH~fh~~Cl~~ 46 (163)
+++....|.+|...+.-..+.-.--.||+.||..|...
T Consensus 5 ~d~~~~~C~~C~~~F~~~~rrhhCr~CG~~vC~~Cs~~ 42 (69)
T PF01363_consen 5 PDSEASNCMICGKKFSLFRRRHHCRNCGRVVCSSCSSQ 42 (69)
T ss_dssp SGGG-SB-TTT--B-BSSS-EEE-TTT--EEECCCS-E
T ss_pred CCCCCCcCcCcCCcCCCceeeEccCCCCCEECCchhCC
Confidence 44566899999987421122222338999999888654
No 174
>cd00065 FYVE FYVE domain; Zinc-binding domain; targets proteins to membrane lipids via interaction with phosphatidylinositol-3-phosphate, PI3P; present in Fab1, YOTB, Vac1, and EEA1;
Probab=48.59 E-value=11 Score=23.05 Aligned_cols=34 Identities=18% Similarity=0.278 Sum_probs=22.7
Q ss_pred cccccccccccCcCCccEEecCCChhhHHHHHHH
Q 031240 14 HNCPICFEFIFDTMKDITVLRCGHTIHLECLKEM 47 (163)
Q Consensus 14 ~~CpIC~e~l~~s~~~~~~L~CGH~fh~~Cl~~~ 47 (163)
..|.+|...|....+...--.||+.||..|....
T Consensus 3 ~~C~~C~~~F~~~~rk~~Cr~Cg~~~C~~C~~~~ 36 (57)
T cd00065 3 SSCMGCGKPFTLTRRRHHCRNCGRIFCSKCSSNR 36 (57)
T ss_pred CcCcccCccccCCccccccCcCcCCcChHHcCCe
Confidence 5688887654322334444589999999887654
No 175
>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=48.17 E-value=8 Score=19.04 Aligned_cols=14 Identities=50% Similarity=1.127 Sum_probs=9.7
Q ss_pred CCCCCCCCCccchh
Q 031240 53 YTCPVCSKSLWDMS 66 (163)
Q Consensus 53 ~~CPiCr~~~~~~~ 66 (163)
+.||.|.+.+....
T Consensus 1 y~C~~C~~~f~~~~ 14 (23)
T PF00096_consen 1 YKCPICGKSFSSKS 14 (23)
T ss_dssp EEETTTTEEESSHH
T ss_pred CCCCCCCCccCCHH
Confidence 35888888876543
No 176
>PRK05580 primosome assembly protein PriA; Validated
Probab=48.13 E-value=17 Score=33.85 Aligned_cols=25 Identities=24% Similarity=0.683 Sum_probs=19.2
Q ss_pred ceeeCCCCCCCCcccceeeeccCCCCCCCc
Q 031240 90 VWILCNDCGANSHVQFHVIAHKCLSCKSYN 119 (163)
Q Consensus 90 ~~i~C~dC~~~~~~~~h~~~~kC~~C~syn 119 (163)
....|+.||.+...+ ..|++|||..
T Consensus 407 ~~l~Ch~Cg~~~~~~-----~~Cp~Cg~~~ 431 (679)
T PRK05580 407 RRLRCHHCGYQEPIP-----KACPECGSTD 431 (679)
T ss_pred CeEECCCCcCCCCCC-----CCCCCCcCCe
Confidence 567899999876544 4799999864
No 177
>PLN02400 cellulose synthase
Probab=47.20 E-value=13 Score=36.72 Aligned_cols=53 Identities=19% Similarity=0.355 Sum_probs=36.5
Q ss_pred CCCccccccccccccCcCCc---cEEecCCChhhHHHHHHHHhcCCCCCCCCCCCc
Q 031240 10 RAMHHNCPICFEFIFDTMKD---ITVLRCGHTIHLECLKEMEKHYRYTCPVCSKSL 62 (163)
Q Consensus 10 ~s~~~~CpIC~e~l~~s~~~---~~~L~CGH~fh~~Cl~~~~~~~~~~CPiCr~~~ 62 (163)
+.....|.||.|++-..... +..--||=-.|+.|++-=.+.++..||.|+..+
T Consensus 33 ~~~gqiCqICGD~VG~t~dGe~FVAC~eCaFPVCRpCYEYERkeGnq~CPQCkTrY 88 (1085)
T PLN02400 33 NLNGQICQICGDDVGVTETGDVFVACNECAFPVCRPCYEYERKDGTQCCPQCKTRY 88 (1085)
T ss_pred ccCCceeeecccccCcCCCCCEEEEEccCCCccccchhheecccCCccCcccCCcc
Confidence 33456999999986322222 233377788999999643444678899999887
No 178
>COG1656 Uncharacterized conserved protein [Function unknown]
Probab=46.73 E-value=17 Score=28.16 Aligned_cols=42 Identities=29% Similarity=0.593 Sum_probs=24.5
Q ss_pred CCCCCCCCCCccchhHHHHhHHHHHhcCCCC-hhhhcCcceeeCCCCCCC
Q 031240 52 RYTCPVCSKSLWDMSKLWSKIDQEIASTPMP-AMYQNKMVWILCNDCGAN 100 (163)
Q Consensus 52 ~~~CPiCr~~~~~~~~~~~~l~~~~~~~~~p-~e~~~~~~~i~C~dC~~~ 100 (163)
..+||.|+..+..++. +.....+| ..|.+......|..|++.
T Consensus 97 ~~RCp~CN~~L~~vs~-------eev~~~Vp~~~~~~~~~f~~C~~Cgki 139 (165)
T COG1656 97 FSRCPECNGELEKVSR-------EEVKEKVPEKVYRNYEEFYRCPKCGKI 139 (165)
T ss_pred cccCcccCCEeccCcH-------HHHhhccchhhhhcccceeECCCCccc
Confidence 4679999988754322 22222233 345555556678888763
No 179
>PF12773 DZR: Double zinc ribbon
Probab=45.92 E-value=18 Score=21.53 Aligned_cols=11 Identities=36% Similarity=0.921 Sum_probs=6.8
Q ss_pred ceeeCCCCCCC
Q 031240 90 VWILCNDCGAN 100 (163)
Q Consensus 90 ~~i~C~dC~~~ 100 (163)
..+.|..|++.
T Consensus 28 ~~~~C~~Cg~~ 38 (50)
T PF12773_consen 28 SKKICPNCGAE 38 (50)
T ss_pred CCCCCcCCcCC
Confidence 34567777765
No 180
>KOG1812 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=45.62 E-value=13 Score=32.41 Aligned_cols=44 Identities=27% Similarity=0.533 Sum_probs=27.5
Q ss_pred ccccccccccc-CcCCccEEecCCChhhHHHHHHHHhcCCCCCCCC
Q 031240 14 HNCPICFEFIF-DTMKDITVLRCGHTIHLECLKEMEKHYRYTCPVC 58 (163)
Q Consensus 14 ~~CpIC~e~l~-~s~~~~~~L~CGH~fh~~Cl~~~~~~~~~~CPiC 58 (163)
..||.|.-.+. ...-..++=.|||-||..|...|...+ ..|..|
T Consensus 307 r~CpkC~~~ie~~~GCnhm~CrC~~~fcy~C~~~~~~~~-~~~~~~ 351 (384)
T KOG1812|consen 307 RQCPKCKFMIELSEGCNHMTCRCGHQFCYMCGGDWKTHN-GECYEC 351 (384)
T ss_pred CcCcccceeeeecCCcceEEeeccccchhhcCcchhhCC-ccccCc
Confidence 47888875421 111233444799999999999997743 334433
No 181
>PRK01110 rpmF 50S ribosomal protein L32; Validated
Probab=45.59 E-value=18 Score=23.17 Aligned_cols=29 Identities=14% Similarity=0.066 Sum_probs=21.2
Q ss_pred eeeCCCCCCCCcccceeeeccCCCCCCCccccccC
Q 031240 91 WILCNDCGANSHVQFHVIAHKCLSCKSYNTRQTRG 125 (163)
Q Consensus 91 ~i~C~dC~~~~~~~~h~~~~kC~~C~synt~~~~~ 125 (163)
.+.|..|++.. ..|-+ |. ||-|+.+++-.
T Consensus 27 ~~~c~~cg~~~--~pH~v---c~-cG~Y~gr~v~~ 55 (60)
T PRK01110 27 LSVDKTTGEYH--LPHHV---SP-KGYYKGRKVLK 55 (60)
T ss_pred eeEcCCCCcee--cccee---cC-CcccCCeEeec
Confidence 56799998753 33444 88 99999998743
No 182
>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=45.27 E-value=19 Score=20.33 Aligned_cols=27 Identities=26% Similarity=0.469 Sum_probs=13.1
Q ss_pred eeeCCCCCCCCcccce---eeeccCCCCCC
Q 031240 91 WILCNDCGANSHVQFH---VIAHKCLSCKS 117 (163)
Q Consensus 91 ~i~C~dC~~~~~~~~h---~~~~kC~~C~s 117 (163)
...|.+|+....+... ..-..|..||+
T Consensus 5 ~y~C~~Cg~~fe~~~~~~~~~~~~CP~Cg~ 34 (41)
T smart00834 5 EYRCEDCGHTFEVLQKISDDPLATCPECGG 34 (41)
T ss_pred EEEcCCCCCEEEEEEecCCCCCCCCCCCCC
Confidence 3456666654432211 11245777776
No 183
>PLN02195 cellulose synthase A
Probab=44.58 E-value=27 Score=34.13 Aligned_cols=53 Identities=19% Similarity=0.258 Sum_probs=37.1
Q ss_pred CCccccccccccccCcCCc---cEEecCCChhhHHHHHHHHhcCCCCCCCCCCCcc
Q 031240 11 AMHHNCPICFEFIFDTMKD---ITVLRCGHTIHLECLKEMEKHYRYTCPVCSKSLW 63 (163)
Q Consensus 11 s~~~~CpIC~e~l~~s~~~---~~~L~CGH~fh~~Cl~~~~~~~~~~CPiCr~~~~ 63 (163)
+....|.||.+.+-..... +.---||--.|+.|++-=.+.++..||.|+..+.
T Consensus 4 ~~~~~c~~cgd~~~~~~~g~~fvaC~eC~~pvCrpCyeyer~eg~q~CpqCkt~Yk 59 (977)
T PLN02195 4 SGAPICATCGEEVGVDSNGEAFVACHECSYPLCKACLEYEIKEGRKVCLRCGGPYD 59 (977)
T ss_pred CCCccceecccccCcCCCCCeEEEeccCCCccccchhhhhhhcCCccCCccCCccc
Confidence 4456899999975322222 2233788889999996545556788999998874
No 184
>PF09986 DUF2225: Uncharacterized protein conserved in bacteria (DUF2225); InterPro: IPR018708 This conserved bacterial family has no known function.
Probab=44.55 E-value=4.8 Score=32.10 Aligned_cols=12 Identities=50% Similarity=1.132 Sum_probs=9.8
Q ss_pred CCCCCCCCCCcc
Q 031240 52 RYTCPVCSKSLW 63 (163)
Q Consensus 52 ~~~CPiCr~~~~ 63 (163)
..+||+|++.+.
T Consensus 5 ~~~CPvC~~~F~ 16 (214)
T PF09986_consen 5 KITCPVCGKEFK 16 (214)
T ss_pred ceECCCCCCeee
Confidence 478999999873
No 185
>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=44.30 E-value=13 Score=20.96 Aligned_cols=12 Identities=25% Similarity=0.509 Sum_probs=8.5
Q ss_pred ceeeCCCCCCCC
Q 031240 90 VWILCNDCGANS 101 (163)
Q Consensus 90 ~~i~C~dC~~~~ 101 (163)
..+.|..|+...
T Consensus 24 ~~v~C~~C~~~~ 35 (38)
T TIGR02098 24 GKVRCGKCGHVW 35 (38)
T ss_pred CEEECCCCCCEE
Confidence 467888887643
No 186
>KOG1873 consensus Ubiquitin-specific protease [Posttranslational modification, protein turnover, chaperones]
Probab=44.22 E-value=10 Score=35.99 Aligned_cols=63 Identities=19% Similarity=0.284 Sum_probs=39.1
Q ss_pred ceeeCCCCCCCCc------------ccceeeeccCCC--CCC-CccccccCCCCC---CCccccccccccceeccccccc
Q 031240 90 VWILCNDCGANSH------------VQFHVIAHKCLS--CKS-YNTRQTRGDTAT---TCSSGDELTILSHHWDYQQHAS 151 (163)
Q Consensus 90 ~~i~C~dC~~~~~------------~~~h~~~~kC~~--C~s-ynt~~~~~~~~~---~~~~~~~~~~~~~~~~~~~~~~ 151 (163)
.|+.|.+|.+... ..--|++++|+. ||. --..|...|+.. +.|.-++-+++...|=|..+.+
T Consensus 65 ~~~~C~eC~e~~~~k~g~s~~~~~~~~~iWLCLkCG~q~CG~~~~~~halkH~~~~r~~~Hclvin~~n~~~WCy~Cd~k 144 (877)
T KOG1873|consen 65 LWIKCSECNEEVKVKDGGSSDQFEFDNAIWLCLKCGYQGCGRNSESQHALKHFLTPRSEPHCLVINLINWLIWCYSCDAK 144 (877)
T ss_pred HHHHHHHhhhcceeccCCCccccccccceeeecccCCeeeCCCcccchhhhhhcccCCCCeeEEEEeeeeeeEEEeccch
Confidence 4667777764221 223499999987 886 445555566652 2333344445666699999885
Q ss_pred c
Q 031240 152 V 152 (163)
Q Consensus 152 ~ 152 (163)
+
T Consensus 145 l 145 (877)
T KOG1873|consen 145 L 145 (877)
T ss_pred h
Confidence 4
No 187
>PRK14892 putative transcription elongation factor Elf1; Provisional
Probab=43.88 E-value=30 Score=24.45 Aligned_cols=35 Identities=20% Similarity=0.427 Sum_probs=21.3
Q ss_pred ceeeCCCCCCCCcc-cc--eeeeccCCCCCCCcccccc
Q 031240 90 VWILCNDCGANSHV-QF--HVIAHKCLSCKSYNTRQTR 124 (163)
Q Consensus 90 ~~i~C~dC~~~~~~-~~--h~~~~kC~~C~synt~~~~ 124 (163)
....|..|++.+.. ++ ...-..|..||-|+.+++.
T Consensus 20 t~f~CP~Cge~~v~v~~~k~~~h~~C~~CG~y~~~~V~ 57 (99)
T PRK14892 20 KIFECPRCGKVSISVKIKKNIAIITCGNCGLYTEFEVP 57 (99)
T ss_pred cEeECCCCCCeEeeeecCCCcceEECCCCCCccCEECC
Confidence 45678899853220 00 0112359999999888864
No 188
>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=43.82 E-value=13 Score=20.78 Aligned_cols=23 Identities=26% Similarity=0.742 Sum_probs=11.0
Q ss_pred eCCCCCCCCcccceeeeccCCCCC
Q 031240 93 LCNDCGANSHVQFHVIAHKCLSCK 116 (163)
Q Consensus 93 ~C~dC~~~~~~~~h~~~~kC~~C~ 116 (163)
.|.+|+....... --..+|.+||
T Consensus 2 ~C~~Cg~~~~~~~-~~~irC~~CG 24 (32)
T PF03604_consen 2 ICGECGAEVELKP-GDPIRCPECG 24 (32)
T ss_dssp BESSSSSSE-BST-SSTSSBSSSS
T ss_pred CCCcCCCeeEcCC-CCcEECCcCC
Confidence 4666665543222 1223666666
No 189
>PLN02915 cellulose synthase A [UDP-forming], catalytic subunit
Probab=43.58 E-value=22 Score=35.01 Aligned_cols=51 Identities=16% Similarity=0.359 Sum_probs=36.2
Q ss_pred CccccccccccccCcCCcc---EEecCCChhhHHHHHHHHhcCCCCCCCCCCCc
Q 031240 12 MHHNCPICFEFIFDTMKDI---TVLRCGHTIHLECLKEMEKHYRYTCPVCSKSL 62 (163)
Q Consensus 12 ~~~~CpIC~e~l~~s~~~~---~~L~CGH~fh~~Cl~~~~~~~~~~CPiCr~~~ 62 (163)
....|.||.|.+-.....- .---||--.|+.|++-=.+.++..||.|+..+
T Consensus 14 ~~~~c~iCGd~vg~~~~Ge~FVAC~eC~fpvCr~cyeye~~~g~~~cp~c~t~y 67 (1044)
T PLN02915 14 DAKTCRVCGDEVGVKEDGQPFVACHVCGFPVCKPCYEYERSEGNQCCPQCNTRY 67 (1044)
T ss_pred CcchhhccccccCcCCCCCEEEEeccCCCccccchhhhhhhcCCccCCccCCch
Confidence 4678999999863322222 22367778999999654555678899999886
No 190
>PRK03564 formate dehydrogenase accessory protein FdhE; Provisional
Probab=43.28 E-value=29 Score=29.47 Aligned_cols=24 Identities=33% Similarity=0.910 Sum_probs=14.9
Q ss_pred ceeeCCCCCCCCcccceeeeccCCCCCC
Q 031240 90 VWILCNDCGANSHVQFHVIAHKCLSCKS 117 (163)
Q Consensus 90 ~~i~C~dC~~~~~~~~h~~~~kC~~C~s 117 (163)
....|.-|+ ..+|+.-.+|.+||+
T Consensus 211 RyL~CslC~----teW~~~R~~C~~Cg~ 234 (309)
T PRK03564 211 RYLHCNLCE----SEWHVVRVKCSNCEQ 234 (309)
T ss_pred eEEEcCCCC----CcccccCccCCCCCC
Confidence 455677775 345566667777774
No 191
>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=42.52 E-value=14 Score=23.37 Aligned_cols=27 Identities=30% Similarity=0.842 Sum_probs=19.4
Q ss_pred cCcceeeCCCCCCCCcccceeeeccCCCCC
Q 031240 87 NKMVWILCNDCGANSHVQFHVIAHKCLSCK 116 (163)
Q Consensus 87 ~~~~~i~C~dC~~~~~~~~h~~~~kC~~C~ 116 (163)
+.+..++|.-||.. .||+--..|..||
T Consensus 11 ~~ktH~~CrRCG~~---syH~qK~~CasCG 37 (55)
T PF01907_consen 11 HNKTHTLCRRCGRR---SYHIQKKTCASCG 37 (55)
T ss_dssp -S-SEEE-TTTSSE---EEETTTTEETTTB
T ss_pred CCccEeeecccCCe---eeecCCCcccccC
Confidence 34578999999984 5677777899998
No 192
>PF14952 zf-tcix: Putative treble-clef, zinc-finger, Zn-binding
Probab=42.33 E-value=13 Score=22.48 Aligned_cols=14 Identities=36% Similarity=0.850 Sum_probs=11.1
Q ss_pred ccCCCCCCCccccc
Q 031240 110 HKCLSCKSYNTRQT 123 (163)
Q Consensus 110 ~kC~~C~synt~~~ 123 (163)
.||+.||-||....
T Consensus 12 rkCp~CGt~NG~R~ 25 (44)
T PF14952_consen 12 RKCPKCGTYNGTRG 25 (44)
T ss_pred ccCCcCcCccCccc
Confidence 48999999996553
No 193
>PF13240 zinc_ribbon_2: zinc-ribbon domain
Probab=42.31 E-value=15 Score=18.86 Aligned_cols=19 Identities=37% Similarity=0.894 Sum_probs=9.2
Q ss_pred CCCCCCCCcccceeeeccCCCCC
Q 031240 94 CNDCGANSHVQFHVIAHKCLSCK 116 (163)
Q Consensus 94 C~dC~~~~~~~~h~~~~kC~~C~ 116 (163)
|..||++-... ...|.+||
T Consensus 2 Cp~CG~~~~~~----~~fC~~CG 20 (23)
T PF13240_consen 2 CPNCGAEIEDD----AKFCPNCG 20 (23)
T ss_pred CcccCCCCCCc----CcchhhhC
Confidence 56666543221 12366665
No 194
>PF08792 A2L_zn_ribbon: A2L zinc ribbon domain; InterPro: IPR014900 This zinc ribbon protein is found associated with some viral A2L transcription factors [].
Probab=42.30 E-value=21 Score=20.07 Aligned_cols=27 Identities=30% Similarity=0.540 Sum_probs=13.5
Q ss_pred eeeCCCCCCCCcccceeeeccCCCCCC
Q 031240 91 WILCNDCGANSHVQFHVIAHKCLSCKS 117 (163)
Q Consensus 91 ~i~C~dC~~~~~~~~h~~~~kC~~C~s 117 (163)
.+.|..|+....+.----+..|.+||+
T Consensus 3 ~~~C~~C~~~~i~~~~~~~~~C~~Cg~ 29 (33)
T PF08792_consen 3 LKKCSKCGGNGIVNKEDDYEVCIFCGS 29 (33)
T ss_pred ceEcCCCCCCeEEEecCCeEEcccCCc
Confidence 345777765433211113456777763
No 195
>COG0333 RpmF Ribosomal protein L32 [Translation, ribosomal structure and biogenesis]
Probab=42.06 E-value=18 Score=22.99 Aligned_cols=28 Identities=32% Similarity=0.776 Sum_probs=20.5
Q ss_pred eeeCCCCCCCCcccceeeeccCCCCCCCccccc
Q 031240 91 WILCNDCGANSHVQFHVIAHKCLSCKSYNTRQT 123 (163)
Q Consensus 91 ~i~C~dC~~~~~~~~h~~~~kC~~C~synt~~~ 123 (163)
...|..||+.. .-...|..||.|+.+++
T Consensus 27 ~~~c~~cG~~~-----l~Hrvc~~cg~Y~g~~v 54 (57)
T COG0333 27 LSVCPNCGEYK-----LPHRVCLKCGYYKGRQV 54 (57)
T ss_pred ceeccCCCCcc-----cCceEcCCCCCccCeEe
Confidence 46699998643 23456999999998875
No 196
>KOG1829 consensus Uncharacterized conserved protein, contains C1, PH and RUN domains [Signal transduction mechanisms]
Probab=41.41 E-value=11 Score=34.63 Aligned_cols=43 Identities=28% Similarity=0.620 Sum_probs=26.0
Q ss_pred cccccccccc--c--cCcCCccEEecCCChhhHHHHHHHHhcCCCCCCCCC
Q 031240 13 HHNCPICFEF--I--FDTMKDITVLRCGHTIHLECLKEMEKHYRYTCPVCS 59 (163)
Q Consensus 13 ~~~CpIC~e~--l--~~s~~~~~~L~CGH~fh~~Cl~~~~~~~~~~CPiCr 59 (163)
-..|.+|... + |....-..-..||+.||..|+.. .+..||.|-
T Consensus 511 gfiCe~Cq~~~iiyPF~~~~~~rC~~C~avfH~~C~~r----~s~~CPrC~ 557 (580)
T KOG1829|consen 511 GFICELCQHNDIIYPFETRNTRRCSTCLAVFHKKCLRR----KSPCCPRCE 557 (580)
T ss_pred eeeeeeccCCCcccccccccceeHHHHHHHHHHHHHhc----cCCCCCchH
Confidence 3567788432 1 11111123458999999999765 334599993
No 197
>smart00647 IBR In Between Ring fingers. the domains occurs between pairs og RING fingers
Probab=41.18 E-value=7.3 Score=24.09 Aligned_cols=15 Identities=20% Similarity=0.687 Sum_probs=13.1
Q ss_pred cCCChhhHHHHHHHH
Q 031240 34 RCGHTIHLECLKEME 48 (163)
Q Consensus 34 ~CGH~fh~~Cl~~~~ 48 (163)
.||+.||..|..+|-
T Consensus 45 ~C~~~fC~~C~~~~H 59 (64)
T smart00647 45 KCGFSFCFRCKVPWH 59 (64)
T ss_pred CCCCeECCCCCCcCC
Confidence 789999999988873
No 198
>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=41.08 E-value=34 Score=20.84 Aligned_cols=10 Identities=50% Similarity=1.361 Sum_probs=7.7
Q ss_pred CCCCCCCCCC
Q 031240 52 RYTCPVCSKS 61 (163)
Q Consensus 52 ~~~CPiCr~~ 61 (163)
.++||.|.+.
T Consensus 2 ~f~CP~C~~~ 11 (54)
T PF05605_consen 2 SFTCPYCGKG 11 (54)
T ss_pred CcCCCCCCCc
Confidence 4789999884
No 199
>KOG3842 consensus Adaptor protein Pellino [Signal transduction mechanisms]
Probab=40.29 E-value=28 Score=29.95 Aligned_cols=56 Identities=23% Similarity=0.490 Sum_probs=33.5
Q ss_pred eecCCC--ccccccccccc--------------cCcC-CccEEecCCChhhHHHHHHHHhc--------CCCCCCCCCCC
Q 031240 7 CVERAM--HHNCPICFEFI--------------FDTM-KDITVLRCGHTIHLECLKEMEKH--------YRYTCPVCSKS 61 (163)
Q Consensus 7 c~e~s~--~~~CpIC~e~l--------------~~s~-~~~~~L~CGH~fh~~Cl~~~~~~--------~~~~CPiCr~~ 61 (163)
+.|+.. +..||+|+..= .|.. -.-..-||||.-=..=..-|... .+..||.|-..
T Consensus 333 ~~e~~g~~~r~CPmC~~~gp~V~L~lG~E~~f~vD~G~pthaF~PCGHv~sekt~~YWs~iplPhGT~~f~a~CPFC~~~ 412 (429)
T KOG3842|consen 333 VRENTGQRERECPMCRVVGPYVPLWLGCEAGFYVDAGPPTHAFNPCGHVCSEKTVKYWSQIPLPHGTHAFHAACPFCATQ 412 (429)
T ss_pred cccccCcccCcCCeeeeecceeeeeccccceeEecCCCcccccCCcccccchhhhhHhhcCcCCCccccccccCcchhhh
Confidence 455554 78999998640 0110 11134599998777766667542 13569999655
Q ss_pred c
Q 031240 62 L 62 (163)
Q Consensus 62 ~ 62 (163)
+
T Consensus 413 L 413 (429)
T KOG3842|consen 413 L 413 (429)
T ss_pred h
Confidence 4
No 200
>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=39.73 E-value=25 Score=18.46 Aligned_cols=6 Identities=33% Similarity=1.104 Sum_probs=3.7
Q ss_pred cCCCCC
Q 031240 111 KCLSCK 116 (163)
Q Consensus 111 kC~~C~ 116 (163)
+|++||
T Consensus 18 ~CPnCG 23 (24)
T PF07754_consen 18 PCPNCG 23 (24)
T ss_pred eCCCCC
Confidence 566665
No 201
>cd02338 ZZ_PCMF_like Zinc finger, ZZ type. Zinc finger present in potassium channel modulatory factor (PCMF) 1 and related proteins. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding. Human potassium channel modulatory factor 1 or FIGC has been shown to possess intrinsic E3 ubiquitin ligase activity and to promote ubiquitination.
Probab=39.34 E-value=25 Score=21.28 Aligned_cols=28 Identities=29% Similarity=0.727 Sum_probs=16.4
Q ss_pred eeCCCCCCCCcccceeeeccCCCCCCCcccc
Q 031240 92 ILCNDCGANSHVQFHVIAHKCLSCKSYNTRQ 122 (163)
Q Consensus 92 i~C~dC~~~~~~~~h~~~~kC~~C~synt~~ 122 (163)
|.|+.|+.....- +-.+|..|..|+--+
T Consensus 1 i~C~~C~~~~i~g---~R~~C~~C~d~dlC~ 28 (49)
T cd02338 1 VSCDGCGKSNFTG---RRYKCLICYDYDLCA 28 (49)
T ss_pred CCCCCCcCCCcEE---eeEEeCCCCCCccch
Confidence 4688887554432 334666666666554
No 202
>PRK14873 primosome assembly protein PriA; Provisional
Probab=39.24 E-value=27 Score=32.67 Aligned_cols=28 Identities=25% Similarity=0.423 Sum_probs=20.4
Q ss_pred ceeeCCCCCCCCcccceeeeccCCCCCCCccccc
Q 031240 90 VWILCNDCGANSHVQFHVIAHKCLSCKSYNTRQT 123 (163)
Q Consensus 90 ~~i~C~dC~~~~~~~~h~~~~kC~~C~synt~~~ 123 (163)
....|+.||... . ...|++|||.+-+..
T Consensus 409 ~~l~Ch~CG~~~-~-----p~~Cp~Cgs~~l~~~ 436 (665)
T PRK14873 409 GTPRCRWCGRAA-P-----DWRCPRCGSDRLRAV 436 (665)
T ss_pred CeeECCCCcCCC-c-----CccCCCCcCCcceee
Confidence 457799999753 2 348999999765554
No 203
>cd02344 ZZ_HERC2 Zinc finger, ZZ type. Zinc finger present in HERC2 and related proteins. HERC2 is a potential E3 ubiquitin protein ligase and/or guanine nucleotide exchange factor. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding.
Probab=38.92 E-value=26 Score=21.15 Aligned_cols=28 Identities=18% Similarity=0.530 Sum_probs=18.4
Q ss_pred eeCCCCCCCCcccceeeeccCCCCCCCcccc
Q 031240 92 ILCNDCGANSHVQFHVIAHKCLSCKSYNTRQ 122 (163)
Q Consensus 92 i~C~dC~~~~~~~~h~~~~kC~~C~synt~~ 122 (163)
+.|+.|+....+- .-.||..|..|+--+
T Consensus 1 V~Cd~C~~~pI~G---~RykC~~C~dyDLC~ 28 (45)
T cd02344 1 VTCDGCQMFPING---PRFKCRNCDDFDFCE 28 (45)
T ss_pred CCCCCCCCCCCcc---CeEECCCCCCccchH
Confidence 4688998654432 334788888777665
No 204
>PF10497 zf-4CXXC_R1: Zinc-finger domain of monoamine-oxidase A repressor R1; InterPro: IPR018866 R1 is a transcription factor repressor that inhibits monoamine oxidase A gene expression. This domain is a four-CXXC zinc finger putative DNA-binding domain found at the C-terminal end of R1. The domain carries 12 cysteines of which four pairs are of the CXXC type [].
Probab=38.84 E-value=32 Score=24.41 Aligned_cols=25 Identities=20% Similarity=0.470 Sum_probs=16.7
Q ss_pred CChhhHHHHHHHHh--------cCCCCCCCCCC
Q 031240 36 GHTIHLECLKEMEK--------HYRYTCPVCSK 60 (163)
Q Consensus 36 GH~fh~~Cl~~~~~--------~~~~~CPiCr~ 60 (163)
.=.||..||..... ...+.||.||.
T Consensus 37 ~~~fC~~CL~~ryge~~~ev~~~~~W~CP~Crg 69 (105)
T PF10497_consen 37 RGKFCGGCLRNRYGENVEEVLEDPNWKCPKCRG 69 (105)
T ss_pred cceehHhHHHHHHhhhHHHHhcCCceECCCCCC
Confidence 55688888776432 23567888876
No 205
>PF13719 zinc_ribbon_5: zinc-ribbon domain
Probab=38.12 E-value=28 Score=19.80 Aligned_cols=13 Identities=23% Similarity=0.437 Sum_probs=8.9
Q ss_pred CcceeeCCCCCCC
Q 031240 88 KMVWILCNDCGAN 100 (163)
Q Consensus 88 ~~~~i~C~dC~~~ 100 (163)
....+.|..|+..
T Consensus 22 ~~~~vrC~~C~~~ 34 (37)
T PF13719_consen 22 GGRKVRCPKCGHV 34 (37)
T ss_pred CCcEEECCCCCcE
Confidence 3457788888754
No 206
>KOG0269 consensus WD40 repeat-containing protein [Function unknown]
Probab=37.63 E-value=33 Score=32.64 Aligned_cols=41 Identities=27% Similarity=0.344 Sum_probs=27.1
Q ss_pred cccccccccccCcCCccEEecCCChhhHHHHHHHHhcCCCCCCC
Q 031240 14 HNCPICFEFIFDTMKDITVLRCGHTIHLECLKEMEKHYRYTCPV 57 (163)
Q Consensus 14 ~~CpIC~e~l~~s~~~~~~L~CGH~fh~~Cl~~~~~~~~~~CPi 57 (163)
..|.+|-..+. ....---.|||..|.+++.+|+.. ...||.
T Consensus 780 ~~CtVC~~vi~--G~~~~c~~C~H~gH~sh~~sw~~~-~s~ca~ 820 (839)
T KOG0269|consen 780 AKCTVCDLVIR--GVDVWCQVCGHGGHDSHLKSWFFK-ASPCAK 820 (839)
T ss_pred cCceeecceee--eeEeecccccccccHHHHHHHHhc-CCCCcc
Confidence 37888875431 111122389999999999999974 355655
No 207
>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=37.19 E-value=27 Score=25.32 Aligned_cols=26 Identities=19% Similarity=0.520 Sum_probs=14.3
Q ss_pred CCCCCCCCCccchhHHHHhHHHHHhcCCCChhhh
Q 031240 53 YTCPVCSKSLWDMSKLWSKIDQEIASTPMPAMYQ 86 (163)
Q Consensus 53 ~~CPiCr~~~~~~~~~~~~l~~~~~~~~~p~e~~ 86 (163)
..|+.|+.++ .+|++++...+.+.|.
T Consensus 86 D~CM~C~~pL--------TLd~~legkef~~~yn 111 (114)
T PF11023_consen 86 DACMHCKEPL--------TLDPSLEGKEFDEKYN 111 (114)
T ss_pred hccCcCCCcC--------ccCchhhcchhhHhhc
Confidence 5677777775 3344444444444443
No 208
>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=36.50 E-value=19 Score=27.17 Aligned_cols=18 Identities=28% Similarity=0.255 Sum_probs=14.9
Q ss_pred ccCCCCCCCccccccCCC
Q 031240 110 HKCLSCKSYNTRQTRGDT 127 (163)
Q Consensus 110 ~kC~~C~synt~~~~~~~ 127 (163)
-.|+.|||-||+.++.-.
T Consensus 106 ~~cp~c~s~~t~~~s~fg 123 (146)
T TIGR02159 106 VQCPRCGSADTTITSIFG 123 (146)
T ss_pred CcCCCCCCCCcEeecCCC
Confidence 489999999999986433
No 209
>PRK00420 hypothetical protein; Validated
Probab=35.91 E-value=34 Score=24.77 Aligned_cols=9 Identities=44% Similarity=1.121 Sum_probs=4.7
Q ss_pred CCCCCCCCC
Q 031240 53 YTCPVCSKS 61 (163)
Q Consensus 53 ~~CPiCr~~ 61 (163)
..||+|..+
T Consensus 24 ~~CP~Cg~p 32 (112)
T PRK00420 24 KHCPVCGLP 32 (112)
T ss_pred CCCCCCCCc
Confidence 346666544
No 210
>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=35.84 E-value=17 Score=21.98 Aligned_cols=37 Identities=32% Similarity=0.705 Sum_probs=25.5
Q ss_pred cccccccccCcCCccEEecCCChhhHHHHHHHHhcCCCCCCCCCCCcc
Q 031240 16 CPICFEFIFDTMKDITVLRCGHTIHLECLKEMEKHYRYTCPVCSKSLW 63 (163)
Q Consensus 16 CpIC~e~l~~s~~~~~~L~CGH~fh~~Cl~~~~~~~~~~CPiCr~~~~ 63 (163)
|+.|.+.+. ....++..=|..||..| ++|-.|++++.
T Consensus 1 C~~C~~~I~--~~~~~~~~~~~~~H~~C---------f~C~~C~~~l~ 37 (58)
T PF00412_consen 1 CARCGKPIY--GTEIVIKAMGKFWHPEC---------FKCSKCGKPLN 37 (58)
T ss_dssp BTTTSSBES--SSSEEEEETTEEEETTT---------SBETTTTCBTT
T ss_pred CCCCCCCcc--CcEEEEEeCCcEEEccc---------cccCCCCCccC
Confidence 667777754 23333347788899888 56999998864
No 211
>PF13901 DUF4206: Domain of unknown function (DUF4206)
Probab=35.70 E-value=28 Score=27.41 Aligned_cols=42 Identities=26% Similarity=0.755 Sum_probs=26.5
Q ss_pred ccccccccc--cccC--cCCccEEecCCChhhHHHHHHHHhcCCCCCCCCCC
Q 031240 13 HHNCPICFE--FIFD--TMKDITVLRCGHTIHLECLKEMEKHYRYTCPVCSK 60 (163)
Q Consensus 13 ~~~CpIC~e--~l~~--s~~~~~~L~CGH~fh~~Cl~~~~~~~~~~CPiCr~ 60 (163)
...|-||.+ .+|. ...-..-..|+-.||..|+.+ ..||-|..
T Consensus 152 GfiCe~C~~~~~IfPF~~~~~~~C~~C~~v~H~~C~~~------~~CpkC~R 197 (202)
T PF13901_consen 152 GFICEICNSDDIIFPFQIDTTVRCPKCKSVFHKSCFRK------KSCPKCAR 197 (202)
T ss_pred CCCCccCCCCCCCCCCCCCCeeeCCcCccccchhhcCC------CCCCCcHh
Confidence 357888873 3332 112122248999999999773 35999953
No 212
>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=35.68 E-value=14 Score=20.25 Aligned_cols=24 Identities=33% Similarity=0.701 Sum_probs=9.4
Q ss_pred eCCCCCCCCcccceeeeccCCCCC
Q 031240 93 LCNDCGANSHVQFHVIAHKCLSCK 116 (163)
Q Consensus 93 ~C~dC~~~~~~~~h~~~~kC~~C~ 116 (163)
+|.-||.+....-.-....|..|+
T Consensus 5 fC~~CG~~t~~~~~g~~r~C~~Cg 28 (32)
T PF09297_consen 5 FCGRCGAPTKPAPGGWARRCPSCG 28 (32)
T ss_dssp B-TTT--BEEE-SSSS-EEESSSS
T ss_pred ccCcCCccccCCCCcCEeECCCCc
Confidence 456666554332223445566665
No 213
>KOG3842 consensus Adaptor protein Pellino [Signal transduction mechanisms]
Probab=35.29 E-value=16 Score=31.32 Aligned_cols=49 Identities=22% Similarity=0.521 Sum_probs=30.8
Q ss_pred CCCccccccccccc----------cCcCCccEEecCCChhhHHHHHHHHhc-----CCCCCCCCCCC
Q 031240 10 RAMHHNCPICFEFI----------FDTMKDITVLRCGHTIHLECLKEMEKH-----YRYTCPVCSKS 61 (163)
Q Consensus 10 ~s~~~~CpIC~e~l----------~~s~~~~~~L~CGH~fh~~Cl~~~~~~-----~~~~CPiCr~~ 61 (163)
|+....|||=+..| .+..++-+.|.|||+--. ..|-.. ....||+|+..
T Consensus 287 NA~RPQCPVglnTL~~P~~~~~~~~~~~QP~vYl~CGHV~G~---H~WG~~e~~g~~~r~CPmC~~~ 350 (429)
T KOG3842|consen 287 NAARPQCPVGLNTLAFPSKRRKRVVDEKQPWVYLNCGHVHGY---HNWGVRENTGQRERECPMCRVV 350 (429)
T ss_pred hccCCCCCcccceeecccccccccccccCCeEEEeccccccc---cccccccccCcccCcCCeeeee
Confidence 45677888887765 122345678999986432 235322 14679999864
No 214
>PRK00415 rps27e 30S ribosomal protein S27e; Reviewed
Probab=34.95 E-value=26 Score=22.48 Aligned_cols=35 Identities=26% Similarity=0.571 Sum_probs=20.7
Q ss_pred CcceeeCCCCCCCCcccce-eeeccCCCCCCCcccc
Q 031240 88 KMVWILCNDCGANSHVQFH-VIAHKCLSCKSYNTRQ 122 (163)
Q Consensus 88 ~~~~i~C~dC~~~~~~~~h-~~~~kC~~C~synt~~ 122 (163)
....+.|.||+....+.-| -.--+|..||.--.+.
T Consensus 8 ~F~~VkCp~C~n~q~vFsha~t~V~C~~Cg~~L~~P 43 (59)
T PRK00415 8 RFLKVKCPDCGNEQVVFSHASTVVRCLVCGKTLAEP 43 (59)
T ss_pred eEEEEECCCCCCeEEEEecCCcEEECcccCCCcccC
Confidence 4568889999875533222 1223688887644333
No 215
>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=34.23 E-value=22 Score=23.08 Aligned_cols=14 Identities=36% Similarity=0.589 Sum_probs=12.0
Q ss_pred ccCCCCCCCccccc
Q 031240 110 HKCLSCKSYNTRQT 123 (163)
Q Consensus 110 ~kC~~C~synt~~~ 123 (163)
++|+.|+|.||+.-
T Consensus 6 ~~CPRC~S~nTKFc 19 (63)
T PF02701_consen 6 LPCPRCDSTNTKFC 19 (63)
T ss_pred CCCCCcCCCCCEEE
Confidence 58999999999874
No 216
>KOG3005 consensus GIY-YIG type nuclease [General function prediction only]
Probab=33.83 E-value=45 Score=27.82 Aligned_cols=47 Identities=34% Similarity=0.599 Sum_probs=32.1
Q ss_pred cccccccccccCcCCccEEe-----cCCChhhHHHHHHHHhc---C-----CCCCCCCCCCc
Q 031240 14 HNCPICFEFIFDTMKDITVL-----RCGHTIHLECLKEMEKH---Y-----RYTCPVCSKSL 62 (163)
Q Consensus 14 ~~CpIC~e~l~~s~~~~~~L-----~CGH~fh~~Cl~~~~~~---~-----~~~CPiCr~~~ 62 (163)
..|-+|.+.+.+. +...+ .|+-.+|..|+...+.. + .-.||.|++.+
T Consensus 183 ~~celc~~ei~e~--~~~~a~c~~~~c~~~~h~~CLa~~~~~~e~g~~~p~eg~cp~C~~~~ 242 (276)
T KOG3005|consen 183 VECELCEKEILET--DWSRATCPNPDCDSLNHLTCLAEELLEVEPGQLIPLEGMCPKCEKFL 242 (276)
T ss_pred hhhHHHHHHhccc--cceeccCCCCCCCchhhhhhhhHHHhccCCCceeccCCCCCchhcee
Confidence 5899998886322 22233 57789999999984322 1 35699999865
No 217
>smart00653 eIF2B_5 domain present in translation initiation factor eIF2B and eIF5.
Probab=33.56 E-value=36 Score=24.40 Aligned_cols=27 Identities=26% Similarity=0.742 Sum_probs=18.2
Q ss_pred eeeCCCCCCCCccc---ceeeeccCCCCCC
Q 031240 91 WILCNDCGANSHVQ---FHVIAHKCLSCKS 117 (163)
Q Consensus 91 ~i~C~dC~~~~~~~---~h~~~~kC~~C~s 117 (163)
-++|..|+.+...- --.+.++|..||+
T Consensus 80 yVlC~~C~spdT~l~k~~r~~~l~C~aCGa 109 (110)
T smart00653 80 YVLCPECGSPDTELIKENRLFFLKCEACGA 109 (110)
T ss_pred cEECCCCCCCCcEEEEeCCeEEEEccccCC
Confidence 57899998764211 1246778998885
No 218
>KOG3039 consensus Uncharacterized conserved protein [Function unknown]
Probab=33.29 E-value=27 Score=28.97 Aligned_cols=33 Identities=15% Similarity=0.196 Sum_probs=27.8
Q ss_pred cccccccccccCcCCccEEecCCChhhHHHHHHHHhc
Q 031240 14 HNCPICFEFIFDTMKDITVLRCGHTIHLECLKEMEKH 50 (163)
Q Consensus 14 ~~CpIC~e~l~~s~~~~~~L~CGH~fh~~Cl~~~~~~ 50 (163)
.-|..|+.. .++|++.+=||.|+++||.+++..
T Consensus 44 dcCsLtLqP----c~dPvit~~GylfdrEaILe~ila 76 (303)
T KOG3039|consen 44 DCCSLTLQP----CRDPVITPDGYLFDREAILEYILA 76 (303)
T ss_pred ceeeeeccc----ccCCccCCCCeeeeHHHHHHHHHH
Confidence 468888876 688899999999999999998753
No 219
>PRK11788 tetratricopeptide repeat protein; Provisional
Probab=32.72 E-value=33 Score=28.43 Aligned_cols=29 Identities=28% Similarity=0.710 Sum_probs=21.7
Q ss_pred eeeCCCCCCCCcccceeeeccCCCCCCCccccc
Q 031240 91 WILCNDCGANSHVQFHVIAHKCLSCKSYNTRQT 123 (163)
Q Consensus 91 ~i~C~dC~~~~~~~~h~~~~kC~~C~synt~~~ 123 (163)
...|..||-++.. ....|++|++.+|-.-
T Consensus 354 ~~~c~~cg~~~~~----~~~~c~~c~~~~~~~~ 382 (389)
T PRK11788 354 RYRCRNCGFTART----LYWHCPSCKAWETIKP 382 (389)
T ss_pred CEECCCCCCCCcc----ceeECcCCCCccCcCC
Confidence 3459999987754 3347999999998653
No 220
>cd02340 ZZ_NBR1_like Zinc finger, ZZ type. Zinc finger present in Drosophila ref(2)P, NBR1, Human sequestosome 1 and related proteins. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding. Drosophila ref(2)P appears to control the multiplication of sigma rhabdovirus. NBR1 (Next to BRCA1 gene 1 protein) interacts with fasciculation and elongation protein zeta-1 (FEZ1) and calcium and integrin binding protein (CIB), and may function in cell signalling pathways. Sequestosome 1 is a phosphotyrosine independent ligand for the Lck SH2 domain and binds noncovalently to ubiquitin via its UBA domain.
Probab=32.56 E-value=32 Score=20.30 Aligned_cols=27 Identities=30% Similarity=0.822 Sum_probs=16.2
Q ss_pred eeCCCCCCCCcccceeeeccCCCCCCCcccc
Q 031240 92 ILCNDCGANSHVQFHVIAHKCLSCKSYNTRQ 122 (163)
Q Consensus 92 i~C~dC~~~~~~~~h~~~~kC~~C~synt~~ 122 (163)
|.|+.|++ ... .+-.+|..|..|+--+
T Consensus 1 v~Cd~C~~-~i~---G~ry~C~~C~d~dLC~ 27 (43)
T cd02340 1 VICDGCQG-PIV---GVRYKCLVCPDYDLCE 27 (43)
T ss_pred CCCCCCCC-cCc---CCeEECCCCCCccchH
Confidence 45888876 222 2344777777776544
No 221
>PF15353 HECA: Headcase protein family homologue
Probab=32.32 E-value=32 Score=24.69 Aligned_cols=17 Identities=29% Similarity=0.645 Sum_probs=14.4
Q ss_pred cCCChhhHHHHHHHHhc
Q 031240 34 RCGHTIHLECLKEMEKH 50 (163)
Q Consensus 34 ~CGH~fh~~Cl~~~~~~ 50 (163)
|.|+.||.+|++.|-++
T Consensus 39 p~~~~MH~~CF~~wE~~ 55 (107)
T PF15353_consen 39 PFGQYMHRECFEKWEDS 55 (107)
T ss_pred CCCCchHHHHHHHHHHH
Confidence 55899999999999653
No 222
>PF04981 NMD3: NMD3 family ; InterPro: IPR007064 The NMD3 protein is involved in nonsense mediated mRNA decay. This N-terminal region contains four conserved CXXC motifs that could be metal binding. NMD3 is involved in export of the 60S ribosomal subunit is mediated by the adapter protein Nmd3p in a Crm1p-dependent pathway [].
Probab=31.88 E-value=27 Score=28.11 Aligned_cols=29 Identities=24% Similarity=0.572 Sum_probs=16.6
Q ss_pred eCCCCCCCC----cccceeeeccCCCCCCCccc
Q 031240 93 LCNDCGANS----HVQFHVIAHKCLSCKSYNTR 121 (163)
Q Consensus 93 ~C~dC~~~~----~~~~h~~~~kC~~C~synt~ 121 (163)
+|.+|-.+. .++-.+--..|..||+|-..
T Consensus 15 lC~~C~~~~~~i~ei~~~i~v~~C~~Cg~~~~~ 47 (236)
T PF04981_consen 15 LCPDCYLKRFDIIEIPDRIEVTICPKCGRYRIG 47 (236)
T ss_pred cChHHhcccCCeeecCCccCceECCCCCCEECC
Confidence 577774322 12222334578888888776
No 223
>cd02342 ZZ_UBA_plant Zinc finger, ZZ type. Zinc finger present in plant ubiquitin-associated (UBA) proteins. The ZZ motif coordinates a zinc ion and most likely participates in ligand binding or molecular scaffolding.
Probab=31.70 E-value=35 Score=20.48 Aligned_cols=28 Identities=21% Similarity=0.344 Sum_probs=18.8
Q ss_pred eeCCCCCCCCcccceeeeccCCCCCCCcccc
Q 031240 92 ILCNDCGANSHVQFHVIAHKCLSCKSYNTRQ 122 (163)
Q Consensus 92 i~C~dC~~~~~~~~h~~~~kC~~C~synt~~ 122 (163)
|.|+.|+....+- .-.||..|..|+-.+
T Consensus 1 I~CDgCg~~PI~G---~RykC~~C~dyDLC~ 28 (43)
T cd02342 1 IQCDGCGVLPITG---PRYKSKVKEDYDLCT 28 (43)
T ss_pred CCCCCCCCCcccc---cceEeCCCCCCccHH
Confidence 5689998766543 334788888776554
No 224
>COG2051 RPS27A Ribosomal protein S27E [Translation, ribosomal structure and biogenesis]
Probab=31.63 E-value=28 Score=22.91 Aligned_cols=34 Identities=26% Similarity=0.602 Sum_probs=20.5
Q ss_pred hcCcceeeCCCCCCCCcccce-eeeccCCCCCCCc
Q 031240 86 QNKMVWILCNDCGANSHVQFH-VIAHKCLSCKSYN 119 (163)
Q Consensus 86 ~~~~~~i~C~dC~~~~~~~~h-~~~~kC~~C~syn 119 (163)
+.+...+.|.||+....+.-| -..-+|..||.--
T Consensus 14 ~s~Fl~VkCpdC~N~q~vFshast~V~C~~CG~~l 48 (67)
T COG2051 14 RSRFLRVKCPDCGNEQVVFSHASTVVTCLICGTTL 48 (67)
T ss_pred CceEEEEECCCCCCEEEEeccCceEEEecccccEE
Confidence 345578889999875433222 1223688887543
No 225
>cd02334 ZZ_dystrophin Zinc finger, ZZ type. Zinc finger present in dystrophin and dystrobrevin. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding. Dystrophin attaches actin filaments to an integral membrane glycoprotein complex in muscle cells. The ZZ domain in dystrophin has been shown to be essential for binding to the membrane protein beta-dystroglycan.
Probab=30.86 E-value=45 Score=20.34 Aligned_cols=28 Identities=29% Similarity=0.544 Sum_probs=18.0
Q ss_pred eeCCCCCCCCcccceeeeccCCCCCCCcccc
Q 031240 92 ILCNDCGANSHVQFHVIAHKCLSCKSYNTRQ 122 (163)
Q Consensus 92 i~C~dC~~~~~~~~h~~~~kC~~C~synt~~ 122 (163)
+.|+.|++.... .+-.||..|..|+--+
T Consensus 1 ~~Cd~C~~~pi~---g~RykC~~C~d~DLC~ 28 (49)
T cd02334 1 AKCNICKEFPIT---GFRYRCLKCFNYDLCQ 28 (49)
T ss_pred CCCCCCCCCCce---eeeEECCCCCCcCchH
Confidence 358888864433 3455777777777665
No 226
>COG3813 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=30.81 E-value=76 Score=21.35 Aligned_cols=48 Identities=21% Similarity=0.396 Sum_probs=32.4
Q ss_pred CccccccccccccCcCCccEEecCCChhhHHHHHHHHhcCCCCCCCCCCCc
Q 031240 12 MHHNCPICFEFIFDTMKDITVLRCGHTIHLECLKEMEKHYRYTCPVCSKSL 62 (163)
Q Consensus 12 ~~~~CpIC~e~l~~s~~~~~~L~CGH~fh~~Cl~~~~~~~~~~CPiCr~~~ 62 (163)
...+|--|-.+|-....+..+-.=-|+||..|.+.-+. ..||-|.-.+
T Consensus 4 LRPnCECCDrDLpp~s~dA~ICtfEcTFCadCae~~l~---g~CPnCGGel 51 (84)
T COG3813 4 LRPNCECCDRDLPPDSTDARICTFECTFCADCAENRLH---GLCPNCGGEL 51 (84)
T ss_pred ccCCCcccCCCCCCCCCceeEEEEeeehhHhHHHHhhc---CcCCCCCchh
Confidence 35667777666543334444434458999999997665 4799998775
No 227
>PRK01343 zinc-binding protein; Provisional
Probab=30.79 E-value=29 Score=22.09 Aligned_cols=11 Identities=36% Similarity=0.869 Sum_probs=9.1
Q ss_pred CCCCCCCCCCc
Q 031240 52 RYTCPVCSKSL 62 (163)
Q Consensus 52 ~~~CPiCr~~~ 62 (163)
..+||+|++.+
T Consensus 9 ~~~CP~C~k~~ 19 (57)
T PRK01343 9 TRPCPECGKPS 19 (57)
T ss_pred CCcCCCCCCcC
Confidence 46799999986
No 228
>KOG3507 consensus DNA-directed RNA polymerase, subunit RPB7.0 [Transcription]
Probab=30.42 E-value=35 Score=21.98 Aligned_cols=28 Identities=21% Similarity=0.669 Sum_probs=17.5
Q ss_pred CcceeeCCCCCCCCcccceeeeccCCCCC
Q 031240 88 KMVWILCNDCGANSHVQFHVIAHKCLSCK 116 (163)
Q Consensus 88 ~~~~i~C~dC~~~~~~~~h~~~~kC~~C~ 116 (163)
.....+|.||+.+...+.--+ ..|..||
T Consensus 17 ~~miYiCgdC~~en~lk~~D~-irCReCG 44 (62)
T KOG3507|consen 17 ATMIYICGDCGQENTLKRGDV-IRCRECG 44 (62)
T ss_pred ccEEEEeccccccccccCCCc-Eehhhcc
Confidence 346778999987654332211 3688887
No 229
>PF06844 DUF1244: Protein of unknown function (DUF1244); InterPro: IPR009654 This family consists of several short bacterial proteins of around 100 residues in length. The function of this family is unknown.; PDB: 2O35_A 3FYB_B.
Probab=30.40 E-value=34 Score=22.53 Aligned_cols=13 Identities=15% Similarity=0.348 Sum_probs=9.0
Q ss_pred hhhHHHHHHHHhc
Q 031240 38 TIHLECLKEMEKH 50 (163)
Q Consensus 38 ~fh~~Cl~~~~~~ 50 (163)
-||+.||.+|...
T Consensus 11 gFCRNCLskWy~~ 23 (68)
T PF06844_consen 11 GFCRNCLSKWYRE 23 (68)
T ss_dssp S--HHHHHHHHHH
T ss_pred HHHHHHHHHHHHH
Confidence 4999999999753
No 230
>PRK00418 DNA gyrase inhibitor; Reviewed
Probab=29.84 E-value=29 Score=22.51 Aligned_cols=10 Identities=40% Similarity=1.192 Sum_probs=8.7
Q ss_pred CCCCCCCCCc
Q 031240 53 YTCPVCSKSL 62 (163)
Q Consensus 53 ~~CPiCr~~~ 62 (163)
..||+|++.+
T Consensus 7 v~CP~C~k~~ 16 (62)
T PRK00418 7 VNCPTCGKPV 16 (62)
T ss_pred ccCCCCCCcc
Confidence 5799999986
No 231
>PF13790 DUF4182: Domain of unknown function (DUF4182)
Probab=29.79 E-value=81 Score=18.41 Aligned_cols=28 Identities=25% Similarity=0.571 Sum_probs=17.7
Q ss_pred cceeeCCCCCCCC----cccceeeeccCCCCC
Q 031240 89 MVWILCNDCGANS----HVQFHVIAHKCLSCK 116 (163)
Q Consensus 89 ~~~i~C~dC~~~~----~~~~h~~~~kC~~C~ 116 (163)
|..|.|..|++.- .-+--.++-+|..|.
T Consensus 1 MGtIvCq~C~~~Id~~e~ekV~~lYg~C~~~e 32 (38)
T PF13790_consen 1 MGTIVCQHCNETIDHFETEKVTTLYGKCGKCE 32 (38)
T ss_pred CCEEEeccccceeeeecCCcEEEEEEECCCCc
Confidence 4678999998631 122235777888754
No 232
>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=29.18 E-value=63 Score=29.49 Aligned_cols=28 Identities=32% Similarity=0.598 Sum_probs=20.3
Q ss_pred eeCCCCCCCCcccceeeeccCCCCCCCccccc
Q 031240 92 ILCNDCGANSHVQFHVIAHKCLSCKSYNTRQT 123 (163)
Q Consensus 92 i~C~dC~~~~~~~~h~~~~kC~~C~synt~~~ 123 (163)
..|++||.... ..+.+|+.|||-+...+
T Consensus 519 ~~C~~CG~~~~----~~~~~CP~CGs~~~~~~ 546 (555)
T cd01675 519 DICNDCGYIGE----GEGFKCPKCGSEDVEVI 546 (555)
T ss_pred ccCCCCCCCCc----CCCCCCcCCCCcCceEE
Confidence 38999997543 24579999998775444
No 233
>PF09779 Ima1_N: Ima1 N-terminal domain; InterPro: IPR018617 Members of this family of uncharacterised novel proteins have no known function.
Probab=29.13 E-value=36 Score=25.02 Aligned_cols=32 Identities=31% Similarity=0.612 Sum_probs=21.8
Q ss_pred eCCCCCCCCccccee-ee-ccCCCCCCCcccccc
Q 031240 93 LCNDCGANSHVQFHV-IA-HKCLSCKSYNTRQTR 124 (163)
Q Consensus 93 ~C~dC~~~~~~~~h~-~~-~kC~~C~synt~~~~ 124 (163)
-|-.||+.+.+.+-- .- -.|.+|+.||.-.-.
T Consensus 2 ~C~fC~~~s~~~~~~~~~~w~C~~C~q~N~f~e~ 35 (131)
T PF09779_consen 2 NCWFCGQNSKVPYDNRNSNWTCPHCEQYNGFDED 35 (131)
T ss_pred eeccCCCCCCCCCCCCCCeeECCCCCCccCcccc
Confidence 488898877654421 11 469999999976643
No 234
>COG3058 FdhE Uncharacterized protein involved in formate dehydrogenase formation [Posttranslational modification, protein turnover, chaperones]
Probab=29.04 E-value=14 Score=31.12 Aligned_cols=29 Identities=21% Similarity=0.713 Sum_probs=15.1
Q ss_pred eeeCCCCCCCCcccceeeec---------cCCCCCCCc
Q 031240 91 WILCNDCGANSHVQFHVIAH---------KCLSCKSYN 119 (163)
Q Consensus 91 ~i~C~dC~~~~~~~~h~~~~---------kC~~C~syn 119 (163)
-+.|..|+......|..+-. .|+.|+||-
T Consensus 225 R~KC~nC~~t~~l~y~sl~s~E~A~vkAEtC~~C~sYl 262 (308)
T COG3058 225 RVKCSNCEQSKKLHYWSLESSELAAVKAETCGDCNSYL 262 (308)
T ss_pred HHHhccccccCCccceeccchhhhHhhhhcCCcHHHHH
Confidence 34455555554444433333 567777764
No 235
>KOG0825 consensus PHD Zn-finger protein [General function prediction only]
Probab=28.50 E-value=30 Score=33.29 Aligned_cols=50 Identities=12% Similarity=0.224 Sum_probs=32.2
Q ss_pred ccccccccccccCcCCccEEe---cCCChhhHHHHHHHHhc-----CCCCCCCCCCCc
Q 031240 13 HHNCPICFEFIFDTMKDITVL---RCGHTIHLECLKEMEKH-----YRYTCPVCSKSL 62 (163)
Q Consensus 13 ~~~CpIC~e~l~~s~~~~~~L---~CGH~fh~~Cl~~~~~~-----~~~~CPiCr~~~ 62 (163)
...|+||.-.+-+.....-++ .|+|.||..||..|... ..-.|++|..-|
T Consensus 96 s~Ss~~C~~E~S~~~ds~~i~P~~~~~~~~CP~Ci~s~~DqL~~~~k~c~H~FC~~Ci 153 (1134)
T KOG0825|consen 96 SDTSPVCEKEHSPDVDSSNICPVQTHVENQCPNCLKSCNDQLEESEKHTAHYFCEECV 153 (1134)
T ss_pred ccccchhheecCCcccccCcCchhhhhhhhhhHHHHHHHHHhhccccccccccHHHHh
Confidence 346777765543211112233 59999999999999864 134588887766
No 236
>KOG2462 consensus C2H2-type Zn-finger protein [Transcription]
Probab=28.25 E-value=33 Score=28.72 Aligned_cols=56 Identities=23% Similarity=0.414 Sum_probs=33.3
Q ss_pred CccccccccccccCcCCc------cEEecCCChhhHHHHHH-HHhcC---------CCCCCCCCCCccchhHH
Q 031240 12 MHHNCPICFEFIFDTMKD------ITVLRCGHTIHLECLKE-MEKHY---------RYTCPVCSKSLWDMSKL 68 (163)
Q Consensus 12 ~~~~CpIC~e~l~~s~~~------~~~L~CGH~fh~~Cl~~-~~~~~---------~~~CPiCr~~~~~~~~~ 68 (163)
--..|++|-..+ .+.-. ...|+|--.+|..-+.+ |+..+ -+.||.|++.|.|.+.+
T Consensus 160 ka~~C~~C~K~Y-vSmpALkMHirTH~l~c~C~iCGKaFSRPWLLQGHiRTHTGEKPF~C~hC~kAFADRSNL 231 (279)
T KOG2462|consen 160 KAFSCKYCGKVY-VSMPALKMHIRTHTLPCECGICGKAFSRPWLLQGHIRTHTGEKPFSCPHCGKAFADRSNL 231 (279)
T ss_pred ccccCCCCCcee-eehHHHhhHhhccCCCcccccccccccchHHhhcccccccCCCCccCCcccchhcchHHH
Confidence 345788886542 11110 12356666666666554 77543 36799999999886543
No 237
>PF13717 zinc_ribbon_4: zinc-ribbon domain
Probab=27.94 E-value=51 Score=18.64 Aligned_cols=10 Identities=40% Similarity=1.002 Sum_probs=7.5
Q ss_pred CCCCCCCCCc
Q 031240 53 YTCPVCSKSL 62 (163)
Q Consensus 53 ~~CPiCr~~~ 62 (163)
.+||-|.+.+
T Consensus 3 i~Cp~C~~~y 12 (36)
T PF13717_consen 3 ITCPNCQAKY 12 (36)
T ss_pred EECCCCCCEE
Confidence 4688888775
No 238
>PRK12336 translation initiation factor IF-2 subunit beta; Provisional
Probab=27.75 E-value=1.1e+02 Score=24.21 Aligned_cols=34 Identities=21% Similarity=0.647 Sum_probs=23.0
Q ss_pred eeeCCCCCCCCcc---cceeeeccCCCCCCCcccccc
Q 031240 91 WILCNDCGANSHV---QFHVIAHKCLSCKSYNTRQTR 124 (163)
Q Consensus 91 ~i~C~dC~~~~~~---~~h~~~~kC~~C~synt~~~~ 124 (163)
-++|..|+.+... .--.+.++|..||.--+....
T Consensus 98 yV~C~~C~~pdT~l~k~~~~~~l~C~aCGa~~~v~~~ 134 (201)
T PRK12336 98 YVICSECGLPDTRLVKEDRVLMLRCDACGAHRPVKKR 134 (201)
T ss_pred eEECCCCCCCCcEEEEcCCeEEEEcccCCCCcccccc
Confidence 6899999975421 112467899999966665543
No 239
>smart00355 ZnF_C2H2 zinc finger.
Probab=27.74 E-value=69 Score=15.11 Aligned_cols=14 Identities=43% Similarity=0.921 Sum_probs=9.8
Q ss_pred CCCCCCCCCccchh
Q 031240 53 YTCPVCSKSLWDMS 66 (163)
Q Consensus 53 ~~CPiCr~~~~~~~ 66 (163)
+.|+.|.+.+....
T Consensus 1 ~~C~~C~~~f~~~~ 14 (26)
T smart00355 1 YRCPECGKVFKSKS 14 (26)
T ss_pred CCCCCCcchhCCHH
Confidence 36888988875543
No 240
>COG2126 RPL37A Ribosomal protein L37E [Translation, ribosomal structure and biogenesis]
Probab=26.98 E-value=36 Score=21.84 Aligned_cols=29 Identities=34% Similarity=0.705 Sum_probs=22.5
Q ss_pred cCcceeeCCCCCCCCcccceeeeccCCCCCCC
Q 031240 87 NKMVWILCNDCGANSHVQFHVIAHKCLSCKSY 118 (163)
Q Consensus 87 ~~~~~i~C~dC~~~~~~~~h~~~~kC~~C~sy 118 (163)
++...|.|.-||.. .||+--..|..||=-
T Consensus 12 nk~tH~~CRRCGr~---syhv~k~~CaaCGfg 40 (61)
T COG2126 12 NKKTHIRCRRCGRR---SYHVRKKYCAACGFG 40 (61)
T ss_pred CCcceehhhhccch---heeeccceecccCCC
Confidence 44678999999985 467777789999844
No 241
>cd02669 Peptidase_C19M A subfamily of Peptidase C19. Peptidase C19 contains ubiquitinyl hydrolases. They are intracellular peptidases that remove ubiquitin molecules from polyubiquinated peptides by cleavage of isopeptide bonds. They hydrolyze bonds involving the carboxyl group of the C-terminal Gly residue of ubiquitin. The purpose of the de-ubiquitination is thought to be editing of the ubiquitin conjugates, which could rescue them from degradation, as well as recycling of the ubiquitin. The ubiquitin/proteasome system is responsible for most protein turnover in the mammalian cell, and with over 50 members, family C19 is one of the largest families of peptidases in the human genome.
Probab=26.90 E-value=49 Score=29.06 Aligned_cols=57 Identities=7% Similarity=-0.078 Sum_probs=40.6
Q ss_pred eCCCCCCCCcccceeeeccCC--CCCCCccccccCCCCCCCccccccccccceecccccccc
Q 031240 93 LCNDCGANSHVQFHVIAHKCL--SCKSYNTRQTRGDTATTCSSGDELTILSHHWDYQQHASV 152 (163)
Q Consensus 93 ~C~dC~~~~~~~~h~~~~kC~--~C~synt~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 152 (163)
.|..|....++ |+++.|+ .+|.-...++..|+..+.|-....+.+-.++-++..-.|
T Consensus 18 ~C~~~~~~~n~---~~CL~cg~~~~g~~~~~ha~~H~~~~~H~~~v~l~t~~~yc~~~~~~v 76 (440)
T cd02669 18 VCSVSLSNLNV---YACLVCGKYFQGRGKGSHAYTHSLEDNHHVFLNLETLKFYCLPDNYEI 76 (440)
T ss_pred cccccCCCCcE---EEEcccCCeecCCCCCcHHHHHhhccCCCEEEECCCCCEEEeCCCCEE
Confidence 48888766665 6888888 577777778888888888777766666555655554443
No 242
>PRK14714 DNA polymerase II large subunit; Provisional
Probab=26.87 E-value=46 Score=33.58 Aligned_cols=9 Identities=33% Similarity=1.047 Sum_probs=5.4
Q ss_pred CCCCCCCCC
Q 031240 53 YTCPVCSKS 61 (163)
Q Consensus 53 ~~CPiCr~~ 61 (163)
.+||-|...
T Consensus 668 rkCPkCG~~ 676 (1337)
T PRK14714 668 RRCPSCGTE 676 (1337)
T ss_pred EECCCCCCc
Confidence 457777654
No 243
>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=26.60 E-value=50 Score=27.96 Aligned_cols=22 Identities=23% Similarity=0.416 Sum_probs=12.8
Q ss_pred hhhHHHHHHHHhcCCCCCCCCCC
Q 031240 38 TIHLECLKEMEKHYRYTCPVCSK 60 (163)
Q Consensus 38 ~fh~~Cl~~~~~~~~~~CPiCr~ 60 (163)
..|.-|-.+|.- ....||.|..
T Consensus 211 L~CslC~teW~~-~R~~C~~Cg~ 232 (305)
T TIGR01562 211 LSCSLCATEWHY-VRVKCSHCEE 232 (305)
T ss_pred EEcCCCCCcccc-cCccCCCCCC
Confidence 344456666654 3566777754
No 244
>TIGR01206 lysW lysine biosynthesis protein LysW. This very small, poorly characterized protein has been shown essential in Thermus thermophilus for an unusual pathway of Lys biosynthesis from aspartate by way of alpha-aminoadipate (AAA) rather than diaminopimelate. It is found also in Deinococcus radiodurans and Pyrococcus horikoshii, which appear to share the AAA pathway.
Probab=26.56 E-value=55 Score=20.49 Aligned_cols=10 Identities=30% Similarity=1.188 Sum_probs=7.9
Q ss_pred CCCCCCCCCc
Q 031240 53 YTCPVCSKSL 62 (163)
Q Consensus 53 ~~CPiCr~~~ 62 (163)
++||.|...+
T Consensus 3 ~~CP~CG~~i 12 (54)
T TIGR01206 3 FECPDCGAEI 12 (54)
T ss_pred cCCCCCCCEE
Confidence 5799998865
No 245
>PF09567 RE_MamI: MamI restriction endonuclease; InterPro: IPR019067 There are four classes of restriction endonucleases: types I, II,III and IV. All types of enzymes recognise specific short DNA sequences and carry out the endonucleolytic cleavage of DNA to give specific double-stranded fragments with terminal 5'-phosphates. They differ in their recognition sequence, subunit composition, cleavage position, and cofactor requirements [, ], as summarised below: Type I enzymes (3.1.21.3 from EC) cleave at sites remote from recognition site; require both ATP and S-adenosyl-L-methionine to function; multifunctional protein with both restriction and methylase (2.1.1.72 from EC) activities. Type II enzymes (3.1.21.4 from EC) cleave within or at short specific distances from recognition site; most require magnesium; single function (restriction) enzymes independent of methylase. Type III enzymes (3.1.21.5 from EC) cleave at sites a short distance from recognition site; require ATP (but doesn't hydrolyse it); S-adenosyl-L-methionine stimulates reaction but is not required; exists as part of a complex with a modification methylase methylase (2.1.1.72 from EC). Type IV enzymes target methylated DNA. Type II restriction endonucleases (3.1.21.4 from EC) are components of prokaryotic DNA restriction-modification mechanisms that protect the organism against invading foreign DNA. These site-specific deoxyribonucleases catalyse the endonucleolytic cleavage of DNA to give specific double-stranded fragments with terminal 5'-phosphates. Of the 3000 restriction endonucleases that have been characterised, most are homodimeric or tetrameric enzymes that cleave target DNA at sequence-specific sites close to the recognition site. For homodimeric enzymes, the recognition site is usually a palindromic sequence 4-8 bp in length. Most enzymes require magnesium ions as a cofactor for catalysis. Although they can vary in their mode of recognition, many restriction endonucleases share a similar structural core comprising four beta-strands and one alpha-helix, as well as a similar mechanism of cleavage, suggesting a common ancestral origin []. However, there is still considerable diversity amongst restriction endonucleases [, ]. The target site recognition process triggers large conformational changes of the enzyme and the target DNA, leading to the activation of the catalytic centres. Like other DNA binding proteins, restriction enzymes are capable of non-specific DNA binding as well, which is the prerequisite for efficient target site location by facilitated diffusion. Non-specific binding usually does not involve interactions with the bases but only with the DNA backbone []. This entry includes the MamI restriction endonuclease which recognises and cleaves GATNN^NNATC. ; GO: 0003677 DNA binding, 0009036 Type II site-specific deoxyribonuclease activity, 0009307 DNA restriction-modification system
Probab=26.43 E-value=31 Score=28.71 Aligned_cols=28 Identities=36% Similarity=0.748 Sum_probs=20.1
Q ss_pred eeeCCCCCCCCcccceeeeccCCCCCCCcccc
Q 031240 91 WILCNDCGANSHVQFHVIAHKCLSCKSYNTRQ 122 (163)
Q Consensus 91 ~i~C~dC~~~~~~~~h~~~~kC~~C~synt~~ 122 (163)
.-.|++||.... -+-.-|++|+|-|-..
T Consensus 82 l~~C~~CGa~V~----~~e~~Cp~C~StnI~r 109 (314)
T PF09567_consen 82 LGKCNNCGANVS----RLEESCPNCGSTNIKR 109 (314)
T ss_pred hhhhccccceee----ehhhcCCCCCcccccc
Confidence 456999986532 2567899999988654
No 246
>PF01485 IBR: IBR domain; InterPro: IPR002867 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents a cysteine-rich (C6HC) zinc finger domain that is present in Triad1, and which is conserved in other proteins encoded by various eukaryotes. The C6HC consensus pattern is: C-x(4)-C-x(14-30)-C-x(1-4)-C-x(4)-C-x(2)-C-x(4)-H-x(4)-C The C6HC zinc finger motif is the fourth family member of the zinc-binding RING, LIM, and LAP/PHD fingers. Strikingly, in most of the proteins the C6HC domain is flanked by two RING finger structures IPR001841 from INTERPRO. The novel C6HC motif has been called DRIL (double RING finger linked). The strong conservation of the larger tripartite TRIAD (twoRING fingers and DRIL) structure indicates that the three subdomains are functionally linked and identifies a novel class of proteins []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 2CT7_A 1WD2_A 2JMO_A 1WIM_A.
Probab=25.92 E-value=4.1 Score=25.20 Aligned_cols=34 Identities=24% Similarity=0.391 Sum_probs=15.9
Q ss_pred ccccc--ccccccCcCCccE--Ee-c-CCChhhHHHHHHH
Q 031240 14 HNCPI--CFEFIFDTMKDIT--VL-R-CGHTIHLECLKEM 47 (163)
Q Consensus 14 ~~CpI--C~e~l~~s~~~~~--~L-~-CGH~fh~~Cl~~~ 47 (163)
.-||- |...+.-...... +. + ||+.||..|-..|
T Consensus 19 ~~Cp~~~C~~~~~~~~~~~~~~~~C~~C~~~fC~~C~~~~ 58 (64)
T PF01485_consen 19 RWCPNPDCEYIIEKDDGCNSPIVTCPSCGTEFCFKCGEPW 58 (64)
T ss_dssp C--TTSST---ECS-SSTTS--CCTTSCCSEECSSSTSES
T ss_pred cCCCCCCCcccEEecCCCCCCeeECCCCCCcCccccCccc
Confidence 36766 7655422222211 22 4 8888888887766
No 247
>PF14354 Lar_restr_allev: Restriction alleviation protein Lar
Probab=25.43 E-value=53 Score=20.26 Aligned_cols=10 Identities=50% Similarity=1.348 Sum_probs=6.5
Q ss_pred ceeeCCCCCC
Q 031240 90 VWILCNDCGA 99 (163)
Q Consensus 90 ~~i~C~dC~~ 99 (163)
..|.|.+|+.
T Consensus 28 ~~V~C~~Cga 37 (61)
T PF14354_consen 28 YYVECTDCGA 37 (61)
T ss_pred EEEEcCCCCC
Confidence 5566777765
No 248
>PRK00432 30S ribosomal protein S27ae; Validated
Probab=25.34 E-value=41 Score=20.62 Aligned_cols=23 Identities=26% Similarity=0.726 Sum_probs=10.1
Q ss_pred eCCCCCCCCcccceeeeccCCCCC
Q 031240 93 LCNDCGANSHVQFHVIAHKCLSCK 116 (163)
Q Consensus 93 ~C~dC~~~~~~~~h~~~~kC~~C~ 116 (163)
.|..|+.. -...|.-.+.|+.||
T Consensus 22 fCP~Cg~~-~m~~~~~r~~C~~Cg 44 (50)
T PRK00432 22 FCPRCGSG-FMAEHLDRWHCGKCG 44 (50)
T ss_pred cCcCCCcc-hheccCCcEECCCcC
Confidence 45555542 222233334555554
No 249
>smart00291 ZnF_ZZ Zinc-binding domain, present in Dystrophin, CREB-binding protein. Putative zinc-binding domain present in dystrophin-like proteins, and CREB-binding protein/p300 homologues. The ZZ in dystrophin appears to bind calmodulin. A missense mutation of one of the conserved cysteines in dystrophin results in a patient with Duchenne muscular dystrophy [3].
Probab=24.82 E-value=74 Score=18.58 Aligned_cols=28 Identities=32% Similarity=0.737 Sum_probs=16.7
Q ss_pred eeeCCCCCCCCcccceeeeccCCCCCCCcccc
Q 031240 91 WILCNDCGANSHVQFHVIAHKCLSCKSYNTRQ 122 (163)
Q Consensus 91 ~i~C~dC~~~~~~~~h~~~~kC~~C~synt~~ 122 (163)
.+.|+.|+. .... +-.+|..|..|+.-+
T Consensus 4 ~~~C~~C~~-~i~g---~ry~C~~C~d~dlC~ 31 (44)
T smart00291 4 SYSCDTCGK-PIVG---VRYHCLVCPDYDLCQ 31 (44)
T ss_pred CcCCCCCCC-CCcC---CEEECCCCCCccchH
Confidence 456888887 3332 223677777766544
No 250
>PRK03988 translation initiation factor IF-2 subunit beta; Validated
Probab=24.81 E-value=68 Score=23.95 Aligned_cols=29 Identities=21% Similarity=0.678 Sum_probs=18.1
Q ss_pred eeeCCCCCCCCcc---cceeeeccCCCCCCCc
Q 031240 91 WILCNDCGANSHV---QFHVIAHKCLSCKSYN 119 (163)
Q Consensus 91 ~i~C~dC~~~~~~---~~h~~~~kC~~C~syn 119 (163)
-++|..|+.+... .--.+.++|..||.--
T Consensus 102 yVlC~~C~spdT~l~k~~r~~~l~C~ACGa~~ 133 (138)
T PRK03988 102 YVICPECGSPDTKLIKEGRIWVLKCEACGAET 133 (138)
T ss_pred cEECCCCCCCCcEEEEcCCeEEEEcccCCCCC
Confidence 5788888875421 1124567888888543
No 251
>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=24.74 E-value=54 Score=16.83 Aligned_cols=14 Identities=21% Similarity=0.607 Sum_probs=10.4
Q ss_pred CCCCCCCCCccchh
Q 031240 53 YTCPVCSKSLWDMS 66 (163)
Q Consensus 53 ~~CPiCr~~~~~~~ 66 (163)
+.|++|.+.+.+..
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 57999998876543
No 252
>TIGR00311 aIF-2beta translation initiation factor aIF-2, beta subunit, putative.
Probab=24.67 E-value=69 Score=23.77 Aligned_cols=28 Identities=21% Similarity=0.566 Sum_probs=17.5
Q ss_pred eeeCCCCCCCCccc---ceeeeccCCCCCCC
Q 031240 91 WILCNDCGANSHVQ---FHVIAHKCLSCKSY 118 (163)
Q Consensus 91 ~i~C~dC~~~~~~~---~h~~~~kC~~C~sy 118 (163)
-++|..|+.+...- --.+.++|..||.-
T Consensus 97 yVlC~~C~sPdT~l~k~~r~~~l~C~ACGa~ 127 (133)
T TIGR00311 97 YVICRECNRPDTRIIKEGRVSLLKCEACGAK 127 (133)
T ss_pred eEECCCCCCCCcEEEEeCCeEEEecccCCCC
Confidence 57899998754211 11345688888854
No 253
>PF09082 DUF1922: Domain of unknown function (DUF1922); InterPro: IPR015166 Members of this family consist of a beta-sheet region followed by an alpha-helix and an unstructured C terminus. The beta-sheet region contains a CXCX...XCXC sequence with Cys residues located in two proximal loops and pointing towards each other. This precise function of this set of bacterial proteins is, as yet, unknown []. ; PDB: 1GH9_A.
Probab=24.24 E-value=27 Score=23.03 Aligned_cols=32 Identities=25% Similarity=0.582 Sum_probs=17.6
Q ss_pred eeeCCCCCCCCcccceeeeccCCCCC-CCcccccc
Q 031240 91 WILCNDCGANSHVQFHVIAHKCLSCK-SYNTRQTR 124 (163)
Q Consensus 91 ~i~C~dC~~~~~~~~h~~~~kC~~C~-synt~~~~ 124 (163)
.+.| |||....+.--.--.+| .|| ..|-.+.+
T Consensus 3 ifrC-~Cgr~lya~e~~kTkkC-~CG~~l~vk~~r 35 (68)
T PF09082_consen 3 IFRC-DCGRYLYAKEGAKTKKC-VCGKTLKVKERR 35 (68)
T ss_dssp EEEE-TTS--EEEETT-SEEEE-TTTEEEE--SSS
T ss_pred EEEe-cCCCEEEecCCcceeEe-cCCCeeeeeeEE
Confidence 4678 89986654433455789 999 45555544
No 254
>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=24.14 E-value=63 Score=23.97 Aligned_cols=12 Identities=33% Similarity=0.797 Sum_probs=8.3
Q ss_pred CCCCCCCCCccc
Q 031240 53 YTCPVCSKSLWD 64 (163)
Q Consensus 53 ~~CPiCr~~~~~ 64 (163)
.+||.|+..+..
T Consensus 92 sRC~~CN~~L~~ 103 (147)
T PF01927_consen 92 SRCPKCNGPLRP 103 (147)
T ss_pred CccCCCCcEeee
Confidence 468888876543
No 255
>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional
Probab=23.65 E-value=1e+02 Score=19.80 Aligned_cols=10 Identities=50% Similarity=1.132 Sum_probs=6.2
Q ss_pred CCCCCCCCCC
Q 031240 51 YRYTCPVCSK 60 (163)
Q Consensus 51 ~~~~CPiCr~ 60 (163)
..|+||-|..
T Consensus 47 ~~Y~CP~CGF 56 (59)
T PRK14890 47 NPYTCPKCGF 56 (59)
T ss_pred CceECCCCCC
Confidence 3467777753
No 256
>COG4311 SoxD Sarcosine oxidase delta subunit [Amino acid transport and metabolism]
Probab=23.45 E-value=51 Score=23.22 Aligned_cols=20 Identities=25% Similarity=0.582 Sum_probs=16.0
Q ss_pred ceeeCCCCCCCCcccceeee
Q 031240 90 VWILCNDCGANSHVQFHVIA 109 (163)
Q Consensus 90 ~~i~C~dC~~~~~~~~h~~~ 109 (163)
..|.|..|+.++...|++.|
T Consensus 2 lLI~CP~Cg~R~e~EFt~~G 21 (97)
T COG4311 2 LLIPCPYCGERPEEEFTYAG 21 (97)
T ss_pred ceecCCCCCCCchhheeecc
Confidence 46889999998888887655
No 257
>KOG2593 consensus Transcription initiation factor IIE, alpha subunit [Transcription]
Probab=22.97 E-value=73 Score=28.36 Aligned_cols=14 Identities=36% Similarity=0.916 Sum_probs=11.2
Q ss_pred CCCCCCCCCCccch
Q 031240 52 RYTCPVCSKSLWDM 65 (163)
Q Consensus 52 ~~~CPiCr~~~~~~ 65 (163)
+|.||.|.+.+..+
T Consensus 128 ~Y~Cp~C~kkyt~L 141 (436)
T KOG2593|consen 128 GYVCPNCQKKYTSL 141 (436)
T ss_pred cccCCccccchhhh
Confidence 68999999987543
No 258
>PF14369 zf-RING_3: zinc-finger
Probab=22.77 E-value=62 Score=18.27 Aligned_cols=6 Identities=33% Similarity=1.193 Sum_probs=3.2
Q ss_pred CCCCCC
Q 031240 112 CLSCKS 117 (163)
Q Consensus 112 C~~C~s 117 (163)
|+.|++
T Consensus 24 CP~C~~ 29 (35)
T PF14369_consen 24 CPRCHG 29 (35)
T ss_pred CcCCCC
Confidence 555553
No 259
>COG3809 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=22.73 E-value=76 Score=21.68 Aligned_cols=13 Identities=31% Similarity=0.596 Sum_probs=9.2
Q ss_pred CCCCCCCCCccch
Q 031240 53 YTCPVCSKSLWDM 65 (163)
Q Consensus 53 ~~CPiCr~~~~~~ 65 (163)
..||-||-.-.+.
T Consensus 22 D~CPrCrGVWLDr 34 (88)
T COG3809 22 DYCPRCRGVWLDR 34 (88)
T ss_pred eeCCccccEeecc
Confidence 4699998775543
No 260
>cd02343 ZZ_EF Zinc finger, ZZ type. Zinc finger present in proteins with an EF_hand motif. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding.
Probab=22.73 E-value=65 Score=19.72 Aligned_cols=27 Identities=22% Similarity=0.586 Sum_probs=17.5
Q ss_pred eeCCCCCCCCcccceeeeccCCCCCCCcccc
Q 031240 92 ILCNDCGANSHVQFHVIAHKCLSCKSYNTRQ 122 (163)
Q Consensus 92 i~C~dC~~~~~~~~h~~~~kC~~C~synt~~ 122 (163)
|.|+.|++... .+-.||..|..|+-.+
T Consensus 1 i~CdgC~~~~~----~~RykCl~C~d~DlC~ 27 (48)
T cd02343 1 ISCDGCDEIAP----WHRYRCLQCTDMDLCK 27 (48)
T ss_pred CCCCCCCCcCC----CceEECCCCCCchhHH
Confidence 46899987432 2455788877776554
No 261
>KOG4118 consensus Uncharacterized conserved protein [Function unknown]
Probab=22.69 E-value=26 Score=23.08 Aligned_cols=35 Identities=17% Similarity=0.397 Sum_probs=22.9
Q ss_pred CCCCCCCCCCccchhHHHHhHHHHHhcCCCChhhh
Q 031240 52 RYTCPVCSKSLWDMSKLWSKIDQEIASTPMPAMYQ 86 (163)
Q Consensus 52 ~~~CPiCr~~~~~~~~~~~~l~~~~~~~~~p~e~~ 86 (163)
.+.|-+|+....+...+.......-..+++|+++.
T Consensus 38 ~~kCtVC~~~mpdpktfkqhfe~kHpk~~~P~eL~ 72 (74)
T KOG4118|consen 38 HHKCTVCMVQMPDPKTFKQHFENKHPKEPLPEELS 72 (74)
T ss_pred HhhhHhhHhhCCCCchHHHHHhhcCCCCCCCHhhc
Confidence 46799998887775555444444444567787764
No 262
>KOG2079 consensus Vacuolar assembly/sorting protein VPS8 [Intracellular trafficking, secretion, and vesicular transport]
Probab=22.36 E-value=59 Score=32.30 Aligned_cols=40 Identities=28% Similarity=0.716 Sum_probs=33.3
Q ss_pred ccccccccccccCcCCccEEecCCChhhHHHHHHHHhcCCCCCC
Q 031240 13 HHNCPICFEFIFDTMKDITVLRCGHTIHLECLKEMEKHYRYTCP 56 (163)
Q Consensus 13 ~~~CpIC~e~l~~s~~~~~~L~CGH~fh~~Cl~~~~~~~~~~CP 56 (163)
..+|.+|.+.|.....+...+.|||.-|.+|...... +||
T Consensus 1133 t~~c~~c~q~~~~h~~~~~Fl~wgh~qh~qc~~~~d~----~c~ 1172 (1206)
T KOG2079|consen 1133 TDDCEICGQKIWAHLDPLLFLAWGHVQHHQCMISVDL----KCP 1172 (1206)
T ss_pred CcchHhhhhhhhccCcchheeeccchhhHHHHHHHhh----cCC
Confidence 4689999999876667777889999999999888764 477
No 263
>COG1545 Predicted nucleic-acid-binding protein containing a Zn-ribbon [General function prediction only]
Probab=22.35 E-value=41 Score=25.01 Aligned_cols=10 Identities=30% Similarity=0.846 Sum_probs=5.4
Q ss_pred ceeeCCCCCC
Q 031240 90 VWILCNDCGA 99 (163)
Q Consensus 90 ~~i~C~dC~~ 99 (163)
.-..|..||.
T Consensus 28 ~g~kC~~CG~ 37 (140)
T COG1545 28 LGTKCKKCGR 37 (140)
T ss_pred EEEEcCCCCe
Confidence 4455666653
No 264
>PRK12496 hypothetical protein; Provisional
Probab=22.33 E-value=73 Score=24.32 Aligned_cols=28 Identities=21% Similarity=0.463 Sum_probs=18.1
Q ss_pred eeCCCCCCCCcccceeeeccCCCCCCCccc
Q 031240 92 ILCNDCGANSHVQFHVIAHKCLSCKSYNTR 121 (163)
Q Consensus 92 i~C~dC~~~~~~~~h~~~~kC~~C~synt~ 121 (163)
..|..|++.....+ -+..|+.|||--.+
T Consensus 128 ~~C~gC~~~~~~~~--~~~~C~~CG~~~~r 155 (164)
T PRK12496 128 KVCKGCKKKYPEDY--PDDVCEICGSPVKR 155 (164)
T ss_pred EECCCCCccccCCC--CCCcCCCCCChhhh
Confidence 44999998664322 22469999975443
No 265
>PF01422 zf-NF-X1: NF-X1 type zinc finger; InterPro: IPR000967 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 domain presumed to be a zinc binding domain. The following pattern describes the zinc finger: C-X(1-6)-H-X-C-X3-C(H/C)-X(3-4)-(H/C)-X(1-10)-C where X can be any amino acid, and numbers in brackets indicate the number of residues. The two position can be either His or Cys. This domain is found in the human transcriptional repressor NK-X1, a repressor of HLA-DRA transcription; the Drosophila shuttle craft protein, which plays an essential role during the late stages of embryonic neurogenesis; and a yeast hypothetical protein YNL023C. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0008270 zinc ion binding, 0006355 regulation of transcription, DNA-dependent, 0005634 nucleus
Probab=22.29 E-value=60 Score=16.27 Aligned_cols=18 Identities=28% Similarity=0.671 Sum_probs=12.6
Q ss_pred CCcceecCCCcccccccc
Q 031240 3 DKHRCVERAMHHNCPICF 20 (163)
Q Consensus 3 ~~H~c~e~s~~~~CpIC~ 20 (163)
.+|+|.+.=-...|+.|.
T Consensus 2 G~H~C~~~CH~G~C~pC~ 19 (20)
T PF01422_consen 2 GNHTCQQLCHPGPCPPCP 19 (20)
T ss_pred CCcccCCcccCCcCCCCC
Confidence 367887766667777775
No 266
>PF12088 DUF3565: Protein of unknown function (DUF3565); InterPro: IPR021948 This family of proteins is functionally uncharacterised. This protein is found in bacteria. Proteins in this family are typically between 30 to 78 amino acids in length. This protein has two conserved sequence motifs: WVA and CGH.
Probab=21.79 E-value=45 Score=21.48 Aligned_cols=14 Identities=43% Similarity=0.793 Sum_probs=11.0
Q ss_pred ccEEecCCChhhHH
Q 031240 29 DITVLRCGHTIHLE 42 (163)
Q Consensus 29 ~~~~L~CGH~fh~~ 42 (163)
-+..|.|||+-|.+
T Consensus 11 WVA~L~CGH~QHvR 24 (61)
T PF12088_consen 11 WVAELSCGHTQHVR 24 (61)
T ss_pred EEEEeccccccccc
Confidence 36789999988765
No 267
>PF12756 zf-C2H2_2: C2H2 type zinc-finger (2 copies); PDB: 2DMI_A.
Probab=21.53 E-value=52 Score=21.62 Aligned_cols=17 Identities=29% Similarity=0.790 Sum_probs=11.3
Q ss_pred CCCCCCCCCccchhHHH
Q 031240 53 YTCPVCSKSLWDMSKLW 69 (163)
Q Consensus 53 ~~CPiCr~~~~~~~~~~ 69 (163)
+.|++|.+.+.+...+.
T Consensus 51 ~~C~~C~~~f~s~~~l~ 67 (100)
T PF12756_consen 51 FRCPYCNKTFRSREALQ 67 (100)
T ss_dssp EEBSSSS-EESSHHHHH
T ss_pred CCCCccCCCCcCHHHHH
Confidence 67999998876654443
No 268
>PHA00616 hypothetical protein
Probab=21.52 E-value=50 Score=19.86 Aligned_cols=17 Identities=18% Similarity=0.487 Sum_probs=12.1
Q ss_pred CCCCCCCCCccchhHHH
Q 031240 53 YTCPVCSKSLWDMSKLW 69 (163)
Q Consensus 53 ~~CPiCr~~~~~~~~~~ 69 (163)
+.||.|.+.+.+.+.+.
T Consensus 2 YqC~~CG~~F~~~s~l~ 18 (44)
T PHA00616 2 YQCLRCGGIFRKKKEVI 18 (44)
T ss_pred CccchhhHHHhhHHHHH
Confidence 67999999876544443
No 269
>PF12874 zf-met: Zinc-finger of C2H2 type; PDB: 1ZU1_A 2KVG_A.
Probab=21.38 E-value=34 Score=16.98 Aligned_cols=13 Identities=31% Similarity=0.715 Sum_probs=9.1
Q ss_pred CCCCCCCCccchh
Q 031240 54 TCPVCSKSLWDMS 66 (163)
Q Consensus 54 ~CPiCr~~~~~~~ 66 (163)
.|.+|++.+.+..
T Consensus 2 ~C~~C~~~f~s~~ 14 (25)
T PF12874_consen 2 YCDICNKSFSSEN 14 (25)
T ss_dssp EETTTTEEESSHH
T ss_pred CCCCCCCCcCCHH
Confidence 5888888776543
No 270
>KOG2231 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=21.14 E-value=68 Score=30.18 Aligned_cols=44 Identities=25% Similarity=0.609 Sum_probs=32.8
Q ss_pred ccccccccccCcCCccEEecCCC-hhhHHHHHHHHhc-C----CCCCCCCCCCc
Q 031240 15 NCPICFEFIFDTMKDITVLRCGH-TIHLECLKEMEKH-Y----RYTCPVCSKSL 62 (163)
Q Consensus 15 ~CpIC~e~l~~s~~~~~~L~CGH-~fh~~Cl~~~~~~-~----~~~CPiCr~~~ 62 (163)
.|+||-.. ..-+..-.||| ..+..|..+...- . ...||+||..+
T Consensus 2 ~c~ic~~s----~~~~~~~s~~h~~v~~~~~~R~~~~~~~~~~~~~~~vcr~~~ 51 (669)
T KOG2231|consen 2 SCAICAFS----PDFVGRGSCGHNEVCATCVVRLRFELNNRKCSNECPVCRREV 51 (669)
T ss_pred CcceeecC----ccccccccccccccchhhhhhhhhhcccccccccCcccccce
Confidence 68999854 34445669999 9999999887532 2 35689999976
No 271
>PRK06393 rpoE DNA-directed RNA polymerase subunit E''; Validated
Probab=21.09 E-value=57 Score=21.26 Aligned_cols=26 Identities=15% Similarity=0.335 Sum_probs=17.2
Q ss_pred eeeCCCCCCCCcccceeeeccCCCCCCCcccc
Q 031240 91 WILCNDCGANSHVQFHVIAHKCLSCKSYNTRQ 122 (163)
Q Consensus 91 ~i~C~dC~~~~~~~~h~~~~kC~~C~synt~~ 122 (163)
...|..|..-.+. .+|+.|||-+|..
T Consensus 5 ~~AC~~C~~i~~~------~~Cp~Cgs~~~S~ 30 (64)
T PRK06393 5 YRACKKCKRLTPE------KTCPVHGDEKTTT 30 (64)
T ss_pred hhhHhhCCcccCC------CcCCCCCCCcCCc
Confidence 3458888765433 3799999965443
No 272
>PF09237 GAGA: GAGA factor; InterPro: IPR015318 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. Members of this entry bind to a 5'-GAGAG-3' DNA consensus binding site, and contain a Cys2-His2 zinc finger core as well as an N-terminal extension containing two highly basic regions. The zinc finger core binds in the DNA major groove and recognises the first three GAG bases of the consensus in a manner similar to that seen in other classical zinc finger-DNA complexes. The second basic region forms a helix that interacts in the major groove recognising the last G of the consensus, while the first basic region wraps around the DNA in the minor groove and recognises the A in the fourth position of the consensus sequence []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; PDB: 1YUI_A 1YUJ_A.
Probab=21.01 E-value=54 Score=20.58 Aligned_cols=12 Identities=33% Similarity=0.974 Sum_probs=6.6
Q ss_pred CCCCCCCCCccc
Q 031240 53 YTCPVCSKSLWD 64 (163)
Q Consensus 53 ~~CPiCr~~~~~ 64 (163)
-+||+|...+..
T Consensus 25 atCP~C~a~~~~ 36 (54)
T PF09237_consen 25 ATCPICGAVIRQ 36 (54)
T ss_dssp EE-TTT--EESS
T ss_pred CCCCcchhhccc
Confidence 469999987754
No 273
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=20.91 E-value=65 Score=23.93 Aligned_cols=10 Identities=40% Similarity=1.221 Sum_probs=5.6
Q ss_pred CCCCCCCCCc
Q 031240 53 YTCPVCSKSL 62 (163)
Q Consensus 53 ~~CPiCr~~~ 62 (163)
|.||.|...+
T Consensus 100 Y~Cp~C~~~y 109 (147)
T smart00531 100 YKCPNCQSKY 109 (147)
T ss_pred EECcCCCCEe
Confidence 4566665554
No 274
>TIGR03830 CxxCG_CxxCG_HTH putative zinc finger/helix-turn-helix protein, YgiT family. This model describes a family of predicted regulatory proteins with a conserved zinc finger/HTH architecture. The amino-terminal region contains a novel domain, featuring two CXXC motifs and occuring in a number of small bacterial proteins as well as in the present family. The carboxyl-terminal region consists of a helix-turn-helix domain, modeled by pfam01381. The predicted function is DNA binding and transcriptional regulation.
Probab=20.78 E-value=64 Score=22.66 Aligned_cols=43 Identities=30% Similarity=0.592 Sum_probs=26.5
Q ss_pred cccccc-cccCcCCccEEecCCChhhHHHHHHHHhcCCCCCCCCCCCccch
Q 031240 16 CPICFE-FIFDTMKDITVLRCGHTIHLECLKEMEKHYRYTCPVCSKSLWDM 65 (163)
Q Consensus 16 CpIC~e-~l~~s~~~~~~L~CGH~fh~~Cl~~~~~~~~~~CPiCr~~~~~~ 65 (163)
||+|.+ .+..........-.|+.+-. ....+.||.|...+.+.
T Consensus 1 C~~C~~~~~~~~~~~~~~~~~G~~~~v-------~~~~~~C~~CGe~~~~~ 44 (127)
T TIGR03830 1 CPICGSGELVRDVKDEPYTYKGESITI-------GVPGWYCPACGEELLDP 44 (127)
T ss_pred CCCCCCccceeeeecceEEEcCEEEEE-------eeeeeECCCCCCEEEcH
Confidence 899983 44444444444567765532 22346799999887553
No 275
>PRK11088 rrmA 23S rRNA methyltransferase A; Provisional
Probab=20.56 E-value=67 Score=25.96 Aligned_cols=26 Identities=15% Similarity=0.383 Sum_probs=15.9
Q ss_pred ccccccccccccCcCCccEEecCCChh
Q 031240 13 HHNCPICFEFIFDTMKDITVLRCGHTI 39 (163)
Q Consensus 13 ~~~CpIC~e~l~~s~~~~~~L~CGH~f 39 (163)
...||||.+.|... .....-..||+|
T Consensus 2 ~~~CP~C~~~l~~~-~~~~~C~~~h~f 27 (272)
T PRK11088 2 SYQCPLCHQPLTLE-ENSWICPQNHQF 27 (272)
T ss_pred cccCCCCCcchhcC-CCEEEcCCCCCC
Confidence 36799999987422 222222447888
No 276
>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=20.55 E-value=47 Score=18.55 Aligned_cols=12 Identities=17% Similarity=0.775 Sum_probs=5.3
Q ss_pred eeeccCCCCCCC
Q 031240 107 VIAHKCLSCKSY 118 (163)
Q Consensus 107 ~~~~kC~~C~sy 118 (163)
+++.+|..||.+
T Consensus 9 l~~~rC~~Cg~~ 20 (37)
T PF12172_consen 9 LLGQRCRDCGRV 20 (37)
T ss_dssp EEEEE-TTT--E
T ss_pred EEEEEcCCCCCE
Confidence 455666666644
No 277
>cd00730 rubredoxin Rubredoxin; nonheme iron binding domains containing a [Fe(SCys)4] center. Rubredoxins are small nonheme iron proteins. The iron atom is coordinated by four cysteine residues (Fe(S-Cys)4), but iron can also be replaced by cobalt, nickel or zinc. They are believed to be involved in electron transfer.
Probab=20.45 E-value=59 Score=19.95 Aligned_cols=11 Identities=36% Similarity=1.072 Sum_probs=8.8
Q ss_pred CCCCCCCCCCC
Q 031240 51 YRYTCPVCSKS 61 (163)
Q Consensus 51 ~~~~CPiCr~~ 61 (163)
..++||+|+.+
T Consensus 33 ~~w~CP~C~a~ 43 (50)
T cd00730 33 DDWVCPVCGAG 43 (50)
T ss_pred CCCCCCCCCCc
Confidence 35899999875
No 278
>COG1571 Predicted DNA-binding protein containing a Zn-ribbon domain [General function prediction only]
Probab=20.44 E-value=59 Score=28.87 Aligned_cols=34 Identities=18% Similarity=0.398 Sum_probs=23.4
Q ss_pred ceeeCCCCCCCCcccceeeeccCCCCC-CCcccccc
Q 031240 90 VWILCNDCGANSHVQFHVIAHKCLSCK-SYNTRQTR 124 (163)
Q Consensus 90 ~~i~C~dC~~~~~~~~h~~~~kC~~C~-synt~~~~ 124 (163)
....|..||..-...=-- |.+|..|| .+++....
T Consensus 349 ~~p~Cp~Cg~~m~S~G~~-g~rC~kCg~~~~~~~~~ 383 (421)
T COG1571 349 VNPVCPRCGGRMKSAGRN-GFRCKKCGTRARETLIK 383 (421)
T ss_pred cCCCCCccCCchhhcCCC-CcccccccccCCccccc
Confidence 456899999754432223 77999999 77776643
No 279
>PRK00464 nrdR transcriptional regulator NrdR; Validated
Probab=20.41 E-value=36 Score=25.92 Aligned_cols=10 Identities=30% Similarity=0.923 Sum_probs=7.0
Q ss_pred CCCCCCCCCc
Q 031240 53 YTCPVCSKSL 62 (163)
Q Consensus 53 ~~CPiCr~~~ 62 (163)
+.||.|..+.
T Consensus 1 m~cp~c~~~~ 10 (154)
T PRK00464 1 MRCPFCGHPD 10 (154)
T ss_pred CcCCCCCCCC
Confidence 3699998653
No 280
>PRK04179 rpl37e 50S ribosomal protein L37e; Reviewed
Probab=20.38 E-value=54 Score=21.23 Aligned_cols=26 Identities=27% Similarity=0.698 Sum_probs=20.6
Q ss_pred cceeeCCCCCCCCcccceeeeccCCCCCC
Q 031240 89 MVWILCNDCGANSHVQFHVIAHKCLSCKS 117 (163)
Q Consensus 89 ~~~i~C~dC~~~~~~~~h~~~~kC~~C~s 117 (163)
...++|.-||.. .||+--..|..||=
T Consensus 15 ~tHt~CrRCG~~---syh~qK~~CasCGy 40 (62)
T PRK04179 15 KTHIRCRRCGRH---SYNVRKKYCAACGF 40 (62)
T ss_pred cccchhcccCcc---cccccccchhhcCC
Confidence 378999999985 56777788988873
No 281
>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=20.36 E-value=55 Score=17.98 Aligned_cols=10 Identities=40% Similarity=1.252 Sum_probs=8.0
Q ss_pred CCCCCCCCCC
Q 031240 52 RYTCPVCSKS 61 (163)
Q Consensus 52 ~~~CPiCr~~ 61 (163)
...||+|..+
T Consensus 17 ~~~CP~Cg~~ 26 (33)
T cd00350 17 PWVCPVCGAP 26 (33)
T ss_pred CCcCcCCCCc
Confidence 4689999875
No 282
>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=20.31 E-value=62 Score=18.41 Aligned_cols=24 Identities=33% Similarity=0.714 Sum_probs=14.5
Q ss_pred ccccccccccCcCCccEEe-cCCCh
Q 031240 15 NCPICFEFIFDTMKDITVL-RCGHT 38 (163)
Q Consensus 15 ~CpIC~e~l~~s~~~~~~L-~CGH~ 38 (163)
.|++|...++.+...-..= .|||.
T Consensus 10 ~C~~C~~~~~~~~dG~~yC~~cG~~ 34 (36)
T PF11781_consen 10 PCPVCGSRWFYSDDGFYYCDRCGHQ 34 (36)
T ss_pred cCCCCCCeEeEccCCEEEhhhCceE
Confidence 3999988765544433333 66764
No 283
>PF01873 eIF-5_eIF-2B: Domain found in IF2B/IF5; InterPro: IPR002735 The beta subunit of archaeal and eukaryotic translation initiation factor 2 (IF2beta) and the N-terminal domain of translation initiation factor 5 (IF5) show significant sequence homology []. Archaeal IF2beta contains two independent structural domains: an N-terminal mixed alpha/beta core domain (topological similarity to the common core of ribosomal proteins L23 and L15e), and a C-terminal domain consisting of a zinc-binding C4 finger []. Archaeal IF2beta is a ribosome-dependent GTPase that stimulates the binding of initiator Met-tRNA(i)(Met) to the ribosomes, even in the absence of other factors []. The C-terminal domain of eukaryotic IF5 is involved in the formation of the multi-factor complex (MFC), an important intermediate for the 43S pre-initiation complex assembly []. IF5 interacts directly with IF1, IF2beta and IF3c, which together with IF2-bound Met-tRNA(i)(Met) form the MFC. This entry represents both the N-terminal and zinc-binding domains of IF2, as well as a domain in IF5.; GO: 0003743 translation initiation factor activity, 0006413 translational initiation; PDB: 2DCU_B 2D74_B 2E9H_A 2G2K_A 1NEE_A 3CW2_L 2QMU_C 3V11_C 2NXU_A 2QN6_C ....
Probab=20.16 E-value=50 Score=24.18 Aligned_cols=27 Identities=30% Similarity=0.805 Sum_probs=15.8
Q ss_pred eeeCCCCCCCCc---ccceeeeccCCCCCC
Q 031240 91 WILCNDCGANSH---VQFHVIAHKCLSCKS 117 (163)
Q Consensus 91 ~i~C~dC~~~~~---~~~h~~~~kC~~C~s 117 (163)
-++|..|+.+.. ..--.+.++|..||+
T Consensus 93 yVlC~~C~spdT~l~k~~r~~~l~C~aCGa 122 (125)
T PF01873_consen 93 YVLCPECGSPDTELIKEGRLIFLKCKACGA 122 (125)
T ss_dssp HSSCTSTSSSSEEEEEETTCCEEEETTTSC
T ss_pred EEEcCCCCCCccEEEEcCCEEEEEecccCC
Confidence 467888876542 111245667887875
Done!