Query 031236
Match_columns 163
No_of_seqs 248 out of 897
Neff 5.3
Searched_HMMs 46136
Date Fri Mar 29 11:13:38 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/031236.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/031236hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF12428 DUF3675: Protein of u 99.9 1.4E-27 3E-32 181.6 6.8 82 74-157 1-84 (118)
2 smart00744 RINGv The RING-vari 99.7 6.9E-19 1.5E-23 114.9 3.1 49 20-69 1-49 (49)
3 PHA02825 LAP/PHD finger-like p 99.7 4.5E-18 9.8E-23 135.0 5.3 61 13-77 3-63 (162)
4 PF12906 RINGv: RING-variant d 99.7 1.6E-18 3.4E-23 112.3 2.0 47 21-68 1-47 (47)
5 PHA02862 5L protein; Provision 99.7 2.1E-17 4.6E-22 129.7 3.5 54 18-75 2-55 (156)
6 KOG1609 Protein involved in mR 99.6 6.6E-18 1.4E-22 141.7 -2.2 143 12-155 72-218 (323)
7 KOG3053 Uncharacterized conser 99.5 4.1E-15 8.9E-20 126.0 3.4 69 12-80 14-89 (293)
8 COG5183 SSM4 Protein involved 99.4 6.2E-14 1.3E-18 133.0 3.2 60 13-73 7-66 (1175)
9 PF13639 zf-RING_2: Ring finge 98.7 7.5E-09 1.6E-13 65.0 2.2 44 19-69 1-44 (44)
10 KOG4628 Predicted E3 ubiquitin 98.5 1.4E-07 3.1E-12 83.3 4.8 52 19-76 230-281 (348)
11 COG5243 HRD1 HRD ubiquitin lig 98.3 1.6E-06 3.5E-11 77.6 5.9 59 16-81 285-353 (491)
12 COG5540 RING-finger-containing 98.1 1.8E-06 4E-11 75.5 3.5 52 16-73 321-372 (374)
13 PF12678 zf-rbx1: RING-H2 zinc 98.1 3.7E-06 8.1E-11 58.6 3.8 45 18-69 19-73 (73)
14 PHA02929 N1R/p28-like protein; 98.0 4.8E-06 1E-10 70.4 3.5 51 17-74 173-228 (238)
15 cd00162 RING RING-finger (Real 97.9 1.5E-05 3.2E-10 47.9 2.9 44 20-71 1-44 (45)
16 PF12861 zf-Apc11: Anaphase-pr 97.9 1.4E-05 3E-10 58.0 3.3 54 17-74 20-83 (85)
17 PF11793 FANCL_C: FANCL C-term 97.7 9.1E-06 2E-10 56.4 0.8 54 18-74 2-67 (70)
18 PF13920 zf-C3HC4_3: Zinc fing 97.7 2.9E-05 6.4E-10 49.8 2.8 46 18-73 2-48 (50)
19 smart00184 RING Ring finger. E 97.6 6.9E-05 1.5E-09 43.3 2.8 39 21-68 1-39 (39)
20 PLN03208 E3 ubiquitin-protein 97.5 7.4E-05 1.6E-09 61.5 3.5 49 16-72 16-78 (193)
21 PF00097 zf-C3HC4: Zinc finger 97.5 6.4E-05 1.4E-09 45.9 2.4 41 21-68 1-41 (41)
22 COG5219 Uncharacterized conser 97.5 1.5E-05 3.3E-10 78.1 -1.6 60 12-74 1463-1524(1525)
23 PHA02926 zinc finger-like prot 97.4 0.00016 3.5E-09 61.0 3.3 54 17-75 169-232 (242)
24 KOG0802 E3 ubiquitin ligase [P 97.3 0.00013 2.8E-09 67.6 2.3 49 17-72 290-340 (543)
25 KOG0317 Predicted E3 ubiquitin 97.1 0.00049 1.1E-08 59.7 3.7 53 12-74 233-285 (293)
26 PF13923 zf-C3HC4_2: Zinc fing 97.1 0.00035 7.7E-09 42.6 1.8 38 21-68 1-39 (39)
27 PF14634 zf-RING_5: zinc-RING 97.0 0.00049 1.1E-08 43.2 2.2 44 20-70 1-44 (44)
28 KOG0828 Predicted E3 ubiquitin 96.8 0.00076 1.6E-08 62.6 2.8 58 10-73 563-634 (636)
29 KOG1493 Anaphase-promoting com 96.8 0.00035 7.5E-09 50.1 0.2 52 19-74 21-82 (84)
30 smart00504 Ubox Modified RING 96.5 0.0038 8.2E-08 40.9 3.5 44 20-73 3-46 (63)
31 KOG0827 Predicted E3 ubiquitin 96.4 0.0019 4.1E-08 58.4 2.3 46 18-69 4-52 (465)
32 COG5194 APC11 Component of SCF 96.0 0.0059 1.3E-07 44.2 2.8 27 46-74 56-82 (88)
33 KOG0823 Predicted E3 ubiquitin 95.9 0.011 2.4E-07 49.9 4.4 50 15-72 44-94 (230)
34 PF13445 zf-RING_UBOX: RING-ty 95.7 0.0083 1.8E-07 38.1 2.2 41 21-66 1-43 (43)
35 KOG1734 Predicted RING-contain 95.6 0.0035 7.5E-08 54.5 0.2 61 9-74 215-282 (328)
36 TIGR00599 rad18 DNA repair pro 95.4 0.0092 2E-07 54.0 2.3 49 16-74 24-72 (397)
37 KOG0804 Cytoplasmic Zn-finger 95.0 0.0083 1.8E-07 55.1 0.6 47 16-71 173-220 (493)
38 PF15227 zf-C3HC4_4: zinc fing 94.2 0.029 6.2E-07 35.1 1.6 40 21-68 1-42 (42)
39 KOG1785 Tyrosine kinase negati 93.9 0.018 4E-07 52.6 0.4 48 18-73 369-416 (563)
40 KOG4445 Uncharacterized conser 93.8 0.034 7.5E-07 49.1 1.8 53 17-74 114-187 (368)
41 KOG4265 Predicted E3 ubiquitin 93.1 0.093 2E-06 46.8 3.5 50 14-73 286-336 (349)
42 PF05883 Baculo_RING: Baculovi 93.1 0.046 9.9E-07 42.8 1.3 42 17-60 25-69 (134)
43 PF14570 zf-RING_4: RING/Ubox 92.8 0.087 1.9E-06 34.4 2.1 46 21-73 1-48 (48)
44 KOG2930 SCF ubiquitin ligase, 92.6 0.056 1.2E-06 40.9 1.2 27 46-74 83-109 (114)
45 KOG1645 RING-finger-containing 92.4 0.12 2.6E-06 47.2 3.2 53 17-73 3-56 (463)
46 PLN02189 cellulose synthase 91.9 0.23 4.9E-06 49.9 4.7 67 4-74 18-88 (1040)
47 TIGR00570 cdk7 CDK-activating 91.5 0.18 4E-06 44.3 3.3 51 18-74 3-55 (309)
48 PLN02436 cellulose synthase A 91.2 0.29 6.3E-06 49.3 4.7 68 3-74 17-90 (1094)
49 KOG0320 Predicted E3 ubiquitin 91.2 0.18 3.9E-06 41.4 2.7 49 16-72 129-177 (187)
50 KOG0825 PHD Zn-finger protein 90.8 0.055 1.2E-06 53.0 -0.7 27 46-74 146-172 (1134)
51 PF04564 U-box: U-box domain; 90.3 0.23 4.9E-06 34.2 2.2 47 19-74 5-51 (73)
52 KOG2177 Predicted E3 ubiquitin 89.3 0.15 3.3E-06 40.1 0.8 45 16-70 11-55 (386)
53 KOG1002 Nucleotide excision re 87.0 0.41 8.8E-06 45.5 2.2 58 15-80 533-593 (791)
54 PLN02400 cellulose synthase 86.8 0.82 1.8E-05 46.3 4.2 68 3-74 17-90 (1085)
55 KOG1941 Acetylcholine receptor 86.4 0.34 7.4E-06 44.4 1.3 48 18-70 365-413 (518)
56 PF14569 zf-UDP: Zinc-binding 86.2 0.93 2E-05 32.6 3.2 55 17-75 8-64 (80)
57 COG5432 RAD18 RING-finger-cont 86.0 0.41 9E-06 42.4 1.6 47 17-73 24-70 (391)
58 PF05290 Baculo_IE-1: Baculovi 85.3 0.66 1.4E-05 36.5 2.2 54 18-74 80-133 (140)
59 PLN02195 cellulose synthase A 84.5 1.1 2.5E-05 44.8 4.0 53 17-73 5-59 (977)
60 KOG1039 Predicted E3 ubiquitin 84.3 0.83 1.8E-05 40.8 2.7 52 16-72 159-220 (344)
61 KOG1428 Inhibitor of type V ad 83.9 0.98 2.1E-05 47.7 3.2 55 14-73 3482-3544(3738)
62 KOG0287 Postreplication repair 83.6 0.43 9.3E-06 43.0 0.6 46 18-73 23-68 (442)
63 PLN02638 cellulose synthase A 82.4 1.7 3.7E-05 44.0 4.3 54 17-74 16-71 (1079)
64 PF10367 Vps39_2: Vacuolar sor 82.3 0.59 1.3E-05 33.1 0.8 33 17-55 77-109 (109)
65 PF10272 Tmpp129: Putative tra 81.7 1.3 2.8E-05 39.8 2.9 33 37-72 307-350 (358)
66 COG5574 PEX10 RING-finger-cont 81.0 1.7 3.7E-05 37.7 3.3 49 15-72 212-261 (271)
67 PF08746 zf-RING-like: RING-li 79.2 1.4 3E-05 27.7 1.6 23 46-68 21-43 (43)
68 PLN02915 cellulose synthase A 78.6 2.4 5.3E-05 42.8 3.9 56 15-74 12-69 (1044)
69 KOG2164 Predicted E3 ubiquitin 76.1 2.5 5.4E-05 39.7 3.0 49 18-74 186-237 (513)
70 KOG1952 Transcription factor N 72.2 3.7 8E-05 40.9 3.2 55 15-73 188-247 (950)
71 PF14447 Prok-RING_4: Prokaryo 71.1 3.6 7.7E-05 27.7 2.1 46 18-75 7-52 (55)
72 PF07800 DUF1644: Protein of u 69.4 6.9 0.00015 31.6 3.8 42 17-60 1-49 (162)
73 KOG1940 Zn-finger protein [Gen 65.2 3.1 6.6E-05 36.2 1.0 43 21-70 161-204 (276)
74 PLN02248 cellulose synthase-li 63.3 22 0.00048 36.6 6.6 35 35-74 144-178 (1135)
75 COG5236 Uncharacterized conser 61.6 10 0.00023 34.5 3.7 55 12-74 55-109 (493)
76 KOG4172 Predicted E3 ubiquitin 61.3 4.9 0.00011 27.4 1.2 47 18-73 7-54 (62)
77 KOG3899 Uncharacterized conser 60.7 5 0.00011 35.7 1.6 31 40-73 324-365 (381)
78 smart00782 PhnA_Zn_Ribbon PhnA 57.1 9.4 0.0002 24.7 2.0 24 59-82 4-28 (47)
79 PF05191 ADK_lid: Adenylate ki 56.4 5.4 0.00012 24.3 0.7 19 63-81 2-20 (36)
80 KOG3268 Predicted E3 ubiquitin 53.6 14 0.0003 30.8 3.0 28 46-73 192-228 (234)
81 KOG2879 Predicted E3 ubiquitin 52.6 17 0.00037 31.9 3.4 51 16-73 237-287 (298)
82 PF03854 zf-P11: P-11 zinc fin 52.1 10 0.00022 25.0 1.6 27 46-74 21-47 (50)
83 COG5175 MOT2 Transcriptional r 50.1 12 0.00027 34.0 2.3 59 8-73 4-64 (480)
84 KOG1100 Predicted E3 ubiquitin 48.3 8.2 0.00018 32.0 0.8 39 19-71 159-198 (207)
85 PF01440 Gemini_AL2: Geminivir 45.0 3.6 7.8E-05 32.2 -1.7 33 34-69 32-64 (134)
86 KOG3970 Predicted E3 ubiquitin 44.2 28 0.00061 30.1 3.4 53 15-73 47-105 (299)
87 KOG4692 Predicted E3 ubiquitin 44.2 15 0.00033 33.6 1.9 48 16-73 420-467 (489)
88 PF04532 DUF587: Protein of un 43.8 7.1 0.00015 32.7 -0.2 29 24-52 93-122 (215)
89 PF10215 Ost4: Oligosaccaryltr 42.4 32 0.0007 21.0 2.6 24 135-158 9-32 (35)
90 KOG0956 PHD finger protein AF1 41.6 17 0.00036 35.9 1.9 58 17-74 116-183 (900)
91 PF13894 zf-C2H2_4: C2H2-type 41.0 12 0.00025 18.9 0.5 11 64-74 2-12 (24)
92 KOG0824 Predicted E3 ubiquitin 40.3 18 0.0004 32.1 1.8 53 16-77 5-57 (324)
93 COG5152 Uncharacterized conser 38.6 19 0.00042 30.5 1.6 42 20-71 198-239 (259)
94 KOG0802 E3 ubiquitin ligase [P 38.3 14 0.0003 34.5 0.8 46 16-75 477-522 (543)
95 PF04641 Rtf2: Rtf2 RING-finge 37.5 45 0.00097 28.1 3.7 51 15-73 110-161 (260)
96 PF00096 zf-C2H2: Zinc finger, 36.8 14 0.0003 19.1 0.4 11 64-74 2-12 (23)
97 KOG2068 MOT2 transcription fac 36.2 37 0.00081 30.3 3.1 53 17-75 248-300 (327)
98 PHA03375 hypothetical protein; 36.0 12 0.00027 36.7 0.1 29 24-52 99-128 (844)
99 PF10795 DUF2607: Protein of u 35.9 37 0.0008 25.3 2.6 19 135-154 11-29 (99)
100 KOG4443 Putative transcription 35.7 23 0.0005 34.5 1.8 33 35-69 34-75 (694)
101 KOG0978 E3 ubiquitin ligase in 34.7 17 0.00038 35.5 0.8 48 18-74 643-690 (698)
102 PF00301 Rubredoxin: Rubredoxi 33.7 22 0.00048 22.9 1.0 17 63-79 2-18 (47)
103 KOG1814 Predicted E3 ubiquitin 33.7 29 0.00063 32.1 2.1 47 18-69 184-236 (445)
104 PF13956 Ibs_toxin: Toxin Ibs, 33.4 23 0.00051 18.8 0.8 11 140-150 4-14 (19)
105 PF04423 Rad50_zn_hook: Rad50 32.6 29 0.00063 22.2 1.4 21 53-73 9-31 (54)
106 PF05715 zf-piccolo: Piccolo Z 32.1 30 0.00064 23.7 1.4 18 62-79 2-19 (61)
107 PF10571 UPF0547: Uncharacteri 31.7 23 0.00051 20.0 0.7 13 61-73 13-25 (26)
108 smart00249 PHD PHD zinc finger 31.6 15 0.00034 21.3 -0.0 28 20-53 1-29 (47)
109 KOG4159 Predicted E3 ubiquitin 31.4 32 0.00068 31.5 1.9 47 17-73 83-129 (398)
110 PF02891 zf-MIZ: MIZ/SP-RING z 30.4 36 0.00079 21.8 1.6 35 34-71 11-50 (50)
111 PTZ00382 Variant-specific surf 28.4 33 0.00071 25.0 1.2 16 140-155 77-92 (96)
112 KOG3039 Uncharacterized conser 28.3 55 0.0012 28.6 2.7 50 17-73 220-270 (303)
113 PF13878 zf-C2H2_3: zinc-finge 27.4 36 0.00077 21.0 1.1 15 61-75 12-26 (41)
114 KOG0955 PHD finger protein BR1 27.0 23 0.0005 36.2 0.3 51 16-70 217-268 (1051)
115 PF14446 Prok-RING_1: Prokaryo 26.4 97 0.0021 20.7 3.1 47 17-73 4-52 (54)
116 PF11789 zf-Nse: Zinc-finger o 25.9 42 0.00092 22.1 1.3 43 18-67 11-53 (57)
117 PF00628 PHD: PHD-finger; Int 24.9 23 0.00051 21.8 -0.1 44 20-69 1-49 (51)
118 PF12907 zf-met2: Zinc-binding 24.9 18 0.00039 22.7 -0.6 12 62-73 1-12 (40)
119 cd00730 rubredoxin Rubredoxin; 24.8 57 0.0012 21.2 1.7 17 63-79 2-18 (50)
120 PF13913 zf-C2HC_2: zinc-finge 24.8 32 0.00069 19.0 0.5 12 63-74 3-14 (25)
121 PF10497 zf-4CXXC_R1: Zinc-fin 24.4 1.3E+02 0.0027 22.3 3.8 51 16-70 5-69 (105)
122 PF15353 HECA: Headcase protei 22.9 48 0.001 25.1 1.3 14 46-59 42-55 (107)
123 PF01363 FYVE: FYVE zinc finge 21.7 24 0.00052 23.3 -0.5 20 55-74 2-21 (69)
124 PF12874 zf-met: Zinc-finger o 20.5 41 0.00089 17.6 0.4 10 64-73 2-11 (25)
125 PF13912 zf-C2H2_6: C2H2-type 20.2 42 0.00091 17.9 0.4 11 64-74 3-13 (27)
126 PLN02294 cytochrome c oxidase 20.0 27 0.00059 28.6 -0.6 27 56-82 135-161 (174)
No 1
>PF12428 DUF3675: Protein of unknown function (DUF3675) ; InterPro: IPR022143 This domain family is found in eukaryotes, and is approximately 120 amino acids in length. The family is found in association with PF00097 from PFAM. There are two completely conserved residues (R and L) that may be functionally important.
Probab=99.94 E-value=1.4e-27 Score=181.57 Aligned_cols=82 Identities=44% Similarity=0.644 Sum_probs=76.8
Q ss_pred CCccCCCCCccchhhceeccccCccccccCCCCCchhHHHH--hhhhccCCCCcccCCCCCCchhHHHHHHHHHHHHHHh
Q 031236 74 PGYTAPSKKSQLIEAAVTIRDSLQIPRREHVPRNPRLVAIA--ERLSAESHYPQCSSAAGRTAACCRSLALTVRFLFCEW 151 (163)
Q Consensus 74 ~~y~~p~~~~~~~~~~i~i~~~~~~~r~~~~~~~~~~~a~~--~~~~~~~~~~~~~~~~~~~~~~CR~~ai~lm~lLll~ 151 (163)
|+||+|||+.+.++++|+||++|+++|+ |++|+|++||+ |++++|+||+||+++++||++||||+|||||+|||||
T Consensus 1 PgYTaPp~~~~~~~~~i~ir~~we~~~~--d~~~~~~~a~~~ae~~~l~~~y~e~~~~~~~~a~~CRsvAli~m~LLllR 78 (118)
T PF12428_consen 1 PGYTAPPKKFQPGETAIDIRGNWEISRR--DLRDPRFLAMAAAERQFLESEYDEYAASNTRGAACCRSVALIFMVLLLLR 78 (118)
T ss_pred CCCCCCCCCCCcCccceEecCCcccccc--CccchhhhhhhhhhhhccccccccccccCCCceeHHHHHHHHHHHHHHHH
Confidence 6899999999999999999999997665 78999999995 6899999999999999999999999999999999999
Q ss_pred hhhhhe
Q 031236 152 SSYRVS 157 (163)
Q Consensus 152 h~l~~~ 157 (163)
|++.+-
T Consensus 79 hal~l~ 84 (118)
T PF12428_consen 79 HALALV 84 (118)
T ss_pred HHHHHh
Confidence 999864
No 2
>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=99.75 E-value=6.9e-19 Score=114.86 Aligned_cols=49 Identities=49% Similarity=1.249 Sum_probs=44.2
Q ss_pred eeeEcccCcccCCCceeecccCCCCCceecHHHHHHHHHHhCCccccCcc
Q 031236 20 HCRICHEEEFESCNSLEAPCACSGTVKFAHRDCIQRWCYEKGNTTCEICL 69 (163)
Q Consensus 20 ~CRIC~~~~~~~~~~l~~PC~C~Gsl~~vH~~CL~~Wl~~k~~~~CeiCk 69 (163)
+||||++++ ++++++++||+|+||++|||++||++|+.++++.+||+|+
T Consensus 1 ~CrIC~~~~-~~~~~l~~PC~C~G~~~~vH~~Cl~~W~~~~~~~~C~iC~ 49 (49)
T smart00744 1 ICRICHDEG-DEGDPLVSPCRCKGSLKYVHQECLERWINESGNKTCEICK 49 (49)
T ss_pred CccCCCCCC-CCCCeeEeccccCCchhHHHHHHHHHHHHHcCCCcCCCCC
Confidence 599999933 3457899999999999999999999999999999999996
No 3
>PHA02825 LAP/PHD finger-like protein; Provisional
Probab=99.72 E-value=4.5e-18 Score=135.03 Aligned_cols=61 Identities=25% Similarity=0.613 Sum_probs=53.5
Q ss_pred CCCCCCCeeeEcccCcccCCCceeecccCCCCCceecHHHHHHHHHHhCCccccCccccccCCcc
Q 031236 13 SNPETTSHCRICHEEEFESCNSLEAPCACSGTVKFAHRDCIQRWCYEKGNTTCEICLQEYGPGYT 77 (163)
Q Consensus 13 ~~s~~~~~CRIC~~~~~~~~~~l~~PC~C~Gsl~~vH~~CL~~Wl~~k~~~~CeiCk~~y~~~y~ 77 (163)
+.+..++.||||++++. .+.+||+|+||++|+|++||++|++.+++..||+|+++|++...
T Consensus 3 ~~s~~~~~CRIC~~~~~----~~~~PC~CkGs~k~VH~sCL~rWi~~s~~~~CeiC~~~Y~i~~~ 63 (162)
T PHA02825 3 DVSLMDKCCWICKDEYD----VVTNYCNCKNENKIVHKECLEEWINTSKNKSCKICNGPYNIKKN 63 (162)
T ss_pred CcCCCCCeeEecCCCCC----CccCCcccCCCchHHHHHHHHHHHhcCCCCcccccCCeEEEEEe
Confidence 34567899999998854 25789999999999999999999999999999999999987643
No 4
>PF12906 RINGv: RING-variant domain; PDB: 2D8S_A 1VYX_A.
Probab=99.72 E-value=1.6e-18 Score=112.29 Aligned_cols=47 Identities=53% Similarity=1.220 Sum_probs=38.5
Q ss_pred eeEcccCcccCCCceeecccCCCCCceecHHHHHHHHHHhCCccccCc
Q 031236 21 CRICHEEEFESCNSLEAPCACSGTVKFAHRDCIQRWCYEKGNTTCEIC 68 (163)
Q Consensus 21 CRIC~~~~~~~~~~l~~PC~C~Gsl~~vH~~CL~~Wl~~k~~~~CeiC 68 (163)
||||++++++++ +|++||+|+||++|||++||++|+.++++.+||+|
T Consensus 1 CrIC~~~~~~~~-~li~pC~C~Gs~~~vH~~CL~~W~~~~~~~~C~~C 47 (47)
T PF12906_consen 1 CRICLEGEEEDE-PLISPCRCKGSMKYVHRSCLERWIRESGNRKCEIC 47 (47)
T ss_dssp ETTTTEE-SSSS--EE-SSS-SSCCGSEECCHHHHHHHHHT-SB-TTT
T ss_pred CeEeCCcCCCCC-ceecccccCCCcchhHHHHHHHHHHhcCCCcCCCC
Confidence 899999987654 89999999999999999999999999999999998
No 5
>PHA02862 5L protein; Provisional
Probab=99.68 E-value=2.1e-17 Score=129.67 Aligned_cols=54 Identities=26% Similarity=0.639 Sum_probs=48.6
Q ss_pred CCeeeEcccCcccCCCceeecccCCCCCceecHHHHHHHHHHhCCccccCccccccCC
Q 031236 18 TSHCRICHEEEFESCNSLEAPCACSGTVKFAHRDCIQRWCYEKGNTTCEICLQEYGPG 75 (163)
Q Consensus 18 ~~~CRIC~~~~~~~~~~l~~PC~C~Gsl~~vH~~CL~~Wl~~k~~~~CeiCk~~y~~~ 75 (163)
...||||++++++. .+||+|+||+||||++||++|++.+++..||+|+++|.+.
T Consensus 2 ~diCWIC~~~~~e~----~~PC~C~GS~K~VHq~CL~~WIn~S~k~~CeLCkteY~Ik 55 (156)
T PHA02862 2 SDICWICNDVCDER----NNFCGCNEEYKVVHIKCMQLWINYSKKKECNLCKTKYNIK 55 (156)
T ss_pred CCEEEEecCcCCCC----cccccccCcchhHHHHHHHHHHhcCCCcCccCCCCeEEEE
Confidence 46899999987542 6999999999999999999999999999999999999753
No 6
>KOG1609 consensus Protein involved in mRNA turnover and stability [RNA processing and modification]
Probab=99.65 E-value=6.6e-18 Score=141.70 Aligned_cols=143 Identities=24% Similarity=0.306 Sum_probs=101.3
Q ss_pred CCCCCCCCeeeEcccCcccCCC-ceeecccCCCCCceecHHHHHHHHHHhCCccccCccccccCCccCCCCCccchhhce
Q 031236 12 KSNPETTSHCRICHEEEFESCN-SLEAPCACSGTVKFAHRDCIQRWCYEKGNTTCEICLQEYGPGYTAPSKKSQLIEAAV 90 (163)
Q Consensus 12 ~~~s~~~~~CRIC~~~~~~~~~-~l~~PC~C~Gsl~~vH~~CL~~Wl~~k~~~~CeiCk~~y~~~y~~p~~~~~~~~~~i 90 (163)
...+.++..||||+++.++... .++.||.|+|+++++|+.|+++|+..|++..||+|++.|...++.+++...+....+
T Consensus 72 ~~~~~~~~~cRIc~~~~~~~~~~~l~~pC~C~g~l~~vH~~cl~~W~~~~~~~~CeiC~~~~~~~~~~~~~~~~~~~~~~ 151 (323)
T KOG1609|consen 72 EESPSSGPICRICHEEDEESNGLLLISPCSCKGSLAYVHRSCLEKWFSIKGNITCEICKSFFINVGTKLKPLIVISKVRS 151 (323)
T ss_pred ccCCCCCCcEEEEecccccccccccccCccccCcHHHHHHHHHHhhhccccCeeeecccccceecceeecceeehhhhhh
Confidence 3344446899999998765422 689999999999999999999999999999999999999998888777766555555
Q ss_pred eccccCccccccCCCCCchhHHHH--hhhhccCCCCcccCCCCCCchhHHHHH-HHHHHHHHHhhhhh
Q 031236 91 TIRDSLQIPRREHVPRNPRLVAIA--ERLSAESHYPQCSSAAGRTAACCRSLA-LTVRFLFCEWSSYR 155 (163)
Q Consensus 91 ~i~~~~~~~r~~~~~~~~~~~a~~--~~~~~~~~~~~~~~~~~~~~~~CR~~a-i~lm~lLll~h~l~ 155 (163)
...+.|...+. ....+...+++. ...++...+++.....+.++..+++.+ ..++++.+.++.+.
T Consensus 152 ~~~~~~~~~~~-~~~~~~~~~~i~~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~ 218 (323)
T KOG1609|consen 152 GALSERTLSGM-ILLKVALLVAIIVSVLPLLLGLLFELVLGVPSLVVESPLANPLALVALGLLGFKIW 218 (323)
T ss_pred Hhhhheeeehh-hhhhhhhhheeeEEeehhhhhhhHHHhccccccccCCCccCchhheeecceechHH
Confidence 45555555442 123444444432 355666666666666666667777766 66666666555443
No 7
>KOG3053 consensus Uncharacterized conserved protein [Function unknown]
Probab=99.53 E-value=4.1e-15 Score=126.03 Aligned_cols=69 Identities=30% Similarity=0.673 Sum_probs=58.5
Q ss_pred CCCCCCCCeeeEcccCcccCCC-ceeecccCCCCCceecHHHHHHHHHHhC------CccccCccccccCCccCCC
Q 031236 12 KSNPETTSHCRICHEEEFESCN-SLEAPCACSGTVKFAHRDCIQRWCYEKG------NTTCEICLQEYGPGYTAPS 80 (163)
Q Consensus 12 ~~~s~~~~~CRIC~~~~~~~~~-~l~~PC~C~Gsl~~vH~~CL~~Wl~~k~------~~~CeiCk~~y~~~y~~p~ 80 (163)
.++.+.++.||||+..++|... .++.||.|+||.|+||+.||.+|+.+|. ...|++|+++|.+.++...
T Consensus 14 ~~~~e~eR~CWiCF~TdeDn~~a~WV~PCrCRGt~KWVHqsCL~rWiDEK~~~n~~q~V~C~QCqTEYiiv~P~l~ 89 (293)
T KOG3053|consen 14 SDNQELERCCWICFATDEDNRLAAWVHPCRCRGTTKWVHQSCLSRWIDEKQRGNPLQTVSCPQCQTEYIIVFPQLG 89 (293)
T ss_pred CCccccceeEEEEeccCcccchhhhcccccccCccHHHHHHHHHHHHhHHhcCCCCceeechhhcchheeeccccC
Confidence 4556788999999999877533 3899999999999999999999999883 4789999999998875443
No 8
>COG5183 SSM4 Protein involved in mRNA turnover and stability [RNA processing and modification]
Probab=99.42 E-value=6.2e-14 Score=133.00 Aligned_cols=60 Identities=38% Similarity=0.937 Sum_probs=53.7
Q ss_pred CCCCCCCeeeEcccCcccCCCceeecccCCCCCceecHHHHHHHHHHhCCccccCcccccc
Q 031236 13 SNPETTSHCRICHEEEFESCNSLEAPCACSGTVKFAHRDCIQRWCYEKGNTTCEICLQEYG 73 (163)
Q Consensus 13 ~~s~~~~~CRIC~~~~~~~~~~l~~PC~C~Gsl~~vH~~CL~~Wl~~k~~~~CeiCk~~y~ 73 (163)
...++...||||+.++.+ ++++.+||+|+||+||+|++||..|+..+++++|+||+++|+
T Consensus 7 ~mN~d~~~CRICr~e~~~-d~pLfhPCKC~GSIkYiH~eCL~eW~~~s~~~kCdiChy~~~ 66 (1175)
T COG5183 7 PMNEDKRSCRICRTEDIR-DDPLFHPCKCSGSIKYIHRECLMEWMECSGTKKCDICHYEYK 66 (1175)
T ss_pred CCCccchhceeecCCCCC-CCcCcccccccchhHHHHHHHHHHHHhcCCCcceeeecceee
Confidence 344567899999998765 468999999999999999999999999999999999999875
No 9
>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=98.71 E-value=7.5e-09 Score=64.95 Aligned_cols=44 Identities=32% Similarity=0.833 Sum_probs=35.8
Q ss_pred CeeeEcccCcccCCCceeecccCCCCCceecHHHHHHHHHHhCCccccCcc
Q 031236 19 SHCRICHEEEFESCNSLEAPCACSGTVKFAHRDCIQRWCYEKGNTTCEICL 69 (163)
Q Consensus 19 ~~CRIC~~~~~~~~~~l~~PC~C~Gsl~~vH~~CL~~Wl~~k~~~~CeiCk 69 (163)
.+|.||+++..+++.....||+ |.+|.+|+++|++.+ .+||+|+
T Consensus 1 d~C~IC~~~~~~~~~~~~l~C~-----H~fh~~Ci~~~~~~~--~~CP~CR 44 (44)
T PF13639_consen 1 DECPICLEEFEDGEKVVKLPCG-----HVFHRSCIKEWLKRN--NSCPVCR 44 (44)
T ss_dssp -CETTTTCBHHTTSCEEEETTS-----EEEEHHHHHHHHHHS--SB-TTTH
T ss_pred CCCcCCChhhcCCCeEEEccCC-----CeeCHHHHHHHHHhC--CcCCccC
Confidence 3699999998766666788876 999999999999764 5999996
No 10
>KOG4628 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=98.48 E-value=1.4e-07 Score=83.33 Aligned_cols=52 Identities=25% Similarity=0.576 Sum_probs=44.9
Q ss_pred CeeeEcccCcccCCCceeecccCCCCCceecHHHHHHHHHHhCCccccCccccccCCc
Q 031236 19 SHCRICHEEEFESCNSLEAPCACSGTVKFAHRDCIQRWCYEKGNTTCEICLQEYGPGY 76 (163)
Q Consensus 19 ~~CRIC~~~~~~~~~~l~~PC~C~Gsl~~vH~~CL~~Wl~~k~~~~CeiCk~~y~~~y 76 (163)
..|-||+|++.+++..-+.||+ |.+|..|+..|+... .+.||+||+.....-
T Consensus 230 ~~CaIClEdY~~GdklRiLPC~-----H~FH~~CIDpWL~~~-r~~CPvCK~di~~~~ 281 (348)
T KOG4628|consen 230 DTCAICLEDYEKGDKLRILPCS-----HKFHVNCIDPWLTQT-RTFCPVCKRDIRTDS 281 (348)
T ss_pred ceEEEeecccccCCeeeEecCC-----CchhhccchhhHhhc-CccCCCCCCcCCCCC
Confidence 6999999999988877799999 999999999999865 567999999765433
No 11
>COG5243 HRD1 HRD ubiquitin ligase complex, ER membrane component [Posttranslational modification, protein turnover, chaperones]
Probab=98.25 E-value=1.6e-06 Score=77.64 Aligned_cols=59 Identities=25% Similarity=0.647 Sum_probs=44.4
Q ss_pred CCCCeeeEcccCcccC----------CCceeecccCCCCCceecHHHHHHHHHHhCCccccCccccccCCccCCCC
Q 031236 16 ETTSHCRICHEEEFES----------CNSLEAPCACSGTVKFAHRDCIQRWCYEKGNTTCEICLQEYGPGYTAPSK 81 (163)
Q Consensus 16 ~~~~~CRIC~~~~~~~----------~~~l~~PC~C~Gsl~~vH~~CL~~Wl~~k~~~~CeiCk~~y~~~y~~p~~ 81 (163)
.++..|-||.++--.+ ..+-..||+ |..|-.||+.|++ ++.+||||+.+.-+.-..|-+
T Consensus 285 n~D~~C~ICmde~~h~~~~~~~~~~~~~pKrLpCG-----HilHl~CLknW~E--RqQTCPICr~p~ifd~~~~~~ 353 (491)
T COG5243 285 NSDRTCTICMDEMFHPDHEPLPRGLDMTPKRLPCG-----HILHLHCLKNWLE--RQQTCPICRRPVIFDQSSPTP 353 (491)
T ss_pred CCCCeEEEecccccCCCCccCcccccCCccccccc-----ceeeHHHHHHHHH--hccCCCcccCccccccCCCCc
Confidence 4678999999983221 245688999 9999999999995 567999999886554444443
No 12
>COG5540 RING-finger-containing ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=98.13 E-value=1.8e-06 Score=75.48 Aligned_cols=52 Identities=19% Similarity=0.532 Sum_probs=43.6
Q ss_pred CCCCeeeEcccCcccCCCceeecccCCCCCceecHHHHHHHHHHhCCccccCcccccc
Q 031236 16 ETTSHCRICHEEEFESCNSLEAPCACSGTVKFAHRDCIQRWCYEKGNTTCEICLQEYG 73 (163)
Q Consensus 16 ~~~~~CRIC~~~~~~~~~~l~~PC~C~Gsl~~vH~~CL~~Wl~~k~~~~CeiCk~~y~ 73 (163)
+.+.+|.||.+..-..+..+++||+ |-+|..|+.+|+.- ....||.|+++.+
T Consensus 321 ~~GveCaICms~fiK~d~~~vlPC~-----H~FH~~Cv~kW~~~-y~~~CPvCrt~iP 372 (374)
T COG5540 321 DKGVECAICMSNFIKNDRLRVLPCD-----HRFHVGCVDKWLLG-YSNKCPVCRTAIP 372 (374)
T ss_pred CCCceEEEEhhhhcccceEEEeccC-----ceechhHHHHHHhh-hcccCCccCCCCC
Confidence 4569999999988766667899999 99999999999962 3468999997754
No 13
>PF12678 zf-rbx1: RING-H2 zinc finger; InterPro: IPR024766 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This domain constitutes a conserved region found in proteins that participate in diverse functions relevant to chromosome metabolism and cell cycle control [].The domain contains 8 cysteine/ histidine residues which are proposed to be the conserved residues involved in zinc binding.; PDB: 4A0C_D 4A0L_I 4A0K_B 2ECL_A 1LDK_C 3RTR_F 3DQV_Y 1U6G_B 1LDJ_B 2HYE_D ....
Probab=98.09 E-value=3.7e-06 Score=58.58 Aligned_cols=45 Identities=31% Similarity=0.745 Sum_probs=32.0
Q ss_pred CCeeeEcccCcccC---------CCc-eeecccCCCCCceecHHHHHHHHHHhCCccccCcc
Q 031236 18 TSHCRICHEEEFES---------CNS-LEAPCACSGTVKFAHRDCIQRWCYEKGNTTCEICL 69 (163)
Q Consensus 18 ~~~CRIC~~~~~~~---------~~~-l~~PC~C~Gsl~~vH~~CL~~Wl~~k~~~~CeiCk 69 (163)
...|-||++...+. +-+ ...+|+ |.+|..||.+|++ .+.+||+|+
T Consensus 19 ~d~C~IC~~~l~~~~~~~~~~~~~~~i~~~~C~-----H~FH~~Ci~~Wl~--~~~~CP~CR 73 (73)
T PF12678_consen 19 DDNCAICREPLEDPCPECQAPQDECPIVWGPCG-----HIFHFHCISQWLK--QNNTCPLCR 73 (73)
T ss_dssp CSBETTTTSBTTSTTCCHHHCTTTS-EEEETTS-----EEEEHHHHHHHHT--TSSB-TTSS
T ss_pred CCcccccChhhhChhhhhcCCccccceEecccC-----CCEEHHHHHHHHh--cCCcCCCCC
Confidence 45699999886321 112 345776 9999999999995 445999996
No 14
>PHA02929 N1R/p28-like protein; Provisional
Probab=98.00 E-value=4.8e-06 Score=70.37 Aligned_cols=51 Identities=22% Similarity=0.589 Sum_probs=38.8
Q ss_pred CCCeeeEcccCcccCCC-----ceeecccCCCCCceecHHHHHHHHHHhCCccccCccccccC
Q 031236 17 TTSHCRICHEEEFESCN-----SLEAPCACSGTVKFAHRDCIQRWCYEKGNTTCEICLQEYGP 74 (163)
Q Consensus 17 ~~~~CRIC~~~~~~~~~-----~l~~PC~C~Gsl~~vH~~CL~~Wl~~k~~~~CeiCk~~y~~ 74 (163)
.+.+|.||+++..+... ....||+ |.+|..|+.+|++ .+.+||+|+..+..
T Consensus 173 ~~~eC~ICle~~~~~~~~~~~~~vl~~C~-----H~FC~~CI~~Wl~--~~~tCPlCR~~~~~ 228 (238)
T PHA02929 173 KDKECAICMEKVYDKEIKNMYFGILSNCN-----HVFCIECIDIWKK--EKNTCPVCRTPFIS 228 (238)
T ss_pred CCCCCccCCcccccCccccccceecCCCC-----CcccHHHHHHHHh--cCCCCCCCCCEeeE
Confidence 46899999997543211 2345676 9999999999995 45699999988763
No 15
>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=97.86 E-value=1.5e-05 Score=47.86 Aligned_cols=44 Identities=36% Similarity=0.825 Sum_probs=33.9
Q ss_pred eeeEcccCcccCCCceeecccCCCCCceecHHHHHHHHHHhCCccccCcccc
Q 031236 20 HCRICHEEEFESCNSLEAPCACSGTVKFAHRDCIQRWCYEKGNTTCEICLQE 71 (163)
Q Consensus 20 ~CRIC~~~~~~~~~~l~~PC~C~Gsl~~vH~~CL~~Wl~~k~~~~CeiCk~~ 71 (163)
.|.||++...+ .....||+ |.+|..|+++|++. ++..||+|+..
T Consensus 1 ~C~iC~~~~~~--~~~~~~C~-----H~~c~~C~~~~~~~-~~~~Cp~C~~~ 44 (45)
T cd00162 1 ECPICLEEFRE--PVVLLPCG-----HVFCRSCIDKWLKS-GKNTCPLCRTP 44 (45)
T ss_pred CCCcCchhhhC--ceEecCCC-----ChhcHHHHHHHHHh-CcCCCCCCCCc
Confidence 48899887622 22455577 89999999999975 67789999964
No 16
>PF12861 zf-Apc11: Anaphase-promoting complex subunit 11 RING-H2 finger
Probab=97.85 E-value=1.4e-05 Score=57.99 Aligned_cols=54 Identities=24% Similarity=0.438 Sum_probs=39.4
Q ss_pred CCCeeeEcccCcccC---------CCceeecccCCCCCceecHHHHHHHHHHh-CCccccCccccccC
Q 031236 17 TTSHCRICHEEEFES---------CNSLEAPCACSGTVKFAHRDCIQRWCYEK-GNTTCEICLQEYGP 74 (163)
Q Consensus 17 ~~~~CRIC~~~~~~~---------~~~l~~PC~C~Gsl~~vH~~CL~~Wl~~k-~~~~CeiCk~~y~~ 74 (163)
.+..|-||....+.. +-+++ -+.|+ |.+|..||.+|+++. .+..||+|++++++
T Consensus 20 ~dd~CgICr~~fdg~Cp~Ck~Pgd~Cplv-~g~C~---H~FH~hCI~kWl~~~~~~~~CPmCR~~w~~ 83 (85)
T PF12861_consen 20 NDDVCGICRMPFDGCCPDCKFPGDDCPLV-WGKCS---HNFHMHCILKWLSTQSSKGQCPMCRQPWKF 83 (85)
T ss_pred CCCceeeEecccccCCCCccCCCCCCcee-eccCc---cHHHHHHHHHHHccccCCCCCCCcCCeeee
Confidence 367899998765421 11222 23566 999999999999874 56899999999875
No 17
>PF11793 FANCL_C: FANCL C-terminal domain; PDB: 3K1L_A.
Probab=97.74 E-value=9.1e-06 Score=56.38 Aligned_cols=54 Identities=19% Similarity=0.394 Sum_probs=25.4
Q ss_pred CCeeeEcccCcccCCCceeec---ccCCCCCceecHHHHHHHHHHhC---------CccccCccccccC
Q 031236 18 TSHCRICHEEEFESCNSLEAP---CACSGTVKFAHRDCIQRWCYEKG---------NTTCEICLQEYGP 74 (163)
Q Consensus 18 ~~~CRIC~~~~~~~~~~l~~P---C~C~Gsl~~vH~~CL~~Wl~~k~---------~~~CeiCk~~y~~ 74 (163)
+.+|.||++...+.+.....- .+|. +.+|..||.+|+.... ...||.|++++..
T Consensus 2 ~~~C~IC~~~~~~~~~~p~~~C~n~~C~---~~fH~~CL~~wf~~~~~~~~~~~~~~G~CP~C~~~i~~ 67 (70)
T PF11793_consen 2 ELECGICYSYRLDDGEIPDVVCPNPSCG---KKFHLLCLSEWFLSLEKSRQSFIPIFGECPYCSSPISW 67 (70)
T ss_dssp --S-SSS--SS-TT-----B--S-TT-------B-SGGGHHHHHHHHSSS-TTT--EEE-TTT-SEEEG
T ss_pred CCCCCcCCcEecCCCCcCceEcCCcccC---CHHHHHHHHHHHHHcccCCeeecccccCCcCCCCeeeE
Confidence 468999998754222222333 4677 8999999999997631 1469999987753
No 18
>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=97.71 E-value=2.9e-05 Score=49.78 Aligned_cols=46 Identities=26% Similarity=0.623 Sum_probs=37.3
Q ss_pred CCeeeEcccCcccCCCceeecccCCCCCce-ecHHHHHHHHHHhCCccccCcccccc
Q 031236 18 TSHCRICHEEEFESCNSLEAPCACSGTVKF-AHRDCIQRWCYEKGNTTCEICLQEYG 73 (163)
Q Consensus 18 ~~~CRIC~~~~~~~~~~l~~PC~C~Gsl~~-vH~~CL~~Wl~~k~~~~CeiCk~~y~ 73 (163)
...|.||++... +....||+ |. +-..|+.+|++ ....||+|+++++
T Consensus 2 ~~~C~iC~~~~~---~~~~~pCg-----H~~~C~~C~~~~~~--~~~~CP~Cr~~i~ 48 (50)
T PF13920_consen 2 DEECPICFENPR---DVVLLPCG-----HLCFCEECAERLLK--RKKKCPICRQPIE 48 (50)
T ss_dssp HSB-TTTSSSBS---SEEEETTC-----EEEEEHHHHHHHHH--TTSBBTTTTBB-S
T ss_pred cCCCccCCccCC---ceEEeCCC-----ChHHHHHHhHHhcc--cCCCCCcCChhhc
Confidence 458999999854 35889998 88 99999999996 7789999998764
No 19
>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=97.57 E-value=6.9e-05 Score=43.28 Aligned_cols=39 Identities=44% Similarity=0.999 Sum_probs=31.5
Q ss_pred eeEcccCcccCCCceeecccCCCCCceecHHHHHHHHHHhCCccccCc
Q 031236 21 CRICHEEEFESCNSLEAPCACSGTVKFAHRDCIQRWCYEKGNTTCEIC 68 (163)
Q Consensus 21 CRIC~~~~~~~~~~l~~PC~C~Gsl~~vH~~CL~~Wl~~k~~~~CeiC 68 (163)
|.||++.. .+....||+ |.+|..|+++|++ .+...||+|
T Consensus 1 C~iC~~~~---~~~~~~~C~-----H~~c~~C~~~~~~-~~~~~CP~C 39 (39)
T smart00184 1 CPICLEEL---KDPVVLPCG-----HTFCRSCIRKWLK-SGNNTCPIC 39 (39)
T ss_pred CCcCccCC---CCcEEecCC-----ChHHHHHHHHHHH-hCcCCCCCC
Confidence 67898873 245788988 8999999999997 566789887
No 20
>PLN03208 E3 ubiquitin-protein ligase RMA2; Provisional
Probab=97.54 E-value=7.4e-05 Score=61.51 Aligned_cols=49 Identities=20% Similarity=0.645 Sum_probs=39.8
Q ss_pred CCCCeeeEcccCcccCCCceeecccCCCCCceecHHHHHHHHHHh--------------CCccccCccccc
Q 031236 16 ETTSHCRICHEEEFESCNSLEAPCACSGTVKFAHRDCIQRWCYEK--------------GNTTCEICLQEY 72 (163)
Q Consensus 16 ~~~~~CRIC~~~~~~~~~~l~~PC~C~Gsl~~vH~~CL~~Wl~~k--------------~~~~CeiCk~~y 72 (163)
++.-+|.||++... ++.+++|+ |.+...||.+|+..+ +...||+|+..+
T Consensus 16 ~~~~~CpICld~~~---dPVvT~CG-----H~FC~~CI~~wl~~s~~s~~~~~~~~~~k~~~~CPvCR~~I 78 (193)
T PLN03208 16 GGDFDCNICLDQVR---DPVVTLCG-----HLFCWPCIHKWTYASNNSRQRVDQYDHKREPPKCPVCKSDV 78 (193)
T ss_pred CCccCCccCCCcCC---CcEEcCCC-----chhHHHHHHHHHHhccccccccccccccCCCCcCCCCCCcC
Confidence 45689999999764 35789988 999999999998632 346899999976
No 21
>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=97.53 E-value=6.4e-05 Score=45.89 Aligned_cols=41 Identities=32% Similarity=0.861 Sum_probs=34.7
Q ss_pred eeEcccCcccCCCceeecccCCCCCceecHHHHHHHHHHhCCccccCc
Q 031236 21 CRICHEEEFESCNSLEAPCACSGTVKFAHRDCIQRWCYEKGNTTCEIC 68 (163)
Q Consensus 21 CRIC~~~~~~~~~~l~~PC~C~Gsl~~vH~~CL~~Wl~~k~~~~CeiC 68 (163)
|.||++...+. ....||+ |.+...|+.+|++.++...||+|
T Consensus 1 C~iC~~~~~~~--~~~~~C~-----H~fC~~C~~~~~~~~~~~~CP~C 41 (41)
T PF00097_consen 1 CPICLEPFEDP--VILLPCG-----HSFCRDCLRKWLENSGSVKCPLC 41 (41)
T ss_dssp ETTTSSBCSSE--EEETTTS-----EEEEHHHHHHHHHHTSSSBTTTT
T ss_pred CCcCCccccCC--CEEecCC-----CcchHHHHHHHHHhcCCccCCcC
Confidence 78998876543 2489999 99999999999998788899988
No 22
>COG5219 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=97.47 E-value=1.5e-05 Score=78.12 Aligned_cols=60 Identities=23% Similarity=0.493 Sum_probs=43.7
Q ss_pred CCCCCCCCeeeEcccCcccCCCce-eeccc-CCCCCceecHHHHHHHHHHhCCccccCccccccC
Q 031236 12 KSNPETTSHCRICHEEEFESCNSL-EAPCA-CSGTVKFAHRDCIQRWCYEKGNTTCEICLQEYGP 74 (163)
Q Consensus 12 ~~~s~~~~~CRIC~~~~~~~~~~l-~~PC~-C~Gsl~~vH~~CL~~Wl~~k~~~~CeiCk~~y~~ 74 (163)
...-++..+|.||..-..--+..+ -..|+ |+ +-+|..||.+|++++++.+||+|+..+++
T Consensus 1463 ~~~fsG~eECaICYsvL~~vdr~lPskrC~TCk---nKFH~~CLyKWf~Ss~~s~CPlCRseitf 1524 (1525)
T COG5219 1463 DEKFSGHEECAICYSVLDMVDRSLPSKRCATCK---NKFHTRCLYKWFASSARSNCPLCRSEITF 1524 (1525)
T ss_pred hhhcCCcchhhHHHHHHHHHhccCCccccchhh---hhhhHHHHHHHHHhcCCCCCCcccccccc
Confidence 334457889999986543111112 24455 66 88999999999999999999999977654
No 23
>PHA02926 zinc finger-like protein; Provisional
Probab=97.35 E-value=0.00016 Score=61.00 Aligned_cols=54 Identities=22% Similarity=0.518 Sum_probs=40.8
Q ss_pred CCCeeeEcccCccc----CC--CceeecccCCCCCceecHHHHHHHHHHhC----CccccCccccccCC
Q 031236 17 TTSHCRICHEEEFE----SC--NSLEAPCACSGTVKFAHRDCIQRWCYEKG----NTTCEICLQEYGPG 75 (163)
Q Consensus 17 ~~~~CRIC~~~~~~----~~--~~l~~PC~C~Gsl~~vH~~CL~~Wl~~k~----~~~CeiCk~~y~~~ 75 (163)
.+.+|-||++.-.+ ++ -.+..+|+ |.+...|+.+|.+.+. ...||+|++.+...
T Consensus 169 kE~eCgICmE~I~eK~~~~eRrFGIL~~Cn-----HsFCl~CIr~Wr~~r~~~~~~rsCPiCR~~f~~I 232 (242)
T PHA02926 169 KEKECGICYEVVYSKRLENDRYFGLLDSCN-----HIFCITCINIWHRTRRETGASDNCPICRTRFRNI 232 (242)
T ss_pred CCCCCccCccccccccccccccccccCCCC-----chHHHHHHHHHHHhccccCcCCcCCCCcceeeee
Confidence 56899999987422 11 13567888 9999999999998642 46799999998754
No 24
>KOG0802 consensus E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=97.29 E-value=0.00013 Score=67.55 Aligned_cols=49 Identities=29% Similarity=0.682 Sum_probs=40.6
Q ss_pred CCCeeeEcccCcccCCC--ceeecccCCCCCceecHHHHHHHHHHhCCccccCccccc
Q 031236 17 TTSHCRICHEEEFESCN--SLEAPCACSGTVKFAHRDCIQRWCYEKGNTTCEICLQEY 72 (163)
Q Consensus 17 ~~~~CRIC~~~~~~~~~--~l~~PC~C~Gsl~~vH~~CL~~Wl~~k~~~~CeiCk~~y 72 (163)
....|.||.|+...+.+ +-..||. |.+|..||++|++. ..+||+|+..+
T Consensus 290 ~~~~C~IC~e~l~~~~~~~~~rL~C~-----Hifh~~CL~~W~er--~qtCP~CR~~~ 340 (543)
T KOG0802|consen 290 SDELCIICLEELHSGHNITPKRLPCG-----HIFHDSCLRSWFER--QQTCPTCRTVL 340 (543)
T ss_pred cCCeeeeechhhccccccccceeecc-----cchHHHHHHHHHHH--hCcCCcchhhh
Confidence 46899999998765433 5789998 99999999999965 67999999843
No 25
>KOG0317 consensus Predicted E3 ubiquitin ligase, integral peroxisomal membrane protein [Posttranslational modification, protein turnover, chaperones]
Probab=97.09 E-value=0.00049 Score=59.70 Aligned_cols=53 Identities=34% Similarity=0.876 Sum_probs=43.6
Q ss_pred CCCCCCCCeeeEcccCcccCCCceeecccCCCCCceecHHHHHHHHHHhCCccccCccccccC
Q 031236 12 KSNPETTSHCRICHEEEFESCNSLEAPCACSGTVKFAHRDCIQRWCYEKGNTTCEICLQEYGP 74 (163)
Q Consensus 12 ~~~s~~~~~CRIC~~~~~~~~~~l~~PC~C~Gsl~~vH~~CL~~Wl~~k~~~~CeiCk~~y~~ 74 (163)
++.++....|-+|++.-.+ +--+||+ |.+=-.|+..|+.+|. .||+|+..+++
T Consensus 233 ~~i~~a~~kC~LCLe~~~~---pSaTpCG-----HiFCWsCI~~w~~ek~--eCPlCR~~~~p 285 (293)
T KOG0317|consen 233 SSIPEATRKCSLCLENRSN---PSATPCG-----HIFCWSCILEWCSEKA--ECPLCREKFQP 285 (293)
T ss_pred ccCCCCCCceEEEecCCCC---CCcCcCc-----chHHHHHHHHHHcccc--CCCcccccCCC
Confidence 4456777999999998654 3589999 9999999999997665 59999988764
No 26
>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=97.06 E-value=0.00035 Score=42.61 Aligned_cols=38 Identities=29% Similarity=0.858 Sum_probs=30.0
Q ss_pred eeEcccCcccCCCc-eeecccCCCCCceecHHHHHHHHHHhCCccccCc
Q 031236 21 CRICHEEEFESCNS-LEAPCACSGTVKFAHRDCIQRWCYEKGNTTCEIC 68 (163)
Q Consensus 21 CRIC~~~~~~~~~~-l~~PC~C~Gsl~~vH~~CL~~Wl~~k~~~~CeiC 68 (163)
|.||++...+ + ...||+ |.+...|+++|++. +..||+|
T Consensus 1 C~iC~~~~~~---~~~~~~CG-----H~fC~~C~~~~~~~--~~~CP~C 39 (39)
T PF13923_consen 1 CPICLDELRD---PVVVTPCG-----HSFCKECIEKYLEK--NPKCPVC 39 (39)
T ss_dssp ETTTTSB-SS---EEEECTTS-----EEEEHHHHHHHHHC--TSB-TTT
T ss_pred CCCCCCcccC---cCEECCCC-----CchhHHHHHHHHHC--cCCCcCC
Confidence 7799887654 4 579998 99999999999975 5799987
No 27
>PF14634 zf-RING_5: zinc-RING finger domain
Probab=97.00 E-value=0.00049 Score=43.17 Aligned_cols=44 Identities=25% Similarity=0.616 Sum_probs=37.5
Q ss_pred eeeEcccCcccCCCceeecccCCCCCceecHHHHHHHHHHhCCccccCccc
Q 031236 20 HCRICHEEEFESCNSLEAPCACSGTVKFAHRDCIQRWCYEKGNTTCEICLQ 70 (163)
Q Consensus 20 ~CRIC~~~~~~~~~~l~~PC~C~Gsl~~vH~~CL~~Wl~~k~~~~CeiCk~ 70 (163)
.|-||++...+...+++++|+ |.+...|++++. .....||+|++
T Consensus 1 ~C~~C~~~~~~~~~~~l~~Cg-----H~~C~~C~~~~~--~~~~~CP~C~k 44 (44)
T PF14634_consen 1 HCNICFEKYSEERRPRLTSCG-----HIFCEKCLKKLK--GKSVKCPICRK 44 (44)
T ss_pred CCcCcCccccCCCCeEEcccC-----CHHHHHHHHhhc--CCCCCCcCCCC
Confidence 488999998555567899998 999999999998 67789999984
No 28
>KOG0828 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=96.84 E-value=0.00076 Score=62.57 Aligned_cols=58 Identities=22% Similarity=0.498 Sum_probs=41.8
Q ss_pred cCCCCCCCCCeeeEcccCcc----c----------CCCceeecccCCCCCceecHHHHHHHHHHhCCccccCcccccc
Q 031236 10 DFKSNPETTSHCRICHEEEF----E----------SCNSLEAPCACSGTVKFAHRDCIQRWCYEKGNTTCEICLQEYG 73 (163)
Q Consensus 10 d~~~~s~~~~~CRIC~~~~~----~----------~~~~l~~PC~C~Gsl~~vH~~CL~~Wl~~k~~~~CeiCk~~y~ 73 (163)
+++.-.+....|-||...-+ . +.+-+.+||+ |.+|+.||++|.+. .+..||.|+...+
T Consensus 563 h~~~~~~~t~dC~ICMt~I~l~~~~s~~~~~~~~~~~nYm~tPC~-----HifH~~CL~~WMd~-ykl~CPvCR~pLP 634 (636)
T KOG0828|consen 563 HLEAFVRRTNDCVICMTPIDLRSTGSDCMVASMMVRRNYMLTPCH-----HIFHRQCLLQWMDT-YKLICPVCRCPLP 634 (636)
T ss_pred cccchhhccccceEeccccceeeccCcchhhhhhhhccccccchH-----HHHHHHHHHHHHhh-hcccCCccCCCCC
Confidence 33333456789999987542 1 1234677999 99999999999973 3478999997654
No 29
>KOG1493 consensus Anaphase-promoting complex (APC), subunit 11 [Cell cycle control, cell division, chromosome partitioning; Posttranslational modification, protein turnover, chaperones]
Probab=96.80 E-value=0.00035 Score=50.12 Aligned_cols=52 Identities=23% Similarity=0.430 Sum_probs=38.4
Q ss_pred CeeeEcccCccc---------CCCceeecccCCCCCceecHHHHHHHHHHhC-CccccCccccccC
Q 031236 19 SHCRICHEEEFE---------SCNSLEAPCACSGTVKFAHRDCIQRWCYEKG-NTTCEICLQEYGP 74 (163)
Q Consensus 19 ~~CRIC~~~~~~---------~~~~l~~PC~C~Gsl~~vH~~CL~~Wl~~k~-~~~CeiCk~~y~~ 74 (163)
..|-||..+.+. ++-+++.- .|. +.+|..|+.+|++.+. +..||.|++++++
T Consensus 21 e~CGiCRm~Fdg~Cp~Ck~PgDdCPLv~G-~C~---h~fh~hCI~~wl~~~tsq~~CPmcRq~~~~ 82 (84)
T KOG1493|consen 21 ETCGICRMPFDGCCPDCKLPGDDCPLVWG-YCL---HAFHAHCILKWLNTPTSQGQCPMCRQTWQF 82 (84)
T ss_pred CccceEecccCCcCCCCcCCCCCCccHHH-HHH---HHHHHHHHHHHhcCccccccCCcchheeEe
Confidence 488898876542 12345433 454 8999999999998764 5789999999875
No 30
>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=96.47 E-value=0.0038 Score=40.86 Aligned_cols=44 Identities=20% Similarity=0.292 Sum_probs=36.3
Q ss_pred eeeEcccCcccCCCceeecccCCCCCceecHHHHHHHHHHhCCccccCcccccc
Q 031236 20 HCRICHEEEFESCNSLEAPCACSGTVKFAHRDCIQRWCYEKGNTTCEICLQEYG 73 (163)
Q Consensus 20 ~CRIC~~~~~~~~~~l~~PC~C~Gsl~~vH~~CL~~Wl~~k~~~~CeiCk~~y~ 73 (163)
.|.||.+-..+ +...||+ +.+-+.|+.+|++. +.+||+|++.+.
T Consensus 3 ~Cpi~~~~~~~---Pv~~~~G-----~v~~~~~i~~~~~~--~~~cP~~~~~~~ 46 (63)
T smart00504 3 LCPISLEVMKD---PVILPSG-----QTYERRAIEKWLLS--HGTDPVTGQPLT 46 (63)
T ss_pred CCcCCCCcCCC---CEECCCC-----CEEeHHHHHHHHHH--CCCCCCCcCCCC
Confidence 68999887643 5888886 89999999999976 568999998764
No 31
>KOG0827 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=96.40 E-value=0.0019 Score=58.40 Aligned_cols=46 Identities=24% Similarity=0.665 Sum_probs=33.9
Q ss_pred CCeeeEcccCcccCCCce--eecccCCCCCceecHHHHHHHHHHhCC-ccccCcc
Q 031236 18 TSHCRICHEEEFESCNSL--EAPCACSGTVKFAHRDCIQRWCYEKGN-TTCEICL 69 (163)
Q Consensus 18 ~~~CRIC~~~~~~~~~~l--~~PC~C~Gsl~~vH~~CL~~Wl~~k~~-~~CeiCk 69 (163)
...|.||-+. .+....+ +..|+ |.+|..||.+|+..-.. +.||||+
T Consensus 4 ~A~C~Ic~d~-~p~~~~l~~i~~cG-----hifh~~cl~qwfe~~Ps~R~cpic~ 52 (465)
T KOG0827|consen 4 MAECHICIDG-RPNDHELGPIGTCG-----HIFHTTCLTQWFEGDPSNRGCPICQ 52 (465)
T ss_pred cceeeEeccC-Cccccccccccchh-----hHHHHHHHHHHHccCCccCCCCcee
Confidence 5789999433 3322223 55566 99999999999987665 6999999
No 32
>COG5194 APC11 Component of SCF ubiquitin ligase and anaphase-promoting complex [Posttranslational modification, protein turnover, chaperones / Cell division and chromosome partitioning]
Probab=96.03 E-value=0.0059 Score=44.21 Aligned_cols=27 Identities=33% Similarity=0.614 Sum_probs=24.2
Q ss_pred ceecHHHHHHHHHHhCCccccCccccccC
Q 031236 46 KFAHRDCIQRWCYEKGNTTCEICLQEYGP 74 (163)
Q Consensus 46 ~~vH~~CL~~Wl~~k~~~~CeiCk~~y~~ 74 (163)
|.+|..|+.+|+++|+ .||++++++..
T Consensus 56 HaFH~HCI~rWL~Tk~--~CPld~q~w~~ 82 (88)
T COG5194 56 HAFHDHCIYRWLDTKG--VCPLDRQTWVL 82 (88)
T ss_pred hHHHHHHHHHHHhhCC--CCCCCCceeEE
Confidence 8999999999998855 89999998864
No 33
>KOG0823 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=95.91 E-value=0.011 Score=49.91 Aligned_cols=50 Identities=18% Similarity=0.518 Sum_probs=41.6
Q ss_pred CCCCCeeeEcccCcccCCCceeecccCCCCCceecHHHHHHHHHHhC-CccccCccccc
Q 031236 15 PETTSHCRICHEEEFESCNSLEAPCACSGTVKFAHRDCIQRWCYEKG-NTTCEICLQEY 72 (163)
Q Consensus 15 s~~~~~CRIC~~~~~~~~~~l~~PC~C~Gsl~~vH~~CL~~Wl~~k~-~~~CeiCk~~y 72 (163)
.+..-.|-||++.-.+ +.+++|+ |.+==.||.+|+..+. ...||+||...
T Consensus 44 ~~~~FdCNICLd~akd---PVvTlCG-----HLFCWpClyqWl~~~~~~~~cPVCK~~V 94 (230)
T KOG0823|consen 44 DGGFFDCNICLDLAKD---PVVTLCG-----HLFCWPCLYQWLQTRPNSKECPVCKAEV 94 (230)
T ss_pred CCCceeeeeeccccCC---CEEeecc-----cceehHHHHHHHhhcCCCeeCCcccccc
Confidence 3556799999998654 6999999 9999999999998875 46679999865
No 34
>PF13445 zf-RING_UBOX: RING-type zinc-finger; PDB: 2CT2_A.
Probab=95.73 E-value=0.0083 Score=38.10 Aligned_cols=41 Identities=27% Similarity=0.631 Sum_probs=23.5
Q ss_pred eeEcccCcccCCCceeecccCCCCCceecHHHHHHHHHHh--CCcccc
Q 031236 21 CRICHEEEFESCNSLEAPCACSGTVKFAHRDCIQRWCYEK--GNTTCE 66 (163)
Q Consensus 21 CRIC~~~~~~~~~~l~~PC~C~Gsl~~vH~~CL~~Wl~~k--~~~~Ce 66 (163)
|.||.+-.++++.+++.||+ |-+=++||+++.+.+ +..+||
T Consensus 1 CpIc~e~~~~~n~P~~L~CG-----H~~c~~cl~~l~~~~~~~~~kCP 43 (43)
T PF13445_consen 1 CPICKEFSTEENPPMVLPCG-----HVFCKDCLQKLSKKSDRNRFKCP 43 (43)
T ss_dssp -TTT----TTSS-EEE-SSS------EEEHHHHHHHHHH-S-S-B--T
T ss_pred CCccccccCCCCCCEEEeCc-----cHHHHHHHHHHHhcCCCCeeeCc
Confidence 77898843444557899988 999999999999865 455664
No 35
>KOG1734 consensus Predicted RING-containing E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=95.60 E-value=0.0035 Score=54.51 Aligned_cols=61 Identities=23% Similarity=0.526 Sum_probs=46.1
Q ss_pred ccCCCCCCCCCeeeEcccCcccC-------CCceeecccCCCCCceecHHHHHHHHHHhCCccccCccccccC
Q 031236 9 EDFKSNPETTSHCRICHEEEFES-------CNSLEAPCACSGTVKFAHRDCIQRWCYEKGNTTCEICLQEYGP 74 (163)
Q Consensus 9 ~d~~~~s~~~~~CRIC~~~~~~~-------~~~l~~PC~C~Gsl~~vH~~CL~~Wl~~k~~~~CeiCk~~y~~ 74 (163)
+..+.+.-+...|.+|-.....+ ++.....|+ |-+|+.|++-|+-.-++.+||-||++...
T Consensus 215 ~glPtkhl~d~vCaVCg~~~~~s~~eegvienty~LsCn-----HvFHEfCIrGWcivGKkqtCPYCKekVdl 282 (328)
T KOG1734|consen 215 SGLPTKHLSDSVCAVCGQQIDVSVDEEGVIENTYKLSCN-----HVFHEFCIRGWCIVGKKQTCPYCKEKVDL 282 (328)
T ss_pred CCCCCCCCCcchhHhhcchheeecchhhhhhhheeeecc-----cchHHHhhhhheeecCCCCCchHHHHhhH
Confidence 34455566788999996543222 244567777 99999999999988788999999987653
No 36
>TIGR00599 rad18 DNA repair protein rad18. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=95.42 E-value=0.0092 Score=53.96 Aligned_cols=49 Identities=22% Similarity=0.455 Sum_probs=39.7
Q ss_pred CCCCeeeEcccCcccCCCceeecccCCCCCceecHHHHHHHHHHhCCccccCccccccC
Q 031236 16 ETTSHCRICHEEEFESCNSLEAPCACSGTVKFAHRDCIQRWCYEKGNTTCEICLQEYGP 74 (163)
Q Consensus 16 ~~~~~CRIC~~~~~~~~~~l~~PC~C~Gsl~~vH~~CL~~Wl~~k~~~~CeiCk~~y~~ 74 (163)
+....|.||++...+ +.+.||. |.+...|+..|+.. ...||+|+..+..
T Consensus 24 e~~l~C~IC~d~~~~---PvitpCg-----H~FCs~CI~~~l~~--~~~CP~Cr~~~~~ 72 (397)
T TIGR00599 24 DTSLRCHICKDFFDV---PVLTSCS-----HTFCSLCIRRCLSN--QPKCPLCRAEDQE 72 (397)
T ss_pred ccccCCCcCchhhhC---ccCCCCC-----CchhHHHHHHHHhC--CCCCCCCCCcccc
Confidence 345799999987643 4688998 99999999999965 3489999997753
No 37
>KOG0804 consensus Cytoplasmic Zn-finger protein BRAP2 (BRCA1 associated protein) [General function prediction only]
Probab=94.99 E-value=0.0083 Score=55.08 Aligned_cols=47 Identities=23% Similarity=0.566 Sum_probs=35.5
Q ss_pred CCCCeeeEcccCcccC-CCceeecccCCCCCceecHHHHHHHHHHhCCccccCcccc
Q 031236 16 ETTSHCRICHEEEFES-CNSLEAPCACSGTVKFAHRDCIQRWCYEKGNTTCEICLQE 71 (163)
Q Consensus 16 ~~~~~CRIC~~~~~~~-~~~l~~PC~C~Gsl~~vH~~CL~~Wl~~k~~~~CeiCk~~ 71 (163)
.+.+.|.+|++.-+++ ...+-.+|. |-+|-.|+++|-. .+||+|++.
T Consensus 173 tELPTCpVCLERMD~s~~gi~t~~c~-----Hsfh~~cl~~w~~----~scpvcR~~ 220 (493)
T KOG0804|consen 173 TELPTCPVCLERMDSSTTGILTILCN-----HSFHCSCLMKWWD----SSCPVCRYC 220 (493)
T ss_pred ccCCCcchhHhhcCccccceeeeecc-----cccchHHHhhccc----CcChhhhhh
Confidence 3569999999986554 334567777 9999999999964 478888743
No 38
>PF15227 zf-C3HC4_4: zinc finger of C3HC4-type, RING; PDB: 2EGP_A 2ECV_A 2ECJ_A 2YSL_A 2YSJ_A.
Probab=94.25 E-value=0.029 Score=35.11 Aligned_cols=40 Identities=28% Similarity=0.664 Sum_probs=28.8
Q ss_pred eeEcccCcccCCCceeecccCCCCCceecHHHHHHHHHHhCC--ccccCc
Q 031236 21 CRICHEEEFESCNSLEAPCACSGTVKFAHRDCIQRWCYEKGN--TTCEIC 68 (163)
Q Consensus 21 CRIC~~~~~~~~~~l~~PC~C~Gsl~~vH~~CL~~Wl~~k~~--~~CeiC 68 (163)
|.||++-..+ +...+|+ |.+=+.||++|.++.+. ..||+|
T Consensus 1 CpiC~~~~~~---Pv~l~CG-----H~FC~~Cl~~~~~~~~~~~~~CP~C 42 (42)
T PF15227_consen 1 CPICLDLFKD---PVSLPCG-----HSFCRSCLERLWKEPSGSGFSCPEC 42 (42)
T ss_dssp ETTTTSB-SS---EEE-SSS-----SEEEHHHHHHHHCCSSSST---SSS
T ss_pred CCccchhhCC---ccccCCc-----CHHHHHHHHHHHHccCCcCCCCcCC
Confidence 7789887653 5889998 99999999999976544 589887
No 39
>KOG1785 consensus Tyrosine kinase negative regulator CBL [Defense mechanisms]
Probab=93.94 E-value=0.018 Score=52.59 Aligned_cols=48 Identities=25% Similarity=0.638 Sum_probs=40.3
Q ss_pred CCeeeEcccCcccCCCceeecccCCCCCceecHHHHHHHHHHhCCccccCcccccc
Q 031236 18 TSHCRICHEEEFESCNSLEAPCACSGTVKFAHRDCIQRWCYEKGNTTCEICLQEYG 73 (163)
Q Consensus 18 ~~~CRIC~~~~~~~~~~l~~PC~C~Gsl~~vH~~CL~~Wl~~k~~~~CeiCk~~y~ 73 (163)
-..|.||-+.+.+ .-+-||+ |..-..||..|..+.+...||.|+.+.+
T Consensus 369 FeLCKICaendKd---vkIEPCG-----HLlCt~CLa~WQ~sd~gq~CPFCRcEIK 416 (563)
T KOG1785|consen 369 FELCKICAENDKD---VKIEPCG-----HLLCTSCLAAWQDSDEGQTCPFCRCEIK 416 (563)
T ss_pred HHHHHHhhccCCC---ccccccc-----chHHHHHHHhhcccCCCCCCCceeeEec
Confidence 3679999877543 4689999 8889999999999888899999997664
No 40
>KOG4445 consensus Uncharacterized conserved protein, contains RWD domain [Function unknown]
Probab=93.81 E-value=0.034 Score=49.07 Aligned_cols=53 Identities=21% Similarity=0.427 Sum_probs=40.6
Q ss_pred CCCeeeEcccCcccCCCceeecccCCCCCceecHHHHHHHHHHh---------------------CCccccCccccccC
Q 031236 17 TTSHCRICHEEEFESCNSLEAPCACSGTVKFAHRDCIQRWCYEK---------------------GNTTCEICLQEYGP 74 (163)
Q Consensus 17 ~~~~CRIC~~~~~~~~~~l~~PC~C~Gsl~~vH~~CL~~Wl~~k---------------------~~~~CeiCk~~y~~ 74 (163)
...+|-||+-...++....+++|- ||+|..||.|.+++- -...|++|+.....
T Consensus 114 p~gqCvICLygfa~~~~ft~T~C~-----Hy~H~~ClaRyl~~~~~~lrqe~q~~~~~~qh~~~~~eavcpVcre~i~~ 187 (368)
T KOG4445|consen 114 PNGQCVICLYGFASSPAFTVTACD-----HYMHFACLARYLTECLTGLRQEIQDAQKERQHMKEQVEAVCPVCRERIKI 187 (368)
T ss_pred CCCceEEEEEeecCCCceeeehhH-----HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhHhhhhhHhhhhccc
Confidence 356788888777666556789998 999999999888652 13679999976643
No 41
>KOG4265 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=93.13 E-value=0.093 Score=46.84 Aligned_cols=50 Identities=24% Similarity=0.558 Sum_probs=35.3
Q ss_pred CCCCCCeeeEcccCcccCCCceeecccCCCCCce-ecHHHHHHHHHHhCCccccCcccccc
Q 031236 14 NPETTSHCRICHEEEFESCNSLEAPCACSGTVKF-AHRDCIQRWCYEKGNTTCEICLQEYG 73 (163)
Q Consensus 14 ~s~~~~~CRIC~~~~~~~~~~l~~PC~C~Gsl~~-vH~~CL~~Wl~~k~~~~CeiCk~~y~ 73 (163)
.++..++|-||+.+..+ .++.||+ |. .=..|.+.-. -....||||++.+.
T Consensus 286 ~~~~gkeCVIClse~rd---t~vLPCR-----HLCLCs~Ca~~Lr--~q~n~CPICRqpi~ 336 (349)
T KOG4265|consen 286 ESESGKECVICLSESRD---TVVLPCR-----HLCLCSGCAKSLR--YQTNNCPICRQPIE 336 (349)
T ss_pred cccCCCeeEEEecCCcc---eEEecch-----hhehhHhHHHHHH--HhhcCCCccccchH
Confidence 44668999999998654 4899988 21 2346766555 23567999998775
No 42
>PF05883 Baculo_RING: Baculovirus U-box/Ring-like domain; InterPro: IPR008573 This family consists of several Baculovirus proteins of around 130 residues in length. The function of this family is unknown, but it appears to be related to the U-box and ring finger domain by profile-profile comparison.
Probab=93.10 E-value=0.046 Score=42.81 Aligned_cols=42 Identities=29% Similarity=0.532 Sum_probs=31.4
Q ss_pred CCCeeeEcccCcccCCCceeecccCCCCC---ceecHHHHHHHHHHh
Q 031236 17 TTSHCRICHEEEFESCNSLEAPCACSGTV---KFAHRDCIQRWCYEK 60 (163)
Q Consensus 17 ~~~~CRIC~~~~~~~~~~l~~PC~C~Gsl---~~vH~~CL~~Wl~~k 60 (163)
-..+|+||++.-.+.++....+|+ |.+ |.+|..|+++|-+++
T Consensus 25 ~~~EC~IC~~~I~~~~GvV~vt~~--g~lnLEkmfc~~C~~rw~~~~ 69 (134)
T PF05883_consen 25 CTVECQICFDRIDNNDGVVYVTDG--GTLNLEKMFCADCDKRWRRER 69 (134)
T ss_pred cCeeehhhhhhhhcCCCEEEEecC--CeehHHHHHHHHHHHHHHhhc
Confidence 468999999997664556677766 444 469999999996443
No 43
>PF14570 zf-RING_4: RING/Ubox like zinc-binding domain; PDB: 1E4U_A 1UR6_B.
Probab=92.77 E-value=0.087 Score=34.44 Aligned_cols=46 Identities=26% Similarity=0.512 Sum_probs=20.6
Q ss_pred eeEcccCcccCCCceeecccCCCCCceecHHHHHHHHHHh--CCccccCcccccc
Q 031236 21 CRICHEEEFESCNSLEAPCACSGTVKFAHRDCIQRWCYEK--GNTTCEICLQEYG 73 (163)
Q Consensus 21 CRIC~~~~~~~~~~l~~PC~C~Gsl~~vH~~CL~~Wl~~k--~~~~CeiCk~~y~ 73 (163)
|.+|-++.+. .+.-..||.|. ++-|+.=|.+.+ .+..||-||++|+
T Consensus 1 cp~C~e~~d~-~d~~~~PC~Cg------f~IC~~C~~~i~~~~~g~CPgCr~~Y~ 48 (48)
T PF14570_consen 1 CPLCDEELDE-TDKDFYPCECG------FQICRFCYHDILENEGGRCPGCREPYK 48 (48)
T ss_dssp -TTTS-B--C-CCTT--SSTTS----------HHHHHHHTTSS-SB-TTT--B--
T ss_pred CCCccccccc-CCCccccCcCC------CcHHHHHHHHHHhccCCCCCCCCCCCC
Confidence 5677666533 33468999997 345555565544 4789999999884
No 44
>KOG2930 consensus SCF ubiquitin ligase, Rbx1 component [Posttranslational modification, protein turnover, chaperones]
Probab=92.61 E-value=0.056 Score=40.89 Aligned_cols=27 Identities=26% Similarity=0.502 Sum_probs=23.0
Q ss_pred ceecHHHHHHHHHHhCCccccCccccccC
Q 031236 46 KFAHRDCIQRWCYEKGNTTCEICLQEYGP 74 (163)
Q Consensus 46 ~~vH~~CL~~Wl~~k~~~~CeiCk~~y~~ 74 (163)
|-+|..|+.+|++. ...||+|.++..+
T Consensus 83 HaFH~hCisrWlkt--r~vCPLdn~eW~~ 109 (114)
T KOG2930|consen 83 HAFHFHCISRWLKT--RNVCPLDNKEWVF 109 (114)
T ss_pred hHHHHHHHHHHHhh--cCcCCCcCcceeE
Confidence 89999999999965 4599999987754
No 45
>KOG1645 consensus RING-finger-containing E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=92.39 E-value=0.12 Score=47.25 Aligned_cols=53 Identities=19% Similarity=0.535 Sum_probs=40.9
Q ss_pred CCCeeeEcccCcccCC-CceeecccCCCCCceecHHHHHHHHHHhCCccccCcccccc
Q 031236 17 TTSHCRICHEEEFESC-NSLEAPCACSGTVKFAHRDCIQRWCYEKGNTTCEICLQEYG 73 (163)
Q Consensus 17 ~~~~CRIC~~~~~~~~-~~l~~PC~C~Gsl~~vH~~CL~~Wl~~k~~~~CeiCk~~y~ 73 (163)
....|.||+++..-+. .-++.| .|. +.+-..|+++|+-.+....|++|+..-.
T Consensus 3 ~g~tcpiclds~~~~g~hr~vsl-~cg---hlFgs~cie~wl~k~~~~~cp~c~~kat 56 (463)
T KOG1645|consen 3 CGTTCPICLDSYTTAGNHRIVSL-QCG---HLFGSQCIEKWLGKKTKMQCPLCSGKAT 56 (463)
T ss_pred ccccCceeeeeeeecCceEEeee-ccc---ccccHHHHHHHHhhhhhhhCcccCChhH
Confidence 4578999999976443 346666 554 9999999999997666789999997543
No 46
>PLN02189 cellulose synthase
Probab=91.94 E-value=0.23 Score=49.91 Aligned_cols=67 Identities=22% Similarity=0.393 Sum_probs=44.2
Q ss_pred cceeeccCCC--CCCCCCeeeEcccCcc-cCCCceeeccc-CCCCCceecHHHHHHHHHHhCCccccCccccccC
Q 031236 4 VVLFVEDFKS--NPETTSHCRICHEEEF-ESCNSLEAPCA-CSGTVKFAHRDCIQRWCYEKGNTTCEICLQEYGP 74 (163)
Q Consensus 4 ~vl~v~d~~~--~s~~~~~CRIC~~~~~-~~~~~l~~PC~-C~Gsl~~vH~~CL~~Wl~~k~~~~CeiCk~~y~~ 74 (163)
|++..+++.. ..-....|+||-++-. +.++.....|+ |. --+=+.|.+. =.+.|+..||.||++|+-
T Consensus 18 ~~~~~~~~~k~~~~~~~~~C~iCgd~vg~~~~g~~fvaC~~C~---fpvCr~Cyey-er~eg~q~CpqCkt~Y~r 88 (1040)
T PLN02189 18 VVIHGHEEPKPLRNLDGQVCEICGDEIGLTVDGDLFVACNECG---FPVCRPCYEY-ERREGTQNCPQCKTRYKR 88 (1040)
T ss_pred eeeccccCCCCcccccCccccccccccCcCCCCCEEEeeccCC---Cccccchhhh-hhhcCCccCcccCCchhh
Confidence 5555554321 1234569999988743 22334668888 75 4488899843 334589999999999983
No 47
>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=91.50 E-value=0.18 Score=44.34 Aligned_cols=51 Identities=14% Similarity=0.434 Sum_probs=38.4
Q ss_pred CCeeeEcccCcccC--CCceeecccCCCCCceecHHHHHHHHHHhCCccccCccccccC
Q 031236 18 TSHCRICHEEEFES--CNSLEAPCACSGTVKFAHRDCIQRWCYEKGNTTCEICLQEYGP 74 (163)
Q Consensus 18 ~~~CRIC~~~~~~~--~~~l~~PC~C~Gsl~~vH~~CL~~Wl~~k~~~~CeiCk~~y~~ 74 (163)
+..|.+|..+.--+ ...+++||+ |-+=..|+.+.+. ++...||.|+..+..
T Consensus 3 ~~~CP~Ck~~~y~np~~kl~i~~CG-----H~~C~sCv~~l~~-~~~~~CP~C~~~lrk 55 (309)
T TIGR00570 3 DQGCPRCKTTKYRNPSLKLMVNVCG-----HTLCESCVDLLFV-RGSGSCPECDTPLRK 55 (309)
T ss_pred CCCCCcCCCCCccCcccccccCCCC-----CcccHHHHHHHhc-CCCCCCCCCCCccch
Confidence 46899999864322 234677887 8899999999764 467799999987754
No 48
>PLN02436 cellulose synthase A
Probab=91.25 E-value=0.29 Score=49.32 Aligned_cols=68 Identities=21% Similarity=0.420 Sum_probs=45.3
Q ss_pred ccceeeccC-CC---CCCCCCeeeEcccCcc-cCCCceeeccc-CCCCCceecHHHHHHHHHHhCCccccCccccccC
Q 031236 3 DVVLFVEDF-KS---NPETTSHCRICHEEEF-ESCNSLEAPCA-CSGTVKFAHRDCIQRWCYEKGNTTCEICLQEYGP 74 (163)
Q Consensus 3 ~~vl~v~d~-~~---~s~~~~~CRIC~~~~~-~~~~~l~~PC~-C~Gsl~~vH~~CL~~Wl~~k~~~~CeiCk~~y~~ 74 (163)
-|++..|+. .. +.-....|.||-++-. ..++.+.-.|+ |. --+=+.|.+. -.+.|+..||.||++|+-
T Consensus 17 ~~~~~~d~~~~~k~~~~~~~~iCqICGD~Vg~t~dGe~FVACn~C~---fpvCr~Cyey-er~eg~~~Cpqckt~Y~r 90 (1094)
T PLN02436 17 FVLINADEIARIRSVQELSGQTCQICGDEIELTVDGEPFVACNECA---FPVCRPCYEY-ERREGNQACPQCKTRYKR 90 (1094)
T ss_pred eeEeccccccCCCCccccCCccccccccccCcCCCCCEEEeeccCC---Cccccchhhh-hhhcCCccCcccCCchhh
Confidence 466776632 12 2234579999988732 22334667888 75 4488899843 334589999999999984
No 49
>KOG0320 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=91.21 E-value=0.18 Score=41.43 Aligned_cols=49 Identities=24% Similarity=0.530 Sum_probs=37.6
Q ss_pred CCCCeeeEcccCcccCCCceeecccCCCCCceecHHHHHHHHHHhCCccccCccccc
Q 031236 16 ETTSHCRICHEEEFESCNSLEAPCACSGTVKFAHRDCIQRWCYEKGNTTCEICLQEY 72 (163)
Q Consensus 16 ~~~~~CRIC~~~~~~~~~~l~~PC~C~Gsl~~vH~~CL~~Wl~~k~~~~CeiCk~~y 72 (163)
++..-|.||++...+. .+.-+-|+ |.|=++|++.-+ |...+||+|++..
T Consensus 129 ~~~~~CPiCl~~~sek-~~vsTkCG-----HvFC~~Cik~al--k~~~~CP~C~kkI 177 (187)
T KOG0320|consen 129 EGTYKCPICLDSVSEK-VPVSTKCG-----HVFCSQCIKDAL--KNTNKCPTCRKKI 177 (187)
T ss_pred ccccCCCceecchhhc-cccccccc-----hhHHHHHHHHHH--HhCCCCCCccccc
Confidence 4458899999987652 12335566 999999999998 6778999999744
No 50
>KOG0825 consensus PHD Zn-finger protein [General function prediction only]
Probab=90.81 E-value=0.055 Score=53.01 Aligned_cols=27 Identities=22% Similarity=0.720 Sum_probs=23.6
Q ss_pred ceecHHHHHHHHHHhCCccccCccccccC
Q 031236 46 KFAHRDCIQRWCYEKGNTTCEICLQEYGP 74 (163)
Q Consensus 46 ~~vH~~CL~~Wl~~k~~~~CeiCk~~y~~ 74 (163)
||+|..|+..|. +...+|++|+..|..
T Consensus 146 H~FC~~Ci~sWs--R~aqTCPiDR~EF~~ 172 (1134)
T KOG0825|consen 146 HYFCEECVGSWS--RCAQTCPVDRGEFGE 172 (1134)
T ss_pred cccHHHHhhhhh--hhcccCchhhhhhhe
Confidence 899999999999 456699999999853
No 51
>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=90.28 E-value=0.23 Score=34.19 Aligned_cols=47 Identities=21% Similarity=0.254 Sum_probs=32.6
Q ss_pred CeeeEcccCcccCCCceeecccCCCCCceecHHHHHHHHHHhCCccccCccccccC
Q 031236 19 SHCRICHEEEFESCNSLEAPCACSGTVKFAHRDCIQRWCYEKGNTTCEICLQEYGP 74 (163)
Q Consensus 19 ~~CRIC~~~~~~~~~~l~~PC~C~Gsl~~vH~~CL~~Wl~~k~~~~CeiCk~~y~~ 74 (163)
-.|.|+++--. ++.+.|++ +.+=+.++++|++. ++.+||+|++....
T Consensus 5 f~CpIt~~lM~---dPVi~~~G-----~tyer~~I~~~l~~-~~~~~P~t~~~l~~ 51 (73)
T PF04564_consen 5 FLCPITGELMR---DPVILPSG-----HTYERSAIERWLEQ-NGGTDPFTRQPLSE 51 (73)
T ss_dssp GB-TTTSSB-S---SEEEETTS-----EEEEHHHHHHHHCT-TSSB-TTT-SB-SG
T ss_pred cCCcCcCcHhh---CceeCCcC-----CEEcHHHHHHHHHc-CCCCCCCCCCcCCc
Confidence 35777766554 35888876 89999999999975 57899999976653
No 52
>KOG2177 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=89.32 E-value=0.15 Score=40.10 Aligned_cols=45 Identities=29% Similarity=0.578 Sum_probs=39.1
Q ss_pred CCCCeeeEcccCcccCCCceeecccCCCCCceecHHHHHHHHHHhCCccccCccc
Q 031236 16 ETTSHCRICHEEEFESCNSLEAPCACSGTVKFAHRDCIQRWCYEKGNTTCEICLQ 70 (163)
Q Consensus 16 ~~~~~CRIC~~~~~~~~~~l~~PC~C~Gsl~~vH~~CL~~Wl~~k~~~~CeiCk~ 70 (163)
++...|.||++...+. .+.||. |.+=+.|+..+.. ....||.|+.
T Consensus 11 ~~~~~C~iC~~~~~~p---~~l~C~-----H~~c~~C~~~~~~--~~~~Cp~cr~ 55 (386)
T KOG2177|consen 11 QEELTCPICLEYFREP---VLLPCG-----HNFCRACLTRSWE--GPLSCPVCRP 55 (386)
T ss_pred cccccChhhHHHhhcC---cccccc-----chHhHHHHHHhcC--CCcCCcccCC
Confidence 4678999999988764 789999 9999999999997 7789999993
No 53
>KOG1002 consensus Nucleotide excision repair protein RAD16 [Replication, recombination and repair]
Probab=87.04 E-value=0.41 Score=45.47 Aligned_cols=58 Identities=22% Similarity=0.558 Sum_probs=46.6
Q ss_pred CCCCCeeeEcccCcccCCCceeecccCCCCCceecHHHHHHHHHH---hCCccccCccccccCCccCCC
Q 031236 15 PETTSHCRICHEEEFESCNSLEAPCACSGTVKFAHRDCIQRWCYE---KGNTTCEICLQEYGPGYTAPS 80 (163)
Q Consensus 15 s~~~~~CRIC~~~~~~~~~~l~~PC~C~Gsl~~vH~~CL~~Wl~~---k~~~~CeiCk~~y~~~y~~p~ 80 (163)
..+..+|.+|++..++ .+++.|+ |-+-+.|+..++.. ..+.+||.|........+.|.
T Consensus 533 nk~~~~C~lc~d~aed---~i~s~Ch-----H~FCrlCi~eyv~~f~~~~nvtCP~C~i~LsiDlse~a 593 (791)
T KOG1002|consen 533 NKGEVECGLCHDPAED---YIESSCH-----HKFCRLCIKEYVESFMENNNVTCPVCHIGLSIDLSEPA 593 (791)
T ss_pred ccCceeecccCChhhh---hHhhhhh-----HHHHHHHHHHHHHhhhcccCCCCccccccccccccchh
Confidence 3467899999998654 4789998 88999999999865 356999999988877666554
No 54
>PLN02400 cellulose synthase
Probab=86.80 E-value=0.82 Score=46.25 Aligned_cols=68 Identities=19% Similarity=0.387 Sum_probs=41.6
Q ss_pred ccceeecc-CCCCC---CCCCeeeEcccCcc-cCCCceeeccc-CCCCCceecHHHHHHHHHHhCCccccCccccccC
Q 031236 3 DVVLFVED-FKSNP---ETTSHCRICHEEEF-ESCNSLEAPCA-CSGTVKFAHRDCIQRWCYEKGNTTCEICLQEYGP 74 (163)
Q Consensus 3 ~~vl~v~d-~~~~s---~~~~~CRIC~~~~~-~~~~~l~~PC~-C~Gsl~~vH~~CL~~Wl~~k~~~~CeiCk~~y~~ 74 (163)
-|++..|+ ...++ -....|.||-++-. ..++.+.--|+ |. --|=+.|.+-=. ..|+..||+||++|+-
T Consensus 17 lv~i~~d~~~g~kp~~~~~gqiCqICGD~VG~t~dGe~FVAC~eCa---FPVCRpCYEYER-keGnq~CPQCkTrYkR 90 (1085)
T PLN02400 17 LVRIRHDSDSGPKPLKNLNGQICQICGDDVGVTETGDVFVACNECA---FPVCRPCYEYER-KDGTQCCPQCKTRYRR 90 (1085)
T ss_pred eeeecccccccCCCccccCCceeeecccccCcCCCCCEEEEEccCC---Cccccchhheec-ccCCccCcccCCcccc
Confidence 46666552 22222 34569999988732 12233555565 43 347778874322 2488999999999984
No 55
>KOG1941 consensus Acetylcholine receptor-associated protein of the synapse (rapsyn) [Extracellular structures]
Probab=86.35 E-value=0.34 Score=44.38 Aligned_cols=48 Identities=23% Similarity=0.499 Sum_probs=38.1
Q ss_pred CCeeeEcccCcccCCCc-eeecccCCCCCceecHHHHHHHHHHhCCccccCccc
Q 031236 18 TSHCRICHEEEFESCNS-LEAPCACSGTVKFAHRDCIQRWCYEKGNTTCEICLQ 70 (163)
Q Consensus 18 ~~~CRIC~~~~~~~~~~-l~~PC~C~Gsl~~vH~~CL~~Wl~~k~~~~CeiCk~ 70 (163)
+-.|-.|-+.....++. ...||. |.+|..|++..+...+..+||-|++
T Consensus 365 ~L~Cg~CGe~~Glk~e~LqALpCs-----HIfH~rCl~e~L~~n~~rsCP~Crk 413 (518)
T KOG1941|consen 365 ELYCGLCGESIGLKNERLQALPCS-----HIFHLRCLQEILENNGTRSCPNCRK 413 (518)
T ss_pred hhhhhhhhhhhcCCcccccccchh-----HHHHHHHHHHHHHhCCCCCCccHHH
Confidence 45688887765433333 478998 9999999999998889999999994
No 56
>PF14569 zf-UDP: Zinc-binding RING-finger; PDB: 1WEO_A.
Probab=86.22 E-value=0.93 Score=32.61 Aligned_cols=55 Identities=22% Similarity=0.462 Sum_probs=22.7
Q ss_pred CCCeeeEcccCcc-cCCCceeeccc-CCCCCceecHHHHHHHHHHhCCccccCccccccCC
Q 031236 17 TTSHCRICHEEEF-ESCNSLEAPCA-CSGTVKFAHRDCIQRWCYEKGNTTCEICLQEYGPG 75 (163)
Q Consensus 17 ~~~~CRIC~~~~~-~~~~~l~~PC~-C~Gsl~~vH~~CL~~Wl~~k~~~~CeiCk~~y~~~ 75 (163)
....|.||-++-. ..+..+..-|+ |. --+=+.|.+-=.+ -|+..|+.|+++|+..
T Consensus 8 ~~qiCqiCGD~VGl~~~Ge~FVAC~eC~---fPvCr~CyEYErk-eg~q~CpqCkt~ykr~ 64 (80)
T PF14569_consen 8 NGQICQICGDDVGLTENGEVFVACHECA---FPVCRPCYEYERK-EGNQVCPQCKTRYKRH 64 (80)
T ss_dssp SS-B-SSS--B--B-SSSSB--S-SSS--------HHHHHHHHH-TS-SB-TTT--B----
T ss_pred CCcccccccCccccCCCCCEEEEEcccC---CccchhHHHHHhh-cCcccccccCCCcccc
Confidence 5789999987632 12233555555 43 4588899876664 3889999999999743
No 57
>COG5432 RAD18 RING-finger-containing E3 ubiquitin ligase [Signal transduction mechanisms]
Probab=86.02 E-value=0.41 Score=42.38 Aligned_cols=47 Identities=23% Similarity=0.441 Sum_probs=38.0
Q ss_pred CCCeeeEcccCcccCCCceeecccCCCCCceecHHHHHHHHHHhCCccccCcccccc
Q 031236 17 TTSHCRICHEEEFESCNSLEAPCACSGTVKFAHRDCIQRWCYEKGNTTCEICLQEYG 73 (163)
Q Consensus 17 ~~~~CRIC~~~~~~~~~~l~~PC~C~Gsl~~vH~~CL~~Wl~~k~~~~CeiCk~~y~ 73 (163)
..-.|+||.+-..- +.++||+ |-+-.-|+.+-+. .+..||+|+..+.
T Consensus 24 s~lrC~IC~~~i~i---p~~TtCg-----HtFCslCIR~hL~--~qp~CP~Cr~~~~ 70 (391)
T COG5432 24 SMLRCRICDCRISI---PCETTCG-----HTFCSLCIRRHLG--TQPFCPVCREDPC 70 (391)
T ss_pred hHHHhhhhhheeec---ceecccc-----cchhHHHHHHHhc--CCCCCccccccHH
Confidence 35689999887643 4789998 8899999999994 4568999997664
No 58
>PF05290 Baculo_IE-1: Baculovirus immediate-early protein (IE-0); InterPro: IPR007954 This entry contains the Baculovirus immediate-early protein IE-0.
Probab=85.32 E-value=0.66 Score=36.54 Aligned_cols=54 Identities=20% Similarity=0.523 Sum_probs=40.6
Q ss_pred CCeeeEcccCcccCCCceeecccCCCCCceecHHHHHHHHHHhCCccccCccccccC
Q 031236 18 TSHCRICHEEEFESCNSLEAPCACSGTVKFAHRDCIQRWCYEKGNTTCEICLQEYGP 74 (163)
Q Consensus 18 ~~~CRIC~~~~~~~~~~l~~PC~C~Gsl~~vH~~CL~~Wl~~k~~~~CeiCk~~y~~ 74 (163)
.-+|-||+|...| +.+..|=.|-|. ..-.-=|.+-|--.+-...||.||+.|+.
T Consensus 80 lYeCnIC~etS~e--e~FLKPneCCgY-~iCn~Cya~LWK~~~~ypvCPvCkTSFKs 133 (140)
T PF05290_consen 80 LYECNICKETSAE--ERFLKPNECCGY-SICNACYANLWKFCNLYPVCPVCKTSFKS 133 (140)
T ss_pred ceeccCcccccch--hhcCCcccccch-HHHHHHHHHHHHHcccCCCCCcccccccc
Confidence 7799999998765 348888667762 23344556788877778899999999974
No 59
>PLN02195 cellulose synthase A
Probab=84.51 E-value=1.1 Score=44.82 Aligned_cols=53 Identities=25% Similarity=0.464 Sum_probs=36.1
Q ss_pred CCCeeeEcccCcc-cCCCceeeccc-CCCCCceecHHHHHHHHHHhCCccccCcccccc
Q 031236 17 TTSHCRICHEEEF-ESCNSLEAPCA-CSGTVKFAHRDCIQRWCYEKGNTTCEICLQEYG 73 (163)
Q Consensus 17 ~~~~CRIC~~~~~-~~~~~l~~PC~-C~Gsl~~vH~~CL~~Wl~~k~~~~CeiCk~~y~ 73 (163)
....|+||-++-. +.++...--|+ |. --|=+.|.+-=. ..|+..||.||++|+
T Consensus 5 ~~~~c~~cgd~~~~~~~g~~fvaC~eC~---~pvCrpCyeyer-~eg~q~CpqCkt~Yk 59 (977)
T PLN02195 5 GAPICATCGEEVGVDSNGEAFVACHECS---YPLCKACLEYEI-KEGRKVCLRCGGPYD 59 (977)
T ss_pred CCccceecccccCcCCCCCeEEEeccCC---Cccccchhhhhh-hcCCccCCccCCccc
Confidence 4569999987632 22233555566 54 447889984333 348999999999998
No 60
>KOG1039 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=84.29 E-value=0.83 Score=40.80 Aligned_cols=52 Identities=23% Similarity=0.570 Sum_probs=37.4
Q ss_pred CCCCeeeEcccCcccCC---Cce-eec-ccCCCCCceecHHHHHHHHHHhC-----CccccCccccc
Q 031236 16 ETTSHCRICHEEEFESC---NSL-EAP-CACSGTVKFAHRDCIQRWCYEKG-----NTTCEICLQEY 72 (163)
Q Consensus 16 ~~~~~CRIC~~~~~~~~---~~l-~~P-C~C~Gsl~~vH~~CL~~Wl~~k~-----~~~CeiCk~~y 72 (163)
..++.|-||++...+.. ..+ +.| |+ |.+=..|+.+|-..+. ...||+|+..-
T Consensus 159 s~~k~CGICme~i~ek~~~~~rfgilpnC~-----H~~Cl~Cir~wr~~~q~~~~~sksCP~CRv~s 220 (344)
T KOG1039|consen 159 SSEKECGICMETINEKAASERRFGILPNCN-----HSFCLNCIRKWRQATQFESKTSKSCPFCRVPS 220 (344)
T ss_pred cccccceehhhhccccchhhhhcccCCCcc-----hhhhhcHhHhhhhhhccccccccCCCcccCcc
Confidence 34789999999865422 011 335 66 8888899999997655 68999999543
No 61
>KOG1428 consensus Inhibitor of type V adenylyl cyclases/Neuronal presynaptic protein Highwire/PAM/RPM-1 [Signal transduction mechanisms]
Probab=83.85 E-value=0.98 Score=47.72 Aligned_cols=55 Identities=22% Similarity=0.599 Sum_probs=38.6
Q ss_pred CCCCCCeeeEcccCcccCCCceeecccCCCCCceecHHHHHHHHHHh--------CCccccCcccccc
Q 031236 14 NPETTSHCRICHEEEFESCNSLEAPCACSGTVKFAHRDCIQRWCYEK--------GNTTCEICLQEYG 73 (163)
Q Consensus 14 ~s~~~~~CRIC~~~~~~~~~~l~~PC~C~Gsl~~vH~~CL~~Wl~~k--------~~~~CeiCk~~y~ 73 (163)
+.+.+..|-||+.+--.....+..-|. |.+|-.|..+-+..+ +-..||||+++.+
T Consensus 3482 kQD~DDmCmICFTE~L~AAP~IqL~C~-----HiFHlqC~R~vLE~RW~GPRItF~FisCPiC~n~In 3544 (3738)
T KOG1428|consen 3482 KQDADDMCMICFTEALSAAPAIQLDCS-----HIFHLQCCRRVLENRWLGPRITFGFISCPICKNKIN 3544 (3738)
T ss_pred hcccCceEEEEehhhhCCCcceecCCc-----cchhHHHHHHHHHhcccCCeeEEeeeecccccchhh
Confidence 456789999999875432212334444 999999998766554 3578999998764
No 62
>KOG0287 consensus Postreplication repair protein RAD18 [Replication, recombination and repair]
Probab=83.56 E-value=0.43 Score=43.05 Aligned_cols=46 Identities=22% Similarity=0.447 Sum_probs=37.3
Q ss_pred CCeeeEcccCcccCCCceeecccCCCCCceecHHHHHHHHHHhCCccccCcccccc
Q 031236 18 TSHCRICHEEEFESCNSLEAPCACSGTVKFAHRDCIQRWCYEKGNTTCEICLQEYG 73 (163)
Q Consensus 18 ~~~CRIC~~~~~~~~~~l~~PC~C~Gsl~~vH~~CL~~Wl~~k~~~~CeiCk~~y~ 73 (163)
.-.|-||++=..- ++++||. |-+-.-|+...+ +.+..||.|..+++
T Consensus 23 lLRC~IC~eyf~i---p~itpCs-----HtfCSlCIR~~L--~~~p~CP~C~~~~~ 68 (442)
T KOG0287|consen 23 LLRCGICFEYFNI---PMITPCS-----HTFCSLCIRKFL--SYKPQCPTCCVTVT 68 (442)
T ss_pred HHHHhHHHHHhcC---ceecccc-----chHHHHHHHHHh--ccCCCCCceecccc
Confidence 3579999987643 5999988 889999999999 45679999997653
No 63
>PLN02638 cellulose synthase A (UDP-forming), catalytic subunit
Probab=82.40 E-value=1.7 Score=44.03 Aligned_cols=54 Identities=22% Similarity=0.451 Sum_probs=36.5
Q ss_pred CCCeeeEcccCcc-cCCCceeeccc-CCCCCceecHHHHHHHHHHhCCccccCccccccC
Q 031236 17 TTSHCRICHEEEF-ESCNSLEAPCA-CSGTVKFAHRDCIQRWCYEKGNTTCEICLQEYGP 74 (163)
Q Consensus 17 ~~~~CRIC~~~~~-~~~~~l~~PC~-C~Gsl~~vH~~CL~~Wl~~k~~~~CeiCk~~y~~ 74 (163)
....|+||-++-. ..++.+.--|+ |. --|=+.|.+-=. ..|+..||+||++|+-
T Consensus 16 ~~qiCqICGD~vg~~~~Ge~FVAC~eC~---FPVCrpCYEYEr-~eG~q~CPqCktrYkr 71 (1079)
T PLN02638 16 GGQVCQICGDNVGKTVDGEPFVACDVCA---FPVCRPCYEYER-KDGNQSCPQCKTKYKR 71 (1079)
T ss_pred CCceeeecccccCcCCCCCEEEEeccCC---Cccccchhhhhh-hcCCccCCccCCchhh
Confidence 4569999988742 12233555666 43 347788984333 3489999999999983
No 64
>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=82.29 E-value=0.59 Score=33.14 Aligned_cols=33 Identities=27% Similarity=0.639 Sum_probs=25.2
Q ss_pred CCCeeeEcccCcccCCCceeecccCCCCCceecHHHHHH
Q 031236 17 TTSHCRICHEEEFESCNSLEAPCACSGTVKFAHRDCIQR 55 (163)
Q Consensus 17 ~~~~CRIC~~~~~~~~~~l~~PC~C~Gsl~~vH~~CL~~ 55 (163)
+...|.+|......+ .-.+-||+ +.+|..|++|
T Consensus 77 ~~~~C~vC~k~l~~~-~f~~~p~~-----~v~H~~C~~r 109 (109)
T PF10367_consen 77 ESTKCSVCGKPLGNS-VFVVFPCG-----HVVHYSCIKR 109 (109)
T ss_pred CCCCccCcCCcCCCc-eEEEeCCC-----eEEecccccC
Confidence 456899999887653 34578887 8999999864
No 65
>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=81.75 E-value=1.3 Score=39.76 Aligned_cols=33 Identities=21% Similarity=0.802 Sum_probs=26.4
Q ss_pred ecccCCCCCceecHHHHHHHHHHh-----------CCccccCccccc
Q 031236 37 APCACSGTVKFAHRDCIQRWCYEK-----------GNTTCEICLQEY 72 (163)
Q Consensus 37 ~PC~C~Gsl~~vH~~CL~~Wl~~k-----------~~~~CeiCk~~y 72 (163)
.+|.|+ -.-=.+|+-+|+.++ ++..||.|++.|
T Consensus 307 ~~C~CR---PmWC~~Cm~kwFasrQd~~~~~~Wl~~~~~CPtCRa~F 350 (358)
T PF10272_consen 307 QQCYCR---PMWCLECMGKWFASRQDQQHPETWLSGKCPCPTCRAKF 350 (358)
T ss_pred cccccc---chHHHHHHHHHhhhcCCCCChhhhhcCCCCCCCCcccc
Confidence 467777 556679999999876 468999999887
No 66
>COG5574 PEX10 RING-finger-containing E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=81.00 E-value=1.7 Score=37.69 Aligned_cols=49 Identities=22% Similarity=0.543 Sum_probs=38.1
Q ss_pred CCCCCeeeEcccCcccCCCceeecccCCCCCceecHHHHHH-HHHHhCCccccCccccc
Q 031236 15 PETTSHCRICHEEEFESCNSLEAPCACSGTVKFAHRDCIQR-WCYEKGNTTCEICLQEY 72 (163)
Q Consensus 15 s~~~~~CRIC~~~~~~~~~~l~~PC~C~Gsl~~vH~~CL~~-Wl~~k~~~~CeiCk~~y 72 (163)
+.....|-||++..+. +.-+||+ |.+=-.||.. |... ....||+|++.-
T Consensus 212 p~~d~kC~lC~e~~~~---ps~t~Cg-----HlFC~~Cl~~~~t~~-k~~~CplCRak~ 261 (271)
T COG5574 212 PLADYKCFLCLEEPEV---PSCTPCG-----HLFCLSCLLISWTKK-KYEFCPLCRAKV 261 (271)
T ss_pred cccccceeeeecccCC---ccccccc-----chhhHHHHHHHHHhh-ccccCchhhhhc
Confidence 3456789999998654 4689998 9999999999 8853 345699999653
No 67
>PF08746 zf-RING-like: RING-like domain; InterPro: IPR014857 This is a zinc finger domain that is related to the C3HC4 RING finger domain (IPR001841 from INTERPRO). ; PDB: 3NW0_A 2CT0_A.
Probab=79.19 E-value=1.4 Score=27.71 Aligned_cols=23 Identities=26% Similarity=0.720 Sum_probs=16.0
Q ss_pred ceecHHHHHHHHHHhCCccccCc
Q 031236 46 KFAHRDCIQRWCYEKGNTTCEIC 68 (163)
Q Consensus 46 ~~vH~~CL~~Wl~~k~~~~CeiC 68 (163)
.-+|..|++++++.+.+..||.|
T Consensus 21 ~r~H~~C~~~y~r~~~~~~CP~C 43 (43)
T PF08746_consen 21 VRLHDDCFKKYFRHRSNPKCPNC 43 (43)
T ss_dssp -EE-HHHHHHHTTT-SS-B-TTT
T ss_pred chHHHHHHHHHHhcCCCCCCcCC
Confidence 45999999999988777789987
No 68
>PLN02915 cellulose synthase A [UDP-forming], catalytic subunit
Probab=78.64 E-value=2.4 Score=42.82 Aligned_cols=56 Identities=21% Similarity=0.468 Sum_probs=37.6
Q ss_pred CCCCCeeeEcccCcc-cCCCceeeccc-CCCCCceecHHHHHHHHHHhCCccccCccccccC
Q 031236 15 PETTSHCRICHEEEF-ESCNSLEAPCA-CSGTVKFAHRDCIQRWCYEKGNTTCEICLQEYGP 74 (163)
Q Consensus 15 s~~~~~CRIC~~~~~-~~~~~l~~PC~-C~Gsl~~vH~~CL~~Wl~~k~~~~CeiCk~~y~~ 74 (163)
+-....|.||-++-. +.++.+.--|+ |. --+=+.|.+-= ...|+..||.||++|+-
T Consensus 12 ~~~~~~c~iCGd~vg~~~~Ge~FVAC~eC~---fpvCr~cyeye-~~~g~~~cp~c~t~y~~ 69 (1044)
T PLN02915 12 SADAKTCRVCGDEVGVKEDGQPFVACHVCG---FPVCKPCYEYE-RSEGNQCCPQCNTRYKR 69 (1044)
T ss_pred CCCcchhhccccccCcCCCCCEEEEeccCC---Cccccchhhhh-hhcCCccCCccCCchhh
Confidence 346789999988732 22233555566 43 44778898433 33488999999999984
No 69
>KOG2164 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=76.12 E-value=2.5 Score=39.66 Aligned_cols=49 Identities=22% Similarity=0.504 Sum_probs=37.6
Q ss_pred CCeeeEcccCcccCCCceeecccCCCCCceecHHHHHHHHHHh---CCccccCccccccC
Q 031236 18 TSHCRICHEEEFESCNSLEAPCACSGTVKFAHRDCIQRWCYEK---GNTTCEICLQEYGP 74 (163)
Q Consensus 18 ~~~CRIC~~~~~~~~~~l~~PC~C~Gsl~~vH~~CL~~Wl~~k---~~~~CeiCk~~y~~ 74 (163)
..+|.||+++..-. ..+-|+ |.+=-.||-+.++.. +-..||||...+.+
T Consensus 186 ~~~CPICL~~~~~p---~~t~CG-----HiFC~~CiLqy~~~s~~~~~~~CPiC~s~I~~ 237 (513)
T KOG2164|consen 186 DMQCPICLEPPSVP---VRTNCG-----HIFCGPCILQYWNYSAIKGPCSCPICRSTITL 237 (513)
T ss_pred CCcCCcccCCCCcc---cccccC-----ceeeHHHHHHHHhhhcccCCccCCchhhhccc
Confidence 67999999986542 445577 899999998877553 56899999987654
No 70
>KOG1952 consensus Transcription factor NF-X1, contains NFX-type Zn2+-binding and R3H domains [Transcription]
Probab=72.24 E-value=3.7 Score=40.87 Aligned_cols=55 Identities=20% Similarity=0.507 Sum_probs=40.0
Q ss_pred CCCCCeeeEcccCcccCCCceeecccCCCCCceecHHHHHHHHHHh-----CCccccCcccccc
Q 031236 15 PETTSHCRICHEEEFESCNSLEAPCACSGTVKFAHRDCIQRWCYEK-----GNTTCEICLQEYG 73 (163)
Q Consensus 15 s~~~~~CRIC~~~~~~~~~~l~~PC~C~Gsl~~vH~~CL~~Wl~~k-----~~~~CeiCk~~y~ 73 (163)
+....+|-||.+........| +|+.--+.+|-.|+++|-.++ ..+.||-|+..++
T Consensus 188 ~~~~yeCmIC~e~I~~t~~~W----SC~sCYhVFHl~CI~~WArs~ek~~~~~WrCP~Cqsv~~ 247 (950)
T KOG1952|consen 188 SNRKYECMICTERIKRTAPVW----SCKSCYHVFHLNCIKKWARSSEKTGQDGWRCPACQSVSK 247 (950)
T ss_pred hcCceEEEEeeeeccccCCce----ecchhhhhhhHHHHHHHHHHhhhccCccccCCcccchhc
Confidence 345689999999876544344 222233899999999999764 3589999997665
No 71
>PF14447 Prok-RING_4: Prokaryotic RING finger family 4
Probab=71.14 E-value=3.6 Score=27.67 Aligned_cols=46 Identities=15% Similarity=0.424 Sum_probs=32.2
Q ss_pred CCeeeEcccCcccCCCceeecccCCCCCceecHHHHHHHHHHhCCccccCccccccCC
Q 031236 18 TSHCRICHEEEFESCNSLEAPCACSGTVKFAHRDCIQRWCYEKGNTTCEICLQEYGPG 75 (163)
Q Consensus 18 ~~~CRIC~~~~~~~~~~l~~PC~C~Gsl~~vH~~CL~~Wl~~k~~~~CeiCk~~y~~~ 75 (163)
...|-.|-.... ...++||+ |++=+.|..- ++-.-||+|+.++++.
T Consensus 7 ~~~~~~~~~~~~---~~~~~pCg-----H~I~~~~f~~----~rYngCPfC~~~~~~~ 52 (55)
T PF14447_consen 7 EQPCVFCGFVGT---KGTVLPCG-----HLICDNCFPG----ERYNGCPFCGTPFEFD 52 (55)
T ss_pred ceeEEEcccccc---cccccccc-----ceeeccccCh----hhccCCCCCCCcccCC
Confidence 456777755543 34789999 8888888433 3456799999998753
No 72
>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=69.45 E-value=6.9 Score=31.62 Aligned_cols=42 Identities=24% Similarity=0.638 Sum_probs=26.5
Q ss_pred CCCeeeEcccCcccCC----Cceeeccc---CCCCCceecHHHHHHHHHHh
Q 031236 17 TTSHCRICHEEEFESC----NSLEAPCA---CSGTVKFAHRDCIQRWCYEK 60 (163)
Q Consensus 17 ~~~~CRIC~~~~~~~~----~~l~~PC~---C~Gsl~~vH~~CL~~Wl~~k 60 (163)
++..|.||+|-.-..- -.....|. |. ..|-|..||.|..+..
T Consensus 1 ed~~CpICme~PHNAVLLlCSS~~kgcRpymc~--Ts~rhSNCLdqfkka~ 49 (162)
T PF07800_consen 1 EDVTCPICMEHPHNAVLLLCSSHEKGCRPYMCD--TSYRHSNCLDQFKKAY 49 (162)
T ss_pred CCccCceeccCCCceEEEEeccccCCccccccC--CccchhHHHHHHHHHh
Confidence 3568999998764310 00123333 54 3688999999998764
No 73
>KOG1940 consensus Zn-finger protein [General function prediction only]
Probab=65.21 E-value=3.1 Score=36.22 Aligned_cols=43 Identities=33% Similarity=0.702 Sum_probs=32.2
Q ss_pred eeEcccCcccCC-CceeecccCCCCCceecHHHHHHHHHHhCCccccCccc
Q 031236 21 CRICHEEEFESC-NSLEAPCACSGTVKFAHRDCIQRWCYEKGNTTCEICLQ 70 (163)
Q Consensus 21 CRIC~~~~~~~~-~~l~~PC~C~Gsl~~vH~~CL~~Wl~~k~~~~CeiCk~ 70 (163)
|.||.+...++. .+-..||+ ++.|..|++.-..+ +..||+|+.
T Consensus 161 cPic~e~l~~s~~~~~~~~Cg-----H~~h~~cf~e~~~~--~y~CP~C~~ 204 (276)
T KOG1940|consen 161 CPICKEYLFLSFEDAGVLKCG-----HYMHSRCFEEMICE--GYTCPICSK 204 (276)
T ss_pred CchhHHHhccccccCCccCcc-----cchHHHHHHHHhcc--CCCCCcccc
Confidence 888887755443 23477888 99998888777743 399999997
No 74
>PLN02248 cellulose synthase-like protein
Probab=63.26 E-value=22 Score=36.57 Aligned_cols=35 Identities=26% Similarity=0.453 Sum_probs=28.4
Q ss_pred eeecccCCCCCceecHHHHHHHHHHhCCccccCccccccC
Q 031236 35 LEAPCACSGTVKFAHRDCIQRWCYEKGNTTCEICLQEYGP 74 (163)
Q Consensus 35 l~~PC~C~Gsl~~vH~~CL~~Wl~~k~~~~CeiCk~~y~~ 74 (163)
-+.||.|. .-+-++|...=++. .-.||=||.+|+.
T Consensus 144 ~~~~~~~~---~~~~~~~~~~~~~~--~~~~~~~~~~~~~ 178 (1135)
T PLN02248 144 DLLPCECG---FKICRDCYIDAVKS--GGICPGCKEPYKV 178 (1135)
T ss_pred cCCccccc---chhHHhHhhhhhhc--CCCCCCCcccccc
Confidence 48999998 66889998777754 5599999999953
No 75
>COG5236 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=61.56 E-value=10 Score=34.54 Aligned_cols=55 Identities=22% Similarity=0.402 Sum_probs=38.5
Q ss_pred CCCCCCCCeeeEcccCcccCCCceeecccCCCCCceecHHHHHHHHHHhCCccccCccccccC
Q 031236 12 KSNPETTSHCRICHEEEFESCNSLEAPCACSGTVKFAHRDCIQRWCYEKGNTTCEICLQEYGP 74 (163)
Q Consensus 12 ~~~s~~~~~CRIC~~~~~~~~~~l~~PC~C~Gsl~~vH~~CL~~Wl~~k~~~~CeiCk~~y~~ 74 (163)
.+..++...|-||-+...-+ -..||+ |-.-..|--+-...-.+..|++|+++.+.
T Consensus 55 ddtDEen~~C~ICA~~~TYs---~~~PC~-----H~~CH~Ca~RlRALY~~K~C~~CrTE~e~ 109 (493)
T COG5236 55 DDTDEENMNCQICAGSTTYS---ARYPCG-----HQICHACAVRLRALYMQKGCPLCRTETEA 109 (493)
T ss_pred cccccccceeEEecCCceEE---EeccCC-----chHHHHHHHHHHHHHhccCCCccccccce
Confidence 34456778999998775433 589998 44445566555555567789999988764
No 76
>KOG4172 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=61.28 E-value=4.9 Score=27.36 Aligned_cols=47 Identities=23% Similarity=0.452 Sum_probs=28.9
Q ss_pred CCeeeEcccCcccCCCceeecccCCCCCce-ecHHHHHHHHHHhCCccccCcccccc
Q 031236 18 TSHCRICHEEEFESCNSLEAPCACSGTVKF-AHRDCIQRWCYEKGNTTCEICLQEYG 73 (163)
Q Consensus 18 ~~~CRIC~~~~~~~~~~l~~PC~C~Gsl~~-vH~~CL~~Wl~~k~~~~CeiCk~~y~ 73 (163)
..+|-||.+...++ ..--|+ |. .-.+|-.+-.+ .....||||+.+.+
T Consensus 7 ~dECTICye~pvds---VlYtCG-----HMCmCy~Cg~rl~~-~~~g~CPiCRapi~ 54 (62)
T KOG4172|consen 7 SDECTICYEHPVDS---VLYTCG-----HMCMCYACGLRLKK-ALHGCCPICRAPIK 54 (62)
T ss_pred ccceeeeccCcchH---HHHHcc-----hHHhHHHHHHHHHH-ccCCcCcchhhHHH
Confidence 38999999987654 344454 11 12345433332 26679999997765
No 77
>KOG3899 consensus Uncharacterized conserved protein [Function unknown]
Probab=60.72 E-value=5 Score=35.69 Aligned_cols=31 Identities=19% Similarity=0.642 Sum_probs=24.3
Q ss_pred cCCCCCceecHHHHHHHHHHh-----------CCccccCcccccc
Q 031236 40 ACSGTVKFAHRDCIQRWCYEK-----------GNTTCEICLQEYG 73 (163)
Q Consensus 40 ~C~Gsl~~vH~~CL~~Wl~~k-----------~~~~CeiCk~~y~ 73 (163)
-|+ ..--++||.+|+..+ ++-+||.|++.|=
T Consensus 324 ~cr---p~wc~~cla~~f~~rq~~v~r~~~~~~~~~cp~cr~~fc 365 (381)
T KOG3899|consen 324 ICR---PLWCRSCLAQIFIGRQDNVYRYEYHRGSAQCPTCRKNFC 365 (381)
T ss_pred ccc---cHHHHHHHHHHHhhcccchhHHHHHhcCCCCcchhhceE
Confidence 366 566789999999653 5789999998874
No 78
>smart00782 PhnA_Zn_Ribbon PhnA Zinc-Ribbon. This protein family includes an uncharacterised member designated phnA in Escherichia coli, part of a large operon associated with alkylphosphonate uptake and carbon-phosphorus bond cleavage. This protein is not related to the characterised phosphonoacetate hydrolase designated PhnA.
Probab=57.08 E-value=9.4 Score=24.66 Aligned_cols=24 Identities=21% Similarity=0.545 Sum_probs=15.3
Q ss_pred HhCCccccCcccccc-CCccCCCCC
Q 031236 59 EKGNTTCEICLQEYG-PGYTAPSKK 82 (163)
Q Consensus 59 ~k~~~~CeiCk~~y~-~~y~~p~~~ 82 (163)
.+...+||+|+..-+ ..|..||..
T Consensus 4 ~Rs~~kCELC~a~~~L~vy~Vpp~~ 28 (47)
T smart00782 4 ARCESKCELCGSDSPLVVYAVPPSS 28 (47)
T ss_pred HHcCCcccCcCCCCCceEEecCCCC
Confidence 344578999997665 345555543
No 79
>PF05191 ADK_lid: Adenylate kinase, active site lid; InterPro: IPR007862 Adenylate kinases (ADK; 2.7.4.3 from EC) are phosphotransferases that catalyse the Mg-dependent reversible conversion of ATP and AMP to two molecules of ADP, an essential reaction for many processes in living cells. In large variants of adenylate kinase, the AMP and ATP substrates are buried in a domain that undergoes conformational changes from an open to a closed state when bound to substrate; the ligand is then contained within a highly specific environment required for catalysis. Adenylate kinase is a 3-domain protein consisting of a large central CORE domain flanked by a LID domain on one side and the AMP-binding NMPbind domain on the other []. The LID domain binds ATP and covers the phosphates at the active site. The substrates first bind the CORE domain, followed by closure of the active site by the LID and NMPbind domains. Comparisons of adenylate kinases have revealed a particular divergence in the active site lid. In some organisms, particularly the Gram-positive bacteria, residues in the lid domain have been mutated to cysteines and these cysteine residues (two CX(n)C motifs) are responsible for the binding of a zinc ion. The bound zinc ion in the lid domain is clearly structurally homologous to Zinc-finger domains. However, it is unclear whether the adenylate kinase lid is a novel zinc-finger DNA/RNA binding domain, or that the lid bound zinc serves a purely structural function [].; GO: 0004017 adenylate kinase activity; PDB: 3BE4_A 2OSB_B 2ORI_A 2EU8_A 3DL0_A 1P3J_A 2QAJ_A 2OO7_A 2P3S_A 3DKV_A ....
Probab=56.37 E-value=5.4 Score=24.25 Aligned_cols=19 Identities=21% Similarity=0.508 Sum_probs=13.9
Q ss_pred ccccCccccccCCccCCCC
Q 031236 63 TTCEICLQEYGPGYTAPSK 81 (163)
Q Consensus 63 ~~CeiCk~~y~~~y~~p~~ 81 (163)
.+|+.|+..|...+..|..
T Consensus 2 r~C~~Cg~~Yh~~~~pP~~ 20 (36)
T PF05191_consen 2 RICPKCGRIYHIEFNPPKV 20 (36)
T ss_dssp EEETTTTEEEETTTB--SS
T ss_pred cCcCCCCCccccccCCCCC
Confidence 4799999999988765443
No 80
>KOG3268 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=53.59 E-value=14 Score=30.82 Aligned_cols=28 Identities=21% Similarity=0.446 Sum_probs=20.5
Q ss_pred ceecHHHHHHHHHHh---C------CccccCcccccc
Q 031236 46 KFAHRDCIQRWCYEK---G------NTTCEICLQEYG 73 (163)
Q Consensus 46 ~~vH~~CL~~Wl~~k---~------~~~CeiCk~~y~ 73 (163)
+-+|+-||-.|++.- + -..||-|..+..
T Consensus 192 kpFHqiCL~dWLRgilTsRQSFdiiFGeCPYCS~Pia 228 (234)
T KOG3268|consen 192 KPFHQICLTDWLRGILTSRQSFDIIFGECPYCSDPIA 228 (234)
T ss_pred CcHHHHHHHHHHHHHhhccceeeeeeccCCCCCCcce
Confidence 899999999999642 1 146888876543
No 81
>KOG2879 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=52.61 E-value=17 Score=31.95 Aligned_cols=51 Identities=18% Similarity=0.384 Sum_probs=38.8
Q ss_pred CCCCeeeEcccCcccCCCceeecccCCCCCceecHHHHHHHHHHhCCccccCcccccc
Q 031236 16 ETTSHCRICHEEEFESCNSLEAPCACSGTVKFAHRDCIQRWCYEKGNTTCEICLQEYG 73 (163)
Q Consensus 16 ~~~~~CRIC~~~~~~~~~~l~~PC~C~Gsl~~vH~~CL~~Wl~~k~~~~CeiCk~~y~ 73 (163)
....+|.+|.+...-+ ..+.||. |.+=..|+..=+...-.-+|+.|+..-+
T Consensus 237 t~~~~C~~Cg~~PtiP--~~~~~C~-----HiyCY~Ci~ts~~~~asf~Cp~Cg~~~~ 287 (298)
T KOG2879|consen 237 TSDTECPVCGEPPTIP--HVIGKCG-----HIYCYYCIATSRLWDASFTCPLCGENVE 287 (298)
T ss_pred cCCceeeccCCCCCCC--eeecccc-----ceeehhhhhhhhcchhhcccCccCCCCc
Confidence 4579999997765432 2467788 8888999987776666789999997665
No 82
>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=52.10 E-value=10 Score=24.96 Aligned_cols=27 Identities=15% Similarity=0.423 Sum_probs=19.1
Q ss_pred ceecHHHHHHHHHHhCCccccCccccccC
Q 031236 46 KFAHRDCIQRWCYEKGNTTCEICLQEYGP 74 (163)
Q Consensus 46 ~~vH~~CL~~Wl~~k~~~~CeiCk~~y~~ 74 (163)
||.=..||..-+ +.+..||||+++.+.
T Consensus 21 HYLCl~CLt~ml--~~s~~C~iC~~~LPt 47 (50)
T PF03854_consen 21 HYLCLNCLTLML--SRSDRCPICGKPLPT 47 (50)
T ss_dssp -EEEHHHHHHT---SSSSEETTTTEE---
T ss_pred hhHHHHHHHHHh--ccccCCCcccCcCcc
Confidence 899999998777 567799999977654
No 83
>COG5175 MOT2 Transcriptional repressor [Transcription]
Probab=50.07 E-value=12 Score=34.01 Aligned_cols=59 Identities=20% Similarity=0.450 Sum_probs=39.6
Q ss_pred eccCCCCCCCCCeeeEcccCcccCCCceeecccCCCCCceecHHHHHHHHHHh--CCccccCcccccc
Q 031236 8 VEDFKSNPETTSHCRICHEEEFESCNSLEAPCACSGTVKFAHRDCIQRWCYEK--GNTTCEICLQEYG 73 (163)
Q Consensus 8 v~d~~~~s~~~~~CRIC~~~~~~~~~~l~~PC~C~Gsl~~vH~~CL~~Wl~~k--~~~~CeiCk~~y~ 73 (163)
+++..+..+++..|..|.++-+-.+ .-..||.|. .-+-+-| |-.-+ =+..||-|+..|.
T Consensus 4 ~qei~~sedeed~cplcie~mditd-knf~pc~cg---y~ic~fc---~~~irq~lngrcpacrr~y~ 64 (480)
T COG5175 4 VQEIHNSEDEEDYCPLCIEPMDITD-KNFFPCPCG---YQICQFC---YNNIRQNLNGRCPACRRKYD 64 (480)
T ss_pred hhhccccccccccCccccccccccc-CCcccCCcc---cHHHHHH---HHHHHhhccCCChHhhhhcc
Confidence 4555555567778999999876543 457899996 2244444 54333 3679999999884
No 84
>KOG1100 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=48.27 E-value=8.2 Score=31.99 Aligned_cols=39 Identities=33% Similarity=0.653 Sum_probs=25.5
Q ss_pred CeeeEcccCcccCCCceeecccCCCCCceec-HHHHHHHHHHhCCccccCcccc
Q 031236 19 SHCRICHEEEFESCNSLEAPCACSGTVKFAH-RDCIQRWCYEKGNTTCEICLQE 71 (163)
Q Consensus 19 ~~CRIC~~~~~~~~~~l~~PC~C~Gsl~~vH-~~CL~~Wl~~k~~~~CeiCk~~ 71 (163)
..||.|.+.+. ..+..||+ |+.| ..| .. +..+||+|+..
T Consensus 159 ~~Cr~C~~~~~---~VlllPCr-----Hl~lC~~C-----~~-~~~~CPiC~~~ 198 (207)
T KOG1100|consen 159 RSCRKCGEREA---TVLLLPCR-----HLCLCGIC-----DE-SLRICPICRSP 198 (207)
T ss_pred ccceecCcCCc---eEEeeccc-----ceEecccc-----cc-cCccCCCCcCh
Confidence 44999988764 36899998 5543 122 11 15679999943
No 85
>PF01440 Gemini_AL2: Geminivirus AL2 protein; InterPro: IPR000942 Geminiviruses are characterised by a genome of circular single-stranded DNA encapsidated in twinned (geminate) quasi-isometric particles, from which the group derives its name []. Most geminiviruses can be divided into two subgroups on the basis of host range and/or insect vector: i.e. those that infect dicotyledenous plants and are transmitted by the same whitefly species, and those that infect monocotyledenous plants and are transmitted by different leafhopper vectors. The genomes of the whitefly-transmitted African cassava mosaic virus, Tomato golden mosaic virus (TGMV) and Bean golden mosaic virus (BGMV) possess a bipartite genome. By contrast, only a single DNA component has been identified for the leafhopper-transmitted Maize streak virus (MSV) and Wheat dwarf virus (WDV) [, ]. Beet curly top virus (BCTV), and Tobacco yellow dwarf virus belong to a third possible subgroup. Like MSV and WDV, BCTV is transmitted by a specific leafhopper species, yet like the whitefly-transmitted geminiviruses it has a host range confined to dicotyledenous plants. Sequence comparison of the whitefly-transmitted Squash leaf curl virus (SqLCV) and Tomato yellow leaf curl virus (TYLCV) with the genomic components of TGMV and BGMV reveals a close evolutionary relationship [, , ]. Amino acid sequence alignments of Potato yellow mosaic virus (PYMV) proteins with those encoded by other geminiviruses show that PYMV is closely related to geminiviruses isolated from the New World, especially in the putative coat protein gene regions []. Comparison of MSV DNA-encoded proteins with those of other geminiviruses infecting monocotyledonous plants, including Panicum streak virus [] and Miscanthus streak virus (MiSV) [], reveal high levels of similarity.; GO: 0005198 structural molecule activity, 0019028 viral capsid
Probab=45.02 E-value=3.6 Score=32.24 Aligned_cols=33 Identities=24% Similarity=0.674 Sum_probs=28.0
Q ss_pred ceeecccCCCCCceecHHHHHHHHHHhCCccccCcc
Q 031236 34 SLEAPCACSGTVKFAHRDCIQRWCYEKGNTTCEICL 69 (163)
Q Consensus 34 ~l~~PC~C~Gsl~~vH~~CL~~Wl~~k~~~~CeiCk 69 (163)
.+-+||+|+ -|+|-.|-...+.++|...|---+
T Consensus 32 RIDL~CGCS---yyihinC~~hGFTHRGthhCsS~~ 64 (134)
T PF01440_consen 32 RIDLPCGCS---YYIHINCHNHGFTHRGTHHCSSSR 64 (134)
T ss_pred ccccCCCCE---EEeecccCCCCcCCCcCccCCCcC
Confidence 356899999 999999999999999877776555
No 86
>KOG3970 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=44.17 E-value=28 Score=30.07 Aligned_cols=53 Identities=19% Similarity=0.431 Sum_probs=39.5
Q ss_pred CCCCCeeeEcccCcccCCCceeecccCCCCCceecHHHHHHHHHHh------CCccccCcccccc
Q 031236 15 PETTSHCRICHEEEFESCNSLEAPCACSGTVKFAHRDCIQRWCYEK------GNTTCEICLQEYG 73 (163)
Q Consensus 15 s~~~~~CRIC~~~~~~~~~~l~~PC~C~Gsl~~vH~~CL~~Wl~~k------~~~~CeiCk~~y~ 73 (163)
++..+-|+.|-....+++ ....-|- +.+|=+||..|-..- ....||-|.++.-
T Consensus 47 sDY~pNC~LC~t~La~gd-t~RLvCy-----hlfHW~ClneraA~lPanTAPaGyqCP~Cs~eiF 105 (299)
T KOG3970|consen 47 SDYNPNCRLCNTPLASGD-TTRLVCY-----HLFHWKCLNERAANLPANTAPAGYQCPCCSQEIF 105 (299)
T ss_pred cCCCCCCceeCCccccCc-ceeehhh-----hhHHHHHhhHHHhhCCCcCCCCcccCCCCCCccC
Confidence 345688999987766543 4566666 999999999998653 2478999998653
No 87
>KOG4692 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=44.17 E-value=15 Score=33.57 Aligned_cols=48 Identities=21% Similarity=0.451 Sum_probs=36.5
Q ss_pred CCCCeeeEcccCcccCCCceeecccCCCCCceecHHHHHHHHHHhCCccccCcccccc
Q 031236 16 ETTSHCRICHEEEFESCNSLEAPCACSGTVKFAHRDCIQRWCYEKGNTTCEICLQEYG 73 (163)
Q Consensus 16 ~~~~~CRIC~~~~~~~~~~l~~PC~C~Gsl~~vH~~CL~~Wl~~k~~~~CeiCk~~y~ 73 (163)
.++..|.||....-. .+..||+ |-.-..|+.+=+ -+...|=.||++..
T Consensus 420 sEd~lCpICyA~pi~---Avf~PC~-----H~SC~~CI~qHl--mN~k~CFfCktTv~ 467 (489)
T KOG4692|consen 420 SEDNLCPICYAGPIN---AVFAPCS-----HRSCYGCITQHL--MNCKRCFFCKTTVI 467 (489)
T ss_pred cccccCcceecccch---hhccCCC-----CchHHHHHHHHH--hcCCeeeEecceee
Confidence 357899999987643 4899998 666668887777 35678999997654
No 88
>PF04532 DUF587: Protein of unknown function (DUF587); InterPro: IPR007618 This domain is found at the N-termini of some human herpesvirus U58 proteins, and some cytomegalovirus UL87 proteins. This region is always found N-terminal to the UL87 (IPR004285 from INTERPRO), which has no known function.
Probab=43.78 E-value=7.1 Score=32.74 Aligned_cols=29 Identities=28% Similarity=0.634 Sum_probs=21.1
Q ss_pred cccCcccCCCce-eecccCCCCCceecHHH
Q 031236 24 CHEEEFESCNSL-EAPCACSGTVKFAHRDC 52 (163)
Q Consensus 24 C~~~~~~~~~~l-~~PC~C~Gsl~~vH~~C 52 (163)
|..++.+.++-| +.|+.|.|.+-|+|+++
T Consensus 93 CyCdeWd~~eyl~~~~~~C~GP~LYVhr~r 122 (215)
T PF04532_consen 93 CYCDEWDTNEYLAECAYFCRGPLLYVHRKR 122 (215)
T ss_pred eeecceehhhHHhhCCcccCCceEEEEccc
Confidence 666655543333 78899999999999943
No 89
>PF10215 Ost4: Oligosaccaryltransferase ; InterPro: IPR018943 Ost4 is a very short, approximately 30 residues, enzyme found from fungi to vertebrates. It is a member of the ER oligosaccaryltansferase complex, 2.4.1.119 from EC, that catalyses the asparagine-linked glycosylation of proteins. It appears to be an integral membrane protein that mediates the en bloc transfer of a pre-assembled high-mannose oligosaccharide onto asparagine residues of nascent polypeptides as they enter the lumen of the rough endoplasmic reticulum. ; PDB: 1RKL_A 2LAT_A.
Probab=42.41 E-value=32 Score=20.99 Aligned_cols=24 Identities=13% Similarity=0.123 Sum_probs=20.1
Q ss_pred hhHHHHHHHHHHHHHHhhhhhhee
Q 031236 135 ACCRSLALTVRFLFCEWSSYRVSM 158 (163)
Q Consensus 135 ~~CR~~ai~lm~lLll~h~l~~~~ 158 (163)
.++.++-++.|+|-++-|++-+|.
T Consensus 9 ~lan~lG~~~~~LIVlYH~v~~n~ 32 (35)
T PF10215_consen 9 TLANFLGVAAMVLIVLYHFVEVNA 32 (35)
T ss_dssp HHHHHHHHHHHHHHHHHHHHCCH-
T ss_pred HHHHHHHHHHHHHHHHHHHhhccc
Confidence 567888999999999999998763
No 90
>KOG0956 consensus PHD finger protein AF10 [General function prediction only]
Probab=41.64 E-value=17 Score=35.88 Aligned_cols=58 Identities=28% Similarity=0.488 Sum_probs=36.9
Q ss_pred CCCeeeEcccCcccCCCc--eeecccCCCCCceecHHHHHHH---HHHh-----CCccccCccccccC
Q 031236 17 TTSHCRICHEEEFESCNS--LEAPCACSGTVKFAHRDCIQRW---CYEK-----GNTTCEICLQEYGP 74 (163)
Q Consensus 17 ~~~~CRIC~~~~~~~~~~--l~~PC~C~Gsl~~vH~~CL~~W---l~~k-----~~~~CeiCk~~y~~ 74 (163)
.-+.|.||.|+..++... --.-|+=.|--+-||..|.|+- +++. +-..|--|++-|..
T Consensus 116 fnKtCYIC~E~GrpnkA~~GACMtCNKs~CkqaFHVTCAQ~~GLLCEE~gn~~dNVKYCGYCk~HfsK 183 (900)
T KOG0956|consen 116 FNKTCYICNEEGRPNKAAKGACMTCNKSGCKQAFHVTCAQRAGLLCEEEGNISDNVKYCGYCKYHFSK 183 (900)
T ss_pred hcceeeeecccCCccccccccceecccccchhhhhhhHhhhhccceeccccccccceechhHHHHHHH
Confidence 468999998886543211 1234442222289999999874 3333 24789999988853
No 91
>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=41.01 E-value=12 Score=18.93 Aligned_cols=11 Identities=27% Similarity=0.857 Sum_probs=7.0
Q ss_pred cccCccccccC
Q 031236 64 TCEICLQEYGP 74 (163)
Q Consensus 64 ~CeiCk~~y~~ 74 (163)
.|++|+..|..
T Consensus 2 ~C~~C~~~~~~ 12 (24)
T PF13894_consen 2 QCPICGKSFRS 12 (24)
T ss_dssp E-SSTS-EESS
T ss_pred CCcCCCCcCCc
Confidence 59999988753
No 92
>KOG0824 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=40.28 E-value=18 Score=32.13 Aligned_cols=53 Identities=17% Similarity=0.293 Sum_probs=35.2
Q ss_pred CCCCeeeEcccCcccCCCceeecccCCCCCceecHHHHHHHHHHhCCccccCccccccCCcc
Q 031236 16 ETTSHCRICHEEEFESCNSLEAPCACSGTVKFAHRDCIQRWCYEKGNTTCEICLQEYGPGYT 77 (163)
Q Consensus 16 ~~~~~CRIC~~~~~~~~~~l~~PC~C~Gsl~~vH~~CL~~Wl~~k~~~~CeiCk~~y~~~y~ 77 (163)
...++|-||+....- +...||. |-+=..||+-=.. .+...|.+|++++.-.+.
T Consensus 5 ~~~~eC~IC~nt~n~---Pv~l~C~-----HkFCyiCiKGsy~-ndk~~CavCR~pids~i~ 57 (324)
T KOG0824|consen 5 TKKKECLICYNTGNC---PVNLYCF-----HKFCYICIKGSYK-NDKKTCAVCRFPIDSTID 57 (324)
T ss_pred ccCCcceeeeccCCc---Ccccccc-----chhhhhhhcchhh-cCCCCCceecCCCCcchh
Confidence 346899999987532 3567777 6666777643332 145679999998864443
No 93
>COG5152 Uncharacterized conserved protein, contains RING and CCCH-type Zn-fingers [General function prediction only]
Probab=38.55 E-value=19 Score=30.50 Aligned_cols=42 Identities=19% Similarity=0.455 Sum_probs=34.1
Q ss_pred eeeEcccCcccCCCceeecccCCCCCceecHHHHHHHHHHhCCccccCcccc
Q 031236 20 HCRICHEEEFESCNSLEAPCACSGTVKFAHRDCIQRWCYEKGNTTCEICLQE 71 (163)
Q Consensus 20 ~CRIC~~~~~~~~~~l~~PC~C~Gsl~~vH~~CL~~Wl~~k~~~~CeiCk~~ 71 (163)
.|-||...... +.++-|+ |++-..|..+=. +....|-+|+..
T Consensus 198 ~C~iCKkdy~s---pvvt~CG-----H~FC~~Cai~~y--~kg~~C~~Cgk~ 239 (259)
T COG5152 198 LCGICKKDYES---PVVTECG-----HSFCSLCAIRKY--QKGDECGVCGKA 239 (259)
T ss_pred eehhchhhccc---hhhhhcc-----hhHHHHHHHHHh--ccCCcceecchh
Confidence 89999888754 4889898 899999987655 567899999964
No 94
>KOG0802 consensus E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=38.33 E-value=14 Score=34.46 Aligned_cols=46 Identities=28% Similarity=0.770 Sum_probs=33.6
Q ss_pred CCCCeeeEcccCcccCCCceeecccCCCCCceecHHHHHHHHHHhCCccccCccccccCC
Q 031236 16 ETTSHCRICHEEEFESCNSLEAPCACSGTVKFAHRDCIQRWCYEKGNTTCEICLQEYGPG 75 (163)
Q Consensus 16 ~~~~~CRIC~~~~~~~~~~l~~PC~C~Gsl~~vH~~CL~~Wl~~k~~~~CeiCk~~y~~~ 75 (163)
+....|+||.++- . .-+.||. |..|+..|...+ ..||+|+.....+
T Consensus 477 ~~~~~~~~~~~~~-~---~~~~~~~--------~~~~l~~~~~~~--~~~pl~~~~~~~~ 522 (543)
T KOG0802|consen 477 EPNDVCAICYQEM-S---ARITPCS--------HALCLRKWLYVQ--EVCPLCHTYMKED 522 (543)
T ss_pred cccCcchHHHHHH-H---hcccccc--------chhHHHhhhhhc--cccCCCchhhhcc
Confidence 4568999998776 1 1356666 999999999644 4899999766543
No 95
>PF04641 Rtf2: Rtf2 RING-finger
Probab=37.52 E-value=45 Score=28.13 Aligned_cols=51 Identities=18% Similarity=0.402 Sum_probs=35.2
Q ss_pred CCCCCeeeEcccCcccCC-CceeecccCCCCCceecHHHHHHHHHHhCCccccCcccccc
Q 031236 15 PETTSHCRICHEEEFESC-NSLEAPCACSGTVKFAHRDCIQRWCYEKGNTTCEICLQEYG 73 (163)
Q Consensus 15 s~~~~~CRIC~~~~~~~~-~~l~~PC~C~Gsl~~vH~~CL~~Wl~~k~~~~CeiCk~~y~ 73 (163)
....-.|.|...+..... -..+.||+| .+-..+|++- +....|++|+.+|.
T Consensus 110 ~~~~~~CPvt~~~~~~~~~fv~l~~cG~-----V~s~~alke~---k~~~~Cp~c~~~f~ 161 (260)
T PF04641_consen 110 SEGRFICPVTGKEFNGKHKFVYLRPCGC-----VFSEKALKEL---KKSKKCPVCGKPFT 161 (260)
T ss_pred CCceeECCCCCcccCCceeEEEEcCCCC-----EeeHHHHHhh---cccccccccCCccc
Confidence 455677888776653221 134789995 7778888766 24567999999996
No 96
>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=36.81 E-value=14 Score=19.10 Aligned_cols=11 Identities=27% Similarity=0.902 Sum_probs=9.1
Q ss_pred cccCccccccC
Q 031236 64 TCEICLQEYGP 74 (163)
Q Consensus 64 ~CeiCk~~y~~ 74 (163)
.|+.|+..|..
T Consensus 2 ~C~~C~~~f~~ 12 (23)
T PF00096_consen 2 KCPICGKSFSS 12 (23)
T ss_dssp EETTTTEEESS
T ss_pred CCCCCCCccCC
Confidence 69999988864
No 97
>KOG2068 consensus MOT2 transcription factor [Transcription]
Probab=36.15 E-value=37 Score=30.34 Aligned_cols=53 Identities=25% Similarity=0.454 Sum_probs=35.2
Q ss_pred CCCeeeEcccCcccCCCceeecccCCCCCceecHHHHHHHHHHhCCccccCccccccCC
Q 031236 17 TTSHCRICHEEEFESCNSLEAPCACSGTVKFAHRDCIQRWCYEKGNTTCEICLQEYGPG 75 (163)
Q Consensus 17 ~~~~CRIC~~~~~~~~~~l~~PC~C~Gsl~~vH~~CL~~Wl~~k~~~~CeiCk~~y~~~ 75 (163)
..+.|.||-+.... .+....||.|. ...+..|+..=. .++..|+.|+++|..+
T Consensus 248 v~~s~p~~~~~~~~-~d~~~lP~~~~---~~~~l~~~~t~~--~~~~~~~~~rk~~~~~ 300 (327)
T KOG2068|consen 248 VPPSCPICYEDLDL-TDSNFLPCPCG---FRLCLFCHKTIS--DGDGRCPGCRKPYERN 300 (327)
T ss_pred cCCCCCCCCCcccc-ccccccccccc---ccchhhhhhccc--ccCCCCCccCCccccC
Confidence 45899999887632 33468999987 334444443322 3678999999887654
No 98
>PHA03375 hypothetical protein; Provisional
Probab=36.00 E-value=12 Score=36.74 Aligned_cols=29 Identities=28% Similarity=0.729 Sum_probs=21.6
Q ss_pred cccCcccCCCce-eecccCCCCCceecHHH
Q 031236 24 CHEEEFESCNSL-EAPCACSGTVKFAHRDC 52 (163)
Q Consensus 24 C~~~~~~~~~~l-~~PC~C~Gsl~~vH~~C 52 (163)
|..++.+.++-| ..+|.|.|.+-|+|+.+
T Consensus 99 CycdeWd~~eyl~~~~~~C~gP~LYvhr~r 128 (844)
T PHA03375 99 CYCDEWDVNEYLAKTACNCRGPLLYIHRSR 128 (844)
T ss_pred ccccchhhhhhhhhcccccCCceEEEEecc
Confidence 666665544333 79999999999999943
No 99
>PF10795 DUF2607: Protein of unknown function (DUF2607); InterPro: IPR019731 This entry represents conserved protein found in in Gammaproteobacteria. The function is not known.
Probab=35.90 E-value=37 Score=25.25 Aligned_cols=19 Identities=16% Similarity=0.340 Sum_probs=12.0
Q ss_pred hhHHHHHHHHHHHHHHhhhh
Q 031236 135 ACCRSLALTVRFLFCEWSSY 154 (163)
Q Consensus 135 ~~CR~~ai~lm~lLll~h~l 154 (163)
-++|.++ +|+++|++|+-+
T Consensus 11 ~~~r~~~-l~~vaLlL~lnf 29 (99)
T PF10795_consen 11 HWRRTVA-LFAVALLLWLNF 29 (99)
T ss_pred HHHHHHH-HHHHHHHHHHHH
Confidence 3455555 677777777654
No 100
>KOG4443 consensus Putative transcription factor HALR/MLL3, involved in embryonic development [General function prediction only]
Probab=35.67 E-value=23 Score=34.47 Aligned_cols=33 Identities=24% Similarity=0.563 Sum_probs=25.2
Q ss_pred eeecccCCCCCceecHHHHHHHHHHh---------CCccccCcc
Q 031236 35 LEAPCACSGTVKFAHRDCIQRWCYEK---------GNTTCEICL 69 (163)
Q Consensus 35 l~~PC~C~Gsl~~vH~~CL~~Wl~~k---------~~~~CeiCk 69 (163)
...-|.+.| +..|..|+.-|+++. +-+.||-|+
T Consensus 34 ~m~ac~~c~--~~yH~~cvt~~~~~~~l~~gWrC~~crvCe~c~ 75 (694)
T KOG4443|consen 34 RLLACSDCG--QKYHPYCVTSWAQHAVLSGGWRCPSCRVCEACG 75 (694)
T ss_pred cchhhhhhc--ccCCcchhhHHHhHHHhcCCcccCCceeeeecc
Confidence 355677665 899999999999875 236777777
No 101
>KOG0978 consensus E3 ubiquitin ligase involved in syntaxin degradation [Posttranslational modification, protein turnover, chaperones]
Probab=34.67 E-value=17 Score=35.45 Aligned_cols=48 Identities=17% Similarity=0.508 Sum_probs=36.4
Q ss_pred CCeeeEcccCcccCCCceeecccCCCCCceecHHHHHHHHHHhCCccccCccccccC
Q 031236 18 TSHCRICHEEEFESCNSLEAPCACSGTVKFAHRDCIQRWCYEKGNTTCEICLQEYGP 74 (163)
Q Consensus 18 ~~~CRIC~~~~~~~~~~l~~PC~C~Gsl~~vH~~CL~~Wl~~k~~~~CeiCk~~y~~ 74 (163)
.-.|..|....-+ ..+.-|. |.|=..|++.-+.. +.++||.|+..|.+
T Consensus 643 ~LkCs~Cn~R~Kd---~vI~kC~-----H~FC~~Cvq~r~et-RqRKCP~Cn~aFga 690 (698)
T KOG0978|consen 643 LLKCSVCNTRWKD---AVITKCG-----HVFCEECVQTRYET-RQRKCPKCNAAFGA 690 (698)
T ss_pred ceeCCCccCchhh---HHHHhcc-----hHHHHHHHHHHHHH-hcCCCCCCCCCCCc
Confidence 4679999744322 3566676 99999999998875 56899999988853
No 102
>PF00301 Rubredoxin: Rubredoxin; InterPro: IPR004039 Rubredoxin is a low molecular weight iron-containing bacterial protein involved in electron transfer [, ], sometimes replacing ferredoxin as an electron carrier []. The 3-D structures of a number of rubredoxins have been solved [, ]. The fold belongs to the alpha+beta class, with 2 alpha-helices and 2-3 beta-strands. Its active site contains an iron ion which is co-ordinated by the sulphurs of four conserved cysteine residues forming an almost regular tetrahedron. The conserved cysteines reside on two loops, which are the most conserved regions of the protein. In addition, a ring of acidic residues in the proximity of the [Fe(Cys)4] centre is also well-conserved []. ; GO: 0009055 electron carrier activity, 0046872 metal ion binding; PDB: 2RDV_C 1RDV_A 1S24_A 1T9O_B 1B2J_A 1SMW_A 2PVE_B 1BFY_A 1T9P_C 1C09_C ....
Probab=33.70 E-value=22 Score=22.86 Aligned_cols=17 Identities=29% Similarity=0.677 Sum_probs=12.9
Q ss_pred ccccCccccccCCccCC
Q 031236 63 TTCEICLQEYGPGYTAP 79 (163)
Q Consensus 63 ~~CeiCk~~y~~~y~~p 79 (163)
..|.+|++.|.+....|
T Consensus 2 y~C~~CgyvYd~~~Gd~ 18 (47)
T PF00301_consen 2 YQCPVCGYVYDPEKGDP 18 (47)
T ss_dssp EEETTTSBEEETTTBBG
T ss_pred cCCCCCCEEEcCCcCCc
Confidence 36999999998766543
No 103
>KOG1814 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=33.65 E-value=29 Score=32.10 Aligned_cols=47 Identities=19% Similarity=0.380 Sum_probs=36.2
Q ss_pred CCeeeEcccCcccCCCceeecccCCCCCceecHHHHHHHHHHh------CCccccCcc
Q 031236 18 TSHCRICHEEEFESCNSLEAPCACSGTVKFAHRDCIQRWCYEK------GNTTCEICL 69 (163)
Q Consensus 18 ~~~CRIC~~~~~~~~~~l~~PC~C~Gsl~~vH~~CL~~Wl~~k------~~~~CeiCk 69 (163)
.-.|-||+++..-.......||. |++=+.|++..+..- ....|+-++
T Consensus 184 lf~C~ICf~e~~G~~c~~~lpC~-----Hv~Ck~C~kdY~~~~i~eg~v~~l~Cp~~~ 236 (445)
T KOG1814|consen 184 LFDCCICFEEQMGQHCFKFLPCS-----HVFCKSCLKDYFTIQIQEGQVSCLKCPDPK 236 (445)
T ss_pred cccceeeehhhcCcceeeecccc-----hHHHHHHHHHHHHHhhhcceeeeecCCCCC
Confidence 36899999987543445689999 999999999998652 346788877
No 104
>PF13956 Ibs_toxin: Toxin Ibs, type I toxin-antitoxin system
Probab=33.40 E-value=23 Score=18.81 Aligned_cols=11 Identities=18% Similarity=0.244 Sum_probs=7.7
Q ss_pred HHHHHHHHHHH
Q 031236 140 LALTVRFLFCE 150 (163)
Q Consensus 140 ~ai~lm~lLll 150 (163)
++|||.+|||.
T Consensus 4 ~vIIlvvLLli 14 (19)
T PF13956_consen 4 LVIILVVLLLI 14 (19)
T ss_pred ehHHHHHHHhc
Confidence 35777888774
No 105
>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=32.56 E-value=29 Score=22.22 Aligned_cols=21 Identities=14% Similarity=0.464 Sum_probs=10.2
Q ss_pred HHHHHHHh-C-CccccCcccccc
Q 031236 53 IQRWCYEK-G-NTTCEICLQEYG 73 (163)
Q Consensus 53 L~~Wl~~k-~-~~~CeiCk~~y~ 73 (163)
+++++..- + ...||+|+.++.
T Consensus 9 ~~k~i~~l~~~~~~CPlC~r~l~ 31 (54)
T PF04423_consen 9 LKKYIEELKEAKGCCPLCGRPLD 31 (54)
T ss_dssp HHHHHHHHTT-SEE-TTT--EE-
T ss_pred HHHHHHHHhcCCCcCCCCCCCCC
Confidence 45555442 2 239999998775
No 106
>PF05715 zf-piccolo: Piccolo Zn-finger; InterPro: IPR008899 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 (predicted) zinc finger is found in the bassoon and piccolo proteins, both of which are components of the presynaptic cytoskeletal matrix (PCM) assembled at the active zone of neurotransmitter release, where Piccolo plays a role in the trafficking of synaptic vesicles (SVs) [, , ]. The Piccolo zinc fingers were found to interact with the dual prenylated rab3A and VAMP2/Synaptobrevin II receptor PRA1. There are eight conserved cysteines in Piccolo-type zinc fingers, suggesting that they coordinates two zinc ligands. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0046872 metal ion binding, 0045202 synapse
Probab=32.11 E-value=30 Score=23.73 Aligned_cols=18 Identities=22% Similarity=0.645 Sum_probs=11.7
Q ss_pred CccccCccccccCCccCC
Q 031236 62 NTTCEICLQEYGPGYTAP 79 (163)
Q Consensus 62 ~~~CeiCk~~y~~~y~~p 79 (163)
+..||+||.....+.+.|
T Consensus 2 k~~CPlCkt~~n~gsk~~ 19 (61)
T PF05715_consen 2 KSLCPLCKTTLNVGSKDP 19 (61)
T ss_pred CccCCcccchhhcCCCCC
Confidence 357888888776554433
No 107
>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=31.72 E-value=23 Score=19.99 Aligned_cols=13 Identities=15% Similarity=0.493 Sum_probs=9.9
Q ss_pred CCccccCcccccc
Q 031236 61 GNTTCEICLQEYG 73 (163)
Q Consensus 61 ~~~~CeiCk~~y~ 73 (163)
....||.|++.|.
T Consensus 13 ~~~~Cp~CG~~F~ 25 (26)
T PF10571_consen 13 SAKFCPHCGYDFE 25 (26)
T ss_pred hcCcCCCCCCCCc
Confidence 4568999997764
No 108
>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 KOG4159 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=31.36 E-value=32 Score=31.45 Aligned_cols=47 Identities=21% Similarity=0.581 Sum_probs=34.9
Q ss_pred CCCeeeEcccCcccCCCceeecccCCCCCceecHHHHHHHHHHhCCccccCcccccc
Q 031236 17 TTSHCRICHEEEFESCNSLEAPCACSGTVKFAHRDCIQRWCYEKGNTTCEICLQEYG 73 (163)
Q Consensus 17 ~~~~CRIC~~~~~~~~~~l~~PC~C~Gsl~~vH~~CL~~Wl~~k~~~~CeiCk~~y~ 73 (163)
.+-+|-||..-.. ++..+||+ |-+=..||++=+ .....||+|+..|.
T Consensus 83 sef~c~vc~~~l~---~pv~tpcg-----hs~c~~Cl~r~l--d~~~~cp~Cr~~l~ 129 (398)
T KOG4159|consen 83 SEFECCVCSRALY---PPVVTPCG-----HSFCLECLDRSL--DQETECPLCRDELV 129 (398)
T ss_pred chhhhhhhHhhcC---CCcccccc-----ccccHHHHHHHh--ccCCCCcccccccc
Confidence 4578999966554 34788998 666667888833 46789999998875
No 110
>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=30.43 E-value=36 Score=21.78 Aligned_cols=35 Identities=17% Similarity=0.435 Sum_probs=14.5
Q ss_pred ceeecccCCCCCceecHHHH--HHHHHH---hCCccccCcccc
Q 031236 34 SLEAPCACSGTVKFAHRDCI--QRWCYE---KGNTTCEICLQE 71 (163)
Q Consensus 34 ~l~~PC~C~Gsl~~vH~~CL--~~Wl~~---k~~~~CeiCk~~ 71 (163)
.+..|.+=+ .-.|..|. +.|+.. ++...||+|+++
T Consensus 11 ~i~~P~Rg~---~C~H~~CFDl~~fl~~~~~~~~W~CPiC~~~ 50 (50)
T PF02891_consen 11 RIRIPVRGK---NCKHLQCFDLESFLESNQRTPKWKCPICNKP 50 (50)
T ss_dssp B-SSEEEET---T--SS--EEHHHHHHHHHHS---B-TTT---
T ss_pred EEEeCccCC---cCcccceECHHHHHHHhhccCCeECcCCcCc
Confidence 466676622 45677774 567644 466899999863
No 111
>PTZ00382 Variant-specific surface protein (VSP); Provisional
Probab=28.37 E-value=33 Score=25.04 Aligned_cols=16 Identities=13% Similarity=-0.058 Sum_probs=9.1
Q ss_pred HHHHHHHHHHHhhhhh
Q 031236 140 LALTVRFLFCEWSSYR 155 (163)
Q Consensus 140 ~ai~lm~lLll~h~l~ 155 (163)
+.+..++.||.|||++
T Consensus 77 ~~v~~lv~~l~w~f~~ 92 (96)
T PTZ00382 77 AVVGGLVGFLCWWFVC 92 (96)
T ss_pred hHHHHHHHHHhheeEE
Confidence 3344555567777763
No 112
>KOG3039 consensus Uncharacterized conserved protein [Function unknown]
Probab=28.31 E-value=55 Score=28.63 Aligned_cols=50 Identities=6% Similarity=0.225 Sum_probs=36.8
Q ss_pred CCCeeeEcccCcccC-CCceeecccCCCCCceecHHHHHHHHHHhCCccccCcccccc
Q 031236 17 TTSHCRICHEEEFES-CNSLEAPCACSGTVKFAHRDCIQRWCYEKGNTTCEICLQEYG 73 (163)
Q Consensus 17 ~~~~CRIC~~~~~~~-~~~l~~PC~C~Gsl~~vH~~CL~~Wl~~k~~~~CeiCk~~y~ 73 (163)
..-.|.+|++..... .-....||+ +.|-.+|+++.+ +++..|++|..+..
T Consensus 220 ~ryiCpvtrd~LtNt~~ca~Lr~sg-----~Vv~~ecvEkli--r~D~v~pv~d~plk 270 (303)
T KOG3039|consen 220 KRYICPVTRDTLTNTTPCAVLRPSG-----HVVTKECVEKLI--RKDMVDPVTDKPLK 270 (303)
T ss_pred cceecccchhhhcCccceEEeccCC-----cEeeHHHHHHhc--cccccccCCCCcCc
Confidence 346899999886432 112356665 889999999999 67889999996654
No 113
>PF13878 zf-C2H2_3: zinc-finger of acetyl-transferase ESCO
Probab=27.41 E-value=36 Score=21.03 Aligned_cols=15 Identities=53% Similarity=1.052 Sum_probs=12.3
Q ss_pred CCccccCccccccCC
Q 031236 61 GNTTCEICLQEYGPG 75 (163)
Q Consensus 61 ~~~~CeiCk~~y~~~ 75 (163)
+.++|+.|+-.|.++
T Consensus 12 ~~~~C~~CgM~Y~~~ 26 (41)
T PF13878_consen 12 GATTCPTCGMLYSPG 26 (41)
T ss_pred CCcCCCCCCCEECCC
Confidence 468999999888764
No 114
>KOG0955 consensus PHD finger protein BR140/LIN-49 [General function prediction only]
Probab=26.96 E-value=23 Score=36.16 Aligned_cols=51 Identities=29% Similarity=0.611 Sum_probs=36.1
Q ss_pred CCCCeeeEcccCcccCCCceeeccc-CCCCCceecHHHHHHHHHHhCCccccCccc
Q 031236 16 ETTSHCRICHEEEFESCNSLEAPCA-CSGTVKFAHRDCIQRWCYEKGNTTCEICLQ 70 (163)
Q Consensus 16 ~~~~~CRIC~~~~~~~~~~l~~PC~-C~Gsl~~vH~~CL~~Wl~~k~~~~CeiCk~ 70 (163)
+....|-||.+.+.+..+ .+.-|. |. .+||++|.-.=+...|...|--|.+
T Consensus 217 ~~D~~C~iC~~~~~~n~n-~ivfCD~Cn---l~VHq~Cygi~~ipeg~WlCr~Cl~ 268 (1051)
T KOG0955|consen 217 EEDAVCCICLDGECQNSN-VIVFCDGCN---LAVHQECYGIPFIPEGQWLCRRCLQ 268 (1051)
T ss_pred CCCccceeecccccCCCc-eEEEcCCCc---chhhhhccCCCCCCCCcEeehhhcc
Confidence 567899999999876433 455565 65 9999999873333345677777774
No 115
>PF14446 Prok-RING_1: Prokaryotic RING finger family 1
Probab=26.42 E-value=97 Score=20.66 Aligned_cols=47 Identities=21% Similarity=0.479 Sum_probs=30.5
Q ss_pred CCCeeeEcccCcccCCCceeecccCCCCCceecHHHHHHHHHHhCCccccC--cccccc
Q 031236 17 TTSHCRICHEEEFESCNSLEAPCACSGTVKFAHRDCIQRWCYEKGNTTCEI--CLQEYG 73 (163)
Q Consensus 17 ~~~~CRIC~~~~~~~~~~l~~PC~C~Gsl~~vH~~CL~~Wl~~k~~~~Cei--Ck~~y~ 73 (163)
....|-+|-+...+.++..+=| .|. .-.||.|- - ....|-+ |+..|.
T Consensus 4 ~~~~C~~Cg~~~~~~dDiVvCp-~Cg---apyHR~C~---~---~~g~C~~~~c~~~~~ 52 (54)
T PF14446_consen 4 EGCKCPVCGKKFKDGDDIVVCP-ECG---APYHRDCW---E---KAGGCINYSCGTGFE 52 (54)
T ss_pred cCccChhhCCcccCCCCEEECC-CCC---CcccHHHH---h---hCCceEeccCCCCcc
Confidence 4567999988875555555655 455 78999994 2 2345666 665553
No 116
>PF11789 zf-Nse: Zinc-finger of the MIZ type in Nse subunit; PDB: 2YU4_A 3HTK_C.
Probab=25.87 E-value=42 Score=22.14 Aligned_cols=43 Identities=14% Similarity=0.420 Sum_probs=27.2
Q ss_pred CCeeeEcccCcccCCCceeecccCCCCCceecHHHHHHHHHHhCCccccC
Q 031236 18 TSHCRICHEEEFESCNSLEAPCACSGTVKFAHRDCIQRWCYEKGNTTCEI 67 (163)
Q Consensus 18 ~~~CRIC~~~~~~~~~~l~~PC~C~Gsl~~vH~~CL~~Wl~~k~~~~Cei 67 (163)
...|.|......+ +..+. .|. |.+-++.+.+|++.++...||+
T Consensus 11 ~~~CPiT~~~~~~---PV~s~-~C~---H~fek~aI~~~i~~~~~~~CPv 53 (57)
T PF11789_consen 11 SLKCPITLQPFED---PVKSK-KCG---HTFEKEAILQYIQRNGSKRCPV 53 (57)
T ss_dssp -SB-TTTSSB-SS---EEEES-SS-----EEEHHHHHHHCTTTS-EE-SC
T ss_pred ccCCCCcCChhhC---CcCcC-CCC---CeecHHHHHHHHHhcCCCCCCC
Confidence 4678887766543 45542 333 9999999999997778899998
No 117
>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=24.91 E-value=23 Score=21.83 Aligned_cols=44 Identities=20% Similarity=0.601 Sum_probs=24.6
Q ss_pred eeeEcccCcccCCCceeeccc-CCCCCceecHHHHHHHHHH----hCCccccCcc
Q 031236 20 HCRICHEEEFESCNSLEAPCA-CSGTVKFAHRDCIQRWCYE----KGNTTCEICL 69 (163)
Q Consensus 20 ~CRIC~~~~~~~~~~l~~PC~-C~Gsl~~vH~~CL~~Wl~~----k~~~~CeiCk 69 (163)
.|.||.....++ ...-|. |. .++|..|+.-=... .+...|+.|.
T Consensus 1 ~C~vC~~~~~~~---~~i~C~~C~---~~~H~~C~~~~~~~~~~~~~~w~C~~C~ 49 (51)
T PF00628_consen 1 YCPVCGQSDDDG---DMIQCDSCN---RWYHQECVGPPEKAEEIPSGDWYCPNCR 49 (51)
T ss_dssp EBTTTTSSCTTS---SEEEBSTTS---CEEETTTSTSSHSHHSHHSSSBSSHHHH
T ss_pred eCcCCCCcCCCC---CeEEcCCCC---hhhCcccCCCChhhccCCCCcEECcCCc
Confidence 377887743322 233343 44 89999998543321 1256666664
No 118
>PF12907 zf-met2: Zinc-binding
Probab=24.90 E-value=18 Score=22.67 Aligned_cols=12 Identities=42% Similarity=0.910 Sum_probs=9.6
Q ss_pred CccccCcccccc
Q 031236 62 NTTCEICLQEYG 73 (163)
Q Consensus 62 ~~~CeiCk~~y~ 73 (163)
+..|.||++.|-
T Consensus 1 ~i~C~iC~qtF~ 12 (40)
T PF12907_consen 1 NIICKICRQTFM 12 (40)
T ss_pred CcCcHHhhHHHH
Confidence 357999998885
No 119
>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=24.84 E-value=57 Score=21.18 Aligned_cols=17 Identities=35% Similarity=0.708 Sum_probs=12.6
Q ss_pred ccccCccccccCCccCC
Q 031236 63 TTCEICLQEYGPGYTAP 79 (163)
Q Consensus 63 ~~CeiCk~~y~~~y~~p 79 (163)
..|.+|++.|.+....|
T Consensus 2 y~C~~CgyiYd~~~Gd~ 18 (50)
T cd00730 2 YECRICGYIYDPAEGDP 18 (50)
T ss_pred cCCCCCCeEECCCCCCc
Confidence 46999999998765433
No 120
>PF13913 zf-C2HC_2: zinc-finger of a C2HC-type
Probab=24.83 E-value=32 Score=18.98 Aligned_cols=12 Identities=33% Similarity=1.054 Sum_probs=9.7
Q ss_pred ccccCccccccC
Q 031236 63 TTCEICLQEYGP 74 (163)
Q Consensus 63 ~~CeiCk~~y~~ 74 (163)
..|++|+..|.+
T Consensus 3 ~~C~~CgR~F~~ 14 (25)
T PF13913_consen 3 VPCPICGRKFNP 14 (25)
T ss_pred CcCCCCCCEECH
Confidence 479999998854
No 121
>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=24.35 E-value=1.3e+02 Score=22.28 Aligned_cols=51 Identities=20% Similarity=0.509 Sum_probs=35.1
Q ss_pred CCCCeeeEcccCcccCCCceeecc-------cCCCCCceecHHHHHHHHHHh-------CCccccCccc
Q 031236 16 ETTSHCRICHEEEFESCNSLEAPC-------ACSGTVKFAHRDCIQRWCYEK-------GNTTCEICLQ 70 (163)
Q Consensus 16 ~~~~~CRIC~~~~~~~~~~l~~PC-------~C~Gsl~~vH~~CL~~Wl~~k-------~~~~CeiCk~ 70 (163)
.....|..|.....+ ....| .|.+....+=..||..+..+. ++..||-|+-
T Consensus 5 ~~g~~CHqCrqKt~~----~~~~C~~~~~~~~C~~~~~~fC~~CL~~ryge~~~ev~~~~~W~CP~Crg 69 (105)
T PF10497_consen 5 VNGKTCHQCRQKTLD----FKTICTGHWKNSSCRGCRGKFCGGCLRNRYGENVEEVLEDPNWKCPKCRG 69 (105)
T ss_pred CCCCCchhhcCCCCC----CceEcCCCCCCCCCccCcceehHhHHHHHHhhhHHHHhcCCceECCCCCC
Confidence 356788888776543 23455 354445678889999998763 5788998885
No 122
>PF15353 HECA: Headcase protein family homologue
Probab=22.93 E-value=48 Score=25.10 Aligned_cols=14 Identities=29% Similarity=1.066 Sum_probs=12.2
Q ss_pred ceecHHHHHHHHHH
Q 031236 46 KFAHRDCIQRWCYE 59 (163)
Q Consensus 46 ~~vH~~CL~~Wl~~ 59 (163)
.|.|+.|++.|=..
T Consensus 42 ~~MH~~CF~~wE~~ 55 (107)
T PF15353_consen 42 QYMHRECFEKWEDS 55 (107)
T ss_pred CchHHHHHHHHHHH
Confidence 89999999999643
No 123
>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=21.69 E-value=24 Score=23.27 Aligned_cols=20 Identities=20% Similarity=0.699 Sum_probs=10.3
Q ss_pred HHHHHhCCccccCccccccC
Q 031236 55 RWCYEKGNTTCEICLQEYGP 74 (163)
Q Consensus 55 ~Wl~~k~~~~CeiCk~~y~~ 74 (163)
.|...+....|.+|+..|..
T Consensus 2 ~W~~d~~~~~C~~C~~~F~~ 21 (69)
T PF01363_consen 2 HWVPDSEASNCMICGKKFSL 21 (69)
T ss_dssp -SSSGGG-SB-TTT--B-BS
T ss_pred CcCCCCCCCcCcCcCCcCCC
Confidence 57766677888888888853
No 124
>PF12874 zf-met: Zinc-finger of C2H2 type; PDB: 1ZU1_A 2KVG_A.
Probab=20.48 E-value=41 Score=17.61 Aligned_cols=10 Identities=30% Similarity=1.065 Sum_probs=8.1
Q ss_pred cccCcccccc
Q 031236 64 TCEICLQEYG 73 (163)
Q Consensus 64 ~CeiCk~~y~ 73 (163)
.|++|+..|.
T Consensus 2 ~C~~C~~~f~ 11 (25)
T PF12874_consen 2 YCDICNKSFS 11 (25)
T ss_dssp EETTTTEEES
T ss_pred CCCCCCCCcC
Confidence 5999998775
No 125
>PF13912 zf-C2H2_6: C2H2-type zinc finger; PDB: 1JN7_A 1FU9_A 2L1O_A 1NJQ_A 2EN8_A 2EMM_A 1FV5_A 1Y0J_B 2L6Z_B.
Probab=20.16 E-value=42 Score=17.93 Aligned_cols=11 Identities=18% Similarity=0.782 Sum_probs=9.0
Q ss_pred cccCccccccC
Q 031236 64 TCEICLQEYGP 74 (163)
Q Consensus 64 ~CeiCk~~y~~ 74 (163)
.|..|+..|..
T Consensus 3 ~C~~C~~~F~~ 13 (27)
T PF13912_consen 3 ECDECGKTFSS 13 (27)
T ss_dssp EETTTTEEESS
T ss_pred CCCccCCccCC
Confidence 69999998863
No 126
>PLN02294 cytochrome c oxidase subunit Vb
Probab=20.00 E-value=27 Score=28.56 Aligned_cols=27 Identities=19% Similarity=0.480 Sum_probs=19.1
Q ss_pred HHHHhCCccccCccccccCCccCCCCC
Q 031236 56 WCYEKGNTTCEICLQEYGPGYTAPSKK 82 (163)
Q Consensus 56 Wl~~k~~~~CeiCk~~y~~~y~~p~~~ 82 (163)
|+.+.....|+.|++.|+..|-.|...
T Consensus 135 ~L~kGkp~RCpeCG~~fkL~~vG~~~~ 161 (174)
T PLN02294 135 WLEKGKSFECPVCTQYFELEVVGPGGP 161 (174)
T ss_pred EecCCCceeCCCCCCEEEEEEeCCCCC
Confidence 344434577999999999887666543
Done!