DUF4912 - PFAM28P - GREMLIN Contacts

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DUF4912 - Domain of unknown function (DUF4912)

PFAM:	PF16258	Sequences: YGEDRLVLLARDPHWLFAYWEITPETLAALGAAWGGARLVLRVYDVTGIDFDGTNAHSVFDIEVHPGARNWYIHVPRPGRSYRVELGYLSPDGRFVSLARSNPVTTPRDGPSDDIDE	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	117 (113)
Sequences:	7293 (5192)
Seq/√Len:	488.4
META:	0.928

GREMLIN Results:

Legend: The darker and larger the blue dots, the higher coevolution strength.

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
87_G	95_F	3.969	1.00
11_R	15_W	2.751	1.00
42_R	61_D	2.649	1.00
38_R	63_E	2.576	1.00
4_D	26_T	2.556	1.00
14_H	109_D	2.541	1.00
85_E	100_R	2.536	1.00
8_L	84_V	2.375	1.00
45_D	80_R	2.233	1.00
85_E	97_S	2.211	1.00
81_S	105_T	2.033	1.00
12_D	15_W	2.000	1.00
6_L	99_A	1.944	1.00
16_L	75_V	1.914	1.00
61_D	89_L	1.891	1.00
8_L	18_A	1.875	1.00
15_W	74_H	1.846	1.00
18_A	84_V	1.814	1.00
83_R	103_P	1.808	1.00
6_L	84_V	1.773	1.00
40_V	61_D	1.708	1.00
81_S	103_P	1.654	1.00
77_R	80_R	1.546	1.00
8_L	16_L	1.486	1.00
65_H	68_A	1.400	1.00
43_V	73_I	1.388	1.00
62_I	73_I	1.381	1.00
90_S	94_R	1.374	1.00
79_G	105_T	1.369	1.00
4_D	99_A	1.360	1.00
51_F	55_N	1.358	1.00
49_I	57_H	1.340	1.00
83_R	100_R	1.332	1.00
43_V	60_F	1.306	1.00
17_F	72_Y	1.290	1.00
88_Y	98_L	1.279	1.00
15_W	71_W	1.261	1.00
40_V	89_L	1.236	1.00
79_G	108_R	1.221	1.00
44_Y	85_E	1.195	1.00
39_L	66_P	1.179	1.00
16_L	106_T	1.170	1.00
38_R	89_L	1.163	1.00
86_L	99_A	1.161	1.00
9_L	17_F	1.159	1.00
4_D	23_T	1.147	1.00
44_Y	83_R	1.145	1.00
39_L	88_Y	1.140	1.00
76_P	82_Y	1.110	1.00
78_P	109_D	1.091	1.00
60_F	76_P	1.063	1.00
53_G	56_A	1.059	1.00
51_F	56_A	1.052	1.00
7_V	19_Y	1.039	1.00
18_A	41_L	1.029	1.00
30_L	33_A	1.023	1.00
8_L	104_V	1.021	1.00
97_S	100_R	1.018	1.00
23_T	26_T	1.014	1.00
52_D	55_N	1.009	1.00
9_L	19_Y	1.005	1.00
34_W	37_A	0.992	1.00
46_V	83_R	0.987	1.00
21_E	69_R	0.984	1.00
14_H	74_H	0.974	1.00
41_L	84_V	0.967	1.00
45_D	49_I	0.961	1.00
85_E	95_F	0.949	1.00
110_G	113_D	0.944	1.00
6_L	18_A	0.944	1.00
82_Y	106_T	0.936	1.00
49_I	55_N	0.931	1.00
42_R	87_G	0.926	1.00
43_V	84_V	0.906	1.00
28_A	31_G	0.894	1.00
30_L	37_A	0.883	1.00
15_W	76_P	0.882	1.00
30_L	34_W	0.876	1.00
29_A	33_A	0.849	1.00
49_I	53_G	0.842	1.00
14_H	78_P	0.836	1.00
6_L	86_L	0.833	1.00
45_D	57_H	0.813	1.00
75_V	106_T	0.809	1.00
68_A	71_W	0.805	1.00
33_A	92_D	0.790	1.00
22_I	86_L	0.780	1.00
90_S	96_V	0.777	1.00
29_A	32_A	0.772	1.00
5_R	21_E	0.768	1.00
63_E	89_L	0.763	1.00
16_L	43_V	0.757	1.00
49_I	52_D	0.746	1.00
73_I	84_V	0.742	1.00
76_P	106_T	0.733	1.00
87_G	97_S	0.722	1.00
17_F	70_N	0.721	1.00
51_F	54_T	0.719	1.00
51_F	57_H	0.717	1.00
58_S	61_D	0.714	1.00
64_V	86_L	0.704	1.00
24_P	27_L	0.702	1.00
39_L	86_L	0.698	1.00
1_Y	21_E	0.697	1.00
64_V	71_W	0.696	1.00
36_G	91_P	0.692	1.00
56_A	83_R	0.692	1.00
65_H	71_W	0.690	1.00
48_G	57_H	0.688	1.00
48_G	80_R	0.688	1.00
66_P	69_R	0.674	1.00
37_A	88_Y	0.668	1.00
13_P	17_F	0.667	1.00
50_D	53_G	0.665	1.00
6_L	41_L	0.663	1.00
2_G	23_T	0.659	1.00
44_Y	56_A	0.656	1.00
77_R	82_Y	0.656	1.00
13_P	107_P	0.655	1.00
44_Y	61_D	0.652	1.00
46_V	53_G	0.640	1.00
78_P	107_P	0.639	1.00
30_L	90_S	0.634	1.00
26_T	99_A	0.631	1.00
60_F	74_H	0.626	1.00
11_R	17_F	0.618	0.99
34_W	39_L	0.613	0.99
62_I	71_W	0.611	0.99
33_A	90_S	0.610	0.99
6_L	101_S	0.610	0.99
22_I	26_T	0.607	0.99
35_G	91_P	0.605	0.99
58_S	77_R	0.603	0.99
44_Y	58_S	0.597	0.99
49_I	56_A	0.592	0.99
60_F	75_V	0.591	0.99
19_Y	72_Y	0.580	0.99
7_V	10_A	0.569	0.99
63_E	68_A	0.569	0.99
32_A	36_G	0.568	0.99
50_D	55_N	0.567	0.99
31_G	35_G	0.565	0.99
71_W	74_H	0.565	0.99
14_H	82_Y	0.562	0.99
31_G	34_W	0.560	0.99
29_A	34_W	0.560	0.99
16_L	104_V	0.554	0.99
26_T	86_L	0.551	0.99
19_Y	70_N	0.546	0.99
18_A	73_I	0.535	0.99
11_R	72_Y	0.525	0.98
34_W	88_Y	0.525	0.98
41_L	73_I	0.523	0.98
13_P	78_P	0.521	0.98
24_P	35_G	0.518	0.98
47_T	55_N	0.514	0.98
53_G	57_H	0.514	0.98
15_W	72_Y	0.514	0.98
27_L	67_G	0.513	0.98
13_P	19_Y	0.512	0.98
64_V	69_R	0.512	0.98
5_R	11_R	0.510	0.98
10_A	104_V	0.509	0.98
28_A	96_V	0.509	0.98
21_E	72_Y	0.506	0.98
9_L	72_Y	0.506	0.98
109_D	112_S	0.505	0.98
37_A	91_P	0.505	0.98
63_E	66_P	0.501	0.98
40_V	63_E	0.500	0.98

Legend: The i and j are positions as given in the UniProt sequence. Only predictions with Prob ≥ 0.7 are listed. For all 3L/2 predictions, click on one of the links below.

Sco = ((raw_sco - min_sco)/(avg_sco - min_sco))/2 + 0.5
Prob = P(contact | Sco, seq80/√len)
seq80 = effective number of sequences, after reducing redundancy to 80% identity

Text file of predictions (all 3L/2 predictions)
Generate restraints for ROSETTA Structure Modeling
Upload PDB model overlay contacts on the model

HHsearch Results:

Legend: GREMLIN results (Prob ≥ 0.7) overlaid on top PDB hits. The grey/red filled circles underneath are pdb residue contacts (min distance < 5 Angstroms). The shade of the circles is based on the top 10 (or top 20 if e-value < 1E-20) HHsearch results which uses the overall probability and per-site alignment prob. Inter oligomeric contacts in the pdb are in shades of red.

PDB	Chains	Cov	%	HHΔ
3up1A	2	0.8462	33.2	0.876	Contact Map
4nn5B	1	0.8376	16.8	0.893	Contact Map
2rb8A	1	0.7692	14	0.896	Contact Map
4s0sD	1	0.735	13.1	0.897	Contact Map
3l5iA	1	0.7949	11.3	0.9	Contact Map
1mukA	1	0.8632	10.2	0.902	Contact Map
2cuiA	1	0.8718	10	0.903	Contact Map
4m4pA	1	0.8632	9.6	0.904	Contact Map
2b5iB	1	0.8376	9.4	0.904	Contact Map
1j8kA	1	0.7778	9	0.905	Contact Map

Sequence Conservation (Image Generated using WebLogo v3)

Legend: Color is used to show Hydrophobicity (Blue: Hydrophilic, Green: Neutral and Black: Hydrophobic). Amount of gaps is represented by width.

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