DUF962 - PFAM28P - GREMLIN Contacts

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DUF962 - Protein of unknown function (DUF962)

PFAM:	PF06127	Sequences: MRSFAEFYPFYLSEHRNPTNRALHFIGTPLILLSLVAALATGPWWLLLALFVVGYGFAWVGHFFFEGNKPATFKDPLWSLLGDPRMLLAMLTGRL	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	95 (93)
Sequences:	16521 (8981)
Seq/√Len:	931.3
META:	0.905

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
29_P	87_L	3.162	1.00
88_L	92_T	3.086	1.00
17_N	20_N	2.717	1.00
25_F	90_M	2.579	1.00
60_V	64_F	2.330	1.00
34_S	53_V	2.245	1.00
85_R	89_A	1.949	1.00
3_S	6_E	1.947	1.00
20_N	61_G	1.865	1.00
85_R	88_L	1.849	1.00
8_Y	89_A	1.817	1.00
18_P	22_A	1.808	1.00
31_I	50_L	1.769	1.00
25_F	87_L	1.712	1.00
87_L	91_L	1.640	1.00
19_T	65_F	1.633	1.00
4_F	82_G	1.524	1.00
45_W	48_L	1.516	1.00
10_F	14_E	1.498	1.00
30_L	53_V	1.495	1.00
4_F	85_R	1.467	1.00
37_A	47_L	1.461	1.00
89_A	94_R	1.420	1.00
19_T	22_A	1.403	1.00
28_T	84_P	1.385	1.00
14_E	71_A	1.382	1.00
5_A	9_P	1.291	1.00
72_T	75_D	1.276	1.00
32_L	84_P	1.245	1.00
59_W	63_F	1.241	1.00
27_G	57_F	1.172	1.00
37_A	46_L	1.170	1.00
3_S	7_F	1.160	1.00
23_L	61_G	1.124	1.00
10_F	13_S	1.108	1.00
22_A	26_I	1.107	1.00
48_L	51_F	1.106	1.00
59_W	73_F	1.085	1.00
21_R	90_M	1.084	1.00
77_L	81_L	1.073	1.00
10_F	71_A	1.065	1.00
19_T	23_L	1.046	1.00
60_V	65_F	1.044	1.00
21_R	25_F	1.037	1.00
10_F	74_K	1.032	1.00
4_F	8_Y	1.027	1.00
14_E	74_K	1.022	1.00
82_G	85_R	1.022	1.00
37_A	41_T	1.007	1.00
41_T	44_W	1.004	1.00
53_V	57_F	0.997	1.00
81_L	84_P	0.994	1.00
35_L	50_L	0.990	1.00
23_L	57_F	0.984	1.00
31_I	51_F	0.977	1.00
22_A	90_M	0.970	1.00
34_S	38_A	0.942	1.00
8_Y	12_L	0.937	1.00
22_A	25_F	0.926	1.00
4_F	78_W	0.915	1.00
64_F	67_G	0.899	1.00
45_W	49_A	0.892	1.00
63_F	69_K	0.891	1.00
27_G	54_G	0.890	1.00
38_A	47_L	0.886	1.00
80_L	84_P	0.885	1.00
26_I	29_P	0.869	1.00
2_R	6_E	0.866	1.00
44_W	48_L	0.862	1.00
31_I	84_P	0.860	1.00
55_Y	59_W	0.857	1.00
33_L	37_A	0.856	1.00
34_S	50_L	0.855	1.00
13_S	16_R	0.849	1.00
56_G	60_V	0.845	1.00
38_A	44_W	0.839	1.00
38_A	42_G	0.831	1.00
89_A	92_T	0.819	1.00
84_P	87_L	0.811	1.00
23_L	60_V	0.811	1.00
16_R	66_E	0.810	1.00
4_F	7_F	0.807	1.00
49_A	53_V	0.792	1.00
36_V	40_A	0.784	1.00
20_N	65_F	0.783	1.00
83_D	86_M	0.778	1.00
75_D	78_W	0.772	1.00
52_V	56_G	0.772	1.00
28_T	83_D	0.736	1.00
38_A	46_L	0.736	1.00
26_I	57_F	0.734	1.00
84_P	88_L	0.720	1.00
42_G	45_W	0.706	1.00
49_A	52_V	0.700	1.00
46_L	49_A	0.698	1.00
69_K	74_K	0.692	1.00
17_N	65_F	0.692	1.00
51_F	55_Y	0.690	1.00
34_S	46_L	0.685	1.00
43_P	46_L	0.675	1.00
6_E	9_P	0.672	1.00
86_M	90_M	0.665	1.00
23_L	65_F	0.657	1.00
32_L	87_L	0.654	1.00
38_A	41_T	0.653	1.00
25_F	91_L	0.651	1.00
90_M	94_R	0.646	1.00
15_H	24_H	0.645	1.00
9_P	13_S	0.639	1.00
38_A	51_F	0.633	1.00
28_T	32_L	0.629	1.00
61_G	65_F	0.607	1.00
53_V	56_G	0.596	1.00
7_F	10_F	0.596	1.00
37_A	40_A	0.589	1.00
78_W	85_R	0.588	1.00
29_P	91_L	0.586	1.00
80_L	83_D	0.579	1.00
30_L	34_S	0.576	1.00
20_N	66_E	0.573	1.00
34_S	49_A	0.567	1.00
14_E	68_N	0.567	1.00
30_L	50_L	0.565	1.00
33_L	50_L	0.563	1.00
76_P	79_S	0.556	1.00
63_F	73_F	0.555	1.00
81_L	85_R	0.554	1.00
32_L	36_V	0.551	1.00
26_I	30_L	0.550	1.00
30_L	57_F	0.550	1.00
55_Y	58_A	0.542	1.00
39_L	42_G	0.532	1.00
12_L	16_R	0.532	1.00
89_A	93_G	0.531	1.00
30_L	54_G	0.524	1.00
78_W	81_L	0.522	1.00
2_R	5_A	0.514	1.00
10_F	75_D	0.512	1.00
10_F	79_S	0.505	1.00
34_S	37_A	0.500	1.00

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
3wxwA	1	0.9474	11.2	0.892	Contact Map
2y8nA	2	0.9895	3.7	0.914	Contact Map
2ls4A	1	0.2526	3.1	0.917	Contact Map
2nrgA	1	0.8632	2.7	0.92	Contact Map
4ltoA	3	0.5368	2.6	0.92	Contact Map
1kdlA	1	0.2105	2.6	0.92	Contact Map
1j6wA	2	0.9789	2.3	0.923	Contact Map
4nfuA	1	0.3053	2.1	0.925	Contact Map
3j9pD	4	0.7474	2	0.925	Contact Map
2wxfA	1	0.1579	1.7	0.928	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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