GldH_lipo - PFAM28P - GREMLIN Contacts

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GldH_lipo - GldH lipoprotein

PFAM:	PF14109	Sequences: TVYEEYKSIPNNGWNKDDTLSFEFEITDTTSPYNLYLNLRNTNDYPYSNLYLFVTTTFPDGKTITDTLEYELADPDGKWLGKGFGDIYENRLPYKENRFPKKGTYTFTIEQAMREDPLPGITDVGLRI	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	128 (127)
Sequences:	7412 (5806)
Seq/√Len:	515.2
META:	0.926

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
83_G	88_Y	2.853	1.00
74_D	78_K	2.635	1.00
25_E	104_T	2.622	1.00
23_E	104_T	2.510	1.00
23_E	106_T	2.464	1.00
57_T	108_T	2.354	1.00
13_G	117_P	2.232	1.00
41_N	90_N	2.173	1.00
53_F	112_A	2.159	1.00
19_T	110_E	2.119	1.00
55_T	108_T	2.038	1.00
42_T	122_T	2.006	1.00
60_D	101_K	2.003	1.00
15_N	117_P	1.976	1.00
55_T	110_E	1.941	1.00
21_S	108_T	1.909	1.00
73_A	79_W	1.836	1.00
21_S	106_T	1.783	1.00
55_T	65_T	1.738	1.00
38_N	91_R	1.711	1.00
42_T	120_G	1.676	1.00
24_F	107_F	1.654	1.00
70_Y	92_L	1.654	1.00
19_T	108_T	1.647	1.00
57_T	106_T	1.584	1.00
15_N	18_D	1.580	1.00
51_Y	69_E	1.574	1.00
46_P	119_P	1.557	1.00
93_P	96_E	1.547	1.00
7_K	20_L	1.544	1.00
40_R	123_D	1.543	1.00
4_E	127_R	1.480	1.00
32_P	98_R	1.479	1.00
91_R	127_R	1.457	1.00
41_N	79_W	1.449	1.00
36_Y	93_P	1.398	1.00
47_Y	115_E	1.398	1.00
49_N	69_E	1.387	1.00
87_I	122_T	1.377	1.00
109_I	124_V	1.359	1.00
54_V	109_I	1.342	1.00
115_E	119_P	1.333	1.00
9_I	20_L	1.316	1.00
10_P	18_D	1.272	1.00
43_N	88_Y	1.271	1.00
29_T	102_K	1.271	1.00
107_F	126_L	1.253	1.00
46_P	115_E	1.237	1.00
8_S	123_D	1.231	1.00
36_Y	91_R	1.231	1.00
57_T	63_T	1.189	1.00
6_Y	38_N	1.188	1.00
3_Y	22_F	1.178	1.00
40_R	87_I	1.178	1.00
53_F	67_T	1.150	1.00
40_R	89_E	1.144	1.00
16_K	116_D	1.139	1.00
32_P	97_N	1.119	1.00
4_E	38_N	1.112	1.00
59_P	103_G	1.086	1.00
80_L	90_N	1.061	1.00
55_T	63_T	1.053	1.00
35_L	126_L	1.039	1.00
48_S	71_E	1.038	1.00
67_T	112_A	1.038	1.00
54_V	68_L	1.037	1.00
46_P	120_G	1.036	1.00
53_F	110_E	1.033	1.00
20_L	124_V	1.022	1.00
2_V	33_Y	1.016	1.00
10_P	13_G	1.010	1.00
39_L	50_L	0.999	1.00
90_N	93_P	0.999	1.00
24_F	128_I	0.992	1.00
109_I	126_L	0.962	1.00
74_D	80_L	0.955	1.00
7_K	18_D	0.948	1.00
41_N	88_Y	0.931	1.00
29_T	32_P	0.924	1.00
51_Y	112_A	0.901	1.00
7_K	22_F	0.882	1.00
34_N	97_N	0.881	1.00
56_T	107_F	0.875	1.00
28_D	31_S	0.873	1.00
34_N	95_K	0.870	1.00
66_D	95_K	0.855	1.00
58_F	62_K	0.854	1.00
34_N	93_P	0.854	1.00
34_N	96_E	0.843	1.00
50_L	121_I	0.829	1.00
52_L	70_Y	0.824	1.00
37_L	124_V	0.823	1.00
48_S	75_P	0.822	1.00
41_N	72_L	0.820	1.00
44_D	120_G	0.819	1.00
37_L	52_L	0.817	1.00
51_Y	114_R	0.810	1.00
51_Y	113_M	0.808	1.00
53_F	65_T	0.808	1.00
41_N	121_I	0.792	1.00
45_Y	49_N	0.782	1.00
37_L	54_V	0.777	1.00
53_F	66_D	0.776	1.00
56_T	95_K	0.774	1.00
38_N	127_R	0.774	1.00
6_Y	123_D	0.763	1.00
12_N	122_T	0.762	1.00
111_Q	118_L	0.757	1.00
9_I	18_D	0.756	1.00
33_Y	99_F	0.755	1.00
45_Y	113_M	0.751	1.00
100_P	105_Y	0.739	1.00
99_F	107_F	0.738	1.00
26_I	103_G	0.734	1.00
50_L	118_L	0.726	1.00
36_Y	127_R	0.724	1.00
37_L	109_I	0.711	1.00
84_F	88_Y	0.708	1.00
37_L	94_Y	0.706	1.00
13_G	119_P	0.701	1.00
71_E	80_L	0.700	1.00
9_I	124_V	0.699	1.00
111_Q	114_R	0.699	1.00
26_I	99_F	0.696	1.00
95_K	98_R	0.694	1.00
58_F	101_K	0.693	1.00
27_T	102_K	0.687	1.00
59_P	105_Y	0.687	1.00
35_L	128_I	0.683	1.00
40_R	122_T	0.681	1.00
43_N	86_D	0.662	1.00
38_N	89_E	0.658	1.00
64_I	95_K	0.645	1.00
18_D	21_S	0.642	1.00
71_E	92_L	0.635	1.00
113_M	118_L	0.629	1.00
48_S	73_A	0.624	1.00
30_T	33_Y	0.618	1.00
49_N	114_R	0.612	1.00
76_D	80_L	0.607	1.00
68_L	95_K	0.604	1.00
49_N	113_M	0.592	0.99
41_N	73_A	0.589	0.99
61_G	64_I	0.589	0.99
39_L	70_Y	0.588	0.99
9_I	13_G	0.583	0.99
39_L	121_I	0.580	0.99
45_Y	50_L	0.579	0.99
86_D	89_E	0.579	0.99
98_R	102_K	0.575	0.99
43_N	83_G	0.575	0.99
9_I	12_N	0.572	0.99
24_F	56_T	0.569	0.99
84_F	89_E	0.564	0.99
20_L	24_F	0.563	0.99
37_L	70_Y	0.561	0.99
95_K	107_F	0.561	0.99
81_G	90_N	0.560	0.99
69_E	73_A	0.560	0.99
54_V	107_F	0.559	0.99
80_L	92_L	0.559	0.99
10_P	15_N	0.558	0.99
62_K	101_K	0.555	0.99
73_A	80_L	0.552	0.99
87_I	123_D	0.551	0.99
47_Y	118_L	0.551	0.99
125_G	128_I	0.549	0.99
4_E	91_R	0.544	0.99
4_E	7_K	0.544	0.99
71_E	74_D	0.544	0.99
86_D	122_T	0.541	0.99
16_K	19_T	0.536	0.99
71_E	75_P	0.536	0.99
54_V	94_Y	0.536	0.99
30_T	98_R	0.535	0.99
50_L	70_Y	0.535	0.99
99_F	103_G	0.530	0.99
48_S	69_E	0.530	0.99
35_L	94_Y	0.528	0.99
16_K	110_E	0.523	0.99
35_L	99_F	0.520	0.99
35_L	95_K	0.520	0.99
39_L	90_N	0.517	0.98
89_E	123_D	0.515	0.98
15_N	116_D	0.508	0.98
54_V	72_L	0.507	0.98
42_T	86_D	0.502	0.98
43_N	85_G	0.502	0.98
77_G	81_G	0.501	0.98
41_N	81_G	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
2ebkA	1	0.7812	16.7	0.907	Contact Map
3nkgA	1	0.8594	13.9	0.91	Contact Map
2p9rA	1	0.7422	11.8	0.913	Contact Map
4ziqA	2	0.75	10.1	0.916	Contact Map
3payA	4	0.7578	7.5	0.92	Contact Map
1ukxA	1	0.8203	6.7	0.922	Contact Map
2b39A	1	0.9453	6.5	0.923	Contact Map
2yroA	1	0.5781	5.8	0.924	Contact Map
3prxB	1	0.8984	5.7	0.925	Contact Map
4bq2A	4	0.8828	5.5	0.925	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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