HPP - PFAM28P - GREMLIN Contacts

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HPP - HPP family

PFAM:	PF04982	Sequences: LLIASFGASAVLLFAVPASPLAQPRNVIGGHLISALVGVACAKLFWLAAALAVGLAIALMHLTRTLHPPAGATALIAVLGGPIHALGYLFLLVPVLLGALLLLLVALLFNNLTGRRYP	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	118 (118)
Sequences:	9491 (5682)
Seq/√Len:	523.1
META:	0.799

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
31_H	73_T	3.878	1.00
40_A	88_Y	3.048	1.00
29_G	65_T	2.862	1.00
34_S	56_A	2.640	1.00
28_I	103_L	2.065	1.00
41_C	55_L	2.039	1.00
13_L	27_V	2.035	1.00
32_L	96_L	2.007	1.00
37_V	59_L	1.919	1.00
27_V	103_L	1.866	1.00
33_I	59_L	1.855	1.00
25_R	65_T	1.848	1.00
9_S	27_V	1.805	1.00
6_F	98_G	1.762	1.00
16_V	21_L	1.672	1.00
11_V	71_G	1.641	1.00
50_A	54_G	1.612	1.00
95_V	99_A	1.592	1.00
33_I	63_T	1.540	1.00
49_A	75_L	1.533	1.00
42_A	84_H	1.511	1.00
109_F	113_T	1.511	1.00
3_I	95_V	1.488	1.00
35_A	73_T	1.485	1.00
12_L	22_A	1.473	1.00
36_L	91_L	1.453	1.00
37_V	55_L	1.428	1.00
52_A	78_V	1.426	1.00
31_H	99_A	1.410	1.00
46_W	50_A	1.382	1.00
19_S	22_A	1.382	1.00
9_S	31_H	1.370	1.00
89_L	93_V	1.369	1.00
25_R	29_G	1.369	1.00
61_H	66_L	1.365	1.00
111_N	116_R	1.352	1.00
56_A	60_M	1.338	1.00
41_C	51_L	1.319	1.00
10_A	14_F	1.317	1.00
13_L	106_A	1.310	1.00
41_C	48_A	1.290	1.00
16_V	19_S	1.277	1.00
40_A	44_L	1.237	1.00
45_F	48_A	1.226	1.00
34_S	70_A	1.224	1.00
93_V	97_L	1.215	1.00
37_V	41_C	1.205	1.00
105_V	109_F	1.203	1.00
35_A	95_V	1.202	1.00
91_L	94_P	1.145	1.00
11_V	66_L	1.143	1.00
13_L	102_L	1.140	1.00
5_S	8_A	1.137	1.00
39_V	43_K	1.136	1.00
10_A	102_L	1.119	1.00
93_V	96_L	1.117	1.00
21_L	68_P	1.108	1.00
111_N	114_G	1.098	1.00
4_A	76_I	1.092	1.00
90_F	94_P	1.092	1.00
9_S	67_H	1.066	1.00
11_V	57_I	1.056	1.00
107_L	111_N	1.053	1.00
32_L	91_L	1.052	1.00
29_G	32_L	1.038	1.00
41_C	45_F	1.034	1.00
107_L	110_N	1.025	1.00
45_F	51_L	1.006	1.00
40_A	43_K	0.995	1.00
35_A	77_A	0.981	1.00
74_A	78_V	0.979	1.00
88_Y	91_L	0.975	1.00
38_G	77_A	0.969	1.00
87_G	90_F	0.968	1.00
107_L	117_Y	0.965	1.00
8_A	12_L	0.962	1.00
23_Q	26_N	0.944	1.00
5_S	72_A	0.934	1.00
42_A	77_A	0.932	1.00
83_I	87_G	0.925	1.00
85_A	89_L	0.917	1.00
99_A	103_L	0.907	1.00
7_G	71_G	0.888	1.00
83_I	86_L	0.883	1.00
77_A	90_F	0.879	1.00
43_K	88_Y	0.867	1.00
47_L	50_A	0.859	1.00
8_A	72_A	0.855	1.00
3_I	6_F	0.852	1.00
48_A	78_V	0.842	1.00
25_R	64_R	0.840	1.00
5_S	76_I	0.838	1.00
13_L	103_L	0.823	1.00
34_S	73_T	0.814	1.00
39_V	77_A	0.812	1.00
28_I	100_L	0.801	1.00
15_A	57_I	0.799	1.00
110_N	115_R	0.753	1.00
82_P	87_G	0.751	1.00
88_Y	94_P	0.750	1.00
38_G	42_A	0.746	1.00
82_P	85_A	0.741	1.00
27_V	99_A	0.737	1.00
11_V	15_A	0.736	1.00
41_C	52_A	0.735	1.00
49_A	78_V	0.733	1.00
36_L	40_A	0.733	1.00
32_L	36_L	0.721	1.00
49_A	79_L	0.718	1.00
17_P	22_A	0.718	1.00
88_Y	92_L	0.712	1.00
58_A	62_L	0.707	1.00
70_A	74_A	0.704	1.00
89_L	92_L	0.701	1.00
52_A	56_A	0.700	1.00
108_L	111_N	0.696	1.00
15_A	61_H	0.694	1.00
7_G	75_L	0.694	1.00
60_M	70_A	0.693	1.00
39_V	88_Y	0.691	1.00
34_S	74_A	0.689	1.00
113_T	116_R	0.687	1.00
73_T	95_V	0.685	1.00
13_L	17_P	0.680	1.00
42_A	78_V	0.673	1.00
12_L	16_V	0.668	1.00
4_A	7_G	0.667	1.00
39_V	91_L	0.666	1.00
4_A	8_A	0.666	1.00
55_L	59_L	0.660	1.00
56_A	74_A	0.659	1.00
63_T	66_L	0.645	1.00
106_A	110_N	0.637	1.00
20_P	26_N	0.637	1.00
73_T	77_A	0.636	1.00
21_L	26_N	0.634	1.00
8_A	21_L	0.625	1.00
75_L	79_L	0.611	1.00
31_H	67_H	0.607	1.00
56_A	71_G	0.606	1.00
21_L	66_L	0.605	1.00
52_A	74_A	0.605	1.00
6_F	13_L	0.603	1.00
20_P	64_R	0.601	1.00
101_L	105_V	0.599	1.00
61_H	64_R	0.597	1.00
41_C	44_L	0.589	0.99
19_S	26_N	0.589	0.99
34_S	37_V	0.584	0.99
57_I	78_V	0.578	0.99
74_A	77_A	0.577	0.99
4_A	72_A	0.571	0.99
84_H	88_Y	0.569	0.99
24_P	28_I	0.561	0.99
42_A	81_G	0.560	0.99
33_I	65_T	0.553	0.99
53_V	56_A	0.551	0.99
18_A	116_R	0.550	0.99
5_S	31_H	0.547	0.99
53_V	71_G	0.547	0.99
30_G	67_H	0.547	0.99
16_V	22_A	0.545	0.99
94_P	97_L	0.543	0.99
30_G	34_S	0.533	0.99
94_P	98_G	0.528	0.99
29_G	33_I	0.527	0.99
37_V	40_A	0.526	0.99
80_G	83_I	0.521	0.99
60_M	71_G	0.519	0.99
96_L	99_A	0.518	0.99
15_A	66_L	0.517	0.99
26_N	65_T	0.510	0.98
15_A	30_G	0.503	0.98
104_L	108_L	0.503	0.98
86_L	89_L	0.502	0.98
37_V	56_A	0.501	0.98
104_L	107_L	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
2kncA	1	0.3559	22	0.885	Contact Map
2k1aA	1	0.339	17.5	0.89	Contact Map
2l8sA	1	0.3305	14.7	0.894	Contact Map
2m3eA	1	0.3559	6.2	0.91	Contact Map
2k9jB	1	0.3644	4.4	0.916	Contact Map
2kv5A	1	0.2797	4.1	0.917	Contact Map
4b19A	1	0.2542	3.6	0.919	Contact Map
1fftB	1	0.4153	3.5	0.92	Contact Map
1afoA	2	0.3305	2.4	0.927	Contact Map
4fvyA	2	0.3475	2.4	0.927	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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