GBS_Bsp-like - PFAM28P - GREMLIN Contacts

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GBS_Bsp-like - GBS Bsp-like repeat

PFAM:	PF08481	Sequences: TIENTNVTAGTFDVTVSNVSSPSGVKSVQFPVWSEANGQDDLKWYTATKQSDGTYKVTVNISNHKNETGTYNVHVYATDNNGNLVGVGGTTF	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	92 (87)
Sequences:	2463 (2014)
Seq/√Len:	215.9
META:	0.693

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
34_S	67_E	3.341	1.00
13_D	58_T	2.640	1.00
30_F	47_A	2.393	1.00
35_E	72_N	2.132	1.00
13_D	56_K	2.078	1.00
16_V	30_F	1.910	1.00
27_S	46_T	1.878	1.00
31_P	44_W	1.837	1.00
79_D	83_N	1.828	1.00
35_E	70_T	1.816	1.00
29_Q	46_T	1.810	1.00
32_V	73_V	1.806	1.00
15_T	56_K	1.778	1.00
34_S	40_D	1.699	1.00
43_K	63_N	1.564	1.00
40_D	67_E	1.553	1.00
50_Q	56_K	1.524	1.00
60_N	63_N	1.519	1.00
86_G	89_G	1.500	1.00
36_A	67_E	1.488	1.00
45_Y	63_N	1.486	1.00
12_F	73_V	1.420	1.00
27_S	78_T	1.405	1.00
77_A	87_V	1.389	1.00
50_Q	54_T	1.378	1.00
26_K	80_N	1.374	1.00
29_Q	78_T	1.362	1.00
39_Q	74_H	1.341	1.00
33_W	39_Q	1.299	1.00
14_V	59_V	1.264	1.00
31_P	74_H	1.250	1.00
45_Y	64_H	1.249	1.00
37_N	40_D	1.243	1.00
39_Q	42_L	1.241	1.00
44_W	74_H	1.224	1.00
32_V	59_V	1.224	1.00
29_Q	84_L	1.209	1.00
39_Q	44_W	1.204	1.00
61_I	68_T	1.169	1.00
31_P	42_L	1.168	1.00
49_K	55_Y	1.126	1.00
34_S	41_D	1.122	1.00
4_N	11_T	1.096	1.00
11_T	58_T	1.076	1.00
35_E	38_G	1.072	1.00
78_T	84_L	1.070	1.00
17_S	54_T	1.058	1.00
30_F	57_V	1.041	1.00
11_T	60_N	1.026	1.00
30_F	73_V	1.012	1.00
30_F	75_V	1.008	1.00
24_G	80_N	0.989	1.00
25_V	77_A	0.977	1.00
50_Q	53_G	0.967	1.00
49_K	52_D	0.958	1.00
61_I	66_N	0.955	1.00
23_S	81_N	0.951	1.00
42_L	74_H	0.938	1.00
79_D	85_V	0.917	0.99
44_W	76_Y	0.913	0.99
31_P	39_Q	0.903	0.99
64_H	67_E	0.869	0.99
4_N	10_G	0.868	0.99
45_Y	57_V	0.859	0.99
6_N	9_A	0.854	0.99
35_E	40_D	0.841	0.99
33_W	41_D	0.838	0.99
4_N	13_D	0.826	0.99
21_S	24_G	0.819	0.99
17_S	53_G	0.795	0.98
40_D	65_K	0.791	0.98
23_S	80_N	0.785	0.98
33_W	74_H	0.772	0.98
4_N	7_V	0.758	0.98
23_S	79_D	0.752	0.98
31_P	47_A	0.752	0.98
10_G	61_I	0.730	0.97
62_S	66_N	0.723	0.97
47_A	55_Y	0.721	0.97
41_D	67_E	0.716	0.97
23_S	83_N	0.716	0.97
14_V	73_V	0.714	0.97
16_V	19_V	0.702	0.96
16_V	75_V	0.701	0.96
64_H	69_G	0.699	0.96
26_K	82_G	0.693	0.96
15_T	54_T	0.688	0.96
26_K	78_T	0.687	0.96
16_V	28_V	0.685	0.96
33_W	42_L	0.684	0.96
12_F	59_V	0.680	0.96
33_W	44_W	0.678	0.96
18_N	22_P	0.667	0.95
31_P	76_Y	0.637	0.94
66_N	71_Y	0.626	0.93
49_K	53_G	0.623	0.93
34_S	72_N	0.617	0.93
39_Q	76_Y	0.613	0.93
65_K	71_Y	0.603	0.92
53_G	56_K	0.602	0.92
21_S	25_V	0.601	0.92
49_K	54_T	0.597	0.92
28_V	77_A	0.596	0.92
40_D	64_H	0.585	0.91
19_V	25_V	0.582	0.91
22_P	79_D	0.580	0.90
28_V	47_A	0.580	0.90
6_N	11_T	0.567	0.89
32_V	45_Y	0.566	0.89
37_N	41_D	0.565	0.89
33_W	76_Y	0.561	0.89
5_T	8_T	0.559	0.89
72_N	89_G	0.557	0.89
41_D	64_H	0.557	0.89
46_T	55_Y	0.555	0.88
7_V	10_G	0.547	0.88
57_V	60_N	0.537	0.87
74_H	86_G	0.536	0.87
5_T	68_T	0.532	0.86
8_T	20_S	0.529	0.86
59_V	63_N	0.529	0.86
79_D	82_G	0.526	0.86
41_D	44_W	0.525	0.86
31_P	41_D	0.521	0.85
43_K	64_H	0.519	0.85
25_V	78_T	0.516	0.85
13_D	16_V	0.509	0.84
4_N	8_T	0.508	0.84
25_V	79_D	0.508	0.84
24_G	79_D	0.500	0.83

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
4kdwA	1	0.9022	59.2	0.816	Contact Map
4p99A	3	0.9022	57.3	0.818	Contact Map
3pe9A	1	0.837	34.4	0.841	Contact Map
2yn5A	3	0.8913	32.7	0.843	Contact Map
3pddA	1	0.837	26.6	0.85	Contact Map
3vmnA	1	0.9891	17.3	0.863	Contact Map
2k7pA	1	0.6739	16.7	0.864	Contact Map
2k9uA	1	0.6957	15	0.867	Contact Map
2bp3A	1	0.6739	14.7	0.867	Contact Map
2di8A	1	0.6739	14.5	0.867	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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