GtrA - PFAM28P - GREMLIN Contacts

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GtrA - GtrA-like protein

PFAM:	PF04138	Sequences: RFALVGGLGTLVDLGVLALLLELLGLPYLLANAIAFLVAVLVNFLLNRRWTFRDRGRRGLLRELLRFLLVSLVGLLLNLGLLALLVELLGLPYLLAKLIAIAVVTVWNFLLSRLWVF	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	117 (117)
Sequences:	81657 (61323)
Seq/√Len:	5669.3
META:	0.904

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
8_L	42_V	2.775	1.00
48_R	63_E	2.756	1.00
70_V	111_L	2.572	1.00
112_S	116_V	2.399	1.00
5_V	46_L	2.385	1.00
47_N	51_T	2.370	1.00
42_V	46_L	2.349	1.00
37_L	68_L	2.184	1.00
12_V	42_V	2.101	1.00
9_G	43_N	2.068	1.00
33_A	79_L	2.043	1.00
16_V	38_V	2.018	1.00
83_A	87_E	1.977	1.00
18_A	22_E	1.928	1.00
41_L	64_L	1.925	1.00
110_L	114_L	1.877	1.00
29_L	83_A	1.869	1.00
13_D	32_N	1.817	1.00
28_Y	82_L	1.795	1.00
29_L	79_L	1.779	1.00
13_D	97_K	1.758	1.00
81_L	100_A	1.724	1.00
45_L	49_R	1.649	1.00
92_P	95_L	1.554	1.00
14_L	18_A	1.519	1.00
85_L	96_A	1.468	1.00
9_G	42_V	1.460	1.00
64_L	68_L	1.446	1.00
32_N	97_K	1.445	1.00
84_L	88_L	1.442	1.00
32_N	79_L	1.434	1.00
100_A	104_V	1.389	1.00
62_R	66_R	1.384	1.00
32_N	82_L	1.368	1.00
40_V	68_L	1.348	1.00
40_V	71_S	1.342	1.00
79_L	83_A	1.334	1.00
21_L	93_Y	1.324	1.00
66_R	115_W	1.290	1.00
27_P	30_L	1.289	1.00
54_D	63_E	1.275	1.00
18_A	94_L	1.223	1.00
33_A	75_L	1.178	1.00
97_K	101_I	1.173	1.00
77_L	107_W	1.160	1.00
106_V	110_L	1.143	1.00
36_F	75_L	1.139	1.00
13_D	78_N	1.131	1.00
17_L	97_K	1.097	1.00
37_L	41_L	1.090	1.00
52_F	113_R	1.089	1.00
73_V	107_W	1.079	1.00
9_G	13_D	1.075	1.00
36_F	40_V	1.064	1.00
16_V	20_L	1.063	1.00
61_L	65_L	1.053	1.00
28_Y	86_V	1.042	1.00
5_V	51_T	1.041	1.00
66_R	116_V	1.034	1.00
20_L	34_I	1.022	1.00
19_L	23_L	1.019	1.00
35_A	39_A	1.013	1.00
18_A	21_L	1.012	1.00
17_L	93_Y	1.011	1.00
74_G	108_N	1.009	1.00
75_L	79_L	1.000	1.00
10_T	101_I	0.985	1.00
44_F	63_E	0.984	1.00
107_W	111_L	0.974	1.00
17_L	35_A	0.973	1.00
20_L	26_L	0.967	1.00
10_T	14_L	0.963	1.00
48_R	117_F	0.962	1.00
48_R	56_G	0.938	1.00
74_G	107_W	0.923	1.00
83_A	88_L	0.911	1.00
82_L	86_V	0.900	1.00
65_L	68_L	0.899	1.00
81_L	85_L	0.898	1.00
32_N	78_N	0.896	1.00
30_L	33_A	0.895	1.00
26_L	30_L	0.890	1.00
41_L	45_L	0.877	1.00
3_A	105_T	0.864	1.00
71_S	112_S	0.862	1.00
102_A	106_V	0.842	1.00
24_L	31_A	0.839	1.00
41_L	68_L	0.831	1.00
4_L	8_L	0.820	1.00
40_V	64_L	0.813	1.00
37_L	40_V	0.796	1.00
62_R	65_L	0.796	1.00
44_F	67_F	0.792	1.00
7_G	11_L	0.783	1.00
87_E	90_G	0.776	1.00
21_L	31_A	0.776	1.00
4_L	7_G	0.773	1.00
101_I	105_T	0.770	1.00
88_L	91_L	0.756	1.00
111_L	114_L	0.755	1.00
13_D	39_A	0.747	1.00
98_L	102_A	0.737	1.00
107_W	110_L	0.736	1.00
22_E	93_Y	0.732	1.00
24_L	27_P	0.725	1.00
18_A	23_L	0.716	1.00
17_L	82_L	0.712	1.00
9_G	46_L	0.711	1.00
76_L	80_G	0.703	1.00
78_N	97_K	0.696	1.00
108_N	112_S	0.692	1.00
80_G	84_L	0.687	1.00
3_A	7_G	0.682	1.00
8_L	11_L	0.679	1.00
101_I	104_V	0.677	1.00
96_A	100_A	0.676	1.00
72_L	76_L	0.675	1.00
67_F	71_S	0.667	1.00
80_G	83_A	0.666	1.00
70_V	116_V	0.666	1.00
14_L	97_K	0.663	1.00
85_L	89_L	0.663	1.00
61_L	64_L	0.662	1.00
33_A	37_L	0.661	1.00
87_E	91_L	0.657	1.00
29_L	33_A	0.657	1.00
28_Y	87_E	0.655	1.00
65_L	69_L	0.653	1.00
17_L	21_L	0.647	1.00
22_E	25_G	0.643	1.00
48_R	54_D	0.638	1.00
70_V	74_G	0.633	1.00
111_L	115_W	0.629	1.00
31_A	35_A	0.627	1.00
70_V	112_S	0.627	1.00
73_V	76_L	0.612	1.00
1_R	50_W	0.606	1.00
11_L	15_G	0.602	1.00
20_L	31_A	0.601	1.00
85_L	88_L	0.598	1.00
19_L	24_L	0.596	1.00
12_V	39_A	0.591	1.00
68_L	72_L	0.585	1.00
13_D	35_A	0.581	1.00
21_L	28_Y	0.581	1.00
91_L	95_L	0.580	1.00
81_L	103_V	0.572	1.00
20_L	24_L	0.570	1.00
26_L	31_A	0.570	1.00
29_L	87_E	0.565	1.00
14_L	98_L	0.564	1.00
46_L	49_R	0.564	1.00
9_G	12_V	0.559	1.00
22_E	94_L	0.558	1.00
16_V	35_A	0.558	1.00
59_G	62_R	0.556	1.00
56_G	63_E	0.555	1.00
20_L	38_V	0.553	1.00
15_G	19_L	0.546	1.00
15_G	18_A	0.546	1.00
58_R	63_E	0.543	1.00
33_A	36_F	0.532	1.00
8_L	12_V	0.532	1.00
86_V	96_A	0.532	1.00
63_E	66_R	0.527	1.00
43_N	47_N	0.519	1.00
85_L	91_L	0.514	1.00
43_N	71_S	0.514	1.00
96_A	99_I	0.511	1.00
6_G	105_T	0.511	1.00
16_V	39_A	0.508	1.00
57_R	60_L	0.508	1.00
7_G	10_T	0.506	1.00
5_V	50_W	0.504	1.00
81_L	84_L	0.503	1.00
2_F	108_N	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
3w4tA	1	0.4872	5.4	0.879	Contact Map
3mktA	1	0.547	4.2	0.885	Contact Map
4lz6A	1	0.4872	3.4	0.89	Contact Map
4humA	1	0.547	3.3	0.891	Contact Map
3aqpA	1	1	3.1	0.893	Contact Map
4k0jA	3	0.9744	2.6	0.897	Contact Map
4il3A	1	0.9915	1.8	0.905	Contact Map
4av3A	2	0.7265	1.5	0.91	Contact Map
3iyzA	3	0.8547	1.4	0.911	Contact Map
2voyD	1	0.1368	1.3	0.912	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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