TniQ - PFAM28P - GREMLIN Contacts

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TniQ - TniQ

PFAM:	PF06527	Sequences: PIRPPPYPDESLSSYLARLAAANGLSPRELLRDLGGPRRRSLADRDLPLHLERLAALTGLSPEELRAHTLLPYYAAMLLGPGGRLRLLLGLLLSRRGLRRRGLRYCPACLAEDGEPYWRRLWQLPGVTVCPKHGCLL	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	137 (136)
Sequences:	9654 (8508)
Seq/√Len:	729.5
META:	0.773

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
108_A	135_C	4.965	1.00
113_D	119_R	4.721	1.00
20_A	30_L	2.617	1.00
112_E	132_K	2.606	1.00
10_E	18_R	2.544	1.00
103_L	118_W	2.510	1.00
106_C	109_C	2.274	1.00
100_R	104_R	2.259	1.00
64_E	67_A	2.226	1.00
6_P	15_Y	2.212	1.00
127_V	131_P	2.175	1.00
108_A	111_A	2.093	1.00
9_D	121_L	2.040	1.00
6_P	68_H	2.030	1.00
4_P	19_L	2.025	1.00
11_S	14_S	1.977	1.00
26_S	29_E	1.969	1.00
119_R	122_W	1.952	1.00
9_D	120_R	1.897	1.00
105_Y	110_L	1.876	1.00
105_Y	118_W	1.866	1.00
121_L	131_P	1.844	1.00
19_L	23_N	1.804	1.00
110_L	122_W	1.796	1.00
15_Y	19_L	1.787	1.00
11_S	123_Q	1.736	1.00
48_P	51_L	1.596	1.00
9_D	119_R	1.523	1.00
129_V	136_L	1.517	1.00
61_S	64_E	1.511	1.00
53_R	57_L	1.460	1.00
4_P	22_A	1.451	1.00
25_L	30_L	1.402	1.00
19_L	58_T	1.387	1.00
11_S	103_L	1.387	1.00
107_P	135_C	1.373	1.00
103_L	123_Q	1.350	1.00
31_L	35_G	1.348	1.00
54_L	58_T	1.321	1.00
55_A	62_P	1.314	1.00
3_R	15_Y	1.302	1.00
40_R	43_A	1.294	1.00
41_S	44_D	1.287	1.00
121_L	127_V	1.268	1.00
118_W	123_Q	1.256	1.00
14_S	118_W	1.252	1.00
30_L	34_L	1.234	1.00
16_L	31_L	1.227	1.00
60_L	64_E	1.198	1.00
27_P	30_L	1.188	1.00
53_R	56_A	1.119	1.00
112_E	133_H	1.104	1.00
128_T	136_L	1.081	1.00
81_P	85_L	1.078	1.00
55_A	60_L	1.056	1.00
130_C	133_H	1.052	1.00
30_L	35_G	1.047	1.00
75_A	78_L	1.034	1.00
11_S	15_Y	1.033	1.00
25_L	28_R	1.012	1.00
52_E	56_A	1.012	1.00
110_L	118_W	1.007	1.00
17_A	21_A	1.005	1.00
11_S	120_R	1.004	1.00
13_S	103_L	0.995	1.00
13_S	123_Q	0.987	1.00
77_M	80_G	0.977	1.00
6_P	9_D	0.972	1.00
15_Y	68_H	0.969	1.00
104_R	123_Q	0.965	1.00
112_E	116_P	0.963	1.00
13_S	17_A	0.961	1.00
55_A	59_G	0.948	1.00
129_V	134_G	0.946	1.00
86_R	91_L	0.932	1.00
2_I	22_A	0.928	1.00
55_A	58_T	0.926	1.00
72_P	120_R	0.926	1.00
15_Y	65_L	0.920	1.00
40_R	44_D	0.917	1.00
86_R	89_L	0.903	1.00
70_L	74_Y	0.902	1.00
70_L	73_Y	0.896	1.00
69_T	72_P	0.893	1.00
133_H	137_L	0.871	1.00
91_L	94_S	0.868	1.00
66_R	71_L	0.866	1.00
118_W	121_L	0.865	1.00
45_R	48_P	0.862	1.00
2_I	23_N	0.856	1.00
85_L	93_L	0.851	1.00
43_A	46_D	0.849	1.00
42_L	45_R	0.836	1.00
8_P	119_R	0.836	1.00
25_L	29_E	0.835	1.00
80_G	83_G	0.834	1.00
92_L	95_R	0.829	1.00
12_L	65_L	0.828	1.00
94_S	97_G	0.828	1.00
17_A	118_W	0.823	1.00
28_R	33_D	0.814	1.00
113_D	132_K	0.803	1.00
109_C	133_H	0.797	1.00
88_L	93_L	0.790	1.00
123_Q	126_G	0.782	1.00
86_R	94_S	0.782	1.00
62_P	65_L	0.780	1.00
82_G	87_L	0.776	1.00
71_L	74_Y	0.776	1.00
114_G	117_Y	0.773	1.00
27_P	32_R	0.772	1.00
29_E	33_D	0.772	1.00
11_S	118_W	0.762	1.00
110_L	113_D	0.757	1.00
4_P	15_Y	0.734	1.00
19_L	30_L	0.727	1.00
93_L	96_R	0.722	1.00
17_A	103_L	0.719	1.00
111_A	115_E	0.714	1.00
63_E	66_R	0.712	1.00
128_T	131_P	0.711	1.00
52_E	62_P	0.706	1.00
87_L	92_L	0.705	1.00
55_A	63_E	0.705	1.00
125_P	128_T	0.701	1.00
45_R	50_H	0.696	1.00
20_A	23_N	0.695	1.00
68_H	71_L	0.684	1.00
14_S	123_Q	0.680	1.00
75_A	79_L	0.679	1.00
27_P	35_G	0.678	1.00
15_Y	122_W	0.676	1.00
78_L	82_G	0.669	1.00
47_L	50_H	0.659	1.00
79_L	87_L	0.657	1.00
122_W	131_P	0.653	1.00
76_A	81_P	0.653	1.00
69_T	120_R	0.651	1.00
86_R	95_R	0.646	1.00
3_R	23_N	0.643	1.00
27_P	31_L	0.641	1.00
43_A	47_L	0.641	1.00
47_L	51_L	0.640	1.00
119_R	132_K	0.639	1.00
106_C	133_H	0.638	1.00
67_A	72_P	0.634	1.00
92_L	97_G	0.634	1.00
84_R	90_G	0.634	1.00
68_H	73_Y	0.627	1.00
54_L	65_L	0.625	1.00
76_A	88_L	0.621	1.00
39_R	43_A	0.619	1.00
3_R	19_L	0.613	1.00
32_R	38_R	0.613	1.00
79_L	82_G	0.609	1.00
8_P	117_Y	0.599	1.00
20_A	27_P	0.596	1.00
87_L	90_G	0.596	1.00
127_V	137_L	0.592	1.00
92_L	96_R	0.590	1.00
55_A	65_L	0.575	1.00
114_G	119_R	0.572	1.00
78_L	85_L	0.569	1.00
60_L	65_L	0.568	1.00
69_T	73_Y	0.565	1.00
46_D	49_L	0.564	1.00
75_A	80_G	0.562	1.00
77_M	81_P	0.557	1.00
69_T	74_Y	0.556	1.00
55_A	61_S	0.554	1.00
86_R	90_G	0.552	1.00
113_D	117_Y	0.549	1.00
65_L	68_H	0.549	1.00
29_E	32_R	0.548	1.00
116_P	132_K	0.548	1.00
66_R	69_T	0.547	1.00
11_S	70_L	0.546	1.00
16_L	118_W	0.540	1.00
120_R	123_Q	0.539	1.00
78_L	81_P	0.539	1.00
7_Y	113_D	0.536	1.00
88_L	91_L	0.534	1.00
12_L	15_Y	0.534	1.00
31_L	36_G	0.534	1.00
8_P	132_K	0.533	1.00
14_S	17_A	0.532	1.00
55_A	64_E	0.531	1.00
99_R	104_R	0.528	1.00
86_R	97_G	0.524	1.00
82_G	88_L	0.522	1.00
62_P	66_R	0.521	1.00
87_L	94_S	0.520	1.00
52_E	55_A	0.519	1.00
39_R	42_L	0.517	1.00
12_L	69_T	0.511	1.00
25_L	35_G	0.508	1.00
79_L	85_L	0.508	1.00
46_D	50_H	0.507	1.00
108_A	112_E	0.506	1.00
44_D	47_L	0.506	1.00
84_R	88_L	0.501	0.99
80_G	85_L	0.501	0.99
25_L	32_R	0.500	0.99
91_L	95_R	0.500	0.99

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
3ttcA	1	0.2774	8.1	0.899	Contact Map
4g9iA	1	0.9197	6.5	0.904	Contact Map
4pd2A	1	0.8978	5.6	0.907	Contact Map
5aj3p	1	0.5912	5	0.909	Contact Map
4kiyR	1	0.1679	4.2	0.912	Contact Map
1e5rA	2	0.6277	3.8	0.914	Contact Map
2kkeA	2	0.2847	3.7	0.915	Contact Map
3vthA	1	0.9489	3.2	0.917	Contact Map
3f2gA	1	0.8978	3.1	0.917	Contact Map
5c56A	1	0.5474	2.5	0.921	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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