Tim17 - PFAM28P - GREMLIN Contacts

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Tim17 - Tim17/Tim22/Tim23/Pmp24 family

PFAM:	PF02466	Sequences: SCLYKTGLAFLMGAALGGVYGLFKGFLKLRLNGVLNAVGRRGPSLGGNFAVFGGLYSGIECLLEKLRKEDPWNSIIAGALTGALLAARAGPRAAAQAAVLGGALFAAFSGAID	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	113 (109)
Sequences:	2913 (1887)
Seq/√Len:	180.7
META:	0.246

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
79_A	102_G	4.569	1.00
67_R	70_D	3.608	1.00
67_R	73_N	3.132	1.00
63_L	76_I	2.935	1.00
59_I	80_L	2.918	1.00
63_L	77_A	2.424	1.00
70_D	73_N	2.297	1.00
59_I	84_L	2.151	1.00
53_G	57_S	1.996	1.00
95_A	98_A	1.818	1.00
42_G	46_G	1.783	1.00
15_A	19_V	1.721	1.00
21_G	25_G	1.608	1.00
64_E	69_E	1.604	1.00
41_R	45_L	1.560	1.00
7_G	10_F	1.559	1.00
32_N	36_N	1.554	1.00
77_A	81_T	1.517	1.00
97_A	101_G	1.515	1.00
39_G	43_P	1.494	1.00
27_L	31_L	1.486	1.00
41_R	44_S	1.465	1.00
83_A	98_A	1.437	1.00
105_F	109_S	1.401	1.00
12_M	16_L	1.392	1.00
21_G	24_K	1.367	1.00
16_L	20_Y	1.351	1.00
12_M	15_A	1.336	1.00
28_K	32_N	1.311	1.00
84_L	87_A	1.283	1.00
96_Q	99_V	1.264	1.00
100_L	104_L	1.250	1.00
75_I	102_G	1.229	1.00
8_L	12_M	1.219	1.00
56_Y	74_S	1.214	1.00
51_V	54_G	1.194	1.00
100_L	103_A	1.193	1.00
29_L	32_N	1.180	1.00
55_L	59_I	1.170	1.00
62_L	66_L	1.165	1.00
101_G	105_F	1.164	1.00
99_V	102_G	1.163	1.00
22_L	25_G	1.161	1.00
72_W	76_I	1.161	1.00
58_G	62_L	1.120	1.00
59_I	77_A	1.098	1.00
95_A	102_G	1.098	1.00
80_L	83_A	1.085	1.00
62_L	65_K	1.072	1.00
14_A	43_P	1.068	1.00
92_R	95_A	1.067	1.00
94_A	98_A	1.054	1.00
27_L	30_R	1.037	1.00
39_G	44_S	1.029	1.00
95_A	99_V	1.020	0.99
34_V	38_V	1.012	0.99
92_R	96_Q	1.007	0.99
75_I	79_A	1.001	0.99
11_L	15_A	0.994	0.99
107_A	110_G	0.987	0.99
9_A	12_M	0.965	0.99
59_I	62_L	0.961	0.99
73_N	77_A	0.955	0.99
14_A	46_G	0.942	0.99
11_L	14_A	0.941	0.99
64_E	73_N	0.938	0.99
60_E	77_A	0.938	0.99
91_P	95_A	0.933	0.99
63_L	73_N	0.914	0.99
78_G	82_G	0.912	0.99
55_L	84_L	0.911	0.99
56_Y	60_E	0.897	0.99
60_E	74_S	0.882	0.98
23_F	26_F	0.876	0.98
5_K	8_L	0.874	0.98
4_Y	50_A	0.873	0.98
81_T	85_L	0.872	0.98
36_N	39_G	0.867	0.98
43_P	47_G	0.867	0.98
33_G	37_A	0.863	0.98
22_L	38_V	0.862	0.98
31_L	35_L	0.858	0.98
74_S	77_A	0.849	0.98
40_R	44_S	0.848	0.98
91_P	94_A	0.845	0.98
31_L	38_V	0.836	0.98
53_G	60_E	0.835	0.98
98_A	101_G	0.831	0.98
75_I	110_G	0.830	0.98
30_R	33_G	0.816	0.97
31_L	34_V	0.814	0.97
36_N	40_R	0.802	0.97
28_K	36_N	0.771	0.96
8_L	11_L	0.769	0.96
42_G	45_L	0.756	0.96
6_T	54_G	0.754	0.96
83_A	87_A	0.750	0.96
96_Q	100_L	0.748	0.96
97_A	109_S	0.739	0.95
15_A	18_G	0.729	0.95
96_Q	101_G	0.724	0.95
103_A	108_F	0.710	0.94
102_G	105_F	0.708	0.94
37_A	41_R	0.704	0.94
17_G	21_G	0.700	0.94
37_A	44_S	0.687	0.93
101_G	108_F	0.686	0.93
22_L	34_V	0.677	0.93
9_A	53_G	0.673	0.93
55_L	81_T	0.672	0.93
30_R	34_V	0.672	0.93
18_G	21_G	0.670	0.93
71_P	110_G	0.669	0.92
79_A	98_A	0.665	0.92
20_Y	24_K	0.658	0.92
39_G	42_G	0.657	0.92
42_G	47_G	0.653	0.92
14_A	18_G	0.651	0.91
3_L	6_T	0.650	0.91
5_K	9_A	0.647	0.91
18_G	22_L	0.646	0.91
17_G	20_Y	0.645	0.91
96_Q	102_G	0.645	0.91
29_L	35_L	0.636	0.90
58_G	61_C	0.632	0.90
101_G	109_S	0.627	0.90
50_A	88_R	0.624	0.90
11_L	16_L	0.618	0.89
19_V	62_L	0.618	0.89
35_L	39_G	0.617	0.89
33_G	43_P	0.615	0.89
68_K	72_W	0.609	0.88
19_V	23_F	0.595	0.87
107_A	111_A	0.594	0.87
48_N	58_G	0.594	0.87
92_R	100_L	0.588	0.87
26_F	30_R	0.588	0.87
48_N	52_F	0.586	0.87
24_K	41_R	0.576	0.86
32_N	39_G	0.576	0.86
29_L	62_L	0.574	0.85
103_A	110_G	0.570	0.85
10_F	21_G	0.570	0.85
71_P	107_A	0.570	0.85
51_V	58_G	0.569	0.85
21_G	26_F	0.568	0.85
5_K	10_F	0.564	0.84
34_V	37_A	0.557	0.84
6_T	61_C	0.555	0.83
61_C	65_K	0.551	0.83
89_A	93_A	0.549	0.83
57_S	60_E	0.541	0.82
97_A	102_G	0.528	0.80
104_L	108_F	0.528	0.80
69_E	73_N	0.526	0.80
29_L	34_V	0.524	0.80
4_Y	10_F	0.522	0.80
63_L	66_L	0.516	0.79
29_L	36_N	0.516	0.79
103_A	107_A	0.515	0.79
105_F	108_F	0.515	0.79
52_F	86_A	0.513	0.78
90_G	98_A	0.511	0.78
38_V	44_S	0.500	0.77

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
1okcA	1	0.8319	3.2	0.904	Contact Map
2lckA	1	0.8319	2.7	0.908	Contact Map
4c9gA	1	0.8319	2.6	0.908	Contact Map
1jb0L	1	0.354	1.7	0.917	Contact Map
4cz8A	2	0.885	1.6	0.918	Contact Map
4p6vB	1	0.9469	1.4	0.92	Contact Map
2lbgA	1	0.2389	1.4	0.921	Contact Map
2m0wA	1	0.2035	0.9	0.931	Contact Map
2nwlA	3	0.3451	0.9	0.931	Contact Map
1q90R	1	0.3451	0.8	0.931	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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