TctB - PFAM28P - GREMLIN Contacts

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TctB - Tripartite tricarboxylate transporter TctB family

PFAM:	PF07331	Sequences: FIAGLLLLALAGLAFAWGALRTGAGPGPGFFPFLLGVLLALLGLLLLVRAARAGGEPPEPFVWRGLLRRVLAVLAALVAYALLLEPLGFLLATALFLFALLGLGRRRWLRALLVAVVLTVVIYLLFVKLLGVPLP	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	135 (132)
Sequences:	47168 (37106)
Seq/√Len:	3229.7
META:	0.893

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
80_Y	93_T	3.490	1.00
18_G	21_R	3.368	1.00
107_R	110_R	3.017	1.00
124_L	128_K	2.986	1.00
17_W	20_L	2.965	1.00
8_L	40_A	2.308	1.00
128_K	131_G	2.293	1.00
37_V	41_L	2.276	1.00
111_A	115_A	2.123	1.00
94_A	119_T	2.076	1.00
29_G	33_F	2.070	1.00
109_L	113_L	2.051	1.00
115_A	119_T	2.002	1.00
123_Y	127_V	1.947	1.00
98_F	115_A	1.806	1.00
91_L	94_A	1.791	1.00
63_W	67_L	1.773	1.00
73_V	100_L	1.699	1.00
64_R	68_R	1.651	1.00
83_L	92_A	1.632	1.00
83_L	86_P	1.598	1.00
110_R	113_L	1.593	1.00
110_R	114_V	1.561	1.00
98_F	111_A	1.540	1.00
123_Y	128_K	1.527	1.00
63_W	66_L	1.516	1.00
4_G	47_L	1.505	1.00
105_R	111_A	1.480	1.00
125_L	129_L	1.479	1.00
113_L	117_V	1.465	1.00
33_F	37_V	1.443	1.00
15_F	36_G	1.435	1.00
16_A	33_F	1.429	1.00
31_F	35_L	1.423	1.00
97_L	101_L	1.415	1.00
96_F	100_L	1.324	1.00
76_A	99_A	1.319	1.00
62_V	66_L	1.295	1.00
65_G	69_R	1.287	1.00
8_L	43_G	1.283	1.00
26_P	30_F	1.280	1.00
30_F	34_L	1.272	1.00
16_A	36_G	1.263	1.00
106_R	110_R	1.259	1.00
17_W	21_R	1.257	1.00
79_A	83_L	1.211	1.00
94_A	116_V	1.211	1.00
108_W	111_A	1.209	1.00
117_V	121_V	1.208	1.00
7_L	43_G	1.206	1.00
12_G	40_A	1.164	1.00
44_L	48_V	1.160	1.00
107_R	111_A	1.144	1.00
26_P	29_G	1.130	1.00
20_L	33_F	1.121	1.00
89_F	93_T	1.121	1.00
34_L	37_V	1.119	1.00
14_A	18_G	1.113	1.00
33_F	36_G	1.105	1.00
65_G	68_R	1.066	1.00
82_L	86_P	1.057	1.00
41_L	45_L	1.057	1.00
68_R	72_A	1.053	1.00
124_L	129_L	1.051	1.00
101_L	111_A	1.046	1.00
69_R	72_A	1.042	1.00
90_L	119_T	1.031	1.00
38_L	42_L	1.029	1.00
87_L	92_A	1.024	1.00
101_L	114_V	1.021	1.00
116_V	119_T	1.015	1.00
105_R	110_R	1.014	1.00
67_L	71_L	1.012	1.00
94_A	98_F	1.011	1.00
90_L	123_Y	1.000	1.00
121_V	125_L	0.992	1.00
83_L	87_L	0.990	1.00
55_G	58_P	0.973	1.00
80_Y	92_A	0.957	1.00
49_R	52_R	0.957	1.00
4_G	43_G	0.945	1.00
43_G	47_L	0.926	1.00
3_A	7_L	0.916	1.00
60_P	63_W	0.910	1.00
52_R	55_G	0.903	1.00
93_T	119_T	0.900	1.00
19_A	33_F	0.900	1.00
94_A	115_A	0.884	1.00
109_L	112_L	0.861	1.00
13_L	17_W	0.861	1.00
129_L	133_P	0.854	1.00
89_F	122_I	0.852	1.00
117_V	120_V	0.852	1.00
58_P	61_F	0.851	1.00
62_V	67_L	0.850	1.00
36_G	40_A	0.845	1.00
24_A	27_G	0.843	1.00
66_L	69_R	0.839	1.00
34_L	38_L	0.838	1.00
62_V	65_G	0.822	1.00
15_F	19_A	0.816	1.00
96_F	99_A	0.813	1.00
16_A	19_A	0.806	1.00
40_A	44_L	0.801	1.00
51_A	54_G	0.801	1.00
121_V	124_L	0.800	1.00
97_L	100_L	0.797	1.00
90_L	127_V	0.793	1.00
55_G	60_P	0.790	1.00
43_G	46_L	0.783	1.00
61_F	65_G	0.767	1.00
3_A	6_L	0.764	1.00
51_A	55_G	0.755	1.00
97_L	118_L	0.748	1.00
61_F	66_L	0.747	1.00
125_L	130_L	0.745	1.00
42_L	46_L	0.745	1.00
15_F	20_L	0.742	1.00
106_R	111_A	0.740	1.00
82_L	85_E	0.738	1.00
102_G	105_R	0.737	1.00
120_V	124_L	0.734	1.00
16_A	20_L	0.733	1.00
59_E	62_V	0.729	1.00
8_L	47_L	0.726	1.00
114_V	117_V	0.716	1.00
98_F	108_W	0.715	1.00
80_Y	84_L	0.715	1.00
87_L	91_L	0.714	1.00
64_R	67_L	0.712	1.00
76_A	96_F	0.705	1.00
112_L	115_A	0.696	1.00
106_R	109_L	0.695	1.00
98_F	101_L	0.688	1.00
45_L	48_V	0.687	1.00
68_R	71_L	0.676	1.00
108_W	112_L	0.671	1.00
98_F	112_L	0.664	1.00
54_G	60_P	0.657	1.00
31_F	36_G	0.649	1.00
127_V	131_G	0.649	1.00
102_G	106_R	0.641	1.00
25_G	30_F	0.640	1.00
105_R	108_W	0.630	1.00
24_A	30_F	0.629	1.00
16_A	40_A	0.629	1.00
71_L	75_A	0.628	1.00
15_F	18_G	0.625	1.00
114_V	118_L	0.625	1.00
5_L	9_A	0.622	1.00
37_V	40_A	0.618	1.00
96_F	101_L	0.610	1.00
86_P	92_A	0.600	1.00
112_L	116_V	0.597	1.00
60_P	65_G	0.596	1.00
39_L	43_G	0.596	1.00
54_G	57_P	0.595	1.00
72_A	75_A	0.592	1.00
84_L	89_F	0.591	1.00
71_L	74_L	0.586	1.00
119_T	123_Y	0.583	1.00
4_G	7_L	0.581	1.00
50_A	53_A	0.576	1.00
78_V	81_A	0.575	1.00
57_P	60_P	0.575	1.00
61_F	64_R	0.575	1.00
77_L	96_F	0.569	1.00
79_A	82_L	0.568	1.00
127_V	133_P	0.568	1.00
95_L	99_A	0.564	1.00
84_L	92_A	0.558	1.00
60_P	64_R	0.557	1.00
81_A	84_L	0.556	1.00
76_A	100_L	0.552	1.00
49_R	53_A	0.550	1.00
88_G	92_A	0.547	1.00
76_A	130_L	0.546	1.00
70_V	74_L	0.542	1.00
53_A	57_P	0.538	1.00
31_F	130_L	0.536	1.00
69_R	73_V	0.535	1.00
70_V	73_V	0.529	1.00
64_R	69_R	0.528	1.00
16_A	37_V	0.527	1.00
75_A	79_A	0.527	1.00
97_L	115_A	0.524	1.00
36_G	39_L	0.523	1.00
51_A	56_E	0.523	1.00
50_A	54_G	0.522	1.00
25_G	29_G	0.521	1.00
95_L	98_F	0.518	1.00
90_L	94_A	0.515	1.00
118_L	122_I	0.512	1.00
78_V	82_L	0.509	1.00
35_L	39_L	0.507	1.00
53_A	56_E	0.505	1.00
51_A	57_P	0.501	1.00
76_A	79_A	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
4djkA	2	0.8667	4.6	0.899	Contact Map
2a65A	2	0.4444	4.4	0.899	Contact Map
2xq2A	2	0.3481	3.8	0.903	Contact Map
3giaA	1	0.4148	3.7	0.903	Contact Map
4o6yA	2	0.3778	3	0.908	Contact Map
3l1lA	2	0.8519	2.8	0.909	Contact Map
3bo0B	1	0.4815	2.1	0.915	Contact Map
3dinD	1	0.4148	2.1	0.915	Contact Map
3j01B	1	0.7185	2	0.916	Contact Map
4qi1A	3	0.9926	1.9	0.917	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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