Sm_multidrug_ex - PFAM28P - GREMLIN Contacts

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Sm_multidrug_ex - Putative small multi-drug export protein

PFAM:	PF06695	Sequences: ELRGAIPLGIALGLPPWLAFLIAVIGNILPVPFILLFLRKILKWLRKIKFFKKFFDWLFERARKKGKKIEKYGFLGLALFVAIPLPGTGAWTGALAAFLLGLDFKKAFLAILLGVLIAGII	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	121 (121)
Sequences:	8591 (6263)
Seq/√Len:	569.4
META:	0.895

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
78_A	117_I	3.371	1.00
9_G	19_A	2.863	1.00
28_I	112_L	2.782	1.00
103_D	106_K	2.766	1.00
8_L	12_L	2.732	1.00
52_K	56_D	2.690	1.00
78_A	110_A	2.546	1.00
74_F	110_A	2.276	1.00
65_K	69_I	2.241	1.00
27_N	115_V	2.142	1.00
74_F	106_K	2.069	1.00
78_A	113_L	2.060	1.00
20_F	119_G	2.052	1.00
66_G	69_I	2.046	1.00
81_V	93_G	1.873	1.00
24_V	116_L	1.826	1.00
20_F	24_V	1.744	1.00
82_A	117_I	1.738	1.00
7_P	10_I	1.725	1.00
15_P	18_L	1.704	1.00
2_L	119_G	1.678	1.00
10_I	16_P	1.671	1.00
28_I	115_V	1.652	1.00
18_L	22_I	1.645	1.00
90_A	115_V	1.591	1.00
40_K	43_K	1.518	1.00
46_R	52_K	1.501	1.00
97_A	107_A	1.492	1.00
30_P	34_I	1.443	1.00
42_L	98_F	1.429	1.00
39_R	101_G	1.346	1.00
44_W	48_I	1.342	1.00
105_K	109_L	1.318	1.00
66_G	70_E	1.311	1.00
42_L	55_F	1.280	1.00
48_I	51_F	1.266	1.00
58_L	62_A	1.263	1.00
46_R	56_D	1.243	1.00
63_R	66_G	1.222	1.00
70_E	73_G	1.204	1.00
20_F	116_L	1.192	1.00
60_E	63_R	1.181	1.00
90_A	111_I	1.172	1.00
5_A	23_A	1.168	1.00
44_W	47_K	1.163	1.00
14_L	18_L	1.154	1.00
81_V	111_I	1.153	1.00
59_F	63_R	1.111	1.00
46_R	59_F	1.090	1.00
17_W	21_L	1.076	1.00
56_D	60_E	1.060	1.00
107_A	111_I	1.060	1.00
39_R	43_K	1.041	1.00
36_L	104_F	1.040	1.00
42_L	46_R	1.039	1.00
35_L	94_A	1.034	1.00
14_L	19_A	1.026	1.00
24_V	112_L	1.019	1.00
74_F	102_L	1.012	1.00
67_K	70_E	1.005	1.00
53_K	57_W	0.998	1.00
65_K	68_K	0.972	1.00
37_F	40_K	0.969	1.00
94_A	111_I	0.964	1.00
39_R	104_F	0.952	1.00
74_F	78_A	0.942	1.00
31_V	90_A	0.934	1.00
36_L	40_K	0.927	1.00
78_A	82_A	0.927	1.00
72_Y	76_G	0.926	1.00
6_I	19_A	0.921	1.00
54_F	58_L	0.921	1.00
8_L	11_A	0.910	1.00
23_A	26_G	0.903	1.00
30_P	33_F	0.900	1.00
10_I	19_A	0.888	1.00
49_K	52_K	0.887	1.00
69_I	76_G	0.886	1.00
63_R	101_G	0.884	1.00
18_L	21_L	0.883	1.00
62_A	96_A	0.880	1.00
60_E	64_K	0.857	1.00
54_F	57_W	0.849	1.00
68_K	76_G	0.836	1.00
112_L	116_L	0.827	1.00
57_W	60_E	0.826	1.00
34_I	94_A	0.824	1.00
31_V	111_I	0.820	1.00
32_P	108_F	0.816	1.00
57_W	61_R	0.813	1.00
24_V	119_G	0.812	1.00
80_F	88_T	0.799	1.00
19_A	23_A	0.799	1.00
106_K	109_L	0.798	1.00
25_I	29_L	0.794	1.00
31_V	94_A	0.791	1.00
80_F	96_A	0.789	1.00
35_L	104_F	0.788	1.00
9_G	14_L	0.784	1.00
27_N	31_V	0.780	1.00
38_L	98_F	0.778	1.00
75_L	78_A	0.777	1.00
27_N	90_A	0.767	1.00
22_I	26_G	0.766	1.00
24_V	115_V	0.763	1.00
42_L	59_F	0.762	1.00
109_L	112_L	0.760	1.00
104_F	108_F	0.760	1.00
55_F	59_F	0.759	1.00
31_V	35_L	0.752	1.00
21_L	25_I	0.747	1.00
4_G	7_P	0.741	1.00
33_F	37_F	0.740	1.00
48_I	52_K	0.730	1.00
112_L	115_V	0.722	1.00
108_F	112_L	0.721	1.00
38_L	42_L	0.717	1.00
39_R	42_L	0.716	1.00
102_L	107_A	0.706	1.00
34_I	38_L	0.706	1.00
40_K	44_W	0.705	1.00
46_R	51_F	0.704	1.00
102_L	110_A	0.701	1.00
81_V	88_T	0.698	1.00
43_K	46_R	0.695	1.00
65_K	96_A	0.694	1.00
16_P	20_F	0.686	1.00
74_F	113_L	0.685	1.00
50_F	53_K	0.683	1.00
51_F	55_F	0.681	1.00
45_L	48_I	0.669	1.00
59_F	98_F	0.668	1.00
32_P	104_F	0.665	1.00
24_V	27_N	0.658	1.00
114_G	118_A	0.636	1.00
2_L	7_P	0.632	1.00
110_A	113_L	0.628	1.00
28_I	108_F	0.625	1.00
50_F	54_F	0.624	1.00
66_G	96_A	0.619	1.00
103_D	109_L	0.618	1.00
19_A	22_I	0.617	1.00
14_L	22_I	0.608	1.00
38_L	41_I	0.599	1.00
5_A	9_G	0.598	1.00
61_R	65_K	0.597	1.00
31_V	108_F	0.593	1.00
34_I	91_W	0.592	1.00
77_L	97_A	0.591	1.00
73_G	102_L	0.588	1.00
45_L	55_F	0.587	1.00
73_G	106_K	0.585	1.00
98_F	101_G	0.581	1.00
84_P	88_T	0.579	1.00
104_F	109_L	0.577	1.00
58_L	99_L	0.575	1.00
32_P	36_L	0.572	1.00
96_A	100_L	0.572	1.00
55_F	58_L	0.568	0.99
6_I	9_G	0.565	0.99
115_V	118_A	0.565	0.99
80_F	92_T	0.559	0.99
59_F	95_L	0.559	0.99
38_L	95_L	0.557	0.99
72_Y	75_L	0.557	0.99
43_K	47_K	0.548	0.99
45_L	52_K	0.547	0.99
76_G	96_A	0.545	0.99
26_G	30_P	0.541	0.99
17_W	20_F	0.540	0.99
3_R	118_A	0.539	0.99
42_L	51_F	0.537	0.99
22_I	25_I	0.534	0.99
87_G	92_T	0.530	0.99
52_K	55_F	0.524	0.99
62_A	95_L	0.522	0.99
45_L	51_F	0.521	0.99
39_R	98_F	0.520	0.99
6_I	20_F	0.513	0.99
69_I	72_Y	0.504	0.99
73_G	76_G	0.502	0.99
6_I	23_A	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
2jlnA	1	0.562	54.3	0.847	Contact Map
4k0jA	3	0.3388	8.6	0.898	Contact Map
4dx5A	3	0.438	8.3	0.898	Contact Map
2cfqA	1	0.9835	6	0.905	Contact Map
3giaA	1	0.438	5.5	0.907	Contact Map
4mt1A	3	0.3471	5	0.908	Contact Map
3ze3A	4	0.7025	4.3	0.911	Contact Map
2kluA	1	0.2645	3.8	0.914	Contact Map
4fc4A	3	0.6033	3.8	0.914	Contact Map
2kncA	1	0.4463	3.6	0.914	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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