PDR_CDR - PFAM28P - GREMLIN Contacts

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PDR_CDR - CDR ABC transporter

PFAM:	PF06422	Sequences: LVPSGPGYENVSGANQVCAVVGAVPGQTTVSGDAYLETSYGYSYSHLWRNFGILIAFWVFFLALYLVATELNSAAKSGGEVLVFKRGHKPKKKKKEE	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	97 (94)
Sequences:	2126 (1574)
Seq/√Len:	162.4
META:	0.238

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
37_E	43_S	3.915	1.00
24_V	34_A	3.662	1.00
31_S	34_A	3.605	1.00
51_F	55_I	3.566	1.00
44_Y	47_L	3.170	1.00
24_V	27_Q	2.406	1.00
33_D	44_Y	2.130	1.00
13_G	16_Q	2.061	1.00
56_A	60_F	2.013	1.00
21_V	39_S	2.004	1.00
17_V	25_P	1.968	1.00
60_F	64_L	1.938	1.00
63_A	67_V	1.881	1.00
53_I	60_F	1.869	1.00
5_G	8_Y	1.773	1.00
87_G	90_P	1.745	1.00
46_H	49_R	1.701	1.00
21_V	38_T	1.646	1.00
85_K	88_H	1.626	1.00
67_V	71_L	1.625	1.00
19_A	23_A	1.622	1.00
58_W	62_L	1.526	1.00
53_I	56_A	1.483	1.00
43_S	46_H	1.470	1.00
34_A	37_E	1.403	1.00
90_P	93_K	1.396	1.00
34_A	38_T	1.365	1.00
11_V	16_Q	1.349	1.00
35_Y	40_Y	1.343	1.00
12_S	15_N	1.338	1.00
47_L	51_F	1.331	1.00
59_V	63_A	1.313	1.00
49_R	53_I	1.243	1.00
55_I	59_V	1.219	1.00
48_W	51_F	1.168	1.00
1_L	16_Q	1.095	1.00
9_E	16_Q	1.081	0.99
12_S	16_Q	1.060	0.99
72_N	75_A	1.030	0.99
6_P	9_E	1.021	0.99
62_L	66_L	1.007	0.99
55_I	58_W	1.002	0.99
79_G	82_L	0.994	0.99
11_V	15_N	0.972	0.99
74_A	78_G	0.953	0.99
4_S	8_Y	0.931	0.98
40_Y	84_F	0.927	0.98
54_L	58_W	0.921	0.98
50_N	53_I	0.907	0.98
9_E	14_A	0.895	0.98
57_F	61_F	0.895	0.98
64_L	68_A	0.894	0.98
37_E	41_G	0.864	0.98
10_N	15_N	0.864	0.98
56_A	61_F	0.859	0.97
10_N	14_A	0.842	0.97
1_L	28_T	0.837	0.97
27_Q	34_A	0.827	0.97
42_Y	49_R	0.826	0.97
9_E	13_G	0.825	0.97
47_L	76_K	0.819	0.97
9_E	12_S	0.818	0.97
74_A	80_E	0.811	0.96
66_L	76_K	0.810	0.96
1_L	5_G	0.790	0.96
68_A	73_S	0.782	0.96
90_P	94_K	0.774	0.95
56_A	59_V	0.772	0.95
65_Y	80_E	0.769	0.95
32_G	48_W	0.757	0.95
72_N	77_S	0.752	0.94
51_F	62_L	0.750	0.94
16_Q	20_V	0.742	0.94
82_L	88_H	0.735	0.94
77_S	80_E	0.703	0.92
16_Q	28_T	0.702	0.92
42_Y	65_Y	0.695	0.92
73_S	83_V	0.688	0.91
69_T	82_L	0.688	0.91
33_D	37_E	0.681	0.91
48_W	52_G	0.675	0.91
23_A	39_S	0.668	0.90
17_V	21_V	0.666	0.90
7_G	11_V	0.665	0.90
49_R	56_A	0.664	0.90
69_T	72_N	0.663	0.90
58_W	69_T	0.662	0.90
59_V	62_L	0.659	0.90
65_Y	73_S	0.659	0.90
89_K	93_K	0.655	0.89
80_E	84_F	0.651	0.89
83_V	87_G	0.650	0.89
58_W	76_K	0.648	0.89
22_G	30_V	0.646	0.89
79_G	83_V	0.642	0.88
64_L	69_T	0.634	0.88
3_P	7_G	0.623	0.87
66_L	73_S	0.617	0.86
73_S	77_S	0.614	0.86
91_K	94_K	0.610	0.86
77_S	82_L	0.604	0.85
82_L	85_K	0.603	0.85
51_F	54_L	0.603	0.85
49_R	52_G	0.602	0.85
1_L	4_S	0.600	0.85
37_E	44_Y	0.598	0.85
17_V	23_A	0.589	0.84
2_V	19_A	0.589	0.84
68_A	71_L	0.587	0.83
75_A	78_G	0.587	0.83
86_R	90_P	0.587	0.83
75_A	79_G	0.584	0.83
80_E	85_K	0.577	0.82
40_Y	64_L	0.576	0.82
69_T	75_A	0.569	0.82
38_T	91_K	0.566	0.81
55_I	70_E	0.565	0.81
45_S	50_N	0.558	0.80
47_L	66_L	0.557	0.80
4_S	9_E	0.554	0.80
65_Y	77_S	0.554	0.80
40_Y	70_E	0.553	0.80
39_S	69_T	0.550	0.79
65_Y	72_N	0.547	0.79
43_S	59_V	0.541	0.78
87_G	92_K	0.538	0.78
74_A	77_S	0.536	0.78
89_K	94_K	0.535	0.77
12_S	93_K	0.535	0.77
9_E	15_N	0.531	0.77
77_S	81_V	0.530	0.77
51_F	61_F	0.530	0.77
42_Y	52_G	0.529	0.77
21_V	91_K	0.526	0.76
89_K	92_K	0.524	0.76
50_N	54_L	0.521	0.76
35_Y	62_L	0.519	0.75
79_G	86_R	0.519	0.75
58_W	68_A	0.512	0.74
88_H	93_K	0.507	0.74
5_G	9_E	0.500	0.73

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
1qb3A	2	0.8557	14.7	0.918	Contact Map
4bw5A	2	0.5258	12	0.921	Contact Map
1cksA	5	0.7629	8.6	0.926	Contact Map
3qy2A	4	0.8454	7.2	0.929	Contact Map
4yc6B	1	0.7113	7.2	0.929	Contact Map
1pucA	2	0.7835	6.6	0.93	Contact Map
4e6zA	1	0	4.8	0.934	Contact Map
4reoA	1	0.7732	4.6	0.935	Contact Map
4h6qA	1	0.2062	3.5	0.938	Contact Map
2kncA	1	0.5361	3.5	0.939	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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