ABC_cobalt - PFAM28P - GREMLIN Contacts

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ABC_cobalt - ABC-type cobalt transport system, permease component

PFAM:	PF09819	Sequences: VDIVVAAVLAVAFGVVFWAWGPLYNALSAALGPLGLGGLLYGVWLLAGVLAALIIRKPGAALLAELVAALVEALLGSQWGLLTLLSGLVQGLGAELVFALFRYRRWGLPVALLAGALAGLAAFV	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	124 (121)
Sequences:	3233 (2032)
Seq/√Len:	184.7
META:	0.757

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
51_A	64_A	5.016	1.00
97_V	117_L	3.816	1.00
62_L	95_E	3.721	1.00
7_A	63_L	3.650	1.00
101_F	110_V	3.094	1.00
69_A	87_G	2.509	1.00
66_L	88_L	2.446	1.00
32_G	35_G	2.132	1.00
13_F	46_L	2.095	1.00
53_L	111_A	2.057	1.00
13_F	47_A	2.037	1.00
52_A	61_A	1.976	1.00
82_L	85_L	1.719	1.00
103_Y	106_W	1.674	1.00
38_G	41_Y	1.656	1.00
108_L	112_L	1.591	1.00
29_A	32_G	1.562	1.00
65_E	68_A	1.560	1.00
21_G	72_E	1.530	1.00
112_L	116_A	1.523	1.00
81_L	85_L	1.520	1.00
107_G	110_V	1.487	1.00
25_N	28_S	1.485	1.00
6_A	55_I	1.416	1.00
62_L	88_L	1.363	1.00
97_V	110_V	1.362	1.00
81_L	84_L	1.332	1.00
9_L	54_I	1.331	1.00
97_V	114_A	1.329	1.00
70_L	84_L	1.327	1.00
14_G	17_F	1.327	1.00
17_F	47_A	1.288	1.00
103_Y	107_G	1.286	1.00
94_A	118_A	1.283	1.00
73_A	83_T	1.279	1.00
20_W	43_V	1.268	1.00
93_G	117_L	1.263	1.00
115_G	119_G	1.250	1.00
32_G	36_L	1.250	1.00
6_A	64_A	1.239	1.00
14_G	18_W	1.238	1.00
41_Y	122_A	1.230	1.00
93_G	121_A	1.185	1.00
17_F	21_G	1.182	1.00
11_V	15_V	1.178	1.00
19_A	22_P	1.177	1.00
13_F	50_L	1.157	1.00
22_P	25_N	1.157	1.00
89_V	121_A	1.145	1.00
49_V	114_A	1.123	1.00
94_A	114_A	1.119	1.00
14_G	71_V	1.111	1.00
23_L	27_L	1.109	1.00
52_A	60_A	1.095	1.00
52_A	98_F	1.094	1.00
75_L	78_Q	1.083	1.00
68_A	72_E	1.083	1.00
49_V	111_A	1.075	1.00
73_A	78_Q	1.069	1.00
48_G	65_E	1.067	1.00
65_E	69_A	1.059	1.00
70_L	73_A	1.050	1.00
73_A	81_L	1.031	1.00
13_F	17_F	1.028	1.00
6_A	63_L	1.026	1.00
117_L	121_A	0.995	0.99
82_L	86_S	0.981	0.99
15_V	18_W	0.965	0.99
18_W	75_L	0.963	0.99
6_A	51_A	0.961	0.99
18_W	21_G	0.956	0.99
3_I	63_L	0.942	0.99
17_F	44_W	0.926	0.99
62_L	92_L	0.916	0.99
26_A	29_A	0.915	0.99
23_L	40_L	0.914	0.99
37_G	41_Y	0.910	0.99
24_Y	27_L	0.905	0.99
97_V	113_L	0.904	0.99
77_S	83_T	0.901	0.99
61_A	94_A	0.881	0.99
47_A	64_A	0.881	0.99
24_Y	28_S	0.872	0.98
112_L	115_G	0.851	0.98
72_E	90_Q	0.844	0.98
52_A	106_W	0.841	0.98
21_G	24_Y	0.840	0.98
55_I	64_A	0.830	0.98
15_V	19_A	0.813	0.98
79_W	83_T	0.793	0.97
96_L	99_A	0.790	0.97
6_A	67_V	0.779	0.97
44_W	65_E	0.777	0.97
117_L	120_L	0.772	0.97
104_R	109_P	0.771	0.97
10_A	51_A	0.767	0.97
48_G	52_A	0.766	0.97
17_F	72_E	0.757	0.96
46_L	50_L	0.752	0.96
31_L	35_G	0.739	0.96
44_W	68_A	0.729	0.95
2_D	57_K	0.721	0.95
21_G	77_S	0.720	0.95
25_N	37_G	0.719	0.95
48_G	94_A	0.718	0.95
63_L	67_V	0.716	0.95
16_V	20_W	0.709	0.95
78_Q	83_T	0.709	0.95
96_L	100_L	0.704	0.94
65_E	90_Q	0.702	0.94
52_A	62_L	0.695	0.94
6_A	54_I	0.693	0.94
28_S	32_G	0.691	0.94
97_V	100_L	0.689	0.94
111_A	115_G	0.689	0.94
36_L	40_L	0.687	0.94
18_W	77_S	0.686	0.94
52_A	94_A	0.684	0.94
61_A	98_F	0.667	0.93
55_I	58_P	0.663	0.93
47_A	65_E	0.661	0.92
69_A	84_L	0.658	0.92
43_V	46_L	0.658	0.92
6_A	9_L	0.658	0.92
87_G	90_Q	0.657	0.92
47_A	68_A	0.656	0.92
106_W	110_V	0.654	0.92
73_A	79_W	0.652	0.92
23_L	26_A	0.652	0.92
104_R	107_G	0.641	0.91
86_S	90_Q	0.639	0.91
13_F	18_W	0.635	0.91
42_G	69_A	0.634	0.91
23_L	28_S	0.630	0.91
4_V	8_V	0.626	0.90
16_V	19_A	0.619	0.90
66_L	84_L	0.617	0.90
55_I	60_A	0.609	0.89
5_V	9_L	0.608	0.89
105_R	110_V	0.605	0.89
97_V	102_R	0.603	0.89
25_N	78_Q	0.602	0.88
114_A	118_A	0.602	0.88
38_G	119_G	0.599	0.88
109_P	112_L	0.597	0.88
25_N	31_L	0.596	0.88
113_L	116_A	0.589	0.87
27_L	92_L	0.588	0.87
98_F	114_A	0.583	0.87
8_V	12_A	0.580	0.87
101_F	105_R	0.580	0.87
58_P	103_Y	0.579	0.86
92_L	100_L	0.578	0.86
24_Y	79_W	0.575	0.86
41_Y	45_L	0.563	0.85
48_G	90_Q	0.561	0.85
107_G	112_L	0.560	0.85
29_A	35_G	0.558	0.84
114_A	117_L	0.555	0.84
110_V	114_A	0.553	0.84
4_V	20_W	0.549	0.83
84_L	91_G	0.549	0.83
66_L	86_S	0.544	0.83
45_L	118_A	0.542	0.83
65_E	72_E	0.542	0.83
117_L	122_A	0.540	0.82
101_F	113_L	0.535	0.82
29_A	37_G	0.528	0.81
10_A	66_L	0.527	0.81
28_S	37_G	0.526	0.81
86_S	89_V	0.525	0.81
85_L	89_V	0.522	0.80
32_G	37_G	0.521	0.80
50_L	53_L	0.520	0.80
8_V	81_L	0.518	0.80
7_A	19_A	0.517	0.80
16_V	41_Y	0.517	0.80
113_L	117_L	0.514	0.79
72_E	87_G	0.509	0.79
74_L	77_S	0.504	0.78
38_G	85_L	0.502	0.78
52_A	88_L	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
3rlbA	1	0.8952	77.5	0.842	Contact Map
4z7fA	2	0.8629	76.9	0.843	Contact Map
3p5nA	2	0.9032	69.1	0.852	Contact Map
4huqS	1	0.8468	68.9	0.852	Contact Map
4hzuS	1	0.879	66.1	0.855	Contact Map
4rfsS	1	0.9194	59.8	0.861	Contact Map
4tkrA	2	0.871	56.9	0.863	Contact Map
4dveA	3	0.9032	16.2	0.898	Contact Map
4m5bA	1	0.879	8	0.911	Contact Map
3orgA	2	0.9839	3.6	0.925	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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