TraD - PFAM28P - GREMLIN Contacts

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TraD - Conjugal transfer protein TraD

PFAM:	PF06412	Sequences: DKARRLRTRHLIELGGLVVKAGLDDLDRATLLGALLEAAEKLDSDEREAAWRRRGAAAFQA	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	61 (59)
Sequences:	3194 (1541)
Seq/√Len:	200.6
META:	0.813

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
34_A	38_A	4.897	1.00
7_R	11_L	3.575	1.00
8_T	12_I	3.153	1.00
40_E	54_R	2.730	1.00
37_E	41_K	2.476	1.00
29_A	56_A	2.220	1.00
10_H	24_D	1.844	1.00
31_L	35_L	1.799	1.00
14_L	18_V	1.709	1.00
56_A	60_Q	1.705	1.00
27_D	30_T	1.657	1.00
3_A	6_L	1.611	1.00
27_D	52_R	1.588	1.00
9_R	13_E	1.548	1.00
36_L	58_A	1.498	1.00
2_K	6_L	1.259	1.00
10_H	13_E	1.235	1.00
18_V	35_L	1.149	1.00
37_E	51_W	1.104	1.00
29_A	52_R	1.099	1.00
15_G	18_V	1.064	1.00
13_E	28_R	1.025	1.00
46_E	49_A	0.980	1.00
20_K	32_L	0.973	0.99
6_L	10_H	0.964	0.99
46_E	50_A	0.960	0.99
12_I	16_G	0.956	0.99
30_T	42_L	0.947	0.99
43_D	46_E	0.943	0.99
32_L	36_L	0.935	0.99
30_T	52_R	0.922	0.99
53_R	57_A	0.916	0.99
20_K	58_A	0.916	0.99
26_L	30_T	0.881	0.99
7_R	19_V	0.871	0.99
52_R	56_A	0.835	0.98
10_H	28_R	0.822	0.98
48_E	51_W	0.820	0.98
43_D	48_E	0.766	0.97
47_R	50_A	0.766	0.97
41_K	47_R	0.754	0.97
44_S	47_R	0.751	0.97
11_L	19_V	0.749	0.97
8_T	11_L	0.747	0.97
4_R	12_I	0.744	0.97
45_D	49_A	0.740	0.97
57_A	60_Q	0.723	0.96
21_A	32_L	0.721	0.96
14_L	19_V	0.718	0.96
9_R	16_G	0.713	0.96
44_S	48_E	0.712	0.96
42_L	47_R	0.712	0.96
19_V	24_D	0.706	0.96
28_R	32_L	0.696	0.95
30_T	51_W	0.691	0.95
41_K	48_E	0.687	0.95
8_T	16_G	0.682	0.95
41_K	46_E	0.662	0.94
20_K	59_F	0.645	0.93
7_R	12_I	0.643	0.93
40_E	43_D	0.636	0.93
15_G	23_L	0.631	0.92
5_R	11_L	0.630	0.92
45_D	53_R	0.603	0.90
36_L	54_R	0.601	0.90
24_D	27_D	0.596	0.90
16_G	20_K	0.586	0.89
4_R	16_G	0.583	0.89
16_G	19_V	0.576	0.88
32_L	59_F	0.574	0.88
14_L	24_D	0.573	0.88
23_L	32_L	0.570	0.88
8_T	13_E	0.567	0.88
4_R	8_T	0.563	0.87
29_A	58_A	0.562	0.87
41_K	49_A	0.559	0.87
18_V	31_L	0.551	0.86
5_R	12_I	0.545	0.86
6_L	53_R	0.536	0.85
31_L	56_A	0.536	0.85
37_E	50_A	0.535	0.84
39_A	47_R	0.523	0.83
3_A	38_A	0.517	0.82
14_L	31_L	0.512	0.82
13_E	20_K	0.509	0.81
50_A	56_A	0.507	0.81
55_G	59_F	0.504	0.81
26_L	42_L	0.500	0.80

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
4o5pA	1	0.0492	12.7	0.827	Contact Map
3i9wA	1	0.541	5	0.856	Contact Map
2j0jA	1	1	3.3	0.868	Contact Map
1rm6B	1	0.918	3	0.871	Contact Map
3ilkA	2	0.6721	3	0.871	Contact Map
3nr7A	2	0.5738	3	0.871	Contact Map
3mkqB	1	0.7705	2.7	0.874	Contact Map
3mkqA	2	1	2.6	0.874	Contact Map
3onpA	2	0	2.3	0.879	Contact Map
3gjxA	1	0.2131	2.2	0.879	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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