CCMD - ECOLI - GREMLIN Contacts

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CCMD - Heme exporter protein D

UniProt:	P0ABM5	Sequences: MTPAFASWNEFFAMGGYAFFVWLAVVMTVIPLVVLVVHSVMQHRAILRGVAQQRAREARLRAAQQQEAA	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG12169
Length:	69 (64)
Sequences:	219 (149)
Seq/√Len:	18.6

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
8_W	12_F	5.530	1.00
19_F	23_L	2.932	0.99
35_L	42_Q	2.288	0.94
24_A	53_Q	2.210	0.93
27_M	31_P	1.992	0.89
50_V	60_L	1.850	0.85
4_A	52_Q	1.822	0.84
30_I	40_V	1.769	0.82
30_I	34_V	1.652	0.77
28_T	64_Q	1.551	0.73
23_L	32_L	1.543	0.72
16_G	59_R	1.517	0.71
33_V	36_V	1.431	0.66
44_R	51_A	1.409	0.65
4_A	53_Q	1.397	0.64
4_A	8_W	1.379	0.63
3_P	6_A	1.351	0.62
25_V	39_S	1.332	0.61
38_H	53_Q	1.282	0.58
57_E	61_R	1.236	0.55
25_V	57_E	1.181	0.51
4_A	38_H	1.179	0.51
60_L	63_A	1.179	0.51
45_A	48_R	1.143	0.49
3_P	63_A	1.126	0.48
4_A	27_M	1.123	0.48
4_A	19_F	1.094	0.46
18_A	23_L	1.092	0.46
54_R	61_R	1.091	0.46
9_N	63_A	1.059	0.44
10_E	13_A	0.988	0.39
3_P	25_V	0.982	0.39
25_V	28_T	0.966	0.38
37_V	44_R	0.957	0.38
18_A	44_R	0.954	0.37
9_N	18_A	0.937	0.36
8_W	66_Q	0.927	0.36
18_A	28_T	0.923	0.36
27_M	64_Q	0.911	0.35
29_V	53_Q	0.910	0.35
49_G	53_Q	0.900	0.34
19_F	32_L	0.888	0.34
24_A	54_R	0.878	0.33
9_N	12_F	0.866	0.32
20_F	47_L	0.866	0.32
19_F	24_A	0.848	0.31
26_V	54_R	0.843	0.31
41_M	52_Q	0.830	0.30
36_V	60_L	0.829	0.30
43_H	58_A	0.825	0.30
10_E	37_V	0.812	0.29
42_Q	66_Q	0.809	0.29
38_H	52_Q	0.797	0.29
24_A	29_V	0.790	0.28
45_A	52_Q	0.767	0.27
33_V	51_A	0.723	0.25
9_N	31_P	0.721	0.25
13_A	55_A	0.717	0.25
30_I	36_V	0.713	0.25
46_I	60_L	0.712	0.25
25_V	38_H	0.695	0.24
58_A	62_A	0.694	0.24
46_I	62_A	0.693	0.24
45_A	62_A	0.686	0.23
43_H	49_G	0.678	0.23
28_T	31_P	0.664	0.22
18_A	42_Q	0.662	0.22
27_M	66_Q	0.654	0.22
7_S	13_A	0.648	0.22
46_I	51_A	0.647	0.22
50_V	53_Q	0.642	0.21
19_F	36_V	0.640	0.21
28_T	47_L	0.638	0.21
6_A	43_H	0.610	0.20
20_F	31_P	0.606	0.20
4_A	23_L	0.603	0.20
26_V	37_V	0.603	0.20
47_L	50_V	0.601	0.20
40_V	62_A	0.596	0.20
13_A	48_R	0.590	0.19
15_G	23_L	0.588	0.19
10_E	27_M	0.577	0.19
13_A	60_L	0.571	0.19
20_F	49_G	0.569	0.19
44_R	58_A	0.567	0.18
20_F	64_Q	0.564	0.18
6_A	41_M	0.559	0.18
49_G	55_A	0.558	0.18
6_A	32_L	0.552	0.18
13_A	39_S	0.548	0.18
3_P	26_V	0.544	0.18
41_M	46_I	0.540	0.17
25_V	46_I	0.538	0.17
29_V	54_R	0.536	0.17
46_I	58_A	0.509	0.16
16_G	32_L	0.500	0.16

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
1v8kA	3	0	19.5	0.907	Contact Map
4oh3A	2	0.8261	14.1	0.913	Contact Map
3pieA	1	0.7536	12	0.916	Contact Map
2y35A	1	0.7971	10.1	0.919	Contact Map
4i5sA	2	0.4783	8.8	0.921	Contact Map
4tphA	2	0.6667	8.3	0.922	Contact Map
4dzoA	2	0.4638	7.7	0.923	Contact Map
3x29A	1	0.5362	7.6	0.923	Contact Map
3fqdA	1	0.8406	6.9	0.924	Contact Map
5amrA	1	0	6.8	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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