PspB - PFAM28P - GREMLIN Contacts

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PspB - Phage shock protein B

PFAM:	PF06667	Sequences: MEDFLFVPLIVFLLFVAPPWLILHYITKWKTAATLSEEDEKLLEELWELARRLEDRIETLERILDAENPDWRQ	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	73 (69)
Sequences:	2697 (1453)
Seq/√Len:	175.0
META:	0.871

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
28_K	31_T	3.631	1.00
10_I	13_L	2.501	1.00
22_I	26_I	1.995	1.00
7_V	10_I	1.906	1.00
20_W	24_H	1.856	1.00
46_L	50_A	1.831	1.00
55_D	58_E	1.828	1.00
65_D	71_W	1.820	1.00
38_E	41_K	1.801	1.00
13_L	17_A	1.699	1.00
11_V	14_L	1.689	1.00
53_L	57_I	1.669	1.00
13_L	18_P	1.632	1.00
65_D	72_R	1.621	1.00
47_W	51_R	1.621	1.00
37_E	41_K	1.583	1.00
64_L	71_W	1.575	1.00
12_F	17_A	1.531	1.00
12_F	16_V	1.481	1.00
60_L	64_L	1.464	1.00
59_T	62_R	1.413	1.00
20_W	25_Y	1.401	1.00
7_V	11_V	1.308	1.00
41_K	45_E	1.278	1.00
16_V	25_Y	1.269	1.00
26_I	29_W	1.265	1.00
19_P	22_I	1.243	1.00
6_F	10_I	1.194	1.00
9_L	12_F	1.185	1.00
45_E	49_L	1.185	1.00
33_A	37_E	1.165	1.00
48_E	52_R	1.159	1.00
57_I	60_L	1.142	1.00
8_P	12_F	1.085	1.00
64_L	67_E	1.040	0.99
39_D	42_L	1.013	0.99
40_E	44_E	1.005	0.99
58_E	63_I	0.986	0.99
49_L	54_E	0.962	0.99
23_L	26_I	0.962	0.99
4_F	9_L	0.940	0.99
18_P	21_L	0.920	0.99
17_A	21_L	0.918	0.99
15_F	18_P	0.902	0.99
18_P	22_I	0.899	0.99
19_P	23_L	0.884	0.98
40_E	45_E	0.875	0.98
33_A	36_S	0.870	0.98
42_L	47_W	0.870	0.98
11_V	15_F	0.869	0.98
57_I	65_D	0.852	0.98
15_F	19_P	0.828	0.97
31_T	34_T	0.817	0.97
51_R	55_D	0.814	0.97
35_L	43_L	0.812	0.97
59_T	63_I	0.812	0.97
60_L	68_N	0.803	0.97
42_L	45_E	0.793	0.97
53_L	60_L	0.792	0.97
23_L	28_K	0.745	0.95
41_K	48_E	0.743	0.95
49_L	53_L	0.728	0.95
14_L	19_P	0.724	0.94
6_F	9_L	0.719	0.94
55_D	62_R	0.707	0.94
12_F	18_P	0.701	0.93
37_E	48_E	0.691	0.93
47_W	53_L	0.685	0.93
44_E	63_I	0.677	0.92
42_L	58_E	0.675	0.92
34_T	38_E	0.675	0.92
54_E	58_E	0.673	0.92
9_L	13_L	0.670	0.92
57_I	71_W	0.656	0.91
63_I	71_W	0.651	0.91
49_L	64_L	0.648	0.91
32_A	45_E	0.638	0.90
60_L	65_D	0.632	0.89
14_L	18_P	0.629	0.89
56_R	61_E	0.627	0.89
42_L	54_E	0.624	0.89
44_E	47_W	0.622	0.89
54_E	62_R	0.611	0.88
37_E	57_I	0.607	0.87
67_E	71_W	0.602	0.87
7_V	12_F	0.592	0.86
15_F	20_W	0.587	0.86
4_F	7_V	0.581	0.85
10_I	18_P	0.580	0.85
32_A	38_E	0.577	0.85
41_K	46_L	0.563	0.83
38_E	63_I	0.561	0.83
47_W	68_N	0.557	0.83
28_K	43_L	0.552	0.82
21_L	30_K	0.550	0.82
68_N	72_R	0.544	0.81
7_V	13_L	0.536	0.80
8_P	11_V	0.535	0.80
65_D	68_N	0.527	0.79
10_I	14_L	0.517	0.78
62_R	67_E	0.510	0.77
5_L	27_T	0.502	0.76
62_R	66_A	0.502	0.76
48_E	71_W	0.500	0.75

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
4bgnA	3	0.5342	74.8	0.786	Contact Map
3rvyA	3	0.3562	70.8	0.792	Contact Map
3pjsK	4	0.9452	70.7	0.793	Contact Map
3effK	4	0.9452	50.3	0.817	Contact Map
4ltoA	3	0.8767	48.4	0.819	Contact Map
4cbcA	3	0.3151	46.1	0.822	Contact Map
3cveA	4	0.5068	36.7	0.832	Contact Map
3layA	5	0.5479	34.1	0.835	Contact Map
4i5sA	2	0.7671	26.7	0.843	Contact Map
2mfrA	1	0.5753	26.6	0.843	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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