SpoVIF - PFAM28P - GREMLIN Contacts

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SpoVIF - Stage VI sporulation protein F

PFAM:	PF14069	Sequences: FKKVEKKTNVNKEDIKKLANGVQKADLKDEATLRELIKQVSKMAGKPVSKEKEDKIVKAIINDKVPNNLEKL	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	72 (72)
Sequences:	911 (575)
Seq/√Len:	67.7
META:	0.64

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
38_K	53_E	4.111	1.00
26_D	29_D	3.094	1.00
58_K	62_N	2.773	1.00
50_K	54_D	2.753	1.00
34_R	53_E	2.477	1.00
32_T	35_E	2.429	1.00
50_K	53_E	2.341	1.00
30_E	34_R	2.161	1.00
4_V	8_T	2.065	1.00
34_R	54_D	2.035	1.00
33_L	57_V	1.607	0.99
22_V	36_L	1.589	0.99
29_D	32_T	1.547	0.99
18_L	40_V	1.531	0.99
33_L	61_I	1.358	0.98
17_K	20_N	1.303	0.97
13_E	17_K	1.281	0.97
20_N	23_Q	1.261	0.96
27_L	33_L	1.240	0.96
25_A	32_T	1.233	0.96
56_I	60_I	1.214	0.95
54_D	58_K	1.211	0.95
33_L	37_I	1.186	0.95
18_L	43_M	1.182	0.95
5_E	11_N	1.175	0.94
14_D	41_S	1.124	0.93
35_E	38_K	1.107	0.92
34_R	50_K	1.101	0.92
38_K	42_K	1.100	0.92
19_A	22_V	1.094	0.92
21_G	39_Q	1.074	0.91
4_V	15_I	1.066	0.91
23_Q	46_K	1.021	0.89
37_I	56_I	1.018	0.89
28_K	31_A	1.018	0.89
2_K	6_K	1.003	0.88
5_E	8_T	0.998	0.88
34_R	38_K	0.971	0.86
14_D	44_A	0.965	0.86
1_F	13_E	0.963	0.86
14_D	18_L	0.958	0.86
48_V	59_A	0.939	0.84
12_K	65_V	0.935	0.84
68_N	72_L	0.934	0.84
34_R	57_V	0.922	0.83
25_A	36_L	0.908	0.82
37_I	40_V	0.902	0.82
31_A	42_K	0.885	0.81
15_I	40_V	0.874	0.80
5_E	12_K	0.853	0.78
20_N	24_K	0.840	0.77
2_K	5_E	0.825	0.76
31_A	49_S	0.820	0.75
34_R	47_P	0.817	0.75
3_K	6_K	0.786	0.72
7_K	12_K	0.782	0.72
32_T	60_I	0.778	0.72
47_P	58_K	0.774	0.71
4_V	72_L	0.757	0.69
11_N	14_D	0.751	0.69
7_K	68_N	0.747	0.68
31_A	35_E	0.732	0.67
37_I	48_V	0.728	0.66
64_K	67_N	0.720	0.66
10_V	34_R	0.713	0.65
19_A	26_D	0.702	0.64
12_K	15_I	0.698	0.63
32_T	36_L	0.694	0.63
27_L	36_L	0.684	0.62
5_E	9_N	0.675	0.61
19_A	51_E	0.669	0.60
2_K	11_N	0.654	0.58
52_K	59_A	0.650	0.58
27_L	59_A	0.647	0.57
18_L	37_I	0.640	0.57
18_L	45_G	0.620	0.54
16_K	23_Q	0.616	0.54
42_K	72_L	0.613	0.53
21_G	32_T	0.612	0.53
30_E	57_V	0.610	0.53
21_G	45_G	0.609	0.53
59_A	65_V	0.607	0.53
1_F	5_E	0.606	0.53
12_K	66_P	0.601	0.52
49_S	66_P	0.600	0.52
29_D	71_K	0.599	0.52
16_K	46_K	0.599	0.52
45_G	51_E	0.584	0.50
8_T	49_S	0.582	0.50
12_K	16_K	0.579	0.49
15_I	42_K	0.573	0.49
38_K	47_P	0.572	0.48
13_E	46_K	0.571	0.48
40_V	56_I	0.566	0.48
69_L	72_L	0.566	0.48
25_A	33_L	0.562	0.47
2_K	55_K	0.557	0.47
67_N	71_K	0.551	0.46
45_G	54_D	0.548	0.46
26_D	63_D	0.546	0.45
58_K	61_I	0.542	0.45
3_K	27_L	0.538	0.44
8_T	19_A	0.528	0.43
39_Q	52_K	0.524	0.43
11_N	42_K	0.524	0.43
4_V	27_L	0.516	0.42
5_E	22_V	0.507	0.41
10_V	53_E	0.500	0.40

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
3ip4B	1	1	27.8	0.859	Contact Map
2zc2A	1	0.5417	26.4	0.861	Contact Map
3al0B	1	1	25.7	0.861	Contact Map
3h0lB	1	1	20.5	0.868	Contact Map
2hz7A	1	0	20.4	0.868	Contact Map
1s4kA	2	0.9583	17.5	0.872	Contact Map
4ut1A	1	0.8889	13.1	0.879	Contact Map
4cr2I	1	0.9167	12.8	0.879	Contact Map
3h5qA	2	0.5972	12.2	0.88	Contact Map
2d6fC	1	0.5972	11.9	0.881	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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