Spore_YtfJ - PFAM28P - GREMLIN Contacts

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Spore_YtfJ - Sporulation protein YtfJ (Spore_YtfJ)

PFAM:	PF09579	Sequences: IETGDGTTIIPVSKVSFGFGAGGGEGGGKKGGEGFGGGGGGGVSITPVAFLVIKDGGVRLLPVKDSTLDKLIDMVPDLID	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	80 (77)
Sequences:	6803 (4194)
Seq/√Len:	477.9
META:	0.892

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
49_A	60_L	4.107	1.00
17_F	43_V	2.982	1.00
14_K	46_T	2.878	1.00
16_S	44_S	2.808	1.00
19_F	41_G	2.770	1.00
7_T	54_K	2.609	1.00
54_K	57_G	2.081	1.00
66_S	69_D	1.714	1.00
3_T	6_G	1.686	1.00
26_G	34_G	1.675	1.00
25_E	35_F	1.651	1.00
24_G	36_G	1.598	1.00
5_D	55_D	1.591	1.00
70_K	73_D	1.584	1.00
70_K	74_M	1.573	1.00
52_V	58_V	1.539	1.00
27_G	33_E	1.469	1.00
54_K	59_R	1.458	1.00
52_V	61_L	1.432	1.00
49_A	63_V	1.396	1.00
12_V	50_F	1.383	1.00
15_V	45_I	1.373	1.00
18_G	42_G	1.342	1.00
74_M	77_D	1.277	1.00
14_K	44_S	1.274	1.00
60_L	63_V	1.212	1.00
51_L	63_V	1.211	1.00
21_A	39_G	1.194	1.00
28_G	31_G	1.139	1.00
48_V	63_V	1.130	1.00
71_L	75_V	1.122	1.00
14_K	48_V	1.059	1.00
12_V	51_L	1.052	1.00
66_S	70_K	1.040	1.00
5_D	54_K	0.988	1.00
5_D	56_G	0.978	1.00
6_G	55_D	0.949	1.00
67_T	77_D	0.949	1.00
12_V	48_V	0.933	1.00
68_L	72_I	0.926	1.00
7_T	58_V	0.919	1.00
28_G	32_G	0.911	1.00
25_E	34_G	0.909	1.00
51_L	61_L	0.905	1.00
67_T	70_K	0.899	1.00
24_G	34_G	0.899	1.00
24_G	41_G	0.896	1.00
9_I	50_F	0.886	1.00
28_G	33_E	0.885	1.00
53_I	58_V	0.873	1.00
4_G	56_G	0.868	1.00
13_S	45_I	0.868	1.00
20_G	36_G	0.838	1.00
67_T	75_V	0.831	1.00
23_G	37_G	0.828	1.00
3_T	10_I	0.825	1.00
51_L	60_L	0.824	1.00
22_G	38_G	0.804	1.00
75_V	79_I	0.800	1.00
20_G	40_G	0.798	1.00
9_I	52_V	0.794	1.00
52_V	59_R	0.785	1.00
14_K	43_V	0.777	1.00
27_G	30_K	0.773	1.00
9_I	51_L	0.761	1.00
14_K	64_K	0.751	1.00
74_M	78_L	0.750	1.00
26_G	32_G	0.747	1.00
27_G	32_G	0.738	1.00
26_G	36_G	0.735	1.00
23_G	35_F	0.733	1.00
9_I	53_I	0.728	1.00
20_G	41_G	0.724	1.00
50_F	58_V	0.716	1.00
3_T	8_T	0.705	1.00
72_I	75_V	0.704	1.00
29_K	32_G	0.701	1.00
25_E	33_E	0.700	1.00
50_F	63_V	0.685	1.00
25_E	37_G	0.682	1.00
7_T	52_V	0.680	1.00
14_K	45_I	0.677	1.00
50_F	60_L	0.669	1.00
29_K	33_E	0.663	1.00
70_K	76_P	0.662	1.00
69_D	72_I	0.661	1.00
19_F	23_G	0.643	1.00
54_K	58_V	0.634	1.00
73_D	76_P	0.629	1.00
10_I	53_I	0.626	1.00
59_R	69_D	0.621	0.99
71_L	76_P	0.617	0.99
13_S	49_A	0.616	0.99
26_G	33_E	0.611	0.99
73_D	79_I	0.601	0.99
65_D	74_M	0.594	0.99
13_S	48_V	0.592	0.99
16_S	42_G	0.588	0.99
27_G	31_G	0.585	0.99
12_V	45_I	0.571	0.99
18_G	40_G	0.565	0.99
9_I	13_S	0.560	0.99
68_L	76_P	0.560	0.99
73_D	77_D	0.545	0.99
13_S	52_V	0.542	0.99
43_V	59_R	0.531	0.98
68_L	77_D	0.529	0.98
46_T	64_K	0.512	0.98
66_S	79_I	0.510	0.98
10_I	13_S	0.509	0.98
10_I	45_I	0.506	0.98
3_T	9_I	0.503	0.98
8_T	53_I	0.501	0.98
15_V	21_A	0.501	0.98
22_G	36_G	0.500	0.98
11_P	78_L	0.500	0.98

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
2p51A	1	0.325	5.4	0.886	Contact Map
1uvqC	1	0.25	3.2	0.898	Contact Map
2c5qA	3	0.975	2.8	0.901	Contact Map
4ae2A	3	0.45	2.5	0.903	Contact Map
1uocA	1	0.4125	2	0.908	Contact Map
3smtA	2	0.3875	1.9	0.909	Contact Map
2v7kA	1	0.3375	1.9	0.909	Contact Map
4zcfA	2	0.35	1.7	0.912	Contact Map
1vw44	1	1	1.7	0.912	Contact Map
4d0i1	1	0.2625	1.6	0.913	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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