SpoVA - PFAM28P - GREMLIN Contacts

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SpoVA - SpoVA protein

PFAM:	PF03862	Sequences: NYLKAFLVGGLICVIGQILIDLTIKLEETTPARTLVTLVFLGALLTGLGLYDKLAKFAGAGATVPITGFGNSLASGAIEFKSEGGVLGVGTGMFTIAGPVIVAGIVFSFLVGLI	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	114 (114)
Sequences:	5859 (3197)
Seq/√Len:	299.4
META:	0.77

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
46_T	71_N	3.323	1.00
23_T	37_T	3.282	1.00
4_K	57_F	3.171	1.00
43_A	74_A	2.651	1.00
4_K	7_L	2.537	1.00
92_G	95_T	2.383	1.00
72_S	97_A	2.278	1.00
52_D	56_K	2.140	1.00
17_Q	21_D	2.133	1.00
18_I	22_L	2.115	1.00
55_A	62_A	1.971	1.00
8_V	58_A	1.920	1.00
93_M	102_V	1.877	1.00
45_L	50_L	1.845	1.00
8_V	57_F	1.585	1.00
20_I	34_T	1.582	1.00
11_L	15_I	1.564	1.00
103_A	107_F	1.540	1.00
46_T	75_S	1.513	1.00
23_T	33_R	1.508	1.00
16_G	38_L	1.467	1.00
40_F	44_L	1.461	1.00
42_G	51_Y	1.398	1.00
3_L	7_L	1.391	1.00
51_Y	62_A	1.369	1.00
19_L	23_T	1.368	1.00
55_A	63_T	1.350	1.00
86_V	89_V	1.343	1.00
37_T	41_L	1.340	1.00
91_T	99_P	1.337	1.00
54_L	62_A	1.303	1.00
80_F	95_T	1.298	1.00
80_F	84_G	1.288	1.00
12_I	38_L	1.278	1.00
85_G	89_V	1.276	1.00
97_A	101_I	1.263	1.00
45_L	54_L	1.261	1.00
20_I	24_I	1.255	1.00
35_L	66_I	1.253	1.00
11_L	14_V	1.241	1.00
55_A	71_N	1.239	1.00
79_E	83_E	1.237	1.00
44_L	48_L	1.237	1.00
19_L	38_L	1.193	1.00
90_G	103_A	1.183	1.00
14_V	18_I	1.179	1.00
4_K	8_V	1.154	1.00
77_A	81_K	1.153	1.00
24_I	27_E	1.147	1.00
38_L	67_T	1.139	1.00
22_L	26_L	1.137	1.00
7_L	57_F	1.121	1.00
107_F	111_V	1.115	1.00
80_F	83_E	1.102	1.00
101_I	105_I	1.100	1.00
8_V	54_L	1.090	1.00
84_G	91_T	1.085	1.00
60_A	64_V	1.066	1.00
41_L	45_L	1.063	1.00
38_L	42_G	1.061	1.00
7_L	11_L	1.030	1.00
22_L	25_K	1.010	1.00
52_D	75_S	1.010	1.00
17_Q	20_I	0.993	1.00
5_A	59_G	0.992	1.00
20_I	30_T	0.991	1.00
12_I	62_A	0.979	1.00
27_E	31_P	0.977	1.00
54_L	58_A	0.977	1.00
31_P	35_L	0.959	1.00
21_D	24_I	0.935	1.00
20_I	27_E	0.925	1.00
23_T	34_T	0.922	1.00
4_K	58_A	0.918	1.00
50_L	53_K	0.915	1.00
19_L	34_T	0.891	1.00
77_A	93_M	0.891	1.00
96_I	99_P	0.890	1.00
85_G	103_A	0.879	1.00
43_A	70_G	0.878	1.00
78_I	81_K	0.877	1.00
71_N	75_S	0.876	1.00
47_G	74_A	0.873	1.00
75_S	79_E	0.868	1.00
52_D	71_N	0.864	1.00
78_I	82_S	0.856	1.00
75_S	78_I	0.851	1.00
14_V	21_D	0.844	1.00
5_A	60_A	0.837	1.00
32_A	35_L	0.835	1.00
109_F	113_L	0.830	1.00
58_A	62_A	0.830	1.00
19_L	37_T	0.826	1.00
70_G	74_A	0.815	1.00
106_V	109_F	0.804	1.00
46_T	78_I	0.792	0.99
46_T	74_A	0.791	0.99
86_V	90_G	0.784	0.99
20_I	31_P	0.780	0.99
19_L	22_L	0.773	0.99
90_G	102_V	0.773	0.99
79_E	82_S	0.767	0.99
53_K	56_K	0.763	0.99
19_L	33_R	0.761	0.99
49_G	52_D	0.736	0.99
24_I	29_T	0.735	0.99
29_T	32_A	0.732	0.99
93_M	98_G	0.729	0.99
24_I	30_T	0.729	0.99
81_K	89_V	0.722	0.99
94_F	97_A	0.718	0.99
104_G	108_S	0.716	0.99
91_T	95_T	0.699	0.99
24_I	28_E	0.698	0.99
21_D	25_K	0.691	0.99
94_F	98_G	0.687	0.99
7_L	14_V	0.678	0.98
106_V	110_L	0.665	0.98
77_A	89_V	0.663	0.98
33_R	36_V	0.663	0.98
85_G	90_G	0.658	0.98
18_I	25_K	0.658	0.98
80_F	89_V	0.657	0.98
73_L	101_I	0.655	0.98
73_L	93_M	0.647	0.98
23_T	26_L	0.636	0.98
30_T	35_L	0.635	0.98
40_F	48_L	0.633	0.98
16_G	67_T	0.611	0.97
16_G	19_L	0.608	0.97
60_A	63_T	0.601	0.97
53_K	57_F	0.597	0.97
15_I	19_L	0.595	0.96
6_F	14_V	0.595	0.96
15_I	41_L	0.591	0.96
31_P	34_T	0.588	0.96
28_E	32_A	0.586	0.96
8_V	12_I	0.579	0.96
63_T	73_L	0.578	0.96
42_G	70_G	0.577	0.96
94_F	102_V	0.574	0.96
33_R	37_T	0.568	0.95
102_V	106_V	0.568	0.95
81_K	86_V	0.566	0.95
50_L	54_L	0.563	0.95
26_L	29_T	0.561	0.95
87_L	90_G	0.560	0.95
39_V	66_I	0.560	0.95
98_G	102_V	0.559	0.95
19_L	24_I	0.555	0.95
100_V	103_A	0.547	0.94
9_G	65_P	0.547	0.94
101_I	104_G	0.544	0.94
8_V	11_L	0.538	0.94
8_V	62_A	0.536	0.94
79_E	84_G	0.535	0.94
36_V	40_F	0.532	0.94
4_K	11_L	0.521	0.93
99_P	102_V	0.521	0.93
84_G	97_A	0.520	0.93
20_I	33_R	0.515	0.92
80_F	92_G	0.515	0.92
67_T	71_N	0.514	0.92
44_L	47_G	0.513	0.92
51_Y	71_N	0.512	0.92
24_I	33_R	0.507	0.92
68_G	71_N	0.505	0.92
53_K	62_A	0.503	0.92
7_L	28_E	0.501	0.91
15_I	38_L	0.501	0.91
46_T	72_S	0.500	0.91

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
3tqjA	2	0.1842	1.6	0.943	Contact Map
1lnqA	6	0.6404	1.5	0.944	Contact Map
3wxwA	1	0.3158	1.4	0.945	Contact Map
3wu2X	1	0.2719	1.3	0.946	Contact Map
3bz1X	1	0.2632	1.3	0.946	Contact Map
4dx5A	3	0.9123	1.3	0.946	Contact Map
4mt1A	3	0.9386	1	0.949	Contact Map
1u7gA	3	1	1	0.949	Contact Map
2qi9A	2	0.4386	1	0.95	Contact Map
2onkC	2	0.4561	1	0.95	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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