SdpI - PFAM28P - GREMLIN Contacts

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SdpI - SdpI/YhfL protein family

PFAM:	PF13630	Sequences: KVKPNYFIGIRTPWTLSSEEVWYKTHRLGGKLFVAAGLLLLLAALGAAFLVLLVALLLAALVPVVYS	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	67 (65)
Sequences:	15581 (13209)
Seq/√Len:	1638.4
META:	0.898

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
4_P	19_E	3.545	1.00
19_E	23_Y	3.079	1.00
20_E	24_K	2.601	1.00
28_L	62_V	1.945	1.00
18_S	21_V	1.898	1.00
2_V	8_I	1.869	1.00
59_A	63_P	1.716	1.00
23_Y	27_R	1.660	1.00
6_Y	17_S	1.640	1.00
10_I	29_G	1.608	1.00
12_T	15_T	1.570	1.00
28_L	32_L	1.555	1.00
14_W	21_V	1.497	1.00
6_Y	16_L	1.467	1.00
12_T	64_V	1.465	1.00
3_K	23_Y	1.453	1.00
20_E	23_Y	1.440	1.00
15_T	25_T	1.418	1.00
50_L	54_V	1.404	1.00
56_L	60_A	1.381	1.00
15_T	26_H	1.328	1.00
22_W	26_H	1.328	1.00
45_L	48_A	1.297	1.00
21_V	24_K	1.265	1.00
40_L	44_A	1.253	1.00
53_L	57_L	1.207	1.00
37_G	44_A	1.195	1.00
51_V	55_A	1.177	1.00
4_P	17_S	1.113	1.00
55_A	59_A	1.057	1.00
52_L	56_L	1.049	1.00
10_I	25_T	1.048	1.00
15_T	21_V	1.033	1.00
28_L	31_K	1.026	1.00
36_A	59_A	1.020	1.00
62_V	65_V	0.995	1.00
27_R	31_K	0.991	1.00
45_L	49_F	0.972	1.00
13_P	17_S	0.966	1.00
14_W	25_T	0.955	1.00
24_K	28_L	0.941	1.00
21_V	25_T	0.927	1.00
17_S	21_V	0.908	1.00
49_F	53_L	0.895	1.00
32_L	35_A	0.892	1.00
41_L	44_A	0.892	1.00
30_G	37_G	0.873	1.00
12_T	21_V	0.870	1.00
4_P	16_L	0.865	1.00
31_K	34_V	0.842	1.00
4_P	23_Y	0.837	1.00
10_I	26_H	0.821	1.00
47_A	50_L	0.819	1.00
4_P	8_I	0.802	1.00
51_V	54_V	0.798	1.00
28_L	66_Y	0.772	1.00
50_L	53_L	0.764	1.00
61_L	64_V	0.739	1.00
60_A	64_V	0.732	1.00
2_V	23_Y	0.729	1.00
48_A	51_V	0.720	1.00
34_V	38_L	0.717	1.00
54_V	57_L	0.702	1.00
36_A	40_L	0.696	1.00
36_A	55_A	0.690	1.00
49_F	52_L	0.686	1.00
11_R	15_T	0.686	1.00
57_L	61_L	0.684	1.00
60_A	63_P	0.681	1.00
29_G	33_F	0.680	1.00
54_V	58_L	0.661	1.00
2_V	34_V	0.656	1.00
46_G	49_F	0.641	1.00
53_L	60_A	0.637	1.00
10_I	15_T	0.637	1.00
32_L	59_A	0.628	1.00
3_K	6_Y	0.619	1.00
27_R	35_A	0.603	1.00
47_A	51_V	0.598	1.00
32_L	36_A	0.593	1.00
11_R	16_L	0.591	1.00
6_Y	13_P	0.590	1.00
29_G	63_P	0.570	1.00
56_L	59_A	0.560	1.00
52_L	55_A	0.557	1.00
38_L	42_L	0.543	1.00
46_G	50_L	0.539	1.00
55_A	63_P	0.537	1.00
12_T	17_S	0.522	1.00
26_H	33_F	0.520	1.00
37_G	55_A	0.518	1.00
29_G	32_L	0.517	1.00
2_V	5_N	0.514	1.00
32_L	40_L	0.504	1.00
49_F	56_L	0.502	1.00
9_G	22_W	0.502	1.00
33_F	59_A	0.501	1.00
3_K	19_E	0.500	1.00

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
4o6yA	2	1	11.5	0.844	Contact Map
2y69D	1	0.3433	5.2	0.867	Contact Map
1v54D	1	0.3433	4.6	0.87	Contact Map
3htsB	2	0.3881	2.5	0.886	Contact Map
1uhvA	3	0.4627	2.3	0.888	Contact Map
3wguB	1	0.806	2.2	0.89	Contact Map
3terA	2	0.4179	2.1	0.89	Contact Map
1oq1A	1	0.403	1.9	0.893	Contact Map
3wxwA	1	0.9701	1.8	0.894	Contact Map
4us3A	1	0.6567	1.8	0.894	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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