FlgD - PFAM28P - GREMLIN Contacts

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FlgD - Flagellar hook capping protein - N-terminal region

PFAM:	PF03963	Sequences: SATTTSSSTTSSTSSSSSSATSSSALGKDDFLKLLVTQLQNQDPLNPMDNTQFTAQLAQFSSVEQLTNLNTSLES	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	75 (67)
Sequences:	26863 (17822)
Seq/√Len:	2177.2
META:	0.905

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
66_L	69_L	3.406	1.00
26_L	30_D	2.870	1.00
46_N	49_D	2.594	1.00
62_S	66_L	2.497	1.00
27_G	30_D	2.286	1.00
49_D	52_Q	2.203	1.00
52_Q	55_A	2.172	1.00
65_Q	70_N	2.132	1.00
69_L	73_L	2.040	1.00
43_D	46_N	1.782	1.00
64_E	68_N	1.731	1.00
37_T	40_Q	1.622	1.00
55_A	59_Q	1.611	1.00
48_M	51_T	1.518	1.00
37_T	41_N	1.509	1.00
67_T	71_T	1.478	1.00
59_Q	62_S	1.444	1.00
28_K	64_E	1.432	1.00
33_K	37_T	1.324	1.00
50_N	54_T	1.280	1.00
71_T	74_E	1.250	1.00
68_N	71_T	1.181	1.00
25_A	30_D	1.157	1.00
10_T	13_T	1.092	1.00
29_D	33_K	1.069	1.00
69_L	72_S	1.022	1.00
61_S	65_Q	1.020	1.00
54_T	57_L	1.020	1.00
30_D	33_K	1.017	1.00
68_N	74_E	1.016	1.00
70_N	74_E	1.011	1.00
68_N	72_S	1.009	1.00
65_Q	68_N	1.008	1.00
38_Q	51_T	0.983	1.00
32_L	36_V	0.958	1.00
39_L	53_F	0.957	1.00
55_A	58_A	0.952	1.00
22_S	25_A	0.949	1.00
21_T	24_S	0.936	1.00
34_L	54_T	0.893	1.00
51_T	54_T	0.879	1.00
53_F	60_F	0.870	1.00
67_T	70_N	0.855	1.00
33_K	36_V	0.855	1.00
11_S	14_S	0.853	1.00
16_S	19_S	0.840	1.00
52_Q	56_Q	0.840	1.00
10_T	14_S	0.822	1.00
17_S	20_A	0.808	1.00
19_S	22_S	0.793	1.00
18_S	21_T	0.790	1.00
61_S	67_T	0.782	1.00
44_P	47_P	0.777	1.00
24_S	27_G	0.767	1.00
12_S	15_S	0.758	1.00
11_S	15_S	0.750	1.00
8_S	11_S	0.748	1.00
13_T	16_S	0.747	1.00
28_K	68_N	0.742	1.00
64_E	67_T	0.741	1.00
36_V	40_Q	0.734	1.00
38_Q	50_N	0.713	1.00
20_A	23_S	0.709	1.00
33_K	40_Q	0.706	1.00
9_T	13_T	0.705	1.00
28_K	31_F	0.699	1.00
25_A	28_K	0.693	1.00
53_F	57_L	0.689	1.00
14_S	18_S	0.677	1.00
23_S	26_L	0.677	1.00
61_S	70_N	0.671	1.00
15_S	18_S	0.666	1.00
21_T	25_A	0.656	1.00
9_T	12_S	0.651	1.00
42_Q	47_P	0.649	1.00
28_K	44_P	0.647	1.00
58_A	63_V	0.635	1.00
35_L	53_F	0.635	1.00
70_N	73_L	0.634	1.00
61_S	64_E	0.632	1.00
15_S	19_S	0.629	1.00
28_K	36_V	0.618	1.00
66_L	73_L	0.617	1.00
51_T	55_A	0.605	1.00
60_F	63_V	0.596	1.00
14_S	17_S	0.570	1.00
35_L	58_A	0.569	1.00
54_T	58_A	0.567	1.00
32_L	44_P	0.559	1.00
48_M	52_Q	0.548	1.00
13_T	17_S	0.546	1.00
16_S	20_A	0.533	1.00
11_S	16_S	0.526	1.00
66_L	70_N	0.525	1.00
10_T	16_S	0.519	1.00
45_L	50_N	0.517	1.00
22_S	26_L	0.517	1.00
32_L	63_V	0.509	1.00
8_S	12_S	0.503	1.00
9_T	14_S	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
2lc5A	1	0.5733	2.2	0.9	Contact Map
1utaA	1	0.3733	2	0.902	Contact Map
1vt0M	4	0.8533	1.4	0.911	Contact Map
1dd3A	6	0.36	1.3	0.912	Contact Map
2z6gA	1	0	1.3	0.912	Contact Map
3si5X	1	0.24	1.2	0.915	Contact Map
1dd4C	7	0.36	1.2	0.915	Contact Map
4qdyA	2	0	1.1	0.915	Contact Map
2jgqA	2	0.5067	1.1	0.915	Contact Map
2jojA	1	0.56	1.1	0.915	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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