MHYT - PFAM28P - GREMLIN Contacts

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MHYT - Bacterial signalling protein N terminal repeat

PFAM:	PF03707	Sequences: GLGIWAMHYTGMAAMRLPAPVSYDPGLVALSLLIAIVASGLALWLAFRLRDRRRRLLAG	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	59 (54)
Sequences:	42325 (27682)
Seq/√Len:	3767.1
META:	0.871

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
24_D	27_L	3.065	1.00
34_I	38_A	2.755	1.00
40_G	44_W	2.323	1.00
7_M	11_G	2.027	1.00
23_Y	28_V	1.850	1.00
33_L	37_V	1.607	1.00
5_W	9_Y	1.581	1.00
13_A	16_R	1.560	1.00
2_L	5_W	1.558	1.00
22_S	25_P	1.508	1.00
2_L	32_L	1.467	1.00
4_I	12_M	1.399	1.00
26_G	30_L	1.396	1.00
2_L	6_A	1.393	1.00
20_P	23_Y	1.374	1.00
6_A	10_T	1.359	1.00
51_D	54_R	1.350	1.00
32_L	36_I	1.341	1.00
26_G	29_A	1.306	1.00
25_P	29_A	1.269	1.00
10_T	13_A	1.244	1.00
9_Y	28_V	1.233	1.00
48_R	51_D	1.219	1.00
25_P	28_V	1.213	1.00
27_L	30_L	1.184	1.00
24_D	28_V	1.164	1.00
44_W	48_R	1.133	1.00
47_F	50_R	1.070	1.00
42_A	45_L	1.034	1.00
39_S	43_L	1.034	1.00
8_H	12_M	1.011	1.00
48_R	54_R	1.008	1.00
50_R	54_R	0.993	1.00
9_Y	31_S	0.955	1.00
44_W	47_F	0.942	1.00
27_L	31_S	0.924	1.00
1_G	36_I	0.924	1.00
23_Y	29_A	0.902	1.00
23_Y	27_L	0.860	1.00
49_L	52_R	0.844	1.00
38_A	41_L	0.840	1.00
5_W	32_L	0.835	1.00
50_R	53_R	0.827	1.00
4_I	8_H	0.814	1.00
39_S	42_A	0.812	1.00
1_G	7_M	0.806	1.00
5_W	13_A	0.804	1.00
35_A	39_S	0.793	1.00
37_V	41_L	0.757	1.00
7_M	17_L	0.753	1.00
16_R	20_P	0.736	1.00
49_L	54_R	0.731	1.00
11_G	14_A	0.719	1.00
23_Y	26_G	0.699	1.00
38_A	46_A	0.686	1.00
41_L	44_W	0.673	1.00
47_F	52_R	0.651	1.00
35_A	45_L	0.636	1.00
41_L	45_L	0.633	1.00
32_L	43_L	0.624	1.00
34_I	46_A	0.614	1.00
22_S	26_G	0.612	1.00
46_A	51_D	0.610	1.00
48_R	52_R	0.609	1.00
4_I	7_M	0.608	1.00
4_I	42_A	0.595	1.00
49_L	53_R	0.589	1.00
28_V	31_S	0.586	1.00
6_A	13_A	0.578	1.00
36_I	39_S	0.557	1.00
3_G	15_M	0.557	1.00
9_Y	12_M	0.555	1.00
36_I	40_G	0.545	1.00
3_G	7_M	0.545	1.00
3_G	6_A	0.542	1.00
4_I	39_S	0.534	1.00
7_M	15_M	0.522	1.00
35_A	43_L	0.514	1.00
25_P	30_L	0.510	1.00
23_Y	31_S	0.508	1.00
39_S	44_W	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
4i0uA	4	0.7288	8.1	0.808	Contact Map
4ev6A	3	0.7627	6.1	0.819	Contact Map
3ig5A	1	1	3.2	0.842	Contact Map
4p02B	1	0.8475	2.8	0.846	Contact Map
3o7qA	1	0.8814	2.1	0.857	Contact Map
1fftA	1	0.9831	1.8	0.861	Contact Map
2l2tA	2	0.678	1.8	0.862	Contact Map
2lx0A	1	0.5424	1.5	0.869	Contact Map
2kluA	1	0.678	1.4	0.871	Contact Map
3d79A	1	0.322	1.2	0.875	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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