Whib - PFAM28P - GREMLIN Contacts

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Whib - Transcription factor WhiB

PFAM:	PF02467	Sequences: WRDRAACRGVDPELFFPEGGAREAAAKAICAGCPVRAECLEYALENREPYGVWGGLTERERRRL	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	64 (63)
Sequences:	30229 (18143)
Seq/√Len:	2285.7
META:	0.925

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
42_Y	46_N	2.688	1.00
42_Y	53_W	2.677	1.00
6_A	32_G	2.297	1.00
36_R	40_L	1.966	1.00
23_E	52_V	1.930	1.00
10_V	29_I	1.871	1.00
40_L	56_L	1.814	1.00
26_A	52_V	1.687	1.00
40_L	44_L	1.642	1.00
6_A	9_G	1.627	1.00
31_A	36_R	1.585	1.00
44_L	56_L	1.582	1.00
2_R	42_Y	1.525	1.00
56_L	60_E	1.515	1.00
27_K	60_E	1.458	1.00
50_Y	58_E	1.420	1.00
23_E	57_T	1.413	1.00
23_E	27_K	1.369	1.00
42_Y	48_E	1.360	1.00
41_E	45_E	1.322	1.00
35_V	38_E	1.287	1.00
27_K	57_T	1.283	1.00
11_D	14_L	1.257	1.00
27_K	52_V	1.254	1.00
43_A	53_W	1.247	1.00
36_R	54_G	1.218	1.00
30_C	33_C	1.217	1.00
14_L	25_A	1.211	1.00
10_V	14_L	1.183	1.00
5_A	35_V	1.167	1.00
46_N	49_P	1.158	1.00
5_A	8_R	1.157	1.00
43_A	54_G	1.157	1.00
12_P	16_F	1.068	1.00
4_R	34_P	1.067	1.00
17_P	20_G	1.064	1.00
57_T	60_E	1.055	1.00
22_R	25_A	1.038	1.00
58_E	62_R	1.002	1.00
25_A	28_A	0.997	1.00
6_A	29_I	0.990	1.00
17_P	23_E	0.951	1.00
10_V	15_F	0.950	1.00
1_W	5_A	0.855	1.00
37_A	41_E	0.848	1.00
6_A	34_P	0.843	1.00
18_E	22_R	0.842	1.00
24_A	27_K	0.834	1.00
27_K	31_A	0.832	1.00
48_E	53_W	0.829	1.00
36_R	56_L	0.797	1.00
19_G	22_R	0.786	1.00
59_R	62_R	0.784	1.00
16_F	53_W	0.770	1.00
13_E	16_F	0.763	1.00
24_A	28_A	0.762	1.00
14_L	26_A	0.734	1.00
16_F	51_G	0.723	1.00
17_P	22_R	0.713	1.00
16_F	50_Y	0.713	1.00
33_C	39_C	0.711	1.00
10_V	13_E	0.671	1.00
1_W	35_V	0.666	1.00
52_V	57_T	0.664	1.00
31_A	55_G	0.663	1.00
9_G	12_P	0.647	1.00
6_A	35_V	0.646	1.00
4_R	35_V	0.639	1.00
3_D	8_R	0.638	1.00
36_R	55_G	0.633	1.00
32_G	36_R	0.622	1.00
37_A	40_L	0.611	1.00
49_P	53_W	0.604	1.00
25_A	29_I	0.599	1.00
56_L	61_R	0.593	1.00
28_A	32_G	0.589	1.00
29_I	32_G	0.586	1.00
15_F	29_I	0.584	1.00
23_E	58_E	0.563	1.00
40_L	54_G	0.559	1.00
28_A	31_A	0.557	1.00
9_G	34_P	0.557	1.00
21_A	25_A	0.550	1.00
26_A	29_I	0.545	1.00
38_E	41_E	0.534	1.00
30_C	39_C	0.532	1.00
21_A	24_A	0.531	1.00
47_R	50_Y	0.516	1.00
1_W	4_R	0.513	1.00
46_N	53_W	0.511	1.00
38_E	42_Y	0.505	1.00
44_L	48_E	0.502	1.00
20_G	59_R	0.501	1.00
34_P	37_A	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
1pxqA	1	0.4062	14.2	0.84	Contact Map
1keaA	2	0.7031	5.6	0.867	Contact Map
4lixA	1	0.9375	5.2	0.869	Contact Map
2abkA	1	0.7344	3.8	0.877	Contact Map
2wj8A	4	1	3.6	0.879	Contact Map
3sdrA	1	0.8906	3.4	0.88	Contact Map
3fspA	1	1	3.2	0.882	Contact Map
4r5qA	1	0.4844	3.1	0.882	Contact Map
1kg2A	1	0.8594	2.8	0.885	Contact Map
1nqzA	1	0.5312	2.6	0.886	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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