Q9HI14 - HALSA - GREMLIN Contacts

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Q9HI14 - Transcription initiation factor IID

UniProt:	Q9HI14	Sequences: MDLEGADYDPEQFPGLVYRLDEPSVVALLFGSGKLVITGGKHPVDAEHAVDTIDSRLEDLGLLDGYGDRAK	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	71 (59)
Sequences:	842 (493)
Seq/√Len:	64.2

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
13_F	30_F	3.102	1.00
25_V	40_G	2.954	1.00
20_L	23_P	2.648	1.00
30_F	38_T	2.394	1.00
25_V	49_A	2.312	1.00
37_I	46_A	2.122	1.00
13_F	28_L	2.081	1.00
6_A	16_L	1.880	1.00
28_L	36_V	1.770	1.00
25_V	53_I	1.709	0.99
20_L	53_I	1.639	0.99
51_D	55_S	1.542	0.99
17_V	28_L	1.476	0.98
37_I	50_V	1.424	0.98
27_A	53_I	1.404	0.98
7_D	20_L	1.402	0.98
30_F	36_V	1.314	0.96
51_D	59_D	1.267	0.96
13_F	36_V	1.175	0.94
15_G	30_F	1.105	0.91
20_L	25_V	1.103	0.91
45_D	48_H	1.097	0.91
7_D	19_R	1.085	0.90
15_G	28_L	1.051	0.89
9_D	12_Q	1.021	0.88
35_L	55_S	1.007	0.87
6_A	18_Y	1.003	0.87
37_I	40_G	1.002	0.87
12_Q	16_L	0.995	0.86
7_D	32_S	0.994	0.86
16_L	38_T	0.969	0.85
41_K	45_D	0.968	0.85
22_E	48_H	0.933	0.82
21_D	48_H	0.927	0.82
7_D	46_A	0.926	0.82
44_V	47_E	0.915	0.81
4_E	11_E	0.904	0.80
56_R	59_D	0.903	0.80
14_P	36_V	0.898	0.80
42_H	47_E	0.892	0.79
11_E	15_G	0.887	0.79
48_H	51_D	0.873	0.78
44_V	48_H	0.864	0.77
42_H	48_H	0.844	0.76
14_P	18_Y	0.832	0.75
11_E	31_G	0.812	0.73
18_Y	56_R	0.792	0.71
33_G	39_G	0.783	0.70
13_F	32_S	0.776	0.69
43_P	47_E	0.771	0.69
9_D	18_Y	0.766	0.68
47_E	59_D	0.764	0.68
26_V	32_S	0.754	0.67
27_A	35_L	0.735	0.65
27_A	55_S	0.720	0.63
21_D	46_A	0.715	0.63
46_A	54_D	0.713	0.63
11_E	24_S	0.676	0.59
14_P	30_F	0.673	0.58
55_S	58_E	0.664	0.57
7_D	17_V	0.664	0.57
43_P	46_A	0.651	0.56
10_P	19_R	0.642	0.55
48_H	59_D	0.636	0.54
22_E	55_S	0.630	0.53
23_P	45_D	0.625	0.53
47_E	51_D	0.623	0.53
5_G	35_L	0.621	0.52
36_V	49_A	0.617	0.52
53_I	60_L	0.613	0.51
25_V	41_K	0.612	0.51
40_G	49_A	0.602	0.50
48_H	56_R	0.600	0.50
9_D	27_A	0.590	0.49
13_F	34_K	0.584	0.48
51_D	62_L	0.572	0.47
13_F	41_K	0.567	0.46
14_P	28_L	0.561	0.45
5_G	32_S	0.555	0.45
31_G	62_L	0.551	0.44
15_G	19_R	0.539	0.43
6_A	12_Q	0.533	0.42
48_H	52_T	0.529	0.42
30_F	34_K	0.527	0.41
55_S	60_L	0.523	0.41
19_R	28_L	0.505	0.39
17_V	34_K	0.501	0.39
10_P	31_G	0.500	0.38

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
1rm1A	1	1	99.9	0.167	Contact Map
3eikA	2	0.9859	99.9	0.168	Contact Map
4b0aA	1	0.9859	99.9	0.17	Contact Map
1ytbA	1	1	99.9	0.172	Contact Map
2z8uA	2	0.8592	99.9	0.173	Contact Map
1mp9A	2	1	99.9	0.175	Contact Map
1aisA	1	1	99.8	0.195	Contact Map
2d0bA	1	1	89.8	0.802	Contact Map
3vn5A	1	0.9155	88.3	0.808	Contact Map
4py5A	1	0.9577	83.7	0.82	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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