Q9HMD0 - HALSA - GREMLIN Contacts

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Q9HMD0 - Thioredoxin

UniProt:	Q9HMD0	Sequences: MTVTLKDFYADWCGPCKTQDPILEELEADYDEDVSFEKIDVDEAEDVANEYQVRSIPTIVVENDDGVVERFVGVTQREQLEDAIESAGA	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	89 (83)
Sequences:	5052 (3258)
Seq/√Len:	357.6

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
41_V	48_A	4.040	1.00
4_T	35_S	2.636	1.00
60_V	70_R	2.489	1.00
13_C	16_C	2.456	1.00
76_Q	79_Q	2.319	1.00
22_I	77_R	2.239	1.00
74_V	79_Q	2.214	1.00
5_L	23_L	2.165	1.00
4_T	37_E	2.099	1.00
7_D	38_K	2.083	1.00
25_E	77_R	2.022	1.00
29_D	77_R	1.973	1.00
22_I	25_E	1.950	1.00
51_Y	62_E	1.870	1.00
39_I	47_V	1.868	1.00
26_L	36_F	1.864	1.00
7_D	20_D	1.757	1.00
29_D	81_E	1.699	1.00
5_L	59_I	1.699	1.00
23_L	36_F	1.534	1.00
26_L	80_L	1.508	1.00
20_D	24_E	1.497	1.00
19_Q	80_L	1.473	1.00
26_L	81_E	1.418	1.00
26_L	77_R	1.355	1.00
6_K	62_E	1.352	1.00
34_V	84_I	1.342	1.00
30_Y	81_E	1.298	1.00
20_D	38_K	1.262	1.00
61_V	83_A	1.228	1.00
19_Q	22_I	1.210	1.00
40_D	43_E	1.152	1.00
24_E	38_K	1.147	1.00
22_I	76_Q	1.142	1.00
30_Y	85_E	1.120	1.00
19_Q	59_I	1.116	1.00
22_I	26_L	1.106	1.00
11_D	40_D	1.092	1.00
41_V	56_I	1.078	1.00
9_Y	38_K	1.059	1.00
44_A	47_V	1.033	1.00
79_Q	82_D	1.029	1.00
61_V	84_I	1.023	1.00
78_E	82_D	1.004	1.00
7_D	19_Q	0.999	1.00
26_L	30_Y	0.997	1.00
47_V	50_E	0.914	1.00
18_T	22_I	0.910	1.00
71_F	83_A	0.857	1.00
11_D	42_D	0.851	1.00
15_P	55_S	0.832	1.00
48_A	51_Y	0.822	1.00
42_D	45_E	0.803	1.00
5_L	36_F	0.775	1.00
45_E	48_A	0.775	1.00
30_Y	36_F	0.771	1.00
53_V	56_I	0.767	1.00
60_V	68_V	0.765	1.00
7_D	15_P	0.745	1.00
5_L	84_I	0.744	1.00
81_E	85_E	0.738	1.00
60_V	67_V	0.735	1.00
8_F	53_V	0.732	1.00
39_I	48_A	0.729	1.00
14_G	18_T	0.729	1.00
73_G	79_Q	0.725	1.00
77_R	81_E	0.710	0.99
63_N	66_G	0.709	0.99
6_K	37_E	0.706	0.99
47_V	51_Y	0.704	0.99
27_E	36_F	0.698	0.99
12_W	17_K	0.696	0.99
8_F	51_Y	0.692	0.99
71_F	74_V	0.685	0.99
23_L	59_I	0.683	0.99
23_L	84_I	0.679	0.99
7_D	23_L	0.655	0.99
15_P	75_T	0.648	0.99
39_I	44_A	0.646	0.99
5_L	80_L	0.635	0.99
33_D	64_D	0.634	0.99
53_V	58_T	0.632	0.99
19_Q	23_L	0.624	0.99
15_P	18_T	0.620	0.98
28_A	63_N	0.618	0.98
10_A	42_D	0.613	0.98
67_V	70_R	0.611	0.98
19_Q	75_T	0.611	0.98
12_W	42_D	0.597	0.98
10_A	13_C	0.592	0.98
14_G	17_K	0.591	0.98
72_V	78_E	0.588	0.98
25_E	29_D	0.575	0.97
77_R	80_L	0.571	0.97
25_E	28_A	0.571	0.97
59_I	80_L	0.570	0.97
13_C	58_T	0.570	0.97
14_G	21_P	0.565	0.97
55_S	75_T	0.565	0.97
45_E	49_N	0.562	0.97
46_D	50_E	0.561	0.97
62_E	68_V	0.559	0.97
29_D	33_D	0.559	0.97
39_I	46_D	0.554	0.97
14_G	55_S	0.552	0.97
69_E	83_A	0.552	0.97
42_D	56_I	0.551	0.97
9_Y	13_C	0.550	0.97
34_V	61_V	0.541	0.96
8_F	41_V	0.540	0.96
34_V	38_K	0.539	0.96
11_D	43_E	0.537	0.96
71_F	79_Q	0.536	0.96
29_D	85_E	0.533	0.96
51_Y	60_V	0.529	0.96
82_D	85_E	0.528	0.96
27_E	30_Y	0.526	0.96
8_F	62_E	0.526	0.96
50_E	62_E	0.520	0.95
6_K	39_I	0.518	0.95
10_A	21_P	0.517	0.95
82_D	86_S	0.508	0.95
33_D	85_E	0.503	0.95
10_A	16_C	0.500	0.94

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
3f8uA	2	1	99.8	0.169	Contact Map
3apoA	1	0.9101	99.8	0.176	Contact Map
2r2jA	2	1	99.8	0.187	Contact Map
2b5eA	1	1	99.8	0.189	Contact Map
4ekzA	1	1	99.8	0.216	Contact Map
3ed3A	1	1	99.8	0.223	Contact Map
1sjiA	2	0.9888	99.7	0.23	Contact Map
3us3A	2	0.9888	99.7	0.232	Contact Map
3uemA	1	0.9775	99.7	0.236	Contact Map
4i6xA	1	0.9888	99.7	0.238	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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