Q9HNL2 - HALSA - GREMLIN Contacts

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Q9HNL2 - Transcription elongation factor Spt4

UniProt:	Q9HNL2	Sequences: MASNRLACHDCHRIVEPDEEMCPYCSSNSLTEDWAGYVVITHPDTSEIADKMEVHEAGEFALKVR	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	65 (58)
Sequences:	103 (61)
Seq/√Len:	8.0

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
7_A	13_R	2.423	0.73
5_R	52_M	2.266	0.68
15_V	59_E	2.140	0.63
15_V	23_P	2.114	0.62
40_I	64_V	2.034	0.59
6_L	31_T	2.030	0.59
61_A	64_V	1.942	0.55
12_H	52_M	1.785	0.49
30_L	33_D	1.715	0.46
10_D	28_N	1.676	0.45
7_A	58_G	1.594	0.41
38_V	48_I	1.578	0.41
34_W	48_I	1.544	0.39
14_I	24_Y	1.526	0.39
6_L	50_D	1.429	0.35
44_D	55_H	1.383	0.33
40_I	45_T	1.370	0.33
37_Y	58_G	1.342	0.32
7_A	14_I	1.336	0.32
24_Y	35_A	1.317	0.31
48_I	53_E	1.316	0.31
10_D	21_M	1.259	0.29
52_M	58_G	1.205	0.27
6_L	30_L	1.204	0.27
27_S	38_V	1.155	0.25
26_S	39_V	1.145	0.25
20_E	23_P	1.143	0.25
42_H	45_T	1.096	0.24
26_S	51_K	1.077	0.23
26_S	44_D	1.054	0.22
7_A	16_E	1.043	0.22
33_D	62_L	1.030	0.22
16_E	59_E	1.000	0.21
13_R	24_Y	0.979	0.20
20_E	58_G	0.974	0.20
5_R	51_K	0.965	0.20
36_G	63_K	0.945	0.19
5_R	42_H	0.932	0.19
32_E	48_I	0.931	0.19
36_G	62_L	0.926	0.19
16_E	23_P	0.918	0.19
54_V	59_E	0.891	0.18
40_I	54_V	0.868	0.18
17_P	41_T	0.863	0.17
37_Y	62_L	0.863	0.17
28_N	62_L	0.845	0.17
6_L	23_P	0.822	0.16
32_E	51_K	0.816	0.16
6_L	14_I	0.809	0.16
32_E	64_V	0.794	0.16
45_T	54_V	0.749	0.15
6_L	32_E	0.732	0.15
10_D	33_D	0.731	0.15
47_E	50_D	0.722	0.14
37_Y	41_T	0.688	0.14
16_E	28_N	0.686	0.14
14_I	31_T	0.677	0.13
12_H	41_T	0.677	0.13
17_P	29_S	0.676	0.13
10_D	20_E	0.674	0.13
17_P	63_K	0.662	0.13
30_L	64_V	0.655	0.13
35_A	63_K	0.652	0.13
26_S	60_F	0.645	0.13
12_H	29_S	0.643	0.13
39_V	56_E	0.640	0.13
23_P	38_V	0.629	0.13
35_A	42_H	0.617	0.12
5_R	53_E	0.613	0.12
9_H	24_Y	0.603	0.12
21_M	51_K	0.590	0.12
29_S	52_M	0.578	0.12
20_E	54_V	0.571	0.12
9_H	32_E	0.562	0.11
41_T	51_K	0.555	0.11
7_A	29_S	0.549	0.11
10_D	39_V	0.548	0.11
20_E	31_T	0.543	0.11
20_E	41_T	0.542	0.11
29_S	37_Y	0.541	0.11
50_D	53_E	0.535	0.11
7_A	56_E	0.534	0.11
30_L	54_V	0.532	0.11
16_E	60_F	0.529	0.11
38_V	63_K	0.506	0.11
29_S	33_D	0.501	0.10
50_D	56_E	0.500	0.10

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
3p8bA	1	0.9231	99.9	0.313	Contact Map
1ryqA	1	0.9077	99.9	0.316	Contact Map
3lpeB	1	0.8923	99.9	0.345	Contact Map
3h7hA	1	1	99.8	0.395	Contact Map
2exuA	2	0.9538	99.7	0.451	Contact Map
2ayjA	1	0.6462	87.2	0.851	Contact Map
4u3eA	2	0.8615	86.3	0.852	Contact Map
2lcqA	1	0.5538	75.3	0.869	Contact Map
1h7bA	2	0.2769	72.4	0.872	Contact Map
5aunA	1	0.6462	71.8	0.872	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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