YGIN - ECOLI - GREMLIN Contacts

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YGIN - Probable quinol monooxygenase YgiN

UniProt:	P0ADU2	Sequences: MLTVIAEIRTRPGQHHRQAVLDQFAKIVPTVLKEEGCHGYAPMVDCAAGVSFQSMAPDSIVMIEQWESIAHLEAHLQTPHMKAYSEAVKGDVLEMNIRILQPGI	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG12657
Length:	104 (100)
Sequences:	121 (80)
Seq/√Len:	8.0

ECOLI - YGIN

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
28_V	42_P	3.964	0.97
39_G	65_Q	2.725	0.82
35_E	67_E	2.682	0.81
35_E	63_I	2.191	0.65
44_V	63_I	2.152	0.63
17_R	21_L	2.090	0.61
92_V	95_M	1.926	0.55
84_Y	95_M	1.871	0.52
54_S	88_V	1.768	0.48
27_I	30_T	1.744	0.47
24_F	53_Q	1.718	0.46
5_I	19_A	1.705	0.46
10_T	20_V	1.682	0.45
79_P	102_P	1.651	0.43
18_Q	22_D	1.560	0.40
82_K	85_S	1.532	0.39
7_E	62_M	1.528	0.38
84_Y	88_V	1.509	0.38
3_T	7_E	1.468	0.36
8_I	53_Q	1.448	0.35
32_L	62_M	1.442	0.35
3_T	62_M	1.438	0.35
17_R	89_K	1.437	0.35
24_F	74_A	1.400	0.34
33_K	94_E	1.381	0.33
65_Q	90_G	1.326	0.31
12_P	93_L	1.316	0.31
14_Q	19_A	1.300	0.30
26_K	33_K	1.294	0.30
62_M	71_H	1.293	0.30
78_T	102_P	1.280	0.29
87_A	90_G	1.248	0.28
14_Q	91_D	1.246	0.28
14_Q	22_D	1.233	0.28
66_W	72_L	1.233	0.28
49_G	61_V	1.230	0.28
2_L	46_C	1.228	0.28
49_G	84_Y	1.223	0.27
2_L	39_G	1.223	0.27
23_Q	86_E	1.212	0.27
30_T	33_K	1.207	0.27
59_S	92_V	1.188	0.26
19_A	91_D	1.187	0.26
11_R	57_P	1.182	0.26
51_S	54_S	1.179	0.26
2_L	87_A	1.171	0.26
43_M	62_M	1.161	0.26
79_P	83_A	1.157	0.25
47_A	90_G	1.150	0.25
27_I	88_V	1.144	0.25
20_V	97_I	1.141	0.25
7_E	56_A	1.135	0.25
33_K	67_E	1.133	0.25
32_L	71_H	1.132	0.25
10_T	58_D	1.122	0.24
1_M	6_A	1.090	0.23
11_R	35_E	1.036	0.22
7_E	98_R	1.029	0.22
22_D	25_A	1.019	0.21
44_V	87_A	1.014	0.21
28_V	84_Y	1.007	0.21
38_H	60_I	1.003	0.21
93_L	96_N	1.003	0.21
28_V	94_E	0.995	0.21
51_S	69_I	0.933	0.19
61_V	83_A	0.905	0.18
24_F	61_V	0.898	0.18
13_G	80_H	0.891	0.18
12_P	29_P	0.883	0.18
83_A	86_E	0.879	0.18
82_K	98_R	0.862	0.17
25_A	33_K	0.851	0.17
25_A	71_H	0.839	0.17
59_S	88_V	0.830	0.17
49_G	73_E	0.821	0.16
69_I	88_V	0.819	0.16
50_V	90_G	0.811	0.16
2_L	30_T	0.809	0.16
61_V	74_A	0.806	0.16
63_I	88_V	0.804	0.16
44_V	65_Q	0.787	0.16
10_T	93_L	0.783	0.16
18_Q	99_I	0.780	0.15
18_Q	90_G	0.774	0.15
14_Q	88_V	0.773	0.15
42_P	76_L	0.772	0.15
32_L	43_M	0.766	0.15
67_E	86_E	0.765	0.15
33_K	86_E	0.763	0.15
8_I	17_R	0.761	0.15
42_P	86_E	0.752	0.15
25_A	79_P	0.748	0.15
85_S	88_V	0.745	0.15
20_V	59_S	0.742	0.15
39_G	43_M	0.736	0.15
70_A	74_A	0.736	0.15
77_Q	85_S	0.733	0.15
53_Q	99_I	0.726	0.14
25_A	48_A	0.714	0.14
26_K	67_E	0.713	0.14
88_V	94_E	0.712	0.14
20_V	98_R	0.709	0.14
88_V	95_M	0.704	0.14
4_V	13_G	0.701	0.14
13_G	17_R	0.680	0.13
48_A	76_L	0.676	0.13
4_V	63_I	0.668	0.13
14_Q	43_M	0.656	0.13
12_P	17_R	0.648	0.13
27_I	76_L	0.642	0.13
22_D	38_H	0.642	0.13
30_T	94_E	0.641	0.13
5_I	74_A	0.640	0.13
69_I	78_T	0.639	0.13
17_R	33_K	0.638	0.13
9_R	71_H	0.636	0.13
84_Y	89_K	0.632	0.13
47_A	86_E	0.627	0.12
11_R	19_A	0.622	0.12
2_L	98_R	0.612	0.12
18_Q	39_G	0.608	0.12
12_P	71_H	0.602	0.12
53_Q	76_L	0.602	0.12
32_L	92_V	0.602	0.12
48_A	54_S	0.596	0.12
92_V	97_I	0.595	0.12
42_P	82_K	0.592	0.12
28_V	82_K	0.588	0.12
28_V	58_D	0.588	0.12
27_I	91_D	0.587	0.12
47_A	55_M	0.583	0.12
71_H	84_Y	0.583	0.12
35_E	86_E	0.568	0.11
43_M	63_I	0.565	0.11
48_A	51_S	0.554	0.11
69_I	76_L	0.553	0.11
69_I	99_I	0.550	0.11
41_A	96_N	0.542	0.11
28_V	68_S	0.538	0.11
55_M	97_I	0.530	0.11
11_R	90_G	0.525	0.11
57_P	73_E	0.525	0.11
23_Q	46_C	0.523	0.11
2_L	20_V	0.523	0.11
24_F	78_T	0.518	0.11
6_A	13_G	0.516	0.11
59_S	97_I	0.514	0.11
13_G	74_A	0.511	0.11
54_S	87_A	0.501	0.10
52_F	73_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
1tuvA	2	0.9712	99.9	0.532	Contact Map
3mcsA	1	0.9038	99.8	0.585	Contact Map
3f44A	1	0.9038	99.7	0.607	Contact Map
1q8bA	2	0.875	99.7	0.611	Contact Map
2omoA	2	0.9038	99.7	0.613	Contact Map
2gffA	2	0.9038	99.7	0.613	Contact Map
3kkfA	3	0.9038	99.7	0.619	Contact Map
2fb0A	2	0.875	99.7	0.62	Contact Map
3e8oA	2	0.9038	99.7	0.623	Contact Map
2bbeA	3	0.9038	99.7	0.624	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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