HYCF - ECOLI - GREMLIN Contacts

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HYCF - Formate hydrogenlyase subunit 6

UniProt:	P16432	Sequences: MFTFIKKVIKTGTATSSYPLEPIAVDKNFRGKPEQNPQQCIGCAACVNACPSNALTVETDLATGELAWEFNLGHCIFCGRCEEVCPTAAIKLSQEYELAVWKKEDFLQQSRFALCNCRVCNRPFAVQKEIDYAIALLKHNGDSRAENHRESFETCPECKRQKCLVPSDRIELTRHMKEAI	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG10479
Length:	180 (149)
Sequences:	628 (430)
Seq/√Len:	35.3

ECOLI - HYCF HYFH NUOI
HALSA - Q9HRL7
SULSO - Q980H1

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
82_E	90_I	3.824	1.00
155_C	158_C	3.545	1.00
47_V	55_L	3.490	1.00
39_Q	89_A	3.046	1.00
35_Q	90_I	2.490	1.00
117_C	120_C	2.423	1.00
134_I	153_E	2.260	0.99
131_D	138_K	2.167	0.99
49_A	84_V	2.145	0.99
27_K	94_Q	2.029	0.98
151_S	162_K	1.918	0.98
82_E	92_L	1.904	0.98
155_C	159_K	1.757	0.96
140_N	143_S	1.735	0.96
97_E	106_F	1.726	0.96
17_S	20_L	1.674	0.95
117_C	121_N	1.624	0.94
36_N	39_Q	1.615	0.94
117_C	155_C	1.605	0.94
123_P	127_Q	1.604	0.94
119_V	161_Q	1.541	0.92
113_A	127_Q	1.532	0.92
49_A	80_R	1.513	0.91
41_I	87_T	1.506	0.91
120_C	155_C	1.463	0.90
54_A	76_I	1.453	0.90
159_K	162_K	1.441	0.89
138_K	148_H	1.434	0.89
148_H	151_S	1.427	0.89
16_S	23_I	1.396	0.88
14_A	122_R	1.369	0.87
70_F	92_L	1.357	0.86
134_I	139_H	1.352	0.86
42_G	77_F	1.348	0.86
120_C	158_C	1.339	0.85
157_E	161_Q	1.326	0.85
154_T	159_K	1.311	0.84
102_K	105_D	1.301	0.84
13_T	20_L	1.291	0.83
111_R	118_R	1.200	0.78
153_E	161_Q	1.178	0.77
53_N	105_D	1.175	0.77
118_R	121_N	1.174	0.77
99_A	102_K	1.160	0.76
142_D	146_E	1.146	0.75
143_S	146_E	1.144	0.75
140_N	144_R	1.143	0.75
161_Q	165_V	1.143	0.75
52_S	76_I	1.140	0.75
34_E	93_S	1.101	0.72
43_C	81_C	1.099	0.72
43_C	85_C	1.099	0.72
46_C	50_C	1.099	0.72
43_C	78_C	1.099	0.72
43_C	50_C	1.099	0.72
46_C	78_C	1.099	0.72
46_C	81_C	1.099	0.72
46_C	85_C	1.099	0.72
43_C	46_C	1.099	0.72
50_C	78_C	1.099	0.72
50_C	81_C	1.099	0.72
78_C	81_C	1.099	0.72
78_C	85_C	1.099	0.72
81_C	85_C	1.099	0.72
50_C	85_C	1.099	0.72
40_C	78_C	1.099	0.72
40_C	46_C	1.099	0.72
40_C	50_C	1.099	0.72
40_C	43_C	1.099	0.72
40_C	81_C	1.099	0.72
40_C	85_C	1.099	0.72
144_R	165_V	1.085	0.71
39_Q	90_I	1.068	0.70
34_E	91_K	1.063	0.69
132_Y	140_N	1.062	0.69
138_K	142_D	1.061	0.69
90_I	153_E	1.059	0.69
75_C	78_C	1.057	0.69
40_C	75_C	1.057	0.69
46_C	75_C	1.057	0.69
50_C	75_C	1.057	0.69
43_C	75_C	1.057	0.69
75_C	85_C	1.057	0.69
75_C	81_C	1.057	0.69
35_Q	44_A	1.040	0.68
86_P	89_A	1.032	0.67
58_E	67_A	1.028	0.67
134_I	138_K	1.027	0.67
146_E	153_E	1.016	0.66
162_K	165_V	1.013	0.66
144_R	151_S	1.011	0.65
152_F	155_C	1.002	0.65
122_R	157_E	0.999	0.64
133_A	151_S	0.995	0.64
157_E	160_R	0.993	0.64
147_N	150_E	0.990	0.64
145_A	151_S	0.978	0.63
89_A	92_L	0.978	0.63
15_T	18_Y	0.976	0.63
154_T	162_K	0.952	0.61
45_A	49_A	0.950	0.60
79_G	92_L	0.946	0.60
77_F	98_L	0.939	0.60
54_A	92_L	0.935	0.59
147_N	151_S	0.933	0.59
33_P	80_R	0.928	0.59
117_C	137_L	0.925	0.58
119_V	165_V	0.923	0.58
144_R	149_R	0.917	0.58
146_E	149_R	0.916	0.58
117_C	126_V	0.915	0.58
131_D	135_A	0.905	0.57
119_V	127_Q	0.888	0.55
57_V	68_W	0.885	0.55
114_L	117_C	0.877	0.54
29_F	83_E	0.870	0.54
35_Q	93_S	0.863	0.53
151_S	159_K	0.863	0.53
25_V	96_Y	0.857	0.53
145_A	149_R	0.857	0.53
47_V	57_V	0.849	0.52
117_C	158_C	0.845	0.52
146_E	152_F	0.845	0.52
144_R	153_E	0.843	0.51
138_K	147_N	0.839	0.51
45_A	76_I	0.836	0.51
116_N	123_P	0.833	0.51
148_H	154_T	0.832	0.50
37_P	89_A	0.829	0.50
38_Q	91_K	0.828	0.50
154_T	158_C	0.827	0.50
117_C	124_F	0.821	0.50
72_L	77_F	0.809	0.49
21_E	24_A	0.808	0.48
84_V	89_A	0.807	0.48
29_F	33_P	0.803	0.48
52_S	74_H	0.795	0.47
32_K	95_E	0.774	0.46
76_I	80_R	0.772	0.45
77_F	92_L	0.772	0.45
124_F	128_K	0.762	0.44
120_C	123_P	0.749	0.43
145_A	152_F	0.748	0.43
118_R	131_D	0.746	0.43
77_F	87_T	0.738	0.42
38_Q	70_F	0.733	0.42
54_A	155_C	0.725	0.41
148_H	162_K	0.719	0.41
22_P	88_A	0.715	0.41
131_D	134_I	0.713	0.40
16_S	21_E	0.712	0.40
15_T	19_P	0.709	0.40
160_R	164_L	0.708	0.40
127_Q	131_D	0.708	0.40
73_G	77_F	0.707	0.40
59_T	72_L	0.705	0.40
67_A	111_R	0.694	0.39
51_P	76_I	0.693	0.39
144_R	147_N	0.692	0.39
148_H	152_F	0.692	0.39
138_K	149_R	0.691	0.39
88_A	93_S	0.688	0.38
150_E	153_E	0.683	0.38
159_K	163_C	0.680	0.38
31_G	36_N	0.679	0.38
149_R	153_E	0.679	0.38
41_I	80_R	0.677	0.37
119_V	162_K	0.676	0.37
41_I	44_A	0.671	0.37
20_L	103_K	0.669	0.37
154_T	157_E	0.654	0.36
126_V	129_E	0.650	0.35
150_E	165_V	0.647	0.35
115_C	120_C	0.646	0.35
18_Y	97_E	0.638	0.34
160_R	163_C	0.637	0.34
120_C	124_F	0.632	0.34
49_A	128_K	0.630	0.34
157_E	165_V	0.630	0.34
117_C	130_I	0.629	0.34
17_S	22_P	0.628	0.34
38_Q	104_E	0.628	0.34
120_C	126_V	0.625	0.33
59_T	73_G	0.624	0.33
74_H	84_V	0.622	0.33
55_L	70_F	0.621	0.33
44_A	98_L	0.621	0.33
120_C	137_L	0.620	0.33
121_N	125_A	0.619	0.33
122_R	126_V	0.618	0.33
135_A	147_N	0.614	0.32
147_N	161_Q	0.612	0.32
92_L	120_C	0.612	0.32
33_P	83_E	0.611	0.32
53_N	97_E	0.608	0.32
45_A	87_T	0.598	0.31
76_I	92_L	0.596	0.31
68_W	76_I	0.596	0.31
146_E	164_L	0.592	0.31
79_G	82_E	0.588	0.31
122_R	135_A	0.576	0.30
45_A	120_C	0.573	0.29
157_E	163_C	0.573	0.29
134_I	146_E	0.565	0.29
70_F	108_Q	0.563	0.29
135_A	150_E	0.560	0.29
146_E	150_E	0.557	0.28
15_T	30_R	0.549	0.28
53_N	107_L	0.545	0.28
127_Q	135_A	0.538	0.27
108_Q	113_A	0.537	0.27
44_A	48_N	0.529	0.26
111_R	117_C	0.527	0.26
152_F	157_E	0.526	0.26
150_E	156_P	0.525	0.26
33_P	68_W	0.524	0.26
24_A	94_Q	0.524	0.26
137_L	155_C	0.512	0.25
134_I	141_G	0.512	0.25
121_N	135_A	0.508	0.25
27_K	138_K	0.506	0.25
38_Q	164_L	0.506	0.25
60_D	84_V	0.505	0.25
118_R	150_E	0.500	0.25

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
3i9v9	1	0.7611	99.9	0.554	Contact Map
1gteA	4	0.5556	99.6	0.679	Contact Map
5c4iB	1	0.5111	99.6	0.679	Contact Map
4omfG	2	0.5278	99.5	0.693	Contact Map
1hfeL	2	0.9056	99.5	0.697	Contact Map
1xerA	2	0.5222	99.5	0.701	Contact Map
2gmhA	1	0.5889	99.5	0.702	Contact Map
3i9v3	1	0.9	99.4	0.708	Contact Map
1rgvA	1	0.4111	99.4	0.709	Contact Map
1jb0C	1	0.4333	99.4	0.711	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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