OPENSEQ.org - HYFA - ECOLI GREMLIN

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HYFA - Hydrogenase-4 component A

UniProt:	P23481	Sequence MNRFVVAEPLWCTGCNTCLAACSDVHKTQGLQQHPRLALAKTSTITAPVVCHHCEEAPCLQVCPVNAISQRDDAIQLNESLCIGCKLCAVVCPFGAISASGSRPVNAHAQYVFQAEGSLKDGEENAPTQHALLRWEPGVQTVAVKCDLCDFLPEGPACVRACPNQALRLITGDSLQRQMKEKQRLAASWFANGGEDPLSLTQEQR	Download Alignment We filter this alignment to remove sites that have > 75% gaps before running GREMLIN.
EcoGene:	EG11150
Length:	205 (188)
Sequences:	534
Seq/Len:	2.84

HYFA
Paralog alert: 0.73 [within 20: 0.36] - ratio of genomes with paralogs
Cluster includes: DMSB HYCB HYDN HYFA NRFC YDHX YDHY YGFS YNFG YSAA

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Scaled Score	Prob
152_L	160_R	3.043	1.00
21_A	161_A	2.364	1.00
12_C	18_C	2.312	1.00
12_C	15_C	2.263	1.00
68_I	97_I	2.126	1.00
15_C	18_C	2.106	1.00
62_V	87_L	2.037	1.00
69_S	78_N	2.03	1.00
12_C	162_C	1.918	0.99
34_H	38_A	1.9	0.99
152_L	157_A	1.864	0.99
156_P	159_V	1.856	0.99
18_C	162_C	1.778	0.99
15_C	162_C	1.736	0.98
177_R	180_K	1.696	0.98
171_T	174_S	1.668	0.98
25_V	151_F	1.667	0.98
174_S	177_R	1.663	0.98
14_G	18_C	1.647	0.98
7_A	50_V	1.615	0.97
13_T	164_N	1.604	0.97
23_S	28_T	1.56	0.96
33_Q	36_R	1.549	0.96
138_G	144_V	1.521	0.96
100_S	144_V	1.454	0.94
175_L	180_K	1.45	0.94
27_K	144_V	1.431	0.93
70_Q	75_I	1.401	0.92
14_G	162_C	1.362	0.91
49_V	52_H	1.362	0.91
74_A	153_P	1.337	0.90
36_R	39_L	1.335	0.90
13_T	163_P	1.325	0.89
124_E	128_T	1.322	0.89
7_A	167_L	1.278	0.87
125_N	128_T	1.277	0.87
86_K	101_G	1.268	0.86
21_A	83_I	1.221	0.83
12_C	163_P	1.218	0.83
124_E	127_P	1.217	0.83
106_N	118_S	1.204	0.82
17_T	164_N	1.2	0.82
81_L	138_G	1.186	0.81
87_L	90_V	1.185	0.81
73_D	186_A	1.182	0.81
110_Q	113_F	1.179	0.80
79_E	142_V	1.175	0.80
34_H	37_L	1.174	0.80
86_K	99_A	1.167	0.79
73_D	170_I	1.166	0.79
117_G	120_K	1.162	0.79
60_L	143_A	1.16	0.79
85_C	143_A	1.158	0.79
180_K	183_Q	1.157	0.79
175_L	182_K	1.152	0.78
71_R	76_Q	1.151	0.78
184_R	188_S	1.151	0.78
100_S	138_G	1.14	0.77
114_Q	117_G	1.137	0.77
78_N	89_A	1.127	0.76
24_D	161_A	1.125	0.76
13_T	16_N	1.123	0.76
14_G	17_T	1.117	0.75
176_Q	181_E	1.11	0.74
122_G	125_N	1.1	0.74
165_Q	168_R	1.096	0.73
180_K	184_R	1.096	0.73
174_S	179_M	1.094	0.73
53_H	168_R	1.093	0.73
79_E	97_I	1.09	0.73
36_R	40_A	1.084	0.72
63_C	82_C	1.072	0.71
62_V	65_V	1.065	0.70
34_H	40_A	1.064	0.70
68_I	77_L	1.058	0.69
83_I	86_K	1.042	0.68
21_A	157_A	1.041	0.68
175_L	179_M	1.039	0.67
53_H	76_Q	1.037	0.67
77_L	143_A	1.035	0.67
112_V	115_A	1.028	0.66
148_L	169_L	1.027	0.66
126_A	129_Q	1.027	0.66
85_C	91_V	1.019	0.65
94_F	184_R	1.013	0.64
159_V	167_L	1.01	0.64
65_V	68_I	1.009	0.64
25_V	53_H	1.001	0.63
20_A	69_S	1	0.63

Legend: The i and j are positions as given in the UniProt sequence. Only predictions with Scaled Score = (raw_score/average(raw_scores)) > 1 are listed. For all 3L/2 predictions, click on one of the links below.

Text file of predictions (all 3L/2 predictions)
Generate restraints for ROSETTA Structure Modeling

HHsearch Results: GREMLIN results overlayed on top 10 PDB hits:

Legend: Blue filled circles are GREMLIN results (Scaled_score >1). The grey/red filled circles underneath are pdb residue contacts (min distance < 5 Angstroms). The shade of the circles is based on 10 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	P(%)	HHΔ		Acc
1ti6B	6	0.8049	100	0.508	Contact Map	0.362
1h0hB	2	0.8146	100	0.516	Contact Map	0.413
2ivfB	1	0.8195	100	0.524	Contact Map	0.443
1kqfB	1	0.8195	100	0.542	Contact Map	0.404
2vpzB	2	0.8146	100	0.561	Contact Map	0.449
1q16B	1	0.8195	99.9	0.637	Contact Map	0.382
3mm5B	2	0.8195	99.7	0.746	Contact Map	0.187
3gyxB	6	0.7366	99.2	0.813	Contact Map	0.253
1rgvA	1	0.3805	99.2	0.815	Contact Map	0.253
2fgoA	1	0.3902	99.2	0.816	Contact Map	0.282

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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