YFIT - BACSU - GREMLIN Contacts

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YFIT - Putative metal-dependent hydrolase YfiT

UniProt:	O31562	Sequences: MTSVNLSYPIGEYKPRESISKEQKDKWIQVLEEVPAKLKQAVEVMTDSQLDTPYRDGGWTVRQVVHHLADSHMNSYIRFKLSLTEETPAIRPYDEKAWSELKDSKTADPSGSLALLQELHGRWTALLRTLTDQQFKRGFYHPDTKEIITLENALGLYVWHSHHHIAHITELSRRMGWS	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	178 (146)
Sequences:	1054 (867)
Seq/√Len:	71.8

BACSU - YFIT

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
94_D	97_A	5.040	1.00
32_E	128_R	4.931	1.00
39_K	117_Q	4.065	1.00
46_T	49_Q	3.619	1.00
134_Q	137_R	3.433	1.00
131_T	134_Q	3.163	1.00
51_D	62_R	3.147	1.00
135_F	154_L	2.963	1.00
79_F	150_L	2.492	1.00
71_S	93_Y	2.351	1.00
37_K	162_H	2.349	1.00
136_K	151_E	2.309	1.00
97_A	100_E	2.000	1.00
116_L	161_S	1.966	1.00
87_T	138_G	1.940	1.00
72_H	120_H	1.918	1.00
66_H	112_S	1.898	1.00
140_Y	145_K	1.813	1.00
79_F	127_L	1.790	1.00
71_S	157_Y	1.740	1.00
81_L	88_P	1.722	1.00
66_H	104_S	1.720	1.00
82_S	139_F	1.690	1.00
130_L	135_F	1.649	1.00
86_E	137_R	1.609	0.99
93_Y	157_Y	1.535	0.99
61_V	168_I	1.523	0.99
24_K	151_E	1.517	0.99
34_V	161_S	1.456	0.99
92_P	142_P	1.412	0.98
49_Q	52_T	1.392	0.98
71_S	75_S	1.356	0.98
42_V	65_V	1.346	0.98
30_V	162_H	1.342	0.98
73_M	77_I	1.336	0.98
50_L	109_P	1.320	0.98
27_W	155_G	1.317	0.98
136_K	149_T	1.317	0.98
75_S	153_A	1.308	0.97
31_L	158_V	1.297	0.97
53_P	63_Q	1.275	0.97
60_T	105_K	1.246	0.97
110_S	114_A	1.236	0.96
53_P	57_G	1.228	0.96
139_F	153_A	1.197	0.96
72_H	123_W	1.175	0.95
148_I	153_A	1.172	0.95
111_G	118_E	1.165	0.95
81_L	86_E	1.156	0.95
69_A	112_S	1.154	0.95
75_S	93_Y	1.149	0.95
115_L	118_E	1.139	0.94
51_D	105_K	1.129	0.94
74_N	98_W	1.129	0.94
41_A	44_V	1.122	0.94
103_D	106_T	1.115	0.94
81_L	91_R	1.112	0.94
81_L	92_P	1.107	0.93
115_L	119_L	1.099	0.93
68_L	165_I	1.083	0.93
39_K	110_S	1.078	0.92
64_V	168_I	1.070	0.92
107_A	115_L	1.063	0.92
29_Q	33_E	1.051	0.92
30_V	158_V	1.050	0.91
24_K	135_F	1.041	0.91
127_L	154_L	1.037	0.91
39_K	113_L	1.032	0.91
40_Q	43_E	1.027	0.91
114_A	117_Q	1.020	0.90
45_M	166_A	1.011	0.90
38_L	165_I	1.003	0.89
87_T	140_Y	1.001	0.89
63_Q	99_S	0.994	0.89
28_I	127_L	0.985	0.89
75_S	156_L	0.985	0.89
107_A	111_G	0.970	0.88
53_P	60_T	0.969	0.88
45_M	49_Q	0.957	0.87
114_A	121_G	0.927	0.85
34_V	165_I	0.925	0.85
69_A	115_L	0.920	0.85
32_E	121_G	0.918	0.85
130_L	134_Q	0.910	0.84
85_E	137_R	0.895	0.83
46_T	168_I	0.893	0.83
29_Q	43_E	0.891	0.83
35_P	38_L	0.882	0.82
133_Q	137_R	0.880	0.82
54_Y	159_W	0.879	0.82
47_D	51_D	0.864	0.81
30_V	161_S	0.860	0.81
80_K	126_L	0.856	0.81
65_V	112_S	0.847	0.80
120_H	161_S	0.844	0.80
29_Q	166_A	0.842	0.79
75_S	79_F	0.833	0.79
71_S	156_L	0.832	0.79
37_K	169_T	0.827	0.78
36_A	117_Q	0.822	0.78
154_L	158_V	0.822	0.78
38_L	161_S	0.810	0.77
41_A	165_I	0.809	0.77
62_R	109_P	0.800	0.76
73_M	115_L	0.797	0.76
31_L	161_S	0.794	0.75
71_S	74_N	0.776	0.74
36_A	136_K	0.768	0.73
53_P	61_V	0.768	0.73
126_L	130_L	0.765	0.73
45_M	61_V	0.760	0.72
85_E	88_P	0.759	0.72
54_Y	163_H	0.756	0.72
83_L	130_L	0.747	0.71
123_W	157_Y	0.742	0.70
36_A	40_Q	0.739	0.70
77_I	120_H	0.738	0.70
34_V	68_L	0.737	0.70
133_Q	146_E	0.737	0.70
42_V	129_T	0.735	0.70
42_V	50_L	0.727	0.69
126_L	129_T	0.720	0.68
83_L	126_L	0.718	0.68
35_P	64_V	0.717	0.68
64_V	68_L	0.716	0.68
57_G	163_H	0.715	0.67
119_L	126_L	0.713	0.67
26_K	29_Q	0.708	0.67
138_G	149_T	0.702	0.66
130_L	150_L	0.699	0.66
159_W	163_H	0.692	0.65
62_R	112_S	0.691	0.65
58_G	159_W	0.685	0.64
25_D	128_R	0.685	0.64
27_W	56_D	0.683	0.64
26_K	30_V	0.681	0.64
62_R	76_Y	0.680	0.64
74_N	90_I	0.677	0.63
68_L	161_S	0.674	0.63
76_Y	122_R	0.670	0.62
99_S	104_S	0.670	0.62
116_L	120_H	0.670	0.62
84_T	163_H	0.669	0.62
58_G	163_H	0.663	0.62
80_K	98_W	0.653	0.60
71_S	95_E	0.651	0.60
70_D	98_W	0.636	0.58
41_A	169_T	0.633	0.58
54_Y	167_H	0.632	0.58
119_L	123_W	0.627	0.57
95_E	120_H	0.626	0.57
38_L	68_L	0.623	0.57
35_P	116_L	0.623	0.57
148_I	152_N	0.619	0.56
67_H	160_H	0.618	0.56
27_W	37_K	0.618	0.56
49_Q	64_V	0.609	0.55
55_R	159_W	0.607	0.55
31_L	115_L	0.604	0.55
120_H	139_F	0.603	0.54
35_P	161_S	0.602	0.54
54_Y	58_G	0.601	0.54
82_S	150_L	0.600	0.54
128_R	135_F	0.597	0.54
68_L	116_L	0.596	0.54
72_H	167_H	0.586	0.52
141_H	145_K	0.583	0.52
120_H	123_W	0.579	0.51
55_R	58_G	0.576	0.51
52_T	61_V	0.572	0.51
74_N	157_Y	0.572	0.51
29_Q	113_L	0.571	0.50
117_Q	121_G	0.570	0.50
51_D	99_S	0.565	0.50
107_A	125_A	0.561	0.49
103_D	137_R	0.560	0.49
86_E	104_S	0.559	0.49
121_G	125_A	0.556	0.49
80_K	122_R	0.555	0.49
38_L	116_L	0.554	0.48
82_S	87_T	0.553	0.48
67_H	164_H	0.552	0.48
133_Q	136_K	0.552	0.48
90_I	95_E	0.548	0.48
84_T	159_W	0.548	0.48
53_P	58_G	0.546	0.47
72_H	157_Y	0.545	0.47
29_Q	32_E	0.544	0.47
43_E	128_R	0.543	0.47
150_L	157_Y	0.543	0.47
55_R	163_H	0.541	0.47
30_V	34_V	0.541	0.47
33_E	37_K	0.540	0.47
70_D	99_S	0.538	0.46
63_Q	100_E	0.537	0.46
24_K	165_I	0.535	0.46
29_Q	40_Q	0.533	0.46
27_W	30_V	0.532	0.46
26_K	43_E	0.530	0.45
75_S	157_Y	0.528	0.45
73_M	122_R	0.528	0.45
139_F	152_N	0.525	0.45
94_D	114_A	0.525	0.45
79_F	153_A	0.520	0.44
132_D	152_N	0.518	0.44
36_A	51_D	0.514	0.44
72_H	161_S	0.513	0.43
42_V	158_V	0.512	0.43
85_E	91_R	0.511	0.43
43_E	113_L	0.510	0.43
24_K	108_D	0.510	0.43
125_A	137_R	0.509	0.43
25_D	29_Q	0.507	0.43
123_W	161_S	0.506	0.43
66_H	71_S	0.506	0.43
160_H	164_H	0.504	0.42
28_I	39_K	0.504	0.42
76_Y	119_L	0.501	0.42
68_L	158_V	0.500	0.42

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
1rxqA	3	0.9831	100	0.427	Contact Map
2rd9A	4	0.9663	99.9	0.554	Contact Map
2yqyA	2	0.7079	99.9	0.581	Contact Map
2ou6A	2	0.9157	99.7	0.648	Contact Map
3dkaA	2	0.7809	99.7	0.649	Contact Map
3gorA	2	0.8202	99.7	0.65	Contact Map
3di5A	1	0.809	99.7	0.653	Contact Map
2hkvA	2	0.7921	99.7	0.654	Contact Map
4n6cA	1	0.9326	99.7	0.655	Contact Map
3cexA	2	0.8596	99.7	0.66	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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