YXBD - BACSU - GREMLIN Contacts

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YXBD - Uncharacterized protein YxbD

UniProt:	P46328	Sequences: MNIIPTCQVPKDLVSAFFQKHWGSPQMVISSGIYNCDELDGYGMLNDDNQIVGLITYIFEEDACEIISLDSVIENKGIGTALLEKAEEACRERNIKQIKLITTNDNIHALAFYQKRGYRLDRLFVNAVETARKMKPEIPLLADNKIPIRDELLLVKELQ	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	159 (153)
Sequences:	178 (153)
Seq/√Len:	12.4

BACSU - YXBD YDHI

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
110_L	154_L	5.499	1.00
64_C	95_I	4.675	1.00
103_T	128_V	4.167	1.00
126_N	129_E	4.006	0.99
130_T	133_K	3.972	0.99
87_E	156_K	3.378	0.98
119_R	150_D	3.202	0.97
53_G	79_G	2.692	0.93
87_E	118_Y	2.672	0.93
56_T	70_D	2.645	0.92
55_I	86_A	2.288	0.85
30_S	124_F	2.246	0.84
118_Y	156_K	2.196	0.82
27_M	68_S	2.173	0.82
39_L	67_I	2.173	0.82
124_F	153_L	2.128	0.80
97_Q	155_V	1.859	0.70
17_F	21_H	1.705	0.63
18_F	36_C	1.649	0.61
36_C	68_S	1.648	0.61
29_I	67_I	1.639	0.60
30_S	101_I	1.581	0.57
86_A	90_C	1.577	0.57
55_I	66_I	1.540	0.55
83_L	91_R	1.487	0.52
120_L	154_L	1.470	0.52
24_S	103_T	1.450	0.51
6_T	11_K	1.422	0.49
24_S	54_L	1.422	0.49
52_V	143_D	1.419	0.49
22_W	105_D	1.410	0.49
66_I	118_Y	1.409	0.49
128_V	131_A	1.346	0.45
12_D	16_A	1.346	0.45
54_L	70_D	1.327	0.44
120_L	147_P	1.318	0.44
71_S	74_E	1.311	0.44
111_A	142_A	1.287	0.42
49_N	60_E	1.280	0.42
120_L	152_L	1.273	0.42
32_G	67_I	1.240	0.40
42_Y	55_I	1.238	0.40
35_N	38_E	1.229	0.39
68_S	74_E	1.205	0.38
40_D	67_I	1.202	0.38
30_S	128_V	1.196	0.38
80_T	116_R	1.188	0.38
29_I	34_Y	1.184	0.37
97_Q	122_R	1.174	0.37
110_L	120_L	1.165	0.36
91_R	98_I	1.124	0.34
59_F	64_C	1.122	0.34
18_F	156_K	1.113	0.34
86_A	98_I	1.111	0.34
4_I	10_P	1.108	0.34
87_E	150_D	1.097	0.33
107_I	144_N	1.092	0.33
56_T	68_S	1.070	0.32
18_F	87_E	1.064	0.32
42_Y	71_S	1.029	0.30
32_G	156_K	1.026	0.30
95_I	100_L	1.023	0.30
120_L	123_L	1.007	0.29
32_G	36_C	0.992	0.29
54_L	103_T	0.984	0.28
107_I	121_D	0.980	0.28
108_H	144_N	0.969	0.28
119_R	149_R	0.965	0.28
32_G	87_E	0.965	0.28
27_M	36_C	0.952	0.27
42_Y	83_L	0.945	0.27
45_L	96_K	0.944	0.27
10_P	85_K	0.931	0.26
14_V	24_S	0.929	0.26
101_I	124_F	0.925	0.26
61_E	93_R	0.923	0.26
94_N	157_E	0.920	0.26
24_S	128_V	0.919	0.26
62_D	95_I	0.916	0.26
31_S	67_I	0.915	0.26
14_V	123_L	0.909	0.25
37_D	152_L	0.907	0.25
28_V	33_I	0.905	0.25
74_E	144_N	0.899	0.25
126_N	149_R	0.899	0.25
75_N	154_L	0.898	0.25
44_M	97_Q	0.898	0.25
73_I	76_K	0.893	0.25
63_A	99_K	0.889	0.25
142_A	148_I	0.880	0.24
36_C	150_D	0.880	0.24
90_C	95_I	0.879	0.24
8_Q	61_E	0.874	0.24
150_D	156_K	0.870	0.24
26_Q	71_S	0.869	0.24
59_F	63_A	0.865	0.24
49_N	62_D	0.861	0.24
6_T	41_G	0.856	0.23
38_E	62_D	0.852	0.23
35_N	40_D	0.850	0.23
30_S	67_I	0.847	0.23
25_P	35_N	0.844	0.23
62_D	80_T	0.836	0.23
66_I	126_N	0.832	0.22
59_F	95_I	0.829	0.22
17_F	36_C	0.828	0.22
57_Y	88_E	0.828	0.22
30_S	34_Y	0.827	0.22
41_G	66_I	0.824	0.22
82_L	151_E	0.824	0.22
42_Y	70_D	0.820	0.22
103_T	123_L	0.819	0.22
55_I	78_I	0.812	0.22
4_I	18_F	0.810	0.22
34_Y	87_E	0.810	0.22
131_A	156_K	0.809	0.22
11_K	148_I	0.801	0.21
61_E	96_K	0.789	0.21
32_G	118_Y	0.789	0.21
45_L	84_E	0.787	0.21
120_L	125_V	0.787	0.21
86_A	95_I	0.783	0.21
115_K	126_N	0.783	0.21
76_K	115_K	0.778	0.21
79_G	102_T	0.773	0.20
111_A	144_N	0.771	0.20
80_T	108_H	0.770	0.20
26_Q	33_I	0.765	0.20
30_S	36_C	0.759	0.20
52_V	67_I	0.755	0.20
36_C	40_D	0.750	0.20
115_K	134_M	0.746	0.20
46_N	96_K	0.746	0.20
92_E	98_I	0.741	0.19
30_S	150_D	0.738	0.19
21_H	126_N	0.737	0.19
11_K	31_S	0.734	0.19
98_I	120_L	0.724	0.19
59_F	100_L	0.720	0.19
128_V	148_I	0.717	0.19
65_E	102_T	0.715	0.19
61_E	94_N	0.711	0.18
16_A	48_D	0.711	0.18
76_K	96_K	0.704	0.18
41_G	71_S	0.699	0.18
57_Y	89_A	0.699	0.18
91_R	123_L	0.697	0.18
80_T	89_A	0.692	0.18
34_Y	67_I	0.689	0.18
64_C	86_A	0.685	0.18
74_E	108_H	0.685	0.18
60_E	66_I	0.682	0.18
89_A	118_Y	0.676	0.17
36_C	72_V	0.675	0.17
90_C	142_A	0.674	0.17
21_H	72_V	0.665	0.17
49_N	121_D	0.664	0.17
57_Y	135_K	0.662	0.17
107_I	120_L	0.661	0.17
125_V	155_V	0.658	0.17
18_F	54_L	0.658	0.17
49_N	89_A	0.653	0.17
31_S	34_Y	0.652	0.17
75_N	108_H	0.652	0.17
108_H	155_V	0.650	0.17
57_Y	131_A	0.648	0.17
85_K	94_N	0.647	0.17
85_K	142_A	0.645	0.17
4_I	8_Q	0.644	0.17
94_N	141_L	0.642	0.16
67_I	99_K	0.640	0.16
20_K	137_E	0.633	0.16
147_P	155_V	0.632	0.16
119_R	129_E	0.630	0.16
61_E	88_E	0.629	0.16
34_Y	156_K	0.624	0.16
49_N	92_E	0.623	0.16
86_A	154_L	0.619	0.16
18_F	31_S	0.618	0.16
41_G	137_E	0.613	0.16
58_I	108_H	0.611	0.16
71_S	75_N	0.609	0.16
124_F	152_L	0.603	0.15
4_I	19_Q	0.595	0.15
21_H	70_D	0.595	0.15
17_F	83_L	0.588	0.15
120_L	142_A	0.587	0.15
18_F	30_S	0.582	0.15
79_G	100_L	0.581	0.15
34_Y	99_K	0.575	0.15
12_D	20_K	0.575	0.15
53_G	102_T	0.556	0.14
41_G	116_R	0.555	0.14
88_E	141_L	0.554	0.14
21_H	149_R	0.554	0.14
93_R	107_I	0.552	0.14
73_I	96_K	0.550	0.14
68_S	156_K	0.550	0.14
37_D	60_E	0.550	0.14
58_I	145_K	0.545	0.14
33_I	72_V	0.545	0.14
4_I	43_G	0.542	0.14
46_N	50_Q	0.540	0.14
21_H	54_L	0.538	0.14
68_S	140_L	0.536	0.14
60_E	67_I	0.536	0.14
131_A	135_K	0.535	0.14
63_A	71_S	0.534	0.14
88_E	91_R	0.532	0.14
102_T	151_E	0.531	0.14
16_A	141_L	0.531	0.14
111_A	146_I	0.526	0.13
14_V	35_N	0.525	0.13
81_A	137_E	0.525	0.13
107_I	147_P	0.521	0.13
8_Q	140_L	0.521	0.13
111_A	116_R	0.521	0.13
49_N	134_M	0.518	0.13
25_P	37_D	0.517	0.13
124_F	149_R	0.515	0.13
125_V	157_E	0.511	0.13
64_C	90_C	0.510	0.13
41_G	55_I	0.509	0.13
139_P	151_E	0.507	0.13
121_D	127_A	0.506	0.13
10_P	136_P	0.504	0.13
23_G	154_L	0.503	0.13
98_I	122_R	0.502	0.13
111_A	143_D	0.502	0.13
6_T	123_L	0.500	0.13

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
1y9kA	1	0.9245	99.6	0.769	Contact Map
3dr6A	2	0.9057	99.6	0.772	Contact Map
2j8mA	2	0.9119	99.6	0.772	Contact Map
2oh1A	1	0.8616	99.5	0.778	Contact Map
1n71A	4	0.8805	99.5	0.778	Contact Map
4luaA	1	0.8868	99.5	0.781	Contact Map
3zj0A	1	0.8428	99.5	0.781	Contact Map
2fiaA	1	0.8931	99.5	0.784	Contact Map
1s3zA	2	0.8176	99.5	0.784	Contact Map
3g8wA	2	0.8931	99.5	0.784	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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