XKDA - BACSU - GREMLIN Contacts

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XKDA - Phage-like element PBSX protein XkdA

UniProt:	P39780	Sequences: MGDYLSHLEEYVKNLYGRLGITSPHHIDMLKIAKDLDIWVHFEDMGSMMVKYDGMYSIVLNQKKSREEQWEDFGHELCHVLKHAGNHFQMNKLFRELQEFQANQFMYHFCVPTFMLLQMELPQWRSQALATIAAVFRVTKEFADKRLDMFERRKAGIQFQKRLAYLLSHKRPNAYEEGDQQHLQVAEEKALYHIGKNI	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	198 (157)
Sequences:	164 (133)
Seq/√Len:	10.6

BACSU - XKDA YQAB

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
97_L	101_Q	3.711	0.98
5_L	10_E	3.649	0.98
71_E	139_T	3.465	0.97
108_H	150_F	3.014	0.94
6_S	153_R	2.917	0.93
87_H	98_Q	2.594	0.88
109_F	149_M	2.410	0.83
101_Q	109_F	2.347	0.82
138_V	143_A	2.259	0.79
85_G	98_Q	2.247	0.78
13_K	114_F	2.169	0.76
108_H	113_T	2.146	0.75
28_D	33_A	2.142	0.75
125_R	151_E	2.128	0.74
114_F	143_A	2.092	0.73
90_M	147_L	2.088	0.73
113_T	150_F	2.038	0.71
74_G	109_F	2.016	0.70
15_L	36_L	2.005	0.70
94_F	97_L	1.927	0.67
24_P	115_M	1.793	0.61
149_M	153_R	1.787	0.60
58_I	135_V	1.674	0.55
74_G	108_H	1.624	0.53
111_V	132_I	1.616	0.53
19_L	36_L	1.616	0.53
40_V	60_L	1.588	0.51
16_Y	32_I	1.581	0.51
16_Y	109_F	1.565	0.50
39_W	57_S	1.554	0.50
16_Y	73_F	1.534	0.49
44_D	62_Q	1.512	0.48
50_V	72_D	1.481	0.46
5_L	13_K	1.456	0.45
76_E	99_E	1.445	0.45
24_P	138_V	1.445	0.45
70_W	74_G	1.435	0.44
20_G	35_D	1.423	0.43
101_Q	108_H	1.413	0.43
82_K	91_N	1.405	0.43
3_D	82_K	1.398	0.42
44_D	64_K	1.347	0.40
82_K	101_Q	1.330	0.39
74_G	101_Q	1.317	0.39
4_Y	65_S	1.292	0.38
133_A	151_E	1.290	0.37
13_K	129_L	1.275	0.37
38_I	103_N	1.258	0.36
119_M	135_V	1.232	0.35
42_F	94_F	1.223	0.35
150_F	153_R	1.219	0.34
16_Y	82_K	1.192	0.33
105_F	109_F	1.191	0.33
110_C	113_T	1.189	0.33
11_Y	82_K	1.187	0.33
80_V	93_L	1.178	0.33
97_L	159_F	1.169	0.32
74_G	150_F	1.168	0.32
5_L	78_C	1.167	0.32
42_F	121_L	1.149	0.31
79_H	99_E	1.148	0.31
107_Y	142_F	1.148	0.31
105_F	143_A	1.138	0.31
70_W	142_F	1.129	0.31
14_N	33_A	1.120	0.30
40_V	71_E	1.120	0.30
110_C	142_F	1.114	0.30
113_T	142_F	1.112	0.30
132_I	143_A	1.107	0.30
16_Y	105_F	1.097	0.29
75_H	99_E	1.088	0.29
8_L	16_Y	1.085	0.29
114_F	119_M	1.080	0.29
54_G	143_A	1.074	0.28
61_N	69_Q	1.070	0.28
128_A	143_A	1.065	0.28
6_S	149_M	1.055	0.28
111_V	118_Q	1.037	0.27
78_C	105_F	1.037	0.27
57_S	84_A	1.013	0.26
29_M	109_F	1.011	0.26
8_L	82_K	1.005	0.26
117_L	150_F	1.001	0.26
64_K	68_E	0.996	0.26
96_E	135_V	0.994	0.25
74_G	113_T	0.988	0.25
122_P	131_T	0.985	0.25
74_G	110_C	0.973	0.25
36_L	51_K	0.970	0.25
107_Y	139_T	0.962	0.24
109_F	150_F	0.962	0.24
11_Y	137_R	0.959	0.24
20_G	81_L	0.957	0.24
27_I	64_K	0.954	0.24
11_Y	78_C	0.946	0.24
10_E	25_H	0.931	0.23
108_H	149_M	0.924	0.23
51_K	59_V	0.911	0.23
108_H	153_R	0.897	0.22
156_G	159_F	0.890	0.22
87_H	94_F	0.889	0.22
33_A	93_L	0.881	0.22
19_L	57_S	0.881	0.22
78_C	82_K	0.880	0.22
19_L	32_I	0.871	0.21
16_Y	78_C	0.870	0.21
6_S	9_E	0.869	0.21
80_V	116_L	0.862	0.21
109_F	113_T	0.862	0.21
90_M	115_M	0.855	0.21
29_M	70_W	0.855	0.21
12_V	130_A	0.853	0.21
77_L	109_F	0.851	0.21
97_L	150_F	0.850	0.21
70_W	104_Q	0.841	0.20
92_K	134_A	0.829	0.20
87_H	99_E	0.823	0.20
138_V	142_F	0.821	0.20
5_L	114_F	0.821	0.20
110_C	137_R	0.812	0.20
105_F	115_M	0.805	0.19
83_H	87_H	0.800	0.19
48_M	153_R	0.795	0.19
11_Y	36_L	0.790	0.19
58_I	83_H	0.782	0.19
40_V	106_M	0.780	0.19
26_H	70_W	0.779	0.19
44_D	63_K	0.767	0.18
35_D	123_Q	0.763	0.18
112_P	146_R	0.747	0.18
112_P	136_F	0.747	0.18
136_F	146_R	0.747	0.18
33_A	90_M	0.747	0.18
113_T	143_A	0.746	0.18
122_P	128_A	0.744	0.18
6_S	107_Y	0.743	0.18
50_V	57_S	0.737	0.17
49_M	80_V	0.736	0.17
60_L	77_L	0.734	0.17
103_N	134_A	0.734	0.17
37_D	81_L	0.729	0.17
114_F	120_E	0.727	0.17
46_G	60_L	0.724	0.17
94_F	147_L	0.723	0.17
55_M	144_D	0.714	0.17
82_K	153_R	0.711	0.17
39_W	55_M	0.708	0.17
9_E	115_M	0.703	0.16
76_E	87_H	0.702	0.16
94_F	98_Q	0.700	0.16
18_R	148_D	0.688	0.16
128_A	132_I	0.687	0.16
28_D	44_D	0.680	0.16
94_F	105_F	0.678	0.16
61_N	148_D	0.676	0.16
82_K	97_L	0.676	0.16
35_D	92_K	0.673	0.16
59_V	149_M	0.671	0.16
103_N	130_A	0.670	0.16
14_N	92_K	0.670	0.16
18_R	64_K	0.666	0.16
108_H	116_L	0.665	0.16
82_K	109_F	0.659	0.15
148_D	152_R	0.659	0.15
20_G	80_V	0.656	0.15
32_I	78_C	0.655	0.15
68_E	118_Q	0.655	0.15
62_Q	65_S	0.651	0.15
47_S	72_D	0.648	0.15
119_M	143_A	0.644	0.15
60_L	122_P	0.636	0.15
113_T	118_Q	0.635	0.15
101_Q	150_F	0.629	0.15
152_R	157_I	0.627	0.15
101_Q	149_M	0.622	0.14
75_H	105_F	0.622	0.14
60_L	140_K	0.620	0.14
62_Q	145_K	0.618	0.14
26_H	35_D	0.616	0.14
15_L	95_R	0.607	0.14
133_A	141_E	0.606	0.14
79_H	112_P	0.606	0.14
79_H	136_F	0.606	0.14
79_H	146_R	0.606	0.14
16_Y	33_A	0.604	0.14
73_F	97_L	0.604	0.14
20_G	144_D	0.598	0.14
14_N	27_I	0.593	0.14
15_L	26_H	0.593	0.14
109_F	153_R	0.592	0.14
70_W	109_F	0.586	0.14
91_N	101_Q	0.584	0.14
14_N	18_R	0.582	0.14
54_G	130_A	0.582	0.14
51_K	80_V	0.579	0.14
65_S	116_L	0.578	0.13
42_F	68_E	0.577	0.13
73_F	94_F	0.574	0.13
103_N	116_L	0.573	0.13
24_P	111_V	0.566	0.13
69_Q	94_F	0.566	0.13
4_Y	44_D	0.561	0.13
31_K	62_Q	0.560	0.13
97_L	108_H	0.555	0.13
59_V	109_F	0.555	0.13
20_G	66_R	0.555	0.13
4_Y	92_K	0.553	0.13
13_K	134_A	0.552	0.13
73_F	82_K	0.551	0.13
111_V	145_K	0.550	0.13
73_F	83_H	0.547	0.13
29_M	110_C	0.547	0.13
28_D	89_Q	0.545	0.13
104_Q	150_F	0.545	0.13
70_W	110_C	0.545	0.13
142_F	149_M	0.543	0.13
110_C	114_F	0.541	0.13
110_C	150_F	0.538	0.13
38_I	124_W	0.525	0.12
30_L	42_F	0.523	0.12
34_K	53_D	0.518	0.12
69_Q	119_M	0.517	0.12
74_G	149_M	0.515	0.12
13_K	131_T	0.512	0.12
119_M	132_I	0.512	0.12
137_R	140_K	0.511	0.12
63_K	91_N	0.509	0.12
35_D	44_D	0.508	0.12
128_A	133_A	0.506	0.12
113_T	153_R	0.505	0.12
86_N	117_L	0.503	0.12
96_E	116_L	0.503	0.12
75_H	143_A	0.502	0.12
95_R	138_V	0.501	0.12
32_I	138_V	0.501	0.12
48_M	88_F	0.500	0.12

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
3dteA	2	0.9899	99.7	0.758	Contact Map
4aw6A	2	0.7121	92.7	0.923	Contact Map
4il3A	1	0.7475	90.2	0.928	Contact Map
3cqbA	4	0.404	80.2	0.938	Contact Map
4jixA	2	0.5253	70.6	0.942	Contact Map
3c37A	1	0.7879	61.4	0.946	Contact Map
4qhjA	2	0.4899	60.4	0.946	Contact Map
4jiuA	1	0.4899	59.1	0.946	Contact Map
4in9A	1	0.5808	35	0.954	Contact Map
1j7nA	2	0.8182	29.6	0.955	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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