YXKA - BACSU - GREMLIN Contacts

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YXKA - Uncharacterized protein YxkA

UniProt:	P55185	Sequences: MNIYVEANPYLHDKYSKYADEKYKREGNPFVSFPIHFDDIPSGAKTLALTFIDHDAIPVCGFSWIHWTAANIPAYIGELPEHASEERQDLMIQGQNSFASPLAGSNDPKVIHQYCGPTPPDKDHAYTLTVYALDAELNLQPGFYLNELYQEMKEHILAETSIELLARV	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	168 (141)
Sequences:	2538 (1756)
Seq/√Len:	147.9

ECOLI - YBHB YBCL
BACSU - YXKA
HALSA - Q9HND1
SULSO - Q7LXJ9

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
134_D	155_H	5.518	1.00
40_I	47_L	4.213	1.00
51_F	128_L	3.019	1.00
17_K	118_T	2.947	1.00
14_K	81_E	2.919	1.00
49_L	130_V	2.892	1.00
98_F	115_C	2.692	1.00
10_Y	165_L	2.566	1.00
4_Y	81_E	2.291	1.00
71_N	138_N	2.244	1.00
6_E	9_P	2.164	1.00
45_K	135_A	2.081	1.00
127_T	163_E	2.014	1.00
4_Y	34_P	1.977	1.00
47_L	74_A	1.964	1.00
129_T	161_S	1.955	1.00
5_V	164_L	1.849	1.00
48_A	148_L	1.809	1.00
40_I	77_G	1.797	1.00
133_L	152_M	1.796	1.00
34_P	78_E	1.781	1.00
11_L	117_P	1.729	1.00
70_A	94_G	1.666	1.00
30_F	116_G	1.654	1.00
94_G	148_L	1.618	1.00
36_H	78_E	1.617	1.00
32_S	79_L	1.560	1.00
71_N	136_E	1.535	1.00
37_F	79_L	1.514	1.00
129_T	159_E	1.465	1.00
48_A	152_M	1.461	1.00
72_I	76_I	1.427	1.00
55_D	125_A	1.375	1.00
82_H	85_E	1.346	1.00
123_D	167_R	1.339	1.00
70_A	148_L	1.335	1.00
130_V	160_T	1.324	1.00
148_L	152_M	1.297	1.00
46_T	71_N	1.295	1.00
11_L	164_L	1.283	1.00
15_Y	81_E	1.232	1.00
65_I	145_L	1.228	1.00
151_E	154_E	1.191	1.00
46_T	136_E	1.187	1.00
152_M	156_I	1.169	1.00
52_I	63_S	1.168	1.00
41_P	132_A	1.155	1.00
53_D	66_H	1.152	1.00
131_Y	152_M	1.150	1.00
70_A	143_F	1.131	0.99
80_P	83_A	1.125	0.99
144_Y	147_E	1.123	0.99
114_Y	117_P	1.122	0.99
48_A	133_L	1.119	0.99
40_I	44_A	1.116	0.99
17_K	115_C	1.071	0.99
68_T	148_L	1.068	0.99
95_Q	99_A	1.065	0.99
10_Y	167_R	1.057	0.99
5_V	12_H	1.057	0.99
127_T	161_S	1.056	0.99
62_F	146_N	1.051	0.99
137_L	152_M	1.051	0.99
47_L	130_V	1.040	0.99
44_A	157_L	1.038	0.99
14_K	31_V	1.037	0.99
47_L	77_G	1.029	0.99
64_W	98_F	1.025	0.99
84_S	93_Q	1.018	0.99
71_N	137_L	1.008	0.99
41_P	44_A	1.006	0.99
15_Y	34_P	1.006	0.99
71_N	92_I	0.993	0.99
68_T	94_G	0.991	0.99
131_Y	156_I	0.990	0.99
88_Q	91_M	0.989	0.99
93_Q	113_Q	0.967	0.98
100_S	113_Q	0.966	0.98
66_H	124_H	0.957	0.98
119_P	124_H	0.956	0.98
40_I	43_G	0.946	0.98
37_F	47_L	0.945	0.98
66_H	119_P	0.945	0.98
52_I	65_I	0.943	0.98
31_V	81_E	0.941	0.98
14_K	20_D	0.916	0.98
7_A	163_E	0.905	0.97
125_A	163_E	0.899	0.97
13_D	18_Y	0.891	0.97
43_G	157_L	0.888	0.97
33_F	128_L	0.885	0.97
67_W	93_Q	0.882	0.97
16_S	166_A	0.876	0.97
143_F	148_L	0.869	0.97
53_D	124_H	0.868	0.97
35_I	162_I	0.861	0.97
52_I	129_T	0.859	0.97
17_K	98_F	0.858	0.97
43_G	158_A	0.857	0.97
52_I	60_C	0.851	0.96
10_Y	123_D	0.848	0.96
17_K	30_F	0.835	0.96
16_S	19_A	0.827	0.96
8_N	163_E	0.826	0.96
61_G	149_Y	0.824	0.96
16_S	20_D	0.820	0.96
44_A	132_A	0.817	0.95
56_A	60_C	0.806	0.95
38_D	77_G	0.806	0.95
51_F	114_Y	0.804	0.95
35_I	128_L	0.804	0.95
44_A	47_L	0.790	0.95
68_T	145_L	0.784	0.94
32_S	67_W	0.773	0.94
86_E	89_D	0.768	0.94
70_A	92_I	0.760	0.93
134_D	156_I	0.744	0.93
54_H	127_T	0.741	0.92
112_H	142_G	0.738	0.92
147_E	151_E	0.722	0.91
84_S	91_M	0.717	0.91
143_F	147_E	0.713	0.91
64_W	115_C	0.712	0.91
140_Q	143_F	0.711	0.91
10_Y	13_D	0.711	0.91
5_V	9_P	0.710	0.91
11_L	15_Y	0.705	0.90
121_D	167_R	0.703	0.90
35_I	49_L	0.700	0.90
56_A	64_W	0.699	0.90
32_S	83_A	0.699	0.90
62_F	65_I	0.690	0.89
5_V	162_I	0.690	0.89
67_W	84_S	0.686	0.89
95_Q	142_G	0.682	0.89
53_D	119_P	0.682	0.89
69_A	91_M	0.682	0.89
86_E	91_M	0.678	0.89
139_L	143_F	0.675	0.88
30_F	98_F	0.674	0.88
50_T	152_M	0.674	0.88
145_L	149_Y	0.665	0.88
30_F	115_C	0.661	0.87
31_V	82_H	0.653	0.87
122_K	167_R	0.650	0.87
71_N	135_A	0.649	0.86
41_P	47_L	0.641	0.86
69_A	93_Q	0.638	0.85
139_L	148_L	0.636	0.85
19_A	115_C	0.636	0.85
96_N	100_S	0.631	0.85
48_A	94_G	0.623	0.84
17_K	20_D	0.622	0.84
156_I	159_E	0.621	0.84
49_L	72_I	0.620	0.84
41_P	158_A	0.617	0.84
4_Y	15_Y	0.616	0.83
66_H	116_G	0.612	0.83
13_D	16_S	0.607	0.83
92_I	95_Q	0.604	0.82
56_A	63_S	0.604	0.82
12_H	15_Y	0.603	0.82
39_D	47_L	0.598	0.82
15_Y	117_P	0.597	0.82
154_E	157_L	0.592	0.81
69_A	72_I	0.592	0.81
53_D	56_A	0.591	0.81
147_E	150_Q	0.589	0.81
92_I	97_S	0.588	0.81
36_H	77_G	0.584	0.80
18_Y	166_A	0.577	0.79
37_F	130_V	0.576	0.79
9_P	165_L	0.572	0.79
37_F	158_A	0.568	0.78
37_F	70_A	0.563	0.78
20_D	147_E	0.562	0.78
87_R	91_M	0.559	0.77
100_S	115_C	0.558	0.77
64_W	150_Q	0.557	0.77
153_K	159_E	0.555	0.77
123_D	165_L	0.555	0.77
69_A	84_S	0.554	0.77
15_Y	31_V	0.553	0.76
5_V	11_L	0.552	0.76
96_N	115_C	0.552	0.76
120_P	124_H	0.550	0.76
93_Q	112_H	0.546	0.75
48_A	131_Y	0.542	0.75
139_L	142_G	0.542	0.75
54_H	120_P	0.539	0.75
64_W	120_P	0.535	0.74
64_W	147_E	0.534	0.74
52_I	145_L	0.534	0.74
46_T	155_H	0.534	0.74
73_P	77_G	0.533	0.74
39_D	77_G	0.530	0.73
52_I	127_T	0.526	0.73
129_T	149_Y	0.524	0.73
66_H	120_P	0.524	0.73
55_D	124_H	0.523	0.72
52_I	149_Y	0.520	0.72
31_V	85_E	0.517	0.72
64_W	97_S	0.517	0.72
57_I	63_S	0.514	0.71
33_F	37_F	0.510	0.71
84_S	87_R	0.509	0.70
46_T	135_A	0.509	0.70
84_S	88_Q	0.508	0.70
10_Y	16_S	0.507	0.70
12_H	114_Y	0.505	0.70
133_L	154_E	0.502	0.69
56_A	120_P	0.500	0.69

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
1fjjA	2	0.8929	100	0.22	Contact Map
2evvA	2	0.9762	100	0.227	Contact Map
3n08A	2	0.8571	100	0.236	Contact Map
1fuxA	2	0.8988	100	0.245	Contact Map
4begA	4	0.8988	100	0.254	Contact Map
1wpxB	1	0.875	99.9	0.546	Contact Map
2jyzA	1	0.7679	99.9	0.569	Contact Map
2gzqA	1	0.8512	99.9	0.585	Contact Map
1vw41	1	0.8571	99.9	0.586	Contact Map
3axyA	1	0.756	99.9	0.591	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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