YNJA - ECOLI - GREMLIN Contacts

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YNJA - Uncharacterized protein YnjA

UniProt:	P76222	Sequences: MGLPPLSKIPLILRPQAWLHRRHYGEVLSPIRWWGRIPFIFYLVSMFVGWLERKRSPLDPVVRSLVSARIAQMCLCEFCVDITSMKVAERTGSSDKLLAVADWRQSPLFSDEERLALEYAEAASVTPPTVDDALRTRLAAHFDAQALTELTALIGLQNLSARFNSAMDIPAQGLCRIPEKRS	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG14003
Length:	182 (148)
Sequences:	4876 (3152)
Seq/√Len:	259.1

ECOLI - YNJA
BACSU - YDFG

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
122_A	134_L	4.036	1.00
139_A	144_A	3.455	1.00
88_A	94_S	3.314	1.00
143_D	146_A	2.784	1.00
118_E	137_R	2.546	1.00
122_A	131_D	2.384	1.00
69_R	121_E	2.321	1.00
119_Y	151_T	2.307	1.00
94_S	98_L	2.273	1.00
66_V	150_L	2.241	1.00
112_E	142_F	2.094	1.00
132_D	136_T	2.068	1.00
136_T	140_A	2.066	1.00
62_V	116_A	1.942	1.00
92_G	96_K	1.927	1.00
124_S	158_N	1.789	1.00
70_I	120_A	1.765	1.00
155_G	159_L	1.762	1.00
164_N	169_I	1.760	1.00
73_M	125_V	1.759	1.00
61_V	113_E	1.727	1.00
57_P	149_E	1.722	1.00
64_S	83_T	1.686	1.00
62_V	112_E	1.671	1.00
131_D	134_L	1.639	1.00
123_A	166_A	1.638	1.00
115_L	134_L	1.636	1.00
132_D	168_D	1.627	1.00
112_E	146_A	1.626	1.00
119_Y	138_L	1.611	1.00
40_I	152_A	1.598	1.00
93_S	96_K	1.589	1.00
59_D	62_V	1.565	1.00
137_R	140_A	1.564	1.00
110_S	113_E	1.544	1.00
139_A	147_L	1.501	1.00
63_R	153_L	1.492	1.00
138_L	147_L	1.487	1.00
116_A	150_L	1.467	1.00
119_Y	130_V	1.462	1.00
66_V	116_A	1.456	1.00
116_A	142_F	1.400	1.00
71_A	161_A	1.395	1.00
61_V	96_K	1.387	1.00
112_E	141_H	1.372	1.00
76_C	79_C	1.356	1.00
99_A	108_L	1.313	1.00
65_L	117_L	1.294	1.00
73_M	121_E	1.256	1.00
87_V	92_G	1.229	1.00
145_Q	149_E	1.207	1.00
158_N	162_R	1.202	1.00
142_F	150_L	1.174	1.00
47_F	156_L	1.142	1.00
37_I	149_E	1.140	1.00
88_A	98_L	1.133	1.00
70_I	124_S	1.127	1.00
48_V	156_L	1.126	1.00
134_L	137_R	1.126	1.00
99_A	106_S	1.112	1.00
64_S	90_R	1.109	1.00
129_T	168_D	1.093	1.00
74_C	161_A	1.092	1.00
57_P	146_A	1.091	1.00
67_S	157_Q	1.083	1.00
114_R	118_E	1.083	1.00
50_W	149_E	1.070	1.00
42_Y	46_M	1.051	1.00
44_V	159_L	1.046	1.00
111_D	141_H	1.030	1.00
139_A	143_D	1.029	1.00
69_R	73_M	1.024	1.00
69_R	117_L	1.015	1.00
119_Y	166_A	1.006	1.00
57_P	145_Q	1.006	1.00
120_A	154_I	1.002	1.00
48_V	67_S	0.993	1.00
135_R	139_A	0.992	1.00
115_L	137_R	0.971	1.00
37_I	145_Q	0.963	1.00
62_V	113_E	0.952	1.00
57_P	143_D	0.947	1.00
72_Q	80_V	0.936	1.00
118_E	134_L	0.932	1.00
65_L	113_E	0.931	1.00
36_R	144_A	0.930	1.00
111_D	114_R	0.923	1.00
85_M	89_E	0.922	1.00
111_D	137_R	0.903	1.00
36_R	148_T	0.899	1.00
96_K	113_E	0.897	1.00
104_R	118_E	0.897	1.00
84_S	88_A	0.895	1.00
62_V	142_F	0.894	1.00
71_A	157_Q	0.892	1.00
72_Q	121_E	0.884	1.00
86_K	89_E	0.883	1.00
82_I	172_Q	0.877	1.00
98_L	101_A	0.872	1.00
68_A	97_L	0.870	1.00
136_T	139_A	0.859	1.00
56_S	149_E	0.853	0.99
98_L	102_D	0.852	0.99
105_Q	118_E	0.851	0.99
124_S	162_R	0.844	0.99
120_A	124_S	0.833	0.99
51_L	153_L	0.832	0.99
151_T	167_M	0.822	0.99
76_C	161_A	0.820	0.99
81_D	95_D	0.818	0.99
64_S	67_S	0.812	0.99
115_L	141_H	0.812	0.99
86_K	90_R	0.807	0.99
111_D	140_A	0.805	0.99
148_T	163_F	0.804	0.99
29_S	32_R	0.802	0.99
74_C	158_N	0.801	0.99
60_P	63_R	0.798	0.99
132_D	135_R	0.795	0.99
46_M	49_G	0.794	0.99
133_A	140_A	0.789	0.99
65_L	100_V	0.784	0.99
58_L	63_R	0.781	0.99
87_V	91_T	0.772	0.99
35_G	41_F	0.770	0.99
73_M	124_S	0.768	0.99
82_I	160_S	0.758	0.99
84_S	97_L	0.758	0.99
123_A	151_T	0.747	0.99
67_S	79_C	0.745	0.99
130_V	134_L	0.744	0.99
143_D	147_L	0.742	0.99
99_A	109_F	0.729	0.98
61_V	92_G	0.724	0.98
95_D	98_L	0.723	0.98
68_A	84_S	0.721	0.98
118_E	121_E	0.719	0.98
78_F	82_I	0.719	0.98
49_G	55_R	0.713	0.98
29_S	78_F	0.709	0.98
70_I	157_Q	0.707	0.98
40_I	50_W	0.706	0.98
48_V	160_S	0.704	0.98
74_C	124_S	0.703	0.98
69_R	72_Q	0.702	0.98
43_L	46_M	0.700	0.98
37_I	148_T	0.698	0.98
68_A	80_V	0.696	0.98
46_M	50_W	0.687	0.98
118_E	122_A	0.687	0.98
79_C	161_A	0.687	0.98
79_C	164_N	0.682	0.98
64_S	86_K	0.677	0.97
131_D	136_T	0.674	0.97
74_C	162_R	0.674	0.97
67_S	83_T	0.672	0.97
138_L	142_F	0.662	0.97
87_V	97_L	0.654	0.97
137_R	141_H	0.653	0.97
126_T	129_T	0.648	0.97
119_Y	123_A	0.635	0.96
133_A	136_T	0.634	0.96
60_P	90_R	0.633	0.96
81_D	172_Q	0.631	0.96
71_A	79_C	0.624	0.96
59_D	112_E	0.620	0.96
84_S	98_L	0.619	0.96
81_D	171_A	0.615	0.96
104_R	121_E	0.612	0.95
34_W	163_F	0.610	0.95
109_F	117_L	0.608	0.95
116_A	120_A	0.605	0.95
129_T	165_S	0.602	0.95
76_C	164_N	0.597	0.95
148_T	152_A	0.596	0.95
133_A	137_R	0.594	0.95
24_Y	28_L	0.594	0.95
150_L	154_I	0.593	0.95
148_T	167_M	0.589	0.94
78_F	172_Q	0.587	0.94
99_A	107_P	0.586	0.94
29_S	82_I	0.581	0.94
42_Y	45_S	0.575	0.94
60_P	64_S	0.573	0.94
44_V	48_V	0.568	0.93
119_Y	167_M	0.567	0.93
41_F	164_N	0.564	0.93
96_K	109_F	0.562	0.93
51_L	149_E	0.561	0.93
83_T	157_Q	0.559	0.93
151_T	166_A	0.556	0.92
34_W	41_F	0.553	0.92
71_A	76_C	0.550	0.92
157_Q	160_S	0.548	0.92
114_R	117_L	0.545	0.92
47_F	159_L	0.544	0.92
24_Y	27_V	0.542	0.92
109_F	113_E	0.539	0.91
119_Y	150_L	0.535	0.91
95_D	107_P	0.534	0.91
156_L	160_S	0.533	0.91
128_P	134_L	0.533	0.91
85_M	172_Q	0.531	0.91
36_R	145_Q	0.529	0.91
138_L	150_L	0.528	0.90
121_E	125_V	0.527	0.90
103_W	106_S	0.525	0.90
70_I	154_I	0.525	0.90
43_L	47_F	0.524	0.90
135_R	168_D	0.521	0.90
152_A	163_F	0.521	0.90
152_A	155_G	0.513	0.89
33_W	169_I	0.511	0.89
95_D	99_A	0.510	0.89
153_L	157_Q	0.510	0.89
39_F	145_Q	0.509	0.89
63_R	67_S	0.508	0.89
112_E	116_A	0.508	0.89
79_C	157_Q	0.505	0.88
80_V	102_D	0.505	0.88
44_V	47_F	0.501	0.88
135_R	147_L	0.500	0.88

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
3c1lA	5	0.978	100	0.226	Contact Map
2pfxA	3	0.978	100	0.229	Contact Map
2oyoA	4	0.978	100	0.231	Contact Map
2prrA	5	0.9835	100	0.236	Contact Map
3lvyA	2	0.967	100	0.25	Contact Map
2o4dA	3	0.7857	100	0.317	Contact Map
2gmyA	3	0.8077	100	0.32	Contact Map
2ouwA	6	0.7033	99.9	0.516	Contact Map
3bjxA	2	0.7473	99.8	0.568	Contact Map
4n2xA	4	0.7473	99.7	0.579	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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