YDDH - ECOLI - GREMLIN Contacts

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YDDH - Uncharacterized protein YddH

UniProt:	P76121	Sequences: MSRFIPIELHHASRLLNHGPTVLITSFDEQSQRRNIMAAAWSMPVEFEPPRVAIVVDKSTWTRELIEHNGKFGIVIPGVAATNWTWAVGSVSGRDEDKFNCYGIPVVRGPVFGLPLVEEKCLAWMECRLLPATSAQEEYDTLFGEVVSAAADARVFVEGRWQFDDDKLNTLHHLGAGTFVTSGKRVTAG	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG13779
Length:	189 (168)
Sequences:	3968 (2861)
Seq/√Len:	220.7

ECOLI - YDDH
BACSU - YWRF YDFE

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
105_P	120_K	3.940	1.00
111_V	147_V	3.456	1.00
72_F	144_G	3.419	1.00
128_R	145_E	3.196	1.00
29_E	33_R	3.136	1.00
79_V	169_N	2.889	1.00
128_R	147_V	2.807	1.00
30_Q	68_H	2.586	1.00
107_V	118_E	2.543	1.00
130_L	145_E	2.481	1.00
97_D	100_N	2.325	1.00
34_R	106_V	2.307	1.00
25_T	73_G	2.307	1.00
67_E	132_A	2.106	1.00
36_I	117_V	2.084	1.00
27_F	34_R	2.069	1.00
79_V	181_T	2.023	1.00
71_K	128_R	2.014	1.00
77_P	85_T	2.014	1.00
109_G	116_L	2.006	1.00
92_S	101_C	2.000	1.00
105_P	118_E	1.992	1.00
73_G	112_F	1.892	1.00
53_A	141_T	1.854	1.00
99_F	106_V	1.810	1.00
27_F	113_G	1.732	1.00
52_V	74_I	1.696	1.00
116_L	124_W	1.685	1.00
71_K	113_G	1.619	1.00
64_E	94_R	1.589	1.00
109_G	126_E	1.555	1.00
25_T	36_I	1.550	1.00
34_R	115_P	1.540	1.00
45_V	53_A	1.536	1.00
92_S	96_E	1.528	1.00
110_P	148_S	1.514	1.00
112_F	126_E	1.500	1.00
51_R	143_F	1.472	1.00
23_L	36_I	1.472	1.00
172_H	180_V	1.450	1.00
72_F	127_C	1.428	1.00
12_A	44_P	1.386	1.00
132_A	140_D	1.358	1.00
23_L	88_V	1.351	1.00
78_G	81_A	1.349	1.00
51_R	130_L	1.349	1.00
109_G	114_L	1.347	1.00
181_T	184_K	1.330	1.00
157_V	164_D	1.325	1.00
66_I	129_L	1.302	1.00
64_E	68_H	1.277	1.00
109_G	112_F	1.271	1.00
77_P	171_L	1.260	1.00
116_L	150_A	1.259	1.00
125_M	146_V	1.247	1.00
97_D	106_V	1.240	1.00
111_V	148_S	1.232	1.00
15_L	123_A	1.224	1.00
63_R	67_E	1.223	1.00
71_K	112_F	1.194	1.00
37_M	62_T	1.178	1.00
66_I	72_F	1.176	1.00
157_V	167_K	1.168	1.00
26_S	66_I	1.165	1.00
75_V	124_W	1.156	1.00
45_V	143_F	1.155	1.00
164_D	167_K	1.154	1.00
81_A	120_K	1.151	1.00
36_I	99_F	1.127	1.00
34_R	97_D	1.098	1.00
125_M	149_A	1.088	1.00
107_V	116_L	1.088	1.00
82_T	171_L	1.082	1.00
80_A	169_N	1.056	1.00
77_P	121_C	1.050	1.00
22_V	42_S	1.048	1.00
26_S	65_L	1.032	1.00
127_C	144_G	1.028	1.00
174_L	180_V	1.028	1.00
96_E	101_C	1.028	1.00
129_L	132_A	1.023	1.00
63_R	140_D	1.021	1.00
52_V	125_M	1.017	1.00
88_V	102_Y	1.015	1.00
58_K	134_S	1.008	1.00
61_W	94_R	1.000	1.00
58_K	140_D	0.976	1.00
73_G	116_L	0.970	1.00
84_W	102_Y	0.967	1.00
172_H	182_S	0.961	1.00
155_V	168_L	0.953	1.00
129_L	142_L	0.952	1.00
63_R	142_L	0.949	1.00
23_L	81_A	0.949	1.00
84_W	104_I	0.948	1.00
132_A	142_L	0.932	1.00
78_G	122_L	0.928	1.00
43_M	53_A	0.916	0.99
169_N	181_T	0.899	0.99
26_S	62_T	0.893	0.99
61_W	64_E	0.890	0.99
151_A	155_V	0.879	0.99
52_V	146_V	0.874	0.99
39_A	54_I	0.866	0.99
39_A	56_V	0.865	0.99
157_V	162_Q	0.861	0.99
133_T	143_F	0.861	0.99
69_N	113_G	0.854	0.99
152_D	155_V	0.852	0.99
27_F	108_R	0.847	0.99
73_G	109_G	0.846	0.99
24_I	54_I	0.843	0.99
134_S	140_D	0.836	0.99
27_F	114_L	0.834	0.99
87_A	92_S	0.826	0.99
107_V	124_W	0.820	0.99
79_V	82_T	0.816	0.99
73_G	124_W	0.815	0.99
27_F	69_N	0.807	0.99
87_A	101_C	0.804	0.99
29_E	32_Q	0.799	0.99
61_W	65_L	0.794	0.98
47_F	57_D	0.790	0.98
25_T	117_V	0.780	0.98
33_R	95_D	0.780	0.98
71_K	114_L	0.779	0.98
57_D	139_Y	0.779	0.98
53_A	143_F	0.775	0.98
108_R	113_G	0.775	0.98
46_E	135_A	0.774	0.98
45_V	51_R	0.774	0.98
65_L	69_N	0.772	0.98
123_A	168_L	0.769	0.98
22_V	74_I	0.767	0.98
74_I	127_C	0.760	0.98
165_D	170_T	0.747	0.98
34_R	99_F	0.744	0.98
76_I	168_L	0.742	0.98
25_T	75_V	0.735	0.97
54_I	142_L	0.735	0.97
46_E	139_Y	0.733	0.97
155_V	163_F	0.731	0.97
122_L	152_D	0.730	0.97
87_A	102_Y	0.730	0.97
80_A	122_L	0.726	0.97
16_L	44_P	0.713	0.97
135_A	143_F	0.712	0.97
105_P	117_V	0.710	0.97
67_E	134_S	0.709	0.97
174_L	178_T	0.706	0.97
111_V	126_E	0.704	0.97
155_V	167_K	0.701	0.97
85_T	171_L	0.698	0.97
29_E	68_H	0.694	0.96
45_V	55_V	0.694	0.96
25_T	114_L	0.692	0.96
76_I	170_T	0.689	0.96
23_L	121_C	0.688	0.96
81_A	121_C	0.686	0.96
67_E	70_G	0.684	0.96
33_R	94_R	0.682	0.96
70_G	128_R	0.680	0.96
117_V	120_K	0.678	0.96
75_V	117_V	0.677	0.96
83_N	87_A	0.677	0.96
85_T	121_C	0.674	0.96
23_L	117_V	0.672	0.96
25_T	99_F	0.666	0.95
84_W	120_K	0.665	0.95
170_T	182_S	0.664	0.95
87_A	96_E	0.663	0.95
45_V	141_T	0.654	0.95
154_R	167_K	0.653	0.95
124_W	150_A	0.653	0.95
70_G	129_L	0.652	0.95
76_I	123_A	0.652	0.95
17_N	170_T	0.646	0.95
131_P	134_S	0.640	0.94
71_K	126_E	0.638	0.94
16_L	76_I	0.631	0.94
62_T	65_L	0.631	0.94
107_V	110_P	0.627	0.94
92_S	98_K	0.627	0.94
34_R	114_L	0.627	0.94
55_V	139_Y	0.623	0.94
174_L	182_S	0.619	0.93
42_S	53_A	0.618	0.93
66_I	144_G	0.613	0.93
109_G	124_W	0.610	0.93
106_V	120_K	0.607	0.93
63_R	132_A	0.606	0.93
15_L	125_M	0.604	0.92
159_G	162_Q	0.600	0.92
61_W	98_K	0.598	0.92
51_R	135_A	0.598	0.92
55_V	141_T	0.597	0.92
43_M	55_V	0.597	0.92
42_S	76_I	0.594	0.92
43_M	141_T	0.593	0.92
73_G	114_L	0.590	0.92
23_L	85_T	0.586	0.91
87_A	90_S	0.585	0.91
16_L	52_V	0.584	0.91
41_W	44_P	0.576	0.91
165_D	174_L	0.575	0.91
21_T	38_A	0.573	0.90
100_N	103_G	0.571	0.90
110_P	126_E	0.568	0.90
111_V	128_R	0.568	0.90
58_K	63_R	0.568	0.90
16_L	22_V	0.568	0.90
166_D	184_K	0.562	0.90
13_S	47_F	0.561	0.89
56_V	142_L	0.560	0.89
39_A	62_T	0.555	0.89
106_V	115_P	0.555	0.89
104_I	117_V	0.553	0.89
23_L	104_I	0.553	0.89
24_I	39_A	0.552	0.89
46_E	51_R	0.552	0.89
27_F	32_Q	0.551	0.89
99_F	102_Y	0.551	0.89
38_A	77_P	0.550	0.89
81_A	104_I	0.550	0.89
163_F	168_L	0.546	0.88
108_R	115_P	0.545	0.88
93_G	98_K	0.542	0.88
110_P	150_A	0.541	0.88
64_E	67_E	0.541	0.88
59_S	63_R	0.541	0.88
26_S	37_M	0.541	0.88
93_G	96_E	0.537	0.87
14_R	175_G	0.536	0.87
86_W	90_S	0.533	0.87
54_I	66_I	0.533	0.87
130_L	143_F	0.532	0.87
115_P	146_V	0.529	0.87
89_G	92_S	0.525	0.86
102_Y	117_V	0.524	0.86
86_W	179_F	0.524	0.86
123_A	151_A	0.523	0.86
15_L	149_A	0.520	0.86
155_V	165_D	0.517	0.85
100_N	106_V	0.517	0.85
17_N	165_D	0.513	0.85
46_E	57_D	0.512	0.85
156_F	163_F	0.509	0.84
104_I	120_K	0.509	0.84
33_R	61_W	0.505	0.84
36_I	88_V	0.503	0.84
80_A	154_R	0.502	0.84
89_G	98_K	0.500	0.83

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
3bpkA	2	0.9683	100	0.248	Contact Map
3fgeA	2	0.9841	100	0.268	Contact Map
3hmzA	2	0.9683	100	0.275	Contact Map
2r6vA	2	0.9524	100	0.291	Contact Map
1ejeA	2	0.9683	100	0.294	Contact Map
2d5mA	2	0.9365	100	0.302	Contact Map
3e4vA	2	0.9101	100	0.327	Contact Map
3bnkA	2	0.9365	100	0.34	Contact Map
1uscA	2	0.9365	100	0.354	Contact Map
3cb0A	2	0.8571	100	0.417	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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