YCSD - BACSU - GREMLIN Contacts

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YCSD - Uncharacterized protein YcsD

UniProt:	P42961	Sequences: MNSLSLPHRYPFLFIDGVTDSEPGKHAAAYKLISENDWFITDTQTEMPFSLVIEALAQTAAFTGITDENSLGLLSSVKKAEKLGEAVPGDRLDLTFEVTRNRRGFVFGHAKASVGEQPVAEAEIGIYIEK	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	130 (123)
Sequences:	3487 (1916)
Seq/√Len:	172.8

ECOLI - FABZ FABA
BACSU - YCSD FABZ

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
84_G	117_Q	2.773	1.00
22_E	25_K	2.762	1.00
29_A	59_T	2.542	1.00
79_K	123_E	2.306	1.00
30_Y	91_R	2.286	1.00
28_A	93_D	2.264	1.00
55_A	94_L	2.243	1.00
56_L	94_L	2.231	1.00
77_V	80_A	2.149	1.00
39_F	47_M	2.060	1.00
111_K	118_P	2.041	1.00
52_V	92_L	1.970	1.00
97_E	109_H	1.943	1.00
113_S	118_P	1.896	1.00
80_A	122_A	1.835	1.00
95_T	113_S	1.827	1.00
109_H	123_E	1.814	1.00
28_A	95_T	1.793	1.00
60_A	108_G	1.717	1.00
99_T	109_H	1.667	1.00
113_S	116_E	1.665	1.00
30_Y	93_D	1.664	1.00
52_V	120_A	1.619	1.00
44_Q	85_E	1.604	1.00
26_H	97_E	1.589	1.00
38_W	41_T	1.584	1.00
26_H	95_T	1.552	1.00
19_T	30_Y	1.550	1.00
95_T	111_K	1.547	1.00
20_D	26_H	1.494	1.00
17_G	30_Y	1.484	1.00
27_A	63_T	1.474	1.00
32_L	91_R	1.459	1.00
96_F	110_A	1.457	1.00
20_D	28_A	1.451	1.00
22_E	26_H	1.405	1.00
106_V	126_I	1.361	1.00
18_V	62_F	1.340	1.00
10_Y	41_T	1.337	1.00
73_L	85_E	1.291	1.00
31_K	37_D	1.274	1.00
47_M	51_L	1.272	1.00
93_D	113_S	1.224	1.00
25_K	97_E	1.206	1.00
44_Q	87_V	1.205	1.00
90_D	114_V	1.151	1.00
94_L	112_A	1.145	1.00
46_E	73_L	1.144	1.00
101_N	106_V	1.140	1.00
83_L	121_E	1.136	1.00
110_A	124_I	1.128	1.00
18_V	29_A	1.090	1.00
76_S	125_G	1.089	1.00
15_I	59_T	1.085	1.00
84_G	119_V	1.084	1.00
44_Q	71_L	1.074	1.00
10_Y	36_N	1.071	1.00
44_Q	73_L	1.066	1.00
33_I	47_M	1.064	1.00
93_D	116_E	1.061	1.00
52_V	112_A	1.057	1.00
27_A	59_T	1.051	1.00
19_T	93_D	1.040	0.99
75_S	125_G	1.031	0.99
112_A	120_A	1.028	0.99
72_G	126_I	1.026	0.99
60_A	96_F	1.026	0.99
47_M	55_A	1.025	0.99
17_G	32_L	1.002	0.99
92_L	112_A	0.997	0.99
5_S	62_F	0.992	0.99
10_Y	35_E	0.992	0.99
53_I	77_V	0.987	0.99
5_S	65_I	0.986	0.99
19_T	28_A	0.982	0.99
74_L	77_V	0.964	0.99
86_A	119_V	0.942	0.99
99_T	107_F	0.938	0.99
118_P	121_E	0.928	0.99
65_I	106_V	0.906	0.99
91_R	115_G	0.897	0.98
108_G	126_I	0.887	0.98
98_V	106_V	0.885	0.98
67_D	70_S	0.880	0.98
101_N	104_G	0.870	0.98
111_K	121_E	0.869	0.98
21_S	27_A	0.868	0.98
107_F	125_G	0.865	0.98
81_E	125_G	0.865	0.98
56_L	122_A	0.861	0.98
27_A	62_F	0.857	0.98
53_I	80_A	0.853	0.98
78_K	123_E	0.850	0.98
10_Y	32_L	0.843	0.98
97_E	111_K	0.842	0.98
21_S	66_T	0.833	0.97
8_H	14_F	0.829	0.97
99_T	123_E	0.824	0.97
78_K	107_F	0.819	0.97
42_D	50_S	0.813	0.97
15_I	62_F	0.809	0.97
6_L	61_A	0.807	0.97
80_A	120_A	0.805	0.97
75_S	126_I	0.790	0.96
75_S	105_F	0.779	0.96
86_A	92_L	0.754	0.95
56_L	120_A	0.752	0.95
100_R	103_R	0.750	0.95
64_G	106_V	0.748	0.95
46_E	49_F	0.740	0.95
17_G	91_R	0.728	0.94
39_F	51_L	0.717	0.94
83_L	118_P	0.697	0.93
109_H	121_E	0.692	0.93
31_K	34_S	0.690	0.93
102_R	105_F	0.689	0.93
33_I	39_F	0.689	0.93
34_S	37_D	0.686	0.93
5_S	66_T	0.684	0.92
8_H	12_F	0.683	0.92
35_E	45_T	0.680	0.92
18_V	59_T	0.680	0.92
63_T	108_G	0.676	0.92
42_D	49_F	0.671	0.92
35_E	39_F	0.671	0.92
31_K	36_N	0.663	0.91
10_Y	17_G	0.662	0.91
10_Y	34_S	0.655	0.91
84_G	87_V	0.652	0.91
53_I	122_A	0.649	0.90
40_I	49_F	0.648	0.90
72_G	108_G	0.643	0.90
8_H	61_A	0.638	0.90
64_G	126_I	0.636	0.89
77_V	82_K	0.635	0.89
36_N	39_F	0.630	0.89
87_V	90_D	0.628	0.89
23_P	66_T	0.628	0.89
64_G	108_G	0.628	0.89
14_F	51_L	0.625	0.89
27_A	60_A	0.623	0.88
64_G	72_G	0.623	0.88
33_I	86_A	0.618	0.88
35_E	38_W	0.618	0.88
50_S	81_E	0.615	0.88
15_I	94_L	0.610	0.87
56_L	112_A	0.602	0.87
35_E	41_T	0.601	0.87
4_L	43_T	0.601	0.87
56_L	110_A	0.596	0.86
76_S	81_E	0.596	0.86
81_E	121_E	0.596	0.86
45_T	49_F	0.592	0.86
32_L	36_N	0.588	0.85
60_A	110_A	0.587	0.85
59_T	94_L	0.578	0.84
49_F	81_E	0.577	0.84
67_D	126_I	0.567	0.83
105_F	125_G	0.565	0.83
40_I	88_P	0.561	0.83
93_D	115_G	0.561	0.83
49_F	83_L	0.557	0.82
46_E	50_S	0.552	0.82
17_G	115_G	0.552	0.82
100_R	107_F	0.547	0.81
62_F	66_T	0.546	0.81
59_T	63_T	0.544	0.81
5_S	70_S	0.540	0.80
42_D	46_E	0.535	0.80
72_G	106_V	0.532	0.79
6_L	96_F	0.521	0.78
74_L	124_I	0.519	0.78
49_F	86_A	0.519	0.78
32_L	35_E	0.518	0.77
96_F	108_G	0.518	0.77
21_S	26_H	0.517	0.77
4_L	66_T	0.514	0.77
24_G	98_V	0.513	0.77
72_G	75_S	0.509	0.76
84_G	115_G	0.506	0.76
34_S	89_G	0.505	0.76
63_T	66_T	0.501	0.75
65_I	108_G	0.501	0.75
59_T	96_F	0.500	0.75

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
2gllA	3	1	100	0.228	Contact Map
1u1zA	3	1	100	0.234	Contact Map
1z6bA	3	0.9846	100	0.279	Contact Map
2cf2C	2	0.9923	100	0.283	Contact Map
3d6xA	3	1	100	0.292	Contact Map
3q62A	2	0.9923	100	0.311	Contact Map
4h4gA	3	0.9846	100	0.332	Contact Map
4i83A	3	0.9846	100	0.335	Contact Map
4b0bA	2	0.9923	99.9	0.359	Contact Map
3esiA	4	0.8923	99.8	0.536	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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