YABR - BACSU - GREMLIN Contacts

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YABR - Uncharacterized protein YabR

UniProt:	P37560	Sequences: MSIEVGSKLQGKITGITNFGAFVELPGGSTGLVHISEVADNYVKDINDHLKVGDQVEVKVINVEKDGKIGLSIKKAKDRPQARPRNDFRPKESFEQKMNKFLKDSEDRLSSLKRNTESKRGGRGARRG	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	128 (107)
Sequences:	2282 (1848)
Seq/√Len:	178.6

ECOLI - PNP YHGF RS1
BACSU - YABR GS13 RS1H PNP YDCI YITL
HALSA - Q9HNL1 IF2A
SULSO - IF2A Q980A3

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
10_Q	57_E	4.307	1.00
10_Q	55_Q	4.301	1.00
12_K	55_Q	3.241	1.00
8_K	59_K	2.998	1.00
11_G	23_V	2.756	1.00
51_K	54_D	2.711	1.00
25_L	71_L	2.617	1.00
31_G	71_L	2.582	1.00
4_E	7_S	2.307	1.00
21_A	50_L	2.203	1.00
61_I	72_S	2.192	1.00
19_F	32_L	2.114	1.00
37_E	75_K	2.063	1.00
44_K	48_D	1.995	1.00
45_D	48_D	1.886	1.00
38_V	50_L	1.808	1.00
8_K	57_E	1.743	1.00
72_S	77_K	1.688	1.00
106_E	109_L	1.684	1.00
40_D	76_A	1.679	1.00
38_V	46_I	1.659	1.00
37_E	77_K	1.631	1.00
56_V	73_I	1.498	1.00
33_V	73_I	1.424	1.00
85_R	88_F	1.412	1.00
105_S	108_R	1.412	1.00
98_M	101_F	1.398	1.00
14_T	24_E	1.359	1.00
3_I	60_V	1.343	1.00
20_G	32_L	1.324	1.00
59_K	75_K	1.313	1.00
3_I	26_P	1.263	1.00
93_S	96_Q	1.232	1.00
24_E	28_G	1.232	1.00
19_F	34_H	1.228	1.00
11_G	71_L	1.217	1.00
34_H	70_G	1.214	1.00
22_F	32_L	1.199	1.00
62_N	70_G	1.161	1.00
104_D	108_R	1.120	1.00
99_N	102_L	1.120	1.00
33_V	58_V	1.114	1.00
40_D	80_P	1.098	1.00
9_L	60_V	1.092	1.00
24_E	30_T	1.086	1.00
18_N	47_N	1.076	1.00
23_V	33_V	1.075	1.00
37_E	74_K	1.068	1.00
43_V	49_H	1.044	1.00
88_F	91_K	1.037	1.00
104_D	107_D	1.007	0.99
37_E	62_N	1.003	0.99
103_K	109_L	0.976	0.99
102_L	105_S	0.971	0.99
16_I	46_I	0.962	0.99
94_F	98_M	0.931	0.99
85_R	91_K	0.915	0.99
38_V	73_I	0.907	0.99
19_F	22_F	0.902	0.99
103_K	108_R	0.897	0.99
100_K	106_E	0.882	0.98
61_I	70_G	0.875	0.98
29_S	67_G	0.867	0.98
58_V	73_I	0.862	0.98
25_L	69_I	0.854	0.98
97_K	101_F	0.840	0.98
9_L	58_V	0.816	0.97
13_I	50_L	0.808	0.97
89_R	92_E	0.806	0.97
92_E	99_N	0.793	0.97
13_I	33_V	0.779	0.97
47_N	52_V	0.777	0.96
90_P	93_S	0.775	0.96
27_G	30_T	0.775	0.96
14_T	30_T	0.762	0.96
41_N	48_D	0.762	0.96
93_S	101_F	0.759	0.96
86_N	90_P	0.757	0.96
95_E	101_F	0.748	0.96
12_K	24_E	0.747	0.96
81_Q	85_R	0.746	0.96
39_A	43_V	0.744	0.96
16_I	52_V	0.738	0.95
91_K	95_E	0.733	0.95
105_S	109_L	0.733	0.95
91_K	96_Q	0.731	0.95
8_K	76_A	0.730	0.95
5_V	66_D	0.726	0.95
37_E	61_I	0.714	0.94
94_F	105_S	0.712	0.94
41_N	49_H	0.706	0.94
5_V	62_N	0.705	0.94
22_F	34_H	0.700	0.94
14_T	17_T	0.693	0.93
104_D	109_L	0.692	0.93
26_P	29_S	0.691	0.93
11_G	31_G	0.688	0.93
99_N	105_S	0.680	0.93
9_L	25_L	0.674	0.93
29_S	65_K	0.671	0.92
93_S	100_K	0.668	0.92
29_S	63_V	0.666	0.92
58_V	63_V	0.665	0.92
102_L	106_E	0.661	0.92
5_V	63_V	0.651	0.91
94_F	101_F	0.650	0.91
32_L	70_G	0.646	0.91
32_L	36_S	0.641	0.91
100_K	104_D	0.640	0.90
85_R	89_R	0.630	0.90
24_E	27_G	0.629	0.90
101_F	105_S	0.617	0.89
52_V	55_Q	0.616	0.89
94_F	108_R	0.615	0.89
3_I	9_L	0.611	0.88
81_Q	84_P	0.600	0.87
88_F	92_E	0.597	0.87
16_I	25_L	0.594	0.87
90_P	96_Q	0.588	0.86
83_R	90_P	0.586	0.86
92_E	95_E	0.577	0.85
35_I	43_V	0.576	0.85
89_R	97_K	0.575	0.85
84_P	89_R	0.575	0.85
83_R	89_R	0.568	0.84
21_A	38_V	0.566	0.84
84_P	87_D	0.561	0.84
18_N	35_I	0.559	0.84
95_E	98_M	0.556	0.83
15_G	30_T	0.554	0.83
76_A	80_P	0.554	0.83
98_M	107_D	0.551	0.83
60_V	63_V	0.550	0.83
101_F	106_E	0.547	0.82
98_M	102_L	0.547	0.82
81_Q	86_N	0.546	0.82
90_P	94_F	0.544	0.82
11_G	22_F	0.542	0.82
64_E	68_K	0.540	0.81
100_K	107_D	0.540	0.81
93_S	108_R	0.536	0.81
95_E	100_K	0.534	0.81
35_I	38_V	0.533	0.81
97_K	103_K	0.530	0.80
99_N	108_R	0.518	0.79
94_F	102_L	0.516	0.78
36_S	74_K	0.514	0.78
16_I	45_D	0.511	0.78
94_F	97_K	0.508	0.77
17_T	22_F	0.508	0.77
84_P	88_F	0.507	0.77
93_S	97_K	0.507	0.77
19_F	39_A	0.507	0.77
95_E	102_L	0.506	0.77
88_F	98_M	0.505	0.77
82_A	87_D	0.505	0.77
21_A	49_H	0.505	0.77
83_R	86_N	0.505	0.77
5_V	61_I	0.500	0.76
89_R	103_K	0.500	0.76

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
3cdiA	3	0	99.7	0.286	Contact Map
4nbqA	3	0.5	99.7	0.288	Contact Map
4aidA	3	0	99.7	0.292	Contact Map
3psfA	1	0.2344	99.7	0.305	Contact Map
1e3pA	3	0.3047	99.7	0.311	Contact Map
3psiA	1	0.6172	99.7	0.331	Contact Map
2khjA	1	0.6406	99.6	0.362	Contact Map
2k4kA	1	0.9609	99.6	0.374	Contact Map
4q7jD	1	0	99.6	0.377	Contact Map
2khiA	1	0.6875	99.6	0.378	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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