GSIB - BACSU - GREMLIN Contacts

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GSIB - Glucose starvation-inducible protein B

UniProt:	P26907	Sequences: MADNNKMSREEAGRKGGETTSKNHDKEFYQEIGQKGGEATSKNHDKEFYQEIGEKGGEATSKNHDKEFYQEIGEKGGEATSENHDKEFYQEIGRKGGEATSKNHDKEFYQEIGSKGGNARNND	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	123 (96)
Sequences:	41303 (36151)
Seq/√Len:	3689.7

ECOLI - YFBP YBGF LPSRP NRFG NLPI YGEH YBBN YGEG BAMD HEMY YFGM BEPA YPHG CADC CCMH BCSC SIRB1 YBEQ PGAA YJCO MALT YIBG DJLC
BACSU - GSIB RAPC YSOA RAPF YVCD RAPK RAPI RAPA RAPH RAPD RAPG RAPB RAPJ RAPE YPIA SUNS YRRB GUTR GLUP
HALSA - Q9HMM8
SULSO - Q97WM3 Q97V36 Q97ZS3 Q97VC4

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
62_K	81_S	3.182	1.00
34_Q	37_G	2.895	1.00
22_K	41_S	2.819	1.00
74_E	77_G	2.765	1.00
26_K	42_K	2.610	1.00
66_K	82_E	2.414	1.00
29_Y	41_S	2.397	1.00
25_D	41_S	2.361	1.00
69_Y	81_S	2.348	1.00
65_D	81_S	2.269	1.00
43_N	65_D	2.232	1.00
69_Y	77_G	2.174	1.00
29_Y	37_G	2.136	1.00
42_K	64_H	2.009	1.00
39_A	43_N	1.805	1.00
39_A	69_Y	1.721	1.00
62_K	84_H	1.675	1.00
69_Y	74_E	1.667	1.00
39_A	72_I	1.645	1.00
79_A	83_N	1.601	1.00
22_K	44_H	1.460	1.00
23_N	64_H	1.352	1.00
29_Y	34_Q	1.337	1.00
15_K	18_E	1.303	1.00
27_E	64_H	1.249	1.00
28_F	32_I	1.227	1.00
18_E	21_S	1.220	1.00
95_K	98_E	1.212	1.00
46_K	62_K	1.184	1.00
39_A	65_D	1.184	1.00
25_D	29_Y	1.145	1.00
45_D	61_S	1.120	1.00
82_E	104_H	1.110	1.00
19_T	49_Y	1.091	1.00
49_Y	57_G	1.086	1.00
109_Y	114_S	1.080	1.00
65_D	69_Y	1.077	1.00
36_G	72_I	1.076	1.00
79_A	112_I	1.073	1.00
37_G	40_T	1.070	1.00
23_N	27_E	1.066	1.00
39_A	68_F	1.063	1.00
44_H	48_F	1.062	1.00
19_T	45_D	1.051	1.00
59_A	89_Y	1.044	1.00
84_H	88_F	1.037	1.00
49_Y	61_S	1.024	1.00
49_Y	58_E	0.984	1.00
58_E	61_S	0.977	1.00
30_Q	71_E	0.968	1.00
22_K	48_F	0.955	1.00
59_A	85_D	0.950	1.00
90_Q	98_E	0.945	1.00
20_T	60_T	0.941	1.00
77_G	80_T	0.938	1.00
83_N	105_D	0.908	1.00
42_K	68_F	0.904	1.00
35_K	71_E	0.894	1.00
98_E	102_K	0.892	1.00
81_S	84_H	0.888	1.00
66_K	85_D	0.885	1.00
99_A	106_K	0.866	1.00
63_N	67_E	0.854	1.00
30_Q	68_F	0.848	1.00
89_Y	101_S	0.839	1.00
84_H	87_E	0.838	1.00
107_E	111_E	0.836	1.00
46_K	61_S	0.828	1.00
30_Q	35_K	0.821	1.00
30_Q	64_H	0.815	1.00
63_N	85_D	0.810	1.00
35_K	68_F	0.806	1.00
79_A	109_Y	0.805	1.00
68_F	72_I	0.803	1.00
67_E	71_E	0.802	1.00
27_E	30_Q	0.791	1.00
77_G	81_S	0.786	1.00
26_K	38_E	0.783	1.00
33_G	73_G	0.778	1.00
44_H	47_E	0.774	1.00
22_K	45_D	0.770	1.00
37_G	41_S	0.767	1.00
41_S	44_H	0.758	1.00
89_Y	97_G	0.757	1.00
30_Q	38_E	0.751	1.00
23_N	61_S	0.750	1.00
62_K	88_F	0.748	1.00
43_N	83_N	0.741	1.00
70_Q	78_E	0.739	1.00
76_G	112_I	0.730	1.00
103_N	107_E	0.723	1.00
108_F	112_I	0.723	1.00
27_E	31_E	0.715	1.00
67_E	70_Q	0.712	1.00
30_Q	42_K	0.706	1.00
70_Q	75_K	0.706	1.00
70_Q	82_E	0.705	1.00
18_E	58_E	0.701	1.00
79_A	105_D	0.698	1.00
86_K	102_K	0.687	1.00
62_K	85_D	0.679	1.00
36_G	76_G	0.662	1.00
96_G	100_T	0.660	1.00
46_K	65_D	0.649	1.00
89_Y	92_I	0.645	1.00
35_K	75_K	0.644	1.00
105_D	109_Y	0.644	1.00
70_Q	111_E	0.630	1.00
107_E	110_Q	0.630	1.00
41_S	81_S	0.624	1.00
69_Y	72_I	0.615	1.00
24_H	27_E	0.614	1.00
27_E	67_E	0.612	1.00
35_K	72_I	0.611	1.00
40_T	44_H	0.606	1.00
23_N	45_D	0.604	1.00
47_E	87_E	0.601	1.00
40_T	80_T	0.600	1.00
39_A	74_E	0.587	1.00
80_T	84_H	0.585	1.00
109_Y	112_I	0.584	1.00
29_Y	32_I	0.581	1.00
66_K	78_E	0.575	1.00
45_D	48_F	0.564	1.00
94_R	97_G	0.559	1.00
63_N	104_H	0.549	1.00
100_T	104_H	0.545	1.00
45_D	85_D	0.540	1.00
83_N	87_E	0.537	1.00
48_F	88_F	0.530	1.00
43_N	47_E	0.523	1.00
82_E	108_F	0.518	1.00
35_K	39_A	0.518	1.00
85_D	89_Y	0.509	1.00
49_Y	89_Y	0.508	1.00
86_K	90_Q	0.507	1.00
104_H	107_E	0.505	1.00
42_K	61_S	0.505	1.00
23_N	58_E	0.505	1.00
56_G	96_G	0.504	1.00
43_N	69_Y	0.503	1.00
38_E	68_F	0.502	1.00
96_G	99_A	0.502	1.00
18_E	22_K	0.500	1.00

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
2pziA	1	0.8943	99.5	0.189	Contact Map
4l9pA	1	0.9024	99.4	0.235	Contact Map
2vsyA	1	0.7724	99.4	0.241	Contact Map
3q7aA	1	0.9024	99.4	0.241	Contact Map
3dssA	1	0.9024	99.4	0.242	Contact Map
4j8eA	2	0.6911	99.4	0.242	Contact Map
3ulqA	1	1	99.4	0.243	Contact Map
4j8fA	2	0.935	99.4	0.244	Contact Map
4jhrA	2	1	99.4	0.245	Contact Map
1dceA	1	0.9024	99.4	0.246	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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