YUSE - BACSU - GREMLIN Contacts

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YUSE - Thioredoxin-like protein YusE

UniProt:	O32171	Sequences: MKELQEHELDHIEDDVYLLYLYTPFCGTCQLASKMLTVVKEMLPDVAFYQNNVNYSPTFAKAYQIESVPCFLLFKGGKMVERGYAFHSVSYLYELIKQKSSSASHL	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	106 (97)
Sequences:	9055 (5924)
Seq/√Len:	601.5

ECOLI - THIO2 THIO YBBN
BACSU - YUSE YTPP THIO YDFQ YDBP BDBA YNEN RESA STOA
HALSA - O46709 Q9HMD0 Q9HQ69
SULSO - Q97WI4 Q980T5 Q980E5

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
53_V	60_A	2.901	1.00
10_D	62_A	2.420	1.00
38_V	89_V	2.337	1.00
72_L	82_R	2.211	1.00
88_S	91_Y	2.088	1.00
42_M	93_Y	1.986	1.00
6_E	58_T	1.982	1.00
42_M	89_V	1.949	1.00
52_N	55_Y	1.924	1.00
26_C	29_C	1.872	1.00
17_Y	47_A	1.852	1.00
6_E	59_F	1.846	1.00
72_L	79_M	1.783	1.00
63_Y	74_F	1.768	1.00
4_L	49_Y	1.741	1.00
43_L	93_Y	1.739	1.00
79_M	82_R	1.732	1.00
15_D	47_A	1.691	1.00
20_Y	50_Q	1.688	1.00
35_M	38_V	1.635	1.00
36_L	48_F	1.622	1.00
39_V	48_F	1.598	1.00
18_L	36_L	1.585	1.00
93_Y	97_K	1.527	1.00
12_I	47_A	1.503	1.00
35_M	89_V	1.489	1.00
16_V	73_L	1.484	1.00
43_L	97_K	1.465	1.00
17_Y	49_Y	1.461	1.00
91_Y	94_E	1.459	1.00
24_P	52_N	1.442	1.00
5_Q	8_E	1.442	1.00
18_L	71_F	1.420	1.00
6_E	56_S	1.405	1.00
86_F	91_Y	1.373	1.00
83_G	87_H	1.371	1.00
8_E	12_I	1.368	1.00
53_V	68_V	1.290	1.00
12_I	17_Y	1.263	1.00
39_V	93_Y	1.232	1.00
83_G	95_L	1.216	1.00
20_Y	33_S	1.172	1.00
73_L	99_K	1.129	1.00
81_E	95_L	1.127	1.00
19_L	74_F	1.127	1.00
89_V	93_Y	1.089	1.00
51_N	59_F	1.088	1.00
39_V	43_L	1.078	1.00
57_P	61_K	1.050	1.00
78_K	81_E	1.046	1.00
32_A	35_M	1.011	1.00
3_E	50_Q	0.996	1.00
33_S	37_T	0.990	1.00
39_V	89_V	0.982	1.00
71_F	92_L	0.974	1.00
73_L	95_L	0.968	1.00
32_A	71_F	0.956	1.00
46_V	96_I	0.950	1.00
36_L	71_F	0.950	1.00
5_Q	56_S	0.946	1.00
37_T	50_Q	0.944	1.00
32_A	92_L	0.937	1.00
16_V	75_K	0.913	1.00
51_N	60_A	0.892	1.00
22_Y	50_Q	0.890	1.00
87_H	91_Y	0.877	1.00
4_L	12_I	0.875	1.00
39_V	92_L	0.874	1.00
33_S	50_Q	0.872	1.00
90_S	94_E	0.848	1.00
73_L	96_I	0.825	1.00
14_D	17_Y	0.798	1.00
35_M	88_S	0.797	1.00
14_D	76_G	0.788	1.00
21_L	63_Y	0.787	1.00
35_M	39_V	0.777	1.00
18_L	48_F	0.770	1.00
20_Y	32_A	0.770	1.00
94_E	97_K	0.766	1.00
45_D	97_K	0.746	1.00
75_K	80_V	0.734	1.00
20_Y	28_T	0.723	1.00
77_G	81_E	0.719	1.00
24_P	54_N	0.716	1.00
9_L	21_L	0.714	1.00
32_A	36_L	0.712	1.00
41_E	44_P	0.711	1.00
31_L	86_F	0.707	1.00
15_D	45_D	0.700	1.00
40_K	48_F	0.699	1.00
43_L	46_V	0.694	1.00
58_T	62_A	0.690	1.00
75_K	78_K	0.687	1.00
81_E	99_K	0.684	1.00
15_D	76_G	0.680	1.00
87_H	95_L	0.680	1.00
16_V	76_G	0.680	1.00
8_E	49_Y	0.679	1.00
24_P	30_Q	0.674	1.00
59_F	62_A	0.674	1.00
3_E	55_Y	0.661	1.00
95_L	99_K	0.661	1.00
65_I	70_C	0.659	1.00
32_A	87_H	0.658	1.00
18_L	73_L	0.634	1.00
38_V	41_E	0.633	1.00
25_F	30_Q	0.627	1.00
8_E	11_H	0.626	1.00
27_G	30_Q	0.623	1.00
31_L	35_M	0.622	1.00
18_L	96_I	0.618	1.00
28_T	67_S	0.612	1.00
58_T	61_K	0.611	1.00
4_L	19_L	0.608	1.00
42_M	97_K	0.608	1.00
57_P	60_A	0.605	1.00
9_L	63_Y	0.599	1.00
27_G	31_L	0.599	1.00
3_E	49_Y	0.596	1.00
28_T	31_L	0.595	1.00
66_E	82_R	0.595	1.00
56_S	59_F	0.595	1.00
74_F	79_M	0.586	1.00
9_L	59_F	0.580	1.00
22_Y	52_N	0.576	1.00
23_T	26_C	0.572	1.00
83_G	86_F	0.571	1.00
18_L	92_L	0.560	1.00
25_F	68_V	0.550	0.99
60_A	63_Y	0.543	0.99
36_L	39_V	0.542	0.99
23_T	34_K	0.541	0.99
81_E	98_Q	0.540	0.99
96_I	99_K	0.530	0.99
54_N	57_P	0.526	0.99
61_K	66_E	0.523	0.99
59_F	63_Y	0.523	0.99
51_N	56_S	0.519	0.99
83_G	91_Y	0.519	0.99
29_C	34_K	0.519	0.99
9_L	19_L	0.514	0.99
21_L	65_I	0.512	0.99
90_S	93_Y	0.511	0.99
36_L	96_I	0.506	0.99
22_Y	68_V	0.505	0.99
28_T	87_H	0.500	0.99

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
2r2jA	2	0.9906	99.8	0.17	Contact Map
3f8uA	2	1	99.8	0.173	Contact Map
2b5eA	1	1	99.8	0.176	Contact Map
3apoA	1	0.9245	99.8	0.184	Contact Map
4ekzA	1	1	99.8	0.202	Contact Map
3us3A	2	0.9906	99.8	0.213	Contact Map
3ed3A	1	1	99.8	0.216	Contact Map
1sjiA	2	0.9906	99.8	0.217	Contact Map
4tveA	1	1	99.7	0.243	Contact Map
4tw5A	3	1	99.7	0.254	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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