YKUV - BACSU - GREMLIN Contacts

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YKUV - Thiol-disulfide oxidoreductase YkuV

UniProt:	O31699	Sequences: MKLRQPMPELTGEKAWLNGEVTREQLIGEKPTLIHFWSISCHLCKEAMPQVNEFRDKYQDQLNVVAVHMPRSEDDLDPGKIKETAAEHDITQPIFVDSDHALTDAFENEYVPAYYVFDKTGQLRHFQAGGSGMKMLEKRVNRVLAETE	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	148 (131)
Sequences:	13879 (10371)
Seq/√Len:	906.1

ECOLI - DSBE TPX BCP AHPC
BACSU - YKUV RESA STOA YNEN TPX BCP AHPC YKUU SCO1
HALSA - Q9HP28 Q9HQE6 Q9HRG4 Q9HN00
SULSO - Q97WP9 Q97VL0 Q97WG5

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
31_P	119_K	3.891	1.00
11_T	21_V	2.674	1.00
16_W	20_E	2.655	1.00
52_N	91_T	2.595	1.00
30_K	63_N	2.539	1.00
118_D	122_Q	2.494	1.00
78_P	82_K	2.373	1.00
118_D	124_R	2.317	1.00
15_A	21_V	2.301	1.00
11_T	23_R	2.214	1.00
6_P	122_Q	2.066	1.00
117_F	123_L	2.055	1.00
17_L	85_A	2.006	1.00
7_M	106_F	1.994	1.00
23_R	26_L	1.981	1.00
52_N	56_D	1.934	1.00
22_T	27_I	1.871	1.00
57_K	137_E	1.854	1.00
32_T	63_N	1.815	1.00
16_W	22_T	1.748	1.00
55_R	59_Q	1.721	1.00
9_E	25_Q	1.684	1.00
137_E	141_N	1.670	1.00
66_A	92_Q	1.626	1.00
45_K	88_H	1.556	1.00
77_D	80_K	1.505	1.00
48_M	90_I	1.505	1.00
35_H	47_A	1.490	1.00
33_L	116_V	1.487	1.00
82_K	86_A	1.425	1.00
9_E	23_R	1.391	1.00
113_A	126_F	1.370	1.00
31_P	124_R	1.365	1.00
35_H	114_Y	1.356	1.00
69_M	103_T	1.336	1.00
50_Q	53_E	1.328	1.00
69_M	100_H	1.279	1.00
125_H	139_R	1.258	1.00
101_A	105_A	1.249	1.00
31_P	116_V	1.247	1.00
53_E	133_M	1.219	1.00
55_R	91_T	1.200	1.00
68_H	81_I	1.199	1.00
45_K	87_E	1.198	1.00
78_P	96_V	1.187	1.00
45_K	84_T	1.163	1.00
115_Y	123_L	1.137	1.00
33_L	114_Y	1.135	1.00
12_G	95_F	1.126	1.00
32_T	117_F	1.124	1.00
84_T	88_H	1.122	1.00
54_F	136_L	1.119	1.00
139_R	142_R	1.116	1.00
79_G	83_E	1.103	1.00
41_C	88_H	1.101	1.00
31_P	62_L	1.099	1.00
27_I	32_T	1.072	1.00
27_I	65_V	1.069	1.00
38_S	111_V	1.064	1.00
33_L	62_L	1.059	1.00
135_M	138_K	1.057	1.00
63_N	93_P	1.050	1.00
36_F	106_F	1.029	1.00
135_M	139_R	1.027	1.00
47_A	114_Y	1.022	1.00
59_Q	63_N	1.019	1.00
25_Q	28_G	1.018	1.00
50_Q	133_M	1.003	1.00
33_L	51_V	1.002	1.00
39_I	81_I	1.000	1.00
22_T	26_L	0.996	1.00
54_F	57_K	0.993	1.00
52_N	92_Q	0.992	1.00
46_E	130_G	0.970	1.00
40_S	81_I	0.966	1.00
70_P	76_L	0.953	1.00
32_T	65_V	0.948	1.00
83_E	86_A	0.932	1.00
9_E	24_E	0.911	1.00
85_A	94_I	0.910	1.00
133_M	137_E	0.908	1.00
83_E	87_E	0.904	1.00
16_W	95_F	0.896	1.00
34_I	117_F	0.875	1.00
56_D	59_Q	0.874	1.00
81_I	96_V	0.873	1.00
29_E	121_G	0.866	1.00
55_R	63_N	0.864	1.00
36_F	67_V	0.863	1.00
48_M	84_T	0.860	1.00
46_E	49_P	0.849	1.00
125_H	142_R	0.848	1.00
49_P	53_E	0.837	1.00
97_D	100_H	0.830	1.00
12_G	102_L	0.823	1.00
15_A	78_P	0.821	1.00
100_H	104_D	0.820	1.00
51_V	64_V	0.820	1.00
10_L	102_L	0.820	1.00
29_E	119_K	0.814	1.00
18_N	82_K	0.813	1.00
24_E	32_T	0.810	1.00
53_E	56_D	0.808	1.00
16_W	93_P	0.792	1.00
53_E	57_K	0.786	1.00
52_N	89_D	0.784	1.00
41_C	44_C	0.775	1.00
58_Y	137_E	0.772	1.00
27_I	63_N	0.768	1.00
58_Y	141_N	0.767	1.00
58_Y	61_Q	0.767	1.00
102_L	105_A	0.762	1.00
56_D	91_T	0.761	1.00
117_F	121_G	0.758	1.00
101_A	104_D	0.756	1.00
138_K	142_R	0.753	1.00
12_G	15_A	0.750	1.00
123_L	126_F	0.749	1.00
108_N	113_A	0.747	1.00
69_M	111_V	0.742	1.00
7_M	117_F	0.740	1.00
79_G	82_K	0.736	1.00
50_Q	54_F	0.732	1.00
136_L	139_R	0.731	1.00
35_H	48_M	0.730	1.00
10_L	24_E	0.728	1.00
132_G	135_M	0.728	1.00
39_I	84_T	0.724	1.00
6_P	28_G	0.724	1.00
138_K	141_N	0.723	1.00
7_M	24_E	0.712	1.00
48_M	88_H	0.707	1.00
35_H	43_L	0.705	1.00
17_L	82_K	0.696	1.00
36_F	108_N	0.691	1.00
134_K	138_K	0.690	1.00
22_T	95_F	0.689	1.00
100_H	103_T	0.686	1.00
24_E	27_I	0.684	1.00
134_K	137_E	0.679	1.00
49_P	52_N	0.672	1.00
54_F	58_Y	0.664	1.00
116_V	127_Q	0.663	1.00
110_Y	113_A	0.662	1.00
41_C	80_K	0.653	1.00
42_H	46_E	0.649	1.00
103_T	108_N	0.649	1.00
28_G	121_G	0.648	1.00
11_T	15_A	0.645	1.00
113_A	128_A	0.644	1.00
58_Y	62_L	0.643	1.00
50_Q	130_G	0.643	1.00
29_E	118_D	0.634	1.00
47_A	51_V	0.616	1.00
24_E	28_G	0.614	1.00
16_W	19_G	0.614	1.00
48_M	52_N	0.613	1.00
85_A	90_I	0.613	1.00
116_V	125_H	0.613	1.00
49_P	88_H	0.610	1.00
37_W	94_I	0.607	1.00
35_H	92_Q	0.596	1.00
10_L	106_F	0.596	1.00
33_L	64_V	0.595	1.00
52_N	88_H	0.594	1.00
66_A	90_I	0.593	1.00
102_L	106_F	0.590	1.00
80_K	83_E	0.589	1.00
28_G	32_T	0.585	1.00
15_A	18_N	0.575	1.00
136_L	140_V	0.574	1.00
32_T	121_G	0.570	1.00
37_W	81_I	0.570	1.00
127_Q	139_R	0.570	1.00
104_D	109_E	0.566	1.00
66_A	94_I	0.565	1.00
36_F	102_L	0.562	1.00
54_F	137_E	0.557	1.00
52_N	55_R	0.557	1.00
67_V	102_L	0.554	1.00
40_S	43_L	0.554	1.00
81_I	94_I	0.552	1.00
40_S	111_V	0.550	1.00
50_Q	134_K	0.529	1.00
41_C	87_E	0.524	1.00
30_K	119_K	0.523	1.00
35_H	51_V	0.520	1.00
127_Q	131_S	0.516	1.00
131_S	136_L	0.516	1.00
43_L	130_G	0.513	1.00
55_R	92_Q	0.509	1.00
57_K	133_M	0.507	1.00
70_P	100_H	0.504	1.00
39_I	80_K	0.502	1.00
5_Q	126_F	0.500	1.00
42_H	45_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
3eytA	4	0.9797	100	0.222	Contact Map
3lorA	3	0.973	100	0.222	Contact Map
2b5xA	1	0.9865	100	0.229	Contact Map
3fw2A	2	0.9257	100	0.234	Contact Map
2p5qA	3	0.9527	100	0.239	Contact Map
2hyxA	2	0.9865	100	0.24	Contact Map
2f9sA	1	0.9324	100	0.245	Contact Map
3hczA	2	0.9459	100	0.245	Contact Map
3gl3A	3	0.9324	100	0.246	Contact Map
2f8aA	3	0.9527	100	0.248	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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