YWPF - BACSU - GREMLIN Contacts

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YWPF - Uncharacterized protein YwpF

UniProt:	P94588	Sequences: MKTFKLVDLNVERVDKEEQSIEQFPLIDGLIINKEDGENHWLIEALVQKEHLSFFEQLQNSQSEAKVFVTITKKSNRPAQLTAAVKNIVKLEESIQVLLYGQMVTRKQQGTETILESLVKEGYTGTKLIEAFKQKL	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	136 (130)
Sequences:	147 (110)
Seq/√Len:	9.6

BACSU - YWPF

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
119_V	129_I	3.801	0.98
110_G	114_I	3.800	0.98
5_K	28_D	3.380	0.96
9_L	97_V	2.838	0.90
11_V	25_P	2.441	0.81
115_L	128_L	2.281	0.76
7_V	34_K	2.279	0.76
6_L	30_L	2.240	0.74
5_K	79_A	2.188	0.73
6_L	45_A	2.107	0.70
52_L	56_E	2.094	0.69
67_V	99_L	2.079	0.69
59_Q	85_V	1.974	0.64
81_L	110_G	1.885	0.61
30_L	45_A	1.821	0.58
39_N	73_K	1.816	0.58
73_K	133_K	1.805	0.57
67_V	83_A	1.736	0.54
60_N	129_I	1.726	0.54
42_L	100_Y	1.691	0.52
6_L	69_V	1.689	0.52
31_I	112_E	1.688	0.52
116_E	120_K	1.681	0.52
3_T	51_H	1.674	0.51
42_L	56_E	1.634	0.50
47_V	62_Q	1.621	0.49
52_L	90_K	1.614	0.49
9_L	45_A	1.592	0.48
6_L	73_K	1.437	0.41
49_K	90_K	1.434	0.41
44_E	81_L	1.420	0.40
67_V	129_I	1.393	0.39
81_L	114_I	1.375	0.38
57_Q	60_N	1.366	0.38
27_I	56_E	1.364	0.38
34_K	100_Y	1.350	0.37
126_T	130_E	1.307	0.35
118_L	132_F	1.305	0.35
42_L	86_K	1.305	0.35
28_D	112_E	1.292	0.35
97_V	127_K	1.278	0.34
119_V	126_T	1.268	0.34
23_Q	42_L	1.235	0.32
15_D	120_K	1.214	0.32
85_V	88_I	1.191	0.31
37_G	70_T	1.170	0.30
91_L	99_L	1.151	0.29
28_D	132_F	1.148	0.29
82_T	131_A	1.143	0.29
34_K	123_Y	1.122	0.28
22_E	55_F	1.120	0.28
15_D	93_E	1.108	0.28
75_S	105_T	1.107	0.28
34_K	77_R	1.105	0.27
53_S	56_E	1.094	0.27
96_Q	100_Y	1.091	0.27
99_L	130_E	1.090	0.27
72_T	104_V	1.077	0.26
96_Q	103_M	1.059	0.26
106_R	130_E	1.044	0.25
63_S	127_K	1.027	0.25
70_T	96_Q	1.020	0.25
33_N	78_P	1.018	0.24
74_K	100_Y	1.010	0.24
47_V	57_Q	1.006	0.24
52_L	97_V	0.976	0.23
85_V	99_L	0.971	0.23
8_D	31_I	0.954	0.22
33_N	103_M	0.953	0.22
74_K	117_S	0.953	0.22
9_L	46_L	0.945	0.22
23_Q	43_I	0.942	0.22
107_K	123_Y	0.938	0.22
111_T	114_I	0.932	0.22
30_L	133_K	0.931	0.22
98_L	103_M	0.929	0.22
36_D	98_L	0.927	0.22
37_G	54_F	0.924	0.21
45_A	133_K	0.908	0.21
36_D	46_L	0.904	0.21
55_F	85_V	0.897	0.21
15_D	43_I	0.891	0.20
14_V	20_S	0.891	0.20
89_V	96_Q	0.886	0.20
24_F	42_L	0.874	0.20
57_Q	65_A	0.874	0.20
34_K	111_T	0.869	0.20
96_Q	111_T	0.865	0.20
26_L	29_G	0.865	0.20
87_N	95_I	0.841	0.19
105_T	108_Q	0.829	0.19
15_D	127_K	0.826	0.19
40_H	84_A	0.812	0.18
109_Q	131_A	0.809	0.18
37_G	85_V	0.809	0.18
47_V	92_E	0.808	0.18
110_G	116_E	0.806	0.18
106_R	123_Y	0.801	0.18
72_T	102_Q	0.800	0.18
54_F	123_Y	0.798	0.18
60_N	65_A	0.795	0.18
99_L	127_K	0.794	0.18
14_V	72_T	0.790	0.18
61_S	87_N	0.787	0.18
51_H	82_T	0.785	0.18
91_L	95_I	0.785	0.18
39_N	75_S	0.778	0.17
131_A	134_Q	0.777	0.17
35_E	118_L	0.769	0.17
25_P	98_L	0.755	0.17
6_L	66_K	0.755	0.17
31_I	122_G	0.754	0.17
51_H	68_F	0.754	0.17
10_N	85_V	0.753	0.17
85_V	98_L	0.749	0.17
55_F	122_G	0.745	0.17
6_L	133_K	0.742	0.16
30_L	73_K	0.737	0.16
115_L	118_L	0.737	0.16
5_K	103_M	0.735	0.16
11_V	120_K	0.729	0.16
26_L	81_L	0.726	0.16
81_L	91_L	0.725	0.16
67_V	109_Q	0.722	0.16
47_V	124_T	0.718	0.16
107_K	111_T	0.716	0.16
46_L	64_E	0.713	0.16
72_T	98_L	0.709	0.16
45_A	73_K	0.700	0.15
120_K	129_I	0.697	0.15
58_L	65_A	0.696	0.15
30_L	74_K	0.695	0.15
42_L	52_L	0.677	0.15
43_I	67_V	0.673	0.15
119_V	125_G	0.671	0.15
24_F	107_K	0.665	0.15
7_V	64_E	0.660	0.15
43_I	131_A	0.659	0.15
26_L	69_V	0.655	0.14
25_P	129_I	0.648	0.14
39_N	108_Q	0.643	0.14
116_E	129_I	0.639	0.14
62_Q	94_S	0.636	0.14
123_Y	130_E	0.631	0.14
69_V	82_T	0.630	0.14
46_L	108_Q	0.629	0.14
13_R	51_H	0.628	0.14
92_E	131_A	0.615	0.14
91_L	109_Q	0.615	0.14
88_I	106_R	0.614	0.14
36_D	73_K	0.613	0.14
11_V	125_G	0.612	0.13
9_L	58_L	0.611	0.13
30_L	77_R	0.611	0.13
30_L	37_G	0.610	0.13
70_T	91_L	0.610	0.13
57_Q	121_E	0.607	0.13
20_S	130_E	0.606	0.13
12_E	126_T	0.605	0.13
24_F	59_Q	0.605	0.13
3_T	85_V	0.602	0.13
72_T	95_I	0.600	0.13
112_E	130_E	0.598	0.13
69_V	113_T	0.589	0.13
8_D	12_E	0.588	0.13
65_A	129_I	0.586	0.13
70_T	100_Y	0.585	0.13
111_T	116_E	0.583	0.13
9_L	30_L	0.582	0.13
57_Q	84_A	0.574	0.13
48_Q	87_N	0.570	0.13
49_K	87_N	0.564	0.13
46_L	131_A	0.560	0.12
3_T	20_S	0.557	0.12
15_D	90_K	0.550	0.12
36_D	39_N	0.546	0.12
44_E	115_L	0.546	0.12
81_L	89_V	0.544	0.12
30_L	34_K	0.539	0.12
7_V	110_G	0.536	0.12
74_K	83_A	0.536	0.12
42_L	125_G	0.535	0.12
6_L	39_N	0.524	0.12
34_K	74_K	0.524	0.12
43_I	94_S	0.523	0.12
24_F	55_F	0.522	0.12
25_P	55_F	0.520	0.12
86_K	100_Y	0.518	0.12
53_S	130_E	0.516	0.12
28_D	115_L	0.511	0.12
5_K	126_T	0.508	0.11
59_Q	69_V	0.507	0.11
28_D	128_L	0.502	0.11
7_V	82_T	0.501	0.11
31_I	72_T	0.500	0.11

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
4qxzA	2	0.9779	100	0.051	Contact Map
1w5rA	2	0.9853	16.7	0.944	Contact Map
4dmoA	1	0.9559	12.9	0.947	Contact Map
4am6A	1	0.9706	8.2	0.952	Contact Map
1g2yA	4	0.2279	7.7	0.952	Contact Map
2mjfB	1	0.6103	7.4	0.953	Contact Map
4c5pA	1	0.9853	6.8	0.953	Contact Map
4nv8A	2	0.9779	5.7	0.955	Contact Map
2wgoA	1	0.2574	5.3	0.956	Contact Map
1e2tA	5	0.9779	5.2	0.956	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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