CVPA - ECOLI - GREMLIN Contacts

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CVPA - Colicin V production protein

UniProt:	P08550	Sequences: MVWIDYAIIAVIAFSSLVSLIRGFVREALSLVTWGCAFFVASHYYTYLSVWFTGFEDELVRNGIAIAVLFIATLIVGAIVNFVIGQLVEKTGLSGTDRVLGVCFGALRGVLIVAAILFFLDSFTGVSKSEDWSKSQLIPQFSFIIRCFFDYLQSSSSFLPRA	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG10169
Length:	162 (152)
Sequences:	2076 (1626)
Seq/√Len:	131.9

ECOLI - CVPA
BACSU - YSHB

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
15_S	108_R	4.906	1.00
16_S	102_V	4.059	1.00
40_V	73_T	4.007	1.00
85_G	97_D	3.567	1.00
33_T	77_G	3.517	1.00
12_I	106_A	3.056	1.00
40_V	69_L	2.948	1.00
16_S	106_A	2.747	1.00
24_F	100_L	2.709	1.00
15_S	105_G	2.681	1.00
48_L	69_L	2.516	1.00
8_I	137_L	2.481	1.00
15_S	109_G	2.434	1.00
27_E	104_F	2.271	1.00
29_L	81_N	2.260	1.00
41_A	66_I	2.153	1.00
22_R	27_E	2.077	1.00
11_V	116_I	2.039	1.00
48_L	51_W	1.984	1.00
91_T	97_D	1.981	1.00
39_F	43_H	1.917	1.00
47_Y	50_V	1.893	1.00
135_S	138_I	1.771	1.00
6_Y	10_A	1.768	1.00
3_W	7_A	1.740	1.00
9_I	13_A	1.736	1.00
18_V	22_R	1.648	1.00
11_V	15_S	1.626	1.00
69_L	73_T	1.576	1.00
45_Y	65_A	1.545	1.00
55_F	64_I	1.545	1.00
132_W	138_I	1.543	1.00
49_S	62_N	1.528	1.00
11_V	109_G	1.525	1.00
45_Y	62_N	1.503	1.00
92_G	95_G	1.491	1.00
45_Y	66_I	1.467	1.00
37_A	70_F	1.453	1.00
48_L	65_A	1.437	1.00
130_E	134_K	1.436	1.00
114_A	141_F	1.421	1.00
36_C	77_G	1.387	1.00
49_S	65_A	1.383	1.00
17_L	21_I	1.383	1.00
88_V	91_T	1.382	1.00
99_V	103_C	1.367	1.00
12_I	109_G	1.366	1.00
8_I	113_V	1.340	1.00
37_A	73_T	1.311	1.00
4_I	8_I	1.302	1.00
27_E	108_R	1.228	1.00
41_A	65_A	1.222	1.00
114_A	144_I	1.206	1.00
137_L	140_Q	1.191	0.99
11_V	113_V	1.179	0.99
105_G	109_G	1.178	0.99
52_F	68_V	1.162	0.99
55_F	61_R	1.157	0.99
18_V	21_I	1.131	0.99
60_V	64_I	1.111	0.99
29_L	37_A	1.090	0.99
84_I	87_L	1.069	0.99
26_R	81_N	1.063	0.99
142_S	145_I	1.062	0.99
110_V	114_A	1.049	0.99
72_A	139_P	1.025	0.98
72_A	80_V	1.017	0.98
25_V	88_V	1.015	0.98
140_Q	144_I	0.986	0.98
26_R	85_G	0.978	0.98
88_V	93_L	0.970	0.98
52_F	65_A	0.969	0.98
52_F	61_R	0.949	0.97
34_W	108_R	0.941	0.97
2_V	6_Y	0.926	0.97
133_S	139_P	0.925	0.97
70_F	74_L	0.921	0.97
65_A	69_L	0.919	0.97
29_L	84_I	0.906	0.96
41_A	117_L	0.906	0.96
118_F	145_I	0.901	0.96
44_Y	69_L	0.897	0.96
97_D	131_D	0.879	0.96
78_A	108_R	0.876	0.96
135_S	141_F	0.865	0.95
34_W	37_A	0.863	0.95
7_A	10_A	0.859	0.95
44_Y	47_Y	0.859	0.95
104_F	108_R	0.859	0.95
124_T	132_W	0.857	0.95
120_L	123_F	0.857	0.95
114_A	138_I	0.856	0.95
37_A	41_A	0.851	0.95
53_T	58_E	0.848	0.95
16_S	20_L	0.843	0.95
5_D	136_Q	0.834	0.94
20_L	102_V	0.829	0.94
5_D	37_A	0.817	0.94
66_I	93_L	0.816	0.94
42_S	45_Y	0.804	0.93
6_Y	151_Y	0.803	0.93
83_V	86_Q	0.777	0.92
70_F	73_T	0.773	0.92
121_D	142_S	0.771	0.92
26_R	114_A	0.769	0.92
91_T	142_S	0.766	0.91
10_A	32_V	0.760	0.91
103_C	107_L	0.750	0.91
5_D	135_S	0.741	0.90
47_Y	65_A	0.739	0.90
142_S	146_R	0.739	0.90
67_A	152_L	0.737	0.90
110_V	144_I	0.728	0.89
11_V	112_I	0.724	0.89
89_E	130_E	0.720	0.89
83_V	93_L	0.718	0.89
37_A	74_L	0.717	0.88
24_F	28_A	0.711	0.88
24_F	104_F	0.709	0.88
34_W	100_L	0.702	0.87
24_F	81_N	0.700	0.87
13_A	17_L	0.693	0.87
143_F	146_R	0.691	0.87
6_Y	33_T	0.682	0.86
29_L	41_A	0.682	0.86
113_V	137_L	0.681	0.86
12_I	16_S	0.679	0.86
54_G	60_V	0.676	0.85
25_V	84_I	0.676	0.85
7_A	141_F	0.674	0.85
45_Y	69_L	0.661	0.84
38_F	42_S	0.659	0.84
32_V	77_G	0.656	0.84
80_V	88_V	0.655	0.84
38_F	41_A	0.655	0.84
109_G	113_V	0.637	0.82
34_W	74_L	0.636	0.82
74_L	78_A	0.636	0.82
10_A	149_F	0.634	0.82
124_T	127_S	0.630	0.81
88_V	97_D	0.629	0.81
148_F	153_Q	0.627	0.81
50_V	53_T	0.627	0.81
51_W	54_G	0.626	0.81
113_V	141_F	0.625	0.81
58_E	130_E	0.625	0.81
20_L	98_R	0.623	0.80
58_E	148_F	0.619	0.80
125_G	128_K	0.618	0.80
11_V	60_V	0.618	0.80
40_V	56_E	0.615	0.80
49_S	53_T	0.613	0.79
59_L	129_S	0.609	0.79
25_V	97_D	0.603	0.78
48_L	118_F	0.601	0.78
85_G	94_S	0.599	0.78
60_V	119_F	0.598	0.78
10_A	151_Y	0.594	0.77
72_A	151_Y	0.591	0.77
10_A	52_F	0.590	0.77
42_S	115_A	0.589	0.77
114_A	146_R	0.589	0.77
79_I	82_F	0.588	0.77
37_A	92_G	0.585	0.76
60_V	63_G	0.584	0.76
126_V	132_W	0.583	0.76
32_V	86_Q	0.581	0.76
118_F	149_F	0.580	0.76
74_L	108_R	0.580	0.76
29_L	108_R	0.579	0.75
133_S	136_Q	0.579	0.75
38_F	50_V	0.576	0.75
81_N	85_G	0.576	0.75
84_I	88_V	0.575	0.75
43_H	80_V	0.570	0.74
91_T	94_S	0.569	0.74
41_A	78_A	0.569	0.74
8_I	117_L	0.568	0.74
116_I	120_L	0.567	0.74
64_I	78_A	0.566	0.74
107_L	143_F	0.565	0.74
74_L	81_N	0.565	0.74
22_R	108_R	0.564	0.74
10_A	14_F	0.562	0.73
44_Y	73_T	0.561	0.73
148_F	152_L	0.558	0.73
28_A	136_Q	0.556	0.72
34_W	70_F	0.555	0.72
102_V	129_S	0.554	0.72
127_S	153_Q	0.552	0.72
12_I	110_V	0.551	0.72
33_T	73_T	0.551	0.72
5_D	137_L	0.551	0.72
13_A	128_K	0.550	0.72
53_T	61_R	0.547	0.71
50_V	80_V	0.540	0.70
23_G	101_G	0.536	0.70
22_R	122_S	0.530	0.69
104_F	112_I	0.530	0.69
27_E	30_S	0.529	0.69
15_S	34_W	0.528	0.69
94_S	97_D	0.526	0.68
114_A	145_I	0.521	0.68
4_I	131_D	0.521	0.68
4_I	138_I	0.521	0.68
39_F	85_G	0.521	0.68
120_L	124_T	0.521	0.68
43_H	47_Y	0.520	0.67
31_L	82_F	0.518	0.67
54_G	79_I	0.518	0.67
40_V	115_A	0.515	0.67
82_F	99_V	0.514	0.67
9_I	137_L	0.513	0.66
111_L	114_A	0.511	0.66
26_R	93_L	0.510	0.66
100_L	141_F	0.509	0.66
19_S	23_G	0.509	0.66
121_D	132_W	0.508	0.66
117_L	145_I	0.507	0.66
33_T	123_F	0.507	0.66
85_G	102_V	0.506	0.65
72_A	107_L	0.506	0.65
18_V	115_A	0.503	0.65
144_I	148_F	0.503	0.65
18_V	37_A	0.503	0.65
38_F	140_Q	0.502	0.65
51_W	130_E	0.501	0.65
76_V	118_F	0.500	0.64

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
3j9pD	4	0.9938	32.9	0.907	Contact Map
3j5pB	3	0.9815	18	0.918	Contact Map
4aw6A	2	0.8272	15.1	0.92	Contact Map
4il3A	1	0.8827	9.3	0.928	Contact Map
2kluA	1	0.4074	7.4	0.931	Contact Map
3udcA	3	0.6605	6.8	0.932	Contact Map
2m20A	2	0.3704	4.8	0.937	Contact Map
3j01B	1	0.6173	4.7	0.937	Contact Map
3behA	3	0.784	4.5	0.938	Contact Map
3tuiA	2	0.7284	3.3	0.941	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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