Colicin_V - PFAM28P - GREMLIN Contacts

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Colicin_V - Colicin V production protein

PFAM:	PF02674	Sequences: LDIIILAILLLSALLGFRRGFVRELLSLAGWVLGLLLALRFYPPLAPLLSGFILSPALAAILAFLLIFLVVLILGSLLGRLLRKLVKASGLGGLDRLLGAVFGLLRGLLIVSLLLLLLALFPLPSLPEWIQESRLAPYLESVAP	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	144 (140)
Sequences:	46325 (33719)
Seq/√Len:	2849.8
META:	0.918

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
13_A	100_A	4.071	1.00
12_S	107_G	3.044	1.00
24_E	106_R	2.983	1.00
30_G	75_G	2.686	1.00
44_P	47_P	2.511	1.00
37_L	71_V	2.511	1.00
14_L	18_R	2.458	1.00
13_A	104_L	2.407	1.00
36_L	40_R	2.048	1.00
135_L	138_Y	2.013	1.00
83_R	95_D	1.930	1.00
21_F	98_L	1.930	1.00
11_L	15_L	1.922	1.00
3_I	7_A	1.902	1.00
19_R	24_E	1.893	1.00
17_F	100_A	1.890	1.00
41_F	44_P	1.876	1.00
42_Y	60_A	1.857	1.00
130_I	136_A	1.731	1.00
136_A	140_E	1.624	1.00
15_L	18_R	1.550	1.00
46_A	60_A	1.530	1.00
56_P	60_A	1.479	1.00
80_R	84_K	1.476	1.00
6_L	10_L	1.434	1.00
90_G	93_G	1.414	1.00
5_I	111_V	1.404	1.00
133_S	136_A	1.392	1.00
41_F	67_I	1.383	1.00
131_Q	134_R	1.376	1.00
34_G	38_A	1.376	1.00
37_L	41_F	1.354	1.00
45_L	48_L	1.348	1.00
9_L	107_G	1.332	1.00
77_L	81_L	1.322	1.00
5_I	135_L	1.320	1.00
26_L	79_G	1.319	1.00
44_P	48_L	1.311	1.00
67_I	71_V	1.307	1.00
45_L	67_I	1.289	1.00
12_S	16_G	1.288	1.00
47_P	50_S	1.273	1.00
7_A	11_L	1.243	1.00
12_S	106_R	1.237	1.00
16_G	99_G	1.235	1.00
57_A	60_A	1.233	1.00
76_S	80_R	1.230	1.00
72_L	76_S	1.213	1.00
103_G	107_G	1.212	1.00
40_R	44_P	1.212	1.00
134_R	137_P	1.206	1.00
11_L	14_L	1.201	1.00
134_R	138_Y	1.198	1.00
68_F	72_L	1.186	1.00
49_L	66_L	1.177	1.00
15_L	19_R	1.169	1.00
114_L	118_L	1.152	1.00
59_A	63_A	1.145	1.00
66_L	69_L	1.143	1.00
22_V	95_D	1.135	1.00
128_E	132_E	1.098	1.00
17_F	96_R	1.091	1.00
115_L	119_A	1.087	1.00
73_I	77_L	1.081	1.00
9_L	104_L	1.081	1.00
123_L	126_L	1.074	1.00
50_S	56_P	1.074	1.00
1_L	129_W	1.071	1.00
116_L	119_A	1.070	1.00
50_S	59_A	1.057	1.00
35_L	39_L	1.051	1.00
8_I	107_G	1.045	1.00
23_R	27_S	1.041	1.00
34_G	71_V	1.040	1.00
19_R	27_S	1.025	1.00
119_A	122_P	1.024	1.00
114_L	117_L	1.021	1.00
42_Y	64_F	1.003	1.00
38_A	64_F	0.999	1.00
70_V	73_I	0.993	1.00
48_L	51_G	0.986	1.00
24_E	103_G	0.981	1.00
89_S	93_G	0.977	1.00
107_G	111_V	0.976	1.00
45_L	63_A	0.964	1.00
37_L	40_R	0.953	1.00
89_S	92_G	0.952	1.00
23_R	83_R	0.951	1.00
56_P	59_A	0.948	1.00
13_A	17_F	0.936	1.00
129_W	132_E	0.932	1.00
10_L	14_L	0.918	1.00
12_S	103_G	0.917	1.00
46_A	50_S	0.915	1.00
121_F	124_P	0.908	1.00
21_F	95_D	0.903	1.00
15_L	24_E	0.896	1.00
94_L	97_L	0.889	1.00
55_S	58_L	0.887	1.00
76_S	79_G	0.885	1.00
46_A	63_A	0.885	1.00
43_P	47_P	0.883	1.00
16_G	24_E	0.881	1.00
93_G	97_L	0.876	1.00
19_R	23_R	0.874	1.00
101_V	105_L	0.873	1.00
118_L	122_P	0.872	1.00
127_P	131_Q	0.870	1.00
24_E	102_F	0.867	1.00
106_R	109_L	0.856	1.00
53_I	59_A	0.835	1.00
83_R	87_K	0.830	1.00
3_I	6_L	0.826	1.00
40_R	43_P	0.826	1.00
39_L	64_F	0.820	1.00
120_L	124_P	0.820	1.00
8_I	111_V	0.808	1.00
22_V	86_V	0.808	1.00
23_R	79_G	0.795	1.00
122_P	125_S	0.786	1.00
103_G	106_R	0.785	1.00
106_R	110_I	0.779	1.00
42_Y	46_A	0.767	1.00
30_G	34_G	0.765	1.00
97_L	101_V	0.760	1.00
81_L	84_K	0.752	1.00
8_I	12_S	0.746	1.00
108_L	112_S	0.737	1.00
75_G	79_G	0.737	1.00
9_L	13_A	0.735	1.00
71_V	75_G	0.733	1.00
85_L	88_A	0.731	1.00
43_P	60_A	0.727	1.00
47_P	51_G	0.727	1.00
81_L	85_L	0.721	1.00
14_L	17_F	0.718	1.00
39_L	43_P	0.717	1.00
114_L	119_A	0.716	1.00
42_Y	63_A	0.709	1.00
121_F	125_S	0.706	1.00
58_L	62_L	0.702	1.00
4_I	8_I	0.701	1.00
60_A	64_F	0.700	1.00
17_F	93_G	0.697	1.00
112_S	139_L	0.694	1.00
122_P	126_L	0.684	1.00
74_L	78_L	0.678	1.00
85_L	89_S	0.674	1.00
58_L	61_I	0.672	1.00
101_V	104_L	0.671	1.00
38_A	68_F	0.670	1.00
34_G	68_F	0.669	1.00
80_R	83_R	0.668	1.00
20_G	99_G	0.668	1.00
30_G	79_G	0.663	1.00
37_L	67_I	0.652	1.00
93_G	96_R	0.645	1.00
63_A	67_I	0.644	1.00
9_L	12_S	0.642	1.00
1_L	5_I	0.640	1.00
34_G	72_L	0.636	1.00
120_L	123_L	0.633	1.00
115_L	118_L	0.623	1.00
92_G	96_R	0.621	1.00
98_L	102_F	0.621	1.00
119_A	124_P	0.616	1.00
104_L	107_G	0.614	1.00
49_L	63_A	0.608	1.00
9_L	111_V	0.600	1.00
124_P	127_P	0.599	1.00
79_G	82_L	0.598	1.00
64_F	67_I	0.595	1.00
117_L	121_F	0.593	1.00
102_F	106_R	0.587	1.00
33_L	37_L	0.586	1.00
91_L	95_D	0.583	1.00
55_S	59_A	0.583	1.00
115_L	136_A	0.573	1.00
51_G	54_L	0.572	1.00
61_I	64_F	0.571	1.00
33_L	75_G	0.570	1.00
29_A	33_L	0.564	1.00
131_Q	137_P	0.563	1.00
25_L	102_F	0.562	1.00
35_L	64_F	0.559	1.00
21_F	102_F	0.558	1.00
6_L	135_L	0.557	1.00
95_D	99_G	0.554	1.00
119_A	140_E	0.553	1.00
43_P	46_A	0.549	1.00
31_W	72_L	0.545	1.00
137_P	140_E	0.544	1.00
46_A	49_L	0.543	1.00
104_L	108_L	0.540	1.00
13_A	16_G	0.539	1.00
72_L	75_G	0.539	1.00
98_L	101_V	0.537	1.00
57_A	61_I	0.535	1.00
8_I	11_L	0.533	1.00
24_E	27_S	0.531	1.00
60_A	63_A	0.526	1.00
113_L	116_L	0.524	1.00
29_A	32_V	0.521	1.00
74_L	77_L	0.518	1.00
9_L	108_L	0.516	1.00
54_L	59_A	0.509	1.00
78_L	81_L	0.507	1.00
136_A	139_L	0.503	1.00
38_A	42_Y	0.502	1.00
13_A	103_G	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
2kluA	1	0.3889	18.1	0.87	Contact Map
3udcA	3	0.6319	7.6	0.891	Contact Map
4tkrA	2	0.8889	3.1	0.909	Contact Map
4hfiA	3	0.7778	2.1	0.917	Contact Map
2nwlA	3	0.7569	1.9	0.919	Contact Map
3wajA	1	0.7778	1.9	0.919	Contact Map
3rlbA	1	0.8472	1.7	0.921	Contact Map
2zy9A	2	0.7361	1.5	0.924	Contact Map
3j9pD	4	0.9792	1.5	0.924	Contact Map
4rp9A	2	0.9236	1.4	0.925	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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