Tape_meas_lam_C - PFAM28P - GREMLIN Contacts

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Tape_meas_lam_C - Lambda phage tail tape-measure protein (Tape_meas_lam_C)

PFAM:	PF09718	Sequences: GDWSAGAKRALADYADSATDAAKQAEDAFTSAFSGMEDALVDFVTTGKLSFKDLADSIIADLARIAIQQAITGPLA	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	76 (72)
Sequences:	4937 (4033)
Seq/√Len:	475.3
META:	0.872

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
63_A	66_A	2.449	1.00
55_A	65_I	2.330	1.00
57_S	61_D	2.225	1.00
34_S	37_E	2.155	1.00
71_I	74_P	2.146	1.00
20_D	23_K	2.142	1.00
45_T	60_A	2.102	1.00
50_S	53_D	1.958	1.00
69_Q	73_G	1.825	1.00
61_D	64_R	1.699	1.00
52_K	56_D	1.654	1.00
9_R	26_E	1.644	1.00
67_I	70_A	1.627	1.00
48_K	53_D	1.575	1.00
36_M	43_F	1.495	1.00
55_A	59_I	1.454	1.00
66_A	70_A	1.452	1.00
41_V	45_T	1.448	1.00
29_F	36_M	1.372	1.00
13_D	17_S	1.371	1.00
53_D	56_D	1.326	1.00
9_R	13_D	1.296	1.00
42_D	45_T	1.288	1.00
55_A	58_I	1.288	1.00
54_L	58_I	1.284	1.00
26_E	30_T	1.264	1.00
38_D	64_R	1.223	1.00
21_A	25_A	1.217	1.00
38_D	41_V	1.214	1.00
23_K	26_E	1.196	1.00
58_I	65_I	1.190	1.00
61_D	68_Q	1.184	1.00
56_D	60_A	1.137	1.00
17_S	20_D	1.100	1.00
44_V	54_L	1.082	1.00
37_E	41_V	1.061	1.00
8_K	17_S	1.041	1.00
27_D	30_T	1.021	1.00
8_K	12_A	1.012	1.00
13_D	26_E	1.009	1.00
12_A	16_D	1.005	1.00
55_A	61_D	0.992	1.00
22_A	29_F	0.987	1.00
11_L	15_A	0.982	1.00
5_A	9_R	0.978	1.00
12_A	15_A	0.941	1.00
19_T	24_Q	0.937	1.00
47_G	54_L	0.904	1.00
31_S	35_G	0.902	1.00
5_A	8_K	0.883	1.00
23_K	27_D	0.880	1.00
15_A	19_T	0.878	1.00
41_V	44_V	0.876	1.00
40_L	67_I	0.869	1.00
14_Y	18_A	0.845	1.00
59_I	63_A	0.825	1.00
41_V	64_R	0.805	1.00
4_S	8_K	0.797	1.00
8_K	13_D	0.786	1.00
56_D	64_R	0.784	1.00
25_A	28_A	0.783	1.00
46_T	49_L	0.781	1.00
64_R	68_Q	0.774	1.00
70_A	74_P	0.768	1.00
65_I	69_Q	0.763	1.00
45_T	49_L	0.760	1.00
36_M	39_A	0.749	1.00
60_A	64_R	0.749	1.00
7_A	10_A	0.737	1.00
25_A	29_F	0.727	1.00
9_R	12_A	0.725	1.00
67_I	74_P	0.719	1.00
19_T	23_K	0.718	1.00
62_L	66_A	0.713	1.00
56_D	59_I	0.710	1.00
41_V	67_I	0.709	1.00
66_A	69_Q	0.700	1.00
42_D	60_A	0.698	1.00
15_A	21_A	0.671	1.00
29_F	33_F	0.666	1.00
12_A	17_S	0.662	1.00
45_T	63_A	0.651	1.00
42_D	46_T	0.646	1.00
10_A	26_E	0.642	1.00
66_A	72_T	0.629	1.00
27_D	31_S	0.625	0.99
44_V	50_S	0.623	0.99
45_T	56_D	0.594	0.99
72_T	75_L	0.593	0.99
37_E	68_Q	0.586	0.99
44_V	51_F	0.578	0.99
31_S	34_S	0.574	0.99
70_A	73_G	0.568	0.99
5_A	12_A	0.562	0.99
22_A	25_A	0.561	0.99
65_I	72_T	0.561	0.99
38_D	42_D	0.560	0.99
60_A	63_A	0.546	0.99
48_K	57_S	0.543	0.99
53_D	57_S	0.538	0.98
30_T	34_S	0.531	0.98
18_A	22_A	0.525	0.98
14_Y	33_F	0.525	0.98
16_D	19_T	0.518	0.98
22_A	26_E	0.518	0.98
39_A	42_D	0.507	0.98
14_Y	37_E	0.501	0.98
29_F	32_A	0.500	0.98

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
3g1gA	2	0.5132	9.9	0.839	Contact Map
3g21A	2	0.5263	8.9	0.842	Contact Map
3favB	1	0.5789	8	0.846	Contact Map
3ogiB	1	0.6842	7.1	0.849	Contact Map
4lwsB	1	0.5789	6.5	0.852	Contact Map
3h6pC	1	0.4605	6.5	0.852	Contact Map
3gwkC	2	0.7368	5.1	0.859	Contact Map
2vs0A	2	0.6184	5	0.86	Contact Map
2a01A	1	0.8553	4.8	0.86	Contact Map
1d1dA	1	0.9868	4.7	0.861	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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