Phg_2220_C - PFAM28P - GREMLIN Contacts

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Phg_2220_C - Conserved phage C-terminus (Phg_2220_C)

PFAM:	PF09524	Sequences: IIDYLNEKTGKNYRPTTKKTLKLIKARLKEGFTLEDFKKVIDKKVAEWLNDTKMEKYLRPETLFRGTKFESYLN	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	74 (73)
Sequences:	3639 (3206)
Seq/√Len:	375.3
META:	0.883

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
4_Y	42_D	3.055	1.00
39_K	43_K	2.573	1.00
44_K	47_E	2.405	1.00
27_R	30_E	2.403	1.00
61_E	71_S	2.375	1.00
41_I	64_F	2.372	1.00
59_R	71_S	2.090	1.00
47_E	56_K	2.073	1.00
28_L	33_T	1.932	1.00
8_K	42_D	1.870	1.00
9_T	45_V	1.857	1.00
50_N	55_E	1.836	1.00
34_L	38_K	1.802	1.00
45_V	49_L	1.723	1.00
68_K	71_S	1.709	1.00
8_K	45_V	1.582	1.00
61_E	68_K	1.523	1.00
18_K	22_K	1.465	1.00
4_Y	38_K	1.438	1.00
45_V	58_L	1.426	1.00
19_K	22_K	1.423	1.00
1_I	28_L	1.414	1.00
4_Y	8_K	1.315	1.00
33_T	36_D	1.284	1.00
4_Y	64_F	1.210	1.00
51_D	55_E	1.209	1.00
9_T	58_L	1.139	1.00
19_K	61_E	1.118	1.00
13_Y	60_P	1.117	1.00
48_W	54_M	1.115	1.00
54_M	57_Y	1.113	1.00
37_F	69_F	1.091	1.00
4_Y	41_I	1.087	1.00
35_E	39_K	1.075	1.00
14_R	32_F	1.039	1.00
52_T	55_E	1.034	1.00
25_K	29_K	1.020	1.00
3_D	7_E	1.005	1.00
36_D	39_K	1.000	1.00
59_R	62_T	0.930	1.00
3_D	16_T	0.924	1.00
17_T	20_T	0.923	1.00
40_V	69_F	0.916	1.00
38_K	42_D	0.912	1.00
45_V	50_N	0.911	1.00
35_E	38_K	0.907	1.00
28_L	34_L	0.904	1.00
44_K	63_L	0.878	1.00
43_K	74_N	0.869	1.00
3_D	15_P	0.861	1.00
11_K	55_E	0.855	1.00
19_K	23_L	0.853	1.00
43_K	47_E	0.847	1.00
18_K	25_K	0.833	1.00
70_E	74_N	0.817	1.00
14_R	17_T	0.808	1.00
5_L	13_Y	0.788	1.00
21_L	25_K	0.787	1.00
51_D	54_M	0.786	1.00
34_L	37_F	0.778	1.00
10_G	49_L	0.772	1.00
53_K	56_K	0.768	1.00
40_V	44_K	0.760	1.00
16_T	21_L	0.757	1.00
2_I	20_T	0.757	1.00
1_I	37_F	0.749	1.00
22_K	66_G	0.740	1.00
5_L	60_P	0.738	1.00
24_I	37_F	0.736	1.00
18_K	21_L	0.735	1.00
32_F	70_E	0.734	1.00
20_T	70_E	0.732	1.00
37_F	41_I	0.709	1.00
40_V	73_L	0.687	0.99
23_L	67_T	0.685	0.99
61_E	67_T	0.683	0.99
5_L	63_L	0.682	0.99
49_L	55_E	0.654	0.99
5_L	58_L	0.632	0.99
15_P	21_L	0.629	0.99
55_E	58_L	0.628	0.99
5_L	9_T	0.606	0.98
23_L	61_E	0.605	0.98
32_F	36_D	0.598	0.98
42_D	46_A	0.595	0.98
25_K	28_L	0.589	0.98
5_L	8_K	0.585	0.98
36_D	73_L	0.580	0.98
6_N	11_K	0.560	0.97
33_T	37_F	0.555	0.97
18_K	66_G	0.536	0.97
27_R	37_F	0.535	0.97
5_L	45_V	0.535	0.97
30_E	70_E	0.532	0.97
26_A	66_G	0.531	0.96
36_D	40_V	0.528	0.96
32_F	69_F	0.522	0.96
19_K	30_E	0.519	0.96
24_I	64_F	0.519	0.96
40_V	63_L	0.518	0.96
12_N	16_T	0.517	0.96
60_P	63_L	0.516	0.96
11_K	43_K	0.515	0.96
48_W	51_D	0.514	0.96
48_W	53_K	0.508	0.96
2_I	15_P	0.506	0.95
57_Y	62_T	0.505	0.95
49_L	52_T	0.502	0.95
20_T	24_I	0.501	0.95
48_W	62_T	0.500	0.95

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
3dfgA	1	0.5811	12.4	0.877	Contact Map
3c1dA	2	0.5541	9.7	0.882	Contact Map
3h0gD	1	0.8919	8.8	0.884	Contact Map
1wthD	3	0.8108	5.9	0.893	Contact Map
3mqzA	1	0.6081	5.7	0.894	Contact Map
2ragA	2	0.7838	5.3	0.896	Contact Map
4nomA	2	0.6081	5.2	0.896	Contact Map
4jdfA	1	0.9459	4.7	0.898	Contact Map
2i2oA	2	0.7973	4.6	0.899	Contact Map
3ttnA	1	0.9459	4.6	0.899	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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