Phage_holin_Dp1 - PFAM28P - GREMLIN Contacts

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Phage_holin_Dp1 - Putative phage holin Dp-1

PFAM:	PF16938	Sequences: LSNKVYDILKWIALIVLPALGTLYFALAGIWGLPYGEEVVGTITAVDTFLGALLGISTANYNK	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	63 (63)
Sequences:	1828 (1459)
Seq/√Len:	183.9
META:	0.955

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
26_A	45_A	3.300	1.00
31_W	42_T	2.809	1.00
23_L	49_F	2.781	1.00
25_F	40_V	2.197	1.00
28_A	36_G	2.193	1.00
11_W	16_V	2.149	1.00
2_S	5_V	1.948	1.00
58_T	62_N	1.893	1.00
13_A	47_D	1.861	1.00
24_Y	28_A	1.838	1.00
3_N	7_D	1.779	1.00
30_I	41_G	1.703	1.00
19_A	52_A	1.664	1.00
23_L	45_A	1.606	1.00
4_K	8_I	1.521	1.00
35_Y	38_E	1.493	1.00
10_K	14_L	1.485	1.00
11_W	55_G	1.479	1.00
23_L	46_V	1.440	1.00
16_V	53_L	1.342	1.00
25_F	41_G	1.299	1.00
29_G	37_E	1.293	1.00
28_A	33_L	1.252	1.00
21_G	43_I	1.228	1.00
24_Y	39_V	1.187	1.00
31_W	38_E	1.157	1.00
5_V	8_I	1.149	1.00
8_I	12_I	1.107	1.00
50_L	54_L	1.105	1.00
10_K	58_T	1.097	1.00
44_T	47_D	1.072	1.00
55_G	59_A	1.053	1.00
21_G	44_T	0.986	0.99
44_T	48_T	0.950	0.99
1_L	5_V	0.940	0.99
17_L	21_G	0.929	0.99
40_V	44_T	0.919	0.99
17_L	43_I	0.914	0.99
56_I	60_N	0.903	0.99
27_L	42_T	0.886	0.99
24_Y	34_P	0.865	0.98
21_G	40_V	0.864	0.98
15_I	51_G	0.851	0.98
27_L	33_L	0.844	0.98
14_L	47_D	0.786	0.97
35_Y	39_V	0.782	0.97
16_V	49_F	0.777	0.97
14_L	51_G	0.733	0.96
48_T	52_A	0.703	0.94
36_G	40_V	0.700	0.94
38_E	42_T	0.699	0.94
22_T	45_A	0.698	0.94
5_V	9_L	0.690	0.94
59_A	62_N	0.690	0.94
17_L	47_D	0.683	0.93
14_L	54_L	0.676	0.93
19_A	49_F	0.669	0.93
24_Y	38_E	0.665	0.93
22_T	25_F	0.661	0.92
8_I	11_W	0.661	0.92
22_T	44_T	0.659	0.92
24_Y	35_Y	0.659	0.92
37_E	41_G	0.657	0.92
20_L	43_I	0.650	0.92
22_T	26_A	0.634	0.91
59_A	63_K	0.627	0.90
6_Y	10_K	0.626	0.90
26_A	41_G	0.620	0.90
28_A	34_P	0.611	0.89
4_K	7_D	0.605	0.89
30_I	45_A	0.603	0.88
13_A	50_L	0.600	0.88
49_F	53_L	0.582	0.87
11_W	14_L	0.582	0.87
13_A	54_L	0.575	0.86
40_V	43_I	0.568	0.85
24_Y	33_L	0.564	0.85
24_Y	43_I	0.564	0.85
26_A	48_T	0.548	0.83
60_N	63_K	0.542	0.83
30_I	36_G	0.535	0.82
22_T	52_A	0.535	0.82
33_L	36_G	0.534	0.82
10_K	51_G	0.534	0.82
20_L	49_F	0.532	0.81
34_P	38_E	0.532	0.81
12_I	16_V	0.525	0.81
22_T	48_T	0.525	0.81
43_I	46_V	0.521	0.80
21_G	25_F	0.518	0.80
25_F	29_G	0.516	0.79
15_I	55_G	0.507	0.78
24_Y	40_V	0.504	0.78
12_I	47_D	0.500	0.77

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
1mhsA	2	1	10	0.871	Contact Map
4r0cA	3	1	4.8	0.889	Contact Map
2xq2A	2	0.9206	4.7	0.889	Contact Map
4ev6A	3	0.9683	4.5	0.891	Contact Map
1mqmB	3	0	4	0.893	Contact Map
4i0uA	4	0.9365	2.9	0.9	Contact Map
3dh4A	3	0.9048	2.5	0.904	Contact Map
4he8L	1	0.9841	2.4	0.905	Contact Map
4r1iA	2	1	2.2	0.906	Contact Map
3b8cA	1	0.9683	2.1	0.907	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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