Phage_Mu_F - PFAM28P - GREMLIN Contacts

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Phage_Mu_F - Phage Mu protein F like protein

PFAM:	PF04233	Sequences: QDIRDALAQGIAEGESIDEIAKRIRKRGGVTSRSRAETIARTETARAYNAGRLEAYAANLGVGPKKWEWVATLDERTRPIHAALDGKVFPLDDPFWGTGYPPNHPNCRCTVI	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	112 (109)
Sequences:	25057 (21781)
Seq/√Len:	2086.3
META:	0.911

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_E	23_R	3.331	1.00
71_A	77_T	2.927	1.00
78_R	81_H	2.835	1.00
69_W	103_N	2.700	1.00
78_R	109_C	2.534	1.00
68_E	88_V	2.456	1.00
15_E	19_E	2.341	1.00
10_G	20_I	2.305	1.00
38_T	105_P	2.278	1.00
6_A	23_R	2.238	1.00
38_T	106_N	1.908	1.00
89_F	95_F	1.746	1.00
35_R	38_T	1.741	1.00
80_I	103_N	1.738	1.00
8_A	12_A	1.719	1.00
16_S	19_E	1.716	1.00
70_V	110_T	1.697	1.00
71_A	85_D	1.688	1.00
9_Q	13_E	1.651	1.00
41_R	106_N	1.640	1.00
81_H	104_H	1.627	1.00
78_R	104_H	1.595	1.00
73_L	77_T	1.569	1.00
34_S	38_T	1.558	1.00
74_D	108_R	1.555	1.00
90_P	93_D	1.486	1.00
17_I	21_A	1.458	1.00
10_G	15_E	1.397	1.00
4_R	8_A	1.382	1.00
6_A	9_Q	1.372	1.00
45_A	49_N	1.352	1.00
6_A	27_R	1.352	1.00
70_V	85_D	1.350	1.00
73_L	85_D	1.312	1.00
21_A	37_E	1.287	1.00
95_F	99_G	1.277	1.00
35_R	39_I	1.274	1.00
42_T	105_P	1.274	1.00
69_W	109_C	1.273	1.00
66_K	88_V	1.250	1.00
66_K	90_P	1.215	1.00
97_G	100_Y	1.206	1.00
56_Y	60_L	1.199	1.00
49_N	52_R	1.187	1.00
84_L	87_K	1.168	1.00
72_T	77_T	1.165	1.00
79_P	83_A	1.148	1.00
57_A	60_L	1.147	1.00
6_A	20_I	1.140	1.00
56_Y	59_N	1.136	1.00
89_F	93_D	1.125	1.00
50_A	54_E	1.117	1.00
74_D	77_T	1.116	1.00
39_I	43_E	1.112	1.00
38_T	42_T	1.048	1.00
77_T	82_A	1.038	1.00
59_N	63_G	1.032	1.00
46_R	50_A	1.032	1.00
37_E	41_R	1.030	1.00
43_E	46_R	1.020	1.00
101_P	105_P	1.001	1.00
50_A	53_L	0.993	1.00
47_A	51_G	0.981	1.00
28_G	31_T	0.979	1.00
68_E	86_G	0.974	1.00
85_D	88_V	0.972	1.00
5_D	9_Q	0.954	1.00
87_K	96_W	0.939	1.00
84_L	89_F	0.929	1.00
80_I	83_A	0.922	1.00
45_A	48_Y	0.899	1.00
52_R	55_A	0.893	1.00
19_E	23_R	0.888	1.00
80_I	84_L	0.884	1.00
23_R	27_R	0.882	1.00
67_W	91_L	0.879	1.00
21_A	25_R	0.874	1.00
103_N	109_C	0.871	1.00
27_R	30_V	0.865	1.00
37_E	106_N	0.828	1.00
44_T	48_Y	0.827	1.00
42_T	46_R	0.826	1.00
18_D	21_A	0.826	1.00
59_N	62_V	0.821	1.00
41_R	45_A	0.791	1.00
53_L	57_A	0.768	1.00
60_L	63_G	0.768	1.00
71_A	109_C	0.753	1.00
73_L	82_A	0.737	1.00
15_E	20_I	0.733	1.00
84_L	98_T	0.730	1.00
84_L	99_G	0.727	1.00
9_Q	23_R	0.718	1.00
96_W	100_Y	0.716	1.00
59_N	64_P	0.714	1.00
20_I	40_A	0.709	1.00
27_R	31_T	0.703	1.00
78_R	105_P	0.693	1.00
81_H	109_C	0.689	1.00
84_L	97_G	0.687	1.00
79_P	82_A	0.683	1.00
76_R	108_R	0.663	1.00
25_R	33_R	0.662	1.00
65_K	90_P	0.661	1.00
43_E	105_P	0.654	1.00
65_K	88_V	0.648	1.00
34_S	106_N	0.646	1.00
9_Q	12_A	0.643	1.00
28_G	32_S	0.639	1.00
49_N	110_T	0.637	1.00
72_T	108_R	0.636	1.00
20_I	24_I	0.634	1.00
77_T	108_R	0.634	1.00
34_S	37_E	0.633	1.00
20_I	44_T	0.631	1.00
57_A	91_L	0.630	1.00
58_A	61_G	0.628	1.00
102_P	105_P	0.624	1.00
69_W	84_L	0.618	1.00
23_R	26_K	0.615	1.00
30_V	34_S	0.614	1.00
62_V	65_K	0.613	1.00
17_I	20_I	0.610	1.00
54_E	57_A	0.610	1.00
8_A	11_I	0.601	1.00
32_S	35_R	0.594	1.00
17_I	37_E	0.586	1.00
51_G	55_A	0.580	1.00
3_I	24_I	0.579	1.00
18_D	22_K	0.579	1.00
19_E	22_K	0.578	1.00
6_A	10_G	0.572	1.00
71_A	74_D	0.571	1.00
24_I	27_R	0.566	1.00
7_L	10_G	0.566	1.00
103_N	107_C	0.566	1.00
89_F	96_W	0.563	1.00
84_L	103_N	0.563	1.00
25_R	36_A	0.560	1.00
17_I	45_A	0.559	1.00
6_A	15_E	0.558	1.00
41_R	108_R	0.558	1.00
101_P	104_H	0.557	1.00
72_T	75_E	0.555	1.00
33_R	37_E	0.544	1.00
78_R	82_A	0.536	1.00
67_W	89_F	0.534	1.00
95_F	98_T	0.533	1.00
18_D	37_E	0.529	1.00
5_D	8_A	0.528	1.00
11_I	48_Y	0.527	1.00
58_A	62_V	0.523	1.00
61_G	64_P	0.521	1.00
89_F	94_P	0.521	1.00
45_A	102_P	0.518	1.00
91_L	94_P	0.517	1.00
52_R	110_T	0.516	1.00
57_A	61_G	0.516	1.00
71_A	82_A	0.515	1.00
12_A	15_E	0.512	1.00
10_G	23_R	0.510	1.00
52_R	56_Y	0.501	1.00
9_Q	15_E	0.500	1.00
31_T	35_R	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
3ob4A	2	0.75	6.7	0.899	Contact Map
2hl7A	1	0.3304	6.5	0.9	Contact Map
4tmaI	1	0.2768	5.2	0.905	Contact Map
3g2bA	2	0.4821	5.2	0.905	Contact Map
2b3fA	1	0.3125	5.1	0.905	Contact Map
2xd3A	1	0.2857	5	0.905	Contact Map
3i3vA	3	0.2857	4.9	0.906	Contact Map
4aq4A	1	0.3571	4.3	0.908	Contact Map
2kw0A	1	0.3571	4.3	0.908	Contact Map
4g9qA	3	0.4643	4.2	0.908	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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