Cas_VVA1548 - PFAM28P - GREMLIN Contacts

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Cas_VVA1548 - Putative CRISPR-associated protein (Cas_VVA1548)

PFAM:	PF09652	Sequences: YFVTRHPGAVEWLREQGIAVDRVVAHLDPAEVVPGDTVIGTLPVHLAAEVCARGARYTHLSLDLPPELRGRELTAEEMRAYGARLEEYRVQ	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	91 (89)
Sequences:	932 (800)
Seq/√Len:	84.7
META:	0.907

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
65_P	68_L	3.564	1.00
15_E	79_R	3.521	1.00
56_R	87_E	3.432	1.00
68_L	81_Y	3.138	1.00
65_P	81_Y	2.657	1.00
58_T	87_E	2.640	1.00
68_L	77_E	2.620	1.00
77_E	80_A	2.454	1.00
2_F	13_L	2.451	1.00
16_Q	79_R	2.416	1.00
50_V	55_A	2.218	1.00
8_G	75_A	2.100	1.00
47_A	51_C	2.057	1.00
15_E	76_E	1.903	1.00
71_R	77_E	1.861	1.00
47_A	50_V	1.833	1.00
37_T	58_T	1.827	1.00
74_T	77_E	1.818	1.00
37_T	56_R	1.787	1.00
61_S	86_E	1.785	1.00
62_L	78_M	1.685	1.00
44_V	47_A	1.667	1.00
44_V	57_Y	1.574	1.00
54_G	57_Y	1.428	0.99
4_T	41_T	1.216	0.98
12_W	78_M	1.190	0.97
4_T	13_L	1.184	0.97
12_W	16_Q	1.183	0.97
22_R	31_E	1.160	0.97
5_R	72_E	1.156	0.97
9_A	78_M	1.098	0.96
39_I	58_T	1.078	0.95
5_R	69_R	1.040	0.94
9_A	41_T	1.032	0.94
63_D	84_R	1.003	0.93
68_L	71_R	0.998	0.93
39_I	85_L	0.988	0.92
9_A	60_L	0.972	0.92
45_H	59_H	0.959	0.91
37_T	87_E	0.952	0.91
49_E	52_A	0.933	0.90
11_E	14_R	0.914	0.89
27_L	55_A	0.906	0.89
10_V	23_V	0.899	0.88
13_L	18_I	0.883	0.87
34_P	49_E	0.874	0.87
20_V	23_V	0.872	0.87
10_V	20_V	0.869	0.87
61_S	88_Y	0.847	0.85
12_W	83_A	0.839	0.85
28_D	31_E	0.834	0.84
37_T	55_A	0.828	0.84
32_V	55_A	0.828	0.84
26_H	69_R	0.827	0.84
25_A	66_P	0.817	0.83
29_P	32_V	0.808	0.82
45_H	64_L	0.797	0.82
44_V	90_V	0.789	0.81
73_L	77_E	0.787	0.81
47_A	90_V	0.780	0.80
38_V	42_L	0.774	0.80
64_L	73_L	0.773	0.80
15_E	75_A	0.763	0.79
76_E	80_A	0.761	0.78
3_V	24_V	0.753	0.78
10_V	25_A	0.745	0.77
27_L	32_V	0.744	0.77
5_R	70_G	0.727	0.75
12_W	82_G	0.719	0.74
22_R	25_A	0.713	0.74
36_D	55_A	0.703	0.73
61_S	85_L	0.697	0.72
61_S	84_R	0.692	0.72
18_I	39_I	0.687	0.71
18_I	21_D	0.674	0.70
47_A	57_Y	0.673	0.69
50_V	57_Y	0.670	0.69
78_M	83_A	0.666	0.69
6_H	69_R	0.666	0.69
61_S	83_A	0.657	0.68
45_H	61_S	0.653	0.67
6_H	72_E	0.652	0.67
41_T	57_Y	0.649	0.67
11_E	15_E	0.649	0.67
8_G	12_W	0.647	0.66
78_M	81_Y	0.647	0.66
59_H	86_E	0.646	0.66
7_P	72_E	0.639	0.65
45_H	57_Y	0.639	0.65
56_R	89_R	0.637	0.65
36_D	54_G	0.635	0.65
33_V	52_A	0.634	0.65
48_A	52_A	0.634	0.65
11_E	89_R	0.632	0.65
74_T	79_R	0.623	0.64
31_E	34_P	0.620	0.63
82_G	85_L	0.619	0.63
52_A	80_A	0.614	0.62
32_V	36_D	0.611	0.62
7_P	11_E	0.609	0.62
44_V	59_H	0.597	0.60
8_G	72_E	0.593	0.60
8_G	78_M	0.592	0.60
63_D	68_L	0.588	0.59
7_P	38_V	0.583	0.58
45_H	49_E	0.579	0.58
3_V	42_L	0.574	0.57
47_A	54_G	0.570	0.57
29_P	33_V	0.562	0.56
58_T	85_L	0.559	0.55
24_V	31_E	0.559	0.55
32_V	54_G	0.556	0.55
45_H	63_D	0.556	0.55
77_E	81_Y	0.554	0.55
85_L	88_Y	0.550	0.54
41_T	45_H	0.547	0.54
33_V	54_G	0.546	0.54
45_H	62_L	0.545	0.53
29_P	49_E	0.543	0.53
64_L	68_L	0.543	0.53
78_M	82_G	0.543	0.53
33_V	49_E	0.538	0.53
19_A	22_R	0.535	0.52
26_H	32_V	0.513	0.49
18_I	78_M	0.511	0.49
8_G	83_A	0.511	0.49
26_H	66_P	0.510	0.49
70_G	73_L	0.509	0.49
29_P	46_L	0.507	0.48
13_L	85_L	0.503	0.48
39_I	54_G	0.502	0.48
41_T	59_H	0.502	0.48
11_E	75_A	0.501	0.48
19_A	88_Y	0.500	0.47

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
3j3iA	6	0.6484	15.8	0.907	Contact Map
4tp8M	1	0.7143	13.5	0.91	Contact Map
4rb5M	1	0.7143	12.1	0.911	Contact Map
4ov4A	2	0.5934	12.1	0.912	Contact Map
2fi0A	1	0.6703	11.8	0.912	Contact Map
1kjwA	1	0.978	11	0.913	Contact Map
2c5qA	3	0.956	10.9	0.913	Contact Map
1qwdA	1	0.3297	8.8	0.917	Contact Map
3nojA	5	0.956	7.6	0.919	Contact Map
1zrtD	1	0.7912	6.7	0.921	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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