T6SS_Vgr - PFAM28P - GREMLIN Contacts

Home
GREMLIN
- Submit - Monomer
- Submit - Complex
Contacts
Metagenomics
- Contacts
- Structures
Structures
- List
Old Projects
- Complexes (2014)
- PFAM (2013)

T6SS_Vgr - Putative type VI secretion system Rhs element Vgr

PFAM:	PF13296	Sequences: KEVGGGGYNQLRFDDTPGQIRAQLASEHGKSQLNLGHLVHQRDNGRGDPRGEGFELRTDAWGAVRAGKGLLISTDARPGAQGQQLDMAEALAQLEQALQLAESLSDAA	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	108 (106)
Sequences:	2761 (1544)
Seq/√Len:	149.9
META:	0.587

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
54_F	62_G	3.411	1.00
11_L	24_L	3.383	1.00
29_G	60_A	3.201	1.00
77_R	89_E	3.151	1.00
66_A	70_L	2.563	1.00
33_L	56_L	2.436	1.00
10_Q	23_Q	2.294	1.00
7_G	20_I	2.193	1.00
38_L	84_Q	2.124	1.00
9_N	26_S	2.038	1.00
58_T	62_G	2.035	1.00
7_G	27_E	1.949	1.00
102_E	106_D	1.845	1.00
87_M	90_A	1.779	1.00
50_R	55_E	1.766	1.00
98_L	102_E	1.736	1.00
13_F	22_A	1.655	1.00
12_R	21_R	1.621	1.00
16_T	19_Q	1.611	1.00
8_Y	27_E	1.579	1.00
28_H	52_E	1.540	1.00
95_E	98_L	1.533	1.00
60_A	68_K	1.527	1.00
100_L	103_S	1.460	1.00
25_A	32_Q	1.458	1.00
94_L	97_A	1.454	1.00
11_L	22_A	1.446	1.00
21_R	41_Q	1.441	1.00
77_R	86_D	1.415	1.00
12_R	41_Q	1.387	1.00
62_G	66_A	1.333	1.00
9_N	22_A	1.314	1.00
40_H	48_D	1.305	1.00
71_L	75_D	1.286	1.00
86_D	89_E	1.268	1.00
75_D	90_A	1.267	1.00
34_N	55_E	1.232	1.00
44_N	47_G	1.205	1.00
39_V	47_G	1.162	1.00
99_Q	103_S	1.160	1.00
73_S	90_A	1.142	1.00
49_P	52_E	1.141	1.00
75_D	93_Q	1.140	1.00
25_A	30_K	1.113	0.99
27_E	30_K	1.110	0.99
95_E	99_Q	1.109	0.99
3_V	10_Q	1.081	0.99
66_A	69_G	1.069	0.99
64_V	70_L	1.064	0.99
77_R	82_G	1.058	0.99
56_L	62_G	1.056	0.99
21_R	37_H	1.053	0.99
61_W	85_L	1.047	0.99
92_A	96_Q	1.022	0.99
14_D	19_Q	1.021	0.99
77_R	80_A	1.014	0.99
23_Q	32_Q	1.007	0.99
97_A	101_A	1.003	0.99
75_D	89_E	0.978	0.99
32_Q	57_R	0.973	0.99
104_L	108_A	0.968	0.98
98_L	101_A	0.961	0.98
37_H	49_P	0.960	0.98
34_N	38_L	0.958	0.98
93_Q	96_Q	0.948	0.98
39_V	49_P	0.933	0.98
95_E	102_E	0.898	0.97
30_K	59_D	0.881	0.97
91_L	95_E	0.869	0.97
31_S	35_L	0.861	0.97
102_E	105_S	0.847	0.96
61_W	68_K	0.834	0.96
101_A	105_S	0.828	0.96
3_V	6_G	0.821	0.96
31_S	57_R	0.810	0.95
101_A	107_A	0.807	0.95
26_S	31_S	0.799	0.95
62_G	70_L	0.795	0.95
82_G	86_D	0.788	0.95
95_E	103_S	0.787	0.95
71_L	90_A	0.781	0.94
87_M	91_L	0.779	0.94
103_S	107_A	0.776	0.94
23_Q	30_K	0.774	0.94
93_Q	105_S	0.757	0.93
82_G	88_A	0.749	0.93
94_L	98_L	0.747	0.93
93_Q	101_A	0.744	0.93
41_Q	46_R	0.741	0.93
67_G	76_A	0.740	0.93
21_R	39_V	0.735	0.92
93_Q	97_A	0.734	0.92
55_E	65_R	0.732	0.92
103_S	106_D	0.724	0.92
63_A	70_L	0.723	0.92
13_F	16_T	0.720	0.92
92_A	95_E	0.717	0.91
45_G	48_D	0.716	0.91
50_R	57_R	0.716	0.91
17_P	47_G	0.712	0.91
69_G	90_A	0.700	0.90
93_Q	98_L	0.700	0.90
88_A	106_D	0.698	0.90
54_F	64_V	0.692	0.90
96_Q	101_A	0.671	0.88
35_L	54_F	0.667	0.88
19_Q	37_H	0.654	0.87
12_R	38_L	0.651	0.87
8_Y	30_K	0.650	0.87
40_H	47_G	0.650	0.87
93_Q	107_A	0.648	0.87
19_Q	49_P	0.648	0.87
44_N	63_A	0.642	0.86
25_A	34_N	0.640	0.86
100_L	105_S	0.638	0.86
96_Q	99_Q	0.629	0.85
67_G	73_S	0.626	0.85
90_A	96_Q	0.613	0.84
96_Q	100_L	0.612	0.83
13_F	24_L	0.611	0.83
57_R	73_S	0.600	0.82
54_F	61_W	0.595	0.82
23_Q	27_E	0.593	0.82
17_P	25_A	0.581	0.80
8_Y	25_A	0.574	0.79
59_D	76_A	0.567	0.79
42_R	47_G	0.561	0.78
6_G	17_P	0.559	0.78
32_Q	54_F	0.558	0.78
54_F	70_L	0.557	0.77
6_G	16_T	0.554	0.77
63_A	71_L	0.548	0.76
88_A	92_A	0.548	0.76
21_R	40_H	0.547	0.76
25_A	72_I	0.546	0.76
73_S	87_M	0.543	0.76
21_R	46_R	0.543	0.76
18_G	22_A	0.542	0.75
28_H	42_R	0.542	0.75
90_A	93_Q	0.538	0.75
6_G	10_Q	0.535	0.75
82_G	89_E	0.532	0.74
96_Q	105_S	0.530	0.74
100_L	104_L	0.529	0.74
71_L	74_T	0.526	0.73
32_Q	35_L	0.525	0.73
78_P	81_Q	0.524	0.73
96_Q	103_S	0.524	0.73
31_S	62_G	0.523	0.73
21_R	42_R	0.514	0.72
20_I	23_Q	0.514	0.72
10_Q	21_R	0.513	0.71
102_E	107_A	0.513	0.71
91_L	105_S	0.509	0.71
52_E	60_A	0.507	0.71
84_Q	94_L	0.505	0.70
91_L	101_A	0.502	0.70
4_G	17_P	0.500	0.70
62_G	69_G	0.500	0.70

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
4mtkA	4	0.9537	85.5	0.869	Contact Map
1wthA	3	0.9259	9.7	0.93	Contact Map
2f9zC	1	0.287	6.1	0.936	Contact Map
1tnsA	1	0.3611	5.6	0.937	Contact Map
3dgpB	1	0.3519	3	0.945	Contact Map
4bgbA	1	0.5185	2.5	0.947	Contact Map
2o14A	1	0.8056	2.2	0.948	Contact Map
1g4dA	1	0.2963	2.1	0.949	Contact Map
2kbnA	1	0.7407	1.7	0.952	Contact Map
2jtvA	1	0.463	1.6	0.952	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.

Page generated in 0.0051 seconds.