GREMLIN Database
T6SS_Vgr - Putative type VI secretion system Rhs element Vgr
PFAM: PF13296 Sequences:
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_F62_G3.4111.00
11_L24_L3.3831.00
29_G60_A3.2011.00
77_R89_E3.1511.00
66_A70_L2.5631.00
33_L56_L2.4361.00
10_Q23_Q2.2941.00
7_G20_I2.1931.00
38_L84_Q2.1241.00
9_N26_S2.0381.00
58_T62_G2.0351.00
7_G27_E1.9491.00
102_E106_D1.8451.00
87_M90_A1.7791.00
50_R55_E1.7661.00
98_L102_E1.7361.00
13_F22_A1.6551.00
12_R21_R1.6211.00
16_T19_Q1.6111.00
8_Y27_E1.5791.00
28_H52_E1.5401.00
95_E98_L1.5331.00
60_A68_K1.5271.00
100_L103_S1.4601.00
25_A32_Q1.4581.00
94_L97_A1.4541.00
11_L22_A1.4461.00
21_R41_Q1.4411.00
77_R86_D1.4151.00
12_R41_Q1.3871.00
62_G66_A1.3331.00
9_N22_A1.3141.00
40_H48_D1.3051.00
71_L75_D1.2861.00
86_D89_E1.2681.00
75_D90_A1.2671.00
34_N55_E1.2321.00
44_N47_G1.2051.00
39_V47_G1.1621.00
99_Q103_S1.1601.00
73_S90_A1.1421.00
49_P52_E1.1411.00
75_D93_Q1.1401.00
25_A30_K1.1130.99
27_E30_K1.1100.99
95_E99_Q1.1090.99
3_V10_Q1.0810.99
66_A69_G1.0690.99
64_V70_L1.0640.99
77_R82_G1.0580.99
56_L62_G1.0560.99
21_R37_H1.0530.99
61_W85_L1.0470.99
92_A96_Q1.0220.99
14_D19_Q1.0210.99
77_R80_A1.0140.99
23_Q32_Q1.0070.99
97_A101_A1.0030.99
75_D89_E0.9780.99
32_Q57_R0.9730.99
104_L108_A0.9680.98
98_L101_A0.9610.98
37_H49_P0.9600.98
34_N38_L0.9580.98
93_Q96_Q0.9480.98
39_V49_P0.9330.98
95_E102_E0.8980.97
30_K59_D0.8810.97
91_L95_E0.8690.97
31_S35_L0.8610.97
102_E105_S0.8470.96
61_W68_K0.8340.96
101_A105_S0.8280.96
3_V6_G0.8210.96
31_S57_R0.8100.95
101_A107_A0.8070.95
26_S31_S0.7990.95
62_G70_L0.7950.95
82_G86_D0.7880.95
95_E103_S0.7870.95
71_L90_A0.7810.94
87_M91_L0.7790.94
103_S107_A0.7760.94
23_Q30_K0.7740.94
93_Q105_S0.7570.93
82_G88_A0.7490.93
94_L98_L0.7470.93
93_Q101_A0.7440.93
41_Q46_R0.7410.93
67_G76_A0.7400.93
21_R39_V0.7350.92
93_Q97_A0.7340.92
55_E65_R0.7320.92
103_S106_D0.7240.92
63_A70_L0.7230.92
13_F16_T0.7200.92
92_A95_E0.7170.91
45_G48_D0.7160.91
50_R57_R0.7160.91
17_P47_G0.7120.91
69_G90_A0.7000.90
93_Q98_L0.7000.90
88_A106_D0.6980.90
54_F64_V0.6920.90
96_Q101_A0.6710.88
35_L54_F0.6670.88
19_Q37_H0.6540.87
12_R38_L0.6510.87
8_Y30_K0.6500.87
40_H47_G0.6500.87
93_Q107_A0.6480.87
19_Q49_P0.6480.87
44_N63_A0.6420.86
25_A34_N0.6400.86
100_L105_S0.6380.86
96_Q99_Q0.6290.85
67_G73_S0.6260.85
90_A96_Q0.6130.84
96_Q100_L0.6120.83
13_F24_L0.6110.83
57_R73_S0.6000.82
54_F61_W0.5950.82
23_Q27_E0.5930.82
17_P25_A0.5810.80
8_Y25_A0.5740.79
59_D76_A0.5670.79
42_R47_G0.5610.78
6_G17_P0.5590.78
32_Q54_F0.5580.78
54_F70_L0.5570.77
6_G16_T0.5540.77
63_A71_L0.5480.76
88_A92_A0.5480.76
21_R40_H0.5470.76
25_A72_I0.5460.76
73_S87_M0.5430.76
21_R46_R0.5430.76
18_G22_A0.5420.75
28_H42_R0.5420.75
90_A93_Q0.5380.75
6_G10_Q0.5350.75
82_G89_E0.5320.74
96_Q105_S0.5300.74
100_L104_L0.5290.74
71_L74_T0.5260.73
32_Q35_L0.5250.73
78_P81_Q0.5240.73
96_Q103_S0.5240.73
31_S62_G0.5230.73
21_R42_R0.5140.72
20_I23_Q0.5140.72
10_Q21_R0.5130.71
102_E107_A0.5130.71
91_L105_S0.5090.71
52_E60_A0.5070.71
84_Q94_L0.5050.70
91_L101_A0.5020.70
4_G17_P0.5000.70
62_G69_G0.5000.70
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

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.

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