GREMLIN Database
PPDD - Prepilin peptidase-dependent protein D
UniProt: P36647 Sequences:
Download Alignment
We filter this alignment to remove sites that have many gaps before running GREMLIN.

Date: 2015_01
EcoGene: EG12107
Length: 146 (129)
Sequences: 2109 (1834)
Seq/√Len: 161.5

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:
i j Sco Prob
55_L59_E4.1631.00
42_M96_G3.9471.00
124_C132_L2.8901.00
41_D45_T2.8301.00
34_L37_A2.7351.00
47_V50_R2.6881.00
56_C60_H2.5821.00
56_C66_C2.5031.00
97_Q100_L2.4481.00
108_T123_N2.4241.00
40_T44_Q2.2631.00
32_N130_S2.1031.00
104_S125_N1.9011.00
90_G94_L1.8891.00
36_K55_L1.8401.00
35_R131_A1.7871.00
95_T104_S1.7701.00
110_G121_T1.7421.00
92_V96_G1.7291.00
67_D70_S1.6851.00
29_A32_N1.6771.00
35_R38_A1.6061.00
66_C69_G1.5131.00
79_T82_V1.5021.00
129_D132_L1.4791.00
48_P52_A1.4631.00
66_C71_N1.4361.00
46_F94_L1.4051.00
90_G109_P1.4011.00
56_C64_D1.3991.00
15_V18_I1.3951.00
93_S106_V1.3511.00
103_L125_N1.3311.00
38_A81_Y1.3111.00
56_C62_G1.2761.00
3_K27_I1.2591.00
31_Q36_K1.2471.00
31_Q34_L1.2381.00
90_G96_G1.2331.00
6_G9_L1.2321.00
39_L42_M1.2151.00
51_T55_L1.2001.00
52_A56_C1.1961.00
105_V109_P1.1961.00
92_V95_T1.1941.00
64_D67_D1.1831.00
3_K20_A1.1721.00
13_M16_I1.1701.00
41_D46_F1.1461.00
63_L66_C1.1441.00
44_Q54_E1.1371.00
106_V123_N1.1231.00
91_V106_V1.1081.00
48_P51_T1.1051.00
96_G103_L1.1011.00
67_D71_N1.0981.00
13_M23_S1.0901.00
20_A34_L1.0870.99
91_V108_T1.0820.99
8_T14_V1.0700.99
53_V58_L1.0650.99
43_L107_M1.0450.99
54_E118_T1.0360.99
74_P77_T1.0280.99
42_M94_L1.0240.99
32_N35_R1.0220.99
93_S104_S1.0190.99
126_I132_L1.0120.99
81_Y84_A1.0080.99
110_G119_G0.9970.99
56_C63_L0.9870.99
96_G100_L0.9860.99
83_S87_V0.9790.99
41_D47_V0.9670.99
57_A118_T0.9640.99
109_P118_T0.9330.98
6_G11_E0.9320.98
38_A45_T0.9210.98
123_N129_D0.9090.98
39_L43_L0.8950.98
124_C127_Q0.8890.98
34_L38_A0.8880.98
36_K54_E0.8880.98
33_Y36_K0.8870.98
36_K59_E0.8860.98
24_A33_Y0.8860.98
57_A61_G0.8850.98
67_D72_G0.8810.98
92_V109_P0.8690.98
39_L105_V0.8630.97
7_F11_E0.8600.97
73_I76_P0.8600.97
43_L47_V0.8590.97
46_F92_V0.8490.97
87_V109_P0.8490.97
86_S95_T0.8470.97
27_I44_Q0.8400.97
62_G65_T0.8370.97
42_M46_F0.8310.97
68_G72_G0.8310.97
124_C129_D0.8250.97
63_L90_G0.8190.97
39_L103_L0.8160.96
83_S86_S0.8100.96
41_D94_L0.8080.96
16_I42_M0.7990.96
127_Q132_L0.7870.96
64_D70_S0.7830.95
16_I23_S0.7770.95
38_A100_L0.7740.95
38_A41_D0.7640.95
15_V23_S0.7560.95
91_V109_P0.7510.94
39_L96_G0.7470.94
54_E109_P0.7470.94
43_L46_F0.7420.94
3_K23_S0.7370.94
8_T12_L0.7290.93
30_Y34_L0.7280.93
105_V126_I0.7180.93
13_M32_N0.7130.93
57_A63_L0.7100.93
47_V54_E0.7070.92
66_C70_S0.7050.92
62_G67_D0.7020.92
45_T48_P0.6940.92
121_T130_S0.6910.91
72_G77_T0.6900.91
44_Q47_V0.6890.91
41_D109_P0.6840.91
42_M45_T0.6800.91
41_D44_Q0.6610.90
26_G30_Y0.6530.89
39_L133_Q0.6520.89
122_R133_Q0.6520.89
27_I47_V0.6370.88
75_S78_T0.6370.88
4_Q34_L0.6310.87
64_D69_G0.6250.87
32_N37_A0.6210.87
96_G102_G0.6190.86
79_T83_S0.6150.86
76_P84_A0.6140.86
77_T85_M0.6130.86
53_V64_D0.6090.85
52_A55_L0.6030.85
69_G74_P0.6010.85
45_T96_G0.6000.85
123_N127_Q0.5970.84
8_T11_E0.5960.84
69_G72_G0.5910.84
36_K132_L0.5900.84
21_I24_A0.5870.83
76_P83_S0.5840.83
43_L50_R0.5790.82
112_D119_G0.5780.82
68_G71_N0.5690.81
103_L132_L0.5690.81
45_T58_L0.5650.81
53_V57_A0.5630.81
45_T94_L0.5510.79
20_A44_Q0.5500.79
62_G88_A0.5490.79
125_N132_L0.5480.79
39_L132_L0.5460.79
100_L103_L0.5450.79
50_R107_M0.5410.78
125_N129_D0.5410.78
35_R103_L0.5380.78
32_N47_V0.5370.78
66_C72_G0.5350.77
112_D116_G0.5300.77
60_H63_L0.5280.76
76_P85_M0.5260.76
68_G88_A0.5230.76
49_Y72_G0.5210.75
117_V122_R0.5200.75
53_V109_P0.5200.75
5_R12_L0.5200.75
4_Q16_I0.5200.75
43_L58_L0.5170.75
45_T49_Y0.5170.75
111_W119_G0.5160.75
15_V19_I0.5120.74
94_L105_V0.5110.74
105_V122_R0.5110.74
17_G32_N0.5070.73
127_Q130_S0.5060.73
13_M51_T0.5050.73
118_T122_R0.5040.73
23_S26_G0.5040.73
39_L126_I0.5020.73
34_L58_L0.5010.73
91_V96_G0.5000.72
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  
2hi2A 1 0.9178 100 0.389 Contact Map
3sokA 1 0.8836 100 0.404 Contact Map
1oqwA 1 0.8699 99.9 0.43 Contact Map
3jyzA 1 0.7397 99.8 0.581 Contact Map
1qveA 2 0.7603 99.7 0.601 Contact Map
1x6zA 1 0.6986 99.7 0.614 Contact Map
2m7gA 1 0.4178 99.6 0.643 Contact Map
3sojA 1 0.6781 99.5 0.658 Contact Map
3g20A 1 0.7055 98.9 0.749 Contact Map
4noaA 1 0.6644 98.5 0.773 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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