GREMLIN Database
PPDA - Prepilin peptidase-dependent protein A
UniProt: P33554 Sequences:
Download Alignment
We filter this alignment to remove sites that have many gaps before running GREMLIN.

Date: 2015_01
EcoGene: EG12081
Length: 156 (146)
Sequences: 1341 (1144)
Seq/√Len: 94.7

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:
i j Sco Prob
71_E74_L4.1671.00
56_D60_H4.0381.00
40_W44_S3.1831.00
56_D59_W3.0331.00
137_V145_R2.9801.00
76_C87_C2.7421.00
32_Y36_S2.5741.00
19_L23_S2.3011.00
71_E80_S2.2641.00
113_F117_R2.2101.00
46_A127_F2.1581.00
78_V82_A2.1271.00
124_H135_W2.0881.00
53_L66_I2.0651.00
76_C79_S1.9411.00
39_L127_F1.9101.00
78_V81_A1.9081.00
23_S26_G1.8831.00
71_E78_V1.8571.00
15_A19_L1.8541.00
47_R144_L1.8321.00
63_D112_A1.8161.00
43_A146_L1.7651.00
128_K133_E1.7001.00
60_H64_H1.6991.00
128_K147_C1.6951.00
15_A18_I1.6911.00
139_S143_R1.6341.00
76_C80_S1.6331.00
42_T102_V1.5691.00
117_R120_A1.5641.00
84_A88_H1.5211.00
17_L20_V1.5051.00
53_L64_H1.4551.00
74_L77_L1.4531.00
75_W81_A1.4351.00
49_Y77_L1.4150.99
136_L144_L1.4020.99
37_Q40_W1.3720.99
74_L78_V1.3700.99
47_R136_L1.3210.99
91_S94_V1.3180.99
61_N115_G1.2900.99
93_L96_V1.2760.99
10_I13_L1.2750.99
50_L66_I1.2700.99
47_R51_L1.2670.99
6_G9_L1.2380.99
80_S85_N1.2230.98
44_S134_W1.2010.98
34_Q38_R1.1820.98
137_V143_R1.1750.98
14_V18_I1.1740.98
22_L25_S1.1740.98
92_P98_R1.1480.98
15_A22_L1.1430.98
43_A47_R1.1400.98
71_E77_L1.1350.97
77_L81_A1.1320.97
80_S88_H1.1180.97
67_S76_C1.1160.97
78_V87_C1.1150.97
43_A134_W1.0930.97
71_E76_C1.0880.97
39_L129_N1.0850.97
74_L80_S1.0660.96
69_I76_C1.0620.96
135_W147_C1.0540.96
30_W34_Q1.0520.96
15_A30_W1.0360.96
115_G118_N1.0330.96
44_S48_D1.0250.95
75_W78_V1.0230.95
27_L31_Q1.0060.95
97_P101_E1.0010.95
19_L22_L0.9970.95
123_G137_V0.9970.95
39_L48_D0.9790.94
40_W134_W0.9460.93
37_Q44_S0.9380.93
113_F144_L0.9340.92
39_L132_G0.9320.92
114_F117_R0.9250.92
28_Y53_L0.9250.92
114_F118_N0.9250.92
65_S112_A0.9170.92
77_L80_S0.9090.91
34_Q45_Q0.9050.91
13_L18_I0.9020.91
29_G54_R0.9000.91
71_E82_A0.8800.90
58_N143_R0.8700.90
111_L125_I0.8610.89
7_Y38_R0.8580.89
10_I14_V0.8510.88
57_A117_R0.8460.88
106_D109_P0.8440.88
8_T11_E0.8350.88
80_S87_C0.8290.87
91_S96_V0.8260.87
23_S27_L0.8240.87
104_M127_F0.8240.87
26_G29_G0.8120.86
91_S95_F0.8080.86
128_K137_V0.8050.86
110_S122_A0.8050.86
49_Y66_I0.8000.85
29_G32_Y0.7960.85
136_L146_L0.7830.84
15_A125_I0.7780.84
111_L117_R0.7770.84
114_F120_A0.7740.83
94_V97_P0.7720.83
18_I61_N0.7700.83
63_D115_G0.7680.83
15_A20_V0.7550.82
62_R101_E0.7540.82
121_W138_V0.7530.82
68_V117_R0.7520.81
139_S145_R0.7480.81
72_G105_S0.7430.81
124_H137_V0.7420.81
82_A88_H0.7410.81
34_Q44_S0.7350.80
35_Q38_R0.7350.80
7_Y11_E0.7270.79
5_R38_R0.7260.79
104_M137_V0.7170.78
55_E144_L0.7130.78
44_S56_D0.7090.78
38_R54_R0.7090.78
28_Y58_N0.7080.77
19_L51_L0.7070.77
18_I26_G0.7000.77
59_W141_W0.6980.76
24_A45_Q0.6960.76
82_A90_S0.6940.76
125_I130_S0.6910.76
21_M29_G0.6900.76
34_Q58_N0.6890.76
50_L111_L0.6810.75
77_L82_A0.6730.74
128_K135_W0.6700.73
110_S123_G0.6650.73
67_S128_K0.6650.73
51_L61_N0.6600.72
123_G129_N0.6550.72
138_V144_L0.6550.72
54_R57_A0.6510.71
117_R142_G0.6500.71
113_F137_V0.6390.70
119_T136_L0.6390.70
12_T15_A0.6380.70
45_Q49_Y0.6340.69
98_R104_M0.6330.69
110_S121_W0.6310.69
135_W144_L0.6300.69
36_S133_E0.6300.69
124_H139_S0.6250.68
80_S84_A0.6230.68
14_V17_L0.6200.68
6_G11_E0.6200.68
123_G138_V0.6200.68
31_Q52_Y0.6190.68
62_R81_A0.6180.67
122_A137_V0.6130.67
16_M89_G0.6110.67
14_V131_T0.6060.66
10_I37_Q0.6020.65
38_R129_N0.6020.65
124_H143_R0.5960.65
39_L116_L0.5940.64
31_Q34_Q0.5930.64
93_L99_W0.5930.64
16_M19_L0.5870.63
35_Q39_L0.5860.63
20_V39_L0.5850.63
67_S78_V0.5810.63
134_W146_L0.5780.62
92_P95_F0.5770.62
34_Q37_Q0.5750.62
61_N143_R0.5680.61
105_S109_P0.5650.60
20_V29_G0.5610.60
26_G91_S0.5540.59
24_A60_H0.5520.59
54_R58_N0.5500.58
44_S59_W0.5500.58
35_Q129_N0.5470.58
28_Y54_R0.5450.58
40_W59_W0.5440.58
15_A23_S0.5430.57
85_N89_G0.5400.57
17_L24_A0.5400.57
10_I16_M0.5390.57
18_I116_L0.5390.57
39_L46_A0.5380.57
46_A66_I0.5380.57
7_Y21_M0.5370.57
99_W107_L0.5370.57
121_W140_P0.5340.56
75_W79_S0.5340.56
4_Q115_G0.5260.55
69_I140_P0.5240.55
38_R73_T0.5240.55
51_L54_R0.5210.54
95_F112_A0.5200.54
49_Y52_Y0.5200.54
30_W120_A0.5140.53
73_T77_L0.5110.53
80_S90_S0.5100.53
50_L144_L0.5100.53
49_Y68_V0.5090.53
129_N132_G0.5050.52
25_S141_W0.5020.52
52_Y92_P0.5020.52
39_L131_T0.5010.52
105_S128_K0.5010.52
15_A27_L0.5000.51
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  
4ipuA 1 0.8077 99.8 0.517 Contact Map
1oqwA 1 0.8397 99.3 0.683 Contact Map
3sokA 1 0.8526 99.1 0.709 Contact Map
2hi2A 1 0.8077 98.8 0.739 Contact Map
2m7gA 1 0.391 98.6 0.751 Contact Map
4dq9A 2 0.7628 97.9 0.797 Contact Map
2knqA 1 0.8013 94.4 0.861 Contact Map
3g20A 1 0.6538 33.1 0.923 Contact Map
2yevB 1 0.8141 14.4 0.934 Contact Map
3j27B 2 0.1795 14 0.935 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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