GREMLIN Database
PgaD - PgaD-like protein
PFAM: PF13994 Sequences:
Download Alignment
We filter this alignment to remove sites that have many gaps before running GREMLIN.

Date: 2015_10
Length: 148 (136)
Sequences: 1233 (974)
Seq/√Len: 83.5
META: 0.788

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:
i j Sco Prob
114_D132_R3.4991.00
139_V147_I3.3261.00
142_D146_R3.2621.00
28_W34_P3.1081.00
113_T116_E3.0141.00
96_N100_F2.6041.00
115_E119_R2.4301.00
28_W33_L2.3001.00
86_A89_L2.2991.00
21_T25_W2.2591.00
131_L137_L2.2251.00
37_T41_W2.2031.00
96_N105_R2.1301.00
41_W48_F2.0671.00
96_N99_R1.9751.00
100_F106_R1.8681.00
124_D127_E1.8571.00
9_Q13_Q1.7981.00
17_D28_W1.7941.00
92_W96_N1.7621.00
21_T24_A1.7361.00
112_V117_L1.6591.00
94_L97_R1.6231.00
46_R51_E1.5841.00
28_W141_H1.5741.00
40_A44_G1.5451.00
95_Y100_F1.5401.00
26_A29_L1.5381.00
48_F52_M1.5210.99
100_F105_R1.5070.99
96_N106_R1.4960.99
127_E130_A1.4860.99
141_H145_G1.4690.99
9_Q17_D1.4540.99
115_E125_P1.4500.99
5_R8_L1.4200.99
10_P13_Q1.4020.99
6_P9_Q1.3730.99
16_L117_L1.3520.99
131_L139_V1.3470.99
78_Y85_L1.3340.99
78_Y81_V1.3250.99
4_D9_Q1.3230.99
118_A128_L1.3200.99
92_W106_R1.3060.98
11_R15_L1.3030.98
116_E119_R1.2900.98
132_R145_G1.2800.98
19_L23_L1.2450.98
125_P129_A1.2410.98
49_Y53_L1.2360.98
108_A111_P1.2320.98
32_W40_A1.2270.98
47_L53_L1.2230.98
51_E65_L1.2120.97
89_L93_A1.1470.96
13_Q17_D1.1450.96
82_I86_A1.1310.96
37_T40_A1.1290.96
86_A90_L1.1090.96
123_L137_L1.1060.96
48_F53_L1.1040.96
123_L131_L1.0980.95
70_A73_E1.0740.95
41_W44_G1.0580.94
112_V132_R1.0370.94
116_E120_S1.0310.94
87_L125_P0.9860.92
30_Y33_L0.9610.91
36_L43_L0.9520.91
38_L41_W0.9400.90
3_I6_P0.9240.89
22_L102_G0.9220.89
24_A82_I0.9210.89
17_D40_A0.9150.89
143_E146_R0.9020.88
41_W51_E0.8950.88
6_P10_P0.8850.87
45_V48_F0.8790.87
28_W79_L0.8750.87
94_L98_R0.8700.86
76_L79_L0.8680.86
27_L140_H0.8650.86
92_W95_Y0.8640.86
127_E131_L0.8580.85
117_L132_R0.8370.84
42_L45_V0.8360.84
9_Q14_R0.8360.84
133_Q143_E0.8330.84
101_R135_R0.8320.84
46_R50_D0.8240.83
118_A125_P0.8230.83
22_L80_L0.8210.83
78_Y82_I0.8100.82
92_W121_F0.8080.82
129_A133_Q0.8080.82
138_V141_H0.8040.82
129_A137_L0.8040.82
134_A141_H0.7970.81
29_L65_L0.7930.81
28_W44_G0.7900.80
87_L111_P0.7880.80
35_L41_W0.7880.80
34_P38_L0.7880.80
12_R40_A0.7840.80
21_T32_W0.7800.80
85_L88_L0.7800.80
37_T44_G0.7740.79
21_T89_L0.7730.79
82_I128_L0.7680.79
34_P41_W0.7660.78
93_A97_R0.7580.78
97_R100_F0.7570.78
30_Y78_Y0.7560.77
114_D128_L0.7520.77
95_Y101_R0.7510.77
46_R78_Y0.7450.76
107_K110_P0.7430.76
34_P37_T0.7380.76
29_L132_R0.7330.75
37_T51_E0.7270.75
38_L52_M0.7270.75
67_G71_L0.7150.73
16_L33_L0.6970.72
71_L77_L0.6960.71
135_R144_D0.6840.70
33_L37_T0.6800.70
74_L81_V0.6780.69
35_L38_L0.6740.69
43_L47_L0.6740.69
6_P34_P0.6730.69
29_L84_V0.6710.69
130_A134_A0.6700.69
72_L91_L0.6700.69
17_D131_L0.6680.68
114_D118_A0.6650.68
15_L18_G0.6630.68
26_A117_L0.6580.67
25_W31_L0.6580.67
114_D129_A0.6460.66
23_L70_A0.6430.65
93_A99_R0.6350.64
23_L26_A0.6340.64
83_L125_P0.6320.64
30_Y38_L0.6320.64
93_A100_F0.6310.64
90_L94_L0.6240.63
45_V49_Y0.6210.63
101_R104_E0.6210.63
30_Y93_A0.6200.63
44_G53_L0.6160.62
128_L132_R0.6160.62
23_L107_K0.6140.62
114_D125_P0.6110.61
52_M67_G0.6090.61
128_L145_G0.6090.61
52_M78_Y0.6070.61
89_L99_R0.6070.61
29_L33_L0.6050.61
112_V116_E0.6020.60
45_V80_L0.6010.60
92_W105_R0.5930.59
102_G106_R0.5920.59
6_P35_L0.5900.59
130_A133_Q0.5860.58
96_N101_R0.5840.58
26_A129_A0.5840.58
79_L90_L0.5800.57
13_Q28_W0.5790.57
76_L88_L0.5760.57
134_A137_L0.5720.56
74_L86_A0.5710.56
65_L71_L0.5660.56
30_Y71_L0.5640.55
131_L134_A0.5640.55
22_L69_L0.5610.55
115_E133_Q0.5590.55
17_D20_L0.5560.54
31_L34_P0.5550.54
10_P17_D0.5510.54
122_G146_R0.5490.53
18_G91_L0.5460.53
31_L99_R0.5460.53
42_L46_R0.5460.53
71_L128_L0.5390.52
46_R121_F0.5330.51
131_L141_H0.5270.50
66_G82_I0.5260.50
69_L73_E0.5250.50
24_A93_A0.5230.50
17_D34_P0.5230.50
108_A147_I0.5220.50
24_A97_R0.5220.50
123_L147_I0.5210.50
16_L127_E0.5190.49
126_E130_A0.5180.49
109_P115_E0.5180.49
31_L53_L0.5140.49
69_L114_D0.5130.49
19_L28_W0.5100.48
71_L75_L0.5070.48
25_W92_W0.5030.47
83_L132_R0.5010.47
14_R31_L0.5000.47
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

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  
3f2gA 1 0.4865 48.8 0.893 Contact Map
4r4eB 2 0.3243 27 0.907 Contact Map
2jmlA 1 0.2838 23.4 0.91 Contact Map
1j9iA 2 0.2635 23.2 0.91 Contact Map
4r24B 2 0.3041 17.2 0.915 Contact Map
4j2nA 4 0.2905 15.6 0.917 Contact Map
3ucsA 2 0.2905 15.5 0.917 Contact Map
3g74A 3 0.3986 13.7 0.919 Contact Map
4a0zA 2 0.3716 12 0.921 Contact Map
4i5sA 2 0.4122 11.3 0.922 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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