GREMLIN Database
NRDI - Protein NrdI
UniProt: P0A772 Sequences:
Download Alignment
We filter this alignment to remove sites that have many gaps before running GREMLIN.

Date: 2015_01
EcoGene: EG13287
Length: 136 (125)
Sequences: 898 (578)
Seq/√Len: 51.7

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:
i j Sco Prob
20_R118_I4.3951.00
15_Q19_E3.4551.00
80_A94_G3.3901.00
75_L101_C2.6271.00
94_G105_W2.6061.00
37_Q68_D2.5931.00
41_P74_L2.5831.00
18_I45_I2.4821.00
69_E73_A2.3301.00
80_A105_W2.2241.00
5_V38_V2.1711.00
95_D108_R2.1461.00
84_R90_Y1.9280.99
58_V63_I1.8920.99
75_L103_V1.8840.99
119_E123_K1.8720.99
17_F121_V1.8010.99
79_I121_V1.7980.99
8_S62_V1.7680.99
60_R63_I1.7100.99
15_Q27_R1.6990.99
44_L66_L1.6540.98
46_V97_I1.6480.98
4_L45_I1.6290.98
44_L62_V1.5480.97
23_L122_R1.5410.97
12_E112_M1.5320.97
80_A91_G1.5060.97
92_R96_V1.4280.96
95_D105_W1.4170.96
50_G89_A1.4090.96
59_P62_V1.4060.95
58_V96_V1.3590.95
89_A92_R1.3470.94
38_V65_F1.3280.94
43_I125_V1.3140.93
90_Y108_R1.3050.93
81_S109_F1.2820.93
57_A89_A1.2760.92
70_H73_A1.2550.92
12_E15_Q1.2180.91
48_S78_V1.2030.90
106_L124_G1.1780.89
63_I100_K1.1660.89
83_N111_L1.1470.88
79_I107_Y1.1410.87
8_S47_P1.1320.87
107_Y121_V1.1300.87
52_G81_S1.1210.87
120_N123_K1.0860.85
17_F109_F1.0720.84
78_V97_I1.0670.84
53_G89_A1.0670.84
6_Y38_V1.0640.84
66_L97_I1.0620.83
45_I79_I1.0260.81
62_V80_A1.0190.81
8_S61_Q1.0160.81
47_P86_F1.0080.80
123_K127_E0.9990.79
14_T47_P0.9940.79
63_I96_V0.9890.79
33_R91_G0.9860.79
107_Y120_N0.9760.78
115_Q119_E0.9680.77
32_E35_R0.9650.77
37_Q70_H0.9650.77
38_V71_N0.9610.77
124_G128_F0.9570.76
46_V52_G0.9460.76
16_R112_M0.9450.76
126_T129_W0.9390.75
10_S49_Y0.9360.75
49_Y86_F0.9320.74
64_R68_D0.9270.74
6_Y28_I0.9020.72
83_N110_E0.8970.72
63_I67_N0.8930.71
59_P87_G0.8920.71
91_G108_R0.8830.70
80_A95_D0.8810.70
81_S106_L0.8690.69
70_H102_G0.8680.69
11_S40_E0.8630.69
22_G25_A0.8620.69
8_S49_Y0.8610.68
56_G89_A0.8590.68
51_G86_F0.8580.68
30_L61_Q0.8530.68
46_V53_G0.8460.67
88_E91_G0.8390.66
66_L72_R0.8240.65
54_T89_A0.8230.65
13_N111_L0.8200.65
12_E19_E0.8170.64
85_N111_L0.8130.64
17_F49_Y0.8100.64
41_P124_G0.8050.63
99_R102_G0.8040.63
67_N94_G0.7920.62
53_G95_D0.7910.62
24_P40_E0.7860.61
9_S81_S0.7810.61
12_E54_T0.7780.61
43_I106_L0.7730.60
35_R68_D0.7510.58
57_A129_W0.7500.58
19_E22_G0.7490.58
123_K126_T0.7470.57
44_L97_I0.7390.57
57_A92_R0.7310.56
42_Y114_T0.7230.55
51_G94_G0.7220.55
41_P76_R0.7190.55
75_L108_R0.7150.54
35_R64_R0.7070.53
21_L120_N0.7070.53
54_T96_V0.6970.52
56_G60_R0.6940.52
5_V40_E0.6940.52
81_S91_G0.6910.52
79_I109_F0.6820.51
17_F118_I0.6780.50
35_R127_E0.6630.49
66_L103_V0.6630.49
77_G117_D0.6570.48
33_R46_V0.6540.48
53_G56_G0.6520.48
85_N110_E0.6480.47
32_E64_R0.6480.47
64_R123_K0.6390.46
14_T49_Y0.6380.46
43_I77_G0.6320.46
18_I25_A0.6300.45
49_Y107_Y0.6250.45
5_V68_D0.6230.45
11_S57_A0.6150.44
74_L122_R0.6140.44
98_A116_S0.6130.44
90_Y95_D0.6030.43
91_G106_L0.6000.42
18_I124_G0.6000.42
37_Q40_E0.5950.42
95_D99_R0.5930.42
50_G59_P0.5900.41
29_P61_Q0.5890.41
73_A127_E0.5880.41
53_G81_S0.5880.41
41_P101_C0.5830.41
78_V91_G0.5830.41
6_Y100_K0.5820.40
17_F117_D0.5760.40
107_Y117_D0.5760.40
35_R53_G0.5730.40
83_N86_F0.5710.39
101_C108_R0.5650.39
107_Y128_F0.5630.39
25_A74_L0.5610.38
34_E68_D0.5570.38
23_L126_T0.5560.38
44_L87_G0.5560.38
83_N109_F0.5520.37
125_V128_F0.5460.37
72_R93_A0.5450.37
77_G124_G0.5420.36
72_R101_C0.5420.36
61_Q100_K0.5410.36
70_H98_A0.5390.36
59_P93_A0.5380.36
80_A98_A0.5360.36
94_G108_R0.5360.36
8_S86_F0.5330.36
105_W116_S0.5330.36
34_E126_T0.5310.35
7_F20_R0.5280.35
67_N100_K0.5190.34
35_R123_K0.5170.34
42_Y103_V0.5140.34
91_G105_W0.5110.34
73_A76_R0.5110.34
43_I124_G0.5090.33
48_S103_V0.5080.33
14_T81_S0.5080.33
105_W108_R0.5070.33
47_P61_Q0.5070.33
52_G69_E0.5060.33
23_L26_V0.5030.33
73_A115_Q0.5000.33
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  
3n3aC 1 0.9632 99.9 0.52 Contact Map
1rljA 1 0.9338 99.9 0.589 Contact Map
2xodA 1 0.8676 99.8 0.64 Contact Map
4n82B 1 0.9779 99.7 0.65 Contact Map
3hr4A 2 0.9632 99.5 0.717 Contact Map
1bvyF 1 0.9632 99.4 0.723 Contact Map
2bpoA 1 0.9632 99.4 0.724 Contact Map
2bmvA 1 0.9485 99.4 0.728 Contact Map
3qe2A 1 0.9559 99.4 0.731 Contact Map
1yobA 1 0.9706 99.3 0.735 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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