GREMLIN Database
YBAB - Nucleoid-associated protein YbaB
UniProt: P0A8B5 Sequences:
Download Alignment
We filter this alignment to remove sites that have many gaps before running GREMLIN.

Date: 2015_01
EcoGene: EG11100
Length: 109 (99)
Sequences: 2300 (1443)
Seq/√Len: 145.0

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:
i j Sco Prob
62_L66_K2.5981.00
33_V87_T2.2891.00
32_E45_T2.0851.00
20_K23_K2.0581.00
34_T43_K2.0411.00
23_K27_E2.0271.00
16_Q20_K2.0071.00
50_H85_E1.9991.00
91_K94_S1.8811.00
46_I52_C1.8781.00
35_G79_D1.8341.00
43_K56_E1.8151.00
56_E70_E1.7661.00
47_N53_R1.7411.00
29_A49_A1.7291.00
79_D83_R1.7131.00
45_T54_R1.7001.00
31_L91_K1.6971.00
34_T45_T1.6831.00
26_E29_A1.6711.00
32_E53_R1.6681.00
22_Q26_E1.6541.00
31_L87_T1.6041.00
59_P66_K1.5251.00
36_E43_K1.5171.00
50_H84_I1.4451.00
100_Q103_P1.4451.00
86_E90_E1.4431.00
10_L14_A1.4371.00
19_E23_K1.4241.00
44_V77_F1.4041.00
52_C77_F1.4001.00
46_I80_A1.3821.00
27_E31_L1.3821.00
51_N82_R1.3381.00
44_V52_C1.3111.00
6_G9_N1.3021.00
44_V55_V1.2931.00
26_E30_Q1.2921.00
79_D82_R1.2881.00
27_E91_K1.2821.00
46_I81_A1.2801.00
37_S75_A1.1961.00
82_R86_E1.1911.00
46_I84_I1.1851.00
66_K70_E1.1501.00
87_T91_K1.1440.99
19_E22_Q1.1430.99
65_D68_M1.0870.99
5_G9_N1.0500.99
38_G75_A1.0350.99
13_Q16_Q1.0340.99
86_E89_K1.0260.99
45_T53_R1.0160.99
15_Q19_E1.0130.99
46_I77_F1.0110.99
24_M95_V0.9970.99
56_E66_K0.9900.99
87_T90_E0.9820.98
50_H81_A0.9800.98
77_F81_A0.9800.98
54_R70_E0.9700.98
48_G84_I0.9490.98
27_E30_Q0.9000.97
9_N12_K0.8910.97
57_I73_V0.8860.97
55_V74_A0.8820.97
52_C55_V0.8610.96
16_Q19_E0.8480.96
47_N51_N0.8450.96
83_R86_E0.8430.96
24_M91_K0.8420.96
49_A85_E0.8370.96
81_A85_E0.8360.96
78_N81_A0.8340.96
23_K26_E0.8210.95
62_L69_L0.8130.95
63_E68_M0.7900.94
66_K69_L0.7870.94
51_N78_N0.7860.94
33_V48_G0.7840.94
11_M14_A0.7700.93
43_K58_D0.7700.93
35_G76_A0.7620.93
5_G8_G0.7510.93
84_I88_Q0.7440.92
9_N13_Q0.7420.92
12_K15_Q0.7420.92
31_L48_G0.7280.91
8_G11_M0.7260.91
41_L60_S0.7230.91
73_V77_F0.7160.91
61_L69_L0.7160.91
97_S100_Q0.7030.90
44_V73_V0.6920.89
39_A75_A0.6860.89
48_G87_T0.6850.89
32_E54_R0.6740.88
24_M92_M0.6740.88
38_G72_L0.6710.88
89_K93_A0.6710.88
6_G16_Q0.6700.88
68_M71_D0.6690.87
57_I66_K0.6560.86
64_D67_E0.6560.86
61_L72_L0.6550.86
33_V84_I0.6480.86
24_M27_E0.6440.85
36_E83_R0.6420.85
45_T56_E0.6410.85
41_L58_D0.6330.84
28_I88_Q0.6270.84
10_L13_Q0.6260.84
80_A84_I0.6260.84
28_I84_I0.6210.83
34_T83_R0.6210.83
36_E40_G0.6200.83
29_A97_S0.6150.83
58_D61_L0.6070.82
6_G12_K0.6020.81
28_I31_L0.5820.79
17_M21_M0.5730.78
90_E94_S0.5650.77
62_L65_D0.5640.77
55_V77_F0.5620.77
52_C74_A0.5570.76
61_L65_D0.5530.76
22_Q25_Q0.5520.76
44_V74_A0.5470.75
46_I74_A0.5450.75
14_A41_L0.5440.74
28_I91_K0.5430.74
24_M94_S0.5400.74
37_S76_A0.5390.74
74_A78_N0.5390.74
24_M88_Q0.5360.73
33_V46_I0.5350.73
55_V70_E0.5340.73
9_N16_Q0.5280.72
58_D75_A0.5220.71
71_D75_A0.5200.71
28_I48_G0.5140.70
83_R87_T0.5130.70
48_G81_A0.5090.70
6_G92_M0.5070.69
10_L16_Q0.5050.69
82_R85_E0.5050.69
91_K95_V0.5000.68
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  
1j8bA 2 0.844 100 0.131 Contact Map
1ybxA 2 0.8349 100 0.198 Contact Map
3f42A 4 0.8532 100 0.271 Contact Map
2kzxA 1 0.5872 12 0.933 Contact Map
2zzrA 1 0.5138 8.6 0.937 Contact Map
4oe8C 1 0.5413 7.5 0.939 Contact Map
2kzfA 1 0.844 6.5 0.94 Contact Map
3oeqA 3 0.7615 4.8 0.944 Contact Map
4chgG 2 0.2294 4.7 0.944 Contact Map
2nrjA 1 0.844 4.4 0.945 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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