GREMLIN Database
YAAK - Nucleoid-associated protein YaaK
UniProt: P24281 Sequences:
Download Alignment
We filter this alignment to remove sites that have many gaps before running GREMLIN.

Date: 2015_01
Length: 107 (100)
Sequences: 2325 (1466)
Seq/√Len: 146.6

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:
i j Sco Prob
63_V68_I2.6351.00
34_V89_I2.3091.00
21_D24_K2.1151.00
33_V46_K2.0951.00
24_K28_E2.0621.00
35_E44_T2.0501.00
51_K87_D2.0481.00
17_K21_D2.0001.00
47_A53_I1.9341.00
93_T96_Q1.8911.00
36_G81_E1.8681.00
44_T57_I1.8301.00
57_I72_Q1.7781.00
35_E46_K1.7691.00
48_N54_L1.7691.00
81_E85_K1.7631.00
27_E30_A1.7351.00
30_A50_Q1.7331.00
23_A27_E1.7171.00
32_K93_T1.7171.00
46_K55_D1.6871.00
33_V54_L1.6781.00
32_K89_I1.6271.00
37_T44_T1.5401.00
60_E68_I1.5161.00
45_V79_T1.5051.00
51_K86_V1.4991.00
20_K24_K1.4631.00
88_E92_E1.4331.00
53_I79_T1.4111.00
47_A82_A1.4081.00
28_E32_K1.4031.00
11_M15_M1.3911.00
45_V53_I1.3671.00
7_N10_K1.3501.00
52_E84_K1.3291.00
45_V56_V1.3231.00
81_E84_K1.3111.00
27_E31_E1.3071.00
28_E93_T1.2801.00
38_A77_A1.2581.00
47_A83_L1.2391.00
47_A86_V1.1861.00
84_K88_E1.1721.00
67_D70_M1.1340.99
89_I93_T1.1000.99
88_E91_N1.0900.99
20_K23_A1.0680.99
14_Q17_K1.0660.99
68_I72_Q1.0640.99
16_Q20_K1.0550.99
89_I92_E1.0360.99
39_G77_A1.0250.99
55_D72_Q1.0140.99
46_K54_L1.0090.99
57_I68_I1.0010.99
25_A97_F0.9920.99
47_A79_T0.9840.98
49_G86_V0.9550.98
51_K83_L0.9410.98
79_T83_L0.9340.98
6_G10_K0.9190.98
28_E31_E0.9100.97
50_Q87_D0.8950.97
53_I56_V0.8800.97
58_I75_V0.8800.97
85_K88_E0.8770.97
56_V76_L0.8730.97
17_K20_K0.8720.97
48_N52_E0.8690.97
10_K13_K0.8630.97
80_N83_L0.8520.96
25_A93_T0.8520.96
83_L87_D0.8470.96
52_E80_N0.8230.95
39_G74_L0.8160.95
36_G78_A0.8130.95
12_M15_M0.8090.95
34_V49_G0.8060.95
24_K27_E0.7950.95
10_K14_Q0.7760.94
42_M61_E0.7720.94
68_I71_L0.7670.93
44_T59_K0.7560.93
32_K49_G0.7560.93
75_V79_T0.7480.93
7_N17_K0.7450.92
13_K16_Q0.7450.92
70_M73_D0.7290.92
86_V90_T0.7290.92
40_G77_A0.7220.91
62_V71_L0.7190.91
9_Q12_M0.7140.91
25_A94_M0.7120.91
37_T85_K0.7010.90
45_V75_V0.6960.90
46_K57_I0.6940.90
30_A99_K0.6930.89
62_V74_L0.6890.89
49_G89_I0.6800.89
63_V71_L0.6780.88
33_V55_D0.6720.88
64_D70_M0.6690.88
7_N13_K0.6650.87
59_K62_V0.6640.87
82_A86_V0.6620.87
66_E69_D0.6620.87
6_G9_Q0.6510.86
99_K102_N0.6450.86
35_E85_K0.6440.86
29_L86_V0.6380.85
91_N95_G0.6300.85
29_L90_T0.6290.84
42_M59_K0.6260.84
37_T41_G0.6090.82
34_V47_A0.6090.82
11_M14_Q0.6070.82
29_L32_K0.6050.82
53_I76_L0.5950.81
47_A76_L0.5930.81
56_V72_Q0.5910.81
18_M22_M0.5900.80
58_I68_I0.5880.80
34_V86_V0.5860.80
76_L80_N0.5800.79
65_P68_I0.5730.79
45_V76_L0.5720.78
92_E96_Q0.5720.78
63_V66_E0.5700.78
60_E65_P0.5690.78
63_V67_D0.5620.77
38_A78_A0.5580.77
25_A28_E0.5570.77
73_D77_A0.5570.77
11_M17_K0.5540.76
56_V79_T0.5510.76
23_A26_Q0.5510.76
25_A96_Q0.5380.74
29_L49_G0.5340.74
36_G85_K0.5320.73
29_L93_T0.5310.73
72_Q76_L0.5290.73
37_T81_E0.5290.73
8_M15_M0.5280.73
36_G43_V0.5230.72
15_M42_M0.5230.72
25_A90_T0.5180.71
37_T40_G0.5150.71
36_G56_V0.5010.69
85_K89_I0.5000.69
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  
1ybxA 2 0.8598 100 0.107 Contact Map
1j8bA 2 0.8598 100 0.185 Contact Map
3f42A 4 0.8692 100 0.256 Contact Map
4chgG 2 0.2056 18.4 0.923 Contact Map
4bjqA 2 0.5047 14.4 0.926 Contact Map
3efmA 1 0.6262 11.5 0.93 Contact Map
4xcoC 1 0.9346 10.3 0.931 Contact Map
2kzxA 1 0.729 10.1 0.931 Contact Map
3r07C 1 0.7383 9.8 0.932 Contact Map
3txsA 5 0.271 8.5 0.933 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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