GREMLIN Database
BofA - SigmaK-factor processing regulatory protein BofA
PFAM: PF07441 Sequences:
Download Alignment
We filter this alignment to remove sites that have many gaps before running GREMLIN.

Date: 2015_10
Length: 75 (73)
Sequences: 3704 (2803)
Seq/√Len: 328.0
META: 0.812

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:
i j Sco Prob
37_V66_V3.4321.00
58_V66_V3.4231.00
51_N54_T2.9061.00
41_G44_F2.4541.00
57_I65_G2.3411.00
30_G59_G2.1011.00
10_L14_L2.0381.00
34_L50_I1.9441.00
7_L11_K1.7681.00
61_L68_L1.7481.00
61_L64_P1.6641.00
31_L55_A1.6221.00
49_P54_T1.5831.00
2_G6_L1.5721.00
46_L70_I1.5531.00
40_L44_F1.5461.00
48_I69_L1.4341.00
30_G58_V1.4341.00
55_A59_G1.4321.00
58_V69_L1.3571.00
48_I73_K1.3441.00
33_L66_V1.3281.00
8_L12_L1.3091.00
57_I69_L1.2761.00
33_L37_V1.2351.00
49_P52_P1.2121.00
33_L63_I1.1781.00
41_G47_H1.1661.00
48_I70_I1.1571.00
27_A55_A1.1511.00
11_K15_K1.1151.00
4_L8_L1.0971.00
31_L50_I1.0941.00
16_P22_K1.0541.00
33_L58_V1.0521.00
64_P67_I1.0511.00
50_I54_T1.0101.00
13_L16_P0.9991.00
23_L27_A0.9841.00
41_G62_G0.9771.00
68_L72_L0.9531.00
37_V41_G0.9361.00
11_K14_L0.9251.00
48_I54_T0.9221.00
21_L24_L0.9161.00
9_I12_L0.9041.00
29_L33_L0.9031.00
33_L36_L0.8941.00
5_L9_I0.8881.00
38_N50_I0.8661.00
40_L43_F0.8571.00
68_L71_L0.8491.00
6_L10_L0.8471.00
42_G45_G0.8451.00
10_L13_L0.8281.00
14_L19_L0.8101.00
61_L65_G0.7961.00
63_I67_I0.7801.00
32_V36_L0.7681.00
24_L67_I0.7661.00
8_L11_K0.7560.99
53_I57_I0.7420.99
35_F50_I0.7420.99
26_N29_L0.7350.99
35_F38_N0.7320.99
24_L27_A0.7240.99
38_N48_I0.7240.99
4_L11_K0.7210.99
19_L22_K0.7160.99
41_G45_G0.7110.99
69_L73_K0.7060.99
28_V32_V0.6880.99
34_L69_L0.6730.99
51_N61_L0.6710.99
16_P20_L0.6650.99
34_L58_V0.6640.99
15_K26_N0.6580.99
2_G9_I0.6490.98
25_I35_F0.6470.98
56_L60_I0.6400.98
54_T65_G0.6400.98
34_L70_I0.6250.98
5_L8_L0.6120.98
67_I74_L0.6110.98
6_L14_L0.6050.98
24_L64_P0.5920.97
44_F74_L0.5840.97
7_L12_L0.5780.97
14_L18_K0.5760.97
2_G10_L0.5730.97
28_V31_L0.5700.97
23_L59_G0.5650.96
32_V60_I0.5610.96
49_P70_I0.5600.96
19_L28_V0.5560.96
7_L10_L0.5520.96
52_P55_A0.5500.96
53_I56_L0.5470.96
36_L39_L0.5330.95
17_L23_L0.5230.94
4_L7_L0.5220.94
13_L17_L0.5220.94
30_G65_G0.5200.94
63_I68_L0.5190.94
2_G7_L0.5170.94
51_N68_L0.5140.94
60_I64_P0.5070.93
26_N62_G0.5060.93
65_G69_L0.5050.93
6_L12_L0.5000.93
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  
4k0jA 3 0.88 4.9 0.847 Contact Map
5a63B 1 0.6 4.1 0.853 Contact Map
4dx5A 3 0.9067 3.2 0.861 Contact Map
3w9iA 3 0.9067 3.1 0.862 Contact Map
4mt1A 3 0.9733 3 0.862 Contact Map
2kluA 1 0.3867 3 0.863 Contact Map
3ne5A 3 0.9067 2.5 0.868 Contact Map
2jwaA 2 0.2933 2.2 0.872 Contact Map
1ji6A 1 0.4133 1.6 0.882 Contact Map
4dveA 3 0.9733 1.5 0.883 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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