GREMLIN Database
BOFA - Sigma-K factor-processing regulatory protein BofA
UniProt: P24282 Sequences:
Download Alignment
We filter this alignment to remove sites that have many gaps before running GREMLIN.

Date: 2015_01
Length: 87 (87)
Sequences: 124 (100)
Seq/√Len: 10.7

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:
i j Sco Prob
33_T70_I3.4900.98
47_V83_K2.8120.92
14_V82_I2.8090.91
40_G69_G2.5740.87
19_L65_T2.5690.87
3_P21_G2.4460.84
56_I83_K2.2720.80
7_I68_S1.9310.67
50_F85_F1.8160.62
43_L47_V1.8050.62
51_G57_H1.7770.60
78_A82_I1.7420.59
22_S26_P1.7310.58
22_S25_K1.7150.57
23_A32_I1.6710.55
63_V86_I1.5400.49
10_I15_I1.5290.49
63_V85_F1.5100.48
14_V17_L1.4400.45
73_I87_I1.3880.42
41_A65_T1.3520.40
34_A56_I1.3520.40
16_L25_K1.3360.40
18_F21_G1.2980.38
4_I8_G1.2970.38
33_T87_I1.2670.37
77_A82_I1.2290.35
22_S39_A1.2220.35
41_A69_G1.2100.34
31_G44_L1.1790.33
12_G19_L1.1650.32
46_C50_F1.1590.32
56_I80_V1.1470.32
49_M86_I1.1330.31
20_S24_A1.1270.31
66_A85_F1.0790.29
6_I10_I1.0730.29
14_V18_F1.0450.28
33_T37_F1.0410.27
9_I30_I1.0330.27
29_W42_L1.0140.26
50_F65_T1.0090.26
30_I56_I0.9960.26
63_V84_Q0.9930.26
19_L41_A0.9850.25
43_L76_I0.9730.25
31_G74_P0.9600.24
81_V86_I0.9590.24
80_V83_K0.9540.24
7_I38_V0.9500.24
2_E33_T0.9490.24
5_F30_I0.9450.24
36_K55_G0.9370.24
84_Q87_I0.9360.24
63_V83_K0.9320.23
25_K28_K0.8980.22
16_L87_I0.8970.22
42_L49_M0.8420.21
14_V78_A0.8380.20
58_V83_K0.8380.20
52_G56_I0.8360.20
33_T54_L0.8310.20
17_L36_K0.8280.20
29_W77_A0.8230.20
23_A46_C0.8230.20
18_F46_C0.8200.20
9_I12_G0.8140.20
5_F9_I0.8140.20
51_G69_G0.8110.20
35_V52_G0.8050.19
30_I33_T0.8050.19
22_S76_I0.8050.19
21_G42_L0.7950.19
5_F20_S0.7910.19
29_W70_I0.7800.19
36_K73_I0.7720.18
49_M81_V0.7710.18
43_L65_T0.7670.18
13_L63_V0.7540.18
9_I38_V0.7530.18
18_F28_K0.7480.18
10_I42_L0.7440.18
77_A81_V0.7420.18
2_E5_F0.7260.17
55_G80_V0.7240.17
53_S85_F0.7230.17
15_I66_A0.7200.17
68_S76_I0.7150.17
55_G81_V0.7090.17
1_M86_I0.6960.16
31_G83_K0.6900.16
15_I38_V0.6870.16
4_I49_M0.6820.16
8_G27_L0.6770.16
4_I19_L0.6690.16
52_G65_T0.6610.15
11_L55_G0.6580.15
16_L20_S0.6570.15
46_C85_F0.6480.15
19_L28_K0.6390.15
24_A42_L0.6330.15
18_F72_G0.6200.14
36_K50_F0.6120.14
6_I24_A0.6110.14
19_L24_A0.6010.14
41_A76_I0.6000.14
58_V68_S0.5940.14
21_G72_G0.5940.14
36_K72_G0.5920.14
16_L81_V0.5880.14
27_L37_F0.5870.14
14_V23_A0.5820.14
41_A78_A0.5820.14
6_I62_L0.5760.13
81_V85_F0.5740.13
54_L68_S0.5690.13
55_G83_K0.5580.13
78_A81_V0.5560.13
27_L34_A0.5490.13
38_V74_P0.5470.13
63_V66_A0.5450.13
8_G53_S0.5430.13
12_G63_V0.5370.13
50_F55_G0.5360.13
49_M52_G0.5340.13
24_A50_F0.5200.12
65_T73_I0.5140.12
19_L52_G0.5130.12
70_I77_A0.5020.12
50_F87_I0.5000.12
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  
2wwbC 1 0.3333 4.3 0.934 Contact Map
2ww9C 1 0.2299 3.3 0.938 Contact Map
4mt1A 3 0.9655 2.9 0.94 Contact Map
4k0jA 3 0.8506 2.4 0.942 Contact Map
3w9iA 3 0.8736 2 0.945 Contact Map
1ji6A 1 0.3793 1.7 0.947 Contact Map
3ne5A 3 0.8736 1.6 0.948 Contact Map
3b5dA 2 0.5287 1.3 0.95 Contact Map
4dveA 3 0.977 1.2 0.951 Contact Map
4dx5A 3 0.8736 1.2 0.951 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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