GREMLIN Database
YgbA_NO - Nitrous oxide-stimulated promoter
PFAM: PF11756 Sequences:
Download Alignment
We filter this alignment to remove sites that have many gaps before running GREMLIN.

Date: 2015_10
Length: 106 (100)
Sequences: 4292 (3156)
Seq/√Len: 315.6
META: 0.874

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_D78_Y3.4831.00
49_F61_V3.0451.00
68_M71_K2.5881.00
65_K68_M2.2901.00
11_E37_L2.2791.00
36_L72_I2.2141.00
34_A38_D2.1811.00
36_L75_V2.1271.00
70_E73_R2.0111.00
71_K74_E1.9901.00
7_K45_D1.9651.00
11_E15_R1.8881.00
30_C33_C1.8541.00
32_E71_K1.8331.00
7_K41_L1.7881.00
42_K46_K1.7811.00
89_I93_R1.7421.00
37_L41_L1.6851.00
10_V72_I1.6641.00
55_T98_G1.6271.00
12_A90_L1.5971.00
35_E68_M1.5211.00
22_H33_C1.5041.00
2_R97_D1.4651.00
12_A16_I1.4591.00
91_A95_L1.4571.00
18_C22_H1.4451.00
5_R97_D1.4091.00
14_I37_L1.3831.00
22_H30_C1.3181.00
18_C30_C1.3161.00
87_H90_L1.2561.00
18_C33_C1.2221.00
17_Y21_H1.2121.00
39_Y43_R1.2061.00
70_E74_E1.2001.00
55_T58_K1.1641.00
4_E8_K1.1621.00
11_E41_L1.1521.00
16_I86_R1.1431.00
78_Y82_R1.1121.00
62_H69_R1.1021.00
8_K12_A1.0911.00
3_L50_G1.0881.00
14_I75_V1.0761.00
3_L7_K1.0731.00
14_I36_L1.0631.00
14_I72_I1.0611.00
10_V40_A1.0511.00
48_P61_V1.0451.00
4_E7_K1.0291.00
50_G54_P1.0211.00
44_L50_G1.0101.00
5_R93_R1.0031.00
12_A15_R0.9781.00
29_L37_L0.9691.00
57_A98_G0.9581.00
10_V14_I0.9451.00
83_M87_H0.9381.00
95_L99_R0.9241.00
42_K45_D0.9131.00
9_T90_L0.9091.00
19_R86_R0.9091.00
32_E35_E0.9021.00
20_D82_R0.9001.00
35_E71_K0.8881.00
44_L64_Y0.8821.00
21_H74_E0.8741.00
49_F60_P0.8691.00
16_I20_D0.8621.00
20_D86_R0.8611.00
31_P34_A0.8591.00
92_L96_L0.8561.00
34_A37_L0.8521.00
67_E71_K0.8341.00
15_R19_R0.8161.00
56_C59_C0.8131.00
66_P69_R0.8101.00
16_I78_Y0.8071.00
93_R96_L0.8061.00
15_R37_L0.8051.00
58_K98_G0.8011.00
83_M91_A0.7881.00
96_L99_R0.7811.00
94_H98_G0.7791.00
13_M88_P0.7791.00
13_M83_M0.7710.99
15_R29_L0.7660.99
3_L44_L0.7490.99
56_C63_C0.7380.99
54_P60_P0.7370.99
41_L45_D0.7370.99
99_R102_K0.6970.99
47_C59_C0.6930.99
54_P102_K0.6820.99
59_C63_C0.6730.99
38_D42_K0.6700.99
31_P35_E0.6670.99
47_C56_C0.6620.98
93_R97_D0.6600.98
44_L49_F0.6600.98
87_H91_A0.6590.98
6_E53_K0.6580.98
3_L9_T0.6500.98
36_L71_K0.6490.98
58_K101_K0.6490.98
54_P61_V0.6460.98
2_R5_R0.6430.98
13_M81_P0.6360.98
24_T27_G0.6340.98
55_T97_D0.6310.98
29_L33_C0.6300.98
68_M75_V0.6200.98
8_K90_L0.6140.97
38_D41_L0.6120.97
21_H78_Y0.6040.97
62_H72_I0.5970.97
92_L95_L0.5930.97
16_I79_S0.5930.97
8_K11_E0.5870.97
40_A72_I0.5860.97
98_G101_K0.5850.97
66_P70_E0.5840.97
57_A97_D0.5820.97
55_T62_H0.5790.96
76_M80_G0.5770.96
74_E78_Y0.5730.96
47_C63_C0.5720.96
22_H78_Y0.5690.96
12_A87_H0.5670.96
90_L93_R0.5660.96
67_E70_E0.5640.96
57_A69_R0.5570.96
10_V36_L0.5520.95
58_K102_K0.5520.95
97_D100_R0.5440.95
98_G102_K0.5430.95
54_P97_D0.5380.95
6_E13_M0.5360.95
97_D101_K0.5340.94
5_R90_L0.5330.94
46_K98_G0.5310.94
84_L95_L0.5220.94
16_I91_A0.5200.94
49_F53_K0.5190.94
9_T55_T0.5110.93
79_S86_R0.5070.93
84_L92_L0.5060.93
82_R86_R0.5030.93
28_G35_E0.5000.92
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  
1oywA 1 0.7642 5.1 0.94 Contact Map
3avrA 1 0.8679 2.5 0.948 Contact Map
4uf0A 2 0.8679 1.9 0.952 Contact Map
2ykgA 1 0.9623 1.6 0.953 Contact Map
4f7uE 1 0.2264 1.6 0.954 Contact Map
2cupA 1 0.566 1.5 0.954 Contact Map
2hl7A 1 0.2453 1.5 0.954 Contact Map
2plxB 1 0.2453 1.4 0.955 Contact Map
4bujB 1 0.783 1.4 0.955 Contact Map
1t6uA 6 0.4245 1.4 0.955 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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