GREMLIN Database
bPH_4 - Bacterial PH domain
PFAM: PF06713 Sequences:
Download Alignment
We filter this alignment to remove sites that have many gaps before running GREMLIN.

Date: 2015_10
Length: 74 (73)
Sequences: 3975 (3269)
Seq/√Len: 382.6
META: 0.866

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_D65_E4.1291.00
5_I23_I2.5461.00
28_S49_R2.5321.00
9_E20_R2.3401.00
69_E72_K2.1481.00
31_P63_K2.1411.00
30_E47_E2.1401.00
23_I73_R2.0721.00
44_D63_K1.9931.00
27_T51_G1.9221.00
22_P25_D1.8861.00
12_I56_I1.6661.00
32_T57_L1.6471.00
38_S45_R1.5191.00
45_R57_L1.5061.00
34_N57_L1.5041.00
47_E55_S1.4231.00
69_E73_R1.3931.00
33_R44_D1.3911.00
25_D51_G1.3441.00
50_Y56_I1.3381.00
30_E49_R1.3261.00
11_I20_R1.2841.00
5_I69_E1.2411.00
9_E23_I1.2351.00
2_R13_R1.2261.00
29_I70_L1.2011.00
26_I48_I1.1661.00
31_P46_L1.1181.00
6_T11_I1.1161.00
64_E68_E1.0781.00
51_G54_D1.0681.00
68_E71_K1.0341.00
4_T11_I1.0221.00
65_E68_E1.0101.00
29_I46_L1.0041.00
9_E22_P1.0011.00
27_T49_R0.9881.00
21_I50_Y0.9871.00
8_D24_S0.9851.00
65_E69_E0.9811.00
46_L58_I0.9591.00
40_A59_S0.9331.00
29_I67_I0.9151.00
1_T41_L0.9121.00
32_T43_L0.8971.00
42_S45_R0.8961.00
7_D23_I0.8781.00
13_R18_R0.8751.00
37_S45_R0.8751.00
11_I18_R0.8681.00
6_T9_E0.8641.00
42_S59_S0.8621.00
19_W56_I0.8501.00
40_A45_R0.8451.00
34_N37_S0.8291.00
14_S19_W0.8071.00
10_L48_I0.7971.00
4_T13_R0.7821.00
32_T36_L0.7561.00
12_I39_P0.7551.00
35_P43_L0.7441.00
68_E72_K0.7421.00
49_R55_S0.7411.00
47_E57_L0.7341.00
31_P64_E0.7271.00
48_I58_I0.7241.00
12_I19_W0.7191.00
6_T23_I0.7121.00
26_I70_L0.7111.00
46_L67_I0.7041.00
31_P67_I0.7031.00
1_T14_S0.6990.99
32_T35_P0.6880.99
67_I71_K0.6720.99
39_P45_R0.6720.99
52_K55_S0.6680.99
38_S57_L0.6530.99
27_T54_D0.6410.99
8_D22_P0.6380.99
50_Y54_D0.6270.99
36_L57_L0.6250.99
34_N38_S0.6180.99
59_S66_F0.6180.99
32_T47_E0.6160.99
32_T38_S0.6080.99
8_D73_R0.6080.99
21_I56_I0.6060.99
42_S58_I0.5930.98
60_P66_F0.5870.98
5_I73_R0.5860.98
32_T45_R0.5850.98
62_D69_E0.5730.98
38_S41_L0.5680.98
63_K67_I0.5660.98
5_I29_I0.5600.98
12_I21_I0.5540.97
6_T20_R0.5420.97
19_W39_P0.5390.97
8_D23_I0.5370.97
38_S43_L0.5370.97
43_L57_L0.5360.97
23_I26_I0.5350.97
10_L58_I0.5310.97
41_L59_S0.5180.96
2_R6_T0.5150.96
25_D54_D0.5070.96
37_S57_L0.5050.96
2_R11_I0.5020.95
21_I26_I0.5000.95
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  
4chmA 1 1 32.7 0.815 Contact Map
4chjA 1 0.9189 29.3 0.819 Contact Map
4r8gE 1 0.7838 26.4 0.824 Contact Map
4tyzA 1 0.9324 26 0.824 Contact Map
3a98B 1 1 19.6 0.834 Contact Map
1icwA 2 0.8514 18.8 0.835 Contact Map
1cq3A 2 0.8649 16.8 0.839 Contact Map
4y93A 1 1 13.2 0.846 Contact Map
1maiA 1 1 12.8 0.847 Contact Map
2w42A 1 0.7838 12.7 0.848 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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