GREMLIN Database
PHB_acc_N - PHB/PHA accumulation regulator DNA-binding domain
PFAM: PF07879 Sequences:
Download Alignment
We filter this alignment to remove sites that have many gaps before running GREMLIN.

Date: 2015_10
Length: 61 (60)
Sequences: 9887 (4213)
Seq/√Len: 543.9
META: 0.971

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:
i j Sco Prob
26_E30_E3.0421.00
25_A29_R2.2991.00
2_I24_L2.1501.00
12_D15_T2.1471.00
14_E32_E2.0881.00
6_A40_K1.9421.00
23_D26_E1.8841.00
9_R39_A1.8181.00
3_K13_T1.8001.00
37_V42_G1.7991.00
2_I10_L1.6021.00
27_L32_E1.6001.00
57_E60_K1.5541.00
25_A57_E1.5501.00
38_D41_T1.5061.00
9_R18_Y1.4111.00
25_A53_I1.3991.00
38_D43_E1.3171.00
9_R47_R1.2751.00
28_V34_F1.2541.00
1_V35_Q1.2401.00
19_V23_D1.2271.00
29_R57_E1.1981.00
51_T55_L1.1771.00
22_D60_K1.1331.00
16_S39_A1.1181.00
15_T27_L1.1071.00
51_T58_E1.0961.00
17_R23_D1.0941.00
35_Q44_D1.0781.00
5_Y16_S1.0721.00
6_A20_T1.0251.00
4_K7_N1.0031.00
10_L24_L1.0001.00
1_V37_V1.0001.00
3_K39_A0.9811.00
26_E29_R0.9481.00
45_L49_V0.9291.00
8_R16_S0.9261.00
38_D45_L0.9221.00
28_V53_I0.9181.00
47_R51_T0.8891.00
48_S58_E0.8751.00
35_Q42_G0.8671.00
7_N45_L0.8661.00
50_L53_I0.8591.00
22_D26_E0.8541.00
48_S59_K0.8461.00
18_Y39_A0.8411.00
20_T51_T0.8251.00
55_L59_K0.8201.00
18_Y25_A0.7571.00
47_R54_I0.7471.00
4_K13_T0.7451.00
15_T59_K0.7321.00
4_K8_R0.6991.00
28_V50_L0.6921.00
47_R60_K0.6891.00
20_T40_K0.6861.00
50_L56_E0.6841.00
23_D34_F0.6821.00
27_L30_E0.6781.00
36_V49_V0.6781.00
4_K9_R0.6731.00
7_N40_K0.6661.00
2_I19_V0.6601.00
34_F59_K0.6501.00
21_L25_A0.6491.00
9_R51_T0.6401.00
45_L58_E0.5881.00
10_L18_Y0.5881.00
31_G34_F0.5850.99
13_T18_Y0.5730.99
6_A39_A0.5640.99
7_N49_V0.5640.99
24_L34_F0.5610.99
20_T23_D0.5570.99
52_Q56_E0.5550.99
29_R51_T0.5480.99
21_L28_V0.5430.99
5_Y18_Y0.5430.99
15_T23_D0.5390.99
12_D19_V0.5310.99
8_R28_V0.5200.99
23_D27_L0.5190.99
55_L60_K0.5170.99
4_K38_D0.5130.99
12_D25_A0.5110.99
24_L29_R0.5040.99
6_A58_E0.5000.98
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  
3k6mA 2 0.7377 14.5 0.859 Contact Map
4trbA 2 0.8361 12 0.865 Contact Map
1poiA 3 0.7213 11.4 0.866 Contact Map
4i2yA 1 0.8361 11.1 0.867 Contact Map
3u0kA 1 0.8033 11 0.867 Contact Map
4ae5A 1 0.9508 10.4 0.868 Contact Map
1vw4J 1 0.9344 10.3 0.868 Contact Map
1o6dA 2 0.8689 10 0.869 Contact Map
1k6dA 2 0.7541 9.9 0.87 Contact Map
1qv0A 1 0.7705 8.7 0.872 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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