GREMLIN Database
PTR - Phage tail repeat like
PFAM: PF12789 Sequences:
Download Alignment
We filter this alignment to remove sites that have many gaps before running GREMLIN.

Date: 2015_10
Length: 60 (57)
Sequences: 1415 (1127)
Seq/√Len: 149.3
META: 0.881

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:
i j Sco Prob
18_Q22_D2.7671.00
25_A28_S2.4981.00
40_Q44_D2.2811.00
3_A6_S2.1751.00
38_G42_A2.0121.00
16_G20_A1.9921.00
47_A50_S1.8561.00
33_I40_Q1.8251.00
32_T35_D1.5731.00
33_I42_A1.5181.00
55_I58_I1.5131.00
9_H13_D1.4771.00
11_I18_Q1.4641.00
54_T57_D1.4301.00
12_S34_A1.3291.00
10_A13_D1.3251.00
19_T41_T1.3131.00
20_A42_A1.2891.00
11_I33_I1.2781.00
15_T37_T1.2211.00
8_T30_T1.2161.00
28_S50_S1.2141.00
39_L43_L1.1741.00
47_A51_H1.1651.00
27_T49_T1.1030.99
26_D48_D1.0950.99
11_I20_A1.0600.99
33_I55_I1.0460.99
31_H35_D1.0300.99
33_I39_L1.0270.99
16_G38_G0.9990.99
24_K46_K0.9810.99
5_T27_T0.9650.98
18_Q40_Q0.9500.98
54_T59_T0.9240.98
22_D44_D0.9120.98
32_T37_T0.9100.98
14_V36_V0.8860.97
11_I22_D0.8820.97
9_H53_H0.8710.97
53_H57_D0.8480.96
43_L46_K0.8450.96
6_S28_S0.8350.96
30_T52_T0.8220.96
47_A53_H0.8150.95
25_A29_H0.8130.95
54_T58_I0.8130.95
11_I14_V0.7840.94
8_T52_T0.7700.94
7_H13_D0.7690.94
23_G45_G0.7660.94
10_A54_T0.7640.94
14_V58_I0.7620.94
10_A15_T0.7580.93
11_I17_L0.7430.93
20_A23_G0.7420.93
33_I43_L0.7250.92
10_A32_T0.7160.91
39_L46_K0.7120.91
4_A26_D0.7120.91
33_I44_D0.6880.90
5_T49_T0.6840.89
16_G21_L0.6820.89
13_D35_D0.6820.89
17_L39_L0.6790.89
19_T23_G0.6770.89
17_L24_K0.6720.88
21_L24_K0.6720.88
52_T56_S0.6490.87
11_I16_G0.6310.85
36_V39_L0.6250.85
11_I55_I0.6210.84
17_L21_L0.6090.83
29_H36_V0.6060.83
31_H53_H0.6020.82
6_S12_S0.5980.82
34_A37_T0.5960.82
14_V17_L0.5940.82
35_D57_D0.5820.80
31_H36_V0.5700.79
41_T45_G0.5700.79
7_H51_H0.5680.79
13_D57_D0.5440.76
5_T8_T0.5360.75
6_S50_S0.5020.70
34_A56_S0.5000.69
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  
3cveA 4 0.6667 1.2 0.9 Contact Map
2r6fA 2 1 1 0.904 Contact Map
3zqjA 1 1 1 0.907 Contact Map
3pihA 2 0.9833 0.9 0.907 Contact Map
3v6bA 2 0.3 0.9 0.907 Contact Map
2makB 2 0.3833 0.9 0.908 Contact Map
4ecgA 1 0.9667 0.9 0.91 Contact Map
4bgoA 1 0.9833 0.8 0.91 Contact Map
3he1A 3 0.3667 0.8 0.911 Contact Map
3qh9A 2 0.5167 0.8 0.911 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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