GREMLIN Database
Phage_r1t_holin - Putative lactococcus lactis phage r1t holin
PFAM: PF16945 Sequences:
Download Alignment
We filter this alignment to remove sites that have many gaps before running GREMLIN.

Date: 2015_10
Length: 72 (62)
Sequences: 2791 (1984)
Seq/√Len: 252.0
META: 0.923

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:
i j Sco Prob
16_F47_A3.9811.00
14_K53_T3.0151.00
15_T18_Q2.0751.00
16_F43_A2.0261.00
18_Q53_T1.7271.00
14_K57_G1.6981.00
50_S54_S1.6231.00
21_L56_A1.6021.00
20_A39_V1.5681.00
2_K6_K1.5121.00
30_G41_S1.4971.00
8_A54_S1.4801.00
8_A51_L1.4651.00
20_A52_L1.4331.00
12_A51_L1.4071.00
15_T19_T1.3971.00
19_T46_A1.3951.00
4_F8_A1.3371.00
12_A54_S1.3101.00
20_A43_A1.2761.00
43_A47_A1.2471.00
38_Q42_V1.2301.00
35_D38_Q1.1941.00
17_A52_L1.1891.00
53_T57_G1.1411.00
25_G29_V1.1401.00
34_V45_L1.1261.00
25_G49_L1.1021.00
22_A46_A1.0741.00
21_L49_L1.0651.00
7_A57_G1.0431.00
37_L40_L1.0321.00
25_G28_A1.0121.00
6_K9_G1.0051.00
30_G33_D1.0011.00
4_F57_G0.9781.00
34_V39_V0.9701.00
15_T46_A0.9621.00
12_A50_S0.9361.00
19_T23_L0.9181.00
16_F40_L0.8981.00
32_L41_S0.8871.00
18_Q50_S0.8660.99
40_L43_A0.8650.99
30_G45_L0.8640.99
7_A58_L0.8550.99
16_F44_A0.8520.99
18_Q49_L0.8380.99
22_A26_A0.8320.99
7_A11_R0.8320.99
40_L44_A0.8210.99
39_V43_A0.8210.99
22_A42_V0.8190.99
9_G51_L0.8160.99
11_R15_T0.8000.99
3_K7_A0.7960.99
41_S45_L0.7890.99
19_T43_A0.7650.99
23_L42_V0.7630.99
4_F58_L0.7450.98
14_K18_Q0.7370.98
4_F10_E0.7320.98
44_A47_A0.7150.98
31_L44_A0.7050.98
31_L45_L0.7000.98
21_L25_G0.6960.98
58_L61_G0.6880.97
4_F54_S0.6830.97
19_T22_A0.6820.97
60_V63_P0.6730.97
42_V46_A0.6700.97
42_V45_L0.6690.97
44_A48_V0.6430.96
6_K10_E0.6310.96
10_E57_G0.6290.96
10_E14_K0.6270.96
13_V17_A0.6240.96
5_W10_E0.5940.94
9_G13_V0.5850.94
16_F46_A0.5840.94
11_R18_Q0.5800.93
8_A55_I0.5790.93
12_A47_A0.5690.93
53_T56_A0.5660.93
31_L42_V0.5650.93
17_A56_A0.5390.91
28_A31_L0.5370.91
3_K6_K0.5270.90
37_L44_A0.5250.90
41_S48_V0.5190.89
8_A50_S0.5110.88
14_K50_S0.5030.88
26_A45_L0.5000.87
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  
2lo0A 2 0.3333 5 0.888 Contact Map
5aj3d 1 0 2.7 0.901 Contact Map
1iflA 10 0.7361 1.9 0.91 Contact Map
4grdA 5 0.9861 1.8 0.911 Contact Map
1o4vA 5 0.9861 1.7 0.911 Contact Map
4ay3A 2 0.9861 1.6 0.914 Contact Map
3bboD 1 0 1.4 0.916 Contact Map
4ja0A 6 0.9583 1.4 0.916 Contact Map
3orsA 5 0.9861 1.4 0.917 Contact Map
4rhpA 2 0.4167 1.4 0.917 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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