GREMLIN Database
Phage_holin_4_1 - Bacteriophage holin family
PFAM: PF05105 Sequences:
Download Alignment
We filter this alignment to remove sites that have many gaps before running GREMLIN.

Date: 2015_10
Length: 114 (111)
Sequences: 7556 (5736)
Seq/√Len: 544.4
META: 0.857

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:
i j Sco Prob
31_A96_R3.9871.00
60_A78_V2.9781.00
27_T93_N2.6371.00
40_S92_E2.5201.00
28_G32_A2.5001.00
21_M54_L2.4811.00
43_G85_N2.4691.00
35_N96_R2.3201.00
20_L83_I2.2841.00
16_A62_L2.2241.00
25_Y43_G2.1371.00
31_A35_N2.0231.00
34_K97_L2.0031.00
52_L94_A1.9111.00
25_Y46_G1.8981.00
94_A99_V1.8821.00
38_L88_I1.8791.00
46_G50_K1.8501.00
34_K45_K1.8111.00
61_H65_K1.8071.00
17_L82_Y1.7871.00
39_S42_K1.6091.00
50_K86_E1.5931.00
29_V38_L1.5751.00
13_L79_I1.5341.00
44_F53_Y1.5131.00
103_K107_K1.4841.00
53_Y82_Y1.4711.00
30_L48_A1.4521.00
24_D89_S1.2941.00
104_K107_K1.2651.00
59_V87_G1.2571.00
33_I108_A1.2451.00
11_D75_R1.2401.00
84_A88_I1.2231.00
19_I62_L1.2151.00
6_L58_A1.2081.00
95_G106_K1.2051.00
15_I19_I1.2031.00
51_V56_L1.2001.00
3_L7_F1.1761.00
87_G109_L1.1561.00
61_H75_R1.1411.00
62_L65_K1.1271.00
87_G91_L1.1271.00
28_G89_S1.1151.00
56_L94_A1.1021.00
12_G15_I1.0981.00
57_V79_I1.0981.00
33_I38_L1.0931.00
11_D15_I1.0891.00
17_L57_V1.0881.00
103_K106_K1.0871.00
23_I55_L1.0761.00
23_I90_I1.0711.00
30_L97_L1.0421.00
80_F84_A1.0241.00
21_M53_Y1.0101.00
29_V33_I0.9671.00
16_A20_L0.9571.00
28_G31_A0.9461.00
95_G112_L0.9451.00
26_I30_L0.9301.00
45_K48_A0.9271.00
22_V26_I0.9191.00
106_K110_E0.9181.00
95_G101_I0.9101.00
41_R45_K0.9071.00
104_K108_A0.9001.00
31_A93_N0.8871.00
91_L101_I0.8751.00
33_I36_G0.8711.00
27_T92_E0.8501.00
8_G11_D0.8451.00
17_L79_I0.8401.00
50_K54_L0.8301.00
44_F85_N0.8181.00
24_D28_G0.8091.00
83_I87_G0.8071.00
38_L43_G0.8001.00
46_G89_S0.8001.00
46_G49_K0.7991.00
39_S110_E0.7931.00
40_S89_S0.7831.00
110_E113_K0.7791.00
94_A101_I0.7791.00
13_L76_T0.7681.00
21_M50_K0.7611.00
45_K49_K0.7491.00
27_T52_L0.7301.00
56_L82_Y0.7221.00
48_A52_L0.7191.00
25_Y29_V0.7181.00
20_L87_G0.7181.00
91_L95_G0.7081.00
16_A66_L0.7051.00
3_L6_L0.7011.00
42_K45_K0.6981.00
47_I81_F0.6971.00
59_V90_I0.6911.00
40_S44_F0.6841.00
25_Y47_I0.6801.00
52_L97_L0.6771.00
27_T31_A0.6711.00
53_Y85_N0.6701.00
62_L66_L0.6691.00
27_T94_A0.6671.00
43_G46_G0.6661.00
29_V43_G0.6651.00
76_T80_F0.6611.00
53_Y86_E0.6591.00
30_L33_I0.6581.00
31_A97_L0.6571.00
32_A37_K0.6541.00
43_G47_I0.6461.00
44_F49_K0.6421.00
13_L80_F0.6371.00
43_G88_I0.6361.00
34_K48_A0.6341.00
66_L83_I0.6231.00
55_L59_V0.6221.00
32_A38_L0.6221.00
23_I59_V0.6191.00
107_K111_Q0.6151.00
48_A82_Y0.6121.00
14_L79_I0.6101.00
95_G98_G0.6091.00
47_I85_N0.6061.00
19_I23_I0.6051.00
37_K110_E0.5991.00
27_T90_I0.5861.00
88_I91_L0.5840.99
84_A109_L0.5820.99
64_D75_R0.5790.99
63_L87_G0.5780.99
63_L67_L0.5780.99
64_D68_G0.5770.99
24_D86_E0.5720.99
88_I92_E0.5720.99
8_G75_R0.5710.99
68_G71_G0.5700.99
70_D73_Y0.5680.99
64_D76_T0.5650.99
56_L78_V0.5620.99
37_K42_K0.5530.99
91_L109_L0.5530.99
6_L9_G0.5520.99
20_L59_V0.5490.99
58_A66_L0.5390.99
44_F48_A0.5360.99
60_A74_L0.5280.99
94_A97_L0.5280.99
66_L69_G0.5280.99
94_A100_P0.5270.99
20_L90_I0.5270.99
50_K53_Y0.5230.99
40_S46_G0.5210.99
64_D79_I0.5120.99
85_N88_I0.5110.99
101_I106_K0.5110.99
49_K53_Y0.5030.99
30_L34_K0.5020.98
4_G80_F0.5020.98
47_I51_V0.5020.98
29_V88_I0.5000.98
91_L105_L0.5000.98
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  
1iojA 1 0.2719 4.3 0.899 Contact Map
1ezeA 1 0.2719 3.6 0.902 Contact Map
2k5jA 2 0.2368 2.5 0.91 Contact Map
4p02B 1 0.3158 2.5 0.911 Contact Map
4k7jA 1 0.1754 2.4 0.911 Contact Map
4mndA 2 0.9211 2.4 0.911 Contact Map
3mz1A 2 0 2.2 0.913 Contact Map
3plaA 2 0.386 2.2 0.913 Contact Map
1yy3A 1 0.4298 2.2 0.913 Contact Map
3id6A 2 0.3947 2.1 0.914 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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