GREMLIN Database
Phage_holin_4_2 - Mycobacterial 4 TMS phage holin, superfamily IV
PFAM: PF04020 Sequences:
Download Alignment
We filter this alignment to remove sites that have many gaps before running GREMLIN.

Date: 2015_10
Length: 105 (104)
Sequences: 37561 (24461)
Seq/√Len: 2398.6
META: 0.925

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:
i j Sco Prob
74_L95_G2.9761.00
58_T66_L2.7781.00
26_V32_A2.3201.00
51_K66_L2.2671.00
75_W79_W2.2451.00
88_G91_A2.1501.00
71_A93_L2.1451.00
15_L19_Y2.1211.00
74_L99_I2.0751.00
47_R51_K2.0241.00
42_L73_M2.0181.00
90_W94_L1.9351.00
72_L75_W1.9301.00
13_A17_A1.8561.00
28_G31_T1.8561.00
14_L35_A1.7771.00
13_A102_V1.7211.00
35_A84_F1.7091.00
24_I95_G1.6971.00
15_L32_A1.6861.00
21_V91_A1.6461.00
91_A94_L1.6091.00
39_L77_A1.5731.00
25_S85_H1.5601.00
17_A98_V1.5351.00
7_W11_A1.5161.00
23_G91_A1.4901.00
17_A99_I1.4791.00
87_D91_A1.4401.00
7_W37_L1.3361.00
25_S87_D1.3231.00
42_L77_A1.2891.00
38_V77_A1.2861.00
65_F68_V1.2691.00
86_V92_A1.2571.00
76_L79_W1.2011.00
75_W89_F1.1991.00
6_R10_N1.1941.00
3_L7_W1.1861.00
23_G87_D1.1771.00
35_A77_A1.1631.00
14_L39_L1.1371.00
51_K69_I1.1301.00
38_V81_V1.1291.00
30_G34_I1.1111.00
54_T58_T1.1081.00
14_L95_G1.1031.00
75_W92_A1.0831.00
75_W78_A1.0611.00
17_A95_G1.0511.00
96_A100_S1.0211.00
16_V19_Y1.0151.00
18_A22_P1.0081.00
51_K54_T1.0081.00
7_W10_N0.9951.00
43_N70_N0.9871.00
21_V94_L0.9861.00
55_L58_T0.9651.00
98_V102_V0.9531.00
51_K58_T0.9481.00
14_L99_I0.9311.00
31_T81_V0.9291.00
91_A95_G0.9261.00
11_A36_A0.9251.00
17_A21_V0.9181.00
61_T65_F0.9171.00
89_F93_L0.9091.00
45_L48_P0.9081.00
10_N14_L0.8891.00
7_W36_A0.8871.00
54_T65_F0.8831.00
92_A96_A0.8731.00
72_L76_L0.8611.00
27_D31_T0.8561.00
12_L16_V0.8451.00
50_L73_M0.8421.00
27_D85_H0.8261.00
18_A26_V0.8241.00
78_A86_V0.8201.00
21_V98_V0.8171.00
71_A92_A0.8171.00
29_F33_L0.8121.00
35_A39_L0.7991.00
36_A40_G0.7991.00
26_V31_T0.7971.00
67_L93_L0.7671.00
11_A33_L0.7671.00
58_T69_I0.7601.00
79_W82_P0.7601.00
99_I103_S0.7591.00
39_L43_N0.7531.00
95_G99_I0.7491.00
40_G44_A0.7461.00
50_L69_I0.7401.00
58_T65_F0.7361.00
64_L68_V0.7331.00
16_V20_L0.7261.00
42_L76_L0.7211.00
73_M76_L0.7131.00
66_L70_N0.7101.00
56_P60_L0.7071.00
24_I86_V0.6931.00
34_I81_V0.6901.00
18_A32_A0.6881.00
78_A84_F0.6861.00
82_P85_H0.6831.00
52_L55_L0.6821.00
31_T83_G0.6811.00
61_T64_L0.6711.00
67_L100_S0.6711.00
7_W33_L0.6681.00
17_A20_L0.6571.00
55_L59_I0.6561.00
67_L97_L0.6511.00
71_A75_W0.6491.00
3_L37_L0.6451.00
24_I74_L0.6421.00
52_L56_P0.6391.00
10_N99_I0.6371.00
78_A82_P0.6341.00
70_N100_S0.6341.00
8_L12_L0.6321.00
11_A32_A0.6261.00
41_L44_A0.6221.00
48_P52_L0.5971.00
51_K55_L0.5921.00
47_R73_M0.5891.00
57_L65_F0.5891.00
47_R69_I0.5861.00
2_R6_R0.5841.00
21_V24_I0.5831.00
27_D83_G0.5811.00
78_A92_A0.5721.00
4_L8_L0.5711.00
31_T34_I0.5691.00
19_Y22_P0.5681.00
26_V84_F0.5671.00
78_A85_H0.5661.00
3_L44_A0.5611.00
34_I38_V0.5611.00
66_L104_W0.5531.00
66_L103_S0.5471.00
9_I13_A0.5371.00
30_G79_W0.5331.00
13_A16_V0.5301.00
41_L45_L0.5291.00
42_L46_V0.5281.00
12_L15_L0.5201.00
10_N13_A0.5201.00
57_L60_L0.5171.00
30_G33_L0.5131.00
31_T35_A0.5121.00
32_A36_A0.5101.00
87_D90_W0.5061.00
69_I73_M0.5011.00
79_W83_G0.5001.00
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  
4czbA 2 0.981 3 0.892 Contact Map
4p6vD 1 0.8571 2.7 0.894 Contact Map
4cz8A 2 0.9619 2.4 0.896 Contact Map
4lz6A 1 0.9905 2 0.901 Contact Map
4humA 1 1 1.7 0.905 Contact Map
3w4tA 1 0.9905 1.6 0.907 Contact Map
3mktA 1 0.9905 1.4 0.909 Contact Map
4bwzA 2 0.9524 1.2 0.913 Contact Map
3hzqA 3 0.6381 1.2 0.914 Contact Map
1oedC 1 0.7429 1.2 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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