GREMLIN Database
Phage_term_smal - Phage small terminase subunit
PFAM: PF05944 Sequences:
Download Alignment
We filter this alignment to remove sites that have many gaps before running GREMLIN.

Date: 2015_10
Length: 130 (129)
Sequences: 1112 (829)
Seq/√Len: 73.0
META: 0.517

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:
i j Sco Prob
57_L65_G3.0501.00
73_A88_T2.9231.00
44_G72_Y2.7631.00
71_E117_R2.7461.00
23_L27_L2.7141.00
7_D31_Y2.6081.00
50_L69_I2.4191.00
70_A92_V2.3361.00
3_Q7_D2.2671.00
51_M73_A2.1661.00
62_D65_G2.1141.00
87_T90_T2.0561.00
17_I21_A2.0181.00
55_V84_F1.9951.00
46_Q79_A1.9641.00
14_I23_L1.9291.00
3_Q30_K1.9181.00
10_R26_E1.8871.00
7_D27_L1.8811.00
7_D30_K1.8681.00
15_Q87_T1.8661.00
80_M91_L1.8231.00
12_K20_K1.7511.00
90_T128_P1.7251.00
68_D117_R1.6841.00
36_E40_A1.6511.00
51_M88_T1.6080.99
35_V69_I1.5880.99
35_V53_V1.5740.99
58_I66_A1.5650.99
22_E25_R1.5550.99
57_L62_D1.5300.99
42_G75_R1.5110.99
77_G125_W1.4790.99
63_F99_A1.4630.99
23_L26_E1.4590.99
50_L73_A1.4480.99
8_R83_R1.4450.99
10_R23_L1.4210.99
28_L60_A1.4090.99
67_L118_V1.4080.99
21_A60_A1.3910.98
111_D116_S1.3800.98
33_P36_E1.3730.98
65_G68_D1.3700.98
7_D10_R1.3630.98
55_V80_M1.3420.98
32_L65_G1.3320.98
52_T84_F1.3030.98
28_L53_V1.2390.97
55_V91_L1.2080.96
94_E97_A1.2070.96
94_E127_M1.1990.96
17_I20_K1.1850.96
19_R22_E1.1770.95
36_E65_G1.1700.95
42_G45_A1.1580.95
93_A127_M1.1540.95
63_F114_Y1.1440.95
96_V118_V1.1210.94
15_Q90_T1.1200.94
103_A110_V1.0970.93
126_D129_D1.0890.93
42_G76_H1.0830.93
5_A9_R1.0730.93
54_M80_M1.0290.91
119_E123_A1.0060.90
103_A108_E0.9710.88
9_R12_K0.9670.88
6_E9_R0.9630.88
58_I96_V0.9430.87
15_Q128_P0.9140.85
5_A8_R0.9110.85
120_E123_A0.9090.85
53_V57_L0.8680.82
63_F110_V0.8680.82
38_V47_D0.8670.82
32_L57_L0.8610.81
100_A110_V0.8600.81
72_Y78_L0.8490.81
58_I63_F0.8460.80
51_M54_M0.8320.79
86_R94_E0.8290.79
17_I84_F0.8280.79
10_R13_Q0.8170.78
3_Q6_E0.8020.77
71_E75_R0.7950.76
36_E68_D0.7920.76
44_G78_L0.7880.75
64_E68_D0.7860.75
113_P116_S0.7850.75
19_R23_L0.7820.75
111_D114_Y0.7750.74
3_Q31_Y0.7750.74
34_W37_G0.7660.73
32_L53_V0.7640.73
27_L30_K0.7590.73
8_R52_T0.7500.72
122_T126_D0.7450.71
34_W128_P0.7450.71
64_E117_R0.7420.71
38_V45_A0.7240.69
52_T83_R0.7220.69
54_M88_T0.7200.69
3_Q23_L0.7200.69
2_A6_E0.7200.69
58_I92_V0.7190.69
38_V50_L0.7180.68
57_L68_D0.7150.68
19_R27_L0.7130.68
71_E120_E0.7110.68
72_Y76_H0.7090.67
109_S121_L0.7080.67
80_M88_T0.6990.66
35_V57_L0.6980.66
4_L49_V0.6970.66
37_G66_A0.6960.66
14_I21_A0.6940.66
54_M73_A0.6830.65
4_L52_T0.6820.64
63_F96_V0.6800.64
100_A115_L0.6770.64
113_P117_R0.6700.63
22_E26_E0.6630.62
74_L125_W0.6610.62
112_L116_S0.6600.62
42_G50_L0.6560.61
16_S129_D0.6550.61
86_R95_E0.6530.61
85_K130_Q0.6480.61
46_Q51_M0.6460.60
35_V124_D0.6410.60
58_I91_L0.6410.60
51_M55_V0.6350.59
99_A103_A0.6320.59
47_D78_L0.6320.59
82_D85_K0.6290.58
102_K106_A0.6220.57
44_G76_H0.6210.57
74_L89_A0.6190.57
125_W128_P0.6170.57
100_A107_G0.6140.56
20_K23_L0.6130.56
64_E111_D0.6090.56
33_P37_G0.6020.55
14_I82_D0.5920.54
47_D72_Y0.5830.53
42_G90_T0.5800.52
30_K130_Q0.5790.52
32_L36_E0.5730.51
104_L107_G0.5710.51
11_L20_K0.5700.51
39_L78_L0.5640.50
114_Y130_Q0.5600.50
122_T129_D0.5580.50
11_L56_W0.5570.49
118_V122_T0.5540.49
16_S128_P0.5540.49
98_D101_L0.5530.49
39_L67_L0.5530.49
99_A113_P0.5520.49
101_L105_K0.5520.49
16_S97_A0.5510.49
34_W84_F0.5500.49
99_A114_Y0.5500.49
79_A88_T0.5480.48
30_K49_V0.5480.48
119_E122_T0.5400.47
69_I79_A0.5380.47
24_K81_P0.5370.47
64_E107_G0.5370.47
19_R77_G0.5350.47
58_I99_A0.5350.47
122_T127_M0.5320.46
78_L82_D0.5310.46
63_F111_D0.5290.46
34_W58_I0.5240.45
110_V118_V0.5240.45
9_R19_R0.5240.45
116_S120_E0.5230.45
32_L62_D0.5210.45
26_E64_E0.5190.45
83_R90_T0.5170.44
117_R120_E0.5170.44
38_V76_H0.5150.44
114_Y117_R0.5150.44
56_W59_D0.5060.43
54_M72_Y0.5060.43
53_V65_G0.5060.43
72_Y82_D0.5040.43
5_A13_Q0.5030.43
57_L69_I0.5030.43
88_T92_V0.5030.43
107_G110_V0.5000.42
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  
3o0yA 3 0.9154 17.4 0.931 Contact Map
3gnlA 1 0.3231 6.6 0.943 Contact Map
1x4qA 1 0.6538 4.6 0.947 Contact Map
2x5hA 2 0.3231 4.5 0.947 Contact Map
1mwqA 2 0.6615 4.3 0.948 Contact Map
3pvzA 2 0.3154 4.3 0.948 Contact Map
1hdhA 1 0.3 4.2 0.948 Contact Map
1z8uA 1 0.1923 3.1 0.952 Contact Map
3qwpA 1 0.9077 3 0.952 Contact Map
1xngA 2 0.3154 3 0.952 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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