GREMLIN Database
HOLD - DNA polymerase III subunit psi
UniProt: P28632 Sequences:
Download Alignment
We filter this alignment to remove sites that have many gaps before running GREMLIN.

Date: 2015_01
Length: 137 (127)
Sequences: 209 (150)
Seq/√Len: 13.3

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:
i j Sco Prob
60_A67_Q2.4460.90
30_A71_L2.3810.89
5_R8_Q2.3160.88
12_L105_S2.2430.86
17_W23_G2.1890.85
57_V75_K2.0620.81
54_V105_S2.0170.79
40_V51_D2.0080.79
10_Q72_T1.9820.78
103_V108_L1.9810.78
13_G117_A1.9550.77
47_P73_P1.9380.76
43_A47_P1.8940.75
54_V68_V1.8260.72
39_L79_L1.8180.72
6_D16_Q1.7800.70
108_L114_N1.7540.69
49_L68_V1.7360.68
42_V63_V1.7010.66
19_L119_A1.6660.65
57_V60_A1.6260.63
10_Q39_L1.5810.60
53_L57_V1.5670.60
24_A27_G1.5530.59
106_P125_I1.5520.59
53_L61_L1.4930.56
12_L18_S1.4880.56
12_L89_R1.4800.55
64_S76_I1.4590.54
54_V104_A1.4350.53
36_H43_A1.4250.52
57_V88_W1.3970.51
86_N89_R1.3870.50
12_L76_I1.3860.50
95_P102_Q1.3810.50
13_G22_P1.3650.49
17_W86_N1.3590.49
75_K119_A1.3560.49
24_A111_L1.3290.47
83_S118_R1.3100.46
56_D61_L1.2990.46
45_D49_L1.2960.45
28_E78_M1.2920.45
58_L124_Q1.2920.45
12_L23_G1.2810.45
26_Q42_V1.2680.44
21_R24_A1.2500.43
25_L119_A1.2390.42
17_W114_N1.2350.42
62_T82_G1.2210.41
12_L119_A1.2150.41
12_L17_W1.2110.41
37_V41_M1.2090.41
44_N93_D1.2000.40
63_V103_V1.1880.40
66_D93_D1.1880.40
31_I58_L1.1830.40
62_T69_L1.1780.39
53_L118_R1.1740.39
8_Q118_R1.1730.39
44_N53_L1.1620.38
19_L27_G1.1590.38
32_A71_L1.1540.38
16_Q56_D1.1540.38
64_S118_R1.1430.38
21_R29_I1.1240.37
40_V108_L1.1180.36
33_I113_A1.1040.36
69_L118_R1.1030.36
57_V106_P1.1030.36
77_A107_A1.0970.35
16_Q29_I1.0830.35
49_L60_A1.0790.34
8_Q41_M1.0230.32
92_T103_V1.0190.32
17_W60_A1.0120.31
15_T129_E0.9980.31
51_D79_L0.9980.31
72_T111_L0.9740.30
116_T120_A0.9730.30
65_P105_S0.9620.29
85_C101_A0.9590.29
42_V61_L0.9530.29
25_L31_I0.9410.28
16_Q28_E0.9180.27
41_M56_D0.8960.26
3_S11_Q0.8950.26
43_A121_L0.8890.26
50_T116_T0.8820.26
89_R95_P0.8770.25
49_L74_E0.8680.25
91_G125_I0.8630.25
40_V114_N0.8630.25
37_V76_I0.8620.25
120_A123_Q0.8580.25
63_V66_D0.8500.24
18_S115_P0.8390.24
36_H123_Q0.8370.24
8_Q75_K0.8280.24
63_V113_A0.8260.23
93_D121_L0.8160.23
40_V60_A0.8150.23
75_K79_L0.8080.23
68_V126_C0.7960.22
13_G91_G0.7880.22
34_P125_I0.7820.22
11_Q109_T0.7780.22
8_Q27_G0.7770.22
25_L56_D0.7720.22
56_D90_L0.7660.21
69_L83_S0.7480.21
40_V89_R0.7470.21
32_A110_D0.7380.20
56_D59_R0.7380.20
71_L107_A0.7350.20
55_S65_P0.7310.20
120_A124_Q0.7220.20
24_A118_R0.7210.20
76_I129_E0.7190.20
71_L79_L0.7140.20
7_W11_Q0.7110.19
56_D78_M0.7110.19
56_D118_R0.7070.19
21_R111_L0.6990.19
91_G103_V0.6930.19
20_R48_A0.6920.19
102_Q107_A0.6900.19
38_R95_P0.6900.19
70_Q118_R0.6900.19
5_R14_I0.6850.19
74_E101_A0.6830.18
78_M90_L0.6820.18
19_L59_R0.6770.18
92_T127_T0.6750.18
11_Q83_S0.6610.18
42_V83_S0.6500.17
73_P126_C0.6440.17
57_V118_R0.6440.17
25_L79_L0.6440.17
87_S125_I0.6390.17
34_P92_T0.6370.17
10_Q15_T0.6360.17
16_Q27_G0.6270.17
35_A40_V0.6270.17
12_L86_N0.6250.17
18_S26_Q0.6230.17
36_H63_V0.6210.17
24_A41_M0.6200.17
7_W17_W0.6200.17
37_V56_D0.6190.17
12_L129_E0.6170.16
57_V71_L0.6140.16
43_A64_S0.6130.16
60_A74_E0.6100.16
5_R16_Q0.6070.16
69_L114_N0.6040.16
88_W105_S0.6020.16
88_W106_P0.5990.16
3_S6_D0.5970.16
45_D93_D0.5940.16
28_E80_P0.5900.16
34_P91_G0.5870.16
20_R71_L0.5850.16
64_S73_P0.5840.16
73_P91_G0.5830.16
35_A93_D0.5820.15
35_A96_L0.5750.15
103_V124_Q0.5730.15
66_D101_A0.5700.15
44_N57_V0.5640.15
10_Q71_L0.5580.15
14_I25_L0.5570.15
17_W117_A0.5530.15
60_A66_D0.5520.15
118_R126_C0.5520.15
88_W124_Q0.5480.15
19_L77_A0.5470.15
16_Q19_L0.5410.14
72_T75_K0.5380.14
19_L38_R0.5340.14
88_W121_L0.5320.14
23_G78_M0.5270.14
42_V118_R0.5240.14
58_L103_V0.5230.14
54_V74_E0.5230.14
50_T95_P0.5200.14
6_D9_L0.5160.14
37_V112_R0.5110.14
53_L107_A0.5070.14
55_S62_T0.5000.13
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  
3sxuB 1 0.7445 100 0.137 Contact Map
3mn1A 4 0.9343 20.5 0.945 Contact Map
3n1uA 3 0.9051 19.1 0.945 Contact Map
4navD 3 0.9124 13.8 0.949 Contact Map
1k1eA 5 0.9635 13.1 0.949 Contact Map
2hdoA 1 0.8321 13.1 0.949 Contact Map
3l2oB 2 0.438 13 0.95 Contact Map
4hgnA 3 0.854 12.9 0.95 Contact Map
4um7A 3 0.9124 12.5 0.95 Contact Map
2j8pA 1 0.3577 11.4 0.951 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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