GREMLIN Database
HOLC - DNA polymerase III subunit chi
UniProt: P28905 Sequences:
Download Alignment
We filter this alignment to remove sites that have many gaps before running GREMLIN.

Date: 2015_01
EcoGene: EG11413
Length: 147 (138)
Sequences: 825 (594)
Seq/√Len: 50.6

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:
i j Sco Prob
49_A82_I4.7581.00
40_L83_A3.8811.00
65_V80_V3.8741.00
29_A41_I3.6241.00
131_Y135_R3.2171.00
117_V127_A3.1391.00
96_L104_A2.3671.00
131_Y141_L2.2821.00
127_A130_R2.2231.00
41_I52_L2.1381.00
21_V123_L2.1181.00
107_A139_F2.1051.00
53_D67_H2.0861.00
30_A60_P2.0501.00
131_Y143_T1.9030.99
44_E101_T1.8690.99
94_D111_T1.8350.99
115_D134_Y1.7820.99
43_C49_A1.7350.99
49_A84_W1.7260.99
119_Y124_K1.6500.98
23_Q55_A1.6180.98
118_P123_L1.6020.98
60_P63_S1.5850.98
133_A137_A1.5560.97
46_E50_Y1.5550.97
26_C53_D1.5530.97
96_L110_F1.5100.97
43_C52_L1.4570.96
42_A100_R1.4540.96
53_D66_P1.4420.96
29_A39_V1.4320.96
129_E132_K1.4210.95
33_W66_P1.4130.95
8_L143_T1.4050.95
32_R95_I1.4030.95
49_A69_L1.3840.95
4_A107_A1.3630.94
68_N78_A1.3560.94
26_C59_R1.3120.93
25_V99_L1.3120.93
46_E84_W1.2710.92
26_C56_L1.2610.92
27_E31_E1.2390.91
103_F134_Y1.2340.91
29_A65_V1.1880.89
22_E55_A1.1790.89
11_N14_T1.1760.88
98_S115_D1.1490.87
37_K94_D1.1200.86
49_A71_G1.1080.85
7_Y24_L1.1000.85
121_D125_Q1.0860.84
129_E135_R1.0800.84
98_S117_V1.0770.84
109_A137_A1.0700.83
116_F124_K1.0690.83
31_E35_S1.0580.82
32_R39_V1.0490.82
68_N114_V1.0480.82
44_E48_Q1.0460.82
113_V137_A1.0240.80
126_L132_K1.0230.80
103_F133_A1.0130.80
112_E144_A1.0090.79
122_S125_Q1.0070.79
5_T112_E0.9970.79
73_G77_G0.9950.78
133_A136_V0.9940.78
107_A137_A0.9800.77
23_Q59_R0.9720.77
4_A134_Y0.9710.77
106_F110_F0.9570.76
116_F143_T0.9500.75
27_E112_E0.9480.75
125_Q132_K0.9470.75
124_K143_T0.9390.74
24_L30_A0.9370.74
21_V118_P0.9330.74
85_P89_S0.9300.74
40_L143_T0.9250.73
68_N73_G0.9220.73
133_A139_F0.9200.73
122_S129_E0.9160.72
27_E144_A0.9080.72
42_A106_F0.8920.70
39_V97_I0.8700.68
118_P127_A0.8690.68
124_K127_A0.8670.68
13_T19_S0.8650.68
109_A133_A0.8650.68
106_F131_Y0.8570.67
45_D48_Q0.8560.67
68_N81_E0.8530.67
96_L106_F0.8390.66
29_A96_L0.8360.65
92_R110_F0.8350.65
31_E112_E0.8340.65
41_I97_I0.8210.64
25_V29_A0.8150.63
8_L24_L0.8110.63
43_C82_I0.8060.62
80_V86_Q0.7980.62
108_T113_V0.7880.61
59_R80_V0.7870.61
10_D14_T0.7790.60
4_A141_L0.7760.60
5_T142_N0.7670.59
92_R140_N0.7650.58
6_F14_T0.7630.58
118_P130_R0.7590.58
105_D108_T0.7540.57
107_A133_A0.7530.57
53_D69_L0.7420.56
3_N142_N0.7380.56
48_Q66_P0.7350.55
93_R97_I0.7350.55
5_T144_A0.7350.55
21_V104_A0.7320.55
77_G80_V0.7300.55
24_L27_E0.7250.54
125_Q129_E0.7250.54
44_E100_R0.7240.54
26_C55_A0.7180.54
22_E51_R0.7140.53
31_E144_A0.7050.52
56_L104_A0.7020.52
32_R112_E0.6950.51
20_A25_V0.6920.51
81_E116_F0.6920.51
75_R78_A0.6870.50
83_A100_R0.6850.50
68_N74_P0.6700.49
32_R94_D0.6670.48
62_E121_D0.6660.48
74_P77_G0.6650.48
103_F130_R0.6630.48
55_A136_V0.6620.48
5_T115_D0.6550.47
58_A62_E0.6550.47
13_T52_L0.6500.47
48_Q95_I0.6450.46
71_G74_P0.6430.46
92_R137_A0.6430.46
107_A115_D0.6370.45
30_A63_S0.6360.45
22_E52_L0.6290.45
30_A65_V0.6290.45
31_E39_V0.6210.44
114_V144_A0.6210.44
71_G102_S0.6200.44
69_L140_N0.6160.43
121_D124_K0.6140.43
12_D120_E0.6130.43
105_D129_E0.6110.43
28_I97_I0.6060.42
26_C67_H0.6040.42
44_E131_Y0.6030.42
19_S123_L0.6020.42
64_F135_R0.6020.42
29_A97_I0.5910.41
72_E135_R0.5900.41
8_L78_A0.5890.40
38_R142_N0.5880.40
27_E30_A0.5870.40
94_D136_V0.5820.40
47_K72_E0.5820.40
113_V134_Y0.5810.40
44_E66_P0.5800.40
33_W47_K0.5700.39
83_A89_S0.5690.39
41_I56_L0.5660.38
14_T19_S0.5660.38
57_W67_H0.5650.38
4_A7_Y0.5610.38
3_N10_D0.5560.37
68_N72_E0.5530.37
115_D119_Y0.5520.37
45_D76_G0.5500.37
87_K90_S0.5470.36
9_L27_E0.5440.36
126_L129_E0.5420.36
115_D130_R0.5410.36
99_L116_F0.5390.36
53_D103_F0.5380.36
50_Y68_N0.5360.35
73_G80_V0.5320.35
108_T125_Q0.5300.35
36_G117_V0.5290.35
90_S129_E0.5270.34
5_T127_A0.5240.34
108_T137_A0.5240.34
61_A80_V0.5240.34
45_D137_A0.5230.34
3_N112_E0.5220.34
59_R112_E0.5200.34
56_L65_V0.5190.34
61_A136_V0.5190.34
33_W65_V0.5180.34
64_F131_Y0.5180.34
54_E95_I0.5150.33
8_L123_L0.5140.33
51_R142_N0.5120.33
55_A105_D0.5090.33
25_V116_F0.5050.32
23_Q27_E0.5000.32
6_F128_R0.5000.32
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  
3sxuA 1 0.9932 100 0.113 Contact Map
2ocaA 1 0.9864 83.9 0.906 Contact Map
1nktA 3 0.9252 75 0.914 Contact Map
2eyqA 1 1 55.9 0.925 Contact Map
1ofdA 1 0.9456 51.3 0.926 Contact Map
2ipcA 2 0.9456 49.8 0.927 Contact Map
4ernA 1 0.9252 47.5 0.928 Contact Map
2fsfA 2 0.9456 36.9 0.933 Contact Map
4pxaA 1 0.9456 35.3 0.933 Contact Map
4ys0A 1 0.9456 35.3 0.933 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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