GREMLIN Database
UvsY - Recombination, repair and ssDNA binding protein UvsY
PFAM: PF11056 Sequences:
Download Alignment
We filter this alignment to remove sites that have many gaps before running GREMLIN.

Date: 2015_10
Length: 129 (127)
Sequences: 3398 (2138)
Seq/√Len: 189.7
META: 0.985

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:
i j Sco Prob
117_K121_E3.5301.00
121_E124_K3.2491.00
107_K110_N2.7501.00
16_E19_K2.7021.00
62_P66_K2.5431.00
52_K84_D2.2681.00
101_Y105_I2.2541.00
34_E95_Q2.0381.00
40_K44_D2.0191.00
42_E96_E2.0011.00
123_R126_T1.9711.00
3_E29_K1.9661.00
61_D64_V1.9341.00
51_E68_K1.7421.00
47_K83_E1.7211.00
18_L119_A1.7001.00
79_L85_L1.6661.00
45_Y85_L1.6231.00
14_D123_R1.6041.00
64_V68_K1.5791.00
19_K22_Q1.5791.00
54_E78_Y1.5711.00
46_K80_D1.5531.00
2_W6_S1.5501.00
103_E107_K1.5481.00
83_E87_K1.5421.00
118_N121_E1.5261.00
45_Y88_L1.5231.00
62_P65_Y1.5101.00
34_E98_K1.4791.00
111_N114_F1.4351.00
7_K22_Q1.4071.00
60_A65_Y1.4071.00
76_D80_D1.3971.00
38_L92_I1.3701.00
1_M30_I1.3701.00
117_K124_K1.3571.00
13_L119_A1.3371.00
64_V67_E1.3361.00
100_D103_E1.3131.00
45_Y89_E1.3041.00
38_L96_E1.2991.00
12_E15_E1.2961.00
48_L52_K1.2611.00
69_I72_K1.2611.00
50_K54_E1.2351.00
65_Y68_K1.2141.00
57_T75_I1.2001.00
36_L94_Y1.1841.00
41_A88_L1.1761.00
39_K93_E1.1751.00
17_S118_N1.1751.00
51_E60_A1.1651.00
35_K97_E1.1371.00
2_W105_I1.1201.00
41_A91_K1.1001.00
71_K74_D1.0961.00
31_L103_E1.0761.00
60_A64_V1.0731.00
50_K81_A1.0691.00
95_Q98_K1.0631.00
41_A95_Q1.0621.00
100_D104_S1.0591.00
89_E93_E1.0521.00
29_K33_T1.0521.00
52_K85_L1.0481.00
47_K51_E1.0361.00
43_F90_L1.0141.00
30_I102_L1.0071.00
53_W59_K1.0071.00
63_E67_E0.9970.99
4_K7_K0.9900.99
96_E100_D0.9890.99
93_E96_E0.9860.99
25_A29_K0.9820.99
45_Y49_K0.9820.99
15_E19_K0.9790.99
10_D123_R0.9780.99
28_L101_Y0.9660.99
48_L88_L0.9650.99
16_E112_R0.9550.99
44_D47_K0.9470.99
107_K111_N0.9430.99
34_E99_V0.9390.99
54_E59_K0.9300.99
123_R127_S0.9290.99
42_E46_K0.9190.99
44_D91_K0.9050.99
17_S119_A0.9040.99
70_L74_D0.8920.99
36_L97_E0.8920.99
36_L40_K0.8720.99
20_I112_R0.8610.98
37_L40_K0.8550.98
5_D26_K0.8540.98
52_K82_D0.8500.98
84_D87_K0.8460.98
9_D12_E0.8440.98
35_K39_K0.8390.98
46_K89_E0.8390.98
35_K100_D0.8380.98
108_Q115_Q0.8260.98
49_K77_K0.8230.98
113_T117_K0.8230.98
63_E66_K0.8220.98
5_D27_Y0.8120.98
55_Y58_G0.7990.98
38_L95_Q0.7950.97
13_L116_I0.7830.97
114_F117_K0.7820.97
55_Y60_A0.7750.97
43_F86_I0.7670.97
10_D15_E0.7620.97
38_L99_V0.7250.96
122_W126_T0.7210.95
87_K90_L0.7200.95
27_Y102_L0.7150.95
43_F93_E0.7120.95
40_K90_L0.7120.95
28_L106_L0.7110.95
94_Y98_K0.7070.95
125_F128_G0.6890.94
74_D77_K0.6790.94
60_A68_K0.6780.94
111_N115_Q0.6740.94
41_A44_D0.6740.94
37_L87_K0.6700.93
53_W57_T0.6670.93
24_H27_Y0.6660.93
39_K42_E0.6620.93
17_S116_I0.6610.93
69_I74_D0.6590.93
10_D14_D0.6510.92
31_L35_K0.6470.92
56_Y82_D0.6450.92
53_W77_K0.6390.92
32_S97_E0.6360.91
7_K10_D0.6340.91
14_D122_W0.6320.91
114_F124_K0.6290.91
119_A123_R0.6150.90
14_D119_A0.6130.90
15_E18_L0.6100.90
48_L85_L0.6080.90
49_K76_D0.6040.89
34_E41_A0.6010.89
1_M4_K0.6000.89
50_K77_K0.6000.89
34_E38_L0.6000.89
3_E7_K0.5960.89
51_E64_V0.5900.88
49_K80_D0.5850.88
34_E102_L0.5850.88
104_S110_N0.5840.88
9_D16_E0.5760.87
116_I120_I0.5710.86
62_P68_K0.5690.86
95_Q99_V0.5660.86
39_K90_L0.5660.86
91_K94_Y0.5640.86
2_W24_H0.5640.86
75_I79_L0.5620.86
52_K79_L0.5590.85
113_T121_E0.5590.85
49_K85_L0.5550.85
97_E100_D0.5540.85
104_S107_K0.5520.85
43_F89_E0.5510.85
21_P115_Q0.5480.84
38_L42_E0.5460.84
48_L84_D0.5460.84
27_Y30_I0.5420.84
8_I16_E0.5390.83
28_L32_S0.5370.83
110_N114_F0.5360.83
36_L39_K0.5350.83
107_K114_F0.5270.82
47_K86_I0.5260.82
52_K68_K0.5240.81
31_L99_V0.5230.81
34_E37_L0.5210.81
86_I90_L0.5190.81
98_K102_L0.5150.80
88_L92_I0.5100.80
3_E25_A0.5060.79
37_L95_Q0.5030.79
56_Y79_L0.5020.79
41_A92_I0.5020.79
37_L41_A0.5020.79
33_T37_L0.5000.78
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  
4r3zA 1 0.3721 4.3 0.927 Contact Map
3jsrA 1 0.6744 3.3 0.93 Contact Map
3ov9A 3 0.3721 3 0.932 Contact Map
4n78F 1 0.6047 2.6 0.934 Contact Map
1z96A 1 0.2248 2.6 0.934 Contact Map
3mnfA 4 0.2791 2.6 0.934 Contact Map
2gw6A 2 0.4264 2.5 0.934 Contact Map
2o3lA 1 0.6357 2.4 0.935 Contact Map
3b2eE 1 0.5349 2.4 0.935 Contact Map
2rklA 2 0.3411 2.4 0.935 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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