GREMLIN Database
YRAI - Uncharacterized protein YraI
UniProt: O07909 Sequences:
Download Alignment
We filter this alignment to remove sites that have many gaps before running GREMLIN.

Date: 2015_01
Length: 119 (89)
Sequences: 768 (687)
Seq/√Len: 72.8

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:
i j Sco Prob
45_G50_W4.4621.00
47_G50_W3.3851.00
66_C74_T2.7691.00
104_Y107_T2.5741.00
41_N55_T2.4201.00
62_I75_G2.3811.00
73_V86_T2.3061.00
40_V88_R2.2921.00
73_V89_T2.1881.00
56_I62_I2.1111.00
104_Y108_G2.0251.00
54_T77_Y1.8301.00
42_M75_G1.8271.00
85_Y88_R1.7991.00
105_M108_G1.7091.00
42_M56_I1.6671.00
41_N52_I1.6391.00
44_S51_G1.6130.99
62_I89_T1.5770.99
63_P76_K1.5250.99
64_I73_V1.5110.99
74_T81_N1.5010.99
75_G82_I1.4940.99
37_G40_V1.4580.99
103_T107_T1.4420.99
71_T86_T1.4310.99
40_V84_N1.4210.99
39_P57_P1.3860.98
33_S64_I1.2960.97
66_C69_T1.2220.96
53_V82_I1.1810.96
40_V85_Y1.1720.95
39_P55_T1.1710.95
106_Y109_S1.1590.95
77_Y82_I1.1410.95
34_T92_S1.1190.94
83_W86_T1.1000.93
103_T108_G1.0750.93
42_M54_T1.0610.92
42_M53_V1.0540.92
53_V77_Y1.0510.92
57_P60_T1.0430.92
64_I89_T1.0320.91
36_S90_L1.0250.91
68_K91_A1.0230.91
40_V43_R0.9980.90
48_T85_Y0.9910.89
56_I84_N0.9890.89
71_T85_Y0.9540.87
103_T106_Y0.9540.87
69_T83_W0.9360.86
84_N87_E0.9330.86
74_T83_W0.9200.85
105_M109_S0.8940.84
43_R88_R0.8930.84
33_S62_I0.8890.83
41_N47_G0.8710.82
31_T91_A0.8700.82
61_R92_S0.8690.82
33_S73_V0.8450.80
35_S38_A0.8060.77
104_Y109_S0.7980.76
76_K82_I0.7940.76
56_I60_T0.7890.75
46_P69_T0.7800.75
103_T109_S0.7760.74
21_S24_A0.7750.74
42_M84_N0.7690.74
84_N89_T0.7610.73
66_C83_W0.7470.71
40_V54_T0.7420.71
59_G97_P0.7350.70
34_T59_G0.7120.68
99_F102_D0.7050.67
93_G99_F0.6970.66
21_S25_L0.6940.66
75_G84_N0.6900.65
65_Y74_T0.6870.65
59_G93_G0.6770.64
27_A83_W0.6760.64
70_G85_Y0.6670.63
60_T66_C0.6650.62
32_V63_P0.6620.62
33_S91_A0.6610.62
43_R46_P0.6570.61
35_S39_P0.6530.61
102_D106_Y0.6390.59
42_M82_I0.6360.59
85_Y89_T0.6260.58
25_L76_K0.6250.58
69_T73_V0.6230.57
83_W87_E0.6160.57
95_I98_G0.6130.56
42_M77_Y0.6070.55
52_I60_T0.5970.54
20_F71_T0.5860.53
95_I100_V0.5860.53
22_S26_A0.5790.52
45_G83_W0.5760.52
49_S87_E0.5740.51
30_Y36_S0.5740.51
45_G70_G0.5690.51
37_G71_T0.5680.51
27_A47_G0.5640.50
38_A49_S0.5640.50
24_A98_G0.5640.50
100_V103_T0.5600.50
96_V101_S0.5560.49
44_S81_N0.5550.49
23_H51_G0.5550.49
101_S104_Y0.5540.49
57_P90_L0.5530.49
58_S96_V0.5490.48
49_S96_V0.5480.48
34_T37_G0.5470.48
35_S42_M0.5400.47
66_C70_G0.5350.47
35_S62_I0.5330.46
76_K79_T0.5320.46
22_S25_L0.5310.46
39_P59_G0.5280.46
26_A88_R0.5250.45
23_H28_Q0.5250.45
46_P63_P0.5240.45
95_I102_D0.5240.45
27_A44_S0.5230.45
48_T51_G0.5180.45
102_D105_M0.5110.44
52_I79_T0.5110.44
99_F103_T0.5100.44
77_Y80_S0.5070.43
22_S28_Q0.5050.43
48_T71_T0.5040.43
53_V97_P0.5000.42
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  
2kt8A 1 0.6303 99.4 0.493 Contact Map
2kq8A 1 0.5882 99.3 0.5 Contact Map
2krsA 1 0.6134 99.3 0.508 Contact Map
3npfA 2 0.8151 98.9 0.588 Contact Map
4krtA 1 0.7143 98.8 0.602 Contact Map
3h41A 1 0.9496 98.7 0.61 Contact Map
2hbwA 1 0.7227 98.4 0.647 Contact Map
3m1uA 2 0.9496 98 0.685 Contact Map
4mt7A 1 0 94.1 0.79 Contact Map
1xovA 1 0.9664 93.9 0.792 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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