GREMLIN Database
YRDA - Uncharacterized protein YrdA
UniProt: O07079 Sequences:
Download Alignment
We filter this alignment to remove sites that have many gaps before running GREMLIN.

Date: 2015_01
Length: 167 (143)
Sequences: 617 (519)
Seq/√Len: 43.4

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:
i j Sco Prob
103_T106_E3.8751.00
78_Q82_D3.5641.00
107_R114_Q3.3451.00
109_N114_Q2.8331.00
76_S79_F2.5521.00
24_N85_H2.5111.00
82_D86_Q2.5051.00
13_E92_V2.4391.00
100_T103_T2.2951.00
89_N93_Q2.2911.00
20_Q24_N2.2211.00
11_S122_M2.1791.00
133_G136_T2.1611.00
81_A85_H2.0940.99
19_T132_R2.0770.99
24_N81_A1.9950.99
34_E41_T1.9620.99
48_H127_H1.8030.98
28_D78_Q1.7630.98
15_E126_Q1.7350.98
116_P119_S1.7180.98
92_V96_K1.6980.97
79_F82_D1.6940.97
31_L80_I1.6630.97
86_Q90_A1.6550.97
20_Q85_H1.6460.97
9_L96_K1.6220.97
7_H118_G1.5900.96
50_V53_I1.4860.95
37_S143_G1.4740.94
26_L77_A1.4590.94
127_H133_G1.4590.94
110_F120_L1.4380.93
33_Q141_Q1.4180.93
107_R116_P1.4080.93
33_Q142_A1.4030.93
56_I60_T1.3750.92
31_L46_A1.3720.92
35_I138_L1.3480.91
57_T60_T1.3450.91
9_L92_V1.3150.90
31_L43_G1.3140.90
34_E37_S1.3080.90
46_A135_M1.2760.89
115_M120_L1.2440.87
36_T39_N1.2400.87
23_L50_V1.2070.86
132_R139_M1.2030.85
41_T44_R1.1820.84
8_F121_L1.1800.84
88_S128_Q1.1640.83
28_D77_A1.1550.83
21_K24_N1.1510.83
6_D10_K1.1370.82
18_A149_I1.1360.82
107_R110_F1.1300.82
27_T147_P1.1150.81
23_L46_A1.0960.80
23_L31_L1.0850.79
22_L133_G1.0840.79
130_H134_Q1.0760.78
34_E84_Y1.0690.78
16_A128_Q1.0550.77
115_M119_S1.0390.76
20_Q81_A1.0390.76
49_T135_M1.0360.76
136_T149_I1.0340.75
13_E96_K1.0310.75
42_L77_A1.0260.75
16_A88_S1.0230.75
55_I111_I0.9970.73
10_K119_S0.9940.72
42_L45_I0.9710.71
26_L31_L0.9680.70
31_L77_A0.9680.70
45_I79_F0.9680.70
69_E79_F0.9670.70
9_L93_Q0.9530.69
35_I135_M0.9470.69
50_V87_A0.9370.68
23_L84_Y0.9370.68
127_H136_T0.9360.68
45_I134_Q0.9360.68
30_S142_A0.9270.67
56_I123_F0.9240.67
84_Y128_Q0.9200.67
40_W123_F0.9140.66
83_S86_Q0.8940.64
15_E18_A0.8920.64
101_D118_G0.8900.64
27_T77_A0.8900.64
96_K129_N0.8890.64
74_P79_F0.8820.63
138_L142_A0.8810.63
26_L139_M0.8780.63
6_D25_S0.8760.63
93_Q98_Q0.8730.62
19_T36_T0.8610.61
78_Q102_H0.8470.60
27_T30_S0.8450.60
25_S146_V0.8380.59
34_E141_Q0.8320.59
138_L141_Q0.8310.59
26_L42_L0.8310.59
42_L135_M0.8250.58
77_A81_A0.8180.57
42_L146_V0.8150.57
93_Q96_K0.8080.56
11_S126_Q0.8040.56
17_D109_N0.8010.56
113_Q122_M0.7970.55
146_V149_I0.7930.55
15_E88_S0.7920.55
51_A69_E0.7910.55
126_Q129_N0.7850.54
47_W80_I0.7830.54
88_S125_I0.7800.54
12_W39_N0.7740.53
22_L146_V0.7710.53
73_V121_L0.7690.53
10_K17_D0.7660.52
76_S107_R0.7610.52
55_I113_Q0.7600.52
60_T110_F0.7590.52
70_D102_H0.7560.51
94_A98_Q0.7510.51
37_S107_R0.7460.51
41_T48_H0.7450.50
34_E138_L0.7420.50
15_E132_R0.7400.50
22_L149_I0.7400.50
79_F83_S0.7330.49
15_E128_Q0.7310.49
27_T81_A0.7210.48
82_D100_T0.7010.46
39_N126_Q0.6970.46
52_A113_Q0.6970.46
62_L101_D0.6930.45
108_I117_N0.6910.45
52_A55_I0.6900.45
23_L26_L0.6880.45
127_H149_I0.6790.44
32_K93_Q0.6770.44
55_I59_N0.6720.44
39_N135_M0.6680.43
7_H137_V0.6660.43
33_Q138_L0.6610.42
26_L127_H0.6600.42
137_V141_Q0.6580.42
54_G94_A0.6550.42
9_L89_N0.6520.42
120_L124_L0.6450.41
51_A55_I0.6430.41
22_L143_G0.6360.40
41_T78_Q0.6330.40
48_H52_A0.6290.40
19_T139_M0.6280.39
73_V76_S0.6270.39
108_I116_P0.6270.39
61_D100_T0.6260.39
6_D83_S0.6250.39
99_W139_M0.6150.38
22_L60_T0.6080.38
43_G133_G0.6070.38
28_D31_L0.6030.37
12_W128_Q0.6010.37
108_I120_L0.6010.37
25_S147_P0.6000.37
31_L74_P0.5970.37
81_A102_H0.5960.37
72_P90_A0.5930.36
11_S119_S0.5900.36
64_F91_F0.5870.36
46_A80_I0.5830.35
41_T58_S0.5820.35
39_N146_V0.5810.35
19_T23_L0.5810.35
36_T141_Q0.5780.35
75_T82_D0.5730.35
40_W44_R0.5720.34
58_S144_L0.5690.34
24_N77_A0.5680.34
45_I140_R0.5660.34
109_N121_L0.5650.34
75_T86_Q0.5650.34
135_M147_P0.5640.34
83_S87_A0.5610.34
25_S143_G0.5600.33
18_A88_S0.5600.33
120_L123_F0.5580.33
78_Q89_N0.5510.33
104_L136_T0.5500.33
6_D93_Q0.5490.32
63_T105_Q0.5460.32
35_I38_Q0.5440.32
76_S118_G0.5440.32
49_T68_A0.5430.32
145_T148_G0.5370.31
63_T108_I0.5360.31
56_I115_M0.5300.31
106_E144_L0.5300.31
47_W73_V0.5250.31
52_A111_I0.5240.30
35_I45_I0.5240.30
61_D64_F0.5200.30
41_T72_P0.5170.30
30_S33_Q0.5160.30
6_D96_K0.5130.30
56_I124_L0.5070.29
6_D57_T0.5060.29
36_T139_M0.5030.29
18_A146_V0.5030.29
49_T109_N0.5010.29
21_K64_F0.5000.29
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  
3di5A 1 0.8982 100 0.451 Contact Map
2p1aA 2 0.8563 99.9 0.566 Contact Map
3dkaA 2 0.8802 99.9 0.595 Contact Map
2f22A 2 0.8563 99.9 0.599 Contact Map
2hkvA 2 0.8802 99.9 0.608 Contact Map
3gorA 2 0.9042 99.9 0.61 Contact Map
2qnlA 2 0.8263 99.8 0.63 Contact Map
2qe9A 2 0.9521 99.8 0.637 Contact Map
2ou6A 2 0.8383 99.8 0.647 Contact Map
3cexA 2 0.8563 99.8 0.661 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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