GREMLIN Database
YJDB - Uncharacterized protein YjdB
UniProt: O31643 Sequences:
Download Alignment
We filter this alignment to remove sites that have many gaps before running GREMLIN.

Date: 2015_01
Length: 115 (92)
Sequences: 2341 (2165)
Seq/√Len: 225.7

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:
i j Sco Prob
55_P87_L3.1071.00
62_Y65_K2.9611.00
48_K90_A2.8831.00
80_A88_V2.7391.00
36_V60_E2.4961.00
75_D96_A2.2181.00
81_E91_K2.2021.00
46_V54_L2.1131.00
66_N70_T1.8211.00
66_N69_A1.7631.00
80_A96_A1.7501.00
95_K111_Y1.7471.00
82_V88_V1.6821.00
75_D99_T1.6661.00
56_L88_V1.6641.00
83_D87_L1.6421.00
74_T77_Q1.6361.00
79_V96_A1.5851.00
72_Y100_L1.5341.00
70_T100_L1.5301.00
47_I113_T1.5271.00
73_W101_F1.5001.00
38_N61_T1.4631.00
50_Q93_K1.4391.00
76_N79_V1.4201.00
74_T98_I1.4071.00
58_V72_Y1.3991.00
41_I110_V1.3861.00
43_P46_V1.3721.00
97_T111_Y1.2911.00
49_I52_Y1.2841.00
43_P110_V1.2661.00
40_S61_T1.2501.00
80_A98_I1.2231.00
82_V86_G1.1741.00
56_L82_V1.1471.00
53_N89_T1.1401.00
75_D97_T1.1271.00
102_K105_A1.0951.00
36_V65_K1.0931.00
79_V114_V1.0821.00
99_T107_F1.0751.00
27_H31_S1.0741.00
97_T109_K1.0721.00
74_T82_V1.0631.00
50_Q90_A1.0581.00
34_T64_V1.0541.00
39_I108_G1.0321.00
55_P86_G1.0281.00
58_V100_L1.0131.00
73_W99_T0.9881.00
23_V26_A0.9791.00
48_K52_Y0.9751.00
36_V62_Y0.9721.00
79_V94_G0.9721.00
48_K54_L0.9591.00
43_P54_L0.9551.00
40_S59_G0.9501.00
53_N87_L0.9461.00
36_V106_V0.9411.00
60_E102_K0.9311.00
96_A114_V0.9221.00
77_Q81_E0.9171.00
69_A103_G0.9110.99
95_K113_T0.8910.99
74_T80_A0.8890.99
71_R101_F0.8750.99
46_V112_V0.8740.99
100_L108_G0.8370.99
41_I108_G0.8340.99
56_L72_Y0.8110.99
42_S57_K0.7970.99
62_Y102_K0.7970.99
105_A108_G0.7810.98
34_T63_S0.7430.98
62_Y67_N0.7400.98
46_V110_V0.7390.98
39_I106_V0.7310.98
44_T108_G0.7240.97
41_I56_L0.7220.97
74_T96_A0.7200.97
41_I58_V0.7070.97
49_I93_K0.7010.97
48_K88_V0.6830.96
31_S34_T0.6810.96
39_I58_V0.6770.96
35_E66_N0.6760.96
106_V110_V0.6690.96
99_T109_K0.6620.96
32_T49_I0.6600.96
32_T35_E0.6590.95
39_I60_E0.6560.95
23_V27_H0.6520.95
27_H30_N0.6470.95
41_I72_Y0.6440.95
60_E66_N0.6420.95
67_N103_G0.6360.95
24_A31_S0.6330.94
75_D78_K0.6240.94
32_T52_Y0.6230.94
101_F104_T0.6220.94
37_K62_Y0.6210.94
108_G112_V0.6200.94
101_F107_F0.6180.94
60_E65_K0.6160.94
25_S30_N0.6160.94
56_L110_V0.6060.93
35_E63_S0.6030.93
82_V96_A0.6010.93
74_T79_V0.5970.92
50_Q92_S0.5870.92
34_T62_Y0.5850.92
79_V92_S0.5790.91
28_E31_S0.5790.91
74_T86_G0.5740.91
84_Q91_K0.5720.91
106_V114_V0.5720.91
63_S67_N0.5640.90
47_I92_S0.5610.90
42_S59_G0.5600.90
70_T102_K0.5550.90
80_A94_G0.5460.89
98_I112_V0.5440.89
43_P56_L0.5440.89
23_V29_I0.5430.88
34_T66_N0.5430.88
60_E69_A0.5390.88
74_T99_T0.5390.88
102_K106_V0.5340.88
43_P100_L0.5320.87
83_D89_T0.5250.87
74_T91_K0.5180.86
110_V114_V0.5140.86
39_I66_N0.5090.85
44_T109_K0.5080.85
36_V104_T0.5070.85
81_E86_G0.5000.84
24_A27_H0.5000.84
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  
2l04A 1 0.7391 99.5 0.356 Contact Map
2mogA 1 0.7217 99.4 0.373 Contact Map
2mh4A 1 0.7217 99.4 0.383 Contact Map
3ncxA 1 0.7913 98.9 0.502 Contact Map
1f00I 1 0.9565 97.5 0.66 Contact Map
4aq1A 1 1 97 0.69 Contact Map
1f1sA 1 0.6435 96.1 0.718 Contact Map
2l7yA 1 0.6696 89.4 0.781 Contact Map
4r5oA 3 0.8 74.9 0.815 Contact Map
1cwvA 1 0.6957 72.8 0.819 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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