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DHFR

ID: 1517327157 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 187 (180)
Sequences: 1486 (1112.3)
Seq/Len: 8.256
Nf(neff/√len): 82.9

HHblits Results: (2016_02)
Sequences per length for each position, BEFORE the coverage/gap filter was applied

Legend: Dots above the red line, indicates positions where there is > 5 sequences per length (if visible, green bar = 20 seq/len). Point of this graphic is to give you an idea if resubmitting a sub-portion of your sequence might help increase the overall Seq/Len (which after applying the coverage filter is at: 8.256).

Sequences per length for each position, AFTER the coverage/gap filter was applied
Legend: If visible, the positions blocked in grey are regions that have > 75% gaps and were automatically trimmed and excluded in the GREMLIN analysis.

Trim query Generate MSA using: Filter MSA GREMLIN
Start: End: E-value: Iterations: Coverage: Remove gaps: Prior:

GREMLIN Results:
Residue pairs sorted by coevolution strength:

Legend: The darker and larger the blue dots, the higher strength in covariance. Below we provide the list of the top [1.5 x length] covarying residues with sequence seperation > 3. The i and j are positions as given in the input sequence.

ij Scaled score Prob
16_G145_S4.2331.00
40_T70_G3.6141.00
13_Q140_M3.2091.00
55_K59_F2.8861.00
76_L121_V2.7271.00
50_L72_I2.6801.00
34_Y38_M2.5951.00
94_L125_A2.3541.00
9_V136_V2.3001.00
34_Y182_V2.2701.00
12_S16_G2.2281.00
159_L181_E2.2091.00
93_S96_D2.1181.00
138_R181_E2.1171.00
51_V73_N2.1071.00
33_R37_R2.0411.00
119_S123_K2.0161.00
7_C131_H2.0121.00
34_Y135_F1.9231.00
6_N135_F1.9001.00
97_A125_A1.8801.00
134_L152_I1.8441.00
49_N114_W1.8001.00
16_G148_F1.7641.00
11_V15_M1.7631.00
6_N112_M1.7381.00
68_L71_R1.6981.00
72_I88_H1.6621.00
59_F82_E1.6621.00
133_K184_E1.6571.00
78_R120_S1.6251.00
133_K182_V1.6051.00
67_P73_N1.6001.00
39_T71_R1.5941.00
19_K144_E1.5931.00
36_Q40_T1.5711.00
35_F116_V1.5671.00
53_M116_V1.5591.00
6_N133_K1.5231.00
115_I125_A1.4951.00
120_S123_K1.4670.99
160_L184_E1.4660.99
14_N142_D1.4600.99
52_I113_V1.4590.99
24_P145_S1.4510.99
77_S92_R1.4510.99
29_R33_R1.4300.99
91_S97_A1.4150.99
6_N114_W1.4040.99
119_S147_T1.3940.99
38_M135_F1.3930.99
56_K59_F1.3820.99
52_I97_A1.3450.99
9_V149_F1.3420.99
12_S143_F1.3360.99
52_I74_L1.3240.99
49_N112_M1.3200.99
159_L162_E1.3000.98
53_M61_I1.2990.98
30_N178_Y1.2940.98
61_I73_N1.2790.98
158_K186_N1.2650.98
11_V138_R1.2550.98
136_V183_Y1.2510.98
120_S124_E1.2350.98
135_F182_V1.2260.97
8_I114_W1.2180.97
23_L32_F1.1980.97
34_Y114_W1.1900.97
92_R96_D1.1870.97
76_L125_A1.1820.97
114_W135_F1.1800.97
13_Q142_D1.1740.96
94_L124_E1.1590.96
73_N116_V1.1480.96
77_S90_L1.1440.96
158_K184_E1.1330.95
140_M179_K1.1230.95
121_V124_E1.1220.95
58_W65_N1.1180.95
51_V116_V1.1120.95
11_V149_F1.1110.95
7_C122_Y1.0980.94
31_E34_Y1.0920.94
76_L97_A1.0860.94
31_E180_F1.0770.93
53_M60_S1.0670.93
62_P65_N1.0580.93
49_N111_D1.0540.92
21_G147_T1.0350.92
32_F73_N1.0340.91
35_F71_R1.0300.91
32_F60_S1.0300.91
29_R173_E1.0140.90
112_M133_K1.0070.90
135_F180_F1.0060.90
34_Y180_F1.0050.90
Legend: Only predictions with Scaled Score > 1 are listed. For all 3L/2 predictions, click on one of the links below.
Prob = P(contact | scaled_score, seq/len).
Scaled Score = (raw_score/average(raw_scores)).
NEW Features
HHsearch Results: (06Aug15)
GREMLIN results overlayed on top 10 PDB hits:
Legend: Blue filled circles are GREMLIN results (Scaled Score > 1). The grey/red filled circles underneath are pdb residue contacts (min distance < 5 Angstroms). The shade of the circles is based on 10 HHsearch results which uses the overall probability and per-position alignment confidence. Inter oligomeric contacts in the pdb are in shades of red.
PDB M Cov P(%) HHΔ  
4eilA80.94651000.224Contact Map
2bl9A10.93581000.235Contact Map
3irmA40.97331000.237Contact Map
1j3kA20.95191000.241Contact Map
3rg9A20.9841000.255Contact Map
3qg2A20.94651000.284Contact Map
3cseA20.97331000.305Contact Map
1kmvA10.9841000.306Contact Map
3nzbX10.99471000.306Contact Map
3ia4A40.8611000.312Contact Map
M = number of chains, if homo-oligomer
Cov = coverage of hit
P(%) = probability

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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