GREMLIN.BAKERLAB.org
Powered by OPENSEQ.org
pilD

ID: 1513896282 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 290 (263)
Sequences: 1866 (1327)
Seq/Len: 7.095
Nf(neff/√len): 81.8

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: 7.095).

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
83_E98_S5.1351.00
107_R151_D4.1951.00
145_M155_L3.2651.00
69_N78_E3.2161.00
141_G159_M3.0361.00
163_L219_M2.9461.00
33_V147_L2.8471.00
119_S140_W2.6881.00
19_I116_A2.6211.00
157_D215_K2.5191.00
211_Y214_F2.4851.00
220_L232_T2.4481.00
83_E99_S2.4151.00
77_H83_E2.4041.00
241_A244_G2.2741.00
15_V120_G2.2611.00
139_T270_W2.2421.00
23_L87_L2.1201.00
90_Y106_K2.1101.00
115_T143_L2.1081.00
18_A123_A2.1061.00
25_V29_L2.0741.00
134_A170_A2.0681.00
83_E93_L1.9741.00
77_H99_S1.9311.00
200_F204_T1.9191.00
79_I84_N1.8851.00
52_L55_E1.8641.00
167_G223_W1.8221.00
146_S266_A1.7921.00
119_S136_L1.7591.00
80_R83_E1.7551.00
114_A147_L1.7511.00
19_I120_G1.7231.00
115_T119_S1.7211.00
204_T208_G1.7171.00
29_L144_A1.6881.00
74_R102_A1.6791.00
65_L68_P1.6711.00
106_K110_L1.6251.00
220_L269_G1.6161.00
155_L160_V1.6001.00
79_I99_S1.5971.00
132_A136_L1.5801.00
77_H80_R1.5601.00
122_V132_A1.4780.99
22_G116_A1.4640.99
122_V139_T1.4470.99
118_L143_L1.4330.99
120_G124_W1.4290.99
137_L166_L1.4230.99
142_L266_A1.4100.99
200_F208_G1.3930.99
84_N93_L1.3780.99
111_V147_L1.3600.98
94_G101_K1.3450.98
167_G219_M1.3410.98
34_H63_Y1.3380.98
75_C100_C1.3310.98
155_L262_G1.3270.98
18_A120_G1.3170.98
169_I187_V1.3080.98
118_L139_T1.3030.98
197_F207_E1.2970.98
105_G109_P1.2970.98
30_N108_Y1.2850.98
72_C100_C1.2800.97
73_P108_Y1.2730.97
85_I89_S1.2720.97
72_C75_C1.2700.97
228_I272_A1.2690.97
80_R98_S1.2680.97
83_E89_S1.2550.97
51_A54_L1.2440.97
51_A55_E1.2440.97
19_I23_L1.2410.97
88_V92_A1.2380.97
105_G108_Y1.2360.97
147_L151_D1.2320.97
135_M273_L1.2250.96
156_P215_K1.2240.96
240_G244_G1.2200.96
198_W201_K1.2150.96
33_V111_V1.1880.96
23_L116_A1.1770.95
148_I263_P1.1740.95
33_V144_A1.1690.95
43_N50_E1.1570.95
82_W98_S1.1570.95
80_R99_S1.1560.95
27_S70_S1.1550.95
234_L237_S1.1500.94
45_K55_E1.1440.94
107_R111_V1.1430.94
69_N80_R1.1400.94
93_L104_I1.1280.94
23_L109_P1.1240.94
110_L114_A1.1180.93
189_G221_G1.1160.93
32_V36_L1.1150.93
89_S93_L1.1060.93
33_V148_I1.0980.92
41_E45_K1.0880.92
197_F211_Y1.0870.92
186_A222_A1.0700.91
153_Q260_P1.0660.91
138_L220_L1.0640.91
193_L217_L1.0620.91
123_A132_A1.0600.91
185_G189_G1.0550.90
107_R147_L1.0520.90
138_L219_M1.0480.90
72_C97_C1.0480.90
115_T140_W1.0470.90
239_V271_I1.0450.90
30_N111_V1.0350.89
87_L113_L1.0350.89
44_W50_E1.0240.89
190_Y214_F1.0240.89
79_I83_E1.0120.88
164_L218_A1.0050.87
237_S241_A1.0040.87
239_V264_Y1.0030.87
82_W92_A1.0010.87
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  
3s0xA20.520799.40.795Contact Map
3py7A10.320748.50.95Contact Map
2ct0A10.2483300.955Contact Map
2k5cA10.241424.40.957Contact Map
1iymA10.144823.90.958Contact Map
2l0bA10.272422.60.958Contact Map
4xlgA10.224119.90.959Contact Map
2lcqA10.310317.40.96Contact Map
3u6pA10.172416.20.961Contact Map
2fiyA20.515.80.961Contact 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.

Page generated in 0.0396 seconds.