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India-Argentina

ID: 1515595952 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 270 (228)
Sequences: 2951 (2042.2)
Seq/Len: 12.943
Nf(neff/√len): 135.2

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: 12.943).

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
118_V129_M4.4251.00
181_K199_D3.6471.00
234_R263_A3.5831.00
89_V119_T3.3091.00
202_D244_S3.0391.00
143_A170_E3.0211.00
91_T116_A2.8261.00
169_V194_I2.7371.00
53_Q56_P2.6991.00
138_A167_G2.3151.00
89_V196_V2.2371.00
87_L180_L2.1231.00
225_D228_H2.0421.00
77_G205_F2.0021.00
78_L105_I1.9651.00
104_W107_Q1.9451.00
83_G177_F1.9351.00
53_Q57_N1.9241.00
142_N184_Y1.9211.00
115_L138_A1.8861.00
125_K208_C1.8841.00
86_V109_I1.8781.00
237_G260_T1.8761.00
90_D120_H1.8041.00
115_L140_Y1.7961.00
172_A179_P1.7771.00
85_R114_A1.7721.00
198_I201_T1.7651.00
235_A238_A1.7551.00
174_A179_P1.7391.00
98_T131_A1.7341.00
57_N178_G1.7201.00
125_K250_H1.6941.00
248_M251_S1.6871.00
197_G204_A1.6721.00
234_R267_D1.6691.00
124_D250_H1.6611.00
117_V196_V1.6491.00
120_H208_C1.6431.00
203_I245_M1.6301.00
185_P195_T1.6131.00
178_G201_T1.6081.00
99_A103_N1.5971.00
230_A267_D1.5921.00
254_D258_A1.5571.00
53_Q59_W1.5571.00
172_A181_K1.5381.00
140_Y167_G1.5291.00
89_V205_F1.5251.00
142_N194_I1.5191.00
119_T196_V1.5111.00
87_L117_V1.5001.00
234_R238_A1.4871.00
144_L147_Q1.4831.00
126_M149_A1.4421.00
182_V194_I1.4361.00
233_A259_I1.4151.00
122_H125_K1.4141.00
120_H125_K1.4131.00
179_P200_G1.4111.00
95_D99_A1.3910.99
57_N201_T1.3820.99
133_H166_N1.3740.99
237_G263_A1.3600.99
204_A246_I1.3570.99
55_A201_T1.3490.99
197_G202_D1.3450.99
179_P199_D1.3440.99
102_L106_K1.3290.99
174_A177_F1.3080.99
182_V196_V1.3040.99
85_R115_L1.2900.99
78_L86_V1.2840.99
116_A132_L1.2800.99
145_S192_D1.2790.99
188_G232_S1.2750.99
86_V105_I1.2670.99
115_L167_G1.2640.99
146_N150_P1.2330.98
143_A168_W1.2290.98
185_P232_S1.2150.98
117_V182_V1.2060.98
193_N207_G1.1800.98
102_L132_L1.1790.98
87_L175_P1.1670.97
76_N92_A1.1650.97
178_G200_G1.1650.97
178_G198_I1.1620.97
102_L131_A1.1590.97
183_F239_A1.1570.97
116_A129_M1.1520.97
90_D208_C1.1410.97
90_D125_K1.1400.97
58_V198_I1.1380.97
181_K197_G1.1330.97
119_T125_K1.1320.97
195_T204_A1.1280.97
189_H208_C1.1260.97
198_I203_I1.1190.96
87_L115_L1.1100.96
91_T129_M1.1050.96
124_D208_C1.0850.96
84_G114_A1.0790.95
197_G243_A1.0750.95
195_T236_F1.0690.95
83_G111_L1.0680.95
141_A145_S1.0400.94
120_H189_H1.0310.94
208_C250_H1.0140.93
119_T207_G1.0130.93
98_T132_L1.0110.93
103_N107_Q1.0070.93
109_I112_P1.0070.93
188_G209_L1.0040.93
120_H124_D1.0040.93
59_W108_E1.0030.93
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  
4eybA20.88521000.418Contact Map
4d1tA10.84811000.444Contact Map
4hl2A20.89261000.462Contact Map
1a7tA20.82221000.479Contact Map
2fhxA20.81000.484Contact Map
4c1dA20.84811000.485Contact Map
2yntA20.80741000.487Contact Map
1m2xA40.79631000.491Contact Map
2yheA60.94811000.491Contact Map
3iogA10.78521000.494Contact 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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