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ctaa_rod_sph

ID: 1500395376 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 391 (345)
Sequences: 1325 (867.8)
Seq/Len: 3.841
Nf(neff/√len): 46.7

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: 3.841).

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
187_A244_A3.3451.00
125_R163_G2.9241.00
131_W159_G2.9221.00
53_V362_V2.8381.00
336_A370_L2.6441.00
52_I365_V2.6361.00
98_Y104_G2.5061.00
54_V123_L2.4961.00
258_W305_Y2.4511.00
191_G241_V2.4291.00
97_Q180_T2.4261.00
260_D265_F2.3891.00
355_Q359_A2.3831.00
232_L310_L2.3281.00
235_V307_L2.3201.00
132_A156_G2.2671.00
82_E86_A2.2201.00
86_A90_D2.2041.00
90_D93_R2.1651.00
235_V310_L2.0701.00
161_L165_I2.0511.00
71_R74_T2.0461.00
61_T116_W2.0091.00
338_L342_L1.9971.00
165_I168_W1.9221.00
165_I188_T1.7480.99
49_M362_V1.7330.99
129_L133_V1.7330.99
329_A373_H1.7320.99
350_S353_E1.7210.99
242_L303_A1.7210.99
197_L369_V1.7050.99
165_I192_L1.6720.99
48_V200_I1.6580.99
51_M124_G1.6450.99
183_S249_I1.6400.99
42_M204_A1.6360.99
315_W334_A1.6310.99
132_A163_G1.6160.99
269_E295_F1.6110.99
97_Q101_M1.5770.98
98_Y103_A1.5700.98
257_T262_N1.5630.98
336_A366_V1.5120.98
106_T109_E1.4950.97
232_L311_G1.4930.97
137_G141_A1.4920.97
194_F365_V1.4840.97
197_L365_V1.4820.97
230_T375_R1.4750.97
97_Q179_V1.4580.97
159_G196_I1.4540.97
236_A371_I1.4510.97
155_L199_L1.4480.97
173_G248_G1.4360.96
58_T173_G1.4350.96
346_G350_S1.4290.96
231_V234_G1.4260.96
168_W185_R1.4220.96
311_G337_L1.4220.96
318_G330_F1.4180.96
260_D263_G1.4120.96
99_R103_A1.4110.96
313_I317_F1.3940.95
41_L134_G1.3940.95
47_L123_L1.3910.95
229_T375_R1.3700.95
332_L370_L1.3670.95
168_W188_T1.3650.95
118_W122_Q1.3610.95
298_F302_M1.3400.94
58_T61_T1.3380.94
163_G167_W1.3380.94
79_P110_F1.3330.94
90_D107_L1.3290.94
333_L374_A1.3290.94
115_W119_G1.3160.93
100_L103_A1.3140.93
191_G237_F1.3120.93
201_A369_V1.3090.93
184_T291_Q1.3050.93
161_L164_G1.3020.93
54_V116_W1.3020.93
308_A341_I1.2990.93
270_M295_F1.2950.92
264_T268_A1.2950.92
67_I75_G1.2900.92
67_I73_V1.2900.92
308_A338_L1.2870.92
315_W319_R1.2710.92
45_F201_A1.2580.91
329_A377_L1.2570.91
336_A363_G1.2520.91
198_G368_W1.2370.90
62_D250_D1.2370.90
302_M306_T1.2310.90
77_V80_L1.2300.90
47_L130_V1.2240.89
258_W267_P1.2130.89
135_F153_L1.2100.89
198_G372_L1.2100.89
279_D288_G1.2090.89
135_F156_G1.2010.88
167_W173_G1.1940.88
342_L346_G1.1860.87
123_L126_V1.1850.87
331_D335_M1.1820.87
67_I74_T1.1710.86
225_L318_G1.1670.86
333_L367_I1.1540.85
353_E356_V1.1530.85
235_V303_A1.1500.85
96_P174_L1.1490.85
156_G159_G1.1480.85
341_I345_V1.1460.85
201_A373_H1.1460.85
236_A311_G1.1460.85
314_F317_F1.1390.84
346_G356_V1.1330.84
125_R167_W1.1320.84
151_R203_Q1.1250.83
47_L51_M1.1240.83
57_L358_I1.1240.83
288_G292_N1.1230.83
337_L341_I1.1210.83
146_R150_P1.1180.83
133_V306_T1.1160.83
144_I152_L1.1050.82
182_E256_P1.1050.82
297_Q348_V1.1010.81
265_F302_M1.0990.81
233_I375_R1.0950.81
312_L338_L1.0880.80
373_H377_L1.0880.80
57_L116_W1.0880.80
329_A370_L1.0850.80
232_L314_F1.0790.80
328_G331_D1.0770.79
35_R38_R1.0760.79
181_V248_G1.0740.79
309_A312_L1.0670.79
198_G202_W1.0620.78
135_F139_L1.0570.78
201_A205_L1.0570.78
74_T114_Y1.0540.77
260_D267_P1.0520.77
308_A337_L1.0500.77
239_Q242_L1.0450.77
190_L244_A1.0450.77
315_W331_D1.0440.76
187_A245_L1.0440.76
234_G329_A1.0440.76
86_A107_L1.0380.76
72_P122_Q1.0350.76
46_L50_A1.0330.75
234_G238_L1.0310.75
139_L153_L1.0290.75
181_V256_P1.0290.75
253_R357_A1.0250.75
59_R64_G1.0230.74
136_L139_L1.0210.74
124_G127_I1.0170.74
302_M305_Y1.0170.74
316_I319_R1.0170.74
249_I293_P1.0130.73
51_M159_G1.0120.73
332_L336_A1.0110.73
61_T246_V1.0100.73
100_L179_V1.0060.73
258_W302_M1.0060.73
98_Y106_T1.0050.72
68_T95_S1.0040.72
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  
1kqfC10.373414.70.977Contact Map
4kt0K10.08958.90.979Contact Map
3cx5C20.235380.979Contact Map
1pp9C20.21485.60.981Contact Map
4ogqA10.24814.90.981Contact Map
4gd3A20.33764.70.981Contact Map
2qjyA60.2664.20.982Contact Map
2l8sA10.11253.90.982Contact Map
1kxfA10.19183.70.982Contact Map
1jb0K10.09973.60.983Contact 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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