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RNF -force run

ID: 1504816623 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 442 (379)
Sequences: 82 (49.4)
Seq/Len: 0.216
Nf(neff/√len): 2.5

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: 0.216).

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
43_S93_T1.9370.60
4_A12_L1.7850.51
153_E159_E1.7060.46
151_R345_Y1.6560.43
34_Q52_H1.6110.40
91_L108_F1.6010.39
249_L254_Q1.5770.38
289_E359_R1.5360.36
124_L127_R1.5230.35
88_L128_L1.5220.35
318_Y349_I1.5180.35
108_F117_F1.5160.35
127_R131_I1.4880.33
337_T349_I1.4870.33
8_G19_V1.4850.33
114_K344_P1.4620.32
249_L260_L1.4600.32
371_L376_D1.4540.31
127_R140_P1.4510.31
62_L240_R1.4490.31
321_Q324_D1.4490.31
12_L51_I1.4420.31
156_R162_L1.4370.30
240_R270_E1.4230.30
305_E324_D1.4220.30
152_A193_C1.4190.29
22_L30_I1.4180.29
368_S372_Q1.4140.29
104_I107_S1.4130.29
91_L94_L1.4120.29
110_S118_L1.4120.29
13_E120_L1.3970.28
286_I342_I1.3970.28
19_V22_L1.3820.28
91_L117_F1.3750.27
123_E133_T1.3660.27
371_L374_T1.3580.26
14_Q50_A1.3560.26
126_E139_R1.3500.26
1_L180_A1.3470.26
96_P108_F1.3430.26
99_Q300_F1.3410.26
101_H105_C1.2990.24
13_E104_I1.2940.23
23_Q39_E1.2880.23
365_D369_E1.2870.23
186_K189_T1.2860.23
205_V240_R1.2860.23
128_L144_S1.2780.23
369_E375_H1.2710.22
370_S378_S1.2690.22
19_V35_A1.2640.22
304_W310_R1.2630.22
213_S234_H1.2610.22
367_Q371_L1.2580.22
23_Q28_E1.2570.22
3_S104_I1.2540.22
127_R158_L1.2500.22
373_N377_D1.2440.21
146_I331_E1.2430.21
367_Q375_H1.2370.21
160_P228_F1.2350.21
232_C314_E1.2330.21
369_E377_D1.2290.21
78_E317_I1.2280.21
228_F306_E1.2270.21
87_Q91_L1.2250.21
37_V48_E1.2200.20
349_I358_P1.2170.20
19_V106_S1.2160.20
140_P158_L1.2160.20
185_P197_V1.2130.20
106_S350_A1.2120.20
195_S198_G1.2120.20
366_E371_L1.2060.20
20_K48_E1.2030.20
270_E339_T1.2030.20
12_L117_F1.1990.19
305_E348_S1.1980.19
153_E161_L1.1930.19
4_A117_F1.1850.19
29_A48_E1.1720.18
193_C346_V1.1690.18
20_K36_M1.1630.18
254_Q261_T1.1620.18
316_E348_S1.1590.18
263_H272_M1.1570.18
315_Q349_I1.1570.18
125_M128_L1.1540.18
366_E376_D1.1520.18
194_P199_K1.1500.18
309_Q318_Y1.1470.18
34_Q166_P1.1430.17
8_G350_A1.1420.17
223_G263_H1.1420.17
275_V335_L1.1400.17
363_P373_N1.1380.17
4_A8_G1.1340.17
236_E311_V1.1340.17
80_K128_L1.1340.17
337_T358_P1.1290.17
72_A293_L1.1290.17
34_Q60_D1.1270.17
223_G265_S1.1270.17
125_M142_Q1.1260.17
70_L94_L1.1220.17
127_R162_L1.1210.17
33_L50_A1.1210.17
370_S375_H1.1180.17
123_E134_R1.1170.17
125_M144_S1.1170.17
180_A195_S1.1160.16
306_E310_R1.1160.16
108_F114_K1.1160.16
186_K192_H1.1140.16
304_W315_Q1.1120.16
93_T337_T1.1120.16
2_E76_Q1.1110.16
32_L84_F1.1110.16
25_A113_N1.1090.16
297_R357_E1.1060.16
48_E55_F1.1020.16
20_K55_F1.1000.16
371_L378_S1.1000.16
2_E302_E1.0990.16
155_A158_L1.0990.16
336_T342_I1.0990.16
240_R252_Q1.0980.16
70_L91_L1.0970.16
253_V260_L1.0970.16
265_S297_R1.0910.16
131_I140_P1.0890.16
14_Q162_L1.0850.15
69_L162_L1.0830.15
186_K193_C1.0780.15
233_R300_F1.0720.15
81_D225_N1.0690.15
15_A114_K1.0680.15
372_Q375_H1.0680.15
134_R269_A1.0660.15
15_A140_P1.0650.15
40_V282_L1.0640.15
245_E311_V1.0630.15
316_E338_I1.0610.15
13_E25_A1.0600.15
91_L96_P1.0600.15
212_R345_Y1.0590.15
108_F118_L1.0590.15
4_A96_P1.0580.15
154_F256_L1.0580.15
237_D244_A1.0560.15
189_T192_H1.0550.15
293_L307_A1.0550.15
338_I358_P1.0540.14
318_Y358_P1.0530.14
367_Q372_Q1.0530.14
84_F215_S1.0530.14
366_E372_Q1.0510.14
8_G106_S1.0500.14
88_L91_L1.0490.14
341_Q345_Y1.0490.14
79_E85_K1.0470.14
124_L311_V1.0460.14
308_Y351_K1.0460.14
249_L253_V1.0410.14
339_T344_P1.0390.14
5_Y12_L1.0380.14
131_I138_L1.0370.14
305_E312_A1.0340.14
62_L72_A1.0320.14
81_D291_A1.0320.14
50_A69_L1.0310.14
304_W311_V1.0300.14
87_Q108_F1.0270.14
101_H122_Y1.0270.14
128_L314_E1.0250.14
80_K88_L1.0240.14
22_L47_E1.0220.14
305_E309_Q1.0210.13
255_E261_T1.0200.13
351_K356_L1.0200.13
4_A47_E1.0190.13
220_L236_E1.0190.13
54_L349_I1.0170.13
314_E319_E1.0160.13
62_L108_F1.0150.13
25_A30_I1.0150.13
107_S111_L1.0100.13
296_M306_E1.0100.13
371_L375_H1.0100.13
153_E160_P1.0090.13
13_E184_G1.0080.13
316_E331_E1.0080.13
322_L352_V1.0080.13
58_M205_V1.0060.13
375_H378_S1.0060.13
62_L293_L1.0060.13
217_K223_G1.0060.13
91_L114_K1.0040.13
22_L60_D1.0030.13
56_G307_A1.0020.13
25_A33_L1.0010.13
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  
4nqjA30.380196.90.958Contact Map
3okqA10.280596.40.961Contact Map
4ltbA20.375695.90.963Contact Map
4tn3A20.68192.10.969Contact Map
4kblA20.289673.50.975Contact Map
4m3lA40.135743.60.98Contact Map
4rsiB10.717243.60.98Contact Map
1t3jA10.1403350.981Contact Map
2dfsA20.176531.70.981Contact Map
4iffA40.185529.90.981Contact 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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