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OPENSEQ.org

mgI457

ID: 1402528473 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 449 (420)
Sequences: 490 (354)
Seq/Len: 1.167
Nf(neff/√len): 17.3

HHblits Results: (2013_03)
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: 1.167).

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
409_C412_C2.3770.99
398_C409_C2.3350.99
313_E341_V2.2910.99
398_C412_C2.2350.99
197_E200_A2.2200.99
349_A362_M2.0700.97
31_V38_V2.0070.97
16_V20_L1.9260.96
13_S16_V1.7630.92
29_V45_L1.7550.92
189_F201_A1.7300.91
345_H349_A1.7110.90
281_A296_C1.6820.89
254_Q283_V1.6460.88
288_P315_L1.6210.87
395_C409_C1.5990.86
319_A322_H1.5990.86
228_E243_L1.5960.86
326_H349_A1.5740.85
165_K168_P1.5690.84
243_L385_H1.5670.84
57_S61_R1.5390.83
395_C398_C1.5280.82
16_V19_T1.5190.82
415_V418_I1.5130.81
326_H345_H1.5090.81
138_P141_L1.4960.80
70_P89_L1.4900.80
395_C412_C1.4850.80
338_K341_V1.4680.79
409_C415_V1.4470.77
7_V15_V1.4420.77
338_K345_H1.4350.76
271_G350_L1.4290.76
105_R136_V1.4250.76
377_A381_R1.4210.75
150_A191_A1.4210.75
414_G417_T1.4200.75
8_L15_V1.3920.73
409_C418_I1.3800.72
93_L205_I1.3790.72
420_W423_S1.3780.72
334_F362_M1.3750.72
239_P243_L1.3660.71
323_P352_I1.3650.71
421_T424_V1.3640.71
205_I219_A1.3620.71
280_L292_L1.3560.70
334_F364_E1.3530.70
96_A176_A1.3500.70
260_A279_L1.3390.69
7_V144_A1.3360.69
51_V55_I1.3330.69
394_V404_A1.3180.67
337_Q340_G1.3170.67
73_L106_R1.3030.66
411_S418_I1.3020.66
326_H348_A1.2940.65
290_R322_H1.2790.64
296_C315_L1.2750.64
277_E280_L1.2710.63
167_Q171_V1.2670.63
296_C312_L1.2670.63
392_A401_V1.2650.63
412_C415_V1.2540.62
398_C418_I1.2520.61
33_W50_L1.2510.61
395_C417_T1.2460.61
421_T426_A1.2400.60
215_T218_V1.2380.60
410_P414_G1.2260.59
161_P168_P1.2240.59
343_R347_M1.2170.58
11_F15_V1.2150.58
398_C415_V1.2110.58
204_W347_M1.2070.57
214_L271_G1.2050.57
422_R425_K1.2010.57
92_A104_G1.2000.57
89_L125_D1.2000.57
6_I15_V1.1990.57
409_C414_G1.1970.56
36_W93_L1.1940.56
219_A337_Q1.1910.56
412_C418_I1.1890.56
15_V203_A1.1880.55
222_W243_L1.1880.55
105_R141_L1.1870.55
21_W332_A1.1810.55
30_Q37_H1.1810.55
315_L326_H1.1790.55
410_P419_E1.1720.54
359_C379_I1.1700.54
312_L345_H1.1690.54
267_E331_E1.1690.54
122_A125_D1.1680.54
411_S415_V1.1650.53
142_E145_K1.1640.53
327_L358_G1.1610.53
179_A354_P1.1600.53
394_V424_V1.1600.53
9_L291_V1.1590.53
401_V404_A1.1550.52
398_C411_S1.1530.52
400_R409_C1.1480.52
130_R197_E1.1440.51
101_V188_A1.1440.51
331_E361_L1.1430.51
40_S44_V1.1390.51
43_P77_R1.1330.50
394_V403_E1.1330.50
88_A111_A1.1310.50
4_R12_M1.1300.50
65_L76_S1.1300.50
400_R411_S1.1260.50
412_C417_T1.1250.49
46_L66_V1.1200.49
42_M57_S1.1190.49
309_L332_A1.1170.49
194_R305_Q1.1170.49
361_L364_E1.1140.48
392_A395_C1.1120.48
98_S349_A1.1110.48
92_A108_A1.1070.48
10_I214_L1.1070.48
185_D208_A1.1060.48
271_G320_P1.1060.48
248_E252_A1.1060.48
398_C414_G1.1040.47
404_A422_R1.1040.47
110_E116_N1.1010.47
146_G149_F1.0990.47
142_E165_K1.0990.47
272_R275_E1.0980.47
411_S414_G1.0940.46
414_G418_I1.0920.46
4_R7_V1.0920.46
4_R46_L1.0910.46
51_V59_L1.0860.46
122_A183_R1.0860.46
296_C308_C1.0840.45
276_A320_P1.0840.45
400_R406_A1.0810.45
98_S183_R1.0800.45
333_A338_K1.0790.45
168_P172_E1.0780.45
400_R417_T1.0780.45
46_L334_F1.0770.45
28_S39_D1.0760.45
408_C422_R1.0740.44
304_D307_A1.0740.44
57_S60_S1.0700.44
411_S417_T1.0680.44
279_L363_A1.0680.44
35_G40_S1.0670.44
389_L401_V1.0670.44
54_L58_A1.0660.44
297_A331_E1.0650.44
238_D280_L1.0650.44
403_E406_A1.0640.44
158_P176_A1.0610.43
29_V41_N1.0610.43
9_L100_D1.0600.43
54_L66_V1.0600.43
4_R299_L1.0590.43
143_A146_G1.0580.43
96_A132_P1.0570.43
92_A336_V1.0560.43
394_V400_R1.0550.43
394_V406_A1.0550.43
216_P283_V1.0550.43
52_V110_E1.0550.43
34_L350_L1.0480.42
309_L330_G1.0440.42
90_L366_E1.0430.42
316_A326_H1.0420.41
118_P125_D1.0420.41
395_C400_R1.0410.41
92_A101_V1.0410.41
349_A384_E1.0360.41
88_A97_E1.0320.41
61_R338_K1.0310.40
105_R145_K1.0290.40
98_S345_H1.0290.40
173_K208_A1.0280.40
404_A421_T1.0260.40
53_F61_R1.0250.40
8_L12_M1.0250.40
19_T384_E1.0240.40
83_E321_H1.0240.40
411_S425_K1.0230.40
29_V132_P1.0200.39
406_A425_K1.0130.39
31_V199_G1.0120.39
51_V140_R1.0120.39
403_E411_S1.0110.39
30_Q41_N1.0090.38
395_C418_I1.0070.38
414_G422_R1.0070.38
92_A161_P1.0070.38
202_Q251_A1.0060.38
392_A409_C1.0060.38
133_A292_L1.0050.38
193_I201_A1.0050.38
31_V295_A1.0040.38
394_V401_V1.0040.38
51_V54_L1.0030.38
312_L349_A1.0030.38
404_A408_C1.0020.38
395_C410_P1.0020.38
395_C403_E1.0000.38
347_M362_M1.0000.38
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: (07Jun14)
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  
3iegA20.703899.90.794Contact Map
1w3bA20.826399.80.81Contact Map
2y4tA30.786299.80.814Contact Map
1fchA20.623699.80.815Contact Map
4jsnB20.68699.80.818Contact Map
4horA10.866499.80.819Contact Map
4g1tA20.806299.80.819Contact Map
3hymB60.616999.80.819Contact Map
3fp2A10.824199.80.823Contact Map
2xpiA20.944399.80.824Contact 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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