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OPENSEQ.org
Mumps V Protein -force run
ID: 1434680047 Query Sequence

 Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 224 (221)
Sequences: 87 (41.8)
Seq/Len: 0.394
Nf(neff/√len): 2.8
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: 0.394).

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
173_E193_C1.9110.76
189_C207_C1.7140.64
189_C193_C1.6370.59
189_C205_C1.6220.58
190_N193_C1.6200.58
173_E189_C1.6190.58
188_W193_C1.6020.56
210_C214_C1.5990.56
178_W188_W1.5960.56
188_W205_C1.5870.55
188_W207_C1.5870.55
170_H189_C1.5790.55
170_H188_W1.5620.54
171_R205_C1.5530.53
173_E188_W1.5360.52
188_W210_C1.5270.51
172_R207_C1.5270.51
189_C210_C1.5270.51
190_N207_C1.5080.50
188_W195_P1.5010.49
188_W196_I1.4940.49
189_C196_I1.4850.48
205_C214_C1.4830.48
205_C210_C1.4790.48
170_H193_C1.4790.48
173_E190_N1.4740.47
190_N205_C1.4730.47
196_I205_C1.4660.47
170_H190_N1.4630.46
207_C210_C1.4540.46
193_C205_C1.4530.46
193_C207_C1.4510.46
172_R189_C1.4500.46
170_H207_C1.4260.44
171_R189_C1.4250.44
178_W189_C1.4210.43
171_R188_W1.4080.43
172_R188_W1.4060.42
170_H205_C1.4050.42
190_N210_C1.3980.42
178_W190_N1.3950.42
170_H210_C1.3850.41
190_N196_I1.3840.41
173_E207_C1.3840.41
173_E205_C1.3820.41
193_C210_C1.3790.40
196_I207_C1.3730.40
171_R207_C1.3650.40
170_H173_E1.3630.39
172_R210_C1.3580.39
193_C196_I1.3430.38
178_W220_D1.3370.38
188_W220_D1.3350.37
170_H196_I1.3220.37
189_C214_C1.3210.37
172_R190_N1.3160.36
173_E210_C1.3130.36
170_H214_C1.3080.36
178_W207_C1.3080.36
171_R190_N1.3020.35
196_I210_C1.3020.35
193_C214_C1.2970.35
188_W214_C1.2950.35
189_C195_P1.2900.34
36_S45_A1.2770.34
190_N214_C1.2760.34
172_R205_C1.2710.33
207_C214_C1.2600.33
195_P205_C1.2590.32
173_E196_I1.2570.32
178_W193_C1.2570.32
187_E220_D1.2540.32
171_R193_C1.2370.31
170_H178_W1.2360.31
172_R193_C1.2350.31
178_W205_C1.2320.31
187_E197_T1.2300.31
210_C220_D1.2300.31
171_R210_C1.2290.31
171_R214_C1.2240.30
170_H195_P1.2200.30
190_N195_P1.2200.30
195_P207_C1.2070.29
193_C217_C1.1980.29
173_E214_C1.1940.28
173_E178_W1.1920.28
7_Q10_T1.1870.28
189_C220_D1.1870.28
205_C220_D1.1710.27
196_I214_C1.1630.27
172_R214_C1.1590.26
214_C220_D1.1520.26
171_R196_I1.1500.26
191_P205_C1.1490.26
178_W196_I1.1490.26
188_W218_E1.1430.26
178_W210_C1.1390.25
207_C220_D1.1350.25
170_H220_D1.1280.25
172_R220_D1.1260.25
189_C197_T1.1170.24
173_E195_P1.1160.24
195_P210_C1.1160.24
193_C220_D1.1090.24
190_N220_D1.1080.24
185_V205_C1.1060.24
172_R196_I1.1000.23
43_G53_E1.0980.23
178_W218_E1.0960.23
172_R178_W1.0880.23
41_I51_N1.0660.22
178_W195_P1.0630.21
171_R178_W1.0570.21
34_S37_K1.0350.20
190_N217_C1.0290.20
185_V188_W1.0230.20
37_K52_P1.0160.19
197_T210_C1.0160.19
185_V196_I1.0150.19
187_E218_E1.0120.19
185_V189_C1.0120.19
172_R195_P1.0110.19
210_C215_D1.0080.19
195_P214_C1.0070.19
170_H217_C1.0060.19
173_E220_D1.0040.19
210_C218_E1.0010.19
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: (31Jan15)
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  
2b5lC20.78571000.35Contact Map
4i1sB10.232199.30.821Contact Map
4co6D30.169695.20.919Contact Map
2knjA10.133923.90.96Contact Map
2amhA10.267910.70.966Contact Map
1wveC20.102710.30.966Contact Map
2fdoB20.16965.50.97Contact Map
4p0eA20.29024.60.971Contact Map
3qhqA20.21884.20.971Contact Map
2y9tA10.30840.972Contact 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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