OPENSEQ.org
MdfA

ID: 1516178710 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 391 (358)
Sequences: 75775 (48036)
Seq/Len: 211.662
Nf(neff/√len): 2538.8

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: 211.662).

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
94_Q98_Q3.8981.00
89_A102_L3.7381.00
82_W109_S3.4211.00
91_L166_V3.3921.00
72_R123_E3.0341.00
55_G104_F2.9121.00
84_I172_A2.9021.00
79_G112_F2.7871.00
86_T102_L2.7871.00
97_E101_L2.7711.00
95_N98_Q2.7611.00
129_V132_K2.5951.00
125_F133_I2.5411.00
258_A312_S2.5271.00
244_S247_E2.4651.00
131_I271_S2.3801.00
63_L112_F2.3401.00
292_V310_G2.2791.00
220_G351_I2.2721.00
86_T109_S2.2451.00
159_L163_G2.2341.00
59_L108_I2.2141.00
126_E129_V2.1801.00
77_L180_Q2.1391.00
86_T105_L2.1251.00
40_A96_I2.1151.00
262_G316_F2.1021.00
93_A98_Q2.0531.00
285_P317_G2.0231.00
88_L169_A2.0201.00
51_A104_F2.0181.00
44_W96_I2.0141.00
68_D338_G2.0021.00
90_I102_L1.9871.00
73_R77_L1.9761.00
41_G44_W1.9341.00
224_L355_G1.9291.00
96_I100_T1.8991.00
228_A359_S1.8601.00
90_I99_F1.8531.00
177_F181_R1.8271.00
81_V176_F1.7921.00
48_S99_F1.7891.00
204_K208_K1.7661.00
71_G74_P1.7301.00
84_I169_A1.7021.00
77_L176_F1.6961.00
84_I176_F1.6921.00
282_G320_L1.6841.00
65_P69_R1.6581.00
205_L336_S1.6581.00
33_A36_E1.6541.00
268_R272_R1.6221.00
216_A347_L1.5981.00
51_A100_T1.5911.00
93_A102_L1.5741.00
67_S116_V1.5631.00
243_L247_E1.5581.00
127_E130_C1.5581.00
30_G156_I1.5451.00
160_P163_G1.5291.00
98_Q102_L1.5201.00
59_L111_C1.5121.00
157_H246_Y1.5081.00
289_G310_G1.4801.00
247_E250_L1.4781.00
121_I137_M1.4571.00
55_G59_L1.4501.00
97_E100_T1.4501.00
67_S72_R1.4461.00
155_W163_G1.4461.00
166_V170_A1.4391.00
267_A271_S1.4371.00
74_P78_A1.4341.00
255_I315_A1.4161.00
84_I173_A1.3930.99
40_A44_W1.3910.99
179_L183_M1.3900.99
305_L309_A1.3800.99
89_A98_Q1.3780.99
66_L70_I1.3510.99
275_V331_F1.3480.99
86_T106_Q1.3450.99
289_G317_G1.3430.99
88_L92_L1.3060.99
274_T277_S1.3030.99
303_A306_W1.3020.99
289_G314_Y1.2950.99
238_I248_Y1.2860.99
213_V217_L1.2850.99
91_L169_A1.2780.99
66_L75_V1.2750.99
178_G182_A1.2560.99
132_K268_R1.2540.99
33_A37_Q1.2470.99
78_A82_W1.2450.98
55_G107_G1.2350.98
305_L308_T1.2340.98
154_A246_Y1.2310.98
266_L320_L1.2300.98
282_G321_A1.2290.98
80_V176_F1.2260.98
59_L62_L1.2250.98
74_P185_E1.2210.98
64_G68_D1.2210.98
154_A158_V1.2100.98
210_G214_A1.2090.98
265_L268_R1.2060.98
85_V89_A1.2050.98
222_V321_A1.2000.98
68_D339_T1.2000.98
70_I75_V1.1990.98
79_G109_S1.1990.98
333_S336_S1.1950.98
92_L166_V1.1940.98
35_V40_A1.1940.98
243_L251_L1.1880.98
70_I74_P1.1860.98
277_S280_I1.1820.98
74_P77_L1.1790.98
73_R185_E1.1780.98
120_A183_M1.1780.98
286_I317_G1.1750.98
227_L352_F1.1730.98
71_G75_V1.1660.97
87_C168_F1.1660.97
336_S339_T1.1660.97
212_F216_A1.1650.97
236_I241_E1.1590.97
170_A174_I1.1570.97
269_L273_R1.1500.97
122_R130_C1.1500.97
262_G265_L1.1490.97
43_D364_L1.1480.97
37_Q162_E1.1460.97
205_L208_K1.1450.97
21_Y141_A1.1360.97
219_L344_M1.1360.97
37_Q161_W1.1340.97
207_L213_V1.1320.97
250_L254_P1.1300.97
251_L308_T1.1210.97
329_T344_M1.1210.97
68_D72_R1.1190.96
82_W86_T1.1170.96
35_V45_V1.1150.96
330_L341_S1.1130.96
54_A353_T1.1060.96
209_N213_V1.0990.96
163_G166_V1.0960.96
281_M284_W1.0910.96
361_H365_N1.0790.95
30_G164_M1.0780.95
77_L81_V1.0760.95
78_A81_V1.0740.95
72_R119_A1.0730.95
89_A92_L1.0710.95
52_Y110_L1.0620.95
132_K271_S1.0620.95
238_I245_S1.0600.95
258_A262_G1.0560.95
289_G313_I1.0550.95
282_G317_G1.0520.95
26_M152_G1.0500.94
123_E337_K1.0500.94
333_S340_V1.0440.94
132_K136_L1.0390.94
94_Q97_E1.0350.94
274_T278_L1.0320.94
287_M291_L1.0250.93
130_C331_F1.0240.93
177_F180_Q1.0230.93
304_Y308_T1.0220.93
101_L105_L1.0220.93
277_S281_M1.0200.93
237_I243_L1.0150.93
76_M179_L1.0140.93
75_V78_A1.0140.93
47_T51_A1.0130.93
169_A173_A1.0120.93
220_G347_L1.0090.93
309_A312_S1.0090.93
72_R185_E1.0070.93
88_L166_V1.0050.93
219_L348_Q1.0050.93
247_E251_L1.0020.92
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  
2gfpA20.95911000.184Contact Map
1pw4A10.97191000.191Contact Map
3o7qA10.97441000.219Contact Map
3wdoA10.97951000.221Contact Map
4pypA10.98471000.244Contact Map
4j05A20.92841000.244Contact Map
2cfqA10.97441000.261Contact Map
4xnjA101000.285Contact Map
4zw9A101000.291Contact Map
4gc0A10.98721000.296Contact 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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