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T0808 -force run

ID: 1402092408 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 418 (411)
Sequences: 81 (70.6)
Seq/Len: 0.197
Nf(neff/√len): 3.5

Jackhmmer Results: (2014_04_16)
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: 0.197).

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
61_F117_I2.2460.74
215_L258_Q2.0550.64
174_W290_Y1.9870.60
353_T401_C1.9190.56
351_R401_C1.9180.56
190_S245_V1.9120.56
220_S255_S1.8970.55
25_V57_V1.8110.50
174_W316_R1.7970.49
226_N229_E1.7900.48
363_A371_Y1.7400.45
277_I314_Y1.7380.45
239_L305_F1.6820.42
175_F317_P1.6700.41
173_E276_Q1.6380.39
275_M289_A1.6360.39
252_N301_L1.6270.39
34_T283_G1.6030.37
248_G252_N1.5870.36
220_S227_P1.5680.35
94_L382_Y1.5420.34
163_L335_V1.5400.34
220_S230_I1.5130.32
305_F367_V1.4700.30
261_L302_I1.4700.30
283_G383_L1.4450.29
119_L300_K1.4440.29
269_N293_A1.4430.29
362_T399_F1.4240.28
290_Y352_L1.4220.28
189_H385_M1.4000.27
154_W236_I1.3930.26
186_E385_M1.3720.25
34_T58_S1.3520.25
67_T139_N1.3480.24
186_E206_Y1.3470.24
309_K386_G1.3450.24
174_W352_L1.3420.24
227_P255_S1.3410.24
290_Y317_P1.3330.24
230_I255_S1.3260.23
165_Y177_N1.3250.23
359_H395_M1.3220.23
199_E312_T1.3210.23
62_Y132_I1.3190.23
25_V173_E1.3140.23
220_S224_T1.3080.23
204_M214_I1.3060.23
158_G373_G1.2930.22
158_G307_R1.2920.22
353_T405_G1.2830.22
155_G220_S1.2770.21
328_Q386_G1.2760.21
175_F290_Y1.2740.21
186_E189_H1.2650.21
157_R307_R1.2590.21
249_E287_Y1.2530.20
238_L294_T1.2510.20
158_G221_P1.2500.20
337_F383_L1.2420.20
154_W372_Q1.2380.20
43_T81_I1.2380.20
146_Y318_H1.2280.19
206_Y314_Y1.2280.19
213_R304_S1.2260.19
109_I344_S1.2250.19
63_L117_I1.2190.19
314_Y317_P1.2180.19
121_G129_F1.2170.19
58_S118_D1.2080.19
277_I284_N1.2080.19
32_Y275_M1.2070.19
30_N389_F1.2050.19
147_V155_G1.1980.18
77_G397_T1.1970.18
337_F344_S1.1950.18
224_T255_S1.1950.18
157_R373_G1.1940.18
255_S301_L1.1920.18
288_T305_F1.1880.18
194_A273_F1.1780.18
157_R389_F1.1750.18
215_L415_L1.1730.17
189_H225_Q1.1720.17
84_S382_Y1.1710.17
158_G389_F1.1670.17
92_V260_Y1.1660.17
180_T270_T1.1650.17
28_S290_Y1.1640.17
271_Y310_T1.1610.17
47_V393_V1.1580.17
155_G363_A1.1500.17
275_M314_Y1.1490.17
155_G305_F1.1480.17
261_L326_P1.1470.17
33_V214_I1.1470.17
258_Q415_L1.1470.17
119_L222_F1.1470.17
208_S388_F1.1450.17
307_R373_G1.1430.16
340_Q355_A1.1420.16
187_T386_G1.1400.16
109_I204_M1.1390.16
47_V318_H1.1380.16
220_S301_L1.1370.16
215_L260_Y1.1350.16
249_E252_N1.1340.16
32_Y328_Q1.1340.16
221_P307_R1.1330.16
231_P252_N1.1320.16
149_D393_V1.1280.16
47_V375_N1.1280.16
176_Y272_K1.1230.16
252_N255_S1.1220.16
157_R221_P1.1190.16
231_P255_S1.1180.16
84_S143_K1.1140.15
52_N382_Y1.1130.15
313_W362_T1.1120.15
204_M232_D1.1110.15
247_I315_K1.1080.15
61_F137_A1.1070.15
342_A406_K1.1020.15
58_S120_Q1.1010.15
32_Y139_N1.1000.15
30_N157_R1.1000.15
221_P257_G1.0980.15
153_Y310_T1.0960.15
167_L383_L1.0960.15
94_L185_G1.0950.15
149_D152_D1.0940.15
204_M337_F1.0920.15
236_I248_G1.0900.15
155_G255_S1.0880.15
190_S236_I1.0870.15
34_T383_L1.0870.15
236_I249_E1.0850.15
227_P252_N1.0840.15
184_E192_Y1.0840.15
326_P383_L1.0840.15
283_G412_W1.0810.14
277_I313_W1.0810.14
261_L378_D1.0790.14
318_H412_W1.0790.14
25_V82_K1.0760.14
236_I252_N1.0740.14
199_E222_F1.0730.14
207_N213_R1.0720.14
159_P258_Q1.0710.14
307_R389_F1.0710.14
359_H372_Q1.0690.14
30_N158_G1.0690.14
231_P415_L1.0670.14
290_Y316_R1.0670.14
155_G230_I1.0670.14
206_Y385_M1.0660.14
159_P215_L1.0660.14
78_H179_I1.0650.14
146_Y315_K1.0650.14
20_P117_I1.0640.14
221_P373_G1.0630.14
117_I152_D1.0630.14
32_Y386_G1.0620.14
373_G389_F1.0610.14
195_A415_L1.0600.14
44_Q292_Y1.0600.14
150_F367_V1.0580.14
90_F107_I1.0570.14
259_S355_A1.0560.14
290_Y416_K1.0540.14
192_Y342_A1.0540.14
122_V188_M1.0530.14
239_L316_R1.0530.14
66_P337_F1.0530.14
84_S337_F1.0510.14
26_G342_A1.0500.14
32_Y313_W1.0500.14
227_P230_I1.0490.14
94_L209_P1.0490.14
67_T210_T1.0460.13
317_P335_V1.0450.13
69_A146_Y1.0450.13
46_G212_R1.0390.13
298_E313_W1.0370.13
372_Q416_K1.0360.13
362_T388_F1.0350.13
155_G321_L1.0340.13
220_S307_R1.0330.13
52_N60_Y1.0330.13
341_W353_T1.0320.13
173_E278_R1.0320.13
25_V102_V1.0300.13
75_A94_L1.0280.13
271_Y373_G1.0280.13
30_N220_S1.0280.13
213_R252_N1.0260.13
195_A215_L1.0250.13
109_I407_E1.0240.13
210_T235_K1.0240.13
56_I120_Q1.0220.13
220_S231_P1.0210.13
337_F392_S1.0210.13
227_P301_L1.0200.13
58_S116_R1.0200.13
277_I317_P1.0190.13
383_L399_F1.0180.13
271_Y291_F1.0170.13
220_S252_N1.0160.13
225_Q315_K1.0160.13
211_E308_P1.0160.13
174_W317_P1.0130.13
288_T312_T1.0130.13
324_F388_F1.0120.13
69_A139_N1.0120.13
105_G303_A1.0120.13
213_R255_S1.0120.13
31_G135_L1.0110.13
232_D409_E1.0100.12
288_T301_L1.0100.12
337_F356_T1.0100.12
182_P289_A1.0100.12
202_F212_R1.0100.12
155_G207_N1.0090.12
327_E399_F1.0080.12
193_M215_L1.0080.12
159_P182_P1.0080.12
292_Y366_Q1.0070.12
231_P305_F1.0070.12
53_P209_P1.0070.12
155_G221_P1.0060.12
233_D236_I1.0060.12
202_F355_A1.0050.12
221_P255_S1.0040.12
344_S350_S1.0030.12
154_W168_P1.0010.12
189_H192_Y1.0000.12
218_V302_I1.0000.12
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: (05Jul14)
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  
2bgoA10.267993.50.968Contact Map
4kmqA10.301482.50.974Contact Map
2w87A20.303879.30.975Contact Map
2vzpA20.277574.90.976Contact Map
2vzsA20.059871.30.977Contact Map
2w47A10.296764.20.978Contact Map
2wz8A10.270363.80.978Contact Map
2w3jA10.303859.40.978Contact Map
2y8kA10.320637.10.981Contact Map
2xwxA20.32334.70.981Contact 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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