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T0848 -force run

ID: 1404967707 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 354 (351)
Sequences: 52 (47.4)
Seq/Len: 0.148
Nf(neff/√len): 2.5

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: 0.148).

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
276_L327_M2.1060.58
80_K85_V1.8660.45
50_V71_V1.8460.44
47_I173_D1.7820.40
20_A109_E1.7080.36
177_A189_K1.6930.35
345_A351_F1.6790.35
123_E346_E1.5310.28
176_K283_K1.5270.27
263_I282_D1.5190.27
93_Y120_K1.5120.27
347_L351_F1.4750.25
39_S174_S1.4630.25
126_L341_D1.4370.24
346_E351_F1.4360.24
5_K29_A1.4340.24
132_K247_N1.4340.24
126_L179_S1.4270.23
113_G153_V1.4070.22
80_K146_G1.3830.22
39_S180_A1.3780.21
247_N316_P1.3720.21
4_K198_T1.3660.21
69_L93_Y1.3550.20
71_V252_A1.3550.20
81_D311_F1.3390.20
121_S304_L1.3120.19
348_V351_F1.3100.19
271_V301_K1.2930.18
51_S200_A1.2760.18
177_A180_A1.2710.18
23_S207_N1.2670.17
98_K140_Y1.2670.17
45_V72_N1.2670.17
232_A272_D1.2650.17
175_A178_L1.2640.17
190_D198_T1.2600.17
267_T315_G1.2560.17
116_I311_F1.2550.17
217_Y316_P1.2530.17
83_L325_V1.2390.17
94_Q334_Q1.2350.16
326_K351_F1.2290.16
176_K192_A1.2290.16
46_K123_E1.2280.16
79_G267_T1.2280.16
229_D300_V1.2270.16
215_D309_E1.2260.16
21_A324_E1.2240.16
135_Q158_D1.2230.16
80_K188_G1.2200.16
97_T273_A1.2200.16
11_L196_K1.2170.16
151_K209_F1.2100.16
207_N301_K1.2060.16
137_E156_K1.2040.16
68_V334_Q1.2010.15
23_S126_L1.2000.15
284_V337_L1.1950.15
45_V193_D1.1940.15
71_V297_E1.1940.15
32_K209_F1.1930.15
265_E269_K1.1930.15
50_V268_V1.1890.15
50_V252_A1.1870.15
68_V217_Y1.1860.15
157_I247_N1.1860.15
47_I126_L1.1840.15
16_M116_I1.1780.15
185_L244_L1.1720.15
65_D114_S1.1690.15
50_V162_K1.1640.14
118_A202_K1.1610.14
92_L262_A1.1600.14
145_Y309_E1.1560.14
229_D235_N1.1500.14
118_A125_N1.1490.14
96_D121_S1.1480.14
71_V268_V1.1450.14
83_L138_L1.1440.14
89_D156_K1.1420.14
38_K43_A1.1400.14
227_Y230_S1.1380.14
92_L96_D1.1370.14
79_G99_M1.1350.14
42_I128_F1.1340.14
47_I109_E1.1340.14
89_D296_Y1.1340.14
96_D126_L1.1330.14
169_D299_A1.1300.14
4_K196_K1.1300.14
88_M116_I1.1300.14
99_M276_L1.1290.13
53_T179_S1.1270.13
98_K329_K1.1270.13
243_G271_V1.1240.13
14_L17_M1.1190.13
43_A325_V1.1180.13
167_T268_V1.1160.13
197_I318_S1.1140.13
124_G199_G1.1110.13
106_D138_L1.1070.13
148_K349_E1.1050.13
265_E322_T1.1050.13
75_V125_N1.1040.13
53_T126_L1.1030.13
61_S172_Q1.1020.13
26_K33_E1.1010.13
50_V280_I1.1000.13
96_D211_E1.1000.13
14_L235_N1.0990.13
9_V271_V1.0940.13
100_S250_I1.0930.13
173_D231_K1.0920.13
271_V324_E1.0910.13
69_L76_K1.0900.12
39_S47_I1.0890.12
70_K117_N1.0890.12
73_V256_S1.0890.12
121_S158_D1.0880.12
327_M342_Y1.0880.12
21_A151_K1.0850.12
51_S116_I1.0780.12
127_F177_A1.0780.12
71_V162_K1.0770.12
38_K324_E1.0760.12
146_G198_T1.0750.12
249_S255_T1.0750.12
128_F202_K1.0740.12
171_L178_L1.0740.12
128_F162_K1.0720.12
101_D298_E1.0710.12
133_G152_S1.0710.12
125_N248_S1.0690.12
154_T172_Q1.0690.12
128_F219_S1.0680.12
47_I107_Y1.0670.12
244_L259_K1.0670.12
98_K120_K1.0620.12
190_D208_D1.0610.12
50_V117_N1.0580.12
182_V302_Y1.0570.12
119_D147_D1.0550.12
176_K188_G1.0550.12
146_G338_D1.0540.12
47_I152_S1.0500.12
183_D191_N1.0490.12
128_F283_K1.0480.12
43_A140_Y1.0460.11
171_L177_A1.0460.11
236_I316_P1.0460.11
41_D264_V1.0460.11
14_L293_S1.0430.11
30_E37_E1.0430.11
72_N134_K1.0430.11
154_T249_S1.0410.11
171_L174_S1.0400.11
81_D146_G1.0390.11
41_D87_S1.0390.11
116_I250_I1.0380.11
177_A259_K1.0360.11
41_D86_D1.0350.11
90_F116_I1.0340.11
269_K322_T1.0330.11
308_P311_F1.0330.11
180_A265_E1.0310.11
229_D302_Y1.0300.11
93_Y137_E1.0290.11
64_D309_E1.0270.11
148_K267_T1.0270.11
73_V327_M1.0270.11
123_E199_G1.0270.11
255_T324_E1.0260.11
162_K254_T1.0250.11
294_A305_Q1.0240.11
342_Y351_F1.0240.11
187_F247_N1.0230.11
43_A83_L1.0220.11
284_V287_Y1.0220.11
126_L152_S1.0200.11
162_K333_D1.0200.11
49_D56_S1.0190.11
291_N323_V1.0140.11
20_A193_D1.0120.11
242_E283_K1.0120.11
71_V259_K1.0120.11
236_I245_S1.0120.11
325_V340_D1.0120.11
87_S264_V1.0110.11
67_L349_E1.0090.11
318_S323_V1.0080.11
32_K151_K1.0060.11
67_L122_V1.0040.11
93_Y140_Y1.0040.11
75_V287_Y1.0020.11
325_V333_D1.0020.11
67_L133_G1.0010.10
97_T240_I1.0010.10
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  
3cfuA20.364499.50.855Contact Map
4lesA10.324998.90.886Contact Map
2llgA10.367296.50.934Contact Map
3qfgA20.341896.30.935Contact Map
3o0lA20.310778.30.957Contact Map
2x3cA10.576378.10.957Contact Map
3zbiC140.0763770.957Contact Map
3nrfA20.285367.60.96Contact Map
3isyA10.293866.60.961Contact Map
4eaeA20.429446.60.965Contact 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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