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T0807

ID: 1401990655 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 284 (272)
Sequences: 14207 (10450.8)
Seq/Len: 52.232
Nf(neff/√len): 633.7

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: 52.232).

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
96_E135_K3.1521.00
40_A250_V2.8151.00
79_S107_L2.7441.00
95_C130_L2.6941.00
69_R103_Q2.5281.00
77_L104_T2.5241.00
219_R264_E2.5141.00
31_R66_Q2.4141.00
92_H133_E2.3141.00
218_A267_Q2.3061.00
40_A44_H2.3021.00
7_R13_A2.2561.00
218_A264_E2.2231.00
261_S264_E2.2171.00
79_S98_S2.2141.00
229_A258_I2.0701.00
92_H129_K1.9751.00
107_L136_I1.9621.00
111_L163_T1.8621.00
95_C110_Y1.8511.00
49_I64_V1.8001.00
97_N101_R1.7941.00
111_L191_M1.7581.00
129_K133_E1.7231.00
35_V67_A1.7211.00
213_I217_N1.7101.00
182_W186_H1.7061.00
221_I258_I1.6961.00
189_P238_L1.6891.00
262_G266_A1.6851.00
41_G46_L1.6841.00
129_K132_A1.6751.00
215_M226_L1.6731.00
6_V16_A1.6691.00
78_V111_L1.6671.00
222_T251_Q1.6661.00
44_H253_A1.6611.00
18_G48_V1.6441.00
183_C190_V1.6381.00
214_N267_Q1.6321.00
35_V66_Q1.6301.00
71_L74_R1.6251.00
62_E101_R1.6231.00
95_C107_L1.5761.00
150_Q154_R1.5611.00
53_E94_A1.5511.00
44_H250_V1.5461.00
128_E132_A1.5381.00
92_H126_A1.5371.00
59_G62_E1.5371.00
246_I250_V1.5331.00
38_L67_A1.5301.00
88_K92_H1.5291.00
106_Y137_R1.5231.00
5_T13_A1.4871.00
81_V91_M1.4861.00
35_V70_G1.4721.00
130_L136_I1.4571.00
12_A138_R1.4441.00
37_A249_V1.4411.00
61_E98_S1.4101.00
150_Q182_W1.4070.99
243_A248_H1.3940.99
136_I139_W1.3910.99
88_K129_K1.3860.99
166_V190_V1.3770.99
150_Q185_Q1.3690.99
221_I225_Q1.3650.99
222_T225_Q1.3630.99
243_A249_V1.3610.99
249_V253_A1.3610.99
42_I75_V1.3540.99
233_R265_L1.3470.99
40_A43_D1.3420.99
39_R67_A1.3200.99
72_R104_T1.3130.99
21_T49_I1.3050.99
96_E100_R1.2950.99
35_V39_R1.2930.99
181_P185_Q1.2920.99
266_A270_R1.2890.99
250_V254_A1.2840.99
92_H96_E1.2830.99
72_R106_Y1.2670.99
12_A76_V1.2650.99
127_M139_W1.2510.99
126_A129_K1.2490.99
170_L268_L1.2490.99
88_K126_A1.2420.98
39_R43_D1.2400.98
40_A246_I1.2390.98
33_Q36_A1.2350.98
234_H265_L1.2340.98
30_Q33_Q1.2170.98
212_I223_V1.2080.98
62_E100_R1.2010.98
76_V109_M1.1950.98
247_E250_V1.1950.98
214_N217_N1.1850.98
254_A257_D1.1850.98
178_D181_P1.1800.98
88_K122_E1.1770.98
97_N100_R1.1700.97
211_D214_N1.1640.97
212_I268_L1.1610.97
221_I226_L1.1570.97
93_R97_N1.1550.97
10_E138_R1.1540.97
173_R176_E1.1540.97
81_V110_Y1.1440.97
145_D148_D1.1290.97
218_A261_S1.1290.97
228_L255_A1.1270.97
9_G162_A1.1230.97
62_E66_Q1.1220.97
267_Q270_R1.1200.96
138_R162_A1.1110.96
88_K125_E1.1080.96
102_L107_L1.1010.96
215_M219_R1.0930.96
143_N193_Y1.0930.96
66_Q103_Q1.0930.96
96_E133_E1.0920.96
229_A255_A1.0810.95
78_V191_M1.0780.95
219_R261_S1.0770.95
226_L258_I1.0620.95
79_S110_Y1.0590.95
48_V191_M1.0560.95
153_W186_H1.0530.95
123_T126_A1.0510.94
38_L49_I1.0510.94
48_V78_V1.0490.94
99_L135_K1.0470.94
109_M163_T1.0450.94
53_E90_A1.0380.94
87_G90_A1.0360.94
171_A209_H1.0340.94
89_A93_R1.0270.94
15_P46_L1.0260.94
225_Q251_Q1.0210.93
65_G103_Q1.0190.93
221_I229_A1.0180.93
130_L133_E1.0150.93
15_P47_T1.0080.93
94_A110_Y1.0050.93
130_L135_K1.0050.93
234_H269_D1.0010.92
266_A269_D1.0000.92
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: (29May14)
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  
1pyfA10.94371000.152Contact Map
3n2tA10.98591000.157Contact Map
1ur3M10.96831000.158Contact Map
3eauA10.97181000.162Contact Map
1pz1A20.97541000.164Contact Map
1lqaA20.97181000.171Contact Map
1ynpA20.95421000.173Contact Map
3lutA10.96831000.176Contact Map
3erpA20.96481000.178Contact Map
3o0kA40.89791000.18Contact 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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