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T0801

ID: 1403053534 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 376 (373)
Sequences: 4167 (3352.4)
Seq/Len: 11.172
Nf(neff/√len): 173.6

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: 11.172).

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
113_E144_K3.6071.00
265_Y293_F3.4461.00
39_W244_W3.3931.00
267_A368_I3.1871.00
136_D162_K2.8271.00
296_K349_R2.8131.00
112_I138_I2.8091.00
134_E137_T2.7511.00
139_M149_V2.7391.00
43_R251_D2.6411.00
19_S32_F2.6151.00
263_N364_Q2.5491.00
48_K197_K2.4581.00
98_V115_A2.3961.00
123_I142_A2.3491.00
263_N365_R2.3401.00
345_K349_R2.3301.00
160_T165_A2.2551.00
139_M143_K2.2101.00
132_A166_L2.2001.00
40_L191_A2.1891.00
192_T203_A2.1621.00
73_E120_T2.1501.00
108_D111_L2.1481.00
47_A195_N2.1341.00
185_A243_L2.1221.00
47_A197_K2.0981.00
256_Q259_A2.0841.00
58_S174_C2.0321.00
142_A149_V2.0231.00
194_I200_I2.0011.00
111_L114_A1.9711.00
14_L18_Q1.9701.00
39_W248_E1.9521.00
360_S363_N1.9431.00
171_H196_D1.9301.00
11_G15_D1.9031.00
53_P57_A1.9001.00
100_V346_E1.8961.00
35_R39_W1.8791.00
68_I93_A1.8651.00
101_R104_T1.8571.00
117_T120_T1.8551.00
32_F244_W1.8411.00
313_A370_T1.8401.00
148_F171_H1.8331.00
309_F374_Y1.8191.00
156_G166_L1.8151.00
66_L148_F1.8141.00
12_T248_E1.8021.00
197_K201_E1.7981.00
110_T137_T1.7901.00
177_F191_A1.7621.00
306_L374_Y1.7591.00
366_T370_T1.7581.00
14_L22_G1.7501.00
308_N312_E1.7461.00
62_A172_I1.7391.00
111_L115_A1.7381.00
313_A373_N1.7311.00
49_V191_A1.7241.00
175_F193_L1.7171.00
43_R165_A1.7151.00
116_I141_L1.6911.00
38_Q42_Q1.6881.00
326_G344_T1.6801.00
236_S239_Q1.6621.00
50_L200_I1.6441.00
80_T324_L1.6421.00
127_H135_M1.6331.00
73_E117_T1.6271.00
107_I112_I1.6201.00
143_K171_H1.6091.00
60_E233_Y1.6041.00
267_A365_R1.5911.00
306_L371_L1.5901.00
40_L157_V1.5841.00
309_F312_E1.5831.00
138_I149_V1.5721.00
136_D161_Y1.5631.00
140_A144_K1.5611.00
127_H170_G1.5461.00
72_D121_R1.5451.00
364_Q368_I1.5381.00
306_L351_L1.5121.00
109_E141_L1.5021.00
160_T287_V1.4951.00
125_P149_V1.4791.00
263_N267_A1.4771.00
78_S343_T1.4691.00
35_R244_W1.4631.00
122_V150_V1.4551.00
77_P88_F1.4541.00
256_Q361_P1.4501.00
142_A147_L1.4501.00
13_E245_A1.4391.00
73_E119_K1.4281.00
41_E49_V1.4271.00
309_F313_A1.4171.00
172_I199_L1.4131.00
270_P372_L1.4131.00
263_N361_P1.4101.00
69_Q93_A1.4050.99
262_Q266_D1.3970.99
325_H344_T1.3880.99
76_M88_F1.3780.99
196_D199_L1.3720.99
200_I204_E1.3700.99
18_Q22_G1.3670.99
182_N291_H1.3590.99
16_Y245_A1.3540.99
60_E90_L1.3440.99
62_A150_V1.3390.99
259_A361_P1.3320.99
75_I112_I1.3300.99
256_Q260_L1.3250.99
268_L371_L1.3200.99
61_M206_I1.3150.99
365_R369_A1.2830.99
310_L317_A1.2830.99
61_M203_A1.2640.99
102_P342_Y1.2560.99
66_L150_V1.2460.98
98_V111_L1.2460.98
48_K200_I1.2450.98
302_D305_A1.2350.98
40_L175_F1.2340.98
112_I141_L1.2270.98
307_I317_A1.2150.98
32_F35_R1.2150.98
263_N368_I1.2040.98
267_A372_L1.2030.98
137_T140_A1.1980.98
66_L172_I1.1950.98
359_L367_V1.1930.98
69_Q72_D1.1930.98
113_E145_H1.1920.98
34_R38_Q1.1900.98
255_Q259_A1.1820.98
51_L235_M1.1780.98
78_S325_H1.1680.97
53_P233_Y1.1600.97
157_V250_A1.1570.97
73_E94_K1.1510.97
78_S340_D1.1450.97
307_I351_L1.1450.97
12_T249_A1.1450.97
340_D343_T1.1370.97
36_C243_L1.1370.97
278_E296_K1.1370.97
105_M346_E1.1320.97
44_F193_L1.1310.97
16_Y248_E1.1230.97
109_E133_C1.1230.97
15_D19_S1.1170.96
60_E231_S1.1130.96
202_R228_D1.1060.96
41_E44_F1.1020.96
46_S168_T1.0990.96
185_A189_G1.0990.96
260_L355_L1.0980.96
10_V13_E1.0940.96
313_A366_T1.0930.96
297_L306_L1.0840.96
306_L309_F1.0820.96
105_M296_K1.0810.95
338_G344_T1.0810.95
139_M169_I1.0770.95
182_N254_N1.0770.95
260_L364_Q1.0740.95
258_L287_V1.0650.95
141_L145_H1.0650.95
325_H340_D1.0650.95
28_G207_R1.0640.95
86_N209_K1.0630.95
131_V283_P1.0600.95
60_E64_L1.0560.95
164_R168_T1.0550.95
326_G338_G1.0530.95
55_C58_S1.0420.94
50_L204_E1.0400.94
294_Y350_L1.0320.94
133_C138_I1.0300.94
255_Q258_L1.0270.94
102_P345_K1.0230.93
64_L91_R1.0230.93
245_A248_E1.0220.93
65_L203_A1.0200.93
165_A168_T1.0110.93
277_I295_I1.0100.93
162_K285_G1.0050.93
75_I120_T1.0010.92
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: (14Jun14)
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  
2c81A10.97871000.476Contact Map
3b8xA20.97071000.485Contact Map
3bb8A20.97871000.487Contact Map
3frkA20.95211000.494Contact Map
1b9hA10.97071000.495Contact Map
1o69A20.93091000.521Contact Map
4lc3A20.97071000.525Contact Map
1mdoA10.96011000.532Contact Map
3nytA10.93881000.536Contact Map
3dr4A40.96811000.538Contact 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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