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ID: 1513690427 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 373 (334)
Sequences: 1054 (663.6)
Seq/Len: 3.156
Nf(neff/√len): 36.3

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: 3.156).

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
210_S213_D3.6091.00
18_N21_E3.4551.00
212_E279_H3.1491.00
236_T257_Q2.9611.00
296_S299_E2.7541.00
42_T46_K2.7511.00
215_F337_M2.7491.00
6_K9_D2.7171.00
19_E58_P2.5981.00
213_D220_K2.5881.00
299_E304_F2.4091.00
5_T9_D2.3451.00
294_P354_K2.3101.00
59_Q62_E2.3001.00
327_S355_V2.2951.00
364_A371_E2.2831.00
331_T348_N2.1751.00
294_P356_D2.1421.00
62_E66_Q2.0801.00
311_I349_L2.0151.00
14_S21_E2.0061.00
362_N365_Q1.9871.00
290_I352_K1.9831.00
289_L349_L1.9801.00
364_A367_R1.9181.00
330_S353_Y1.9060.99
297_F301_L1.8380.99
287_D339_T1.8130.99
13_V22_L1.7830.99
361_L365_Q1.7800.99
202_T268_K1.7670.99
71_A74_S1.7660.99
283_K292_T1.7620.99
17_A22_L1.7510.99
368_A371_E1.7130.99
204_Q273_V1.7050.99
311_I346_R1.7010.99
57_D60_K1.6880.98
214_L276_E1.6750.98
215_F346_R1.6660.98
329_T352_K1.6490.98
7_L54_I1.6380.98
16_S21_E1.6370.98
211_L279_H1.6310.98
209_V213_D1.6160.98
6_K15_P1.5700.97
325_Q359_I1.5660.97
314_R335_Q1.5430.97
38_P41_D1.5190.96
248_A275_Q1.5050.96
23_K60_K1.4940.96
113_N116_S1.4920.96
367_R371_E1.4880.96
63_I72_A1.4790.96
211_L214_L1.4790.96
243_K246_W1.4370.95
207_L242_L1.4350.95
246_W250_T1.4250.94
334_G348_N1.4070.94
214_L337_M1.3940.93
44_K48_I1.3810.93
54_I63_I1.3690.93
58_P62_E1.3690.93
248_A276_E1.3620.92
366_K370_D1.3430.92
5_T47_E1.3420.92
288_D350_I1.3240.91
273_V370_D1.3100.90
69_L72_A1.3060.90
9_D15_P1.2920.90
215_F311_I1.2890.89
256_N268_K1.2880.89
254_Y257_Q1.2850.89
342_N345_Q1.2850.89
37_K52_F1.2710.88
7_L73_R1.2640.88
27_R31_L1.2540.88
361_L366_K1.2530.88
4_E50_E1.2520.87
238_I254_Y1.2520.87
76_G79_F1.2420.87
58_P61_R1.2420.87
21_E24_K1.2410.87
250_T254_Y1.2380.87
326_P357_Y1.2280.86
337_M349_L1.2230.86
4_E69_L1.2150.85
171_P174_M1.2140.85
206_N275_Q1.2100.85
228_G260_Y1.2080.85
238_I252_I1.2070.85
114_I117_Q1.1930.84
223_K237_Q1.1900.84
14_S306_K1.1850.83
8_Y11_L1.1770.83
69_L73_R1.1730.82
291_Y349_L1.1690.82
301_L357_Y1.1620.82
329_T350_I1.1600.81
31_L37_K1.1480.80
43_E355_V1.1480.80
301_L369_I1.1350.79
219_K241_Q1.1350.79
286_G332_Y1.1240.79
369_I372_N1.1140.78
312_D346_R1.1120.77
322_Q330_S1.1060.77
260_Y288_D1.1020.77
23_K36_D1.1010.77
170_M175_G1.0940.76
247_K250_T1.0920.76
299_E370_D1.0910.76
27_R56_N1.0870.75
285_D288_D1.0810.75
218_K365_Q1.0810.75
114_I118_F1.0800.75
368_A372_N1.0770.74
16_S242_L1.0750.74
65_D68_G1.0730.74
2_V6_K1.0730.74
324_V353_Y1.0700.74
9_D14_S1.0650.73
295_L324_V1.0590.72
363_D367_R1.0580.72
15_P29_A1.0540.72
211_L215_F1.0500.72
251_K277_K1.0450.71
331_T353_Y1.0450.71
75_G79_F1.0450.71
336_G347_G1.0450.71
36_D46_K1.0440.71
228_G234_E1.0430.71
63_I67_Y1.0420.71
7_L50_E1.0400.71
276_E337_M1.0320.70
211_L337_M1.0300.69
17_A48_I1.0240.69
349_L353_Y1.0220.69
172_G175_G1.0190.68
292_T352_K1.0160.68
21_E280_P1.0120.68
209_V274_I1.0120.68
259_D305_S1.0060.67
302_L357_Y1.0040.67
200_E268_K1.0010.66
121_G355_V1.0010.66
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  
3lz8A20.46381000.322Contact Map
4j80A40.70511000.337Contact Map
2q2gA20.46381000.563Contact Map
3agxA20.45311000.572Contact Map
1c3gA10.45581000.575Contact Map
1nltA10.43161000.585Contact Map
4j7zA60.27881000.748Contact Map
1bq0A10.198499.90.76Contact Map
4rwuA10.217299.90.76Contact Map
3i38A120.246699.90.762Contact 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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