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T0831 -force run

ID: 1403740918 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 419 (419)
Sequences: 107 (84.5)
Seq/Len: 0.255
Nf(neff/√len): 4.1

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: 0.255).

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
104_R360_T2.1320.75
364_R370_E1.8610.60
49_R68_Q1.8000.57
244_F350_V1.7580.54
22_R30_G1.6980.50
49_R93_D1.6570.47
69_R100_A1.5760.42
163_V222_N1.5730.42
359_A366_R1.5660.42
70_L410_Q1.5530.41
299_E336_Y1.5470.40
70_L103_L1.5420.40
233_R346_L1.5410.40
27_A103_L1.5180.39
21_H70_L1.5080.38
233_R350_V1.4970.37
49_R90_T1.4840.37
339_L350_V1.4730.36
143_W335_E1.4710.36
233_R244_F1.4570.35
227_A234_P1.4550.35
38_K387_E1.4390.34
6_L31_L1.4170.33
63_K348_N1.4170.33
96_L404_L1.4100.32
18_E33_G1.4070.32
1_T36_I1.4060.32
187_C194_L1.4060.32
1_T184_F1.3880.31
258_L396_D1.3880.31
4_E143_W1.3840.31
19_E369_R1.3610.30
33_G379_H1.3580.29
233_R339_L1.3510.29
30_G393_L1.3510.29
305_I325_S1.3500.29
45_A79_L1.3470.29
106_H162_R1.3370.28
293_W336_Y1.3320.28
51_V199_E1.3270.28
30_G208_V1.3240.28
6_L190_L1.3190.27
231_H350_V1.3190.27
191_Q397_K1.3170.27
244_F339_L1.3120.27
352_A358_M1.3000.26
18_E404_L1.2930.26
119_Q397_K1.2890.26
160_V320_D1.2790.25
58_H233_R1.2770.25
103_L366_R1.2750.25
233_R239_L1.2750.25
21_H58_H1.2720.25
57_E102_Q1.2710.25
18_E96_L1.2700.25
409_G413_Y1.2690.25
14_G18_E1.2640.25
33_G380_I1.2640.25
18_E63_K1.2610.25
49_R89_P1.2550.24
233_R293_W1.2540.24
5_L322_G1.2420.24
20_A198_M1.2410.24
412_L416_N1.2410.24
18_E22_R1.2350.23
4_E25_V1.2330.23
108_M411_L1.2240.23
355_E358_M1.2240.23
239_L350_V1.2210.23
52_L77_M1.2200.23
25_V79_L1.2200.23
70_L360_T1.2160.22
14_G37_I1.2150.22
93_D96_L1.2150.22
309_A363_L1.2130.22
143_W408_L1.2070.22
28_L35_H1.2060.22
309_A369_R1.2060.22
53_R291_G1.2020.22
122_L335_E1.2020.22
70_L244_F1.2000.22
381_I396_D1.1970.22
212_V345_A1.1940.21
100_A366_R1.1880.21
232_L337_K1.1880.21
142_W299_E1.1850.21
1_T38_K1.1830.21
334_K340_H1.1830.21
5_L343_W1.1780.21
21_H234_P1.1770.21
12_K18_E1.1760.21
301_S396_D1.1750.21
365_V413_Y1.1680.20
206_K225_E1.1620.20
166_E391_I1.1610.20
163_V304_A1.1580.20
122_L233_R1.1550.20
233_R291_G1.1550.20
5_L26_C1.1540.20
10_Q39_G1.1540.20
194_L400_A1.1540.20
184_F410_Q1.1510.20
26_C30_G1.1480.20
291_G358_M1.1480.20
232_L350_V1.1420.19
323_S359_A1.1420.19
337_K343_W1.1420.19
90_T370_E1.1400.19
56_E181_S1.1380.19
5_L232_L1.1360.19
343_W413_Y1.1360.19
104_R197_Q1.1340.19
163_V220_S1.1330.19
72_A350_V1.1320.19
364_R410_Q1.1300.19
102_Q163_V1.1290.19
21_H244_F1.1280.19
70_L190_L1.1280.19
11_K21_H1.1200.18
70_L329_F1.1190.18
259_F336_Y1.1170.18
272_E278_E1.1170.18
311_S413_Y1.1160.18
80_L143_W1.1140.18
333_K404_L1.1100.18
51_V134_R1.1100.18
68_Q347_R1.1100.18
5_L17_C1.1080.18
104_R215_L1.1070.18
294_A364_R1.1010.18
94_G167_I1.0990.18
58_H350_V1.0960.18
142_W410_Q1.0940.17
231_H244_F1.0930.17
1_T188_R1.0930.17
335_E414_L1.0910.17
5_L233_R1.0830.17
104_R294_A1.0790.17
103_L364_R1.0780.17
92_R361_E1.0770.17
227_A293_W1.0770.17
234_P239_L1.0770.17
414_L417_L1.0770.17
16_E100_A1.0760.17
97_E303_K1.0760.17
184_F359_A1.0760.17
260_S298_T1.0740.17
45_A302_M1.0730.17
131_E168_T1.0730.17
37_I78_E1.0730.17
129_I161_Q1.0730.17
299_E333_K1.0710.17
246_K413_Y1.0690.17
234_P322_G1.0670.16
21_H103_L1.0660.16
232_L291_G1.0660.16
45_A80_L1.0650.16
259_F362_R1.0640.16
269_I276_D1.0640.16
21_H233_R1.0610.16
251_F261_N1.0600.16
33_G206_K1.0580.16
33_G406_K1.0580.16
43_L381_I1.0560.16
224_I227_A1.0560.16
150_A253_E1.0520.16
35_H66_S1.0520.16
244_F410_Q1.0500.16
255_E291_G1.0490.16
46_E233_R1.0440.16
64_T343_W1.0430.16
74_H352_A1.0420.16
189_G262_T1.0420.16
194_L368_P1.0410.16
10_Q336_Y1.0410.16
73_T99_E1.0400.16
70_L216_E1.0380.15
147_I276_D1.0340.15
5_L231_H1.0320.15
5_L413_Y1.0320.15
129_I135_K1.0320.15
49_R100_A1.0310.15
10_Q194_L1.0300.15
270_F381_I1.0290.15
143_W366_R1.0260.15
22_R67_L1.0250.15
146_V163_V1.0250.15
228_T233_R1.0250.15
28_L310_K1.0240.15
45_A194_L1.0240.15
233_R396_D1.0240.15
233_R389_N1.0230.15
99_E297_E1.0220.15
147_I194_L1.0220.15
158_E222_N1.0220.15
219_P239_L1.0220.15
100_A385_E1.0210.15
294_A360_T1.0210.15
409_G414_L1.0210.15
136_I317_E1.0210.15
293_W393_L1.0210.15
208_V266_Q1.0190.15
354_D358_M1.0190.15
49_R87_I1.0180.15
205_Q233_R1.0180.15
345_A400_A1.0180.15
80_L335_E1.0180.15
333_K393_L1.0180.15
33_G373_P1.0170.15
73_T90_T1.0150.15
227_A231_H1.0150.15
50_E251_F1.0140.15
376_P380_I1.0140.15
215_L357_A1.0130.15
185_R341_E1.0120.15
34_I352_A1.0120.15
68_Q90_T1.0100.15
130_H209_R1.0090.14
236_R322_G1.0080.14
205_Q239_L1.0070.14
227_A232_L1.0070.14
251_F254_Y1.0070.14
259_F333_K1.0060.14
247_A386_V1.0050.14
291_G337_K1.0050.14
12_K19_E1.0040.14
25_V103_L1.0030.14
51_V131_E1.0020.14
353_V404_L1.0010.14
186_D192_F1.0000.14
185_R249_E1.0000.14
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  
3qwwA10.279293.90.952Contact Map
3qwpA10.2959930.954Contact Map
3n71A10.338988.80.958Contact Map
3ro3A10.379586.30.96Contact Map
3u3wA20.360482.90.962Contact Map
3ro2A10.415377.40.964Contact Map
3nf1A10.2315700.966Contact Map
4jhrA20.439167.90.966Contact Map
3sf4A30.436866.30.966Contact Map
4a1sA20.131356.60.968Contact 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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