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PilM

ID: 1513362434 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 352 (330)
Sequences: 4277 (3094.1)
Seq/Len: 12.961
Nf(neff/√len): 170.3

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: 12.961).

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
92_L162_L3.4281.00
36_I79_I3.2351.00
89_Q168_S3.1931.00
231_I257_V3.0761.00
224_L296_G2.9961.00
228_K245_M2.9421.00
39_V348_A2.9251.00
196_V272_I2.5371.00
227_L261_Y2.4981.00
73_S164_G2.4201.00
243_M247_N2.4151.00
227_L265_I2.4071.00
224_L245_M2.3161.00
105_Q144_K2.2571.00
269_I306_F2.2511.00
206_L213_P2.1891.00
89_Q170_K2.1881.00
237_D240_M2.1821.00
54_G82_V2.1551.00
289_V315_K2.1541.00
54_G78_N2.1261.00
91_N171_N2.1081.00
290_V310_L2.1051.00
40_V49_T2.0591.00
199_G295_G2.0331.00
266_N309_K2.0321.00
230_E264_Y2.0181.00
32_Y200_E2.0131.00
275_T278_F2.0041.00
234_L260_I1.9961.00
162_L169_I1.9941.00
26_G348_A1.9301.00
155_A172_M1.9141.00
224_L228_K1.9131.00
27_V162_L1.9131.00
242_E246_V1.8931.00
242_E245_M1.8901.00
240_M243_M1.8831.00
228_K242_E1.8671.00
93_S347_A1.8511.00
92_L172_M1.8311.00
37_A344_A1.8021.00
27_V90_I1.7961.00
90_I167_F1.7611.00
193_K291_Y1.7181.00
217_R275_T1.7111.00
111_S116_R1.6911.00
27_V76_L1.6491.00
249_S261_Y1.6461.00
80_F167_F1.6451.00
38_E87_S1.6331.00
298_R338_N1.6211.00
40_V47_I1.5981.00
271_E274_Y1.5721.00
196_V290_V1.5671.00
303_E316_K1.5591.00
150_I155_A1.5361.00
301_D304_K1.5361.00
26_G37_A1.5221.00
119_L132_Y1.5111.00
76_L161_L1.5081.00
35_K295_G1.5071.00
79_I83_F1.5041.00
163_K168_S1.5001.00
191_K288_E1.4921.00
30_G295_G1.4701.00
194_L276_I1.4601.00
52_I79_I1.4591.00
93_S175_D1.4581.00
293_V342_A1.4541.00
103_S146_L1.4431.00
73_S161_L1.4421.00
265_I302_I1.4411.00
36_I83_F1.4301.00
25_I38_E1.4241.00
68_D71_Y1.4221.00
152_K156_Q1.4151.00
105_Q142_S1.3990.99
303_E307_T1.3860.99
39_V46_I1.3830.99
194_L205_L1.3790.99
37_A48_L1.3670.99
291_Y317_I1.3610.99
28_D344_A1.3480.99
178_N347_A1.3400.99
292_L302_I1.3390.99
61_I66_I1.3380.99
60_V72_L1.3310.99
99_L174_A1.3210.99
30_G199_G1.3190.99
76_L165_L1.3110.99
103_S144_K1.2930.99
70_Q164_G1.2890.99
27_V36_I1.2820.99
38_E50_N1.2780.99
302_I306_F1.2730.99
23_A49_T1.2720.99
62_V67_N1.2670.99
169_I172_M1.2590.99
61_I64_G1.2570.99
235_V260_I1.2560.99
196_V203_V1.2520.99
161_L165_L1.2490.99
306_F314_T1.2470.99
232_R241_V1.2410.98
159_E169_I1.2400.98
38_E83_F1.2390.98
224_L295_G1.2370.98
101_Y146_L1.2130.98
118_K121_E1.2120.98
75_N79_I1.2100.98
182_L317_I1.2080.98
26_G344_A1.2000.98
131_Y156_Q1.1980.98
74_T77_K1.1980.98
266_N305_I1.1950.98
53_Q341_G1.1930.98
269_I302_I1.1910.98
188_G315_K1.1910.98
162_L167_F1.1830.98
36_I80_F1.1590.97
28_D199_G1.1550.97
39_V48_L1.1540.97
34_I75_N1.1500.97
173_D350_R1.1430.97
28_D35_K1.1370.97
131_Y152_K1.1330.97
29_I61_I1.1300.97
31_T201_S1.1280.97
273_Q277_E1.1280.97
173_D181_N1.1230.97
28_D197_D1.1210.97
95_S175_D1.1210.97
29_I158_F1.1120.96
73_S165_L1.1120.96
184_E291_Y1.1120.96
228_K241_V1.1100.96
179_I343_N1.1060.96
292_L303_E1.0980.96
222_L268_I1.0970.96
270_K274_Y1.0940.96
200_E295_G1.0730.95
35_K53_Q1.0710.95
26_G29_I1.0640.95
343_N347_A1.0640.95
25_I87_S1.0640.95
290_V312_L1.0530.95
36_I52_I1.0510.94
52_I82_V1.0480.94
69_F73_S1.0420.94
256_E259_E1.0420.94
205_L217_R1.0420.94
51_F341_G1.0410.94
24_Y91_N1.0390.94
53_Q340_Q1.0390.94
129_D149_V1.0370.94
31_T295_G1.0330.94
27_V167_F1.0310.94
209_T214_V1.0190.93
162_L166_N1.0180.93
101_Y174_A1.0180.93
31_T61_I1.0130.93
203_V223_G1.0080.93
222_L226_N1.0080.93
306_F310_L1.0070.93
72_L161_L1.0030.93
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  
2ychA10.90911000.383Contact Map
3wt0A401000.474Contact Map
3wqtA40.8751000.477Contact Map
4a2aA20.89491000.498Contact Map
2d0oA20.94699.90.59Contact Map
1nbwA20.943299.90.592Contact Map
3h1qA20.741599.90.654Contact Map
1jceA10.798399.70.721Contact Map
2zgyA20.786999.70.723Contact Map
4j8fA10.823999.60.726Contact 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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