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1lth-jackhmmer

ID: 1506720722 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 313 (306)
Sequences: 6516 (3665.5)
Seq/Len: 21.294
Nf(neff/√len): 209.5

Jackhmmer Results: (2016_04)
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: 21.294).

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
5_A70_A3.9541.00
72_M242_I2.7321.00
294_L298_K2.7221.00
214_Q218_N2.6011.00
74_V242_I2.3661.00
23_R243_E2.3571.00
95_V127_V2.3271.00
79_P93_A2.2951.00
250_N277_N2.2331.00
302_E306_E2.1471.00
104_N107_K2.1471.00
67_C109_A2.1421.00
215_E222_K2.1421.00
117_I238_G2.1361.00
5_A67_C2.1091.00
136_E260_K2.0981.00
206_A210_E2.0871.00
265_I297_L2.0851.00
158_Q208_K2.0591.00
171_A181_L2.0501.00
102_M128_A2.0391.00
277_N282_N2.0201.00
270_M297_L2.0001.00
168_A185_A1.9531.00
250_N282_N1.9431.00
275_L283_N1.9111.00
129_Q269_C1.9041.00
159_T187_I1.8801.00
106_V134_L1.8631.00
106_V133_G1.8621.00
99_K103_P1.8531.00
259_L272_V1.8081.00
274_T281_V1.8011.00
211_E215_E1.7791.00
103_P131_L1.7581.00
100_A104_N1.7561.00
134_L138_Q1.7401.00
295_A299_R1.7351.00
298_K302_E1.7121.00
270_M301_A1.7101.00
257_S274_T1.6981.00
102_M132_T1.6941.00
114_Y128_A1.6841.00
228_G231_N1.6721.00
91_V307_T1.6671.00
4_L26_A1.6661.00
279_Q282_N1.6601.00
113_I245_V1.6491.00
85_Q93_A1.6481.00
144_T271_S1.6071.00
296_A299_R1.5901.00
258_M269_C1.5811.00
125_T269_C1.5761.00
103_P107_K1.5661.00
179_V293_E1.5581.00
64_P108_V1.5411.00
6_V17_A1.5391.00
265_I298_K1.5311.00
291_D295_A1.5281.00
291_D294_L1.5241.00
16_L238_G1.5031.00
126_H130_K1.4961.00
141_G256_S1.4961.00
47_Q157_Q1.4881.00
98_L128_A1.4861.00
39_V43_V1.4691.00
142_S238_G1.4601.00
96_N99_K1.4591.00
243_E247_H1.4551.00
4_L20_A1.4231.00
299_R302_E1.4201.00
205_D208_K1.4131.00
81_Q220_A1.3950.99
9_A31_L1.3790.99
145_N237_S1.3740.99
145_N253_L1.3640.99
113_I138_Q1.3600.99
210_E214_Q1.3540.99
292_K296_A1.3510.99
170_I180_P1.3510.99
72_M115_M1.3410.99
65_E68_R1.3390.99
3_K30_V1.3390.99
47_Q153_F1.3210.99
73_V105_L1.3190.99
98_L102_M1.3120.99
177_S303_T1.2970.99
127_V131_L1.2940.99
260_K266_S1.2910.99
105_L114_Y1.2880.99
49_G236_M1.2800.99
248_D278_R1.2780.99
41_A226_G1.2750.99
37_E225_N1.2700.99
75_I116_L1.2660.99
214_Q217_K1.2650.99
16_L242_I1.2640.99
265_I301_A1.2630.99
183_E293_E1.2600.99
20_A29_I1.2550.99
218_N221_Y1.2490.99
208_K211_E1.2450.98
155_I166_V1.2270.98
222_K225_N1.2240.98
100_A103_P1.2220.98
36_K63_D1.2220.98
64_P107_K1.2190.98
37_E226_G1.2110.98
162_N165_N1.1970.98
86_S89_E1.1930.98
180_P213_H1.1880.98
275_L282_N1.1860.98
295_A298_K1.1860.98
93_A96_N1.1700.97
259_L262_F1.1670.97
156_A166_V1.1660.97
37_E40_E1.1550.97
158_Q211_E1.1540.97
167_H186_T1.1540.97
109_A112_A1.1510.97
16_L74_V1.1420.97
38_R42_E1.1400.97
79_P82_K1.1380.97
3_K28_E1.1380.97
35_A38_R1.1320.97
292_K295_A1.1270.97
257_S281_V1.1240.97
3_K69_D1.1230.97
73_V112_A1.1220.97
18_F235_G1.1190.96
129_Q258_M1.1180.96
48_H219_A1.1160.96
99_K131_L1.1130.96
67_C70_A1.1120.96
299_R303_T1.1110.96
116_L128_A1.1060.96
183_E290_S1.1020.96
165_N188_G1.1010.96
255_V274_T1.0960.96
85_Q89_E1.0940.96
56_V59_D1.0930.96
18_F22_Q1.0920.96
30_V66_I1.0910.96
89_E92_G1.0700.95
32_E64_P1.0680.95
20_A25_I1.0640.95
71_D111_N1.0540.95
153_F157_Q1.0500.94
121_V141_G1.0420.94
177_S300_S1.0400.94
243_E249_T1.0380.94
87_R119_N1.0380.94
90_L94_T1.0380.94
252_I275_L1.0320.94
222_K226_G1.0310.94
154_L215_E1.0290.94
14_S42_E1.0270.94
30_V70_A1.0260.94
181_L289_V1.0210.93
190_V194_D1.0190.93
11_A231_N1.0180.93
75_I128_A1.0120.93
121_V125_T1.0100.93
240_D251_R1.0030.93
74_V115_M1.0010.92
63_D66_I1.0000.92
106_V132_T1.0000.92
92_G96_N1.0000.92
171_A179_V1.0000.92
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: (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  
2d4aB40.96491000.229Contact Map
1lldA20.99361000.236Contact Map
1a5zA10.98721000.241Contact Map
3nepX10.94891000.243Contact Map
4plzA10.96171000.245Contact Map
4cl3A20.97121000.248Contact Map
4aj2A40.99681000.25Contact Map
1guzA40.96491000.256Contact Map
2v6bA40.90421000.258Contact Map
3vpgA40.99041000.258Contact 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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