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1lth

ID: 1506711094 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 313 (308)
Sequences: 5096 (2736.4)
Seq/Len: 16.545
Nf(neff/√len): 155.9

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: 16.545).

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_A4.1151.00
72_M242_I2.9761.00
214_Q218_N2.7821.00
294_L298_K2.6781.00
74_V242_I2.6581.00
95_V127_V2.5291.00
102_M128_A2.5231.00
79_P93_A2.4391.00
5_A67_C2.3861.00
117_I238_G2.3821.00
275_L283_N2.3571.00
104_N107_K2.2711.00
270_M297_L2.2371.00
215_E222_K2.2181.00
168_A185_A2.1791.00
171_A181_L2.1761.00
67_C109_A2.1641.00
250_N277_N2.0951.00
158_Q208_K2.0741.00
302_E306_E2.0671.00
134_L138_Q1.9761.00
99_K103_P1.9491.00
102_M132_T1.8491.00
277_N282_N1.8211.00
3_K28_E1.8051.00
250_N282_N1.7901.00
23_R243_E1.7831.00
259_L272_V1.7661.00
270_M301_A1.7551.00
206_A210_E1.7541.00
295_A299_R1.7391.00
129_Q269_C1.7371.00
16_L238_G1.7221.00
100_A104_N1.7151.00
126_H130_K1.7021.00
98_L128_A1.6931.00
113_I245_V1.6891.00
265_I297_L1.6571.00
3_K30_V1.6541.00
103_P131_L1.6521.00
274_T281_V1.6501.00
141_G256_S1.6381.00
298_K302_E1.6361.00
39_V43_V1.6231.00
291_D294_L1.6141.00
211_E215_E1.6051.00
114_Y128_A1.6031.00
91_V307_T1.5961.00
4_L20_A1.5951.00
222_K225_N1.5751.00
142_S238_G1.5751.00
99_K131_L1.5731.00
179_V293_E1.5691.00
145_N253_L1.5381.00
296_A299_R1.5331.00
6_V17_A1.5161.00
106_V133_G1.4971.00
170_I180_P1.4951.00
49_G236_M1.4851.00
243_E247_H1.4741.00
125_T269_C1.4691.00
98_L102_M1.4521.00
75_I116_L1.4511.00
73_V105_L1.4511.00
144_T271_S1.4441.00
279_Q282_N1.4441.00
103_P107_K1.4401.00
47_Q157_Q1.4331.00
96_N99_K1.4291.00
79_P82_K1.4141.00
222_K226_G1.4111.00
258_M269_C1.4020.99
18_F235_G1.3990.99
126_H308_A1.3900.99
3_K69_D1.3860.99
20_A29_I1.3830.99
93_A96_N1.3810.99
116_L128_A1.3810.99
47_Q153_F1.3800.99
291_D295_A1.3770.99
159_T187_I1.3750.99
156_A166_V1.3730.99
67_C70_A1.3710.99
127_V131_L1.3670.99
295_A298_K1.3540.99
145_N237_S1.3450.99
299_R302_E1.3420.99
218_N221_Y1.3370.99
113_I138_Q1.3280.99
155_I166_V1.3260.99
109_A112_A1.3230.99
105_L114_Y1.3190.99
158_Q211_E1.3100.99
86_S89_E1.3040.99
2_T246_L1.2980.99
48_H219_A1.2970.99
214_Q217_K1.2940.99
16_L242_I1.2890.99
121_V141_G1.2800.99
28_E57_S1.2650.99
305_K309_A1.2600.99
90_L94_T1.2570.99
180_P213_H1.2480.99
41_A226_G1.2440.98
16_L235_G1.2250.98
177_S303_T1.2250.98
129_Q139_I1.2210.98
16_L74_V1.2100.98
125_T141_G1.2100.98
83_P225_N1.2090.98
85_Q93_A1.2010.98
183_E293_E1.2000.98
257_S274_T1.1970.98
59_D66_I1.1860.98
306_E309_A1.1770.98
81_Q220_A1.1740.98
205_D208_K1.1720.98
14_S42_E1.1690.97
135_P138_Q1.1570.97
18_F22_Q1.1570.97
105_L134_L1.1550.97
30_V66_I1.1480.97
73_V112_A1.1420.97
100_A103_P1.1410.97
75_I128_A1.1400.97
272_V284_T1.1390.97
162_N165_N1.1390.97
292_K296_A1.1350.97
240_D251_R1.1250.97
32_E64_P1.1180.96
89_E92_G1.1170.96
248_D278_R1.1150.96
252_I275_L1.1140.96
266_S305_K1.1130.96
11_A231_N1.1120.96
85_Q89_E1.1110.96
208_K211_E1.1110.96
65_E68_R1.1040.96
87_R174_H1.1030.96
289_V297_L1.1000.96
306_E310_Q1.0990.96
292_K295_A1.0940.96
220_A224_I1.0910.96
299_R303_T1.0900.96
75_I101_I1.0870.96
298_K301_A1.0870.96
30_V70_A1.0830.96
183_E290_S1.0750.95
102_M131_L1.0700.95
38_R42_E1.0680.95
121_V125_T1.0550.95
154_L157_Q1.0510.94
92_G96_N1.0480.94
241_I255_V1.0470.94
119_N174_H1.0430.94
210_E214_Q1.0400.94
265_I298_K1.0380.94
98_L124_A1.0310.94
154_L215_E1.0290.94
156_A163_V1.0270.94
87_R119_N1.0260.94
115_M241_I1.0240.93
223_I233_A1.0230.93
262_F286_N1.0230.93
243_E249_T1.0160.93
74_V115_M1.0130.93
161_V166_V1.0080.93
72_M115_M1.0050.93
106_V132_T1.0020.92
17_A31_L1.0000.92
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  
2d4aB40.96491000.183Contact Map
1a5zA10.98721000.189Contact Map
4cl3A20.97121000.194Contact Map
3nepX10.94891000.195Contact Map
1lldA20.99041000.196Contact Map
4aj2A40.99041000.198Contact Map
4plzA10.96171000.202Contact Map
1guzA40.96491000.205Contact Map
3vpgA40.99041000.21Contact Map
2v6bA40.90421000.211Contact 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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