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OPENSEQ.org

1sbp_ex7

ID: 1484037990 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 310 (262)
Sequences: 14608 (8546.4)
Seq/Len: 55.756
Nf(neff/√len): 528.0

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: 55.756).

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
103_K209_E4.2261.00
79_D236_K3.5051.00
23_A245_Y3.4091.00
4_Q39_D3.3231.00
104_G207_K3.1751.00
157_D161_A3.0341.00
34_D238_V2.9051.00
6_L39_D2.7821.00
18_E22_K2.7601.00
248_S251_G2.5931.00
4_Q35_N2.5891.00
241_A244_K2.5451.00
23_A26_A2.4521.00
236_K240_E2.4251.00
25_S35_N2.3471.00
101_V209_E2.3201.00
28_W241_A2.3201.00
24_F241_A2.3111.00
23_A254_I2.2571.00
249_P253_E2.2221.00
21_N242_Y2.1981.00
28_W32_T2.1721.00
235_T238_V2.1401.00
105_N187_D2.1231.00
102_R105_N2.0571.00
19_Q22_K2.0491.00
154_K157_D2.0361.00
110_H214_S2.0351.00
24_F242_Y1.9951.00
22_K26_A1.9731.00
21_N25_S1.9711.00
237_A240_E1.9401.00
123_I186_G1.9221.00
253_E257_K1.9151.00
101_V211_V1.9021.00
78_I224_S1.8951.00
103_K207_K1.8791.00
114_D117_K1.8791.00
225_V239_A1.8511.00
240_E244_K1.8431.00
23_A27_H1.8361.00
79_D227_D1.8201.00
22_K25_S1.8191.00
24_F34_D1.8071.00
3_I238_V1.7921.00
158_F161_A1.7871.00
160_K164_K1.7861.00
27_H248_S1.7641.00
111_D114_D1.7301.00
223_V243_L1.7121.00
59_D235_T1.6981.00
254_I257_K1.6951.00
27_H32_T1.6781.00
32_T241_A1.6551.00
225_V243_L1.6391.00
249_P264_D1.6261.00
249_P266_D1.6261.00
110_H114_D1.6261.00
237_A241_A1.6071.00
5_L238_V1.5951.00
180_F185_I1.5931.00
116_I161_A1.5841.00
89_D222_T1.5811.00
60_T239_A1.5701.00
6_L41_S1.5591.00
153_A157_D1.5341.00
229_V235_T1.5331.00
3_I235_T1.5321.00
72_I78_I1.5211.00
157_D160_K1.5201.00
242_Y246_L1.5041.00
53_I75_R1.4781.00
27_H250_E1.4761.00
229_V236_K1.4691.00
25_S32_T1.4661.00
60_T242_Y1.4621.00
76_G227_D1.4541.00
34_D241_A1.4541.00
121_S187_D1.4511.00
180_F186_G1.4291.00
98_V210_I1.4271.00
116_I162_L1.4241.00
24_F245_Y1.3990.99
238_V241_A1.3920.99
251_G254_I1.3800.99
225_V240_E1.3580.99
23_A250_E1.3510.99
253_E267_V1.3470.99
161_A164_K1.3460.99
14_R18_E1.3370.99
19_Q23_A1.3310.99
44_G47_K1.3020.99
50_T54_N1.2930.99
158_F162_L1.2900.99
161_A165_N1.2890.99
23_A251_G1.2820.99
116_I158_F1.2620.99
59_D229_V1.2620.99
116_I165_N1.2590.99
35_N39_D1.2350.98
106_P188_V1.2320.98
250_E253_E1.2210.98
223_V246_L1.1970.98
60_T243_L1.1940.98
28_W33_G1.1880.98
102_R207_K1.1860.98
264_D267_V1.1790.98
172_G176_S1.1790.98
2_D35_N1.1710.98
27_H245_Y1.1680.97
250_E254_I1.1520.97
225_V236_K1.1410.97
95_S219_A1.1280.97
79_D229_V1.1260.97
226_V229_V1.1180.96
100_L191_A1.1170.96
61_V226_V1.0950.96
73_A88_D1.0940.96
113_N117_K1.0860.96
113_N116_I1.0820.96
21_N38_I1.0810.95
21_N40_Q1.0760.95
229_V234_D1.0650.95
101_V108_Q1.0650.95
245_Y251_G1.0650.95
20_Y245_Y1.0590.95
100_L196_A1.0590.95
179_T183_R1.0530.95
20_Y251_G1.0480.94
9_S40_Q1.0460.94
117_K120_V1.0370.94
156_E160_K1.0350.94
252_Q263_R1.0270.94
79_D240_E1.0150.93
24_F32_T1.0140.93
19_Q258_N1.0100.93
103_K107_K1.0010.92
177_T189_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  
1sbpA10.98061000.342Contact Map
1potA10.92581000.412Contact Map
2qryA40.91611000.414Contact Map
3rpwA10.90971000.424Contact Map
3waeA20.89681000.424Contact Map
4r6yA10.92581000.426Contact Map
4edpA20.92261000.426Contact Map
3pu5A10.92261000.427Contact Map
4eqbA20.92261000.43Contact Map
3c9hA20.91611000.433Contact 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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