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1sbp from pdb

ID: 1513748048 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 309 (261)
Sequences: 14944 (8772.8)
Seq/Len: 57.257
Nf(neff/√len): 543.0

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: 57.257).

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_E4.1961.00
23_A245_Y3.5281.00
79_D236_K3.5011.00
4_Q39_D3.2121.00
104_G207_K3.0681.00
157_D161_A2.9391.00
34_D238_V2.9051.00
18_E22_K2.8991.00
6_L39_D2.7331.00
241_A244_K2.5971.00
4_Q35_N2.5961.00
248_S251_G2.4961.00
23_A26_A2.4761.00
236_K240_E2.4371.00
25_S35_N2.3881.00
249_P253_E2.3461.00
23_A254_I2.3421.00
101_V209_E2.3391.00
28_W241_A2.3071.00
24_F241_A2.3001.00
21_N242_Y2.2311.00
28_W32_T2.2241.00
235_T238_V2.1891.00
105_N187_D2.1651.00
19_Q22_K2.1301.00
154_K157_D2.1061.00
110_H214_S2.0951.00
102_R105_N2.0901.00
123_I186_G2.0561.00
22_K26_A2.0351.00
253_E257_K1.9991.00
24_F242_Y1.9761.00
101_V211_V1.9621.00
27_H248_S1.9601.00
114_D117_K1.9351.00
21_N25_S1.9331.00
78_I224_S1.9211.00
223_V243_L1.8861.00
237_A240_E1.8761.00
23_A27_H1.8671.00
22_K25_S1.8471.00
225_V239_A1.8251.00
24_F34_D1.8201.00
79_D227_D1.7991.00
160_K164_K1.7591.00
3_I238_V1.7541.00
103_K207_K1.7401.00
158_F161_A1.7211.00
240_E244_K1.6951.00
32_T241_A1.6841.00
254_I257_K1.6811.00
59_D235_T1.6631.00
110_H114_D1.6501.00
237_A241_A1.6481.00
111_D114_D1.6361.00
249_P264_D1.6291.00
53_I75_R1.6021.00
249_P266_D1.5881.00
5_L238_V1.5821.00
116_I162_L1.5771.00
98_V210_I1.5681.00
27_H32_T1.5651.00
225_V243_L1.5491.00
180_F185_I1.5411.00
157_D160_K1.5361.00
229_V235_T1.5341.00
153_A157_D1.5241.00
121_S187_D1.5151.00
89_D222_T1.4991.00
25_S32_T1.4981.00
76_G227_D1.4941.00
60_T239_A1.4811.00
72_I78_I1.4731.00
27_H250_E1.4691.00
34_D241_A1.4681.00
238_V241_A1.4671.00
60_T242_Y1.4651.00
180_F186_G1.4571.00
3_I235_T1.4431.00
116_I161_A1.4341.00
229_V236_K1.4271.00
242_Y246_L1.4211.00
24_F245_Y1.3960.99
253_E267_V1.3690.99
6_L41_S1.3670.99
23_A250_E1.3530.99
14_R18_E1.3510.99
225_V240_E1.3500.99
161_A164_K1.3460.99
23_A251_G1.3390.99
251_G254_I1.3390.99
19_Q23_A1.3190.99
156_E160_K1.3150.99
158_F162_L1.3070.99
116_I165_N1.2820.99
223_V246_L1.2810.99
35_N39_D1.2680.99
161_A165_N1.2460.98
116_I158_F1.2450.98
100_L191_A1.2390.98
50_T54_N1.2100.98
172_G176_S1.2030.98
102_R207_K1.1820.98
59_D229_V1.1820.98
95_S219_A1.1800.98
264_D267_V1.1780.98
226_V229_V1.1770.98
250_E254_I1.1580.97
27_H245_Y1.1510.97
28_W33_G1.1510.97
106_P188_V1.1490.97
44_G47_K1.1470.97
177_T189_L1.1430.97
60_T243_L1.1420.97
2_D35_N1.1370.97
229_V234_D1.1350.97
245_Y251_G1.1170.96
250_E253_E1.1130.96
225_V236_K1.1080.96
100_L196_A1.1060.96
9_S40_Q1.1020.96
21_N40_Q1.1000.96
79_D229_V1.0960.96
73_A88_D1.0940.96
61_V224_S1.0890.96
21_N38_I1.0810.95
61_V226_V1.0720.95
24_F32_T1.0610.95
101_V108_Q1.0510.94
113_N117_K1.0440.94
179_T183_R1.0430.94
20_Y251_G1.0410.94
7_N223_V1.0070.93
166_V169_L1.0040.93
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  
1sbpA10.98381000.354Contact Map
3waeA20.88671000.419Contact Map
4edpA20.90611000.425Contact Map
1potA10.92231000.43Contact Map
3rpwA10.89971000.433Contact Map
2qryA40.92561000.437Contact Map
4r6yA10.90941000.439Contact Map
3pu5A10.90611000.44Contact Map
4eqbA20.90291000.441Contact Map
4i1dA40.92231000.442Contact 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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