OPENSEQ.org
1a0l

ID: 1516175609 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 244 (237)
Sequences: 13941 (10070.8)
Seq/Len: 58.823
Nf(neff/√len): 654.2

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: 58.823).

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
125_C200_C4.5111.00
29_C45_C3.6971.00
38_W96_E3.0301.00
75_S96_E2.9881.00
38_W94_L2.8861.00
11_K147_Q2.8581.00
31_G39_V2.8321.00
6_E146_K2.7411.00
46_V93_A2.6011.00
73_P98_E2.5251.00
15_Q128_T2.4821.00
17_S27_H2.4821.00
32_S208_Q2.4601.00
12_W147_Q2.4411.00
90_A233_Y2.3381.00
33_L101_V2.3101.00
60_L101_V2.2961.00
190_C218_C2.2411.00
40_L208_Q2.2321.00
37_Q100_P2.2011.00
76_R96_E2.1991.00
148_V187_R2.1811.00
37_Q96_E2.1551.00
44_H194_S2.1271.00
16_V31_G2.1111.00
214_W226_I2.1001.00
12_W128_T2.0901.00
158_C181_C2.0851.00
97_L101_V2.0771.00
6_E144_P2.0461.00
36_P100_P2.0041.00
35_H38_W1.9951.00
127_V189_S1.9931.00
81_P240_Y1.9631.00
78_I240_Y1.9231.00
92_I233_Y1.9111.00
59_Q71_L1.9041.00
16_V60_L1.8981.00
1_I4_G1.8871.00
178_D232_Y1.8221.00
75_S98_E1.8101.00
234_L238_H1.8041.00
128_T199_V1.7921.00
74_V95_L1.7661.00
103_V109_T1.7471.00
72_L101_V1.7361.00
89_G178_D1.7241.00
72_L98_E1.7141.00
82_Q90_A1.6971.00
125_C152_I1.6831.00
16_V39_V1.5951.00
14_W199_V1.5541.00
127_V148_V1.5501.00
19_R27_H1.5081.00
228_T233_Y1.5051.00
198_L227_Y1.5041.00
7_A12_W1.4951.00
110_V208_Q1.4791.00
59_Q62_E1.4461.00
80_H90_A1.4141.00
41_T46_V1.4050.99
10_S63_Q1.4010.99
62_E69_D1.3990.99
180_L198_L1.3930.99
229_R232_Y1.3910.99
189_S212_V1.3820.99
64_H143_F1.3540.99
126_W149_K1.3480.99
188_D225_G1.3320.99
200_C209_A1.3310.99
79_V93_A1.3280.99
9_R63_Q1.3260.99
46_V79_V1.3190.99
212_V215_G1.3180.99
133_V146_K1.3130.99
14_W111_T1.3110.99
15_Q145_L1.3100.99
8_P11_K1.3090.99
57_R71_L1.3050.99
78_I96_E1.3040.99
32_S110_V1.2880.99
92_I228_T1.2880.99
124_P149_K1.2870.99
42_A211_V1.2750.99
66_Y143_F1.2690.99
179_M214_W1.2680.99
44_H91_D1.2540.99
32_S211_V1.2510.99
153_M224_P1.2480.99
110_V199_V1.2430.98
15_Q130_W1.2380.98
15_Q30_G1.2040.98
137_E220_Q1.1960.98
77_I95_L1.1930.98
33_L60_L1.1880.98
18_L58_V1.1730.98
72_L99_E1.1730.98
127_V150_V1.1650.97
90_A178_D1.1640.97
14_W206_W1.1560.97
32_S40_L1.1430.97
38_W240_Y1.1400.97
195_G198_L1.1390.97
236_W240_Y1.1290.97
216_E223_R1.1210.97
5_Q147_Q1.1090.96
64_H144_P1.1060.96
154_E157_I1.1050.96
80_H83_F1.0810.95
39_V58_V1.0780.95
84_Y87_Q1.0780.95
125_C198_L1.0630.95
6_E63_Q1.0600.95
12_W126_W1.0560.95
142_P146_K1.0510.94
124_P151_P1.0430.94
201_K206_W1.0420.94
151_P183_G1.0350.94
199_V206_W1.0330.94
10_S106_H1.0280.94
155_N229_R1.0230.93
89_G176_R1.0210.93
19_R59_Q1.0130.93
33_L39_V1.0130.93
7_A147_Q1.0110.93
12_W206_W1.0090.93
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  
2f83A10.8689100-0.017Contact Map
2f9nA40.98361000.012Contact Map
4nzqA10.94671000.012Contact Map
2xxlA20.94261000.012Contact Map
4kkdA20.96311000.019Contact Map
3nxpA10.93851000.021Contact Map
2b9lA10.97131000.026Contact Map
4crgA10.93851000.027Contact Map
2anyA10.95491000.03Contact Map
3gylB10.97131000.031Contact 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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