D-I-TASSER Q6B0K9-D1

D-I-TASSER results for Q6B0K9-D1

[Click result.zip to download all results on this page]

Input Sequence in FASTA format

>Q6B0K9 (141 residues)
MLSAQERAQIAQVWDLIAGHEAQFGAELLLRLFTVYPSTKVYFPHLSACQDATQLLSHGQ
RMLAAVGAAVQHVDNLRAALSPLADLHALVLRVDPANFPLLIQCFHVVLASHLQDEFTVQ
MQAAWDKFLTGVAVVLTEKYR

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 \| \| \| \| \| \| \| MLSAQERAQIAQVWDLIAGHEAQFGAELLLRLFTVYPSTKVYFPHLSACQDATQLLSHGQRMLAAVGAAVQHVDNLRAALSPLADLHALVLRVDPANFPLLIQCFHVVLASHLQDEFTVQMQAAWDKFLTGVAVVLTEKYR
Prediction	CCCHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHCHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHHCHCHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHCC
Confidence	989999999999999986248899999999999978348888874422677768999999999999999981220899999999984872099967888999999999999823459999999999999999999998639
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 \| \| \| \| \| \| \| MLSAQERAQIAQVWDLIAGHEAQFGAELLLRLFTVYPSTKVYFPHLSACQDATQLLSHGQRMLAAVGAAVQHVDNLRAALSPLADLHALVLRVDPANFPLLIQCFHVVLASHLQDEFTVQMQAAWDKFLTGVAVVLTEKYR
Prediction	723762352046026304631551023003300442253442144154256354144102300320240043145145104500531064260446305401400130024226741232023004301210021026528
	Values range from 0 (buried residue) to 8 (highly exposed residue)

Predicted Contact, Hydrogen and Distance Map Used in D-I-TASSER simulation

Contact Map

Distance Map

Hydrogen bond networks

D-I-TASSER simulation is guided by the consensus contact map (left figure), distance map (middle figure) and Hydrogen bond network (right figure) derived based on confidence scores of DeepPotential. In the contact, distance map and hydrogen bond networks, the axes mark the residue index along the sequence. For the contact map, each dot represents a residue pair with predicted contact, while for the distance map and hydrogen bond network, a color scale represents a distance of 1-20+ angstroms or a angle of 0-180 degree.

Top 10 threading templates used by D-I-TASSER

Rank

PDB
hit

ID1

ID2

Cov

Norm.
Zscore

Download
alignment

                  20                  40                  60                  80                 100                 120                 140

                   |                   |                   |                   |                   |                   |                   |

SS
Seq

CCCHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHCHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHHCHCHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHCC
MLSAQERAQIAQVWDLIAGHEAQFGAELLLRLFTVYPSTKVYFPHLSACQDATQLLSHGQRMLAAVGAAVQHVDNLRAALSPLADLHALVLRVDPANFPLLIQCFHVVLASHLQDEFTVQMQAAWDKFLTGVAVVLTEKYR

1jebA

0.48

13.83

1.67

DEthreader

SLTKTERTIIVSMWAKISTQADTIGTETLERLFLSHPQTKTYFPHFDLHPGSAQLRAHGSKVVAAVGDAVKSIDDIGGALSKLSELHAYILRVDPVNFKLLSHCLLVTLAARFPADFTAEAHAAWDKFLSVVSSVLTEKYR

1jebA

0.48

13.83

1.69

SPARKS-K

SLTKTERTIIVSMWAKISTQADTIGTETLERLFLSHPQTKTYFPHFDLHPGSAQLRAHGSKVVAAVGDAVKSIDDIGGALSKLSELHAYILRVDPVNFKLLSHCLLVTLAARFPADFTAEAHAAWDKFLSVVSSVLTEKYR

5jggA

0.37

10.95

0.92

MapAlign

TLTSADKSHVKSIWSKASGKAEELGAEALGRMLEVFPNTKTYFHYADLSVTSGQVHTHGKKILDAITTAVNHIDDITGVLTALSTLHAKTLRVDPANFKILSHTILVVLALYFPADFTPEVHLACDKFLASVSHTLATKY-

5jggA

0.38

11.15

0.61

CEthreader

TLTSADKSHVKSIWSKASGKAEELGAEALGRMLEVFPNTKTYFSYADLSVTSGQVHTHGKKILDAITTAVNHIDDITGVLTALSTLHAKTLRVDPANFKILSHTILVVLALYFPADFTPEVHLACDKFLASVSHTLATKYR

1jebA

0.48

13.83

1.65

MUSTER

SLTKTERTIIVSMWAKISTQADTIGTETLERLFLSHPQTKTYFPHFDLHPGSAQLRAHGSKVVAAVGDAVKSIDDIGGALSKLSELHAYILRVDPVNFKLLSHCLLVTLAARFPADFTAEAHAAWDKFLSVVSSVLTEKYR

1c7dA

0.45

13.26

1.33

HHsearch

VLSPADKTNVKAAWGKVGAHAGEYGAEALERMFLSFPTTKTYFPHFDLSHGSAQVKGHGKKVADALTNAVAHVDDMPNALSALSDLHAHKLRVDPVNFKLLSHCLLVTLAAHLPAEFTPAVHASLDKFLASVSTVLTSKYR

1hv4A

0.47

13.64

2.16

FFAS-3D

VLSAADKTNVKGVFSKISGHAEEYGAETLERMFTAYPQTKTYFPHFDLQHGSAQIKAHGKKVVAALVEAVNHIDDIAGALSKLSDLHAQKLRVDPVNFKFLGHCFLVVVAIHHPSALTAEVHASLDKFLCAVGTVLTAKYR

1ouuB

0.29

8.84

1.00

EigenThreader

EWTDAEKSTISAVWGKV--NIDEIGPLALARVLIVYPWTQRYFGSFGNVSTNPKVAAHGKVVCGALDKAVKNMGNILATYKSLSETHANKLFVDPDNFRVLADVLTIVIAAKFGASFTPEIQATWQKFMKVVVAAMGSRYF

1hbrA

0.50

14.60

1.10

CNFpred

MLTAEDKKLIQQAWEKAASHQEEFGAEALTRMFTTYPQTKTYFPHFDLSPGSDQVRGHGKKVLGALGNAVKNVDNLSQAMAELSNLHAYNLRVDPVNFKLLSQCIQVVLAVHMGKDYTPEVHAAFDKFLSAVSAVLAEKYR

1hbrA

0.50

14.60

1.50

DEthreader

MLTAEDKKLIQQAWEKAASHQEEFGAEALTRMFTTYPQTKTYFPHFDLSPGSDQVRGHGKKVLGALGNAVKNVDNLSQAMAELSNLHAYNLRVDPVNFKLLSQCIQVVLAVHMGKDYTPEVHAAFDKFLSAVSAVLAEKYR

(a)	ID1 is the number of template residues identical to query divided by number of aligned residues.
(b)	ID2 is the number of template residues identical to query divided by query sequence length.
(c)	Cov is equal the number of aligned template residues divided by query sequence length.
(d)	Norm. Zscore is the normalized Z-score of the threading alignments. A Normalized Z-score >1 means a good alignment and is highlighted in bold.
(e)	Download alignment lists the threading program used to identify the template, and provide the 3D structure of aligned regions of threading templates (threading[1-10].pdb.gz).
(f)	Template residues identical to query sequence are highlighted in color.

Top 1 final models from D-I-TASSER

Click to view	Rank^a	Download	Estimated TM-score^b
	1	model1.pdb.gz	0.8886

(a)

D-I-TASSER simulations generate a large ensemble of structural conformations, i.e. decoys. These decoys are clustered by SPICKER based on pairwise structure similarity to report up to five final models from the five largest clusters. Models are ranked in descending order of cluster size. If the simulations converge well, it is possible to have less than 5 models generated, which is usually an indication of good model quality.

(b)

The model confidence is quantitatified by estimated TM-score (eTM-score), calculated based on significance of threading template alignments, contact map satisfaction rate, mean absolute error between distance of model and distance of DeepPotential, and convergence of D-I-TASSER simulations. eTM-score is typically in the range of [0, 1], with higher eTM-score signifies higher model confidence.

Proteins with similar structure

Top 10 structural analogs in PDB (as identified by TM-align)

Rank	PDB Hit	TM-score	RMSD^a	IDEN^a	Cov.	Download Alignment
1	1jebA	0.99	0.55	0.475	1.000	model1_1jebA.pdb.gz
2	1hbrA	0.97	0.78	0.504	1.000	model1_1hbrA.pdb.gz
3	1c7dA	0.97	0.74	0.454	1.000	model1_1c7dA.pdb.gz
4	5jggA	0.97	0.78	0.383	1.000	model1_5jggA.pdb.gz
5	6nbdA	0.97	0.68	0.450	0.993	model1_6nbdA.pdb.gz
6	1hv4A	0.96	0.98	0.468	1.000	model1_1hv4A.pdb.gz
7	2r1hA	0.96	0.93	0.376	1.000	model1_2r1hA.pdb.gz
8	1ouuA	0.96	0.95	0.397	1.000	model1_1ouuA.pdb.gz
9	1xq5A	0.96	0.97	0.369	1.000	model1_1xq5A.pdb.gz
10	6hitA	0.96	0.97	0.397	1.000	model1_6hitA.pdb.gz

(a)	Query structure is shown in cartoon, while the structural analog is displayed using backbone trace.
(b)	Ranking of proteins is based on TM-score of the structural alignment between the query structure and known structures in the PDB library.
(c)	RMSD^a is the RMSD between residues that are structurally aligned by TM-align.
(d)	IDEN^a is the percentage sequence identity in the structurally aligned region.
(e)	Cov. represents the coverage of the alignment by TM-align and is equal to the number of structurally aligned residues divided by length of the query protein.

Predicted Gene Ontology (GO) Terms

Molecular Function (MF)

GO term	Cscore^GO	Name
GO:0020037	1.00	heme binding
GO:0019825	1.00	oxygen binding
GO:0005506	1.00	iron ion binding
GO:0005344	1.00	oxygen transporter activity
GO:0003824	0.67	catalytic activity
GO:0016491	0.62	oxidoreductase activity
GO:0016209	0.54	antioxidant activity
GO:0004601	0.53	peroxidase activity
GO:0031720	0.50	haptoglobin binding

Download full result of the above consensus prediction.

Click the graph to show a high resolution version.

(a)

Cscore^GO is the confidence score of predicted GO terms. Cscore^GO values range in between [0-1]; where a higher value indicates a better confidence in predicting the function using the template.

(b)

The graph shows the predicted terms within the Gene Ontology hierachy for Molecular Function. Confidently predicted terms are color coded by Cscore^GO:

[0.4,0.5)

[0.5,0.6)

[0.6,0.7)

[0.7,0.8)

[0.8,0.9)

[0.9,1.0]

Biological Process (BP)

GO term	Cscore^GO	Name
GO:0015671	1.00	oxygen transport
GO:0009987	0.79	cellular process
GO:0065007	0.73	biological regulation
GO:0008152	0.71	metabolic process
GO:0050789	0.68	regulation of biological process
GO:0050794	0.65	regulation of cellular process
GO:0044763	0.65	single-organism cellular process
GO:0050896	0.64	response to stimulus
GO:0044237	0.61	cellular metabolic process
GO:0006950	0.60	response to stress
GO:0044767	0.57	single-organism developmental process
GO:0019222	0.57	regulation of metabolic process
GO:0016043	0.56	cellular component organization
GO:0060255	0.55	regulation of macromolecule metabolic process
GO:0051171	0.55	regulation of nitrogen compound metabolic process
GO:0031323	0.55	regulation of cellular metabolic process
GO:0009889	0.55	regulation of biosynthetic process
GO:0080090	0.54	regulation of primary metabolic process
GO:0051291	0.54	protein heterooligomerization
GO:0042221	0.54	response to chemical
GO:0031326	0.54	regulation of cellular biosynthetic process
GO:0010556	0.54	regulation of macromolecule biosynthetic process
GO:2000112	0.53	regulation of cellular macromolecule biosynthetic process
GO:0048869	0.53	cellular developmental process
GO:0010468	0.53	regulation of gene expression
GO:0009056	0.52	catabolic process
GO:0006979	0.52	response to oxidative stress
GO:1901700	0.51	response to oxygen-containing compound
GO:0048523	0.51	negative regulation of cellular process
GO:0048518	0.51	positive regulation of biological process
GO:0048522	0.50	positive regulation of cellular process
GO:0044248	0.50	cellular catabolic process
GO:0019219	0.50	regulation of nucleobase-containing compound metabolic process
GO:0010941	0.50	regulation of cell death
GO:0010558	0.50	negative regulation of macromolecule biosynthetic process
GO:0010035	0.50	response to inorganic substance

Download full result of the above consensus prediction.

Click the graph to show a high resolution version.

(a)

Cscore^GO is the confidence score of predicted GO terms. Cscore^GO values range in between [0-1]; where a higher value indicates a better confidence in predicting the function using the template.

(b)

The graph shows the predicted terms within the Gene Ontology hierachy for Biological Process. Confidently predicted terms are color coded by Cscore^GO:

[0.4,0.5)

[0.5,0.6)

[0.6,0.7)

[0.7,0.8)

[0.8,0.9)

[0.9,1.0]

Cellular Component (CC)

GO term	Cscore^GO	Name
GO:0044464	0.97	cell part
GO:0044424	0.96	intracellular part
GO:0044444	0.76	cytoplasmic part
GO:0032991	0.50	macromolecular complex
GO:0043234	0.49	protein complex
GO:0005833	0.47	hemoglobin complex
GO:0043226	0.42	organelle
GO:0005737	0.41	cytoplasm
GO:0043227	0.40	membrane-bounded organelle
GO:0044421	0.34	extracellular region part
GO:0044446	0.30	intracellular organelle part

Download full result of the above consensus prediction.

Click the graph to show a high resolution version.

(a)

Cscore^GO is the confidence score of predicted GO terms. Cscore^GO values range in between [0-1]; where a higher value indicates a better confidence in predicting the function using the template.

(b)

The graph shows the predicted terms within the Gene Ontology hierachy for Cellular Component. Confidently predicted terms are color coded by Cscore^GO:

[0.4,0.5)

[0.5,0.6)

[0.6,0.7)

[0.7,0.8)

[0.8,0.9)

[0.9,1.0]

Predicted Enzyme Commission (EC) Numbers

Top 5 enzyme homologs in PDB

Rank	Cscore^EC	PDB Hit	TM-score	RMSD^a	IDEN^a	Cov.	EC Number	Predicted Active Site Residues
1	0.060	1xl7A	0.422	4.47	0.043	0.681	2.3.1.137	29
2	0.060	3hhsB	0.480	5.04	0.064	0.858	1.14.18.1	NA
3	0.060	3k2wB	0.488	4.30	0.053	0.766	1.2.1.8	NA
4	0.060	2ztgA	0.484	4.40	0.082	0.816	6.1.1.7	NA
5	0.060	2o2rC	0.483	4.48	0.043	0.759	1.5.1.6	NA

	Click on the radio buttons to visualize predicted active site residues.
(a)	Cscore^EC is the confidence score for the Enzyme Commission (EC) number prediction. Cscore^EC values range in between [0-1]; where a higher score indicates a more reliable EC number prediction.
(b)	TM-score is a measure of global structural similarity between query and template protein.
(c)	RMSD^a is the RMSD between residues that are structurally aligned by TM-align.
(d)	IDEN^a is the percentage sequence identity in the structurally aligned region.
(e)	Cov. represents the coverage of global structural alignment and is equal to the number of structurally aligned residues divided by length of the query protein.

Predicted Ligand Binding Sites

Template proteins with similar binding site:

Rank	Cscore^LB	PDB Hit	TM-score	RMSD^a	IDEN^a	Cov.	BS-score	Lig. Name	Download Complex	Predicted binding site residues
1	0.91	1v75A	0.974	0.75	0.525	1.000	1.58	HEM	complex1.pdb.gz	32,42,43,45,46,58,61,65,83,87,91,93,97,98,101,136
2	0.62	1hdsA	0.950	1.05	0.404	1.000	1.13	HEM	complex2.pdb.gz	39,43,58,61,62,66,86,87,93,97,101,136
3	0.09	1ird0	0.975	0.81	0.454	1.000	1.47	III	complex3.pdb.gz	30,31,34,35,36,103,107,110,111,114,117,118,119,122,123,126

	Click on the radio buttons to visualize predicted binding site and residues.
(a)	Cscore^LB is the confidence score of predicted binding site. Cscore^LB values range in between [0-1]; where a higher score indicates a more reliable ligand-binding site prediction.
(b)	BS-score is a measure of local similarity (sequence & structure) between template binding site and predicted binding site in the query structure. Based on large scale benchmarking analysis, we have observed that a BS-score >1 reflects a significant local match between the predicted and template binding site.
(c)	TM-score is a measure of global structural similarity between query and template protein.
(d)	RMSD^a the RMSD between residues that are structurally aligned by TM-align.
(e)	IDEN^a is the percentage sequence identity in the structurally aligned region.
(f)	Cov. represents the coverage of global structural alignment and is equal to the number of structurally aligned residues divided by length of the query protein.

[Click result.zip to download all results on this page]

References:
1.	Wei Zheng, Qiqige Wuyun, Yang Li, Quancheng Liu, Xiaogen Zhou, Yiheng Zhu, P. Lydia Freddolino, Yang Zhang. Integrating deep learning potentials with I-TASSER for single- and multi-domain protein structure prediction. Submitted. 2023.