D-I-TASSER Q9NPI7-D1

D-I-TASSER results for Q9NPI7-D1

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

Input Sequence in FASTA format

>Q9NPI7 (259 residues)
MKHSKKTYDSFQDELEDYIKVQKARGLEPKTCFRKMKGDYLETCGYKGEVNSRPTYRMFD
QRLPSETIQTYPRSCNIPQTVENRLPQWLPAHDSRLRLDSLSYCQFTRDCFSEKPVPLNF
NQQEYICGSHGVEHRVYKHFSSDNSTSTHQASHKQIHQKRKRHPEEGREKSEEERSKHKR
KKSCEEIDLDKHKSIQRKKTEVEIETVHVSTEKLKNRKEKKSRDVVSKKEERKRTKKKKE
QGQERTEEEMLWDQSILGF

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 160 180 200 220 240 \| \| \| \| \| \| \| \| \| \| \| \| MKHSKKTYDSFQDELEDYIKVQKARGLEPKTCFRKMKGDYLETCGYKGEVNSRPTYRMFDQRLPSETIQTYPRSCNIPQTVENRLPQWLPAHDSRLRLDSLSYCQFTRDCFSEKPVPLNFNQQEYICGSHGVEHRVYKHFSSDNSTSTHQASHKQIHQKRKRHPEEGREKSEEERSKHKRKKSCEEIDLDKHKSIQRKKTEVEIETVHVSTEKLKNRKEKKSRDVVSKKEERKRTKKKKEQGQERTEEEMLWDQSILGF
Prediction	CCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCCCCHHHHHHHCCCCCCCCCCCCHHHHCCCCCCCCCCCCCCCCCCCHHHHCCCCCCCCCCCCCCCCCCCCCCCCCHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHCCCCCCCCCHHHHHHCCCCCCCCHHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHCCCHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHCC
Confidence	9975321067999999999998861588753211110123343265423466753011125688655456888765330232258888876556677777775555433236789887855444678987655565445666776444321134667877743421244433210245531123335411345677764311121113343115677776521311368899888877633000038877666654069
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 160 180 200 220 240 \| \| \| \| \| \| \| \| \| \| \| \| MKHSKKTYDSFQDELEDYIKVQKARGLEPKTCFRKMKGDYLETCGYKGEVNSRPTYRMFDQRLPSETIQTYPRSCNIPQTVENRLPQWLPAHDSRLRLDSLSYCQFTRDCFSEKPVPLNFNQQEYICGSHGVEHRVYKHFSSDNSTSTHQASHKQIHQKRKRHPEEGREKSEEERSKHKRKKSCEEIDLDKHKSIQRKKTEVEIETVHVSTEKLKNRKEKKSRDVVSKKEERKRTKKKKEQGQERTEEEMLWDQSILGF
Prediction	5654654254035305511424524615244203424642253462653456443241166413373243244424344424641242144455524175152142346415754343615464545244445473354145665455454545444554553466466568665554545555655515555544655464555545155544544555465645665554544555566465425331013321356
	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 AttentionPotential. 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                 160                 180                 200                 220                 240

                   |                   |                   |                   |                   |                   |                   |                   |                   |                   |                   |                   |

SS
Seq

CCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCCCCHHHHHHHCCCCCCCCCCCCHHHHCCCCCCCCCCCCCCCCCCCHHHHCCCCCCCCCCCCCCCCCCCCCCCCCHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHCCCCCCCCCHHHHHHCCCCCCCCHHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHCCCHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHCC
MKHSKKTYDSFQDELEDYIKVQKARGLEPKTCFRKMKGDYLETCGYKGEVNSRPTYRMFDQRLPSETIQTYPRSCNIPQTVENRLPQWLPAHDSRLRLDSLSYCQFTRDCFSEKPVPLNFNQQEYICGSHGVEHRVYKHFSSDNSTSTHQASHKQIHQKRKRHPEEGREKSEEERSKHKRKKSCEEIDLDKHKSIQRKKTEVEIETVHVSTEKLKNRKEKKSRDVVSKKEERKRTKKKKEQGQERTEEEMLWDQSILGF

3ttoA1

0.03

1.94

0.51

CEthreader

PMVTEGHYGTITLKQGQDTKTAWVYRDQNNTILKGLQNINGTLQFFDPYTGEQLKGGVAKYDDKLFYFESGKGNLVSTVAGDYQDGHYISQDGQTRYADKQNQLVKGLVTVNGALQYFDNATGNQIKNQQVIVDGKTYYFDDKGNGEYLFTNTLDMSTNAFSTKSILANGTTWRDSTDKDMRPLITVWWPNKNVQVNYLNFMKANGLLTTAAQYTLHSDQYDLNQAAQDVQVAIERRIASEHGTDWLQKLLFESQNNNP

7ko4P

0.07

2.77

0.72

EigenThreader

DRAEQAEADKKAAEDRSKQLEDELVSLQKKLKGTEDELDKYSEALKDAQEKLELAEKKATDAEADVASLNRRIQLVEEELDRAQERLATALQKLEEAEKAADESERGMKVIESRAQKDEEKMEIQEIQLKEAKHIAEDADRKYEEVARKLVIIESDLERAEERAELSEGKCAELEEELKTVTNNLKSLEAQAEKYSQKEDRYEEEIKVLSDKLKEAETRAEFAERSVTKLEKSIDDLEDELYAQKLKYKAISEELDHAL

5hmoA

0.17

0.07

2.28

0.36

FFAS-3D

-----------------------------------------------------------------------------------------------------------------------------------------------------AEKRAEEEKRKREEEEKRKREEEERERERERREAELRAQQEEAARKQRELEALQQESQRAAELSRELEKQKENKQVEEEKEIEDLQRMKERQELSLTEAQQLRDE-----

5jcss

0.09

0.08

3.27

1.35

SPARKS-K

KPDQLIQSSVYDSIFSEAADCFAGAIGEFKALSLDIASSRISLFLTQHVPTLENLDDSIKIGRAVLLKEKLNIQKKSMNST-----LFAFTNHSLRLMEQISVCIQMTEPVGETAKMLAKKLTVINVSQQTETGDLLGYKPKTVAVPIQENFETLFNATFSLKKNEKFHKMLHRCFNKNQWKNVVKLWNEAYKMAQSILKITNTENENENAKKKKRRLNTHEKKLLLDNDSVKKFEAQSSSIENRAGEWLLLDEVNLAT

6rw8A

0.03

0.02

1.22

0.83

DEthreader

----------------HAVIMRCG----ILLTAEQ-----------------------TQAQTDGLLAGLSDQLQAAQVKTT--RYSTAGVSELAPYIDPRIGQTG-FEDVANLSYY---WKK-IEIPINVNIRPL-W------------------DLVPNI--VGGSRFGALFNASAIGIEISASATRIAADKISQSEIYRRRRQEWEIQRNNAEAEIKQIDAQLATLAVRREAAVLQKNYLTQAQTQAQLA------

3ttoA1

0.05

2.44

0.95

MapAlign

DLTTGIQAKGQFVTIQETYYFSKDHGDAQLLPMVTEGHYGTITLKQGQDTKTAWVYRDQNNTILKGLQNINGTLQFFDPYTGEQLYISQDGQTRYADKQNQLVKGLVTVNGALQYFDNIKNQQVIVDGKTYYFDDKGNGEYLFTNTTVWWPNKNVQVNYLNFMKANGLLTT----AAQYTLHSDQYDLNQAAQDVQVAIERRIASEHGTDWLQKLLFESQNNNPSFFIWNKDSEYHGNGMGYVLKDWHNGQYFKLDGDK

2tmaA

0.14

4.73

0.86

MUSTER

MDAIKKKMQMLKLDKENA-RAEQAEADK-KAAEDRSKQLEDELVSLQKKLKGTEDELDKYSEALKDAQEKLELAEKKATDAEADVAS---NRRIQLVEEELDRAQERLATALQKLEEAEKAADESERGMKVIESRAQKDEEKMEIQEIQLKEAKHIAEDADRKYEEVARKLVIIESDLERAEERAELSEGKCAELEEEIKTVTNNLKSLEAQAEKYSQKEDKYEEEIKVLSDKLKEAETRAEFAERSVTKL-EKSILED

6b3oA

0.12

0.06

2.17

0.51

HHsearch

VKSQTTRINFCGYVPISFTTANVSPGLAPKGYFVQDDGEW----------KFTGS-SYYYPEPITDKNSVIMSSCAVNYAPEVFLNTSIPNPDFKEELDKWF---------KNQTSIPDLDFEKLNVT--------LLDLTYEMNR----------IQDAIKK---------------------------------------------LNES-----------------------------------------------

1e6vB

0.06

0.05

2.43

0.49

CEthreader

YPQTIDYFGGNVASMLDVPMKQEGVGYALRNI--------MVNHIVAATRKNTMQAVCLAATLQQTAMFEMGDALGPFERLHLLGYAYQGLNADNMVYDIVKKHGKEGTVGTVVREVVERALEDGVIEVKEELPSFKVYKANDMDLWNAYAAAGLVAAVMVNQGAARAAQGVSATILYYNDLLEYETGLPGVDFGRAEGTAVGFSFFSHSIYGGGGPGIFHGNHIVTRHSKGFAIPPVAAAMALDAGTQMFSPEVTSKL

2tmaA

0.07

2.85

0.67

EigenThreader

AEDRSKQLEDELVSLQKKLKGTEDELDKYSEALKDAQEKLELAEKKATDAEADVASLNRRIQLVEEELDRAQERLATALQKLEEAEKAADESERGMKVIESRAQKDEEKMEIQEIQLKEAKHIAEDADRKYEEVARKLVIIESDLERAEERAELSEGKCAELEEEIKTVTNNLKSLEAQAEKYSQKEDKYEEEIKVLSDKLKEAETRAEFAERSVTKLEKSIDDLEDELYAQKLKYKAISEELDHAL--------NDMT

(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	0.2943

(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 AttentionPotential, 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	6vr4A	0.46	5.82	0.056	0.776	model1_6vr4A.pdb.gz
2	5lr8A	0.45	6.46	0.052	0.807	model1_5lr8A.pdb.gz
3	5azaA	0.44	5.86	0.045	0.730	model1_5azaA.pdb.gz
4	4kf7A	0.44	5.56	0.046	0.707	model1_4kf7A.pdb.gz
5	3s4wA	0.43	5.86	0.046	0.734	model1_3s4wA.pdb.gz
6	6tnfB	0.43	5.72	0.045	0.707	model1_6tnfB.pdb.gz
7	2b3yA	0.42	6.20	0.065	0.730	model1_2b3yA.pdb.gz
8	4iglA	0.42	6.40	0.045	0.757	model1_4iglA.pdb.gz
9	2c4mC	0.42	5.94	0.025	0.703	model1_2c4mC.pdb.gz
10	2aw3A	0.42	6.32	0.044	0.734	model1_2aw3A.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:1901363	0.94	heterocyclic compound binding
GO:0097159	0.94	organic cyclic compound binding
GO:0003676	0.93	nucleic acid binding
GO:0003723	0.92	RNA binding
GO:0002039	0.90	p53 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:0050794	0.83	regulation of cellular process
GO:0007165	0.81	signal transduction
GO:0072332	0.80	intrinsic apoptotic signaling pathway by p53 class mediator
GO:0044699	0.67	single-organism process
GO:0009987	0.56	cellular process

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	0.99	cell part
GO:0044424	0.91	intracellular part
GO:0044425	0.87	membrane part
GO:0032991	0.76	macromolecular complex
GO:0043234	0.75	protein complex
GO:0042597	0.75	periplasmic space
GO:0044459	0.71	plasma membrane part
GO:0044422	0.67	organelle part
GO:0043226	0.67	organelle
GO:1902495	0.64	transmembrane transporter complex
GO:1902494	0.64	catalytic complex
GO:0098797	0.64	plasma membrane protein complex
GO:0044446	0.64	intracellular organelle part
GO:0043229	0.64	intracellular organelle
GO:1990060	0.62	maltose transport complex
GO:0055052	0.62	ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing
GO:0030288	0.62	outer membrane-bounded periplasmic space
GO:0044444	0.60	cytoplasmic part
GO:0043227	0.60	membrane-bounded organelle
GO:0043231	0.57	intracellular membrane-bounded organelle
GO:0016020	0.56	membrane

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	1g87B	0.366	6.53	0.050	0.664	3.2.1.4	NA
2	0.060	1t3tA	0.360	6.48	0.047	0.649	6.3.5.3	NA
3	0.060	1xmeA	0.368	5.68	0.043	0.591	1.9.3.1	NA
4	0.060	2azdB	0.410	6.50	0.036	0.738	2.4.1.1	NA
5	0.060	2c4mC	0.420	5.94	0.025	0.703	2.4.1.1	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:

No Binding sites was predicted

Click to view	Rank	Cscore^LB	PDB Hit	TM-score	RMSD^a	IDEN^a	Cov.	BS-score	Lig. Name	Download Complex	Predicted binding site residues

	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, Chengxin Zhang, Yang Li, Robin Pearce, Eric W. Bell, Yang Zhang. Folding non-homology proteins by coupling deep-learning contact maps with I-TASSER assembly simulations. In preparation, 2020.