D-I-TASSER Q9GZT9-D1

D-I-TASSER results for Q9GZT9-D1

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

Input Sequence in FASTA format

>Q9GZT9 (292 residues)
MANDSGGPGGPSPSERDRQYCELCGKMENLLRCSRCRSSFYCCKEHQRQDWKKHKLVCQG
SEGALGHGVGPHQHSGPAPPAAVPPPRAGAREPRKAAARRDNASGDAAKGKVKAKPPADP
AAAASPCRAAAGGQGSAVAAEAEPGKEEPPARSSLFQEKANLYPPSNTPGDALSPGGGLR
PNGQTKPLPALKLALEYIVPCMNKHGICVVDDFLGKETGQQIGDEVRALHDTGKFTDGQL
VSQKSDSSKDIRGDKITWIEGKEPGCETIGLLMSSMDDLIRHCNGKLGSYKI

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 160 180 200 220 240 260 280 \| \| \| \| \| \| \| \| \| \| \| \| \| \| MANDSGGPGGPSPSERDRQYCELCGKMENLLRCSRCRSSFYCCKEHQRQDWKKHKLVCQGSEGALGHGVGPHQHSGPAPPAAVPPPRAGAREPRKAAARRDNASGDAAKGKVKAKPPADPAAAASPCRAAAGGQGSAVAAEAEPGKEEPPARSSLFQEKANLYPPSNTPGDALSPGGGLRPNGQTKPLPALKLALEYIVPCMNKHGICVVDDFLGKETGQQIGDEVRALHDTGKFTDGQLVSQKSDSSKDIRGDKITWIEGKEPGCETIGLLMSSMDDLIRHCNGKLGSYKI
Prediction	CCCCCCCCCCCCCCCCCCCSCCCCCCCCCCCCCCCCCCSSSCCHHHHHHHCCCCCCCCCCHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHCCCCHHHCCSSSSSCCCCHHHHHHHHHHHHHHHHCCCCCCCSSSCCCCCCCCCCCCCSSSSSCCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCSC
Confidence	9887888889997655677255689901212124787476769899986611000223332321355555555666665211333222234555555555665421011012356631123456742236777664322223434467864321123433344555676545676311012233555301111133112244343437750325768999999999999971998787673368898876544258995589877378999999999999996233488619
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 160 180 200 220 240 260 280 \| \| \| \| \| \| \| \| \| \| \| \| \| \| MANDSGGPGGPSPSERDRQYCELCGKMENLLRCSRCRSSFYCCKEHQRQDWKKHKLVCQGSEGALGHGVGPHQHSGPAPPAAVPPPRAGAREPRKAAARRDNASGDAAKGKVKAKPPADPAAAASPCRAAAGGQGSAVAAEAEPGKEEPPARSSLFQEKANLYPPSNTPGDALSPGGGLRPNGQTKPLPALKLALEYIVPCMNKHGICVVDDFLGKETGQQIGDEVRALHDTGKFTDGQLVSQKSDSSKDIRGDKITWIEGKEPGCETIGLLMSSMDDLIRHCNGKLGSYKI
Prediction	6354565554465464554114314446414442302201220361044214333320432442344534333444434444444444444344444454554444434443534434533434433344444444334334443344443444333443443334324444244444344434434354444435222530342010002300356105301510340175240431302244565554010020201235163052033004200300330244046154
	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                 260                 280

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

SS
Seq

CCCCCCCCCCCCCCCCCCCSCCCCCCCCCCCCCCCCCCSSSCCHHHHHHHCCCCCCCCCCHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHCCCCHHHCCSSSSSCCCCHHHHHHHHHHHHHHHHCCCCCCCSSSCCCCCCCCCCCCCSSSSSCCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCSC
MANDSGGPGGPSPSERDRQYCELCGKMENLLRCSRCRSSFYCCKEHQRQDWKKHKLVCQGSEGALGHGVGPHQHSGPAPPAAVPPPRAGAREPRKAAARRDNASGDAAKGKVKAKPPADPAAAASPCRAAAGGQGSAVAAEAEPGKEEPPARSSLFQEKANLYPPSNTPGDALSPGGGLRPNGQTKPLPALKLALEYIVPCMNKHGICVVDDFLGKETGQQIGDEVRALHDTGKFTDGQLVSQKSDSSKDIRGDKITWIEGKEPGCETIGLLMSSMDDLIRHCNGKLGSYKI

3hqrA

1.00

0.37

10.45

1.26

CNFpred

---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------QTKPLPALKLALEYIVPCMNKHGICVVDDFLGKETGQQIGDEVRALHDTGKFTDGQLVSQKSDSSKDIRGDKITWIEGKEPGCETIGLLMSSMDDLIRHCNGKLGSYKI

7bj1A

0.12

4.32

1.03

MapAlign

LLFRSDPLAYTVCKGSRGVVCDRCLLGKKLMRCSQCRVAKYCSAKCQKKAWPDHKRECRQLVMTFQHFMREEIQDASQLPPAFDLFEAFAKVICNSFTICNAEMQEVGVGLYPSISLLNHSCDPNCSIVFNGPHLLLRAVRDIEVGEELTICYLSEERRKQLRDQYCFECDCFRCQTQDKDADMLTGDEQVWKEVQESLKKIEELSNSERLPDINIYQLKVLDCAMDACINLGLALGTRTMFPGSHPVRGVQVMKVGKLQLHQGMFPQAMKNLRLAFDIMRVTHGREHSL--

2dj8A

0.32

0.07

1.96

2.06

HHsearch

---GSSGSSGINQQEDSSESCWNCGRK-ASETCSGCNTARYCGSFCQHKDWEKHHHICSGPSSG------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------

2hbtA

1.00

0.36

10.07

0.61

CEthreader

-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------LPALKLALEYIVPCMNKHGICVVDDFLGKETGQQIGDEVRALHDTGKFTDGQLVSQKSDSSKDIRGDKITWIEGKEPGCETIGLLMSSMDDLIRHCNGKLGSYKI

1ryxA

0.05

2.35

0.60

EigenThreader

SCHTGLGRSAGWNIPIGTCVPGATIEQKLCRQCKGDPKTKCARNAPYSGYSGAFHCLKDGKGDVAFVKHTQKDEYELLCLDGSRQPVDNYKTCNWAQSDFGVDTKSDFHLFGPPGKKDPVLKDLLDSQLYLGFEYYSAIQSMRKDQLTPSPREN------RIQWCAVGKDEKSKCDRWSVVSNGDETKDCIIKIMKGVYTAGVCGKSCHTAVGRTAGWVIPMGLIHNR----TEYFSEGCAPGSPPNSRLCQLCQGCVASSHEKYFGYTGALRCLVESTVEENTGGKNKADW

2hbtA

1.00

0.36

9.97

0.67

FFAS-3D

-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------LPALKLALEYIVPCMNKHGICVVDDFLGKETGQQIGDEVRALHDTGKFTDGQLVSQKSDSSKDIRGDKITWIEGKEPGCETIGLLMSSMDDLIRHCNGKLGSYK-

2hbtA

1.00

0.36

10.07

0.90

SPARKS-K

-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------LPALKLALEYIVPCMNKHGICVVDDFLGKETGQQIGDEVRALHDTGKFTDGQLVSQKSDSSKDIRGDKITWIEGKEPGCETIGLLMSSMDDLIRHCNGKLGSYKI

5lb6A

1.00

0.36

10.07

1.21

CNFpred

-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------LPALKLALEYIVPCMNKHGICVVDDFLGKETGQQIGDEVRALHDTGKFTDGQLVSQKSDSSKDIRGDKITWIEGKEPGCETIGLLMSSMDDLIRHCNGKLGSYKI

4a5bA

0.09

0.06

2.24

0.67

DEthreader

GSGRDFRDFTRPITGAEEGLF-----A---FI------TLNHLSRLGEDARSMIKHSRNDLFPLQEGTVLPSSV---------------------------------------------LFKGFQQ--SC------S-AG--EV---E-VRPDG--SASVNE--KNRLKPLANCQVSILVAPKLPAASGFVQVFRFASSTAP-----MFIT---G----REMLASIDTLKD-HRLLR-S--DFSG-DVEEL-AEAAREFCSSIFLCKTMALTVSLLRHMAA-G-ENQPSFIK

6yuhA

0.11

3.95

1.00

MapAlign

LLFRSDPLAYTVCKGSRGVVCDRCLLGKKLMRCSQCRVAKYCSAKCQKKAKRECKCLKSCKVMTFQHFMREEIQDASQLPPAFDLFEAFAKVICNSFTICNAEMQEVGVGLYPSISLLNHSCDPNCSIVFNGPHLLLRAVRDIEVGEELTICYLSEERRKQLRDQYCFECDCFRCQTQDKDADMLTGDEQVWKEVQESLKKIEELSNSERLPDINIYQLKVLDCAMDACINLEEAEPYRIFFPGSHPVRGVQVMKVGKLQLHQGMFPQAMKNLRLAFDIMRVTHGREHSL--

(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	0.577

(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	4a5bA	0.45	4.78	0.068	0.630	model1_4a5bA.pdb.gz
2	3agrA	0.44	5.16	0.071	0.647	model1_3agrA.pdb.gz
3	3cj9A	0.37	5.71	0.037	0.582	model1_3cj9A.pdb.gz
4	3aapA	0.35	5.31	0.066	0.520	model1_3aapA.pdb.gz
5	1o0yA	0.25	6.11	0.041	0.407	model1_1o0yA.pdb.gz
6	3renA	0.25	6.38	0.061	0.425	model1_3renA.pdb.gz
7	1a6rA2	0.22	5.68	0.037	0.336	model1_1a6rA2.pdb.gz
8	3zx0A1	0.21	5.22	0.075	0.301	model1_3zx0A1.pdb.gz
9	1feuD	0.20	6.27	0.064	0.343	model1_1feuD.pdb.gz
10	4kfcA2	0.19	4.08	0.077	0.253	model1_4kfcA2.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:0003824	0.81	catalytic activity
GO:0016491	0.70	oxidoreductase activity
GO:0016706	0.68	oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, 2-oxoglutarate as one donor, and incorporation of one atom each of oxygen into both donors
GO:0031543	0.62	peptidyl-proline dioxygenase activity
GO:0031545	0.54	peptidyl-proline 4-dioxygenase activity

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:0065007	0.99	biological regulation
GO:0050789	0.98	regulation of biological process
GO:0050794	0.94	regulation of cellular process
GO:0009987	0.85	cellular process
GO:0044699	0.79	single-organism process
GO:0060255	0.78	regulation of macromolecule metabolic process
GO:0080090	0.75	regulation of primary metabolic process
GO:0044763	0.72	single-organism cellular process
GO:0031323	0.72	regulation of cellular metabolic process
GO:0008152	0.72	metabolic process
GO:0071704	0.69	organic substance metabolic process
GO:0044238	0.68	primary metabolic process
GO:0044237	0.68	cellular metabolic process
GO:0010468	0.68	regulation of gene expression
GO:0043170	0.67	macromolecule metabolic process
GO:0044260	0.66	cellular macromolecule metabolic process
GO:0050896	0.65	response to stimulus
GO:2001141	0.64	regulation of RNA biosynthetic process
GO:2000112	0.64	regulation of cellular macromolecule biosynthetic process
GO:0006950	0.63	response to stress
GO:0006355	0.63	regulation of transcription, DNA-templated
GO:0043412	0.62	macromolecule modification
GO:0009628	0.61	response to abiotic stimulus
GO:0001666	0.60	response to hypoxia
GO:0006807	0.59	nitrogen compound metabolic process
GO:0006464	0.59	cellular protein modification process
GO:0018193	0.57	peptidyl-amino acid modification
GO:0048518	0.55	positive regulation of biological process
GO:0044710	0.55	single-organism metabolic process
GO:0006357	0.55	regulation of transcription from RNA polymerase II promoter
GO:0044281	0.54	small molecule metabolic process
GO:1901564	0.51	organonitrogen compound metabolic process
GO:0048519	0.51	negative regulation of biological process
GO:0051239	0.50	regulation of multicellular organismal process
GO:0018401	0.50	peptidyl-proline hydroxylation to 4-hydroxy-L-proline

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:0044424	1.00	intracellular part
GO:0043226	0.65	organelle
GO:0043229	0.63	intracellular organelle
GO:0043227	0.61	membrane-bounded organelle
GO:0043231	0.59	intracellular membrane-bounded organelle
GO:0044444	0.57	cytoplasmic part
GO:0005634	0.55	nucleus

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	1qo9A	0.345	5.81	0.054	0.548	3.1.1.7	NA
2	0.060	1n0hA	0.345	6.02	0.050	0.569	2.2.1.6	NA
3	0.060	1ea0A	0.402	6.49	0.043	0.699	1.4.1.13	NA
4	0.060	1lgfA	0.344	5.36	0.038	0.514	1.14.-.-	NA
5	0.060	2ji6A	0.344	5.86	0.045	0.555	4.1.1.8	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	0.01	2ckjA	0.344	6.53	0.031	0.596	0.65	FES	complex1.pdb.gz	23,24,25,27,30
2	0.01	2ckjA	0.344	6.53	0.031	0.596	0.53	FES	complex2.pdb.gz	26,27,29,43
3	0.01	2vdcA	0.402	6.58	0.043	0.706	0.56	F3S	complex3.pdb.gz	229,234,235,236,237,256
4	0.01	2ckjC	0.352	6.95	0.047	0.661	0.66	FES	complex4.pdb.gz	231,232,233,235,257,258
5	0.01	3eubS	0.199	5.15	0.038	0.288	0.73	FES	complex5.pdb.gz	259,261,262,263,264,266,269
6	0.01	2ckjC	0.352	6.95	0.047	0.661	0.52	FES	complex6.pdb.gz	226,232,233,235,237

	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.