D-I-TASSER Q9ULI3-D2

D-I-TASSER results for Q9ULI3-D2

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

Input Sequence in FASTA format

>Q9ULI3 (122 residues)
LAPLAGAGLELQLERRPEREPPPTPPRERRGPACKSSAEVCQLLGSQRRIFRAGSLCKRK
SPECDKDTSICTDLDGVALCQCKSGYFQFNKMDHSCRACEDGYRLENETCMSCPFGLGGL
NC

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 \| \| \| \| \| \| LAPLAGAGLELQLERRPEREPPPTPPRERRGPACKSSAEVCQLLGSQRRIFRAGSLCKRKSPECDKDTSICTDLDGVALCQCKSGYFQFNKMDHSCRACEDGYRLENETCMSCPFGLGGLNC
Prediction	CCCCCCCCCSSSSCCCCCCCCCCCCCCCCCCCCCCCCCCCCCSSSCCCCSSSSCCCSSCCCCCCCCCCCSSSCCCCCSSSSSCCCCCCCCCCCCCCCCCCCCCSSSCCSSSSCCCCCCCCCC
Confidence	98766775155530155568989886333461101400045153236413651540324899877766534658884688737883467977676110668754439877407997777789
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 \| \| \| \| \| \| LAPLAGAGLELQLERRPEREPPPTPPRERRGPACKSSAEVCQLLGSQRRIFRAGSLCKRKSPECDKDTSICTDLDGVALCQCKSGYFQFNKMDHSCRACEDGYRLENETCMSCPFGLGGLNC
Prediction	74424434142315534775477744564346415433630311254424233430155455715464441334723330313532374347534154065334144441451343334445
	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

                   |                   |                   |                   |                   |                   |

SS
Seq

CCCCCCCCCSSSSCCCCCCCCCCCCCCCCCCCCCCCCCCCCCSSSCCCCSSSSCCCSSCCCCCCCCCCCSSSCCCCCSSSSSCCCCCCCCCCCCCCCCCCCCCSSSCCSSSSCCCCCCCCCC
LAPLAGAGLELQLERRPEREPPPTPPRERRGPACKSSAEVCQLLGSQRRIFRAGSLCKRKSPECDKDTSICTDLDGVALCQCKSGYFQFNKMDHSCRACEDGYRLENETCMSCPFGLGGLNC

2vj3A

0.25

0.19

5.85

1.96

SPARKS-K

----------------------------QDVDECSLGANPCEINTLGSFECQTGPRCEIDVNECVSNDATCLDQIGEFQCICMPGYEGVHCEVNT-DECASSPCLHNGRCLECPTGFTGHLC

5uk5A

0.23

0.13

4.11

1.77

CNFpred

---------------------------------------------------QDVDECALGANPCEH-AGKCLNTLGSFECQCLQGYTGPRCE-IDVNECISNPCQNDATCLICMPGYEGVYC

2vj3A

0.26

0.20

6.07

1.49

MUSTER

----------------------------QDVDECSLGANPCESFECQCLQGYTGPRCEIDVNECCQNDATCLDQIGEFQCICMPGYEGVHCEV-NTDECASSPCLHNGRCLDCPTGFTGHLC

5uk5A

0.17

0.16

5.12

1.08

HHsearch

SAACGATCHDRRTGLCHLNDA----C---ISNPCNE-GSNCDTNPVCPSGYQDVDECALGANPCE-HAGKCLNTLGSFECQCLQGYTGPRCEID-VNECISNPCQNDATCLDCMPGYEGVYC

1lmjA

0.22

0.12

3.89

0.51

CEthreader

---------------------------------------------------TDIDECRISPDLCG--RGQCVNTPGDFECKCDEGYESGFMMMKNCMDCRGGVCHNTEGSYRCELSPNISAC

1w0yL

0.10

0.08

3.01

0.65

EigenThreader

ANAF-------LLRPGSLRCKQCS----------FARIFKDAERTKLFWISYSDGDQ--CASSPCQNGGSCKDQLQSYICFCLPAFEGRNC--ETDDQLICGGCE----QYCSDHTGTKRSC

2vj3A

0.26

0.15

4.55

0.63

FFAS-3D

----------------------------------------------------DVDECSLGANPCE-HAGKCINTLGSFECQCLQGYTGPRCEEVNTDECASSPCLHNGRCCECPTGFTGHLC

4d90A

0.18

0.16

5.32

1.92

SPARKS-K

-----CDPNPCENGGICLPSFSCECPDGFTDPNCSSVVE----VASDEEEPTSAGPCTP--NPCH-NGGTCEISEIGYVCKCPRGFNGIHCQHNI-NECEVEPCKNGGICTECPGEFMGRNC

5mwbA

0.25

0.14

4.31

1.76

CNFpred

-----------------------------------------------------VDECAMASNPCEH-AGKCVNTDGAFHCECLKGYAGPRCE-MDINECHSDPCQNDATCLLCMPGFKGVHC

4av3A

0.08

0.07

2.56

0.83

DEthreader

DDGDNVGDVGLGALLFVAIVSIASYMFPIYV--QKENL-VHQ-VPKETILIYPFP--S--------VFTTLGAALGMLS-----IKGIGSAA-AAITANSG-GAW-----DNAKHKLGDTGD

(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	0.4452

(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	7ckqC	0.47	4.88	0.094	0.885	model1_7ckqC.pdb.gz
2	2zzgA1	0.47	4.98	0.035	0.869	model1_2zzgA1.pdb.gz
3	4ezcA	0.47	4.53	0.046	0.811	model1_4ezcA.pdb.gz
4	6lodB	0.47	4.74	0.035	0.820	model1_6lodB.pdb.gz
5	6vvsC	0.46	4.92	0.060	0.885	model1_6vvsC.pdb.gz
6	2ztgA1	0.45	5.00	0.061	0.869	model1_2ztgA1.pdb.gz
7	3i39X	0.45	5.04	0.061	0.861	model1_3i39X.pdb.gz
8	2d1gA	0.45	5.12	0.050	0.828	model1_2d1gA.pdb.gz
9	3k3fA	0.44	4.51	0.027	0.770	model1_3k3fA.pdb.gz
10	3cf4A1	0.40	5.13	0.067	0.762	model1_3cf4A1.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	0.49	heterocyclic compound binding
GO:0097159	0.49	organic cyclic compound binding
GO:0003824	0.43	catalytic activity
GO:0097367	0.42	carbohydrate derivative binding
GO:0035639	0.38	purine ribonucleoside triphosphate binding
GO:0032559	0.38	adenyl ribonucleotide binding
GO:0032550	0.38	purine ribonucleoside binding
GO:0016876	0.38	ligase activity, forming aminoacyl-tRNA and related compounds

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:0044699	0.89	single-organism process
GO:0009987	0.89	cellular process
GO:0032502	0.87	developmental process
GO:0044763	0.86	single-organism cellular process
GO:0044767	0.84	single-organism developmental process
GO:0048856	0.81	anatomical structure development
GO:0016043	0.78	cellular component organization
GO:0048513	0.74	animal organ development
GO:0045216	0.71	cell-cell junction organization
GO:0065007	0.70	biological regulation
GO:0050789	0.70	regulation of biological process
GO:0007507	0.70	heart development
GO:0051239	0.59	regulation of multicellular organismal process
GO:0009653	0.58	anatomical structure morphogenesis
GO:0048518	0.57	positive regulation of biological process
GO:0032501	0.57	multicellular organismal process
GO:0048869	0.56	cellular developmental process
GO:0044707	0.56	single-multicellular organism process
GO:0051240	0.54	positive regulation of multicellular organismal process
GO:0048731	0.54	system development
GO:0048589	0.54	developmental growth
GO:0065008	0.53	regulation of biological quality
GO:0048729	0.53	tissue morphogenesis
GO:0032989	0.53	cellular component morphogenesis
GO:0030154	0.53	cell differentiation
GO:0009888	0.53	tissue development
GO:0003008	0.53	system process
GO:0048468	0.52	cell development
GO:0060429	0.51	epithelium development
GO:0050878	0.51	regulation of body fluid levels
GO:0048845	0.51	venous blood vessel morphogenesis
GO:0009791	0.51	post-embryonic development
GO:0003222	0.51	ventricular trabecula myocardium morphogenesis
GO:0003209	0.51	cardiac atrium morphogenesis
GO:0003013	0.51	circulatory system process
GO:0002064	0.51	epithelial cell development
GO:0001817	0.51	regulation of cytokine production
GO:0001701	0.51	in utero embryonic development
GO:0001570	0.51	vasculogenesis
GO:0000904	0.51	cell morphogenesis involved in differentiation
GO:0090271	0.50	positive regulation of fibroblast growth factor production
GO:0060039	0.50	pericardium development
GO:0055017	0.50	cardiac muscle tissue growth
GO:0035264	0.50	multicellular organism growth
GO:0030324	0.50	lung development
GO:0003281	0.50	ventricular septum development
GO:0003017	0.50	lymph circulation
GO:0001945	0.50	lymph vessel development
GO:0001944	0.50	vasculature development
GO:0001886	0.50	endothelial cell morphogenesis
GO:0001885	0.50	endothelial cell development

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	1.00	cell part
GO:0044424	0.65	intracellular part
GO:0044425	0.57	membrane part
GO:0044459	0.56	plasma membrane part
GO:0030054	0.55	cell junction
GO:0009986	0.54	cell surface
GO:0005911	0.54	cell-cell junction
GO:0009897	0.53	external side of plasma 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	1cgtA	0.426	4.78	0.044	0.770	2.4.1.19	NA
2	0.060	3lk5A	0.443	3.86	0.047	0.705	2.5.1.1	53,72
3	0.060	2q80A	0.432	3.77	0.083	0.689	2.5.1.29 2.5.1.10 2.5.1.1	NA
4	0.060	3eqvA	0.433	5.19	0.099	0.861	3.4.16.4	85
5	0.060	2puwB	0.424	4.73	0.071	0.754	2.6.1.16	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	1c4cA	0.437	4.61	0.090	0.779	0.53	SF4	complex1.pdb.gz	99,118,119,120,121
2	0.01	1c4aA	0.435	5.07	0.063	0.836	0.41	SF4	complex2.pdb.gz	42,43,44,45,46,79
3	0.01	3n1vF	0.421	4.40	0.042	0.721	0.49	3N1	complex3.pdb.gz	85,99,100,110
4	0.01	1pieA	0.435	4.11	0.044	0.705	0.41	PO4	complex4.pdb.gz	85,86,98
5	0.01	1c4aA	0.435	5.07	0.063	0.836	0.45	FES	complex5.pdb.gz	105,112,113,114,120
6	0.01	2z8yC	0.449	5.00	0.034	0.836	0.52	SF4	complex6.pdb.gz	102,113,116

	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.