D-I-TASSER Q03112-D3

D-I-TASSER results for Q03112-D3

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

Input Sequence in FASTA format

>Q03112 (173 residues)
LVTSQNSDLLDDEEVEDEVLLDEEDEDNDITGKTGKEPVTSNLHEGNPEDDYEETSALEM
SCKTSPVRYKEEEYKSGLSALDHIRHFTDSLKMRKMEDNQYSEAELSSFSTSHVPEELKQ
PLHRKSKSQAYAMMLSLSDKESLHSTSHSSSNVWHSMARAAAESSAIQSISHV

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 160 \| \| \| \| \| \| \| \| LVTSQNSDLLDDEEVEDEVLLDEEDEDNDITGKTGKEPVTSNLHEGNPEDDYEETSALEMSCKTSPVRYKEEEYKSGLSALDHIRHFTDSLKMRKMEDNQYSEAELSSFSTSHVPEELKQPLHRKSKSQAYAMMLSLSDKESLHSTSHSSSNVWHSMARAAAESSAIQSISHV
Prediction	CCCCCCCCCCCCHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCSCCCCCCCCHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCHHHHHHHCCCCCCCCCCCCCCCC
Confidence	98765555543012213342154432123567667889999867788642224688864102679863102221345333456678897311010220246534565237755704531167788887999998720468877877789657888622577666665556679
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 160 \| \| \| \| \| \| \| \| LVTSQNSDLLDDEEVEDEVLLDEEDEDNDITGKTGKEPVTSNLHEGNPEDDYEETSALEMSCKTSPVRYKEEEYKSGLSALDHIRHFTDSLKMRKMEDNQYSEAELSSFSTSHVPEELKQPLHRKSKSQAYAMMLSLSDKESLHSTSHSSSNVWHSMARAAAESSAIQSISHV
Prediction	74446544215476263422345755656355547654355534574554446546435132534453344654641133143244245415245256651545315414443447514541344254302210131256552444444434112314434444432432446
	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                 160

                   |                   |                   |                   |                   |                   |                   |                   |

SS
Seq

CCCCCCCCCCCCHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCSCCCCCCCCHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCHHHHHHHCCCCCCCCCCCCCCCC
LVTSQNSDLLDDEEVEDEVLLDEEDEDNDITGKTGKEPVTSNLHEGNPEDDYEETSALEMSCKTSPVRYKEEEYKSGLSALDHIRHFTDSLKMRKMEDNQYSEAELSSFSTSHVPEELKQPLHRKSKSQAYAMMLSLSDKESLHSTSHSSSNVWHSMARAAAESSAIQSISHV

3cuqC

0.06

0.05

2.31

0.43

CEthreader

LQPNVDTRQKQLAAWCSLVLSFCRLHKQSSMTVMEAQESPLFNNVKLQRKLPVESIQIVLEELRKKGNLEWLDKSKSSFLIMWRRPEEWGKLIYQWVSRSGQNNSVFTLYELTNGEDTEEEFHGLDEATLLRALQALQQEHKAEIITVSDGRGVKFF----------------

6yvuB

0.04

2.09

0.52

EigenThreader

LNVVMKNLERLRGEYNDLQSETKTKKEKIKGLQDEIMKIIKLQMQNSKVESVCQKLDILVAKLKKVKSASKKSGGDVVKFQKLLQNSERDVELSSDELKVIEEQLKHTKLALAENDTNMNETLNLKVELKEQSEQLKEQMEDMEESINEFKSIEIEMKNKLEKLNSLLTYIKS

4btgA2

0.12

0.11

3.88

0.43

FFAS-3D

-------------KNRTAVYEAVSQWHEASTEFAYEDAYSVTIRNKRYTAEVKEFELLGLGQRRERVRILKPTVAHAIIQMWYSWFVEDDRTLAAARRTSRDDAEKLAIDGRRMQNAV--TLLRKIEMASAVHLAQIDDSSDLHVGINRRIRIWAGLAEAEALTKVLGDSNAL

6ybwz

0.13

0.12

4.18

0.99

SPARKS-K

DEDEDVKDNWDDDDDEKKEEAEVKPEVKISEKKKIAEKIKEKERQQKKRQEEIKQ------LADKLRLKKLQEESDLELAKETRDDFTEFGKLLKDKITQYEKSLYYASFLEVLCISLEIDDLKKITNSLTVLCSEKQKQEKQSKAKKKKKGVVPGGGLKAT-----------

5cwnA

0.15

0.10

3.29

0.64

CNFpred

------------ESLERAREASERGDEEEFRKAAEK--------------------ALELAKRLVEQAKKEGDPELVLEAAKVALRVAELAAKNG-----------------------DKEVFKKAAESALEVAKRLVEVASKEG----DPELVLEAAKVALRVAELAA----

7jgdA

0.05

0.04

1.94

0.83

DEthreader

TDDLIKTENDLIPQYLRFLQEWVTRWDQYYTTNVDRKEYNCKENEST-------PNGLPKGCIYPECISAN-DKYIVRQQLCEAYYLWKQYNPTG--K--------------GID-DANKKACCAIRGSFYDLEDIIKGDLNTKRARTDWWEN-KTIRQLVWDAMQSGVPCMG

5dwbA

0.09

3.34

0.74

MapAlign

HVMLDNVSEEQYQQISDYFVPLVNKPKLKSRDAIGQAFVMATEVCPDANPSDLWHHVLYRIYIREKIGTDPSQSWVRTSGEAFEVALVERYNPVLARHGIRVMIEKQGGGRSPDAEGFGVVGGIHAKVDIPASRIMMGEGLLSLGTPDRPSDKRNYIEGHGDTTPSGRHIYVS

5n5xA2

0.13

4.58

0.64

MUSTER

-IIVDHPEWASLFNNADEREKESIGALVSQIKLKERERISRVQNLIEHENSHDEDKYLRLS-IATNELLESWQKTKDESILSGSLSHSKLKNLLENSDSFASIPEFSDVTFIGFEKLLHLFLHEDVPGIFYNKLLQCWVLVSPQAELEIVKDIIWSLARLEKPSLFEPIQNEI

2pffB

0.16

5.18

0.67

HHsearch

CLTEFENCYLEGNDIHALAAKLLQE-NDTTAKRPFDKKSGEGNAQLVATDDYFEERDLYQTYHVLVDLIKSAETLSERTTLDAEKVFTQGLNILEWLENPSNTPDK-DYLLS-IPISCFFVSVRKAITVLFFIGVRCYEAYPNTSL--PPSILEDSLENNEGVPSPMLSISNL

1itkB

0.10

3.65

0.41

CEthreader

EDKAVNWGPEDEFETQERFDEPGEIQEGLGASVMGLIYVNPEGPDGNPDPEASAKNIRQTFDRMAMNDKETAALIAGGHTFGKVHGADDPEENLGPEPEAAPIEQQGLGWQNKNGNSKGGEMITSGIEGPWGYINNLLDYEWEPEKGPGGAWQWAPKSEELKNSVPDAHDPDE

(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	0.436

(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	4k6jA	0.50	5.19	0.044	0.832	model1_4k6jA.pdb.gz
2	6vbu7	0.50	4.98	0.065	0.786	model1_6vbu7.pdb.gz
3	6tnfA	0.50	5.00	0.072	0.850	model1_6tnfA.pdb.gz
4	6lq8A	0.49	5.42	0.048	0.879	model1_6lq8A.pdb.gz
5	6sd8X	0.49	5.41	0.048	0.856	model1_6sd8X.pdb.gz
6	5ez3A	0.49	5.47	0.049	0.861	model1_5ez3A.pdb.gz
7	6ijcA	0.48	5.34	0.062	0.838	model1_6ijcA.pdb.gz
8	3djlA	0.48	5.21	0.065	0.821	model1_3djlA.pdb.gz
9	5ys9A	0.47	5.02	0.063	0.763	model1_5ys9A.pdb.gz
10	6ajfA3	0.47	5.31	0.034	0.815	model1_6ajfA3.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:0003677	1.00	DNA binding
GO:0003700	0.82	transcription factor activity, sequence-specific DNA binding
GO:0042803	0.81	protein homodimerization activity
GO:0003824	0.60	catalytic activity
GO:0016740	0.56	transferase activity
GO:0018024	0.53	histone-lysine N-methyltransferase 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:0044699	1.00	single-organism process
GO:0065007	0.87	biological regulation
GO:0050789	0.86	regulation of biological process
GO:0050794	0.85	regulation of cellular process
GO:0080090	0.81	regulation of primary metabolic process
GO:0060255	0.81	regulation of macromolecule metabolic process
GO:0031323	0.81	regulation of cellular metabolic process
GO:0048519	0.80	negative regulation of biological process
GO:0006355	0.80	regulation of transcription, DNA-templated
GO:0031324	0.79	negative regulation of cellular metabolic process
GO:0010605	0.79	negative regulation of macromolecule metabolic process
GO:0045892	0.78	negative regulation of transcription, DNA-templated
GO:0044767	0.71	single-organism developmental process
GO:0048856	0.70	anatomical structure development
GO:0044707	0.69	single-multicellular organism process
GO:0048518	0.67	positive regulation of biological process
GO:0048522	0.66	positive regulation of cellular process
GO:0031325	0.65	positive regulation of cellular metabolic process
GO:0051173	0.64	positive regulation of nitrogen compound metabolic process
GO:0048583	0.64	regulation of response to stimulus
GO:0010604	0.64	positive regulation of macromolecule metabolic process
GO:0045893	0.63	positive regulation of transcription, DNA-templated
GO:0009966	0.63	regulation of signal transduction
GO:0009968	0.62	negative regulation of signal transduction
GO:0009888	0.62	tissue development
GO:0009653	0.62	anatomical structure morphogenesis
GO:0060429	0.61	epithelium development
GO:0031399	0.52	regulation of protein modification process
GO:0019220	0.52	regulation of phosphate metabolic process
GO:0006357	0.52	regulation of transcription from RNA polymerase II promoter
GO:1902531	0.51	regulation of intracellular signal transduction
GO:0051726	0.51	regulation of cell cycle
GO:0009987	0.51	cellular process
GO:0001932	0.51	regulation of protein phosphorylation
GO:0071425	0.50	hematopoietic stem cell proliferation
GO:0046329	0.50	negative regulation of JNK cascade
GO:0043069	0.50	negative regulation of programmed cell death

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:0043231	1.00	intracellular membrane-bounded organelle
GO:0044444	0.97	cytoplasmic part
GO:0044446	0.93	intracellular organelle part
GO:0005737	0.92	cytoplasm
GO:0005654	0.92	nucleoplasm
GO:0016235	0.91	aggresome
GO:0005794	0.91	Golgi apparatus
GO:0005634	0.57	nucleus
GO:0032991	0.54	macromolecular complex
GO:0043234	0.53	protein complex

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	1w07B	0.438	5.55	0.042	0.792	1.3.3.6	NA
2	0.060	1ej6A	0.433	5.33	0.028	0.769	2.7.7.50	NA
3	0.060	1j36A	0.432	5.20	0.070	0.734	3.4.15.1	NA
4	0.060	3hq2B	0.434	4.84	0.113	0.705	3.4.24.-	NA
5	0.060	2eabA	0.460	4.96	0.093	0.769	3.2.1.63	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:

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
	1	0.01	2olcA	0.472	5.36	0.054	0.775	0.21	ADP	complex1.pdb.gz	78,79,82,84,85
	2	0.01	2pupA	0.468	5.33	0.048	0.763	0.22	ADP	complex2.pdb.gz	32,121,122,124

	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.