D-I-TASSER Q9H9V9-D2

D-I-TASSER results for Q9H9V9-D2

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

Input Sequence in FASTA format

>Q9H9V9 (133 residues)
VNGFNLANMWRFLQQELCAVQEEVSEWRDSMPDWHHHCQVIMRSCSGINFEEFYHFLKVI
AEKRLLVLREAAAEDGAGLGFEQAAFDVGRITEVLASLVAHPDFQRVDTSAFSPQPKELL
QQLREAVDAAAAP

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 \| \| \| \| \| \| VNGFNLANMWRFLQQELCAVQEEVSEWRDSMPDWHHHCQVIMRSCSGINFEEFYHFLKVIAEKRLLVLREAAAEDGAGLGFEQAAFDVGRITEVLASLVAHPDFQRVDTSAFSPQPKELLQQLREAVDAAAAP
Prediction	CCCCHHHHHHHHHHHHHHHHHHHHHHHHHHCHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCHHHHHHHHHHHHHHHHHHHCCHHHHHCCHHHCCHCHHHHHHHHHHHHHHHCCC
Confidence	9611199999999999999999999999735049999999998605999999999999999999999985124343456677999989999999999971844644275437911999999999999973389
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 \| \| \| \| \| \| VNGFNLANMWRFLQQELCAVQEEVSEWRDSMPDWHHHCQVIMRSCSGINFEEFYHFLKVIAEKRLLVLREAAAEDGAGLGFEQAAFDVGRITEVLASLVAHPDFQRVDTSAFSPQPKELLQQLREAVDAAAAP
Prediction	6402204200420362054036206403640751351013103133212142014003200541152046245564341233002211530350044016464155243640465055015404531543668
	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

                   |                   |                   |                   |                   |                   |

SS
Seq

CCCCHHHHHHHHHHHHHHHHHHHHHHHHHHCHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCHHHHHHHHHHHHHHHHHHHCCHHHHHCCHHHCCHCHHHHHHHHHHHHHHHCCC
VNGFNLANMWRFLQQELCAVQEEVSEWRDSMPDWHHHCQVIMRSCSGINFEEFYHFLKVIAEKRLLVLREAAAEDGAGLGFEQAAFDVGRITEVLASLVAHPDFQRVDTSAFSPQPKELLQQLREAVDAAAAP

1yvlB2

0.07

2.78

1.17

DEthreader

DKVMCIEHEIKSLEDLQDEYDFKCKTLQKQEQLLLKKMYLMLD----NKRKEVVHKIIELLNVTELTQNALINDEQLQNWFTIVAESLQQVRQQLKKLEELQKY-TYE-HDPTKNKQVLWDRTFSLFQQLIQS

2yu2A

0.09

0.08

2.85

1.11

HHsearch

LHSFNIPMQLKIYN---------IEDR--------------TRVPNKFRYPFYYEMCWYVLERYVYCITNRSHLTKELEQVHLTHFELEGLRCLVDKLESLPLHKKCVPTG-IEDEDALIADVKILLEELANS

1y1uA

0.09

0.08

3.17

1.17

DEthreader

LITQDTENELKKLQQTQEYFIIQYQESLQVETWL-QREAQTLQ----QYRVELAEKHQKTLQLLRKQQTIILDELVLQSWCEKLAEIIWQNRQQIRRAEHLQL--PIPG-PVEEMLAEVNATITDIISALVTT

6ff6A2

0.07

2.73

0.76

SPARKS-K

--QSFYQAFFDMADVMLKVMEQLLKLDAAMLNAIFRAAHFIKGAAGTFGFTILQETTHLMENLLDEARRG--EMQLNTDIINLFLETKDIMQEQLDAYKNSEEPDA-------ASFEYICNALRQLALEAK--

5dlqB

0.11

3.84

0.68

MapAlign

IPSELFSSFVNCLTHLTCSFGRSAALEEVLDMVYMEAYDKLLESLGRIAAEHCMPLLTSLLEERVTRLHGQLRHQQDNKMLDDLYEDIHWLILVTGYLLIPPEIMEYSRTDSVIRLLSAVLRVSEVMGKDIVW

2jqqA

0.07

0.06

2.55

0.59

CEthreader

-------KTQSDLQKFMTQLDHLIKDTQEIIKDVLEYLKKLDEIYGSLRNHSQLTEALSLGKRLSKSLHEMCGIEPLEEICSGLIEQLYKLITASRRILE---SCADSNSPYIHHLRNDYQDLLQEFQISLKI

3kyjA

0.14

0.12

4.13

0.55

MUSTER

-----MDEIWALYADDGAQALDAMEASLLALQDAAAHVGPLFRA--GLGLSVVESRAHLCEDLIGLVRDA--GVPMDGEIVEILLFASDTLRAMLEETAASR------ADVEGTGSEALMDQLRSKIARCSR-

3kv6D

0.14

0.11

3.83

0.84

HHsearch

LHNLNIGMQLRCYEMEK-----------------------RLKTPDLFKFPFFEAICWFVAKNLLETLKELREDG--FQPQTYLVQGVKALHTALKLWMKKELVSEIP-DN--VRPGHLIKELSKVIRAIEEE

3ay5A2

0.13

0.12

4.16

0.75

FFAS-3D

----NKAAALLMLTKNVDFVKDAHEEMEQAVEEWSEDDQELIIP-----CLALVRASKACL-KKIRMLVAENGKKDQVAQLDDIVDISDEISPSVDDLALS-IYPPMSHLTVRINSAKLVSVLKKALEITKA-

1bg1A1

0.08

3.02

0.88

EigenThreader

KRVQDLEQKMKVVENLQDDFDFNYKTLKSVTRQKMQQLE-QMLTALDQMRRSIVSELAGLLSAMEYVQKTLTDEDRLENWITSLAESQLQTRQQIKKLEELQQKVSYKGDPIVQHRPMLEERIVELFRNLMKS

(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	0.7908

(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	1y1uA	0.78	2.66	0.087	0.947	model1_1y1uA.pdb.gz
2	1yvlB	0.77	2.84	0.070	0.962	model1_1yvlB.pdb.gz
3	1bg1A	0.77	2.86	0.063	0.962	model1_1bg1A.pdb.gz
4	1uusA	0.59	3.58	0.041	0.804	model1_1uusA.pdb.gz
5	3hhmB	0.44	3.00	0.027	0.556	model1_3hhmB.pdb.gz
6	1a38A2	0.42	2.83	0.067	0.534	model1_1a38A2.pdb.gz
7	2btpA2	0.41	2.85	0.040	0.534	model1_2btpA2.pdb.gz
8	1g8pA1	0.36	5.09	0.050	0.677	model1_1g8pA1.pdb.gz
9	2blmA	0.35	4.71	0.080	0.609	model1_2blmA.pdb.gz
10	4h7uA	0.35	5.15	0.076	0.654	model1_4h7uA.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	0.63	heterocyclic compound binding
GO:0097159	0.63	organic cyclic compound binding
GO:0003676	0.62	nucleic acid binding
GO:0003677	0.59	DNA binding
GO:0003682	0.53	chromatin binding
GO:0000987	0.53	core promoter proximal region sequence-specific DNA binding
GO:0000977	0.53	RNA polymerase II regulatory region sequence-specific DNA binding
GO:0008134	0.52	transcription factor binding
GO:0000982	0.52	transcription factor activity, RNA polymerase II core promoter proximal region sequence-specific binding
GO:0098531	0.51	transcription factor activity, direct ligand regulated sequence-specific DNA binding
GO:0070491	0.51	repressing transcription factor binding
GO:0048020	0.51	CCR chemokine receptor binding
GO:0043566	0.51	structure-specific DNA binding
GO:0035258	0.51	steroid hormone receptor binding
GO:0019900	0.51	kinase binding
GO:0001085	0.51	RNA polymerase II transcription factor 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:0009987	0.95	cellular process
GO:0065007	0.93	biological regulation
GO:0050789	0.93	regulation of biological process
GO:0016043	0.93	cellular component organization
GO:0048518	0.92	positive regulation of biological process
GO:2000026	0.91	regulation of multicellular organismal development
GO:0071704	0.87	organic substance metabolic process
GO:0044238	0.87	primary metabolic process
GO:0044237	0.87	cellular metabolic process
GO:0044260	0.86	cellular macromolecule metabolic process
GO:0006325	0.85	chromatin organization
GO:0016570	0.83	histone modification
GO:0043985	0.81	histone H4-R3 methylation
GO:0010030	0.81	positive regulation of seed germination
GO:0044699	0.65	single-organism process
GO:0050794	0.63	regulation of cellular process
GO:0044763	0.61	single-organism cellular process
GO:0080090	0.59	regulation of primary metabolic process
GO:0060255	0.59	regulation of macromolecule metabolic process
GO:0031323	0.59	regulation of cellular metabolic process
GO:2000112	0.58	regulation of cellular macromolecule biosynthetic process
GO:0019219	0.58	regulation of nucleobase-containing compound metabolic process
GO:0006355	0.57	regulation of transcription, DNA-templated
GO:0044767	0.56	single-organism developmental process
GO:0006810	0.56	transport
GO:0048523	0.55	negative regulation of cellular process
GO:0045935	0.55	positive regulation of nucleobase-containing compound metabolic process
GO:0031328	0.55	positive regulation of cellular biosynthetic process
GO:0010604	0.55	positive regulation of macromolecule metabolic process
GO:0048856	0.54	anatomical structure development
GO:0044707	0.54	single-multicellular organism process
GO:0006950	0.54	response to stress
GO:0048584	0.53	positive regulation of response to stimulus
GO:0031324	0.53	negative regulation of cellular metabolic process
GO:0010605	0.53	negative regulation of macromolecule metabolic process
GO:0006954	0.53	inflammatory response
GO:2000113	0.52	negative regulation of cellular macromolecule biosynthetic process
GO:0060968	0.52	regulation of gene silencing
GO:0051716	0.52	cellular response to stimulus
GO:0051704	0.52	multi-organism process
GO:0048878	0.52	chemical homeostasis
GO:0045934	0.52	negative regulation of nucleobase-containing compound metabolic process
GO:0044765	0.52	single-organism transport
GO:0032269	0.52	negative regulation of cellular protein metabolic process
GO:0031399	0.52	regulation of protein modification process
GO:0030182	0.52	neuron differentiation
GO:0010941	0.52	regulation of cell death
GO:0010629	0.52	negative regulation of gene expression
GO:0010033	0.52	response to organic substance
GO:0009653	0.52	anatomical structure morphogenesis
GO:0006886	0.52	intracellular protein transport
GO:0006357	0.52	regulation of transcription from RNA polymerase II promoter
GO:2001222	0.51	regulation of neuron migration
GO:2001169	0.51	regulation of ATP biosynthetic process
GO:2000736	0.51	regulation of stem cell differentiation
GO:1905050	0.51	positive regulation of metallopeptidase activity
GO:1904683	0.51	regulation of metalloendopeptidase activity
GO:1903580	0.51	positive regulation of ATP metabolic process
GO:1903579	0.51	negative regulation of ATP metabolic process
GO:1903427	0.51	negative regulation of reactive oxygen species biosynthetic process
GO:1902893	0.51	regulation of pri-miRNA transcription from RNA polymerase II promoter
GO:1902593	0.51	single-organism nuclear import
GO:1901214	0.51	regulation of neuron death
GO:1900373	0.51	positive regulation of purine nucleotide biosynthetic process
GO:0098727	0.51	maintenance of cell number
GO:0097305	0.51	response to alcohol
GO:0090559	0.51	regulation of membrane permeability
GO:0071354	0.51	cellular response to interleukin-6
GO:0060964	0.51	regulation of gene silencing by miRNA
GO:0060148	0.51	positive regulation of posttranscriptional gene silencing
GO:0051198	0.51	negative regulation of coenzyme metabolic process
GO:0050795	0.51	regulation of behavior
GO:0050768	0.51	negative regulation of neurogenesis
GO:0048871	0.51	multicellular organismal homeostasis
GO:0048592	0.51	eye morphogenesis
GO:0046530	0.51	photoreceptor cell differentiation
GO:0044744	0.51	protein targeting to nucleus
GO:0044703	0.51	multi-organism reproductive process
GO:0042531	0.51	positive regulation of tyrosine phosphorylation of STAT protein
GO:0042516	0.51	regulation of tyrosine phosphorylation of Stat3 protein
GO:0042326	0.51	negative regulation of phosphorylation
GO:0042127	0.51	regulation of cell proliferation
GO:0040033	0.51	negative regulation of translation, ncRNA-mediated
GO:0033993	0.51	response to lipid
GO:0033500	0.51	carbohydrate homeostasis
GO:0030336	0.51	negative regulation of cell migration
GO:0017038	0.51	protein import
GO:0010950	0.51	positive regulation of endopeptidase activity
GO:0010728	0.51	regulation of hydrogen peroxide biosynthetic process
GO:0010727	0.51	negative regulation of hydrogen peroxide metabolic process
GO:0010677	0.51	negative regulation of cellular carbohydrate metabolic process
GO:0010001	0.51	glial cell differentiation
GO:0009895	0.51	negative regulation of catabolic process
GO:0008593	0.51	regulation of Notch signaling pathway
GO:0007631	0.51	feeding behavior
GO:0007417	0.51	central nervous system development
GO:0007049	0.51	cell cycle
GO:0007006	0.51	mitochondrial membrane organization
GO:0006839	0.51	mitochondrial transport
GO:0006110	0.51	regulation of glycolytic process
GO:0002526	0.51	acute inflammatory response

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	0.99	intracellular part
GO:0005634	0.97	nucleus
GO:0044422	0.74	organelle part
GO:0044446	0.73	intracellular organelle part
GO:0005737	0.70	cytoplasm
GO:0032991	0.65	macromolecular complex
GO:0044444	0.60	cytoplasmic part
GO:0005829	0.59	cytosol
GO:0044428	0.57	nuclear 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	0.066	3eabA	0.485	2.67	0.073	0.617	3.6.4.3	4,17,51
2	0.066	1cxzB	0.477	3.25	0.094	0.624	2.7.11.13	57,61
3	0.066	1wcrA	0.512	2.64	0.119	0.632	2.7.1.69	NA
4	0.066	2e2aA	0.512	2.99	0.100	0.669	2.7.1.69	NA
5	0.060	1ahpA	0.513	3.94	0.063	0.737	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:

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	3n9qA	0.598	3.33	0.088	0.850	0.18	III	complex1.pdb.gz	3,4,5,11,12,15,16
2	0.01	1lvkA	0.410	3.75	0.046	0.571	0.11	UUU	complex2.pdb.gz	48,49,50
3	0.01	1mmaA	0.441	4.53	0.062	0.639	0.11	ADP	complex3.pdb.gz	14,15,16,17
4	0.01	1rke0	0.503	4.26	0.042	0.804	0.11	III	complex4.pdb.gz	7,10,13,14
5	0.01	1d0xA	0.432	5.13	0.083	0.752	0.15	MNQ	complex5.pdb.gz	9,10,11,47,48,52
6	0.01	1mmnA	0.397	4.92	0.040	0.707	0.16	ANP	complex6.pdb.gz	43,44,46,47,48,49
7	0.01	1u6hA	0.498	4.30	0.034	0.820	0.23	III	complex7.pdb.gz	5,6,9,11,12,13,15,64
8	0.01	1jwyA	0.420	4.00	0.039	0.594	0.11	ADP	complex8.pdb.gz	48,49,51,52
9	0.01	1xwjA	0.492	4.31	0.034	0.812	0.32	III	complex9.pdb.gz	4,5,8,9,12,15
10	0.01	1w9jA	0.399	4.65	0.062	0.669	0.12	UUU	complex10.pdb.gz	48,53,54,55

	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.