D-I-TASSER P16234-D1

D-I-TASSER results for P16234-D1

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

Input Sequence in FASTA format

>P16234 (246 residues)
MGTSHPAFLVLGCLLTGLSLILCQLSLPSILPNENEKVVQLNSSFSLRCFGESEVSWQYP
MSEEESSDVEIRNEENNSGLFVTVLEVSSASAAHTGLYTCYYNHTQTEENELEGRHIYIY
VPDPDVAFVPLGMTDYLVIVEDDDSAIIPCRTTDPETPVTLHNSEGVVPASYDSRQGFNG
TFTVGPYICEATVKGKKFQTIPFNVYALKATSELDLEMEALKTVYKSGETIVVTCAVFNN
EVVDLQ

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 160 180 200 220 240 \| \| \| \| \| \| \| \| \| \| \| \| MGTSHPAFLVLGCLLTGLSLILCQLSLPSILPNENEKVVQLNSSFSLRCFGESEVSWQYPMSEEESSDVEIRNEENNSGLFVTVLEVSSASAAHTGLYTCYYNHTQTEENELEGRHIYIYVPDPDVAFVPLGMTDYLVIVEDDDSAIIPCRTTDPETPVTLHNSEGVVPASYDSRQGFNGTFTVGPYICEATVKGKKFQTIPFNVYALKATSELDLEMEALKTVYKSGETIVVTCAVFNNEVVDLQ
Prediction	CCCCCCSCSSSSSSSSCCSSSSCCCCCCSSSSCCCCSSSCCCCCSSSSSSCCCCSSSSSCCCCCCCCCCSSSSSSCCCCCSSSSSSSCCCCHHHCSSSSSSSSCCCCCSCCCSSSSSSSSSCCCCCCCSCCCCCCCSSSSSCCCSSSSSSSCCCCCCSSSSSSCCSSSCCCCCCCCCCSSSCCCSSSSSSSSSCCSSSSSSSSSSSSSCCCCCCSSSSCCCCCSSCCCCSSSSSSSSSCCCCCCCC
Confidence	998742012333422043799735789889827992899199419999984895689825654456663167641367613789998446845555899999747651123079999999778987510467776349994894499980438998669999899141476444224102314669999999899489978999999726988669982686288178149999999678888719
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 160 180 200 220 240 \| \| \| \| \| \| \| \| \| \| \| \| MGTSHPAFLVLGCLLTGLSLILCQLSLPSILPNENEKVVQLNSSFSLRCFGESEVSWQYPMSEEESSDVEIRNEENNSGLFVTVLEVSSASAAHTGLYTCYYNHTQTEENELEGRHIYIYVPDPDVAFVPLGMTDYLVIVEDDDSAIIPCRTTDPETPVTLHNSEGVVPASYDSRQGFNGTFTVGPYICEATVKGKKFQTIPFNVYALKATSELDLEMEALKTVYKSGETIVVTCAVFNNEVVDLQ
Prediction	853433000000011222213144243040316674230446440303041635040214435444564514444454442212020440346221302020323424545534230101033353221434344331203454403030304335230203257541424342342132334312020203366443313302020344353150404166331434450403030465442637
	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                 180                 200                 220                 240

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

SS
Seq

CCCCCCSCSSSSSSSSCCSSSSCCCCCCSSSSCCCCSSSCCCCCSSSSSSCCCCSSSSSCCCCCCCCCCSSSSSSCCCCCSSSSSSSCCCCHHHCSSSSSSSSCCCCCSCCCSSSSSSSSSCCCCCCCSCCCCCCCSSSSSCCCSSSSSSSCCCCCCSSSSSSCCSSSCCCCCCCCCCSSSCCCSSSSSSSSSCCSSSSSSSSSSSSSCCCCCCSSSSCCCCCSSCCCCSSSSSSSSSCCCCCCCC
MGTSHPAFLVLGCLLTGLSLILCQLSLPSILPNENEKVVQLNSSFSLRCFGESEVSWQYPMSEEESSDVEIRNEENNSGLFVTVLEVSSASAAHTGLYTCYYNHTQTEENELEGRHIYIYVPDPDVAFVPLGMTDYLVIVEDDDSAIIPCRTTDPETPVTLHNSEGVVPASYDSRQGFNGTFTVGPYICEATVKGKKFQTIPFNVYALKATSELDLEMEALKTVYKSGETIVVTCAVFNNEVVDLQ

7lbfD

0.97

0.85

23.70

1.56

SPARKS-K

--------------------------LPSILPNENEKVVQLNSSFSLRCFGESEVSWQYPMSSD----VEIRNEENNSGLFVTVLEVSSASAAHTGLYTCYYNHTQTEENELEGRHIYIYVPDPDVAFVPLGMTDYLVIVEDDDSAIIPCRTTDPETPVTLHNSEGVVPASYDSRQGFNGTFTVGPYICEATVKK-KFQTIPFNVYALKATSELDLEMEALKTVYKSGETIVVTCAVFNNEVLQWT

3mjgX

0.34

0.28

8.52

1.14

MUSTER

---------------------------LVVTPPGPELVLNVSSTFVLTCSGSAPVVWERMSQEPPQ-----EMAKAQDGTFSSVLTLTNLTGLDTGEYFCTHND-------DERKRLYIFVPDPTVGFLPNDAEELFIFLTEITEITIPCRVTDPQLVVTLHEKKGDVPVPYDHQRGFSGIFEDRSYICKTTIGDREVDSDAYYVYRLQVSS-INVSVNAVQTVVRQGENITLMCIVIGNEVVNFE

7lbfD

0.99

0.86

24.03

1.93

FFAS-3D

---------------------------PSILPNENEKVVQLNSSFSLRCFGESEVSWQYPMSSD----VEIRNEENNSGLFVTVLEVSSASAAHTGLYTCYYNHTQTEENELEGRHIYIYVPDPDVAFVPLGMTDYLVIVEDDDSAIIPCRTTDPETPVTLHNSEGVVPASYDSRQGFNGTFTVGPYICEATVKK-KFQTIPFNVYALKATSELDLEMEALKTVYKSGETIVVTCAVFNNEVVDLQ

4liqE

0.27

0.22

6.73

2.55

CNFpred

--------------------------IPVIEPSVPELVVKPGATVTLRCVGNGSVEWDGPPSPHWTLYS---------DGSSSILSTNNATFQNTGTYRCTEPG---------SAAIHLYVKDPARPWNVL---AQEVVVFEDQDALLPCLLTDPEAGVSLVRV-RHTNYSFSPWHGFTIH-QSQDYQCSALMGGRKVMSISIRLKVQKVIGPPALTLVPAELVRIRGEAAQIVCSASSVVNFDVF

5lf5A

0.13

0.11

3.65

1.00

DEthreader

----PKNYPPVVHESFRSLLLLDIVNTPNIVVPP--EVVAG-TEVEVSCMVPPELSWLGH-E---GLGEPTVLGRLRTWVQVSLLHF-VPTREANGHRLGCQAAFPNTTLQFEGYASLDVKY-P-PVIVEMN-S-SVEAIEGSHVSLLCGADSNPPPLLTWMRDG-MVLREAVAKSLYLDLEVEDVYACLAENAYG-QDNRTVELSVMYA----------------------------ENQY----

3mjgX

0.33

0.27

8.19

1.38

SPARKS-K

---------------------------LVVTPPGPELVLNVSSTFVLTCSGSAPVVWERMSQEPP-----QEMAKAQDGTFSSVLTLTNLTGLDTGEYFCTHNDDER-------KRLYIFVPDPTVGFLPNDAEELFIFLTEITEITIPCRVTDPQLVVTLHEKKGALPVPYDHQRGFSGIFEDRSYICKTTIGDREVDSDAYYVYRLQVS-SINVSVNAVQTVVRQGENITLMCIVIGNEVVNFE

4hjjH

0.11

0.09

3.36

0.47

MapAlign

------------------------EVTLRESG---PALVKPTQTLTLTCTFSMGVSWIRQPPGKALEWLTISKD---TSKNQVVLTMTNMDPVDTATYYCARRGI--RSAMDYWGGTTVTVSSPEVQLVQ----SGTEVKKPGESLKISCKGSGTSYWIGWVRQMEWMQVTISATAFLQWSLDTAMYYCARVGSTFDIWGQGTMVTVSS-ASTKGPSVFP--LAPSGTAALGCLVKDYFPLYSLS-

7lbfD

1.00

0.87

24.36

0.56

CEthreader

--------------------------LPSILPNENEKVVQLNSSFSLRCFGESEVSWQYPMSS----DVEIRNEENNSGLFVTVLEVSSASAAHTGLYTCYYNHTQTEENELEGRHIYIYVPDPDVAFVPLGMTDYLVIVEDDDSAIIPCRTTDPETPVTLHNSEGVVPASYDSRQGFNGTFTVGPYICEATVK-KKFQTIPFNVYALKATSELDLEMEALKTVYKSGETIVVTCAVFNNEVVDLQ

4bskA

0.26

0.17

5.38

1.00

MUSTER

-------------------------TPPTLNITEESHVIDTGDSLSISCRGQHPLEWAWPGAQEAPATGDK----DSERPYCKVLLLHEVHANDTGSYVCYYTA----------ASSYVFVRDFEQPFINKPDT---LLVNRKDAMWVPCLVSIPGLNVTLRSQSSVLWPVWDDRRGMLVSHDALYLQCETTWQD--FLSNPFLVHI---------------------------------------

3b43A

0.11

0.10

3.50

0.54

HHsearch

-----------------------AMEPPYFIEPLEHVEAAIGEPITLQCKVDGRIAWYKEHTKLRS---APAYK-MQFKNNVASLVINKVDHSDVGEYTCKAENSVGA----VASSAVLVIKERKPPSFARKLK--DVHETLGFPVAFECRINSEPLQVSWYKDGLDDANQFIHNATLQILSHVGQYNCSASNPLGTA-SSSAKLTLSEHEVPPFFDLKPVSVDLALGESGTFKCHVTTAPKITWA

(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	0.7578

(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	7lbfD	0.78	2.30	0.939	0.862	model1_7lbfD.pdb.gz
2	3mjgX	0.64	2.09	0.290	0.699	model1_3mjgX.pdb.gz
3	5t89X	0.62	2.40	0.234	0.695	model1_5t89X.pdb.gz
4	4bskA	0.61	1.95	0.258	0.663	model1_4bskA.pdb.gz
5	4liqE	0.60	2.87	0.236	0.699	model1_4liqE.pdb.gz
6	3dmkA	0.59	4.05	0.075	0.797	model1_3dmkA.pdb.gz
7	4dkdC	0.59	2.70	0.235	0.683	model1_4dkdC.pdb.gz
8	3ejjX	0.56	2.80	0.211	0.667	model1_3ejjX.pdb.gz
9	2e9wB	0.56	2.99	0.197	0.679	model1_2e9wB.pdb.gz
10	2o26X	0.56	3.04	0.195	0.671	model1_2o26X.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:0016740	0.92	transferase activity
GO:0004713	0.91	protein tyrosine kinase activity
GO:0004888	0.87	transmembrane signaling receptor activity
GO:0004714	0.86	transmembrane receptor protein tyrosine kinase activity
GO:0005021	0.56	vascular endothelial growth factor-activated receptor 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	0.98	single-organism process
GO:0032502	0.94	developmental process
GO:0065007	0.93	biological regulation
GO:0009987	0.93	cellular process
GO:0050789	0.92	regulation of biological process
GO:0044767	0.91	single-organism developmental process
GO:0050794	0.85	regulation of cellular process
GO:0044763	0.83	single-organism cellular process
GO:0008152	0.83	metabolic process
GO:0071704	0.82	organic substance metabolic process
GO:0044260	0.81	cellular macromolecule metabolic process
GO:0044238	0.81	primary metabolic process
GO:0048518	0.78	positive regulation of biological process
GO:0007165	0.78	signal transduction
GO:0048522	0.77	positive regulation of cellular process
GO:0007166	0.77	cell surface receptor signaling pathway
GO:0007169	0.76	transmembrane receptor protein tyrosine kinase signaling pathway
GO:0006464	0.76	cellular protein modification process
GO:0048856	0.75	anatomical structure development
GO:0048583	0.75	regulation of response to stimulus
GO:0019222	0.75	regulation of metabolic process
GO:0006468	0.75	protein phosphorylation
GO:0080090	0.74	regulation of primary metabolic process
GO:0060255	0.74	regulation of macromolecule metabolic process
GO:0051239	0.74	regulation of multicellular organismal process
GO:0031323	0.74	regulation of cellular metabolic process
GO:0009966	0.74	regulation of signal transduction
GO:0048584	0.73	positive regulation of response to stimulus
GO:0031325	0.73	positive regulation of cellular metabolic process
GO:0010604	0.73	positive regulation of macromolecule metabolic process
GO:0009967	0.72	positive regulation of signal transduction
GO:0001934	0.72	positive regulation of protein phosphorylation
GO:0050896	0.70	response to stimulus
GO:0043410	0.70	positive regulation of MAPK cascade
GO:0009653	0.66	anatomical structure morphogenesis
GO:0006928	0.66	movement of cell or subcellular component
GO:0016477	0.64	cell migration
GO:0065008	0.60	regulation of biological quality
GO:0050793	0.60	regulation of developmental process
GO:0042221	0.60	response to chemical
GO:0016043	0.59	cellular component organization
GO:0018108	0.58	peptidyl-tyrosine phosphorylation
GO:0070887	0.57	cellular response to chemical stimulus
GO:0035556	0.56	intracellular signal transduction
GO:0048869	0.54	cellular developmental process
GO:0010033	0.53	response to organic substance
GO:0022414	0.52	reproductive process
GO:0006950	0.52	response to stress
GO:0051128	0.51	regulation of cellular component organization
GO:0048513	0.51	animal organ development
GO:0046777	0.51	protein autophosphorylation
GO:0022603	0.51	regulation of anatomical structure morphogenesis
GO:0048519	0.50	negative regulation of biological process
GO:0044702	0.50	single organism reproductive 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	1.00	cell part
GO:0044424	0.86	intracellular part
GO:0016020	0.83	membrane
GO:0005886	0.75	plasma membrane
GO:0043226	0.70	organelle
GO:0043229	0.69	intracellular organelle
GO:0043227	0.69	membrane-bounded organelle
GO:0043231	0.68	intracellular membrane-bounded organelle
GO:0044425	0.62	membrane part
GO:0044459	0.60	plasma membrane part
GO:0005634	0.58	nucleus
GO:0031224	0.54	intrinsic component of membrane
GO:0031226	0.53	intrinsic component 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	0.287	3mjgX	0.643	2.09	0.290	0.699	2.7.10.1	128,137,160,166,172,180,182,188
2	0.060	2fhbA	0.391	5.99	0.045	0.683	3.2.1.41	NA
3	0.060	2z8gB	0.393	5.03	0.036	0.585	3.2.1.57	NA
4	0.060	3l4uA	0.412	5.51	0.039	0.654	3.2.1.20 3.2.1.3	113
5	0.060	1n8zA	0.392	4.56	0.086	0.528	2.7.10.1	99

	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	0.10	2o262	0.557	3.04	0.195	0.671	0.38	III	complex1.pdb.gz	138,184,185,201,203,205

	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.