D-I-TASSER P10600-D2

D-I-TASSER results for P10600-D2

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

Input Sequence in FASTA format

>P10600 (192 residues)
KFDMIQGLAEHNELAVCPKGITSKVFRFNVSSVEKNRTNLFRAEFRVLRVPNPSSKRNEQ
RIELFQILRPDEHIAKQRYIGGKNLPTRGTAEWLSFDVTDTVREWLLRRESNLGLEISIH
CPCHTFQPNGDILENIHEVMEIKFKGVDNEDDHGRGDLGRLKKQKDHHNPHLILMMIPPH
RLDNPGQGGQRK

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 160 180 \| \| \| \| \| \| \| \| \| KFDMIQGLAEHNELAVCPKGITSKVFRFNVSSVEKNRTNLFRAEFRVLRVPNPSSKRNEQRIELFQILRPDEHIAKQRYIGGKNLPTRGTAEWLSFDVTDTVREWLLRRESNLGLEISIHCPCHTFQPNGDILENIHEVMEIKFKGVDNEDDHGRGDLGRLKKQKDHHNPHLILMMIPPHRLDNPGQGGQRK
Prediction	CCCSSCCCCCCCCCCCCCCCCCSSSSSSSCCCCCCCCCHSHHHSSSSSSCCCCCCCCCCSSSSSSSSSCCCCCCCCCSSSSSSSSCCCCCCCSSSSSHHHHHHHHHHCCCCCCSSSSSSSCCCCCCCCCCCCCCCCCCCCSSSSSSCCCCCCCCCCCCCCCCCCCCCCCCSSSSSSCCCCCCCCCCHHHCCC
Confidence	987303660113566677887459999847889798310021201102447877787637999999644899986424651377315898716999718989999847898714999998289842456765677776402799860587765665310012332358987999834766677742110159
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 160 180 \| \| \| \| \| \| \| \| \| KFDMIQGLAEHNELAVCPKGITSKVFRFNVSSVEKNRTNLFRAEFRVLRVPNPSSKRNEQRIELFQILRPDEHIAKQRYIGGKNLPTRGTAEWLSFDVTDTVREWLLRRESNLGLEISIHCPCHTFQPNGDILENIHEVMEIKFKGVDNEDDHGRGDLGRLKKQKDHHNPHLILMMIPPHRLDNPGQGGQRK
Prediction	734314224554434543755412202020341366353033000200334456545452302002134578544332003233144544721231302400440264665421020102064444355544474565413030322455654444445526646645300000002235437454554658
	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

                   |                   |                   |                   |                   |                   |                   |                   |                   |

SS
Seq

CCCSSCCCCCCCCCCCCCCCCCSSSSSSSCCCCCCCCCHSHHHSSSSSSCCCCCCCCCCSSSSSSSSSCCCCCCCCCSSSSSSSSCCCCCCCSSSSSHHHHHHHHHHCCCCCCSSSSSSSCCCCCCCCCCCCCCCCCCCCSSSSSSCCCCCCCCCCCCCCCCCCCCCCCCSSSSSSCCCCCCCCCCHHHCCC
KFDMIQGLAEHNELAVCPKGITSKVFRFNVSSVEKNRTNLFRAEFRVLRVPNPSSKRNEQRIELFQILRPDEHIAKQRYIGGKNLPTRGTAEWLSFDVTDTVREWLLRRESNLGLEISIHCPCHTFQPNGDILENIHEVMEIKFKGVDNEDDHGRGDLGRLKKQKDHHNPHLILMMIPPHRLDNPGQGGQRK

4ycgA

0.13

0.10

3.43

1.00

DEthreader

SNIVRSF--SVEDAISTAAFFQKHILIFNI-SIPRH-EQITRAELRLYVSCQDSTHGLEGSMVVYDVLEDSETTGTKTFLVSQDIR---DEGWETLEVSSAVKRWVRADSNKNKLEVTVQSHRE------------CDTLDISVP-------------------GSKNLPFFVVFSNDRSNGT---------

4ycgA

0.11

0.09

3.35

1.36

SPARKS-K

ASNIVRSFSVEDAIAATEDFPQKHILIFNIS-IPRHE-QITRAELRLYVSCQNDVDGLEGSMVVYDVLEDSETWGTKTFLVSQDIR---DEGWETLEVSSAVKRWVRADTNKNKLEVTVQSHRESCDT-------------LDISVP----------------PGSKNLPFFVVFSNDRSNGTKETRLELKE

4ycgA

0.13

0.10

3.43

1.05

MapAlign

---VRSFSVEDAISTAADFPFQKHILIFNI-SI-PRHEQITRAELRLYVSCQNDTHGLEGSMVVYDVLTWDQATGTKTFLVSQDIRD---EGWETLEVSSAVKRWVRATTNKNKLEVTVQSHRESC-----------DTLDISV------------------PPGSKNLPFFVVFSNDRSNG----------

5hlyA2

0.20

0.14

4.51

0.98

CEthreader

--SEIITFAESGT--------ARKTLHFEISKEGSDLSVVERAEVWLFLKVPKANRRTKVTIRLFQQQKH---ERSELLLSEKVVDAR-KSTWHVFPVSSSIQRLLDQGKSSLDVRIACEQCQ-------------ESGASLVLLG---------------EEKEQSHRPFLLQARQS--------------

5ntuA2

0.20

0.15

4.67

1.29

MUSTER

TTETIITMPTEK------------CCFFKFSSKIQ-YNKVVKAQLWIYLRPVET--PTTVFVQILRLIKPMKDGTRYTGIRSLKLDMPGTGIWQSIDVKTVLQNWLAAPASNLGIEIKALDENGHDL-----------------------------AVTFPGPGEDGLNPFLEVKV-------TDTPKRSRR

3rjrA1

0.30

0.24

7.26

4.11

HHsearch

YAKEVTRVLMVESGNKFKGTPHSLYMLFNTSELREPV-LLSRAELRLLRLKLK----VEQHVELYQKYSQ----DSWRYLSNRLLAPSDSPEWLSFDVTGVVRQWLTRREAIEGFRLSAHCSCDSKDN----------TLHVEINGDL-------------ATIHGMNRPFLLLMATPLERAQH--------

5ntuA2

0.20

0.15

4.68

1.50

FFAS-3D

TTETIITMPTEK------------CCFFKFSSKIQYN-KVVKAQLWIYLRPVETP--TTVFVQILRLIKPMKDGTRYTGIRSLKLMNPGTGIWQSIDVKTVLQNWLAAPASNLGIEIKALDENGHDLAVTFP-----------------------------GPGEDGLNPFLEVKV------TDTPKRSRRD

3rjrA1

0.30

0.23

7.11

0.90

EigenThreader

PEAVLMVESGNQIYDKFKGTPHSLYMLFNTSELREAVPEPSRAELRLLRLK----LKVEQHVELYQKYSQDS----WRYLSNRLLAPSDSPEWLSFDVTGVVRQWLTRREAIEGFRLSAH----------CSCDN---TLHVEIN-----GDLATIH--------GMNRPFLLLMATPLERAQH--------

4ycgA

0.11

0.09

3.35

1.99

CNFpred

ASNIVRSFSVEDAISTAATPFQKHILIFNISIPR--HEQITRAELRLYVSCQNSTHGLEGSMVVYDVLEDSEATGTKTFLVSQDIRD---EGWETLEVSSAVKRWVRADSNKNKLEVTVQSHRESC-------------DTLDISVPPGS----------------KNLPFFVVFSNDRSNGTKETRLELKE

3rjrA

0.32

0.25

7.53

1.00

DEthreader

AKEVTRVLMVESNQIYFKGTPHSLYMLFNTSEREVPEPLLSRAELRLLRLKLK-V---EQHVELYQKYSQD---S-WRYLSNRLLAPSDSPEWLSFDVTGVVRQWLTRREAIEGFRLSAH---CSCD------VEI-NGDLATI--------------------HGMNRPFLLLMATPLERAQH-TQY----

(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	0.7587

(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	4ycgA	0.70	2.48	0.127	0.802	model1_4ycgA.pdb.gz
2	3rjrA	0.63	3.23	0.301	0.755	model1_3rjrA.pdb.gz
3	5ntuA2	0.62	2.72	0.183	0.719	model1_5ntuA2.pdb.gz
4	5hlyA	0.62	2.87	0.179	0.734	model1_5hlyA.pdb.gz
5	2inyA	0.53	4.24	0.106	0.745	model1_2inyA.pdb.gz
6	2obeA2	0.53	4.14	0.093	0.745	model1_2obeA2.pdb.gz
7	6ybaH	0.53	4.26	0.093	0.755	model1_6ybaH.pdb.gz
8	3ks7D1	0.53	3.23	0.094	0.677	model1_3ks7D1.pdb.gz
9	3zifA	0.52	4.32	0.097	0.776	model1_3zifA.pdb.gz
10	1pnfA	0.51	3.76	0.121	0.667	model1_1pnfA.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:0005102	1.00	receptor binding
GO:0005160	0.99	transforming growth factor beta receptor binding
GO:0005114	0.87	type II transforming growth factor beta receptor binding
GO:0034714	0.82	type III transforming growth factor beta receptor binding
GO:0042802	0.70	identical protein binding
GO:0034713	0.58	type I transforming growth factor beta receptor 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:0050794	0.99	regulation of cellular process
GO:0048518	0.99	positive regulation of biological process
GO:0044767	0.99	single-organism developmental process
GO:0009987	0.99	cellular process
GO:0080090	0.98	regulation of primary metabolic process
GO:0048583	0.98	regulation of response to stimulus
GO:0044763	0.98	single-organism cellular process
GO:0031325	0.98	positive regulation of cellular metabolic process
GO:0010604	0.98	positive regulation of macromolecule metabolic process
GO:0007165	0.98	signal transduction
GO:0007178	0.96	transmembrane receptor protein serine/threonine kinase signaling pathway
GO:0010556	0.92	regulation of macromolecule biosynthetic process
GO:0051239	0.86	regulation of multicellular organismal process
GO:0048523	0.86	negative regulation of cellular process
GO:0007179	0.86	transforming growth factor beta receptor signaling pathway
GO:2000026	0.85	regulation of multicellular organismal development
GO:0031324	0.84	negative regulation of cellular metabolic process
GO:0051240	0.83	positive regulation of multicellular organismal process
GO:0050896	0.83	response to stimulus
GO:0030278	0.83	regulation of ossification
GO:0016043	0.83	cellular component organization
GO:0010557	0.83	positive regulation of macromolecule biosynthetic process
GO:0009653	0.83	anatomical structure morphogenesis
GO:0051241	0.82	negative regulation of multicellular organismal process
GO:0051094	0.82	positive regulation of developmental process
GO:0048585	0.82	negative regulation of response to stimulus
GO:0045597	0.82	positive regulation of cell differentiation
GO:0010033	0.82	response to organic substance
GO:0009719	0.82	response to endogenous stimulus
GO:0051128	0.81	regulation of cellular component organization
GO:0045778	0.81	positive regulation of ossification
GO:0022603	0.81	regulation of anatomical structure morphogenesis
GO:0010720	0.81	positive regulation of cell development
GO:0006950	0.81	response to stress
GO:0002682	0.81	regulation of immune system process
GO:1901654	0.80	response to ketone
GO:0051130	0.80	positive regulation of cellular component organization
GO:0050776	0.80	regulation of immune response
GO:0048545	0.80	response to steroid hormone
GO:0044707	0.80	single-multicellular organism process
GO:0007435	0.80	salivary gland morphogenesis
GO:0002697	0.80	regulation of immune effector process
GO:0002683	0.80	negative regulation of immune system process
GO:0001817	0.80	regulation of cytokine production
GO:0045216	0.79	cell-cell junction organization
GO:0032570	0.79	response to progesterone
GO:0010936	0.79	negative regulation of macrophage cytokine production
GO:0010718	0.79	positive regulation of epithelial to mesenchymal transition
GO:2000112	0.71	regulation of cellular macromolecule biosynthetic process
GO:0019219	0.71	regulation of nucleobase-containing compound metabolic process
GO:0010468	0.71	regulation of gene expression
GO:0006355	0.70	regulation of transcription, DNA-templated
GO:0048584	0.65	positive regulation of response to stimulus
GO:0045937	0.65	positive regulation of phosphate metabolic process
GO:0032270	0.65	positive regulation of cellular protein metabolic process
GO:0009966	0.65	regulation of signal transduction
GO:0001932	0.65	regulation of protein phosphorylation
GO:0009967	0.64	positive regulation of signal transduction
GO:0001934	0.64	positive regulation of protein phosphorylation
GO:0048869	0.63	cellular developmental process
GO:0043408	0.63	regulation of MAPK cascade
GO:0010605	0.63	negative regulation of macromolecule metabolic process
GO:2000113	0.62	negative regulation of cellular macromolecule biosynthetic process
GO:0045934	0.62	negative regulation of nucleobase-containing compound metabolic process
GO:0045893	0.62	positive regulation of transcription, DNA-templated
GO:0030501	0.59	positive regulation of bone mineralization
GO:0051054	0.58	positive regulation of DNA metabolic process
GO:0048856	0.58	anatomical structure development
GO:0032967	0.58	positive regulation of collagen biosynthetic process
GO:0006275	0.58	regulation of DNA replication
GO:0001503	0.58	ossification
GO:0043932	0.57	ossification involved in bone remodeling
GO:0008156	0.57	negative regulation of DNA replication
GO:0042981	0.54	regulation of apoptotic process
GO:0042127	0.54	regulation of cell proliferation
GO:0070482	0.50	response to oxygen levels

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:0044421	1.00	extracellular region part
GO:0031012	0.73	extracellular matrix
GO:0005615	0.66	extracellular space
GO:0044464	0.62	cell part
GO:0044424	0.52	intracellular 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	0.060	2bbaA	0.487	3.37	0.048	0.641	2.7.10.1	10,48
2	0.060	1pmjX	0.462	4.17	0.053	0.667	3.2.1.78	48
3	0.060	1d3i1	0.464	4.46	0.056	0.693	3.6.1.15	NA
4	0.060	1sg3A	0.449	4.31	0.038	0.646	3.5.3.4	NA
5	0.060	2v5yA	0.461	3.52	0.030	0.609	3.1.3.48	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	0.02	1j5qB	0.514	3.97	0.090	0.703	0.44	UUU	complex1.pdb.gz	64,102,114,115
2	0.01	1m3yA	0.509	3.97	0.082	0.708	0.53	UUU	complex2.pdb.gz	80,114,115
3	0.01	1ga2A	0.485	4.32	0.053	0.698	0.43	BGC	complex3.pdb.gz	45,64,65,80,81,102,105,114

	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.