D-I-TASSER P01019-D2

D-I-TASSER results for P01019-D2

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

Input Sequence in FASTA format

>P01019 (202 residues)
SPTAVFGTLASLYLGALDHTADRLQAILGVPWKDKNCTSRLDAHKVLSALQAVQGLLVAQ
GRADSQAQLLLSTVVGVFTAPGLHLKQPFVQGLALYTPVVLPRSLDFTELDVAAEKIDRF
MQAVTGWKTGCSLMGASVDSTLAFNTYVHFQGLVLQGSYDLQDLLAQAELPAILHTELNL
QKLSNDRIRVGEVLNSIFFELE

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 160 180 200 \| \| \| \| \| \| \| \| \| \| SPTAVFGTLASLYLGALDHTADRLQAILGVPWKDKNCTSRLDAHKVLSALQAVQGLLVAQGRADSQAQLLLSTVVGVFTAPGLHLKQPFVQGLALYTPVVLPRSLDFTELDVAAEKIDRFMQAVTGWKTGCSLMGASVDSTLAFNTYVHFQGLVLQGSYDLQDLLAQAELPAILHTELNLQKLSNDRIRVGEVLNSIFFELE
Prediction	CCHHHHHHHHHHHHCCCCHHHHHHHHHHCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCCCSSSSSSSSSSSCCCCCCCHHHHHHHHHHHCHCCSSCCCCCCHHHHHHHHHHHHHHHHCCCCHHHCCCCCCCCSSSSSSCSSSCSSCCCCCCCHHHHHCCCCCCSSSCCSCCCCCCCCCCCHHHHHHHHHHHCCC
Confidence	9166999999999607853599999994999777654321026789999999999998633678986055553332210189882199999999996211211069999799999999999999768601206689987446442022333222678864244300455334421101112223796238899887775069
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 160 180 200 \| \| \| \| \| \| \| \| \| \| SPTAVFGTLASLYLGALDHTADRLQAILGVPWKDKNCTSRLDAHKVLSALQAVQGLLVAQGRADSQAQLLLSTVVGVFTAPGLHLKQPFVQGLALYTPVVLPRSLDFTELDVAAEKIDRFMQAVTGWKTGCSLMGASVDSTLAFNTYVHFQGLVLQGSYDLQDLLAQAELPAILHTELNLQKLSNDRIRVGEVLNSIFFELE
Prediction	4241011011102112445025203611514464553444443441252044025214545456743412011101011377061265015204611453304414164275026302510474074305520671345020000000202031555245354124544123222443504414375030141013232528
	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

                   |                   |                   |                   |                   |                   |                   |                   |                   |                   |

SS
Seq

CCHHHHHHHHHHHHCCCCHHHHHHHHHHCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCCCSSSSSSSSSSSCCCCCCCHHHHHHHHHHHCHCCSSCCCCCCHHHHHHHHHHHHHHHHCCCCHHHCCCCCCCCSSSSSSCSSSCSSCCCCCCCHHHHHCCCCCCSSSCCSCCCCCCCCCCCHHHHHHHHHHHCCC
SPTAVFGTLASLYLGALDHTADRLQAILGVPWKDKNCTSRLDAHKVLSALQAVQGLLVAQGRADSQAQLLLSTVVGVFTAPGLHLKQPFVQGLALYTPVVLPRSLDFTELDVAAEKIDRFMQAVTGWKTGCSLMGASVDSTLAFNTYVHFQGLVLQGSYDLQDLLAQAELPAILHTELNLQKLSNDRIRVGEVLNSIFFELE

6ssvA

0.14

0.13

4.57

1.33

DEthreader

CPLGILFTLGILLGGAQGKTGHQIGKAIRLKSTSNPFGAQEEMKSLYKELNDSLGS-EK--TF----EKVVRISTGLFVQRTHEIETSFNESIKNDF-KGELIPVNFLNRTSATLSINRWVDQQSNGLLEKFFMDDIPDTGMILVNVFYFRDFTLKNTLDLVQTLKSMGIVDLFNPAANLSGITHHQLYVDKFMQTNILEAT

6ssvA1

0.13

0.12

4.15

2.36

SPARKS-K

CPLGILFTLGILLGSAQGKTGHQIGKAIRLKSTSSSWNPFGAQEEMKSLYKELNDSLGSE-KTFDKEEKVVRISTGLFVQRTHEIETSFNESIKNDFK-GELIPVNFLNRTSATLSINRWVDQQSNGLLEKFMDDIPDDTGMILVNVFYFR----KNTLDLVQTLKSMGIVDLFNPAANLSGITHDQLYVDKFMQTN-----

4au2A

0.18

0.17

5.46

0.97

MapAlign

SPVVVASSLGLVSLGGKATTASQAKAVLSA-E-------QLRDEEVHAGLGELLRSLS---------NVTWKLGSRLYGPSSVSFAEDFVRSSKQHY-NCEHSKINFRDKRSALQSINEWAAQTTDGKLPEVTKDVERTDGALLVNAMFFKKGVVEVTHDLQKHLAGLGLTEAIDKKADLSRMSGKKLYLASVFHATAFEWD

4au2A

0.18

0.17

5.46

0.59

CEthreader

SPVVVASSLGLVSLGGKATTASQAKAVLSAEQ--------LRDEEVHAGLGELLRSLS---------NVTWKLGSRLYGPSSVSFAEDFVRSSKQHY-NCEHSKINFRDKRSALQSINEWAAQTTDGKLPEVTKDVERTDGALLVNAMFFKPHVVEVTHDLQKHLAGLGLTEAIDKKADLSRMSGKKLYLASVFHATAFEWD

2zv6B1

0.21

0.19

5.97

2.01

MUSTER

SPISITSALGMVLLGAKDNTAQQIKKVLHFDQV-------------HHQFQKLLTEFNK-----STDAYELKIANKLFGEKTYLFLQEYLDAIKKFYQTS-VESVDFAAPEESRKKINSWVESQTNEKIKNLIPNIGSNTTLVLVNAIYFKGK-VEESYDLKDTLRTMGMVDIFNGDADLSGMTGRGLVLSGVLHKAFVE--

4if8A1

0.19

0.17

5.59

1.59

HHsearch

SPLSISTAFSMLCLGAQDSTLDEIKQGFNFRKMPE--------KDLHEGFHYIIHELTQ-----KTQDLKLSIGNTLFIDQRLQPQRKFLEDAKNFYS-AETILTNFQNLEMAQKQINDFISQKTHGKINNLIENIDPGTVMLLANYIFFRH--MTGTFDLKKTLSYIGVSKIFEEHGDLTKIAPHSLKVGEAVHKAELK--

2zv6B1

0.18

0.16

5.17

2.35

FFAS-3D

SPISITSALGMVLLGAKDNTAQQIKKVLHFDQV----------------HHQFQKLLTEFNKSTDAYE--LKIANKLFGEKTYLFLQEYLDAIKKFYQTSVESVDFANAPEESRKKINSWVESQTNEKIKNLIPEIGSNTTLVLVNAIYFKGKVEESYDLKDTL-RTMGMVDIFNGDADLSGMTGSGLVLSGVLHKAFVE--

5inwA

0.22

0.19

6.10

1.30

EigenThreader

SPLSIASALGVVTAGANGSTRAELDTALGFK-----------SMKYFARLNGALY-----------KGFELMGKNVVFSKKGLWLYRQFTRTVAHLFK-SNVRSVDFGDSKNAVELMNAYIEKVTSKKFPDVISDVDTDTSLVIVNVIYFKGSWISVSYDLKAYLSAMGMSSMFSYGADLSRITGQKLHVDKITHKSVLHVN

5m3yA

0.98

0.95

26.63

1.73

CNFpred

SPTAVFGTLASLYLGALDHTADRLQAILGVPWKDKQCTSRLDAHKVLSALQAVQGLLVAQ-------QLLLSTVVGVFTAPGLHLKQPFVQGLALYTPVVLPRSLDFTELDVAAEKIDRFMQAVTGWKTGSSLMGASVDSTLAFNTYVHFQGKVLQGSYDLQDLLAQAELPAILHTELNLQKLSNDRIRVGEVLNSIFFELE

1ovaD

0.16

0.15

5.11

1.33

DEthreader

CPIAIMSALAMVYLGAKDSTRTQINKVVRFDKLFGDSIEAQCSVNVHSSLRDILNQITK-NDV-----YSFSLASRLYAEERYPILPEYLQCVKELY-RGGLEPINFQAADQARELINSWVESQTNGIIRNVLQSVDSQTAMVLVNAIVFKGMKMEEKYNLTSVLMAMGITDVFSSSANLSGISSAELKISQAVHAAHAEIN

(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	0.8594

(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	2wxwA	0.97	1.10	0.960	0.995	model1_2wxwA.pdb.gz
2	2wxxA	0.92	1.40	0.622	0.970	model1_2wxxA.pdb.gz
3	4if8A	0.80	2.40	0.187	0.921	model1_4if8A.pdb.gz
4	3fgqA	0.79	2.59	0.197	0.931	model1_3fgqA.pdb.gz
5	1ophA	0.78	2.63	0.206	0.931	model1_1ophA.pdb.gz
6	6ssvA	0.78	2.93	0.132	0.975	model1_6ssvA.pdb.gz
7	7rbwA	0.78	2.66	0.164	0.936	model1_7rbwA.pdb.gz
8	2ceoA	0.78	2.64	0.191	0.931	model1_2ceoA.pdb.gz
9	5hgcA	0.78	2.73	0.170	0.931	model1_5hgcA.pdb.gz
10	1yxaA	0.77	2.73	0.175	0.936	model1_1yxaA.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:0004867	1.00	serine-type endopeptidase inhibitor 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:0065007	0.96	biological regulation
GO:0050789	0.95	regulation of biological process
GO:0080090	0.94	regulation of primary metabolic process
GO:0060255	0.94	regulation of macromolecule metabolic process
GO:0050794	0.94	regulation of cellular process
GO:0048519	0.94	negative regulation of biological process
GO:0048523	0.93	negative regulation of cellular process
GO:0031323	0.93	regulation of cellular metabolic process
GO:0044699	0.91	single-organism process
GO:0050896	0.90	response to stimulus
GO:0050790	0.90	regulation of catalytic activity
GO:0048583	0.90	regulation of response to stimulus
GO:0032501	0.90	multicellular organismal process
GO:0009987	0.90	cellular process
GO:0065008	0.89	regulation of biological quality
GO:0044763	0.89	single-organism cellular process
GO:0051239	0.88	regulation of multicellular organismal process
GO:0048522	0.88	positive regulation of cellular process
GO:0032502	0.88	developmental process
GO:0023051	0.88	regulation of signaling
GO:0010646	0.88	regulation of cell communication
GO:0010468	0.88	regulation of gene expression
GO:0003008	0.88	system process
GO:2000026	0.87	regulation of multicellular organismal development
GO:0051240	0.87	positive regulation of multicellular organismal process
GO:0051171	0.87	regulation of nitrogen compound metabolic process
GO:0051128	0.87	regulation of cellular component organization
GO:0044767	0.87	single-organism developmental process
GO:0042127	0.87	regulation of cell proliferation
GO:0010941	0.87	regulation of cell death
GO:0010604	0.87	positive regulation of macromolecule metabolic process
GO:0007165	0.87	signal transduction
GO:1903053	0.86	regulation of extracellular matrix organization
GO:0051130	0.86	positive regulation of cellular component organization
GO:0051049	0.86	regulation of transport
GO:0050880	0.86	regulation of blood vessel size
GO:0048584	0.86	positive regulation of response to stimulus
GO:0045893	0.86	positive regulation of transcription, DNA-templated
GO:0043085	0.86	positive regulation of catalytic activity
GO:0043065	0.86	positive regulation of apoptotic process
GO:0030335	0.86	positive regulation of cell migration
GO:0022603	0.86	regulation of anatomical structure morphogenesis
GO:0008152	0.86	metabolic process
GO:0008016	0.86	regulation of heart contraction
GO:0007186	0.86	G-protein coupled receptor signaling pathway
GO:0002018	0.86	renin-angiotensin regulation of aldosterone production
GO:0051046	0.85	regulation of secretion
GO:0040008	0.85	regulation of growth
GO:0008217	0.85	regulation of blood pressure
GO:0051246	0.78	regulation of protein metabolic process
GO:0032268	0.77	regulation of cellular protein metabolic process
GO:0048585	0.72	negative regulation of response to stimulus
GO:0051094	0.71	positive regulation of developmental process
GO:0009968	0.71	negative regulation of signal transduction
GO:1902531	0.70	regulation of intracellular signal transduction
GO:0038166	0.70	angiotensin-activated signaling pathway
GO:2001238	0.69	positive regulation of extrinsic apoptotic signaling pathway
GO:2000379	0.69	positive regulation of reactive oxygen species metabolic process
GO:1903779	0.69	regulation of cardiac conduction
GO:1903598	0.69	positive regulation of gap junction assembly
GO:1901201	0.69	regulation of extracellular matrix assembly
GO:0090190	0.69	positive regulation of branching involved in ureteric bud morphogenesis
GO:0061098	0.69	positive regulation of protein tyrosine kinase activity
GO:0051387	0.69	negative regulation of neurotrophin TRK receptor signaling pathway
GO:0048146	0.69	positive regulation of fibroblast proliferation
GO:0045742	0.69	positive regulation of epidermal growth factor receptor signaling pathway
GO:0044237	0.69	cellular metabolic process
GO:0035813	0.69	regulation of renal sodium excretion
GO:0035556	0.69	intracellular signal transduction
GO:0019538	0.69	protein metabolic process
GO:0014873	0.69	response to muscle activity involved in regulation of muscle adaptation
GO:0014068	0.69	positive regulation of phosphatidylinositol 3-kinase signaling
GO:0010959	0.69	regulation of metal ion transport
GO:0010873	0.69	positive regulation of cholesterol esterification
GO:0010613	0.69	positive regulation of cardiac muscle hypertrophy
GO:0010595	0.69	positive regulation of endothelial cell migration
GO:0010535	0.69	positive regulation of activation of JAK2 kinase activity
GO:0001558	0.69	regulation of cell growth
GO:0080134	0.67	regulation of response to stress
GO:0016043	0.67	cellular component organization
GO:0032101	0.66	regulation of response to external stimulus
GO:0031347	0.66	regulation of defense response
GO:0002019	0.66	regulation of renal output by angiotensin
GO:0050727	0.65	regulation of inflammatory response
GO:0044707	0.65	single-multicellular organism process
GO:0010817	0.65	regulation of hormone levels
GO:0001819	0.65	positive regulation of cytokine production
GO:0048856	0.64	anatomical structure development
GO:0042445	0.64	hormone metabolic process
GO:0006950	0.63	response to stress
GO:0010605	0.62	negative regulation of macromolecule metabolic process
GO:1903532	0.60	positive regulation of secretion by cell
GO:0044092	0.60	negative regulation of molecular function
GO:0042756	0.60	drinking behavior
GO:0042310	0.60	vasoconstriction
GO:0022414	0.60	reproductive process
GO:0009628	0.60	response to abiotic stimulus
GO:0006939	0.60	smooth muscle contraction
GO:0048513	0.58	animal organ development
GO:0001822	0.57	kidney development
GO:1902632	0.54	positive regulation of membrane hyperpolarization
GO:0051336	0.52	regulation of hydrolase activity
GO:0045777	0.52	positive regulation of blood pressure
GO:0010629	0.50	negative regulation of gene expression

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:0005615	1.00	extracellular space

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	2jc4A	0.434	5.20	0.060	0.723	3.1.11.2	NA
2	0.060	2ewgA	0.456	4.25	0.066	0.663	2.5.1.10	23
3	0.060	2q3uA	0.460	5.61	0.034	0.772	3.5.3.12	NA
4	0.060	1cbgA	0.439	5.33	0.062	0.713	3.2.1.21	NA
5	0.060	1fpsA	0.434	4.37	0.101	0.629	2.5.1.1 2.5.1.10	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	0.04	3evjI	0.755	2.72	0.156	0.911	0.91	UUU	complex1.pdb.gz	14,86,92,181,182,184,185

	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.