D-I-TASSER P09603-D2

D-I-TASSER results for P09603-D2

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

Input Sequence in FASTA format

>P09603 (302 residues)
DVVTKPDCNCLYPKAIPSSDPASVSPHQPLAPSMAPVAGLTWEDSEGTEGSSLLPGEQPL
HTVDPGSAKQRPPRSTCQSFEPPETPVVKDSTIGGSPQPRPSVGAFNPGMEDILDSAMGT
NWVPEEASGEASEIPVPQGTELSPSRPGGGSMQTEPARPSNFLSASSPLPASAKGQQPAD
VTGTALPRVGPVRPTGQDWNHTPQKTDHPSALLRDPPEPGSPRISSLRPQGLSNPSTLSA
QPQLSRSHSSGSVLPLGELEGRRSTRDRRSPAEPEGGPASEGAARPLPRFNSVPLTDTGH
ER

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 160 180 200 220 240 260 280 300 \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| DVVTKPDCNCLYPKAIPSSDPASVSPHQPLAPSMAPVAGLTWEDSEGTEGSSLLPGEQPLHTVDPGSAKQRPPRSTCQSFEPPETPVVKDSTIGGSPQPRPSVGAFNPGMEDILDSAMGTNWVPEEASGEASEIPVPQGTELSPSRPGGGSMQTEPARPSNFLSASSPLPASAKGQQPADVTGTALPRVGPVRPTGQDWNHTPQKTDHPSALLRDPPEPGSPRISSLRPQGLSNPSTLSAQPQLSRSHSSGSVLPLGELEGRRSTRDRRSPAEPEGGPASEGAARPLPRFNSVPLTDTGHER
Prediction	CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
Confidence	96668887888988888888888899899999888888888888888888888988889988899887889999988988999899989899999999999988999988887777778888887888888899989998889888898988889999988988999889998778999888889988999899988878898888898889999889999988999988889998999899999889998879988888888888899987878888887767898888888876788899
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 160 180 200 220 240 260 280 300 \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| DVVTKPDCNCLYPKAIPSSDPASVSPHQPLAPSMAPVAGLTWEDSEGTEGSSLLPGEQPLHTVDPGSAKQRPPRSTCQSFEPPETPVVKDSTIGGSPQPRPSVGAFNPGMEDILDSAMGTNWVPEEASGEASEIPVPQGTELSPSRPGGGSMQTEPARPSNFLSASSPLPASAKGQQPADVTGTALPRVGPVRPTGQDWNHTPQKTDHPSALLRDPPEPGSPRISSLRPQGLSNPSTLSAQPQLSRSHSSGSVLPLGELEGRRSTRDRRSPAEPEGGPASEGAARPLPRFNSVPLTDTGHER
Prediction	83344271414415523476256454664654454445545455566465454336743465555644655446544764545654647754566445454455444354654465535454435645474565434676644445367554546455457445564445464664425745755456554452665446444664644564465465555464354656647545544654743664455444357527576446656435636756457436424562542434543578
	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                 260                 280                 300

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

SS
Seq

CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
DVVTKPDCNCLYPKAIPSSDPASVSPHQPLAPSMAPVAGLTWEDSEGTEGSSLLPGEQPLHTVDPGSAKQRPPRSTCQSFEPPETPVVKDSTIGGSPQPRPSVGAFNPGMEDILDSAMGTNWVPEEASGEASEIPVPQGTELSPSRPGGGSMQTEPARPSNFLSASSPLPASAKGQQPADVTGTALPRVGPVRPTGQDWNHTPQKTDHPSALLRDPPEPGSPRISSLRPQGLSNPSTLSAQPQLSRSHSSGSVLPLGELEGRRSTRDRRSPAEPEGGPASEGAARPLPRFNSVPLTDTGHER

5jcss

0.09

3.37

1.40

SPARKS-K

LKAINNNWPLVLVGPSNSGKLASILGPRVDVFSM----------NSDIDSMDILGG---YEQVDLTRQISYITEELTNIVREISMNMKLSPNATAILNNIVTPEKFQDFRNRFNRFFSHLEGHPLLKTMSMNIEKMTEIITKEASVKDGMLVKAVEKGHSQEDGQPRVLKPHPNDELHSRSTAFDRLTLGFELGENIDFVSIDDGIKKIKLNEPDMSIPLKHYVPSYLSRPCIFAQVHDILLLSDEEPIEESLIPISHLEVGKWANNVLNCTEYSEKKIAERLYVFITFLTDMGVLEKINNL

2oajA

0.07

2.95

1.03

MapAlign

----TPRYSITSYEGMKNYYANPKQMKIFPLPTNVPIVNILPIPRQSPYFAGCHNPGLILLILGNGEIETVRTKRQKLPAEYGTAFITGHSNGSVRIYDASHGDIQDAVDKISFAAETLELAVSIETGDVVVGIAYAAGSLMLIDRRGPAIIYMENIREISGAQSACVTCIEFVIMEYGDDGYSSILMVCGTDMGEVITYNVTSKGPIHKIDAFSKETKSSCLATIPKMQNLSKGLCIPGIVLITGFDDIRLITLGKSKSFKYPLAATGLSYISTVEKNNDRKNLTVIITLEINGHLRVFTI

2nbiA

0.13

4.57

1.05

MUSTER

NPSSQPS-ECADVLEECPIDECFLPYSDASRPPSCLSFGRPDCDVLPTPQNINCPRCCATECRPDNPMFTPSPDGSPPICSPTMLPTNQPTPPEPSSAPSDCGEVIECPLDTCFLPTSDPARPTAVGRPDCDVLPFPNNLGCPACCPFECSPDNPMFTPSPDGSPPNCSPTMLPTPQPSTPTVITSPAPSSQPSQAEVIEQCPPYGDSSRPLDCTDPAVNRPDCDVLPPQNINCPACCAFECR--PDNPMFTPSPDGSPPICSPTMMPSPEPSSQPSDCGEVIEECPIDACFLPKSDSARPP

5gyyA

0.08

3.23

0.61

CEthreader

TLVSPGNIFELGFFRTNSRWYLGMWYKKLSGRTYDNPLSNSIGTLKISNMNLVLLDHSNKSVWSTNLTRENVRSPVVAELLANGNFVVRDPSGFLWQSFDYPTDTLLPEMKLGYDLKTGLNRFLVSWRSSDDPSSGDFSYKLDIQ---RGLPEFYTFKDNTLVHRTGPWNGIRFSGIPEEQQLSYMVYNFTENSEEVAYTFLVTNNSIYSRLTINFSGFFERLTWTPSLVIWNPIWSSPASFQCDPYMICGPGSYCDVNTLPLCNCIQGFKPLNVQEWDMRDHTRGCIRRTRLSCRGDGFTR

5jhqA

0.05

2.43

0.60

EigenThreader

AANVNAKDGANVHARDDGGLIPLHNACSFGHARDNWNYTPLHEAAIKGKALDLADPSAKAVLTGEYKTPLNVNCHASDGRKSTPLHLAAGYNRVRIVADVHAKDKGGLVPLHNACSYGHYEVTELLLKHGACVNAMDLWQFTPLHEAASKNRADPTLVNYEFKGHSLLQAAREADLAKVKKTLALEIINFKQPQSHETALHCAVASLHPKRKQVTELLLRKGANVNEKNKDFMTPLHVAAERAHNDVMEVLHKHGAKMNALDTLGQTALHRAALAGHLQTCRLLLSYGSDPSIISLQGFTAA

2xd8A

0.13

4.34

0.61

FFAS-3D

---GATDKYALYLKLF-SGEMFKGFQHETIARDLVTKRTLKNGKSGRMTSSFHTPGTPILGNADKAPPVAEKTIVMDDLLISSAFVYDLDETLAHYELRGEISKKIGYALAEKYDRLIFRSITRGARSASPVSATNFVEPGGTQIRVGSGTNESDAFTANGLVNRDVQGSALQSGNGVIEIAGIHIMNIPFLGKYGVKYGGTTGETSPGNLGSHIGPTPENANATGGVNNDYGTNAELGAKSCIFQKEAAGVVEAIGQVQVTNGDVSVIYQGDVILGRMAMGADNPAA--------------

6ezoE

0.10

3.58

1.40

SPARKS-K

--MEFQAVVMAVGGGSRMTDLTSSIPKPLLPVGNKPLYPLNLLERVGFEEVIVVTTRDVQKALCAEFKMKMKPDIV--CIPDDADMGTADSKLKTDSCDLITDVALHEVVDLFRAMLMRKRDFIGVDSTGKRLLFMANEADLDEELVIKGSILQKHPRIRFHLKKYIVDFLMENGSITSELIPYLVRKVHIMKEGLCSRVSTLGLYMEANRQVPKLLSSAQIVSKHLVGVDIGPETQIGEKSSIKRSVIGSSCLIKDRVTITNCLLMNSEGSNIQGSVICNNAIEKGADIKDCLIGSGQRIE

1wygA

0.08

0.06

2.25

0.67

DEthreader

----LGLCGTVCTITGYRP-----------------------QLFQ-E-----VPKDQDMVGRP-LPHLAANMQGEAVYCDRLSLRLVTAKFVC-VADIAVLFVSTMTQFVRVRMGGFGGFRGFGGPQGMGISFTLPFLNQGGGTSTNVPNT-SPTAA-SASADLNGQGVYEA-CQTILKRLEPFK--------------WVMDAYSAVSLSATGFY------------FHYFSYGVAFVQGLGLEIPA-GEPPLFLASSIFFAIKDAIRAARAQHGDNAKQ----------LDSPA-----

5gyyA

0.06

2.40

0.89

MapAlign

--GFFRTNSRWYLGMWYKKLSGRTYVWVANRDNPLSNSIGTLKISNMNLVLLDHSNKSVWSTNLTRENV-------------RSPVVAELLANGNFVVRDPSGFLWQSFDYPTDTLLPEMKLGYDLKTGLNRFLVSGDFSYKLDIQRGLPEFYTFKDNTLVHRTGPWNGIRFSGIPEEQQLSYMVYNFTENSEEVAYTFSRLTINFSGFFERLTWTPSLVIWNPIWSSPASFQCDPYMICGPGSYCDVNTLPLC----------NCIQGFKPLNVQEWDMRDHTRGCIRRT-----------

2nbiA1

0.12

4.13

1.04

MUSTER

NPSSQPS-ECADVLEECPIDECFLPYSDASRPPSCLSFGRPDCDVLPTPQNINCPRCCATECRPDNPMFTPSPDGSPPICSPTMLPTNQPTPPEPSSAPSDCGEVIECPLDTCFLPTSDPARPTAVGRPDCDVLPFPNNLGCPACCPFECSPDNPTPSPDGSPPNCSPTMLPTPQPSTPTVITSPAPSSQPSQCAEVIEQCPIDECFLPYGDSSRPLDCTDPAVNRPDCDVLPTPQNINCPACCAFECRPDNPMFTPSPDGSPPSPTMMPSPEPSSQPSDCGEVIEECPIDALPKSDSARPP

(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	0.469

(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	5mz61	0.44	6.50	0.034	0.768	model1_5mz61.pdb.gz
2	1kb0A	0.43	6.29	0.045	0.709	model1_1kb0A.pdb.gz
3	5l56A	0.42	6.36	0.060	0.715	model1_5l56A.pdb.gz
4	5wlcLH	0.42	6.70	0.041	0.729	model1_5wlcLH.pdb.gz
5	2eabA	0.42	6.46	0.026	0.712	model1_2eabA.pdb.gz
6	7bwmA	0.41	6.19	0.056	0.692	model1_7bwmA.pdb.gz
7	6pcvA	0.41	6.23	0.063	0.692	model1_6pcvA.pdb.gz
8	6rutB1	0.41	6.08	0.043	0.666	model1_6rutB1.pdb.gz
9	3w37A	0.41	5.95	0.078	0.672	model1_3w37A.pdb.gz
10	4wjlA	0.41	6.64	0.039	0.695	model1_4wjlA.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:0042803	1.00	protein homodimerization activity
GO:0005102	0.78	receptor binding
GO:0005126	0.75	cytokine receptor binding
GO:0008083	0.73	growth factor activity
GO:0005157	0.73	macrophage colony-stimulating factor receptor binding
GO:0005125	0.73	cytokine 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:0044767	1.00	single-organism developmental process
GO:0030316	1.00	osteoclast differentiation
GO:0008283	1.00	cell proliferation
GO:0065007	0.86	biological regulation
GO:0050789	0.86	regulation of biological process
GO:0050794	0.83	regulation of cellular process
GO:0048518	0.79	positive regulation of biological process
GO:0080090	0.77	regulation of primary metabolic process
GO:0060255	0.77	regulation of macromolecule metabolic process
GO:0048522	0.77	positive regulation of cellular process
GO:0031323	0.77	regulation of cellular metabolic process
GO:0031325	0.76	positive regulation of cellular metabolic process
GO:0010604	0.76	positive regulation of macromolecule metabolic process
GO:0051239	0.75	regulation of multicellular organismal process
GO:0048583	0.75	regulation of response to stimulus
GO:0007165	0.75	signal transduction
GO:0001932	0.75	regulation of protein phosphorylation
GO:0051240	0.74	positive regulation of multicellular organismal process
GO:0048856	0.74	anatomical structure development
GO:0010628	0.74	positive regulation of gene expression
GO:0009967	0.74	positive regulation of signal transduction
GO:0001934	0.74	positive regulation of protein phosphorylation
GO:1902107	0.73	positive regulation of leukocyte differentiation
GO:0051338	0.73	regulation of transferase activity
GO:0050769	0.73	positive regulation of neurogenesis
GO:0045785	0.73	positive regulation of cell adhesion
GO:0043085	0.73	positive regulation of catalytic activity
GO:0032879	0.73	regulation of localization
GO:0032101	0.73	regulation of response to external stimulus
GO:0008284	0.73	positive regulation of cell proliferation
GO:0007167	0.73	enzyme linked receptor protein signaling pathway
GO:1904141	0.72	positive regulation of microglial cell migration
GO:1902228	0.72	positive regulation of macrophage colony-stimulating factor signaling pathway
GO:0045860	0.72	positive regulation of protein kinase activity
GO:0045672	0.72	positive regulation of osteoclast differentiation
GO:0045657	0.72	positive regulation of monocyte differentiation
GO:0045651	0.72	positive regulation of macrophage differentiation
GO:0032946	0.72	positive regulation of mononuclear cell proliferation
GO:0030225	0.72	macrophage differentiation
GO:0010759	0.72	positive regulation of macrophage chemotaxis
GO:0010744	0.72	positive regulation of macrophage derived foam cell differentiation
GO:0007169	0.72	transmembrane receptor protein tyrosine kinase signaling pathway
GO:0003006	0.72	developmental process involved in reproduction
GO:0001954	0.72	positive regulation of cell-matrix adhesion
GO:0009653	0.58	anatomical structure morphogenesis
GO:0032501	0.57	multicellular organismal process
GO:0044707	0.56	single-multicellular organism 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:0005615	1.00	extracellular space
GO:0044464	0.90	cell part
GO:0044424	0.86	intracellular part
GO:0044444	0.79	cytoplasmic part
GO:0043226	0.78	organelle
GO:0043227	0.77	membrane-bounded organelle
GO:0032991	0.76	macromolecular complex
GO:0043234	0.75	protein complex
GO:0070062	0.73	extracellular exosome
GO:1990682	0.72	CSF1-CSF1R complex
GO:0048471	0.72	perinuclear region of cytoplasm
GO:0016020	0.54	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	0.060	3cuzA	0.384	6.51	0.037	0.662	2.3.3.9	NA
2	0.060	2vdcF	0.374	6.77	0.044	0.666	1.4.1.13	NA
3	0.060	2sqcA	0.380	6.42	0.026	0.646	5.4.99.17	NA
4	0.060	1w6sC	0.392	6.64	0.048	0.679	1.1.99.8	NA
5	0.060	1kv9A	0.383	6.52	0.039	0.669	1.1.99.-	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:

No Binding sites was predicted

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

	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.