D-I-TASSER P17535-D1

D-I-TASSER results for P17535-D1

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

Input Sequence in FASTA format

>P17535 (347 residues)
METPFYGDEALSGLGGGASGSGGSFASPGRLFPGAPPTAAAGSMMKKDALTLSLSEQVAA
ALKPAAAPPPTPLRADGAPSAAPPDGLLASPDLGLLKLASPELERLIIQSNGLVTTTPTS
SQFLYPKVAASEEQEFAEGFVKALEDLHKQNQLGAGAAAAAAAAAAGGPSGTATGSAPPG
ELAPAAAAPEAPVYANLSSYAGGAGGAGGAATVAFAAEPVPFPPPPPPGALGPPRLAALK
DEPQTVPDVPSFGESPPLSPIDMDTQERIKAERKRLRNRIAASKCRKRKLERISRLEEKV
KTLKSQNTELASTASLLREQVAQLKQKVLSHVNSGCQLLPQHQVPAY

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 160 180 200 220 240 260 280 300 320 340 \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| METPFYGDEALSGLGGGASGSGGSFASPGRLFPGAPPTAAAGSMMKKDALTLSLSEQVAAALKPAAAPPPTPLRADGAPSAAPPDGLLASPDLGLLKLASPELERLIIQSNGLVTTTPTSSQFLYPKVAASEEQEFAEGFVKALEDLHKQNQLGAGAAAAAAAAAAGGPSGTATGSAPPGELAPAAAAPEAPVYANLSSYAGGAGGAGGAATVAFAAEPVPFPPPPPPGALGPPRLAALKDEPQTVPDVPSFGESPPLSPIDMDTQERIKAERKRLRNRIAASKCRKRKLERISRLEEKVKTLKSQNTELASTASLLREQVAQLKQKVLSHVNSGCQLLPQHQVPAY
Prediction	CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHCCCC
Confidence	99987774100256778788777788876567888776544444456667878788764445655578887655666655567545578966344667898403321025788789999877348887776543334454321002455677899887788888888888777778888777777788887644556677888888888776677888878888998766777766766667765567777677766788882146899999999999999999999999999999999999999999999999999999999999999995489702466510249
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 160 180 200 220 240 260 280 300 320 340 \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| METPFYGDEALSGLGGGASGSGGSFASPGRLFPGAPPTAAAGSMMKKDALTLSLSEQVAAALKPAAAPPPTPLRADGAPSAAPPDGLLASPDLGLLKLASPELERLIIQSNGLVTTTPTSSQFLYPKVAASEEQEFAEGFVKALEDLHKQNQLGAGAAAAAAAAAAGGPSGTATGSAPPGELAPAAAAPEAPVYANLSSYAGGAGGAGGAATVAFAAEPVPFPPPPPPGALGPPRLAALKDEPQTVPDVPSFGESPPLSPIDMDTQERIKAERKRLRNRIAASKCRKRKLERISRLEEKVKTLKSQNTELASTASLLREQVAQLKQKVLSHVNSGCQLLPQHQVPAY
Prediction	87440234312423444444443444444433334444444444244441525254544543444444444434554444434454325335344242321313311233443334324444123264345444424432333354344444344544444444444444444444444443343433243433333332344444444333333444434444444544444544444454544444344345444434254665654345523541340045134213520550263055046315504521540451044025103503737153056252656
	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                 320                 340

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

SS
Seq

CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHCCCC
METPFYGDEALSGLGGGASGSGGSFASPGRLFPGAPPTAAAGSMMKKDALTLSLSEQVAAALKPAAAPPPTPLRADGAPSAAPPDGLLASPDLGLLKLASPELERLIIQSNGLVTTTPTSSQFLYPKVAASEEQEFAEGFVKALEDLHKQNQLGAGAAAAAAAAAAGGPSGTATGSAPPGELAPAAAAPEAPVYANLSSYAGGAGGAGGAATVAFAAEPVPFPPPPPPGALGPPRLAALKDEPQTVPDVPSFGESPPLSPIDMDTQERIKAERKRLRNRIAASKCRKRKLERISRLEEKVKTLKSQNTELASTASLLREQVAQLKQKVLSHVNSGCQLLPQHQVPAY

5yfpB

0.07

0.05

2.30

1.29

SPARKS-K

NELSGHMISKIIHSQRLILQNNTNQDKSQGCVELSYYLKIN------QLFQIISDTGKDSEGLKSTVEPNKVNTISGTSYLNLNCQ-----------------------PSSQGLT---------DSPTIIEMWLLILKYINDLWKICDQFILDGTYQNSIINEKRKENILIGDSNIIESYQKSLILKEEQINEVRLKGEEFITSVSQNLISFFTSSQSSLPSSLKDSTGDITRSNKDSGS-----PLDYGFIPPNCNGLSCLRYLPKIVEPILKFSTELAQLNITTNGI-----------------TICRNTLSTIINRCVGAISSTKLRDIS--NFYQLENWQVY

1vt4I3

0.10

3.57

1.13

MapAlign

GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG

2vkyB2

0.12

0.02

0.61

2.24

HHsearch

----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------LKYDPDQYSIEADKKFKLIKQIEDKIEEILSKIYHIENEIARIKKLIG-------------------------

1vt4I3

0.10

0.09

3.38

0.62

CEthreader

GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG--------------------------------------

5o9zG

0.07

2.87

0.58

EigenThreader

RHIWITAAKLEEANGNTQMVEKIIDRAITSLRANGVEINREQWIQDAEECDRAGSVATCQAVMRAVIGIGIEEEDRKAHNALECARAIYAYALQVFPSKKSVWLRAAYFEKNHGTLLQRAVAHCPKAEVLWLMGAKSKWLAGLALAFQANPNSEEIWLAAVKLESENDEYERARRLLAKARSSAPTARVFMKSVKLEWVQDNIRAAQDLCEEALRHYEDFPKLWMMKGQIEEQKEMMEKAREAYNQGLKKCPHSTPLWLLLSRLEEKIRARAILEKSRLKNLWLESVRLEYIANTLMAKALQEVAKLFWSQKAREWFHRTVKIWAFFYKFELQHGTRKRCESAEPRH

2wt7B

0.27

0.06

1.77

0.73

FFAS-3D

-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------LRGFTKDEVIRLKQKRRTLKNRGYAQSCRYKRVQQKHHLENEKTQLIQQVEQLKQEVSRLARERDAYKVKSEK-----------------

4btgA

0.12

0.11

3.94

1.06

SPARKS-K

EVSPFKLRPITSYIGQTSAIDHMGQPSDWQFAKEITTPVKLANNSNQRFLDPGISDRMSATLAPIGNTFAVSAVYEAVSQRGTVNSNGA---EMTLGFPS------VVERDYALDRDP----------------------MVAIAALRTGIVDESLEARAVAHNPEQGVAAEQNVRTELRIPVGYNAIEGGSIRTPEPAYNKPIQPSEVLQAKVLASTEFAYEDAYSVTIRNKRYTAEVK-EFELLGLGQRRERVRILKPIQMEDDRTLAAARRTSRDDAEKLAIDGRRMQNAVTLLRKIEMIGTTGASAVHLAQSRIVDQMAGRNRHRIRIWAGLAVLQMMGLLSR

5j65A

0.11

0.02

0.83

0.55

CNFpred

-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------EIKKQLDSAQHDLDRDVKIIGMLNSINTDIDNLYSQGQEAIKVFQKLQGIWATIGAQIENLRTTSLQEVQD-------------

2ycuA

0.05

0.03

1.44

0.67

DEthreader

-----WTARRLVAALRDEVELRRLRLPRDQI-------------ASVLHNRERYYSGLI--------------------YTEAIVMYR-VPPHV-AVT--A-SQSILVILAINFIGANIEVLRLNRALDRSPR-QGASFLG-------------------------------------------------ILFQEFRQRY-----EILTPN--------IPKGFMDGKQAC---LDPNYRVG---------------------QS--KI-FFRAGVLAQLEEERASEQTKSDYLKRANELVQWINDKQASLESLAEHGQSNSDLLSILAQLTELNYN----------

4xpoA

0.08

3.09

1.05

MapAlign

LQKEEQLYGFGLNFQTVHQRGKILELHVDHYGGKDSGRTHAPTPFYVSSNGYGVFINSARYIKVWAGTGVRTWSSRPYSDAVEILVPAEGVEVYVFGGKPIDAVKRYNLLNGGGYLPPRWGLGFTQRVMTRYTDKDVEKEVNDFKEKPLDFVGLEPGWQSKAYPGTFSWDKSRYPDPTSFVKKMKDQGIRLNLWKEIKPYTGSHTVWLGLVPDFTMAEARKPFFNQLLKDQIERGVSGYKIDEVDGYDYYLWPDAAKFPSGLSAEQMRQTYGLLVQRYSAELYKQNHQDFITALEEWLRRFQSNVEVEADVKKFALLRMQMMPYWYSAFARYHFEGMPPFRG-----

(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	0.4656

(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	2ycuA	0.39	5.93	0.047	0.599	model1_2ycuA.pdb.gz
2	7kveB	0.38	6.87	0.020	0.671	model1_7kveB.pdb.gz
3	5m59A	0.38	6.08	0.038	0.599	model1_5m59A.pdb.gz
4	4bgdA	0.38	6.36	0.042	0.620	model1_4bgdA.pdb.gz
5	6mf0A	0.37	6.61	0.055	0.614	model1_6mf0A.pdb.gz
6	5oqlO	0.37	6.80	0.064	0.617	model1_5oqlO.pdb.gz
7	5wlcLT	0.37	6.36	0.055	0.585	model1_5wlcLT.pdb.gz
8	6pzkA	0.36	6.78	0.044	0.614	model1_6pzkA.pdb.gz
9	3hmjA	0.36	6.65	0.045	0.602	model1_3hmjA.pdb.gz
10	1g8kA	0.36	6.39	0.040	0.579	model1_1g8kA.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:0003677	0.97	DNA binding
GO:0044212	0.94	transcription regulatory region DNA binding
GO:0003700	0.93	transcription factor activity, sequence-specific DNA binding
GO:0043565	0.91	sequence-specific DNA binding
GO:0000976	0.90	transcription regulatory region sequence-specific DNA binding
GO:0000977	0.79	RNA polymerase II regulatory region sequence-specific DNA binding
GO:0000981	0.75	RNA polymerase II transcription factor activity, sequence-specific DNA binding
GO:0001159	0.72	core promoter proximal region DNA binding
GO:0000978	0.71	RNA polymerase II core promoter proximal region sequence-specific DNA binding
GO:0008134	0.69	transcription factor binding
GO:0003713	0.66	transcription coactivator 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	0.92	biological regulation
GO:0050789	0.92	regulation of biological process
GO:0050794	0.91	regulation of cellular process
GO:0009987	0.90	cellular process
GO:0080090	0.86	regulation of primary metabolic process
GO:0060255	0.86	regulation of macromolecule metabolic process
GO:0031323	0.86	regulation of cellular metabolic process
GO:0006355	0.85	regulation of transcription, DNA-templated
GO:0048522	0.82	positive regulation of cellular process
GO:0006357	0.82	regulation of transcription from RNA polymerase II promoter
GO:0045893	0.81	positive regulation of transcription, DNA-templated
GO:0050896	0.76	response to stimulus
GO:0051716	0.71	cellular response to stimulus
GO:0048523	0.71	negative regulation of cellular process
GO:0042221	0.71	response to chemical
GO:0045944	0.70	positive regulation of transcription from RNA polymerase II promoter
GO:0070887	0.68	cellular response to chemical stimulus
GO:0045892	0.68	negative regulation of transcription, DNA-templated
GO:0010033	0.68	response to organic substance
GO:0000122	0.67	negative regulation of transcription from RNA polymerase II promoter
GO:0009605	0.66	response to external stimulus
GO:1901700	0.65	response to oxygen-containing compound
GO:0071495	0.65	cellular response to endogenous stimulus
GO:0071310	0.65	cellular response to organic substance
GO:0051726	0.65	regulation of cell cycle
GO:0045595	0.65	regulation of cell differentiation
GO:0010941	0.65	regulation of cell death
GO:0009725	0.65	response to hormone
GO:0009628	0.65	response to abiotic stimulus
GO:0045597	0.64	positive regulation of cell differentiation
GO:0042493	0.64	response to drug
GO:0042127	0.64	regulation of cell proliferation
GO:0034097	0.64	response to cytokine
GO:0032870	0.64	cellular response to hormone stimulus
GO:0014070	0.64	response to organic cyclic compound
GO:0010243	0.64	response to organonitrogen compound
GO:0009314	0.64	response to radiation
GO:0051591	0.63	response to cAMP
GO:0043207	0.63	response to external biotic stimulus
GO:0009612	0.63	response to mechanical stimulus
GO:0032496	0.62	response to lipopolysaccharide

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:0044424	1.00	intracellular part
GO:0032991	0.80	macromolecular complex
GO:0043234	0.79	protein complex
GO:0044446	0.77	intracellular organelle part
GO:0044428	0.74	nuclear part
GO:0005667	0.72	transcription factor complex
GO:0044427	0.69	chromosomal part
GO:0000790	0.68	nuclear chromatin
GO:0043226	0.66	organelle
GO:0043229	0.65	intracellular organelle
GO:0043231	0.64	intracellular membrane-bounded organelle
GO:0005634	0.62	nucleus

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	3eifA	0.328	6.83	0.049	0.565	3.4.21.110	NA
2	0.060	3b9jI	0.131	5.85	0.046	0.207	1.17.1.4 1.17.3.2	NA
3	0.060	2j5wA	0.334	6.72	0.048	0.568	1.16.3.1	NA
4	0.060	1t3tA	0.327	6.61	0.056	0.548	6.3.5.3	NA
5	0.060	1ug9A	0.326	7.14	0.036	0.591	3.2.1.70	102,138

	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	0.01	2a6h8	0.201	6.78	0.059	0.352	0.13	III	complex1.pdb.gz	119,135,137,138,140,146,150

	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.