D-I-TASSER Q6P1J9-D1

D-I-TASSER results for Q6P1J9-D1

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

Input Sequence in FASTA format

>Q6P1J9 (343 residues)
MADVLSVLRQYNIQKKEIVVKGDEVIFGEFSWPKNVKTNYVVWGTGKEGQPREYYTLDSI
LFLLNNVHLSHPVYVRRAATENIPVVRRPDRKDLLGYLNGEASTSASIDRSAPLEIGLQR
STQVKRAADEVLAEAKKPRIEDEECVRLDKERLAARLEGHKEGIVQTEQIRSLSEAMSVE
KIAAIKAKIMAKKRSTIKTDLDDDITALKQRSFVDAEVDVTRDIVSRERVWRTRTTILQS
TGKNFSKNIFAILQSVKAREEGRAPEQRPAPNAAPVDPTLRTKQPIPAAYNRYDQERFKG
KEETEGFKIDTMGTYHGMTLKSVTEGASARKTQTPAAQPVPRP

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 160 180 200 220 240 260 280 300 320 340 \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| MADVLSVLRQYNIQKKEIVVKGDEVIFGEFSWPKNVKTNYVVWGTGKEGQPREYYTLDSILFLLNNVHLSHPVYVRRAATENIPVVRRPDRKDLLGYLNGEASTSASIDRSAPLEIGLQRSTQVKRAADEVLAEAKKPRIEDEECVRLDKERLAARLEGHKEGIVQTEQIRSLSEAMSVEKIAAIKAKIMAKKRSTIKTDLDDDITALKQRSFVDAEVDVTRDIVSRERVWRTRTTILQSTGKNFSKNIFAILQSVKAREEGRAPEQRPAPNAAPVDPTLRTKQPIPAAYNRYDQERFKGKEETEGFKIDTMGTYHGMTLKSVTEGASARKTQTPAAQPVPRP
Prediction	CCCHHHHHHHHHHCCCCSSSSCCSSSSCCSSSCCCCCCSSSSCCCCCCCCCCCCSCHHHHHHHHHHCCCCHHHHHHHHHHHCCCCCCCCCHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHCCCCCCCCHHHHHHHCCCCCCCCHHHHHHHHHHHHCCCCCCHHHHHHHCCCHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
Confidence	9738999999984399548868889977645047774114635887677877521289999999822687799999999919995134224689999618888863346556643244565555677655555334567763444321267776431244433334333212212230788888654222201233233305555310445542124699999985300246287898634741789999999999999850255556677778888887777776312322214334553224573315665423455533557888877889999999999
	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 \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| MADVLSVLRQYNIQKKEIVVKGDEVIFGEFSWPKNVKTNYVVWGTGKEGQPREYYTLDSILFLLNNVHLSHPVYVRRAATENIPVVRRPDRKDLLGYLNGEASTSASIDRSAPLEIGLQRSTQVKRAADEVLAEAKKPRIEDEECVRLDKERLAARLEGHKEGIVQTEQIRSLSEAMSVEKIAAIKAKIMAKKRSTIKTDLDDDITALKQRSFVDAEVDVTRDIVSRERVWRTRTTILQSTGKNFSKNIFAILQSVKAREEGRAPEQRPAPNAAPVDPTLRTKQPIPAAYNRYDQERFKGKEETEGFKIDTMGTYHGMTLKSVTEGASARKTQTPAAQPVPRP
Prediction	7630042034003665504346540302523042614131334545454455310101000000214726215004303756052042234540152043635336404452546354554554454565445645444354564454445435543555554434454345357534363134144443544444344445553544645533524352055026443525423200434445225401410530344355645645545544546455544454444352245441545644751514340243244154156455365464365544668
	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

CCCHHHHHHHHHHCCCCSSSSCCSSSSCCSSSCCCCCCSSSSCCCCCCCCCCCCSCHHHHHHHHHHCCCCHHHHHHHHHHHCCCCCCCCCHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHCCCCCCCCHHHHHHHCCCCCCCCHHHHHHHHHHHHCCCCCCHHHHHHHCCCHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
MADVLSVLRQYNIQKKEIVVKGDEVIFGEFSWPKNVKTNYVVWGTGKEGQPREYYTLDSILFLLNNVHLSHPVYVRRAATENIPVVRRPDRKDLLGYLNGEASTSASIDRSAPLEIGLQRSTQVKRAADEVLAEAKKPRIEDEECVRLDKERLAARLEGHKEGIVQTEQIRSLSEAMSVEKIAAIKAKIMAKKRSTIKTDLDDDITALKQRSFVDAEVDVTRDIVSRERVWRTRTTILQSTGKNFSKNIFAILQSVKAREEGRAPEQRPAPNAAPVDPTLRTKQPIPAAYNRYDQERFKGKEETEGFKIDTMGTYHGMTLKSVTEGASARKTQTPAAQPVPRP

5ydeA

1.00

0.32

9.06

1.76

FFAS-3D

MADVLSVLRQYNIQKKEIVVKGDEVIFGEFSWPKNVKTNYVVWGTGKEGQPREYYTLDSILFLLNNVHLSHPVYVRRAATENIPVVRRPDRKDLLGYLNGEASTSASIDRS----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------

5ydeA

1.00

0.32

9.06

1.38

SPARKS-K

MADVLSVLRQYNIQKKEIVVKGDEVIFGEFSWPKNVKTNYVVWGTGKEGQPREYYTLDSILFLLNNVHLSHPVYVRRAATENIPVVRRPDRKDLLGYLNGEASTSASIDRS----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------

5ydeA

1.00

0.32

9.06

1.59

CNFpred

MADVLSVLRQYNIQKKEIVVKGDEVIFGEFSWPKNVKTNYVVWGTGKEGQPREYYTLDSILFLLNNVHLSHPVYVRRAATENIPVVRRPDRKDLLGYLNGEASTSASIDRS----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------

5ydeA

1.00

0.32

9.06

5.20

HHsearch

MADVLSVLRQYNIQKKEIVVKGDEVIFGEFSWPKNVKTNYVVWGTGKEGQPREYYTLDSILFLLNNVHLSHPVYVRRAATENIPVVRRPDRKDLLGYLNGEASTSASIDRS----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------

5ydeA

1.00

0.32

9.06

0.84

CEthreader

MADVLSVLRQYNIQKKEIVVKGDEVIFGEFSWPKNVKTNYVVWGTGKEGQPREYYTLDSILFLLNNVHLSHPVYVRRAATENIPVVRRPDRKDLLGYLNGEASTSASIDRS----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------

1hz4A

0.05

0.04

2.08

0.75

EigenThreader

AEFNALRAQVAINDGN-------------PDEAERLAKLALEE--LPPGWFYSRIVATSVLGEVLHCKGELTRSLALMQQTEQMARQHDVSLIQQSEILFAQGF---------------LQTAWETQEKAFQLINEQEQLPMHEFLVRIRAQLLWAWARLDEAEASARSGIEVLSSYQPQQQLQCLAMLIQCSLARGDLDNARSQLNRLENLLGNGKYHSDWISNA----NKVRVIYWQMTGDKAAAANWLRHTNIARAQILLGEFEPAEIVLEELNENARSLRLMSDLNRNLLLLNQLYWQAGRKSDAQRVLLDAEGEAMAQQLRQLIQLNTLPELEQHRAQ

6em5n

0.11

0.08

3.07

0.60

FFAS-3D

-------------------------------------------KKNTRGNARNFITRSQAV---RKLQVSLADFRRLCIFKGIYPREPRNKKKA-----NKGSTAPTTFYYAKDIQYLMHEPVLAKFREHKTFARKL-----TRALGRGEVSSAKRLEENRDSYTLDHIIKERYPSF-PDAIRDIDDALNMLFLFSNLPSTNQVSSKIINDAQKICNQWLAYVAKERDVDFRIMLTFLE-----FYSTLLHFVLYKLYTDSGLIYPPKLDLKKDKIISGLSSYILESRYDSP-VASLFSAFV----FYVSREVPIDILEFLILSCGGNVISEAAMDSK-----

6em5I

0.09

0.08

2.92

0.78

SPARKS-K

SNAAPIQVSLGILATQAAKELISTASHFNFRTDIFTLLLRRICKPRISTDPTSIQIIQTFETLLNEEEGSISFEILRIFNKILKTRNFNIEESVLNMLLSKKKDRVHLSKKQRKARKEMQQIEEEMRNAEQAVSAEERERNQSEILKIVFTIYLNILKNNAKTLIGSEGLTKFGNMANFDLLGDFLEVMKELISD----------TEFDAEVRKALLCIVSAFSLISNTQ--------YMKLSKFV----DGLYALLPYICLDADIELSYRSLRLADPLNNEIIKPSVN----------------------VSTKAELLLKALDHVFFRSKSGTKERATAFTK

1bk6A

0.11

0.04

1.57

0.60

CNFpred

------------------------------------------------------PALRAVGNIVTG----NDLQTQVVINA-------GVLPALRLLLSSP----------------------------------------KENIKKEACWTISNITAGNTEQIIDANLIPPLVKLLTKKEACWAISNASSGG---------------------LQRPDIIRYLVSQG-CIKPLCDLLEIADNRIIEVTLDALENIIKM------------------------------------------------------------------------------------

6reyc

0.06

0.03

1.56

0.67

DEthreader

-----------E--S--LILLKKKELSRADLE------------------------PW-RPLYDMVERILYEFPNSVENILKTLVK----------EM-LEEWRPLMAIF-LPTSLPPELPSWLTP--------------R--Q-IATFST-VLQFMDRCFGLIESSTLEQTTET---SHIFEAGMVADMCRAAVKCCPTEYCPGGIQWIDVMLQHELRTLTVEGCAGAYNFCCRDIIPLVACLAQTWPAIILLGLLSLLAAGILKQLKRTHKKLTINPCEIGCP----------------------------------------------------------

(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	0.6286

(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	2vdcA	0.38	6.14	0.067	0.601	model1_2vdcA.pdb.gz
2	6r9tA	0.37	6.33	0.051	0.609	model1_6r9tA.pdb.gz
3	6v85A	0.37	6.08	0.024	0.589	model1_6v85A.pdb.gz
4	6z2wE	0.37	6.48	0.048	0.604	model1_6z2wE.pdb.gz
5	4d0jA	0.36	6.68	0.049	0.609	model1_4d0jA.pdb.gz
6	3ffzA	0.36	7.06	0.030	0.638	model1_3ffzA.pdb.gz
7	6bcuA	0.36	6.71	0.042	0.609	model1_6bcuA.pdb.gz
8	7abiE	0.35	6.47	0.028	0.583	model1_7abiE.pdb.gz
9	6hqvA	0.35	6.45	0.048	0.580	model1_6hqvA.pdb.gz
10	6rflA3	0.35	6.55	0.053	0.571	model1_6rflA3.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:0044877	0.86	macromolecular complex binding
GO:0000993	0.85	RNA polymerase II core 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:0065007	1.00	biological regulation
GO:0050789	1.00	regulation of biological process
GO:0050794	0.99	regulation of cellular process
GO:0044699	0.99	single-organism process
GO:0006355	0.98	regulation of transcription, DNA-templated
GO:0009987	0.96	cellular process
GO:0044763	0.90	single-organism cellular process
GO:0048869	0.89	cellular developmental process
GO:0034243	0.89	regulation of transcription elongation from RNA polymerase II promoter
GO:0032502	0.87	developmental process
GO:0044767	0.85	single-organism developmental process
GO:0008152	0.77	metabolic process
GO:0071704	0.76	organic substance metabolic process
GO:0048518	0.76	positive regulation of biological process
GO:0044238	0.76	primary metabolic process
GO:0044237	0.76	cellular metabolic process
GO:0044260	0.75	cellular macromolecule metabolic process
GO:0048522	0.74	positive regulation of cellular process
GO:0031325	0.73	positive regulation of cellular metabolic process
GO:0010604	0.73	positive regulation of macromolecule metabolic process
GO:0045893	0.72	positive regulation of transcription, DNA-templated
GO:0034641	0.72	cellular nitrogen compound metabolic process
GO:0090304	0.71	nucleic acid metabolic process
GO:0009967	0.71	positive regulation of signal transduction
GO:0016070	0.70	RNA metabolic process
GO:2000026	0.63	regulation of multicellular organismal development
GO:0048523	0.63	negative regulation of cellular process
GO:0045944	0.63	positive regulation of transcription from RNA polymerase II promoter
GO:0032501	0.63	multicellular organismal process
GO:0016071	0.63	mRNA metabolic process
GO:0006396	0.63	RNA processing
GO:0044707	0.62	single-multicellular organism process
GO:0032968	0.62	positive regulation of transcription elongation from RNA polymerase II promoter
GO:0031324	0.62	negative regulation of cellular metabolic process
GO:0010948	0.62	negative regulation of cell cycle process
GO:0010605	0.62	negative regulation of macromolecule metabolic process
GO:0006397	0.62	mRNA processing
GO:2000134	0.61	negative regulation of G1/S transition of mitotic cell cycle
GO:0045638	0.61	negative regulation of myeloid cell differentiation
GO:0031442	0.61	positive regulation of mRNA 3'-end processing
GO:0030177	0.61	positive regulation of Wnt signaling pathway
GO:0019827	0.61	stem cell population maintenance
GO:0008285	0.61	negative regulation of cell proliferation
GO:0006378	0.61	mRNA polyadenylation
GO:0001711	0.61	endodermal cell fate commitment
GO:0000122	0.61	negative regulation of transcription from RNA polymerase II promoter

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:0016593	1.00	Cdc73/Paf1 complex
GO:0005634	1.00	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	2jfdA	0.198	6.52	0.042	0.327	2.3.1.85	NA
2	0.060	1dmrA	0.300	6.59	0.025	0.493	1.7.2.3	NA
3	0.060	2pmzQ	0.321	6.91	0.047	0.542	2.7.7.6	NA
4	0.060	2vz9B	0.316	6.50	0.047	0.531	2.3.1.85	NA
5	0.060	3dlaD	0.310	6.37	0.050	0.498	6.3.5.1	8

	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	0.01	2hgu5	0.120	4.13	0.076	0.154	0.68	III	complex1.pdb.gz	91,92,95,98,99
2	0.01	2hgu3	0.128	5.04	0.017	0.181	0.66	III	complex2.pdb.gz	89,90,91,92,96,101
3	0.01	2hdnA	0.071	2.68	0.030	0.079	0.49	GDP	complex3.pdb.gz	93,96,97
4	0.01	2hcjB	0.203	6.64	0.041	0.338	0.52	GDP	complex4.pdb.gz	96,97,98
5	0.01	2ja50	0.078	4.21	0.089	0.102	0.41	III	complex5.pdb.gz	96,97,100

	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.