D-I-TASSER Q14164-D5

D-I-TASSER results for Q14164-D5

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

Input Sequence in FASTA format

>Q14164 (311 residues)
VDLQADYNTAKGVLGAGYQALRLARALLDGQELMFRGLHWVMEVLQATCRRTLEVARTSL
LYLSSSLGTERFSSVAGTPEIQELKAAAELRSRLRTLAEVLSRCSQNITETQESLSSLNR
ELVKSRDQVHEDRSIQQIQCCLDKMNFIYKQFKKSRMRPGLGYNEEQIHKLDKVNFSHLA
KRLLQVFQEECVQKYQASLVTHGKRMRVVHETRNHLRLVGCSVAACNTEAQGVQESLSKL
LEELSHQLLQDRAKGAQASPPPIAPYPSPTRKDLLLHMQELCEGMKLLASDLLDNNRIIE
RLNRVPAPPDV

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 160 180 200 220 240 260 280 300 \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| VDLQADYNTAKGVLGAGYQALRLARALLDGQELMFRGLHWVMEVLQATCRRTLEVARTSLLYLSSSLGTERFSSVAGTPEIQELKAAAELRSRLRTLAEVLSRCSQNITETQESLSSLNRELVKSRDQVHEDRSIQQIQCCLDKMNFIYKQFKKSRMRPGLGYNEEQIHKLDKVNFSHLAKRLLQVFQEECVQKYQASLVTHGKRMRVVHETRNHLRLVGCSVAACNTEAQGVQESLSKLLEELSHQLLQDRAKGAQASPPPIAPYPSPTRKDLLLHMQELCEGMKLLASDLLDNNRIIERLNRVPAPPDV
Prediction	CCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCC
Confidence	96264689999999989999999999999999999999999999999999999999999998766777777887516764046788999999999999999987556788888885899999996321001127999999999999999999998860689985899999999889999999999999878999999999999999999999999999997999999999999999999999999998740113566787755667786258899999999999999999999954999971368999999
	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 \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| VDLQADYNTAKGVLGAGYQALRLARALLDGQELMFRGLHWVMEVLQATCRRTLEVARTSLLYLSSSLGTERFSSVAGTPEIQELKAAAELRSRLRTLAEVLSRCSQNITETQESLSSLNRELVKSRDQVHEDRSIQQIQCCLDKMNFIYKQFKKSRMRPGLGYNEEQIHKLDKVNFSHLAKRLLQVFQEECVQKYQASLVTHGKRMRVVHETRNHLRLVGCSVAACNTEAQGVQESLSKLLEELSHQLLQDRAKGAQASPPPIAPYPSPTRKDLLLHMQELCEGMKLLASDLLDNNRIIERLNRVPAPPDV
Prediction	74254004202100000020120042033014002300410031035304520443442133032113153244036445264154035125405503530452354045334416403431353364156543351043004204500440352534671523441013023430353043025004750143044105302500420240242044035304403540451352034025403551263555635454543434547425402420450153054003304502410532551445667
	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 AttentionPotential. 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

CCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCC
VDLQADYNTAKGVLGAGYQALRLARALLDGQELMFRGLHWVMEVLQATCRRTLEVARTSLLYLSSSLGTERFSSVAGTPEIQELKAAAELRSRLRTLAEVLSRCSQNITETQESLSSLNRELVKSRDQVHEDRSIQQIQCCLDKMNFIYKQFKKSRMRPGLGYNEEQIHKLDKVNFSHLAKRLLQVFQEECVQKYQASLVTHGKRMRVVHETRNHLRLVGCSVAACNTEAQGVQESLSKLLEELSHQLLQDRAKGAQASPPPIAPYPSPTRKDLLLHMQELCEGMKLLASDLLDNNRIIERLNRVPAPPDV

6cq0A

0.27

0.20

6.22

1.17

DEthreader

YDLDGDASMAKAITGVVCYACRIASTLLLYQELMRKGIRWLIELIKDDYNETVHKKTEVVITLDFCIRNIEKTV-------EL-GEISDIHTKLLRLSSSQGTIETSLQDIDSRLSGLADAWAHQE-GTHKDRNVEKLQVLLNCMTEIYYQFKKDKAERRLAYNEEQIHKFDKQKLYYHATKAMTHFTDECVKKYEAFLNKSEEWIRKMLHLRKQLLSLTNQCFDIEEEVSKYQEYTNE--LQ--E--T--------------------------------------------------------------

6cq0A3

0.29

0.22

6.57

1.46

SPARKS-K

YDLDGDASMAKAITGVVCYACRIASTLLLYQELMRKGIRWLIELIKDDYNETVHKKTEVVITLDFCIRNIEKTV--------ELGEISDIHTKLLRLSSSQGTIETSLQDIDSRLSSLADAWAHQEGTHPKDRNVEKLQVLLNCMTEIYYQFKKDKAERRLAYNEEQIHKFDKQKLYYHATKAMTHFTDECVKKYEAFLNKSEEWIRKMLHLRKQLLSLTNQCFDIEEEVSKYQEYTNELQET--------------------------------------------------------------------

4hpqC

0.09

3.32

1.32

MapAlign

AVIEKLLENSRKFLTGAKLICQESNDHLTTTKLRLDCIQQQTKFLSILLRGIGRLIEEWSQVLVRLVNDMKFWQNEITKMMDSSHILDSKLNEIPTIRKQVENITRQYQTMLAKVQQLVSRMKGLRDEFTNEALEQELADFLKSFTDHFDKCSALSSRSVSPEDAQNLFEIVERDDKDLAAILQDAA-IDVASFVRKVNMLLAKMQATLSKLLTEHEEYISVFEGISALIQKFKASCLEDIRQTRNLLDFYANFERSYHNLLKEVKRRKETAAKLSQILKSCETQLEQINTADLRERQMFLLENG------

4iw0A

0.27

0.21

6.41

0.85

CEthreader

YDLDGDASMAKAITGVVCYACRIASTLLLYQELMRKGIRWLIELIKDDYNETVHKKTEVVITLDFCIRNIEKTVK----VYEKLGEISDIHTKLLRLSSSQGTIETSLQDIDSRLGSLADAWAHQEGTHPKDRNVEKLQVLLNCMTEIYYQFKKDKAERRLAYNEEQIHKFDKQKLYYHATKAMTHFTDECVKKYEAFLNKSEEWIRKMLHLRKQLLSLTNQCFDIEEEVSKYQEYTNELQET--------------------------------------------------------------------

4iw0A3

0.27

0.21

6.41

1.27

MUSTER

YDLDGDASMAKAITGVVCYACRIASTLLLYQELMRKGIRWLIELIKDDYNETVHKKTEVVITLDFCIRNIEKTVKV----YEKLGEISDIHTKLLRLSSSQGTIETSLQDIDSRLGSLADAWAHQEGTHPKDRNVEKLQVLLNCMTEIYYQFKKDKAERRLAYNEEQIHKFDKQKLYYHATKAMTHFTDECVKKYEAFLNKSEEWIRKMLHLRKQLLSLTNQCFDIEEEVSKYQEYTNELQET--------------------------------------------------------------------

4iw0A3

0.28

0.21

6.50

5.59

HHsearch

YDLDGDASMAKAITGVVCYACRIASTLLLYQELMRKGIRWLIELIKDDYNETVHKKTEVVITLDFCIRNIEKVKV-----YEKLGEISDIHTKLLRLSSSQGTIETSLQDIDSRLSPLADAWAHQEGTHPKDRNVEKLQVLLNCMTEIYYQFKKDKAERRLAYNEEQIHKFDKQKLYYHATKAMTHFTDECVKKYEAFLNKSEEWIRKMLHLRKQLLSLTNQCFDIEEEVSKYQEYTNELQET--------------------------------------------------------------------

4iw0A3

0.27

0.21

6.41

2.57

FFAS-3D

YDLDGDASMAKAITGVVCYACRIASTLLLYQELMRKGIRWLIELIKDDYNETVHKKTEVVITLDFCIRNIEKTV----KVYEKLGEISDIHTKLLRLSSSQGTIETSLQDIDSRLGSLADAWAHQEGTHPKDRNVEKLQVLLNCMTEIYYQFKKDKAERRLAYNEEQIHKFDKQKLYYHATKAMTHFTDECVKKYEAFLNKSEEWIRKMLHLRKQLLSLTNQCFDIEEEVSKYQEYTNELQE---------------------------------------------------------------------

5ebzA3

0.12

0.09

3.19

1.47

EigenThreader

LPIIQLRKVWAEAVHYVSGLKEDYSRLFQGQRAAMLSLLRYNANLTKMKNTLISASQQLKAKLEFFHKSIQLDLERYSEQMKMLKAWKEMEEKAIHYA-----EVGVIGYLEDQIMSLHAEIMELQKSPYGRRQGDLMESLEQRAIDLYKQLKH---RPSDHSYS------DSTEMVKIIVHTVQSQD-RVLKELFGHLSKLLGCKQKIIDLLPKVEVALSNIKEADNTVMFMQGKRQKEIWH--------------------LLKIACTQ----------------------------------------

4im0A

0.27

0.20

6.22

1.28

CNFpred

YDLDGDASMAKAITGVVCYACRIASTLLLYQELMRKGIRWLIELIKDDYNETVHKKTEVVITLDFCIRNIEKTVKV---------EISDIHTKLLRLSSSQGTIETSLQDIDSRLSPGADAWAHQEGTHPKDRNVEKLQVLLNCMTEIYYQFKKDKAERRLAYNEEQIHKFDKQKLYYHATKAMTHFTDECVKKYEAFLNKSEEWIRKMLHLRKQLLSLTNQCFDIEEEVSKYQEYTNELQET--------------------------------------------------------------------

4iw0A

0.22

0.17

5.36

1.00

DEthreader

YDLDGDASMAKAITGVVCYACRIASTLLLYQELMRKGIRWLIELIKDDYNETVHKKTEVVITLDFCIRNIEKTVKVYEKL-G---EISDIHTKLLRLSSSQGTIETSLQDIDSRLSGSLA-DAWAHQEGTH-PKDRNVEKLQVLLNCMTEIYYQFKKDERLAYNEEQIHKFDKQKLYYHATKAMTHFTDECVKKYEAFLNKSEEWIRKMLHLRKQLLSLTNQCFDIEEEVSKYQEYTNE-LQE--T-----------------------------------------------------------------

(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	0.7128

(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 AttentionPotential, 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	6cq0A	0.72	1.54	0.268	0.756	model1_6cq0A.pdb.gz
2	5ebzA3	0.64	3.16	0.088	0.765	model1_5ebzA3.pdb.gz
3	4hpqC	0.61	3.91	0.060	0.781	model1_4hpqC.pdb.gz
4	6iknA	0.56	4.68	0.065	0.743	model1_6iknA.pdb.gz
5	6xj1A	0.55	4.27	0.073	0.714	model1_6xj1A.pdb.gz
6	4e40A	0.55	3.65	0.082	0.672	model1_4e40A.pdb.gz
7	4wpcA	0.55	4.50	0.027	0.733	model1_4wpcA.pdb.gz
8	2q13A	0.44	5.67	0.047	0.672	model1_2q13A.pdb.gz
9	3ghgJ	0.36	3.18	0.056	0.428	model1_3ghgJ.pdb.gz
10	4gf2A	0.29	5.84	0.026	0.457	model1_4gf2A.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:0003824	0.84	catalytic activity
GO:0016740	0.83	transferase activity
GO:0004674	0.81	protein serine/threonine kinase activity
GO:0019899	0.64	enzyme binding
GO:0004871	0.63	signal transducer activity
GO:0031625	0.62	ubiquitin protein ligase binding
GO:0036435	0.61	K48-linked polyubiquitin binding
GO:0004704	0.61	NF-kappaB-inducing kinase 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:0048584	1.00	positive regulation of response to stimulus
GO:0048522	1.00	positive regulation of cellular process
GO:0006950	1.00	response to stress
GO:0009987	0.93	cellular process
GO:0071704	0.92	organic substance metabolic process
GO:0044238	0.92	primary metabolic process
GO:0044237	0.92	cellular metabolic process
GO:0044260	0.91	cellular macromolecule metabolic process
GO:0006468	0.90	protein phosphorylation
GO:0007165	0.82	signal transduction
GO:0035556	0.80	intracellular signal transduction
GO:0023056	0.80	positive regulation of signaling
GO:0010647	0.80	positive regulation of cell communication
GO:0009966	0.80	regulation of signal transduction
GO:0043123	0.79	positive regulation of I-kappaB kinase/NF-kappaB signaling
GO:0051239	0.74	regulation of multicellular organismal process
GO:0048519	0.74	negative regulation of biological process
GO:0002376	0.73	immune system process
GO:0001817	0.73	regulation of cytokine production
GO:0080134	0.72	regulation of response to stress
GO:0050776	0.72	regulation of immune response
GO:0032479	0.72	regulation of type I interferon production
GO:0002684	0.72	positive regulation of immune system process
GO:0002218	0.71	activation of innate immune response
GO:0051260	0.68	protein homooligomerization
GO:0035456	0.68	response to interferon-beta
GO:0008630	0.68	intrinsic apoptotic signaling pathway in response to DNA damage
GO:0051707	0.62	response to other organism
GO:0001818	0.51	negative regulation of cytokine production
GO:0032480	0.50	negative regulation of type I interferon production
GO:0006955	0.50	immune response
GO:0002224	0.50	toll-like receptor signaling pathway

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:0005737	1.00	cytoplasm
GO:0044444	0.87	cytoplasmic part
GO:0016020	0.74	membrane
GO:0044446	0.73	intracellular organelle part
GO:0031090	0.70	organelle membrane
GO:0043229	0.69	intracellular organelle
GO:0043231	0.68	intracellular membrane-bounded organelle
GO:0005634	0.66	nucleus
GO:0005829	0.65	cytosol
GO:0044428	0.61	nuclear part
GO:0031966	0.60	mitochondrial membrane
GO:0016605	0.59	PML body

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	3gtdA	0.425	4.51	0.062	0.569	4.2.1.2	NA
2	0.060	1w27A	0.498	5.76	0.045	0.736	4.3.1.24	NA
3	0.060	3no9A	0.424	5.28	0.050	0.614	4.2.1.2	NA
4	0.060	1i0aA	0.421	5.24	0.069	0.605	4.3.2.1	NA
5	0.060	1dcnB	0.417	4.71	0.072	0.566	4.3.2.1	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	0.01	1zww0	0.472	4.15	0.109	0.617	0.62	III	complex1.pdb.gz	19,20,23,25,26,29,30,34,37,40,47,51,196,199,200,202,203,206,207,210,211,212
2	0.01	1i490	0.450	3.66	0.097	0.556	0.75	III	complex2.pdb.gz	13,16,20,23,26,27,30,33,34,38,115,118,119,121,122,125,129,141,173,174
3	0.01	1wdz0	0.494	4.52	0.062	0.669	0.65	III	complex3.pdb.gz	33,34,37,41,44,48,51,52,55,58,59,61,62,65,68,69,72,73,79,80,83,86,89,90,93,97,111,199,200,203,206,207,208,211
4	0.01	1i4d0	0.463	3.91	0.059	0.592	0.79	III	complex4.pdb.gz	23,24,30,34,37,40,44,47,48,54,55,58,187,192,193,196,197,200,204
5	0.01	2raj0	0.535	3.60	0.052	0.656	0.41	III	complex5.pdb.gz	27,30,31,34,37,38,45,55,56,58,62,66,69,70,73,87,90,101,192,198,202,203,206,207,210

	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, Chengxin Zhang, Yang Li, Robin Pearce, Eric W. Bell, Yang Zhang. Folding non-homology proteins by coupling deep-learning contact maps with I-TASSER assembly simulations. In preparation, 2020.