D-I-TASSER Q12891-D1

D-I-TASSER results for Q12891-D1

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

Input Sequence in FASTA format

>Q12891 (252 residues)
MRAGPGPTVTLALVLAVSWAMELKPTAPPIFTGRPFVVAWDVPTQDCGPRLKVPLDLNAF
DVQASPNEGFVFTRPTYSRRLTGLSEMDLISTIGESAALGAAGVILWGDAGYTTSTETCQ
YLKDYLTRLLVPYVVNVSWATQYCSRAQCHGHGRCVRRNPSASTFLHLSTNSFRLVPGHA
PGEPQLRPVGELSWADIDHLQTHFRCQCYLGWSGEQCQWDHRQAAGGASEAWAGSHLTSL
LALAALAFTWTL

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 160 180 200 220 240 \| \| \| \| \| \| \| \| \| \| \| \| MRAGPGPTVTLALVLAVSWAMELKPTAPPIFTGRPFVVAWDVPTQDCGPRLKVPLDLNAFDVQASPNEGFVFTRPTYSRRLTGLSEMDLISTIGESAALGAAGVILWGDAGYTTSTETCQYLKDYLTRLLVPYVVNVSWATQYCSRAQCHGHGRCVRRNPSASTFLHLSTNSFRLVPGHAPGEPQLRPVGELSWADIDHLQTHFRCQCYLGWSGEQCQWDHRQAAGGASEAWAGSHLTSLLALAALAFTWTL
Prediction	CCCCCCCCSHHHHHHHHHHHHHCCCCCCCCCCCCCCSSSSCCCHHHHHHHHHHHHHHHHCCCCCCCCCSSSSSSSSSCCCCCCCCHHHHHHHHHHHHHCCCCSSSSSCCCCCCCCHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHCCCCSSSCCCCCCCCCCCCCCCCCSSSSCCCCCCCCSSSCCCCCHHHHHHHHHCCSSSCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHCC
Confidence	988878742246888887752057677986468851566247647887777777656631578888732557867625755555899999999999971897799935765567988999999998616515899999999999799855898053269998545026975532574257888736770459999999976173787248988988756876567777788877317899999999997339
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 160 180 200 220 240 \| \| \| \| \| \| \| \| \| \| \| \| MRAGPGPTVTLALVLAVSWAMELKPTAPPIFTGRPFVVAWDVPTQDCGPRLKVPLDLNAFDVQASPNEGFVFTRPTYSRRLTGLSEMDLISTIGESAALGAAGVILWGDAGYTTSTETCQYLKDYLTRLLVPYVVNVSWATQYCSRAQCHGHGRCVRRNPSASTFLHLSTNSFRLVPGHAPGEPQLRPVGELSWADIDHLQTHFRCQCYLGWSGEQCQWDHRQAAGGASEAWAGSHLTSLLALAALAFTWTL
Prediction	744230020000000011103514233323146310000010006303500200120232544634320100021214442410334202300320372401000000223424347205403510563011001102400430044105633303344451521020437314133464665441324240445215403750302003415165054456555445342233330210001001133134
	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

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

SS
Seq

CCCCCCCCSHHHHHHHHHHHHHCCCCCCCCCCCCCCSSSSCCCHHHHHHHHHHHHHHHHCCCCCCCCCSSSSSSSSSCCCCCCCCHHHHHHHHHHHHHCCCCSSSSSCCCCCCCCHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHCCCCSSSCCCCCCCCCCCCCCCCCSSSSCCCCCCCCSSSCCCCCHHHHHHHHHCCSSSCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHCC
MRAGPGPTVTLALVLAVSWAMELKPTAPPIFTGRPFVVAWDVPTQDCGPRLKVPLDLNAFDVQASPNEGFVFTRPTYSRRLTGLSEMDLISTIGESAALGAAGVILWGDAGYTTSTETCQYLKDYLTRLLVPYVVNVSWATQYCSRAQCHGHGRCVRRNPSASTFLHLSTNSFRLVPGHAPGEPQLRPVGELSWADIDHLQTHFRCQCYLGWSGEQCQWDHRQAAGGASEAWAGSHLTSLLALAALAFTWTL

2pe4A

0.29

0.21

6.53

0.83

DEthreader

------------------------------LLPNRTTVWNAPQTIFYSSQLGDAAIPADFSGGLRALPVLPYVQIFYDTTNHFLPLDELEHSLGESAAQGAAGVVLWVSWENTRTKESCQAIKEYMDTTLGPFILNVTSGALLCSQALCSGHGRCVRRTSHPKALLLLNPASFSIQLTPG-GGPLSLRGALSLE-DQAQMAVEFKCRCYPGWQA-PWCER--------------------------------

2pe4A

0.29

0.24

7.38

1.79

SPARKS-K

AQDQFQGAARAWMAGTLQLGRALRP--------RGLWGFYGFPTGQCPVQHRVAEAFRVAVAGDPNLPVLPYVQIFYDTTNHFLPLDELEHSLGESAAQGAAGVVLWVSWENTRTKESCQAIKEYMDTTLGPFILNVTSGALLCSQALCSGHGRCVRRTSHPKALLLLNPASFSIQLTP--GGGPLSLRGALSLEDQAQMAVEFKCRCYPGWQAPWCERKSMWT----------------------------

2pe4A

0.26

0.23

7.10

1.26

MapAlign

QFQGAARAWMAGTLQLGRALRPRGLWGFYGFPDCYNALYPSIYMPAVLEGTGKSQMYVQHRVGDPNLPVLPYVQIFYDTTNHFLPLDELEHSLGESAAQGAAGVVLWVSWENTRTKESCQAIKEYMDTTLGPFILNVTSGALLCSQALCSGHGRCVRRTSHPKALLLLNPASFSIQLT--PGGGPLSLRGALSLEDQAQMAVEFKCRCYPGWQAPWCERKSMWT----------------------------

2pe4A

0.25

0.22

6.88

1.43

CEthreader

DCYNYDFLSPNYTGQCPSGIRAQNDQLGWLWGQSRALYPSIYMPAVLEGTGKSQMYVQHRVAEAFNLPVLPYVQIFYDTTNHFLPLDELEHSLGESAAQGAAGVVLWVSWENTRTKESCQAIKEYMDTTLGPFILNVTSGALLCSQALCSGHGRCVRRTSHPKALLLLNPASFSIQLTPGG--GPLSLRGALSLEDQAQMAVEFKCRCYPGWQAPWCERKSMWT----------------------------

2pe4A

0.36

0.28

8.40

0.89

MUSTER

-----------------------RSFRGPLLPNRPFTTVWNANTQWCLERHGVDVDVSVFDVVANPGPVLPYVQIFYDTTNHFLPLDELEHSLGESAAQGAAGVVLWVSWENTRTKESCQAIKEYMDTTLGPFILNVTSGALLCSQALCSGHGRCVRRTSHPKALLLLNPASFSIQLT--PGGGPLSLRGALSLEDQAQMAVEFKCRCYPGWQAPWCERKSMWT----------------------------

2pe4A

0.36

0.28

8.40

7.40

HHsearch

-----------------------RSFRGPLLPNRPFTTVWNANTQWCLERHGVDVDVSVFDVVANPGQTFPYVQIFYDTTNHFLPLDELEHSLGESAAQGAAGVVLWVSWENTRTKESCQAIKEYMDTTLGPFILNVTSGALLCSQALCSGHGRCVRRTSHPKALLLLNPASFSIQLTP--GGGPLSLRGALSLEDQAQMAVEFKCRCYPGWQAPWCERKSMWT----------------------------

2pe4A

0.28

0.24

7.40

1.79

FFAS-3D

-YTGQCPSGIRAQNDQLGWLWGQSRALYPSIYMPAVLEGTGKSQMYVQHRVAEAFRVAV-AAGDPNLPVLPYVQIFYDTTNHFLPLDELEHSLGESAAQGAAGVVLWVSWENTRTKESCQAIKEYMDTTLGPFILNVTSGALLCSQALCSGHGRCVRRTSHPKALLLLNPASFSIQLT--PGGGPLSLRGALSLEDQAQMAVEFKCRCYPGWQAPWCERKS-------------------------------

2pe4A

0.26

0.22

6.87

1.12

EigenThreader

HPDWPAPQVEAVAQDQGRALRPRGNYDFLSPNYTGQCYPSIYMPAVLEG---TGKSQMYVQHRVANLPVLPYVQIFYDTTNHFLPLDELEHSLGESAAQGAAGVVLWVSWENTRTKESCQAIKEYMDTTLGPFILNVTSGALLCSQALCSGHGRCVRRTSHPKALLLLNPASFSIQLTPG--GGPLSLRGALSLEDQAQMAVEFKCRCYPGWQAPWC-----ERKSMWT-----------------------

2pe4A

0.31

0.24

7.21

2.36

CNFpred

----------LGWLWGQSRAL------------YPSIYMPAV-KSQMYVQHRVAEAFRVAVAADPNLPVLPYVQIFYDTTNHFLPLDELEHSLGESAAQGAAGVVLWVSWENTRTKESCQAIKEYMDTTLGPFILNVTSGALLCSQALCSGHGRCVRRTSHPKALLLLNPASFSIQLTP--GGGPLSLRGALSLEDQAQMAVEFKCRCYPGWQAPWCERKS-------------------------------

2x2hA

0.06

0.05

2.19

0.83

DEthreader

------YLNYNQNPDYIPMYYAAPV-RSVMPPKYVFGFGADNWQDMTVPAMHALCTRISYIIGGNLPLVGSDIGFSYDNQRTPCTGDLMVRYVQAGCL-LPWFRNHY-D--RWIESKDHGKD-YQELYMYEMTLRKFVEFRYRWQEV-TGGHDGRILCAPRELKFGPD----------------------FDTK--PLEGAMIFVREGA------FPLGNNRAEQDGTETIYVRVRGQVDQETDS-------

(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	0.6133

(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	2pe4A	0.74	2.98	0.262	0.849	model1_2pe4A.pdb.gz
2	2x2hA	0.49	5.53	0.036	0.774	model1_2x2hA.pdb.gz
3	3a23A	0.49	4.73	0.054	0.702	model1_3a23A.pdb.gz
4	4jcmA	0.48	5.60	0.063	0.758	model1_4jcmA.pdb.gz
5	4jclA	0.48	5.60	0.039	0.762	model1_4jclA.pdb.gz
6	1cygA	0.48	5.62	0.044	0.762	model1_1cygA.pdb.gz
7	3lpoA	0.48	5.77	0.058	0.782	model1_3lpoA.pdb.gz
8	5awoA	0.48	5.66	0.059	0.794	model1_5awoA.pdb.gz
9	3l4uA	0.48	5.68	0.072	0.766	model1_3l4uA.pdb.gz
10	2dijA	0.48	5.51	0.027	0.746	model1_2dijA.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	1.00	catalytic activity
GO:0015929	0.99	hexosaminidase activity
GO:0004415	0.98	hyalurononglucosaminidase activity
GO:0001618	0.90	virus receptor activity
GO:0033906	0.70	hyaluronoglucuronidase activity
GO:0030294	0.67	receptor signaling protein tyrosine kinase inhibitor activity
GO:0005540	0.67	hyaluronic acid 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:0071704	0.96	organic substance metabolic process
GO:0043170	0.95	macromolecule metabolic process
GO:0030203	0.94	glycosaminoglycan metabolic process
GO:0006027	0.93	glycosaminoglycan catabolic process
GO:0009987	0.92	cellular process
GO:1903510	0.91	mucopolysaccharide metabolic process
GO:0051704	0.91	multi-organism process
GO:0030212	0.90	hyaluronan metabolic process
GO:0071493	0.88	cellular response to UV-B
GO:0071347	0.88	cellular response to interleukin-1
GO:0030214	0.88	hyaluronan catabolic process
GO:0009615	0.88	response to virus
GO:0006950	0.88	response to stress
GO:0051216	0.87	cartilage development
GO:0071495	0.86	cellular response to endogenous stimulus
GO:0071363	0.86	cellular response to growth factor stimulus
GO:0051240	0.86	positive regulation of multicellular organismal process
GO:0048522	0.86	positive regulation of cellular process
GO:0030334	0.86	regulation of cell migration
GO:0030308	0.86	negative regulation of cell growth
GO:0000302	0.86	response to reactive oxygen species
GO:0044699	0.70	single-organism process
GO:0044763	0.68	single-organism cellular process
GO:0044344	0.68	cellular response to fibroblast growth factor stimulus
GO:0032501	0.68	multicellular organismal process
GO:0061025	0.67	membrane fusion
GO:2000778	0.66	positive regulation of interleukin-6 secretion
GO:2000484	0.66	positive regulation of interleukin-8 secretion
GO:0071560	0.66	cellular response to transforming growth factor beta stimulus
GO:0070295	0.66	renal water absorption
GO:0061099	0.66	negative regulation of protein tyrosine kinase activity
GO:0051898	0.66	negative regulation of protein kinase B signaling
GO:0050729	0.66	positive regulation of inflammatory response
GO:0046718	0.66	viral entry into host cell
GO:0043407	0.66	negative regulation of MAP kinase activity
GO:0042117	0.66	monocyte activation
GO:0035810	0.66	positive regulation of urine volume
GO:0019087	0.66	transformation of host cell by virus
GO:0019064	0.66	fusion of virus membrane with host plasma membrane
GO:0010764	0.66	negative regulation of fibroblast migration

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:0044464	0.99	cell part
GO:0031982	0.97	vesicle
GO:0043231	0.96	intracellular membrane-bounded organelle
GO:0031410	0.96	cytoplasmic vesicle
GO:0005764	0.93	lysosome
GO:0031988	0.79	membrane-bounded vesicle
GO:0016020	0.76	membrane
GO:0044459	0.75	plasma membrane part
GO:0031224	0.72	intrinsic component of membrane
GO:0016324	0.72	apical plasma membrane
GO:0016023	0.72	cytoplasmic, membrane-bounded vesicle
GO:0045121	0.70	membrane raft
GO:0048471	0.69	perinuclear region of cytoplasm
GO:0046658	0.69	anchored component of plasma membrane
GO:0030139	0.69	endocytic vesicle
GO:0005902	0.69	microvillus
GO:0005829	0.69	cytosol

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	3h6oA	0.440	5.25	0.062	0.667	2.7.1.40	NA
2	0.060	2oykB	0.428	5.25	0.084	0.643	3.2.1.123	77
3	0.060	1xc6A	0.470	5.32	0.057	0.722	3.2.1.23	69,94,100
4	0.060	2ze0A	0.427	5.07	0.036	0.635	3.2.1.20	NA
5	0.060	1iq8A	0.440	5.64	0.075	0.691	2.4.2.29	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	1cgvA	0.476	5.59	0.036	0.754	0.55	MAL	complex1.pdb.gz	55,56,58,100,101,104
2	0.01	1eo7A	0.483	5.52	0.036	0.758	0.47	GLC	complex2.pdb.gz	102,103,105
3	0.01	1cdgA	0.476	5.63	0.045	0.758	0.58	MAL	complex3.pdb.gz	100,101,102,103,104,144,145,155
4	0.01	1v3mB	0.484	5.58	0.054	0.762	0.45	GAL	complex4.pdb.gz	100,101,144,155
5	0.01	3a23B	0.486	5.42	0.060	0.750	0.42	GAL	complex5.pdb.gz	77,80,109,119

	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.