D-I-TASSER Q13144-D2

D-I-TASSER results for Q13144-D2

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

Input Sequence in FASTA format

>Q13144 (219 residues)
SNLHMYSAVCADVIRRWVYPLTPEANFTDSTTQSCTHSRHNIYRGPEVSLGHGSILEENV
LLGSGTVIGSNCFITNSVIGPGCHIGDNVVLDQTYLWQGVRVAAGAQIHQSLLCDNAEVK
ERVTLKPRSVLTSQVVVGPNITLPEGSVISLHPPDAEEDEDDGEFSDDSGADQEKDKVKM
KGYNPAEVGAAGKGYLWKAAGMNMEEEEELQQNLWGLKI

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 160 180 200 \| \| \| \| \| \| \| \| \| \| SNLHMYSAVCADVIRRWVYPLTPEANFTDSTTQSCTHSRHNIYRGPEVSLGHGSILEENVLLGSGTVIGSNCFITNSVIGPGCHIGDNVVLDQTYLWQGVRVAAGAQIHQSLLCDNAEVKERVTLKPRSVLTSQVVVGPNITLPEGSVISLHPPDAEEDEDDGEFSDDSGADQEKDKVKMKGYNPAEVGAAGKGYLWKAAGMNMEEEEELQQNLWGLKI
Prediction	CCHHHHHHHHHHHHHCCCCCCCCCCCCCCCCSSSSSSSCCCSSSCCCSSSCCCCSSCCCSSSCCCCSSCCCCSSSCCSSCCCCSSCCCCSSSCCSSCCCCSSCCCCSSCCCSSCCCCSSCCCCSSCCCCSSCCCCSSCCCCSSCCCCSSCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCSSCCCCCSSSSCCCCCCCCHHHHHHHHHHCCCC
Confidence	988999999999986445555775545688416679964998988980995883995987986995997992991839989979989929944098799699899299183984997998992999992987994998994998993980675543211455411356553112343211345641566897277515788884137899987536779
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 160 180 200 \| \| \| \| \| \| \| \| \| \| SNLHMYSAVCADVIRRWVYPLTPEANFTDSTTQSCTHSRHNIYRGPEVSLGHGSILEENVLLGSGTVIGSNCFITNSVIGPGCHIGDNVVLDQTYLWQGVRVAAGAQIHQSLLCDNAEVKERVTLKPRSVLTSQVVVGPNITLPEGSVISLHPPDAEEDEDDGEFSDDSGADQEKDKVKMKGYNPAEVGAAGKGYLWKAAGMNMEEEEELQQNLWGLKI
Prediction	843620330022004410200002131367423312244540321540402340403430300440411440303401015404025404043020124040254030440101340402540404610301540402650404630302534454564455451445554454455252554443411540312114367463543552364247067
	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

                   |                   |                   |                   |                   |                   |                   |                   |                   |                   |

SS
Seq

CCHHHHHHHHHHHHHCCCCCCCCCCCCCCCCSSSSSSSCCCSSSCCCSSSCCCCSSCCCSSSCCCCSSCCCCSSSCCSSCCCCSSCCCCSSSCCSSCCCCSSCCCCSSCCCSSCCCCSSCCCCSSCCCCSSCCCCSSCCCCSSCCCCSSCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCSSCCCCCSSSSCCCCCCCCHHHHHHHHHHCCCC
SNLHMYSAVCADVIRRWVYPLTPEANFTDSTTQSCTHSRHNIYRGPEVSLGHGSILEENVLLGSGTVIGSNCFITNSVIGPGCHIGDNVVLDQTYLWQGVRVAAGAQIHQSLLCDNAEVKERVTLKPRSVLTSQVVVGPNITLPEGSVISLHPPDAEEDEDDGEFSDDSGADQEKDKVKMKGYNPAEVGAAGKGYLWKAAGMNMEEEEELQQNLWGLKI

3t57A

0.11

0.09

3.16

1.17

DEthreader

-------------HPN-AV--IGKGVSVGPYCPSSHVFG-NTELGESCVLMTGAVVGDYTFIGCNNIIGHHAVVGFLCIGNNNEIREFCSIHRTVIGDNNLIMGSCHIAHCKIGDRNIFANNTLLAGHVVVEDNTHTAGASVVHQFCHIGSAFIGGVAGERAELRGLAYRKIFVSFEER-------PAV-----SIRDS--F---TES-RR-GI-----

5b04I2

0.20

0.14

4.37

2.38

SPARKS-K

------------------------VPDSNLLNQTFSYQRHQIYKEEDVVLARSCIIKARTLIGAYTKVGDASVVANTIIGRNCTIGSNCSIDSAFLWEDVVIGDNCRIGKAILANSVKIGNNCSIEDGAIVAAGVVIGDNTIIEKNKRLT-------TFESHSQGTLNDPSLVGIGGR-----------------------------------------

6iveA

0.19

0.13

4.14

0.53

MapAlign

----------------------------------SVYRFKTPAVHPTAFIAPGAYVVGAVEVGEGASIWFGAVVRGVVVGPGTNVQDGAVLHACLLGPEVTVGHRAVVHGAVVEEGALVGMGAVVLNGARIGKNAVVGAGAVVPPGMEVGRLA---------------------------------LGVPARVVRPIDPPGNAPRYRALAERYRKAL--

7a23q

0.12

0.11

4.03

0.30

CEthreader

GFWIRETGQALDRLGCRLQGKNYFREQLSRHRTLMNVFDKAPIVDKEAFVAPSASVIGDVHIGRGSSIWYGCVLRGVSVGSGTNIQDNSLVHVTIIGDNVTIGHSAVLHGCTVEDETFIGMGATLLDGVVVEKHGMVAAGALVRQNTRIPSGEVWGGNPARFLRKLTDEEIAFISQSATNYSNLAQAHAAENAKPLNVIEFEKVLRK------------

6jlwJ3

1.00

0.75

21.10

1.84

MUSTER

-NLHMYSAVCADVIRRWVYPLTPEANFTDSTTQSCTHSRHNIYRGPEVSLGHGSILEENVLLGSGTVIGSNCFITNSVIGPGCHIGDNVVLDQTYLWQGVRVAAGAQIHQSLLCDNAEVKERVTLKPRSVLTSQVVVGPNITLPEGSVISLHPPDAEEDEDDGEFS-----------------------------------------------------

6jlwJ

0.78

21.96

1.35

HHsearch

SNLHMYSAVCADVIRRWVYPLTPEANFTDSTTQSCTHSRHNIYRGPEVSLGHGSILEENVLLGSGTVIGSNCFITNSVIGPGCHIGDNVVLDQTYLWQGVRVAAGAQIHQSLLCDNAEVKERVTLKPRSVLTSQVVVGPNITLPEGSVISLHPPDAEEDEDDKVFQNEGTLQRGKEENKYANISLKEVMQVSHVVLEPLQQMDLDSLLLPLLKAWSPVF

6jlwJ3

1.00

0.75

21.10

1.93

FFAS-3D

-NLHMYSAVCADVIRRWVYPLTPEANFTDSTTQSCTHSRHNIYRGPEVSLGHGSILEENVLLGSGTVIGSNCFITNSVIGPGCHIGDNVVLDQTYLWQGVRVAAGAQIHQSLLCDNAEVKERVTLKPRSVLTSQVVVGPNITLPEGSVISLHPPDAEEDEDDGEFS-----------------------------------------------------

4e75A

0.15

0.14

4.61

1.00

EigenThreader

DNPYLAFAILTHVFD----KKISSTSTAETAHYVVIG--ENCVVGDNTVIQSHTKLDDNVEVGKDCFIDSYVTITGSSLRDRVRIHSSTVIGQGSVLNDVRIGSNCSIDRGNTIDGVIIDNLVQIAHNVHIGSNTAIAAKCGIAGSTKIGKNCIGA--------CGGHLDNVTLT------GMSMVTKNISEAGTYSSGTGLFKKTIVRLRQLADVPLT

5b04I

0.28

0.19

5.73

4.40

CNFpred

RSLQTYDAISKDVLSRWVYPFVPDSNLLN---QTFSYQRHQIYKEEDVVLARSCIIKARTLIGAYTKVGDASVVANTIIGRNCTIGSNCSIDSAFLWEDVVIGDNCRIGKAILANSVKIGNNCSIEDGAIVAAGVVIGDNTIIEKNKRLTT--------------------------------------------------------------------

5demA

0.11

0.09

3.13

1.00

DEthreader

-------------DP-SA--RLAADVQVG-P-WS-IVGA-EVEIGEGTVIGPHVVLKGPTKIGKHNRIYQFSSVGRLVIGDHNVIREGVTIHRTTIGDHNLIMAYAHIGHSVIGNHCILVNNTALAGHVHVDDWAILSGYTLVHQYCRIGHSFSGMVFG-AEARSMLRRAKVVGHTVEEA---L-AF-E----FR-SI----------QSAT-G-----

(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	0.7256

(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	2ggoA	0.68	2.19	0.127	0.749	model1_2ggoA.pdb.gz
2	3fsbA	0.67	3.94	0.090	0.822	model1_3fsbA.pdb.gz
3	4e75A	0.67	3.94	0.061	0.831	model1_4e75A.pdb.gz
4	5f42A	0.66	3.83	0.131	0.813	model1_5f42A.pdb.gz
5	5demA	0.66	3.75	0.131	0.804	model1_5demA.pdb.gz
6	2jf2A	0.66	3.87	0.131	0.813	model1_2jf2A.pdb.gz
7	3i3xA	0.66	3.62	0.137	0.794	model1_3i3xA.pdb.gz
8	1j2zA	0.66	3.72	0.126	0.799	model1_1j2zA.pdb.gz
9	4eqyA	0.66	3.75	0.105	0.799	model1_4eqyA.pdb.gz
10	5jxxA	0.66	3.55	0.163	0.790	model1_5jxxA.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:1901363	0.95	heterocyclic compound binding
GO:0097159	0.95	organic cyclic compound binding
GO:0005085	0.94	guanyl-nucleotide exchange factor activity
GO:0003723	0.92	RNA binding
GO:0003743	0.91	translation initiation factor 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:0009987	0.98	cellular process
GO:0044237	0.96	cellular metabolic process
GO:0006413	0.89	translational initiation
GO:0044699	0.88	single-organism process
GO:0044763	0.85	single-organism cellular process
GO:0048869	0.80	cellular developmental process
GO:0048856	0.80	anatomical structure development
GO:0044767	0.80	single-organism developmental process
GO:0014003	0.79	oligodendrocyte development
GO:0050896	0.75	response to stimulus
GO:0051716	0.74	cellular response to stimulus
GO:0065007	0.73	biological regulation
GO:0050789	0.72	regulation of biological process
GO:0050794	0.71	regulation of cellular process
GO:0006950	0.71	response to stress
GO:0042221	0.70	response to chemical
GO:0009408	0.69	response to heat
GO:2000112	0.68	regulation of cellular macromolecule biosynthetic process
GO:0080090	0.68	regulation of primary metabolic process
GO:0051171	0.68	regulation of nitrogen compound metabolic process
GO:0033554	0.68	cellular response to stress
GO:0010468	0.68	regulation of gene expression
GO:0048708	0.66	astrocyte differentiation
GO:0042552	0.66	myelination
GO:0035690	0.66	cellular response to drug
GO:0034976	0.66	response to endoplasmic reticulum stress
GO:0014002	0.66	astrocyte development
GO:0006417	0.65	regulation of translation
GO:0006446	0.64	regulation of translational initiation
GO:0010033	0.61	response to organic substance
GO:0043434	0.60	response to peptide hormone
GO:0009749	0.60	response to glucose
GO:0048518	0.59	positive regulation of biological process
GO:0048522	0.58	positive regulation of cellular process
GO:0051247	0.57	positive regulation of protein metabolic process
GO:0051173	0.57	positive regulation of nitrogen compound metabolic process
GO:0044702	0.57	single organism reproductive process
GO:0031328	0.57	positive regulation of cellular biosynthetic process
GO:0010628	0.57	positive regulation of gene expression
GO:0010557	0.57	positive regulation of macromolecule biosynthetic process
GO:0003006	0.57	developmental process involved in reproduction
GO:0045948	0.56	positive regulation of translational initiation
GO:0001541	0.56	ovarian follicle development

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:0044444	0.98	cytoplasmic part
GO:0043234	0.92	protein complex
GO:0005851	0.89	eukaryotic translation initiation factor 2B complex
GO:0005737	0.76	cytoplasm

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	0.079	2vheA	0.545	2.59	0.145	0.607	2.7.7.23	NA
2	0.066	2jf2A	0.658	3.87	0.131	0.813	2.3.1.129	NA
3	0.060	3eg4A	0.603	3.30	0.130	0.712	2.3.1.117	NA
4	0.060	1v3wA	0.568	2.03	0.105	0.616	4.2.1.1	NA
5	0.060	3fttA	0.486	3.53	0.086	0.585	2.3.1.-	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	0.22	1hv9A	0.631	3.54	0.103	0.753	1.34	COA	complex1.pdb.gz	87,103,104,120,122
2	0.20	3fsbA	0.669	3.94	0.090	0.822	1.36	COA	complex2.pdb.gz	45,63,64,80,81,97
3	0.12	3i3xA	0.657	3.62	0.137	0.794	1.11	U22	complex3.pdb.gz	67,69,70,86,87,101,102,103,104,105,118
4	0.10	3i3xC	0.657	3.63	0.132	0.794	0.93	U22	complex4.pdb.gz	84,87,101,103,104,105,119,120,121,122,136
5	0.10	3mqgA	0.583	2.67	0.132	0.662	1.34	U5P	complex5.pdb.gz	80,81,98,112,115
6	0.09	1j2zA	0.657	3.72	0.126	0.799	0.81	SOG	complex6.pdb.gz	61,63,64,79,80,97,98
7	0.08	2wlfA	0.585	3.31	0.096	0.717	1.08	ACO	complex7.pdb.gz	49,51,67,69,70,84,86,87,101,119
8	0.06	2oi7A	0.633	3.42	0.100	0.753	1.33	GN1	complex8.pdb.gz	61,64,78,79,80,81

	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.