D-I-TASSER Q9HCC8-D3

D-I-TASSER results for Q9HCC8-D3

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

Input Sequence in FASTA format

>Q9HCC8 (257 residues)
LVGHRGAPMLAPENTLMSLRKTAECGATVFETDVMVSSDGVPFLMHDEHLSRTTNVASVF
PTRITAHSSDFSWTELKRLNAGSWFLERRPFWGAKPLAGPDQKEAESQTVPALEELLEEA
AALNLSIMFDLRRPPQNHTYYDTFVIQTLETVLNARVPQAMVFWLPDEDRANVQRRAPGM
RQIYGRQGGNRTERPQFLNLPYQDLPLLDIKALHKDNVSVNLFVVNKPWLFSLLWCAGVD
SVTTNDCQLLQQMRYPI

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 160 180 200 220 240 \| \| \| \| \| \| \| \| \| \| \| \| LVGHRGAPMLAPENTLMSLRKTAECGATVFETDVMVSSDGVPFLMHDEHLSRTTNVASVFPTRITAHSSDFSWTELKRLNAGSWFLERRPFWGAKPLAGPDQKEAESQTVPALEELLEEAAALNLSIMFDLRRPPQNHTYYDTFVIQTLETVLNARVPQAMVFWLPDEDRANVQRRAPGMRQIYGRQGGNRTERPQFLNLPYQDLPLLDIKALHKDNVSVNLFVVNKPWLFSLLWCAGVDSVTTNDCQLLQQMRYPI
Prediction	CSSCCCCCCCCCCHHHHHHHHHHHHCCCSSSSSSSSCCCCCSSSSCCCCCCCCCCCCCCCCCCCCCCHHHCCHHHHHHCCCCCCCCCCCCCCCCCCCCCCCHHHCCCCCCCCHHHHHHHHHHCCCSSSSSSCCCCCCCCHHHHHHHHHHHHHHHCCCCCSSSSSCCHHHHHHHHHHCCCCCSSCCCCCCCCCCCCCSSCCCCCCCCHHHHHHHHHHCCSSSSSCCCCHHHHHHHHHHCCCSSSSCCHHHHHHHHCCC
Confidence	94258998899621399999999919899998661847995999579998776799876565566725559899998577874457667543345543221343189867989999999771198899983799876522779999999999971999779995399999999997999413211134300128929836710099999999999099899965797999999998199999818799999854529
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 160 180 200 220 240 \| \| \| \| \| \| \| \| \| \| \| \| LVGHRGAPMLAPENTLMSLRKTAECGATVFETDVMVSSDGVPFLMHDEHLSRTTNVASVFPTRITAHSSDFSWTELKRLNAGSWFLERRPFWGAKPLAGPDQKEAESQTVPALEELLEEAAALNLSIMFDLRRPPQNHTYYDTFVIQTLETVLNARVPQAMVFWLPDEDRANVQRRAPGMRQIYGRQGGNRTERPQFLNLPYQDLPLLDIKALHKDNVSVNLFVVNKPWLFSLLWCAGVDSVTTNDCQLLQQMRYPI
Prediction	21003213332222014003300614030000101003441000002640510031544246545230250216204402022323643444444424434344157130110430052047370200000122454442044003300530274514300000023500430262045022010233434323020000415302460053027342412544253351032014101413426235214556578
	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

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

SS
Seq

CSSCCCCCCCCCCHHHHHHHHHHHHCCCSSSSSSSSCCCCCSSSSCCCCCCCCCCCCCCCCCCCCCCHHHCCHHHHHHCCCCCCCCCCCCCCCCCCCCCCCHHHCCCCCCCCHHHHHHHHHHCCCSSSSSSCCCCCCCCHHHHHHHHHHHHHHHCCCCCSSSSSCCHHHHHHHHHHCCCCCSSCCCCCCCCCCCCCSSCCCCCCCCHHHHHHHHHHCCSSSSSCCCCHHHHHHHHHHCCCSSSSCCHHHHHHHHCCC
LVGHRGAPMLAPENTLMSLRKTAECGATVFETDVMVSSDGVPFLMHDEHLSRTTNVASVFPTRITAHSSDFSWTELKRLNAGSWFLERRPFWGAKPLAGPDQKEAESQTVPALEELLEEAAALNLSIMFDLRRPPQNHTYYDTFVIQTLETVLNARVPQAMVFWLPDEDRANVQRRAPGMRQIYGRQGGNRTERPQFLNLPYQDLPLLDIKALHKDNVSVNLFVVNKPWLFSLLWCAGVDSVTTNDCQLLQQMRYPI

2oogD

0.26

0.24

7.43

1.50

DEthreader

TIAHRGASGYAPEHTFQAYDKSHELKASYIEIDLQRTKDGHLVAMHDETVNRTTNG-------H-GKVEDYTLDELKQLDAGSWFN-K-KYPKY------ARASYKNAKVPTLDEILERYGP-NANYYIETKS----PDVYPGMEEQLLASLKKHHLKHVMIQSFSDESLKKIHRQNKHVPLVKLVELFRLIRSAIGLGPDYTDLTEQNTHHLKDLGFIVHPYTVNEKADMLRLNKYGVDGVFTNFADKYKEVIKEG

2pz0B

0.22

0.19

6.15

2.09

SPARKS-K

VIAHRGDSKNVPENTIAAFKRAMELGADGIELDVQLTKDGHLVVIHDETVDRTTNGEGF--------VKDFTLEEIKKLDAGI----------------KFGEKFAGERIPTLYEVFELIGDKDFLVNIEIKSGIVLYP---GIEEKLIKAIKEYNFERVIISSFNHYSLRDVKKMAPHLKIGLLYQCGLVEMEAYSLHPFYFNIIPELVEGCKKNGVKLFPWTVDRKEDMERMIKAGVDGIITDDPETLINLVRKG

2pz0B

0.23

0.20

6.24

1.18

MapAlign

VIAHRGDSKNVPENTIAAFKRAMELGADGIELDVQLTKDGHLVVIHDETVDRTTNG--------EGFVKDFTLEEIKKLDAGIKF----------------GEKFAGERIPTLYEVFELIGDKDFLVNIEIKSG---IVLYPGIEEKLIKAIKEYNFERVIISSFNHYSLRDVKKMAPHLKIGLLYQWHMALRMAYSLHPFYFNIIPELVEGCKKNGVKLFPWTVDRKEDMERMIKAGVDGIITDDPETLINL----

2oogD

0.28

0.25

7.75

0.98

CEthreader

TIAHRGASGYAPEHTFQAYDKSHELKASYIEIDLQRTKDGHLVAMHDETVNRTTNG--------HGKVEDYTLDELKQLDAGSWFNKKYPKY--------ARASYKNAKVPTLDEILERYG-PNANYYIETKSPD----VYPGMEEQLLASLKKHHLGHVMIQSFSDESLKKIHRQNKHVPLVKLVDKGEIRSYAIGLGPDYTDLTEQNTHHLKDLGFIVHPYTVNEKADMLRLNKYGVDGVFTNFADKYKEVIKEG

2pz0B

0.23

0.20

6.36

1.82

MUSTER

VIAHRGDSKNVPENTIAAFKRAMELGADGIELDVQLTKDGHLVVIHDETVDRTTNGEG--------FVKDFTLEEIKKLDAGIKFGEK----------------FAGERIPTLYEVFELIGDKDFLVNIEIKSGIVLYPG---IEEKLIKAIKEYNFERVIISSFNHYSLRDVKKMAPHLKIGLLYQCGLLRMEAYSLHPFYFNIIPELVEGCKKNGVKLFPWTVDRKEDMERMIKAGVDGIITDDPETLINLVRKG

5t91A

0.23

0.21

6.70

2.54

HHsearch

TVAHRGASGYVPEHTILSYETAQKMKADFIELDLQMTKDGKLIVMHDEKLDRTTNGMG--------WVKDHTLADIKKLDAGSWFNEAYPEKAK--------PQYVGLKVPTLEEVLDRFGK-HANYYIETKSPDTY----PGMEEKLIASLQKHKLGQVIIQSFSKESLVKVHQLQPNLPTVQLLEAKQIKTYAVGAGPDYKALNQENVRMIRSHGLLLHPYTVNNEADMHRLLDWGVTGVFTNYPDLFHKVKKGY

3qvqA

0.24

0.21

6.67

2.54

FFAS-3D

VIAHRGSSGQAPENTLASLHLAGQQGIKWVEIDVL-SGDGIPVIFHDDYLSRTTDGDG--------LIYKTPLAELKQLDAGSWKG----------------QEYQQETIPTLLEAIEVISQYGGLNLELKPCEGLEEETIAASVEVLKQH--WPQDLPLLFSSFNYFALVSAKALWPEIARGYNVSAIPEHLDCAGLHIHQSFFDVQQVSDIKAAGYKVLAFTINDESLALKLYNQGLDAVFSDYPQKIQSIDSHI

2pz0B

0.22

0.20

6.25

1.12

EigenThreader

TLAHRGDSKNVPENTIAAFKRAMELGADGIELDVQLTKDGHLVVIHDETVDRTTNGE--------GFVKDFTLEEIKKLDAGIKFGEK----------------FAGERIPTLYEVFELIGDKDFLVNIEIKSGIVLYPG---IEEKLIKAIKEYNFEERVIISSNHYSLRDVKKMAPHLKIGLLYCGLVEPMEAYSLHPFYFNIIPELVEGCKKNGVKLFPWTVDRKEDMERMIKAGVDGIITDDPETLINLVRKG

3qvqA

0.24

0.21

6.67

2.31

CNFpred

VIAHRGSSGQAPENTLASLHLAGQQGIKWVEIDVMLSGDGIPVIFHDDYLSRTTDGDG--------LIYKTPLAELKQLDAGSWKGQE----------------YQQETIPTLLEAIEVISQYGMGLNLELKPCE---GLEEETIAASVEVLKQHWPLPLLFSSFNYFALVSAKALWPEIARGYNVSAIPS-LDCAGLHIHQSFFDVQQVSDIKAAGYKVLAFTINDESLALKLYNQGLDAVFSDYPQKIQSAIDSH

3l12A

0.25

0.23

7.25

1.50

DEthreader

VIGHRGARGV-PENTLEGFAFTLAAGVRALEFDVV-TADGVPVVTHNHHLANATRDGQHWLTGAERQVAE-TYAEIRALDVG-GLDGRTGRFPDQA-----F--LTGIHVPRLGELLDLCAGYAPYLLLELKSDPALHDAARAEVAAVLADVRRYREPRTV-HSFDWALLGECRRQAPDLPTSYLSQSLQAVAGGQLWCPYFLDVTPELVAEAHDLGLIVLTWTVNEPEDIRR-ATTGVDGIVTDYPGRTQRILIDG

(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	0.8869

(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	2oogD	0.88	1.31	0.271	0.918	model1_2oogD.pdb.gz
2	4r7oA	0.88	1.38	0.209	0.914	model1_4r7oA.pdb.gz
3	3l12A	0.87	2.19	0.238	0.949	model1_3l12A.pdb.gz
4	5t91A	0.87	1.50	0.237	0.918	model1_5t91A.pdb.gz
5	1t8qB	0.87	2.36	0.215	0.957	model1_1t8qB.pdb.gz
6	2pz0B	0.86	1.36	0.226	0.895	model1_2pz0B.pdb.gz
7	3ch0A	0.85	2.15	0.189	0.926	model1_3ch0A.pdb.gz
8	3qvqA	0.85	1.25	0.250	0.887	model1_3qvqA.pdb.gz
9	2otdA	0.81	1.75	0.232	0.872	model1_2otdA.pdb.gz
10	2o55A	0.81	1.77	0.235	0.860	model1_2o55A.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	0.98	catalytic activity
GO:0016788	0.97	hydrolase activity, acting on ester bonds
GO:0008081	0.96	phosphoric diester hydrolase activity
GO:0008889	0.94	glycerophosphodiester phosphodiesterase activity
GO:0047389	0.60	glycerophosphocholine phosphodiesterase 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	0.94	cellular process
GO:0044699	0.91	single-organism process
GO:0008152	0.88	metabolic process
GO:0071704	0.86	organic substance metabolic process
GO:0065007	0.85	biological regulation
GO:0044710	0.85	single-organism metabolic process
GO:0044238	0.85	primary metabolic process
GO:0044763	0.83	single-organism cellular process
GO:0044237	0.83	cellular metabolic process
GO:0006629	0.82	lipid metabolic process
GO:0044255	0.77	cellular lipid metabolic process
GO:0019637	0.77	organophosphate metabolic process
GO:0006796	0.77	phosphate-containing compound metabolic process
GO:0044242	0.76	cellular lipid catabolic process
GO:0006644	0.76	phospholipid metabolic process
GO:0009395	0.75	phospholipid catabolic process
GO:0006650	0.67	glycerophospholipid metabolic process
GO:0046475	0.66	glycerophospholipid catabolic process
GO:0065008	0.57	regulation of biological quality
GO:0030643	0.56	cellular phosphate ion homeostasis

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	0.98	cell part
GO:0044424	0.89	intracellular part
GO:0016020	0.71	membrane
GO:0044444	0.63	cytoplasmic part
GO:0044446	0.61	intracellular organelle part
GO:0042995	0.50	cell projection

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	0.257	2v81A	0.555	2.96	0.108	0.650	4.1.2.21	31
2	0.184	3ch0A	0.855	2.15	0.189	0.926	3.1.4.46	5,226
3	0.067	1wx0A	0.553	3.30	0.117	0.685	2.2.1.2	NA
4	0.067	1v5xA	0.546	3.21	0.105	0.665	5.3.1.24	NA
5	0.067	1g69B	0.566	3.11	0.092	0.673	2.5.1.3	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	0.05	1ydy0	0.877	2.33	0.201	0.965	1.01	III	complex1.pdb.gz	10,11,16,17,20,21,24,77,93,94,106,108,115,118,119,122,123
2	0.04	1vd60	0.758	1.78	0.210	0.817	0.45	III	complex2.pdb.gz	191,205,226,232,233,235
3	0.02	1wq5A	0.603	3.41	0.126	0.728	0.52	SO4	complex3.pdb.gz	6,7,28
4	0.02	1wq5A	0.603	3.41	0.126	0.728	0.49	GOL	complex4.pdb.gz	2,3,4,7,22,25,28,29,30
5	0.02	1r3wA	0.621	3.64	0.084	0.786	0.41	CP3	complex5.pdb.gz	4,6,7,8,34,50,164
6	0.01	1gjwA	0.610	4.33	0.061	0.813	0.46	GLC	complex6.pdb.gz	21,22,25,27

	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.