D-I-TASSER Q6UXH9-D2

D-I-TASSER results for Q6UXH9-D2

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

Input Sequence in FASTA format

>Q6UXH9 (105 residues)
KACREPKISDLVRRRVLPMQVQSRETPLHQLYSAAFSKQKLQSAPTKKPALPFGDLPMGY
QHLHTQLQYECISPFYRRLGSSRRTCLRTGKWSGRAPSCIPICGK

Predicted Secondary Structure

Sequence	20 40 60 80 100 \| \| \| \| \| KACREPKISDLVRRRVLPMQVQSRETPLHQLYSAAFSKQKLQSAPTKKPALPFGDLPMGYQHLHTQLQYECISPFYRRLGSSRRTCLRTGKWSGRAPSCIPICGK
Prediction	CCCCCCCCCCCSSSSSSCCCCCCCCCCCCCCSCCCCCCCCCCCCCCCCCCCCCCCCCCCSSSSCCSSSSSSCCCCSSSSCCCSSSSCCCCCSCCCCCSSSSCCCC
Confidence	987689865101456515888887575544203677765655456789988877557862774638999975998488558728977999673799713822388
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 \| \| \| \| \| KACREPKISDLVRRRVLPMQVQSRETPLHQLYSAAFSKQKLQSAPTKKPALPFGDLPMGYQHLHTQLQYECISPFYRRLGSSRRTCLRTGKWSGRAPSCIPICGK
Prediction	852673714630444214463664634234312443553447526266461444423423242433030404543153445542312753614354340433148
	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

                   |                   |                   |                   |                   |

SS
Seq

CCCCCCCCCCCSSSSSSCCCCCCCCCCCCCCSCCCCCCCCCCCCCCCCCCCCCCCCCCCSSSSCCSSSSSSCCCCSSSSCCCSSSSCCCCCSCCCCCSSSSCCCC
KACREPKISDLVRRRVLPMQVQSRETPLHQLYSAAFSKQKLQSAPTKKPALPFGDLPMGYQHLHTQLQYECISPFYRRLGSSRRTCLRTGKWSGRAPSCIPICGK

3govA

0.17

5.63

1.85

SPARKS-K

NECPELQPPVHGKIEPSQAKFKDQVLVSCKVLKECLKDGTWSNKCRAPGELEHGLIRNNLTTYKSEIKYSCQEPYYKMLNTGIYTCSAQGVWMRSLPTCLPVCGL

3erbA

0.17

5.62

1.02

MUSTER

VRCPAPVSFENGIYTPRLGPVGGNVSFECILRGSPRPNGMWDGETPNPGISLGAVRTGFRFGHGDKVRYRCSSN-LVLTGSSERECQGNGVWSGTEPICRQPYSY

2q7zA

0.12

0.11

4.08

1.27

HHsearch

AACPHPPKIQNGHYIGSLYLPGMTISYIYLLVGKCTDQGIWSQLCSFPLFMNGISKMKKVYHYGDYVTLKCEDG-YTLEGSPWSQCQADDRWDPPLAKCTSRAHD

1c1zA

0.17

0.16

5.35

1.88

CNFpred

RTCPKPDDLPFSTVVPLKTFYEPGEEITYSRKFICPLTGLWP-VCPFAGILENGAVRYTTFEYPNTISFSCNT-GFYLNGADSAKCTEEGKWSPELPVCAPIICP

1zjkA

0.23

0.16

5.09

0.83

DEthreader

--------PPGELPLK---------------ACSIV-------DCGPPDDLPSGRVEYGVTTYKAVIQYSCEETFYTMKVNGKYVCEADGFWTKSLPVCEPVCGR

2o39C

0.15

0.14

4.80

1.81

SPARKS-K

--CEEPPTFEAMELIYYEIGERVDYKCKYFYHTICDRNHTWLETCPYIRDPLNGQAVPANYEFGYQMHFICNEG-YYLIGEEILYCELKGIWSGKPPICEKV---

1e5gA

0.15

0.14

4.79

0.68

MapAlign

NGQLDIGGVDFGSSITYSCNGYHLIGESKSYCELGSTGSMVSVKCQSPPSISNGRHNGDFYTDGSVVTYSCNS-GYSLIGNSGVLCSG-GEWSD-PPTCQI----

1c1zA

0.16

5.36

0.41

CEthreader

RTCPKPDDLPFSTVVPLKTFYEPGEEITYSCKPGYVTLKCTPRVCPFAGILENGAVRYTTFEYPNTISFSCNTG-FYLNGADSAKCTEEGKWSPELPVCAPIICP

1c1zA

0.17

0.16

5.31

1.01

MUSTER

RTCPKPDDLPFSTVVPLKTFYEP-----YVSRGGMRLTGLWPINTPFAGILENGAVRYTTFEYPNTISFSCNTG-FYLNGADSAKCTEEGKWSPELPVCAPICPP

2q7zA

0.18

5.88

1.23

HHsearch

IFCPNPPAILNGRHTGTDIPYGKEISTTFNLIGECTSNGVWSSACPHPPKIQNGHYIGSLYLPGMTISYICDPG-YLLVGKGFIFCTDQGIWSQLDHYCKEVCSF

(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	0.531

(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	2a55A	0.57	2.66	0.128	0.695	model1_2a55A.pdb.gz
2	1ojyC	0.56	2.18	0.115	0.638	model1_1ojyC.pdb.gz
3	3o8eB	0.56	2.42	0.125	0.648	model1_3o8eB.pdb.gz
4	2o39C	0.55	2.20	0.119	0.638	model1_2o39C.pdb.gz
5	2q7zA	0.55	3.31	0.129	0.752	model1_2q7zA.pdb.gz
6	1c1zA	0.54	2.15	0.133	0.638	model1_1c1zA.pdb.gz
7	3erbA	0.54	2.74	0.149	0.667	model1_3erbA.pdb.gz
8	4kkdA	0.54	1.57	0.190	0.600	model1_4kkdA.pdb.gz
9	3govA	0.54	1.50	0.190	0.600	model1_3govA.pdb.gz
10	4c16A	0.54	2.76	0.107	0.657	model1_4c16A.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:0043167	0.56	ion binding
GO:0097367	0.55	carbohydrate derivative binding
GO:0004871	0.54	signal transducer activity
GO:0004888	0.53	transmembrane signaling receptor 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:0065007	0.87	biological regulation
GO:0050789	0.80	regulation of biological process
GO:0009987	0.79	cellular process
GO:0044699	0.78	single-organism process
GO:0050794	0.73	regulation of cellular process
GO:0032502	0.69	developmental process
GO:0050896	0.67	response to stimulus
GO:0048856	0.67	anatomical structure development
GO:0044763	0.67	single-organism cellular process
GO:0048518	0.65	positive regulation of biological process
GO:0019222	0.63	regulation of metabolic process
GO:0080090	0.62	regulation of primary metabolic process
GO:0048583	0.62	regulation of response to stimulus
GO:0048519	0.61	negative regulation of biological process
GO:0044767	0.61	single-organism developmental process
GO:0065008	0.60	regulation of biological quality
GO:0048523	0.60	negative regulation of cellular process
GO:0016043	0.60	cellular component organization
GO:0031323	0.59	regulation of cellular metabolic process
GO:0048522	0.57	positive regulation of cellular process
GO:0032501	0.57	multicellular organismal process
GO:0031324	0.57	negative regulation of cellular metabolic process
GO:0042221	0.55	response to chemical
GO:0007155	0.55	cell adhesion
GO:0045934	0.53	negative regulation of nucleobase-containing compound metabolic process
GO:0044707	0.53	single-multicellular organism process
GO:0031327	0.53	negative regulation of cellular biosynthetic process
GO:1901700	0.52	response to oxygen-containing compound
GO:0060255	0.52	regulation of macromolecule metabolic process
GO:0007165	0.52	signal transduction
GO:0002682	0.52	regulation of immune system process
GO:0065009	0.51	regulation of molecular function
GO:0010033	0.51	response to organic substance
GO:0008152	0.51	metabolic process
GO:0050790	0.50	regulation of catalytic activity
GO:0048869	0.50	cellular developmental process
GO:0032879	0.50	regulation of localization
GO:0023051	0.50	regulation of signaling
GO:0010817	0.50	regulation of hormone levels
GO:0010646	0.50	regulation of cell communication
GO:0009719	0.50	response to endogenous stimulus

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:0044421	0.89	extracellular region part
GO:0044464	0.88	cell part
GO:0043226	0.81	organelle
GO:0043227	0.76	membrane-bounded organelle
GO:0016020	0.73	membrane
GO:0044424	0.67	intracellular part
GO:0005576	0.64	extracellular region
GO:0031988	0.63	membrane-bounded vesicle
GO:0044425	0.60	membrane part
GO:0070062	0.59	extracellular exosome
GO:0031224	0.51	intrinsic component of membrane
GO:0005886	0.51	plasma membrane
GO:0005615	0.51	extracellular space

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	1c7gA	0.451	3.85	0.073	0.724	4.1.99.2	NA
2	0.060	2ywfA	0.427	4.32	0.079	0.771	3.6.5.-	NA
3	0.060	2zyjA	0.431	3.80	0.056	0.686	2.6.1.39	NA
4	0.060	3ecrA	0.431	3.87	0.054	0.705	2.5.1.61	NA
5	0.060	1rtkA	0.325	5.29	0.033	0.705	3.4.21.47	55,61

	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:

Click to view	Rank	Cscore^LB	PDB Hit	TM-score	RMSD^a	IDEN^a	Cov.	BS-score	Lig. Name	Download Complex	Predicted binding site residues
	1	0.21	1elvA	0.524	1.63	0.222	0.600	0.90	UUU	complex1.pdb.gz	85,87,89,91,94

	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.