D-I-TASSER Q9UPR5-D2

D-I-TASSER results for Q9UPR5-D2

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

Input Sequence in FASTA format

>Q9UPR5 (302 residues)
NETVSNLTLMALGSSAPEILLSVIEVCGHNFQAGELGPGTIVGSAAFNMFVVIAVCIYVI
PAGESRKIKHLRVFFVTASWSIFAYVWLYLILAVFSPGVVQVWEALLTLVFFPVCVVFAW
MADKRLLFYKYVYKRYRTDPRSGIIIGAEGDPPKSIELDGKDSVNAVVFVALGTSIPDTF
ASKVAALQDQCADASIGNVTGSNAVNVFLGLGVAWSVAAVYWAVQGRPFEVRTGTLAFSV
TLFTVFAFVGIAVLLYRRRPHIGGELGGPRGPKLATTALFLGLWLLYILFASLEAYCHIR
GF

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 160 180 200 220 240 260 280 300 \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| NETVSNLTLMALGSSAPEILLSVIEVCGHNFQAGELGPGTIVGSAAFNMFVVIAVCIYVIPAGESRKIKHLRVFFVTASWSIFAYVWLYLILAVFSPGVVQVWEALLTLVFFPVCVVFAWMADKRLLFYKYVYKRYRTDPRSGIIIGAEGDPPKSIELDGKDSVNAVVFVALGTSIPDTFASKVAALQDQCADASIGNVTGSNAVNVFLGLGVAWSVAAVYWAVQGRPFEVRTGTLAFSVTLFTVFAFVGIAVLLYRRRPHIGGELGGPRGPKLATTALFLGLWLLYILFASLEAYCHIRGF
Prediction	CCCSSSSSSHHHHCCHHHHHHHHHHHHHCCCCCCCCSSSHHHHHHHHHHHHHHHHHHHHHCCCSCCCSSSSHHHHHHHHHHHHHHHHHHHHHHHCCCCSSSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHSSSCCCCCCSSSSSSSCCCCCCCCCSSSCCCCCCHHHHHHHHHHHHCCCCCSSSSSHHHHHHHHHHHHHHHHHHHCCSSSSCCCSSSSSCHCHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCSCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCC
Confidence	95322011101414318999999999807888876122015878999999999999973111010303441257899999999999999999961699786467889999999999999875443344455666654200100111333221222331576310001010268885578999999982678875776123436999999986887622113203664899703089999999999999999999961334235411650478999999999999999999999996883799
	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 \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| NETVSNLTLMALGSSAPEILLSVIEVCGHNFQAGELGPGTIVGSAAFNMFVVIAVCIYVIPAGESRKIKHLRVFFVTASWSIFAYVWLYLILAVFSPGVVQVWEALLTLVFFPVCVVFAWMADKRLLFYKYVYKRYRTDPRSGIIIGAEGDPPKSIELDGKDSVNAVVFVALGTSIPDTFASKVAALQDQCADASIGNVTGSNAVNVFLGLGVAWSVAAVYWAVQGRPFEVRTGTLAFSVTLFTVFAFVGIAVLLYRRRPHIGGELGGPRGPKLATTALFLGLWLLYILFASLEAYCHIRGF
Prediction	85300000010320130121000000133435431000000101011000000100000121323441332301000111112221223111101222200200000000000000010123335343453333423132232032223222212221314423432431444342331110001023543110000000000001000010110000002122442303030101131333132223322210112334403241224302100001102321231010000202220655
	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

CCCSSSSSSHHHHCCHHHHHHHHHHHHHCCCCCCCCSSSHHHHHHHHHHHHHHHHHHHHHCCCSCCCSSSSHHHHHHHHHHHHHHHHHHHHHHHCCCCSSSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHSSSCCCCCCSSSSSSSCCCCCCCCCSSSCCCCCCHHHHHHHHHHHHCCCCCSSSSSHHHHHHHHHHHHHHHHHHHCCSSSSCCCSSSSSCHCHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCSCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCC
NETVSNLTLMALGSSAPEILLSVIEVCGHNFQAGELGPGTIVGSAAFNMFVVIAVCIYVIPAGESRKIKHLRVFFVTASWSIFAYVWLYLILAVFSPGVVQVWEALLTLVFFPVCVVFAWMADKRLLFYKYVYKRYRTDPRSGIIIGAEGDPPKSIELDGKDSVNAVVFVALGTSIPDTFASKVAALQDQCADASIGNVTGSNAVNVFLGLGVAWSVAAVYWAVQGRPFEVRTGTLAFSVTLFTVFAFVGIAVLLYRRRPHIGGELGGPRGPKLATTALFLGLWLLYILFASLEAYCHIRGF

4kppA

0.10

0.08

3.08

1.17

DEthreader

EMPFSLAIVALLAVEYAVDGYFAWKAGSVGGEYVHYATANMTGANRLLIGIGWSLVAFIATLKSKEVELD-DGIRLEIFFLFLATLYAFT-LPL--KGHISPFDALVFVSLYAIYIYLSTKA-E-RE--EV---------EVGGV----------TAAGIDEFLAVQWIAPLASESPELIVAIYFVRR-FRVSASMNALISSKVNQWTLLIGTIAIIYSISAFK-L-QSLPLDARQSEEVLLTAAQSLFAVAILLDLKI------------SW-KEASALFLLFIVQLLF-PGV--EVRYIS

4k1cA

0.12

0.11

3.74

2.12

SPARKS-K

AGNTIGGLLNATFGNAVELIVSIIALKK---GQVRIVQASMLGSLLSNLLLVLGLCFIFGGYNRVQQTFNQTAAQTMSSLLAIACASLLIPAAFRATLELSRGTSIVILIVYVLFLYFQLFEQQEEETDEVMSTISR---------NPHHSLSVKSSTGLSKTFIGLIVIPIVGNAAEHVTSVLVAMK-DKMDLALGVAIGSSLQVALFVTPFMVLVGWMI----DVPMTLNFST---FETATLFIAVFLSNYLILDGESN------------WLEGVMSLAMYILIAMAFFYYPDE-----

3v5sA2

0.22

0.16

4.91

1.37

MapAlign

SNFVIGATVMAIGTSLPEILTSAYASY---MHAPGISIGNAIGSCICNIGLVLGLSAIISP-----IIVDKNLQKNIL-VYLLFVIFAAVIGI----DGFSWIDGVVLLILFIIYLRWTVKNG--------------------------------------DKVIGFTLVAFGTSLPELMVSLAAAK-RNLGGMVLGNVIGSNIADIGGALAVGSLFM---------HLPA----ENVQMAVLVIMSLLLYLFAKYSK-------------IGRWQGILFLALYIIAIALRM----------

4k1cA

0.11

0.10

3.59

0.97

CEthreader

AGNTIGGLLNATFGNAVELIVSIIALKK---GQVRIVQASMLGSLLSNLLLVLGLCFIFGGYNRVQQTFNQTAAQTMSSLLAIACASLLIPAAFRAILELSRGTSIVILIVYVLFLYFQLGSHHALFEQQEEETDEVMSTISRNPHHSLSVKSSVESTGLSKTFIGLIVIPIVGNAAEHVTSVLVAMKD-KMDLALGVAIGSSLQVALFVTPFMVLVGWMI---DVPMTLNFSTFETATLFIAVFLSNYLILDGE----------------SNWLEGVMSLAMYILIAMAFFYYPDE-----

3v5sA2

0.22

0.16

4.91

1.32

MUSTER

SNFVIGATVMAIGTSLPEILTSAYASYM---HAPGISIGNAIGSCICNIGLVLGLSAIISPIIVDKN---------LQKNILVYLLFVIFAAVIGIDG-FSWIDGVVLLILFIIYLRWTVKN--------------------------------------GDKVIGFTLVAFGTSLPELMVSLAAAKRN-LGGMVLGNVIGSNIADIGGALAVGSLFM---------HLPAENVQMAVLVIMSLLLYLFAKY------------------KIGRWQGILFLALYIIAIASLRM---------

4k1cA

0.12

0.11

3.76

4.54

HHsearch

GNTIGGLLNATFG-NAVELIVSIIALKK---GQVRIVQASMLGSLLSNLLLVLGLCFIFGGYNRVQQTFNQTAAQTMSSLLAIACALIPAAFRATLPFELSRGTSIVILIVYVLFLYFQLGSHHALFEQQEE-ETDEVMSTISRNPHHSLSVKSSESTGLSKTFIGLIVIPIVGNAAEHVTSVLVAMK-DKMDLALGVAIGSSLQVALFVTPFMVLVGWM----IDVPMTLNFS--TFET-ATLFIAVFLSNYLILDGE--S---------NW-LEGVMSLAMYILIAMAFFYYPDE-----

4kppA

0.12

0.11

3.95

1.89

FFAS-3D

--RSFSLAIVALLAVLPEYAVDGYFAWKAGSVGGEYATANMTGANRLLIGIGWSLVAFIAFRTLKSKEVELDDGIRLEIFFLFLATLYAFTLPL--KGHISPFDALVFVSLYAIYIYLSTKAETRRLSVVVLFLFAGFTILMSVEAFSEGLLETARIAGIDEFLAVQWIAPLASESPELIVAIYFVRRF-RVSASMNALISSKVNQWTLLIGTIAIIYS---ISAFKLQSLPLDARQSEEVLLTAAQSLFAVAIL------------LDLKISWKEASALFLLFIVQLLFPGVEV-------

4k1cA

0.10

0.09

3.39

1.93

EigenThreader

AGNTIGGLLNATFGNAVELIVSIIALK---KGQVRIVQASMLGSLLSNLLLVLGLCFIFGGYNRVQQNQT--AAQTMSSLLAIACASLLIPAAFRATLPFIRGTSIVILIVYVLFLYFQLGTDEVMSTISRTVIISFCADFLVGT-----IDNVVESTGLSKTFIGLIVIPIVGNAAEHVTSVLVAMK-DKMDLALGVAIGSSLQVALFVTPFMVLVGWMID---VPMTLNFSTFETATLFIAVFLSNYLILDG--------------------ESNWLEGVMSLAMYILIAMAFFYYPDE-

4kppA

0.11

0.10

3.70

1.63

CNFpred

---SFSLAIVALLAVLPEYAVDGYFAWKAGSVYVHYATANMTGANRLLIGIGWSLVAFIAFRTLSKEVELDDGIRLEIFFLFLATLYAFTLPLKG---HISPFDALVFVSLYAIYIYLSTKAEREEVEVGGVPAYLCSLKTETRRL-SEGLLETARIAGIDEFLAVQWIAPLASESPELIVAIYFVRR-FRVSASMNALISSKVNQWTLLIGTIAIIYSISAFK-LQSLPLD-ARQSEEVLLTAAQSLFAVAILLDL-------------KISWKEASALFLLFIVQLLFPGVEVRYIISAI

4k1cA

0.13

0.11

3.78

1.17

DEthreader

-E--ADGGLNATFGNAVELIVSIIALK-K-G-QVRIVQASMLGSLLSNLLLVLGLCFIFGGNRVQQTFNQT-AAQTMSSLLAIACASLLIPAAFRIDILESRGTSIVILIVYVLFLYFQLSHHALFEQQ-E--------V-STISRN---------VSTGLSKFIGLIVIPIVGNAAEHVTSVLVAMK-DKMDLALGVAIGSSLQVALFVTPFMVLVGWMID-----VPMTL-NFSTFETATLFIAVFLSNYLILD-GE------------SNWLEGVMSLAMYILIAMAFFYYPDE-----

(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	0.8147

(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	4k1cA	0.76	3.17	0.117	0.881	model1_4k1cA.pdb.gz
2	4kppA	0.76	2.99	0.108	0.868	model1_4kppA.pdb.gz
3	4kjsA	0.71	3.19	0.113	0.815	model1_4kjsA.pdb.gz
4	3v5sA	0.68	2.94	0.193	0.775	model1_3v5sA.pdb.gz
5	5j65A	0.49	5.57	0.059	0.729	model1_5j65A.pdb.gz
6	4lz6A	0.48	5.85	0.082	0.745	model1_4lz6A.pdb.gz
7	6w08A	0.47	5.69	0.058	0.699	model1_6w08A.pdb.gz
8	6ezvX	0.46	5.50	0.068	0.679	model1_6ezvX.pdb.gz
9	2ibzC	0.46	5.81	0.089	0.738	model1_2ibzC.pdb.gz
10	3vvnA1	0.37	5.17	0.078	0.536	model1_3vvnA1.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:0015368	1.00	calcium:cation antiporter activity
GO:0015081	1.00	sodium ion transmembrane transporter activity
GO:0046872	0.82	metal ion binding
GO:0005509	0.74	calcium ion binding
GO:0022821	0.71	potassium ion antiporter activity
GO:0005261	0.70	cation channel activity
GO:0031420	0.68	alkali metal ion binding
GO:0008273	0.61	calcium, potassium:sodium antiporter activity
GO:0005262	0.60	calcium channel activity
GO:0031402	0.57	sodium ion binding
GO:0030955	0.57	potassium ion 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:0065007	0.98	biological regulation
GO:0009987	0.97	cellular process
GO:0055074	0.91	calcium ion homeostasis
GO:0044699	0.91	single-organism process
GO:0072503	0.90	cellular divalent inorganic cation homeostasis
GO:0006875	0.90	cellular metal ion homeostasis
GO:0006874	0.87	cellular calcium ion homeostasis
GO:0050789	0.63	regulation of biological process
GO:0006810	0.58	transport
GO:0050794	0.53	regulation of cellular process
GO:0006811	0.53	ion transport
GO:0006816	0.51	calcium ion transport

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:0031224	0.99	intrinsic component of membrane
GO:0016021	0.97	integral component of membrane
GO:0044464	0.92	cell part
GO:0031226	0.83	intrinsic component of plasma membrane
GO:0016020	0.83	membrane
GO:0005887	0.76	integral component of plasma membrane

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	1qleA	0.363	6.27	0.038	0.593	1.9.3.1	NA
2	0.060	2np0A	0.376	5.25	0.050	0.553	3.4.24.69	NA
3	0.060	3fg3A	0.339	5.26	0.027	0.490	4.2.1.92 1.13.11.40	NA
4	0.060	1qleC	0.431	5.06	0.069	0.632	1.9.3.1	176,180
5	0.060	1z0hB	0.268	6.68	0.028	0.477	3.4.24.69	19,206

	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	0.02	1p84C	0.459	5.81	0.089	0.738	0.75	CDL	complex1.pdb.gz	6,12,204,209,210
2	0.01	3cx5N	0.457	5.77	0.093	0.735	0.46	HEM	complex2.pdb.gz	18,19,38,41,42,45,48,202,203,206,207
3	0.01	2qjyD	0.458	5.79	0.072	0.735	0.41	UQ2	complex3.pdb.gz	42,211,214,215
4	0.01	1zrtC	0.459	5.83	0.081	0.745	0.41	HEM	complex4.pdb.gz	45,48,49,51,81,82,84,88
5	0.01	1ezvC	0.448	5.89	0.063	0.725	0.42	HEM	complex5.pdb.gz	13,112,113,116,117,202,205,206,209
6	0.01	2qjkA	0.456	6.02	0.076	0.745	0.41	HEM	complex6.pdb.gz	25,33,36,37,40,41,43,44,163
7	0.01	2qjpD	0.459	5.86	0.076	0.742	0.45	HEM	complex7.pdb.gz	38,41,42,45,84,88,89,91,92
8	0.01	2qjyD	0.458	5.79	0.072	0.735	0.46	HEM	complex8.pdb.gz	37,41,42,45,210,211,214
9	0.01	2yiuD	0.457	5.98	0.068	0.742	0.47	HEM	complex9.pdb.gz	44,45,48,49,52,171,178,180,206
10	0.01	2yiuA	0.457	5.91	0.064	0.738	0.41	HEM	complex10.pdb.gz	37,44,45,47,78,81,82,85,86,88,89,92,108

	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.