D-I-TASSER Q9UPU7-D2

D-I-TASSER results for Q9UPU7-D2

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

Input Sequence in FASTA format

>Q9UPU7 (277 residues)
AREPARLCGYLQKLSGKGPLRGYRSRWFVFDARRCYLYYFKSPQDALPLGHLDIADACFS
YQGPDEAAEPGTEPPAHFQVHSAGAVTVLKAPNRQLMTYWLQELQQKRWEYCNSLKKDLS
SQKELVRLLQQTVRSSQYDKYFTSSRLCEGVPKDTLELLHQKDDQILGLTSQLERFSLEK
ESLQQEVRTLKSKVGELNEQLGMLMETIQAKDEVIIKLSEGEGNGPPPTVAPSSPSVVPV
ARDQLELDRLKDNLQGYKTQNKFLNKEILELSALRRN

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 160 180 200 220 240 260 \| \| \| \| \| \| \| \| \| \| \| \| \| AREPARLCGYLQKLSGKGPLRGYRSRWFVFDARRCYLYYFKSPQDALPLGHLDIADACFSYQGPDEAAEPGTEPPAHFQVHSAGAVTVLKAPNRQLMTYWLQELQQKRWEYCNSLKKDLSSQKELVRLLQQTVRSSQYDKYFTSSRLCEGVPKDTLELLHQKDDQILGLTSQLERFSLEKESLQQEVRTLKSKVGELNEQLGMLMETIQAKDEVIIKLSEGEGNGPPPTVAPSSPSVVPVARDQLELDRLKDNLQGYKTQNKFLNKEILELSALRRN
Prediction	CCCCCCSSSSSSSSCCCCCCCCCCSSSSSSSCCCCSSSSSCCCCCCCCCCCSSCCCCSSSSSCCCCCCCCCCCCCCSSSSSCCCSSSSSCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHC
Confidence	9998644578996369988777521589995897489996687765667625237728998346666665545553145426961576315999999999999999999999764222321246777642223321355310123320356045789998888999999999999999999999999999999999999999999999999999999999998532254311001110267899999999999999999999999999999998609
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 160 180 200 220 240 260 \| \| \| \| \| \| \| \| \| \| \| \| \| AREPARLCGYLQKLSGKGPLRGYRSRWFVFDARRCYLYYFKSPQDALPLGHLDIADACFSYQGPDEAAEPGTEPPAHFQVHSAGAVTVLKAPNRQLMTYWLQELQQKRWEYCNSLKKDLSSQKELVRLLQQTVRSSQYDKYFTSSRLCEGVPKDTLELLHQKDDQILGLTSQLERFSLEKESLQQEVRTLKSKVGELNEQLGMLMETIQAKDEVIIKLSEGEGNGPPPTVAPSSPSVVPVARDQLELDRLKDNLQGYKTQNKFLNKEILELSALRRN
Prediction	8653452001010336544242142020003764120000233445414230424412221324444455444442123130432112233334631442231012014422532444353455215324443544635544455446564455335224534531550453155154534414641541553154046415413542553443134025435644554455555445535544452550364155255334403520440451368
	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

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

SS
Seq

CCCCCCSSSSSSSSCCCCCCCCCCSSSSSSSCCCCSSSSSCCCCCCCCCCCSSCCCCSSSSSCCCCCCCCCCCCCCSSSSSCCCSSSSSCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHC
AREPARLCGYLQKLSGKGPLRGYRSRWFVFDARRCYLYYFKSPQDALPLGHLDIADACFSYQGPDEAAEPGTEPPAHFQVHSAGAVTVLKAPNRQLMTYWLQELQQKRWEYCNSLKKDLSSQKELVRLLQQTVRSSQYDKYFTSSRLCEGVPKDTLELLHQKDDQILGLTSQLERFSLEKESLQQEVRTLKSKVGELNEQLGMLMETIQAKDEVIIKLSEGEGNGPPPTVAPSSPSVVPVARDQLELDRLKDNLQGYKTQNKFLNKEILELSALRRN

6pbcA

0.09

0.08

3.05

1.12

EigenThreader

CRSLEVGTVMTLFYSKKSQRP--ERKTFQVKLETRQITWS-------IEGSIDIREIKEIRPGKTSDPAFRPDQSHCFVILYGLKTLSLQATSEDEVNMWIKGLTWLMEDTLQAATPLQIERWLRKQFYSVGQFAQLYRSLMYSAQKTMDLPFEFQQFLLEYQGELWAVDRLQVQEFMLSFLREAYARCLRMSDVLHTIKEHAAQQRNMAQHFRKVLGDTLLTKPLHSSEKWFHGKLGAGRDGRHIAERLLTEYCIETG-----------------A

3a8pA

0.10

0.08

2.92

1.32

FFAS-3D

--------GWLFFKPLVVARRKWKQYWVTLK--GCTLLFYETYGKSAPRCALFAEDSIVQSVPEHPK------KEHVFCLSNSCDVYLFQATSQTDLENWVTAIHSACASLFAKKHGKEDTVRLLKSQTRSLLQKIDMDSKMKK--------------MAELQLSVVSDPKNRKAIENQIRQWEQNLEKFHMDLFRMRCYLASLQGGELPNPKSLL--------------------AATSRPSKLALGRLGVSVSSF---HALVCSR----------

3a8pA

0.14

0.10

3.57

1.08

SPARKS-K

---VVRKAGWLFFKPELVARRKWKQYWVTLKG--CTLLFYETYGKSAPRCALFAEDSIVQSV------PEHPKKEHVFCLSNSCDVYLFQATSQTDLENWVTAIHSACASLFAKKHGKVRLLKSQTRSLLQKIDMDSKMKKMAELQLSVVSDP---KNRKAIENQIRQWEQNLEKFHMDLFRMRCYLASLQKSLLPSKLALGRLVLSVSSFHALVCSRD----------------------------------------------------------

2lkoA

0.14

0.06

2.11

1.30

HHsearch

ITSIPELADYIKVFKPKKTLKGYKQYWCTFKDTS--ISCYKSKEESSPAHQMNLRGCEVTPDVNIS------GQKFNIKLLIPMNEIWLRCDNEKQYAHWMAACRLASKGKTMADS---SYNL---------------EVQNILSFLKMQH------------------------------------------------------------------------------------------------------------------------------

7ctpA

0.10

3.62

0.61

CEthreader

LDERIVFSGNLFQHQEDS--KKWRNRFSLVPHNYGLVLYENKAAQVPPRAVINSAGYKILTSVDQTAKLKCPTQFPLILWHPYARHYYFCMMTEAEQDKWQAVLQDCIRHCNNGWEMLCGNEVQILSNLVMEELGPELKAELGPRLKGKPQERQRQWIQISDAVYHMVYEQAKARFEEVLSKVQQVQPAMQAVIRTDMDQIITSKEHLASKIRAFILPKAEVCVRNHVQPYIPSILEALMVPTSQGFTEVRDVFFKEVTDMNLNVINEGGIDKLGEY

3qr0A

0.11

0.10

3.81

1.10

EigenThreader

IELKWPKVKFLKWEEGSS---GFIEILLRVDPKGYFLYWK--IEGKEDTQLLDLAYVRDIRCAKYAKPPKIPLQDKCVTICHGLEWTHLVAENSSVAKKWSEEVFSYAYLSLNKNQLGEWEKLYFRLTTVQKCLSDDRARISKALEKIGWPSGDTFFKFYLALLERSEIEGIFKELSVMFRDFLNDMAQCEALINDYESAVNKKGKEGLLYFLMCHRLDLGANMKLTLAAGHQLTGKSSVEIYRQVLLTDVVYAIAESAQQKLLAQYCNEAFGELLL

3a8nA

0.08

0.06

2.39

1.10

FFAS-3D

--------GALAVKNESATRRKWKHYWVSLK--GCTLFFYETDSV--PKHAVWVENSIV------QAVPEHPKKDFVFCLSNSLDAFLFQTTSQTELENWITAIHSACAAAVARHHHKEDTLRLLKSEIKKLEQKIDMDEKMKK--------------MGEMQLSSVTDSKKKKTILDQIFVWEQNLEQFQMDLFRFRCYLASLQGGELPNPKRLLAFASRPTKVAMGRLGIFSVS-----------------------------------------

7ctpA

0.10

0.09

3.50

0.91

SPARKS-K

LDERIVFSGNLFQHQED--SKKWRNRFSLVPHN-YGLVLYENKRQVPPRAVINSAGYKILTSLPGTTAKLKCPTQFPLILWHPARHYYFCMMTEAEQDKWQAVLQDCIRHCNNGIPEEGPAFTDAIRMYRQSQILSNLVMEELGPELKAKGKPQERQRQWIQISDAVYHMVYEQAKARFEEVLSKVQQVQPAMQAVIRTDMDQIITSKEHLASKIRAFILPKAEVCVRNHV-------QPYIPSILEALMVPTSQGFTEVRDVFFKEVTDMNLNVIN

2tmaA

0.10

0.06

2.40

0.78

CNFpred

---------------------------------------------------------------------------------------------TEDELDKYSEALKDAQEKLELAEKKATDAEADVASLNRRIQLVEEELDRAQERLATALQEEAEKAADESERGMKVIESRAQKDEEKMEIQEIQLKEAKHIAEDADRKYEEVARKLVIIESDLERAEERAELSEGKCAELEEE----IKTVTNNLKSLEAQAEKYSQKEDKYEEEIKVLSDKLKE

6j72A

0.03

0.02

1.24

0.83

DEthreader

---VVIAGQ-K-------------GKSQLLN----IVARVGDDESTVLATVVSYGPSPL--------------LRSHAI--------SLND-ELNEESNFPAIVKFLSEVLSRQNDRIRDQIVDEIRSAAEHLLLAVESELSSFNDP---G--ERERLTAELERRKQEAQDALALWQQVLSDGIADLTADVDHDLRHRFRIIAAHTEKVIDGCD-PT---------LHWEIAEL--A---A--DN--W---R-------------------------

(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	0.6199

(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	1f31A	0.44	5.75	0.095	0.715	model1_1f31A.pdb.gz
2	6j72A	0.44	5.30	0.033	0.661	model1_6j72A.pdb.gz
3	2j69A	0.43	5.92	0.052	0.682	model1_2j69A.pdb.gz
4	5nrlA	0.43	6.06	0.043	0.715	model1_5nrlA.pdb.gz
5	6rw9A	0.43	6.20	0.052	0.722	model1_6rw9A.pdb.gz
6	1vw1A	0.43	5.62	0.046	0.668	model1_1vw1A.pdb.gz
7	6r4lA	0.43	6.38	0.037	0.744	model1_6r4lA.pdb.gz
8	3qmzA	0.43	5.03	0.046	0.610	model1_3qmzA.pdb.gz
9	3jd8A	0.43	6.43	0.029	0.740	model1_3jd8A.pdb.gz
10	4aurA	0.28	5.84	0.064	0.451	model1_4aurA.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:0098772	0.72	molecular function regulator
GO:0030234	0.68	enzyme regulator activity
GO:0019899	0.66	enzyme binding
GO:0008047	0.66	enzyme activator activity
GO:0005096	0.65	GTPase activator activity
GO:0017137	0.63	Rab GTPase 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	0.90	biological regulation
GO:0050789	0.89	regulation of biological process
GO:0050794	0.82	regulation of cellular process
GO:0006810	0.75	transport
GO:0051049	0.74	regulation of transport
GO:0071702	0.70	organic substance transport
GO:0008104	0.69	protein localization
GO:0015031	0.68	protein transport
GO:0051649	0.66	establishment of localization in cell
GO:0051641	0.65	cellular localization
GO:0051128	0.65	regulation of cellular component organization
GO:0050790	0.64	regulation of catalytic activity
GO:0046907	0.64	intracellular transport
GO:0033043	0.64	regulation of organelle organization
GO:0051336	0.63	regulation of hydrolase activity
GO:0043087	0.62	regulation of GTPase activity
GO:0043085	0.62	positive regulation of catalytic activity
GO:0060627	0.61	regulation of vesicle-mediated transport
GO:0043547	0.61	positive regulation of GTPase activity
GO:0006886	0.61	intracellular protein transport
GO:0090630	0.60	activation of GTPase activity
GO:0031338	0.60	regulation of vesicle fusion

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:0005576	0.71	extracellular region
GO:0005622	0.64	intracellular
GO:0012505	0.60	endomembrane system

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	1kogH	0.239	6.29	0.020	0.408	6.1.1.3	11
2	0.060	3hmjA	0.352	6.52	0.042	0.628	2.3.1.86	NA
3	0.060	3ixzA	0.397	6.00	0.053	0.657	3.6.3.10	31
4	0.060	1qf6A	0.358	6.30	0.047	0.625	6.1.1.3	NA
5	0.060	1f1sA	0.297	6.51	0.053	0.531	4.2.2.1	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	0.01	2ckjA	0.368	6.01	0.045	0.610	0.60	FES	complex1.pdb.gz	15,17,18,20,23
2	0.01	1fiqA	0.154	5.88	0.046	0.245	0.56	FES	complex2.pdb.gz	14,15,16,18,19,21,23
3	0.01	2ckjA	0.368	6.01	0.045	0.610	0.57	FES	complex3.pdb.gz	8,9,26,28,39

	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.