D-I-TASSER Q9UPW5-D4

D-I-TASSER results for Q9UPW5-D4

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

Input Sequence in FASTA format

>Q9UPW5 (305 residues)
VFEGKVRGPIVVPTAGEETSGNSGNLRKVVMKENISSKGDEGEKKSTFMDLAKEDIKDND
RTLQQQPGDQNRTISSVHGLNNDIVKALDRITLQNIPSQTAPGFTAEMKKDCSLPLTVLT
CAKACPHMATCGNVLFEGRTVQLGKLCCTGVETEDDEDTESNSSVEQASVEVPDGPTLHD
PDLYIEIVKNTKSVPEYSEVAYPDYFGHIPPPFKEPILERPYGVQRTKIAQDIERLIHQS
DIIDRVVYDLDNPNYTIPEEGDILKFNSKFESGNLRKVIQIRKNEYDLILNSDINSNHYH
QWFYF

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 160 180 200 220 240 260 280 300 \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| VFEGKVRGPIVVPTAGEETSGNSGNLRKVVMKENISSKGDEGEKKSTFMDLAKEDIKDNDRTLQQQPGDQNRTISSVHGLNNDIVKALDRITLQNIPSQTAPGFTAEMKKDCSLPLTVLTCAKACPHMATCGNVLFEGRTVQLGKLCCTGVETEDDEDTESNSSVEQASVEVPDGPTLHDPDLYIEIVKNTKSVPEYSEVAYPDYFGHIPPPFKEPILERPYGVQRTKIAQDIERLIHQSDIIDRVVYDLDNPNYTIPEEGDILKFNSKFESGNLRKVIQIRKNEYDLILNSDINSNHYHQWFYF
Prediction	CCCCCCCCCSSSCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCSCCCCCCCCCCHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHCCCCCCCCCCCHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHCCCCCCCCSSSSCCCCCCCCCCCCCSSSSSCCCCCCCCCCSSSSCCCSSSSSSCCCCCCCCCCSSSCC
Confidence	98888898567258888778887765666544578866677778873346541124446630102556654311222334310111110011356655568764332223345777754566567653443233334566534531114666676655544234432210379999888878998863478755662224788667998999778776899552130455417887444444133145468987777788983578511365552203473485789997167899986310119
	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 \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| VFEGKVRGPIVVPTAGEETSGNSGNLRKVVMKENISSKGDEGEKKSTFMDLAKEDIKDNDRTLQQQPGDQNRTISSVHGLNNDIVKALDRITLQNIPSQTAPGFTAEMKKDCSLPLTVLTCAKACPHMATCGNVLFEGRTVQLGKLCCTGVETEDDEDTESNSSVEQASVEVPDGPTLHDPDLYIEIVKNTKSVPEYSEVAYPDYFGHIPPPFKEPILERPYGVQRTKIAQDIERLIHQSDIIDRVVYDLDNPNYTIPEEGDILKFNSKFESGNLRKVIQIRKNEYDLILNSDINSNHYHQWFYF
Prediction	44635350000001244544344541553544752544665454442324144643564545345445545332322432445135325524355344554443445445535351424334532543442242335444241342224414454554454444344324534741312313101420641512240450120312233624432122456453344302520430263551144000203415342566552020104010100220141263301000110321552200023
	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

CCCCCCCCCSSSCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCSCCCCCCCCCCHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHCCCCCCCCCCCHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHCCCCCCCCSSSSCCCCCCCCCCCCCSSSSSCCCCCCCCCCSSSSCCCSSSSSSCCCCCCCCCCSSSCC
VFEGKVRGPIVVPTAGEETSGNSGNLRKVVMKENISSKGDEGEKKSTFMDLAKEDIKDNDRTLQQQPGDQNRTISSVHGLNNDIVKALDRITLQNIPSQTAPGFTAEMKKDCSLPLTVLTCAKACPHMATCGNVLFEGRTVQLGKLCCTGVETEDDEDTESNSSVEQASVEVPDGPTLHDPDLYIEIVKNTKSVPEYSEVAYPDYFGHIPPPFKEPILERPYGVQRTKIAQDIERLIHQSDIIDRVVYDLDNPNYTIPEEGDILKFNSKFESGNLRKVIQIRKNEYDLILNSDINSNHYHQWFYF

1vt4I3

0.06

2.46

1.03

MapAlign

----------GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG--GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG--GGGGGGG

4a37A1

0.24

0.03

1.02

3.10

HHsearch

-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------MQIRADFDSGNIQVIDASDPRRIRLAIRPDL-ASQHFQWFHF

1vt4I3

0.06

2.66

0.87

CEthreader

GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG------GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG

5b5ec

0.05

0.04

1.96

0.52

EigenThreader

------------------------------------NSIFATNRDQESSGFAWWAGNARLINLSGKLLGAHVAHAGLIVFWAGAMTLFELAHFIPEKPMQGLILIPHIATLGWGVDTFPFFVVGVVHLISSAVLGFGGVYHAIRG---PETLEEYSSFFGYDWKDKNKMTTILGFHLIVLGIGALLLVAKAMFFGGHIWIGLICIAGGIWHILTTPFNTVYPPTGPEASQAQAMTFLIRDQKLGANV--------GSAQGPTGLG----------KYLMRSP-TGEIIFGGFRGPWLEPLRGPNG

4a37A1

0.27

0.04

1.11

0.49

FFAS-3D

-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------MQIRADFDSGNIQVIDASDPRRIRLAIRPDLASQ-HFQWFHF

6y4bA

0.11

0.09

3.07

0.95

SPARKS-K

LIKNKPIKIVIGISMQSPHQISNEHFVDLLRKTNEQCIRDENIRISELIVVITDGLHRHNLRLYKNVSTTSEAAGLGQKWVADNRQFLEAIGQCGISYKVI-HWEELKSVAF------NRYLQIVEEEYEKPNSEFRSIIDNLTQTHLEKLVNFLLETRDSS-FTQEDCVSATRKYLLEEAASAFEFASLKADG-----MTYP--------------GPCSPG-----FKYIYDTYLSES-------NPLPFIEYGMRGGKKLPSFWKEESP---------------------------------

3w4rA

0.11

0.03

0.94

0.58

CNFpred

-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------STRMAFVRSVVDFLNKYN-FDGLDLDWEYPGAADRGGSFSDKDKFLYLVQELRRAFIREGKGWELTAAVPL-----------

4knhA

0.06

0.04

1.76

0.67

DEthreader

VHRFLLELEQDAIAKPA--IFGIPPKKFIRCEAKGRSMLRLVEQHLALHAVQHAYTEFSGMGFQDLRGINLDDEQRTK-FLALKGAFDFIL----SVAADC---KA-Q-EWQ-P-LGARQWLQLLREEDEQRQLR--PNHEQDM---RP----------EIEPESALECRLIKLATESE------------------------------RACIFVLKLMRKTHPPESLNDSVLI-GNDDAMAATAVRFSREWNRVLRYQGE-AGVRRKPVANY--------------------------------

2pffB

0.06

2.55

0.92

MapAlign

GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG-------------GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG

2atyA

0.11

0.10

3.70

0.56

MUSTER

SGTFRLIGEKSLLCITKDKVDGTWDKPAPKCEYFNKYSSCPEPIVPGGYKIRGSTPYRHGDSCKTNFSMNNNMWGPTRLPTCVSVFPLEGSIEGRGGSELADPEVPRDCGCKPCICTVPEVSSVFIFPPKPKDVLTITLTPKVVVVDISKDDPEVQDDVEVHTAQTQPREEQFNSTFRSVSELPIMHQDNSAAFPAPIEKTISKTKGRPKAPQLYTIPPPKEQMAKDKVS-MITDFFPEDITVGQPAENYKNTQPIMNTNESKLNVQKNWEGNTFTSVL-----------HEGLHNHHTEK--SL

(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	0.437

(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	1w6jA	0.43	6.56	0.034	0.751	model1_1w6jA.pdb.gz
2	6riwA	0.43	6.55	0.056	0.741	model1_6riwA.pdb.gz
3	1t3tA	0.42	6.48	0.036	0.721	model1_1t3tA.pdb.gz
4	4o5pA	0.41	6.19	0.037	0.679	model1_4o5pA.pdb.gz
5	1r76A	0.32	6.67	0.037	0.551	model1_1r76A.pdb.gz
6	3sqcA1	0.31	7.29	0.033	0.574	model1_3sqcA1.pdb.gz
7	1dceB	0.30	7.08	0.046	0.544	model1_1dceB.pdb.gz
8	1pmiA	0.30	6.86	0.031	0.544	model1_1pmiA.pdb.gz
9	1r9jB	0.30	6.85	0.036	0.528	model1_1r9jB.pdb.gz
10	2cjpA	0.28	5.89	0.047	0.453	model1_2cjpA.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:0004181	1.00	metallocarboxypeptidase activity
GO:0008092	0.88	cytoskeletal protein binding
GO:0015631	0.87	tubulin 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:0009987	0.94	cellular process
GO:0008152	0.92	metabolic process
GO:0071704	0.91	organic substance metabolic process
GO:0044237	0.91	cellular metabolic process
GO:0044238	0.90	primary metabolic process
GO:0043170	0.90	macromolecule metabolic process
GO:0044260	0.89	cellular macromolecule metabolic process
GO:0044699	0.88	single-organism process
GO:0019538	0.88	protein metabolic process
GO:0035608	0.87	protein deglutamylation
GO:0035610	0.85	protein side chain deglutamylation
GO:0048856	0.82	anatomical structure development
GO:0044767	0.82	single-organism developmental process
GO:0032501	0.82	multicellular organismal process
GO:0035609	0.76	C-terminal protein deglutamylation
GO:0044763	0.74	single-organism cellular process
GO:0016043	0.72	cellular component organization
GO:0006996	0.71	organelle organization
GO:0007005	0.69	mitochondrion organization
GO:0050905	0.68	neuromuscular process
GO:0021772	0.68	olfactory bulb development
GO:0021702	0.68	cerebellar Purkinje cell differentiation
GO:0001754	0.68	eye photoreceptor cell differentiation

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:0044444	1.00	cytoplasmic part
GO:0043229	1.00	intracellular organelle
GO:0005829	0.98	cytosol
GO:0043231	0.94	intracellular membrane-bounded organelle
GO:0005739	0.92	mitochondrion
GO:0005634	0.91	nucleus
GO:0005737	0.90	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	0.060	2vdcA	0.385	6.60	0.035	0.672	1.4.1.13	NA
2	0.060	1kyaA	0.401	6.40	0.050	0.685	1.10.3.2	NA
3	0.060	3cskA	0.381	6.41	0.036	0.652	3.4.14.4	NA
4	0.060	2hrgA	0.402	6.17	0.055	0.669	1.10.3.2	NA
5	0.060	1fokA	0.386	6.16	0.062	0.639	3.1.21.4	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	1ydiA	0.216	5.85	0.029	0.351	0.17	III	complex1.pdb.gz	70,73,76,79,80,83,87
2	0.01	2ivfA	0.400	6.89	0.056	0.721	0.26	SF4	complex2.pdb.gz	252,254,267,268,277
3	0.01	3s90B	0.211	5.81	0.017	0.321	0.12	III	complex3.pdb.gz	81,85,89,92,93,96
4	0.01	1syqA	0.226	5.82	0.017	0.357	0.21	III	complex4.pdb.gz	15,19,78,85,89,93,96
5	0.01	3rf3A	0.213	6.38	0.036	0.361	0.15	III	complex5.pdb.gz	8,11,12,14,89

	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.