D-I-TASSER Q9ULK5-D2

D-I-TASSER results for Q9ULK5-D2

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

Input Sequence in FASTA format

>Q9ULK5 (146 residues)
VPLDCSRHLGVAAGATLALLSFLTPLAFLLLPPLLWREELEPCGTACEGLFISVAFKLLI
LLLGSWALFFRRPKASLPRVFVLRALLMVLVFLLVVSYWLFYGVRILDARERSYQGVVQF
AVSLVDALLFVHYLAVVLLELRQLQP

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 \| \| \| \| \| \| \| VPLDCSRHLGVAAGATLALLSFLTPLAFLLLPPLLWREELEPCGTACEGLFISVAFKLLILLLGSWALFFRRPKASLPRVFVLRALLMVLVFLLVVSYWLFYGVRILDARERSYQGVVQFAVSLVDALLFVHYLAVVLLELRQLQP
Prediction	CCCCCSSSHHHHHHHHHHHHHHHHHHHHHHHCHCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHSSSCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCC
Confidence	99874440577999999999999499999832103644334478555400146999999999999999824777888636999999999999999999999851231164211578999999999999999999999999983299
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 \| \| \| \| \| \| \| VPLDCSRHLGVAAGATLALLSFLTPLAFLLLPPLLWREELEPCGTACEGLFISVAFKLLILLLGSWALFFRRPKASLPRVFVLRALLMVLVFLLVVSYWLFYGVRILDARERSYQGVVQFAVSLVDALLFVHYLAVVLLELRQLQP
Prediction	75350433033321331133133323313301332344615514450422001133333313311200012455140010213313113313333333332110102344464042003102230010033323101001035358
	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

                   |                   |                   |                   |                   |                   |                   |

SS
Seq

CCCCCSSSHHHHHHHHHHHHHHHHHHHHHHHCHCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHSSSCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCC
VPLDCSRHLGVAAGATLALLSFLTPLAFLLLPPLLWREELEPCGTACEGLFISVAFKLLILLLGSWALFFRRPKASLPRVFVLRALLMVLVFLLVVSYWLFYGVRILDARERSYQGVVQFAVSLVDALLFVHYLAVVLLELRQLQP

4tweA

0.09

0.08

3.13

1.17

DEthreader

APQDLRRDSFFLPL-KVSDY-SETLRSFLQAAQQDLGA--LLESISLGPLVTAVEKFEAEAAALGQRISTLQKGSPDPLQVRMLNDQLMLLERTFLHVLWAFPGLSNACRAWAEVQRQLSIVVTALEGAAATLR--PVA-------

6tbuA

0.11

3.96

0.44

CEthreader

DTLSHDTFVAICLAMAASLAVLLCSLSIFNTVAVLILLGWQLNILESIAVSTAIGLAVDFSLHYGIHYRMSPVKERLAATQFVLSRIIGPTVMAATTTGLAGGIMMASNILPYIQIGVFLVVVMIVSWFYATFFLMSLLRVAGPQH

5y50A1

0.05

2.29

0.70

EigenThreader

DGFLRETKKLSYIAGAMIAVNSSMYVLQVISIMMVGHLGELFLSSTAIAVSFCSVTGSVVFGLASLCGQANGAKQYEKLGVHTYTGIVSLFLVCIPLSLLWTYIGDILSLIGQDEAGKFATWLIPALFGYATLQPLVRFFQAQSLI

6qkcI

0.19

0.17

5.55

0.70

FFAS-3D

--------VQVLLTTIGAFAAFGLMTIAISTDYWLYTRGLTHSGLICRASSIFPILSAILLLLGGVCVAASRVYKSKRNIILGAGILFVAAGLSNIIGVIVYISANAGKNHYSYGWSFYFGGLSFILAEVIGVLAVNIYIERS---

6zg3C

0.10

3.77

0.83

SPARKS-K

PAITTIPLTVAVFASLRPKAGAAFGLVWGLTSLLRAYVAPNGLVTILLFQNPLIALLPRLAAGWAAGLAGQESRKPLAYALSGLLASAVNTLIVILLSDLVYFIHPLALGAKSGQSLLVILFTALAVNGILEAVFSGLITPLITAP

3rkoC

0.11

0.09

3.24

0.87

CNFpred

-----SQAPTAGSVDLAGILLKTAAYGLLRFSLPLFPN--------ASAEFAPIAMWLGVIGIFYGAWMAFAQ--DIKRLIAYTSVSHMGFVLIAIYTGSQLAYQG---------AVIQMIAHGLSAAGLFILCGQLYERIHTRDM

7anzD

0.06

0.05

2.44

1.17

DEthreader

YLKMFHFLWKLRQLNNLLNWHFEMFNELNHNVVTKL----S-SR-NRRPLAKSLSIITSIRFHFTQFLNELYLVLLYIDQIFNILQTIFNFINTSQEFYSLVVTFGLLVSDQDEDLEFQLHKIKRKIYKDIYQHDYKRQLNDLKND

6ajfA3

0.12

4.33

0.66

MapAlign

PLASELTGTIGEDAAALPAIIGGLAIAGALGIMRLVAEFTPVHFFAQPVVTLGLGIAIDYGLFIVSRFREEIAEGYDTEVRRTVMTSGRTVVFSAVIIVASSVPLLLFPQGFLKSITYAIIASVMLAAILSIVLAAALAILGPRVD

4lz6A2

0.13

0.12

4.06

0.74

MUSTER

YS-RLRETVMLGFKVATIFSIGIFALLMLFPEALLFTADREVIQAGVSAMHILFCVTFLIGAQIVAGGLYQSLGKP---KQALILSLSRQIIFLIPLVLIL-------PHIFGLSGVW-WAFPIADVLSFILTVVLLYRDRNVFFL

4cofA

0.20

0.13

4.16

0.71

HHsearch

INYDSAARVALGITTVLTMTTINTH-LRETLPKIPYVKA------IDMYLMGCFVFVFLALLEYAFVNYISQPRAAIDRW--SRIVFPFTFSLFNLVYWLYYV-------------------------------------------

(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	0.5982

(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	4q25A	0.70	2.90	0.088	0.931	model1_4q25A.pdb.gz
2	7jh5A	0.70	3.58	0.048	1.000	model1_7jh5A.pdb.gz
3	1sumB	0.69	3.16	0.080	0.938	model1_1sumB.pdb.gz
4	1xwmA	0.67	3.14	0.096	0.925	model1_1xwmA.pdb.gz
5	1t72A	0.67	2.94	0.069	0.890	model1_1t72A.pdb.gz
6	3l39A	0.67	3.35	0.080	0.925	model1_3l39A.pdb.gz
7	2i0mA	0.66	3.22	0.126	0.925	model1_2i0mA.pdb.gz
8	2oltC	0.64	3.89	0.070	0.959	model1_2oltC.pdb.gz
9	2bkpA1	0.48	3.20	0.082	0.637	model1_2bkpA1.pdb.gz
10	4wrtA	0.38	3.81	0.082	0.534	model1_4wrtA.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:0005102	0.35	receptor binding
GO:0046983	0.31	protein dimerization activity
GO:0042802	0.31	identical protein binding
GO:0005109	0.30	frizzled 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:0044699	0.94	single-organism process
GO:0065007	0.93	biological regulation
GO:0050789	0.93	regulation of biological process
GO:0032502	0.93	developmental process
GO:0050794	0.92	regulation of cellular process
GO:0044767	0.92	single-organism developmental process
GO:0009653	0.92	anatomical structure morphogenesis
GO:0002009	0.83	morphogenesis of an epithelium
GO:0001736	0.82	establishment of planar polarity
GO:0048583	0.72	regulation of response to stimulus
GO:0051239	0.69	regulation of multicellular organismal process
GO:0050793	0.69	regulation of developmental process
GO:2000027	0.68	regulation of organ morphogenesis
GO:0090175	0.67	regulation of establishment of planar polarity
GO:0048598	0.64	embryonic morphogenesis
GO:0009987	0.64	cellular process
GO:0044763	0.59	single-organism cellular process
GO:0048518	0.57	positive regulation of biological process
GO:0048522	0.56	positive regulation of cellular process
GO:0048646	0.54	anatomical structure formation involved in morphogenesis
GO:0035148	0.53	tube formation
GO:0009966	0.53	regulation of signal transduction
GO:0007165	0.53	signal transduction
GO:0006928	0.53	movement of cell or subcellular component
GO:0016477	0.52	cell migration
GO:0060027	0.51	convergent extension involved in gastrulation
GO:0048584	0.51	positive regulation of response to stimulus
GO:0030111	0.51	regulation of Wnt signaling pathway
GO:0007166	0.50	cell surface receptor signaling pathway

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	1.00	cell part
GO:0016020	0.93	membrane
GO:0005886	0.92	plasma membrane
GO:0044425	0.62	membrane part

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	0.066	1wcrA	0.464	3.23	0.113	0.644	2.7.1.69	NA
2	0.060	1q2vA	0.512	4.29	0.065	0.808	3.6.4.9	NA
3	0.060	3btaA	0.518	4.13	0.035	0.753	3.4.24.69	NA
4	0.060	2epoA	0.544	3.23	0.057	0.712	3.2.1.52	NA
5	0.060	1ygeA	0.445	5.01	0.057	0.781	1.13.11.12	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	148lE	0.322	4.61	0.061	0.514	0.29	III	complex1.pdb.gz	23,53,56,57,61
2	0.01	3htgA	0.273	5.23	0.067	0.514	0.18	JZ7	complex2.pdb.gz	49,50,106
3	0.01	1nhbA	0.274	5.48	0.037	0.514	0.20	PYL	complex3.pdb.gz	48,99,104
4	0.01	1ovhA	0.273	5.55	0.037	0.520	0.38	2CM	complex4.pdb.gz	49,52,53,101,104
5	0.01	2rh1A	0.561	4.52	0.043	0.870	0.35	CLR	complex5.pdb.gz	49,52,123
6	0.01	1li2A	0.273	5.55	0.046	0.520	0.29	IPH	complex6.pdb.gz	48,49,97,104
7	0.01	186lA	0.272	5.46	0.046	0.514	0.40	N4B	complex7.pdb.gz	49,52,98,102
8	0.01	1li3A	0.273	5.21	0.057	0.514	0.37	3CH	complex8.pdb.gz	49,98,101

	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.