D-I-TASSER Q8IYU8-D1

D-I-TASSER results for Q8IYU8-D1

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

Input Sequence in FASTA format

>Q8IYU8 (272 residues)
MAAAAGSCARVAAWGGKLRRGLAVSRQAVRSPGPLAAAVAGAALAGAGAAWHHSRVSVAA
RDGSFTVSAQKNVEHGIIYIGKPSLRKQRFMQFSSLEHEGEYYMTPRDFLFSVMFEQMER
KTSVKKLTKKDIEDTLSGIQTAGCGSTFFRDLGDKGLISYTEYLFLLTILTKPHSGFHVA
FKMLDTDGNEMIEKREFFKLQKIISKQDDLMTVKTNETGYQEAIVKEPEINTTLQMRFFG
KRGQRKLHYKEFRRFMENLQTEIQEMEFLQFS

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 160 180 200 220 240 260 \| \| \| \| \| \| \| \| \| \| \| \| \| MAAAAGSCARVAAWGGKLRRGLAVSRQAVRSPGPLAAAVAGAALAGAGAAWHHSRVSVAARDGSFTVSAQKNVEHGIIYIGKPSLRKQRFMQFSSLEHEGEYYMTPRDFLFSVMFEQMERKTSVKKLTKKDIEDTLSGIQTAGCGSTFFRDLGDKGLISYTEYLFLLTILTKPHSGFHVAFKMLDTDGNEMIEKREFFKLQKIISKQDDLMTVKTNETGYQEAIVKEPEINTTLQMRFFGKRGQRKLHYKEFRRFMENLQTEIQEMEFLQFS
Prediction	CCCCHCHHHHHCCCCCCCCCCCCCCCCCCCCCCCHHHHSCCCCCCHHHHHHHHHCCCCCCCCCCHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCSCCCCCSSCCHHHHHHHHCCCCCCCCHCHHHHHHHHHHHHHHHCCCCCCHHHHSSSCCCCCSSSHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCSSCHHHHHHHHHHHCCCCCHHHCCCCCCCCCCCCCHHHHHHHHHHHHHHCCCCCCCSCHHHHHHHHHHHHHHHHHHHHHHCC
Confidence	96420012310034666564212466445677622331013332115677774111101245304567777666412113782789999998432321893643999999983255433110111211555888775223321113313525999517399999999972121899999999837999982269999999998612320210333323444321001322247899860788998227999999999999999999998519
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 160 180 200 220 240 260 \| \| \| \| \| \| \| \| \| \| \| \| \| MAAAAGSCARVAAWGGKLRRGLAVSRQAVRSPGPLAAAVAGAALAGAGAAWHHSRVSVAARDGSFTVSAQKNVEHGIIYIGKPSLRKQRFMQFSSLEHEGEYYMTPRDFLFSVMFEQMERKTSVKKLTKKDIEDTLSGIQTAGCGSTFFRDLGDKGLISYTEYLFLLTILTKPHSGFHVAFKMLDTDGNEMIEKREFFKLQKIISKQDDLMTVKTNETGYQEAIVKEPEINTTLQMRFFGKRGQRKLHYKEFRRFMENLQTEIQEMEFLQFS
Prediction	63333321220132344344434244432444222100001021000021234444424446452354345424542443451541450044101344635420214200410034333462425404443155125424434423200202365030203000000121343453032004000324554032500330152144545345244444445542444440322023321356454403172035005603531043006528
	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                 160                 180                 200                 220                 240                 260

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

SS
Seq

CCCCHCHHHHHCCCCCCCCCCCCCCCCCCCCCCCHHHHSCCCCCCHHHHHHHHHCCCCCCCCCCHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCSCCCCCSSCCHHHHHHHHCCCCCCCCHCHHHHHHHHHHHHHHHCCCCCCHHHHSSSCCCCCSSSHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCSSCHHHHHHHHHHHCCCCCHHHCCCCCCCCCCCCCHHHHHHHHHHHHHHCCCCCCCSCHHHHHHHHHHHHHHHHHHHHHHCC
MAAAAGSCARVAAWGGKLRRGLAVSRQAVRSPGPLAAAVAGAALAGAGAAWHHSRVSVAARDGSFTVSAQKNVEHGIIYIGKPSLRKQRFMQFSSLEHEGEYYMTPRDFLFSVMFEQMERKTSVKKLTKKDIEDTLSGIQTAGCGSTFFRDLGDKGLISYTEYLFLLTILTKPHSGFHVAFKMLDTDGNEMIEKREFFKLQKIISKQDDLMTVKTNETGYQEAIVKEPEINTTLQMRFFGKRGQRKLHYKEFRRFMENLQTEIQEMEFLQFS

1gqiA

0.06

0.05

2.04

0.67

DEthreader

TINAAAAELQRG------LSGLLNIVALVIIVVLYGHLLRLIQTQ-----DYARINASLGINGTV---V--LVKASER-QGVINPTVQSSWYAFGRMWDHQISAATAADEWL-RM--T-----FSNQP-AFI-EPV-KQ-------MMLV------------SREAGVNYRHYGPAPWTTAVYYHRASK-TGI-GF-NR-------ALAQYP--E-----PIAKAWGSVPEDLIL---MQSGRNLWQELVHKYYQGVEQVRAMQRTWDQQEA

6aghA1

1.00

0.62

17.29

1.47

SPARKS-K

-----------------------------------------------------------------------------------SLRKQRFMQFSSLEHEGEYYMTPRDFLFSVMFEQMERKTSVKKLTKKDIEDTLSGIQTAGCGSTFFRDLGDKGLISYTEYLFLLTILTKPHSGFHVAFKMLDTDGNEMIEKREFFKLQKIISKQ---------------------EINTTLQMRFFGKRGQRKLHYKEFRRFMENLQTEIQEMEFLQFS

6lb8A

0.25

0.21

6.50

0.89

MapAlign

--NQDVDAAVRGILRNAKLKPVYDS----LDAVRRAALINMVFQMGETGVAGFTNSLRMLQQKRWDEAAVNLAKSRWYRIRAYSTPDKIFRYFATLKVEAEVFMTPEDFVRSITP---------------NQYIIKRFREKFADEGSIFYTLGECGLISFSDYIFLTTVLSTPQRNFEIAFKMFDLNGDGEVDMEEFEQVQSIIR---------------------SQGLCSALTTYFFGADLKGKLTIKNFLEFQRKLQHDVLKLEFER--

6lb8A

0.23

0.20

6.33

0.56

CEthreader

VFQMGETGVAGFTNSLRMLQQKRWDEAAVNLAKSRWYNQTPNRAKRVITTFRTGTWDAYHMEEKKSGFRDRKVMEYENRIRAYSTPDKIFRYFATLKVIAEVFMTPEDFVRSITPNQYI---------------IKRFREKFADEGSIFYTLGECGLISFSDYIFLTTVLSTPQRNFEIAFKMFDLNGDGEVDMEEFEQVQSIIRSQ---------------------GLCSALTTYFFGADLKGKLTIKNFLEFQRKLQHDVLKLEFERHD

6iihA

0.71

0.62

17.65

1.07

MUSTER

FNQDVDAAVRGILRNAKLKP-VYDSLDAVRRAALINTGVAGFTNSLRMAAVNLAKSIWYNQTPNRAKRVITTFRTGT-WDAYHMLRKQRFMQFSSLEHEGEYYMTPRDFLFSVMFEQM---TSVKKLTKKDIEDTLSGIQTAGCGSTFFRDLGDKGLISYTEYLFLLTILTKPHSGFHVAFKMLDTDGNEMIEKREFFKL-----------------------------INTTLQMRFFGKRGQRKLHYKEFRRFMENLQTEIQEMEFLQFS

6iihA

0.71

0.61

17.24

1.27

HHsearch

VDAAV--RGILRNA-KLK--PVYDSLDAVRRAALIETGVAGFTNSLRMLQQKRWEAAVNLA--KSIWYNQTKITTFRTGTAYHMLRKQRFMQFSSLEHEGEYYMTPRDFLFSVMFEQMT---SVKKLTKKDIEDTLSGIQTAGCGSTFFRDLGDKGLISYTEYLFLLTILTKPHSGFHVAFKMLDTDGNEMIEKREFFKLI-----------------------------NTTLQMRFFGKRGQRKLHYKEFRRFMENLQTEIQEMEFLQFS

6iihA

0.47

0.40

11.67

0.77

EigenThreader

NAKLKPVYDSLVRRAALINMVFQMGETGVAGFTNSLRMLQQDEAAVNLA------KSIWYNQTPNRAKRVITTFRTGTWDAYHMLRKQRFMQFSSLEHEGEYYMTPRDFLFSVMFEQMTSVKKL---TKKDIEDTLSGIQTAGCGSTFFRDLGDKGLISYTEYLFLLTILT------------------KP----------HSGFHVAFKMLDTDGNEMIEKREFFKLINTTLQMRFFG---KRGQRKLKEFRRFMENLQTEIQEMEFLQFS

6aghA1

1.00

0.62

17.29

2.01

FFAS-3D

-----------------------------------------------------------------------------------SLRKQRFMQFSSLEHEGEYYMTPRDFLFSVMFEQMERKTSVKKLTKKDIEDTLSGIQTAGCGSTFFRDLGDKGLISYTEYLFLLTILTKPHSGFHVAFKMLDTDGNEMIEKREFFKLQKIISKQ---------------------EINTTLQMRFFGKRGQRKLHYKEFRRFMENLQTEIQEMEFLQFS

6lb8A

0.29

0.23

6.95

1.18

HHsearch

MVFQMGETGVTNSLR---------------MLQQKRWDEAAVNLAK--SRWYNQTPNRA--KRVITTFRTHMEMEYENRIRAYSTPDKIFRYFATLKVEAEVFMTPEDFVRSITPNQYIIKR----F-----------REKFADEGSIFYTLGECGLISFSDYIFLTTVLSTPQRNFEIAFKMFDLNGDGEVDMEEFEQVQSIIRSQG--------------------LC-SALTTYFFGADLKGKLTIKNFLEFQRKLQHDVLKLEFERHD

6aghA

1.00

0.62

17.29

1.76

CNFpred

-----------------------------------------------------------------------------------SLRKQRFMQFSSLEHEGEYYMTPRDFLFSVMFEQMERKTSVKKLTKKDIEDTLSGIQTAGCGSTFFRDLGDKGLISYTEYLFLLTILTKPHSGFHVAFKMLDTDGNEMIEKREFFKLQKIISKQ---------------------EINTTLQMRFFGKRGQRKLHYKEFRRFMENLQTEIQEMEFLQFS

(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	0.5892

(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	6iihA	0.74	3.09	0.695	0.849	model1_6iihA.pdb.gz
2	6agiA	0.59	2.47	0.455	0.643	model1_6agiA.pdb.gz
3	6aghA1	0.59	1.42	0.946	0.614	model1_6aghA1.pdb.gz
4	6k7yI	0.46	2.47	0.314	0.500	model1_6k7yI.pdb.gz
5	5x0mA2	0.44	6.00	0.050	0.739	model1_5x0mA2.pdb.gz
6	6lb8A	0.43	4.14	0.188	0.559	model1_6lb8A.pdb.gz
7	1ygpA	0.43	6.26	0.052	0.743	model1_1ygpA.pdb.gz
8	2aw3A	0.43	6.42	0.057	0.757	model1_2aw3A.pdb.gz
9	4l22A	0.43	6.24	0.060	0.739	model1_4l22A.pdb.gz
10	1llwA	0.42	6.64	0.067	0.743	model1_1llwA.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:0005198	0.63	structural molecule activity
GO:0003735	0.62	structural constituent of ribosome
GO:0043167	0.52	ion binding
GO:0046872	0.51	metal 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:0009987	0.97	cellular process
GO:0044699	0.77	single-organism process
GO:0065007	0.70	biological regulation
GO:0044763	0.66	single-organism cellular process
GO:0006810	0.63	transport
GO:0008152	0.59	metabolic process
GO:0071704	0.58	organic substance metabolic process
GO:0044237	0.58	cellular metabolic process
GO:0006811	0.58	ion transport
GO:0044238	0.57	primary metabolic process
GO:0006807	0.57	nitrogen compound metabolic process
GO:0034641	0.56	cellular nitrogen compound metabolic process
GO:1901564	0.55	organonitrogen compound metabolic process
GO:1901576	0.54	organic substance biosynthetic process
GO:0065008	0.54	regulation of biological quality
GO:0044260	0.54	cellular macromolecule metabolic process
GO:0044249	0.54	cellular biosynthetic process
GO:1901566	0.53	organonitrogen compound biosynthetic process
GO:0044271	0.53	cellular nitrogen compound biosynthetic process
GO:0055074	0.52	calcium ion homeostasis
GO:0051560	0.50	mitochondrial calcium ion homeostasis
GO:0006412	0.50	translation

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:0044446	0.88	intracellular organelle part
GO:0044429	0.86	mitochondrial part
GO:0016020	0.85	membrane
GO:0031090	0.83	organelle membrane
GO:0044425	0.82	membrane part
GO:0043231	0.82	intracellular membrane-bounded organelle
GO:0005743	0.82	mitochondrial inner membrane
GO:0005739	0.81	mitochondrion
GO:0098796	0.73	membrane protein complex
GO:0044455	0.73	mitochondrial membrane part
GO:1990246	0.72	uniplex complex
GO:0031974	0.71	membrane-enclosed lumen
GO:0070013	0.70	intracellular organelle lumen
GO:0005758	0.70	mitochondrial intermembrane 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	2w0aA	0.369	5.77	0.059	0.596	1.14.13.70	NA
2	0.060	2azdB	0.433	6.26	0.049	0.746	2.4.1.1	156
3	0.060	1e9xA	0.387	5.70	0.060	0.618	1.14.13.70	239
4	0.060	3ctzA	0.391	6.35	0.061	0.691	3.4.11.9	NA
5	0.060	1fuiA	0.399	6.41	0.048	0.710	5.3.1.25	162

	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	0.01	1ofdA	0.426	6.37	0.041	0.728	0.42	F3S	complex1.pdb.gz	139,141,142,143,148,153,155,157
	2	0.01	1llwA	0.424	6.64	0.067	0.743	0.50	F3S	complex2.pdb.gz	241,242,243,244,245,246,247

	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.