D-I-TASSER Q13239-D1

D-I-TASSER results for Q13239-D1

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

Input Sequence in FASTA format

>Q13239 (276 residues)
MGNSMKSTPAPAERPLPNPEGLDSDFLAVLSDYPSPDISPPIFRRGEKLRVISDEGGWWK
AISLSTGRESYIPGICVARVYHGWLFEGLGRDKAEELLQLPDTKVGSFMIRESETKKGFY
SLSVRHRQVKHYRIFRLPNNWYYISPRLTFQCLEDLVNHYSEVADGLCCVLTTPCLTQST
AAPAVRASSSPVTLRQKTVDWRRVSRLQEDPEGTENPLGVDESLFSYGLRESIASYLSLT
SEDNTSFDRKKKSISLMYGGSKRKSSFFSSPPYFED

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 160 180 200 220 240 260 \| \| \| \| \| \| \| \| \| \| \| \| \| MGNSMKSTPAPAERPLPNPEGLDSDFLAVLSDYPSPDISPPIFRRGEKLRVISDEGGWWKAISLSTGRESYIPGICVARVYHGWLFEGLGRDKAEELLQLPDTKVGSFMIRESETKKGFYSLSVRHRQVKHYRIFRLPNNWYYISPRLTFQCLEDLVNHYSEVADGLCCVLTTPCLTQSTAAPAVRASSSPVTLRQKTVDWRRVSRLQEDPEGTENPLGVDESLFSYGLRESIASYLSLTSEDNTSFDRKKKSISLMYGGSKRKSSFFSSPPYFED
Prediction	CCCCCCCCCCCCCCCCCCCCCCCCSSSSSSCCCCCCCCCCCCSCCCCSSSSSSCCCCSSSSSCCCCCCSCCSSCCCCCCCCCSSCCCCCCHHHHHHHHHCCCCCCCCSSSSCCCCCCCCSSSSSSCCCCSSSSSSSCCCCCSSSCCCCSSCCHHHHHHHHHHCCCCCCSSCCSCCCCCCCCCCCCCCCCCCCCCCHHHCCHHHHHHHCCCCCCSSSSSCCCCCSSSSSSCCCCCCHHHHHHHHHHHHHCCCCCSSSSSSSSCCCCCSSSSSSCCCC
Confidence	998889999998789999999897499993368999988775338919999947998798231789932225044455444201035579899999985359999816851578899829999846980299999959995997698322999999999964679971556810368999998534578863224200577775322124660461334765057888427888999999999999763897654699896599957999635689
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 160 180 200 220 240 260 \| \| \| \| \| \| \| \| \| \| \| \| \| MGNSMKSTPAPAERPLPNPEGLDSDFLAVLSDYPSPDISPPIFRRGEKLRVISDEGGWWKAISLSTGRESYIPGICVARVYHGWLFEGLGRDKAEELLQLPDTKVGSFMIRESETKKGFYSLSVRHRQVKHYRIFRLPNNWYYISPRLTFQCLEDLVNHYSEVADGLCCVLTTPCLTQSTAAPAVRASSSPVTLRQKTVDWRRVSRLQEDPEGTENPLGVDESLFSYGLRESIASYLSLTSEDNTSFDRKKKSISLMYGGSKRKSSFFSSPPYFED
Prediction	744636454446654336365464310000010606566401043513030135254102133364443020123333322230233303264125103445354012201416533000000022643220202237622010266443720420051036445113130330033564543545445451505455143640532552242321414364420141136524435402500520461626300200000266300000011278
	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

CCCCCCCCCCCCCCCCCCCCCCCCSSSSSSCCCCCCCCCCCCSCCCCSSSSSSCCCCSSSSSCCCCCCSCCSSCCCCCCCCCSSCCCCCCHHHHHHHHHCCCCCCCCSSSSCCCCCCCCSSSSSSCCCCSSSSSSSCCCCCSSSCCCCSSCCHHHHHHHHHHCCCCCCSSCCSCCCCCCCCCCCCCCCCCCCCCCHHHCCHHHHHHHCCCCCCSSSSSCCCCCSSSSSSCCCCCCHHHHHHHHHHHHHCCCCCSSSSSSSSCCCCCSSSSSSCCCC
MGNSMKSTPAPAERPLPNPEGLDSDFLAVLSDYPSPDISPPIFRRGEKLRVISDEGGWWKAISLSTGRESYIPGICVARVYHGWLFEGLGRDKAEELLQLPDTKVGSFMIRESETKKGFYSLSVRHRQVKHYRIFRLPNNWYYISPRLTFQCLEDLVNHYSEVADGLCCVLTTPCLTQSTAAPAVRASSSPVTLRQKTVDWRRVSRLQEDPEGTENPLGVDESLFSYGLRESIASYLSLTSEDNTSFDRKKKSISLMYGGSKRKSSFFSSPPYFED

2shpA

0.18

0.11

3.41

0.67

DEthreader

-------------------------------------------------------------------------------KSRRWFHPNITGVEAENLLLT-RGVDGSFLARPSKSNPGDLTLSVRRGAVTHIKIQNTGD-YYDLYGGEKFATLAELVQYYMEHGQLKEIELKYPLNC-------------ADPTSFHGHLALLEKGKHRTGD--NDGK--QLKQPLNTTRILGFWEEFET---P-HGVGTVIDVPKTQMV-------------I--

2ptkA1

0.39

0.24

6.96

2.81

SPARKS-K

-----------------------VTTFVALYDYESRTETDLSFKKGERLQIVNNTGDWWLAHSLTTGQTGYIPSNYVAPSDEEWYFGKITRRESERLLLNPENPRGTFLVRESETTKGAYCLSVSDLNVKHYKIRKLDSGGFYITSRTQFSSLQQLVAYYSKHADGLCHRLTNVCPTSKPQTQGLAKDA---------------------------------------------------------------------------------------

2ptkA

0.29

0.26

8.05

1.24

MapAlign

-----------------------VTTFVALYDYESRTETDLSFKKGERLQIVNNEGDWWLAHSLTTGQTGYIPSNYVAPSDEEWYFGKITRRESERLLLNPENPRGTFLVRESETTKGAYCLSVSDFNVKHYKIRKLDSGGFYITSRTQFSSLQQLVAYYSKHADGLCHRLTNVCPTLRLEVKLGQGCFGEVWMGTWNGTTRVAIKTLVVSEEPIYIVTEYMRLPQLVDMAAQIASGMAYVERMNYVHRDLRAANILVGENLVCKVADFGLFP---

1qcfA

0.32

0.29

8.85

0.79

CEthreader

--------------------SGIRIIVVALYDYEAIHHEDLSFQKGDQMVVLEESGEWWKARSLATRKEGYIPSNYVARVTEEWFFKGISRKDAERQLLAPGNMLGSFMIRDSETTKGSYSLSVRDDTVKHYKIRTLDNGGFYISPRSTFSTLQELVDHYKKGNDGLCQKLSVPCMSSKPQKPWEKDAWEIPRESLKLEKFGEVWMATYNKHTKVAVKTMKPGSMSVEAFLAEANVMKTLQHDKLVKLHAVVTKEPIYIITEFMAKGSLLDFLKSD

2ptkA1

0.40

0.24

7.06

1.69

MUSTER

-----------------------VTTFVALYDYESRTETDLSFKKGERLQIVNNEGDWWLAHSLTTGQTGYIPSNYVAPSAEEWYFGKITRRESERLLLNPENPRGTFLVRESETTKGAYCLSVSDLNVKHYKIRKLDSGGFYITSRTQFSSLQQLVAYYSKHADGLCHRLTNVCPTSKPQTQGLAKDA---------------------------------------------------------------------------------------

2ptkA

0.32

0.28

8.29

1.98

HHsearch

-----------------------VTTFVALYDYESRTETDLSFKKGERLQIVNNEGDWWLAHSLTTGQTGYIPSNYVAPSAEEWYFGKITRRESERLLLNPENPRGTFLVRESETTKGAYCLSVSDDNVKHYKIRKLDSGGFYITSRTQFSSLQQLVAYYSKHADGLCHRLTNVCPTSKPQTQ------------GLAKDAWEIPRESLR--LEVKLGQGCFGEVWMGTWNGTTRVAIKTLKPPEAFLRHEKLVQLYAVVSE-E-PIYIVTEYMSK

1lckA

0.45

0.25

7.41

2.17

FFAS-3D

-----------------------DNLVIALHSYEPSHDGDLGFEKGEQLRILEQSGEWWKAQSLTTGQEGFIPFNFVAKANEPWFFKNLSRKDAERQLLAPGNTHGSFLIRESESTAGSFSLSVRGEVVKHYKIRNLDNGGFYISPRITFPGLHELVRHYTNASDGLCTRLSRPCQT---------------------------------------------------------------------------------------------------

1qcfA

0.30

0.28

8.45

1.27

EigenThreader

--------------------SGIRIIVVALYDYEAIHHEDLSFQKGDQMVVLEESGEWWKARSLATRKEGYIPSNYVARVDSLETEEWISRKDAERQLLAPGNMLGSFMIRDSETTKGSYSLSVRDRQGKHYKIRTLDNGGFYISPRSTFSTLQELVDHYKKGNDGLCQKLSVPCMSSKPQKPWEKDTLQHDKLVKFMAKG---SLLDFLKSDEGSKQPLPKLIDFSAQIAEGMAFIEQRNYIHRDLRAANASLVCKIAIEDNEYTAREGAKFPIK

2h8hA

0.33

0.26

7.82

3.31

CNFpred

-------------------------TFVALYDYESRTETDLSFKKGERLQIVNTEGDWWLAHSLSTGQTGYIPSNYVAPSAEEWYFGKITRRESERLLLNAENPRGTFLVRESETTKGAYCLSVSDFNVKHYKIRKLDSGGFYITSRTQFNSLQQLVAYYSKHADGLCHRLTTVCPTSKPQTQGL------------AKDAWEIPRESLR--LEVKLGQGCFGEVWMGTWN--------------------GTTRVAIKTL--KPGTMSPEAFLQE

6md7A

0.17

0.10

3.22

0.67

DEthreader

--------------------------------------------------------------------------------SRRWFHPNITGVEAENLLLT-RGVDGSFLARPSKSNPGDFTLSVRRGAVTHIKIQNTGD-YYDLYGGEKFATLAELVQYYMEHGQLKEIELKYPLNC-------------ADPTSFHGHLAKLLKGKHRTGDDGKSK--QLKQPLNTTR--LQGFWEEFE---P-HGVGRTIDVPKTIQMV------------I--

(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	0.647

(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	2ptkA	0.69	3.68	0.301	0.819	model1_2ptkA.pdb.gz
2	1qcfA	0.67	3.95	0.331	0.830	model1_1qcfA.pdb.gz
3	2fo0A	0.66	3.89	0.240	0.793	model1_2fo0A.pdb.gz
4	3cf4A	0.43	5.92	0.059	0.721	model1_3cf4A.pdb.gz
5	4z32A	0.43	4.35	0.136	0.562	model1_4z32A.pdb.gz
6	6e9eA	0.42	6.30	0.045	0.721	model1_6e9eA.pdb.gz
7	3bkbA	0.41	4.61	0.156	0.547	model1_3bkbA.pdb.gz
8	6pbcA	0.41	3.74	0.177	0.500	model1_6pbcA.pdb.gz
9	2b3oA	0.41	3.83	0.149	0.496	model1_2b3oA.pdb.gz
10	2f48B	0.41	6.29	0.052	0.703	model1_2f48B.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:0003824	0.87	catalytic activity
GO:0016773	0.85	phosphotransferase activity, alcohol group as acceptor
GO:0016301	0.85	kinase activity
GO:0005102	0.84	receptor binding
GO:0004713	0.84	protein tyrosine kinase activity
GO:0004715	0.81	non-membrane spanning protein tyrosine kinase activity

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:0050794	0.97	regulation of cellular process
GO:0009987	0.94	cellular process
GO:0007165	0.90	signal transduction
GO:0044699	0.89	single-organism process
GO:0008152	0.89	metabolic process
GO:0071704	0.88	organic substance metabolic process
GO:0044238	0.88	primary metabolic process
GO:0044237	0.88	cellular metabolic process
GO:0044260	0.87	cellular macromolecule metabolic process
GO:0019538	0.87	protein metabolic process
GO:0016310	0.87	phosphorylation
GO:0044763	0.86	single-organism cellular process
GO:0007166	0.86	cell surface receptor signaling pathway
GO:0006468	0.86	protein phosphorylation
GO:0050896	0.84	response to stimulus
GO:0002376	0.82	immune system process
GO:0006950	0.81	response to stress
GO:0046777	0.80	protein autophosphorylation
GO:0018193	0.80	peptidyl-amino acid modification
GO:0007169	0.80	transmembrane receptor protein tyrosine kinase signaling pathway
GO:0018108	0.79	peptidyl-tyrosine phosphorylation
GO:0048869	0.78	cellular developmental process
GO:0038083	0.78	peptidyl-tyrosine autophosphorylation
GO:0042127	0.77	regulation of cell proliferation
GO:0006955	0.75	immune response
GO:0048583	0.68	regulation of response to stimulus
GO:0006952	0.68	defense response
GO:0045087	0.64	innate immune response
GO:0048518	0.62	positive regulation of biological process
GO:0030154	0.61	cell differentiation
GO:0032502	0.58	developmental process
GO:0048584	0.57	positive regulation of response to stimulus
GO:0002682	0.56	regulation of immune system process
GO:0050776	0.55	regulation of immune response
GO:0048522	0.55	positive regulation of cellular process
GO:0048856	0.53	anatomical structure development
GO:0044767	0.53	single-organism developmental process
GO:0048523	0.52	negative regulation of cellular process
GO:0031323	0.52	regulation of cellular metabolic process
GO:0009966	0.52	regulation of signal transduction
GO:0002684	0.52	positive regulation of immune system process
GO:0080090	0.51	regulation of primary metabolic process
GO:0050778	0.51	positive regulation of immune response
GO:0032879	0.51	regulation of localization
GO:0002764	0.51	immune response-regulating signaling pathway
GO:0065008	0.50	regulation of biological quality
GO:0060255	0.50	regulation of macromolecule metabolic process
GO:0007229	0.50	integrin-mediated signaling pathway
GO:0002768	0.50	immune response-regulating 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:0044444	1.00	cytoplasmic part
GO:0005737	1.00	cytoplasm
GO:0044425	0.94	membrane part
GO:0044459	0.90	plasma membrane part
GO:0016020	0.90	membrane
GO:0043229	0.81	intracellular organelle
GO:0043227	0.81	membrane-bounded organelle
GO:0043231	0.80	intracellular membrane-bounded organelle
GO:0005829	0.80	cytosol
GO:0031234	0.78	extrinsic component of cytoplasmic side of plasma membrane
GO:0005886	0.69	plasma membrane
GO:0044446	0.62	intracellular organelle part
GO:0005634	0.62	nucleus

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	0.369	1g83A	0.475	2.40	0.456	0.540	2.7.10.2	86,90,95,112,114,121,129,132,136
2	0.060	1bljA	0.345	2.15	0.462	0.377	2.7.10.2	91,111,113,121,129,132,142,144,157
3	0.060	3cf4A	0.433	5.92	0.059	0.721	1.2.99.2	NA
4	0.060	3dh9A	0.390	6.50	0.060	0.703	1.8.1.9	NA
5	0.060	2zvaA	0.275	6.62	0.059	0.500	2.7.10.2	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	0.05	2oi3A	0.214	1.98	0.277	0.228	1.38	III	complex1.pdb.gz	31,33,36,37,38,39,40,55,56,57,58,71,73,74,75,76
2	0.01	2qlqA	0.294	6.10	0.036	0.500	0.48	SR2	complex2.pdb.gz	157,158,159,160
3	0.01	3en6B	0.246	6.19	0.073	0.431	0.41	KS5	complex3.pdb.gz	107,123,125,130,131,132,166
4	0.01	3ac2A	0.288	6.18	0.037	0.500	0.43	KSE	complex4.pdb.gz	107,123,131,132
5	0.01	3acjA	0.289	6.46	0.022	0.518	0.41	KSS	complex5.pdb.gz	106,124,131,132

	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.