I-TASSER-MTD Results for job ITM118

[Click on ITM118_results.tar.bz2 to download the tarball file including all results listed on this page]

Query Sequence and Predicted Domain Definition

>example (230 residues)
MNELVDTTEMYLRTIYDLEEEGVTPLRARIAERLDQSGPTVSQTVSRMERDGLLRVAGDRHLELTEKGRALAIAVMRKHRLAERLLVDVIGLPWEEVHAEACRWEHVMSEDVERRLVKVLNNPTTSPFGNPIPGLDELGVGPEPGADDANLVRLTELPAGSPVAVVVRQLTEHVQGDIDLITRLKDAGVVPNARVTVETTPGGGVTIVIPGHENVTLPHEMAHAVKVEKV
domain 1: 1-66 domain 2: 67-141 domain 3: 142-230
3 domains in total. Different colors represent different domains. The domain definition is used for the domain structure modeling, see the domain boundary prediction part for details.

Final Full-length Models Predicted by I-TASSER-MTD

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Top 5 models constructed by I-TASSER-MTD

Click to view	eTM-score	eRMSD(Å)	P-score	PDB file
Model 1	0.92+-0.08	2.8+-0.7	0.25	Download model
Model 2	0.78+-0.11	4.2+-1.2	0.24	Download model
Model 3	0.74+-0.15	4.8+-1.1	0.20	Download model
Model 4	0.72+-0.14	5.0+-1.4	0.19	Download model
Model 5	0.70+-0.16	5.3+-1.6	0.12	Download model

Probabilties of inter-domain interactions

domain1-domain2: 1.00; domain1-domain3: 0.17; domain2-domain3: 0.85;

(a)	Colored by domain: domain 1 in red; domain 2 in blue; domain 3 in green.
(b)	For each target, I-TASSER-MTD generates an ensemble of structural conformations by starting from a set of initial models generated by different templates. The server reports up to five final models sorted by the energy. The accuracy of each model is quantitatively evaluated by estimated TM-score (eTM-score) and estimated RMSD (eRMSD) that are calculated based on the significance of the structural analogous templates for domain models assembly, convergence parameters of the domain assembly simulations, satisfaction degrees of the inter-domain distances/interfaces, and the estimated accuracy of the individual domain model. eTM-score is typically in the range of [0,1], where an eTM-score of higher value signifies a model with a high confidence and vice-versa.
(d)	Since the top 5 models are ranked by the energy or cluster size, it is possible that the lower-rank models have a higher eTM-score in rare cases. Although the first model has a better quality in most cases, it is also possible that the lower-rank models have a better quality than the higher-rank models as seen in our benchmark tests.
	More about eTM-score
(e)	P-score is used to estimate the population formed in the modeling simulations based on the structural similarity or SPICKER clustering. P-score ranges from 0 to 1, and a higher value means the structure occurs more often in the simulation trajectory.
(f)	The inter-domain interaction is defined as ≥1 residue pairs with distance <8Å apart from the linker region. The probability ranges from 0 to 1, and a large value indicates the two domains have a large probability of interaction.

Predicted Individual Domain Structures

Structure of domain 1

Download dom1.pdb
eTM-score=0.76

Estimated distance error of domain 1 Download distance error of domain 1

Click to view the predicted function

Structure of domain 2

Download dom2.pdb
eTM-score=0.77

Estimated distance error of domain 2 Download distance error of domain 2

Click to view the predicted function

Structure of domain 3

Download dom3.pdb
eTM-score=0.7

Estimated distance error of domain 3 Download distance error of domain 3

Click to view the predicted function

Predicted Secondary Structure

	1 20 40 60 80 100 120 140 160 180 200 220 \| \| \| \| \| \| \| \| \| \| \| \|
Sequence	MNELVDTTEMYLRTIYDLEEEGVTPLRARIAERLDQSGPTVSQTVSRMERDGLLRVAGDRHLELTEKGRALAIAVMRKHRLAERLLVDVIGLPWEEVHAEACRWEHVMSEDVERRLVKVLNNPTTSPFGNPIPGLDELGVGPEPGADDANLVRLTELPAGSPVAVVVRQLTEHVQGDIDLITRLKDAGVVPNARVTVETTPGGGVTIVIPGHENVTLPHEMAHAVKVEKV
Prediction	CCCCCHHHHHHHHHHHHHHHHCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCSSSCCCCCSSSCHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHCCCCHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHCCCCCSSSSSSSSSCCCCCCCHHHHHHHHHHCCCCCCSSSSSSSCCCCSSSSSSCCSSSSCCHHHHCCCSSSSC
Conf.Score	97567689999999999996189866999999979993799999999999197898179726458889999999999999779999998499989999999998636989999999998379887999997897333666676543221211044348994289999994112357999999999909999829999995699749999699389848888412047759
	H: Helix; S: Strand; C: Coil

Predicted Solvent Accessibility

	1 20 40 60 80 100 120 140 160 180 200 220 \| \| \| \| \| \| \| \| \| \| \| \|
Sequence	MNELVDTTEMYLRTIYDLEEEGVTPLRARIAERLDQSGPTVSQTVSRMERDGLLRVAGDRHLELTEKGRALAIAVMRKHRLAERLLVDVIGLPWEEVHAEACRWEHVMSEDVERRLVKVLNNPTTSPFGNPIPGLDELGVGPEPGADDANLVRLTELPAGSPVAVVVRQLTEHVQGDIDLITRLKDAGVVPNARVTVETTPGGGVTIVIPGHENVTLPHEMAHAVKVEKV
Conf.Score	87524643130020003026675413143006317144210140043036431022254330202640351044004202002410341060436302620240111326500510261173054044342025364324245443334222303404644402000210253265244004203726031424030343574311021466541502460054020558
	Values range from 0 (buried residue) to 8 (highly exposed residue)

Information for Domain Boundary Detection

Predicted domain boundary on contact map

FU-score curve of continuous domain

FU-score heatmap of discontinuous domain

Predicted domain(s)

Download contact map

Download the FU-score (continuous)

Download the FU-score (discontinuous)

Modeling^a
Domain 1(D1): 1-66
Domain 2(D2): 67-141
Domain 3(D3): 142-230
Without linker^b
Domain 1(D1): 1-64
Domain 2(D2): 73-141
Domain 3(D3): 151-230

(a) Domain definition for the domain structure modeling. (b) Domain definition without including the linker.

Top 10 Full-length Templates for Domain Assembly

Rank

Template

SeqId

TplScore

                1                 20                  40                  60                  80                 100                 120                 140                 160                 180                 200                 220                 
|                  |                   |                   |                   |                   |                   |                   |                   |                   |                   |                   |

Query

MNELVDTTEMYLRTIYDLEEEGVTPLRARIAERLDQSGPTVSQTVSRMERDGLLRVAGDRHLELTEKGRALAIAVMRKHRLAERLLVDVIGLPWEEVHAEACRWEHVMSEDVERRLVKVLNNPTTSPFGNPIPGLDELGVGPEPGADDANLVRLTELPAGSPVAVVVRQLTEHVQGDIDLITRLKDAGVVPNARVTVETTPGGGVTIVIPGHENVTLPHEMAHAVKVEKV

4o6jA

0.29

0.76

-----VTEEDYLKIIQELVLYKGYATLADISRSLNVKRQSVRDEINHLISLSMAEK----------SGDREANRFLRKHRTAEILLSRCIGIPWERVDEEAMGIE-HGM--T-EEIIQRTEGVDRCPHGNP--------------PV--ADVRITSL-L-PDSTARISRIVYE-T--DDILHFLALNGLIPGKDIKIESVK-DTVRVLV-DGRSIEIPTD----------

6o5cA

0.27

0.76

----TPNKEDYLKCIYEIGEQEPKITNKMVAEKMHVSAPAVSEMIKKMISQGWIVK----------KGYALVANLYRKHRLIEVFLIHQLGYNTQEVHQEAEVLEHTVSDTFIDRLDKILDFPDFCPHGGT--------------EM--NTTTLNTITE-L-GRFRLSRIHD--H-FD-LIQYLETHHLNINTELTLTIDTFKTYTICY-GDKELVIPEN----------

5cviB

0.27

0.72

-----PNKEDYLKIIYELSERDEKISNKQIAEK-SVSAPAVSE-VKKLLLEDLVLK----------KKQILASSLYRKHRLIEVFL-NHLNYTADEIHEEAEVLEHTVSDVFVERLDKFLNYPKVCPHGGT--------------ER--YRTTLKGVTE---GVYLLKRVQDN-F--Q-LLKY-EQHHLKIGDELRLLYDAFGAYTIEK-DGEQLQVTSA----------

6ndlA

0.19

0.54

----SKYSQDVLQLLYKNK--PNYISGQSIAESLNISRTAVKKVIDQLKLEGCKID-----------AFSMISKFNLFIALGIRDAIQ-HFSQFLERLLQEIEKRYNQLFSEIREEYIAASNI------------------GRF-RH-----KWPND---WNRTLLFTEN-------------------DKQFKGQAIDLDYGYLIVRDEAGESHRL-I-----------

3rirA

0.19

0.53

----SKYSQDVLQLLYKNK--PNYISGQSIAESLNISRTAVKKVIDQLKLEGCKID-----------AFSMISKFNLFIALGIRDAIQ-HFSQFLERLLQEIEKRYNQLFSEIREEYNAASNI------------------GRF-RH-----KWPND---WNRTLLFTEN-------------------DKQFKGQAIDLDYDYLIVRDEAGESHRL-I-----------

2ewnA

0.21

0.51

---DNTVPLKLIALLANGE----FHSGEQLGETLGMSRAAINKHIQTLRDWGVDVF----------QGPAAAIGLSLVIGIVMAEVLRKLGILLAAMLIRELRAALELELAPYLSRWEKL-DNF-----------------NDLY-LQDRK-----------INRPV-KL-I--I-GD--KE-I----F---G-ISRGIDKQGALLLEQ-DGIIKPWM-G----------

3qphA

0.24

0.50

KEILTYWTLLVYGPSTAKE-----IST-KSGIPY-NR--VY-DTISSLKLRGFVTE--------------------------EVIGMTVVKSIIFSQYSLIIEIFKESTLEK-EI-IG--DIRFFA---MF----------NTVNF-NPK--HAVDFVKNLKRNIYAE-I-T----GKNLGRLET---LT--G-RVVGYTLSVNNIHLETENGVVKVGGM----------

4gygA

0.26

0.48

TMRLTAEDWRVLTAVEMGSKNHEIVPTPLIEKI------GVHKSIATLAKAGLIAR----------WMYLSRLAAIKEFAFMKALYEEGF---------EPAVMS---FNIDFPQ-MV-SMLDAAL--ASG---------------------KL------------DRAH-LTGGLDLALHTH-ADVYS---VGSRIGV-GKESDIMIVAKQKVLKIHRL----------

6k8nA

0.29

0.48

VSSAGRVQSPTLVQVVNSEIERSRYTKVSLLKWMSNTEATRGRIIEILVKRKYLTN----------ELCKYHYEAKVRLLDAVEIWKERTKYDHKKILKRISSSTGK--------------------M-------------TKSDILS----GLISFPTNSQKIPSIYNKGEN-SSYRKLVDLVRKITGG-KYVVKQAI--KILIRFSVSADNWIYH-------------

4xgcC

0.29

0.47

HTALPPDLSVVYKLHLECGR---MINLFDWLQAFRVIQARFTRAVAELQFLGYIKM----------RDLLHFLLFRCSLEFLTELVGDLPRC--GKLRRELYVNCLAII---------KVNALERT---QF----------FHFFGG--NAFAL-CTDYSKLGKLTMETRLP--SFRP-YVEI-CRIAVLTDD----------------DYLKKKQLLCP----------

(a)	All the residues are colored in black; however, those residues in template which are identical to the residue in the query sequence are highlighted in color. Coloring scheme is based on the property of amino acids, where polar are brightly coloured while non-polar residues are colored in dark shade. (more about the colors used)
(b)	Rank of templates represents the top five structural aligenment templates identified by using TM-align.
(c)	SeqId is the ratio between the number of identical residues and query length.
(d)	TplScore is the score of the template calculated based on harmonic mean of TM-scores between all domain models and the template.

Predicted Distance/Interface Map for Domain Assembly

CA distance map with distance < 20Å	CB distance map with distance < 20Å	CA interface map with distance < 18Å	CB interface map with distance < 18Å
Download CA distance map	Download CB distance map	Download CA interface map	Download CB interface map

Proteins Structurally Close to the Query Protein

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Top 10 structural analogs in PDB (as identified by TM-align)

Rank	PDB Hit	TM-score	RMSD^a	IDEN^a	Cov.	Download Alignment
1	1c0wB	0.89	1.59	0.589	0.952	model1_1c0wB.pdb.gz
2	3hrsA	0.77	2.86	0.241	0.922	model1_3hrsA.pdb.gz
3	7b1vA	0.77	3.10	0.619	0.926	model1_7b1vA.pdb.gz
4	1fx7A	0.76	3.21	0.778	0.930	model1_1fx7A.pdb.gz
5	6o5cA	0.72	3.30	0.244	0.887	model1_6o5cA.pdb.gz
6	5zr4A	0.72	1.96	0.291	0.791	model1_5zr4A.pdb.gz
7	4o6jA	0.72	3.31	0.271	0.909	model1_4o6jA.pdb.gz
8	5cviA	0.70	3.32	0.238	0.878	model1_5cviA.pdb.gz
9	2f5cA	0.48	1.93	0.221	0.517	model1_2f5cA.pdb.gz
10	2x4hA	0.48	2.39	0.252	0.552	model1_2x4hA.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:1901363	0.89	heterocyclic compound binding
GO:0097159	0.89	organic cyclic compound binding
GO:0003700	0.86	transcription factor activity, sequence-specific DNA binding
GO:0003677	0.86	DNA binding
GO:0046983	0.84	protein dimerization 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:0008152 0.83 metabolic process

GO:0050896 0.81 response to stimulus

GO:0009987 0.81 cellular process

GO:0044237 0.80 cellular metabolic process

GO:0071704 0.77 organic substance metabolic process

GO:0009058 0.73 biosynthetic process

GO:0044249 0.72 cellular biosynthetic process

GO:0006807 0.72 nitrogen compound metabolic process

GO:0010043 0.70 response to zinc ion

GO:1901576 0.69 organic substance biosynthetic process

GO:0034641 0.64 cellular nitrogen compound metabolic process

GO:1901360 0.63 organic cyclic compound metabolic process

GO:0006725 0.63 cellular aromatic compound metabolic process

GO:0044271 0.60 cellular nitrogen compound biosynthetic process

GO:0044699 0.55 single-organism process

GO:0044238 0.55 primary metabolic process

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:0044424 1.00 intracellular part

GO:0005886 0.93 plasma membrane

GO:0005737 0.87 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

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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	1fxxA	0.411	5.68	0.100	0.674	3.1.11.1	9,79
2	0.060	2a1sC	0.275	6.52	0.029	0.530	3.1.13.4	NA
3	0.060	1mdwA	0.316	6.26	0.043	0.574	3.4.22.53	NA
4	0.060	2qxfA	0.414	5.68	0.017	0.713	3.1.11.1	NA
5	0.060	1mioD	0.409	6.11	0.055	0.726	1.18.6.1	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

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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	0.37	1c0wD	0.741	1.03	0.697	0.761	1.91	QNA	complex1.pdb.gz	7,36,37,39,40,43,47,50
2	0.10	1c0wA	0.734	0.97	0.705	0.752	0.80	CO	complex2.pdb.gz	79,98,172,175
3	0.04	2h090	0.462	2.36	0.258	0.517	0.94	III	complex3.pdb.gz	32,34,85,90,92,93,96,100,103,104,107,108,109
4	0.03	3jsoB	0.297	3.25	0.119	0.348	1.23	QNA	complex4.pdb.gz	5,7,36,37,39,40,43,44,50,59
5	0.01	2ff4B	0.414	5.27	0.069	0.648	0.66	III	complex5.pdb.gz	51,52,53,54,55,66,67

	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.

[Back to server]

Reference:

Xiaogen Zhou, Wei Zheng, Yang Li, Robin Pearce, Chengxin Zhang, Eric W. Bell, Guijun Zhang, and Yang Zhang. I-TASSER-MTD: A deep-learning based platform for multi-domain protein structure and function prediction, to be submitted.

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