D-I-TASSER results for Q4G0Z9

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

Summary of the Protein

Uniprot ID: Q4G0Z9
Protein Name: Minichromosome maintenance domain-containing protein 2
Gene Name: MCMDC2

Input Sequence in FASTA format

>Q4G0Z9 (681 residues)
MSNLKMKEAALIYLDRSGGLQKFIDDCKYYNDSKQSYAVYRFKILINPSDVVELDAELGN
HILHQPLKAAEVFQSVCFIAVKTLSLIGQLQTETQINIVLKLTHLPPLPSYGLDLCEFPL
DYTSQRFYMMQGIVIAMTTITKYTQGARFLCSDEACPLSKGFQYIRVHVPGATESATIRN
DFLCNLCASSLQEDRKFRVLGDKQIVEIIATKALRAFQGYSNNQPFRFQSLTIFLRDESV
NKMNIGNEYKIIGIPTCVKTSQTAVCIEANSITFCNSKVPSGISDNFRCLLSLTSSSCWK
FTAILANIFASQITPPGTYNLLKLCLLMSLVQTTDRNKELEDCLDILIITSDTLLIDRLL
NFSINLVPRGIRHLVSTEIFPTLSRNKYGTGAVSIQAGSALLAKGGICFIGDLASHKKDK
LEQLQTVLESRSITVYIPGKKFGEDIDQQMTFPVQCSFWSFVDVDSSSRRNAQKINTLIG
QMDCSLIPANLVEAFGLLINCNESSPCHPFLPTVQHTLNKAINPEGLFYAASRQFTTEDF
EKLLAFAKNLNVEFSLEAERMTHGYYLASRRIRTGSVCGSKLSASALKYLVFLSEAHARL
NLRNKVLKEDVLIAALLFETSLTLKYGATVFCVAPNAVFPFELYNEEYLEQRDLYLTQCQ
QQLEQFIATYGPGTTIFSSDE

Predicted Contact and Distance Map Used in D-I-TASSER simulation

Contact Map

Distance Map

D-I-TASSER simulation is guided by the consensus contact map (left figure) and distance map (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.

Information of Domain

No. of Domain	Domain	Domain Boundary	Length of Domain	Models of Domain	Sequence
1	Q4G0Z9-D1	1-282	282		MSNLKMKEAALIYLDRSGGLQKFIDDCKYYNDSKQSYAVYRFKILINPSDVVELDAELGNHILHQPLKAAEVFQSVCFIAVKTLSLIGQLQTETQINIVLKLTHLPPLPSYGLDLCEFPLDYTSQRFYMMQGIVIAMTTITKYTQGARFLCSDEACPLSKGFQYIRVHVPGATESATIRNDFLCNLCASSLQEDRKFRVLGDKQIVEIIATKALRAFQGYSNNQPFRFQSLTIFLRDESVNKMNIGNEYKIIGIPTCVKTSQTAVCIEANSITFCNSKVPSG
2	Q4G0Z9-D2	283-331,501-681	230		ISDNFRCLLSLTSSSCWKFTAILANIFASQITPPGTYNLLKLCLLMSLVCNESSPCHPFLPTVQHTLNKAINPEGLFYAASRQFTTEDFEKLLAFAKNLNVEFSLEAERMTHGYYLASRRIRTGSVCGSKLSASALKYLVFLSEAHARLNLRNKVLKEDVLIAALLFETSLTLKYGATVFCVAPNAVFPFELYNEEYLEQRDLYLTQCQQQLEQFIATYGPGTTIFSSDE
3	Q4G0Z9-D3	332-500	169		QTTDRNKELEDCLDILIITSDTLLIDRLLNFSINLVPRGIRHLVSTEIFPTLSRNKYGTGAVSIQAGSALLAKGGICFIGDLASHKKDKLEQLQTVLESRSITVYIPGKKFGEDIDQQMTFPVQCSFWSFVDVDSSSRRNAQKINTLIGQMDCSLIPANLVEAFGLLIN

Top 1 final models from D-I-TASSER

SpinHigh qualityWhite background

Click to view	Rank^a	Download	Estimated TM-score^b
	1	model1.pdb.gz	0.56

(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

script 1 started

FileManager.getAtomSetCollectionFromFile(model1_6xtx2.pdb.gz)

FileManager opening 1 https://zhanglab.comp.nus.edu.sg/HPmod/data/Q4G0Z9/model1_6xtx2.pdb.gz

/jmol//j2s/core/corezip.z.js

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The Resolver thinks Pdb

/jmol//j2s/core/corebio.z.js

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/jmol//j2s/J/render/MeshRenderer.js

-- required by J.renderbio.BioShapeRenderer ajax=true async=false

/jmol//j2s/J/shape/Mesh.js

-- required by J.renderbio.BioShapeRenderer ajax=true async=false

Time for openFile(model1_6xtx2.pdb.gz): 1523 ms

reading 16281 atoms

ModelSet: haveSymmetry:false haveUnitcells:false haveFractionalCoord:false

1 model in this collection. Use getProperty "modelInfo" or getProperty "auxiliaryInfo" to inspect them.

Default Van der Waals type for model set to Babel

16281 atoms created

ModelSet: autobonding; use autobond=false to not generate bonds automatically

Jmol 14.2.13_2015.03.07 2015-03-07 10:45 DSSP analysis for model 1.1 - null

W. Kabsch and C. Sander, Biopolymers, vol 22, 1983, pp 2577-2637

We thank Wolfgang Kabsch and Chris Sander for writing the DSSP software,

and we thank the CMBI for maintaining it to the extent that it was easy to

re-engineer for our purposes. At this point in time, we make no guarantee

that this code gives precisely the same analysis as the code available via license

from CMBI at http://swift.cmbi.ru.nl/gv/dssp

All bioshapes have been deleted and must be regenerated.

NOTE: Backbone amide hydrogen positions are present and will be ignored. Their positions will be approximated, as in standard DSSP analysis.

Use SET dsspCalculateHydrogenAlways FALSE to not use this approximation.

null

JSmol exec jmolApplet2 start applet null

Jmol JavaScript applet jmolApplet2__6861478512079136__ initializing

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SpinHigh qualityWhite background

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

Rank	PDB Hit	TM-score	RMSD^a	IDEN^a	Cov.	Download Alignment
1	6xtx2	0.71	4.18	0.128	0.830	model1_6xtx2.pdb.gz
2	3ja86	0.68	3.62	0.130	0.759	model1_3ja86.pdb.gz
3	6raw7	0.67	4.12	0.142	0.775	model1_6raw7.pdb.gz
4	6xtx6	0.67	3.98	0.120	0.771	model1_6xtx6.pdb.gz
5	3ja82	0.64	4.76	0.112	0.786	model1_3ja82.pdb.gz
6	3ja87	0.64	4.90	0.116	0.783	model1_3ja87.pdb.gz
7	6raw3	0.63	4.38	0.128	0.740	model1_6raw3.pdb.gz
8	3ja85	0.62	5.00	0.111	0.771	model1_3ja85.pdb.gz
9	6raw5	0.62	4.43	0.121	0.733	model1_6raw5.pdb.gz
10	3f9vA	0.60	5.65	0.115	0.783	model1_3f9vA.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	0.76	heterocyclic compound binding
GO:0097159	0.76	organic cyclic compound binding
GO:0003824	0.71	catalytic activity
GO:0044877	0.69	macromolecular complex binding
GO:0016787	0.68	hydrolase activity
GO:0017111	0.67	nucleoside-triphosphatase activity
GO:0036094	0.56	small molecule binding
GO:0003676	0.56	nucleic acid binding
GO:0035639	0.55	purine ribonucleoside triphosphate binding
GO:0032555	0.55	purine ribonucleotide binding
GO:0032550	0.55	purine ribonucleoside binding
GO:0016887	0.55	ATPase activity
GO:0003678	0.55	DNA helicase activity
GO:0005524	0.51	ATP binding
GO:0003677	0.50	DNA 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:0008152	0.77	metabolic process
GO:0071704	0.76	organic substance metabolic process
GO:0044238	0.76	primary metabolic process
GO:0044237	0.76	cellular metabolic process
GO:0044260	0.75	cellular macromolecule metabolic process
GO:0006139	0.74	nucleobase-containing compound metabolic process
GO:0090304	0.73	nucleic acid metabolic process
GO:0016043	0.73	cellular component organization
GO:0006259	0.72	DNA metabolic process
GO:0044699	0.71	single-organism process
GO:0065007	0.68	biological regulation
GO:0006996	0.68	organelle organization
GO:0050794	0.66	regulation of cellular process
GO:0044763	0.60	single-organism cellular process
GO:0022402	0.59	cell cycle process
GO:0051276	0.58	chromosome organization
GO:0071103	0.57	DNA conformation change
GO:0032508	0.56	DNA duplex unwinding
GO:0019222	0.56	regulation of metabolic process
GO:0060255	0.54	regulation of macromolecule metabolic process
GO:0031323	0.54	regulation of cellular metabolic process
GO:0080090	0.53	regulation of primary metabolic process
GO:0050896	0.53	response to stimulus
GO:0006310	0.53	DNA recombination
GO:0019219	0.51	regulation of nucleobase-containing compound metabolic process
GO:2000112	0.50	regulation of cellular macromolecule biosynthetic process
GO:0051716	0.50	cellular response to stimulus

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	0.99	intracellular part
GO:0032991	0.96	macromolecular complex
GO:0043234	0.95	protein complex
GO:0042555	0.92	MCM complex
GO:0044446	0.89	intracellular organelle part
GO:0043226	0.87	organelle
GO:0043229	0.86	intracellular organelle
GO:0043231	0.85	intracellular membrane-bounded organelle
GO:0005634	0.84	nucleus
GO:0044428	0.83	nuclear part
GO:0044427	0.81	chromosomal part
GO:0005737	0.77	cytoplasm
GO:0044454	0.76	nuclear chromosome part
GO:0005654	0.76	nucleoplasm
GO:0032993	0.72	protein-DNA complex
GO:0005656	0.71	nuclear pre-replicative complex
GO:0031298	0.70	replication fork protection complex
GO:0031261	0.70	DNA replication preinitiation complex

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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script 1 started

FileManager.getAtomSetCollectionFromFile(model1.pdb.gz)

FileManager opening 1 https://zhanglab.comp.nus.edu.sg/HPmod/data/Q4G0Z9/model1.pdb.gz

The Resolver thinks Pdb

Time for openFile(model1.pdb.gz): 1349 ms

reading 10767 atoms

ModelSet: haveSymmetry:false haveUnitcells:false haveFractionalCoord:false

1 model in this collection. Use getProperty "modelInfo" or getProperty "auxiliaryInfo" to inspect them.

Default Van der Waals type for model set to Babel

10767 atoms created

ModelSet: autobonding; use autobond=false to not generate bonds automatically

Jmol 14.2.13_2015.03.07 2015-03-07 10:45 DSSP analysis for model 1.1 - null

W. Kabsch and C. Sander, Biopolymers, vol 22, 1983, pp 2577-2637

We thank Wolfgang Kabsch and Chris Sander for writing the DSSP software,

and we thank the CMBI for maintaining it to the extent that it was easy to

re-engineer for our purposes. At this point in time, we make no guarantee

that this code gives precisely the same analysis as the code available via license

from CMBI at http://swift.cmbi.ru.nl/gv/dssp

All bioshapes have been deleted and must be regenerated.

NOTE: Backbone amide hydrogen positions are present and will be ignored. Their positions will be approximated, as in standard DSSP analysis.

Use SET dsspCalculateHydrogenAlways FALSE to not use this approximation.

null

SpinHigh qualityWhite background

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	0.111	3f9vA	0.600	5.65	0.115	0.783	3.-.-.-	NA
2	0.060	2vdcA	0.317	8.48	0.044	0.521	1.4.1.13	NA
3	0.060	2g25A	0.289	8.17	0.029	0.468	1.2.4.1	NA
4	0.060	2vkzG	0.328	8.49	0.046	0.554	2.3.1.38 3.1.2.14	233
5	0.060	2vz9B	0.298	7.36	0.031	0.449	2.3.1.85	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:

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	1g9aA	0.268	8.28	0.029	0.441	0.11	BAB	complex1.pdb.gz	128,130,131,249

	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.