D-I-TASSER Q9NS73-D1

D-I-TASSER results for Q9NS73-D1

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

Input Sequence in FASTA format

>Q9NS73 (344 residues)
MAAATELNRPSSGDRNLERRCRPNLSREVLYEIFRSLHTLVGQLDLRDDVVKITIDWNKL
QSLSAFQPALLFSALEQHILYLQPFLAKLQSPIKEENTTAVEEIGRTEMGNKNEVNDKFS
IGDLQEEEKHKESDLRDVKKTQIHFDPEVVQIKAGKAEIDRRISAFIERKQAEINENNVR
EFCNVIDCNQENSCARTDAIFTPYPGFKSHVKVSRVVNTYGPQTRPEGIPGSGHKPNSML
RDCGNQAVEERLQNIEAHLRLQTGGPVPRDIYQRIKKLEDKILELEGISPEYFQSVSFSG
KRRKVQPPQQNYSLAELDEKISALKQALLRKSREAESMATHHLP

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 160 180 200 220 240 260 280 300 320 340 \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| MAAATELNRPSSGDRNLERRCRPNLSREVLYEIFRSLHTLVGQLDLRDDVVKITIDWNKLQSLSAFQPALLFSALEQHILYLQPFLAKLQSPIKEENTTAVEEIGRTEMGNKNEVNDKFSIGDLQEEEKHKESDLRDVKKTQIHFDPEVVQIKAGKAEIDRRISAFIERKQAEINENNVREFCNVIDCNQENSCARTDAIFTPYPGFKSHVKVSRVVNTYGPQTRPEGIPGSGHKPNSMLRDCGNQAVEERLQNIEAHLRLQTGGPVPRDIYQRIKKLEDKILELEGISPEYFQSVSFSGKRRKVQPPQQNYSLAELDEKISALKQALLRKSREAESMATHHLP
Prediction	CCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCCCCSSSSSSHHHHCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCHHHHHCCCCCCCCCCCCCCCCCCCCSSSSSCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCSSCCCCCCCCCSSSSSSSCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHCCCCCCCCCHCHHHHHHHHHHHHHHHHCCCHHHHHHHCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCC
Confidence	96411114766565551015882479999999999999999984587771358862454225654322679999999999999999997899987423457763144434433334677732003331023344100124445688120554259899999999999999998634788886236888755764111100103689875146898745877733677777666777755567777249999999999968888999953199999999999999963797899885025667788986334799999999999999999998875412334598
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 160 180 200 220 240 260 280 300 320 340 \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| MAAATELNRPSSGDRNLERRCRPNLSREVLYEIFRSLHTLVGQLDLRDDVVKITIDWNKLQSLSAFQPALLFSALEQHILYLQPFLAKLQSPIKEENTTAVEEIGRTEMGNKNEVNDKFSIGDLQEEEKHKESDLRDVKKTQIHFDPEVVQIKAGKAEIDRRISAFIERKQAEINENNVREFCNVIDCNQENSCARTDAIFTPYPGFKSHVKVSRVVNTYGPQTRPEGIPGSGHKPNSMLRDCGNQAVEERLQNIEAHLRLQTGGPVPRDIYQRIKKLEDKILELEGISPEYFQSVSFSGKRRKVQPPQQNYSLAELDEKISALKQALLRKSREAESMATHHLP
Prediction	74443644345644432555152520240022004103400540504450131203142033044242210121145005403400540443145534432551656243345424463546614654546636275356345504561030405574034205401541354135302320144366666210000101145376460302022041431314346445445444454465443520430041004104045744233400510350152014017321401222424475554534634130630452055025403542553553546628
	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                 280                 300                 320                 340

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

SS
Seq

CCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCCCCSSSSSSHHHHCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCHHHHHCCCCCCCCCCCCCCCCCCCCSSSSSCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCSSCCCCCCCCCSSSSSSSCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHCCCCCCCCCHCHHHHHHHHHHHHHHHHCCCHHHHHHHCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCC
MAAATELNRPSSGDRNLERRCRPNLSREVLYEIFRSLHTLVGQLDLRDDVVKITIDWNKLQSLSAFQPALLFSALEQHILYLQPFLAKLQSPIKEENTTAVEEIGRTEMGNKNEVNDKFSIGDLQEEEKHKESDLRDVKKTQIHFDPEVVQIKAGKAEIDRRISAFIERKQAEINENNVREFCNVIDCNQENSCARTDAIFTPYPGFKSHVKVSRVVNTYGPQTRPEGIPGSGHKPNSMLRDCGNQAVEERLQNIEAHLRLQTGGPVPRDIYQRIKKLEDKILELEGISPEYFQSVSFSGKRRKVQPPQQNYSLAELDEKISALKQALLRKSREAESMATHHLP

2pffB

0.06

2.62

1.03

MapAlign

-------TDDYFEELRDLYQTYHVLVGDLIKFSAAHYVVTAKLLGFTPGELRSVTAVAIAETDSWESFFVSVRKAITVLFFIQVQDYVNKTNSHLPAGKQVEISLVNGAKNLVVSGPPQSLYGLNLTLRGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGMDLYKTSKAAQDVWNRADNHFKEINEHSTSYTFRSEKGLLSATQFTQPALTLMEKAAFEDLKESLVEVVFYRGMTMQV---

2pffB

0.15

0.14

4.63

1.33

HHsearch

FFIASQLQ--EQFNKILPEPTEPTTPAELVGKFLGYVSSLVEPSKVGQFDQVLNLEFENCYLE-GNDIHALAAKLLQENDTTELIKNYITARIMAKRPFDKK-SNSALFEGNAQLVAIFG---GQGNTDDYFEELRDLYQTYVLVDKVFTQGLNYLLSIPISCIGVIQLAHYVVT-AKLLGFTPGLKGATGHSQGLVTAVAIAETDFVSVRKAITGVRCYEAYPNTSLPPSINNEPSPMLSNLTQEQVQDYVNKTNSHLPAGKVSGPPQSLYGLNLTL-------RKAKAPSGLDQSRIPERKKASPFHSHLLVPASDLIN-----KDLVKNVSFNAKDI-QIP

4or2A

0.07

2.85

0.48

CEthreader

---DLEDNWETLNDNLKVIEKADNAAQVKDALTKMRAAALDAQKATPPKLEDKSPDSPEMKDFRHGFDILVGQIDDALKLANEGKVKEAQAAAEQLKTTRNAYIQKYLIPVRYLEWSLYRDTPVVKSSSRELCYIILAGIFLGYVCPFTLIAKPTTTSCYLQRLLVGLSSAMCYSALVTKTNRIARILARKPRFMSAWAQVIIASILQLTLVVTLIIMEPPMPILSYPSIKEVYLICNTSNLGVVAPLGYNGLLIMSCTYYAFKTRNVPANFNEAKYIAFTMYTTCIIWLAFVPIYFGSNYKIITTCFAVSLSVTVALGCMFTPKMYIIIAKPE----------

6w5cA

0.06

2.55

0.58

EigenThreader

SYRKLRIRCSRKGATPSILKIVQDYELGTKLGREKIKAFLASKVGPYY--------LGSYSAMLENALSPIKGMTTKNCKFVLKQIDAKNDIKYENEPFGKIVEGFFDSVLHPHHIGESNTINTYCEEVGKTPLVQLLRYLYSRKDDIAVDKIIDGITFLSKKHKVEKKVKKRQMRLEAARQQICKRGNNFEVTLYKVVLGYDANIRKNTYAAIEADQLSYNGVKLLYCNMKDFEAIADDETSLYYFNMKYCKLLQSSIRNHVLKLSSLSNLSFVMFKVAKSLIGTYFGHLLMVMMHQGLEARYSRCTPSELTEKNRKEILSFLSNAYYNEGAMAFLATYGLKK

5nl6A

0.08

0.05

2.04

0.78

FFAS-3D

-----------------------HDYEQRAQALKENIEAAINKMEPSDEYHQVKEQINETKNY----RKGDKRAFIKEQGDLATLFGQINSKLRGMKRPV--------------------------YVAPEGLDPKSLEGYIANI-----------SEAERALRSKLNTAMRNCLIALRKAFADPAN-----------------------------------------------------------ATDAKINEYRTFVTDETSEAPLEEQVATLKAKLEELKQVEAQLPPIEEAEKACEDANIEDNEYTDVSFDDLQFNYEQTVSMFEKKIVYIEAQ------

4m0mA

0.11

3.85

0.74

SPARKS-K

FKQLYPKSFNWFFEKNHGGQTKKEEVIVELKSLSEFFSSLAKHFQINENNITLGIDRDEKSSFGQPPVRDRLSYLQHSLTSIANYYHYHCDEKSSTNESVKNLLLERVKESRTKPDSEHLEQTDEVRQILESKNEKGFLWQQIN------HISPNARQYCEQVKAALREHLEHVLSDTQKEEIRKADRDN----------IVNDSSKDSQQKRREVIELNAKATTPEDTRSHFQKAYFEGDTQKTLNLESLSQTLNQLSKAHYGETSTDKITQRLDGYKNRNWFWNSVKEVLNFF---NIPLPKLHSEVKEQIADKLKERLVDLKEAITRELGKAREDLIEHYK

4k1pA

0.11

0.08

2.74

0.73

CNFpred

--------------------------NQEMMRYSIRFNSYYSKLY--ELAGNINEDE--------QSKADFTNAYGKLQLQVQSIQENMEQDLLELNR----------------------KTVLDKDSNNLSIKADEAIKTLQGS--------GDIVKLREDIKRIQGEIQA-----ELTTILNRP---QEIIKGSINIGKQVF---TKTIDFVSIGTLS---NEIVNAADSQTREAALRIQQKQKELLPLIQKLSQT----------EAEATQITFVEDQVSSFTELIDRQITTLETL------------TDWKVLNNNMIQIQKNVEEGTYTDSSLLQKHFN

3javA

0.05

0.04

1.73

0.67

DEthreader

DILKGGDVVR-------TSATS----------DLDFANDASK-VLGSIAGKLEGTITQNER------RS-VTKLLEDLVYFCRVLRHSQTALLHNNRDLCVSMDSNKEYRYQLNLFASKDFGFYNFSDL-------SE-GNSSQEPSRYRNIIERL-QDIVSALEDRLRPLVQAELSVLVDVLHELFEKCESGGFIKQTETKDRGGEMSLECHLGSNLVID--M-----------------DKKSEKFFKV-YHRDLQNFLRQNNK-------------------------------NQTLESTNLLLMLQLARLQTMLKPGGQVDGDE---------------

1v9pA

0.07

2.70

0.92

MapAlign

-----------------------MTREEARRRINELRDLIRYH-----------NYRYYVLADPEISDAEYDRLLRELKELEERFVLAFEERLERALGRKRPFLYTVEHKVDGLSVNLYYEEGVLVFGATRGDGEVGEEVTQNLLTIPTIEVYMPIEAFLRLNEELEERGAEGVEEVYRRLLDVVFQVGRTGRVTPVGVLEPVFIEGSEVSRVTLHNEWPETCPECGHRLVKEGKVHRCPNPLCPAKRFEAIRHYADLYHLRKEDLLGMGEKSAQNLLRQIEESKHRGLERLLYMDRLLEASLEELLEVEEVGELTARAILETLKDPAFRDLVRRLKEAGVSM-

5yz0A

0.10

3.56

0.62

MUSTER

LNMLLEKLCVMFEDGVLMRLKS-DLLKAALCHLLQYFLKYESALQVRKVYVR-NICKALLDVLGIEVDAEYLL--GPLYAALKMESMEIIEEIQCQTQQENLSSNSDGISPKRRRLSSSLNPSKRAPKQTEEIKHVDMNQKSILWSA----LKQKAESLQISLEYSGLKNPVIEMLEGIAVVLQLTALCTVHCSHQNMNCRTFKDCQHKSKKKPSVVITWMSLDFYTKVLKSCRSLESVQKLDLEATIDKVVKIYDALIYMQVNSSFEDHILEDLCGMLSL-IYSHSDDGCLKLTTF---AANLLTLSCRISDSYSPQAQSRCVFLLTLFPRRIFLEWRTAVYN

(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	0.4517

(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	3ffzA	0.43	6.36	0.034	0.686	model1_3ffzA.pdb.gz
2	5x0mA2	0.41	6.38	0.040	0.651	model1_5x0mA2.pdb.gz
3	6rc9A	0.41	7.16	0.033	0.738	model1_6rc9A.pdb.gz
4	7c6oA	0.41	6.71	0.042	0.701	model1_7c6oA.pdb.gz
5	6rutB1	0.41	6.77	0.025	0.698	model1_6rutB1.pdb.gz
6	5julA	0.40	6.86	0.032	0.698	model1_5julA.pdb.gz
7	3ucqA	0.40	6.28	0.068	0.657	model1_3ucqA.pdb.gz
8	6uz0A	0.40	6.26	0.050	0.634	model1_6uz0A.pdb.gz
9	7dtdA	0.40	6.28	0.051	0.628	model1_7dtdA.pdb.gz
10	5twvB	0.40	6.81	0.052	0.663	model1_5twvB.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	0.66	catalytic activity
GO:0016740	0.65	transferase activity
GO:0030366	0.58	molybdopterin synthase 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:0071704	1.00	organic substance metabolic process
GO:0044238	1.00	primary metabolic process
GO:0044237	1.00	cellular metabolic process
GO:0043170	0.96	macromolecule metabolic process
GO:0019538	0.95	protein metabolic process
GO:0006807	0.70	nitrogen compound metabolic process
GO:1901576	0.69	organic substance biosynthetic process
GO:1901360	0.69	organic cyclic compound metabolic process
GO:0046483	0.69	heterocycle metabolic process
GO:0044249	0.69	cellular biosynthetic process
GO:1901362	0.66	organic cyclic compound biosynthetic process
GO:0018130	0.66	heterocycle biosynthetic process
GO:0044260	0.65	cellular macromolecule metabolic process
GO:0006796	0.60	phosphate-containing compound metabolic process
GO:1901564	0.59	organonitrogen compound metabolic process
GO:0019637	0.59	organophosphate metabolic process
GO:1901566	0.58	organonitrogen compound biosynthetic process
GO:0090407	0.58	organophosphate biosynthetic process
GO:0051188	0.58	cofactor biosynthetic process
GO:0043545	0.58	molybdopterin cofactor metabolic process
GO:0016043	0.55	cellular component organization
GO:0006777	0.52	Mo-molybdopterin cofactor biosynthetic process
GO:0043933	0.51	macromolecular complex subunit organization
GO:0006464	0.51	cellular protein modification process
GO:0006325	0.50	chromatin organization

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:0044446	0.67	intracellular organelle part
GO:0044444	0.66	cytoplasmic part
GO:0032991	0.63	macromolecular complex
GO:0043234	0.62	protein complex
GO:0005829	0.62	cytosol
GO:0044428	0.60	nuclear part
GO:0043226	0.60	organelle
GO:0044451	0.58	nucleoplasm part
GO:0043229	0.58	intracellular organelle
GO:1990234	0.57	transferase complex
GO:0000123	0.55	histone acetyltransferase complex
GO:0043227	0.54	membrane-bounded organelle
GO:0005671	0.54	Ada2/Gcn5/Ada3 transcription activator complex
GO:0043231	0.52	intracellular membrane-bounded organelle
GO:0005634	0.51	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	0.060	1hxgA	0.350	6.57	0.042	0.587	4.2.3.9 4.1.99.7	NA
2	0.060	1ug9A	0.359	6.34	0.056	0.576	3.2.1.70	NA
3	0.060	5coxA	0.374	6.69	0.063	0.637	1.14.99.1	NA
4	0.060	1eqrA	0.352	6.73	0.031	0.596	6.1.1.12	47
5	0.060	2wyhA	0.379	6.01	0.032	0.593	3.2.1.24	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:

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	3o8nB	0.351	6.93	0.040	0.602	0.16	ADP	complex1.pdb.gz	196,197,219

	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.