D-I-TASSER results for O00408-D4

Input Sequence in FASTA format

>O00408 (365 residues)
VSDDEYTKLLHDGIQPVAAIDSNFASFTYTPRSLPEDDTSMAILSMLQDMNFINNYKIDC
PTLARFCLMVKKGYRDPPYHNWMHAFSVSHFCYLLYKNLELTNYLEDIEIFALFISCMCH
DLDHRGTNNSFQVASKSVLAALYSSEGSVMERHHFAQAIAILNTHGCNIFDHFSRKDYQR
MLDLMRDIILATDLAHHLRIFKDLQKMAEVGYDRNNKQHHRLLLCLLMTSCDLSDQTKGW
KTTRKIAELIYKEFFSQGDLEKAMGNRPMEMMDREKAYIPELQISFMEHIAMPIYKLLQD
LFPKAAELYERVASNREHWTKVSHKFTIRGLPSNNSLDFLDEEYEVPDLDGTRAPINGCC
SLDAE

Predicted Secondary Structure

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Sequence
VSDDEYTKLLHDGIQPVAAIDSNFASFTYTPRSLPEDDTSMAILSMLQDMNFINNYKIDCPTLARFCLMVKKGYRDPPYHNWMHAFSVSHFCYLLYKNLELTNYLEDIEIFALFISCMCHDLDHRGTNNSFQVASKSVLAALYSSEGSVMERHHFAQAIAILNTHGCNIFDHFSRKDYQRMLDLMRDIILATDLAHHLRIFKDLQKMAEVGYDRNNKQHHRLLLCLLMTSCDLSDQTKGWKTTRKIAELIYKEFFSQGDLEKAMGNRPMEMMDREKAYIPELQISFMEHIAMPIYKLLQDLFPKAAELYERVASNREHWTKVSHKFTIRGLPSNNSLDFLDEEYEVPDLDGTRAPINGCCSLDAE
Prediction
CCHHHHHHHHHCCCCCHHHHHHCCCCCCCCCCCCCCHHHHHHHHHHHHHCCCHHHCCCCHHHHHHHHHHHHHCCCCCCCCCHHHHHHHHHHHHHHHHCCCHHHCCCHHHHHHHHHHHHHHCCCCCCCCCHHHHHHCCHHHHHHCCCCCHHHHHHHHHHHHHHHCCCCCHHHCCCHHHHHHHHHHHHHHHHHHCHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHCHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
Confidence
98899999971775228999850122754645488038999999999981941430989999999999999717999973389999999999999964432212898999999999998137889988477886341899984578854563789999999961487332069999999999999999997218999999999999987431122358999999997578752233300899999999999999987678998299987667877431335778999999999999999981527999999999999999999998751577754322345445777778998988886333479

H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

                  20                  40                  60                  80                 100                 120                 140                 160                 180                 200                 220                 240                 260                 280                 300                 320                 340                 360
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Sequence
VSDDEYTKLLHDGIQPVAAIDSNFASFTYTPRSLPEDDTSMAILSMLQDMNFINNYKIDCPTLARFCLMVKKGYRDPPYHNWMHAFSVSHFCYLLYKNLELTNYLEDIEIFALFISCMCHDLDHRGTNNSFQVASKSVLAALYSSEGSVMERHHFAQAIAILNTHGCNIFDHFSRKDYQRMLDLMRDIILATDLAHHLRIFKDLQKMAEVGYDRNNKQHHRLLLCLLMTSCDLSDQTKGWKTTRKIAELIYKEFFSQGDLEKAMGNRPMEMMDREKAYIPELQISFMEHIAMPIYKLLQDLFPKAAELYERVASNREHWTKVSHKFTIRGLPSNNSLDFLDEEYEVPDLDGTRAPINGCCSLDAE
Prediction
74572254027351641540253034040201505631001000000341400540504361023002102522440101002000000000000011230442032010000000000121312122220132142200210234411210000000010023331200340336103301400120011113420151053045005223324342012000100020010020033040024003100300133343145371412423544413113112000100010003000400440440051045016204611652556536557416435674546647556444732551578

Values range from 0 (buried residue) to 8 (highly exposed residue)

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

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 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.

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                 360                    |                   |                   |                   |                   |                   |                   |                   |                   |                   |                   |                   |                   |                   |                   |                   |                   |                   |
							SS	CCHHHHHHHHHCCCCCHHHHHHCCCCCCCCCCCCCCHHHHHHHHHHHHHCCCHHHCCCCHHHHHHHHHHHHHCCCCCCCCCHHHHHHHHHHHHHHHHCCCHHHCCCHHHHHHHHHHHHHHCCCCCCCCCHHHHHHCCHHHHHHCCCCCHHHHHHHHHHHHHHHCCCCCHHHCCCHHHHHHHHHHHHHHHHHHCHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHCHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
							Seq	VSDDEYTKLLHDGIQPVAAIDSNFASFTYTPRSLPEDDTSMAILSMLQDMNFINNYKIDCPTLARFCLMVKKGYRDPPYHNWMHAFSVSHFCYLLYKNLELTNYLEDIEIFALFISCMCHDLDHRGTNNSFQVASKSVLAALYSSEGSVMERHHFAQAIAILNTHGCNIFDHFSRKDYQRMLDLMRDIILATDLAHHLRIFKDLQKMAEVGYDRNNKQHHRLLLCLLMTSCDLSDQTKGWKTTRKIAELIYKEFFSQGDLEKAMGNRPMEMMDREKAYIPELQISFMEHIAMPIYKLLQDLFPKAAELYERVASNREHWTKVSHKFTIRGLPSNNSLDFLDEEYEVPDLDGTRAPINGCCSLDAE
1	6mzbB	0.29	0.26	8.01	1.50	DEthreader		REEIQLIPTREILKVLPGPAKFDIYEFHFSDLECTELELVKCGIQMYYELGVVRKFQIPQEVLVRFLFSVSKGYRRITYHNWRHGFNVAQTMFTLLMTGKLKSYYTDLEAFAMVTAGLCHDIDHRGTNNLYQMKSQNPLAKL-HGS-SILERHHLEFGKFLLSEETLNIYQNLNRRQHEHVIHLMDIAIIATDLALYFKKRTMFQKIVDESWYLLETTRKEIVMAMMMTACDLSAITKPWEVQSKVALLVAAEFWEQGDLERTVLQQPIPMMDRNKAELPKLQVGFIDFVCTFVYKEFSRFHEEILPMFDRLQNNRKEWKALADEYEAKVKAL--------------------------------
2	3jsiA	0.25	0.23	7.04	3.40	SPARKS-K		---GSHMTYPKYLLS--PETIEALRKPTFDVWLWEPNEMLSCLEHMYHDLGLVRDFSINPVTLRRWLFCVHDNYRNNPFHNFRHCFCVAQMMYSMVWLCSLQEKFSQTDILILMTAAICHDLDHPGYNNTYQINARTELAVRYN-DISPLENHHCAVAFQILAEPECNIFSNIPPDGFKQIRQGMITLILATDMARHAEIMDSFKEKME-NFDYSNEEHMTLLKMILIKCCDISNEVRPMEVAEPWVDCLLEEYFMQSDREKSEGLPVAPFMDRDKVTKATAQIGFIKFVLIPMFETVTKLFPMEEIMLQPLWESRDRYEELKRIDDAMKELQK-------------------------------
3	1t9sA	0.33	0.29	8.72	1.55	MapAlign		E-TRELQSLAAAVVPSAQTL--KITDFSFSDFELSDLETALCTIRMFTDLNLVQNFQMKHEVLCRWILSVKKNYRKVAYHNWRHAFNTAQCMFAALKAGKIQNKLTDLEILALLIAALSHDLDHPGVSNQFLINTNSELALMYND-ESVLEHHHFDQCLMILNSPGNQILSGLSIEEYKTTLKIIKQAILATDLALYIKRRGEFFELIRNQFNLEDPHQKELFLAMLMTACDLSAITKPWPIQQRIAELVATEFFDQGDRERKLNIEPTDLMNREKKKIPSMQVGFIDAICLQLYEALTHVSEDCFPLLDGCRKNRQKWQALA------------------------------------------
4	3jsiA	0.25	0.22	6.96	0.90	CEthreader		-----GSHMTYPKYLLSPETIEALRKPTFDVWLWEPNEMLSCLEHMYHDLGLVRDFSINPVTLRRWLFCVHDNYRNNPFHNFRHCFCVAQMMYSMVWLCSLQEKFSQTDILILMTAAICHDLDHPGYNNTYQINARTELAVRYN-DISPLENHHCAVAFQILAEPECNIFSNIPPDGFKQIRQGMITLILATDMARHAEIMDSFKEKME-NFDYSNEEHMTLLKMILIKCCDISNEVRPMEVAEPWVDCLLEEYFMQSDREKSEGLPVAPFMDRDKVTKATAQIGFIKFVLIPMFETVTKLFMVEEIMLQPLWESRDRYEELKRIDDAMKELQK-------------------------------
5	3ibjA3	1.00	0.86	24.01	2.52	MUSTER		VSDDEYTKLLHDGIQPVAAIDSNFASFTYTPRSLPEDDTSMAILSMLQDMNFINNYKIDCPTLARFCLMVKKGYRDPPYHNWMHAFSVSHFCYLLYKNLELTNYLEDIEIFALFISCMCHDLDHRGTNNSFQVASKSVLAALYSSEGSVMERHHFAQAIAILNTHGCNIFDHFSRKDYQRMLDLMRDIILATDLAHHLRIFKDLQKMAEVGYDRNNKQHHRLLLCLLMTSCDLSDQTKGWKTTRKIAELIYKEFFSQGDLEKA-----------EKAYIPELQISFMEHIAMPIYKLLQDLFPKAAELYERVASNREHWTKVSH-----------------------------------------
6	7jsnA	0.29	0.26	8.01	2.78	HHsearch		CEEEELAEILQGELPDAD--KYEINKFHFSDLPLTELELVKCGIQMYYELKVVDKFHIPQEALVRFMYSLSKGYRRITYHNWRHGFNVGQTMFSLLVTGKLKRYFTDLEALAMVTAAFCHDIDHRGTNNLYQMKSQNPLAKLHG-S-SILERHHLEFGKTLLRDESLNIFQNLNRRQHEHAIHMMDIAIIATDLALYFKKRTMFQKIVDSKTYETDQTRKEIVMAMMMTACDLSAITKPWEVQSKVALLVAAEFWEQGDLERTLQQNPIPMMDRNKADLPKLQVGFIDFVCTFVYKEFSRFHEEITPMLDGITNNRKEWKALADEYETKMKGLEEEK----------------------------
7	1t9sA	0.33	0.29	8.72	3.74	FFAS-3D		-ETRELQSLAAAVVPSAQTL--KITDFSFSDFELSDLETALCTIRMFTDLNLVQNFQMKHEVLCRWILSVKKNYRNVAYHNWRHAFNTAQCMFAALKAGKIQNKLTDLEILALLIAALSHDLDHPGVSNQFLINTNSELALMYN-DESVLEHHHFDQCLMILNSPGNQILSGLSIEEYKTTLKIIKQAILATDLALYIKRRGEFFELIRKQFNLEDPHQKELFLAMLMTACDLSAITKPWPIQQRIAELVATEFFDQGDRERELNIEPTDLMNREKKKIPSMQVGFIDAICLQLYEALTHVSEDCFPLLDGCRKNRQKWQALAE-----------------------------------------
8	3jsiA	0.26	0.23	7.02	1.92	EigenThreader		TYP---------KYLLSPETIEALRKPTFDVWLWEPNEMLSCLEHMYHDLGLVRDFSINPVTLRRWLFCVHDNYRNNPFHNFRHCFCVAQMMYSMVWLCSLQEKFSQTDILILMTAAICHDLDHPGYNNTYQINARTELAVRYND-ISPLENHHCAVAFQILAEPECNIFSNIPPDGFKQIRQGMITLILATDMARHAEIMDSFKEKME-NFDYSNEEHMTLLKMILIKCCDISNEVRPMEVAEPWVDCLLEEYFMQSDREKSEGLPVAPFMDRDKVTKATAQIGFIKFVLIPMFETVTKLFPMEEIMLQPLWESRDRYEELKRIDDAMKELQK-------------------------------
9	6b96A	1.00	0.92	25.70	2.59	CNFpred		-----YTKLLHDGIQPVAAIDSNFASFTYTPRSLPEDDTSMAILSMLQDMNFINNYKIDCPTLARFCLMVKKGYRDPPYHNWMHAFSVSHFCYLLYKNLELTNYLEDIEIFALFISCMCHDLDHRGTNNSFQVASKSVLAALYSSEGSVMERHHFAQAIAILNTHGCNIFDHFSRKDYQRMLDLMRDIILATDLAHHLRIFKDLQKMAEVGYDRNNKQHHRLLLCLLMTSCDLSDQTKGWKTTRKIAELIYKEFFSQGDLEKAMGNRPMEMMDREKAYIPELQISFMEHIAMPIYKLLQDLFPKAAELYERVASNREHWTKVSHKFTIRGLPSNNSLDFL-------------------------
10	2ouyA	0.33	0.30	8.87	1.33	DEthreader		CTSEEWQGLMQ--FTLPVRLCKEIELFHFDIGPFE-NMWPGIFVYMVHRSCGTS-C-FELEKLCRFIMSVKKNYRRVPYHNWKHAVTVAHCMYAILQN-N-HTLFTDLERKGLLIACLCHNLDHRGFSNSYLQKFDHPLAA-LYS-TSTMEQHHFSQTVSILQLEGHNIFSTLSSSEYEQVLEIIRKAIIATDLALYFGNRKQLEEMYTGSLNLNNQSHRDRVIGLMMTACDLCSVTKLWPVTKLTANDIYAEFWAEGDEMKKLGIQPIPMMDRDKKEVPQGQLGFYNAVAIPCYTTLTQILPPTEPLLKACRDNLSQWEKVIRGE------------ETATWI---------------------


(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

Rank^a	Estimated TM-score^b
1	0.8491


(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

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


Rank	PDB Hit	TM-score	RMSD^a	IDEN^a	Cov.
1	6mzbB	0.87	1.77	0.289	0.910
2	3jsiA	0.86	1.24	0.254	0.879
3	7jsnA	0.86	1.82	0.284	0.907
4	1t9sA	0.86	1.24	0.333	0.879
5	2ouyA	0.85	1.55	0.343	0.885
6	2r8qA	0.84	1.74	0.289	0.882
7	3g45A	0.83	1.85	0.250	0.871
8	6ezuA	0.83	1.84	0.259	0.869
9	4i15A	0.83	1.88	0.272	0.877
10	5vydA	0.82	1.34	0.261	0.849



(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	1.00	catalytic activity
GO:0004112	0.99	cyclic-nucleotide phosphodiesterase activity
GO:0004114	0.98	3',5'-cyclic-nucleotide phosphodiesterase activity
GO:1901363	0.75	heterocyclic compound binding
GO:0097159	0.75	organic cyclic compound binding
GO:0097367	0.66	carbohydrate derivative binding
GO:0000166	0.66	nucleotide binding
GO:0032555	0.65	purine ribonucleotide binding
GO:0030551	0.55	cyclic nucleotide binding






(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:

Biological Process (BP)


GO term	Cscore^GO	Name
GO:0044699	0.94	single-organism process
GO:0009987	0.94	cellular process
GO:0044763	0.88	single-organism cellular process
GO:0008152	0.88	metabolic process
GO:0071704	0.87	organic substance metabolic process
GO:0044238	0.87	primary metabolic process
GO:0044237	0.87	cellular metabolic process
GO:0006139	0.86	nucleobase-containing compound metabolic process
GO:0044281	0.81	small molecule metabolic process
GO:0055086	0.80	nucleobase-containing small molecule metabolic process
GO:0009117	0.79	nucleotide metabolic process
GO:0065007	0.78	biological regulation
GO:1901564	0.77	organonitrogen compound metabolic process
GO:0050789	0.77	regulation of biological process
GO:0050794	0.76	regulation of cellular process
GO:0009187	0.76	cyclic nucleotide metabolic process
GO:0009150	0.76	purine ribonucleotide metabolic process
GO:0007165	0.62	signal transduction
GO:0032501	0.61	multicellular organismal process
GO:0046058	0.58	cAMP metabolic process
GO:0046068	0.57	cGMP metabolic process
GO:0009214	0.57	cyclic nucleotide catabolic process
GO:0009154	0.57	purine ribonucleotide catabolic process
GO:0050896	0.56	response to stimulus
GO:0003008	0.54	system process
GO:0006198	0.50	cAMP catabolic process






(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:

Cellular Component (CC)


GO term	Cscore^GO	Name
GO:0044464	0.97	cell part
GO:0044424	0.89	intracellular part
GO:0016020	0.77	membrane
GO:0043226	0.74	organelle
GO:0044444	0.71	cytoplasmic part
GO:0043229	0.70	intracellular organelle
GO:0043227	0.70	membrane-bounded organelle
GO:0043231	0.68	intracellular membrane-bounded organelle
GO:0005634	0.61	nucleus
GO:0005886	0.54	plasma membrane
GO:0005829	0.52	cytosol






(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:

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	0.196	2qykB	0.830	1.67	0.259	0.866	3.1.4.17	NA
2	0.193	2r8qA	0.838	1.74	0.289	0.882	3.1.4.17	NA
3	0.153	2qymA	0.706	2.31	0.275	0.756	3.1.4.17	NA
4	0.060	2cseW	0.416	6.50	0.054	0.674	3.6.4.13	NA
5	0.060	2f89F	0.395	6.28	0.060	0.622	2.5.1.1 2.5.1.10	NA



(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:

No Binding sites was predicted

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.