D-I-TASSER results for P04406-D2

Input Sequence in FASTA format

>P04406 (186 residues)
ASCTTNCLAPLAKVIHDNFGIVEGLMTTVHAITATQKTVDGPSGKLWRDGRGALQNIIPA
STGAAKAVGKVIPELNGKLTGMAFRVPTANVSVVDLTCRLEKPAKYDDIKKVVKQASEGP
LKGILGYTEHQVVSSDFNSDTHSSTFDAGAGIALNDHFVKLISWYDNEFGYSNRVVDLMA
HMASKE

Predicted Secondary Structure

                  20                  40                  60                  80                 100                 120                 140                 160                 180
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Sequence
ASCTTNCLAPLAKVIHDNFGIVEGLMTTVHAITATQKTVDGPSGKLWRDGRGALQNIIPASTGAAKAVGKVIPELNGKLTGMAFRVPTANVSVVDLTCRLEKPAKYDDIKKVVKQASEGPLKGILGYTEHQVVSSDFNSDTHSSTFDAGAGIALNDHFVKLISWYDNEFGYSNRVVDLMAHMASKE
Prediction
CCCHHHHHHHHHHHHHHHCCSSSSSSSCSCCCCCCCCCCCCCCCCCCCCCHHHHHCCCCCCHHHHHHHHHHCHHHCCCCCSSSSSCCCCCCCSSSSSSSSCCCCCHHHHHHHHHHHHCCCCCCSSCCCCCCCCCCCCCCCCCCSSSSCCCCSSSCCCSSSSSSSSCCHHHHHHHHHHHHHHHHHCC
Confidence
985124456789876631364565542111123887355676877543201255357657569999999963510798751689636899416978999778799999999999996098886041327875321358999653464045736679789999972551667799999999998169

H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

                  20                  40                  60                  80                 100                 120                 140                 160                 180
                   |                   |                   |                   |                   |                   |                   |                   |                   |
Sequence
ASCTTNCLAPLAKVIHDNFGIVEGLMTTVHAITATQKTVDGPSGKLWRDGRGALQNIIPASTGAAKAVGKVIPELNGKLTGMAFRVPTANVSVVDLTCRLEKPAKYDDIKKVVKQASEGPLKGILGYTEHQVVSSDFNSDTHSSTFDAGAGIALNDHFVKLISWYDNEFGYSNRVVDLMAHMASKE
Prediction
741310130110000345221342300121031341431122144121301000300123322003010302230633031201101234000000003063603163025004500734131102036440002003425200100151033145400000002200311021002004303758

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                    |                   |                   |                   |                   |                   |                   |                   |                   |
							SS	CCCHHHHHHHHHHHHHHHCCSSSSSSSCSCCCCCCCCCCCCCCCCCCCCCHHHHHCCCCCCHHHHHHHHHHCHHHCCCCCSSSSSCCCCCCCSSSSSSSSCCCCCHHHHHHHHHHHHCCCCCCSSCCCCCCCCCCCCCCCCCCSSSSCCCCSSSCCCSSSSSSSSCCHHHHHHHHHHHHHHHHHCC
							Seq	ASCTTNCLAPLAKVIHDNFGIVEGLMTTVHAITATQKTVDGPSGKLWRDGRGALQNIIPASTGAAKAVGKVIPELNGKLTGMAFRVPTANVSVVDLTCRLEKPAKYDDIKKVVKQASEGPLKGILGYTEHQVVSSDFNSDTHSSTFDAGAGIALNDHFVKLISWYDNEFGYSNRVVDLMAHMASKE
1	6m5xO	0.65	0.64	18.26	1.50	DEthreader		PSCTTNCLAPLAKTLNDKFTIVEGLMTAIHAYTASQ-KTV-DGPSSWRGGRAAAQNLIPSSTGAAKAVGKVIPELAGKVTGMSVRVPTVNVSLVDFTVRFAKDVTYDEVKAAIKEASEGPLKGILAYTEDDIVSTDILTDPHSSTFDAKAGIALNKNFVKVMSWYDNEYGYSRRVVDLIVFVSKKG
2	6ok4A2	0.66	0.66	18.70	3.27	SPARKS-K		-SCTTNCLAPLAKVLLDNFGIEEGLMTTVHAATATQSVVDGPSRKDWRGGRGAFQNIIPASTGAAKAVGLCLPELKGKLTGMAFRVPVADVSVVDLTVKLSSATTYEAICEAVKHAANTSMKNIMYYTEEAVVSSDFIGCEYSSIFDAQAGVALNDRFFKLVAWYDNEIGYATRIVDLLEYVQEN-
3	3docA	0.49	0.48	14.05	0.84	MapAlign		ASCTTNCLAPVAQVLNDTIGIEKGFMTTIHSYTGDQPTLDTMH-KDLYRARAAALSMIPTSTGAAKAVGLVLPELKGKLDGVAIRVPTPNVSVVDLTFIAKRETTVEEVNNAIREAANGRLKGILGYTDEKLVSHDFNHDSHSSVFHTDQTKVMDGTMVRILSWYDNEWGFSSRMSDTAVALGK--
4	3docA	0.49	0.48	14.06	0.57	CEthreader		ASCTTNCLAPVAQVLNDTIGIEKGFMTTIHSYTGDQPTLDTMH-KDLYRARAAALSMIPTSTGAAKAVGLVLPELKGKLDGVAIRVPTPNVSVVDLTFIAKRETTVEEVNNAIREAANGRLKGILGYTDEKLVSHDFNHDSHSSVFHTDQTKVMDGTMVRILSWYDNEWGFSSRMSDTAVALGKLI
5	1j0xO2	0.96	0.95	26.53	3.16	MUSTER		---TTNCLAPLAKVIHDHFGIVEGLMTTVHAITATQKTVDGPSGKLWRDGRGAAQNIIPASTGAAKAVGKVIPELNGKLTGMAFRVPTPNVSVVDLTCRLEKAAKYDDIKKVVKQASEGPLKGILGYTEDQVVSCDFNSDTHSSTFDAGAGIALNDHFVKLISWYDNEFGYSNRVVDLMVHMASKE
6	3cifA2	0.71	0.71	20.16	1.70	HHsearch		-SSTTNCLAPLAKIINDKFGIVEGLMTTVHSLTANQLTVDGPSGKDWRAGRCAGNNIIPASTGAAKAVGKVIPALNGKLTGMAIRVPTPDVSVVDLTCKLAKPASIEEIYQAVKEASNGPMKGIMGYTSDDVVSTDFIGCKYSSILDKNACIALNDSFVKLISWYDNESGYSNRLVDLAVYVASRG
7	1hdgO2	0.51	0.50	14.48	3.04	FFAS-3D		-SCTTNSIAPIVKVLHEKFGIVSGMLTTVHSYTNDQRVLDLPH-KDLRRARAAAVNIIPTTTGAAKAVALVVPEVKGKLDGMAIRVPTPDGSITDLTVLVEKETTVEEVNAVMKEATEGRLKGIIGYNDEPIVSSDIIGTTFSGIFDATITNVIGGKLVKVASWYDNEYGYSNRVVDTLELLLK--
8	6m5xO2	0.69	0.69	19.58	1.15	EigenThreader		ASCTTNCLAPLAKTLNDKFTIVEGLMTAIHAYTASQKTVDGPSSKDWRGGRAAAQNLIPSSTGAAKAVGKVIPELAGKVTGMSVRVPTVNVSLVDFTVRFAKDVTYDEVKAAIKEASEGPLKGILAYTEDDIVSTDILTDPHSSTFDAKAGIALNKNFVKVMSWYDNEYGYSRRVVDLIVFVSKKD
9	4k9dA	0.81	0.80	22.62	2.97	CNFpred		ASCTTNCLAPLAKVIHDKFGIIEGLMTTVHATTATQKTVDGPSGKLWRDGRGAGQNIIPASTGAAKAVGKVIPDLNGKLTGMAFRVPTPDVSVVDLTCRLQKGATMDEIKAAVKEAANGPMKGILEYTEDQVVSTDFTGDTHSSIFDALACISLNPNFVKLIAWYDNEYGYSNRVVDLISYIASR-
10	6m5xO2	0.65	0.64	18.26	1.50	DEthreader		PSCTTNCLAPLAKTLNDKFTIVEGLMTAIHAYTASQ-KTV-DGPSSWRGGRAAAQNLIPSSTGAAKAVGKVIPELAGKVTGMSVRVPTVNVSLVDFTVRFAKDVTYDEVKAAIKEASEGPLKGILAYTEDDIVSTDILTDPHSSTFDAKAGIALNKNFVKVMSWYDNEYGYSRRVVDLIVFVSKKG


(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	0.8876


(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	6m5xO2	0.99	0.46	0.688	1.000
2	3h9eB	0.99	0.47	0.785	1.000
3	6ok4A	0.99	0.46	0.665	0.995
4	1ywgO	0.98	0.54	0.741	0.995
5	1j0xO	0.98	0.74	0.946	1.000
6	1gd1O	0.98	0.56	0.578	0.995
7	3docA	0.98	0.58	0.481	0.995
8	3cifA	0.98	0.71	0.715	1.000
9	2d2iA	0.98	0.60	0.524	0.995
10	3e6aO	0.98	0.63	0.762	0.995



(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:0016620	0.98	oxidoreductase activity, acting on the aldehyde or oxo group of donors, NAD or NADP as acceptor
GO:0004365	0.97	glyceraldehyde-3-phosphate dehydrogenase (NAD+) (phosphorylating) activity
GO:1901363	0.70	heterocyclic compound binding
GO:0097159	0.70	organic cyclic compound binding
GO:0036094	0.65	small molecule binding
GO:0000166	0.64	nucleotide binding
GO:0048037	0.60	cofactor binding
GO:0051287	0.59	NAD 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:0008152	0.92	metabolic process
GO:0071704	0.89	organic substance metabolic process
GO:0044238	0.89	primary metabolic process
GO:0009987	0.88	cellular process
GO:0044763	0.84	single-organism cellular process
GO:0044237	0.84	cellular metabolic process
GO:0065007	0.70	biological regulation
GO:0065008	0.53	regulation of biological quality
GO:0044710	0.53	single-organism metabolic process
GO:0043170	0.53	macromolecule metabolic process
GO:0044260	0.52	cellular macromolecule metabolic process
GO:0006915	0.50	apoptotic 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	0.98	cell part
GO:0044424	0.95	intracellular part
GO:0044444	0.84	cytoplasmic part
GO:0043226	0.81	organelle
GO:0043229	0.80	intracellular organelle
GO:0043227	0.75	membrane-bounded organelle
GO:0043231	0.74	intracellular membrane-bounded organelle
GO:0005829	0.65	cytosol
GO:0005737	0.56	cytoplasm
GO:0043232	0.53	intracellular non-membrane-bounded organelle
GO:0005634	0.53	nucleus






(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	0.624	3docA	0.982	0.58	0.481	0.995	1.2.1.12	3,30
2	0.606	2vynD	0.992	0.47	0.801	1.000	1.2.1.12	30
3	0.605	3h9eB	0.992	0.47	0.785	1.000	1.2.1.12	3,30
4	0.603	1crwG	0.990	0.52	0.753	1.000	1.2.1.12	3,30
5	0.593	3l0dA	0.980	0.63	0.454	0.995	1.2.1.12	3,30



(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	Predicted binding site residues
1	0.76	3cifC	0.988	0.58	0.715	1.000	1.27	G3H	2,3,4,30,33,62,64,85
2	0.68	1qxsA	0.978	0.79	0.591	1.000	0.87	S70	3,4,28,30,62



(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.

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.