D-I-TASSER Q5TC82-D2

D-I-TASSER results for Q5TC82-D2

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

Input Sequence in FASTA format

>Q5TC82 (194 residues)
AKPKDVVAAGSVEMMNVESKGMRDQRLDLQRRAAETSDDDLIPFGDRPTVSRFGAISRTS
KTIYQGAGPMQAMAPQGAPTKSINISDYSPYGTHGGWGASPYSPHQNIPSQGHFSERERI
SMSEVASHGKPLPSAEREQLRLELQQLNHQISQQTQLRGLEAVSNRLVLQREANTLAGQS
QPPPPPPPKWPGMI

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 160 180 \| \| \| \| \| \| \| \| \| AKPKDVVAAGSVEMMNVESKGMRDQRLDLQRRAAETSDDDLIPFGDRPTVSRFGAISRTSKTIYQGAGPMQAMAPQGAPTKSINISDYSPYGTHGGWGASPYSPHQNIPSQGHFSERERISMSEVASHGKPLPSAEREQLRLELQQLNHQISQQTQLRGLEAVSNRLVLQREANTLAGQSQPPPPPPPKWPGMI
Prediction	CCCCCCCCCCCHHHSCCCCCCCCHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCSSHHHHHCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHCCCCCCCCCCCCCCCCC
Confidence	99755567774110003355531111245543134577884468999864445532210114666799856778999998764201156544557777778887678887666421100110111124688997425678889999998886654566553031157787777765159999999998788889
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 160 180 \| \| \| \| \| \| \| \| \| AKPKDVVAAGSVEMMNVESKGMRDQRLDLQRRAAETSDDDLIPFGDRPTVSRFGAISRTSKTIYQGAGPMQAMAPQGAPTKSINISDYSPYGTHGGWGASPYSPHQNIPSQGHFSERERISMSEVASHGKPLPSAEREQLRLELQQLNHQISQQTQLRGLEAVSNRLVLQREANTLAGQSQPPPPPPPKWPGMI
Prediction	86355244444142242555625454153444346367330122374241343231443243424554335333464445441414423221423423334345455344643334443122332344444356454540313054145514564444425444441214343543545563475544614637
	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 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
Seq

CCCCCCCCCCCHHHSCCCCCCCCHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCSSHHHHHCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHCCCCCCCCCCCCCCCCC
AKPKDVVAAGSVEMMNVESKGMRDQRLDLQRRAAETSDDDLIPFGDRPTVSRFGAISRTSKTIYQGAGPMQAMAPQGAPTKSINISDYSPYGTHGGWGASPYSPHQNIPSQGHFSERERISMSEVASHGKPLPSAEREQLRLELQQLNHQISQQTQLRGLEAVSNRLVLQREANTLAGQSQPPPPPPPKWPGMI

1vt4I3

0.08

3.23

0.62

CEthreader

GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG

4kvmA

0.06

2.53

0.55

EigenThreader

TTLLWTYYFLAQHFDHVGELEKAEKYVDLAIDHTPTLVELFMTKARISKHKGELQTAMEIMDHARKLINGKCAKYMLRNDENELAAKTVSLFTRNEAVGGAVGDLADMQCIFDTWADDQFDFHFFAFRKGSLRTYLDLMSWEDLKEAQKCLEAYILAAQLYTRLDTASKYLEQAKVILGQNDPTVISTEKFYNS

6w1sF

0.15

0.05

1.56

0.50

FFAS-3D

-------------------------------------------------------------------------------------------------------------------------VIKCMDKDSPDLHQDLNALKTKFQELRKLIGPEQQQQQLHSLREQVRTKNELLQ-------------KYKSL-

5yfpH2

0.12

0.11

3.80

1.00

SPARKS-K

RDRSSVLILEKF----------WDTELDQLFKNVEGAQKFI---NSTK----------GRHILMNSANWMELNTTTGKPLQMVQLNDLVLIADKSRDKQNDFIVSQCYPLKDVTVTQEELLFKFSNSNSSLYECRDADECSRLLDVIRKAKDDLCDIFHVEEE-NSKRIRESFRYLQSTQQTPGRENNRSPNKN

5vjuA

0.29

0.08

2.52

0.42

CNFpred

--------------------------------------------------------------------------------------------------------------------------------GSPELRQEHQQLAQEFQQLLQEIQQL-GRELLKGELQGIKQLREASEKARNPEKKSV---------

7cu3A

0.08

0.06

2.27

0.83

DEthreader

--ICMNTPQGMQCFRAFMSMFQITQTLLCMGLTFVVVNF-IIGMFLLLLCYA-FA-------------------G----VLFGFAITVLFRI-------------------VTGEDWNIMDCMVQCTWATCGNYAGALMYFCSFYVIAYIMLNLLVAIIVENFSLFYSTELSYNDLRHFQIIWVDDKRE-----

6jr6A

0.03

1.69

0.95

MapAlign

--TYEIFTEQLRIRVNKAPFQLQIFALTGKPIMPPKWALGFSQCRGDYTIPCDIIYQDIGWTEGLQDFDWRKNNYANQQQWKEADALGHLVKDVRTGKSYDMPWPWGGNCGVVDFTKPEVADWWGSYAVDRLNMKHHLGHNEIHNVYGFTWDKVVTEQFYKHQMANQIPVGLSAGMGLIPFWTCDISGYCGDIK

6etxG

0.11

4.06

0.67

MUSTER

FSFLRFIDISPAEMANLMLQGLLARWLALFLSLKASYRLHQLRSWGAPEGESHQRYLRNKDFLLGVNFPLSFLKSLVFSSHCKAVSGYSDQVVHQRRSATSSLRRCLLTELPSFLCVASPRVTAVPLDSYCNDRSAEYERRVLKEGGSLAAKQCLLNGAPELAADWLNRRSQFFPEPAGGLWSIRPQNGWSFIR

2pffA1

0.22

0.20

6.19

0.44

HHsearch

RFSKQVTAKGSTLIFNQGSKQDVEALIETEKNGGLGWDDAIIPFAAIPEDSKAHRIMRMVKKRGIETRPAQVILPMSPGTFGGLFRWHSSCGAIIGWTRGTGLMSANIISQKEMAGLLTPEVVELCQKSVMADLNGGLQFVPELKEFTKELVETSEVRKAV--SIETALEHKV--VNGN---------------

6jdaA

0.07

2.95

0.46

CEthreader

ASTGIINHGVLTALNPKNLGGLAEFPLKESIARHTDKPIGLLNDVQAAACAEYKDEDKNAVQNFVFITVVGGGIILERRLLTEPNGVAGHIGHTLADPNGPVCGCGRVGCVEAVAAGRAIEAVSSQWNPPCTPKQAFELFRKNDEKATALIQRSASAIANLIADLVIGLDVQKVVVGGSVGLAEGYLPLVKQYL

(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	0.4409

(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.	Download Alignment
1	4pmwA	0.45	6.08	0.080	0.830	model1_4pmwA.pdb.gz
2	5f0oA	0.45	5.97	0.039	0.820	model1_5f0oA.pdb.gz
3	6es9A	0.44	5.52	0.053	0.747	model1_6es9A.pdb.gz
4	6xiwA	0.43	5.03	0.033	0.691	model1_6xiwA.pdb.gz
5	1f31A	0.43	4.96	0.027	0.660	model1_1f31A.pdb.gz
6	4za4A	0.43	5.82	0.052	0.778	model1_4za4A.pdb.gz
7	6f3hA	0.43	6.00	0.050	0.799	model1_6f3hA.pdb.gz
8	3k1qB	0.43	5.43	0.048	0.717	model1_3k1qB.pdb.gz
9	2cseW	0.35	5.28	0.092	0.603	model1_2cseW.pdb.gz
10	2id0A	0.34	6.27	0.032	0.649	model1_2id0A.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:0044822	1.00	poly(A) RNA binding
GO:0003729	0.89	mRNA binding
GO:0003730	0.78	mRNA 3'-UTR binding
GO:0035613	0.77	RNA stem-loop binding
GO:0003824	0.60	catalytic activity
GO:0016740	0.57	transferase activity
GO:0004842	0.55	ubiquitin-protein transferase 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:0044260	1.00	cellular macromolecule metabolic process
GO:0044238	1.00	primary metabolic process
GO:0065007	0.93	biological regulation
GO:0050789	0.93	regulation of biological process
GO:0050794	0.92	regulation of cellular process
GO:0060255	0.90	regulation of macromolecule metabolic process
GO:0048518	0.90	positive regulation of biological process
GO:0065008	0.89	regulation of biological quality
GO:0048522	0.89	positive regulation of cellular process
GO:0010608	0.89	posttranscriptional regulation of gene expression
GO:0016070	0.84	RNA metabolic process
GO:0080090	0.80	regulation of primary metabolic process
GO:0048519	0.80	negative regulation of biological process
GO:0031323	0.80	regulation of cellular metabolic process
GO:0016071	0.80	mRNA metabolic process
GO:2000112	0.79	regulation of cellular macromolecule biosynthetic process
GO:0051171	0.79	regulation of nitrogen compound metabolic process
GO:0050896	0.79	response to stimulus
GO:0032268	0.79	regulation of cellular protein metabolic process
GO:0031324	0.79	negative regulation of cellular metabolic process
GO:0010605	0.79	negative regulation of macromolecule metabolic process
GO:0070887	0.78	cellular response to chemical stimulus
GO:0051254	0.78	positive regulation of RNA metabolic process
GO:0017148	0.78	negative regulation of translation
GO:0010033	0.78	response to organic substance
GO:0000956	0.78	nuclear-transcribed mRNA catabolic process
GO:0071347	0.77	cellular response to interleukin-1
GO:0061158	0.77	3'-UTR-mediated mRNA destabilization
GO:0061014	0.77	positive regulation of mRNA catabolic process
GO:0000288	0.77	nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay
GO:0009966	0.72	regulation of signal transduction
GO:0051239	0.62	regulation of multicellular organismal process
GO:0051241	0.61	negative regulation of multicellular organismal process
GO:0022407	0.61	regulation of cell-cell adhesion
GO:0006996	0.61	organelle organization
GO:0002682	0.61	regulation of immune system process
GO:0050856	0.60	regulation of T cell receptor signaling pathway
GO:0046007	0.60	negative regulation of activated T cell proliferation
GO:0045623	0.60	negative regulation of T-helper cell differentiation
GO:0033962	0.60	cytoplasmic mRNA processing body assembly
GO:0030889	0.60	negative regulation of B cell proliferation
GO:0002635	0.60	negative regulation of germinal center formation

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:0043226	0.82	organelle
GO:0043229	0.81	intracellular organelle
GO:0044444	0.77	cytoplasmic part
GO:0032991	0.74	macromolecular complex
GO:0030529	0.72	intracellular ribonucleoprotein complex
GO:0043232	0.71	intracellular non-membrane-bounded organelle
GO:0010494	0.70	cytoplasmic stress granule
GO:0000932	0.70	cytoplasmic mRNA processing body
GO:0005737	0.56	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

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	1w27A	0.416	5.56	0.066	0.742	4.3.1.24	NA
2	0.060	1rr8C	0.360	5.55	0.084	0.619	5.99.1.2	NA
3	0.060	1gthA	0.401	5.79	0.037	0.732	1.3.1.2	NA
4	0.060	1dgjA	0.399	6.07	0.041	0.732	1.2.-.-	NA
5	0.060	1yfeA	0.403	5.37	0.025	0.675	4.2.1.2	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:

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	2x2iC	0.408	5.54	0.077	0.717	0.29	QPS	complex1.pdb.gz	51,53,54,146
2	0.01	2x2iD	0.403	5.71	0.045	0.722	0.28	QPS	complex2.pdb.gz	55,84,87,88,89,96,97,144
3	0.01	1uzeA	0.327	5.30	0.049	0.541	0.13	EAL	complex3.pdb.gz	53,87,88,89,113
4	0.01	1i1eA	0.390	5.60	0.032	0.701	0.34	DM2	complex4.pdb.gz	54,66,67,76
5	0.01	2x2iA	0.406	5.55	0.070	0.722	0.29	QPS	complex5.pdb.gz	87,88,89,92
6	0.01	1g9aA	0.399	5.39	0.006	0.691	0.13	BAB	complex6.pdb.gz	110,113,114,115,116,118
7	0.01	2z1qB	0.420	4.85	0.061	0.655	0.11	FAD	complex7.pdb.gz	33,41,42,55,97,142
8	0.01	2z1qA	0.418	4.93	0.073	0.655	0.10	FAD	complex8.pdb.gz	60,62,63,68,151

	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.