D-I-TASSER O60235-D2

D-I-TASSER results for O60235-D2

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

Input Sequence in FASTA format

>O60235 (259 residues)
LTDQAAANWLINECGAGPDLITLSEQRILGGTEAEEGSWPWQVSLRLNNAHHCGGSLINN
MWILTAAHCFRSNSNPRDWIATSGISTTFPKLRMRVRNILIHNNYKSATHENDIALVRLE
NSVTFTKDIHSVCLPAATQNIPPGSTAYVTGWGAQEYAGHTVPELRQGQVRIISNDVCNA
PHSYNGAILSGMLCAGVPQGGVDACQGDSGGPLVQEDSRRLWFIVGIVSWGDQCGLPDKP
GVYTRVTAYLDWIRQQTGI

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 160 180 200 220 240 \| \| \| \| \| \| \| \| \| \| \| \| LTDQAAANWLINECGAGPDLITLSEQRILGGTEAEEGSWPWQVSLRLNNAHHCGGSLINNMWILTAAHCFRSNSNPRDWIATSGISTTFPKLRMRVRNILIHNNYKSATHENDIALVRLENSVTFTKDIHSVCLPAATQNIPPGSTAYVTGWGAQEYAGHTVPELRQGQVRIISNDVCNAPHSYNGAILSGMLCAGVPQGGVDACQGDSGGPLVQEDSRRLWFIVGIVSWGDQCGLPDKPGVYTRVTAYLDWIRQQTGI
Prediction	CCCCCCCCCCCCCCCCCCCCCCCCCCCSSCCSSCCCCCCCCSSSSSSCCSSSSSSSSCCCCSSSSCCCCCCCCCCCSSSSSSSCCSSCCCCSSSSSSSSSSCCCCCCCCCCCSSSSSSSCCCCCCCCCSSSSSCCCCCCCCCCCCSSSSSCCCSCCCCCCCCCSCSSSSSSSCCHHHHCCCCCCCCCCCCCSSSCCCCCCCCSCCCCCCCCCSSSSCCCCSSSSSSSSSSCCCCCCCCCCSSSSSHHHHHHHHHHHHCC
Confidence	9841114354668899987777889954598658999997389999899688557982399799912216899982489999775766993899999999798999998887079999688766789844455899999899963899981721357999995136998553098885321247997799836415777997286788998425654998499999996063559999892665446878899986298
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 160 180 200 220 240 \| \| \| \| \| \| \| \| \| \| \| \| LTDQAAANWLINECGAGPDLITLSEQRILGGTEAEEGSWPWQVSLRLNNAHHCGGSLINNMWILTAAHCFRSNSNPRDWIATSGISTTFPKLRMRVRNILIHNNYKSATHENDIALVRLENSVTFTKDIHSVCLPAATQNIPPGSTAYVTGWGAQEYAGHTVPELRQGQVRIISNDVCNAPHSYNGAILSGMLCAGVPQGGVDACQGDSGGPLVQEDSRRLWFIVGIVSWGDQCGLPDKPGVYTRVTAYLDWIRQQTGI
Prediction	8456535513345213444435456410041450544411100001146411010040253000000000454541420102022344665241404301303512543240100302353305037301000004574614543301002424134525336342304020134731544433644036200100157333001205132130044763200000000213010346342230200312763564256
	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                 200                 220                 240

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

SS
Seq

CCCCCCCCCCCCCCCCCCCCCCCCCCCSSCCSSCCCCCCCCSSSSSSCCSSSSSSSSCCCCSSSSCCCCCCCCCCCSSSSSSSCCSSCCCCSSSSSSSSSSCCCCCCCCCCCSSSSSSSCCCCCCCCCSSSSSCCCCCCCCCCCCSSSSSCCCSCCCCCCCCCSCSSSSSSSCCHHHHCCCCCCCCCCCCCSSSCCCCCCCCSCCCCCCCCCSSSSCCCCSSSSSSSSSSCCCCCCCCCCSSSSSHHHHHHHHHHHHCC
LTDQAAANWLINECGAGPDLITLSEQRILGGTEAEEGSWPWQVSLRLNNAHHCGGSLINNMWILTAAHCFRSNSNPRDWIATSGISTTFPKLRMRVRNILIHNNYKSATHENDIALVRLENSVTFTKDIHSVCLPAATQNIPPGSTAYVTGWGAQEYAGHTVPELRQGQVRIISNDVCNAPHSYNGAILSGMLCAGVPQGGVDACQGDSGGPLVQEDSRRLWFIVGIVSWGDQCGLPDKPGVYTRVTAYLDWIRQQTGI

1z8gA

0.45

0.44

12.75

1.50

DEthreader

NAGCALTAICQ-DCGRRKLP-------IVGGRDTSLGRWPWQVSLRYDGAHLCGGSLLSGDWVLTAAHCFPENRVLSRWRVFAGAVASPHGLQLGVQAVVYHGGYLPEENSNDIALVHLSSPLPLTEYIQPVCLPAAGQALVDGKICTVTGWGNTQYYGQQAGVLQEARVPIISNDVCNGADFYGNQIKPKMFCAGYPEGGIDACQGDSGGPFVCEDSTPRWRLCGIVSWGTGCALAQKPGVYTKVSDFREWIFQAIKS

2oq5A

0.50

0.45

13.09

2.69

SPARKS-K

---------------------------IVGGTEVEEGEWPWQASLQWDGSHRCGATLINATWLVSAAHCFTTYKNPARWTASFGVTIKPSKMKRGLRRIIVHEKYKHPSHDYDISLAELSSPVPYTNAVHRVCLPDASYEFQPGDVMFVTGFGALKNDGYSQNHLRQAQVTLIDATTCNEPQAYNDAITPRMLCAGSLEGKTDACQGDSGGPLVSSDARDIWYLAGIVSWGDECAKPNKPGVYTRVTALRDWITSKTGI

1z8gA

0.45

0.43

12.64

0.66

MapAlign

--VAGLSCEEMGFCGRRK-------LPIVGGRDTSLGRWPWQVSLRYDGAHLCGGSLLSGDWVLTAAHCFERNRVLSRWRVFAGAVAQASGLQLGVQAVVYHGGYLSEENSNDIALVHLSSPLPLTEYIQPVCLPAAGQALVDGKICTVTGWGNTQYYGQQAGVLQEARVPIISNDVCNGADFYGNQIKPKMFCAGYPEGGIDACQGDSGGPFVCEDRTPRWRLCGIVSWGTGCALAQKPGVYTKVSDFREWIFQAIKT

1z8gA2

0.47

0.43

12.60

0.36

CEthreader

-------------CGRRKL-------PIVGGRDTSLGRWPWQVSLRYDGAHLCGGSLLSGDWVLTAAHCFPENRVLSRWRVFAGAVASPHGLQLGVQAVVYHGGYLPEENSNDIALVHLSSPLPLTEYIQPVCLPAAGQALVDGKICTVTGWGNTQYYGQQAGVLQEARVPIISNDVCNGADFYGNQIKPKMFCAGYPEGGIDACQGDSGGPFVCEDSTPRWRLCGIVSWGTGCALAQKPGVYTKVSDFREWIFQAIKT

2oq5A

0.50

0.45

13.09

2.24

MUSTER

---------------------------IVGGTEVEEGEWPWQASLQWDGSHRCGATLINATWLVSAAHCFTTYKNPARWTASFGVTIKPSKMKRGLRRIIVHEKYKHPSHDYDISLAELSSPVPYTNAVHRVCLPDASYEFQPGDVMFVTGFGALKNDGYSQNHLRQAQVTLIDATTCNEPQAYNDAITPRMLCAGSLEGKTDACQGDSGGPLVSSDARDIWYLAGIVSWGDECAKPNKPGVYTRVTALRDWITSKTGI

6esoA

0.38

0.36

10.65

1.55

HHsearch

SPTRGSSGYSLRLCNTGD------VCTIVGGTNSSWGEWPWQVSLQVKQRHLCGGSLIGHQWVLTAAHCFDGLPLQDVWRIYSGILNLKDTPFSQIKEIIIHQNYKVSEGNHDIALIKLQAPLNYTEFQKPICLPSKGDTSTIYTNCWVTGWGFSKEKGEIQNILQKVNIPLVTNEECQKRYQ-DYKITQRMVCA----GGKDACKGDSGGPLVCKH-NGMWRLVGITSWGEGCARREQPGVYTKVAEYMDWILEKTQS

1ekbB

0.37

0.33

9.74

2.96

FFAS-3D

---------------------------IVGGSDSREGAWPWVVALYFDDQQVCGASLVSRDWLVSAAHCVYGRNMEPSKWKAASNLTSPQIETRLIDQIVINPHYNKRRKNNDIAMMHLEMKVNYTDYIQPICLPEENQVFPPGRICSIAGWGALIYQGSTADVLQEADVPLLSNEKCQQQMP-EYNITENMVCAGYEAGGVDSCQGDSGGPLMCQE-NNRWLLAGVTSFGYQCALPNRPGVYARVPRFTEWIQSFL--

1jwtA

0.34

0.33

9.83

0.98

EigenThreader

TFG-----SGEADCGLRPLFEKKSLEDIVEGSDAEIGMSPWQVMLFRKSELLCGASLISDRWVLTAAHCLLPWDKNFTLLVRIGKHSRNIEKISMLEKIYIHPRYWRENLDRDIALMKLKKPVAFSDYIHPVCLPDAASLLQAGYKGRVTGWGNLKETWGQPSVLQVVNLPIVERPVCKDS--TRIRITDNMFCAGYKPKRGDACEGDSGGPFVMKSPNNRWYQMGIVSWGEGCDRDGKYGFYTHVFRLKKWIQKVIDQ

2oq5A

0.50

0.45

13.09

4.91

CNFpred

---------------------------IVGGTEVEEGEWPWQASLQWDGSHRCGATLINATWLVSAAHCFTTYKNPARWTASFGVTIKPSKMKRGLRRIIVHEKYKHPSHDYDISLAELSSPVPYTNAVHRVCLPDASYEFQPGDVMFVTGFGALKNDGYSQNHLRQAQVTLIDATTCNEPQAYNDAITPRMLCAGSLEGKTDACQGDSGGPLVSSDARDIWYLAGIVSWGDECAKPNKPGVYTRVTALRDWITSKTGI

7meqA

0.40

0.39

11.49

1.50

DEthreader

YRAACNFYSRCIACGVNLN--------IVGGESALPGAWPWQVSLHVQNVHVCGGSIITPEWIVTAAHCVEKLNNPWHWTAFAGILRSFMFAGYQVEKVISHPNYDSKTKNNDIALMKLQKPLTFNDLVKPVCLPNPGMMLQPEQLCWISGWGATEEKGKTSEVLNAAKVLLIETQRCNSRYVYDNLITPAMICAGFLQGNVDSCQGDSGGPLVTSKNN-IWWLIGDTSWGSGCAKAYRPGVYGNVMVFTDWIYRQMRA

(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	0.8916

(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	1z8gA	0.94	1.33	0.448	0.973	model1_1z8gA.pdb.gz
2	7meqA	0.92	1.61	0.410	0.961	model1_7meqA.pdb.gz
3	1jwtA	0.91	1.80	0.337	0.961	model1_1jwtA.pdb.gz
4	2vntC	0.89	1.43	0.357	0.927	model1_2vntC.pdb.gz
5	1bmlA	0.89	1.93	0.352	0.934	model1_1bmlA.pdb.gz
6	1a5iA	0.89	1.74	0.336	0.942	model1_1a5iA.pdb.gz
7	2oq5A	0.88	0.93	0.504	0.896	model1_2oq5A.pdb.gz
8	1yc0A	0.88	1.31	0.329	0.911	model1_1yc0A.pdb.gz
9	1fizA	0.87	1.15	0.418	0.896	model1_1fizA.pdb.gz
10	1cgiE	0.87	1.74	0.397	0.915	model1_1cgiE.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:0008233	0.98	peptidase activity
GO:0070011	0.96	peptidase activity, acting on L-amino acid peptides
GO:0008236	0.93	serine-type peptidase activity
GO:0004175	0.83	endopeptidase activity
GO:0004252	0.80	serine-type endopeptidase 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:0008152	0.83	metabolic process
GO:0071704	0.82	organic substance metabolic process
GO:0044238	0.81	primary metabolic process
GO:0043170	0.79	macromolecule metabolic process
GO:0019538	0.76	protein metabolic process
GO:0006508	0.71	proteolysis
GO:0044699	0.55	single-organism process
GO:0065007	0.53	biological regulation

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:0044464	0.84	cell part
GO:0044424	0.69	intracellular part
GO:0044421	0.53	extracellular region part
GO:0043226	0.46	organelle
GO:0005615	0.46	extracellular space
GO:0043227	0.42	membrane-bounded organelle
GO:0043229	0.36	intracellular organelle
GO:0044444	0.34	cytoplasmic part
GO:0043231	0.33	intracellular membrane-bounded organelle
GO:0005737	0.30	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	0.592	2eekA	0.801	1.42	0.361	0.826	3.4.21.4	68,113,205,207,208
2	0.575	2qxgA	0.811	1.26	0.390	0.842	3.4.21.117	68,113,205,207,208
3	0.563	2zgcA	0.833	1.50	0.330	0.876	3.4.21.-	68,113,207,209,210
4	0.562	1bitA	0.806	1.76	0.373	0.838	3.4.21.4	68,113,205,207,208
5	0.559	1trnA	0.815	1.12	0.378	0.838	3.4.21.4	68,113,205,207,208

	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	0.65	1z8gA	0.944	1.33	0.448	0.973	1.48	III	complex1.pdb.gz	68,105,110,157,187,203,204,205,206,207,209,229,230,231,232,233,234,241
2	0.57	1uvsH	0.834	1.31	0.375	0.865	1.27	I11	complex2.pdb.gz	110,203,204,205,206,228,229,230,231,233,234
3	0.56	2zfpH	0.851	1.35	0.367	0.884	1.37	19U	complex3.pdb.gz	68,110,204,209,228,229,230,231,241,242
4	0.53	1bmmH	0.853	1.40	0.361	0.888	1.21	BM2	complex4.pdb.gz	68,108,109,110,203,206,209,229,230,231,232,233
5	0.40	1dwcH	0.855	1.30	0.361	0.888	1.11	MIT	complex5.pdb.gz	68,203,204,205,209,230,231,232,233
6	0.39	1nroH	0.851	1.38	0.361	0.888	1.00	III	complex6.pdb.gz	68,72,209,229,231,233
7	0.39	2c93B	0.848	1.33	0.368	0.880	0.93	C4M	complex7.pdb.gz	68,206,230,231
8	0.34	1p8vC	0.847	1.35	0.368	0.880	1.31	DFP	complex8.pdb.gz	53,68,205,206,207,209,229,230
9	0.28	1nrnH	0.843	1.35	0.366	0.876	0.99	III	complex9.pdb.gz	68,110,206,230,231,232,233
10	0.25	3p70B	0.851	1.36	0.362	0.884	1.69	NA	complex10.pdb.gz	55,56,64,65,210,211,212,227

	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.