D-I-TASSER P22413-D3

D-I-TASSER results for P22413-D3

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

Input Sequence in FASTA format

>P22413 (306 residues)
QGEKSWVEEPCESINEPQCPAGFETPPTLLFSLDGFRAEYLHTWGGLLPVISKLKKCGTY
TKNMRPVYPTKTFPNHYSIVTGLYPESHGIIDNKMYDPKMNASFSLKSKEKFNPEWYKGE
PIWVTAKYQGLKSGTFFWPGSDVEINGIFPDIYKMYNGSVPFEERILAVLQWLQLPKDER
PHFYTLYLEEPDSSGHSYGPVSSEVIKALQRVDGMVGMLMDGLKELNLHRCLNLILISDH
GHGSDNVFSNMQALFVGYGPGFKHGIEADTFENIEVYNLMCDLLNLTPAPNNGTHGSLNH
LLKNPV

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 160 180 200 220 240 260 280 300 \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| QGEKSWVEEPCESINEPQCPAGFETPPTLLFSLDGFRAEYLHTWGGLLPVISKLKKCGTYTKNMRPVYPTKTFPNHYSIVTGLYPESHGIIDNKMYDPKMNASFSLKSKEKFNPEWYKGEPIWVTAKYQGLKSGTFFWPGSDVEINGIFPDIYKMYNGSVPFEERILAVLQWLQLPKDERPHFYTLYLEEPDSSGHSYGPVSSEVIKALQRVDGMVGMLMDGLKELNLHRCLNLILISDHGHGSDNVFSNMQALFVGYGPGFKHGIEADTFENIEVYNLMCDLLNLTPAPNNGTHGSLNHLLKNPV
Prediction	CCCCCCCCCCCCCCCCCCCCCCCCCCCSSSSSSCCCCHHHHHHHHHCCCHHHHHHHCCCCCCCSSSCCCCCCCCHHHHHHCCCCCCCCSSSCCCCCCCCCCCCSSCCCCCCCCHHHHCCCCHHHHHHHHCCCSSSSSCCCCSSSCCCCCCCCSCCCCCCCCHHHHHHHHHHHHHHHHCCCCCSSSSSSCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHCCCCCSSSSSSSCCCCCCCCCCCCCCCHHHHHCCCCCCCCCCCCCCHHHHHHHHHHHHCCCCCCCCCCHHHHHHHHHCCC
Confidence	985444557764446788987779995899992589989998642039179999980964264051466524551556621678852123168644676685132145444784562577389999861972478745873121267777500111244314899999999986122269958999606787445778999999999999999999999999999598788279999357888888754222114440753125876787213349999999919998998997578999962789
	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 \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| QGEKSWVEEPCESINEPQCPAGFETPPTLLFSLDGFRAEYLHTWGGLLPVISKLKKCGTYTKNMRPVYPTKTFPNHYSIVTGLYPESHGIIDNKMYDPKMNASFSLKSKEKFNPEWYKGEPIWVTAKYQGLKSGTFFWPGSDVEINGIFPDIYKMYNGSVPFEERILAVLQWLQLPKDERPHFYTLYLEEPDSSGHSYGPVSSEVIKALQRVDGMVGMLMDGLKELNLHRCLNLILISDHGHGSDNVFSNMQALFVGYGPGFKHGIEADTFENIEVYNLMCDLLNLTPAPNNGTHGSLNHLLKNPV
Prediction	855532254416536436346636444122100302112104514641313420152103043031222011100100000022012000000221224244312122232132310303200210443423000000122213132120222221222222441031014003315754010000000100320022013063024004302400330151047241443000000023321324312222232022012034426274041010000002117051223403363035105628
	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

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

SS
Seq

CCCCCCCCCCCCCCCCCCCCCCCCCCCSSSSSSCCCCHHHHHHHHHCCCHHHHHHHCCCCCCCSSSCCCCCCCCHHHHHHCCCCCCCCSSSCCCCCCCCCCCCSSCCCCCCCCHHHHCCCCHHHHHHHHCCCSSSSSCCCCSSSCCCCCCCCSCCCCCCCCHHHHHHHHHHHHHHHHCCCCCSSSSSSCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHCCCCCSSSSSSSCCCCCCCCCCCCCCCHHHHHCCCCCCCCCCCCCCHHHHHHHHHHHHCCCCCCCCCCHHHHHHHHHCCC
QGEKSWVEEPCESINEPQCPAGFETPPTLLFSLDGFRAEYLHTWGGLLPVISKLKKCGTYTKNMRPVYPTKTFPNHYSIVTGLYPESHGIIDNKMYDPKMNASFSLKSKEKFNPEWYKGEPIWVTAKYQGLKSGTFFWPGSDVEINGIFPDIYKMYNGSVPFEERILAVLQWLQLPKDERPHFYTLYLEEPDSSGHSYGPVSSEVIKALQRVDGMVGMLMDGLKELNLHRCLNLILISDHGHGSDNVFSNMQALFVGYGPGFKHGIEADTFENIEVYNLMCDLLNLTPAPNNGTHGSLNHLLKNPV

6c01A

0.61

0.57

16.28

1.33

DEthreader

-------------------Q--FDLPPVILFSMDGFRAEYLYTWDTLMPNINKLKTCGIHSKYMRAMYPTKTFPNHYTIVTGLYPESHGIIDNNMYD-VNLNKNFSLSKEQNNPAWWHGQPMWLTAMYQGLKAATYFWPGSEVAINGSFPSIYMPYNGSVPFEERISTLLKWLDLPKAERPRFYTMYFEEPDSSGHAGGPVSARVIKALQVVDHAFGMLMEGLKQRNLHNCVNIILLADHGMDHGYNFRSMEAIFLAHGPSFKEKTEVEPFENIEVYNLMCDLLRIQPAP-NNGTHGSLNHLLKVE

4b56A3

0.87

0.86

24.20

2.63

SPARKS-K

---KSWVEETCESIDTPECPAEFESPPTLLFSLDGFRAEYLHTWGGLLPVISKLKNCGTYTKNMRPMYPTKTFPNHYSIVTGLYPESHGIIDNKMYDPKMNASFSLKSKEKFNPLWYKGQPIWVTANHQEVKSGTYFWPGSDVEIDGILPDIYKVYNGSVPFEERILAVLEWLQLPSHERPHFYTLYLEEPDSSGHSHGPVSSEVIKALQKVDRLVGMLMDGLKDLGLDKCLNLILISDHGHGSDNLFSNMQALFIGYGPAFKHGAEVDSFENIEVYNLMCDLLGLIPAPNNGSHGSLNHLLKKPI

6c01A

0.62

0.60

17.11

0.87

MapAlign

----------CDTAQQSQCPEGFDLPPVILFSMDGFRAEYLYTWDTLMPNINKLKTCGIHSKYMRAMYPTKTFPNHYTIVTGLYPESHGIIDNNMYDVNLNKNFSLSSKEQNNPAWWHGQPMWLTAMYQGLKAATYFWPGSEVAINGSFPSIYMPYNGSVPFEERISTLLKWLDLPKAERPRFYTMYFEEPDSSGHAGGPVSARVIKALQVVDHAFGMLMEGLKQRNLHNCVNIILLADHGMDYNNEFRSMEAIFLAHGPSFKEKTEVEPFENIEVYNLMCDLLRIQPA-PNNGTHGSLNHLLKVP

6c01A

0.67

19.09

0.56

CEthreader

QGETSWLEENCDTAQQSQCPEGFDLPPVILFSMDGFRAEYLYTWDTLMPNINKLKTCGIHSKYMRAMYPTKTFPNHYTIVTGLYPESHGIIDNNMYDVNLNKNFSLSSKEQNNPAWWHGQPMWLTAMYQGLKAATYFWPGSEVAINGSFPSIYMPYNGSVPFEERISTLLKWLDLPKAERPRFYTMYFEEPDSSGHAGGPVSARVIKALQVVDHAFGMLMEGLKQRNLHNCVNIILLADHGHGYNNEFRSMEAIFLAHGPSFKEKTEVEPFENIEVYNLMCDLLRIQPAPNNGTHGSLNHLLKVPF

4b56A3

0.86

24.11

2.11

MUSTER

---KSWVEETCESIDTPECPAEFESPPTLLFSLDGFRAEYLHTWGGLLPVISKLKNCGTYTKNMRPMYPTKTFPNHYSIVTGLYPESHGIIDNKMYDPKMNASFSLKSKEKFNPLWYKGQPIWVTANHQEVKSGTYFWPGSDVEIDGILPDIYKVYNGSVPFEERILAVLEWLQLPSHERPHFYTLYLEEPDSSGHSHGPVSSEVIKALQKVDRLVGMLMDGLKDLGLDKCLNLILISDHGMGSDNLFSNMQALFIGYGPAFKHGAEVDSFENIEVYNLMCDLLGLIPAPNNGSHGSLNHLLKKPI

6c01A

0.67

19.09

1.95

HHsearch

QGETSWLEENCDTAQQSQCPEGFDLPPVILFSMDGFRAEYLYTWDTLMPNINKLKTCGIHSKYMRAMYPTKTFPNHYTIVTGLYPESHGIIDNNMYDVNLNKNFSLSSKEQNNPAWWHGQPMWLTAMYQGLKAATYFWPGSEVAINGSFPSIYMPYNGSVPFEERISTLLKWLDLPKAERPRFYTMYFEEPDSSGHAGGPVSARVIKALQVVDHAFGMLMEGLKQRNLHNCVNIILLADHGHGYNNEFRSMEAIFLAHGPSFKEKTEVEPFENIEVYNLMCDLLRIQPAPNNGTHGSLNHLLKVPF

4b56A3

0.87

0.86

24.20

3.37

FFAS-3D

---KSWVEETCESIDTPECPAEFESPPTLLFSLDGFRAEYLHTWGGLLPVISKLKNCGTYTKNMRPMYPTKTFPNHYSIVTGLYPESHGIIDNKMYDPKMNASFSLKSKEKFNPLWYKGQPIWVTANHQEVKSGTYFWPGSDVEIDGILPDIYKVYNGSVPFEERILAVLEWLQLPSHERPHFYTLYLEEPDSSGHSHGPVSSEVIKALQKVDRLVGMLMDGLKDLGLDKCLNLILISDHGHGSDNLFSNMQALFIGYGPAFKHGAEVDSFENIEVYNLMCDLLGLIPAPNNGSHGSLNHLLKKPI

4b56A3

0.86

24.11

1.38

EigenThreader

---KSWVEETCESIDTPECPAEFESPPTLLFSLDGFRAEYLHTWGGLLPVISKLKNCGTYTKNMRPMYPTKTFPNHYSIVTGLYPESHGIIDNKMYDPKMNASFSLKSKEKFNPLWYKGQPIWVTANHQEVKSGTYFWPGSDVEIDGILPDIYKVYNGSVPFEERILAVLEWLQLPSHERPHFYTLYLEEPDSSGHSHGPVSSEVIKALQKVDRLVGMLMDGLKDLGLDKCLNLILISDHGMGSDNLFSNMQALFIGYGPAFKHGAEVDSFENIEVYNLMCDLLGLIPAPNNGSHGSLNHLLKKPI

6c01A

0.56

0.54

15.52

2.33

CNFpred

QGETSWLEENCDTAQQSQCPEGFDLPPVILFSMDGFRAEYLYTWDTLMPNINKLKTCGIHSKYMRAMYPTKTFPNHYTIVTGLYPESHGIIDNNMYDVNLNKNFSLSSKEQNNPAWWHGQPMWLTAMYQGLKAATYFWPGSEVAINGSFPSIYMPYNGSVPFEERISTLLKWLDLPKAERPRFYTMYFEEPDSSGHAGGPVSARVIKALQVVDHAFGMLMEGLKQRNLHNCVNIILLADHGMDQTY---CNKMEYMTDYFPR--------INFFYMYEGPAPRIRAHNIPHDFFSFNSEEIVRNLS

6c01A2

0.62

0.57

16.27

1.33

DEthreader

-------------------Q--FDLPPVILFSMDGFRAEYLYTWDTLMPNINKLKTCGIHSKYMRAMYPTKTFPNHYTIVTGLYPESHGIIDNNMYD-VNLNKNFSLSKEQNNPAWWHGQPMWLTAMYQGLKAATYFWPGSEVAINGSFPSIYMPYNGSVPFEERISTLLKWLDLPKAERPRFYTMYFEEPDSSGHAGGPVSARVIKALQVVDHAFGMLMEGLKQRNLHNCVNIILLADHGMDHGYNFRSMEAIFLAHGPSFKEKTEVEPFENIEVYNLMCDLLRIQPAP-NNGTHGSLNHLLKV-

(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	0.8941

(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	6c01A	0.99	0.61	0.663	1.000	model1_6c01A.pdb.gz
2	4b56A	0.99	0.67	0.856	1.000	model1_4b56A.pdb.gz
3	5gz4A	0.98	0.66	0.637	0.990	model1_5gz4A.pdb.gz
4	2xr9A	0.92	1.01	0.573	0.941	model1_2xr9A.pdb.gz
5	2rh6A	0.88	1.13	0.371	0.908	model1_2rh6A.pdb.gz
6	3q3qA	0.81	3.03	0.164	0.935	model1_3q3qA.pdb.gz
7	1p49A	0.76	3.19	0.145	0.876	model1_1p49A.pdb.gz
8	1n2lA	0.75	2.98	0.126	0.863	model1_1n2lA.pdb.gz
9	2qzuA1	0.74	3.30	0.166	0.873	model1_2qzuA1.pdb.gz
10	4uphA	0.74	2.94	0.174	0.843	model1_4uphA.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	1.00	catalytic activity
GO:0016787	0.93	hydrolase activity
GO:0016788	0.83	hydrolase activity, acting on ester bonds
GO:0008081	0.82	phosphoric diester hydrolase activity
GO:0016462	0.69	pyrophosphatase activity
GO:0004551	0.66	nucleotide diphosphatase activity
GO:0004528	0.64	phosphodiesterase I activity
GO:0008270	0.59	zinc ion binding
GO:0005509	0.59	calcium ion binding
GO:0047429	0.52	nucleoside-triphosphate diphosphatase 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:0044699	0.90	single-organism process
GO:0008152	0.88	metabolic process
GO:0071704	0.83	organic substance metabolic process
GO:0009987	0.83	cellular process
GO:0044710	0.82	single-organism metabolic process
GO:0044238	0.81	primary metabolic process
GO:0044763	0.80	single-organism cellular process
GO:0044237	0.79	cellular metabolic process
GO:0006807	0.77	nitrogen compound metabolic process
GO:0006793	0.74	phosphorus metabolic process
GO:0006796	0.72	phosphate-containing compound metabolic process
GO:0019637	0.70	organophosphate metabolic process
GO:0065007	0.67	biological regulation
GO:0050789	0.67	regulation of biological process
GO:0009056	0.65	catabolic process
GO:0034641	0.64	cellular nitrogen compound metabolic process
GO:1901575	0.62	organic substance catabolic process
GO:0044712	0.62	single-organism catabolic process
GO:0044248	0.62	cellular catabolic process
GO:0050794	0.59	regulation of cellular process
GO:0046434	0.59	organophosphate catabolic process
GO:0006139	0.59	nucleobase-containing compound metabolic process
GO:0051239	0.58	regulation of multicellular organismal process
GO:0044281	0.57	small molecule metabolic process
GO:0006629	0.56	lipid metabolic process
GO:1901135	0.55	carbohydrate derivative metabolic process
GO:0055086	0.55	nucleobase-containing small molecule metabolic process
GO:1901564	0.53	organonitrogen compound metabolic process
GO:0080090	0.53	regulation of primary metabolic process
GO:0060255	0.53	regulation of macromolecule metabolic process
GO:0031323	0.53	regulation of cellular metabolic process
GO:0048523	0.52	negative regulation of cellular process
GO:0034655	0.52	nucleobase-containing compound catabolic process
GO:0006753	0.52	nucleoside phosphate metabolic process
GO:0097164	0.51	ammonium ion metabolic process
GO:0065008	0.51	regulation of biological quality
GO:0050896	0.51	response to stimulus
GO:0006810	0.51	transport
GO:2000113	0.50	negative regulation of cellular macromolecule biosynthetic process
GO:1901292	0.50	nucleoside phosphate catabolic process
GO:0043170	0.50	macromolecule metabolic process
GO:0009141	0.50	nucleoside triphosphate metabolic process

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	0.92	cell part
GO:0044444	0.62	cytoplasmic part
GO:0016020	0.62	membrane
GO:0044421	0.57	extracellular region part
GO:0044425	0.55	membrane part

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	0.073	2i09B	0.707	3.54	0.133	0.846	5.4.2.7	192
2	0.067	2zktB	0.664	3.57	0.150	0.791	5.4.2.1	NA
3	0.060	3igyB	0.700	3.85	0.112	0.856	5.4.2.1	NA
4	0.060	1dioA	0.410	6.37	0.059	0.690	4.2.1.28	NA
5	0.060	1iwpA	0.411	6.54	0.049	0.716	4.2.1.30	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	0.49	2gsuB	0.882	1.17	0.371	0.908	1.26	AMP	complex1.pdb.gz	72,73,93,106,137,156,158,187,192,193,196
	2	0.49	2gsoB	0.882	1.15	0.371	0.908	1.18	VO4	complex2.pdb.gz	34,72,192,196,240

	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.