D-I-TASSER P26440-D1

D-I-TASSER results for P26440-D1

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

Input Sequence in FASTA format

>P26440 (282 residues)
MAEMATATRLLGWRVASWRLRPPLAGFVSQRAHSLLPVDDAINGLSEEQRQLRQTMAKFL
QEHLAPKAQEIDRSNEFKNLREFWKQLGNLGVLGITAPVQYGGSGLGYLEHVLVMEEISR
ASGAVGLSYGAHSNLCINQLVRNGNEAQKEKYLPKLISGEYIGALAMSEPNAGSDVVSMK
LKAEKKGNHYILNGNKFWITNGPDADVLIVYAKTDLAAVPASRGITAFIVEKGMPGFSTS
KKLDKLGMRGSNTCELIFEDCKIPAANILGHENKGVYVLMSG

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 160 180 200 220 240 260 280 \| \| \| \| \| \| \| \| \| \| \| \| \| \| MAEMATATRLLGWRVASWRLRPPLAGFVSQRAHSLLPVDDAINGLSEEQRQLRQTMAKFLQEHLAPKAQEIDRSNEFKNLREFWKQLGNLGVLGITAPVQYGGSGLGYLEHVLVMEEISRASGAVGLSYGAHSNLCINQLVRNGNEAQKEKYLPKLISGEYIGALAMSEPNAGSDVVSMKLKAEKKGNHYILNGNKFWITNGPDADVLIVYAKTDLAAVPASRGITAFIVEKGMPGFSTSKKLDKLGMRGSNTCELIFEDCKIPAANILGHENKGVYVLMSG
Prediction	CCHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHCHCHHHHHHHCCCCCHHHHHHHHHHCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHCCCCSSSSHHHHHHHHHHHHHHCCHHHHHHHCHCCCCCCSSSSSSSCCCCCCCCHHHCSSSSSSSCCSSSSSCSSSSSCCCCCCCSSSSSSSSCCCCCCCCCCSSSSSSSCCCCCSSCCCCCCCCCCCCCCCSSSSSCCCSSCHHHCCCCCCCCHHHHCCC
Confidence	921456555431233421246653432222323467888655799999999999999999998021089998608999569999999980998998880008999479999999999984074110221122334388999869999998763310466612578715999885244264399994997999016755617887879999999489867898825899993899973316766656778888126884171735898289999643211389
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 160 180 200 220 240 260 280 \| \| \| \| \| \| \| \| \| \| \| \| \| \| MAEMATATRLLGWRVASWRLRPPLAGFVSQRAHSLLPVDDAINGLSEEQRQLRQTMAKFLQEHLAPKAQEIDRSNEFKNLREFWKQLGNLGVLGITAPVQYGGSGLGYLEHVLVMEEISRASGAVGLSYGAHSNLCINQLVRNGNEAQKEKYLPKLISGEYIGALAMSEPNAGSDVVSMKLKAEKKGNHYILNGNKFWITNGPDADVLIVYAKTDLAAVPASRGITAFIVEKGMPGFSTSKKLDKLGMRGSNTCELIFEDCKIPAANILGHENKGVYVLMSG
Prediction	653024023303441434424442443344444441427423350452052016102500652032204512666513523400420251101003103611011112100000000002110000000000010002002420162025410240031120000000014012113313030325644000012110001043000000000014536532100000002471510430451511012004002030430501441202543410320068
	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

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

SS
Seq

CCHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHCHCHHHHHHHCCCCCHHHHHHHHHHCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHCCCCSSSSHHHHHHHHHHHHHHCCHHHHHHHCHCCCCCCSSSSSSSCCCCCCCCHHHCSSSSSSSCCSSSSSCSSSSSCCCCCCCSSSSSSSSCCCCCCCCCCSSSSSSSCCCCCSSCCCCCCCCCCCCCCCSSSSSCCCSSCHHHCCCCCCCCHHHHCCC
MAEMATATRLLGWRVASWRLRPPLAGFVSQRAHSLLPVDDAINGLSEEQRQLRQTMAKFLQEHLAPKAQEIDRSNEFKNLREFWKQLGNLGVLGITAPVQYGGSGLGYLEHVLVMEEISRASGAVGLSYGAHSNLCINQLVRNGNEAQKEKYLPKLISGEYIGALAMSEPNAGSDVVSMKLKAEKKGNHYILNGNKFWITNGPDADVLIVYAKTDLAAVPASRGITAFIVEKGMPGFSTSKKLDKLGMRGSNTCELIFEDCKIPAANILGHENKGVYVLMSG

1ivhA1

0.99

0.86

24.13

1.33

DEthreader

------------------------------------VD-DAINGLSEEQRQLRQTMAKFLQEHLAPKAQEIDRSNEFKNLREFWKQLGNLGVLGITAPVQYGGSGLGYLEHVLVMEEISRASGAVGLSYGAHSNLCINQLVRNGNEAQKEKYLPKLISGEYIGALAMSEPNAGSDVVSMKLKAEKKGNHYILNGNKFWITNGPDADVLIVYAKTDLAAVPASRGITAFIVEKGMPGFSTSKKLDKLGMRGSNTCELIFEDCKIPAANILGHENKGVYVLMSG

1ivhA1

1.00

0.87

24.33

2.63

SPARKS-K

-------------------------------------VDDAINGLSEEQRQLRQTMAKFLQEHLAPKAQEIDRSNEFKNLREFWKQLGNLGVLGITAPVQYGGSGLGYLEHVLVMEEISRASGAVGLSYGAHSNLCINQLVRNGNEAQKEKYLPKLISGEYIGALAMSEPNAGSDVVSMKLKAEKKGNHYILNGNKFWITNGPDADVLIVYAKTDLAAVPASRGITAFIVEKGMPGFSTSKKLDKLGMRGSNTCELIFEDCKIPAANILGHENKGVYVLMSG

4n5fA

0.36

0.30

8.98

0.84

MapAlign

-----------------------------------------DELYTEDQRMIRDAARAFATEMLAPNAAQWDHDAHLP--DAIVAQLGELGLLGMIVPQELGGSYTDYVAYALAMEEVAAGDAACATMMSVHNSVGCGPILGFGTPAQKDRWLADMAAGRVIGAFCLTEPHAGSEANNLRTRAELRDGQWVLNGAKQFVTNGQRAGVAIVFAMTDP--EAGKRGISAFLVPTDTPGFIVGKPEKKMGIRASDTCPITFENCAIPEDNLLGNRGEGLKIALSN

4n5fA

0.36

0.30

9.08

0.46

CEthreader

---------------------------------------HMDELYTEDQRMIRDAARAFATEMLAPNAAQWDHDAHLP--DAIVAQLGELGLLGMIVPQELGGSYTDYVAYALAMEEVAAGDAACATMMSVHNSVGCGPILGFGTPAQKDRWLADMAAGRVIGAFCLTEPHAGSEANNLRTRAELRDGQWVLNGAKQFVTNGQRAGVAIVFAMTDPEA--GKRGISAFLVPTDTPGFIVGKPEKKMGIRASDTCPITFENCAIPEDNLLGNRGEGLKIALSN

1ivhA1

1.00

0.87

24.33

2.12

MUSTER

-------------------------------------VDDAINGLSEEQRQLRQTMAKFLQEHLAPKAQEIDRSNEFKNLREFWKQLGNLGVLGITAPVQYGGSGLGYLEHVLVMEEISRASGAVGLSYGAHSNLCINQLVRNGNEAQKEKYLPKLISGEYIGALAMSEPNAGSDVVSMKLKAEKKGNHYILNGNKFWITNGPDADVLIVYAKTDLAAVPASRGITAFIVEKGMPGFSTSKKLDKLGMRGSNTCELIFEDCKIPAANILGHENKGVYVLMSG

1ivhA1

1.00

0.87

24.33

1.27

HHsearch

-------------------------------------VDDAINGLSEEQRQLRQTMAKFLQEHLAPKAQEIDRSNEFKNLREFWKQLGNLGVLGITAPVQYGGSGLGYLEHVLVMEEISRASGAVGLSYGAHSNLCINQLVRNGNEAQKEKYLPKLISGEYIGALAMSEPNAGSDVVSMKLKAEKKGNHYILNGNKFWITNGPDADVLIVYAKTDLAAVPASRGITAFIVEKGMPGFSTSKKLDKLGMRGSNTCELIFEDCKIPAANILGHENKGVYVLMSG

1ivhA1

1.00

0.86

24.13

3.22

FFAS-3D

--------------------------------------DDAINGLSEEQRQLRQTMAKFLQEHLAPKAQEIDRSNEFKNLREFWKQLGNLGVLGITAPVQYGGSGLGYLEHVLVMEEISRASGAVGLSYGAHSNLCINQLVRNGNEAQKEKYLPKLISGEYIGALAMSEPNAGSDVVSMKLKAEKKGNHYILNGNKFWITNGPDADVLIVYAKTDLAAVPASRGITAFIVEKGMPGFSTSKKLDKLGMRGSNTCELIFEDCKIPAANILGHENKGVYVLMS-

2pg0A1

0.38

0.32

9.56

1.23

EigenThreader

------------------------------------TARY----LREEHHMFRAAFRKFLEKEAYPHYNDWEKRGIIP--RSFWAKMGENGFLCPWVDEKYGGLNADFAYSVVINEELEKVGSSL-VGIGLHNDIVTPYIASYGTEEQKQKWLPKCVTGELITAIAMTEPGAGSDLANISTTAVKDGDYYIVNGQKTFITNGIHADLIVVACKTDPQAKPPHRGISLLVVERDTPGFTRGRKLEKVGLHAQDTAELFFQDAKVPAYNLLGEEGKGFYYLMEK

1ivhA

1.00

0.87

24.33

2.72

CNFpred

-------------------------------------VDDAINGLSEEQRQLRQTMAKFLQEHLAPKAQEIDRSNEFKNLREFWKQLGNLGVLGITAPVQYGGSGLGYLEHVLVMEEISRASGAVGLSYGAHSNLCINQLVRNGNEAQKEKYLPKLISGEYIGALAMSEPNAGSDVVSMKLKAEKKGNHYILNGNKFWITNGPDADVLIVYAKTDLAAVPASRGITAFIVEKGMPGFSTSKKLDKLGMRGSNTCELIFEDCKIPAANILGHENKGVYVLMSG

1ivhA

0.99

0.86

24.13

1.33

DEthreader

------------------------------------VD-DAINGLSEEQRQLRQTMAKFLQEHLAPKAQEIDRSNEFKNLREFWKQLGNLGVLGITAPVQYGGSGLGYLEHVLVMEEISRASGAVGLSYGAHSNLCINQLVRNGNEAQKEKYLPKLISGEYIGALAMSEPNAGSDVVSMKLKAEKKGNHYILNGNKFWITNGPDADVLIVYAKTDLAAVPASRGITAFIVEKGMPGFSTSKKLDKLGMRGSNTCELIFEDCKIPAANILGHENKGVYVLMSG

(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	0.906

(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	1ivhA	0.87	0.22	0.988	0.869	model1_1ivhA.pdb.gz
2	2ix5A	0.83	2.16	0.250	0.894	model1_2ix5A.pdb.gz
3	1jqiA	0.82	1.17	0.367	0.851	model1_1jqiA.pdb.gz
4	4n5fA	0.82	1.22	0.364	0.848	model1_4n5fA.pdb.gz
5	1rx0A	0.82	1.50	0.324	0.851	model1_1rx0A.pdb.gz
6	2pg0A1	0.82	1.19	0.382	0.844	model1_2pg0A1.pdb.gz
7	2d29A	0.81	1.57	0.365	0.855	model1_2d29A.pdb.gz
8	2jifA	0.81	1.25	0.340	0.840	model1_2jifA.pdb.gz
9	5ol2C	0.81	1.25	0.409	0.837	model1_5ol2C.pdb.gz
10	4l1fA	0.81	1.34	0.399	0.840	model1_4l1fA.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:0016627	1.00	oxidoreductase activity, acting on the CH-CH group of donors
GO:0003995	0.99	acyl-CoA dehydrogenase activity
GO:1901363	0.98	heterocyclic compound binding
GO:0097159	0.98	organic cyclic compound binding
GO:0052890	0.97	oxidoreductase activity, acting on the CH-CH group of donors, with a flavin as acceptor
GO:0050660	0.97	flavin adenine dinucleotide binding
GO:0009055	0.96	electron carrier activity
GO:0000062	0.96	fatty-acyl-CoA binding

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	1.00	single-organism process
GO:0008152	1.00	metabolic process
GO:1901575	0.99	organic substance catabolic process
GO:0044763	0.99	single-organism cellular process
GO:0044281	0.99	small molecule metabolic process
GO:0044237	0.99	cellular metabolic process
GO:0009062	0.98	fatty acid catabolic process
GO:0065007	0.97	biological regulation
GO:0006635	0.97	fatty acid beta-oxidation
GO:0055088	0.96	lipid homeostasis
GO:0033539	0.96	fatty acid beta-oxidation using acyl-CoA dehydrogenase

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	1.00	cell part
GO:0044424	0.98	intracellular part
GO:0044444	0.97	cytoplasmic part
GO:0043231	0.94	intracellular membrane-bounded organelle
GO:0005739	0.85	mitochondrion

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	0.141	1rx0A	0.817	1.50	0.324	0.851	1.3.99.-	NA
2	0.128	2jifA	0.814	1.25	0.340	0.840	1.3.99.-	NA
3	0.104	1jqiA	0.824	1.17	0.367	0.851	1.3.99.2	NA
4	0.103	1ukwA	0.797	1.57	0.384	0.837	1.3.99.3	NA
5	0.098	3mddA	0.803	1.56	0.363	0.844	1.3.99.3	135,172,174,176,198,200

	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	0.73	1ivhB	0.868	0.23	0.988	0.869	1.27	FAD	complex1.pdb.gz	165,167,168,173,174,198,199,200,245
2	0.61	1ivhB	0.868	0.23	0.988	0.869	1.20	COS	complex2.pdb.gz	167,173,174,176,177,222,276,277,280
3	0.22	1egcA	0.798	1.64	0.349	0.844	0.86	CO8	complex3.pdb.gz	127,130,135,165,174,176,200,276,280
4	0.07	3mpjB	0.809	1.35	0.412	0.840	0.80	III	complex4.pdb.gz	74,76,77,80,160,203,204,206,233

	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.