D-I-TASSER P35558-D2

D-I-TASSER results for P35558-D2

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

Input Sequence in FASTA format

>P35558 (174 residues)
GWLAEHMLILGITNPEGEKKYLAAAFPSACGKTNLAMMNPSLPGWKVECVGDDIAWMKFD
AQGHLRAINPENGFFGVAPGTSVKTNPNAIKTIQKNTIFTNVAETSDGGVYWEGIDEPLA
SGVTITSWKNKEWSSEDGEPCAHPNSRFCTPASQCPIIDAAWESPEGVPIEGII

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 160 \| \| \| \| \| \| \| \| GWLAEHMLILGITNPEGEKKYLAAAFPSACGKTNLAMMNPSLPGWKVECVGDDIAWMKFDAQGHLRAINPENGFFGVAPGTSVKTNPNAIKTIQKNTIFTNVAETSDGGVYWEGIDEPLASGVTITSWKNKEWSSEDGEPCAHPNSRFCTPASQCPIIDAAWESPEGVPIEGII
Prediction	CCHHHHHHHHSSCCCCCCSSSSSSSCCCCCCCCCHHHCCCCCCCCSSSSSSCCSSSSSSCCCCSSSSSCCCCCSSSSCCCCCCCCCHHHHHHHHHCCSSSSSSSCCCCCSSSCCCCCCCCCCCCSSCCCCCCCCCCCCCCCCCCCCCCCCCHHHCCCCCCCCCCCCCCCSSSSC
Confidence	705565475323279995899987537776710255508999981899984436777658998399963677757764699988798999998618648866785999866147898999996220378997889999957787411021265599779412599996132569
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 160 \| \| \| \| \| \| \| \| GWLAEHMLILGITNPEGEKKYLAAAFPSACGKTNLAMMNPSLPGWKVECVGDDIAWMKFDAQGHLRAINPENGFFGVAPGTSVKTNPNAIKTIQKNTIFTNVAETSDGGVYWEGIDEPLASGVTITSWKNKEWSSEDGEPCAHPNSRFCTPASQCPIIDAAWESPEGVPIEGII
Prediction	732021000110434744321000011122331120013362541303110220010314574302020233200000132347312200400463000000030674402011256526762413204345346757431002000001106402311661633730304137
	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

                   |                   |                   |                   |                   |                   |                   |                   |

SS
Seq

CCHHHHHHHHSSCCCCCCSSSSSSSCCCCCCCCCHHHCCCCCCCCSSSSSSCCSSSSSSCCCCSSSSSCCCCCSSSSCCCCCCCCCHHHHHHHHHCCSSSSSSSCCCCCSSSCCCCCCCCCCCCSSCCCCCCCCCCCCCCCCCCCCCCCCCHHHCCCCCCCCCCCCCCCSSSSC
GWLAEHMLILGITNPEGEKKYLAAAFPSACGKTNLAMMNPSLPGWKVECVGDDIAWMKFDAQGHLRAINPENGFFGVAPGTSVKTNPNAIKTIQKNTIFTNVAETSDGGVYWEGIDEPLASGVTITSWKNKEWSSEDGEPCAHPNSRFCTPASQCPIIDAAWESPEGVPIEGII

2zciA

0.40

0.38

11.20

1.17

DEthreader

EKALEHMLILKLINPEGKAYHIAAAFSACGKTNLMITPTI-P-G-WTAQVVGDDIAWLKLREDGLYAVNPENGFFGVAPGTNYASNPIAMKTMPGNTLFTNVALT-DDGDIWWMDGDAPAH-L-IDW--MGNDWTESDENAAHPNSRYCVAIDQSPAAAPEFNDWEGVKIDAIL

2zciA3

0.53

0.51

14.77

4.03

SPARKS-K

--MAEHMLILKLINPEGKAYHIAAAFPSACGKTNLAMITPTIPGWTAQVVGDDIAWLKLREDG-LYAVNPENGFFGVAPGTNYASNPIAMKTMEPGTLFTNVALTDDGDIWWEGMDGDAPA--HLIDWMGNDWTPESDENAAHPNSRYCVAIDQSPAAAPEFNDWEGVKIDA--

3dt7A

0.89

0.87

24.41

1.45

MapAlign

---AEHMLILGITNPEGKKKYLAAAPSACGKTNLA-MMNPTLPGWKVECVGDDIAWMKFDAQGNLRAINPENGFFGVAPGTSVKTNPNAIKTIQKNTIFTNVAETSDGGVYWEGIDEPLAPGVTITSWKNKEWRPQDEEPCAHPNSRFCTPASQCPIIDPAWESPEGVPIEGII

3dt7A

0.95

26.60

1.28

CEthreader

GWLAEHMLILGITNPEGKKKYLAAAFPSACGKTNLAMMNPTLPGWKVECVGDDIAWMKFDAQGNLRAINPENGFFGVAPGTSVKTNPNAIKTIQKNTIFTNVAETSDGGVYWEGIDEPLAPGVTITSWKNKEWRPQDEEPCAHPNSRFCTPASQCPIIDPAWESPEGVPIEGII

3dt7A

0.95

26.60

2.81

MUSTER

GWLAEHMLILGITNPEGKKKYLAAAFPSACGKTNLAMMNPTLPGWKVECVGDDIAWMKFDAQGNLRAINPENGFFGVAPGTSVKTNPNAIKTIQKNTIFTNVAETSDGGVYWEGIDEPLAPGVTITSWKNKEWRPQDEEPCAHPNSRFCTPASQCPIIDPAWESPEGVPIEGII

2fahA

0.75

21.17

4.46

HHsearch

GWLAEHMLILGVTSPSGEKRYMAAAFPSACGKTNLAMMTPSLPGWRIHCVGDDIAWMKFDDEGRLRAINPERGFFGVAPGTSSRTNPNAMATIARNTIFTNVGLRSDGGVYWDGLDEPTEPGVTYTSWLGKPWKHGDPEPCAHPNSRFCAPADQCPIMDPRWDDPEGVPIDAII

2zciA3

0.53

0.51

14.77

2.67

FFAS-3D

--MAEHMLILKLINPEGKAYHIAAAFPSACGKTNLAMITPTIPGWTAQVVGDDIAWLKLR-EDGLYAVNPENGFFGVAPGTNYASNPIAMKTMPGNTLFTNVALTDDGDIWWEGMDGDAPA--HLIDWMGNDWTPESDENAAHPNSRYCVAIDQSPAAAPEFNDWEGVKIDA--

2zciA3

0.51

0.49

14.15

1.68

EigenThreader

MAEH--MLILKLINPEGKAYHIAAAFPSACGKTNLAMITPTIPGWTAQVVGDDIAWLKLRE-DGLYAVNPENGFFGVAPGTNYASNPIAMKTMEPGTLFTNVALTDDGDIWWEGMDGDAP--AHLIDWMGNDWTPESDENAAHPNSRYCVAIDQSPAAAPEFNDWEGVKIDA--

1khbA

0.99

27.84

5.38

CNFpred

GWLAEHMLVLGITNPEGEKKYLAAAFPSACGKTNLAMMNPSLPGWKVECVGDDIAWMKFDAQGHLRAINPENGFFGVAPGTSVKTNPNAIKTIQKNTIFTNVAETSDGGVYWEGIDEPLASGVTITSWKNKEWSSEDGEPCAHPNSRFCTPASQCPIIDAAWESPEGVPIEGII

4wieA

0.46

0.44

12.91

1.17

DEthreader

EKSLEHMLILKLISPENKAYYFAAAFPSAGKTNLAMLQPT-IPGWRAETLGDDIAWMRFGKDGRLYAVNPEFGFFGVAPGTNWKSNPNAMRTIAAGNTVFTNVAL-DDGDVWWLEGDPQH--LIDWK--G-NDWYETETNAAHPNSRYCTPMSQCPILAPEWDDPQGVPISGIL

(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	0.8315

(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	3dt7A	0.99	0.58	0.948	1.000	model1_3dt7A.pdb.gz
2	2fahA	0.97	0.99	0.747	1.000	model1_2fahA.pdb.gz
3	2zciA	0.95	1.12	0.538	0.983	model1_2zciA.pdb.gz
4	4wieA	0.94	1.17	0.602	0.983	model1_4wieA.pdb.gz
5	1aylA1	0.66	1.86	0.211	0.736	model1_1aylA1.pdb.gz
6	1ko7A	0.45	2.67	0.118	0.534	model1_1ko7A.pdb.gz
7	4iibA	0.38	5.71	0.057	0.741	model1_4iibA.pdb.gz
8	2v5jA	0.32	5.42	0.042	0.581	model1_2v5jA.pdb.gz
9	2b39A3	0.31	4.70	0.115	0.506	model1_2b39A3.pdb.gz
10	3x17B	0.31	5.96	0.035	0.598	model1_3x17B.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:0004611	1.00	phosphoenolpyruvate carboxykinase activity
GO:0004613	0.77	phosphoenolpyruvate carboxykinase (GTP) activity
GO:1901363	0.69	heterocyclic compound binding
GO:0097159	0.69	organic cyclic compound binding
GO:0043167	0.66	ion binding
GO:0000166	0.66	nucleotide binding
GO:0046872	0.65	metal ion binding
GO:0035639	0.65	purine ribonucleoside triphosphate binding
GO:0032555	0.65	purine ribonucleotide binding
GO:0032550	0.65	purine ribonucleoside binding
GO:0046914	0.63	transition metal ion binding
GO:0005525	0.62	GTP binding
GO:0030145	0.61	manganese ion 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:0008152	0.85	metabolic process
GO:0044699	0.81	single-organism process
GO:0009987	0.81	cellular process
GO:0071704	0.80	organic substance metabolic process
GO:0044238	0.78	primary metabolic process
GO:0050896	0.74	response to stimulus
GO:0044237	0.74	cellular metabolic process
GO:0065007	0.73	biological regulation
GO:0044710	0.71	single-organism metabolic process
GO:0044281	0.68	small molecule metabolic process
GO:0010033	0.63	response to organic substance
GO:1901700	0.62	response to oxygen-containing compound
GO:1901576	0.62	organic substance biosynthetic process
GO:0044763	0.62	single-organism cellular process
GO:0044711	0.57	single-organism biosynthetic process
GO:0006006	0.57	glucose metabolic process
GO:0006094	0.56	gluconeogenesis
GO:0044260	0.52	cellular macromolecule metabolic process
GO:0019752	0.52	carboxylic acid metabolic process
GO:0050789	0.51	regulation of biological process
GO:0032787	0.50	monocarboxylic acid 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:0044444	1.00	cytoplasmic part
GO:0043226	0.64	organelle
GO:0043227	0.63	membrane-bounded organelle
GO:0044422	0.57	organelle part
GO:0043229	0.51	intracellular organelle
GO:0043231	0.50	intracellular membrane-bounded organelle

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	1lnsA	0.391	5.59	0.052	0.718	3.4.14.11	NA
2	0.060	1pl6A	0.319	6.04	0.046	0.638	1.1.1.14	NA
3	0.060	1euzF	0.402	4.93	0.081	0.661	1.4.1.3	20,159
4	0.060	2i2xA	0.390	5.55	0.013	0.730	2.1.1.90	30,34,113
5	0.060	1ytmA	0.674	2.13	0.226	0.764	4.1.1.49	32

	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	0.82	2fahB	0.969	1.02	0.747	1.000	1.56	MN	complex1.pdb.gz	33,76,77,147
2	0.69	2qeyA	0.984	0.65	0.948	1.000	1.06	GTP	complex2.pdb.gz	6,27,28,29,30,31,32,33,34,53,77,147
3	0.58	2rk8A	0.988	0.55	0.948	1.000	0.91	PPF	complex3.pdb.gz	6,28,53,75,147
4	0.54	2gmvA	0.974	0.90	0.994	1.000	0.89	UN8	complex4.pdb.gz	30,31,34,35,38,84,85
5	0.17	1aq2A	0.680	1.82	0.214	0.753	1.02	MG	complex5.pdb.gz	33,52,74

	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.