D-I-TASSER P35609-D1

D-I-TASSER results for P35609-D1

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

Input Sequence in FASTA format

>P35609 (151 residues)
MNQIEPGVQYNYVYDEDEYMIQEEEWDRDLLLDPAWEKQQRKTFTAWCNSHLRKAGTQIE
NIEEDFRNGLKLMLLLEVISGERLPKPDRGKMRFHKIANVNKALDYIASKGVKLVSIGAE
EIVDGNVKMTLGMIWTIILRFAIQDISVEET

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 \| \| \| \| \| \| \| MNQIEPGVQYNYVYDEDEYMIQEEEWDRDLLLDPAWEKQQRKTFTAWCNSHLRKAGTQIENIEEDFRNGLKLMLLLEVISGERLPKPDRGKMRFHKIANVNKALDYIASKGVKLVSIGAEEIVDGNVKMTLGMIWTIILRFAIQDISVEET
Prediction	CCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHCHCCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHCCCCCCCC
Confidence	9977888776655676542211103456765202489999999999999997013998452788764439999999996499887667997689999999999999998398777897320107985699999999999974203673459
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 \| \| \| \| \| \| \| MNQIEPGVQYNYVYDEDEYMIQEEEWDRDLLLDPAWEKQQRKTFTAWCNSHLRKAGTQIENIEEDFRNGLKLMLLLEVISGERLPKPDRGKMRFHKIANVNKALDYIASKGVKLVSIGAEEIVDGNVKMTLGMIWTIILRFAIQDISVEET
Prediction	7544457354644445754446545544544256634530242015301520574725053025304511100100120253434345434343322300430141045344434644353024243410010012003303155145768
	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

                   |                   |                   |                   |                   |                   |                   |

SS
Seq

CCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHCHCCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHCCCCCCCC
MNQIEPGVQYNYVYDEDEYMIQEEEWDRDLLLDPAWEKQQRKTFTAWCNSHLRKAGTQIENIEEDFRNGLKLMLLLEVISGERLPKPDRGKMRFHKIANVNKALDYIASKGVKLVSIGAEEIVDGNVKMTLGMIWTIILRFAIQDISVEET

5nl7A

0.48

0.38

11.18

1.17

DEthreader

----------------------------DS-LVAQWEKVQIKTFTKWVNMHLAKKGRKINDVTTDFKNGVELCALLEIIGETTIKCVTNPKMRIQMTENLDKALRFIQSRDVKLTGIGPTDIVDGNVKLTLGLVWTLILRFAISEYKFSSN

6anuf

0.47

0.42

12.15

2.09

SPARKS-K

---------------NDSSSARLFERSRIKALADEREAVQKKTFTKWVNSHLARVTCRVGDLYSDLRDGRNLLRLLEVLSGEILPKPTKGRMRIHCLENVDKALQFLKEQKVHLENMGSHDIVDGNHRLTLGLVWTIILRFQIQDISV---

1pxyB

0.16

0.15

4.86

0.89

MapAlign

---NWKHASKPPIKMPFRKVENCNQVIKIGKQWQLMRFHMDADILSWANRKVRTMKLQIESFKDSLSSGLFFLNLLWAVEPRVVNWVTKGETDDEKRLNATYIVSVARKLGCSV-FLLPEDIVEVNQKMILILTASIMYWSLQR-------

5nl7A

0.48

0.40

11.55

0.62

CEthreader

---------------------------ADSELVAQWEKVQIKTFTKWVNMHLAKKGRKINDVTTDFKNGVELCALLEIIGETTIKCVTNPKMRIQMTENLDKALRFIQSRDVKLTGIGPTDIVDGNVKLTLGLVWTLILRFAISELSAEGL

6anuf

0.47

0.42

12.15

2.12

MUSTER

---------------NDSSSARLFERSRIKALADEREAVQKKTFTKWVNSHLARVTCRVGDLYSDLRDGRNLLRLLEVLSGEILPKPTKGRMRIHCLENVDKALQFLKEQKVHLENMGSHDIVDGNHRLTLGLVWTIILRFQIQDISV---

1sjjA

0.95

0.75

21.18

2.09

HHsearch

-------------------------------LDPAWEKQQRKTFTAWCNSHLRKAGTQIENIEEDFRDGLKLMLLLEVISGERLAKPERGKMRVHKISNVNKALDFIASKGVKLVSIGAEEIVDGNVKMTLGMIWTIILRFAIQDISVEET

5nl7A1

0.49

0.40

11.54

2.01

FFAS-3D

----------------------------DSELVAQWEKVQIKTFTKWVNMHLAKKGRKINDVTTDFKNGVELCALLEIIGETTIKCVTNPKMRIQMTENLDKALRFIQSRDVKLTGIGPTDIVDGNVKLTLGLVWTLILRFAISELSAEGL

2eyiA

0.15

4.92

1.22

EigenThreader

LDFIASKGVKLVSIGAEEIVDGNVKMTLGMIWTIILRFAIKEGLLLWCQRKTAPYNVNIQNFHISWKDGLGFCALIHRHRPELIDYGKLRKDD--PLTNLNTAFDVAEKYLDIPKMLDAEDIVGTDEKAIMTYVSSFYHAFSGAQEFLEPG

5a36A

1.00

0.88

24.66

1.28

CNFpred

------------------YMIQEEEWDRDLLLDPAWEKQQRKTFTAWCNSHLRKAGTQIENIEEDFRNGLKLMLLLEVISGERLPKPDRGKMRFHKIANVNKALDYIASKGVKLVSIGAEEIVDGNVKMTLGMIWTIILRFAIQDISVEET

4z6gA

0.50

0.38

11.15

1.17

DEthreader

---------------------------------DERDRVQKKTFTKWVNKHLMKVRKHINDLYEDLRDGHNLISLLEVLSGIKLPREK-GRMRFHRLQNVQIALDFLKQRQVKLVNIRNDDITDGNPKLTLGLIWTIILHFQISDIYKPEG

(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	0.7455

(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	5nl7A	0.74	2.00	0.468	0.801	model1_5nl7A.pdb.gz
2	6anuf	0.74	2.46	0.470	0.861	model1_6anuf.pdb.gz
3	6sl2A	0.74	2.07	0.448	0.808	model1_6sl2A.pdb.gz
4	2wa5A	0.73	2.28	0.362	0.801	model1_2wa5A.pdb.gz
5	1mb8A	0.73	2.15	0.460	0.795	model1_1mb8A.pdb.gz
6	2eyiA	0.72	1.81	0.856	0.781	model1_2eyiA.pdb.gz
7	4z6gA	0.72	1.66	0.496	0.755	model1_4z6gA.pdb.gz
8	4b7lA	0.71	1.85	0.393	0.762	model1_4b7lA.pdb.gz
9	1dxxA	0.71	1.64	0.412	0.755	model1_1dxxA.pdb.gz
10	5bvrA	0.70	1.90	0.440	0.748	model1_5bvrA.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:0008092	0.88	cytoskeletal protein binding
GO:0046983	0.62	protein dimerization activity
GO:0042802	0.62	identical protein binding
GO:0042803	0.61	protein homodimerization activity
GO:0017166	0.57	vinculin binding
GO:0042805	0.54	actinin binding
GO:0051393	0.53	alpha-actinin 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	0.95	single-organism process
GO:0009987	0.92	cellular process
GO:0044763	0.89	single-organism cellular process
GO:0016043	0.84	cellular component organization
GO:0032502	0.83	developmental process
GO:0044767	0.81	single-organism developmental process
GO:0048856	0.74	anatomical structure development
GO:0048869	0.69	cellular developmental process
GO:0006996	0.69	organelle organization
GO:0030029	0.68	actin filament-based process
GO:0007010	0.68	cytoskeleton organization
GO:1902589	0.67	single-organism organelle organization
GO:0030036	0.65	actin cytoskeleton organization
GO:0048468	0.58	cell development
GO:0031032	0.56	actomyosin structure organization
GO:0065007	0.53	biological regulation
GO:0055002	0.53	striated muscle cell development
GO:0045214	0.53	sarcomere organization
GO:0048747	0.52	muscle fiber development
GO:0048741	0.51	skeletal muscle fiber development

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	0.89	cytoplasmic part
GO:0044422	0.88	organelle part
GO:0044446	0.84	intracellular organelle part
GO:0043226	0.83	organelle
GO:0044430	0.78	cytoskeletal part
GO:0043229	0.78	intracellular organelle
GO:0016020	0.76	membrane
GO:0043232	0.70	intracellular non-membrane-bounded organelle
GO:0030054	0.70	cell junction
GO:0005856	0.68	cytoskeleton
GO:0044425	0.67	membrane part
GO:0044459	0.65	plasma membrane part
GO:0005912	0.65	adherens junction
GO:0005886	0.65	plasma membrane
GO:0042995	0.64	cell projection
GO:0030055	0.64	cell-substrate junction
GO:0044449	0.63	contractile fiber part
GO:0005924	0.62	cell-substrate adherens junction
GO:0044448	0.59	cell cortex part
GO:0005925	0.57	focal adhesion
GO:0032432	0.53	actin filament bundle
GO:0042383	0.52	sarcolemma
GO:0030863	0.52	cortical cytoskeleton
GO:0005911	0.52	cell-cell junction
GO:0001725	0.51	stress fiber
GO:0030864	0.50	cortical actin cytoskeleton
GO:0005913	0.50	cell-cell adherens junction

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	1jswB	0.476	3.93	0.028	0.709	4.3.1.1	NA
2	0.060	1sf2A	0.468	4.81	0.031	0.788	2.6.1.19 2.6.1.22	NA
3	0.060	1dofA	0.469	4.89	0.077	0.808	4.3.2.2	NA
4	0.060	2ebsB	0.471	4.90	0.077	0.815	3.2.1.150	110
5	0.060	3bs8A	0.475	4.77	0.070	0.808	5.4.3.8	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	0.08	2vziB	0.738	1.88	0.203	0.815	0.90	III	complex1.pdb.gz	9,10,43,135,138,142
2	0.04	2k2rA	0.667	2.70	0.206	0.808	0.55	III	complex2.pdb.gz	69,70,99,102,105,106,109,137
3	0.01	1zvzA	0.326	4.75	0.045	0.497	0.43	III	complex3.pdb.gz	50,51,61,100,103,104,107,110,111,121,126,133,137,144

	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.