D-I-TASSER O15520-D1

D-I-TASSER results for O15520-D1

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

Input Sequence in FASTA format

>O15520 (208 residues)
MWKWILTHCASAFPHLPGCCCCCFLLLFLVSSVPVTCQALGQDMVSPEATNSSSSSFSSP
SSAGRHVRSYNHLQGDVRWRKLFSFTKYFLKIEKNGKVSGTKKENCPYSILEITSVEIGV
VAVKAINSNYYLAMNKKGKLYGSKEFNNDCKLKERIEENGYNTYASFNWQHNGRQMYVAL
NGKGAPRRGQKTRRKNTSAHFLPMVVHS

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 160 180 200 \| \| \| \| \| \| \| \| \| \| MWKWILTHCASAFPHLPGCCCCCFLLLFLVSSVPVTCQALGQDMVSPEATNSSSSSFSSPSSAGRHVRSYNHLQGDVRWRKLFSFTKYFLKIEKNGKVSGTKKENCPYSILEITSVEIGVVAVKAINSNYYLAMNKKGKLYGSKEFNNDCKLKERIEENGYNTYASFNWQHNGRQMYVALNGKGAPRRGQKTRRKNTSAHFLPMVVHS
Prediction	CCSSSSSSCCCCCCCCCHHHHHHHHHHHHHSCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCSSSSSSSCCCSSSSSCCCCCSSCSCCCCCCCSSSSSSSCCCCSSSSSSSCCCSSSSSCCCCCSCCCCCCCCCCSSSSSSCCCCCSSSSSSSCCCCCCCSSSSSCCCCCCCCCCCCCCCCCCCSSSSCCCCC
Confidence	9356662013445555447899988865421366667755423357544444454445665456765536544676158999945882899879984801216888630568998028769998631363773579994303331155414899972589257875213567862489977999988377778898320164124789
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 160 180 200 \| \| \| \| \| \| \| \| \| \| MWKWILTHCASAFPHLPGCCCCCFLLLFLVSSVPVTCQALGQDMVSPEATNSSSSSFSSPSSAGRHVRSYNHLQGDVRWRKLFSFTKYFLKIEKNGKVSGTKKENCPYSILEITSVEIGVVAVKAINSNYYLAMNKKGKLYGSKEFNNDCKLKERIEENGYNTYASFNWQHNGRQMYVALNGKGAPRRGQKTRRKNTSAHFLPMVVHS
Prediction	7231203212523432301000111001000102132453354324472444444444446635444453531434322120104232201025614041244644442323241343220103124222010136504321453144402031314652110020232555542010103562534635434663410100323378
	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

                   |                   |                   |                   |                   |                   |                   |                   |                   |                   |

SS
Seq

CCSSSSSSCCCCCCCCCHHHHHHHHHHHHHSCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCSSSSSSSCCCSSSSSCCCCCSSCSCCCCCCCSSSSSSSCCCCSSSSSSSCCCSSSSSCCCCCSCCCCCCCCCCSSSSSSCCCCCSSSSSSSCCCCCCCSSSSSCCCCCCCCCCCCCCCCCCCSSSSCCCCC
MWKWILTHCASAFPHLPGCCCCCFLLLFLVSSVPVTCQALGQDMVSPEATNSSSSSFSSPSSAGRHVRSYNHLQGDVRWRKLFSFTKYFLKIEKNGKVSGTKKENCPYSILEITSVEIGVVAVKAINSNYYLAMNKKGKLYGSKEFNNDCKLKERIEENGYNTYASFNWQHNGRQMYVALNGKGAPRRGQKTRRKNTSAHFLPMVVHS

6p25A

0.06

0.04

1.95

1.00

DEthreader

------KEKLLVAC------AVFTAVIRATVILMYTLAVFTVTGLPFA-----------------------VG--IGSIISLRHLSMGYLHSHSHQQSTLYPH-MDANNDWLLELYNGTKVRLFHTVTRCRLHSHDHKEVSCYGYGDANDDWVVEIDKSQKFRLRHAMT-----GCYLFSHEKQEVTCASSGR--HDLTLWYVENNSN

1nunA

1.00

0.67

18.71

2.83

SPARKS-K

--------------------------------------------------------------------SYNHLQGDVRWRKLFSFTKYFLKIEKNGKVSGTKKENCPYSILEITSVEIGVVAVKAINSNYYLAMNKKGKLYGSKEFNNDCKLKERIEENGYNTYASFNWQHNGRQMYVALNGKGAPRRGQKTRRKNTSAHFLPMVVH-

3f1rA

0.40

0.26

7.79

0.76

MapAlign

----------------------------------------------------------------------LAHLHGIRRRQLYCRTGFHLQILPDGSVQGTRQDHSLFGILEFISVAVGLVSIRGVDSGLYLGMNDKGELYGSEKLTSECIFREQFEENWYNTYSSNIYKHTGRRYFVALNKDGTPRDGARSKRHQKFTHFLPRPV--

1qqlA

0.44

0.28

8.16

0.59

CEthreader

---------------------------------------------------------------------------DIRVRRLFCRTQWYLRIDKRGKVKGTQEMRNSYNIMEIRTVAVGIVAIKGVESEYYLAMNKEGKLYAKQTPNEECLFLERLEENHYNTYISKKHAE--KNWFVGLKKNGSCKRGPRTHYGQKAILFLPLPVSS

1nunA

1.00

0.67

18.71

2.22

MUSTER

--------------------------------------------------------------------SYNHLQGDVRWRKLFSFTKYFLKIEKNGKVSGTKKENCPYSILEITSVEIGVVAVKAINSNYYLAMNKKGKLYGSKEFNNDCKLKERIEENGYNTYASFNWQHNGRQMYVALNGKGAPRRGQKTRRKNTSAHFLPMVVH-

1nunA

1.00

0.67

18.71

3.47

HHsearch

--------------------------------------------------------------------SYNHLQGDVRWRKLFSFTKYFLKIEKNGKVSGTKKENCPYSILEITSVEIGVVAVKAINSNYYLAMNKKGKLYGSKEFNNDCKLKERIEENGYNTYASFNWQHNGRQMYVALNGKGAPRRGQKTRRKNTSAHFLPMVVH-

1nunA

1.00

0.67

18.71

2.20

FFAS-3D

--------------------------------------------------------------------SYNHLQGDVRWRKLFSFTKYFLKIEKNGKVSGTKKENCPYSILEITSVEIGVVAVKAINSNYYLAMNKKGKLYGSKEFNNDCKLKERIEENGYNTYASFNWQHNGRQMYVALNGKGAPRRGQKTRRKNTSAHFLPMVVH-

5foyA1

0.04

0.03

1.48

1.02

EigenThreader

-------------------------------------------------------------MRNLDFIDSFIPTEGKYIRVMDFYNSFCIHAPSAPNIMTEICSRENNQYFIFFPTDDGRVIIANRHNGSVFTGEATSVVSDIYTGSPLQFFREVKRTMATYYLAIQNPESATDVRALEPHSHPSRLYYTNIENNSNILISNKEQIL-

1nunA

1.00

0.67

18.71

2.86

CNFpred

--------------------------------------------------------------------SYNHLQGDVRWRKLFSFTKYFLKIEKNGKVSGTKKENCPYSILEITSVEIGVVAVKAINSNYYLAMNKKGKLYGSKEFNNDCKLKERIEENGYNTYASFNWQHNGRQMYVALNGKGAPRRGQKTRRKNTSAHFLPMVVH-

1qqlA

0.44

0.28

8.16

1.00

DEthreader

---------------------------------------------------------------------------DIRVRRLFCRTQWYLRIDKRGKVKGTQEMRNSYNIMEIRTVAVGIVAIKGVESEYYLAMNKEGKLYAKQTPNEECLFLERLEENHYNTYISKKHA--EKNWFVGLKKNGSCKRGPRTHYGQKAILFLPLPVSS

(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

script 1 started

FileManager.getAtomSetCollectionFromFile(model1.pdb.gz)

FileManager opening 1 https://zhanglab.comp.nus.edu.sg/HPmod/data/O15520/O15520-D1/model1.pdb.gz

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The Resolver thinks Pdb

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Time for openFile(model1.pdb.gz): 2277 ms

reading 3280 atoms

ModelSet: haveSymmetry:false haveUnitcells:false haveFractionalCoord:false

1 model in this collection. Use getProperty "modelInfo" or getProperty "auxiliaryInfo" to inspect them.

Default Van der Waals type for model set to Babel

3280 atoms created

ModelSet: autobonding; use autobond=false to not generate bonds automatically

Jmol 14.2.13_2015.03.07 2015-03-07 10:45 DSSP analysis for model 1.1 - null

W. Kabsch and C. Sander, Biopolymers, vol 22, 1983, pp 2577-2637

We thank Wolfgang Kabsch and Chris Sander for writing the DSSP software,

and we thank the CMBI for maintaining it to the extent that it was easy to

re-engineer for our purposes. At this point in time, we make no guarantee

that this code gives precisely the same analysis as the code available via license

from CMBI at http://swift.cmbi.ru.nl/gv/dssp

All bioshapes have been deleted and must be regenerated.

NOTE: Backbone amide hydrogen positions are present and will be ignored. Their positions will be approximated, as in standard DSSP analysis.

Use SET dsspCalculateHydrogenAlways FALSE to not use this approximation.

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Click to view	Rank^a	Download	Estimated TM-score^b
	1	model1.pdb.gz	0.6323

(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

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Top 10 structural analogs in PDB (as identified by TM-align)

Rank	PDB Hit	TM-score	RMSD^a	IDEN^a	Cov.	Download Alignment
1	1nunA	0.64	1.44	0.950	0.668	model1_1nunA.pdb.gz
2	3f1rA	0.63	1.76	0.382	0.668	model1_3f1rA.pdb.gz
3	2vseA	0.62	4.14	0.072	0.808	model1_2vseA.pdb.gz
4	3hbwA	0.61	1.37	0.346	0.639	model1_3hbwA.pdb.gz
5	1qqlA	0.61	1.18	0.443	0.630	model1_1qqlA.pdb.gz
6	1e0oA	0.59	1.08	0.336	0.615	model1_1e0oA.pdb.gz
7	1ijtA	0.59	1.01	0.341	0.606	model1_1ijtA.pdb.gz
8	4cjmA	0.59	1.09	0.286	0.606	model1_4cjmA.pdb.gz
9	2ehiB1	0.57	2.45	0.066	0.649	model1_2ehiB1.pdb.gz
10	2ihoA	0.56	1.99	0.077	0.625	model1_2ihoA.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:0005102	0.85	receptor binding
GO:0008083	0.61	growth factor activity
GO:0005104	0.58	fibroblast growth factor receptor 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	0.94	single-organism process
GO:0065007	0.92	biological regulation
GO:0050789	0.91	regulation of biological process
GO:0050794	0.88	regulation of cellular process
GO:0032502	0.84	developmental process
GO:0009987	0.80	cellular process
GO:0044767	0.77	single-organism developmental process
GO:0048518	0.75	positive regulation of biological process
GO:0048856	0.74	anatomical structure development
GO:0044763	0.74	single-organism cellular process
GO:0048522	0.69	positive regulation of cellular process
GO:0007165	0.65	signal transduction
GO:0051239	0.61	regulation of multicellular organismal process
GO:0048583	0.60	regulation of response to stimulus
GO:0042127	0.60	regulation of cell proliferation
GO:0023051	0.57	regulation of signaling
GO:0019222	0.57	regulation of metabolic process
GO:0010646	0.57	regulation of cell communication
GO:0060255	0.55	regulation of macromolecule metabolic process
GO:0009966	0.55	regulation of signal transduction
GO:0080090	0.54	regulation of primary metabolic process
GO:0031323	0.54	regulation of cellular metabolic process
GO:0009893	0.54	positive regulation of metabolic process
GO:0008284	0.54	positive regulation of cell proliferation
GO:0010604	0.53	positive regulation of macromolecule metabolic process
GO:0009653	0.52	anatomical structure morphogenesis

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	0.90	cell part
GO:0044424	0.85	intracellular part
GO:0044421	0.71	extracellular region part
GO:0043226	0.71	organelle
GO:0043227	0.69	membrane-bounded organelle
GO:0005615	0.67	extracellular space
GO:0043229	0.66	intracellular organelle
GO:0043231	0.64	intracellular membrane-bounded organelle
GO:0005634	0.57	nucleus

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

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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	0.294	1nunA	0.641	1.44	0.950	0.668	2.7.10.1	81,83,85,89,91,99,161,181,185,187,202,204
2	0.180	1knnA	0.486	1.96	0.054	0.538	3.2.1.8	139
3	0.060	1abrB	0.505	2.69	0.055	0.582	3.2.2.22	138,145
4	0.060	1ry7A	0.613	1.69	0.295	0.654	2.7.10.1	131,140,162,203
5	0.060	1v6yA	0.296	5.57	0.020	0.519	3.2.1.8	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

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Jmol Version: 14.2.13_2015.03.07 2015-03-07 10:45

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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	0.18	1bfcA	0.577	0.89	0.366	0.591	1.45	UUU	complex1.pdb.gz	85,86,181,182,187,196,197,198
2	0.18	1e0o2	0.598	1.12	0.341	0.620	1.36	III	complex2.pdb.gz	83,86,87,89,102,104,154,156,157,158,160,161,162,202
3	0.16	1hknC	0.591	1.21	0.336	0.615	1.12	N2M	complex3.pdb.gz	183,187,195,196,197,198
4	0.10	1iil0	0.610	1.30	0.346	0.635	1.39	III	complex4.pdb.gz	83,85,89,102,113,114,115,116,117,118,121,122,131,146,154,156,157,159,160,161,162,202,204
5	0.07	1ihk0	0.637	1.75	0.404	0.673	1.25	III	complex5.pdb.gz	80,83,85,89,104,159,160,202,203,204,205,206
6	0.05	1e0oC	0.598	1.12	0.341	0.620	0.91	UUU	complex6.pdb.gz	177,182,187,190,191
7	0.05	1rmlA	0.536	2.45	0.341	0.620	0.98	NTS	complex7.pdb.gz	91,93,94,107,108,109,110
8	0.04	3aj5B	0.581	2.88	0.082	0.688	0.87	NGA	complex8.pdb.gz	180,181,182,186,188,193,196,198
9	0.02	3ah1A	0.580	2.84	0.082	0.683	0.95	SLB	complex9.pdb.gz	133,134,135,142,149
10	0.02	1f31A	0.576	4.10	0.058	0.779	0.84	UUU	complex10.pdb.gz	134,135,141,143,145

	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.

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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.