D-I-TASSER Q13099-D2

D-I-TASSER results for Q13099-D2

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

Input Sequence in FASTA format

>Q13099 (287 residues)
ASPLEAKKKDSPEEKIKQLEKEVNELVEESCIANSCGDLKLALEKAKDAGRKERVLVRQR
EQVTTPENINLDLTYSVLFNLASQYSVNEMYAEALNTYQVIVKNKMFSNAGILKMNMGNI
YLKQRNYSKAIKFYRMALDQVPSVNKQMRIKIMQNIGVTFIQAGQYSDAINSYEHIMSMA
PNLKAGYNLTICYFAIGDREKMKKAFQKLITVPLEIDEDKYISPSDDPHTNLVTEAIKND
HLRQMERERKAMAEKYIMTSAKLIAPVIETSFAAGYDWCVEVVKASQ

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 160 180 200 220 240 260 280 \| \| \| \| \| \| \| \| \| \| \| \| \| \| ASPLEAKKKDSPEEKIKQLEKEVNELVEESCIANSCGDLKLALEKAKDAGRKERVLVRQREQVTTPENINLDLTYSVLFNLASQYSVNEMYAEALNTYQVIVKNKMFSNAGILKMNMGNIYLKQRNYSKAIKFYRMALDQVPSVNKQMRIKIMQNIGVTFIQAGQYSDAINSYEHIMSMAPNLKAGYNLTICYFAIGDREKMKKAFQKLITVPLEIDEDKYISPSDDPHTNLVTEAIKNDHLRQMERERKAMAEKYIMTSAKLIAPVIETSFAAGYDWCVEVVKASQ
Prediction	CCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHCHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHCHHHHHHHHHHHHHHHHHHHHHCC
Confidence	98630112379999999999999999999999998254999999999999999999999999987886267755589988999999909999999999999932679854899999999999909999999999999972866787047999999999999919999999999999982986699989999999909999999999999952743664102023347885729999717499999999999999999999987004432009999999999998069
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 160 180 200 220 240 260 280 \| \| \| \| \| \| \| \| \| \| \| \| \| \| ASPLEAKKKDSPEEKIKQLEKEVNELVEESCIANSCGDLKLALEKAKDAGRKERVLVRQREQVTTPENINLDLTYSVLFNLASQYSVNEMYAEALNTYQVIVKNKMFSNAGILKMNMGNIYLKQRNYSKAIKFYRMALDQVPSVNKQMRIKIMQNIGVTFIQAGQYSDAINSYEHIMSMAPNLKAGYNLTICYFAIGDREKMKKAFQKLITVPLEIDEDKYISPSDDPHTNLVTEAIKNDHLRQMERERKAMAEKYIMTSAKLIAPVIETSFAAGYDWCVEVVKASQ
Prediction	75435645753144004401640361154012023253034005204501522510430351152066143534122000001004536416401610440162443272030100001004526516401610430051147245523020000002003426516401610440061245141000001004426526402600540051357257541344333443431330244441432345424302400220041005403740240010004304738
	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                 220                 240                 260                 280

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

SS
Seq

CCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHCHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHCHHHHHHHHHHHHHHHHHHHHHCC
ASPLEAKKKDSPEEKIKQLEKEVNELVEESCIANSCGDLKLALEKAKDAGRKERVLVRQREQVTTPENINLDLTYSVLFNLASQYSVNEMYAEALNTYQVIVKNKMFSNAGILKMNMGNIYLKQRNYSKAIKFYRMALDQVPSVNKQMRIKIMQNIGVTFIQAGQYSDAINSYEHIMSMAPNLKAGYNLTICYFAIGDREKMKKAFQKLITVPLEIDEDKYISPSDDPHTNLVTEAIKNDHLRQMERERKAMAEKYIMTSAKLIAPVIETSFAAGYDWCVEVVKASQ

3sf4A

0.14

0.12

4.18

1.17

DEthreader

---------ATIGDQLGEAKASGNLGNTLKVLGN-------F-DEAIVCCQRHLDISRELN----DKVGEARALYNLGNVYHAKGKSVRDLQAAVDFYEENLSLVDRAAQGRAFGNLGNTHYLLGNFRDAVIAHEQRLLIAKFGDKAAERRAYSNLGNAYIFLGEFETASEYYKKTLLLAREAQSCYSLGNTYTLLQDYEKAIDYHLKHLAIAQELND--RI------GEGRACWSLGNAYTALG---NHDQAMHFAEKHLEISREVGDKSGELTARLNLSDLQMVL

5dseA

0.13

0.11

3.96

1.33

SPARKS-K

QEVLQRKALLAFQRAHSLSPTDHQAAFYLALQLAISRQIPEALGYVRQALQLQGD------------------DANSLHLLALLLSAQKHYHDALNIIDMALSEY--PENFILLFSKVKLQSLCRGPDEALLTCKHMLQIWYLHPWMTLAQIWLHAAEVYIGIGKPAEATACTQEAANLFPMSNVLYMRGQIAELRGSMDEARRWYEEALAISPTH-----------------VKSMQRLALILHQLGRYSLAEKILRDAVQVNS-----TAHEVWNGLGEVLQAQG

6t3hA

0.12

0.11

3.96

0.58

MapAlign

QEASMGDVVNMLSKGSHDLLINFYFELFAGDYEFFKKNYVKAISFYEKAEQKLSSI----------PNIEETKFAEFHYKIGVAYYEIDQHLVSVNKVTKARDIYWNLEAIQCSLVVGINLYDMGRLDDADAYFRDALTEALDHYDKPITKIYHNLGLVHWQKGSLELALHYFREAYSHEKGQQTVYMLSRVLYTMGQNEEAYHWYELGIEMARKFDDHEY-----KAKHDILYHLYEQPSIDEVKQSLWPDVSKIAKGISELYEKKGDLVTSHEFLKRAFYAKEQI

4a1sA

0.14

0.13

4.49

0.48

CEthreader

CRAGVAFFQAAIQAGTEDLRTLSAIYSQLGNAYFYLGDYNKAMQYHKHDLTLAKSMN------------DRLGEAKSSGNLGNTLKVMGRFDEAAICCERHLTLGDRLSEGRALYNLGNVYHAKGKLTRAVEFYQENLKLMRLGDRGAQGRACGNLGNTYYLLGDFQAAIEHHQERLRIAAERRANSNLGNSHIFLGQFEDAAEHYKRTLALAVELGE-----------REVEAQSCYSLGNTYTLLHEFNTAIEYHNRHLAIAQELGDRIGEARACWSLGNAHSAI

5o09C

0.15

0.14

4.84

1.06

MUSTER

GDTALERQIASASRSVEEARRLAYHVGALVEQISVLADLRQKEGDFRKAESLYREALFRAQELRKQDPDLL---TGIYSLLAHLYDRWGRMDKAAEFYELALKISESDKVATIKNNLAMIFKQLRKFERAEGYYCEALETFQRLDGARVASVYNNLGVLYYSHMDVDRAQVMHERALAIRQNLQTFINLGAVYKAAGDFQKAEACVDRAKRIRAAMNGDTALERQIASASRSVEEARRLAYHDPIR--VGALVEQISVLADLRQKEGDFRKAESLYREALFRAQELR

5o09C

0.15

5.14

0.74

HHsearch

SHMDVDRAQVMHERALAIRADLSQTFINLGAVYKAAGDFQKAEACVDRAKRIRAAALEQISVLADREALKQDPDTGIYSLLAHLYDRWGRMDKAAEFYELALKIEESDKVATIKNNLAMIFKQLRKFERAEGYYCEALETFQREQSARVASVYNNLGVLYYSHMDVDRAQVMHERALAIRADLSTFINLGAVYKAAGDFQKAEACVDRAKRIRAAMNGTLRQKEGDRKQDPDLTGIYSLLAHLYDRWGRMDKAAEFYELALKISAENGLDKVATIKNNLAMIFKQLR

2c0mC

0.13

0.11

3.96

2.11

FFAS-3D

--GLRRLQEGDLPNAVLLFEAAVQQDPKHMEAWQYLGTTQAENEQELLAISALRRCLELK-----------PDNQTALMALAVSFTNESLQREVKELFLAAVRLDPTSIDPDVQCGLGVLFNLSGEYDKAVDCFTAALSVRPND-----YLLWNKLGATLANGNQSEEAVAAYRRALELQPGIRSRYNLGISCINLGAHREAVEHFLEALNMQRKSRGPRGEGGAMS------ENIWSTLRLALSMLGQSDAYGAADARDLSTLLTMFG------------------

6t3hA

0.11

0.10

3.76

0.77

EigenThreader

QEASMGDVVNMLSKGSHDLLINFYFELFAGDYEFFKKNYVKAISFYEKAEQKL----------SSIPNIEETKFAEFHYKIGVAYYEIDQHLVSVNKVTKARDIYKKSDMIQCSLVVGINLYDMGRLDDADAYFRDALTEALDHYDKPITKIYHNLGLVHWQKGSLELALHYFREAYSHEKGQQTVYMLSRVLYTMGQNEEAYHWYELGIEMARKFDD-------HEYKAKHDILYHLYEQDEVKQSLAFLEEVSKIAKGISELYEKKGDLVTSHEFLKRAFYAKEQ

4a1sA

0.15

0.13

4.24

1.40

CNFpred

------------------LRTLSAIYSQLGNAYFYLGDYNKAMQYHKHDLTLAKSM------------NDRLGEAKSSGNLGNTLKVMGRFDEAAICCERHLTLADRLSEGRALYNLGNVYHAKGALTRAVEFYQENLKLMRDLDRGAQGRACGNLGNTYYLLGDFQAAIEHHQERLRIARERRANSNLGNSHIFLGQFEDAAEHYKRTLALAVEL-----------GEREVEAQSCYSLGNTYTLLHEFNTAIEYHNRHLAIAQELDRIGEARACWSLGNAHSAIG

6zpgA

0.07

0.06

2.60

1.17

DEthreader

CEKFQALASRVFVQNNGITHNLYYLAQVYQHLE-------MFEKAAHYCHSTLKRQLEH------------E-WAINAATLSQFYINKLCFMEARHCLSAANVFTQRKGIARCWIKYCLTLMQNALFLLGQHYVFEAKEFFQDGYVTDHIEVVQDHSALFKLAMRCKMHKRRIAMLEPLTNRQFEIAHAYYDMMDLKKINNLNKSALKYYQLFLDSLR---V--LRP-AMLAKFRVARLYGK-II-TADPKKELENLATSLEHYFIVYCKHPAQIEVELELSKEMVS

(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	0.8055

(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	3sf4A	0.79	2.55	0.139	0.899	model1_3sf4A.pdb.gz
2	4a1sA	0.78	1.98	0.148	0.850	model1_4a1sA.pdb.gz
3	6mfvA1	0.71	2.55	0.142	0.801	model1_6mfvA1.pdb.gz
4	7k10A	0.71	4.14	0.077	0.916	model1_7k10A.pdb.gz
5	6z2wE	0.70	4.27	0.106	0.906	model1_6z2wE.pdb.gz
6	5dseA	0.70	2.85	0.097	0.805	model1_5dseA.pdb.gz
7	4xdnA	0.70	3.91	0.077	0.892	model1_4xdnA.pdb.gz
8	4bujB	0.70	3.33	0.088	0.833	model1_4bujB.pdb.gz
9	4n5cA	0.69	4.60	0.113	0.944	model1_4n5cA.pdb.gz
10	3q15A	0.69	3.98	0.134	0.864	model1_3q15A.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	0.53	catalytic 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:0044763	1.00	single-organism cellular process
GO:0016043	0.86	cellular component organization
GO:0032502	0.83	developmental process
GO:0044767	0.82	single-organism developmental process
GO:0065007	0.77	biological regulation
GO:0030030	0.77	cell projection organization
GO:0050789	0.73	regulation of biological process
GO:0050794	0.71	regulation of cellular process
GO:0006996	0.70	organelle organization
GO:1902589	0.68	single-organism organelle organization
GO:0022607	0.68	cellular component assembly
GO:0009653	0.68	anatomical structure morphogenesis
GO:0051179	0.67	localization
GO:0048869	0.67	cellular developmental process
GO:0048646	0.67	anatomical structure formation involved in morphogenesis
GO:0060271	0.66	cilium morphogenesis
GO:0042384	0.66	cilium assembly
GO:0032501	0.65	multicellular organismal process
GO:0008104	0.65	protein localization
GO:0007017	0.64	microtubule-based process
GO:0035058	0.61	nonmotile primary cilium assembly
GO:0048518	0.57	positive regulation of biological process
GO:0006810	0.57	transport
GO:0051641	0.56	cellular localization
GO:0048522	0.56	positive regulation of cellular process
GO:0044707	0.56	single-multicellular organism process
GO:0051649	0.55	establishment of localization in cell
GO:0048856	0.55	anatomical structure development
GO:0015031	0.55	protein transport
GO:0006928	0.55	movement of cell or subcellular component
GO:0046907	0.54	intracellular transport
GO:0044765	0.54	single-organism transport
GO:0007018	0.54	microtubule-based movement
GO:1902582	0.53	single-organism intracellular transport
GO:0006886	0.53	intracellular protein transport
GO:0050896	0.52	response to stimulus
GO:0048583	0.52	regulation of response to stimulus
GO:0042073	0.52	intraciliary transport
GO:0030705	0.52	cytoskeleton-dependent intracellular transport
GO:0098840	0.51	protein transport along microtubule
GO:0009966	0.50	regulation of signal transduction

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	0.92	intracellular part
GO:0043226	0.92	organelle
GO:0044422	0.87	organelle part
GO:0044446	0.86	intracellular organelle part
GO:0042995	0.84	cell projection
GO:0005929	0.83	cilium
GO:0044430	0.71	cytoskeletal part
GO:0044441	0.66	ciliary part
GO:0005815	0.64	microtubule organizing center
GO:0036064	0.63	ciliary basal body
GO:0032991	0.52	macromolecular complex
GO:0043234	0.51	protein complex

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	2pziA	0.633	3.44	0.089	0.787	2.7.11.1	114
2	0.060	2dqmA	0.491	5.53	0.063	0.777	3.4.11.2	NA
3	0.060	1gaiA	0.488	5.37	0.055	0.735	3.2.1.3	NA
4	0.060	2sqcA	0.493	5.14	0.085	0.725	5.4.99.17	NA
5	0.060	1slyA	0.503	5.23	0.074	0.773	4.2.2.-	172

	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	0.07	3fp4A	0.619	3.68	0.106	0.784	1.14	III	complex1.pdb.gz	114,119,122,134,151,155,185,189
2	0.05	2bptA	0.633	4.87	0.067	0.920	0.98	III	complex2.pdb.gz	154,157,158,161,162,188,191
3	0.04	1o6oB	0.550	5.41	0.079	0.843	0.73	III	complex3.pdb.gz	112,115,116,120,151,154
4	0.03	1f59A	0.547	5.83	0.065	0.885	0.71	III	complex4.pdb.gz	111,114,115,118,119,152,156
5	0.02	1o6pB	0.547	5.75	0.059	0.888	0.75	III	complex5.pdb.gz	119,123,154,157,158

	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.