D-I-TASSER Q13049-D2

D-I-TASSER results for Q13049-D2

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

Input Sequence in FASTA format

>Q13049 (252 residues)
LLMCRSCGRRLPRQFCRSCGLVLCEPCREADHQPPGHCTLPVKEAAEERRRDFGEKLTRL
RELMGELQRRKAALEGVSKDLQARYKAVLQEYGHEERRVQDELARSRKFFTGSLAEVEKS
NSQVVEEQSYLLNIAEVQAVSRCDYFLAKIKQADVALLEETADEEEPELTASLPRELTLQ
DVELLKVGHVGPLQIGQAVKKPRTVNVEDSWAMEATASAASTSVTFREMDMSPEEVVASP
RASPAKQRGPEA

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 160 180 200 220 240 \| \| \| \| \| \| \| \| \| \| \| \| LLMCRSCGRRLPRQFCRSCGLVLCEPCREADHQPPGHCTLPVKEAAEERRRDFGEKLTRLRELMGELQRRKAALEGVSKDLQARYKAVLQEYGHEERRVQDELARSRKFFTGSLAEVEKSNSQVVEEQSYLLNIAEVQAVSRCDYFLAKIKQADVALLEETADEEEPELTASLPRELTLQDVELLKVGHVGPLQIGQAVKKPRTVNVEDSWAMEATASAASTSVTFREMDMSPEEVVASPRASPAKQRGPEA
Prediction	CCCCCCCCCCCSSSSCCCCCCSSCHHHCCCCCCCCCCCSSSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHCCCCCCCCCCCCCSSCCCCCCCCHHHHSCCCCCCCCCCCCCCCCCCCCCCCCSSSSSCCCCCCCCCCCCCCCCCCCCCCCC
Confidence	983855799321478376993003552124777899762469999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999997629999997646899999850320144543054323466611100244454201022035642123212234334555554146531467876678999999876689999
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 160 180 200 220 240 \| \| \| \| \| \| \| \| \| \| \| \| LLMCRSCGRRLPRQFCRSCGLVLCEPCREADHQPPGHCTLPVKEAAEERRRDFGEKLTRLRELMGELQRRKAALEGVSKDLQARYKAVLQEYGHEERRVQDELARSRKFFTGSLAEVEKSNSQVVEEQSYLLNIAEVQAVSRCDYFLAKIKQADVALLEETADEEEPELTASLPRELTLQDVELLKVGHVGPLQIGQAVKKPRTVNVEDSWAMEATASAASTSVTFREMDMSPEEVVASPRASPAKQRGPEA
Prediction	522374276431510165063003333344616376342330440055226404610550362155045235415512541453154136304521540363046216414541551364355315514521532454245414412430455115304534754355135513550426514134155244251352244344252755154454345344423144344546534364643455354478
	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

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

SS
Seq

CCCCCCCCCCCSSSSCCCCCCSSCHHHCCCCCCCCCCCSSSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHCCCCCCCCCCCCCSSCCCCCCCCHHHHSCCCCCCCCCCCCCCCCCCCCCCCCSSSSSCCCCCCCCCCCCCCCCCCCCCCCC
LLMCRSCGRRLPRQFCRSCGLVLCEPCREADHQPPGHCTLPVKEAAEERRRDFGEKLTRLRELMGELQRRKAALEGVSKDLQARYKAVLQEYGHEERRVQDELARSRKFFTGSLAEVEKSNSQVVEEQSYLLNIAEVQAVSRCDYFLAKIKQADVALLEETADEEEPELTASLPRELTLQDVELLKVGHVGPLQIGQAVKKPRTVNVEDSWAMEATASAASTSVTFREMDMSPEEVVASPRASPAKQRGPEA

2dfsA

0.08

0.05

2.02

0.83

DEthreader

LYARVWSPPLRN----------PDILVGEN---------VEKIRADKLRAACIRIQKTIRGWLMRKKYMRMRRAAITIQRYVRGHQARCYATFLRRTRAAIIIQKFQRMYVVRKRYQCMRDATIALQALLRGYLVRNKYQMMLREHKSIIIQKHVRGWLARVHYHRTLKAIVYLQY--M-------------------------------------------------------------------------

4uosA

0.11

0.08

2.72

1.04

SPARKS-K

--------------------------------GDNEEVKKMLEKMIEEIKKMLEKAIKKVKEMLEKMIKEIKKMLEILKKAKEMAEKILKMVIELAEKILKKAKEMAEKILKKVKELGEEVKKMLEKMIEEIKKMLEKAIKKVKEMLEKMIKEIKKMLEEKILKKAKEMAEKILKMVIELAEKILKKAKEMAEKILKKVKELGVG-----------------------------------------------

4tn3A

0.11

0.10

3.74

1.13

MapAlign

-DHCARHG-EKLLLFCQEDSKVICWLCKDSQE-HRGHHTFLMEEVAQEYHVKLQTALEMLRQKQQEAEKLEADIREEKASWKIQIDYDKTNVSADFEQLREILDWEESNELQNLEKEEEDILKSLTKSETEMVQQTQYMRELISELEHR-----LQMMDLLQGVDGIIKRI---ENMTLFRAPDLKGMLDMFRDAAAEESPVLLAMNIFEMLRIDEGLRLKIYKNTEGYYTIGIGHLLTKSPSLNAAKSELD

4tn3A

0.12

4.21

0.82

CEthreader

VDHCARH-GEKLLLFCQEDSKVICWLCKDSQ-EHRGHHTFLMEEVAQEYHVKLQTALEMLRQKQQEAEKLEADIREEKASWKIQIDYDKTNVSADFEQLREILDWEESNELQNLEKEEEDILKSLTKSETEMVQQTQYMRELISELEHRLQMMDIENMTLFRAPDLKGMLDMFRDAAAEESPVLLAMNIFEMLRIDEGLRLKIYKNTEGYYTILLTKSPSLNAAKSELDKAIGRNTNGVITKDEAEKLFNQD

6h3aA

0.12

0.10

3.48

1.08

MUSTER

TVYCNVHKHEPLVLFCESCDTLTCRDCQLNAHK--DHQYQFLEDAVRNQRKLLASLVKRLGDKHATLQKSTKEVRSSIRQVSDVQKRVQVDVKMAILQIMKELNKRGRVLVNDAQKVTEGQQERLERQHWTMTKIQKHQEHILRFASWALESDNNTALLLSKKLIYFQLHRALKMIVDPVEP-----------------HGEMKFQWDLNAWTKSAEAFGKI------------------------------

6qajA

0.13

0.10

3.43

2.68

HHsearch

TVYCNVHKHEPLVLFCESCDTLTCRDCQLNA--HKDHQYQFLEDAVRNQRKLLASLVKRLGDKHATLQKSTKEVRSSIRQVSDVQKRVQVDVKMAILQIMKELNKRGRVLVNDAQKVTEGQQERLERQHWTMTKIQKHQEHILRFASWALESDNTALLLSKKIYFQLHRALKM--IVDPVEPEFQWTKSAEAF-----------------------------------------------------------

4tn3A

0.15

0.10

3.36

1.35

FFAS-3D

VDHCARH-GEKLLLFCQEDSKVICWLCKDSQ-EHRGHHTFLMEEVAQEYHVKLQTALEMLRQKQQEAEKLEADIREEKASWKIQIDYDKTNVSADFEQLREILDWEESNELQNLEKEEEDILKSLTKSETEMVQQTQYMRELISELEHRLQMMD--LLQGVDGIIKRIENMTLFRA----------------------------------------------------------------------------

4tn3A

0.11

0.09

3.32

1.03

EigenThreader

-VDHCARHGEKLLLFCQEDSKVICWLCKD--SQEHRGHHTFLMEEVAQEYHVKLQTALEMLRQKQQEAEKLEADIREEKASWKIQIDYDKTNVSADFEQLREILDWEESNELQNLEKEEEDILKSLTKSETEMVQQTQYMRELISELEHRLQ-MMDLLQ---GVDGIIKRIENMTLFRAPD--------------------------LKGMLDMFRDAAAE---ESPVLLAMNLRIDEGLRLKIYKNTEGYY

4tn3A

0.15

0.09

3.08

0.86

CNFpred

VDHCARHG-EKLLLFCQEDSKVICWLCKDSQ-EHRGHHTFLMEEVAQEYHVKLQTALEMLRQKQQEAEKLEADIREEKASWKIQIDYDKTNVSADFEQLREILDWEESNELQNLEKEEEDILKSLTKSETEMVQQTQYMRELISELEHRLQ--MMDLLQ---------------------------------------------------------------------------------------------

6z9lA

0.12

0.08

2.83

0.83

DEthreader

NA--------QAATK-------QAQTLDINQEKLA-TAQQAE-SDAQQARSASQQALNTAKTTQATAEKELSVHKATLANLQAVATKSTTNYEEKVRQTATAEKSLQQTKDQLATINELIQNRAAVLEKAKTNVAEAQAIEQTSAKVLKEKQEAQKAEENTLNSLKEVLDLAENNQKQVALKTSTRSLS---------------------------------------------------------------

(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	0.4549

(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	4tn3A	0.57	3.20	0.113	0.691	model1_4tn3A.pdb.gz
2	6h3aA	0.55	4.17	0.102	0.762	model1_6h3aA.pdb.gz
3	6qajA	0.54	4.30	0.109	0.750	model1_6qajA.pdb.gz
4	4ltbA	0.50	3.40	0.089	0.623	model1_4ltbA.pdb.gz
5	6flnA	0.49	3.60	0.069	0.615	model1_6flnA.pdb.gz
6	6sl2A	0.45	5.12	0.065	0.667	model1_6sl2A.pdb.gz
7	1sjjA	0.45	5.22	0.063	0.663	model1_1sjjA.pdb.gz
8	4cg4A1	0.44	4.32	0.076	0.607	model1_4cg4A1.pdb.gz
9	2eflA	0.44	3.99	0.043	0.583	model1_2eflA.pdb.gz
10	2efkA	0.43	4.20	0.042	0.587	model1_2efkA.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:0031369	1.00	translation initiation factor binding
GO:0097159	0.74	organic cyclic compound binding
GO:1901363	0.73	heterocyclic compound binding
GO:0003824	0.73	catalytic activity
GO:0016740	0.70	transferase activity
GO:0004842	0.69	ubiquitin-protein transferase activity
GO:0003723	0.69	RNA binding
GO:0008092	0.68	cytoskeletal protein binding
GO:0061630	0.67	ubiquitin protein ligase activity
GO:0043621	0.67	protein self-association
GO:0043130	0.67	ubiquitin binding
GO:0017022	0.67	myosin 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:0065007	0.85	biological regulation
GO:0050789	0.84	regulation of biological process
GO:0044699	0.83	single-organism process
GO:0048518	0.78	positive regulation of biological process
GO:0080090	0.77	regulation of primary metabolic process
GO:0060255	0.77	regulation of macromolecule metabolic process
GO:0051246	0.76	regulation of protein metabolic process
GO:0010604	0.76	positive regulation of macromolecule metabolic process
GO:0051247	0.75	positive regulation of protein metabolic process
GO:0045732	0.74	positive regulation of protein catabolic process
GO:0009987	0.68	cellular process
GO:0050794	0.66	regulation of cellular process
GO:0008152	0.60	metabolic process
GO:0071704	0.58	organic substance metabolic process
GO:0044763	0.58	single-organism cellular process
GO:0044238	0.58	primary metabolic process
GO:0044237	0.58	cellular metabolic process
GO:0044260	0.57	cellular macromolecule metabolic process
GO:0031323	0.56	regulation of cellular metabolic process
GO:0048519	0.55	negative regulation of biological process
GO:0048583	0.54	regulation of response to stimulus
GO:0048523	0.54	negative regulation of cellular process
GO:0019538	0.54	protein metabolic process
GO:0051239	0.53	regulation of multicellular organismal process
GO:0051171	0.53	regulation of nitrogen compound metabolic process
GO:0050896	0.53	response to stimulus
GO:0048584	0.53	positive regulation of response to stimulus
GO:0048522	0.53	positive regulation of cellular process
GO:0044267	0.53	cellular protein metabolic process
GO:0032268	0.53	regulation of cellular protein metabolic process
GO:0023051	0.53	regulation of signaling
GO:0010468	0.53	regulation of gene expression
GO:2001141	0.52	regulation of RNA biosynthetic process
GO:2000112	0.52	regulation of cellular macromolecule biosynthetic process
GO:1902531	0.52	regulation of intracellular signal transduction
GO:0080134	0.52	regulation of response to stress
GO:0031325	0.52	positive regulation of cellular metabolic process
GO:0031324	0.52	negative regulation of cellular metabolic process
GO:0023056	0.52	positive regulation of signaling
GO:0016567	0.52	protein ubiquitination
GO:0010647	0.52	positive regulation of cell communication
GO:0002376	0.52	immune system process
GO:0001817	0.52	regulation of cytokine production
GO:2000026	0.51	regulation of multicellular organismal development
GO:1902533	0.51	positive regulation of intracellular signal transduction
GO:0080135	0.51	regulation of cellular response to stress
GO:0065009	0.51	regulation of molecular function
GO:0051726	0.51	regulation of cell cycle
GO:0051240	0.51	positive regulation of multicellular organismal process
GO:0051128	0.51	regulation of cellular component organization
GO:0045934	0.51	negative regulation of nucleobase-containing compound metabolic process
GO:0045595	0.51	regulation of cell differentiation
GO:0045087	0.51	innate immune response
GO:0042981	0.51	regulation of apoptotic process
GO:0032879	0.51	regulation of localization
GO:0032270	0.51	positive regulation of cellular protein metabolic process
GO:0031327	0.51	negative regulation of cellular biosynthetic process
GO:0030154	0.51	cell differentiation
GO:0010605	0.51	negative regulation of macromolecule metabolic process
GO:0010033	0.51	response to organic substance
GO:0006355	0.51	regulation of transcription, DNA-templated
GO:1902230	0.50	negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage
GO:1902187	0.50	negative regulation of viral release from host cell
GO:0051092	0.50	positive regulation of NF-kappaB transcription factor activity
GO:0048147	0.50	negative regulation of fibroblast proliferation
GO:0045862	0.50	positive regulation of proteolysis
GO:0045787	0.50	positive regulation of cell cycle
GO:0045666	0.50	positive regulation of neuron differentiation
GO:0045444	0.50	fat cell differentiation
GO:0043123	0.50	positive regulation of I-kappaB kinase/NF-kappaB signaling
GO:0042787	0.50	protein ubiquitination involved in ubiquitin-dependent protein catabolic process
GO:0034612	0.50	response to tumor necrosis factor
GO:0032897	0.50	negative regulation of viral transcription
GO:0030335	0.50	positive regulation of cell migration
GO:0030307	0.50	positive regulation of cell growth
GO:0009411	0.50	response to UV
GO:0000209	0.50	protein polyubiquitination

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:0005863	1.00	striated muscle myosin thick filament
GO:0005634	1.00	nucleus
GO:0005737	0.68	cytoplasm

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	1hbmB	0.315	5.37	0.053	0.488	2.8.4.1	NA
2	0.060	3b8eC	0.357	5.21	0.038	0.544	3.6.3.9	NA
3	0.060	1mroB	0.314	5.69	0.079	0.504	2.8.4.1	20
4	0.060	3ffzA	0.315	4.17	0.022	0.417	3.4.24.69	NA
5	0.060	3g61A	0.336	3.82	0.033	0.436	3.6.3.44	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	0.01	1ic20	0.284	2.02	0.101	0.309	0.75	III	complex1.pdb.gz	63,64,67,70,71,74,75,77,78,81,85,88,92,95,96,98,99,106
2	0.01	3aoiN	0.442	5.63	0.054	0.714	0.64	ZN	complex2.pdb.gz	32,33,36,38
3	0.01	2p9i3	0.135	4.75	0.078	0.186	0.70	III	complex3.pdb.gz	52,53,54,56
4	0.01	1ynjD	0.399	5.74	0.052	0.655	0.73	ZN	complex4.pdb.gz	16,19,32,35
5	0.01	1w7i0	0.281	5.81	0.047	0.472	0.79	III	complex5.pdb.gz	47,49,51,52,53,55,56,57,58,60,61,64,67

	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.