D-I-TASSER P19544-D1

D-I-TASSER results for P19544-D1

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

Input Sequence in FASTA format

>P19544 (143 residues)
MGSDVRDLNALLPAVPSLGGGGGCALPVSGAAQWAPVLDFAPPGASAYGSLGGPAPPPAP
PPPPPPPPHSFIKQEPSWGGAEPHEEQCLSAFTVHFSGQFTGTAGACRYGPFGPPPPSQA
SSGQARMFPNAPYLPSCLESQPA

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 \| \| \| \| \| \| \| MGSDVRDLNALLPAVPSLGGGGGCALPVSGAAQWAPVLDFAPPGASAYGSLGGPAPPPAPPPPPPPPPHSFIKQEPSWGGAEPHEEQCLSAFTVHFSGQFTGTAGACRYGPFGPPPPSQASSGQARMFPNAPYLPSCLESQPA
Prediction	CCCCHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCSCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHCCSSSSSSSSCSSCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
Confidence	97303445653788877789998766667888876421157888888765667888888888899997421114888899995321121225888612332677763346788999999998887546899777654467999
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 \| \| \| \| \| \| \| MGSDVRDLNALLPAVPSLGGGGGCALPVSGAAQWAPVLDFAPPGASAYGSLGGPAPPPAPPPPPPPPPHSFIKQEPSWGGAEPHEEQCLSAFTVHFSGQFTGTAGACRYGPFGPPPPSQASSGQARMFPNAPYLPSCLESQPA
Prediction	74542541431133146245444131314434413220413355443244034444445445554443341145447144543344301120212232413344331431323424456347444421463421342365668
	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 DeepPotential. 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

CCCCHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCSCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHCCSSSSSSSSCSSCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
MGSDVRDLNALLPAVPSLGGGGGCALPVSGAAQWAPVLDFAPPGASAYGSLGGPAPPPAPPPPPPPPPHSFIKQEPSWGGAEPHEEQCLSAFTVHFSGQFTGTAGACRYGPFGPPPPSQASSGQARMFPNAPYLPSCLESQPA

1yi7A

0.08

3.08

0.49

CEthreader

AKIIYKGTDIKYTEGPHIYHIGDYYYLFTAEGGTTYEHSETVARSKNIDGPYEIDPEYPLLTSWHDPRNSLQKCGHASLVHTHTDEWYLAHLVGRYCPLGRETSIQRIEWVDNWPRVVGGKQGSVNVEAPKIPEVKWEKTYDE

1ubmS

0.07

2.89

0.60

EigenThreader

ECTGCSESVLRAFAGDAAEAALEQAVNSPHGFIAVVEGGIPTAANGIYGKNHTMLDICSRILPKAQAVIAYGTCATFGGVQAAKPNPTGAKGNIAGCPPLNRPTVHWCLYELGCKGPWPVDAGHPCIGCSEPDFWDAMTPFYQ

6b40M1

0.24

0.16

5.00

0.39

FFAS-3D

----VCDRVPLRDPSPTVQSGAMSTLPIDVGGEGISLSDMKEVKAMPHIA-SGCTAVWGPPLPPKPGKDT--KQVILWGGLDKRRWCCLTQVDITITPKTT------------------------------------------

7jjvA

0.20

0.16

5.16

0.95

SPARKS-K

DGADGTS-NG---QAGASGLAGGPNCNGGKGGKGAPG----VGTAGGAGGVGGAGGT-GNTNGGAGGSGGNSDVAAGGAGAA----GGAAG------GAGTGGTGGGGAGPGGAPGAGGAGTPAGSAGSPGQTTVL-------

5c42A

0.20

0.06

1.79

0.17

CNFpred

KLVDFRELNKRTQDFWEVQLGIPHPAGLP-KKKSVTVLDVG------------------------------------------------------------------------------------------------------

3ifeA

0.07

0.06

2.54

0.83

DEthreader

QSAMKEELIERFRYVIDTQSNPTQFGLLVLVATLFLAHL-DTATDFTGK--NVKPNTDGTTL-L-GADDKAGEIMVAFTPDEEIGRGP-F----------AYM--MDG-GPLGLEYEMGLSLPTPNIF-TGGEVSVDVME---

1n9wB2

0.13

4.38

0.68

MapAlign

EDLMRLEEALLAEMLEEALNTAGDEIRLLGATWPIPRLTHAEAKRILKEELGYPVERLLGEYAKERWGSDWLFVTRYPRYTYPEEDGTTRSFDLLFRGLEITSGGQRIHRYEELLESLKAKGMDPEAFHGYLEVFKYGMP---

2nbiA

0.20

6.47

0.71

MUSTER

CLSFGRPDCDVLPTPQNINCPRCCATERPDNPMFTPSPDGSPPICSP-TMLPTNQPTPPEPSSAPSDCGEVIEECPLDTCFLPSDPARPPDCTVLPFPNNLGCPACCPFECSPDNPMFTPSPDGSPPNCSPTMLPTPQPSTPT

2jr3A

0.37

0.10

3.12

0.54

HHsearch

--------------------------------------DDTPS---------------------------SRCGSGGWGPCLPIDLLCIVHVTVGCSGGF----GCCRIG---------------------------------

3h7nA1

0.07

0.06

2.34

0.48

CEthreader

QDYDMVSQSDSDPSHFRKVEAVGEYLSLYNNTLVTLLGLFQMGTLLVDSSGILTYTFQNNIPTNLSASAIWSIVDLVLTRPLELASYLNLIVLWKSGTASKLQILNVNDESFKNYEWI-------------------------

(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	0.5072

(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 DeepPotential, 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	2gqdA	0.47	4.77	0.056	0.811	model1_2gqdA.pdb.gz
2	2uv9D3	0.47	4.83	0.070	0.825	model1_2uv9D3.pdb.gz
3	3lrfA	0.47	5.08	0.071	0.832	model1_3lrfA.pdb.gz
4	2pffA	0.47	5.02	0.069	0.846	model1_2pffA.pdb.gz
5	1e5mA	0.47	4.84	0.063	0.818	model1_1e5mA.pdb.gz
6	6kxdA	0.47	5.09	0.047	0.839	model1_6kxdA.pdb.gz
7	4b7vA	0.47	5.01	0.063	0.825	model1_4b7vA.pdb.gz
8	3hmjA6	0.46	4.97	0.085	0.832	model1_3hmjA6.pdb.gz
9	4ewgA	0.46	4.88	0.047	0.825	model1_4ewgA.pdb.gz
10	3o04A	0.46	4.94	0.063	0.818	model1_3o04A.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:0070742	1.00	C2H2 zinc finger domain binding
GO:0044212	1.00	transcription regulatory region DNA binding
GO:0043565	1.00	sequence-specific DNA binding
GO:0008270	1.00	zinc ion binding
GO:0001077	1.00	transcriptional activator activity, RNA polymerase II core promoter proximal region sequence-specific binding
GO:0003723	0.65	RNA binding
GO:0003690	0.65	double-stranded DNA 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	1.00	single-organism process
GO:0048856	0.94	anatomical structure development
GO:0044767	0.94	single-organism developmental process
GO:0001822	0.93	kidney development
GO:0009987	0.91	cellular process
GO:0065007	0.89	biological regulation
GO:0044763	0.89	single-organism cellular process
GO:0050789	0.88	regulation of biological process
GO:0050794	0.87	regulation of cellular process
GO:0030154	0.87	cell differentiation
GO:0072112	0.86	glomerular visceral epithelial cell differentiation
GO:0048523	0.83	negative regulation of cellular process
GO:0080090	0.74	regulation of primary metabolic process
GO:0060255	0.74	regulation of macromolecule metabolic process
GO:0031323	0.74	regulation of cellular metabolic process
GO:0051171	0.73	regulation of nitrogen compound metabolic process
GO:0006355	0.72	regulation of transcription, DNA-templated
GO:0031324	0.71	negative regulation of cellular metabolic process
GO:0010605	0.71	negative regulation of macromolecule metabolic process
GO:0006357	0.71	regulation of transcription from RNA polymerase II promoter
GO:0045892	0.70	negative regulation of transcription, DNA-templated
GO:0008285	0.68	negative regulation of cell proliferation
GO:0008152	0.66	metabolic process
GO:0071704	0.65	organic substance metabolic process
GO:0048468	0.65	cell development
GO:0009888	0.65	tissue development
GO:0072073	0.64	kidney epithelium development
GO:0044238	0.64	primary metabolic process
GO:0044237	0.64	cellular metabolic process
GO:0035295	0.64	tube development
GO:0032835	0.64	glomerulus development
GO:0030325	0.64	adrenal gland development
GO:0051239	0.63	regulation of multicellular organismal process
GO:0048518	0.63	positive regulation of biological process
GO:0043170	0.63	macromolecule metabolic process
GO:0032501	0.63	multicellular organismal process
GO:2000026	0.62	regulation of multicellular organismal development
GO:0051241	0.62	negative regulation of multicellular organismal process
GO:0048522	0.62	positive regulation of cellular process
GO:0044707	0.62	single-multicellular organism process
GO:0044260	0.62	cellular macromolecule metabolic process
GO:0006807	0.62	nitrogen compound metabolic process
GO:0090304	0.61	nucleic acid metabolic process
GO:0090185	0.61	negative regulation of kidney development
GO:0048731	0.61	system development
GO:0003002	0.61	regionalization
GO:0050896	0.60	response to stimulus
GO:0031325	0.60	positive regulation of cellular metabolic process
GO:0016070	0.60	RNA metabolic process
GO:0010604	0.60	positive regulation of macromolecule metabolic process
GO:0045893	0.59	positive regulation of transcription, DNA-templated
GO:0032268	0.59	regulation of cellular protein metabolic process
GO:0016043	0.59	cellular component organization
GO:0051716	0.58	cellular response to stimulus
GO:0032269	0.58	negative regulation of cellular protein metabolic process
GO:0022414	0.58	reproductive process
GO:0010033	0.58	response to organic substance
GO:0009653	0.58	anatomical structure morphogenesis
GO:2001076	0.57	positive regulation of metanephric ureteric bud development
GO:2000195	0.57	negative regulation of female gonad development
GO:2000020	0.57	positive regulation of male gonad development
GO:0072302	0.57	negative regulation of metanephric glomerular mesangial cell proliferation
GO:0072284	0.57	metanephric S-shaped body morphogenesis
GO:0072166	0.57	posterior mesonephric tubule development
GO:0072075	0.57	metanephric mesenchyme development
GO:0071371	0.57	cellular response to gonadotropin stimulus
GO:0061032	0.57	visceral serous pericardium development
GO:0060421	0.57	positive regulation of heart growth
GO:0060231	0.57	mesenchymal to epithelial transition
GO:0043066	0.57	negative regulation of apoptotic process
GO:0043065	0.57	positive regulation of apoptotic process
GO:0043010	0.57	camera-type eye development
GO:0035802	0.57	adrenal cortex formation
GO:0032836	0.57	glomerular basement membrane development
GO:0030539	0.57	male genitalia development
GO:0030308	0.57	negative regulation of cell growth
GO:0017148	0.57	negative regulation of translation
GO:0008406	0.57	gonad development
GO:0008380	0.57	RNA splicing
GO:0007530	0.57	sex determination
GO:0007507	0.57	heart development
GO:0007356	0.57	thorax and anterior abdomen determination
GO:0007281	0.57	germ cell development
GO:0003156	0.57	regulation of organ formation
GO:0001658	0.57	branching involved in ureteric bud morphogenesis
GO:0001657	0.57	ureteric bud development
GO:0001570	0.57	vasculogenesis
GO:0000122	0.57	negative regulation of transcription from RNA polymerase II promoter
GO:0045165	0.51	cell fate commitment
GO:0008584	0.50	male gonad 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:0016607	1.00	nuclear speck
GO:0005737	1.00	cytoplasm
GO:0005654	1.00	nucleoplasm
GO:0005634	1.00	nucleus
GO:0043232	0.54	intracellular non-membrane-bounded organelle
GO:0005730	0.53	nucleolus

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	2ahbA	0.433	5.36	0.088	0.811	2.3.1.180 2.3.1.41	NA
2	0.060	2ebdA	0.425	5.29	0.032	0.811	2.3.1.180	NA
3	0.060	2p0uA	0.429	5.44	0.047	0.839	2.3.1.74	NA
4	0.060	2iikB	0.444	5.26	0.055	0.818	2.3.1.16	NA
5	0.060	2gp6A	0.459	4.91	0.046	0.825	2.3.1.41	100

	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:

Click to view	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	2vba0	0.458	4.82	0.073	0.804	0.42	III	complex1.pdb.gz	111,113,114

	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, Qiqige Wuyun, Yang Li, Quancheng Liu, Xiaogen Zhou, Yiheng Zhu, P. Lydia Freddolino, Yang Zhang. Integrating deep learning potentials with I-TASSER for single- and multi-domain protein structure prediction. Submitted. 2023.