D-I-TASSER Q96MD2-D2

D-I-TASSER results for Q96MD2-D2

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

Input Sequence in FASTA format

>Q96MD2 (115 residues)
SPLESSFQLEVDVLCHLLKAQAQVSEWKFLPSLVNLHSAHTKLQTWGQIFEKQRETKKHL
FGGQSQKAVQPPHLFLWLMKLKNMLLAKFSFYFHEALSRQTTASEMKTLTAKANP

Predicted Secondary Structure

Sequence	20 40 60 80 100 \| \| \| \| \| SPLESSFQLEVDVLCHLLKAQAQVSEWKFLPSLVNLHSAHTKLQTWGQIFEKQRETKKHLFGGQSQKAVQPPHLFLWLMKLKNMLLAKFSFYFHEALSRQTTASEMKTLTAKANP
Prediction	CCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHCCC
Confidence	9335568999999999999999999832699999999889999999999874222455313766556678856999999999999999898877877436997899999974088
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 \| \| \| \| \| SPLESSFQLEVDVLCHLLKAQAQVSEWKFLPSLVNLHSAHTKLQTWGQIFEKQRETKKHLFGGQSQKAVQPPHLFLWLMKLKNMLLAKFSFYFHEALSRQTTASEMKTLTAKANP
Prediction	8434541410030033014033203514214001303504431530453156455434432444444446333012103413432233113201420374444741342256558
	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

                   |                   |                   |                   |                   |

SS
Seq

CCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHCCC
SPLESSFQLEVDVLCHLLKAQAQVSEWKFLPSLVNLHSAHTKLQTWGQIFEKQRETKKHLFGGQSQKAVQPPHLFLWLMKLKNMLLAKFSFYFHEALSRQTTASEMKTLTAKANP

1y1uA

0.05

2.37

1.33

DEthreader

QKHLQINQRFEELRLITQDTENELKKLYRVELAEKHQKTLQLLRKQQTIILDELIQWKRAGPPEGSLDLQWCEKLAEIIWQNRQQIRRAEHLCQQL-P-IPG--PVEEMLAEVAT

2gnxA

0.88

0.73

20.56

1.22

SPARKS-K

SPLESSFQLEVGVLSHLLKAQAQISEWKFLPSLVTLHNAHTKLQSWGQTFEK-------------QRPP---HLFLWL-KLKT-LLAKFSFYFHEALSRQTTASE-KALTAKANP

2gnxA

0.86

0.72

20.32

1.16

MUSTER

SPLESSFQLEVGVLSHLLKAQAQISEWKFLPSLVTLHNAHTKLQSWGQTFEKQ----------------RPPHLFLWLKLK--TLLAKFSFYFHEALSRQTTASE-KALTAKANP

2gnxA

0.90

0.75

21.03

4.82

HHsearch

SPLESSFQLEVGVLSHLLKAQAQISEWKFLPSLVTLHNAHTKLQSWGQTFEKQ----------------RPPHLFLWL-KLKT-LLAKFSFYFHEALSRQTTASE-KALTAKANP

2gnxA

0.73

0.62

17.51

1.21

FFAS-3D

SPLESSFQLEVGVLSHLLKAQAQISEWKFLPSLVTLHNAHTKLQSWGQTFE----------------KQRPPHLFLWL--KLKTLLAKFSFYFHEALSRQTTFGKISSFIRKYDA

2gnxA

0.91

0.77

21.75

1.04

CNFpred

-PLESSFQLEVGVLSHLLKAQAQISEWKFLPSLVTLHNAHTKLQSWGQTFEKQR----------------PPHLFLWLMKLKTMLLAKFSFYFHEALSRQTTASEMKALTAKANP

6ux2A1

0.11

0.10

3.75

1.17

DEthreader

SQQHEIESRILDLRAMMEKLVKSISQLRRKEVLDASKALLGRLTTLIELLLPKLEEWKAQK-AC--GLLEWFTAGAKLLFHLRQLLKELKGLSCLV-Q--DD--PLTKGVDLRAQ

6ux2A

0.11

0.10

3.75

1.17

DEthreader

SQQHEIESRILDLRAMMEKLVKSISQLRRKEVLDASKALLGRLTTLIELLLPKLEEWKAQK-AC--GLLEWFTAGAKLLFHLRQLLKELKGLSCLV-Q--DD--PLTKGVDLRAQ

4am2A

0.09

3.35

0.65

SPARKS-K

EYLNRGLRSELTAVSQYWLHYRMLEDWGYKDLAKKWRAESIEEMAHADKFVERILFLEGLPNLQTLDPLRIGEVLESDLAAEREARALYQEGAAYAASVGDFKNLFEELMGDEEH

4av3A3

0.07

2.88

0.87

MapAlign

LGAVMSASAGIVGMKMATRANVRVAEAPAKVAYQGGSVMGLSVGFAALGCSIIAMFDRNVGDVAGLGADLLESFVGVATSVSVDSYGPIADNAGGISEDPEVRKITDHLDAVGNT

(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	0.7712

(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	1y1uA	0.80	2.42	0.063	0.974	model1_1y1uA.pdb.gz
2	6ux2A1	0.77	2.67	0.117	0.965	model1_6ux2A1.pdb.gz
3	1yvlB2	0.77	2.75	0.063	0.974	model1_1yvlB2.pdb.gz
4	2xheB	0.75	2.85	0.036	0.948	model1_2xheB.pdb.gz
5	1fioA	0.74	2.85	0.082	0.957	model1_1fioA.pdb.gz
6	4r61A	0.73	2.11	0.122	0.852	model1_4r61A.pdb.gz
7	3c98B	0.73	2.80	0.101	0.930	model1_3c98B.pdb.gz
8	1bg1A1	0.72	2.97	0.088	0.983	model1_1bg1A1.pdb.gz
9	1uusA	0.61	2.88	0.075	0.809	model1_1uusA.pdb.gz
10	1cnt1	0.51	2.88	0.050	0.626	model1_1cnt1.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:0004871	0.73	signal transducer activity
GO:1901363	0.72	heterocyclic compound binding
GO:0097159	0.72	organic cyclic compound binding
GO:0003676	0.70	nucleic acid binding
GO:0003677	0.66	DNA binding
GO:0098531	0.59	transcription factor activity, direct ligand regulated sequence-specific DNA binding
GO:0070491	0.59	repressing transcription factor binding
GO:0048020	0.59	CCR chemokine receptor binding
GO:0043566	0.59	structure-specific DNA binding
GO:0035258	0.59	steroid hormone receptor binding
GO:0019902	0.59	phosphatase binding
GO:0019900	0.59	kinase binding
GO:0003824	0.59	catalytic activity
GO:0003682	0.59	chromatin binding
GO:0001228	0.59	transcriptional activator activity, RNA polymerase II transcription regulatory region sequence-specific binding
GO:0001085	0.59	RNA polymerase II transcription factor binding
GO:0000987	0.59	core promoter proximal region sequence-specific DNA binding
GO:0000982	0.59	transcription factor activity, RNA polymerase II core promoter proximal region sequence-specific binding
GO:0000977	0.59	RNA polymerase II regulatory region sequence-specific DNA binding
GO:0046872	0.56	metal ion binding
GO:0046914	0.55	transition metal ion binding
GO:0016740	0.53	transferase activity
GO:0051536	0.52	iron-sulfur cluster binding
GO:0016782	0.52	transferase activity, transferring sulfur-containing groups
GO:0005506	0.52	iron ion 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:0009987	0.82	cellular process
GO:0044699	0.76	single-organism process
GO:0008152	0.71	metabolic process
GO:0071704	0.70	organic substance metabolic process
GO:0044238	0.70	primary metabolic process
GO:0044237	0.70	cellular metabolic process
GO:0044763	0.67	single-organism cellular process
GO:0043170	0.66	macromolecule metabolic process
GO:0006810	0.66	transport
GO:0065007	0.63	biological regulation
GO:0050789	0.63	regulation of biological process
GO:0044767	0.63	single-organism developmental process
GO:0048856	0.62	anatomical structure development
GO:0044707	0.62	single-multicellular organism process
GO:0044249	0.62	cellular biosynthetic process
GO:0016043	0.62	cellular component organization
GO:0015031	0.62	protein transport
GO:0050794	0.61	regulation of cellular process
GO:0022414	0.61	reproductive process
GO:0006996	0.61	organelle organization
GO:2000026	0.60	regulation of multicellular organismal development
GO:0051241	0.60	negative regulation of multicellular organismal process
GO:0051093	0.60	negative regulation of developmental process
GO:0048522	0.60	positive regulation of cellular process
GO:0044765	0.60	single-organism transport
GO:0007165	0.60	signal transduction
GO:2001222	0.59	regulation of neuron migration
GO:2001169	0.59	regulation of ATP biosynthetic process
GO:2000736	0.59	regulation of stem cell differentiation
GO:1905050	0.59	positive regulation of metallopeptidase activity
GO:1904683	0.59	regulation of metalloendopeptidase activity
GO:1903580	0.59	positive regulation of ATP metabolic process
GO:1903579	0.59	negative regulation of ATP metabolic process
GO:1903508	0.59	positive regulation of nucleic acid-templated transcription
GO:1903427	0.59	negative regulation of reactive oxygen species biosynthetic process
GO:1902893	0.59	regulation of pri-miRNA transcription from RNA polymerase II promoter
GO:1902593	0.59	single-organism nuclear import
GO:1901214	0.59	regulation of neuron death
GO:1900373	0.59	positive regulation of purine nucleotide biosynthetic process
GO:0098727	0.59	maintenance of cell number
GO:0097305	0.59	response to alcohol
GO:0090559	0.59	regulation of membrane permeability
GO:0071378	0.59	cellular response to growth hormone stimulus
GO:0071354	0.59	cellular response to interleukin-6
GO:0060964	0.59	regulation of gene silencing by miRNA
GO:0060148	0.59	positive regulation of posttranscriptional gene silencing
GO:0051198	0.59	negative regulation of coenzyme metabolic process
GO:0050795	0.59	regulation of behavior
GO:0050768	0.59	negative regulation of neurogenesis
GO:0048871	0.59	multicellular organismal homeostasis
GO:0048638	0.59	regulation of developmental growth
GO:0048592	0.59	eye morphogenesis
GO:0046530	0.59	photoreceptor cell differentiation
GO:0044744	0.59	protein targeting to nucleus
GO:0044703	0.59	multi-organism reproductive process
GO:0043069	0.59	negative regulation of programmed cell death
GO:0042981	0.59	regulation of apoptotic process
GO:0042531	0.59	positive regulation of tyrosine phosphorylation of STAT protein
GO:0042516	0.59	regulation of tyrosine phosphorylation of Stat3 protein
GO:0042326	0.59	negative regulation of phosphorylation
GO:0042127	0.59	regulation of cell proliferation
GO:0040033	0.59	negative regulation of translation, ncRNA-mediated
GO:0035264	0.59	multicellular organism growth
GO:0033993	0.59	response to lipid
GO:0033500	0.59	carbohydrate homeostasis
GO:0030336	0.59	negative regulation of cell migration
GO:0019221	0.59	cytokine-mediated signaling pathway
GO:0017038	0.59	protein import
GO:0014070	0.59	response to organic cyclic compound
GO:0010950	0.59	positive regulation of endopeptidase activity
GO:0010728	0.59	regulation of hydrogen peroxide biosynthetic process
GO:0010727	0.59	negative regulation of hydrogen peroxide metabolic process
GO:0010677	0.59	negative regulation of cellular carbohydrate metabolic process
GO:0010628	0.59	positive regulation of gene expression
GO:0010001	0.59	glial cell differentiation
GO:0009895	0.59	negative regulation of catabolic process
GO:0008593	0.59	regulation of Notch signaling pathway
GO:0007631	0.59	feeding behavior
GO:0007417	0.59	central nervous system development
GO:0007169	0.59	transmembrane receptor protein tyrosine kinase signaling pathway
GO:0007049	0.59	cell cycle
GO:0007006	0.59	mitochondrial membrane organization
GO:0006839	0.59	mitochondrial transport
GO:0006110	0.59	regulation of glycolytic process
GO:0002526	0.59	acute inflammatory response
GO:0022607	0.54	cellular component assembly
GO:0019538	0.54	protein metabolic process
GO:0051186	0.53	cofactor metabolic process
GO:0016192	0.53	vesicle-mediated transport
GO:0055072	0.52	iron ion homeostasis
GO:0051604	0.52	protein maturation
GO:0051188	0.52	cofactor biosynthetic process
GO:0046916	0.52	cellular transition metal ion homeostasis
GO:0032940	0.52	secretion by cell
GO:0031163	0.52	metallo-sulfur cluster assembly
GO:0006790	0.52	sulfur compound metabolic process

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:0045171	1.00	intercellular bridge
GO:0015630	1.00	microtubule cytoskeleton

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	0.114	2e2aA	0.663	2.33	0.108	0.800	2.7.1.69	NA
2	0.101	3k1sA	0.654	2.59	0.052	0.817	2.7.1.69	NA
3	0.066	3eabA	0.526	2.80	0.085	0.704	3.6.4.3	NA
4	0.066	1cxzB	0.482	2.91	0.145	0.626	2.7.11.13	NA
5	0.060	3e08A	0.640	3.92	0.096	1.000	1.13.11.11	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:

No Binding sites was predicted

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

	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.