D-I-TASSER Q5R3I4-D1

D-I-TASSER results for Q5R3I4-D1

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

Input Sequence in FASTA format

>Q5R3I4 (106 residues)
MAAASPLRDCQAWKDARLPLSTTSNEACKLFDATLTQYVKWTNDKSLGGIEGCLSKLKAA
DPTFVMGHAMATGLVLIGTGSSVKLDKELDLAVKTMVEISRTQPLT

Predicted Secondary Structure

Sequence	20 40 60 80 100 \| \| \| \| \| MAAASPLRDCQAWKDARLPLSTTSNEACKLFDATLTQYVKWTNDKSLGGIEGCLSKLKAADPTFVMGHAMATGLVLIGTGSSVKLDKELDLAVKTMVEISRTQPLT
Prediction	CCCCHHHHHHHHHHHCCCCCCCCCHHHHHHHHHHHHHHHHCCCCCCCCCHHHHHHHHHHCCCHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHCCCCC
Confidence	9861256778999972987666752899999999999850125887665799999998459178999999976543027963123289999999999997127899
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 \| \| \| \| \| MAAASPLRDCQAWKDARLPLSTTSNEACKLFDATLTQYVKWTNDKSLGGIEGCLSKLKAADPTFVMGHAMATGLVLIGTGSSVKLDKELDLAVKTMVEISRTQPLT
Prediction	8645542541640474615142445420421321034214245363142254115404744142010301133033224543342264045304402523655648
	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

CCCCHHHHHHHHHHHCCCCCCCCCHHHHHHHHHHHHHHHHCCCCCCCCCHHHHHHHHHHCCCHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHCCCCC
MAAASPLRDCQAWKDARLPLSTTSNEACKLFDATLTQYVKWTNDKSLGGIEGCLSKLKAADPTFVMGHAMATGLVLIGTGSSVKLDKELDLAVKTMVEISRTQPLT

6bqsA

0.07

2.67

1.17

DEthreader

------AAYYTAYCRII-----GGDLSEIACLRSMAASARLLPRQTYAESSRQLAVALEANPANPRAYFLQAQSLLYTPAQGGGKD-KALPFAEKSVSCYAAATVS

6vl6A

0.09

0.08

3.20

0.73

SPARKS-K

NLAEKMYKAGNAMYRKG-----QYTIAIIAYTLALLLGNAAYKKGEYDEAIEAYQKALELDPNNAEAWYNLGNAYYKQGD-----YDEAIEYYKKALRLDPRNVDA

5dseA

0.11

0.10

3.71

0.50

MapAlign

-----TIPLLAAKLCMEATVVTSEFKAKGYLALGLTYSLQAGMQEVLQKALLAFQRAHSLSPTDHQAAFYLALQLAISR-----QIPEALGYVRQALQLQGDDANS

7cc7A

0.06

2.53

0.31

CEthreader

LHRGDEQGKREGFQLLLNNKLVYGSRQDFLWRLARAYSDMCELTEYALDGKEEAEAALEKGDESADCHLWYAVLCGQLAESIQRSGFSFKEHVDKAIALQPENPMA

3ly7A

0.15

0.14

4.79

0.55

MUSTER

KALNQPWP--QRMQETLQKILPHRGALLTNFYQAHDYLLHGD-DKSLNRASELLGEIVQSSPEFTYARAEKALVDIVRHSQHPLDEKQLAALNTEIDNIVPELNNL

3ly7A2

0.14

0.11

3.86

0.78

HHsearch

--------------------LPHRGALLTNFYQAHDYLLHGDD-KSLNRASELLGEIVQSSPEFTYARAEKALVDIVRHSQHPLDEKQLAALNTEIDNIVTLPELN

3ly7A2

0.17

0.13

4.35

0.83

FFAS-3D

----------------------HRGALLTNFYQA-HDYLLHGDDKSLNRASELLGEIVQSSPEFTYARAEKALVDIVRHSQHPLDEKQLAALNTEIDNIVTLPELN

3qwvA2

0.08

2.99

0.50

EigenThreader

SPPQARNVIEEFRRAKHYKSVFNVYMLHMMYQAMGVCLYMQD----WEGALKYGQKIIKPHYPVASMWLKLGRLYMGL-ENKAAGEKALKKAIAIMEVAHGKDHPY

3ly7A

0.15

0.11

3.82

0.64

CNFpred

------------------------GALLTNFYQAHDYLLHGDD-KSLNRASELLGEIVQSSPEFTYARAEKALVDIVRHSQHPLDEKQLAALNTEIDNIVTLPELN

6r80A

0.09

0.08

2.91

1.17

DEthreader

DLQEKLHNA-------------RFEKAVYYLDAVVSFIECGNSPFPYSETVDLIKYT-KLKYKTVLCLRCESLLYLRLFKKVTSNFLYATEIWDQAEQLSKEQEFD

(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	0.7184

(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	6bqsA	0.71	2.55	0.057	0.887	model1_6bqsA.pdb.gz
2	4l7tA	0.71	2.88	0.047	0.924	model1_4l7tA.pdb.gz
3	3fdhA	0.70	2.61	0.071	0.859	model1_3fdhA.pdb.gz
4	6t5hB	0.69	2.97	0.059	0.887	model1_6t5hB.pdb.gz
5	4bujB	0.68	2.65	0.079	0.840	model1_4bujB.pdb.gz
6	6zwmA	0.68	3.04	0.066	0.877	model1_6zwmA.pdb.gz
7	3myvA	0.68	2.76	0.060	0.868	model1_3myvA.pdb.gz
8	2npmA	0.68	3.01	0.050	0.887	model1_2npmA.pdb.gz
9	3lewA	0.66	2.68	0.050	0.849	model1_3lewA.pdb.gz
10	3ehnA	0.63	2.49	0.094	0.802	model1_3ehnA.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	0.66	catalytic activity
GO:0016740	0.60	transferase activity
GO:0098772	0.58	molecular function regulator
GO:0036094	0.58	small molecule binding
GO:1901981	0.56	phosphatidylinositol phosphate binding
GO:0033218	0.56	amide binding
GO:0030246	0.56	carbohydrate binding
GO:0030234	0.56	enzyme regulator activity
GO:0016758	0.56	transferase activity, transferring hexosyl groups
GO:0010485	0.56	H4 histone acetyltransferase activity
GO:0008194	0.56	UDP-glycosyltransferase 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:0044699	0.76	single-organism process
GO:0009987	0.74	cellular process
GO:0008152	0.72	metabolic process
GO:0065007	0.70	biological regulation
GO:0050789	0.70	regulation of biological process
GO:0071704	0.68	organic substance metabolic process
GO:0050794	0.68	regulation of cellular process
GO:0044237	0.67	cellular metabolic process
GO:0048583	0.66	regulation of response to stimulus
GO:0044763	0.66	single-organism cellular process
GO:0044238	0.65	primary metabolic process
GO:0044710	0.63	single-organism metabolic process
GO:0044260	0.63	cellular macromolecule metabolic process
GO:0048519	0.62	negative regulation of biological process
GO:0051179	0.61	localization
GO:0048856	0.61	anatomical structure development
GO:0044767	0.61	single-organism developmental process
GO:0034641	0.61	cellular nitrogen compound metabolic process
GO:0009966	0.61	regulation of signal transduction
GO:1901576	0.60	organic substance biosynthetic process
GO:0080134	0.60	regulation of response to stress
GO:0044281	0.60	small molecule metabolic process
GO:0044249	0.60	cellular biosynthetic process
GO:0006139	0.60	nucleobase-containing compound metabolic process
GO:0002682	0.60	regulation of immune system process
GO:1902531	0.59	regulation of intracellular signal transduction
GO:1901575	0.59	organic substance catabolic process
GO:0048585	0.59	negative regulation of response to stimulus
GO:0048523	0.59	negative regulation of cellular process
GO:0034645	0.59	cellular macromolecule biosynthetic process
GO:0019538	0.59	protein metabolic process
GO:0007165	0.59	signal transduction
GO:0002684	0.59	positive regulation of immune system process
GO:0051641	0.58	cellular localization
GO:0048513	0.58	animal organ development
GO:0010941	0.58	regulation of cell death
GO:0010468	0.58	regulation of gene expression
GO:0006996	0.58	organelle organization
GO:0006464	0.58	cellular protein modification process
GO:1901564	0.57	organonitrogen compound metabolic process
GO:0065009	0.57	regulation of molecular function
GO:0051716	0.57	cellular response to stimulus
GO:0051128	0.57	regulation of cellular component organization
GO:0046578	0.57	regulation of Ras protein signal transduction
GO:0032880	0.57	regulation of protein localization
GO:0019637	0.57	organophosphate metabolic process
GO:0010605	0.57	negative regulation of macromolecule metabolic process
GO:0006796	0.57	phosphate-containing compound metabolic process
GO:0006355	0.57	regulation of transcription, DNA-templated
GO:0006090	0.57	pyruvate metabolic process
GO:2000379	0.56	positive regulation of reactive oxygen species metabolic process
GO:1903829	0.56	positive regulation of cellular protein localization
GO:1903578	0.56	regulation of ATP metabolic process
GO:1903426	0.56	regulation of reactive oxygen species biosynthetic process
GO:1903321	0.56	negative regulation of protein modification by small protein conjugation or removal
GO:1901071	0.56	glucosamine-containing compound metabolic process
GO:1900180	0.56	regulation of protein localization to nucleus
GO:1900076	0.56	regulation of cellular response to insulin stimulus
GO:1900037	0.56	regulation of cellular response to hypoxia
GO:0090317	0.56	negative regulation of intracellular protein transport
GO:0090313	0.56	regulation of protein targeting to membrane
GO:0071396	0.56	cellular response to lipid
GO:0071331	0.56	cellular response to hexose stimulus
GO:0071229	0.56	cellular response to acid chemical
GO:0071219	0.56	cellular response to molecule of bacterial origin
GO:0070206	0.56	protein trimerization
GO:0061085	0.56	regulation of histone H3-K27 methylation
GO:0051569	0.56	regulation of histone H3-K4 methylation
GO:0051291	0.56	protein heterooligomerization
GO:0051260	0.56	protein homooligomerization
GO:0051196	0.56	regulation of coenzyme metabolic process
GO:0051129	0.56	negative regulation of cellular component organization
GO:0050790	0.56	regulation of catalytic activity
GO:0048311	0.56	mitochondrion distribution
GO:0048017	0.56	inositol lipid-mediated signaling
GO:0045893	0.56	positive regulation of transcription, DNA-templated
GO:0044093	0.56	positive regulation of molecular function
GO:0043967	0.56	histone H4 acetylation
GO:0043470	0.56	regulation of carbohydrate catabolic process
GO:0043467	0.56	regulation of generation of precursor metabolites and energy
GO:0043413	0.56	macromolecule glycosylation
GO:0042327	0.56	positive regulation of phosphorylation
GO:0042326	0.56	negative regulation of phosphorylation
GO:0033135	0.56	regulation of peptidyl-serine phosphorylation
GO:0032526	0.56	response to retinoic acid
GO:0032496	0.56	response to lipopolysaccharide
GO:0031667	0.56	response to nutrient levels
GO:0031396	0.56	regulation of protein ubiquitination
GO:0031062	0.56	positive regulation of histone methylation
GO:0030852	0.56	regulation of granulocyte differentiation
GO:0030162	0.56	regulation of proteolysis
GO:0018023	0.56	peptidyl-lysine trimethylation
GO:0016601	0.56	Rac protein signal transduction
GO:0012501	0.56	programmed cell death
GO:0010799	0.56	regulation of peptidyl-threonine phosphorylation
GO:0009749	0.56	response to glucose
GO:0009636	0.56	response to toxic substance
GO:0009101	0.56	glycoprotein biosynthetic process
GO:0008361	0.56	regulation of cell size
GO:0008286	0.56	insulin receptor signaling pathway
GO:0007623	0.56	circadian rhythm
GO:0007420	0.56	brain development
GO:0006357	0.56	regulation of transcription from RNA polymerase II promoter
GO:0006111	0.56	regulation of gluconeogenesis
GO:0006096	0.56	glycolytic process
GO:0002763	0.56	positive regulation of myeloid leukocyte differentiation
GO:0001678	0.56	cellular glucose homeostasis

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:0070062	1.00	extracellular exosome
GO:0044464	0.75	cell part
GO:0044424	0.63	intracellular part

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	2epoB	0.561	3.59	0.058	0.868	3.2.1.52	32
2	0.060	2c0lA	0.633	3.11	0.063	0.802	2.3.1.176	46
3	0.060	2f4eA	0.268	5.07	0.061	0.519	5.2.1.8	47
4	0.060	2vn7A	0.539	3.45	0.087	0.840	3.2.1.3	NA
5	0.060	1ksdA	0.551	3.73	0.108	0.830	3.2.1.4	64

	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	0.26	3fp4A	0.696	2.45	0.119	0.840	0.75	III	complex1.pdb.gz	31,35,38,54,66,71
2	0.09	2c2lB	0.655	2.68	0.104	0.821	0.49	III	complex2.pdb.gz	32,35,40,66,70,71
3	0.07	2c63B	0.681	2.84	0.079	0.877	0.45	III	complex3.pdb.gz	38,69,70,73
4	0.07	3e6yB	0.600	2.89	0.090	0.840	0.58	III	complex4.pdb.gz	31,38,39,66,69,70,73,77
5	0.02	1hz40	0.639	2.72	0.071	0.840	0.72	III	complex5.pdb.gz	50,70,73,77
6	0.02	1fchA	0.625	2.74	0.052	0.783	0.70	III	complex6.pdb.gz	28,29,31,32,68,70
7	0.01	1qz2A	0.627	2.92	0.041	0.802	0.46	III	complex7.pdb.gz	42,73,76
8	0.01	2fi70	0.633	2.31	0.031	0.774	0.49	III	complex8.pdb.gz	33,49,52,53,56

	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.