D-I-TASSER O94919-D2

D-I-TASSER results for O94919-D2

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

Input Sequence in FASTA format

>O94919 (93 residues)
VIRALLRILCCLLKAICRVLSIPVRVLVDVATFPVYTMGAIPIVCKDIALGLGGTVSLLF
DTAFGTLGGLFQVVFSVCKRIGYKVTFDNSGEL

Predicted Secondary Structure

Sequence	20 40 60 80 \| \| \| \| VIRALLRILCCLLKAICRVLSIPVRVLVDVATFPVYTMGAIPIVCKDIALGLGGTVSLLFDTAFGTLGGLFQVVFSVCKRIGYKVTFDNSGEL
Prediction	CHHHHHHHHHHHHHHHHHHHCCCCSSSSSSSCCCSSSSSCCCHHHHHHHHHHCHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCSSCCCCCCCC
Confidence	655999999999999999976730578874047514540222367778751012246779988987636999999999985771215899989
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 \| \| \| \| VIRALLRILCCLLKAICRVLSIPVRVLVDVATFPVYTMGAIPIVCKDIALGLGGTVSLLFDTAFGTLGGLFQVVFSVCKRIGYKVTFDNSGEL
Prediction	633120301111042003124131310121343333330212310442133332331133323323322313102200442235133646567
	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

                   |                   |                   |                   |

SS
Seq

CHHHHHHHHHHHHHHHHHHHCCCCSSSSSSSCCCSSSSSCCCHHHHHHHHHHCHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCSSCCCCCCCC
VIRALLRILCCLLKAICRVLSIPVRVLVDVATFPVYTMGAIPIVCKDIALGLGGTVSLLFDTAFGTLGGLFQVVFSVCKRIGYKVTFDNSGEL

1ik9A

0.05

2.44

1.17

DEthreader

-RIHLITHFLTLTAWTGLEKVENPAEVIRELIAYALDTIAENQAKNEHLQKENERLLRDWNDVQGRFEKAVSAKEALETDLYKRFLVLNKKTR

5a63C

0.17

5.65

0.56

CEthreader

LQEVFRFAYYKLLKKADEGLAISIRQMAYVSGLSFGIISGVFSVINILADALYFLTSAFLTAAIILLHTFWGVVFFDACERRRYWALGLVVGS

6mzcK

0.10

3.61

0.52

EigenThreader

YHLARRRTLQVVVSSLLTEAGAEKASVETLTEMLQSYISEIGRSAKSYCPTLSDIVVTLVEMREKAASQRRDVERALTRFMAKTGETQSFPLI

5loiA1

0.12

4.15

0.50

FFAS-3D

-TSLLVDFADTLIDLWHQCLSGPIYHLVSLLLYTLNAVEVAPHILSSLIPVCATTCRLVALPRLNSVTQCLSVLYLAASGCLPQPLPQDT---

5uj9A3

0.12

4.19

0.71

SPARKS-K

FIRQSDLKVDENQKAYYPSIVANRWLAVRLECVGNCIVLFASLFAVILSAGLVGLSVSYSLQVTTYLNWLVRMSSEMETNIVKEYSETEKEAP

5xtcr

0.14

0.13

4.43

0.65

CNFpred

AYPFLVLSLWGMIMTSSICLRTDLKSLI-----AYSSISHMALVVTAILIQTSFTGAVILMIAHGLTSSLLFCLANSNYERTHSRIMILSQGL

4ke2A

0.06

0.05

2.33

1.17

DEthreader

--A-AVASAAKALET-IN--VAAYAAATTANTAAAAAAATATTAAAAAAAKATIDNAAAAKAAAVATAVSDAAATAATAAAVAAATEA-----

2g0dA

0.11

3.90

0.74

MapAlign

MGLAGLAGVGCILAYAHIKGYSSLSALQKIIFDAWCYGGPGISLLYLYGGLDYFVDKAEKILESAMYSGLIEICSLFKRLLNTKKFDSYMEEF

6idpA

0.11

3.84

0.47

MUSTER

LASAWTGAMLYFYYSVCRANGNTLLPG--TLMM----VTSVLNLILDPIFIFTGIDGAAIATIIAFGVGIAIVAPKVAQRQWTSYQWQDLNIS

5dfzA

0.10

0.08

2.80

0.35

HHsearch

YVNSQLGYYLLFLHLTIQIFKAPLPYRLMYYQYPLYFTDQMI-S---------KHQAKLIKAIHYFNADILQFKQILENYR------------

(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	0.5644

(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	3thfA	0.77	2.35	0.054	0.989	model1_3thfA.pdb.gz
2	3g67A	0.71	2.11	0.011	0.828	model1_3g67A.pdb.gz
3	6tgzF	0.71	2.37	0.077	0.903	model1_6tgzF.pdb.gz
4	6z9lA	0.71	2.44	0.076	0.839	model1_6z9lA.pdb.gz
5	6f1tX	0.71	2.34	0.022	0.806	model1_6f1tX.pdb.gz
6	3pikA	0.70	2.75	0.055	0.850	model1_3pikA.pdb.gz
7	4e29B	0.70	2.84	0.057	0.925	model1_4e29B.pdb.gz
8	5azoA	0.70	2.55	0.086	0.839	model1_5azoA.pdb.gz
9	6yvuB	0.70	2.14	0.043	0.796	model1_6yvuB.pdb.gz
10	2qihB	0.70	2.16	0.032	0.796	model1_2qihB.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:1901363	0.77	heterocyclic compound binding
GO:0097159	0.77	organic cyclic compound binding
GO:0003676	0.71	nucleic acid binding
GO:0003677	0.69	DNA binding
GO:0003690	0.64	double-stranded DNA binding
GO:0001191	0.64	transcriptional repressor activity, RNA polymerase II transcription factor binding
GO:0042802	0.60	identical protein binding
GO:0003682	0.60	chromatin binding
GO:0001190	0.60	transcriptional activator activity, RNA polymerase II transcription factor binding
GO:0001135	0.60	transcription factor activity, RNA polymerase II transcription factor recruiting
GO:0001084	0.60	transcription factor activity, TFIID-class binding
GO:0000981	0.60	RNA polymerase II transcription factor activity, sequence-specific DNA binding
GO:0000978	0.60	RNA polymerase II core promoter proximal region sequence-specific DNA binding
GO:0003779	0.55	actin binding
GO:0032403	0.53	protein complex binding
GO:0008134	0.53	transcription factor binding
GO:0003712	0.53	transcription cofactor 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:0009987	0.89	cellular process
GO:0071704	0.77	organic substance metabolic process
GO:0044238	0.77	primary metabolic process
GO:0044237	0.77	cellular metabolic process
GO:0044260	0.70	cellular macromolecule metabolic process
GO:0006807	0.70	nitrogen compound metabolic process
GO:0065007	0.69	biological regulation
GO:0050789	0.69	regulation of biological process
GO:1901576	0.68	organic substance biosynthetic process
GO:0044699	0.68	single-organism process
GO:0044249	0.68	cellular biosynthetic process
GO:0050794	0.67	regulation of cellular process
GO:0044763	0.66	single-organism cellular process
GO:0016043	0.66	cellular component organization
GO:0048523	0.65	negative regulation of cellular process
GO:0051128	0.64	regulation of cellular component organization
GO:0031323	0.63	regulation of cellular metabolic process
GO:0080134	0.62	regulation of response to stress
GO:0050896	0.62	response to stimulus
GO:0045944	0.62	positive regulation of transcription from RNA polymerase II promoter
GO:0043254	0.62	regulation of protein complex assembly
GO:0031324	0.62	negative regulation of cellular metabolic process
GO:0090304	0.61	nucleic acid metabolic process
GO:1903833	0.60	positive regulation of cellular response to amino acid starvation
GO:0045899	0.60	positive regulation of RNA polymerase II transcriptional preinitiation complex assembly
GO:0010691	0.60	negative regulation of ribosomal protein gene transcription from RNA polymerase II promoter in response to nutrient levels
GO:0008652	0.60	cellular amino acid biosynthetic process
GO:0001080	0.60	nitrogen catabolite activation of transcription from RNA polymerase II promoter
GO:0048869	0.58	cellular developmental process
GO:0034645	0.58	cellular macromolecule biosynthetic process
GO:0044767	0.56	single-organism developmental process
GO:1902414	0.53	protein localization to cell junction
GO:0048870	0.53	cell motility
GO:0048753	0.53	pigment granule organization
GO:0034613	0.53	cellular protein localization
GO:0032989	0.53	cellular component morphogenesis
GO:0030952	0.53	establishment or maintenance of cytoskeleton polarity
GO:0030036	0.53	actin cytoskeleton organization
GO:0001736	0.53	establishment of planar polarity
GO:0006260	0.52	DNA replication
GO:0048856	0.50	anatomical structure 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:0070062	1.00	extracellular exosome
GO:0016020	1.00	membrane
GO:0044464	0.90	cell part
GO:0044424	0.86	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	0.196	1z56A	0.602	2.35	0.055	0.763	6.5.1.1	NA
2	0.155	2h8nA	0.559	2.27	0.045	0.699	3.5.1.98	67
3	0.060	1z0hB	0.281	4.54	0.038	0.538	3.4.24.69	50
4	0.060	3g61A	0.666	3.52	0.022	0.957	3.6.3.44	NA
5	0.060	2iw5A	0.615	3.48	0.066	0.882	1.-.-.-	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	0.04	1ic20	0.689	2.07	0.051	0.785	1.00	III	complex1.pdb.gz	23,26,29,30,33,34,36,37,40,41,43,44,47,50,51,54,55,57,58,61,65,68,72,75,76,78,79,86
2	0.02	1zv8C	0.477	0.68	0.087	0.495	1.21	III	complex2.pdb.gz	43,46,49,50,53,56,57,60,61,63,64,67,68,71,74,75,78,82,85
3	0.01	1zv8A	0.506	0.74	0.020	0.527	1.23	III	complex3.pdb.gz	49,52,53,56,59,60,63,64,66,67,70,71,74,77,78
4	0.01	1zv8E	0.503	0.80	0.020	0.527	1.20	III	complex4.pdb.gz	26,29,30,32,33,36,40,43,44,47,50,51,54,58,61,65,68

	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.