D-I-TASSER A8MVW5-D2

D-I-TASSER results for A8MVW5-D2

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

Input Sequence in FASTA format

>A8MVW5 (94 residues)
PVTKPVVQIHPPSGAVEYVGNMTLTCHVEGGTRLAYQWLKNGRPVHTSSTYSFSPQNNTL
HIAPVTKEDIGNYSCLVRNPVSEMESDIIMPIIY

Predicted Secondary Structure

Sequence	20 40 60 80 \| \| \| \| PVTKPVVQIHPPSGAVEYVGNMTLTCHVEGGTRLAYQWLKNGRPVHTSSTYSFSPQNNTLHIAPVTKEDIGNYSCLVRNPVSEMESDIIMPIIY
Prediction	CCCCCSSSSCCCCSSSSCCCCSSSSSSSSCCCCCSSSSSSCCSSCCCCCCSSSSCCCCSSSSCCCCHHHCSSSSSSSSSCCCCSSSSSSSSSSC
Confidence	9689879967886899499409999991255998899999999958899889982899899932775557799999998796199999999839
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 \| \| \| \| PVTKPVVQIHPPSGAVEYVGNMTLTCHVEGGTRLAYQWLKNGRPVHTSSTYSFSPQNNTLHIAPVTKEDIGNYSCLVRNPVSEMESDIIMPIIY
Prediction	8534440445156341544551455150665350414423455505577414034763204045045545443333041433444040403134
	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

                   |                   |                   |                   |

SS
Seq

CCCCCSSSSCCCCSSSSCCCCSSSSSSSSCCCCCSSSSSSCCSSCCCCCCSSSSCCCCSSSSCCCCHHHCSSSSSSSSSCCCCSSSSSSSSSSC
PVTKPVVQIHPPSGAVEYVGNMTLTCHVEGGTRLAYQWLKNGRPVHTSSTYSFSPQNNTLHIAPVTKEDIGNYSCLVRNPVSEMESDIIMPIIY

6efzA

0.20

6.45

1.50

DEthreader

VHFPPMIWIQNQLVGAALTQNITLECQSEAYPKSINYWMKNDTIIVPGERFVPETFTMRLTIYEVDIQDFGAYRCVAKNSLGDTDG-AIKLYHI

3pxjA2

0.25

0.24

7.60

1.15

SPARKS-K

PAGFPVITQGPGTRVIEVGHTVLMTCKAIGNPTPNIYWIKNQTKVDMSNPR-YSLKDGFLQIENSREEDQGKYECVAENSMGTEHSKATNLYVK

4u7mA3

0.21

0.20

6.44

1.67

FFAS-3D

--ETPSLVVPLEDRVVSVGETVALQCKATGNPPPRITWFKGDRPLSLTERHHLTPDNQLLVVQNVVAEDAGRYTCEMSNTLGTERAHSQLSVLL

2rikA

0.24

0.23

7.31

1.62

CNFpred

AMAPPFFDLKPVSVDLALGESGTFKCHVTGTAPIKITWAKDNREIRGNYKMTLVENTATLTVLKVTKGDAGQYTCYASNV-AGKDSCSAQLGVQ

1qz1A

0.25

0.24

7.60

1.50

DEthreader

VNVPPTVQARQSIVNATALQSVTLVCDADGFPEPTMSWTKDGEPIENDEKHIFSDDSSELTIRNVDKNDEAEYVCIAENKAGEQDA-SIHLKVF

2v44A2

0.20

0.19

6.14

1.13

SPARKS-K

--QKLTFREVVSPQEFKQGEDAEVVCRVSSSPAPAVSWLYHNVTTISDNRF-AMLANNNLQILNINKSDEGIYRCEGRVEARGIDFRDIIVIVN

3dmkA

0.21

0.20

6.44

0.53

MapAlign

-FDPPVIRQAFQEETMEPGPSVFLKCVAGGNPTPEISWELDGKKIANNDRYQVGQVVSYLNITSVHANDGGLYKCIAKSKVGVAEH-SAKLNVY

3dmkA2

0.20

6.45

0.36

CEthreader

RFDPPVIRQAFQEETMEPGPSVFLKCVAGGNPTPEISWELDGKKIANNDRYQVGQVVSYLNITSVHANDGGLYKCIAKSKVGVAEHS-AKLNVY

3pxjA

0.25

0.24

7.60

0.95

MUSTER

PAGFPVITQGPGTRVIEVGHTVLMTCKAIGNPTPNIYWIKNQTKVDMSNPR-YSLKDGFLQIENSREEDQGKYECVAENSMGTEHSKATNLYVK

6iaaA2

0.21

0.20

6.41

0.41

HHsearch

--APPQFVVRPRDQIVAQGRTVTFPCETKGNPQPAVFWQKEGSQNLPNSRCSVS-PTGDLTITNIQRSDAGYYICQALTVAGSI-LAKAQLEVT

(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	0.9166

(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	3pxhA	0.92	1.20	0.226	0.989	model1_3pxhA.pdb.gz
2	1u2hA	0.92	0.98	0.174	0.979	model1_1u2hA.pdb.gz
3	3pucA	0.91	1.05	0.226	0.989	model1_3pucA.pdb.gz
4	1tlkA	0.91	1.23	0.237	0.989	model1_1tlkA.pdb.gz
5	2yd9A	0.91	1.28	0.226	0.989	model1_2yd9A.pdb.gz
6	2wwkO	0.91	1.11	0.226	0.989	model1_2wwkO.pdb.gz
7	1g1cA	0.91	1.14	0.204	0.989	model1_1g1cA.pdb.gz
8	2wwmD	0.91	1.21	0.204	0.989	model1_2wwmD.pdb.gz
9	2vraA	0.90	1.27	0.280	0.989	model1_2vraA.pdb.gz
10	3pxjA	0.90	1.21	0.250	0.979	model1_3pxjA.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:0042802	0.81	identical protein binding
GO:0003824	0.68	catalytic activity
GO:0016740	0.63	transferase activity
GO:0004872	0.63	receptor activity
GO:0038023	0.62	signaling receptor activity
GO:0016772	0.61	transferase activity, transferring phosphorus-containing groups
GO:0004888	0.61	transmembrane signaling receptor activity
GO:0005198	0.60	structural molecule activity
GO:0004672	0.60	protein kinase activity
GO:1901363	0.59	heterocyclic compound binding
GO:0097159	0.59	organic cyclic compound binding
GO:0008046	0.57	axon guidance receptor activity
GO:0043167	0.56	ion binding
GO:0008307	0.56	structural constituent of muscle
GO:0046872	0.55	metal ion binding
GO:0008092	0.55	cytoskeletal protein binding
GO:0097367	0.54	carbohydrate derivative binding
GO:0051371	0.54	muscle alpha-actinin binding
GO:0051015	0.54	actin filament binding
GO:0004674	0.54	protein serine/threonine kinase activity
GO:0097493	0.53	structural molecule activity conferring elasticity
GO:0019899	0.53	enzyme binding
GO:0019901	0.51	protein kinase binding
GO:0005524	0.51	ATP binding
GO:0005509	0.51	calcium ion binding
GO:0004713	0.51	protein tyrosine kinase activity
GO:0002020	0.51	protease binding
GO:0043621	0.50	protein self-association
GO:0031433	0.50	telethonin binding
GO:0005516	0.50	calmodulin 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	0.88	cellular process
GO:0044699	0.86	single-organism process
GO:0044763	0.78	single-organism cellular process
GO:0065007	0.68	biological regulation
GO:0032502	0.67	developmental process
GO:0050789	0.66	regulation of biological process
GO:0050794	0.65	regulation of cellular process
GO:0044767	0.64	single-organism developmental process
GO:0048869	0.56	cellular developmental process
GO:0048856	0.54	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:0044464	0.97	cell part
GO:0044424	0.70	intracellular part
GO:0044425	0.55	membrane part
GO:0044459	0.51	plasma membrane part
GO:0044444	0.49	cytoplasmic part
GO:0031224	0.49	intrinsic component of membrane
GO:0016021	0.48	integral component of membrane
GO:0031226	0.45	intrinsic component of plasma membrane
GO:0043226	0.44	organelle
GO:0005887	0.44	integral component of plasma membrane
GO:0043227	0.42	membrane-bounded organelle
GO:0097458	0.40	neuron part
GO:0042995	0.40	cell projection
GO:0044422	0.39	organelle part
GO:0043025	0.38	neuronal cell body
GO:0030424	0.38	axon
GO:0030425	0.36	dendrite
GO:0016020	0.34	membrane
GO:0043229	0.33	intracellular organelle
GO:0044446	0.32	intracellular organelle 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	0.322	2wwmD	0.905	1.21	0.204	0.989	2.7.11.1	43,71
2	0.307	1tnnA	0.716	2.39	0.250	0.936	2.7.11.1	39,59,72,85
3	0.284	2bk8A	0.848	1.39	0.222	0.957	2.7.11.1	43
4	0.258	2edwA	0.785	1.70	0.161	0.925	2.7.11.1	26,51,69,74,90
5	0.243	2gqhA	0.744	2.12	0.161	0.925	2.7.11.1	23,51,74

	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	0.06	3lafA	0.898	1.24	0.215	0.989	0.62	UUU	complex1.pdb.gz	38,40,70,72
2	0.06	2fdb1	0.864	1.54	0.228	0.979	0.61	III	complex2.pdb.gz	30,31,32,34,35,37,39,43,45,53,54,55,58,76,78,79,80,86
3	0.06	1tlk0	0.914	1.23	0.237	0.989	0.96	III	complex3.pdb.gz	3,6,29,31,33,35,36,37,45
4	0.05	2iep0	0.903	1.29	0.215	0.989	0.49	III	complex4.pdb.gz	7,8,11,25,27,29
5	0.05	2j8o0	0.888	1.20	0.217	0.979	0.47	III	complex5.pdb.gz	11,16,17,20,21,25,59
6	0.05	1evt3	0.868	1.59	0.204	0.989	0.54	III	complex6.pdb.gz	13,14,15,16,17,91,93
7	0.03	2jccL	0.841	1.59	0.089	0.957	0.44	III	complex7.pdb.gz	38,40,41,73

	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.