D-I-TASSER Q96FV9-D4

D-I-TASSER results for Q96FV9-D4

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

Input Sequence in FASTA format

>Q96FV9 (129 residues)
TSDTKPTRIIRKRTAPEDFLGKGPTKKILMGNEELTRLWNLCPDNMEACKSETREHMPTL
EEFFEEAIEQADPENMVENEYKAVNNSNYGWRALRLLARRSPHFFQPTNQQFKSLPEYLE
NMVIKLAKE

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 \| \| \| \| \| \| TSDTKPTRIIRKRTAPEDFLGKGPTKKILMGNEELTRLWNLCPDNMEACKSETREHMPTLEEFFEEAIEQADPENMVENEYKAVNNSNYGWRALRLLARRSPHFFQPTNQQFKSLPEYLENMVIKLAKE
Prediction	CCCCCCCCCCCCCCCCHHHCCCCCCCCSSCCCHHHHHHHHCCCCCHHHCCCHHHHCCCCHHHHHHHHHHHCCHHHCCHHHHHHHCCCHHHHHHHHHHHHHCHHHCCCCCCCCCCHHHHHHHHHHHHHCC
Confidence	987799864213677401113464443334988999887238751654152332128999999999999649443655776541131257899999996090221455666665689999999998419
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 \| \| \| \| \| \| TSDTKPTRIIRKRTAPEDFLGKGPTKKILMGNEELTRLWNLCPDNMEACKSETREHMPTLEEFFEEAIEQADPENMVENEYKAVNNSNYGWRALRLLARRSPHFFQPTNQQFKSLPEYLENMVIKLAKE
Prediction	866664564566463465157454623130237304501623574174144752633440451155115524475424762453656313120010003523520343464355145204402442368
	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

                   |                   |                   |                   |                   |                   |

SS
Seq

CCCCCCCCCCCCCCCCHHHCCCCCCCCSSCCCHHHHHHHHCCCCCHHHCCCHHHHCCCCHHHHHHHHHHHCCHHHCCHHHHHHHCCCHHHHHHHHHHHHHCHHHCCCCCCCCCCHHHHHHHHHHHHHCC
TSDTKPTRIIRKRTAPEDFLGKGPTKKILMGNEELTRLWNLCPDNMEACKSETREHMPTLEEFFEEAIEQADPENMVENEYKAVNNSNYGWRALRLLARRSPHFFQPTNQQFKSLPEYLENMVIKLAKE

4uylA1

0.10

3.72

0.48

CEthreader

LRSYVPLITDEVESFVKNSPAFQGHKGVFDVCKTIAEITIYTASRSLQGKEVRSKFDSTFAELYHNLDMGFAPINFMHNRKRDAAQRKLTETYMEIIKARSEDMVWNLMSCVYKDEEIAHMMIALLMAG

7btsA

0.04

2.05

0.58

EigenThreader

RNTNGVITQDVDAAVRGILRNAKLKPVYDSLDAVRRAALINMVFQMGITTFRTGTWALIVLLIVAGNVLVIVAIAKIMSLASADLVMGLLVVPFGATIVVWGFFCELWTSVDVLCVTASIETLCVIALD

5y6pa2

0.10

0.09

3.49

0.53

FFAS-3D

ASAGSPLVKPKRTASMSAIMQAEQQDRF-LQLGELNEIVAFLNSGSKRLEIANV-ISNNSNLMVSKAADKIFNVVRYGSTRMQKRDLDWFLRALREMRKVAVTLFDNDSASQELVKEYFNVIINEFDQ-

2ojeD1

0.14

0.12

4.24

0.74

SPARKS-K

--SMKLRVENPKKAQKHFVQNLNN---VVFTNKELEDIYNLSN-------KEETKEV--LKLFKLKVNQFYRHAFGIVNDYNGLLEYKEIFNMMFLKLSVVFDTQRKEANNVKRNIAILDEIMAKADND

5cwoA

0.13

0.09

2.96

0.49

CNFpred

---------------------------------EVEKVAQRAEEGNPDLRDS----AKELRRAVEEAIEEAKKQGNPELVEWVARAAKVAAEVIKVAIQANRDLFRA-------ALELVRAVIEAIEEA

5fnoA

0.05

0.04

1.89

0.83

DEthreader

ATLLGISDQWEAQSLRTDAAKVANIFVYQIARGQSENYT----NNNWLLAK--IMFNNDLFHGQIFHVAPHAIEIVHMMLTGCAHH-VLNGEPVASGVMHPSVQVTLA--NRPNIP--SV---------

4jspB

0.05

0.04

1.86

0.71

MapAlign

-----------------VDPSRQLDHPLPTVHPQVTYAY-----MKNMWKSARKDAFM-QHFVQTMQQQAHAIATEDQQHKQELH-KLMARCFLKLGEWQLIPKVLQYYSAATEHDKAWHAWAVMNFEA

4didB

0.13

0.12

4.30

0.58

MUSTER

---ARPEIIVLREPGATWGNYLQHQKAS---NHSLHNLYNLQRDLLTVAATVLGKQDPVLTSMANQMELAKVKADRPATKQEEAAAKALKKNLIELIAARQQQDGLPAKEAHRFAAVAFRDAQVKQLNN

7apxB

0.16

0.11

3.60

2.44

HHsearch

FQNFRISKEKPPPAFD---ETFKKFTFIKMGNKLINNVWKIP-TGLDKIEQEV----KKPEGVY---------------------EIIRQWQTLRFLRSRYLFDFDKVNE-KTGVD-------------

1e6vA1

0.09

3.30

0.46

CEthreader

AAMQQMWDDIRRTNMGEMLPARRARGENEPGGVPFGVLADCVQTMRKYPDDPAKVALEVLDDYVYYGLEYVIAEAEPSMDVVKDVATEVTLYGLEQYERYPAAMETHFGGSQRAVCAAAAGCSTAFATG

(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	0.5899

(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	5fx8A	0.54	3.99	0.067	0.861	model1_5fx8A.pdb.gz
2	5fnoA	0.54	4.16	0.025	0.884	model1_5fnoA.pdb.gz
3	3qe7A	0.53	4.24	0.049	0.845	model1_3qe7A.pdb.gz
4	2p0mA2	0.51	4.63	0.067	0.891	model1_2p0mA2.pdb.gz
5	1no3A2	0.51	4.50	0.026	0.853	model1_1no3A2.pdb.gz
6	3d3lA	0.51	4.03	0.047	0.830	model1_3d3lA.pdb.gz
7	5medA	0.50	4.52	0.026	0.837	model1_5medA.pdb.gz
8	6ns2A	0.50	4.58	0.034	0.861	model1_6ns2A.pdb.gz
9	1j36A	0.49	4.73	0.053	0.853	model1_1j36A.pdb.gz
10	5d06A2	0.49	4.17	0.068	0.791	model1_5d06A2.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	0.60	catalytic activity
GO:0016491	0.58	oxidoreductase activity
GO:0016701	0.57	oxidoreductase activity, acting on single donors with incorporation of molecular oxygen
GO:1901363	0.56	heterocyclic compound binding
GO:0097159	0.56	organic cyclic compound binding
GO:0003676	0.50	nucleic acid 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	1.00	cellular process
GO:0006950	1.00	response to stress
GO:0006406	1.00	mRNA export from nucleus
GO:0033554	0.94	cellular response to stress
GO:0044260	0.93	cellular macromolecule metabolic process
GO:0044238	0.93	primary metabolic process
GO:0090304	0.92	nucleic acid metabolic process
GO:0065007	0.91	biological regulation
GO:0050789	0.91	regulation of biological process
GO:0060255	0.89	regulation of macromolecule metabolic process
GO:0010605	0.88	negative regulation of macromolecule metabolic process
GO:0010468	0.88	regulation of gene expression
GO:0050794	0.85	regulation of cellular process
GO:0048518	0.84	positive regulation of biological process
GO:0080134	0.83	regulation of response to stress
GO:0051239	0.83	regulation of multicellular organismal process
GO:0051172	0.83	negative regulation of nitrogen compound metabolic process
GO:0050776	0.83	regulation of immune response
GO:0048522	0.83	positive regulation of cellular process
GO:0045786	0.83	negative regulation of cell cycle
GO:0031324	0.83	negative regulation of cellular metabolic process
GO:0006355	0.83	regulation of transcription, DNA-templated
GO:2000002	0.82	negative regulation of DNA damage checkpoint
GO:0048297	0.82	negative regulation of isotype switching to IgA isotypes
GO:0032786	0.82	positive regulation of DNA-templated transcription, elongation
GO:0031297	0.82	replication fork processing
GO:0044699	0.68	single-organism process
GO:0044763	0.67	single-organism cellular process
GO:0051704	0.65	multi-organism process
GO:0016032	0.59	viral process
GO:0046784	0.58	viral mRNA export from host cell nucleus
GO:0006915	0.58	apoptotic process
GO:0016070	0.57	RNA metabolic process
GO:0006396	0.50	RNA processing

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:0000347	1.00	THO complex
GO:0043231	0.93	intracellular membrane-bounded organelle
GO:0005634	0.92	nucleus
GO:0000445	0.73	THO complex part of transcription export complex
GO:0044421	0.71	extracellular region part
GO:0005654	0.71	nucleoplasm
GO:0000346	0.71	transcription export complex
GO:0005737	0.70	cytoplasm
GO:0045171	0.69	intercellular bridge
GO:0000784	0.69	nuclear chromosome, telomeric region

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	3d3lA	0.506	4.03	0.047	0.830	1.13.11.31	NA
2	0.060	3bkkA	0.478	4.75	0.054	0.822	3.4.15.1	NA
3	0.060	1rx0A	0.460	4.10	0.032	0.721	1.3.99.-	NA
4	0.060	2r0nA	0.427	4.52	0.056	0.729	1.3.99.7	NA
5	0.060	2qz6A	0.487	4.32	0.073	0.791	3.5.2.6	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	0.01	1xwjA	0.374	4.79	0.088	0.651	0.10	III	complex1.pdb.gz	12,16,20,23
2	0.01	3s90B	0.375	4.83	0.011	0.643	0.13	III	complex2.pdb.gz	22,24,91,102,115
3	0.01	2iagA	0.481	4.70	0.065	0.814	0.11	HEM	complex3.pdb.gz	117,119,122,123,127
4	0.01	1zvzA	0.370	4.84	0.089	0.651	0.18	III	complex4.pdb.gz	30,31,94,101
5	0.01	1loxA	0.470	4.56	0.080	0.798	0.17	RS7	complex5.pdb.gz	90,94,97,102
6	0.01	2ibfA	0.374	4.82	0.078	0.659	0.27	III	complex6.pdb.gz	43,91,98
7	0.01	1zw2A	0.352	4.59	0.114	0.612	0.18	III	complex7.pdb.gz	19,22,23,90,116
8	0.01	1t01A	0.371	4.87	0.087	0.667	0.17	III	complex8.pdb.gz	24,31,98
9	0.01	3s90A	0.383	5.03	0.054	0.698	0.16	III	complex9.pdb.gz	31,97,101
10	0.01	1zw3A	0.371	4.87	0.088	0.667	0.15	III	complex10.pdb.gz	24,27,28,94,98,101

	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.