D-I-TASSER Q9BT04-D1

D-I-TASSER results for Q9BT04-D1

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

Input Sequence in FASTA format

>Q9BT04 (153 residues)
MGEEGTGGTVHLLCLAASSGVPLFCRSSRGGAPARQQLPFSVIGSLNGVHMFGQNLEVQL
SSARTENTTVVWKSFHDSITLIVLSSEVGISELRLERLLQMVFGAMVLLVGLEELTNIRN
VERLKKDLRASYCLIDSFLGDSELIGDLTQCVD

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 \| \| \| \| \| \| \| MGEEGTGGTVHLLCLAASSGVPLFCRSSRGGAPARQQLPFSVIGSLNGVHMFGQNLEVQLSSARTENTTVVWKSFHDSITLIVLSSEVGISELRLERLLQMVFGAMVLLVGLEELTNIRNVERLKKDLRASYCLIDSFLGDSELIGDLTQCVD
Prediction	CCCCCCCCCSSSSSSSCCCCCSSSSSCCCCCCCCCCCCCCCSSSSSCSSSSSSCCCCCSSSSSSCCCCSSSSSSSCCSSSSSSSSCCCCCCHHHHHHHHHHHHHHHHHHHCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHCCC
Confidence	976688871899999749980689816899877533687314554101222203568489987719948998872683999999458994178999999999877776534888753234899999998877999999987554411541369
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 \| \| \| \| \| \| \| MGEEGTGGTVHLLCLAASSGVPLFCRSSRGGAPARQQLPFSVIGSLNGVHMFGQNLEVQLSSARTENTTVVWKSFHDSITLIVLSSEVGISELRLERLLQMVFGAMVLLVGLEELTNIRNVERLKKDLRASYCLIDSFLGDSELIGDLTQCVD
Prediction	736634422020100135330100014467535546523133113230101115437140421427623000322441010000135542344304300430131000102364055354264035404400200030054353224135138
	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                 140

                   |                   |                   |                   |                   |                   |                   |

SS
Seq

CCCCCCCCCSSSSSSSCCCCCSSSSSCCCCCCCCCCCCCCCSSSSSCSSSSSSCCCCCSSSSSSCCCCSSSSSSSCCSSSSSSSSCCCCCCHHHHHHHHHHHHHHHHHHHCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHCCC
MGEEGTGGTVHLLCLAASSGVPLFCRSSRGGAPARQQLPFSVIGSLNGVHMFGQNLEVQLSSARTENTTVVWKSFHDSITLIVLSSEVGISELRLERLLQMVFGAMVLLVGLEELTNIRNVERLKKDLRASYCLIDSFLGDSELIGDLTQCVD

5lddB

0.10

0.09

3.36

1.17

DEthreader

----IIPAQLFLAIYNPATLQIVYYAT-A--STLVERERLRQIGLAQGMVEFAKSDGEPVDTIDTEKARVILVEVEEGWWILASIDLSVKPPSLLRADLLRAYDLFLLHGSS-LSSLL-ASQGRAQLVASLTRFWDHFLATWNVL--------

5mu7B

0.09

0.08

2.96

1.16

MapAlign

-------VVLAASICTRG-GKAVLARAFHD-----IKR-SRVEALLASFPK-AANSGTQHTTVEQDNVRFVYQPLD-ELYMVLITNK-QSNILQDIDTLHLFAQVVTNTC--RTLE----EREILRNAYELISAFDEIINLGYRENLTINQI-

5mu7B

0.10

0.08

3.14

1.03

CEthreader

--------VVLAASICTRGGKAVLARAFHDIKRSRV---EALLASFPKAAN----SGTQHTTVEQDNVRFVYQPL-DELYMVLITNKQ-SNILQDIDTLHLFAQVVTNTCRTLE------EREILRNAYELISAFDEIINLGYRENLTINQIK

5lddA

0.20

0.18

5.65

1.10

HHsearch

RLALWKGKLKHYLILS-SAGKPIWSRH-GD-----LSLVNSTMGVVQTIISFYEGARNPLLGFTAGKVRFVILIKG-PLYFVAISRL-RESDAQLRAQLEALYMQILSTLTLPILTNIPSTD-LRGPLQGTESLLASLADSFTKGS-------

1w63M1

0.14

0.12

4.03

1.02

EigenThreader

-------SASAVYVLDLK-GKVLICRNYRGD-----VDMSEVEHFMPILMEKEEEGMLSPILAHGG-VRFMWIKHNN-LYLVATSK-KNACVSLVFSFLYKVVQVFSEYFKE------LEEESIRDNFVIIYELLDELMDFGYPQTTDSKILQ

2hf6A

0.15

0.13

4.42

1.17

DEthreader

-AILEPSLYVAILILDN-DGDRLFAKYY-DDT-YPSVEQKAFEKNIFNKTHRT----DSEIALLEG--LTVVYKSSIDLYFYVIGS-SYENELMLMAVLNCLFDSLSQMLRKN-VE-K--R-ALLENMEGLFLAVDEIVDGVILESDPQQVVH

2hf6A

0.21

0.18

5.80

1.08

MapAlign

------LYTVAILILDN-DGDRLFAKYYDDT-----YPSVKEQKAFEKNIFNKT-HRTDSEIALLEGLTVVYKSSI-DLYFYVIGSSY-ENELMLMAVLNCLFDSLSQMLRK-NVE----KRALLENMEGLFLAVDEIVGGVILESDPQQVV-

2jktI

0.08

0.07

2.80

1.17

DEthreader

-------MIRFILIQNR-AGKTRLAKWYM--Q--FDDEKQKLIEEVHAVVTVR--DAKHTNFVEFRNFKIIYRRY-AGLYFCICVD-VNDNNLAYLEAIHNFVEVLNEYFHN-VCE-L----DLVFNFYKVYTVVDEMFLAEIRETSQTKVLK

2hf6A

0.19

0.17

5.47

0.96

SPARKS-K

LILEPSLYTVKAILILDNDGDRLFAKYYDDTYPSVKEQKAFEKNIFNKTH---RTDS---EIALLEGLTVVYKSSID-LYFYVIGSSYENE-LMLMAVLNCLFDSLSQMLEKRALLE--NM-------EGLFLAVDEIVDGPQQVVHRVALR-

2jkrM

0.15

0.12

3.99

1.08

MapAlign

-------MIGGLFIYNH-KGEVLISRVYR------DDIGRNAVDAFRNVIH-ARQQVR-SPVTNIARTSFFHVKRS-NIWLAAVTKQ-NVNAAMVFEFLYKMCDVMAAYFGK--IS----EENIKNNFVLIYELLDEILD-FGYPQNSE----

(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	0.87

(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	7q3dC	0.91	1.04	1.000	0.954	model1_7q3dC.pdb.gz
2	7qlaA	0.75	2.36	0.162	0.889	model1_7qlaA.pdb.gz
3	8c7gC	0.74	2.54	0.197	0.895	model1_8c7gC.pdb.gz
4	7qlaC	0.72	3.31	0.109	0.954	model1_7qlaC.pdb.gz
5	8c7gB	0.72	3.18	0.134	0.928	model1_8c7gB.pdb.gz
6	5lddB	0.68	3.48	0.128	0.908	model1_5lddB.pdb.gz
7	7p3xS	0.67	2.92	0.101	0.837	model1_7p3xS.pdb.gz
8	7b6xD2	0.67	3.33	0.109	0.863	model1_7b6xD2.pdb.gz
9	2hf6A	0.66	3.06	0.167	0.850	model1_2hf6A.pdb.gz
10	7b6dD	0.65	3.59	0.123	0.876	model1_7b6dD.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	0.84	heterocyclic compound binding
GO:0097159	0.84	organic cyclic compound binding
GO:0003676	0.82	nucleic acid binding
GO:0003723	0.81	RNA 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:0044699	0.96	single-organism process
GO:0044763	0.95	single-organism cellular process
GO:0065007	0.86	biological regulation
GO:0044767	0.86	single-organism developmental process
GO:0009653	0.86	anatomical structure morphogenesis
GO:0050789	0.85	regulation of biological process
GO:0016043	0.85	cellular component organization
GO:0001736	0.85	establishment of planar polarity
GO:0070925	0.84	organelle assembly
GO:0050794	0.84	regulation of cellular process
GO:0009966	0.79	regulation of signal transduction
GO:0048704	0.78	embryonic skeletal system morphogenesis
GO:0042384	0.78	cilium assembly
GO:0010172	0.78	embryonic body morphogenesis
GO:0008589	0.78	regulation of smoothened signaling pathway
GO:0001843	0.78	neural tube closure
GO:0048522	0.67	positive regulation of cellular process
GO:0048519	0.66	negative regulation of biological process
GO:0051239	0.65	regulation of multicellular organismal process
GO:0048856	0.65	anatomical structure development
GO:0048523	0.65	negative regulation of cellular process
GO:0044707	0.65	single-multicellular organism process
GO:2000026	0.64	regulation of multicellular organismal development
GO:0045595	0.64	regulation of cell differentiation
GO:0032879	0.64	regulation of localization
GO:0023057	0.64	negative regulation of signaling
GO:0022603	0.64	regulation of anatomical structure morphogenesis
GO:0010648	0.64	negative regulation of cell communication
GO:2000314	0.63	negative regulation of fibroblast growth factor receptor signaling pathway involved in neural plate anterior/posterior pattern formation
GO:0090301	0.63	negative regulation of neural crest formation
GO:0090090	0.63	negative regulation of canonical Wnt signaling pathway
GO:0045724	0.63	positive regulation of cilium assembly
GO:0035058	0.63	nonmotile primary cilium assembly
GO:0030336	0.63	negative regulation of cell migration
GO:0008285	0.63	negative regulation of cell proliferation
GO:0001942	0.63	hair follicle 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:0043226	1.00	organelle
GO:0043227	0.90	membrane-bounded organelle
GO:0044421	0.88	extracellular region part
GO:0031982	0.88	vesicle
GO:0070062	0.87	extracellular exosome
GO:0044464	0.77	cell part
GO:0044424	0.60	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	2veaA	0.489	3.97	0.055	0.706	2.7.13.3	NA
2	0.060	1vjpA	0.490	5.12	0.080	0.869	5.5.1.4	125
3	0.060	3d64A	0.494	4.80	0.028	0.824	3.3.1.1	NA
4	0.060	1qbaA	0.504	4.69	0.055	0.830	3.2.1.52	NA
5	0.060	1rypV	0.480	4.50	0.091	0.771	3.4.25.1	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	0.07	2jkrI	0.636	3.08	0.076	0.817	0.89	III	complex1.pdb.gz	16,17,75,77,79,103,104
2	0.01	3r7wD	0.509	2.49	0.049	0.621	0.41	GNP	complex2.pdb.gz	19,48,78,82
3	0.01	3h9uB	0.449	5.11	0.072	0.765	0.44	NAD	complex3.pdb.gz	114,125,131

	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.