D-I-TASSER Q9BT04-D3

D-I-TASSER results for Q9BT04-D3

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

Input Sequence in FASTA format

>Q9BT04 (134 residues)
ALPSGFPLHTDILGLLLLHLELKRCLFTVEPLGDKEPSPEQRRRLLRNFYTLVTSTHFPP
EPGPPEKTEDEVYQAQLPRACYLVLGTEEPGTGVRLVALQLGLRRLLLLLSPQSPTHGLR
SLATHTLHALTPLL

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 \| \| \| \| \| \| ALPSGFPLHTDILGLLLLHLELKRCLFTVEPLGDKEPSPEQRRRLLRNFYTLVTSTHFPPEPGPPEKTEDEVYQAQLPRACYLVLGTEEPGTGVRLVALQLGLRRLLLLLSPQSPTHGLRSLATHTLHALTPLL
Prediction	CCCCCCCCCHHHHSSSSSSCCCCSSSSSSCCCCCCCCCHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCSSSSSSSSCCCCCSSSSSSSCCCCSSSSSSCCCCCHHHHHHHHHHHHHHHHHCC
Confidence	99987767863431234515553578875678888875899999999999998853157888972223566554567641578752112678517999973992799997499971799999999999974129
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 \| \| \| \| \| \| ALPSGFPLHTDILGLLLLHLELKRCLFTVEPLGDKEPSPEQRRRLLRNFYTLVTSTHFPPEPGPPEKTEDEVYQAQLPRACYLVLGTEEPGTGVRLVALQLGLRRLLLLLSPQSPTHGLRSLATHTLHALTPLL
Prediction	84367151344000000023644300102433667644453025003401430243313455555554556455454343223233423246313020243542100000244222300230044015303646
	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

CCCCCCCCCHHHHSSSSSSCCCCSSSSSSCCCCCCCCCHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCSSSSSSSSCCCCCSSSSSSSCCCCSSSSSSCCCCCHHHHHHHHHHHHHHHHHCC
ALPSGFPLHTDILGLLLLHLELKRCLFTVEPLGDKEPSPEQRRRLLRNFYTLVTSTHFPPEPGPPEKTEDEVYQAQLPRACYLVLGTEEPGTGVRLVALQLGLRRLLLLLSPQSPTHGLRSLATHTLHALTPLL

5u47A2

0.10

0.09

3.34

1.17

DEthreader

SLQTFLTMDFMTASATVVNAKTGEILTTQRPTKKGYDWVN-RLYTQVQMLRAFTAISNIMVIG----K--SK-QAASTRMTVKS--GTAQVETLNSVVAMVPEYIMYVTVQEPWNNNFFATVVNPVLEEAMSMG

1tvfA1

0.06

2.57

1.08

MapAlign

QYGYAGLSAAYPTSAVNVSQTGQLLYQYNILYPGQVWTIADLLQIARDYAILDLHVIKHAVTYYTFNFSLEGAKMSLPGTDGLKTG--SSDTANYNHTITTKRINQVIMGAYLGGEKQRNMMGNALMERSF---

1vt4I3

0.11

0.10

3.80

1.20

HHsearch

ALHRSIVDHYNIPKTFDSDDLIPPYLDQYFYSHIHHLKNIEHPERMTLDFRFLEQKIRHDSTAWASGSILNTLQQLKFYKPYICDNDPKYE---RLVAILLPKIEENLICSKYTDLLRIAAIFEEAHKQVQRGG

6ekkA1

0.07

0.06

2.41

0.89

CEthreader

GSRIKQNPETTFEVYVEVAYD-PEVQRQFPED----YSDQEVLQTLTKFCF---------------------PFYVDVGQNFTFVLTDIDSKQRFGFCRLSSKSCFCILSYLPW-FEVFYKLLNILADYTTKRQ

3cueM

0.06

0.05

2.29

0.88

EigenThreader

----------AIETILVINKSGGLIYQRNFTNDEQKLNSNEYLILASTLHGVFAIASQLTIPYIDDFFKEPFTNWNKSGLRQLCTD------QFTMFIYQTTGLKFVAISSSVMNIQIADNFLRKVYCLYSDYV

1j3wB

0.13

0.11

3.88

0.53

FFAS-3D

-VEPSLVLYGGARYALLIDRKGFVLAHKEALWAPKPPPLDTLATLVAGNAAATQAL---AKLLGEARFQEEVHQGERMGLYVDEAG---------------EHALLVLVFDETAPLGKVKLHGKRASEALARIA

3f73A1

0.09

0.08

3.18

0.68

SPARKS-K

LMGRRAVSKPADALRVGFYRAQETALALLRLDGAQGWP-----EFLRRALLRAFGASLRLHTLHAHPSQGLAFREEGVQAVLVLTPPMEDRNRLKALLLREGPSQILNVPLREEERHRWENALLGLLAKAGLQV

4b93A

0.06

0.04

1.66

0.74

CNFpred

-----------AILFAVVARG-TTILAKHAWCG----------GNFLEVTEQILAKIP-----------------ENNKLTYSHG-------NYLFHYICQDRIVYLCITDDDFERSRAFSFLNEVKKRFQTTY

5u47A

0.10

0.09

3.34

1.17

DEthreader

SLQTFLTMDFMTASATVVNAKTGEILTTQRPTKKGYDWVN-RLYTQVQMLRAFTAISNIMVIG----K--SK-QAASTRMTVKS--GTAQVETLNSVVAMVPEYIMYVTVQEPWNNNFFATVVNPVLEEAMSMG

4k91A1

0.07

2.73

1.08

MapAlign

----PAPPQLAAKSYVLMDGESGQVVENNFIKVGSQVSVSDLLHGARDMAVLARAIIKEFLWNNIKQPNRNLLLWRDKTVDGLKTG--HTDEAGYCLVASAQRMIAVVFGTN--SEQARAAETQKLLTYGF---

(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	0.682

(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	7q3dC3	0.81	1.28	0.939	0.858	model1_7q3dC3.pdb.gz
2	7qlaA2	0.65	3.24	0.110	0.881	model1_7qlaA2.pdb.gz
3	7q3dB	0.65	3.23	0.109	0.866	model1_7q3dB.pdb.gz
4	3ue3A	0.65	3.60	0.045	0.925	model1_3ue3A.pdb.gz
5	8c7gC	0.63	2.52	0.076	0.784	model1_8c7gC.pdb.gz
6	5u47A	0.63	3.62	0.061	0.918	model1_5u47A.pdb.gz
7	8bh1B	0.62	3.67	0.061	0.918	model1_8bh1B.pdb.gz
8	7kisA	0.62	3.72	0.047	0.910	model1_7kisA.pdb.gz
9	5lp4A	0.62	3.66	0.109	0.895	model1_5lp4A.pdb.gz
10	5uy7A	0.62	3.51	0.039	0.873	model1_5uy7A.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:0003723	1.00	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:0070925	1.00	organelle assembly
GO:0065007	0.94	biological regulation
GO:0044699	0.94	single-organism process
GO:0050794	0.93	regulation of cellular process
GO:0044763	0.92	single-organism cellular process
GO:0044767	0.91	single-organism developmental process
GO:0048704	0.90	embryonic skeletal system morphogenesis
GO:0042384	0.90	cilium assembly
GO:0010172	0.90	embryonic body morphogenesis
GO:0008589	0.90	regulation of smoothened signaling pathway
GO:0001843	0.90	neural tube closure
GO:0001736	0.90	establishment of planar polarity
GO:0048522	0.82	positive regulation of cellular process
GO:2000026	0.81	regulation of multicellular organismal development
GO:0048856	0.81	anatomical structure development
GO:0048523	0.81	negative regulation of cellular process
GO:0044707	0.81	single-multicellular organism process
GO:0032879	0.81	regulation of localization
GO:2000314	0.80	negative regulation of fibroblast growth factor receptor signaling pathway involved in neural plate anterior/posterior pattern formation
GO:0090301	0.80	negative regulation of neural crest formation
GO:0090090	0.80	negative regulation of canonical Wnt signaling pathway
GO:0045724	0.80	positive regulation of cilium assembly
GO:0035058	0.80	nonmotile primary cilium assembly
GO:0030336	0.80	negative regulation of cell migration
GO:0008285	0.80	negative regulation of cell proliferation
GO:0001942	0.80	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	0.89	membrane-bounded organelle
GO:0044421	0.86	extracellular region part
GO:0031988	0.86	membrane-bounded vesicle
GO:0070062	0.85	extracellular exosome
GO:0044464	0.79	cell part
GO:0044424	0.62	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	1k38A	0.552	3.71	0.050	0.813	3.5.2.6	NA
2	0.060	2wzxA	0.583	3.58	0.108	0.828	3.5.2.6	NA
3	0.060	1mfoA	0.553	4.01	0.099	0.813	3.5.2.6	NA
4	0.060	1m6kA	0.579	3.42	0.061	0.821	3.5.2.6	NA
5	0.060	3lezA	0.549	4.00	0.117	0.813	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	0.02	2xd1A	0.615	3.49	0.071	0.881	0.17	CEF	complex1.pdb.gz	109,120,122
2	0.02	2y2qA	0.614	3.66	0.071	0.888	0.26	Z06	complex2.pdb.gz	11,96,118,119
3	0.01	2y2qB	0.613	3.54	0.071	0.881	0.25	Z06	complex3.pdb.gz	82,98,119
4	0.01	2zc4B	0.609	3.80	0.068	0.918	0.19	TEB	complex4.pdb.gz	13,15,96,97,98
5	0.01	2jchA	0.613	3.53	0.071	0.881	0.20	PL7	complex5.pdb.gz	124,125,126
6	0.01	1k6sA	0.572	3.94	0.091	0.858	0.22	IAP	complex6.pdb.gz	41,42,45
7	0.01	1k6rA	0.578	3.85	0.091	0.851	0.15	MX1	complex7.pdb.gz	42,92,93,94
8	0.01	1h5xA	0.578	3.92	0.082	0.858	0.24	IM2	complex8.pdb.gz	82,83,84
9	0.01	2xd5A	0.615	3.65	0.071	0.888	0.20	S2D	complex9.pdb.gz	2,14,26
10	0.01	2y2jA	0.615	3.65	0.071	0.888	0.20	ZA4	complex10.pdb.gz	82,95,97

	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.