D-I-TASSER O95487

D-I-TASSER results for O95487

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

Summary of the Protein

Uniprot ID: O95487
Protein Name: Protein transport protein Sec24B
Gene Name: SEC24B

Input Sequence in FASTA format

>O95487 (1268 residues)
MSAPAGSSHPAASARIPPKFGGAAVSGAAAPAGPGAGPAPHQQNGPAQNQMQVPSGYGLH
HQNYIAPSGHYSQGPGKMTSLPLDTQCGDYYSALYTVPTQNVTPNTVNQQPGAQQLYSRG
PPAPHIVGSTLGSFQGAASSASHLHTSASQPYSSFVNHYNSPAMYSASSSVASQGFPSTC
GHYAMSTVSNAAYPSVSYPSLPAGDTYGQMFTSQNAPTVRPVKDNSFSGQNTAISHPSPL
PPLPSQQHHQQQSLSGYSTLTWSSPGLPSTQDNLIRNHTGSLAVANNNPTITVADSLSCP
VMQNVQPPKSSPVVSTVLSGSSGSSSTRTPPTANHPVEPVTSVTQPSELLQQKGVQYGEY
VNNQASSAPTPLSSTSDDEEEEEEDEEAGVDSSSTTSSASPMPNSYDALEGGSYPDMLSS
SASSPAPDPAPEPDPASAPAPASAPAPVVPQPSKMAKPFGYGYPTLQPGYQNATAPLISG
VQPSNPVYSGFQQYPQQYPGVNQLSSSIGGLSLQSSPQPESLRPVNLTQERNILPMTPVW
APVPNLNADLKKLNCSPDSFRCTLTNIPQTQALLNKAKLPLGLLLHPFRDLTQLPVITSN
TIVRCRSCRTYINPFVSFIDQRRWKCNLCYRVNDVPEEFMYNPLTRSYGEPHKRPEVQNS
TVEFIASSDYMLRPPQPAVYLFVLDVSHNAVEAGYLTILCQSLLENLDKLPGDSRTRIGF
MTFDSTIHFYNLQEGLSQPQMLIVSDIDDVFLPTPDSLLVNLYESKELIKDLLNALPNMF
TNTRETHSALGPALQAAFKLMSPTGGRVSVFQTQLPSLGAGLLQSREDPNQRSSTKVVQH
LGPATDFYKKLALDCSGQQTAVDLFLLSSQYSDLASLACMSKYSAGCIYYYPSFHYTHNP
SQAEKLQKDLKRYLTRKIGFEAVMRIRCTKGLSMHTFHGNFFVRSTDLLSLANINPDAGF
AVQLSIEESLTDTSLVCFQTALLYTSSKGERRIRVHTLCLPVVSSLADVYAGVDVQAAIC
LLANMAVDRSVSSSLSDARDALVNAVVDSLSAYGSTVSNLQHSALMAPSSLKLFPLYVLA
LLKQKAFRTGTSTRLDDRVYAMCQIKSQPLVHLMKMIHPNLYRIDRLTDEGAVHVNDRIV
PQPPLQKLSAEKLTREGAFLMDCGSVFYIWVGKGCDNNFIEDVLGYTNFASIPQKMTHLP
ELDTLSSERARSFITWLRDSRPLSPILHIVKDESPAKAEFFQHLIEDRTEAAFSYYEFLL
HVQQQICK

Predicted Contact and Distance Map Used in D-I-TASSER simulation

Contact Map

Distance Map

D-I-TASSER simulation is guided by the consensus contact map (left figure) and distance map (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.

Information of Domain

No. of Domain	Domain	Domain Boundary	Length of Domain	Models of Domain	Sequence
1	O95487-D1	1-49,108-137	79		MSAPAGSSHPAASARIPPKFGGAAVSGAAAPAGPGAGPAPHQQNGPAQNNQQPGAQQLYSRGPPAPHIVGSTLGSFQGA
2	O95487-D2	50-107	58		QMQVPSGYGLHHQNYIAPSGHYSQGPGKMTSLPLDTQCGDYYSALYTVPTQNVTPNTV
3	O95487-D3	138-218,563-666	185		ASSASHLHTSASQPYSSFVNHYNSPAMYSASSSVASQGFPSTCGHYAMSTVSNAAYPSVSYPSLPAGDTYGQMFTSQNAPTTLTNIPQTQALLNKAKLPLGLLLHPFRDLTQLPVITSNTIVRCRSCRTYINPFVSFIDQRRWKCNLCYRVNDVPEEFMYNPLTRSYGEPHKRPEVQNSTVEFIA
4	O95487-D4	219-562,891-992	446		VRPVKDNSFSGQNTAISHPSPLPPLPSQQHHQQQSLSGYSTLTWSSPGLPSTQDNLIRNHTGSLAVANNNPTITVADSLSCPVMQNVQPPKSSPVVSTVLSGSSGSSSTRTPPTANHPVEPVTSVTQPSELLQQKGVQYGEYVNNQASSAPTPLSSTSDDEEEEEEDEEAGVDSSSTTSSASPMPNSYDALEGGSYPDMLSSSASSPAPDPAPEPDPASAPAPASAPAPVVPQPSKMAKPFGYGYPTLQPGYQNATAPLISGVQPSNPVYSGFQQYPQQYPGVNQLSSSIGGLSLQSSPQPESLRPVNLTQERNILPMTPVWAPVPNLNADLKKLNCSPDSFRCYPSFHYTHNPSQAEKLQKDLKRYLTRKIGFEAVMRIRCTKGLSMHTFHGNFFVRSTDLLSLANINPDAGFAVQLSIEESLTDTSLVCFQTALLYTSSKGERR
5	O95487-D5	667-806	140		SSDYMLRPPQPAVYLFVLDVSHNAVEAGYLTILCQSLLENLDKLPGDSRTRIGFMTFDSTIHFYNLQEGLSQPQMLIVSDIDDVFLPTPDSLLVNLYESKELIKDLLNALPNMFTNTRETHSALGPALQAAFKLMSPTGG
6	O95487-D6	807-841,993-1268	311		RVSVFQTQLPSLGAGLLQSREDPNQRSSTKVVQHLIRVHTLCLPVVSSLADVYAGVDVQAAICLLANMAVDRSVSSSLSDARDALVNAVVDSLSAYGSTVSNLQHSALMAPSSLKLFPLYVLALLKQKAFRTGTSTRLDDRVYAMCQIKSQPLVHLMKMIHPNLYRIDRLTDEGAVHVNDRIVPQPPLQKLSAEKLTREGAFLMDCGSVFYIWVGKGCDNNFIEDVLGYTNFASIPQKMTHLPELDTLSSERARSFITWLRDSRPLSPILHIVKDESPAKAEFFQHLIEDRTEAAFSYYEFLLHVQQQICK
7	O95487-D7	842-890	49		GPATDFYKKLALDCSGQQTAVDLFLLSSQYSDLASLACMSKYSAGCIYY

Top 1 final models from D-I-TASSER

Click to view	Rank^a	Download	Estimated TM-score^b
	1	model1.pdb.gz	0.46

(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	3eh1A	0.29	5.40	0.410	0.333	model1_3eh1A.pdb.gz
2	1pcxA	0.29	5.37	0.132	0.327	model1_1pcxA.pdb.gz
3	3efoB	0.28	5.75	0.120	0.330	model1_3efoB.pdb.gz
4	3eh2A	0.28	5.79	0.120	0.325	model1_3eh2A.pdb.gz
5	2j5wA	0.27	9.35	0.043	0.412	model1_2j5wA.pdb.gz
6	1t3tA	0.27	9.52	0.038	0.408	model1_1t3tA.pdb.gz
7	4bxsV	0.27	9.80	0.040	0.418	model1_4bxsV.pdb.gz
8	2cseW	0.26	9.38	0.057	0.400	model1_2cseW.pdb.gz
9	6fb3A	0.26	9.83	0.034	0.410	model1_6fb3A.pdb.gz
10	7c6oA	0.26	9.72	0.050	0.405	model1_7c6oA.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	0.27	heterocyclic compound binding
GO:0097159	0.27	organic cyclic compound binding
GO:0005048	0.19	signal sequence binding
GO:0036094	0.18	small molecule binding
GO:0005215	0.18	transporter activity
GO:0000166	0.17	nucleotide binding
GO:0032555	0.16	purine ribonucleotide binding
GO:0032550	0.16	purine ribonucleoside binding
GO:0035639	0.15	purine ribonucleoside triphosphate binding
GO:0098772	0.13	molecular function regulator
GO:0046872	0.13	metal ion binding
GO:0032561	0.11	guanyl ribonucleotide 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	0.85	cellular process
GO:0044699	0.72	single-organism process
GO:0016043	0.69	cellular component organization
GO:0051234	0.67	establishment of localization
GO:0006810	0.66	transport
GO:0044763	0.64	single-organism cellular process
GO:0065007	0.60	biological regulation
GO:0050789	0.58	regulation of biological process
GO:0050794	0.57	regulation of cellular process
GO:0044767	0.54	single-organism developmental process

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:0044444	1.00	cytoplasmic part
GO:0044446	0.86	intracellular organelle part
GO:0044425	0.81	membrane part
GO:0044433	0.77	cytoplasmic vesicle part
GO:0043226	0.69	organelle
GO:0043229	0.67	intracellular organelle
GO:0043234	0.65	protein complex
GO:0043227	0.65	membrane-bounded organelle
GO:0043231	0.64	intracellular membrane-bounded organelle
GO:0030117	0.63	membrane coat
GO:0030120	0.62	vesicle coat
GO:0030127	0.61	COPII vesicle coat
GO:0031982	0.50	vesicle

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	2pffA	0.241	9.77	0.018	0.376	2.3.1.41 2.3.1.86	NA
2	0.060	2ivfA	0.239	8.96	0.036	0.357	1.17.99.2	NA
3	0.060	1bxrA	0.240	9.35	0.041	0.365	6.3.5.5	NA
4	0.060	2eabA	0.241	9.12	0.042	0.364	3.2.1.63	NA
5	0.060	1kqfA	0.246	9.40	0.048	0.376	1.2.1.2	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:

Click to view	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	3b9jB	0.127	6.05	0.072	0.155	0.12	FAD	complex1.pdb.gz	46,47,48

	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.