ASpdb: an integrative knowledgebase of human protein isoforms from experimental and AI-predicted structures

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	Protein Summary
	AS Summary
	Protein Functional Features
	Gene Isoform Structures and Expression Levels
	Protein Structures
	pLDDT Score Distribution
	Ramachandran Plot of Protein Structures
	Potential Active Site Information
	Protein Structure and Feature Comparision
	Protein-Protein Interaction
	Related Drugs
	Related Diseases
	Clinically Important Variants

Protein:API5

Protein Summary

Gene summary

Gene name: API5
ASpdb.0 ID: 8539
	Gene
Gene symbol	API5
Gene ID	8539
Gene name	apoptosis inhibitor 5
Synonyms	AAC-11\|AAC11
Cytomap	11p12
Type of gene	protein-coding
Description	apoptosis inhibitor 5FIFantiapoptosis clone 11 proteincell migration-inducing gene 8 proteinfibroblast growth factor 2-interacting factor 2migration-inducing protein MIG8
Modification date	20240305
UniProtAcc	Q9BZZ5

Gene ontology of this gene with evidence of Inferred from Direct Assay (IDA) from Entrez

Partner	Gene	GO ID	GO term	PubMed ID
Gene	API5	GO:0005634	nucleus	11075807
Gene	API5	GO:0016607	nuclear speck	-

AS Summary

Information of the canonical protein with experimentally identified structure from PDB (2023).

UniProt Acc	File name	PDB ID	Method	Resolution	Chain	Start	End
Q9BZZ5-4	Q9BZZ5-4_3u0r_A.pdb	3U0R	X-ray	2.5	A	2	446

ASpdb's canonical and alternatively spliced isoform information.

accession_id	gene_name	canonical_id	alternative_id	canonical_length	alternative_length	canonical_start	canonical_end	type	originalSEQ	variationSEQ	alternative_start	alternative_end
Q9BZZ5	API5	Q9BZZ5-4	Q9BZZ5-1	524	438	1	72	Deletion	none	none	0	0
Q9BZZ5	API5	Q9BZZ5-4	Q9BZZ5-1	524	438	498	510	Substitution	EQRGAFRGSRGGR	GERFRLGTRNMRD	426	438
Q9BZZ5	API5	Q9BZZ5-4	Q9BZZ5-1	524	438	511	524	Deletion	none	none	438	438
Q9BZZ5	API5	Q9BZZ5-4	Q9BZZ5-2	524	504	499	504	Substitution	QRGAFR	RSLQGK	499	504
Q9BZZ5	API5	Q9BZZ5-4	Q9BZZ5-2	524	504	505	524	Deletion	none	none	504	504
Q9BZZ5	API5	Q9BZZ5-4	Q9BZZ5-3	524	445	427	431	Substitution	DLFHI	AKESQ	427	431
Q9BZZ5	API5	Q9BZZ5-4	Q9BZZ5-3	524	445	432	510	Deletion	none	none	431	431
Q9BZZ5	API5	Q9BZZ5-4	Q9BZZ5-5	524	450	24	77	Deletion	none	none	23	23
Q9BZZ5	API5	Q9BZZ5-4	Q9BZZ5-5	524	450	499	504	Substitution	QRGAFR	RSLQGK	445	450
Q9BZZ5	API5	Q9BZZ5-4	Q9BZZ5-5	524	450	505	524	Deletion	none	none	450	450
Q9BZZ5	API5	Q9BZZ5-4	Q9BZZ5-6	524	513	1	23	Substitution	MPTVEELYRNYGILADATEQVGQ	MKQRWRENGIGK	1	12

Multiple sequence alignment of our canonical and alternatively spliced API5

Matched gene isoform IDs with Ensembl and RefSeq of our canonical and alternative spliced genes of API5

UniProt-id	ENSG	ENST	ENSP
Q9BZZ5-4	ENSG00000166181.13	ENST00000531273.6	ENSP00000431391.1
Q9BZZ5-1	ENSG00000166181.13	ENST00000534600.5	ENSP00000434462.1
Q9BZZ5-2	ENSG00000166181.13	ENST00000378852.7	ENSP00000368129.3
Q9BZZ5-5	ENSG00000166181.13	ENST00000420461.6	ENSP00000402540.2
Q9BZZ5-6	ENSG00000166181.13	ENST00000455725.6	ENSP00000399341.2

UniProt-id	NM ID	NP ID
Q9BZZ5-4	NM_001142930.1	NP_001136402.1
Q9BZZ5-2	NM_006595.3	NP_006586.1
Q9BZZ5-5	NM_001142931.1	NP_001136403.1

Amino acid sequences of our canonical and alternatively spliced API5

accession_id	Protein sequence
Q9BZZ5-4	MPTVEELYRNYGILADATEQVGQHKDAYQVILDGVKGGTKEKRLAAQFIPKFFKHFPELADSAINAQLDLCEDEDVSIRRQAIKELPQFA TGENLPRVADILTQLLQTDDSAEFNLVNNALLSIFKMDAKGTLGGLFSQILQGEDIVRERAIKFLSTKLKTLPDEVLTKEVEELILTESK KVLEDVTGEEFVLFMKILSGLKSLQTVSGRQQLVELVAEQADLEQTFNPSDPDCVDRLLQCTRQAVPLFSKNVHSTRFVTYFCEQVLPNL GTLTTPVEGLDIQLEVLKLLAEMSSFCGDMEKLETNLRKLFDKLLEYMPLPPEEAENGENAGNEEPKLQFSYVECLLYSFHQLGRKLPDF LTAKLNAEKLKDFKIRLQYFARGLQVYIRQLRLALQGKTGEALKTEENKIKVVALKITNNINVLIKDLFHIPPSYKSTVTLSWKPVQKVE
Q9BZZ5-1	DEDVSIRRQAIKELPQFATGENLPRVADILTQLLQTDDSAEFNLVNNALLSIFKMDAKGTLGGLFSQILQGEDIVRERAIKFLSTKLKTL PDEVLTKEVEELILTESKKVLEDVTGEEFVLFMKILSGLKSLQTVSGRQQLVELVAEQADLEQTFNPSDPDCVDRLLQCTRQAVPLFSKN VHSTRFVTYFCEQVLPNLGTLTTPVEGLDIQLEVLKLLAEMSSFCGDMEKLETNLRKLFDKLLEYMPLPPEEAENGENAGNEEPKLQFSY VECLLYSFHQLGRKLPDFLTAKLNAEKLKDFKIRLQYFARGLQVYIRQLRLALQGKTGEALKTEENKIKVVALKITNNINVLIKDLFHIP
Q9BZZ5-2	MPTVEELYRNYGILADATEQVGQHKDAYQVILDGVKGGTKEKRLAAQFIPKFFKHFPELADSAINAQLDLCEDEDVSIRRQAIKELPQFA TGENLPRVADILTQLLQTDDSAEFNLVNNALLSIFKMDAKGTLGGLFSQILQGEDIVRERAIKFLSTKLKTLPDEVLTKEVEELILTESK KVLEDVTGEEFVLFMKILSGLKSLQTVSGRQQLVELVAEQADLEQTFNPSDPDCVDRLLQCTRQAVPLFSKNVHSTRFVTYFCEQVLPNL GTLTTPVEGLDIQLEVLKLLAEMSSFCGDMEKLETNLRKLFDKLLEYMPLPPEEAENGENAGNEEPKLQFSYVECLLYSFHQLGRKLPDF LTAKLNAEKLKDFKIRLQYFARGLQVYIRQLRLALQGKTGEALKTEENKIKVVALKITNNINVLIKDLFHIPPSYKSTVTLSWKPVQKVE
Q9BZZ5-3	MPTVEELYRNYGILADATEQVGQHKDAYQVILDGVKGGTKEKRLAAQFIPKFFKHFPELADSAINAQLDLCEDEDVSIRRQAIKELPQFA TGENLPRVADILTQLLQTDDSAEFNLVNNALLSIFKMDAKGTLGGLFSQILQGEDIVRERAIKFLSTKLKTLPDEVLTKEVEELILTESK KVLEDVTGEEFVLFMKILSGLKSLQTVSGRQQLVELVAEQADLEQTFNPSDPDCVDRLLQCTRQAVPLFSKNVHSTRFVTYFCEQVLPNL GTLTTPVEGLDIQLEVLKLLAEMSSFCGDMEKLETNLRKLFDKLLEYMPLPPEEAENGENAGNEEPKLQFSYVECLLYSFHQLGRKLPDF
Q9BZZ5-5	MPTVEELYRNYGILADATEQVGQIRRQAIKELPQFATGENLPRVADILTQLLQTDDSAEFNLVNNALLSIFKMDAKGTLGGLFSQILQGE DIVRERAIKFLSTKLKTLPDEVLTKEVEELILTESKKVLEDVTGEEFVLFMKILSGLKSLQTVSGRQQLVELVAEQADLEQTFNPSDPDC VDRLLQCTRQAVPLFSKNVHSTRFVTYFCEQVLPNLGTLTTPVEGLDIQLEVLKLLAEMSSFCGDMEKLETNLRKLFDKLLEYMPLPPEE AENGENAGNEEPKLQFSYVECLLYSFHQLGRKLPDFLTAKLNAEKLKDFKIRLQYFARGLQVYIRQLRLALQGKTGEALKTEENKIKVVA LKITNNINVLIKDLFHIPPSYKSTVTLSWKPVQKVEIGQKRASEDTTSGSPPKKSSAGPKRDARQIYNPPSGKYSSNLGNFNYERSLQGK
Q9BZZ5-6	MKQRWRENGIGKHKDAYQVILDGVKGGTKEKRLAAQFIPKFFKHFPELADSAINAQLDLCEDEDVSIRRQAIKELPQFATGENLPRVADI LTQLLQTDDSAEFNLVNNALLSIFKMDAKGTLGGLFSQILQGEDIVRERAIKFLSTKLKTLPDEVLTKEVEELILTESKKVLEDVTGEEF VLFMKILSGLKSLQTVSGRQQLVELVAEQADLEQTFNPSDPDCVDRLLQCTRQAVPLFSKNVHSTRFVTYFCEQVLPNLGTLTTPVEGLD IQLEVLKLLAEMSSFCGDMEKLETNLRKLFDKLLEYMPLPPEEAENGENAGNEEPKLQFSYVECLLYSFHQLGRKLPDFLTAKLNAEKLK DFKIRLQYFARGLQVYIRQLRLALQGKTGEALKTEENKIKVVALKITNNINVLIKDLFHIPPSYKSTVTLSWKPVQKVEIGQKRASEDTT

Protein Functional Features

Main function of this protein. (from UniProt)

API5 (go to UniProt):Q9BZZ5

Retention analysis result of protein across 39 protein features of UniProt such as six molecule processing features, 13 region features, four site features, six amino acid modification features, two natural variation features, five experimental info features, and 3 secondary structure features. Here, because of limited space for viewing, we only show the protein feature retention information belong to the 13 regional features. All retention annotation result can be downloaded at
download page
* Minus value of BPloci means that the break pointn is located before the CDS.

- Retained protein feature among the 13 regional features.

Accession_id	Subsection	Start	End	Funcitonal feature	Splicing information
Q9BZZ5	Region	2	360	Note=ARM-like and Heat-like helical repeats	Type=Deletion;Start=1;End=72
Q9BZZ5	Region	2	360	Note=ARM-like and Heat-like helical repeats	Type=Deletion;Start=24;End=77
Q9BZZ5	Region	2	360	Note=ARM-like and Heat-like helical repeats	Type=Substitution;Start=1;End=23
Q9BZZ5	Region	452	524	Note=Disordered;Ontology_term=ECO:0000256;evidence=ECO:0000256\|SAM:MobiDB-lite	Type=Substitution;Start=498;End=510
Q9BZZ5	Region	452	524	Note=Disordered;Ontology_term=ECO:0000256;evidence=ECO:0000256\|SAM:MobiDB-lite	Type=Deletion;Start=511;End=524
Q9BZZ5	Region	452	524	Note=Disordered;Ontology_term=ECO:0000256;evidence=ECO:0000256\|SAM:MobiDB-lite	Type=Substitution;Start=499;End=504
Q9BZZ5	Region	452	524	Note=Disordered;Ontology_term=ECO:0000256;evidence=ECO:0000256\|SAM:MobiDB-lite	Type=Deletion;Start=505;End=524
Q9BZZ5	Region	452	524	Note=Disordered;Ontology_term=ECO:0000256;evidence=ECO:0000256\|SAM:MobiDB-lite	Type=Deletion;Start=432;End=510
Q9BZZ5	Region	452	524	Note=Disordered;Ontology_term=ECO:0000256;evidence=ECO:0000256\|SAM:MobiDB-lite	Type=Substitution;Start=499;End=504
Q9BZZ5	Region	452	524	Note=Disordered;Ontology_term=ECO:0000256;evidence=ECO:0000256\|SAM:MobiDB-lite	Type=Deletion;Start=505;End=524
Q9BZZ5	Motif	454	475	Note=Nuclear localization signal;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:22334682;Dbxref=PMID:22334682	Type=Deletion;Start=432;End=510
Q9BZZ5	Compositional bias	483	497	Note=Polar residues;Ontology_term=ECO:0000256;evidence=ECO:0000256\|SAM:MobiDB-lite	Type=Deletion;Start=432;End=510

Gene Isoform Structures and Expression Levels for API5

Gene structures of our canonical and alternative spliced genes of API5
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.

Expression levels of gene isoforms across GTEx.

Expression levels of gene isoforms across TCGA.

Protein Structures

PDB and CIF files of the predicted protein structures
* Here we show the 3D structure of the proteins using Mol*. AlphaFold produces a per-residue confidence score (pLDDT) between 0 and 100. Model confidence is shown from the pLDDT values per residue. pLDDT corresponds to the model’s prediction of its score on the local Distance Difference Test. It is a measure of local accuracy (from AlphfaFold website). To color code individual residues, we transformed individual PDB files into CIF format.

3D view using mol* of Q9BZZ5-4

3D view using mol* of Q9BZZ5-1

3D view using mol* of Q9BZZ5-2

3D view using mol* of Q9BZZ5-3

3D view using mol* of Q9BZZ5-5

3D view using mol* of Q9BZZ5-6

pLDDT Score Distribution

pLDDT score distribution of the predicted protein structures from AlphaFold2
* AlphaFold produces a per-residue confidence score (pLDDT) between 0 and 100.

pLDDT distribution across the protein length of Q9BZZ5-4

pLDDT distribution across the protein length of Q9BZZ5-1

pLDDT distribution across the protein length of Q9BZZ5-2

pLDDT distribution across the protein length of Q9BZZ5-3

pLDDT distribution across the protein length of Q9BZZ5-5

pLDDT distribution across the protein length of Q9BZZ5-6

Ramachandran Plot of Protein Structures

Ramachandran plot of the torsional angles - phi (φ)and psi (ψ) - of the residues (amino acids) contained in this protein peptide.

Ramachandran plot of Q9BZZ5-4

Ramachandran plot of Q9BZZ5-2

Ramachandran plot of Q9BZZ5-6

Potential Active Site Information

The potential binding sites of these proteins were identified using SiteMap, a module of the Schrodinger suite.

UniProt-id	Site score	Size	D score	Volume	Exposure	Enclosure	Contact	Phobic	Philic	Balance	Don/Acc	Residues
Q9BZZ5-4	1.045	304	1.091	1000.188	0.554	0.706	0.908	0.95	0.837	1.135	0.841	243,246,284,285,288,289,292,341,344,345,381,385,38 8,392,395,396,397,398,399,403,404,409,412,413,415, 416,417,418,419,420,422,423,426,439,440,442,443,44 4,445,446,447,448,481,483,484,485,486,488,489,492, 493,494,495,496,497,498
Q9BZZ5-1	1.001	199	1.056	669.193	0.664	0.632	0.801	0.596	0.806	0.739	0.693	212,216,263,264,265,266,267,268,269,273,307,310,31 1,314,315,318,327,328,331,332,337,338,340,341,342, 344,345,370,371,372,373,374,375,376,416,417,418,41 9,420,421,422,423,424,425,426,427,429
Q9BZZ5-2	0.791	66	0.785	198.254	0.746	0.58	0.77	0.279	1.002	0.279	1.132	322,323,324,325,328,329,330,331,332,333,334,335,33 6,337,338,340,379,382,383,386,387
Q9BZZ5-3	1.019	96	1.067	284.69	0.628	0.681	0.89	0.615	0.805	0.763	1.066	284,288,291,292,335,336,337,338,339,340,341,342,34 4,345,379,382,383,386,387,390,410,413,414,417,444, 445
Q9BZZ5-5	0.969	146	1.009	466.823	0.71	0.621	0.767	0.264	0.932	0.283	1.087	230,234,268,269,270,271,274,276,277,278,279,280,28 1,282,283,284,285,286,287,291,325,328,329,332,333, 336,352,355,356,358,359,360,362,363,388,389,390,39 1,392,443
Q9BZZ5-6	0.9	67	0.96	200.655	0.676	0.595	0.809	1.36	0.509	2.671	0.522	1,2,4,5,6,10,13,16,19,20,23,30,33,34,37,40,41

Protein Structure and Feature Comparision

Protein Structure Comparision Using Template Modeling Scores (TM-score).

Protein Structure Comparision Visualization with mol*. between Canonical predicted structure (AF2)(orange) vs Canonical validated structure (PDB)(green)

3D view using mol* of Q9BZZ5-4_Q9BZZ5-4_3u0r_A.pdb

Protein Structure Comparision Visualization with mol*. between Canonical validated structure (PDB)(orange) vs Alternative predicted structure (AF2)(green)

3D view using mol* of Q9BZZ5-4_3u0r_A_Q9BZZ5-1.pdb

3D view using mol* of Q9BZZ5-4_3u0r_A_Q9BZZ5-2.pdb

3D view using mol* of Q9BZZ5-4_3u0r_A_Q9BZZ5-3.pdb

3D view using mol* of Q9BZZ5-4_3u0r_A_Q9BZZ5-5.pdb

3D view using mol* of Q9BZZ5-4_3u0r_A_Q9BZZ5-6.pdb

Protein Structure Comparision Visualization with mol*. between Canonical predicted structure (AF2)(orange) vs Alternative predicted structure (AF2)(green)

3D view using mol* of Q9BZZ5-4_Q9BZZ5-1.pdb

3D view using mol* of Q9BZZ5-4_Q9BZZ5-2.pdb

3D view using mol* of Q9BZZ5-4_Q9BZZ5-3.pdb

3D view using mol* of Q9BZZ5-4_Q9BZZ5-5.pdb

3D view using mol* of Q9BZZ5-4_Q9BZZ5-6.pdb

Protein Feature Comparison of the protein sequendary structures among the protiens.

./stats/secondary_structure/figure/Q9BZZ5-4_vs_Q9BZZ5-1.png