NucPred on Proteomes

Authors: Andrea Krings, Amine Heddad, Markus Brameier and Bob MacCallum, Stockholm Bioinformatics Center, Stockholm University, Sweden.

NucPred - predictions for eukaryotic proteomes

Species:

Note: All filters/tests are combined with AND unless otherwise stated

Show only the proteins with links to database(s):
OMIM - human disease genes
PDB - protein 3D structure
( AND OR combination )

Annotation filters (can be slow! - Perl regexps allowed: e.g. nucleus|nucleolus)

UniProt ID (e.g. "PK3B_")
UniProt description (e.g. "kinase")
UniProt subcellular location
AND
UniProt GO component
AND
AND the
AND the

Only show proteins where the PredictNLS prediction is:

positive
negative

Only show proteins where the PSORT II predicted location

is is not

Click here: to filter by NucPred score

exclude all transmembrane proteins predicted by TMHMM
don't exclude lone N-terminal predicted transmembrane helices
(these could be signal peptides)

export all ACs and IDs as text file

Show proteins (ordered by NucPred score ) from to (currently 98716 matches)

You can bookmark/save your search criteria with this link. You can also start again with default settings.

UniProt accession	UniProt ID	UniProt description	NucPred score	Predict- NLS	PSORT II	TMHMM #helices	UniProt annotation for subcellular location	Uniprot GO cellular component	OMIM	PDB	sequence length
P22970 UniProt NPD GO	LEC1_CYTSE	Anti-H(O) lectin I (CSA-I)	0.05	-	cyt	0					244
Q9BKJ1 UniProt NPD GO	SCN2_MESMA	Anti-neuroexcitation peptide 2 precursor (Anti-neuroexcitation peptide II) (ANEPII)	0.05	-	exc	0	Secreted protein (By similarity)				85
Q28433 UniProt NPD GO	TAP1_GORGO	Antigen peptide transporter 1 (APT1) (Peptide transporter TAP1) (ATP-binding cassette sub-family B m ...	0.05	-	end	5 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein. The transmembran ...				748
Q03518 UniProt NPD GO	TAP1_HUMAN	Antigen peptide transporter 1 (APT1) (Peptide transporter TAP1) (ATP-binding cassette sub-family B m ...	0.05	-	end	5 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein. The transmembran ...	integral to membrane [NAS]	170260	1JJ7	748
P84524 UniProt NPD GO	AMP1_PHYHY	Antimicrobial peptide 1	0.05	-		0	Secreted protein				12
P83880 UniProt NPD GO	AMP1_PINMO	Antimicrobial peptide 1 (PMAP1) (10.6 kDa protein) (Fragment)	0.05	-	nuc	0	Secreted protein (By similarity)				23
P81567 UniProt NPD GO	DEFD6_SPIOL	Antimicrobial peptide D6 (So-D6) (Defensin D6) (Fragment)	0.05	-	cyt	0	Cell wall				24
P81050 UniProt NPD GO	ANT3_MESAU	Antithrombin-III (ATIII) (Fragment)	0.05	-	nuc	0	Secreted protein; extracellular space				25
P32261 UniProt NPD GO	ANT3_MOUSE	Antithrombin-III precursor (ATIII)	0.05	-	mit	0	Secreted protein; extracellular space				465
P10297 UniProt NPD GO	RIP1_PHYAM	Antiviral protein I precursor (EC 3.2.2.22) (PAP-I) (PAP-C) (Ribosome-inactivating protein) (rRNA N- ...	0.05	-	exc	1 *				1QCJ	313
P23339 UniProt NPD GO	RIPS_PHYAM	Antiviral protein S (EC 3.2.2.22) (PAP-S) (Ribosome-inactivating protein) (rRNA N-glycosidase)	0.05	-	nuc	0				1J1S	261
O35484 UniProt NPD GO	AZIN1_MOUSE	Antizyme inhibitor 1 (AZI) (Ornithine decarboxylase antizyme inhibitor)	0.05	-	cyt	0					448
P01500 UniProt NPD GO	APAM_APIME	Apamin precursor	0.05	-	nuc	1 *	Secreted protein				46
P06246 UniProt NPD GO	CYF_MARPO	Apocytochrome f precursor	0.05	-	end	2 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				320
P09813 UniProt NPD GO	APOA2_MOUSE	Apolipoprotein A-II precursor (Apo-AII) (ApoA-II)	0.05	-	cyt	0	Secreted protein				102
O02718 UniProt NPD GO	BCL2_BOVIN	Apoptosis regulator Bcl-2	0.05	-	cyt	1	Mitochondrion; mitochondrial outer membrane; single-pass membrane protein (By similarity). Nucleus; ...				229
Q9JJV8 UniProt NPD GO	BCL2_CRIGR	Apoptosis regulator Bcl-2	0.05	-	nuc	1	Mitochondrion; mitochondrial outer membrane; single-pass membrane protein. Nucleus; nuclear membrane ...				236
P10415 UniProt NPD GO	BCL2_HUMAN	Apoptosis regulator Bcl-2	0.05	-	nuc	1	Mitochondrion; mitochondrial outer membrane; single-pass membrane protein. Nucleus; nuclear membrane ...	mitochondrial outer membrane [IDA]	151430	1YSW	239
P10417 UniProt NPD GO	BCL2_MOUSE	Apoptosis regulator Bcl-2	0.05	-	nuc	1	Mitochondrion; mitochondrial outer membrane; single-pass membrane protein. Nucleus; nuclear membrane ...	cytosol [IDA] mitochondrion [IDA]			236
P83691 UniProt NPD GO	GANA_HUMIN	Arabinogalactan endo-1,4-beta-galactosidase (EC 3.2.1.89) (Endo-1,4-beta-galactanase) (Galactanase)	0.05	-	cyt	0		extraorganismal space [IC]		1HJQ	332
P19329 UniProt NPD GO	ARC1_PHAVU	Arcelin-1 precursor	0.05	-	exc	0				1AVB	265
P19330 UniProt NPD GO	ARC2_PHAVU	Arcelin-2 precursor	0.05	-	exc	0					265
Q6FMP0 UniProt NPD GO	RMT2_CANGA	Arginine N-methyltransferase 2 (EC 2.1.1.-)	0.05	-	cyt	0	Cytoplasm (By similarity). Nucleus (By similarity)				412
Q6CPN1 UniProt NPD GO	RMT2_KLULA	Arginine N-methyltransferase 2 (EC 2.1.1.-)	0.05	-	cyt	0	Cytoplasm (By similarity). Nucleus (By similarity)				407
O82475 UniProt NPD GO	SPE1_BRAJU	Arginine decarboxylase (EC 4.1.1.19) (ARGDC) (ADC)	0.05	-	cyt	0					702
Q9SNN0 UniProt NPD GO	SPE1_ORYSA	Arginine decarboxylase (EC 4.1.1.19) (ARGDC) (ADC)	0.05	-	cyt	0					702
Q43075 UniProt NPD GO	SPE1_PEA	Arginine decarboxylase (EC 4.1.1.19) (ARGDC) (ADC)	0.05	-	cyt	0					728
Q05506 UniProt NPD GO	SYRC_YEAST	Arginyl-tRNA synthetase, cytoplasmic (EC 6.1.1.19) (Arginine--tRNA ligase) (ArgRS)	0.05	-	cyt	0	Cytoplasm	cytoplasm [IC] mitochondrion [IDA]		1BS2	607
Q8NCT1 UniProt NPD GO	ARRD4_HUMAN	Arrestin domain-containing protein 4	0.05	-	cyt	0					418
O54984 UniProt NPD GO	ARSA1_MOUSE	Arsenical pump-driving ATPase (EC 3.6.3.16) (Arsenite-translocating ATPase) (Arsenical resistance AT ...	0.05	-	cyt	0					348
O43681 UniProt NPD GO	ARSA1_HUMAN	Arsenical pump-driving ATPase (EC 3.6.3.16) (Arsenite-translocating ATPase) (Arsenical resistance AT ...	0.05	-	cyt	0		cytoplasm [TAS] nucleolus [TAS] soluble fraction [TAS]	601913		348
Q06598 UniProt NPD GO	ACR3_YEAST	Arsenical-resistance protein ACR3	0.05	-	end	9 *	Membrane; multi-pass membrane protein (Potential)				404
P49091 UniProt NPD GO	ASNS_BRAOL	Asparagine synthetase [glutamine-hydrolyzing] (EC 6.3.5.4) (Glutamine-dependent asparagine synthetas ...	0.05	-	mit	0					585
O24338 UniProt NPD GO	ASNS_SANAU	Asparagine synthetase [glutamine-hydrolyzing] (EC 6.3.5.4) (Glutamine-dependent asparagine synthetas ...	0.05	-	mit	0					524
Q9SW96 UniProt NPD GO	SYNC1_ARATH	Asparaginyl-tRNA synthetase, cytoplasmic 1 (EC 6.1.1.22) (Asparagine--tRNA ligase 1) (AsnRS 1)	0.05	-	cyt	0	Cytoplasm (Probable)				572
P37833 UniProt NPD GO	AATC_ORYSA	Aspartate aminotransferase, cytoplasmic (EC 2.6.1.1) (Transaminase A)	0.05	-	nuc	0	Cytoplasm (By similarity)				407
P49077 UniProt NPD GO	PYRB_ARATH	Aspartate carbamoyltransferase, chloroplast precursor (EC 2.1.3.2) (Aspartate transcarbamylase) (ATC ...	0.05	-	mit	0	Plastid; chloroplast				390
Q8R3P0 UniProt NPD GO	ACY2_MOUSE	Aspartoacylase (EC 3.5.1.15) (Aminoacylase-2) (ACY-2)	0.05	-	cyt	0					312
P07584 UniProt NPD GO	ASTA_ASTFL	Astacin precursor (EC 3.4.24.21) (Crayfish small-molecule proteinase)	0.05	-	exc	0				1QJJ	251
P36107 UniProt NPD GO	AUR1_YEAST	Aureobasidin A resistance protein	0.05	-	end	6 *	Membrane; multi-pass membrane protein (Potential)	Golgi apparatus [IDA]			401
Q6FJZ6 UniProt NPD GO	ATG5_CANGA	Autophagy protein 5	0.05	-	cyt	0	Cytoplasm (By similarity). Membrane; peripheral membrane protein (By similarity)				270
Q9P6N1 UniProt NPD GO	ATG21_SCHPO	Autophagy-related protein 21	0.05	-	cyt	0	Cytoplasm (By similarity). Membrane; peripheral membrane protein (By similarity). Vacuole; vacuolar ...				335
Q6BM18 UniProt NPD GO	ATG27_DEBHA	Autophagy-related protein 27 precursor	0.05	-	end	1	Intracytoplasmic membrane; single-pass type I membrane protein (By similarity). Perivacuolar punctat ...				282
Q6CXQ8 UniProt NPD GO	ATG27_KLULA	Autophagy-related protein 27 precursor	0.05	-	end	1	Intracytoplasmic membrane; single-pass type I membrane protein (By similarity). Perivacuolar punctat ...				285
P33080 UniProt NPD GO	AX10A_SOYBN	Auxin-induced protein X10A	0.05	-	mit	0					92
O24407 UniProt NPD GO	IAA16_ARATH	Auxin-responsive protein IAA16 (Indoleacetic acid-induced protein 16)	0.05	-	nuc	0	Nucleus (By similarity)				236
P50080 UniProt NPD GO	AZR1_YEAST	Azole resistance protein 1	0.05	-	end	13	Cell membrane; multi-pass membrane protein	plasma membrane [IDA]			613
Q80UN1 UniProt NPD GO	KCTD9_MOUSE	BTB/POZ domain-containing protein KCTD9	0.05	-	mit	0					339
Q42372 UniProt NPD GO	LCB2_ROBPS	Bark agglutinin I, polypeptide B precursor (RPbAI) (LECRPA2)	0.05	-	vac	1 *					286
Q5HZM3 UniProt NPD GO	BAFL_XENLA	Barrier-to-autointegration factor-like protein (BAF-L)	0.05	-	cyt	0	Nucleus (By similarity)				91

You are viewing entries 73851 to 73900 of 98716. You can see more proteins by changing the limits in the form at the top of this page, or click here for the next page of proteins .

If you find NucPred useful, please cite this paper:

NucPred - Predicting Nuclear Localization of Proteins. Brameier M, Krings A, Maccallum RM. Bioinformatics, 2007. PubMed id: 17332022

The authors also look forward to your comments and suggestions.

What does the NucPred score mean?

You have to decide on a NucPred score threshold. Sequences which score greater than or equal to this threshold are predicted to spend some time in the nucleus. Higher thresholds yield fewer predicted nuclear proteins, but these predictions are more accurate (you can have higher confidence in them). The table below gives more details of the performance of NucPred estimated using the sequences it was trained on (by cross-validation). Another benchmark is available in the Bioinformatics 2007 paper.

NucPred score threshold	Specificity	Sensitivity
see above	fraction of proteins predicted to be nuclear that actually are nuclear	fraction of true nuclear proteins that are predicted (coverage)
0.10	0.45	0.88
0.20	0.52	0.83
0.30	0.57	0.77
0.40	0.63	0.69
0.50	0.70	0.62
0.60	0.71	0.53
0.70	0.81	0.44
0.80	0.84	0.32
0.90	0.88	0.21
1.00	1.00	0.02

Sequences which score >= 0.8 with NucPred and which are predicted by PredictNLS to contain an NLS have been shown to be 93% correct with a coverage of 16%. (PredictNLS by itself is 87% correct with 26% coverage on the same data.)

Go back to the NucPred Home Page.