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
P16167 UniProt NPD GO	UFO3_MAIZE	Anthocyanidin 3-O-glucosyltransferase (EC 2.4.1.115) (Flavonol 3-O-glucosyltransferase) (UDP-glucose ...	0.02	-	mit	0					471
P51094 UniProt NPD GO	UFOG_VITVI	Anthocyanidin 3-O-glucosyltransferase (EC 2.4.1.115) (Flavonol 3-O-glucosyltransferase) (UDP-glucose ...	0.02	-	cyt	0					154
Q4R1I9 UniProt NPD GO	ANGLT_ROSHC	Anthocyanidin 5,3-O-glucosyltransferase (EC 2.4.1.-) (UDP-glucose: anthocyanidin 5,3-O-glucosyltrans ...	0.02	-	cyt	0					473
P01532 UniProt NPD GO	TXAC_ANTEL	Anthopleurin-C (Toxin AP-C)	0.02	-	nuc	0	Secreted protein. Found in nematocyst				47
P51362 UniProt NPD GO	TRPG_PORPU	Anthranilate synthase component II (EC 4.1.3.27) (Glutamine amido-transferase)	0.02	-	cyt	0	Plastid; chloroplast				189
P48821 UniProt NPD GO	CECE_BOMMO	Antibacterial peptide enbocin precursor (Moricin)	0.02	-	end	1 *	Secreted protein				59
P82965 UniProt NPD GO	ADFA_TENMO	Antidiuretic factor A (ADFa) (ADF) (Antidiuretic hormone A) (ADHA)	0.02	-		0	Secreted protein	extracellular region [NAS]			14
P84869 UniProt NPD GO	PVAP_PHAVU	Antifungal lectin PVAP (Fragment)	0.02	-		0					10
P81493 UniProt NPD GO	AX1_BETVU	Antifungal protein AX1	0.02	-	nuc	0					46
P33044 UniProt NPD GO	THHR_HORVU	Antifungal protein R (Fragment)	0.02	-	cyt	0					44
Q08617 UniProt NPD GO	ANTF_SARPE	Antifungal protein precursor (AFP)	0.02	-	vac	0					85
Q9DGI0 UniProt NPD GO	BJ46A_BOTJA	Antihemorragic factor BJ46a precursor (Metalloproteinase inhibitor)	0.02	-	exc	0					341
P59084 UniProt NPD GO	BDS2_ANESU	Antihypertensive protein BDS-2 (BDS-II) (Blood depressing substance II)	0.02	-	nuc	0	Secreted protein. Found in nematocyst				43
P22922 UniProt NPD GO	A1AT_BOMMO	Antitrypsin precursor (AT)	0.02	-	end	0	Secreted protein				392
P24475 UniProt NPD GO	RIP3_GELMU	Antiviral protein GAP-31 (EC 3.2.2.22) (Ribosome-inactivating protein) (rRNA N-glycosidase) (Fragmen ...	0.02	-	nuc	0					55
Q86QT2 UniProt NPD GO	APAM_APICC	Apamin precursor	0.02	-	nuc	1 *	Secreted protein				46
P18647 UniProt NPD GO	APOA1_ERYPA	Apolipoprotein A-I (Apo-AI) (ApoA-I) (Fragment)	0.02	-		0	Secreted protein				20
P19939 UniProt NPD GO	APOC1_RAT	Apolipoprotein C-I precursor (Apo-CI) (ApoC-I)	0.02	-	gol	0	Secreted protein				88
Q9XSN5 UniProt NPD GO	APOC1_TUPGL	Apolipoprotein C-I precursor (Apo-CI) (ApoC-I)	0.02	-	exc	0	Secreted protein (By similarity)				88
Q8SPI0 UniProt NPD GO	APOD_MACFA	Apolipoprotein D precursor (Apo-D) (ApoD)	0.02	-	exc	0	Secreted protein (By similarity)				189
P23593 UniProt NPD GO	APOD_RAT	Apolipoprotein D precursor (Apo-D) (ApoD)	0.02	-	end	0	Secreted protein				189
Q07816 UniProt NPD GO	BCLX_CHICK	Apoptosis regulator Bcl-X (Bcl-2-like 1 protein)	0.02	-	cyt	1	Mitochondrion; mitochondrial membrane (By similarity). Mitochondrial membranes and perinuclear envel ...				229
P53563 UniProt NPD GO	BCLX_RAT	Apoptosis regulator Bcl-X (Bcl-2-like 1 protein)	0.02	-	cyt	1	Mitochondrion; mitochondrial membrane (By similarity). Mitochondrial membranes and perinuclear envel ...	integral to membrane of membrane fraction [TAS] mitochondrial envelope [IDA] mitochondrial outer membrane [IDA]		1AF3	233
Q8BUE4 UniProt NPD GO	AMID_MOUSE	Apoptosis-inducing factor-like mitochondrion-associated inducer of death (EC 1.-.-.-) (Apoptosis-ind ...	0.02	-	cyt	1 *	Cytoplasm. Mitochondrion; mitochondrial outer membrane (By similarity)				373
P02658 UniProt NPD GO	APOV1_ANAPL	Apovitellenin-1 (Apovitellenin I)	0.02	-	cyt	0					82
Q9NHW7 UniProt NPD GO	AQP_AEDAE	Aquaporin AQPAe.a	0.02	-	end	6 *	Membrane; multi-pass membrane protein				249
Q8LFP7 UniProt NPD GO	NIP12_ARATH	Aquaporin NIP1.2 (NOD26-like intrinsic protein 1.2) (Nodulin-26-like major intrinsic protein 2) (AtN ...	0.02	-	end	6	Membrane; multi-pass membrane protein (Probable)				294
P61837 UniProt NPD GO	PIP11_ARATH	Aquaporin PIP1.1 (Plasma membrane intrinsic protein 1a) (PIP1a) (Aquaporin 1) (Plasma membrane aquap ...	0.02	-	end	6	Cell membrane; multi-pass membrane protein				286
P61838 UniProt NPD GO	PIP11_VICFA	Aquaporin PIP1.1 (Plasma membrane intrinsic protein 1a) (PIP1a) (Aquaporin 1) (Plasma membrane aquap ...	0.02	-	end	6	Cell membrane; multi-pass membrane protein				286
Q06611 UniProt NPD GO	PIP12_ARATH	Aquaporin PIP1.2 (Plasma membrane intrinsic protein 1b) (PIP1b) (Transmembrane protein A) (TMP-A) (A ...	0.02	-	end	6	Cell membrane; multi-pass membrane protein				286
Q96PS8 UniProt NPD GO	AQP10_HUMAN	Aquaporin-10 (AQP-10) (Small intestine aquaporin)	0.02	-	end	5 *	Membrane; multi-pass membrane protein		606578		301
Q8CHJ2 UniProt NPD GO	AQP12_MOUSE	Aquaporin-12A (AQP-12)	0.02	-	end	4 *	Membrane; multi-pass membrane protein (Potential)	cytoplasm [IDA]			290
P33280 UniProt NPD GO	ARGI_NEUCR	Arginase (EC 3.5.3.1)	0.02	-	mit	0	Cytoplasm				358
O81160 UniProt NPD GO	SPE2_THECC	Arginine decarboxylase (EC 4.1.1.19) (ARGDC) (ADC) (Fragment)	0.02	-	cyt	0					406
P04817 UniProt NPD GO	CAN1_YEAST	Arginine permease	0.02	-	end	10	Membrane; multi-pass membrane protein	lipid raft [IDA] mitochondrion [IDA]			590
P16639 UniProt NPD GO	ATE1_YEAST	Arginyl-tRNA--protein transferase 1 (EC 2.3.2.8) (R-transferase 1) (Arginyltransferase 1) (Arginine- ...	0.02	-	cyt	0	Cytoplasm	cytoplasm [TAS]			503
O96571 UniProt NPD GO	DDC_DROLE	Aromatic-L-amino-acid decarboxylase (EC 4.1.1.28) (AADC) (DOPA decarboxylase) (DDC) (Fragment)	0.02	-	cyt	1 *					403
P51481 UniProt NPD GO	ARRC_RANCA	Arrestin-C (Cone arrestin)	0.02	-	cyt	0					389
P51482 UniProt NPD GO	ARRC_RANPI	Arrestin-C (Cone arrestin)	0.02	-	cyt	0					389
P51483 UniProt NPD GO	ARRC_XENLA	Arrestin-C (Cone arrestin)	0.02	-	cyt	0					387
Q3TYD4 UniProt NPD GO	ARSG_MOUSE	Arylsulfatase G precursor (EC 3.1.6.-) (ASG)	0.02	-	end	0	Endoplasmic reticulum (By similarity)	endoplasmic reticulum [ISS]			525
Q9NS82 UniProt NPD GO	AAA1_HUMAN	Asc-type amino acid transporter 1 (Asc-1)	0.02	-	end	12 *	Membrane; multi-pass membrane protein (Probable)	integral to plasma membrane [NAS] membrane [TAS]	607959		523
Q61024 UniProt NPD GO	ASNS_MOUSE	Asparagine synthetase [glutamine-hydrolyzing] (EC 6.3.5.4) (Glutamine-dependent asparagine synthetas ...	0.02	-	cyt	0					560
Q43011 UniProt NPD GO	ASNS_ORYSA	Asparagine synthetase [glutamine-hydrolyzing] (EC 6.3.5.4) (Glutamine-dependent asparagine synthetas ...	0.02	-	mit	0					590
Q5R6W9 UniProt NPD GO	ASNS_PONPY	Asparagine synthetase [glutamine-hydrolyzing] (EC 6.3.5.4) (Glutamine-dependent asparagine synthetas ...	0.02	-	cyt	0					560
P08243 UniProt NPD GO	ASNS_HUMAN	Asparagine synthetase [glutamine-hydrolyzing] (EC 6.3.5.4) (Glutamine-dependent asparagine synthetas ...	0.02	-	cyt	0		soluble fraction [IDA]	108370		560
P49092 UniProt NPD GO	ASNS1_LOTJA	Asparagine synthetase [glutamine-hydrolyzing] 1 (EC 6.3.5.4) (Glutamine-dependent asparagine synthet ...	0.02	-	mit	0					585
P19251 UniProt NPD GO	ASNS1_PEA	Asparagine synthetase, nodule [glutamine-hydrolyzing] (EC 6.3.5.4) (Glutamine-dependent asparagine s ...	0.02	-	mit	0					585
P46248 UniProt NPD GO	AAT5_ARATH	Aspartate aminotransferase, chloroplast precursor (EC 2.6.1.1) (Transaminase A)	0.02	-	mit	0	Plastid; chloroplast				453
P17174 UniProt NPD GO	AATC_HUMAN	Aspartate aminotransferase, cytoplasmic (EC 2.6.1.1) (Transaminase A) (Glutamate oxaloacetate transa ...	0.02	-	cyt	0	Cytoplasm		138180		412

You are viewing entries 82501 to 82550 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.