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
Q01355 UniProt NPD GO	AOX_NEUCR	Alternative oxidase, mitochondrial precursor (EC 1.-.-.-) (ALTOX)	0.23	-	mit	0	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein; matrix side				362
Q708S6 UniProt NPD GO	ACC2C_BRARE	Amiloride-sensitive cation channel 2-C, neuronal (Acid-sensing ion channel 1.3) (ZASIC1.3)	0.23	-	nuc	2 *	Cell membrane; multi-pass membrane protein (Probable)	integral to plasma membrane [IDA]			529
Q80ZD8 UniProt NPD GO	AMGO1_MOUSE	Amphoterin-induced protein 1 precursor (AMIGO-1) (Alivin-2)	0.23	-	exc	2 *	Membrane; single-pass type I membrane protein (Potential). Associated with axons of neuronal cells ( ...	integral to plasma membrane [ISS]			492
Q8WME8 UniProt NPD GO	ANGI_PANTR	Angiogenin precursor (EC 3.1.27.-) (Ribonuclease 5) (RNase 5)	0.23	-	exc	1 *	Secreted protein	basal lamina [ISS] extracellular space [ISS] nucleolus [ISS] nucleus [ISS]			147
Q9GKY1 UniProt NPD GO	B3A4_RABIT	Anion exchange protein 4 (Anion exchanger 4) (Solute carrier family 4 member 9)	0.23	-	end	11	Cell membrane; apical cell membrane; multi-pass membrane protein. In contrast to the rat ortholog, i ...				955
Q9D1A4 UniProt NPD GO	ASB5_MOUSE	Ankyrin repeat and SOCS box protein 5 (ASB-5)	0.23	-	nuc	1 *					329
Q91ZU0 UniProt NPD GO	ASB7_MOUSE	Ankyrin repeat and SOCS box protein 7 (ASB-7)	0.23	-	mit	0					318
O97529 UniProt NPD GO	ANXA8_RABIT	Annexin A8 (Annexin VIII)	0.23	-	cyt	0					327
Q5R7P1 UniProt NPD GO	AGR2_PONPY	Anterior gradient protein 2 homolog precursor	0.23	-	exc	0	Secreted protein (Probable)				175
Q92370 UniProt NPD GO	TRPG_SCHPO	Anthranilate synthase component 2 (EC 4.1.3.27) (Anthranilate synthase component II) [Includes: Glut ...	0.23	-	cyt	0					759
Q8HZQ3 UniProt NPD GO	NKL_HORSE	Antimicrobial peptide NK-lysin precursor	0.23	-	exc	0	Secreted protein (By similarity)				145
Q4MYA8 UniProt NPD GO	RK36_THEPA	Apicoplast 50S ribosomal protein L36	0.23	-	nuc	0	Plastid; apicoplast				38
O77248 UniProt NPD GO	APL3_SPOLT	Apolipophorin-3 precursor (Apolipophorin-III) (ApoLp-III)	0.23	-	exc	0	Secreted protein (By similarity)				188
O42175 UniProt NPD GO	APOA1_SPAAU	Apolipoprotein A-I precursor (Apo-AI) (ApoA-I)	0.23	-	exc	0	Secreted protein (By similarity)				260
Q9Y5M1 UniProt NPD GO	APR2_HUMAN	Apoptosis-related protein 2 (APR-2)	0.23	-	cyt	0					114
Q9QYH7 UniProt NPD GO	GHRL_RAT	Appetite-regulating hormone precursor (Growth hormone secretagogue) (Growth hormone-releasing peptid ...	0.23	-	exc	0	Secreted protein	extracellular space [IC]			117
P61798 UniProt NPD GO	APTX_CHICK	Aprataxin homolog (Forkhead-associated domain histidine triad-like protein) (FHA-HIT) (Fragment)	0.23	-	nuc	0	Nucleus (Probable)				316
P49269 UniProt NPD GO	TXP4_APTSC	Aptotoxin-4 (Aptotoxin IV) (Paralytic peptide IV) (PP IV)	0.23	-	nuc	0	Secreted protein				76
Q58DL1 UniProt NPD GO	ARGI2_BOVIN	Arginase-2, mitochondrial precursor (EC 3.5.3.1) (Arginase II)	0.23	-	mit	0	Mitochondrion (By similarity)				354
P48861 UniProt NPD GO	DDC_MANSE	Aromatic-L-amino-acid decarboxylase (EC 4.1.1.28) (AADC) (DOPA decarboxylase) (DDC)	0.23	-	cyt	0					508
Q95MN7 UniProt NPD GO	AIPL1_SAIBB	Aryl-hydrocarbon-interacting protein-like 1	0.23	-	cyt	0	Cytoplasm (By similarity). Nucleus (By similarity)				372
P11246 UniProt NPD GO	ARY2_RABIT	Arylamine N-acetyltransferase 2 (EC 2.3.1.5) (Arylamide acetylase 2) (Arylamine N-acetyltransferase, ...	0.23	-	nuc	1	Cytoplasm				290
P15848 UniProt NPD GO	ARSB_HUMAN	Arylsulfatase B precursor (EC 3.1.6.12) (ASB) (N-acetylgalactosamine-4-sulfatase) (G4S)	0.23	-	mit	0	Lysosome	lysosome [TAS]	253200	1FSU	533
P07307 UniProt NPD GO	ASGR2_HUMAN	Asialoglycoprotein receptor 2 (ASGP-R 2) (ASGPR 2) (Hepatic lectin H2)	0.23	-	mit	1	Membrane; single-pass type II membrane protein		108361		311
P49089 UniProt NPD GO	ASNS1_YEAST	Asparagine synthetase [glutamine-hydrolyzing] 1 (EC 6.3.5.4) (Glutamine-dependent asparagine synthet ...	0.23	-	cyt	0		cytoplasm [IDA]			571
P10869 UniProt NPD GO	AK_YEAST	Aspartokinase (EC 2.7.2.4) (Aspartate kinase)	0.23	-	mit	0		cytoplasm [IDA]			527
Q6HA08 UniProt NPD GO	ASTL_HUMAN	Astacin-like metalloendopeptidase precursor (EC 3.4.-.-) (Oocyte astacin) (Ovastacin)	0.23	-	nuc	1 *			608860		431
Q60HD2 UniProt NPD GO	SPG3A_MACFA	Atlastin (GTP-binding protein 3) (Guanine nucleotide-binding protein 3)	0.23	-	end	2					558
P07499 UniProt NPD GO	ANF_CANFA	Atrial natriuretic factor precursor (ANF) (Atrial natriuretic peptide) (ANP) (Prepronatriodilatin)	0.23	-	exc	0	Secreted protein				149
P46197 UniProt NPD GO	ANPRB_BOVIN	Atrial natriuretic peptide receptor B precursor (ANP-B) (ANPRB) (GC-B) (Guanylate cyclase B) (EC 4.6 ...	0.23	-	end	0	Membrane; single-pass type I membrane protein				1047
P20594 UniProt NPD GO	ANPRB_HUMAN	Atrial natriuretic peptide receptor B precursor (ANP-B) (ANPRB) (GC-B) (Guanylate cyclase B) (EC 4.6 ...	0.23	-	end	0	Membrane; single-pass type I membrane protein	plasma membrane [TAS]	602875		1047
Q6VVW5 UniProt NPD GO	ANPRB_MOUSE	Atrial natriuretic peptide receptor B precursor (ANP-B) (ANPRB) (GC-B) (Guanylate cyclase B) (EC 4.6 ...	0.23	-	end	0	Membrane; single-pass type I membrane protein (By similarity)	plasma membrane [TAS]			1047
P16067 UniProt NPD GO	ANPRB_RAT	Atrial natriuretic peptide receptor B precursor (ANP-B) (ANPRB) (GC-B) (Guanylate cyclase B) (EC 4.6 ...	0.23	-	end	2	Membrane; single-pass type I membrane protein				1047
Q7M4A6 UniProt NPD GO	ATT_APLBR	Attractin	0.23	-	nuc	0	Secreted protein (By similarity)				58
Q7M460 UniProt NPD GO	ATT_APLDE	Attractin	0.23	-	nuc	0	Secreted protein (By similarity)				56
Q5R792 UniProt NPD GO	ATG5_PONPY	Autophagy protein 5 (APG5-like)	0.23	-	cyt	0	Cytoplasm (By similarity)				275
Q6BJP0 UniProt NPD GO	ATG10_DEBHA	Autophagy-related protein 10 (Autophagy-related E2-like-conjugating enzyme ATG10)	0.23	-	nuc	0	Cytoplasm (By similarity)				221
O93922 UniProt NPD GO	ATG7_PICPA	Autophagy-related protein 7 (Autophagy-related E1-like-activating enzyme ATG7) (Glucose-induced sele ...	0.23	-	cyt	0	Cytoplasm (By similarity)				654
Q9LG86 UniProt NPD GO	IAA2_ORYSA	Auxin-responsive protein IAA2 (Indoleacetic acid-induced protein 2)	0.23	-	nuc	0	Nucleus (By similarity)				238
Q9N1E4 UniProt NPD GO	CD22_GORGO	B-cell receptor CD22 precursor (Siglec-2) (Fragment)	0.23	-	cyt	0	Membrane; single-pass type I membrane protein				332
Q3C2E2 UniProt NPD GO	CD20_CANFA	B-lymphocyte antigen CD20	0.23	-	mit	4	Membrane; multi-pass membrane protein (By similarity)				297
O70201 UniProt NPD GO	BIRC5_MOUSE	Baculoviral IAP repeat-containing protein 5 (Apoptosis inhibitor survivin) (Apoptosis inhibitor 4) ( ...	0.23	-	nuc	0	Cytoplasm. Nucleus. Localizes on chromosome arms and inner centromeres from prophase through metapha ...	cytoplasm [IDA]		1M4M	140
P35613 UniProt NPD GO	BASI_HUMAN	Basigin precursor (Leukocyte activation antigen M6) (Collagenase stimulatory factor) (Extracellular ...	0.23	+	end	2 *	Cell membrane; single-pass type I membrane protein (By similarity). Colocalizes with SLC16A1 and SLC ...		111380		385
P26444 UniProt NPD GO	CRBA2_BOVIN	Beta crystallin A2 (Beta-A2-crystallin)	0.23	-	cyt	0					196
Q91316 UniProt NPD GO	CRB31_RANCA	Beta crystallin A3-1	0.23	-	cyt	0					215
P02522 UniProt NPD GO	CRBB2_BOVIN	Beta crystallin B2 (Beta-crystallin Bp)	0.23	-	nuc	0				2BB2	204
Q8NES3 UniProt NPD GO	LFNG_HUMAN	Beta-1,3-N-acetylglucosaminyltransferase lunatic fringe (EC 2.4.1.222) (O-fucosylpeptide 3-beta-N-ac ...	0.23	-	exc	1 *	Golgi apparatus; Golgi membrane; single-pass type II membrane protein (By similarity)	extracellular region [NAS]	609813		379
Q80WN8 UniProt NPD GO	B4GT3_CRIGR	Beta-1,4-galactosyltransferase 3 (EC 2.4.1.-) (Beta-1,4-GalTase 3) (Beta4Gal-T3) (b4Gal-T3) (UDP-gal ...	0.23	-	mit	1 *	Golgi apparatus; Golgi stack; Golgi stack membrane; single-pass type II membrane protein (By similar ...				395
Q6P768 UniProt NPD GO	B4GT3_RAT	Beta-1,4-galactosyltransferase 3 (EC 2.4.1.-) (Beta-1,4-GalTase 3) (Beta4Gal-T3) (b4Gal-T3) (UDP-gal ...	0.23	-	mit	1 *	Golgi apparatus; Golgi stack; Golgi stack membrane; single-pass type II membrane protein (By similar ...				395
P05814 UniProt NPD GO	CASB_HUMAN	Beta-casein precursor	0.23	-	exc	0	Secreted protein		115460		226

You are viewing entries 47101 to 47150 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.