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
P23927 UniProt NPD GO	CRYAB_MOUSE	Alpha crystallin B chain (Alpha(B)-crystallin) (P23)	0.27	-	mit	0		contractile fiber [IDA] insoluble fraction [IDA] plasma membrane [IDA] soluble fraction [IDA] Z disc [IDA]			175
P26572 UniProt NPD GO	MGAT1_HUMAN	Alpha-1,3-mannosyl-glycoprotein 2-beta-N-acetylglucosaminyltransferase (EC 2.4.1.101) (N-glycosyl-ol ...	0.27	-	end	1 *	Golgi apparatus; Golgi membrane; single-pass type II membrane protein	integral to membrane [TAS]	160995		445
P27115 UniProt NPD GO	MGAT1_RABIT	Alpha-1,3-mannosyl-glycoprotein 2-beta-N-acetylglucosaminyltransferase (EC 2.4.1.101) (N-glycosyl-ol ...	0.27	-	end	1 *	Golgi apparatus; Golgi membrane; single-pass type II membrane protein			2APC	447
Q8GW72 UniProt NPD GO	FUCO1_ARATH	Alpha-L-fucosidase 1 precursor (EC 3.2.1.51) (Alpha-L-fucoside fucohydrolase) (Alpha-1,3/4-fucosidas ...	0.27	-	exc	0	Secreted protein; extracellular space; apoplast				506
Q01634 UniProt NPD GO	IDUA_CANFA	Alpha-L-iduronidase precursor (EC 3.2.1.76)	0.27	-	exc	0	Lysosome				655
P35475 UniProt NPD GO	IDUA_HUMAN	Alpha-L-iduronidase precursor (EC 3.2.1.76)	0.27	-	exc	0	Lysosome		607016		653
P18626 UniProt NPD GO	CAS1_CAPHI	Alpha-S1-casein precursor (Alpha-S1-CN) (Variants A, B, C, D, E and F)	0.27	-	exc	0	Secreted protein				214
Q9SMZ4 UniProt NPD GO	AASS_ARATH	Alpha-aminoadipic semialdehyde synthase (LKR/SDH) (cAt-LKR/SDH) [Includes: Lysine ketoglutarate redu ...	0.27	-	cyt	0	Cytoplasm				1064
P32936 UniProt NPD GO	IAAB_HORVU	Alpha-amylase/trypsin inhibitor CMb precursor (Chloroform/methanol-soluble protein CMb)	0.27	-	exc	0	Secreted protein				149
O55189 UniProt NPD GO	AMBN_MOUSE	Ameloblastin precursor	0.27	-	exc	0	Secreted protein; extracellular space; extracellular matrix	extracellular matrix (sensu Metazoa) [ISS]			407
Q86WK6 UniProt NPD GO	AMGO1_HUMAN	Amphoterin-induced protein 1 precursor (AMIGO-1) (Alivin-2)	0.27	-	exc	1	Membrane; single-pass type I membrane protein (Potential). Associated with axons of neuronal cells ( ...	integral to plasma membrane [ISS]			493
P22968 UniProt NPD GO	ACET_RABIT	Angiotensin-converting enzyme, testis-specific isoform precursor (EC 3.4.15.1) (EC 3.2.1.-) (ACE-T) ...	0.27	-	end	1	Cell membrane; single-pass type I membrane protein (By similarity). Processed form: Secreted protein ...				737
Q92108 UniProt NPD GO	ANXA1_CHICK	Annexin A1 (Annexin I) (Lipocortin I) (Calpactin II) (Chromobindin-9) (p35) (Phospholipase A2 inhibi ...	0.27	-	nuc	0					130
P32069 UniProt NPD GO	TRPX_ARATH	Anthranilate synthase component I-2, chloroplast precursor (EC 4.1.3.27)	0.27	-	cyt	0	Plastid; chloroplast (Probable)				621
P81591 UniProt NPD GO	AMP_IPONI	Antimicrobial protein PN-AMP1 [Contains: Antimicrobial protein PN-AMP2]	0.27	-	mit	0					41
P38977 UniProt NPD GO	ANTA_HYDMA	Antistasin precursor (ATS) (Blood coagulation factor Xa/proclotting enzyme inhibitor)	0.27	-	nuc	0	Secreted protein				220
Q6BEG7 UniProt NPD GO	GHRL_CAPHI	Appetite-regulating hormone precursor (Growth hormone secretagogue) (Growth hormone-releasing peptid ...	0.27	-	exc	0	Secreted protein				116
O08701 UniProt NPD GO	ARGI2_RAT	Arginase-2, mitochondrial precursor (EC 3.5.3.1) (Arginase II) (Non-hepatic arginase) (Kidney-type a ...	0.27	-	mit	0	Mitochondrion	mitochondrion [IMP]			354
Q95MN8 UniProt NPD GO	AIPL1_PAPCY	Aryl-hydrocarbon-interacting protein-like 1	0.27	-	cyt	0	Cytoplasm (By similarity). Nucleus (By similarity)				372
P13913 UniProt NPD GO	ARY1_CHICK	Arylamine N-acetyltransferase, pineal gland isozyme NAT-10 (EC 2.3.1.5) (Arylamine acetylase)	0.27	+	cyt	0					290
P14217 UniProt NPD GO	ARS_CHLRE	Arylsulfatase precursor (EC 3.1.6.1) (AS) (Aryl-sulfate sulphohydrolase)	0.27	-	vac	0	Periplasm				647
P01160 UniProt NPD GO	ANF_HUMAN	Atrial natriuretic factor precursor (ANF) (Atrial natriuretic peptide) (ANP) (Prepronatriodilatin) ( ...	0.27	-	exc	1 *	Secreted protein	extracellular region [NAS]	108780	1ANP	153
Q7SG38 UniProt NPD GO	ATG22_NEUCR	Autophagy-related protein 22	0.27	-	end	12	Vacuole; vacuolar membrane; multi-pass membrane protein (By similarity). Vacuole and punctate struct ...				737
Q4P2U6 UniProt NPD GO	ATG8_USTMA	Autophagy-related protein 8 precursor (Autophagy-related ubiquitin-like modifier atg8)	0.27	-	nuc	0	Membrane-associated through a lipid anchor. Cvt vesicles, autophagosomes and vacuolar (By similarity ...				118
Q38827 UniProt NPD GO	IAA9_ARATH	Auxin-responsive protein IAA9 (Indoleacetic acid-induced protein 9)	0.27	-	nuc	0	Nucleus (By similarity)				338
Q8JGM8 UniProt NPD GO	BID_CHICK	BH3-interacting domain death agonist	0.27	-	mit	0	Cytoplasm (By similarity)				193
Q20681 UniProt NPD GO	BAT38_CAEEL	BTB and MATH domain-containing protein 38	0.27	-	cyt	0					387
Q7TPL3 UniProt NPD GO	KCD10_RAT	BTB/POZ domain-containing protein KCTD10	0.27	-	cyt	0	Nucleus (Probable)				315
P04281 UniProt NPD GO	PRP5_HUMAN	Basic proline-rich peptide IB-1	0.27	-	nuc	0					96
P18572 UniProt NPD GO	BASI_MOUSE	Basigin precursor (Basic immunoglobulin superfamily) (Membrane glycoprotein gp42) (HT7 antigen) (CD1 ...	0.27	+	end	1 *	Cell membrane; single-pass type I membrane protein. Colocalizes with SLC16A1 and SLC16A8. In spermat ...				389
Q9BXK5 UniProt NPD GO	B2L13_HUMAN	Bcl-2-like 13 protein (Protein Mil1) (Bcl-rambo)	0.27	-	nuc	1	Isoform 2: Mitochondrion. Isoform 2, isoform 3: Nucleus (Probable)	integral to membrane [IDA] mitochondrion [NAS]			485
Q96LC9 UniProt NPD GO	BMF_HUMAN	Bcl-2-modifying factor	0.27	-	nuc	0		myosin [ISS]	606266		184
Q9R1U9 UniProt NPD GO	RFNG_RAT	Beta-1,3-N-acetylglucosaminyltransferase radical fringe (EC 2.4.1.222) (O-fucosylpeptide 3-beta-N-ac ...	0.27	-	mit	1 *	Golgi apparatus; Golgi membrane; single-pass type II membrane protein (Potential)				334
O60909 UniProt NPD GO	B4GT2_HUMAN	Beta-1,4-galactosyltransferase 2 (EC 2.4.1.-) (Beta-1,4-GalTase 2) (Beta4Gal-T2) (b4Gal-T2) (UDP-gal ...	0.27	-	cyt	1 *	Golgi apparatus; Golgi stack; Golgi stack membrane; single-pass type II membrane protein. Trans cist ...		604013		372
Q91YY2 UniProt NPD GO	B4GT3_MOUSE	Beta-1,4-galactosyltransferase 3 (EC 2.4.1.-) (Beta-1,4-GalTase 3) (Beta4Gal-T3) (b4Gal-T3) (UDP-gal ...	0.27	-	mit	1 *	Golgi apparatus; Golgi stack; Golgi stack membrane; single-pass type II membrane protein (By similar ...				395
Q13425 UniProt NPD GO	SNTB2_HUMAN	Beta-2-syntrophin (59 kDa dystrophin-associated protein A1 basic component 2) (Syntrophin 3) (SNT3) ...	0.27	-	mit	0	Membrane-associated. In muscle, it is exclusively localized at the neuromuscular junction (By simila ...	dystrophin-associated glycoprotein complex [TAS] membrane fraction [TAS]	600027		540
P29067 UniProt NPD GO	ARRB2_RAT	Beta-arrestin-2 (Arrestin, beta 2)	0.27	-	mit	0	Cytoplasm (By similarity). Nucleus (By similarity)	postsynaptic membrane [IDA]			410
Q9NSA3 UniProt NPD GO	CNBP1_HUMAN	Beta-catenin-interacting protein 1 (Inhibitor of beta-catenin and Tcf-4)	0.27	-	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity)		607758	1T08	81
O97946 UniProt NPD GO	BD01_CAPHI	Beta-defensin 1 precursor (BD-1) (Defensin, beta 1)	0.27	-	mit	1 *	Secreted protein				64
Q8N690 UniProt NPD GO	DB119_HUMAN	Beta-defensin 119 precursor (Defensin, beta 119) (Beta-defensin 19) (DEFB-19)	0.27	-	nuc	0	Secreted protein (Potential)				84
Q29548 UniProt NPD GO	HEXB_PIG	Beta-hexosaminidase beta chain precursor (EC 3.2.1.52) (N-acetyl-beta-glucosaminidase) (Beta-N-acety ...	0.27	-	cyt	0	Lysosome				531
P07382 UniProt NPD GO	DRTS_LEIMA	Bifunctional dihydrofolate reductase-thymidylate synthase (DHFR-TS) [Includes: Dihydrofolate reducta ...	0.27	-	cyt	0					520
Q9ES83 UniProt NPD GO	POPD1_MOUSE	Blood vessel epicardial substance (Popeye domain-containing protein 1) (Popeye protein 1)	0.27	-	end	3 *	Membrane; multi-pass membrane protein (Potential)	membrane [IDA]			358
Q61711 UniProt NPD GO	SIAL_MOUSE	Bone sialoprotein-2 precursor (Bone sialoprotein II) (BSP II) (Cell-binding sialoprotein) (Integrin- ...	0.27	-	exc	0	Secreted protein				324
P01056 UniProt NPD GO	IBB_PHALU	Bowman-Birk type proteinase inhibitor	0.27	-	nuc	0				1H34	83
P80321 UniProt NPD GO	IBB_MEDSC	Bowman-Birk type proteinase inhibitor (MSTI)	0.27	-	nuc	0				1MVZ	62
P81484 UniProt NPD GO	IBB3_PHAVU	Bowman-Birk type proteinase inhibitor PVI-3(2)	0.27	-	nuc	0					85
P81483 UniProt NPD GO	IBB4_PHAVU	Bowman-Birk type proteinase inhibitor PVI-4	0.27	-	nuc	0					85
P01062 UniProt NPD GO	IBB_PHAAU	Bowman-Birk type trypsin inhibitor	0.27	-	nuc	0				1SMF	72
P14082 UniProt NPD GO	BDNF_PIG	Brain-derived neurotrophic factor precursor (BDNF)	0.27	-	nuc	0	Secreted protein				252

You are viewing entries 42951 to 43000 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.