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
Q9EPV9 UniProt NPD GO	BD05_MOUSE	Beta-defensin 5 precursor (Defensin, beta 5) (BD-5) (mBD-5)	0.09	-	exc	0	Secreted protein (By similarity)				64
O19015 UniProt NPD GO	BGAL_FELCA	Beta-galactosidase precursor (EC 3.2.1.23) (Lactase) (Acid beta-galactosidase)	0.09	-	exc	0	Lysosome				669
P06865 UniProt NPD GO	HEXA_HUMAN	Beta-hexosaminidase alpha chain precursor (EC 3.2.1.52) (N-acetyl-beta-glucosaminidase) (Beta-N-acet ...	0.09	-	cyt	0	Lysosome		272800	1QBC	529
Q5RC84 UniProt NPD GO	HEXA_PONPY	Beta-hexosaminidase alpha chain precursor (EC 3.2.1.52) (N-acetyl-beta-glucosaminidase) (Beta-N-acet ...	0.09	-	cyt	0	Lysosome (By similarity)				529
P02754 UniProt NPD GO	LACB_BOVIN	Beta-lactoglobulin precursor (Beta-LG) (Allergen Bos d 5)	0.09	-	nuc	0	Secreted protein			3BLG	178
P19647 UniProt NPD GO	LACB2_EQUAS	Beta-lactoglobulin-2 (Beta-LG-2) (Beta-lactoglobulin II, minor monomeric)	0.09	-	cyt	0					163
Q95327 UniProt NPD GO	MANBA_CAPHI	Beta-mannosidase precursor (EC 3.2.1.25) (Lysosomal beta A mannosidase) (Mannanase) (Mannase)	0.09	-	nuc	0	Lysosome				879
Q16585 UniProt NPD GO	SGCB_HUMAN	Beta-sarcoglycan (Beta-SG) (43 kDa dystrophin-associated glycoprotein) (43DAG) (A3b)	0.09	-	gol	1	Sarcolemma; sarcolemmal membrane; single-pass type II membrane protein (By similarity)	integral to plasma membrane [TAS] sarcoglycan complex [TAS]	604286		318
Q05763 UniProt NPD GO	DRTS2_ARATH	Bifunctional dihydrofolate reductase-thymidylate synthase 2 (DHFR-TS 2) [Includes: Dihydrofolate red ...	0.09	-	cyt	0					518
Q02353 UniProt NPD GO	NDST1_RAT	Bifunctional heparan sulfate N-deacetylase/N-sulfotransferase 1 (EC 2.8.2.8) (Glucosaminyl N-deacety ...	0.09	-	gol	1 *	Golgi apparatus; Golgi membrane; single-pass type II membrane protein				882
Q06520 UniProt NPD GO	ST2A1_HUMAN	Bile salt sulfotransferase (EC 2.8.2.14) (Hydroxysteroid Sulfotransferase) (HST) (Dehydroepiandroste ...	0.09	-	cyt	0	Cytoplasm		125263	1OV4	284
P07882 UniProt NPD GO	CEL_RAT	Bile salt-activated lipase precursor (EC 3.1.1.3) (EC 3.1.1.13) (BAL) (Bile salt-stimulated lipase) ...	0.09	-	mit	0		cytoplasm [IDA]			612
P53004 UniProt NPD GO	BIEA_HUMAN	Biliverdin reductase A precursor (EC 1.3.1.24) (Biliverdin-IX alpha-reductase) (BVR A)	0.09	-	cyt	0	Cytoplasm		109750		296
P50583 UniProt NPD GO	AP4A_HUMAN	Bis(5'-nucleosyl)-tetraphosphatase [Asymmetrical] (EC 3.6.1.17) (Diadenosine 5',5'''-P1,P4-tetraphos ...	0.09	-	mit	0			602852	1XSC	146
P33718 UniProt NPD GO	BXA1_SAMCY	Bombyxin A-1 homolog precursor [Contains: Bombyxin A-1 homolog B chain; Bombyxin A-1 homolog A chain ...	0.09	-	mit	1 *	Secreted protein				99
P26732 UniProt NPD GO	BXA9_BOMMO	Bombyxin A-9 precursor (BBX-A9) (4K-prothoracicotropic hormone) (4K-PTTH) [Contains: Bombyxin A-9 B ...	0.09	-	exc	0	Secreted protein				92
Q8W4Y8 UniProt NPD GO	IBB_LENCU	Bowman-Birk type proteinase inhibitor precursor (Trypsin/chymotrypsin inhibitor)	0.09	-	exc	0					110
P01021 UniProt NPD GO	BPPB_AGKHA	Bradykinin-potentiating peptide B (Angiotensin-converting enzyme inhibitor)	0.09	-		0					11
Q9M401 UniProt NPD GO	BCAT3_ARATH	Branched-chain-amino-acid aminotransferase 3, chloroplast precursor (EC 2.6.1.42) (Atbcat-3)	0.09	-	mit	0	Plastid; chloroplast				413
P54688 UniProt NPD GO	BCAT_CAEEL	Branched-chain-amino-acid aminotransferase, cytosolic (EC 2.6.1.42) (BCAT) (ECA39 protein)	0.09	-	mit	0	Cytoplasm				415
Q9ASR4 UniProt NPD GO	BCAL2_ARATH	Branched-chain-amino-acid aminotransferase-like protein 2	0.09	-	cyt	0					559
Q13410 UniProt NPD GO	BT1A1_HUMAN	Butyrophilin subfamily 1 member A1 precursor (BT)	0.09	-	end	1	Membrane; single-pass type I membrane protein	integral to plasma membrane [TAS]	601610		526
Q2Y2P0 UniProt NPD GO	CCR1_MACFA	C-C chemokine receptor type 1 (C-C CKR-1) (CC-CKR-1) (CCR-1) (CCR1) (CD191 antigen)	0.09	-	end	6 *	Membrane; multi-pass membrane protein				355
P56482 UniProt NPD GO	CCR1_MACMU	C-C chemokine receptor type 1 (C-C CKR-1) (CC-CKR-1) (CCR-1) (CCR1) (CD191 antigen)	0.09	-	end	6 *	Membrane; multi-pass membrane protein				355
O55193 UniProt NPD GO	CCR2_RAT	C-C chemokine receptor type 2 (C-C CKR-2) (CC-CKR-2) (CCR-2) (CCR2) (CD192 antigen)	0.09	-	end	6	Membrane; multi-pass membrane protein				373
P02742 UniProt NPD GO	CRP_RABIT	C-reactive protein precursor	0.09	-	mit	0	Secreted protein				225
Q6UXB4 UniProt NPD GO	CLC4G_HUMAN	C-type lectin domain family 4 member G	0.09	-	mit	1 *	Membrane; single-pass type II membrane protein (Potential)				293
Q8AXR3 UniProt NPD GO	ANFC1_ONCMY	C-type natriuretic peptide 1 precursor (C-type natriuretic peptide I) (CNP-22 I)	0.09	-	exc	0	Secreted protein				131
O97605 UniProt NPD GO	CD40L_FELCA	CD40 ligand (CD40-L) (Tumor necrosis factor ligand superfamily member 5) (CD154 antigen) [Contains: ...	0.09	-	mit	1 *	Cell membrane; single-pass type II membrane protein (By similarity). Processed form: Secreted protei ...	integral to membrane [ISS]			260
Q9Z0M6 UniProt NPD GO	CD97_MOUSE	CD97 antigen precursor	0.09	-	end	7	Membrane; multi-pass membrane protein	integral to membrane [TAS]			818
Q95ZE2 UniProt NPD GO	PSS_ENCCU	CDP-diacylglycerol--serine O-phosphatidyltransferase (EC 2.7.8.8) (Phosphatidylserine synthase)	0.09	-	end	9 *	Membrane; peripheral membrane protein (By similarity)				384
Q9NX76 UniProt NPD GO	CKLF6_HUMAN	CKLF-like MARVEL transmembrane domain-containing protein 6 (Chemokine-like factor superfamily member ...	0.09	-	end	3	Membrane; multi-pass membrane protein		607889		183
Q6Z4G8 UniProt NPD GO	COBL1_ORYSA	COBRA-like 1 protein precursor (BRITTLE CULM1-like 6 protein)	0.09	-	end	1	Cell membrane; lipid-anchor; GPI-anchor (Potential)				446
Q86VX2 UniProt NPD GO	COMD7_HUMAN	COMM domain-containing protein 7	0.09	-	cyt	0					200
P68358 UniProt NPD GO	CSN3_BRAOL	COP9 signalosome complex subunit 3 (Signalosome subunit 3) (FUSCA protein 11) (FUSCA11) (Fragments)	0.09	-	nuc	0	Cytoplasm. Nucleus				55
O74638 UniProt NPD GO	PYRG_GIBZE	CTP synthase (EC 6.3.4.2) (UTP--ammonia ligase) (CTP synthetase)	0.09	-	mit	1 *					580
O93319 UniProt NPD GO	CAD11_CHICK	Cadherin-11 precursor	0.09	-	nuc	1 *	Membrane; single-pass type I membrane protein (Potential)				792
O88338 UniProt NPD GO	CAD16_MOUSE	Cadherin-16 precursor (Kidney-specific cadherin) (Ksp-cadherin)	0.09	-	cyt	1	Membrane; single-pass type I membrane protein (Probable)				830
Q28634 UniProt NPD GO	CAD16_RABIT	Cadherin-16 precursor (Kidney-specific cadherin) (Ksp-cadherin)	0.09	-	end	1	Membrane; single-pass type I membrane protein				829
P42322 UniProt NPD GO	CANB1_NAEGR	Calcineurin subunit B (Protein phosphatase 2B regulatory subunit) (Calcineurin regulatory subunit)	0.09	-	nuc	0					177
Q63811 UniProt NPD GO	CANB2_MOUSE	Calcineurin subunit B isoform 2 (Protein phosphatase 2B regulatory subunit 2) (Protein phosphatase 3 ...	0.09	-	cyt	0					178
Q10063 UniProt NPD GO	EHS1_SCHPO	Calcium influx-promoting protein ehs1 precursor	0.09	-	nuc	0					486
Q09011 UniProt NPD GO	CAST_SOLTU	Calcium-binding protein CAST	0.09	-	cyt	0					199
Q9D424 UniProt NPD GO	CABYR_MOUSE	Calcium-binding tyrosine phosphorylation-regulated protein (Calcium-binding protein 86) (Testis-spec ...	0.09	-	nuc	0	Cytoplasm. Localizes to fibrous sheath including the surface of the longitudinal columns and ribs of ...	flagellum (sensu Eukaryota) [IDA]			453
Q292Q0 UniProt NPD GO	ATC1_DROPS	Calcium-transporting ATPase sarcoplasmic/endoplasmic reticulum type (EC 3.6.3.8) (Calcium pump)	0.09	-	end	8	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein. Sarcoplasmic ret ...	sarcoplasmic reticulum [ISS]			1020
P57709 UniProt NPD GO	AT2C1_BOVIN	Calcium-transporting ATPase type 2C member 1 (EC 3.6.3.8) (ATPase 2C1) (Secretory pathway Ca(2+)-tra ...	0.09	-	end	8	Golgi apparatus; Golgi membrane; multi-pass membrane protein (By similarity)				953
P04630 UniProt NPD GO	CALL_CAEEL	Calmodulin-like protein	0.09	-	cyt	0					161
P49258 UniProt NPD GO	CALL_DROME	Calmodulin-related protein 97A (Protein androcam)	0.09	-	cyt	0		cytoplasm [IDA] nucleus [IDA]			148
Q759K3 UniProt NPD GO	PALB_ASHGO	Calpain-like protease palB/RIM13 (EC 3.4.22.-) (Cysteine protease RIM13)	0.09	-	cyt	0					694
P52193 UniProt NPD GO	CALR_BOVIN	Calreticulin precursor (CRP55) (Calregulin) (HACBP)	0.09	-	end	0	Endoplasmic reticulum; endoplasmic reticulum lumen				417

You are viewing entries 65801 to 65850 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.