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
Q7Z465 UniProt NPD GO	BNIPL_HUMAN	Bcl-2/adenovirus E1B 19 kDa-interacting protein 2-like protein	0.34	-	nuc	0		cytosol [IDA] nucleus [IDA]			357
P11843 UniProt NPD GO	CRBA1_BOVIN	Beta crystallin A3 [Contains: Beta crystallin A3, isoform A1, Delta4 form; Beta crystallin A3, isofo ...	0.34	-	nuc	0					215
P48646 UniProt NPD GO	CRBS1_CHICO	Beta crystallin S-1 (Gamma crystallin S-1)	0.34	-	nuc	0					172
Q30KL5 UniProt NPD GO	DB112_PANTR	Beta-defensin 112 precursor (Defensin, beta 112)	0.34	-	nuc	0	Secreted protein (By similarity)				113
Q39693 UniProt NPD GO	INV3_DAUCA	Beta-fructofuranosidase, insoluble isoenzyme 3 precursor (EC 3.2.1.26) (Sucrose hydrolase 3) (Invert ...	0.34	-	mit	1 *	Cell wall. Ionically bound to the cell wall				583
P08236 UniProt NPD GO	BGLR_HUMAN	Beta-glucuronidase precursor (EC 3.2.1.31) (Beta-G1)	0.34	-	end	1 *	Lysosome		253220	1BHG	651
O77695 UniProt NPD GO	BGLR_CERAE	Beta-glucuronidase precursor (EC 3.2.1.31) (Fragment)	0.34	-	vac	0	Lysosome				648
P21664 UniProt NPD GO	LACB2_FELCA	Beta-lactoglobulin-2 (Beta-LG-2) (Beta-lactoglobulin II)	0.34	-	nuc	0					163
O54820 UniProt NPD GO	PAPS1_CAVPO	Bifunctional 3'-phosphoadenosine 5'-phosphosulfate synthetase 1 (PAPS synthetase 1) (PAPSS 1) (Sulfu ...	0.34	-	cyt	0		intracellular [ISS]			624
Q66KB9 UniProt NPD GO	BL1S2_XENTR	Biogenesis of lysosome-related organelles complex-1 subunit 2	0.34	-	nuc	0	Centrosome (By similarity)				147
Q8BGS2 UniProt NPD GO	BOLA2_MOUSE	BolA-like protein 2	0.34	-	cyt	0				1V9J	86
P01063 UniProt NPD GO	IBBC2_SOYBN	Bowman-Birk type proteinase inhibitor C-II precursor	0.34	-	nuc	0					83
P09863 UniProt NPD GO	IBB1_WHEAT	Bowman-Birk type proteinase inhibitor I-2B (Fragment)	0.34	-	nuc	0					56
P80492 UniProt NPD GO	BRAC2_BRAFL	Brachyury protein homolog 2 (AmBra-2)	0.34	-	nuc	0	Nucleus (By similarity)				440
Q95106 UniProt NPD GO	BDNF_BOVIN	Brain-derived neurotrophic factor precursor (BDNF)	0.34	-	nuc	0	Secreted protein				250
P63054 UniProt NPD GO	PEP19_MOUSE	Brain-specific polypeptide PEP-19 (Brain-specific antigen PCP-4) (Purkinje cell protein 4)	0.34	-	nuc	0					61
P63055 UniProt NPD GO	PEP19_RAT	Brain-specific polypeptide PEP-19 (Brain-specific antigen PCP-4) (Purkinje cell protein 4)	0.34	-	nuc	0					61
Q805D6 UniProt NPD GO	ANFC1_FUGRU	C-type natriuretic peptide 1 precursor	0.34	-	nuc	0	Secreted protein				126
P20968 UniProt NPD GO	ANFC_RANCA	C-type natriuretic peptide 1 precursor (CNP I)	0.34	-	nuc	0	Secreted protein				129
P23259 UniProt NPD GO	ANFC_SCYCA	C-type natriuretic peptide prohormone precursor (CNP-115) [Contains: CNP-39; CNP-38; CNP-22]	0.34	-	nuc	0	Secreted protein				115
P51749 UniProt NPD GO	CD40L_BOVIN	CD40 ligand (CD40-L) (Tumor necrosis factor ligand superfamily member 5) (CD154 antigen) [Contains: ...	0.34	-	nuc	1 *	Cell membrane; single-pass type II membrane protein (By similarity). Processed form: Secreted protei ...	integral to membrane [ISS]			261
P13750 UniProt NPD GO	1B01_PANTR	CHLA class I histocompatibility antigen, B-1 alpha chain precursor (Fragment)	0.34	-	end	1	Membrane; single-pass type I membrane protein				359
Q8BXC6 UniProt NPD GO	COMD2_MOUSE	COMM domain-containing protein 2	0.34	-	cyt	0					199
Q5R610 UniProt NPD GO	COMD2_PONPY	COMM domain-containing protein 2	0.34	-	cyt	0					199
Q8SYG2 UniProt NPD GO	CSN3_DROME	COP9 signalosome complex subunit 3 (Signalosome subunit 3) (Dch3)	0.34	-	cyt	0	Cytoplasm (Probable). Nucleus (Probable)	signalosome complex [IMP]			445
Q8VBV7 UniProt NPD GO	CSN8_MOUSE	COP9 signalosome complex subunit 8 (Signalosome subunit 8) (SGN8) (JAB1-containing signalosome subun ...	0.34	-	cyt	0	Cytoplasm (By similarity). Nucleus (By similarity)	nucleus [IDA] signalosome complex [IDA]			209
Q03981 UniProt NPD GO	CSN9_YEAST	COP9 signalosome complex subunit 9	0.34	-	nuc	0	Cytoplasm (Probable). Nucleus (Probable)	signalosome complex [IDA]			162
P19535 UniProt NPD GO	CADH3_BOVIN	Cadherin-3 (Placental-cadherin) (P-cadherin) (Fragment)	0.34	-	nuc	1	Membrane; single-pass type I membrane protein				491
Q9ESK8 UniProt NPD GO	KCMB4_RAT	Calcium-activated potassium channel subunit beta 4 (Calcium-activated potassium channel, subfamily M ...	0.34	-	end	2 *	Membrane; multi-pass membrane protein (By similarity)	voltage-gated potassium channel complex [ISS]			210
Q8RUN1 UniProt NPD GO	ACA3_ORYSA	Calcium-transporting ATPase 3, plasma membrane-type (EC 3.6.3.8) (Ca(2+)-ATPase isoform 3)	0.34	-	end	8	Membrane; multi-pass membrane protein (By similarity)				1043
Q91VB2 UniProt NPD GO	KCC1G_MOUSE	Calcium/calmodulin-dependent protein kinase type 1G (EC 2.7.11.17) (CaM kinase IG) (CaM kinase I gam ...	0.34	-	nuc	0	Cytoplasm. Golgi apparatus; Golgi membrane; peripheral membrane protein. Cell membrane; peripheral m ...	calcium- and calmodulin-dependent protein k... [IDA] endomembrane system [IDA] plasma membrane [IDA]			477
Q8L3R2 UniProt NPD GO	CML41_ARATH	Calmodulin-like protein 41	0.34	-	mit	0					205
P14211 UniProt NPD GO	CALR_MOUSE	Calreticulin precursor (CRP55) (Calregulin) (HACBP) (ERp60)	0.34	-	end	0	Endoplasmic reticulum; endoplasmic reticulum lumen. Associated with the lytic granules in the cytoly ...	external side of plasma membrane [IDA] extracellular space [IDA]			416
P18418 UniProt NPD GO	CALR_RAT	Calreticulin precursor (CRP55) (Calregulin) (HACBP) (ERp60) (CALBP) (Calcium-binding protein 3) (CAB ...	0.34	-	end	0	Endoplasmic reticulum; endoplasmic reticulum lumen	endoplasmic reticulum [TAS] soluble fraction [TAS]		1K9C	416
Q08331 UniProt NPD GO	CALB2_MOUSE	Calretinin (CR)	0.34	-	cyt	0		gap junction [IDA]			271
P47728 UniProt NPD GO	CALB2_RAT	Calretinin (CR)	0.34	-	cyt	0					271
P22676 UniProt NPD GO	CALB2_HUMAN	Calretinin (CR) (29 kDa calbindin)	0.34	-	cyt	0			114051		271
P16870 UniProt NPD GO	CBPE_HUMAN	Carboxypeptidase E precursor (EC 3.4.17.10) (CPE) (Carboxypeptidase H) (CPH) (Enkephalin convertase) ...	0.34	-	mit	0	Secretory granules of pancreatic islets, adrenal gland, pituitary and brain	plasma membrane [TAS]	114855		476
Q8N436 UniProt NPD GO	CPXM2_HUMAN	Carboxypeptidase-like protein X2 precursor	0.34	-	exc	1 *	Secreted protein (Probable)				756
Q7Z692 UniProt NPD GO	CEA19_HUMAN	Carcinoembryonic antigen-related cell adhesion molecule 19 precursor (Carcinoembryonic antigen-like ...	0.34	-	nuc	1	Membrane; single-pass type I membrane protein (Potential)		606691		300
P43639 UniProt NPD GO	CSK2B_YEAST	Casein kinase II subunit beta (CK II beta)	0.34	-	cyt	0		protein kinase CK2 complex [IDA]			278
Q9CQC5 UniProt NPD GO	BORG2_MOUSE	Cdc42 effector protein 3 (Binder of Rho GTPases 2)	0.34	-	nuc	0	Intracytoplasmic membrane; peripheral membrane protein (By similarity)				254
Q96AQ7 UniProt NPD GO	CIDEC_HUMAN	Cell death activator CIDE-3 (Cell death-inducing DFFA-like effector protein C) (Fat-specific protein ...	0.34	-	mit	0	Cytoplasm. Cytoplasmic in a punctate manner	cytosol [IDA]			238
O75794 UniProt NPD GO	CD123_HUMAN	Cell division cycle protein 123 homolog (Protein D123) (HT-1080) (PZ32)	0.34	-	cyt	0	Cytoplasm (By similarity)				336
Q9UJX2 UniProt NPD GO	CDC23_HUMAN	Cell division cycle protein 23 homolog (Anaphase-promoting complex subunit 8) (APC8) (Cyclosome subu ...	0.34	-	nuc	0		anaphase-promoting complex [IDA]	603462		591
O78516 UniProt NPD GO	FTSH_GUITH	Cell division protein ftsH homolog (EC 3.4.24.-)	0.34	-	end	2 *	Plastid; chloroplast; chloroplast membrane; multi-pass membrane protein (Potential)				631
Q12798 UniProt NPD GO	CETN1_HUMAN	Centrin-1 (Caltractin isoform 2)	0.34	-	cyt	0	Centrosome. Centrosome of interphase and mitotic cells	centrosome [TAS] cytoskeleton [TAS] spindle pole body [TAS]	603187		172
Q8N0S6 UniProt NPD GO	CENPL_HUMAN	Centromere protein L (CENP-L)	0.34	-	cyt	0					344
Q8NI60 UniProt NPD GO	CABC1_HUMAN	Chaperone-activity of bc1 complex-like, mitochondrial precursor (Chaperone-ABC1-like)	0.34	-	cyt	0	Mitochondrion		606980		647
Q4R574 UniProt NPD GO	CHMP3_MACFA	Charged multivesicular body protein 3 (Chromatin-modifying protein 3) (Vacuolar protein sorting 24)	0.34	-	nuc	0	Cytoplasm; cytosol. Membrane; lipid-anchor				221

You are viewing entries 36501 to 36550 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.