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
P09440 UniProt NPD GO	C1TM_YEAST	C-1-tetrahydrofolate synthase, mitochondrial precursor (C1-THF synthase) [Includes: Methylenetetrahy ...	0.15	-	mit	0	Mitochondrion	mitochondrion [IDA]			975
Q924I3 UniProt NPD GO	CCRL1_MOUSE	C-C chemokine receptor type 11 (C-C CKR-11) (CC-CKR-11) (CCR-11) (CC chemokine receptor-like 1) (CCR ...	0.15	+	end	7 *	Membrane; multi-pass membrane protein (By similarity)				350
Q95NC6 UniProt NPD GO	CCR5_TRAJO	C-C chemokine receptor type 5 (C-C CKR-5) (CC-CKR-5) (CCR-5) (CCR5) (CD195 antigen)	0.15	-	end	6 *	Membrane; multi-pass membrane protein				352
O54689 UniProt NPD GO	CCR6_MOUSE	C-C chemokine receptor type 6 (C-C CKR-6) (CC-CKR-6) (CCR-6) (KY411) (CD196 antigen)	0.15	-	end	7 *	Membrane; multi-pass membrane protein				367
P51684 UniProt NPD GO	CCR6_HUMAN	C-C chemokine receptor type 6 (C-C CKR-6) (CC-CKR-6) (CCR-6) (LARC receptor) (GPR-CY4) (GPRCY4) (Che ...	0.15	-	end	7 *	Membrane; multi-pass membrane protein	integral to plasma membrane [TAS] plasma membrane [TAS]	601835		374
Q04683 UniProt NPD GO	CXCR5_MOUSE	C-X-C chemokine receptor type 5 (CXC-R5) (CXCR-5) (Burkitt lymphoma receptor 1 homolog) (CD185 antig ...	0.15	+	end	7	Membrane; multi-pass membrane protein				374
P28557 UniProt NPD GO	PHCA_AGLNE	C-phycocyanin alpha chain	0.15	-	nuc	0	Plastid; chloroplast				162
Q13166 UniProt NPD GO	CATR1_HUMAN	CATR tumorigenic conversion 1 protein (CATR1.3)	0.15	-	nuc	0			600676		79
Q9UGN4 UniProt NPD GO	CM35H_HUMAN	CMRF35-H antigen precursor (CMRF35-H9) (CMRF-35-H9) (CD300a antigen) (Inhibitory receptor protein 60 ...	0.15	-	end	1	Membrane; single-pass type I membrane protein (Potential)		606790		299
Q9H0A8 UniProt NPD GO	COMD4_HUMAN	COMM domain-containing protein 4	0.15	-	mit	0					199
Q9CQ02 UniProt NPD GO	COMD4_MOUSE	COMM domain-containing protein 4	0.15	-	mit	0					199
P68352 UniProt NPD GO	CSN1_BRAOL	COP9 signalosome complex subunit 1 (CSN complex subunit 1) (Constitutive photomorphogenesis protein ...	0.15	-	nuc	0	Cytoplasm. Nucleus				37
Q4IJM4 UniProt NPD GO	CSN5_GIBZE	COP9 signalosome complex subunit 5 (EC 3.4.-.-)	0.15	-	cyt	0	Cytoplasm (By similarity). Nucleus (By similarity)				340
Q7KTH8 UniProt NPD GO	CSN8_DROME	COP9 signalosome complex subunit 8 (Signalosome subunit 8) (Dch8)	0.15	-	cyt	0	Cytoplasm (Probable). Nucleus (Probable)	signalosome complex [IMP]			182
O15194 UniProt NPD GO	CTDSL_HUMAN	CTD small phosphatase-like protein (CTDSP-like) (Small C-terminal domain phosphatase 3) (Small CTD p ...	0.15	-	cyt	0	Nucleus (Potential)		608592		276
O75309 UniProt NPD GO	CAD16_HUMAN	Cadherin-16 precursor (Kidney-specific cadherin) (Ksp-cadherin)	0.15	-	end	1	Membrane; single-pass type I membrane protein (Probable)		603118		829
Q28067 UniProt NPD GO	KCMB1_BOVIN	Calcium-activated potassium channel subunit beta 1 (Calcium-activated potassium channel, subfamily M ...	0.15	-	end	2 *	Membrane; multi-pass membrane protein				190
Q16558 UniProt NPD GO	KCMB1_HUMAN	Calcium-activated potassium channel subunit beta 1 (Calcium-activated potassium channel, subfamily M ...	0.15	-	end	2 *	Membrane; multi-pass membrane protein		608622		190
Q9NPB3 UniProt NPD GO	CABP2_HUMAN	Calcium-binding protein 2 (CaBP2)	0.15	-	mit	0			607314		219
O75952 UniProt NPD GO	CABYR_HUMAN	Calcium-binding tyrosine phosphorylation-regulated protein (Calcium-binding protein 86) (Testis-spec ...	0.15	-	nuc	0	Cytoplasm. Localized to fibrous sheath including the surface of the longitudinal columns and ribs of ...				493
Q16974 UniProt NPD GO	KPC1_APLCA	Calcium-dependent protein kinase C (EC 2.7.11.13) (APL I)	0.15	-	mit	0	Cytoplasm. Translocated to neuronal membranes				649
P41150 UniProt NPD GO	CAYP1_RABIT	Calcyphosin (Calcyphosine) (R2D5 antigen)	0.15	-	cyt	0	Cytoplasm				189
P60206 UniProt NPD GO	CALM_AJECA	Calmodulin (CaM)	0.15	-	cyt	0					148
P60205 UniProt NPD GO	CALM_ASPOR	Calmodulin (CaM)	0.15	-	cyt	0					148
P60204 UniProt NPD GO	CALM_EMENI	Calmodulin (CaM)	0.15	-	cyt	0					148
P30188 UniProt NPD GO	CALL1_ARATH	Calmodulin-like protein 1	0.15	-	mit	0					216
Q9JJG7 UniProt NPD GO	CALN1_MOUSE	Calneuron-1	0.15	-	nuc	1					219
P04632 UniProt NPD GO	CPNS1_HUMAN	Calpain small subunit 1 (CSS1) (Calcium-dependent protease small subunit 1) (Calcium-dependent prote ...	0.15	-	cyt	0	Cytoplasm (By similarity). Cell membrane (By similarity). Translocates to the plasma membrane upon c ...		114170	1KFX	268
Q64537 UniProt NPD GO	CPNS1_RAT	Calpain small subunit 1 (CSS1) (Calcium-dependent protease small subunit 1) (Calcium-dependent prote ...	0.15	-	cyt	0	Cytoplasm. Cell membrane. Translocates to the plasma membrane upon calcium binding (By similarity). ...			1U5I	270
P37803 UniProt NPD GO	CNN1_MELGA	Calponin-1 (Calponin, smooth muscle) (Fragment)	0.15	-	nuc	0					176
Q9D9Q6 UniProt NPD GO	CALR3_MOUSE	Calreticulin-3 precursor (Calreticulin-2)	0.15	-	exc	0	Endoplasmic reticulum; endoplasmic reticulum lumen (By similarity)				380
Q9Y2W7 UniProt NPD GO	CSEN_HUMAN	Calsenilin (DRE-antagonist modulator) (DREAM) (Kv channel-interacting protein 3) (KChIP3) (A-type po ...	0.15	-	cyt	0	Cytoplasm. Cell membrane; lipid-anchor (By similarity). Also membrane-bound; associated with the pla ...		604662		256
P43645 UniProt NPD GO	CATR_SPESI	Caltractin (Centrin) (Fragment)	0.15	-	cyt	0					148
O75638 UniProt NPD GO	CTAG2_HUMAN	Cancer/testis antigen 2 (L antigen family member 1) (LAGE-1 protein) (ESO-2 protein)	0.15	-	nuc	0			300396	2BNQ	210
P43095 UniProt NPD GO	CARP6_CANAL	Candidapepsin-6 precursor (EC 3.4.23.24) (Aspartate protease 6) (ACP 6) (Secreted aspartic protease ...	0.15	-	mit	0	Secreted protein				418
Q8C196 UniProt NPD GO	CPSM_MOUSE	Carbamoyl-phosphate synthase [ammonia], mitochondrial precursor (EC 6.3.4.16) (Carbamoyl-phosphate s ...	0.15	-	mit	0	Mitochondrion (By similarity)				1500
Q5RBZ6 UniProt NPD GO	CHSTA_PONPY	Carbohydrate sulfotransferase 10 (EC 2.8.2.-) (HNK-1 sulfotransferase) (HNK1ST) (HNK-1ST)	0.15	-	cyt	1 *	Golgi apparatus; Golgi membrane; single-pass type II membrane protein (By similarity)				356
O43529 UniProt NPD GO	CHSTA_HUMAN	Carbohydrate sulfotransferase 10 (EC 2.8.2.-) (HNK-1 sulfotransferase) (HNK1ST) (HNK-1ST) (huHNK-1ST ...	0.15	-	cyt	1 *	Golgi apparatus; Golgi membrane; single-pass type II membrane protein (By similarity)	Golgi apparatus [TAS] membrane fraction [TAS]	606376		356
O54702 UniProt NPD GO	CHSTA_RAT	Carbohydrate sulfotransferase 10 (EC 2.8.2.-) (HNK-1 sulfotransferase) (HNK1ST) (HNK-1ST) (raHNK-1ST ...	0.15	-	cyt	1 *	Golgi apparatus; Golgi membrane; single-pass type II membrane protein (By similarity)				356
P84537 UniProt NPD GO	CAH_LOBCS	Carbonic anhydrase (EC 4.2.1.1) (Carbonate dehydratase) (Matrix protein MPL-2) (Fragment)	0.15	-	cyt	0					175
P13634 UniProt NPD GO	CAH1_MOUSE	Carbonic anhydrase 1 (EC 4.2.1.1) (Carbonic anhydrase I) (Carbonate dehydratase I) (CA-I)	0.15	-	nuc	0	Cytoplasm				260
Q8N1Q1 UniProt NPD GO	CAH13_HUMAN	Carbonic anhydrase 13 (EC 4.2.1.1) (Carbonic anhydrase XIII) (Carbonate dehydratase XIII) (CA-XIII)	0.15	-	cyt	0					262
Q9D6N1 UniProt NPD GO	CAH13_MOUSE	Carbonic anhydrase 13 (EC 4.2.1.1) (Carbonic anhydrase XIII) (Carbonate dehydratase XIII) (CA-XIII)	0.15	-	cyt	0					262
P27139 UniProt NPD GO	CAH2_RAT	Carbonic anhydrase 2 (EC 4.2.1.1) (Carbonic anhydrase II) (Carbonate dehydratase II) (CA-II)	0.15	-	cyt	0	Cytoplasm	cytoplasm [IDA]			259
P15085 UniProt NPD GO	CBPA1_HUMAN	Carboxypeptidase A1 precursor (EC 3.4.17.1)	0.15	-	end	0	Secreted protein	extracellular space [IDA]	114850		419
P00731 UniProt NPD GO	CBPA1_RAT	Carboxypeptidase A1 precursor (EC 3.4.17.1)	0.15	-	end	0	Secreted protein				419
P35509 UniProt NPD GO	KC1G3_BOVIN	Casein kinase I isoform gamma-3 (EC 2.7.11.1) (CKI-gamma 3) (Fragment)	0.15	-	mit	0	Cytoplasm				276
Q96528 UniProt NPD GO	CATA1_ARATH	Catalase-1 (EC 1.11.1.6)	0.15	-	cyt	0	Cytoplasm (Potential)				492
O48561 UniProt NPD GO	CATA4_SOYBN	Catalase-4 (EC 1.11.1.6)	0.15	-	cyt	0	Peroxisome (By similarity). Glyoxysome (By similarity)				492
P22195 UniProt NPD GO	PER1_ARAHY	Cationic peroxidase 1 precursor (EC 1.11.1.7) (PNPC1)	0.15	-	exc	0	Secreted protein (By similarity)			1SCH	316

You are viewing entries 56701 to 56750 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.