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
P47043 UniProt NPD GO	ZAP1_YEAST	Zinc-responsive transcriptional regulator ZAP1	0.88	-	nuc	0	Nucleus (Potential)	nucleus [IDA]		1ZW8	880
Q08499 UniProt NPD GO	PDE4D_HUMAN	cAMP-specific 3',5'-cyclic phosphodiesterase 4D (EC 3.1.4.17) (DPDE3) (PDE43)	0.88	-	nuc	0	Cytoplasm (By similarity). Membrane (By similarity). Cytoskeleton (By similarity). Centrosome (By si ...	insoluble fraction [TAS] soluble fraction [TAS]	600129	2FM5	809
O14233 UniProt NPD GO	RNA14_SCHPO	mRNA 3'-end-processing protein rna14	0.88	-	nuc	0	Nucleus (By similarity). Cytoplasm (By similarity). Nucleus and/or cytoplasm (By similarity)				733
Q96X49 UniProt NPD GO	PACC_CEPAC	pH-response transcription factor pacC/RIM101	0.88	-	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity)				621
Q9C1A4 UniProt NPD GO	PACC_TRIRU	pH-response transcription factor pacC/RIM101	0.88	-	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity)				758
Q6H8R9 UniProt NPD GO	PACC_USTMA	pH-response transcription factor pacC/RIM101	0.88	-	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity)				791
Q6FQB2 UniProt NPD GO	TRM10_CANGA	tRNA (guanine-N(1)-)-methyltransferase (EC 2.1.1.31) (tRNA methyltransferase 10)	0.88	+	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity)				287
Q15147 UniProt NPD GO	PLCB4_HUMAN	1-phosphatidylinositol-4,5-bisphosphate phosphodiesterase beta 4 (EC 3.1.4.11) (Phosphoinositide pho ...	0.87	+	nuc	0			600810		1175
Q9QW07 UniProt NPD GO	PLCB4_RAT	1-phosphatidylinositol-4,5-bisphosphate phosphodiesterase beta 4 (EC 3.1.4.11) (Phosphoinositide pho ...	0.87	+	nuc	0					1175
P16885 UniProt NPD GO	PLCG2_HUMAN	1-phosphatidylinositol-4,5-bisphosphate phosphodiesterase gamma 2 (EC 3.1.4.11) (Phosphoinositide ph ...	0.87	-	cyt	0			600220		1265
O15530 UniProt NPD GO	PDPK1_HUMAN	3-phosphoinositide-dependent protein kinase 1 (EC 2.7.11.1) (hPDK1)	0.87	-	exc	0	Cytoplasm. Membrane; peripheral membrane protein. Membrane-associated after cell stimulation leading ...	cytoplasm [IEP] plasma membrane [IEP]	605213	2BIY	556
Q5E995 UniProt NPD GO	RS6_BOVIN	40S ribosomal protein S6	0.87	+	nuc	0					249
P62755 UniProt NPD GO	RS6_RAT	40S ribosomal protein S6	0.87	+	nuc	0					249
P39017 UniProt NPD GO	RS6_XENLA	40S ribosomal protein S6	0.87	+	nuc	0					249
P62753 UniProt NPD GO	RS6_HUMAN	40S ribosomal protein S6 (Phosphoprotein NP33)	0.87	+	nuc	0		cytosolic small ribosomal subunit (sensu Eu... [IDA] nucleus [IDA]	180460		249
P62754 UniProt NPD GO	RS6_MOUSE	40S ribosomal protein S6 (Phosphoprotein NP33)	0.87	+	nuc	0		cytoplasm [IDA]			249
Q8WQI5 UniProt NPD GO	RS8_SPOFR	40S ribosomal protein S8	0.87	+	nuc	0					208
Q91WG5 UniProt NPD GO	AAKG2_MOUSE	5'-AMP-activated protein kinase subunit gamma-2 (AMPK gamma-2 chain) (AMPK gamma2)	0.87	-	nuc	0					566
Q02204 UniProt NPD GO	RM13_YEAST	60S ribosomal protein L13, mitochondrial precursor (YmL13)	0.87	-	mit	0	Mitochondrion	mitochondrial large ribosomal subunit [TAS]			264
O02639 UniProt NPD GO	RL19_CAEEL	60S ribosomal protein L19	0.87	-	nuc	0					198
O82713 UniProt NPD GO	RL41_QUESU	60S ribosomal protein L41	0.87	+	nuc	0					25
Q9Y710 UniProt NPD GO	RL41_SCHPO	60S ribosomal protein L41	0.87	+	nuc	0					25
Q7KF89 UniProt NPD GO	RL41_SPOFR	60S ribosomal protein L41	0.87	+	nuc	0					25
Q9ULX6 UniProt NPD GO	AKP8L_HUMAN	A-kinase anchor protein 8-like (AKAP8-like protein) (Neighbor of A-kinase-anchoring protein 95) (Nei ...	0.87	+	nuc	0	Nucleus; nucleoplasm; nuclear matrix. Cytoplasm. Nuclear at steady state but shuttles between the nu ...	nucleus [TAS]	609475		646
P43145 UniProt NPD GO	ADML_RAT	ADM precursor [Contains: Adrenomedullin (AM); Proadrenomedullin N-20 terminal peptide (ProAM-N20) (P ...	0.87	-	exc	0	Secreted protein				185
Q03935 UniProt NPD GO	YAP6_YEAST	AP-1-like transcription factor YAP6	0.87	-	nuc	0	Nucleus	nucleus [IDA]			383
Q9Z1T1 UniProt NPD GO	AP3B1_MOUSE	AP-3 complex subunit beta-1 (Adapter-related protein complex 3 beta-1 subunit) (Beta3A-adaptin) (Ada ...	0.87	-	nuc	0	Component of the coat surrounding the cytoplasmic face of coated vesicles located at the Golgi compl ...	Golgi trans face [TAS]			1105
Q10213 UniProt NPD GO	SRS2_SCHPO	ATP-dependent DNA helicase srs2 (EC 3.6.1.-)	0.87	-	nuc	0	Nucleus (By similarity)				887
Q6BLM5 UniProt NPD GO	DBP9_DEBHA	ATP-dependent RNA helicase DBP9 (EC 3.6.1.-)	0.87	-	nuc	0	Nucleus; nucleolus (By similarity)				586
Q99MJ9 UniProt NPD GO	DDX50_MOUSE	ATP-dependent RNA helicase DDX50 (EC 3.6.1.-) (DEAD box protein 50) (Nucleolar protein Gu2) (Gu-beta ...	0.87	-	nuc	0	Nucleus; nucleolus (By similarity)				734
Q6FN65 UniProt NPD GO	ROK1_CANGA	ATP-dependent RNA helicase ROK1 (EC 3.6.1.-)	0.87	-	nuc	0	Nucleus; nucleolus (By similarity)				565
Q873H9 UniProt NPD GO	SPB4_NEUCR	ATP-dependent rRNA helicase spb-4 (EC 3.6.1.-)	0.87	+	nuc	0	Nucleus; nucleolus (By similarity)				654
Q9Y4K1 UniProt NPD GO	AIM1_HUMAN	Absent in melanoma 1 protein	0.87	-	nuc	0			601797		1723
Q07732 UniProt NPD GO	ADY3_YEAST	Accumulates dyads protein 3	0.87	-	nuc	0	Localizes to prospore membrane and SPB. Localizes to the leading edge, which cover the ring-shape op ...	prospore membrane [IDA] spindle [IDA]			790
P15699 UniProt NPD GO	AMDR_EMENI	Acetamidase regulatory protein	0.87	-	nuc	0	Nucleus				765
P53946 UniProt NPD GO	ARP5_YEAST	Actin-like protein ARP5	0.87	-	nuc	0	Nucleus	INO80 complex [IDA] nucleus [IDA]			755
Q07912 UniProt NPD GO	ACK1_HUMAN	Activated CDC42 kinase 1 (EC 2.7.10.2) (ACK-1) (Tyrosine kinase non-receptor protein 2)	0.87	-	nuc	0			606994	1U54	1036
Q5R9Y3 UniProt NPD GO	ABT1_PONPY	Activator of basal transcription 1	0.87	-	nuc	0	Nucleus (By similarity). Nucleus; nucleolus (By similarity)				272
Q9Y2D8 UniProt NPD GO	ADIP_HUMAN	Afadin- and alpha-actinin-binding protein (ADIP) (Afadin DIL domain-interacting protein) (SSX2-inter ...	0.87	-	nuc	0	Cell membrane; cell-cell junction; adherens junction (By similarity). Not found at cell-matrix AJs ( ...		608690		614
Q3TSG4 UniProt NPD GO	ALKB5_MOUSE	Alkylated repair protein alkB homolog 5	0.87	-	nuc	0					395
Q96Q35 UniProt NPD GO	AL2SB_HUMAN	Amyotrophic lateral sclerosis 2 chromosomal region candidate gene 12 protein	0.87	-	nuc	0					445
Q9P2G1 UniProt NPD GO	AKIB1_HUMAN	Ankyrin repeat and IBR domain-containing protein 1 (Fragment)	0.87	-	nuc	0		ubiquitin ligase complex [ISS]			1214
Q13625 UniProt NPD GO	ASPP2_HUMAN	Apoptosis-stimulating of p53 protein 2 (Tumor suppressor p53-binding protein 2) (p53-binding protein ...	0.87	-	nuc	0	Cytoplasm; perinuclear region. Predominantly. Nucleus. Some small fraction is nuclear	cytoplasm [TAS]	602143	1YCS	1128
P92965 UniProt NPD GO	RSP40_ARATH	Arginine/serine-rich-splicing factor RSP40	0.87	-	nuc	0	Nucleus (Potential)				350
Q96SD1 UniProt NPD GO	DCR1C_HUMAN	Artemis protein (EC 3.1.-.-) (DNA cross-link repair 1C protein) (SNM1-like protein) (A-SCID protein) ...	0.87	-	nuc	0	Nucleus		605988		692
O00327 UniProt NPD GO	BMAL1_HUMAN	Aryl hydrocarbon receptor nuclear translocator-like protein 1 (Brain and muscle ARNT-like 1) (Member ...	0.87	-	nuc	0	Nucleus (By similarity)		602550		626
O14525 UniProt NPD GO	ASTN_HUMAN	Astrotactin-1 precursor	0.87	+	end	2	Membrane; multi-pass membrane protein (Potential)		600904		1302
Q63540 UniProt NPD GO	ATX1_RAT	Ataxin-1 (Spinocerebellar ataxia type 1 protein homolog)	0.87	-	nuc	0	Cytoplasm. Nucleus				789
Q59X11 UniProt NPD GO	ATG2_CANAL	Autophagy-related protein 2	0.87	-	nuc	0	Perivacuolar compartment (By similarity)				1856
Q6CNX6 UniProt NPD GO	ATG20_KLULA	Autophagy-related protein 20	0.87	-	nuc	0	Cytoplasm (By similarity). Membrane; peripheral membrane protein (By similarity). Endosome; endosoma ...				636

You are viewing entries 5451 to 5500 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.