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
Q9P6V8 UniProt NPD GO	SPB1_NEUCR	AdoMet-dependent rRNA methyltransferase spb-1 (EC 2.1.1.-) (2'-O-ribose RNA methyltransferase) (S-ad ...	0.65	+	nuc	0	Nucleus; nucleolus (By similarity)				831
Q1XGV3 UniProt NPD GO	ASIP_MACFA	Agouti signaling protein precursor (ASP) (Agouti switch protein)	0.65	-	nuc	1 *	Secreted protein (By similarity)				132
Q1XGV4 UniProt NPD GO	ASIP_PONPY	Agouti signaling protein precursor (ASP) (Agouti switch protein)	0.65	-	nuc	0	Secreted protein (By similarity)				132
Q1XGU8 UniProt NPD GO	ASIP_SEMEN	Agouti signaling protein precursor (ASP) (Agouti switch protein)	0.65	-	nuc	1 *	Secreted protein (By similarity)				132
Q9NSC7 UniProt NPD GO	SIA7A_HUMAN	Alpha-N-acetylgalactosaminide alpha-2,6-sialyltransferase 1 (EC 2.4.99.3) (GalNAc alpha-2,6-sialyltr ...	0.65	-	mit	1 *	Golgi apparatus; Golgi membrane; single-pass type II membrane protein (Potential)				600
P02773 UniProt NPD GO	FETA_RAT	Alpha-fetoprotein precursor (Alpha-fetoglobulin) (Alpha-1-fetoprotein)	0.65	-	exc	0	Isoform 1: Secreted protein. Isoform 2: Cytoplasm	extracellular space [TAS]			611
Q12800 UniProt NPD GO	TFCP2_HUMAN	Alpha-globin transcription factor CP2 (Transcription factor LSF) (SAA3 enhancer factor)	0.65	-	nuc	0	Nucleus		189889		502
Q96Q42 UniProt NPD GO	ALS2_HUMAN	Alsin (Amyotrophic lateral sclerosis protein 2)	0.65	-	nuc	0		cytosol [IDA] early endosome [IDA] vesicular fraction [IDA]	607225		1657
P32450 UniProt NPD GO	AUA1_YEAST	Ammonia regulation of amino acid uptake protein	0.65	-	nuc	0					94
P49418 UniProt NPD GO	AMPH_HUMAN	Amphiphysin	0.65	-	nuc	0	Synaptic vesicle; synaptic vesicle membrane; peripheral membrane protein; cytoplasmic side	actin cytoskeleton [TAS] synaptic vesicle [TAS]	600418	1UTC	695
Q6TMA8 UniProt NPD GO	ANGL4_RAT	Angiopoietin-related protein 4 precursor (Angiopoietin-like 4) (Hepatic fibrinogen/angiopoietin-rela ...	0.65	-	nuc	0	Secreted protein				405
Q8R3P9 UniProt NPD GO	ANR32_MOUSE	Ankyrin repeat domain-containing protein 32	0.65	-	nuc	0					421
Q02357 UniProt NPD GO	ANK1_MOUSE	Ankyrin-1 (Erythrocyte ankyrin)	0.65	+	cyt	0	Isoform Er1: Cytoplasm (By similarity). Cytoplasm (By similarity). Probably the other erythrocyte (E ...	basolateral plasma membrane [ISS]			1862
P07356 UniProt NPD GO	ANXA2_MOUSE	Annexin A2 (Annexin II) (Lipocortin II) (Calpactin I heavy chain) (Chromobindin-8) (p36) (Protein I) ...	0.65	-	nuc	0	Secreted protein; extracellular space; extracellular matrix; basement membrane. In the lamina beneat ...	cytoplasm [IDA] early endosome [IDA] sarcolemma [IDA]			338
Q9V496 UniProt NPD GO	APLP_DROME	Apolipophorins precursor (Retinoid- and fatty acid-binding glycoprotein) [Contains: Apolipophorin-2 ...	0.65	-	nuc	1 *	Secreted protein. Secreted in hemolymph	extracellular region [NAS]			3351
Q9I9H8 UniProt NPD GO	APAF_BRARE	Apoptotic protease-activating factor 1 (Apaf-1)	0.65	-	cyt	0	Cytoplasm (By similarity)				1261
Q9UKV5 UniProt NPD GO	AMFR2_HUMAN	Autocrine motility factor receptor, isoform 2 (EC 6.3.2.-) (AMF receptor) (gp78)	0.65	-	end	5 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein	integral to endoplasmic reticulum membrane [IDA]	603243		643
Q06671 UniProt NPD GO	ATG23_YEAST	Autophagy-related protein 23 (Cytoplasm to vacuole targeting protein 23)	0.65	-	nuc	0	Cytoplasm. Membrane; peripheral membrane protein. Found in pre-autophagosomal structure and other pu ...	extrinsic to membrane [IDA]			453
Q9YGY0 UniProt NPD GO	AXN_XENLA	Axin (Axis inhibition protein) (xAxin)	0.65	-	nuc	0	Cytoplasm (By similarity)			1QZ7	842
Q9QYN5 UniProt NPD GO	BCL10_RAT	B-cell lymphoma/leukemia 10 (B-cell CLL/lymphoma 10) (Bcl-10) (R-RCD1) (RCD)	0.65	-	nuc	0	Cytoplasm (By similarity)				233
O94812 UniProt NPD GO	BAIP3_HUMAN	BAI1-associated protein 3 (BAP3)	0.65	-	cyt	0			604009		1187
Q8K0E1 UniProt NPD GO	KCD15_MOUSE	BTB/POZ domain-containing protein KCTD15	0.65	-	nuc	0					283
Q9BZE3 UniProt NPD GO	BARH1_HUMAN	BarH-like 1 homeobox protein	0.65	+	nuc	0	Nucleus (Probable)		605211		327
P63157 UniProt NPD GO	BARH1_MOUSE	BarH-like 1 homeobox protein (Bar-class homeodomain protein MBH2) (BarH-related homeobox protein 1)	0.65	+	nuc	0	Nucleus (Probable)				327
P63156 UniProt NPD GO	BARH1_RAT	BarH-like 1 homeobox protein (Bar-class homeodomain protein MBH2) (BarH-related homeobox protein 1)	0.65	+	nuc	0	Nucleus (Probable)				327
P21146 UniProt NPD GO	ARBK1_BOVIN	Beta-adrenergic receptor kinase 1 (EC 2.7.11.15) (Beta-ARK-1) (G-protein-coupled receptor kinase 2)	0.65	-	cyt	0		cytoplasm [ISS] soluble fraction [ISS]		2BCJ	689
Q60641 UniProt NPD GO	NR1H4_MOUSE	Bile acid receptor (Farnesoid X-activated receptor) (Farnesol receptor HRR-1) (Retinoid X receptor-i ...	0.65	-	nuc	0	Nucleus (Probable)				488
Q2KJH1 UniProt NPD GO	BMP4_BOVIN	Bone morphogenetic protein 4 precursor (BMP-4)	0.65	-	vac	0	Secreted protein; extracellular space; extracellular matrix (By similarity)				409
Q8MQJ9 UniProt NPD GO	BRAT_DROME	Brain tumor protein	0.65	-	nuc	0	Cytoplasm	cytoplasm [IDA]		1Q7F	1037
Q5EAD0 UniProt NPD GO	BAIP2_BOVIN	Brain-specific angiogenesis inhibitor 1-associated protein 2 (BAI1-associated protein 2) (BAI-associ ...	0.65	-	nuc	0	Cytoplasm (By similarity). Membrane; peripheral membrane protein (By similarity). Detected throughou ...				521
O35732 UniProt NPD GO	CFLAR_MOUSE	CASP8 and FADD-like apoptosis regulator precursor (Cellular FLICE-like inhibitory protein) (c-FLIP) ...	0.65	-	nuc	0		cytoplasm [IDA]			484
Q8K4F0 UniProt NPD GO	CD226_MOUSE	CD226 antigen precursor (Platelet and T-cell activation antigen 1)	0.65	+	end	1	Membrane; single-pass type I membrane protein (Potential)				333
P26051 UniProt NPD GO	CD44_RAT	CD44 antigen precursor (Phagocytic glycoprotein 1) (PGP-1) (HUTCH-I) (Extracellular matrix receptor ...	0.65	-	end	1	Membrane; single-pass type I membrane protein				503
Q6NRT5 UniProt NPD GO	CSN1_XENLA	COP9 signalosome complex subunit 1 (Signalosome subunit 1)	0.65	-	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity)				487
Q9PTG8 UniProt NPD GO	MASK_XENLA	CPEB-associated factor Maskin (Cytoplasmic polyadenylation element-binding protein-associated factor ...	0.65	-	nuc	0	Cytoplasm. When interacting with EIF4E				931
P27164 UniProt NPD GO	CALM3_PETHY	Calmodulin-related protein	0.65	-	nuc	0					183
P20807 UniProt NPD GO	CAN3_HUMAN	Calpain-3 (EC 3.4.22.-) (Calpain L3) (Calpain p94) (Calcium-activated neutral proteinase 3) (CANP 3) ...	0.65	-	cyt	0	Cytoplasm	intracellular [TAS]	253600		821
Q20471 UniProt NPD GO	KIN20_CAEEL	Casein kinase I isoform delta (EC 2.7.11.1) (Protein kinase 20)	0.65	-	nuc	0	Cytoplasm (By similarity)				497
Q9WUR6 UniProt NPD GO	P53_CAVPO	Cellular tumor antigen p53 (Tumor suppressor p53)	0.65	+	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity)	cytoplasm [ISS] mitochondrion [ISS] nucleolus [ISS] nucleus [ISS]			391
Q9H444 UniProt NPD GO	CHM4B_HUMAN	Charged multivesicular body protein 4b (Chromatin-modifying protein 4b) (CHMP4b) (Vacuolar protein s ...	0.65	-	nuc	0	Cytoplasm				224
Q01285 UniProt NPD GO	CHS4_NEUCR	Chitin synthase 4 (EC 2.4.1.16) (Chitin-UDP acetyl-glucosaminyl transferase 4) (Class-IV chitin synt ...	0.65	+	end	6	Cell membrane; multi-pass membrane protein				1195
O13394 UniProt NPD GO	CHS5_USTMA	Chitin synthase 5 (EC 2.4.1.16) (Chitin-UDP acetyl-glucosaminyl transferase 5) (Class-IV chitin synt ...	0.65	-	end	6	Cell membrane; multi-pass membrane protein				1239
Q6B914 UniProt NPD GO	RR16_GRATL	Chloroplast 30S ribosomal protein S16	0.65	-	nuc	0	Plastid; chloroplast				78
Q85X35 UniProt NPD GO	RR18_PINKO	Chloroplast 30S ribosomal protein S18	0.65	+	mit	0	Plastid; chloroplast				93
O47027 UniProt NPD GO	RR2A_CHLRE	Chloroplast 30S ribosomal protein S2	0.65	-	mit	0	Plastid; chloroplast				570
P12145 UniProt NPD GO	RR2_ORYSA	Chloroplast 30S ribosomal protein S2	0.65	-	mit	0	Plastid; chloroplast				236
P56355 UniProt NPD GO	RR7_CHLVU	Chloroplast 30S ribosomal protein S7	0.65	-	nuc	0	Plastid; chloroplast				156
Q9MUP1 UniProt NPD GO	RR7_MESVI	Chloroplast 30S ribosomal protein S7	0.65	-	mit	0	Plastid; chloroplast				156
Q85WV2 UniProt NPD GO	RR7_PINKO	Chloroplast 30S ribosomal protein S7	0.65	-	nuc	0	Plastid; chloroplast				155
Q6B8V6 UniProt NPD GO	RK2_GRATL	Chloroplast 50S ribosomal protein L2	0.65	+	nuc	0	Plastid; chloroplast				275

You are viewing entries 16201 to 16250 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.