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
Q8VI02 UniProt NPD GO	PP4R1_RAT	Serine/threonine-protein phosphatase 4 regulatory subunit 1	0.60	-	cyt	0					951
Q8K1K6 UniProt NPD GO	SPB10_MOUSE	Serpin B10	0.60	-	cyt	0	Cytoplasm (By similarity)				397
Q6TC41 UniProt NPD GO	SRY_MONSC	Sex-determining region Y protein (Testis-determining factor)	0.60	-	nuc	0	Nucleus				221
P36391 UniProt NPD GO	SRY_MACFA	Sex-determining region Y protein (Testis-determining factor) (Fragment)	0.60	-	nuc	0	Nucleus				55
P23253 UniProt NPD GO	TCNA_TRYCR	Sialidase (EC 3.2.1.18) (Neuraminidase) (NA) (Major surface antigen)	0.60	-	nuc	1	Cell membrane; lipid-anchor; GPI-anchor (Potential)				1162
O08562 UniProt NPD GO	SCN9A_RAT	Sodium channel protein type 9 subunit alpha (Sodium channel protein type IX subunit alpha) (Voltage- ...	0.60	+	end	21	Membrane; multi-pass membrane protein (By similarity). In neurite terminals				1984
Q28644 UniProt NPD GO	SCN9A_RABIT	Sodium channel protein type 9 subunit alpha (Sodium channel protein type IX subunit alpha) (Voltage- ...	0.60	-	end	21	Membrane; multi-pass membrane protein. In neurite terminals (By similarity)				1984
Q9Y5X0 UniProt NPD GO	SNX10_HUMAN	Sorting nexin-10	0.60	-	nuc	0					201
Q96RF0 UniProt NPD GO	SNX18_HUMAN	Sorting nexin-18 (Sorting nexin-associated Golgi protein 1)	0.60	-	cyt	0					628
Q6CY25 UniProt NPD GO	SNX3_KLULA	Sorting nexin-3	0.60	-	nuc	0	Cytoplasm (By similarity)				164
Q5KJJ8 UniProt NPD GO	SNX4_CRYNE	Sorting nexin-4 (Autophagy-related protein 24)	0.60	-	cyt	0	Cytoplasm (By similarity). Membrane; peripheral membrane protein (By similarity). Endosome; endosoma ...				493
Q9NY59 UniProt NPD GO	NSMA2_HUMAN	Sphingomyelin phosphodiesterase 3 (EC 3.1.4.12) (Neutral sphingomyelinase 2) (Neutral sphingomyelina ...	0.60	-	nuc	2 *	Golgi apparatus; Golgi membrane; multi-pass membrane protein. May localize to detergent-resistant su ...		605777		655
P01129 UniProt NPD GO	CDC10_SCHPO	Start control protein cdc10	0.60	-	nuc	0		MBF transcription complex [TAS]			767
P24899 UniProt NPD GO	SCL_CHICK	Stem cell protein	0.60	-	nuc	0					311
P21801 UniProt NPD GO	DHSB_YEAST	Succinate dehydrogenase [ubiquinone] iron-sulfur protein, mitochondrial precursor (EC 1.3.5.1) (IP)	0.60	-	mit	0	Mitochondrion; mitochondrial inner membrane	respiratory chain complex II (sensu Eukaryota) [TAS]		1PB4	266
Q68FE8 UniProt NPD GO	SUHW4_MOUSE	Suppressor of hairy wing homolog 4	0.60	-	nuc	0	Nucleus (Potential)				974
Q9D5V6 UniProt NPD GO	SYAP1_MOUSE	Synapse-associated protein 1	0.60	-	nuc	0		nucleus [IDA]			365
Q7TN84 UniProt NPD GO	SYT14_MOUSE	Synaptotagmin-14 (Synaptotagmin XIV) (SytXIV)	0.60	+	nuc	1 *	Membrane; single-pass type III membrane protein (Potential)				555
Q8R5A6 UniProt NPD GO	TB22A_MOUSE	TBC1 domain family member 22A	0.60	-	nuc	0					516
P70196 UniProt NPD GO	TRAF6_MOUSE	TNF receptor-associated factor 6	0.60	-	nuc	0	Cytoplasm (Probable)				530
Q8VIG6 UniProt NPD GO	TRAIP_MOUSE	TRAF-interacting protein	0.60	-	nuc	0	Cytoplasm; perinuclear region (By similarity)				470
Q2KJE0 UniProt NPD GO	TAXB1_BOVIN	Tax1-binding protein 1 homolog	0.60	-	nuc	0					817
Q15554 UniProt NPD GO	TERF2_HUMAN	Telomeric repeat-binding factor 2 (TTAGGG repeat-binding factor 2) (Telomeric DNA-binding protein)	0.60	-	nuc	0	Nucleus. Colocalizes with telomeric DNA in interphase cells and is located at chromosome ends during ...	chromosome, telomeric region [TAS]	602027	1XG1	500
P37243 UniProt NPD GO	THB2_HUMAN	Thyroid hormone receptor beta-2	0.60	+	cyt	0	Nucleus	nucleus [TAS]	274300		476
P18119 UniProt NPD GO	THBB_XENLA	Thyroid hormone receptor beta-B	0.60	+	mit	0	Nucleus				414
Q8QFQ9 UniProt NPD GO	TRH_ONCNE	Thyroliberin type A precursor [Contains: Prothyroliberin type A; Thyroliberin (Thyrotropin-releasing ...	0.60	-	exc	0	Secreted protein				258
P34056 UniProt NPD GO	AP2A_MOUSE	Transcription factor AP-2 alpha (AP2-alpha) (Activating enhancer-binding protein 2 alpha) (Activator ...	0.60	-	nuc	0	Nucleus	transcription factor complex [TAS]			437
P46153 UniProt NPD GO	GATA6_RAT	Transcription factor GATA-6 (GATA-binding factor 6) (DNA-binding protein GATA-GT2)	0.60	-	nuc	0	Nucleus				441
Q9ULX9 UniProt NPD GO	MAFF_HUMAN	Transcription factor MafF (V-maf musculoaponeurotic fibrosarcoma oncogene homolog F) (U-Maf)	0.60	-	nuc	0	Nucleus		604877		164
Q90596 UniProt NPD GO	MAFK_CHICK	Transcription factor MafK	0.60	-	nuc	0	Nucleus				156
Q6PKU1 UniProt NPD GO	SPI1_PIG	Transcription factor PU.1	0.60	+	nuc	0	Nucleus (By similarity)				270
Q9Y651 UniProt NPD GO	SOX21_HUMAN	Transcription factor SOX-21 (SOX-A)	0.60	+	mit	0	Nucleus (Potential)	nucleus [NAS]	604974		276
Q8N5J4 UniProt NPD GO	SPIC_HUMAN	Transcription factor Spi-C	0.60	-	nuc	0	Nucleus (Probable)				248
Q39140 UniProt NPD GO	TGA6_ARATH	Transcription factor TGA6 (AtbZIP45)	0.60	-	nuc	0	Nucleus				330
Q9UL49 UniProt NPD GO	TCFL5_HUMAN	Transcription factor-like 5 protein (Cha transcription factor) (HPV-16 E2-binding protein 1) (E2BP-1 ...	0.60	+	nuc	0	Nucleus	nucleus [IDA]	604745		452
O94759 UniProt NPD GO	TRPM2_HUMAN	Transient receptor potential cation channel subfamily M member 2 (EC 3.6.1.13) (Long transient recep ...	0.60	-	end	6	Membrane; multi-pass membrane protein	integral to plasma membrane [TAS]	603749		1503
Q9H1D0 UniProt NPD GO	TRPV6_HUMAN	Transient receptor potential cation channel subfamily V member 6 (TrpV6) (Epithelial calcium channel ...	0.60	-	end	7	Cell membrane; multi-pass membrane protein (By similarity)	integral to plasma membrane [TAS]	606680		725
Q5R4X4 UniProt NPD GO	SSRA_PONPY	Translocon-associated protein subunit alpha precursor (TRAP-alpha) (Signal sequence receptor subunit ...	0.60	-	end	1 *	Endoplasmic reticulum; endoplasmic reticulum membrane; single-pass type I membrane protein (By simil ...				291
O75949 UniProt NPD GO	TMM28_HUMAN	Transmembrane protein 28 (TED protein)	0.60	-	end	0	Membrane; multi-pass membrane protein (Potential)				473
P68874 UniProt NPD GO	S230_PLAF7	Transmission-blocking target antigen S230 precursor	0.60	+	nuc	0	Cell surface				3135
P68875 UniProt NPD GO	S230_PLAFO	Transmission-blocking target antigen S230 precursor	0.60	+	nuc	0	Cell surface				3135
Q8K4K4 UniProt NPD GO	TRIB1_MOUSE	Tribbles homolog 1 (TRB-1)	0.60	-	mit	0					372
Q96RU8 UniProt NPD GO	TRIB1_HUMAN	Tribbles homolog 1 (TRB-1) (SKIP1) (G-protein-coupled receptor-induced protein 2) (GIG-2)	0.60	-	mit	0			609461		372
Q26503 UniProt NPD GO	TPM_SCHHA	Tropomyosin	0.60	-	nuc	0					284
Q8CGU9 UniProt NPD GO	TPH2_RAT	Tryptophan 5-hydroxylase 2 (EC 1.14.16.4) (Tryptophan 5-monooxygenase 2) (Neuronal tryptophan hydrox ...	0.60	-	mit	0					485
Q5FVQ9 UniProt NPD GO	TBCE_RAT	Tubulin-specific chaperone E (Tubulin-folding cofactor E)	0.60	-	nuc	0					524
Q3SZI1 UniProt NPD GO	TINAG_BOVIN	Tubulointerstitial nephritis antigen (TIN-Ag)	0.60	-	nuc	0	Secreted protein; extracellular space; extracellular matrix; basement membrane (By similarity)				476
Q9ERA6 UniProt NPD GO	TFP11_MOUSE	Tuftelin-interacting protein 11 (Tuftelin-interacting protein 39)	0.60	-	cyt	0	Cytoplasm. Nucleus	extracellular matrix (sensu Metazoa) [IDA] intracellular [NAS]			838
Q5EAF2 UniProt NPD GO	IP5PB_ARATH	Type I inositol-1,4,5-trisphosphate 5-phosphatase 11 (EC 3.1.3.56) (At5PTase11)	0.60	-	nuc	0					334
Q02256 UniProt NPD GO	PVH1_YEAST	Tyrosine-protein phosphatase YVH1 (EC 3.1.3.48) (PTPase YVH1)	0.60	-	nuc	0		cytoplasm [IDA]			364

You are viewing entries 19301 to 19350 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.