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
P40749 UniProt NPD GO	SYT4_MOUSE	Synaptotagmin-4 (Synaptotagmin IV) (SytIV)	0.42	+	nuc	1 *	Synaptic vesicle; synaptic vesicle membrane; multi-pass membrane protein	integral to membrane [TAS] neuron projection [IDA] perinuclear region [IDA]			425
P49415 UniProt NPD GO	SDC_DROME	Syndecan precursor	0.42	-	exc	2 *	Membrane; single-pass type I membrane protein				399
P20974 UniProt NPD GO	NAR2B_RAT	T-cell ecto-ADP-ribosyltransferase 2 precursor (EC 2.4.2.31) (T-cell NAD(P)(+)--arginine ADP-ribosyl ...	0.42	-	exc	0	Cell membrane; lipid-anchor; GPI-anchor			1OG4	275
Q62312 UniProt NPD GO	TGFR2_MOUSE	TGF-beta receptor type-2 precursor (EC 2.7.11.30) (TGF-beta receptor type II) (TGFR-2) (TGF-beta typ ...	0.42	-	nuc	1	Membrane; single-pass type I membrane protein				592
Q13077 UniProt NPD GO	TRAF1_HUMAN	TNF receptor-associated factor 1 (Epstein-Barr virus-induced protein 6)	0.42	-	nuc	0		cytoplasm [TAS]	601711		416
Q02335 UniProt NPD GO	YOL8_CAEEL	TPR repeat-containing protein ZK370.8	0.42	-	cyt	1 *					569
Q4QQV1 UniProt NPD GO	TX1B3_RAT	Tax1-binding protein 3	0.42	-	mit	0	Cytoplasm (By similarity). Nucleus (By similarity)				98
O14530 UniProt NPD GO	TXND9_HUMAN	Thioredoxin domain-containing protein 9 (Protein 1-4) (ATP-binding protein associated with cell diff ...	0.42	-	cyt	0					226
P40225 UniProt NPD GO	TPO_HUMAN	Thrombopoietin precursor (Megakaryocyte colony-stimulating factor) (Myeloproliferative leukemia viru ...	0.42	-	nuc	0	Secreted protein		187950	1V7N	353
P40226 UniProt NPD GO	TPO_MOUSE	Thrombopoietin precursor (Megakaryocyte colony-stimulating factor) (Myeloproliferative leukemia viru ...	0.42	-	nuc	0	Secreted protein				356
P97273 UniProt NPD GO	TITF1_CAVPO	Thyroid transcription factor 1 (Thyroid nuclear factor 1) (TTF-1) (Homeobox protein Nkx-2.1) (Fragme ...	0.42	-	nuc	0	Nucleus				112
Q9BGN4 UniProt NPD GO	TSHR_FELCA	Thyrotropin receptor precursor (TSH-R) (Thyroid-stimulating hormone receptor)	0.42	-	end	7	Membrane; multi-pass membrane protein				763
P47750 UniProt NPD GO	TSHR_MOUSE	Thyrotropin receptor precursor (TSH-R) (Thyroid-stimulating hormone receptor)	0.42	-	end	7	Membrane; multi-pass membrane protein	plasma membrane [IDA]			764
P24055 UniProt NPD GO	TF_RABIT	Tissue factor precursor (TF) (Coagulation factor III) (CD142 antigen)	0.42	+	end	1	Membrane; single-pass type I membrane protein			1A21	292
Q9VH14 UniProt NPD GO	TIMP_DROME	Tissue inhibitor of metalloproteases precursor	0.42	-	exc	0	Secreted protein (By similarity)				210
Q8LHP0 UniProt NPD GO	ELOF1_ORYSA	Transcription elongation factor 1 homolog	0.42	-	nuc	0	Nucleus (By similarity)				89
Q9ESX2 UniProt NPD GO	SP6_MOUSE	Transcription factor Sp6 (Krueppel-like factor 14) (Epiprofin)	0.42	-	nuc	0	Nucleus				376
P56721 UniProt NPD GO	COLL_DROME	Transcription factor collier (Transcription factor knot)	0.42	-	nuc	0	Nucleus (Potential)				575
P32367 UniProt NPD GO	TFC1_YEAST	Transcription factor tau 95 kDa subunit (TFIIIC 95 kDa subunit)	0.42	-	nuc	0	Nucleus	transcription factor TFIIIC complex [TAS]			649
P41900 UniProt NPD GO	T2FB_DROME	Transcription initiation factor IIF subunit beta (EC 3.6.1.-) (ATP-dependent helicase TfIIF-beta) (T ...	0.42	-	nuc	0	Nucleus	transcription factor TFIIF complex [NAS]			277
Q94KR8 UniProt NPD GO	IF1C_MESCR	Translation initiation factor IF-1, chloroplast precursor	0.42	-	nuc	0	Plastid; chloroplast (By similarity)				156
Q75D26 UniProt NPD GO	SEC62_ASHGO	Translocation protein SEC62	0.42	+	end	2	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (By similarity)				244
Q7TPJ0 UniProt NPD GO	SSRA_RAT	Translocon-associated protein subunit alpha precursor (TRAP-alpha) (Signal sequence receptor subunit ...	0.42	-	end	1 *	Endoplasmic reticulum; endoplasmic reticulum membrane; single-pass type I membrane protein (By simil ...				319
Q3T113 UniProt NPD GO	TMIGD_BOVIN	Transmembrane and immunoglobulin domain-containing protein precursor	0.42	-	mit	2 *	Membrane; single-pass type I membrane protein (Potential)				261
Q9WTQ6 UniProt NPD GO	TRIB3_RAT	Tribbles homolog 3 (TRB-3) (Neuronal cell death-inducible putative kinase)	0.42	-	nuc	0		nucleus [ISS]			349
Q9QXA7 UniProt NPD GO	TRI44_MOUSE	Tripartite motif-containing protein 44 (Protein DIPB) (Protein Mc7)	0.42	-	nuc	0					346
P49813 UniProt NPD GO	TMOD1_MOUSE	Tropomodulin-1 (Erythrocyte tropomodulin) (E-Tmod)	0.42	-	nuc	0		cytoskeleton [TAS] myofibril [IDA]			359
O97162 UniProt NPD GO	TPM_BOOMI	Tropomyosin	0.42	-	nuc	0					284
P84335 UniProt NPD GO	TPM1_LIZAU	Tropomyosin 1 alpha chain (Alpha-tropomyosin)	0.42	-	nuc	0					284
P58771 UniProt NPD GO	TPM1_MOUSE	Tropomyosin 1 alpha chain (Alpha-tropomyosin)	0.42	-	nuc	0		muscle thin filament tropomyosin [TAS]			284
P58772 UniProt NPD GO	TPM1_RABIT	Tropomyosin 1 alpha chain (Alpha-tropomyosin)	0.42	-	nuc	0				2TMA	284
P04692 UniProt NPD GO	TPM1_RAT	Tropomyosin 1 alpha chain (Alpha-tropomyosin)	0.42	-	nuc	0				2B9C	284
P38057 UniProt NPD GO	ITRY_SINAR	Trypsin inhibitor (TISA) [Contains: Trypsin inhibitor small chain; Trypsin inhibitor large chain]	0.42	-	nuc	0					130
P21643 UniProt NPD GO	T23O_RAT	Tryptophan 2,3-dioxygenase (EC 1.13.11.11) (TO) (Tryptophan pyrrolase) (Tryptophanase) (Tryptophan o ...	0.42	-	cyt	0					406
Q50EL0 UniProt NPD GO	DMAW_ASPFU	Tryptophan dimethylallyltransferase (EC 2.5.1.34) (DMATS) (All-trans-hexaprenyl-diphosphate synthase ...	0.42	-	nuc	0					459
Q6X2E3 UniProt NPD GO	DMAW_EPINE	Tryptophan dimethylallyltransferase (EC 2.5.1.34) (DMATS) (All-trans-hexaprenyl-diphosphate synthase ...	0.42	-	cyt	0					450
Q6X2E1 UniProt NPD GO	DMAW2_ACRCO	Tryptophan dimethylallyltransferase 2 (EC 2.5.1.34) (DMATS 2) (All-trans-hexaprenyl-diphosphate synt ...	0.42	-	cyt	0					450
Q5R4J1 UniProt NPD GO	SYW_PONPY	Tryptophanyl-tRNA synthetase (EC 6.1.1.2) (Tryptophan--tRNA ligase) (TrpRS)	0.42	-	cyt	0					472
P21148 UniProt NPD GO	TBB_LEIME	Tubulin beta chain (Beta tubulin)	0.42	-	cyt	0	Cytoplasm				445
Q5I3B1 UniProt NPD GO	IOD3_BOVIN	Type III iodothyronine deiodinase (EC 1.97.1.11) (Type-III 5'deiodinase) (DIOIII) (Type 3 DI) (5DIII ...	0.42	-	nuc	0	Cell membrane; single-pass type II membrane protein (By similarity). Endosome; endosomal membrane; s ...				278
Q91ZI8 UniProt NPD GO	IOD3_MOUSE	Type III iodothyronine deiodinase (EC 1.97.1.11) (Type-III 5'deiodinase) (DIOIII) (Type 3 DI) (5DIII ...	0.42	-	nuc	0	Cell membrane; single-pass type II membrane protein (By similarity). Endosome; endosomal membrane; s ...				278
Q6DN07 UniProt NPD GO	IOD3_SHEEP	Type III iodothyronine deiodinase (EC 1.97.1.11) (Type-III 5'deiodinase) (DIOIII) (Type 3 DI) (5DIII ...	0.42	-	nuc	0	Cell membrane; single-pass type II membrane protein (By similarity). Endosome; endosomal membrane; s ...				278
Q00234 UniProt NPD GO	TYRO_ASPOR	Tyrosinase (EC 1.14.18.1) (Monophenol monooxygenase)	0.42	-	cyt	0					539
Q08881 UniProt NPD GO	ITK_HUMAN	Tyrosine-protein kinase ITK/TSK (EC 2.7.10.2) (T-cell-specific kinase) (Tyrosine-protein kinase Lyk) ...	0.42	-	cyt	0	Cell membrane (By similarity). Localizes to cell surface receptors in the plasma membrane after stim ...		186973	1SNX	620
P34925 UniProt NPD GO	RYK_HUMAN	Tyrosine-protein kinase RYK precursor (EC 2.7.10.1)	0.42	-	mit	1	Membrane; single-pass type I membrane protein (Potential)	integral to plasma membrane [TAS]	600524		604
Q06124 UniProt NPD GO	PTN11_HUMAN	Tyrosine-protein phosphatase non-receptor type 11 (EC 3.1.3.48) (Protein-tyrosine phosphatase 2C) (P ...	0.42	-	mit	0	Cytoplasm		151100	2SHP	597
Q04177 UniProt NPD GO	UTP5_YEAST	U3 small nucleolar RNA-associated protein 5 (U3 snoRNA-associated protein 5)	0.42	-	cyt	0	Nucleus; nucleolus	small nucleolar ribonucleoprotein complex [IPI]			643
Q04228 UniProt NPD GO	UBX2_YEAST	UBX domain-containing protein 2 (Secretion lowering protein 1)	0.42	-	cyt	0	Endoplasmic reticulum	endoplasmic reticulum [IDA] mitochondrial outer membrane [IDA]			584
Q9NYU1 UniProt NPD GO	UGGG2_HUMAN	UDP-glucose:glycoprotein glucosyltransferase 2 precursor (EC 2.4.1.-) (UDP-glucose ceramide glucosyl ...	0.42	-	end	0	Endoplasmic reticulum; endoplasmic reticulum lumen (By similarity). Endoplasmic reticulum-Golgi inte ...	endoplasmic reticulum lumen [ISS]	605898		1516
Q6DF08 UniProt NPD GO	UXS1_XENTR	UDP-glucuronic acid decarboxylase 1 (EC 4.1.1.35) (UDP-glucuronate decarboxylase 1) (UXS-1)	0.42	-	mit	1 *	Golgi apparatus; Golgi stack; Golgi stack membrane; single-pass type II membrane protein (By similar ...				421

You are viewing entries 30751 to 30800 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.