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
Q9NS26 UniProt NPD GO	SPNXA_HUMAN	Sperm protein associated with the nucleus on the X chromosome A (Nuclear-associated protein SPAN-Xa) ...	0.45	-	nuc	0	Cytoplasm. Nucleus. Associated with nuclear craters	cytoplasm [TAS] nucleus [TAS]	300493		97
Q9WTP2 UniProt NPD GO	SPY4_MOUSE	Sprouty homolog 4 (Spry-4)	0.45	-	nuc	0	Cytoplasm. Membrane; peripheral membrane protein. Found in the cytoplasm in unstimulated cells but i ...				300
Q9H6Q3 UniProt NPD GO	SLAP2_HUMAN	Src-like-adapter 2 (Src-like adapter protein 2) (SLAP-2) (Modulator of antigen receptor signaling) ( ...	0.45	-	nuc	0	Cytoplasm. Isoform 1: Cell membrane. Cytoplasmic vesicle. Isoform 1 is localized to the plasma membr ...	cytoplasm [TAS] endosome membrane [NAS] plasma membrane [TAS]	606577		260
Q8LB02 UniProt NPD GO	DHSB2_ARATH	Succinate dehydrogenase [ubiquinone] iron-sulfur protein 2, mitochondrial precursor (EC 1.3.5.1) (IP ...	0.45	-	mit	0	Mitochondrion; mitochondrial inner membrane	mitochondrion [IDA]			280
Q3T189 UniProt NPD GO	DHSB_BOVIN	Succinate dehydrogenase [ubiquinone] iron-sulfur protein, mitochondrial precursor (EC 1.3.5.1) (Ip) ...	0.45	-	mit	0	Mitochondrion; mitochondrial inner membrane (By similarity)				280
P07768 UniProt NPD GO	SUIS_RABIT	Sucrase-isomaltase, intestinal [Contains: Sucrase (EC 3.2.1.48); Isomaltase (EC 3.2.1.10)]	0.45	-	mit	1 *	Cell membrane; single-pass type II membrane protein. Brush border				1826
P31927 UniProt NPD GO	SPS_MAIZE	Sucrose-phosphate synthase (EC 2.4.1.14) (UDP-glucose-fructose-phosphate glucosyltransferase)	0.45	+	cyt	0					1068
O04933 UniProt NPD GO	SPS2_CRAPL	Sucrose-phosphate synthase 2 (EC 2.4.1.14) (UDP-glucose-fructose-phosphate glucosyltransferase 2)	0.45	+	cyt	0					1081
O35876 UniProt NPD GO	SMN_RAT	Survival motor neuron protein	0.45	-	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity). Localized in subnuclear structures next to coile ...				289
O14350 UniProt NPD GO	SWI3_SCHPO	Swi1-interacting protein swi3 (Replication fork protection complex subunit swi3)	0.45	+	nuc	0	Nucleus. Nuclear throughout the cell cycle. Associated with chromatin during S phase	nucleus [IDA] replication fork protection complex [TAS]			181
Q4R720 UniProt NPD GO	RIC8A_MACFA	Synembryn-A (Protein Ric-8A)	0.45	-	nuc	0	Cytoplasm (By similarity)				530
Q9SA23 UniProt NPD GO	SYP51_ARATH	Syntaxin-51 (AtSYP51)	0.45	-	nuc	1	Golgi apparatus; trans-Golgi network; trans-Golgi network membrane; single-pass type IV membrane pro ...				232
P31377 UniProt NPD GO	STX8_YEAST	Syntaxin-8 (SNARE protein related to mammalian syntaxin 8) (ULP1-interacting protein 2)	0.45	-	nuc	1	Endosome; endosomal membrane; single-pass type IV membrane protein	endosome [TAS]			255
P58500 UniProt NPD GO	TAK1L_MOUSE	TAK1-like protein	0.45	-	nuc	0					142
Q921F2 UniProt NPD GO	TADBP_MOUSE	TAR DNA-binding protein 43 (TDP-43)	0.45	-	nuc	0	Nucleus (By similarity)				414
Q9CZB3 UniProt NPD GO	THUM2_MOUSE	THUMP domain-containing protein 2	0.45	+	nuc	0					498
Q8VXP3 UniProt NPD GO	TBC2_CHLRE	Tbc2 translation factor, chloroplast precursor	0.45	-	nuc	0	Plastid; chloroplast; chloroplast stroma				1115
Q99JD2 UniProt NPD GO	TEKT1_RAT	Tektin-1	0.45	-	nuc	0					418
Q9WTJ6 UniProt NPD GO	MTL5_MOUSE	Tesmin (Metallothionein-like 5, testis-specific) (Testis-specific metallothionein-like protein)	0.45	-	nuc	0		cytoplasm [IDA] nucleus [IDA] soluble fraction [IDA]			295
Q92563 UniProt NPD GO	TICN2_HUMAN	Testican-2 precursor (SPARC/osteonectin, CWCV, and Kazal-like domains proteoglycan 2)	0.45	-	exc	0	Secreted protein; extracellular space; extracellular matrix (Probable)	extracellular matrix (sensu Metazoa) [NAS]	607988		424
Q9H892 UniProt NPD GO	TTC12_HUMAN	Tetratricopeptide repeat protein 12 (TPR repeat protein 12)	0.45	-	cyt	0					705
Q8R1G1 UniProt NPD GO	TASP1_MOUSE	Threonine aspartase 1 (EC 3.4.25.-) (Taspase-1) [Contains: Threonine aspartase subunit alpha; Threon ...	0.45	+	cyt	0					420
Q00643 UniProt NPD GO	TRHB_XENLA	Thyroliberin type B precursor [Contains: Prothyroliberin type B; Thyroliberin (Thyrotropin-releasing ...	0.45	-	exc	0	Secreted protein				224
O57337 UniProt NPD GO	HES1_CHICK	Transcription factor HES-1 (C-HAIRY1)	0.45	-	nuc	0	Nucleus (Probable)				290
Q01750 UniProt NPD GO	T2FB_RAT	Transcription initiation factor IIF subunit beta (EC 3.6.1.-) (ATP-dependent helicase GTF2F2) (TFIIF ...	0.45	-	nuc	0	Nucleus				249
Q00577 UniProt NPD GO	PURA_HUMAN	Transcriptional activator protein Pur-alpha (Purine-rich single-stranded DNA-binding protein alpha)	0.45	-	cyt	0	Nucleus	DNA replication factor A complex [ISS] nuclear chromosome, telomeric region [IC] nucleus [IDA]	600473		322
Q04725 UniProt NPD GO	TLE2_HUMAN	Transducin-like enhancer protein 2 (ESG2)	0.45	-	nuc	0	Nucleus	nucleus [TAS]	601041		743
P51231 UniProt NPD GO	IF3C_PORPU	Translation initiation factor IF-3, chloroplast	0.45	-	nuc	0	Plastid; chloroplast				182
Q8TDI8 UniProt NPD GO	TMC1_HUMAN	Transmembrane cochlear-expressed protein 1	0.45	+	end	6	Membrane; multi-pass membrane protein (Potential)		606706		760
Q8BFY9 UniProt NPD GO	TNPO1_MOUSE	Transportin-1 (Importin beta-2) (Karyopherin beta-2)	0.45	-	cyt	0	Cytoplasm (By similarity). Nucleus (By similarity)				890
Q92973 UniProt NPD GO	TNPO1_HUMAN	Transportin-1 (Importin beta-2) (Karyopherin beta-2) (M9 region interaction protein) (MIP)	0.45	-	cyt	0	Cytoplasm. Nucleus	cytoplasm [TAS] nucleus [TAS]	602901	1QBK	890
Q27181 UniProt NPD GO	T2C_PARTE	Trichocyst matrix protein T2-C precursor (Secretory granule protein T2-C) (TMP 2-C) [Contains: Trich ...	0.45	-	vac	0	Trichocyst. These are architecturally complex secretory storage granules-docked at the plasma membra ...				387
Q9C019 UniProt NPD GO	TRI15_HUMAN	Tripartite motif-containing protein 15 (Zinc finger protein B7) (RING finger protein 93) (Zinc finge ...	0.45	-	cyt	0					465
Q80WG7 UniProt NPD GO	TRI36_MOUSE	Tripartite motif-containing protein 36 (Haprin) (Acrosome RBCC protein)	0.45	-	nuc	0	Cytoplasm. Found in the acrosomal region of elongated spermatids and mature sperm	acrosome [IDA]			729
P22893 UniProt NPD GO	TTP_MOUSE	Tristetraproline (TTP) (Zinc finger protein 36) (Zfp-36) (TIS11A protein) (TIS11) (Growth factor-ind ...	0.45	-	nuc	0	Nucleus	cytoplasm [IDA] cytosol [IDA] nucleus [IDA]		1M9O	319
Q9NYL9 UniProt NPD GO	TMOD3_HUMAN	Tropomodulin-3 (Ubiquitous tropomodulin) (U-Tmod)	0.45	+	nuc	0			605112		352
Q23939 UniProt NPD GO	TPM_DERFA	Tropomyosin (Allergen Der f 10) (Mag44)	0.45	-	nuc	0					284
O61379 UniProt NPD GO	TPM_PANST	Tropomyosin (Allergen Pan s 1) (Pan s I)	0.45	-	nuc	0					274
P43689 UniProt NPD GO	TPM2_BIOGL	Tropomyosin 2 (TMII)	0.45	-	nuc	0					284
P09495 UniProt NPD GO	TPM4_RAT	Tropomyosin alpha-4 chain (Tropomyosin-4) (TM-4)	0.45	-	nuc	0					247
P32921 UniProt NPD GO	SYW_MOUSE	Tryptophanyl-tRNA synthetase (EC 6.1.1.2) (Tryptophan--tRNA ligase) (TrpRS)	0.45	-	cyt	0					481
P23381 UniProt NPD GO	SYW_HUMAN	Tryptophanyl-tRNA synthetase (EC 6.1.1.2) (Tryptophan--tRNA ligase) (TrpRS) (IFP53) (hWRS)	0.45	-	cyt	0		cytoplasm [TAS] soluble fraction [TAS]	191050	1ULH	471
P18695 UniProt NPD GO	TBG_EMENI	Tubulin gamma chain (Gamma tubulin)	0.45	+	cyt	0					454
Q9UJW2 UniProt NPD GO	TINAG_HUMAN	Tubulointerstitial nephritis antigen (TIN-Ag)	0.45	-	nuc	0	Secreted protein; extracellular space; extracellular matrix; basement membrane	basement membrane [IDA]	606749		476
Q8NHU6 UniProt NPD GO	TDRD7_HUMAN	Tudor domain-containing protein 7 (Tudor repeat associator with PCTAIRE 2) (Trap)	0.45	-	cyt	0	Cytoplasm (By similarity)				1098
P41272 UniProt NPD GO	TNR7_MOUSE	Tumor necrosis factor receptor superfamily member 7 precursor (CD27L receptor) (T-cell activation an ...	0.45	-	exc	1 *	Membrane; single-pass type I membrane protein	extracellular region [ISS] integral to plasma membrane [ISS]			250
Q25321 UniProt NPD GO	OAR1_LOCMI	Tyramine receptor 1 (Tyr-Loc1)	0.45	+	end	7	Membrane; multi-pass membrane protein				484
P43404 UniProt NPD GO	ZAP70_MOUSE	Tyrosine-protein kinase ZAP-70 (EC 2.7.10.2) (70 kDa zeta-associated protein) (Syk-related tyrosine ...	0.45	-	mit	0		cytosol [IDA]			618
Q61152 UniProt NPD GO	PTN18_MOUSE	Tyrosine-protein phosphatase non-receptor type 18 (EC 3.1.3.48) (Fetal liver phosphatase 1) (FLP-1) ...	0.45	-	nuc	0	Nucleus. Cytoplasm	cytoplasm [IDA] nucleus [IDA]			453
Q5A449 UniProt NPD GO	RU2A_CANAL	U2 small nuclear ribonucleoprotein A' (U2 snRNP-A')	0.45	-	nuc	0	Nucleus (By similarity)				233

You are viewing entries 28651 to 28700 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.