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
Q9H106 UniProt NPD GO	SIRPD_HUMAN	Signal-regulatory protein delta precursor (Protein tyrosine phosphatase non-receptor type substrate ...	0.20	-	nuc	0					197
Q4V892 UniProt NPD GO	SIGIR_RAT	Single Ig IL-1-related receptor (Single Ig IL-1R-related molecule) (Single immunoglobulin domain-con ...	0.20	-	cyt	1	Membrane; single-pass type III membrane protein (Potential)	membrane [ISS]			409
Q6EEV6 UniProt NPD GO	SUMO4_HUMAN	Small ubiquitin-related modifier 4 precursor (SUMO-4) (Small ubiquitin-like protein 4)	0.20	-	nuc	0			608829		95
P05024 UniProt NPD GO	AT1A1_PIG	Sodium/potassium-transporting ATPase alpha-1 chain precursor (EC 3.6.3.9) (Sodium pump 1) (Na+/K+ AT ...	0.20	-	end	10	Membrane; multi-pass membrane protein	sodium:potassium-exchanging ATPase complex [ISS]			1021
P04074 UniProt NPD GO	AT1A1_SHEEP	Sodium/potassium-transporting ATPase alpha-1 chain precursor (EC 3.6.3.9) (Sodium pump 1) (Na+/K+ AT ...	0.20	-	end	10	Membrane; multi-pass membrane protein	sodium:potassium-exchanging ATPase complex [ISS]			1021
Q6PIC6 UniProt NPD GO	AT1A3_MOUSE	Sodium/potassium-transporting ATPase alpha-3 chain (EC 3.6.3.9) (Sodium pump 3) (Na+/K+ ATPase 3) (A ...	0.20	-	end	8	Membrane; multi-pass membrane protein	cytoplasm [IDA] nucleus [IDA]			1013
P06687 UniProt NPD GO	AT1A3_RAT	Sodium/potassium-transporting ATPase alpha-3 chain (EC 3.6.3.9) (Sodium pump 3) (Na+/K+ ATPase 3) (A ...	0.20	-	end	8	Membrane; multi-pass membrane protein	plasma membrane [TAS] sodium:potassium-exchanging ATPase complex [ISS]			1013
P14672 UniProt NPD GO	GTR4_HUMAN	Solute carrier family 2, facilitated glucose transporter member 4 (Glucose transporter type 4, insul ...	0.20	-	end	12 *	Membrane; perinuclear region; multi-pass membrane protein. Localizes primarily to the perinuclear re ...	external side of plasma membrane [IDA] integral to plasma membrane [TAS] membrane fraction [TAS] perinuclear region [IDA] vesicle membrane [IDA]	138190		509
P63293 UniProt NPD GO	SLIB_CAPHI	Somatoliberin (Growth hormone-releasing factor) (GRF) (Growth hormone-releasing hormone) (GHRH)	0.20	-	nuc	0	Secreted protein				44
P30937 UniProt NPD GO	SSR4_RAT	Somatostatin receptor type 4 (SS4R)	0.20	-	end	7 *	Membrane; multi-pass membrane protein				384
Q99523 UniProt NPD GO	SORT_HUMAN	Sortilin precursor (Neurotensin receptor 3) (NTR3) (NT3) (Glycoprotein 95) (Gp95) (100 kDa NT recept ...	0.20	-	end	1	Membrane; single-pass type I membrane protein. Localized to membranes of the endoplasmic reticulum, ...	endosome [NAS] integral to membrane [NAS]	602458		831
Q8R1X6 UniProt NPD GO	SPG20_MOUSE	Spartin	0.20	-	nuc	0					671
P36425 UniProt NPD GO	SP17_RABIT	Sperm surface protein Sp17 (Sperm autoantigenic protein 17)	0.20	+	nuc	0	Membrane; peripheral membrane protein (Potential)				146
Q9JLI7 UniProt NPD GO	SPAG6_MOUSE	Sperm-associated antigen 6 (PF16 protein homolog) (Axoneme central apparatus protein)	0.20	-	nuc	0	Cytoplasm. Associated with microtubules. Flagellum. Detected on the sperm flagellum				507
P83429 UniProt NPD GO	SPHE1_APTPA	Spheniscin-1 (Sphe-1) (pBD-1)	0.20	-	mit	0	Secreted protein				38
Q9TYV2 UniProt NPD GO	SMSR2_CAEEL	Sphingomyelin synthase-related 2	0.20	-	end	3	Membrane; multi-pass membrane protein (Potential)	integral to membrane [NAS]			381
O95470 UniProt NPD GO	SGPL1_HUMAN	Sphingosine-1-phosphate lyase 1 (EC 4.1.2.27) (SP-lyase) (hSPL) (Sphingosine-1-phosphate aldolase)	0.20	-	cyt	0	Endoplasmic reticulum; endoplasmic reticulum membrane; single-pass type III membrane protein	integral to endoplasmic reticulum membrane [NAS]	603729		568
Q02769 UniProt NPD GO	FDFT_RAT	Squalene synthetase (EC 2.5.1.21) (SQS) (SS) (Farnesyl-diphosphate farnesyltransferase) (FPP:FPP far ...	0.20	-	cyt	0	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein				416
Q91WG4 UniProt NPD GO	STTP1_MOUSE	Stat3-interacting protein (StIP1)	0.20	-	cyt	0					831
Q9NIV2 UniProt NPD GO	STELO_DROME	Stellate orphon protein at 12D	0.20	-	nuc	0		cytoplasm [ISS] nucleus [ISS] protein kinase CK2 complex [ISS]			172
Q7KV23 UniProt NPD GO	STEL9_DROME	Stellate protein CG33247	0.20	-	nuc	0		cytoplasm [ISS] nucleus [ISS] protein kinase CK2 complex [ISS]			171
Q9DG08 UniProt NPD GO	STAR_XENLA	Steroidogenic acute regulatory protein (StAR) (StARD1) (Fragment)	0.20	-	mit	0	Mitochondrion (By similarity)				289
P15003 UniProt NPD GO	PER1_LYCES	Suberization-associated anionic peroxidase 1 precursor (EC 1.11.1.7) (TMP1)	0.20	-	exc	1 *	Secreted protein (By similarity)				364
Q27236 UniProt NPD GO	SYBL_SCHMA	Synaptobrevin-like protein	0.20	-	mit	1	Synaptic vesicle; synaptic vesicle membrane; single-pass type IV membrane protein (By similarity). N ...				131
P34740 UniProt NPD GO	SDC1_MESAU	Syndecan-1 precursor (SYND1)	0.20	-	end	1	Membrane; single-pass type I membrane protein				309
P25518 UniProt NPD GO	TSYL3_DENPO	Synergistic-like venom protein CM-3	0.20	-	nuc	0	Secreted protein				65
P01734 UniProt NPD GO	TVB1_MOUSE	T-cell receptor beta chain V region 3H.25 precursor	0.20	-	mit	0					135
P18438 UniProt NPD GO	CD3D_SHEEP	T-cell surface glycoprotein CD3 delta chain precursor (T-cell receptor T3 delta chain)	0.20	-	end	1	Membrane; single-pass type I membrane protein	T cell receptor complex [ISS]		1XMW	167
Q28071 UniProt NPD GO	CD28_BOVIN	T-cell-specific surface glycoprotein CD28 precursor	0.20	-	nuc	1	Membrane; single-pass type I membrane protein	integral to plasma membrane [ISS]			219
P10747 UniProt NPD GO	CD28_HUMAN	T-cell-specific surface glycoprotein CD28 precursor (TP44)	0.20	-	nuc	1	Membrane; single-pass type I membrane protein	external side of plasma membrane [IDA] integral to plasma membrane [TAS] plasma membrane [IDA]	186760	1YJD	220
P48605 UniProt NPD GO	TCPG_DROME	T-complex protein 1 subunit gamma (TCP-1-gamma) (CCT-gamma)	0.20	-	cyt	0	Cytoplasm				544
Q92526 UniProt NPD GO	TCPW_HUMAN	T-complex protein 1 subunit zeta-2 (TCP-1-zeta-2) (CCT-zeta-2) (TCP-1-zeta-like) (CCT-zeta-like) (Te ...	0.20	-	cyt	0	Cytoplasm				529
P26354 UniProt NPD GO	TBP_ACACA	TATA-box-binding protein (TATA-box factor) (TATA-binding factor) (TATA sequence-binding protein) (TB ...	0.20	-	nuc	0	Nucleus				258
O43133 UniProt NPD GO	TBP_CANAL	TATA-box-binding protein (TATA-box factor) (TATA-binding factor) (TATA sequence-binding protein) (TB ...	0.20	-	cyt	0	Nucleus				238
Q9JKT3 UniProt NPD GO	TA2R4_MOUSE	Taste receptor type 2 member 4 (T2R4) (Taste receptor type 2 member 8) (T2R8)	0.20	-	end	7 *	Membrane; multi-pass membrane protein	integral to membrane [NAS]			297
Q645U8 UniProt NPD GO	TA2R8_PONPY	Taste receptor type 2 member 8 (T2R8)	0.20	-	end	7 *	Membrane; multi-pass membrane protein				309
Q646G5 UniProt NPD GO	TA2R9_PAPHA	Taste receptor type 2 member 9 (T2R9)	0.20	-	end	7 *	Membrane; multi-pass membrane protein				311
Q8W4T9 UniProt NPD GO	T13H_TAXCU	Taxane 13-alpha-hydroxylase (EC 1.14.13.77) (Cytochrome P450 725A2)	0.20	-	nuc	1 *					485
Q2YDE9 UniProt NPD GO	TES_BOVIN	Testin	0.20	-	nuc	0					421
Q8VIG3 UniProt NPD GO	TSGA2_MOUSE	Testis-specific gene A2 protein (Male meiotic metaphase chromosome-associated acidic protein) (Meich ...	0.20	-	cyt	0	Cytoplasm. Cytoplasmic in late spermatocytes, secondary spermatocytes and round spermatids. Gathered ...				301
Q9UI38 UniProt NPD GO	TSP50_HUMAN	Testis-specific protease-like protein 50 precursor	0.20	-	mit	0			607950		385
P70537 UniProt NPD GO	TSX_RAT	Testis-specific protein TSX	0.20	-	nuc	0					144
Q69AB1 UniProt NPD GO	TXND8_RAT	Thioredoxin domain-containing protein 8 (Spermatid-specific thioredoxin-3) (Sptrx-3)	0.20	-	cyt	0	Cytoplasm (By similarity). Golgi apparatus (By similarity)				127
Q9R088 UniProt NPD GO	KITM_MOUSE	Thymidine kinase 2, mitochondrial precursor (EC 2.7.1.21) (Mt-TK)	0.20	-	mit	0	Mitochondrion	mitochondrial inner membrane [IDA] mitochondrion [IDA]			270
Q9P4T7 UniProt NPD GO	TYSY_AGABI	Thymidylate synthase (EC 2.1.1.45) (TS) (TSase)	0.20	-	cyt	0					296
P04818 UniProt NPD GO	TYSY_HUMAN	Thymidylate synthase (EC 2.1.1.45) (TS) (TSase)	0.20	-	cyt	0			188350	1JUJ	312
P06785 UniProt NPD GO	TYSY_YEAST	Thymidylate synthase (EC 2.1.1.45) (TS) (TSase)	0.20	-	cyt	0		nucleus [IDA]			304
Q9W7M8 UniProt NPD GO	TYB_BRARE	Thymosin beta	0.20	-	nuc	0	Cytoplasm (By similarity)				44
Q9H0E2 UniProt NPD GO	TOLIP_HUMAN	Toll-interacting protein	0.20	-	cyt	0	Cytoplasm (Probable)	cytoplasm [IC] interleukin-1 receptor complex [NAS] interleukin-18 receptor complex [NAS]	606277	1WGL	274
Q9Y6L7 UniProt NPD GO	TLL2_HUMAN	Tolloid-like protein 2 precursor (EC 3.4.24.-)	0.20	-	exc	0	Secreted protein (Probable)		606743		1015

You are viewing entries 51251 to 51300 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.