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
P29508 UniProt NPD GO	SPB3_HUMAN	Serpin B3 (Squamous cell carcinoma antigen 1) (SCCA-1) (Protein T4-A)	0.22	-	cyt	0	Cytoplasm. Seems to also be secreted in plasma by cancerous cells but at a low level		600517		390
O61374 UniProt NPD GO	SXL_CERCA	Sex-lethal homolog (CCSXL)	0.22	+	nuc	0	Nucleus				348
P01424 UniProt NPD GO	NXS1_NAJME	Short neurotoxin 1 (Neurotoxin D)	0.22	-	nuc	0	Secreted protein				61
P32879 UniProt NPD GO	NXS1_AIPLA	Short neurotoxin A	0.22	-	nuc	0	Secreted protein				60
P10456 UniProt NPD GO	NXSD_LATCO	Short neurotoxin D precursor	0.22	-	nuc	0	Secreted protein				83
Q9YGX0 UniProt NPD GO	NXS4_LATCO	Short neurotoxin NCA-04 precursor	0.22	-	nuc	0	Secreted protein				83
P47758 UniProt NPD GO	SRPRB_MOUSE	Signal recognition particle receptor subunit beta (SR-beta)	0.22	-	mit	1 *	Endoplasmic reticulum; endoplasmic reticulum membrane; single-pass membrane protein (By similarity)			2FH5	269
P43321 UniProt NPD GO	SMD3_YEAST	Small nuclear ribonucleoprotein Sm D3 (snRNP core protein D3) (Sm-D3)	0.22	+	nuc	0	Cytoplasm. Nucleus	commitment complex [IPI] snRNP U1 [IDA] snRNP U5 [IPI] U4/U6 x U5 tri-snRNP complex [IDA]			101
Q9BYE4 UniProt NPD GO	SPR2G_HUMAN	Small proline-rich protein 2G (SPR-2G)	0.22	-	nuc	0	Cytoplasm (By similarity)	cornified envelope [NAS]			73
P21925 UniProt NPD GO	SIA3_SORBI	Small protein inhibitor of insect alpha-amylases 3 (SI alpha-3)	0.22	-	mit	0					47
O97596 UniProt NPD GO	S20A1_FELCA	Sodium-dependent phosphate transporter 1 (Solute carrier family 20 member 1) (Phosphate transporter ...	0.22	-	end	8 *	Membrane; multi-pass membrane protein (By similarity)				681
P48761 UniProt NPD GO	SL9A1_CRIGR	Sodium/hydrogen exchanger 1 (Na(+)/H(+) exchanger 1) (NHE-1) (Solute carrier family 9 member 1)	0.22	-	end	12 *	Membrane; multi-pass membrane protein				822
P28774 UniProt NPD GO	AT1B_ARTSF	Sodium/potassium-transporting ATPase alpha chain (EC 3.6.3.9) (Sodium pump) (Na+/K+ ATPase)	0.22	-	end	8	Membrane; multi-pass membrane protein				1004
Q71RS6 UniProt NPD GO	NCKX5_HUMAN	Sodium/potassium/calcium exchanger 5 precursor (Na(+)/K(+)/Ca(2+)-exchange protein 5) (Solute carrie ...	0.22	-	end	9	Membrane; multi-pass membrane protein (By similarity)		609802		500
Q23983 UniProt NPD GO	SNAP_DROME	Soluble NSF attachment protein (SNAP) (N-ethylmaleimide-sensitive factor attachment protein)	0.22	-	nuc	0	Membrane; peripheral membrane protein (By similarity)				292
Q43187 UniProt NPD GO	IPYR_SOLTU	Soluble inorganic pyrophosphatase (EC 3.6.1.1) (Pyrophosphate phospho-hydrolase) (PPase)	0.22	-	nuc	0	Cytoplasm				211
Q9NYB5 UniProt NPD GO	SO1C1_HUMAN	Solute carrier organic anion transporter family member 1C1 (Solute carrier family 21 member 14) (Org ...	0.22	-	end	10	Membrane; multi-pass membrane protein				712
Q9I8J9 UniProt NPD GO	SOML_ICTPU	Somatolactin precursor (SL)	0.22	-	cyt	0	Secreted protein				230
P07217 UniProt NPD GO	SLIB_SHEEP	Somatoliberin (Growth hormone-releasing factor) (GRF) (Growth hormone-releasing hormone) (GHRH)	0.22	-	nuc	0	Secreted protein				44
P46407 UniProt NPD GO	SOMA_RABIT	Somatotropin precursor (Growth hormone)	0.22	-	exc	0	Secreted protein				216
Q08826 UniProt NPD GO	SNX3_YEAST	Sorting nexin-3 (Golgi retention deficient protein 19)	0.22	-	nuc	0	Cytoplasm. Mainly. Membrane; peripheral membrane protein. A minor amount associates with membranes	cytosol [IDA]		1OCU	162
Q8N0X2 UniProt NPD GO	SPG16_HUMAN	Sperm-associated antigen 16 protein (PF20 protein homolog)	0.22	-	mit	0	Cytoplasm (By similarity). Flagellum (By similarity). Detected on the sperm flagellum. Detected in t ...				631
P15744 UniProt NPD GO	ANSP_EIMTE	Sporozoite antigen	0.22	-	nuc	0					216
P53800 UniProt NPD GO	FDFT_NICBE	Squalene synthetase (EC 2.5.1.21) (SQS) (SS) (Farnesyl-diphosphate farnesyltransferase) (FPP:FPP far ...	0.22	-	nuc	1	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (By similarity)				411
P59095 UniProt NPD GO	STAR6_HUMAN	StAR-related lipid transfer protein 6 (StARD6) (START domain-containing protein 6)	0.22	-	nuc	0			607051		220
Q7KV12 UniProt NPD GO	STEL1_DROME	Stellate protein CG33236/CG33244	0.22	-	nuc	0		cytoplasm [ISS] nucleus [ISS] protein kinase CK2 complex [ISS]			177
Q61263 UniProt NPD GO	SOAT1_MOUSE	Sterol O-acyltransferase 1 (EC 2.3.1.26) (Cholesterol acyltransferase 1) (Acyl coenzyme A:cholestero ...	0.22	-	end	8	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein	microsome [IDA]			540
Q91453 UniProt NPD GO	STXB_SYNHO	Stonustoxin subunit beta (SNTX subunit beta)	0.22	-	cyt	0	Secreted protein. Secreted into the venom gland lumen. The secretion is proved by the fact that the ...				699
Q11005 UniProt NPD GO	MMP11_XENLA	Stromelysin-3 precursor (EC 3.4.24.-) (Matrix metalloproteinase-11) (MMP-11) (ST3)	0.22	+	cyt	0					477
Q02853 UniProt NPD GO	MMP11_MOUSE	Stromelysin-3 precursor (EC 3.4.24.-) (ST3) (SL-3) (Matrix metalloproteinase-11) (MMP-11)	0.22	+	nuc	1 *				1HV5	492
O57593 UniProt NPD GO	SURF1_FUGRU	Surfeit locus protein 1 (Fragment)	0.22	-	mit	1	Mitochondrion; mitochondrial inner membrane (By similarity)				240
Q9UH64 UniProt NPD GO	NSGX_HUMAN	Susceptibility protein NSG-x	0.22	-	nuc	0					79
O95988 UniProt NPD GO	TCL1B_HUMAN	T-cell leukemia/lymphoma protein 1B (TCL1B oncogene) (Syncytiotrophoblast-specific protein) (SYN-1)	0.22	-	cyt	0			603769		128
Q5XKA2 UniProt NPD GO	TI21L_XENLA	TIM21-like protein, mitochondrial precursor	0.22	-	mit	1	Mitochondrion; mitochondrial membrane; single-pass membrane protein (Potential)				232
Q8I6S3 UniProt NPD GO	TKN1_OCTVU	Tachykinin-1 precursor (Tachykinin I) (OctTK-I)	0.22	-	mit	0	Secreted protein				87
Q645V0 UniProt NPD GO	T2R10_PONPY	Taste receptor type 2 member 10 (T2R10)	0.22	-	end	7 *	Membrane; multi-pass membrane protein				308
Q645Y9 UniProt NPD GO	T2R40_GORGO	Taste receptor type 2 member 40 (T2R40)	0.22	-	end	6 *	Membrane; multi-pass membrane protein				323
Q646D4 UniProt NPD GO	T2R40_PANPA	Taste receptor type 2 member 40 (T2R40)	0.22	-	end	6 *	Membrane; multi-pass membrane protein				323
Q646B1 UniProt NPD GO	T2R40_PANTR	Taste receptor type 2 member 40 (T2R40)	0.22	-	end	6 *	Membrane; multi-pass membrane protein				323
Q645V7 UniProt NPD GO	T2R50_PONPY	Taste receptor type 2 member 50 (T2R50)	0.22	-	end	7 *	Membrane; multi-pass membrane protein				299
Q8WYR4 UniProt NPD GO	TSGA2_HUMAN	Testis-specific gene A2 protein (Male meiotic metaphase chromosome-associated acidic protein) (Meich ...	0.22	-	cyt	0	Cytoplasm (By similarity). Cytoplasmic in late spermatocytes, secondary spermatocytes and round sper ...		609314		309
Q9SEU8 UniProt NPD GO	TRXM2_ARATH	Thioredoxin M-type 2, chloroplast precursor (TRX-M2)	0.22	-	nuc	0	Plastid; chloroplast (By similarity)				186
Q17745 UniProt NPD GO	TRXR_CAEEL	Thioredoxin reductase (EC 1.8.1.9) (TR-Se) (TRR)	0.22	-	cyt	0	Cytoplasm (By similarity)	cytosol [ISS]			667
Q8LEK4 UniProt NPD GO	TRXL2_ARATH	Thioredoxin-like 2, chloroplast precursor	0.22	-	mit	0	Plastid; chloroplast (Potential)				221
P15306 UniProt NPD GO	TRBM_MOUSE	Thrombomodulin precursor (TM) (Fetomodulin) (CD141 antigen)	0.22	-	end	1	Membrane; single-pass type I membrane protein	plasma membrane [TAS]			577
P35442 UniProt NPD GO	TSP2_HUMAN	Thrombospondin-2 precursor	0.22	-	exc	0			188061	1YO8	1172
Q3SX26 UniProt NPD GO	TRIP6_BOVIN	Thyroid receptor-interacting protein 6 (TRIP6)	0.22	-	nuc	0		focal adhesion [ISS]			481
Q96423 UniProt NPD GO	TCMO_GLYEC	Trans-cinnamate 4-monooxygenase (EC 1.14.13.11) (Cinnamic acid 4-hydroxylase) (CA4H) (C4H) (P450C4H) ...	0.22	-	end	0					505
Q42797 UniProt NPD GO	TCMO_SOYBN	Trans-cinnamate 4-monooxygenase (EC 1.14.13.11) (Cinnamic acid 4-hydroxylase) (CA4H) (C4H) (P450C4H) ...	0.22	-	end	1 *					506
Q12363 UniProt NPD GO	WTM1_YEAST	Transcriptional modulator WTM1	0.22	-	mit	0		nucleus [IDA]			437

You are viewing entries 48951 to 49000 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.