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
Q6IFV3 UniProt NPD GO	K1C15_RAT	Keratin, type I cytoskeletal 15 (Cytokeratin-15) (CK-15) (Keratin-15) (K15) (Type I keratin Ka15)	0.40	-	cyt	0					447
P08778 UniProt NPD GO	K1C5_XENLA	Keratin, type I cytoskeletal 47 kDa	0.40	-	mit	0					433
Q9Z2T6 UniProt NPD GO	KRHB5_MOUSE	Keratin, type II cuticular Hb5 (Hair keratin, type II Hb5)	0.40	-	mit	0					507
P04259 UniProt NPD GO	K2C6B_HUMAN	Keratin, type II cytoskeletal 6B (Cytokeratin-6B) (CK 6B) (K6b keratin)	0.40	-	nuc	0			167210		563
P48668 UniProt NPD GO	K2C6E_HUMAN	Keratin, type II cytoskeletal 6E (Cytokeratin-6E) (CK 6E) (K6e keratin) (Keratin K6h)	0.40	-	nuc	0		intermediate filament [NAS]			563
Q3LI83 UniProt NPD GO	KR241_HUMAN	Keratin-associated protein 24-1	0.40	-	nuc	0					254
Q9BYR5 UniProt NPD GO	KRA42_HUMAN	Keratin-associated protein 4-2 (Keratin-associated protein 4.2) (Ultrahigh sulfur keratin-associated ...	0.40	-	nuc	0					136
Q9BYR4 UniProt NPD GO	KRA43_HUMAN	Keratin-associated protein 4-3 (Keratin-associated protein 4.3) (Ultrahigh sulfur keratin-associated ...	0.40	-	mit	0					98
Q9BYQ2 UniProt NPD GO	KRA94_HUMAN	Keratin-associated protein 9-4 (Keratin-associated protein 9.4) (Ultrahigh sulfur keratin-associated ...	0.40	-	mit	0					154
Q8WN03 UniProt NPD GO	KCIP2_MUSPF	Kv channel-interacting protein 2 (KChIP2) (A-type potassium channel modulatory protein 2) (Potassium ...	0.40	-	nuc	0	Cell membrane; peripheral membrane protein (By similarity)				270
O15229 UniProt NPD GO	KMO_HUMAN	Kynurenine 3-monooxygenase (EC 1.14.13.9) (Kynurenine 3-hydroxylase)	0.40	-	end	2	Mitochondrion; mitochondrial outer membrane; multi-pass membrane protein		603538		486
Q9WVM8 UniProt NPD GO	AADAT_MOUSE	Kynurenine/alpha-aminoadipate aminotransferase mitochondrial precursor (KAT/AadAT) (Kynurenine--oxog ...	0.40	-	mit	0	Mitochondrion (Potential)	mitochondrion [IDA]			425
O88951 UniProt NPD GO	LIN7B_MOUSE	LIN-7 homolog B (LIN-7B) (Mammalian LIN-seven protein 2) (MALS-2) (Vertebrate LIN 7 homolog 2) (Veli ...	0.40	-	cyt	0	Cell membrane; peripheral membrane protein. Cell membrane; cell-cell junction; peripheral membrane p ...	plasma membrane [IDA]		1Y74	207
Q9Z252 UniProt NPD GO	LIN7B_RAT	LIN-7 homolog B (LIN-7B) (Mammalian LIN-seven protein 2) (MALS-2) (Vertebrate LIN 7 homolog 2) (Veli ...	0.40	-	cyt	0	Cell membrane; peripheral membrane protein. Mainly basolateral in renal epithelial cells (By similar ...	intercellular junction [IDA] synapse [IDA]			207
Q9CQB7 UniProt NPD GO	YG01_MOUSE	LYR family protein A-211C6.1 homolog	0.40	-	nuc	0					122
P21298 UniProt NPD GO	DHLE_RAPSA	Late embryogenesis abundant protein (Protein LEA)	0.40	-	nuc	0					184
Q8K4K5 UniProt NPD GO	L2GL1_RAT	Lethal(2) giant larvae protein homolog 1 (LLGL) (Rgl-1)	0.40	-	nuc	0	Cytoplasm. Localized to the lateral membrane during the polarization and formation cell-cell contact ...				1036
Q8MII8 UniProt NPD GO	LRC25_BOVIN	Leucine-rich repeat-containing protein 25 precursor (Monocyte and plasmacytoid-activated protein)	0.40	-	exc	1	Membrane; single-pass type I membrane protein (Potential)				307
Q4V8I7 UniProt NPD GO	LRC8A_RAT	Leucine-rich repeat-containing protein 8A	0.40	-	end	4 *	Membrane; multi-pass membrane protein (Potential)				810
Q6P9F7 UniProt NPD GO	LRC8B_HUMAN	Leucine-rich repeat-containing protein 8B (T-cell activation leucine repeat-rich protein)	0.40	-	end	4 *	Membrane; multi-pass membrane protein (Potential)				803
Q9JHL0 UniProt NPD GO	NTAL_MOUSE	Linker for activation of T-cells family member 2 (Non-T-cell activation linker) (Linker for activati ...	0.40	-	nuc	1 *	Cell membrane; single-pass type III membrane protein. Present in lipid rafts				203
P32875 UniProt NPD GO	LIP5_YEAST	Lipoic acid synthetase, mitochondrial precursor (Lip-syn) (Lipoate synthase)	0.40	-	mit	0	Mitochondrion	mitochondrion [IDA]			414
Q9NPH0 UniProt NPD GO	PPA6_HUMAN	Lysophosphatidic acid phosphatase type 6 precursor (EC 3.1.3.2) (Acid phosphatase 6, lysophosphatidi ...	0.40	-	mit	0	Secreted protein (Probable)				428
Q8K5E0 UniProt NPD GO	EDG7_RAT	Lysophosphatidic acid receptor Edg-7 (LPA receptor 3) (LPA-3) (snGPCR32)	0.40	-	end	7 *	Membrane; multi-pass membrane protein (Probable)				354
Q15013 UniProt NPD GO	MD2BP_HUMAN	MAD2L1-binding protein (Caught by MAD2 protein)	0.40	-	cyt	0	Nucleus. During early mitosis, unevenly distributed throughout the nucleoplasm. From metaphase to an ...	cytoplasm [IDA] nucleus [IDA]			274
Q9JLB0 UniProt NPD GO	MPP6_MOUSE	MAGUK p55 subfamily member 6 (Protein associated with Lin-7 2) (Dlgh4 protein) (P55T protein)	0.40	-	cyt	0	Membrane; peripheral membrane protein	plasma membrane [IDA]			553
O49914 UniProt NPD GO	MLOH1_ORYSA	MLO protein homolog 1 (OsMLO1)	0.40	-	end	7 *	Membrane; multi-pass membrane protein (By similarity)				540
Q9NV56 UniProt NPD GO	MRGBP_HUMAN	MRG-binding protein	0.40	-	nuc	0	Nucleus				204
P38157 UniProt NPD GO	MAL33_YEAST	Maltose fermentation regulatory protein MAL33	0.40	-	nuc	0	Nucleus				468
Q9N0C7 UniProt NPD GO	EPDR1_MACFA	Mammalian ependymin-related protein 1 precursor (MERP-1) (UCC1 protein)	0.40	-	exc	1 *	Secreted protein				224
Q9P446 UniProt NPD GO	MAT1_COCSA	Mating-type protein MAT-1	0.40	-	nuc	0	Nucleus (Potential)				378
Q9CQA5 UniProt NPD GO	MED4_MOUSE	Mediator complex subunit 4 (Mediator of RNA polymerase II transcription subunit 4)	0.40	-	nuc	0	Nucleus (By similarity)				270
Q9Z2A8 UniProt NPD GO	MBTP1_CRIGR	Membrane-bound transcription factor site 1 protease precursor (EC 3.4.21.-) (S1P endopeptidase) (Sit ...	0.40	+	vac	1	Endoplasmic reticulum; endoplasmic reticulum membrane; single-pass type I membrane protein (By simil ...				1052
Q03643 UniProt NPD GO	MSA2_PLAFK	Merozoite surface antigen 2 precursor (MSA-2)	0.40	-	nuc	0	Cell membrane; lipid-anchor; GPI-anchor				280
P47802 UniProt NPD GO	MTX1_MOUSE	Metaxin-1	0.40	-	nuc	1	Mitochondrion; mitochondrial outer membrane	mitochondrial inner membrane [IDA]			317
Q3ZC89 UniProt NPD GO	AMPM2_BOVIN	Methionine aminopeptidase 2 (EC 3.4.11.18) (MetAP 2) (Peptidase M 2)	0.40	+	cyt	0					477
P50579 UniProt NPD GO	AMPM2_HUMAN	Methionine aminopeptidase 2 (EC 3.4.11.18) (MetAP 2) (Peptidase M 2) (Initiation factor 2-associated ...	0.40	+	cyt	0		cytoplasm [TAS]	601870	2ADU	478
Q96DP5 UniProt NPD GO	FMT_HUMAN	Methionyl-tRNA formyltransferase, mitochondrial precursor (EC 2.1.2.9) (MtFMT)	0.40	-	mit	0	Mitochondrion (By similarity)				389
Q28022 UniProt NPD GO	MFAP5_BOVIN	Microfibrillar-associated protein 5 precursor (MFAP-5) (Microfibril-associated glycoprotein 2) (MAGP ...	0.40	-	exc	0	Secreted protein; extracellular space; extracellular matrix				170
Q92552 UniProt NPD GO	RT27_HUMAN	Mitochondrial 28S ribosomal protein S27 (S27mt) (MRP-S27)	0.40	-	mit	0	Mitochondrion				414
Q6CY37 UniProt NPD GO	GEM1_KLULA	Mitochondrial Rho GTPase 1 (EC 3.6.5.-) (GTPase EF-hand protein of mitochondria 1)	0.40	+	nuc	1	Mitochondrion; mitochondrial outer membrane; single-pass type IV membrane protein (By similarity)				659
P41800 UniProt NPD GO	MMM1_YEAST	Mitochondrial outer membrane protein MMM1 (Yeast mitochondrial escape protein 6)	0.40	-	nuc	1	Mitochondrion; mitochondrial outer membrane; multi-pass membrane protein. Punctate structures in the ...	mitochondrial outer membrane [IDA]			426
Q66H23 UniProt NPD GO	MFRN1_RAT	Mitoferrin-1 (Mitochondrial iron transporter 1) (Solute carrier family 25 member 37)	0.40	-	cyt	0	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein (By similarity)				338
P39745 UniProt NPD GO	SUR1_CAEEL	Mitogen-activated protein kinase mpk-1 (EC 2.7.11.24) (MAP kinase sur-1)	0.40	-	mit	0					444
P97471 UniProt NPD GO	SMAD4_MOUSE	Mothers against decapentaplegic homolog 4 (SMAD 4) (Mothers against DPP homolog 4) (Deletion target ...	0.40	-	nuc	0	Cytoplasm (By similarity). In the cytoplasm in the absence of ligand. Nucleus (By similarity). Migra ...	nucleus [IDA] transcription factor complex [IDA]			551
O70437 UniProt NPD GO	SMAD4_RAT	Mothers against decapentaplegic homolog 4 (SMAD 4) (Mothers against DPP homolog 4) (Smad4)	0.40	-	nuc	0	Cytoplasm (By similarity). In the cytoplasm in the absence of ligand. Nucleus (By similarity). Migra ...				552
Q9QYM0 UniProt NPD GO	MRP5_RAT	Multidrug resistance-associated protein 5	0.40	-	end	11	Membrane; multi-pass membrane protein				1436
P30544 UniProt NPD GO	ACM4_XENLA	Muscarinic acetylcholine receptor M4	0.40	-	end	7 *	Membrane; multi-pass membrane protein				484
Q25452 UniProt NPD GO	CAC1M_MUSDO	Muscle calcium channel alpha-1 subunit (MDL-alpha-1)	0.40	+	end	20	Membrane; multi-pass membrane protein				1687
Q62838 UniProt NPD GO	MUSK_RAT	Muscle, skeletal receptor tyrosine protein kinase precursor (EC 2.7.10.1) (Muscle-specific kinase re ...	0.40	-	end	2	Membrane; single-pass type I membrane protein (Potential)			1LUF	868

You are viewing entries 31951 to 32000 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.