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
Q59VW7 UniProt NPD GO	TIM21_CANAL	Import inner membrane translocase subunit TIM21, mitochondrial precursor	0.50	-	nuc	1	Mitochondrion; mitochondrial inner membrane; single-pass membrane protein (By similarity)				268
Q01852 UniProt NPD GO	TIM44_YEAST	Import inner membrane translocase subunit TIM44, mitochondrial precursor (Mitochondrial protein impo ...	0.50	-	mit	0	Mitochondrion; mitochondrial inner membrane	mitochondrial matrix [TAS] presequence translocase-associated import m... [IPI]			431
Q9V9P3 UniProt NPD GO	TI50A_DROME	Import inner membrane translocase subunit TIM50-A, mitochondrial precursor	0.50	-	mit	1	Mitochondrion; mitochondrial inner membrane; single-pass membrane protein (By similarity)	mitochondrial inner membrane presequence tr... [ISS]			343
O00410 UniProt NPD GO	IMB3_HUMAN	Importin beta-3 (Karyopherin beta-3) (Ran-binding protein 5) (RanBP5)	0.50	-	mit	0	Cytoplasm. Nucleus. Nucleus; nucleoplasm; nuclear rim. Nucleus; nucleolus. Found particularly in the ...	cytoplasm [TAS] nuclear pore [TAS] nucleus [TAS]	602008		1096
P52295 UniProt NPD GO	IMA_DROME	Importin subunit alpha (Karyopherin subunit alpha) (Pendulin)	0.50	-	nuc	0	Cytoplasm. Nucleus. Shuttles between the cytoplasm and nucleus in a cell cycle-dependent manner				522
Q8TEX9 UniProt NPD GO	IPO4_HUMAN	Importin-4 (Importin 4b) (Imp4b) (Ran-binding protein 4) (RanBP4)	0.50	-	cyt	0	Cytoplasm (By similarity). Nucleus (By similarity)				1081
Q6NXK7 UniProt NPD GO	DPP10_MOUSE	Inactive dipeptidyl peptidase 10 (Dipeptidyl peptidase X)	0.50	-	mit	1 *	Membrane; single-pass type II membrane protein (By similarity)				797
Q5TEJ8 UniProt NPD GO	ICB1_HUMAN	Induced by contact to basement membrane 1 protein (Protein ICB-1)	0.50	+	cyt	0					643
P22618 UniProt NPD GO	IGF_MYXGL	Insulin-like growth factor precursor (IGF) (Fragment)	0.50	-	exc	0	Secreted protein				139
P17852 UniProt NPD GO	ITA3_CRIGR	Integrin alpha-3 precursor (Galactoprotein B3) (GAPB3) (VLA-3 alpha chain) (CD49c antigen) [Contains ...	0.50	-	end	2 *	Membrane; single-pass type I membrane protein				1066
P49879 UniProt NPD GO	IFNA1_PIG	Interferon alpha-1 precursor (IFN-alpha-1)	0.50	-	nuc	0	Secreted protein				189
Q64287 UniProt NPD GO	IRF4_MOUSE	Interferon regulatory factor 4 (IRF-4) (Lymphocyte-specific interferon regulatory factor) (LSIRF) (N ...	0.50	-	nuc	0	Nucleus	nucleus [ISS]			450
P48551 UniProt NPD GO	INAR2_HUMAN	Interferon-alpha/beta receptor beta chain precursor (IFN-alpha-REC) (Type I interferon receptor) (IF ...	0.50	-	end	1 *	Membrane; single-pass type I membrane protein	extracellular region [TAS] integral to plasma membrane [TAS] plasma membrane [TAS]	602376	1N6V	515
P48089 UniProt NPD GO	IL1A_MACMU	Interleukin-1 alpha precursor (IL-1 alpha) (Hematopoietin-1)	0.50	-	nuc	0	Secreted protein. The lack of a specific hydrophobic segment in the precursor sequence suggests that ...				271
Q8K4B2 UniProt NPD GO	IRAK3_MOUSE	Interleukin-1 receptor-associated kinase 3 (EC 2.7.11.1) (IRAK-3) (IL-1 receptor-associated kinase M ...	0.50	-	nuc	0					609
Q8MJS1 UniProt NPD GO	I12R2_PIG	Interleukin-12 receptor beta-2 chain precursor (IL-12 beta2 receptor) (IL-12Rbeta2)	0.50	-	nuc	0	Membrane; single-pass type I membrane protein				861
P16872 UniProt NPD GO	IL7RA_MOUSE	Interleukin-7 receptor alpha chain precursor (IL-7R-alpha) (CD127 antigen)	0.50	-	exc	1	Membrane; single-pass type I membrane protein	external side of plasma membrane [IDA]			459
P78411 UniProt NPD GO	IRX5_HUMAN	Iroquois-class homeodomain protein IRX-5 (Iroquois homeobox protein 5) (Homeodomain protein IRXB2) ( ...	0.50	-	nuc	0	Nucleus (Probable)		606195		482
Q12350 UniProt NPD GO	JID1_YEAST	J domain-containing protein 1	0.50	-	nuc	0	Mitochondrion; mitochondrial membrane; single-pass membrane protein (Potential)	mitochondrion [IDA]			301
Q9QYE5 UniProt NPD GO	JAG2_MOUSE	Jagged-2 precursor (Jagged2)	0.50	+	nuc	1	Membrane; single-pass type I membrane protein	integral to plasma membrane [IDA]			1247
Q9ET80 UniProt NPD GO	JPH1_MOUSE	Junctophilin-1 (Junctophilin type 1) (JP-1)	0.50	-	nuc	1	Cell membrane; peripheral membrane protein. Endoplasmic reticulum; endoplasmic reticulum membrane; s ...	microsome [IDA] sarcoplasmic reticulum [TAS] Z disc [IDA]			660
P14692 UniProt NPD GO	KAF8_SORBI	Kafirin PSK8 precursor (Fragment)	0.50	-	exc	0					267
Q64291 UniProt NPD GO	K1C12_MOUSE	Keratin, type I cytoskeletal 12 (Cytokeratin-12) (CK-12) (Keratin-12) (K12)	0.50	-	nuc	0					483
Q90303 UniProt NPD GO	K1C1_CARAU	Keratin, type I cytoskeletal 50 kDa (GK50)	0.50	-	cyt	0					467
Q01546 UniProt NPD GO	K22O_HUMAN	Keratin, type II cytoskeletal 2 oral (Cytokeratin-2P) (K2P) (CK 2P)	0.50	-	nuc	0		intermediate filament [NAS]			638
P11679 UniProt NPD GO	K2C8_MOUSE	Keratin, type II cytoskeletal 8 (Cytokeratin-8) (CK-8) (Keratin-8) (K8) (Cytokeratin endo A)	0.50	-	mit	0		sarcolemma [IDA] Z disc [IDA]			489
Q5R8E2 UniProt NPD GO	KLC3_PONPY	Kinesin light chain 3	0.50	-	nuc	0	Elongating spermatid tail midpiece, localized in outer dense fibers (ODFs) and associates with mitoc ...				504
P09442 UniProt NPD GO	DH11_GOSHI	Late embryogenesis abundant protein D-11 (LEA D-11)	0.50	-	nuc	0					145
P07794 UniProt NPD GO	H2BL1_PSAMI	Late histone H2B.2.1	0.50	+	nuc	0	Nucleus				123
O60157 UniProt NPD GO	LCMT2_SCHPO	Leucine carboxyl methyltransferase 2 (EC 2.1.1.-)	0.50	-	nuc	0					681
Q80VQ1 UniProt NPD GO	LRRC1_MOUSE	Leucine-rich repeat-containing protein 1	0.50	-	nuc	0	Cytoplasm (By similarity). Membrane; peripheral membrane protein (By similarity). Localized at the b ...				524
Q5XI54 UniProt NPD GO	LRC48_RAT	Leucine-rich repeat-containing protein 48	0.50	-	cyt	0					523
Q8NHL6 UniProt NPD GO	LIRB1_HUMAN	Leukocyte immunoglobulin-like receptor subfamily B member 1 precursor (Leukocyte immunoglobulin-like ...	0.50	-	exc	1	Membrane; single-pass type I membrane protein	integral to membrane [TAS]	604811	1VDG	650
Q5SCY8 UniProt NPD GO	CHLN_HUPLU	Light-independent protochlorophyllide reductase subunit N (EC 1.18.-.-) (LI-POR subunit N) (DPOR sub ...	0.50	-	cyt	0	Plastid; chloroplast				471
Q8BFW7 UniProt NPD GO	LPP_MOUSE	Lipoma-preferred partner homolog	0.50	-	nuc	0	Nucleus (By similarity). Cytoplasm (By similarity). Cell membrane; cell-cell junction (By similarity ...				613
P32067 UniProt NPD GO	LA_MOUSE	Lupus La protein homolog (La ribonucleoprotein) (La autoantigen homolog)	0.50	-	nuc	0	Nucleus (Probable)	nucleus [IDA]			415
Q920P9 UniProt NPD GO	LY75_MESAU	Lymphocyte antigen 75 precursor (DEC-205) (CD205 antigen)	0.50	-	end	1	Membrane; single-pass type I membrane protein				1722
Q9UVX1 UniProt NPD GO	PLB3_CANAL	Lysophospholipase 3 precursor (EC 3.1.1.5) (Phospholipase B 3)	0.50	-	exc	0	Secreted protein (Probable)				754
O80805 UniProt NPD GO	PHE1_ARATH	MADS-box transcription factor PHERES1	0.50	-	nuc	0					279
P35566 UniProt NPD GO	MRP_RABIT	MARCKS-related protein (MARCKS-like protein 1) (Macrophage myristoylated alanine-rich C kinase subst ...	0.50	+	nuc	0					198
Q9EPH2 UniProt NPD GO	MRP_RAT	MARCKS-related protein (MARCKS-like protein 1) (Macrophage myristoylated alanine-rich C kinase subst ...	0.50	+	nuc	0					198
Q32KV2 UniProt NPD GO	MAEL_BOVIN	Maelstrom homolog	0.50	-	mit	0	Nucleus (Potential)				420
Q5R447 UniProt NPD GO	MRS2L_PONPY	Magnesium transporter MRS2L, mitochondrial precursor (MRS2-like protein)	0.50	-	mit	2	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein (By similarity)				443
Q9ET09 UniProt NPD GO	MRS2L_RAT	Magnesium transporter MRS2L, mitochondrial precursor (MRS2-like protein)	0.50	-	mit	2	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein (By similarity)				434
Q707Y3 UniProt NPD GO	MATA1_YARLI	Mating-type protein A1 (MATA1 transcription factor)	0.50	-	mit	0	Nucleus (By similarity)				176
Q874P0 UniProt NPD GO	MTAL1_CANGA	Mating-type-like protein ALPHA1	0.50	-	mit	0	Nucleus (By similarity)				191
Q9ULZ9 UniProt NPD GO	MMP17_HUMAN	Matrix metalloproteinase-17 precursor (EC 3.4.24.-) (MMP-17) (Membrane-type matrix metalloproteinase ...	0.50	-	mit	0	Isoform 1: Cell membrane; lipid-anchor; GPI-anchor; extracellular side	integral to plasma membrane [TAS]	602285		606
Q9Y5R2 UniProt NPD GO	MMP24_HUMAN	Matrix metalloproteinase-24 precursor (EC 3.4.24.-) (MMP-24) (Membrane-type matrix metalloproteinase ...	0.50	+	end	1 *	Cell membrane; single-pass type I membrane protein (By similarity). Processed form: Secreted protein ...	integral to plasma membrane [TAS]	604871		645
Q99PW6 UniProt NPD GO	MMP24_RAT	Matrix metalloproteinase-24 precursor (EC 3.4.24.-) (MMP-24) (Membrane-type matrix metalloproteinase ...	0.50	+	end	1	Cell membrane; single-pass type I membrane protein (By similarity). Processed form: Secreted protein ...	integral to membrane [TAS]			618
Q5J2X4 UniProt NPD GO	MATK_CHEBH	Maturase K (Intron maturase)	0.50	-	nuc	0	Plastid; chloroplast				505

You are viewing entries 25051 to 25100 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.