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
P02533 UniProt NPD GO	K1C14_HUMAN	Keratin, type I cytoskeletal 14 (Cytokeratin-14) (CK-14) (Keratin-14) (K14)	0.38	-	nuc	0			601001		471
P08802 UniProt NPD GO	K1C18_XENLA	Keratin, type I cytoskeletal 18 (Cytokeratin-18) (CK-18) (Keratin-18) (K18) (Keratin, type I cytoske ...	0.38	-	cyt	0					368
P78385 UniProt NPD GO	KRHB3_HUMAN	Keratin, type II cuticular Hb3 (Hair keratin, type II Hb3)	0.38	-	nuc	0			602765		493
P48666 UniProt NPD GO	K2C6C_HUMAN	Keratin, type II cytoskeletal 6C (Cytokeratin-6C) (CK 6C) (K6c keratin)	0.38	-	nuc	0		intermediate filament [NAS]			563
P60372 UniProt NPD GO	KR104_HUMAN	Keratin-associated protein 10-4 (Keratin-associated protein 10.4) (High sulfur keratin-associated pr ...	0.38	-	nuc	0					401
P13134 UniProt NPD GO	KEX2_YEAST	Kexin precursor (EC 3.4.21.61) (KEX2 protease) (Proteinase YSCF)	0.38	-	exc	1	Golgi apparatus; trans-Golgi network; trans-Golgi network membrane; single-pass type I membrane prot ...	Golgi trans face [IDA]		1R64	814
P08934 UniProt NPD GO	KNG1_RAT	Kininogen-1 precursor [Contains: Kininogen-1 heavy chain; Bradykinin; Kininogen-1 light chain]	0.38	-	exc	0	Secreted protein; extracellular space				639
P83059 UniProt NPD GO	KNL2_BOMOR	Kininogen-2 precursor (BOK-2) [Contains: [Thr6]-bradykinin]	0.38	-	exc	0	Secreted protein	extracellular region [IDA]			161
P21583 UniProt NPD GO	SCF_HUMAN	Kit ligand precursor (C-kit ligand) (Stem cell factor) (SCF) (Mast cell growth factor) (MGF)	0.38	-	nuc	1	Isoform 1, isoform 2: Cell membrane; single-pass type I membrane protein (By similarity). Processed ...	plasma membrane [NAS]	184745	1SCF	273
Q9MZS9 UniProt NPD GO	KMO_PIG	Kynurenine 3-monooxygenase (EC 1.14.13.9) (Kynurenine 3-hydroxylase) (Fpk)	0.38	-	cyt	2	Mitochondrion; mitochondrial outer membrane; multi-pass membrane protein (By similarity)				471
Q9M2J7 UniProt NPD GO	LBD29_ARATH	LOB domain-containing protein 29	0.38	-	nuc	0					218
P48450 UniProt NPD GO	ERG7_RAT	Lanosterol synthase (EC 5.4.99.7) (Oxidosqualene--lanosterol cyclase) (2,3-epoxysqualene--lanosterol ...	0.38	-	cyt	0					733
Q15048 UniProt NPD GO	LRC14_HUMAN	Leucine-rich repeat-containing protein 14	0.38	-	cyt	0					493
Q86YC3 UniProt NPD GO	LRC33_HUMAN	Leucine-rich repeat-containing protein 33 precursor	0.38	-	nuc	1	Membrane; single-pass type I membrane protein (Potential)				692
Q5BK65 UniProt NPD GO	LRC33_RAT	Leucine-rich repeat-containing protein 33 precursor	0.38	-	end	1	Membrane; single-pass type I membrane protein (Potential)				692
Q6DHL5 UniProt NPD GO	LRC57_BRARE	Leucine-rich repeat-containing protein 57	0.38	-	nuc	0					238
Q8IWT6 UniProt NPD GO	LRC8A_HUMAN	Leucine-rich repeat-containing protein 8A	0.38	-	end	4 *	Membrane; multi-pass membrane protein (Potential)		608360		810
Q05310 UniProt NPD GO	L10K_RAT	Leydig cell tumor 10 kDa protein	0.38	-	nuc	0					93
P25848 UniProt NPD GO	PHY1_CERPU	Light-sensor Protein kinase [Includes: Phytochrome; Protein kinase (EC 2.7.11.1)]	0.38	-	mit	0	Located in a fixed position close to the plasma membrane				1307
P38419 UniProt NPD GO	LOXC1_ORYSA	Lipoxygenase 7, chloroplast precursor (EC 1.13.11.12)	0.38	-	mit	0	Plastid; chloroplast (Potential)				924
Q28CM3 UniProt NPD GO	MCM6M_XENTR	Maternal DNA replication licensing factor mcm6 (Maternal minichromosome maintenance protein 6) (mMCM ...	0.38	-	cyt	0	Nucleus. Associated with chromatin before the formation of nuclei and detaches from it as DNA replic ...	chromatin [ISS] MCM complex [ISS]			821
P68943 UniProt NPD GO	MED28_RAT	Mediator of RNA polymerase II transcription subunit 28 (Mediator complex subunit 28) (Med23 homolog) ...	0.38	-	nuc	0	Nucleus (By similarity). Cytoplasm (By similarity). Membrane (By similarity). May be also cytoplasmi ...				178
Q92379 UniProt NPD GO	RE104_SACPS	Meiotic recombination protein REC104	0.38	-	nuc	0					185
P50499 UniProt NPD GO	MSA2_PLAFJ	Merozoite surface antigen 2 precursor (MSA-2)	0.38	-	nuc	0	Cell membrane; lipid-anchor; GPI-anchor			1LDV	264
Q99319 UniProt NPD GO	MSA2_PLAFH	Merozoite surface antigen 2 precursor (MSA-2) (Allelic form 3)	0.38	-	nuc	0	Cell membrane; lipid-anchor; GPI-anchor				281
Q90YI3 UniProt NPD GO	SYMM_FUGRU	Methionyl-tRNA synthetase, mitochondrial precursor (EC 6.1.1.10) (Methionine--tRNA ligase 2) (Mitoch ...	0.38	-	nuc	0	Mitochondrion; mitochondrial matrix (By similarity)				590
P10636 UniProt NPD GO	TAU_HUMAN	Microtubule-associated protein tau (Neurofibrillary tangle protein) (Paired helical filament-tau) (P ...	0.38	-	nuc	0	Cytoplasm; cytosol. Cell membrane. Mostly found in the axons of neurons, in the cytosol and in assoc ...	axon [IDA] cytosol [TAS] growth cone [IDA] microtubule associated complex [TAS] plasma membrane [IDA] tubulin [IDA]	157140	1I8H	757
P57786 UniProt NPD GO	TAU_MACMU	Microtubule-associated protein tau (Neurofibrillary tangle protein) (Paired helical filament-tau) (P ...	0.38	-	nuc	0	Cytoplasm; cytosol. Cell membrane. Mostly found in the axons of neurons, in the cytosol and in assoc ...				458
P39722 UniProt NPD GO	GEM1_YEAST	Mitochondrial Rho GTPase 1 (EC 3.6.5.-) (GTPase EF-hand protein of mitochondria 1)	0.38	-	nuc	1	Mitochondrion; mitochondrial outer membrane; single-pass type IV membrane protein	mitochondrial outer membrane [IDA]			662
Q9Y276 UniProt NPD GO	BCS1_HUMAN	Mitochondrial chaperone BCS1 (BCS1-like protein) (H-BCS1)	0.38	-	cyt	0	Mitochondrion; mitochondrial inner membrane; single-pass membrane protein	respiratory chain complex III (sensu Eukary... [TAS]	603647		419
Q9VF08 UniProt NPD GO	TIM16_DROME	Mitochondrial import inner membrane translocase subunit TIM16 (Protein black pearl)	0.38	-	nuc	0	Mitochondrion; mitochondrial inner membrane; peripheral membrane protein (By similarity)				141
Q568N4 UniProt NPD GO	TIM9B_BRARE	Mitochondrial import inner membrane translocase subunit Tim9 B (TIMM10B) (Tim10b)	0.38	-	nuc	0	Mitochondrion; mitochondrial inner membrane; peripheral membrane protein (By similarity)				202
Q15785 UniProt NPD GO	OM34_HUMAN	Mitochondrial import receptor subunit TOM34 (Translocase of outer membrane 34 kDa subunit) (hTom34)	0.38	-	nuc	0	Cytoplasm. Mitochondrion; mitochondrial outer membrane; peripheral membrane protein; cytoplasmic sid ...	integral to membrane [TAS] mitochondrial outer membrane [TAS]			309
Q5REK3 UniProt NPD GO	MPPB_PONPY	Mitochondrial-processing peptidase subunit beta, mitochondrial precursor (EC 3.4.24.64) (Beta-MPP)	0.38	-	mit	0	Mitochondrion; mitochondrial matrix (By similarity)				489
O75439 UniProt NPD GO	MPPB_HUMAN	Mitochondrial-processing peptidase subunit beta, mitochondrial precursor (EC 3.4.24.64) (Beta-MPP) ( ...	0.38	-	mit	0	Mitochondrion; mitochondrial matrix (By similarity)		603131		489
Q06060 UniProt NPD GO	MAPK_PEA	Mitogen-activated protein kinase homolog D5 (EC 2.7.11.24)	0.38	-	cyt	0					394
Q15750 UniProt NPD GO	TAB1_HUMAN	Mitogen-activated protein kinase kinase kinase 7-interacting protein 1 (TGF-beta-activated kinase 1- ...	0.38	-	nuc	0			602615		504
Q9D752 UniProt NPD GO	MD2L2_MOUSE	Mitotic spindle assembly checkpoint protein MAD2B (MAD2-like 2)	0.38	-	cyt	0					211
P27114 UniProt NPD GO	MOTI_RABIT	Motilin precursor [Contains: Motilin; Motilin-associated peptide (MAP)]	0.38	-	exc	1 *	Secreted protein				133
Q9C7F2 UniProt NPD GO	MDR12_ARATH	Multidrug resistance protein 12 (P-glycoprotein 14)	0.38	-	end	11 *	Membrane; multi-pass membrane protein (Potential)				1247
O35217 UniProt NPD GO	MINP1_RAT	Multiple inositol polyphosphate phosphatase 1 precursor (EC 3.1.3.62) (Inositol (1,3,4,5)-tetrakisph ...	0.38	-	exc	0	Endoplasmic reticulum; endoplasmic reticulum lumen				481
P30606 UniProt NPD GO	ITR2_YEAST	Myo-inositol transporter 2	0.38	-	end	12	Membrane; multi-pass membrane protein	plasma membrane [IDA]			612
P42522 UniProt NPD GO	MYOC_DICDI	Myosin IC heavy chain	0.38	-	nuc	0					1181
P18432 UniProt NPD GO	MLR_DROME	Myosin regulatory light chain 2 (MLC-2)	0.38	-	cyt	0					221
Q90688 UniProt NPD GO	MYPC3_CHICK	Myosin-binding protein C, cardiac-type (Cardiac MyBP-C) (C-protein, cardiac muscle isoform)	0.38	-	cyt	0					1271
P12624 UniProt NPD GO	MARCS_BOVIN	Myristoylated alanine-rich C-kinase substrate (MARCKS) (ACAMP-81)	0.38	+	nuc	0	Cell membrane; lipid-anchor. Cytoplasm				331
Q8MV48 UniProt NPD GO	GALT7_DROME	N-acetylgalactosaminyltransferase 7 (EC 2.4.1.-) (Protein-UDP acetylgalactosaminyltransferase 7) (UD ...	0.38	-	mit	1 *	Golgi apparatus; Golgi membrane; single-pass type II membrane protein (By similarity)	Golgi stack [NAS]			591
Q9DCS9 UniProt NPD GO	NDUBA_MOUSE	NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 10 (EC 1.6.5.3) (EC 1.6.99.3) (NADH-ubiqui ...	0.38	-	nuc	0	Mitochondrion; mitochondrial inner membrane; matrix side	mitochondrial inner membrane [IDA] mitochondrion [IDA]			175
O24143 UniProt NPD GO	NUIM_TOBAC	NADH-ubiquinone oxidoreductase 23 kDa subunit, mitochondrial precursor (EC 1.6.5.3) (EC 1.6.99.3) (C ...	0.38	-	mit	0					230
Q8VCM2 UniProt NPD GO	NOXO1_MOUSE	NADPH oxidase organizer 1 (Nox organizer 1) (Sorting nexin-28)	0.38	-	nuc	0	Cell membrane (By similarity). Associates with the plasma membrane in a lipid-dependent manner (By s ...				349

You are viewing entries 33551 to 33600 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.