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
P01189 UniProt NPD GO	COLI_HUMAN	Corticotropin-lipotropin precursor (Pro-opiomelanocortin) (POMC) [Contains: NPP; Melanotropin gamma ...	0.58	-	nuc	0		soluble fraction [TAS]	176830		267
Q10423 UniProt NPD GO	CCE1_SCHPO	Cruciform cutting endonuclease 1, mitochondrial precursor (EC 3.1.-.-) (Protein ydc2)	0.58	-	nuc	0	Mitochondrion	mitochondrion [IDA]		1KCF	258
Q13619 UniProt NPD GO	CUL4A_HUMAN	Cullin-4A (CUL-4A)	0.58	-	cyt	0			603137		759
P47050 UniProt NPD GO	CUL8_YEAST	Cullin-8	0.58	-	nuc	0		cytoplasm [IDA] nucleus [IDA]			842
P41890 UniProt NPD GO	SCN1_SCHPO	Cut9-interacting protein scn1	0.58	-	nuc	0					335
P48129 UniProt NPD GO	RK28_CYAPA	Cyanelle 50S ribosomal protein L28	0.58	-	nuc	0	Plastid; cyanelle				70
O14976 UniProt NPD GO	GAK_HUMAN	Cyclin G-associated kinase (EC 2.7.11.1)	0.58	-	mit	0	Cytoplasm; perinuclear region. Golgi apparatus; trans-Golgi network. Cell membrane; cell-matrix junc ...		602052		1311
O60028 UniProt NPD GO	NFS1_ASHGO	Cysteine desulfurase, mitochondrial precursor (EC 2.8.1.7) (tRNA-splicing protein SPL1)	0.58	-	mit	0	Mitochondrion (By similarity)				490
P15393 UniProt NPD GO	C11B1_RAT	Cytochrome P450 11B1, mitochondrial precursor (EC 1.14.15.4) (CYPXIB1) (P450C11) (Steroid 11-beta-hy ...	0.58	-	mit	0	Mitochondrion	integral to endoplasmic reticulum membrane [IDA]			499
Q64441 UniProt NPD GO	CP24A_MOUSE	Cytochrome P450 24A1, mitochondrial precursor (EC 1.14.-.-) (P450-CC24) (Vitamin D(3) 24-hydroxylase ...	0.58	-	nuc	0	Mitochondrion				514
P51589 UniProt NPD GO	CP2J2_HUMAN	Cytochrome P450 2J2 (EC 1.14.14.1) (CYPIIJ2) (Arachidonic acid epoxygenase)	0.58	+	cyt	2 *	Endoplasmic reticulum; endoplasmic reticulum membrane; peripheral membrane protein		601258		502
Q9VRM7 UniProt NPD GO	CP307_DROME	Cytochrome P450 307a1 (EC 1.14.-.-) (CYPCCCVIIA1) (Spook protein)	0.58	-	mit	2 *	Endoplasmic reticulum; endoplasmic reticulum membrane; peripheral membrane protein (Potential)				543
O35728 UniProt NPD GO	CP4AE_MOUSE	Cytochrome P450 4A14 precursor (EC 1.14.15.3) (CYPIVA14) (Lauric acid omega-hydroxylase 3) (P450-LA- ...	0.58	-	nuc	2 *	Endoplasmic reticulum; endoplasmic reticulum membrane; peripheral membrane protein				507
Q9VWE0 UniProt NPD GO	DOME_DROME	Cytokine receptor precursor (Protein domeless)	0.58	-	nuc	1	Cell membrane; apicolateral cell membrane; single-pass type I membrane protein. Apicolateral membran ...	apical plasma membrane [TAS] apicolateral plasma membrane [IDA]			1282
O88485 UniProt NPD GO	DC1I1_MOUSE	Cytoplasmic dynein 1 intermediate chain 1 (Dynein intermediate chain 1, cytosolic) (DH IC-1) (Cytopl ...	0.58	+	cyt	0		dynein complex [TAS]			628
Q8H136 UniProt NPD GO	RH14_ARATH	DEAD-box ATP-dependent RNA helicase 14 (EC 3.6.1.-)	0.58	-	nuc	0	Nucleus (By similarity)				619
Q8BPN8 UniProt NPD GO	DMXL2_MOUSE	DMX-like-2 protein (Rabconnectin-3) (Fragment)	0.58	-	nuc	0	Synaptic vesicle; synaptic vesicle membrane; peripheral membrane protein (By similarity)				1485
Q6BIP4 UniProt NPD GO	DPB4_DEBHA	DNA polymerase epsilon subunit D (EC 2.7.7.7) (DNA polymerase II subunit D)	0.58	+	nuc	0	Nucleus (By similarity)				247
O89043 UniProt NPD GO	DPOA2_RAT	DNA polymerase subunit alpha B (DNA polymerase alpha 70 kDa subunit) (DNA polymerase subunit II)	0.58	-	nuc	0	Nucleus	alpha DNA polymerase:primase complex [TAS]			600
Q9QZM2 UniProt NPD GO	DPOG2_MOUSE	DNA polymerase subunit gamma 2, mitochondrial precursor (EC 2.7.7.7) (Mitochondrial DNA polymerase a ...	0.58	-	mit	0	Mitochondrion	mitochondrion [TAS]		1G5I	459
P36592 UniProt NPD GO	RAD22_SCHPO	DNA repair and recombination protein rad22	0.58	-	nuc	0					469
P40377 UniProt NPD GO	MCM2_SCHPO	DNA replication licensing factor mcm2 (Minichromosome maintenance protein 2) (Cell division control ...	0.58	-	mit	0	Nucleus (Probable)	MCM complex [IDA]			830
P30182 UniProt NPD GO	TOP2_ARATH	DNA topoisomerase 2 (EC 5.99.1.3) (DNA topoisomerase II)	0.58	+	nuc	0					1473
Q85X62 UniProt NPD GO	RPOC2_PINKO	DNA-directed RNA polymerase beta'' chain (EC 2.7.7.6) (PEP) (Plastid-encoded RNA polymerase beta'' s ...	0.58	-	nuc	0	Plastid; chloroplast				1209
P23025 UniProt NPD GO	XPA_HUMAN	DNA-repair protein complementing XP-A cells (Xeroderma pigmentosum group A-complementing protein)	0.58	-	nuc	0	Nucleus	nucleus [TAS]	278700	1XPA	273
Q06409 UniProt NPD GO	YL422_YEAST	DOCK-like protein YLR422W	0.58	-	end	0	Cytoplasm	cytoplasm [IDA]			1932
Q13316 UniProt NPD GO	DMP1_HUMAN	Dentin matrix acidic phosphoprotein 1 precursor (Dentin matrix protein 1) (DMP-1)	0.58	-	exc	0		extracellular matrix (sensu Metazoa) [TAS]	600980		513
Q8BHN5 UniProt NPD GO	DRBP1_MOUSE	Developmentally-regulated RNA-binding protein 1 (RB-1)	0.58	-	cyt	0	Cytoplasm (By similarity). Predominantly. Nucleus (By similarity). May shuttle between cytoplasm and ...	cytoplasm [ISS] nucleus [ISS]			476
O88797 UniProt NPD GO	DAB2_RAT	Disabled homolog 2 (DOC-2) (Mitogen-responsive phosphoprotein) (C9)	0.58	-	nuc	0					768
Q91284 UniProt NPD GO	DLX3_PLEWA	Distal-less-like protein DLX-3	0.58	+	nuc	0	Nucleus (Potential)				274
Q9Y2G8 UniProt NPD GO	DJC16_HUMAN	DnaJ homolog subfamily C member 16 precursor	0.58	-	end	1 *	Membrane; single-pass type IV membrane protein (Potential)				782
Q84JQ8 UniProt NPD GO	DOF18_ARATH	Dof zinc finger protein DOF1.8 (AtDOF1.8)	0.58	-	nuc	0	Nucleus (Probable)				352
P0C1Q2 UniProt NPD GO	PDE11_MOUSE	Dual 3',5'-cyclic-AMP and -GMP phosphodiesterase 11A (EC 3.1.4.17) (EC 3.1.4.35) (cAMP and cGMP phos ...	0.58	-	end	0	Cytoplasm; cytosol (By similarity)				933
Q8HZK2 UniProt NPD GO	DUOX2_PIG	Dual oxidase 2 precursor (EC 1.6.3.1) (EC 1.11.1.-) (NADH/NADPH thyroid oxidase p138-tox)	0.58	-	end	6	Cell membrane; apical cell membrane; multi-pass membrane protein. Localizes to the apical membrane o ...	apical plasma membrane [ISS]			1545
P36506 UniProt NPD GO	MP2K2_RAT	Dual specificity mitogen-activated protein kinase kinase 2 (EC 2.7.12.2) (MAP kinase kinase 2) (MAPK ...	0.58	-	exc	0					400
Q07192 UniProt NPD GO	MP2K2_XENLA	Dual specificity mitogen-activated protein kinase kinase 2 (EC 2.7.12.2) (MAP kinase kinase 2) (MAPK ...	0.58	-	nuc	0					446
Q924U5 UniProt NPD GO	TESK2_RAT	Dual specificity testis-specific protein kinase 2 (EC 2.7.12.1) (Testicular protein kinase 2)	0.58	-	nuc	0	Nucleus (By similarity)	cytoplasm [IMP] nucleus [IDA]			570
P45897 UniProt NPD GO	SMA4_CAEEL	Dwarfin sma-4 (MAD protein homolog 3)	0.58	-	nuc	0					570
P39057 UniProt NPD GO	DYHC_ANTCR	Dynein beta chain, ciliary	0.58	+	nuc	0	Flagellum				4466
P23098 UniProt NPD GO	DYHC_TRIGR	Dynein beta chain, ciliary	0.58	+	nuc	0	Flagellum			1HN5	4466
Q96JC9 UniProt NPD GO	EAF1_HUMAN	ELL-associated factor 1	0.58	-	nuc	0	Nucleus; nucleoplasm; nuclear speckle. Colocalizes with ELL to nuclear speckles. Nucleus; nucleoplas ...		608315		268
Q9D4C5 UniProt NPD GO	EAF1_MOUSE	ELL-associated factor 1	0.58	-	nuc	0	Nucleus; nucleoplasm; Cajal body (By similarity). Nucleus; nucleoplasm; nuclear speckle (By similari ...				268
Q5RAM8 UniProt NPD GO	EAF1_PONPY	ELL-associated factor 1	0.58	-	nuc	0	Nucleus; nucleoplasm; nuclear speckle (By similarity). Colocalizes with ELL to nuclear speckles. Nuc ...				268
Q3V1U8 UniProt NPD GO	ELMD1_MOUSE	ELMO domain-containing protein 1	0.58	-	mit	0					326
Q9Y6R1 UniProt NPD GO	S4A4_HUMAN	Electrogenic sodium bicarbonate cotransporter 1 (Sodium bicarbonate cotransporter) (Na(+)/HCO3(-) co ...	0.58	+	end	9	Cell membrane; basolateral cell membrane; multi-pass membrane protein		604278		1079
Q06706 UniProt NPD GO	IKI3_YEAST	Elongator complex protein 1 (Gamma-toxin target 1) (Protein IKI3)	0.58	-	nuc	0	Cytoplasm. Nucleus	DNA-directed RNA polymerase II, holoenzyme [IDA] transcription elongation factor complex [IDA]			1349
Q9C1W8 UniProt NPD GO	PPN1_SCHPO	Endopolyphosphatase (EC 3.6.1.10)	0.58	+	nuc	0	Vacuole; vacuolar membrane; single-pass type II membrane protein				577
O09100 UniProt NPD GO	GATA2_MOUSE	Endothelial transcription factor GATA-2 (GATA-binding protein 2)	0.58	-	nuc	0	Nucleus				480
Q924Y4 UniProt NPD GO	GATA2_RAT	Endothelial transcription factor GATA-2 (GATA-binding protein 2)	0.58	-	nuc	0	Nucleus (By similarity)	nucleus [ISS]			480
P97425 UniProt NPD GO	ECP2_MOUSE	Eosinophil cationic protein 2 precursor (EC 3.1.27.-) (ECP 2) (Ribonuclease 3-2) (RNase 3-2) (Eosino ...	0.58	-	exc	0	Matrix of eosinophil's large specific granule (By similarity)				156

You are viewing entries 20101 to 20150 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.