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
P60320 UniProt NPD GO	SMG_DROYA	Protein Smaug (Fragment)	0.52	-	nuc	0	Cytoplasm (By similarity)				126
P48614 UniProt NPD GO	WN10B_MOUSE	Protein Wnt-10b precursor (Wnt-12)	0.52	-	nuc	0	Secreted protein; extracellular space; extracellular matrix				389
O42122 UniProt NPD GO	WNT5B_ORYLA	Protein Wnt-5b precursor	0.52	-	nuc	0	Secreted protein; extracellular space; extracellular matrix				371
P51030 UniProt NPD GO	WNT8C_CHICK	Protein Wnt-8c precursor (CWnt-8)	0.52	-	exc	1 *	Secreted protein; extracellular space; extracellular matrix				357
P31318 UniProt NPD GO	ARG56_SCHPO	Protein arg11, mitochondrial precursor [Contains: N-acetyl-gamma-glutamyl-phosphate reductase (EC 1. ...	0.52	-	nuc	0	Mitochondrion	mitochondrial matrix [IDA]			885
O46232 UniProt NPD GO	HUNB_DROAD	Protein hunchback (Fragments)	0.52	-	nuc	0	Nucleus (By similarity)				192
Q8R4R9 UniProt NPD GO	PP14C_RAT	Protein phosphatase 1 regulatory subunit 14C (PKC-potentiated PP1 inhibitory protein) (Kinase-enhanc ...	0.52	-	nuc	0	Intracytoplasmic membrane; peripheral membrane protein (By similarity)				164
Q10136 UniProt NPD GO	STE7_SCHPO	Protein ste7	0.52	-	nuc	0					569
Q96QU1 UniProt NPD GO	PCD15_HUMAN	Protocadherin-15 precursor	0.52	-	end	1 *	Membrane; single-pass type I membrane protein (By similarity)		609533		1955
Q6BNX8 UniProt NPD GO	PUS5_DEBHA	Pseudouridylate synthase PUS5 (EC 5.4.99.-) (Pseudouridine synthase 5) (Uracil hydrolyase PUS5)	0.52	-	nuc	0	Mitochondrion (By similarity)				339
O94260 UniProt NPD GO	G3BP_SCHPO	Putative G3BP-like protein	0.52	-	nuc	0					434
Q9NAH2 UniProt NPD GO	TBX34_CAEEL	Putative T-box protein 34	0.52	-	nuc	0	Nucleus (Potential)				302
Q07825 UniProt NPD GO	XPP_YEAST	Putative Xaa-Pro aminopeptidase (EC 3.4.11.9)	0.52	+	mit	0	Cytoplasm	cytoplasm [IDA]			749
Q9FRH3 UniProt NPD GO	CAP13_ARATH	Putative clathrin assembly protein At1g25240	0.52	-	mit	0					376
Q9T048 UniProt NPD GO	DRL27_ARATH	Putative disease resistance protein At4g27190	0.52	-	cyt	0					985
O74940 UniProt NPD GO	NADE_SCHPO	Putative glutamine-dependent NAD(+) synthetase (EC 6.3.5.1) (NAD(+) synthase [glutamine-hydrolyzing] ...	0.52	-	cyt	0					700
Q9VGG6 UniProt NPD GO	IDLC_DROME	Putative inner dynein arm light chain, axonemal	0.52	-	nuc	0					250
Q6L403 UniProt NPD GO	R1B17_SOLDE	Putative late blight resistance protein homolog R1B-17	0.52	-	nuc	0	Cytoplasm (By similarity)				1312
Q9LVK9 UniProt NPD GO	ALA7_ARATH	Putative phospholipid-transporting ATPase 7 (EC 3.6.3.1) (Aminophospholipid flippase 7)	0.52	+	end	10	Membrane; multi-pass membrane protein				1247
P40557 UniProt NPD GO	YIA5_YEAST	Putative protein disulfide-isomerase YIL005W precursor (EC 5.3.4.1)	0.52	-	mit	1 *		endoplasmic reticulum membrane [IDA]			701
Q9Y7J6 UniProt NPD GO	KOIA_SCHPO	Putative serine/threonine-protein kinase C1778.10c (EC 2.7.11.1)	0.52	-	nuc	0					550
Q20024 UniProt NPD GO	STX1_CAEEL	Putative syntaxin-1	0.52	-	nuc	1	Membrane; single-pass type IV membrane protein (Potential)	integral to membrane [ISS]			306
Q19673 UniProt NPD GO	TYR3_CAEEL	Putative tyrosinase-like protein tyr-3 precursor	0.52	-	exc	0					683
Q5T4H9 UniProt NPD GO	CJ114_HUMAN	Putative uncharacterized protein C10orf114	0.52	-	nuc	0					136
P38895 UniProt NPD GO	YAN0_YEAST	Putative uncharacterized protein YAR060C/YHR212C	0.52	-	nuc	0					111
O14077 UniProt NPD GO	YEAC_SCHPO	Putative zinc-protease UNK4.12c (EC 3.4.99.-)	0.52	-	cyt	0					969
P53331 UniProt NPD GO	REXO1_YEAST	RNA exonuclease 1 (EC 3.1.-.-) (RNase H(70))	0.52	+	cyt	0	Nucleus	nucleus [IDA]			553
Q6CD24 UniProt NPD GO	TFB4_YARLI	RNA polymerase II transcription factor B subunit 4 (RNA polymerase II transcription factor B p34 sub ...	0.52	+	nuc	0	Nucleus (By similarity)				340
Q62799 UniProt NPD GO	ERBB3_RAT	Receptor tyrosine-protein kinase erbB-3 precursor (EC 2.7.10.1) (c-erbB3)	0.52	+	exc	1	Membrane; single-pass type I membrane protein	integral to membrane [TAS]			1339
Q61526 UniProt NPD GO	ERBB3_MOUSE	Receptor tyrosine-protein kinase erbB-3 precursor (EC 2.7.10.1) (c-erbB3) (Glial growth factor recep ...	0.52	+	exc	1	Membrane; single-pass type I membrane protein (By similarity)	apical plasma membrane [IDA] lateral plasma membrane [IDA]			1339
Q92729 UniProt NPD GO	PTPRU_HUMAN	Receptor-type tyrosine-protein phosphatase U precursor (EC 3.1.3.48) (R-PTP-U) (Protein-tyrosine pho ...	0.52	-	end	2	Membrane; single-pass type I membrane protein	integral to plasma membrane [TAS]	602454		1430
Q15262 UniProt NPD GO	PTPRK_HUMAN	Receptor-type tyrosine-protein phosphatase kappa precursor (EC 3.1.3.48) (Protein-tyrosine phosphata ...	0.52	-	end	2 *	Cell membrane; cell-cell junction; adherens junction; single-pass type I membrane protein	integral to plasma membrane [TAS]	602545	2C7S	1439
P56722 UniProt NPD GO	PTPRN_BOVIN	Receptor-type tyrosine-protein phosphatase-like N precursor (R-PTP-N) (Islet cell autoantigen 512) ( ...	0.52	-	nuc	1	Membrane; single-pass type I membrane protein. Neuroendocrine secretory granules				979
Q9CX84 UniProt NPD GO	RGS19_MOUSE	Regulator of G-protein signaling 19 (RGS19)	0.52	-	nuc	0	Membrane; lipid-anchor (By similarity)				216
O70521 UniProt NPD GO	RGS19_RAT	Regulator of G-protein signaling 19 (RGS19) (G-alpha-interacting protein) (GAIP protein)	0.52	-	nuc	0	Membrane; lipid-anchor (By similarity)	clathrin-coated vesicle [IDA] Golgi membrane [TAS]			216
Q9EPU0 UniProt NPD GO	RENT1_MOUSE	Regulator of nonsense transcripts 1 (EC 3.6.1.-) (ATP-dependent helicase RENT1) (Nonsense mRNA reduc ...	0.52	-	nuc	0	Cytoplasm	chromatin [ISS] cytoplasm [ISS]			1113
P40938 UniProt NPD GO	RFC3_HUMAN	Replication factor C subunit 3 (Replication factor C 38 kDa subunit) (RFC38) (Activator 1 38 kDa sub ...	0.52	-	nuc	0	Nucleus (Probable)	DNA replication factor C complex [TAS]	600405		356
Q99PI8 UniProt NPD GO	RTN4R_MOUSE	Reticulon-4 receptor precursor (Nogo receptor) (NgR) (Nogo-66 receptor)	0.52	-	exc	0	Cell membrane; lipid-anchor; GPI-anchor (By similarity)	plasma membrane [IDA]			473
Q9JLT7 UniProt NPD GO	RX_RAT	Retinal homeobox protein Rx (Retina and anterior neural fold homeobox protein)	0.52	+	nuc	0	Nucleus				342
Q9PVX0 UniProt NPD GO	RX2_CHICK	Retinal homeobox protein Rx2 (cRax2)	0.52	+	nuc	0	Nucleus (By similarity)				317
P78363 UniProt NPD GO	ABCA4_HUMAN	Retinal-specific ATP-binding cassette transporter (ATP-binding cassette sub-family A member 4) (RIM ...	0.52	+	end	11 *	Membrane; multi-pass membrane protein	membrane fraction [TAS]	604116		2273
P19793 UniProt NPD GO	RXRA_HUMAN	Retinoic acid receptor RXR-alpha (Retinoid X receptor alpha)	0.52	+	nuc	0	Nucleus		180245	2NLL	462
P10403 UniProt NPD GO	ENV1_DROME	Retrovirus-related Env polyprotein from transposon gypsy	0.52	-	mit	1					509
Q8R2S1 UniProt NPD GO	RPKL1_MOUSE	Ribosomal protein S6 kinase-like 1 (EC 2.7.11.1)	0.52	-	nuc	0					544
P97452 UniProt NPD GO	BOP1_MOUSE	Ribosome biogenesis protein BOP1 (Block of proliferation 1 protein)	0.52	-	cyt	0	Nucleus; nucleolus	nucleolus [IDA]			732
Q12464 UniProt NPD GO	RUVB2_YEAST	RuvB-like protein 2 (EC 3.6.1.-) (RUVBL2) (TIP49b homolog) (TIP49-homology protein 2)	0.52	-	cyt	0	Nucleus; nucleoplasm	INO80 complex [IPI] nucleus [IDA] SWR1 complex [IPI]			471
Q9NP31 UniProt NPD GO	SH22A_HUMAN	SH2 domain protein 2A (T cell-specific adapter protein) (TSAd) (VEGF receptor-associated protein) (S ...	0.52	-	nuc	0	Cytoplasm	cytoplasm [TAS] soluble fraction [TAS]	604514		389
Q9Y6D0 UniProt NPD GO	SELK_HUMAN	Selenoprotein K	0.52	-	nuc	1 *			607916		94
Q62179 UniProt NPD GO	SEM4B_MOUSE	Semaphorin-4B precursor (Semaphorin C) (Sema C)	0.52	-	mit	2 *	Membrane; single-pass type I membrane protein				823
Q6X2M3 UniProt NPD GO	SEMG2_HYLKL	Semenogelin-2 precursor (Semenogelin II) (SGII)	0.52	-	nuc	0	Secreted protein (By similarity)				522

You are viewing entries 23951 to 24000 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.