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
Q00078 UniProt NPD GO	KPC1_ASPNG	Protein kinase C-like (EC 2.7.11.13)	0.78	-	nuc	0					1096
P49757 UniProt NPD GO	NUMB_HUMAN	Protein numb homolog (h-Numb) (Protein S171)	0.78	-	nuc	0	Membrane; peripheral membrane protein	integral to plasma membrane [TAS]	603728		651
Q32PL1 UniProt NPD GO	PP1R7_BRARE	Protein phosphatase 1 regulatory subunit 7 (Protein phosphatase 1 regulatory subunit 22)	0.78	-	nuc	0	Nucleus (By similarity)				345
Q9DCL8 UniProt NPD GO	IPP2_MOUSE	Protein phosphatase inhibitor 2 (IPP-2)	0.78	-	nuc	0					205
O44783 UniProt NPD GO	SPY_DROME	Protein sprouty (Spry)	0.78	-	nuc	0	Cell membrane; peripheral membrane protein; cytoplasmic side	intracellular [TAS]			589
P11075 UniProt NPD GO	SEC7_YEAST	Protein transport protein SEC7	0.78	-	nuc	0	Cytoplasm. Golgi apparatus. Associated with the peripheral Golgi membrane	cytosol [IDA] Golgi-associated vesicle [IDA] late endosome [IDA]			2009
P53450 UniProt NPD GO	FOS_FUGRU	Proto-oncogene protein c-fos (Cellular oncogene fos)	0.78	+	nuc	0	Nucleus				376
Q09449 UniProt NPD GO	YQ12_CAEEL	Putative ATP-dependent helicase C05C10.2 (EC 3.6.1.-)	0.78	-	nuc	0					1551
P38766 UniProt NPD GO	YHJ1_YEAST	Putative ATP-dependent helicase YHR031C (EC 3.6.1.-)	0.78	-	nuc	0		nuclear telomeric heterochromatin [IPI]			723
Q9UUI7 UniProt NPD GO	TPSY_SCHPO	Putative alpha,alpha-trehalose-phosphate synthase [UDP-forming] subunit 100 kDa subunit (EC 2.4.1.15 ...	0.78	-	cyt	0					891
P43151 UniProt NPD GO	GPA_LEIDO	Putative guanine nucleotide-binding protein subunit alpha	0.78	-	nuc	1					464
Q9CY21 UniProt NPD GO	WBS22_MOUSE	Putative methyltransferase WBSCR22 (EC 2.1.1.-) (Williams-Beuren syndrome chromosome region 22 prote ...	0.78	+	nuc	0	Nucleus (Potential)				281
Q19238 UniProt NPD GO	YS3J_CAEEL	Putative tyrosine-protein kinase F09A5.2 in chromosome X (EC 2.7.10.1)	0.78	-	mit	2 *	Membrane; multi-pass membrane protein (Potential)				894
Q6NRZ0 UniProt NPD GO	RCOR2_XENLA	REST corepressor 2	0.78	-	nuc	0	Nucleus (By similarity)				503
P93823 UniProt NPD GO	ATL1A_ARATH	RING-H2 finger protein ATL1A	0.78	-	nuc	1 *					381
P40992 UniProt NPD GO	RRN7_YEAST	RNA polymerase I-specific transcription initiation factor RRN7	0.78	-	nuc	0	Nucleus; nucleolus	RNA polymerase I transcription factor complex [TAS]			514
Q9P376 UniProt NPD GO	FCP1_SCHPO	RNA polymerase II subunit A C-terminal domain phosphatase (EC 3.1.3.16) (CTD phosphatase fcp1)	0.78	+	nuc	0	Nucleus (Probable)				723
Q6BP96 UniProt NPD GO	TFB3_DEBHA	RNA polymerase II transcription factor B subunit 3 (RNA polymerase II transcription factor B p38 sub ...	0.78	-	nuc	0	Nucleus (By similarity)				345
Q8C5L7 UniProt NPD GO	RBM34_MOUSE	RNA-binding protein 34 (RNA-binding motif protein 34)	0.78	-	nuc	0	Nucleus; nucleolus (By similarity)				375
Q15276 UniProt NPD GO	RABE1_HUMAN	Rab GTPase-binding effector protein 1 (Rabaptin-5) (Rabaptin-5alpha) (Rabaptin-4) (NY-REN-17 antigen ...	0.78	-	nuc	0	Cytoplasm. Endosome; early endosome. Endosome; recycling endosome	early endosome [TAS]	603616	1X79	862
O15211 UniProt NPD GO	RGL2_HUMAN	Ral guanine nucleotide dissociation stimulator-like 2 (RalGDS-like factor) (RAS-associated protein R ...	0.78	-	nuc	0			602306		777
Q9ERU9 UniProt NPD GO	RBP2_MOUSE	Ran-binding protein 2 (RanBP2)	0.78	-	nuc	0	Nucleus; nuclear envelope; nuclear pore complex (By similarity). Cytoplasmic filaments (By similarit ...				3053
P49758 UniProt NPD GO	RGS6_HUMAN	Regulator of G-protein signaling 6 (RGS6) (S914)	0.78	-	cyt	0	Cytoplasm. Membrane; peripheral membrane protein		603894	2ES0	567
P21691 UniProt NPD GO	SIR1_YEAST	Regulatory protein SIR1 (Silent information regulator 1)	0.78	-	mit	0		chromatin silencing complex [IDA]		1ZHI	678
Q8WUF5 UniProt NPD GO	IASPP_HUMAN	RelA-associated inhibitor (Inhibitor of ASPP protein) (Protein iASPP) (PPP1R13B-like protein) (NFkB- ...	0.78	+	nuc	0	Isoform 1: Cytoplasm. Predominantly cytoplasmic but also nuclear (isoform 1). Isoform 1, isoform 2: ...	nucleus [TAS]	607463		828
Q5I1X5 UniProt NPD GO	IASPP_MOUSE	RelA-associated inhibitor (Inhibitor of ASPP protein) (Protein iASPP) (PPP1R13B-like protein) (NFkB- ...	0.78	+	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity). Predominantly cytoplasmic but also nuclear (By s ...				824
P38630 UniProt NPD GO	RFC1_YEAST	Replication factor C subunit 1 (Replication factor C1) (Activator 1 95 kDa subunit) (Cell division c ...	0.78	+	nuc	0	Nucleus (Probable)	DNA replication factor C complex [IDA]		1SXJ	861
Q03278 UniProt NPD GO	PO21_NASVI	Retrovirus-related Pol polyprotein from type-1 retrotransposable element R2 (Retrovirus-related Pol ...	0.78	+	nuc	0					1025
Q9BRR9 UniProt NPD GO	RHG09_HUMAN	Rho-GTPase-activating protein 9	0.78	-	nuc	0					750
Q8R040 UniProt NPD GO	RPP21_MOUSE	Ribonuclease P protein subunit p21 (EC 3.1.26.5) (RNaseP protein p21) (Ribonucleoprotein V)	0.78	-	nuc	0	Nucleus; nucleolus (By similarity)				150
P78345 UniProt NPD GO	RPP38_HUMAN	Ribonuclease P protein subunit p38 (EC 3.1.26.5) (RNaseP protein p38)	0.78	+	nuc	0	Nucleus; nucleolus (Potential)	nucleolar ribonuclease P complex [TAS] nucleus [TAS]	606116		283
Q9Z2B9 UniProt NPD GO	KS6A4_MOUSE	Ribosomal protein S6 kinase alpha-4 (EC 2.7.11.1) (Nuclear mitogen-and stress-activated protein kina ...	0.78	-	cyt	0	Nucleus (By similarity)	nucleus [ISS]			773
Q08932 UniProt NPD GO	RSA1_YEAST	Ribosome assembly 1 protein	0.78	-	nuc	0	Nucleus	nucleoplasm [IDA]			381
Q96MS0 UniProt NPD GO	ROBO3_HUMAN	Roundabout homolog 3 precursor (Roundabout-like protein 3)	0.78	-	nuc	1	Membrane; single-pass type I membrane protein (Potential)	integral to membrane [NAS]	608630		1386
Q5F471 UniProt NPD GO	SAPS3_CHICK	SAPS domain family member 3	0.78	-	nuc	0					873
Q15464 UniProt NPD GO	SHB_HUMAN	SH2 domain-containing adapter protein B	0.78	-	nuc	0	Cytoplasm. Associates with membrane lipid rafts upon TCR stimulation		600314		509
Q810B9 UniProt NPD GO	SLIK3_MOUSE	SLIT and NTRK-like protein 3 precursor	0.78	+	nuc	2 *	Membrane; single-pass membrane protein (Potential)				980
Q59P11 UniProt NPD GO	HSV2_CANAL	SVP1-like protein 2	0.78	-	nuc	0	Vacuole; vacuolar membrane; peripheral membrane protein (By similarity). Cytoplasmic vesicle; cytopl ...				595
Q8BJL0 UniProt NPD GO	SMAL1_MOUSE	SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A-like protein 1 ...	0.78	-	nuc	0	Nucleus (By similarity)				910
Q9P0W2 UniProt NPD GO	HM20B_HUMAN	SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily E member 1-relate ...	0.78	+	nuc	0	Nucleus. Localized to condensed chromosomes in mitosis in conjunction with BRCA2	nucleus [NAS]	605535		317
P13730 UniProt NPD GO	SGS3_DROER	Salivary glue protein Sgs-3 precursor	0.78	-	nuc	0					328
Q9VCR6 UniProt NPD GO	SAV_DROME	Scaffold protein salvador (Shar-pei)	0.78	-	nuc	0					608
Q9BQE4 UniProt NPD GO	SELS_HUMAN	Selenoprotein S (VCP-interacting membrane protein)	0.78	-	nuc	1 *	Endoplasmic reticulum; endoplasmic reticulum membrane; single-pass membrane protein	integral to endoplasmic reticulum membrane [IDA]	607918		189
Q9P283 UniProt NPD GO	SEM5B_HUMAN	Semaphorin-5B precursor	0.78	-	exc	1	Membrane; single-pass type I membrane protein				1093
Q60519 UniProt NPD GO	SEM5B_MOUSE	Semaphorin-5B precursor (Semaphorin G) (Sema G)	0.78	-	exc	1	Membrane; single-pass type I membrane protein				1093
Q9H2E6 UniProt NPD GO	SEM6A_HUMAN	Semaphorin-6A precursor (Semaphorin VIA) (Sema VIA) (Semaphorin 6A-1) (SEMA6A-1)	0.78	-	exc	1	Membrane; single-pass type I membrane protein	axon [NAS] integral to membrane [NAS]	605885		1030
O35464 UniProt NPD GO	SEM6A_MOUSE	Semaphorin-6A precursor (Semaphorin VIA) (Sema VIA) (Semaphorin 6A-1) (SEMA6A-1) (Semaphorin Q) (Sem ...	0.78	-	exc	1	Membrane; single-pass type I membrane protein	axon [NAS] integral to membrane [ISS] membrane [NAS]			1031
Q8C650 UniProt NPD GO	SEP10_MOUSE	Septin-10	0.78	-	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity)				452
Q8BG48 UniProt NPD GO	ST17B_MOUSE	Serine/threonine-protein kinase 17B (EC 2.7.11.1) (DAP kinase-related apoptosis-inducing protein kin ...	0.78	-	mit	0	Nucleus (By similarity)	nucleus [ISS]			372
Q5EAK6 UniProt NPD GO	ATM_DROME	Serine/threonine-protein kinase ATM (EC 2.7.11.1) (Telomere fusion protein)	0.78	-	nuc	0	Nucleus (Probable)				2767

You are viewing entries 10051 to 10100 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.