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
Q10955 UniProt NPD GO	RGS5_CAEEL	Regulator of G-protein signaling rgs-5	0.87	+	nuc	0					492
P39113 UniProt NPD GO	CAT8_YEAST	Regulatory protein CAT8	0.87	-	nuc	0	Nucleus	nucleus [IC]			1433
P53035 UniProt NPD GO	MIG2_YEAST	Regulatory protein MIG2	0.87	-	nuc	0	Nucleus (Potential)	nucleus [TAS]			382
P30622 UniProt NPD GO	REST_HUMAN	Restin (Cytoplasmic linker protein 170 alpha-2) (CLIP-170) (Reed-Sternberg intermediate filament-ass ...	0.87	-	nuc	0	Cytoplasm. Cytoskeleton. Associated with the cytoskeleton	endosome [TAS] intermediate filament [TAS] kinetochore [TAS] microtubule cytoskeleton [TAS]	179838	2CP6	1427
Q05654 UniProt NPD GO	RT21_SCHPO	Retrotransposable element Tf2 155 kDa protein type 1	0.87	-	nuc	0					1333
Q9C0R2 UniProt NPD GO	RT22_SCHPO	Retrotransposable element Tf2 155 kDa protein type 2	0.87	-	nuc	0					1333
Q09763 UniProt NPD GO	GEF1_SCHPO	Rho guanine nucleotide exchange factor gef1	0.87	-	nuc	0	Septum	cell septum [IDA] cytoplasm [IDA] medial ring [IDA]			753
Q63744 UniProt NPD GO	RHG07_RAT	Rho-GTPase-activating protein 7 (Rho-type GTPase-activating protein 7) (p122-RhoGAP) (Deleted in liv ...	0.87	+	nuc	0	Cytoplasm (Potential)	cytoplasm [NAS]			1091
Q80UU2 UniProt NPD GO	RPP38_MOUSE	Ribonuclease P protein subunit p38 (EC 3.1.26.5) (RNaseP protein p38)	0.87	+	nuc	0	Nucleus; nucleolus (Potential)				280
Q6BIF5 UniProt NPD GO	RLP7_DEBHA	Ribosome biogenesis protein RLP7	0.87	+	nuc	0	Nucleus; nucleolus (By similarity)				275
Q15050 UniProt NPD GO	RRS1_HUMAN	Ribosome biogenesis regulatory protein homolog	0.87	+	nuc	0	Nucleus; nucleolus				365
Q8CJ40 UniProt NPD GO	CROCC_MOUSE	Rootletin (Ciliary rootlet coiled-coil protein)	0.87	-	nuc	0	Centrosome. In ciliated cells, associated with ciliary rootlets. In non-ciliated cells, localized be ...	centriole [IDA] ciliary rootlet [IDA]			2009
O55005 UniProt NPD GO	ROBO1_RAT	Roundabout homolog 1 precursor	0.87	-	exc	0	Membrane; single-pass type I membrane protein (Potential)				1651
Q9UNE7 UniProt NPD GO	STUB1_HUMAN	STIP1 homology and U box-containing protein 1 (EC 6.3.2.-) (STIP1 homology and U-box-containing prot ...	0.87	-	nuc	0	Cytoplasm	ubiquitin conjugating enzyme complex [TAS]	607207		303
Q91ZW3 UniProt NPD GO	SMCA5_MOUSE	SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A member 5 (EC 3. ...	0.87	+	nuc	0	Nucleus	nucleus [IDA]			1051
Q6PDG5 UniProt NPD GO	SMRC2_MOUSE	SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily C member 2 (SWI/S ...	0.87	+	nuc	0	Nucleus				1213
Q6BWZ7 UniProt NPD GO	SWC5_DEBHA	SWR1-complex protein 5	0.87	-	nuc	0	Nucleus (By similarity)				341
Q9JLC8 UniProt NPD GO	SACS_MOUSE	Sacsin	0.87	-	nuc	0					3830
Q8VEB2 UniProt NPD GO	SAV1_MOUSE	Salvador homolog 1 protein (45 kDa WW domain protein) (mWW45)	0.87	-	nuc	0					386
Q14151 UniProt NPD GO	SAFB2_HUMAN	Scaffold attachment factor B2	0.87	+	nuc	0	Cytoplasm. Nucleus		608066		953
Q9UHJ3 UniProt NPD GO	SMBT1_HUMAN	Scm-like with four MBT domains protein 1 (Renal ubiquitous protein 1)	0.87	+	nuc	0			607319		866
P51140 UniProt NPD GO	DSH_DROME	Segment polarity protein dishevelled	0.87	-	nuc	0	Cytoplasm. Membrane; peripheral membrane protein. Associated with the membrane when hyperphosphoryla ...	adherens junction [TAS] cytoplasm [TAS]			623
Q9QZR6 UniProt NPD GO	SEPT9_RAT	Septin-9 (Eseptin) (eighth septin) (Septin-like protein) (SLP)	0.87	-	nuc	0	Cell membrane				564
Q9Y7W4 UniProt NPD GO	BUR1_CANAL	Serine/threonine-protein kinase BUR1 (EC 2.7.11.22) (EC 2.7.11.23)	0.87	-	nuc	0	Nucleus (By similarity)				746
O01510 UniProt NPD GO	SMG1_CAEEL	Serine/threonine-protein kinase smg-1 (EC 2.7.11.1) (Suppressor with morphogenetic effect on genital ...	0.87	-	mit	0	Cytoplasm				2322
Q6GLQ4 UniProt NPD GO	PP1RA_XENLA	Serine/threonine-protein phosphatase 1 regulatory subunit 10	0.87	+	nuc	0	Nucleus (By similarity)				819
Q03256 UniProt NPD GO	SRY_CAPHI	Sex-determining region Y protein (Testis-determining factor)	0.87	+	nuc	0	Nucleus				240
Q864Q7 UniProt NPD GO	SRY_EUBAS	Sex-determining region Y protein (Testis-determining factor)	0.87	+	nuc	0	Nucleus				204
P48046 UniProt NPD GO	SRY_GORGO	Sex-determining region Y protein (Testis-determining factor)	0.87	+	nuc	0	Nucleus				204
Q05066 UniProt NPD GO	SRY_HUMAN	Sex-determining region Y protein (Testis-determining factor)	0.87	+	nuc	0	Nucleus	nucleus [NAS]	163950	1J47	204
Q67EX6 UniProt NPD GO	SRY_MOSCH	Sex-determining region Y protein (Testis-determining factor)	0.87	+	nuc	0	Nucleus				227
Q28778 UniProt NPD GO	SRY_PANPA	Sex-determining region Y protein (Testis-determining factor)	0.87	+	nuc	0	Nucleus				204
Q28798 UniProt NPD GO	SRY_PANTR	Sex-determining region Y protein (Testis-determining factor)	0.87	+	nuc	0	Nucleus				204
Q864Q6 UniProt NPD GO	SRY_PHYCA	Sex-determining region Y protein (Testis-determining factor)	0.87	+	nuc	0	Nucleus				216
P36395 UniProt NPD GO	SRY_SMIMA	Sex-determining region Y protein (Testis-determining factor)	0.87	-	nuc	0	Nucleus				208
O35119 UniProt NPD GO	TRPC4_RAT	Short transient receptor potential channel 4 (TrpC4) (Trp4) (Capacitative calcium entry channel 1) ( ...	0.87	-	end	8	Membrane; multi-pass membrane protein (Probable)				977
O62852 UniProt NPD GO	TRPC5_RABIT	Short transient receptor potential channel 5 (TrpC5) (Rtrp5) (Capacitative calcium entry channel 2) ...	0.87	-	end	7	Membrane; multi-pass membrane protein (Probable)				974
Q80TE4 UniProt NPD GO	SI1L2_MOUSE	Signal-induced proliferation-associated 1-like protein 2	0.87	-	nuc	0					1722
P40959 UniProt NPD GO	MVP1_YEAST	Sorting nexin MVP1	0.87	-	nuc	0	Cytoplasm	cytoplasm [IDA]			511
Q9UBP0 UniProt NPD GO	SPAST_HUMAN	Spastin	0.87	-	nuc	1	Nucleus. Cytoplasm; perinuclear region	nucleus [TAS]	604277		616
P16546 UniProt NPD GO	SPTA2_MOUSE	Spectrin alpha chain, brain (Spectrin, non-erythroid alpha chain) (Alpha-II spectrin) (Fodrin alpha ...	0.87	-	nuc	0		Z disc [IDA]			1458
Q8NHX4 UniProt NPD GO	SPTA3_HUMAN	Spermatogenesis-associated protein 3 (Testis spermatocyte apoptosis-related protein 1) (Testis and s ...	0.87	-	nuc	0					183
Q9S7A9 UniProt NPD GO	SPL4_ARATH	Squamosa promoter-binding-like protein 4	0.87	-	nuc	0	Nucleus (Probable)			1UL4	174
Q15020 UniProt NPD GO	SART3_HUMAN	Squamous cell carcinoma antigen recognized by T-cells 3 (SART-3) (hSART-3) (Tat-interacting protein ...	0.87	+	cyt	0	Cytoplasm. Nucleus. Localized in speckles. Expressed in the nucleus of all of the malignant tumor ce ...				963
Q15772 UniProt NPD GO	SPEG_HUMAN	Striated muscle preferentially expressed protein kinase (EC 2.7.11.1) (Aortic preferentially express ...	0.87	-	end	0	Isoform 4: Nucleus	nucleus [TAS]		1U2H	3223
Q9NTJ3 UniProt NPD GO	SMC4_HUMAN	Structural maintenance of chromosomes 4-like 1 protein (Chromosome-associated polypeptide C) (hCAP-C ...	0.87	-	nuc	0	Nucleus. Cytoplasm. In interphase cells, the majority of the condensin complex is found in the cytop ...	condensin complex [TAS] nucleus [TAS]	605575		1288
Q8N3V7 UniProt NPD GO	SYNPO_HUMAN	Synaptopodin	0.87	-	nuc	0	Cytoplasm (By similarity). Cell membrane; cell-cell junction; tight junction (By similarity). Locali ...		608155		929
Q8N103 UniProt NPD GO	TAGAP_HUMAN	T-cell activation Rho GTPase-activating protein (T-cell activation GTPase-activating protein)	0.87	+	nuc	0			609667		731
O55144 UniProt NPD GO	TLX3_MOUSE	T-cell leukemia homeobox protein 3 (Homeobox TLX-3) (Homeobox protein Hox-11L2) (Respiratory neuron ...	0.87	+	nuc	0	Nucleus (Probable)	nucleus [IDA]			291
O43711 UniProt NPD GO	TLX3_HUMAN	T-cell leukemia homeobox protein 3 (Homeobox protein Hox-11L2)	0.87	+	nuc	0	Nucleus (Probable)		604640		291

You are viewing entries 5801 to 5850 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.