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
P06701 UniProt NPD GO	SIR3_YEAST	Regulatory protein SIR3 (Silent information regulator 3)	0.93	-	nuc	0	Nucleus	chromatin silencing complex [IDA] mitochondrion [IDA] nuclear telomere cap complex [IDA] nuclear telomeric heterochromatin [IDA] nucleolus [IDA]		2FL7	977
P26307 UniProt NPD GO	VIV1_MAIZE	Regulatory protein viviparous-1	0.93	-	nuc	0	Or: Cytoplasm. Or: Nucleus				691
Q9VJE5 UniProt NPD GO	CL190_DROME	Restin homolog (Cytoplasmic linker protein 190) (Microtubule-binding protein 190) (d-CLIP-190)	0.93	-	nuc	0	Cytoplasm. Microtubule-associated. Golgi apparatus. Lva-CLIP-190 complexes are found at the Golgi	fusome [IDA] Golgi apparatus [IDA] microtubule associated complex [IDA] spindle microtubule [IDA]			1690
Q64700 UniProt NPD GO	RBL2_MOUSE	Retinoblastoma-like protein 2 (130 kDa retinoblastoma-associated protein) (PRB2) (P130) (RBR-2)	0.93	+	nuc	0	Nucleus	nucleus [IDA] transcription factor complex [IDA]			1135
O55081 UniProt NPD GO	RBL2_RAT	Retinoblastoma-like protein 2 (130 kDa retinoblastoma-associated protein) (PRB2) (P130) (RBR-2) (PPA ...	0.93	-	nuc	0	Nucleus				1135
P70336 UniProt NPD GO	ROCK2_MOUSE	Rho-associated protein kinase 2 (EC 2.7.11.1) (Rho-associated, coiled-coil-containing protein kinase ...	0.93	-	nuc	0	Cytoplasm (By similarity). Cell membrane; peripheral membrane protein (By similarity). Cytoplasmic, ...				1388
Q62868 UniProt NPD GO	ROCK2_RAT	Rho-associated protein kinase 2 (EC 2.7.11.1) (Rho-associated, coiled-coil-containing protein kinase ...	0.93	-	nuc	0	Cytoplasm. Cell membrane; peripheral membrane protein. Cytoplasmic, and associated with actin microf ...				1379
Q06407 UniProt NPD GO	RGA2_YEAST	Rho-type GTPase-activating protein 2	0.93	-	nuc	0		intracellular [TAS]			1009
O01326 UniProt NPD GO	RNC_CAEEL	Ribonuclease III (EC 3.1.26.3) (RNase III)	0.93	-	nuc	0	Nucleus (Probable)				1086
Q9QX72 UniProt NPD GO	SEBP2_RAT	SECIS-binding protein 2 (Selenocysteine insertion sequence-binding protein 2)	0.93	+	nuc	0	Nucleus (Potential)				846
P46995 UniProt NPD GO	SET2_YEAST	SET domain-containing protein 2	0.93	+	nuc	0		nucleus [IPI]		2C5Z	733
Q80Z38 UniProt NPD GO	SHAN2_MOUSE	SH3 and multiple ankyrin repeat domains protein 2 (Shank2) (Cortactin-binding protein 1) (CortBP1)	0.93	+	nuc	0	Cytoplasm; postsynaptic density of neuronal cells. Colocalizes with cortactin in growth cones in dif ...				1476
Q8VDU5 UniProt NPD GO	SNRK_MOUSE	SNF-related serine/threonine-protein kinase (EC 2.7.11.1) (SNF1-related kinase)	0.93	-	nuc	0	Nucleus (By similarity)				748
Q92925 UniProt NPD GO	SMRD2_HUMAN	SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily D member 2 (60 kD ...	0.93	+	nuc	0	Nucleus	nucleoplasm [TAS]	601736		456
O54772 UniProt NPD GO	SMRD2_RAT	SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily D member 2 (60 kD ...	0.93	+	nuc	0	Nucleus (By similarity)	SWI/SNF complex [TAS]			456
Q5AAJ7 UniProt NPD GO	SWC4_CANAL	SWR1-complex protein 4	0.93	+	nuc	0	Nucleus (By similarity)				635
Q6CSS3 UniProt NPD GO	SWC4_KLULA	SWR1-complex protein 4	0.93	-	nuc	0	Nucleus (By similarity)				497
Q91ZX6 UniProt NPD GO	SENP2_MOUSE	Sentrin-specific protease 2 (EC 3.4.22.-) (Sentrin/SUMO-specific protease SENP2) (SUMO-1/Smt3-specif ...	0.93	-	nuc	0	Nucleus. Isoform 1: Nucleus; nuclear envelope; nuclear pore complex; nucleoplasmic side (By similari ...	nuclear pore [ISS]			588
Q22258 UniProt NPD GO	ATR_CAEEL	Serine/threonine-protein kinase ATR (EC 2.7.11.1) (Ataxia telangiectasia and Rad3-related protein ho ...	0.93	-	nuc	0	Nucleus. Recruited to stalled replication forks by rpa-1-coated single-stranded DNA. Recruited to pr ...				2531
Q01919 UniProt NPD GO	KIN4_YEAST	Serine/threonine-protein kinase KIN4 (EC 2.7.11.1)	0.93	-	nuc	0		bud neck [IDA] cell cortex [IDA] spindle pole body [IDA]			800
P20794 UniProt NPD GO	MAK_HUMAN	Serine/threonine-protein kinase MAK (EC 2.7.11.22) (Male germ cell-associated kinase)	0.93	-	nuc	0			154235		623
P51957 UniProt NPD GO	NEK4_HUMAN	Serine/threonine-protein kinase Nek4 (EC 2.7.11.1) (NimA-related protein kinase 4) (Serine/threonine ...	0.93	-	nuc	0	Nucleus (Probable)		601959		841
Q5F2E8 UniProt NPD GO	TAOK1_MOUSE	Serine/threonine-protein kinase TAO1 (EC 2.7.11.1) (Thousand and one amino acid protein 1)	0.93	-	nuc	0	Cytoplasm (By similarity)				1001
O88664 UniProt NPD GO	TAOK1_RAT	Serine/threonine-protein kinase TAO1 (EC 2.7.11.1) (Thousand and one amino acid protein 1)	0.93	-	nuc	0	Cytoplasm (By similarity)				1001
Q7L7X3 UniProt NPD GO	TAOK1_HUMAN	Serine/threonine-protein kinase TAO1 (EC 2.7.11.1) (Thousand and one amino acid protein 1) (STE20-li ...	0.93	-	nuc	0	Cytoplasm				1001
Q7ZYJ0 UniProt NPD GO	TAO1B_XENLA	Serine/threonine-protein kinase TAO1-B (EC 2.7.11.1) (Thousand and one amino acid protein 1-B)	0.93	-	nuc	0	Cytoplasm (By similarity)				1001
Q9JIH7 UniProt NPD GO	WNK1_RAT	Serine/threonine-protein kinase WNK1 (EC 2.7.11.1) (Protein kinase with no lysine 1) (Protein kinase ...	0.93	-	nuc	0	Cytoplasm	cytoplasm [IEP]		1T4H	2126
P0C1B1 UniProt NPD GO	CBK1_EMENI	Serine/threonine-protein kinase cbk1 (EC 2.7.11.1)	0.93	-	nuc	0					884
Q7RZD3 UniProt NPD GO	STE20_NEUCR	Serine/threonine-protein kinase ste-20 (EC 2.7.11.1)	0.93	-	mit	0	Cytoplasm (By similarity). Nucleus (By similarity)				954
Q7RZT9 UniProt NPD GO	ATM_NEUCR	Serine/threonine-protein kinase tel-1 (EC 2.7.11.1) (DNA-damage checkpoint kinase tel-1) (Telomere l ...	0.93	+	nuc	0	Nucleus. Localizes to nuclear DNA repair foci with other DNA repair proteins in response to DNA doub ...				2953
P33329 UniProt NPD GO	PPZ2_YEAST	Serine/threonine-protein phosphatase PP-Z2 (EC 3.1.3.16)	0.93	-	nuc	0					709
Q80UF4 UniProt NPD GO	SDCG8_MOUSE	Serologically defined colon cancer antigen 8 (Centrosomal colon cancer autoantigen protein) (mCCCAP) ...	0.93	+	nuc	0	Centrosome	centrosome [IDA]			717
Q864Q9 UniProt NPD GO	SRY_BALPH	Sex-determining region Y protein (Testis-determining factor)	0.93	+	nuc	0	Nucleus				204
Q864Q8 UniProt NPD GO	SRY_MEGNO	Sex-determining region Y protein (Testis-determining factor)	0.93	+	nuc	0	Nucleus				204
P34708 UniProt NPD GO	TRA1_CAEEL	Sex-determining transformer protein 1 (Hermaphrodization of XO animals protein 2)	0.93	+	nuc	0	Cytoplasm. Nucleus	cytoplasm [IDA] nucleus [IDA]			1110
Q9NIW4 UniProt NPD GO	TRA2_CAERE	Sex-determining transformer protein 2 precursor (Cr-tra-2)	0.93	+	end	10 *	Membrane; multi-pass membrane protein (Potential)	integral to membrane [IDA]			1485
Q9P7A0 UniProt NPD GO	SGO1_SCHPO	Shugoshin-1	0.93	-	nuc	0	Nucleus. Localizes to the centromere. Bub1 is required for centromeric localization. At the onset of ...	kinetochore [TAS]			319
P40349 UniProt NPD GO	URB1_USTMA	Siderophore biosynthesis regulatory protein URBS1	0.93	-	nuc	0	Nucleus (Probable)				950
Q60665 UniProt NPD GO	SKIL_MOUSE	Ski-like protein (Ski-related protein) (Ski-related oncogene)	0.93	-	nuc	0					675
Q8TAD8 UniProt NPD GO	SNIP1_HUMAN	Smad nuclear-interacting protein 1	0.93	-	nuc	0	Nucleus		608241		396
P58391 UniProt NPD GO	KCNN3_MOUSE	Small conductance calcium-activated potassium channel protein 3 (SK3)	0.93	+	nuc	5	Membrane; multi-pass membrane protein				731
P70605 UniProt NPD GO	KCNN3_RAT	Small conductance calcium-activated potassium channel protein 3 (SK3)	0.93	+	nuc	5	Membrane; multi-pass membrane protein	plasma membrane [IMP]			732
Q9WV80 UniProt NPD GO	SNX1_MOUSE	Sorting nexin-1	0.93	-	nuc	0		endosome [IDA]			522
Q99N27 UniProt NPD GO	SNX1_RAT	Sorting nexin-1	0.93	-	nuc	0		early endosome [IDA]			522
P02549 UniProt NPD GO	SPTA1_HUMAN	Spectrin alpha chain, erythrocyte (Erythroid alpha-spectrin)	0.93	-	nuc	0		spectrin [TAS]	130600	1OWA	2418
P11277 UniProt NPD GO	SPTB1_HUMAN	Spectrin beta chain, erythrocyte (Beta-I spectrin)	0.93	-	cyt	0		spectrin [TAS]	130600	1S35	2136
Q64213 UniProt NPD GO	SF01_MOUSE	Splicing factor 1 (Zinc finger protein 162) (Transcription factor ZFM1) (mZFM) (Zinc finger gene in ...	0.93	+	nuc	0	Nucleus				652
Q08170 UniProt NPD GO	SFRS4_HUMAN	Splicing factor, arginine/serine-rich 4 (Pre-mRNA-splicing factor SRP75) (SRP001LB)	0.93	+	nuc	0	Nucleus; nucleoplasm; nuclear speckle	nucleus [TAS]	601940		494
P43620 UniProt NPD GO	RMD8_YEAST	Sporulation protein RMD8	0.93	-	nuc	1		cytoplasm [IDA]			662
Q5KK25 UniProt NPD GO	ATG26_CRYNE	Sterol 3-beta-glucosyltransferase (EC 2.4.1.173) (Autophagy-related protein 26)	0.93	+	nuc	0	Cytoplasm (By similarity). Membrane; peripheral membrane protein (By similarity)				1585

You are viewing entries 3001 to 3050 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.