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
P34268 UniProt NPD GO	FLII_CAEEL	Protein flightless-1 homolog	0.79	-	nuc	0					1257
Q9JJ28 UniProt NPD GO	FLII_MOUSE	Protein flightless-1 homolog	0.79	+	cyt	0	Nucleus. Cytoplasm. Centrosome. Colocalizes to actin-rich structures in blastocysts and, together wi ...				1271
Q9ZRT1 UniProt NPD GO	GR1_ARATH	Protein gamma response 1 (Protein gamma response I)	0.79	-	nuc	0	Nucleus (Probable)				589
Q7KRY7 UniProt NPD GO	LAP4_DROME	Protein lap4 (Protein scribble) (Protein smell-impaired)	0.79	-	nuc	0	Cytoplasm. Cell membrane; peripheral membrane protein. Localized to epithelial septate junction at t ...	apicolateral plasma membrane [IDA] basolateral plasma membrane [TAS] cytoplasm [NAS] extracellular region [IDA] lateral plasma membrane [IDA] septate junction [IDA] subapical complex [TAS]			1851
P54936 UniProt NPD GO	LIN2_CAEEL	Protein lin-2 (Abnormal cell lineage protein 2)	0.79	-	nuc	0					961
P87320 UniProt NPD GO	MSP1_SCHPO	Protein msp1, mitochondrial precursor	0.79	-	mit	0	Mitochondrion	mitochondrial intermembrane space [IDA]			903
Q9GRW7 UniProt NPD GO	NONA_DROVI	Protein no-on-transient A	0.79	+	nuc	0					697
Q9ERT9 UniProt NPD GO	IPP1_MOUSE	Protein phosphatase inhibitor 1 (IPP-1) (I-1)	0.79	-	nuc	0					171
Q623U2 UniProt NPD GO	PTDSR_CAEBR	Protein psr-1	0.79	+	nuc	0	Nucleus (By similarity)	nucleus [ISS]			397
Q09743 UniProt NPD GO	STE16_SCHPO	Protein ste16	0.79	-	nuc	0	Membrane; multi-pass membrane protein (Potential)				1309
Q08875 UniProt NPD GO	SUHW_DROAN	Protein suppressor of hairy wing	0.79	+	nuc	0	Nucleus				886
Q09835 UniProt NPD GO	GOS1_SCHPO	Protein transport protein gos1 (Golgi SNARE protein 1) (Golgi SNAP receptor complex member 1)	0.79	-	nuc	1	Golgi apparatus; Golgi membrane; single-pass type IV membrane protein (By similarity)				182
Q05063 UniProt NPD GO	LYOX_CHICK	Protein-lysine 6-oxidase precursor (EC 1.4.3.13) (Lysyl oxidase)	0.79	+	nuc	0	Secreted protein; extracellular space				420
P10911 UniProt NPD GO	MCF2_HUMAN	Proto-oncogene DBL (Proto-oncogene MCF-2) [Contains: MCF2-transforming protein; DBL-transforming pro ...	0.79	-	mit	0	Cytoplasm	cytoskeleton [TAS] cytosol [TAS] membrane fraction [TAS]	311030		925
Q6P158 UniProt NPD GO	DHX57_HUMAN	Putative ATP-dependent RNA helicase DHX57 (EC 3.6.1.-) (DEAH box protein 57)	0.79	-	nuc	0					1386
Q6P5D3 UniProt NPD GO	DHX57_MOUSE	Putative ATP-dependent RNA helicase DHX57 (EC 3.6.1.-) (DEAH box protein 57)	0.79	-	nuc	0					1388
O45291 UniProt NPD GO	TBX33_CAEEL	Putative T-box protein 33	0.79	-	nuc	0	Nucleus (Potential)				507
O50052 UniProt NPD GO	DRL25_ARATH	Putative disease resistance protein At4g19050	0.79	-	nuc	0					1181
Q5SQS8 UniProt NPD GO	CJ120_HUMAN	Putative uncharacterized protein C10orf120	0.79	-	nuc	0					335
Q07967 UniProt NPD GO	YL030_YEAST	Putative uncharacterized protein YLR030W	0.79	-	nuc	0					263
Q95QY7 UniProt NPD GO	YKKA_CAEEL	Putative zinc finger protein C02F5.12	0.79	-	nuc	0	Nucleus (Potential)				380
Q9D0P5 UniProt NPD GO	PYGO1_MOUSE	Pygopus homolog 1	0.79	-	nuc	0	Nucleus (Probable)				417
Q67YI6 UniProt NPD GO	ATL3G_ARATH	RING-H2 finger protein ATL3G	0.79	+	nuc	1 *					411
Q03254 UniProt NPD GO	FCP1_YEAST	RNA polymerase II subunit A C-terminal domain phosphatase (EC 3.1.3.16) (CTD phosphatase FCP1)	0.79	-	nuc	0	Nucleus	nucleus [IPI]			732
Q8NG57 UniProt NPD GO	ELOA3_HUMAN	RNA polymerase II transcription factor SIII subunit A3 (Elongin-A3) (EloA3) (Transcription elongatio ...	0.79	-	nuc	0	Nucleus				546
Q05672 UniProt NPD GO	RBS1_YEAST	RNA-binding suppressor of PAS kinase protein 1	0.79	-	nuc	0	Cytoplasm	cytoplasm [IDA]			457
Q80U22 UniProt NPD GO	RUSC2_MOUSE	RUN and SH3 domain-containing protein 2	0.79	-	nuc	0					1514
Q642R9 UniProt NPD GO	RB3GP_XENLA	Rab3 GTPase-activating protein catalytic subunit	0.79	-	nuc	0	Cytoplasm (Probable)				978
P26044 UniProt NPD GO	RADI_PIG	Radixin (Moesin-B)	0.79	-	nuc	0	Highly concentrated in the undercoat of the cell-to-cell adherens junction and the cleavage furrow i ...				583
Q15283 UniProt NPD GO	RASA2_HUMAN	Ras GTPase-activating protein 2 (GAP1m)	0.79	-	nuc	0	Cytoplasm. Cytoplasm; perinuclear region		601589		849
O43353 UniProt NPD GO	RIPK2_HUMAN	Receptor-interacting serine/threonine-protein kinase 2 (EC 2.7.11.1) (RIP-like-interacting CLARP kin ...	0.79	-	nuc	0	Cytoplasm (Probable)		603455		540
P16664 UniProt NPD GO	RGP1_YEAST	Reduced growth phenotype protein (Protein RGP1)	0.79	-	nuc	0		Golgi apparatus [IDA] Golgi membrane [IPI] guanyl-nucleotide exchange factor complex [IDA]			663
Q9Z2H2 UniProt NPD GO	RGS6_MOUSE	Regulator of G-protein signaling 6 (RGS6)	0.79	-	nuc	0	Cytoplasm (By similarity). Membrane; peripheral membrane protein (By similarity)				472
O42184 UniProt NPD GO	REST_CHICK	Restin (Cytoplasmic linker protein 170) (CLIP-170)	0.79	-	nuc	0	Cytoplasm (By similarity). Associated with the cytoskeleton (By similarity)				1433
Q9W5Z3 UniProt NPD GO	RARA_FUGRU	Retinoic acid receptor alpha (RAR-alpha)	0.79	+	nuc	0	Nucleus				447
P20828 UniProt NPD GO	GAG2_DROME	Retrovirus-related Gag polyprotein from transposon 297	0.79	-	nuc	0					414
Q12774 UniProt NPD GO	ARHG5_HUMAN	Rho guanine nucleotide exchange factor 5 (Guanine nucleotide regulatory protein TIM) (Oncogene TIM) ...	0.79	-	nuc	0			600888		519
P11459 UniProt NPD GO	RHOA_PLAFA	Rhoptry antigen protein (Fragment)	0.79	+	nuc	0					134
Q02555 UniProt NPD GO	RNT1_YEAST	Ribonuclease III (EC 3.1.26.3) (RNase III)	0.79	-	nuc	0		nucleolus [IDA] nucleoplasm [IDA]		1T4O	471
Q9CW46 UniProt NPD GO	RAVR1_MOUSE	Ribonucleoprotein PTB-binding 1 (Protein raver-1)	0.79	-	nuc	0	Nucleus. Cytoplasm. Nuclear, in perinucleolar structures. Shuttles between nucleus and cytoplasm. Cy ...			1WI6	748
P40693 UniProt NPD GO	RLP7_YEAST	Ribosome biogenesis protein RLP7 (Ribosomal protein L7-like)	0.79	+	nuc	0	Nucleus; nucleolus	nucleolus [IDA]			322
P13831 UniProt NPD GO	RESA_PLAFN	Ring-infected erythrocyte surface antigen (Fragment)	0.79	+	nuc	0	Cell membrane; cytoplasmic side. Probably located on the cytoplasmic face of the membrane where it a ...				760
Q9HCK4 UniProt NPD GO	ROBO2_HUMAN	Roundabout homolog 2 precursor	0.79	-	mit	1	Membrane; single-pass type I membrane protein (Potential)	cell surface [IDA]	602431	1UJT	1378
Q15413 UniProt NPD GO	RYR3_HUMAN	Ryanodine receptor 3 (Brain-type ryanodine receptor) (RyR3) (RYR-3) (Brain ryanodine receptor-calciu ...	0.79	+	end	6	Membrane; multi-pass membrane protein (Probable)		180903		4870
Q9NSI8 UniProt NPD GO	SAMN1_HUMAN	SAM domain-containing protein SAMSN-1 (SAM domain, SH3 domain and nuclear localization signals prote ...	0.79	-	nuc	0			607978		373
Q9Y6Y8 UniProt NPD GO	S23IP_HUMAN	SEC23-interacting protein (p125)	0.79	-	nuc	0	Endoplasmic reticulum-Golgi intermediate compartment. Golgi apparatus	cytoplasm [TAS] ER-Golgi intermediate compartment [TAS]			1000
Q6PD21 UniProt NPD GO	SHB_MOUSE	SH2 domain-containing adapter protein B	0.79	-	nuc	0	Cytoplasm. Associates with membrane lipid rafts upon TCR stimulation (By similarity)				503
Q96B97 UniProt NPD GO	SH3K1_HUMAN	SH3-domain kinase-binding protein 1 (Cbl-interacting protein of 85 kDa) (Human Src-family kinase-bin ...	0.79	-	nuc	0	Membrane; peripheral membrane protein. Nucleus		300374	2BZ8	665
Q12766 UniProt NPD GO	SMF_HUMAN	SMF protein (Fragment)	0.79	-	nuc	0	Nucleus (Potential)				1435
Q4I650 UniProt NPD GO	SWC5_GIBZE	SWR1-complex protein 5	0.79	+	nuc	0	Nucleus (By similarity)				327

You are viewing entries 9551 to 9600 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.