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
P43564 UniProt NPD GO	YFD4_YEAST	Uncharacterized protein YFL034W	0.84	+	nuc	4	Membrane; multi-pass membrane protein (Potential)				1073
P53253 UniProt NPD GO	YG2K_YEAST	Uncharacterized protein YGR089W	0.84	-	nuc	3 *	Membrane; multi-pass membrane protein (Potential)	membrane fraction [IDA]			936
Q03694 UniProt NPD GO	YM57_YEAST	Uncharacterized protein YMR204C	0.84	-	nuc	0		extrinsic to intraperoxisomal membrane [IDA] peroxisome [IDA]			420
O13783 UniProt NPD GO	BRO1_SCHPO	Vacuolar protein-sorting protein bro1 (BRO domain-containing protein 1)	0.84	-	nuc	0	Cytoplasm (By similarity). Endosome (By similarity)				775
Q90243 UniProt NPD GO	VIT_ACITR	Vitellogenin precursor (VTG) [Contains: Lipovitellin I (LVI); Phosvitin (PV); Lipovitellin II (LVII) ...	0.84	-	nuc	0					1677
O00555 UniProt NPD GO	CAC1A_HUMAN	Voltage-dependent P/Q-type calcium channel subunit alpha-1A (Voltage-gated calcium channel subunit a ...	0.84	+	end	17	Membrane; multi-pass membrane protein	integral to membrane [ISS]	601011		2505
P27884 UniProt NPD GO	CAC1A_RABIT	Voltage-dependent P/Q-type calcium channel subunit alpha-1A (Voltage-gated calcium channel subunit a ...	0.84	+	end	19 *	Membrane; multi-pass membrane protein	integral to membrane [ISS]			2424
Q6VNB8 UniProt NPD GO	WDFY3_MOUSE	WD repeat and FYVE domain-containing protein 3 (Beach domain, WD repeat and FYVE domain-containing p ...	0.84	-	mit	0	Membrane; peripheral membrane protein; cytoplasmic side. Co-localizes with autophagic structures in ...	cytoplasm [IDA]			3508
Q9Z0H1 UniProt NPD GO	WDR46_MOUSE	WD repeat protein 46 (WD repeat protein BING4)	0.84	+	nuc	0					622
Q8BH43 UniProt NPD GO	WASF2_MOUSE	Wiskott-Aldrich syndrome protein family member 2 (WASP-family protein member 2) (Protein WAVE-2)	0.84	+	nuc	0	Cytoplasm (By similarity)	early endosome [IDA] ruffle [IDA]			497
Q3TXX3 UniProt NPD GO	ZFY27_MOUSE	Zinc finger FYVE domain-containing protein 27	0.84	-	mit	3	Membrane; multi-pass membrane protein (Potential)				415
Q14119 UniProt NPD GO	ZN161_HUMAN	Zinc finger protein 161 (Putative transcription factor DB1)	0.84	+	nuc	0	Nucleus		606747		516
P98182 UniProt NPD GO	ZN200_HUMAN	Zinc finger protein 200	0.84	-	nuc	0	Nucleus (Probable)	nucleus [NAS]	603231		394
Q9UL58 UniProt NPD GO	ZN215_HUMAN	Zinc finger protein 215 (BWSCR2-associated zinc-finger protein 2) (BAZ 2)	0.84	-	nuc	0	Nucleus (Probable)	nucleus [NAS]	605016		517
P17028 UniProt NPD GO	ZNF24_HUMAN	Zinc finger protein 24 (Zinc finger protein 191) (Zinc finger protein KOX17) (Retinoic acid suppress ...	0.84	-	nuc	0	Nucleus (Potential)	nucleus [IC]	194534	1X6E	368
Q96GC6 UniProt NPD GO	ZN274_HUMAN	Zinc finger protein 274 (Zinc finger protein HFB101) (Zinc finger protein zfp2) (Zf2)	0.84	+	nuc	0	Nucleus; nucleolus	nucleolus [TAS]	605467		653
Q9Y6Q3 UniProt NPD GO	ZFP37_HUMAN	Zinc finger protein 37 homolog (Zfp-37)	0.84	-	nuc	0	Nucleus (Probable)	nucleus [NAS]	602951		597
Q8TAU3 UniProt NPD GO	ZN417_HUMAN	Zinc finger protein 417	0.84	-	nuc	0	Nucleus (Probable)				575
Q9UJL9 UniProt NPD GO	ZN643_HUMAN	Zinc finger protein 643	0.84	-	nuc	0	Nucleus (Potential)				432
P17098 UniProt NPD GO	ZNF8_HUMAN	Zinc finger protein 8 (Zinc finger protein HF.18)	0.84	-	nuc	0	Nucleus (Probable)	nucleus [NAS]	194532		575
Q61967 UniProt NPD GO	ZFP90_MOUSE	Zinc finger protein 90 (Zfp-90) (Zinc finger protein NK10)	0.84	-	nuc	0	Nucleus				636
O08900 UniProt NPD GO	AIOL_MOUSE	Zinc finger protein Aiolos	0.84	-	nuc	0	Nucleus (Probable)				507
Q6FUZ2 UniProt NPD GO	CET1_CANGA	mRNA capping enzyme subunit beta (EC 3.1.3.33) (Polynucleotide 5'-triphosphatase) (mRNA 5'-triphosph ...	0.84	-	nuc	0	Nucleus (By similarity)				602
P82914 UniProt NPD GO	RT15_HUMAN	28S ribosomal protein S15, mitochondrial precursor (S15mt) (MRP-S15)	0.83	-	nuc	0	Mitochondrion	mitochondrial small ribosomal subunit [IDA]			257
Q9NEN6 UniProt NPD GO	RS6_CAEEL	40S ribosomal protein S6	0.83	-	nuc	0					246
Q90YR6 UniProt NPD GO	RS8_ICTPU	40S ribosomal protein S8	0.83	+	nuc	0					207
P70290 UniProt NPD GO	EM55_MOUSE	55 kDa erythrocyte membrane protein (p55) (Membrane protein, palmitoylated 1) (Palmitoylated protein ...	0.83	-	nuc	0	Membrane; peripheral membrane protein (By similarity)				466
P50888 UniProt NPD GO	RL24_HORVU	60S ribosomal protein L24	0.83	-	nuc	0	Cytoplasm				162
Q962T1 UniProt NPD GO	RL32_SPOFR	60S ribosomal protein L32	0.83	-	nuc	0					134
Q8WRF3 UniProt NPD GO	RL32_APIME	60S ribosomal protein L32 (Ribosomal protein 49)	0.83	-	nuc	0					134
O35598 UniProt NPD GO	ADA10_MOUSE	ADAM 10 precursor (EC 3.4.24.81) (A disintegrin and metalloproteinase domain 10) (Mammalian disinteg ...	0.83	-	exc	1	Membrane; single-pass type I membrane protein	cell surface [ISS] cytoplasm [IDA] Golgi apparatus [ISS] Golgi-associated vesicle [ISS] nucleus [IDA] plasma membrane [IDA]			749
Q01433 UniProt NPD GO	AMPD2_HUMAN	AMP deaminase 2 (EC 3.5.4.6) (AMP deaminase isoform L)	0.83	-	mit	0			102771		879
P19880 UniProt NPD GO	YAP1_YEAST	AP-1-like transcription factor YAP1 (Phenanthroline resistance protein PAR1) (Pleiotropic drug resis ...	0.83	-	nuc	0	Nucleus. Cytoplasm. Oxidized YAP1 is found predominantly in the nucleus, while reduced YAP1 is conti ...	cytoplasm [IDA] nucleus [IDA]		1SSE	650
Q9JME5 UniProt NPD GO	AP3B2_MOUSE	AP-3 complex subunit beta-2 (Adapter-related protein complex 3 beta-2 subunit) (Beta3B-adaptin) (Ada ...	0.83	-	nuc	0	Component of the coat surrounding the cytoplasmic face of coated vesicles located at the Golgi compl ...	Golgi trans face [TAS]			1082
Q755A1 UniProt NPD GO	AP3D_ASHGO	AP-3 complex subunit delta (Adapter-related protein complex 3 subunit delta) (Delta-adaptin 3) (AP-3 ...	0.83	+	nuc	0	Component of the coat surrounding the cytoplasmic face of coated vesicles located at the Golgi compl ...				899
Q6MG08 UniProt NPD GO	ABCF1_RAT	ATP-binding cassette sub-family F member 1 (ATP-binding cassette 50)	0.83	+	nuc	0					839
Q9BQ39 UniProt NPD GO	DDX50_HUMAN	ATP-dependent RNA helicase DDX50 (EC 3.6.1.-) (DEAD box protein 50) (Nucleolar protein Gu2) (Gu-beta ...	0.83	-	nuc	0	Nucleus; nucleolus				737
Q6BP45 UniProt NPD GO	ROK1_DEBHA	ATP-dependent RNA helicase ROK1 (EC 3.6.1.-)	0.83	+	nuc	0	Nucleus; nucleolus (By similarity)				550
Q09719 UniProt NPD GO	DBP10_SCHPO	ATP-dependent RNA helicase dbp10 (EC 3.6.1.-)	0.83	+	nuc	0	Nucleus; nucleolus (By similarity)				848
Q8CG07 UniProt NPD GO	WRIP1_RAT	ATPase WRNIP1 (Werner helicase-interacting protein 1)	0.83	+	nuc	0	Nucleus (By similarity). Colocalizes with WRN in granular structures in the nucleus (By similarity)	nucleus [ISS]			660
P54244 UniProt NPD GO	ACH3_CAEEL	Acetylcholine receptor subunit alpha-type deg-3 precursor	0.83	-	end	4 *	Membrane; multi-pass membrane protein				564
Q8K4G5 UniProt NPD GO	ABLM1_MOUSE	Actin-binding LIM protein 1 (Actin-binding LIM protein family member 1) (abLIM-1)	0.83	-	nuc	0	Cytoplasm. Cytoskeleton. In a striped pattern along the myofibril axis in cardiac myocytes. Associat ...	actin cytoskeleton [IDA]			861
Q6CV12 UniProt NPD GO	SPB1_KLULA	AdoMet-dependent rRNA methyltransferase SPB1 (EC 2.1.1.-) (2'-O-ribose RNA methyltransferase) (S-ade ...	0.83	-	nuc	0	Nucleus; nucleolus (By similarity)				833
Q66JG8 UniProt NPD GO	ALKB5_XENTR	Alkylated repair protein alkB homolog 5	0.83	+	nuc	0					358
P35405 UniProt NPD GO	ADA2C_DIDMA	Alpha-2C adrenergic receptor (Alpha-2C adrenoceptor) (Alpha-2C adrenoreceptor)	0.83	-	end	7 *	Membrane; multi-pass membrane protein				469
Q9UI47 UniProt NPD GO	CTN3_HUMAN	Alpha-3 catenin (Alpha T-catenin) (Cadherin-associated protein)	0.83	-	nuc	0	Localizes to intercalated disks of cardiomyocytes and in peritubular myoid cells of testis, and colo ...	fascia adherens [IDA]	607667		895
P20111 UniProt NPD GO	ACTN2_CHICK	Alpha-actinin-2 (Alpha actinin skeletal muscle isoform 2) (F-actin cross linking protein)	0.83	-	nuc	0					897
P40222 UniProt NPD GO	TXLNA_HUMAN	Alpha-taxilin	0.83	-	nuc	0		extracellular region [NAS]	608676		546
Q28738 UniProt NPD GO	SCNNG_RABIT	Amiloride-sensitive sodium channel gamma-subunit (Epithelial Na+ channel subunit gamma) (Gamma ENaC) ...	0.83	-	end	1	Cell membrane; apical cell membrane; multi-pass membrane protein (By similarity). Apical membrane of ...				653
P98084 UniProt NPD GO	APBA2_MOUSE	Amyloid beta A4 precursor protein-binding family A member 2 (Neuron-specific X11L protein) (Neuronal ...	0.83	-	nuc	0					750

You are viewing entries 7251 to 7300 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.