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
O17931 UniProt NPD GO	NH197_CAEEL	Nuclear hormone receptor family member nhr-197	0.44	-	mit	0	Nucleus (Potential)				340
O17934 UniProt NPD GO	NH199_CAEEL	Nuclear hormone receptor family member nhr-199	0.44	-	nuc	0	Nucleus (Potential)				405
Q7ZU29 UniProt NPD GO	NUP93_BRARE	Nuclear pore complex protein Nup93 (Nucleoporin Nup93) (93 kDa nucleoporin) (Dead eye protein)	0.44	-	cyt	0	Nucleus; nuclear envelope; nuclear pore complex (By similarity). Localizes at the nuclear basket and ...				820
Q9WU00 UniProt NPD GO	NRF1_MOUSE	Nuclear respiratory factor 1 (NRF-1) (Alpha palindromic-binding protein) (Alpha-pal)	0.44	-	cyt	0	Nucleus	transcription factor complex [TAS]			503
Q9SMP0 UniProt NPD GO	NFYC1_ARATH	Nuclear transcription factor Y subunit C-1 (AtNF-YC-1) (Transcriptional activator HAP5A)	0.44	+	cyt	0	Nucleus (By similarity)				234
P25207 UniProt NPD GO	NFYB_CHICK	Nuclear transcription factor Y subunit beta (Nuclear transcription factor Y subunit B) (NF-YB) (CAAT ...	0.44	-	nuc	0	Nucleus				205
P25208 UniProt NPD GO	NFYB_HUMAN	Nuclear transcription factor Y subunit beta (Nuclear transcription factor Y subunit B) (NF-YB) (CAAT ...	0.44	-	nuc	0	Nucleus	CCAAT-binding factor complex [IDA] nucleus [IEP]	189904	1N1J	207
P14907 UniProt NPD GO	NSP1_YEAST	Nucleoporin NSP1 (Nuclear pore protein NSP1) (Nucleoskeletal-like protein) (p110)	0.44	-	mit	0	Nucleus; nuclear envelope; nuclear pore complex; cytoplasmic side; nucleoplasmic side. Symmetric dis ...	nuclear pore [IDA]		1O6O	823
O15504 UniProt NPD GO	NUPL2_HUMAN	Nucleoporin-like 2 (NLP-1) (hCG1) (NUP42 homolog)	0.44	-	nuc	0	Nucleus; nuclear envelope; nuclear pore complex; cytoplasmic side. Excluded from the nucleolus	nucleus [TAS]			423
Q42712 UniProt NPD GO	FATA_CORSA	Oleoyl-acyl carrier protein thioesterase, chloroplast precursor (EC 3.1.2.14) (18:0-acyl-carrier pro ...	0.44	-	mit	0	Plastid; chloroplast				369
P18749 UniProt NPD GO	ZO6_XENLA	Oocyte zinc finger protein XLCOF6 (Fragment)	0.44	-	nuc	0	Nucleus (Potential)				453
P58874 UniProt NPD GO	OPT_BOVIN	Opticin precursor (Oculoglycan)	0.44	-	exc	0	Secreted protein; extracellular space; extracellular matrix (By similarity)				321
P11725 UniProt NPD GO	OTC_MOUSE	Ornithine carbamoyltransferase, mitochondrial precursor (EC 2.1.3.3) (OTCase) (Ornithine transcarbam ...	0.44	-	mit	0	Mitochondrion; mitochondrial matrix	mitochondrial inner membrane [IDA] mitochondrion [IDA]			354
O35627 UniProt NPD GO	NR1I3_MOUSE	Orphan nuclear receptor NR1I3 (Constitutive androstane receptor) (CAR)	0.44	-	cyt	0	Nucleus (By similarity)	cytosol [IDA] nucleus [IDA]		1XNX	358
Q14994 UniProt NPD GO	NR1I3_HUMAN	Orphan nuclear receptor NR1I3 (Constitutive androstane receptor) (Constitutive activator of retinoid ...	0.44	-	cyt	0	Nucleus (By similarity)		603881	1XVP	352
Q9Z101 UniProt NPD GO	PAR6A_MOUSE	Partitioning defective 6 homolog alpha (PAR-6 alpha) (PAR-6A) (PAR-6)	0.44	-	nuc	0	Cytoplasm (By similarity). Cell membrane (By similarity). Cell membrane; cell-cell junction; tight j ...	cell cortex [IDA] cytoplasm [IDA] nucleus [IDA] tight junction [IDA]			346
Q2M591 UniProt NPD GO	KB2_MESMA	Peptide BmKb2 precursor	0.44	-	mit	0	Secreted protein (By similarity)				74
Q7RXA6 UniProt NPD GO	PPIL2_NEUCR	Peptidyl-prolyl cis-trans isomerase-like 2 (EC 5.2.1.8) (PPIase) (Rotamase) (Cyclophilin-60) (Cyclop ...	0.44	-	cyt	0	Nucleus (By similarity)				597
Q75A74 UniProt NPD GO	CWC27_ASHGO	Peptidyl-prolyl isomerase CWC27 (EC 5.2.1.8)	0.44	-	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity)				303
Q7DMA9 UniProt NPD GO	PAS1_ARATH	Peptidyl-prolyl isomerase PASTICCINO1 (EC 5.2.1.8) (Peptidyl-prolyl cis-trans isomerase) (PPIase) (R ...	0.44	+	cyt	1					635
Q9C1X1 UniProt NPD GO	PWP2_SCHPO	Periodic tryptophan protein 2 homolog	0.44	-	cyt	0					854
P37231 UniProt NPD GO	PPARG_HUMAN	Peroxisome proliferator-activated receptor gamma (PPAR-gamma)	0.44	+	cyt	0	Nucleus		601487	4PRG	505
O18924 UniProt NPD GO	PPARG_MACMU	Peroxisome proliferator-activated receptor gamma (PPAR-gamma)	0.44	+	cyt	0	Nucleus				505
P07219 UniProt NPD GO	PHSA_PHAVU	Phaseolin, alpha-type precursor	0.44	-	end	0	Protein body. Vacuole. Cotyledonary membrane-bound vacuolar protein bodies				436
P37215 UniProt NPD GO	AROF_LYCES	Phospho-2-dehydro-3-deoxyheptonate aldolase 1, chloroplast precursor (EC 2.5.1.54) (Phospho-2-keto-3 ...	0.44	-	mit	0	Plastid; chloroplast				511
P58766 UniProt NPD GO	PLDZ1_ARATH	Phospholipase D zeta (EC 3.1.4.4) (AtPLDzeta) (PLD zeta)	0.44	-	nuc	0	Cytoplasm (By similarity). Membrane; peripheral membrane protein (By similarity)				820
P14272 UniProt NPD GO	KLKB1_RAT	Plasma kallikrein precursor (EC 3.4.21.34) (Plasma prekallikrein) (Kininogenin) (Fletcher factor) [C ...	0.44	-	exc	1 *					638
Q8NC51 UniProt NPD GO	PAIRB_HUMAN	Plasminogen activator inhibitor 1 RNA-binding protein (PAI1 RNA-binding protein 1) (PAI-RBP1) (SERPI ...	0.44	+	nuc	0	Cytoplasm. Nucleus. Cytoplasm; perinuclear region. Also found in perinuclear regions		607378		408
Q6Q308 UniProt NPD GO	PLEK_CANFA	Pleckstrin	0.44	-	cyt	0					351
Q4KM33 UniProt NPD GO	PLEK_RAT	Pleckstrin	0.44	-	cyt	0					350
Q9QY40 UniProt NPD GO	PLXB3_MOUSE	Plexin-B3 precursor (Plexin-6)	0.44	-	end	2	Membrane; single-pass type I membrane protein (By similarity)				1892
Q9WTQ2 UniProt NPD GO	PODXL_RAT	Podocalyxin precursor	0.44	-	exc	1	Membrane; single-pass type I membrane protein (Potential)	integral to membrane [NAS]			485
O08832 UniProt NPD GO	GALT4_MOUSE	Polypeptide N-acetylgalactosaminyltransferase 4 (EC 2.4.1.41) (Protein-UDP acetylgalactosaminyltrans ...	0.44	-	exc	1 *	Golgi apparatus; Golgi membrane; single-pass type II membrane protein (By similarity)				578
Q6WV17 UniProt NPD GO	GALT5_DROME	Polypeptide N-acetylgalactosaminyltransferase 5 (EC 2.4.1.41) (Protein-UDP acetylgalactosaminyltrans ...	0.44	-	gol	1 *	Golgi apparatus; Golgi membrane; single-pass type II membrane protein (By similarity)	Golgi stack [NAS]			630
P43309 UniProt NPD GO	PPO_MALDO	Polyphenol oxidase, chloroplast precursor (EC 1.10.3.1) (PPO) (Catechol oxidase)	0.44	-	mit	0	Plastid; chloroplast; chloroplast thylakoid lumen				593
P92960 UniProt NPD GO	KAT3_ARATH	Potassium channel KAT3 (AKT4) (AtKC1) (Potassium channel TKC)	0.44	-	mit	5	Membrane; multi-pass membrane protein				662
P22459 UniProt NPD GO	KCNA4_HUMAN	Potassium voltage-gated channel subfamily A member 4 (Voltage-gated potassium channel subunit Kv1.4) ...	0.44	-	end	4	Membrane; multi-pass membrane protein	voltage-gated potassium channel complex [TAS]	176266		653
Q6FVL2 UniProt NPD GO	CWC15_CANGA	Pre-mRNA-splicing factor CWC15	0.44	+	nuc	0	Nucleus (Probable)				143
Q751G9 UniProt NPD GO	CWC21_ASHGO	Pre-mRNA-splicing factor CWC21	0.44	-	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity)				125
Q5KH46 UniProt NPD GO	SYF1_CRYNE	Pre-mRNA-splicing factor SYF1	0.44	-	nuc	0	Nucleus (By similarity)				1031
O94539 UniProt NPD GO	PAM17_SCHPO	Presequence translocated-associated motor subunit pam17, mitochondrial precursor	0.44	+	mit	2	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein (By similarity)				197
Q14147 UniProt NPD GO	DHX34_HUMAN	Probable ATP-dependent RNA helicase DHX34 (EC 3.6.1.-) (DEAH box protein 34)	0.44	-	end	0					576
Q9DD18 UniProt NPD GO	DTD1_MOUSE	Probable D-tyrosyl-tRNA(Tyr) deacylase (EC 3.1.-.-)	0.44	-	nuc	0	Cytoplasm (Potential)				201
Q6NV75 UniProt NPD GO	GP153_HUMAN	Probable G-protein coupled receptor 153 (G-protein coupled receptor PGR1)	0.44	-	end	7 *	Membrane; multi-pass membrane protein				609
Q9LQ54 UniProt NPD GO	DRL12_ARATH	Probable disease resistance protein At1g59620 (CW9)	0.44	-	cyt	0					695
O61820 UniProt NPD GO	IF36_CAEEL	Probable eukaryotic translation initiation factor 3 subunit 6 (eIF-3 p48) (eIF3e)	0.44	-	cyt	0					432
P78588 UniProt NPD GO	FREL_CANAL	Probable ferric reductase transmembrane component (EC 1.16.1.7) (Ferric-chelate reductase)	0.44	-	end	5	Membrane; multi-pass membrane protein (Potential)				669
Q6CNJ1 UniProt NPD GO	SPC24_KLULA	Probable kinetochore protein SPC24	0.44	-	nuc	0	Nucleus (By similarity). Associated with kinetochores (By similarity)				189
Q10234 UniProt NPD GO	RT05_SCHPO	Probable mitochondrial 40S ribosomal protein S5	0.44	-	mit	0	Mitochondrion (Potential)				387
Q9LJ42 UniProt NPD GO	PEL10_ARATH	Probable pectate lyase 10 precursor (EC 4.2.2.2)	0.44	-	mit	0					440

You are viewing entries 29151 to 29200 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.