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
Q9U5Y0 UniProt NPD GO	U239_DROER	Protein anon-73B1	0.18	+	mit	1 *		integral to membrane [NAS]			87
Q9NVM4 UniProt NPD GO	ANM7_HUMAN	Protein arginine N-methyltransferase 7 (EC 2.1.1.-)	0.18	-	cyt	0		cytoplasm [TAS] nucleus [TAS]			692
Q24207 UniProt NPD GO	BOULE_DROME	Protein boule	0.18	-	nuc	0	Nucleus. Cytoplasm. Nuclear in primary spermatocytes until near the end of the meiotic prophase and ...				228
Q24522 UniProt NPD GO	BUN1_DROME	Protein bunched, class 1/class 3 isoforms (Protein shortsighted)	0.18	-	cyt	0	Cytoplasm. Nucleus	cytoplasm [IDA]			219
P27773 UniProt NPD GO	PDIA3_MOUSE	Protein disulfide-isomerase A3 precursor (EC 5.3.4.1) (Disulfide isomerase ER-60) (ERp60) (58 kDa mi ...	0.18	-	exc	0	Endoplasmic reticulum; endoplasmic reticulum lumen (By similarity)	endoplasmic reticulum [IDA]			504
P30101 UniProt NPD GO	PDIA3_HUMAN	Protein disulfide-isomerase A3 precursor (EC 5.3.4.1) (Disulfide isomerase ER-60) (ERp60) (58 kDa mi ...	0.18	-	mit	0	Endoplasmic reticulum; endoplasmic reticulum lumen (By similarity)	endoplasmic reticulum [TAS]	602046		505
P11598 UniProt NPD GO	PDIA3_RAT	Protein disulfide-isomerase A3 precursor (EC 5.3.4.1) (Disulfide isomerase ER-60) (ERp60) (58 kDa mi ...	0.18	-	exc	0	Endoplasmic reticulum; endoplasmic reticulum lumen				505
Q02936 UniProt NPD GO	HH_DROME	Protein hedgehog precursor [Contains: Protein hedgehog N-product (Hh-Np) (N-Hh); Protein hedgehog C- ...	0.18	-	mit	1 *	Nucleus. Nuclear up to embryonic stage 10 and then at stage 11 shifts to the cytoplasm. C-terminal p ...	cytoplasm [IEP] cytoplasmic membrane-bound vesicle [IDA] extracellular region [NAS] nucleus [IEP] plasma membrane [NAS]		1AT0	421
Q01777 UniProt NPD GO	HUNB_LOCMI	Protein hunchback (Fragment)	0.18	-	nuc	0	Nucleus (Probable)				56
P20444 UniProt NPD GO	KPCA_MOUSE	Protein kinase C alpha type (EC 2.7.11.13) (PKC-alpha) (PKC-A)	0.18	-	cyt	0		cytoplasm [IDA] mitochondrion [IDA] nucleus [IDA]			671
P05771 UniProt NPD GO	KPCB_HUMAN	Protein kinase C beta type (EC 2.7.11.13) (PKC-beta) (PKC-B)	0.18	-	cyt	0	Cytoplasm (By similarity). Membrane; peripheral membrane protein (By similarity)	cytoplasm [TAS] plasma membrane [TAS]	176970		670
P68404 UniProt NPD GO	KPCB_MOUSE	Protein kinase C beta type (EC 2.7.11.13) (PKC-beta) (PKC-B)	0.18	-	cyt	0	Cytoplasm (By similarity). Membrane; peripheral membrane protein (By similarity)	cytoplasm [IDA] nucleus [IDA]			672
P05129 UniProt NPD GO	KPCG_HUMAN	Protein kinase C gamma type (EC 2.7.11.13) (PKC-gamma)	0.18	-	cyt	0			605361		697
Q90XF2 UniProt NPD GO	KPCI_BRARE	Protein kinase C iota type (EC 2.7.11.13) (nPKC-iota) (Atypical protein kinase C-lambda/iota) (aPKC- ...	0.18	-	cyt	0		cytosol [ISS] nucleus [ISS] polarisome [ISS]			588
P38089 UniProt NPD GO	PP2C4_YEAST	Protein phosphatase 2C homolog 4 (EC 3.1.3.16) (PP2C-4)	0.18	-	cyt	0		cytoplasm [IDA]			393
Q9C3Y4 UniProt NPD GO	RHOA_EMENI	Protein rhoA (Rho1 protein homolog)	0.18	-	mit	0	Cell membrane; lipid-anchor; cytoplasmic side (Potential)				193
Q17320 UniProt NPD GO	WHITE_CERCA	Protein white	0.18	-	end	5	Membrane; multi-pass membrane protein				679
Q25533 UniProt NPD GO	WNTG_MANSE	Protein wingless (Fragment)	0.18	-	nuc	0	Secreted protein; extracellular space; extracellular matrix				141
Q5VTY9 UniProt NPD GO	HHAT_HUMAN	Protein-cysteine N-palmitoyltransferase HHAT (EC 2.3.1.-) (Hedgehog acyltransferase) (Skinny hedgeho ...	0.18	-	mit	8 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (By similarity)		605743		493
Q96PF1 UniProt NPD GO	TGM7_HUMAN	Protein-glutamine gamma-glutamyltransferase Z (EC 2.3.2.13) (TGase Z) (TGZ) (TG(Z)) (Transglutaminas ...	0.18	-	cyt	0			606776		710
P56615 UniProt NPD GO	IP21_CAPAN	Proteinase inhibitor PSI-1.1	0.18	-	nuc	0	Secreted protein				55
P00734 UniProt NPD GO	THRB_HUMAN	Prothrombin precursor (EC 3.4.21.5) (Coagulation factor II) [Contains: Activation peptide fragment 1 ...	0.18	-	vac	0	Secreted protein; extracellular space	extracellular region [NAS] extracellular space [TAS] soluble fraction [TAS]	176930	8KME	622
Q5DRD1 UniProt NPD GO	PCDB3_PANTR	Protocadherin beta 3 precursor (PCDH-beta3)	0.18	-	nuc	1	Membrane; single-pass type I membrane protein (By similarity)				796
Q9Y5E5 UniProt NPD GO	PCDB4_HUMAN	Protocadherin beta 4 precursor (PCDH-beta4)	0.18	-	end	1	Membrane; single-pass type I membrane protein (By similarity)	integral to plasma membrane [TAS]	606330		795
Q5DRB6 UniProt NPD GO	PCDG4_PANTR	Protocadherin gamma A4 precursor (PCDH-gamma-A4)	0.18	-	nuc	1	Membrane; single-pass type I membrane protein (By similarity)				931
Q94IG7 UniProt NPD GO	PPOCM_SPIOL	Protoporphyrinogen oxidase, chloroplast/mitochondrial precursor (EC 1.3.3.4) (Protox II) (SO-POX2)	0.18	-	cyt	0	Isoform L: Plastid; chloroplast; chloroplast inner membrane; peripheral membrane protein; stromal si ...	chloroplast inner membrane [IDA] mitochondrial inner membrane [IDA]			531
Q6CQC4 UniProt NPD GO	PUS5_KLULA	Pseudouridylate synthase PUS5 (EC 5.4.99.-) (Pseudouridine synthase 5) (Uracil hydrolyase PUS5)	0.18	-	mit	0	Mitochondrion (By similarity)				299
Q09865 UniProt NPD GO	RM06_SCHPO	Putative 60S ribosomal protein L6, mitochondrial precursor	0.18	-	mit	0	Mitochondrion (By similarity)				213
Q61B10 UniProt NPD GO	NOLA1_CAEBR	Putative H/ACA ribonucleoprotein complex subunit 1-like protein	0.18	+	cyt	0	Nucleus; nucleolus (By similarity)				246
Q09670 UniProt NPD GO	OYEA_SCHPO	Putative NADPH dehydrogenase C5H10.04 (EC 1.6.99.1) (Old yellow enzyme homolog)	0.18	-	cyt	0					382
P98179 UniProt NPD GO	RBM3_HUMAN	Putative RNA-binding protein 3 (RNA-binding motif protein 3) (RNPL)	0.18	-	cyt	0			300027		157
P49191 UniProt NPD GO	ELO3_CAEEL	Putative fatty acid elongation protein 3	0.18	-	end	6 *	Membrane; multi-pass membrane protein (Potential)				320
P84180 UniProt NPD GO	GR22B_DROME	Putative gustatory receptor 22b	0.18	-	end	7 *	Membrane; multi-pass membrane protein (Potential)				386
P58955 UniProt NPD GO	GR36A_DROME	Putative gustatory receptor 36a	0.18	-	end	7 *	Membrane; multi-pass membrane protein (Potential)	integral to membrane [NAS]			391
Q6FPI6 UniProt NPD GO	ATG15_CANGA	Putative lipase ATG15 (EC 3.1.1.3) (Autophagy-related protein 15)	0.18	-	mit	0	Endoplasmic reticulum; endoplasmic reticulum membrane; single-pass type II membrane protein (By simi ...				504
Q9T0E3 UniProt NPD GO	LCR17_ARATH	Putative low-molecular-weight cysteine-rich protein LCR17	0.18	-	nuc	1 *					96
P82748 UniProt NPD GO	LCR33_ARATH	Putative low-molecular-weight cysteine-rich protein LCR33 precursor	0.18	-	exc	1 *					78
P82789 UniProt NPD GO	LCR80_ARATH	Putative low-molecular-weight cysteine-rich protein LCR80 precursor	0.18	-	exc	0					122
Q04900 UniProt NPD GO	MUC24_HUMAN	Putative mucin core protein 24 precursor (Multi-glycosylated core protein 24) (MGC-24) (MUC-24) (CD1 ...	0.18	-	mit	0	Secreted protein	integral to plasma membrane [TAS] plasma membrane [IDA]	603356		189
Q8BQC3 UniProt NPD GO	PUNC_MOUSE	Putative neuronal cell adhesion molecule precursor	0.18	-	mit	1	Membrane; single-pass type I membrane protein				813
P0C025 UniProt NPD GO	NUD17_HUMAN	Putative nucleoside diphosphate-linked moiety X motif 17, mitochondrial precursor (EC 3.6.1.-) (Nudi ...	0.18	-	cyt	0	Mitochondrion (Potential)				295
Q8N2Z3 UniProt NPD GO	NUD9P_HUMAN	Putative nucleoside diphosphate-linked moiety X motif 9P1	0.18	-	cyt	0					120
P52913 UniProt NPD GO	NTP4_TOXGO	Putative nucleoside-triphosphatase (EC 3.6.1.15) (Nucleoside triphosphate phosphohydrolase) (NTPase) ...	0.18	-	nuc	0					592
P52716 UniProt NPD GO	YPP3_CAEEL	Putative serine carboxypeptidase F32A5.3 precursor (EC 3.4.16.-)	0.18	-	exc	0					574
Q80ZM7 UniProt NPD GO	T2AG_MOUSE	Putative transcription initiation factor IIA gamma chain (TFIIA P12 subunit) (TFIIA-12) (TFIIAS) (TF ...	0.18	-	mit	0	Nucleus (By similarity)				109
P93748 UniProt NPD GO	SINA1_ARATH	Putative ubiquitin ligase SINAT1 (EC 6.3.2.-) (Seven in absentia homolog 1)	0.18	-	nuc	0					305
O88794 UniProt NPD GO	PNPO_RAT	Pyridoxine-5'-phosphate oxidase (EC 1.4.3.5) (Pyridoxamine-phosphate oxidase)	0.18	-	cyt	0					261
Q29RK2 UniProt NPD GO	PYC_BOVIN	Pyruvate carboxylase, mitochondrial precursor (EC 6.4.1.1) (Pyruvic carboxylase) (PCB)	0.18	-	mit	0	Mitochondrion; mitochondrial matrix (By similarity)				1178
P11498 UniProt NPD GO	PYC_HUMAN	Pyruvate carboxylase, mitochondrial precursor (EC 6.4.1.1) (Pyruvic carboxylase) (PCB)	0.18	-	mit	0	Mitochondrion; mitochondrial matrix		608786		1178
P52901 UniProt NPD GO	ODPA_ARATH	Pyruvate dehydrogenase E1 component alpha subunit, mitochondrial precursor (EC 1.2.4.1) (PDHE1-A)	0.18	-	mit	0	Mitochondrion; mitochondrial matrix				389

You are viewing entries 53551 to 53600 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.