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
P93766 UniProt NPD GO	MLO_HORVU	Protein MLO	0.32	-	end	7 *	Membrane; multi-pass membrane protein				533
Q9PU58 UniProt NPD GO	NIPS2_BRARE	Protein NipSnap2 (Glioblastoma amplified sequence)	0.32	-	mit	0					286
P50116 UniProt NPD GO	S10A9_RAT	Protein S100-A9 (S100 calcium-binding protein A9) (Calgranulin-B) (Migration inhibitory factor-relat ...	0.32	-	nuc	0					112
Q91029 UniProt NPD GO	WNT1_CHICK	Protein Wnt-1 (Fragment)	0.32	-	nuc	0	Secreted protein; extracellular space; extracellular matrix				134
P24257 UniProt NPD GO	WNT1_BRARE	Protein Wnt-1 precursor	0.32	-	exc	0	Secreted protein; extracellular space; extracellular matrix				370
P28101 UniProt NPD GO	WNT3A_ALOVU	Protein Wnt-3a (Fragment)	0.32	-	nuc	0	Secreted protein; extracellular space; extracellular matrix				123
P28121 UniProt NPD GO	WNT53_EPTST	Protein Wnt-5(III) (Fragment)	0.32	-	nuc	0	Secreted protein; extracellular space; extracellular matrix				116
P33945 UniProt NPD GO	WNT5C_XENLA	Protein Wnt-5c precursor (XWnt-5c)	0.32	-	exc	0	Secreted protein; extracellular space; extracellular matrix				360
O35468 UniProt NPD GO	WNT9B_MOUSE	Protein Wnt-9b precursor (Wnt-15) (Wnt-14b)	0.32	-	nuc	1 *	Secreted protein; extracellular space; extracellular matrix				359
P18487 UniProt NPD GO	A37C_DROME	Protein anon-37Cs	0.32	-	nuc	0	Cytoplasm	cytoplasm [IDA]			504
O22034 UniProt NPD GO	CFXQ2_CYACA	Protein cfxQ homolog	0.32	-	cyt	0	Plastid; chloroplast				286
P51228 UniProt NPD GO	CFXQ_PORPU	Protein cfxQ homolog	0.32	-	cyt	0	Plastid; chloroplast				301
Q2KIL5 UniProt NPD GO	PDIA5_BOVIN	Protein disulfide-isomerase A5 precursor (EC 5.3.4.1)	0.32	-	mit	1 *	Endoplasmic reticulum; endoplasmic reticulum lumen (By similarity)				521
Q02956 UniProt NPD GO	KPCZ_MOUSE	Protein kinase C zeta type (EC 2.7.11.13) (nPKC-zeta)	0.32	-	nuc	0	Cytoplasm (By similarity). Endosome (By similarity). In the retina, localizes in the terminals of th ...	apical cortex [IDA] cell cortex [IDA] cytoplasm [IDA] tight junction [IDA]			592
Q01871 UniProt NPD GO	KRUP_EUSPL	Protein krueppel (Fragment)	0.32	-	nuc	0	Nucleus (Probable)				74
Q13635 UniProt NPD GO	PTC1_HUMAN	Protein patched homolog 1 (PTC1) (PTC)	0.32	-	end	12	Membrane; multi-pass membrane protein	integral to plasma membrane [TAS]	605462		1447
O95685 UniProt NPD GO	PPR3D_HUMAN	Protein phosphatase 1 regulatory subunit 3D (Protein phosphatase 1, regulatory subunit 6) (Protein p ...	0.32	-	mit	0			603326		299
P38796 UniProt NPD GO	PPME1_YEAST	Protein phosphatase methylesterase 1 (EC 3.1.1.-) (PME-1) (Yms2)	0.32	-	cyt	0		mitochondrial small ribosomal subunit [IPI]			400
P15258 UniProt NPD GO	RAL2_SCHPO	Protein ral2	0.32	-	cyt	0					611
Q10658 UniProt NPD GO	UN119_CAEEL	Protein unc-119	0.32	-	cyt	0		axon [IDA]			219
Q16928 UniProt NPD GO	WHITE_ANOAL	Protein white	0.32	-	end	6	Membrane; multi-pass membrane protein				709
O02761 UniProt NPD GO	FOS_SHEEP	Proto-oncogene protein c-fos (Cellular oncogene fos) (Fragment)	0.32	+	nuc	0	Nucleus				195
P00540 UniProt NPD GO	MOS_HUMAN	Proto-oncogene serine/threonine-protein kinase mos (EC 2.7.11.1) (c-mos) (Oocyte maturation factor m ...	0.32	-	mit	0			190060		346
P00539 UniProt NPD GO	MOS_RAT	Proto-oncogene serine/threonine-protein kinase mos (EC 2.7.11.1) (c-mos) (Oocyte maturation factor m ...	0.32	-	nuc	0		cytosol [IDA]			339
Q9Y5H8 UniProt NPD GO	PCDA3_HUMAN	Protocadherin alpha 3 precursor (PCDH-alpha3)	0.32	+	nuc	0	Membrane; single-pass type I membrane protein (By similarity)	integral to plasma membrane [TAS]	606309		950
Q9Y5F3 UniProt NPD GO	PCDB1_HUMAN	Protocadherin beta 1 precursor (PCDH-beta1)	0.32	-	nuc	1 *	Membrane; single-pass type I membrane protein (By similarity)		606327		818
Q6KEQ9 UniProt NPD GO	PC11X_PIG	Protocadherin-11 X-linked precursor (Protocadherin-11) (Protocadherin on the X chromosome)	0.32	+	end	1	Membrane; single-pass type I membrane protein (Potential)				1117
P56529 UniProt NPD GO	CXP3E_CONPU	Psi-conotoxin PIIIE precursor (Conotoxin P3.8)	0.32	-	exc	1 *	Secreted protein			1JLO	75
P07988 UniProt NPD GO	PSPB_HUMAN	Pulmonary surfactant-associated protein B precursor (SP-B) (6 kDa protein) (Pulmonary surfactant-ass ...	0.32	-	cyt	0	Secreted protein; extracellular space		178640	1SSZ	381
P82281 UniProt NPD GO	TL29_ARATH	Putative L-ascorbate peroxidase, chloroplast precursor (EC 1.11.1.11) (Thylakoid lumenal 29 kDa prot ...	0.32	-	mit	0	Plastid; chloroplast; chloroplast thylakoid lumen				349
Q9LMI7 UniProt NPD GO	ACO32_ARATH	Putative acyl-coenzyme A oxidase 3.2, peroxisomal precursor (EC 1.3.3.6)	0.32	-	cyt	0	Peroxisome (Probable)				675
O64474 UniProt NPD GO	AHM2_ARATH	Putative cadmium/zinc-transporting ATPase 2 (EC 3.6.3.3) (EC 3.6.3.5)	0.32	+	end	6	Membrane; multi-pass membrane protein				1172
Q9LT02 UniProt NPD GO	ATY1_ARATH	Putative cation-transporting ATPase (EC 3.6.3.-)	0.32	-	end	10 *	Membrane; multi-pass membrane protein				1179
Q9W594 UniProt NPD GO	GR02A_DROME	Putative gustatory receptor 2a	0.32	-	nuc	4 *	Membrane; multi-pass membrane protein (Potential)	integral to membrane [NAS]			414
Q9W2B1 UniProt NPD GO	GR58B_DROME	Putative gustatory receptor 58b	0.32	-	end	7 *	Membrane; multi-pass membrane protein (Potential)	integral to membrane [NAS]			408
P27469 UniProt NPD GO	G0S2_HUMAN	Putative lymphocyte G0/G1 switch protein 2	0.32	-	mit	1 *					103
Q9LHK4 UniProt NPD GO	MDR22_ARATH	Putative multidrug resistance protein 22 (P-glycoprotein 8)	0.32	-	end	9 *	Membrane; multi-pass membrane protein (Potential)				1241
Q18179 UniProt NPD GO	YXX5_CAEEL	Putative neuropeptide Y receptor (NPY-R)	0.32	-	end	7 *	Membrane; multi-pass membrane protein				455
P35731 UniProt NPD GO	YKF5_YEAST	Putative oxidoreductase YKL055C (EC 1.-.-.-)	0.32	-	nuc	0		mitochondrion [IMP]			278
Q8N5I3 UniProt NPD GO	KCNRG_HUMAN	Putative potassium channel regulatory protein (Potassium channel regulator) (Protein CLLD4)	0.32	-	cyt	0			607947		272
P51237 UniProt NPD GO	YCXD_PORPU	Putative single-stranded DNA-binding protein in psbI-ycf39 intergenic region (ORF111)	0.32	-	nuc	0	Plastid; chloroplast				111
Q09545 UniProt NPD GO	DHSB_CAEEL	Putative succinate dehydrogenase [ubiquinone] iron-sulfur protein, mitochondrial precursor (EC 1.3.5 ...	0.32	-	nuc	0	Mitochondrion; mitochondrial inner membrane (By similarity)				298
P32327 UniProt NPD GO	PYC2_YEAST	Pyruvate carboxylase 2 (EC 6.4.1.1) (Pyruvic carboxylase 2) (PCB 2)	0.32	-	cyt	0	Cytoplasm	cytosol [IDA]			1180
Q9WUA6 UniProt NPD GO	AKT3_MOUSE	RAC-gamma serine/threonine-protein kinase (EC 2.7.11.1) (RAC-PK-gamma) (Protein kinase Akt-3) (Prote ...	0.32	-	cyt	0	Cytoplasm. Membrane; peripheral membrane protein. Membrane-associated after cell stimulation leading ...				479
Q9FL07 UniProt NPD GO	ATL5I_ARATH	RING-H2 finger protein ATL5I	0.32	-	nuc	1 *					376
Q757I9 UniProt NPD GO	REXO4_ASHGO	RNA exonuclease 4 (EC 3.1.-.-)	0.32	-	nuc	0	Nucleus (By similarity)				285
Q9NYV6 UniProt NPD GO	RRN3_HUMAN	RNA polymerase I-specific transcription initiation factor RRN3 (Transcription initiation factor IA) ...	0.32	-	cyt	0	Nucleus (By similarity)				651
Q9VLR5 UniProt NPD GO	TCP4_DROME	RNA polymerase II transcriptional coactivator (p11)	0.32	-	nuc	0	Nucleus				110
Q67VP4 UniProt NPD GO	RAC4_ORYSA	Rac-like GTP-binding protein 4 (OsRac4) (GTPase protein ROP4)	0.32	-	cyt	0	Cytoplasm (By similarity). Membrane; peripheral membrane protein (By similarity). Associated with th ...				215
P22279 UniProt NPD GO	RAS2_RHIRA	Ras-like protein 2	0.32	-	cyt	0	Cell membrane; lipid-anchor				198

You are viewing entries 38851 to 38900 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.