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
P53961 UniProt NPD GO	GPI15_YEAST	Phosphatidylinositol N-acetylglucosaminyltransferase subunit GPI15 (EC 2.4.1.198) (PIGH homolog)	0.31	-	end	2	Membrane; multi-pass membrane protein (Potential)	glycosylphosphatidylinositol-N-acetylglucos... [TAS]			229
O70172 UniProt NPD GO	PI52A_MOUSE	Phosphatidylinositol-4-phosphate 5-kinase type-2 alpha (EC 2.7.1.68) (Phosphatidylinositol-4-phospha ...	0.31	-	mit	0					405
P78356 UniProt NPD GO	PI52B_HUMAN	Phosphatidylinositol-4-phosphate 5-kinase type-2 beta (EC 2.7.1.68) (Phosphatidylinositol-4-phosphat ...	0.31	-	mit	0	Endoplasmic reticulum; endoplasmic reticulum membrane; peripheral membrane protein (By similarity). ...		603261	1BO1	416
P60043 UniProt NPD GO	PA21B_NAJSG	Phospholipase A2 isoform 1 precursor (EC 3.1.1.4) (Phosphatidylcholine 2-acylhydrolase) (Fragment)	0.31	-	mit	0	Secreted protein			1XXW	126
P93733 UniProt NPD GO	PLDB1_ARATH	Phospholipase D beta 1 (EC 3.1.4.4) (AtPLDbeta1) (PLD beta 1) (PLDbeta)	0.31	-	nuc	0	Cytoplasm (By similarity). Membrane; peripheral membrane protein (By similarity)				967
P98204 UniProt NPD GO	ALA1_ARATH	Phospholipid-transporting ATPase 1 (EC 3.6.3.1) (Aminophospholipid flippase 1)	0.31	-	end	10	Membrane; multi-pass membrane protein				1158
O35621 UniProt NPD GO	PMM1_MOUSE	Phosphomannomutase 1 (EC 5.4.2.8) (PMM 1)	0.31	-	cyt	0	Cytoplasm (By similarity)				262
P33579 UniProt NPD GO	PRLPC_RAT	Placental prolactin-like protein C precursor (PRL-like protein C) (PLP-C) (Growth hormone-related pl ...	0.31	-	mit	0	Secreted protein				238
Q7FMW4 UniProt NPD GO	PDR15_ORYSA	Pleiotropic drug resistance protein 15	0.31	-	end	13	Membrane; multi-pass membrane protein (By similarity)				1509
Q9XIE2 UniProt NPD GO	PDR8_ARATH	Pleiotropic drug resistance protein 8	0.31	-	end	13	Cell membrane; multi-pass membrane protein	chloroplast [IDA] plasma membrane [IDA]			1469
Q8CJH3 UniProt NPD GO	PLXB1_MOUSE	Plexin-B1 precursor	0.31	-	end	0	Membrane; single-pass type I membrane protein				2119
Q91X05 UniProt NPD GO	PODO_MOUSE	Podocin	0.31	-	nuc	1	Membrane; multi-pass membrane protein	plasma membrane [IDA]			385
Q8MTP3 UniProt NPD GO	PTP3_ENCCU	Polar tube protein 3 precursor	0.31	-	nuc	0					1256
Q9GM01 UniProt NPD GO	GALT9_MACFA	Polypeptide N-acetylgalactosaminyltransferase 9 (EC 2.4.1.41) (Protein-UDP acetylgalactosaminyltrans ...	0.31	-	end	1 *	Golgi apparatus; Golgi membrane; single-pass type II membrane protein (By similarity)				606
O14649 UniProt NPD GO	KCNK3_HUMAN	Potassium channel subfamily K member 3 (Acid-sensitive potassium channel protein TASK-1) (TWIK-relat ...	0.31	-	end	5 *	Membrane; multi-pass membrane protein (Potential)	integral to plasma membrane [TAS]	603220		394
P59867 UniProt NPD GO	KAX63_HETSP	Potassium channel toxin alpha-KTx 6.3 (Neurotoxin HsTX1)	0.31	-	nuc	0	Secreted protein			1Y2P	34
Q28293 UniProt NPD GO	KCNA2_CANFA	Potassium voltage-gated channel subfamily A member 2 (Voltage-gated potassium channel subunit Kv1.2) ...	0.31	-	end	5	Membrane; multi-pass membrane protein (By similarity)				499
Q8R1C0 UniProt NPD GO	KCNC4_MOUSE	Potassium voltage-gated channel subfamily C member 4 (Voltage-gated potassium channel subunit Kv3.4) ...	0.31	+	end	3	Membrane; multi-pass membrane protein				628
Q63734 UniProt NPD GO	KCNC4_RAT	Potassium voltage-gated channel subfamily C member 4 (Voltage-gated potassium channel subunit Kv3.4) ...	0.31	+	end	3	Membrane; multi-pass membrane protein			1ZTN	625
Q9JMJ4 UniProt NPD GO	PRP19_RAT	Pre-mRNA-splicing factor 19 (PRP19/PSO4 homolog) (Neuronal differentiation-related gene protein)	0.31	-	cyt	0	Nucleus (By similarity). Nucleoplasmic in interphase cells. Irregularly distributed in anaphase cell ...				504
Q99KP6 UniProt NPD GO	PRP19_MOUSE	Pre-mRNA-splicing factor 19 (PRP19/PSO4 homolog) (Nuclear matrix protein 200) (Nuclear matrix protei ...	0.31	-	cyt	0	Nucleus (By similarity). Nucleoplasmic in interphase cells. Irregularly distributed in anaphase cell ...				504
Q9UMS4 UniProt NPD GO	PRP19_HUMAN	Pre-mRNA-splicing factor 19 (PRP19/PSO4 homolog) (Nuclear matrix protein 200) (hPso4)	0.31	-	cyt	0	Nucleus. Nucleoplasmic in interphase cells. Irregularly distributed in anaphase cells. In prophase c ...		608330		504
Q02521 UniProt NPD GO	SPP2_YEAST	Pre-mRNA-splicing factor SPP2 (Spliceosome maturation protein SPP2) (Suppressor of PRP protein 2)	0.31	-	nuc	0	Cytoplasm. Nucleus	spliceosome complex [IDA]			185
P11465 UniProt NPD GO	PSG2_HUMAN	Pregnancy-specific beta-1-glycoprotein 2 precursor (PSBG-2) (Pregnancy-specific beta-1 glycoprotein ...	0.31	-	nuc	0	Secreted protein (Potential)		176391		335
Q6CXR8 UniProt NPD GO	PAM17_KLULA	Presequence translocated-associated motor subunit PAM17, mitochondrial precursor	0.31	-	nuc	2	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein (By similarity)				196
Q95Y71 UniProt NPD GO	RM45_CAEEL	Probable 39S ribosomal protein L45, mitochondrial precursor	0.31	-	mit	0	Mitochondrion (By similarity)	mitochondrion [ISS]			357
P55842 UniProt NPD GO	RL14_TRYBB	Probable 60S ribosomal protein L14 (23 kDa cell surface protein homolog)	0.31	-	nuc	0					189
Q9BKQ8 UniProt NPD GO	DHX35_CAEEL	Probable ATP-dependent RNA helicase DHX35 homolog (EC 3.6.1.-)	0.31	-	nuc	0					732
Q9NRW3 UniProt NPD GO	ABC3C_HUMAN	Probable DNA dC->dU-editing enzyme APOBEC-3C (EC 3.5.4.-) (APOBEC1-like) (Phorbolin I protein)	0.31	+	cyt	0			607750		190
P30322 UniProt NPD GO	DPOM_AGABT	Probable DNA polymerase (EC 2.7.7.7) (Fragment)	0.31	-	nuc	0					797
Q9M9G7 UniProt NPD GO	CAPZB_ARATH	Probable F-actin capping protein subunit beta (CapZ-beta)	0.31	-	nuc	0					256
Q7TQN7 UniProt NPD GO	GP135_RAT	Probable G-protein coupled receptor 135	0.31	-	end	7	Membrane; multi-pass membrane protein				457
P0C0W8 UniProt NPD GO	GP139_RAT	Probable G-protein coupled receptor 139 (G(q)-coupled orphan receptor GPRg1)	0.31	-	end	6 *	Membrane; multi-pass membrane protein				345
Q8C131 UniProt NPD GO	GPR81_MOUSE	Probable G-protein coupled receptor 81	0.31	+	end	7 *	Membrane; multi-pass membrane protein				343
Q03613 UniProt NPD GO	YN84_CAEEL	Probable G-protein coupled receptor ZC84.4	0.31	-	end	7 *	Membrane; multi-pass membrane protein (Potential)				395
Q8VWQ5 UniProt NPD GO	WRK50_ARATH	Probable WRKY transcription factor 50 (WRKY DNA-binding protein 50)	0.31	+	nuc	0	Nucleus (Probable)				173
P34346 UniProt NPD GO	KADX_CAEEL	Probable adenylate kinase isoenzyme C29E4.8 (EC 2.7.4.3) (ATP-AMP transphosphorylase)	0.31	-	cyt	0					251
Q2KIG4 UniProt NPD GO	ALLC_BOVIN	Probable allantoicase (EC 3.5.3.4) (Allantoate amidinohydrolase)	0.31	-	cyt	0					412
Q21153 UniProt NPD GO	CMC1_CAEEL	Probable calcium-binding mitochondrial carrier K02F3.2	0.31	-	nuc	0	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein (By similarity)				707
Q9HD20 UniProt NPD GO	AT131_HUMAN	Probable cation-transporting ATPase 13A1 (EC 3.6.3.-)	0.31	-	end	7	Membrane; multi-pass membrane protein (By similarity)				1204
Q9VKD3 UniProt NPD GO	NFS1_DROME	Probable cysteine desulfurase, mitochondrial precursor (EC 2.8.1.7)	0.31	+	mit	0	Mitochondrion (By similarity)				462
Q9VAQ5 UniProt NPD GO	DIMH_DROME	Probable dimethyladenosine transferase (EC 2.1.1.-) (S-adenosylmethionine-6-N',N'-adenosyl(rRNA) dim ...	0.31	-	nuc	0	Nucleus; nucleolus (By similarity)				306
Q9FF17 UniProt NPD GO	ALG6_ARATH	Probable dolichyl pyrophosphate Man9GlcNAc2 alpha-1,3-glucosyltransferase (EC 2.4.1.-) (Dolichyl-P-G ...	0.31	-	end	9 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (Potential)				533
Q9HAH7 UniProt NPD GO	FBSH_HUMAN	Probable fibrosin-1 long transcript protein	0.31	-	nuc	0			608601		372
O62431 UniProt NPD GO	SYQ_CAEEL	Probable glutaminyl-tRNA synthetase (EC 6.1.1.18) (Glutamine--tRNA ligase) (GlnRS)	0.31	-	cyt	0					786
Q9H7Z6 UniProt NPD GO	MYST1_HUMAN	Probable histone acetyltransferase MYST1 (EC 2.3.1.48) (MYST protein 1) (MOZ, YBF2/SAS3, SAS2 and TI ...	0.31	-	cyt	0	Nucleus	nucleus [IDA]	609912	2GIV	458
Q9GYS9 UniProt NPD GO	RM23_CAEEL	Probable mitochondrial 39S ribosomal protein L23 (L23mt) (MRP-L23)	0.31	-	mit	0	Mitochondrion (By similarity)				159
Q9SRH4 UniProt NPD GO	PEL7_ARATH	Probable pectate lyase 7 precursor (EC 4.2.2.2)	0.31	-	exc	0					475
Q9VCA5 UniProt NPD GO	SYFB_DROME	Probable phenylalanyl-tRNA synthetase beta chain (EC 6.1.1.20) (Phenylalanine--tRNA ligase beta chai ...	0.31	-	cyt	0	Cytoplasm (By similarity)				589
Q9VPY8 UniProt NPD GO	TGT_DROME	Probable queuine tRNA-ribosyltransferase (EC 2.4.2.29) (tRNA-guanine transglycosylase) (Guanine inse ...	0.31	+	mit	0					427

You are viewing entries 39701 to 39750 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.