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
P51164 UniProt NPD GO	ATP4B_HUMAN	Potassium-transporting ATPase subunit beta (Proton pump beta chain) (Gastric H(+)/K(+) ATPase beta s ...	0.07	-	cyt	1 *	Membrane; single-pass type II membrane protein		137217		291
Q92989 UniProt NPD GO	CLP1_HUMAN	Pre-mRNA cleavage complex II protein Clp1	0.07	-	cyt	0	Nucleus		608757		425
O70591 UniProt NPD GO	PFD2_MOUSE	Prefoldin subunit 2	0.07	-	cyt	0		cytosol [TAS]			154
P40005 UniProt NPD GO	PFD2_YEAST	Prefoldin subunit 2 (Genes involved in microtubule biogenesis protein 4) (Gim complex subunit 4) (Gi ...	0.07	-	mit	1 *		cytoplasm [IDA] prefoldin complex [IPI]			123
P83202 UniProt NPD GO	PAG55_SHEEP	Pregnancy-associated glycoprotein 55 (EC 3.4.23.-) (ovPAG-55) (Fragment)	0.07	-		0	Secreted protein				18
P84291 UniProt NPD GO	BPAP_BOVIN	Pregnancy-associated protein bPAP (Fragments)	0.07	-	cyt	0					100
Q9Z0S9 UniProt NPD GO	PRAF1_MOUSE	Prenylated Rab acceptor protein 1 (PRA1 family protein 1) (Prenylin)	0.07	-	end	2	Cell membrane; multi-pass membrane protein (By similarity). Cytoplasm (By similarity). Golgi apparat ...	Golgi apparatus [IDA] integral to membrane [IDA]			185
P49768 UniProt NPD GO	PSN1_HUMAN	Presenilin-1 (EC 3.4.23.-) (PS-1) (Protein S182) [Contains: Presenilin-1 NTF subunit; Presenilin-1 C ...	0.07	-	end	9	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein. Golgi apparatus; ...	endoplasmic reticulum [IDA] Golgi apparatus [IDA] integral to nuclear inner membrane [TAS] integral to plasma membrane [IDA] kinetochore [TAS] membrane fraction [TAS] mitochondrion [IDA]	607822		467
P97887 UniProt NPD GO	PSN1_RAT	Presenilin-1 (EC 3.4.23.-) (PS-1) (Protein S182) [Contains: Presenilin-1 NTF subunit; Presenilin-1 C ...	0.07	-	end	9	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein. Golgi apparatus; ...	endoplasmic reticulum [ISS] Golgi apparatus [ISS] integral to nuclear inner membrane [ISS] integral to plasma membrane [ISS] kinetochore [ISS] lysosomal membrane [IDA] membrane fraction [ISS] mitochondrial inner membrane [IDA] mitochondrion [ISS]			468
Q9GJY2 UniProt NPD GO	PRND_SHEEP	Prion-like protein doppel precursor (PrPLP)	0.07	-	exc	1 *	Cell membrane; lipid-anchor; GPI-anchor (By similarity)				178
Q9HDU6 UniProt NPD GO	PANE_SCHPO	Probable 2-dehydropantoate 2-reductase (EC 1.1.1.169) (Ketopantoate reductase) (KPA reductase) (KPR) ...	0.07	-	nuc	0					350
Q93Y35 UniProt NPD GO	PSD6_ARATH	Probable 26S proteasome non-ATPase regulatory subunit 6	0.07	-	cyt	0					387
Q10920 UniProt NPD GO	PSD9_CAEEL	Probable 26S proteasome non-ATPase regulatory subunit 9	0.07	-	nuc	0					197
P78774 UniProt NPD GO	ARPC1_SCHPO	Probable ARP2/3 complex 41 kDa subunit (p41-ARC)	0.07	-	cyt	0		Arp2/3 protein complex [TAS]			377
Q09693 UniProt NPD GO	YA26_SCHPO	Probable DNA polymerase family X C2F7.06c (EC 2.7.7.7)	0.07	-	cyt	1					506
Q9VIZ0 UniProt NPD GO	RPO1D_DROME	Probable DNA-directed RNA polymerase I subunit D (EC 2.7.7.6)	0.07	-	cyt	0	Nucleus (By similarity)	DNA-directed RNA polymerase I complex [ISS] DNA-directed RNA polymerase III complex [ISS]			105
Q60SM4 UniProt NPD GO	RPO2J_CAEBR	Probable DNA-directed RNA polymerase II subunit J (EC 2.7.7.6)	0.07	-	nuc	0	Nucleus (By similarity)				122
Q7TQP0 UniProt NPD GO	GP141_MOUSE	Probable G-protein coupled receptor 141 (G-protein coupled receptor PGR13)	0.07	-	end	7 *	Membrane; multi-pass membrane protein				305
Q8C206 UniProt NPD GO	GP157_MOUSE	Probable G-protein coupled receptor 157	0.07	-	end	7 *	Membrane; multi-pass membrane protein				330
Q8GXG1 UniProt NPD GO	ASPG2_ARATH	Probable L-asparaginase 2 precursor (EC 3.5.1.1) (L-asparagine amidohydrolase 2) [Contains: L-aspara ...	0.07	-	cyt	0					325
Q7G764 UniProt NPD GO	NADO1_ORYSA	Probable NAD(P)H-dependent oxidoreductase 1 (EC 1.1.1.-)	0.07	-	cyt	0					321
P87153 UniProt NPD GO	TCPH_SCHPO	Probable T-complex protein 1 subunit eta (TCP-1-eta) (CCT-eta)	0.07	-	nuc	0	Cytoplasm (Potential)				558
Q9BSD7 UniProt NPD GO	U334_HUMAN	Probable UPF0334 kinase-like protein C1orf57	0.07	-	cyt	0					190
Q02332 UniProt NPD GO	PDK_CAEEL	Probable [pyruvate dehydrogenase [lipoamide]] kinase, mitochondrial precursor (EC 2.7.11.2) (Pyruvat ...	0.07	-	mit	0	Mitochondrion; mitochondrial matrix (By similarity)				401
Q7PVX8 UniProt NPD GO	ARPC2_ANOGA	Probable actin-related protein 2/3 complex subunit 2 (ARP2/3 complex 34 kDa subunit) (p34-ARC)	0.07	-	cyt	0					304
P0C0X5 UniProt NPD GO	PIN1B_ORYSA	Probable auxin efflux carrier component 1b (OsPIN1b)	0.07	-	end	9 *	Membrane; multi-pass membrane protein (Potential)				554
Q9XFR0 UniProt NPD GO	KCO3_ARATH	Probable calcium-activated outward-rectifying potassium channel 3 (AtKCO3)	0.07	-	end	4	Membrane; multi-pass membrane protein				260
Q9FLK2 UniProt NPD GO	CX5C3_ARATH	Probable cytochrome c oxidase polypeptide Vc-3 (EC 1.9.3.1) (Cytochrome c oxidase subunit 5c-3)	0.07	-	mit	1 *	Mitochondrion; mitochondrial inner membrane (By similarity)				64
Q9XXJ0 UniProt NPD GO	DHYS_CAEEL	Probable deoxyhypusine synthase (EC 2.5.1.46) (DHS)	0.07	-	cyt	0					371
Q5E982 UniProt NPD GO	DPH5_BOVIN	Probable diphthine synthase (EC 2.1.1.98) (Diphthamide biosynthesis methyltransferase)	0.07	-	cyt	0					285
P42940 UniProt NPD GO	ETFB_YEAST	Probable electron transfer flavoprotein subunit beta (Beta-ETF)	0.07	-	mit	0	Mitochondrion; mitochondrial matrix (By similarity)	mitochondrion [IDA]			261
P54412 UniProt NPD GO	EF1G_CAEEL	Probable elongation factor 1-gamma (EF-1-gamma) (eEF-1B gamma)	0.07	-	cyt	0					398
Q9ERY9 UniProt NPD GO	ERG28_MOUSE	Probable ergosterol biosynthetic protein 28	0.07	-	end	4 *	Membrane; multi-pass membrane protein (Potential)				140
Q8SRY1 UniProt NPD GO	G6PI_ENCCU	Probable glucose-6-phosphate isomerase (EC 5.3.1.9) (GPI) (Phosphoglucose isomerase) (PGI) (Phosphoh ...	0.07	-	nuc	0	Cytoplasm (By similarity)				508
Q9LYB4 UniProt NPD GO	GPX5_ARATH	Probable glutathione peroxidase 5 (EC 1.11.1.9)	0.07	-	cyt	0					173
Q9SII0 UniProt NPD GO	H2AV2_ARATH	Probable histone H2A variant 2 (H2A.F/Z 2) (HTA8)	0.07	-	nuc	0	Nucleus (By similarity)				136
Q6ZL42 UniProt NPD GO	H2A2_ORYSA	Probable histone H2A.2	0.07	-	cyt	0	Nucleus (By similarity)				135
O04848 UniProt NPD GO	H2AXA_ARATH	Probable histone H2AXa (HTA5)	0.07	-	nuc	0	Nucleus (By similarity)				142
Q2QPG9 UniProt NPD GO	H2AXB_ORYSA	Probable histone H2AXb	0.07	-	nuc	0	Nucleus (By similarity)				138
Q9LX12 UniProt NPD GO	INO3_ARATH	Probable inositol-3-phosphate synthase isozyme 3 (EC 5.5.1.4) (Myo-inositol-1-phosphate synthase 3) ...	0.07	-	cyt	0	Cytoplasm (By similarity)				510
P07192 UniProt NPD GO	MAL3_DROME	Probable maltase L precursor (EC 3.2.1.20) (Larval visceral protein L)	0.07	-	vac	0					574
O14255 UniProt NPD GO	GCS1_SCHPO	Probable mannosyl-oligosaccharide glucosidase (EC 3.2.1.106) (Processing A-glucosidase I)	0.07	-	vac	1 *	Endoplasmic reticulum; endoplasmic reticulum membrane; single-pass type II membrane protein (Potenti ...				808
Q9ZTS1 UniProt NPD GO	SYM_ORYSA	Probable methionyl-tRNA synthetase (EC 6.1.1.10) (Methionine--tRNA ligase) (MetRS)	0.07	-	mit	0	Cytoplasm (Probable)				801
O59856 UniProt NPD GO	RM33_SCHPO	Probable mitochondrial 60S ribosomal protein L33	0.07	-	mit	0	Mitochondrion (By similarity)				97
Q9VN97 UniProt NPD GO	TI17D_DROME	Probable mitochondrial import inner membrane translocase subunit Tim17 4	0.07	-	mit	1	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein (By similarity)				224
O04308 UniProt NPD GO	MPPA2_ARATH	Probable mitochondrial-processing peptidase alpha subunit 2, mitochondrial precursor (EC 3.4.24.64) ...	0.07	-	mit	0	Mitochondrion; mitochondrial inner membrane (By similarity)				499
Q9FJD1 UniProt NPD GO	OPT8_ARATH	Probable oligopeptide transporter 8 (AtOPT8)	0.07	-	end	12 *	Membrane; multi-pass membrane protein (Probable)				733
Q5RAP5 UniProt NPD GO	CJ033_PONPY	Probable oxidoreductase C10orf33 homolog (EC 1.-.-.-)	0.07	-	mit	0					581
Q09795 UniProt NPD GO	YAA1_SCHPO	Probable peptidase C22G7.01c (EC 3.4.-.-)	0.07	-	nuc	0					598
Q09859 UniProt NPD GO	MSRA_SCHPO	Probable peptide methionine sulfoxide reductase (EC 1.8.4.6) (Protein-methionine-S-oxide reductase) ...	0.07	-	cyt	0					170

You are viewing entries 70751 to 70800 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.