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
P28128 UniProt NPD GO	WNT5A_MELGA	Protein Wnt-5a (Fragment)	0.22	-	nuc	0	Secreted protein; extracellular space; extracellular matrix				116
Q5NVK2 UniProt NPD GO	WNT5B_PONPY	Protein Wnt-5b precursor	0.22	-	exc	0	Secreted protein; extracellular space; extracellular matrix (By similarity)				359
P28105 UniProt NPD GO	WNT7A_ALOVU	Protein Wnt-7a (Fragment)	0.22	-	nuc	0	Secreted protein; extracellular space; extracellular matrix				123
P31288 UniProt NPD GO	WNT7A_XENLA	Protein Wnt-7a (XWnt-7a) (Fragment)	0.22	-	nuc	0	Secreted protein; extracellular space; extracellular matrix				135
P28146 UniProt NPD GO	WNT8_THUTH	Protein Wnt-8 (Fragment)	0.22	-	nuc	0	Secreted protein; extracellular space; extracellular matrix				128
P32795 UniProt NPD GO	YME1_YEAST	Protein YME1 (EC 3.4.24.-) (TAT-binding homolog 11) (Protein OSD1)	0.22	-	mit	0		i-AAA complex [IDA] mitochondrion [IDA]			747
Q8CIG8 UniProt NPD GO	ANM5_MOUSE	Protein arginine N-methyltransferase 5 (EC 2.1.1.-) (Shk1 kinase-binding protein 1 homolog) (SKB1 ho ...	0.22	-	cyt	0	Cytoplasm (By similarity)				636
Q8WP23 UniProt NPD GO	BOLL_MACFA	Protein boule-like	0.22	-	nuc	0	Cytoplasm (By similarity)				283
O60052 UniProt NPD GO	PFTA_SCHPO	Protein farnesyltransferase/geranylgeranyltransferase type I alpha subunit (EC 2.5.1.58) (EC 2.5.1.5 ...	0.22	-	cyt	0					294
O35595 UniProt NPD GO	PTC2_MOUSE	Protein patched homolog 2 (PTC2)	0.22	-	end	10	Membrane; multi-pass membrane protein				1182
Q2URJ0 UniProt NPD GO	PPME1_ASPOR	Protein phosphatase methylesterase 1 (EC 3.1.1.-) (PME-1)	0.22	-	cyt	0					427
Q09914 UniProt NPD GO	RHO1_SCHPO	Protein rho1	0.22	-	mit	0	Cell membrane; lipid-anchor. Found at the growing tips of interphase cells and at the septum prior t ...	site of polarized growth [TAS]			202
Q755R1 UniProt NPD GO	SUI1_ASHGO	Protein translation factor SUI1	0.22	-	nuc	0					108
P32915 UniProt NPD GO	SC61A_YEAST	Protein transport protein SEC61 (Sec61 complex subunit SEC61) (Sec61 complex subunit alpha)	0.22	-	end	5 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein	endoplasmic reticulum lumen [IDA] integral to endoplasmic reticulum membrane [IDA] Sec complex-associated translocon complex [TAS]			480
P43682 UniProt NPD GO	SFT1_YEAST	Protein transport protein SFT1 (P14)	0.22	-	nuc	1	Golgi apparatus; Golgi membrane; single-pass type IV membrane protein	Golgi membrane [TAS]			97
P21980 UniProt NPD GO	TGM2_HUMAN	Protein-glutamine gamma-glutamyltransferase 2 (EC 2.3.2.13) (Tissue transglutaminase) (TGase C) (TGC ...	0.22	-	mit	0		cytosol [ISS] extracellular matrix (sensu Metazoa) [ISS] membrane [ISS]	190196	1KV3	687
Q60805 UniProt NPD GO	MERTK_MOUSE	Proto-oncogene tyrosine-protein kinase MER precursor (EC 2.7.10.1) (C-mer) (Receptor tyrosine kinase ...	0.22	-	end	1	Membrane; single-pass type I membrane protein (By similarity)				994
Q5DRD8 UniProt NPD GO	PCDBB_PANTR	Protocadherin beta 11 precursor (PCDH-beta11)	0.22	-	nuc	1	Membrane; single-pass type I membrane protein (By similarity)				797
Q8CFY5 UniProt NPD GO	COX10_MOUSE	Protoheme IX farnesyltransferase, mitochondrial precursor (EC 2.5.1.-) (Heme O synthase)	0.22	-	end	4	Mitochondrion; mitochondrial membrane; multi-pass membrane protein (By similarity)	mitochondrion [IDA]			443
Q7S5E7 UniProt NPD GO	COX10_NEUCR	Protoheme IX farnesyltransferase, mitochondrial precursor (EC 2.5.1.-) (Heme O synthase)	0.22	-	mit	8	Mitochondrion; mitochondrial membrane; multi-pass membrane protein (By similarity)				535
Q8AVA3 UniProt NPD GO	CRVP_PSEPO	Pseudecin precursor	0.22	-	exc	0	Secreted protein				238
Q12298 UniProt NPD GO	YD061_YEAST	Putative ABC transporter ATP-binding protein YDR061W	0.22	-	cyt	0	Mitochondrion	mitochondrion [IDA]			539
O78432 UniProt NPD GO	YCF30_GUITH	Putative HTH-type transcriptional regulator ycf30	0.22	-	cyt	0	Plastid; chloroplast				310
Q9C7E9 UniProt NPD GO	ATL1E_ARATH	Putative RING-H2 finger protein ATL1E	0.22	-	mit	1 *					336
Q94B78 UniProt NPD GO	GCSP2_ARATH	Putative glycine dehydrogenase [decarboxylating] 2, mitochondrial precursor (EC 1.4.4.2) (Glycine de ...	0.22	-	mit	0	Mitochondrion				1037
P53993 UniProt NPD GO	YMP8_CAEEL	Putative glycosyl transferase B0361.8 in chromosome III (EC 2.-.-.-)	0.22	-	end	2 *	Membrane; multi-pass membrane protein (Potential)				470
P84181 UniProt NPD GO	GR22D_DROME	Putative gustatory receptor 22d	0.22	-	end	8 *	Membrane; multi-pass membrane protein (Potential)				387
Q9SSC9 UniProt NPD GO	AHP6_ARATH	Putative histidine-containing phosphotransfer protein 6	0.22	-	nuc	0					154
P83104 UniProt NPD GO	M3LK7_DROME	Putative mitogen-activated protein kinase kinase kinase 7-like (EC 2.7.11.25)	0.22	-	cyt	0					393
Q9C6B9 UniProt NPD GO	PEAM3_ARATH	Putative phosphoethanolamine N-methyltransferase 3 (EC 2.1.1.103)	0.22	-	cyt	0	Cytoplasm (By similarity)				490
Q9UI43 UniProt NPD GO	RRMJ2_HUMAN	Putative ribosomal RNA methyltransferase 2 (EC 2.1.1.-) (rRNA (uridine-2'-O-)-methyltransferase)	0.22	-	cyt	0	Nucleus; nucleolus		606906		246
O36015 UniProt NPD GO	YEK3_SCHPO	Putative ribosomal RNA methyltransferase C4F10.03c (EC 2.1.1.-) (rRNA (uridine-2'-O-)-methyltransfer ...	0.22	-	nuc	0					285
Q7S5N8 UniProt NPD GO	GLYM_NEUCR	Putative serine hydroxymethyltransferase, mitochondrial precursor (EC 2.1.2.1) (Serine methylase) (G ...	0.22	-	mit	0	Mitochondrion				527
P83528 UniProt NPD GO	STX5_CAEEL	Putative syntaxin C15C7.1	0.22	-	nuc	1	Membrane; single-pass type IV membrane protein (Potential)	integral to membrane [ISS]			122
Q5G234 UniProt NPD GO	P2OX_TRAPU	Pyranose 2-oxidase precursor (EC 1.1.3.10) (P2Ox) (Pyranose oxidase) (PROD) (POD) (POx) (Pyranose:ox ...	0.22	-	cyt	0	Hyphal periplasmic space (By similarity)				622
Q9HES8 UniProt NPD GO	PYC_ASPNG	Pyruvate carboxylase (EC 6.4.1.1) (Pyruvic carboxylase) (PCB)	0.22	-	mit	0	Cytoplasm (By similarity)				1192
O54965 UniProt NPD GO	RNF13_MOUSE	RING finger protein 13	0.22	+	nuc	1					381
P0C034 UniProt NPD GO	ATL1K_ARATH	RING-H2 finger protein ATL1K (RING-H2 finger protein ATL10)	0.22	-	end	1					251
Q6NKR1 UniProt NPD GO	ATL2H_ARATH	RING-H2 finger protein ATL2H	0.22	-	nuc	1 *					254
Q6FQA0 UniProt NPD GO	REXO4_CANGA	RNA exonuclease 4 (EC 3.1.-.-)	0.22	-	nuc	0	Nucleus (By similarity)				263
O94375 UniProt NPD GO	REXO4_SCHPO	RNA exonuclease 4 (EC 3.1.-.-)	0.22	-	nuc	0	Nucleus (By similarity)				260
P47822 UniProt NPD GO	MED21_YEAST	RNA polymerase II mediator complex subunit 21 (RNAPII complex component SRB7) (Suppressor of RNA pol ...	0.22	-	nuc	0	Nucleus	mediator complex [IDA]		1YKH	140
Q24491 UniProt NPD GO	RX21_DROME	RNA-binding protein Rsf1 (RNA-binding protein Rox21)	0.22	-	nuc	0	Nucleus	nucleus [IDA]			197
Q93062 UniProt NPD GO	RBPMS_HUMAN	RNA-binding protein with multiple splicing (RBP-MS)	0.22	-	nuc	0			601558	1BNY	196
O82481 UniProt NPD GO	RAC10_ARATH	Rac-like GTP-binding protein ARAC10 (GTPase protein ROP11)	0.22	-	cyt	0	Membrane; lipid-anchor				215
P43487 UniProt NPD GO	RANG_HUMAN	Ran-specific GTPase-activating protein (Ran-binding protein 1) (RanBP1)	0.22	+	nuc	0		cytoplasm [TAS] nucleus [TAS]	601180	1K5G	201
P40517 UniProt NPD GO	YRB2_YEAST	Ran-specific GTPase-activating protein 2 (Ran-binding protein 2) (RANBP2)	0.22	-	nuc	0	Nucleus	nuclear pore [IDA] nucleus [IDA]			327
P0C0R1 UniProt NPD GO	ERFD_YARLI	Ras modification protein ERF4	0.22	-	cyt	0	Endoplasmic reticulum; endoplasmic reticulum membrane; peripheral membrane protein (By similarity)				180
P38976 UniProt NPD GO	RAS2_HYDMA	Ras-like protein RAS2	0.22	-	cyt	0	Cell membrane; lipid-anchor; cytoplasmic side (Potential)				192
Q92737 UniProt NPD GO	RR22_HUMAN	Ras-like protein RRP22 (RAS-related protein on chromosome 22)	0.22	-	cyt	0	Cell membrane; lipid-anchor; cytoplasmic side (Potential)		602220		203

You are viewing entries 48851 to 48900 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.