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
P30065 UniProt NPD GO	RK2_EPIVI	Plastid 50S ribosomal protein L2	0.32	-	mit	0	Plastid				274
P02775 UniProt NPD GO	SCYB7_HUMAN	Platelet basic protein precursor (PBP) (Small inducible cytokine B7) (CXCL7) (Leukocyte-derived grow ...	0.32	-	nuc	1 *	Secreted protein		121010	1TVX	128
P43310 UniProt NPD GO	PPO_SPIOL	Polyphenol oxidase, chloroplast precursor (EC 1.10.3.1) (PPO) (Catechol oxidase)	0.32	-	nuc	0	Plastid; chloroplast; chloroplast thylakoid lumen				639
P17225 UniProt NPD GO	PTBP1_MOUSE	Polypyrimidine tract-binding protein 1 (PTB) (Heterogeneous nuclear ribonucleoprotein I) (hnRNP I)	0.32	-	nuc	0	Nucleus	nucleus [IDA]			527
Q9UJ96 UniProt NPD GO	KCNG2_HUMAN	Potassium voltage-gated channel subfamily G member 2 (Voltage-gated potassium channel subunit Kv6.2) ...	0.32	-	end	5	Membrane; multi-pass membrane protein	voltage-gated potassium channel complex [TAS]	605696		466
Q7SAX8 UniProt NPD GO	FIP1_NEUCR	Pre-mRNA polyadenylation factor fip-1	0.32	-	nuc	0	Nucleus (By similarity)				423
Q52DF3 UniProt NPD GO	SYF1_MAGGR	Pre-mRNA-splicing factor SYF1	0.32	-	cyt	0	Nucleus (By similarity)				816
Q4WP02 UniProt NPD GO	SPP2_ASPFU	Pre-mRNA-splicing factor spp2	0.32	-	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity)				541
Q4SPU8 UniProt NPD GO	PFD1_TETNG	Prefoldin subunit 1	0.32	-	nuc	0					122
Q2T9V8 UniProt NPD GO	DTD1_BOVIN	Probable D-tyrosyl-tRNA(Tyr) deacylase (EC 3.1.-.-)	0.32	-	nuc	0	Cytoplasm (Potential)				209
Q22019 UniProt NPD GO	PSF1_CAEEL	Probable DNA replication complex GINS protein PSF1	0.32	-	nuc	0	Nucleus (By similarity)				201
Q9HGP5 UniProt NPD GO	CAPZB_SCHPO	Probable F-actin capping protein subunit beta	0.32	-	nuc	0		actin cortical patch [IDA] actin filament [IDA] cell tip [IDA] F-actin capping protein complex [IDA]			268
Q80WT4 UniProt NPD GO	GP176_MOUSE	Probable G-protein coupled receptor 176 (G-protein coupled receptor AGR9)	0.32	-	end	7 *	Membrane; multi-pass membrane protein				515
Q14330 UniProt NPD GO	GPR18_HUMAN	Probable G-protein coupled receptor 18	0.32	-	end	7 *	Membrane; multi-pass membrane protein	integral to membrane [NAS]	602042		331
Q93127 UniProt NPD GO	GPR18_BALAM	Probable G-protein coupled receptor No18	0.32	-	end	7 *	Membrane; multi-pass membrane protein (By similarity)				379
P41941 UniProt NPD GO	GOSR2_CAEEL	Probable Golgi SNAP receptor complex member 2	0.32	-	nuc	1	Golgi apparatus; Golgi membrane; single-pass type IV membrane protein (Potential)				213
Q4WU59 UniProt NPD GO	TAH18_ASPFU	Probable NADPH reductase tah18 (EC 1.-.-.-)	0.32	-	cyt	0					654
Q9VIM5 UniProt NPD GO	ARPC2_DROME	Probable actin-related protein 2/3 complex subunit 2 (ARP2/3 complex 34 kDa subunit) (p34-ARC)	0.32	-	cyt	0					301
Q7XSQ9 UniProt NPD GO	PIP12_ORYSA	Probable aquaporin PIP1.2 (Plasma membrane intrinsic protein 1.2) (OsPIP1.2)	0.32	+	mit	4	Cell membrane; multi-pass membrane protein (By similarity)				282
Q19825 UniProt NPD GO	SYR_CAEEL	Probable arginyl-tRNA synthetase (EC 6.1.1.19) (Arginine--tRNA ligase) (ArgRS)	0.32	-	cyt	0	Cytoplasm (Potential)				713
Q9EPE9 UniProt NPD GO	AT131_MOUSE	Probable cation-transporting ATPase 13A1 (EC 3.6.3.-) (CATP)	0.32	-	end	6	Membrane; multi-pass membrane protein (By similarity)				1200
Q95050 UniProt NPD GO	ATX9_TETTH	Probable cation-transporting ATPase 9 (EC 3.6.3.-)	0.32	-	end	8	Membrane; multi-pass membrane protein				1133
Q9VG40 UniProt NPD GO	CP134_DROME	Probable cytochrome P450 313a4 (EC 1.14.-.-) (CYPCCCXIIIA4)	0.32	-	end	2 *	Endoplasmic reticulum; endoplasmic reticulum membrane; peripheral membrane protein (Potential)				478
Q25225 UniProt NPD GO	IF4A_LEIBR	Probable eukaryotic initiation factor 4A (EC 3.6.1.-) (ATP-dependent RNA helicase eIF4A) (eIF-4A)	0.32	-	cyt	0					403
Q09704 UniProt NPD GO	RRP4_SCHPO	Probable exosome complex exonuclease rrp4 (EC 3.1.13.-) (Ribosomal RNA-processing protein 4)	0.32	-	cyt	0					329
Q94L32 UniProt NPD GO	NMT2_ARATH	Probable glycylpeptide N-tetradecanoyltransferase 2 (EC 2.3.1.97) (Peptide N-myristoyltransferase 2) ...	0.32	-	cyt	0					430
P47016 UniProt NPD GO	NIT2_YEAST	Probable hydrolase NIT2 (EC 3.5.-.-)	0.32	-	nuc	0					307
Q6C7C3 UniProt NPD GO	SPC24_YARLI	Probable kinetochore protein SPC24	0.32	-	nuc	0	Nucleus (By similarity). Associated with kinetochores (By similarity)				189
Q91WB2 UniProt NPD GO	PPAC3_MOUSE	Probable lipid phosphate phosphatase PPAPDC3 (EC 3.1.3.-) (Phosphatidic acid phosphatase type 2 doma ...	0.32	-	end	4	Membrane; multi-pass membrane protein (Potential)				271
Q61DA8 UniProt NPD GO	RM23_CAEBR	Probable mitochondrial 39S ribosomal protein L23 (L23mt) (MRP-L23)	0.32	-	mit	0	Mitochondrion (By similarity)				159
Q9M8Z8 UniProt NPD GO	PEL8_ARATH	Probable pectate lyase 8 precursor (EC 4.2.2.2)	0.32	-	exc	0					416
Q29449 UniProt NPD GO	AT8A1_BOVIN	Probable phospholipid-transporting ATPase IA (EC 3.6.3.1) (Chromaffin granule ATPase II) (ATPase cla ...	0.32	+	end	8	Integral membrane protein. Chromaffin granules				1149
Q17827 UniProt NPD GO	PFD1_CAEEL	Probable prefoldin subunit 1	0.32	-	nuc	0					117
P53233 UniProt NPD GO	KG1Z_YEAST	Probable serine/threonine-protein kinase YGR052W (EC 2.7.11.1)	0.32	-	mit	0		mitochondrion [IDA]			369
Q00714 UniProt NPD GO	STCS_EMENI	Probable sterigmatocystin biosynthesis P450 monooxygenase stcS (EC 1.14.-.-) (Cytochrome P450 59)	0.32	-	cyt	0					505
P56344 UniProt NPD GO	CYSA_CHLVU	Probable sulfate/thiosulfate import ATP-binding protein cysA (EC 3.6.3.25) (Sulfate-transporting ATP ...	0.32	-	cyt	0	Plastid; chloroplast				236
O77263 UniProt NPD GO	TRMB_DROME	Probable tRNA (guanine-N(7)-)-methyltransferase (EC 2.1.1.33) (tRNA(m7G46)-methyltransferase)	0.32	-	cyt	0					256
Q84ZC0 UniProt NPD GO	VATH_ORYSA	Probable vacuolar ATP synthase subunit H (EC 3.6.3.14) (V-ATPase H subunit) (Vacuolar proton pump su ...	0.32	-	cyt	0					452
Q8UW81 UniProt NPD GO	GON2_VERMO	Progonadoliberin-2 precursor (Progonadoliberin II) (Chicken-type II gonadotropin-releasing hormone) ...	0.32	-	exc	0	Secreted protein	extracellular region [ISS]			85
P22393 UniProt NPD GO	PRL_CAMDR	Prolactin (PRL)	0.32	-	nuc	0	Secreted protein				199
P70597 UniProt NPD GO	PE2R1_RAT	Prostaglandin E2 receptor, EP1 subtype (Prostanoid EP1 receptor) (PGE receptor, EP1 subtype)	0.32	-	end	6 *	Membrane; multi-pass membrane protein				405
P13475 UniProt NPD GO	3F_DICDI	Protein 3F precursor (Fragment)	0.32	-	exc	0					215
P78586 UniProt NPD GO	ARG56_CANAL	Protein ARG5,6, mitochondrial precursor [Contains: N-acetyl-gamma-glutamyl-phosphate reductase (EC 1 ...	0.32	-	mit	0	Mitochondrion				857
Q9LUJ3 UniProt NPD GO	Y3268_ARATH	Protein At3g22680	0.32	-	nuc	0				1VK5	163
Q68UT5 UniProt NPD GO	CU045_PANTR	Protein C21orf45 homolog	0.32	-	nuc	0					232
Q91VH6 UniProt NPD GO	CB004_MOUSE	Protein C2orf4 homolog	0.32	-	nuc	0					297
Q6FM20 UniProt NPD GO	CIS1_CANGA	Protein CIS1	0.32	-	cyt	0	Punctate structures (By similarity)				182
Q8IUH2 UniProt NPD GO	CREG2_HUMAN	Protein CREG2 precursor	0.32	-	nuc	0	Secreted protein				290
P35843 UniProt NPD GO	HES1_YEAST	Protein HES1 (Oxysterol-binding protein homolog 5)	0.32	-	nuc	0					434
Q75A44 UniProt NPD GO	LDB17_ASHGO	Protein LDB17	0.32	-	nuc	0	Cytoplasm (By similarity)				361

You are viewing entries 38801 to 38850 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.