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
O46480 UniProt NPD GO	NDEL1_RABIT	Nuclear distribution protein nudE-like 1 (Protein Nudel)	0.55	-	nuc	0	Cytoplasm (By similarity). Centrosome (By similarity). Spindle (By similarity). Localizes to the int ...				345
Q78PB6 UniProt NPD GO	NDEL1_RAT	Nuclear distribution protein nudE-like 1 (Protein Nudel)	0.55	-	nuc	0	Localizes to the mitotic spindle and to the to the microtubules of the manchette in elongated sperma ...				345
Q9ERR1 UniProt NPD GO	NDEL1_MOUSE	Nuclear distribution protein nudE-like 1 (Protein Nudel) (Protein mNudE-like) (mNudE-L)	0.55	-	nuc	0	Cytoplasm. Centrosome. Spindle. Localizes to the interphase centrosome and the mitotic spindle. Loca ...	axon [IDA] centrosome [IDA] microtubule associated complex [IDA]			345
Q8VYK4 UniProt NPD GO	NFYB8_ARATH	Nuclear transcription factor Y subunit B-8 (AtNF-YB-8)	0.55	-	nuc	0	Nucleus (Probable)				173
Q74ZK6 UniProt NPD GO	NOG1_ASHGO	Nucleolar GTP-binding protein 1	0.55	-	nuc	0	Nucleus; nucleolus (By similarity)				642
Q6TGJ8 UniProt NPD GO	NOG2_CRYGA	Nucleolar GTP-binding protein 2	0.55	-	cyt	0	Nucleus; nucleolus (By similarity)				731
Q6C036 UniProt NPD GO	NOG2_YARLI	Nucleolar GTP-binding protein 2	0.55	-	cyt	0	Nucleus; nucleolus (By similarity)				509
Q7S2L7 UniProt NPD GO	NOP12_NEUCR	Nucleolar protein 12	0.55	-	nuc	0	Nucleus; nucleolus (By similarity)				594
Q8BTS4 UniProt NPD GO	NUP54_MOUSE	Nucleoporin p54 (54 kDa nucleoporin)	0.55	-	cyt	0	Nucleus; nuclear envelope; nuclear pore complex; cytoplasmic side; nucleoplasmic side. Biased toward ...				510
P33034 UniProt NPD GO	TOG3A_AGEAP	Omega-agatoxin-3A (Omega-agatoxin IIIA) (Omega-Aga-IIIA)	0.55	-	nuc	0	Secreted protein				76
Q5M7B7 UniProt NPD GO	OPTN_XENLA	Optineurin	0.55	-	nuc	0	Cytoplasm (By similarity)				532
P20393 UniProt NPD GO	NR1D1_HUMAN	Orphan nuclear receptor NR1D1 (V-erbA-related protein EAR-1) (Rev-erbA-alpha)	0.55	-	nuc	0	Nucleus (Potential)	nucleus [TAS]	602408	1HLZ	614
P13056 UniProt NPD GO	TR2_HUMAN	Orphan nuclear receptor TR2 (Testicular receptor 2)	0.55	-	nuc	0	Nucleus (Potential)		601529		483
P49116 UniProt NPD GO	TR4_HUMAN	Orphan nuclear receptor TR4 (Orphan nuclear receptor TAK1)	0.55	-	nuc	0	Nucleus (Probable)		601426		596
P49117 UniProt NPD GO	TR4_MOUSE	Orphan nuclear receptor TR4 (Orphan nuclear receptor TAK1)	0.55	-	nuc	0	Nucleus (Probable)				596
Q8CIE2 UniProt NPD GO	ZIMP7_MOUSE	PIAS-like protein Zimp7	0.55	-	nuc	0	Nucleus (By similarity)				920
O60813 UniProt NPD GO	PRA11_HUMAN	PRAME family member 11 (Fragment)	0.55	-	nuc	0					435
O14603 UniProt NPD GO	PRY_HUMAN	PTPN13-like protein, Y-linked (Testis-specific PTP-BL-related Y protein)	0.55	-	nuc	0			400019		147
Q9M0R2 UniProt NPD GO	PATL5_ARATH	Patellin-5	0.55	-	nuc	0	Membrane; peripheral membrane protein (By similarity). Mainly membrane-associated. Cytoplasm (By sim ...				668
P78723 UniProt NPD GO	PEX14_PICAN	Peroxisomal membrane protein PER10 (Peroxin-14)	0.55	-	nuc	0	Peroxisome; peroxisomal membrane; peripheral membrane protein; cytoplasmic side				351
Q96V77 UniProt NPD GO	PALY_USTMA	Phenylalanine ammonia-lyase (EC 4.3.1.5)	0.55	-	cyt	0	Cytoplasm (Probable)				724
O00459 UniProt NPD GO	P85B_HUMAN	Phosphatidylinositol 3-kinase regulatory subunit beta (PI3-kinase p85-subunit beta) (PtdIns-3-kinase ...	0.55	-	nuc	0		phosphoinositide 3-kinase complex [ISS]	603157		728
P70458 UniProt NPD GO	IPSP_MOUSE	Plasma serine protease inhibitor precursor (PCI) (Protein C inhibitor) (Serpin A5) (Plasminogen acti ...	0.55	-	mit	0	Secreted protein				405
P12919 UniProt NPD GO	PDGFB_FELCA	Platelet-derived growth factor B chain precursor (PDGF B-chain) (Platelet-derived growth factor beta ...	0.55	-	exc	0				1OWU	245
Q96AC1 UniProt NPD GO	PKHC1_HUMAN	Pleckstrin homology domain-containing family C member 1 (Kindlin-2) (Mitogen-inducible gene 2 protei ...	0.55	+	cyt	0	Cytoplasm; cell cortex. Within actin stress fibers at cell-ECM focal adhesion sites	stress fiber [NAS]	607746		680
Q9H0J9 UniProt NPD GO	PRP12_HUMAN	Poly [ADP-ribose] polymerase 12 (EC 2.4.2.30) (PARP-12) (Zinc finger CCCH domain-containing protein ...	0.55	+	nuc	0	Nucleus (Probable)				701
Q02096 UniProt NPD GO	PGLR_PERAE	Polygalacturonase precursor (EC 3.2.1.15) (PG) (Pectinase)	0.55	-	mit	0	Secreted protein				462
Q06215 UniProt NPD GO	PPO_VICFA	Polyphenol oxidase A1, chloroplast precursor (EC 1.10.3.1) (PPO) (Catechol oxidase)	0.55	-	mit	0	Plastid; chloroplast; chloroplast thylakoid lumen				606
P42837 UniProt NPD GO	FIG4_YEAST	Polyphosphoinositide phosphatase (EC 3.1.3.-) (Phosphatidylinositol 3,5-bisphosphate 5-phosphatase) ...	0.55	-	cyt	0	Vacuole; vacuolar membrane; peripheral membrane protein. Localized to the limiting membrane of the v ...	extrinsic to membrane [IDA] vacuolar membrane (sensu Fungi) [IDA]			879
Q61762 UniProt NPD GO	KCNA5_MOUSE	Potassium voltage-gated channel subfamily A member 5 (Voltage-gated potassium channel subunit Kv1.5) ...	0.55	-	end	3	Membrane; multi-pass membrane protein				602
Q9JKA9 UniProt NPD GO	HCN2_RAT	Potassium/sodium hyperpolarization-activated cyclic nucleotide-gated channel 2	0.55	-	end	3	Membrane; multi-pass membrane protein				863
P23394 UniProt NPD GO	PRP28_YEAST	Pre-mRNA-splicing ATP-dependent RNA helicase PRP28 (EC 3.6.1.-) (Helicase CA8)	0.55	-	nuc	0	Cytoplasm. Nucleus	snRNP U5 [IPI] spliceosome complex [TAS]			588
O35181 UniProt NPD GO	NRG3_MOUSE	Pro-neuregulin-3, membrane-bound isoform precursor (Pro-NRG3) [Contains: Neuregulin-3 (NRG-3)]	0.55	-	nuc	2	Pro-neuregulin-3, membrane-bound isoform: Cell membrane; single-pass type I membrane protein (By sim ...				713
O61470 UniProt NPD GO	PSD3_ANOGA	Probable 26S proteasome non-ATPase regulatory subunit 3 (26S proteasome subunit S3) (Diphenol oxidas ...	0.55	-	cyt	0					496
Q9JJY4 UniProt NPD GO	DDX20_MOUSE	Probable ATP-dependent RNA helicase DDX20 (EC 3.6.1.-) (DEAD box protein 20) (DEAD box protein DP 10 ...	0.55	-	nuc	0	Cytoplasm. Nucleus. Localized in subnuclear structures next to coiled bodies, called Gemini of Cajal ...	transcriptional repressor complex [IDA]			825
Q4R4T6 UniProt NPD GO	DDX28_MACFA	Probable ATP-dependent RNA helicase DDX28 (EC 3.6.1.-) (Mitochondrial DEAD box protein 28)	0.55	-	mit	0	Nucleus (By similarity). Mitochondrion (By similarity). Transported between these two compartments. ...				546
Q9H0S4 UniProt NPD GO	DDX47_HUMAN	Probable ATP-dependent RNA helicase DDX47 (EC 3.6.1.-) (DEAD box protein 47)	0.55	+	cyt	0	Nucleus; nucleolus				455
Q9CWX9 UniProt NPD GO	DDX47_MOUSE	Probable ATP-dependent RNA helicase DDX47 (EC 3.6.1.-) (DEAD box protein 47)	0.55	+	cyt	0	Nucleus; nucleolus (By similarity)				455
P38735 UniProt NPD GO	YHD5_YEAST	Probable ATP-dependent permease YHL035C	0.55	-	end	14 *	Membrane; multi-pass membrane protein (Potential)	mitochondrion [IDA]			1592
O03685 UniProt NPD GO	RPOP_GELSP	Probable DNA-directed RNA polymerase (EC 2.7.7.6)	0.55	-	cyt	0					831
Q99680 UniProt NPD GO	GPR22_HUMAN	Probable G-protein coupled receptor 22	0.55	-	end	7 *	Membrane; multi-pass membrane protein	integral to plasma membrane [TAS]	601910		433
P60838 UniProt NPD GO	DRL1_ARATH	Probable disease resistance protein At1g12280	0.55	-	cyt	0					894
P20262 UniProt NPD GO	GLRK_RANBE	Probable glutamate receptor precursor (Kainate-binding protein) (KBP)	0.55	-	end	3	Membrane; multi-pass membrane protein				487
Q19426 UniProt NPD GO	GCS1_CAEEL	Probable mannosyl-oligosaccharide glucosidase (EC 3.2.1.106) (Processing A-glucosidase I)	0.55	-	nuc	1 *	Endoplasmic reticulum; endoplasmic reticulum membrane; single-pass type II membrane protein (Potenti ...				781
P46592 UniProt NPD GO	MNT2_CANAL	Probable mannosyltransferase MNT2 (EC 2.4.1.131)	0.55	-	mit	1 *					461
Q43802 UniProt NPD GO	SPS_ORYSA	Probable sucrose-phosphate synthase (EC 2.4.1.14) (UDP-glucose-fructose-phosphate glucosyltransferas ...	0.55	+	cyt	0					1084
P06186 UniProt NPD GO	PRGR_RABIT	Progesterone receptor (PR)	0.55	+	nuc	0	Nucleus				930
Q9W6C5 UniProt NPD GO	PDC6I_XENLA	Programmed cell death 6-interacting protein (Signal transduction protein Xp95)	0.55	-	nuc	0					867
Q8L3U3 UniProt NPD GO	BBM1_BRANA	Protein BABY BOOM 1 (BnBBM1)	0.55	-	nuc	0	Nucleus (Probable)				579
Q5R590 UniProt NPD GO	BEX4_PONPY	Protein BEX4 (Brain-expressed X-linked protein 4 homolog) (BEX1-like 1)	0.55	-	nuc	0	Nucleus (By similarity). Cytoplasm (By similarity)				119

You are viewing entries 22101 to 22150 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.