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
Q58CZ2 UniProt NPD GO	PCMD2_BOVIN	Protein-L-isoaspartate O-methyltransferase domain-containing protein 2	0.53	+	cyt	0	Cytoplasm (By similarity)				361
Q8WP22 UniProt NPD GO	ABEC4_MACFA	Putative C->U-editing enzyme APOBEC-4 (EC 3.5.4.-) (Apolipoprotein B mRNA-editing enzyme catalytic p ...	0.53	-	nuc	0					363
P51376 UniProt NPD GO	RPOZ_PORPU	Putative DNA-directed RNA polymerase omega chain (EC 2.7.7.6) (PEP) (Plastid-encoded RNA polymerase ...	0.53	-	nuc	0	Plastid; chloroplast				75
Q06374 UniProt NPD GO	CG1_COLGL	Putative G1/S-specific cyclin	0.53	-	nuc	0					245
Q9VEW2 UniProt NPD GO	SERFL_DROME	Putative SERF-like protein	0.53	-	nuc	0					60
Q9LQE8 UniProt NPD GO	ARFN_ARATH	Putative auxin response factor 14	0.53	-	nuc	0	Nucleus				605
Q9LQE3 UniProt NPD GO	ARFO_ARATH	Putative auxin response factor 15	0.53	-	nuc	0	Nucleus				593
P42839 UniProt NPD GO	YN61_YEAST	Putative cation exchanger YNL321W	0.53	-	end	13	Membrane; multi-pass membrane protein (Potential)				908
P18664 UniProt NPD GO	RK23_SPIOL	Putative chloroplast 50S ribosomal protein L23	0.53	-	nuc	0	Plastid; chloroplast				90
Q9V564 UniProt NPD GO	COG6_DROME	Putative conserved oligomeric Golgi complex component 6	0.53	-	cyt	0	Golgi apparatus (By similarity)				630
Q9SL29 UniProt NPD GO	CNG15_ARATH	Putative cyclic nucleotide-gated ion channel 15 (Cyclic nucleotide-and calmodulin-regulated ion chan ...	0.53	+	end	5	Cell membrane; multi-pass membrane protein (Potential)				678
Q6L3X3 UniProt NPD GO	R1B8_SOLDE	Putative late blight resistance protein homolog R1B-8	0.53	-	mit	0	Cytoplasm (By similarity)				1202
Q7XV13 UniProt NPD GO	LOX5_ORYSA	Putative lipoxygenase 5 (EC 1.13.11.12)	0.53	+	cyt	0					899
Q9LFP5 UniProt NPD GO	PEL19_ARATH	Putative pectate lyase 19 precursor (EC 4.2.2.2)	0.53	-	mit	0					472
Q9M1K2 UniProt NPD GO	PI5K4_ARATH	Putative phosphatidylinositol-4-phosphate 5-kinase 4 (EC 2.7.1.68) (AtPIP5K4) (1-phosphatidylinosito ...	0.53	-	nuc	0					779
O14753 UniProt NPD GO	OVOL1_HUMAN	Putative transcription factor Ovo-like 1 (hOvo1)	0.53	-	nuc	0	Nucleus (By similarity)	nucleus [NAS]	602313		267
Q9WTJ2 UniProt NPD GO	OVOL1_MOUSE	Putative transcription factor Ovo-like 1 (mOvo1) (mOvo1a)	0.53	-	nuc	0	Nucleus	nucleus [IDA]			267
P38899 UniProt NPD GO	YH18_YEAST	Putative uncharacterized protein YHR218W	0.53	-	nuc	0					603
Q9QZR0 UniProt NPD GO	RNF25_MOUSE	RING finger protein 25 (EC 6.3.2.-) (RING finger protein AO7)	0.53	-	nuc	0					456
Q4PER6 UniProt NPD GO	REXO4_USTMA	RNA exonuclease 4 (EC 3.1.-.-)	0.53	-	nuc	0	Nucleus (By similarity)				375
Q03290 UniProt NPD GO	TFB3_YEAST	RNA polymerase II transcription factor B subunit 3 (RNA polymerase II transcription factor B p38 sub ...	0.53	-	nuc	0	Nucleus (By similarity)	nucleotide-excision repair factor 3 complex [TAS] transcription factor TFIIH complex [IDA]			321
P26374 UniProt NPD GO	RAE2_HUMAN	Rab proteins geranylgeranyltransferase component A 2 (Rab escort protein 2) (REP-2) (Choroideraemia- ...	0.53	-	nuc	0			118825		656
Q93538 UniProt NPD GO	RB3GP_CAEEL	Rab3 GTPase-activating protein catalytic subunit (Rab3 GTPase-activating protein 1)	0.53	-	nuc	0	Cytoplasm (Probable)	soluble fraction [ISS]			915
Q9CT10 UniProt NPD GO	RANB3_MOUSE	Ran-binding protein 3 (RanBP3)	0.53	+	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity)				491
Q8GZ43 UniProt NPD GO	YZR3_ARATH	RanBP2-type zinc-finger protein At1g67325	0.53	-	nuc	0					288
Q99P51 UniProt NPD GO	RASF3_MOUSE	Ras association domain-containing protein 3	0.53	-	nuc	0	Cytoplasm. Localized to microtubules in vascular endothelial cells (By similarity)				232
Q60673 UniProt NPD GO	PTPRN_MOUSE	Receptor-type tyrosine-protein phosphatase-like N precursor (R-PTP-N) (PTP IA-2)	0.53	-	end	1	Membrane; single-pass type I membrane protein	membrane fraction [TAS] plasma membrane [TAS]			979
P13770 UniProt NPD GO	FLP_ZYGFE	Recombinase Flp protein	0.53	-	cyt	0					372
Q08116 UniProt NPD GO	RGS1_HUMAN	Regulator of G-protein signaling 1 (RGS1) (Early response protein 1R20) (B-cell activation protein B ...	0.53	+	nuc	0		plasma membrane [TAS]	600323	2BV1	196
Q9VYS3 UniProt NPD GO	RENT1_DROME	Regulator of nonsense transcripts 1 homolog	0.53	-	nuc	0	Cytoplasm (Potential)				1180
P91124 UniProt NPD GO	RIC19_CAEEL	Resistance to inhibitors of cholinesterase protein 19 (ICA1 homolog)	0.53	-	nuc	0	Cytoplasm	cytoplasm [IDA]			430
O35600 UniProt NPD GO	ABCA4_MOUSE	Retinal-specific ATP-binding cassette transporter (ATP-binding cassette sub-family A member 4) (RIM ...	0.53	+	end	11 *	Membrane; multi-pass membrane protein (By similarity)	integral to plasma membrane [TAS]			2310
Q99969 UniProt NPD GO	TIG2_HUMAN	Retinoic acid receptor responder protein 2 precursor (Tazarotene-induced gene 2 protein) (RAR-respon ...	0.53	+	exc	0	Secreted protein (Potential)		601973		163
Q03279 UniProt NPD GO	PO21_SCICO	Retrovirus-related Pol polyprotein from type-1 retrotransposable element R2 (Retrovirus-related Pol ...	0.53	-	nuc	0					869
Q03274 UniProt NPD GO	PO22_POPJA	Retrovirus-related Pol polyprotein from type-1 retrotransposable element R2 (Retrovirus-related Pol ...	0.53	+	nuc	0					711
P34096 UniProt NPD GO	RNAS4_HUMAN	Ribonuclease 4 precursor (EC 3.1.27.-) (RNase 4)	0.53	-	exc	1 *	Secreted protein		601030	2RNF	147
Q5NVS4 UniProt NPD GO	RNAS4_PONPY	Ribonuclease 4 precursor (EC 3.1.27.-) (RNase 4)	0.53	-	exc	1 *	Secreted protein (By similarity)				147
Q02926 UniProt NPD GO	RB97D_DROME	Ribonucleoprotein RB97D	0.53	-	nuc	0					471
Q9M1X0 UniProt NPD GO	RRFC_ARATH	Ribosome recycling factor, chloroplast precursor (Ribosome-releasing factor, chloroplast) (RRF) (CpF ...	0.53	-	nuc	0	Plastid; chloroplast (By similarity)				275
Q01196 UniProt NPD GO	RUNX1_HUMAN	Runt-related transcription factor 1 (Core-binding factor, alpha 2 subunit) (CBF-alpha 2) (Acute myel ...	0.53	-	nuc	0	Nucleus	nucleus [NAS]	151385	1LJM	453
O75170 UniProt NPD GO	SAPS2_HUMAN	SAPS domain family member 2	0.53	-	nuc	0					927
P37839 UniProt NPD GO	SOX1_PLEWA	SOX-1 protein (Fragment)	0.53	-	nuc	0	Nucleus (Probable)				56
P04109 UniProt NPD GO	SPE1A_STRPU	SPEC 1A protein	0.53	-	nuc	0					152
P40637 UniProt NPD GO	AES1_ALLMI	SRY-related protein AES1 (Fragment)	0.53	-	nuc	0	Nucleus (Potential)				72
P40639 UniProt NPD GO	AES4_ALLMI	SRY-related protein AES4 (Fragment)	0.53	-	nuc	0	Nucleus (Potential)				72
Q9D666 UniProt NPD GO	UN84A_MOUSE	Sad1/unc-84 protein-like 1 (Unc-84 homolog A)	0.53	-	mit	2	Nucleus; nuclear membrane; multi-pass membrane protein. Membrane; perinuclear region; multi-pass mem ...	cytoplasm [IDA] nucleus [IDA]			913
Q5U7N1 UniProt NPD GO	SEMG2_HYLLA	Semenogelin-2 precursor (Semenogelin II) (SGII)	0.53	-	nuc	0	Secreted protein (By similarity)				582
O60165 UniProt NPD GO	SPN7_SCHPO	Septin homolog spn7	0.53	-	nuc	0	Cortices of developing spores				428
Q07964 UniProt NPD GO	SRYA_DROPS	Serendipity locus protein alpha	0.53	+	nuc	0	Cytoplasm (By similarity). Cell membrane; peripheral membrane protein; cytoplasmic side (By similari ...				551
Q8LF36 UniProt NPD GO	2A5T_ARATH	Serine/threonine protein phosphatase 2A 57 kDa regulatory subunit B' theta isoform (PP2A, B' subunit ...	0.53	-	nuc	0					492

You are viewing entries 23351 to 23400 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.