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
Q3SXZ3 UniProt NPD GO	ZF718_HUMAN	Zinc finger protein 718	0.62	-	nuc	0	Nucleus (Potential)				478
Q9SSE5 UniProt NPD GO	COL9_ARATH	Zinc finger protein CONSTANS-LIKE 9	0.62	-	nuc	0	Nucleus (Potential)				372
Q5R9M9 UniProt NPD GO	S39A6_PONPY	Zinc transporter SLC39A6 precursor (Solute carrier family 39 member 6)	0.62	+	end	6	Cell membrane; multi-pass membrane protein (By similarity)				743
Q64595 UniProt NPD GO	KGP2_RAT	cGMP-dependent protein kinase 2 (EC 2.7.11.12) (CGK 2) (cGKII) (Type II cGMP-dependent protein kinas ...	0.62	-	cyt	0					762
Q5KM87 UniProt NPD GO	RNA14_CRYNE	mRNA 3'-end processing protein RNA14	0.62	-	nuc	0	Nucleus (By similarity). Cytoplasm (By similarity). Nucleus and/or cytoplasm (By similarity)				1064
Q9NPI6 UniProt NPD GO	DCP1A_HUMAN	mRNA decapping enzyme 1A (EC 3.-.-.-) (Transcription factor SMIF) (Smad4-interacting transcriptional ...	0.62	-	nuc	0	Cytoplasm. Predominantly cytoplasmic, in processing bodies (PB). Nucleus. Nuclear, after TGFB1 treat ...		607010		582
P53179 UniProt NPD GO	PALF_YEAST	pH-response regulator protein palF/RIM8 (Regulator of IME2 protein 8)	0.62	-	nuc	0					542
Q52E66 UniProt NPD GO	PALH_MAGGR	pH-response regulator protein palH/RIM21	0.62	-	nuc	4	Cell membrane; multi-pass membrane protein (By similarity)				829
Q753Y2 UniProt NPD GO	PACC_ASHGO	pH-response transcription factor pacC/RIM101	0.62	-	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity)				432
Q9MUR3 UniProt NPD GO	TILS_MESVI	tRNA(Ile)-lysidine synthase (EC 6.3.4.-) (tRNA(Ile)-lysidine synthetase) (tRNA(Ile)-2-lysyl-cytidine ...	0.62	-	cyt	0	Plastid; chloroplast				310
Q02158 UniProt NPD GO	PIPA_DICDI	1-phosphatidylinositol-4,5-bisphosphate phosphodiesterase (EC 3.1.4.11) (PLC) (Phosphoinositide phos ...	0.61	+	nuc	0					801
Q9XFM4 UniProt NPD GO	13S3_FAGES	13S globulin seed storage protein 3 precursor (Legumin-like protein 3) (Allergen Fag e 1) [Contains: ...	0.61	-	nuc	0					538
P12694 UniProt NPD GO	ODBA_HUMAN	2-oxoisovalerate dehydrogenase alpha subunit, mitochondrial precursor (EC 1.2.4.4) (Branched-chain a ...	0.61	-	mit	0	Mitochondrion; mitochondrial matrix	alpha-ketoglutarate dehydrogenase complex (... [TAS] mitochondrion [TAS]	248600	2BFF	445
P08090 UniProt NPD GO	MEI3_SCHPO	21 kDa protein inducing meiosis and sporulation	0.61	-	mit	0					148
Q5R8M4 UniProt NPD GO	RM19_PONPY	39S ribosomal protein L19, mitochondrial precursor (L19mt) (MRP-L19)	0.61	-	nuc	0	Mitochondrion (By similarity)				292
Q9DCI9 UniProt NPD GO	RM32_MOUSE	39S ribosomal protein L32, mitochondrial precursor (L32mt) (MRP-L32) (Heart expressed gene 1 protein ...	0.61	-	exc	0	Mitochondrion	mitochondrial inner membrane [ISS] mitochondrial large ribosomal subunit [IDA]			187
Q9XEG7 UniProt NPD GO	RS3A_TORRU	40S ribosomal protein S3a	0.61	-	nuc	0					247
Q4UFS9 UniProt NPD GO	RS8_THEAN	40S ribosomal protein S8	0.61	+	nuc	0					184
Q6FL25 UniProt NPD GO	RT09_CANGA	40S ribosomal protein S9, mitochondrial precursor	0.61	-	nuc	0	Mitochondrion (Potential)				288
Q01240 UniProt NPD GO	NF60_LOLPE	60 kDa neurofilament protein (NF60)	0.61	-	nuc	0					511
P41129 UniProt NPD GO	RL132_BRANA	60S ribosomal protein L13-2 (Cold-induced protein C24B)	0.61	-	mit	0					206
Q9SVR0 UniProt NPD GO	R13A3_ARATH	60S ribosomal protein L13a-3	0.61	+	cyt	0					206
P52818 UniProt NPD GO	RL15_ANOGA	60S ribosomal protein L15 (RL10)	0.61	-	nuc	0					203
O23515 UniProt NPD GO	RL151_ARATH	60S ribosomal protein L15-1	0.61	-	nuc	0					204
Q8VYF1 UniProt NPD GO	RL152_ARATH	60S ribosomal protein L15-2	0.61	-	nuc	0					204
O48557 UniProt NPD GO	RL17_MAIZE	60S ribosomal protein L17	0.61	-	nuc	0					171
Q95WA0 UniProt NPD GO	RL26_LITLI	60S ribosomal protein L26	0.61	-	nuc	0					144
Q69CJ9 UniProt NPD GO	RL35_OPHHA	60S ribosomal protein L35	0.61	-	nuc	0					122
O80929 UniProt NPD GO	RL361_ARATH	60S ribosomal protein L36-1	0.61	-	nuc	0					113
P36578 UniProt NPD GO	RL4_HUMAN	60S ribosomal protein L4 (L1)	0.61	+	nuc	0		cytosolic large ribosomal subunit (sensu Eu... [TAS]	180479		426
O88845 UniProt NPD GO	AKA10_MOUSE	A kinase anchor protein 10, mitochondrial precursor (Protein kinase A-anchoring protein 10) (PRKA10) ...	0.61	-	nuc	0	Mitochondrion. Membrane. Cytoplasm. Predominantly mitochondrial but also membrane associated and cyt ...	mitochondrion [IDA]			662
Q9UNA0 UniProt NPD GO	ATS5_HUMAN	ADAMTS-5 precursor (EC 3.4.24.-) (A disintegrin and metalloproteinase with thrombospondin motifs 5) ...	0.61	-	nuc	0	Secreted protein; extracellular space; extracellular matrix (By similarity)	extracellular matrix (sensu Metazoa) [TAS]	605007		930
O43747 UniProt NPD GO	AP1G1_HUMAN	AP-1 complex subunit gamma-1 (Adapter-related protein complex 1 gamma-1 subunit) (Gamma-adaptin) (Ad ...	0.61	-	nuc	0	Component of the coat surrounding the cytoplasmic face of coated vesicles located at the Golgi compl ...	clathrin-coated vesicle [IDA] cytoplasm [TAS] Golgi apparatus [IDA] membrane coat adaptor complex [TAS]	603533	1IU1	821
Q12028 UniProt NPD GO	AP1G1_YEAST	AP-1 complex subunit gamma-1 (Gamma(1)-adaptin) (Clathrin assembly protein large gamma-1 chain) (Cla ...	0.61	-	nuc	0	Cytoplasm (By similarity). Golgi apparatus; Golgi membrane; peripheral membrane protein; cytoplasmic ...	AP-1 adaptor complex [IPI]			832
P48084 UniProt NPD GO	ATPF_CYAPA	ATP synthase B chain (EC 3.6.3.14) (Subunit I)	0.61	-	nuc	1 *	Plastid; cyanelle; cyanelle thylakoid membrane; single-pass membrane protein (By similarity)				185
Q12039 UniProt NPD GO	HMI1_YEAST	ATP-dependent DNA helicase HMI1, mitochondrial precursor (EC 3.6.1.-)	0.61	-	nuc	0	Mitochondrion; mitochondrial inner membrane; peripheral membrane protein (Probable)	mitochondrial matrix [IDA]			706
Q6CXW0 UniProt NPD GO	DBP8_KLULA	ATP-dependent RNA helicase DBP8 (EC 3.6.1.-)	0.61	-	cyt	0	Nucleus; nucleolus (By similarity)				435
Q06218 UniProt NPD GO	DBP9_YEAST	ATP-dependent RNA helicase DBP9 (EC 3.6.1.-) (DEAD box protein 9)	0.61	-	cyt	0	Nucleus; nucleolus	nucleolus [TAS]			594
Q6FY67 UniProt NPD GO	MAK5_CANGA	ATP-dependent RNA helicase MAK5 (EC 3.6.1.-)	0.61	-	nuc	0	Nucleus; nucleolus (By similarity)				733
Q4WXW1 UniProt NPD GO	DBP8_ASPFU	ATP-dependent RNA helicase dbp8 (EC 3.6.1.-)	0.61	+	nuc	0	Nucleus; nucleolus (By similarity)				526
Q2UFL0 UniProt NPD GO	DBP9_ASPOR	ATP-dependent RNA helicase dbp9 (EC 3.6.1.-)	0.61	-	cyt	0	Nucleus; nucleolus (By similarity)				605
Q5BCI0 UniProt NPD GO	MAK5_EMENI	ATP-dependent RNA helicase mak5 (EC 3.6.1.-)	0.61	-	mit	0	Nucleus; nucleolus (By similarity)				770
Q8NEB7 UniProt NPD GO	ACRBP_HUMAN	Acrosin-binding protein precursor (Proacrosin-binding protein sp32) (Cancer testis antigen OY-TES-1) ...	0.61	-	exc	0	Secreted protein (By similarity). Acrosome (By similarity). Colocalizes with proacrosin in the acros ...		608352		543
O43734 UniProt NPD GO	CIKS_HUMAN	Adapter protein CIKS (Connection to IKK and SAPK/JNK) (TRAF3-interacting protein 2) (Nuclear factor ...	0.61	-	nuc	0			607043		574
P02772 UniProt NPD GO	FETA_MOUSE	Alpha-fetoprotein precursor (Alpha-fetoglobulin) (Alpha-1-fetoprotein)	0.61	-	exc	0	Secreted protein	extracellular space [IDA]			605
Q9R1N2 UniProt NPD GO	SCNNA_CAVPO	Amiloride-sensitive sodium channel subunit alpha (Epithelial Na+ channel subunit alpha) (Alpha ENaC) ...	0.61	-	exc	1	Cell membrane; apical cell membrane; multi-pass membrane protein (By similarity). Apical membrane of ...	integral to membrane [ISS]			682
P50478 UniProt NPD GO	AMPH_CHICK	Amphiphysin	0.61	-	nuc	0	Synaptic vesicle; synaptic vesicle membrane; peripheral membrane protein; cytoplasmic side	soluble fraction [IDA] synaptosome [IDA]			682
Q8N187 UniProt NPD GO	AL2S8_HUMAN	Amyotrophic lateral sclerosis 2 chromosomal region candidate gene 8 protein (Calcium-response factor ...	0.61	-	nuc	0	Nucleus (Potential)		607586		725
Q8VHI4 UniProt NPD GO	AL2S8_MOUSE	Amyotrophic lateral sclerosis 2 chromosomal region candidate gene 8 protein homolog (Calcium-respons ...	0.61	-	nuc	0	Nucleus (Potential)	nucleolus [IDA] nucleoplasm [IDA]			689
Q9Y264 UniProt NPD GO	ANGP4_HUMAN	Angiopoietin-4 precursor (ANG-4) (ANG-3)	0.61	-	nuc	0	Secreted protein (Probable)		603705		503

You are viewing entries 18301 to 18350 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.)

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