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
O44248 UniProt NPD GO	RL5_ANOGA	60S ribosomal protein L5	0.79	-	nuc	0					325
P19949 UniProt NPD GO	RL5_RABIT	60S ribosomal protein L5 (Fragments)	0.79	-	nuc	0	Cytoplasm				101
O42596 UniProt NPD GO	ADA22_XENLA	ADAM 22 precursor (A disintegrin and metalloproteinase domain 22) (Metalloprotease-disintegrin MDC11 ...	0.79	-	exc	1	Membrane; single-pass type I membrane protein				935
O75077 UniProt NPD GO	ADA23_HUMAN	ADAM 23 precursor (A disintegrin and metalloproteinase domain 23) (Metalloproteinase-like, disintegr ...	0.79	-	exc	1	Cell membrane; single-pass type I membrane protein (Potential). Isoform Gamma: Secreted protein	integral to plasma membrane [TAS]	603710		832
P53366 UniProt NPD GO	ADML_PIG	ADM precursor [Contains: Adrenomedullin (AM); Proadrenomedullin N-20 terminal peptide (ProAM-N20) (P ...	0.79	-	nuc	0	Secreted protein				188
Q91X58 UniProt NPD GO	ZFN2B_MOUSE	AN1-type zinc finger protein 2B	0.79	-	nuc	0					257
Q9USY4 UniProt NPD GO	ABP2_SCHPO	ARS-binding protein 2	0.79	-	nuc	0	Nucleus				527
O93257 UniProt NPD GO	KU70_CHICK	ATP-dependent DNA helicase 2 subunit 1 (EC 3.6.1.-) (ATP-dependent DNA helicase II 70 kDa subunit) ( ...	0.79	+	cyt	0	Nucleus (By similarity)				632
Q4WV71 UniProt NPD GO	DBP7_ASPFU	ATP-dependent RNA helicase dbp7 (EC 3.6.1.-)	0.79	-	nuc	0	Nucleus; nucleolus (By similarity)				758
O60080 UniProt NPD GO	DBP9_SCHPO	ATP-dependent RNA helicase dbp9 (EC 3.6.1.-)	0.79	+	nuc	0	Nucleus; nucleolus (By similarity)				595
Q5AZY1 UniProt NPD GO	MRH4_EMENI	ATP-dependent RNA helicase mrh4, mitochondrial precursor (EC 3.6.1.-)	0.79	+	mit	0	Mitochondrion (By similarity)				630
Q91XU0 UniProt NPD GO	WRIP1_MOUSE	ATPase WRNIP1 (Werner helicase-interacting protein 1)	0.79	+	nuc	0	Nucleus. Colocalizes with WRN in granular structures in the nucleus	nucleus [IDA]			660
Q6CIF3 UniProt NPD GO	AEP3_KLULA	ATPase expression protein 3	0.79	-	nuc	0	Mitochondrion; mitochondrial inner membrane; peripheral membrane protein; matrix side (By similarity ...				593
P33737 UniProt NPD GO	MS2A_DROSI	Accessory gland-specific peptide 26Aa precursor (Male accessory gland secretory protein 355A)	0.79	-	exc	0	Secreted protein; extracellular space				255
Q15650 UniProt NPD GO	TRIP4_HUMAN	Activating signal cointegrator 1 (ASC-1) (Thyroid receptor-interacting protein 4) (TRIP-4)	0.79	-	nuc	0	Nucleus. Cytoplasm. Cytoplasmic under conditions of serum deprivation	cytoplasm [IDA] nucleus [IDA]	604501		581
Q52C47 UniProt NPD GO	SPB1_MAGGR	AdoMet-dependent rRNA methyltransferase SPB1 (EC 2.1.1.-) (2'-O-ribose RNA methyltransferase) (S-ade ...	0.79	-	nuc	0	Nucleus; nucleolus (By similarity)				884
Q38847 UniProt NPD GO	AGL15_ARATH	Agamous-like MADS-box protein AGL15	0.79	-	nuc	0	Nucleus				268
Q865F0 UniProt NPD GO	ASIP_FELCA	Agouti signaling protein precursor (ASP) (Agouti switch protein)	0.79	-	exc	0	Secreted protein (By similarity)				135
Q65CL1 UniProt NPD GO	CTN3_MOUSE	Alpha-3 catenin (Alpha T-catenin) (Cadherin-associated protein)	0.79	-	nuc	0	Localizes to intercalated disks of cardiomyocytes and in peritubular myoid cells of testis, and colo ...	fascia adherens [ISS] lamellipodium [IDA]			895
P35609 UniProt NPD GO	ACTN2_HUMAN	Alpha-actinin-2 (Alpha actinin skeletal muscle isoform 2) (F-actin cross linking protein)	0.79	-	cyt	0	Colocalizes with MYOZ1 and FLNC at the Z-lines of skeletal muscle	actin filament [TAS] cytoskeleton [NAS]	102573	1QUU	894
Q7ZYD9 UniProt NPD GO	A13CB_XENLA	Ankyrin repeat domain-containing protein 13C-B	0.79	-	nuc	0					513
P13526 UniProt NPD GO	ARLC_MAIZE	Anthocyanin regulatory Lc protein	0.79	+	nuc	0					610
P13027 UniProt NPD GO	ARRS_MAIZE	Anthocyanin regulatory R-S protein	0.79	+	nuc	0					612
P07249 UniProt NPD GO	ARGR1_YEAST	Arginine metabolism regulation protein I	0.79	-	nuc	1	Nucleus	nucleus [IDA]			177
Q99700 UniProt NPD GO	ATX2_HUMAN	Ataxin-2 (Spinocerebellar ataxia type 2 protein) (Trinucleotide repeat-containing gene 13 protein)	0.79	-	nuc	0	Cytoplasm (By similarity)	cytoplasm [TAS] nucleus [TAS]	601517		1312
Q9DCJ7 UniProt NPD GO	AKIP_MOUSE	Aurora kinase A-interacting protein (AURKA-interacting protein)	0.79	+	mit	0	Nucleus	anaphase-promoting complex [ISS]			200
Q5ABA6 UniProt NPD GO	ATG18_CANAL	Autophagy-related protein 18	0.79	-	nuc	0	Membrane-associated. Peripheral membrane protein of pre-autophagosomal structure (PAS) and vacuole ( ...				558
Q12142 UniProt NPD GO	ATG9_YEAST	Autophagy-related protein 9 (Cytoplasm to vacuole targeting protein 7)	0.79	-	end	6	Membrane; multi-pass membrane protein. Pre-autophagosomal and other perivacuolar punctate structures ...	cytoplasm [IDA] integral to membrane [IDA] membrane fraction [IDA]			997
Q9QYE3 UniProt NPD GO	BC11A_MOUSE	B-cell lymphoma/leukemia 11A (B-cell CLL/lymphoma 11A) (COUP-TF-interacting protein 1) (Ecotropic vi ...	0.79	+	nuc	0	Cytoplasm. Nucleus	nucleus [IDA]			773
Q9NSY1 UniProt NPD GO	BMP2K_HUMAN	BMP-2-inducible protein kinase (EC 2.7.11.1) (BIKe)	0.79	-	nuc	0	Nucleus				1161
Q9Y0A7 UniProt NPD GO	AMOS_DROME	Basic helix-loop-helix transcription factor amos (Reduced olfactory organs protein) (Rough eye prote ...	0.79	+	nuc	0	Nucleus (Probable)				198
Q9QYB8 UniProt NPD GO	ADDB_MOUSE	Beta-adducin (Erythrocyte adducin subunit beta) (Add97)	0.79	+	nuc	0		membrane [IDA]			724
P14599 UniProt NPD GO	A4_DROME	Beta-amyloid-like protein precursor	0.79	-	cyt	1	Membrane; single-pass type I membrane protein	extracellular region [IDA] plasma membrane [IDA]			887
Q9CWL8 UniProt NPD GO	CTBL1_MOUSE	Beta-catenin-like protein 1 (Nuclear-associated protein) (NAP)	0.79	-	cyt	0	Nucleus (By similarity)				563
P12643 UniProt NPD GO	BMP2_HUMAN	Bone morphogenetic protein 2 precursor (BMP-2) (BMP-2A)	0.79	+	nuc	1 *	Secreted protein		112261	3BMP	396
P30884 UniProt NPD GO	BMP2B_XENLA	Bone morphogenetic protein 2-B precursor (BMP-2-II)	0.79	+	nuc	0	Secreted protein (By similarity)				398
Q9H0E9 UniProt NPD GO	BRD8_HUMAN	Bromodomain-containing protein 8 (p120) (Skeletal muscle abundant protein) (Thyroid hormone receptor ...	0.79	+	nuc	0	Nucleus	nucleus [NAS]	602848		1235
Q99LJ0 UniProt NPD GO	CT2NL_MOUSE	CTTNBP2 N-terminal-like protein	0.79	-	exc	0					638
Q8C078 UniProt NPD GO	KKCC2_MOUSE	Calcium/calmodulin-dependent protein kinase kinase 2 (EC 2.7.11.17) (Calcium/calmodulin-dependent pr ...	0.79	-	nuc	0	Cytoplasm (By similarity)	intracellular [ISS]			588
Q7T3S3 UniProt NPD GO	CHSTB_BRARE	Carbohydrate sulfotransferase 11 (EC 2.8.2.5) (Chondroitin 4-O-sulfotransferase 1) (Chondroitin 4-su ...	0.79	-	nuc	1 *	Golgi apparatus; Golgi membrane; single-pass type II membrane protein (By similarity)				352
Q8AXM9 UniProt NPD GO	CTND1_XENLA	Catenin delta-1 (p120 catenin) (p120(ctn)) (Xp120(ctn))	0.79	+	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity)				859
O36006 UniProt NPD GO	P53_MARMO	Cellular tumor antigen p53 (Tumor suppressor p53)	0.79	+	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity)	cytoplasm [ISS] mitochondrion [ISS] nucleolus [ISS] nucleus [ISS]			391
P02340 UniProt NPD GO	P53_MOUSE	Cellular tumor antigen p53 (Tumor suppressor p53)	0.79	+	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity)	cytoplasm [ISS] cytosol [IDA] mitochondrion [ISS] nucleolus [ISS] nucleus [ISS] replication fork [IDA]		2GEQ	390
P25035 UniProt NPD GO	P53_ONCMY	Cellular tumor antigen p53 (Tumor suppressor p53)	0.79	+	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity)				396
P82963 UniProt NPD GO	CHAO_TRICA	Chaoptin (Photoreceptor cell-specific membrane protein) (Fragment)	0.79	+	nuc	0	Cell membrane; extracellular side (By similarity). Extracellular surface of R-cell plasma membrane ( ...				782
P05638 UniProt NPD GO	RR14_PEA	Chloroplast 30S ribosomal protein S14	0.79	+	nuc	0	Plastid; chloroplast				100
Q7YJV4 UniProt NPD GO	RR18_CALFE	Chloroplast 30S ribosomal protein S18	0.79	-	nuc	0	Plastid; chloroplast				100
Q70XY3 UniProt NPD GO	RK20_AMBTC	Chloroplast 50S ribosomal protein L20	0.79	-	nuc	0	Plastid; chloroplast				119
Q9BBR0 UniProt NPD GO	RK20_LOTJA	Chloroplast 50S ribosomal protein L20	0.79	+	mit	0	Plastid; chloroplast				120
Q9TKX4 UniProt NPD GO	RK20_NEPOL	Chloroplast 50S ribosomal protein L20	0.79	-	nuc	0	Plastid; chloroplast				113

You are viewing entries 9251 to 9300 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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