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
Q02206 UniProt NPD GO	RSC4_YEAST	Chromatin structure remodeling complex protein RSC4 (Remodel the structure of chromatin complex subu ...	0.79	-	nuc	0	Nucleus. Localizes to centromeric and flanking chromatin. Association with these loci is dependent o ...	RSC complex [IDA]			625
Q8BMK0 UniProt NPD GO	CCD21_MOUSE	Coiled-coil domain-containing protein 21	0.79	-	nuc	0					761
Q8IWP9 UniProt NPD GO	CC28A_HUMAN	Coiled-coil domain-containing protein 28A (CCRL1AP)	0.79	-	nuc	0					274
Q9D6J3 UniProt NPD GO	CCD94_MOUSE	Coiled-coil domain-containing protein 94	0.79	-	nuc	0					314
P61134 UniProt NPD GO	CO6_PANTR	Complement component C6 precursor	0.79	-	mit	0	Secreted protein				934
Q15021 UniProt NPD GO	CND1_HUMAN	Condensin complex subunit 1 (Chromosome condensation-related SMC-associated protein 1) (Chromosome-a ...	0.79	-	nuc	0	Nucleus. Cytoplasm. In interphase cells, the majority of the condensin complex is found in the cytop ...	condensed chromosome [IDA] condensin core heterodimer [NAS] cytoplasm [NAS] nucleus [NAS]			1401
Q9XSK0 UniProt NPD GO	CRX_BOVIN	Cone-rod homeobox protein	0.79	-	nuc	0	Nucleus (By similarity)				299
P11115 UniProt NPD GO	CPC1_NEUCR	Cross-pathway control protein 1	0.79	-	nuc	0	Nucleus				270
Q5B8L2 UniProt NPD GO	MUS81_EMENI	Crossover junction endonuclease mus81 (EC 3.1.22.-)	0.79	-	nuc	0	Nucleus (By similarity)				677
P14809 UniProt NPD GO	RK20_CYAPA	Cyanelle 50S ribosomal protein L20	0.79	-	nuc	0	Plastid; cyanelle				113
Q60765 UniProt NPD GO	ATF3_MOUSE	Cyclic AMP-dependent transcription factor ATF-3 (Activating transcription factor 3) (Transcription f ...	0.79	+	nuc	0	Nucleus	transcription factor complex [IC]			181
P03874 UniProt NPD GO	CBP2_YEAST	Cytochrome B pre-mRNA-processing protein 2	0.79	-	mit	0	Mitochondrion	mitochondrion [IDA]			630
Q6CTH8 UniProt NPD GO	ASK1_KLULA	DASH complex subunit ASK1 (Outer kinetochore protein ASK1) (Associated with spindles and kinetochore ...	0.79	-	nuc	0	Nucleus (By similarity). Associates with the mitotic spindle and the kinetochore (By similarity)				218
Q5RE62 UniProt NPD GO	DJBP_PONPY	DJ-1-binding protein	0.79	-	nuc	0	Nucleus (By similarity)				1013
P97386 UniProt NPD GO	DNL3_MOUSE	DNA ligase 3 (EC 6.5.1.1) (DNA ligase III) (Polydeoxyribonucleotide synthase [ATP] 3)	0.79	-	nuc	0	Nucleus				1015
Q5RKI3 UniProt NPD GO	DPOLL_RAT	DNA polymerase lambda (EC 2.7.7.7) (EC 4.2.99.-) (Pol Lambda)	0.79	-	nuc	0	Nucleus (By similarity)				573
P30261 UniProt NPD GO	DPOD3_SCHPO	DNA polymerase subunit delta 3 (Cell division control protein 27)	0.79	+	nuc	0	Nucleus (By similarity)	delta DNA polymerase complex [TAS]			372
Q9QZD4 UniProt NPD GO	ERCC4_MOUSE	DNA repair endonuclease XPF (EC 3.1.-.-) (DNA excision repair protein ERCC-4)	0.79	-	cyt	0	Nucleus (By similarity)				906
Q09683 UniProt NPD GO	RAD32_SCHPO	DNA repair protein rad32	0.79	+	nuc	0	Nucleus	Mre11 complex [TAS]			649
P24279 UniProt NPD GO	MCM3_YEAST	DNA replication licensing factor MCM3 (Minichromosome maintenance protein 3)	0.79	+	nuc	0	Nucleus	cytoplasm [IDA] MCM complex [IDA] nucleus [IDA] pre-replicative complex [IDA]			971
P33992 UniProt NPD GO	MCM5_HUMAN	DNA replication licensing factor MCM5 (CDC46 homolog) (P1-CDC46)	0.79	-	cyt	0	Nucleus	nucleus [TAS]	602696		734
O46374 UniProt NPD GO	TOP2A_PIG	DNA topoisomerase 2-alpha (EC 5.99.1.3) (DNA topoisomerase II, alpha isozyme)	0.79	+	nuc	0					1533
P41516 UniProt NPD GO	TOP2A_RAT	DNA topoisomerase 2-alpha (EC 5.99.1.3) (DNA topoisomerase II, alpha isozyme)	0.79	+	nuc	0	Nucleus	nucleus [IDA]			1526
Q68G58 UniProt NPD GO	APEX2_MOUSE	DNA-(apurinic or apyrimidinic site) lyase 2 (EC 4.2.99.18) (Apurinic-apyrimidinic endonuclease 2) (A ...	0.79	-	nuc	0	Nucleus (Probable). Mitochondrion (Probable). Co-localizated partly with PCNA in nuclear foci	mitochondrial inner membrane [IDA] nucleus [IDA]			516
P29775 UniProt NPD GO	ETS4_DROME	DNA-binding protein D-ETS-4	0.79	+	nuc	0	Nucleus				518
Q24312 UniProt NPD GO	EWG_DROME	DNA-binding protein Ewg (Protein erect wing)	0.79	-	nuc	0	Nucleus. Not in nucleolus	nucleus [IDA]			733
P24928 UniProt NPD GO	RPB1_HUMAN	DNA-directed RNA polymerase II largest subunit (EC 2.7.7.6) (RPB1)	0.79	-	nuc	0	Nucleus	DNA-directed RNA polymerase II, core complex [TAS] nucleus [NAS]	180660		1970
P08775 UniProt NPD GO	RPB1_MOUSE	DNA-directed RNA polymerase II largest subunit (EC 2.7.7.6) (RPB1)	0.79	-	nuc	0	Nucleus	nucleus [ISS]			1970
Q85BW1 UniProt NPD GO	RPOB_ANTFO	DNA-directed RNA polymerase beta chain (EC 2.7.7.6) (PEP) (Plastid-encoded RNA polymerase subunit be ...	0.79	-	mit	0	Plastid; chloroplast				1071
Q20EX1 UniProt NPD GO	RPOB_OLTVI	DNA-directed RNA polymerase beta chain (EC 2.7.7.6) (PEP) (Plastid-encoded RNA polymerase subunit be ...	0.79	-	nuc	0	Plastid; chloroplast				1416
Q589B8 UniProt NPD GO	RPOC2_SILLA	DNA-directed RNA polymerase beta'' chain (EC 2.7.7.6) (PEP) (Plastid-encoded RNA polymerase beta'' s ...	0.79	-	cyt	0	Plastid; chloroplast				1373
Q9NYF0 UniProt NPD GO	DACT1_HUMAN	Dapper homolog 1 (hDPR1) (Heptacellular carcinoma novel gene 3 protein)	0.79	-	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity)		607861		836
Q96JH7 UniProt NPD GO	VCIP1_HUMAN	Deubiquitinating protein VCIP135 (EC 3.4.22.-) (Valosin-containing protein p97/p47 complex-interacti ...	0.79	-	nuc	0	Endoplasmic reticulum (By similarity). Golgi apparatus; Golgi stack (By similarity). Associated with ...				1222
Q8TDY4 UniProt NPD GO	DDFL1_HUMAN	Development and differentiation-enhancing factor-like 1 (Protein up-regulated in liver cancer 1)	0.79	-	nuc	0	Cytoplasm			2B0O	903
Q811T9 UniProt NPD GO	DISC1_MOUSE	Disrupted in schizophrenia 1 homolog	0.79	+	nuc	0	Localizes to neurites (By similarity). Cytoplasm. Localizes to punctate cytoplasmic foci which overl ...				852
Q60829 UniProt NPD GO	IPPD_MOUSE	Dopamine- and cAMP-regulated neuronal phosphoprotein (DARPP-32)	0.79	-	nuc	0	Cytoplasm	cytoplasm [TAS]			194
P25723 UniProt NPD GO	TLD_DROME	Dorsal-ventral patterning protein tolloid precursor (EC 3.4.24.-)	0.79	-	mit	1 *					1067
Q9ESN1 UniProt NPD GO	DOC2G_MOUSE	Double C2-like domain-containing protein gamma (Doc2-gamma)	0.79	+	nuc	0					387
Q8CJ67 UniProt NPD GO	STAU2_MOUSE	Double-stranded RNA-binding protein Staufen homolog 2	0.79	-	nuc	0	Cytoplasm. Nucleus. Nucleus; nucleolus. Shuttles between the nucleolus, nucleus and the cytoplasm. N ...			1UHZ	570
O14733 UniProt NPD GO	MP2K7_HUMAN	Dual specificity mitogen-activated protein kinase kinase 7 (EC 2.7.12.2) (MAP kinase kinase 7) (MAPK ...	0.79	-	nuc	0			603014		419
Q6PCJ1 UniProt NPD GO	DYNA_XENLA	Dynactin-1	0.79	-	nuc	0	Cytoplasm (By similarity)				1232
Q9LQ55 UniProt NPD GO	DRP2B_ARATH	Dynamin-2B (EC 3.6.5.5) (Dynamin-related protein 2B) (Dynamin-like protein 3)	0.79	-	nuc	0					920
P37276 UniProt NPD GO	DYHC_DROME	Dynein heavy chain, cytosolic (DYHC)	0.79	-	cyt	0	Cytoplasm	fusome [TAS] microtubule associated complex [IDA] ring canal (sensu Insecta) [TAS]			4639
Q16960 UniProt NPD GO	DYI3_ANTCR	Dynein intermediate chain 3, ciliary	0.79	-	nuc	0					597
P84060 UniProt NPD GO	DTNB_RAT	Dystrobrevin beta (Beta-dystrobrevin) (DTN-B)	0.79	-	nuc	0	Cytoplasm (By similarity)				654
O70585 UniProt NPD GO	DTNB_MOUSE	Dystrobrevin beta (Beta-dystrobrevin) (DTN-B) (MDTN-B)	0.79	-	nuc	0	Cytoplasm	cytoplasm [IDA] synapse [IDA]			700
P49881 UniProt NPD GO	ECR_BOMMO	Ecdysone receptor (Ecdysteroid receptor) (20-hydroxy-ecdysone receptor) (20E receptor) (EcRH)	0.79	-	nuc	0	Nucleus				606
Q02884 UniProt NPD GO	ELP4_YEAST	Elongator complex protein 4 (Gamma-toxin target 7) (HAT-associated protein 1)	0.79	-	nuc	0	Cytoplasm. Nucleus	cytoplasm [IDA] transcription elongation factor complex [IDA]			456
Q9NRM1 UniProt NPD GO	ENAM_HUMAN	Enamelin precursor	0.79	-	nuc	0	Secreted protein; extracellular space; extracellular matrix	extracellular matrix (sensu Metazoa) [NAS]	608563		1142
Q867D0 UniProt NPD GO	EDN2_HORSE	Endothelin-2 precursor (ET-2) (Preproendothelin-2) (PPET2)	0.79	-	exc	0	Secreted protein				178

You are viewing entries 9301 to 9350 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.