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
Q6JUT9 UniProt NPD GO	ATG25_PICAN	Autophagy-related protein 25 (Peroxisome degradation deficient protein 4)	0.77	-	nuc	0	Cytoplasm (Probable)				384
Q9H165 UniProt NPD GO	BC11A_HUMAN	B-cell lymphoma/leukemia 11A (B-cell CLL/lymphoma 11A) (COUP-TF-interacting protein 1) (Ecotropic vi ...	0.77	+	nuc	0	Cytoplasm. Nucleus	cytoplasm [NAS] nucleus [NAS]	606557		835
Q9I969 UniProt NPD GO	TXLNB_CHICK	Beta-taxilin (Muscle-derived protein 77)	0.77	-	nuc	0	Cytoplasm				676
P23117 UniProt NPD GO	BIND_LYTVA	Bindin precursor	0.77	+	exc	0	Acrosome; acrosomal lumen				462
Q810B3 UniProt NPD GO	BSH_MOUSE	Brain-specific homeobox protein homolog	0.77	+	nuc	0	Nucleus (By similarity)	nucleus [ISS]			232
O75815 UniProt NPD GO	BCAR3_HUMAN	Breast cancer anti-estrogen resistance protein 3 (SH2 domain-containing protein 3B) (Novel SH2-conta ...	0.77	-	nuc	0			604704		825
Q9DCA5 UniProt NPD GO	BXDC2_MOUSE	Brix domain-containing protein 2 (Ribosome biogenesis protein Brix)	0.77	+	nuc	0	Nucleus; nucleolus (By similarity)				276
P25337 UniProt NPD GO	BUD31_YEAST	Bud site selection protein BUD31	0.77	-	nuc	0	Nucleus (Potential)	nucleus [IDA]			157
P41698 UniProt NPD GO	BUD8_YEAST	Bud site selection protein BUD8	0.77	-	nuc	2	Cell membrane; multi-pass membrane protein. Found at presumptive bud sites, bud tips, and the distal ...	bud tip [IDA] incipient bud site [IDA]			603
Q9QZT0 UniProt NPD GO	CUZD1_RAT	CUB and zona pellucida-like domain-containing protein 1 precursor (Uterus/ovary-specific protein 44) ...	0.77	-	nuc	1	Membrane; single-pass type I membrane protein (Potential). Associated with zymogen granule membranes ...	integral to membrane [NAS] zymogen granule membrane [ISS]			607
O13798 UniProt NPD GO	CID16_SCHPO	Caffeine-induced protein 16	0.77	-	nuc	0					1202
P23292 UniProt NPD GO	KC12_YEAST	Casein kinase I homolog 2 (EC 2.7.11.1)	0.77	-	mit	0	Cell membrane; lipid-anchor	bud neck [IDA] mating projection [IDA] plasma membrane [IDA]			546
P40230 UniProt NPD GO	RAG8_KLULA	Casein kinase I homolog RAG8 (EC 2.7.11.1)	0.77	-	nuc	0					536
Q9BX69 UniProt NPD GO	CARD6_HUMAN	Caspase recruitment domain-containing protein 6	0.77	-	nuc	0					1037
P30999 UniProt NPD GO	CTND1_MOUSE	Catenin delta-1 (p120 catenin) (p120(ctn)) (Cadherin-associated Src substrate) (CAS) (p120(cas))	0.77	+	nuc	0	Cytoplasm. Nucleus	lamellipodium [IDA] membrane fraction [IDA]			911
Q9BWU1 UniProt NPD GO	CD2L6_HUMAN	Cell division cycle 2-like protein kinase 6 (EC 2.7.11.22) (CDC2-related protein kinase 6) (Death-pr ...	0.77	-	nuc	0					502
P33520 UniProt NPD GO	RES1_SCHPO	Cell division cycle-related protein res1/sct1	0.77	-	nuc	0		MBF transcription complex [TAS]			637
Q10719 UniProt NPD GO	FUS1_SCHPO	Cell fusion protein fus1	0.77	-	nuc	0	Cytoplasm	cytoplasm [IDA] mating projection [IDA]			1372
O93379 UniProt NPD GO	P53_ICTPU	Cellular tumor antigen p53 (Tumor suppressor p53)	0.77	+	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity)				376
P10361 UniProt NPD GO	P53_RAT	Cellular tumor antigen p53 (Tumor suppressor p53)	0.77	+	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity)	cytoplasm [ISS] mitochondrion [ISS] nucleolus [ISS] nucleus [ISS]			391
Q9TTA1 UniProt NPD GO	P53_TUPGB	Cellular tumor antigen p53 (Tumor suppressor p53)	0.77	+	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity)	cytoplasm [ISS] mitochondrion [ISS] nucleolus [ISS] nucleus [ISS]			393
Q96P50 UniProt NPD GO	CENB5_HUMAN	Centaurin-beta 5 (Cnt-b5)	0.77	-	nuc	0					759
P40969 UniProt NPD GO	CBF3B_YEAST	Centromere DNA-binding protein complex CBF3 subunit B (Centromere protein 3)	0.77	-	mit	0	Nucleus (Probable)	CBF3 complex [TAS] condensed nuclear chromosome kinetochore [IDA]			608
P49379 UniProt NPD GO	CBF1_KLULA	Centromere-binding protein 1 (CBP-1) (Centromere-binding factor 1) (Centromere promoter factor 1)	0.77	+	nuc	0	Nucleus				359
Q9BYV8 UniProt NPD GO	CEP41_HUMAN	Centrosomal protein of 41 kDa (Cep41 protein) (Testis-specific gene A14 protein)	0.77	-	nuc	0	Centrosome	centrosome [IDA]			373
Q8NHQ1 UniProt NPD GO	CEP70_HUMAN	Centrosomal protein of 70 kDa (Cep70 protein) (p10-binding protein)	0.77	-	nuc	0	Centrosome				597
Q6NU11 UniProt NPD GO	CHM6B_XENLA	Charged multivesicular body protein 6-B (Chromatin-modifying protein 6-B)	0.77	-	nuc	0	Intracytoplasmic membrane; lipid-anchor (By similarity)				199
Q9BBT3 UniProt NPD GO	RR14_LOTJA	Chloroplast 30S ribosomal protein S14	0.77	-	nuc	0	Plastid; chloroplast				100
P56807 UniProt NPD GO	RR18_ARATH	Chloroplast 30S ribosomal protein S18	0.77	-	nuc	0	Plastid; chloroplast; chloroplast stroma				101
Q6EW31 UniProt NPD GO	RR18_NYMAL	Chloroplast 30S ribosomal protein S18	0.77	-	nuc	0	Plastid; chloroplast				101
P26565 UniProt NPD GO	RK20_CHLRE	Chloroplast 50S ribosomal protein L20	0.77	-	mit	0	Plastid; chloroplast				111
P28803 UniProt NPD GO	RK20_SPIOL	Chloroplast 50S ribosomal protein L20	0.77	-	mit	0	Plastid; chloroplast				127
Q6B8T5 UniProt NPD GO	RK35_GRATL	Chloroplast 50S ribosomal protein L35	0.77	+	mit	0	Plastid; chloroplast				66
O55229 UniProt NPD GO	CHKB_MOUSE	Choline/ethanolamine kinase [Includes: Choline kinase beta (EC 2.7.1.32) (CK); Ethanolamine kinase ( ...	0.77	-	cyt	0					393
Q6BI21 UniProt NPD GO	EAF6_DEBHA	Chromatin modification-related protein EAF6	0.77	-	nuc	0	Nucleus (By similarity)				170
Q6C5V7 UniProt NPD GO	YNG2_YARLI	Chromatin modification-related protein YNG2 (ING1 homolog 2)	0.77	-	nuc	0	Nucleus (By similarity)				283
P26339 UniProt NPD GO	CMGA_MOUSE	Chromogranin A precursor (CgA) [Contains: Pancreastatin; Beta-granin; WE-14]	0.77	-	exc	0	Neuroendocrine and endocrine secretory granules				463
P22058 UniProt NPD GO	CPD1_DROME	Chromosomal protein D1	0.77	-	nuc	0	Nucleus				355
Q8IYE1 UniProt NPD GO	CCD13_HUMAN	Coiled-coil domain-containing protein 13	0.77	-	nuc	0					715
Q63ZM9 UniProt NPD GO	CCD16_XENLA	Coiled-coil domain-containing protein 16	0.77	-	nuc	0	Nucleus (By similarity). Excluded from nucleolus (By similarity)				356
P81269 UniProt NPD GO	ATF1_MOUSE	Cyclic AMP-dependent transcription factor ATF-1 (Activating transcription factor 1) (TCR-ATF1)	0.77	+	nuc	0	Nucleus	transcription factor complex [IDA]			269
Q6P788 UniProt NPD GO	ATF5_RAT	Cyclic AMP-dependent transcription factor ATF-5 (Activating transcription factor 5) (Transcription f ...	0.77	+	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity)				281
O70191 UniProt NPD GO	ATF5_MOUSE	Cyclic AMP-dependent transcription factor ATF-5 (Activating transcription factor 5-alpha/beta) (Tran ...	0.77	+	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity)	transcription factor complex [IDA]			283
P13569 UniProt NPD GO	CFTR_HUMAN	Cystic fibrosis transmembrane conductance regulator (CFTR) (cAMP-dependent chloride channel) (ATP-bi ...	0.77	-	end	11	Membrane; multi-pass membrane protein	apical plasma membrane [NAS] basolateral plasma membrane [NAS]	219700	2BBT	1480
Q2IBE4 UniProt NPD GO	CFTR_PONPY	Cystic fibrosis transmembrane conductance regulator (CFTR) (cAMP-dependent chloride channel) (ATP-bi ...	0.77	-	end	11	Membrane; multi-pass membrane protein				1480
P35734 UniProt NPD GO	ASK1_YEAST	DASH complex subunit ASK1 (Outer kinetochore protein ASK1) (Associated with spindles and kinetochore ...	0.77	-	nuc	0	Nucleus. Associates with the mitotic spindle and the kinetochore	DASH complex [IDA] spindle [IDA]			292
Q9SW44 UniProt NPD GO	RH16_ARATH	DEAD-box ATP-dependent RNA helicase 16 (EC 3.6.1.-)	0.77	+	nuc	0					626
P93008 UniProt NPD GO	RH21_ARATH	DEAD-box ATP-dependent RNA helicase 21 (EC 3.6.1.-)	0.77	+	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity)				733
Q92466 UniProt NPD GO	DDB2_HUMAN	DNA damage-binding protein 2 (Damage-specific DNA-binding protein 2) (DDB p48 subunit) (DDBb) (UV-da ...	0.77	-	nuc	0	Nucleus		600811		427
P43351 UniProt NPD GO	RAD52_HUMAN	DNA repair protein RAD52 homolog	0.77	-	nuc	0	Nucleus (Potential)	nucleus [TAS]	600392	1KN0	418

You are viewing entries 10251 to 10300 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.