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
Q8WXS8 UniProt NPD GO	ATS14_HUMAN	ADAMTS-14 precursor (EC 3.4.24.-) (A disintegrin and metalloproteinase with thrombospondin motifs 14 ...	0.75	-	nuc	0	Secreted protein; extracellular space; extracellular matrix (By similarity)		607506		1223
P35318 UniProt NPD GO	ADML_HUMAN	ADM precursor [Contains: Adrenomedullin (AM); Proadrenomedullin N-20 terminal peptide (ProAM-N20) (P ...	0.75	-	exc	0	Secreted protein	extracellular space [TAS] soluble fraction [TAS]	103275	2FLY	185
P49777 UniProt NPD GO	ABP1_SCHPO	ARS-binding protein 1	0.75	-	nuc	0	Nucleus	condensed nuclear chromosome, pericentric r... [IDA]		1IUF	522
Q26228 UniProt NPD GO	KU70_RHIAP	ATP-dependent DNA helicase 2 subunit 1 (EC 3.6.1.-) (ATP-dependent DNA helicase II 70 kDa subunit) ( ...	0.75	-	nuc	0	Nucleus (By similarity)				600
Q6CK32 UniProt NPD GO	DBP7_KLULA	ATP-dependent RNA helicase DBP7 (EC 3.6.1.-)	0.75	+	nuc	0	Nucleus; nucleolus (By similarity)				740
Q5KPU1 UniProt NPD GO	DBP8_CRYNE	ATP-dependent RNA helicase DBP8 (EC 3.6.1.-)	0.75	-	nuc	0	Nucleus; nucleolus (By similarity)				619
Q6BV94 UniProt NPD GO	MRH4_DEBHA	ATP-dependent RNA helicase MRH4, mitochondrial precursor (EC 3.6.1.-)	0.75	-	nuc	0	Mitochondrion (By similarity)				593
Q4IPI1 UniProt NPD GO	ROK1_GIBZE	ATP-dependent RNA helicase ROK1 (EC 3.6.1.-)	0.75	+	nuc	0	Nucleus; nucleolus (By similarity)				693
Q7S9J4 UniProt NPD GO	DBP10_NEUCR	ATP-dependent RNA helicase dbp-10 (EC 3.6.1.-)	0.75	-	nuc	0	Nucleus; nucleolus (By similarity)				934
P51533 UniProt NPD GO	PDR10_YEAST	ATP-dependent permease PDR10	0.75	-	end	11	Membrane; multi-pass membrane protein (Potential)				1564
Q8BUZ1 UniProt NPD GO	ABRA_MOUSE	Actin-binding Rho-activating protein (Striated muscle activator of Rho-dependent signaling) (STARS)	0.75	-	nuc	0	Localized to the I-band of the sarcomere and to a lesser extent to the sarcomeric structure between ...	actin cytoskeleton [IDA] sarcomere [ISS]			375
Q9QYC0 UniProt NPD GO	ADDA_MOUSE	Alpha-adducin (Erythrocyte adducin subunit alpha)	0.75	+	nuc	0		cytoskeleton [IDA] membrane [IDA]			735
Q99767 UniProt NPD GO	APBA2_HUMAN	Amyloid beta A4 precursor protein-binding family A member 2 (Neuron-specific X11L protein) (Neuronal ...	0.75	-	nuc	0			602712		749
O94556 UniProt NPD GO	APC8_SCHPO	Anaphase-promoting complex subunit 8 (20S cyclosome/APC complex protein apc8) (Cell untimely torn pr ...	0.75	-	cyt	0		anaphase-promoting complex [TAS]			565
Q9XWN6 UniProt NPD GO	ANI3_CAEEL	Anillin-like protein 3	0.75	-	nuc	0					709
P16283 UniProt NPD GO	B3A3_MOUSE	Anion exchange protein 3 (Neuronal band 3-like protein) (Solute carrier family 4 member 3)	0.75	+	end	12	Membrane; multi-pass membrane protein				1227
P48751 UniProt NPD GO	B3A3_HUMAN	Anion exchange protein 3 (Neuronal band 3-like protein) (Solute carrier family 4 member 3) (Cardiac/ ...	0.75	+	end	11	Membrane; multi-pass membrane protein	integral to plasma membrane [TAS] membrane fraction [TAS]	106195		1232
P45951 UniProt NPD GO	ARP_ARATH	Apurinic endonuclease-redox protein (DNA-(apurinic or apyrimidinic site) lyase) (EC 4.2.99.18)	0.75	-	mit	0	Nucleus				536
Q9W689 UniProt NPD GO	ATX3_CHICK	Ataxin-3 (EC 3.4.22.-) (Machado-Joseph disease protein 1 homolog)	0.75	-	nuc	0	Nucleus (By similarity)				363
Q9C5W9 UniProt NPD GO	ARFR_ARATH	Auxin response factor 18	0.75	-	nuc	0	Nucleus				602
P15056 UniProt NPD GO	BRAF1_HUMAN	B-Raf proto-oncogene serine/threonine-protein kinase (EC 2.7.11.1) (p94) (v-Raf murine sarcoma viral ...	0.75	-	nuc	0	Cytoplasm		115150	1UWJ	766
Q9C0K0 UniProt NPD GO	BC11B_HUMAN	B-cell lymphoma/leukemia 11B (B-cell CLL/lymphoma 11B) (Radiation-induced tumor suppressor gene 1 pr ...	0.75	-	nuc	0	Nucleus (Potential)		606558		894
Q5QJC9 UniProt NPD GO	BAG5_RAT	BAG family molecular chaperone regulator 5 (BCL2-associated athanogene 5) (BAG-5)	0.75	-	nuc	0					447
Q9QZH2 UniProt NPD GO	BARD1_RAT	BRCA1-associated RING domain protein 1 (BARD-1)	0.75	-	nuc	0	Nucleus (By similarity). Cytoplasm (By similarity). Can translocate to the cytoplasm (By similarity) ...	BRCA1-BARD1 complex [ISS] cytoplasm [ISS] nucleus [ISS] ubiquitin ligase complex [ISS]			768
P97737 UniProt NPD GO	BMP3B_MOUSE	Bone morphogenetic protein 3b precursor (BMP-3b) (Growth/differentiation factor 10) (GDF-10)	0.75	+	exc	0	Secreted protein				476
P20722 UniProt NPD GO	BMP6_MOUSE	Bone morphogenetic protein 6 precursor (BMP-6) (VG-1-related protein) (VGR-1)	0.75	-	exc	0	Secreted protein (By similarity)				510
Q3ZB98 UniProt NPD GO	BCAS1_RAT	Breast carcinoma amplified sequence 1 homolog (Protein whose mRNA is enriched in synaptosomes 2) (Pm ...	0.75	+	nuc	0	Cytoplasm				555
Q8R3B7 UniProt NPD GO	BRD8_MOUSE	Bromodomain-containing protein 8	0.75	+	nuc	0	Nucleus (By similarity)				951
P25300 UniProt NPD GO	BUD5_YEAST	Bud site selection protein BUD5	0.75	-	cyt	0	Bud neck. Cytoplasm; cell cortex. In haploid cells, forms double rings that encircle the mother-bud ...	bud neck [IDA] incipient bud site [IDA]			642
P51951 UniProt NPD GO	MAT1_XENLA	CDK-activating kinase assembly factor MAT1 (RING finger protein MAT1) (Menage a trois) (CDK7/cyclin ...	0.75	-	nuc	0	Nucleus				309
Q8K389 UniProt NPD GO	CK5P2_MOUSE	CDK5 regulatory subunit-associated protein 2 (CDK5 activator-binding protein C48)	0.75	+	nuc	0	Centrosome (By similarity)	cytoskeleton [ISS]			1822
Q9FG23 UniProt NPD GO	CK5P3_ARATH	CDK5RAP3-like protein	0.75	-	nuc	0					522
P07390 UniProt NPD GO	PT494_YEAST	COX3 mRNA-specific translational activator PET494	0.75	-	mit	1	Mitochondrion; mitochondrial inner membrane; peripheral membrane protein	mitochondrial inner membrane [IDA]			489
Q68ED7 UniProt NPD GO	CRTC1_MOUSE	CREB-regulated transcription coactivator 1 (Mucoepidermoid carcinoma translocated protein 1 homolog) ...	0.75	-	nuc	0	Nucleus (By similarity)	nucleus [ISS]			630
Q9P2B4 UniProt NPD GO	CT2NL_HUMAN	CTTNBP2 N-terminal-like protein	0.75	-	exc	0					639
Q5RDH2 UniProt NPD GO	CT2NL_PONPY	CTTNBP2 N-terminal-like protein	0.75	-	exc	0					639
O23463 UniProt NPD GO	CMTA5_ARATH	Calmodulin-binding transcription activator 5 (Signal-responsive protein 6) (Ethylene-induced calmodu ...	0.75	-	cyt	0	Nucleus				923
Q9LSP8 UniProt NPD GO	CMTA6_ARATH	Calmodulin-binding transcription activator 6 (Signal-responsive protein 3) (Ethylene-induced calmodu ...	0.75	-	nuc	0	Nucleus				838
P27321 UniProt NPD GO	ICAL_RAT	Calpastatin (Calpain inhibitor)	0.75	-	nuc	0					654
Q8WRC7 UniProt NPD GO	CCAP_MANSE	Cardioactive peptide precursor (CCAP) (Crustacean cardioactive peptide) (Cardioacceleratory peptide ...	0.75	-	exc	1 *	Secreted protein	extracellular region [IDA]			125
O14011 UniProt NPD GO	CWF8_SCHPO	Cell cycle control protein cwf8	0.75	-	nuc	0	Nucleus (Probable)	spliceosome complex [TAS] ubiquitin ligase complex [TAS]			488
Q15057 UniProt NPD GO	CENB2_HUMAN	Centaurin-beta 2 (Cnt-b2)	0.75	-	nuc	0			607766		778
Q9QYM8 UniProt NPD GO	CENPH_MOUSE	Centromere protein H (Kinetochore protein CENP-H) (Centromere autoantigen H)	0.75	-	nuc	0	Nucleus. Associates with active centromere-kinetochore complexes throughout the cell cycle. Colocali ...	kinetochore [IDA] nucleus [IDA]			241
Q8K1K4 UniProt NPD GO	CENPI_MOUSE	Centromere protein I (CENP-I) (Follicle-stimulating hormone primary response protein) (FSH primary r ...	0.75	-	nuc	0					746
Q96MT8 UniProt NPD GO	CEP63_HUMAN	Centrosomal protein of 63 kDa (Cep63 protein)	0.75	-	nuc	0	Centrosome	centrosome [IDA]			703
P08004 UniProt NPD GO	CHS1_YEAST	Chitin synthase 1 (EC 2.4.1.16) (Chitin-UDP acetyl-glucosaminyl transferase 1)	0.75	-	end	7	Cell membrane; multi-pass membrane protein	chitosome [IDA] plasma membrane [IDA]			1131
P14180 UniProt NPD GO	CHS2_YEAST	Chitin synthase 2 (EC 2.4.1.16) (Chitin-UDP acetyl-glucosaminyl transferase 2)	0.75	-	end	7	Membrane; multi-pass membrane protein	bud neck [IDA]			963
O13353 UniProt NPD GO	CHS4_MAGGR	Chitin synthase 4 (EC 2.4.1.16) (Chitin-UDP acetyl-glucosaminyl transferase 4) (Class-IV chitin synt ...	0.75	-	end	4	Cell membrane; multi-pass membrane protein				1198
P78611 UniProt NPD GO	CHSD_EMENI	Chitin synthase D (EC 2.4.1.16) (Chitin-UDP acetyl-glucosaminyl transferase D) (Class-V chitin synth ...	0.75	+	end	5	Cell membrane; multi-pass membrane protein				1184
Q9MTK1 UniProt NPD GO	RR18_OENHO	Chloroplast 30S ribosomal protein S18	0.75	-	nuc	0	Plastid; chloroplast				101

You are viewing entries 11201 to 11250 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.