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
P46682 UniProt NPD GO	AP3B_YEAST	AP-3 complex subunit beta (Beta-adaptin) (Adapter-related protein complex 3 beta subunit) (Clathrin ...	0.56	-	nuc	0	Component of the coat surrounding the cytoplasmic face of coated vesicles located at the Golgi compl ...				809
P47102 UniProt NPD GO	GEA1_YEAST	ARF guanine-nucleotide exchange factor 1	0.56	-	end	0	Cytoplasm; cytosol. Membrane; peripheral membrane protein. Soluble and partially membrane-bound	Golgi cis cisterna [IDA] Golgi-associated vesicle [IPI]		1RE0	1408
Q5KBP5 UniProt NPD GO	DBP5_CRYNE	ATP-dependent RNA helicase DBP5 (EC 3.6.1.-)	0.56	-	nuc	0	Cytoplasm. Nucleus; nuclear envelope; nuclear pore complex; cytoplasmic side. Nuclear pore complex c ...				546
Q6CX73 UniProt NPD GO	FAL1_KLULA	ATP-dependent RNA helicase FAL1 (EC 3.6.1.-)	0.56	-	cyt	0	Nucleus; nucleolus (By similarity)				398
Q5KDK3 UniProt NPD GO	ROK1_CRYNE	ATP-dependent RNA helicase ROK1 (EC 3.6.1.-)	0.56	+	nuc	0	Nucleus; nucleolus (By similarity)				620
Q4WJE9 UniProt NPD GO	RRP3_ASPFU	ATP-dependent rRNA helicase rrp3 (EC 3.6.1.-)	0.56	-	cyt	0	Nucleus (Probable)				472
Q28XE2 UniProt NPD GO	AN32A_DROPS	Acidic leucine-rich nuclear phosphoprotein 32 family member A	0.56	-	nuc	0	Nucleus. Cytoplasm. Shuttles between nucleus and cytoplasm (By similarity)				241
Q6CSB9 UniProt NPD GO	ARP4_KLULA	Actin-like protein ARP4	0.56	-	nuc	0	Nucleus (By similarity)				520
Q12406 UniProt NPD GO	ARP7_YEAST	Actin-like protein ARP7 (Chromatin structure remodeling complex protein ARP7) (SWI/SNF complex compo ...	0.56	-	nuc	0	Nucleus. Localizes to centromeric and flanking chromatin. Association with these loci is dependent o ...	nucleus [IDA] RSC complex [IDA] SWI/SNF complex [IDA]			477
Q03489 UniProt NPD GO	AGL9_PETHY	Agamous-like MADS-box protein AGL9 homolog (Floral homeotic protein FBP2) (Floral-binding protein 2) ...	0.56	-	nuc	0	Nucleus				241
P55302 UniProt NPD GO	AMRP_MOUSE	Alpha-2-macroglobulin receptor-associated protein precursor (Alpha-2-MRAP) (Low density lipoprotein ...	0.56	-	nuc	0	Endoplasmic reticulum (By similarity). Cytoplasm (By similarity). Cell surface (By similarity). Intr ...				360
O77715 UniProt NPD GO	ADA2B_DIDMA	Alpha-2B adrenergic receptor (Alpha-2B adrenoceptor) (Alpha-2B adrenoreceptor) (Fragment)	0.56	-	end	6 *	Membrane; multi-pass membrane protein				382
Q9QYJ1 UniProt NPD GO	SIA7E_MOUSE	Alpha-N-acetylgalactosaminide alpha-2,6-sialyltransferase 5 (EC 2.4.99.-) (GalNAc alpha-2,6-sialyltr ...	0.56	-	exc	1 *	Golgi apparatus; Golgi membrane; single-pass type II membrane protein				336
P05095 UniProt NPD GO	ACTN_DICDI	Alpha-actinin, non-muscular (F-actin cross linking protein)	0.56	-	cyt	0				1G8X	862
Q9AWA5 UniProt NPD GO	GWD1_SOLTU	Alpha-glucan water dikinase, chloroplast precursor (EC 2.7.9.4) (EC 2.7.13.3) (Starch-related R1 pro ...	0.56	-	cyt	0	Plastid; chloroplast. Starch granules. Binds to starch granules isolated from either illuminated or ...				1464
O13262 UniProt NPD GO	SCNNC_XENLA	Amiloride-sensitive sodium channel beta-2-subunit (Epithelial Na(+) channel beta-2 subunit) (Beta-2 ...	0.56	+	mit	2	Cell membrane; apical cell membrane; multi-pass membrane protein (By similarity). Apical membrane of ...				646
Q8NDH6 UniProt NPD GO	AL2SE_HUMAN	Amyotrophic lateral sclerosis 2 chromosomal region candidate gene 15 protein	0.56	-	nuc	0					482
Q6ZP36 UniProt NPD GO	AL2SF_HUMAN	Amyotrophic lateral sclerosis 2 chromosomal region candidate gene 16 protein	0.56	-	mit	0					381
Q9UJX5 UniProt NPD GO	ANC4_HUMAN	Anaphase-promoting complex subunit 4 (APC4) (Cyclosome subunit 4)	0.56	-	mit	0		anaphase-promoting complex [TAS]	606947		808
P70295 UniProt NPD GO	AUP1_MOUSE	Ancient ubiquitous protein 1 precursor	0.56	-	nuc	1 *					410
Q9BDY7 UniProt NPD GO	ANGP2_PIG	Angiopoietin-2 precursor (ANG-2)	0.56	-	exc	0	Secreted protein				496
Q9Z0S8 UniProt NPD GO	B3A2_CAVPO	Anion exchange protein 2 (Non-erythroid band 3-like protein) (AE2 anion exchanger) (Solute carrier f ...	0.56	-	end	11	Membrane; multi-pass membrane protein				1238
P23347 UniProt NPD GO	B3A2_RAT	Anion exchange protein 2 (Non-erythroid band 3-like protein) (AE2 anion exchanger) (Solute carrier f ...	0.56	-	end	11	Membrane; multi-pass membrane protein	integral to membrane [IEP]			1234
Q8VHS5 UniProt NPD GO	ASB16_MOUSE	Ankyrin repeat and SOCS box protein 16 (ASB-16)	0.56	-	cyt	0					453
Q3UX43 UniProt NPD GO	AN13C_MOUSE	Ankyrin repeat domain-containing protein 13C	0.56	-	nuc	0					541
Q1LZH7 UniProt NPD GO	ANR25_BOVIN	Ankyrin repeat domain-containing protein 25	0.56	-	nuc	0					858
Q6AI12 UniProt NPD GO	ANR40_HUMAN	Ankyrin repeat domain-containing protein 40	0.56	-	nuc	0					368
Q2M3V2 UniProt NPD GO	ANR43_HUMAN	Ankyrin repeat domain-containing protein 43	0.56	-	nuc	0					332
P04272 UniProt NPD GO	ANXA2_BOVIN	Annexin A2 (Annexin II) (Lipocortin II) (Calpactin I heavy chain) (Chromobindin-8) (p36) (Protein I) ...	0.56	-	nuc	0	Secreted protein; extracellular space; extracellular matrix; basement membrane. In the lamina beneat ...				338
P27006 UniProt NPD GO	ANX2A_XENLA	Annexin A2-A (Annexin II type I) (Lipocortin II) (Calpactin I heavy chain)	0.56	-	nuc	0	Secreted protein; extracellular space; extracellular matrix; basement membrane. In the lamina beneat ...				339
Q12092 UniProt NPD GO	ATG29_YEAST	Autophagy-related protein 29	0.56	-	nuc	0	Pre-autophagosomal and other perivacuolar punctate structures	cytoplasm [IDA]			213
P25918 UniProt NPD GO	CD19_MOUSE	B-lymphocyte antigen CD19 precursor (Differentiation antigen CD19)	0.56	+	end	1	Membrane; single-pass type I membrane protein	external side of plasma membrane [IDA]			547
O59739 UniProt NPD GO	BAG1B_SCHPO	BAG-family molecular chaperone regulator 1B (BAG-1B)	0.56	-	nuc	0					206
Q9Y2F9 UniProt NPD GO	BTBD3_HUMAN	BTB/POZ domain-containing protein 3	0.56	+	cyt	0					522
Q80ZG6 UniProt NPD GO	BBC3_RAT	Bcl-2-binding component 3 (p53 up-regulated modulator of apoptosis)	0.56	-	nuc	0	Mitochondrion. Localized to the mitochondria in order to induce cytochrome c release (By similarity) ...				193
O35417 UniProt NPD GO	PDYN_MOUSE	Beta-neoendorphin-dynorphin precursor (Proenkephalin B) (Preprodynorphin) [Contains: Alpha-neoendorp ...	0.56	-	exc	0	Secreted protein				248
Q60478 UniProt NPD GO	PDYN_CAVPO	Beta-neoendorphin-dynorphin precursor (Proenkephalin B) (Preprodynorphin) [Contains: Beta-neoendorph ...	0.56	-	exc	0	Secreted protein				245
P01138 UniProt NPD GO	NGF_HUMAN	Beta-nerve growth factor precursor (Beta-NGF)	0.56	-	exc	0	Secreted protein		162030	1WWW	241
Q9N2F1 UniProt NPD GO	NGF_PANTR	Beta-nerve growth factor precursor (Beta-NGF)	0.56	-	exc	0	Secreted protein				241
P22003 UniProt NPD GO	BMP5_HUMAN	Bone morphogenetic protein 5 precursor (BMP-5)	0.56	-	nuc	0	Secreted protein		112265		454
Q03484 UniProt NPD GO	CEBPD_RAT	CCAAT/enhancer-binding protein delta (C/EBP delta) (Transcription factor CELF)	0.56	+	nuc	0	Nucleus	nucleus [IDA]			268
Q9ULM6 UniProt NPD GO	CNOT6_HUMAN	CCR4-NOT transcription complex subunit 6 (EC 3.1.-.-) (Cytoplasmic deadenylase) (Carbon catabolite r ...	0.56	-	nuc	0	Cytoplasm (Probable). Nucleus (Probable)		608951		557
Q8K3P5 UniProt NPD GO	CNOT6_MOUSE	CCR4-NOT transcription complex subunit 6 (EC 3.1.-.-) (Cytoplasmic deadenylase) (Carbon catabolite r ...	0.56	-	nuc	0	Cytoplasm (Probable). Nucleus (Probable)				557
Q6AXU9 UniProt NPD GO	CNOT6_RAT	CCR4-NOT transcription complex subunit 6 (EC 3.1.-.-) (Cytoplasmic deadenylase) (Carbon catabolite r ...	0.56	-	nuc	0	Cytoplasm (Probable). Nucleus (Probable)				557
Q05078 UniProt NPD GO	CD44_HORSE	CD44 antigen precursor (Phagocytic glycoprotein I) (PGP-1) (HUTCH-I) (Extracellular matrix receptor- ...	0.56	-	end	1	Membrane; single-pass type I membrane protein				359
Q6IQT4 UniProt NPD GO	CSN2_BRARE	COP9 signalosome complex subunit 2 (Signalosome subunit 2)	0.56	-	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity)				443
P61201 UniProt NPD GO	CSN2_HUMAN	COP9 signalosome complex subunit 2 (Signalosome subunit 2) (SGN2) (JAB1-containing signalosome subun ...	0.56	-	nuc	0	Cytoplasm. Nucleus	cytoplasm [IDA] signalosome complex [IDA]	604508		443
P61202 UniProt NPD GO	CSN2_MOUSE	COP9 signalosome complex subunit 2 (Signalosome subunit 2) (SGN2) (JAB1-containing signalosome subun ...	0.56	-	nuc	0	Cytoplasm. Nucleus	cytoplasm [ISS] nucleus [IDA] signalosome complex [ISS]			443
P61203 UniProt NPD GO	CSN2_RAT	COP9 signalosome complex subunit 2 (Signalosome subunit 2) (SGN2) (JAB1-containing signalosome subun ...	0.56	-	nuc	0	Cytoplasm. Nucleus				443
Q6FT36 UniProt NPD GO	CSN5_CANGA	COP9 signalosome complex subunit 5 (EC 3.4.-.-)	0.56	-	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity)				465

You are viewing entries 21201 to 21250 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.