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
P33477 UniProt NPD GO	ANX11_RABIT	Annexin A11 (Annexin XI) (Calcyclin-associated annexin 50) (CAP-50)	0.37	-	nuc	0	Nucleus; nucleoplasm (By similarity). Found throughout the nucleoplasm at interphase and at the mito ...	nuclear envelope [ISS] nucleoplasm [ISS]			503
P08132 UniProt NPD GO	ANXA4_PIG	Annexin A4 (Annexin IV) (Lipocortin IV) (Endonexin I) (Chromobindin-4) (Protein II) (P32.5) (Placent ...	0.37	-	cyt	0					318
P09525 UniProt NPD GO	ANXA4_HUMAN	Annexin A4 (Annexin IV) (Lipocortin IV) (Endonexin I) (Chromobindin-4) (Protein II) (P32.5) (Placent ...	0.37	-	cyt	0		cytoplasm [TAS]	106491		318
P48037 UniProt NPD GO	ANXA6_RAT	Annexin A6 (Annexin VI) (Lipocortin VI) (P68) (P70) (Protein III) (Chromobindin-20) (67 kDa calelect ...	0.37	-	cyt	0	Stress fibers	apical plasma membrane [IDA] cytoplasm [IDA]			672
P83142 UniProt NPD GO	AFP2S_MALPA	Antifungal protein 2 small subunit (CW-2) (Fragment)	0.37	-		0					16
Q06602 UniProt NPD GO	APD73_APIME	Apidaecins type 73 precursor [Contains: Apidaecin; Apidaecin-1B (Apidaecin IB); Apidaecin-1A (Apidae ...	0.37	-	nuc	0	Secreted protein				283
P02647 UniProt NPD GO	APOA1_HUMAN	Apolipoprotein A-I precursor (Apo-AI) (ApoA-I) [Contains: Apolipoprotein A-I(1-242)]	0.37	-	exc	0	Secreted protein	extracellular region [NAS] extracellular space [NAS]	105200	2A01	267
O57523 UniProt NPD GO	APA11_ONCMY	Apolipoprotein A-I-1 precursor (Apo-AI-1) (ApoA-I-1)	0.37	-	exc	0	Secreted protein (By similarity)				262
P02651 UniProt NPD GO	APOA4_RAT	Apolipoprotein A-IV precursor (Apo-AIV) (ApoA-IV)	0.37	-	exc	0	Secreted protein	chylomicron [IDA]			391
Q9JHU5 UniProt NPD GO	ARFP1_RAT	Arfaptin-1 (ADP-ribosylation factor-interacting protein 1)	0.37	-	nuc	0					366
P43061 UniProt NPD GO	ARLY_CANAL	Argininosuccinate lyase (EC 4.3.2.1) (Arginosuccinase) (ASAL)	0.37	-	cyt	0					468
Q5T2S8 UniProt NPD GO	ARMC4_HUMAN	Armadillo repeat-containing protein 4	0.37	-	nuc	0					1044
P18605 UniProt NPD GO	ARY1_RABIT	Arylamine N-acetyltransferase 1 (EC 2.3.1.5) (Arylamide acetylase 1) (Arylamine N-acetyltransferase, ...	0.37	-	cyt	0	Cytoplasm				290
Q5RBQ8 UniProt NPD GO	ASGR1_PONPY	Asialoglycoprotein receptor 1 (ASGPR 1) (ASGP-R 1)	0.37	-	cyt	1 *	Membrane; single-pass type II membrane protein (By similarity)				290
Q9Z297 UniProt NPD GO	PEA15_CRIGR	Astrocytic phosphoprotein PEA-15 (Phosphoprotein enriched in astrocytes, 15 kDa)	0.37	-	nuc	0	Cytoplasm. Associated with microtubules (By similarity)			1N3K	130
Q15121 UniProt NPD GO	PEA15_HUMAN	Astrocytic phosphoprotein PEA-15 (Phosphoprotein enriched in diabetes) (PED)	0.37	-	nuc	0	Cytoplasm. Associated with microtubules	microtubule associated complex [NAS]	603434		130
P80015 UniProt NPD GO	CAP7_PIG	Azurocidin (Cationic antimicrobial protein CAP37) (Heparin-binding protein) (HBP)	0.37	+	nuc	0		azurophil granule [ISS] extracellular region [ISS]			219
P19437 UniProt NPD GO	CD20_MOUSE	B-cell surface protein CD20 homolog (B-cell differentiation antigen Ly-44)	0.37	-	end	4 *	Membrane; multi-pass membrane protein				291
O60238 UniProt NPD GO	BNI3L_HUMAN	BCL2/adenovirus E1B 19 kDa protein-interacting protein 3-like (NIP3L) (NIP3-like protein X) (BCL2/ad ...	0.37	-	nuc	1	Mitochondrion	mitochondrion [IDA]	605368		219
P19660 UniProt NPD GO	BCTN5_BOVIN	Bactenecin-5 precursor (Bac5) (Cathelicidin-2) (PR-42)	0.37	-	nuc	0	Secreted protein				176
P79362 UniProt NPD GO	BCTN5_SHEEP	Bactenecin-5 precursor (Bac5) (OaBac5) (Cathelicidin-2)	0.37	-	nuc	1 *	Secreted protein				176
Q8RVH5 UniProt NPD GO	7SBG2_SOYBN	Basic 7S globulin 2 precursor (Bg) (SBg7S) [Contains: Basic 7S globulin 2 high kDa subunit; Basic 7S ...	0.37	-	nuc	0					433
Q99PA3 UniProt NPD GO	BASI_CRIGR	Basigin (CD147 antigen) (Fragment)	0.37	+	nuc	1	Cell membrane; single-pass type I membrane protein (By similarity). Colocalizes with SLC16A1 and SLC ...				249
Q99L88 UniProt NPD GO	SNTB1_MOUSE	Beta-1-syntrophin (59 kDa dystrophin-associated protein A1 basic component 1) (DAPA1B) (Syntrophin 2 ...	0.37	-	mit	0	Sarcolemma; sarcolemmal membrane; peripheral membrane protein; cytoplasmic side. In skeletal muscle, ...	synapse [IDA]			536
P39037 UniProt NPD GO	CASB_PIG	Beta-casein precursor	0.37	-	exc	0	Secreted protein				232
O95803 UniProt NPD GO	NDST3_HUMAN	Bifunctional heparan sulfate N-deacetylase/N-sulfotransferase 3 (EC 2.8.2.8) (Glucosaminyl N-deacety ...	0.37	-	gol	1 *	Golgi apparatus; Golgi membrane; single-pass type II membrane protein (By similarity)		603950		873
Q96T60 UniProt NPD GO	PNKP_HUMAN	Bifunctional polynucleotide phosphatase/kinase (Polynucleotide kinase-3'-phosphatase) (DNA 5'-kinase ...	0.37	-	cyt	0	Nucleus	nucleus [IDA]	605610	2BRF	521
Q9N0V3 UniProt NPD GO	ABCBB_RABIT	Bile salt export pump (ATP-binding cassette sub-family B member 11) (Sister of P-glycoprotein)	0.37	-	end	9	Membrane; multi-pass membrane protein				1321
Q9MZE2 UniProt NPD GO	BMP15_SHEEP	Bone morphogenetic protein 15 precursor (BMP-15) (Growth/differentiation factor 9B) (GDF-9B)	0.37	-	nuc	0	Secreted protein			1EHU	393
Q63767 UniProt NPD GO	BCAR1_RAT	Breast cancer anti-estrogen resistance protein 1 (CRK-associated substrate) (p130cas)	0.37	-	nuc	0	Cell membrane; cell-matrix junction; focal adhesion. Focal adhesions and stress fibers. Cytoplasm. U ...	cytoplasm [ISS] focal adhesion [IDA] membrane fraction [ISS] ruffle [ISS]		1Z23	968
O75934 UniProt NPD GO	BCAS2_HUMAN	Breast carcinoma amplified sequence 2 (DNA amplified in mammary carcinoma 1 protein) (Spliceosome-as ...	0.37	-	nuc	0	Nucleus; nucleolus	spliceosome complex [IDA]	605783		225
Q5RAX7 UniProt NPD GO	BCAS2_PONPY	Breast carcinoma amplified sequence 2 homolog	0.37	-	nuc	0	Nucleus; nucleolus (By similarity)				226
Q9D287 UniProt NPD GO	BCAS2_MOUSE	Breast carcinoma amplified sequence 2 homolog (DNA amplified in mammary carcinoma 1 protein)	0.37	-	nuc	0	Nucleus; nucleolus (By similarity)				225
Q9UMR7 UniProt NPD GO	CLC4A_HUMAN	C-type lectin domain family 4 member A (C-type lectin superfamily member 6) (Dendritic cell immunore ...	0.37	-	nuc	1 *	Membrane; single-pass type II membrane protein (Probable)	integral to plasma membrane [TAS]	605306		237
Q8VBX4 UniProt NPD GO	CLC4K_MOUSE	C-type lectin domain family 4 member K (Langerin) (CD207 antigen)	0.37	-	nuc	1 *	Membrane; single-pass type II membrane protein. Found in Birbeck granules (BGs), which are organelle ...				331
O15255 UniProt NPD GO	CXX1_HUMAN	CAAX box protein 1 (Cerebral protein 5)	0.37	-	nuc	0	Cell membrane; lipid-anchor (Potential)		300213		209
Q8R395 UniProt NPD GO	COMD5_MOUSE	COMM domain-containing protein 5	0.37	-	nuc	0	Nucleus (By similarity)				224
P22223 UniProt NPD GO	CADH3_HUMAN	Cadherin-3 precursor (Placental-cadherin) (P-cadherin)	0.37	-	end	1	Membrane; single-pass type I membrane protein		601553		829
P06881 UniProt NPD GO	CALCA_HUMAN	Calcitonin gene-related peptide 1 precursor (Calcitonin gene-related peptide I) (CGRP-I) (Alpha-type ...	0.37	-	exc	0		endoplasmic reticulum [TAS] extracellular space [TAS] soluble fraction [TAS]	114130	1LS7	128
Q9H9S4 UniProt NPD GO	CB39L_HUMAN	Calcium-binding protein 39-like (Mo25-like protein) (Antigen MLAA-34)	0.37	-	nuc	0					337
Q5R6Z8 UniProt NPD GO	CYBP_PONPY	Calcyclin-binding protein (CacyBP)	0.37	-	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity)				228
Q39817 UniProt NPD GO	CALX_SOYBN	Calnexin homolog precursor	0.37	-	end	2 *	Endoplasmic reticulum; endoplasmic reticulum membrane; single-pass type I membrane protein (By simil ...				546
Q9Y6W3 UniProt NPD GO	CAN7_HUMAN	Calpain-7 (EC 3.4.22.-) (PalB homolog) (PalBH)	0.37	-	nuc	0	Nucleus		606400		813
Q55IT8 UniProt NPD GO	PALB_CRYNE	Calpain-like protease palB/RIM13 (EC 3.4.22.-) (Cysteine protease RIM13)	0.37	-	cyt	0					814
Q8K3H7 UniProt NPD GO	CALR_CRIGR	Calreticulin precursor (CRP55) (Calregulin) (HACBP) (ERp60)	0.37	-	end	0	Endoplasmic reticulum; endoplasmic reticulum lumen				417
O43916 UniProt NPD GO	CHST1_HUMAN	Carbohydrate sulfotransferase 1 (EC 2.8.2.21) (Keratan sulfate Gal-6 sulfotransferase) (KSST) (KSGal ...	0.37	-	nuc	1 *	Golgi apparatus; Golgi membrane; single-pass type II membrane protein (By similarity)	integral to membrane [NAS] intrinsic to Golgi membrane [ISS]	603797		411
Q8NCG5 UniProt NPD GO	CHST4_HUMAN	Carbohydrate sulfotransferase 4 (EC 2.8.2.-) (N-acetylglucosamine 6-O-sulfotransferase 2) (GlcNAc6ST ...	0.37	-	vac	1 *	Golgi apparatus; Golgi membrane; single-pass type II membrane protein	Golgi trans face [IDA] intrinsic to Golgi membrane [NAS]			386
O70354 UniProt NPD GO	CAH11_MOUSE	Carbonic anhydrase-related protein 2 precursor (CARP-2) (CA-RP II) (CA-XI) (Carbonic anhydrase-relat ...	0.37	-	exc	0	Secreted protein (Potential)				328
Q6UY09 UniProt NPD GO	CEA20_HUMAN	Carcinoembryonic antigen-related cell adhesion molecule 20 precursor	0.37	-	nuc	1	Membrane; single-pass type I membrane protein (Potential)				585
Q16619 UniProt NPD GO	CTF1_HUMAN	Cardiotrophin-1 (CT-1)	0.37	-	nuc	0	Secreted protein	extracellular region [TAS]	600435		201

You are viewing entries 34001 to 34050 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.