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
Q6FQY7 UniProt NPD GO	ATG7_CANGA	Autophagy-related protein 7 (Autophagy-related E1-like-activating enzyme ATG7)	0.30	-	cyt	0	Cytoplasm (By similarity)				623
Q755X2 UniProt NPD GO	ATG8_ASHGO	Autophagy-related protein 8 precursor (Autophagy-related ubiquitin-like modifier ATG8)	0.30	-	cyt	0	Membrane-associated through a lipid anchor. Cvt vesicles, autophagosomes and vacuolar (By similarity ...				120
P87068 UniProt NPD GO	ATG8_LACBI	Autophagy-related protein 8 precursor (Autophagy-related ubiquitin-like modifier ATG8)	0.30	-	cyt	0	Membrane; lipid-anchor. Associated through a lipid anchor				184
Q51MW4 UniProt NPD GO	ATG8_MAGGR	Autophagy-related protein 8 precursor (Autophagy-related ubiquitin-like modifier ATG8)	0.30	-	cyt	0	Membrane-associated through a lipid anchor. Cvt vesicles, autophagosomes and vacuolar (By similarity ...				123
Q8NJJ4 UniProt NPD GO	ATG8_PICPA	Autophagy-related protein 8 precursor (Autophagy-related ubiquitin-like modifier ATG8) (Pexophagy ze ...	0.30	-	cyt	0	Membrane; lipid-anchor (By similarity). Associated through a lipid anchor (By similarity)				125
Q8WZY7 UniProt NPD GO	ATG8_NEUCR	Autophagy-related protein 8 precursor (Autophagy-related ubiquitin-like modifier atg-8)	0.30	-	nuc	0	Membrane-associated through a lipid anchor. Cvt vesicles, autophagosomes and vacuolar (By similarity ...				121
Q922M3 UniProt NPD GO	KCD10_MOUSE	BTB/POZ domain-containing protein KCTD10	0.30	-	nuc	0	Nucleus (By similarity)				315
P48647 UniProt NPD GO	CRBS2_CHICO	Beta crystallin S-2 (Gamma crystallin S-2)	0.30	-	nuc	0					172
P08588 UniProt NPD GO	ADRB1_HUMAN	Beta-1 adrenergic receptor (Beta-1 adrenoceptor) (Beta-1 adrenoreceptor)	0.30	-	end	7	Cell membrane; multi-pass membrane protein. Localized at the plasma membrane. Found in the Golgi upo ...	integral to plasma membrane [TAS] plasma membrane [TAS]	607276		477
Q8JHF2 UniProt NPD GO	LFNG_BRARE	Beta-1,3-N-acetylglucosaminyltransferase lunatic fringe (EC 2.4.1.222) (O-fucosylpeptide 3-beta-N-ac ...	0.30	-	exc	1 *					374
Q24157 UniProt NPD GO	BRN_DROME	Beta-1,3-galactosyltransferase brn (EC 2.4.1.62) (Neurogenic secreted signaling protein brn) (Braini ...	0.30	-	exc	1 *	Golgi apparatus; Golgi membrane; single-pass type II membrane protein (Potential)	Golgi stack [ISS]			325
O43286 UniProt NPD GO	B4GT5_HUMAN	Beta-1,4-galactosyltransferase 5 (EC 2.4.1.-) (Beta-1,4-GalTase 5) (Beta4Gal-T5) (b4Gal-T5) (UDP-gal ...	0.30	-	mit	1 *	Golgi apparatus; Golgi stack; Golgi stack membrane; single-pass type II membrane protein. Trans cist ...		604016		388
Q9JJN6 UniProt NPD GO	CNBP1_MOUSE	Beta-catenin-interacting protein 1 (Inhibitor of beta-catenin and Tcf-4)	0.30	-	nuc	0	Cytoplasm. Nucleus	cytoplasm [TAS] nucleus [TAS]			81
Q30KK7 UniProt NPD GO	DB120_PANTR	Beta-defensin 120 precursor (Defensin, beta 120)	0.30	-	mit	0	Secreted protein (Potential)				88
Q8N689 UniProt NPD GO	DB120_HUMAN	Beta-defensin 120 precursor (Defensin, beta 120) (Beta-defensin 20) (DEFB-20)	0.30	-	mit	0	Secreted protein (Potential)				88
P28668 UniProt NPD GO	SYEP_DROME	Bifunctional aminoacyl-tRNA synthetase [Includes: Glutamyl-tRNA synthetase (EC 6.1.1.17) (Glutamate- ...	0.30	-	cyt	0					1714
P29002 UniProt NPD GO	BMNL1_BOMOR	Bombinin-like peptides 1 precursor [Contains: Acidic peptide 1; Bombinin-like peptide 1 (BLP-1); Oct ...	0.30	-	exc	0	Secreted protein				204
P01067 UniProt NPD GO	IBB2_ARAHY	Bowman-Birk type proteinase inhibitor B-II	0.30	-	nuc	0					63
O18752 UniProt NPD GO	BDNF_URSAR	Brain-derived neurotrophic factor precursor (BDNF)	0.30	-	nuc	0	Secreted protein				247
Q9EPW4 UniProt NPD GO	CLC3A_MOUSE	C-type lectin domain family 3 member A precursor (C-type lectin superfamily member 1) (Cartilage-der ...	0.30	-	exc	0					196
O46651 UniProt NPD GO	CD166_RABIT	CD166 antigen (Activated leukocyte-cell adhesion molecule) (ALCAM) (SB-10 antigen) (Fragment)	0.30	-	nuc	1	Membrane; single-pass type I membrane protein (By similarity)				521
P10252 UniProt NPD GO	CD48_RAT	CD48 antigen precursor (MRC OX-45 surface antigen) (BCM1 surface antigen) (BLAST-1)	0.30	-	exc	0	Cell membrane; lipid-anchor; GPI-anchor	anchored to plasma membrane [IDA] plasma membrane [IDA]			240
Q2R1U4 UniProt NPD GO	CK5P1_ORYSA	CDK5RAP1-like protein	0.30	-	mit	0					600
Q566E6 UniProt NPD GO	CLM1_RAT	CMRF35-like-molecule 1 precursor (CLM-1) (CD300 antigen like family member F)	0.30	-	exc	1	Membrane; single-pass type I membrane protein (Potential)				332
Q9VVU5 UniProt NPD GO	CSN1_DROME	COP9 signalosome complex subunit 1b (Signalosome subunit 1b) (Dch1-2)	0.30	-	nuc	0	Cytoplasm (Probable). Nucleus (Probable)	signalosome complex [IMP]			525
Q9UNS2 UniProt NPD GO	CSN3_HUMAN	COP9 signalosome complex subunit 3 (Signalosome subunit 3) (SGN3) (JAB1-containing signalosome subun ...	0.30	-	nuc	0	Cytoplasm. Nucleus		604665		422
O88543 UniProt NPD GO	CSN3_MOUSE	COP9 signalosome complex subunit 3 (Signalosome subunit 3) (SGN3) (JAB1-containing signalosome subun ...	0.30	-	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity)	signalosome complex [IDA]			422
P03875 UniProt NPD GO	AI1M_YEAST	COX1/OXI3 intron 1 protein	0.30	-	nuc	1 *		mitochondrion [TAS]			834
Q9HBT6 UniProt NPD GO	CAD20_HUMAN	Cadherin-20 precursor	0.30	-	nuc	1 *	Membrane; single-pass type I membrane protein	integral to membrane [NAS]	605807		801
P33151 UniProt NPD GO	CADH5_HUMAN	Cadherin-5 precursor (Vascular endothelial-cadherin) (VE-cadherin) (7B4 antigen) (CD144 antigen)	0.30	+	end	2 *	Cell membrane; cell-cell junction; single-pass type I membrane protein. Cell membrane; cell-matrix j ...	membrane fraction [TAS] plasma membrane [TAS]	601120		784
P70407 UniProt NPD GO	CADH9_MOUSE	Cadherin-9 (T1-cadherin) (Fragment)	0.30	-	nuc	0	Membrane; single-pass type I membrane protein (Potential)				109
Q9D869 UniProt NPD GO	CHP2_MOUSE	Calcineurin B homologous protein 2 (Hepatocellular carcinoma-associated antigen 520 homolog)	0.30	-	cyt	0					195
Q7FZF1 UniProt NPD GO	CNBL5_ARATH	Calcineurin B-like protein 5 (SOS3-like calcium-binding protein 4)	0.30	-	nuc	0	Cell membrane; lipid-anchor (By similarity)				202
O75575 UniProt NPD GO	CRCP_HUMAN	Calcitonin gene-related peptide-receptor component protein (CGRP-receptor component protein) (CGRP-R ...	0.30	-	nuc	0			606121		148
Q8VHM6 UniProt NPD GO	CRCP_RAT	Calcitonin gene-related peptide-receptor component protein (CGRP-receptor component protein) (CGRP-R ...	0.30	-	nuc	0					148
P08414 UniProt NPD GO	KCC4_MOUSE	Calcium/calmodulin-dependent protein kinase type IV (EC 2.7.11.17) (CAM kinase-GR) (CaMK IV)	0.30	-	cyt	0	Cytoplasm. Nucleus. Substantial localization in certain neuronal nuclei (By similarity). In spermati ...	cytoplasm [IDA] nucleus [IDA]			469
P13234 UniProt NPD GO	KCC4_RAT	Calcium/calmodulin-dependent protein kinase type IV (EC 2.7.11.17) (CAM kinase-GR) (CaMK IV) (Calspe ...	0.30	-	mit	0	Cytoplasm (By similarity). Nucleus (By similarity). Substantial localization in certain neuronal nuc ...				474
P52194 UniProt NPD GO	CLGN_MOUSE	Calmegin precursor (MEG 1 antigen) (Calnexin-T) (A2/6)	0.30	+	end	1	Endoplasmic reticulum; endoplasmic reticulum membrane; single-pass type I membrane protein				611
Q96L12 UniProt NPD GO	CALR3_HUMAN	Calreticulin-3 precursor (Calreticulin-2)	0.30	-	mit	0	Endoplasmic reticulum; endoplasmic reticulum lumen (By similarity)				384
Q27179 UniProt NPD GO	CATR2_PARTE	Caltractin ICL1B (Centrin)	0.30	-	mit	0	ICL, innermost fibrous network of the cortical cytoskeleton				182
P43155 UniProt NPD GO	CACP_HUMAN	Carnitine O-acetyltransferase (EC 2.3.1.7) (Carnitine acetylase) (CAT) (Carnitine acetyltransferase) ...	0.30	-	pox	0	Endoplasmic reticulum (Potential). Peroxisome (Potential). Mitochondrion; mitochondrial inner membra ...	endoplasmic reticulum [NAS] peroxisome [NAS]	600184	1S5O	626
Q9CYD3 UniProt NPD GO	CRTAP_MOUSE	Cartilage-associated protein precursor	0.30	-	end	0	Secreted protein; extracellular space; extracellular matrix				400
P54367 UniProt NPD GO	KC1A_DROME	Casein kinase I isoform alpha (EC 2.7.11.1) (CKI-alpha) (DmCK1)	0.30	-	cyt	0	Cytoplasm (By similarity)	cytoplasm [IDA] nucleus [IDA]			337
P40232 UniProt NPD GO	CSK2B_SCHPO	Casein kinase II subunit beta (CK II beta)	0.30	-	cyt	0					231
Q8BIG7 UniProt NPD GO	CMTD1_MOUSE	Catechol-O-methyltransferase domain-containing protein 1 (EC 2.1.1.-)	0.30	-	mit	1 *	Membrane; single-pass type II membrane protein (Potential)				262
P49928 UniProt NPD GO	SC51_SHEEP	Cathelin-related peptide SC5 precursor 1 (Antibacterial peptide SMAP-29) (Myeloid antibacterial pept ...	0.30	-	nuc	0	Secreted protein			1FRY	160
P19092 UniProt NPD GO	CYSP1_HAECO	Cathepsin B-like cysteine proteinase 1 precursor (EC 3.4.22.-)	0.30	-	vac	0				1MNW	342
Q5EDC3 UniProt NPD GO	CCRK_MACMU	Cell cycle-related kinase (EC 2.7.11.22) (Cyclin-kinase-activating kinase p42) (CDK-activating kinas ...	0.30	-	cyt	0	Nucleus (By similarity)				243
Q641C9 UniProt NPD GO	CD123_XENLA	Cell division cycle protein 123 homolog	0.30	-	cyt	0	Cytoplasm (By similarity)				338
Q39085 UniProt NPD GO	DIM_ARATH	Cell elongation protein DIMINUTO (Cell elongation protein Dwarf1)	0.30	-	mit	1 *					561

You are viewing entries 40151 to 40200 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.