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
Q91V70 UniProt NPD GO	BD07_MOUSE	Beta-defensin 7 precursor (Defensin, beta 7) (BD-7) (mBD-7) (mBD7)	0.13	-	end	1 *	Secreted protein (Potential)			1E4T	71
Q9NQQ0 UniProt NPD GO	GUSL1_HUMAN	Beta-glucuronidase-like protein 1 (SMA3-like protein)	0.13	-	nuc	0					140
P49009 UniProt NPD GO	HEXA_ENTHI	Beta-hexosaminidase alpha chain precursor (EC 3.2.1.52) (N-acetyl-beta-glucosaminidase) (Beta-GlcNAc ...	0.13	-	end	0	Cytoplasmic granule				564
Q8R079 UniProt NPD GO	BFAR_MOUSE	Bifunctional apoptosis regulator	0.13	-	end	3	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (By similarity)			1V85	450
Q27828 UniProt NPD GO	DRTS_PARTE	Bifunctional dihydrofolate reductase-thymidylate synthase (DHFR-TS) [Includes: Dihydrofolate reducta ...	0.13	-	mit	0					462
O46390 UniProt NPD GO	PGS1_SHEEP	Biglycan precursor (Bone/cartilage proteoglycan I) (PG-S1)	0.13	-	exc	0	Secreted protein; extracellular space; extracellular matrix (By similarity)				369
P21809 UniProt NPD GO	PGS1_BOVIN	Biglycan precursor (Bone/cartilage proteoglycan I) (PG-S1) (Leucine-rich PG I)	0.13	-	nuc	0	Secreted protein; extracellular space; extracellular matrix			2FT3	369
Q3SZ84 UniProt NPD GO	BOLA3_BOVIN	BolA-like protein 3	0.13	-	mit	0					110
P29006 UniProt NPD GO	BMNL1_BOMVA	Bombinin-like peptides 1 precursor [Contains: Acidic peptide 1-1; Bombinin-like peptide 1 (BLP-1); O ...	0.13	-	end	0	Secreted protein				137
P33719 UniProt NPD GO	BXA2_SAMCY	Bombyxin A-2 homolog precursor [Contains: Bombyxin A-2 homolog B chain; Bombyxin A-2 homolog A chain ...	0.13	-	exc	0	Secreted protein				100
P07084 UniProt NPD GO	IBBR_ORYSA	Bowman-Birk type bran trypsin inhibitor precursor (RBTI) (OSE727A)	0.13	-	nuc	0					195
P24661 UniProt NPD GO	IBB_VICFA	Bowman-Birk type proteinase inhibitor (FBI)	0.13	-	nuc	0					63
P25432 UniProt NPD GO	BDNF_XENLA	Brain-derived neurotrophic factor (BDNF) (Fragment)	0.13	-	nuc	0	Secreted protein				114
P82269 UniProt NPD GO	BR2TB_RANTE	Brevinin-2Tb precursor	0.13	-	exc	0	Secreted protein				74
P83346 UniProt NPD GO	BCIN_BUNCA	Bucain	0.13	-	nuc	0	Secreted protein			1VYC	65
Q9NPB9 UniProt NPD GO	CCRL1_HUMAN	C-C chemokine receptor type 11 (C-C CKR-11) (CC-CKR-11) (CCR-11) (CC chemokine receptor-like 1) (CCR ...	0.13	+	end	7 *	Membrane; multi-pass membrane protein	integral to plasma membrane [TAS] plasma membrane [TAS]	606065		350
Q9BDS8 UniProt NPD GO	CCR3_MACFA	C-C chemokine receptor type 3 (C-C CKR-3) (CC-CKR-3) (CCR-3) (CCR3) (CKR3) (CD193 antigen)	0.13	-	end	7 *	Membrane; multi-pass membrane protein				355
P56483 UniProt NPD GO	CCR3_MACMU	C-C chemokine receptor type 3 (C-C CKR-3) (CC-CKR-3) (CCR-3) (CCR3) (CKR3) (CD193 antigen)	0.13	-	end	7 *	Membrane; multi-pass membrane protein				355
O97883 UniProt NPD GO	CCR5_HYLLE	C-C chemokine receptor type 5 (C-C CKR-5) (CC-CKR-5) (CCR-5) (CCR5) (CD195 antigen)	0.13	-	end	6 *	Membrane; multi-pass membrane protein				352
Q95NC0 UniProt NPD GO	CCR5_HYLML	C-C chemokine receptor type 5 (C-C CKR-5) (CC-CKR-5) (CCR-5) (CCR5) (CD195 antigen)	0.13	-	end	6 *	Membrane; multi-pass membrane protein				352
Q95NC5 UniProt NPD GO	CCR5_HYLSY	C-C chemokine receptor type 5 (C-C CKR-5) (CC-CKR-5) (CCR-5) (CCR5) (CD195 antigen)	0.13	-	end	6 *	Membrane; multi-pass membrane protein				352
P51682 UniProt NPD GO	CCR5_MOUSE	C-C chemokine receptor type 5 (C-C CKR-5) (CC-CKR-5) (CCR-5) (MIP-1 alpha receptor) (CD195 antigen)	0.13	-	end	6 *	Membrane; multi-pass membrane protein				354
O00421 UniProt NPD GO	CCRL2_HUMAN	C-C chemokine receptor-like 2 (Putative MCP-1 chemokine receptor) (Chemokine receptor CCR11) (Chemok ...	0.13	-	end	6 *	Membrane; multi-pass membrane protein (By similarity)	integral to plasma membrane [TAS]	608379		344
Q9Z2F5 UniProt NPD GO	CTBP1_RAT	C-terminal-binding protein 1 (EC 1.1.1.-) (CtBP1) (C-terminal-binding protein 3) (CtBP3) (50 kDa BFA ...	0.13	-	cyt	0	Cytoplasm. Nucleus	cytosol [IDA]		1HL3	430
Q6TAC8 UniProt NPD GO	C3AR_MACFA	C3a anaphylatoxin chemotactic receptor (C3a-R) (C3AR)	0.13	-	end	7 *	Membrane; multi-pass membrane protein				481
O09047 UniProt NPD GO	C3AR_MOUSE	C3a anaphylatoxin chemotactic receptor (C3a-R) (C3AR) (Complement component 3a receptor 1)	0.13	-	end	7 *	Membrane; multi-pass membrane protein				477
P79234 UniProt NPD GO	C5AR_PONPY	C5a anaphylatoxin chemotactic receptor (C5a-R) (C5aR) (CD88 antigen) (Fragment)	0.13	-	end	7 *	Membrane; multi-pass membrane protein				340
P09326 UniProt NPD GO	CD48_HUMAN	CD48 antigen precursor (B-lymphocyte activation marker BLAST-1) (BCM1 surface antigen) (Leukocyte an ...	0.13	-	end	1	Cell membrane; lipid-anchor; GPI-anchor	integral to plasma membrane [TAS] plasma membrane [TAS]	109530		243
P14209 UniProt NPD GO	CD99_HUMAN	CD99 antigen precursor (T-cell surface glycoprotein E2) (E2 antigen) (Protein MIC2) (12E7)	0.13	-	end	2 *	Membrane; single-pass type I membrane protein (Potential)	cytoplasm [TAS] integral to plasma membrane [TAS] plasma membrane [TAS]	450000		185
P61131 UniProt NPD GO	SIA4C_RAT	CMP-N-acetylneuraminate-beta-galactosamide-alpha-2,3-sialyltransferase (EC 2.4.99.-) (Beta-galactosi ...	0.13	-	end	1 *	Golgi apparatus; Golgi stack; Golgi stack membrane; single-pass type II membrane protein (By similar ...				333
Q6SJQ7 UniProt NPD GO	CLM1_MOUSE	CMRF35-like-molecule 1 precursor (CLM-1) (CD300 antigen like family member F)	0.13	-	end	1	Membrane; single-pass type I membrane protein (Potential)			1ZOX	337
Q92905 UniProt NPD GO	CSN5_HUMAN	COP9 signalosome complex subunit 5 (EC 3.4.-.-) (Signalosome subunit 5) (SGN5) (Jun activation domai ...	0.13	-	nuc	0	Cytoplasm. Nucleus	eukaryotic translation initiation factor 3 ... [TAS]	604850		333
Q5R5W6 UniProt NPD GO	CAD13_PONPY	Cadherin-13 precursor	0.13	-	exc	0	Cell membrane; lipid-anchor; GPI-anchor (By similarity)				713
P55290 UniProt NPD GO	CAD13_HUMAN	Cadherin-13 precursor (Truncated-cadherin) (T-cadherin) (T-cad) (Heart-cadherin) (H-cadherin) (P105) ...	0.13	-	exc	0	Cell membrane; lipid-anchor; GPI-anchor		601364		713
Q86UP0 UniProt NPD GO	CAD24_HUMAN	Cadherin-24 precursor	0.13	-	end	1	Membrane; single-pass type I membrane protein (Potential)	intercellular junction [IDA]			819
Q63149 UniProt NPD GO	CADH4_RAT	Cadherin-4 (Retinal-cadherin) (R-cadherin) (R-CAD) (Fragment)	0.13	-	cyt	0	Membrane; single-pass type I membrane protein (Potential)				296
P33187 UniProt NPD GO	MTCD_HELPO	Cadmium-metallothionein (CD-MT)	0.13	-	nuc	0					66
P41044 UniProt NPD GO	CAB32_DROME	Calbindin-32	0.13	-	nuc	0					310
Q9C5P6 UniProt NPD GO	CNBL6_ARATH	Calcineurin B-like protein 6 (SOS3-like calcium-binding protein 2)	0.13	-	cyt	0					226
Q757B7 UniProt NPD GO	CANB_ASHGO	Calcineurin subunit B (Protein phosphatase 2B regulatory subunit) (Calcineurin regulatory subunit)	0.13	-	cyt	0					175
Q5RE25 UniProt NPD GO	CCP2_PONPY	Calcipressin-2 (Down syndrome candidate region 1-like protein 1)	0.13	-	nuc	0					197
Q28266 UniProt NPD GO	KCMB1_CANFA	Calcium-activated potassium channel subunit beta 1 (Calcium-activated potassium channel, subfamily M ...	0.13	-	end	2 *	Membrane; multi-pass membrane protein (By similarity)				190
Q4R3X7 UniProt NPD GO	CABYR_MACFA	Calcium-binding tyrosine phosphorylation-regulated protein	0.13	-	nuc	0	Cytoplasm (By similarity). Localized to fibrous sheath including the surface of the longitudinal col ...				487
P53682 UniProt NPD GO	CDPK1_ORYSA	Calcium-dependent protein kinase, isoform 1 (EC 2.7.11.1) (CDPK 1)	0.13	-	cyt	0					534
P92939 UniProt NPD GO	ECA1_ARATH	Calcium-transporting ATPase 1, endoplasmic reticulum-type (EC 3.6.3.8)	0.13	-	end	8	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein	integral to endoplasmic reticulum membrane [IDA]			1061
P27466 UniProt NPD GO	KCC1_YEAST	Calcium/calmodulin-dependent protein kinase I (EC 2.7.11.17)	0.13	-	cyt	0		cytoplasm [IPI]			446
Q9NZT1 UniProt NPD GO	CALL5_HUMAN	Calmodulin-like protein 5 (Calmodulin-like skin protein)	0.13	-	cyt	0			605183	2B1U	146
P06813 UniProt NPD GO	CPNS1_RABIT	Calpain small subunit 1 (CSS1) (Calcium-dependent protease small subunit 1) (Calcium-dependent prote ...	0.13	-	cyt	0	Cytoplasm. Cell membrane. Translocates to the plasma membrane upon calcium binding (By similarity). ...				266
Q02910 UniProt NPD GO	CPN_DROME	Calphotin	0.13	-	end	0	Cytoplasm. Hypodense compartment				864
Q9XF98 UniProt NPD GO	CALR_PRUAR	Calreticulin precursor	0.13	-	end	0	Endoplasmic reticulum; endoplasmic reticulum lumen (By similarity)				421

You are viewing entries 59451 to 59500 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.