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
O15263 UniProt NPD GO	BD02_HUMAN	Beta-defensin 2 precursor (BD-2) (hBD-2) (Defensin, beta 2) (Skin-antimicrobial peptide 1) (SAP1)	0.03	-	end	1 *	Secreted protein		602215	1FQQ	64
Q7TMD2 UniProt NPD GO	BD37_MOUSE	Beta-defensin 37 precursor (Defensin, beta 37) (BD-37) (mBD-37)	0.03	-	exc	0	Secreted protein (By similarity)				62
P82019 UniProt NPD GO	BD04_MOUSE	Beta-defensin 4 precursor (Defensin, beta 4) (BD-4) (mBD-4)	0.03	-	mit	1 *	Secreted protein (By similarity)				63
P46163 UniProt NPD GO	BD05_BOVIN	Beta-defensin 5 precursor (BNDB-5) (BNBD-5)	0.03	-	exc	1 *	Secreted protein				64
Q43089 UniProt NPD GO	INV1_PEA	Beta-fructofuranosidase, cell wall isozyme precursor (EC 3.2.1.26) (Sucrose hydrolase) (Acid inverta ...	0.03	-	exc	0					555
Q6EU76 UniProt NPD GO	INV1_ORYSA	Beta-fructofuranosidase, insoluble isoenzyme 1 precursor (EC 3.2.1.26) (Sucrose hydrolase 1) (Invert ...	0.03	-	exc	0	Secreted protein; extracellular space; apoplast (Probable). Cell wall (Probable). Associated to the ...				577
P22507 UniProt NPD GO	BGL2_SACFI	Beta-glucosidase 2 precursor (EC 3.2.1.21) (Gentiobiase) (Cellobiase) (Beta-D-glucoside glucohydrola ...	0.03	-	gol	0					880
Q29614 UniProt NPD GO	LACB_MACEU	Beta-lactoglobulin precursor (Beta-LG)	0.03	-	exc	0					174
Q29146 UniProt NPD GO	LACB_TRIVU	Beta-lactoglobulin precursor (Beta-LG)	0.03	-	exc	0					174
P69392 UniProt NPD GO	PMTXB_BATMC	Beta-pompilidotoxin (Beta-PMTX)	0.03	-		0	Secreted protein				13
Q5RBM6 UniProt NPD GO	BUP1_PONPY	Beta-ureidopropionase (EC 3.5.1.6) (Beta-alanine synthase) (N-carbamoyl-beta-alanine amidohydrolase) ...	0.03	-	mit	0	Cytoplasm (By similarity)				384
Q9UBR1 UniProt NPD GO	BUP1_HUMAN	Beta-ureidopropionase (EC 3.5.1.6) (Beta-alanine synthase) (N-carbamoyl-beta-alanine amidohydrolase) ...	0.03	-	mit	0	Cytoplasm		606673		384
Q5I597 UniProt NPD GO	BHMT_BOVIN	Betaine--homocysteine S-methyltransferase (EC 2.1.1.5)	0.03	-	cyt	0	Cytoplasm (By similarity)				407
O35490 UniProt NPD GO	BHMT_MOUSE	Betaine--homocysteine S-methyltransferase (EC 2.1.1.5)	0.03	-	cyt	0	Cytoplasm				407
O09171 UniProt NPD GO	BHMT_RAT	Betaine--homocysteine S-methyltransferase (EC 2.1.1.5)	0.03	-	cyt	0	Cytoplasm			1UMY	407
O04895 UniProt NPD GO	BADH_AMAHP	Betaine-aldehyde dehydrogenase, chloroplast precursor (EC 1.2.1.8) (BADH)	0.03	-	cyt	0	Plastid; chloroplast				501
Q9S795 UniProt NPD GO	BADH_ARATH	Betaine-aldehyde dehydrogenase, chloroplast precursor (EC 1.2.1.8) (BADH)	0.03	-	cyt	0	Plastid; chloroplast				501
P28237 UniProt NPD GO	BADH_BETVU	Betaine-aldehyde dehydrogenase, chloroplast precursor (EC 1.2.1.8) (BADH)	0.03	-	cyt	0	Plastid; chloroplast				500
P46103 UniProt NPD GO	DRTS_PLAVN	Bifunctional dihydrofolate reductase-thymidylate synthase (DHFR-TS) [Includes: Dihydrofolate reducta ...	0.03	-	nuc	0					182
Q04448 UniProt NPD GO	MTDC_DROME	Bifunctional methylenetetrahydrofolate dehydrogenase/cyclohydrolase, mitochondrial precursor (DNMDMC ...	0.03	-	cyt	0	Mitochondrion	mitochondrion [ISS]			309
Q4LDG0 UniProt NPD GO	S27A5_MOUSE	Bile acyl-CoA synthetase (EC 6.2.1.7) (BACS) (Bile acid CoA ligase) (BA-CoA ligase) (BAL) (Cholate-- ...	0.03	-	end	3 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (By similarity)	endoplasmic reticulum [TAS]			689
P15709 UniProt NPD GO	ST2A1_RAT	Bile salt sulfotransferase (EC 2.8.2.14) (Hydroxysteroid sulfotransferase) (ST) (ST-20)	0.03	-	cyt	0	Cytoplasm				283
P84521 UniProt NPD GO	BIOP1_PHYHY	Bioactive peptide 1	0.03	-		0	Secreted protein				17
P70645 UniProt NPD GO	BLMH_RAT	Bleomycin hydrolase (EC 3.4.22.40) (BLM hydrolase) (BMH) (BH)	0.03	-	cyt	0	Cytoplasm				454
P18577 UniProt NPD GO	RHCE_HUMAN	Blood group Rh(CE) polypeptide (Rhesus C/E antigens) (Rh30A) (RhIXB) (Rh polypeptide 1) (RhPI) (CD24 ...	0.03	-	end	12 *	Membrane; multi-pass membrane protein	integral to plasma membrane [TAS]	111700		416
Q02161 UniProt NPD GO	RHD_HUMAN	Blood group Rh(D) polypeptide (Rhesus D antigen) (RHXIII) (Rh polypeptide 2) (RhPII) (CD240D antigen ...	0.03	-	end	10 *	Membrane; multi-pass membrane protein	integral to plasma membrane [TAS]	111680		416
P26727 UniProt NPD GO	BXA4_BOMMO	Bombyxin A-4 precursor (BBX-A4) (4K-prothoracicotropic hormone) (4K-PTTH) [Contains: Bombyxin A-4 B ...	0.03	-	exc	0	Secreted protein				92
P26734 UniProt NPD GO	BXB2_BOMMO	Bombyxin B-2 precursor (BBX-B2) (4K-prothoracicotropic hormone) (4K-PTTH) [Contains: Bombyxin B-2 B ...	0.03	-	exc	0	Secreted protein				89
P22030 UniProt NPD GO	BOTB_BOTJA	Botrocetin, beta chain (Platelet coagglutinin)	0.03	-	cyt	0	Secreted protein			1U0O	125
Q7LZ54 UniProt NPD GO	BRK1_RANNI	Bradykinin-like peptide 1	0.03	-		0	Secreted protein				9
O95258 UniProt NPD GO	UCP5_HUMAN	Brain mitochondrial carrier protein 1 (BMCP-1) (Mitochondrial uncoupling protein 5) (UCP 5) (Solute ...	0.03	-	end	0	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein (By similarity)	integral to plasma membrane [TAS] mitochondrion [TAS]	300242		325
Q9Z2B2 UniProt NPD GO	UCP5_MOUSE	Brain mitochondrial carrier protein 1 (BMCP-1) (Mitochondrial uncoupling protein 5) (UCP 5) (Solute ...	0.03	-	end	0	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein (By similarity)	mitochondrial envelope [IDA]			325
Q5R4Z3 UniProt NPD GO	BR44_PONPY	Brain protein 44	0.03	-	cyt	0					127
Q9Y5U8 UniProt NPD GO	BR44L_HUMAN	Brain protein 44-like protein	0.03	-	nuc	0					109
Q93Y32 UniProt NPD GO	BCAT1_ARATH	Branched-chain-amino-acid aminotransferase 1, mitochondrial precursor (EC 2.6.1.42) (Atbcat-1)	0.03	-	mit	0	Mitochondrion				384
P84839 UniProt NPD GO	BR1E_RANSA	Brevinin-1E	0.03	-	mit	0	Secreted protein	extracellular region [IDA]			24
P32413 UniProt NPD GO	BR2E_RANES	Brevinin-2E	0.03	-	nuc	0	Secreted protein				33
O23791 UniProt NPD GO	BROM1_ANACO	Bromelain precursor (EC 3.4.22.32) (Allergen Ana c 2)	0.03	-	exc	1 *					351
Q754B9 UniProt NPD GO	ERG3_ASHGO	C-5 sterol desaturase (EC 1.3.3.-) (Sterol-C5-desaturase) (Ergosterol delta 5,6 desaturase)	0.03	-	end	4	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (Probable)				351
P56484 UniProt NPD GO	CCR8_MOUSE	C-C chemokine receptor type 8 (C-C CKR-8) (CC-CKR-8) (CCR-8)	0.03	-	end	7 *	Membrane; multi-pass membrane protein				353
P51686 UniProt NPD GO	CCR9_HUMAN	C-C chemokine receptor type 9 (C-C CKR-9) (CC-CKR-9) (CCR-9) (GPR-9-6) (G-protein coupled receptor 2 ...	0.03	-	end	7 *	Membrane; multi-pass membrane protein	integral to plasma membrane [TAS] plasma membrane [TAS]	604738		357
Q867B2 UniProt NPD GO	CXCR3_CAPHI	C-X-C chemokine receptor type 3 (CXC-R3) (CXCR-3) (Interferon-inducible protein 10 receptor) (IP-10 ...	0.03	-	end	7	Membrane; multi-pass membrane protein (By similarity)				366
O88410 UniProt NPD GO	CXCR3_MOUSE	C-X-C chemokine receptor type 3 (CXC-R3) (CXCR-3) (Interferon-inducible protein 10 receptor) (IP-10 ...	0.03	-	end	7	Membrane; multi-pass membrane protein (By similarity)				367
O19024 UniProt NPD GO	CXCR6_MACNE	C-X-C chemokine receptor type 6 (CXC-R6) (CXCR-6) (G-protein coupled receptor bonzo)	0.03	-	end	7 *	Membrane; multi-pass membrane protein				342
Q9BDS6 UniProt NPD GO	CXCR6_MACFA	C-X-C chemokine receptor type 6 (CXC-R6) (CXCR-6) (G-protein coupled receptor bonzo) (G-protein coup ...	0.03	-	end	7 *	Membrane; multi-pass membrane protein				343
Q9XT45 UniProt NPD GO	CXCR6_MACMU	C-X-C chemokine receptor type 6 (CXC-R6) (CXCR-6) (G-protein coupled receptor bonzo) (G-protein coup ...	0.03	-	end	7 *	Membrane; multi-pass membrane protein				343
Q36698 UniProt NPD GO	PHCB_RHOVL	C-phycocyanin beta chain	0.03	-	cyt	0	Plastid; chloroplast				172
P06206 UniProt NPD GO	CRP4_LIMPO	C-reactive protein 1.4 precursor	0.03	-	exc	0	Secreted protein				242
P49262 UniProt NPD GO	CRP_MESAU	C-reactive protein precursor	0.03	-	mit	0	Secreted protein				225
Q9R007 UniProt NPD GO	CLC5A_MOUSE	C-type lectin domain family 5 member A (C-type lectin superfamily member 5) (Myeloid DAP12-associati ...	0.03	-	cyt	1 *	Membrane; single-pass type II membrane protein (Probable)				165

You are viewing entries 79251 to 79300 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.