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
O77531 UniProt NPD GO	B2MG_PITIR	Beta-2-microglobulin precursor	0.00	-	exc	0	Secreted protein				119
Q9TSX4 UniProt NPD GO	B2MG_SAGFU	Beta-2-microglobulin precursor	0.00	-	exc	0	Secreted protein				119
O77518 UniProt NPD GO	B2MG_SAGIM	Beta-2-microglobulin precursor	0.00	-	exc	0	Secreted protein				119
Q863A9 UniProt NPD GO	B2M_EQUGR	Beta-2-microglobulin precursor	0.00	-	end	0	Secreted protein				118
P25853 UniProt NPD GO	AMYB_ARATH	Beta-amylase (EC 3.2.1.2) (1,4-alpha-D-glucan maltohydrolase)	0.00	-	mit	0					498
P10537 UniProt NPD GO	AMYB_IPOBA	Beta-amylase (EC 3.2.1.2) (1,4-alpha-D-glucan maltohydrolase)	0.00	-	cyt	0				1FA2	498
P10538 UniProt NPD GO	AMYB_SOYBN	Beta-amylase (EC 3.2.1.2) (1,4-alpha-D-glucan maltohydrolase)	0.00	-	cyt	0				1WDS	495
Q5J5C9 UniProt NPD GO	DB121_HUMAN	Beta-defensin 121 precursor (Defensin, beta 121) (Beta-defensin 21) (DEFB-21)	0.00	-	exc	0	Secreted protein (Potential)	extracellular region [ISS]			76
Q5J5Z9 UniProt NPD GO	DB122_MACMU	Beta-defensin 122 precursor (Defensin, beta 122)	0.00	-	exc	1 *	Secreted protein (Potential)				69
Q30KJ8 UniProt NPD GO	DB131_PANTR	Beta-defensin 131 precursor (Defensin, beta 131)	0.00	-	end	0	Secreted protein (Potential)				71
P59861 UniProt NPD GO	DB131_HUMAN	Beta-defensin 131 precursor (Defensin, beta 131) (Beta-defensin 31) (DEFB-31)	0.00	-	end	0	Secreted protein (Potential)				70
P13929 UniProt NPD GO	ENOB_HUMAN	Beta-enolase (EC 4.2.1.11) (2-phospho-D-glycerate hydro-lyase) (Muscle-specific enolase) (MSE) (Skel ...	0.00	-	cyt	0	Cytoplasm. Localized to the Z line. Some colocalization with CKM at M-band (By similarity)		131370		433
P21550 UniProt NPD GO	ENOB_MOUSE	Beta-enolase (EC 4.2.1.11) (2-phospho-D-glycerate hydro-lyase) (Muscle-specific enolase) (MSE) (Skel ...	0.00	-	cyt	0	Cytoplasm. Localized to the Z line. Some colocalization with CKM at M-band (By similarity)				433
P25704 UniProt NPD GO	ENOB_RABIT	Beta-enolase (EC 4.2.1.11) (2-phospho-D-glycerate hydro-lyase) (Muscle-specific enolase) (MSE) (Skel ...	0.00	-	cyt	0	Cytoplasm. Localized to the Z line (By similarity). Some colocalization with CKM at M-band				433
P15429 UniProt NPD GO	ENOB_RAT	Beta-enolase (EC 4.2.1.11) (2-phospho-D-glycerate hydro-lyase) (Muscle-specific enolase) (MSE) (Skel ...	0.00	-	cyt	0	Cytoplasm. Localized to the Z line. Some colocalization with CKM at M-band (By similarity)				433
P58738 UniProt NPD GO	EXB1A_MAIZE	Beta-expansin 1a precursor (Pollen allergen Zea m 1) (Zea m I)	0.00	-	vac	0					269
Q07154 UniProt NPD GO	EXB1B_MAIZE	Beta-expansin 1b (Pollen allergen Zea m 1) (Zea m I) (Fragment)	0.00	-	cyt	0					191
Q95332 UniProt NPD GO	BHMT_PIG	Betaine--homocysteine S-methyltransferase (EC 2.1.1.5) (Fragment)	0.00	-	cyt	0	Cytoplasm				277
P80163 UniProt NPD GO	BTX_ATRBI	Bibrotoxin (BTX)	0.00	-	cyt	0	Secreted protein				21
P23473 UniProt NPD GO	CHLY_PARTH	Bifunctional chitinase/lysozyme [Includes: Chitinase (EC 3.2.1.14); Lysozyme (EC 3.2.1.17)] (Fragmen ...	0.00	-	cyt	0	Secreted protein; extracellular space				47
P80957 UniProt NPD GO	DEF_TACTR	Big defensin	0.00	-	vac	1 *	Secreted protein. L- and S-granules				79
Q63276 UniProt NPD GO	BAAT_RAT	Bile acid CoA:amino acid N-acyltransferase (EC 2.3.1.65) (BAT) (BACAT) (Glycine N-choloyltransferase ...	0.00	-	nuc	0	Peroxisome				420
P09464 UniProt NPD GO	BBP_PIEBR	Bilin-binding protein precursor (BBP)	0.00	-	exc	0				1T0V	189
P05115 UniProt NPD GO	BCCP_LYCES	Biotin carboxyl carrier protein of acetyl-CoA carboxylase (BCCP) (Fragment)	0.00	-	cyt	0	Plastid; chloroplast				70
P43251 UniProt NPD GO	BTD_HUMAN	Biotinidase precursor (EC 3.5.1.12)	0.00	-	mit	0	Secreted protein; extracellular space		609019		523
P58752 UniProt NPD GO	BIRT_PARTR	Birtoxin	0.00	-	cyt	0	Secreted protein				58
P07096 UniProt NPD GO	APL2_PETMA	Blood plasma apolipoprotein LAL2 precursor	0.00	-	exc	0	Secreted protein				191
P83767 UniProt NPD GO	BP2_PROTR	Blooming-related protein 2 (BP2) (Fragment)	0.00	-		0					20
P51491 UniProt NPD GO	OPSB_MOUSE	Blue-sensitive opsin (BOP) (Blue cone photoreceptor pigment) (Short wavelength-sensitive cone opsin) ...	0.00	-	end	7 *	Membrane; multi-pass membrane protein	photoreceptor outer segment [IDA]			346
Q63652 UniProt NPD GO	OPSB_RAT	Blue-sensitive opsin (BOP) (Blue cone photoreceptor pigment) (Short wavelength-sensitive cone opsin) ...	0.00	-	end	7 *	Membrane; multi-pass membrane protein				346
P51472 UniProt NPD GO	OPSB_ASTFA	Blue-sensitive opsin (Blue cone photoreceptor pigment)	0.00	-	end	7 *	Membrane; multi-pass membrane protein				355
P32310 UniProt NPD GO	OPSB_CARAU	Blue-sensitive opsin (Blue cone photoreceptor pigment)	0.00	-	end	7 *	Membrane; multi-pass membrane protein	integral to membrane [IDA]			351
P28682 UniProt NPD GO	OPSB_CHICK	Blue-sensitive opsin (Blue cone photoreceptor pigment)	0.00	-	end	7 *	Membrane; multi-pass membrane protein				361
O13227 UniProt NPD GO	OPSB_CONCO	Blue-sensitive opsin (Blue cone photoreceptor pigment)	0.00	-	end	7 *	Membrane; multi-pass membrane protein				350
P35357 UniProt NPD GO	OPSB_GECGE	Blue-sensitive opsin P467 (Blue photoreceptor pigment)	0.00	-	end	7 *	Membrane; multi-pass membrane protein				355
O76243 UniProt NPD GO	GLBB_CERLA	Body wall hemoglobin	0.00	-	cyt	0					109
P82282 UniProt NPD GO	BMNH1_BOMVA	Bombinin-H1/H3	0.00	-	nuc	0	Secreted protein				21
P82284 UniProt NPD GO	BMNH4_BOMVA	Bombinin-H4	0.00	-	nuc	0	Secreted protein				21
P82285 UniProt NPD GO	BMNH5_BOMVA	Bombinin-H5	0.00	-	nuc	0	Secreted protein				21
P29003 UniProt NPD GO	BMNL2_BOMOR	Bombinin-like peptide 2 (BLP-2)	0.00	-	cyt	0	Secreted protein				27
P29005 UniProt NPD GO	BMNL4_BOMOR	Bombinin-like peptide 4 (BLP-4)	0.00	-	cyt	0	Secreted protein				25
P07493 UniProt NPD GO	BOL2_MEGPE	Bombolitin-2 (Bombolitin II)	0.00	-		0	Secreted protein				17
P07494 UniProt NPD GO	BOL3_MEGPE	Bombolitin-3 (Bombolitin III)	0.00	-		0	Secreted protein				17
P07495 UniProt NPD GO	BOL4_MEGPE	Bombolitin-4 (Bombolitin IV)	0.00	-		0	Secreted protein				17
P07496 UniProt NPD GO	BOL5_MEGPE	Bombolitin-5 (Bombolitin V)	0.00	-		0	Secreted protein				17
P26742 UniProt NPD GO	BXB8_BOMMO	Bombyxin B-8 precursor (BBX-B8) (4K-prothoracicotropic hormone) (4K-PTTH) [Contains: Bombyxin B-8 B ...	0.00	-	exc	0	Secreted protein				88
P22444 UniProt NPD GO	BMP3_BOVIN	Bone morphogenetic protein 3 (BMP-3) (Osteogenin) (BMP-3A) (Fragment)	0.00	-	cyt	0	Secreted protein				80
P34819 UniProt NPD GO	BMP7_CANFA	Bone morphogenetic protein 7 (BMP-7) (Osteogenic protein 1) (OP-1) (Fragment)	0.00	-	cyt	0	Secreted protein (By similarity)				187
P20416 UniProt NPD GO	HRJ_BOTJA	Bothrolysin (EC 3.4.24.50) (Hemorrhagic metalloproteinase J) (Fragment)	0.00	-	cyt	0	Secreted protein				29
P22028 UniProt NPD GO	BOTR_BOTJA	Botrocetin (Platelet coagglutinin) (Fragment)	0.00	-	nuc	0	Secreted protein				25

You are viewing entries 92851 to 92900 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.