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
P10762 UniProt NPD GO	APL3_LOCMI	Apolipophorin-3b precursor (Apolipophorin-IIIb) (ApoLp-IIIb)	0.24	-	exc	0	Secreted protein			1LS4	179
P04638 UniProt NPD GO	APOA2_RAT	Apolipoprotein A-II precursor (Apo-AII) (ApoA-II)	0.24	-	nuc	0	Secreted protein				102
P55797 UniProt NPD GO	APOC4_RAT	Apolipoprotein C-IV precursor (Apo-CIV) (ApoC-IV) (Apolipoprotein E-linked) (ECL) (Fragment)	0.24	-	exc	0	Secreted protein				88
Q9BZR8 UniProt NPD GO	B2L14_HUMAN	Apoptosis facilitator Bcl-2-like 14 protein (Apoptosis regulator Bcl-G)	0.24	-	cyt	0	Cytoplasm. Isoform 1: Cytoplasm; cytosol. Isoform 2: Intracytoplasmic membrane. Isoform 2 is predomi ...	cytosol [IDA] intracellular organelle [IDA]	606126		327
Q9EPV5 UniProt NPD GO	APAF_RAT	Apoptotic protease-activating factor 1 (Apaf-1)	0.24	-	cyt	0	Cytoplasm (By similarity)				1249
P49272 UniProt NPD GO	TXP9_APTSC	Aptotoxin-9 (Aptotoxin IX) (Paralytic peptide IX) (PP IX)	0.24	-	nuc	0	Secreted protein				76
P56401 UniProt NPD GO	AQP1_SHEEP	Aquaporin-1 (AQP-1) (Aquaporin-CHIP) (Water channel protein for red blood cells and kidney proximal ...	0.24	+	end	6 *	Membrane; multi-pass membrane protein				271
Q5RBE8 UniProt NPD GO	LOX15_PONPY	Arachidonate 15-lipoxygenase (EC 1.13.11.33) (Arachidonate omega-6 lipoxygenase) (15-LOX)	0.24	-	cyt	0	Cytoplasm (By similarity)				661
P04424 UniProt NPD GO	ARLY_HUMAN	Argininosuccinate lyase (EC 4.3.2.1) (Arginosuccinase) (ASAL)	0.24	-	cyt	0		cytoplasm [TAS]	207900	1K62	464
P17720 UniProt NPD GO	ARTM_ARTSA	Artemin	0.24	-	mit	0					229
Q9ULA0 UniProt NPD GO	DNPEP_HUMAN	Aspartyl aminopeptidase (EC 3.4.11.21)	0.24	-	cyt	0	Cytoplasm	cytoplasm [TAS]			475
Q03577 UniProt NPD GO	SYD_CAEEL	Aspartyl-tRNA synthetase (EC 6.1.1.12) (Aspartate--tRNA ligase) (AspRS)	0.24	-	cyt	0	Cytoplasm (By similarity)				531
P81991 UniProt NPD GO	CRVP1_AUSSU	Asurin-1 (Fragment)	0.24	-	nuc	0	Secreted protein				46
P09196 UniProt NPD GO	ANF_RANRI	Atrial natriuretic factor (ANF) (Atrial natriuretic peptide) (ANP)	0.24	-	mit	0	Secreted protein				30
P70180 UniProt NPD GO	ANPRC_MOUSE	Atrial natriuretic peptide clearance receptor precursor (ANP-C) (ANPRC) (NPR-C) (Atrial natriuretic ...	0.24	-	end	1	Membrane; single-pass type I membrane protein				536
P55202 UniProt NPD GO	ANPRB_ANGJA	Atrial natriuretic peptide receptor B precursor (ANP-B) (ANPRB) (GC-B) (Guanylate cyclase) (EC 4.6.1 ...	0.24	-	nuc	0	Membrane; single-pass type I membrane protein				1050
P49677 UniProt NPD GO	IAA1_ARATH	Auxin-responsive protein IAA1 (Indoleacetic acid-induced protein 1)	0.24	-	nuc	0	Nucleus				168
Q38829 UniProt NPD GO	IAA11_ARATH	Auxin-responsive protein IAA11 (Indoleacetic acid-induced protein 11)	0.24	-	nuc	0	Nucleus (By similarity)				246
Q96PM8 UniProt NPD GO	CU118_HUMAN	B lymphocyte activation-related protein BC-1514	0.24	-	nuc	0					130
P11911 UniProt NPD GO	CD79A_MOUSE	B-cell antigen receptor complex-associated protein alpha-chain precursor (IG-alpha) (MB-1 membrane g ...	0.24	-	end	1	Membrane; single-pass type I membrane protein	B cell receptor complex [IDA] external side of plasma membrane [IDA] multivesicular body [IDA]			220
Q61334 UniProt NPD GO	BAP29_MOUSE	B-cell receptor-associated protein 29 (BCR-associated protein Bap29)	0.24	-	end	3 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein				240
Q61335 UniProt NPD GO	BAP31_MOUSE	B-cell receptor-associated protein 31 (BCR-associated protein Bap31) (p28 Bap31)	0.24	-	end	2 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (By similarity). ...	Golgi membrane [IDA] plasma membrane [IPI]			244
Q3MHP8 UniProt NPD GO	BET1L_BOVIN	BET1-like protein	0.24	-	mit	1	Golgi apparatus; Golgi membrane; single-pass type IV membrane protein (By similarity)				111
Q9H3F6 UniProt NPD GO	KCD10_HUMAN	BTB/POZ domain-containing protein KCTD10	0.24	-	cyt	0	Nucleus (By similarity)				313
O88677 UniProt NPD GO	BTG3_RAT	BTG3 protein (Rbtg3)	0.24	-	nuc	0					252
P17453 UniProt NPD GO	BPI_BOVIN	Bactericidal permeability-increasing protein precursor (BPI)	0.24	-	mit	0	Membrane-associated in polymorphonuclear Leukocytes (PMN) granules (By similarity)				482
Q9LD45 UniProt NPD GO	BI1_ARATH	Bax inhibitor 1 (BI-1) (AtBI-1)	0.24	+	end	7 *	Membrane; multi-pass membrane protein (Potential)				247
P02525 UniProt NPD GO	CRBA1_MOUSE	Beta crystallin A1 (Beta-A1-crystallin)	0.24	-	cyt	0					198
Q91317 UniProt NPD GO	CRB32_RANCA	Beta crystallin A3-2	0.24	-	cyt	0					215
P43320 UniProt NPD GO	CRBB2_HUMAN	Beta crystallin B2 (Beta-crystallin Bp)	0.24	-	nuc	0			123620	1YTQ	204
P62698 UniProt NPD GO	CRBB2_MESAU	Beta crystallin B2 (Beta-crystallin Bp)	0.24	-	nuc	0					204
P62696 UniProt NPD GO	CRBB2_MOUSE	Beta crystallin B2 (Beta-crystallin Bp)	0.24	-	nuc	0				1E7N	204
P62697 UniProt NPD GO	CRBB2_RAT	Beta crystallin B2 (Beta-crystallin Bp)	0.24	-	nuc	0				1BD7	204
O09008 UniProt NPD GO	MFNG_MOUSE	Beta-1,3-N-acetylglucosaminyltransferase manic fringe (EC 2.4.1.222) (O-fucosylpeptide 3-beta-N-acet ...	0.24	-	mit	1 *	Golgi apparatus; Golgi membrane; single-pass type II membrane protein (By similarity)				321
Q9Z2Y2 UniProt NPD GO	B4GT2_MOUSE	Beta-1,4-galactosyltransferase 2 (EC 2.4.1.-) (Beta-1,4-GalTase 2) (Beta4Gal-T2) (b4Gal-T2) (UDP-gal ...	0.24	-	cyt	1 *	Golgi apparatus; Golgi stack; Golgi stack membrane; single-pass type II membrane protein (By similar ...				369
Q61235 UniProt NPD GO	SNTB2_MOUSE	Beta-2-syntrophin (59 kDa dystrophin-associated protein A1 basic component 2) (Syntrophin 3) (SNT3) ...	0.24	-	cyt	0	Membrane-associated. In insulinoma cell line, it is enriched in secretory granules (By similarity). ...	synapse [IDA]			520
Q95LI0 UniProt NPD GO	DB118_MACMU	Beta-defensin 118 precursor (Defensin, beta 118) (Epididymal secretory protein 13.6) (ESP13.6)	0.24	-	nuc	0	Secreted protein				123
O95340 UniProt NPD GO	PAPS2_HUMAN	Bifunctional 3'-phosphoadenosine 5'-phosphosulfate synthetase 2 (PAPS synthetase 2) (PAPSS 2) (Sulfu ...	0.24	-	cyt	0		intracellular [ISS]	603005	2AX4	614
O70127 UniProt NPD GO	ABCBB_RAT	Bile salt export pump (ATP-binding cassette sub-family B member 11) (Sister of P-glycoprotein)	0.24	-	end	9	Membrane; multi-pass membrane protein				1321
Q920N2 UniProt NPD GO	BPL1_MOUSE	Biotin--protein ligase (EC 6.3.4.-) (Biotin apo-protein ligase) [Includes: Biotin--[methylmalonyl-Co ...	0.24	-	mit	0	Cytoplasm (By similarity). Mitochondrion (By similarity)				722
Q28862 UniProt NPD GO	SIAL_BOVIN	Bone sialoprotein-2 precursor (Bone sialoprotein II) (BSP II) (Cell-binding sialoprotein) (Integrin- ...	0.24	-	exc	0	Secreted protein				310
P79780 UniProt NPD GO	SIAL_CHICK	Bone sialoprotein-2 precursor (Bone sialoprotein II) (BSP II) (Cell-binding sialoprotein) (Integrin- ...	0.24	-	exc	0	Secreted protein				276
P01060 UniProt NPD GO	IBB2_PHAVU	Bowman-Birk type proteinase inhibitor 2 (Bowman-Birk type proteinase inhibitor II)	0.24	-	nuc	0					79
P09864 UniProt NPD GO	IBB2_WHEAT	Bowman-Birk type proteinase inhibitor II-4 (Fragment)	0.24	-	nuc	0					53
P79777 UniProt NPD GO	BRAC_CHICK	Brachyury protein (T protein)	0.24	-	nuc	0	Nucleus				433
Q07998 UniProt NPD GO	BRAC_BRARE	Brachyury protein homolog (T protein homolog) (T-box protein ZfT) (Zf-T) (No tail protein)	0.24	-	nuc	0	Nucleus	nucleus [IDA]			423
Q91XV3 UniProt NPD GO	BASP_MOUSE	Brain acid soluble protein 1 (BASP1 protein) (Neuronal axonal membrane protein NAP-22) (22 kDa neuro ...	0.24	-	nuc	0	Membrane; lipid-anchor. Associated with the membranes of "growth cones" that form the tips of elonga ...				225
Q805D7 UniProt NPD GO	ANFB_FUGRU	Brain natriuretic peptide precursor (B-type natriuretic peptide)	0.24	-	exc	0	Secreted protein				133
Q9TST3 UniProt NPD GO	BDNF_FELCA	Brain-derived neurotrophic factor precursor (BDNF)	0.24	-	nuc	0	Secreted protein				247
P21237 UniProt NPD GO	BDNF_MOUSE	Brain-derived neurotrophic factor precursor (BDNF)	0.24	-	cyt	0	Secreted protein	cytoplasmic membrane-bound vesicle [IDA]			249

You are viewing entries 46051 to 46100 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.