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
P43883 UniProt NPD GO	ADFP_MOUSE	Adipophilin (Adipose differentiation-related protein) (ADRP)	0.21	-	mit	0	Membrane; peripheral membrane protein	lipid particle [IDA] nucleus [IDA] plasma membrane [IDA]			425
P43142 UniProt NPD GO	ADMR_MOUSE	Adrenomedullin receptor (AM-R) (G10D) (NOW)	0.21	-	end	7 *	Membrane; multi-pass membrane protein				395
Q8TD30 UniProt NPD GO	ALAT2_HUMAN	Alanine aminotransferase 2 (EC 2.6.1.2) (ALT2) (Glutamic--pyruvic transaminase 2) (GPT 2) (Glutamic- ...	0.21	-	mit	0			607438		523
Q940M2 UniProt NPD GO	AGT21_ARATH	Alanine--glyoxylate aminotransferase 2 homolog 1, mitochondrial precursor (EC 2.6.1.44) (Beta-alanin ...	0.21	-	mit	0	Mitochondrion	mitochondrion [IDA]			476
P49588 UniProt NPD GO	SYA_HUMAN	Alanyl-tRNA synthetase (EC 6.1.1.7) (Alanine--tRNA ligase) (AlaRS) (NY-REN-42 antigen)	0.21	-	cyt	0	Cytoplasm (Potential)	cytoplasm [TAS] soluble fraction [TAS]	601065		968
P81116 UniProt NPD GO	ABBB_TRIAB	Alboaggregin-B subunit beta	0.21	-	cyt	0	Secreted protein				118
Q9Z0U5 UniProt NPD GO	ADO_RAT	Aldehyde oxidase (EC 1.2.3.1)	0.21	-	cyt	0	Cytoplasm (By similarity)	cytosol [TAS]			1333
P80456 UniProt NPD GO	ADO_RABIT	Aldehyde oxidase (EC 1.2.3.1) (Retinal oxidase)	0.21	-	nuc	0	Cytoplasm				1334
P40690 UniProt NPD GO	ALKE_BABBO	Aldo-keto reductase (Fragment)	0.21	-	mit	0					285
P02497 UniProt NPD GO	CRYAA_MESAU	Alpha crystallin A chain [Contains: Alpha crystallin A chain, short form]	0.21	-	cyt	0					196
Q6BW42 UniProt NPD GO	ALG10_DEBHA	Alpha-1,2 glucosyltransferase ALG10 (EC 2.4.1.-) (Alpha-2-glucosyltransferase ALG10) (Dolichyl-phosp ...	0.21	-	end	10 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein				461
P04045 UniProt NPD GO	PHSL1_SOLTU	Alpha-1,4 glucan phosphorylase L-1 isozyme, chloroplast precursor (EC 2.4.1.1) (Starch phosphorylase ...	0.21	-	mit	0	Plastid; chloroplast. Plastid; amyloplast				966
P19652 UniProt NPD GO	A1AG2_HUMAN	Alpha-1-acid glycoprotein 2 precursor (AGP 2) (Orosomucoid-2) (OMD 2)	0.21	-	vac	0	Secreted protein	extracellular space [TAS]	138610		201
Q63805 UniProt NPD GO	A1AG3_MOUSE	Alpha-1-acid glycoprotein 3 precursor (AGP 3) (Orosomucoid-3) (OMD 3)	0.21	-	mit	0	Secreted protein				206
Q58DH9 UniProt NPD GO	NAGAB_BOVIN	Alpha-N-acetylgalactosaminidase precursor (EC 3.2.1.49) (Alpha-galactosidase B)	0.21	-	mit	0	Lysosome (By similarity)				411
P20840 UniProt NPD GO	SAG1_YEAST	Alpha-agglutinin precursor (AG-alpha-1)	0.21	-	exc	1	Cell membrane; lipid-anchor; GPI-anchor (Probable)	cell wall (sensu Fungi) [IDA]			650
Q08806 UniProt NPD GO	AMY2_DEBOC	Alpha-amylase 2 precursor (EC 3.2.1.1) (1,4-alpha-D-glucan glucanohydrolase 2)	0.21	-	nuc	0					507
P16159 UniProt NPD GO	IAC16_WHEAT	Alpha-amylase/trypsin inhibitor CM16 precursor (Chloroform/methanol-soluble protein CM16)	0.21	-	exc	1 *	Secreted protein				143
Q27601 UniProt NPD GO	PUR1_DROME	Amidophosphoribosyltransferase precursor (EC 2.4.2.14) (Glutamine phosphoribosylpyrophosphate amidot ...	0.21	-	cyt	0					546
Q64133 UniProt NPD GO	AOFA_MOUSE	Amine oxidase [flavin-containing] A (EC 1.4.3.4) (Monoamine oxidase type A) (MAO-A)	0.21	-	end	0	Mitochondrion; mitochondrial outer membrane	mitochondrion [IDA]			526
Q21988 UniProt NPD GO	AMX1_CAEEL	Amine oxidase family member 1	0.21	-	nuc	0					783
O49849 UniProt NPD GO	GCST_FLAAN	Aminomethyltransferase, mitochondrial precursor (EC 2.1.2.10) (Glycine cleavage system T protein) (G ...	0.21	-	cyt	0	Mitochondrion				407
P49363 UniProt NPD GO	GCST_FLAPR	Aminomethyltransferase, mitochondrial precursor (EC 2.1.2.10) (Glycine cleavage system T protein) (G ...	0.21	-	cyt	0	Mitochondrion				407
Q7TNJ4 UniProt NPD GO	AMGO2_RAT	Amphoterin-induced protein 2 precursor (AMIGO-2) (Alivin-1)	0.21	-	end	1	Cell membrane; single-pass type I membrane protein (Potential). Nucleus. Associated with nucleus as ...	integral to plasma membrane [NAS]			520
P31346 UniProt NPD GO	ANGI_PIG	Angiogenin (EC 3.1.27.-) (Ribonuclease 5) (RNase 5)	0.21	-	nuc	0	Secreted protein				123
Q861Y5 UniProt NPD GO	ANGI_COLGU	Angiogenin precursor (EC 3.1.27.-) (Ribonuclease 5) (RNase 5)	0.21	-	exc	1 *	Secreted protein	basal lamina [ISS] extracellular space [ISS] nucleolus [ISS] nucleus [ISS]			146
Q02763 UniProt NPD GO	TIE2_HUMAN	Angiopoietin-1 receptor precursor (EC 2.7.10.1) (Tyrosine-protein kinase receptor TIE-2) (hTIE2) (Ty ...	0.21	+	end	1	Membrane; single-pass type I membrane protein	integral to plasma membrane [TAS]	600195	2GY5	1124
Q10714 UniProt NPD GO	ACE_DROME	Angiotensin-converting enzyme precursor (EC 3.4.15.1) (Dipeptidyl carboxypeptidase I) (Kininase II)	0.21	-	end	0	Secreted protein; extracellular space			1J38	615
Q862Z2 UniProt NPD GO	ASB5_RABIT	Ankyrin repeat and SOCS box protein 5 (ASB-5)	0.21	-	nuc	1 *					329
P83597 UniProt NPD GO	EAP2_EUCUL	Antifungal peptide 2 (EAFP2)	0.21	-	nuc	0				1P9Z	41
O24006 UniProt NPD GO	AMP_IMPBA	Antimicrobial peptides precursor (IB-AMP) [Contains: Basic peptide AMP3 (IB-AMP3); Basic peptide AMP ...	0.21	-	exc	1 *	Secreted protein				333
Q03352 UniProt NPD GO	ANT3_CHICK	Antithrombin-III precursor (ATIII) (Fragment)	0.21	-	nuc	0	Secreted protein; extracellular space				105
P80703 UniProt NPD GO	APL3_GALME	Apolipophorin-3 precursor (Apolipophorin-III) (ApoLp-III)	0.21	-	exc	0	Secreted protein				186
P49267 UniProt NPD GO	TXP1_APTSC	Aptotoxin-1 (Aptotoxin I) (Paralytic peptide I) (PP I)	0.21	-	nuc	0	Secreted protein				74
P78540 UniProt NPD GO	ARGI2_HUMAN	Arginase-2, mitochondrial precursor (EC 3.5.3.1) (Arginase II) (Non-hepatic arginase) (Kidney-type a ...	0.21	-	nuc	0	Mitochondrion	mitochondrion [TAS]	107830	1PQ3	354
Q91YI0 UniProt NPD GO	ARLY_MOUSE	Argininosuccinate lyase (EC 4.3.2.1) (Arginosuccinase) (ASAL)	0.21	-	cyt	0					464
Q7L311 UniProt NPD GO	ARMX2_HUMAN	Armadillo repeat-containing X-linked protein 2 (Protein ALEX2) (ARM protein lost in epithelial cance ...	0.21	-	mit	1 *			300363		632
Q6NXE6 UniProt NPD GO	ARMC6_HUMAN	Armadillo repeat-containing protein 6	0.21	-	mit	0					501
Q96B67 UniProt NPD GO	ARRD3_HUMAN	Arrestin domain-containing protein 3	0.21	-	nuc	0					414
P51466 UniProt NPD GO	ARR1_ONCMY	Arrestin, red cell isoform 1 (CARR)	0.21	-	cyt	0					407
P51468 UniProt NPD GO	ARR3_ONCMY	Arrestin, red cell isoform 3 (CARR)	0.21	-	cyt	0					415
Q9NWB1 UniProt NPD GO	A2BP1_HUMAN	Ataxin-2-binding protein 1	0.21	-	nuc	0		Golgi apparatus [TAS]	605104	2ERR	397
Q9GLD0 UniProt NPD GO	ANF_FELCA	Atrial natriuretic factor precursor (ANF) (Atrial natriuretic peptide) (ANP) (Prepronatriodilatin)	0.21	-	exc	0	Secreted protein (By similarity)				153
P27596 UniProt NPD GO	ANF_CAVPO	Atrial natriuretic factor precursor (ANF) (Atrial natriuretic peptide) (ANP) (Prepronatriodilatin) [ ...	0.21	-	nuc	0	Secreted protein				128
Q99J83 UniProt NPD GO	ATG5_MOUSE	Autophagy protein 5 (APG5-like)	0.21	-	cyt	0	Cytoplasm. Cytoplasmic or associated with cytoplasmic isolation membrane	autophagic vacuole [IDA] cytoplasm [IDA]			275
O24541 UniProt NPD GO	AX22C_PHAAU	Auxin-induced protein 22C (Indole-3-acetic acid-induced protein ARG12)	0.21	-	cyt	0	Nucleus (By similarity)				188
P15308 UniProt NPD GO	B4_XENLA	B4 protein (Linker histone B4) (Histone H1-like protein)	0.21	+	nuc	0	Nucleus				273
Q07815 UniProt NPD GO	BAXC_HUMAN	BAX protein, cytoplasmic isoform gamma	0.21	-	nuc	0	Cytoplasm		600040		41
P15209 UniProt NPD GO	NTRK2_MOUSE	BDNF/NT-3 growth factors receptor precursor (EC 2.7.10.1) (Neurotrophic tyrosine kinase receptor typ ...	0.21	-	nuc	2 *	Membrane; single-pass type I membrane protein	cytosol [IDA] plasma membrane [IDA]			821
P70444 UniProt NPD GO	BID_MOUSE	BH3-interacting domain death agonist (BID) (p22 BID) [Contains: BH3-interacting domain death agonist ...	0.21	-	mit	0	Cytoplasm. When uncleaved, it is predominantly cytoplasmic. Mitochodrion; mitochondrial membrane. p1 ...			1DDB	195

You are viewing entries 49201 to 49250 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.