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
P02713 UniProt NPD GO	ACHG_CHICK	Acetylcholine receptor protein subunit gamma precursor	0.35	-	end	4	Membrane; multi-pass membrane protein				514
Q23022 UniProt NPD GO	ACH5_CAEEL	Acetylcholine receptor subunit alpha-type unc-38 precursor (Uncoordinated protein 38)	0.35	-	end	4	Membrane; multi-pass membrane protein	synapse [IDA]			511
P51122 UniProt NPD GO	AN32A_BOVIN	Acidic leucine-rich nuclear phosphoprotein 32 family member A (Leucine-rich acidic nuclear protein) ...	0.35	-	nuc	0	Nucleus. Cytoplasm. Shuttles between nucleus and cytoplasm (By similarity)				249
Q2PT36 UniProt NPD GO	AICDA_BOVIN	Activation-induced cytidine deaminase (EC 3.5.4.5) (Cytidine aminohydrolase)	0.35	-	cyt	0					199
Q9Z1N0 UniProt NPD GO	ACOX1_CAVPO	Acyl-coenzyme A oxidase 1, peroxisomal (EC 1.3.3.6) (Palmitoyl-CoA oxidase) (AOX)	0.35	-	pox	0	Peroxisome (By similarity)				661
Q8NFM4 UniProt NPD GO	ADCY4_HUMAN	Adenylate cyclase type 4 (EC 4.6.1.1) (Adenylate cyclase type IV) (ATP pyrophosphate-lyase 4) (Adeny ...	0.35	-	end	12 *	Membrane; multi-pass membrane protein		600292		1077
Q28173 UniProt NPD GO	RAGE_BOVIN	Advanced glycosylation end product-specific receptor precursor (Receptor for advanced glycosylation ...	0.35	-	end	1	Membrane; single-pass type I membrane protein				416
Q38841 UniProt NPD GO	AGL12_ARATH	Agamous-like MADS-box protein AGL12	0.35	-	nuc	0	Nucleus (By similarity)				211
Q9NXW9 UniProt NPD GO	ALKB4_HUMAN	Alkylated repair protein alkB homolog 4	0.35	-	cyt	0					302
Q9V778 UniProt NPD GO	ADAS_DROME	Alkyldihydroxyacetonephosphate synthase (EC 2.5.1.26) (Alkyl-DHAP synthase) (Alkylglycerone-phosphat ...	0.35	-	pox	0	Peroxisome (By similarity)				631
Q9EQR2 UniProt NPD GO	ADAS_RAT	Alkyldihydroxyacetonephosphate synthase, peroxisomal precursor (EC 2.5.1.26) (Alkyl-DHAP synthase) ( ...	0.35	-	cyt	0	Peroxisome (By similarity)	peroxisome [TAS]			644
P02499 UniProt NPD GO	CRYAA_PROCA	Alpha crystallin A chain [Contains: Alpha crystallin A chain, short form]	0.35	-	mit	0					173
P02510 UniProt NPD GO	CRYAB_BOVIN	Alpha crystallin B chain (Alpha(B)-crystallin)	0.35	-	mit	0					175
Q11131 UniProt NPD GO	FUT7_MOUSE	Alpha-(1,3)-fucosyltransferase (EC 2.4.1.-) (Galactoside 3-L-fucosyltransferase) (Fucosyltransferase ...	0.35	-	cyt	1	Golgi apparatus; Golgi stack; Golgi stack membrane; single-pass type II membrane protein. Membrane-b ...				389
P53535 UniProt NPD GO	PHSL2_SOLTU	Alpha-1,4 glucan phosphorylase L-2 isozyme, chloroplast precursor (EC 2.4.1.1) (Starch phosphorylase ...	0.35	-	mit	0	Plastid; chloroplast. Plastid; amyloplast				974
Q61838 UniProt NPD GO	A2MG_MOUSE	Alpha-2-macroglobulin precursor (Alpha-2-M) [Contains: Alpha-2-macroglobulin 165 kDa subunit; Alpha- ...	0.35	-	mit	0	Secreted protein	extracellular region [TAS]			1495
P18089 UniProt NPD GO	ADA2B_HUMAN	Alpha-2B adrenergic receptor (Alpha-2B adrenoceptor) (Alpha-2B adrenoreceptor) (Alpha-2 adrenergic r ...	0.35	-	end	7 *	Membrane; multi-pass membrane protein	integral to plasma membrane [TAS] plasma membrane [TAS]	104260		450
O19012 UniProt NPD GO	ADA2B_ERIEU	Alpha-2B adrenergic receptor (Alpha-2B adrenoceptor) (Alpha-2B adrenoreceptor) (Fragment)	0.35	-	end	6 *	Membrane; multi-pass membrane protein				391
O77830 UniProt NPD GO	ADA2B_RABIT	Alpha-2B adrenergic receptor (Alpha-2B adrenoceptor) (Alpha-2B adrenoreceptor) (Fragment)	0.35	-	end	6 *	Membrane; multi-pass membrane protein (By similarity)				394
P68210 UniProt NPD GO	ENSA_BOVIN	Alpha-endosulfine (ARPP-19e)	0.35	-	nuc	0	Cytoplasm (By similarity)				121
P68211 UniProt NPD GO	ENSA_PIG	Alpha-endosulfine (ARPP-19e)	0.35	-	nuc	0	Cytoplasm (By similarity)				121
P28050 UniProt NPD GO	FETA_GORGO	Alpha-fetoprotein precursor (Alpha-fetoglobulin) (Alpha-1-fetoprotein)	0.35	-	vac	0	Secreted protein				609
P02771 UniProt NPD GO	FETA_HUMAN	Alpha-fetoprotein precursor (Alpha-fetoglobulin) (Alpha-1-fetoprotein)	0.35	-	vac	0	Secreted protein		104150		609
P47710 UniProt NPD GO	CAS1_HUMAN	Alpha-s1-casein precursor [Contains: Casoxin D]	0.35	-	exc	0	Secreted protein		115450		185
O08523 UniProt NPD GO	TECTA_MOUSE	Alpha-tectorin precursor	0.35	-	nuc	0	Cell membrane; lipid-anchor; GPI-anchor; extracellular side (Probable). Found in the non-collagenous ...	extracellular matrix (sensu Metazoa) [IDA]			2155
Q99217 UniProt NPD GO	AMELX_HUMAN	Amelogenin, X isoform precursor	0.35	-	exc	0	Secreted protein; extracellular space; extracellular matrix	extracellular matrix (sensu Metazoa) [NAS]	301200		191
Q5ZL23 UniProt NPD GO	AB1IP_CHICK	Amyloid beta A4 precursor protein-binding family B member 1-interacting protein (APBB1-interacting p ...	0.35	-	nuc	0	Cell membrane; peripheral membrane protein (By similarity)				485
Q8WN66 UniProt NPD GO	ANGI_CERAE	Angiogenin precursor (EC 3.1.27.-) (Ribonuclease 5) (RNase 5)	0.35	-	exc	1 *	Secreted protein	basal lamina [ISS] extracellular space [ISS] nucleolus [ISS] nucleus [ISS]			146
Q8CFN1 UniProt NPD GO	ACET_RAT	Angiotensin-converting enzyme, testis-specific isoform precursor (EC 3.4.15.1) (EC 3.2.1.-) (ACE-T) ...	0.35	-	end	1	Cell membrane; single-pass type I membrane protein (By similarity). Processed form: Secreted protein ...				775
Q810B6 UniProt NPD GO	ANFY1_MOUSE	Ankyrin repeat and FYVE domain-containing protein 1 (Ankyrin repeats hooked to a zinc finger motif)	0.35	-	nuc	0	Cytoplasm. Endosome; endosomal membrane; peripheral membrane protein. Also associated with endosomal ...	endosome membrane [IDA]			1169
Q5ZMD2 UniProt NPD GO	ANKY2_CHICK	Ankyrin repeat and MYND domain-containing protein 2	0.35	-	nuc	0					460
Q8IZ07 UniProt NPD GO	ANR13_HUMAN	Ankyrin repeat domain-containing protein 13 (Protein KE03)	0.35	-	mit	0					590
Q3SWX7 UniProt NPD GO	ANXA3_BOVIN	Annexin A3 (Annexin III)	0.35	-	nuc	0					322
P14824 UniProt NPD GO	ANXA6_MOUSE	Annexin A6 (Annexin VI) (Lipocortin VI) (P68) (P70) (Protein III) (Chromobindin-20) (67 kDa calelect ...	0.35	-	cyt	0	Stress fibers (By similarity)	perinuclear region [IDA]			672
P03973 UniProt NPD GO	ALK1_HUMAN	Antileukoproteinase 1 precursor (ALP) (HUSI-1) (Seminal proteinase inhibitor) (Secretory leukocyte p ...	0.35	-	nuc	0	Secreted protein		107285		132
P81571 UniProt NPD GO	DEFD2_SPIOL	Antimicrobial peptide D2 (So-D2) (Defensin D2) (Fragment)	0.35	-	nuc	0	Cell wall				52
O42363 UniProt NPD GO	APOA1_BRARE	Apolipoprotein A-I precursor (Apo-AI) (ApoA-I)	0.35	-	exc	0	Secreted protein				262
Q6B959 UniProt NPD GO	APLD1_RAT	Apolipoprotein-L domain-containing protein 1 (Vascular early response gene protein)	0.35	-	cyt	2 *	Cell membrane; multi-pass membrane protein (By similarity)				246
Q6UW56 UniProt NPD GO	APR3_HUMAN	Apoptosis-related protein 3 precursor (APR-3) (p18)	0.35	-	end	1					229
P24058 UniProt NPD GO	ARLY2_ANAPL	Argininosuccinate lyase (EC 4.3.2.1) (Arginosuccinase) (ASAL) (Delta-2 crystallin) (Delta crystallin ...	0.35	-	nuc	0				1TJW	468
Q5U310 UniProt NPD GO	ARMX1_RAT	Armadillo repeat-containing X-linked protein 1	0.35	-	mit	1 *					461
P11245 UniProt NPD GO	ARY2_HUMAN	Arylamine N-acetyltransferase 2 (EC 2.3.1.5) (Arylamide acetylase 2) (Arylamine N-acetyltransferase, ...	0.35	-	cyt	1	Cytoplasm		243400		290
Q6UWY0 UniProt NPD GO	ARSK_HUMAN	Arylsulfatase K precursor (EC 3.1.6.-) (ASK) (Telethon sulfatase)	0.35	-	vac	1 *	Secreted protein (Potential)		610011		536
O48593 UniProt NPD GO	SYNO_ARATH	Asparaginyl-tRNA synthetase, chloroplast/mitochondrial precursor (EC 6.1.1.22) (Asparagine--tRNA lig ...	0.35	-	mit	0	Plastid; chloroplast. Mitochondrion				567
Q6HA09 UniProt NPD GO	ASTL_MOUSE	Astacin-like metalloendopeptidase precursor (EC 3.4.-.-) (Oocyte astacin) (Ovastacin)	0.35	-	exc	0					435
P18910 UniProt NPD GO	ANPRA_RAT	Atrial natriuretic peptide receptor A precursor (ANP-A) (ANPRA) (GC-A) (Guanylate cyclase) (EC 4.6.1 ...	0.35	-	nuc	0	Membrane; single-pass type I membrane protein			1T34	1057
Q6C794 UniProt NPD GO	ATG8_YARLI	Autophagy-related protein 8 precursor (Autophagy-related ubiquitin-like modifier ATG8)	0.35	-	cyt	0	Membrane-associated through a lipid anchor. Cvt vesicles, autophagosomes and vacuolar (By similarity ...				137
Q38828 UniProt NPD GO	IAA10_ARATH	Auxin-responsive protein IAA10 (Indoleacetic acid-induced protein 10)	0.35	-	nuc	0	Nucleus (By similarity)				261
Q8H174 UniProt NPD GO	IAA31_ARATH	Auxin-responsive protein IAA31 (Indoleacetic acid-induced protein 31)	0.35	-	nuc	0	Nucleus (By similarity)				158
Q6H543 UniProt NPD GO	IAA7_ORYSA	Auxin-responsive protein IAA7 (Indoleacetic acid-induced protein 7)	0.35	-	nuc	0	Nucleus (By similarity)				300

You are viewing entries 35601 to 35650 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.