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
P62899 UniProt NPD GO	RL31_HUMAN	60S ribosomal protein L31	0.37	-	nuc	0					125
P62900 UniProt NPD GO	RL31_MOUSE	60S ribosomal protein L31	0.37	-	nuc	0					125
P62901 UniProt NPD GO	RL31_PIG	60S ribosomal protein L31	0.37	-	nuc	0					125
P62902 UniProt NPD GO	RL31_RAT	60S ribosomal protein L31	0.37	-	nuc	0					125
Q91309 UniProt NPD GO	F26_RANCA	6PF-2-K/Fru-2,6-P2ASE liver/muscle isozymes [Includes: 6-phosphofructo-2-kinase (EC 2.7.1.105); Fruc ...	0.37	-	cyt	0					470
Q9LZB8 UniProt NPD GO	ATH12_ARATH	ABC2 homolog 12	0.37	+	end	2	Membrane; multi-pass membrane protein (Potential)				634
Q6TUF2 UniProt NPD GO	ACN9_RAT	ACN9 protein homolog, mitochondrial precursor (Liver regeneration-related protein LRRGT00092)	0.37	-	mit	0	Mitochondrion (Potential)	mitochondrial intermembrane space [ISS]			125
Q28478 UniProt NPD GO	ADAM2_MACFA	ADAM 2 precursor (A disintegrin and metalloproteinase domain 2) (Fertilin subunit beta) (PH-30) (PH3 ...	0.37	-	end	1	Membrane; single-pass type I membrane protein				735
Q63202 UniProt NPD GO	ADAM2_RAT	ADAM 2 precursor (A disintegrin and metalloproteinase domain 2) (Fertilin subunit beta) (PH-30) (PH3 ...	0.37	-	end	1	Membrane; single-pass type I membrane protein	acrosome [IDA]			737
Q05910 UniProt NPD GO	ADAM8_MOUSE	ADAM 8 precursor (EC 3.4.24.-) (A disintegrin and metalloproteinase domain 8) (Cell surface antigen ...	0.37	-	end	1	Membrane; single-pass type I membrane protein	plasma membrane [IDA]			826
Q923K9 UniProt NPD GO	ACF_RAT	APOBEC1 complementation factor (APOBEC1-stimulating protein)	0.37	-	nuc	0	Nucleus. Predominantly nuclear where it localizes to heterochromatin. Endoplasmic reticulum. Also cy ...	apolipoprotein B mRNA editing enzyme complex [ISS] cytoplasm [IDA] nuclear heterochromatin [IDA]			594
O62939 UniProt NPD GO	ATPF_PINTH	ATP synthase B chain (EC 3.6.3.14) (ATPase subunit I)	0.37	-	nuc	0	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein				184
Q9TM29 UniProt NPD GO	ATPX_CYACA	ATP synthase B' chain (EC 3.6.3.14) (Subunit II)	0.37	-	nuc	1 *	Plastid; chloroplast; chloroplast thylakoid membrane				157
Q02758 UniProt NPD GO	ATPD_PEA	ATP synthase delta chain, chloroplast precursor (EC 3.6.3.14)	0.37	-	mit	0	Plastid; chloroplast; chloroplast thylakoid membrane				251
Q92337 UniProt NPD GO	ABC1_SCHPO	ATP-binding cassette transporter abc1	0.37	-	end	17 *	Membrane; multi-pass membrane protein (Potential)				1427
Q09427 UniProt NPD GO	ABCC8_CRICR	ATP-binding cassette transporter sub-family C member 8 (Sulfonylurea receptor 1)	0.37	-	end	16 *	Membrane; multi-pass membrane protein				1581
Q59LU0 UniProt NPD GO	DBP2_CANAL	ATP-dependent RNA helicase DBP2 (EC 3.6.1.-)	0.37	+	cyt	0	Cytoplasm (By similarity). Nucleus (By similarity)				562
Q9QY15 UniProt NPD GO	DDX25_MOUSE	ATP-dependent RNA helicase DDX25 (EC 3.6.1.-) (DEAD box protein 25) (Gonadotropin-regulated testicul ...	0.37	-	cyt	0	Cytoplasm				484
Q96TA2 UniProt NPD GO	YMEL1_HUMAN	ATP-dependent metalloprotease YME1L1 (EC 3.4.24.-) (YME1-like protein 1) (ATP-dependent metalloprote ...	0.37	-	mit	0	Mitochondrion		607472		773
P28590 UniProt NPD GO	ABRC_ABRPR	Abrin-c precursor [Contains: Abrin-c A chain (EC 3.2.2.22) (rRNA N-glycosidase); Linker peptide; Abr ...	0.37	-	exc	0					562
Q9TTS3 UniProt NPD GO	COA1_BOVIN	Acetyl-CoA carboxylase 1 (EC 6.4.1.2) (ACC-alpha) [Includes: Biotin carboxylase (EC 6.3.4.14)]	0.37	-	nuc	0	Cytoplasm				2346
O00763 UniProt NPD GO	COA2_HUMAN	Acetyl-CoA carboxylase 2 (EC 6.4.1.2) (ACC-beta) [Includes: Biotin carboxylase (EC 6.3.4.14)]	0.37	-	cyt	0	Intracytoplasmic membrane. May associate with membranes		601557		2483
Q9V895 UniProt NPD GO	AN32A_DROME	Acidic leucine-rich nuclear phosphoprotein 32 family member A	0.37	-	nuc	0	Nucleus. Cytoplasm. Shuttles between nucleus and cytoplasm (By similarity)				261
P39687 UniProt NPD GO	AN32A_HUMAN	Acidic leucine-rich nuclear phosphoprotein 32 family member A (Potent heat-stable protein phosphatas ...	0.37	-	nuc	0	Nucleus. Cytoplasm. Shuttles between nucleus and cytoplasm	cytoplasm [TAS] endoplasmic reticulum [IDA] nucleus [IDA] perinuclear region [IDA]	600832		249
Q86QS6 UniProt NPD GO	AN32_SCHMA	Acidic leucine-rich nuclear phosphoprotein 32-related protein (ANP32/acidic nuclear phosphoprotein-l ...	0.37	-	nuc	0					296
P29108 UniProt NPD GO	STAD_BRANA	Acyl-[acyl-carrier-protein] desaturase, chloroplast precursor (EC 1.14.19.2) (Stearoyl-ACP desaturas ...	0.37	-	mit	0	Plastid; chloroplast. In green tissue, found in chloroplasts. Plastid. In non-photosynthetic tissue, ...				398
Q9R0H0 UniProt NPD GO	ACOX1_MOUSE	Acyl-coenzyme A oxidase 1, peroxisomal (EC 1.3.3.6) (Palmitoyl-CoA oxidase) (AOX)	0.37	-	pox	0	Peroxisome (By similarity)	mitochondrion [IDA] peroxisomal membrane [IDA] peroxisome [TAS]			661
Q91WF3 UniProt NPD GO	ADCY4_MOUSE	Adenylate cyclase type 4 (EC 4.6.1.1) (Adenylate cyclase type IV) (ATP pyrophosphate-lyase 4) (Adeny ...	0.37	-	end	12 *	Membrane; multi-pass membrane protein	dendrite [IDA] intracellular [IDA] plasma membrane [TAS]			1077
P39413 UniProt NPD GO	AEF1_DROME	Adult enhancer factor 1 (AEF-1)	0.37	-	nuc	0	Nucleus				308
Q62151 UniProt NPD GO	RAGE_MOUSE	Advanced glycosylation end product-specific receptor precursor (Receptor for advanced glycosylation ...	0.37	-	end	1 *	Membrane; single-pass type I membrane protein				403
Q61282 UniProt NPD GO	PGCA_MOUSE	Aggrecan core protein precursor (Cartilage-specific proteoglycan core protein) (CSPCP)	0.37	-	exc	0	Secreted protein; extracellular space; extracellular matrix (By similarity)	basement membrane [IDA]			2132
O00253 UniProt NPD GO	AGRP_HUMAN	Agouti-related protein precursor	0.37	-	exc	0	Secreted protein (By similarity)		601665	1MR0	132
Q58DM4 UniProt NPD GO	ALKB2_BOVIN	Alkylated repair protein alkB homolog 2	0.37	-	cyt	0					278
Q70XC3 UniProt NPD GO	ALLT_SPOFR	Allatotropin precursor (Spofr-AT) (AT)	0.37	-	mit	0	Secreted protein (By similarity)				200
Q62994 UniProt NPD GO	FUT4_RAT	Alpha-(1,3)-fucosyltransferase (EC 2.4.1.-) (Galactoside 3-L-fucosyltransferase) (Fucosyltransferase ...	0.37	-	mit	0	Golgi apparatus; Golgi stack; Golgi stack membrane; single-pass type II membrane protein. Membrane-b ...				433
Q5R4N8 UniProt NPD GO	A2MG_PONPY	Alpha-2-macroglobulin precursor (Alpha-2-M)	0.37	-	exc	0	Secreted protein (By similarity)				1474
Q90WY4 UniProt NPD GO	ADA2A_BRARE	Alpha-2A adrenergic receptor (Alpha-2A adrenoceptor) (Alpha-2A adrenoreceptor) (Alpha(2A)AR)	0.37	+	end	7 *	Membrane; multi-pass membrane protein	integral to plasma membrane [IC]			388
Q92185 UniProt NPD GO	SIA8A_HUMAN	Alpha-N-acetylneuraminide alpha-2,8-sialyltransferase (EC 2.4.99.8) (Ganglioside GD3 synthase) (Gang ...	0.37	+	gol	1 *	Golgi apparatus; Golgi membrane; single-pass type II membrane protein (Potential)	integral to membrane [TAS]	601123		356
P53537 UniProt NPD GO	PHSH_VICFA	Alpha-glucan phosphorylase, H isozyme (EC 2.4.1.1) (Starch phosphorylase H)	0.37	-	cyt	0	Cytoplasm				842
P02863 UniProt NPD GO	GDA0_WHEAT	Alpha/beta-gliadin precursor (Prolamin)	0.37	-	exc	0					286
Q9JHS6 UniProt NPD GO	ACCN4_RAT	Amiloride-sensitive cation channel 4 (Acid-sensing ion channel 4) (Spinal chord ASIC)	0.37	-	nuc	0	Membrane; multi-pass membrane protein (By similarity)				539
P46933 UniProt NPD GO	APBB1_RAT	Amyloid beta A4 precursor protein-binding family B member 1 (Fe65 protein)	0.37	-	nuc	0		growth cone [ISS] lamellipodium [ISS] nucleus [ISS] synapse [ISS]			711
Q6FI81 UniProt NPD GO	CPIN1_HUMAN	Anamorsin (Cytokine-induced apoptosis inhibitor 1) (CUA001)	0.37	-	nuc	0	Cytoplasm (By similarity)	cytoplasm [ISS]	608943		312
Q9U8R2 UniProt NPD GO	AGH_ARMVU	Androgenic gland hormone precursor (Arv-AGH) [Contains: Androgenic gland hormone B chain; Androgenic ...	0.37	-	nuc	0	Secreted protein				144
P22967 UniProt NPD GO	ACET_MOUSE	Angiotensin-converting enzyme, testis-specific isoform precursor (EC 3.4.15.1) (EC 3.2.1.-) (ACE-T) ...	0.37	-	end	1	Cell membrane; single-pass type I membrane protein (By similarity). Processed form: Secreted protein ...				732
Q3ZBX7 UniProt NPD GO	ANKR1_BOVIN	Ankyrin repeat domain-containing protein 1	0.37	+	cyt	0	Nucleus (By similarity)				319
Q7ZT11 UniProt NPD GO	ANKR1_CHICK	Ankyrin repeat domain-containing protein 1 (Cardiac ankyrin repeat protein)	0.37	+	nuc	0	Nucleus (By similarity)				319
Q865U8 UniProt NPD GO	ANKR1_PIG	Ankyrin repeat domain-containing protein 1 (Cardiac ankyrin repeat protein)	0.37	+	cyt	0	Nucleus (By similarity)				319
Q80UP5 UniProt NPD GO	ANR13_MOUSE	Ankyrin repeat domain-containing protein 13	0.37	-	mit	0					588
P19619 UniProt NPD GO	ANXA1_PIG	Annexin A1 (Annexin I) (Lipocortin I) (Calpactin II) (Chromobindin-9) (p35) (Phospholipase A2 inhibi ...	0.37	-	cyt	0				1MCX	346

You are viewing entries 33951 to 34000 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.