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
Q6BQ61 UniProt NPD GO	RRP3_DEBHA	ATP-dependent rRNA helicase RRP3 (EC 3.6.1.-)	0.38	-	nuc	0	Nucleus (Probable)				477
P34073 UniProt NPD GO	NXLD_ACAAN	Acanthophin-D (Postsynaptic neurotoxin)	0.38	+	nuc	0	Secreted protein				74
P78820 UniProt NPD GO	COAC_SCHPO	Acetyl-CoA carboxylase (EC 6.4.1.2) (ACC) (Cell untimely torn protein 6) [Includes: Biotin carboxyla ...	0.38	-	mit	0	Cytoplasm				2280
Q00955 UniProt NPD GO	COAC_YEAST	Acetyl-CoA carboxylase (EC 6.4.1.2) (ACC) [Includes: Biotin carboxylase (EC 6.3.4.14)]	0.38	-	nuc	0	Cytoplasm	endoplasmic reticulum membrane [IDA] mitochondrion [IDA]		1W96	2233
Q6B8M3 UniProt NPD GO	ACCA_GRATL	Acetyl-coenzyme A carboxylase carboxyl transferase subunit alpha (EC 6.4.1.2) (Acetyl-CoA carboxylas ...	0.38	-	cyt	0	Plastid; chloroplast				328
O35381 UniProt NPD GO	AN32A_MOUSE	Acidic leucine-rich nuclear phosphoprotein 32 family member A (Potent heat-stable protein phosphatas ...	0.38	-	nuc	0	Nucleus. Cytoplasm. Shuttles between nucleus and cytoplasm. Translocates to the cytoplasm during the ...	nuclear matrix [IPI] nucleus [IDA]			247
Q64G17 UniProt NPD GO	AN32C_MOUSE	Acidic leucine-rich nuclear phosphoprotein 32 family member C	0.38	-	nuc	0					247
P62816 UniProt NPD GO	HRK_MOUSE	Activator of apoptosis harakiri (Neuronal death protein DP5) (BH3-interacting domain protein 3)	0.38	-	nuc	0					92
P62817 UniProt NPD GO	HRK_RAT	Activator of apoptosis harakiri (Neuronal death protein DP5) (BH3-interacting domain protein 3)	0.38	-	nuc	0					92
Q2KHT9 UniProt NPD GO	ACBD4_BOVIN	Acyl-CoA-binding domain-containing protein 4	0.38	-	nuc	1					303
Q04400 UniProt NPD GO	ADCY5_RAT	Adenylate cyclase type 5 (EC 4.6.1.1) (Adenylate cyclase type V) (ATP pyrophosphate-lyase 5) (Adenyl ...	0.38	-	end	11	Membrane; multi-pass membrane protein				1262
P36621 UniProt NPD GO	CAP_SCHPO	Adenylyl cyclase-associated protein (CAP)	0.38	-	nuc	0					551
Q27409 UniProt NPD GO	FP1_MYTGA	Adhesive plaque matrix protein precursor (Foot protein 1) (MGFP1) (MGFP-1)	0.38	-	nuc	0	Secreted protein				751
P51215 UniProt NPD GO	PHAF_PORPU	Allophycocyanin beta 18 chain	0.38	-	nuc	0	Plastid; chloroplast				169
P02503 UniProt NPD GO	CRYAA_DIDMA	Alpha crystallin A chain [Contains: Alpha crystallin A chain, short form]	0.38	-	mit	0					173
Q9EPF3 UniProt NPD GO	CRYAB_SPAJD	Alpha crystallin B chain (Alpha(B)-crystallin)	0.38	-	mit	0					175
Q61234 UniProt NPD GO	SNTA1_MOUSE	Alpha-1-syntrophin (59 kDa dystrophin-associated protein A1 acidic component 1) (Syntrophin 1)	0.38	-	mit	0	Sarcolemma; sarcolemmal membrane; peripheral membrane protein; cytoplasmic side. In skeletal muscle, ...	postsynaptic membrane [IDA]		2PDZ	503
Q60475 UniProt NPD GO	ADA2B_CAVPO	Alpha-2B adrenergic receptor (Alpha-2B adrenoceptor) (Alpha-2B adrenoreceptor)	0.38	-	end	7 *	Membrane; multi-pass membrane protein				448
O43768 UniProt NPD GO	ENSA_HUMAN	Alpha-endosulfine (ARPP-19e)	0.38	-	nuc	0	Cytoplasm (By similarity)		603061		121
P32811 UniProt NPD GO	PHSH_SOLTU	Alpha-glucan phosphorylase, H isozyme (EC 2.4.1.1) (Starch phosphorylase H)	0.38	-	cyt	0	Cytoplasm				838
Q8LPT9 UniProt NPD GO	GWD1_CITRE	Alpha-glucan water dikinase, chloroplast precursor (EC 2.7.9.4) (Starch-related protein R1)	0.38	-	mit	0	Plastid; chloroplast. Starch granules				1475
P38158 UniProt NPD GO	MAL32_YEAST	Alpha-glucosidase MAL32 (EC 3.2.1.20) (Maltase)	0.38	-	cyt	0				1VAD	584
P47186 UniProt NPD GO	MPH23_YEAST	Alpha-glucosides permease MPH2/3 (Maltose transport protein 2/3)	0.38	-	end	12	Membrane; multi-pass membrane protein (Potential)	integral to membrane [NAS]			602
P04728 UniProt NPD GO	GDA8_WHEAT	Alpha/beta-gliadin clone PTO-A10 (Prolamin) (Fragment)	0.38	-	nuc	0					186
Q9QXJ1 UniProt NPD GO	APBB1_MOUSE	Amyloid beta A4 precursor protein-binding family B member 1 (Fe65 protein)	0.38	-	nuc	0		growth cone [ISS] lamellipodium [ISS] nucleus [IDA] synapse [ISS]			710
P14724 UniProt NPD GO	CDC26_YEAST	Anaphase-promoting complex subunit CDC26 (Cell division control protein 26)	0.38	-	nuc	0	Nucleus	anaphase-promoting complex [TAS]			124
P56684 UniProt NPD GO	ANDT_ANDAU	Androctonin	0.38	-	mit	0	Secreted protein			1CZ6	25
Q86SA8 UniProt NPD GO	AGH_PORDI	Androgenic gland hormone precursor (Pod-AGH) [Contains: Androgenic gland hormone B chain; Androgenic ...	0.38	-	exc	0	Secreted protein				146
P47820 UniProt NPD GO	ACE_RAT	Angiotensin-converting enzyme, somatic isoform precursor (EC 3.4.15.1) (Dipeptidyl carboxypeptidase ...	0.38	-	end	1	Cell membrane; single-pass type I membrane protein (By similarity). Processed form: Secreted protein ...				1313
Q5U2S6 UniProt NPD GO	ASB2_RAT	Ankyrin repeat and SOCS box protein 2 (ASB-2)	0.38	-	nuc	0					634
Q8R560 UniProt NPD GO	ANKR1_RAT	Ankyrin repeat domain-containing protein 1 (Cardiac ankyrin repeat protein) (Cardiac adriamycin-resp ...	0.38	+	cyt	0	Nucleus	nucleus [TAS]			319
Q07076 UniProt NPD GO	ANXA7_MOUSE	Annexin A7 (Annexin VII) (Synexin)	0.38	-	nuc	0		cytosol [IDA] nuclear envelope [IDA] nucleus [IDA] plasma membrane [IDA]			463
Q40286 UniProt NPD GO	UFOG4_MANES	Anthocyanidin 3-O-glucosyltransferase (EC 2.4.1.115) (Flavonol 3-O-glucosyltransferase 4) (UDP-gluco ...	0.38	-	mit	0					241
P83137 UniProt NPD GO	AFP3_MALPA	Antifungal protein 3 (CW-3) (Fragment)	0.38	-		0	Secreted protein				15
Q06601 UniProt NPD GO	APD14_APIME	Apidaecins type 14 precursor [Contains: Apidaecin-2 (Apidaecin II); Apidaecin-1B (Apidaecin IB); Api ...	0.38	-	nuc	1 *	Secreted protein				168
Q8BVF9 UniProt NPD GO	AMZ1_MOUSE	Archaemetzincin-1 (EC 3.-.-.-) (Archeobacterial metalloproteinase-like protein 1)	0.38	-	cyt	0					502
P50298 UniProt NPD GO	ARY2_RAT	Arylamine N-acetyltransferase 2 (EC 2.3.1.5) (Arylamide acetylase 2) (N-acetyltransferase type 2) (N ...	0.38	-	cyt	0	Cytoplasm				290
Q12303 UniProt NPD GO	YPS3_YEAST	Aspartic proteinase yapsin-3 precursor (EC 3.4.23.-)	0.38	-	exc	0	Cell membrane; lipid-anchor; GPI-anchor	anchored to plasma membrane [IDA] plasma membrane [IDA]			508
P15178 UniProt NPD GO	SYD_RAT	Aspartyl-tRNA synthetase (EC 6.1.1.12) (Aspartate--tRNA ligase) (AspRS)	0.38	-	cyt	0	Cytoplasm	aminoacyl-tRNA synthetase multienzyme complex [TAS]			501
Q62048 UniProt NPD GO	PEA15_MOUSE	Astrocytic phosphoprotein PEA-15	0.38	-	nuc	0	Cytoplasm. Associated with microtubules	membrane fraction [TAS] microtubule associated complex [NAS]			130
P83964 UniProt NPD GO	ANF_ACITR	Atrial natriuretic factor precursor (ANF) (Atrial natriuretic peptide) (ANP) (Prepronatriodilatin)	0.38	-	nuc	0	Secreted protein				142
Q6BH63 UniProt NPD GO	ATG16_DEBHA	Autophagy protein 16	0.38	-	nuc	0	Vacuole (By similarity). Cytoplasmic vesicle (By similarity). Vesicular and vacuolar. Found in punct ...				183
Q520U5 UniProt NPD GO	ATG16_MAGGR	Autophagy protein 16	0.38	-	nuc	0	Vacuole (By similarity). Cytoplasmic vesicle (By similarity). Vesicular and vacuolar. Found in punct ...				204
Q6BZZ1 UniProt NPD GO	ATG12_YARLI	Autophagy-related protein 12 (Autophagy-related ubiquitin-like modifier ATG12)	0.38	-	nuc	0	Cytoplasm (By similarity)				205
Q7Z3C6 UniProt NPD GO	ATG9A_HUMAN	Autophagy-related protein 9A (APG9-like 1)	0.38	-	end	5	Membrane; multi-pass membrane protein (Potential)				839
Q3T904 UniProt NPD GO	ATG9A_BOVIN	Autophagy-related protein 9A (APG9-like 1) (Autophagy protein 9)	0.38	-	end	5	Membrane; multi-pass membrane protein (Potential)				839
Q8LAL2 UniProt NPD GO	IAA26_ARATH	Auxin-responsive protein IAA26 (Indoleacetic acid-induced protein 26) (Phytochrome-associated protei ...	0.38	-	nuc	0	Nucleus (By similarity)				269
Q5W0U4 UniProt NPD GO	BSPRY_HUMAN	B box and SPRY domain-containing protein	0.38	-	cyt	0	Cytoplasm. Membrane; peripheral membrane protein (By similarity)				402
Q8BGV7 UniProt NPD GO	KCD13_MOUSE	BTB/POZ domain-containing protein KCTD13 (Polymerase delta-interacting protein 1)	0.38	-	nuc	0	Nucleus (By similarity)				329
P19661 UniProt NPD GO	BCTN7_BOVIN	Bactenecin-7 precursor (Bac7) (Cathelicidin-3) (PR-59)	0.38	-	nuc	1 *	Secreted protein				190

You are viewing entries 33201 to 33250 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.