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
Q75BS4 UniProt NPD GO	DHH1_ASHGO	ATP-dependent RNA helicase DHH1 (EC 3.6.1.-)	0.44	-	nuc	0	Cytoplasm. Is concentrated in several cytoplasmic foci called P bodies (or cytoplasmic processing bo ...				484
Q6CXB7 UniProt NPD GO	HAS1_KLULA	ATP-dependent RNA helicase HAS1 (EC 3.6.1.-)	0.44	+	nuc	0	Nucleus; nucleolus (By similarity)				497
Q2UMH8 UniProt NPD GO	DBP3_ASPOR	ATP-dependent RNA helicase dbp3 (EC 3.6.1.-)	0.44	-	nuc	0	Nucleus; nucleolus (By similarity)				498
Q4WWD3 UniProt NPD GO	DHH1_ASPFU	ATP-dependent RNA helicase dhh1 (EC 3.6.1.-)	0.44	-	nuc	0	Cytoplasm. Is concentrated in several cytoplasmic foci called P bodies (or cytoplasmic processing bo ...				507
Q2UAK1 UniProt NPD GO	FAL1_ASPOR	ATP-dependent RNA helicase fal1 (EC 3.6.1.-)	0.44	-	nuc	0	Nucleus; nucleolus (By similarity)				398
Q5BBH7 UniProt NPD GO	ACN9_EMENI	Acetate non-utilizing protein 9, mitochondrial precursor	0.44	-	mit	0	Mitochondrion; mitochondrial intermembrane space (By similarity)				135
Q7ZUP0 UniProt NPD GO	AN32A_BRARE	Acidic leucine-rich nuclear phosphoprotein 32 family member A	0.44	-	nuc	0	Nucleus. Cytoplasm. Shuttles between nucleus and cytoplasm (By similarity)				254
Q07622 UniProt NPD GO	ACK1_YEAST	Activator of C kinase protein 1	0.44	-	nuc	0		mitochondrion [IDA]			623
P54822 UniProt NPD GO	PUR8_MOUSE	Adenylosuccinate lyase (EC 4.3.2.2) (Adenylosuccinase) (ASL) (ASASE)	0.44	-	mit	0					484
Q9SA98 UniProt NPD GO	ALKBH_ARATH	Alkylated DNA repair protein alkB homolog	0.44	-	cyt	0					354
Q05557 UniProt NPD GO	CRYAB_ANAPL	Alpha crystallin B chain (Alpha(B)-crystallin)	0.44	-	nuc	0					174
P39106 UniProt NPD GO	MNN1_YEAST	Alpha-1,3-mannosyltransferase MNN1 (EC 2.4.1.-)	0.44	-	mit	1 *	Golgi apparatus; Golgi membrane; single-pass type II membrane protein (Probable)	Golgi apparatus [IDA]			762
O42470 UniProt NPD GO	AES_XENLA	Amino-terminal enhancer of split (Amino enhancer of split) (GRG protein)	0.44	-	nuc	0	Nucleus (By similarity)				197
Q9D6J4 UniProt NPD GO	AB2BP_MOUSE	Amyloid beta A4 protein-binding family A member 2-binding protein (X11L-binding protein 51) (mXB51)	0.44	-	nuc	0	Cytoplasm (By similarity)	cytoplasm [ISS] endoplasmic reticulum [IDA] endoplasmic reticulum membrane [ISS] Golgi cis cisterna [ISS]			353
Q9UJX3 UniProt NPD GO	APC7_HUMAN	Anaphase-promoting complex subunit 7 (APC7) (Cyclosome subunit 7)	0.44	-	nuc	0			606949		565
O15123 UniProt NPD GO	ANGP2_HUMAN	Angiopoietin-2 precursor (ANG-2)	0.44	-	exc	0	Secreted protein	extracellular space [TAS]	601922		496
Q50JE5 UniProt NPD GO	ACE_MESAU	Angiotensin-converting enzyme, somatic isoform precursor (EC 3.4.15.1) (Dipeptidyl carboxypeptidase ...	0.44	-	end	1	Cell membrane; single-pass type I membrane protein (By similarity). Processed form: Secreted protein ...				1314
P12822 UniProt NPD GO	ACE_RABIT	Angiotensin-converting enzyme, somatic isoform precursor (EC 3.4.15.1) (Dipeptidyl carboxypeptidase ...	0.44	-	mit	1	Cell membrane; single-pass type I membrane protein (By similarity). Processed form: Secreted protein ...				1310
Q8NFD2 UniProt NPD GO	ANKK1_HUMAN	Ankyrin repeat and protein kinase domain-containing protein 1 (EC 2.7.11.1) (Protein kinase PKK2) (X ...	0.44	-	cyt	0			608774		765
P07150 UniProt NPD GO	ANXA1_RAT	Annexin A1 (Annexin I) (Lipocortin I) (Calpactin II) (Chromobindin-9) (p35) (Phospholipase A2 inhibi ...	0.44	-	cyt	0					345
P50995 UniProt NPD GO	ANX11_HUMAN	Annexin A11 (Annexin XI) (Calcyclin-associated annexin 50) (CAP-50) (56 kDa autoantigen)	0.44	-	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity). Found throughout the nucleoplasm at interphase a ...	cytoplasm [TAS] nuclear envelope [NAS] nucleoplasm [NAS] nucleus [TAS]	602572		505
P22621 UniProt NPD GO	AMA1_PLAFF	Apical membrane antigen 1 precursor (Merozoite surface antigen)	0.44	-	nuc	1	Membrane; single-pass type I membrane protein			1YXE	622
P50490 UniProt NPD GO	AMA1_PLAFG	Apical membrane antigen 1 precursor (Merozoite surface antigen)	0.44	-	nuc	1	Membrane; single-pass type I membrane protein				622
P50491 UniProt NPD GO	AMA1_PLAFH	Apical membrane antigen 1 precursor (Merozoite surface antigen)	0.44	-	nuc	1	Membrane; single-pass type I membrane protein				622
Q28758 UniProt NPD GO	APOA4_PAPAN	Apolipoprotein A-IV precursor (Apo-AIV) (ApoA-IV) (Fragment)	0.44	-	nuc	0	Secreted protein				401
Q6Q788 UniProt NPD GO	APOA5_HUMAN	Apolipoprotein A-V precursor (Apolipoprotein A5) (ApoAV) (ApoA-V) (Regeneration-associated protein 3 ...	0.44	-	cyt	0	Secreted protein	chylomicron [IDA] endoplasmic reticulum [IDA] extracellular region [IEP]	606368		366
Q8C7G5 UniProt NPD GO	APOA5_MOUSE	Apolipoprotein A-V precursor (Apolipoprotein A5) (ApoAV) (ApoA-V) (Regeneration-associated protein 3 ...	0.44	-	exc	0	Secreted protein				368
P18287 UniProt NPD GO	APOE_RABIT	Apolipoprotein E precursor (Apo-E)	0.44	-	exc	0	Secreted protein				311
P08519 UniProt NPD GO	APOA_HUMAN	Apolipoprotein(a) precursor (EC 3.4.21.-) (Apo(a)) (Lp(a))	0.44	-	nuc	0		extracellular region [NAS]	152200	4KIV	4548
Q5R644 UniProt NPD GO	API5_PONPY	Apoptosis inhibitor 5 (API-5)	0.44	-	cyt	0	Nucleus (By similarity). Mainly. Cytoplasm (By similarity)	cytoplasm [ISS] nucleus [ISS]			504
Q9BZZ5 UniProt NPD GO	API5_HUMAN	Apoptosis inhibitor 5 (API-5) (Fibroblast growth factor 2-interacting factor) (FIF) (Protein XAGL) ( ...	0.44	-	cyt	0	Nucleus. Mainly nuclear. Cytoplasm. Can also be cytoplasmic. Isoform 3: Cytoplasm	cytoplasm [NAS] nucleus [NAS] spliceosome complex [ISS]	609774		510
Q6PGD0 UniProt NPD GO	APR3_MOUSE	Apoptosis-related protein 3 precursor (APR-3)	0.44	-	end	1					223
Q9Z319 UniProt NPD GO	CORIN_MOUSE	Atrial natriuteric peptide-converting enzyme (EC 3.4.21.-) (pro-ANP-converting enzyme) (Corin) (Low ...	0.44	-	mit	1	Membrane; single-pass type II membrane protein				1113
Q5QA94 UniProt NPD GO	ATG18_PICAN	Autophagy-related protein 18	0.44	-	nuc	0	Membrane-associated. Peripheral membrane protein of pre-autophagosomal structure (PAS) and vacuole ( ...				525
Q5KHR3 UniProt NPD GO	ATG9_CRYNE	Autophagy-related protein 9	0.44	+	end	6	Membrane; multi-pass membrane protein. Pre-autophagosomal and other perivacuolar punctate structures ...				879
Q80YW5 UniProt NPD GO	BSPRY_MOUSE	B box and SPRY domain-containing protein	0.44	-	nuc	0	Cytoplasm. Membrane; peripheral membrane protein. Apical domain of kidney distal tubular cells				473
Q921K9 UniProt NPD GO	BCL7B_MOUSE	B-cell CLL/lymphoma 7 protein family member B	0.44	-	nuc	0					202
P48748 UniProt NPD GO	BKRB1_RABIT	B1 bradykinin receptor (BK-1 receptor) (B1R)	0.44	-	end	7 *	Membrane; multi-pass membrane protein				352
Q09242 UniProt NPD GO	BCL7_CAEEL	BCL7-like protein C28H8.1	0.44	-	nuc	0					146
Q8N5Z5 UniProt NPD GO	KCD17_HUMAN	BTB/POZ domain-containing protein KCTD17	0.44	-	nuc	0					314
Q5XJ34 UniProt NPD GO	KC15A_BRARE	BTB/POZ domain-containing protein kctd15-A	0.44	-	mit	0					257
Q8K2G4 UniProt NPD GO	BBS7_MOUSE	Bardet-Biedl syndrome 7 protein homolog (BBS2-like protein 1)	0.44	-	cyt	0					715
P02812 UniProt NPD GO	PRB2_HUMAN	Basic salivary proline-rich protein 2 (Salivary proline-rich protein) (Con1 glycoprotein) [Contains: ...	0.44	-	nuc	0			168810		382
P05813 UniProt NPD GO	CRBA1_HUMAN	Beta crystallin A3 [Contains: Beta crystallin A3, isoform A1, Delta4 form; Beta crystallin A3, isofo ...	0.44	-	nuc	0			600881		215
Q02742 UniProt NPD GO	GCNT1_HUMAN	Beta-1,3-galactosyl-O-glycosyl-glycoprotein beta-1,6-N-acetylglucosaminyltransferase (EC 2.4.1.102) ...	0.44	-	mit	1 *	Golgi apparatus; Golgi membrane; single-pass type II membrane protein	integral to membrane [TAS]	600391		428
Q91Z92 UniProt NPD GO	B3GT6_MOUSE	Beta-1,3-galactosyltransferase 6 (EC 2.4.1.134) (Beta 3GalT6) (Galactosylxylosylprotein 3-beta-galac ...	0.44	-	mit	1 *	Golgi apparatus; Golgi membrane; single-pass type II membrane protein (By similarity)	Golgi medial cisterna [IDA]			325
P32486 UniProt NPD GO	KRE6_YEAST	Beta-glucan synthesis-associated protein KRE6 (Killer toxin-resistance protein 6)	0.44	-	mit	1	Golgi apparatus; Golgi membrane; single-pass type II membrane protein	Golgi cis cisterna [IDA] integral to membrane [IDA]			720
Q6AZB0 UniProt NPD GO	BOC_MOUSE	Brother of CDO precursor (Protein BOC)	0.44	-	exc	1	Membrane; single-pass type I membrane protein (By similarity)			1X4Z	1110
P41238 UniProt NPD GO	ABEC1_HUMAN	C->U-editing enzyme APOBEC-1 (EC 3.5.4.-) (Apolipoprotein B mRNA-editing enzyme 1) (HEPR)	0.44	-	nuc	0			600130		236
Q8HY11 UniProt NPD GO	CLC4M_HYLSY	C-type lectin domain family 4 member M (CD209 antigen-like protein 1) (CD299 antigen)	0.44	-	nuc	1 *	Membrane; single-pass type II membrane protein (By similarity)				422

You are viewing entries 28801 to 28850 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.