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
P27919 UniProt NPD GO	AVEN_AVESA	Avenin precursor	0.35	-	exc	0					214
Q6P6S3 UniProt NPD GO	BSPRY_RAT	B box and SPRY domain-containing protein (Zetin-1)	0.35	-	nuc	0	Cytoplasm. Membrane; peripheral membrane protein				448
Q8WUZ0 UniProt NPD GO	BCL7C_HUMAN	B-cell CLL/lymphoma 7 protein family member C	0.35	-	nuc	0			605847		217
Q96NJ5 UniProt NPD GO	BKLH5_HUMAN	BTB and kelch domain-containing protein 5	0.35	-	cyt	0					620
Q32L18 UniProt NPD GO	BTBDG_BOVIN	BTB/POZ domain-containing protein 16	0.35	-	nuc	0					499
Q6WVG3 UniProt NPD GO	KCD12_MOUSE	BTB/POZ domain-containing protein KCTD12 (Pfetin) (Predominantly fetal expressed T1 domain)	0.35	-	nuc	0					327
Q6DCX3 UniProt NPD GO	KCD15_XENLA	BTB/POZ domain-containing protein kctd15	0.35	-	mit	0					255
Q6P3P4 UniProt NPD GO	KCD15_XENTR	BTB/POZ domain-containing protein kctd15	0.35	-	mit	0					255
Q6DC02 UniProt NPD GO	KC15B_BRARE	BTB/POZ domain-containing protein kctd15-B	0.35	-	mit	0					257
Q8TAM1 UniProt NPD GO	BBS10_HUMAN	Bardet-Biedl syndrome 10 protein	0.35	-	mit	0			209900		723
P00989 UniProt NPD GO	IVB2_BUNMU	Beta bungarotoxin B2 chain precursor	0.35	-	exc	0	Secreted protein			1BUN	85
P14881 UniProt NPD GO	CRBA1_RAT	Beta crystallin A3 [Contains: Beta crystallin A3, isoform A1, Delta4 form; Beta crystallin A3, isofo ...	0.35	-	cyt	0					215
P07700 UniProt NPD GO	ADRB1_MELGA	Beta-1 adrenergic receptor (Beta-1 adrenoceptor) (Beta-1 adrenoreceptor) (Beta-T)	0.35	-	end	7 *	Membrane; multi-pass membrane protein			1DEP	483
Q5IS64 UniProt NPD GO	MFNG_PANTR	Beta-1,3-N-acetylglucosaminyltransferase manic fringe (EC 2.4.1.222) (O-fucosylpeptide 3-beta-N-acet ...	0.35	-	vac	0	Golgi apparatus; Golgi membrane; single-pass type II membrane protein (By similarity)				321
Q5EA87 UniProt NPD GO	B4GT3_BOVIN	Beta-1,4-galactosyltransferase 3 (EC 2.4.1.-) (Beta-1,4-GalTase 3) (Beta4Gal-T3) (b4Gal-T3) (UDP-gal ...	0.35	-	mit	1 *	Golgi apparatus; Golgi stack; Golgi stack membrane; single-pass type II membrane protein (By similar ...				396
P52757 UniProt NPD GO	CHIO_HUMAN	Beta-chimaerin (Beta-chimerin) (Rho-GTPase-activating protein 3)	0.35	-	cyt	0	Membrane; peripheral membrane protein (Potential)		602857	1XA6	468
Q30KK8 UniProt NPD GO	DB119_PANTR	Beta-defensin 119 precursor (Defensin, beta 119)	0.35	-	nuc	0	Secreted protein (Potential)				84
Q5R5N6 UniProt NPD GO	BGLR_PONPY	Beta-glucuronidase precursor (EC 3.2.1.31)	0.35	-	cyt	1 *	Lysosome (By similarity)				651
Q9JLV6 UniProt NPD GO	PNKP_MOUSE	Bifunctional polynucleotide phosphatase/kinase (Polynucleotide kinase-3'-phosphatase) (DNA 5'-kinase ...	0.35	-	cyt	0	Nucleus (By similarity)			1YJM	522
P54967 UniProt NPD GO	BIOB_ARATH	Biotin synthase (EC 2.8.1.6) (Biotin synthetase)	0.35	-	mit	0					378
P23359 UniProt NPD GO	BMP7_MOUSE	Bone morphogenetic protein 7 precursor (BMP-7) (Osteogenic protein 1) (OP-1)	0.35	-	exc	0	Secreted protein (By similarity)	extracellular space [IDA]			430
P55105 UniProt NPD GO	BMP8B_MOUSE	Bone morphogenetic protein 8B precursor (BMP-8B)	0.35	-	end	1 *	Secreted protein (By similarity)				399
Q9TUI7 UniProt NPD GO	ABEC1_MONDO	C->U-editing enzyme APOBEC-1 (EC 3.5.4.-) (Apolipoprotein B mRNA-editing enzyme 1)	0.35	-	nuc	0					235
Q67EQ1 UniProt NPD GO	CLC4E_RAT	C-type lectin domain family 4 member E (C-type lectin superfamily member 9) (Macrophage-inducible C- ...	0.35	-	nuc	1 *	Membrane; single-pass type II membrane protein (Probable)				215
P55208 UniProt NPD GO	ANFC_TRISC	C-type natriuretic peptide prohormone precursor (CNP-115) [Contains: CNP-39; CNP-38; CNP-22]	0.35	-	exc	0	Secreted protein				136
P16210 UniProt NPD GO	1A02_PANTR	CHLA class I histocompatibility antigen, A-5 alpha chain precursor	0.35	-	end	1	Membrane; single-pass type I membrane protein				362
P45432 UniProt NPD GO	CSN1_ARATH	COP9 signalosome complex subunit 1 (CSN complex subunit 1) (Constitutive photomorphogenesis protein ...	0.35	-	mit	0	Cytoplasm. Nucleus				441
P41547 UniProt NPD GO	CALC_CANFA	Calcitonin precursor	0.35	-	exc	0	Secreted protein				130
Q9JIN6 UniProt NPD GO	KCMB4_MOUSE	Calcium-activated potassium channel subunit beta 4 (Calcium-activated potassium channel, subfamily M ...	0.35	-	end	2 *	Membrane; multi-pass membrane protein (By similarity)	voltage-gated potassium channel complex [ISS]			210
P54653 UniProt NPD GO	CBP2_DICDI	Calcium-binding protein 2	0.35	-	nuc	0					168
Q2QMX9 UniProt NPD GO	ACA1_ORYSA	Calcium-transporting ATPase 1, plasma membrane-type (EC 3.6.3.8) (Ca(2+)-ATPase isoform 1) (Plastid ...	0.35	-	end	8	Membrane; multi-pass membrane protein (By similarity)				1020
O35350 UniProt NPD GO	CAN1_MOUSE	Calpain-1 catalytic subunit (EC 3.4.22.52) (Calpain-1 large subunit) (Calcium-activated neutral prot ...	0.35	-	cyt	0	Cytoplasm (By similarity). Cell membrane (By similarity). Translocates to the plasma membrane upon C ...				713
Q8VHB5 UniProt NPD GO	CAH9_MOUSE	Carbonic anhydrase 9 precursor (EC 4.2.1.1) (Carbonic anhydrase IX) (Carbonate dehydratase IX) (CA-I ...	0.35	-	exc	1					437
Q9N085 UniProt NPD GO	CAH10_MACFA	Carbonic anhydrase-related protein 10	0.35	-	nuc	0					328
Q5R4U0 UniProt NPD GO	CAH10_PONPY	Carbonic anhydrase-related protein 10	0.35	-	nuc	0					328
P61215 UniProt NPD GO	CAH10_MOUSE	Carbonic anhydrase-related protein 10 (Carbonic anhydrase-related protein X) (CARP X) (CA-RP X)	0.35	-	nuc	0					328
Q9NS85 UniProt NPD GO	CAH10_HUMAN	Carbonic anhydrase-related protein 10 (Carbonic anhydrase-related protein X) (CARP X) (CA-RP X) (Cer ...	0.35	-	nuc	0			604642		328
P13688 UniProt NPD GO	CEAM1_HUMAN	Carcinoembryonic antigen-related cell adhesion molecule 1 precursor (Biliary glycoprotein 1) (BGP-1) ...	0.35	-	nuc	1	Isoform A, isoform B, isoform C: Cell membrane; single-pass type I membrane protein. Isoform G, isof ...	integral to plasma membrane [NAS] membrane fraction [TAS]	109770		526
P31809 UniProt NPD GO	CEAM1_MOUSE	Carcinoembryonic antigen-related cell adhesion molecule 1 precursor (Biliary glycoprotein 1) (BGP-1) ...	0.35	-	end	1	Membrane; single-pass type I membrane protein				521
P50416 UniProt NPD GO	CPT1A_HUMAN	Carnitine O-palmitoyltransferase I, liver isoform (EC 2.3.1.21) (CPT I) (CPTI-L) (Carnitine palmitoy ...	0.35	-	nuc	2	Mitochondrion; mitochondrial outer membrane; multi-pass membrane protein	mitochondrion [TAS]	600528		773
P19139 UniProt NPD GO	CSK21_RAT	Casein kinase II subunit alpha (EC 2.7.11.1) (CK II)	0.35	-	mit	0		protein kinase CK2 complex [TAS]			391
O81275 UniProt NPD GO	CSK2D_ARATH	Casein kinase II subunit beta-3 (CK II beta-3)	0.35	-	nuc	0					276
P55865 UniProt NPD GO	CAS1A_XENLA	Caspase-1-A precursor (EC 3.4.22.-) (CASP-1-A) (Interleukin-1 beta convertase homolog A) (xICE-A)	0.35	-	nuc	0	Cytoplasm (By similarity)				386
Q64405 UniProt NPD GO	CATA_CAVPO	Catalase (EC 1.11.1.6)	0.35	-	cyt	0	Peroxisome (By similarity)				526
Q6NZY7 UniProt NPD GO	BORG3_HUMAN	Cdc42 effector protein 5 (Binder of Rho GTPases 3)	0.35	-	nuc	0	Intracytoplasmic membrane; peripheral membrane protein (By similarity)	cytoplasm [IDA] membrane [IDA]	609171		148
Q4KMG0 UniProt NPD GO	CDON_HUMAN	Cell adhesion molecule-related/down-regulated by oncogenes precursor	0.35	-	nuc	1	Membrane; single-pass membrane protein (Potential)		608707		1287
P25342 UniProt NPD GO	CDC10_YEAST	Cell division control protein 10	0.35	-	cyt	0	Membrane; peripheral membrane protein. Bud neck. Present at the bud neck during cell division. Proba ...	septin ring (sensu Saccharomyces) [TAS]			322
P36618 UniProt NPD GO	CDC16_SCHPO	Cell division control protein 16	0.35	-	nuc	0					299
P39826 UniProt NPD GO	CDC3_CANAL	Cell division control protein 3	0.35	-	cyt	0	Bud neck. Present at the bud neck during cell division (By similarity)				416
Q9ZPR1 UniProt NPD GO	CD48B_ARATH	Cell division control protein 48 homolog B (AtCDC48b)	0.35	-	nuc	0	Nucleus (By similarity). Phragmoplast (By similarity). Primarily localized to the nucleus and, durin ...				603

You are viewing entries 35651 to 35700 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.