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
P17177 UniProt NPD GO	CP27A_RABIT	Cytochrome P450 27, mitochondrial precursor (EC 1.14.13.15) (Cytochrome P-450C27/25) (Sterol 26-hydr ...	0.42	-	nuc	0	Mitochondrion				535
Q29473 UniProt NPD GO	CP2DF_CANFA	Cytochrome P450 2D15 (EC 1.14.14.1) (CYPIID15) (P450 DUT2)	0.42	-	end	2 *	Endoplasmic reticulum; endoplasmic reticulum membrane; peripheral membrane protein				499
P51590 UniProt NPD GO	CP2J3_RAT	Cytochrome P450 2J3 (EC 1.14.14.1) (CYPIIJ3)	0.42	-	nuc	2 *	Endoplasmic reticulum; endoplasmic reticulum membrane; peripheral membrane protein				502
O54750 UniProt NPD GO	CP2J6_MOUSE	Cytochrome P450 2J6 (EC 1.14.14.1) (CYPIIJ6) (Arachidonic acid epoxygenase)	0.42	-	mit	2 *	Endoplasmic reticulum; endoplasmic reticulum membrane; peripheral membrane protein				501
Q8K4D6 UniProt NPD GO	CP4X1_RAT	Cytochrome P450 4X1 (EC 1.14.14.1) (CYPIVX1)	0.42	-	nuc	1 *	Endoplasmic reticulum; endoplasmic reticulum membrane; peripheral membrane protein (By similarity)				507
Q42799 UniProt NPD GO	C93A2_SOYBN	Cytochrome P450 93A2 (EC 1.14.-.-)	0.42	-	nuc	1 *					502
O48957 UniProt NPD GO	C99A1_SORBI	Cytochrome P450 CYP99A1 (EC 1.14.-.-) (Fragment)	0.42	-	mit	0					519
Q9FI99 UniProt NPD GO	CNGT1_ARATH	Cytokinin-N-glucosyltransferase 1 (EC 2.4.1.-)	0.42	-	cyt	0					464
P52703 UniProt NPD GO	DRD3_CERAE	D(3) dopamine receptor	0.42	-	end	7 *	Membrane; multi-pass membrane protein				400
Q6CXI8 UniProt NPD GO	DAD2_KLULA	DASH complex subunit DAD2 (Outer kinetochore protein DAD2)	0.42	-	nuc	0	Nucleus (By similarity). Associates with the mitotic spindle and the kinetochore (By similarity)				132
O14285 UniProt NPD GO	SPC34_SCHPO	DASH complex subunit spc34 (Outer kinetochore protein spc34)	0.42	-	nuc	0	Nucleus. Associates with the mitotic spindle and the kinetochore. Kinetochore association occurs onl ...	DASH complex [IDA] spindle pole body [IDA]			164
P87324 UniProt NPD GO	DPOD2_SCHPO	DNA polymerase subunit delta 2 (EC 2.7.7.7)	0.42	-	nuc	0	Nucleus	delta DNA polymerase complex [TAS]			462
O61660 UniProt NPD GO	TOP3_CAEEL	DNA topoisomerase 3 (EC 5.99.1.2) (DNA topoisomerase III)	0.42	-	cyt	0					759
Q5E9N9 UniProt NPD GO	APEX2_BOVIN	DNA-(apurinic or apyrimidinic site) lyase 2 (EC 4.2.99.18) (Apurinic-apyrimidinic endonuclease 2) (A ...	0.42	-	nuc	0	Nucleus (By similarity). Mitochondrion (By similarity). Co-localizated partly with PCNA in nuclear f ...				514
P23571 UniProt NPD GO	3MG_RAT	DNA-3-methyladenine glycosylase (EC 3.2.2.21) (3-methyladenine DNA glycosidase) (ADPG) (3-alkyladeni ...	0.42	-	nuc	0	Nucleus (Potential)				317
Q2T9T3 UniProt NPD GO	RPB5_BOVIN	DNA-directed RNA polymerase II 23 kDa polypeptide (EC 2.7.7.6) (RPB25) (RPB5) (RPABC1)	0.42	-	nuc	0	Nucleus (By similarity)				210
Q80UW8 UniProt NPD GO	RPB5_MOUSE	DNA-directed RNA polymerase II 23 kDa polypeptide (EC 2.7.7.6) (RPB25) (RPB5) (RPABC1)	0.42	-	nuc	0	Nucleus (By similarity)				210
P17890 UniProt NPD GO	RPC8_YEAST	DNA-directed RNA polymerase III 31 kDa polypeptide (EC 2.7.7.6) (C31)	0.42	+	nuc	0	Nucleus	DNA-directed RNA polymerase III complex [TAS]			251
Q8SL94 UniProt NPD GO	RPOA_EUGAN	DNA-directed RNA polymerase alpha chain (EC 2.7.7.6) (PEP) (Plastid-encoded RNA polymerase subunit a ...	0.42	-	nuc	0	Plastid; chloroplast				207
Q68RX5 UniProt NPD GO	RPOA_PANGI	DNA-directed RNA polymerase alpha chain (EC 2.7.7.6) (PEP) (Plastid-encoded RNA polymerase subunit a ...	0.42	-	nuc	0	Plastid; chloroplast				353
Q6L370 UniProt NPD GO	RPOA_SACHY	DNA-directed RNA polymerase alpha chain (EC 2.7.7.6) (PEP) (Plastid-encoded RNA polymerase subunit a ...	0.42	-	cyt	0	Plastid; chloroplast				339
Q6ENT2 UniProt NPD GO	RPOA_SACOF	DNA-directed RNA polymerase alpha chain (EC 2.7.7.6) (PEP) (Plastid-encoded RNA polymerase subunit a ...	0.42	-	cyt	0	Plastid; chloroplast				339
P60315 UniProt NPD GO	RPOA_PHYPA	DNA-directed RNA polymerase alpha chain, chloroplast precursor (EC 2.7.7.6) (PEP) (Plastid-encoded R ...	0.42	-	cyt	0	Plastid; chloroplast				450
Q85FR7 UniProt NPD GO	RPOB_CYAME	DNA-directed RNA polymerase beta chain (EC 2.7.7.6) (PEP) (Plastid-encoded RNA polymerase subunit be ...	0.42	-	cyt	0	Plastid; chloroplast				1036
Q33C46 UniProt NPD GO	RPOB_NICTO	DNA-directed RNA polymerase beta chain (EC 2.7.7.6) (PEP) (Plastid-encoded RNA polymerase subunit be ...	0.42	-	cyt	0	Plastid; chloroplast				1070
Q32RG0 UniProt NPD GO	RPOB_ZYGCR	DNA-directed RNA polymerase beta chain (EC 2.7.7.6) (PEP) (Plastid-encoded RNA polymerase subunit be ...	0.42	-	cyt	0	Plastid; chloroplast				1063
Q4VZP2 UniProt NPD GO	RPOC1_CUCSA	DNA-directed RNA polymerase beta' chain (EC 2.7.7.6) (PEP) (Plastid-encoded RNA polymerase beta' sub ...	0.42	-	mit	0	Plastid; chloroplast				680
Q3V543 UniProt NPD GO	RPOC1_ACOCL	DNA-directed RNA polymerase gamma chain (EC 2.7.7.6) (RNAP gamma subunit) (Transcriptase gamma chain ...	0.42	-	cyt	0	Plastid; chloroplast				682
Q8GY03 UniProt NPD GO	DDPS4_ARATH	Dehydrodolichyl diphosphate synthase 4 (EC 2.5.1.-) (Dedol-PP synthase 4)	0.42	-	exc	0	Endoplasmic reticulum; endoplasmic reticulum membrane; single-pass membrane protein (By similarity)				289
P97399 UniProt NPD GO	DSPP_MOUSE	Dentin sialophosphoprotein precursor (Dentin matrix protein 3) (DMP-3) [Contains: Dentin phosphoprot ...	0.42	-	exc	1 *	Secreted protein (By similarity)				934
P48769 UniProt NPD GO	DCK_RAT	Deoxycytidine kinase (EC 2.7.1.74) (dCK)	0.42	-	cyt	0	Nucleus (By similarity)				260
P79119 UniProt NPD GO	PGLB_BOVIN	Dermatan sulfate proteoglycan 3 precursor (Epiphycan) (Small chondroitin/dermatan sulfate proteoglyc ...	0.42	-	exc	0	Secreted protein; extracellular space; extracellular matrix (By similarity)				321
Q9JIQ3 UniProt NPD GO	DBLOH_MOUSE	Diablo homolog, mitochondrial precursor (Second mitochondria-derived activator of caspase) (Smac pro ...	0.42	-	mit	0	Mitochondrion. But released into the cytosol when cells undergo apoptosis	cytoplasm [IDA] mitochondrion [IDA]			237
Q7XBQ9 UniProt NPD GO	RGA2_SOLBU	Disease resistance protein RGA2 (RGA2-blb) (Blight resistance protein RPI)	0.42	-	cyt	0					970
Q5FVM7 UniProt NPD GO	DJC16_RAT	DnaJ homolog subfamily C member 16 precursor	0.42	-	end	1 *	Membrane; single-pass type IV membrane protein (Potential)				771
Q5EA84 UniProt NPD GO	DOK1_BOVIN	Docking protein 1 (Downstream of tyrosine kinase 1)	0.42	-	nuc	0					483
Q9Y6C2 UniProt NPD GO	EMIL1_HUMAN	EMILIN-1 precursor (Elastin microfibril interface-located protein 1) (Elastin microfibril interfacer ...	0.42	-	mit	0	Secreted protein; extracellular space; extracellular matrix. Found mainly at the interface between a ...		130660		1016
Q9BXX0 UniProt NPD GO	EMIL2_HUMAN	EMILIN-2 precursor (Elastin microfibril interface-located protein 2) (Elastin microfibril interfacer ...	0.42	-	mit	0	Secreted protein; extracellular space; extracellular matrix. Found mainly at the interface between a ...	extracellular region [IDA]	608928		1053
P41970 UniProt NPD GO	ELK3_HUMAN	ETS domain-containing protein Elk-3 (ETS-related protein NET) (ETS-related protein ERP) (SRF accesso ...	0.42	-	nuc	0	Nucleus		600247		407
P43268 UniProt NPD GO	ETV4_HUMAN	ETS translocation variant 4 (Adenovirus E1A enhancer-binding protein) (E1A-F)	0.42	-	nuc	0	Nucleus	nucleus [NAS]	600711		484
Q92838 UniProt NPD GO	EDA_HUMAN	Ectodysplasin-A (Ectodermal dysplasia protein) (EDA protein) [Contains: Ectodysplasin-A, membrane fo ...	0.42	-	nuc	1 *	Cell membrane; single-pass type II membrane protein. Processed form: Secreted protein	cytoskeleton [TAS] integral to membrane [TAS] membrane fraction [TAS] plasma membrane [TAS]	300451	1RJ8	391
O14638 UniProt NPD GO	ENPP3_HUMAN	Ectonucleotide pyrophosphatase/phosphodiesterase 3 (E-NPP 3) (Phosphodiesterase I/nucleotide pyropho ...	0.42	-	mit	1 *	Membrane; single-pass type II membrane protein	integral to plasma membrane [TAS]	602182		875
Q6PE25 UniProt NPD GO	EF1G_BRARE	Elongation factor 1-gamma (EF-1-gamma) (eEF-1B gamma)	0.42	-	cyt	0					442
Q75EV6 UniProt NPD GO	EF3_ASHGO	Elongation factor 3 (EF-3)	0.42	+	nuc	0					1044
O94489 UniProt NPD GO	EF3_SCHPO	Elongation factor 3 (EF-3)	0.42	+	nuc	0					1047
P78549 UniProt NPD GO	NTHL1_HUMAN	Endonuclease III-like protein 1 (EC 4.2.99.18)	0.42	-	nuc	0	Nucleus	nucleus [IDA]	602656		312
Q6BKG0 UniProt NPD GO	PPN1_DEBHA	Endopolyphosphatase (EC 3.6.1.10)	0.42	-	mit	1 *	Vacuole; vacuolar membrane; single-pass type II membrane protein				713
Q07494 UniProt NPD GO	EPHB1_CHICK	Ephrin type-B receptor 1 (EC 2.7.10.1) (Tyrosine-protein kinase receptor EPH-2) (Tyrosine kinase CEK ...	0.42	-	nuc	1	Membrane; single-pass type I membrane protein				984
P0C0K6 UniProt NPD GO	EPHB6_PANTR	Ephrin type-B receptor 6 precursor (Tyrosine-protein kinase-defective receptor EPH-6)	0.42	-	end	1	Membrane; single-pass type I membrane protein (By similarity)				1005
O80338 UniProt NPD GO	ERF2_ARATH	Ethylene-responsive transcription factor 2 (Ethylene-responsive element-binding factor 2) (EREBP-2) ...	0.42	-	nuc	0	Nucleus (Probable)				243

You are viewing entries 30301 to 30350 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.