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
O98452 UniProt NPD GO	RK2_SPIMX	Chloroplast 50S ribosomal protein L2	0.68	-	nuc	0	Plastid; chloroplast				277
Q32RV7 UniProt NPD GO	RK2_STAPU	Chloroplast 50S ribosomal protein L2	0.68	-	nuc	0	Plastid; chloroplast				277
P07133 UniProt NPD GO	RK20_EUGGR	Chloroplast 50S ribosomal protein L20	0.68	+	nuc	0	Plastid; chloroplast				123
Q6L378 UniProt NPD GO	RK20_SACHY	Chloroplast 50S ribosomal protein L20	0.68	-	nuc	0	Plastid; chloroplast				119
P56795 UniProt NPD GO	RK22_ARATH	Chloroplast 50S ribosomal protein L22	0.68	+	nuc	0	Plastid; chloroplast				160
Q85G60 UniProt NPD GO	RK32_CYAME	Chloroplast 50S ribosomal protein L32	0.68	-	nuc	0	Plastid; chloroplast				58
P49164 UniProt NPD GO	RK34_OLILU	Chloroplast 50S ribosomal protein L34	0.68	-	nuc	0	Plastid; chloroplast				42
Q85FL0 UniProt NPD GO	CEMA_ADICA	Chloroplast envelope membrane protein	0.68	-	end	3	Plastid; chloroplast; chloroplast inner membrane; multi-pass membrane protein (By similarity)				464
Q9C0J9 UniProt NPD GO	BHLH3_HUMAN	Class B basic helix-loop-helix protein 3 (bHLHB3) (Differentially expressed in chondrocytes protein ...	0.68	+	nuc	0	Nucleus (By similarity)	nucleus [NAS]	606200		482
Q29549 UniProt NPD GO	CLUS_PIG	Clusterin precursor (Complement cytolysis inhibitor) (CLI) (CP40) [Contains: Clusterin beta chain; C ...	0.68	-	nuc	0	Secreted protein				446
P23252 UniProt NPD GO	CR2_HORVU	Cold-regulated protein 2 (Fragment)	0.68	+	nuc	0					202
P38170 UniProt NPD GO	CND2_YEAST	Condensin complex subunit 2 (Barren homolog) (CAPH homolog)	0.68	-	nuc	0	Nucleus. Cytoplasm. In interphase cells, the majority of the condensin complex is found in the cytop ...	nuclear condensin complex [IPI] nucleus [IDA]			728
P11885 UniProt NPD GO	COLI_RANCA	Corticotropin-lipotropin precursor (Pro-opiomelanocortin) (POMC) [Contains: NPP; Melanotropin gamma ...	0.68	-	nuc	0					263
P79760 UniProt NPD GO	CP1A4_CHICK	Cytochrome P450 1A4 (EC 1.14.14.1) (CYPIA4) (P450 TCDDAHH)	0.68	-	end	0	Endoplasmic reticulum; endoplasmic reticulum membrane; peripheral membrane protein				530
P97504 UniProt NPD GO	BMX_MOUSE	Cytoplasmic tyrosine-protein kinase BMX (EC 2.7.10.2) (Bone marrow tyrosine kinase gene in chromosom ...	0.68	-	nuc	0	Cytoplasm (Probable)				651
Q9FFQ1 UniProt NPD GO	RH31_ARATH	DEAD-box ATP-dependent RNA helicase 31 (EC 3.6.1.-)	0.68	-	mit	0					716
Q9H6A0 UniProt NPD GO	DEN2D_HUMAN	DENN domain-containing protein 2D	0.68	-	mit	0					471
Q4R8T1 UniProt NPD GO	DJBP_MACFA	DJ-1-binding protein	0.68	-	nuc	0	Nucleus (By similarity)				570
Q9XGC9 UniProt NPD GO	MSH2_MAIZE	DNA mismatch repair protein MSH2 (MUS1)	0.68	-	cyt	0					942
O89042 UniProt NPD GO	DPOLA_RAT	DNA polymerase alpha catalytic subunit (EC 2.7.7.7) (Fragment)	0.68	+	nuc	0	Nucleus				1451
P28340 UniProt NPD GO	DPOD1_HUMAN	DNA polymerase delta catalytic subunit (EC 2.7.7.7) (DNA polymerase subunit delta p125)	0.68	+	cyt	0	Nucleus		174761		1107
Q9NP87 UniProt NPD GO	DPOLM_HUMAN	DNA polymerase mu (EC 2.7.7.7) (Pol Mu)	0.68	-	mit	0			606344		494
Q9Y620 UniProt NPD GO	RA54B_HUMAN	DNA repair and recombination protein RAD54B (EC 3.6.1.-) (RAD54 homolog B)	0.68	-	nuc	0	Nucleus (Probable)		604289		910
O42410 UniProt NPD GO	IKAR_CHICK	DNA-binding protein Ikaros	0.68	-	nuc	0	Nucleus				518
Q01826 UniProt NPD GO	SATB1_HUMAN	DNA-binding protein SATB1 (Special AT-rich sequence-binding protein 1)	0.68	-	nuc	0	Nucleus	nucleus [TAS]	602075	1YSE	763
Q9LFV6 UniProt NPD GO	RPOT2_ARATH	DNA-directed RNA polymerase 2, chloroplast/mitochondrial precursor (EC 2.7.7.6)	0.68	+	cyt	0	Plastid; chloroplast. Mitochondrion				1011
Q753Q4 UniProt NPD GO	RPB2_ASHGO	DNA-directed RNA polymerase II polypeptide 2 (EC 2.7.7.6) (RNA polymerase II subunit 2)	0.68	-	cyt	0	Nucleus (By similarity)				1222
P36440 UniProt NPD GO	RPOB_HETCA	DNA-directed RNA polymerase beta chain (EC 2.7.7.6) (PEP) (Plastid-encoded RNA polymerase subunit be ...	0.68	-	mit	0	Plastid; chloroplast				1116
Q9MUS6 UniProt NPD GO	RPOC1_MESVI	DNA-directed RNA polymerase beta' chain (EC 2.7.7.6) (PEP) (Plastid-encoded RNA polymerase beta' sub ...	0.68	-	cyt	0	Plastid; chloroplast				668
P39750 UniProt NPD GO	RAD2_SCHPO	DNA-repair protein rad2	0.68	+	nuc	0	Nucleus (Probable)				380
P53355 UniProt NPD GO	DAPK1_HUMAN	Death-associated protein kinase 1 (EC 2.7.11.1) (DAP kinase 1)	0.68	+	end	0	Cytoplasm. Colocalizes with the actin filament system	actin cytoskeleton [IEP]	600831	1WVY	1432
Q99KU1 UniProt NPD GO	DHDDS_MOUSE	Dehydrodolichyl diphosphate synthase (EC 2.5.1.-) (Dedol-PP synthase)	0.68	+	cyt	0					333
P27526 UniProt NPD GO	PHR_NEUCR	Deoxyribodipyrimidine photo-lyase (EC 4.1.99.3) (DNA photolyase) (Photoreactivating enzyme)	0.68	-	mit	0					642
Q9M667 UniProt NPD GO	RPP13_ARATH	Disease resistance protein RPP13 (Resistance to Peronospora parasitica protein 13)	0.68	+	cyt	0					835
Q42484 UniProt NPD GO	RPS2_ARATH	Disease resistance protein RPS2 (Resistance to Pseudomonas syringae protein 2)	0.68	-	nuc	0	Cytoplasm. Membrane; peripheral membrane protein				909
Q94AR6 UniProt NPD GO	DOF31_ARATH	Dof zinc finger protein DOF3.1 (AtDOF3.1)	0.68	-	nuc	0	Nucleus (Probable)				204
Q9XGM2 UniProt NPD GO	MRE11_ARATH	Double-strand break repair protein MRE11	0.68	+	nuc	0	Nucleus				720
Q84XF3 UniProt NPD GO	DRP1B_ARATH	Dynamin-related protein 1B (Dynamin-like protein B)	0.68	-	mit	0	Cytoplasm (By similarity). Microtubule-associated (By similarity)				610
Q9UJM3 UniProt NPD GO	ERRFI_HUMAN	ERBB receptor feedback inhibitor 1 (Mitogen-inducible gene 6 protein) (Mig-6)	0.68	-	nuc	0	Cytoplasm	cytoplasm [TAS]	608069		462
O73691 UniProt NPD GO	EGR1_CHICK	Early growth response protein 1 (EGR-1) (Zinc finger protein ZENK) (Fragment)	0.68	-	nuc	0	Nucleus				194
O73693 UniProt NPD GO	EGR1_POEGU	Early growth response protein 1 (EGR-1) (Zinc finger protein ZENK) (Fragment)	0.68	-	nuc	0	Nucleus				193
P43300 UniProt NPD GO	EGR3_MOUSE	Early growth response protein 3 (EGR-3)	0.68	-	nuc	0	Nucleus (Probable)				387
P93329 UniProt NPD GO	NO20_MEDTR	Early nodulin 20 precursor (N-20)	0.68	-	mit	0					268
Q98SP8 UniProt NPD GO	EPABA_XENLA	Embryonic polyadenylate-binding protein-A (Embryonic poly(A)-binding protein-A) (ePABP-A) (ePAB-A) ( ...	0.68	-	nuc	0	Cytoplasm. Associated with polysomes	cytoplasm [IDA]			629
Q5KH67 UniProt NPD GO	PPN1_CRYNE	Endopolyphosphatase (EC 3.6.1.10)	0.68	-	exc	0	Vacuole; vacuolar membrane; single-pass type II membrane protein				678
P22388 UniProt NPD GO	EDN1_RAT	Endothelin-1 precursor (ET-1) (Preproendothelin-1) (PPET1)	0.68	-	nuc	0	Secreted protein			6CMH	202
Q6NTZ5 UniProt NPD GO	XPO6B_XENLA	Exportin-6-B	0.68	-	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity). Shuttles between the nucleus and the cytoplasm ( ...				1138
P48442 UniProt NPD GO	CASR_RAT	Extracellular calcium-sensing receptor precursor (CaSR) (Parathyroid Cell calcium-sensing receptor)	0.68	-	end	7	Membrane; multi-pass membrane protein				1079
Q9UKT4 UniProt NPD GO	FBX5_HUMAN	F-box only protein 5 (Early mitotic inhibitor 1)	0.68	-	mit	0			606013		447
Q8X0X6 UniProt NPD GO	SPT16_NEUCR	FACT complex subunit spt-16 (Facilitates chromatin transcription complex subunit spt-16)	0.68	+	cyt	0	Nucleus (By similarity)				1032

You are viewing entries 14651 to 14700 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.