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
Q14678 UniProt NPD GO	ANR15_HUMAN	Ankyrin repeat domain-containing protein 15 (Kidney ankyrin repeat-containing protein)	0.83	-	nuc	0	Cytoplasm		607704		1352
O42115 UniProt NPD GO	ARX_BRARE	Aristaless-related homeobox protein (ARX)	0.83	+	nuc	0	Nucleus (By similarity)				453
Q6BTX0 UniProt NPD GO	ATG2_DEBHA	Autophagy-related protein 2	0.83	-	nuc	0	Perivacuolar compartment (By similarity)				1903
Q51WZ9 UniProt NPD GO	ATG9_MAGGR	Autophagy-related protein 9	0.83	-	end	4	Membrane; multi-pass membrane protein. Pre-autophagosomal and other perivacuolar punctate structures ...				917
Q94A43 UniProt NPD GO	BEH2_ARATH	BES1/BZR1 homolog protein 2	0.83	-	nuc	0					318
O46564 UniProt NPD GO	BMP2_RABIT	Bone morphogenetic protein 2 precursor (BMP-2)	0.83	+	nuc	1 *	Secreted protein (By similarity)				395
Q9VEB3 UniProt NPD GO	BXDC1_DROME	Brix domain-containing protein 1 homolog	0.83	-	nuc	0	Nucleus; nucleolus (By similarity)				320
Q58A65 UniProt NPD GO	JIP4_MOUSE	C-jun-amino-terminal kinase-interacting protein 4 (JNK-interacting protein 4) (JIP-4) (JNK-associate ...	0.83	-	nuc	0	Cytoplasm. Cytoplasm; perinuclear region. Perinuclear distribution in response to stress signals suc ...	cytoplasm [IDA]			1321
Q03012 UniProt NPD GO	SPP1_YEAST	COMPASS component SPP1 (Complex proteins associated with SET1 protein SPP1) (Set1C component SPP1) ( ...	0.83	-	nuc	0	Nucleus (Probable)	COMPASS complex [IPI]			353
Q9NWM3 UniProt NPD GO	CUED1_HUMAN	CUE domain-containing protein 1	0.83	-	nuc	0					386
P55280 UniProt NPD GO	CADH6_RAT	Cadherin-6 precursor (Kidney-cadherin) (K-cadherin)	0.83	-	nuc	1	Membrane; single-pass type I membrane protein	integral to plasma membrane [TAS]			789
Q13555 UniProt NPD GO	KCC2G_HUMAN	Calcium/calmodulin-dependent protein kinase type II gamma chain (EC 2.7.11.17) (CaM-kinase II gamma ...	0.83	-	nuc	0			602123		558
P51125 UniProt NPD GO	ICAL_MOUSE	Calpastatin (Calpain inhibitor)	0.83	-	nuc	0					788
P12675 UniProt NPD GO	ICAL_PIG	Calpastatin (Calpain inhibitor)	0.83	-	nuc	0					713
P23291 UniProt NPD GO	KC11_YEAST	Casein kinase I homolog 1 (EC 2.7.11.1)	0.83	-	nuc	0	Cell membrane; lipid-anchor	endoplasmic reticulum [IDA] plasma membrane [IDA]			538
Q9Y6M4 UniProt NPD GO	KC1G3_HUMAN	Casein kinase I isoform gamma-3 (EC 2.7.11.1) (CKI-gamma 3)	0.83	-	nuc	0	Cytoplasm		604253	2CHL	447
O94508 UniProt NPD GO	CWF11_SCHPO	Cell cycle control protein cwf11	0.83	-	cyt	0	Nucleus (Probable)				1284
P40468 UniProt NPD GO	TAO3_YEAST	Cell morphogenesis protein PAG1 (Protein TAO3)	0.83	-	end	0		bud [IDA] incipient bud site [IDA] mating projection tip [IDA] mitochondrion [IDA]			2376
O12946 UniProt NPD GO	P53_PLAFE	Cellular tumor antigen p53 (Tumor suppressor p53)	0.83	-	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity)				366
P51664 UniProt NPD GO	P53_SHEEP	Cellular tumor antigen p53 (Tumor suppressor p53)	0.83	+	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity)	cytoplasm [ISS] mitochondrion [ISS] nucleolus [ISS] nucleus [ISS]			382
P53298 UniProt NPD GO	OKP1_YEAST	Central kinetochore subunit OKP1 (Outer kinetochore protein 1)	0.83	+	nuc	0	Nucleus. Associated with kinetochores	COMA complex [IDA]			406
Q85CV5 UniProt NPD GO	RK20_ANTFO	Chloroplast 50S ribosomal protein L20	0.83	-	nuc	0	Plastid; chloroplast				112
Q96NB3 UniProt NPD GO	CCD16_HUMAN	Coiled-coil domain-containing protein 16	0.83	-	nuc	0	Nucleus (By similarity). Excluded from nucleolus (By similarity)				372
Q95JL6 UniProt NPD GO	CCD38_MACFA	Coiled-coil domain-containing protein 38	0.83	-	nuc	0					563
Q6P9F0 UniProt NPD GO	CCD62_HUMAN	Coiled-coil domain-containing protein 60 (Aaa-protein) (Protein TSP-NY)	0.83	-	nuc	0					684
P23251 UniProt NPD GO	CR1_HORVU	Cold-regulated protein 1 (Fragment)	0.83	+	nuc	0					127
Q15003 UniProt NPD GO	CND2_HUMAN	Condensin complex subunit 2 (Barren homolog protein 1) (Chromosome-associated protein H) (hCAP-H) (X ...	0.83	+	nuc	0	Nucleus. Cytoplasm. In interphase cells, the majority of the condensin complex is found in the cytop ...		602332		741
Q9YGK4 UniProt NPD GO	COLI1_CYPCA	Corticotropin-lipotropin 1 precursor (Corticotropin-lipotropin I) (Pro-opiomelanocortin I) (POMC I) ...	0.83	-	exc	0					222
Q5ZJP9 UniProt NPD GO	CCNL1_CHICK	Cyclin-L1	0.83	+	nuc	0	Nucleus (By similarity)				534
Q9XT26 UniProt NPD GO	CCNT1_HORSE	Cyclin-T1 (CycT1) (Cyclin-T)	0.83	-	nuc	0	Nucleus (By similarity)				727
O60563 UniProt NPD GO	CCNT1_HUMAN	Cyclin-T1 (CycT1) (Cyclin-T)	0.83	-	nuc	0	Nucleus		602506		726
Q8HXN7 UniProt NPD GO	CCNT1_PANTR	Cyclin-T1 (CycT1) (Cyclin-T)	0.83	-	nuc	0	Nucleus (By similarity)				725
P26363 UniProt NPD GO	CFTR_XENLA	Cystic fibrosis transmembrane conductance regulator (CFTR) (cAMP-dependent chloride channel) (ATP-bi ...	0.83	-	end	11	Membrane; multi-pass membrane protein				1485
O70279 UniProt NPD GO	DGC14_MOUSE	DGCR14 protein (DiGeorge syndrome critical region 14 homolog) (ES2 protein) (Expressed sequence 2 em ...	0.83	-	nuc	0	Nucleus	nucleus [IEP]			479
P04819 UniProt NPD GO	DNLI_YEAST	DNA ligase I, mitochondrial precursor (EC 6.5.1.1) (Polydeoxyribonucleotide synthase [ATP])	0.83	-	mit	0	Nucleus. Mitochondrion	mitochondrion [IDA] nucleus [IDA] replication fork [NAS]			755
Q9LVN7 UniProt NPD GO	DPOD1_ARATH	DNA polymerase delta catalytic subunit (EC 2.7.7.7)	0.83	+	mit	0	Nucleus				1081
Q6BNG2 UniProt NPD GO	DPOE_DEBHA	DNA polymerase epsilon, catalytic subunit A (EC 2.7.7.7) (DNA polymerase II subunit A)	0.83	-	nuc	0	Nucleus (By similarity)				2226
Q4R380 UniProt NPD GO	DPOLL_MACFA	DNA polymerase lambda (EC 2.7.7.7) (EC 4.2.99.-) (Pol Lambda)	0.83	-	nuc	0	Nucleus (By similarity)				575
Q7Z5Q5 UniProt NPD GO	DPOLN_HUMAN	DNA polymerase nu (EC 2.7.7.7)	0.83	-	nuc	0	Nucleus				900
P06778 UniProt NPD GO	RAD52_YEAST	DNA repair and recombination protein RAD52	0.83	-	nuc	0	Nucleus	nuclear chromosome [IDA] nucleus [IDA]			471
P12689 UniProt NPD GO	REV1_YEAST	DNA repair protein REV1 (EC 2.7.7.-)	0.83	-	nuc	0	Nucleus (Probable)	mitochondrion [IDA] nucleus [IC]		2AQ4	985
Q9URU2 UniProt NPD GO	DNA2_SCHPO	DNA replication ATP-dependent helicase dna2 (EC 3.6.1.-)	0.83	-	nuc	0	Nucleus				1398
Q9H211 UniProt NPD GO	CDT1_HUMAN	DNA replication factor Cdt1 (Double parked homolog) (DUP)	0.83	-	nuc	0	Nucleus	nucleus [IDA] replication fork [IPI]	605525		546
P49718 UniProt NPD GO	MCM5_MOUSE	DNA replication licensing factor MCM5 (CDC46 homolog) (P1-CDC46)	0.83	-	nuc	0	Nucleus				733
P29776 UniProt NPD GO	ETS6_DROME	DNA-binding protein D-ETS-6	0.83	+	nuc	0	Nucleus				475
O54889 UniProt NPD GO	RPA1_RAT	DNA-directed RNA polymerase I largest subunit (EC 2.7.7.6) (RNA polymerase I 194 kDa subunit) (RPA19 ...	0.83	-	nuc	0	Nucleus				1716
P32349 UniProt NPD GO	RPC3_YEAST	DNA-directed RNA polymerase III 74 kDa polypeptide (EC 2.7.7.6) (C74)	0.83	-	nuc	0	Nucleus	DNA-directed RNA polymerase III complex [TAS]			654
Q8S8Y1 UniProt NPD GO	RPOC2_ATRBE	DNA-directed RNA polymerase beta'' chain (EC 2.7.7.6) (PEP) (Plastid-encoded RNA polymerase beta'' s ...	0.83	-	nuc	0	Plastid; chloroplast				1389
Q3C1G9 UniProt NPD GO	RPOC2_NICSY	DNA-directed RNA polymerase beta'' chain (EC 2.7.7.6) (PEP) (Plastid-encoded RNA polymerase beta'' s ...	0.83	-	nuc	0	Plastid; chloroplast				1392
Q33C48 UniProt NPD GO	RPOC2_NICTO	DNA-directed RNA polymerase beta'' chain (EC 2.7.7.6) (PEP) (Plastid-encoded RNA polymerase beta'' s ...	0.83	-	nuc	0	Plastid; chloroplast				1392

You are viewing entries 7301 to 7350 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.