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
P33332 UniProt NPD GO	SEC3_YEAST	Exocyst complex component SEC3 (Protein PSL1)	1.00	+	nuc	0		bud neck [IDA] bud tip [IDA] exocyst [IPI] incipient bud site [IDA]			1336
P40020 UniProt NPD GO	FIR1_YEAST	Factor interacting with REF2 (Polymerase-interacting protein 1) (PAP1-interacting protein)	1.00	-	nuc	0	Bud neck	bud neck [IDA]			876
Q08050 UniProt NPD GO	FOXM1_HUMAN	Forkhead box protein M1 (Forkhead-related protein FKHL16) (Hepatocyte nuclear factor 3 forkhead homo ...	1.00	+	nuc	0	Nucleus		602341		763
Q00586 UniProt NPD GO	FRQ_CRESP	Frequency clock protein	1.00	+	nuc	0					1015
P16383 UniProt NPD GO	GCF_HUMAN	GC-rich sequence DNA-binding factor (GCF) (Transcription factor 9) (TCF-9)	1.00	+	mit	0	Nucleus		189901		784
Q9Y5B6 UniProt NPD GO	GCFC_HUMAN	GC-rich sequence DNA-binding factor homolog	1.00	+	nuc	0	Nucleus (Potential)	nucleus [NAS]			917
P58501 UniProt NPD GO	GCFC_MOUSE	GC-rich sequence DNA-binding factor homolog (Fragment)	1.00	+	nuc	0	Nucleus (Potential)				855
Q8CI11 UniProt NPD GO	GNL3_MOUSE	Guanine nucleotide-binding protein-like 3 (Nucleolar GTP-binding protein 3) (Nucleostemin)	1.00	+	nuc	0	Nucleus (By similarity). Nucleus; nucleolus (By similarity). Shuttles between the nucleus and nucleo ...	nucleolus [ISS] nucleus [ISS]			538
Q7Z6Z7 UniProt NPD GO	HUWE1_HUMAN	HECT, UBA and WWE domain-containing protein 1 (EC 6.3.2.-) (E3 ubiquitin protein ligase URE-B1) (Mcl ...	1.00	-	end	0	Nucleus (By similarity). Predominantly cytosolic or perinuclear in some colorectal carcinoma cells	nucleus [ISS]			4374
Q759G7 UniProt NPD GO	SWR1_ASHGO	Helicase SWR1 (EC 3.6.1.-)	1.00	+	nuc	0	Nucleus (By similarity)				1486
Q6BKC2 UniProt NPD GO	SWR1_DEBHA	Helicase SWR1 (EC 3.6.1.-)	1.00	-	nuc	0	Nucleus (By similarity)				1616
Q6CJ38 UniProt NPD GO	SWR1_KLULA	Helicase SWR1 (EC 3.6.1.-)	1.00	+	nuc	0	Nucleus (By similarity)				1572
Q4WAS9 UniProt NPD GO	SWR1_ASPFU	Helicase swr1 (EC 3.6.1.-)	1.00	+	nuc	0	Nucleus (By similarity)				1695
O13682 UniProt NPD GO	SWR1_SCHPO	Helicase swr1 (EC 3.6.1.-)	1.00	+	nuc	0	Nucleus (By similarity)				1288
O15047 UniProt NPD GO	SET1A_HUMAN	Histone-lysine N-methyltransferase, H3 lysine-4 specific SET1 (EC 2.1.1.43) (Set1/Ash2 histone methy ...	1.00	+	nuc	0	Nucleus (Probable)				1707
Q04116 UniProt NPD GO	YHP1_YEAST	Homeobox protein YHP1	1.00	+	nuc	0	Nucleus	nuclear chromosome [IDA]			353
P34161 UniProt NPD GO	YOX1_YEAST	Homeobox protein YOX1	1.00	+	nuc	0	Nucleus	nucleus [IDA]			385
P53148 UniProt NPD GO	YGJ3_YEAST	Hypothetical 104.8 kDa protein in PAN2-NUP145 intergenic region	1.00	+	nuc	0		mitochondrion [IDA] spindle pole body [IDA]			917
P53935 UniProt NPD GO	YNJ1_YEAST	Hypothetical 141.5 kDa protein in YPT53-RHO2 intergenic region	1.00	+	nuc	0		cytoplasm [IDA]			1240
P12222 UniProt NPD GO	YCF1_TOBAC	Hypothetical 226 kDa protein ycf1 (ORF 1901)	1.00	+	nuc	6 *	Plastid; chloroplast				1901
Q10369 UniProt NPD GO	YDBJ_SCHPO	Hypothetical protein C22E12.19 in chromosome I	1.00	+	nuc	0					661
Q09863 UniProt NPD GO	YAFA_SCHPO	Hypothetical protein C29E6.10c in chromosome I	1.00	+	nuc	0		inner kinetochore of condensed chromosome [TAS]			1085
P34478 UniProt NPD GO	YMHA_CAEEL	Hypothetical protein F58A4.11	1.00	+	nuc	1 *					747
Q12072 UniProt NPD GO	IOC2_YEAST	ISWI one complex protein 2	1.00	+	nuc	0	Nucleus	ISW1 complex [IPI]			812
P53125 UniProt NPD GO	ITC1_YEAST	Imitation switch two complex protein 1	1.00	+	nuc	0	Nucleus	chromatin accessibility complex [IPI]			1264
P53352 UniProt NPD GO	INCE_CHICK	Inner centromere protein	1.00	+	nuc	0	Nucleus. Is restricted to the nucleus in interphase, remains tightly bound to the chromosomes until ...				877
Q9NQS7 UniProt NPD GO	INCE_HUMAN	Inner centromere protein	1.00	+	nuc	0	Localizes on chromosome arms and inner centromeres from prophase through metaphase and then transfer ...	centric heterochromatin [IDA] spindle [IDA]	604411		923
Q9WU62 UniProt NPD GO	INCE_MOUSE	Inner centromere protein	1.00	+	nuc	0	Localizes on chromosome arms and inner centromeres from prophase through metaphase and then transfer ...	central element [IDA] chromosome, pericentric region [IDA] midbody [IDA]			880
Q3KRF1 UniProt NPD GO	IPR1_RAT	Intracellular pathogen resistance protein 1	1.00	+	nuc	0	Nucleus (Potential)				478
Q640I9 UniProt NPD GO	JHD1B_XENLA	JmjC domain-containing histone demethylation protein 1B (EC 1.14.11.-) (F-box/LRR-repeat protein 10) ...	1.00	+	nuc	0	Nucleus (By similarity)				1259
Q8NI77 UniProt NPD GO	KI18A_HUMAN	Kinesin family member 18A	1.00	-	nuc	0					898
P46674 UniProt NPD GO	SAC3_YEAST	Leucine permease transcriptional regulator	1.00	-	nuc	0	Nucleus (Potential)	nuclear pore [IDA]			1301
Q4V8G7 UniProt NPD GO	MLFIP_RAT	MLF1-interacting protein	1.00	+	nuc	0	Cytoplasm. Nucleus				410
Q71F23 UniProt NPD GO	MLFIP_HUMAN	MLF1-interacting protein (KSHV latent nuclear antigen-interacting protein 1)	1.00	-	nuc	0	Cytoplasm. Nucleus				418
P21249 UniProt NPD GO	ANT1_ONCVO	Major antigen (Myosin-like antigen)	1.00	+	nuc	0					2022
P40631 UniProt NPD GO	MLH_TETTH	Micronuclear linker histone polyprotein (MIC LH) [Contains: Micronuclear linker histone-alpha; Micro ...	1.00	+	nuc	0	Nucleus. Micronuclei				633
Q3TRR0 UniProt NPD GO	MAP9_MOUSE	Microtubule-associated protein 9 (Aster-associated protein)	1.00	+	nuc	0	Cytoplasm. Localizes to microtubules in interphase, associates with the mitotic spindle during mitos ...				646
P25028 UniProt NPD GO	FSYA_DROME	Mitosis initiation protein fs(1)Ya	1.00	-	nuc	0	Nucleus; nuclear envelope. In the nuclear envelope during interphase to metaphase. Nucleus; nucleopl ...	cytoplasm [IDA] nuclear envelope [IDA]			696
Q62504 UniProt NPD GO	MINT_MOUSE	Msx2-interacting protein (SPEN homolog) (SMART/HDAC1-associated repressor protein)	1.00	+	nuc	0	Nucleus. Associates with chromatin	nucleus [IDA]			3644
Q5FWF5 UniProt NPD GO	ESCO1_HUMAN	N-acetyltransferase ESCO1 (EC 2.3.1.-) (Establishment of cohesion 1 homolog 1) (ECO1 homolog 1) (ESO ...	1.00	-	nuc	0	Nucleus. Nuclear at interphase, associated with chromosomes during mitosis		609674		840
P52919 UniProt NPD GO	NBP1_YEAST	NAP1-binding protein	1.00	+	nuc	0		central plaque of spindle pole body [IDA] nucleus [IDA]			319
Q9Z206 UniProt NPD GO	ARHG8_MOUSE	Neuroepithelial cell-transforming gene 1 protein (Rho guanine nucleotide exchange factor 8)	1.00	+	nuc	0	Cytoplasm. Nucleus				595
Q7Z628 UniProt NPD GO	ARHG8_HUMAN	Neuroepithelial cell-transforming gene 1 protein (p65 Net1 proto-oncogene) (Rho guanine nucleotide e ...	1.00	+	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity)		606450		596
Q6KCD5 UniProt NPD GO	NPBL_MOUSE	Nipped-B-like protein (Delangin homolog) (SCC2 homolog)	1.00	+	nuc	0	Nucleus (By similarity)				2798
Q6KC79 UniProt NPD GO	NIPBL_HUMAN	Nipped-B-like protein (Delangin) (SCC2 homolog)	1.00	+	nuc	0	Nucleus (By similarity)		608667		2804
Q62736 UniProt NPD GO	CALD1_RAT	Non-muscle caldesmon (CDM) (L-caldesmon)	1.00	+	mit	0	On thin filaments in smooth muscle and on stress fibers in fibroblasts (nonmuscle) (By similarity)				531
P23497 UniProt NPD GO	SP100_HUMAN	Nuclear autoantigen Sp-100 (Speckled 100 kDa) (Nuclear dot-associated Sp100 protein) (Lysp100b)	1.00	+	nuc	0	Nucleus. Found in the nuclear body, also known as nuclear domain 10 (ND10), PML oncogenic domain (PO ...	nucleus [TAS] PML body [TAS]	604585	1H5P	879
P32597 UniProt NPD GO	STH1_YEAST	Nuclear protein STH1/NPS1 (EC 3.6.1.-) (ATP-dependent helicase STH1) (Chromatin structure remodeling ...	1.00	+	nuc	0	Nucleus. Localizes to centromeric and flanking chromatin. Association of the RSC complex with these ...	chromosome, pericentric region [IDA] RSC complex [IDA]			1359
Q4KKX4 UniProt NPD GO	NCOR1_XENTR	Nuclear receptor corepressor 1 (N-CoR1) (N-CoR) (xN-CoR)	1.00	+	nuc	0	Nucleus (By similarity)				2494
Q9Y618 UniProt NPD GO	NCOR2_HUMAN	Nuclear receptor corepressor 2 (N-CoR2) (Silencing mediator of retinoic acid and thyroid hormone rec ...	1.00	+	nuc	0	Nucleus	nucleus [TAS]	600848	1R2B	2517

You are viewing entries 51 to 100 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.