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
Q8INR6 UniProt NPD GO	DOT1L_DROME	Histone-lysine N-methyltransferase, H3 lysine-79 specific (EC 2.1.1.43) (Histone H3-K79 methyltransf ...	0.99	+	nuc	0	Nucleus	histone methyltransferase complex [IC]			1848
O60016 UniProt NPD GO	CLR4_SCHPO	Histone-lysine N-methyltransferase, H3 lysine-9 specific (EC 2.1.1.43) (Histone H3-K9 methyltransfer ...	0.99	-	nuc	0	Nucleus (By similarity)	nuclear centric heterochromatin [TAS] Rik1-E3 ubiquitin ligase complex [IDA]		1MVX	490
Q92786 UniProt NPD GO	PROX1_HUMAN	Homeobox prospero-like protein PROX1 (PROX 1)	0.99	+	nuc	0	Nucleus (Probable)		601546		737
P48437 UniProt NPD GO	PROX1_MOUSE	Homeobox prospero-like protein PROX1 (PROX 1)	0.99	+	nuc	0	Nucleus (Probable)	nucleus [IDA]			737
P39881 UniProt NPD GO	CUTL1_CANFA	Homeobox protein cut-like 1 (CCAAT displacement protein) (CDP) (Homeobox protein Clox) (Clox-1) (Fra ...	0.99	+	nuc	0	Nucleus				975
Q00900 UniProt NPD GO	ZEP2_RAT	Human immunodeficiency virus type I enhancer-binding protein 2 homolog (DNA-binding protein AGIE-BP1 ...	0.99	+	nuc	0	Nucleus				2437
Q3UHF7 UniProt NPD GO	ZEP2_MOUSE	Human immunodeficiency virus type I enhancer-binding protein 2 homolog (Myc intron-binding protein 1 ...	0.99	+	nuc	0	Nucleus	transcription factor complex [TAS]			2430
P41647 UniProt NPD GO	YCF1_PINTH	Hypothetical 205.3 kDa protein ycf1 (ORF 1756)	0.99	-	nuc	6 *	Plastid; chloroplast				1756
Q9BBN6 UniProt NPD GO	YCF1_LOTJA	Hypothetical 214.8 kDa protein ycf1	0.99	+	end	6 *	Plastid; chloroplast				1793
Q32065 UniProt NPD GO	YCX9_CHLRE	Hypothetical 341.7 kDa protein in psbD-psbC intergenic region (ORF2971) (ORFB)	0.99	+	end	0	Plastid; chloroplast				2971
Q03213 UniProt NPD GO	YM41_YEAST	Hypothetical 79.4 kDa protein in ALD2-DDR48 intergenic region	0.99	-	nuc	1 *		nuclear chromosome [IDA]			719
Q11102 UniProt NPD GO	YL17_CAEEL	Hypothetical protein C02F12.7	0.99	-	nuc	0					1130
Q11191 UniProt NPD GO	YPDD_CAEEL	Hypothetical protein C05D11.13	0.99	+	nuc	0					270
Q11188 UniProt NPD GO	YPD9_CAEEL	Hypothetical protein C05D11.9	0.99	+	nuc	0					752
Q09459 UniProt NPD GO	YQ38_CAEEL	Hypothetical protein C09G5.8	0.99	+	nuc	0					1531
Q10207 UniProt NPD GO	YBX1_SCHPO	Hypothetical protein C17D1.01 in chromosome II	0.99	+	nuc	0					584
O14206 UniProt NPD GO	YDD3_SCHPO	Hypothetical protein C1B9.03c in chromosome I	0.99	+	nuc	0					389
Q9UUI4 UniProt NPD GO	YIY9_SCHPO	Hypothetical protein C22F8.09 in chromosome I	0.99	+	nuc	0					419
O14009 UniProt NPD GO	YDP6_SCHPO	Hypothetical protein C29A4.06c in chromosome I	0.99	-	nuc	0					355
Q09507 UniProt NPD GO	YQI9_CAEEL	Hypothetical protein C45G9.9	0.99	+	nuc	0					294
Q10218 UniProt NPD GO	YAYB_SCHPO	Hypothetical protein C4H3.11c in chromosome I	0.99	-	nuc	0					783
P87137 UniProt NPD GO	YDM6_SCHPO	Hypothetical protein C57A7.06 in chromosome I	0.99	+	nuc	0					929
Q10076 UniProt NPD GO	YANB_SCHPO	Hypothetical zinc finger protein C3H1.11 in chromosome I	0.99	+	nuc	0	Nucleus (Potential)				582
P43596 UniProt NPD GO	IOC3_YEAST	ISWI one complex protein 3	0.99	+	nuc	0	Nucleus	ISW1 complex [IPI]			787
P09208 UniProt NPD GO	INSR_DROME	Insulin-like receptor precursor (EC 2.7.10.1) (DIR) (DInr) (dIRH) [Contains: Insulin-like receptor s ...	0.99	-	nuc	0	Membrane; single-pass type I membrane protein	insulin receptor complex [IDA] intercellular junction [IDA]			2144
Q9NZM3 UniProt NPD GO	ITSN2_HUMAN	Intersectin-2 (SH3 domain-containing protein 1B) (SH3P18) (SH3P18-like WASP-associated protein)	0.99	+	nuc	0	Cytoplasm		604464	1UHF	1696
P22149 UniProt NPD GO	AFT1_YEAST	Iron-regulated transcriptional activator AFT1 (Activator of iron transcription protein 1)	0.99	+	nuc	0	Nucleus (Potential)	cytoplasm [IDA] nucleus [IDA]			690
Q8NHM5 UniProt NPD GO	JHD1B_HUMAN	JmjC domain-containing histone demethylation protein 1B (EC 1.14.11.-) (F-box/LRR-repeat protein 10) ...	0.99	-	nuc	0	Nucleus (Probable)	nucleus [NAS]	609078		1336
Q9QXL2 UniProt NPD GO	KI21A_MOUSE	Kinesin family member 21A	0.99	+	nuc	0	Cytoplasm. In neurons, localized to axons and dendrites				1672
Q7Z4S6 UniProt NPD GO	KI21A_HUMAN	Kinesin family member 21A (Kinesin-like protein KIF2) (NY-REN-62 antigen)	0.99	+	nuc	0			608283		1674
O75037 UniProt NPD GO	KI21B_HUMAN	Kinesin family member 21B	0.99	+	nuc	0	Cytoplasm (By similarity)		608322		1637
Q9QXL1 UniProt NPD GO	KI21B_MOUSE	Kinesin family member 21B (Kinesin-like protein KIF6)	0.99	+	nuc	0	Cytoplasm. In neurons, localized to dendrites				1668
O35066 UniProt NPD GO	KIF3C_MOUSE	Kinesin-like protein KIF3C	0.99	+	nuc	0					796
O55165 UniProt NPD GO	KIF3C_RAT	Kinesin-like protein KIF3C	0.99	+	nuc	0					796
P24339 UniProt NPD GO	CUT7_SCHPO	Kinesin-like protein cut7 (Cell untimely torn protein 7)	0.99	-	nuc	0		spindle microtubule [IDA]			1085
Q8WWI1 UniProt NPD GO	LMO7_HUMAN	LIM domain only protein 7 (LOMP) (F-box only protein 20)	0.99	+	nuc	0		cytoplasm [TAS] nucleus [TAS] ubiquitin ligase complex [NAS]	604362		1683
Q86UK5 UniProt NPD GO	LBN_HUMAN	Limbin	0.99	+	exc	2 *	Membrane; multi-pass membrane protein (Potential)		607261		1308
P42283 UniProt NPD GO	LOLA1_DROME	Longitudinals lacking protein, isoform G	0.99	-	nuc	0	Nucleus	nucleus [IDA]			894
Q2KIW5 UniProt NPD GO	MLFIP_BOVIN	MLF1-interacting protein (Fragment)	0.99	-	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity)				408
Q9WVG9 UniProt NPD GO	MS3L1_MOUSE	Male-specific lethal 3-like 1 (MSL3-like 1) (Male-specific lethal-3 homolog 1)	0.99	+	nuc	0	Nucleus (By similarity)				525
P35724 UniProt NPD GO	MNR2_YEAST	Manganese resistance protein MNR2	0.99	+	end	2	Membrane; multi-pass membrane protein (Potential)				969
Q9UUM2 UniProt NPD GO	SWI1_SCHPO	Mating-type switching protein swi1 (Replication fork protection complex subunit swi1)	0.99	+	mit	0	Nucleus. Associated with chromatin during S phase. Nuclear accumulation requires swi3	nucleus [IDA] replication fork protection complex [TAS]			971
Q93074 UniProt NPD GO	MED12_HUMAN	Mediator of RNA polymerase II transcription subunit 12 (Thyroid hormone receptor-associated protein ...	0.99	+	nuc	0	Nucleus	mediator complex [IDA] nucleus [IDA]	300188		2212
Q05812 UniProt NPD GO	MSC3_YEAST	Meiotic sister-chromatid recombination protein 3	0.99	-	nuc	0	Cell membrane; peripheral membrane protein. Cell periphery				728
Q91V27 UniProt NPD GO	MELPH_MOUSE	Melanophilin (Exophilin-3) (Leaden protein) (Synaptotagmin-like protein 2a) (Slac2-a) (Slp homolog l ...	0.99	-	nuc	0	Melanosome	actin cytoskeleton [IDA] melanosome [TAS]			590
Q7TT79 UniProt NPD GO	MCPH1_MOUSE	Microcephalin	0.99	+	nuc	0	Centrosome (By similarity)				822
Q49MG5 UniProt NPD GO	MAP9_HUMAN	Microtubule-associated protein 9 (Aster-associated protein)	0.99	+	nuc	0	Cytoplasm. Localizes to microtubules in interphase, associates with the mitotic spindle during mitos ...		610070		647
P80192 UniProt NPD GO	M3K9_HUMAN	Mitogen-activated protein kinase kinase kinase 9 (EC 2.7.11.25) (Mixed lineage kinase 1)	0.99	+	exc	0			600136		1104
Q7TPV4 UniProt NPD GO	MBB1A_MOUSE	Myb-binding protein 1A (Myb-binding protein of 160 kDa)	0.99	+	nuc	0	Nucleus; nucleolus. Predominantly. Cytoplasm. Also shuttles between the nucleus and cytoplasm. Nucle ...	cytoplasm [IDA] NLS-dependent protein nuclear import complex [IDA] nucleolus [IDA] nucleus [IDA]			1344
Q8K3H5 UniProt NPD GO	MYO3A_MOUSE	Myosin IIIA (EC 2.7.11.1)	0.99	+	nuc	0					1613

You are viewing entries 301 to 350 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.