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
Q86VS8 UniProt NPD GO	HOOK3_HUMAN	Hook homolog 3 (hHK3)	0.85	-	nuc	0	Cytoplasm. Golgi apparatus. Associates with the Golgi complex. Enriched in the cis-face of the Golgi ...	Golgi membrane [NAS]	607825		718
Q68UT7 UniProt NPD GO	HUNK_PANTR	Hormonally up-regulated neu tumor-associated kinase (EC 2.7.11.1)	0.85	-	nuc	0					714
P57058 UniProt NPD GO	HUNK_HUMAN	Hormonally up-regulated neu tumor-associated kinase (EC 2.7.11.1) (Serine/threonine-protein kinase M ...	0.85	-	nuc	0			606532		714
P53913 UniProt NPD GO	YNN3_YEAST	Hypothetical 20.0 kDa protein in FPR1-TOM22 intergenic region	0.85	-	nuc	0		nucleus [IDA]			173
P43602 UniProt NPD GO	YFJ2_YEAST	Hypothetical 79.7 kDa protein in FAB1-PES4 intergenic region	0.85	-	nuc	0					733
Q10145 UniProt NPD GO	YAS9_SCHPO	Hypothetical RNA-binding protein C3H8.09c in chromosome I	0.85	-	nuc	0					738
P41993 UniProt NPD GO	YKC2_CAEEL	Hypothetical protein B0280.2	0.85	-	nuc	0					627
Q11091 UniProt NPD GO	YWZ1_CAEEL	Hypothetical protein C02B8.1	0.85	+	nuc	0					112
Q10064 UniProt NPD GO	YAMB_SCHPO	Hypothetical protein C1F5.11c in chromosome I	0.85	-	end	0					3655
Q09726 UniProt NPD GO	YA46_SCHPO	Hypothetical protein C31A2.06 in chromosome I	0.85	-	nuc	0					542
Q10327 UniProt NPD GO	YD72_SCHPO	Hypothetical protein C32A11.02c in chromosome I	0.85	-	nuc	0					851
O14303 UniProt NPD GO	YE87_SCHPO	Hypothetical protein C9G1.07 in chromosome I	0.85	-	nuc	0					418
P34554 UniProt NPD GO	YNP1_CAEEL	Hypothetical protein T05G5.1 precursor	0.85	-	exc	1 *					411
P34561 UniProt NPD GO	YNP8_CAEEL	Hypothetical protein T05G5.8	0.85	-	cyt	0					808
P34631 UniProt NPD GO	YOJ8_CAEEL	Hypothetical protein ZK353.8 in chromosome III	0.85	-	nuc	0					469
Q5JU85 UniProt NPD GO	IQEC2_HUMAN	IQ motif and Sec7 domain-containing protein 2	0.85	-	nuc	0	Cytoplasm (Potential)		300522		1478
Q9D8Y8 UniProt NPD GO	ING5_MOUSE	Inhibitor of growth protein 5	0.85	-	nuc	0					240
P19158 UniProt NPD GO	IRA2_YEAST	Inhibitory regulator protein IRA2	0.85	-	end	0		cytoplasm [IDA] mitochondrion [IDA]			3079
Q9DF49 UniProt NPD GO	IRS2A_XENLA	Insulin receptor substrate 2-A (IRS-2-A) (Insulin receptor substrate-unique) (Insulin receptor subst ...	0.85	-	nuc	0		cytoplasm [ISS] microsome [ISS] nucleus [ISS]			1074
P53705 UniProt NPD GO	INT1_CANAL	Integrin alpha chain-like protein (Alpha-INT1)	0.85	-	nuc	0	Cell surface. Cell-surface of the blastospores				1664
P33417 UniProt NPD GO	IXR1_YEAST	Intrastrand crosslink recognition protein (Structure-specific recognition protein) (SSRP)	0.85	-	nuc	0	Nucleus	nuclear chromosome [IPI]			597
Q9US53 UniProt NPD GO	JMJ2_SCHPO	Jumonji/ARID domain-containing protein 2	0.85	-	mit	0					715
Q90631 UniProt NPD GO	KTN1_CHICK	Kinectin	0.85	+	nuc	1 *	Endoplasmic reticulum; endoplasmic reticulum membrane; single-pass type II membrane protein. Vesicle ...				1364
P46871 UniProt NPD GO	KRP95_STRPU	Kinesin-II 95 kDa subunit (KRP-85/95 95 kDa subunit)	0.85	-	nuc	0					742
O59751 UniProt NPD GO	KLP6_SCHPO	Kinesin-like protein 6	0.85	-	nuc	0	Cytoplasm. Cytoplasmic microtubules in interphase, mitotic kinetochores in metaphase and spindle mid ...	kinetochore [IDA] spindle midzone [IDA]			784
Q9WV04 UniProt NPD GO	KIF9_MOUSE	Kinesin-like protein KIF9	0.85	-	nuc	0					790
Q10430 UniProt NPD GO	SPC25_SCHPO	Kinetochore protein spc25	0.85	-	nuc	0	Nucleus. Associated with kinetochores	Ndc80 complex [TAS]			238
Q8BZ81 UniProt NPD GO	LRTM3_MOUSE	Leucine-rich repeat transmembrane neuronal protein 3 precursor	0.85	-	mit	1	Membrane; single-pass type I membrane protein (Potential)				582
Q96JN0 UniProt NPD GO	LCOR_HUMAN	Ligand-dependent corepressor (LCoR) (Mblk1-related protein 2)	0.85	-	nuc	0	Nucleus		607698	2COB	433
O35711 UniProt NPD GO	LIPB2_MOUSE	Liprin-beta-2 (Protein tyrosine phosphatase receptor type f polypeptide-interacting protein-binding ...	0.85	-	nuc	0					882
Q9FE22 UniProt NPD GO	HFR1_ARATH	Long hypocotyl in far-red 1 (bHLH-like protein HFR1) (Reduced phytochrome signaling) (Basic helix-lo ...	0.85	-	nuc	0	Nucleus				292
Q8IWV1 UniProt NPD GO	LAX1_HUMAN	Lymphocyte transmembrane adapter 1 (Membrane-associated adapter protein LAX) (Linker for activation ...	0.85	-	nuc	1 *	Cell membrane; single-pass type III membrane protein	integral to membrane [IDA]			398
P30634 UniProt NPD GO	MPIP3_CAEEL	M-phase inducer phosphatase cdc-25.3 (EC 3.1.3.48) (Cell division cycle-related protein 25.3)	0.85	-	nuc	0					316
Q9FUY6 UniProt NPD GO	JOIN_LYCES	MADS-box protein JOINTLESS (LeMADS)	0.85	-	nuc	0	Nucleus (Probable)				265
Q5K4R0 UniProt NPD GO	MAD47_ORYSA	MADS-box transcription factor 47 (OsMADS47)	0.85	-	nuc	0	Nucleus (Probable)				246
Q8BGS0 UniProt NPD GO	RBM13_MOUSE	MAK16-like protein RBM13 (RNA-binding motif protein 13)	0.85	+	nuc	0	Nucleus; nucleolus (By similarity)				296
O08605 UniProt NPD GO	MKNK1_MOUSE	MAP kinase-interacting serine/threonine-protein kinase 1 (EC 2.7.11.1) (MAP kinase signal-integratin ...	0.85	+	nuc	0					427
P25158 UniProt NPD GO	OSKA_DROME	Maternal effect protein oskar	0.85	+	nuc	0		polar granule [IDA]			606
Q61846 UniProt NPD GO	MELK_MOUSE	Maternal embryonic leucine zipper kinase (EC 2.7.11.1) (Protein kinase PK38) (mPK38)	0.85	+	nuc	0	Cytoplasm (Potential)	cytoplasm [IDA]			643
Q10668 UniProt NPD GO	SWI2_SCHPO	Mating-type switching protein swi2	0.85	-	nuc	0					722
Q95EE5 UniProt NPD GO	MATK_GRABR	Maturase K (Intron maturase)	0.85	-	nuc	0	Plastid; chloroplast				510
Q9TI97 UniProt NPD GO	MATK_SPOIN	Maturase K (Intron maturase)	0.85	+	nuc	0	Plastid; chloroplast				513
O94452 UniProt NPD GO	MCP1_SCHPO	Meiotic coiled-coil protein 1	0.85	-	nuc	0					661
Q91618 UniProt NPD GO	PMYT1_XENLA	Membrane-associated tyrosine- and threonine-specific cdc2-inhibitory kinase (EC 2.7.11.1) (Myt1 kina ...	0.85	+	nuc	0	Endoplasmic reticulum; endoplasmic reticulum membrane; peripheral membrane protein (Probable). Golgi ...				548
P46662 UniProt NPD GO	MERL_MOUSE	Merlin (Moesin-ezrin-radixin-like protein) (Neurofibromin-2) (Schwannomin)	0.85	-	mit	0		adherens junction [IMP]		1ISN	596
Q8R1S4 UniProt NPD GO	MTSS1_MOUSE	Metastasis suppressor protein 1 (Missing in metastasis protein)	0.85	-	nuc	0		actin cytoskeleton [ISS] cytoplasm [ISS] endocytic vesicle [ISS] ruffle [ISS]			759
Q62599 UniProt NPD GO	MTA1_RAT	Metastasis-associated protein MTA1	0.85	+	nuc	0	Isoform 1: Nucleus. Isoform 2: Zymogen granules, rough endoplasmic reticulum and Golgi apparatus				703
Q9CQU1 UniProt NPD GO	MFAP1_MOUSE	Microfibrillar-associated protein 1	0.85	-	nuc	0	Secreted protein; extracellular space; extracellular matrix (By similarity)				439
P15146 UniProt NPD GO	MAP2_RAT	Microtubule-associated protein 2 (MAP 2) (MAP-2)	0.85	-	nuc	0					1861
Q75AH6 UniProt NPD GO	AGC1_ASHGO	Mitochondrial aspartate-glutamate transporter AGC1 (Aspartate-glutamate carrier 1)	0.85	-	mit	0	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein (By similarity)				911

You are viewing entries 6551 to 6600 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.