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
Q14839 UniProt NPD GO	CHD4_HUMAN	Chromodomain helicase-DNA-binding protein 4 (EC 3.6.1.-) (ATP-dependent helicase CHD4) (CHD-4) (Mi-2 ...	0.97	+	nuc	0	Nucleus		603277	1MM3	1912
Q9USQ1 UniProt NPD GO	CTF18_SCHPO	Chromosome transmission fidelity protein 18	0.97	-	nuc	0	Nucleus	Ctf18 RFC-like complex [TAS]			960
Q9PTD7 UniProt NPD GO	CING_XENLA	Cingulin	0.97	+	nuc	0		tight junction [NAS]			1360
Q3SX41 UniProt NPD GO	CROP_BOVIN	Cisplatin resistance-associated overexpressed protein	0.97	+	nuc	0	Nucleus; nucleoplasm; nuclear speckle (By similarity)				432
Q5SUF2 UniProt NPD GO	CROP_MOUSE	Cisplatin resistance-associated overexpressed protein	0.97	+	nuc	0	Nucleus; nucleoplasm; nuclear speckle (By similarity)				432
Q5R8W6 UniProt NPD GO	CROP_PONPY	Cisplatin resistance-associated overexpressed protein	0.97	+	nuc	0	Nucleus; nucleoplasm; nuclear speckle (By similarity)				432
O95232 UniProt NPD GO	CROP_HUMAN	Cisplatin resistance-associated overexpressed protein (cAMP regulatory element-associated protein 1) ...	0.97	+	nuc	0	Nucleus; nucleoplasm; nuclear speckle. The subnuclear localization is affected by cisplatin		609434		432
P49025 UniProt NPD GO	CTRO_MOUSE	Citron Rho-interacting kinase (EC 2.7.11.1) (CRIK) (Rho-interacting, serine/threonine-protein kinase ...	0.97	-	nuc	0	Cytoplasm	actin cytoskeleton [IDA] cytoplasm [IDA] intracellular [IDA] ruffle [IDA]			2055
Q9D5R3 UniProt NPD GO	CCD41_MOUSE	Coiled-coil domain-containing protein 41	0.97	-	nuc	0					692
Q5ZM86 UniProt NPD GO	CCD50_CHICK	Coiled-coil domain-containing protein 50	0.97	+	nuc	0					301
Q5NCR9 UniProt NPD GO	CCD55_MOUSE	Coiled-coil domain-containing protein 55	0.97	-	nuc	0					542
Q8N4S0 UniProt NPD GO	CCD82_HUMAN	Coiled-coil domain-containing protein 82	0.97	+	nuc	0					544
O13067 UniProt NPD GO	CND2_XENLA	Condensin complex subunit 2 (Chromosome-associated protein H) (Chromosome assembly protein xCAP-H) ( ...	0.97	+	nuc	0	Nucleus (By similarity). Cytoplasm (By similarity). In interphase cells, the majority of the condens ...				699
Q8WXI2 UniProt NPD GO	CNKR2_HUMAN	Connector enhancer of kinase suppressor of ras 2 (Connector enhancer of KSR2) (CNK2)	0.97	-	nuc	0	Cytoplasm. Membrane; peripheral membrane protein				1034
Q80YA9 UniProt NPD GO	CNKR2_MOUSE	Connector enhancer of kinase suppressor of ras 2 (Connector enhancer of KSR2) (CNK2)	0.97	-	nuc	0	Cytoplasm (By similarity). Membrane; peripheral membrane protein (By similarity)				1032
Q9Z1T4 UniProt NPD GO	CNKR2_RAT	Connector enhancer of kinase suppressor of ras 2 (Connector enhancer of KSR2) (CNK2) (Membrane-assoc ...	0.97	-	nuc	0	Cytoplasm (By similarity). Membrane; peripheral membrane protein (By similarity)				1032
Q640B4 UniProt NPD GO	MUS81_XENTR	Crossover junction endonuclease MUS81 (EC 3.1.22.-)	0.97	-	nuc	0	Nucleus (By similarity)				612
P18850 UniProt NPD GO	ATF6A_HUMAN	Cyclic AMP-dependent transcription factor ATF-6 alpha (Activating transcription factor 6 alpha) (ATF ...	0.97	+	nuc	0	Endoplasmic reticulum; endoplasmic reticulum membrane; single-pass type II membrane protein. Process ...	endoplasmic reticulum membrane [TAS] nuclear envelope [TAS] nucleoplasm [TAS] nucleus [TAS]	605537		670
Q7ZVX0 UniProt NPD GO	CCNL1_BRARE	Cyclin-L1	0.97	+	nuc	0	Nucleus (By similarity)				498
P78621 UniProt NPD GO	SEPA_EMENI	Cytokinesis protein sepA (FH1/2 protein) (Forced expression inhibition of growth A)	0.97	+	nuc	0					1790
Q9ZRZ8 UniProt NPD GO	RH28_ARATH	DEAD-box ATP-dependent RNA helicase 28 (EC 3.6.1.-)	0.97	+	nuc	0					789
P26358 UniProt NPD GO	DNMT1_HUMAN	DNA (cytosine-5)-methyltransferase 1 (EC 2.1.1.37) (Dnmt1) (DNA methyltransferase HsaI) (DNA MTase H ...	0.97	+	nuc	0	Nucleus	nucleus [TAS]	126375		1616
Q752B8 UniProt NPD GO	DPOE_ASHGO	DNA polymerase epsilon, catalytic subunit A (EC 2.7.7.7) (DNA polymerase II subunit A)	0.97	+	nuc	0	Nucleus (By similarity)				2180
Q9EQ28 UniProt NPD GO	DPOD3_MOUSE	DNA polymerase subunit delta 3 (DNA polymerase subunit delta p66)	0.97	+	nuc	0	Nucleus	delta DNA polymerase complex [ISS]			462
Q9UUA2 UniProt NPD GO	PIF1_SCHPO	DNA repair and recombination protein pif1, mitochondrial precursor (EC 3.6.1.-) (ATP-dependent helic ...	0.97	-	nuc	0	Mitochondrion (By similarity)	mitochondrion [TAS]			805
P31244 UniProt NPD GO	RAD16_YEAST	DNA repair protein RAD16 (EC 3.6.1.-) (ATP-dependent helicase RAD16)	0.97	+	nuc	0	Nucleus	nucleotide-excision repair factor 4 complex [IDA] repairosome [IDA]			790
Q6FY76 UniProt NPD GO	RAD5_CANGA	DNA repair protein RAD5 (EC 3.6.1.-)	0.97	+	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity)				1151
Q9W252 UniProt NPD GO	RAD50_DROME	DNA repair protein RAD50 (EC 3.6.-.-)	0.97	-	nuc	0	Nucleus. Uniformly distributed along mitotic chromosomes	condensed chromosome [IDA] Mre11 complex [TAS]			1318
Q9UTJ8 UniProt NPD GO	RAD50_SCHPO	DNA repair protein rad50 (EC 3.6.-.-)	0.97	-	nuc	0	Nucleus	Mre11 complex [TAS]			1290
P49717 UniProt NPD GO	MCM4_MOUSE	DNA replication licensing factor MCM4 (CDC21 homolog) (P1-CDC21)	0.97	-	nuc	0	Nucleus (By similarity)				862
O42709 UniProt NPD GO	MCM10_SCHPO	DNA replication licensing factor mcm10 (Minichromosome maintenance protein 10) (Cdc23 protein)	0.97	-	nuc	0	Nucleus. Associates with chromatin				593
Q9ATY5 UniProt NPD GO	UVH3_ARATH	DNA-repair protein UVH3 (EC 3.1.-.-) (UV hypersensitive protein 3) (XPG homolog) (ERCC5 homolog) (RA ...	0.97	+	nuc	0	Nucleus (Probable)				1479
Q8VIB2 UniProt NPD GO	DAXX_RAT	Death domain-associated protein 6 (Daxx)	0.97	-	nuc	0	Nucleus (By similarity). Cytoplasm (By similarity). Translocates from the nucleus to the cytoplasm u ...	nucleus [ISS]			731
Q9Y2H0 UniProt NPD GO	DLGP4_HUMAN	Disks large-associated protein 4 (DAP-4) (SAP90/PSD-95-associated protein 4) (SAPAP4) (PSD-95/SAP90- ...	0.97	+	nuc	0	Membrane; peripheral membrane protein (By similarity)				989
P11532 UniProt NPD GO	DMD_HUMAN	Dystrophin	0.97	-	nuc	0		costamere [IDA] cytoskeleton [TAS] dystrophin-associated glycoprotein complex [TAS]	300376	1EG4	3685
Q5GN48 UniProt NPD GO	DMD_PIG	Dystrophin	0.97	-	nuc	0					3674
Q9VDW6 UniProt NPD GO	DMDA_DROME	Dystrophin, isoforms A/C/DLP1/DLP3	0.97	+	nuc	0		cytoskeleton [ISS]			3497
Q9P4Z1 UniProt NPD GO	TOM1_NEUCR	E3 ubiquitin protein ligase TOM1-like protein (EC 6.3.2.-)	0.97	-	nuc	0	Nucleus (By similarity)				4065
P57680 UniProt NPD GO	EVC_MOUSE	Ellis-van Creveld syndrome protein homolog	0.97	-	nuc	1 *					1005
Q6CEV5 UniProt NPD GO	EPL1_YARLI	Enhancer of polycomb-like protein 1	0.97	-	nuc	0	Nucleus (By similarity)				839
Q5KBL8 UniProt NPD GO	EXO84_CRYNE	Exocyst complex component EXO84	0.97	-	nuc	0	Secretory vesicle (By similarity). Cell periphery. The polarization of EXO84 requires actin cables ( ...				675
Q8K007 UniProt NPD GO	SULF1_MOUSE	Extracellular sulfatase Sulf-1 precursor (EC 3.1.6.-) (MSulf-1)	0.97	+	nuc	0	Endoplasmic reticulum (By similarity). Golgi apparatus; Golgi stack (By similarity). Cell surface (B ...	cell surface [ISS] extracellular space [ISS]			870
Q920B0 UniProt NPD GO	FRM4B_MOUSE	FERM domain-containing protein 4B (GRP1-binding protein GRSP1) (Golgi-associated band 4.1-like prote ...	0.97	-	nuc	0	Cytoplasm				981
Q9Y4F1 UniProt NPD GO	FARP1_HUMAN	FERM, RhoGEF and pleckstrin domain-containing protein 1 (Chondrocyte-derived ezrin-like protein)	0.97	-	nuc	0		cytoskeleton [TAS]	602654		1045
Q7Z7B0 UniProt NPD GO	FLIP1_HUMAN	Filamin-A-interacting protein 1 (FILIP)	0.97	-	nuc	0			607307		1213
Q05858 UniProt NPD GO	FMN_CHICK	Formin (Limb deformity protein)	0.97	-	nuc	0	Nucleus				1213
Q05860 UniProt NPD GO	FMN1A_MOUSE	Formin-1 isoforms I/II/III (Limb deformity protein)	0.97	+	nuc	0	Nucleus	adherens junction [IPI]			1468
Q659K0 UniProt NPD GO	CCNB3_CANFA	G2/mitotic-specific cyclin-B3	0.97	+	nuc	0	Nucleus (By similarity)				1330
P51944 UniProt NPD GO	CCNF_MOUSE	G2/mitotic-specific cyclin-F	0.97	+	nuc	0	Nucleus (By similarity)				776
P38229 UniProt NPD GO	GIP1_YEAST	GLC7-interacting protein 1	0.97	-	nuc	0		prospore membrane [IDA] protein phosphatase type 1 complex [IPI]			573

You are viewing entries 951 to 1000 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.)

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