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
Q9D0F6 UniProt NPD GO	RFC5_MOUSE	Replication factor C subunit 5 (Replication factor C 36 kDa subunit) (RF-C 36 kDa subunit) (RFC36) ( ...	0.27	-	mit	0	Nucleus (Probable)				339
Q8X082 UniProt NPD GO	RFC5_NEUCR	Replication factor C subunit 5 (Replication factor C5) (Probable activator 1 subunit 5)	0.27	-	cyt	0	Nucleus (By similarity)				352
O93434 UniProt NPD GO	RCN1_FUGRU	Reticulocalbin-1 precursor	0.27	-	nuc	0	Endoplasmic reticulum; endoplasmic reticulum lumen (By similarity)				322
Q03275 UniProt NPD GO	PO24_POPJA	Retrovirus-related Pol polyprotein from type-1 retrotransposable element R2 (Retrovirus-related Pol ...	0.27	-	cyt	0					482
P52198 UniProt NPD GO	RND2_HUMAN	Rho-related GTP-binding protein RhoN (Rho family GTPase 2) (Rnd2) (Rho7)	0.27	-	nuc	0	Cell membrane; lipid-anchor; cytoplasmic side (Potential). Colocalizes with RACGAP1 in Golgi-derived ...		601555		227
P38786 UniProt NPD GO	RPP1_YEAST	Ribonuclease P protein subunit RPP1 (EC 3.1.26.5) (RNaseP protein 1)	0.27	-	nuc	0	Nucleus (Potential)	nucleolar ribonuclease P complex [TAS] ribonuclease MRP complex [TAS]			293
P29315 UniProt NPD GO	RINI_RAT	Ribonuclease inhibitor (Ribonuclease/angiogenin inhibitor 1)	0.27	-	nuc	0	Cytoplasm				456
Q8VD87 UniProt NPD GO	RNS1G_RATRT	Ribonuclease pancreatic gamma-type precursor (EC 3.1.27.5) (RNase 1 gamma)	0.27	-	exc	0	Secreted protein (By similarity)				147
Q9WUR4 UniProt NPD GO	RNAS1_CLEGL	Ribonuclease pancreatic precursor (EC 3.1.27.5) (RNase 1) (RNase A)	0.27	-	exc	0	Secreted protein				148
Q7YRG7 UniProt NPD GO	RNAS9_CEBCA	Ribonuclease-like protein 9 precursor	0.27	-	exc	0	Secreted protein (Probable)				205
Q7YRH2 UniProt NPD GO	RNAS9_MACNE	Ribonuclease-like protein 9 precursor	0.27	-	exc	0	Secreted protein (Probable)				204
P51812 UniProt NPD GO	KS6A3_HUMAN	Ribosomal protein S6 kinase alpha-3 (EC 2.7.11.1) (S6K-alpha 3) (90 kDa ribosomal protein S6 kinase ...	0.27	-	cyt	0			303600		740
P18654 UniProt NPD GO	KS6A3_MOUSE	Ribosomal protein S6 kinase alpha-3 (EC 2.7.11.1) (S6K-alpha 3) (90 kDa ribosomal protein S6 kinase ...	0.27	-	cyt	0					740
P09989 UniProt NPD GO	RIPT_TRIKI	Ribosome-inactivating protein alpha-trichosanthin precursor (EC 3.2.2.22) (rRNA N-glycosidase) (Alph ...	0.27	-	exc	0				1TCS	289
P84073 UniProt NPD GO	RIPL_LUFCY	Ribosome-inactivating protein luffacylin (EC 3.2.2.22) (rRNA N-glycosidase) (Fragment)	0.27	-		0					14
Q28263 UniProt NPD GO	PDE6A_CANFA	Rod cGMP-specific 3',5'-cyclic phosphodiesterase alpha-subunit (EC 3.1.4.35) (GMP-PDE alpha)	0.27	-	cyt	0	Cell membrane; lipid-anchor; cytoplasmic side (Potential)				860
P07761 UniProt NPD GO	SLSG6_BRAOL	S-locus-specific glycoprotein S6 precursor (SLSG-6)	0.27	-	exc	1 *					436
Q6GMV2 UniProt NPD GO	SMYD5_HUMAN	SET and MYND domain-containing protein 5 (Protein NN8-4AG)	0.27	-	cyt	0					418
Q9NR46 UniProt NPD GO	SHLB2_HUMAN	SH3 domain GRB2-like protein B2 (Endophilin B2)	0.27	-	cyt	0	Cytoplasm				395
Q9H299 UniProt NPD GO	SH3L3_HUMAN	SH3 domain-binding glutamic acid-rich-like protein 3 (SH3 domain-binding protein 1) (SH3BP-1)	0.27	-	nuc	0	Cytoplasm. Nucleus			1SJ6	93
O35180 UniProt NPD GO	SH3G3_RAT	SH3-containing GRB2-like protein 3 (SH3 domain protein 2C) (SH3p13) (Fragment)	0.27	+	cyt	0					291
Q38997 UniProt NPD GO	KIN10_ARATH	SNF1-related protein kinase catalytic subunit alpha KIN10 (EC 2.7.11.1) (AKIN10) (AKIN alpha2)	0.27	-	nuc	0					535
P40665 UniProt NPD GO	CH01_CHICK	SRY-related protein CH1 (Fragment)	0.27	-	nuc	0	Nucleus (Potential)				54
P40984 UniProt NPD GO	UBC9_SCHPO	SUMO-conjugating enzyme ubc9 (EC 6.3.2.19) (Ubiquitin-conjugating enzyme E2-18 kDa) (Ubiquitin-prote ...	0.27	-	nuc	0	Nucleus	nucleus [IDA]			157
Q8GYE0 UniProt NPD GO	PHF1_ARATH	Sec12-like protein 1 (Protein PHOSPHATE TRANSPORTER TRAFFIC FACILITATOR 1) (PHF-1)	0.27	-	nuc	1	Endoplasmic reticulum; endoplasmic reticulum membrane; single-pass membrane protein				398
Q8C4U3 UniProt NPD GO	SFRP1_MOUSE	Secreted frizzled-related protein 1 precursor (sFRP-1)	0.27	-	exc	0	Secreted protein. Cell membrane or extracellular matrix-associated. Released by heparin-binding (By ...				314
O96615 UniProt NPD GO	SER2_GALME	Sericin-2 (Silk gum protein 2) (Fragment)	0.27	-	mit	0	Secreted protein				220
Q04066 UniProt NPD GO	YD428_YEAST	Serine hydrolase YDR428C (EC 3.1.-.-)	0.27	-	cyt	0				1VKH	261
P53323 UniProt NPD GO	BUD32_YEAST	Serine/threonine-protein kinase BUD32 (EC 2.7.11.1) (Bud site selection protein BUD32) (piD261)	0.27	-	cyt	0		cytoplasm [IDA] nucleus [IDA]			261
Q9WVC6 UniProt NPD GO	SGK1_MOUSE	Serine/threonine-protein kinase Sgk1 (EC 2.7.11.1) (Serum/glucocorticoid-regulated kinase 1)	0.27	-	cyt	0	Cytoplasm (By similarity). Nucleus (By similarity). Nuclear, upon phosphorylation (By similarity)				431
P0C153 UniProt NPD GO	PTPA2_EMENI	Serine/threonine-protein phosphatase 2A activator 2 (EC 5.2.1.8) (Peptidyl-prolyl cis-trans isomeras ...	0.27	-	nuc	0	Cytoplasm (By similarity)				420
P48454 UniProt NPD GO	PP2BC_HUMAN	Serine/threonine-protein phosphatase 2B catalytic subunit gamma isoform (EC 3.1.3.16) (Calmodulin-de ...	0.27	-	mit	0			114107		502
P48455 UniProt NPD GO	PP2BC_MOUSE	Serine/threonine-protein phosphatase 2B catalytic subunit gamma isoform (EC 3.1.3.16) (Calmodulin-de ...	0.27	-	mit	0					513
P53043 UniProt NPD GO	PPT1_YEAST	Serine/threonine-protein phosphatase T (EC 3.1.3.16) (PPT)	0.27	-	nuc	0	Nucleus	cytoplasm [IDA] nucleus [IDA]			513
Q8WUJ0 UniProt NPD GO	STYX_HUMAN	Serine/threonine/tyrosine-interacting protein (Protein tyrosine phosphatase-like protein)	0.27	-	cyt	0					223
Q18881 UniProt NPD GO	SRA31_CAEEL	Serpentine receptor class alpha-31 (Protein sra-31)	0.27	-	end	6 *	Membrane; multi-pass membrane protein (Potential)				338
P15651 UniProt NPD GO	ACADS_RAT	Short-chain specific acyl-CoA dehydrogenase, mitochondrial precursor (EC 1.3.99.2) (SCAD) (Butyryl-C ...	0.27	-	mit	0	Mitochondrion; mitochondrial matrix	mitochondrial matrix [TAS]		1JQI	412
O94607 UniProt NPD GO	STR2_SCHPO	Siderophore iron transporter 2	0.27	-	end	12	Membrane; multi-pass membrane protein (Probable)				597
P09132 UniProt NPD GO	SRP19_HUMAN	Signal recognition particle 19 kDa protein (SRP19)	0.27	-	nuc	0	Cytoplasm	signal recognition particle (sensu Eukaryota) [TAS]	182175	1RY1	144
Q5RBR1 UniProt NPD GO	SRP19_PONPY	Signal recognition particle 19 kDa protein (SRP19)	0.27	-	nuc	0	Cytoplasm (By similarity)				144
P81877 UniProt NPD GO	SSBP2_HUMAN	Single-stranded DNA-binding protein 2 (Sequence-specific single-stranded-DNA-binding protein 2)	0.27	-	nuc	0	Nucleus (By similarity)	nucleus [NAS]	607389		361
Q9CYZ8 UniProt NPD GO	SSBP2_MOUSE	Single-stranded DNA-binding protein 2 (Sequence-specific single-stranded-DNA-binding protein 2)	0.27	-	nuc	0	Nucleus (By similarity)	nucleus [ISS]			361
Q9PUN2 UniProt NPD GO	SMUF1_XENLA	Smad ubiquitination regulatory factor 1 (EC 6.3.2.-) (Ubiquitin--protein ligase SMURF1) (Smad-specif ...	0.27	-	mit	0		intracellular [TAS]			731
P62303 UniProt NPD GO	RUXE_CHICK	Small nuclear ribonucleoprotein E (snRNP-E) (Sm protein E) (Sm-E) (SmE)	0.27	-	mit	0	Nucleus				92
P62304 UniProt NPD GO	RUXE_HUMAN	Small nuclear ribonucleoprotein E (snRNP-E) (Sm protein E) (Sm-E) (SmE)	0.27	-	mit	0	Nucleus	small nuclear ribonucleoprotein complex [NAS] spliceosome complex [NAS]	128260		92
P62305 UniProt NPD GO	RUXE_MOUSE	Small nuclear ribonucleoprotein E (snRNP-E) (Sm protein E) (Sm-E) (SmE)	0.27	-	mit	0	Nucleus				92
Q3SZF8 UniProt NPD GO	SMD2_BOVIN	Small nuclear ribonucleoprotein Sm D2 (snRNP core protein D2) (Sm-D2)	0.27	-	nuc	0	Nucleus (By similarity)				118
P62316 UniProt NPD GO	SMD2_HUMAN	Small nuclear ribonucleoprotein Sm D2 (snRNP core protein D2) (Sm-D2)	0.27	-	nuc	0	Nucleus		601061	1B34	118
P62317 UniProt NPD GO	SMD2_MOUSE	Small nuclear ribonucleoprotein Sm D2 (snRNP core protein D2) (Sm-D2)	0.27	-	nuc	0	Nucleus (By similarity)				118
Q29329 UniProt NPD GO	SMD2_PIG	Small nuclear ribonucleoprotein Sm D2 (snRNP core protein D2) (Sm-D2) (Fragment)	0.27	-	nuc	0	Nucleus (By similarity)				50

You are viewing entries 43651 to 43700 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.