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
Q9QY42 UniProt NPD GO	GPR37_MOUSE	Probable G-protein coupled receptor 37 precursor	0.64	-	end	7	Membrane; multi-pass membrane protein				600
Q9NBX4 UniProt NPD GO	RTXE_DROME	Probable RNA-directed DNA polymerase from transposon X-element (EC 2.7.7.49) (Reverse transcriptase) ...	0.64	+	cyt	0					908
Q19546 UniProt NPD GO	WRN_CAEEL	Probable Werner syndrome ATP-dependent helicase homolog 1 (EC 3.6.1.-)	0.64	-	nuc	0	Nucleus (By similarity)				1056
P50108 UniProt NPD GO	MNN10_YEAST	Probable alpha-1,6-mannosyltransferase MNN10 (EC 2.4.1.-) (Mannan polymerase II complex MNN10 subuni ...	0.64	-	mit	1	Endoplasmic reticulum; endoplasmic reticulum membrane; single-pass type II membrane protein. Golgi a ...	alpha-1,6-mannosyltransferase complex [IDA]			393
Q09860 UniProt NPD GO	SYC_SCHPO	Probable cysteinyl-tRNA synthetase (EC 6.1.1.16) (Cysteine--tRNA ligase) (CysRS)	0.64	-	mit	0					754
Q93YU5 UniProt NPD GO	EXOC4_ARATH	Probable exocyst complex component 4 (Exocyst complex component Sec8)	0.64	-	nuc	0					1053
Q99JT1 UniProt NPD GO	GATB_MOUSE	Probable glutamyl-tRNA(Gln) amidotransferase subunit B, mitochondrial precursor (EC 6.3.5.-) (Glu-AD ...	0.64	-	nuc	0	Mitochondrion (By similarity)				557
P49870 UniProt NPD GO	HR38_BOMMO	Probable nuclear hormone receptor HR38 (bHR38) (Fragment)	0.64	-	nuc	0	Nucleus				360
Q80YA3 UniProt NPD GO	DDHD1_MOUSE	Probable phospholipase DDHD1 (EC 3.1.1.-) (DDHD domain protein 1) (Phosphatidic acid-preferring phos ...	0.64	-	nuc	0					547
O46606 UniProt NPD GO	DDHD1_BOVIN	Probable phospholipase DDHD1 (EC 3.1.1.-) (DDHD domain protein 1) (Phosphatidic acid-preferring phos ...	0.64	-	nuc	0					875
Q9W391 UniProt NPD GO	KPBA_DROME	Probable phosphorylase b kinase regulatory subunit alpha (Phosphorylase kinase subunit alpha)	0.64	-	cyt	0	Cell membrane; lipid-anchor; cytoplasmic side (Potential)				1247
Q7PC82 UniProt NPD GO	PDR14_ARATH	Probable pleiotropic drug resistance protein 14	0.64	-	end	11	Membrane; multi-pass membrane protein (By similarity)				1392
Q3SZ12 UniProt NPD GO	RLP24_BOVIN	Probable ribosome biogenesis protein RLP24	0.64	+	nuc	0	Nucleus; nucleolus (By similarity)				163
Q9VGN9 UniProt NPD GO	RLP24_DROME	Probable ribosome biogenesis protein RLP24	0.64	+	cyt	0	Nucleus; nucleolus (By similarity)				191
Q00453 UniProt NPD GO	RGM1_YEAST	Probable transcription repressor protein RGM1	0.64	-	nuc	0	Nucleus	nucleus [IC]			211
P39961 UniProt NPD GO	YE14_YEAST	Probable transcriptional regulatory protein YER184C	0.64	-	nuc	2	Nucleus (Probable)				794
Q00175 UniProt NPD GO	PRGR_MOUSE	Progesterone receptor (PR)	0.64	+	nuc	0	Nucleus	nucleus [IC]			923
Q04499 UniProt NPD GO	PROD_DROME	Proline oxidase, mitochondrial precursor (EC 1.5.3.-) (Proline dehydrogenase) (Protein sluggish-A)	0.64	-	mit	0	Mitochondrion; mitochondrial matrix				681
O22224 UniProt NPD GO	Y2162_ARATH	Protein At2g41620	0.64	-	cyt	0					861
Q756K9 UniProt NPD GO	BCP1_ASHGO	Protein BCP1	0.64	-	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity)				271
P87128 UniProt NPD GO	YDLD_SCHPO	Protein C3A12.13c in chromosome I	0.64	-	nuc	0					274
Q5VWP3 UniProt NPD GO	CF142_HUMAN	Protein C6orf142	0.64	-	nuc	0					458
Q9D5Y0 UniProt NPD GO	CG031_MOUSE	Protein C7orf31 homolog (Protein TISP74)	0.64	-	nuc	0					588
Q3UHX9 UniProt NPD GO	CI114_MOUSE	Protein C9orf114 homolog	0.64	-	nuc	0					385
P40987 UniProt NPD GO	CIN1_YEAST	Protein CIN1 (Chromosome instability protein 1)	0.64	-	end	0					1014
Q92508 UniProt NPD GO	FA38A_HUMAN	Protein FAM38A	0.64	+	end	23 *	Membrane; multi-pass membrane protein (Potential)				2035
Q8IZT9 UniProt NPD GO	FAM9C_HUMAN	Protein FAM9C	0.64	-	nuc	0	Nucleus		300479		166
Q92636 UniProt NPD GO	FAN_HUMAN	Protein FAN (Factor associated with N-SMase activation) (Factor associated with neutral sphingomyeli ...	0.64	-	cyt	0		cytoplasm [TAS] soluble fraction [TAS]	603043		917
Q5S2C4 UniProt NPD GO	NCKP1_ARATH	Protein NAP1 (Nck-associated protein 1) (AtNAP1) (AtNAP125) (p125Nap1) (NAP of plants) (ARP2/3 regul ...	0.64	-	nuc	0					1425
P53617 UniProt NPD GO	NRD1_YEAST	Protein NRD1	0.64	-	nuc	0	Nucleus (Potential)	nucleus [IPI]			575
P25294 UniProt NPD GO	SIS1_YEAST	Protein SIS1	0.64	-	nuc	0	Nucleus. Localized throughout the cell but is more concentrated at the nucleus	cytosolic small ribosomal subunit (sensu Eu... [IDA]		1C3G	352
Q99176 UniProt NPD GO	SRN2_YEAST	Protein SRN2 (Vacuolar protein sorting-associated protein VPS37)	0.64	-	nuc	0	Cytoplasm	endosome [IPI] ESCRT I complex [IDA]		2F66	213
P11972 UniProt NPD GO	SST2_YEAST	Protein SST2	0.64	-	nuc	0		plasma membrane [IDA]			698
Q5PQS2 UniProt NPD GO	ZN365_RAT	Protein ZNF365	0.64	-	nuc	0	Nucleus (Potential)				408
Q32MQ0 UniProt NPD GO	ZN750_HUMAN	Protein ZNF750	0.64	-	nuc	0			610227		723
P18755 UniProt NPD GO	ETS1A_XENLA	Protein c-ets-1-A (C-ets-1A)	0.64	+	nuc	0	Nucleus	nucleus [ISS]			438
Q86UF2 UniProt NPD GO	CTGE6_HUMAN	Protein cTAGE-6 (cTAGE family member 6)	0.64	-	nuc	0					732
Q9W568 UniProt NPD GO	HFW1_DROME	Protein halfway precursor (Protein singed wings)	0.64	-	exc	0					611
P53009 UniProt NPD GO	SCY1_YEAST	Protein kinase-like protein SCY1	0.64	-	nuc	0					804
Q09564 UniProt NPD GO	PHLPP_CAEEL	Protein phosphatase PHLPP-like protein (EC 3.1.3.16)	0.64	-	nuc	0					1036
Q9GPJ1 UniProt NPD GO	SKEL_DROME	Protein skeletor	0.64	-	nuc	0	Part of a macromolecular complex forming the spindle matrix. Associated with chromosome at interphas ...	nucleus [IDA] polytene chromosome [IDA]			743
P53847 UniProt NPD GO	DSL1_YEAST	Protein transport protein DSL1 (Dependent on SLY1-20 protein 1)	0.64	-	cyt	0	Endoplasmic reticulum; endoplasmic reticulum membrane; peripheral membrane protein	endoplasmic reticulum [IDA]			754
Q3U2P1 UniProt NPD GO	SC24A_MOUSE	Protein transport protein Sec24A (SEC24-related protein A)	0.64	-	nuc	0	Cytoplasm (By similarity). Cytoplasm; perinuclear region (By similarity)				1090
O74786 UniProt NPD GO	SEC9_SCHPO	Protein transport protein sec9	0.64	-	nuc	0					419
P17219 UniProt NPD GO	PTTH_BOMMO	Prothoracicotropic hormone precursor (PTTH) [Contains: P2K; P6K; Prothoracicotropic hormone]	0.64	-	nuc	1 *	PTTH is synthesized by two dorsolateral neurosecretory cells of the Bombyx brain				224
O97930 UniProt NPD GO	FOS_PIG	Proto-oncogene protein c-fos (Cellular oncogene fos)	0.64	+	nuc	0	Nucleus				380
Q9HC56 UniProt NPD GO	PCDH9_HUMAN	Protocadherin-9 precursor	0.64	+	nuc	1	Membrane; single-pass type I membrane protein (By similarity)		603581		1203
Q80U78 UniProt NPD GO	PUM1_MOUSE	Pumilio homolog 1	0.64	-	nuc	0	Cytoplasm (Probable)				1189
Q5R607 UniProt NPD GO	DHX30_PONPY	Putative ATP-dependent RNA helicase DHX30 (EC 3.6.1.-) (DEAH box protein 30)	0.64	-	mit	0					1194
Q9XVD5 UniProt NPD GO	TBX38_CAEEL	Putative T-box protein 38	0.64	-	nuc	0	Nucleus (Potential)				303

You are viewing entries 17051 to 17100 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.