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
P12004 UniProt NPD GO	PCNA_HUMAN	Proliferating cell nuclear antigen (PCNA) (Cyclin)	0.03	-	cyt	0	Nucleus	DNA replication factor C complex [TAS]	176740	1W60	261
P22177 UniProt NPD GO	PCNA_SOYBN	Proliferating cell nuclear antigen (PCNA) (Cyclin) (Fragment)	0.03	-	mit	0	Nucleus				236
P93732 UniProt NPD GO	PIP_ARATH	Proline iminopeptidase (EC 3.4.11.5) (PIP) (Prolyl aminopeptidase) (PAP)	0.03	-	cyt	0	Cytoplasm (By similarity)				329
P18696 UniProt NPD GO	PUTX_EMENI	Proline-specific permease (Proline transport protein)	0.03	-	end	12 *	Membrane; multi-pass membrane protein				550
Q99MN9 UniProt NPD GO	PCCB_MOUSE	Propionyl-CoA carboxylase beta chain, mitochondrial precursor (EC 6.4.1.3) (PCCase subunit beta) (Pr ...	0.03	-	mit	0	Mitochondrion; mitochondrial matrix (By similarity)	mitochondrion [IDA]			541
P07633 UniProt NPD GO	PCCB_RAT	Propionyl-CoA carboxylase beta chain, mitochondrial precursor (EC 6.4.1.3) (PCCase subunit beta) (Pr ...	0.03	-	mit	0	Mitochondrion; mitochondrial matrix	mitochondrion [TAS]			541
Q9JM51 UniProt NPD GO	PTGES_MOUSE	Prostaglandin E synthase (EC 5.3.99.3) (mPGES-1)	0.03	-	nuc	2 *	Membrane; multi-pass membrane protein (Potential)	cytoplasm [IDA] microsome [IDA] nuclear envelope lumen [IDA]			153
P02780 UniProt NPD GO	PSC3_RAT	Prostatic steroid-binding protein C3 chain precursor (Prostatein peptide C3)	0.03	-	vac	1 *	Secreted protein				95
P81162 UniProt NPD GO	CRPTI_BOOMI	Protease inhibitor carrapatin	0.03	-	cyt	0	Secreted protein				69
Q863Z0 UniProt NPD GO	PSME2_PIG	Proteasome activator complex subunit 2 (Proteasome activator 28-beta subunit) (PA28beta) (PA28b)	0.03	-	cyt	0					238
P30656 UniProt NPD GO	PSB5_YEAST	Proteasome component PRE2 precursor (EC 3.4.25.1) (Macropain subunit PRE2) (Proteinase YSCE subunit ...	0.03	+	cyt	0	Cytoplasm. Nucleus	proteasome core complex, beta-subunit compl... [IPI]		2FNY	287
P25451 UniProt NPD GO	PSB3_YEAST	Proteasome component PUP3 (EC 3.4.25.1) (Macropain subunit PUP3) (Multicatalytic endopeptidase compl ...	0.03	-	cyt	0	Cytoplasm. Nucleus	proteasome core complex, beta-subunit compl... [IPI]		2FNY	205
Q95083 UniProt NPD GO	PSA5_DROME	Proteasome subunit alpha type 5 (EC 3.4.25.1)	0.03	-	cyt	0	Cytoplasm (By similarity). Nucleus (By similarity)				244
P28066 UniProt NPD GO	PSA5_HUMAN	Proteasome subunit alpha type 5 (EC 3.4.25.1) (Proteasome zeta chain) (Macropain zeta chain) (Multic ...	0.03	-	cyt	0	Cytoplasm. Nucleus	proteasome complex (sensu Eukaryota) [TAS]	176844		241
Q9Z2U1 UniProt NPD GO	PSA5_MOUSE	Proteasome subunit alpha type 5 (EC 3.4.25.1) (Proteasome zeta chain) (Macropain zeta chain) (Multic ...	0.03	-	cyt	0	Cytoplasm. Nucleus				241
P34064 UniProt NPD GO	PSA5_RAT	Proteasome subunit alpha type 5 (EC 3.4.25.1) (Proteasome zeta chain) (Macropain zeta chain) (Multic ...	0.03	-	cyt	0	Cytoplasm. Nucleus				241
O81147 UniProt NPD GO	PSA6B_ARATH	Proteasome subunit alpha type 6-B (EC 3.4.25.1) (Proteasome subunit alpha type 1) (20S proteasome al ...	0.03	-	cyt	0	Cytoplasm (By similarity). Nucleus (By similarity)				246
O04861 UniProt NPD GO	PSA7_ORYSA	Proteasome subunit alpha type 7 (EC 3.4.25.1) (20S proteasome alpha subunit D) (20S proteasome subun ...	0.03	-	cyt	0	Cytoplasm (By similarity). Nucleus (By similarity)				249
Q9XI05 UniProt NPD GO	PSB3A_ARATH	Proteasome subunit beta type 3-A (EC 3.4.25.1) (20S proteasome beta subunit C-1) (Proteasome compone ...	0.03	-	cyt	0	Cytoplasm (By similarity). Nucleus (By similarity)				204
Q29384 UniProt NPD GO	PSB4_PIG	Proteasome subunit beta type 4 precursor (EC 3.4.25.1) (Proteasome beta chain) (Macropain beta chain ...	0.03	-	cyt	0	Cytoplasm (By similarity). Nucleus (By similarity)				154
P30655 UniProt NPD GO	PSB5_SCHPO	Proteasome subunit beta type 5 precursor (EC 3.4.25.1) (Proteasome component pts1) (Macropain subuni ...	0.03	-	cyt	0	Cytoplasm (By similarity). Nucleus (By similarity)	nucleus [TAS]			272
Q9XZ43 UniProt NPD GO	5NTD_LUTLO	Protein 5NUC precursor [Includes: UDP-sugar hydrolase (EC 3.6.1.45) (UDP-sugar diphosphatase) (UDP-s ...	0.03	-	exc	0					572
P52307 UniProt NPD GO	5NTD_BOOMI	Protein 5NUC precursor [Includes: UDP-sugar hydrolase (EC 3.6.1.45) (UDP-sugar diphosphatase) (UDP-s ...	0.03	-	exc	0	Cell membrane; lipid-anchor; GPI-anchor				580
Q750Q7 UniProt NPD GO	ARV1_ASHGO	Protein ARV1	0.03	-	end	4	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (By similarity). ...				299
Q9SQZ9 UniProt NPD GO	Y3478_ARATH	Protein At3g04780	0.03	-	nuc	0				1XOY	176
Q8LB17 UniProt NPD GO	Y3846_ARATH	Protein At3g58460	0.03	-	end	6 *	Membrane; multi-pass membrane protein (Potential)			1VG5	403
Q32PA8 UniProt NPD GO	CK067_BOVIN	Protein C11orf67 homolog	0.03	-	cyt	0					122
Q7Z3D6 UniProt NPD GO	CN159_HUMAN	Protein C14orf159, mitochondrial precursor	0.03	-	mit	0	Mitochondrion (Potential)				616
Q9NV44 UniProt NPD GO	CU077_HUMAN	Protein C21orf77	0.03	-	nuc	0					126
Q68US2 UniProt NPD GO	CU077_PANTR	Protein C21orf77 homolog	0.03	-	mit	0					126
Q9H3L0 UniProt NPD GO	CB025_HUMAN	Protein C2orf25, mitochondrial precursor	0.03	-	mit	0	Mitochondrion (Potential)				296
Q9H0C6 UniProt NPD GO	CB031_HUMAN	Protein C2orf31	0.03	-	cyt	0					104
Q68FU4 UniProt NPD GO	CG010_RAT	Protein C7orf10 homolog	0.03	-	mit	0					436
O75223 UniProt NPD GO	CG024_HUMAN	Protein C7orf24	0.03	-	cyt	0					188
Q9BW30 UniProt NPD GO	CG38_HUMAN	Protein CGI-38	0.03	-	cyt	0					176
Q9CRB6 UniProt NPD GO	CG38_MOUSE	Protein CGI-38 homolog	0.03	-	cyt	0				1WLM	176
Q755V9 UniProt NPD GO	CIS1_ASHGO	Protein CIS1	0.03	-	cyt	0	Punctate structures (By similarity)				142
Q5ZJ73 UniProt NPD GO	CREG1_CHICK	Protein CREG1 precursor	0.03	-	exc	0	Secreted protein (By similarity)				192
O60888 UniProt NPD GO	CUTA_HUMAN	Protein CutA precursor (Brain acetylcholinesterase putative membrane anchor) (Acetylcholinesterase-a ...	0.03	-	end	1 *		membrane [IDA]		1XK8	179
P54187 UniProt NPD GO	D2_ONCVO	Protein D2 (Fragment)	0.03	-	cyt	0					114
P41771 UniProt NPD GO	ERD1_KLULA	Protein ERD1	0.03	-	end	5 *	Membrane; multi-pass membrane protein				384
Q12450 UniProt NPD GO	ERP4_YEAST	Protein ERP4 precursor	0.03	-	end	1	Endoplasmic reticulum; endoplasmic reticulum membrane; single-pass type I membrane protein (By simil ...				207
Q24JY7 UniProt NPD GO	FM14A_BOVIN	Protein FAM14A precursor	0.03	-	mit	1 *					133
Q9H2X8 UniProt NPD GO	FM14A_HUMAN	Protein FAM14A precursor (Protein ISG12(b)) (Protein TLH29) (pIFI27-like protein)	0.03	-	mit	1 *					130
Q9D8T0 UniProt NPD GO	FAM3A_MOUSE	Protein FAM3A precursor	0.03	-	mit	1 *	Secreted protein (Potential)				230
Q92520 UniProt NPD GO	FAM3C_HUMAN	Protein FAM3C precursor (Protein GS3786)	0.03	-	end	1 *	Secreted protein (Potential)	extracellular region [NAS]	608618		227
Q5ND56 UniProt NPD GO	FA57A_MOUSE	Protein FAM57A	0.03	-	end	7 *	Cell membrane; multi-pass membrane protein (By similarity)				257
Q17040 UniProt NPD GO	G12_ANOGA	Protein G12 precursor (ANG12)	0.03	-	exc	0					211
Q9VVT2 UniProt NPD GO	INDY1_DROME	Protein I'm not dead yet (INDY transporter protein) (drIndy)	0.03	-	end	10 *	Cell membrane; basolateral cell membrane; multi-pass membrane protein. Basolateral membrane of cells ...	integral to plasma membrane [IDA] plasma membrane [IDA]			572
Q9VDQ0 UniProt NPD GO	INDY2_DROME	Protein I'm not dead yet 2	0.03	-	end	11 *	Membrane; multi-pass membrane protein (Probable)	integral to plasma membrane [ISS]			562

You are viewing entries 81301 to 81350 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.