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
O13867 UniProt NPD GO	UPP1_SCHPO	Probable uracil phosphoribosyltransferase 1 (EC 2.4.2.9) (UMP pyrophosphorylase 1) (UPRTase 1)	0.04	-	cyt	0					219
O00469 UniProt NPD GO	PLOD2_HUMAN	Procollagen-lysine,2-oxoglutarate 5-dioxygenase 2 precursor (EC 1.14.11.4) (Lysyl hydroxylase 2) (LH ...	0.04	-	end	0	Endoplasmic reticulum; rough endoplasmic reticulum; rough endoplasmic reticulum cisterna; peripheral ...	endoplasmic reticulum [TAS]	609220		737
Q06084 UniProt NPD GO	PARC_TRYBB	Procyclic form-specific polypeptide B-alpha precursor (Procyclin) (PARP B-alpha) (PSSA-1)	0.04	-	exc	1 *	Cell membrane; lipid-anchor; GPI-anchor				145
P08469 UniProt NPD GO	PAR1_TRYBB	Procyclic form-specific polypeptide B1-alpha precursor (Procyclin B1-alpha) (PARP)	0.04	-	exc	1 *	Cell membrane; lipid-anchor; GPI-anchor				143
P18320 UniProt NPD GO	PROF_ANTCR	Profilin	0.04	-	cyt	0					139
P23412 UniProt NPD GO	PROF_TETPY	Profilin	0.04	-	cyt	0					153
Q8GSL5 UniProt NPD GO	PROF_PRUDU	Profilin (Allergen Pru du 4)	0.04	-	cyt	0					131
Q93YI9 UniProt NPD GO	PROF_CAPAN	Profilin (Minor food allergen Cap a 2)	0.04	-	cyt	0					131
Q84V37 UniProt NPD GO	PROF_CHEAL	Profilin (Minor pollen allergen Che a 2)	0.04	-	cyt	0					131
O65812 UniProt NPD GO	PROF1_HEVBR	Profilin-1 (Pollen allergen Hev b 8.0101)	0.04	-	cyt	0					131
Q9SNW6 UniProt NPD GO	PROF2_LILLO	Profilin-2	0.04	-	cyt	0					131
Q93YG7 UniProt NPD GO	PROF2_LYCES	Profilin-2 (Minor food allergen Lyc e 1)	0.04	-	cyt	0					131
Q64LH2 UniProt NPD GO	PROF2_AMBAR	Profilin-2 (Pollen allergen A0418)	0.04	-	cyt	0					131
Q9SNW5 UniProt NPD GO	PROF3_LILLO	Profilin-3	0.04	-	cyt	0					131
Q9DAD6 UniProt NPD GO	PROF3_MOUSE	Profilin-3 (Profilin III)	0.04	-	cyt	0					137
P51919 UniProt NPD GO	GON1_SPAAU	Progonadoliberin-1 precursor (Progonadoliberin I) [Contains: Gonadoliberin-1 (Gonadoliberin I) (Lute ...	0.04	-	exc	1 *	Secreted protein				95
P51917 UniProt NPD GO	GON3_CARAU	Progonadoliberin-3 precursor (Progonadoliberin III) [Contains: Gonadoliberin-3 (Gonadoliberin III) ( ...	0.04	-	exc	0	Secreted protein				94
Q92106 UniProt NPD GO	GON3_RUTRU	Progonadoliberin-3 precursor (Progonadoliberin III) [Contains: Gonadoliberin-3 (Gonadoliberin III) ( ...	0.04	-	exc	0	Secreted protein				94
P12273 UniProt NPD GO	PIP_HUMAN	Prolactin-inducible protein precursor (Secretory actin-binding protein) (SABP) (Gross cystic disease ...	0.04	-	end	0	Secreted protein (Probable)	extracellular region [NAS]	176720		146
P57761 UniProt NPD GO	PCNA_CRIGR	Proliferating cell nuclear antigen (PCNA)	0.04	-	cyt	0	Nucleus (By similarity)				261
Q6B6N4 UniProt NPD GO	PCNA_HAPBU	Proliferating cell nuclear antigen (PCNA)	0.04	-	cyt	0	Nucleus (By similarity)				260
O82797 UniProt NPD GO	PCNA_TOBAC	Proliferating cell nuclear antigen (PCNA)	0.04	-	mit	0	Nucleus				264
P17918 UniProt NPD GO	PCNA_MOUSE	Proliferating cell nuclear antigen (PCNA) (Cyclin)	0.04	-	cyt	0	Nucleus	cyclin-dependent protein kinase holoenzyme ... [IPI] nuclear lamina [IDA] nucleus [IDA] replication fork [IDA]			261
P04961 UniProt NPD GO	PCNA_RAT	Proliferating cell nuclear antigen (PCNA) (Cyclin)	0.04	-	cyt	0	Nucleus				261
Q9ZW35 UniProt NPD GO	PCNA2_ARATH	Proliferating cell nuclear antigen 2 (PCNA 2)	0.04	-	mit	0	Nucleus				264
Q9Z2Y8 UniProt NPD GO	PROSC_MOUSE	Proline synthetase co-transcribed bacterial homolog protein	0.04	-	cyt	0					274
P15380 UniProt NPD GO	PUT4_YEAST	Proline-specific permease	0.04	-	end	11	Membrane; multi-pass membrane protein				627
P48147 UniProt NPD GO	PPCE_HUMAN	Prolyl endopeptidase (EC 3.4.21.26) (Post-proline cleaving enzyme) (PE)	0.04	-	nuc	0	Cytoplasm	cytoplasm [TAS]	600400		710
P79384 UniProt NPD GO	PCCB_PIG	Propionyl-CoA carboxylase beta chain, mitochondrial precursor (EC 6.4.1.3) (PCCase subunit beta) (Pr ...	0.04	-	mit	0	Mitochondrion; mitochondrial matrix				539
P02781 UniProt NPD GO	PSC2_RAT	Prostatic steroid-binding protein C2 chain precursor (Prostatein peptide C2)	0.04	-	exc	0	Secreted protein				112
Q5E9G3 UniProt NPD GO	PSME2_BOVIN	Proteasome activator complex subunit 2 (Proteasome activator 28-beta subunit) (PA28beta) (PA28b)	0.04	-	cyt	0					238
Q5RDN3 UniProt NPD GO	PSMF1_PONPY	Proteasome inhibitor PI31 subunit	0.04	-	mit	0					271
Q92530 UniProt NPD GO	PSMF1_HUMAN	Proteasome inhibitor PI31 subunit (hPI31)	0.04	-	mit	0		proteasome core complex (sensu Eukaryota) [NAS]			271
Q3T0Y5 UniProt NPD GO	PSA2_BOVIN	Proteasome subunit alpha type 2 (EC 3.4.25.1)	0.04	-	cyt	0	Cytoplasm (By similarity). Nucleus (By similarity)				233
O73672 UniProt NPD GO	PSA2_CARAU	Proteasome subunit alpha type 2 (EC 3.4.25.1)	0.04	-	cyt	0	Cytoplasm (By similarity). Nucleus (By similarity)				233
P25787 UniProt NPD GO	PSA2_HUMAN	Proteasome subunit alpha type 2 (EC 3.4.25.1) (Proteasome component C3) (Macropain subunit C3) (Mult ...	0.04	-	cyt	0	Cytoplasm. Nucleus	proteasome complex (sensu Eukaryota) [TAS]	176842		233
P49722 UniProt NPD GO	PSA2_MOUSE	Proteasome subunit alpha type 2 (EC 3.4.25.1) (Proteasome component C3) (Macropain subunit C3) (Mult ...	0.04	-	cyt	0	Cytoplasm. Nucleus				233
P17220 UniProt NPD GO	PSA2_RAT	Proteasome subunit alpha type 2 (EC 3.4.25.1) (Proteasome component C3) (Macropain subunit C3) (Mult ...	0.04	-	cyt	0	Cytoplasm. Nucleus				233
P24495 UniProt NPD GO	PSA2_XENLA	Proteasome subunit alpha type 2 (EC 3.4.25.1) (Proteasome component C3) (Macropain subunit C3) (Mult ...	0.04	-	cyt	0	Cytoplasm (By similarity). Nucleus (By similarity)				233
Q9N599 UniProt NPD GO	PSA4_CAEEL	Proteasome subunit alpha type 4 (EC 3.4.25.1) (Proteasome subunit alpha 3)	0.04	-	mit	0	Cytoplasm (By similarity). Nucleus (By similarity)				250
P34120 UniProt NPD GO	PSA7_DICDI	Proteasome subunit alpha type 7 (EC 3.4.25.1) (Proteasome component DD5)	0.04	-	cyt	0	Cytoplasm (By similarity). Nucleus (By similarity)				250
P30186 UniProt NPD GO	PSA7A_ARATH	Proteasome subunit alpha type 7-A (EC 3.4.25.1) (Proteasome subunit alpha type 4) (20S proteasome al ...	0.04	-	cyt	0	Cytoplasm (By similarity). Nucleus (By similarity)				250
P40306 UniProt NPD GO	PSB10_HUMAN	Proteasome subunit beta type 10 precursor (EC 3.4.25.1) (Proteasome MECl-1) (Macropain subunit MECl- ...	0.04	-	cyt	0	Cytoplasm (By similarity). Nucleus (By similarity)	proteasome complex (sensu Eukaryota) [TAS]	176847		273
O35955 UniProt NPD GO	PSB10_MOUSE	Proteasome subunit beta type 10 precursor (EC 3.4.25.1) (Proteasome MECl-1) (Macropain subunit MECl- ...	0.04	-	cyt	0	Cytoplasm (By similarity). Nucleus (By similarity)				273
O65084 UniProt NPD GO	PSB3_PICMA	Proteasome subunit beta type 3 (EC 3.4.25.1) (20S proteasome alpha subunit C) (20S proteasome subuni ...	0.04	-	cyt	0	Cytoplasm (By similarity). Nucleus (By similarity)				204
Q9XYN7 UniProt NPD GO	PSB3_DROME	Proteasome subunit beta type 3 (EC 3.4.25.1) (20S proteasome subunit beta-3)	0.04	-	cyt	0	Cytoplasm (By similarity). Nucleus (By similarity)				205
P35183 UniProt NPD GO	AST1_YEAST	Protein AST1	0.04	-	cyt	0	Membrane; peripheral membrane protein	extrinsic to membrane [TAS]			429
Q9FX77 UniProt NPD GO	Y1664_ARATH	Protein At1g16640	0.04	-	cyt	0				1YEL	134
Q9M015 UniProt NPD GO	Y5161_ARATH	Protein At5g01610	0.04	-	cyt	0				1YDU	170
Q53FT3 UniProt NPD GO	CK073_HUMAN	Protein C11orf73	0.04	-	cyt	0	Cytoplasm (By similarity)				197

You are viewing entries 78101 to 78150 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.