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
Q41706 UniProt NPD GO	UPSA3_VIGUN	Probable ureide permease A3 (VuA3) (Fragment)	0.08	-	end	8 *	Membrane; multi-pass membrane protein (Probable)				376
Q40648 UniProt NPD GO	KCAB_ORYSA	Probable voltage-gated potassium channel subunit beta (K(+) channel subunit beta)	0.08	-	cyt	0					328
P41994 UniProt NPD GO	RPIA_CAEEL	Probable-ribose 5-phosphate isomerase (EC 5.3.1.6) (Phosphoriboisomerase)	0.08	-	cyt	0					251
Q6TCH4 UniProt NPD GO	PAQR6_HUMAN	Progestin and adipoQ receptor family member 6 (Progestin and adipoQ receptor family member VI)	0.08	-	end	4	Membrane; multi-pass membrane protein (Potential)				344
O54713 UniProt NPD GO	GON1_CAVPO	Progonadoliberin-1 precursor (Progonadoliberin I) [Contains: Gonadoliberin-1 (Gonadoliberin I) (Lute ...	0.08	-	exc	0	Secreted protein				92
Q28588 UniProt NPD GO	GON1_SHEEP	Progonadoliberin-1 precursor (Progonadoliberin I) [Contains: Gonadoliberin-1 (Gonadoliberin I) (Lute ...	0.08	-	nuc	0	Secreted protein				61
P58369 UniProt NPD GO	ANKH_TETNG	Progressive ankylosis protein homolog (ANK)	0.08	-	end	9 *	Membrane; multi-pass membrane protein (By similarity)				487
P60990 UniProt NPD GO	PIP_RABIT	Prolactin-inducible protein homolog precursor	0.08	-	mit	0	Secreted protein				146
O70417 UniProt NPD GO	PIP_RAT	Prolactin-inducible protein homolog precursor	0.08	-	mit	0	Secreted protein (Probable)				146
Q43266 UniProt NPD GO	PCNA_MAIZE	Proliferating cell nuclear antigen (PCNA)	0.08	-	mit	0	Nucleus				263
P04769 UniProt NPD GO	PLFR_MOUSE	Proliferin-related protein precursor (PRP)	0.08	-	exc	0	Secreted protein				244
O35449 UniProt NPD GO	PRRT1_MOUSE	Proline-rich transmembrane protein 1	0.08	-	end	2	Membrane; multi-pass membrane protein (Potential)				306
Q9W735 UniProt NPD GO	PROML_BRARE	Prominin-like protein (Fragment)	0.08	-	end	5 *	Membrane; multi-pass membrane protein (Potential)				713
P14882 UniProt NPD GO	PCCA_RAT	Propionyl-CoA carboxylase alpha chain, mitochondrial precursor (EC 6.4.1.3) (PCCase subunit alpha) ( ...	0.08	-	mit	0	Mitochondrion; mitochondrial matrix	mitochondrion [IDA]			704
Q8N2E6 UniProt NPD GO	TOR2X_HUMAN	Prosalusin precursor (Torsin-2A) (Torsin family 2 member A) [Contains: Salusin-alpha; Salusin-beta]	0.08	-	exc	1 *	Secreted protein		608052		242
Q6PWL6 UniProt NPD GO	PTGES_MACFA	Prostaglandin E synthase (EC 5.3.99.3) (Microsomal glutathione S-transferase 1-like 1) (MGST1-L1)	0.08	-	nuc	2 *	Membrane; multi-pass membrane protein (Potential)				152
Q6DT45 UniProt NPD GO	KLK3_MACFA	Prostate-specific antigen precursor (EC 3.4.21.77) (PSA) (Kallikrein-3) (Semenogelase)	0.08	-	exc	0	Secreted protein (By similarity)				261
P33619 UniProt NPD GO	KLK3_MACMU	Prostate-specific antigen precursor (EC 3.4.21.77) (PSA) (Kallikrein-3) (Semenogelase)	0.08	-	exc	0	Secreted protein (By similarity)				261
O23712 UniProt NPD GO	PSA1B_ARATH	Proteasome subunit alpha type 1-B (EC 3.4.25.1) (Proteasome subunit alpha type 6) (20S proteasome al ...	0.08	-	cyt	0	Cytoplasm (By similarity). Nucleus (By similarity)				277
Q9R1P0 UniProt NPD GO	PSA4_MOUSE	Proteasome subunit alpha type 4 (EC 3.4.25.1) (Proteasome component C9) (Macropain subunit C9) (Mult ...	0.08	-	mit	0	Cytoplasm. Nucleus				261
P21670 UniProt NPD GO	PSA4_RAT	Proteasome subunit alpha type 4 (EC 3.4.25.1) (Proteasome component C9) (Macropain subunit C9) (Mult ...	0.08	-	mit	0	Cytoplasm. Nucleus				261
Q9VA12 UniProt NPD GO	PSA4L_DROME	Proteasome subunit alpha type 4-like (EC 3.4.25.1)	0.08	-	cyt	0	Nucleus				251
Q3T0T1 UniProt NPD GO	PSB10_BOVIN	Proteasome subunit beta type 10 precursor (EC 3.4.25.1)	0.08	-	cyt	0	Cytoplasm (By similarity). Nucleus (By similarity)				273
Q9LIP2 UniProt NPD GO	PSB5B_ARATH	Proteasome subunit beta type 5-B precursor (EC 3.4.25.1) (20S proteasome beta subunit E-2) (Proteaso ...	0.08	-	cyt	0	Cytoplasm (By similarity). Nucleus (By similarity)				273
Q3T112 UniProt NPD GO	PSB8_BOVIN	Proteasome subunit beta type 8 precursor (EC 3.4.25.1)	0.08	-	cyt	0	Cytoplasm (By similarity). Nucleus (By similarity)				276
P83107 UniProt NPD GO	BOP1_BOVIN	Protein BOP-1 precursor	0.08	-	exc	0	Secreted protein; extracellular space (Potential)				100
Q9GZP1 UniProt NPD GO	CT098_HUMAN	Protein C20orf98	0.08	-	mit	2	Membrane; multi-pass membrane protein (Potential)	integral to membrane [NAS]			204
Q6DV04 UniProt NPD GO	CB025_GECJA	Protein C2orf25 homolog, mitochondrial precursor	0.08	-	mit	0	Mitochondrion (Potential)				296
Q6AYT5 UniProt NPD GO	CF211_RAT	Protein C6orf211 homolog	0.08	-	cyt	0					439
Q91WR6 UniProt NPD GO	CF072_MOUSE	Protein C6orf72 homolog precursor	0.08	-	end	1	Membrane; single-pass type I membrane protein (Potential)				327
Q5RF75 UniProt NPD GO	CI071_PONPY	Protein C9orf71 homolog	0.08	-	end	2 *	Membrane; multi-pass membrane protein (Potential)				170
Q9ZNV5 UniProt NPD GO	CEN_ARATH	Protein CENTRORADIALIS-like	0.08	-	cyt	0	Cytoplasm (By similarity)				175
Q61124 UniProt NPD GO	CLN3_MOUSE	Protein CLN3 (Battenin)	0.08	-	end	8 *	Lysosome; lysosomal membrane; multi-pass membrane protein (By similarity)				438
Q9UBY8 UniProt NPD GO	CLN8_HUMAN	Protein CLN8	0.08	-	end	5 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein. Endoplasmic reti ...	endoplasmic reticulum [TAS] ER-Golgi intermediate compartment [TAS] integral to membrane [TAS]	610003		286
Q96DE9 UniProt NPD GO	CX04B_HUMAN	Protein CXorf40B	0.08	-	cyt	0					158
P40781 UniProt NPD GO	CYPR4_CYNCA	Protein CYPRO4	0.08	-	cyt	0					501
P93009 UniProt NPD GO	CUTA_ARATH	Protein CutA, chloroplast precursor (Copper-binding protein CutA) (AtCUTA)	0.08	-	nuc	0	Plastid; chloroplast; chloroplast intermembrane space				182
P36037 UniProt NPD GO	DOA1_YEAST	Protein DOA1	0.08	-	nuc	0	Nucleus. Cytoplasm	cytoplasm [IDA] nucleus [IDA]			715
Q29S14 UniProt NPD GO	FA18B_BOVIN	Protein FAM18B	0.08	-	end	4 *	Membrane; multi-pass membrane protein (Potential)				208
Q9NYZ1 UniProt NPD GO	FA18B_HUMAN	Protein FAM18B	0.08	-	end	4 *	Membrane; multi-pass membrane protein (Potential)				205
Q9D7J4 UniProt NPD GO	FA36A_MOUSE	Protein FAM36A	0.08	-	cyt	0					117
Q9H5I5 UniProt NPD GO	FA38B_HUMAN	Protein FAM38B	0.08	-	end	4 *	Membrane; multi-pass membrane protein (Potential)				544
Q8TCE6 UniProt NPD GO	FA45A_HUMAN	Protein FAM45A	0.08	-	cyt	0					357
Q9SXZ2 UniProt NPD GO	FT_ARATH	Protein FLOWERING LOCUS T	0.08	-	cyt	0	Cytoplasm. Nucleus			1WKP	175
P12670 UniProt NPD GO	NP24_LYCES	Protein NP24 precursor (Pathogenesis-related protein PR P23) (Salt-induced protein)	0.08	-	exc	1 *	Cytoplasm. Or soluble fractions of cytoplasmic organelles, except mitochondria and plastids				247
P83106 UniProt NPD GO	PIP1_PIG	Protein PIP-1 precursor	0.08	-	exc	0	Secreted protein; extracellular space (Potential)				101
P80310 UniProt NPD GO	S10AC_PIG	Protein S100-A12 (S100 calcium-binding protein A12) (Calgranulin-C) (CAGC)	0.08	-	cyt	0					91
Q96FQ6 UniProt NPD GO	S10AG_HUMAN	Protein S100-A16 (S100 calcium-binding protein A16) (Protein S100F)	0.08	-	nuc	0					103
Q86SG5 UniProt NPD GO	SA7L1_HUMAN	Protein S100-A7-like 1 (S100 calcium-binding protein A7-like 1) (S100 calcium-binding protein A15)	0.08	-	nuc	0	Cytoplasm (By similarity)				100
P29377 UniProt NPD GO	S100G_HUMAN	Protein S100-G (S100 calcium-binding protein G) (Vitamin D-dependent calcium-binding protein, intest ...	0.08	-	nuc	0			302020		78

You are viewing entries 68801 to 68850 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.