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
P48726 UniProt NPD GO	PP2A_PARTE	Serine/threonine-protein phosphatase PP2A catalytic subunit (EC 3.1.3.16) (PPN)	0.23	-	nuc	0					315
Q60969 UniProt NPD GO	STYX_MOUSE	Serine/threonine/tyrosine-interacting protein (Protein tyrosine phosphatase-like protein) (Phosphose ...	0.23	-	mit	0		cytoplasm [IDA]			223
Q19509 UniProt NPD GO	SRD40_CAEEL	Serpentine receptor class delta-40 (Protein srd-40)	0.23	-	end	7 *	Membrane; multi-pass membrane protein (Potential)				320
P54128 UniProt NPD GO	SRG6_CAEEL	Serpentine receptor class gamma-6 (Protein srg-6)	0.23	-	end	7 *	Membrane; multi-pass membrane protein (Probable)				311
P08835 UniProt NPD GO	ALBU_PIG	Serum albumin precursor	0.23	-	exc	0	Secreted protein	extracellular region [ISS] protein complex [ISS]			607
Q10321 UniProt NPD GO	SHG1_SCHPO	Set1 complex component shg1 (Set1C component shg1) (COMPASS component shg1) (Complex proteins associ ...	0.23	-	nuc	0	Nucleus (Probable)	COMPASS complex [IDA]			128
P68415 UniProt NPD GO	NXS1_ENHSC	Short neurotoxin 1 (Toxin 4)	0.23	-	nuc	0	Secreted protein				60
P68416 UniProt NPD GO	NXS1_LAPHA	Short neurotoxin 1 (Toxin 4)	0.23	-	nuc	0	Secreted protein				60
P01434 UniProt NPD GO	NXS1_ACAAN	Short neurotoxin 1 (Toxin Aa c)	0.23	-	mit	0	Secreted protein				62
P62376 UniProt NPD GO	NXS2_HYDCY	Short neurotoxin 2 (Hydrophitoxin b)	0.23	-	nuc	0	Secreted protein				60
Q9YGC7 UniProt NPD GO	NXS5_LATCO	Short neurotoxin NCA-02/NCA-05/UER-05 precursor	0.23	-	nuc	0	Secreted protein				83
Q9HCX4 UniProt NPD GO	TRPC7_HUMAN	Short transient receptor potential channel 7 (TrpC7) (TRP7 protein)	0.23	-	end	5	Membrane; multi-pass membrane protein (Probable)				862
P18839 UniProt NPD GO	LECS_RANJA	Sialic acid-binding lectin (EC 3.1.27.-)	0.23	-	nuc	0	Secreted protein				111
Q9D7A6 UniProt NPD GO	SRP19_MOUSE	Signal recognition particle 19 kDa protein (SRP19)	0.23	-	nuc	0	Cytoplasm				144
Q9Y5M8 UniProt NPD GO	SRPRB_HUMAN	Signal recognition particle receptor subunit beta (SR-beta) (Protein APMCF1)	0.23	-	mit	1 *	Endoplasmic reticulum; endoplasmic reticulum membrane; single-pass membrane protein (By similarity)				271
Q5XHY7 UniProt NPD GO	STAM2_RAT	Signal transducing adapter molecule 2 (STAM-2)	0.23	-	nuc	0	Cytoplasm (By similarity). Membrane; peripheral membrane protein (By similarity)				523
Q9BWG4 UniProt NPD GO	SSBP4_HUMAN	Single-stranded DNA-binding protein 4	0.23	-	nuc	0	Nucleus (By similarity)		607391		385
Q09732 UniProt NPD GO	DCC1_SCHPO	Sister chromatid cohesion protein dcc1 (Defective in sister chromatid cohesion protein 1)	0.23	-	cyt	0	Nucleus (By similarity)	Ctf18 RFC-like complex [TAS]			349
Q5I1Z0 UniProt NPD GO	CCL3_PANTR	Small inducible cytokine A3 precursor (CCL3) (Macrophage inflammatory protein 1-alpha) (MIP-1-alpha) ...	0.23	-	exc	0	Secreted protein (By similarity)				92
O70556 UniProt NPD GO	SPR2E_MOUSE	Small proline-rich protein 2E	0.23	-	nuc	0	Cytoplasm (By similarity)	cornified envelope [NAS]			76
Q09198 UniProt NPD GO	SA21_SORBI	Small protein inhibitor of insect alpha-amylases 2.1 (SI alpha-2.1)	0.23	-	mit	0					47
O00624 UniProt NPD GO	NPT3_HUMAN	Sodium-dependent phosphate transport protein 3 (Sodium/phosphate cotransporter 3) (Na(+)/PI cotransp ...	0.23	-	end	8 *	Membrane; multi-pass membrane protein	integral to plasma membrane [TAS] membrane fraction [TAS]			436
P26434 UniProt NPD GO	SL9A4_RAT	Sodium/hydrogen exchanger 4 (Na(+)/H(+) exchanger 4) (NHE-4) (Solute carrier family 9 member 4)	0.23	-	end	11	Membrane; multi-pass membrane protein				717
Q8R4D1 UniProt NPD GO	SL9A8_MOUSE	Sodium/hydrogen exchanger 8 (Na(+)/H(+) exchanger 8) (NHE-8) (Solute carrier family 9 member 8)	0.23	-	end	11	Golgi apparatus; Golgi membrane; multi-pass membrane protein (By similarity)				576
Q8BXB6 UniProt NPD GO	SO2B1_MOUSE	Solute carrier organic anion transporter family member 2B1 (Solute carrier family 21 member 9)	0.23	-	end	12 *	Membrane; multi-pass membrane protein				683
Q6NUT7 UniProt NPD GO	SORT1_BRARE	Sortilin precursor	0.23	-	end	1	Golgi apparatus; Golgi stack; Golgi stack membrane; single-pass type I membrane protein (By similari ...				814
Q9YGL1 UniProt NPD GO	SPD1B_XENLA	Speedy protein 1-B (Spy1-B) (XSpy1-B) (Rapid inducer of G2/M progression in oocytes B) (RINGO-B) (p3 ...	0.23	-	mit	0	Nucleus (By similarity)	nucleus [ISS]			298
Q62252 UniProt NPD GO	SP17_MOUSE	Sperm surface protein Sp17 (Sperm autoantigenic protein 17)	0.23	+	nuc	0	Membrane; peripheral membrane protein (Potential)				149
Q08648 UniProt NPD GO	SPG11_HUMAN	Sperm-associated antigen 11 precursor (EP2 protein) (Sperm antigen HE2)	0.23	-	exc	0	Secreted protein	extracellular region [NAS]	606560		103
Q8K450 UniProt NPD GO	SPG16_MOUSE	Sperm-associated antigen 16 protein (PF20 protein homolog)	0.23	-	cyt	0	Cytoplasm. Flagellum. Detected on the sperm flagellum. Detected in the central apparatus of the axon ...	cytoplasm [IDA] flagellar axoneme [IDA] microtubule [IDA] nucleus [IDA]			639
Q9BUD6 UniProt NPD GO	SPON2_HUMAN	Spondin-2 precursor (Mindin) (Differentially expressed in cancerous and non-cancerous lung cells 1) ...	0.23	-	nuc	0	Secreted protein; extracellular space; extracellular matrix (By similarity)		605918		331
Q6IA86 UniProt NPD GO	STTP1_HUMAN	Stat3-interacting protein (StIP1) (SHINC-2)	0.23	-	cyt	0					826
P14709 UniProt NPD GO	STAT_MACAR	Statherin	0.23	-	nuc	0	Secreted protein	extracellular region [ISS]			42
P02809 UniProt NPD GO	STAT_MACFA	Statherin precursor	0.23	-	cyt	0	Secreted protein	extracellular region [ISS]			61
Q7YT83 UniProt NPD GO	TX31_CONTE	Substrate-specific endoprotease Tex31 precursor (EC 3.4.-.-)	0.23	-	nuc	0	Secreted protein				300
P31924 UniProt NPD GO	SUS2_ORYSA	Sucrose synthase 2 (EC 2.4.1.13) (Sucrose-UDP glucosyltransferase 2)	0.23	-	cyt	0					816
Q9TKX3 UniProt NPD GO	CYSA_NEPOL	Sulfate/thiosulfate import ATP-binding protein cysA (EC 3.6.3.25) (Sulfate-transporting ATPase)	0.23	-	mit	0	Plastid; chloroplast				343
P97610 UniProt NPD GO	SYT12_RAT	Synaptotagmin-12 (Synaptotagmin XII) (SytXII) (Synaptotagmin-related gene 1 protein) (Srg1)	0.23	-	nuc	1 *	Synaptic vesicle; synaptic vesicle membrane; multi-pass membrane protein (By similarity)				421
Q8NBV8 UniProt NPD GO	SYT8_HUMAN	Synaptotagmin-8 (Synaptotagmin VIII) (SytVIII)	0.23	+	nuc	1 *	Cell membrane; single-pass type III membrane protein (By similarity). Acrosome (By similarity)		607719		172
P33671 UniProt NPD GO	SDC3_RAT	Syndecan-3 precursor (SYND3) (N-syndecan) (Neuroglycan)	0.23	-	end	1	Membrane; single-pass type I membrane protein	integral to membrane [TAS]			442
Q9QZY7 UniProt NPD GO	CD1C2_CAVPO	T-cell surface glycoprotein CD1c2 precursor (CD1-c2 antigen)	0.23	-	end	1	Membrane; single-pass type I membrane protein (By similarity)				332
Q9UTM4 UniProt NPD GO	TCPE_SCHPO	T-complex protein 1 subunit epsilon (TCP-1-epsilon) (CCT-epsilon)	0.23	-	cyt	0	Cytoplasm (Potential)				546
P54411 UniProt NPD GO	TCPE2_AVESA	T-complex protein 1 subunit epsilon (TCP-1-epsilon) (CCT-epsilon) (TCP-K36)	0.23	-	cyt	0	Cytoplasm				535
Q570C0 UniProt NPD GO	TIR1_ARATH	TRANSPORT INHIBITOR RESPONSE 1 protein (F-box/LRR-repeat protein 1)	0.23	-	cyt	0					594
Q7M712 UniProt NPD GO	TR110_MOUSE	Taste receptor type 2 member 110 (T2R110) (mT2r57) (STC 9-1)	0.23	-	end	7 *	Membrane; multi-pass membrane protein				333
Q7TQA8 UniProt NPD GO	TR136_MOUSE	Taste receptor type 2 member 136 (T2R136) (Taste receptor type 2 member 36) (T2R36) (mT2r52)	0.23	-	end	6 *	Membrane; multi-pass membrane protein	integral to membrane [NAS]			305
Q645Z2 UniProt NPD GO	T2R14_GORGO	Taste receptor type 2 member 14 (T2R14)	0.23	-	end	7 *	Membrane; multi-pass membrane protein				317
Q646D9 UniProt NPD GO	T2R14_PANPA	Taste receptor type 2 member 14 (T2R14)	0.23	-	end	7 *	Membrane; multi-pass membrane protein				317
Q646B7 UniProt NPD GO	T2R14_PANTR	Taste receptor type 2 member 14 (T2R14)	0.23	-	end	7 *	Membrane; multi-pass membrane protein				317
Q67ER9 UniProt NPD GO	T2R39_RAT	Taste receptor type 2 member 39 (T2R39) (Taste receptor type 2 member 32) (T2R32)	0.23	-	end	6 *	Membrane; multi-pass membrane protein				319

You are viewing entries 47901 to 47950 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.