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
P31154 UniProt NPD GO	DCAM1_MOUSE	S-adenosylmethionine decarboxylase proenzyme 1 (EC 4.1.1.50) (AdoMetDC 1) (SamdC 1) [Contains: S-ade ...	0.63	-	cyt	0					334
P82184 UniProt NPD GO	DCAM2_MOUSE	S-adenosylmethionine decarboxylase proenzyme 2 (EC 4.1.1.50) (AdoMetDC 2) (SamDC 2) [Contains: S-ade ...	0.63	-	cyt	0					334
P82185 UniProt NPD GO	DCAM2_MUSSP	S-adenosylmethionine decarboxylase proenzyme 2 (EC 4.1.1.50) (AdoMetDC 2) (SamDC 2) [Contains: S-ade ...	0.63	-	cyt	0					334
Q700K0 UniProt NPD GO	SSPO_RAT	SCO-spondin precursor	0.63	-	nuc	0	Secreted protein; extracellular space (By similarity)				5141
Q8N5H7 UniProt NPD GO	SH2D3_HUMAN	SH2 domain-containing protein 3C (Novel SH2-containing protein 3)	0.63	-	mit	0	Cytoplasm (By similarity). Membrane; peripheral membrane protein (By similarity). Associated with th ...		604722		860
Q8TF17 UniProt NPD GO	S3TC2_HUMAN	SH3 domain and tetratricopeptide repeats-containing protein 2	0.63	-	nuc	0			608206		1288
P98083 UniProt NPD GO	SHC1_MOUSE	SHC-transforming protein 1 (SH2 domain protein C1) (Src homology 2 domain-containing-transforming pr ...	0.63	-	nuc	0	Cytoplasm (By similarity). Isoform p46: Mitochondrion; mitochondrial matrix (By similarity). Isoform ...	plasma membrane [ISS]			579
P18897 UniProt NPD GO	SMR2_RAT	SMR2 protein precursor	0.63	-	exc	0	Secreted protein (Probable)				137
O00570 UniProt NPD GO	SOX1_HUMAN	SOX-1 protein	0.63	+	nuc	1	Nucleus (Probable)	nucleus [NAS]	602148		387
Q9H4F8 UniProt NPD GO	SMOC1_HUMAN	SPARC-related modular calcium-binding protein 1 precursor (Secreted modular calcium-binding protein ...	0.63	-	exc	0	Secreted protein; extracellular space; extracellular matrix; basement membrane. In or around the bas ...				434
Q06688 UniProt NPD GO	SRR1L_YEAST	SRR1-like protein	0.63	+	nuc	0	Cytoplasm	cytoplasm [IDA]			274
Q6C7G8 UniProt NPD GO	SWC5_YARLI	SWR1-complex protein 5	0.63	-	nuc	0	Nucleus (By similarity)				194
Q9Y467 UniProt NPD GO	SALL2_HUMAN	Sal-like protein 2 (Zinc finger protein SALL2) (HSal2)	0.63	-	nuc	0	Nucleus (Probable)	nucleus [NAS]	602219		1007
Q96C86 UniProt NPD GO	DCPS_HUMAN	Scavenger mRNA decapping enzyme DcpS (EC 3.-.-.-) (DCS-1) (Hint-related 7meGMP-directed hydrolase) ( ...	0.63	-	nuc	0	Cytoplasm. Nucleus			1XMM	337
Q99985 UniProt NPD GO	SEM3C_HUMAN	Semaphorin-3C precursor (Semaphorin E) (Sema E)	0.63	-	mit	0	Secreted protein		602645		751
Q5U7N3 UniProt NPD GO	SEMG2_GORGO	Semenogelin-2 precursor (Semenogelin II) (SGII)	0.63	-	nuc	0	Secreted protein (By similarity)				474
Q02383 UniProt NPD GO	SEMG2_HUMAN	Semenogelin-2 precursor (Semenogelin II) (SGII)	0.63	-	nuc	0	Secreted protein	extracellular space [TAS]	182141		582
Q15831 UniProt NPD GO	STK11_HUMAN	Serine/threonine-protein kinase 11 (EC 2.7.11.1) (Serine/threonine-protein kinase LKB1) (NY-REN-19 a ...	0.63	-	cyt	0	Cytoplasm (By similarity)		602216		433
Q9Y2H1 UniProt NPD GO	ST38L_HUMAN	Serine/threonine-protein kinase 38-like (EC 2.7.11.1) (NDR2 protein kinase) (Nuclear Dbf2-related ki ...	0.63	-	cyt	0	Cytoplasm. Cytoskeleton. Associated with the actin cytoskeleton	actin cytoskeleton [ISS] cytoplasm [IDA]			464
Q8BWW9 UniProt NPD GO	PKN2_MOUSE	Serine/threonine-protein kinase N2 (EC 2.7.11.13) (Protein kinase C-like 2) (Protein-kinase C-relate ...	0.63	-	nuc	0	Cytoplasm (By similarity)	cytoplasm [IDA] nucleus [IDA]			983
O14305 UniProt NPD GO	SID1_SCHPO	Serine/threonine-protein kinase sid1 (EC 2.7.11.1) (STE20-like kinase sid1)	0.63	-	nuc	0	Spindle pole body. Localizes to the SPB prior to cytokinesis and leaves once septation is complete	spindle pole body [IDA]			471
Q5ZIY5 UniProt NPD GO	2ABD_CHICK	Serine/threonine-protein phosphatase 2A 55 kDa regulatory subunit B delta isoform (PP2A, subunit B, ...	0.63	-	nuc	0	Cytoplasm (By similarity)				451
P97888 UniProt NPD GO	2ABG_RAT	Serine/threonine-protein phosphatase 2A 55 kDa regulatory subunit B gamma isoform (PP2A, subunit B, ...	0.63	-	nuc	0					447
Q28654 UniProt NPD GO	2A5E_RABIT	Serine/threonine-protein phosphatase 2A 56 kDa regulatory subunit epsilon isoform (PP2A, B subunit, ...	0.63	-	nuc	0	Cytoplasm (By similarity)				165
P20424 UniProt NPD GO	SRP54_YEAST	Signal recognition particle subunit SRP54 (Signal recognition particle 54 kDa protein homolog)	0.63	-	nuc	0	Cytoplasm	signal recognition particle (sensu Eukaryota) [IDA]			541
Q95115 UniProt NPD GO	STA5A_BOVIN	Signal transducer and activator of transcription 5A (Mammary gland factor)	0.63	-	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity). Translocated into the nucleus in response to pho ...				794
Q7QDU4 UniProt NPD GO	STAT_ANOGA	Signal transducer and transcription activator (Ag-STAT)	0.63	-	cyt	0	Cytoplasm. Nucleus. Translocated into the nucleus in response to phosphorylation (By similarity)				722
P25555 UniProt NPD GO	GBP2_YEAST	Single-strand telomeric DNA-binding protein GBP2 (G-strand-binding protein 2) (RAP1 localization fac ...	0.63	+	nuc	0	Nucleus (Potential)	nucleus [IDA]			427
Q9BT40 UniProt NPD GO	SKIP_HUMAN	Skeletal muscle and kidney-enriched inositol phosphatase (EC 3.1.3.56)	0.63	-	mit	0	Endoplasmic reticulum. Following stimulation with EGF, translocates to membrane ruffles	cytosol [IDA] neuron projection [IDA]	607875		448
Q8NHG7 UniProt NPD GO	SVIP_HUMAN	Small VCP/p97-interacting protein	0.63	+	nuc	0	Endoplasmic reticulum; smooth endoplasmic reticulum; smooth endoplasmic reticulum membrane; peripher ...				77
Q5R6N0 UniProt NPD GO	SVIP_PONPY	Small VCP/p97-interacting protein	0.63	+	nuc	0	Endoplasmic reticulum; smooth endoplasmic reticulum; smooth endoplasmic reticulum membrane; peripher ...				77
Q95209 UniProt NPD GO	SORL_RABIT	Sortilin-related receptor precursor (Sorting protein-related receptor containing LDLR class A repeat ...	0.63	-	end	2 *	Membrane; single-pass type I membrane protein (Potential)				2213
Q5KF05 UniProt NPD GO	MVP1_CRYNE	Sorting nexin MVP1	0.63	-	mit	0	Cytoplasm (By similarity)				612
Q9CWT3 UniProt NPD GO	SNX10_MOUSE	Sorting nexin-10	0.63	-	nuc	0					201
Q9H3E2 UniProt NPD GO	SNX25_HUMAN	Sorting nexin-25	0.63	-	cyt	0					538
Q6BZE9 UniProt NPD GO	SNX4_DEBHA	Sorting nexin-4 (Autophagy-related protein 24)	0.63	+	nuc	0	Cytoplasm (By similarity). Membrane; peripheral membrane protein (By similarity). Endosome; endosoma ...				582
Q09167 UniProt NPD GO	SFRS5_RAT	Splicing factor, arginine/serine-rich 5 (Pre-mRNA-splicing factor SRP40) (Insulin-induced growth res ...	0.63	+	nuc	0	Nucleus (Potential)				269
O43610 UniProt NPD GO	SPY3_HUMAN	Sprouty homolog 3 (Spry-3)	0.63	-	nuc	0	Cytoplasm. Membrane; peripheral membrane protein. Found in the cytoplasm in unstimulated cells but i ...	membrane [NAS]	300531		288
Q09004 UniProt NPD GO	STMN4_XENLA	Stathmin-4 (Stathmin-like protein B3) (xB3)	0.63	-	nuc	0					185
Q60416 UniProt NPD GO	SRBP1_CRIGR	Sterol regulatory element-binding protein 1 (SREBP-1) (Sterol regulatory element-binding transcripti ...	0.63	+	mit	0	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein. Golgi apparatus; ...				1133
Q70KF8 UniProt NPD GO	DHSB_UROFA	Succinate dehydrogenase [ubiquinone] iron-sulfur protein, mitochondrial precursor (EC 1.3.5.1) (IP)	0.63	-	mit	0	Mitochondrion; mitochondrial inner membrane				283
O04932 UniProt NPD GO	SPS1_CRAPL	Sucrose-phosphate synthase 1 (EC 2.4.1.14) (UDP-glucose-fructose-phosphate glucosyltransferase 1)	0.63	-	cyt	0					1054
P32351 UniProt NPD GO	IMPX_YEAST	Sugar utilization regulatory protein IMP2	0.63	-	nuc	0		cytoplasm [IDA]			346
P17883 UniProt NPD GO	SKI3_YEAST	Superkiller 3 protein	0.63	+	nuc	0	Nucleus	cytoplasm [IDA] nucleus [TAS]			1432
Q9HE02 UniProt NPD GO	SRB9_SCHPO	Suppressor of RNA polymerase B srb9	0.63	-	nuc	0	Nucleus (Probable)				1223
O14994 UniProt NPD GO	SYN3_HUMAN	Synapsin-3 (Synapsin III)	0.63	-	nuc	0	Synapse. Peripheral membrane protein localized to the cytoplasmic surface of synaptic vesicles	synaptic vesicle [TAS]	602705		580
Q8JZP2 UniProt NPD GO	SYN3_MOUSE	Synapsin-3 (Synapsin III)	0.63	-	nuc	0	Synapse. Peripheral membrane protein localized to the cytoplasmic surface of synaptic vesicles (By s ...	synapse [IDA] synaptic vesicle membrane [IDA]			579
Q08144 UniProt NPD GO	TLG2_YEAST	T-SNARE affecting a late Golgi compartment protein 2 (Syntaxin TLG2)	0.63	-	nuc	1	Golgi apparatus; trans-Golgi network; trans-Golgi network membrane; single-pass type IV membrane pro ...	early endosome [TAS] Golgi trans cisterna [TAS] Golgi trans face [TAS]			397
Q91WQ5 UniProt NPD GO	TAF5L_MOUSE	TAF5-like RNA polymerase II p300/CBP-associated factor-associated factor 65 kDa subunit 5L (PCAF-ass ...	0.63	-	nuc	0	Nucleus (By similarity)				589
O95759 UniProt NPD GO	TBCD8_HUMAN	TBC1 domain family member 8 (Vascular Rab-GAP/TBC-containing protein) (AD 3)	0.63	-	mit	0		membrane [TAS]			897

You are viewing entries 17651 to 17700 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.