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
O35326 UniProt NPD GO	SFRS5_MOUSE	Splicing factor, arginine/serine-rich 5 (Pre-mRNA-splicing factor SRP40) (Delayed-early protein HRS) ...	0.75	+	nuc	0	Nucleus (Potential)				270
Q9Y3M8 UniProt NPD GO	STA13_HUMAN	StAR-related lipid transfer protein 13 (StARD13) (START domain-containing protein 13) (46H23.2) (Del ...	0.75	-	nuc	0	Cytoplasm		609866		1113
Q09006 UniProt NPD GO	STM1A_XENLA	Stathmin-1-A (Stathmin clone XO35)	0.75	-	nuc	0	Cytoplasm				145
O15056 UniProt NPD GO	SYNJ2_HUMAN	Synaptojanin-2 (EC 3.1.3.36) (Synaptic inositol-1,4,5-trisphosphate 5-phosphatase 2)	0.75	-	end	0	Membrane (By similarity). Predominantly associated with the particulate fractions (By similarity)			1UFW	1496
O55207 UniProt NPD GO	SYNJ2_RAT	Synaptojanin-2 (EC 3.1.3.36) (Synaptic inositol-1,4,5-trisphosphate 5-phosphatase 2)	0.75	-	mit	0	Cytoplasm. Cell membrane. Isoform 2A: Mitochondrion. Interaction of isoform 2A with OMP25 results in ...	synapse [TAS]			1496
P24507 UniProt NPD GO	SY63_DISOM	Synaptotagmin C (Synaptic vesicle protein O-p65-C)	0.75	+	nuc	1	Synaptic vesicles in neurons				537
Q8BHS8 UniProt NPD GO	SYBU_MOUSE	Syntabulin (Syntaxin-1-binding protein) (Golgi-localized syntaphilin-related protein) (m-Golsyn)	0.75	-	nuc	0	Golgi apparatus; Golgi membrane; single-pass membrane protein (By similarity). Colocalizes with synt ...				665
Q9FFK1 UniProt NPD GO	SYP31_ARATH	Syntaxin-31 (AtSYP31) (AtSED5)	0.75	-	nuc	1	Golgi apparatus; cis-Golgi network; cis-Golgi network membrane; single-pass type IV membrane protein ...				336
Q13207 UniProt NPD GO	TBX2_HUMAN	T-box transcription factor TBX2 (T-box protein 2)	0.75	-	nuc	0	Nucleus (Potential)		600747		702
Q61663 UniProt NPD GO	TLX2_MOUSE	T-cell leukemia homeobox protein 2 (Homeobox protein Hox-11L1) (Homeobox TLX-2) (PMUR10F)	0.75	+	nuc	0	Nucleus (Probable)	cytoplasm [IDA] nucleus [IDA]			284
Q9BYX2 UniProt NPD GO	TBCD2_HUMAN	TBC1 domain family member 2 (Prostate antigen recognized and identified by SEREX) (PARIS-1)	0.75	-	nuc	0			609871		917
O14559 UniProt NPD GO	TCGAP_HUMAN	TC10/CDC42 GTPase-activating protein (Sorting nexin-26)	0.75	-	nuc	0					1287
P54939 UniProt NPD GO	TLN1_CHICK	Talin-1	0.75	-	nuc	0		cytosol [TAS] focal adhesion [IDA] ruffle [IDA]		1ZVZ	2541
Q922G7 UniProt NPD GO	TEKT2_MOUSE	Tektin-2 (Testicular tektin) (Tektin-t)	0.75	-	nuc	0					430
Q15006 UniProt NPD GO	K0103_HUMAN	Tetratricopeptide repeat protein KIAA0103	0.75	-	nuc	0	Nucleus (By similarity)	endoplasmic reticulum [IDA]	607722		297
Q5E993 UniProt NPD GO	K0103_BOVIN	Tetratricopeptide repeat protein KIAA0103 homolog	0.75	-	cyt	0	Nucleus (By similarity)				297
Q66JW3 UniProt NPD GO	TOX_MOUSE	Thymus high mobility group box protein TOX	0.75	+	nuc	0	Nucleus			2CO9	526
Q9DGB6 UniProt NPD GO	TLR22_CHICK	Toll-like receptor 2 type-2 precursor	0.75	-	mit	1	Membrane; single-pass type I membrane protein (By similarity)				781
Q5JTV8 UniProt NPD GO	TOIP1_HUMAN	Torsin-1A-interacting protein 1	0.75	-	nuc	0	Nucleus; nuclear inner membrane; single-pass membrane protein (By similarity)				583
Q15560 UniProt NPD GO	TCEA2_HUMAN	Transcription elongation factor A protein 2 (Transcription elongation factor S-II protein 2) (Testis ...	0.75	-	nuc	0	Nucleus	transcription elongation factor complex [NAS]	604784		299
Q9VCP0 UniProt NPD GO	ELOA1_DROME	Transcription elongation factor B polypeptide 3 (RNA polymerase II transcription factor SIII subunit ...	0.75	-	nuc	0	Nucleus (By similarity)	transcription elongation factor complex [ISS]			643
Q9HCC6 UniProt NPD GO	HES4_HUMAN	Transcription factor HES-4 (Hairy and enhancer of split 4) (bHLH factor Hes4)	0.75	-	nuc	0			608060		221
Q9SM50 UniProt NPD GO	HY5_LYCES	Transcription factor HY5 (LeHY5) (tHY5)	0.75	-	nuc	0	Nucleus				158
P35716 UniProt NPD GO	SOX11_HUMAN	Transcription factor SOX-11	0.75	+	nuc	0	Nucleus (Potential)		600898		441
P41225 UniProt NPD GO	SOX3_HUMAN	Transcription factor SOX-3	0.75	+	mit	0	Nucleus		313430		446
Q39234 UniProt NPD GO	TGA3_ARATH	Transcription factor TGA3 (AtbZIP22)	0.75	-	nuc	0	Nucleus				384
Q8CHZ9 UniProt NPD GO	MTERF_MOUSE	Transcription termination factor, mitochondrial precursor (mTERF) (Mitochondrial transcription termi ...	0.75	-	nuc	0	Mitochondrion				379
Q04724 UniProt NPD GO	TLE1_HUMAN	Transducin-like enhancer protein 1 (ESG1) (E(Sp1) homolog)	0.75	+	nuc	0	Nucleus. Nuclear and chromatin-associated, depending on isoforms and phosphorylation status. Hyperph ...	nucleus [TAS]	600189	2CE9	770
Q9BZY9 UniProt NPD GO	TRI31_HUMAN	Tripartite motif-containing protein 31	0.75	-	nuc	0			609316		425
Q6MFZ5 UniProt NPD GO	TRI39_RAT	Tripartite motif-containing protein 39 (RING finger protein 23)	0.75	-	nuc	0					488
Q27371 UniProt NPD GO	TNNT_CAEEL	Troponin T	0.75	-	nuc	0					405
Q92142 UniProt NPD GO	TPH_XENLA	Tryptophan 5-hydroxylase (EC 1.14.16.4) (Tryptophan 5-monooxygenase)	0.75	-	cyt	0					481
P17752 UniProt NPD GO	TPH1_HUMAN	Tryptophan 5-hydroxylase 1 (EC 1.14.16.4) (Tryptophan 5-monooxygenase 1)	0.75	-	cyt	0			191060	1MLW	444
P49815 UniProt NPD GO	TSC2_HUMAN	Tuberin (Tuberous sclerosis 2 protein)	0.75	-	end	0	Cytoplasm. Membrane; peripheral membrane protein. At steady state found in association with membrane ...	cytoplasm [TAS] cytosol [TAS] membrane fraction [TAS] plasma membrane [TAS]	606690		1807
P25295 UniProt NPD GO	TBG_SCHPO	Tubulin gamma chain (Gamma tubulin)	0.75	+	nuc	0		equatorial microtubule organizing center [IDA] gamma-tubulin complex [TAS] spindle pole body [IDA]			446
O15327 UniProt NPD GO	INP4B_HUMAN	Type II inositol-3,4-bisphosphate 4-phosphatase (EC 3.1.3.66) (Inositol polyphosphate 4-phosphatase ...	0.75	-	mit	0			607494		924
Q5RA60 UniProt NPD GO	INP4B_PONPY	Type II inositol-3,4-bisphosphate 4-phosphatase (EC 3.1.3.66) (Inositol polyphosphate 4-phosphatase ...	0.75	-	nuc	0					924
P20417 UniProt NPD GO	PTN1_RAT	Tyrosine-protein phosphatase non-receptor type 1 (EC 3.1.3.48) (Protein-tyrosine phosphatase 1B) (PT ...	0.75	-	nuc	1	Endoplasmic reticulum; endoplasmic reticulum membrane; peripheral membrane protein; cytoplasmic side ...				432
Q04323 UniProt NPD GO	U33K_HUMAN	UBA/UBX 33.3 kDa protein	0.75	-	nuc	0		cytoplasm [IDA]			297
Q922Y1 UniProt NPD GO	U33K_MOUSE	UBA/UBX 33.3 kDa protein	0.75	-	nuc	0				1WHC	297
Q09140 UniProt NPD GO	UGGG_SCHPO	UDP-glucose:glycoprotein glucosyltransferase precursor (EC 2.4.1.-) (UDP--Glc:glycoprotein glucosylt ...	0.75	-	nuc	0	Endoplasmic reticulum; endoplasmic reticulum lumen	endoplasmic reticulum [TAS]			1448
Q9Y6I4 UniProt NPD GO	UBP3_HUMAN	Ubiquitin carboxyl-terminal hydrolase 3 (EC 3.1.2.15) (Ubiquitin thioesterase 3) (Ubiquitin-specific ...	0.75	-	nuc	0			604728		521
Q13107 UniProt NPD GO	UBP4_HUMAN	Ubiquitin carboxyl-terminal hydrolase 4 (EC 3.1.2.15) (Ubiquitin thioesterase 4) (Ubiquitin-specific ...	0.75	-	nuc	0	Cytoplasm	lysosome [TAS] nucleus [TAS]	603486		963
Q9HAC8 UniProt NPD GO	UBTD1_HUMAN	Ubiquitin domain-containing protein 1	0.75	+	nuc	0					227
Q91WB7 UniProt NPD GO	UBTD1_MOUSE	Ubiquitin domain-containing protein 1	0.75	+	nuc	0					227
O70546 UniProt NPD GO	UTX_MOUSE	Ubiquitously transcribed X chromosome tetratricopeptide repeat protein (Ubiquitously transcribed TPR ...	0.75	-	nuc	0	Nucleus (Potential)				1333
O14607 UniProt NPD GO	UTY_HUMAN	Ubiquitously transcribed Y chromosome tetratricopeptide repeat protein (Ubiquitously transcribed TPR ...	0.75	-	exc	1	Nucleus (Potential)		400009		1347
Q9NVL8 UniProt NPD GO	CN105_HUMAN	Uncharacterized protein C14orf105	0.75	-	nuc	0					296
Q5E9A0 UniProt NPD GO	CT111_BOVIN	Uncharacterized protein C20orf111 homolog	0.75	+	nuc	0					291
Q8N2C7 UniProt NPD GO	CB021_HUMAN	Uncharacterized protein C2orf21	0.75	-	nuc	0					320

You are viewing entries 11601 to 11650 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.