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
Q864Q2 UniProt NPD GO	SRY_PHOPH	Sex-determining region Y protein (Testis-determining factor)	0.84	+	nuc	0	Nucleus				196
Q17308 UniProt NPD GO	TRA1_CAEBR	Sex-determining transformer protein 1	0.84	+	nuc	0	Nucleus	cytoplasm [ISS] nucleus [ISS]			1165
Q00004 UniProt NPD GO	SRP68_CANFA	Signal recognition particle 68 kDa protein (SRP68)	0.84	-	nuc	0	Cytoplasm (By similarity). Nucleus; nucleolus (By similarity)				622
P42228 UniProt NPD GO	STAT4_MOUSE	Signal transducer and activator of transcription 4	0.84	-	nuc	0	Cytoplasm. Nucleus. Translocated into the nucleus in response to phosphorylation	nucleus [IDA]		1BGF	749
P58390 UniProt NPD GO	KCNN2_MOUSE	Small conductance calcium-activated potassium channel protein 2 (SK2)	0.84	+	end	7	Membrane; multi-pass membrane protein				574
Q5AD73 UniProt NPD GO	SNX41_CANAL	Sorting nexin-41	0.84	-	nuc	0	Endosome; endosomal membrane; peripheral membrane protein (By similarity). Intracellular membrane; p ...				681
Q9GKQ5 UniProt NPD GO	HSP1_COLGU	Sperm protamine P1	0.84	+	mit	0	Nucleus (By similarity)				50
P42136 UniProt NPD GO	HSP1_ISOMA	Sperm protamine P1	0.84	+	nuc	0	Nucleus				66
Q7LZB6 UniProt NPD GO	HSP1_ALLMI	Sperm protamine P1-type (Protamine II)	0.84	+	nuc	0	Nucleus (By similarity)				56
P17305 UniProt NPD GO	STP1_BOVIN	Spermatid nuclear transition protein 1 (STP-1) (TP-1)	0.84	-	nuc	0	Nucleus	nucleosome [ISS]			54
O97965 UniProt NPD GO	STP3_SHEEP	Spermatid nuclear transition protein 3 (STP-3) (TP-3) (TP3) (Spermatidal protein 3)	0.84	+	mit	0	Nucleus				109
Q12772 UniProt NPD GO	SRBP2_HUMAN	Sterol regulatory element-binding protein 2 (SREBP-2) (Sterol regulatory element-binding transcripti ...	0.84	-	end	0	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein. Golgi apparatus; ...		600481	1UKL	1141
Q29RN6 UniProt NPD GO	SOCS5_BOVIN	Suppressor of cytokine signaling 5 (SOCS-5)	0.84	-	nuc	0					536
Q8CC35 UniProt NPD GO	SYNPO_MOUSE	Synaptopodin	0.84	-	nuc	0	Cytoplasm. Cell membrane; cell-cell junction; tight junction. Localized at the tight junction of cel ...	actin cytoskeleton [IDA]			929
Q8BJ25 UniProt NPD GO	THAP3_MOUSE	THAP domain-containing protein 3	0.84	-	mit	0					218
Q8R3N6 UniProt NPD GO	THOC1_MOUSE	THO complex subunit 1 (Tho1) (Nuclear matrix protein p84)	0.84	-	nuc	0	Nucleus; nucleoplasm; nuclear speckle (By similarity). Nucleus; nucleoplasm; nuclear matrix (By simi ...				657
O08653 UniProt NPD GO	TEP1_RAT	Telomerase protein component 1 (rTLP1) (Telomerase-associated protein 1) (Telomerase protein 1) (p24 ...	0.84	-	nuc	0					2629
Q9D845 UniProt NPD GO	TEX9_MOUSE	Testis-expressed sequence 9 protein (Testis-specifically expressed protein 1) (Tsec-1)	0.84	-	mit	0					387
Q9UJT2 UniProt NPD GO	TSKS_HUMAN	Testis-specific serine kinase substrate (Testis-specific kinase substrate) (STK22 substrate 1)	0.84	-	nuc	0			608253		592
P43698 UniProt NPD GO	TITF1_CANFA	Thyroid transcription factor 1 (Thyroid nuclear factor 1) (TTF-1) (Homeobox protein Nkx-2.1)	0.84	-	nuc	0	Nucleus				371
P50220 UniProt NPD GO	TITF1_MOUSE	Thyroid transcription factor 1 (Thyroid nuclear factor 1) (TTF-1) (Homeobox protein Nkx-2.1)	0.84	-	nuc	0	Nucleus	nucleus [IDA] transcription factor complex [IDA]			372
P43699 UniProt NPD GO	TITF1_HUMAN	Thyroid transcription factor 1 (Thyroid nuclear factor 1) (TTF-1) (Homeobox protein Nkx-2.1) (Homeob ...	0.84	-	nuc	0	Nucleus	nucleus [NAS]	600635		371
Q9QXY1 UniProt NPD GO	ZO3_MOUSE	Tight junction protein ZO-3 (Zonula occludens 3 protein) (Zona occludens 3 protein) (Tight junction ...	0.84	-	nuc	0					905
Q15170 UniProt NPD GO	TCAL1_HUMAN	Transcription elongation factor A protein-like 1 (TCEA-like protein 1) (Transcription elongation fac ...	0.84	-	nuc	0	Nucleus	nucleus [TAS]	300237		157
Q3MNT0 UniProt NPD GO	SPT6_CANAL	Transcription elongation factor SPT6 (Chromatin elongation factor SPT6)	0.84	+	nuc	0	Nucleus (By similarity)				1401
O00716 UniProt NPD GO	E2F3_HUMAN	Transcription factor E2F3 (E2F-3)	0.84	+	exc	0	Nucleus		600427		465
O35261 UniProt NPD GO	E2F3_MOUSE	Transcription factor E2F3 (E2F-3)	0.84	+	exc	0	Nucleus				457
Q04888 UniProt NPD GO	SOX10_MOUSE	Transcription factor SOX-10 (SOX-21) (Transcription factor SOX-M)	0.84	+	nuc	0	Nucleus				466
O74205 UniProt NPD GO	TOXE_COCCA	Transcription factor TOXE	0.84	-	nuc	0	Nucleus (By similarity)	nucleus [IDA]			441
Q09771 UniProt NPD GO	ATF31_SCHPO	Transcription factor atf31	0.84	-	nuc	0	Nucleus (Potential)				209
Q5EAW9 UniProt NPD GO	TAF3_XENLA	Transcription initiation factor TFIID subunit 3 (TBP-associated factor 3)	0.84	+	nuc	0	Nucleus (By similarity)				845
Q5BKE0 UniProt NPD GO	TAF9_RAT	Transcription initiation factor TFIID subunit 9 (Transcription initiation factor TFIID 31 kDa subuni ...	0.84	-	nuc	0	Nucleus (By similarity)				264
Q8TDI7 UniProt NPD GO	TMC2_HUMAN	Transmembrane cochlear-expressed protein 2	0.84	+	end	9	Membrane; multi-pass membrane protein (Potential)		606707		906
P38427 UniProt NPD GO	TSL1_YEAST	Trehalose synthase complex regulatory subunit TSL1 (Alpha,alpha-trehalose-phosphate synthase [UDP-fo ...	0.84	-	nuc	0	Cytoplasm	alpha,alpha-trehalose-phosphate synthase co... [IGI]			1098
Q9UPQ9 UniProt NPD GO	TNC6B_HUMAN	Trinucleotide repeat-containing 6B protein	0.84	+	nuc	0					1723
O88413 UniProt NPD GO	TULP3_MOUSE	Tubby-related protein 3 (Tubby-like protein 3)	0.84	+	nuc	0					460
Q689G4 UniProt NPD GO	PRR73_ORYSA	Two-component response regulator-like PRR73 (Pseudo-response regulator 73) (OsPRR73)	0.84	+	nuc	0	Nucleus (Probable)				767
P00522 UniProt NPD GO	ABL_DROME	Tyrosine-protein kinase Abl (EC 2.7.10.2) (Abelson protein) (D-ash)	0.84	-	nuc	0	Cytoplasm	adherens junction [TAS] cytoplasm [IDA] extrinsic to plasma membrane [IDA] intercellular junction [IDA] muscle tendon junction [IDA]			1620
Q62136 UniProt NPD GO	PTN21_MOUSE	Tyrosine-protein phosphatase non-receptor type 21 (EC 3.1.3.48) (Protein-tyrosine phosphatase PTP-RL ...	0.84	-	nuc	0					1176
Q5SSI6 UniProt NPD GO	UTP18_MOUSE	U3 small nucleolar RNA-associated protein 18 homolog (WD repeat protein 50)	0.84	+	nuc	0	Nucleus; nucleolus (By similarity)				552
Q8BUV6 UniProt NPD GO	LSM11_MOUSE	U7 snRNA-associated Sm-like protein LSm11	0.84	+	nuc	0	Nucleus (By similarity)				361
O42726 UniProt NPD GO	UBP2_KLULA	Ubiquitin carboxyl-terminal hydrolase 2 (EC 3.1.2.15) (Ubiquitin thioesterase 2) (Ubiquitin-specific ...	0.84	-	cyt	0					1220
P24814 UniProt NPD GO	GRR1_YEAST	Ubiquitin ligase complex F-box protein GRR1	0.84	-	nuc	0	Membrane. Associated with the particulate fraction. Probably forms a complex by protein-protein inte ...	contractile ring (sensu Saccharomyces) [IDA] cytoplasm [IDA] nuclear ubiquitin ligase complex [TAS] nucleus [IDA] SCF ubiquitin ligase complex [IMP]			1151
Q4KLY4 UniProt NPD GO	RING2_RAT	Ubiquitin ligase protein RING2 (EC 6.3.2.-) (RING finger protein 2) (RING finger protein 1B) (RING1b ...	0.84	-	nuc	0	Nucleus. Enriched on inactive X chromosome (Xi) in female trophoblast stem (TS) cells as well as dif ...				308
Q74Z34 UniProt NPD GO	UBC6_ASHGO	Ubiquitin-conjugating enzyme E2 6 (EC 6.3.2.19) (Ubiquitin-protein ligase UBC6) (Ubiquitin carrier p ...	0.84	-	nuc	1	Endoplasmic reticulum; endoplasmic reticulum membrane (By similarity)				242
Q5ZLS3 UniProt NPD GO	BRE1A_CHICK	Ubiquitin-protein ligase BRE1A (EC 6.3.2.-) (BRE1-A) (RING finger protein 20)	0.84	+	nuc	0	Nucleus (By similarity)				984
Q5DTM8 UniProt NPD GO	BRE1A_MOUSE	Ubiquitin-protein ligase BRE1A (EC 6.3.2.-) (BRE1-A) (RING finger protein 20)	0.84	+	nuc	0	Nucleus (By similarity)				973
Q9CWJ3 UniProt NPD GO	CO029_MOUSE	Uncharacterized protein C15orf29 homolog	0.84	-	nuc	0					299
Q5JPB2 UniProt NPD GO	CT174_HUMAN	Uncharacterized protein C20orf174	0.84	-	nuc	0					1082
O60179 UniProt NPD GO	YG44_SCHPO	Uncharacterized protein C23E6.04c	0.84	-	mit	0	Nucleus; nucleolus (By similarity)				1649

You are viewing entries 7201 to 7250 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.