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
P09547 UniProt NPD GO	SWI1_YEAST	Transcription regulatory protein SWI1 (SWI/SNF complex component SWI1) (Transcription regulatory pro ...	0.94	-	nuc	0	Nucleus	SWI/SNF complex [TAS]		1KN5	1314
Q9JJG0 UniProt NPD GO	TACC2_MOUSE	Transforming acidic coiled-coil-containing protein 2	0.94	-	nuc	0	Nucleus (By similarity). Centrosome (By similarity). Concentrated at centrosomes (By similarity)				1035
O93449 UniProt NPD GO	TGFB1_ONCMY	Transforming growth factor beta-1 precursor (TGF-beta-1)	0.94	-	exc	0	Secreted protein				382
P27090 UniProt NPD GO	TGFB2_MOUSE	Transforming growth factor beta-2 precursor (TGF-beta-2)	0.94	-	exc	0	Secreted protein	axon [IDA] cell soma [IDA] extracellular region [ISS]			414
Q38L25 UniProt NPD GO	TGFB2_MUSPF	Transforming growth factor beta-2 precursor (TGF-beta-2)	0.94	-	exc	1 *	Secreted protein				414
P09858 UniProt NPD GO	TGFB2_PIG	Transforming growth factor beta-2 precursor (TGF-beta-2)	0.94	-	exc	1 *	Secreted protein	axon [ISS] cell soma [ISS] extracellular region [ISS]			435
Q07257 UniProt NPD GO	TGFB2_RAT	Transforming growth factor beta-2 precursor (TGF-beta-2)	0.94	-	exc	0	Secreted protein	axon [ISS] cell soma [ISS] extracellular region [ISS]			442
P17247 UniProt NPD GO	TGFB2_XENLA	Transforming growth factor beta-2 precursor (TGF-beta-2)	0.94	-	exc	0	Secreted protein				413
P61811 UniProt NPD GO	TGFB2_CERAE	Transforming growth factor beta-2 precursor (TGF-beta-2) (Glioblastoma-derived T-cell suppressor fac ...	0.94	-	exc	1 *	Secreted protein	axon [ISS] cell soma [ISS] extracellular region [ISS]			414
P61812 UniProt NPD GO	TGFB2_HUMAN	Transforming growth factor beta-2 precursor (TGF-beta-2) (Glioblastoma-derived T-cell suppressor fac ...	0.94	-	exc	1 *	Secreted protein	axon [ISS] cell soma [ISS] extracellular region [IDA]	190220	2TGI	414
P38297 UniProt NPD GO	FZO1_YEAST	Transmembrane GTPase FZO1 (EC 3.6.5.-)	0.94	+	nuc	0	Mitochondrion; mitochondrial outer membrane; multi-pass membrane protein	mitochondrial outer membrane [IDA]			855
P22793 UniProt NPD GO	TRHY_SHEEP	Trichohyalin	0.94	+	nuc	0					1549
Q8IN94 UniProt NPD GO	OSA_DROME	Trithorax group protein osa (Protein eyelid)	0.94	-	nuc	0	Nucleus	brahma complex [IDA] nucleus [IDA]			2716
Q9XZ71 UniProt NPD GO	TNNT_PERAM	Troponin T (TnT)	0.94	+	nuc	0					384
Q12888 UniProt NPD GO	TP53B_HUMAN	Tumor suppressor p53-binding protein 1 (p53-binding protein 1) (p53BP1) (53BP1)	0.94	-	nuc	0	Nucleus. Associated with kinetochores. Both nuclear and cytoplasmic in some cells. Recruited to site ...	cytoplasm [IDA] nucleoplasm [IDA]	605230	1XNI	1972
P70399 UniProt NPD GO	TP53B_MOUSE	Tumor suppressor p53-binding protein 1 (p53-binding protein 1) (p53BP1) (53BP1)	0.94	-	nuc	0	Nucleus. Associated with kinetochores. Both nuclear and cytoplasmic in some cells. Recruited to site ...	kinetochore [IDA] replication fork [IDA]		1SSF	1957
Q9LKL2 UniProt NPD GO	APRR1_ARATH	Two-component response regulator-like APRR1 (Pseudo-response regulator 1) (Timing of CAB expression ...	0.94	+	nuc	0	Nucleus				618
Q06187 UniProt NPD GO	BTK_HUMAN	Tyrosine-protein kinase BTK (EC 2.7.10.2) (Bruton tyrosine kinase) (Agammaglobulinaemia tyrosine kin ...	0.94	-	nuc	0	Cytoplasm (By similarity). Membrane; peripheral membrane protein (By similarity)	cytoplasm [TAS] lipid raft [IDA]	300300	1QLY	658
P03949 UniProt NPD GO	ABL1_CAEEL	Tyrosine-protein kinase abl-1 (EC 2.7.10.2)	0.94	-	nuc	0					1224
Q12923 UniProt NPD GO	PTN13_HUMAN	Tyrosine-protein phosphatase non-receptor type 13 (EC 3.1.3.48) (Protein-tyrosine phosphatase 1E) (P ...	0.94	-	nuc	0	Cytoplasm (By similarity)		600267	3PDZ	2485
Q5XIW8 UniProt NPD GO	SNUT1_RAT	U4/U6.U5 tri-snRNP-associated protein 1 (Squamous cell carcinoma antigen recognized by T-cells 1) (S ...	0.94	+	nuc	0	Nucleus (By similarity)				806
Q5BK32 UniProt NPD GO	UBXD8_RAT	UBX domain-containing protein 8	0.94	+	nuc	0	Cytoplasm (By similarity)				346
P87115 UniProt NPD GO	YDK9_SCHPO	UPF0202 protein C20G8.09c	0.94	-	nuc	0	Nucleus (By similarity)				1033
Q9H0E7 UniProt NPD GO	UBP44_HUMAN	Ubiquitin carboxyl-terminal hydrolase 44 (EC 3.1.2.15) (Ubiquitin thioesterase 44) (Ubiquitin-specif ...	0.94	+	nuc	0					712
Q8BY87 UniProt NPD GO	UBP47_MOUSE	Ubiquitin carboxyl-terminal hydrolase 47 (EC 3.1.2.15) (Ubiquitin thioesterase 47) (Ubiquitin-specif ...	0.94	-	nuc	0					1376
Q6P9L4 UniProt NPD GO	UBP49_MOUSE	Ubiquitin carboxyl-terminal hydrolase 49 (EC 3.1.2.15) (Ubiquitin thioesterase 49) (Ubiquitin-specif ...	0.94	+	nuc	0					685
Q99PU7 UniProt NPD GO	BAP1_MOUSE	Ubiquitin carboxyl-terminal hydrolase BAP1 (EC 3.4.19.12) (BRCA1-associated protein 1) (Ubiquitin C- ...	0.94	+	nuc	0	Nucleus (By similarity)				728
Q04511 UniProt NPD GO	UFO1_YEAST	Ubiquitin ligase complex F-box protein UFO1	0.94	-	nuc	0		cytoplasm [IDA] nucleus [IDA] SCF ubiquitin ligase complex [IPI]			668
P56951 UniProt NPD GO	MDM2_HORSE	Ubiquitin-protein ligase E3 Mdm2 (EC 6.3.2.-) (p53-binding protein Mdm2) (Double minute 2 protein) ( ...	0.94	-	nuc	0	Nucleus; nucleoplasm (By similarity). Cytoplasm (By similarity). Expressed predominantly in the nucl ...	nucleolus [ISS] nucleoplasm [ISS]			491
Q60524 UniProt NPD GO	MDM2_MESAU	Ubiquitin-protein ligase E3 Mdm2 (EC 6.3.2.-) (p53-binding protein Mdm2) (Oncoprotein Mdm2) (Double ...	0.94	+	nuc	0	Nucleus; nucleoplasm (By similarity). Cytoplasm (By similarity). Expressed predominantly in the nucl ...	nucleolus [ISS] nucleoplasm [ISS]			466
Q62769 UniProt NPD GO	UN13B_RAT	Unc-13 homolog B (Munc13-2)	0.94	-	nuc	0	Cytoplasm. Membrane; peripheral membrane protein. Cell membrane. Localized to synapses. Translocated ...				1622
Q9Z1N9 UniProt NPD GO	UN13B_MOUSE	Unc-13 homolog B (Munc13-2) (munc13)	0.94	-	nuc	0	Cytoplasm. Membrane; peripheral membrane protein. Golgi apparatus. Localized to synapses (By similar ...				1591
Q6AXP3 UniProt NPD GO	CO033_RAT	Uncharacterized protein C15orf33 homolog	0.94	+	nuc	0					573
Q8NC74 UniProt NPD GO	CT151_HUMAN	Uncharacterized protein C20orf151	0.94	-	nuc	0					664
P40050 UniProt NPD GO	YEQ7_YEAST	Uncharacterized protein YER077C	0.94	-	nuc	0					688
P40497 UniProt NPD GO	YIJ2_YEAST	Uncharacterized protein YIL092W	0.94	+	nuc	0	Membrane; multi-pass membrane protein (Potential)	cytoplasm [IDA] nucleus [IDA]			633
Q08206 UniProt NPD GO	YO036_YEAST	Uncharacterized protein YOL036W	0.94	-	nuc	0					761
Q99326 UniProt NPD GO	YO338_YEAST	Uncharacterized protein YOR338W	0.94	+	nuc	0					363
Q02875 UniProt NPD GO	YP105_YEAST	Uncharacterized protein YPL105C	0.94	+	nuc	0	Cytoplasm	cytoplasm [IDA] mitochondrion [IDA]			849
Q6GNJ8 UniProt NPD GO	VPS72_XENLA	Vacuolar protein sorting protein 72 homolog (Transcription factor-like 1)	0.94	+	nuc	0	Nucleus (By similarity)				353
O13786 UniProt NPD GO	PEP7_SCHPO	Vacuolar segregation protein pep7	0.94	-	nuc	0					536
Q2TA49 UniProt NPD GO	VASP_BOVIN	Vasodilator-stimulated phosphoprotein (VASP)	0.94	-	nuc	0	Cytoplasm. Targeted to stress fibers and focal adhesions through interaction with a number of protei ...				382
Q29RL0 UniProt NPD GO	WDR67_BOVIN	WD repeat protein 67	0.94	-	cyt	0					1063
Q6DDI6 UniProt NPD GO	WDR67_XENLA	WD repeat protein 67	0.94	-	nuc	0					1089
Q6DEY8 UniProt NPD GO	WDR67_XENTR	WD repeat protein 67	0.94	-	nuc	0					1088
Q9C5T4 UniProt NPD GO	WRK18_ARATH	WRKY transcription factor 18 (WRKY DNA-binding protein 18) (AtWRKY18)	0.94	-	nuc	0	Nucleus (Probable)				310
Q63802 UniProt NPD GO	WEE1_RAT	Wee1-like protein kinase (EC 2.7.10.2)	0.94	-	nuc	0	Nucleus (By similarity)				646
P30291 UniProt NPD GO	WEE1_HUMAN	Wee1-like protein kinase (EC 2.7.10.2) (WEE1hu)	0.94	-	nuc	0	Nucleus	nucleus [TAS]	193525	1X8B	646
Q9NP71 UniProt NPD GO	WBS14_HUMAN	Williams-Beuren syndrome chromosome region 14 protein (WS basic-helix-loop-helix leucine zipper prot ...	0.94	-	nuc	0	Nucleus	transcription factor complex [NAS]	605678		852
Q7Z5K2 UniProt NPD GO	WAPL_HUMAN	Wings apart-like protein homolog (Friend of EBNA2 protein)	0.94	+	nuc	0	Isoform 2: Nucleus				1190

You are viewing entries 2601 to 2650 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.