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
Q71JP6 UniProt NPD GO	TPP1_BOVIN	Tripeptidyl-peptidase 1 precursor (EC 3.4.14.9) (Tripeptidyl-peptidase I) (TPP-I) (Tripeptidyl amino ...	0.34	-	mit	0	Lysosome (By similarity)				563
O14773 UniProt NPD GO	TPP1_HUMAN	Tripeptidyl-peptidase 1 precursor (EC 3.4.14.9) (Tripeptidyl-peptidase I) (TPP-I) (Tripeptidyl amino ...	0.34	-	mit	0	Lysosome	lysosome [TAS]	204500	1R60	563
P35394 UniProt NPD GO	TBB_OCTDO	Tubulin beta chain (Beta tubulin)	0.34	-	cyt	0					447
O49068 UniProt NPD GO	TBG2_ORYSA	Tubulin gamma-2 chain (Gamma-2 tubulin)	0.34	-	cyt	0					469
P80584 UniProt NPD GO	TBCA_RABIT	Tubulin-specific chaperone A (Tubulin-folding cofactor A) (CFA) (TCP1-chaperonin cofactor A)	0.34	-	nuc	0					107
Q15628 UniProt NPD GO	TRADD_HUMAN	Tumor necrosis factor receptor type 1-associated DEATH domain protein (TNFR1-associated DEATH domain ...	0.34	-	cyt	0			603500	1F3V	312
Q5RCT1 UniProt NPD GO	TPD54_PONPY	Tumor protein D54 (Tumor protein D52-like 2)	0.34	-	nuc	0		cytoplasm [ISS] perinuclear region [ISS]			206
P42687 UniProt NPD GO	SPK1_DUGTI	Tyrosine-protein kinase SPK-1 (EC 2.7.10.2)	0.34	-	nuc	0					497
P55146 UniProt NPD GO	TYRO3_RAT	Tyrosine-protein kinase receptor TYRO3 precursor (EC 2.7.10.1) (Tyrosine-protein kinase SKY)	0.34	+	end	1 *	Membrane; single-pass type I membrane protein				880
P28204 UniProt NPD GO	PTP12_STYPL	Tyrosine-protein phosphatase 12 (EC 3.1.3.48) (Fragment)	0.34	-	cyt	0					105
P28197 UniProt NPD GO	PTP5_STYPL	Tyrosine-protein phosphatase 5 (EC 3.1.3.48) (Fragment)	0.34	-	nuc	0					108
P53965 UniProt NPD GO	SIW14_YEAST	Tyrosine-protein phosphatase SIW14 (EC 3.1.3.48)	0.34	-	nuc	0	Cytoplasm	cytoplasm [IDA]			281
P54830 UniProt NPD GO	PTN5_MOUSE	Tyrosine-protein phosphatase non-receptor type 5 (EC 3.1.3.48) (Protein-tyrosine phosphatase striatu ...	0.34	-	end	0					541
Q5R947 UniProt NPD GO	IMP4_PONPY	U3 small nucleolar ribonucleoprotein protein IMP4 (U3 snoRNP protein IMP4)	0.34	-	mit	0	Nucleus; nucleolus (By similarity)				291
Q8NBZ7 UniProt NPD GO	UXS1_HUMAN	UDP-glucuronic acid decarboxylase 1 (EC 4.1.1.35) (UDP-glucuronate decarboxylase 1) (UGD) (UXS-1)	0.34	-	cyt	1 *	Golgi apparatus; Golgi stack; Golgi stack membrane; single-pass type II membrane protein (By similar ...		609749	2B69	420
Q91XL3 UniProt NPD GO	UXS1_MOUSE	UDP-glucuronic acid decarboxylase 1 (EC 4.1.1.35) (UDP-glucuronate decarboxylase 1) (UGD) (UXS-1)	0.34	-	mit	1 *	Golgi apparatus; Golgi stack; Golgi stack membrane; single-pass type II membrane protein (By similar ...				420
Q5PQX0 UniProt NPD GO	UXS1_RAT	UDP-glucuronic acid decarboxylase 1 (EC 4.1.1.35) (UDP-glucuronate decarboxylase 1) (UGD) (UXS-1)	0.34	-	mit	1 *	Golgi apparatus; Golgi stack; Golgi stack membrane; single-pass type II membrane protein				420
P01146 UniProt NPD GO	UTS1_CYPCA	UI precursor [Contains: Urophysin; Urotensin-1 (Urotensin I)]	0.34	-	nuc	0	Secreted protein				145
Q12257 UniProt NPD GO	YD177_YEAST	UPF0029 protein YDL177C	0.34	-	nuc	0					170
O82314 UniProt NPD GO	U082_ARATH	UPF0082 protein At2g25830	0.34	-	mit	0					331
Q8IV20 UniProt NPD GO	U124_HUMAN	UPF0124 protein	0.34	-	mit	0					430
Q9SR25 UniProt NPD GO	U195B_ARATH	UPF0195 protein At3g09380	0.34	-	nuc	0					149
Q9VH39 UniProt NPD GO	U240_DROME	UPF0240 protein CG11722	0.34	-	nuc	0					203
Q9NW38 UniProt NPD GO	FANCL_HUMAN	Ubiquitin ligase protein FANCL (EC 6.3.2.-) (Fanconi anemia group L protein) (Fanconi anemia-associa ...	0.34	-	cyt	0	Cytoplasm. Nucleus		608111		375
Q8LBL5 UniProt NPD GO	PRT1_ARATH	Ubiquitin protein ligase PRT1 (EC 6.3.2.-) (Proteolysis 1 protein)	0.34	-	nuc	0	Cytoplasm (Probable)				410
Q4R6B2 UniProt NPD GO	CS015_MACFA	Uncharacterized protein C19orf15 homolog precursor	0.34	-	end	1	Membrane; single-pass type I membrane protein (Potential)				1159
Q9H3Z7 UniProt NPD GO	CT135_HUMAN	Uncharacterized protein C20orf135	0.34	-	cyt	0					469
Q8CHX7 UniProt NPD GO	CB011_MOUSE	Uncharacterized protein C2orf11 homolog	0.34	-	nuc	0					500
P25649 UniProt NPD GO	YCX2_YEAST	Uncharacterized protein YCR082W	0.34	-	cyt	0		cytoplasm [IDA] nucleus [IDA]			128
Q08001 UniProt NPD GO	YL072_YEAST	Uncharacterized protein YLR072W	0.34	-	nuc	1	Membrane; single-pass membrane protein (Potential). Localizes to cytoplasmic punctate structures	cytoplasm [IDA]			693
Q3E736 UniProt NPD GO	YO192_YEAST	Uncharacterized protein YOR192C-C	0.34	-	nuc	0					78
Q08954 UniProt NPD GO	YP199_YEAST	Uncharacterized protein YPL199C	0.34	-	nuc	0	Cytoplasm	cytoplasm [IDA]			240
P35456 UniProt NPD GO	UPAR_MOUSE	Urokinase plasminogen activator surface receptor, GPI-anchored form precursor (uPAR) (U-PAR) (CD87 a ...	0.34	-	exc	1	Cell membrane; lipid-anchor; GPI-anchor				327
Q5DID3 UniProt NPD GO	UROL1_MOUSE	Uromodulin-like 1 precursor (Olfactorin)	0.34	-	end	1	Cell membrane; single-pass type I membrane protein				1319
P33715 UniProt NPD GO	UTS2_RANRI	Urotensin-2 precursor (Urotensin-II) (U-II) (UII)	0.34	-	mit	0	Secreted protein				127
Q90523 UniProt NPD GO	RAG1_GINCI	V(D)J recombination-activating protein 1 (RAG-1) (Fragment)	0.34	-	nuc	0	Nucleus				106
P39942 UniProt NPD GO	VATD_BOVIN	Vacuolar ATP synthase subunit D (EC 3.6.3.14) (V-ATPase D subunit) (Vacuolar proton pump D subunit) ...	0.34	-	cyt	0					247
Q9V7D2 UniProt NPD GO	VATD1_DROME	Vacuolar ATP synthase subunit D 1 (EC 3.6.3.14) (V-ATPase D subunit 1) (Vacuolar proton pump D subun ...	0.34	-	cyt	0					246
O74174 UniProt NPD GO	VATG_SCHPO	Vacuolar ATP synthase subunit G (EC 3.6.3.14) (V-ATPase G subunit) (Vacuolar proton pump G subunit)	0.34	-	nuc	0					108
P49754 UniProt NPD GO	VPS41_HUMAN	Vacuolar assembly protein VPS41 homolog (S53)	0.34	-	cyt	0		integral to membrane [TAS]	605485		854
Q9CQ80 UniProt NPD GO	VPS25_MOUSE	Vacuolar protein sorting protein 25	0.34	-	mit	0	Cytoplasm (By similarity). Nucleus (By similarity). Distributes diffusely throughout the cytoplasm a ...	mitochondrion [IDA]			176
Q9BRG1 UniProt NPD GO	VPS25_HUMAN	Vacuolar protein sorting protein 25 (hVps25) (ELL-associated protein of 20 kDa) (Dermal papilla-deri ...	0.34	-	mit	0	Cytoplasm. Nucleus; nucleoplasm. Distributes diffusely throughout the cytoplasm and nucleoplasm, but ...				176
Q10243 UniProt NPD GO	VPS26_SCHPO	Vacuolar protein sorting/targeting protein VPS26 homolog	0.34	-	cyt	0					298
Q8VEJ9 UniProt NPD GO	VPS4A_MOUSE	Vacuolar sorting protein 4a	0.34	-	nuc	0	Cytoplasm. Membrane; peripheral membrane protein. Membrane-associated in the prevacuolar endosomal c ...	cytoplasm [IDA] perinuclear region [IDA]			437
P26640 UniProt NPD GO	SYV_HUMAN	Valyl-tRNA synthetase (EC 6.1.1.9) (Valine--tRNA ligase) (ValRS) (Protein G7a)	0.34	-	cyt	0		intracellular [NAS]	192150		1264
P52583 UniProt NPD GO	VGFR2_COTJA	Vascular endothelial growth factor receptor 2 precursor (EC 2.7.10.1) (VEGFR-2) (Endothelial kinase ...	0.34	-	end	2 *	Membrane; single-pass type I membrane protein				1348
P67861 UniProt NPD GO	TXVE_DABRR	Vascular endothelial growth factor toxin (svVEGF) (VR-1)	0.34	-	nuc	0	Secreted protein				109
P40898 UniProt NPD GO	YJV1_YEAST	Very hypothetical protein YJL211C	0.34	-	nuc	0					147
P46459 UniProt NPD GO	NSF_HUMAN	Vesicle-fusing ATPase (EC 3.6.4.6) (Vesicular-fusion protein NSF) (N-ethylmaleimide sensitive fusion ...	0.34	-	cyt	0	Cytoplasm		601633		744
O70280 UniProt NPD GO	WFDC1_RAT	WAP four-disulfide core domain protein 1 precursor (Prostate stromal protein ps20) (ps20 growth inhi ...	0.34	-	exc	0	Secreted protein				212

You are viewing entries 37201 to 37250 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.