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
O95478 UniProt NPD GO	TIP1_HUMAN	TGF-beta-inducible nuclear protein 1 (Hairy cell leukemia protein 1)	0.63	+	nuc	0	Nucleus; nucleolus				260
Q9QYU7 UniProt NPD GO	TIP1_RAT	TGF-beta-inducible nuclear protein 1 (Protein CDK105)	0.63	+	nuc	0	Nucleus; nucleolus (By similarity)				260
Q8TBB0 UniProt NPD GO	THAP6_HUMAN	THAP domain-containing protein 6	0.63	-	nuc	0					222
Q24K03 UniProt NPD GO	THUM1_BOVIN	THUMP domain-containing protein 1	0.63	-	nuc	0					357
O74804 UniProt NPD GO	EST1_SCHPO	Telomere elongation protein est1 (EC 2.7.7.-) (Ever shorter telomeres protein 1)	0.63	-	nuc	0	Nucleus				490
P07202 UniProt NPD GO	PERT_HUMAN	Thyroid peroxidase precursor (EC 1.11.1.8) (TPO)	0.63	-	end	1 *	Membrane; single-pass type I membrane protein	integral to plasma membrane [TAS]	606765		933
Q9JLC6 UniProt NPD GO	TEF_MOUSE	Thyrotroph embryonic factor	0.63	+	nuc	0	Nucleus (Probable)	nucleus [IC]			301
Q9BRU2 UniProt NPD GO	TCAL7_HUMAN	Transcription elongation factor A protein-like 7 (TCEA-like protein 7) (Transcription elongation fac ...	0.63	-	nuc	0	Nucleus (Probable)				100
Q5ZI08 UniProt NPD GO	SPT5H_CHICK	Transcription elongation factor SPT5 (DRB sensitivity-inducing factor large subunit) (DSIF large sub ...	0.63	-	nuc	0	Nucleus (By similarity)				1079
O55201 UniProt NPD GO	SPT5H_MOUSE	Transcription elongation factor SPT5 (DRB sensitivity-inducing factor large subunit) (DSIF large sub ...	0.63	-	nuc	0	Nucleus (By similarity)				1082
P40630 UniProt NPD GO	TFAM_MOUSE	Transcription factor A, mitochondrial precursor (mtTFA) (Testis-specific high mobility group protein ...	0.63	+	nuc	0	Nucleus. Mitochondrion	mitochondrion [IDA] transcription factor complex [TAS]			243
Q76HI7 UniProt NPD GO	AP2B_CANFA	Transcription factor AP-2 beta (AP2-beta) (Activating enhancer-binding protein 2 beta)	0.63	-	nuc	0	Nucleus (Probable)				449
Q92481 UniProt NPD GO	AP2B_HUMAN	Transcription factor AP-2 beta (AP2-beta) (Activating enhancer-binding protein 2 beta)	0.63	-	nuc	0	Nucleus (Probable)		601601		449
Q62814 UniProt NPD GO	E2F5_RAT	Transcription factor E2F5 (E2F-5) (Fragment)	0.63	-	nuc	0	Nucleus				300
P46152 UniProt NPD GO	GATA4_RAT	Transcription factor GATA-4 (GATA-binding factor 4) (DNA-binding protein GATA-GT2)	0.63	-	nuc	0	Nucleus				440
P17947 UniProt NPD GO	SPI1_HUMAN	Transcription factor PU.1 (31 kDa transforming protein)	0.63	+	nuc	0	Nucleus		165170		270
Q811W0 UniProt NPD GO	SOX21_MOUSE	Transcription factor SOX-21	0.63	+	nuc	0	Nucleus (Potential)	nucleus [IC]			276
Q62445 UniProt NPD GO	SP4_MOUSE	Transcription factor Sp4	0.63	-	nuc	0	Nucleus				782
Q02446 UniProt NPD GO	SP4_HUMAN	Transcription factor Sp4 (SPR-1)	0.63	-	nuc	0	Nucleus		600540		784
P09450 UniProt NPD GO	JUNB_MOUSE	Transcription factor jun-B	0.63	+	nuc	0	Nucleus				344
P24898 UniProt NPD GO	JUNB_RAT	Transcription factor jun-B	0.63	+	nuc	0	Nucleus				344
P49846 UniProt NPD GO	TAF5_DROME	Transcription initiation factor TFIID subunit 5 (Transcription initiation factor TFIID 85 kDa subuni ...	0.63	+	nuc	0	Nucleus	SAGA complex [IPI]			704
P16176 UniProt NPD GO	TGFB1_XENLA	Transforming growth factor beta-1 precursor (TGF-beta-1) (TGF-beta-5)	0.63	-	nuc	0	Secreted protein				382
P09032 UniProt NPD GO	EI2BG_YEAST	Translation initiation factor eIF-2B subunit gamma (eIF-2B GDP-GTP exchange factor subunit gamma) (G ...	0.63	-	nuc	0		eukaryotic translation initiation factor 2B... [IDA] ribosome [TAS]			578
P03934 UniProt NPD GO	TC1A_CAEEL	Transposable element Tc1 transposase	0.63	-	nuc	0	Nucleus	nucleus [NAS]			273
Q9ET35 UniProt NPD GO	TR13B_MOUSE	Tumor necrosis factor receptor superfamily member 13B (Transmembrane activator and CAML interactor)	0.63	-	nuc	1	Membrane; single-pass type III membrane protein (Probable)	external side of plasma membrane [IDA] integral to plasma membrane [IDA]			249
P53250 UniProt NPD GO	TWF1_YEAST	Twinfilin-1 (Twinfilin-A)	0.63	-	nuc	0		actin cortical patch [IDA]			332
Q8MIU0 UniProt NPD GO	TYRO_BOVIN	Tyrosinase precursor (EC 1.14.18.1) (Monophenol monooxygenase)	0.63	-	end	1	Melanosome; melanosomal membrane; single-pass type I membrane protein (By similarity)	integral to membrane [ISS] melanosome [ISS]			530
P24604 UniProt NPD GO	TEC_MOUSE	Tyrosine-protein kinase Tec (EC 2.7.10.2)	0.63	-	cyt	0	Cytoplasm (Probable)			1GL5	630
P16621 UniProt NPD GO	LAR_DROME	Tyrosine-protein phosphatase Lar precursor (EC 3.1.3.48) (Protein-tyrosine-phosphate phosphohydrolas ...	0.63	-	end	0	Membrane; single-pass type I membrane protein				2029
Q9H3S7 UniProt NPD GO	PTN23_HUMAN	Tyrosine-protein phosphatase non-receptor type 23 (EC 3.1.3.48) (His-domain-containing protein tyros ...	0.63	-	nuc	0	Cytoplasmic vesicle		606584		1636
P09012 UniProt NPD GO	SNRPA_HUMAN	U1 small nuclear ribonucleoprotein A (U1 snRNP protein A) (U1A protein) (U1-A)	0.63	+	nuc	0	Nucleus	spliceosome complex [IDA]	182285	3UTR	281
Q9XIK4 UniProt NPD GO	U202A_ARATH	UPF0202 protein At1g10490	0.63	+	mit	0	Nucleus (By similarity)				1058
O75208 UniProt NPD GO	COQ9_HUMAN	Ubiquinone biosynthesis protein COQ9, mitochondrial precursor	0.63	-	mit	0	Mitochondrion (By similarity)				318
P39538 UniProt NPD GO	UBP12_YEAST	Ubiquitin carboxyl-terminal hydrolase 12 (EC 3.1.2.15) (Ubiquitin thioesterase 12) (Ubiquitin-specif ...	0.63	-	nuc	0		cytoplasm [IDA] nucleus [IDA]			1254
P39944 UniProt NPD GO	UBP5_YEAST	Ubiquitin carboxyl-terminal hydrolase 5 (EC 3.1.2.15) (Ubiquitin thioesterase 5) (Ubiquitin-specific ...	0.63	-	nuc	0		cytoplasm [IC]			805
P35130 UniProt NPD GO	UBC2_MEDSA	Ubiquitin-conjugating enzyme E2-17 kDa (EC 6.3.2.19) (Ubiquitin-protein ligase) (Ubiquitin carrier p ...	0.63	-	nuc	0					152
Q9D915 UniProt NPD GO	CH004_MOUSE	Uncharacterized protein C8orf4 homolog	0.63	-	nuc	0					106
P40019 UniProt NPD GO	YEM0_YEAST	Uncharacterized protein YER030W	0.63	+	nuc	0		nucleus [IDA]			160
P87275 UniProt NPD GO	YES3A_YEAST	Uncharacterized protein YER093C-A	0.63	-	nuc	2 *	Membrane; multi-pass membrane protein (Potential)				137
P38883 UniProt NPD GO	YHZ7_YEAST	Uncharacterized protein YHR197W	0.63	-	mit	0		nucleoplasm [IDA] nucleus [IDA]			763
P53958 UniProt NPD GO	YNE2_YEAST	Uncharacterized protein YNL042W	0.63	-	nuc	0		cytoplasm [IDA] nucleus [IDA]			396
Q07468 UniProt NPD GO	VPS39_YEAST	Vacuolar assembly protein VPS39 (Vacuolar morphogenesis protein 6)	0.63	-	nuc	0		HOPS complex [IPI] vacuole (sensu Fungi) [IDA]			1049
Q6BRL3 UniProt NPD GO	BRO1_DEBHA	Vacuolar protein-sorting protein BRO1 (BRO domain-containing protein 1)	0.63	-	nuc	0	Cytoplasm (By similarity). Endosome (By similarity)				970
Q6BSH2 UniProt NPD GO	SNF7_DEBHA	Vacuolar sorting protein SNF7 (Vacuolar protein sorting-associated protein VPS32)	0.63	+	nuc	0	Cytoplasm (By similarity). Endosome; endosomal membrane; peripheral membrane protein (By similarity) ...				226
O73682 UniProt NPD GO	VEGFA_BRARE	Vascular endothelial growth factor precursor	0.63	-	nuc	0	Secreted protein (By similarity)	extracellular region [NAS]			188
P81282 UniProt NPD GO	CSPG2_BOVIN	Versican core protein precursor (Large fibroblast proteoglycan) (Chondroitin sulfate proteoglycan co ...	0.63	-	nuc	0	Secreted protein; extracellular space; extracellular matrix				3381
P19826 UniProt NPD GO	VINC_CAEEL	Vinculin (P107B)	0.63	-	nuc	0	Cytoskeleton. Cell membrane; cell-cell junction; adherens junction; cytoplasmic side. Cell membrane; ...	cytoskeleton [IDA]			1010
Q9N4J2 UniProt NPD GO	VIT3_CAEEL	Vitellogenin-3 precursor	0.63	-	cyt	0	Secreted protein				1603
Q5ZMV9 UniProt NPD GO	WDR24_CHICK	WD repeat protein 24	0.63	-	nuc	0					705

You are viewing entries 17701 to 17750 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.