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
Q9VH70 UniProt NPD GO	TOPI_DROME	Testis-specific zinc finger protein topi (Protein matotopetli)	0.81	-	nuc	0	Nucleus. Binds to chromatin	nucleus [NAS]			814
P01266 UniProt NPD GO	THYG_HUMAN	Thyroglobulin precursor	0.81	-	nuc	0	Secreted protein	extracellular region [NAS]	188450		2768
O60296 UniProt NPD GO	TRAK2_HUMAN	Trafficking kinesin-binding protein 2 (Amyotrophic lateral sclerosis 2 chromosomal region candidate ...	0.81	-	nuc	0	Cytoplasm (By similarity)	cytoplasm [ISS] plasma membrane [ISS]	607334		914
Q5KLR1 UniProt NPD GO	SPT6_CRYNE	Transcription elongation factor SPT6 (Chromatin elongation factor SPT6)	0.81	+	nuc	0	Nucleus (By similarity)				1506
Q00059 UniProt NPD GO	TFAM_HUMAN	Transcription factor A, mitochondrial precursor (mtTFA) (Mitochondrial transcription factor 1) (MtTF ...	0.81	-	nuc	0	Mitochondrion	mitochondrion [TAS]	600438		246
P26375 UniProt NPD GO	BAF1_KLULA	Transcription factor BAF1 (ARS-binding factor 1) (Protein ABF1) (Bidirectionally acting factor)	0.81	-	nuc	0	Nucleus				494
Q08605 UniProt NPD GO	GAGA_DROME	Transcription factor GAGA (Trithorax-like protein) (GAGA factor) (GAF) (Adh transcription factor 2) ...	0.81	-	nuc	0	Nucleus	centric heterochromatin [IDA] euchromatin [IDA] nucleus [IDA] polytene chromosome [IDA]		1YUJ	581
Q9LSE2 UniProt NPD GO	ICE1_ARATH	Transcription factor ICE1 (Inducer of CBF expression 1) (Basic helix-loop-helix protein 116) (bHLH11 ...	0.81	+	nuc	0	Nucleus (Probable)				494
P43680 UniProt NPD GO	SOX18_MOUSE	Transcription factor SOX-18	0.81	+	nuc	0	Nucleus	nucleus [IC]			377
Q9U405 UniProt NPD GO	GRAU_DROME	Transcription factor grauzone	0.81	+	nuc	0	Nucleus	nucleus [IDA]		1PZW	570
Q09926 UniProt NPD GO	PCR1_SCHPO	Transcription factor pcr1 (Transcription factor mts2)	0.81	+	nuc	0	Nucleus (Potential)				171
Q5F489 UniProt NPD GO	TAF3_CHICK	Transcription initiation factor TFIID subunit 3 (TBP-associated factor 3)	0.81	+	nuc	0	Nucleus (By similarity)				930
Q16594 UniProt NPD GO	TAF9_HUMAN	Transcription initiation factor TFIID subunit 9 (Transcription initiation factor TFIID 31 kDa subuni ...	0.81	-	nuc	0	Nucleus	transcription factor TFIID complex [IDA]	600822		264
Q5R9U8 UniProt NPD GO	MTERF_PONPY	Transcription termination factor, mitochondrial precursor (mTERF) (Mitochondrial transcription termi ...	0.81	-	nuc	0	Mitochondrion (By similarity)				398
O13862 UniProt NPD GO	RDP1_SCHPO	Transcriptional activator protein rdp1 (Rhp51-DRE-binding protein 1)	0.81	-	nuc	0	Nucleus (Potential)				478
Q03833 UniProt NPD GO	GIS1_YEAST	Transcriptional activator/repressor GIS1	0.81	-	nuc	0	Nucleus	mitochondrion [IDA] nucleus [IDA]			894
Q96QT4 UniProt NPD GO	TRPM7_HUMAN	Transient receptor potential cation channel subfamily M member 7 (EC 2.7.11.1) (Long transient recep ...	0.81	+	end	6	Membrane; multi-pass membrane protein (Probable)		605692		1865
P46944 UniProt NPD GO	TRS85_YEAST	Transport protein particle 85 kDa subunit (TRAPP 85 kDa subunit) (Sporulation protein GSG1)	0.81	-	nuc	0	Golgi apparatus; cis-Golgi network	TRAPP complex [IDA]			698
P46686 UniProt NPD GO	TULP2_MOUSE	Tubby-related protein 2 (Tubby-like protein 2) (P4-6 protein) (Fragment)	0.81	-	nuc	0					564
P49816 UniProt NPD GO	TSC2_RAT	Tuberin (Tuberous sclerosis 2 homolog protein)	0.81	-	end	0					1809
P62598 UniProt NPD GO	ARR12_ARATH	Two-component response regulator ARR12	0.81	-	nuc	0	Nucleus				596
Q8L500 UniProt NPD GO	APRR9_ARATH	Two-component response regulator-like APRR9 (Pseudo-response regulator 9)	0.81	-	nuc	0	Nucleus (Probable)				468
Q9LR47 UniProt NPD GO	IP5P3_ARATH	Type I inositol-1,4,5-trisphosphate 5-phosphatase CVP2 (EC 3.1.3.56) (Cotyledon vascular pattern 2 p ...	0.81	-	nuc	0					609
Q24488 UniProt NPD GO	ROR1_DROME	Tyrosine-protein kinase transmembrane receptor Ror precursor (EC 2.7.10.1) (dRor)	0.81	+	nuc	1	Membrane; single-pass type I membrane protein (Potential)	integral to membrane [NAS]			685
Q62728 UniProt NPD GO	PTN21_RAT	Tyrosine-protein phosphatase non-receptor type 21 (EC 3.1.3.48) (Protein-tyrosine phosphatase 2E)	0.81	-	nuc	0					1175
Q8CCF0 UniProt NPD GO	PRP31_MOUSE	U4/U6 small nuclear ribonucleoprotein Prp31 (Pre-mRNA-processing factor 31) (U4/U6 snRNP 61 kDa prot ...	0.81	-	nuc	0	Nucleus; nucleoplasm; nuclear speckle (By similarity). Nucleus; nucleoplasm; Cajal body (By similari ...				499
Q6AZH6 UniProt NPD GO	UBX8A_XENLA	UBX domain-containing protein 8-A	0.81	+	cyt	0	Cytoplasm (By similarity)				445
Q803I4 UniProt NPD GO	RING2_BRARE	Ubiquitin ligase protein RING2 (EC 6.3.2.-) (RING finger protein 2) (RING finger protein 1B) (RING1b ...	0.81	-	nuc	0	Nucleus (By similarity)				336
Q4WDD7 UniProt NPD GO	BRE1_ASPFU	Ubiquitin-protein ligase bre1 (EC 6.3.2.-)	0.81	-	nuc	0	Nucleus (By similarity)				725
P32788 UniProt NPD GO	YBB0_YEAST	Uncharacterized protein YBL010C	0.81	-	nuc	0	Nucleus (Potential)				280
P53313 UniProt NPD GO	YG58_YEAST	Uncharacterized protein YGR245C	0.81	+	nuc	0		nucleus [IDA]			767
P53955 UniProt NPD GO	YNE7_YEAST	Uncharacterized protein YNL047C	0.81	-	nuc	0		plasma membrane [IDA] TORC 2 complex [IPI]			656
Q18685 UniProt NPD GO	UN112_CAEEL	Uncoordinated protein 112 (Mitogen-inducible mig-2 protein-like)	0.81	-	nuc	0	Intracytoplasmic membrane; peripheral membrane protein. Colocalizes with pat-3/beta-integrin in body ...	cell-matrix junction [IDA] cytoplasm [IDA] plasma membrane [IDA]			720
Q5TM18 UniProt NPD GO	VATG2_MACMU	Vacuolar ATP synthase subunit G 2 (EC 3.6.3.14) (V-ATPase G subunit 2) (Vacuolar proton pump G subun ...	0.81	-	nuc	0					118
Q8TAA9 UniProt NPD GO	VANG1_HUMAN	Vang-like protein 1 (Van Gogh-like protein 1) (Strabismus 2) (Loop-tail protein 2 homolog) (LPP2)	0.81	+	end	4	Membrane; multi-pass membrane protein (Potential)		610132		524
P17948 UniProt NPD GO	VGFR1_HUMAN	Vascular endothelial growth factor receptor 1 precursor (EC 2.7.10.1) (VEGFR-1) (Vascular permeabili ...	0.81	-	end	0	Isoform Flt1: Cell membrane; single-pass type I membrane protein. Isoform SFlt1: Secreted protein	extracellular space [TAS] integral to plasma membrane [TAS]	165070	1RV6	1338
Q9WTP9 UniProt NPD GO	VAX2_MOUSE	Ventral anterior homeobox 2 (Ventral retina homeodomain protein)	0.81	+	nuc	0	Nucleus (Probable)				292
P22458 UniProt NPD GO	VTNC_RABIT	Vitronectin precursor (Serum-spreading factor) (S-protein) (Glycoprotein 66)	0.81	+	exc	0	Secreted protein; extracellular space				475
P27732 UniProt NPD GO	CAC1D_RAT	Voltage-dependent L-type calcium channel subunit alpha-1D (Voltage-gated calcium channel subunit alp ...	0.81	+	end	19	Membrane; multi-pass membrane protein	voltage-gated calcium channel complex [TAS]			2203
P97445 UniProt NPD GO	CAC1A_MOUSE	Voltage-dependent P/Q-type calcium channel subunit alpha-1A (Voltage-gated calcium channel subunit a ...	0.81	+	end	17	Membrane; multi-pass membrane protein	integral to membrane [ISS] voltage-gated calcium channel complex [TAS]			2164
O88427 UniProt NPD GO	CAC1H_MOUSE	Voltage-dependent T-type calcium channel subunit alpha-1H (Voltage-gated calcium channel subunit alp ...	0.81	+	end	15	Membrane; multi-pass membrane protein				2365
O75554 UniProt NPD GO	WBP4_HUMAN	WW domain-binding protein 4 (WBP-4) (Formin-binding protein 21)	0.81	+	nuc	0	Nucleus; nucleoplasm; nuclear speckle		604981		376
O35426 UniProt NPD GO	XBP1_MOUSE	X box-binding protein 1 (XBP-1) (Tax-responsive element-binding protein 5 homolog)	0.81	+	exc	0	Nucleus				267
P17861 UniProt NPD GO	XBP1_HUMAN	X box-binding protein 1 (XBP-1) (Tax-responsive element-binding protein 5)	0.81	+	nuc	0	Nucleus		194355		261
Q5QQ53 UniProt NPD GO	XYLT_DROPS	Xylosyltransferase oxt (EC 2.4.2.26) (Peptide O-xylosyltransferase)	0.81	-	mit	1 *	Or: Endoplasmic reticulum; endoplasmic reticulum membrane; single-pass type II membrane protein (By ...	integral to membrane [ISS]			880
O14709 UniProt NPD GO	ZN197_HUMAN	Zinc finger protein 197 (ZnF20)	0.81	+	nuc	0	Nucleus (Probable)				1029
O94822 UniProt NPD GO	ZN294_HUMAN	Zinc finger protein 294	0.81	-	nuc	0					1766
Q6U7Q0 UniProt NPD GO	Z322A_HUMAN	Zinc finger protein 322A	0.81	-	nuc	0	Cytoplasm. Nucleus				402
Q5ZJ02 UniProt NPD GO	ZN326_CHICK	Zinc finger protein 326	0.81	+	nuc	0	Nucleus (By similarity)				565
Q92610 UniProt NPD GO	ZN592_HUMAN	Zinc finger protein 592	0.81	-	nuc	0	Nucleus (Probable)				1267

You are viewing entries 8701 to 8750 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.