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
Q8SW18 UniProt NPD GO	HD10_ENCCU	Homeobox protein HD-10 (EcHD-10)	0.72	+	nuc	0	Nucleus				227
Q9IA24 UniProt NPD GO	HXA6_HETFR	Homeobox protein Hox-A6	0.72	+	nuc	0	Nucleus (By similarity)				229
P31259 UniProt NPD GO	HXB1_CHICK	Homeobox protein Hox-B1 (Ghox-lab)	0.72	+	nuc	0	Nucleus				309
P09019 UniProt NPD GO	HXB5_XENLA	Homeobox protein Hox-B5 (XlHbox-4) (Xhox-1B) (Fragment)	0.72	+	nuc	0	Nucleus				230
P28174 UniProt NPD GO	HXC3A_BRARE	Homeobox protein Hox-C3a (Hox-114) (Zf-114)	0.72	+	nuc	0	Nucleus (By similarity)				250
Q91994 UniProt NPD GO	OTX1_BRARE	Homeobox protein OTX1 (ZOTX1)	0.72	-	nuc	0	Nucleus (Probable)				323
P43120 UniProt NPD GO	HHEX_MOUSE	Homeobox protein PRH (Hematopoietically expressed homeobox) (Homeobox protein HEX)	0.72	+	nuc	0	Nucleus (Probable)	nucleus [IDA]			271
Q62232 UniProt NPD GO	SIX2_MOUSE	Homeobox protein SIX2 (Sine oculis homeobox homolog 2)	0.72	-	nuc	0	Nucleus				296
P56915 UniProt NPD GO	GSC_HUMAN	Homeobox protein goosecoid	0.72	+	nuc	0	Nucleus	nucleus [NAS]	138890		257
Q3LU38 UniProt NPD GO	PROP1_ALOBE	Homeobox protein prophet of Pit-1 (PROP-1) (Pituitary-specific homeodomain factor)	0.72	+	nuc	0	Nucleus (By similarity)				226
P09081 UniProt NPD GO	BCD_DROME	Homeotic protein bicoid (PRD-4)	0.72	-	nuc	0	Nucleus			1ZQ3	494
P24345 UniProt NPD GO	KN1_MAIZE	Homeotic protein knotted-1	0.72	-	nuc	0	Nucleus				359
Q9UJC3 UniProt NPD GO	HOOK1_HUMAN	Hook homolog 1 (h-hook1) (hHK1)	0.72	-	nuc	0	Cytoplasm (By similarity). Does not associate with the Golgi complex. During spermiogenesis, it loca ...		607820		728
P50503 UniProt NPD GO	F10A1_RAT	Hsc70-interacting protein (Hip) (Protein ST13 homolog) (Protein FAM10A1)	0.72	-	nuc	0	Cytoplasm				368
O59836 UniProt NPD GO	HIM1_SCHPO	Hsk1-interacting molecule 1 (DNA repair protein rad35)	0.72	-	nuc	0	Nucleus	Dbf4-dependent protein kinase complex [IDA]			545
P36117 UniProt NPD GO	YK01_YEAST	Hypothetical 102.5 kDa protein in YPT52-DBP7 intergenic region	0.72	-	nuc	0		cytoplasm [IDA]			915
P47168 UniProt NPD GO	YJ9E_YEAST	Hypothetical 48.6 kDa protein in NMD5-HOM6 intergenic region	0.72	-	cyt	0		cytoplasm [IDA]			421
Q03823 UniProt NPD GO	YM35_YEAST	Hypothetical 95.1 kDa protein in IMP1-HLJ1 intergenic region	0.72	-	nuc	0		vacuolar membrane (sensu Fungi) [IDA]			816
Q09417 UniProt NPD GO	YRM8_CAEEL	Hypothetical WD repeat protein R06F6.8	0.72	-	nuc	0					1470
P34347 UniProt NPD GO	YK6B_CAEEL	Hypothetical protein C29E4.11	0.72	+	nuc	0					208
O14173 UniProt NPD GO	YE57_SCHPO	Hypothetical protein C4D7.07c in chromosome I	0.72	-	end	1	Membrane; multi-pass membrane protein (Potential)				600
Q10237 UniProt NPD GO	YD14_SCHPO	Hypothetical protein C4G9.04c in chromosome I	0.72	-	nuc	0					638
O14061 UniProt NPD GO	YC35_SCHPO	Hypothetical protein C962.05 in chromosome III	0.72	+	mit	0					536
P34483 UniProt NPD GO	YMJ8_CAEEL	Hypothetical protein F59B2.8	0.72	-	cyt	0					435
Q09423 UniProt NPD GO	YRO6_CAEEL	Hypothetical protein R07G3.6	0.72	-	nuc	0					304
Q09651 UniProt NPD GO	YS19_CAEEL	Hypothetical protein ZK1307.9	0.72	-	nuc	0					369
Q9UTM0 UniProt NPD GO	YIV2_SCHPO	Hypothetical zinc finger protein C144.02 in chromosome I	0.72	-	nuc	0	Nucleus (Potential)				249
P53409 UniProt NPD GO	ISL3_ONCTS	Insulin gene enhancer protein ISL-3 (Islet-3)	0.72	+	nuc	0	Nucleus				363
P20591 UniProt NPD GO	MX1_HUMAN	Interferon-induced GTP-binding protein Mx1 (Interferon-regulated resistance GTP-binding protein MxA) ...	0.72	-	cyt	0	Cytoplasm		147150		661
Q9WVP9 UniProt NPD GO	MX2_MOUSE	Interferon-induced GTP-binding protein Mx2	0.72	-	cyt	0	Cytoplasm	cytoplasm [TAS]			655
Q8JZL1 UniProt NPD GO	I17RD_MOUSE	Interleukin-17 receptor D precursor (IL-17 receptor D) (IL-17RD) (Interleukin-17D receptor) (IL-17D ...	0.72	-	exc	0	Golgi apparatus; Golgi membrane; single-pass type I membrane protein (By similarity). Cell membrane; ...				738
P48997 UniProt NPD GO	INVO_MOUSE	Involucrin	0.72	-	nuc	0	Cytoplasm. Constituent of the scaffolding of the cornified envelope				467
Q80ZQ5 UniProt NPD GO	JAZF1_MOUSE	Juxtaposed with another zinc finger protein 1	0.72	-	nuc	0	Nucleus (Potential)				243
Q5RDF5 UniProt NPD GO	JAZF1_PONPY	Juxtaposed with another zinc finger protein 1	0.72	-	nuc	0	Nucleus (Potential)				243
Q86VZ6 UniProt NPD GO	JAZF1_HUMAN	Juxtaposed with another zinc finger protein 1 (TAK1-interacting protein 27)	0.72	-	nuc	0	Nucleus (Potential)	transcriptional repressor complex [IDA]	606246		243
Q6CDX0 UniProt NPD GO	SMI1_YARLI	KNR4/SMI1 homolog	0.72	+	nuc	0					713
Q9PUL2 UniProt NPD GO	KTNA1_XENLA	Katanin p60 ATPase-containing subunit (EC 3.6.4.3) (Katanin p60 subunit) (p60 katanin) (Fragment)	0.72	-	nuc	0	Cytoplasm. Predominantly. Centrosome. Also localized to the interphase centrosome. Spindle. Enhanced ...				486
Q9LIJ0 UniProt NPD GO	LBD26_ARATH	LOB domain-containing protein 26	0.72	+	nuc	0					153
Q9SN23 UniProt NPD GO	LBD38_ARATH	LOB domain-containing protein 38	0.72	-	nuc	0					247
P40796 UniProt NPD GO	LA_DROME	La protein homolog (La ribonucleoprotein) (La autoantigen homolog)	0.72	-	cyt	0	Nucleus (Probable)				390
P84550 UniProt NPD GO	LBXCO_HUMAN	Ladybird homeobox corepressor 1	0.72	-	nuc	0	Nucleus (By similarity)				965
O13765 UniProt NPD GO	DBR1_SCHPO	Lariat debranching enzyme (EC 3.1.-.-)	0.72	-	nuc	0					466
O97827 UniProt NPD GO	LPHN3_BOVIN	Latrophilin-3 precursor	0.72	-	end	7	Membrane; multi-pass membrane protein				1580
Q9ZPI1 UniProt NPD GO	SYK_ARATH	Lysyl-tRNA synthetase (EC 6.1.1.6) (Lysine--tRNA ligase) (LysRS)	0.72	-	nuc	0	Cytoplasm (By similarity)				626
P20483 UniProt NPD GO	MPIP_DROME	M-phase inducer phosphatase (EC 3.1.3.48) (Protein string) (Cdc25-like protein)	0.72	-	nuc	0		chromosome [IDA] nucleus [IDA]			479
Q9CR33 UniProt NPD GO	MANS1_MOUSE	MANSC domain-containing protein 1 precursor	0.72	-	end	1	Membrane; single-pass type I membrane protein (Potential)				414
Q58D94 UniProt NPD GO	MKNK1_BOVIN	MAP kinase-interacting serine/threonine-protein kinase 1 (EC 2.7.11.1) (MAP kinase signal-integratin ...	0.72	+	nuc	0					420
Q9YGW0 UniProt NPD GO	MKNK1_XENLA	MAP kinase-interacting serine/threonine-protein kinase 1 (EC 2.7.11.1) (MAP kinase signal-integratin ...	0.72	+	cyt	0					418
Q9UBG0 UniProt NPD GO	MRC2_HUMAN	Macrophage mannose receptor 2 precursor (Urokinase receptor-associated protein) (Endocytic receptor ...	0.72	-	nuc	1	Membrane; single-pass type I membrane protein				1479
Q02991 UniProt NPD GO	MAT2_COCHE	Mating-type protein MAT-2	0.72	-	nuc	0	Nucleus (Potential)				343

You are viewing entries 12801 to 12850 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.