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
P15861 UniProt NPD GO	HXB6A_BRARE	Homeobox protein Hox-B6a (Hox-B6) (Zf-22)	0.75	+	nuc	0	Nucleus				228
Q6JIY4 UniProt NPD GO	HXCDB_BRARE	Homeobox protein Hox-C13b	0.75	+	nuc	0	Nucleus (By similarity)				273
P49925 UniProt NPD GO	HXC6_SHEEP	Homeobox protein Hox-C6	0.75	+	nuc	0	Nucleus				153
O42502 UniProt NPD GO	HXC9_FUGRU	Homeobox protein Hox-C9 (HOXC-9)	0.75	+	nuc	0	Nucleus				261
Q91981 UniProt NPD GO	OTX2_BRARE	Homeobox protein OTX2 (ZOTX2)	0.75	-	nuc	0	Nucleus (Probable)				289
Q96KN3 UniProt NPD GO	PKNX2_HUMAN	Homeobox protein PKNOX2 (PBX/knotted homeobox 2) (Homeobox protein PREP-2)	0.75	-	nuc	0	Nucleus				460
Q26600 UniProt NPD GO	SMOX1_SCHMA	Homeobox protein SMOX-1 (Fragment)	0.75	-	nuc	0	Nucleus (By similarity)				280
P35993 UniProt NPD GO	HOX7P_XENLA	Homeobox protein XHOX-7.1' (Fragment)	0.75	+	exc	0	Nucleus (Probable)				291
P56667 UniProt NPD GO	KNX10_MAIZE	Homeobox protein knotted-1-like 10 (Fragment)	0.75	-	nuc	0	Nucleus (Probable)				88
P56661 UniProt NPD GO	KNOX3_MAIZE	Homeobox protein knotted-1-like 3 (Fragment)	0.75	+	nuc	0	Nucleus (Probable)				88
Q9DGQ7 UniProt NPD GO	CDC37_TETFL	Hsp90 co-chaperone Cdc37 (Hsp90 chaperone protein kinase-targeting subunit) (p50Cdc37)	0.75	-	nuc	0	Cytoplasm (By similarity)				377
O00291 UniProt NPD GO	HIP1_HUMAN	Huntingtin-interacting protein 1 (HIP-I)	0.75	+	nuc	0	Intracytoplasmic membrane	cytoplasm [IDA] cytoskeleton [TAS] Golgi apparatus [IDA] membrane fraction [TAS]	601767		1030
P40355 UniProt NPD GO	YJ31_YEAST	Hypothetical 108.4 kDa protein in CBF1-NTA1 intergenic region	0.75	-	mit	1 *					935
Q03673 UniProt NPD GO	YMO3_YEAST	Hypothetical 22.7 kDa protein in CDC5-MVP1 intergenic region	0.75	-	nuc	0		mitochondrion [IDA]			198
Q03208 UniProt NPD GO	YML9_YEAST	Hypothetical 40.1 kDa protein in NDI1-ATR1 intergenic region	0.75	-	nuc	0					357
P53850 UniProt NPD GO	YNZ4_YEAST	Hypothetical 46.2 kDa protein in SIP3-MRPL30 intergenic region	0.75	-	nuc	0		cytoplasm [IDA] nucleus [IDA]			401
P53963 UniProt NPD GO	YND4_YEAST	Hypothetical 69.4 kDa protein in NCE3-HHT2 intergenic region	0.75	-	nuc	0					612
Q9Y7I8 UniProt NPD GO	YOI1_SCHPO	Hypothetical J domain-containing protein C1778.01c	0.75	-	nuc	0					442
Q18079 UniProt NPD GO	YXT1_CAEEL	Hypothetical protein C18B2.1	0.75	+	nuc	1 *					321
Q9USW8 UniProt NPD GO	YHY1_SCHPO	Hypothetical protein C19C7.01 in chromosome II	0.75	-	nuc	0					196
P87145 UniProt NPD GO	YB03_SCHPO	Hypothetical protein C25H2.03 in chromosome II	0.75	+	mit	0					811
O74361 UniProt NPD GO	YNU4_SCHPO	Hypothetical protein C28E12.04 in chromosome II	0.75	-	nuc	0					356
Q9Y7S8 UniProt NPD GO	YCX5_SCHPO	Hypothetical protein C2H8.05c in chromosome III	0.75	-	nuc	0					217
Q09729 UniProt NPD GO	YA4C_SCHPO	Hypothetical protein C31A2.12 in chromosome I	0.75	-	nuc	0					596
Q09262 UniProt NPD GO	YQD1_CAEEL	Hypothetical protein C32D5.1	0.75	-	nuc	0					260
Q09265 UniProt NPD GO	YQD5_CAEEL	Hypothetical protein C32D5.5	0.75	-	nuc	0					288
Q9HFF2 UniProt NPD GO	YL92_SCHPO	Hypothetical protein C683.02c in chromosome I	0.75	+	nuc	0					218
O14256 UniProt NPD GO	YE6A_SCHPO	Hypothetical protein C6G10.10c in chromosome I	0.75	-	nuc	0					194
Q8SW85 UniProt NPD GO	Y301_ENCCU	Hypothetical protein ECU03_0010	0.75	-	nuc	0					276
P46505 UniProt NPD GO	YLX9_CAEEL	Hypothetical protein F23F12.9 in chromosome III	0.75	-	nuc	0					176
Q09394 UniProt NPD GO	YR75_CAEEL	Hypothetical protein F43C1.5	0.75	-	nuc	0					221
O62518 UniProt NPD GO	YHPK_CAEEL	Hypothetical protein ZK795.3 in chromosome IV	0.75	-	nuc	0					292
P01855 UniProt NPD GO	IGHE_RAT	Ig epsilon chain C region	0.75	-	nuc	0					429
Q5B4P0 UniProt NPD GO	TIM50_EMENI	Import inner membrane translocase subunit tim50, mitochondrial precursor	0.75	-	mit	0	Mitochondrion; mitochondrial inner membrane; single-pass membrane protein (By similarity)				532
Q60960 UniProt NPD GO	IMA1_MOUSE	Importin alpha-1 subunit (Karyopherin alpha-1 subunit) (SRP1-beta) (RAG cohort protein 2) (Nucleopro ...	0.75	-	nuc	0	Cytoplasm. Nucleus				538
Q9UK53 UniProt NPD GO	ING1_HUMAN	Inhibitor of growth protein 1	0.75	+	nuc	0	Nucleus (Probable)	nucleus [NAS]	601566		422
Q7SFQ9 UniProt NPD GO	MRS2_NEUCR	Inner membrane magnesium transporter MRS2, mitochondrial precursor (RNA-splicing protein MRS2)	0.75	-	cyt	1	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein (By similarity)				547
Q9TU34 UniProt NPD GO	ITPR1_BOVIN	Inositol 1,4,5-trisphosphate receptor type 1 (Type 1 inositol 1,4,5-trisphosphate receptor) (Type 1 ...	0.75	-	end	6	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein. Secretory vesicl ...				2709
Q14573 UniProt NPD GO	ITPR3_HUMAN	Inositol 1,4,5-trisphosphate receptor type 3 (Type 3 inositol 1,4,5-trisphosphate receptor) (Type 3 ...	0.75	+	end	7	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein	brush border [TAS] endoplasmic reticulum [TAS] plasma membrane [TAS]	147267		2671
P50211 UniProt NPD GO	ISL1_CHICK	Insulin gene enhancer protein ISL-1 (Islet-1)	0.75	+	nuc	0	Nucleus				349
Q90WV8 UniProt NPD GO	IBP5_XENLA	Insulin-like growth factor-binding protein 5 precursor (IGFBP-5) (IBP-5) (IGF-binding protein 5) (xI ...	0.75	-	nuc	0	Secreted protein	extracellular region [IDA]			265
Q8K2A7 UniProt NPD GO	INT10_MOUSE	Integrator complex subunit 10	0.75	-	cyt	0	Nucleus (By similarity)				710
P63309 UniProt NPD GO	IFNG_MACFA	Interferon gamma precursor (IFN-gamma)	0.75	-	exc	0	Secreted protein				165
P63310 UniProt NPD GO	IFNG_MACMU	Interferon gamma precursor (IFN-gamma)	0.75	-	exc	0	Secreted protein				165
P63311 UniProt NPD GO	IFNG_MACNE	Interferon gamma precursor (IFN-gamma)	0.75	-	exc	0	Secreted protein				165
Q5I6S9 UniProt NPD GO	IFNG_MACTH	Interferon gamma precursor (IFN-gamma)	0.75	-	exc	0	Secreted protein (By similarity)				165
O73915 UniProt NPD GO	IFNG_NUMME	Interferon gamma precursor (IFN-gamma)	0.75	-	nuc	1 *	Secreted protein (By similarity)				164
Q90876 UniProt NPD GO	IRF1_CHICK	Interferon regulatory factor 1 (IRF-1)	0.75	+	nuc	0	Nucleus				313
Q9Z0E6 UniProt NPD GO	GBP2_MOUSE	Interferon-induced guanylate-binding protein 2 (GTP-binding protein 2) (Guanine nucleotide-binding p ...	0.75	-	nuc	0	Cell membrane; lipid-anchor; cytoplasmic side (Potential)				589
Q6NXA4 UniProt NPD GO	ILF3_BRARE	Interleukin enhancer-binding factor 3 homolog	0.75	+	nuc	0	Nucleus (By similarity)				833

You are viewing entries 11351 to 11400 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.