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
P28818 UniProt NPD GO	GNRP_RAT	Guanine nucleotide-releasing protein (GNRP) (P140 Ras-GRF)	0.92	-	nuc	0					1244
Q870J1 UniProt NPD GO	STE11_PNECA	HMG-box protein STE11	0.92	+	nuc	0	Nucleus (Probable)				501
Q8VDM6 UniProt NPD GO	HNRL1_MOUSE	Heterogeneous nuclear ribonucleoprotein U-like protein 1	0.92	-	nuc	0	Nucleus (By similarity)				859
Q9NP66 UniProt NPD GO	HM20A_HUMAN	High mobility group protein 20A (HMG box-containing protein 20A) (HMG domain-containing protein HMGX ...	0.92	+	nuc	0	Nucleus (By similarity)	nucleus [NAS]	605534		347
Q9DC33 UniProt NPD GO	HM20A_MOUSE	High mobility group protein 20A (HMG box-containing protein 20A) (iBRAF) (Inhibitor of BRAF35) (HMG ...	0.92	+	nuc	0	Nucleus (By similarity)				346
Q08649 UniProt NPD GO	ESA1_YEAST	Histone acetyltransferase ESA1 (EC 2.3.1.48)	0.92	+	nuc	0		H4/H2A histone acetyltransferase complex [IPI]		1MJB	445
Q8CHK4 UniProt NPD GO	TIP60_MOUSE	Histone acetyltransferase HTATIP (EC 2.3.1.48) (EC 2.3.1.-) (60 kDa Tat interactive protein) (Tip60) ...	0.92	-	nuc	0	Nucleus (By similarity). Cytoplasm; perinuclear region (By similarity). Upon stimulation with EDN1, ...	transcription factor complex [IDA]			513
Q99MK2 UniProt NPD GO	TIP60_RAT	Histone acetyltransferase HTATIP (EC 2.3.1.48) (EC 2.3.1.-) (60 kDa Tat interactive protein) (Tip60) ...	0.92	-	nuc	0	Nucleus (By similarity). Cytoplasm; perinuclear region (By similarity). Upon stimulation with EDN1, ...	chromatin [IDA] histone acetyltransferase complex [TAS]			513
Q92993 UniProt NPD GO	TIP60_HUMAN	Histone acetyltransferase HTATIP (EC 2.3.1.48) (EC 2.3.1.-) (60 kDa Tat interactive protein) (Tip60) ...	0.92	-	nuc	0	Nucleus. Cytoplasm; perinuclear region. Upon stimulation with EDN1, it is exported from the nucleus ...	nucleus [TAS] TIP60 histone acetyltransferase complex [IDA]	601409		513
Q9YGT0 UniProt NPD GO	HXCCB_BRARE	Homeobox protein Hox-C12b	0.92	+	nuc	0	Nucleus (By similarity)				283
Q8MIE9 UniProt NPD GO	TF2LX_GORGO	Homeobox protein TGIF2LX (TGFB-induced factor 2-like protein, X-linked) (TGF(beta)induced transcript ...	0.92	-	nuc	0	Nucleus (By similarity)				241
Q8IUE1 UniProt NPD GO	TF2LX_HUMAN	Homeobox protein TGIF2LX (TGFB-induced factor 2-like protein, X-linked) (TGF(beta)induced transcript ...	0.92	-	nuc	0	Nucleus (By similarity)		300411		241
P09087 UniProt NPD GO	ABDB_DROME	Homeobox protein abdominal-B (P3) (Infraabdominal 7) (IAB-7) (PH189)	0.92	+	nuc	0	Nucleus				493
P41935 UniProt NPD GO	HM10_CAEEL	Homeobox protein ceh-10	0.92	+	nuc	0	Nucleus (Probable)				344
Q19720 UniProt NPD GO	HM38_CAEEL	Homeobox protein ceh-38	0.92	-	nuc	0	Nucleus (Potential)				641
Q26601 UniProt NPD GO	SMOX2_SCHMA	Homeobox protein engrailed-like SMOX-2	0.92	+	nuc	0	Nucleus (By similarity)				524
P46897 UniProt NPD GO	ATHB7_ARATH	Homeobox-leucine zipper protein ATHB-7 (Homeodomain transcription factor ATHB-7) (HD-ZIP protein ATH ...	0.92	-	nuc	0	Nucleus				258
Q9W539 UniProt NPD GO	HR4_DROME	Hormone receptor 4 (dHR4)	0.92	+	nuc	0	Nucleus	nucleus [IDA]			1518
P97924 UniProt NPD GO	HAPIP_RAT	Huntingtin-associated protein-interacting protein (Protein Duo) (Kalirin) (PAM COOH-terminal interac ...	0.92	-	nuc	0	Cytoplasm	cell soma [IDA] neuron projection [IDA] perinuclear region [IDA]		1U3O	1919
P36168 UniProt NPD GO	YK76_YEAST	Hypothetical 137.5 kDa protein in MPL1-PPC1 intergenic region	0.92	-	nuc	0		cytoplasm [IDA] nucleus [IDA]			1195
P36066 UniProt NPD GO	YKN3_YEAST	Hypothetical 54.4 kDa protein in APL2-MYO3 intergenic region	0.92	-	nuc	1					463
P53919 UniProt NPD GO	YNM4_YEAST	Hypothetical 54.9 kDa protein in SPC98-TOM70 intergenic region	0.92	+	nuc	0		nucleoplasm [TAS]			492
Q11103 UniProt NPD GO	YL18_CAEEL	Hypothetical protein C02F12.8	0.92	+	nuc	0					687
Q10183 UniProt NPD GO	YAW8_SCHPO	Hypothetical protein C3F10.08c in chromosome I	0.92	-	nuc	0					259
Q10221 UniProt NPD GO	YAYE_SCHPO	Hypothetical protein C4H3.14c in chromosome I	0.92	+	nuc	0					345
P41950 UniProt NPD GO	YLK2_CAEEL	Hypothetical protein D1044.2 precursor	0.92	-	mit	2 *	Membrane; single-pass type I membrane protein (Potential)				1090
Q10125 UniProt NPD GO	YSM5_CAEEL	Hypothetical protein F52C9.5 precursor	0.92	-	exc	0					618
P34520 UniProt NPD GO	YM44_CAEEL	Hypothetical protein K11H3.4	0.92	-	nuc	0					717
P34656 UniProt NPD GO	YOTA_CAEEL	Hypothetical protein ZK632.11	0.92	+	nuc	0					453
Q59W44 UniProt NPD GO	TIM50_CANAL	Import inner membrane translocase subunit TIM50, mitochondrial precursor	0.92	+	mit	0	Mitochondrion; mitochondrial inner membrane; single-pass membrane protein (By similarity)				469
Q9ESK4 UniProt NPD GO	ING2_MOUSE	Inhibitor of growth protein 2 (p33ING2) (Inhibitor of growth 1-like protein)	0.92	+	nuc	0	Nucleus (By similarity). Predominantly. Localized to chromatin and nuclear matrix. Upon reduced PtdI ...			1WES	281
Q9H160 UniProt NPD GO	ING2_HUMAN	Inhibitor of growth protein 2 (p33ING2) (Inhibitor of growth 1-like protein) (ING1Lp) (p32)	0.92	+	nuc	0	Nucleus. Predominantly. Localized to chromatin and nuclear matrix. Upon reduced PtdIns(5)P levels se ...	CCAAT-binding factor complex [IDA] chromosome [TAS] nucleus [IEP]	604215		280
Q8N201 UniProt NPD GO	INT1_HUMAN	Integrator complex subunit 1 (Int1)	0.92	-	end	0	Nucleus; nuclear membrane; single-pass membrane protein (Potential)				2190
Q6P4S8 UniProt NPD GO	INT1_MOUSE	Integrator complex subunit 1 (Int1)	0.92	-	end	0	Nucleus; nuclear membrane; single-pass membrane protein (Potential)				2126
Q71S22 UniProt NPD GO	INVSA_XENLA	Inversin-A	0.92	+	nuc	0	Cytoplasm (By similarity). Associates with the cytoskeleton (By similarity)				1007
Q5RD88 UniProt NPD GO	JHD3A_PONPY	JmjC domain-containing histone demethylation protein 3A (EC 1.14.11.-) (Jumonji domain-containing pr ...	0.92	+	nuc	0	Nucleus (By similarity)				1064
Q9BWU0 UniProt NPD GO	NADAP_HUMAN	Kanadaptin (Kidney anion exchanger adapter protein) (Solute carrier family 4 anion exchanger member ...	0.92	+	nuc	0	Nucleus. Mainly. Cytoplasm. Small amounts are found in the cytoplasm		602655		796
P32526 UniProt NPD GO	KAR9_YEAST	Karyogamy protein KAR9 (Cortical protein KAR9)	0.92	-	nuc	0	Nucleus. Localizes to the tip of shmoo projections and to the tip of budding cells in a cell-cycle d ...	cell cortex [IDA] mating projection tip [IDA]			644
Q5R9K7 UniProt NPD GO	KIF5A_PONPY	Kinesin heavy chain isoform 5A	0.92	-	nuc	0	Cytoplasm; perinuclear region (By similarity). Concentrated in the cell body of the neurons, particu ...				1032
P33175 UniProt NPD GO	KIF5A_MOUSE	Kinesin heavy chain isoform 5A (Neuronal kinesin heavy chain) (NKHC) (Kinesin heavy chain neuron-spe ...	0.92	-	nuc	0	Cytoplasm; perinuclear region. Concentrated in the cell body of the neurons, particularly in the per ...	ciliary rootlet [IDA] cytoplasm [IDA] kinesin complex [TAS] neuron projection [IDA]			1027
Q9P2E2 UniProt NPD GO	KIF17_HUMAN	Kinesin-like protein KIF17 (KIF3-related motor protein)	0.92	-	nuc	0			605037		1029
O88658 UniProt NPD GO	KIF1B_RAT	Kinesin-like protein KIF1B	0.92	-	nuc	0	Cytoplasmic vesicle (By similarity). Predominantly found on the vesicle- and tubule-like structures ...				1816
Q922S8 UniProt NPD GO	KIF2C_MOUSE	Kinesin-like protein KIF2C (Mitotic centromere-associated kinesin) (MCAK)	0.92	-	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity)			1V8K	721
Q4R628 UniProt NPD GO	KIF3A_MACFA	Kinesin-like protein KIF3A (Microtubule plus end-directed kinesin motor 3A)	0.92	+	nuc	0					702
Q5R4H3 UniProt NPD GO	KIF3A_PONPY	Kinesin-like protein KIF3A (Microtubule plus end-directed kinesin motor 3A)	0.92	+	nuc	0					702
O15066 UniProt NPD GO	KIF3B_HUMAN	Kinesin-like protein KIF3B (Microtubule plus end-directed kinesin motor 3B) (HH0048)	0.92	+	nuc	0		plus-end kinesin complex [TAS]	603754		747
P57682 UniProt NPD GO	KLF3_HUMAN	Krueppel-like factor 3 (Basic krueppel-like factor) (CACCC-box-binding protein BKLF) (TEF-2)	0.92	-	nuc	0	Nucleus (Probable)		609392		345
P35805 UniProt NPD GO	MYCLB_XENLA	L-myc B protein (L-myc 2 protein)	0.92	-	nuc	0	Nucleus				344
Q9UHB6 UniProt NPD GO	LIMA1_HUMAN	LIM domain and actin-binding protein 1 (Epithelial protein lost in neoplasm)	0.92	-	nuc	0	Cytoplasm. Cell membrane; cell-matrix junction; focal adhesion. This cytoskeletal protein co-localiz ...	focal adhesion [IDA] stress fiber [IDA]	608364		759
O55203 UniProt NPD GO	LDB2_MOUSE	LIM domain-binding protein 2 (Carboxyl-terminal LIM domain-binding protein 1) (CLIM-1) (LIM-domain-b ...	0.92	+	nuc	0	Nucleus				373

You are viewing entries 3251 to 3300 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.