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
P36141 UniProt NPD GO	YK29_YEAST	Uncharacterized protein YKR049C	0.32	-	mit	0		mitochondrion [IDA]		1WPI	133
P53970 UniProt NPD GO	YNC4_YEAST	Uncharacterized protein YNL024C	0.32	+	cyt	0		cytoplasm [IDA]			246
Q9GK78 UniProt NPD GO	UPAR_MACFA	Urokinase plasminogen activator surface receptor precursor (uPAR) (U-PAR)	0.32	-	exc	0	Cell membrane; lipid-anchor; GPI-anchor (By similarity)				335
Q9UK41 UniProt NPD GO	VPS28_HUMAN	VPS28 protein homolog	0.32	-	cyt	0		cytosol [IDA] endosome [IDA]			221
Q8C0E2 UniProt NPD GO	VP26B_MOUSE	Vacuolar protein sorting 26B (Vesicle protein sorting 26B)	0.32	-	cyt	0	Cytoplasm. Membrane; peripheral membrane protein. Does not localize to endosomes				336
Q7ZV03 UniProt NPD GO	V26BA_BRARE	Vacuolar protein sorting 26B-A (Vesicle protein sorting 26B-A)	0.32	-	cyt	0	Cytoplasm. Membrane; peripheral membrane protein. Does not localize to endosomes (By similarity)				331
Q86VN1 UniProt NPD GO	VPS36_HUMAN	Vacuolar protein sorting protein 36 (ELL-associated protein of 45 kDa)	0.32	-	cyt	0	Cytoplasm. Endosome; late endosome. Colocalizes with ubiquitinated proteins on late endosomes. Nucle ...				386
O13954 UniProt NPD GO	YEHD_SCHPO	Very hypothetical protein C23H4.13c in chromosome I	0.32	-	nuc	1 *					184
O75396 UniProt NPD GO	SC22B_HUMAN	Vesicle-trafficking protein SEC22b (SEC22 vesicle-trafficking protein-like 1)	0.32	-	nuc	1	Membrane; single-pass type IV membrane protein (Probable)	ER-Golgi intermediate compartment [IDA]	604029		214
O08547 UniProt NPD GO	SC22B_MOUSE	Vesicle-trafficking protein SEC22b (SEC22 vesicle-trafficking protein-like 1)	0.32	-	nuc	1	Membrane; single-pass type IV membrane protein (Probable)	endoplasmic reticulum membrane [IDA] Golgi membrane [IDA]		1IFQ	214
Q5RAI9 UniProt NPD GO	SC22B_PONPY	Vesicle-trafficking protein SEC22b (SEC22 vesicle-trafficking protein-like 1)	0.32	-	nuc	1	Membrane; single-pass type IV membrane protein (Probable)				214
P02856 UniProt NPD GO	VCL1_PEA	Vicilin, 14 kDa component	0.32	-	nuc	0	Protein body. Vacuole. Cotyledonary membrane-bound vacuolar protein bodies				124
P53813 UniProt NPD GO	PROS_RAT	Vitamin K-dependent protein S precursor	0.32	-	mit	0	Secreted protein				675
Q13303 UniProt NPD GO	KCAB2_HUMAN	Voltage-gated potassium channel subunit beta-2 (K(+) channel subunit beta-2) (Kv-beta-2) (HKvbeta2)	0.32	-	nuc	0	Cytoplasm (Potential)		601142	1ZSX	367
Q2KIY3 UniProt NPD GO	WDFY1_BOVIN	WD repeat and FYVE domain-containing protein 1 (WD40- and FYVE domain-containing protein 1)	0.32	-	mit	0	Endosome; early endosome (By similarity)				410
Q9H7D7 UniProt NPD GO	WDR26_HUMAN	WD repeat protein 26	0.32	-	cyt	0					514
Q5XII5 UniProt NPD GO	WDR79_RAT	WD repeat protein 79	0.32	-	nuc	0					532
Q9UN42 UniProt NPD GO	AT1B4_HUMAN	X/potassium-transporting ATPase subunit beta-m (X,K-ATPase beta-m subunit)	0.32	-	nuc	1	Membrane; single-pass type II membrane protein (Potential)	integral to plasma membrane [TAS]			357
P47989 UniProt NPD GO	XDH_HUMAN	Xanthine dehydrogenase/oxidase [Includes: Xanthine dehydrogenase (EC 1.17.1.4) (XD); Xanthine oxidas ...	0.32	-	cyt	0	Peroxisome		607633		1332
O65493 UniProt NPD GO	XCP1_ARATH	Xylem cysteine proteinase 1 precursor (EC 3.4.22.-) (AtXCP1)	0.32	-	exc	0	Vacuole. Predominantly. Cell membrane. May be associated to plasma membrane				355
P06674 UniProt NPD GO	ZEA3_MAIZE	Zein-alpha 19A2 precursor (19 kDa zein 19A2) (Fragment)	0.32	-	exc	0					230
P24450 UniProt NPD GO	ZEAD_MAIZE	Zein-alpha PMS2 precursor (19 kDa zein PMS2)	0.32	-	exc	1 *					233
Q84W91 UniProt NPD GO	ZFNL1_ARATH	Zinc finger CCCH domain-containing protein ZFN-like 1	0.32	-	nuc	0	Nucleus (By similarity)				468
Q8VCM3 UniProt NPD GO	ZFY21_MOUSE	Zinc finger FYVE domain-containing protein 21	0.32	-	mit	0					234
Q9QY66 UniProt NPD GO	ZNHI2_MOUSE	Zinc finger HIT domain-containing protein 2 (Protein FON)	0.32	-	cyt	0					399
Q96E35 UniProt NPD GO	ZMY19_HUMAN	Zinc finger MYND domain-containing protein 19 (Melanin-concentrating hormone receptor 1-interacting ...	0.32	-	cyt	0	Cytoplasm. Cell membrane; peripheral membrane protein				227
Q9CQG3 UniProt NPD GO	ZMY19_MOUSE	Zinc finger MYND domain-containing protein 19 (Melanin-concentrating hormone receptor 1-interacting ...	0.32	-	cyt	0	Cytoplasm (By similarity). Cell membrane; peripheral membrane protein (By similarity)	cytoplasm [IDA] synaptosome [IDA]			227
Q7TSV3 UniProt NPD GO	ZMY19_RAT	Zinc finger MYND domain-containing protein 19 (Melanin-concentrating hormone receptor 1-interacting ...	0.32	-	cyt	0	Cytoplasm (By similarity). Cell membrane; peripheral membrane protein (By similarity)				227
Q4U5R4 UniProt NPD GO	ZN313_BOVIN	Zinc finger protein 313	0.32	-	nuc	0					230
P16372 UniProt NPD GO	ZFP58_MOUSE	Zinc finger protein 58 (Zfp-58) (Zinc finger protein Mfg-1) (Fragment)	0.32	-	nuc	0	Nucleus (Probable)				169
Q8L7N8 UniProt NPD GO	ZFN3_ARATH	Zinc finger type domain-containing protein ZFN3	0.32	-	nuc	0	Nucleus (By similarity)				375
P55113 UniProt NPD GO	NAS7_CAEEL	Zinc metalloproteinase nas-7 precursor (EC 3.4.24.21) (Nematode astacin 7)	0.32	-	nuc	0	Secreted protein (Potential)				382
O13724 UniProt NPD GO	ZPR1_SCHPO	Zinc-finger protein zpr1	0.32	-	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity). Translocates to the nucleus after nutrient stimu ...				459
Q9BH10 UniProt NPD GO	ZP2_BOVIN	Zona pellucida sperm-binding protein 2 precursor (Zona pellucida glycoprotein ZP2) (Zona pellucida p ...	0.32	-	nuc	1	Cell membrane; single-pass type I membrane protein. Processed form: Secreted protein; extracellular ...				713
P47983 UniProt NPD GO	ZP2_CANFA	Zona pellucida sperm-binding protein 2 precursor (Zona pellucida glycoprotein ZP2) (Zona pellucida p ...	0.32	-	end	1 *	Cell membrane; single-pass type I membrane protein. Processed form: Secreted protein; extracellular ...				715
Q2KJG8 UniProt NPD GO	BCKD_BOVIN	[3-methyl-2-oxobutanoate dehydrogenase [lipoamide]] kinase, mitochondrial precursor (EC 2.7.11.4) (B ...	0.32	-	nuc	0	Mitochondrion; mitochondrial matrix (By similarity)				412
Q64536 UniProt NPD GO	PDK2_RAT	[Pyruvate dehydrogenase [lipoamide]] kinase isozyme 2, mitochondrial precursor (EC 2.7.11.2) (Pyruva ...	0.32	-	mit	0	Mitochondrion; mitochondrial matrix			1JM6	407
O88484 UniProt NPD GO	PDP2_RAT	[Pyruvate dehydrogenase [lipoamide]]-phosphatase 2, mitochondrial precursor (EC 3.1.3.43) (PDP 2) (P ...	0.32	-	mit	0	Mitochondrion; mitochondrial matrix	pyruvate dehydrogenase (lipoamide) phosphat... [TAS]			530
P06245 UniProt NPD GO	KAPB_YEAST	cAMP-dependent protein kinase type 2 (EC 2.7.11.11) (PKA 2)	0.32	-	cyt	0		cAMP-dependent protein kinase complex [IMP] cytoplasm [TAS]			380
Q9Z0Z0 UniProt NPD GO	KGP1B_MOUSE	cGMP-dependent protein kinase 1, beta isozyme (EC 2.7.11.12) (cGK 1 beta) (cGKI-beta)	0.32	-	cyt	0		Golgi apparatus [IDA]			686
Q9HGN3 UniProt NPD GO	TLG1_SCHPO	t-SNARE affecting a late Golgi compartment protein 1 (Syntaxin tlg1)	0.32	-	nuc	1	Golgi apparatus; trans-Golgi network; trans-Golgi network membrane; single-pass type IV membrane pro ...				225
Q9Z120 UniProt NPD GO	TRMB_MOUSE	tRNA (guanine-N(7)-)-methyltransferase (EC 2.1.1.33) (tRNA(m7G46)-methyltransferase) (Methyltransfer ...	0.32	-	nuc	0					268
P53167 UniProt NPD GO	PUS2_YEAST	tRNA pseudouridine synthase 2 (EC 5.4.99.-) (tRNA-uridine isomerase 2) (tRNA pseudouridylate synthas ...	0.32	-	cyt	0	Nucleus				370
Q7ZWS1 UniProt NPD GO	DUS3L_XENLA	tRNA-dihydrouridine synthase 3-like (EC 1.-.-.-)	0.32	+	cyt	0					640
P93665 UniProt NPD GO	DCS1_GOSHI	(+)-delta-cadinene synthase (EC 4.2.3.13) (D-cadinene synthase)	0.31	-	cyt	0					554
Q8GXU8 UniProt NPD GO	LPAT1_ARATH	1-acyl-sn-glycerol-3-phosphate acyltransferase 1, chloroplast precursor (EC 2.3.1.51) (Lysophosphati ...	0.31	-	end	2	Plastid; chloroplast; chloroplast membrane; multi-pass membrane protein				356
Q5ZLQ6 UniProt NPD GO	1433B_CHICK	14-3-3 protein beta/alpha	0.31	-	nuc	0	Cytoplasm (By similarity)				244
P35213 UniProt NPD GO	1433B_RAT	14-3-3 protein beta/alpha (Protein kinase C inhibitor protein 1) (KCIP-1) (Prepronerve growth factor ...	0.31	-	nuc	0	Cytoplasm				245
P29307 UniProt NPD GO	1433_OENHO	14-3-3-like protein	0.31	-	nuc	0					260
O88685 UniProt NPD GO	PRS6A_MOUSE	26S protease regulatory subunit 6A (TAT-binding protein 1) (TBP-1)	0.31	-	cyt	0	Cytoplasm (Potential). Nucleus (Potential)				442

You are viewing entries 39051 to 39100 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.