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
O45903 UniProt NPD GO	MECR1_CAEEL	Probable trans-2-enoyl-CoA reductase 1, mitochondrial precursor (EC 1.3.1.38)	0.19	-	mit	0	Mitochondrion (By similarity)				344
Q9SMP1 UniProt NPD GO	XTH11_ARATH	Probable xyloglucan endotransglucosylase/hydrolase protein 11 precursor (EC 2.4.1.207) (At-XTH11) (X ...	0.19	-	vac	0	Secreted protein; extracellular space; apoplast (Probable)				267
Q38910 UniProt NPD GO	XTH23_ARATH	Probable xyloglucan endotransglucosylase/hydrolase protein 23 precursor (EC 2.4.1.207) (At-XTH23) (X ...	0.19	-	exc	1 *	Secreted protein; extracellular space; apoplast (Probable)				286
P01148 UniProt NPD GO	GON1_HUMAN	Progonadoliberin-1 precursor (Progonadoliberin I) [Contains: Gonadoliberin-1 (Gonadoliberin I) (Lute ...	0.19	-	exc	0	Secreted protein	soluble fraction [TAS]	152760		92
Q9EP73 UniProt NPD GO	PDL1_MOUSE	Programmed cell death 1 ligand 1 precursor (Programmed death ligand 1) (PD-L1) (PDCD1 ligand 1) (B7 ...	0.19	-	end	1	Cell membrane; single-pass type I membrane protein (By similarity)				290
P40961 UniProt NPD GO	PHB1_YEAST	Prohibitin-1	0.19	-	cyt	0	Mitochondrion; mitochondrial inner membrane; peripheral membrane protein; intermembrane side	mitochondrial inner membrane [IDA] mitochondrion [IDA]			287
Q8SPN2 UniProt NPD GO	PKR1_BOVIN	Prokineticin receptor 1 (PK-R1) (G-protein coupled receptor 73) (G-protein coupled receptor ZAQ)	0.19	+	end	7	Membrane; multi-pass membrane protein				393
P81277 UniProt NPD GO	PRRP_HUMAN	Prolactin-releasing peptide precursor (PrRP) (Prolactin-releasing hormone) [Contains: Prolactin-rele ...	0.19	-	mit	1 *	Secreted protein		602663		87
Q8WN12 UniProt NPD GO	PRRP_SHEEP	Prolactin-releasing peptide precursor (PrRP) (Prolactin-releasing hormone) [Contains: Prolactin-rele ...	0.19	-	exc	1 *	Secreted protein				98
P18689 UniProt NPD GO	PRO1_DACGL	Prolamin alpha-1 (Fragment)	0.19	-	nuc	0					29
Q80W65 UniProt NPD GO	PCSK9_MOUSE	Proprotein convertase subtilisin/kexin type 9 precursor (EC 3.4.21.-) (Proprotein convertase PC9) (S ...	0.19	-	exc	1 *	Secreted protein	extracellular region [IDA]			694
Q9WV91 UniProt NPD GO	FPRP_MOUSE	Prostaglandin F2 receptor negative regulator precursor (Prostaglandin F2-alpha receptor regulatory p ...	0.19	-	end	1	Endoplasmic reticulum; endoplasmic reticulum membrane; single-pass type I membrane protein (By simil ...				879
Q63797 UniProt NPD GO	PSME1_RAT	Proteasome activator complex subunit 1 (Proteasome activator 28-alpha subunit) (PA28alpha) (PA28a) ( ...	0.19	-	cyt	0					249
P28062 UniProt NPD GO	PSB8_HUMAN	Proteasome subunit beta type 8 precursor (EC 3.4.25.1) (Proteasome component C13) (Macropain subunit ...	0.19	-	cyt	0	Cytoplasm (By similarity). Nucleus (By similarity)	proteasome complex (sensu Eukaryota) [TAS]	177046		276
Q9H386 UniProt NPD GO	CU116_HUMAN	Protein C21orf116	0.19	-	mit	0					69
P58622 UniProt NPD GO	CU015_HUMAN	Protein C21orf15 (Fragment)	0.19	-	nuc	0					110
Q5R9Q8 UniProt NPD GO	CF089_PONPY	Protein C6orf89 homolog	0.19	-	mit	1	Membrane; single-pass membrane protein (Potential)				347
P36034 UniProt NPD GO	COS9_YEAST	Protein COS9	0.19	-	end	4	Membrane; multi-pass membrane protein (Potential)				407
Q8CD54 UniProt NPD GO	FA38B_MOUSE	Protein FAM38B	0.19	-	end	8 *	Membrane; multi-pass membrane protein (Potential)				607
Q3ZCA1 UniProt NPD GO	FA84A_BOVIN	Protein FAM84A	0.19	-	cyt	0					297
Q8BI06 UniProt NPD GO	K1199_MOUSE	Protein KIAA1199 homolog precursor (Protein 12H19.01.T7)	0.19	-	mit	0					1361
Q9FML4 UniProt NPD GO	LOB_ARATH	Protein LATERAL ORGAN BOUNDARIES	0.19	-	nuc	0					186
Q12117 UniProt NPD GO	MRH1_YEAST	Protein MRH1 (Membrane protein related to HSP30)	0.19	-	end	7 *	Cell membrane; multi-pass membrane protein. Localized primarily to the plasma membrane. Mitochondrio ...	mitochondrion [IDA] plasma membrane [IDA]			320
P08593 UniProt NPD GO	MSS18_YEAST	Protein MSS18	0.19	-	cyt	0	Mitochondrion	mitochondrion [IDA]			268
Q7ZWV3 UniProt NPD GO	NDR1B_XENLA	Protein NDRG1-B (xNDRG1-B)	0.19	-	nuc	0					396
Q3ZBA8 UniProt NPD GO	NDRG2_BOVIN	Protein NDRG2	0.19	-	nuc	0	Cytoplasm (By similarity)				357
P27004 UniProt NPD GO	S10AA_XENLA	Protein S100-A10 (S100 calcium-binding protein A10) (Calpactin-1 light chain) (Calpactin I light cha ...	0.19	-	nuc	1					96
Q8GZA8 UniProt NPD GO	ULT1_ARATH	Protein ULTRAPETALA1	0.19	-	nuc	0	Cytoplasm. Nucleus				237
Q96X44 UniProt NPD GO	URE2_SACDO	Protein URE2	0.19	-	nuc	0					359
Q7LLZ8 UniProt NPD GO	URE2_SACPA	Protein URE2	0.19	-	nuc	0					359
Q9QXQ5 UniProt NPD GO	WNT4_RAT	Protein Wnt-4 precursor	0.19	-	gol	1 *	Secreted protein; extracellular space; extracellular matrix				351
Q9QXQ7 UniProt NPD GO	WNT5A_RAT	Protein Wnt-5a precursor	0.19	-	exc	0	Secreted protein; extracellular space; extracellular matrix				379
P28136 UniProt NPD GO	WNT5B_PLEJO	Protein Wnt-5b (Fragment)	0.19	-	nuc	0	Secreted protein; extracellular space; extracellular matrix				116
P28107 UniProt NPD GO	WNT9_ALOVU	Protein Wnt-9 (Fragment)	0.19	-	nuc	0	Secreted protein; extracellular space; extracellular matrix				120
Q12245 UniProt NPD GO	YP144_YEAST	Protein YPL144W	0.19	-	nuc	0	Cytoplasm	cytoplasm [IDA]			148
Q08245 UniProt NPD GO	ZEO1_YEAST	Protein ZEO1 (Zeocin resistance protein 1)	0.19	-	nuc	0	Cell membrane; peripheral membrane protein	extrinsic to plasma membrane [IDA] mitochondrial outer membrane [IDA] mitochondrion [IDA]			112
P29746 UniProt NPD GO	BNB_DROME	Protein bangles and beads	0.19	-	exc	0					442
O24304 UniProt NPD GO	PFTA_PEA	Protein farnesyltransferase/geranylgeranyltransferase type I alpha subunit (EC 2.5.1.58) (EC 2.5.1.5 ...	0.19	-	cyt	0					333
P68403 UniProt NPD GO	KPCB_RAT	Protein kinase C beta type (EC 2.7.11.13) (PKC-beta) (PKC-B)	0.19	-	cyt	0	Cytoplasm. Membrane; peripheral membrane protein			1A25	670
P05128 UniProt NPD GO	KPCG_BOVIN	Protein kinase C gamma type (EC 2.7.11.13) (PKC-gamma) (Fragment)	0.19	-	mit	0					682
Q9WVG7 UniProt NPD GO	OSR1_MOUSE	Protein odd-skipped-related 1	0.19	-	nuc	0	Nucleus (Potential)				266
Q9Y6C5 UniProt NPD GO	PTC2_HUMAN	Protein patched homolog 2 (PTC2)	0.19	-	end	11 *	Membrane; multi-pass membrane protein	integral to plasma membrane [TAS]	605462		1203
P25646 UniProt NPD GO	YCW9_YEAST	Protein phosphatase 2C-like protein YCR079W	0.19	-	nuc	0		mitochondrion [IDA]			442
Q9HE04 UniProt NPD GO	RHO5_SCHPO	Protein rho5	0.19	-	mit	0	Cell membrane; lipid-anchor; cytoplasmic side (Potential)	cell tip [IDA] plasma membrane [TAS]			200
Q9VIP8 UniProt NPD GO	VLS_DROME	Protein valois (MEP50 homolog)	0.19	-	cyt	0	Cytoplasm	cytoplasm [IDA]			367
Q26366 UniProt NPD GO	VG_DROME	Protein vestigial	0.19	-	nuc	0	Nucleus	nucleus [IDA]			453
Q27256 UniProt NPD GO	WHITE_ANOGA	Protein white	0.19	-	end	6	Membrane; multi-pass membrane protein				695
Q01841 UniProt NPD GO	TGM2_CHICK	Protein-glutamine gamma-glutamyltransferase 2 (EC 2.3.2.13) (Tissue transglutaminase) (TGase C) (TGC ...	0.19	-	mit	0					689
P56488 UniProt NPD GO	PAR1_PAPHA	Proteinase-activated receptor 1 precursor (PAR-1) (Thrombin receptor)	0.19	-	end	7	Membrane; multi-pass membrane protein				425
P57097 UniProt NPD GO	MERTK_RAT	Proto-oncogene tyrosine-protein kinase MER precursor (EC 2.7.10.1) (C-mer) (Receptor tyrosine kinase ...	0.19	-	end	1	Membrane; single-pass type I membrane protein (By similarity)				994

You are viewing entries 52301 to 52350 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.