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
P60048 UniProt NPD GO	PABP5_HYLLA	Polyadenylate-binding protein 5 (Poly(A)-binding protein 5) (PABP 5)	0.26	-	nuc	0	Cytoplasm (By similarity)				382
P60049 UniProt NPD GO	PABP5_PANTR	Polyadenylate-binding protein 5 (Poly(A)-binding protein 5) (PABP 5)	0.26	-	nuc	0	Cytoplasm (By similarity)				382
P60050 UniProt NPD GO	PABP5_PONPY	Polyadenylate-binding protein 5 (Poly(A)-binding protein 5) (PABP 5)	0.26	-	nuc	0	Cytoplasm (By similarity)				382
Q4I7X1 UniProt NPD GO	PFS2_GIBZE	Polyadenylation factor subunit 2	0.26	-	nuc	0	Nucleus (By similarity)				612
Q26458 UniProt NPD GO	ESC_DROVI	Polycomb protein esc (Protein extra sex combs)	0.26	-	cyt	0	Nucleus (Probable)	nuclear chromatin [ISS] nucleus [IDA]			425
P98161 UniProt NPD GO	PKD1_HUMAN	Polycystin-1 precursor (Autosomal dominant polycystic kidney disease protein 1)	0.26	-	end	10	Membrane; multi-pass membrane protein (Potential)	integral to plasma membrane [TAS]	173900	1B4R	4303
P01833 UniProt NPD GO	PIGR_HUMAN	Polymeric-immunoglobulin receptor precursor (Poly-Ig receptor) (PIGR) (Hepatocellular carcinoma-asso ...	0.26	-	end	1	Cell membrane; single-pass type I membrane protein. Processed form: Secreted protein	integral to plasma membrane [TAS]	173880	1XED	764
Q6WV20 UniProt NPD GO	GALT1_DROME	Polypeptide N-acetylgalactosaminyltransferase 1 (EC 2.4.1.41) (Protein-UDP acetylgalactosaminyltrans ...	0.26	-	mit	1 *	Golgi apparatus; Golgi membrane; single-pass type II membrane protein (By similarity)	Golgi stack [NAS]			601
Q00024 UniProt NPD GO	PPO1_AGABI	Polyphenol oxidase (EC 1.10.3.1) (PPO) (Catechol oxidase)	0.26	-	cyt	0					568
Q9DG25 UniProt NPD GO	POPD3_CHICK	Popeye domain-containing protein 3 (Popeye protein 3)	0.26	-	end	2 *	Membrane; multi-pass membrane protein (Potential)				305
Q9NYG8 UniProt NPD GO	KCNK4_HUMAN	Potassium channel subfamily K member 4 (TWIK-related arachidonic acid-stimulated potassium channel p ...	0.26	-	end	6 *	Membrane; multi-pass membrane protein (Potential)		605720		393
Q8W4I4 UniProt NPD GO	POT6_ARATH	Potassium transporter 6 (AtPOT6) (AtHAK6)	0.26	+	end	12 *	Cell membrane; multi-pass membrane protein (Potential)				782
Q09081 UniProt NPD GO	KCNA2_RABIT	Potassium voltage-gated channel subfamily A member 2 (Voltage-gated potassium channel subunit Kv1.2) ...	0.26	-	end	3	Membrane; multi-pass membrane protein				273
Q14003 UniProt NPD GO	KCNC3_HUMAN	Potassium voltage-gated channel subfamily C member 3 (Voltage-gated potassium channel subunit Kv3.3) ...	0.26	-	end	4	Membrane; multi-pass membrane protein	voltage-gated potassium channel complex [TAS]	176264		757
Q6C784 UniProt NPD GO	FIP1_YARLI	Pre-mRNA polyadenylation factor FIP1	0.26	-	nuc	0	Nucleus (By similarity)				221
Q06835 UniProt NPD GO	RDS3_YEAST	Pre-mRNA-splicing factor RDS3 (Regulator of drug sensitivity 3)	0.26	+	nuc	0	Nucleus	spliceosome complex [TAS]			107
P46988 UniProt NPD GO	PFD1_YEAST	Prefoldin subunit 1 (Genes involved in microtubule biogenesis protein 6) (Gim complex subunit 6) (Gi ...	0.26	-	nuc	0		prefoldin complex [IMP]			109
P53900 UniProt NPD GO	PFD4_YEAST	Prefoldin subunit 4 (Genes involved in microtubule biogenesis protein 3) (Gim complex subunit 3) (Gi ...	0.26	-	nuc	0		cytoplasm [IDA] prefoldin complex [IPI]			129
Q04493 UniProt NPD GO	PFD5_YEAST	Prefoldin subunit 5 (Genes involved in microtubule biogenesis protein 5) (Gim complex subunit 5) (Gi ...	0.26	-	nuc	0		cytoplasm [IDA] prefoldin complex [IPI]			163
Q15238 UniProt NPD GO	PSG5_HUMAN	Pregnancy-specific beta-1-glycoprotein 5 precursor (PSBG-5) (Fetal liver non-specific cross-reactive ...	0.26	-	nuc	0	Secreted protein (Potential)		176394		335
P38397 UniProt NPD GO	SECY_PYRSA	Preprotein translocase secY subunit (Fragment)	0.26	-	end	8 *	Plastid; chloroplast; chloroplast membrane; multi-pass membrane protein				412
Q6CFW6 UniProt NPD GO	PAM17_YARLI	Presequence translocated-associated motor subunit PAM17, mitochondrial precursor	0.26	-	mit	2	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein (By similarity)				185
Q58DI5 UniProt NPD GO	PPAC2_BOVIN	Presqualene diphosphate phosphatase (EC 3.1.3.-) (Phosphatidic acid phosphatase type 2 domain-contai ...	0.26	-	end	3	Membrane; multi-pass membrane protein (Potential)				289
P02889 UniProt NPD GO	PSD8_DICDI	Probable 26S proteasome non-ATPase regulatory subunit 8 (Vegetative cell protein X) (M4 protein)	0.26	-	nuc	0					263
Q5RBD4 UniProt NPD GO	DHX35_PONPY	Probable ATP-dependent RNA helicase DHX35 (EC 3.6.1.-) (DEAH box protein 35)	0.26	-	cyt	0					720
P51241 UniProt NPD GO	ABCX_PORPU	Probable ATP-dependent transporter ycf16	0.26	-	cyt	0	Plastid; chloroplast				251
Q84WJ2 UniProt NPD GO	PRI2_ARATH	Probable DNA primase large subunit (EC 2.7.7.-)	0.26	-	cyt	0					454
Q16538 UniProt NPD GO	GP162_HUMAN	Probable G-protein coupled receptor 162 (Gene-rich cluster gene A protein)	0.26	-	end	7 *	Membrane; multi-pass membrane protein (By similarity)				588
Q10904 UniProt NPD GO	YWO1_CAEEL	Probable G-protein coupled receptor AH9.1	0.26	-	end	7 *	Membrane; multi-pass membrane protein (Potential)				361
P34311 UniProt NPD GO	YKR5_CAEEL	Probable G-protein coupled receptor C06G4.5	0.26	+	end	7	Membrane; multi-pass membrane protein (Potential)				436
Q9VXD9 UniProt NPD GO	MTH1_DROME	Probable G-protein coupled receptor Mth-like 1 precursor (Protein methuselah-like 1)	0.26	-	end	6	Membrane; multi-pass membrane protein (Potential)				676
Q8SYV9 UniProt NPD GO	MTH14_DROME	Probable G-protein coupled receptor Mth-like 14 precursor (Protein methuselah-like 14)	0.26	-	end	7	Membrane; multi-pass membrane protein (Potential)				533
Q9VRN2 UniProt NPD GO	MTH2_DROME	Probable G-protein coupled receptor Mth-like 2 precursor (Protein methuselah-like 2)	0.26	-	end	7	Membrane; multi-pass membrane protein (Potential)				518
O61397 UniProt NPD GO	GALT7_CAEEL	Probable N-acetylgalactosaminyltransferase 7 (EC 2.4.1.-) (Protein-UDP acetylgalactosaminyltransfera ...	0.26	-	mit	1 *	Golgi apparatus; Golgi membrane; single-pass type II membrane protein (By similarity)				601
Q4R964 UniProt NPD GO	ALLC_MACFA	Probable allantoicase (EC 3.5.3.4) (Allantoate amidinohydrolase)	0.26	-	cyt	0					410
Q2RAS0 UniProt NPD GO	ACA5_ORYSA	Probable calcium-transporting ATPase 5, plasma membrane-type (EC 3.6.3.8) (Ca(2+)-ATPase isoform 5)	0.26	-	end	8	Membrane; multi-pass membrane protein (By similarity)				1017
Q9SZR0 UniProt NPD GO	CHMO_ARATH	Probable choline monooxygenase, chloroplast precursor (EC 1.14.15.7)	0.26	-	cyt	0	Plastid; chloroplast; chloroplast stroma (By similarity)				422
Q9VB31 UniProt NPD GO	C6A18_DROME	Probable cytochrome P450 6a18 (EC 1.14.-.-) (CYPVIA18)	0.26	-	mit	1 *	Endoplasmic reticulum; endoplasmic reticulum membrane; peripheral membrane protein (Potential)				507
Q9VRI9 UniProt NPD GO	CP6T1_DROME	Probable cytochrome P450 6t1 (EC 1.14.-.-) (CYPVIT1)	0.26	-	end	1 *	Endoplasmic reticulum; endoplasmic reticulum membrane; peripheral membrane protein (Potential)				529
Q9VG82 UniProt NPD GO	CP9F2_DROME	Probable cytochrome P450 9f2 (EC 1.14.-.-) (CYPIXF2)	0.26	-	end	0	Endoplasmic reticulum; endoplasmic reticulum membrane; peripheral membrane protein (Potential)				516
O94681 UniProt NPD GO	ODO2_SCHPO	Probable dihydrolipoyllysine-residue succinyltransferase component of 2-oxoglutarate dehydrogenase c ...	0.26	-	mit	0	Mitochondrion (By similarity)				452
Q9FG90 UniProt NPD GO	DRL33_ARATH	Probable disease resistance protein At5g43740	0.26	-	nuc	0					862
P78795 UniProt NPD GO	IF34_SCHPO	Probable eukaryotic translation initiation factor 3 RNA-binding subunit (eIF-3 RNA-binding subunit) ...	0.26	-	nuc	0					282
Q1S053 UniProt NPD GO	H2A3_MEDTR	Probable histone H2A.3	0.26	+	nuc	0	Nucleus (By similarity)				152
Q9T0G7 UniProt NPD GO	SUVH9_ARATH	Probable histone-lysine N-methyltransferase, H3 lysine-9 specific SUVH9 (EC 2.1.1.43) (Histone H3-K9 ...	0.26	-	cyt	0	Nucleus (By similarity). Associates with centromeric constitutive heterochromatin (By similarity)				650
P56174 UniProt NPD GO	ILB5_CAEEL	Probable insulin-like peptide beta-type 5 precursor	0.26	-	exc	0	Secreted protein (Potential)				112
P34275 UniProt NPD GO	IVD_CAEEL	Probable isovaleryl-CoA dehydrogenase (EC 1.3.99.10) (IVD)	0.26	-	mit	0					408
Q9VDV3 UniProt NPD GO	NUPL1_DROME	Probable nucleoporin Nup58	0.26	-	mit	0	Nucleus; nuclear envelope; nuclear pore complex (By similarity). Localizes to the nuclear pore compl ...	nuclear pore [ISS]			546
Q9SGE9 UniProt NPD GO	SYFB_ARATH	Probable phenylalanyl-tRNA synthetase beta chain (EC 6.1.1.20) (Phenylalanine--tRNA ligase beta chai ...	0.26	-	cyt	0	Cytoplasm (By similarity)				598
Q10270 UniProt NPD GO	MET16_SCHPO	Probable phosphoadenosine phosphosulfate reductase (EC 1.8.4.8) (PAPS reductase, thioredoxin depende ...	0.26	-	cyt	0					266

You are viewing entries 44501 to 44550 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.