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
Q925R7 UniProt NPD GO	GLT10_RAT	Polypeptide N-acetylgalactosaminyltransferase 10 (EC 2.4.1.41) (Protein-UDP acetylgalactosaminyltran ...	0.52	-	mit	1 *	Golgi apparatus; Golgi membrane; single-pass type II membrane protein (By similarity)				603
P17970 UniProt NPD GO	KCNAB_DROME	Potassium voltage-gated channel protein Shab	0.52	-	end	6	Membrane; multi-pass membrane protein	voltage-gated potassium channel complex [TAS]			985
P15385 UniProt NPD GO	KCNA4_RAT	Potassium voltage-gated channel subfamily A member 4 (Voltage-gated potassium channel subunit Kv1.4) ...	0.52	-	end	3	Membrane; multi-pass membrane protein	integral to plasma membrane [IDA]		1ZTO	655
O95259 UniProt NPD GO	KCNH1_HUMAN	Potassium voltage-gated channel subfamily H member 1 (Voltage-gated potassium channel subunit Kv10.1 ...	0.52	-	end	4	Membrane; multi-pass membrane protein	voltage-gated potassium channel complex [TAS]	603305		989
Q9UL51 UniProt NPD GO	HCN2_HUMAN	Potassium/sodium hyperpolarization-activated cyclic nucleotide-gated channel 2 (Brain cyclic nucleot ...	0.52	-	nuc	2	Membrane; multi-pass membrane protein	voltage-gated potassium channel complex [TAS]	602781		889
P39682 UniProt NPD GO	PRP39_YEAST	Pre-mRNA-processing protein PRP39	0.52	-	cyt	0	Nucleus	commitment complex [IGI] snRNP U1 [IDA]			629
Q6C9T0 UniProt NPD GO	SLU7_YARLI	Pre-mRNA-splicing factor SLU7	0.52	-	nuc	0	Nucleus (By similarity)				416
Q4WVF4 UniProt NPD GO	SYF1_ASPFU	Pre-mRNA-splicing factor syf1	0.52	-	cyt	0	Nucleus (By similarity)				839
P61759 UniProt NPD GO	PFD3_MOUSE	Prefoldin subunit 3 (Von Hippel-Lindau-binding protein 1) (VHL-binding protein 1) (VBP-1)	0.52	+	nuc	0	Cytoplasm. Nucleus. In complex with VHL can translocate to the nucleus	cytoplasm [TAS] nucleus [TAS]			196
Q55PU1 UniProt NPD GO	PAM17_CRYNE	Presequence translocated-associated motor subunit PAM17, mitochondrial precursor	0.52	-	mit	2	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein (By similarity)				217
Q4P983 UniProt NPD GO	PAM17_USTMA	Presequence translocated-associated motor subunit PAM17, mitochondrial precursor	0.52	-	mit	2	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein (By similarity)				232
Q9TLX1 UniProt NPD GO	ABCX_CYACA	Probable ATP-dependent transporter ycf16	0.52	-	cyt	0	Plastid; chloroplast				254
Q9S763 UniProt NPD GO	WRK45_ARATH	Probable WRKY transcription factor 45 (WRKY DNA-binding protein 45) (AT.I.24-4)	0.52	-	nuc	0	Nucleus (Probable)				147
Q9SKD9 UniProt NPD GO	WRK46_ARATH	Probable WRKY transcription factor 46 (WRKY DNA-binding protein 46)	0.52	-	nuc	0	Nucleus (Probable)				295
O74431 UniProt NPD GO	ATC9_SCHPO	Probable cation-transporting ATPase C1672.11c (EC 3.6.3.-)	0.52	-	end	10	Membrane; multi-pass membrane protein				1315
Q9V4T3 UniProt NPD GO	C4AD1_DROME	Probable cytochrome P450 4ad1 (EC 1.14.-.-) (CYPIVAD1)	0.52	-	nuc	1 *	Endoplasmic reticulum; endoplasmic reticulum membrane; peripheral membrane protein (Potential)				516
Q9C8F1 UniProt NPD GO	IF5Y_ARATH	Probable eukaryotic translation initiation factor 5-1 (eIF-5 1)	0.52	-	nuc	0					439
Q9VT53 UniProt NPD GO	INSL4_DROME	Probable insulin-like peptide 4 precursor (Insulin-related peptide) (DILP4) [Contains: Probable insu ...	0.52	-	exc	0	Secreted protein (Potential)	extracellular region [ISS]			134
Q4IMM0 UniProt NPD GO	SPC25_GIBZE	Probable kinetochore protein SPC25	0.52	-	nuc	0	Nucleus (By similarity). Associated with kinetochores (By similarity)				257
Q873B7 UniProt NPD GO	SPC25_NEUCR	Probable kinetochore protein spc-25	0.52	-	mit	0	Nucleus (By similarity). Associated with kinetochores (By similarity)				259
O19898 UniProt NPD GO	LIPB_CYACA	Probable lipoyltransferase (EC 2.3.1.-) (Lipoyl-[acyl-carrier protein]-protein -N-lipoyltransferase) ...	0.52	-	cyt	0	Plastid; chloroplast				214
P53966 UniProt NPD GO	KTR5_YEAST	Probable mannosyltransferase KTR5 (EC 2.4.1.131)	0.52	-	mit	1 *	Membrane; single-pass type II membrane protein (Probable)				522
Q8IZN3 UniProt NPD GO	ZDH14_HUMAN	Probable palmitoyltransferase ZDHHC14 (EC 2.3.1.-) (Zinc finger DHHC domain-containing protein 14) ( ...	0.52	-	nuc	4	Membrane; multi-pass membrane protein (Potential)				488
Q8VDZ4 UniProt NPD GO	ZDHC5_MOUSE	Probable palmitoyltransferase ZDHHC5 (EC 2.3.1.-) (Zinc finger DHHC domain-containing protein 5) (DH ...	0.52	-	mit	4 *	Membrane; multi-pass membrane protein (Potential)				715
O22165 UniProt NPD GO	RLP24_ARATH	Probable ribosome biogenesis protein RLP24	0.52	-	nuc	0	Nucleus; nucleolus (By similarity)				159
Q9W107 UniProt NPD GO	SYYM_DROME	Probable tyrosyl-tRNA synthetase, mitochondrial precursor (EC 6.1.1.1) (Tyrosine--tRNA ligase) (TyrR ...	0.52	-	mit	0	Mitochondrion (Potential)	mitochondrion [ISS]			464
O14737 UniProt NPD GO	PDCD5_HUMAN	Programmed cell death protein 5 (Protein TFAR19) (TF-1 cell apoptosis-related gene 19 protein)	0.52	-	nuc	0			604583	2CRU	124
Q62053 UniProt NPD GO	PE2R2_MOUSE	Prostaglandin E2 receptor, EP2 subtype (Prostanoid EP2 receptor) (PGE receptor, EP2 subtype)	0.52	-	end	7 *	Membrane; multi-pass membrane protein				362
P35408 UniProt NPD GO	PE2R4_HUMAN	Prostaglandin E2 receptor, EP4 subtype (Prostanoid EP4 receptor) (PGE receptor, EP4 subtype)	0.52	-	end	6 *	Membrane; multi-pass membrane protein	integral to membrane [TAS]	601586		488
Q5F3J5 UniProt NPD GO	PSME3_CHICK	Proteasome activator complex subunit 3 (Proteasome activator 28-gamma subunit) (PA28gamma) (PA28g) ( ...	0.52	-	cyt	0					254
Q5RFD3 UniProt NPD GO	PSME3_PONPY	Proteasome activator complex subunit 3 (Proteasome activator 28-gamma subunit) (PA28gamma) (PA28g) ( ...	0.52	-	cyt	0					254
P27091 UniProt NPD GO	60A_DROME	Protein 60A precursor (Protein glass bottom boat)	0.52	+	exc	1 *	Secreted protein (By similarity)				455
Q8S8M5 UniProt NPD GO	ABIL1_ARATH	Protein ABIL1 (Abl interactor-like protein 1) (AtABIL1)	0.52	-	nuc	0					298
Q2PG52 UniProt NPD GO	BEX1_MACFA	Protein BEX1 (Brain-expressed X-linked protein 1 homolog)	0.52	-	nuc	0	Nucleus. Cytoplasm. Shuttles between the cytoplasm and the nucleus (By similarity)				128
Q3MKQ2 UniProt NPD GO	BEX1_RAT	Protein BEX1 (Brain-expressed X-linked protein 1 homolog) (EG2RVC)	0.52	-	nuc	0	Nucleus. Cytoplasm. Shuttles between the cytoplasm and the nucleus. Predominantly nuclear				128
Q9HBH7 UniProt NPD GO	BEX1_HUMAN	Protein BEX1 (Brain-expressed X-linked protein 1)	0.52	-	nuc	0	Nucleus. Cytoplasm. Shuttles between the cytoplasm and the nucleus (By similarity)				125
Q3MKQ1 UniProt NPD GO	BEX2_RAT	Protein BEX2 (Brain-expressed X-linked protein 2 homolog)	0.52	-	nuc	0	Nucleus. Cytoplasm				129
Q3TZW7 UniProt NPD GO	BEX6_MOUSE	Protein BEX6 (Brain-expressed X-linked protein 6 homolog)	0.52	-	nuc	0	Cytoplasm				114
Q6C9G2 UniProt NPD GO	BFR2_YARLI	Protein BFR2	0.52	-	nuc	0	Nucleus; nucleolus (By similarity)				495
Q75E41 UniProt NPD GO	BRE4_ASHGO	Protein BRE4	0.52	-	end	8	Membrane; multi-pass membrane protein (Potential)				1053
Q8BGK9 UniProt NPD GO	CC018_MOUSE	Protein C3orf18 homolog	0.52	-	nuc	1	Membrane; single-pass membrane protein (Potential)				164
O36019 UniProt NPD GO	YEK7_SCHPO	Protein C4F10.07c in chromosome I	0.52	-	nuc	0	Nucleus; nucleolus				758
Q6ZRZ4 UniProt NPD GO	CI047_HUMAN	Protein C9orf47 precursor	0.52	-	nuc	0					202
Q08226 UniProt NPD GO	CRT10_YEAST	Protein CRT10 (Constitutive RNR transcription regulator 10)	0.52	-	cyt	0					957
Q12403 UniProt NPD GO	ERP3_YEAST	Protein ERP3 precursor	0.52	-	end	1	Endoplasmic reticulum; endoplasmic reticulum membrane; single-pass type I membrane protein (By simil ...				225
Q6IFS5 UniProt NPD GO	HSN2_HUMAN	Protein HSN2 precursor	0.52	-	nuc	0	Secreted protein (Potential)		608620		434
O60268 UniProt NPD GO	K0513_HUMAN	Protein KIAA0513	0.52	-	nuc	0					411
O60299 UniProt NPD GO	K0552_HUMAN	Protein KIAA0552	0.52	-	nuc	0					673
Q6C3B0 UniProt NPD GO	SEY1_YARLI	Protein SEY1	0.52	-	nuc	1	Membrane; multi-pass membrane protein (Potential)				938
Q12212 UniProt NPD GO	SIA1_YEAST	Protein SIA1 precursor	0.52	-	mit	0					622

You are viewing entries 23901 to 23950 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.