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
P13557 UniProt NPD GO	HBB_TARSY	Hemoglobin subunit beta (Hemoglobin beta chain) (Beta-globin)	0.02	-	cyt	0					146
P04245 UniProt NPD GO	HBB_TRAST	Hemoglobin subunit beta (Hemoglobin beta chain) (Beta-globin)	0.02	-	cyt	0					145
P18990 UniProt NPD GO	HBB_TURTR	Hemoglobin subunit beta (Hemoglobin beta chain) (Beta-globin)	0.02	-	cyt	0					146
P18991 UniProt NPD GO	HBB1_UROHA	Hemoglobin subunit beta-1 (Hemoglobin beta-1 chain) (Beta-1-globin) (Fragments)	0.02	-	cyt	0					146
P02091 UniProt NPD GO	HBB1_RAT	Hemoglobin subunit beta-1 (Hemoglobin beta-1 chain) (Beta-1-globin) (Hemoglobin beta chain, major-fo ...	0.02	-	cyt	0					146
P68087 UniProt NPD GO	HBB1_CHAMP	Hemoglobin subunit beta-1 (Hemoglobin beta-1 chain) (Beta-1-globin) (Hemoglobin beta-I chain)	0.02	-	cyt	0					146
P02088 UniProt NPD GO	HBB1_MOUSE	Hemoglobin subunit beta-1 (Hemoglobin beta-1 chain) (Beta-1-globin) (Hemoglobin beta-major chain)	0.02	-	cyt	0		hemoglobin complex [IDA] mitochondrion [IDA]		1JEB	146
P02064 UniProt NPD GO	HBB1_TAPTE	Hemoglobin subunit beta-1 (Hemoglobin beta-1 chain) (Beta-1-globin) (Hemoglobin beta-major chain)	0.02	-	cyt	0					146
P10785 UniProt NPD GO	HBB1_TRICR	Hemoglobin subunit beta-1 (Hemoglobin beta-1 chain) (Beta-1-globin) (Hemoglobin beta-major chain)	0.02	-	cyt	0					145
P02057 UniProt NPD GO	HBB_RABIT	Hemoglobin subunit beta-1/2 (Hemoglobin beta-1/2 chain) (Beta-1/2-globin)	0.02	-	cyt	0					146
P84604 UniProt NPD GO	HBB2_ARCGL	Hemoglobin subunit beta-2 (Hemoglobin beta-2 chain) (Beta-2-globin)	0.02	-	cyt	0					146
Q1AGS6 UniProt NPD GO	HBB2_BORSA	Hemoglobin subunit beta-2 (Hemoglobin beta-2 chain) (Beta-2-globin)	0.02	-	cyt	0					146
P84611 UniProt NPD GO	HBB2_GADMO	Hemoglobin subunit beta-2 (Hemoglobin beta-2 chain) (Beta-2-globin)	0.02	-	cyt	0					146
P18988 UniProt NPD GO	HBB2_PANLE	Hemoglobin subunit beta-2 (Hemoglobin beta-2 chain) (Beta-2-globin)	0.02	-	cyt	0					146
P20247 UniProt NPD GO	HBB2_TORMA	Hemoglobin subunit beta-2 (Hemoglobin beta-2 chain) (Beta-2-globin)	0.02	-	cyt	0					142
Q7M2Y5 UniProt NPD GO	HBB2_CHAMP	Hemoglobin subunit beta-2 (Hemoglobin beta-2 chain) (Beta-2-globin) (Hemoglobin beta-II chain)	0.02	-	cyt	0					146
P02089 UniProt NPD GO	HBB2_MOUSE	Hemoglobin subunit beta-2 (Hemoglobin beta-2 chain) (Beta-2-globin) (Hemoglobin beta-minor chain)	0.02	-	cyt	0					146
P02065 UniProt NPD GO	HBB2_TAPTE	Hemoglobin subunit beta-2 (Hemoglobin beta-2 chain) (Beta-2-globin) (Hemoglobin beta-minor chain)	0.02	-	cyt	0					146
P04346 UniProt NPD GO	HBBA_BOSJA	Hemoglobin subunit beta-A (Hemoglobin beta-A chain) (Beta-A-globin)	0.02	-	cyt	0					145
Q9PVM2 UniProt NPD GO	HBBA_SERQU	Hemoglobin subunit beta-A (Hemoglobin beta-A chain) (Beta-A-globin)	0.02	-	cyt	0					147
Q5XLE5 UniProt NPD GO	HBD_AILME	Hemoglobin subunit delta (Hemoglobin delta chain) (Delta-globin)	0.02	-	cyt	0					146
P33499 UniProt NPD GO	HBD_ATEFU	Hemoglobin subunit delta (Hemoglobin delta chain) (Delta-globin)	0.02	-	cyt	0					146
P02044 UniProt NPD GO	HBD_ATEGE	Hemoglobin subunit delta (Hemoglobin delta chain) (Delta-globin)	0.02	-	cyt	0					146
P13558 UniProt NPD GO	HBD_TARSY	Hemoglobin subunit delta (Hemoglobin delta chain) (Delta-globin)	0.02	-	cyt	0					146
P14261 UniProt NPD GO	HBE_CAIMO	Hemoglobin subunit epsilon (Hemoglobin epsilon chain) (Epsilon-globin)	0.02	-	cyt	0					146
P51442 UniProt NPD GO	HBE_PITIR	Hemoglobin subunit epsilon (Hemoglobin epsilon chain) (Epsilon-globin)	0.02	-	cyt	0					146
P08054 UniProt NPD GO	HBP1_CASGL	Hemoglobin-1 (Hemoglobin I)	0.02	-	cyt	0					151
P80527 UniProt NPD GO	HGLB1_FASHE	Hemoglobinase-like protein 1 (EC 3.4.22.34) (Newly excysted juvenile protein 3) (Fragment)	0.02	-		0					20
P18651 UniProt NPD GO	FGF1_CANFA	Heparin-binding growth factor 1 (HBGF-1) (Acidic fibroblast growth factor) (aFGF) (Alpha-endothelial ...	0.02	-		0					15
Q801Y3 UniProt NPD GO	HEPC1_SALSA	Hepcidin-1 precursor	0.02	-	exc	1 *	Secreted protein				86
P60993 UniProt NPD GO	TX2_HETMC	Heteroscodratoxin-2 (HmTx2)	0.02	-	cyt	0	Secreted protein				38
Q17020 UniProt NPD GO	HEXA_ANOGA	Hexamerin 1.1 precursor (HEX-1.1)	0.02	-	cyt	0	Secreted protein; extracellular space (By similarity)				692
Q9NZJ6 UniProt NPD GO	COQ3_HUMAN	Hexaprenyldihydroxybenzoate methyltransferase, mitochondrial precursor (EC 2.1.1.114) (Dihydroxyhexa ...	0.02	-	mit	0	Mitochondrion; mitochondrial matrix (Probable)		605196		369
O74421 UniProt NPD GO	COQ3_SCHPO	Hexaprenyldihydroxybenzoate methyltransferase, mitochondrial precursor (EC 2.1.1.114) (Dihydroxyhexa ...	0.02	-	mit	0	Mitochondrion; mitochondrial matrix (Probable)				271
Q09756 UniProt NPD GO	HXK1_SCHPO	Hexokinase-1 (EC 2.7.1.1)	0.02	-	cyt	0					484
Q9SEK3 UniProt NPD GO	HXK1_SPIOL	Hexokinase-1 (EC 2.7.1.1) (SoHxK1)	0.02	-	nuc	1 *	Plastid; chloroplast; chloroplast outer membrane; single-pass membrane protein				498
Q9SQ76 UniProt NPD GO	HXK2_SOLTU	Hexokinase-2 (EC 2.7.1.1) (StHK2)	0.02	-	nuc	1 *	Plastid; chloroplast; chloroplast outer membrane; single-pass membrane protein (By similarity)				496
Q6Q8A5 UniProt NPD GO	HXK2_TOBAC	Hexokinase-2, chloroplast precursor (EC 2.7.1.1) (NtHxK2)	0.02	-	mit	0	Plastid; chloroplast; chloroplast stroma (Probable)				499
Q1WM15 UniProt NPD GO	HXK8_ORYSA	Hexokinase-8 (EC 2.7.1.1) (Hexokinase-4)	0.02	-	cyt	0					458
Q06575 UniProt NPD GO	HP20_TAMSI	Hibernation-associated plasma protein HP-20 precursor (Hibernator-specific blood complex, 20 kDa sub ...	0.02	-	end	0	Secreted protein				196
Q06576 UniProt NPD GO	HP25_TAMSI	Hibernation-associated plasma protein HP-25 precursor (Hibernator-specific blood complex, 25 kDa sub ...	0.02	-	exc	0	Secreted protein				215
Q06577 UniProt NPD GO	HP27_TAMSI	Hibernation-associated plasma protein HP-27 precursor (Hibernator-specific blood complex, 27 kDa sub ...	0.02	-	exc	0	Secreted protein				215
P20489 UniProt NPD GO	FCERA_MOUSE	High affinity immunoglobulin epsilon receptor alpha-subunit precursor (FcERI) (IgE Fc receptor, alph ...	0.02	-	end	1	Membrane; single-pass type I membrane protein	external side of plasma membrane [IDA] integral to plasma membrane [IDA] lipid raft [TAS]			250
Q8SPW1 UniProt NPD GO	FCERG_MACFA	High affinity immunoglobulin epsilon receptor gamma-subunit precursor (FceRI gamma) (IgE Fc receptor ...	0.02	-	end	1 *	Membrane; single-pass type I membrane protein (By similarity)				86
P13386 UniProt NPD GO	FCERB_RAT	High affinity immunoglobulin epsilon receptor subunit beta (FcERI) (IgE Fc receptor, subunit beta) ( ...	0.02	-	end	4	Membrane; multi-pass membrane protein				243
Q8UWF0 UniProt NPD GO	SC5A7_TORMA	High-affinity choline transporter 1	0.02	-	end	12 *	Membrane; multi-pass membrane protein (By similarity)	integral to membrane [NAS]			584
Q8BGY9 UniProt NPD GO	SC5A7_MOUSE	High-affinity choline transporter 1 (Solute carrier family 5 member 7) (Hemicholinium-3-sensitive ch ...	0.02	-	end	12 *	Membrane; multi-pass membrane protein (By similarity)	integral to membrane [NAS]			580
Q8CIA9 UniProt NPD GO	HIAL1_MOUSE	Hippocampus abundant transcript-like protein 1	0.02	-	end	12 *	Membrane; multi-pass membrane protein (Potential)				484
P28501 UniProt NPD GO	ITHA_HIRME	Hirudin I (Fragments)	0.02	-	cyt	0	Secreted protein			1WBG	65
P28502 UniProt NPD GO	ITHB_HIRME	Hirudin IA (Fragment)	0.02	-		0	Secreted protein				17

You are viewing entries 83851 to 83900 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.