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
Q63969 UniProt NPD GO	A1AT_MUSSA	Alpha-1-antiproteinase precursor (Alpha-1-antitrypsin) (Alpha-1-proteinase inhibitor)	0.06	-	end	0	Secreted protein (By similarity)				413
O54760 UniProt NPD GO	ALSI_TAMSI	Alpha-1-antitrypsin-like protein CM55-SI precursor	0.06	-	end	0					413
P20848 UniProt NPD GO	A1ATR_HUMAN	Alpha-1-antitrypsin-related protein precursor	0.06	-	vac	0			107410		420
P35348 UniProt NPD GO	ADA1A_HUMAN	Alpha-1A adrenergic receptor (Alpha 1A-adrenoceptor) (Alpha 1A-adrenoreceptor) (Alpha-1C adrenergic ...	0.06	-	end	7 *	Membrane; multi-pass membrane protein	integral to plasma membrane [TAS]	104221		466
O76284 UniProt NPD GO	AMYR_DROBC	Alpha-amylase-related protein precursor (EC 3.2.1.1)	0.06	-	cyt	0	Secreted protein (Probable)				494
Q9NJP0 UniProt NPD GO	AMYR_DROEL	Alpha-amylase-related protein precursor (EC 3.2.1.1)	0.06	-	cyt	0	Secreted protein (Probable)				493
Q9GQV3 UniProt NPD GO	AMYR_DROJA	Alpha-amylase-related protein precursor (EC 3.2.1.1)	0.06	-	cyt	0	Secreted protein (Probable)				494
O77013 UniProt NPD GO	AMYR_DROKI	Alpha-amylase-related protein precursor (EC 3.2.1.1)	0.06	-	cyt	0	Secreted protein (Probable)				494
O76459 UniProt NPD GO	AMYR_DROSR	Alpha-amylase-related protein precursor (EC 3.2.1.1)	0.06	-	cyt	0	Secreted protein (Probable)				494
O77018 UniProt NPD GO	AMYR_DROTK	Alpha-amylase-related protein precursor (EC 3.2.1.1)	0.06	-	nuc	0	Secreted protein (Probable)				493
P60274 UniProt NPD GO	CXAD_CONGE	Alpha-conotoxin GID	0.06	-		0	Secreted protein			1MTQ	19
O22874 UniProt NPD GO	EXPA8_ARATH	Alpha-expansin 8 precursor (AtEXPA8) (At-EXP8) (AtEx8) (Ath-ExpAlpha-1.11)	0.06	-	vac	0	Cell wall; peripheral membrane protein				253
Q9UUZ4 UniProt NPD GO	AGALC_ASPNG	Alpha-galactosidase C precursor (EC 3.2.1.22) (Melibiase)	0.06	-	cyt	0					747
Q02751 UniProt NPD GO	MALT_CANAL	Alpha-glucosidase (EC 3.2.1.20) (Maltase)	0.06	-	cyt	0					569
Q43763 UniProt NPD GO	AGLU_HORVU	Alpha-glucosidase precursor (EC 3.2.1.20) (Maltase)	0.06	-	exc	0					877
Q12558 UniProt NPD GO	AGLU_ASPOR	Alpha-glucosidase precursor (EC 3.2.1.20) (Maltase) (AGL)	0.06	-	exc	0					985
Q99024 UniProt NPD GO	AGUA_TRIRE	Alpha-glucuronidase precursor (EC 3.2.1.139) (Alpha-glucosiduronase) (GLRI)	0.06	-	exc	1 *	Secreted protein				847
Q9XZK7 UniProt NPD GO	CXA2_CONTE	Alpha-type conotoxin Tx2 precursor	0.06	-	mit	1 *	Secreted protein				66
Q39219 UniProt NPD GO	AOX1A_ARATH	Alternative oxidase 1a, mitochondrial precursor (EC 1.-.-.-)	0.06	-	mit	0	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein (Probable). Mitochondrial, ...				354
Q40578 UniProt NPD GO	AOX2_TOBAC	Alternative oxidase 2, mitochondrial precursor (EC 1.-.-.-)	0.06	-	cyt	0	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein (Probable). Mitochondrial, ...				297
P34054 UniProt NPD GO	INDA1_TRIAT	Amino-acid permease inda1	0.06	-	end	11	Membrane; multi-pass membrane protein				573
Q8WSV0 UniProt NPD GO	ANDP_DROOR	Andropin precursor	0.06	-	exc	1 *	Secreted protein	extracellular region [ISS]			67
Q10715 UniProt NPD GO	ACE_HAEIE	Angiotensin-converting enzyme precursor (EC 3.4.15.1) (Dipeptidyl carboxypeptidase I) (Kininase II)	0.06	-	mit	0	Secreted protein; extracellular space (Probable)				611
Q8WXH4 UniProt NPD GO	ASB11_HUMAN	Ankyrin repeat and SOCS box protein 11 (ASB-11)	0.06	-	nuc	1 *					323
Q3SX00 UniProt NPD GO	ANR46_BOVIN	Ankyrin repeat domain-containing protein 46	0.06	-	nuc	1	Membrane; single-pass membrane protein (Potential)				228
Q76K24 UniProt NPD GO	ANR46_RAT	Ankyrin repeat domain-containing protein 46 (Ankyrin repeat small protein) (ANK-S)	0.06	-	nuc	1	Membrane; single-pass membrane protein (Potential)				228
Q9H9E1 UniProt NPD GO	ANRA2_HUMAN	Ankyrin repeat family A protein 2 (RFXANK-like 2)	0.06	-	cyt	0	Cytoplasm (By similarity). Membrane; peripheral membrane protein (By similarity)	cytosol [IDA] membrane [IDA]	605787		313
O82106 UniProt NPD GO	ZM33_MAIZE	Anther-specific protein MZm3-3 precursor	0.06	-	exc	1 *					109
P14726 UniProt NPD GO	UFOG_HORVU	Anthocyanidin 3-O-glucosyltransferase (EC 2.4.1.115) (Flavonol 3-O-glucosyltransferase) (UDP-glucose ...	0.06	-	cyt	0					455
P07285 UniProt NPD GO	TRPD_YEAST	Anthranilate phosphoribosyltransferase (EC 2.4.2.18)	0.06	-	cyt	0		cytoplasm [IDA] nucleus [IDA]			380
P22973 UniProt NPD GO	LEC2_ULEEU	Anti-H(O) lectin 2 (Anti-H(O) lectin II) (UEA-II)	0.06	-	cyt	0				1QNW	249
P83651 UniProt NPD GO	ALO1_ACRLO	Antimicrobial peptide Alo-1	0.06	-	nuc	0	Secreted protein				34
P81569 UniProt NPD GO	DEFD4_SPIOL	Antimicrobial peptide D4 (So-D4) (Defensin D4) (Fragment)	0.06	-	nuc	0	Cell wall				23
P81568 UniProt NPD GO	DEFD5_SPIOL	Antimicrobial peptide D5 (So-D5) (Defensin D5) (Fragment)	0.06	-	nuc	0	Cell wall				24
P80391 UniProt NPD GO	AMP1_MELGA	Antimicrobial peptide THP1 precursor (Turkey heterophil peptide 1)	0.06	-	end	1 *	Secreted protein				65
P56928 UniProt NPD GO	ENA2_HORSE	Antimicrobial peptide eNAP-2 (Fragment)	0.06	-	nuc	0					46
O14977 UniProt NPD GO	AZIN1_HUMAN	Antizyme inhibitor 1 (AZI) (Ornithine decarboxylase antizyme inhibitor)	0.06	-	cyt	0			607909		448
Q5R7K3 UniProt NPD GO	AZIN1_PONPY	Antizyme inhibitor 1 (AZI) (Ornithine decarboxylase antizyme inhibitor)	0.06	-	cyt	0					448
Q63764 UniProt NPD GO	AZIN1_RAT	Antizyme inhibitor 1 (AZI) (Ornithine decarboxylase antizyme inhibitor)	0.06	-	cyt	0					448
P19034 UniProt NPD GO	APOC2_BOVIN	Apolipoprotein C-II (Apo-CII) (ApoC-II) [Contains: Apolipoprotein C-II short form]	0.06	-	cyt	0	Secreted protein				79
P18658 UniProt NPD GO	APOC2_MACFA	Apolipoprotein C-II precursor (Apo-CII) (ApoC-II)	0.06	-	exc	0	Secreted protein				101
Q05020 UniProt NPD GO	APOC2_MOUSE	Apolipoprotein C-II precursor (Apo-CII) (ApoC-II)	0.06	-	exc	0	Secreted protein				97
P27917 UniProt NPD GO	APOC3_PIG	Apolipoprotein C-III precursor (Apo-CIII) (ApoC-III)	0.06	-	exc	0	Secreted protein				96
P06759 UniProt NPD GO	APOC3_RAT	Apolipoprotein C-III precursor (Apo-CIII) (ApoC-III)	0.06	-	exc	0	Secreted protein				101
O02703 UniProt NPD GO	BAXA_BOVIN	Apoptosis regulator BAX, membrane isoform alpha	0.06	-	end	1	Membrane; single-pass membrane protein (By similarity)				192
Q63690 UniProt NPD GO	BAXA_RAT	Apoptosis regulator BAX, membrane isoform alpha	0.06	-	end	1	Membrane; single-pass membrane protein				192
Q9I9N6 UniProt NPD GO	ASC_BRARE	Apoptosis-associated speck-like protein containing a CARD (PYD and CARD domain-containing protein)	0.06	-	nuc	0	Cytoplasm				203
Q23808 UniProt NPD GO	AQP_CICVR	Aquaporin AQPcic	0.06	-	end	6 *	Membrane; multi-pass membrane protein				255
Q9WTY4 UniProt NPD GO	AQP5_MOUSE	Aquaporin-5 (AQP-5)	0.06	-	end	6 *	Membrane; multi-pass membrane protein	apical plasma membrane [IDA] basal plasma membrane [IDA] integral to plasma membrane [TAS] microvillus [IDA]			265
P47864 UniProt NPD GO	AQP5_RAT	Aquaporin-5 (AQP-5)	0.06	-	end	6 *	Membrane; multi-pass membrane protein	apical plasma membrane [IDA]			265

You are viewing entries 71551 to 71600 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.