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
Q9M5P8 UniProt NPD GO	SNAA_SOLTU	Alpha-soluble NSF attachment protein (Alpha-SNAP) (N-ethylmaleimide-sensitive factor attachment prot ...	0.04	-	cyt	0	Membrane; peripheral membrane protein (By similarity)				288
Q9SPE6 UniProt NPD GO	SNAA2_ARATH	Alpha-soluble NSF attachment protein 2 (Alpha-SNAP2) (N-ethylmaleimide-sensitive factor attachment p ...	0.04	-	cyt	0	Membrane; peripheral membrane protein (By similarity)				289
Q41224 UniProt NPD GO	AOX1_TOBAC	Alternative oxidase 1, mitochondrial precursor (EC 1.-.-.-)	0.04	-	mit	0	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein (Probable). Mitochondrial, ...				353
O22049 UniProt NPD GO	AOX2_ARATH	Alternative oxidase 2, mitochondrial precursor (EC 1.-.-.-)	0.04	-	mit	0	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein (Probable). Mitochondrial, ...				353
Q8LEE7 UniProt NPD GO	AOX3_ARATH	Alternative oxidase 3, mitochondrial precursor (EC 1.-.-.-)	0.04	-	mit	2	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein (Probable). Mitochondrial, ...				318
Q9P959 UniProt NPD GO	AOX_EMENI	Alternative oxidase, mitochondrial precursor (EC 1.-.-.-)	0.04	-	mit	1	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein; matrix side (By similarity ...				354
Q95165 UniProt NPD GO	SCNNB_CANFA	Amiloride-sensitive sodium channel subunit beta (Epithelial Na+ channel subunit beta) (Beta ENaC) (N ...	0.04	-	nuc	0	Cell membrane; apical cell membrane; multi-pass membrane protein (By similarity). Apical membrane of ...				88
P58028 UniProt NPD GO	AOFB_CAVPO	Amine oxidase [flavin-containing] B (EC 1.4.3.4) (Monoamine oxidase type B) (MAO-B)	0.04	-	end	0	Mitochondrion; mitochondrial outer membrane				519
P32454 UniProt NPD GO	APE2_YEAST	Aminopeptidase 2 (EC 3.4.11.-) (Aminopeptidase II) (AP-II) (YscII)	0.04	-	cyt	0		cytoplasm [NAS] mitochondrion [IDA] periplasmic space (sensu Fungi) [NAS]			844
Q9UT86 UniProt NPD GO	APC11_SCHPO	Anaphase-promoting complex subunit 11 (20S cyclosome/APC complex protein apc11)	0.04	-	nuc	0		anaphase-promoting complex [IDA]			94
O04795 UniProt NPD GO	PERA_IPOBA	Anionic peroxidase precursor (EC 1.11.1.7) (SwPA1)	0.04	-	exc	0	Secreted protein (By similarity)				364
Q8WXK1 UniProt NPD GO	ASB15_HUMAN	Ankyrin repeat and SOCS box protein 15 (ASB-15)	0.04	-	cyt	0					588
Q6TNT2 UniProt NPD GO	ANR46_BRARE	Ankyrin repeat domain-containing protein 46	0.04	-	nuc	1	Membrane; single-pass membrane protein (Potential)				228
Q99PE2 UniProt NPD GO	ANRA2_MOUSE	Ankyrin repeat family A protein 2 (RFXANK-like 2)	0.04	-	cyt	0	Cytoplasm. Membrane; peripheral membrane protein	membrane fraction [IDA]			312
P19620 UniProt NPD GO	ANXA2_PIG	Annexin A2 (Annexin II) (Lipocortin II) (Calpactin I heavy chain) (Chromobindin-8) (p36) (Protein I) ...	0.04	-	nuc	0	Secreted protein; extracellular space; extracellular matrix; basement membrane. In the lamina beneat ...				91
Q43641 UniProt NPD GO	UFOG_SOLME	Anthocyanidin 3-O-glucosyltransferase (EC 2.4.1.115) (Flavonol 3-O-glucosyltransferase) (UDP-glucose ...	0.04	-	nuc	0					433
Q9S9P6 UniProt NPD GO	FORT_ARATH	Anthocyanidin 3-O-glucosyltransferase (EC 2.4.1.115) (Flavonol-3-O-rhamnosyltransferase) (UDP glucos ...	0.04	-	mit	0					453
P01530 UniProt NPD GO	TXAA_ANTXA	Anthopleurin-A (Toxin AP-A)	0.04	-	nuc	0	Secreted protein. Found in nematocyst			1AHL	49
P22971 UniProt NPD GO	LEC2_CYTSE	Anti-H(O) lectin II (CSA-II)	0.04	-	cyt	0					243
P07087 UniProt NPD GO	ALPS_TACTR	Anti-lipopolysaccharide factor (anti-LPS)	0.04	-	cyt	0					102
Q9BKJ0 UniProt NPD GO	SCN3_MESMA	Anti-neuroexcitation peptide 3 precursor (Anti-neuroexcitation peptide III) (ANEPIII) (Anti-epilepsy ...	0.04	-	exc	0	Secreted protein (By similarity)				85
P83141 UniProt NPD GO	AFP1L_MALPA	Antifungal protein 1 large subunit (CW-1) (Fragment)	0.04	-		0					15
P83652 UniProt NPD GO	ALO2_ACRLO	Antimicrobial peptide Alo-2	0.04	-	nuc	0	Secreted protein				34
Q8NIL3 UniProt NPD GO	AES1_SCHPO	Antisense-enhancing sequence 1 (AES factor 1)	0.04	-	cyt	0					296
Q40772 UniProt NPD GO	RIP2_PHYAM	Antiviral protein 2 precursor (EC 3.2.2.22) (PAP-II) (Ribosome-inactivating protein) (rRNA N-glycosi ...	0.04	-	exc	0				1LLN	310
P24476 UniProt NPD GO	RIP0_DIACA	Antiviral protein DAP-30 precursor (EC 3.2.2.22) (Ribosome-inactivating protein) (rRNA N-glycosidase ...	0.04	-	vac	0				1RL0	293
P21326 UniProt NPD GO	RIPP_MIRJA	Antiviral protein MAP precursor (EC 3.2.2.22) (Ribosome-inactivating protein) (rRNA N-glycosidase)	0.04	-	mit	0					278
Q03464 UniProt NPD GO	RIPA_PHYAM	Antiviral protein alpha precursor (EC 3.2.2.22) (PAP-alpha) (Ribosome-inactivating protein) (rRNA N- ...	0.04	-	exc	0	Cell wall			1APA	294
Q8MIQ5 UniProt NPD GO	APOA2_PANTR	Apolipoprotein A-II precursor (Apo-AII) (ApoA-II)	0.04	-	nuc	0	Secreted protein				100
Q03472 UniProt NPD GO	APOR_PIG	Apolipoprotein R precursor (Apo-R)	0.04	-	exc	0	Secreted protein				202
Q07812 UniProt NPD GO	BAXA_HUMAN	Apoptosis regulator BAX, membrane isoform alpha	0.04	-	end	1	Membrane; single-pass membrane protein		600040	1F16	192
Q00709 UniProt NPD GO	BCL2_CHICK	Apoptosis regulator Bcl-2	0.04	-	nuc	1	Mitochondrion; mitochondrial outer membrane; single-pass membrane protein. Nucleus; nuclear membrane ...				233
Q1RMX3 UniProt NPD GO	BCLW_BOVIN	Apoptosis regulator Bcl-W (Bcl-2-like 2 protein)	0.04	-	cyt	1	Mitochondrion; mitochondrial membrane; peripheral membrane protein (By similarity). Loosely associat ...				193
Q45T69 UniProt NPD GO	BCLW_CANFA	Apoptosis regulator Bcl-W (Bcl-2-like 2 protein)	0.04	-	cyt	1	Mitochondrion; mitochondrial membrane; peripheral membrane protein (By similarity). Loosely associat ...				193
Q92843 UniProt NPD GO	BCLW_HUMAN	Apoptosis regulator Bcl-W (Bcl-2-like 2 protein)	0.04	-	cyt	1	Mitochondrion; mitochondrial membrane; peripheral membrane protein. Loosely associated with the mito ...	cytoplasm [NAS]	601931	1ZY3	193
P70345 UniProt NPD GO	BCLW_MOUSE	Apoptosis regulator Bcl-W (Bcl-2-like 2 protein) (c98)	0.04	-	cyt	1	Mitochondrion; mitochondrial membrane; peripheral membrane protein (By similarity). Loosely associat ...				193
Q9BRQ8 UniProt NPD GO	AMID_HUMAN	Apoptosis-inducing factor-like mitochondrion-associated inducer of death (EC 1.-.-.-) (Apoptosis-ind ...	0.04	-	cyt	1 *	Cytoplasm. Mitochondrion; mitochondrial outer membrane	cytoplasm [IDA] cytosol [IDA] mitochondrial outer membrane [IDA] mitochondrion [IDA]	605159		373
P43287 UniProt NPD GO	PIP22_ARATH	Aquaporin PIP2.2 (Plasma membrane intrinsic protein 2b) (PIP2b) (TMP2b)	0.04	-	end	6 *	Cell membrane; multi-pass membrane protein				285
P30302 UniProt NPD GO	PIP23_ARATH	Aquaporin PIP2.3 (Plasma membrane intrinsic protein 2c) (PIP2c) (TMP2C) (RD28-PIP) (Water stress-ind ...	0.04	-	end	6 *	Cell membrane; multi-pass membrane protein				285
P55088 UniProt NPD GO	AQP4_MOUSE	Aquaporin-4 (AQP-4) (WCH4) (Mercurial-insensitive water channel) (MIWC)	0.04	-	end	6 *	Membrane; multi-pass membrane protein	integral to plasma membrane [TAS]			323
P47863 UniProt NPD GO	AQP4_RAT	Aquaporin-4 (AQP-4) (WCH4) (Mercurial-insensitive water channel) (MIWC)	0.04	-	end	6 *	Membrane; multi-pass membrane protein	integral to plasma membrane [IDA] membrane [IDA]		2D57	323
O14520 UniProt NPD GO	AQP7_HUMAN	Aquaporin-7 (AQP-7) (Aquaporin-7-like) (Aquaporin adipose) (AQPap)	0.04	-	end	6 *	Membrane; multi-pass membrane protein	integral to plasma membrane [TAS]	602974		342
P42256 UniProt NPD GO	ABNA_ASPNG	Arabinan endo-1,5-alpha-L-arabinosidase A precursor (EC 3.2.1.99) (Endo-1,5-alpha-L-arabinanase A) ( ...	0.04	-	cyt	0					321
P83692 UniProt NPD GO	GANA_THIHE	Arabinogalactan endo-1,4-beta-galactosidase (EC 3.2.1.89) (Endo-1,4-beta-galactanase) (Galactanase)	0.04	-	cyt	0		extraorganismal space [IC]		1HJU	332
P48842 UniProt NPD GO	GANA_ASPAC	Arabinogalactan endo-1,4-beta-galactosidase precursor (EC 3.2.1.89) (Endo-1,4-beta-galactanase) (Gal ...	0.04	-	exc	0				1FOB	350
P83184 UniProt NPD GO	AGPE_WHEAT	Arabinogalactan peptide	0.04	-		0					15
P83573 UniProt NPD GO	ARALB_ARAEL	Aralin B chain (Fragment)	0.04	-	nuc	0					26
P46637 UniProt NPD GO	ARGI1_ARATH	Arginase (EC 3.5.3.1)	0.04	-	mit	0					342
Q03305 UniProt NPD GO	RMT2_YEAST	Arginine N-methyltransferase 2 (EC 2.1.1.-)	0.04	-	cyt	0	Cytoplasm. Nucleus	cytoplasm [IDA] nucleus [IDA]			412
Q04728 UniProt NPD GO	ARGJ_YEAST	Arginine biosynthesis bifunctional protein ARG7, mitochondrial precursor (Extracellular matrix prote ...	0.04	-	mit	0	Mitochondrion; mitochondrial matrix	mitochondrial matrix [NAS]			441

You are viewing entries 76301 to 76350 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.