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
P27581 UniProt NPD GO	ADH2_DROAR	Alcohol dehydrogenase 2 (EC 1.1.1.1)	0.07	-	cyt	0					253
Q6XQ67 UniProt NPD GO	ADH5_SACPS	Alcohol dehydrogenase 5 (EC 1.1.1.1) (Alcohol dehydrogenase V)	0.07	-	cyt	0					351
P38113 UniProt NPD GO	ADH5_YEAST	Alcohol dehydrogenase 5 (EC 1.1.1.1) (Alcohol dehydrogenase V)	0.07	-	cyt	0		cytoplasm [IDA] nucleus [IDA]			351
P47895 UniProt NPD GO	AL1A3_HUMAN	Aldehyde dehydrogenase 1A3 (EC 1.2.1.5) (Aldehyde dehydrogenase 6) (Retinaldehyde dehydrogenase 3) ( ...	0.07	-	cyt	0	Cytoplasm (By similarity)		600463		512
Q9JHW9 UniProt NPD GO	AL1A3_MOUSE	Aldehyde dehydrogenase 1A3 (EC 1.2.1.5) (Aldehyde dehydrogenase 6) (Retinaldehyde dehydrogenase 3) ( ...	0.07	-	cyt	0	Cytoplasm				512
Q8K4D8 UniProt NPD GO	AL1A3_RAT	Aldehyde dehydrogenase 1A3 (EC 1.2.1.5) (Aldehyde dehydrogenase 6) (Retinaldehyde dehydrogenase 3) ( ...	0.07	-	cyt	0	Cytoplasm (By similarity)				512
P48448 UniProt NPD GO	AL3B2_HUMAN	Aldehyde dehydrogenase 3B2 (EC 1.2.1.5) (Aldehyde dehydrogenase 8)	0.07	-	cyt	0			601917		385
P12762 UniProt NPD GO	ALDH2_HORSE	Aldehyde dehydrogenase, mitochondrial (EC 1.2.1.3) (ALDH class 2) (ALDHI) (ALDH-E2)	0.07	-	cyt	0	Mitochondrion; mitochondrial matrix				500
P47738 UniProt NPD GO	ALDH2_MOUSE	Aldehyde dehydrogenase, mitochondrial precursor (EC 1.2.1.3) (ALDH class 2) (AHD-M1) (ALDHI) (ALDH-E ...	0.07	-	mit	0	Mitochondrion; mitochondrial matrix	mitochondrion [IDA]			519
P20000 UniProt NPD GO	ALDH2_BOVIN	Aldehyde dehydrogenase, mitochondrial precursor (EC 1.2.1.3) (ALDH class 2) (ALDHI) (ALDH-E2)	0.07	-	mit	0	Mitochondrion; mitochondrial matrix			1AG8	520
P27800 UniProt NPD GO	ALDX_SPOSA	Aldehyde reductase 1 (EC 1.1.1.2) (Aldehyde reductase I) (Alcohol dehydrogenase [NADP+]) (ALR)	0.07	-	cyt	0		cell [IDA]			322
O08782 UniProt NPD GO	ALD2_CRIGR	Aldose reductase-related protein 2 (EC 1.1.1.21) (AR) (Aldehyde reductase) (Aldo-keto reductase)	0.07	-	cyt	0	Cytoplasm (By similarity)			1C9W	315
P45377 UniProt NPD GO	ALD2_MOUSE	Aldose reductase-related protein 2 (EC 1.1.1.21) (AR) (Aldehyde reductase) (Fibroblast growth factor ...	0.07	-	cyt	0	Cytoplasm (By similarity)			1FRB	315
Q24238 UniProt NPD GO	APH4_DROME	Alkaline phosphatase 4 precursor (EC 3.1.3.1)	0.07	-	exc	0	Cell membrane; lipid-anchor; GPI-anchor (By similarity)				596
P05187 UniProt NPD GO	PPB1_HUMAN	Alkaline phosphatase, placental type precursor (EC 3.1.3.1) (PLAP-1) (Regan isozyme)	0.07	-	exc	0	Cell membrane; lipid-anchor; GPI-anchor		171800	2GLQ	535
Q9D099 UniProt NPD GO	APHC_MOUSE	Alkaline phytoceramidase (EC 3.5.1.-) (aPHC) (Alkaline ceramidase)	0.07	-	end	7 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (By similarity). ...				267
P42559 UniProt NPD GO	ALLS_MANSE	Allatostatin (Mas-AS)	0.07	-		0	Secreted protein				15
Q25641 UniProt NPD GO	CRPI_PERAM	Allergen Cr-PI precursor (Allergen Per a 3)	0.07	-	cyt	0	Secreted protein; extracellular space (By similarity)				685
Q96WK6 UniProt NPD GO	TPS1_ZYGRO	Alpha,alpha-trehalose-phosphate synthase [UDP-forming] (EC 2.4.1.15) (Trehalose-6-phosphate synthase ...	0.07	-	cyt	0					485
Q00217 UniProt NPD GO	TPSB_ASPNG	Alpha,alpha-trehalose-phosphate synthase [UDP-forming] 2 (EC 2.4.1.15) (Trehalose-6-phosphate syntha ...	0.07	-	cyt	0					480
Q8R2R3 UniProt NPD GO	P34_MOUSE	Alpha- and gamma-adaptin-binding protein p34	0.07	-	cyt	0					316
P38031 UniProt NPD GO	A1AT4_HORSE	Alpha-1-antiproteinase 4 (Alpha-1-antitrypsin 4) (Alpha-1-proteinase inhibitor 4) (SPI4) (Fragments) ...	0.07	-	cyt	0	Secreted protein				43
P26595 UniProt NPD GO	A1AT_MUSCR	Alpha-1-antiproteinase precursor (Alpha-1-antitrypsin) (Alpha-1-proteinase inhibitor) (AAT)	0.07	-	exc	1 *	Secreted protein				412
P32759 UniProt NPD GO	A1AT_CYPCA	Alpha-1-antitrypsin homolog precursor	0.07	-	mit	0	Secreted protein				372
P61648 UniProt NPD GO	SIA8F_PANTR	Alpha-2,8-sialyltransferase 8F (EC 2.4.99.-) (ST8Sia VI)	0.07	-	mit	1 *	Golgi apparatus; Golgi membrane; single-pass type II membrane protein (Potential)				398
P79019 UniProt NPD GO	AXHA_ASPNG	Alpha-L-arabinofuranosidase precursor (EC 3.2.1.55) (Arabinoxylan arabinofuranohydrolase)	0.07	-	exc	0	Secreted protein				332
Q9FXE5 UniProt NPD GO	FUCO2_ARATH	Alpha-L-fucosidase 2 precursor (EC 3.2.1.51) (Alpha-L-fucoside fucohydrolase 2) (Alpha-1,2-fucosidas ...	0.07	-	exc	0	Secreted protein; extracellular space; apoplast				372
P54802 UniProt NPD GO	ANAG_HUMAN	Alpha-N-acetylglucosaminidase precursor (EC 3.2.1.50) (N-acetyl-alpha-glucosaminidase) (NAG) [Contai ...	0.07	-	mit	0		lysosome [TAS]	609701		743
P01085 UniProt NPD GO	IAA1_WHEAT	Alpha-amylase inhibitor 0.19 (0.19 AI) (0.19 alpha-AI)	0.07	-	cyt	0	Secreted protein			1HSS	124
O18408 UniProt NPD GO	AMYR_DROME	Alpha-amylase-related protein precursor (EC 3.2.1.1)	0.07	-	cyt	0	Secreted protein (Probable)				493
Q7T3J2 UniProt NPD GO	NXLA_BUNCA	Alpha-bungarotoxin, isoform A31 precursor	0.07	-	nuc	0	Secreted protein				95
P60615 UniProt NPD GO	NXL1A_BUNMU	Alpha-bungarotoxin, isoform A31 precursor (Alpha-BTX A31) (BGTX A31) (Alpha-Bgt(A31)) (Long neurotox ...	0.07	-	nuc	0	Secreted protein			2BTX	95
P60616 UniProt NPD GO	NXL1V_BUNMU	Alpha-bungarotoxin, isoform V31 precursor (Alpha-BTX V31) (BGTX V31) (Alpha-Bgt(V31)) (Long neurotox ...	0.07	-	nuc	0	Secreted protein			1HC9	95
P01519 UniProt NPD GO	CXAA_CONGE	Alpha-conotoxin GIA [Contains: Alpha-conotoxin GI (G1)]	0.07	-		0	Secreted protein			1XGC	15
Q9FL76 UniProt NPD GO	EXP24_ARATH	Alpha-expansin 24 precursor (AtEXPA24) (At-EXP24) (AtEx24) (Ath-ExpAlpha-1.19)	0.07	-	mit	0	Cell wall; peripheral membrane protein				312
Q9LN94 UniProt NPD GO	EXPA7_ARATH	Alpha-expansin 7 precursor (AtEXPA7) (At-EXP7) (AtEx7) (Ath-ExpAlpha-1.26)	0.07	-	cyt	1 *	Cell wall; peripheral membrane protein				262
Q9LZ99 UniProt NPD GO	EXPA9_ARATH	Alpha-expansin 9 precursor (AtEXPA9) (At-EXP9) (AtEx9) (Ath-ExpAlpha-1.10)	0.07	-	mit	0	Cell wall; peripheral membrane protein				258
P41945 UniProt NPD GO	MEL2_YEAST	Alpha-galactosidase 2 precursor (EC 3.2.1.22) (Melibiase 2) (Alpha-D-galactoside galactohydrolase 2) ...	0.07	-	mit	0					471
O42814 UniProt NPD GO	AGUA_ASPTU	Alpha-glucuronidase precursor (EC 3.2.1.139) (Alpha-glucosiduronase)	0.07	-	exc	0	Secreted protein				841
P81646 UniProt NPD GO	LALBA_TACAC	Alpha-lactalbumin (Lactose synthase B protein)	0.07	-	cyt	0	Secreted protein				126
P08334 UniProt NPD GO	LALB1_HORSE	Alpha-lactalbumin A (Lactose synthase B protein)	0.07	-	cyt	0	Secreted protein				123
Q9PUB7 UniProt NPD GO	NXAH1_MICCO	Alpha-neurotoxin homolog 1 precursor	0.07	-	nuc	1 *	Secreted protein				78
Q9PRI1 UniProt NPD GO	NXAH7_MICCO	Alpha-neurotoxin homolog 7 precursor	0.07	-	nuc	1 *	Secreted protein				78
Q9XZK6 UniProt NPD GO	CXA1_CONTE	Alpha-type conotoxin Tx1 precursor	0.07	-	mit	1 *	Secreted protein				69
P22185 UniProt NPD GO	AOX1_SAUGU	Alternative oxidase, mitochondrial precursor (EC 1.-.-.-)	0.07	-	mit	0	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein (Probable). Mitochondrial, ...				349
O59942 UniProt NPD GO	AAP2_NEUCR	Amino acid permease 2	0.07	-	end	12	Membrane; multi-pass membrane protein (Probable)				541
Q9CSB4 UniProt NPD GO	PAR3L_MOUSE	Amyotrophic lateral sclerosis 2 chromosome region candidate gene 19 protein homolog (Partitioning-de ...	0.07	-	cyt	0	Intracytoplasmic membrane (By similarity). Cell membrane; cell-cell junction (By similarity). Partia ...				213
P01015 UniProt NPD GO	ANGT_RAT	Angiotensinogen precursor [Contains: Angiotensin-1 (Angiotensin I) (Ang I); Angiotensin-2 (Angiotens ...	0.07	-	exc	0	Secreted protein				477
Q502M6 UniProt NPD GO	ANR29_BRARE	Ankyrin repeat domain-containing protein 29	0.07	-	cyt	0					298
Q810N6 UniProt NPD GO	ANR45_MOUSE	Ankyrin repeat domain-containing protein 45	0.07	-	cyt	0					248

You are viewing entries 69501 to 69550 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.