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
P26532 UniProt NPD GO	ATPB_PYLLI	ATP synthase subunit beta (EC 3.6.3.14) (ATPase subunit beta) (ATP synthase F1 sector subunit beta)	0.05	-	mit	0	Plastid; chloroplast; chloroplast thylakoid membrane; peripheral membrane protein (By similarity)				481
P20858 UniProt NPD GO	ATPB_WHEAT	ATP synthase subunit beta (EC 3.6.3.14) (ATPase subunit beta) (ATP synthase F1 sector subunit beta)	0.05	-	cyt	0	Plastid; chloroplast; chloroplast thylakoid membrane; peripheral membrane protein (By similarity)				498
P19023 UniProt NPD GO	ATPBM_MAIZE	ATP synthase subunit beta, mitochondrial precursor (EC 3.6.3.14)	0.05	-	mit	0	Mitochondrion				553
P23704 UniProt NPD GO	ATPB_NEUCR	ATP synthase subunit beta, mitochondrial precursor (EC 3.6.3.14)	0.05	-	mit	0	Mitochondrion				519
Q5XIM4 UniProt NPD GO	ATP5S_RAT	ATP synthase subunit s, mitochondrial precursor (ATP synthase coupling factor B) (Mitochondrial ATP ...	0.05	-	cyt	0	Mitochondrion (By similarity)				200
Q9NP78 UniProt NPD GO	ABCB9_HUMAN	ATP-binding cassette sub-family B member 9 precursor (ATP-binding cassette transporter 9) (ABC trans ...	0.05	-	end	7 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (Probable). Lysos ...	ATP-binding cassette (ABC) transporter complex [NAS] integral to membrane [NAS]	605453		766
Q4R579 UniProt NPD GO	ATPBB_MACFA	ATP-binding domain 1 family member B	0.05	-	cyt	0					310
Q96IU4 UniProt NPD GO	AB14B_HUMAN	Abhydrolase domain-containing protein 14B (CCG1-interacting factor B)	0.05	-	cyt	0	Cytoplasm. Nucleus			1IMJ	210
P37220 UniProt NPD GO	ASR3_LYCES	Abscisic stress ripening protein 3	0.05	-	nuc	0					78
Q12559 UniProt NPD GO	AMDS_ASPOR	Acetamidase (EC 3.5.1.4)	0.05	-	cyt	0					545
Q96VC7 UniProt NPD GO	ACS2_ZYGBA	Acetyl-coenzyme A synthetase 2 (EC 6.2.1.1) (Acetate--CoA ligase 2) (Acyl-activating enzyme 2)	0.05	-	nuc	0					675
P09479 UniProt NPD GO	ACHA_CHICK	Acetylcholine receptor protein subunit alpha precursor	0.05	-	end	4	Membrane; multi-pass membrane protein				456
P09660 UniProt NPD GO	ACHE_RAT	Acetylcholine receptor protein subunit epsilon precursor	0.05	-	end	4	Membrane; multi-pass membrane protein	nicotinic acetylcholine-gated receptor-chan... [IMP]			494
Q27677 UniProt NPD GO	ACES_LEPDE	Acetylcholinesterase precursor (EC 3.1.1.7) (AChE)	0.05	-	exc	0	Cell membrane; lipid-anchor; GPI-anchor (By similarity). Attached to the membrane of the neuronal ch ...				629
P23604 UniProt NPD GO	ACH1_LONAC	Achelase-1 (EC 3.4.21.-) (Achelase I)	0.05	-	cyt	0					213
P52291 UniProt NPD GO	PPA1_PICPA	Acid phosphatase PHO1 precursor (EC 3.1.3.2)	0.05	-	mit	0					468
Q8X176 UniProt NPD GO	PHOA_ASPFU	Acid phosphatase precursor (EC 3.1.3.2)	0.05	-	nuc	0	Cell membrane; lipid-anchor; GPI-anchor				447
P34724 UniProt NPD GO	PHOA_ASPNG	Acid phosphatase precursor (EC 3.1.3.2)	0.05	-	vac	0	Secreted protein				417
P36910 UniProt NPD GO	CHIE_BETVU	Acidic endochitinase SE2 precursor (EC 3.2.1.14)	0.05	-	exc	0	Secreted protein; extracellular space. Intercellular fluid of leaves				293
P29024 UniProt NPD GO	CHIA_PHAAN	Acidic endochitinase precursor (EC 3.2.1.14)	0.05	-	end	0	Secreted protein; extracellular space				298
P82611 UniProt NPD GO	ACON_CANAL	Aconitate hydratase, mitochondrial (EC 4.2.1.3) (Citrate hydro-lyase) (Aconitase) (Fragments)	0.05	-	nuc	0	Mitochondrion				28
P19414 UniProt NPD GO	ACON_YEAST	Aconitate hydratase, mitochondrial precursor (EC 4.2.1.3) (Citrate hydro-lyase) (Aconitase)	0.05	-	mit	0	Mitochondrion. Cytoplasm. Mitochondrial and extramitochondrial	cytosol [TAS] mitochondrial nucleoid [IDA]			778
Q05214 UniProt NPD GO	ACT1_TOBAC	Actin	0.05	-	cyt	0	Cytoplasm				377
O13419 UniProt NPD GO	ACT_BOTCI	Actin	0.05	-	cyt	0	Cytoplasm				375
Q9UVX4 UniProt NPD GO	ACT_COPCI	Actin	0.05	-	cyt	0	Cytoplasm				375
P26183 UniProt NPD GO	ACT_CRYPV	Actin	0.05	-	cyt	0	Cytoplasm				376
Q6TCF2 UniProt NPD GO	ACT_GAEGA	Actin	0.05	-	cyt	0	Cytoplasm				375
O00937 UniProt NPD GO	ACT_HISCA	Actin	0.05	-	cyt	0	Cytoplasm				375
P78711 UniProt NPD GO	ACT_NEUCR	Actin	0.05	-	cyt	0	Cytoplasm				375
P10365 UniProt NPD GO	ACT_THELA	Actin	0.05	-	cyt	0	Cytoplasm				375
Q92192 UniProt NPD GO	ACT_CALFI	Actin (Fragment)	0.05	-	cyt	0	Cytoplasm				278
Q964E2 UniProt NPD GO	ACTC_BIOPF	Actin, cytoplasmic	0.05	-	cyt	0	Cytoplasm				376
P53466 UniProt NPD GO	ACT2_LYTPI	Actin, cytoskeletal 2 (LPC2)	0.05	-	cyt	0	Cytoplasm. Cytoskeleton				376
Q9UVW9 UniProt NPD GO	ACTG_CEPAC	Actin, gamma	0.05	-	cyt	0	Cytoplasm				375
P20359 UniProt NPD GO	ACTG_EMENI	Actin, gamma	0.05	-	cyt	0	Cytoplasm				375
Q9URS0 UniProt NPD GO	ACTG_PENCH	Actin, gamma	0.05	-	cyt	0	Cytoplasm				375
P12431 UniProt NPD GO	ACTM_STRPU	Actin, muscle	0.05	-	cyt	0	Cytoplasm				374
P53461 UniProt NPD GO	ACTC_HALRO	Actin, nonmuscle	0.05	-	cyt	0	Cytoplasm				376
P30162 UniProt NPD GO	ACT1_ONCVO	Actin-1	0.05	-	cyt	0	Cytoplasm				376
P13362 UniProt NPD GO	ACT1_ORYSA	Actin-1	0.05	-	cyt	0	Cytoplasm	actin cytoskeleton [IEP] cytoplasm [IEP]			377
Q9Y701 UniProt NPD GO	ACT1_SUIBO	Actin-1	0.05	-	cyt	0	Cytoplasm				375
Q9Y702 UniProt NPD GO	ACT1_SCHCO	Actin-1 (Beta-actin)	0.05	-	cyt	0	Cytoplasm				375
P10671 UniProt NPD GO	ACT1_ARATH	Actin-1/3	0.05	-	cyt	0	Cytoplasm				377
P10983 UniProt NPD GO	ACT1_CAEEL	Actin-1/3	0.05	-	cyt	0	Cytoplasm			1D4X	376
P41341 UniProt NPD GO	ACTY_LIMPO	Actin-11	0.05	-	cyt	0	Cytoplasm				376
P53497 UniProt NPD GO	ACT12_ARATH	Actin-12	0.05	-	cyt	0	Cytoplasm				377
P92176 UniProt NPD GO	ACT2_LUMTE	Actin-2	0.05	-	cyt	0	Cytoplasm				376
P53494 UniProt NPD GO	ACT4_ARATH	Actin-4	0.05	-	cyt	0	Cytoplasm				377
P10986 UniProt NPD GO	ACT4_CAEEL	Actin-4	0.05	-	cyt	0	Cytoplasm				376
P02572 UniProt NPD GO	ACT2_DROME	Actin-42A	0.05	-	cyt	0	Cytoplasm				376

You are viewing entries 73701 to 73750 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.