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
P22748 UniProt NPD GO	CAH4_HUMAN	Carbonic anhydrase 4 precursor (EC 4.2.1.1) (Carbonic anhydrase IV) (Carbonate dehydratase IV) (CA-I ...	0.14	-	exc	1	Cell membrane; lipid-anchor; GPI-anchor	membrane fraction [TAS]	114760	1ZNC	312
P17067 UniProt NPD GO	CAHC_PEA	Carbonic anhydrase, chloroplast precursor (EC 4.2.1.1) (Carbonate dehydratase) [Contains: Carbonic a ...	0.14	-	mit	0	Plastid; chloroplast; chloroplast stroma			1EKJ	328
P48052 UniProt NPD GO	CBPA2_HUMAN	Carboxypeptidase A2 precursor (EC 3.4.17.15)	0.14	-	end	0	Secreted protein		600688	1O6X	417
P19222 UniProt NPD GO	CBPA2_RAT	Carboxypeptidase A2 precursor (EC 3.4.17.15)	0.14	-	exc	0	Secreted protein				417
Q9UI42 UniProt NPD GO	CBPA4_HUMAN	Carboxypeptidase A4 precursor (EC 3.4.17.-) (Carboxypeptidase A3)	0.14	-	end	0	Secreted protein (By similarity)		607635	2BOA	421
Q8R4H4 UniProt NPD GO	CBPA5_MOUSE	Carboxypeptidase A5 precursor (EC 3.4.17.1)	0.14	-	exc	0	Secreted protein (By similarity)				436
Q96IY4 UniProt NPD GO	CBPB2_HUMAN	Carboxypeptidase B2 precursor (EC 3.4.17.20) (Carboxypeptidase U) (Thrombin-activable fibrinolysis i ...	0.14	-	cyt	0	Secreted protein		603101		423
P27516 UniProt NPD GO	CBR_DUNBA	Carotene biosynthesis-related protein CBR, chloroplast precursor	0.14	-	nuc	2	Plastid; chloroplast				172
Q9N2I1 UniProt NPD GO	CASP1_PIG	Caspase-1 precursor (EC 3.4.22.36) (CASP-1) (Interleukin-1 beta convertase) (IL-1BC) (IL-1 beta-conv ...	0.14	-	cyt	0	Cytoplasm				404
P55306 UniProt NPD GO	CATA_SCHPO	Catalase (EC 1.11.1.6)	0.14	-	cyt	0					512
Q9Y7C2 UniProt NPD GO	CATB_AJECA	Catalase B (EC 1.11.1.6)	0.14	-	mit	0	Secreted protein				728
P49317 UniProt NPD GO	CATA3_NICPL	Catalase isozyme 3 (EC 1.11.1.6)	0.14	-	cyt	0	Peroxisome (Potential)				492
P55097 UniProt NPD GO	CATK_MOUSE	Cathepsin K precursor (EC 3.4.22.38)	0.14	-	vac	0	Lysosome (By similarity)				329
Q5R7I7 UniProt NPD GO	CCRK_PONPY	Cell cycle-related kinase (EC 2.7.11.22)	0.14	-	cyt	0	Nucleus (By similarity)				346
Q4KM34 UniProt NPD GO	CCRK_RAT	Cell cycle-related kinase (EC 2.7.11.22)	0.14	-	cyt	0	Nucleus (By similarity)				346
Q9JHU3 UniProt NPD GO	CCRK_MOUSE	Cell cycle-related kinase (EC 2.7.11.22) (Cyclin-kinase-activating kinase p42) (CDK-activating kinas ...	0.14	-	cyt	0	Nucleus (By similarity)				346
P04551 UniProt NPD GO	CDC2_SCHPO	Cell division control protein 2 (EC 2.7.11.22) (EC 2.7.11.23) (p34 protein kinase)	0.14	-	cyt	0					297
P24923 UniProt NPD GO	CDC21_MEDSA	Cell division control protein 2 homolog 1 (EC 2.7.11.22) (EC 2.7.11.23) (Fragment)	0.14	-	cyt	0					291
P47178 UniProt NPD GO	DAN1_YEAST	Cell wall protein DAN1 precursor (Covalently-linked cell wall protein 13)	0.14	-	exc	1 *	Cell membrane; lipid-anchor; GPI-anchor	cell wall (sensu Fungi) [IDA]			298
P17818 UniProt NPD GO	CHSY_MATIN	Chalcone synthase (EC 2.3.1.74) (Naringenin-chalcone synthase)	0.14	-	cyt	0					394
Q01286 UniProt NPD GO	CHS1_PEA	Chalcone synthase 1 (EC 2.3.1.74) (Naregenin-chalcone synthase 1)	0.14	-	nuc	0					389
P24826 UniProt NPD GO	CHS1_SOYBN	Chalcone synthase 1 (EC 2.3.1.74) (Naringenin-chalcone synthase 1)	0.14	-	cyt	0					388
P17957 UniProt NPD GO	CHS2_SOYBN	Chalcone synthase 2 (EC 2.3.1.74) (Naringenin-chalcone synthase 2)	0.14	-	cyt	0					388
P19168 UniProt NPD GO	CHS3_SOYBN	Chalcone synthase 3 (EC 2.3.1.74) (Naringenin-chalcone synthase 3)	0.14	-	cyt	0					388
P48406 UniProt NPD GO	CHS5_SOYBN	Chalcone synthase 5 (EC 2.3.1.74) (Naringenin-chalcone synthase 5)	0.14	-	cyt	0					388
P30080 UniProt NPD GO	CHS6_SOYBN	Chalcone synthase 6 (EC 2.3.1.74) (Naringenin-chalcone synthase 6)	0.14	-	cyt	0					388
P22927 UniProt NPD GO	CHSG_PETHY	Chalcone synthase G (EC 2.3.1.74) (Naringenin-chalcone synthase G)	0.14	-	nuc	0					393
Q06702 UniProt NPD GO	CDA1_YEAST	Chitin deacetylase 1 precursor (EC 3.5.1.41)	0.14	-	cyt	0					301
P81729 UniProt NPD GO	CHAL_BRARA	Chitin-binding allergen Bra r 2 (Fragments)	0.14	-	nuc	0					91
Q59Q79 UniProt NPD GO	ALG1_CANAL	Chitobiosyldiphosphodolichol beta-mannosyltransferase (EC 2.4.1.142) (GDP-mannose-dolichol diphospho ...	0.14	-	end	1 *	Endoplasmic reticulum; endoplasmic reticulum membrane; single-pass type II membrane protein (By simi ...				456
O45405 UniProt NPD GO	EXL1_CAEEL	Chloride intracellular channel exl-1 (Exc-4-like protein)	0.14	-	cyt	0	Cytoplasm. Membrane. Can be translocated to membranes, possibly as integral membrane proteins, with ...				238
P51305 UniProt NPD GO	RR17_PORPU	Chloroplast 30S ribosomal protein S17	0.14	-	nuc	0	Plastid; chloroplast				83
Q6EN80 UniProt NPD GO	RR19_ORYNI	Chloroplast 30S ribosomal protein S19	0.14	-	mit	0	Plastid; chloroplast				93
O22020 UniProt NPD GO	RR4_CYAME	Chloroplast 30S ribosomal protein S4	0.14	-	mit	0	Plastid; chloroplast				190
O46904 UniProt NPD GO	RK14_GUITH	Chloroplast 50S ribosomal protein L14	0.14	-	cyt	0	Plastid; chloroplast				121
Q9BBQ0 UniProt NPD GO	RK14_LOTJA	Chloroplast 50S ribosomal protein L14	0.14	-	cyt	0	Plastid; chloroplast				122
Q9MUN9 UniProt NPD GO	RK19_MESVI	Chloroplast 50S ribosomal protein L19	0.14	-	nuc	0	Plastid; chloroplast				119
O19884 UniProt NPD GO	RK21_CYACA	Chloroplast 50S ribosomal protein L21	0.14	-	cyt	0	Plastid; chloroplast				108
Q85FI3 UniProt NPD GO	RK22_ADICA	Chloroplast 50S ribosomal protein L22	0.14	-	nuc	0	Plastid; chloroplast				122
Q9TLT7 UniProt NPD GO	RK22_CYACA	Chloroplast 50S ribosomal protein L22	0.14	-	mit	0	Plastid; chloroplast				103
Q4G364 UniProt NPD GO	RK3_EMIHU	Chloroplast 50S ribosomal protein L3	0.14	-	nuc	0	Plastid; chloroplast				207
P51302 UniProt NPD GO	RK5_PORPU	Chloroplast 50S ribosomal protein L5	0.14	-	cyt	0	Plastid; chloroplast				181
Q9MTK9 UniProt NPD GO	CEMA_OENHO	Chloroplast envelope membrane protein	0.14	-	end	4 *	Plastid; chloroplast; chloroplast inner membrane; multi-pass membrane protein (By similarity)				229
P49160 UniProt NPD GO	CEMA_SOYBN	Chloroplast envelope membrane protein	0.14	-	end	4 *	Plastid; chloroplast; chloroplast inner membrane; multi-pass membrane protein (By similarity)				229
Q8WWI5 UniProt NPD GO	CTL1_HUMAN	Choline transporter-like protein 1 (Solute carrier family 44 member 1) (CD92 antigen) (CDw92)	0.14	-	end	9 *	Membrane; multi-pass membrane protein (By similarity)		606105		657
P06276 UniProt NPD GO	CHLE_HUMAN	Cholinesterase precursor (EC 3.1.1.8) (Acylcholine acylhydrolase) (Choline esterase II) (Butyrylchol ...	0.14	+	exc	2 *		extracellular region [NAS]	177400	1XLW	602
P13428 UniProt NPD GO	CH19_DROSU	Chorion protein S19	0.14	-	mit	0					180
P28777 UniProt NPD GO	AROC_YEAST	Chorismate synthase (EC 4.2.3.5) (5-enolpyruvylshikimate-3-phosphate phospholyase)	0.14	-	cyt	0		cytoplasm [IDA]		1R53	376
P56435 UniProt NPD GO	MCPT1_MACFA	Chymase precursor (EC 3.4.21.39) (Mast cell protease I)	0.14	-	vac	0	Mast cell granules (By similarity)				247
P16240 UniProt NPD GO	CION_CIOIN	Cionin precursor	0.14	-	nuc	1 *	Secreted protein				128

You are viewing entries 58101 to 58150 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.