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
O43108 UniProt NPD GO	ATC1_YARLI	Calcium-transporting ATPase 1 (EC 3.6.3.8) (P-type calcium ATPase)	0.12	-	end	7	Golgi apparatus; Golgi membrane; multi-pass membrane protein				928
O22218 UniProt NPD GO	ACA4_ARATH	Calcium-transporting ATPase 4, plasma membrane-type (EC 3.6.3.8) (Ca(2+)-ATPase isoform 4)	0.12	-	end	8	Vacuole; vacuolar membrane; multi-pass membrane protein. Tonoplast. Small vacuoles				1030
Q13938 UniProt NPD GO	CAYP1_HUMAN	Calcyphosin (Calcyphosine)	0.12	-	cyt	0	Cytoplasm		114212		189
P04574 UniProt NPD GO	CPNS1_PIG	Calpain small subunit 1 (CSS1) (Calcium-dependent protease small subunit 1) (Calcium-dependent prote ...	0.12	-	cyt	0	Cytoplasm (By similarity). Cell membrane (By similarity). Translocates to the plasma membrane upon c ...			1NX3	266
O35783 UniProt NPD GO	CALU_RAT	Calumenin precursor (Crocalbin) (CBP-50)	0.12	-	end	0	Endoplasmic reticulum; endoplasmic reticulum lumen	endoplasmic reticulum lumen [IDA]			315
Q00663 UniProt NPD GO	CARP_CANTR	Candidapepsin precursor (EC 3.4.23.24) (Aspartate protease) (ACP)	0.12	-	vac	0	Secreted protein			1J71	394
P43094 UniProt NPD GO	CARP5_CANAL	Candidapepsin-5 precursor (EC 3.4.23.24) (Aspartate protease 5) (ACP 5) (Secreted aspartic protease ...	0.12	-	vac	0	Secreted protein				418
P00921 UniProt NPD GO	CAH2_BOVIN	Carbonic anhydrase 2 (EC 4.2.1.1) (Carbonic anhydrase II) (Carbonate dehydratase II) (CA-II)	0.12	-	nuc	0	Cytoplasm			1V9I	259
P00920 UniProt NPD GO	CAH2_MOUSE	Carbonic anhydrase 2 (EC 4.2.1.1) (Carbonic anhydrase II) (Carbonate dehydratase II) (CA-II)	0.12	-	nuc	0	Cytoplasm				259
P00922 UniProt NPD GO	CAH2_SHEEP	Carbonic anhydrase 2 (EC 4.2.1.1) (Carbonic anhydrase II) (Carbonate dehydratase II) (CA-II)	0.12	-	cyt	0	Cytoplasm				259
P35218 UniProt NPD GO	CAH5A_HUMAN	Carbonic anhydrase 5A, mitochondrial precursor (EC 4.2.1.1) (Carbonic anhydrase VA) (Carbonate dehyd ...	0.12	-	mit	0	Mitochondrion	mitochondrial matrix [NAS] mitochondrion [TAS]	114761		305
P43165 UniProt NPD GO	CAH5A_RAT	Carbonic anhydrase 5A, mitochondrial precursor (EC 4.2.1.1) (Carbonic anhydrase VA) (Carbonate dehyd ...	0.12	-	mit	0	Mitochondrion	mitochondrion [IDA]			304
Q7TPZ8 UniProt NPD GO	CBPA1_MOUSE	Carboxypeptidase A1 precursor (EC 3.4.17.1)	0.12	-	end	0	Secreted protein (By similarity)				419
P09954 UniProt NPD GO	CBPA1_PIG	Carboxypeptidase A1 precursor (EC 3.4.17.1)	0.12	-	exc	0	Secreted protein			1PCA	419
Q5RAV7 UniProt NPD GO	CARD8_PONPY	Caspase recruitment domain-containing protein 8	0.12	-	cyt	0	Cytoplasm (By similarity). Nucleus (By similarity)				427
O35397 UniProt NPD GO	CASP6_RAT	Caspase-6 precursor (EC 3.4.22.-) (CASP-6) (Apoptotic protease Mch-2) [Contains: Caspase-6 subunit p ...	0.12	-	cyt	0	Cytoplasm (By similarity)				277
P09668 UniProt NPD GO	CATH_HUMAN	Cathepsin H precursor (EC 3.4.22.16) [Contains: Cathepsin H mini chain; Cathepsin H heavy chain; Cat ...	0.12	-	cyt	0	Lysosome		116820	1BZN	335
Q9GL24 UniProt NPD GO	CATL_CANFA	Cathepsin L precursor (EC 3.4.22.15) [Contains: Cathepsin L heavy chain; Cathepsin L light chain]	0.12	-	exc	0	Lysosome (By similarity)				333
Q8IZL9 UniProt NPD GO	CCRK_HUMAN	Cell cycle-related kinase (EC 2.7.11.22) (Cyclin-kinase-activating kinase p42) (CDK-activating kinas ...	0.12	-	cyt	0	Nucleus		610076		346
Q4Z6R1 UniProt NPD GO	CDC2H_PLABA	Cell division control protein 2 homolog (EC 2.7.11.22) (EC 2.7.11.23)	0.12	-	nuc	0	Cytoplasm (By similarity)				288
P25859 UniProt NPD GO	CDC2B_ARATH	Cell division control protein 2 homolog B (EC 2.7.11.22) (EC 2.7.11.23)	0.12	-	cyt	0					309
Q9MUM4 UniProt NPD GO	FTSW_MESVI	Cell division protein ftsW homolog	0.12	-	end	8 *	Membrane; multi-pass membrane protein (Potential)				415
P97587 UniProt NPD GO	CGRF1_RAT	Cell growth regulator with RING finger domain 1 (Cell growth regulatory gene 19 protein)	0.12	-	cyt	1 *					332
Q9ES57 UniProt NPD GO	MOX2R_MOUSE	Cell surface glycoprotein OX2 receptor precursor (CD200 cell surface glycoprotein receptor)	0.12	-	mit	1 *	Membrane; single-pass type I membrane protein	external side of plasma membrane [IDA]			326
Q9Z275 UniProt NPD GO	CRAL_MOUSE	Cellular retinaldehyde-binding protein (CRALBP)	0.12	-	nuc	0	Cytoplasm				316
Q9ZRS4 UniProt NPD GO	CHSY_CATRO	Chalcone synthase (EC 2.3.1.74) (Naringenin-chalcone synthase)	0.12	-	cyt	0					389
Q9LKP7 UniProt NPD GO	CHSY_DIAMO	Chalcone synthase (EC 2.3.1.74) (Naringenin-chalcone synthase)	0.12	-	cyt	0					391
O04111 UniProt NPD GO	CHSY_PERFR	Chalcone synthase (EC 2.3.1.74) (Naringenin-chalcone synthase)	0.12	-	cyt	0					391
Q9XJ58 UniProt NPD GO	CHS1_CITSI	Chalcone synthase 1 (EC 2.3.1.74) (Naringenin-chalcone synthase 1)	0.12	-	cyt	0					389
P23418 UniProt NPD GO	CHS1_LYCES	Chalcone synthase 1 (EC 2.3.1.74) (Naringenin-chalcone synthase 1)	0.12	-	mit	0					389
P30073 UniProt NPD GO	CHS1_MEDSA	Chalcone synthase 1 (EC 2.3.1.74) (Naringenin-chalcone synthase 1)	0.12	-	nuc	0					389
Q9FSB9 UniProt NPD GO	CHS1_RUTGR	Chalcone synthase 1 (EC 2.3.1.74) (Naringenin-chalcone synthase 1)	0.12	-	cyt	0					393
Q01287 UniProt NPD GO	CHS2_PEA	Chalcone synthase 2 (EC 2.3.1.74) (Naregenin-chalcone synthase 2)	0.12	-	mit	0					389
P30074 UniProt NPD GO	CHS2_MEDSA	Chalcone synthase 2 (EC 2.3.1.74) (Naringenin-chalcone synthase 2)	0.12	-	mit	0				1U0W	389
P30075 UniProt NPD GO	CHS4_MEDSA	Chalcone synthase 4 (EC 2.3.1.74) (Naringenin-chalcone synthase 4) (CHS12-1)	0.12	-	mit	0					389
P48395 UniProt NPD GO	CHSA_IPONI	Chalcone synthase A (EC 2.3.1.74) (Naringenin-chalcone synthase A) (CHS-A) (Fragment)	0.12	-	nuc	0					344
O08878 UniProt NPD GO	CML2_RAT	Chemokine receptor-like 2 (G-protein coupled receptor 30) (G-protein coupled receptor 41)	0.12	-	end	7	Membrane; multi-pass membrane protein				375
Q99527 UniProt NPD GO	CML2_HUMAN	Chemokine receptor-like 2 (G-protein coupled receptor 30) (IL8-related receptor DRY12) (Flow-induced ...	0.12	-	end	7	Membrane; multi-pass membrane protein	integral to plasma membrane [TAS]	601805		375
P19169 UniProt NPD GO	RR3_EUGGR	Chloroplast 30S ribosomal protein S3	0.12	-	cyt	0	Plastid; chloroplast				218
Q6B922 UniProt NPD GO	RR6_GRATL	Chloroplast 30S ribosomal protein S6	0.12	-	nuc	0	Plastid; chloroplast				103
O46909 UniProt NPD GO	RK18_GUITH	Chloroplast 50S ribosomal protein L18	0.12	-	nuc	0	Plastid; chloroplast				107
Q1XDH7 UniProt NPD GO	RK2_PORYE	Chloroplast 50S ribosomal protein L2	0.12	-	mit	0	Plastid; chloroplast				293
Q6B8W4 UniProt NPD GO	RK24_GRATL	Chloroplast 50S ribosomal protein L24	0.12	-	nuc	0	Plastid; chloroplast				92
P51210 UniProt NPD GO	RK27_PORPU	Chloroplast 50S ribosomal protein L27	0.12	-	nuc	0	Plastid; chloroplast				86
Q7YJV5 UniProt NPD GO	RK33_CALFE	Chloroplast 50S ribosomal protein L33	0.12	-	nuc	0	Plastid; chloroplast				66
O78487 UniProt NPD GO	RK33_GUITH	Chloroplast 50S ribosomal protein L33	0.12	-	nuc	0	Plastid; chloroplast				56
Q6B8P8 UniProt NPD GO	CEMA_GRATL	Chloroplast envelope membrane protein	0.12	-	end	4	Plastid; chloroplast; chloroplast inner membrane; multi-pass membrane protein (By similarity)				278
P32756 UniProt NPD GO	CLAT_CAEEL	Choline O-acetyltransferase (EC 2.3.1.6) (CHOACTase) (Choline acetylase) (ChAT)	0.12	-	cyt	0					627
O62761 UniProt NPD GO	CHLE_PANTT	Cholinesterase precursor (EC 3.1.1.8) (Acylcholine acylhydrolase) (Choline esterase II) (Butyrylchol ...	0.12	+	vac	0					602
P21927 UniProt NPD GO	CHLE_RABIT	Cholinesterase precursor (EC 3.1.1.8) (Acylcholine acylhydrolase) (Choline esterase II) (Butyrylchol ...	0.12	+	cyt	1 *					581

You are viewing entries 60951 to 61000 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.