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
P03930 UniProt NPD GO	ATP8_MOUSE	ATP synthase protein 8 (EC 3.6.3.14) (ATPase subunit 8) (A6L)	0.14	-	nuc	1 *	Mitochondrion; mitochondrial membrane; single-pass membrane protein				67
Q9MJB2 UniProt NPD GO	ATP8_TALEU	ATP synthase protein 8 (EC 3.6.3.14) (ATPase subunit 8) (A6L)	0.14	-	nuc	1 *	Mitochondrion; mitochondrial membrane; single-pass membrane protein				67
P11608 UniProt NPD GO	ATP8_RAT	ATP synthase protein 8 (EC 3.6.3.14) (ATPase subunit 8) (A6L) (Chargerin II)	0.14	-	nuc	1 *	Mitochondrion; mitochondrial membrane; single-pass membrane protein				67
P48080 UniProt NPD GO	ATPA_CYAPA	ATP synthase subunit alpha (EC 3.6.3.14) (ATPase subunit alpha) (ATP synthase F1 sector subunit alph ...	0.14	-	cyt	0	Plastid; cyanelle; cyanelle thylakoid membrane; peripheral membrane protein (By similarity)				505
Q37380 UniProt NPD GO	ATPAM_ACACA	ATP synthase subunit alpha, mitochondrial (EC 3.6.3.14)	0.14	-	mit	0	Mitochondrion				522
P35381 UniProt NPD GO	ATPA_DROME	ATP synthase subunit alpha, mitochondrial precursor (EC 3.6.3.14) (Protein bellwether)	0.14	-	mit	0	Mitochondrion; mitochondrial inner membrane				552
O75027 UniProt NPD GO	ABCB7_HUMAN	ATP-binding cassette sub-family B member 7, mitochondrial precursor (ATP-binding cassette transporte ...	0.14	-	end	5	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein (Potential)	mitochondrial inner membrane [TAS]	301310		752
Q07478 UniProt NPD GO	SUB2_YEAST	ATP-dependent RNA helicase SUB2 (EC 3.6.1.-) (Suppressor of BRR1 protein 2)	0.14	-	cyt	0	Nucleus	chromosome, telomeric region [IPI] nucleus [IDA] spliceosome complex [TAS] transcription export complex [IPI]			446
P87206 UniProt NPD GO	IF4A_CANAL	ATP-dependent RNA helicase eIF4A (EC 3.6.1.-) (Eukaryotic initiation factor 4A) (eIF-4A) (Translatio ...	0.14	-	cyt	0	Cytoplasm (By similarity)				397
Q5ASK8 UniProt NPD GO	SUB2_EMENI	ATP-dependent RNA helicase sub2 (EC 3.6.1.-)	0.14	-	cyt	0	Nucleus (By similarity)				451
Q61743 UniProt NPD GO	IRK11_MOUSE	ATP-sensitive inward rectifier potassium channel 11 (Potassium channel, inwardly rectifying subfamil ...	0.14	-	end	2	Membrane; multi-pass membrane protein				390
Q9JHJ9 UniProt NPD GO	IRK11_CAVPO	ATP-sensitive inward rectifier potassium channel 11 (Potassium channel, inwardly rectifying subfamil ...	0.14	-	end	2	Membrane; multi-pass membrane protein				390
P10334 UniProt NPD GO	MS2B_DROME	Accessory gland-specific peptide 26Ab precursor (Male accessory gland secretory protein 355B)	0.14	-	exc	0	Secreted protein; extracellular space				90
Q9QXG4 UniProt NPD GO	ACSA_MOUSE	Acetyl-coenzyme A synthetase, cytoplasmic (EC 6.2.1.1) (Acetate--CoA ligase) (Acyl-activating enzyme ...	0.14	-	cyt	1	Cytoplasm (By similarity)	cytoplasm [IDA]			701
P22929 UniProt NPD GO	CARP_SACFI	Acid protease precursor (EC 3.4.23.-)	0.14	-	exc	0					390
Q24733 UniProt NPD GO	ACT_DICVI	Actin (Fragment)	0.14	-	nuc	0	Cytoplasm				33
Q9Y614 UniProt NPD GO	ACL7B_HUMAN	Actin-like protein 7B (Actin-like-7-beta)	0.14	-	cyt	0		actin cytoskeleton [TAS]	604304		415
Q99PD4 UniProt NPD GO	ARC1A_RAT	Actin-related protein 2/3 complex subunit 1A	0.14	-	cyt	0					370
P52413 UniProt NPD GO	ACP3_CUPLA	Acyl carrier protein 3, chloroplast precursor (ACP)	0.14	-	mit	0	Plastid; chloroplast				143
P07088 UniProt NPD GO	ACP_BRACM	Acyl carrier protein SF2, chloroplast precursor (ACP)	0.14	-	mit	0	Plastid; chloroplast				134
O00767 UniProt NPD GO	ACOD_HUMAN	Acyl-CoA desaturase (EC 1.14.19.1) (Stearoyl-CoA desaturase) (Fatty acid desaturase) (Delta(9)-desat ...	0.14	-	nuc	4	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (Probable)		604031		359
Q64420 UniProt NPD GO	ACOD_MESAU	Acyl-CoA desaturase (EC 1.14.19.1) (Stearoyl-CoA desaturase) (Fatty acid desaturase) (Delta(9)-desat ...	0.14	-	end	4	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (Probable)				354
P21147 UniProt NPD GO	ACO1_YEAST	Acyl-CoA desaturase 1 (EC 1.14.19.1) (Stearoyl-CoA desaturase 1) (Fatty acid desaturase 1)	0.14	-	mit	4	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (Probable)	endoplasmic reticulum membrane [TAS]			510
P13516 UniProt NPD GO	ACOD1_MOUSE	Acyl-CoA desaturase 1 (EC 1.14.19.1) (Stearoyl-CoA desaturase 1) (Fatty acid desaturase 1) (Delta(9) ...	0.14	-	end	4	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (Probable)				355
O65202 UniProt NPD GO	ACOX1_ARATH	Acyl-coenzyme A oxidase 1, peroxisomal (EC 1.3.3.6) (AOX 1) (Long-chain acyl-CoA oxidase) (AtCX1)	0.14	-	cyt	0	Peroxisome (Probable)			1W07	664
Q9HFJ5 UniProt NPD GO	APTH1_NEUCR	Acyl-protein thioesterase 1 (EC 3.1.2.-)	0.14	-	mit	0	Cytoplasm (By similarity)				245
Q2R2W1 UniProt NPD GO	ADO3_ORYSA	Adagio-like protein 3	0.14	-	cyt	0	Nucleus (By similarity)				630
P53909 UniProt NPD GO	ADA_YEAST	Adenosine deaminase (EC 3.5.4.4) (Adenosine aminohydrolase)	0.14	-	cyt	0		cytoplasm [IDA] nucleus [IDA]			347
P78825 UniProt NPD GO	ADK_SCHPO	Adenosine kinase (EC 2.7.1.20)	0.14	-	cyt	0					340
Q9WUS0 UniProt NPD GO	KAD4_RAT	Adenylate kinase isoenzyme 4, mitochondrial (EC 2.7.4.3) (Adenylate kinase 3-like 1) (ATP-AMP transp ...	0.14	-	cyt	0	Mitochondrion; mitochondrial matrix (Potential)				223
P31392 UniProt NPD GO	ADMR_RAT	Adrenomedullin receptor (AM-R) (G10D) (NOW)	0.14	-	end	7 *	Membrane; multi-pass membrane protein				395
Q94688 UniProt NPD GO	ALDH9_POLMI	Aldehyde dehydrogenase 9 (EC 1.2.1.3) (PM-ALDH9) (Fragment)	0.14	-	mit	0					228
Q9LS01 UniProt NPD GO	AOC3_ARATH	Allene oxide cyclase 3, chloroplast precursor (EC 5.3.99.6)	0.14	-	mit	0	Plastid; chloroplast				258
Q10359 UniProt NPD GO	GMH3_SCHPO	Alpha-1,2-galactosyltransferase gmh3 (EC 2.4.1.-)	0.14	-	cyt	1 *	Golgi apparatus; Golgi membrane; single-pass type II membrane protein (Potential)				332
Q9SC19 UniProt NPD GO	UPTG1_SOLTU	Alpha-1,4-glucan-protein synthase [UDP-forming] 1 (EC 2.4.1.112) (UDP-glucose:protein transglucosyla ...	0.14	-	cyt	0	Cell wall (By similarity). Cell wall; cell-cell junction; plasmodesma (By similarity). Cell wall-ass ...				365
Q8NDV1 UniProt NPD GO	SIA7C_HUMAN	Alpha-N-acetylgalactosaminide alpha-2,6-sialyltransferase 3 (EC 2.4.99.-) (GalNAc alpha-2,6-sialyltr ...	0.14	-	mit	1 *	Golgi apparatus; Golgi membrane; single-pass type II membrane protein (Potential)				305
Q9UDR5 UniProt NPD GO	AASS_HUMAN	Alpha-aminoadipic semialdehyde synthase, mitochondrial precursor (LKR/SDH) [Includes: Lysine ketoglu ...	0.14	-	nuc	0	Mitochondrion (By similarity)	mitochondrion [TAS]	605113		926
O81086 UniProt NPD GO	TPSD1_ABIGR	Alpha-bisabolene synthase (EC 4.2.3.-) ((E)-alpha-bisabolene synthase) (AgfEabis)	0.14	-	cyt	0	Cytoplasm (Probable)				817
P15571 UniProt NPD GO	ELIA_PHYCP	Alpha-elicitin capsicein	0.14	-	exc	0	Secreted protein				98
P21139 UniProt NPD GO	MA2C1_RAT	Alpha-mannosidase 2C1 (EC 3.2.1.24) (Alpha-D-mannoside mannohydrolase) (Mannosidase alpha class 2C m ...	0.14	-	nuc	0	Endoplasmic reticulum	endoplasmic reticulum [NAS]			1040
Q41266 UniProt NPD GO	AOX2_SOYBN	Alternative oxidase 2, mitochondrial precursor (EC 1.-.-.-)	0.14	-	mit	2	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein (Probable). Mitochondrial, ...				333
Q9Y711 UniProt NPD GO	AOX_AJECA	Alternative oxidase, mitochondrial precursor (EC 1.-.-.-)	0.14	-	mit	2	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein; matrix side (By similarity ...				356
Q12698 UniProt NPD GO	PUR1_SACKL	Amidophosphoribosyltransferase (EC 2.4.2.14) (Glutamine phosphoribosylpyrophosphate amidotransferase ...	0.14	-	cyt	0					510
Q9H4A4 UniProt NPD GO	AMPB_HUMAN	Aminopeptidase B (EC 3.4.11.6) (Ap-B) (Arginyl aminopeptidase) (Arginine aminopeptidase)	0.14	-	cyt	0	Secreted protein (By similarity)	extracellular region [TAS] Golgi apparatus [ISS] plasma membrane [TAS]	602675		650
Q6UKI2 UniProt NPD GO	AMNLS_CANFA	Amnionless protein precursor	0.14	-	end	1	Membrane; single-pass type I membrane protein (Potential)				458
Q92624 UniProt NPD GO	APBP2_HUMAN	Amyloid protein-binding protein 2 (Amyloid beta precursor protein-binding protein 2) (APP-BP2) (Prot ...	0.14	-	cyt	0	Nucleus. Cytoplasm. Associated with membranes and microtubules	cytoplasm [NAS] microtubule associated complex [TAS] nucleus [NAS]	605324		585
Q9ZPW2 UniProt NPD GO	APC10_ARATH	Anaphase-promoting complex subunit 10 (APC10) (Cyclosome subunit 10)	0.14	-	nuc	0					192
Q86XS5 UniProt NPD GO	ANGL5_HUMAN	Angiopoietin-related protein 5 precursor (Angiopoietin-like 5)	0.14	-	cyt	0	Secreted protein (Potential)		607666		388
Q5EA33 UniProt NPD GO	ANR49_BOVIN	Ankyrin repeat domain-containing protein 49	0.14	-	cyt	0					238
Q8VD46 UniProt NPD GO	ASZ1_MOUSE	Ankyrin repeat, SAM and basic leucine zipper domain-containing protein 1 (Germ cell-specific ankyrin ...	0.14	-	nuc	0	Cytoplasm	cytoplasm [IDA]			475

You are viewing entries 57951 to 58000 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.