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
Q6C2X0 UniProt NPD GO	KAPR_YARLI	cAMP-dependent protein kinase regulatory subunit (PKA regulatory subunit)	0.16	-	cyt	0					375
P05986 UniProt NPD GO	KAPC_YEAST	cAMP-dependent protein kinase type 3 (EC 2.7.11.11) (PKA 3)	0.16	-	cyt	0		cAMP-dependent protein kinase complex [IMP] cytoplasm [TAS]			398
Q6CXK7 UniProt NPD GO	PALH_KLULA	pH-response regulator protein palH/RIM21	0.16	-	end	6	Cell membrane; multi-pass membrane protein (By similarity)				519
Q4WHH9 UniProt NPD GO	GEL4_ASPFU	1,3-beta-glucanosyltransferase gel4 precursor (EC 2.4.1.-) (Glucan elongating glucanosyltransferase ...	0.15	-	exc	0	Cell membrane; lipid-anchor; GPI-anchor				548
Q6C2U0 UniProt NPD GO	HIS4_YARLI	1-(5-phosphoribosyl)-5-[(5-phosphoribosylamino)methylideneamino] imidazole-4-carboxamide isomerase ( ...	0.15	-	cyt	0	Cytoplasm (By similarity)				264
Q9SYC8 UniProt NPD GO	LPAT3_ARATH	1-acyl-sn-glycerol-3-phosphate acyltransferase 3 (EC 2.3.1.51) (Lysophosphatidyl acyltransferase 3)	0.15	-	end	3 *	Membrane; multi-pass membrane protein (Potential)				376
Q6DCK1 UniProt NPD GO	PLCG_XENLA	1-acyl-sn-glycerol-3-phosphate acyltransferase eta (EC 2.3.1.51) (1-AGP acyltransferase 7) (1-AGPAT ...	0.15	-	cyt	2 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (By similarity)				522
P13813 UniProt NPD GO	110KD_PLAKN	110 kDa antigen (PK110) (Fragment)	0.15	-	cyt	0					296
Q8GYB8 UniProt NPD GO	OPR2_ARATH	12-oxophytodienoate reductase 2 (EC 1.3.1.42) (12-oxophytodienoate-10,11-reductase 2) (OPDA-reductas ...	0.15	-	cyt	0	Cytoplasm				374
Q6X4M3 UniProt NPD GO	RTP12_ONCMY	12.5 kDa retinal tissue protein (Rtp12.5)	0.15	-	nuc	0					112
P92177 UniProt NPD GO	1433E_DROME	14-3-3 protein epsilon (Suppressor of Ras1 3-9)	0.15	-	nuc	0		chromosome [IDA] cytoplasm [IDA] nucleus [IDA] ring canal (sensu Insecta) [IDA]			262
Q60856 UniProt NPD GO	OAS1B_MOUSE	2'-5'-oligoadenylate synthetase 1B (EC 2.7.7.-) ((2-5')oligo(A) synthetase 1b) (2-5A synthetase 1B) ...	0.15	-	nuc	0					192
O88986 UniProt NPD GO	KBL_MOUSE	2-amino-3-ketobutyrate coenzyme A ligase, mitochondrial precursor (EC 2.3.1.29) (AKB ligase) (Glycin ...	0.15	-	cyt	0	Mitochondrion	mitochondrial inner membrane [IDA] mitochondrion [IDA]			416
Q6IYF8 UniProt NPD GO	OXGR1_MOUSE	2-oxoglutarate receptor 1 (Alpha-ketoglutarate receptor 1) (G-protein coupled receptor 99)	0.15	-	end	7 *	Membrane; multi-pass membrane protein				337
P11955 UniProt NPD GO	CHI1_HORVU	26 kDa endochitinase 1 precursor (EC 3.2.1.14)	0.15	-	mit	0					318
O64982 UniProt NPD GO	PRS7_PRUPE	26S protease regulatory subunit 7 (26S proteasome subunit 7) (26S proteasome AAA-ATPase subunit RPT1 ...	0.15	-	cyt	0	Cytoplasm (Potential). Nucleus (Potential)				425
Q9SSB5 UniProt NPD GO	PRS7_ARATH	26S protease regulatory subunit 7 (26S proteasome subunit 7) (26S proteasome AAA-ATPase subunit RPT1 ...	0.15	-	cyt	0	Cytoplasm (Potential). Nucleus (Potential)				426
P46470 UniProt NPD GO	PRS8_XENLA	26S protease regulatory subunit 8 (SUG1 homolog) (xSUG1)	0.15	-	cyt	0	Cytoplasm (Potential). Nucleus (Potential)				461
Q23449 UniProt NPD GO	PSD8_CAEEL	26S proteasome non-ATPase regulatory subunit 8 (26S proteasome regulatory subunit rpn-12)	0.15	-	cyt	0					250
P14891 UniProt NPD GO	HMDH1_ARATH	3-hydroxy-3-methylglutaryl-coenzyme A reductase 1 (EC 1.1.1.34) (HMG-CoA reductase 1) (HMGR1)	0.15	-	end	3	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein				592
Q921H8 UniProt NPD GO	THIKA_MOUSE	3-ketoacyl-CoA thiolase A, peroxisomal precursor (EC 2.3.1.16) (Beta-ketothiolase A) (Acetyl-CoA acy ...	0.15	-	nuc	0	Peroxisome (By similarity)	peroxisome [TAS]			424
Q26646 UniProt NPD GO	SM30A_STRPU	30 kDa spicule matrix protein-alpha precursor (SM30-alpha)	0.15	-	exc	0					290
P29344 UniProt NPD GO	RR1_SPIOL	30S ribosomal protein S1, chloroplast precursor (CS1)	0.15	-	mit	0	Plastid; chloroplast				411
Q5M818 UniProt NPD GO	RM16_RAT	39S ribosomal protein L16, mitochondrial precursor (L16mt) (MRP-L16)	0.15	-	mit	0	Mitochondrion (By similarity)				251
Q60Y65 UniProt NPD GO	HPPD_CAEBR	4-hydroxyphenylpyruvate dioxygenase (EC 1.13.11.27) (4HPPD) (HPD) (HPPDase) (4-hydroxyphenylpyruvic ...	0.15	-	cyt	0					393
Q01661 UniProt NPD GO	RS0_PNECA	40S ribosomal protein S0 (Extracellular matrix receptor protein)	0.15	-	cyt	0					295
O14112 UniProt NPD GO	RS10A_SCHPO	40S ribosomal protein S10-A	0.15	-	cyt	0					144
P79013 UniProt NPD GO	RS11_SCHPO	40S ribosomal protein S11	0.15	-	cyt	0					152
O65569 UniProt NPD GO	RS11B_ARATH	40S ribosomal protein S11-2	0.15	-	nuc	0	Cytoplasm (By similarity)				159
P10735 UniProt NPD GO	RT12_DROME	40S ribosomal protein S12, mitochondrial precursor (MT-RPS12) (Protein technical knockout locus)	0.15	-	nuc	0	Mitochondrion				140
Q8MUR2 UniProt NPD GO	RS13_CHOPR	40S ribosomal protein S13	0.15	-	mit	0					150
Q08699 UniProt NPD GO	RS14_PODCA	40S ribosomal protein S14	0.15	-	cyt	0					151
P46793 UniProt NPD GO	RS15A_DICDI	40S ribosomal protein S15a (Ribosomal protein S24)	0.15	-	mit	0					129
P50891 UniProt NPD GO	RS15A_PARLI	40S ribosomal protein S15a (Ribosomal protein S24)	0.15	-	mit	0					129
O18650 UniProt NPD GO	RS19_CAEEL	40S ribosomal protein S19	0.15	-	nuc	0					146
Q9M337 UniProt NPD GO	RS21B_ARATH	40S ribosomal protein S21-2	0.15	-	cyt	0					82
P51405 UniProt NPD GO	RS4_DICDI	40S ribosomal protein S4	0.15	-	mit	0	Cytoplasm (By similarity)				266
P26783 UniProt NPD GO	RS5_YEAST	40S ribosomal protein S5 (S2) (YS8) (RP14)	0.15	-	cyt	0		cytosolic small ribosomal subunit (sensu Eu... [TAS]		1K5X	224
O14277 UniProt NPD GO	RS5A_SCHPO	40S ribosomal protein S5-A	0.15	-	nuc	0					203
O43741 UniProt NPD GO	AAKB2_HUMAN	5'-AMP-activated protein kinase subunit beta-2 (AMPK beta-2 chain)	0.15	-	nuc	0			602741	2F15	272
Q9QZH4 UniProt NPD GO	AAKB2_RAT	5'-AMP-activated protein kinase subunit beta-2 (AMPK beta-2 chain)	0.15	-	nuc	0		cAMP-dependent protein kinase complex [IDA]			271
Q2TBU5 UniProt NPD GO	NT5D1_BOVIN	5'-nucleotidase domain-containing protein 1	0.15	-	cyt	0					452
Q92403 UniProt NPD GO	HEM1_AGABI	5-aminolevulinate synthase, mitochondrial precursor (EC 2.3.1.37) (5-aminolevulinic acid synthase) ( ...	0.15	-	cyt	0	Mitochondrion; mitochondrial matrix				621
Q9N297 UniProt NPD GO	5HT1A_GORGO	5-hydroxytryptamine 1A receptor (5-HT-1A) (Serotonin receptor 1A) (5-HT1A)	0.15	-	end	7 *	Membrane; multi-pass membrane protein				422
Q9N296 UniProt NPD GO	5HT1A_PONPY	5-hydroxytryptamine 1A receptor (5-HT-1A) (Serotonin receptor 1A) (5-HT1A)	0.15	-	end	7 *	Membrane; multi-pass membrane protein				422
P08908 UniProt NPD GO	5HT1A_HUMAN	5-hydroxytryptamine 1A receptor (5-HT-1A) (Serotonin receptor 1A) (5-HT1A) (G-21)	0.15	-	end	7 *	Membrane; multi-pass membrane protein	integral to plasma membrane [TAS]	109760		422
O08892 UniProt NPD GO	5HT1B_CAVPO	5-hydroxytryptamine 1B receptor (5-HT-1B) (Serotonin receptor 1B) (5-HT1B)	0.15	-	end	7 *	Membrane; multi-pass membrane protein				389
P79250 UniProt NPD GO	5HT1B_CANFA	5-hydroxytryptamine 1B receptor (5-HT-1B) (Serotonin receptor 1B) (5-HT1B) (5-HTR1B) (5-HT1D subtype ...	0.15	-	end	7 *	Membrane; multi-pass membrane protein				389
P31164 UniProt NPD GO	RK11_SPIOL	50S ribosomal protein L11, chloroplast precursor (CL11)	0.15	-	mit	0	Plastid; chloroplast (Probable)				224
P22367 UniProt NPD GO	MSAS_PENPA	6-methylsalicylic acid synthase (EC 2.3.1.165) (6-MSAS)	0.15	-	cyt	0					1774

You are viewing entries 56501 to 56550 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.