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
P62198 UniProt NPD GO	PRS8_RAT	26S protease regulatory subunit 8 (Proteasome subunit p45) (p45/SUG) (Proteasome 26S subunit ATPase ...	0.10	-	cyt	0	Cytoplasm (Potential). Nucleus (Potential)	cytoplasm [ISS] nucleus [ISS] proteasome complex (sensu Eukaryota) [ISS]			406
P62196 UniProt NPD GO	PRS8_MOUSE	26S protease regulatory subunit 8 (Proteasome subunit p45) (p45/SUG) (Proteasome 26S subunit ATPase ...	0.10	-	cyt	0	Cytoplasm (Potential). Nucleus (Potential)	cytoplasm [ISS] nucleus [ISS] proteasome complex (sensu Eukaryota) [ISS]			406
P34124 UniProt NPD GO	PRS8_DICDI	26S protease regulatory subunit 8 (TAT-binding protein homolog 10) (Fragment)	0.10	-	nuc	0	Cytoplasm (Potential). Nucleus (Potential)				389
Q9UNM6 UniProt NPD GO	PSD13_HUMAN	26S proteasome non-ATPase regulatory subunit 13 (26S proteasome regulatory subunit S11) (26S proteas ...	0.10	-	cyt	0		proteasome regulatory particle (sensu Eukar... [TAS]	603481		376
Q75CF3 UniProt NPD GO	RPN2_ASHGO	26S proteasome regulatory subunit RPN2	0.10	-	cyt	0					930
P50524 UniProt NPD GO	RPN12_SCHPO	26S proteasome regulatory subunit rpn12	0.10	-	cyt	0					270
P82911 UniProt NPD GO	RT11_BOVIN	28S ribosomal protein S11, mitochondrial precursor (S11mt) (MRP-S11)	0.10	-	mit	0	Mitochondrion	mitochondrial small ribosomal subunit [IDA]			197
Q9Y2R5 UniProt NPD GO	RT17_HUMAN	28S ribosomal protein S17, mitochondrial precursor (S17mt) (MRP-S17)	0.10	-	mit	0	Mitochondrion	mitochondrial small ribosomal subunit [NAS]			130
O76819 UniProt NPD GO	HMDH_AGRIP	3-hydroxy-3-methylglutaryl-coenzyme A reductase (EC 1.1.1.34) (HMG-CoA reductase)	0.10	-	end	4	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein				833
P48021 UniProt NPD GO	HMDH_CAMAC	3-hydroxy-3-methylglutaryl-coenzyme A reductase (EC 1.1.1.34) (HMG-CoA reductase)	0.10	-	end	2 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein				593
Q01237 UniProt NPD GO	HMDH_MOUSE	3-hydroxy-3-methylglutaryl-coenzyme A reductase (EC 1.1.1.34) (HMG-CoA reductase)	0.10	-	end	5 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein	microsome [IDA]			887
Q12649 UniProt NPD GO	HMDH_PHYBL	3-hydroxy-3-methylglutaryl-coenzyme A reductase (EC 1.1.1.34) (HMG-CoA reductase)	0.10	-	end	5 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein				1176
P51639 UniProt NPD GO	HMDH_RAT	3-hydroxy-3-methylglutaryl-coenzyme A reductase (EC 1.1.1.34) (HMG-CoA reductase)	0.10	-	end	5 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein	microsome [IDA]			887
Q62904 UniProt NPD GO	DHB7_RAT	3-keto-steroid reductase (EC 1.1.1.270) (Estradiol 17-beta-dehydrogenase 7) (EC 1.1.1.62) (17-beta-H ...	0.10	-	mit	0	Membrane; single-pass membrane protein				334
O00107 UniProt NPD GO	PHYA_THIHE	3-phytase A precursor (EC 3.1.3.8) (Myo-inositol-hexaphosphate 3-phosphohydrolase A) (3 phytase A) ( ...	0.10	-	cyt	0	Secreted protein				487
Q25116 UniProt NPD GO	SM30_HEMPU	30 kDa spicule matrix protein precursor	0.10	-	end	0					288
O44126 UniProt NPD GO	LEG1_HAECO	32 kDa beta-galactoside-binding lectin (Galectin 1)	0.10	-	cyt	0					283
P80836 UniProt NPD GO	CWP14_ARATH	36 kDa cell wall protein (Fragment)	0.10	-		0	Cell wall				10
Q9DB15 UniProt NPD GO	RM12_MOUSE	39S ribosomal protein L12, mitochondrial precursor (L12mt) (MRP-L12)	0.10	-	mit	0	Mitochondrion				201
P52827 UniProt NPD GO	RM12_CRICR	39S ribosomal protein L12, mitochondrial precursor (L12mt) (MRP-L12) (P2A1)	0.10	-	mit	0	Mitochondrion				203
Q5EA20 UniProt NPD GO	HPPD_BOVIN	4-hydroxyphenylpyruvate dioxygenase (EC 1.13.11.27) (4HPPD) (HPD) (HPPDase) (4-hydroxyphenylpyruvic ...	0.10	-	cyt	0					392
P32754 UniProt NPD GO	HPPD_HUMAN	4-hydroxyphenylpyruvate dioxygenase (EC 1.13.11.27) (4HPPD) (HPD) (HPPDase) (4-hydroxyphenylpyruvic ...	0.10	-	nuc	0			609695		392
Q5BKL0 UniProt NPD GO	HPPD_XENTR	4-hydroxyphenylpyruvate dioxygenase (EC 1.13.11.27) (4HPPD) (HPD) (HPPDase) (4-hydroxyphenylpyruvic ...	0.10	+	cyt	0					394
Q29228 UniProt NPD GO	AL9A1_PIG	4-trimethylaminobutyraldehyde dehydrogenase (EC 1.2.1.47) (TMABADH) (Aldehyde dehydrogenase 9A1) (EC ...	0.10	-	nuc	0	Cytoplasm (By similarity)				69
P62279 UniProt NPD GO	RS13_PIG	40S ribosomal protein S13 (Fragment)	0.10	-	nuc	0					106
P42798 UniProt NPD GO	RS15A_ARATH	40S ribosomal protein S15a	0.10	-	cyt	0	Cytoplasm				129
Q00332 UniProt NPD GO	RS15A_BRANA	40S ribosomal protein S15a (PPCB8)	0.10	-	cyt	0	Cytoplasm				129
P49202 UniProt NPD GO	RS18_CHLRE	40S ribosomal protein S18	0.10	-	cyt	0	Cytoplasm				153
Q9SGA6 UniProt NPD GO	RS191_ARATH	40S ribosomal protein S19-1	0.10	-	cyt	0					143
Q7ZUG5 UniProt NPD GO	RS21_BRARE	40S ribosomal protein S21	0.10	-	cyt	0					81
P0C0X0 UniProt NPD GO	RS28B_YEAST	40S ribosomal protein S28-B (S33) (YS27)	0.10	-	cyt	0		cytosolic small ribosomal subunit (sensu Eu... [TAS]			67
P38980 UniProt NPD GO	RSSA_TRIGR	40S ribosomal protein SA (p40) (34/67 kDa laminin-binding protein)	0.10	-	nuc	0	Cytoplasm				316
P46770 UniProt NPD GO	RSSA_ECHGR	40S ribosomal protein SA (p40) (Laminin-binding protein)	0.10	-	cyt	0	Cytoplasm				268
P22108 UniProt NPD GO	APA2_YEAST	5',5'''-P-1,P-4-tetraphosphate phosphorylase 2 (EC 2.7.7.53) (Diadenosine 5',5'''-P1,P4-tetraphospha ...	0.10	-	nuc	0		cytoplasm [IDA] nucleus [IDA]			325
P50407 UniProt NPD GO	5HT7R_CAVPO	5-hydroxytryptamine 7 receptor (5-HT-7) (Serotonin receptor 7) (5-HT-X)	0.10	-	end	7	Membrane; multi-pass membrane protein				446
P82192 UniProt NPD GO	RK5_SPIOL	50S ribosomal protein L5, chloroplast	0.10	-	cyt	0	Plastid; chloroplast				220
P53319 UniProt NPD GO	6PGD2_YEAST	6-phosphogluconate dehydrogenase, decarboxylating 2 (EC 1.1.1.44)	0.10	-	cyt	0		cytosol [TAS]			492
P56378 UniProt NPD GO	68MP_HUMAN	6.8 kDa mitochondrial proteolipid	0.10	-	cyt	1 *	Mitochondrion (By similarity)		604573		58
P10155 UniProt NPD GO	RO60_HUMAN	60 kDa SS-A/Ro ribonucleoprotein (60 kDa Ro protein) (60 kDa ribonucleoprotein Ro) (RoRNP) (Ro 60 kD ...	0.10	-	cyt	0	Cytoplasm	ribonucleoprotein complex [TAS]	600063		538
Q5NVM5 UniProt NPD GO	CH60_PONPY	60 kDa heat shock protein, mitochondrial precursor (Hsp60) (60 kDa chaperonin) (CPN60) (Heat shock p ...	0.10	-	cyt	0	Mitochondrion; mitochondrial matrix (By similarity)				573
P10809 UniProt NPD GO	CH60_HUMAN	60 kDa heat shock protein, mitochondrial precursor (Hsp60) (60 kDa chaperonin) (CPN60) (Heat shock p ...	0.10	-	cyt	0	Mitochondrion; mitochondrial matrix	cytoplasm [TAS] mitochondrion [TAS]	605280		573
P25642 UniProt NPD GO	IMG2_YEAST	60S ribosomal protein IMG2, mitochondrial precursor	0.10	-	mit	0	Mitochondrion	mitochondrial large ribosomal subunit [IPI]			146
O14363 UniProt NPD GO	RL1A_SCHPO	60S ribosomal protein L1-A (L10a)	0.10	+	nuc	0					216
O50003 UniProt NPD GO	RL12_PRUAR	60S ribosomal protein L12	0.10	-	cyt	0					166
Q3T057 UniProt NPD GO	RL23_BOVIN	60S ribosomal protein L23	0.10	-	cyt	0					140
Q6PC14 UniProt NPD GO	RL23_BRARE	60S ribosomal protein L23	0.10	-	mit	0					140
Q9XSU3 UniProt NPD GO	RL23_CANFA	60S ribosomal protein L23	0.10	-	mit	0					140
Q90YU5 UniProt NPD GO	RL23_ICTPU	60S ribosomal protein L23	0.10	-	mit	0					140
P62830 UniProt NPD GO	RL23_MOUSE	60S ribosomal protein L23	0.10	-	mit	0		nucleolus [IDA]			140
Q5REU2 UniProt NPD GO	RL23_PONPY	60S ribosomal protein L23	0.10	-	mit	0					140

You are viewing entries 63801 to 63850 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.