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
Q9FPR6 UniProt NPD GO	ARR17_ARATH	Two-component response regulator ARR17	0.07	-	nuc	0	Nucleus (Probable)				153
Q9M8Y4 UniProt NPD GO	ARR22_ARATH	Two-component response regulator ARR22	0.07	-	cyt	0	Nucleus (Probable)				142
Q8VIB3 UniProt NPD GO	SIA10_MOUSE	Type 2 lactosamine alpha-2,3-sialyltransferase (EC 2.4.99.-) (CMP-NeuAc:beta-galactoside alpha-2,3-s ...	0.07	-	mit	1 *	Golgi apparatus; Golgi membrane; single-pass type II membrane protein (Potential)				329
Q29467 UniProt NPD GO	I5P1_CANFA	Type I inositol-1,4,5-trisphosphate 5-phosphatase (EC 3.1.3.56) (5PTase)	0.07	-	cyt	0	Membrane; lipid-anchor				412
P43240 UniProt NPD GO	AGTR1_CANFA	Type-1 angiotensin II receptor (AT1)	0.07	-	end	7 *	Membrane; multi-pass membrane protein				359
P79785 UniProt NPD GO	AGTR1_CHICK	Type-1 angiotensin II receptor (AT1)	0.07	-	end	7 *	Membrane; multi-pass membrane protein				359
P33396 UniProt NPD GO	AGTR1_MELGA	Type-1 angiotensin II receptor (AT1)	0.07	-	end	7 *	Membrane; multi-pass membrane protein				359
Q9Z0Z6 UniProt NPD GO	AGTR2_MERUN	Type-2 angiotensin II receptor (AT2)	0.07	-	end	7 *	Membrane; multi-pass membrane protein				363
P35351 UniProt NPD GO	AGTR2_RAT	Type-2 angiotensin II receptor (AT2)	0.07	-	end	7 *	Membrane; multi-pass membrane protein	perinuclear region [IDA] plasma membrane [IDA]			363
P81765 UniProt NPD GO	POI_MUSDO	Tyrosinase inhibitor (Phenol oxidase inhibitor) (Phenoloxidase inhibitor) (POI)	0.07	-	nuc	0	Secreted protein				38
O73792 UniProt NPD GO	TIE1_BRARE	Tyrosine-protein kinase receptor Tie-1 (EC 2.7.10.1) (Fragment)	0.07	-	cyt	0	Membrane; single-pass type I membrane protein				184
P28208 UniProt NPD GO	PTP16_STYPL	Tyrosine-protein phosphatase 16 (EC 3.1.3.48) (Fragment)	0.07	-	cyt	0					109
P28218 UniProt NPD GO	PTP26_STYPL	Tyrosine-protein phosphatase 26 (EC 3.1.3.48) (Fragment)	0.07	-	cyt	0					117
Q29465 UniProt NPD GO	SYYC_BOVIN	Tyrosyl-tRNA synthetase, cytoplasmic (EC 6.1.1.1) (Tyrosyl--tRNA ligase) (TyrRS)	0.07	-	cyt	0	Cytoplasm (By similarity)				527
Q5ADN8 UniProt NPD GO	HUT1_CANAL	UDP-galactose transporter homolog 1	0.07	-	end	10 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (By similarity)				370
Q9NTN3 UniProt NPD GO	S35D1_HUMAN	UDP-glucuronic acid/UDP-N-acetylgalactosamine transporter (UDP-GlcA/UDP-GalNAc transporter) (Solute ...	0.07	-	end	8 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein	integral to endoplasmic reticulum membrane [NAS]			355
Q91280 UniProt NPD GO	UGT3_PLEPL	UDP-glucuronosyltransferase (EC 2.4.1.17) (UDPGT) (Fragment)	0.07	-	cyt	1	Microsome (By similarity)				472
Q64550 UniProt NPD GO	UD11_RAT	UDP-glucuronosyltransferase 1-1 precursor (EC 2.4.1.17) (UDPGT) (UGT1*1) (UGT1-01) (UGT1.1) (UGT1A1) ...	0.07	-	end	2 *	Microsome				535
Q63886 UniProt NPD GO	UD11_MOUSE	UDP-glucuronosyltransferase 1-1 precursor (EC 2.4.1.17) (UDPGT) (UGT1*1) (UGT1-01) (UGT1.1) (UGT1A1) ...	0.07	-	end	2 *	Microsome	integral to plasma membrane [IDA]			535
P54855 UniProt NPD GO	UDB15_HUMAN	UDP-glucuronosyltransferase 2B15 precursor (EC 2.4.1.17) (UDPGT) (UDPGTh-3) (HLUG4)	0.07	-	nuc	1	Microsome		600069		530
O19103 UniProt NPD GO	UDB16_RABIT	UDP-glucuronosyltransferase 2B16 precursor (EC 2.4.1.17) (UDPGT) (Fragment)	0.07	-	end	1	Microsome				523
Q9XT55 UniProt NPD GO	UDB19_MACFA	UDP-glucuronosyltransferase 2B19 precursor (EC 2.4.1.17) (UDPGT)	0.07	-	end	1	Microsome (By similarity)				528
P19488 UniProt NPD GO	UDB5_RAT	UDP-glucuronosyltransferase 2B5 precursor (EC 2.4.1.17) (UDPGT) (17-beta-hydroxysteroid specific) (U ...	0.07	-	end	1	Microsome				530
Q6P6M7 UniProt NPD GO	UGTAP_MOUSE	UGA suppressor tRNA-associated protein	0.07	-	nuc	0	Cytoplasm (By similarity)	cytoplasm [IDA] nucleus [IDA]			504
Q9DBP5 UniProt NPD GO	KCY_MOUSE	UMP-CMP kinase (EC 2.7.4.14) (Cytidylate kinase) (Deoxycytidylate kinase) (Cytidine monophosphate ki ...	0.07	-	cyt	0	Nucleus (By similarity). Mainly. Cytoplasm (By similarity)				196
O08654 UniProt NPD GO	CP070_RAT	UPF0183 protein C16orf70 homolog	0.07	-	cyt	0					422
Q91ZJ5 UniProt NPD GO	UGPA2_MOUSE	UTP--glucose-1-phosphate uridylyltransferase 2 (EC 2.7.7.9) (UDP-glucose pyrophosphorylase 2) (UDPGP ...	0.07	-	cyt	0	Cytoplasm (By similarity)				507
P79303 UniProt NPD GO	UGPA2_PIG	UTP--glucose-1-phosphate uridylyltransferase 2 (EC 2.7.7.9) (UDP-glucose pyrophosphorylase 2) (UDPGP ...	0.07	-	cyt	0	Cytoplasm				507
Q69BJ9 UniProt NPD GO	UCRI_AOTAZ	Ubiquinol-cytochrome c reductase iron-sulfur subunit, mitochondrial precursor (EC 1.10.2.2) (Rieske ...	0.07	-	cyt	0	Mitochondrion; mitochondrial inner membrane (By similarity)				274
Q09154 UniProt NPD GO	UCRI_SCHPO	Ubiquinol-cytochrome c reductase iron-sulfur subunit, mitochondrial precursor (EC 1.10.2.2) (Rieske ...	0.07	-	mit	0	Mitochondrion; mitochondrial inner membrane	mitochondrial inner membrane [IGI] respiratory chain complex III (sensu Eukary... [IGI]			228
P09936 UniProt NPD GO	UCHL1_HUMAN	Ubiquitin carboxyl-terminal hydrolase isozyme L1 (EC 3.4.19.12) (EC 6.-.-.-) (UCH-L1) (Ubiquitin thi ...	0.07	-	nuc	0	Cytoplasm	cytoplasm [TAS]	191342	2ETL	223
Q9M2P4 UniProt NPD GO	SINA2_ARATH	Ubiquitin ligase SINAT2 (EC 6.3.2.-) (Seven in absentia homolog 2)	0.07	-	cyt	0					308
Q9D1C1 UniProt NPD GO	UBE2C_MOUSE	Ubiquitin-conjugating enzyme E2 C (EC 6.3.2.19) (Ubiquitin-protein ligase C) (Ubiquitin carrier prot ...	0.07	-	nuc	0					179
Q3SZ43 UniProt NPD GO	UB2V2_BOVIN	Ubiquitin-conjugating enzyme E2 variant 2	0.07	-	nuc	0					144
Q15819 UniProt NPD GO	UB2V2_HUMAN	Ubiquitin-conjugating enzyme E2 variant 2 (MMS2) (Enterocyte differentiation-associated factor EDAF- ...	0.07	-	nuc	0		cytoplasm [TAS] nucleus [IDA] UBC13-MMS2 complex [IDA]	603001	1ZGU	144
Q6DI37 UniProt NPD GO	UBCP1_BRARE	Ubiquitin-like domain-containing CTD phosphatase 1 (EC 3.1.3.16)	0.07	-	cyt	0	Nucleus (By similarity)				318
O14399 UniProt NPD GO	UBL1_SCHPO	Ubiquitin-like protein 1	0.07	-	nuc	0		SCF ubiquitin ligase complex [IDA]			78
Q4WVZ0 UniProt NPD GO	YA800_ASPFU	Uncharacterized protein Afu5g13800	0.07	-	mit	0					261
Q6P8Y0 UniProt NPD GO	CO026_MOUSE	Uncharacterized protein C15orf26 homolog	0.07	-	cyt	0					303
Q9NUV7 UniProt NPD GO	CT038_HUMAN	Uncharacterized protein C20orf38	0.07	-	cyt	0					175
Q09895 UniProt NPD GO	YAI8_SCHPO	Uncharacterized protein C24B11.08c	0.07	-	mit	2 *	Membrane; multi-pass membrane protein (Potential)				390
Q22004 UniProt NPD GO	AMER1_CAEEL	Uncharacterized protein R166.3	0.07	-	cyt	0					200
P38896 UniProt NPD GO	YAN2_YEAST	Uncharacterized protein YAR062W/YHR213W	0.07	-	nuc	0					198
P38231 UniProt NPD GO	YBP7_YEAST	Uncharacterized protein YBR047W	0.07	-	mit	0		mitochondrion [IDA]			175
P38247 UniProt NPD GO	YBS7_YEAST	Uncharacterized protein YBR077C	0.07	-	nuc	0		cytoplasm [IDA] vacuolar membrane (sensu Fungi) [IDA]			162
P25584 UniProt NPD GO	YCF6_YEAST	Uncharacterized protein YCL056C	0.07	-	mit	0		cytoplasm [IDA]			144
P40008 UniProt NPD GO	YEJ4_YEAST	Uncharacterized protein YER004W	0.07	-	cyt	0		endoplasmic reticulum [IDA] mitochondrial outer membrane [IDA] mitochondrion [IDA]			231
P38745 UniProt NPD GO	YHB7_YEAST	Uncharacterized protein YHL071W precursor	0.07	-	end	7	Golgi apparatus; trans-Golgi network; trans-Golgi network membrane; multi-pass membrane protein (Pro ...				532
Q02598 UniProt NPD GO	YI014_YEAST	Uncharacterized protein YIL014C-A	0.07	-	cyt	0					104
Q2V2P5 UniProt NPD GO	YI102_YEAST	Uncharacterized protein YIL102C-A	0.07	-	mit	2 *	Membrane; multi-pass membrane protein (Potential)				75

You are viewing entries 71201 to 71250 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.