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
P49723 UniProt NPD GO	RIR4_YEAST	Ribonucleoside-diphosphate reductase small chain 2 (EC 1.17.4.1) (Ribonucleotide reductase small sub ...	0.03	-	nuc	0	Nucleus. Found predominantly in the nucleus under normal growth conditions and is redistributed to t ...	cytoplasm [IDA] nucleus [IDA] ribonucleoside-diphosphate reductase complex [IDA]		1ZZD	345
P84531 UniProt NPD GO	RIP_CUCMO	Ribosome-inactivating protein cucurmosin (EC 3.2.2.22) (rRNA N-glycosidase) (Fragment)	0.03	-	nuc	0					27
P20656 UniProt NPD GO	RIP6_SAPOF	Ribosome-inactivating protein saporin-6 precursor (EC 3.2.2.22) (SAP-6) (SO-6) (rRNA N-glycosidase)	0.03	-	vac	0					299
Q9JI75 UniProt NPD GO	NQO2_MOUSE	Ribosyldihydronicotinamide dehydrogenase [quinone] (EC 1.10.99.2) (NRH dehydrogenase [quinone] 2) (Q ...	0.03	-	cyt	0	Cytoplasm (By similarity)				230
Q6AY80 UniProt NPD GO	NQO2_RAT	Ribosyldihydronicotinamide dehydrogenase [quinone] (EC 1.10.99.2) (NRH dehydrogenase [quinone] 2) (Q ...	0.03	-	cyt	0	Cytoplasm (By similarity)				230
P37393 UniProt NPD GO	RBL_CYACA	Ribulose bisphosphate carboxylase large chain (EC 4.1.1.39) (RuBisCO large subunit)	0.03	-	mit	1	Plastid; chloroplast				488
P24673 UniProt NPD GO	RBL_CYLSN	Ribulose bisphosphate carboxylase large chain (EC 4.1.1.39) (RuBisCO large subunit)	0.03	-	nuc	0	Plastid; chloroplast				490
O98945 UniProt NPD GO	RBL_DETCO	Ribulose bisphosphate carboxylase large chain (EC 4.1.1.39) (RuBisCO large subunit)	0.03	-	mit	1	Plastid; chloroplast				490
P00878 UniProt NPD GO	RBL_EUGGR	Ribulose bisphosphate carboxylase large chain (EC 4.1.1.39) (RuBisCO large subunit)	0.03	-	cyt	0	Plastid; chloroplast				475
P92445 UniProt NPD GO	RBL_ASPEL	Ribulose bisphosphate carboxylase large chain (EC 4.1.1.39) (RuBisCO large subunit) (Fragment)	0.03	-	cyt	0	Plastid; chloroplast				449
P51994 UniProt NPD GO	RBL_BAMGL	Ribulose bisphosphate carboxylase large chain (EC 4.1.1.39) (RuBisCO large subunit) (Fragment)	0.03	-	cyt	0	Plastid; chloroplast				440
P48069 UniProt NPD GO	RBL_EUGAN	Ribulose bisphosphate carboxylase large chain (EC 4.1.1.39) (RuBisCO large subunit) (Fragment)	0.03	-	cyt	0	Plastid; chloroplast				436
P48072 UniProt NPD GO	RBL_EUGMY	Ribulose bisphosphate carboxylase large chain (EC 4.1.1.39) (RuBisCO large subunit) (Fragment)	0.03	-	cyt	0	Plastid; chloroplast				436
P48075 UniProt NPD GO	RBL_EUGVI	Ribulose bisphosphate carboxylase large chain (EC 4.1.1.39) (RuBisCO large subunit) (Fragment)	0.03	-	cyt	0	Plastid; chloroplast				436
P50255 UniProt NPD GO	RBL_PORCA	Ribulose bisphosphate carboxylase large chain (EC 4.1.1.39) (RuBisCO large subunit) (Fragment)	0.03	-	nuc	0	Plastid; chloroplast				441
P12466 UniProt NPD GO	RBL_CHLVU	Ribulose bisphosphate carboxylase large chain precursor (EC 4.1.1.39) (RuBisCO large subunit)	0.03	-	cyt	0	Plastid; chloroplast				475
Q37192 UniProt NPD GO	RBL_EUPAT	Ribulose bisphosphate carboxylase large chain precursor (EC 4.1.1.39) (RuBisCO large subunit)	0.03	-	cyt	0	Plastid; chloroplast				485
P19161 UniProt NPD GO	RBL_FLABI	Ribulose bisphosphate carboxylase large chain precursor (EC 4.1.1.39) (RuBisCO large subunit)	0.03	-	cyt	0	Plastid; chloroplast				485
P19162 UniProt NPD GO	RBL_FLAPR	Ribulose bisphosphate carboxylase large chain precursor (EC 4.1.1.39) (RuBisCO large subunit)	0.03	-	cyt	0	Plastid; chloroplast				485
P45738 UniProt NPD GO	RBL_HELAN	Ribulose bisphosphate carboxylase large chain precursor (EC 4.1.1.39) (RuBisCO large subunit)	0.03	-	cyt	0	Plastid; chloroplast				485
Q9T4F2 UniProt NPD GO	RBL_NEPOL	Ribulose bisphosphate carboxylase large chain precursor (EC 4.1.1.39) (RuBisCO large subunit)	0.03	-	cyt	0	Plastid; chloroplast				475
P24395 UniProt NPD GO	RBS_ECTSI	Ribulose bisphosphate carboxylase small chain (EC 4.1.1.39) (RuBisCO small subunit)	0.03	-	cyt	0	Plastid; chloroplast				139
P10797 UniProt NPD GO	RBS2B_ARATH	Ribulose bisphosphate carboxylase small chain 2B, chloroplast precursor (EC 4.1.1.39) (RuBisCO small ...	0.03	-	mit	0	Plastid; chloroplast				181
P07180 UniProt NPD GO	RBS3A_LYCES	Ribulose bisphosphate carboxylase small chain 3A/3C, chloroplast precursor (EC 4.1.1.39) (RuBisCO sm ...	0.03	-	mit	0	Plastid; chloroplast				180
P05349 UniProt NPD GO	RBS3B_LYCES	Ribulose bisphosphate carboxylase small chain 3B, chloroplast precursor (EC 4.1.1.39) (RuBisCO small ...	0.03	-	mit	0	Plastid; chloroplast				180
O64416 UniProt NPD GO	RBS_MARPA	Ribulose bisphosphate carboxylase small chain, chloroplast precursor (EC 4.1.1.39) (RuBisCO small su ...	0.03	-	mit	0	Plastid; chloroplast				180
Q03395 UniProt NPD GO	ROM1_HUMAN	Rod outer segment membrane protein 1 (ROSP1) (Tetraspanin-23) (Tspan-23)	0.03	-	end	4 *	Membrane; multi-pass membrane protein	integral to plasma membrane [TAS]	268000		351
O49065 UniProt NPD GO	RAP_TAROF	Root allergen protein (RAP)	0.03	-	cyt	0					157
Q25264 UniProt NPD GO	DCAM_LEIDO	S-adenosylmethionine decarboxylase proenzyme (EC 4.1.1.50) (AdoMetDC) (SamDC) [Contains: S-adenosylm ...	0.03	-	cyt	0					382
Q9NGA0 UniProt NPD GO	DCAM_LEIIN	S-adenosylmethionine decarboxylase proenzyme (EC 4.1.1.50) (AdoMetDC) (SamDC) [Contains: S-adenosylm ...	0.03	-	cyt	0					392
O43938 UniProt NPD GO	METK_LEIIN	S-adenosylmethionine synthetase (EC 2.5.1.6) (Methionine adenosyltransferase) (AdoMet synthetase)	0.03	-	cyt	0					392
Q4R924 UniProt NPD GO	METK2_MACFA	S-adenosylmethionine synthetase isoform type-2 (EC 2.5.1.6) (Methionine adenosyltransferase 2) (AdoM ...	0.03	-	cyt	0					395
Q3THS6 UniProt NPD GO	METK2_MOUSE	S-adenosylmethionine synthetase isoform type-2 (EC 2.5.1.6) (Methionine adenosyltransferase 2) (AdoM ...	0.03	-	cyt	0					395
Q5R5H1 UniProt NPD GO	METK2_PONPY	S-adenosylmethionine synthetase isoform type-2 (EC 2.5.1.6) (Methionine adenosyltransferase 2) (AdoM ...	0.03	-	cyt	0					395
P31153 UniProt NPD GO	METK2_HUMAN	S-adenosylmethionine synthetase isoform type-2 (EC 2.5.1.6) (Methionine adenosyltransferase 2) (AdoM ...	0.03	-	cyt	0			601468		395
Q42546 UniProt NPD GO	DPNP1_ARATH	SAL1 phosphatase (3'(2'),5'-bisphosphate nucleotidase 1) (EC 3.1.3.7) (3'(2'),5'-bisphosphonucleosid ...	0.03	-	nuc	0					353
Q39255 UniProt NPD GO	SKP1A_ARATH	SKP1-like protein 1A (SKP1-like 1) (UFO-binding protein 1)	0.03	-	cyt	0	Nucleus. Spindle. Phragmoplast. Associated to mitotic spindle and phragmoplasts during cell division ...				160
P15981 UniProt NPD GO	HA2D_PIG	SLA class II histocompatibility antigen, DQ haplotype D alpha chain precursor	0.03	-	end	1	Membrane; single-pass type I membrane protein (Potential)				255
P36377 UniProt NPD GO	SPRC_CHICK	SPARC precursor (Secreted protein acidic and rich in cysteine) (Osteonectin) (ON) (Basement-membrane ...	0.03	-	exc	0					298
P07214 UniProt NPD GO	SPRC_MOUSE	SPARC precursor (Secreted protein acidic and rich in cysteine) (Osteonectin) (ON) (Basement-membrane ...	0.03	-	exc	0					302
P38997 UniProt NPD GO	LYS1_YARLI	Saccharopine dehydrogenase [NAD+, L-lysine-forming] (EC 1.5.1.7) (Lysine--2-oxoglutarate reductase) ...	0.03	-	nuc	0					369
P13211 UniProt NPD GO	SRTD_ATREN	Sarafotoxin-D (S6D) (SRTX-D)	0.03	-	cyt	0	Secreted protein				21
P42532 UniProt NPD GO	SARCO_RABIT	Sarcolipin	0.03	-	cyt	1 *	Sarcoplasmic reticulum; sarcoplasmic reticulum membrane; single-pass membrane protein				31
Q14714 UniProt NPD GO	SSPN_HUMAN	Sarcospan (K-ras oncogene-associated protein) (Kirsten-ras-associated protein)	0.03	-	end	4	Sarcolemma; sarcolemmal membrane; multi-pass membrane protein (By similarity). Also found in myotend ...	dystrophin-associated glycoprotein complex [TAS] integral to plasma membrane [TAS]	601599		243
Q61009 UniProt NPD GO	SCRB1_MOUSE	Scavenger receptor class B member 1 (SRB1) (SR-BI)	0.03	-	end	2 *	Cell membrane; multi-pass membrane protein (By similarity). Predominantly localized to cholesterol a ...	caveolar membrane [IDA] integral to membrane of membrane fraction [IDA] integral to plasma membrane [IDA]			509
Q60417 UniProt NPD GO	SCRB1_CRIGR	Scavenger receptor class B member 1 (SRB1) (SR-BI) (HaSR-BI)	0.03	-	end	2 *	Cell membrane; multi-pass membrane protein (By similarity). Predominantly localized to cholesterol a ...				509
P56972 UniProt NPD GO	SCRP_PANIM	Scorpin precursor (Scorpine)	0.03	-	cyt	1 *	Secreted protein				94
P83939 UniProt NPD GO	SCRN1_BOVIN	Secernin-1 (p50) (Fragments)	0.03	-	cyt	0	Cytoplasm				100
P97401 UniProt NPD GO	SFRP3_MOUSE	Secreted frizzled-related protein 3 precursor (sFRP-3) (Frizzled-related protein 1) (FrzB-1) (Frezzl ...	0.03	-	exc	0	Secreted protein (Probable)	extracellular region [NAS]		1IJX	323
O46502 UniProt NPD GO	SCTR_RABIT	Secretin receptor precursor (SCT-R)	0.03	-	end	7 *	Membrane; multi-pass membrane protein				445

You are viewing entries 81601 to 81650 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.