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
Q40379 UniProt NPD GO	RNS6_NICAL	Ribonuclease S-6 precursor (EC 3.1.27.1) (Stylar glycoprotein 6) (S6-RNase)	0.05	-	exc	1 *	Secreted protein; extracellular space				215
Q70IB3 UniProt NPD GO	RNS10_HORSE	Ribonuclease-like protein 10 precursor (Protein Train A) (Fragment)	0.05	-	exc	1 *	Secreted protein (By similarity)				165
Q70IB1 UniProt NPD GO	RNS10_SHEEP	Ribonuclease-like protein 10 precursor (Protein Train A) (Fragment)	0.05	-	exc	1 *	Secreted protein (By similarity)				161
P09938 UniProt NPD GO	RIR2_YEAST	Ribonucleoside-diphosphate reductase small chain 1 (EC 1.17.4.1) (Ribonucleotide reductase small sub ...	0.05	-	cyt	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]		2CVY	399
Q9XGA1 UniProt NPD GO	KPRS4_SPIOL	Ribose-phosphate pyrophosphokinase 4 (EC 2.7.6.1) (Phosphoribosyl pyrophosphate synthetase 4)	0.05	-	cyt	0	Cytoplasm (Potential)				318
Q00465 UniProt NPD GO	RIPA_LUFCY	Ribosome-inactivating protein luffin-alpha precursor (EC 3.2.2.22) (rRNA N-glycosidase)	0.05	-	end	0					277
P27561 UniProt NPD GO	RIP4_SAPOF	Ribosome-inactivating protein saporin-4 precursor (EC 3.2.2.22) (SAP-4) (SO-3) (rRNA N-glycosidase) ...	0.05	-	exc	0					157
Q42813 UniProt NPD GO	RBL2_GONPO	Ribulose 1,5-bisphosphate carboxylase, chloroplast precursor (EC 4.1.1.39) (Fragment)	0.05	-	cyt	0	Plastid; chloroplast (Probable). In this organism the plastid is the result of a secondary endosymbi ...				547
P48073 UniProt NPD GO	RBL_EUGPI	Ribulose bisphosphate carboxylase large chain (EC 4.1.1.39) (RuBisCO large subunit) (Fragment)	0.05	-	cyt	0	Plastid; chloroplast				435
P26574 UniProt NPD GO	RBS1_SOLTU	Ribulose bisphosphate carboxylase small chain 1, chloroplast precursor (EC 4.1.1.39) (RuBisCO small ...	0.05	-	mit	0	Plastid; chloroplast				181
Q39748 UniProt NPD GO	RBS6_FLAPR	Ribulose bisphosphate carboxylase small chain 6, chloroplast precursor (EC 4.1.1.39) (RuBisCO small ...	0.05	-	cyt	0	Plastid; chloroplast				173
Q08186 UniProt NPD GO	RBS6_MESCR	Ribulose bisphosphate carboxylase small chain 6, chloroplast precursor (EC 4.1.1.39) (RuBisCO small ...	0.05	-	mit	0	Plastid; chloroplast				186
P19310 UniProt NPD GO	RBS4_LEMGI	Ribulose bisphosphate carboxylase small chain SSU40B, chloroplast precursor (EC 4.1.1.39) (RuBisCO s ...	0.05	-	vac	0	Plastid; chloroplast				177
P04714 UniProt NPD GO	RBS1_PETHY	Ribulose bisphosphate carboxylase small chain SSU8, chloroplast precursor (EC 4.1.1.39) (RuBisCO sma ...	0.05	-	mit	0	Plastid; chloroplast				180
P05348 UniProt NPD GO	RBS_MAIZE	Ribulose bisphosphate carboxylase small chain, chloroplast precursor (EC 4.1.1.39) (RuBisCO small su ...	0.05	-	mit	0	Plastid; chloroplast				170
O48550 UniProt NPD GO	RBS_ZANAE	Ribulose bisphosphate carboxylase small chain, chloroplast precursor (EC 4.1.1.39) (RuBisCO small su ...	0.05	-	mit	0	Plastid; chloroplast				178
P00868 UniProt NPD GO	RBS1_PEA	Ribulose bisphosphate carboxylase small chain, chloroplast precursor (EC 4.1.1.39) (RuBisCO small su ...	0.05	-	cyt	0	Plastid; chloroplast				136
Q9ZT00 UniProt NPD GO	RCA_MAIZE	Ribulose bisphosphate carboxylase/oxygenase activase, chloroplast precursor (RuBisCO activase) (RA)	0.05	-	mit	0	Plastid; chloroplast; chloroplast stroma				433
P10871 UniProt NPD GO	RCA_SPIOL	Ribulose bisphosphate carboxylase/oxygenase activase, chloroplast precursor (RuBisCO activase) (RA)	0.05	-	mit	0	Plastid; chloroplast; chloroplast stroma				472
Q5PPM7 UniProt NPD GO	ROM1_RAT	Rod outer segment membrane protein 1 (ROSP1)	0.05	-	end	4 *	Membrane; multi-pass membrane protein (By similarity)				351
P39657 UniProt NPD GO	RUAP_SOYBN	RuBisCO-associated protein	0.05	-	cyt	0					283
Q9AVE3 UniProt NPD GO	SCRA_ARALY	S locus cysteine-rich-like protein a precursor	0.05	-	cyt	1 *					86
Q9AVE2 UniProt NPD GO	SCRB_ARALY	S locus cysteine-rich-like protein b precursor	0.05	-	vac	1 *					81
P32771 UniProt NPD GO	FADH_YEAST	S-(hydroxymethyl)glutathione dehydrogenase (EC 1.1.1.284) (Glutathione-dependent formaldehyde dehydr ...	0.05	-	cyt	0		cytoplasm [IDA] mitochondrion [IDA]			386
Q96555 UniProt NPD GO	DCAM_DATST	S-adenosylmethionine decarboxylase proenzyme (EC 4.1.1.50) (AdoMetDC) (SamDC) [Contains: S-adenosylm ...	0.05	-	cyt	0					362
O24575 UniProt NPD GO	DCAM_MAIZE	S-adenosylmethionine decarboxylase proenzyme (EC 4.1.1.50) (AdoMetDC) (SamDC) [Contains: S-adenosylm ...	0.05	-	cyt	0					400
Q9Z179 UniProt NPD GO	SHCBP_MOUSE	SHC SH2 domain-binding protein 1 (Protein expressed in activated lymphocytes) (mPAL) (SHC-binding pr ...	0.05	-	cyt	0					668
P15980 UniProt NPD GO	HA2C_PIG	SLA class II histocompatibility antigen, DQ haplotype C alpha chain precursor	0.05	-	end	1	Membrane; single-pass type I membrane protein (Potential)				254
P16537 UniProt NPD GO	SPC3_STRPU	SPEC3 protein	0.05	-	cyt	3	Integral membrane protein. In cilia and Golgi complexes				208
Q5E9X6 UniProt NPD GO	SSB1_BOVIN	SPRY domain-containing SOCS box protein 1 (SSB-1)	0.05	-	nuc	0	Cytoplasm (Probable)				273
Q96BD6 UniProt NPD GO	SSB1_HUMAN	SPRY domain-containing SOCS box protein 1 (SSB-1)	0.05	-	nuc	0	Cytoplasm (Probable)				273
Q9D5L7 UniProt NPD GO	SSB1_MOUSE	SPRY domain-containing SOCS box protein 1 (SSB-1)	0.05	-	nuc	0	Cytoplasm (Probable)				273
Q75BV4 UniProt NPD GO	LYS1_ASHGO	Saccharopine dehydrogenase [NAD+, L-lysine-forming] (EC 1.5.1.7) (Lysine--2-oxoglutarate reductase) ...	0.05	-	cyt	0					372
Q870G1 UniProt NPD GO	LYS1_EMENI	Saccharopine dehydrogenase [NAD+, L-lysine-forming] (EC 1.5.1.7) (Lysine--2-oxoglutarate reductase) ...	0.05	-	nuc	0					375
P38998 UniProt NPD GO	LYS1_YEAST	Saccharopine dehydrogenase [NAD+, L-lysine-forming] (EC 1.5.1.7) (Lysine--2-oxoglutarate reductase) ...	0.05	-	nuc	0	Cytoplasm	cytoplasm [IDA]			372
P04569 UniProt NPD GO	SCP1_BRALA	Sarcoplasmic calcium-binding proteins I, III, and IV (SCP I, III, IV)	0.05	-	cyt	0					185
P13585 UniProt NPD GO	AT2A1_CHICK	Sarcoplasmic/endoplasmic reticulum calcium ATPase 1 (EC 3.6.3.8) (Calcium pump 1) (SERCA1) (SR Ca(2+ ...	0.05	-	end	8	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein. Sarcoplasmic ret ...				994
O46674 UniProt NPD GO	AT2A2_CANFA	Sarcoplasmic/endoplasmic reticulum calcium ATPase 2 (EC 3.6.3.8) (Calcium pump 2) (SERCA2) (SR Ca(2+ ...	0.05	-	end	7	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein. Sarcoplasmic ret ...				997
Q00779 UniProt NPD GO	AT2A2_FELCA	Sarcoplasmic/endoplasmic reticulum calcium ATPase 2 (EC 3.6.3.8) (Calcium pump 2) (SERCA2) (SR Ca(2+ ...	0.05	-	end	7	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein. Sarcoplasmic ret ...				997
P16615 UniProt NPD GO	AT2A2_HUMAN	Sarcoplasmic/endoplasmic reticulum calcium ATPase 2 (EC 3.6.3.8) (Calcium pump 2) (SERCA2) (SR Ca(2+ ...	0.05	-	end	8	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein. Sarcoplasmic ret ...	integral to plasma membrane [TAS] membrane fraction [TAS] microsome [TAS] sarcoplasmic reticulum [IDA]	124200		1042
P20647 UniProt NPD GO	AT2A2_RABIT	Sarcoplasmic/endoplasmic reticulum calcium ATPase 2 (EC 3.6.3.8) (Calcium pump 2) (SERCA2) (SR Ca(2+ ...	0.05	-	end	9	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein. Sarcoplasmic ret ...				1042
P11507 UniProt NPD GO	AT2A2_RAT	Sarcoplasmic/endoplasmic reticulum calcium ATPase 2 (EC 3.6.3.8) (Calcium pump 2) (SERCA2) (SR Ca(2+ ...	0.05	-	end	8	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein. Sarcoplasmic ret ...	sarcoplasmic reticulum [TAS]			1043
P24491 UniProt NPD GO	SRX21_SARPE	Sarcotoxin II-1 precursor	0.05	-	nuc	1 *	Secreted protein				265
P08375 UniProt NPD GO	SRX1A_SARPE	Sarcotoxin-1A precursor (Sarcotoxin IA)	0.05	-	vac	1 *	Secreted protein				63
Q8SQC1 UniProt NPD GO	SCRB1_PIG	Scavenger receptor class B member 1 (SRB1) (SR-BI) (High density lipoprotein receptor SR-BI)	0.05	-	end	2 *	Cell membrane; multi-pass membrane protein (By similarity). Predominantly localized to cholesterol a ...				509
P01159 UniProt NPD GO	SCOT_RAT	Scotophobin	0.05	-		0					15
Q80YD6 UniProt NPD GO	SRGEF_MOUSE	Secretion-regulating guanine nucleotide exchange factor (Guanine nucleotide exchange factor-related ...	0.05	-	cyt	0	Cytoplasm (By similarity). Nucleus (By similarity)	cytoplasm [ISS] nucleus [ISS]			464
Q01882 UniProt NPD GO	RA14_ORYSA	Seed allergenic protein RA14 precursor	0.05	-	vac	1 *	Secreted protein (Potential)				165
Q01884 UniProt NPD GO	RAG1_ORYSA	Seed allergenic protein RAG1 precursor (Fragment)	0.05	-	vac	1 *	Secreted protein (Potential)				95
Q01885 UniProt NPD GO	RAG2_ORYSA	Seed allergenic protein RAG2 precursor	0.05	-	vac	1 *	Secreted protein (Potential)				166

You are viewing entries 75601 to 75650 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.