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
P31751 UniProt NPD GO	AKT2_HUMAN	RAC-beta serine/threonine-protein kinase (EC 2.7.11.1) (RAC-PK-beta) (Protein kinase Akt-2) (Protein ...	0.18	-	cyt	0			164731	1O6L	481
Q7ZX15 UniProt NPD GO	AKT2A_XENLA	RAC-beta serine/threonine-protein kinase-A (EC 2.7.11.1) (RAC-PK-beta-A) (Protein kinase Akt-2-A) (P ...	0.18	-	cyt	0					486
Q6IP76 UniProt NPD GO	AKT2B_XENLA	RAC-beta serine/threonine-protein kinase-B (EC 2.7.11.1) (RAC-PK-beta-B) (Protein kinase Akt-2-B) (P ...	0.18	-	cyt	0					485
P01122 UniProt NPD GO	RHO_APLCA	RAS-like GTP-binding protein RHO	0.18	-	cyt	0	Cell membrane; lipid-anchor; cytoplasmic side (Potential)				192
Q23862 UniProt NPD GO	RACE_DICDI	RAS-related protein racE	0.18	-	cyt	0	Cell membrane; lipid-anchor; cytoplasmic side (Potential)				223
Q6PC78 UniProt NPD GO	RN185_BRARE	RING finger protein 185	0.18	-	nuc	2	Membrane; multi-pass membrane protein (Potential)				194
Q8LGA5 UniProt NPD GO	ATL5H_ARATH	RING-H2 finger protein ATL5H precursor	0.18	-	end	2 *					368
Q9Y2P8 UniProt NPD GO	RCL1_HUMAN	RNA 3'-terminal phosphate cyclase-like protein	0.18	-	mit	0	Nucleus; nucleolus (By similarity)	nucleolus [NAS]			373
P38633 UniProt NPD GO	MED31_YEAST	RNA polymerase II mediator complex subunit 31 (Hpr1 suppressor protein 1)	0.18	-	cyt	0	Nucleus	nucleus [IDA]			127
Q9UNT1 UniProt NPD GO	RBL2B_HUMAN	Rab-like protein 2B	0.18	-	cyt	0			605413		228
Q6EP31 UniProt NPD GO	RAC5_ORYSA	Rac-like GTP-binding protein 5 (OsRac5) (GTPase protein RacD)	0.18	-	cyt	0	Cytoplasm (By similarity). Membrane; peripheral membrane protein (By similarity). Associated with th ...				197
Q6ZHA3 UniProt NPD GO	RAC6_ORYSA	Rac-like GTP-binding protein 6 (OsRac6) (GTPase protein RacB)	0.18	-	cyt	0	Cytoplasm (By similarity). Membrane; peripheral membrane protein (By similarity). Associated with th ...				197
Q38902 UniProt NPD GO	RAC1_ARATH	Rac-like GTP-binding protein ARAC1 (GTPase protein ROP3)	0.18	-	cyt	0	Cytoplasm (By similarity). Membrane; peripheral membrane protein (By similarity). Associated with th ...				197
P92978 UniProt NPD GO	RAC11_ARATH	Rac-like GTP-binding protein ARAC11 (GTPase protein ROP1)	0.18	-	cyt	0	Cytoplasm (By similarity). Membrane; peripheral membrane protein (By similarity). Associated with th ...	cytoplasm [IDA] nucleolus [IDA] nucleus [IDA] phragmoplast [IDA] plasma membrane [TAS] spindle [IDA]			197
Q39435 UniProt NPD GO	RAC1_BETVU	Rac-like GTP-binding protein RHO1 (RHO1Bv)	0.18	-	cyt	0	Cytoplasm (By similarity). Membrane; peripheral membrane protein (By similarity). Associated with th ...				197
Q8BIV3 UniProt NPD GO	RNBP6_MOUSE	Ran-binding protein 6 (RanBP6) (Fragment)	0.18	-	cyt	0	Cytoplasm (By similarity). Nucleus (By similarity)				439
P18262 UniProt NPD GO	RAS_ARTSA	Ras-like protein (Fragment)	0.18	-	cyt	0	Cell membrane; lipid-anchor; cytoplasmic side (Potential)				178
Q39433 UniProt NPD GO	RB1BV_BETVU	Ras-related protein RAB1BV	0.18	-	mit	0	Cell membrane; lipid-anchor; cytoplasmic side (Potential)				215
Q969Q5 UniProt NPD GO	RAB24_HUMAN	Ras-related protein Rab-24	0.18	-	cyt	0	Endoplasmic reticulum-Golgi intermediate compartment (By similarity). Endosome; late endosome (By si ...				203
P35290 UniProt NPD GO	RAB24_MOUSE	Ras-related protein Rab-24 (Rab-16)	0.18	-	cyt	0	Endoplasmic reticulum-Golgi intermediate compartment. Endosome; late endosome				203
Q94986 UniProt NPD GO	RAB3_CAEEL	Ras-related protein Rab-3	0.18	-	cyt	0	Cell membrane; lipid-anchor; cytoplasmic side (Potential)	synaptic vesicle [IDA]			219
Q68EK7 UniProt NPD GO	RAB4B_BRARE	Ras-related protein Rab-4B	0.18	-	cyt	0	Cell membrane; lipid-anchor; cytoplasmic side (Potential)				213
P20339 UniProt NPD GO	RAB5A_HUMAN	Ras-related protein Rab-5A	0.18	-	nuc	0	Cell membrane; lipid-anchor; cytoplasmic side (By similarity). Endosome; early endosome; early endos ...	early endosome [IDA]	179512	1TU4	215
Q7ZVX5 UniProt NPD GO	REEP3_BRARE	Receptor expression-enhancing protein 3	0.18	-	gol	2 *	Membrane; multi-pass membrane protein (By similarity)				256
P97844 UniProt NPD GO	RGS1_RAT	Regulator of G-protein signaling 1 (RGS1)	0.18	-	nuc	0					162
P49806 UniProt NPD GO	RGS10_RAT	Regulator of G-protein signaling 10 (RGS10) (Fragment)	0.18	-	nuc	0					66
P27652 UniProt NPD GO	LUCI_RENRE	Renilla-luciferin 2-monooxygenase (EC 1.13.12.5) (Renilla-type luciferase)	0.18	-	cyt	0					311
P53034 UniProt NPD GO	RFC2_DROME	Replication factor C subunit 2 (Replication factor C 40 kDa subunit) (RF-C 40 kDa subunit) (RFC40) ( ...	0.18	-	cyt	0	Nucleus				331
Q96B86 UniProt NPD GO	RGMA_HUMAN	Repulsive guidance molecule A precursor (RGM domain family member A)	0.18	-	nuc	0	Cell membrane; lipid-anchor; GPI-anchor (By similarity)		607362		450
P55203 UniProt NPD GO	GUC2D_BOVIN	Retinal guanylyl cyclase 1 precursor (EC 4.6.1.2) (Guanylate cyclase 2D, retinal) (RETGC-1) (Rod out ...	0.18	-	end	2	Membrane; single-pass type I membrane protein				1110
P10400 UniProt NPD GO	POL1_MOUSE	Retrovirus-related Pol polyprotein [Includes: Reverse transcriptase (EC 2.7.7.49); Endonuclease] (Fr ...	0.18	-	cyt	0					120
Q76C99 UniProt NPD GO	RF1_ORYSA	Rf1 protein, mitochondrial precursor (PPR protein) (Fertility restorer) (Restorer for CMS)	0.18	-	mit	0	Mitochondrion (Potential)				791
P82270 UniProt NPD GO	RTD1A_MACMU	Rhesus theta defensin-1/3, subunit A precursor (RTD-1a) (RTD-1 subunit A) (RTD-3) (Demidefensin-2)	0.18	-	exc	0					76
P97348 UniProt NPD GO	RHOD_MOUSE	Rho-related GTP-binding protein RhoD precursor	0.18	-	cyt	0	Cell membrane. Endosome; early endosome				210
Q8SPZ5 UniProt NPD GO	RNAS8_AOTTR	Ribonuclease 8 precursor (EC 3.1.27.-) (RNase 8)	0.18	-	nuc	0	Secreted protein (Probable)				155
Q9DB28 UniProt NPD GO	POP5_MOUSE	Ribonuclease P/MRP protein subunit POP5 (EC 3.1.26.5)	0.18	-	cyt	0	Nucleus; nucleolus (By similarity)	nucleolar ribonuclease P complex [IDA]			169
P00667 UniProt NPD GO	RNAS1_ALCAA	Ribonuclease pancreatic (EC 3.1.27.5) (RNase 1) (RNase A)	0.18	-	nuc	0	Secreted protein				124
P00668 UniProt NPD GO	RNAS1_ANTAM	Ribonuclease pancreatic (EC 3.1.27.5) (RNase 1) (RNase A)	0.18	-	nuc	0	Secreted protein				124
P00675 UniProt NPD GO	RNAS1_CHIBR	Ribonuclease pancreatic (EC 3.1.27.5) (RNase 1) (RNase A)	0.18	-	nuc	0	Secreted protein				124
P00676 UniProt NPD GO	RNAS1_MYOCO	Ribonuclease pancreatic (EC 3.1.27.5) (RNase 1) (RNase A)	0.18	-	nuc	0	Secreted protein				128
Q8SPJ0 UniProt NPD GO	RNS10_PIG	Ribonuclease-like protein 10 precursor (Protein Train A)	0.18	-	exc	1 *	Secreted protein				213
P31350 UniProt NPD GO	RIR2_HUMAN	Ribonucleoside-diphosphate reductase M2 subunit (EC 1.17.4.1) (Ribonucleotide reductase small subuni ...	0.18	-	cyt	0	Cytoplasm	cytoplasm [NAS]	180390		389
P48591 UniProt NPD GO	RIR1_DROME	Ribonucleoside-diphosphate reductase large subunit (EC 1.17.4.1) (Ribonucleoside-diphosphate reducta ...	0.18	-	mit	0					812
Q42581 UniProt NPD GO	KPRS1_ARATH	Ribose-phosphate pyrophosphokinase 1 (EC 2.7.6.1) (Phosphoribosyl pyrophosphate synthetase 1) (PRS I ...	0.18	-	mit	0					403
Q9CS42 UniProt NPD GO	PRPS2_MOUSE	Ribose-phosphate pyrophosphokinase II (EC 2.7.6.1) (Phosphoribosyl pyrophosphate synthetase II) (PRS ...	0.18	-	cyt	0					317
P09330 UniProt NPD GO	PRPS2_RAT	Ribose-phosphate pyrophosphokinase II (EC 2.7.6.1) (Phosphoribosyl pyrophosphate synthetase II) (PRS ...	0.18	-	cyt	0					317
P25892 UniProt NPD GO	RIP9_MAIZE	Ribosome-inactivating protein 9 (EC 3.2.2.22) (rRNA N-glycosidase) (B-32 protein)	0.18	-	cyt	0	Cytoplasm				304
P16094 UniProt NPD GO	RIP1_MOMCH	Ribosome-inactivating protein momordin I precursor (EC 3.2.2.22) (rRNA N-glycosidase) (Alpha-momorch ...	0.18	-	end	0				1MRI	286
P14960 UniProt NPD GO	RBS_GUITH	Ribulose bisphosphate carboxylase small chain (EC 4.1.1.39) (RuBisCO small subunit)	0.18	-	cyt	0	Plastid; chloroplast				139
P16134 UniProt NPD GO	RBS1_ACEME	Ribulose bisphosphate carboxylase small chain 1, chloroplast precursor (EC 4.1.1.39) (RuBisCO small ...	0.18	-	mit	0	Plastid; chloroplast				182

You are viewing entries 53601 to 53650 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.