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
Q5DRC6 UniProt NPD GO	PCDB8_PANTR	Protocadherin beta 8 precursor (PCDH-beta8)	0.35	-	end	1	Membrane; single-pass type I membrane protein (By similarity)				801
Q8AVA4 UniProt NPD GO	CRVP_PSEAU	Pseudechetoxin precursor (PsTx)	0.35	-	exc	0	Secreted protein				238
O13869 UniProt NPD GO	YE14_SCHPO	Putative GTP-binding protein C1B3.04c	0.35	-	mit	0					646
Q7TNK6 UniProt NPD GO	CF075_RAT	Putative RNA methylase C6orf75 homolog (EC 2.1.1.-)	0.35	-	cyt	0					463
Q19013 UniProt NPD GO	GLS1_CAEEL	Putative glutaminase DH11.1 (EC 3.5.1.2) (GLS) (L-glutamine amidohydrolase)	0.35	-	nuc	0					605
P34344 UniProt NPD GO	TG250_CAEEL	Putative protein tag-250	0.35	+	cyt	0					610
Q10078 UniProt NPD GO	KAND_SCHPO	Putative serine/threonine-protein kinase C3H1.13 (EC 2.7.11.1)	0.35	-	nuc	0					344
O14096 UniProt NPD GO	TGTL_SCHPO	Queuine tRNA-ribosyltransferase-like protein	0.35	-	mit	0					348
P83592 UniProt NPD GO	PHEG_COROI	R-phycoerythrin gamma chain, chloroplast precursor	0.35	-	cyt	0	Plastid; chloroplast				319
P0C074 UniProt NPD GO	RCP10_YEAST	RDS3 complex subunit 10 (Splicing factor 3b subunit)	0.35	-	nuc	0	Nucleus (Probable)				85
Q8BG47 UniProt NPD GO	RN152_MOUSE	RING finger protein 152	0.35	-	cyt	1					203
Q7YR31 UniProt NPD GO	RNF39_PANTR	RING finger protein 39 (Protein HZFw)	0.35	-	mit	0	Cytoplasm (By similarity)				420
Q84W40 UniProt NPD GO	ATL1N_ARATH	RING-H2 finger protein ATL1N precursor	0.35	-	nuc	2 *					404
Q9SN28 UniProt NPD GO	ATL4E_ARATH	RING-H2 finger protein ATL4E	0.35	-	nuc	1 *					236
Q8R4X3 UniProt NPD GO	RBM12_MOUSE	RNA-binding protein 12 (RNA-binding motif protein 12) (SH3/WW domain anchor protein in the nucleus) ...	0.35	+	nuc	0	Nucleus (By similarity)			2CQP	1002
Q80WA4 UniProt NPD GO	NOVA1_RAT	RNA-binding protein Nova-1 (Neuro-oncological ventral antigen 1) (Fragment)	0.35	-	cyt	0	Nucleus				474
Q27294 UniProt NPD GO	CAZ_DROME	RNA-binding protein cabeza (Sarcoma-associated RNA-binding fly homolog) (P19)	0.35	+	cyt	0	Nucleus				399
P82864 UniProt NPD GO	TB48_TRYBB	RNA-editing ligase TbMP48, mitochondrial precursor (EC 6.5.1.3) (RNA ligase)	0.35	-	mit	0	Mitochondrion				416
P50399 UniProt NPD GO	GDIB_RAT	Rab GDP dissociation inhibitor beta (Rab GDI beta) (Guanosine diphosphate dissociation inhibitor 2) ...	0.35	-	nuc	0	Cytoplasm. Membrane; peripheral membrane protein	cytosol [TAS]			445
Q9V8W3 UniProt NPD GO	RABEP_DROME	Rab proteins geranylgeranyltransferase component A (Rab escort protein homolog) (REP)	0.35	-	nuc	0	Cytoplasm; perinuclear region. Coordinated with the cell cycle, located around nuclei during prophas ...	aster [IDA] cytoplasm [ISS] membrane [ISS] perinuclear region [IDA] Rab-protein geranylgeranyltransferase complex [ISS] spindle pole [IDA] synaptic vesicle [NAS]			511
Q24192 UniProt NPD GO	RHOL_DROME	Ras-like GTP-binding protein RhoL	0.35	-	nuc	0	Cell membrane; lipid-anchor; cytoplasmic side (Potential)				190
P35286 UniProt NPD GO	RAB13_RAT	Ras-related protein Rab-13	0.35	-	nuc	0	Cell membrane; cell-cell junction; tight junction; lipid-anchor; cytoplasmic side (By similarity). C ...				203
Q8VHQ4 UniProt NPD GO	RB40C_MOUSE	Ras-related protein Rab-40C (SOCS box-containing protein RAR3)	0.35	-	nuc	0	Cell membrane; lipid-anchor; cytoplasmic side (Potential)				281
Q96S21 UniProt NPD GO	RB40C_HUMAN	Ras-related protein Rab-40C (SOCS box-containing protein RAR3) (Rar-like protein)	0.35	-	nuc	0	Cell membrane; lipid-anchor; cytoplasmic side (Potential)				281
Q68AX7 UniProt NPD GO	REG4_RAT	Regenerating islet-derived protein 4 precursor	0.35	-	exc	0	Secreted protein (By similarity)				157
Q08746 UniProt NPD GO	RRS1_YEAST	Regulator of ribosome biosynthesis	0.35	-	nuc	0	Nucleus	nucleus [IDA]			203
Q9D0U6 UniProt NPD GO	MAF1_MOUSE	Repressor of RNA polymerase III transcription MAF1 homolog	0.35	-	nuc	0	Nucleus (By similarity)				258
Q02846 UniProt NPD GO	GUC2D_HUMAN	Retinal guanylyl cyclase 1 precursor (EC 4.6.1.2) (Guanylate cyclase 2D, retinal) (RETGC-1) (Rod out ...	0.35	-	end	1 *	Membrane; single-pass type I membrane protein	integral to plasma membrane [TAS] nuclear outer membrane [TAS]	204000	1AWL	1103
Q9HBH0 UniProt NPD GO	RHOF_HUMAN	Rho-related GTP-binding protein RhoF (Rho-family GTPase Rif) (Rho in filopodia)	0.35	-	cyt	0	Cell membrane; lipid-anchor; cytoplasmic side (Potential)	cytoskeleton [NAS]			211
Q04740 UniProt NPD GO	RNH1_YEAST	Ribonuclease H (EC 3.1.26.4) (RNase H)	0.35	-	nuc	0		intracellular [TAS] nucleus [IC]		1QHK	348
P00674 UniProt NPD GO	RNAS1_HORSE	Ribonuclease pancreatic (EC 3.1.27.5) (RNase 1) (RNase A)	0.35	-	nuc	0	Secreted protein				128
P00681 UniProt NPD GO	RNAS1_ONDZI	Ribonuclease pancreatic (EC 3.1.27.5) (RNase 1) (RNase A)	0.35	-	nuc	0	Secreted protein				124
Q8VD91 UniProt NPD GO	RNS1A_RATFU	Ribonuclease pancreatic alpha-type precursor (EC 3.1.27.5) (RNase 1 gamma)	0.35	-	exc	0	Secreted protein (By similarity)				149
P00683 UniProt NPD GO	RNAS1_MOUSE	Ribonuclease pancreatic precursor (EC 3.1.27.5) (RNase 1) (RNase A)	0.35	-	exc	0	Secreted protein				149
Q8SQ07 UniProt NPD GO	RNAS1_SAGOE	Ribonuclease pancreatic precursor (EC 3.1.27.5) (RNase 1) (RNase A)	0.35	-	nuc	1 *	Secreted protein (By similarity)				156
Q4KLN6 UniProt NPD GO	RIR2_RAT	Ribonucleoside-diphosphate reductase M2 subunit (EC 1.17.4.1) (Ribonucleotide reductase small subuni ...	0.35	-	cyt	0	Cytoplasm (By similarity)				390
P23921 UniProt NPD GO	RIR1_HUMAN	Ribonucleoside-diphosphate reductase large subunit (EC 1.17.4.1) (Ribonucleoside-diphosphate reducta ...	0.35	-	nuc	0	Cytoplasm	ribonucleoside-diphosphate reductase complex [NAS]	180410		792
P79732 UniProt NPD GO	RIR1_BRARE	Ribonucleoside-diphosphate reductase large subunit (EC 1.17.4.1) (Ribonucleoside-diphosphate reducta ...	0.35	-	cyt	0	Cytoplasm				794
Q4I948 UniProt NPD GO	RUVB2_GIBZE	RuvB-like helicase 2 (EC 3.6.1.-)	0.35	-	cyt	0	Nucleus (By similarity)				464
Q99MS0 UniProt NPD GO	S14L2_RAT	SEC14-like protein 2 (Alpha-tocopherol-associated protein) (TAP) (Supernatant protein factor) (SPF) ...	0.35	-	cyt	0	Cytoplasm (By similarity). Nucleus (By similarity). Cytoplasmic in absence of alpha-tocopherol, and ...	cytoplasm [ISS] cytosol [IDA] nucleus [ISS]			403
P07701 UniProt NPD GO	SGS5_DROME	Salivary glue protein Sgs-5 precursor	0.35	-	exc	0					163
P57772 UniProt NPD GO	SELB_HUMAN	Selenocysteine-specific elongation factor (Elongation factor sec) (Eukaryotic elongation factor, sel ...	0.35	-	cyt	0	Cytoplasm (Potential). Nucleus (Potential)	cytoplasm [NAS] nucleus [NAS]	607695		596
Q96LD8 UniProt NPD GO	SENP8_HUMAN	Sentrin-specific protease 8 (EC 3.4.22.-) (Sentrin/SUMO-specific protease SENP8) (Protease, cysteine ...	0.35	-	cyt	0			608659	2BKR	212
Q9TY95 UniProt NPD GO	SERA_PLAF7	Serine-repeat antigen protein precursor (p126) (111 kDa antigen)	0.35	-	nuc	0	Vacuole (By similarity). Exported antigen that accumulates in the parasitophorous vacuole (By simila ...				997
O88697 UniProt NPD GO	STK16_MOUSE	Serine/threonine-protein kinase 16 (EC 2.7.11.1) (Protein kinase PKL12) (Myristoylated and palmitoyl ...	0.35	-	cyt	0	Membrane; lipid-anchor (By similarity)				304
Q8K1R7 UniProt NPD GO	NEK9_MOUSE	Serine/threonine-protein kinase Nek9 (EC 2.7.11.1) (NimA-related protein kinase 9) (Never in mitosis ...	0.35	-	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity)				984
O94921 UniProt NPD GO	PFTK1_HUMAN	Serine/threonine-protein kinase PFTAIRE-1 (EC 2.7.11.22)	0.35	-	nuc	0	Cytoplasm. Nucleus	cytoplasm [TAS] nucleus [TAS]			469
O35495 UniProt NPD GO	PFTK1_MOUSE	Serine/threonine-protein kinase PFTAIRE-1 (EC 2.7.11.22)	0.35	-	nuc	0	Cytoplasm. Nucleus				469
Q4WTN5 UniProt NPD GO	BUR1_ASPFU	Serine/threonine-protein kinase bur1 (EC 2.7.11.22) (EC 2.7.11.23)	0.35	-	mit	0	Nucleus (By similarity)				580
Q84V18 UniProt NPD GO	STT7_CHLRE	Serine/threonine-protein kinase stt7, chloroplast precursor (EC 2.7.11.1)	0.35	-	nuc	0	Plastid; chloroplast; chloroplast thylakoid membrane				754

You are viewing entries 36201 to 36250 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.