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
Q29JI9 UniProt NPD GO	MCM6_DROPS	DNA replication licensing factor Mcm6 (Minichromosome maintenance 6 protein)	0.45	-	cyt	0	Nucleus. Associated with chromatin during cell cycles (By similarity)	nucleus [ISS]			815
Q3V502 UniProt NPD GO	RPOA_ACOCL	DNA-directed RNA polymerase alpha chain (EC 2.7.7.6) (PEP) (Plastid-encoded RNA polymerase subunit a ...	0.45	-	nuc	0	Plastid; chloroplast				337
P60282 UniProt NPD GO	RPOB_AMBTC	DNA-directed RNA polymerase beta chain (EC 2.7.7.6) (PEP) (Plastid-encoded RNA polymerase subunit be ...	0.45	-	nuc	0	Plastid; chloroplast				1078
Q8S8X9 UniProt NPD GO	RPOB_ATRBE	DNA-directed RNA polymerase beta chain (EC 2.7.7.6) (PEP) (Plastid-encoded RNA polymerase subunit be ...	0.45	-	cyt	0	Plastid; chloroplast				1070
P46818 UniProt NPD GO	RPOB_SINAL	DNA-directed RNA polymerase beta chain (EC 2.7.7.6) (PEP) (Plastid-encoded RNA polymerase subunit be ...	0.45	-	cyt	0	Plastid; chloroplast				1078
P60287 UniProt NPD GO	RPOC1_AMBTC	DNA-directed RNA polymerase beta' chain (EC 2.7.7.6) (PEP) (Plastid-encoded RNA polymerase beta' sub ...	0.45	-	mit	0	Plastid; chloroplast				680
Q589B9 UniProt NPD GO	RPOC1_SILLA	DNA-directed RNA polymerase beta' chain (EC 2.7.7.6) (PEP) (Plastid-encoded RNA polymerase beta' sub ...	0.45	-	cyt	0	Plastid; chloroplast				687
P46819 UniProt NPD GO	RPOC1_SINAL	DNA-directed RNA polymerase beta' chain (EC 2.7.7.6) (PEP) (Plastid-encoded RNA polymerase beta' sub ...	0.45	-	cyt	0	Plastid; chloroplast				688
Q32RG1 UniProt NPD GO	RPOC1_ZYGCR	DNA-directed RNA polymerase beta' chain (EC 2.7.7.6) (PEP) (Plastid-encoded RNA polymerase beta' sub ...	0.45	-	cyt	0	Plastid; chloroplast				715
P48120 UniProt NPD GO	RPOC2_CYAPA	DNA-directed RNA polymerase beta'' chain (EC 2.7.7.6) (PEP) (Plastid-encoded RNA polymerase beta'' s ...	0.45	-	nuc	0	Plastid; cyanelle				1265
P06773 UniProt NPD GO	DCTD_YEAST	Deoxycytidylate deaminase (EC 3.5.4.12) (dCMP deaminase)	0.45	-	cyt	0		cytoplasm [IDA]			312
Q9XZT6 UniProt NPD GO	DNK_DROME	Deoxynucleoside kinase (EC 2.7.1.145) (Deoxyribonucleoside kinase) (Dm-dNK) (Multispecific deoxynucl ...	0.45	-	nuc	0				1ZMX	250
P31001 UniProt NPD GO	DESM_MOUSE	Desmin	0.45	-	mit	0	Cytoplasm	contractile fiber [IDA] cytoskeleton [IDA] insoluble fraction [IDA] sarcolemma [IDA] synapse [IDA] Z disc [IDA]			468
P55850 UniProt NPD GO	DSC3_MOUSE	Desmocollin-3 precursor	0.45	-	cyt	1	Membrane; single-pass type I membrane protein (Potential)	cytoplasm [IDA] desmosome [IDA] plasma membrane [IDA]			895
Q08650 UniProt NPD GO	DGA1_YEAST	Diacylglycerol O-acyltransferase 1 (EC 2.3.1.20)	0.45	+	mit	1	Endoplasmic reticulum; endoplasmic reticulum membrane; single-pass membrane protein (Potential). Lip ...	lipid particle [IDA]			418
P49620 UniProt NPD GO	DGKG_RAT	Diacylglycerol kinase gamma (EC 2.7.1.107) (Diglyceride kinase gamma) (DGK-gamma) (DAG kinase gamma) ...	0.45	-	nuc	0					788
Q9Z218 UniProt NPD GO	DPP6_MOUSE	Dipeptidyl aminopeptidase-like protein 6 (Dipeptidylpeptidase VI) (Dipeptidylpeptidase 6) (Dipeptidy ...	0.45	-	mit	1 *	Membrane; single-pass type II membrane protein (Probable)				804
Q99JF5 UniProt NPD GO	ERG19_MOUSE	Diphosphomevalonate decarboxylase (EC 4.1.1.33) (Mevalonate pyrophosphate decarboxylase) (Mevalonate ...	0.45	-	cyt	0					401
O94625 UniProt NPD GO	SPJ1_SCHPO	DnaJ-related protein spj1	0.45	-	cyt	0	Endoplasmic reticulum (Potential)				381
P97465 UniProt NPD GO	DOK1_MOUSE	Docking protein 1 (Downstream of tyrosine kinase 1) (p62(dok))	0.45	-	nuc	0				1UEF	482
Q8TEW6 UniProt NPD GO	DOK4_HUMAN	Docking protein 4 (Downstream of tyrosine kinase 4)	0.45	-	nuc	0			608333		326
O95456 UniProt NPD GO	DSCR2_HUMAN	Down syndrome critical region protein 2 (Leucine-rich protein C21-LRP)	0.45	-	cyt	0		integral to plasma membrane [TAS] membrane fraction [TAS]	605296		288
Q9JHL4 UniProt NPD GO	DBNL_RAT	Drebrin-like protein (SH3 domain-containing protein 7) (Actin-binding protein 1) (Abp1)	0.45	-	nuc	0	Cytoskeleton. Cortical cytoskeleton. Associates with lamellipodial actin	cell cortex [ISS] cytoplasm [ISS] lamellipodium [ISS]			436
Q9H223 UniProt NPD GO	EHD4_HUMAN	EH-domain-containing protein 4 (Hepatocellular carcinoma-associated protein 10/11)	0.45	-	nuc	0		nucleus [TAS]	605892		541
P41158 UniProt NPD GO	ELK4_MOUSE	ETS domain-containing protein Elk-4 (Serum response factor accessory protein 1) (SAP-1)	0.45	+	nuc	0	Nucleus				430
Q95LN5 UniProt NPD GO	EDAD_MACFA	Ectodysplasin A receptor-associated adapter protein	0.45	-	nuc	0	Cytoplasm (Probable)	cytoplasm [ISS]			206
Q9BEG5 UniProt NPD GO	EDA_BOVIN	Ectodysplasin-A (Ectodysplasin-1) (Ectodermal dysplasia protein) [Contains: Ectodysplasin-A, membran ...	0.45	-	nuc	1 *	Cell membrane; single-pass type II membrane protein (By similarity). Processed form: Secreted protei ...				391
Q64610 UniProt NPD GO	ENPP2_RAT	Ectonucleotide pyrophosphatase/phosphodiesterase 2 (E-NPP 2) (Phosphodiesterase I/nucleotide pyropho ...	0.45	-	mit	1 *	Membrane; single-pass type II membrane protein				885
P70531 UniProt NPD GO	EF2K_RAT	Elongation factor 2 kinase (EC 2.7.11.20) (eEF-2 kinase) (eEF-2K) (Calcium/calmodulin-dependent euka ...	0.45	-	nuc	0					724
P54762 UniProt NPD GO	EPHB1_HUMAN	Ephrin type-B receptor 1 precursor (EC 2.7.10.1) (Tyrosine-protein kinase receptor EPH-2) (NET) (HEK ...	0.45	-	end	1	Membrane; single-pass type I membrane protein	integral to plasma membrane [TAS] plasma membrane [TAS]	600600		984
Q94ID6 UniProt NPD GO	ERF12_ARATH	Ethylene-responsive transcription factor 12 (Ethylene-responsive element-binding factor 12) (EREBP-1 ...	0.45	-	nuc	0	Nucleus (Probable)				189
Q8VZ91 UniProt NPD GO	ERF6_ARATH	Ethylene-responsive transcription factor 6 (Ethylene-responsive element-binding factor 6) (EREBP-6) ...	0.45	-	cyt	0	Nucleus (Probable)				282
O15372 UniProt NPD GO	IF33_HUMAN	Eukaryotic translation initiation factor 3 subunit 3 (eIF-3 gamma) (eIF3 p40 subunit) (eIF3h)	0.45	-	nuc	0		eukaryotic translation initiation factor 3 ... [TAS]	603912		352
Q4G061 UniProt NPD GO	IF39_RAT	Eukaryotic translation initiation factor 3 subunit 9 (eIF-3 eta)	0.45	-	cyt	0					797
Q2QV94 UniProt NPD GO	EXOC5_ORYSA	Exocyst complex component 5 (Exocyst complex component Sec10)	0.45	-	cyt	0					806
Q9WVL6 UniProt NPD GO	EXTL3_MOUSE	Exostosin-like 3 (EC 2.4.1.-) (Multiple exostosis-like protein 3)	0.45	-	mit	1 *	Endoplasmic reticulum; endoplasmic reticulum membrane; single-pass type II membrane protein (By simi ...				918
Q62894 UniProt NPD GO	ECM1_RAT	Extracellular matrix protein 1 precursor (Secretory component P85)	0.45	-	exc	0	Secreted protein; extracellular space				562
Q8BK06 UniProt NPD GO	FBX9_MOUSE	F-box only protein 9	0.45	-	cyt	0					437
O74531 UniProt NPD GO	POF7_SCHPO	F-box protein pof7	0.45	-	nuc	0					361
Q58DG6 UniProt NPD GO	FXL20_BOVIN	F-box/LRR-repeat protein 20 (F-box and leucine-rich repeat protein 20)	0.45	-	nuc	0	Cytoplasm (By similarity)				438
P0C1J7 UniProt NPD GO	FKBP5_RHIOR	FK506-binding protein 5 (EC 5.2.1.8) (Peptidyl-prolyl cis-trans isomerase) (PPIase) (Rotamase)	0.45	-	cyt	0					385
P33573 UniProt NPD GO	FIBA2_PETMA	Fibrinogen alpha-2 chain precursor [Contains: Fibrinopeptide A]	0.45	-	exc	0	Secreted protein				641
P48807 UniProt NPD GO	FGF5_RAT	Fibroblast growth factor 5 precursor (FGF-5) (HBGF-5)	0.45	-	exc	0					266
Q71FD7 UniProt NPD GO	FBLI1_MOUSE	Filamin-binding LIM protein 1 (CSX-associated LIM)	0.45	-	nuc	0	Cytoplasm; cell cortex (By similarity). Associated with actin stress fiber at cell-ECM focal adhesio ...				375
P70054 UniProt NPD GO	FEN1B_XENLA	Flap endonuclease 1-B (EC 3.1.-.-) (Flap structure-specific endonuclease 1-B) (FEN-1-B) (xFEN-1b)	0.45	-	nuc	0	Nucleus	nucleus [IDA]			382
Q9NPG1 UniProt NPD GO	FZD3_HUMAN	Frizzled-3 precursor (Fz-3) (hFz3)	0.45	-	end	8 *	Membrane; multi-pass membrane protein	integral to plasma membrane [TAS]	606143		666
Q8VEC3 UniProt NPD GO	GP110_MOUSE	G-protein coupled receptor 110 precursor	0.45	-	end	7	Membrane; multi-pass membrane protein				908
Q9JJT2 UniProt NPD GO	GFRA4_MOUSE	GDNF family receptor alpha-4 precursor (GFR-alpha-4) (Persephin receptor)	0.45	-	nuc	0	Isoform a1, isoform b1: Cell membrane; lipid-anchor; GPI-anchor. Isoform a3, isoform b3: Secreted pr ...				260
O94661 UniProt NPD GO	GYP10_SCHPO	GTPase-activating protein gyp10	0.45	-	nuc	1		endoplasmic reticulum [IDA]			373
P07315 UniProt NPD GO	CRGC_HUMAN	Gamma crystallin C (Gamma crystallin 2-1) (Gamma crystallin 3)	0.45	-	nuc	0			123680	1LFE	173

You are viewing entries 28251 to 28300 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.