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
Q9UMR2 UniProt NPD GO	DD19B_HUMAN	ATP-dependent RNA helicase DDX19B (EC 3.6.1.-) (DEAD box protein 19B) (DEAD box RNA helicase DEAD5)	0.32	-	cyt	0	Cytoplasm. Nucleus; nuclear envelope; nuclear pore complex; cytoplasmic side. Nuclear pore complex c ...	cytoplasm [TAS] nuclear pore [TAS]	605812		479
Q5A9Z6 UniProt NPD GO	FAL1_CANAL	ATP-dependent RNA helicase FAL1 (EC 3.6.1.-)	0.32	-	cyt	0	Nucleus; nucleolus (By similarity)				399
Q6C347 UniProt NPD GO	FAL1_YARLI	ATP-dependent RNA helicase FAL1 (EC 3.6.1.-)	0.32	-	cyt	0	Nucleus; nucleolus (By similarity)				397
Q4P6N0 UniProt NPD GO	HAS1_USTMA	ATP-dependent RNA helicase HAS1 (EC 3.6.1.-)	0.32	-	nuc	0	Nucleus; nucleolus (By similarity)				517
Q6C7D2 UniProt NPD GO	HAS1_YARLI	ATP-dependent RNA helicase HAS1 (EC 3.6.1.-)	0.32	-	nuc	0	Nucleus; nucleolus (By similarity)				605
Q7S873 UniProt NPD GO	DBP7_NEUCR	ATP-dependent RNA helicase dbp-7 (EC 3.6.1.-)	0.32	-	nuc	0	Nucleus; nucleolus (By similarity)				814
Q4X195 UniProt NPD GO	DBP2_ASPFU	ATP-dependent RNA helicase dbp2 (EC 3.6.1.-)	0.32	+	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity)				547
P34689 UniProt NPD GO	GLH1_CAEEL	ATP-dependent RNA helicase glh-1 (EC 3.6.1.-) (Germline helicase 1)	0.32	-	cyt	0		P granule [IDA]			763
Q966L9 UniProt NPD GO	GLH2_CAEEL	ATP-dependent RNA helicase glh-2 (EC 3.6.1.-) (Germline helicase 2)	0.32	-	cyt	0		P granule [IDA]			974
Q6FNK8 UniProt NPD GO	RRP3_CANGA	ATP-dependent rRNA helicase RRP3 (EC 3.6.1.-)	0.32	-	nuc	0	Nucleus (Probable)				493
P78508 UniProt NPD GO	IRK10_HUMAN	ATP-sensitive inward rectifier potassium channel 10 (Potassium channel, inwardly rectifying subfamil ...	0.32	-	mit	2	Membrane; multi-pass membrane protein	integral to plasma membrane [TAS]	602208		379
Q9SJB3 UniProt NPD GO	PMA5_ARATH	ATPase 5, plasma membrane-type (EC 3.6.3.6) (Proton pump 5)	0.32	-	end	10	Membrane; multi-pass membrane protein				948
Q99LR1 UniProt NPD GO	ABD12_MOUSE	Abhydrolase domain-containing protein 12	0.32	-	mit	1					398
P11140 UniProt NPD GO	ABRA_ABRPR	Abrin-a precursor [Contains: Abrin-a A chain (EC 3.2.2.22) (rRNA N-glycosidase); Linker peptide; Abr ...	0.32	-	nuc	0				1ABR	528
Q06076 UniProt NPD GO	ABRD_ABRPR	Abrin-d precursor [Contains: Abrin-d A chain (EC 3.2.2.22) (rRNA N-glycosidase); Linker peptide; Abr ...	0.32	-	nuc	0					528
Q59L89 UniProt NPD GO	ACN9_CANAL	Acetate non-utilizing protein 9, mitochondrial precursor	0.32	-	nuc	0	Mitochondrion; mitochondrial intermembrane space (By similarity)				122
P51198 UniProt NPD GO	ACCD_PORPU	Acetyl-coenzyme A carboxylase carboxyl transferase subunit beta (EC 6.4.1.2) (ACCase beta chain)	0.32	-	nuc	0	Plastid; chloroplast				288
P23414 UniProt NPD GO	ACH1_SCHGR	Acetylcholine receptor protein subunit alpha-L1 precursor	0.32	-	end	4	Membrane; multi-pass membrane protein				557
P26436 UniProt NPD GO	ASPX_HUMAN	Acrosomal protein SP-10 precursor (Acrosomal vesicle protein 1)	0.32	-	exc	0	Acrosome. Nascent acrosomal vesicle of Golgi phase spermatids		102525		265
P50289 UniProt NPD GO	ASPX_MOUSE	Acrosomal protein SP-10 precursor (Acrosomal vesicle protein 1) (MSA-63)	0.32	-	exc	0		acrosome [IDA]			261
Q9JM76 UniProt NPD GO	ARPC3_MOUSE	Actin-related protein 2/3 complex subunit 3 (ARP2/3 complex 21 kDa subunit) (p21-ARC)	0.32	-	nuc	0		Arp2/3 protein complex [TAS] lamellipodium [IDA]			177
Q6DGF9 UniProt NPD GO	ACBD4_RAT	Acyl-CoA-binding domain-containing protein 4	0.32	-	cyt	1					326
Q99NB7 UniProt NPD GO	ACO12_RAT	Acyl-coenzyme A thioesterase 12 (EC 3.1.2.1) (Acyl-CoA thioesterase 12) (Acyl-CoA thioester hydrolas ...	0.32	-	cyt	0	Cytoplasm	cytosol [IDA]			556
Q08462 UniProt NPD GO	ADCY2_HUMAN	Adenylate cyclase type 2 (EC 4.6.1.1) (Adenylate cyclase type II) (ATP pyrophosphate-lyase 2) (Adeny ...	0.32	-	end	10 *	Membrane; multi-pass membrane protein	integral to membrane [NAS]	103071		1091
Q03343 UniProt NPD GO	ADCY6_RAT	Adenylate cyclase type 6 (EC 4.6.1.1) (Adenylate cyclase type VI) (ATP pyrophosphate-lyase 6) (Ca(2+ ...	0.32	-	end	12	Membrane; multi-pass membrane protein				1166
P29410 UniProt NPD GO	KAD2_RAT	Adenylate kinase isoenzyme 2, mitochondrial (EC 2.7.4.3) (ATP-AMP transphosphorylase)	0.32	-	cyt	0	Mitochondrion; mitochondrial intermembrane space	mitochondrion [IDA]			238
Q21774 UniProt NPD GO	PUR8_CAEEL	Adenylosuccinate lyase (EC 4.3.2.2) (Adenylosuccinase) (ASL) (ASASE)	0.32	-	cyt	0				1YIS	478
O60105 UniProt NPD GO	PUR8_SCHPO	Adenylosuccinate lyase (EC 4.3.2.2) (Adenylosuccinase) (ASL) (ASASE)	0.32	-	cyt	0					482
Q99541 UniProt NPD GO	ADFP_HUMAN	Adipophilin (Adipose differentiation-related protein) (ADRP)	0.32	-	nuc	0	Membrane; peripheral membrane protein	endoplasmic reticulum [TAS] extracellular region [TAS] lipid particle [TAS]	103195		437
P97275 UniProt NPD GO	ADAS_CAVPO	Alkyldihydroxyacetonephosphate synthase, peroxisomal precursor (EC 2.5.1.26) (Alkyl-DHAP synthase) ( ...	0.32	-	nuc	0	Peroxisome				658
P42838 UniProt NPD GO	LEM3_YEAST	Alkylphosphocholine resistance protein LEM3 (Ro-sensitive 3) (Brefeldin-A sensitivity protein 3)	0.32	-	end	2	Cell membrane; multi-pass membrane protein	cytoplasm [IDA] endoplasmic reticulum [IDA] plasma membrane [IDA]			414
P02482 UniProt NPD GO	CRYAA_ARTJA	Alpha crystallin A chain [Contains: Alpha crystallin A chain, short form]	0.32	-	mit	0					173
P02501 UniProt NPD GO	CRYAA_ORYAF	Alpha crystallin A chain [Contains: Alpha crystallin A chain, short form]	0.32	-	mit	0					173
Q5ENZ0 UniProt NPD GO	CRYAA_SHEEP	Alpha crystallin A chain [Contains: Alpha crystallin A chain, short form]	0.32	-	cyt	0					173
Q5B0M8 UniProt NPD GO	ALG10_EMENI	Alpha-1,2 glucosyltransferase alg10 (EC 2.4.1.-) (Alpha-2-glucosyltransferase alg10) (Dolichyl-phosp ...	0.32	-	end	10 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein				608
Q10469 UniProt NPD GO	MGAT2_HUMAN	Alpha-1,6-mannosyl-glycoprotein 2-beta-N-acetylglucosaminyltransferase (EC 2.4.1.143) (Mannoside ace ...	0.32	-	mit	1 *	Golgi apparatus; Golgi membrane; single-pass type II membrane protein	membrane fraction [TAS]	602616		447
P32251 UniProt NPD GO	ADRA2_CARAU	Alpha-2 adrenergic receptor (Alpha-2 adrenoceptor) (Alpha-2 adrenoreceptor)	0.32	-	end	7 *	Membrane; multi-pass membrane protein				436
P08697 UniProt NPD GO	A2AP_HUMAN	Alpha-2-antiplasmin precursor (Alpha-2-plasmin inhibitor) (Alpha-2-PI) (Alpha-2-AP)	0.32	-	end	0	Secreted protein	extracellular region [NAS]	262850		491
P22909 UniProt NPD GO	ADA2A_RAT	Alpha-2A adrenergic receptor (Alpha-2A adrenoceptor) (Alpha-2A adrenoreceptor) (Alpha-2AAR) (CA2-47) ...	0.32	-	end	7 *	Membrane; multi-pass membrane protein	plasma membrane [IDA]			450
O18935 UniProt NPD GO	ADA2B_AMBHO	Alpha-2B adrenergic receptor (Alpha-2B adrenoceptor) (Alpha-2B adrenoreceptor) (Fragment)	0.32	-	end	6 *	Membrane; multi-pass membrane protein				386
Q9LKJ3 UniProt NPD GO	PHSH_WHEAT	Alpha-glucan phosphorylase, H isozyme (EC 2.4.1.1) (Starch phosphorylase H)	0.32	-	cyt	0	Cytoplasm (By similarity)				832
P49638 UniProt NPD GO	TTPA_HUMAN	Alpha-tocopherol transfer protein (Alpha-TTP)	0.32	-	cyt	0	Cytoplasm		277460	1R5L	278
Q8J0I8 UniProt NPD GO	AOX_YARLI	Alternative oxidase, mitochondrial precursor (EC 1.-.-.-)	0.32	-	mit	2	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein; matrix side (By similarity ...				353
Q99218 UniProt NPD GO	AMELY_HUMAN	Amelogenin, Y isoform precursor	0.32	-	exc	0	Secreted protein; extracellular space; extracellular matrix		410000		206
Q99004 UniProt NPD GO	AMELY_BOVIN	Amelogenin, Y isoform precursor (Class II amelogenin)	0.32	-	exc	0	Secreted protein; extracellular space; extracellular matrix				192
P48728 UniProt NPD GO	GCST_HUMAN	Aminomethyltransferase, mitochondrial precursor (EC 2.1.2.10) (Glycine cleavage system T protein) (G ...	0.32	-	mit	0	Mitochondrion	mitochondrion [TAS]	238310	1WSV	403
P91887 UniProt NPD GO	AMPN_PLUXY	Aminopeptidase N precursor (EC 3.4.11.2) (Microsomal aminopeptidase) (APN1)	0.32	-	exc	0	Cell membrane; lipid-anchor; GPI-anchor				946
O35827 UniProt NPD GO	APBB3_RAT	Amyloid beta A4 precursor protein-binding family B member 3 (Fe65-like protein 2) (Fe65L2)	0.32	-	cyt	0					504
Q96BM1 UniProt NPD GO	ANKR9_HUMAN	Ankyrin repeat domain-containing protein 9	0.32	-	cyt	0					317
P25631 UniProt NPD GO	YCU1_YEAST	Ankyrin repeat-containing protein YCR051W	0.32	-	cyt	0		cytoplasm [IDA] nucleus [IDA]			222

You are viewing entries 38251 to 38300 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.