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
P12142 UniProt NPD GO	RK36_MARPO	Chloroplast 50S ribosomal protein L36	0.60	-	mit	0	Plastid; chloroplast				37
Q9Z288 UniProt NPD GO	GCM1_RAT	Chorion-specific transcription factor GCMa (Glial cells missing homolog 1) (GCM motif protein 1)	0.60	-	nuc	0	Nucleus (Potential)				436
O75603 UniProt NPD GO	GCM2_HUMAN	Chorion-specific transcription factor GCMb (Glial cells missing homolog 2) (GCM motif protein 2) (hG ...	0.60	-	nuc	0	Nucleus (By similarity)	nucleus [TAS]	603716		506
Q969X6 UniProt NPD GO	CIR1A_HUMAN	Cirhin	0.60	-	mit	0	Nucleus; nucleolus		607456		686
P25870 UniProt NPD GO	CLH_DICDI	Clathrin heavy chain	0.60	-	cyt	0	Cytoplasmic face of coated pits and vesicles				1694
Q9CZB6 UniProt NPD GO	CSP9_MOUSE	Cofactor required for Sp1 transcriptional activation subunit 9	0.60	-	nuc	0	Nucleus (By similarity)				233
Q8CEG5 UniProt NPD GO	CC28B_MOUSE	Coiled-coil domain-containing protein 28B	0.60	-	nuc	0					200
Q9BQI4 UniProt NPD GO	CCDC3_HUMAN	Coiled-coil domain-containing protein 3 precursor	0.60	-	exc	0					270
Q9CR29 UniProt NPD GO	CCD43_MOUSE	Coiled-coil domain-containing protein 43	0.60	+	cyt	0					222
Q66I12 UniProt NPD GO	CCD47_BRARE	Coiled-coil domain-containing protein 47 precursor	0.60	-	end	0	Membrane; single-pass membrane protein (Potential)				486
Q5E9D3 UniProt NPD GO	CHCH3_BOVIN	Coiled-coil-helix-coiled-coil-helix domain-containing protein 3	0.60	-	nuc	0					227
Q07563 UniProt NPD GO	COHA1_MOUSE	Collagen alpha-1(XVII) chain (Bullous pemphigoid antigen 2) (180 kDa bullous pemphigoid antigen 2)	0.60	+	nuc	1	Membrane; single-pass type II membrane protein (By similarity)	hemidesmosome [IDA]			1470
Q9BPX3 UniProt NPD GO	CND3_HUMAN	Condensin complex subunit 3 (Chromosome-associated protein G) (Condensin subunit CAP-G) (hCAP-G) (XC ...	0.60	-	end	0	Nucleus. Cytoplasm. In interphase cells, the majority of the condensin complex is found in the cytop ...	nucleus [NAS]	606280		1015
Q9Z160 UniProt NPD GO	COG1_MOUSE	Conserved oligomeric Golgi complex component 1 (Low density lipoprotein receptor defect B-complement ...	0.60	-	nuc	0	Golgi apparatus (By similarity)	Golgi transport complex [ISS]			980
Q00096 UniProt NPD GO	CPCA_ASPNG	Cross-pathway control protein A	0.60	-	nuc	0	Nucleus (By similarity)				245
Q28199 UniProt NPD GO	CD5R1_BOVIN	Cyclin-dependent kinase 5 activator 1 precursor (CDK5 activator 1) (Cyclin-dependent kinase 5 regula ...	0.60	-	nuc	0	Cyclin-dependent kinase 5 activator 1, p35: Cell membrane; lipid-anchor; cytoplasmic side (By simila ...	axon [ISS] cell soma [ISS] contractile fiber [ISS] cytoplasm [ISS] dendritic spine [ISS] growth cone [ISS] membrane [ISS] membrane fraction [ISS] neuromuscular junction [ISS] nucleus [ISS]			307
Q2QL74 UniProt NPD GO	CFTR_DIDMA	Cystic fibrosis transmembrane conductance regulator (CFTR) (cAMP-dependent chloride channel) (ATP-bi ...	0.60	-	end	11	Membrane; multi-pass membrane protein				1482
P51869 UniProt NPD GO	CP4F4_RAT	Cytochrome P450 4F4 (EC 1.14.14.1) (CYPIVF4)	0.60	-	nuc	2 *	Endoplasmic reticulum; endoplasmic reticulum membrane; peripheral membrane protein				522
Q27606 UniProt NPD GO	CP4E2_DROME	Cytochrome P450 4e2 (EC 1.14.-.-) (CYPIVE2)	0.60	-	mit	1 *	Endoplasmic reticulum; endoplasmic reticulum membrane; peripheral membrane protein (Potential)				526
Q12587 UniProt NPD GO	CP52Q_CANMA	Cytochrome P450 52C2 (EC 1.14.14.-) (CYPLIIC2) (Alkane-inducible P450-ALK6-A)	0.60	-	nuc	0					510
Q60991 UniProt NPD GO	CP7B1_MOUSE	Cytochrome P450 7B1 (EC 1.14.13.100) (25-hydroxycholesterol 7-alpha-hydroxylase) (Oxysterol 7-alpha- ...	0.60	-	end	3 *	Endoplasmic reticulum; endoplasmic reticulum membrane; peripheral membrane protein	microsome [TAS]			507
Q80YW0 UniProt NPD GO	CYH4_MOUSE	Cytohesin-4	0.60	-	cyt	0					393
P32927 UniProt NPD GO	IL3RB_HUMAN	Cytokine receptor common beta chain precursor (GM-CSF/IL-3/IL-5 receptor common beta-chain) (CD131 a ...	0.60	-	exc	1	Membrane; single-pass type I membrane protein	granulocyte macrophage colony-stimulating f... [TAS]	138981	1GH7	897
Q18317 UniProt NPD GO	CPB2_CAEEL	Cytoplasmic polyadenylation element-binding protein 2	0.60	-	nuc	0					422
Q6E3F0 UniProt NPD GO	CPB2_CAEJA	Cytoplasmic polyadenylation element-binding protein 2	0.60	-	mit	0					594
Q9P6S5 UniProt NPD GO	ASK1_SCHPO	DASH complex subunit ask1 (Outer kinetochore protein ask1) (Associated with spindles and kinetochore ...	0.60	-	nuc	0	Nucleus. Associates with the mitotic spindle and the kinetochore. Kinetochore association occurs onl ...	DASH complex [IDA] spindle pole body [IDA]			307
Q9VUQ8 UniProt NPD GO	DCN1L_DROME	DCN1-like protein (Defective in cullin neddylation protein 1-like protein)	0.60	-	nuc	0		cytoplasm [ISS] nucleus [ISS]			288
Q9LIH9 UniProt NPD GO	RH51_ARATH	DEAD-box ATP-dependent RNA helicase 51 (EC 3.6.1.-)	0.60	+	cyt	0					568
O65607 UniProt NPD GO	MSH3_ARATH	DNA mismatch repair protein MSH3 (AtMsh3)	0.60	-	nuc	0					1081
P36195 UniProt NPD GO	TDT_CHICK	DNA nucleotidylexotransferase (EC 2.7.7.31) (Terminal addition enzyme) (Terminal deoxynucleotidyltra ...	0.60	+	mit	0	Nucleus (By similarity)				506
P25615 UniProt NPD GO	DPO4_YEAST	DNA polymerase IV (EC 2.7.7.7) (POL IV)	0.60	-	cyt	0	Nucleus	nucleus [TAS]			581
Q9Y253 UniProt NPD GO	POLH_HUMAN	DNA polymerase eta (EC 2.7.7.7) (RAD30 homolog A) (Xeroderma pigmentosum variant type protein)	0.60	+	nuc	0	Nucleus. Accumulates at replication forks after DNA damage	nucleoplasm [TAS]	603968		713
O59835 UniProt NPD GO	DPOD4_SCHPO	DNA polymerase subunit delta 4	0.60	-	mit	0	Nucleus (By similarity)	delta DNA polymerase complex [TAS]			160
P10363 UniProt NPD GO	PRI1_YEAST	DNA primase small subunit (EC 2.7.7.-) (DNA primase 48 kDa subunit) (DNA polymerase alpha:primase co ...	0.60	-	nuc	0		alpha DNA polymerase:primase complex [TAS]			409
P49735 UniProt NPD GO	MCM2_DROME	DNA replication licensing factor Mcm2 (Minichromosome maintenance 2 protein) (DmMCM2)	0.60	-	nuc	0	Nucleus (Probable)				887
Q62764 UniProt NPD GO	DBPA_RAT	DNA-binding protein A (Cold shock domain-containing protein A) (Muscle Y-box protein YB2) (Y-box-bin ...	0.60	-	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity)	nucleus [IDA]			361
Q64267 UniProt NPD GO	XPA_MOUSE	DNA-repair protein complementing XP-A cells homolog (Xeroderma pigmentosum group A-complementing pro ...	0.60	-	nuc	0	Nucleus	nucleus [IDA]			272
O74331 UniProt NPD GO	RLP1_SCHPO	DNA-repair protein rlp1 (RecA-like protein 1)	0.60	-	nuc	0	Nucleus (Probable)				363
P51530 UniProt NPD GO	DNA2L_HUMAN	DNA2-like homolog (EC 3.6.1.-) (DNA replication ATP-dependent helicase-like homolog) (Fragment)	0.60	-	nuc	0			601810		1077
Q08554 UniProt NPD GO	DSC1_HUMAN	Desmocollin-1 precursor (Desmosomal glycoprotein 2/3) (DG2/DG3)	0.60	+	end	1	Membrane; single-pass type I membrane protein	gap junction [TAS] membrane fraction [TAS]	125643		894
Q08210 UniProt NPD GO	PYRD_PLAF7	Dihydroorotate dehydrogenase homolog, mitochondrial precursor (EC 1.3.3.1) (Dihydroorotate oxidase) ...	0.60	-	nuc	1	Mitochondrion; mitochondrial inner membrane (Probable)				569
Q9UDY4 UniProt NPD GO	DNJB4_HUMAN	DnaJ homolog subfamily B member 4 (Heat shock 40 kDa protein 1 homolog) (Heat shock protein 40 homol ...	0.60	-	nuc	0					337
Q7Z6W7 UniProt NPD GO	DNJB7_HUMAN	DnaJ homolog subfamily B member 7	0.60	+	nuc	0					309
Q91WT4 UniProt NPD GO	DJC17_MOUSE	DnaJ homolog subfamily C member 17	0.60	-	nuc	0					303
Q95KD5 UniProt NPD GO	DJC18_MACFA	DnaJ homolog subfamily C member 18	0.60	-	nuc	0	Membrane; single-pass membrane protein (Potential)				358
Q9LZ56 UniProt NPD GO	DOF51_ARATH	Dof zinc finger protein DOF5.1 (AtDOF5.1)	0.60	-	nuc	0	Nucleus (Probable)				399
Q9NII1 UniProt NPD GO	ADAR_DROME	Double-stranded RNA-specific editase Adar (EC 3.5.-.-) (Adenosine deaminase that act on RNA) (dsRNA ...	0.60	-	nuc	0		intracellular [IC]			676
Q14919 UniProt NPD GO	DRAP1_HUMAN	Dr1-associated corepressor (Dr1-associated protein 1) (Negative co-factor 2 alpha) (NC2 alpha)	0.60	-	nuc	0			602289	1JFI	204
Q9ESS0 UniProt NPD GO	DUS10_MOUSE	Dual specificity protein phosphatase 10 (EC 3.1.3.48) (EC 3.1.3.16) (Mitogen-activated protein kinas ...	0.60	-	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity)				483
Q8CBY8 UniProt NPD GO	DCTN4_MOUSE	Dynactin subunit 4 (Dynactin subunit p62)	0.60	-	nuc	0	Cytoplasm (By similarity). Centrosome (By similarity). Has a punctate cytoplasmic distribution as we ...				467

You are viewing entries 18951 to 19000 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.