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
P32796 UniProt NPD GO	CACP_YEAST	Carnitine O-acetyltransferase, mitochondrial precursor (EC 2.3.1.7) (Carnitine acetylase)	0.63	-	nuc	0	Peroxisome. Mitochondrion; mitochondrial inner membrane; matrix side	mitochondrion [IDA]			670
P53699 UniProt NPD GO	CDC4_CANAL	Cell division control protein 4	0.63	-	nuc	0					684
Q9SS94 UniProt NPD GO	CD48C_ARATH	Cell division control protein 48 homolog C (AtCDC48c)	0.63	+	cyt	0	Nucleus (By similarity). Phragmoplast (By similarity). Primarily localized to the nucleus and, durin ...				820
Q9Z0H0 UniProt NPD GO	CDC7_MOUSE	Cell division cycle 7-related protein kinase (EC 2.7.11.1) (CDC7-related kinase) (muCdc7)	0.63	-	nuc	0	Nucleus (By similarity)				564
Q9VT57 UniProt NPD GO	CDK8_DROME	Cell division protein kinase 8 (EC 2.7.11.22) (EC 2.7.11.23) (DmCdk8)	0.63	-	nuc	0	Nucleus	nucleus [IDA]			454
P07193 UniProt NPD GO	P53_XENLA	Cellular tumor antigen p53 (Tumor suppressor p53)	0.63	-	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity)				363
Q9H3R5 UniProt NPD GO	CENPH_HUMAN	Centromere protein H (Kinetochore protein CENP-H)	0.63	-	nuc	0	Nucleus. Associates with active centromere-kinetochore complexes throughout the cell cycle. Colocali ...	kinetochore [NAS] nucleus [IDA]	605607		247
Q8C0D9 UniProt NPD GO	CEP68_MOUSE	Centrosomal protein of 68 kDa (Cep68 protein)	0.63	-	nuc	0	Centrosome (By similarity)				733
P34940 UniProt NPD GO	CH60_PLAFG	Chaperonin CPN60, mitochondrial precursor	0.63	-	nuc	1 *	Mitochondrion; mitochondrial matrix (By similarity)				700
Q6ENI1 UniProt NPD GO	RR2_ORYNI	Chloroplast 30S ribosomal protein S2	0.63	-	mit	0	Plastid; chloroplast				236
Q85WZ6 UniProt NPD GO	RR8_PINKO	Chloroplast 30S ribosomal protein S8	0.63	+	nuc	0	Plastid; chloroplast				132
Q6ENF0 UniProt NPD GO	RK20_ORYNI	Chloroplast 50S ribosomal protein L20	0.63	-	nuc	0	Plastid; chloroplast				119
P30378 UniProt NPD GO	1A04_GORGO	Class I histocompatibility antigen, GOGO-A0501 alpha chain precursor	0.63	-	end	1	Membrane; single-pass type I membrane protein				365
Q7T046 UniProt NPD GO	RVXX_VIPLE	Coagulation factor X-activating enzyme heavy chain precursor (EC 3.4.24.58) (VLFXA heavy chain) (Coa ...	0.63	-	nuc	0	Secreted protein (By similarity)				612
Q96MW1 UniProt NPD GO	CCD43_HUMAN	Coiled-coil domain-containing protein 43	0.63	+	cyt	0					224
Q08024 UniProt NPD GO	PEBB_MOUSE	Core-binding factor subunit beta (CBF-beta) (Polyomavirus enhancer-binding protein 2 beta subunit) ( ...	0.63	-	nuc	0	Nucleus (Potential)	nucleus [IDA]		2JHB	187
P01193 UniProt NPD GO	COLI_MOUSE	Corticotropin-lipotropin precursor (Pro-opiomelanocortin) (POMC) [Contains: NPP; Melanotropin gamma ...	0.63	-	exc	0					235
Q17389 UniProt NPD GO	CUL1_CAEEL	Cullin-1 (Abnormal cell lineage protein 19)	0.63	-	cyt	0	Cytoplasm (Potential)	cytosol [NAS]			780
Q17392 UniProt NPD GO	CUL4_CAEEL	Cullin-4	0.63	-	nuc	0					840
O14122 UniProt NPD GO	CUL4_SCHPO	Cullin-4 (Cul-4)	0.63	-	nuc	0	Nucleus	nuclear centric heterochromatin [TAS] nucleus [IDA] Rik1-E3 ubiquitin ligase complex [IDA]			734
Q5RCJ3 UniProt NPD GO	CUL7_PONPY	Cullin-7 (CUL-7)	0.63	-	cyt	0					1729
Q8VE73 UniProt NPD GO	CUL7_MOUSE	Cullin-7 (CUL-7) (p185) (p193) (Fragment)	0.63	-	cyt	0		anaphase-promoting complex [ISS] intracellular [IC]			913
Q86VP6 UniProt NPD GO	CAND1_HUMAN	Cullin-associated NEDD8-dissociated protein 1 (Cullin-associated and neddylation-dissociated protein ...	0.63	-	mit	0	Nucleus (By similarity)	ubiquitin ligase complex [IDA]	607727	1U6G	1230
P14606 UniProt NPD GO	CIGA_DICDI	Cyclic AMP-inducible protein BP74 precursor	0.63	-	nuc	1 *					786
Q15078 UniProt NPD GO	CD5R1_HUMAN	Cyclin-dependent kinase 5 activator 1 precursor (CDK5 activator 1) (Cyclin-dependent kinase 5 regula ...	0.63	-	nuc	0	Cyclin-dependent kinase 5 activator 1, p35: Cell membrane; lipid-anchor; cytoplasmic side (Probable) ...	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]	603460	1UNL	307
Q00552 UniProt NPD GO	CFTR_CAVPO	Cystic fibrosis transmembrane conductance regulator (CFTR) (cAMP-dependent chloride channel) (ATP-bi ...	0.63	-	nuc	0	Membrane; multi-pass membrane protein				180
Q6QHT9 UniProt NPD GO	CP19A_ANGJA	Cytochrome P450 19A1 (EC 1.14.14.1) (Aromatase) (CYPXIX) (Estrogen synthetase) (P-450AROM)	0.63	-	cyt	2 *	Membrane; peripheral membrane protein				511
P05179 UniProt NPD GO	CP2C7_RAT	Cytochrome P450 2C7 (EC 1.14.14.1) (CYPIIC7) (P450F) (PTF1)	0.63	-	nuc	0	Endoplasmic reticulum; endoplasmic reticulum membrane; peripheral membrane protein				490
P08749 UniProt NPD GO	COX2_PARTE	Cytochrome c oxidase subunit 2 (EC 1.9.3.1) (Cytochrome c oxidase polypeptide II)	0.63	-	cyt	0	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				205
Q5YLB5 UniProt NPD GO	GYRA_NICBE	DNA gyrase subunit A, chloroplast/mitochondrial precursor (EC 5.99.1.3)	0.63	-	mit	0	Plastid; chloroplast. Mitochondrion				935
P30315 UniProt NPD GO	DPOD_PLAFK	DNA polymerase delta catalytic subunit (EC 2.7.7.7)	0.63	+	nuc	0	Nucleus				1094
P15436 UniProt NPD GO	DPOD_YEAST	DNA polymerase delta catalytic subunit (EC 2.7.7.7) (DNA polymerase III)	0.63	+	nuc	0	Nucleus	delta DNA polymerase complex [TAS] replication fork [IDA]			1097
Q6R3M4 UniProt NPD GO	POLI_MOUSE	DNA polymerase iota (EC 2.7.7.7) (Rad30 homolog B)	0.63	-	nuc	0	Nucleus (By similarity). Accumulates at replication forks after DNA damage (By similarity)				717
P53709 UniProt NPD GO	RAD14_CANAL	DNA repair protein RAD14 (Fragment)	0.63	+	nuc	0	Nucleus				121
P22276 UniProt NPD GO	RPC2_YEAST	DNA-directed RNA polymerase III 130 kDa polypeptide (EC 2.7.7.6) (C128) (RNA polymerase III subunit ...	0.63	+	mit	0	Nucleus	DNA-directed RNA polymerase III complex [TAS]			1149
Q9MUS5 UniProt NPD GO	RPOB_MESVI	DNA-directed RNA polymerase beta chain (EC 2.7.7.6) (PEP) (Plastid-encoded RNA polymerase subunit be ...	0.63	-	cyt	0	Plastid; chloroplast				1080
Q9NVU0 UniProt NPD GO	RPC5_HUMAN	DNA-directed RNA polymerases III 80 kDa polypeptide (EC 2.7.7.6) (RNA polymerase III subunit 5) (RPC ...	0.63	-	nuc	0	Nucleus				708
Q9CZJ9 UniProt NPD GO	DJC18_MOUSE	DnaJ homolog subfamily C member 18	0.63	-	nuc	0	Membrane; single-pass membrane protein (Potential)				357
Q27968 UniProt NPD GO	DNJC3_BOVIN	DnaJ homolog subfamily C member 3 (Interferon-induced, double-stranded RNA-activated protein kinase ...	0.63	-	mit	0	Cytoplasm (By similarity). Endoplasmic reticulum (By similarity). Associated with the endoplasmic re ...				504
Q24133 UniProt NPD GO	DNAJ1_DROME	DnaJ protein homolog 1 (DROJ1)	0.63	-	nuc	0	Cytoplasm				334
Q43385 UniProt NPD GO	DOF37_ARATH	Dof zinc finger protein DOF3.7 (AtDOF3.7) (Dof affecting germination 1) (Transcription factor BBFa) ...	0.63	-	nuc	0	Nucleus (Probable)				296
Q9W6K1 UniProt NPD GO	MRE11_XENLA	Double-strand break repair protein MRE11	0.63	+	nuc	0	Nucleus (By similarity)				711
Q32LE6 UniProt NPD GO	DMRTD_BOVIN	Doublesex- and mab-3-related transcription factor C2	0.63	-	nuc	0	Nucleus (Potential)				370
Q99956 UniProt NPD GO	DUS9_HUMAN	Dual specificity protein phosphatase 9 (EC 3.1.3.48) (EC 3.1.3.16) (Mitogen-activated protein kinase ...	0.63	-	nuc	0	Cytoplasm	cytoplasm [TAS] nucleus [TAS]	300134		384
O00429 UniProt NPD GO	DNM1L_HUMAN	Dynamin-1-like protein (EC 3.6.5.5) (Dynamin-like protein) (Dnm1p/Vps1p-like protein) (DVLP) (Dynami ...	0.63	-	nuc	0	Cytoplasm; cytosol. Mainly. Intracellular membrane; peripheral membrane protein. Also membrane-assoc ...	endoplasmic reticulum [TAS] Golgi cis-face [TAS]	603850		736
Q9UQ16 UniProt NPD GO	DYN3_HUMAN	Dynamin-3 (EC 3.6.5.5) (Dynamin, testicular) (T-dynamin)	0.63	-	nuc	0	Cytoplasm (Potential). Microtubule-associated (Potential)				859
Q06651 UniProt NPD GO	PIB1_YEAST	E3 ubiquitin--protein ligase PIB1 (EC 6.-.-.-) (Phosphatidylinositol-3-phosphate-binding protein 1)	0.63	-	nuc	0	Endosome; endosomal membrane; peripheral membrane protein. Vacuole; vacuolar membrane; peripheral me ...	late endosome [IDA] vacuolar membrane (sensu Fungi) [IDA]			286
P50548 UniProt NPD GO	ERF_HUMAN	ETS domain-containing transcription factor ERF (Ets2 repressor factor)	0.63	+	nuc	0	Nucleus				548
Q9XSZ4 UniProt NPD GO	S4A4_RABIT	Electrogenic sodium bicarbonate cotransporter 1 (Sodium bicarbonate cotransporter) (Na(+)/HCO3(-) co ...	0.63	+	end	9	Cell membrane; basolateral cell membrane; multi-pass membrane protein (By similarity)				1079
Q8TAT5 UniProt NPD GO	NEIL3_HUMAN	Endonuclease VIII-like 3 (Nei-like 3) (DNA glycosylase FPG2)	0.63	-	nuc	0	Nucleus		608934		605

You are viewing entries 17301 to 17350 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.