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
P0C1D3 UniProt NPD GO	CTF18_EMENI	Chromosome transmission fidelity protein 18	0.94	-	nuc	0	Nucleus (By similarity)				993
O15516 UniProt NPD GO	CLOCK_HUMAN	Circadian locomoter output cycles protein kaput (hCLOCK)	0.94	+	nuc	0	Nucleus (Potential)		601851		846
O08785 UniProt NPD GO	CLOCK_MOUSE	Circadian locomoter output cycles protein kaput (mCLOCK)	0.94	+	nuc	0		cytoplasm [IDA] nucleus [IDA]			855
Q8BVV7 UniProt NPD GO	CCD45_MOUSE	Coiled-coil domain-containing protein 45	0.94	-	nuc	0					827
Q810U5 UniProt NPD GO	CCD50_MOUSE	Coiled-coil domain-containing protein 50 (Protein Ymer)	0.94	-	nuc	0					305
Q810U0 UniProt NPD GO	CCD50_RAT	Coiled-coil domain-containing protein 50 (Protein Ymer)	0.94	+	nuc	0					305
Q567U6 UniProt NPD GO	CCD93_HUMAN	Coiled-coil domain-containing protein 93	0.94	-	nuc	0					631
Q6FYA6 UniProt NPD GO	MUS81_CANGA	Crossover junction endonuclease MUS81 (EC 3.1.22.-)	0.94	-	nuc	0	Nucleus (By similarity)				628
Q09457 UniProt NPD GO	BLI1_CAEEL	Cuticle collagen bli-1 (Blistered cuticle protein 1)	0.94	-	exc	1 *					963
O93602 UniProt NPD GO	ATF2_CHICK	Cyclic AMP-dependent transcription factor ATF-2 (Activating transcription factor 2)	0.94	+	nuc	0	Nucleus				487
O35451 UniProt NPD GO	ATF6B_MOUSE	Cyclic AMP-dependent transcription factor ATF-6 beta (Activating transcription factor 6 beta) (ATF6- ...	0.94	+	nuc	0	Endoplasmic reticulum; endoplasmic reticulum membrane; single-pass type II membrane protein (By simi ...	condensed nuclear chromosome [ISS] early endosome [ISS] endomembrane system [ISS] microtubule organizing center [ISS] nuclear matrix [ISS]			699
Q99941 UniProt NPD GO	ATF6B_HUMAN	Cyclic AMP-dependent transcription factor ATF-6 beta (Activating transcription factor 6 beta) (ATF6- ...	0.94	+	nuc	0	Endoplasmic reticulum; endoplasmic reticulum membrane; single-pass type II membrane protein. Process ...	intracellular [IDA] nucleus [TAS]	600984		703
P35663 UniProt NPD GO	CYLC1_HUMAN	Cylicin-1 (Cylicin I) (Multiple-band polypeptide I)	0.94	+	nuc	0	Calyx. Sperm head cytoskeletal structure	acrosomal matrix [IDA] cytoskeleton [NAS]	603121		651
Q9ULE3 UniProt NPD GO	DEN2A_HUMAN	DENN domain-containing protein 2A	0.94	+	nuc	0					1009
P12000 UniProt NPD GO	DNLI_SCHPO	DNA ligase (EC 6.5.1.1) (Polydeoxyribonucleotide synthase [ATP])	0.94	-	nuc	0	Nucleus	mitochondrion [IDA] nucleus [IDA]			768
O74833 UniProt NPD GO	DNL4_SCHPO	DNA ligase 4 (EC 6.5.1.1) (DNA ligase IV) (Polydeoxyribonucleotide synthase [ATP] 4)	0.94	-	nuc	0	Nucleus (By similarity)				923
P20585 UniProt NPD GO	MSH3_HUMAN	DNA mismatch repair protein Msh3 (Divergent upstream protein) (DUP) (Mismatch repair protein 1) (MRP ...	0.94	+	nuc	0			608089		1137
Q9WVF7 UniProt NPD GO	DPOE1_MOUSE	DNA polymerase epsilon, catalytic subunit A (EC 2.7.7.7) (DNA polymerase II subunit A)	0.94	-	nuc	0	Nucleus				2283
Q9JIL8 UniProt NPD GO	RAD50_RAT	DNA repair protein RAD50 (EC 3.6.-.-)	0.94	-	nuc	0	Nucleus. Localizes to discrete nuclear foci after treatment with genotoxic agents	Mre11 complex [TAS]			1312
Q9SL02 UniProt NPD GO	RAD50_ARATH	DNA repair protein RAD50 (EC 3.6.-.-) (AtRAD50)	0.94	-	nuc	0	Nucleus (Probable)				1316
P41410 UniProt NPD GO	RAD54_SCHPO	DNA repair protein rhp54 (EC 3.6.1.-) (RAD54 homolog 1)	0.94	-	nuc	0	Nucleus				852
Q5XK83 UniProt NPD GO	MCM4A_XENLA	DNA replication licensing factor mcm4-A (Minichromosome maintenance protein 4-A) (xMCM4-A) (CDC21 ho ...	0.94	-	nuc	0	Nucleus. Associated with chromatin before the formation of nuclei and detaches from it as DNA replic ...	chromatin [IDA] MCM complex [IDA]			858
P53135 UniProt NPD GO	SLD3_YEAST	DNA replication regulator SLD3	0.94	+	nuc	0	Nucleus (By similarity)	nuclear chromatin [IDA]			668
P30189 UniProt NPD GO	TOP1_DROME	DNA topoisomerase 1 (EC 5.99.1.2) (DNA topoisomerase I)	0.94	+	nuc	0		cytoplasm [IDA] nucleus [IDA]			972
P07799 UniProt NPD GO	TOP1_SCHPO	DNA topoisomerase 1 (EC 5.99.1.2) (DNA topoisomerase I)	0.94	+	nuc	0					814
P40151 UniProt NPD GO	MGS1_YEAST	DNA-dependent ATPase MGS1 (Maintenance of genome stability protein 1)	0.94	-	nuc	0	Nucleus (Potential)	nucleus [IC]			587
P16025 UniProt NPD GO	RPOC2_MAIZE	DNA-directed RNA polymerase beta'' chain (EC 2.7.7.6) (PEP) (Plastid-encoded RNA polymerase beta'' s ...	0.94	+	nuc	0	Plastid; chloroplast				1527
Q5TJE1 UniProt NPD GO	DAXX_CANFA	Death domain-associated protein 6 (Daxx)	0.94	-	nuc	0	Nucleus (By similarity). Cytoplasm (By similarity). Translocates from the nucleus to the cytoplasm u ...	nucleus [ISS]			737
O94850 UniProt NPD GO	DEND_HUMAN	Dendrin	0.94	+	nuc	0					657
O08560 UniProt NPD GO	DGKZ_RAT	Diacylglycerol kinase zeta (EC 2.7.1.107) (Diglyceride kinase zeta) (DGK-zeta) (DAG kinase zeta) (DG ...	0.94	-	nuc	0	Nucleus	nucleus [IDA]			929
Q9Y4D1 UniProt NPD GO	DAAM1_HUMAN	Disheveled-associated activator of morphogenesis 1	0.94	+	nuc	0			606626		1078
Q3SWX9 UniProt NPD GO	RAD21_BOVIN	Double-strand-break repair protein rad21 homolog	0.94	-	nuc	0	Nucleus. Associates with chromatin. Before prophase it is scattered along chromosome arms. During pr ...				630
Q61550 UniProt NPD GO	RAD21_MOUSE	Double-strand-break repair protein rad21 homolog (Pokeweed agglutinin-binding protein 29) (PW29) (SC ...	0.94	-	nuc	0	Nucleus. Associates with chromatin. Once cleaved by caspase-3, the C-terminal 64 kDa cleavage produc ...				635
Q03373 UniProt NPD GO	DIG2_YEAST	Down-regulator of invasive growth 2 (Regulator of sterile twelve 2) (Regulator of STE12 protein 2)	0.94	-	nuc	0	Nucleus	nucleus [TAS]			323
Q07266 UniProt NPD GO	DREB_RAT	Drebrin (Developmentally-regulated brain protein)	0.94	-	nuc	0	Cytoplasm	actin cytoskeleton [ISS]			706
Q6TXD4 UniProt NPD GO	DNMBP_MOUSE	Dynamin-binding protein (Scaffold protein Tuba)	0.94	-	nuc	0	Cytoplasm. Golgi apparatus; Golgi stack. Localized to synapses and Golgi stacks				1580
P34036 UniProt NPD GO	DYHC_DICDI	Dynein heavy chain, cytosolic (DYHC)	0.94	-	nuc	0	Cytoplasm				4725
P01362 UniProt NPD GO	ELH1_APLCA	ELH precursor [Contains: Alpha-bag cell peptide (Alpha-BCP); Beta-bag cell peptide (Beta-BCP); Gamma ...	0.94	-	mit	0	Secreted protein				271
P53861 UniProt NPD GO	ELOA1_YEAST	Elongin-A	0.94	-	nuc	0					379
Q9UPY3 UniProt NPD GO	DICER_HUMAN	Endoribonuclease Dicer (EC 3.1.26.-) (Helicase with RNase motif) (Helicase-MOI)	0.94	-	nuc	0		intracellular [NAS]	606241		1912
Q9UU94 UniProt NPD GO	EPL1_SCHPO	Enhancer of polycomb-like protein 1	0.94	-	nuc	0	Nucleus (By similarity)				557
Q12929 UniProt NPD GO	EPS8_HUMAN	Epidermal growth factor receptor kinase substrate 8	0.94	+	nuc	0			600206		822
Q5R4H4 UniProt NPD GO	EPS8_PONPY	Epidermal growth factor receptor kinase substrate 8	0.94	+	nuc	0					822
Q6GQV7 UniProt NPD GO	EDRF1_MOUSE	Erythroid differentiation-related factor 1	0.94	-	nuc	0	Nucleus (Probable)				1239
P23116 UniProt NPD GO	IF3A_MOUSE	Eukaryotic translation initiation factor 3 subunit 10 (eIF-3 theta) (eIF3 p167) (eIF3 p180) (eIF3 p1 ...	0.94	-	nuc	0	Centrosomin A: Centrosome. Centrosomin B: Nucleus				1344
Q10475 UniProt NPD GO	IF4G_SCHPO	Eukaryotic translation initiation factor 4 gamma (eIF-4-gamma) (eIF-4G)	0.94	-	nuc	0	Cytoplasm; perinuclear region. Localized to the perinuclear region, the growing tips and septum				1403
Q6NZJ6 UniProt NPD GO	IF4G1_MOUSE	Eukaryotic translation initiation factor 4 gamma 1 (eIF-4-gamma 1) (eIF-4G1) (eIF-4G 1)	0.94	-	nuc	0		cytoplasm [IDA]			1600
Q4HYZ2 UniProt NPD GO	EXO84_GIBZE	Exocyst complex component EXO84	0.94	-	nuc	0	Secretory vesicle (By similarity). Cell periphery. The polarization of EXO84 requires actin cables ( ...				679
Q8IWU5 UniProt NPD GO	SULF2_HUMAN	Extracellular sulfatase Sulf-2 precursor (EC 3.1.6.-) (HSulf-2)	0.94	+	nuc	1 *	Endoplasmic reticulum (By similarity). Golgi apparatus; Golgi stack (By similarity). Cell surface (B ...	cell surface [IDA] extracellular space [NAS]			870
Q8IX29 UniProt NPD GO	FBX16_HUMAN	F-box only protein 16	0.94	-	nuc	0			608519		292

You are viewing entries 2251 to 2300 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.