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
P38781 UniProt NPD GO	RSC30_YEAST	Chromatin structure remodeling complex protein RSC30 (Remodel the structure of chromatin complex sub ...	0.88	-	nuc	0	Nucleus. Localizes to centromeric and flanking chromatin. Association with these loci is dependent o ...	RSC complex [IDA]			883
P25632 UniProt NPD GO	RSC6_YEAST	Chromatin structure remodeling complex protein RSC6 (Remodel the structure of chromatin complex subu ...	0.88	-	nuc	0	Nucleus. Localizes to centromeric and flanking chromatin. Association with these loci is dependent o ...	RSC complex [IDA]			483
Q10103 UniProt NPD GO	CHP1_SCHPO	Chromo domain protein 1	0.88	+	nuc	0	Nucleus	centric heterochromatin [IDA] mating-type region heterochromatin [IDA] nuclear telomeric heterochromatin [IDA] RITS complex [IDA]			960
Q9DGN0 UniProt NPD GO	STAG2_XENLA	Cohesin subunit SA-2 (xSA-2) (Stromal antigen 2 homolog) (SCC3 homolog 2)	0.88	-	nuc	0	Nucleus. Associates with chromatin. Before prophase it is scattered along chromosome arms. During pr ...				1194
P30776 UniProt NPD GO	RAD21_SCHPO	Cohesin subunit rad21 (Double-strand-break repair protein rad21) (SCC1 homolog)	0.88	-	nuc	0	Nucleus. Associates with chromatin. Cohesin complex mainly associates with broad centromere region. ...	mitotic cohesin complex [IDA]			628
Q3MHS2 UniProt NPD GO	CCD16_RAT	Coiled-coil domain-containing protein 16	0.88	-	nuc	0	Nucleus (By similarity). Excluded from nucleolus (By similarity)				370
Q494V2 UniProt NPD GO	CCD37_HUMAN	Coiled-coil domain-containing protein 37	0.88	-	nuc	0					611
Q2HJ91 UniProt NPD GO	CCD71_BOVIN	Coiled-coil domain-containing protein 71	0.88	-	nuc	0					452
Q8IV32 UniProt NPD GO	CCD71_HUMAN	Coiled-coil domain-containing protein 71	0.88	-	nuc	0					467
Q14746 UniProt NPD GO	COG2_HUMAN	Conserved oligomeric Golgi complex component 2 (Low density lipoprotein receptor defect C-complement ...	0.88	-	nuc	0	Golgi apparatus; Golgi membrane; peripheral membrane protein; cytoplasmic side (Probable)	Golgi membrane [TAS] Golgi transport complex [IEP]	606974		738
Q9CWW7 UniProt NPD GO	CXCC1_MOUSE	CpG-binding protein (PHD finger and CXXC domain-containing protein 1) (CXXC finger protein 1)	0.88	-	nuc	0	Nucleus (By similarity)	nuclear matrix [IDA]			660
O02751 UniProt NPD GO	CFDP2_BOVIN	Craniofacial development protein 2 (p97 bucentaur protein)	0.88	-	nuc	0	Cytoplasm. Nucleus				592
Q6FM02 UniProt NPD GO	EME1_CANGA	Crossover junction endonuclease EME1 (EC 3.1.22.-)	0.88	-	nuc	0	Nucleus (By similarity)				580
Q6CNM6 UniProt NPD GO	EME1_KLULA	Crossover junction endonuclease EME1 (EC 3.1.22.-)	0.88	-	nuc	0	Nucleus (By similarity)				690
Q96AY2 UniProt NPD GO	EME1_HUMAN	Crossover junction endonuclease EME1 (EC 3.1.22.-) (hMMS4)	0.88	-	nuc	0	Nucleus; nucleolus. Recruited to regions of DNA damage in S-phase cells				570
Q6BJ48 UniProt NPD GO	MUS81_DEBHA	Crossover junction endonuclease MUS81 (EC 3.1.22.-)	0.88	+	nuc	0	Nucleus (By similarity)				651
Q4INS6 UniProt NPD GO	MUS81_GIBZE	Crossover junction endonuclease MUS81 (EC 3.1.22.-)	0.88	+	nuc	0	Nucleus (By similarity)				581
P52959 UniProt NPD GO	CTF1B_FUSSO	Cutinase transcription factor 1 beta	0.88	-	nuc	0	Nucleus (Potential)				882
Q8IVW4 UniProt NPD GO	CDKL3_HUMAN	Cyclin-dependent kinase-like 3 (EC 2.7.11.22) (Serine/threonine protein kinase NKIAMRE)	0.88	-	nuc	0	Cytoplasm (By similarity)		608459		592
Q3MJ16 UniProt NPD GO	PA24E_HUMAN	Cytosolic phospholipase A2 epsilon (EC 3.1.1.4) (cPLA2-epsilon) (Phospholipase A2 group IVE)	0.88	-	mit	0	Cytoplasm; cytosol. Translocates to lysosomal membranes in a calcium-dependent fashion (By similarit ...				838
Q2KN96 UniProt NPD GO	CYTSA_XENTR	Cytospin-A	0.88	-	nuc	0					1101
Q8H0U8 UniProt NPD GO	RH42_ARATH	DEAD-box ATP-dependent RNA helicase 42 (EC 3.6.1.-)	0.88	+	nuc	0					1166
P30620 UniProt NPD GO	PSO2_YEAST	DNA cross-link repair protein PSO2/SNM1 (EC 3.1.-.-)	0.88	-	nuc	0	Nucleus (Probable)	nucleus [IC]			661
Q62857 UniProt NPD GO	DDIT3_RAT	DNA damage-inducible transcript 3 (DDIT-3) (Growth arrest and DNA-damage-inducible protein GADD153)	0.88	+	nuc	0	Nucleus (By similarity)	nucleus [TAS]			168
O76075 UniProt NPD GO	DFFB_HUMAN	DNA fragmentation factor subunit beta (EC 3.-.-.-) (DNA fragmentation factor 40 kDa subunit) (DFF-40 ...	0.88	-	nuc	0	Cytoplasm. Nucleus	cytosol [TAS] nucleus [IDA]	601883	1IBX	338
P37913 UniProt NPD GO	DNL1_MOUSE	DNA ligase 1 (EC 6.5.1.1) (DNA ligase I) (Polydeoxyribonucleotide synthase [ATP] 1)	0.88	+	nuc	0	Nucleus				916
Q9JI44 UniProt NPD GO	DMAP1_MOUSE	DNA methyltransferase 1-associated protein 1 (DNMT1-associated protein 1) (DNMAP1) (MAT1-mediated tr ...	0.88	-	nuc	0	Nucleus. Targeted to replication foci throughout S phase by DNMT1	replication fork [IDA]			468
P52701 UniProt NPD GO	MSH6_HUMAN	DNA mismatch repair protein MSH6 (MutS-alpha 160 kDa subunit) (G/T mismatch-binding protein) (GTBP) ...	0.88	+	mit	0	Nucleus		608089		1360
P14242 UniProt NPD GO	PMS1_YEAST	DNA mismatch repair protein PMS1 (Postmeiotic segregation protein 1)	0.88	-	nuc	0	Nucleus	nuclear chromosome [TAS]			873
P87154 UniProt NPD GO	DPOE_SCHPO	DNA polymerase epsilon, catalytic subunit A (EC 2.7.7.7) (DNA polymerase II subunit A)	0.88	-	nuc	0	Nucleus (By similarity)	epsilon DNA polymerase complex [TAS]			2199
O12944 UniProt NPD GO	RAD54_CHICK	DNA repair and recombination protein RAD54-like (EC 3.6.1.-) (RAD54 homolog) (Putative recombination ...	0.88	-	nuc	0	Nucleus (Probable)				733
P39022 UniProt NPD GO	RAD52_CHICK	DNA repair protein RAD52 homolog	0.88	-	nuc	0	Nucleus (Potential)				422
Q10445 UniProt NPD GO	RHP41_SCHPO	DNA repair protein rhp41	0.88	+	nuc	0	Nucleus (Potential)				638
P06786 UniProt NPD GO	TOP2_YEAST	DNA topoisomerase 2 (EC 5.99.1.3) (DNA topoisomerase II)	0.88	+	nuc	0	Nucleus	nucleus [IDA] synaptonemal complex [IDA]		1QZR	1428
P90520 UniProt NPD GO	TOP2M_DICDI	DNA topoisomerase II, mitochondrial precursor (EC 5.99.1.3)	0.88	-	nuc	0	Mitochondrion				1282
P25032 UniProt NPD GO	EMBP1_WHEAT	DNA-binding protein EMBP-1 (Histone promoter-binding protein 1a(1)) (HBP-1a(1))	0.88	+	nuc	0	Nucleus				354
Q96TL7 UniProt NPD GO	RAP1_SCHPO	DNA-binding protein rap1	0.88	-	nuc	0	Nucleus	chromosome, telomeric region [IDA] nucleus [IDA]			693
Q49L08 UniProt NPD GO	RPOC2_EUCGG	DNA-directed RNA polymerase beta'' chain (EC 2.7.7.6) (PEP) (Plastid-encoded RNA polymerase beta'' s ...	0.88	-	nuc	0	Plastid; chloroplast				1392
Q8C3J5 UniProt NPD GO	DOCK2_MOUSE	Dedicator of cytokinesis protein 2 (Hch protein)	0.88	+	vac	0	Intracytoplasmic membrane; peripheral membrane protein (By similarity). Colocalizes with F-actin (By ...				1828
P34886 UniProt NPD GO	MEC10_CAEEL	Degenerin mec-10 (Mechanosensory abnormality protein 10)	0.88	-	end	2	Membrane; multi-pass membrane protein				724
Q6NZB0 UniProt NPD GO	DNJC8_MOUSE	DnaJ homolog subfamily C member 8	0.88	-	nuc	0					253
Q642C0 UniProt NPD GO	DNJC8_RAT	DnaJ homolog subfamily C member 8	0.88	-	nuc	0					253
O75937 UniProt NPD GO	DNJC8_HUMAN	DnaJ homolog subfamily C member 8 (Splicing protein spf31)	0.88	-	nuc	0					253
P49761 UniProt NPD GO	CLK3_HUMAN	Dual specificity protein kinase CLK3 (EC 2.7.12.1) (CDC-like kinase 3)	0.88	+	nuc	0	Nucleus (By similarity)		602990	2EXE	490
P50494 UniProt NPD GO	PVDG_PLAKN	Duffy receptor gamma form precursor (Erythrocyte-binding protein)	0.88	-	nuc	1	Membrane; single-pass type I membrane protein				1070
P28023 UniProt NPD GO	DYNA_RAT	Dynactin-1 (150 kDa dynein-associated polypeptide) (DP-150) (DAP-150) (p150-glued)	0.88	-	end	0	Cytoplasm	cytoplasmic dynein complex [IDA]			1280
Q14203 UniProt NPD GO	DYNA_HUMAN	Dynactin-1 (150 kDa dynein-associated polypeptide) (DP-150) (DAP-150) (p150-glued) (p135)	0.88	-	end	0	Cytoplasm	cytoplasm [TAS]	601143	2COY	1278
Q8LFT2 UniProt NPD GO	DRP3B_ARATH	Dynamin-related protein 3B (Dynamin-like protein 2b)	0.88	-	nuc	0	Mitochondrion				780
P54861 UniProt NPD GO	DNM1_YEAST	Dynamin-related protein DNM1 (EC 3.6.5.5)	0.88	-	nuc	0	Mitochondrion; mitochondrial outer membrane; cytoplasmic side. Cytoplasmic, localizes to the cytopla ...	mitochondrial outer membrane [IDA]			757
Q8H0T4 UniProt NPD GO	UPL2_ARATH	E3 ubiquitin protein ligase UPL2 (EC 6.3.2.-) (Ubiquitin-protein ligase 2)	0.88	-	end	0					3658

You are viewing entries 5051 to 5100 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.