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
Q06639 UniProt NPD GO	RSC3_YEAST	Chromatin structure remodeling complex protein RSC3 (Remodel the structure of chromatin complex subu ...	0.99	-	nuc	0	Nucleus. Localizes to centromeric and flanking chromatin. Association with these loci is dependent o ...	nucleus [IDA] RSC complex [IDA]			885
P32657 UniProt NPD GO	CHD1_YEAST	Chromo domain protein 1 (EC 3.6.1.-) (ATP-dependent helicase CHD1)	0.99	-	nuc	0	Nucleus (Probable)	mitochondrion [IDA] SAGA complex [IDA] SLIK (SAGA-like) complex [IDA] transcription elongation factor complex [IPI]			1468
Q9US25 UniProt NPD GO	HRP1_SCHPO	Chromodomain helicase hrp1 (EC 3.6.1.-) (ATP-dependent helicase hrp1)	0.99	+	nuc	0	Nucleus	condensed chromosome, pericentric region [IDA] nucleus [IDA]			1373
O14139 UniProt NPD GO	HRP3_SCHPO	Chromodomain helicase hrp3 (EC 3.6.1.-) (ATP-dependent helicase hrp3)	0.99	-	nuc	0	Nucleus	mating-type region heterochromatin [IDA]			1388
Q9P2D1 UniProt NPD GO	CHD7_HUMAN	Chromodomain-helicase-DNA-binding protein 7 (EC 3.6.1.-) (ATP-dependent helicase CHD7) (CHD-7) (Frag ...	0.99	+	nuc	0	Nucleus (Probable)		608892		2235
Q9HCK8 UniProt NPD GO	CHD8_HUMAN	Chromodomain-helicase-DNA-binding protein 8 (EC 3.6.1.-) (ATP-dependent helicase CHD8) (CHD-8) (Heli ...	0.99	+	nuc	0	Nucleus (Probable)	nucleus [NAS]			2302
Q9V3I5 UniProt NPD GO	JIL1_DROME	Chromosomal serine/threonine-protein kinase JIL-1 (EC 2.7.11.1)	0.99	-	nuc	0	Nucleus. Associates with chromosomes throughout the cell cycle. Localizes to interband regions along ...	dosage compensation complex (sensu Insecta) [IPI] nuclear chromatin [IDA] nuclear chromosome [IDA] polytene chromosome interband [IDA]			1207
Q90640 UniProt NPD GO	KIF4A_CHICK	Chromosome-associated kinesin KIF4A (Chromokinesin)	0.99	+	nuc	0	Nucleus. Associated with mitotic chromosomes				1225
P33174 UniProt NPD GO	KIF4A_MOUSE	Chromosome-associated kinesin KIF4A (Chromokinesin)	0.99	+	nuc	0	Nucleus. Associated with mitotic chromosomes				1231
Q91784 UniProt NPD GO	KIF4A_XENLA	Chromosome-associated kinesin KLP1 (Chromokinesin)	0.99	-	nuc	0	Nucleus. Associated with mitotic chromosomes				1226
Q9UJ98 UniProt NPD GO	STAG3_HUMAN	Cohesin subunit SA-3 (Stromal antigen 3) (Stromalin 3) (SCC3 homolog 3)	0.99	+	vac	0	Nucleus. Associates with chromatin. In prophase I stage of meiosis, it is found along the axial elem ...	nucleus [TAS] synaptonemal complex [TAS]	608489		1225
O70576 UniProt NPD GO	STAG3_MOUSE	Cohesin subunit SA-3 (Stromal antigen 3) (Stromalin 3) (SCC3 homolog 3)	0.99	-	end	0	Nucleus. Associates with chromatin. In prophase I stage of meiosis, it is found along the axial elem ...	transverse filament [IDA]			1240
Q96GE4 UniProt NPD GO	CCD45_HUMAN	Coiled-coil domain-containing protein 45	0.99	+	nuc	0					821
O49498 UniProt NPD GO	DML3_ARATH	DEMETER-like protein 3 (EC 3.2.2.-)	0.99	+	nuc	0	Nucleus (Probable)				1044
P43633 UniProt NPD GO	ALK1_YEAST	DNA damage-responsive protein ALK1	0.99	-	nuc	0					760
P13382 UniProt NPD GO	DPOA_YEAST	DNA polymerase alpha catalytic subunit A (EC 2.7.7.7) (DNA polymerase I subunit A) (DNA polymerase a ...	0.99	+	nuc	0	Nucleus	alpha DNA polymerase:primase complex [TAS] replication fork [IDA]			1468
P14284 UniProt NPD GO	DPOZ_YEAST	DNA polymerase zeta catalytic subunit (EC 2.7.7.7)	0.99	+	nuc	0	Nucleus (Potential)	mitochondrion [IDA] zeta DNA polymerase complex [IDA]			1504
P32863 UniProt NPD GO	RAD54_YEAST	DNA repair and recombination protein RAD54 (EC 3.6.1.-)	0.99	+	nuc	0	Nucleus	nucleus [IMP]			898
P32849 UniProt NPD GO	RAD5_YEAST	DNA repair protein RAD5 (EC 3.6.1.-) (Radiation sensitivity protein 5) (Revertibility protein 2)	0.99	+	nuc	0	Cytoplasm. Nucleus	nuclear chromatin [IDA]			1169
P79051 UniProt NPD GO	RHP16_SCHPO	DNA repair protein rhp16 (RAD16 homolog)	0.99	+	nuc	0	Nucleus (By similarity)				861
P34252 UniProt NPD GO	SLD2_YEAST	DNA replication regulator SLD2 (DNA replication and checkpoint protein 1)	0.99	+	nuc	0	Nucleus (By similarity)	replication fork [IGI]			453
P21538 UniProt NPD GO	REB1_YEAST	DNA-binding protein REB1 (QBP)	0.99	+	nuc	0	Nucleus	nucleus [TAS]			810
Q3ZJ93 UniProt NPD GO	RPOB_PSEAK	DNA-directed RNA polymerase beta chain (EC 2.7.7.6) (PEP) (Plastid-encoded RNA polymerase subunit be ...	0.99	+	nuc	0	Plastid; chloroplast				2178
P14629 UniProt NPD GO	ERCC5_XENLA	DNA-repair protein complementing XP-G cells homolog (Xeroderma pigmentosum group G-complementing pro ...	0.99	+	nuc	0	Nucleus (By similarity)				1196
Q8C9B9 UniProt NPD GO	DIDO1_MOUSE	Death-inducer obliterator 1 (DIO-1) (Death-associated transcription factor 1) (DATF-1) (Fragments)	0.99	+	nuc	0	Cytoplasm. Nucleus. Translocates to the nucleus after pro-apoptotic stimuli	cytoplasm [TAS] nucleus [IDA]		1WEM	1956
P15924 UniProt NPD GO	DESP_HUMAN	Desmoplakin (DP) (250/210 kDa paraneoplastic pemphigus antigen)	0.99	+	nuc	0	Innermost portion of the desmosomal plaque	cornified envelope [IDA]	125647	1LM7	2871
P11531 UniProt NPD GO	DMD_MOUSE	Dystrophin	0.99	-	nuc	0		insoluble fraction [IDA] microsome [IDA] sarcolemma [TAS] synapse [IDA]			3678
Q9H2F5 UniProt NPD GO	EPC1_HUMAN	Enhancer of polycomb homolog 1	0.99	+	nuc	0	Nucleus	nucleus [IDA]			836
Q66JA8 UniProt NPD GO	EPC2_XENLA	Enhancer of polycomb homolog 2	0.99	+	nuc	0	Nucleus (By similarity)				804
Q6CIN8 UniProt NPD GO	EPL1_KLULA	Enhancer of polycomb-like protein 1	0.99	+	nuc	0	Nucleus (By similarity)				806
Q92800 UniProt NPD GO	EZH1_HUMAN	Enhancer of zeste homolog 1 (ENX-2)	0.99	-	nuc	0	Nucleus (Probable)		601674		747
P39935 UniProt NPD GO	IF4F1_YEAST	Eukaryotic initiation factor 4F subunit p150 (eIF4F p150) (eIF-4F p150) (mRNA cap-binding protein co ...	0.99	-	nuc	0		eukaryotic translation initiation factor 4F... [IGI] mitochondrion [IDA] ribosome [TAS]		1RF8	952
Q9VEX0 UniProt NPD GO	SULF1_DROME	Extracellular sulfatase SULF-1 homolog precursor (EC 3.1.6.-) (DmSulf-1)	0.99	+	nuc	1 *	Endoplasmic reticulum (By similarity). Golgi apparatus; Golgi stack (By similarity). Cell surface (B ...	cell surface [ISS] endoplasmic reticulum [ISS] Golgi stack [ISS]			1114
Q90XB6 UniProt NPD GO	SULF1_COTCO	Extracellular sulfatase Sulf-1 precursor (EC 3.1.6.-) (QSulf1)	0.99	+	nuc	0	Endoplasmic reticulum (By similarity). Golgi apparatus; Golgi stack (By similarity). Cell surface. A ...	cell surface [ISS] extracellular space [ISS]			867
Q66H04 UniProt NPD GO	FBX43_RAT	F-box only protein 43 (Endogenous meiotic inhibitor 2)	0.99	-	nuc	0					650
Q3YK19 UniProt NPD GO	FANCJ_CHICK	Fanconi anemia group J protein homolog (EC 3.6.1.-) (ATP-dependent RNA helicase BRIP1) (Protein FACJ ...	0.99	-	nuc	0	Nucleus (By similarity)				1252
Q8IYD8 UniProt NPD GO	FANCM_HUMAN	Fanconi anemia group M protein (EC 3.6.1.-) (ATP-dependent RNA helicase FANCM) (Protein FACM) (Fanco ...	0.99	-	nuc	1	Nucleus		609644		2048
O08696 UniProt NPD GO	FOXM1_MOUSE	Forkhead box protein M1 (Forkhead homolog 16) (Winged-helix transcription factor Trident)	0.99	+	nuc	0	Nucleus (By similarity)				760
Q09033 UniProt NPD GO	FRQ_SORFI	Frequency clock protein	0.99	-	nuc	0					997
Q810T2 UniProt NPD GO	CCNB3_MOUSE	G2/mitotic-specific cyclin-B3	0.99	-	nuc	0	Nucleus (By similarity)				1396
Q3T8J9 UniProt NPD GO	GON4L_HUMAN	GON-4-like protein (GON-4 homolog)	0.99	+	nuc	0	Nucleus (Potential)				2241
Q14789 UniProt NPD GO	GOGB1_HUMAN	Golgin subfamily B member 1 (Giantin) (Macrogolgin) (372 kDa Golgi complex-associated protein) (GCP3 ...	0.99	-	nuc	1	Golgi apparatus; Golgi membrane; single-pass type I membrane protein	ER-Golgi intermediate compartment [IDA] Golgi membrane [TAS] Golgi stack [TAS] integral to membrane [TAS]	602500		3259
Q811S9 UniProt NPD GO	GNL3_RAT	Guanine nucleotide-binding protein-like 3 (Nucleolar GTP-binding protein 3) (Nucleostemin)	0.99	+	nuc	0	Nucleus. Nucleus; nucleolus. Shuttles between the nucleus and nucleolus	nucleolus [IDA] nucleus [IDA]			538
Q7TMY8 UniProt NPD GO	HUWE1_MOUSE	HECT, UBA and WWE domain-containing protein 1 (EC 6.3.2.-) (E3 ubiquitin protein ligase URE-B1) (E3H ...	0.99	-	end	0	Nucleus (By similarity)	nucleus [ISS]			4377
Q59U81 UniProt NPD GO	SWR1_CANAL	Helicase SWR1 (EC 3.6.1.-)	0.99	-	nuc	0	Nucleus (By similarity)				1641
Q4IAK7 UniProt NPD GO	SWR1_GIBZE	Helicase SWR1 (EC 3.6.1.-)	0.99	+	nuc	0	Nucleus (By similarity)				1691
Q4P328 UniProt NPD GO	SWR1_USTMA	Helicase SWR1 (EC 3.6.1.-)	0.99	+	nuc	0	Nucleus (By similarity)				1830
Q5ARK3 UniProt NPD GO	SWR1_EMENI	Helicase swr1 (EC 3.6.1.-)	0.99	+	nuc	0	Nucleus (By similarity)				1656
P12351 UniProt NPD GO	HAP1_YEAST	Heme-responsive zinc finger transcription factor HAP1 (Heme activator protein 1) (CYP1 activatory pr ...	0.99	+	mit	0	Nucleus	nucleus [IDA]		2HAP	1483
Q92794 UniProt NPD GO	MYST3_HUMAN	Histone acetyltransferase MYST3 (EC 2.3.1.48) (EC 2.3.1.-) (MYST protein 3) (MOZ, YBF2/SAS3, SAS2 an ...	0.99	+	nuc	0	Nucleus. Partially concentrated in subnuclear foci distinct from PML bodies, and excluded from the n ...	nucleus [IDA]	601408	1M36	2004

You are viewing entries 251 to 300 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.