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
P63013 UniProt NPD GO	PRRX1_MOUSE	Paired mesoderm homeobox protein 1 (PRX-1) (Paired-related homeobox protein 1) (Homeobox protein mHo ...	0.84	+	nuc	0	Nucleus				245
P63014 UniProt NPD GO	PRRX1_RAT	Paired mesoderm homeobox protein 1 (PRX-1) (Paired-related homeobox protein 1) (rHox)	0.84	+	nuc	0	Nucleus (By similarity)				245
P10567 UniProt NPD GO	MYSP_CAEEL	Paramyosin	0.84	-	nuc	0	Thick filaments of the myofibrils				882
P36166 UniProt NPD GO	PXL1_YEAST	Paxillin-like protein 1	0.84	-	nuc	0		bud neck [IDA] bud tip [IDA] cytoplasm [IDA] incipient bud site [IDA] mating projection tip [IDA]			706
Q871A4 UniProt NPD GO	PPIL4_NEUCR	Peptidyl-prolyl cis-trans isomerase-like 4 (EC 5.2.1.8) (PPIase) (Rotamase)	0.84	+	nuc	0	Nucleus (By similarity)				494
P12349 UniProt NPD GO	PER_DROVI	Period circadian protein	0.84	-	nuc	0	Nucleus (By similarity). Cytoplasm; perinuclear region (By similarity). Nuclear at specific periods ...				1087
Q8CHI5 UniProt NPD GO	PER1_RAT	Period circadian protein 1 (rPER1) (Fragment)	0.84	-	nuc	0	Nucleus (By similarity)				1244
O60437 UniProt NPD GO	PEPL_HUMAN	Periplakin (195 kDa cornified envelope precursor protein) (190 kDa paraneoplastic pemphigus antigen) ...	0.84	-	nuc	0	Cell membrane; cell-cell junction; desmosome. Nucleus. Mitochondrion. Associated with desmosomes and ...	cytoskeleton [TAS]	602871		1756
P52960 UniProt NPD GO	PIP2_YEAST	Peroxisome proliferation transcriptional regulator (Oleate-activated transcription factor 2)	0.84	-	end	0	Nucleus	nucleus [IPI]			996
P35169 UniProt NPD GO	TOR1_YEAST	Phosphatidylinositol 3-kinase TOR1 (EC 2.7.1.137) (PtdIns-3-kinase TOR1) (PI3-kinase TOR1) (PI3K TOR ...	0.84	-	cyt	0		endosome membrane [IDA] extrinsic to internal side of plasma membrane [IDA] Golgi membrane [IDA] plasma membrane [IDA] TORC 1 complex [IPI] vacuolar membrane [IDA]		1W1N	2470
P20033 UniProt NPD GO	PDGFA_MOUSE	Platelet-derived growth factor A chain precursor (PDGF A-chain) (Platelet-derived growth factor alph ...	0.84	+	exc	0		microvillus [IDA]			211
P35226 UniProt NPD GO	PCGF4_HUMAN	Polycomb group RING finger protein 4 (Polycomb complex protein BMI-1) (RING finger protein 51)	0.84	-	nuc	0	Nucleus		164831		326
Q8K214 UniProt NPD GO	SCMH1_MOUSE	Polycomb protein SCMH1 (Sex comb on midleg homolog 1)	0.84	-	nuc	0	Nucleus (Probable)	nucleus [IC]			706
Q9VHA0 UniProt NPD GO	SCM_DROME	Polycomb protein Scm (Sex comb on midleg protein)	0.84	-	mit	0	Nucleus (Probable)	nucleus [IC]		1PK3	877
Q8IXK0 UniProt NPD GO	PHC2_HUMAN	Polyhomeotic-like protein 2 (hPH2) (Early development regulatory protein 2)	0.84	-	nuc	0	Nucleus (Probable)		602979		858
Q9Y117 UniProt NPD GO	GALT3_DROME	Polypeptide N-acetylgalactosaminyltransferase 3 (EC 2.4.1.41) (Protein-UDP acetylgalactosaminyltrans ...	0.84	-	end	1 *	Golgi apparatus; Golgi membrane; single-pass type II membrane protein (By similarity)	Golgi stack [NAS]			667
P20095 UniProt NPD GO	PRP2_YEAST	Pre-mRNA-splicing factor ATP-dependent RNA helicase PRP2 (EC 3.6.1.-)	0.84	-	nuc	0	Nucleus	nucleus [TAS] spliceosome complex [TAS]			876
P53854 UniProt NPD GO	CWC25_YEAST	Pre-mRNA-splicing factor CWC25 (Complexed with CEF1 protein 25)	0.84	-	nuc	0	Nucleus	spliceosome complex [IPI]			179
Q4P9X4 UniProt NPD GO	SPP2_USTMA	Pre-mRNA-splicing factor SPP2	0.84	-	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity)				417
Q93WV0 UniProt NPD GO	WRK20_ARATH	Probable WRKY transcription factor 20 (WRKY DNA-binding protein 20)	0.84	-	nuc	0	Nucleus (Probable)				557
O65590 UniProt NPD GO	WRK34_ARATH	Probable WRKY transcription factor 34 (WRKY DNA-binding protein 34)	0.84	-	nuc	0	Nucleus (Probable)				568
P28370 UniProt NPD GO	SMCA1_HUMAN	Probable global transcription activator SNF2L1 (EC 3.6.1.-) (ATP-dependent helicase SMARCA1) (SWI/SN ...	0.84	-	nuc	0	Nucleus	nucleus [TAS]	300012		976
Q55Z49 UniProt NPD GO	NUF2_CRYNE	Probable kinetochore protein NUF2	0.84	-	nuc	0	Nucleus (By similarity). Associated with kinetochores (By similarity)				467
Q4IBX0 UniProt NPD GO	NUF2_GIBZE	Probable kinetochore protein NUF2	0.84	-	nuc	0	Nucleus (By similarity). Associated with kinetochores (By similarity)				462
Q09630 UniProt NPD GO	MGR1_CAEEL	Probable metabotropic glutamate receptor mgl-1	0.84	-	end	7	Membrane; multi-pass membrane protein (By similarity)				999
Q6C2F4 UniProt NPD GO	NOP14_YARLI	Probable nucleolar complex protein 14	0.84	-	nuc	0	Nucleus; nucleolus (By similarity)				832
Q10571 UniProt NPD GO	MN1_HUMAN	Probable tumor suppressor protein MN1	0.84	-	nuc	0			607174		1319
O75592 UniProt NPD GO	MYCB2_HUMAN	Probable ubiquitin ligase protein MYCBP2 (EC 6.3.2.-) (Myc-binding protein 2) (Protein associated wi ...	0.84	+	nuc	0	Nucleus				4641
Q7TPH6 UniProt NPD GO	MYCB2_MOUSE	Probable ubiquitin ligase protein MYCBP2 (EC 6.3.2.-) (Myc-binding protein 2) (Protein associated wi ...	0.84	+	nuc	0	Nucleus (By similarity)				4711
Q6Q4D0 UniProt NPD GO	BRU1_ARATH	Protein BRUSHY 1 (Protein TONSOKU) (Protein MGOUN 3)	0.84	+	nuc	0	Nucleus				1311
Q8C6C7 UniProt NPD GO	CJ084_MOUSE	Protein C10orf84 homolog	0.84	+	nuc	0					236
Q5R498 UniProt NPD GO	CN140_PONPY	Protein C14orf140 homolog	0.84	-	nuc	0					389
Q5XKR9 UniProt NPD GO	F104B_HUMAN	Protein FAM104B	0.84	+	nuc	0					115
Q5EA89 UniProt NPD GO	FA76A_BOVIN	Protein FAM76A	0.84	-	nuc	0					307
Q4IR18 UniProt NPD GO	GRC3_GIBZE	Protein GRC3	0.84	-	nuc	0	Nucleus (By similarity)				796
O60308 UniProt NPD GO	K0562_HUMAN	Protein KIAA0562	0.84	-	nuc	0					925
Q5ZMG1 UniProt NPD GO	K0776_CHICK	Protein KIAA0776 homolog	0.84	+	cyt	0					789
Q9Y0I1 UniProt NPD GO	MRG15_DROME	Protein MRG15	0.84	-	nuc	0	Nucleus (Probable)	TIP60 histone acetyltransferase complex [IDA]			424
P46954 UniProt NPD GO	SIP4_YEAST	Protein SIP4	0.84	-	nuc	0	Nucleus (Probable)	nucleus [IDA]			829
Q9CTN5 UniProt NPD GO	S6OS1_MOUSE	Protein SIX6OS1 (Six6 opposite strand transcript 1)	0.84	-	nuc	0					574
Q92540 UniProt NPD GO	SMG7_HUMAN	Protein SMG7 (SMG-7 homolog) (EST1-like protein C)	0.84	-	nuc	0	Cytoplasm. Nucleus. Predominantly cytoplasmic, and nuclear. Shuttles between nucleus and cytoplasm	cytoplasm [IDA] nucleus [IDA]		1YA0	1137
Q6BSL1 UniProt NPD GO	VTS1_DEBHA	Protein VTS1	0.84	-	nuc	0	Cytoplasm (By similarity)				577
Q9VUQ5 UniProt NPD GO	AGO2_DROME	Protein argonaute-2	0.84	-	nuc	0		RNA-induced silencing complex [IDA]		1VYN	1214
Q9UU96 UniProt NPD GO	GRC3_SCHPO	Protein grc3	0.84	-	nuc	0	Nucleus	nucleus [IDA]			736
P16371 UniProt NPD GO	GROU_DROME	Protein groucho (Enhancer of split m9/10 protein) (E(spl)m9/10)	0.84	-	nuc	0	Nucleus	nucleus [TAS]			719
O96785 UniProt NPD GO	HUNB_CLOAL	Protein hunchback (Fragment)	0.84	-	nuc	0	Nucleus (Probable)				485
P34683 UniProt NPD GO	LIN31_CAEEL	Protein lin-31 (Abnormal cell lineage protein 31)	0.84	-	nuc	0	Nucleus (Probable)				237
P30630 UniProt NPD GO	LIN9_CAEEL	Protein lin-9 (Abnormal cell lineage protein 9)	0.84	-	nuc	0					644
Q5SW75 UniProt NPD GO	SSH2_MOUSE	Protein phosphatase Slingshot homolog 2 (EC 3.1.3.48) (EC 3.1.3.16) (SSH-2L) (mSSH-2L)	0.84	-	nuc	0	Cytoplasm. Colocalizes with filamentous actin in the cytoplasm and the cell periphery. Cell membrane ...				1423
Q8WMS3 UniProt NPD GO	IPP1_CANFA	Protein phosphatase inhibitor 1 (IPP-1) (I-1)	0.84	-	nuc	0					171

You are viewing entries 7101 to 7150 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.