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
Q7ZVC4 UniProt NPD GO	CHM4B_BRARE	Charged multivesicular body protein 4b (Chromatin-modifying protein 4b) (CHMP4b)	0.76	-	nuc	0	Cytoplasm (By similarity)				220
Q5ZL55 UniProt NPD GO	CHMP6_CHICK	Charged multivesicular body protein 6 (Chromatin-modifying protein 6)	0.76	-	nuc	0	Intracytoplasmic membrane; lipid-anchor (By similarity)				199
Q6ENW5 UniProt NPD GO	RR14_SACOF	Chloroplast 30S ribosomal protein S14	0.76	+	nuc	0	Plastid; chloroplast				103
Q85FK0 UniProt NPD GO	RR18_ADICA	Chloroplast 30S ribosomal protein S18	0.76	-	nuc	0	Plastid; chloroplast				75
P06375 UniProt NPD GO	RR18_MARPO	Chloroplast 30S ribosomal protein S18	0.76	-	nuc	0	Plastid; chloroplast				75
Q68RY4 UniProt NPD GO	RR18_PANGI	Chloroplast 30S ribosomal protein S18	0.76	-	nuc	0	Plastid; chloroplast				101
P49169 UniProt NPD GO	RR18_PEA	Chloroplast 30S ribosomal protein S18	0.76	+	nuc	0	Plastid; chloroplast				110
Q8WHZ9 UniProt NPD GO	RR18_PSINU	Chloroplast 30S ribosomal protein S18	0.76	-	nuc	0	Plastid; chloroplast				75
P02360 UniProt NPD GO	RR7_EUGGR	Chloroplast 30S ribosomal protein S7	0.76	-	nuc	0	Plastid; chloroplast				155
P06385 UniProt NPD GO	RK20_MARPO	Chloroplast 50S ribosomal protein L20	0.76	-	mit	0	Plastid; chloroplast				115
Q6C9N2 UniProt NPD GO	SFH1_YARLI	Chromatin structure remodeling complex protein SFH1 (SNF5 homolog 1)	0.76	+	nuc	0	Nucleus (By similarity)				441
Q8N8U2 UniProt NPD GO	CDYL2_HUMAN	Chromodomain Y-like protein 2 (CDY-like 2)	0.76	-	nuc	0	Nucleus (By similarity)				506
P06915 UniProt NPD GO	CSP_PLABE	Circumsporozoite protein precursor (CS)	0.76	-	exc	1 *					339
P17697 UniProt NPD GO	CLUS_BOVIN	Clusterin precursor (Glycoprotein III) (GpIII) [Contains: Clusterin beta chain; Clusterin alpha chai ...	0.76	-	exc	0	Present in chromaffin granules				439
P43621 UniProt NPD GO	COPD_YEAST	Coatomer subunit delta (Delta-coat protein) (Delta-COP)	0.76	-	nuc	0	Cytoplasm (By similarity). Golgi apparatus; Golgi membrane; peripheral membrane protein; cytoplasmic ...	COPI vesicle coat [IMP]			545
P61135 UniProt NPD GO	CO6_PONPY	Complement component C6 precursor	0.76	-	exc	0	Secreted protein				934
Q5RAD0 UniProt NPD GO	CO7_PONPY	Complement component C7 precursor	0.76	-	nuc	0					843
Q8SQ03 UniProt NPD GO	CRX_CANFA	Cone-rod homeobox protein	0.76	-	nuc	0	Nucleus (By similarity)				299
Q01819 UniProt NPD GO	CONN_DROME	Connectin precursor	0.76	-	end	1 *	Cell membrane; lipid-anchor; GPI-anchor (Potential)	plasma membrane [TAS]			682
Q969H4 UniProt NPD GO	CNKR1_HUMAN	Connector enhancer of kinase suppressor of ras 1 (Connector enhancer of KSR1) (hCNK1) (Connector enh ...	0.76	-	nuc	0	Cytoplasm (By similarity). Membrane; peripheral membrane protein (By similarity)	cell cortex [IDA] intercellular junction [TAS] plasma membrane [TAS]	603272	1WWV	720
Q4WYE5 UniProt NPD GO	MUS81_ASPFU	Crossover junction endonuclease mus81 (EC 3.1.22.-)	0.76	-	nuc	0	Nucleus (By similarity)				596
Q9UIA0 UniProt NPD GO	CYH4_HUMAN	Cytohesin-4	0.76	-	cyt	0			606514		394
Q6CUV9 UniProt NPD GO	LCD1_KLULA	DNA damage checkpoint protein LCD1	0.76	-	vac	0	Cytoplasm (By similarity). Nucleus (By similarity)				664
P39956 UniProt NPD GO	RPH1_YEAST	DNA damage-responsive transcriptional repressor RPH1	0.76	-	nuc	0	Nucleus	nucleus [IC]			796
Q58CZ0 UniProt NPD GO	DFFB_BOVIN	DNA fragmentation factor subunit beta (EC 3.-.-.-)	0.76	-	mit	0	Cytoplasm (By similarity). Nucleus (By similarity)				341
P38920 UniProt NPD GO	MLH1_YEAST	DNA mismatch repair protein MLH1 (MutL protein homolog 1) (Post meiotic segregation protein 2)	0.76	-	nuc	0	Nucleus	mitochondrion [IDA] nucleus [IMP]			769
O04716 UniProt NPD GO	MSH6_ARATH	DNA mismatch repair protein MSH6-1 (AtMsh6-1)	0.76	+	mit	0					1324
Q4PFV5 UniProt NPD GO	DPOE_USTMA	DNA polymerase epsilon, catalytic subunit A (EC 2.7.7.7) (DNA polymerase II subunit A)	0.76	+	nuc	0	Nucleus (By similarity)				2305
Q9FUG4 UniProt NPD GO	XPB2_ARATH	DNA repair helicase XPB2 (EC 3.6.1.-) (XPB homolog 2) (ERCC3 homolog 2) (RAD25 homolog 2) (AtXPB2)	0.76	-	nuc	0	Nucleus (Probable)				766
P14736 UniProt NPD GO	RAD4_YEAST	DNA repair protein RAD4	0.76	+	nuc	0	Nucleus	nucleotide-excision repair factor 2 complex [IDA] repairosome [IDA]			754
Q6C2R8 UniProt NPD GO	RAD5_YARLI	DNA repair protein RAD5 (EC 3.6.1.-)	0.76	-	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity)				1025
O16140 UniProt NPD GO	TOP2_BOMMO	DNA topoisomerase 2 (EC 5.99.1.3) (DNA topoisomerase II) (TOPOII)	0.76	+	nuc	0	Nucleus (By similarity)				1547
P41607 UniProt NPD GO	RPOB_PINTH	DNA-directed RNA polymerase beta chain (EC 2.7.7.6) (PEP) (Plastid-encoded RNA polymerase subunit be ...	0.76	-	nuc	0	Plastid; chloroplast				1075
P06273 UniProt NPD GO	RPOC1_MARPO	DNA-directed RNA polymerase beta' chain (EC 2.7.7.6) (PEP) (Plastid-encoded RNA polymerase beta' sub ...	0.76	-	cyt	0	Plastid; chloroplast				684
Q8HVY4 UniProt NPD GO	RPOC1_SOYBN	DNA-directed RNA polymerase beta' chain (EC 2.7.7.6) (PEP) (Plastid-encoded RNA polymerase beta' sub ...	0.76	-	nuc	0	Plastid; chloroplast				687
Q01923 UniProt NPD GO	RPOC2_SORBI	DNA-directed RNA polymerase beta'' chain (EC 2.7.7.6) (PEP) (Plastid-encoded RNA polymerase beta'' s ...	0.76	-	nuc	0	Plastid; chloroplast				435
O54784 UniProt NPD GO	DAPK3_MOUSE	Death-associated protein kinase 3 (EC 2.7.11.1) (DAP kinase 3) (DAP-like kinase) (Dlk) (ZIP-kinase)	0.76	-	cyt	0	Nucleus. Cytoplasm. Relocates to the cytoplasm on binding PAWR where the complex appears to interact ...	nucleus [IEP]			448
Q68FQ8 UniProt NPD GO	DLEC1_RAT	Deleted in lung and esophageal cancer protein 1 homolog	0.76	-	nuc	0	Cytoplasm (By similarity)	cytoplasm [ISS]			465
Q9W0S9 UniProt NPD GO	DIP2_DROME	Disco-interacting protein 2	0.76	+	end	0	Nucleus (Potential)				1773
Q15398 UniProt NPD GO	DLG7_HUMAN	Discs large homolog 7 (Hepatoma up-regulated protein) (HURP)	0.76	-	nuc	0	Nucleus. Cytoplasm. Localizes to the spindle poles in mitotic cells. Colocalizes with CDH1 at sites ...	nucleus [IDA] spindle pole centrosome [IDA]			846
Q18066 UniProt NPD GO	DIM1_CAEEL	Disorganized muscle protein 1 (2D-page protein spot 8)	0.76	-	nuc	0	Cytoplasm. Localized at the basal membrane region of bodywall muscle cells				640
Q9SE83 UniProt NPD GO	DRP2A_ARATH	Dynamin-2A (EC 3.6.5.5) (Dynamin-related protein 2A) (Dynamin-like protein 6)	0.76	-	nuc	0	Cytoplasm; cytosol. Golgi apparatus; Golgi membrane; peripheral membrane protein				914
Q27171 UniProt NPD GO	DYHC_PARTE	Dynein heavy chain, cytosolic (DYHC) (DHC08)	0.76	-	nuc	0	Cytoplasm				4540
P54703 UniProt NPD GO	DYIN_DICDI	Dynein intermediate chain, cytosolic (DH IC) (Cytoplasmic dynein intermediate chain)	0.76	-	nuc	0					652
Q680Q4 UniProt NPD GO	SIZ1_ARATH	E3 SUMO--protein ligase SIZ1 (EC 6.-.-.-)	0.76	+	nuc	0	Nucleus; nucleoplasm; nuclear speckle			1WEW	884
P50549 UniProt NPD GO	ETV1_HUMAN	ETS translocation variant 1 (ER81 protein)	0.76	-	nuc	0	Nucleus (Probable)		600541		477
Q29W20 UniProt NPD GO	EGR1_BOVIN	Early growth response protein 1 (EGR-1)	0.76	-	nuc	0	Nucleus (By similarity)				540
Q05159 UniProt NPD GO	EGR2B_BRARE	Early growth response protein 2b (EGR-2b) (Krox-20 protein) (KRX-20 protein)	0.76	-	nuc	0	Nucleus				412
P13055 UniProt NPD GO	E75BB_DROME	Ecdysone-induced protein 75B isoform B (E75-C)	0.76	-	nuc	0	Nucleus (Potential)				1412
P13206 UniProt NPD GO	EDN1_CANFA	Endothelin-1 precursor (ET-1) (Preproendothelin-1) (PPET1)	0.76	-	nuc	0	Secreted protein				202

You are viewing entries 10751 to 10800 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.