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
Q8R4S7 UniProt NPD GO	AHR_MUSCR	Aryl hydrocarbon receptor precursor (Ah receptor) (AhR)	0.93	-	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity). First cytoplasmic, upon binding with ligand and ...	nucleus [ISS]			854
Q8R4S2 UniProt NPD GO	AHR_MUSSP	Aryl hydrocarbon receptor precursor (Ah receptor) (AhR)	0.93	-	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity). First cytoplasmic, upon binding with ligand and ...	nucleus [ISS]			854
P54253 UniProt NPD GO	ATX1_HUMAN	Ataxin-1 (Spinocerebellar ataxia type 1 protein)	0.93	+	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity)	cytoplasm [TAS] nucleus [TAS]	164400	1OA8	816
Q7S055 UniProt NPD GO	ATG11_NEUCR	Autophagy-related protein 11	0.93	-	nuc	0	Vacuole; vacuolar membrane; peripheral membrane protein (By similarity). Vacuolar and perivacuolar p ...				1300
Q9VGI8 UniProt NPD GO	BLM_DROME	Bloom syndrome protein homolog (EC 3.6.1.-) (Dmblm) (Mutagen-sensitive protein 309) (RecQ helicase h ...	0.93	-	nuc	0	Nucleus (By similarity)				1487
Q8BHE5 UniProt NPD GO	BMP3_MOUSE	Bone morphogenetic protein 3 precursor (BMP-3)	0.93	+	exc	0	Secreted protein				468
Q6INP9 UniProt NPD GO	BCAR3_XENLA	Breast cancer anti-estrogen resistance protein 3 homolog	0.93	-	nuc	0					806
Q9Y6Y1 UniProt NPD GO	CMTA1_HUMAN	Calmodulin-binding transcription activator 1	0.93	+	nuc	0	Nucleus (Probable). Cytoplasm			2CXK	1673
P79955 UniProt NPD GO	CTK2_XENLA	Carboxy-terminal kinesin 2 (XCTK2)	0.93	-	nuc	0					643
Q9H257 UniProt NPD GO	CARD9_HUMAN	Caspase recruitment domain-containing protein 9 (hCARD9)	0.93	+	nuc	0	Cytoplasm		607212		536
Q9XT62 UniProt NPD GO	RAD17_CERAE	Cell cycle checkpoint protein RAD17	0.93	+	nuc	0	Nucleus. Phosphorylated form redistributes to discrete nuclear foci upon DNA damage (By similarity)				670
O75943 UniProt NPD GO	RAD17_HUMAN	Cell cycle checkpoint protein RAD17 (hRad17) (RF-C/activator 1 homolog)	0.93	+	nuc	0	Nucleus. Phosphorylated form redistributes to discrete nuclear foci upon DNA damage		603139		681
Q9P7C5 UniProt NPD GO	CWF16_SCHPO	Cell cycle control protein cwf16	0.93	-	nuc	0	Nucleus (Probable)				270
Q24106 UniProt NPD GO	HID_DROME	Cell death protein W (Protein head involution defective) (Protein wrinkled)	0.93	-	nuc	1					410
Q02342 UniProt NPD GO	CDC25_SACKL	Cell division control protein 25 (Fragment)	0.93	-	nuc	0					1095
Q99741 UniProt NPD GO	CDC6_HUMAN	Cell division control protein 6 homolog (CDC6-related protein) (p62(cdc6)) (HsCDC6) (HsCDC18)	0.93	-	nuc	0	Nucleus. Cytoplasm. The protein is nuclear in G1 and cytoplasmic in S-phase cells	cytoplasm [TAS] nucleus [TAS]		2CCI	560
Q8BT07 UniProt NPD GO	CEP55_MOUSE	Centrosome protein 55	0.93	-	mit	0	Centrosome (By similarity). Present at the centrosomes at interphase. A small portion is associated ...				462
Q9FL54 UniProt NPD GO	DNAJ6_ARATH	Chaperone protein dnaJ 6 (AtJ6) (AtDjC6)	0.93	+	nuc	0	Nucleus (Potential)				284
Q08365 UniProt NPD GO	RR3_CHLRE	Chloroplast 30S ribosomal protein S3 (ORF 712)	0.93	+	nuc	0	Plastid; chloroplast				712
Q5B4Q8 UniProt NPD GO	VID21_EMENI	Chromatin modification-related protein vid21	0.93	-	nuc	0	Nucleus (Probable)				1447
Q8WVM7 UniProt NPD GO	STAG1_HUMAN	Cohesin subunit SA-1 (Stromal antigen 1) (SCC3 homolog 1)	0.93	-	nuc	0	Nucleus. Associates with chromatin. Before prophase it is scattered along chromosome arms. During pr ...	nucleus [TAS]	604358		1258
Q9DGN1 UniProt NPD GO	STAG1_XENLA	Cohesin subunit SA-1 (xSA-1) (Stromal antigen 1 homolog) (SCC3 homolog 1)	0.93	-	cyt	0	Nucleus. Associates with chromatin. Before prophase it is scattered along chromosome arms. During pr ...				1265
Q3V036 UniProt NPD GO	CCD27_MOUSE	Coiled-coil domain-containing protein 27	0.93	-	nuc	0					639
Q9D5Y1 UniProt NPD GO	CCD39_MOUSE	Coiled-coil domain-containing protein 39	0.93	-	nuc	0					937
Q4FZU3 UniProt NPD GO	CCD55_RAT	Coiled-coil domain-containing protein 55	0.93	-	nuc	0					547
Q9BW85 UniProt NPD GO	CCD94_HUMAN	Coiled-coil domain-containing protein 94	0.93	-	nuc	0					323
O13688 UniProt NPD GO	COR1_SCHPO	Core protein 1	0.93	+	nuc	0					522
Q5I0H5 UniProt NPD GO	CCNL2_RAT	Cyclin-L2	0.93	+	nuc	0	Nucleus; nucleoplasm; nuclear speckle (By similarity)				520
Q4R8T9 UniProt NPD GO	CDKL3_MACFA	Cyclin-dependent kinase-like 3 (EC 2.7.11.22)	0.93	-	nuc	0	Cytoplasm (By similarity)				590
P32790 UniProt NPD GO	SLA1_YEAST	Cytoskeleton assembly control protein SLA1	0.93	+	nuc	0	Cytoplasm. Actin patch. Cytoplasmic and cortical actin patches. Is associated with cortical actin pa ...	actin cortical patch [IDA]		1Z9Z	1244
Q96G01 UniProt NPD GO	BICD1_HUMAN	Cytoskeleton-like bicaudal D protein homolog 1	0.93	-	nuc	0	Golgi apparatus	cytoskeleton [NAS]	602204		975
Q50L42 UniProt NPD GO	PA24E_MOUSE	Cytosolic phospholipase A2 epsilon (EC 3.1.1.4) (cPLA2-epsilon) (Phospholipase A2 group IVE)	0.93	+	nuc	0	Cytoplasm; cytosol. Translocates to lysosomal membranes in a calcium-dependent fashion	cytoplasm [IDA]			875
P53267 UniProt NPD GO	DAM1_YEAST	DASH complex subunit DAM1 (Outer kinetochore protein DAM1) (DUO1 and MPS1-interacting protein 1) (Ki ...	0.93	-	nuc	0	Nucleus. Associates with the mitotic spindle and the kinetochore	DASH complex [IDA] spindle midzone [IDA]			343
P35638 UniProt NPD GO	DDIT3_HUMAN	DNA damage-inducible transcript 3 (DDIT-3) (Growth arrest and DNA-damage-inducible protein GADD153) ...	0.93	+	nuc	0	Nucleus		126337		169
Q9UHC1 UniProt NPD GO	MLH3_HUMAN	DNA mismatch repair protein Mlh3 (MutL protein homolog 3)	0.93	-	nuc	0	Nucleus (Potential)	nucleus [TAS]	604395		1453
Q9FHA3 UniProt NPD GO	DPOLA_ARATH	DNA polymerase alpha catalytic subunit (EC 2.7.7.7)	0.93	-	nuc	0	Nucleus (By similarity)				1492
Q94636 UniProt NPD GO	DPOLA_OXYNO	DNA polymerase alpha catalytic subunit (EC 2.7.7.7)	0.93	+	nuc	0	Nucleus				1492
Q9LKI5 UniProt NPD GO	UVH1_ARATH	DNA repair endonuclease UVH1 (EC 3.1.-.-) (Ultraviolet hypersensitive 1) (AtRAD1) (DNA excision repa ...	0.93	-	nuc	0	Nucleus (Probable)				956
Q4PGG5 UniProt NPD GO	RAD5_USTMA	DNA repair protein RAD5 (EC 3.6.1.-)	0.93	-	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity)				1387
Q92878 UniProt NPD GO	RAD50_HUMAN	DNA repair protein RAD50 (EC 3.6.-.-) (hRAD50)	0.93	-	nuc	0	Nucleus. Localizes to discrete nuclear foci after treatment with genotoxic agents	Mre11 complex [TAS]	604040		1312
O14129 UniProt NPD GO	RAD55_SCHPO	DNA repair protein rhp55 (RAD55 homolog)	0.93	-	nuc	0	Nucleus (Potential)	nucleus [TAS]			350
O13329 UniProt NPD GO	FOB1_YEAST	DNA replication fork-blocking protein FOB1	0.93	-	nuc	0		nucleolus [IDA]			566
P30664 UniProt NPD GO	MCM4B_XENLA	DNA replication licensing factor mcm4-B (Minichromosome maintenance protein 4-B) (xMCM4-B) (CDC21 ho ...	0.93	-	nuc	0	Nucleus. Associated with chromatin before the formation of nuclei and detaches from it as DNA replic ...	chromatin [IDA] MCM complex [IDA]			863
Q01879 UniProt NPD GO	TOP2_PICGU	DNA topoisomerase 2 (EC 5.99.1.3) (DNA topoisomerase II) (Fragment)	0.93	-	nuc	0	Nucleus				389
P14248 UniProt NPD GO	RPB1_PLAFD	DNA-directed RNA polymerase II largest subunit (EC 2.7.7.6)	0.93	+	nuc	0	Nucleus				2452
P27625 UniProt NPD GO	RPC1_PLAFA	DNA-directed RNA polymerase III largest subunit (EC 2.7.7.6)	0.93	-	nuc	0	Nucleus				2339
P49466 UniProt NPD GO	RPOB_ODOSI	DNA-directed RNA polymerase beta chain (EC 2.7.7.6) (PEP) (Plastid-encoded RNA polymerase subunit be ...	0.93	-	nuc	0	Plastid; chloroplast				1379
Q6ENI2 UniProt NPD GO	RPOC2_ORYNI	DNA-directed RNA polymerase beta'' chain (EC 2.7.7.6) (PEP) (Plastid-encoded RNA polymerase beta'' s ...	0.93	+	nuc	0	Plastid; chloroplast				1513
P12093 UniProt NPD GO	RPOC2_ORYSA	DNA-directed RNA polymerase beta'' chain (EC 2.7.7.6) (PEP) (Plastid-encoded RNA polymerase beta'' s ...	0.93	+	nuc	0	Plastid; chloroplast				1513
Q6L3A5 UniProt NPD GO	RPOC2_SACHY	DNA-directed RNA polymerase beta'' chain (EC 2.7.7.6) (PEP) (Plastid-encoded RNA polymerase beta'' s ...	0.93	+	nuc	0	Plastid; chloroplast				1534

You are viewing entries 2701 to 2750 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.