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
Q12427 UniProt NPD GO	STB3_YEAST	Protein STB3 (SIN3-binding protein 3)	0.95	-	nuc	0	Cytoplasm	cytoplasm [IDA]			513
Q4WMI1 UniProt NPD GO	BFR2_ASPFU	Protein bfr2	0.95	+	nuc	0	Nucleus; nucleolus (By similarity)				565
P34545 UniProt NPD GO	CBP1_CAEEL	Protein cbp-1	0.95	-	nuc	0		cytoplasm [IDA]			2056
Q8MX88 UniProt NPD GO	CRM_DROSE	Protein cramped	0.95	-	nuc	0	Nucleus (By similarity). During S-phase in early embryogenesis (By similarity)	nucleus [ISS]			975
Q9VIF5 UniProt NPD GO	DEL_DROME	Protein deadlock	0.95	-	nuc	0	Nucleus. Centrosome. Colocalizes with the oocyte nucleus at midstages of oogenesis and with the cent ...	centrosome [IDA] nucleus [IDA]			981
P48608 UniProt NPD GO	DIA_DROME	Protein diaphanous	0.95	-	nuc	0	Localizes to the site where the metaphase furrow is anticipated to form, to the growing tip of cellu ...				1091
P36582 UniProt NPD GO	PCK1_SCHPO	Protein kinase C-like 1 (EC 2.7.11.13)	0.95	-	nuc	0					988
Q8MSS1 UniProt NPD GO	LVA_DROME	Protein lava lamp	0.95	-	nuc	0	Golgi apparatus. Lva-alpha-spectrin and Lva-CLIP-190 complexes are found at the Golgi	Golgi apparatus [IDA]			2779
P52164 UniProt NPD GO	MAX_RAT	Protein max (Myc-associated factor X)	0.95	+	nuc	0	Nucleus				160
P54705 UniProt NPD GO	SNWA_DICDI	Protein snwA	0.95	+	nuc	0	Nucleus				685
Q6V3V8 UniProt NPD GO	THR_DROVI	Protein three rows	0.95	-	nuc	0	Cytoplasm (By similarity)	cytoplasm [ISS]			1411
Q9U3V9 UniProt NPD GO	XMAS2_DROME	Protein xmas-2	0.95	+	nuc	0					1370
Q59KI4 UniProt NPD GO	INO80_CANAL	Putative DNA helicase INO80 (EC 3.6.1.-)	0.95	-	nuc	0	Nucleus (By similarity)				1387
Q9FJQ5 UniProt NPD GO	EIL5_ARATH	Putative ETHYLENE-INSENSITIVE3-like 5 protein	0.95	-	nuc	0	Nucleus (By similarity)				557
P32606 UniProt NPD GO	PT127_YEAST	Putative mitochondrial translation system component PET127	0.95	-	nuc	0		mitochondrial envelope [IDA]			800
Q9UT43 UniProt NPD GO	YFRD_SCHPO	Putative phospholipid-transporting ATPase C821.13c (EC 3.6.3.1)	0.95	-	end	7	Membrane; multi-pass membrane protein (Potential)				1562
Q6P3B9 UniProt NPD GO	RBFAL_MOUSE	Putative ribosome-binding factor A, mitochondrial precursor	0.95	-	nuc	0	Mitochondrion (Potential)				350
Q09813 UniProt NPD GO	T111_SCHPO	Putative transcription initiation factor TFIID 111 kDa subunit (TBP-associated factor 111 kDa) (TAFI ...	0.95	+	nuc	0	Nucleus (Potential)				979
O00841 UniProt NPD GO	CUDA_DICDI	Putative transcriptional regulator cudA	0.95	+	nuc	0	Nucleus; nucleoplasm				791
P34670 UniProt NPD GO	YO14_CAEEL	Putative zinc finger protein ZK686.4	0.95	-	nuc	0	Nucleus (Potential)				407
Q5R328 UniProt NPD GO	RSPO3_BRARE	R-spondin-3 precursor (Roof plate-specific spondin-3) (Cabriolet)	0.95	+	nuc	0	Secreted protein (By similarity)				317
Q15032 UniProt NPD GO	R3HD1_HUMAN	R3H domain-containing protein 1	0.95	-	nuc	0					1099
Q9Y2K5 UniProt NPD GO	R3HD2_HUMAN	R3H domain-containing protein 2 (Fragment)	0.95	-	nuc	0	Nucleus (Potential)			1WHR	962
Q09555 UniProt NPD GO	DAF19_CAEEL	RFX-like transcription factor daf-19 (Abnormal dauer formation protein 19)	0.95	-	nuc	0	Nucleus (Potential)				805
Q8QFX1 UniProt NPD GO	RIMB2_CHICK	RIM-binding protein 2 (RIM-BP2)	0.95	-	nuc	0	Synaptic plasma membrane				1325
O08856 UniProt NPD GO	ELL_MOUSE	RNA polymerase II elongation factor ELL (Eleven-nineteen lysine-rich leukemia protein)	0.95	-	nuc	0	Nucleus; nucleoplasm; nuclear speckle (By similarity). Colocalizes with EAF2 to nuclear speckles. Nu ...				602
P25046 UniProt NPD GO	MED19_YEAST	RNA polymerase II mediator complex subunit 19 (Hypoxic gene repressor protein 3) (Negative regulator ...	0.95	+	nuc	0	Nucleus	mediator complex [IDA] nucleus [IDA]			220
P32776 UniProt NPD GO	TFB1_YEAST	RNA polymerase II transcription factor B subunit 1 (RNA polymerase II transcription factor B p73 sub ...	0.95	-	nuc	0	Nucleus	nucleotide-excision repair factor 3 complex [TAS] transcription factor TFIIH complex [IDA]		1Y5O	642
Q8IYF1 UniProt NPD GO	ELOA2_HUMAN	RNA polymerase II transcription factor SIII subunit A2 (Elongin-A2) (EloA2) (Transcription elongatio ...	0.95	-	nuc	0	Nucleus (Probable)		609522		753
P38351 UniProt NPD GO	PAF1_YEAST	RNA polymerase-associated protein 1 (Protein PAF1)	0.95	+	nuc	0	Nucleus; nucleoplasm	Cdc73/Paf1 complex [IPI] nucleus [IDA]			445
Q62018 UniProt NPD GO	CTR9_MOUSE	RNA polymerase-associated protein CTR9 homolog (SH2 domain-binding protein 1) (Tetratricopeptide rep ...	0.95	+	nuc	0	Nucleus; nucleoplasm; nuclear speckle	nucleus [IDA]			1173
Q5XG24 UniProt NPD GO	RNPS1_XENLA	RNA-binding protein with serine-rich domain 1	0.95	+	nuc	0	Nucleus (By similarity)				283
Q9NZL6 UniProt NPD GO	RGL1_HUMAN	Ral guanine nucleotide dissociation stimulator-like 1 (RalGDS-like 1)	0.95	-	nuc	0			605667		768
P13769 UniProt NPD GO	FLP_ZYGBA	Recombinase Flp protein	0.95	-	nuc	0					474
P49796 UniProt NPD GO	RGS3_HUMAN	Regulator of G-protein signaling 3 (RGS3) (RGP3)	0.95	+	nuc	0	Cytoplasm. Nucleus. Long isoforms are cytoplasmic and associated with the plasma membrane. Short iso ...	cytosol [TAS]	602189	2F5Y	1198
Q01870 UniProt NPD GO	WETA_PENCH	Regulatory protein wetA	0.95	-	nuc	0					499
P41910 UniProt NPD GO	MAF1_YEAST	Repressor of RNA polymerase III transcription MAF1	0.95	-	nuc	0	Cytoplasm. Nucleus	nucleus [IDA]			395
Q8TA86 UniProt NPD GO	RP9_HUMAN	Retinitis pigmentosa 9 protein (Pim-1-associated protein) (PAP-1)	0.95	+	nuc	0	Nucleus (By similarity)		607331		221
P33568 UniProt NPD GO	RB_RAT	Retinoblastoma-associated protein (PP105) (RB) (Fragment)	0.95	+	nuc	0	Nucleus				899
Q5ZLR6 UniProt NPD GO	ARHG6_CHICK	Rho guanine nucleotide exchange factor 6 (Rac/Cdc42 guanine nucleotide exchange factor 6)	0.95	-	nuc	0					764
P39083 UniProt NPD GO	RGA1_YEAST	Rho-type GTPase-activating protein 1	0.95	+	nuc	0		intracellular [TAS]			1007
Q99575 UniProt NPD GO	POP1_HUMAN	Ribonucleases P/MRP protein subunit POP1 (EC 3.1.26.5) (hPOP1)	0.95	+	nuc	0	Nucleus; nucleolus	nucleolar ribonuclease P complex [IDA] ribonuclease MRP complex [IDA]	602486		1024
Q12176 UniProt NPD GO	MAK21_YEAST	Ribosome biogenesis protein MAK21 (Maintenance of killer protein 21) (Nucleolar complex protein 1)	0.95	+	nuc	0	Nucleus; nucleolus	Noc1p-Noc2p complex [IPI]			1025
P59808 UniProt NPD GO	SASH1_MOUSE	SAM and SH3 domain-containing protein 1	0.95	-	nuc	0					1230
Q91Z69 UniProt NPD GO	SRGP1_MOUSE	SLIT-ROBO Rho GTPase-activating protein 1 (srGAP1) (Rho-GTPase-activating protein 13) (Fragment)	0.95	-	nuc	0					714
O75044 UniProt NPD GO	FNBP2_HUMAN	SLIT-ROBO Rho GTPase-activating protein 2 (srGAP2) (Formin-binding protein 2)	0.95	-	nuc	0			606524		1071
Q80YR5 UniProt NPD GO	SAFB2_MOUSE	Scaffold attachment factor B2	0.95	+	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity)				991
Q9GZR1 UniProt NPD GO	SENP6_HUMAN	Sentrin-specific protease 6 (EC 3.4.22.-) (Sentrin/SUMO-specific protease SENP6) (SUMO-1-specific pr ...	0.95	+	nuc	0	Cytoplasm		605003		1112
Q9UHD8 UniProt NPD GO	SEPT9_HUMAN	Septin-9 (MLL septin-like fusion protein) (MLL septin-like fusion protein MSF-A) (Ovarian/Breast sep ...	0.95	-	nuc	0	Cell membrane (By similarity)	cytoplasm [TAS] microtubule [IDA] perinuclear region [IDA] stress fiber [IDA]	604061		586
Q9NQ38 UniProt NPD GO	ISK5_HUMAN	Serine protease inhibitor Kazal-type 5 precursor (Lympho-epithelial Kazal-type-related inhibitor) (L ...	0.95	-	exc	0	Secreted protein	cell cortex [IDA] cytoplasm [IDA] cytosol [IDA] endoplasmic reticulum [IDA] endoplasmic reticulum membrane [IDA] extracellular region [IDA] lamellar body [TAS] perinuclear region [IDA]	256500	1UVG	1064

You are viewing entries 2051 to 2100 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.