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
Q5R8S0 UniProt NPD GO	K1967_PONPY	Protein KIAA1967 homolog	0.90	-	nuc	0					918
Q12502 UniProt NPD GO	LDB19_YEAST	Protein LDB19 (Low dye-binding protein 19)	0.90	-	nuc	0	Cytoplasm. Golgi apparatus	cytoplasm [IDA]			818
P32521 UniProt NPD GO	PAN1_YEAST	Protein PAN1	0.90	+	nuc	0	Cytoplasm; cell cortex; actin patch. Associates with the actin patches on the cell cortex	actin cortical patch [IDA] plasma membrane [IDA]			1480
P38232 UniProt NPD GO	REG2_YEAST	Protein REG2	0.90	-	nuc	0		protein phosphatase type 1 complex [IPI]			338
P32578 UniProt NPD GO	SIP1_YEAST	Protein SIP1	0.90	-	nuc	0		vacuole [IDA]			863
P35209 UniProt NPD GO	SPT21_YEAST	Protein SPT21	0.90	-	nuc	0		nucleus [IDA]			758
P32917 UniProt NPD GO	STE5_YEAST	Protein STE5	0.90	-	nuc	0	Cytoplasm	cytoplasm [IDA] mating projection tip [IDA] nucleus [IDA] plasma membrane [IDA]			917
Q6GVH5 UniProt NPD GO	ZN403_RAT	Protein ZNF403 (Gametogenetin-binding protein 2)	0.90	+	nuc	0	Cytoplasmic vesicle (By similarity). Associated with vesicular structures (By similarity)				696
P29673 UniProt NPD GO	APTE_DROME	Protein apterous	0.90	+	nuc	0	Nucleus	nucleus [IDA]			469
P48987 UniProt NPD GO	ATO_DROME	Protein atonal	0.90	+	nuc	0	Nucleus				312
Q9UUE2 UniProt NPD GO	CSX2_SCHPO	Protein csx2	0.90	-	nuc	0					870
P19538 UniProt NPD GO	CID_DROME	Protein cubitus interruptus	0.90	-	nuc	0	Nucleus	cytoplasm [IDA] Hedgehog signaling complex [IPI] membrane [IDA] nucleus [IEP]			1397
Q9VMA3 UniProt NPD GO	CUP_DROME	Protein cup (Oskar ribonucleoprotein complex 147 kDa subunit)	0.90	-	nuc	0	Cytoplasm				1132
O61734 UniProt NPD GO	CYCL_DROME	Protein cycle (Brain and muscle ARNT-like 1) (BMAL1) (MOP3)	0.90	-	nuc	0	Nucleus (Potential)	nucleus [NAS]			413
Q02308 UniProt NPD GO	HLES_DROME	Protein hairless	0.90	+	nuc	0	Nucleus (Probable)	nucleus [TAS]			1077
P40140 UniProt NPD GO	NG3_DROME	Protein new-glue 3 precursor (NG-3)	0.90	+	nuc	0	Secreted protein (Potential)				146
Q9W123 UniProt NPD GO	POF_DROME	Protein painting of fourth (Zeste-interacting protein 16) (Zip16 protein)	0.90	-	nuc	0	Nucleus. Specifically binds to the fourth chromosome	autosome [IDA]			495
Q96T49 UniProt NPD GO	PP16B_HUMAN	Protein phosphatase 1 regulatory inhibitor subunit 16B (TGF-beta-inhibited membrane-associated prote ...	0.90	+	nuc	0	Cell membrane; lipid-anchor (Potential)	plasma membrane [NAS]			567
Q9VLT5 UniProt NPD GO	POE_DROME	Protein purity of essence (Protein pushover) (Protein Calossin) (Interaction calmodulin and colossal ...	0.90	-	nuc	0					5322
P26674 UniProt NPD GO	STE6_SCHPO	Protein ste6	0.90	-	cyt	0					911
Q24211 UniProt NPD GO	STNA_DROME	Protein stoned-A (StonedA) (Stn-A)	0.90	+	nuc	0	Cytoplasm. Colocalizes with synaptic vesicle pools. Colocalizes with the endocytic network within sy ...	endocytic vesicle [IDA]			850
P42286 UniProt NPD GO	THR_DROME	Protein three rows	0.90	-	nuc	0	Cytoplasm. Cytoplasmic during interphase and distributed throughout the cell during early mitosis	cytoplasm [IDA]			1379
Q6V3W0 UniProt NPD GO	THR_DROPS	Protein three rows	0.90	+	nuc	0	Cytoplasm (By similarity)	cytoplasm [ISS]			1409
Q9V5N8 UniProt NPD GO	STAN_DROME	Protocadherin-like wing polarity protein stan precursor (Protein starry night) (Protein flamingo)	0.90	+	end	8 *	Membrane; multi-pass membrane protein	integral to membrane [NAS]			3574
Q9NQ29 UniProt NPD GO	LUC7L_HUMAN	Putative RNA-binding protein Luc7-like 1 (SR+89) (Putative SR protein LUC7B1)	0.90	+	nuc	0			607782		371
Q9UMS5 UniProt NPD GO	PHTF1_HUMAN	Putative homeodomain transcription factor 1	0.90	+	end	6	Nucleus (Potential)		604950		762
Q12407 UniProt NPD GO	YD199_YEAST	Putative metabolite transport protein YDL199C	0.90	+	end	11	Membrane; multi-pass membrane protein (Potential)				687
Q19317 UniProt NPD GO	NBEA_CAEEL	Putative neurobeachin homolog	0.90	-	end	0	Cytoplasm (By similarity). Membrane; peripheral membrane protein (By similarity)				2507
Q5ZKM1 UniProt NPD GO	RRMJ3_CHICK	Putative rRNA methyltransferase 3 (EC 2.1.1.-) (rRNA (uridine-2'-O-)-methyltransferase 3)	0.90	+	nuc	0	Nucleus; nucleolus (By similarity)				832
Q8IY81 UniProt NPD GO	RRMJ3_HUMAN	Putative rRNA methyltransferase 3 (EC 2.1.1.-) (rRNA (uridine-2'-O-)-methyltransferase 3)	0.90	+	nuc	0	Nucleus; nucleolus				847
Q8CH09 UniProt NPD GO	SFR14_MOUSE	Putative splicing factor, arginine/serine-rich 14 (Arginine/serine-rich-splicing factor 14)	0.90	+	nuc	0	Nucleus (Potential)				1067
Q9FMB6 UniProt NPD GO	BIM3_ARATH	Putative transcription factor BIM3 (BES1-interacting Myc-like protein 3) (Transcription factor EN 12 ...	0.90	-	nuc	0	Nucleus (Probable)				298
Q9Z132 UniProt NPD GO	RSPO1_MOUSE	R-spondin-1 precursor (Roof plate-specific spondin-1) (Cysteine-rich and single thrombospondin domai ...	0.90	+	nuc	0	Secreted protein. Nucleus. May also localize in the nucleus according to Ref.1				265
P53971 UniProt NPD GO	YNC3_YEAST	RING finger protein YNL023C	0.90	-	nuc	0					965
P53437 UniProt NPD GO	RRN9_YEAST	RNA polymerase I-specific transcription initiation factor RRN9	0.90	-	nuc	0	Nucleus; nucleolus	RNA polymerase I upstream activating factor... [TAS]			365
P53064 UniProt NPD GO	RTF1_YEAST	RNA polymerase-associated protein RTF1	0.90	-	nuc	0	Nucleus; nucleoplasm	Cdc73/Paf1 complex [IPI] nucleus [IDA]			558
O13845 UniProt NPD GO	RSD1_SCHPO	RNA-binding protein rsd1	0.90	+	nuc	0					604
Q9WVM1 UniProt NPD GO	RGAP1_MOUSE	Rac GTPase-activating protein 1 (MgcRacGAP)	0.90	-	nuc	0	Nucleus. Cytoplasm. Spindle. During interphase, localized to the nucleus and cytoplasm along with mi ...	nucleus [ISS]			628
Q62172 UniProt NPD GO	RBP1_MOUSE	RalA-binding protein 1 (RalBP1) (Ral-interacting protein 1) (Dinitrophenyl S-glutathione ATPase) (DN ...	0.90	+	nuc	0	Membrane; peripheral membrane protein (By similarity)	membrane [ISS]			647
Q8WYP3 UniProt NPD GO	RIN2_HUMAN	Ras and Rab interactor 2 (Ras interaction/interference protein 2) (Ras inhibitor JC265) (Ras associa ...	0.90	-	nuc	0	Cytoplasm (Probable)				895
Q6XUX0 UniProt NPD GO	RIPK5_CHICK	Receptor-interacting serine/threonine-protein kinase 5 (EC 2.7.11.1) (Dusty protein kinase) (Dusty P ...	0.90	+	cyt	0	Cytoplasm (Probable)				930
P50898 UniProt NPD GO	MIG1_KLULA	Regulatory protein MIG1	0.90	-	nuc	0	Nucleus				474
P20945 UniProt NPD GO	ABAA_EMENI	Regulatory protein abaA	0.90	-	nuc	0	Nucleus				796
Q8CGM2 UniProt NPD GO	RP1L1_MOUSE	Retinitis pigmentosa 1-like 1 protein (Retinitis pigmentosa 1-like protein 1)	0.90	-	nuc	0					1859
Q64701 UniProt NPD GO	RBL1_MOUSE	Retinoblastoma-like protein 1 (107 kDa retinoblastoma-associated protein) (PRB1) (P107)	0.90	-	nuc	0		nucleus [IDA] transcription factor complex [IDA]			1063
O55043 UniProt NPD GO	ARHG7_RAT	Rho guanine nucleotide exchange factor 7 (PAK-interacting exchange factor beta) (Beta-Pix)	0.90	-	nuc	0		growth cone [IDA]		2G6F	646
P40995 UniProt NPD GO	SCD1_SCHPO	Rho guanine nucleotide exchange factor scd1	0.90	-	nuc	0	Nucleus. Cytoplasm. Located at the growing cell ends and tips of conjugation tubes	mating projection tip [IDA] nucleus [IDA]			872
Q28021 UniProt NPD GO	ROCK2_BOVIN	Rho-associated protein kinase 2 (EC 2.7.11.1) (Rho-associated, coiled-coil-containing protein kinase ...	0.90	-	nuc	0	Cytoplasm. Cell membrane; peripheral membrane protein. Cytoplasmic, and associated with actin microf ...			2F2U	1388
O89026 UniProt NPD GO	ROBO1_MOUSE	Roundabout homolog 1 precursor	0.90	-	nuc	0	Membrane; single-pass type I membrane protein (Potential)	axolemma [IDA]			1612
Q61466 UniProt NPD GO	SMRD1_MOUSE	SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily D member 1 (SWI/S ...	0.90	-	nuc	0	Nucleus (Probable)			1UHR	476

You are viewing entries 4351 to 4400 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.