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
P19174 UniProt NPD GO	PLCG1_HUMAN	1-phosphatidylinositol-4,5-bisphosphate phosphodiesterase gamma 1 (EC 3.1.4.11) (Phosphoinositide ph ...	0.90	-	nuc	0			172420	2HSP	1290
P10686 UniProt NPD GO	PLCG1_RAT	1-phosphatidylinositol-4,5-bisphosphate phosphodiesterase gamma 1 (EC 3.1.4.11) (Phosphoinositide ph ...	0.90	-	nuc	0		cytoplasm [TAS]		2FJL	1290
O97902 UniProt NPD GO	DDEF1_BOVIN	130 kDa phosphatidylinositol 4,5-biphosphate-dependent ARF1 GTPase-activating protein (PIP2-dependen ...	0.90	-	nuc	0	Cytoplasm (By similarity). Predominantly. Membrane (By similarity). Partially membrane-associated (B ...				1129
O55173 UniProt NPD GO	PDPK1_RAT	3-phosphoinositide-dependent protein kinase 1 (EC 2.7.11.1) (Protein kinase B kinase) (PkB kinase)	0.90	-	nuc	0	Cytoplasm (By similarity). Membrane; peripheral membrane protein (By similarity). Membrane-associate ...				559
Q9Z2A0 UniProt NPD GO	PDPK1_MOUSE	3-phosphoinositide-dependent protein kinase 1 (EC 2.7.11.1) (mPDK1)	0.90	-	nuc	0	Cytoplasm. Membrane; peripheral membrane protein. Membrane-associated after cell stimulation leading ...	cytoplasm [IDA] cytoplasmic membrane-bound vesicle [IDA]			559
Q15583 UniProt NPD GO	TGIF_HUMAN	5'-TG-3'-interacting factor (Homeobox protein TGIF)	0.90	-	nuc	0	Nucleus		602630		401
P70284 UniProt NPD GO	TGIF_MOUSE	5'-TG-3'-interacting factor (Homeobox protein TGIF)	0.90	-	nuc	0	Nucleus				272
Q5IS58 UniProt NPD GO	TGIF_PANTR	5'-TG-3'-interacting factor (Homeobox protein TGIF)	0.90	-	nuc	0	Nucleus (By similarity)				401
O60318 UniProt NPD GO	MCM3A_HUMAN	80 kDa MCM3-associated protein (GANP protein)	0.90	+	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity)	nucleus [TAS]	603294		1980
Q63014 UniProt NPD GO	AKAP8_RAT	A-kinase anchor protein 8 (A-kinase anchor protein 95 kDa) (AKAP 95)	0.90	+	nuc	0	Nucleus; nucleoplasm; nuclear matrix. Associated with the nuclear matrix. Redistributed and detached ...	nuclear matrix [IDA]			687
Q7Z4T9 UniProt NPD GO	AAT1_HUMAN	AMY-1-associating protein expressed in testis 1 (AAT-1)	0.90	-	nuc	0	Cytoplasm. Mitochondrion. Isoform 4 is found in the mitochondria and localized in the neck of the sp ...		609910		603
Q95LR0 UniProt NPD GO	AAT1_MACFA	AMY-1-associating protein expressed in testis 1 (AAT-1)	0.90	-	nuc	0	Cytoplasm (By similarity). Mitochondrion (By similarity)				603
P56095 UniProt NPD GO	AP1_KLULA	AP-1-like transcription factor	0.90	-	nuc	0	Nucleus				583
P54362 UniProt NPD GO	AP3D_DROME	AP-3 complex subunit delta (Delta-adaptin) (Garnet protein) (Delta adaptin subunit of AP-3)	0.90	-	nuc	0	Component of the coat surrounding the cytoplasmic face of coated vesicles located at the Golgi compl ...	AP-3 adaptor complex [NAS] endoplasmic reticulum [IDA] Golgi stack [IDA] Golgi-associated vesicle [NAS]			1034
O14497 UniProt NPD GO	ARI1A_HUMAN	AT-rich interactive domain-containing protein 1A (ARID domain-containing protein 1A) (SWI/SNF-relate ...	0.90	-	cyt	0	Nucleus	nucleus [NAS] SWI/SNF complex [ISS]	603024	1RYU	2285
P51979 UniProt NPD GO	HFM1_YEAST	ATP-dependent DNA helicase MER3 (EC 3.6.1.-) (Protein HFM1)	0.90	-	nuc	0	Nucleus (Probable)	nucleus [IDA]			1188
Q4P3W3 UniProt NPD GO	DBP10_USTMA	ATP-dependent RNA helicase DBP10 (EC 3.6.1.-)	0.90	-	nuc	0	Nucleus; nucleolus (By similarity)				1154
Q6C7X8 UniProt NPD GO	DBP10_YARLI	ATP-dependent RNA helicase DBP10 (EC 3.6.1.-)	0.90	+	nuc	0	Nucleus; nucleolus (By similarity)				926
Q9NVP1 UniProt NPD GO	DDX18_HUMAN	ATP-dependent RNA helicase DDX18 (EC 3.6.1.-) (DEAD box protein 18) (Myc-regulated DEAD box protein) ...	0.90	+	nuc	0			606355		670
Q8NJM2 UniProt NPD GO	DBP10_ASPFU	ATP-dependent RNA helicase dbp10 (EC 3.6.1.-)	0.90	+	nuc	0	Nucleus; nucleolus (By similarity)				869
Q8CJ27 UniProt NPD GO	ASPM_MOUSE	Abnormal spindle-like microcephaly-associated protein homolog (Calmodulin-binding protein 1) (Spindl ...	0.90	+	nuc	0	Cytoplasm. Nucleus. The nuclear-cytoplasmic distribution could be regulated by the availability of c ...				3122
Q751U1 UniProt NPD GO	SPB1_ASHGO	AdoMet-dependent rRNA methyltransferase SPB1 (EC 2.1.1.-) (2'-O-ribose RNA methyltransferase) (S-ade ...	0.90	+	nuc	0	Nucleus; nucleolus (By similarity)				845
Q6FX63 UniProt NPD GO	SPB1_CANGA	AdoMet-dependent rRNA methyltransferase SPB1 (EC 2.1.1.-) (2'-O-ribose RNA methyltransferase) (S-ade ...	0.90	+	nuc	0	Nucleus; nucleolus (By similarity)				837
Q15911 UniProt NPD GO	ATBF1_HUMAN	Alpha-fetoprotein enhancer-binding protein (AT motif-binding factor) (AT-binding transcription facto ...	0.90	-	nuc	0	Nucleus	nucleus [TAS]	104155		3703
P37091 UniProt NPD GO	SCNNG_RAT	Amiloride-sensitive sodium channel gamma-subunit (Epithelial Na+ channel subunit gamma) (Gamma ENaC) ...	0.90	-	nuc	2	Cell membrane; apical cell membrane; multi-pass membrane protein (By similarity). Apical membrane of ...				650
Q8MIK0 UniProt NPD GO	ANDR_CROCR	Androgen receptor (Dihydrotestosterone receptor)	0.90	+	nuc	0	Nucleus				912
Q5VUR7 UniProt NPD GO	A20A3_HUMAN	Ankyrin repeat domain-containing protein 20A3	0.90	+	nuc	0					823
Q5SQ80 UniProt NPD GO	A20A4_HUMAN	Ankyrin repeat domain-containing protein 20A4	0.90	+	nuc	0					823
Q96KQ4 UniProt NPD GO	ASPP1_HUMAN	Apoptosis-stimulating of p53 protein 1 (Protein phosphatase 1 regulatory subunit 13B)	0.90	-	nuc	0	Cytoplasm. Predominantly. Nucleus. Some fraction is nuclear	cytoplasm [TAS] nucleus [IDA]	606455		1090
Q9BXP5 UniProt NPD GO	ARS2_HUMAN	Arsenite-resistance protein 2	0.90	+	nuc	0					876
Q99MR6 UniProt NPD GO	ARS2_MOUSE	Arsenite-resistance protein 2	0.90	+	nuc	0					875
Q9DG12 UniProt NPD GO	ARNT2_BRARE	Aryl hydrocarbon receptor nuclear translocator 2 (ARNT protein 2) (zfARNT2)	0.90	+	nuc	0	Nucleus (Probable)	nucleus [IC]			737
Q5B1T9 UniProt NPD GO	ATG2_EMENI	Autophagy-related protein 2	0.90	-	nuc	0	Perivacuolar compartment (By similarity)				2102
Q6BW58 UniProt NPD GO	ATG9_DEBHA	Autophagy-related protein 9	0.90	-	nuc	6	Membrane; multi-pass membrane protein. Pre-autophagosomal and other perivacuolar punctate structures ...				905
Q08696 UniProt NPD GO	MST2_DROHY	Axoneme-associated protein mst101(2)	0.90	+	nuc	0	Cytoplasm	cytoplasm [IDA]			1391
Q7T2X6 UniProt NPD GO	BMP3B_XENLA	Bone morphogenetic protein 3b precursor (BMP-3b) (xBMP-3b)	0.90	-	nuc	1 *	Secreted protein				443
O60242 UniProt NPD GO	BAI3_HUMAN	Brain-specific angiogenesis inhibitor 3 precursor	0.90	-	end	8 *	Membrane; multi-pass membrane protein	integral to membrane [TAS]	602684		1522
P11274 UniProt NPD GO	BCR_HUMAN	Breakpoint cluster region protein (EC 2.7.11.1) (NY-REN-26 antigen)	0.90	+	nuc	0			151410	1K1F	1271
Q95153 UniProt NPD GO	BRCA1_CANFA	Breast cancer type 1 susceptibility protein homolog	0.90	-	nuc	0	Nucleus (Potential)	gamma-tubulin ring complex [ISS] nucleus [ISS]			1878
Q80YN3 UniProt NPD GO	BCAS1_MOUSE	Breast carcinoma amplified sequence 1 homolog (Novel amplified in breast cancer 1 homolog)	0.90	+	nuc	0	Cytoplasm (By similarity)				633
Q9HF61 UniProt NPD GO	BUD3_ASHGO	Bud site selection protein BUD3	0.90	-	nuc	0					1478
Q7Z401 UniProt NPD GO	MYCPP_HUMAN	C-myc promoter-binding protein	0.90	-	nuc	0	Nucleus (Probable)				1863
P51950 UniProt NPD GO	MAT1_MARGL	CDK-activating kinase assembly factor MAT1 (RING finger protein MAT1) (Menage a trois) (CDK7/cyclin ...	0.90	-	nuc	0	Nucleus				324
P50582 UniProt NPD GO	HSK1_SCHPO	Cell cycle serine/threonine-protein kinase hsk1 (EC 2.7.11.1) (Minichromosome maintenance protein ki ...	0.90	-	nuc	0	Nucleus. Nuclear throughout the cell cycle	Dbf4-dependent protein kinase complex [TAS] nucleus [IDA]			507
P41411 UniProt NPD GO	CDC18_SCHPO	Cell division control protein 18	0.90	-	nuc	0					577
P32504 UniProt NPD GO	CBF3A_YEAST	Centromere DNA-binding protein complex CBF3 subunit A (Kinetochore protein CTF14) (Centromere-bindin ...	0.90	-	nuc	0	Nucleus	CBF3 complex [TAS] condensed nuclear chromosome kinetochore [IDA] spindle midzone [IDA]			956
Q53EZ4 UniProt NPD GO	CEP55_HUMAN	Centrosome protein 55 (Up-regulated in colon cancer 6)	0.90	-	nuc	0	Centrosome. Present at the centrosomes at interphase. A small portion is associated preferentially w ...		610000		464
Q33BP8 UniProt NPD GO	FOXN3_PIG	Checkpoint suppressor 1 (Forkhead box protein N3)	0.90	+	nuc	0	Nucleus (Probable)				485
P06507 UniProt NPD GO	RR14_SPIOL	Chloroplast 30S ribosomal protein S14	0.90	-	nuc	0	Plastid; chloroplast				99
Q6CX31 UniProt NPD GO	EAF7_KLULA	Chromatin modification-related protein EAF7	0.90	-	nuc	0	Nucleus (By similarity)				402

You are viewing entries 4051 to 4100 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.