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
P78569 UniProt NPD GO	RL41_AGABI	60S ribosomal protein L41	0.85	+	nuc	0					25
Q10743 UniProt NPD GO	ADA10_RAT	ADAM 10 precursor (EC 3.4.24.81) (A disintegrin and metalloproteinase domain 10) (Mammalian disinteg ...	0.85	-	nuc	1	Membrane; single-pass type I membrane protein	cell surface [ISS] cytoplasm [ISS] Golgi apparatus [ISS] Golgi trans face [IDA] Golgi-associated vesicle [ISS] membrane fraction [IDA] nucleus [ISS]			544
Q811B3 UniProt NPD GO	ATS12_MOUSE	ADAMTS-12 precursor (EC 3.4.24.-) (A disintegrin and metalloproteinase with thrombospondin motifs 12 ...	0.85	-	nuc	0	Secreted protein; extracellular space; extracellular matrix (By similarity)				1600
Q8TE57 UniProt NPD GO	ATS16_HUMAN	ADAMTS-16 precursor (EC 3.4.24.-) (A disintegrin and metalloproteinase with thrombospondin motifs 16 ...	0.85	-	exc	0	Secreted protein; extracellular space; extracellular matrix (By similarity)		607510		1224
O08739 UniProt NPD GO	AMPD3_MOUSE	AMP deaminase 3 (EC 3.5.4.6) (AMP deaminase isoform E) (AMP deaminase H-type) (Heart-type AMPD)	0.85	-	nuc	0					766
Q01432 UniProt NPD GO	AMPD3_HUMAN	AMP deaminase 3 (EC 3.5.4.6) (AMP deaminase isoform E) (Erythrocyte AMP deaminase)	0.85	-	nuc	0			102772		767
Q497H0 UniProt NPD GO	ZFAN3_MOUSE	AN1-type zinc finger protein 3 (Testis-expressed sequence 27)	0.85	-	nuc	0					227
Q5U2M7 UniProt NPD GO	ZFAN3_RAT	AN1-type zinc finger protein 3 (Testis-expressed sequence 27)	0.85	-	nuc	0					227
Q08182 UniProt NPD GO	YAP7_YEAST	AP-1-like transcription factor YAP7	0.85	-	nuc	0	Nucleus	nucleus [IC]			245
Q8NE71 UniProt NPD GO	ABCF1_HUMAN	ATP-binding cassette sub-family F member 1 (ATP-binding cassette 50) (TNF-alpha-stimulated ABC prote ...	0.85	+	nuc	0			603429		845
P32807 UniProt NPD GO	KU70_YEAST	ATP-dependent DNA helicase 2 subunit 1 (EC 3.6.1.-) (Yeast Ku70 protein) (High affinity DNA-binding ...	0.85	-	nuc	0	Nucleus	nuclear chromatin [TAS] nuclear envelope [IDA] nuclear telomeric heterochromatin [TAS]			602
Q6CGD1 UniProt NPD GO	DBP4_YARLI	ATP-dependent RNA helicase DBP4 (EC 3.6.1.-)	0.85	+	nuc	0	Nucleus; nucleolus (By similarity)				740
Q7RZ35 UniProt NPD GO	DBP4_NEUCR	ATP-dependent RNA helicase dbp-4 (EC 3.6.1.-)	0.85	+	nuc	0	Nucleus; nucleolus (By similarity)				823
Q09903 UniProt NPD GO	DRS1_SCHPO	ATP-dependent RNA helicase drs1 (EC 3.6.1.-)	0.85	+	nuc	0	Nucleus; nucleolus (By similarity)				754
Q4WYJ7 UniProt NPD GO	SPB4_ASPFU	ATP-dependent rRNA helicase spb4 (EC 3.6.1.-)	0.85	-	nuc	0	Nucleus; nucleolus (By similarity)				640
Q12089 UniProt NPD GO	AEP3_YEAST	ATPase expression protein 3	0.85	-	nuc	0	Mitochondrion; mitochondrial inner membrane; peripheral membrane protein; matrix side	cytoplasm [IDA] extrinsic to membrane [IDA] mitochondrial inner membrane [IDA] mitochondrion [IDA]			606
P34441 UniProt NPD GO	EMB30_CAEEL	Abnormal embryogenesis protein 30	0.85	-	nuc	0					1027
Q16706 UniProt NPD GO	MA2A1_HUMAN	Alpha-mannosidase 2 (EC 3.2.1.114) (Alpha-mannosidase II) (Mannosyl-oligosaccharide 1,3-1,6-alpha-ma ...	0.85	-	mit	1 *	Golgi apparatus; Golgi membrane; single-pass type II membrane protein (By similarity)		154582		1144
P51170 UniProt NPD GO	SCNNG_HUMAN	Amiloride-sensitive sodium channel gamma-subunit (Epithelial Na+ channel subunit gamma) (Gamma ENaC) ...	0.85	-	mit	2	Cell membrane; apical cell membrane; multi-pass membrane protein. Apical membrane of epithelial cell ...	integral to plasma membrane [TAS]	600761		649
Q96Q45 UniProt NPD GO	AL2S4_HUMAN	Amyotrophic lateral sclerosis 2 chromosomal region candidate gene 4 protein	0.85	+	nuc	4	Membrane; multi-pass membrane protein (Potential)				432
Q9TT90 UniProt NPD GO	ANDR_CANFA	Androgen receptor (Dihydrotestosterone receptor)	0.85	+	nuc	0	Nucleus				907
Q2KJ51 UniProt NPD GO	ANGL4_BOVIN	Angiopoietin-related protein 4 precursor (Angiopoietin-like 4)	0.85	-	exc	0	Secreted protein (By similarity)				410
Q92625 UniProt NPD GO	ANKS1_HUMAN	Ankyrin repeat and SAM domain-containing protein 1A (Odin)	0.85	-	nuc	0	Cytoplasm. Cytoplasmic before and after growth factor treatment		608994		1133
P04114 UniProt NPD GO	APOB_HUMAN	Apolipoprotein B-100 precursor (Apo B-100) [Contains: Apolipoprotein B-48 (Apo B-48)]	0.85	-	nuc	1 *	Secreted protein	endoplasmic reticulum [NAS] extracellular region [NAS] microsome [TAS]	144010		4563
Q61324 UniProt NPD GO	ARNT2_MOUSE	Aryl hydrocarbon receptor nuclear translocator 2 (ARNT protein 2)	0.85	+	nuc	0	Nucleus (Potential)	nucleus [NAS] transcription factor complex [IDA]			712
Q9WTL8 UniProt NPD GO	BMAL1_MOUSE	Aryl hydrocarbon receptor nuclear translocator-like protein 1 (Brain and muscle ARNT-like 1) (Arnt3) ...	0.85	-	nuc	0	Nucleus	nucleus [IDA]			632
Q9EPW1 UniProt NPD GO	BMAL1_RAT	Aryl hydrocarbon receptor nuclear translocator-like protein 1 (Brain and muscle ARNT-like 1) (Tic)	0.85	-	nuc	0	Nucleus (By similarity)				626
P54259 UniProt NPD GO	ATN1_HUMAN	Atrophin-1 (Dentatorubral-pallidoluysian atrophy protein)	0.85	-	nuc	0		cytoplasm [TAS] nucleus [TAS]	607462		1185
Q5IS70 UniProt NPD GO	ATN1_PANTR	Atrophin-1 (Dentatorubral-pallidoluysian atrophy protein)	0.85	-	nuc	0					1186
P54258 UniProt NPD GO	ATN1_RAT	Atrophin-1 (Dentatorubral-pallidoluysian atrophy protein)	0.85	-	nuc	0					1183
Q9C438 UniProt NPD GO	ATG11_PICPA	Autophagy-related protein 11 (Glucose-induced selective autophagy protein 9) (Pexophagy zeocin-resis ...	0.85	-	nuc	0	Vacuole; vacuolar membrane; peripheral membrane protein. Vacuolar and perivacuolar punctate structur ...				1313
Q6CT08 UniProt NPD GO	ATG9_KLULA	Autophagy-related protein 9	0.85	-	nuc	4	Membrane; multi-pass membrane protein. Pre-autophagosomal and other perivacuolar punctate structures ...				908
P57094 UniProt NPD GO	AXN1_BRARE	Axin-1 (Axis inhibition protein 1)	0.85	-	nuc	0	Cytoplasm (By similarity)				835
P25356 UniProt NPD GO	BPH1_YEAST	Beige protein homolog 1	0.85	-	nuc	0		mitochondrion [IDA]			2167
O18017 UniProt NPD GO	BLM_CAEEL	Bloom syndrome protein homolog (EC 3.6.1.-) (RecQ helicase homolog)	0.85	-	nuc	0	Nucleus (By similarity)				988
Q91998 UniProt NPD GO	BRN3_CHICK	Brain-specific homeobox/POU domain protein 3 (Brn-3)	0.85	+	nuc	0	Nucleus				341
P41697 UniProt NPD GO	BUD6_YEAST	Bud site selection protein BUD6 (Actin-interacting protein 3)	0.85	-	nuc	0		actin cap [IDA] polarisome [TAS]			788
Q8K0V4 UniProt NPD GO	CNOT3_MOUSE	CCR4-NOT transcription complex subunit 3 (CCR4-associated factor 3)	0.85	-	nuc	0	Cytoplasm (Probable). Nucleus (Probable)				751
P20810 UniProt NPD GO	ICAL_HUMAN	Calpastatin (Calpain inhibitor) (Sperm BS-17 component)	0.85	-	nuc	0			114090		708
Q91574 UniProt NPD GO	CART1_XENLA	Cartilage homeoprotein 1 (CART-1) (XCART1)	0.85	+	nuc	0	Nucleus (Probable)				335
Q62763 UniProt NPD GO	KC1G3_RAT	Casein kinase I isoform gamma-3 (EC 2.7.11.1) (CKI-gamma 3)	0.85	-	nuc	0	Cytoplasm				448
Q9UQB3 UniProt NPD GO	CTND2_HUMAN	Catenin delta-2 (Delta-catenin) (Neural plakophilin-related ARM-repeat protein) (NPRAP) (Neurojungin ...	0.85	+	nuc	0	Nucleus (By similarity). Cell membrane; cell-cell junction; adherens junction (By similarity)	cytoplasm [TAS]	604275		1225
O35927 UniProt NPD GO	CTND2_MOUSE	Catenin delta-2 (Neural plakophilin-related ARM-repeat protein) (NPRAP) (Neurojungin)	0.85	+	nuc	0	Nucleus. Cell membrane; cell-cell junction; adherens junction				1247
O74113 UniProt NPD GO	CDC45_SCHPO	Cell division control protein 45 homolog (Suppressor of nda4 protein)	0.85	+	mit	0	Nucleus	chromatin [IGI] DNA replication preinitiation complex [IDA]			638
Q9NX58 UniProt NPD GO	LYAR_HUMAN	Cell growth-regulating nucleolar protein	0.85	+	nuc	0	Nucleus; nucleolus				379
P79820 UniProt NPD GO	P53_ORYLA	Cellular tumor antigen p53 (Tumor suppressor p53)	0.85	+	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity)				352
P97817 UniProt NPD GO	CDR2_MOUSE	Cerebellar degeneration-related protein 2	0.85	-	nuc	0		cytoplasm [IDA]			455
O94751 UniProt NPD GO	BUB1_SCHPO	Checkpoint serine/threonine-protein kinase bub1 (EC 2.7.11.1)	0.85	-	nuc	0	Nucleus. Associates with kinetochores and centromeres during the early stages of mitosis	nucleus [IDA]			1044
Q6KGW1 UniProt NPD GO	RR7_SCIVE	Chloroplast 30S ribosomal protein S7	0.85	-	nuc	0	Plastid; chloroplast				159
P12211 UniProt NPD GO	CEMA_MARPO	Chloroplast envelope membrane protein	0.85	+	end	4	Plastid; chloroplast; chloroplast inner membrane; multi-pass membrane protein (By similarity)				434

You are viewing entries 6401 to 6450 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.