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
Q9WTY8 UniProt NPD GO	ZBT10_RAT	Zinc finger and BTB domain-containing protein 10 (Zinc finger protein RIN ZF)	0.78	+	nuc	0	Nucleus (Potential)				836
Q9HC78 UniProt NPD GO	ZBT20_HUMAN	Zinc finger and BTB domain-containing protein 20 (Zinc finger protein 288) (Dendritic-derived BTB/PO ...	0.78	-	nuc	0	Nucleus (Probable)		606025		741
Q9P1Z0 UniProt NPD GO	ZBTB4_HUMAN	Zinc finger and BTB domain-containing protein 4 (KAISO-like zinc finger protein 1) (KAISO-L1)	0.78	+	nuc	0	Nucleus (Potential)				1013
Q9C0A1 UniProt NPD GO	ZFHX2_HUMAN	Zinc finger homeobox protein 2	0.78	-	nuc	0	Nucleus (Probable)				1427
Q14586 UniProt NPD GO	ZN267_HUMAN	Zinc finger protein 267 (Zinc finger protein HZF2)	0.78	-	nuc	0	Nucleus (Probable)		604752		743
Q4R7X8 UniProt NPD GO	Z322A_MACFA	Zinc finger protein 322A	0.78	-	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity)				402
Q9HCZ1 UniProt NPD GO	ZN334_HUMAN	Zinc finger protein 334	0.78	-	nuc	0	Nucleus (Probable)				680
Q569K4 UniProt NPD GO	ZN533_HUMAN	Zinc finger protein 533	0.78	-	nuc	0	Nucleus (Potential)				471
Q96KM6 UniProt NPD GO	K1196_HUMAN	Zinc finger protein KIAA1196	0.78	-	nuc	0	Nucleus (Probable)				892
Q9N658 UniProt NPD GO	GFI1_DROME	Zinc finger protein sens (Protein senseless)	0.78	-	nuc	0	Nucleus				541
Q9UTS5 UniProt NPD GO	ZAS1_SCHPO	Zinc finger protein zas1	0.78	-	nuc	1	Nucleus (Potential)				897
Q92784 UniProt NPD GO	DPF3_HUMAN	Zinc-finger protein DPF3 (cer-d4)	0.78	-	nuc	0	Cytoplasm (Potential). Nucleus (Potential)	nucleus [NAS]	601672		224
Q12033 UniProt NPD GO	PALA_YEAST	pH-response regulator protein palA/RIM20 (Regulator of IME2 protein 20)	0.78	-	nuc	0	Cytoplasm. Nucleus	cytoplasm [IDA] nucleus [IDA]			661
Q7SGZ5 UniProt NPD GO	PALF_NEUCR	pH-response regulator protein palF/rim-8	0.78	-	nuc	0					927
Q52B93 UniProt NPD GO	PACC_MAGGR	pH-response transcription factor pacC/RIM101	0.78	-	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity)				559
Q23917 UniProt NPD GO	REGA_DICDI	3',5'-cyclic-nucleotide phosphodiesterase regA (EC 3.1.4.17) (PDEase regA)	0.77	-	nuc	0					793
Q6BXH8 UniProt NPD GO	RS6_DEBHA	40S ribosomal protein S6	0.77	-	nuc	0					236
O76756 UniProt NPD GO	RS8_APIME	40S ribosomal protein S8	0.77	+	nuc	0					208
Q8MLY8 UniProt NPD GO	RS8_DROME	40S ribosomal protein S8	0.77	+	nuc	0					208
Q6BIJ5 UniProt NPD GO	RT09_DEBHA	40S ribosomal protein S9, mitochondrial precursor	0.77	-	mit	0	Mitochondrion (Potential)				323
Q90Z10 UniProt NPD GO	RL13_BRARE	60S ribosomal protein L13	0.77	-	nuc	0					210
P48535 UniProt NPD GO	RM02_KLULA	60S ribosomal protein L2, mitochondrial precursor	0.77	-	nuc	0	Mitochondrion				364
Q8LEM8 UniProt NPD GO	RL373_ARATH	60S ribosomal protein L37-3	0.77	-	mit	0					95
Q9R1V6 UniProt NPD GO	ADA22_MOUSE	ADAM 22 precursor (A disintegrin and metalloproteinase domain 22)	0.77	-	exc	1	Membrane; single-pass type I membrane protein				904
Q9R1V7 UniProt NPD GO	ADA23_MOUSE	ADAM 23 precursor (A disintegrin and metalloproteinase domain 23) (Metalloproteinase-like, disintegr ...	0.77	-	exc	1	Cell membrane; single-pass type I membrane protein (Potential). Isoform Gamma: Secreted protein				829
Q8TE59 UniProt NPD GO	ATS19_HUMAN	ADAMTS-19 precursor (EC 3.4.24.-) (A disintegrin and metalloproteinase with thrombospondin motifs 19 ...	0.77	-	exc	0	Secreted protein; extracellular space; extracellular matrix (By similarity)		607513		1207
P59509 UniProt NPD GO	ATS19_MOUSE	ADAMTS-19 precursor (EC 3.4.24.-) (A disintegrin and metalloproteinase with thrombospondin motifs 19 ...	0.77	-	nuc	0	Secreted protein; extracellular space; extracellular matrix (By similarity)				1210
Q06596 UniProt NPD GO	YAP8_YEAST	AP-1-like transcription factor YAP8 (Arsenical-resistance protein ARR1) (Arsenic compound resistance ...	0.77	-	nuc	0	Nucleus (Potential)	cytoplasm [IDA] nucleus [IDA]			294
Q9JKC9 UniProt NPD GO	SYNG_RAT	AP1 subunit gamma-binding protein 1 (Gamma-synergin) (Fragment)	0.77	+	nuc	0	Cytoplasm. Golgi apparatus; trans-Golgi network; trans-Golgi network membrane; peripheral membrane p ...	clathrin coat of trans-Golgi network vesicle [IDA]			700
Q68CP9 UniProt NPD GO	ARID2_HUMAN	AT-rich interactive domain-containing protein 2 (ARID domain-containing protein 2) (BRG1-associated ...	0.77	-	nuc	0	Nucleus		609539		1835
Q4HZ68 UniProt NPD GO	DBP7_GIBZE	ATP-dependent RNA helicase DBP7 (EC 3.6.1.-)	0.77	-	nuc	0	Nucleus; nucleolus (By similarity)				744
Q6P9R1 UniProt NPD GO	DDX51_MOUSE	ATP-dependent RNA helicase DDX51 (EC 3.6.1.-) (DEAD box protein 51)	0.77	+	nuc	0	Nucleus; nucleolus (By similarity)				639
Q5KMN6 UniProt NPD GO	HAS1_CRYNE	ATP-dependent RNA helicase HAS1 (EC 3.6.1.-)	0.77	-	nuc	0	Nucleus; nucleolus (By similarity)				607
Q76PD3 UniProt NPD GO	DBP6_SCHPO	ATP-dependent RNA helicase dbp6 (EC 3.6.1.-)	0.77	-	nuc	0	Nucleus; nucleolus (By similarity)				604
Q09916 UniProt NPD GO	HAS1_SCHPO	ATP-dependent RNA helicase has1 (EC 3.6.1.-)	0.77	-	nuc	0	Nucleus; nucleolus (By similarity)				578
Q4HVW2 UniProt NPD GO	SPB4_GIBZE	ATP-dependent rRNA helicase SPB4 (EC 3.6.1.-)	0.77	+	cyt	0	Nucleus; nucleolus (By similarity)				637
Q06234 UniProt NPD GO	ASCL1_XENLA	Achaete-scute homolog 1	0.77	-	nuc	0	Nucleus (Probable)				199
Q8N0Z2 UniProt NPD GO	ABRA_HUMAN	Actin-binding Rho-activating protein (Striated muscle activator of Rho-dependent signaling) (STARS)	0.77	-	nuc	0	Localized to the I-band of the sarcomere and to a lesser extent to the sarcomeric structure between ...	actin cytoskeleton [ISS] sarcomere [ISS]	609747		381
Q12386 UniProt NPD GO	ARP8_YEAST	Actin-like protein ARP8	0.77	-	nuc	0	Nucleus	INO80 complex [IPI] nucleus [IDA]			881
Q9QYL7 UniProt NPD GO	ABT1_MOUSE	Activator of basal transcription 1	0.77	-	nuc	0	Nucleus. Nucleus; nucleolus	transcription factor complex [IDA]			269
O18917 UniProt NPD GO	B3A3_RABIT	Anion exchange protein 3 (Neuronal band 3-like protein) (Solute carrier family 4 member 3) (Anion ex ...	0.77	+	end	11	Membrane; multi-pass membrane protein				1233
Q8N8V4 UniProt NPD GO	ANS4B_HUMAN	Ankyrin repeat and SAM domain-containing protein 4B (Harmonin-interacting ankyrin repeat-containing ...	0.77	-	nuc	0			609901		460
Q7ZUV0 UniProt NPD GO	AN13C_BRARE	Ankyrin repeat domain-containing protein 13C	0.77	-	nuc	0					488
Q7YRZ1 UniProt NPD GO	APTX_PIG	Aprataxin homolog (Forkhead-associated domain histidine triad-like protein) (FHA-HIT)	0.77	+	nuc	0	Nucleus (By similarity). Upon genotoxic stress, it colocalizes with XRCC1 at sites of DNA damage (By ...				356
P62995 UniProt NPD GO	TRA2B_HUMAN	Arginine/serine-rich-splicing factor 10 (Transformer-2-beta) (HTRA2-beta) (Transformer 2 protein hom ...	0.77	-	nuc	0	Nucleus	nucleus [IDA]	602719	2CQC	288
P62997 UniProt NPD GO	TRA2B_RAT	Arginine/serine-rich-splicing factor 10 (Transformer-2-beta) (HTRA2-beta) (Transformer 2 protein hom ...	0.77	-	nuc	0	Nucleus (By similarity)	nucleus [ISS]			288
P62996 UniProt NPD GO	TRA2B_MOUSE	Arginine/serine-rich-splicing factor 10 (Transformer-2-beta) (HTRA2-beta) (Transformer 2 protein hom ...	0.77	-	nuc	0	Nucleus (By similarity)	nucleus [ISS]			288
Q9CVD2 UniProt NPD GO	ATX3_MOUSE	Ataxin-3 (EC 3.4.22.-) (Machado-Joseph disease protein 1 homolog)	0.77	-	nuc	0	Nucleus (By similarity)				355
Q5RAC9 UniProt NPD GO	A16L1_PONPY	Autophagy-related protein 16-1 (APG16-like 1)	0.77	-	nuc	0	Cytoplasm (By similarity). Membrane; peripheral membrane protein (By similarity). Localized to preau ...				607
Q02887 UniProt NPD GO	ATG21_YEAST	Autophagy-related protein 21 (Maturation of proaminopeptidase I protein 1) (Homologous with SVP1 pro ...	0.77	-	nuc	0	Cytoplasm. Vacuole. And perivacuolar punctate structures	cytosol [IDA] vacuolar membrane (sensu Fungi) [IDA]			496

You are viewing entries 10201 to 10250 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.