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
Q9LG05 UniProt NPD GO	WRK10_ARATH	Probable WRKY transcription factor 10 (WRKY DNA-binding protein 10) (Protein MINISEED3)	0.82	-	nuc	0	Nucleus				506
O43065 UniProt NPD GO	MOT1_SCHPO	Probable helicase mot1 (EC 3.6.1.-) (TBP-associated factor mot1) (Modifier of transcription 1)	0.82	+	mit	0	Nucleus. Localized on chromatin				1953
Q8SUE9 UniProt NPD GO	NDC80_ENCCU	Probable kinetochore protein NDC80	0.82	-	mit	0	Nucleus (By similarity). Associated with kinetochores (By similarity)				543
Q9V411 UniProt NPD GO	NOG1_DROME	Probable nucleolar GTP-binding protein 1	0.82	-	nuc	0	Nucleus; nucleolus (By similarity)				652
Q621J7 UniProt NPD GO	ZYG1_CAEBR	Probable serine/threonine-protein kinase zyg-1 (EC 2.7.11.1) (Zygote defective protein 1)	0.82	-	nuc	0	Centrosome (By similarity). Component of the centrosome. Present at centrioles only immediately befo ...				709
P35995 UniProt NPD GO	YKW2_YEAST	Probable transcriptional regulatory protein YKL222C	0.82	-	nuc	0	Nucleus (Probable)				705
Q93008 UniProt NPD GO	USP9X_HUMAN	Probable ubiquitin carboxyl-terminal hydrolase FAF-X (EC 3.1.2.15) (Ubiquitin thioesterase FAF-X) (U ...	0.82	-	end	0			300072		2547
P53119 UniProt NPD GO	HUL5_YEAST	Probable ubiquitin-protein ligase HUL5 (EC 6.3.2.-)	0.82	-	mit	0		cytoplasm [IDA] nucleus [IDA]			910
Q9WTY1 UniProt NPD GO	PDCD7_MOUSE	Programmed cell death protein 7 (ES18)	0.82	+	nuc	0	Nucleus (Potential)	minor (U12-dependent) spliceosome complex [ISS]			482
Q8N8D1 UniProt NPD GO	PDCD7_HUMAN	Programmed cell death protein 7 (ES18) (HES18)	0.82	+	nuc	0	Nucleus (Potential)	minor (U12-dependent) spliceosome complex [IDA]	608138		485
Q92733 UniProt NPD GO	PRCC_HUMAN	Proline-rich protein PRCC (Papillary renal cell carcinoma translocation-associated gene protein)	0.82	+	nuc	0			179755		491
Q6S8J3 UniProt NPD GO	POTE2_HUMAN	Prostate, ovary, testis-expressed protein on chromosome 2 (Fragment)	0.82	-	nuc	0			608914		712
P69006 UniProt NPD GO	PRTB_ACIGU	Protamine-B (Sturine-B)	0.82	+	nuc	0	Nucleus				27
P69007 UniProt NPD GO	PRTB_ACIST	Protamine-B (Sturine-B) (Stellin-B)	0.82	+	nuc	0	Nucleus				27
P48361 UniProt NPD GO	ASK10_YEAST	Protein ASK10	0.82	-	nuc	0		cytoplasm [IDA] DNA-directed RNA polymerase II, holoenzyme [IDA]			1146
Q9H9C1 UniProt NPD GO	CN133_HUMAN	Protein C14orf133	0.82	+	nuc	0					493
Q9H1B7 UniProt NPD GO	CN004_HUMAN	Protein C14orf4	0.82	-	nuc	0	Nucleus (Potential)	nucleus [NAS]		2CS3	796
Q5U2Y9 UniProt NPD GO	CF152_RAT	Protein C6orf152 homolog	0.82	-	nuc	0					727
Q8N865 UniProt NPD GO	CG031_HUMAN	Protein C7orf31	0.82	-	nuc	0					590
Q8K3W3 UniProt NPD GO	CASC3_MOUSE	Protein CASC3 (Cancer susceptibility candidate gene 3 protein homolog) (Metastatic lymph node protei ...	0.82	-	nuc	0	Cytoplasm; perinuclear region. Predominantly. Nucleus. Shuttles between the nucleus and the cytoplas ...	cytoplasm [IDA] nucleus [IDA] ribonucleoprotein complex [IDA]			697
Q61909 UniProt NPD GO	MTG8_MOUSE	Protein CBFA2T1 (Protein MTG8)	0.82	-	nuc	0	Nucleus (Potential)	nucleus [IDA]			577
Q7ZUV7 UniProt NPD GO	EMSY_BRARE	Protein EMSY	0.82	+	nuc	0	Nucleus (By similarity)				1173
Q03111 UniProt NPD GO	ENL_HUMAN	Protein ENL (YEATS domain-containing protein 1)	0.82	-	nuc	0	Nucleus	nucleus [TAS]	159556		559
Q8IXL6 UniProt NPD GO	FA20C_HUMAN	Protein FAM20C precursor	0.82	+	nuc	0	Secreted protein (Potential)				570
Q8TAV0 UniProt NPD GO	FA76A_HUMAN	Protein FAM76A	0.82	-	nuc	0					307
Q12247 UniProt NPD GO	FYV7_YEAST	Protein FYV7 (Function required for viability upon toxin exposure protein 7)	0.82	+	nuc	0	Nucleus; nucleolus	nucleolus [IDA] nucleus [IDA]			151
Q07845 UniProt NPD GO	GRC3_YEAST	Protein GRC3	0.82	-	nuc	0	Nucleus (By similarity)				632
Q12767 UniProt NPD GO	K0195_HUMAN	Protein KIAA0195 (Transmembrane protein 94)	0.82	+	end	10	Membrane; multi-pass membrane protein (Potential)				1356
Q5ZIL9 UniProt NPD GO	K1279_CHICK	Protein KIAA1279 homolog	0.82	-	cyt	0					594
Q8N4X5 UniProt NPD GO	K1914_HUMAN	Protein KIAA1914	0.82	-	nuc	0				2COF	818
P36146 UniProt NPD GO	LAS1_YEAST	Protein LAS1	0.82	+	nuc	0	Nucleus. Mitochondrion	mitochondrion [IDA] nucleus [TAS]			502
P35198 UniProt NPD GO	MTH1_YEAST	Protein MTH1	0.82	-	nuc	0					433
P32909 UniProt NPD GO	SMY2_YEAST	Protein SMY2 (Suppressor of MYO2-66 protein)	0.82	-	nuc	0	Cytoplasm	cytoplasm [IDA]			740
P13574 UniProt NPD GO	STE12_YEAST	Protein STE12	0.82	-	nuc	0	Nucleus	nucleus [TAS]			688
Q9W0K7 UniProt NPD GO	BAB1_DROME	Protein bric-a-brac 1	0.82	-	nuc	0	Nucleus	nucleus [IDA]			977
O08808 UniProt NPD GO	DIAP1_MOUSE	Protein diaphanous homolog 1 (Diaphanous-related formin-1) (DRF1) (mDIA1) (p140mDIA)	0.82	-	nuc	0	Cell membrane. Membrane ruffles, especially at the tip of ruffles, of motile cells			2BNX	1255
Q13045 UniProt NPD GO	FLII_HUMAN	Protein flightless-1 homolog	0.82	+	nuc	0	Nucleus (By similarity). Cytoplasm (By similarity). Centrosome (By similarity). Colocalizes to actin ...		600362		1269
Q24087 UniProt NPD GO	MEI9_DROME	Protein mei-9 (Protein meiotic 9)	0.82	-	nuc	0	Nucleus (Probable)				961
P32845 UniProt NPD GO	NULLO_DROME	Protein nullo	0.82	-	nuc	0	Colocalizes with the structural transitions in the microfilament network during cellularization	adherens junction [TAS]			253
P11845 UniProt NPD GO	IPP2_RABIT	Protein phosphatase inhibitor 2 (IPP-2)	0.82	-	mit	0					204
P24014 UniProt NPD GO	SLIT_DROME	Protein slit precursor [Contains: Protein slit N-product; Protein slit C-product]	0.82	+	nuc	0	Secreted protein	extracellular matrix (sensu Metazoa) [TAS] extracellular region [IDA]		1W8A	1504
Q9P6R7 UniProt NPD GO	VTS1_SCHPO	Protein vts1	0.82	-	nuc	0	Cytoplasm (By similarity)				713
O49289 UniProt NPD GO	RH29_ARATH	Putative DEAD-box ATP-dependent RNA helicase 29 (EC 3.6.1.-)	0.82	+	nuc	0					845
Q9U2G0 UniProt NPD GO	U520_CAEEL	Putative U5 small nuclear ribonucleoprotein 200 kDa helicase (EC 3.6.1.-)	0.82	+	nuc	0	Nucleus (By similarity)	spliceosome complex [ISS]			2145
Q9LDR2 UniProt NPD GO	CNG19_ARATH	Putative cyclic nucleotide-gated ion channel 19 (Cyclic nucleotide-binding transporter 2)	0.82	-	end	5	Cell membrane; multi-pass membrane protein (Potential)				729
Q10238 UniProt NPD GO	YD15_SCHPO	Putative regulatory protein C4G9.05	0.82	-	nuc	0					581
Q9P6P3 UniProt NPD GO	KKB3_SCHPO	Putative serine/threonine-protein kinase C823.03 (EC 2.7.11.1)	0.82	-	nuc	0					534
Q10086 UniProt NPD GO	YAO7_SCHPO	Putative transcriptional regulatory protein C11D3.07c	0.82	-	nuc	0	Nucleus (Probable)				603
O59741 UniProt NPD GO	YN25_SCHPO	Putative transcriptional regulatory protein C530.05	0.82	-	mit	0	Nucleus				743
Q9C0Z1 UniProt NPD GO	YKM1_SCHPO	Putative transcriptional regulatory protein PB24D3.01	0.82	-	nuc	1	Nucleus (Probable)				594

You are viewing entries 8001 to 8050 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.