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
Q8VIL3 UniProt NPD GO	ZWINT_RAT	ZW10 interactor (ZW10-interacting protein 1) (Zwint-1) (SNAP25-interacting protein 30)	0.83	-	nuc	0	Nucleus (By similarity). Associated with the kinetochore (By similarity)				266
Q5HZA3 UniProt NPD GO	ZCH12_RAT	Zinc finger CCHC domain-containing protein 12	0.83	+	mit	0					401
Q8N3Z6 UniProt NPD GO	ZCHC7_HUMAN	Zinc finger CCHC domain-containing protein 7	0.83	-	nuc	0					542
P10925 UniProt NPD GO	ZFY1_MOUSE	Zinc finger Y-chromosomal protein 1	0.83	+	nuc	0	Nucleus				782
O75362 UniProt NPD GO	ZN217_HUMAN	Zinc finger protein 217	0.83	-	nuc	0	Nucleus (Probable)		602967		1048
Q07231 UniProt NPD GO	ZFP38_MOUSE	Zinc finger protein 38 (Zfp-38) (CtFIN51) (Transcription factor RU49)	0.83	-	nuc	0	Nucleus	nucleus [IDA]			555
Q96SQ5 UniProt NPD GO	ZN587_HUMAN	Zinc finger protein 587	0.83	-	nuc	0	Nucleus (Probable)				575
Q8N1G0 UniProt NPD GO	ZN687_HUMAN	Zinc finger protein 687	0.83	-	nuc	0	Nucleus (Probable)				1237
Q39057 UniProt NPD GO	CONS_ARATH	Zinc finger protein CONSTANS	0.83	-	nuc	0	Nucleus (Probable)				373
P47806 UniProt NPD GO	GLI1_MOUSE	Zinc finger protein GLI1 (Glioma-associated oncogene homolog)	0.83	-	nuc	0	Nucleus	cytoplasm [IDA] nucleus [IDA]			1111
Q6XP49 UniProt NPD GO	GLIS3_MOUSE	Zinc finger protein GLIS3 (GLI-similar 3)	0.83	-	nuc	0	Nucleus	nucleus [IDA]			780
P38704 UniProt NPD GO	STP2_YEAST	Zinc finger protein STP2	0.83	-	nuc	0	Nucleus (Potential)	nucleus [IPI]			541
Q21252 UniProt NPD GO	NAS3_CAEEL	Zinc metalloproteinase nas-3 precursor (EC 3.4.24.21) (Nematode astacin 3)	0.83	-	exc	0	Secreted protein (Potential)				292
P58267 UniProt NPD GO	DPF1_CHICK	Zinc-finger protein neuro-d4 (D4, zinc and double PHD fingers family 1)	0.83	+	nuc	0	Cytoplasm (Potential). Nucleus (Potential)				380
Q7T3T9 UniProt NPD GO	ZAR1_FUGRU	Zygote arrest 1 (Oocyte-specific maternal effect factor)	0.83	+	nuc	0	Cytoplasm (By similarity)				320
P16220 UniProt NPD GO	CREB1_HUMAN	cAMP response element-binding protein (CREB)	0.83	+	nuc	0	Nucleus	nucleus [TAS]	123810		341
Q01147 UniProt NPD GO	CREB1_MOUSE	cAMP response element-binding protein (CREB)	0.83	+	nuc	0	Nucleus	nucleus [IDA] transcription factor complex [IDA]		1DH3	341
Q8TF77 UniProt NPD GO	KAPR_RHIRA	cAMP-dependent protein kinase regulatory subunit (PKA regulatory subunit)	0.83	+	cyt	0					427
Q6C8L8 UniProt NPD GO	RNA14_YARLI	mRNA 3'-end-processing protein RNA14	0.83	-	nuc	0	Nucleus (By similarity). Cytoplasm (By similarity). Nucleus and/or cytoplasm (By similarity)				806
Q9UW13 UniProt NPD GO	PALF_CANAL	pH-response regulator protein palF/RIM8	0.83	-	nuc	0					622
Q8K2Y7 UniProt NPD GO	RM47_MOUSE	39S ribosomal protein L47, mitochondrial precursor (L47mt) (MRP-L47)	0.82	-	nuc	0	Mitochondrion (By similarity)				252
O14049 UniProt NPD GO	RS8A_SCHPO	40S ribosomal protein S8-A	0.82	-	nuc	0					200
P25873 UniProt NPD GO	RK15_ARATH	50S ribosomal protein L15, chloroplast precursor (CL15)	0.82	-	mit	0	Plastid; chloroplast				277
Q8JGR4 UniProt NPD GO	RL24_BRARE	60S ribosomal protein L24	0.82	-	nuc	0					157
Q9FUL4 UniProt NPD GO	RL24_PRUAV	60S ribosomal protein L24	0.82	-	nuc	0					186
P62120 UniProt NPD GO	RL41_ARATH	60S ribosomal protein L41	0.82	+	nuc	0					25
Q75AH3 UniProt NPD GO	RL41_ASHGO	60S ribosomal protein L41	0.82	+	nuc	0					25
P62122 UniProt NPD GO	RL41_GOSHI	60S ribosomal protein L41	0.82	+	nuc	0					25
P62124 UniProt NPD GO	RL41_HORVU	60S ribosomal protein L41	0.82	+	nuc	0					25
P62125 UniProt NPD GO	RL41_ORYSA	60S ribosomal protein L41	0.82	+	nuc	0					25
P62123 UniProt NPD GO	RL41_PEA	60S ribosomal protein L41	0.82	+	nuc	0					25
P62121 UniProt NPD GO	RL41_TOBAC	60S ribosomal protein L41	0.82	+	nuc	0					25
P59510 UniProt NPD GO	ATS20_HUMAN	ADAMTS-20 precursor (EC 3.4.24.-) (A disintegrin and metalloproteinase with thrombospondin motifs 20 ...	0.82	-	nuc	0	Secreted protein; extracellular space; extracellular matrix (By similarity)				1911
P59511 UniProt NPD GO	ATS20_MOUSE	ADAMTS-20 precursor (EC 3.4.24.-) (A disintegrin and metalloproteinase with thrombospondin motifs 20 ...	0.82	-	nuc	0	Secreted protein; extracellular space; extracellular matrix (By similarity)				1906
Q66J85 UniProt NPD GO	ZFAN3_XENLA	AN1-type zinc finger protein 3 homolog	0.82	-	nuc	0					226
Q5SV85 UniProt NPD GO	SYNG_MOUSE	AP1 subunit gamma-binding protein 1 (Gamma-synergin)	0.82	+	nuc	0	Cytoplasm; cytosol. Golgi apparatus; trans-Golgi network; trans-Golgi network membrane; peripheral m ...				1306
Q86UK0 UniProt NPD GO	ABCAC_HUMAN	ATP-binding cassette sub-family A member 12 (ATP-binding cassette transporter 12) (ATP-binding casse ...	0.82	-	end	13 *	Membrane; multi-pass membrane protein (Potential)	integral to membrane [NAS]	607800		2595
P32892 UniProt NPD GO	DRS1_YEAST	ATP-dependent RNA helicase DRS1 (EC 3.6.1.-) (Deficiency of ribosomal subunits protein 1)	0.82	+	nuc	0	Nucleus; nucleolus	nucleolus [TAS]			752
Q59ZH9 UniProt NPD GO	MAK5_CANAL	ATP-dependent RNA helicase MAK5 (EC 3.6.1.-)	0.82	-	nuc	0	Nucleus; nucleolus (By similarity)				782
Q5KC99 UniProt NPD GO	MAK5_CRYNE	ATP-dependent RNA helicase MAK5 (EC 3.6.1.-)	0.82	+	nuc	0	Nucleus; nucleolus (By similarity)				772
Q6BV58 UniProt NPD GO	MAK5_DEBHA	ATP-dependent RNA helicase MAK5 (EC 3.6.1.-)	0.82	-	nuc	0	Nucleus; nucleolus (By similarity)				790
Q7RZH4 UniProt NPD GO	MAK5_NEUCR	ATP-dependent RNA helicase mak-5 (EC 3.6.1.-)	0.82	+	nuc	0	Nucleus; nucleolus (By similarity)				805
Q4P3U9 UniProt NPD GO	RRP3_USTMA	ATP-dependent rRNA helicase RRP3 (EC 3.6.1.-)	0.82	-	nuc	0	Nucleus (Probable)				551
Q6FKT1 UniProt NPD GO	AEP3_CANGA	ATPase expression protein 3	0.82	-	nuc	0	Mitochondrion; mitochondrial inner membrane; peripheral membrane protein; matrix side (By similarity ...				623
P10333 UniProt NPD GO	MS2A_DROME	Accessory gland-specific peptide 26Aa precursor (Male accessory gland secretory protein 355A)	0.82	-	exc	0	Secreted protein; extracellular space				264
P09775 UniProt NPD GO	AST8_DROME	Achaete-scute complex protein T8 (Asense)	0.82	-	nuc	0					486
Q9SZJ6 UniProt NPD GO	AGL21_ARATH	Agamous-like MADS-box protein AGL21	0.82	-	nuc	0	Nucleus (By similarity)				228
P50275 UniProt NPD GO	ASE1_YEAST	Anaphase spindle elongation protein	0.82	-	nuc	0		nuclear microtubule [TAS] spindle microtubule [TAS]			885
O97776 UniProt NPD GO	ANDR_EULFC	Androgen receptor (Dihydrotestosterone receptor)	0.82	+	nuc	0	Nucleus				884
Q6QT55 UniProt NPD GO	ANDR_MACMU	Androgen receptor (Dihydrotestosterone receptor)	0.82	+	nuc	0	Nucleus				895

You are viewing entries 7701 to 7750 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.