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
Q589G4 UniProt NPD GO	AS19_ANOSM	Toxin As-fr-19 precursor	0.06	-	mit	0	Secreted protein				75
P60163 UniProt NPD GO	SCX2_CENGR	Toxin Cg2	0.06	-	nuc	0	Secreted protein				68
Q923Y2 UniProt NPD GO	TAA7A_RAT	Trace amine-associated receptor 7a (Trace amine receptor 8) (TaR-8)	0.06	-	end	6 *	Membrane; multi-pass membrane protein				358
Q923X6 UniProt NPD GO	TAA7E_RAT	Trace amine-associated receptor 7e (Trace amine receptor 14) (TaR-14)	0.06	-	end	7 *	Membrane; multi-pass membrane protein				358
Q923Y1 UniProt NPD GO	TAA7G_RAT	Trace amine-associated receptor 7g (Trace amine receptor 9) (TaR-9)	0.06	-	end	6 *	Membrane; multi-pass membrane protein				358
Q9Z311 UniProt NPD GO	MECR_RAT	Trans-2-enoyl-CoA reductase, mitochondrial precursor (EC 1.3.1.38) (Nuclear receptor-binding factor ...	0.06	-	mit	0	Mitochondrion	mitochondrion [IDA]			373
Q9P7K8 UniProt NPD GO	SPT4_SCHPO	Transcription elongation factor spt4 (Chromatin elongation factor spt4)	0.06	-	exc	0	Nucleus. Centromere and heterochromatin (By similarity)				105
Q90YG6 UniProt NPD GO	T2AG_ONCMY	Transcription initiation factor IIA gamma chain (TFIIA P12 subunit) (TFIIA-12) (TFIIAS) (TFIIA-gamma ...	0.06	-	cyt	0	Nucleus				108
Q9W5B9 UniProt NPD GO	T2AH_DROME	Transcription initiation factor IIA gamma-2 chain (TFIIA-gamma-2)	0.06	-	cyt	0	Nucleus (By similarity)				107
Q8HZV3 UniProt NPD GO	TFR1_PIG	Transferrin receptor protein 1 (TfR1) (TR) (TfR) (Trfr) (CD71 antigen)	0.06	-	cyt	1	Cell membrane; single-pass type II membrane (By similarity)				768
P48030 UniProt NPD GO	TGFA_MOUSE	Transforming growth factor alpha precursor (TGF-alpha) (EGF-like TGF) (ETGF) (TGF type 1)	0.06	-	end	1	Precursor form: Cell membrane; single-pass type I membrane protein. Mature form: Secreted protein; e ...			1GK5	159
P55244 UniProt NPD GO	TGFA_MACMU	Transforming growth factor alpha precursor (TGF-alpha) (EGF-like TGF) (ETGF) (TGF type 1) (Fragment) ...	0.06	-	mit	1	Precursor form: Cell membrane; single-pass type I membrane protein. Mature form: Secreted protein; e ...				121
P82198 UniProt NPD GO	BGH3_MOUSE	Transforming growth factor-beta-induced protein ig-h3 precursor (Beta ig-h3)	0.06	-	exc	0	Secreted protein; extracellular space. May be associated both with microfibrils and with the cell su ...	extracellular matrix (sensu Metazoa) [IDA] extracellular space [IDA]			683
Q9QUI0 UniProt NPD GO	RHOA_MOUSE	Transforming protein RhoA precursor	0.06	-	cyt	0	Membrane; peripheral membrane protein (By similarity)	cytosol [IDA] nucleus [IDA] plasma membrane [IDA]			193
P61589 UniProt NPD GO	RHOA_RAT	Transforming protein RhoA precursor	0.06	-	cyt	0	Membrane; peripheral membrane protein (By similarity)				193
P61585 UniProt NPD GO	RHOA_BOVIN	Transforming protein RhoA precursor (Gb) (p21)	0.06	-	cyt	0	Membrane; lipid-anchor				193
P61586 UniProt NPD GO	RHOA_HUMAN	Transforming protein RhoA precursor (H12)	0.06	-	cyt	0	Membrane; lipid-anchor		165390	1XCG	193
P24406 UniProt NPD GO	RHOA_CANFA	Transforming protein RhoA precursor (Rho1)	0.06	-	cyt	0	Membrane; peripheral membrane protein (By similarity)				193
P56290 UniProt NPD GO	IF1C_CHLVU	Translation initiation factor IF-1, chloroplast	0.06	-	cyt	0	Plastid; chloroplast				79
P12134 UniProt NPD GO	IF1C_MARPO	Translation initiation factor IF-1, chloroplast	0.06	-	nuc	0	Plastid; chloroplast				78
Q32RN1 UniProt NPD GO	IF1C_ZYGCR	Translation initiation factor IF-1, chloroplast	0.06	-	cyt	0	Plastid; chloroplast				77
P30070 UniProt NPD GO	IF1C_EPIVI	Translation initiation factor IF-1, plastid	0.06	-	cyt	0	Plastid				77
Q08810 UniProt NPD GO	IF2C_GALSU	Translation initiation factor IF-2, chloroplast (Fragment)	0.06	-	nuc	0	Plastid; chloroplast				259
Q9HD45 UniProt NPD GO	TM9S3_HUMAN	Transmembrane 9 superfamily protein member 3 precursor (SM-11044-binding protein) (EP70-P-iso)	0.06	-	end	9 *	Membrane; multi-pass membrane protein (Probable)				589
Q2HJA8 UniProt NPD GO	TMUB2_BOVIN	Transmembrane and ubiquitin-like domain-containing protein 2	0.06	-	end	3 *	Membrane; multi-pass membrane protein (Potential)				322
Q3UF25 UniProt NPD GO	TM110_MOUSE	Transmembrane protein 110	0.06	-	end	5 *	Membrane; multi-pass membrane protein (Potential)				288
Q7TSW6 UniProt NPD GO	TM110_RAT	Transmembrane protein 110	0.06	-	end	5 *	Membrane; multi-pass membrane protein (Potential)				288
Q9UPQ8 UniProt NPD GO	TMM15_HUMAN	Transmembrane protein 15	0.06	-	end	14 *	Membrane; multi-pass membrane protein (Potential)				538
Q9BQJ4 UniProt NPD GO	TMM47_HUMAN	Transmembrane protein 47 (Transmembrane 4 superfamily member 10)	0.06	-	end	4 *	Membrane; multi-pass membrane protein (Potential)				181
Q9JJG6 UniProt NPD GO	TMM47_MOUSE	Transmembrane protein 47 (Transmembrane 4 superfamily member 10)	0.06	-	end	4 *	Membrane; multi-pass membrane protein (Potential)				181
Q6PBE5 UniProt NPD GO	TMM47_XENTR	Transmembrane protein 47 (Transmembrane 4 superfamily member 10)	0.06	-	end	4 *	Membrane; multi-pass membrane protein (Potential)				179
Q9XSV3 UniProt NPD GO	TMM47_CANFA	Transmembrane protein 47 (Transmembrane 4 superfamily member 10) (Brain cell membrane protein 1)	0.06	-	end	4 *	Membrane; multi-pass membrane protein (Potential)				181
Q4V899 UniProt NPD GO	TPARL_RAT	Transmembrane protein TPARL	0.06	-	end	7 *	Membrane; multi-pass membrane protein (Potential)				323
O46654 UniProt NPD GO	TTHY_SORAR	Transthyretin precursor (Prealbumin)	0.06	-	end	0	Secreted protein				147
P22102 UniProt NPD GO	PUR2_HUMAN	Trifunctional purine biosynthetic protein adenosine-3 [Includes: Phosphoribosylamine--glycine ligase ...	0.06	-	cyt	0			138440	1ZLY	1010
P21797 UniProt NPD GO	TNNC1_BALNU	Troponin C, isoform 1	0.06	-	cyt	0					158
P47949 UniProt NPD GO	TNNC3_DROME	Troponin C, isoform 3	0.06	-	cyt	0					155
P02585 UniProt NPD GO	TNNC2_HUMAN	Troponin C, skeletal muscle	0.06	-	cyt	0			191039		159
P02586 UniProt NPD GO	TNNC2_RABIT	Troponin C, skeletal muscle	0.06	-	cyt	0				2TN4	159
P02589 UniProt NPD GO	TNNC2_RANES	Troponin C, skeletal muscle	0.06	-	cyt	0					162
P20801 UniProt NPD GO	TNNC2_MOUSE	Troponin C, skeletal muscle (STNC)	0.06	-	cyt	0					159
P05936 UniProt NPD GO	TNNC1_COTJA	Troponin C, slow skeletal and cardiac muscles (TN-C)	0.06	-	cyt	0					161
P83348 UniProt NPD GO	TRYP_APIMS	Trypsin (EC 3.4.21.4) (Fragment)	0.06	-	cyt	0	Secreted protein; extracellular space				21
P04814 UniProt NPD GO	TRYA_DROME	Trypsin alpha precursor (EC 3.4.21.4)	0.06	-	exc	0	Secreted protein; extracellular space				256
P54625 UniProt NPD GO	TRYB_DROER	Trypsin beta precursor (EC 3.4.21.4)	0.06	-	exc	0	Secreted protein; extracellular space				253
P01069 UniProt NPD GO	ITRY_TRIKI	Trypsin inhibitor	0.06	-	nuc	0					41
P26771 UniProt NPD GO	ITI1_LAGLE	Trypsin inhibitor 1 (Trypsin inhibitor I) (LLDTI-I) (LLTI-I) [Contains: Trypsin inhibitor 2 (Trypsin ...	0.06	-	nuc	0	Secreted protein				30
P10821 UniProt NPD GO	IT1A_PSOTE	Trypsin inhibitor 1A (WTI-1A)	0.06	-	cyt	0					172
P30709 UniProt NPD GO	ITRA_MOMCH	Trypsin inhibitor A	0.06	-	mit	0	Secreted protein			1MCT	28
P35035 UniProt NPD GO	TRY1_ANOGA	Trypsin-1 precursor (EC 3.4.21.4)	0.06	-	exc	0	Secreted protein				274

You are viewing entries 73351 to 73400 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.