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
P34248 UniProt NPD GO	YKK0_YEAST	Hypothetical 67.5 kDa protein in APE1/LAP4-CWP1 intergenic region	0.33	+	end	7					587
Q03605 UniProt NPD GO	YNN1_CAEEL	Hypothetical RING finger protein T02C1.1 in chromosome III	0.33	-	nuc	0					160
P30631 UniProt NPD GO	YOUD_CAEEL	Hypothetical RING finger protein ZK637.14 in chromosome III	0.33	-	nuc	0					161
P94024 UniProt NPD GO	M170_ARATH	Hypothetical mitochondrial protein AtMg00170/AtMg00620 (ORF139b/ORF139a)	0.33	-	mit	1	Mitochondrion (Potential)				139
P21260 UniProt NPD GO	YPRO_OWEFU	Hypothetical proline-rich protein (Fragment)	0.33	-	mit	0					141
Q11110 UniProt NPD GO	YX03_CAEEL	Hypothetical protein C03B1.3	0.33	-	nuc	0					115
Q09227 UniProt NPD GO	YP89_CAEEL	Hypothetical protein C08B11.9 (1207-1)	0.33	-	nuc	0					186
Q09235 UniProt NPD GO	YQ42_CAEEL	Hypothetical protein C13B9.2	0.33	-	nuc	0					397
O74745 UniProt NPD GO	YHF4_SCHPO	Hypothetical protein C1734.04 in chromosome II	0.33	-	mit	1 *	Membrane; single-pass type II membrane protein (Probable)				430
O13800 UniProt NPD GO	YE03_SCHPO	Hypothetical protein C17H9.03c in chromosome I	0.33	-	nuc	0					230
Q09774 UniProt NPD GO	YA87_SCHPO	Hypothetical protein C22F3.07c in chromosome I	0.33	-	nuc	0					118
O13957 UniProt NPD GO	YEHG_SCHPO	Hypothetical protein C23H4.16c in chromosome I	0.33	-	cyt	0					328
P87156 UniProt NPD GO	YB0F_SCHPO	Hypothetical protein C25H2.15 in chromosome II	0.33	-	nuc	0					396
Q10069 UniProt NPD GO	YAN3_SCHPO	Hypothetical protein C3H1.03 in chromosome I	0.33	-	nuc	0					146
P34422 UniProt NPD GO	YL31_CAEEL	Hypothetical protein F44B9.1 in chromosome III	0.33	-	cyt	0					740
P34445 UniProt NPD GO	YL87_CAEEL	Hypothetical protein F54C8.7	0.33	-	nuc	0					307
P82631 UniProt NPD GO	SCR12_ARATH	Hypothetical protein SCRL12 precursor	0.33	-	mit	1 *					92
P34613 UniProt NPD GO	YOG4_CAEEL	Hypothetical protein ZK112.4	0.33	-	nuc	0					100
Q6FLD4 UniProt NPD GO	ISN1_CANGA	IMP-specific 5'-nucleotidase 1 (EC 3.1.3.-)	0.33	-	mit	0					447
P01860 UniProt NPD GO	IGHG3_HUMAN	Ig gamma-3 chain C region (Heavy chain disease protein) (HDC)	0.33	-	nuc	0		membrane fraction [NAS]	147120		290
P04206 UniProt NPD GO	KV3G_HUMAN	Ig kappa chain V-III region GOL (Rheumatoid factor)	0.33	-	nuc	0		extracellular region [NAS]			109
P01624 UniProt NPD GO	KV3F_HUMAN	Ig kappa chain V-III region POM	0.33	-	nuc	0		extracellular region [NAS]			109
P01622 UniProt NPD GO	KV3D_HUMAN	Ig kappa chain V-III region Ti	0.33	-	nuc	0		extracellular region [NAS]			109
P01641 UniProt NPD GO	KV5H_MOUSE	Ig kappa chain V-V region MOPC 173B precursor	0.33	-	exc	0					117
P04940 UniProt NPD GO	KV6F_MOUSE	Ig kappa chain V-VI region NQ2-17.4.1	0.33	-	nuc	0					107
P04941 UniProt NPD GO	KV6G_MOUSE	Ig kappa chain V-VI region NQ2-48.2.2	0.33	-	mit	0					107
P38217 UniProt NPD GO	IMB2_YEAST	Importin beta-2 subunit (Karyopherin beta-2 subunit) (Importin 104) (Transportin) (TRN)	0.33	-	cyt	0	Cytoplasm	cytosol [IDA]			918
Q8N608 UniProt NPD GO	DPP10_HUMAN	Inactive dipeptidyl peptidase 10 (Dipeptidyl peptidase X) (Dipeptidyl peptidase-like protein 2) (DPL ...	0.33	-	gol	1 *	Membrane; single-pass type II membrane protein	membrane fraction [IDA]	608209		796
Q8LKI3 UniProt NPD GO	ALB32_CHLRE	Inner membrane ALBINO3-like protein 2, chloroplast precursor	0.33	-	end	0	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein (Potential)				422
Q6C2P2 UniProt NPD GO	LPE10_YARLI	Inner membrane magnesium transporter LPE10, mitochondrial precursor	0.33	-	end	2	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein (By similarity)				419
Q21123 UniProt NPD GO	INX7_CAEEL	Innexin-7	0.33	-	end	4 *	Membrane; multi-pass membrane protein				556
Q6P1C1 UniProt NPD GO	IPPK_MOUSE	Inositol-pentakisphosphate 2-kinase (EC 2.7.1.-) (Inositol-1,3,4,5,6-pentakisphosphate 2-kinase) (In ...	0.33	-	cyt	0	Cytoplasm (By similarity). Nucleus (By similarity)	intracellular [ISS]			489
Q9H8X2 UniProt NPD GO	IPPK_HUMAN	Inositol-pentakisphosphate 2-kinase (EC 2.7.1.-) (Inositol-1,3,4,5,6-pentakisphosphate 2-kinase) (In ...	0.33	-	cyt	0	Cytoplasm (By similarity). Nucleus (By similarity)	intracellular [IC]			491
Q13572 UniProt NPD GO	ITPK1_HUMAN	Inositol-tetrakisphosphate 1-kinase (EC 2.7.1.134) (Inositol-triphosphate 5/6-kinase) (EC 2.7.1.-) ( ...	0.33	-	cyt	0			601838		414
P38954 UniProt NPD GO	IPT1_YEAST	Inositolphosphotransferase 1 (EC 2.-.-.-) (Mannosyl diphosphorylinositol ceramide synthase)	0.33	-	end	8 *	Membrane; multi-pass membrane protein (Potential)	membrane fraction [IDA]			527
P14617 UniProt NPD GO	INSRR_CAVPO	Insulin receptor-related protein precursor (EC 2.7.10.1) (IRR) (IR-related receptor) [Contains: Insu ...	0.33	-	end	1 *	Membrane; single-pass type I membrane protein				1300
P47877 UniProt NPD GO	IBP2_MOUSE	Insulin-like growth factor-binding protein 2 precursor (IGFBP-2) (IBP-2) (IGF-binding protein 2)	0.33	-	exc	0	Secreted protein				305
P47879 UniProt NPD GO	IBP4_MOUSE	Insulin-like growth factor-binding protein 4 precursor (IGFBP-4) (IBP-4) (IGF-binding protein 4)	0.33	-	exc	0	Secreted protein				254
Q91VK4 UniProt NPD GO	ITM2C_MOUSE	Integral membrane protein 2C (Transmembrane protein BRI3) [Contains: CT-BRI3]	0.33	-	cyt	1	Membrane; single-pass type II membrane protein (Potential)	membrane fraction [TAS]			269
Q00651 UniProt NPD GO	ITA4_MOUSE	Integrin alpha-4 precursor (Integrin alpha-IV) (VLA-4) (Lymphocyte Peyer patch adhesion molecules su ...	0.33	-	nuc	1	Membrane; single-pass type I membrane protein				1039
Q63258 UniProt NPD GO	ITA7_RAT	Integrin alpha-7 (H36-alpha7) [Contains: Integrin alpha-7 heavy chain; Integrin alpha-7 light chain] ...	0.33	+	nuc	1	Membrane; single-pass type I membrane protein	cytoplasm [IMP] integrin complex [IMP]			1106
Q24247 UniProt NPD GO	ITA1_DROME	Integrin alpha-PS1 precursor (Position-specific antigen 1 alpha chain) (Protein multiple edematous w ...	0.33	-	nuc	1	Membrane; single-pass type I membrane protein	integrin complex [NAS]			1146
Q9QXH4 UniProt NPD GO	ITAX_MOUSE	Integrin alpha-X precursor (Leukocyte adhesion glycoprotein p150,95 alpha chain) (Leukocyte adhesion ...	0.33	-	end	2 *	Membrane; single-pass type I membrane protein (By similarity)	external side of plasma membrane [IDA]			1169
Q9UKP3 UniProt NPD GO	ITBP2_HUMAN	Integrin beta-1-binding protein 2 (Melusin)	0.33	-	nuc	0			300332		347
P05012 UniProt NPD GO	IFNB_HORSE	Interferon beta precursor (IFN-beta)	0.33	-	exc	1 *	Secreted protein				186
P01575 UniProt NPD GO	IFNB_MOUSE	Interferon beta precursor (IFN-beta)	0.33	-	end	1 *	Secreted protein			2HIF	182
Q02556 UniProt NPD GO	IRF8_HUMAN	Interferon regulatory factor 8 (IRF-8) (Interferon consensus sequence-binding protein) (ICSBP)	0.33	-	mit	0	Nucleus		601565		426
Q28594 UniProt NPD GO	IFNT4_SHEEP	Interferon tau-4 precursor (IFN-tau4) (Trophoblast protein 1) (TP-1) (Trophoblastin) (Antiluteolysin ...	0.33	-	mit	1 *	Secreted protein. Secreted into the uterine lumen				195
P20809 UniProt NPD GO	IL11_HUMAN	Interleukin-11 precursor (IL-11) (Adipogenesis inhibitory factor) (AGIF) (Oprelvekin)	0.33	-	exc	0	Secreted protein	extracellular region [IC]	147681		199
Q9BEG2 UniProt NPD GO	I12R2_BOVIN	Interleukin-12 receptor beta-2 chain precursor (IL-12 beta2 receptor) (IL-12Rbeta2)	0.33	-	end	1 *	Membrane; single-pass type I membrane protein	interleukin-12 receptor complex [NAS]			861

You are viewing entries 37651 to 37700 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.