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
P15611 UniProt NPD GO	YM10_PARTE	Hypothetical 12.0 kDa protein (ORF10)	0.43	-	nuc	0					105
P53175 UniProt NPD GO	YGF2_YEAST	Hypothetical 12.1 kDa protein in DUP1-DUP2 intergenic region	0.43	-	nuc	0					101
P36140 UniProt NPD GO	YK27_YEAST	Hypothetical 12.3 kDa protein in GAP1-NAP1 intergenic region	0.43	-	nuc	1 *					101
Q04336 UniProt NPD GO	YM54_YEAST	Hypothetical 126.6 kDa protein in RPL36A-VTI1 intergenic region	0.43	-	cyt	0		cytoplasm [IDA]			1088
P05724 UniProt NPD GO	YCX3_CHLRE	Hypothetical 14.4 kDa protein in 16S rRNA region	0.43	-	nuc	0	Plastid; chloroplast				124
P36071 UniProt NPD GO	YKM3_YEAST	Hypothetical 15.2 kDa protein in RRN3-SRP21 intergenic region	0.43	-	cyt	0					126
P14289 UniProt NPD GO	YPOB_STYLE	Hypothetical 22 kDa protein in overamplified macronuclear DNA POB4	0.43	-	nuc	0					204
P51218 UniProt NPD GO	YCF80_PORPU	Hypothetical 52.1 kDa protein ycf80 (ORF450)	0.43	-	mit	0	Plastid; chloroplast				450
P53304 UniProt NPD GO	YG4K_YEAST	Hypothetical 54.5 kDa protein in ZPR1-RTA1 intergenic region	0.43	-	nuc	0					468
O94621 UniProt NPD GO	YBKC_SCHPO	Hypothetical RNA-binding protein C1289.12 in chromosome II	0.43	-	nuc	0					352
P92560 UniProt NPD GO	M1290_ARATH	Hypothetical mitochondrial protein AtMg01290 (ORF111c)	0.43	-	nuc	0	Mitochondrion (Potential)				111
O74405 UniProt NPD GO	YJ04_SCHPO	Hypothetical protein C1223.04c in chromosome III	0.43	-	cyt	0					381
O74317 UniProt NPD GO	YOGC_SCHPO	Hypothetical protein C15D4.12c in chromosome II	0.43	-	nuc	0					113
O74449 UniProt NPD GO	YCG4_SCHPO	Hypothetical protein C16C4.04 in chromosome III	0.43	-	nuc	0					266
O13973 UniProt NPD GO	YE4D_SCHPO	Hypothetical protein C24C9.13c in chromosome I	0.43	-	mit	0					88
Q10498 UniProt NPD GO	YDGC_SCHPO	Hypothetical protein C26F1.12c in chromosome I	0.43	-	cyt	0					356
Q09858 UniProt NPD GO	YAF4_SCHPO	Hypothetical protein C29E6.04 in chromosome I	0.43	-	nuc	0		inner kinetochore of condensed nuclear chro... [TAS]			145
Q09270 UniProt NPD GO	YQF6_CAEEL	Hypothetical protein C34C12.6 in chromosome III	0.43	-	cyt	0					392
O94668 UniProt NPD GO	YBWA_SCHPO	Hypothetical protein C651.10 in chromosome II	0.43	-	cyt	0					388
Q92346 UniProt NPD GO	YDH1_SCHPO	Hypothetical protein C6G9.01c in chromosome I	0.43	-	nuc	0					95
O14065 UniProt NPD GO	YC31_SCHPO	Hypothetical protein C962.01 in chromosome III	0.43	-	end	2	Membrane; multi-pass membrane protein (Potential)				1429
P34376 UniProt NPD GO	YLM2_CAEEL	Hypothetical protein D2007.2	0.43	-	nuc	0					195
Q09562 UniProt NPD GO	YR45_CAEEL	Hypothetical protein F47D12.5	0.43	-	cyt	0					633
P34487 UniProt NPD GO	YMJB_CAEEL	Hypothetical protein F59B2.12	0.43	-	nuc	0					918
Q21802 UniProt NPD GO	YEYC_CAEEL	Hypothetical protein R07B7.12	0.43	-	gol	1 *					550
P50444 UniProt NPD GO	YNU6_CAEEL	Hypothetical protein R74.6 in chromosome III	0.43	-	cyt	0	Nucleus (Potential)				381
P82626 UniProt NPD GO	SCRL7_ARATH	Hypothetical protein SCRL7 precursor	0.43	+	exc	0					92
Q9M647 UniProt NPD GO	IAR1_ARATH	IAA-alanine resistance protein 1	0.43	+	mit	3 *	Membrane; multi-pass membrane protein (Probable)				338
P53220 UniProt NPD GO	TIM21_YEAST	Import inner membrane translocase subunit TIM21, mitochondrial precursor	0.43	-	nuc	1	Mitochondrion; mitochondrial inner membrane; single-pass membrane protein	mitochondrial inner membrane presequence tr... [IPI] mitochondrion [IDA]			239
Q3ZCQ8 UniProt NPD GO	TIM50_HUMAN	Import inner membrane translocase subunit TIM50, mitochondrial precursor	0.43	-	mit	1	Mitochondrion; mitochondrial inner membrane; single-pass membrane protein. Isoform 2: Nucleus; nucle ...	mitochondrial inner membrane presequence tr... [IPI] nuclear speck [IDA]	607381		353
Q71VM4 UniProt NPD GO	IMA1A_ORYSA	Importin alpha-1a subunit	0.43	-	mit	0	Cytoplasm; perinuclear region				526
Q8VI75 UniProt NPD GO	IPO4_MOUSE	Importin-4 (Importin 4a) (Imp4a) (Ran-binding protein 4) (RanBP4)	0.43	-	cyt	0	Cytoplasm (By similarity). Nucleus (By similarity)				1082
Q8L718 UniProt NPD GO	ALB32_ARATH	Inner membrane ALBINO3-like protein 2, chloroplast precursor (Ath5)	0.43	-	end	4	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein (Potential)				525
Q6FJD1 UniProt NPD GO	LPE10_CANGA	Inner membrane magnesium transporter LPE10, mitochondrial precursor	0.43	-	nuc	2	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein (By similarity)				397
P06799 UniProt NPD GO	IFNA7_MOUSE	Interferon alpha-7 precursor	0.43	-	nuc	0	Secreted protein				190
P51526 UniProt NPD GO	IFN_ANAPL	Interferon precursor	0.43	-	exc	0	Secreted protein (By similarity)				191
P56830 UniProt NPD GO	IFNT2_BOVIN	Interferon tau-2 (IFN-tau2) (Trophoblast protein 1) (TP-1) (Trophoblastin) (Antiluteolysin) (Trophob ...	0.43	-	nuc	0	Secreted protein. Secreted into the uterine lumen				172
P56831 UniProt NPD GO	IFNT3_BOVIN	Interferon tau-3 (IFN-tau3) (Trophoblast protein 1) (TP-1) (Trophoblastin) (Antiluteolysin) (Trophob ...	0.43	-	nuc	0	Secreted protein. Secreted into the uterine lumen				172
P42165 UniProt NPD GO	IFNA1_CHICK	Interferon type A1/A2 precursor	0.43	-	nuc	0	Secreted protein (Probable)				193
Q90872 UniProt NPD GO	IFNA3_CHICK	Interferon type A3 precursor	0.43	-	nuc	0	Secreted protein (Probable)				193
Q8CJE6 UniProt NPD GO	IL12B_MESAU	Interleukin-12 beta chain precursor (IL-12B) (IL-12 p40) (Cytotoxic lymphocyte maturation factor 40 ...	0.43	-	exc	1 *	Secreted protein				327
P42701 UniProt NPD GO	I12R1_HUMAN	Interleukin-12 receptor beta-1 chain precursor (IL-12R-beta1) (Interleukin-12 receptor beta) (IL-12 ...	0.43	-	end	1	Membrane; single-pass type I membrane protein	integral to plasma membrane [TAS]	601604		662
Q8CGK6 UniProt NPD GO	IL28_MOUSE	Interleukin-28 precursor (Interferon lambda) (IFN-lambda)	0.43	-	exc	0	Secreted protein (By similarity)				193
P24712 UniProt NPD GO	INVO_SAGOE	Involucrin	0.43	-	nuc	0	Cytoplasm. Constituent of the scaffolding of the cornified envelope	cornified envelope [ISS] cytoplasm [ISS]			493
Q96WZ5 UniProt NPD GO	ACEA_PENMA	Isocitrate lyase (EC 4.1.3.1) (Isocitrase) (Isocitratase) (ICL)	0.43	-	cyt	0	Peroxisome (By similarity)				540
P45457 UniProt NPD GO	ACEA2_SOYBN	Isocitrate lyase 2 (EC 4.1.3.1) (Isocitrase 2) (Isocitratase 2) (ICL 2) (Fragment)	0.43	-	cyt	0	Glyoxysome				557
Q5A847 UniProt NPD GO	JHD1_CANAL	JmjC domain-containing histone demethylation protein 1 (EC 1.14.11.-)	0.43	-	cyt	0	Nucleus (By similarity)				478
P30998 UniProt NPD GO	PLAK_XENLA	Junction plakoglobin (Desmoplakin III)	0.43	-	nuc	0	Cytoplasm. Cytoplasmic in a soluble and membrane-associated form				738
Q9JHP7 UniProt NPD GO	KDEL1_MOUSE	KDEL motif-containing protein 1 precursor (ER protein 58)	0.43	-	end	0	Endoplasmic reticulum; Endoplasmic reticulum lumen				502
Q6BW41 UniProt NPD GO	SMI1_DEBHA	KNR4/SMI1 homolog 1	0.43	-	nuc	0					451

You are viewing entries 29701 to 29750 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.