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
P21621 UniProt NPD GO	IL1B_SHEEP	Interleukin-1 beta precursor (IL-1 beta)	0.24	-	cyt	0	Secreted protein. The lack of a specific hydrophobic segment in the precursor sequence suggests that ...				266
Q62611 UniProt NPD GO	ILRL1_RAT	Interleukin-1 receptor-like 1 precursor (Fos-responsive gene 1 protein) (Fit-1)	0.24	-	end	2 *	Cell membrane; single-pass type I membrane protein. Isoform B: Secreted protein	cell surface [IMP]			566
P79338 UniProt NPD GO	IL10_MACFA	Interleukin-10 precursor (IL-10) (Cytokine synthesis inhibitory factor) (CSIF)	0.24	-	exc	0	Secreted protein	extracellular region [ISS]			178
Q99MF4 UniProt NPD GO	I11RA_RAT	Interleukin-11 receptor alpha chain precursor (IL-11R-alpha) (IL-11RA)	0.24	-	exc	1	Membrane; single-pass type I membrane protein				431
P46658 UniProt NPD GO	IL12B_CERTO	Interleukin-12 beta chain precursor (IL-12B) (IL-12 p40) (Cytotoxic lymphocyte maturation factor 40 ...	0.24	-	exc	1 *	Secreted protein				328
Q62386 UniProt NPD GO	IL17_MOUSE	Interleukin-17A precursor (IL-17A) (IL-17) (Cytotoxic T-lymphocyte-associated antigen 8) (CTLA-8)	0.24	-	exc	1 *	Secreted protein				158
O97513 UniProt NPD GO	IL2_ORCOR	Interleukin-2 precursor (IL-2) (T-cell growth factor) (TCGF) (Fragment)	0.24	-	exc	0	Secreted protein				152
Q13007 UniProt NPD GO	IL24_HUMAN	Interleukin-24 precursor (Suppression of tumorigenicity 16 protein) (Melanoma differentiation-associ ...	0.24	-	exc	0	Secreted protein (Potential)		604136		206
Q9MZR8 UniProt NPD GO	IL4_RABIT	Interleukin-4 precursor (IL-4)	0.24	-	exc	0	Secreted protein				147
P51744 UniProt NPD GO	IL4_CEREL	Interleukin-4 precursor (IL-4) (B-cell stimulatory factor 1) (BSF-1) (Lymphocyte stimulatory factor ...	0.24	-	exc	0	Secreted protein				135
Q60440 UniProt NPD GO	IL4_MESAU	Interleukin-4 precursor (IL-4) (B-cell stimulatory factor 1) (BSF-1) (Lymphocyte stimulatory factor ...	0.24	-	exc	0	Secreted protein				147
Q8HYB1 UniProt NPD GO	IL4_PANTR	Interleukin-4 precursor (IL-4) (B-cell stimulatory factor 1) (BSF-1) (Lymphocyte stimulatory factor ...	0.24	-	exc	0	Secreted protein (By similarity)	extracellular space [ISS]			153
P05112 UniProt NPD GO	IL4_HUMAN	Interleukin-4 precursor (IL-4) (B-cell stimulatory factor 1) (BSF-1) (Lymphocyte stimulatory factor ...	0.24	-	exc	0	Secreted protein	extracellular space [TAS]	147780	2INT	153
Q28747 UniProt NPD GO	IL6_ORCOR	Interleukin-6 precursor (IL-6) (Fragment)	0.24	-	exc	0	Secreted protein				205
P03956 UniProt NPD GO	MMP1_HUMAN	Interstitial collagenase precursor (EC 3.4.24.7) (Matrix metalloproteinase-1) (MMP-1) (Fibroblast co ...	0.24	-	exc	0			120353	966C	469
Q86ZF1 UniProt NPD GO	ACEA_LEPMC	Isocitrate lyase (EC 4.1.3.1) (Isocitrase) (Isocitratase) (ICL)	0.24	-	cyt	0	Peroxisome (By similarity)				537
Q9HFN2 UniProt NPD GO	ACEA_PICJA	Isocitrate lyase (EC 4.1.3.1) (Isocitrase) (Isocitratase) (ICL)	0.24	-	pox	0	Peroxisome (By similarity)				550
Q6AY06 UniProt NPD GO	IZUM1_RAT	Izumo sperm-egg fusion protein 1 precursor (Sperm-specific protein izumo)	0.24	-	end	1	Membrane; single-pass type I membrane protein (Potential)				383
Q9TVP3 UniProt NPD GO	JDP_DROME	J domain-containing protein (dJDP)	0.24	-	nuc	0					195
Q9SBK6 UniProt NPD GO	JMT_BRARP	Jasmonate O-methyltransferase (EC 2.1.1.141) (S-adenosyl-L-methionine:jasmonic acid carboxyl methylt ...	0.24	-	cyt	0	Cytoplasm. Predominantly. Nucleus. Partially				392
Q7ZVE6 UniProt NPD GO	KDEL1_BRARE	KDEL motif-containing protein 1 precursor	0.24	-	nuc	0	Endoplasmic reticulum; Endoplasmic reticulum lumen (By similarity)				500
Q8UUW7 UniProt NPD GO	SAM68_CHICK	KH domain-containing, RNA-binding, signal transduction-associated protein 1 (Src-associated in mitos ...	0.24	-	nuc	0	Nucleus (By similarity). Membrane (By similarity)	membrane [ISS] nucleus [ISS]			433
P42156 UniProt NPD GO	CASK_CAPCR	Kappa-casein precursor	0.24	-	exc	0	Secreted protein				192
P42157 UniProt NPD GO	CASK_CERNI	Kappa-casein precursor	0.24	-	exc	0	Secreted protein				190
P57790 UniProt NPD GO	KEAP1_RAT	Kelch-like ECH-associated protein 1 (Cytosolic inhibitor of Nrf2) (INrf2)	0.24	-	cyt	0	Cytoplasm (By similarity)				624
Q5F3N5 UniProt NPD GO	KLH14_CHICK	Kelch-like protein 14	0.24	-	mit	0					622
Q90314 UniProt NPD GO	SCF_COTJA	Kit ligand precursor (C-kit ligand) (Stem cell factor) (SCF) (Mast cell growth factor) (MGF)	0.24	-	exc	1	Isoform 1, isoform 2: Cell membrane; single-pass type I membrane protein (By similarity). Processed ...				287
Q6DJH2 UniProt NPD GO	ADPPT_XENLA	L-aminoadipate-semialdehyde dehydrogenase-phosphopantetheinyl transferase (EC 2.7.8.-) (4'-phosphopa ...	0.24	-	mit	0	Cytoplasm (By similarity)				302
Q8IU89 UniProt NPD GO	LASS3_HUMAN	LAG1 longevity assurance homolog 3	0.24	-	nuc	5 *	Nucleus; nuclear membrane; multi-pass membrane protein (Potential)				383
Q9D6K9 UniProt NPD GO	LASS5_MOUSE	LAG1 longevity assurance homolog 5 (Translocating chain-associating membrane protein homolog 4) (TRA ...	0.24	-	end	5 *	Nucleus; nuclear membrane; multi-pass membrane protein (Potential). Endoplasmic reticulum; endoplasm ...	endoplasmic reticulum [IDA]		2CQX	414
Q40153 UniProt NPD GO	LE14B_LITER	LEC14B protein	0.24	-	nuc	0					473
Q19157 UniProt NPD GO	PIN2_CAEEL	LIM protein pin-2	0.24	-	nuc	0	Cytoplasm. Nucleus				329
P38095 UniProt NPD GO	LAMA_EMENI	Lactam utilization protein lamA (Fragment)	0.24	-	nuc	0					41
P48449 UniProt NPD GO	ERG7_HUMAN	Lanosterol synthase (EC 5.4.99.7) (Oxidosqualene--lanosterol cyclase) (2,3-epoxysqualene--lanosterol ...	0.24	-	nuc	0			600909	1W6K	732
P06144 UniProt NPD GO	H1_LYTPI	Late histone H1	0.24	+	nuc	0	Nucleus				210
O94910 UniProt NPD GO	LPHN1_HUMAN	Latrophilin-1 precursor (Calcium-independent alpha-latrotoxin receptor 1) (Lectomedin-2)	0.24	-	end	8 *	Membrane; multi-pass membrane protein	integral to membrane [TAS]			1474
Q9Z2H4 UniProt NPD GO	LGR4_RAT	Leucine-rich repeat-containing G-protein coupled receptor 4 precursor	0.24	-	end	7	Membrane; multi-pass membrane protein				951
O02036 UniProt NPD GO	LCK_AEDAE	Leucokinins precursor [Contains: Leucokinin-1; Leucokinin-3; Leucokinin-2]	0.24	-	exc	0	Secreted protein				228
Q5R614 UniProt NPD GO	SYLC_PONPY	Leucyl-tRNA synthetase, cytoplasmic (EC 6.1.1.4) (Leucine--tRNA ligase) (LeuRS)	0.24	-	cyt	0	Cytoplasm (By similarity)				1176
P05619 UniProt NPD GO	ILEU_HORSE	Leukocyte elastase inhibitor (LEI) (Serpin B1)	0.24	-	nuc	0	Cytoplasm			1HLE	379
P30740 UniProt NPD GO	ILEU_HUMAN	Leukocyte elastase inhibitor (LEI) (Serpin B1) (Monocyte/neutrophil elastase inhibitor) (M/NEI) (EI) ...	0.24	-	nuc	0	Cytoplasm (By similarity)	cytoplasm [NAS]	130135		379
P51188 UniProt NPD GO	CHLN_PORPU	Light-independent protochlorophyllide reductase subunit N (EC 1.18.-.-) (LI-POR subunit N) (DPOR sub ...	0.24	+	cyt	0	Plastid; chloroplast				435
O43766 UniProt NPD GO	LIAS_HUMAN	Lipoic acid synthetase, mitochondrial precursor (Lip-syn) (Lipoate synthase)	0.24	-	mit	0	Mitochondrion (By similarity)		607031		372
O46419 UniProt NPD GO	LIPB_BOVIN	Lipoyltransferase 1, mitochondrial precursor (EC 6.-.-.-) (Lipoate-protein ligase) (Lipoate biosynth ...	0.24	-	cyt	0	Mitochondrion				373
P18165 UniProt NPD GO	LORI_MOUSE	Loricrin	0.24	+	nuc	0		cornified envelope [IDA] internal side of plasma membrane [IDA]			486
Q9JHF9 UniProt NPD GO	LY96_MOUSE	Lymphocyte antigen 96 precursor (MD-2 protein) (ESOP-1)	0.24	-	vac	0	Secreted protein; extracellular space				160
P50745 UniProt NPD GO	LNK_RAT	Lymphocyte-specific adapter protein Lnk (Signal transduction protein Lnk) (Lymphocyte adapter protei ...	0.24	-	mit	0					368
P78854 UniProt NPD GO	PLB1_SCHPO	Lysophospholipase 1 precursor (EC 3.1.1.5) (Phospholipase B 1)	0.24	-	end	0	Secreted protein (Probable)				613
Q13571 UniProt NPD GO	LAPM5_HUMAN	Lysosomal-associated multitransmembrane protein (Retinoic acid-inducible E3 protein) (HA1520)	0.24	-	end	5 *	Lysosome; lysosomal membrane; multi-pass membrane protein	integral to plasma membrane [TAS] lysosome [TAS]	601476		262
Q63341 UniProt NPD GO	MMP12_RAT	Macrophage metalloelastase precursor (EC 3.4.24.65) (MME) (Matrix metalloproteinase-12) (MMP-12)	0.24	-	exc	0					465

You are viewing entries 46451 to 46500 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.