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
Q09381 UniProt NPD GO	YS84_CAEEL	Hypothetical protein ZK945.4	0.20	-	cyt	0					255
Q09382 UniProt NPD GO	YS86_CAEEL	Hypothetical protein ZK945.6	0.20	-	nuc	0					216
Q9TKX7 UniProt NPD GO	YCF81_NEPOL	Hypothetical protein ycf81 (RF81)	0.20	-	mit	0	Plastid; chloroplast				138
Q10040 UniProt NPD GO	YQA4_CAEEL	Hypothetical zinc protease C28F5.4 (EC 3.4.99.-)	0.20	+	cyt	0					745
P59723 UniProt NPD GO	HIF1N_BRARE	Hypoxia-inducible factor 1 alpha inhibitor (EC 1.14.11.16) (Hypoxia-inducible factor asparagine hydr ...	0.20	-	cyt	0	Nucleus (Potential)				344
P18532 UniProt NPD GO	HV61_MOUSE	Ig heavy chain V region 1B43 precursor	0.20	-	exc	0				2EXQ	116
P84750 UniProt NPD GO	KVM5_MOUSE	Ig kappa chain V region Mem5 (Fragment)	0.20	-	nuc	0	Secreted protein				121
P01663 UniProt NPD GO	KV3K_MOUSE	Ig kappa chain V-III region PC 4050	0.20	-	nuc	0					111
P01625 UniProt NPD GO	KV4A_HUMAN	Ig kappa chain V-IV region Len	0.20	-	nuc	0		extracellular region [NAS]		5LVE	114
P01635 UniProt NPD GO	KV5C_MOUSE	Ig kappa chain V-V region K2 precursor (Fragment)	0.20	-	exc	0				1A7R	115
P01872 UniProt NPD GO	MUC_MOUSE	Ig mu chain C region secreted form	0.20	-	nuc	0	Secreted protein (Probable)	B cell receptor complex [IDA] external side of plasma membrane [IDA] immunoglobulin complex, circulating [IDA] perinuclear region [IDA]			454
Q96ID5 UniProt NPD GO	IGS21_HUMAN	Immunoglobulin superfamily member 21 precursor	0.20	-	exc	0	Secreted protein (Potential)				467
P28776 UniProt NPD GO	I23O_MOUSE	Indoleamine 2,3-dioxygenase (EC 1.13.11.42) (IDO) (Indoleamine-pyrrole 2,3-dioxygenase)	0.20	-	nuc	0					407
P39870 UniProt NPD GO	NIA2_SOYBN	Inducible nitrate reductase [NADH] 2 (EC 1.7.1.1) (NR)	0.20	-	cyt	0					890
P12707 UniProt NPD GO	INS2_XENLA	Insulin-2 precursor [Contains: Insulin-2 B chain; Insulin-2 A chain]	0.20	-	vac	0	Secreted protein				106
O77801 UniProt NPD GO	INSL3_BOVIN	Insulin-like 3 precursor (Leydig insulin-like peptide) (Ley-I-L) (Relaxin-like factor) [Contains: In ...	0.20	-	end	1 *	Secreted protein (By similarity)				132
P26009 UniProt NPD GO	ITA8_CHICK	Integrin alpha-8 precursor [Contains: Integrin alpha-8 heavy chain; Integrin alpha-8 light chain]	0.20	-	end	1	Membrane; single-pass type I membrane protein				1044
P26008 UniProt NPD GO	ITAV_CHICK	Integrin alpha-V precursor (Vitronectin receptor subunit alpha) [Contains: Integrin alpha-V heavy ch ...	0.20	-	end	1	Membrane; single-pass type I membrane protein				1034
P18563 UniProt NPD GO	ITB6_CAVPO	Integrin beta-6 (Fragment)	0.20	-	nuc	0	Membrane; single-pass type I membrane protein				577
Q7TSL0 UniProt NPD GO	IFNK_MOUSE	Interferon kappa precursor (IFN-kappa)	0.20	-	vac	1 *	Secreted protein (By similarity)				199
P15091 UniProt NPD GO	II2A_MOUSE	Interferon-activable protein 202a (Ifi-202a) (Interferon-inducible protein p202a)	0.20	-	nuc	0	Cytoplasm. Nucleus. Accumulates first in the cytoplasm, and is translocated to the nucleus after a d ...				445
P09428 UniProt NPD GO	IL1B_BOVIN	Interleukin-1 beta precursor (IL-1 beta)	0.20	-	cyt	0	Secreted protein. The lack of a specific hydrophobic segment in the precursor sequence suggests that ...				266
Q9NWZ3 UniProt NPD GO	IRAK4_HUMAN	Interleukin-1 receptor-associated kinase 4 (EC 2.7.11.1) (IRAK-4) (NY-REN-64 antigen)	0.20	-	mit	0			606883		460
Q64385 UniProt NPD GO	I11RA_MOUSE	Interleukin-11 receptor alpha-1 chain precursor (IL-11R-alpha-1) (IL-11RA1) (IL-11R-alpha) (IL-11RA) ...	0.20	-	exc	1	Membrane; single-pass type I membrane protein				432
P70225 UniProt NPD GO	I11RB_MOUSE	Interleukin-11 receptor alpha-2 chain precursor (IL-11R-alpha-2) (Interleukin-11 receptor beta chain ...	0.20	-	end	1	Membrane; single-pass type I membrane protein				432
Q91ZK7 UniProt NPD GO	IL12B_SIGHI	Interleukin-12 beta chain precursor (IL-12B) (IL-12 p40) (Cytotoxic lymphocyte maturation factor 40 ...	0.20	-	exc	1 *	Secreted protein				327
Q29416 UniProt NPD GO	IL2_CANFA	Interleukin-2 precursor (IL-2) (T-cell growth factor) (TCGF)	0.20	-	exc	0	Secreted protein				155
Q07885 UniProt NPD GO	IL2_FELCA	Interleukin-2 precursor (IL-2) (T-cell growth factor) (TCGF)	0.20	-	exc	0	Secreted protein				154
Q2USJ2 UniProt NPD GO	MIA40_ASPOR	Intermembrane space import and assembly protein 40, mitochondrial precursor (Mitochondrial import in ...	0.20	-	mit	0	Mitochondrion; mitochondrial inner membrane; single-pass type II membrane protein; intermembrane sid ...				187
Q6CFQ0 UniProt NPD GO	ISU1_YARLI	Iron sulfur cluster assembly protein 1, mitochondrial precursor (Iron sulfur cluster scaffold protei ...	0.20	-	mit	0	Mitochondrion; mitochondrial matrix (By similarity)				181
P79089 UniProt NPD GO	IDHP_ASPNG	Isocitrate dehydrogenase [NADP], mitochondrial precursor (EC 1.1.1.42) (Oxalosuccinate decarboxylase ...	0.20	-	mit	0	Mitochondrion				498
P21954 UniProt NPD GO	IDHP_YEAST	Isocitrate dehydrogenase [NADP], mitochondrial precursor (EC 1.1.1.42) (Oxalosuccinate decarboxylase ...	0.20	-	mit	0	Mitochondrion	mitochondrial nucleoid [IDA] mitochondrion [IDA]			428
Q6FPK7 UniProt NPD GO	ACEA_CANGA	Isocitrate lyase (EC 4.1.3.1) (Isocitrase) (Isocitratase) (ICL)	0.20	-	mit	0	Peroxisome (Potential)				576
Q9SWG0 UniProt NPD GO	IVD_ARATH	Isovaleryl-CoA dehydrogenase, mitochondrial precursor (EC 1.3.99.10) (IVD)	0.20	-	mit	0	Mitochondrion				409
Q5EAE5 UniProt NPD GO	JOS1_BOVIN	Josephin-1 (Josephin domain-containing protein 1)	0.20	-	mit	0					202
P29622 UniProt NPD GO	KAIN_HUMAN	Kallistatin precursor (Serpin A4) (Kallikrein inhibitor) (Protease inhibitor 4)	0.20	-	cyt	0	Secreted protein		147935		427
P15817 UniProt NPD GO	NXLR1_BUNMU	Kappa-3-bungarotoxin precursor (Long neurotoxin CR1) (Kappa neurotoxin)	0.20	-	nuc	0	Secreted protein				87
P11841 UniProt NPD GO	CASK_PIG	Kappa-casein precursor	0.20	-	exc	0	Secreted protein				188
Q8NAB2 UniProt NPD GO	KBTB3_HUMAN	Kelch repeat and BTB domain-containing protein 3 (BTB and kelch domain-containing protein 3)	0.20	-	cyt	0					608
P59280 UniProt NPD GO	KLHL8_MOUSE	Kelch-like protein 8	0.20	-	mit	0					629
Q9BYR7 UniProt NPD GO	KRA32_HUMAN	Keratin-associated protein 3-2 (Keratin-associated protein 3.2) (High sulfur keratin-associated prot ...	0.20	-	nuc	0					98
O75690 UniProt NPD GO	KRA58_HUMAN	Keratin-associated protein 5-8 (Keratin-associated protein 5.8) (Ultrahigh sulfur keratin-associated ...	0.20	-	nuc	0		extracellular region [NAS]			187
Q04477 UniProt NPD GO	SPC24_YEAST	Kinetochore protein SPC24	0.20	-	nuc	0	Nucleus. Associated with kinetochores	condensed nuclear chromosome kinetochore [IDA] Ndc80 complex [IDA]		2FV4	213
Q9WU03 UniProt NPD GO	SPIT2_MOUSE	Kunitz-type protease inhibitor 2 precursor (Hepatocyte growth factor activator inhibitor type 2) (HA ...	0.20	-	end	1	Membrane; single-pass type I membrane protein (Potential)				252
O09046 UniProt NPD GO	OXLA_MOUSE	L-amino-acid oxidase precursor (EC 1.4.3.2) (LAAO) (Interleukin-4-induced protein 1) (IL4-induced pr ...	0.20	-	end	0	Isoform 1, isoform 2: Lysosome				630
Q5PQQ7 UniProt NPD GO	LIX1L_RAT	LIX1-like protein	0.20	-	nuc	0					338
O22132 UniProt NPD GO	LBD19_ARATH	LOB domain-containing protein 19	0.20	-	nuc	0					191
Q9N291 UniProt NPD GO	A4GAT_PANTR	Lactosylceramide 4-alpha-galactosyltransferase (EC 2.4.1.228) (Alpha-1,4-galactosyltransferase) (UDP ...	0.20	-	mit	1 *	Golgi apparatus; Golgi membrane; single-pass type II membrane protein (Probable)	integral to Golgi membrane [ISS]			353
Q9N289 UniProt NPD GO	A4GAT_PONPY	Lactosylceramide 4-alpha-galactosyltransferase (EC 2.4.1.228) (Alpha-1,4-galactosyltransferase) (UDP ...	0.20	-	cyt	0	Golgi apparatus; Golgi membrane; single-pass type II membrane protein (Probable)				218
P24627 UniProt NPD GO	TRFL_BOVIN	Lactotransferrin precursor (EC 3.4.21.-) (Lactoferrin) [Contains: Lactoferricin B (Lfcin B)]	0.20	-	exc	0	Secreted protein			2G93	708

You are viewing entries 50751 to 50800 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.