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
P46617 UniProt NPD GO	CYF_MAIZE	Apocytochrome f precursor	0.11	-	cyt	1	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				320
P49476 UniProt NPD GO	CYF_ODOSI	Apocytochrome f precursor	0.11	-	end	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				314
P51265 UniProt NPD GO	CYF_PORPU	Apocytochrome f precursor	0.11	-	mit	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				320
Q6L387 UniProt NPD GO	CYF_SACHY	Apocytochrome f precursor	0.11	-	cyt	1	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				320
Q6ENV1 UniProt NPD GO	CYF_SACOF	Apocytochrome f precursor	0.11	-	cyt	1	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				320
Q9Z2R5 UniProt NPD GO	APOC3_CAVPO	Apolipoprotein C-III precursor (Apo-CIII) (ApoC-III)	0.11	-	exc	0	Secreted protein				91
Q9GKY5 UniProt NPD GO	GHRL_PIG	Appetite-regulating hormone precursor (Growth hormone secretagogue) (Growth hormone-releasing peptid ...	0.11	-	exc	1 *	Secreted protein (By similarity)				118
P42767 UniProt NPD GO	PIP1_ATRCA	Aquaporin PIP-type	0.11	-	end	6 *	Membrane; multi-pass membrane protein				282
P43286 UniProt NPD GO	PIP21_ARATH	Aquaporin PIP2.1 (Plasma membrane intrinsic protein 2a) (PIP2a)	0.11	-	end	6 *	Cell membrane; multi-pass membrane protein				287
P48792 UniProt NPD GO	XYL1_TRIKO	Arabinofuranosidase/B-xylosidase precursor [Includes: Alpha-N-arabinofuranosidase (EC 3.2.1.55) (Ara ...	0.11	-	mit	0					500
Q95JC8 UniProt NPD GO	ARGI1_PIG	Arginase-1 (EC 3.5.3.1) (Type I arginase) (Liver-type arginase)	0.11	-	cyt	0	Cytoplasm (By similarity)				322
P07824 UniProt NPD GO	ARGI1_RAT	Arginase-1 (EC 3.5.3.1) (Type I arginase) (Liver-type arginase)	0.11	-	cyt	0	Cytoplasm			5RLA	323
Q759W1 UniProt NPD GO	RMT2_ASHGO	Arginine N-methyltransferase 2 (EC 2.1.1.-)	0.11	-	mit	0	Cytoplasm (By similarity). Nucleus (By similarity)				413
Q7SCW9 UniProt NPD GO	RMT2_NEUCR	Arginine N-methyltransferase 2 (EC 2.1.1.-)	0.11	-	cyt	0	Cytoplasm (By similarity). Nucleus (By similarity)				429
P48610 UniProt NPD GO	KARG_DROME	Arginine kinase (EC 2.7.3.3) (AK)	0.11	-	cyt	0					356
O15990 UniProt NPD GO	KARG_LIOJA	Arginine kinase (EC 2.7.3.3) (AK)	0.11	-	cyt	0					349
P04076 UniProt NPD GO	ARLY_YEAST	Argininosuccinate lyase (EC 4.3.2.1) (Arginosuccinase) (ASAL)	0.11	-	cyt	0		cytosol [IDA]			463
P00505 UniProt NPD GO	AATM_HUMAN	Aspartate aminotransferase, mitochondrial precursor (EC 2.6.1.1) (Transaminase A) (Glutamate oxaloac ...	0.11	-	cyt	0	Mitochondrion; mitochondrial matrix	mitochondrion [TAS]	138150		430
P05202 UniProt NPD GO	AATM_MOUSE	Aspartate aminotransferase, mitochondrial precursor (EC 2.6.1.1) (Transaminase A) (Glutamate oxaloac ...	0.11	-	cyt	0	Mitochondrion; mitochondrial matrix	mitochondrial inner membrane [IDA] mitochondrion [IDA]			430
P40583 UniProt NPD GO	YPS6_YEAST	Aspartic proteinase yapsin-6 precursor (EC 3.4.23.-)	0.11	-	exc	0	Cell membrane; lipid-anchor; GPI-anchor (Potential)	cell wall (sensu Fungi) [IDA]			537
P17946 UniProt NPD GO	PEPA_ASPAW	Aspergillopepsin A precursor (EC 3.4.23.18)	0.11	-	mit	0	Secreted protein				394
P55325 UniProt NPD GO	PEPA_ASPNG	Aspergillopepsin A precursor (EC 3.4.23.18)	0.11	-	mit	0	Secreted protein				394
Q12567 UniProt NPD GO	PEPA_ASPSA	Aspergillopepsin A precursor (EC 3.4.23.18) (Aspergillopepsin I)	0.11	-	mit	0	Secreted protein			1IBQ	394
Q9VTU1 UniProt NPD GO	APG12_DROME	Autophagy protein 12-like (APG12-like)	0.11	-	mit	1 *	Cytoplasm (By similarity)				106
Q8R1P4 UniProt NPD GO	ATG10_MOUSE	Autophagy-related protein 10 (APG10-like) (mAPG10)	0.11	-	cyt	0	Cytoplasm (Probable)				215
O94817 UniProt NPD GO	ATG12_HUMAN	Autophagy-related protein 12 (APG12-like)	0.11	-	cyt	0	Cytoplasm (By similarity)	cytoplasm [TAS]	609608		140
Q7S083 UniProt NPD GO	ATG12_NEUCR	Autophagy-related protein 12 (Autophagy-related ubiquitin-like modifier atg-12)	0.11	-	cyt	0	Cytoplasm (Probable)				157
P46989 UniProt NPD GO	ATG27_YEAST	Autophagy-related protein 27 precursor (Enhancer of VPS34 missorting protein 1)	0.11	-	end	1	Intracytoplasmic membrane; single-pass type I membrane protein (Potential). Perivacuolar punctate st ...	membrane [IDA]			271
Q75GK0 UniProt NPD GO	IAA11_ORYSA	Auxin-responsive protein IAA11 (Indoleacetic acid-induced protein 11)	0.11	-	cyt	0	Nucleus (By similarity)				233
Q7Y1Y5 UniProt NPD GO	IAA13_ORYSA	Auxin-responsive protein IAA13 (Indoleacetic acid-induced protein 13)	0.11	-	nuc	0	Nucleus	nucleus [IC]			236
P49678 UniProt NPD GO	IAA2_ARATH	Auxin-responsive protein IAA2 (Indoleacetic acid-induced protein 2)	0.11	-	nuc	0	Nucleus				174
Q69TU6 UniProt NPD GO	IAA22_ORYSA	Auxin-responsive protein IAA22 (Indoleacetic acid-induced protein 22)	0.11	-	cyt	0	Nucleus (By similarity)				265
Q93WC4 UniProt NPD GO	IAA29_ARATH	Auxin-responsive protein IAA29 (Indoleacetic acid-induced protein 29)	0.11	-	nuc	0	Nucleus (By similarity)				251
Q16620 UniProt NPD GO	NTRK2_HUMAN	BDNF/NT-3 growth factors receptor precursor (EC 2.7.10.1) (Neurotrophic tyrosine kinase receptor typ ...	0.11	-	nuc	2 *	Membrane; single-pass type I membrane protein	integral to plasma membrane [TAS]	600456	1WWB	822
Q9BQ13 UniProt NPD GO	KCD14_HUMAN	BTB/POZ domain-containing protein KCTD14	0.11	-	cyt	0					225
Q7L273 UniProt NPD GO	KCTD9_HUMAN	BTB/POZ domain-containing protein KCTD9	0.11	-	mit	0					389
Q6I6F4 UniProt NPD GO	BIRC5_FELCA	Baculoviral IAP repeat-containing protein 5 (Apoptosis inhibitor survivin)	0.11	-	nuc	0	Cytoplasm. Nucleus. Localizes on chromosome arms and inner centromeres from prophase through metapha ...				142
Q5RAH9 UniProt NPD GO	BIRC5_PONPY	Baculoviral IAP repeat-containing protein 5 (Apoptosis inhibitor survivin)	0.11	-	cyt	0	Cytoplasm. Nucleus. Localizes on chromosome arms and inner centromeres from prophase through metapha ...				142
O15392 UniProt NPD GO	BIRC5_HUMAN	Baculoviral IAP repeat-containing protein 5 (Apoptosis inhibitor survivin) (Apoptosis inhibitor 4)	0.11	-	cyt	0	Cytoplasm. Nucleus. Localizes on chromosome arms and inner centromeres from prophase through metapha ...	chromosome, pericentric region [IDA] midbody [IDA] spindle microtubule [TAS]	603352	1XOX	142
P29061 UniProt NPD GO	CHIB_TOBAC	Basic endochitinase precursor (EC 3.2.1.14)	0.11	-	vac	0					294
Q9UBX8 UniProt NPD GO	B4GT6_HUMAN	Beta-1,4-galactosyltransferase 6 (EC 2.4.1.-) (Beta-1,4-GalTase 6) (Beta4Gal-T6) (b4Gal-T6) (UDP-gal ...	0.11	-	mit	1 *	Golgi apparatus; Golgi stack; Golgi stack membrane; single-pass type II membrane protein. Trans cist ...		604017		382
Q6QAT4 UniProt NPD GO	B2MG_SHEEP	Beta-2-microglobulin precursor	0.11	-	exc	0	Secreted protein				118
P16098 UniProt NPD GO	AMYB_HORVU	Beta-amylase (EC 3.2.1.2) (1,4-alpha-D-glucan maltohydrolase)	0.11	-	cyt	0				1B1Y	535
Q03070 UniProt NPD GO	CHIO_RAT	Beta-chimaerin (Beta-chimerin) (Rho-GTPase-activating protein 3)	0.11	-	cyt	0	Membrane; peripheral membrane protein (Potential)				295
P46168 UniProt NPD GO	BD10_BOVIN	Beta-defensin 10 precursor (BNDB-10) (BNBD-10) (Neutrophil beta-defensin 10)	0.11	-	gol	0	Secreted protein				62
Q8NES8 UniProt NPD GO	DB124_HUMAN	Beta-defensin 124 precursor (Defensin, beta 124) (Beta-defensin 24) (DEFB-24)	0.11	-	end	0	Secreted protein (Potential)				71
Q8K3I8 UniProt NPD GO	BD19_MOUSE	Beta-defensin 19 precursor (Defensin, beta 19) (BD-19) (mBD-19) (Testis-specific beta-defensin-like ...	0.11	-	exc	0	Secreted protein (By similarity)				83
P15570 UniProt NPD GO	ELIB_PHYCR	Beta-elicitin cryptogein precursor (CRY)	0.11	-	exc	0	Secreted protein			1LRI	118
P80065 UniProt NPD GO	INVB_DAUCA	Beta-fructofuranosidase, soluble isoenzyme I precursor (EC 3.2.1.26) (Sucrose hydrolase) (Invertase) ...	0.11	-	nuc	1 *	Vacuole				661
P49676 UniProt NPD GO	BGAL_BRAOL	Beta-galactosidase precursor (EC 3.2.1.23) (Lactase)	0.11	-	vac	1 *					828

You are viewing entries 62351 to 62400 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.