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
O21246 UniProt NPD GO	RT10_RECAM	Mitochondrial ribosomal protein S10	0.14	-	nuc	0	Mitochondrion				116
Q5R513 UniProt NPD GO	MPPA_PONPY	Mitochondrial-processing peptidase alpha subunit, mitochondrial precursor (EC 3.4.24.64) (Alpha-MPP) ...	0.14	-	mit	0	Mitochondrion; mitochondrial matrix (By similarity)				525
P20069 UniProt NPD GO	MPPA_RAT	Mitochondrial-processing peptidase alpha subunit, mitochondrial precursor (EC 3.4.24.64) (Alpha-MPP) ...	0.14	-	mit	0	Mitochondrion; mitochondrial matrix	mitochondrial matrix [TAS]			524
Q3KQ62 UniProt NPD GO	MORG1_XENLA	Mitogen-activated protein kinase organizer 1 (MAPK organizer 1)	0.14	-	nuc	0	Cytoplasm (By similarity)				314
P82818 UniProt NPD GO	MOR1_BOMMO	Moricin-1 precursor	0.14	-	end	0	Secreted protein			1KV4	66
O96059 UniProt NPD GO	MOR2_BOMMO	Moricin-2 precursor	0.14	-	end	0	Secreted protein				66
Q60SZ2 UniProt NPD GO	MPV17_CAEBR	Mpv17-like protein	0.14	-	mit	4 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein (By similarity)				189
Q99102 UniProt NPD GO	MUC4_HUMAN	Mucin-4 (Tracheobronchial mucin) (Fragment)	0.14	-	nuc	0		integral to plasma membrane [TAS]	158372		610
P43245 UniProt NPD GO	MDR1_RAT	Multidrug resistance protein 1 (EC 3.6.3.44) (P-glycoprotein 1) (CD243 antigen)	0.14	-	end	12 *	Membrane; multi-pass membrane protein	membrane [IDA]			1277
Q9ZR72 UniProt NPD GO	MDR1_ARATH	Multidrug resistance protein 1 (P-glycoprotein 1) (AtPgp1)	0.14	-	end	12 *	Cell membrane; multi-pass membrane protein. Non-polar distribution in apical cells. Predominant basa ...				1286
Q9ERZ4 UniProt NPD GO	ACM2_MOUSE	Muscarinic acetylcholine receptor M2	0.14	-	end	7 *	Membrane; multi-pass membrane protein				466
P08940 UniProt NPD GO	MIM1_CHICK	Myeloid protein 1 precursor (p33)	0.14	-	exc	0	Granules of promyelocytes				326
P06742 UniProt NPD GO	MLC1_DROME	Myosin light chain alkali	0.14	+	cyt	0		muscle myosin [IDA]			155
Q9HFW8 UniProt NPD GO	TRPF_ZYGBA	N-(5'-phosphoribosyl)anthranilate isomerase (EC 5.3.1.24) (PRAI)	0.14	-	cyt	0					205
O54697 UniProt NPD GO	NALDL_RAT	N-acetylated-alpha-linked acidic dipeptidase-like protein (EC 3.4.17.21) (NAALADase L) (Ileal dipept ...	0.14	-	cyt	1 *	Cell membrane; single-pass type II membrane protein. Ileal brush border membrane				745
P51607 UniProt NPD GO	RENBP_RAT	N-acylglucosamine 2-epimerase (EC 5.1.3.8) (GlcNAc 2-epimerase) (N-acetyl-D-glucosamine 2-epimerase) ...	0.14	-	cyt	0					419
Q64669 UniProt NPD GO	NQO1_MOUSE	NAD(P)H dehydrogenase [quinone] 1 (EC 1.6.5.2) (Quinone reductase 1) (NAD(P)H:quinone oxidoreductase ...	0.14	-	mit	0	Cytoplasm			1DXQ	273
Q9B149 UniProt NPD GO	NU2C_LOTJA	NAD(P)H-quinone oxidoreductase chain 2, chloroplast (EC 1.6.5.-) (NAD(P)H dehydrogenase, chain 2) (N ...	0.14	-	end	11 *	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein (By similarity)				510
P10328 UniProt NPD GO	NU2C_SOYBN	NAD(P)H-quinone oxidoreductase chain 2, chloroplast (EC 1.6.5.-) (NAD(P)H dehydrogenase, chain 2) (N ...	0.14	-	end	12 *	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein (By similarity)				510
Q9MUM8 UniProt NPD GO	NU4C_MESVI	NAD(P)H-quinone oxidoreductase chain 4, chloroplast (EC 1.6.5.-) (NAD(P)H dehydrogenase, chain 4) (N ...	0.14	-	end	14 *	Plastid; chloroplast				507
P06264 UniProt NPD GO	NU5C_MARPO	NAD(P)H-quinone oxidoreductase chain 5, chloroplast (EC 1.6.5.-) (NAD(P)H dehydrogenase, chain 5) (N ...	0.14	+	end	16 *	Plastid; chloroplast; chloroplast membrane; multi-pass membrane protein				692
Q9M3J4 UniProt NPD GO	NU5C_SPIOL	NAD(P)H-quinone oxidoreductase chain 5, chloroplast (EC 1.6.5.-) (NAD(P)H dehydrogenase, chain 5) (N ...	0.14	-	end	16 *	Plastid; chloroplast; chloroplast membrane; multi-pass membrane protein				742
Q85UU0 UniProt NPD GO	NUCC_ANTFO	NAD(P)H-quinone oxidoreductase chain H, chloroplast (EC 1.6.5.-) (NAD(P)H dehydrogenase, chain H) (N ...	0.14	-	cyt	0	Plastid; chloroplast				393
Q5R6G3 UniProt NPD GO	SIRT5_PONPY	NAD-dependent deacetylase sirtuin-5 (EC 3.5.1.-)	0.14	-	mit	0					310
Q99LC3 UniProt NPD GO	NDUAA_MOUSE	NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 10, mitochondrial precursor (EC 1.6.5.3) ...	0.14	-	mit	0	Mitochondrion; mitochondrial matrix	mitochondrion [IDA]			355
Q9CQ75 UniProt NPD GO	NDUA2_MOUSE	NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 2 (EC 1.6.5.3) (EC 1.6.99.3) (NADH-ubiqui ...	0.14	-	mit	0	Mitochondrion; mitochondrial inner membrane; matrix side	mitochondrion [IDA] respiratory chain complex I (sensu Eukaryota) [TAS]			98
P42026 UniProt NPD GO	NUKM_BOVIN	NADH-ubiquinone oxidoreductase 20 kDa subunit, mitochondrial precursor (EC 1.6.5.3) (EC 1.6.99.3) (C ...	0.14	-	exc	0					216
O75251 UniProt NPD GO	NUKM_HUMAN	NADH-ubiquinone oxidoreductase 20 kDa subunit, mitochondrial precursor (EC 1.6.5.3) (EC 1.6.99.3) (C ...	0.14	-	mit	0			601825		213
Q5R4J8 UniProt NPD GO	NUKM_PONPY	NADH-ubiquinone oxidoreductase 20 kDa subunit, mitochondrial precursor (EC 1.6.5.3) (EC 1.6.99.3) (C ...	0.14	-	mit	0					213
P23709 UniProt NPD GO	NUGM_BOVIN	NADH-ubiquinone oxidoreductase 30 kDa subunit, mitochondrial precursor (EC 1.6.5.3) (EC 1.6.99.3) (C ...	0.14	-	mit	0	Mitochondrion; mitochondrial inner membrane				266
Q91WD5 UniProt NPD GO	NUCM_MOUSE	NADH-ubiquinone oxidoreductase 49 kDa subunit, mitochondrial precursor (EC 1.6.5.3) (EC 1.6.99.3) (C ...	0.14	-	mit	0	Mitochondrion; mitochondrial inner membrane; matrix side (By similarity)	mitochondrion [IDA]			463
O78695 UniProt NPD GO	NU1M_CEBAP	NADH-ubiquinone oxidoreductase chain 1 (EC 1.6.5.3) (NADH dehydrogenase subunit 1)	0.14	-	end	7 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein (Probable)				318
P03889 UniProt NPD GO	NU1M_RAT	NADH-ubiquinone oxidoreductase chain 1 (EC 1.6.5.3) (NADH dehydrogenase subunit 1)	0.14	-	end	8 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein (Probable)			1MHC	318
Q2TQ14 UniProt NPD GO	NU2M_CROHI	NADH-ubiquinone oxidoreductase chain 2 (EC 1.6.5.3) (NADH dehydrogenase subunit 2)	0.14	-	end	8 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				347
P34187 UniProt NPD GO	NU2M_CROLA	NADH-ubiquinone oxidoreductase chain 2 (EC 1.6.5.3) (NADH dehydrogenase subunit 2)	0.14	-	end	9 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				348
Q330C4 UniProt NPD GO	NU2M_MYOSI	NADH-ubiquinone oxidoreductase chain 2 (EC 1.6.5.3) (NADH dehydrogenase subunit 2)	0.14	-	end	8 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				347
Q330B3 UniProt NPD GO	NU2M_NATTU	NADH-ubiquinone oxidoreductase chain 2 (EC 1.6.5.3) (NADH dehydrogenase subunit 2)	0.14	-	end	9 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				347
Q330C3 UniProt NPD GO	NU2M_NYCAR	NADH-ubiquinone oxidoreductase chain 2 (EC 1.6.5.3) (NADH dehydrogenase subunit 2)	0.14	-	end	8 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				347
Q2TQ12 UniProt NPD GO	NU2M_SUNET	NADH-ubiquinone oxidoreductase chain 2 (EC 1.6.5.3) (NADH dehydrogenase subunit 2)	0.14	-	end	8 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				347
Q2TQ15 UniProt NPD GO	NU2M_SYLOL	NADH-ubiquinone oxidoreductase chain 2 (EC 1.6.5.3) (NADH dehydrogenase subunit 2)	0.14	-	end	8 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				347
Q5ZNA1 UniProt NPD GO	NU4M_ZAGBR	NADH-ubiquinone oxidoreductase chain 4 (EC 1.6.5.3) (NADH dehydrogenase subunit 4)	0.14	-	end	13 *					459
O03773 UniProt NPD GO	NU4M_POROP	NADH-ubiquinone oxidoreductase chain 4 (EC 1.6.5.3) (NADH dehydrogenase subunit 4) (Fragment)	0.14	-	end	6 *					231
Q37024 UniProt NPD GO	NU5M_PICCA	NADH-ubiquinone oxidoreductase chain 5 (EC 1.6.5.3)	0.14	-	end	18 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein (By similarity)				644
P12776 UniProt NPD GO	NU5M_PARLI	NADH-ubiquinone oxidoreductase chain 5 (EC 1.6.5.3) (NADH dehydrogenase subunit 5)	0.14	-	end	15 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein (Probable)				638
Q00542 UniProt NPD GO	NU5M_PHOVI	NADH-ubiquinone oxidoreductase chain 5 (EC 1.6.5.3) (NADH dehydrogenase subunit 5)	0.14	-	end	16 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein (Probable)				609
Q9TDR1 UniProt NPD GO	NU5M_PIG	NADH-ubiquinone oxidoreductase chain 5 (EC 1.6.5.3) (NADH dehydrogenase subunit 5)	0.14	-	end	16 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein (Probable)				606
O79411 UniProt NPD GO	NU5M_SCYCA	NADH-ubiquinone oxidoreductase chain 5 (EC 1.6.5.3) (NADH dehydrogenase subunit 5)	0.14	-	end	15 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein (Probable)				609
Q35813 UniProt NPD GO	NU5M_STRCA	NADH-ubiquinone oxidoreductase chain 5 (EC 1.6.5.3) (NADH dehydrogenase subunit 5)	0.14	-	end	16 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein (Probable)				605
Q4JQH7 UniProt NPD GO	NU5M_TETNG	NADH-ubiquinone oxidoreductase chain 5 (EC 1.6.5.3) (NADH dehydrogenase subunit 5)	0.14	-	end	16 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein (Probable)				612
Q31651 UniProt NPD GO	NU5M_ANSCE	NADH-ubiquinone oxidoreductase chain 5 (EC 1.6.5.3) (NADH dehydrogenase subunit 5) (Fragment)	0.14	-	end	4 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein (Probable)				214

You are viewing entries 58651 to 58700 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.