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
P04355 UniProt NPD GO	MT2_RAT	Metallothionein-2 (MT-2) (Metallothionein-II) (MT-II)	0.13	-	nuc	0				4MT2	61
P80292 UniProt NPD GO	MT2E_RABIT	Metallothionein-2E (MT-2E) (Metallothionein-IIE) (MT-IIE)	0.13	-	nuc	0					61
Q9UJH8 UniProt NPD GO	METRN_HUMAN	Meteorin precursor	0.13	-	mit	0	Secreted protein (By similarity)				293
Q8C1Q4 UniProt NPD GO	METRN_MOUSE	Meteorin precursor (Hypoxia/reoxygenation regulatory factor)	0.13	-	exc	0	Secreted protein	extracellular space [IDA]			291
P26188 UniProt NPD GO	MGMT_YEAST	Methylated-DNA--protein-cysteine methyltransferase (EC 2.1.1.63) (6-O-methylguanine-DNA methyltransf ...	0.13	-	cyt	0	Nucleus	nucleus [IC]			206
Q66HR2 UniProt NPD GO	MARE1_RAT	Microtubule-associated protein RP/EB family member 1 (APC-binding protein EB1) (End-binding protein ...	0.13	-	cyt	0	Cytoplasm (By similarity). Associated with the microtubule network at the growing distal tip of micr ...				267
O75394 UniProt NPD GO	RM33_HUMAN	Mitochondrial 39S ribosomal protein L33 (L33mt) (MRP-L33)	0.13	-	cyt	0	Mitochondrion		610059		65
Q9NYK5 UniProt NPD GO	RM39_HUMAN	Mitochondrial 39S ribosomal protein L39 (L39mt) (MRP-L39) (MRP-L5)	0.13	-	cyt	0	Mitochondrion	mitochondrial ribosome [NAS]			338
P46751 UniProt NPD GO	RM16_PROWI	Mitochondrial 60S ribosomal protein L16	0.13	-	mit	0	Mitochondrion				135
P42793 UniProt NPD GO	RM05_ARATH	Mitochondrial 60S ribosomal protein L5	0.13	-	cyt	0	Mitochondrion				185
Q8IXI1 UniProt NPD GO	MIRO2_HUMAN	Mitochondrial Rho GTPase 2 (EC 3.6.5.-) (MIRO-2) (hMiro-2) (Ras homolog gene family member T2)	0.13	-	cyt	1	Mitochondrion; mitochondrial outer membrane; single-pass type IV membrane protein (Probable)				618
Q5RD81 UniProt NPD GO	GHC1_PONPY	Mitochondrial glutamate carrier 1 (GC-1) (Glutamate/H(+) symporter 1) (Solute carrier family 25 memb ...	0.13	-	mit	1 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein (Potential)				323
Q61BP6 UniProt NPD GO	TIM10_CAEBR	Mitochondrial import inner membrane translocase subunit Tim10	0.13	-	nuc	0	Mitochondrion; mitochondrial inner membrane; peripheral membrane protein; intermembrane side (By sim ...				86
Q9P7K0 UniProt NPD GO	TIM9_SCHPO	Mitochondrial import inner membrane translocase subunit tim9	0.13	-	nuc	0	Mitochondrion; mitochondrial inner membrane; peripheral membrane protein; intermembrane side (By sim ...				84
P82874 UniProt NPD GO	TO203_ARATH	Mitochondrial import receptor subunit TOM20-3 (Translocase of outer membrane 20 kDa subunit 3)	0.13	-	nuc	1	Mitochondrion; mitochondrial outer membrane; multi-pass membrane protein			1ZU2	202
P87292 UniProt NPD GO	MTF1_SACKL	Mitochondrial replication protein MTF1 (Mitochondrial transcription factor mtTFB)	0.13	-	cyt	0	Mitochondrion (By similarity)				337
Q04121 UniProt NPD GO	NAH2_YEAST	Mitochondrial sodium/hydrogen exchanger (Mitochondrial Na(+)/H(+) exchanger) (Vacuolar protein sorti ...	0.13	-	end	8	Mitochondrion; mitochondrial membrane; multi-pass membrane protein	late endosome [IDA]			633
P10507 UniProt NPD GO	MPPB_YEAST	Mitochondrial-processing peptidase subunit beta, mitochondrial precursor (EC 3.4.24.64) (Beta-MPP) ( ...	0.13	-	mit	0	Mitochondrion; mitochondrial matrix	mitochondrial processing peptidase complex [IDA]		1HR9	462
Q5Z859 UniProt NPD GO	MPK4_ORYSA	Mitogen-activated protein kinase 4 (EC 2.7.11.24) (MAP kinase 4) (OsMAP2) (Multiple stress-responsiv ...	0.13	-	cyt	0					369
Q9Z1B5 UniProt NPD GO	MD2L1_MOUSE	Mitotic spindle assembly checkpoint protein MAD2A (MAD2-like 1)	0.13	-	mit	0	Nucleus (By similarity)	kinetochore [IDA] spindle pole body [IDA]			205
P55321 UniProt NPD GO	MIH_CALSI	Molt-inhibiting hormone precursor (MIH)	0.13	-	mit	0	Secreted protein				113
O96605 UniProt NPD GO	MIH_CHAFE	Molt-inhibiting hormone precursor (MIH)	0.13	-	mit	1 *	Secreted protein				113
O95396 UniProt NPD GO	MOCS3_HUMAN	Molybdenum cofactor synthesis protein 3 (Molybdopterin synthase sulfurylase) (MPT synthase sulfuryla ...	0.13	-	end	0					460
Q9GZU1 UniProt NPD GO	MCLN1_HUMAN	Mucolipin-1 (Mucolipidin) (MG-2)	0.13	-	end	5	Cell membrane; multi-pass membrane protein. Endosome; late endosome; late endosomal membrane; multi- ...	integral to plasma membrane [NAS]	605248		580
P37842 UniProt NPD GO	CYTM_SOLTU	Multicystatin (MC)	0.13	-	cyt	0					756
P34712 UniProt NPD GO	MDR1_CAEEL	Multidrug resistance protein 1 (EC 3.6.3.44) (P-glycoprotein A)	0.13	-	end	11	Membrane; multi-pass membrane protein				1321
Q52BY4 UniProt NPD GO	MBF1_MAGGR	Multiprotein-bridging factor 1	0.13	-	nuc	0					161
Q9XYF6 UniProt NPD GO	MYOD_TOXGO	Myosin D (MyoD) (TgM-D)	0.13	-	mit	0					822
Q8VCR8 UniProt NPD GO	MYLK2_MOUSE	Myosin light chain kinase 2, skeletal/cardiac muscle (EC 2.7.11.18) (MLCK2) (Fragment)	0.13	-	cyt	0	Cytoplasm (By similarity). Colocalizes with phosphorylated myosin light chain (RLCP) at filaments of ...				240
P97457 UniProt NPD GO	MLRS_MOUSE	Myosin regulatory light chain 2, skeletal muscle isoform (MLC2F)	0.13	+	cyt	0					169
P54265 UniProt NPD GO	DMPK_MOUSE	Myotonin-protein kinase (EC 2.7.11.1) (Myotonic dystrophy protein kinase) (MDPK) (DM-kinase) (DMK) ( ...	0.13	-	nuc	0					631
Q39513 UniProt NPD GO	FATB_CUPHO	Myristoyl-acyl carrier protein thioesterase, chloroplast precursor (EC 3.1.2.-) (16:0-acyl-carrier p ...	0.13	-	nuc	0	Plastid; chloroplast				415
P00912 UniProt NPD GO	TRPF_YEAST	N-(5'-phosphoribosyl)anthranilate isomerase (EC 5.3.1.24) (PRAI)	0.13	-	mit	0		cytoplasm [TAS]			224
Q7M758 UniProt NPD GO	NALDL_MOUSE	N-acetylated-alpha-linked acidic dipeptidase-like protein (EC 3.4.17.21) (NAALADase L)	0.13	-	end	1 *	Cell membrane; single-pass type II membrane protein (By similarity). Ileal brush border membrane (By ...				745
Q9UQQ1 UniProt NPD GO	NALDL_HUMAN	N-acetylated-alpha-linked acidic dipeptidase-like protein (EC 3.4.17.21) (NAALADase L) (Ileal dipept ...	0.13	-	cyt	1 *	Cell membrane; single-pass type II membrane protein. Ileal brush border membrane	integral to membrane [NAS]	602640		740
P69060 UniProt NPD GO	NEUA_RAT	N-acylneuraminate cytidylyltransferase (EC 2.7.7.43) (CMP-N-acetylneuraminic acid synthetase) (CMP-N ...	0.13	-	mit	0	Nucleus (By similarity)				432
P40205 UniProt NPD GO	NCYM_HUMAN	N-cym protein (N-myc opposite strand)	0.13	-	nuc	0			605374		109
Q9XQ96 UniProt NPD GO	NU2C_BRANA	NAD(P)H-quinone oxidoreductase chain 2, chloroplast (EC 1.6.5.-) (NAD(P)H dehydrogenase, chain 2) (N ...	0.13	-	end	11 *	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein (By similarity)				510
Q49KT7 UniProt NPD GO	NU2C_EUCGG	NAD(P)H-quinone oxidoreductase chain 2, chloroplast (EC 1.6.5.-) (NAD(P)H dehydrogenase, chain 2) (N ...	0.13	-	end	11 *	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein (By similarity)				510
Q332R8 UniProt NPD GO	NU2C_LACSA	NAD(P)H-quinone oxidoreductase chain 2, chloroplast (EC 1.6.5.-) (NAD(P)H dehydrogenase, chain 2) (N ...	0.13	-	end	12 *	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein (By similarity)				510
Q9ME36 UniProt NPD GO	NU2C_OENHO	NAD(P)H-quinone oxidoreductase chain 2, chloroplast (EC 1.6.5.-) (NAD(P)H dehydrogenase, chain 2) (N ...	0.13	-	end	12 *	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein (By similarity)				510
Q68RU6 UniProt NPD GO	NU2C_PANGI	NAD(P)H-quinone oxidoreductase chain 2, chloroplast (EC 1.6.5.-) (NAD(P)H dehydrogenase, chain 2) (N ...	0.13	-	end	12 *	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein (By similarity)				510
Q2VEC1 UniProt NPD GO	NU2C_SOLTU	NAD(P)H-quinone oxidoreductase chain 2, chloroplast (EC 1.6.5.-) (NAD(P)H dehydrogenase, chain 2) (N ...	0.13	-	end	12 *	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein (By similarity)				510
Q9LD71 UniProt NPD GO	NU2C_SPIOL	NAD(P)H-quinone oxidoreductase chain 2, chloroplast (EC 1.6.5.-) (NAD(P)H dehydrogenase, chain 2) (N ...	0.13	-	end	11 *	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein (By similarity)				510
P26288 UniProt NPD GO	NU4C_ARATH	NAD(P)H-quinone oxidoreductase chain 4, chloroplast (EC 1.6.5.-) (NAD(P)H dehydrogenase, chain 4) (N ...	0.13	-	end	14 *	Plastid; chloroplast				500
O03060 UniProt NPD GO	NU4C_HORVU	NAD(P)H-quinone oxidoreductase chain 4, chloroplast (EC 1.6.5.-) (NAD(P)H dehydrogenase, chain 4) (N ...	0.13	-	end	14 *	Plastid; chloroplast				500
Q9BBP3 UniProt NPD GO	NU4C_LOTJA	NAD(P)H-quinone oxidoreductase chain 4, chloroplast (EC 1.6.5.-) (NAD(P)H dehydrogenase, chain 4) (N ...	0.13	-	end	14 *	Plastid; chloroplast				497
P58420 UniProt NPD GO	NU4C_WHEAT	NAD(P)H-quinone oxidoreductase chain 4, chloroplast (EC 1.6.5.-) (NAD(P)H dehydrogenase, chain 4) (N ...	0.13	-	end	14 *	Plastid; chloroplast				500
P11646 UniProt NPD GO	NU4LC_MAIZE	NAD(P)H-quinone oxidoreductase chain 4L, chloroplast (EC 1.6.5.-) (NAD(P)H dehydrogenase, chain 4L) ...	0.13	-	end	3 *	Plastid; chloroplast				101
Q32516 UniProt NPD GO	NU5C_LYCES	NAD(P)H-quinone oxidoreductase chain 5, chloroplast (EC 1.6.5.-) (NAD(P)H dehydrogenase, chain 5) (N ...	0.13	-	end	16 *	Plastid; chloroplast; chloroplast membrane; multi-pass membrane protein				737

You are viewing entries 60001 to 60050 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.