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
P02825 UniProt NPD GO	HSP71_DROME	Major heat shock 70 kDa protein Ab (Heat shock protein 70Ab) (HSP70-87A7)	0.28	-	cyt	0					642
Q9TT91 UniProt NPD GO	MKRN1_MACEU	Makorin-1	0.28	-	nuc	0					478
P04926 UniProt NPD GO	EXP1_PLAFA	Malaria protein EXP-1 precursor (Exported antigen AG 5.1)	0.28	-	end	1					162
P39107 UniProt NPD GO	MNN9_YEAST	Mannan polymerase complexes MNN9 subunit (M-pol I subunit MNN9) (M-Pol II subunit MNN9)	0.28	-	gol	1 *	Endoplasmic reticulum; endoplasmic reticulum membrane; single-pass type II membrane protein. Golgi a ...	alpha-1,6-mannosyltransferase complex [IPI] Golgi cis-face [TAS] membrane [TAS]			394
O60664 UniProt NPD GO	M6PBP_HUMAN	Mannose-6-phosphate receptor-binding protein 1 (Cargo selection protein TIP47) (47 kDa mannose 6-pho ...	0.28	-	nuc	0	Cytoplasm. Endosome. Membrane associated on endosomes. Detected in the envelope and the core of lipi ...	cytoplasm [TAS] endosome [TAS] Golgi apparatus [TAS]	602702		434
P35692 UniProt NPD GO	FMR1_PODAN	Mat- sexual cell fertilization-promoting factor	0.28	-	cyt	0	Nucleus (Potential)				305
Q708A1 UniProt NPD GO	MATA1_KLUDE	Mating-type protein A1 (MATa1 transcription factor)	0.28	-	nuc	0	Nucleus (By similarity)				122
Q06182 UniProt NPD GO	SWI10_SCHPO	Mating-type switching protein swi10	0.28	-	nuc	0	Nucleus				252
Q8MJ39 UniProt NPD GO	MGP_PIG	Matrix Gla-protein precursor (MGP)	0.28	-	exc	0	Secreted protein				103
O43008 UniProt NPD GO	CRS1_SCHPO	Meiosis-specific cyclin crs1 (Meiotically up-regulated protein 17)	0.28	-	cyt	0					229
P01502 UniProt NPD GO	MEL_APIDO	Melittin	0.28	-	mit	0	Secreted protein				26
Q86UD3 UniProt NPD GO	MARH3_HUMAN	Membrane-associated RING finger protein 3 (Membrane-associated RING-CH protein III) (MARCH-III) (RIN ...	0.28	-	end	2	Membrane; multi-pass membrane protein (Potential)				253
Q9H3V2 UniProt NPD GO	MS4A5_HUMAN	Membrane-spanning 4-domains subfamily A member 5 (Testis-expressed transmembrane 4 protein) (CD20 an ...	0.28	-	end	4 *	Membrane; multi-pass membrane protein		606499		200
P68494 UniProt NPD GO	MT_ANAPL	Metallothionein (MT)	0.28	-	nuc	0					63
P68495 UniProt NPD GO	MT_CAIMO	Metallothionein (MT)	0.28	-	nuc	0					63
P68497 UniProt NPD GO	MT_CHICK	Metallothionein (MT)	0.28	-	nuc	0					63
P68498 UniProt NPD GO	MT_MELGA	Metallothionein (MT)	0.28	-	nuc	0					63
P68499 UniProt NPD GO	MT_PHACO	Metallothionein (MT) (Fragment)	0.28	-	nuc	0					49
Q9LTB2 UniProt NPD GO	MMT1_ARATH	Methionine S-methyltransferase (EC 2.1.1.12) (AdoMet:Met S-methyltransferase)	0.28	+	nuc	0	Cytoplasm (By similarity)				1071
Q20970 UniProt NPD GO	SYM_CAEEL	Methionyl-tRNA synthetase (EC 6.1.1.10) (Methionine--tRNA ligase) (MetRS)	0.28	-	nuc	0	Cytoplasm (By similarity)				917
Q96IZ6 UniProt NPD GO	METL2_HUMAN	Methyltransferase-like protein 2 (EC 2.1.1.-)	0.28	-	nuc	0			607846		378
Q13361 UniProt NPD GO	MFAP5_HUMAN	Microfibrillar-associated protein 5 precursor (MFAP-5) (Microfibril-associated glycoprotein 2) (MAGP ...	0.28	-	nuc	0	Secreted protein; extracellular space; extracellular matrix		601103		173
O41515 UniProt NPD GO	MLP3B_BOVIN	Microtubule-associated proteins 1A/1B light chain 3B (Microtubule-associated protein 1 light chain 3 ...	0.28	-	nuc	0	LC3-I: Cytoplasm. LC3-II: Intracytoplasmic membrane; lipid-anchor. LC3-II binds to the autophagic me ...				124
Q9GZQ8 UniProt NPD GO	MLP3B_HUMAN	Microtubule-associated proteins 1A/1B light chain 3B precursor (Microtubule-associated protein 1 lig ...	0.28	-	nuc	0	LC3-I: Cytoplasm. LC3-II: Intracytoplasmic membrane; lipid-anchor. LC3-II binds to the autophagic me ...	autophagic vacuole [ISS] organelle membrane [ISS]	609604	1V49	124
Q32PI6 UniProt NPD GO	RM04_BOVIN	Mitochondrial 39S ribosomal protein L4 (L4mt) (MRP-L4)	0.28	-	mit	0	Mitochondrion (By similarity)				294
P36533 UniProt NPD GO	RM39_YEAST	Mitochondrial 60S ribosomal protein L39 (YmL39)	0.28	-	nuc	0	Mitochondrion	mitochondrial large ribosomal subunit [TAS]			69
P27882 UniProt NPD GO	ERV1_YEAST	Mitochondrial FAD-linked sulfhydryl oxidase ERV1 (EC 1.8.3.-) (14 kDa regulatory protein) (Essential ...	0.28	-	nuc	0	Mitochondrion; mitochondrial intermembrane space	mitochondrial intermembrane space [IDA] mitochondrion [IDA]			189
Q8IXI2 UniProt NPD GO	MIRO1_HUMAN	Mitochondrial Rho GTPase 1 (EC 3.6.5.-) (MIRO-1) (hMiro-1) (Ras homolog gene family member T1) (Rac- ...	0.28	-	cyt	1	Mitochondrion; mitochondrial outer membrane; single-pass type IV membrane protein (Probable)				618
Q6PBL0 UniProt NPD GO	TIM16_BRARE	Mitochondrial import inner membrane translocase subunit TIM16	0.28	-	mit	0	Mitochondrion; mitochondrial inner membrane; peripheral membrane protein (By similarity)				129
Q60RS2 UniProt NPD GO	TIM16_CAEBR	Mitochondrial import inner membrane translocase subunit TIM16	0.28	-	nuc	0	Mitochondrion; mitochondrial inner membrane; peripheral membrane protein (By similarity)				138
Q6BTN1 UniProt NPD GO	TIM54_DEBHA	Mitochondrial import inner membrane translocase subunit TIM54	0.28	-	cyt	0	Mitochondrion; mitochondrial inner membrane; single-pass membrane protein (By similarity)				495
Q6NU12 UniProt NPD GO	MI40A_XENLA	Mitochondrial intermembrane space import and assembly protein 40-A (Coiled-coil-helix-coiled-coil-he ...	0.28	-	nuc	0	Mitochondrion; mitochondrial intermembrane space (By similarity)				139
Q63ZK1 UniProt NPD GO	MI40B_XENLA	Mitochondrial intermembrane space import and assembly protein 40-B (Coiled-coil-helix-coiled-coil-he ...	0.28	-	nuc	0	Mitochondrion; mitochondrial intermembrane space (By similarity)				139
Q35905 UniProt NPD GO	RMAR_SACDO	Mitochondrial ribosomal protein VAR1	0.28	-	nuc	0	Mitochondrion				373
O96772 UniProt NPD GO	HSP70_ENCCU	Mitochondrial-type heat shock protein 70 (mit-hsp70)	0.28	-	nuc	0	Nucleus (Potential)				592
Q84UI5 UniProt NPD GO	MPK1_ORYSA	Mitogen-activated protein kinase 1 (EC 2.7.11.24) (MAP kinase 1) (MAP kinase 6) (OsMAPK6) (OsSIPK)	0.28	-	cyt	0					398
P47812 UniProt NPD GO	MK14_XENLA	Mitogen-activated protein kinase 14 (EC 2.7.11.24) (Mitogen-activated Mitogen-activated protein kina ...	0.28	-	cyt	0					361
O93982 UniProt NPD GO	HOG1_ZYGRO	Mitogen-activated protein kinase HOG1 (EC 2.7.11.24) (MAP kinase HOG1)	0.28	-	cyt	0					380
P27638 UniProt NPD GO	SPK1_SCHPO	Mitogen-activated protein kinase spk1 (EC 2.7.11.24) (MAP kinase spk1) (MAPK)	0.28	-	cyt	0	Nucleus. Mainly	nucleus [IDA]			372
Q39056 UniProt NPD GO	CNX3_ARATH	Molybdopterin biosynthesis protein CNX3 (Molybdenum cofactor biosynthesis enzyme CNX3)	0.28	-	mit	0					270
O35253 UniProt NPD GO	SMAD7_MOUSE	Mothers against decapentaplegic homolog 7 (SMAD 7) (Mothers against DPP homolog 7) (Smad7) (Madh8)	0.28	-	nuc	0	Nucleus. Interaction with NEDD4L induces translocation from the nucleus to the cytoplasm				426
O46617 UniProt NPD GO	MOTI_HORSE	Motilin precursor [Contains: Motilin; Motilin-associated peptide (MAP)] (Fragment)	0.28	-	nuc	0	Secreted protein				92
Q9UDY8 UniProt NPD GO	MALT1_HUMAN	Mucosa-associated lymphoid tissue lymphoma translocation protein 1 (EC 3.4.22.-) (MALT lymphoma-asso ...	0.28	-	cyt	0	Cytoplasm; perinuclear region. Found in perinuclear structures together with Bcl-10	intracellular [NAS]	604860	2G7R	824
Q42093 UniProt NPD GO	MRP2_ARATH	Multidrug resistance-associated protein 2 (EC 3.6.3.44) (Glutathione S-conjugate-transporting ATPase ...	0.28	-	end	14 *	Vacuole; vacuolar membrane; multi-pass membrane protein (Potential). Tonoplast				1623
Q8VZZ4 UniProt NPD GO	MRP8_ARATH	Multidrug resistance-associated protein 8 (EC 3.6.3.44) (Glutathione S-conjugate-transporting ATPase ...	0.28	-	end	12 *	Membrane; multi-pass membrane protein (Potential)				1466
Q9UK23 UniProt NPD GO	NAGPA_HUMAN	N-acetylglucosamine-1-phosphodiester alpha-N-acetylglucosaminidase precursor (EC 3.1.4.45) (Phosphod ...	0.28	-	nuc	1	Golgi apparatus; Golgi stack; Golgi stack membrane; single-pass type I membrane protein. Cis/medial ...	integral to membrane [TAS]	607985		515
Q39013 UniProt NPD GO	NAC2_ARATH	NAC domain-containing protein 2 (ANAC002)	0.28	-	nuc	0					289
Q2QD37 UniProt NPD GO	NUIC_CUCSA	NAD(P)H-quinone oxidoreductase subunit I, chloroplast (EC 1.6.5.-) (NAD(P)H dehydrogenase subunit I) ...	0.28	-	cyt	0	Plastid; chloroplast; chloroplast thylakoid membrane; peripheral membrane protein (By similarity)				160
P06253 UniProt NPD GO	NUIC_MARPO	NAD(P)H-quinone oxidoreductase subunit I, chloroplast (EC 1.6.5.-) (NAD(P)H dehydrogenase subunit I) ...	0.28	-	nuc	0	Plastid; chloroplast; chloroplast thylakoid membrane; peripheral membrane protein (By similarity)				183
Q5RBV5 UniProt NPD GO	NDUB6_PONPY	NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 6 (EC 1.6.5.3) (EC 1.6.99.3) (NADH-ubiquin ...	0.28	-	cyt	1	Mitochondrion; mitochondrial inner membrane; matrix side (By similarity)				127

You are viewing entries 42451 to 42500 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.