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
O76942 UniProt NPD GO	PTP1_ENCCU	Major polar tube protein precursor (Major PTP)	0.24	-	nuc	0	Secreted protein; extracellular space				395
O43123 UniProt NPD GO	MAAI_EMENI	Maleylacetoacetate isomerase (EC 5.2.1.2) (MAAI)	0.24	-	mit	0	Cytoplasm (By similarity)				230
P15685 UniProt NPD GO	MAL61_YEAST	Maltose permease MAL61 (Maltose transport protein MAL61)	0.24	-	end	8	Membrane; multi-pass membrane protein				614
P15089 UniProt NPD GO	CBPA3_MOUSE	Mast cell carboxypeptidase A precursor (EC 3.4.17.1) (MC-CPA) (Carboxypeptidase A3)	0.24	-	cyt	0	Secretory granules				417
Q16655 UniProt NPD GO	MAR1_HUMAN	Melanoma antigen recognized by T-cells 1 (MART-1) (Melan-A protein) (Antigen SK29-AA) (Antigen LB39- ...	0.24	-	nuc	1 *		integral to plasma membrane [TAS]	605513		118
Q5R4D0 UniProt NPD GO	MCP_PONPY	Membrane cofactor protein precursor (CD46 antigen)	0.24	-	end	1	Acrosome; acrosomal inner membrane; single-pass type I membrane protein (By similarity). Inner acros ...				355
Q9NXK6 UniProt NPD GO	MPRG_HUMAN	Membrane progestin receptor gamma (mPR gamma) (Progestin and adipoQ receptor family member V)	0.24	-	cyt	6	Membrane; multi-pass membrane protein (By similarity)		607781		330
Q9DCU0 UniProt NPD GO	MPRG_MOUSE	Membrane progestin receptor gamma (mPR gamma) (Progestin and adipoQ receptor family member V)	0.24	-	cyt	5 *	Membrane; multi-pass membrane protein (By similarity)				330
Q9C6B2 UniProt NPD GO	NRAM2_ARATH	Metal transporter Nramp2 (AtNramp2)	0.24	-	end	9	Membrane; multi-pass membrane protein (Probable)				530
O02722 UniProt NPD GO	TIMP1_HORSE	Metalloproteinase inhibitor 1 precursor (TIMP-1)	0.24	-	exc	0	Secreted protein				207
P27086 UniProt NPD GO	MTA_COLVI	Metallothionein A (MTA) (Fragment)	0.24	-	nuc	0					43
P55950 UniProt NPD GO	MT2_CALSI	Metallothionein-2B (MT-2B) (Metallothionein-IIB) (MT-IIB) [Contains: Metallothionein-2A (MT-2A) (Met ...	0.24	-	nuc	0					58
P34599 UniProt NPD GO	MTX2_CAEEL	Metaxin-2 homolog	0.24	-	cyt	0	Mitochondrion; mitochondrial outer membrane (Potential)				230
Q8BVH9 UniProt NPD GO	METL6_MOUSE	Methyltransferase-like protein 6 (EC 2.1.1.-)	0.24	-	mit	0					282
O02828 UniProt NPD GO	TAU_CAPHI	Microtubule-associated protein tau (Neurofibrillary tangle protein) (Paired helical filament-tau) (P ...	0.24	-	nuc	0	Cytoplasm; cytosol. Cell membrane. Mostly found in the axons of neurons, in the cytosol and in assoc ...				402
Q9DE65 UniProt NPD GO	MIME_COTJA	Mimecan precursor (Osteoglycin)	0.24	-	exc	0	Secreted protein; extracellular space; extracellular matrix (By similarity)				293
Q7TQ82 UniProt NPD GO	RT10_RAT	Mitochondrial 28S ribosomal protein S10 (S10mt) (MRP-S10) (Liver regeneration-related protein LRRG09 ...	0.24	-	mit	0	Mitochondrion (By similarity)				155
Q6BHJ8 UniProt NPD GO	TIM13_DEBHA	Mitochondrial import inner membrane translocase subunit TIM13	0.24	-	nuc	0	Mitochondrion; mitochondrial inner membrane; peripheral membrane protein; intermembrane side (By sim ...				98
Q754J4 UniProt NPD GO	TIM16_ASHGO	Mitochondrial import inner membrane translocase subunit TIM16 (Presequence translocated-associated m ...	0.24	-	mit	0	Mitochondrion; mitochondrial inner membrane; peripheral membrane protein (By similarity)				136
Q6CK35 UniProt NPD GO	TIM16_KLULA	Mitochondrial import inner membrane translocase subunit TIM16 (Presequence translocated-associated m ...	0.24	-	mit	0	Mitochondrion; mitochondrial inner membrane; peripheral membrane protein (By similarity)				139
Q6CWH5 UniProt NPD GO	TIM8_KLULA	Mitochondrial import inner membrane translocase subunit TIM8	0.24	-	nuc	0	Mitochondrion; mitochondrial inner membrane; peripheral membrane protein; intermembrane side (By sim ...				87
P50093 UniProt NPD GO	PHB2_CAEEL	Mitochondrial prohibitin complex protein 2 (Prohibitin-2)	0.24	-	exc	1 *	Mitochondrion; mitochondrial inner membrane				286
P92541 UniProt NPD GO	M1090_ARATH	Mitochondrial protein AtMg01090 (ORF262)	0.24	-	end	3 *	Mitochondrion; mitochondrial membrane; multi-pass membrane protein (Potential)				262
Q08774 UniProt NPD GO	YO305_YEAST	Mitochondrial protein YOR305W	0.24	-	nuc	0	Mitochondrion	mitochondrion [IDA]			242
P21358 UniProt NPD GO	RMAR_CANGA	Mitochondrial ribosomal protein VAR1	0.24	-	nuc	0	Mitochondrion				339
Q63844 UniProt NPD GO	MK03_MOUSE	Mitogen-activated protein kinase 3 (EC 2.7.11.24) (Extracellular signal-regulated kinase 1) (ERK-1) ...	0.24	-	cyt	0		cytoplasm [IDA] nucleus [IDA]			380
Q39027 UniProt NPD GO	MPK7_ARATH	Mitogen-activated protein kinase 7 (EC 2.7.11.24) (MAP kinase 7) (AtMPK7)	0.24	-	cyt	0					368
Q8WXG9 UniProt NPD GO	MASS1_HUMAN	Monogenic audiogenic seizure susceptibility protein 1 homolog precursor (Very large G-protein couple ...	0.24	-	end	7 *	Membrane; multi-pass membrane protein	integral to membrane [TAS] membrane [NAS]	605472		6307
Q8UUG2 UniProt NPD GO	MORO_MORCH	Moronecidin precursor	0.24	-	mit	0	Secreted protein				79
Q8UUG0 UniProt NPD GO	MORO_MORSA	Moronecidin precursor (Piscidin-1)	0.24	-	cyt	0	Secreted protein				79
P03971 UniProt NPD GO	MIS_HUMAN	Muellerian-inhibiting factor precursor (MIS) (Anti-Muellerian hormone) (AMH) (Muellerian-inhibiting ...	0.24	-	exc	0	Secreted protein	extracellular region [NAS] extracellular space [TAS]	600957		560
P53176 UniProt NPD GO	MST27_YEAST	Multicopy suppressor of SEC21 protein 27 (DUP240 protein MST27) (Protein DUP2)	0.24	-	end	2 *	Membrane; multi-pass membrane protein (Potential). Endoplasmic reticulum, endoplasmic reticulum to G ...	endoplasmic reticulum [IDA] Golgi apparatus [IDA] integral to membrane [IDA]			234
P21440 UniProt NPD GO	MDR2_MOUSE	Multidrug resistance protein 2 (EC 3.6.3.44) (P-glycoprotein 2)	0.24	-	end	10	Membrane; multi-pass membrane protein	intercellular canaliculus [IDA]			1276
Q9C8G9 UniProt NPD GO	MRP1_ARATH	Multidrug resistance-associated protein 1 (EC 3.6.3.44) (Glutathione S-conjugate-transporting ATPase ...	0.24	-	end	14 *	Vacuole; vacuolar membrane; multi-pass membrane protein. Tonoplast				1622
P98190 UniProt NPD GO	MBP_CAROB	Myelin basic protein (MBP) (Fragments)	0.24	-	nuc	0	Myelin membrane; peripheral membrane protein; cytoplasmic side. Cytoplasmic side of myelin				128
Q8WTN9 UniProt NPD GO	ST4S6_OMMSL	N-acetylgalactosamine 4-sulfate 6-O-sulfotransferase (EC 2.8.2.33) (GalNAc4S-6ST) (Fragments)	0.24	-	cyt	0	Golgi apparatus; Golgi membrane; single-pass type II membrane protein (Probable)				159
Q80VA0 UniProt NPD GO	GALT7_MOUSE	N-acetylgalactosaminyltransferase 7 (EC 2.4.1.-) (Protein-UDP acetylgalactosaminyltransferase 7) (UD ...	0.24	-	exc	1 *	Golgi apparatus; Golgi membrane; single-pass type II membrane protein (By similarity)				657
Q96PD5 UniProt NPD GO	PGRP2_HUMAN	N-acetylmuramoyl-L-alanine amidase precursor (EC 3.5.1.28) (Peptidoglycan recognition protein long) ...	0.24	-	nuc	0	Secreted protein. Membrane	intracellular [NAS] membrane [NAS]	608199		576
Q866Y3 UniProt NPD GO	PGRP2_PIG	N-acetylmuramoyl-L-alanine amidase precursor (EC 3.5.1.28) (Peptidoglycan recognition protein long) ...	0.24	-	cyt	0	Secreted protein. Membrane	intracellular [ISS] membrane [ISS]			598
Q5SCZ6 UniProt NPD GO	NU4C_HUPLU	NAD(P)H-quinone oxidoreductase chain 4, chloroplast (EC 1.6.5.-) (NAD(P)H dehydrogenase, chain 4) (N ...	0.24	-	end	13 *	Plastid; chloroplast				502
P51100 UniProt NPD GO	NU5C_GERJA	NAD(P)H-quinone oxidoreductase chain 5, chloroplast (EC 1.6.5.-) (NAD(P)H dehydrogenase, chain 5) (N ...	0.24	-	end	15 *	Plastid; chloroplast; chloroplast membrane; multi-pass membrane protein				744
P92251 UniProt NPD GO	NU5C_BRASY	NAD(P)H-quinone oxidoreductase chain 5, chloroplast (EC 1.6.5.-) (NAD(P)H dehydrogenase, chain 5) (N ...	0.24	-	end	2	Plastid; chloroplast; chloroplast membrane; multi-pass membrane protein				214
O94640 UniProt NPD GO	SIR2_SCHPO	NAD-dependent histone deacetylase sir2 (EC 3.5.1.-) (Regulatory protein sir2) (Silent information re ...	0.24	-	nuc	0	Nucleus. Nuclear throughout the cell cycle. Binds to centromeres, telomeric sites and sites between ...	chromosome, pericentric region [IDA] chromosome, telomeric region [IDA] mating-type region heterochromatin [IDA] nucleus [IDA]			475
Q02375 UniProt NPD GO	NUYM_BOVIN	NADH-ubiquinone oxidoreductase 18 kDa subunit, mitochondrial precursor (EC 1.6.5.3) (EC 1.6.99.3) (C ...	0.24	-	mit	0	Mitochondrion; mitochondrial inner membrane; matrix side				175
Q94VK0 UniProt NPD GO	NU1M_VARBA	NADH-ubiquinone oxidoreductase chain 1 (EC 1.6.5.3) (NADH dehydrogenase subunit 1)	0.24	-	end	7 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein (Probable)				321
Q94YT7 UniProt NPD GO	NU1M_VARDU	NADH-ubiquinone oxidoreductase chain 1 (EC 1.6.5.3) (NADH dehydrogenase subunit 1)	0.24	-	end	8 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein (Probable)				321
P03894 UniProt NPD GO	NU2M_XENLA	NADH-ubiquinone oxidoreductase chain 2 (EC 1.6.5.3) (NADH dehydrogenase subunit 2)	0.24	-	end	6 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				345
P03910 UniProt NPD GO	NU4M_BOVIN	NADH-ubiquinone oxidoreductase chain 4 (EC 1.6.5.3) (NADH dehydrogenase subunit 4)	0.24	-	end	12 *					459
P48916 UniProt NPD GO	NU4M_FELCA	NADH-ubiquinone oxidoreductase chain 4 (EC 1.6.5.3) (NADH dehydrogenase subunit 4)	0.24	-	end	12 *					459
P50665 UniProt NPD GO	NU5M_MACFA	NADH-ubiquinone oxidoreductase chain 5 (EC 1.6.5.3) (NADH dehydrogenase subunit 5) (Fragment)	0.24	-	nuc	2 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein (Probable)				79

You are viewing entries 46501 to 46550 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.