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
Q99965 UniProt NPD GO	ADAM2_HUMAN	ADAM 2 precursor (A disintegrin and metalloproteinase domain 2) (Fertilin subunit beta) (PH-30) (PH3 ...	0.27	-	end	1	Membrane; single-pass type I membrane protein	integral to plasma membrane [TAS]	601533		735
Q07959 UniProt NPD GO	IZH3_YEAST	ADIPOR-like receptor IZH3 (Implicated in zinc homeostasis protein 3)	0.27	-	end	7	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (Potential)	endoplasmic reticulum [IDA] membrane [TAS]			543
O22342 UniProt NPD GO	ADT1_GOSHI	ADP,ATP carrier protein 1, mitochondrial precursor (ADP/ATP translocase 1) (Adenine nucleotide trans ...	0.27	-	cyt	3	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein (By similarity)				386
P04366 UniProt NPD GO	AMBP_PIG	AMBP protein precursor [Contains: Alpha-1-microglobulin; Inter-alpha-trypsin inhibitor light chain ( ...	0.27	-	nuc	0	Secreted protein	extracellular region [ISS] plasma membrane [ISS]			337
P63010 UniProt NPD GO	AP2B1_HUMAN	AP-2 complex subunit beta-1 (Adapter-related protein complex 2 beta-1 subunit) (Beta-adaptin) (Plasm ...	0.27	-	end	0	Component of the coat surrounding the cytoplasmic face of coated vesicles in the plasma membrane		601025	2G30	937
Q9DBG3 UniProt NPD GO	AP2B1_MOUSE	AP-2 complex subunit beta-1 (Adapter-related protein complex 2 beta-1 subunit) (Beta-adaptin) (Plasm ...	0.27	-	end	0	Component of the coat surrounding the cytoplasmic face of coated vesicles in the plasma membrane				937
P62944 UniProt NPD GO	AP2B1_RAT	AP-2 complex subunit beta-1 (Adapter-related protein complex 2 beta-1 subunit) (Beta-adaptin) (Plasm ...	0.27	-	end	0	Component of the coat surrounding the cytoplasmic face of coated vesicles in the plasma membrane				937
Q9NQ94 UniProt NPD GO	ACF_HUMAN	APOBEC1 complementation factor (APOBEC1-stimulating protein)	0.27	-	nuc	0	Nucleus. Predominantly nuclear where it localizes to heterochromatin. Endoplasmic reticulum (By simi ...	apolipoprotein B mRNA editing enzyme complex [IDA] cytoplasm [IDA]		2CPD	594
Q5R9H4 UniProt NPD GO	ACF_PONPY	APOBEC1 complementation factor (APOBEC1-stimulating protein)	0.27	-	nuc	0	Nucleus (By similarity). Predominantly nuclear where it localizes to heterochromatin. Endoplasmic re ...	apolipoprotein B mRNA editing enzyme complex [ISS] cytoplasm [ISS]			587
Q00822 UniProt NPD GO	ATPF_ODOSI	ATP synthase B chain (EC 3.6.3.14) (ATPase subunit I)	0.27	-	nuc	0	Plastid; chloroplast; chloroplast thylakoid membrane				179
Q9MTL8 UniProt NPD GO	ATPF_OENHO	ATP synthase B chain (EC 3.6.3.14) (ATPase subunit I)	0.27	-	nuc	1 *	Plastid; chloroplast; chloroplast thylakoid membrane				184
P35012 UniProt NPD GO	ATPX_GALSU	ATP synthase B' chain (EC 3.6.3.14) (Subunit II)	0.27	-	nuc	1 *	Plastid; chloroplast; chloroplast thylakoid membrane				157
P30902 UniProt NPD GO	ATP7_YEAST	ATP synthase D chain, mitochondrial (EC 3.6.3.14)	0.27	-	nuc	0		proton-transporting ATP synthase, stator st... [IMP]			173
P02721 UniProt NPD GO	ATP5J_BOVIN	ATP synthase coupling factor 6, mitochondrial precursor (EC 3.6.3.14) (ATPase subunit F6)	0.27	-	mit	0				1VZS	108
Q01908 UniProt NPD GO	ATPG1_ARATH	ATP synthase gamma chain 1, chloroplast precursor (EC 3.6.3.14)	0.27	-	mit	0	Plastid; chloroplast; chloroplast thylakoid membrane				373
P82451 UniProt NPD GO	ABCC9_RABIT	ATP-binding cassette transporter sub-family C member 9 (Sulfonylurea receptor 2)	0.27	-	end	14 *	Membrane; multi-pass membrane protein (Potential)				1549
Q5KFM6 UniProt NPD GO	DBP2_CRYNE	ATP-dependent RNA helicase DBP2-A (EC 3.6.1.-)	0.27	+	cyt	0	Cytoplasm (By similarity). Nucleus (By similarity)				540
Q4HW67 UniProt NPD GO	DHH1_GIBZE	ATP-dependent RNA helicase DHH1 (EC 3.6.1.-)	0.27	-	cyt	0	Cytoplasm. Is concentrated in several cytoplasmic foci called P bodies (or cytoplasmic processing bo ...				486
Q925S8 UniProt NPD GO	YMEL1_RAT	ATP-dependent metalloprotease YME1L1 (EC 3.4.24.-) (YME1-like protein 1) (ATP-dependent metalloprote ...	0.27	-	mit	0	Mitochondrion (By similarity)				715
P17681 UniProt NPD GO	AGN3_APLBR	Abdominal ganglion neuropeptide R3-14 [Contains: Histidine-rich basic peptide (HRBP); Peptide I; Pep ...	0.27	-	nuc	0	Secreted protein				85
Q6BIY6 UniProt NPD GO	ACN9_DEBHA	Acetate non-utilizing protein 9, mitochondrial precursor	0.27	-	nuc	0	Mitochondrion; mitochondrial intermembrane space (By similarity)				121
P25162 UniProt NPD GO	ACH4_DROME	Acetylcholine receptor protein subunit beta-like 2 precursor	0.27	-	end	4	Membrane; multi-pass membrane protein				519
P48181 UniProt NPD GO	ACH2_CAEEL	Acetylcholine receptor subunit beta-type unc-29 precursor (Uncoordinated protein 29)	0.27	-	end	5 *	Membrane; multi-pass membrane protein	synapse [IDA]			493
P38433 UniProt NPD GO	ACE1_CAEEL	Acetylcholinesterase 1 precursor (EC 3.1.1.7) (AChE 1)	0.27	-	exc	0	Secreted protein (Potential). Membrane; peripheral membrane protein (Potential). May be secreted or ...	cell [IDA]			620
Q9DDE3 UniProt NPD GO	ACES_BRARE	Acetylcholinesterase precursor (EC 3.1.1.7) (AChE)	0.27	-	end	0					634
P10164 UniProt NPD GO	PRP2_RAT	Acidic proline-rich protein PRP25 precursor (Fragment)	0.27	-	exc	0					172
P08001 UniProt NPD GO	ACRO_PIG	Acrosin precursor (EC 3.4.21.10) (53 kDa fucose-binding protein) [Contains: Acrosin light chain; Acr ...	0.27	-	exc	0				1FIZ	415
Q25380 UniProt NPD GO	ACT4_LYTPI	Actin, cytoskeletal 4 (LPC4) (Fragment)	0.27	-	nuc	0	Cytoplasm. Cytoskeleton				154
Q9LQ81 UniProt NPD GO	ADFX_ARATH	Actin-depolymerizing factor-like At1g01750 (ADF-like)	0.27	-	nuc	0					140
Q9WVE0 UniProt NPD GO	AICDA_MOUSE	Activation-induced cytidine deaminase (EC 3.5.4.5) (Cytidine aminohydrolase)	0.27	-	cyt	0					198
Q9W7S2 UniProt NPD GO	ACL1_AGKAC	Acutolysin-1 precursor (EC 3.4.24.-)	0.27	-	nuc	0	Secreted protein (By similarity)				417
Q9TT94 UniProt NPD GO	ACOD_BOVIN	Acyl-CoA desaturase (EC 1.14.19.1) (Stearoyl-CoA desaturase) (Fatty acid desaturase) (Delta(9)-desat ...	0.27	-	end	4	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (Probable)				359
Q42770 UniProt NPD GO	STAD_GOSHI	Acyl-[acyl-carrier-protein] desaturase, chloroplast precursor (EC 1.14.19.2) (Stearoyl-ACP desaturas ...	0.27	-	mit	0	Plastid; chloroplast (By similarity). In green tissue, found in chloroplasts. Plastid (By similarity ...				397
Q6CKK7 UniProt NPD GO	ACOX_KLULA	Acyl-coenzyme A oxidase (EC 1.3.3.6) (Acyl-CoA oxidase)	0.27	-	mit	0	Peroxisome (By similarity)				736
O64894 UniProt NPD GO	ACOX2_CUCMA	Acyl-coenzyme A oxidase, peroxisomal precursor (EC 1.3.3.6) (AOX) (Long-chain acyl-CoA oxidase)	0.27	-	nuc	0	Peroxisome. Glyoxysome				690
P55263 UniProt NPD GO	ADK_HUMAN	Adenosine kinase (EC 2.7.1.20) (AK) (Adenosine 5'-phosphotransferase)	0.27	-	cyt	0			102750	1BX4	362
Q08828 UniProt NPD GO	ADCY1_HUMAN	Adenylate cyclase type 1 (EC 4.6.1.1) (Adenylate cyclase type I) (ATP pyrophosphate-lyase 1) (Ca(2+) ...	0.27	-	end	9	Membrane; multi-pass membrane protein	integral to membrane [NAS]	103072		1119
P40123 UniProt NPD GO	CAP2_HUMAN	Adenylyl cyclase-associated protein 2 (CAP 2)	0.27	-	nuc	0	Cell membrane (By similarity)				477
P52481 UniProt NPD GO	CAP2_RAT	Adenylyl cyclase-associated protein 2 (CAP 2)	0.27	-	nuc	0	Cell membrane (By similarity)				477
Q02196 UniProt NPD GO	KAPS_YEAST	Adenylyl-sulfate kinase (EC 2.7.1.25) (APS kinase) (Adenosine-5'phosphosulfate kinase) (ATP adenosin ...	0.27	-	nuc	0		cytoplasm [TAS] intracellular [IDA]			202
P02876 UniProt NPD GO	AGI2_WHEAT	Agglutinin isolectin 2 precursor (WGA2) (Isolectin D)	0.27	-	exc	1 *				9WGA	213
P07898 UniProt NPD GO	PGCA_CHICK	Aggrecan core protein precursor (Cartilage-specific proteoglycan core protein) (CSPCP)	0.27	-	cyt	0	Secreted protein; extracellular space; extracellular matrix (By similarity)				2109
P23110 UniProt NPD GO	2SS8_HELAN	Albumin-8 precursor (Methionine-rich 2S protein) (SFA8)	0.27	-	exc	0				1S6D	141
P40353 UniProt NPD GO	ATF1_YEAST	Alcohol O-acetyltransferase 1 (EC 2.3.1.84) (AATase 1)	0.27	-	cyt	0	Membrane; peripheral membrane protein	endomembrane system [TAS] lipid particle [IDA]			525
Q5TM25 UniProt NPD GO	AIF1_MACMU	Allograft inflammatory factor 1 (AIF-1)	0.27	-	nuc	0					147
P02508 UniProt NPD GO	CRYAA_RANTE	Alpha crystallin A chain (Fragment)	0.27	-	nuc	0					149
P02472 UniProt NPD GO	CRYAA_CAMDR	Alpha crystallin A chain [Contains: Alpha crystallin A chain, short form]	0.27	-	cyt	0					173
P02486 UniProt NPD GO	CRYAA_CHOHO	Alpha crystallin A chain [Contains: Alpha crystallin A chain, short form]	0.27	-	cyt	0					170
P02477 UniProt NPD GO	CRYAA_PHOPH	Alpha crystallin A chain [Contains: Alpha crystallin A chain, short form]	0.27	-	mit	0					173
P02480 UniProt NPD GO	CRYAA_URSUR	Alpha crystallin A chain [Contains: Alpha crystallin A chain, short form]	0.27	-	mit	0					173

You are viewing entries 42901 to 42950 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.