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
P04749 UniProt NPD GO	AMY5_HORVU	Alpha-amylase type B isozyme (EC 3.2.1.1) (1,4-alpha-D-glucan glucanohydrolase) (Clone 168) (Fragmen ...	0.02	-	cyt	0					135
P04750 UniProt NPD GO	AMY6_HORVU	Alpha-amylase type B isozyme precursor (EC 3.2.1.1) (1,4-alpha-D-glucan glucanohydrolase) (Clones GR ...	0.02	-	exc	1 *					429
O18552 UniProt NPD GO	AMYR_DROPS	Alpha-amylase-related protein precursor (EC 3.2.1.1)	0.02	-	cyt	0	Secreted protein (Probable)				494
O76260 UniProt NPD GO	AMYR_DROTE	Alpha-amylase-related protein precursor (EC 3.2.1.1)	0.02	-	nuc	0	Secreted protein (Probable)				493
P16851 UniProt NPD GO	IAAC2_WHEAT	Alpha-amylase/trypsin inhibitor CM2 precursor (Chloroform/methanol-soluble protein CM2)	0.02	-	exc	1 *	Secreted protein				145
P01520 UniProt NPD GO	CXA2_CONGE	Alpha-conotoxin GII	0.02	-		0	Secreted protein				13
Q6PTD4 UniProt NPD GO	CX12_CONLE	Alpha-conotoxin Lp1.2 precursor	0.02	-	end	1 *	Secreted protein				68
P0C1R7 UniProt NPD GO	CXAA_CONOM	Alpha-conotoxin OmIA precursor	0.02	-		0	Secreted protein				17
Q1L777 UniProt NPD GO	CXA1_CONPR	Alpha-conotoxin PeIA precursor (Fragment)	0.02	-	nuc	0	Secreted protein				38
P28878 UniProt NPD GO	CAS1A_CONST	Alpha-conotoxin SIA (S1A)	0.02	-		0	Secreted protein				13
P17182 UniProt NPD GO	ENOA_MOUSE	Alpha-enolase (EC 4.2.1.11) (2-phospho-D-glycerate hydro-lyase) (Non-neural enolase) (NNE) (Enolase ...	0.02	-	cyt	0	Cytoplasm (By similarity). Cell membrane (By similarity). Can translocate to the plasma membrane in ...				433
P04764 UniProt NPD GO	ENOA_RAT	Alpha-enolase (EC 4.2.1.11) (2-phospho-D-glycerate hydro-lyase) (Non-neural enolase) (NNE) (Enolase ...	0.02	-	mit	0	Cytoplasm. Cell membrane. Can translocate to the plasma membrane in either the homodimeric (alpha/al ...				433
Q9PVK2 UniProt NPD GO	ENOA_ALLMI	Alpha-enolase (EC 4.2.1.11) (2-phospho-D-glycerate hydro-lyase) (Phosphopyruvate hydratase)	0.02	-	nuc	0	Cytoplasm				433
Q9W7L1 UniProt NPD GO	ENOA_TRASC	Alpha-enolase (EC 4.2.1.11) (2-phospho-D-glycerate hydro-lyase) (Phosphopyruvate hydratase)	0.02	-	mit	0	Cytoplasm				433
Q9LQ07 UniProt NPD GO	EXP18_ARATH	Alpha-expansin 18 precursor (AtEXPA18) (At-EXP18) (AtEx18) (Ath-ExpAlpha-1.25)	0.02	-	mit	1 *	Cell wall; peripheral membrane protein				257
P29752 UniProt NPD GO	LALBA_MOUSE	Alpha-lactalbumin precursor (Lactose synthase B protein)	0.02	-	exc	0	Secreted protein			2FYD	143
P81893 UniProt NPD GO	L2AM_DROSI	Alpha-methyldopa hypersensitive protein (EC 4.1.1.-) (Fragment)	0.02	-	cyt	0					328
P60258 UniProt NPD GO	SCXD_BUTOM	Alpha-neurotoxin Bom alpha-6d	0.02	-	nuc	0	Secreted protein				70
P60259 UniProt NPD GO	SCXE_BUTOM	Alpha-neurotoxin Bom alpha-6e	0.02	-	nuc	0	Secreted protein				66
Q9NJC7 UniProt NPD GO	SC11_MESMA	Alpha-neurotoxin TX11 precursor (Toxin BmTX11') (BmKalphaTx11) (BmKalphaTx11') (Alpha-toxin 2) (BmKa ...	0.02	-	exc	0	Secreted protein				85
Q9NJC4 UniProt NPD GO	SC17_MESMA	Alpha-neurotoxin TX17 precursor (BmKalphaTx17) (Fragment)	0.02	-	nuc	0	Secreted protein				74
P58370 UniProt NPD GO	NXAH8_MICCO	Alpha-neurotoxin homolog 8 precursor	0.02	-	mit	0	Secreted protein				86
Q9GUA7 UniProt NPD GO	SCA3_MESMA	Alpha-toxin 3 precursor (BmKalpha3)	0.02	-	exc	0	Secreted protein (By similarity)				85
P84614 UniProt NPD GO	SCX28_BUTSI	Alpha-toxin Bs-Tx28	0.02	-	nuc	0	Secreted protein				65
Q07185 UniProt NPD GO	AOX1_SOYBN	Alternative oxidase 1, mitochondrial precursor (EC 1.-.-.-)	0.02	-	mit	0	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein (Probable). Mitochondrial, ...				321
P08944 UniProt NPD GO	ALYT_ALYOB	Alytesin	0.02	-		0	Secreted protein				14
Q925H0 UniProt NPD GO	ACCN1_MOUSE	Amiloride-sensitive cation channel 1, neuronal (Amiloride-sensitive brain sodium channel) (Acid-sens ...	0.02	-	cyt	0	Cell membrane; multi-pass membrane protein. Localized at the plasma membrane, in the soma and puncta ...	cell soma [IDA] integral to plasma membrane [IDA] neuron projection [IDA]			512
Q62962 UniProt NPD GO	ACCN1_RAT	Amiloride-sensitive cation channel 1, neuronal (Amiloride-sensitive brain sodium channel) (Amiloride ...	0.02	-	cyt	0	Cell membrane; multi-pass membrane protein. Localized at the plasma membrane of neurons, in the soma ...				512
Q7YRB7 UniProt NPD GO	AOFB_CANFA	Amine oxidase [flavin-containing] B (EC 1.4.3.4) (Monoamine oxidase type B) (MAO-B)	0.02	-	cyt	1	Mitochondrion; mitochondrial outer membrane (By similarity)				519
P48015 UniProt NPD GO	GCST_YEAST	Aminomethyltransferase, mitochondrial precursor (EC 2.1.2.10) (Glycine cleavage system T protein) (G ...	0.02	-	mit	0	Mitochondrion	glycine cleavage complex [TAS] mitochondrion [IDA]			400
P37302 UniProt NPD GO	APE3_YEAST	Aminopeptidase Y precursor (EC 3.4.11.15)	0.02	-	cyt	0	Vacuole. Lysosome-like vacuoles	vacuole (sensu Fungi) [IDA]			537
P02738 UniProt NPD GO	SAA_MACMU	Amyloid protein A (Amyloid fibril protein AA)	0.02	-	cyt	0					76
Q9CPX9 UniProt NPD GO	APC11_MOUSE	Anaphase-promoting complex subunit 11 (APC11) (Cyclosome subunit 11)	0.02	-	cyt	0	Cytoplasm (By similarity). Nucleus (By similarity)				84
Q5R8A2 UniProt NPD GO	APC11_PONPY	Anaphase-promoting complex subunit 11 (APC11) (Cyclosome subunit 11)	0.02	-	cyt	0	Cytoplasm (By similarity). Nucleus (By similarity)				84
Q9NYG5 UniProt NPD GO	APC11_HUMAN	Anaphase-promoting complex subunit 11 (APC11) (Cyclosome subunit 11) (Hepatocellular carcinoma-assoc ...	0.02	-	cyt	0	Cytoplasm. Nucleus	anaphase-promoting complex [IDA]			84
Q8WSV1 UniProt NPD GO	ANDP_DROTE	Andropin precursor	0.02	-	vac	0	Secreted protein	extracellular region [ISS]			62
Q10757 UniProt NPD GO	ANGT_THETS	Angiotensin (Fragment)	0.02	-		0					14
Q10582 UniProt NPD GO	ANGT2_BOTJA	Angiotensin-like peptide 2 (Fragment)	0.02	-		0					8
P01016 UniProt NPD GO	ANGT_HORSE	Angiotensinogen [Contains: Angiotensin-1 (Angiotensin I) (Ang I); Angiotensin-2 (Angiotensin II) (An ...	0.02	-		0	Secreted protein			1ER8	14
Q8WXK3 UniProt NPD GO	ASB13_HUMAN	Ankyrin repeat and SOCS box protein 13 (ASB-13)	0.02	-	cyt	0					278
Q8HXA6 UniProt NPD GO	ASB15_BOVIN	Ankyrin repeat and SOCS box protein 15 (ASB-15)	0.02	-	cyt	0					588
Q91ZT9 UniProt NPD GO	ASB8_MOUSE	Ankyrin repeat and SOCS box protein 8 (ASB-8)	0.02	-	cyt	0	Cytoplasm (By similarity)				288
P42998 UniProt NPD GO	OXYT_EISFO	Annetocin	0.02	-		0	Secreted protein				9
P0C005 UniProt NPD GO	ANOP_ANOSM	Anoplin	0.02	-		0	Secreted protein				10
P41507 UniProt NPD GO	BCP1_BRACM	Anther-specific protein BCP1	0.02	-	exc	2 *					119
P58706 UniProt NPD GO	FYRI_ANTEL	Antho-RIamide-1 (Antho-RIamide I) [Contains: Antho-RIamide-2 (Antho-RIamide II)]	0.02	-		0	Secreted protein				4
P58707 UniProt NPD GO	FLRN_ANTEL	Antho-RNamide	0.02	-		0	Secreted protein				4
Q40289 UniProt NPD GO	UFOG7_MANES	Anthocyanidin 3-O-glucosyltransferase (EC 2.4.1.115) (Flavonol 3-O-glucosyltransferase 7) (UDP-gluco ...	0.02	+	nuc	0					287
P16165 UniProt NPD GO	UFO2_MAIZE	Anthocyanidin 3-O-glucosyltransferase (EC 2.4.1.115) (Flavonol 3-O-glucosyltransferase) (UDP-glucose ...	0.02	-	mit	0					471
P16166 UniProt NPD GO	UFO1_MAIZE	Anthocyanidin 3-O-glucosyltransferase (EC 2.4.1.115) (Flavonol 3-O-glucosyltransferase) (UDP-glucose ...	0.02	-	mit	0					471

You are viewing entries 82451 to 82500 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.