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
O04161 UniProt NPD GO	AMT12_LYCES	Ammonium transporter 1 member 2 (LeAMT1;2)	0.00	-	end	11 *	Membrane; multi-pass membrane protein (Probable)				514
Q9FVN0 UniProt NPD GO	AMT13_LYCES	Ammonium transporter 1 member 3 (LeAMT1;3)	0.00	-	end	10 *	Membrane; multi-pass membrane protein (Probable)				460
Q28053 UniProt NPD GO	A4_BOVIN	Amyloid beta A4 protein (APP) (ABPP) (Alzheimer disease amyloid A4 protein homolog) [Contains: Solub ...	0.00	-	nuc	1 *	Membrane; single-pass type I membrane protein				59
Q28280 UniProt NPD GO	A4_CANFA	Amyloid beta A4 protein (APP) (ABPP) (Alzheimer disease amyloid A4 protein homolog) [Contains: Solub ...	0.00	-	mit	1 *	Membrane; single-pass type I membrane protein				58
Q28748 UniProt NPD GO	A4_RABIT	Amyloid beta A4 protein (APP) (ABPP) (Alzheimer disease amyloid A4 protein homolog) [Contains: Solub ...	0.00	-	nuc	1 *	Membrane; single-pass type I membrane protein				58
Q28757 UniProt NPD GO	A4_SHEEP	Amyloid beta A4 protein (APP) (ABPP) (Alzheimer disease amyloid A4 protein homolog) [Contains: Solub ...	0.00	-	nuc	1 *	Membrane; single-pass type I membrane protein				58
Q29149 UniProt NPD GO	A4_URSMA	Amyloid beta A4 protein (APP) (ABPP) (Alzheimer disease amyloid A4 protein homolog) [Contains: Solub ...	0.00	-	mit	1 *	Membrane; single-pass type I membrane protein				57
Q9NVV5 UniProt NPD GO	AIG1_HUMAN	Androgen-induced protein 1 (AIG-1)	0.00	-	end	6 *	Membrane; multi-pass membrane protein (Potential)		608514		245
O16825 UniProt NPD GO	ANDP_DROMA	Andropin precursor	0.00	-	exc	1 *	Secreted protein	extracellular region [ISS]			57
P21663 UniProt NPD GO	ANDP_DROME	Andropin precursor	0.00	-	exc	1 *	Secreted protein	extracellular region [IDA]			57
Q8WSV2 UniProt NPD GO	ANDP_DROSE	Andropin precursor	0.00	-	exc	1 *	Secreted protein	extracellular region [ISS]			57
Q8WSV4 UniProt NPD GO	ANDP_DROSI	Andropin precursor	0.00	-	exc	1 *	Secreted protein	extracellular region [ISS]			60
Q8WPA1 UniProt NPD GO	ANDP_DROYA	Andropin precursor	0.00	-	exc	1 *	Secreted protein	extracellular region [ISS]			60
P12820 UniProt NPD GO	ACE_BOVIN	Angiotensin-converting enzyme, somatic (EC 3.4.15.1) (ACE) (Dipeptidyl carboxypeptidase I) (Kininase ...	0.00	-	cyt	0					22
Q5G8A9 UniProt NPD GO	AP10_TITCO	Anionic peptide clone 10 precursor	0.00	-	exc	1 *	Secreted protein				74
Q5G8B2 UniProt NPD GO	AP7_TITCO	Anionic peptide clone 7 precursor	0.00	-	exc	1 *	Secreted protein				74
Q5G8B1 UniProt NPD GO	AP8_TITCO	Anionic peptide clone 8 precursor	0.00	-	exc	1 *	Secreted protein				74
Q5G8B0 UniProt NPD GO	AP9_TITCO	Anionic peptide clone 9 precursor	0.00	-	exc	1 *	Secreted protein				74
Q9CQ31 UniProt NPD GO	ASB11_MOUSE	Ankyrin repeat and SOCS box protein 11 (ASB-11)	0.00	-	nuc	1 *					323
P81285 UniProt NPD GO	OBPA_MAMBR	Antennal odorant-binding protein (AOBP) (Fragment)	0.00	-		0					15
P13447 UniProt NPD GO	LAT52_LYCES	Anther-specific protein LAT52 precursor	0.00	-	exc	0					161
Q6WY08 UniProt NPD GO	ATLE_AGRAE	Anti-tumor lectin (EC 3.1.21.-) (AAL) (Fragment)	0.00	-	cyt	0					158
P84061 UniProt NPD GO	AFP_DIOTE	Antifungal protein (Fragment)	0.00	-	cyt	0					30
P33045 UniProt NPD GO	THHS_HORVU	Antifungal protein S (Fragment)	0.00	-	cyt	0					37
P17737 UniProt NPD GO	AFP_ASPGI	Antifungal protein precursor	0.00	-	exc	0	Secreted protein			1AFP	94
P81418 UniProt NPD GO	PAFP_PHYAM	Antimicrobial peptide 1 precursor (AMP1) (Pa-AMP-1) (Anti-fungal protein 1) (AFPS-1) (PAFP-S)	0.00	-	exc	1 *	Secreted protein			1DKC	65
P84382 UniProt NPD GO	XT2_XENTR	Antimicrobial peptide 2 (XT-2)	0.00	-	nuc	0	Secreted protein	extracellular region [IDA]			25
P27275 UniProt NPD GO	AMP_AMACA	Antimicrobial peptide 2 precursor (AMP2) [Contains: Antimicrobial peptide 1 (AMP1)]	0.00	-	cyt	1 *				1ZWU	86
P84384 UniProt NPD GO	XT4_XENTR	Antimicrobial peptide 4 (XT-4)	0.00	-	cyt	0	Secreted protein	extracellular region [IDA]			22
P84385 UniProt NPD GO	XT5_XENTR	Antimicrobial peptide 5 (XT-5) (PGLa-like peptide)	0.00	-	cyt	0	Secreted protein	extracellular region [IDA]			22
P84381 UniProt NPD GO	XT7_XENTR	Antimicrobial peptide 7 (XT-7)	0.00	-		0	Secreted protein	extracellular region [IDA]			18
P39080 UniProt NPD GO	PGQ_XENLA	Antimicrobial peptide PGQ	0.00	-	cyt	0	Secreted protein				24
P09465 UniProt NPD GO	APHR_CRICR	Aphrodisin precursor	0.00	-	exc	0	Secreted protein			1E5P	167
Q9Z1I7 UniProt NPD GO	APHR_MESAU	Aphrodisin precursor	0.00	-	exc	0	Secreted protein				167
P18657 UniProt NPD GO	APOC1_MACFA	Apolipoprotein C-I (Apo-CI) (ApoC-I) (Fragment)	0.00	-	nuc	0	Secreted protein				22
P33047 UniProt NPD GO	APOC1_RABIT	Apolipoprotein C-I (Apo-CI) (ApoC-I) (Fragment)	0.00	-	cyt	0	Secreted protein				28
P34928 UniProt NPD GO	APOC1_MOUSE	Apolipoprotein C-I precursor (Apo-CI) (ApoC-I)	0.00	-	mit	0	Secreted protein				88
P51909 UniProt NPD GO	APOD_CAVPO	Apolipoprotein D precursor (Apo-D) (ApoD)	0.00	-	nuc	0	Secreted protein				189
P49268 UniProt NPD GO	TXP3_APTSC	Aptotoxin-3 (Aptotoxin III) (Paralytic peptide III) (PP III)	0.00	-	nuc	0	Secreted protein				37
O96559 UniProt NPD GO	APY_CIMLE	Apyrase precursor (EC 3.6.1.5)	0.00	-	mit	1 *		extracellular space [NAS]			364
Q25074 UniProt NPD GO	AQP_HAEIE	Aquaporin (Water channel 1) (BfWC1)	0.00	-	end	6 *	Membrane; multi-pass membrane protein				251
Q8VZW1 UniProt NPD GO	NIP11_ARATH	Aquaporin NIP1.1 (NOD26-like intrinsic protein 1.1) (Nodulin-26-like major intrinsic protein 1) (AtN ...	0.00	-	end	6	Membrane; multi-pass membrane protein (Probable)				296
P25818 UniProt NPD GO	TIP11_ARATH	Aquaporin TIP1.1 (Tonoplast intrinsic protein 1.1) (Gamma-tonoplast intrinsic protein) (Gamma-TIP) ( ...	0.00	-	end	7 *	Vacuole; vacuolar membrane; multi-pass membrane protein (By similarity). Tonoplast. Specifically loc ...				251
Q41963 UniProt NPD GO	TIP12_ARATH	Aquaporin TIP1.2 (Tonoplast intrinsic protein 1.2) (Gamma-tonoplast intrinsic protein 2) (Gamma-TIP2 ...	0.00	-	end	7 *	Vacuole; vacuolar membrane; multi-pass membrane protein (By similarity). Tonoplast				253
Q41951 UniProt NPD GO	TIP21_ARATH	Aquaporin TIP2.1 (Tonoplast intrinsic protein 2.1) (Delta-tonoplast intrinsic protein) (Delta-TIP)	0.00	-	end	6 *	Vacuole; vacuolar membrane; multi-pass membrane protein (By similarity). Tonoplast. It is specifical ...				250
P26587 UniProt NPD GO	TIP31_ARATH	Aquaporin TIP3.1 (Tonoplast intrinsic protein 3.1) (Alpha-tonoplast intrinsic protein) (Alpha-TIP)	0.00	-	end	5 *	Vacuole; vacuolar membrane; multi-pass membrane protein. Tonoplast. It is specifically located in th ...				268
O77697 UniProt NPD GO	AQP2_AMBHO	Aquaporin-2 (AQP-2) (Aquaporin-CD) (AQP-CD) (Water channel protein for renal collecting duct) (ADH w ...	0.00	-	end	3 *	Membrane; multi-pass membrane protein				109
P79099 UniProt NPD GO	AQP2_BOVIN	Aquaporin-2 (AQP-2) (Aquaporin-CD) (AQP-CD) (Water channel protein for renal collecting duct) (ADH w ...	0.00	-	end	3 *	Membrane; multi-pass membrane protein				109
P79144 UniProt NPD GO	AQP2_CANFA	Aquaporin-2 (AQP-2) (Aquaporin-CD) (AQP-CD) (Water channel protein for renal collecting duct) (ADH w ...	0.00	-	end	3 *	Membrane; multi-pass membrane protein				109
P79164 UniProt NPD GO	AQP2_DASNO	Aquaporin-2 (AQP-2) (Aquaporin-CD) (AQP-CD) (Water channel protein for renal collecting duct) (ADH w ...	0.00	-	end	3 *	Membrane; multi-pass membrane protein				109

You are viewing entries 92701 to 92750 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.