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
Q03144 UniProt NPD GO	SNO1_YEAST	Probable glutamine amidotransferase SNO1 (EC 2.6.-.-)	0.04	-	cyt	0		cytoplasm [IDA]			224
P53823 UniProt NPD GO	SNO2_YEAST	Probable glutamine amidotransferase SNO2 (EC 2.6.-.-)	0.04	-	cyt	0					222
P43544 UniProt NPD GO	SNO3_YEAST	Probable glutamine amidotransferase SNO3 (EC 2.6.-.-)	0.04	-	cyt	0					222
O04922 UniProt NPD GO	GPX2_ARATH	Probable glutathione peroxidase 2 (EC 1.11.1.9)	0.04	-	cyt	0					169
Q21508 UniProt NPD GO	ILA2_CAEEL	Probable insulin-like peptide alpha-type 2 precursor	0.04	-	nuc	0	Secreted protein (Potential)				83
Q9VWH4 UniProt NPD GO	IDH3A_DROME	Probable isocitrate dehydrogenase [NAD] subunit alpha, mitochondrial precursor (EC 1.1.1.41) (Isocit ...	0.04	-	pox	0	Mitochondrion (By similarity)	mitochondrion [ISS]			377
Q68G31 UniProt NPD GO	MAWBP_RAT	Probable isomerase MAWBP (EC 5.1.-.-)	0.04	-	cyt	0					288
Q8H0Q5 UniProt NPD GO	THNX_HORVU	Probable leaf thionin precursor [Contains: Probable leaf thionin; Acidic protein]	0.04	-	nuc	0	Secreted protein (Potential)				137
Q53RB0 UniProt NPD GO	LOX4_ORYSA	Probable lipoxygenase 4 (EC 1.13.11.12)	0.04	-	cyt	0					877
Q9ZUL7 UniProt NPD GO	LCR68_ARATH	Probable low-molecular-weight cysteine-rich protein LCR68 precursor	0.04	-	mit	1 *	Secreted protein (Potential)				77
Q02971 UniProt NPD GO	MTDH1_ARATH	Probable mannitol dehydrogenase 1 (EC 1.1.1.255) (NAD-dependent mannitol dehydrogenase 1)	0.04	-	cyt	0					357
Q02972 UniProt NPD GO	MTDH2_ARATH	Probable mannitol dehydrogenase 2 (EC 1.1.1.255) (NAD-dependent mannitol dehydrogenase 2)	0.04	-	cyt	0					359
P34650 UniProt NPD GO	MANA_CAEEL	Probable mannose-6-phosphate isomerase (EC 5.3.1.8) (Phosphomannose isomerase) (PMI) (Phosphohexomut ...	0.04	-	cyt	0	Cytoplasm (By similarity)				416
P38142 UniProt NPD GO	YB91_YEAST	Probable metabolite transport protein YBR241C	0.04	-	end	11 *	Membrane; multi-pass membrane protein (Probable)	vacuolar membrane (sensu Fungi) [IDA]			488
Q9UUF2 UniProt NPD GO	SYMC_SCHPO	Probable methionyl-tRNA synthetase, cytoplasmic (EC 6.1.1.10) (Methionine--tRNA ligase) (MetRS)	0.04	-	nuc	0	Cytoplasm (Potential)				782
Q7KW39 UniProt NPD GO	MMSA_DROME	Probable methylmalonate-semialdehyde dehydrogenase [acylating], mitochondrial precursor (EC 1.2.1.27 ...	0.04	-	nuc	0	Mitochondrion (By similarity)	mitochondrion [ISS]			520
Q10259 UniProt NPD GO	SPC3_SCHPO	Probable microsomal signal peptidase subunit 3 (EC 3.4.-.-)	0.04	-	mit	1 *	Microsome; microsomal membrane; single-pass type II membrane protein (Potential)				185
Q61Z83 UniProt NPD GO	TOM40_CAEBR	Probable mitochondrial import receptor subunit TOM40 homolog (Translocase of outer membrane 40 kDa s ...	0.04	-	cyt	0	Mitochondrion; mitochondrial outer membrane; multi-pass membrane protein (By similarity)				301
Q18090 UniProt NPD GO	TOM40_CAEEL	Probable mitochondrial import receptor subunit TOM40 homolog (Translocase of outer membrane 40 kDa s ...	0.04	-	cyt	0	Mitochondrion; mitochondrial outer membrane; multi-pass membrane protein (By similarity)				301
Q6P825 UniProt NPD GO	TOM40_XENTR	Probable mitochondrial import receptor subunit TOM40 homolog (Translocase of outer membrane 40 kDa s ...	0.04	-	mit	0	Mitochondrion; mitochondrial outer membrane; multi-pass membrane protein (By similarity)				336
Q2KI08 UniProt NPD GO	TOM7_BOVIN	Probable mitochondrial import receptor subunit TOM7 homolog (Translocase of outer membrane 7 kDa sub ...	0.04	-	cyt	1 *	Mitochondrion; mitochondrial outer membrane; multi-pass membrane protein (By similarity)				55
Q9P0U1 UniProt NPD GO	TOM7_HUMAN	Probable mitochondrial import receptor subunit TOM7 homolog (Translocase of outer membrane 7 kDa sub ...	0.04	-	mit	1 *	Mitochondrion; mitochondrial outer membrane; multi-pass membrane protein		607980		55
Q9D173 UniProt NPD GO	TOM7_MOUSE	Probable mitochondrial import receptor subunit TOM7 homolog (Translocase of outer membrane 7 kDa sub ...	0.04	-	mit	1 *	Mitochondrion; mitochondrial outer membrane; multi-pass membrane protein (By similarity)				55
O04404 UniProt NPD GO	NLT12_PARJU	Probable nonspecific lipid-transfer protein 1 precursor (LTP) (Major pollen allergen Par j 1.0102) ( ...	0.04	-	exc	1 *					176
Q8IUH4 UniProt NPD GO	ZDH13_HUMAN	Probable palmitoyltransferase ZDHHC13 (EC 2.3.1.-) (Zinc finger DHHC domain-containing protein 13) ( ...	0.04	-	end	6	Membrane; multi-pass membrane protein (Potential)				622
Q6UX98 UniProt NPD GO	ZDH24_HUMAN	Probable palmitoyltransferase ZDHHC24 (EC 2.3.1.-) (Zinc finger DHHC domain-containing protein 24) ( ...	0.04	-	end	5 *	Membrane; multi-pass membrane protein (Potential)				284
Q58DT3 UniProt NPD GO	ZDHC4_BOVIN	Probable palmitoyltransferase ZDHHC4 (EC 2.3.1.-) (Zinc finger DHHC domain-containing protein 4) (DH ...	0.04	-	end	5 *	Membrane; multi-pass membrane protein (Potential)				343
Q9NPG8 UniProt NPD GO	ZDHC4_HUMAN	Probable palmitoyltransferase ZDHHC4 (EC 2.3.1.-) (Zinc finger DHHC domain-containing protein 4) (DH ...	0.04	-	end	5 *	Membrane; multi-pass membrane protein (Potential)				344
Q9LRR9 UniProt NPD GO	GOX2_ARATH	Probable peroxisomal (S)-2-hydroxy-acid oxidase 2 (EC 1.1.3.15) (Glycolate oxidase 2) (GOX 2) (Short ...	0.04	-	nuc	0	Peroxisome (By similarity)				367
O74770 UniProt NPD GO	PHK_SCHPO	Probable phosphoketolase (EC 4.1.2.-)	0.04	-	cyt	0					825
P91856 UniProt NPD GO	SERC_CAEEL	Probable phosphoserine aminotransferase (EC 2.6.1.52) (PSAT)	0.04	-	cyt	0					370
Q7XR51 UniProt NPD GO	PHYK1_ORYSA	Probable phytol kinase 1, chloroplast precursor (EC 2.7.-.-)	0.04	-	end	8 *	Plastid; chloroplast; chloroplast membrane; multi-pass membrane protein (Potential)				314
P51351 UniProt NPD GO	RRP3_PORPU	Probable plastid-specific 30S ribosomal protein 3 (PSRP-3)	0.04	-	cyt	0	Plastid; chloroplast				99
Q69RI8 UniProt NPD GO	HAK14_ORYSA	Probable potassium transporter 14 (OsHAK14)	0.04	-	end	12	Membrane; multi-pass membrane protein (By similarity)				859
Q9M4B5 UniProt NPD GO	PFD4_ARATH	Probable prefoldin subunit 4 (ABI3-interacting protein 3)	0.04	-	cyt	0					128
Q00826 UniProt NPD GO	PSB2_CRYNE	Probable proteasome subunit beta type 2 (EC 3.4.25.1)	0.04	-	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity)				224
Q9URX7 UniProt NPD GO	ANM1_SCHPO	Probable protein arginine N-methyltransferase (EC 2.1.1.-)	0.04	-	cyt	0		nucleus [IDA]			339
P55868 UniProt NPD GO	XAG_XENLA	Probable secreted protein XAG precursor	0.04	-	end	0	Secreted protein (Probable)				183
Q9MA96 UniProt NPD GO	SPCS3_ARATH	Probable signal peptidase complex subunit 3 (EC 3.4.-.-) (Microsomal signal peptidase 22 kDa subunit ...	0.04	-	exc	1 *	Microsome; microsomal membrane; single-pass type II membrane protein (Potential)				167
Q9VXE0 UniProt NPD GO	RUXG_DROME	Probable small nuclear ribonucleoprotein G (snRNP-G) (Sm protein G) (Sm-G) (SmG)	0.04	-	cyt	0	Nucleus (By similarity)				76
Q6ZL94 UniProt NPD GO	SUCA_ORYSA	Probable succinyl-CoA ligase [GDP-forming] subunit alpha, mitochondrial precursor (EC 6.2.1.4) (Succ ...	0.04	-	mit	0	Mitochondrion (By similarity)				331
Q09450 UniProt NPD GO	SCOT_CAEEL	Probable succinyl-CoA:3-ketoacid-coenzyme A transferase, mitochondrial precursor (EC 2.8.3.5) (3-oxo ...	0.04	-	mit	0	Mitochondrion (By similarity)				521
Q8GYH8 UniProt NPD GO	SUT42_ARATH	Probable sulfate transporter 4.2	0.04	-	end	12	Membrane; multi-pass membrane protein (Potential)				677
Q9C8D6 UniProt NPD GO	THN24_ARATH	Probable thionin-2.4 precursor [Contains: Probable thionin-2.4; Acidic protein]	0.04	-	nuc	0	Secreted protein (Potential)				134
Q6CIR6 UniProt NPD GO	ETR1_KLULA	Probable trans-2-enoyl-CoA reductase, mitochondrial precursor (EC 1.3.1.38)	0.04	-	mit	0	Mitochondrion (By similarity)				382
Q10488 UniProt NPD GO	ETR1_SCHPO	Probable trans-2-enoyl-CoA reductase, mitochondrial precursor (EC 1.3.1.38)	0.04	-	mit	0	Mitochondrion; mitochondrial matrix (By similarity)				372
Q59MJ2 UniProt NPD GO	MCH1_CANAL	Probable transporter MCH1	0.04	-	end	10 *	Vacuole; vacuolar membrane; multi-pass membrane protein (By similarity)				436
Q6CGU8 UniProt NPD GO	MCH1_YARLI	Probable transporter MCH1	0.04	-	end	11 *	Vacuole; vacuolar membrane; multi-pass membrane protein (By similarity)				486
O74433 UniProt NPD GO	UCR9_SCHPO	Probable ubiquinol-cytochrome c reductase complex subunit 9 (EC 1.10.2.2) (Complex III polypeptide I ...	0.04	-	mit	1 *	Mitochondrion; mitochondrial inner membrane (By similarity)				67
Q5PU89 UniProt NPD GO	UFM1_CHLIN	Probable ubiquitin-fold modifier 1 precursor (Protein PR46A)	0.04	-	cyt	0					99

You are viewing entries 78051 to 78100 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.