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
O75879 UniProt NPD GO	GATB_HUMAN	Probable glutamyl-tRNA(Gln) amidotransferase subunit B, mitochondrial precursor (EC 6.3.5.-) (Glu-AD ...	0.42	-	nuc	0	Mitochondrion	mitochondrion [TAS]	603645		557
Q09250 UniProt NPD GO	SAP18_CAEEL	Probable histone deacetylase complex subunit SAP18 (Sin3-associated polypeptide, 18 kDa)	0.42	-	nuc	0					166
Q6BNN6 UniProt NPD GO	SPC25_DEBHA	Probable kinetochore protein SPC25	0.42	-	cyt	0	Nucleus (By similarity). Associated with kinetochores (By similarity)				241
P46554 UniProt NPD GO	LCMT1_CAEEL	Probable leucine carboxyl methyltransferase 1 (EC 2.1.1.-)	0.42	-	cyt	0					333
Q8MPD6 UniProt NPD GO	MED31_TAESO	Probable mediator of RNA polymerase II transcription subunit 31 (Mediator complex subunit 31)	0.42	-	mit	0	Nucleus (Potential)				148
Q21939 UniProt NPD GO	RM49_CAEEL	Probable mitochondrial 39S ribosomal protein L49 (L49mt)	0.42	-	nuc	0	Mitochondrion (By similarity)				223
Q07534 UniProt NPD GO	YD119_YEAST	Probable mitochondrial carrier YDL119C	0.42	-	mit	0	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				307
P39965 UniProt NPD GO	SYPC_YEAST	Probable prolyl-tRNA synthetase, cytoplasmic (EC 6.1.1.15) (Proline--tRNA ligase) (ProRS)	0.42	-	mit	0	Cytoplasm (Potential)				576
Q9W4J5 UniProt NPD GO	NEP1_DROME	Probable ribosome biogenesis protein NEP1	0.42	-	nuc	0	Nucleus; nucleolus (By similarity)				252
Q7SAK9 UniProt NPD GO	SEN34_NEUCR	Probable tRNA-splicing endonuclease subunit sen-34 (EC 3.1.27.9) (tRNA-intron endonuclease sen-34)	0.42	-	nuc	0					315
O78417 UniProt NPD GO	YCF29_GUITH	Probable transcriptional regulator ycf29	0.42	-	cyt	0	Plastid; chloroplast				208
Q09924 UniProt NPD GO	EI2BD_SCHPO	Probable translation initiation factor eIF-2B subunit delta (eIF-2B GDP-GTP exchange factor subunit ...	0.42	-	nuc	0					467
P40479 UniProt NPD GO	YIL3_YEAST	Probable tyrosine-protein phosphatase YIL113W (EC 3.1.3.48)	0.42	-	nuc	0		cytoplasm [IDA] nucleus [IDA]			209
Q80TQ2 UniProt NPD GO	CYLD_MOUSE	Probable ubiquitin carboxyl-terminal hydrolase CYLD (EC 3.1.2.15) (Ubiquitin thioesterase CYLD) (Ubi ...	0.42	-	cyt	0	Cytoplasm; perinuclear region (By similarity)				952
Q4VBH4 UniProt NPD GO	UBE2W_BRARE	Probable ubiquitin-conjugating enzyme E2 W (EC 6.3.2.19) (Ubiquitin-protein ligase W) (Ubiquitin car ...	0.42	-	nuc	0					151
Q03455 UniProt NPD GO	MSC2_YEAST	Probable zinc transporter MSC2 (Meiotic sister chromatid recombination protein 2)	0.42	-	end	13 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein. Nucleus; nuclear ...	endoplasmic reticulum [IDA] nucleus [IDA]			724
P01210 UniProt NPD GO	PENK_HUMAN	Proenkephalin A precursor [Contains: Synenkephalin; Met-enkephalin (Opioid growth factor) (OGF); Met ...	0.42	-	exc	0	Secreted protein		131330	1PLX	267
P33096 UniProt NPD GO	PRL_ANGAN	Prolactin precursor (PRL)	0.42	-	exc	0	Secreted protein				209
P48096 UniProt NPD GO	PRL_SALSA	Prolactin precursor (PRL)	0.42	-	exc	0	Secreted protein				210
P09584 UniProt NPD GO	PRL2_ONCKE	Prolactin-2 precursor (Prolactin II) (PRL-II)	0.42	-	exc	0	Secreted protein				210
Q9NPJ4 UniProt NPD GO	PNRC2_HUMAN	Proline-rich nuclear receptor coactivator 2	0.42	-	nuc	0	Nucleus (Potential)				139
P05142 UniProt NPD GO	PRP2_MOUSE	Proline-rich protein MP-2 precursor	0.42	-	exc	0					261
Q3V1T4 UniProt NPD GO	P3H1_MOUSE	Prolyl 3-hydroxylase 1 precursor (EC 1.14.11.7) (Leucine proline-enriched proteoglycan 1) (Leprecan- ...	0.42	-	end	0	Endoplasmic reticulum (By similarity). Secreted protein; extracellular space; extracellular matrix ( ...	cytoplasm [IDA] nucleus [IDA] plasma membrane [TAS]			739
P01289 UniProt NPD GO	TKN1_BOVIN	Protachykinin 1 precursor (PPT) [Contains: Substance P; Neurokinin A (NKA) (Substance K) (Neuromedin ...	0.42	-	mit	0	Secreted protein				130
Q4R3H2 UniProt NPD GO	PSA1_MACFA	Proteasome subunit alpha type 1 (EC 3.4.25.1)	0.42	-	cyt	0	Cytoplasm. Nucleus				263
Q9WTZ8 UniProt NPD GO	BEX2_MOUSE	Protein BEX2 (Brain-expressed X-linked protein 2 homolog)	0.42	-	nuc	0	Nucleus (By similarity). Cytoplasm (By similarity)				129
Q3ZBJ6 UniProt NPD GO	BEX3_BOVIN	Protein BEX3 (Brain-expressed X-linked protein 3 homolog) (p75NTR-associated cell death executor) (N ...	0.42	-	nuc	0	Nucleus. Cytoplasm. Shuttles between the cytoplasm and the nucleus. Associates with replicating mito ...				112
Q6PDU5 UniProt NPD GO	BEX3_RAT	Protein BEX3 (Brain-expressed X-linked protein 3 homolog) (rBex3) (p75NTR-associated cell death exec ...	0.42	-	nuc	0	Nucleus (By similarity). Cytoplasm. Shuttles between the cytoplasm and the nucleus. Associates with ...				130
Q8IX90 UniProt NPD GO	CM003_HUMAN	Protein C13orf3	0.42	-	nuc	0					412
Q8BWJ4 UniProt NPD GO	CR001_MOUSE	Protein C18orf1 homolog	0.42	-	nuc	1	Cell membrane; single-pass membrane protein (By similarity)				306
Q8WYQ4 UniProt NPD GO	CV015_HUMAN	Protein C22orf15 (N27C7-3 protein)	0.42	-	nuc	0					148
Q8C5S3 UniProt NPD GO	CC022_MOUSE	Protein C3orf22 homolog	0.42	-	nuc	0					137
Q6ZUJ4 UniProt NPD GO	CC062_HUMAN	Protein C3orf62	0.42	-	nuc	0					267
Q5T9G4 UniProt NPD GO	CF081_HUMAN	Protein C6orf81	0.42	-	nuc	0					340
O95766 UniProt NPD GO	CG028_HUMAN	Protein C7orf28	0.42	-	cyt	0					482
Q8K2P1 UniProt NPD GO	CI150_MOUSE	Protein C9orf150 homolog	0.42	-	nuc	0					221
Q8WW33 UniProt NPD GO	F112B_HUMAN	Protein FAM112B	0.42	-	nuc	0					167
Q4R8M9 UniProt NPD GO	F112B_MACFA	Protein FAM112B	0.42	-	nuc	0					167
Q9NWS6 UniProt NPD GO	F118A_HUMAN	Protein FAM118A	0.42	-	mit	0					357
Q91YN1 UniProt NPD GO	F118A_MOUSE	Protein FAM118A	0.42	-	mit	0					357
Q41822 UniProt NPD GO	IOJAP_MAIZE	Protein Iojap	0.42	-	mit	0					228
P32335 UniProt NPD GO	MSS51_YEAST	Protein MSS51	0.42	-	mit	0	Mitochondrion	extrinsic to membrane [IDA] mitochondrial inner membrane [IDA] mitochondrial matrix [IDA] mitochondrion [IDA]			436
Q9Y2Z2 UniProt NPD GO	MTO1_HUMAN	Protein MTO1 homolog, mitochondrial precursor	0.42	-	mit	0	Mitochondrion (By similarity)				717
O75323 UniProt NPD GO	NIPS2_HUMAN	Protein NipSnap2 (Glioblastoma amplified sequence)	0.42	-	mit	0		integral to plasma membrane [TAS] membrane fraction [TAS] mitochondrion [ISS]	603004		286
O13377 UniProt NPD GO	PT122_SACKL	Protein PET122, mitochondrial precursor	0.42	-	cyt	0	Mitochondrion; mitochondrial inner membrane; peripheral membrane protein (By similarity)				312
Q06208 UniProt NPD GO	RIF2_YEAST	Protein RIF2 (RAP1-interacting factor 2)	0.42	-	nuc	0		nuclear telomere cap complex [IDA]			395
P53997 UniProt NPD GO	SET_DROME	Protein SET	0.42	-	nuc	0					269
Q6NQJ8 UniProt NPD GO	SDG40_ARATH	Protein SET DOMAIN GROUP 40	0.42	-	cyt	0					491
Q8TGM6 UniProt NPD GO	TAR1_YEAST	Protein TAR1 (Transcript antisense to ribosomal RNA protein 1)	0.42	-	nuc	0	Mitochondrion	mitochondrion [IMP]			124
P28099 UniProt NPD GO	WN10A_ALOVU	Protein Wnt-10a (Fragment)	0.42	-	nuc	0	Secreted protein; extracellular space; extracellular matrix				120

You are viewing entries 30601 to 30650 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.