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
Q13487 UniProt NPD GO	SNPC2_HUMAN	snRNA-activating protein complex subunit 2 (SNAPc subunit 2) (snRNA-activating protein complex 45 kD ...	0.64	-	nuc	0	Nucleus	nucleus [TAS]	605076		334
O43242 UniProt NPD GO	PSD3_HUMAN	26S proteasome non-ATPase regulatory subunit 3 (26S proteasome regulatory subunit S3) (Proteasome su ...	0.63	-	nuc	0		proteasome complex (sensu Eukaryota) [TAS]			534
Q2YDF6 UniProt NPD GO	RT35_BOVIN	28S ribosomal protein S35, mitochondrial precursor (Mitochondrial ribosomal protein S28) (MRP-S28)	0.63	-	mit	0	Mitochondrion	mitochondrial small ribosomal subunit [IDA]			325
P49627 UniProt NPD GO	RL13_TOBAC	60S ribosomal protein L13 (Clone 6.2.1)	0.63	-	nuc	0					202
Q9UNX3 UniProt NPD GO	RL26L_HUMAN	60S ribosomal protein L26-like 1	0.63	-	nuc	0					145
Q3T0L7 UniProt NPD GO	RL28_BOVIN	60S ribosomal protein L28	0.63	+	nuc	0		cytosolic large ribosomal subunit (sensu Eu... [ISS]			136
Q9Y3U8 UniProt NPD GO	RL36_HUMAN	60S ribosomal protein L36	0.63	-	nuc	0		cytosolic large ribosomal subunit (sensu Eu... [NAS]			104
Q5RAZ9 UniProt NPD GO	RL36_PONPY	60S ribosomal protein L36	0.63	-	nuc	0					104
P05733 UniProt NPD GO	RL37B_SCHPO	60S ribosomal protein L37-B (L37-2) (YL27)	0.63	-	mit	0					90
P09180 UniProt NPD GO	RL4_DROME	60S ribosomal protein L4 (L1)	0.63	-	cyt	0					401
Q9D8E6 UniProt NPD GO	RL4_MOUSE	60S ribosomal protein L4 (L1)	0.63	+	nuc	0					418
O74676 UniProt NPD GO	CDR4_CANAL	ABC transporter CDR4	0.63	+	end	13	Membrane; multi-pass membrane protein (Potential)				1490
Q8C9W3 UniProt NPD GO	ATS2_MOUSE	ADAMTS-2 precursor (EC 3.4.24.14) (A disintegrin and metalloproteinase with thrombospondin motifs 2) ...	0.63	-	exc	0	Secreted protein; extracellular space; extracellular matrix (By similarity)				1213
Q08422 UniProt NPD GO	YO052_YEAST	AN1-type zinc finger protein YOR052C	0.63	-	nuc	0	Nucleus	nucleus [IDA]			150
Q99LE6 UniProt NPD GO	ABCF2_MOUSE	ATP-binding cassette sub-family F member 2	0.63	-	nuc	0					628
P01097 UniProt NPD GO	ATIF_YEAST	ATPase inhibitor, mitochondrial precursor	0.63	-	mit	0	Mitochondrion	proton-transporting ATP synthase complex (s... [TAS]			85
Q99929 UniProt NPD GO	ASCL2_HUMAN	Achaete-scute homolog 2 (Mash2) (HASH2)	0.63	+	nuc	0	Nucleus	nucleus [NAS]	601886		193
Q9NQ33 UniProt NPD GO	ASCL3_HUMAN	Achaete-scute homolog 3 (bHLH transcriptional regulator Sgn-1)	0.63	-	nuc	0	Nucleus		609154		180
P29381 UniProt NPD GO	AGL1_ARATH	Agamous-like MADS-box protein AGL1 (Protein Shatterproof 1)	0.63	-	nuc	0	Nucleus				248
P42127 UniProt NPD GO	ASIP_HUMAN	Agouti signaling protein precursor (ASP) (Agouti switch protein)	0.63	-	nuc	0	Secreted protein	extracellular space [TAS]	600201	1Y7K	132
Q6ZYM3 UniProt NPD GO	ASIP_PIG	Agouti signaling protein precursor (ASP) (Agouti switch protein)	0.63	-	exc	0	Secreted protein (By similarity)				131
Q32L00 UniProt NPD GO	ALKB3_BOVIN	Alkylated repair protein alkB homolog 3	0.63	-	nuc	0					286
P43238 UniProt NPD GO	ALL12_ARAHY	Allergen Ara h 1, clone P41B precursor (Ara h I)	0.63	-	mit	0					626
P30997 UniProt NPD GO	CTN2_CHICK	Alpha-2 catenin (Alpha N-catenin) (Neural alpha-catenin)	0.63	-	nuc	0					906
P22855 UniProt NPD GO	MAN1_YEAST	Alpha-mannosidase (EC 3.2.1.24) (Alpha-D-mannoside mannohydrolase)	0.63	-	cyt	0	Vacuole	vacuolar membrane [IDA]			1083
Q03157 UniProt NPD GO	APLP1_MOUSE	Amyloid-like protein 1 precursor (APLP) (APLP-1) [Contains: C30]	0.63	-	mit	1	Cell membrane; single-pass type I membrane protein. C30: Cytoplasm. C-terminally processed in the Go ...	Golgi apparatus [IDA] integral to membrane [TAS] membrane fraction [IDA]			653
Q874R3 UniProt NPD GO	APC2_SCHPO	Anaphase-promoting complex subunit 2 (20S cyclosome/APC complex protein apc2)	0.63	-	mit	0		anaphase-promoting complex [IDA]			681
P49699 UniProt NPD GO	ANDR_RABIT	Androgen receptor (Dihydrotestosterone receptor) (Fragment)	0.63	+	nuc	0	Nucleus				709
Q9R182 UniProt NPD GO	ANGL3_MOUSE	Angiopoietin-related protein 3 precursor (Angiopoietin-like 3)	0.63	-	exc	0	Secreted protein (By similarity)	extracellular region [ISS]			455
Q5F259 UniProt NPD GO	AN13B_MOUSE	Ankyrin repeat domain-containing protein 13B	0.63	-	nuc	0					626
Q9GZV1 UniProt NPD GO	ANKR2_HUMAN	Ankyrin repeat domain-containing protein 2 (Skeletal muscle ankyrin repeat protein) (hArpp)	0.63	+	cyt	0		nucleus [ISS]			333
Q966L5 UniProt NPD GO	ARS2_CAEEL	Arsenite-resistance protein 2 homolog	0.63	+	nuc	0					712
Q5FYB1 UniProt NPD GO	ARSI_HUMAN	Arylsulfatase I precursor (EC 3.1.6.-) (ASI)	0.63	-	cyt	0	Secreted protein (Potential)		610009		569
O17850 UniProt NPD GO	ATX3_CAEEL	Ataxin-3 homolog (EC 3.4.22.-) (Machado-Joseph disease-like protein)	0.63	-	nuc	0	Nucleus (By similarity)				317
Q872C6 UniProt NPD GO	ATG5_NEUCR	Autophagy protein 5	0.63	-	nuc	0	Cytoplasm (By similarity). Membrane; peripheral membrane protein (By similarity)				397
Q8RYC8 UniProt NPD GO	ARFS_ARATH	Auxin response factor 19 (Auxin-responsive protein IAA22)	0.63	-	nuc	0	Nucleus	nucleus [TAS]			1086
Q5W670 UniProt NPD GO	IAA18_ORYSA	Auxin-responsive protein IAA18 (Indoleacetic acid-induced protein 18)	0.63	-	nuc	0	Nucleus (By similarity)				327
Q8BVN8 UniProt NPD GO	IDLC_MOUSE	Axonemal dynein light intermediate polypeptide 1 (Inner dynein arm light chain, axonemal)	0.63	-	nuc	0					258
Q4KM52 UniProt NPD GO	BLNK_RAT	B-cell linker protein (Cytoplasmic adapter protein)	0.63	-	nuc	0	Cytoplasm (By similarity). Membrane (By similarity). BCR activation results in the translocation to ...				457
P08726 UniProt NPD GO	BAR6_CHITE	Balbiani ring protein 6 (Giant secretory protein I-C) (GSP-IC) (Fragment)	0.63	-	nuc	0	Secreted protein				235
Q64682 UniProt NPD GO	ARBK1_MESAU	Beta-adrenergic receptor kinase 1 (EC 2.7.11.15) (Beta-ARK-1) (G-protein-coupled receptor kinase 2)	0.63	-	cyt	0					689
P26819 UniProt NPD GO	ARBK2_RAT	Beta-adrenergic receptor kinase 2 (EC 2.7.11.15) (Beta-ARK-2) (G-protein-coupled receptor kinase 3)	0.63	-	cyt	0		axon [IDA] dendritic shaft [IDA] dendritic spine [IDA] synapse [IDA]			688
P42674 UniProt NPD GO	BP10_PARLI	Blastula protease 10 precursor (EC 3.4.24.-)	0.63	-	exc	0	Cytoplasm; perinuclear region. Cytoplasm; cell cortex. Secreted protein; extracellular space. First ...				597
Q29542 UniProt NPD GO	RNBR_GIRCA	Brain ribonuclease (EC 3.1.27.-) (BRB)	0.63	-	nuc	0	Secreted protein				141
Q01295 UniProt NPD GO	BRC1_DROME	Broad-complex core-protein isoforms 1/2/3/4/5	0.63	-	nuc	0	Nucleus				727
P51948 UniProt NPD GO	MAT1_HUMAN	CDK-activating kinase assembly factor MAT1 (RING finger protein MAT1) (Menage a trois) (CDK7/cyclin ...	0.63	-	nuc	0	Nucleus		602659	1G25	309
O14423 UniProt NPD GO	CBH1_SCHPO	CENP-B homolog protein 1 (CBHP-1)	0.63	-	cyt	0	Nucleus	condensed nuclear chromosome, pericentric r... [IDA]			514
P79995 UniProt NPD GO	CAD10_CHICK	Cadherin-10 precursor	0.63	-	end	1	Membrane; single-pass type I membrane protein	integral to membrane [ISS]			789
P43187 UniProt NPD GO	ALLB3_BETVE	Calcium-binding allergen Bet v 3 (Bet v III)	0.63	-	cyt	0					205
P49342 UniProt NPD GO	ICAL_CERAE	Calpastatin (Calpain inhibitor) (Fragment)	0.63	-	nuc	0					283

You are viewing entries 17251 to 17300 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.