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
P40653 UniProt NPD GO	MG44_TARMA	SRY-related protein MG44 (Fragment)	0.42	-	nuc	0	Nucleus (Potential)				72
P13208 UniProt NPD GO	SRTX_ATREN	Sarafotoxins precursor [Contains: Sarafotoxin A, Ser-isoform (Sarafotoxin A) (S6A) (SRTX-A); Sarafot ...	0.42	-	exc	0	Secreted protein			1SRB	543
Q9BG79 UniProt NPD GO	SOST_BOVIN	Sclerostin (Fragment)	0.42	-	nuc	0	Secreted protein (Potential)				176
Q99P67 UniProt NPD GO	SOST_RAT	Sclerostin precursor	0.42	-	exc	0	Secreted protein (Potential)				213
Q863H1 UniProt NPD GO	SFRP2_CANFA	Secreted frizzled-related protein 2 precursor (sFRP-2)	0.42	-	exc	0	Secreted protein				294
Q9Z2G6 UniProt NPD GO	SEL1L_MOUSE	Sel-1 homolog precursor (Suppressor of lin-12-like protein) (Sel-1L)	0.42	-	end	0	Membrane; single-pass type I membrane protein (Potential)				790
Q9R1T4 UniProt NPD GO	SEPT6_MOUSE	Septin-6	0.42	+	cyt	0					433
P51567 UniProt NPD GO	AFC2_ARATH	Serine/threonine-protein kinase AFC2 (EC 2.7.12.1)	0.42	-	cyt	0					427
Q9C0K7 UniProt NPD GO	AL2S2_HUMAN	Serine/threonine-protein kinase ALS2CR2 (EC 2.7.11.1) (Amyotrophic lateral sclerosis 2 chromosomal r ...	0.42	-	nuc	0	Cytoplasm (Potential)		607333		418
Q90XC2 UniProt NPD GO	NEK8_BRARE	Serine/threonine-protein kinase Nek8 (EC 2.7.11.1) (NimA-related protein kinase 8)	0.42	-	cyt	0	Cytoplasm (By similarity). Predominantly (By similarity)				697
Q6P9R2 UniProt NPD GO	OXSR1_MOUSE	Serine/threonine-protein kinase OSR1 (EC 2.7.11.1) (Oxidative stress-responsive 1 protein)	0.42	-	cyt	0					527
P20654 UniProt NPD GO	PP1_EMENI	Serine/threonine-protein phosphatase PP1 (EC 3.1.3.16)	0.42	-	cyt	0					323
Q20410 UniProt NPD GO	SRA12_CAEEL	Serpentine receptor class alpha-12 (Protein sra-12)	0.42	-	end	7 *	Membrane; multi-pass membrane protein (Potential)				327
O17699 UniProt NPD GO	SRG47_CAEEL	Serpentine receptor class gamma-47 (Protein srg-47)	0.42	-	end	5 *	Membrane; multi-pass membrane protein (Probable)				309
Q86U17 UniProt NPD GO	SPA11_HUMAN	Serpin A11 precursor	0.42	-	mit	0	Secreted protein (Potential)				422
Q9GMB8 UniProt NPD GO	SYS_BOVIN	Seryl-tRNA synthetase (EC 6.1.1.11) (Serine--tRNA ligase) (SerRS)	0.42	-	cyt	0					513
Q9N0F3 UniProt NPD GO	SYSM_BOVIN	Seryl-tRNA synthetase, mitochondrial precursor (EC 6.1.1.11) (Serine--tRNA ligase) (SerRSmt)	0.42	-	mit	0	Mitochondrion	mitochondrion [IDA]		1WLE	518
P01432 UniProt NPD GO	NXS3_NAJMO	Short neurotoxin 3 (Neurotoxin III) (NMM III)	0.42	-	nuc	0	Secreted protein				62
Q920G3 UniProt NPD GO	SIGL5_MOUSE	Sialic acid-binding Ig-like lectin 5 precursor (Siglec-5) (Sialic acid-binding Ig-like lectin-F) (mS ...	0.42	-	end	1	Membrane; single-pass type I membrane protein				569
P41922 UniProt NPD GO	SEC65_YARLI	Signal recognition particle SEC65 subunit	0.42	-	nuc	0	Cytoplasm (By similarity)				310
P08240 UniProt NPD GO	SRPR_HUMAN	Signal recognition particle receptor subunit alpha (SR-alpha) (Docking protein alpha) (DP-alpha)	0.42	+	cyt	0	Endoplasmic reticulum; endoplasmic reticulum membrane; peripheral membrane protein. Thought to be an ...	endoplasmic reticulum [TAS] integral to membrane [TAS] signal recognition particle receptor complex [TAS]	182180	2FH5	638
P32916 UniProt NPD GO	SRPR_YEAST	Signal recognition particle receptor subunit alpha homolog (SR-alpha) (Docking protein alpha) (DP-al ...	0.42	-	nuc	0	Endoplasmic reticulum; endoplasmic reticulum membrane	endoplasmic reticulum membrane [IDA] signal recognition particle receptor complex [TAS]		1NRJ	621
Q8MIZ1 UniProt NPD GO	SCYBA_MACMU	Small inducible cytokine B10 precursor (CXCL10) (10 kDa interferon-gamma-induced protein)	0.42	-	mit	1 *	Secreted protein (By similarity)				98
P02778 UniProt NPD GO	SCYBA_HUMAN	Small inducible cytokine B10 precursor (CXCL10) (10 kDa interferon-gamma-induced protein) (Gamma-IP1 ...	0.42	-	mit	1 *	Secreted protein		147310	1O80	98
P97698 UniProt NPD GO	SMO_RAT	Smoothened homolog precursor (SMO)	0.42	+	end	7	Membrane; multi-pass membrane protein				793
Q62968 UniProt NPD GO	SC10A_RAT	Sodium channel protein type 10 subunit alpha (Sodium channel protein type X subunit alpha) (Voltage- ...	0.42	-	end	20	Membrane; multi-pass membrane protein (By similarity). It can be translocated to the extracellular m ...	integral to membrane [IDA]			1956
Q9QZM6 UniProt NPD GO	NCKX1_RAT	Sodium/potassium/calcium exchanger 1 (Na(+)/K(+)/Ca(2+)-exchange protein 1) (Retinal rod Na-Ca+K exc ...	0.42	-	end	11 *	Membrane; multi-pass membrane protein				1181
Q6DNF3 UniProt NPD GO	GCY37_CAEEL	Soluble guanylate cyclase gcy-37 (EC 4.6.1.2)	0.42	-	cyt	0	Cytoplasm (By similarity)				708
P20391 UniProt NPD GO	SOMA_KATPE	Somatotropin (Growth hormone)	0.42	-	nuc	0	Secreted protein				185
Q9I9L5 UniProt NPD GO	SOMA_ODOAR	Somatotropin precursor (Growth hormone)	0.42	-	exc	0	Secreted protein				204
Q98UF6 UniProt NPD GO	SOMA_TRITC	Somatotropin precursor (Growth hormone)	0.42	-	exc	0	Secreted protein				204
O93359 UniProt NPD GO	SOMA1_CARAU	Somatotropin-1 precursor (Somatotropin I) (Growth hormone I)	0.42	-	exc	0	Secreted protein				210
Q99314 UniProt NPD GO	SAS5_YEAST	Something about silencing protein 5	0.42	-	cyt	0	Nucleus	nuclear chromatin [IDA] nuclear chromosome, telomeric region [IC]			248
Q96L94 UniProt NPD GO	SNX22_HUMAN	Sorting nexin-22	0.42	-	nuc	0				2ETT	193
Q5R4C2 UniProt NPD GO	SNX4_PONPY	Sorting nexin-4	0.42	-	cyt	0					450
Q6FPT9 UniProt NPD GO	SNX4_CANGA	Sorting nexin-4 (Autophagy-related protein 24)	0.42	-	nuc	0	Cytoplasm (By similarity). Membrane; peripheral membrane protein (By similarity). Endosome; endosoma ...				430
Q6UW49 UniProt NPD GO	SPESP_HUMAN	Sperm equatorial segment protein 1 precursor (SP-ESP) (Equatorial segment protein) (ESP) (Glycosylat ...	0.42	-	exc	0	Acrosome. Small proacrosomal granules (during the Golgi phase), enlarged acrosomal vesicles (during ...		609399		350
Q6DII2 UniProt NPD GO	SFRS1_XENTR	Splicing factor, arginine/serine-rich 1	0.42	+	nuc	0	Nucleus (By similarity)				267
Q60598 UniProt NPD GO	SRC8_MOUSE	Src substrate cortactin	0.42	-	nuc	0	Cytoplasm. Associated with membrane ruffles and lamellipodia	cell cortex [IDA] cytoplasm [IDA] lamellipodium [IDA] ruffle [IDA]			546
Q9BYL1 UniProt NPD GO	SAM10_HUMAN	Sterile alpha motif domain-containing protein 10	0.42	-	nuc	0					202
Q7TST3 UniProt NPD GO	SAM10_MOUSE	Sterile alpha motif domain-containing protein 10	0.42	-	nuc	0					202
Q28996 UniProt NPD GO	STAR_PIG	Steroidogenic acute regulatory protein, mitochondrial precursor (StAR) (StARD1)	0.42	-	mit	0	Mitochondrion				285
P51557 UniProt NPD GO	STAR_MOUSE	Steroidogenic acute regulatory protein, mitochondrial precursor (StAR) (StARD1) (Luteinizing hormone ...	0.42	-	cyt	0	Mitochondrion	mitochondrion [IDA]			284
Q9GKL2 UniProt NPD GO	STF1_HORSE	Steroidogenic factor 1 (STF-1) (SF-1)	0.42	+	mit	0	Nucleus (By similarity)				461
P18899 UniProt NPD GO	DDR48_YEAST	Stress protein DDR48 (DNA damage-responsive protein 48) (DDRP 48) (YP 75) (Flocculent-specific prote ...	0.42	-	nuc	0		cytoplasm [IDA]			429
Q9ERG2 UniProt NPD GO	STRN3_MOUSE	Striatin-3 (Cell-cycle autoantigen SG2NA) (S/G2 antigen)	0.42	-	cyt	0	Cytoplasm. Membrane; peripheral membrane protein				796
P58404 UniProt NPD GO	STRN4_MOUSE	Striatin-4 (Zinedin)	0.42	-	nuc	0	Cytoplasm. Membrane; peripheral membrane protein				760
P98091 UniProt NPD GO	MUCS_BOVIN	Submaxillary mucin-like protein	0.42	-	nuc	0	Secreted protein				563
P21913 UniProt NPD GO	DHSB_RAT	Succinate dehydrogenase [ubiquinone] iron-sulfur protein (EC 1.3.5.1) (Ip) (Iron-sulfur subunit of c ...	0.42	-	nuc	0	Mitochondrion; mitochondrial inner membrane				143
P41823 UniProt NPD GO	SY65_APLCA	Synaptotagmin-1 (Synaptotagmin I) (p65)	0.42	+	nuc	1	Synaptic vesicles and vesicle-like structures	integral to synaptic vesicle membrane [IDA]			428

You are viewing entries 30701 to 30750 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.