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
P47867 UniProt NPD GO	SCG3_MOUSE	Secretogranin-3 precursor (Secretogranin III) (SgIII)	0.58	-	nuc	0	Secreted protein. Neuroendocrine and endocrine secretory granules				471
Q24322 UniProt NPD GO	SEM1A_DROME	Semaphorin-1A precursor (Semaphorin-I) (Sema I)	0.58	-	nuc	1	Membrane; single-pass type I membrane protein				850
Q63548 UniProt NPD GO	SEM3A_RAT	Semaphorin-3A precursor (Semaphorin III) (Sema III)	0.58	+	mit	0	Secreted protein (By similarity)				772
O08665 UniProt NPD GO	SEM3A_MOUSE	Semaphorin-3A precursor (Semaphorin III) (Sema III) (Semaphorin D) (Sema D)	0.58	+	mit	0	Secreted protein			1Q47	772
Q5U7N4 UniProt NPD GO	SEMG2_PANTR	Semenogelin-2 precursor (Semenogelin II) (SGII)	0.58	-	nuc	0	Secreted protein (By similarity)				407
P02783 UniProt NPD GO	SVP2_RAT	Seminal vesicle protein 2 precursor (Seminal vesicle secretory protein IV) (SVS IV) (SVS protein S) ...	0.58	-	exc	1 *	Secreted protein; extracellular space				112
P22209 UniProt NPD GO	KIN3_YEAST	Serine/threonine-protein kinase KIN3 (EC 2.7.11.1)	0.58	-	nuc	0					435
Q8TD19 UniProt NPD GO	NEK9_HUMAN	Serine/threonine-protein kinase Nek9 (EC 2.7.11.1) (NimA-related protein kinase 9) (Never in mitosis ...	0.58	+	nuc	0	Cytoplasm. Nucleus		609798		979
Q9FE20 UniProt NPD GO	PBS1_ARATH	Serine/threonine-protein kinase PBS1 (EC 2.7.11.1) (AvrPphB susceptible protein 1)	0.58	-	nuc	0					456
Q12701 UniProt NPD GO	KSG1_SCHPO	Serine/threonine-protein kinase ksg1 (EC 2.7.11.1)	0.58	-	nuc	0					592
O75460 UniProt NPD GO	ERN1_HUMAN	Serine/threonine-protein kinase/endoribonuclease IRE1 precursor (Inositol-requiring protein 1) (hIRE ...	0.58	-	end	1 *	Endoplasmic reticulum; endoplasmic reticulum membrane; single-pass type I membrane protein	endoplasmic reticulum membrane [TAS] integral to endoplasmic reticulum membrane [IEP]	604033		977
P50410 UniProt NPD GO	2ABG_RABIT	Serine/threonine-protein phosphatase 2A 55 kDa regulatory subunit B gamma isoform (PP2A, subunit B, ...	0.58	-	nuc	0					447
Q4PCR0 UniProt NPD GO	PTPA2_USTMA	Serine/threonine-protein phosphatase 2A activator 2 (EC 5.2.1.8) (Peptidyl-prolyl cis-trans isomeras ...	0.58	-	cyt	0	Cytoplasm (By similarity)				457
P36622 UniProt NPD GO	STE4_SCHPO	Sexual differentiation protein ste4	0.58	-	nuc	0					264
P81133 UniProt NPD GO	SIM1_HUMAN	Single-minded homolog 1	0.58	-	nuc	0	Nucleus (Potential)		603128		766
Q8C5L6 UniProt NPD GO	SKIP_MOUSE	Skeletal muscle and kidney-enriched inositol phosphatase (EC 3.1.3.56)	0.58	-	nuc	0	Endoplasmic reticulum. Following stimulation with EGF, translocates to membrane ruffles (By similari ...	cytosol [ISS] neuron projection [ISS]			468
O18637 UniProt NPD GO	SLY1_DROVI	Sly1 protein homolog	0.58	-	cyt	0	Cytoplasm (By similarity). Membrane; peripheral membrane protein (By similarity)	cytoplasm [ISS] membrane [ISS]			656
Q8BJU0 UniProt NPD GO	SGTA_MOUSE	Small glutamine-rich tetratricopeptide repeat-containing protein A	0.58	-	exc	0					315
P84443 UniProt NPD GO	CC21A_MOUSE	Small inducible cytokine A21a precursor (CCL21) (Beta chemokine exodus-2) (6Ckine) (Thymus-derived c ...	0.58	-	exc	0	Secreted protein				133
O95149 UniProt NPD GO	SPN1_HUMAN	Snurportin-1 (RNA U transporter 1)	0.58	-	nuc	0	Nucleus. Cytoplasm. Nucleoplasmic shuttling protein. Its nuclear import involves the nucleocytoplasm ...	nuclear pore [TAS]	607902	1XK5	360
Q8BTY2 UniProt NPD GO	S4A7_MOUSE	Sodium bicarbonate cotransporter 3 (Solute carrier family 4 member 7)	0.58	+	end	9	Cell membrane; basolateral cell membrane; multi-pass membrane protein. Also described at the apical ...				1034
P04775 UniProt NPD GO	SCN2A_RAT	Sodium channel protein type 2 subunit alpha (Sodium channel protein type II subunit alpha) (Voltage- ...	0.58	+	end	21	Membrane; multi-pass membrane protein	voltage-gated sodium channel complex [IDA]		1BYY	2005
Q92543 UniProt NPD GO	SNX19_HUMAN	Sorting nexin-19	0.58	-	end	2 *					992
P47057 UniProt NPD GO	SNX4_YEAST	Sorting nexin-4 (Autophagy-related protein 24) (Cytoplasm to vacuole targeting protein 13)	0.58	-	nuc	0	Cytoplasm. Membrane; peripheral membrane protein. Endosome; endosomal membrane; peripheral membrane ...	membrane [IPI]			423
Q8NEY3 UniProt NPD GO	SPAT4_HUMAN	Spermatogenesis-associated protein 4 (Testis spermatocyte apoptosis-related gene 2 protein) (Testis ...	0.58	-	nuc	0			609879		305
Q9JJY3 UniProt NPD GO	NSMA2_MOUSE	Sphingomyelin phosphodiesterase 3 (EC 3.1.4.12) (Neutral sphingomyelinase 2) (Neutral sphingomyelina ...	0.58	-	nuc	2 *	Golgi apparatus; Golgi membrane; multi-pass membrane protein. May localize to detergent-resistant su ...	Golgi apparatus [IDA] Golgi cis cisterna [IDA]			655
O35049 UniProt NPD GO	NSMA2_RAT	Sphingomyelin phosphodiesterase 3 (EC 3.1.4.12) (Neutral sphingomyelinase 2) (Neutral sphingomyelina ...	0.58	-	nuc	2 *	Golgi apparatus; Golgi membrane; multi-pass membrane protein (By similarity). May localize to deterg ...				655
P53540 UniProt NPD GO	SPC98_YEAST	Spindle pole body component SPC98	0.58	-	cyt	0	Nucleus	gamma-tubulin complex (sensu Saccharomyces) [IPI] inner plaque of spindle pole body [IDA] outer plaque of spindle pole body [IDA]			846
O46106 UniProt NPD GO	NOI_DROME	Splicing factor 3A subunit 3 (Protein noisette)	0.58	-	nuc	0	Nucleus. Excluded from the nucleoli				503
Q02651 UniProt NPD GO	SMA1_YEAST	Spore membrane assembly protein 1	0.58	-	nuc	0					245
P08568 UniProt NPD GO	GRPA_RAT	Submandibular gland secretory Glx-rich protein CA precursor (GRP-CA)	0.58	-	exc	0	Secreted protein				246
Q9CX34 UniProt NPD GO	SUGT1_MOUSE	Suppressor of G2 allele of SKP1 homolog	0.58	-	nuc	0					335
Q93212 UniProt NPD GO	SOL1_CAEEL	Suppressor of lurcher protein 1 precursor	0.58	-	end	0	Cell membrane; cell-cell junction; single-pass type I membrane protein. Colocalizes with glr-1 at th ...				594
O75940 UniProt NPD GO	SPF30_HUMAN	Survival of motor neuron-related-splicing factor 30 (SMN-related protein) (30 kDa splicing factor SM ...	0.58	-	nuc	0	Nucleus; nucleoplasm; nuclear speckle. Nucleus; nucleoplasm; Cajal body. Detected in nuclear speckle ...	nucleus [TAS] spliceosome complex [TAS]	603519		238
Q8BGT7 UniProt NPD GO	SPF30_MOUSE	Survival of motor neuron-related-splicing factor 30 (SMN-related protein) (30 kDa splicing factor SM ...	0.58	-	nuc	0	Nucleus; nucleoplasm; nuclear speckle (By similarity). Nucleus; nucleoplasm; Cajal body (By similari ...				238
Q63537 UniProt NPD GO	SYN2_RAT	Synapsin-2 (Synapsin II)	0.58	-	nuc	0	Synapse	synaptic vesicle [IDA]		1I7N	586
O08625 UniProt NPD GO	SYT10_RAT	Synaptotagmin-10 (Synaptotagmin X) (SytX)	0.58	+	nuc	1	Synaptic vesicle; synaptic vesicle membrane; multi-pass membrane protein (By similarity)				523
Q9R0N8 UniProt NPD GO	SYT6_MOUSE	Synaptotagmin-6 (Synaptotagmin VI) (SytVI)	0.58	-	exc	1	Synaptic vesicle; synaptic vesicle membrane; multi-pass membrane protein				511
O43581 UniProt NPD GO	SYT7_HUMAN	Synaptotagmin-7 (Synaptotagmin VII) (SytVII)	0.58	-	nuc	1 *	Synaptic vesicle; synaptic vesicle membrane; multi-pass membrane protein (By similarity)		604146		402
Q80ZG1 UniProt NPD GO	RIC8A_RAT	Synembryn-A (Protein Ric-8A)	0.58	-	nuc	0	Cytoplasm (By similarity)				529
Q12241 UniProt NPD GO	VAM3_YEAST	Syntaxin VAM3	0.58	-	nuc	1	Vacuole; vacuolar membrane; single-pass type IV membrane protein	vacuolar membrane [IDA]		1HS7	283
Q9P2W9 UniProt NPD GO	STX18_HUMAN	Syntaxin-18 (Growth-inhibiting gene 9 protein)	0.58	-	nuc	1	Endoplasmic reticulum; endoplasmic reticulum membrane; single-pass type IV membrane protein (Probabl ...	endoplasmic reticulum [TAS]	606046		335
Q08849 UniProt NPD GO	STX3_RAT	Syntaxin-3	0.58	-	gol	1	Membrane; single-pass type IV membrane protein (Potential)				289
O73718 UniProt NPD GO	TBX3_CHICK	T-box transcription factor TBX3 (T-box protein 3) (Fragment)	0.58	-	nuc	0	Nucleus (Potential)				414
P16004 UniProt NPD GO	CD4_PANTR	T-cell surface glycoprotein CD4 precursor (T-cell surface antigen T4/Leu-3)	0.58	-	end	1	Membrane; single-pass type I membrane protein	T cell receptor complex [ISS]			458
P05540 UniProt NPD GO	CD4_RAT	T-cell surface glycoprotein CD4 precursor (T-cell surface antigen T4/Leu-3) (W3/25 antigen)	0.58	-	nuc	1	Membrane; single-pass type I membrane protein	T cell receptor complex [ISS]		1CID	457
Q3SX11 UniProt NPD GO	TIP1_BOVIN	TGF-beta-inducible nuclear protein 1	0.58	+	nuc	0	Nucleus; nucleolus (By similarity)				260
O95551 UniProt NPD GO	TTRAP_HUMAN	TRAF and TNF receptor-associated protein (ETS1-associated protein 2) (ETS1-associated protein II) (E ...	0.58	-	mit	0	Nucleus		605764		362
Q8VWG3 UniProt NPD GO	TT1_ARATH	TRANSPARENT TESTA 1 protein (Zinc finger protein TT1) (TTL1)	0.58	-	nuc	0	Nucleus				303
Q5KT10 UniProt NPD GO	TRH_CARAU	Thyroliberin precursor [Contains: Prothyroliberin; Thyroliberin (Thyrotropin-releasing hormone) (TRH ...	0.58	-	exc	0	Secreted protein				231

You are viewing entries 20451 to 20500 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.