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
Q522W5 UniProt NPD GO	SNX4_MAGGR	Sorting nexin-4 (Autophagy-related protein 24)	0.48	+	cyt	0	Cytoplasm (By similarity). Membrane; peripheral membrane protein (By similarity). Endosome; endosoma ...				495
P27205 UniProt NPD GO	EM1_ENSMI	Sperm protein EM1 (Fragment)	0.48	+	mit	0	Nucleus				34
Q922B9 UniProt NPD GO	SSFA2_MOUSE	Sperm-specific antigen 2	0.48	-	nuc	0	Cell surface (By similarity). Surface of sperm (By similarity)				264
Q15459 UniProt NPD GO	SF3A1_HUMAN	Splicing factor 3 subunit 1 (Spliceosome-associated protein 114) (SAP 114) (SF3a120)	0.48	-	nuc	0	Nucleus (By similarity)	spliceosome complex [IDA]	605595	1ZKH	793
Q24562 UniProt NPD GO	U2AF2_DROME	Splicing factor U2AF 50 kDa subunit (U2 auxiliary factor 50 kDa subunit) (U2 snRNP auxiliary factor ...	0.48	+	cyt	0	Nucleus	nucleus [IC] snRNP U2 [TAS]			416
Q9QXV9 UniProt NPD GO	SPY1_MOUSE	Sprouty homolog 1 (Spry-1)	0.48	-	nuc	0	Cytoplasm. Membrane; peripheral membrane protein. Found in the cytoplasm in unstimulated cells but i ...				313
Q7RTU9 UniProt NPD GO	STRC_HUMAN	Stereocilin precursor	0.48	-	end	1 *	Cell surface (By similarity). Associated with the hair bundle (By similarity)		606440		1775
Q6QGW5 UniProt NPD GO	SRA1_RAT	Steroid receptor RNA activator 1 (Steroid receptor RNA activator protein) (SRAP)	0.48	-	nuc	0	Nucleus. Cytoplasm (By similarity)	nucleus [ISS] ribonucleoprotein complex [ISS]			231
P49675 UniProt NPD GO	STAR_HUMAN	Steroidogenic acute regulatory protein, mitochondrial precursor (StAR) (StARD1)	0.48	-	mit	0	Mitochondrion		201710	1IMG	285
O35979 UniProt NPD GO	SMR2D_MOUSE	Submaxillary gland androgen-regulated protein 2, isoform delta precursor (Salivary protein MSG2, iso ...	0.48	-	exc	0	Secreted protein				143
P80351 UniProt NPD GO	2SS1_CAPMA	Sweet protein mabinlin-1 (Mabinlin I) (MAB I) [Contains: Sweet protein mabinlin-1 chain A; Sweet pro ...	0.48	-	mit	0					104
P35589 UniProt NPD GO	SYB_APLCA	Synaptobrevin	0.48	-	gol	1	Synaptic vesicle; synaptic vesicle membrane; single-pass type IV membrane protein. Neuronal synaptic ...				180
O95721 UniProt NPD GO	SNP29_HUMAN	Synaptosomal-associated protein 29 (SNAP-29) (Vesicle-membrane fusion protein SNAP-29) (Soluble 29 k ...	0.48	-	nuc	0	Cytoplasm. Membrane; peripheral membrane protein. Appears to be mostly membrane-bound, probably via ...	plasma membrane [TAS]	609528		258
O08835 UniProt NPD GO	SYT11_RAT	Synaptotagmin-11 (Synaptotagmin XI) (SytXI)	0.48	+	nuc	1 *	Synaptic vesicle; synaptic vesicle membrane; multi-pass membrane protein (By similarity)	synaptic vesicle [TAS]			430
Q9BQG1 UniProt NPD GO	SYT3_HUMAN	Synaptotagmin-3 (Synaptotagmin III) (SytIII)	0.48	+	nuc	1	Synaptic vesicle; synaptic vesicle membrane; single-pass membrane protein (By similarity)		600327		590
O35681 UniProt NPD GO	SYT3_MOUSE	Synaptotagmin-3 (Synaptotagmin III) (SytIII)	0.48	+	nuc	1	Synaptic vesicle; synaptic vesicle membrane; single-pass membrane protein				587
Q9GSX9 UniProt NPD GO	RIC8_CAEEL	Synembryn (Resistance to inhibitors of cholinesterase protein 8)	0.48	-	nuc	0	Cytoplasm; cell cortex. Localizes to the cell cortex. Excluded from interphase nuclei and becomes lo ...				566
P41834 UniProt NPD GO	UFE1_YEAST	Syntaxin UFE1	0.48	-	nuc	0	Endoplasmic reticulum; endoplasmic reticulum membrane; single-pass type IV membrane protein	endoplasmic reticulum membrane [TAS]			346
Q00262 UniProt NPD GO	STX2_MOUSE	Syntaxin-2 (Epimorphin)	0.48	-	gol	1	Membrane; single-pass type IV membrane protein				289
O15400 UniProt NPD GO	STX7_HUMAN	Syntaxin-7	0.48	-	nuc	1	Endosome; early endosome; early endosomal membrane; single-pass type IV membrane protein (By similar ...		603217		260
Q5R602 UniProt NPD GO	STX7_PONPY	Syntaxin-7	0.48	-	nuc	1	Endosome; early endosome; early endosomal membrane; single-pass type IV membrane protein (By similar ...				260
Q9Z2Q7 UniProt NPD GO	STX8_RAT	Syntaxin-8	0.48	-	nuc	1	Membrane; single-pass type IV membrane protein. Preferentially associated with the early endosome. T ...			1GL2	236
O88983 UniProt NPD GO	STX8_MOUSE	Syntaxin-8 (Syntaxin-like protein 3I35)	0.48	-	nuc	1	Membrane; single-pass type IV membrane protein (By similarity). Preferentially associated with the e ...				236
O95947 UniProt NPD GO	TBX6_HUMAN	T-box transcription factor TBX6 (T-box protein 6)	0.48	+	nuc	0	Nucleus (Potential)		602427		436
P22091 UniProt NPD GO	TAL1_MOUSE	T-cell acute lymphocytic leukemia-1 protein homolog (TAL-1 protein) (Stem cell protein)	0.48	-	nuc	0					329
Q9NVG8 UniProt NPD GO	TBC13_HUMAN	TBC1 domain family member 13	0.48	-	nuc	0					275
Q9BSI4 UniProt NPD GO	TINF2_HUMAN	TERF1-interacting nuclear factor 2 (TRF1-interacting nuclear protein 2)	0.48	-	nuc	0	Nucleus. Associated with telomeres	chromosome, telomeric region [TAS]	604319		451
Q05546 UniProt NPD GO	TENR_RAT	Tenascin-R precursor (TN-R) (Restrictin) (Janusin) (Neural recognition molecule J1-160/180)	0.48	-	cyt	0	Secreted protein; extracellular space; extracellular matrix	extracellular matrix (sensu Metazoa) [IDA]		1TDQ	1356
Q9BQ16 UniProt NPD GO	TICN3_HUMAN	Testican-3 precursor (SPARC/osteonectin, CWCV, and Kazal-like domains proteoglycan 3)	0.48	-	exc	1 *	Secreted protein; extracellular space; extracellular matrix		607989		436
Q8R3H9 UniProt NPD GO	TTC4_MOUSE	Tetratricopeptide repeat protein 4 (TPR repeat protein 4)	0.48	-	nuc	0					386
Q3ZBV8 UniProt NPD GO	SYTC_BOVIN	Threonyl-tRNA synthetase, cytoplasmic (EC 6.1.1.3) (Threonine--tRNA ligase) (ThrRS)	0.48	-	cyt	0	Cytoplasm (By similarity)				723
Q9WV82 UniProt NPD GO	TLR4_CRIGR	Toll-like receptor 4 precursor (CD284 antigen)	0.48	-	end	1	Membrane; single-pass type I membrane protein (By similarity)				838
P58727 UniProt NPD GO	TLR4_FELCA	Toll-like receptor 4 precursor (CD284 antigen)	0.48	-	nuc	1	Membrane; single-pass type I membrane protein (By similarity)	lipopolysaccharide receptor complex [ISS]			833
Q9TSP2 UniProt NPD GO	TLR4_PAPAN	Toll-like receptor 4 precursor (CD284 antigen)	0.48	-	nuc	1	Membrane; single-pass type I membrane protein (By similarity)	lipopolysaccharide receptor complex [ISS]			826
Q16254 UniProt NPD GO	E2F4_HUMAN	Transcription factor E2F4 (E2F-4)	0.48	-	nuc	0	Nucleus		600659	1CF7	413
Q91605 UniProt NPD GO	HTF4_XENLA	Transcription factor XE1.1 (Fragment)	0.48	-	nuc	0	Nucleus				152
Q16514 UniProt NPD GO	TAF12_HUMAN	Transcription initiation factor TFIID subunit 12 (Transcription initiation factor TFIID 20/15 kDa su ...	0.48	-	nuc	0	Nucleus	transcription factor TFIID complex [IDA]	600773	1H3O	161
Q61179 UniProt NPD GO	IRTF_MOUSE	Transcriptional regulator ISGF3 subunit gamma (IFN-alpha-responsive transcription factor subunit) (I ...	0.48	-	nuc	0	Nucleus				399
Q04727 UniProt NPD GO	TLE4_HUMAN	Transducin-like enhancer protein 4	0.48	-	nuc	0	Nucleus	nucleus [NAS]	605132		766
Q704Y3 UniProt NPD GO	TRPV1_MOUSE	Transient receptor potential cation channel subfamily V member 1 (TrpV1) (osm-9-like TRP channel 1) ...	0.48	-	end	6	Cell membrane; multi-pass membrane protein (By similarity)	integral to membrane [IDA] membrane [IDA]			839
Q9R186 UniProt NPD GO	TRPV6_RAT	Transient receptor potential cation channel subfamily V member 6 (TrpV6) (Epithelial calcium channel ...	0.48	-	end	6	Cell membrane; multi-pass membrane protein (By similarity)				727
O78489 UniProt NPD GO	IF2C_GUITH	Translation initiation factor IF-2, chloroplast	0.48	-	cyt	0	Plastid; chloroplast				735
P32502 UniProt NPD GO	EI2BB_YEAST	Translation initiation factor eIF-2B subunit beta (eIF-2B GDP-GTP exchange factor subunit beta) (Gua ...	0.48	-	mit	0		eukaryotic translation initiation factor 2B... [IDA] mitochondrion [IDA] ribosome [TAS]			381
P53815 UniProt NPD GO	SSRA_RABIT	Translocon-associated protein subunit alpha precursor (TRAP-alpha) (Signal sequence receptor subunit ...	0.48	-	end	1 *	Endoplasmic reticulum; endoplasmic reticulum membrane; single-pass type I membrane protein				286
Q8R500 UniProt NPD GO	MFN2_RAT	Transmembrane GTPase MFN2 (EC 3.6.5.-) (Mitofusin-2) (Mitochondrial transmembrane GTPase FZO1A) (HSG ...	0.48	-	nuc	1	Mitochondrion; mitochondrial outer membrane; multi-pass membrane protein. Colocalizes with BAX durin ...	cytosol [IDA] intrinsic to mitochondrial outer membrane [IDA]			757
Q8R182 UniProt NPD GO	TMG2_MOUSE	Transmembrane gamma-carboxyglutamic acid protein 2 precursor (Proline-rich Gla protein 2) (Proline-r ...	0.48	+	nuc	1	Membrane; single-pass type I membrane protein (By similarity)	integral to membrane [TAS]			198
Q9Y2B1 UniProt NPD GO	TMEM5_HUMAN	Transmembrane protein 5	0.48	-	mit	1 *	Membrane; single-pass type II membrane protein (Potential)	integral to plasma membrane [TAS]	605862		443
P47973 UniProt NPD GO	TTP_RAT	Tristetraproline (TTP) (Zinc finger protein 36) (Zfp-36) (TIS11A protein) (TIS11)	0.48	-	nuc	0	Nucleus	cytoplasm [IDA] nucleus [IDA]			320
Q9WUZ5 UniProt NPD GO	TNNI1_MOUSE	Troponin I, slow skeletal muscle (Troponin I, slow-twitch isoform)	0.48	-	nuc	0					186
P02645 UniProt NPD GO	TNNI1_RABIT	Troponin I, slow skeletal muscle (Troponin I, slow-twitch isoform)	0.48	-	nuc	0					184

You are viewing entries 26601 to 26650 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.