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
Q7TSE6 UniProt NPD GO	ST38L_MOUSE	Serine/threonine-protein kinase 38-like (EC 2.7.11.1) (NDR2 protein kinase) (Nuclear Dbf2-related ki ...	0.53	-	cyt	0	Cytoplasm. Cytoskeleton. Associated with the actin cytoskeleton	actin cytoskeleton [IDA] cytoplasm [IDA]			464
P51568 UniProt NPD GO	AFC3_ARATH	Serine/threonine-protein kinase AFC3 (EC 2.7.12.1)	0.53	+	nuc	0					400
O70405 UniProt NPD GO	ULK1_MOUSE	Serine/threonine-protein kinase ULK1 (EC 2.7.11.1) (Unc-51-like kinase 1) (Serine/threonine-protein ...	0.53	-	nuc	0		cytoplasmic vesicle membrane [IDA] membrane fraction [IDA] neuron projection [IDA]			1051
Q05681 UniProt NPD GO	PP2B_NEUCR	Serine/threonine-protein phosphatase 2B catalytic subunit (EC 3.1.3.16) (Calmodulin-dependent calcin ...	0.53	-	cyt	0					518
Q09212 UniProt NPD GO	SRA9_CAEEL	Serpentine receptor class alpha-9 (Protein sra-9)	0.53	-	end	6 *	Membrane; multi-pass membrane protein (Potential)				331
P16254 UniProt NPD GO	SRP14_MOUSE	Signal recognition particle 14 kDa protein (SRP14)	0.53	-	nuc	0	Cytoplasm			1914	110
Q9NAD6 UniProt NPD GO	STAT1_CAEEL	Signal transducer and activator of transcription 1	0.53	-	nuc	0	Cytoplasm. Nucleus. Translocated into the nucleus in response to phosphorylation				706
Q17241 UniProt NPD GO	SGF1_BOMMO	Silk gland factor 1 (SGF-1)	0.53	+	nuc	0	Nucleus				349
P81564 UniProt NPD GO	CALCR_PHYBI	Skin calcitonin gene-related peptide precursor (S-CGRP)	0.53	-	exc	0	Secreted protein				115
P08104 UniProt NPD GO	SCN3A_RAT	Sodium channel protein type 3 subunit alpha (Sodium channel protein type III subunit alpha) (Voltage ...	0.53	+	end	19	Membrane; multi-pass membrane protein	voltage-gated sodium channel complex [TAS]		1QG9	1951
Q9UQD0 UniProt NPD GO	SCN8A_HUMAN	Sodium channel protein type 8 subunit alpha (Sodium channel protein type VIII subunit alpha) (Voltag ...	0.53	+	end	19	Membrane; multi-pass membrane protein	integral to membrane [TAS] voltage-gated sodium channel complex [IC]	600702		1980
Q9QZX8 UniProt NPD GO	SO1B2_RAT	Solute carrier organic anion transporter family member 1B2 (Solute carrier family 21 member 10) (Sod ...	0.53	-	end	11 *	Cell membrane; basolateral cell membrane; multi-pass membrane protein. Confined to the basolateral p ...				652
Q99JL1 UniProt NPD GO	SPEF1_MOUSE	Sperm flagellar protein 1	0.53	+	nuc	0	Cytoplasm. Present in the tails of developing and epididymal sperm, internal to the fibrous sheath a ...	cytoplasm [IDA] flagellum (sensu Eukaryota) [IDA]			234
P53252 UniProt NPD GO	PIL1_YEAST	Sphingolipid long chain base-responsive protein PIL1	0.53	-	mit	0	Lipid particle	cytoplasm [IDA] mitochondrial outer membrane [IDA] mitochondrion [IDA]			339
P08458 UniProt NPD GO	SPS1_YEAST	Sporulation-specific protein 1 (EC 2.7.11.1)	0.53	-	nuc	0	Nucleus. Cytoplasm	cytoplasm [IDA] nucleus [IDA] prospore membrane [IDA]			490
O08580 UniProt NPD GO	ERR1_MOUSE	Steroid hormone receptor ERR1 (Estrogen-related receptor, alpha) (ERR-alpha) (Estrogen receptor-like ...	0.53	-	cyt	0	Nucleus (By similarity)				462
P08462 UniProt NPD GO	GRPB_RAT	Submandibular gland secretory Glx-rich protein CB precursor (GRP-CB) (Contiguous repeat polypeptide) ...	0.53	-	exc	0	Secreted protein				247
Q9QX78 UniProt NPD GO	SOCS1_RAT	Suppressor of cytokine signaling 1 (SOCS-1)	0.53	+	nuc	0					212
O35718 UniProt NPD GO	SOCS3_MOUSE	Suppressor of cytokine signaling 3 (SOCS-3) (Cytokine-inducible SH2 protein 3) (CIS-3) (Protein EF-1 ...	0.53	-	nuc	0					225
Q7L8C5 UniProt NPD GO	SYT13_HUMAN	Synaptotagmin-13 (Synaptotagmin XIII) (SytXIII)	0.53	-	nuc	1 *	Membrane; single-pass membrane protein (By similarity)		607716	1WFM	426
Q5E9J8 UniProt NPD GO	RIC8A_BOVIN	Synembryn-A (Protein Ric-8A)	0.53	-	nuc	0	Cytoplasm (By similarity)				530
O14662 UniProt NPD GO	STX16_HUMAN	Syntaxin-16 (Syn16)	0.53	-	gol	1	Golgi apparatus; Golgi membrane; single-pass type IV membrane protein. Isoform C: Cytoplasm	cytoplasm [TAS] Golgi apparatus [TAS] microsome [TAS]	603666		325
P31314 UniProt NPD GO	TLX1_HUMAN	T-cell leukemia homeobox protein 1 (Homeobox protein Hox-11) (TCL-3 proto-oncogene)	0.53	+	nuc	0	Nucleus (Probable)		186770		330
Q9BXI6 UniProt NPD GO	TBC10_HUMAN	TBC1 domain family member 10A (EBP50-PDX interactor of 64 kDa) (EPI64 protein)	0.53	-	nuc	0	Localizes to the microvilli-rich region of the syncytiotrophoblast	microvillus [TAS]			508
Q9UJ04 UniProt NPD GO	TSYL4_HUMAN	Testis-specific Y-encoded-like protein 4 (TSPY-like 4)	0.53	-	nuc	0					414
Q01755 UniProt NPD GO	TS13_MOUSE	Testis-specific protein PBS13	0.53	-	nuc	0					566
Q9CSP9 UniProt NPD GO	TTC14_MOUSE	Tetratricopeptide repeat protein 14 (TPR repeat protein 14) (Fragment)	0.53	-	nuc	0					441
Q8TAM2 UniProt NPD GO	TTC8_HUMAN	Tetratricopeptide repeat protein 8 (TPR repeat protein 8) (Bardet-Biedl syndrome 8 protein)	0.53	-	cyt	0	Centrosome		608132		531
Q9PVE4 UniProt NPD GO	THB_BRARE	Thyroid hormone receptor beta	0.53	+	nuc	0	Nucleus				386
P18117 UniProt NPD GO	THBA_XENLA	Thyroid hormone receptor beta-A	0.53	+	cyt	0	Nucleus				373
Q9Y2C9 UniProt NPD GO	TLR6_HUMAN	Toll-like receptor 6 precursor	0.53	-	end	2 *	Cell membrane; single-pass type I membrane protein (By similarity). Phagosome; phagosomal membrane; ...	integral to plasma membrane [TAS] membrane [ISS] phagocytic vesicle [ISS]	605403		796
Q5KNK1 UniProt NPD GO	SPT5_CRYNE	Transcription elongation factor SPT5 (Chromatin elongation factor SPT5)	0.53	+	cyt	0	Nucleus (By similarity)				1152
Q08639 UniProt NPD GO	TDP1_MOUSE	Transcription factor Dp-1 (E2F dimerization partner 1) (DRTF1-polypeptide 1)	0.53	-	nuc	0	Nucleus	nucleus [IDA] transcription factor complex [IDA]			410
P41212 UniProt NPD GO	ETV6_HUMAN	Transcription factor ETV6 (ETS-related protein Tel1) (Tel) (ETS translocation variant 6)	0.53	-	nuc	0	Nucleus		600618	1LKY	452
O54791 UniProt NPD GO	MAFF_MOUSE	Transcription factor MafF (V-maf musculoaponeurotic fibrosarcoma oncogene homolog F)	0.53	-	nuc	0	Nucleus (By similarity)				156
P48380 UniProt NPD GO	RFX3_HUMAN	Transcription factor RFX3	0.53	+	nuc	0	Nucleus (Probable)	nucleus [IC]	601337		749
P48381 UniProt NPD GO	RFX3_MOUSE	Transcription factor RFX3	0.53	+	nuc	0	Nucleus (Probable)	nucleus [ISS]			749
Q39237 UniProt NPD GO	TGA1_ARATH	Transcription factor TGA1 (DNA-binding protein TGA1a-like protein) (AtbZIP47)	0.53	-	cyt	0	Nucleus				368
Q966L8 UniProt NPD GO	CHE1_CAEEL	Transcription factor che-1 (Abnormal chemotaxis protein 1)	0.53	-	nuc	0	Nucleus (Probable)				279
Q12297 UniProt NPD GO	TAF3_YEAST	Transcription initiation factor TFIID subunit 3 (TBP-associated factor 3) (TBP-associated factor 47 ...	0.53	-	nuc	0	Nucleus	transcription factor TFIID complex [IDA]			353
Q62311 UniProt NPD GO	TAF6_MOUSE	Transcription initiation factor TFIID subunit 6 (Transcription initiation factor TFIID 70 kDa subuni ...	0.53	-	nuc	0	Nucleus				678
P54811 UniProt NPD GO	TERA1_CAEEL	Transitional endoplasmic reticulum ATPase homolog 1 (p97/CDC48 homolog 1) (Cell division cycle-relat ...	0.53	-	nuc	0					809
Q7Z403 UniProt NPD GO	TMC6_HUMAN	Transmembrane channel-like protein 6 (Epidermodysplasia verruciformis protein 1) (Protein LAK-4)	0.53	+	end	10	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein		605828		805
P47097 UniProt NPD GO	YJZ6_YEAST	Transposon Ty1 protein A	0.53	-	nuc	0					440
P47099 UniProt NPD GO	YJZ8_YEAST	Transposon Ty1 protein A	0.53	-	nuc	0					440
P08405 UniProt NPD GO	YTY1_YEAST	Transposon Ty1-15 52 kDa hypothetical protein	0.53	-	nuc	0					440
P25383 UniProt NPD GO	YCC0_YEAST	Transposon Ty2 protein A (Ty1-17 protein A)	0.53	-	nuc	0					438
Q96RU7 UniProt NPD GO	TRIB3_HUMAN	Tribbles homolog 3 (TRB-3) (Neuronal cell death-inducible putative kinase) (p65-interacting inhibito ...	0.53	-	mit	0		nucleus [ISS]	607898		358
Q99PP9 UniProt NPD GO	TRI16_MOUSE	Tripartite motif-containing protein 16 (Estrogen-responsive B box protein)	0.53	-	nuc	0	Cytoplasm	cytoplasm [IDA]			556
Q12899 UniProt NPD GO	TRI26_HUMAN	Tripartite motif-containing protein 26 (Zinc finger protein 173) (Acid finger protein) (AFP) (RING f ...	0.53	-	cyt	0			600830		539

You are viewing entries 23401 to 23450 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.