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
Q9USH7 UniProt NPD GO	PSY1_SCHPO	Syntaxin-like protein psy1	0.57	-	nuc	1	Cell membrane; single-pass type IV membrane protein. During vegetative growth located at the plasma ...	plasma membrane [IDA] prospore membrane [IDA]			284
Q19691 UniProt NPD GO	TBX2_CAEEL	T-box protein 2	0.57	-	nuc	0	Nucleus (Potential)				423
Q22292 UniProt NPD GO	TBX8_CAEEL	T-box transcription factor tbx-8	0.57	-	nuc	0	Nucleus	nucleus [IEP]			315
P79779 UniProt NPD GO	TBX6L_CHICK	T-box-containing protein TBX6L (Fragment)	0.57	-	nuc	0	Nucleus (Potential)				361
Q3UU67 UniProt NPD GO	TRAT1_MOUSE	T-cell receptor-associated transmembrane adapter 1 (T-cell receptor-interacting molecule) (TRIM)	0.57	+	nuc	1 *	Cell membrane; single-pass type III membrane protein (By similarity)				187
P97357 UniProt NPD GO	TAF1A_MOUSE	TATA box-binding protein-associated factor RNA polymerase I subunit A (TATA box-binding protein-asso ...	0.57	-	cyt	0	Nucleus (By similarity)	RNA polymerase I transcription factor complex [TAS]			453
Q9Y4K3 UniProt NPD GO	TRAF6_HUMAN	TNF receptor-associated factor 6 (Interleukin 1 signal transducer) (RING finger protein 85)	0.57	-	nuc	0	Cytoplasm (Probable)		602355	1LB6	522
Q86VP1 UniProt NPD GO	TAXB1_HUMAN	Tax1-binding protein 1 (TRAF6-binding protein)	0.57	-	nuc	0			605326		789
Q66HA4 UniProt NPD GO	TAXB1_RAT	Tax1-binding protein 1 homolog (Liver regeneration-related protein LRRG004)	0.57	-	nuc	0					813
Q8BW49 UniProt NPD GO	TTC12_MOUSE	Tetratricopeptide repeat protein 12 (TPR repeat protein 12)	0.57	-	cyt	0					704
Q91279 UniProt NPD GO	THB_PAROL	Thyroid hormone receptor beta (THR-beta)	0.57	+	cyt	0	Nucleus				395
P41224 UniProt NPD GO	TEF_RAT	Thyrotroph embryonic factor	0.57	+	nuc	0	Nucleus	nucleus [IEP]			301
Q6CC84 UniProt NPD GO	SPT5_YARLI	Transcription elongation factor SPT5 (Chromatin elongation factor SPT5)	0.57	+	nuc	0	Nucleus (By similarity)				980
Q9Y242 UniProt NPD GO	TCF19_HUMAN	Transcription factor 19 (Transcription factor SC1)	0.57	+	nuc	0	Nucleus (Potential)		600912		345
O35437 UniProt NPD GO	TCF21_MOUSE	Transcription factor 21 (Podocyte-expressed 1) (Pod-1) (Epicardin) (Capsulin)	0.57	-	nuc	0					179
Q41558 UniProt NPD GO	HBP1C_WHEAT	Transcription factor HBP-1b(c1) (Fragment)	0.57	-	nuc	0	Nucleus				476
Q4JL84 UniProt NPD GO	MYB59_ARATH	Transcription factor MYB59 (Myb-related protein 59) (AtMYB59)	0.57	-	nuc	0	Nucleus. Isoform MYB59-2 and isoform MYB59-3 (harboring both NLS1 and NLS2) are nuclear, werheas iso ...				235
P38129 UniProt NPD GO	TAF5_YEAST	Transcription initiation factor TFIID subunit 5 (TBP-associated factor 5) (TBP-associated factor 90 ...	0.57	-	nuc	0		SAGA complex [IDA] SLIK (SAGA-like) complex [IPI] transcription factor TFIID complex [IDA]			798
P49847 UniProt NPD GO	TAF6_DROME	Transcription initiation factor TFIID subunit 6 (Transcription initiation factor TFIID 62 kDa subuni ...	0.57	-	nuc	0	Nucleus			1TAF	606
Q99594 UniProt NPD GO	TEAD3_HUMAN	Transcriptional enhancer factor TEF-5 (TEA domain family member 3) (TEAD-3) (DTEF-1)	0.57	-	nuc	0	Nucleus		603170		435
Q12041 UniProt NPD GO	MET32_YEAST	Transcriptional regulator MET32 (Methionine-requiring protein 32)	0.57	-	nuc	0	Cytoplasm. Nucleus	nucleus [IPI]			191
Q38895 UniProt NPD GO	SUP_ARATH	Transcriptional regulator SUPERMAN	0.57	-	nuc	0	Nucleus			1NJQ	204
Q09715 UniProt NPD GO	TUP11_SCHPO	Transcriptional repressor tup11	0.57	-	nuc	0		nucleus [IDA]			614
Q04600 UniProt NPD GO	TMA64_YEAST	Translation machinery-associated protein 64	0.57	+	nuc	0					565
Q7YR32 UniProt NPD GO	TRI10_PANTR	Tripartite motif-containing protein 10 (RING finger protein 9) (B30-RING finger protein)	0.57	-	cyt	0					481
P42637 UniProt NPD GO	TPM1_SCHMA	Tropomyosin 1 (TMI) (Polypeptide 49)	0.57	-	nuc	0					284
P34787 UniProt NPD GO	TBG_PLAFO	Tubulin gamma chain (Gamma tubulin)	0.57	-	nuc	0					452
Q8CIV8 UniProt NPD GO	TBCE_MOUSE	Tubulin-specific chaperone E (Tubulin-folding cofactor E)	0.57	-	nuc	0				1WJN	524
O14763 UniProt NPD GO	TR10B_HUMAN	Tumor necrosis factor receptor superfamily member 10B precursor (Death receptor 5) (TNF-related apop ...	0.57	-	nuc	1 *	Membrane; single-pass type I membrane protein	integral to membrane [IC]	275355	1ZA3	440
O35305 UniProt NPD GO	TNR11_MOUSE	Tumor necrosis factor receptor superfamily member 11A precursor (Receptor activator of NF-KB) (Osteo ...	0.57	-	exc	1	Membrane; single-pass type I membrane protein (Potential)				625
Q9EPU5 UniProt NPD GO	TNR21_MOUSE	Tumor necrosis factor receptor superfamily member 21 precursor (TNFR-related death receptor 6) (Deat ...	0.57	-	exc	2 *	Membrane; single-pass type I membrane protein (Probable)				655
Q5RJR2 UniProt NPD GO	TWF1_RAT	Twinfilin-1	0.57	-	nuc	0	Cytoplasm. Diffuse cytoplasmic localization with perinuclear and G-actin-rich cortical actin structu ...				350
Q96PE3 UniProt NPD GO	INP4A_HUMAN	Type I inositol-3,4-bisphosphate 4-phosphatase (EC 3.1.3.66) (Inositol polyphosphate 4-phosphatase t ...	0.57	-	nuc	0			600916		977
P32586 UniProt NPD GO	PYP2_SCHPO	Tyrosine-protein phosphatase 2 (EC 3.1.3.48) (Protein-tyrosine phosphatase 2) (PTPase 2)	0.57	-	nuc	0	Cytoplasm	cytoplasm [IDA]			711
Q3T0M3 UniProt NPD GO	IMP3_BOVIN	U3 small nucleolar ribonucleoprotein protein IMP3 (U3 snoRNP protein IMP3)	0.57	-	cyt	0	Nucleus; nucleolus (By similarity)				184
Q18953 UniProt NPD GO	UGTAP_CAEEL	UGA suppressor tRNA-associated protein homolog	0.57	+	nuc	0	Cytoplasm (By similarity)				481
Q5XIJ1 UniProt NPD GO	DC12_RAT	UPF0361 protein DC12 homolog	0.57	-	nuc	0					353
Q7ZTY7 UniProt NPD GO	USE1_BRARE	USE1-like protein	0.57	-	nuc	1	Endoplasmic reticulum; endoplasmic reticulum membrane; single-pass type II membrane protein (By simi ...				258
Q6BU36 UniProt NPD GO	UBC2_DEBHA	Ubiquitin-conjugating enzyme E2 2 (EC 6.3.2.19) (Ubiquitin-protein ligase UBC2) (Ubiquitin carrier p ...	0.57	-	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity)				168
P59113 UniProt NPD GO	URP1_MOUSE	Unc-112-related protein 1 (Kindlin-1) (Fragment)	0.57	-	cyt	0	Cytoplasm (By similarity). Colocalizes with filamentous actin. Cell membrane; cell-matrix junction; ...				637
P53145 UniProt NPD GO	YGJ9_YEAST	Uncharacterized GTP-binding protein YGL099W	0.57	-	nuc	0		cytoplasm [IDA]			640
P53893 UniProt NPD GO	YNQ3_YEAST	Uncharacterized GTP-binding protein YNL163C	0.57	-	mit	0		cytoplasm [IDA]			1110
P40564 UniProt NPD GO	YIS4_YEAST	Uncharacterized J domain-containing protein YIR004W	0.57	-	cyt	0		cytosol [IDA]			432
Q8IYD9 UniProt NPD GO	CR054_HUMAN	Uncharacterized protein C18orf54 precursor	0.57	-	nuc	0	Secreted protein (Potential)				372
Q96EL1 UniProt NPD GO	CC054_HUMAN	Uncharacterized protein C3orf54	0.57	-	nuc	0					285
Q07799 UniProt NPD GO	YL007_YEAST	Uncharacterized protein YLL007C	0.57	-	nuc	0	Cytoplasm	cytoplasm [IDA]			665
P53735 UniProt NPD GO	YN8N_YEAST	Uncharacterized protein YNR039C	0.57	-	end	6	Membrane; multi-pass membrane protein (Potential)	endoplasmic reticulum [IDA]			605
Q99PM9 UniProt NPD GO	UCK2_MOUSE	Uridine-cytidine kinase 2 (EC 2.7.1.48) (UCK 2) (Uridine monophosphokinase 2) (Cytidine monophosphok ...	0.57	-	cyt	0					261
Q8BUB6 UniProt NPD GO	UST_MOUSE	Uronyl 2-sulfotransferase (EC 2.8.2.-)	0.57	-	mit	1 *	Golgi apparatus; Golgi membrane; single-pass type II membrane protein (By similarity)				407
P59016 UniProt NPD GO	VP33B_MOUSE	Vacuolar protein sorting 33B	0.57	-	cyt	0	Late endosome; late endosomal membrane; peripheral membrane protein (By similarity). Lysosome; lysos ...				617

You are viewing entries 21051 to 21100 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.