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
P19814 UniProt NPD GO	TGON3_RAT	Trans-Golgi network integral membrane protein TGN38 precursor	0.61	-	end	1	Golgi apparatus; trans-Golgi network				357
Q9U501 UniProt NPD GO	ELOF1_MANSE	Transcription elongation factor 1 homolog	0.61	+	nuc	0	Nucleus (By similarity)				82
Q759T6 UniProt NPD GO	SPT5_ASHGO	Transcription elongation factor SPT5 (Chromatin elongation factor SPT5)	0.61	-	nuc	0	Nucleus (By similarity)				959
Q9DDT5 UniProt NPD GO	SPT5H_BRARE	Transcription elongation factor SPT5 (DRB sensitivity-inducing factor large subunit) (DSIF large sub ...	0.61	-	cyt	0	Nucleus				1084
P58197 UniProt NPD GO	AP2A_RAT	Transcription factor AP-2 alpha (AP2-alpha) (Activating enhancer-binding protein 2 alpha) (Activator ...	0.61	-	nuc	0	Nucleus				437
Q92754 UniProt NPD GO	AP2C_HUMAN	Transcription factor AP-2 gamma (AP2-gamma) (Activating enhancer-binding protein 2 gamma) (Transcrip ...	0.61	-	nuc	0	Nucleus (Probable)		601602		450
P33293 UniProt NPD GO	BAF1_KLUMA	Transcription factor BAF1 (ARS-binding factor 1) (Protein ABF1) (Bidirectionally acting factor)	0.61	-	nuc	0	Nucleus				496
O60675 UniProt NPD GO	MAFK_HUMAN	Transcription factor MafK (Erythroid transcription factor NF-E2 p18 subunit)	0.61	-	nuc	0	Nucleus		600197		156
Q61827 UniProt NPD GO	MAFK_MOUSE	Transcription factor MafK (Erythroid transcription factor NF-E2 p18 subunit)	0.61	-	nuc	0	Nucleus	nucleus [IDA]			156
Q01892 UniProt NPD GO	SPIB_HUMAN	Transcription factor Spi-B	0.61	+	nuc	0	Isoform 1: Nucleus. Isoform 2: Cytoplasm	cytoplasm [TAS]	606802		262
Q39162 UniProt NPD GO	TGA4_ARATH	Transcription factor TGA4 (Ocs element-binding factor 4) (OBF4) (AtbZIP57)	0.61	-	nuc	0	Nucleus				364
O75486 UniProt NPD GO	SUPT3_HUMAN	Transcription initiation protein SPT3 homolog (SPT3-like protein)	0.61	+	mit	0	Nucleus	nucleus [IEP]	602947		399
Q13263 UniProt NPD GO	TIF1B_HUMAN	Transcription intermediary factor 1-beta (TIF1-beta) (Tripartite motif-containing protein 28) (Nucle ...	0.61	-	nuc	0	Nucleus. Associated with centromeric heterochromatin during cell differentiation through CBX1 (By si ...		601742	1FP0	834
P40914 UniProt NPD GO	HAP3_KLULA	Transcriptional activator HAP3	0.61	-	nuc	0	Nucleus				205
Q91YD4 UniProt NPD GO	TRPM2_MOUSE	Transient receptor potential cation channel subfamily M member 2 (EC 3.6.1.13) (Long transient recep ...	0.61	-	end	5	Membrane; multi-pass membrane protein				1507
Q9CY50 UniProt NPD GO	SSRA_MOUSE	Translocon-associated protein subunit alpha precursor (TRAP-alpha) (Signal sequence receptor subunit ...	0.61	-	end	1 *	Endoplasmic reticulum; endoplasmic reticulum membrane; single-pass type I membrane protein (By simil ...				286
Q5U405 UniProt NPD GO	TMPSD_MOUSE	Transmembrane protease, serine 13 (EC 3.4.21.-) (Mosaic serine protease) (Membrane-type mosaic serin ...	0.61	-	nuc	1	Membrane; single-pass type II membrane protein (Potential)				543
P38426 UniProt NPD GO	TPS3_YEAST	Trehalose synthase complex regulatory subunit TPS3 (Alpha,alpha-trehalose-phosphate synthase [UDP-fo ...	0.61	+	nuc	0	Cytoplasm	alpha,alpha-trehalose-phosphate synthase co... [IGI]			1054
P82179 UniProt NPD GO	TRDN_CANFA	Triadin	0.61	-	nuc	1 *	Sarcoplasmic reticulum; sarcoplasmic reticulum membrane; single-pass type II membrane protein				700
Q7TPM3 UniProt NPD GO	TRI17_MOUSE	Tripartite motif-containing protein 17	0.61	-	nuc	0					477
Q8C7M3 UniProt NPD GO	TRIM9_MOUSE	Tripartite motif-containing protein 9	0.61	-	nuc	0		cytoplasm [IDA]			817
P36188 UniProt NPD GO	TNNI_DROME	Troponin I (Tn I) (Protein wings apart-A) (Protein heldup)	0.61	+	nuc	0		troponin complex [NAS]			268
P53377 UniProt NPD GO	TBG_NEUCR	Tubulin gamma chain (Gamma tubulin)	0.61	-	cyt	0					461
Q9UBB9 UniProt NPD GO	TFP11_HUMAN	Tuftelin-interacting protein 11	0.61	-	cyt	0	Cytoplasm (By similarity). Nucleus (By similarity)	intracellular [ISS]			837
Q9QZM4 UniProt NPD GO	TR10B_MOUSE	Tumor necrosis factor receptor superfamily member 10B precursor (Death receptor 5) (MK)	0.61	-	mit	2 *	Membrane; single-pass type I membrane protein				381
Q8VCY6 UniProt NPD GO	UTP6_MOUSE	U3 small nucleolar RNA-associated protein 6 homolog (Multiple hat domains protein)	0.61	-	cyt	0	Nucleus; nucleolus (By similarity)				597
Q8R1M0 UniProt NPD GO	DC12_MOUSE	UPF0361 protein DC12 homolog	0.61	-	nuc	0					353
Q5NVR0 UniProt NPD GO	DC12_PONPY	UPF0361 protein DC12 homolog	0.61	-	nuc	0					354
Q9CQ56 UniProt NPD GO	USE1_MOUSE	USE1-like protein (D12 protein)	0.61	-	nuc	1	Endoplasmic reticulum; endoplasmic reticulum membrane; single-pass type II membrane protein (By simi ...				270
P54860 UniProt NPD GO	UFD2_YEAST	Ubiquitin conjugation factor E4 (Ubiquitin fusion degradation protein 2) (UB fusion protein 2)	0.61	-	nuc	0		cytoplasm [IDA] nucleus [IDA]			961
Q14139 UniProt NPD GO	UBE4A_HUMAN	Ubiquitin conjugation factor E4 A	0.61	-	end	0		ubiquitin ligase complex [TAS]	603753	1WGM	1066
Q965X6 UniProt NPD GO	SIA1_CAEEL	Ubiquitin ligase sia-1 (EC 6.3.2.-) (Seven in absentia homolog 1)	0.61	-	nuc	0					339
Q12205 UniProt NPD GO	YL057_YEAST	Uncharacterized glycosyl hydrolase YLR057W (EC 3.2.1.-)	0.61	-	mit	1 *	Membrane; single-pass type II membrane protein (Potential)				849
Q5XKK7 UniProt NPD GO	CO017_HUMAN	Uncharacterized protein C15orf17	0.61	-	nuc	0					198
Q3TEI4 UniProt NPD GO	CO039_MOUSE	Uncharacterized protein C15orf39 homolog	0.61	-	nuc	0					1023
Q9Y2B5 UniProt NPD GO	CP007_HUMAN	Uncharacterized protein C16orf7 (Protein ATP-BL)	0.61	-	nuc	0					438
Q5E969 UniProt NPD GO	CH004_BOVIN	Uncharacterized protein C8orf4 homolog	0.61	-	nuc	0					106
P38330 UniProt NPD GO	YB88_YEAST	Uncharacterized protein YBR238C	0.61	-	nuc	0		cytoplasm [IDA] mitochondrion [IDA]			731
P25617 UniProt NPD GO	YCQ6_YEAST	Uncharacterized protein YCR016W	0.61	+	nuc	0		nucleolus [IDA] nucleus [IDA]			290
P40080 UniProt NPD GO	YEV8_YEAST	Uncharacterized protein YER128W	0.61	-	nuc	0					203
P32343 UniProt NPD GO	YKM4_YEAST	Uncharacterized protein YKL124W	0.61	+	nuc	1 *					579
Q08634 UniProt NPD GO	YO238_YEAST	Uncharacterized protein YOR238W	0.61	-	nuc	0	Cytoplasm	cytoplasm [IDA]			303
Q9BZX2 UniProt NPD GO	UCK2_HUMAN	Uridine-cytidine kinase 2 (EC 2.7.1.48) (UCK 2) (Uridine monophosphokinase 2) (Cytidine monophosphok ...	0.61	-	cyt	0			609329	1XRJ	261
Q25532 UniProt NPD GO	VATG_MANSE	Vacuolar ATP synthase subunit G (EC 3.6.3.14) (V-ATPase G subunit) (Vacuolar proton pump G subunit) ...	0.61	+	cyt	0	Cell membrane; apical cell membrane. Apical plasma membrane of the goblet cells and Malpighian tubul ...				117
P59015 UniProt NPD GO	VPS18_BRARE	Vacuolar protein sorting 18	0.61	-	cyt	0	Late endosome; late endosomal membrane; peripheral membrane protein (By similarity). Lysosome; lysos ...				974
Q5AJC1 UniProt NPD GO	BRO1_CANAL	Vacuolar protein-sorting protein BRO1 (BRO domain-containing protein 1)	0.61	-	nuc	0	Cytoplasm (By similarity). Endosome (By similarity)				945
Q3HXY0 UniProt NPD GO	NGFV1_HOPST	Venom nerve growth factor 1 precursor (vNGF-1)	0.61	-	exc	0	Secreted protein				243
Q3HXY9 UniProt NPD GO	NGFV1_PSETE	Venom nerve growth factor 1 precursor (vNGF-1)	0.61	-	exc	0	Secreted protein				243
Q801E1 UniProt NPD GO	VAX2_BRARE	Ventral anterior homeobox 2	0.61	+	nuc	0	Nucleus (By similarity)				307
Q9BPS0 UniProt NPD GO	VIT2_PERAM	Vitellogenin-2 precursor (Vg-2)	0.61	-	nuc	0	Secreted protein (By similarity)				1876

You are viewing entries 18801 to 18850 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.