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
P35428 UniProt NPD GO	HES1_MOUSE	Transcription factor HES-1 (Hairy and enhancer of split 1)	0.72	-	nuc	0	Nucleus	cytoplasm [IDA] nucleus [IDA]			282
P17842 UniProt NPD GO	TF3A_XENBO	Transcription factor IIIA (Factor A) (TFIIIA)	0.72	-	nuc	0	Nucleus				339
Q01201 UniProt NPD GO	RELB_HUMAN	Transcription factor RelB (I-Rel)	0.72	+	mit	0	Nucleus		604758		579
P0C1G9 UniProt NPD GO	SOX11_RAT	Transcription factor SOX-11	0.72	+	nuc	0	Nucleus (By similarity)				395
P57073 UniProt NPD GO	SOX8_HUMAN	Transcription factor SOX-8	0.72	+	nuc	0	Nucleus (Potential)		605923		446
Q5EBA3 UniProt NPD GO	SPIB_RAT	Transcription factor Spi-B	0.72	+	nuc	0	Nucleus (Probable)				269
Q92172 UniProt NPD GO	TEF_CHICK	Transcription factor VBP (Vitellogenin gene-binding protein) (Thyrotroph embryonic factor homolog)	0.72	+	nuc	0	Nucleus (By similarity)	nucleus [IC]			319
P28515 UniProt NPD GO	ELT1_CAEEL	Transcription factor elt-1	0.72	-	nuc	0	Nucleus				416
Q02796 UniProt NPD GO	LGE1_YEAST	Transcriptional regulatory protein LGE1 (Large cells protein 1)	0.72	-	nuc	0	Nucleus	nucleus [IDA]			332
Q62440 UniProt NPD GO	TLE1_MOUSE	Transducin-like enhancer protein 1 (Groucho-related protein 1) (Grg-1)	0.72	+	nuc	0	Nucleus. Nuclear and chromatin-associated, depending on isoforms and phosphorylation status. Hyperph ...	nucleus [IDA] transcription factor complex [IDA]			770
Q9WVB3 UniProt NPD GO	TLE6_MOUSE	Transducin-like enhancer protein 6 (Groucho-related protein 6)	0.72	-	mit	0	Nucleus (By similarity)				581
Q07258 UniProt NPD GO	TGFB3_RAT	Transforming growth factor beta-3 precursor (TGF-beta-3)	0.72	-	exc	0	Secreted protein				412
Q8K424 UniProt NPD GO	TRPV3_MOUSE	Transient receptor potential cation channel subfamily V member 3 (TrpV3)	0.72	+	end	6	Membrane; multi-pass membrane protein (Probable)	membrane [IDA]			791
Q92545 UniProt NPD GO	TM131_HUMAN	Transmembrane protein 131 (Protein RW1) (Fragment)	0.72	-	end	2	Membrane; multi-pass membrane protein (Potential)				1805
Q61510 UniProt NPD GO	TRI25_MOUSE	Tripartite motif-containing protein 25 (Zinc finger protein 147) (Estrogen-responsive finger protein ...	0.72	-	nuc	0		cytoplasm [IDA]			634
Q9HCM9 UniProt NPD GO	TRI39_HUMAN	Tripartite motif-containing protein 39 (RING finger protein 23) (Testis-abundant finger protein)	0.72	-	nuc	0			605700		518
Q8MKD5 UniProt NPD GO	TNNI3_CANFA	Troponin I, cardiac muscle (Cardiac troponin I)	0.72	-	nuc	0					210
Q9UUG9 UniProt NPD GO	TSC2_SCHPO	Tuberous sclerosis 2 protein homolog	0.72	-	cyt	0					1339
Q4R4D7 UniProt NPD GO	INP4B_MACFA	Type II inositol-3,4-bisphosphate 4-phosphatase (EC 3.1.3.66) (Inositol polyphosphate 4-phosphatase ...	0.72	-	cyt	0					813
P28192 UniProt NPD GO	PTP2_CAEEL	Tyrosine-protein phosphatase 2 (EC 3.1.3.48) (Protein-tyrosine phosphatase 2)	0.72	-	nuc	1					1156
Q00684 UniProt NPD GO	CDC14_YEAST	Tyrosine-protein phosphatase CDC14 (EC 3.1.3.48)	0.72	-	nuc	0	Nucleus; nucleolus. Cytoplasm	nucleolus [IDA] nucleus [IDA] RENT complex [IDA] spindle pole body [IDA]			551
P40055 UniProt NPD GO	UTP7_YEAST	U3 small nucleolar RNA-associated protein 7 (U3 snoRNA-associated protein 7)	0.72	-	nuc	0	Nucleus; nucleolus	small nucleolar ribonucleoprotein complex [IPI]			554
Q04958 UniProt NPD GO	YMF9_YEAST	UPF0028 protein YML059C	0.72	-	nuc	3	Membrane; multi-pass membrane protein (Potential)	endoplasmic reticulum [IDA]			1679
P51784 UniProt NPD GO	UBP11_HUMAN	Ubiquitin carboxyl-terminal hydrolase 11 (EC 3.1.2.15) (Ubiquitin thioesterase 11) (Ubiquitin-specif ...	0.72	-	cyt	0	Nucleus		300050		920
P60051 UniProt NPD GO	UBP14_PANTR	Ubiquitin carboxyl-terminal hydrolase 14 (EC 3.1.2.15) (Ubiquitin thioesterase 14) (Ubiquitin-specif ...	0.72	-	nuc	0					492
Q8R5H1 UniProt NPD GO	UBP15_MOUSE	Ubiquitin carboxyl-terminal hydrolase 15 (EC 3.1.2.15) (Ubiquitin thioesterase 15) (Ubiquitin-specif ...	0.72	-	nuc	0					981
O75604 UniProt NPD GO	UBP2_HUMAN	Ubiquitin carboxyl-terminal hydrolase 2 (EC 3.1.2.15) (Ubiquitin thioesterase 2) (Ubiquitin-specific ...	0.72	-	nuc	0			604725		605
Q8W4N3 UniProt NPD GO	UBP2_ARATH	Ubiquitin carboxyl-terminal hydrolase 2 (EC 3.1.2.15) (Ubiquitin thioesterase 2) (Ubiquitin-specific ...	0.72	-	nuc	0					961
Q93009 UniProt NPD GO	UBP7_HUMAN	Ubiquitin carboxyl-terminal hydrolase 7 (EC 3.1.2.15) (Ubiquitin thioesterase 7) (Ubiquitin-specific ...	0.72	-	cyt	0	Nucleus. Nuclear, present in a minority of ND10 nuclear bodies. Association with Vmw110 at early tim ...	nucleus [TAS]	602519	2FOP	1102
Q9VX91 UniProt NPD GO	UBR1_DROME	Ubiquitin-protein ligase E3 component N-recognin (EC 6.-.-.-) (Ubiquitin-protein ligase E3-alpha)	0.72	-	mit	0					1824
Q09833 UniProt NPD GO	YAD7_SCHPO	Uncharacterized RNA methyltransferase C4G8.07c (EC 2.1.1.-)	0.72	-	mit	0					527
Q8BFT2 UniProt NPD GO	CN094_MOUSE	Uncharacterized protein C14orf94 homolog	0.72	-	cyt	0					363
Q9H079 UniProt NPD GO	CO029_HUMAN	Uncharacterized protein C15orf29	0.72	-	nuc	0					304
Q8BH50 UniProt NPD GO	CR025_MOUSE	Uncharacterized protein C18orf25 homolog	0.72	-	nuc	0					245
P34216 UniProt NPD GO	YBE7_YEAST	Uncharacterized protein YBL047C	0.72	-	nuc	0		actin cortical patch [IDA] bud neck [IDA] bud tip [IDA]		2G3Q	1381
P38753 UniProt NPD GO	YHA2_YEAST	Uncharacterized protein YHL002W	0.72	-	nuc	0		endosome [IDA]			452
Q07074 UniProt NPD GO	YH007_YEAST	Uncharacterized protein YHR007C-A	0.72	+	nuc	1 *	Membrane; single-pass membrane protein (Potential)				71
Q08421 UniProt NPD GO	YO051_YEAST	Uncharacterized protein YOR051C	0.72	-	nuc	0	Nucleus	nucleus [IDA]			412
Q08930 UniProt NPD GO	YP191_YEAST	Uncharacterized protein YPL191C	0.72	-	nuc	0	Cytoplasm	cytoplasm [IDA]			360
Q5B5E0 UniProt NPD GO	VPS32_EMENI	Vacuolar sorting protein 32	0.72	-	nuc	0	Cytoplasm (By similarity). Endosome; endosomal membrane; peripheral membrane protein (By similarity) ...				242
Q06708 UniProt NPD GO	VAC14_YEAST	Vacuole morphology and inheritance protein 14 (Swollen vacuole phenotype 2 protein)	0.72	-	nuc	0	Vacuole; vacuolar membrane; peripheral membrane protein. Limiting membrane of the vacuole. Localizat ...	vacuolar membrane (sensu Fungi) [IDA] vacuole [IDA]			880
Q62059 UniProt NPD GO	CSPG2_MOUSE	Versican core protein precursor (Large fibroblast proteoglycan) (Chondroitin sulfate proteoglycan co ...	0.72	-	nuc	0	Secreted protein; extracellular space; extracellular matrix	extracellular matrix (sensu Metazoa) [IDA]			3357
Q10152 UniProt NPD GO	YAT7_SCHPO	Very hypothetical protein C1D4.07c in chromosome I	0.72	-	mit	0					146
P49646 UniProt NPD GO	YYY1_HUMAN	Very very hypothetical protein RMSA-1	0.72	+	nuc	1 *		chromatin [TAS] nucleus [TAS]			418
P05690 UniProt NPD GO	VIT2_CAEEL	Vitellogenin-2 precursor	0.72	-	exc	0	Secreted protein				1613
O00305 UniProt NPD GO	CACB4_HUMAN	Voltage-dependent L-type calcium channel subunit beta-4 (CAB4) (Calcium channel voltage-dependent su ...	0.72	-	mit	0		voltage-gated calcium channel complex [TAS]	600669	2D46	520
Q12510 UniProt NPD GO	YD156_YEAST	WD repeat protein YDL156W	0.72	-	nuc	0	Cytoplasm. Nucleus	cytoplasm [IDA] nucleus [IDA]			522
Q7XA72 UniProt NPD GO	WBC21_ARATH	White-brown complex homolog protein 21	0.72	-	nuc	0	Membrane; multi-pass membrane protein (By similarity)				467
Q92834 UniProt NPD GO	RPGR_HUMAN	X-linked retinitis pigmentosa GTPase regulator	0.72	-	nuc	0	Golgi apparatus (By similarity)	Golgi apparatus [ISS]	312610		1020
Q8N567 UniProt NPD GO	ZCHC9_HUMAN	Zinc finger CCHC domain-containing protein 9	0.72	-	nuc	0					271

You are viewing entries 13051 to 13100 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.