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
Q5R6D8 UniProt NPD GO	DDX46_PONPY	Probable ATP-dependent RNA helicase DDX46 (EC 3.6.1.-) (DEAD box protein 46)	0.96	+	nuc	0	Nucleus; nucleoplasm; nuclear speckle (By similarity). Nucleus; nucleoplasm; Cajal body (By similari ...				1032
Q62780 UniProt NPD GO	DDX46_RAT	Probable ATP-dependent RNA helicase DDX46 (EC 3.6.1.-) (DEAD box protein 46) (Helicase of 117.4 kDa) ...	0.96	+	nuc	0	Nucleus; nucleoplasm; nuclear speckle (By similarity). Nucleus; nucleoplasm; Cajal body (By similari ...	nucleus [IDA]			1032
Q8T498 UniProt NPD GO	GAP2_DROME	Probable Ras GTPase-activating protein	0.96	-	nuc	0	Cytoplasm (By similarity)	cytoplasm [ISS]			1556
O04336 UniProt NPD GO	WRK21_ARATH	Probable WRKY transcription factor 21 (WRKY DNA-binding protein 21)	0.96	-	nuc	0	Nucleus (Probable)				380
O43051 UniProt NPD GO	NOP14_SCHPO	Probable nucleolar complex protein 14	0.96	-	nuc	0	Nucleus; nucleolus (By similarity)				827
P38994 UniProt NPD GO	MSS4_YEAST	Probable phosphatidylinositol-4-phosphate 5-kinase MSS4 (EC 2.7.1.68) (1-phosphatidylinositol-4-phos ...	0.96	-	nuc	0		plasma membrane [IDA]			779
P25389 UniProt NPD GO	KCC4_YEAST	Probable serine/threonine-protein kinase KCC4 (EC 2.7.11.1)	0.96	-	nuc	0	Bud neck	bud neck [IDA]			1037
P50104 UniProt NPD GO	STB4_YEAST	Probable transcriptional regulatory protein STB4	0.96	+	end	1 *	Nucleus (Probable)	nucleus [IC]			949
Q11076 UniProt NPD GO	UBC17_CAEEL	Probable ubiquitin-conjugating enzyme protein 17	0.96	+	mit	0					679
Q96HE9 UniProt NPD GO	PRR11_HUMAN	Proline-rich protein 11	0.96	+	nuc	0					360
P53858 UniProt NPD GO	BNI4_YEAST	Protein BNI4	0.96	+	nuc	0		bud neck [IDA] incipient bud site [IDA] septin ring [IDA]			892
Q5R9B3 UniProt NPD GO	CJ118_PONPY	Protein C10orf118 homolog (Fragment)	0.96	-	nuc	0					689
Q8NEJ9 UniProt NPD GO	CN120_HUMAN	Protein C14orf120	0.96	+	nuc	0					315
Q9DB96 UniProt NPD GO	CN120_MOUSE	Protein C14orf120 homolog	0.96	+	nuc	0					315
Q8CCG1 UniProt NPD GO	CN140_MOUSE	Protein C14orf140 homolog	0.96	-	nuc	0					527
Q6AYP4 UniProt NPD GO	CN140_RAT	Protein C14orf140 homolog	0.96	-	nuc	0					525
P39013 UniProt NPD GO	END3_YEAST	Protein END3	0.96	-	nuc	0		actin cortical patch [TAS]			349
Q12418 UniProt NPD GO	GIS3_YEAST	Protein GIS3	0.96	-	nuc	0	Cytoplasm. Nucleus	cytoplasm [IDA] nucleus [IDA]			502
Q92617 UniProt NPD GO	K0220_HUMAN	Protein KIAA0220 (Fragment)	0.96	+	nuc	0					884
Q93073 UniProt NPD GO	K0256_HUMAN	Protein KIAA0256	0.96	-	nuc	0					1101
Q9C0H5 UniProt NPD GO	K1688_HUMAN	Protein KIAA1688	0.96	+	nuc	0	Nucleus (Potential)				1083
Q8BQ30 UniProt NPD GO	K1949_MOUSE	Protein KIAA1949 homolog	0.96	-	nuc	0					594
Q9Z1W6 UniProt NPD GO	LYRIC_RAT	Protein LYRIC (Lysine-rich CEACAM1 co-isolated protein) (Metastasis adhesion protein) (Metadherin)	0.96	+	nuc	1 *	Endoplasmic reticulum; endoplasmic reticulum membrane; single-pass type II membrane protein (By simi ...	tight junction [IPI]			581
O94851 UniProt NPD GO	MICA2_HUMAN	Protein MICAL-2	0.96	+	nuc	0	Cytoplasm (By similarity)		608881		1124
P42845 UniProt NPD GO	STB1_YEAST	Protein STB1 (SIN3-binding protein 1)	0.96	-	nuc	0	Cytoplasm. Nucleus	cytoplasm [IDA] nucleus [IDA] Sin3 complex [IPI]			420
Q26307 UniProt NPD GO	ANA_DROME	Protein anachronism precursor	0.96	-	nuc	0	Secreted protein				474
Q9UPA5 UniProt NPD GO	BSN_HUMAN	Protein bassoon (Zinc finger protein 231)	0.96	+	nuc	0	Cytoplasm (By similarity). Localized to the active zone of presynaptic density (By similarity)	nucleus [TAS]	604020		3925
O76906 UniProt NPD GO	CRM_DROME	Protein cramped	0.96	-	nuc	0	Nucleus. During S-phase in early embryogenesis	nucleus [IDA]			982
O60610 UniProt NPD GO	DIAP1_HUMAN	Protein diaphanous homolog 1 (Diaphanous-related formin-1) (DRF1)	0.96	-	nuc	0			602121		1248
Q01820 UniProt NPD GO	GCL_DROME	Protein germ cell-less	0.96	+	cyt	0	Pole plasm	nuclear pore [IDA] nucleus [TAS]			569
P52161 UniProt NPD GO	MAX_BRARE	Protein max (Myc-associated factor X)	0.96	+	nuc	0	Nucleus	nucleus [NAS]			165
P52162 UniProt NPD GO	MAX_CHICK	Protein max (Myc-associated factor X)	0.96	+	nuc	0	Nucleus				160
P61245 UniProt NPD GO	MAX_FELCA	Protein max (Myc-associated factor X)	0.96	+	nuc	0	Nucleus (By similarity)				160
P61244 UniProt NPD GO	MAX_HUMAN	Protein max (Myc-associated factor X)	0.96	+	nuc	0	Nucleus		154950	1R05	160
P28574 UniProt NPD GO	MAX_MOUSE	Protein max (Myc-associated factor X) (Protein myn) (Myc-binding novel HLH/LZ protein)	0.96	+	nuc	0	Nucleus			2A93	160
P31368 UniProt NPD GO	PDM1_DROME	Protein nubbin (Protein twain) (POU domain protein 1) (PDM-1) (dPOU-19) (dOCT1)	0.96	+	nuc	0	Nucleus				601
Q24167 UniProt NPD GO	SIMA_DROME	Protein similar	0.96	-	nuc	0	Nucleus (Potential)				1507
Q86B79 UniProt NPD GO	UNK_DROME	Protein unkempt	0.96	-	nuc	0	Cytoplasm	cytoplasm [IDA]			599
Q9U3V8 UniProt NPD GO	XMAS1_DROME	Protein xmas-1	0.96	-	nuc	0					736
Q859W7 UniProt NPD GO	YCF2_ANTFO	Protein ycf2	0.96	+	end	0	Plastid; chloroplast; chloroplast stroma (By similarity)				2392
Q5KHM0 UniProt NPD GO	INO80_CRYNE	Putative DNA helicase INO80 (EC 3.6.1.-)	0.96	+	nuc	0	Nucleus (By similarity)				1765
Q9LX16 UniProt NPD GO	EIL4_ARATH	Putative ETHYLENE-INSENSITIVE3-like 4 protein	0.96	-	nuc	0	Nucleus (By similarity)				471
O61764 UniProt NPD GO	TBX32_CAEEL	Putative T-box protein 32	0.96	+	nuc	1 *	Nucleus (Potential)				545
Q09219 UniProt NPD GO	TG178_CAEEL	Putative protein tag-178	0.96	-	nuc	1 *					753
Q9U1H0 UniProt NPD GO	CIC_DROME	Putative transcription factor capicua (Protein fettucine)	0.96	-	nuc	0	Nucleus				1403
O74906 UniProt NPD GO	YCS7_SCHPO	Putative zinc-finger protein C613.07	0.96	-	nuc	0					345
Q9JJ26 UniProt NPD GO	MEFV_MOUSE	Pyrin (Marenostrin)	0.96	-	nuc	0	Cytoplasm. Associated with microtubules and with the filamentous actin of perinuclear filaments and ...	microtubule associated complex [ISS]			767
P53046 UniProt NPD GO	ROM1_YEAST	RHO1 GDP-GTP exchange protein 1 (Protein kinase C suppressor SKC1)	0.96	-	nuc	0		intracellular [TAS]			1155
Q3MHI4 UniProt NPD GO	RNUXA_BOVIN	RNA U small nuclear RNA export adapter protein (Phosphorylated adapter RNA export protein)	0.96	-	nuc	0	Nucleus. Cytoplasm. Located in the nucleoplasm and Cajal bodies. Shuttles between the nucleus and th ...				394
Q8N1G1 UniProt NPD GO	REXO1_HUMAN	RNA exonuclease 1 homolog (EC 3.1.-.-) (Elongin A-binding protein 1) (EloA-BP1) (Transcription elong ...	0.96	-	nuc	0	Nucleus		609614		1221

You are viewing entries 1551 to 1600 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.