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
Q91YR7 UniProt NPD GO	PRP6_MOUSE	Pre-mRNA-processing factor 6 homolog (U5 snRNP-associated 102 kDa protein) (U5-102 kDa protein)	0.75	-	cyt	0	Nucleus (By similarity)				941
Q6CUQ5 UniProt NPD GO	CWC25_KLULA	Pre-mRNA-splicing factor CWC25	0.75	-	nuc	0	Nucleus (By similarity)				206
Q5AL13 UniProt NPD GO	CWC26_CANAL	Pre-mRNA-splicing factor CWC26	0.75	+	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity)				281
P32524 UniProt NPD GO	PRP21_YEAST	Pre-mRNA-splicing factor PRP21	0.75	-	nuc	0	Nucleus	snRNP U2 [IDA]			280
Q6BMK7 UniProt NPD GO	SLU7_DEBHA	Pre-mRNA-splicing factor SLU7	0.75	-	nuc	0	Nucleus (By similarity)				370
Q6BQ23 UniProt NPD GO	SYF1_DEBHA	Pre-mRNA-splicing factor SYF1	0.75	-	nuc	0	Nucleus (By similarity)				850
Q5BB35 UniProt NPD GO	CWC2_EMENI	Pre-mRNA-splicing factor cwc2	0.75	+	nuc	0	Nucleus (By similarity)				417
P30645 UniProt NPD GO	PDE2_CAEEL	Probable 3',5'-cyclic phosphodiesterase pde-2 (EC 3.1.4.17)	0.75	-	nuc	0					859
Q8H0Y8 UniProt NPD GO	WRK41_ARATH	Probable WRKY transcription factor 41 (WRKY DNA-binding protein 41)	0.75	-	nuc	0	Nucleus (Probable)				313
Q9FH83 UniProt NPD GO	WRK52_ARATH	Probable WRKY transcription factor 52 (WRKY DNA-binding protein 52) (Disease resistance protein RRS1 ...	0.75	+	cyt	0	Nucleus (Probable)				1288
Q9SJ09 UniProt NPD GO	WRK59_ARATH	Probable WRKY transcription factor 59 (WRKY DNA-binding protein 59)	0.75	-	nuc	0	Nucleus (Probable)				202
Q9SK33 UniProt NPD GO	WRK60_ARATH	Probable WRKY transcription factor 60 (WRKY DNA-binding protein 60)	0.75	-	nuc	0	Nucleus (Potential)				271
Q9LNJ0 UniProt NPD GO	CNG10_ARATH	Probable cyclic nucleotide-gated ion channel 10 (Cyclic nucleotide-and calmodulin-regulated ion chan ...	0.75	-	end	5	Cell membrane; multi-pass membrane protein (Potential)				711
Q18286 UniProt NPD GO	EXOC6_CAEEL	Probable exocyst complex component 6 (Exocyst complex component Sec15)	0.75	-	mit	0					817
Q7S9H0 UniProt NPD GO	NUF2_NEUCR	Probable kinetochore protein nuf-2	0.75	-	nuc	0	Nucleus (By similarity). Associated with kinetochores (By similarity)				464
Q09815 UniProt NPD GO	KAB7_SCHPO	Probable serine/threonine-protein kinase C16C9.07 (EC 2.7.12.1)	0.75	-	nuc	0					836
Q12244 UniProt NPD GO	YL054_YEAST	Probable transcriptional regulatory protein YLL054C	0.75	-	nuc	0	Nucleus (Probable)				769
P19541 UniProt NPD GO	YP133_YEAST	Probable transcriptional regulatory protein YPL133C	0.75	-	nuc	0	Nucleus (Probable)	cytoplasm [IDA] nucleus [IDA]			446
Q811B5 UniProt NPD GO	PRR3_MOUSE	Proline-rich protein 3 (MHC class I region proline-rich protein CAT56)	0.75	-	nuc	0					190
P51454 UniProt NPD GO	REL1_PANTR	Prorelaxin H1 precursor [Contains: Relaxin B chain; Relaxin A chain] (Fragment)	0.75	-	nuc	0	Secreted protein				166
P59278 UniProt NPD GO	Y1745_ARATH	Protein At1g51745	0.75	-	nuc	0					597
Q96NH3 UniProt NPD GO	CF170_HUMAN	Protein C6orf170	0.75	-	mit	0	Membrane; multi-pass membrane protein (Potential)				1247
Q9DB52 UniProt NPD GO	CI042_MOUSE	Protein C9orf42 homolog	0.75	-	nuc	0					284
Q6AYT4 UniProt NPD GO	CI042_RAT	Protein C9orf42 homolog	0.75	-	nuc	0					286
Q8N4H0 UniProt NPD GO	CI068_HUMAN	Protein C9orf68	0.75	-	nuc	0					392
P48969 UniProt NPD GO	DVR1_STRPU	Protein DVR-1 homolog precursor	0.75	-	nuc	1 *	Secreted protein (By similarity)				461
Q8BHE1 UniProt NPD GO	F51A1_MOUSE	Protein FAM51A1	0.75	-	mit	0					238
Q6CRY6 UniProt NPD GO	FYV7_KLULA	Protein FYV7	0.75	-	nuc	0	Nucleus; nucleolus (By similarity)				144
Q9AWL7 UniProt NPD GO	GIGAN_ORYSA	Protein GIGANTEA	0.75	+	nuc	0	Nucleus (By similarity)				1160
Q5S2C3 UniProt NPD GO	PIR_ARATH	Protein PIR (PIR of plants) (Protein PIROGI) (Protein KLUNKER) (AtSRA1)	0.75	-	end	0					1283
P38072 UniProt NPD GO	SCO2_YEAST	Protein SCO2, mitochondrial precursor	0.75	-	mit	0	Mitochondrion; mitochondrial inner membrane (By similarity)	mitochondrial envelope [IDA]			301
Q9FVC1 UniProt NPD GO	SVP_ARATH	Protein SHORT VEGETATIVE PHASE	0.75	-	nuc	0	Nucleus (Probable)				240
P34164 UniProt NPD GO	SIP2_YEAST	Protein SIP2 (Protein SPM2)	0.75	-	nuc	0	Membrane; lipid-anchor	cytoplasm [IDA] plasma membrane [IDA]			414
Q23972 UniProt NPD GO	SMG_DROME	Protein Smaug	0.75	-	nuc	0	Cytoplasm	cytoplasm [IDA]		1OXJ	999
Q9FIE3 UniProt NPD GO	VIN3_ARATH	Protein VERNALIZATION-INSENSITIVE 3	0.75	-	nuc	0	Nucleus. Probably DNA-associated; interacts directly with the FLC regulatory regions				600
P17886 UniProt NPD GO	CRN_DROME	Protein crooked neck	0.75	+	cyt	0	Nucleus; nucleoplasm; nuclear speckle. Concentrated in nuclear speckles	nuclear speck [IDA] nucleus [IC]			702
Q24020 UniProt NPD GO	FLII_DROME	Protein flightless-1 (Flightless-I)	0.75	-	cyt	0					1256
Q00805 UniProt NPD GO	GIL_DROME	Protein giant-lens precursor (Protein argos) (Protein strawberry)	0.75	-	exc	1 *	Secreted protein	extracellular region [TAS]			444
P13508 UniProt NPD GO	GLP1_CAEEL	Protein glp-1 precursor	0.75	+	exc	0	Membrane; single-pass type I membrane protein	cytoplasm [IDA] endomembrane system [IDA] lateral plasma membrane [IDA] plasma membrane [IDA]			1295
O75928 UniProt NPD GO	PIAS2_HUMAN	Protein inhibitor of activated STAT2 (Protein inhibitor of activated STAT x) (Msx-interacting zinc f ...	0.75	-	nuc	0	Nucleus; nucleoplasm; nuclear speckle. Colocalizes at least partially with promyelocytic leukemia nu ...		603567	2ASQ	621
Q9GNL2 UniProt NPD GO	LIN14_CAEBR	Protein lin-14 (Abnormal cell lineage protein 14)	0.75	-	nuc	0	Nucleus				543
Q9QZS3 UniProt NPD GO	NUMB_MOUSE	Protein numb homolog (m-Numb) (m-Nb)	0.75	-	nuc	0	Membrane; peripheral membrane protein	apical part of cell [IDA] cytoplasm [IDA] early endosome [IDA] extrinsic to plasma membrane [IDA] nucleus [IDA]		1WJ1	653
Q6GLB0 UniProt NPD GO	PP1RB_XENTR	Protein phosphatase 1 regulatory subunit 11	0.75	+	nuc	0					119
Q8K1L5 UniProt NPD GO	PP1RB_MOUSE	Protein phosphatase 1 regulatory subunit 11 (T-complex testis expressed protein 5) (Tctex-5)	0.75	+	nuc	0					131
Q9QZ67 UniProt NPD GO	PP2CD_MOUSE	Protein phosphatase 2C isoform delta (EC 3.1.3.16) (PP2C-delta) (p53-induced protein phosphatase 1) ...	0.75	-	nuc	0					598
Q6CSD1 UniProt NPD GO	SEC9_KLULA	Protein transport protein SEC9	0.75	-	nuc	0					556
Q4WJS2 UniProt NPD GO	VTS1_ASPFU	Protein vts1	0.75	-	nuc	0	Cytoplasm (By similarity)				602
Q872F4 UniProt NPD GO	TCP4_NEUCR	Putative RNA polymerase II transcriptional coactivator	0.75	+	nuc	0	Nucleus (By similarity)				172
Q9U2C9 UniProt NPD GO	TBX37_CAEEL	Putative T-box protein 37	0.75	-	nuc	0	Nucleus (Potential)				352
O14081 UniProt NPD GO	TPSX_SCHPO	Putative alpha,alpha-trehalose-phosphate synthase [UDP-forming] subunit 106 kDa subunit (EC 2.4.1.15 ...	0.75	-	nuc	0					944

You are viewing entries 11501 to 11550 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.