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
Q3T0C7 UniProt NPD GO	STMN1_BOVIN	Stathmin	0.73	-	nuc	0	Cytoplasm (By similarity)				148
Q6DUB7 UniProt NPD GO	STMN1_PIG	Stathmin	0.73	-	nuc	0	Cytoplasm (By similarity)				148
P54227 UniProt NPD GO	STMN1_MOUSE	Stathmin (Phosphoprotein p19) (pp19) (Oncoprotein 18) (Op18) (Leukemia-associated phosphoprotein p18 ...	0.73	-	nuc	0	Cytoplasm	cytoplasm [IDA]			148
P16949 UniProt NPD GO	STMN1_HUMAN	Stathmin (Phosphoprotein p19) (pp19) (Oncoprotein 18) (Op18) (Leukemia-associated phosphoprotein p18 ...	0.73	-	nuc	0	Cytoplasm		151442		148
Q7S1I0 UniProt NPD GO	ATG26_NEUCR	Sterol 3-beta-glucosyltransferase (EC 2.4.1.173) (Autophagy-related protein 26)	0.73	-	nuc	0	Membrane; peripheral membrane protein (By similarity)				1553
Q00659 UniProt NPD GO	SCONB_EMENI	Sulfur metabolite repression control protein	0.73	-	nuc	0					678
P39016 UniProt NPD GO	MPT5_YEAST	Suppressor protein MPT5 (Protein HTR1)	0.73	-	nuc	0		cytoplasm [IDA]			834
Q68FW4 UniProt NPD GO	STX18_RAT	Syntaxin-18	0.73	-	nuc	1	Endoplasmic reticulum; endoplasmic reticulum membrane; single-pass type IV membrane protein (By simi ...				334
Q9WU70 UniProt NPD GO	STXB5_RAT	Syntaxin-binding protein 5 (Tomosyn-1) (Lethal(2) giant larvae protein homolog 3)	0.73	-	nuc	0	Cytoplasm. Cell membrane; peripheral membrane protein. Membrane; peripheral membrane protein. Cytopl ...			1URQ	1152
Q3T0G1 UniProt NPD GO	THAP1_BOVIN	THAP domain-containing protein 1	0.73	+	nuc	0	Nucleus; nucleoplasm (By similarity). And PML nuclear bodies (By similarity)				213
Q9FT81 UniProt NPD GO	TT8_ARATH	TRANSPARENT TESTA 8 protein (Basic helix-loop-helix protein 42) (bHLH42) (AtbHLH042)	0.73	+	cyt	0	Nucleus (Potential)				518
Q6P3P1 UniProt NPD GO	TAXB1_XENTR	Tax1-binding protein 1 homolog	0.73	-	nuc	0					841
O14261 UniProt NPD GO	TAF1_SCHPO	Taz1-interacting factor 1 (Protein taf1)	0.73	-	nuc	0					926
Q9Y6F8 UniProt NPD GO	CDY1_HUMAN	Testis-specific chromodomain protein Y 1	0.73	-	nuc	0	Nucleus (By similarity)		400016	2FBM	540
Q9Y6F7 UniProt NPD GO	CDY2_HUMAN	Testis-specific chromodomain protein Y 2	0.73	-	nuc	0	Nucleus (By similarity)		400018	2FW2	541
O62683 UniProt NPD GO	ZO3_CANFA	Tight junction protein ZO-3 (Zonula occludens 3 protein) (Zona occludens 3 protein) (Tight junction ...	0.73	-	nuc	0					898
P10646 UniProt NPD GO	TFPI1_HUMAN	Tissue factor pathway inhibitor precursor (TFPI) (Lipoprotein-associated coagulation inhibitor) (LAC ...	0.73	+	exc	0	Secreted protein		152310	1TFX	304
Q28864 UniProt NPD GO	TFPI1_MACMU	Tissue factor pathway inhibitor precursor (TFPI) (Lipoprotein-associated coagulation inhibitor) (LAC ...	0.73	+	exc	0	Secreted protein				304
Q9DD78 UniProt NPD GO	TLR21_CHICK	Toll-like receptor 2 type-1 precursor	0.73	-	nuc	1	Membrane; single-pass type I membrane protein (By similarity)				793
Q62313 UniProt NPD GO	TGON1_MOUSE	Trans-Golgi network integral membrane protein 1 precursor (TGN38A)	0.73	-	end	1	Cell membrane; single-pass type I membrane protein (By similarity). Golgi apparatus; trans-Golgi net ...				353
Q8CCT4 UniProt NPD GO	TCAL5_MOUSE	Transcription elongation factor A protein-like 5 (TCEA-like protein 5) (Transcription elongation fac ...	0.73	-	nuc	0	Nucleus (Probable)				200
Q6FRZ5 UniProt NPD GO	SPT5_CANGA	Transcription elongation factor SPT5 (Chromatin elongation factor SPT5)	0.73	+	nuc	0	Nucleus (By similarity)				1010
Q6BZG0 UniProt NPD GO	SPT5_DEBHA	Transcription elongation factor SPT5 (Chromatin elongation factor SPT5)	0.73	+	nuc	0	Nucleus (By similarity)				967
Q2UGU3 UniProt NPD GO	SPT5_ASPOR	Transcription elongation factor spt5 (Chromatin elongation factor spt5)	0.73	+	nuc	0	Nucleus (By similarity)				1026
Q60722 UniProt NPD GO	ITF2_MOUSE	Transcription factor 4 (Immunoglobulin transcription factor 2) (ITF-2) (MITF-2) (SL3-3 enhancer fact ...	0.73	-	nuc	0	Nucleus (Probable)	transcription factor complex [IDA]			670
Q62655 UniProt NPD GO	ITF2_RAT	Transcription factor 4 (Immunoglobulin transcription factor 2) (ITF-2) (RITF-2) (SL3-3 enhancer fact ...	0.73	-	nuc	0	Nucleus (Probable)				589
O54917 UniProt NPD GO	E2F6_MOUSE	Transcription factor E2F6 (E2F-6) (E2F-binding site-modulating activity protein) (EMA)	0.73	-	nuc	0	Nucleus (Probable)	DNA replication factor A complex [IC]			272
Q9Y543 UniProt NPD GO	HES2_HUMAN	Transcription factor HES-2 (Hairy and enhancer of split 2)	0.73	-	nuc	0	Nucleus (By similarity)		609970		173
Q7M6Y2 UniProt NPD GO	SOX11_MOUSE	Transcription factor SOX-11	0.73	+	nuc	0	Nucleus				395
Q27355 UniProt NPD GO	LIN26_CAEEL	Transcription factor lin-26 (Abnormal cell lineage protein 26)	0.73	-	nuc	0	Nucleus (Potential)	nucleus [IDA]			438
O14283 UniProt NPD GO	PRR1_SCHPO	Transcription factor prr1 (Pombe response regulator 1)	0.73	-	nuc	0	Nucleus (Potential)				539
Q92750 UniProt NPD GO	TAF4B_HUMAN	Transcription initiation factor TFIID 105 kDa subunit (TAFII-105) (TAFII105) (Fragment)	0.73	-	nuc	0	Nucleus	nucleus [NAS]	601689		801
Q9UGP8 UniProt NPD GO	SEC63_HUMAN	Translocation protein SEC63 homolog	0.73	+	vac	3 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein	endoplasmic reticulum [TAS]	608648		759
Q99PP6 UniProt NPD GO	TRI34_MOUSE	Tripartite motif-containing protein 34	0.73	-	nuc	0					485
Q9ESN2 UniProt NPD GO	TRI39_MOUSE	Tripartite motif-containing protein 39 (RING finger protein 23) (Testis-abundant finger protein)	0.73	-	nuc	0					488
Q8IWZ5 UniProt NPD GO	TRI42_HUMAN	Tripartite motif-containing protein 42	0.73	-	nuc	0					723
P48787 UniProt NPD GO	TNNI3_MOUSE	Troponin I, cardiac muscle (Cardiac troponin I)	0.73	-	nuc	0		troponin complex [TAS]			210
P50754 UniProt NPD GO	TNNI3_XENLA	Troponin I, cardiac muscle (Troponin IC)	0.73	-	nuc	0					243
O77736 UniProt NPD GO	TNR6_PIG	Tumor necrosis factor receptor superfamily member 6 precursor (FASLG receptor) (Apoptosis-mediating ...	0.73	-	exc	1	Membrane; single-pass type I membrane protein				332
P28908 UniProt NPD GO	TNR8_HUMAN	Tumor necrosis factor receptor superfamily member 8 precursor (CD30L receptor) (Lymphocyte activatio ...	0.73	-	exc	1	Isoform Long: Cell membrane; single-pass type I membrane protein. Isoform Short: Cytoplasm		153243	1D01	595
Q90VY2 UniProt NPD GO	EDAR_ORYLA	Tumor necrosis factor receptor superfamily member EDAR precursor (Ectodysplasin-A receptor) (Reduced ...	0.73	-	exc	1	Membrane; single-pass type I membrane protein (Probable)				514
Q8R0Z2 UniProt NPD GO	COVA1_MOUSE	Tumor-associated hydroquinone oxidase (tNOX) (Cytosolic ovarian carcinoma antigen 1) (APK1 antigen) ...	0.73	-	nuc	0	Extracellular and plasma membrane-associated (By similarity)	cytosol [ISS] external side of plasma membrane [ISS]			598
P49960 UniProt NPD GO	PRP24_YEAST	U4/U6 snRNA-associated-splicing factor PRP24 (U4/U6 snRNP protein)	0.73	-	nuc	0	Nucleus	snRNP U6 [IDA]		2GHP	444
P47049 UniProt NPD GO	UBX6_YEAST	UBX domain-containing protein 6	0.73	-	nuc	0		nucleus [IDA]			396
P54578 UniProt NPD GO	UBP14_HUMAN	Ubiquitin carboxyl-terminal hydrolase 14 (EC 3.1.2.15) (Ubiquitin thioesterase 14) (Ubiquitin-specif ...	0.73	-	nuc	0			607274	2AYO	493
Q9P2H5 UniProt NPD GO	UBP35_HUMAN	Ubiquitin carboxyl-terminal hydrolase 35 (EC 3.1.2.15) (Ubiquitin thioesterase 35) (Ubiquitin-specif ...	0.73	-	nuc	0					1017
Q9HE05 UniProt NPD GO	UFD2_SCHPO	Ubiquitin conjugation factor E4 (Ubiquitin fusion degradation protein 2) (UB fusion protein 2)	0.73	-	mit	0		cytoplasm [IDA] nucleus [IDA]			1010
Q9CPZ1 UniProt NPD GO	CN105_MOUSE	Uncharacterized protein C14orf105 homolog	0.73	-	nuc	0					294
P40485 UniProt NPD GO	YIK5_YEAST	Uncharacterized protein YIL105C	0.73	-	nuc	0		cytoplasm [IDA] mitochondrion [IDA] plasma membrane [IDA] TORC 2 complex [IPI]			686
P47006 UniProt NPD GO	YJO8_YEAST	Uncharacterized protein YJL148W	0.73	+	nuc	0		DNA-directed RNA polymerase I complex [TAS] nucleolus [IDA] nucleus [IDA]			233

You are viewing entries 12551 to 12600 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.