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
Q8NJS1 UniProt NPD GO	ATG26_LEPMC	Sterol 3-beta-glucosyltransferase (EC 2.4.1.173) (Autophagy-related protein 26) (UDP-glycosyltransfe ...	0.93	-	nuc	0	Membrane; peripheral membrane protein (By similarity)				1456
Q9P246 UniProt NPD GO	STIM2_HUMAN	Stromal interaction molecule 2 precursor	0.93	-	end	0	Cell membrane; single-pass type I membrane protein (Potential)	integral to membrane [NAS]			746
Q5R4K5 UniProt NPD GO	SMC3_PONPY	Structural maintenance of chromosome 3 (Chondroitin sulfate proteoglycan 6)	0.93	-	nuc	0	Nucleus (By similarity). Associates with chromatin. Before prophase it is scattered along chromosome ...				1217
Q9CW03 UniProt NPD GO	SMC3_MOUSE	Structural maintenance of chromosome 3 (Chondroitin sulfate proteoglycan 6) (Chromosome segregation ...	0.93	-	nuc	0	Nucleus. Associates with chromatin. Before prophase it is scattered along chromosome arms. During pr ...	cohesin complex [ISS] cytoplasm [ISS] lateral element [IDA] nuclear matrix [ISS] nucleus [IDA] spindle pole [ISS]			1217
Q9UQE7 UniProt NPD GO	SMC3_HUMAN	Structural maintenance of chromosome 3 (Chondroitin sulfate proteoglycan 6) (Chromosome-associated p ...	0.93	-	nuc	0	Nucleus. Associates with chromatin. Before prophase it is scattered along chromosome arms. During pr ...	basement membrane [TAS] cohesin complex [NAS] cytoplasm [IDA] nuclear matrix [IDA] nucleus [TAS] spindle pole [IDA]	606062		1217
Q920F6 UniProt NPD GO	SM1L2_MOUSE	Structural maintenance of chromosomes 1-like 2 protein (SMC1beta protein)	0.93	-	nuc	0	Nucleus. Associates with chromatin. In prophase I stage of meiosis, localizes along the AE of synapt ...	chromosome, pericentric region [IDA] lateral element [IDA]			1248
Q9QX27 UniProt NPD GO	ST18_RAT	Suppression of tumorigenicity protein 18 (Neural zinc finger factor 3) (NZF-3) (C2-HC type zinc fing ...	0.93	-	nuc	0	Nucleus				1032
Q8IZU3 UniProt NPD GO	SYCP3_HUMAN	Synaptonemal complex protein 3 (SCP-3)	0.93	-	nuc	0	Nucleus (By similarity). In tripartite segments of synaptonemal complexes, irrespective of whether t ...		604759		236
Q9UMS6 UniProt NPD GO	SYNP2_HUMAN	Synaptopodin-2 (Myopodin) (Genethonin 2)	0.93	+	nuc	0	Nucleus (By similarity). Cytoplasm (By similarity). Shuttles between the nucleus and the cytoplasm i ...				1093
Q8IYJ3 UniProt NPD GO	SYTL1_HUMAN	Synaptotagmin-like protein 1 (Exophilin-7) (Protein JFC1) (SB146)	0.93	-	exc	0	Cell membrane; peripheral membrane protein; cytoplasmic side. Peripheral membrane protein tightly bo ...	extrinsic to plasma membrane [ISS] melanosome [ISS] soluble fraction [ISS]	608042		562
Q96C24 UniProt NPD GO	SYTL4_HUMAN	Synaptotagmin-like protein 4 (Exophilin-2) (Granuphilin)	0.93	-	nuc	0	Membrane; peripheral membrane protein (By similarity). Detected close to the plasma membrane and on ...	extrinsic to plasma membrane [ISS]		2CSZ	671
Q96SF7 UniProt NPD GO	TBX15_HUMAN	T-box transcription factor TBX15 (T-box protein 15)	0.93	-	nuc	0	Nucleus (Potential)		604127		602
O70306 UniProt NPD GO	TBX15_MOUSE	T-box transcription factor TBX15 (T-box protein 15) (MmTBx8)	0.93	-	nuc	0	Nucleus (Potential)				602
Q6SZ61 UniProt NPD GO	CD2_MACFA	T-cell surface antigen CD2 precursor	0.93	+	nuc	1	Membrane; single-pass type I membrane protein				351
P06729 UniProt NPD GO	CD2_HUMAN	T-cell surface antigen CD2 precursor (T-cell surface antigen T11/Leu-5) (LFA-2) (LFA-3 receptor) (Er ...	0.93	+	nuc	1	Membrane; single-pass type I membrane protein	integral to plasma membrane [NAS]	186990	1L2Z	351
Q6P773 UniProt NPD GO	TAF1C_RAT	TATA box-binding protein-associated factor, RNA polymerase I, subunit C (TATA box-binding protein-as ...	0.93	+	nuc	0	Nucleus (By similarity)				842
P38825 UniProt NPD GO	YHR7_YEAST	TPR repeat-containing protein YHR117W	0.93	+	nuc	0		integral to mitochondrial outer membrane [IDA] mitochondrial outer membrane [IDA]			639
P47988 UniProt NPD GO	TEA1_YEAST	TY1 enhancer activator	0.93	+	nuc	0	Nucleus	nucleus [IGI]			759
Q12050 UniProt NPD GO	ELG1_YEAST	Telomere length regulation protein ELG1 (Telomere elongation suppressor ELG1)	0.93	-	nuc	0	Nucleus	cytoplasm [IDA] DNA replication factor C complex [TAS] mitochondrion [IDA] nucleus [IDA]			791
Q8C1F5 UniProt NPD GO	TTC16_MOUSE	Tetratricopeptide repeat protein 16 (TPR repeat protein 16)	0.93	-	nuc	0					767
P39447 UniProt NPD GO	ZO1_MOUSE	Tight junction protein ZO-1 (Zonula occludens 1 protein) (Zona occludens 1 protein) (Tight junction ...	0.93	-	nuc	0	Cell membrane; peripheral membrane protein; cytoplasmic side (By similarity). Movement of ZO-1 from ...	adherens junction [IDA] intercellular canaliculus [IDA] nucleus [IDA] plasma membrane [IDA] tight junction [IDA]			1745
Q8UVK2 UniProt NPD GO	SPT6H_BRARE	Transcription elongation factor SPT6 (Protein pandora)	0.93	+	nuc	0	Nucleus (By similarity)				1726
Q9CAD0 UniProt NPD GO	EGL1_ARATH	Transcription factor EGL1 (ENHANCER OF GLABRA3) (Basic helix-loop-helix protein 2) (bHLH2) (AtbHLH00 ...	0.93	+	nuc	0	Nucleus (Probable)				596
P38128 UniProt NPD GO	SMP1_YEAST	Transcription factor SMP1	0.93	+	nuc	0	Nucleus (Potential)	cytoplasm [IDA] nucleus [IDA]			452
Q9BG89 UniProt NPD GO	SOX9_PANTR	Transcription factor SOX-9	0.93	+	nuc	0	Nucleus (Potential)				509
Q03761 UniProt NPD GO	TAF12_YEAST	Transcription initiation factor TFIID subunit 12 (TBP-associated factor 12) (TBP-associated factor 6 ...	0.93	-	nuc	0	Nucleus	SAGA complex [IDA] SLIK (SAGA-like) complex [IPI] transcription factor TFIID complex [IDA]			539
P50947 UniProt NPD GO	PHO23_YEAST	Transcriptional regulatory protein PHO23	0.93	+	nuc	0	Nucleus	histone deacetylase complex [IDA] nucleus [IDA]			330
P40489 UniProt NPD GO	XBP1_YEAST	Transcriptional repressor XBP1 (XhoI site-binding protein 1)	0.93	-	nuc	0	Nucleus (Probable)	nucleus [IDA]			647
P30371 UniProt NPD GO	TGFB2_CHICK	Transforming growth factor beta-2 precursor (TGF-beta-2)	0.93	-	nuc	0	Secreted protein	axon [ISS] cell soma [ISS] extracellular region [ISS]			412
Q8NDB6 UniProt NPD GO	TMM29_HUMAN	Transmembrane protein 29	0.93	-	nuc	0	Membrane; single-pass membrane protein (Potential)				213
Q04183 UniProt NPD GO	TR120_YEAST	Transport protein particle 120 kDa subunit (TRAPP 120 kDa subunit) (Trafficking protein particle com ...	0.93	-	nuc	0	Golgi apparatus; cis-Golgi network	TRAPP complex [IDA]			1289
P47098 UniProt NPD GO	YJZ7_YEAST	Transposon Ty1 protein B	0.93	-	nuc	0					1755
P47100 UniProt NPD GO	YJZ9_YEAST	Transposon Ty1 protein B	0.93	-	nuc	0					1755
Q04711 UniProt NPD GO	YME4_YEAST	Transposon Ty1 protein B	0.93	-	nuc	0					1328
P02642 UniProt NPD GO	TNNT2_CHICK	Troponin T, cardiac muscle isoforms (TnTC)	0.93	+	nuc	0					301
Q9H7E2 UniProt NPD GO	TDRD3_HUMAN	Tudor domain-containing protein 3	0.93	-	nuc	0				1WJI	651
O88898 UniProt NPD GO	P73L_MOUSE	Tumor protein p73-like (p73L) (p63) (Transformation-related protein 63)	0.93	+	nuc	0	Nucleus	nucleus [IDA]			680
Q9JJP6 UniProt NPD GO	P73L_RAT	Tumor protein p73-like (p73L) (p63) (Transformation-related protein 63) (TP63) (Keratinocyte transcr ...	0.93	+	nuc	0	Nucleus (By similarity)				680
Q9H3D4 UniProt NPD GO	P73L_HUMAN	Tumor protein p73-like (p73L) (p63) (Tumor protein 63) (TP63) (p51) (p40) (Keratinocyte transcriptio ...	0.93	+	nuc	0	Nucleus	nucleus [IDA]	103285	1RG6	680
Q8JH64 UniProt NPD GO	BTK_CHICK	Tyrosine-protein kinase BTK (EC 2.7.10.2) (Bruton tyrosine kinase)	0.93	-	nuc	0	Cytoplasm (By similarity). Membrane; peripheral membrane protein (By similarity)				657
P17133 UniProt NPD GO	RU17_DROME	U1 small nuclear ribonucleoprotein 70 kDa (U1 snRNP 70 kDa) (snRNP70)	0.93	+	nuc	0		nucleus [IC]		2BN5	448
Q9NPG3 UniProt NPD GO	UBN1_HUMAN	Ubinuclein (Ubiquitously expressed nuclear protein) (VT4)	0.93	+	nuc	0	Nucleus		609771		1134
Q9Y2K6 UniProt NPD GO	UBP20_HUMAN	Ubiquitin carboxyl-terminal hydrolase 20 (EC 3.1.2.15) (Ubiquitin thioesterase 20) (Ubiquitin-specif ...	0.93	+	nuc	0					913
Q96K76 UniProt NPD GO	UBP47_HUMAN	Ubiquitin carboxyl-terminal hydrolase 47 (EC 3.1.2.15) (Ubiquitin thioesterase 47) (Ubiquitin-specif ...	0.93	-	nuc	0					1375
O60014 UniProt NPD GO	UBR1_KLULA	Ubiquitin-protein ligase E3 component N-recognin-1 (EC 6.-.-.-) (N-end-recognizing protein)	0.93	+	nuc	0					1945
Q15386 UniProt NPD GO	UBE3C_HUMAN	Ubiquitin-protein ligase E3C (EC 6.3.2.-)	0.93	-	cyt	0	Nucleus (Potential)	intracellular [IC]			1083
Q80U95 UniProt NPD GO	UBE3C_MOUSE	Ubiquitin-protein ligase E3C (EC 6.3.2.-)	0.93	-	cyt	0	Nucleus (Potential)				1083
Q8N715 UniProt NPD GO	CA065_HUMAN	Uncharacterized protein C1orf65	0.93	+	nuc	0					623
Q95LL8 UniProt NPD GO	CC025_MACFA	Uncharacterized protein C3orf25 homolog	0.93	-	nuc	0					569
P38747 UniProt NPD GO	YHB3_YEAST	Uncharacterized protein YHL013C	0.93	-	nuc	0		cytoplasm [IDA]			307

You are viewing entries 3051 to 3100 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.