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
O35526 UniProt NPD GO	STX1A_MOUSE	Syntaxin-1A (Neuron-specific antigen HPC-1)	0.79	-	gol	1	Membrane; single-pass type IV membrane protein	plasma membrane [TAS]			288
P32850 UniProt NPD GO	STX1A_BOVIN	Syntaxin-1A (Synaptotagmin-associated 35 kDa protein) (P35A) (Neuron-specific antigen HPC-1)	0.79	-	gol	1	Membrane; single-pass type IV membrane protein				288
P32851 UniProt NPD GO	STX1A_RAT	Syntaxin-1A (Synaptotagmin-associated 35 kDa protein) (P35A) (Neuron-specific antigen HPC-1)	0.79	-	gol	1	Membrane; single-pass type IV membrane protein	integral to membrane [NAS] secretory granule [IDA]		2BU0	288
Q95LL3 UniProt NPD GO	TB22B_MACFA	TBC1 domain family member 22B	0.79	-	nuc	0					505
P32780 UniProt NPD GO	TF2H1_HUMAN	TFIIH basal transcription factor complex p62 subunit (Basic transcription factor 62 kDa subunit) (BT ...	0.79	-	nuc	0	Nucleus	transcription factor TFIIH complex [TAS]	189972	1PFJ	548
P26039 UniProt NPD GO	TLN1_MOUSE	Talin-1	0.79	-	nuc	0		cytosol [ISS] focal adhesion [ISS] ruffle [ISS]		2G35	2541
Q95Q95 UniProt NPD GO	TOR_CAEEL	Target of rapamycin homolog (EC 2.7.11.1) (CeTOR) (Lethal protein 363)	0.79	-	nuc	0	Nucleus	cytoplasm [IDA]			2697
Q9DCD5 UniProt NPD GO	TJAP1_MOUSE	Tight junction-associated protein 1 (Tight junction protein 4) (Protein incorporated later into tigh ...	0.79	-	nuc	0	Golgi apparatus. Cell membrane; cell-cell junction; tight junction. Recruited to tight junctions (TJ ...				539
Q8R2H7 UniProt NPD GO	TRAK2_RAT	Trafficking kinesin-binding protein 2 (Amyotrophic lateral sclerosis 2 chromosomal region candidate ...	0.79	-	nuc	0	Cytoplasm	cytoplasm [IEP] nucleus [IDA] plasma membrane [IEP]			913
Q8R0A5 UniProt NPD GO	TCAL3_MOUSE	Transcription elongation factor A protein-like 3 (TCEA-like protein 3) (Transcription elongation fac ...	0.79	-	nuc	0	Nucleus (Probable)				200
Q5H9L2 UniProt NPD GO	TCAL5_HUMAN	Transcription elongation factor A protein-like 5 (TCEA-like protein 5) (Transcription elongation fac ...	0.79	-	nuc	0	Nucleus (Probable)				206
Q09413 UniProt NPD GO	ELOA1_CAEEL	Transcription elongation factor B polypeptide 3 (RNA polymerase II transcription factor SIII subunit ...	0.79	+	nuc	0		transcription elongation factor complex [IDA]			434
P18289 UniProt NPD GO	JRA_DROME	Transcription factor AP-1 (Jun-related antigen) (dJRA) (dJun)	0.79	+	nuc	0	Nucleus	cytoplasm [IDA] nucleus [IDA]			289
Q90977 UniProt NPD GO	E2F1_CHICK	Transcription factor E2F1 (E2F-1)	0.79	+	exc	0	Nucleus				403
Q14209 UniProt NPD GO	E2F2_HUMAN	Transcription factor E2F2 (E2F-2)	0.79	-	nuc	0	Nucleus		600426	1N4M	437
P79797 UniProt NPD GO	TF3A_ICTPU	Transcription factor IIIA (Factor A) (TFIIIA)	0.79	+	nuc	0	Nucleus				322
Q9W7R6 UniProt NPD GO	SOX14_CHICK	Transcription factor SOX-14 (SRY-related protein CH60)	0.79	+	nuc	0	Nucleus (Potential)				240
Q9DDD7 UniProt NPD GO	SX19B_BRARE	Transcription factor Sox-19b (Protein sox-31)	0.79	-	nuc	0	Nucleus				292
P34111 UniProt NPD GO	TFC3_YEAST	Transcription factor tau 138 kDa subunit (TFIIIC 138 kDa subunit)	0.79	-	nuc	0	Nucleus	mitochondrion [IDA] transcription factor TFIIIC complex [TAS]			1160
Q03123 UniProt NPD GO	T2FB_XENLA	Transcription initiation factor IIF subunit beta (EC 3.6.1.-) (ATP-dependent helicase gtf2f2) (TFIIF ...	0.79	-	nuc	0	Nucleus				264
O00268 UniProt NPD GO	TAF4_HUMAN	Transcription initiation factor TFIID subunit 4 (TBP-associated factor 4) (Transcription initiation ...	0.79	-	nuc	0	Nucleus	transcription factor TFIID complex [IDA]	601796	1H3O	1085
Q5NC05 UniProt NPD GO	TTF2_MOUSE	Transcription termination factor 2 (EC 3.6.1.-) (RNA polymerase II termination factor) (Transcriptio ...	0.79	-	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity). Cytoplasmic during interphase. Relocates to the ...				1184
Q8W234 UniProt NPD GO	SEUSS_ARATH	Transcriptional corepressor SEUSS	0.79	-	nuc	0	Nucleus (Probable)				877
P40505 UniProt NPD GO	SDS3_YEAST	Transcriptional regulatory protein SDS3 (Suppressor of defective silencing protein 3)	0.79	-	nuc	0	Nucleus	histone deacetylase complex [IPI]			327
Q9JIT3 UniProt NPD GO	TLE3_RAT	Transducin-like enhancer protein 3 (rTLE3)	0.79	-	nuc	0	Nucleus				764
Q80YV3 UniProt NPD GO	TRRAP_MOUSE	Transformation/transcription domain-associated protein (Tra1 homolog)	0.79	-	mit	0	Nucleus (By similarity)	histone acetyltransferase complex [TAS]			2565
Q61749 UniProt NPD GO	EI2BD_MOUSE	Translation initiation factor eIF-2B subunit delta (eIF-2B GDP-GTP exchange factor subunit delta)	0.79	-	nuc	0					524
Q69ZZ6 UniProt NPD GO	TMCC1_MOUSE	Transmembrane and coiled-coil domains protein 1	0.79	-	cyt	2	Membrane; multi-pass membrane protein (Potential)				649
Q8R4P4 UniProt NPD GO	TMC2_MOUSE	Transmembrane cochlear-expressed protein 2	0.79	-	end	7	Membrane; multi-pass membrane protein (Potential)				888
O14523 UniProt NPD GO	TMM24_HUMAN	Transmembrane protein 24 (Protein DLNB23)	0.79	-	nuc	1 *					706
P78875 UniProt NPD GO	TPP1_SCHPO	Trehalose-phosphatase (EC 3.1.3.12) (Trehalose 6-phosphate phosphatase) (TPP)	0.79	-	cyt	0					817
O08550 UniProt NPD GO	TRX2_MOUSE	Trithorax homolog 2 (WW domain-binding protein 7) (Fragment)	0.79	-	nuc	0	Nucleus (By similarity)				290
P68246 UniProt NPD GO	TNNI2_CHICK	Troponin I, fast skeletal muscle (Troponin I, fast-twitch isoform)	0.79	-	nuc	0				1YV0	182
P68247 UniProt NPD GO	TNNI2_COTJA	Troponin I, fast skeletal muscle (Troponin I, fast-twitch isoform)	0.79	-	nuc	0					182
O15697 UniProt NPD GO	GAS8_TRYBR	Trypanin (T lymphocyte-triggering factor) (TLTF)	0.79	+	nuc	0	Cytoplasm. Cytoskeleton. Associated with the cytoskeleton. Localized to the site of attachment of th ...				453
Q9BWV7 UniProt NPD GO	TTLL2_HUMAN	Tubulin--tyrosine ligase-like protein 2 (Testis-specific protein NYD-TSPG)	0.79	-	mit	0					592
Q12199 UniProt NPD GO	TIP41_YEAST	Type 2A phosphatase activator TIP41 (PP2A phosphatase activator TIP41) (TAP42-interacting protein 1) ...	0.79	-	mit	0	Cytoplasm. Nucleus	cytoplasm [IDA] nucleus [IDA]			356
Q9QWG5 UniProt NPD GO	INP4B_RAT	Type II inositol-3,4-bisphosphate 4-phosphatase (EC 3.1.3.66) (Inositol polyphosphate 4-phosphatase ...	0.79	-	nuc	0					928
Q01973 UniProt NPD GO	ROR1_HUMAN	Tyrosine-protein kinase transmembrane receptor ROR1 precursor (EC 2.7.10.1) (Neurotrophic tyrosine k ...	0.79	-	exc	1	Membrane; single-pass type I membrane protein	cytoplasm [TAS] integral to plasma membrane [TAS] plasma membrane [TAS]	602336		937
Q6FWF3 UniProt NPD GO	BRE1_CANGA	Ubiquitin-protein ligase BRE1 (EC 6.3.2.-)	0.79	-	nuc	0	Nucleus (By similarity)				693
Q5KBI0 UniProt NPD GO	BRE1_CRYNE	Ubiquitin-protein ligase BRE1 (EC 6.3.2.-)	0.79	-	nuc	0	Nucleus (By similarity)				820
P48524 UniProt NPD GO	BUL1_YEAST	Ubiquitination pathway protein BUL1 (Respiration deficiency suppressor)	0.79	-	nuc	0		plasma membrane [IPI] ubiquitin ligase complex [IDA]			976
Q8K2W9 UniProt NPD GO	CN093_MOUSE	Uncharacterized protein C14orf93 homolog precursor	0.79	-	nuc	0					541
Q96M60 UniProt NPD GO	CO033_HUMAN	Uncharacterized protein C15orf33	0.79	-	nuc	0					508
Q9D842 UniProt NPD GO	CB013_MOUSE	Uncharacterized protein C2orf13 homolog	0.79	-	nuc	0					499
P38273 UniProt NPD GO	YBY1_YEAST	Uncharacterized protein YBR131W	0.79	-	nuc	0		late endosome [TAS] membrane [TAS] vacuole [IDA]			704
P38306 UniProt NPD GO	YB47_YEAST	Uncharacterized protein YBR197C	0.79	-	nuc	0		cytoplasm [IDA] nucleus [IDA]			217
Q12027 UniProt NPD GO	YD176_YEAST	Uncharacterized protein YDL176W	0.79	-	mit	0					708
P32618 UniProt NPD GO	YEF3_YEAST	Uncharacterized protein YEL043W	0.79	-	nuc	0		endoplasmic reticulum [IDA]			956
P48237 UniProt NPD GO	YG3M_YEAST	Uncharacterized protein YGR150C	0.79	-	mit	0		mitochondrion [IDA]			864

You are viewing entries 9651 to 9700 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.