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
Q9CA19 UniProt NPD GO	RT13_ARATH	Small ribosomal subunit protein S13, mitochondrial precursor (mS13)	0.38	-	nuc	0	Mitochondrion	chloroplast [IDA] mitochondrial small ribosomal subunit [TAS] mitochondrion [IDA]			154
Q64541 UniProt NPD GO	AT1A4_RAT	Sodium/potassium-transporting ATPase alpha-4 chain (EC 3.6.3.9) (Sodium pump 4) (Na+/K+ ATPase 4)	0.38	-	end	10	Membrane; multi-pass membrane protein	sodium:potassium-exchanging ATPase complex [ISS]			1028
P09916 UniProt NPD GO	SLIB_RAT	Somatoliberin precursor (Growth hormone-releasing factor) (GRF) (Growth hormone-releasing hormone) ( ...	0.38	-	mit	0	Secreted protein				104
P55755 UniProt NPD GO	SOMA_CRONO	Somatotropin (Growth hormone)	0.38	-	nuc	0	Secreted protein				190
P09539 UniProt NPD GO	SOMA_SERQU	Somatotropin precursor (Growth hormone)	0.38	-	exc	0	Secreted protein				204
Q2U4K2 UniProt NPD GO	SNX3_ASPOR	Sorting nexin-3	0.38	-	cyt	0	Cytoplasm (By similarity)				142
Q64298 UniProt NPD GO	MCSP_RAT	Sperm mitochondrial-associated cysteine-rich protein	0.38	-	nuc	0	Cytoplasm. Becomes associated with the spermatid mitochondrion capsule at step 16 of spermatogenesis ...	cytoplasm [ISS] mitochondrion [ISS]			145
P16376 UniProt NPD GO	7UP2_DROME	Steroid receptor seven-up, isoform A	0.38	-	nuc	0	Nucleus (Potential)	cytoplasm [IDA]			746
P80477 UniProt NPD GO	DHSB_PORPU	Succinate dehydrogenase [ubiquinone] iron-sulfur protein (EC 1.3.5.1) (IP)	0.38	-	nuc	0	Mitochondrion; mitochondrial inner membrane				239
P80480 UniProt NPD GO	DHSB_RECAM	Succinate dehydrogenase [ubiquinone] iron-sulfur protein (EC 1.3.5.1) (IP)	0.38	-	nuc	0	Mitochondrion; mitochondrial inner membrane				239
P41691 UniProt NPD GO	MLR5_FELCA	Superfast myosin regulatory light chain 2 (MyLC-2) (MYLC2) (Myosin regulatory light chain 5)	0.38	-	mit	0					173
Q9Z0P7 UniProt NPD GO	SUFU_MOUSE	Suppressor of fused homolog	0.38	-	mit	0	Cytoplasm. Nucleus	cytoplasm [IDA]			484
Q09808 UniProt NPD GO	SMN1_SCHPO	Survival motor neuron-like protein 1	0.38	-	nuc	0	Nucleus	nucleus [IDA]			152
P18827 UniProt NPD GO	SDC1_HUMAN	Syndecan-1 precursor (SYND1) (CD138 antigen)	0.38	-	exc	1	Membrane; single-pass type I membrane protein	integral to plasma membrane [TAS]	186355		310
Q80ZG0 UniProt NPD GO	RIC8B_RAT	Synembryn-B (Protein Ric-8B)	0.38	-	cyt	0	Cytoplasm; cell cortex (By similarity). Localizes to the cell cortex (By similarity)				520
O75558 UniProt NPD GO	STX11_HUMAN	Syntaxin-11	0.38	-	nuc	0	Membrane; peripheral membrane protein (Potential)		605014		287
Q27850 UniProt NPD GO	TBP_TETTH	TATA-box-binding protein (TATA-box factor) (TATA-binding factor) (TATA sequence-binding protein) (TB ...	0.38	-	nuc	0	Nucleus				246
Q60452 UniProt NPD GO	ERCC2_CRIGR	TFIIH basal transcription factor complex helicase subunit (EC 3.6.1.-) (DNA-repair protein complemen ...	0.38	-	cyt	0	Nucleus	nucleus [ISS] transcription factor TFIIH complex [ISS]			760
P38438 UniProt NPD GO	TGFR2_RAT	TGF-beta receptor type-2 precursor (EC 2.7.11.30) (TGF-beta receptor type II) (TGFR-2) (TGF-beta typ ...	0.38	-	nuc	0	Membrane; single-pass type I membrane protein				567
Q8VD31 UniProt NPD GO	TPSNR_MOUSE	Tapasin-related protein precursor (TAPASIN-R) (Tapasin-like) (TAP-binding protein-related protein) ( ...	0.38	-	nuc	1	Cell membrane; single-pass type I membrane protein (By similarity). Endoplasmic reticulum; endoplasm ...				451
Q8WVT3 UniProt NPD GO	TTC15_HUMAN	Tetratricopeptide repeat protein 15 (TPR repeat protein 15)	0.38	-	nuc	0					735
P87144 UniProt NPD GO	SYTC_SCHPO	Threonyl-tRNA synthetase, cytoplasmic (EC 6.1.1.3) (Threonine--tRNA ligase) (ThrRS)	0.38	-	nuc	0	Cytoplasm				703
P49745 UniProt NPD GO	TPO_RAT	Thrombopoietin precursor	0.38	-	nuc	0	Secreted protein	extracellular region [IDA]			326
P13100 UniProt NPD GO	TYSY_PNECA	Thymidylate synthase (EC 2.1.1.45) (TS) (TSase)	0.38	-	cyt	0				1F28	297
P14650 UniProt NPD GO	PERT_RAT	Thyroid peroxidase precursor (EC 1.11.1.8) (TPO)	0.38	-	end	2 *	Membrane; single-pass type I membrane protein (By similarity)				914
P56495 UniProt NPD GO	TSHR_SHEEP	Thyrotropin receptor precursor (TSH-R) (Thyroid-stimulating hormone receptor)	0.38	-	end	7	Membrane; multi-pass membrane protein				764
O35536 UniProt NPD GO	TFPI2_MOUSE	Tissue factor pathway inhibitor 2 precursor (TFPI-2)	0.38	-	nuc	0	Secreted protein				230
P13778 UniProt NPD GO	REP1_ZYGRO	Trans-acting factor B (REP1)	0.38	-	nuc	0					410
P17630 UniProt NPD GO	TCO1_PIG	Transcobalamin-1 precursor (Transcobalamin I) (TCI) (TC I) (Haptocorrin) (R protein) (Cobalophilin) ...	0.38	-	exc	0	Secreted protein				416
Q63398 UniProt NPD GO	COE1_RAT	Transcription factor COE1 (OE-1) (O/E-1) (Early B-cell factor) (Olfactory neuronal transcription fac ...	0.38	-	nuc	0	Nucleus				584
Q12415 UniProt NPD GO	TFC7_YEAST	Transcription factor tau 55 kDa subunit (TFIIIC 55 kDa subunit)	0.38	-	nuc	0	Nucleus (By similarity)	transcription factor TFIIIC complex [TAS]			435
Q9Y690 UniProt NPD GO	MORF4_HUMAN	Transcription factor-like protein MORF4 (Mortality factor 4) (Cellular senescence-related protein 1) ...	0.38	-	nuc	0	Nucleus		116960		235
Q99PM3 UniProt NPD GO	TF2AA_MOUSE	Transcription initiation factor IIA subunit 1 (General transcription factor IIA1) [Contains: Transcr ...	0.38	-	nuc	0	Nucleus (By similarity)				378
O16991 UniProt NPD GO	TF2B_CAEEL	Transcription initiation factor IIB (General transcription factor TFIIB)	0.38	-	nuc	0	Nucleus (By similarity)				306
O94424 UniProt NPD GO	T2FB_SCHPO	Transcription initiation factor IIF subunit beta (EC 3.6.1.-) (ATP-dependent helicase TFG2) (TFIIF-b ...	0.38	-	nuc	0	Nucleus (By similarity)				307
P53040 UniProt NPD GO	TAF6_YEAST	Transcription initiation factor TFIID subunit 6 (TBP-associated factor 6) (TBP-associated factor 60 ...	0.38	-	cyt	0	Nucleus	SAGA complex [IDA] SLIK (SAGA-like) complex [IPI] transcription factor TFIID complex [IDA]			516
Q6PAC9 UniProt NPD GO	PURBA_XENLA	Transcriptional activator protein Pur-beta-A (Purine-rich element-binding protein B-A)	0.38	-	nuc	0	Nucleus (By similarity)				322
Q5R4Q3 UniProt NPD GO	SEC62_PONPY	Translocation protein SEC62 (Translocation protein 1) (TP-1)	0.38	+	end	2	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (By similarity)				399
Q99442 UniProt NPD GO	SEC62_HUMAN	Translocation protein SEC62 (Translocation protein 1) (TP-1) (hTP-1)	0.38	+	end	2	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (By similarity)	endoplasmic reticulum [TAS] integral to membrane [TAS]	602173		399
P45433 UniProt NPD GO	SSRA_ONCMY	Translocon-associated protein subunit alpha precursor (TRAP-alpha) (Signal sequence receptor subunit ...	0.38	-	end	1 *	Endoplasmic reticulum; endoplasmic reticulum membrane; single-pass type I membrane protein				288
Q9BYE2 UniProt NPD GO	TMPSD_HUMAN	Transmembrane protease, serine 13 (EC 3.4.21.-) (Mosaic serine protease) (Membrane-type mosaic serin ...	0.38	-	nuc	1	Membrane; single-pass type II membrane protein (Potential)	integral to membrane [NAS]	610050		581
P69526 UniProt NPD GO	TMPS9_RAT	Transmembrane protease, serine 9 (EC 3.4.21.-) (Polyserase-1) (Polyserine protease 1) (Polyserase-I) ...	0.38	-	cyt	0	Cell membrane; single-pass type II membrane protein (By similarity)				1061
Q9ESN6 UniProt NPD GO	TRIM2_MOUSE	Tripartite motif-containing protein 2 (Neural activity-related RING finger protein)	0.38	-	cyt	0	Cytoplasm	cytoplasm [NAS]			744
Q8CH72 UniProt NPD GO	TRI32_MOUSE	Tripartite motif-containing protein 32 (EC 6.3.2.-)	0.38	-	cyt	0	Nucleus (By similarity)				655
Q9NZR1 UniProt NPD GO	TMOD2_HUMAN	Tropomodulin-2 (Neuronal tropomodulin) (N-Tmod)	0.38	-	nuc	0			602928		351
Q8WR63 UniProt NPD GO	TPM_TRIPS	Tropomyosin	0.38	-	nuc	0					284
Q95VA8 UniProt NPD GO	TPM_TRISP	Tropomyosin	0.38	-	nuc	0					284
Q01173 UniProt NPD GO	TPM1_XENLA	Tropomyosin 1 alpha chain (Alpha-tropomyosin)	0.38	-	nuc	0					284
P48775 UniProt NPD GO	T23O_HUMAN	Tryptophan 2,3-dioxygenase (EC 1.13.11.11) (TO) (Tryptophan pyrrolase) (Tryptophanase) (Tryptophan o ...	0.38	-	cyt	0			191070		406
P38557 UniProt NPD GO	TBG1_ARATH	Tubulin gamma-1 chain (Gamma-1 tubulin)	0.38	-	cyt	0					474

You are viewing entries 33801 to 33850 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.