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
Q93ZE8 UniProt NPD GO	SDF2_ARATH	Stromal cell-derived factor 2-like protein precursor (SDF2-like protein)	0.14	-	cyt	0	Secreted protein (Probable)				218
P53312 UniProt NPD GO	SUCB_YEAST	Succinyl-CoA ligase [ADP-forming] subunit beta, mitochondrial precursor (EC 6.2.1.5) (Succinyl-CoA s ...	0.14	-	mit	0	Mitochondrion (By similarity)	mitochondrion [IDA]			427
O65026 UniProt NPD GO	SUSY_MEDSA	Sucrose synthase (EC 2.4.1.13) (Sucrose-UDP glucosyltransferase)	0.14	-	cyt	0					805
P31926 UniProt NPD GO	SUSY_VICFA	Sucrose synthase (EC 2.4.1.13) (Sucrose-UDP glucosyltransferase)	0.14	-	cyt	0					806
Q2QLI1 UniProt NPD GO	SUT2_ORYSA	Sucrose transport protein 2 (Sucrose permease 2) (Sucrose-proton symporter 2) (Sucrose transporter 2 ...	0.14	-	end	8 *	Cell membrane; multi-pass membrane protein (By similarity)				501
O43704 UniProt NPD GO	ST1B1_HUMAN	Sulfotransferase family cytosolic 1B member 1 (EC 2.8.2.-) (Sulfotransferase 1B2) (Thyroid hormone s ...	0.14	-	cyt	0	Cytoplasm (By similarity)	cytosol [NAS]	608436	1XV1	296
Q7RX39 UniProt NPD GO	SVF1_NEUCR	Survival factor 1	0.14	-	cyt	0	Cytoplasm (By similarity). Nucleus (By similarity)				381
Q01827 UniProt NPD GO	VMAT2_RAT	Synaptic vesicular amine transporter (Monoamine transporter) (Vesicular amine transporter 2) (VAT2) ...	0.14	-	end	11 *	Cytoplasmic vesicle; cytoplasmic vesicle membrane; multi-pass membrane protein				515
P47951 UniProt NPD GO	SDC1_CRIGR	Syndecan-1 precursor (SYND1)	0.14	-	end	1	Membrane; single-pass type I membrane protein				309
O00560 UniProt NPD GO	SDCB1_HUMAN	Syntenin-1 (Syndecan-binding protein 1) (Melanoma differentiation-associated protein 9) (MDA-9) (Sca ...	0.14	-	cyt	1	Cell membrane; cell-matrix junction; focal adhesion; peripheral membrane protein. Cell membrane; cel ...	adherens junction [NAS] cytoskeleton [NAS] interleukin-5 receptor complex [ISS] membrane [NAS] nucleus [NAS]	602217	1YBO	298
P11985 UniProt NPD GO	TCX2_MOUSE	T complex testis-specific protein 2 (TCTEX-2)	0.14	-	mit	0	Membrane; peripheral membrane protein	cytoplasmic dynein complex [IDA] flagellum (sensu Eukaryota) [IDA] membrane [IDA]			191
O43435 UniProt NPD GO	TBX1_HUMAN	T-box transcription factor TBX1 (T-box protein 1) (Testis-specific T-box protein)	0.14	-	nuc	0	Nucleus (Potential)		602054		398
O60806 UniProt NPD GO	TBX19_HUMAN	T-box transcription factor TBX19 (T-box protein 19) (T-box factor, pituitary)	0.14	-	nuc	0	Nucleus (Potential)		604614		448
P78371 UniProt NPD GO	TCPB_HUMAN	T-complex protein 1 subunit beta (TCP-1-beta) (CCT-beta)	0.14	-	cyt	0	Cytoplasm	cytosol [NAS]	605139		534
P80314 UniProt NPD GO	TCPB_MOUSE	T-complex protein 1 subunit beta (TCP-1-beta) (CCT-beta)	0.14	-	cyt	0	Cytoplasm	chaperonin-containing T-complex [IDA]			534
P80315 UniProt NPD GO	TCPD_MOUSE	T-complex protein 1 subunit delta (TCP-1-delta) (CCT-delta) (A45)	0.14	-	cyt	0	Cytoplasm	chaperonin-containing T-complex [IDA]			538
P48643 UniProt NPD GO	TCPE_HUMAN	T-complex protein 1 subunit epsilon (TCP-1-epsilon) (CCT-epsilon)	0.14	-	cyt	0	Cytoplasm				541
Q5RF02 UniProt NPD GO	TCPE_PONPY	T-complex protein 1 subunit epsilon (TCP-1-epsilon) (CCT-epsilon)	0.14	-	cyt	0	Cytoplasm (By similarity)				541
P55965 UniProt NPD GO	BYN_DROME	T-related protein (Trp) (Protein brachyenteron)	0.14	-	nuc	0	Nucleus (Potential)	nucleus [IDA]			697
P13393 UniProt NPD GO	TBP_YEAST	TATA-box-binding protein (TATA-box factor) (TATA-binding factor) (TATA sequence-binding protein) (TB ...	0.14	-	nuc	0	Nucleus	nucleus [IDA] RNA polymerase I transcription factor complex [TAS] transcription factor TFIID complex [IDA] transcription factor TFIIIB complex [IDA]		1YTF	239
Q9TU45 UniProt NPD GO	TYOBP_PIG	TYRO protein tyrosine kinase-binding protein precursor (DNAX-activation protein 12)	0.14	-	end	2 *	Membrane; single-pass type I membrane protein (By similarity)				108
P14213 UniProt NPD GO	TAC1_TACTR	Tachyplesin-1 precursor (Tachyplesin I)	0.14	-	cyt	0	Secreted protein. S-granules			1WO1	77
Q93YA3 UniProt NPD GO	TASY_TAXBA	Taxadiene synthase (EC 4.2.3.17) (Taxa-4(5),11(12)-diene synthase)	0.14	-	cyt	0					862
Q03096 UniProt NPD GO	EST3_YEAST	Telomere replication protein EST3 (Ever shorter telomeres protein 3) [Contains: Telomere replication ...	0.14	-	nuc	0	Nucleus (Probable)	chromosome, telomeric region [IMP] nucleus [IDA] telomerase holoenzyme complex [IDA]			181
Q9JMI7 UniProt NPD GO	TX101_MOUSE	Testis-expressed protein 101 precursor (TES101-reactive protein) (TES101RP)	0.14	-	mit	0	Cell membrane; lipid-anchor; GPI-anchor (By similarity). Associated with lipid rafts. Shed from epid ...				250
P07504 UniProt NPD GO	THN_PYRPU	Thionin	0.14	-	mit	0	Secreted protein				47
P09856 UniProt NPD GO	TRXF_SPIOL	Thioredoxin F-type, chloroplast precursor (TRX-F)	0.14	-	cyt	0	Plastid; chloroplast			1FAA	190
O18883 UniProt NPD GO	TXND9_BOVIN	Thioredoxin domain-containing protein 9 (Protein 1-4) (Fragment)	0.14	-	cyt	0					179
Q9BG99 UniProt NPD GO	TREX1_BOVIN	Three prime repair exonuclease 1 (EC 3.1.11.2) (3'-5' exonuclease TREX1)	0.14	-	nuc	1	Nucleus (By similarity)	nuclear envelope [ISS]			315
O13427 UniProt NPD GO	GLY1_CANAL	Threonine aldolase (EC 4.1.2.5)	0.14	-	cyt	0					374
Q8BH55 UniProt NPD GO	THNSL_MOUSE	Threonine synthase-like 1	0.14	-	cyt	0					747
P49430 UniProt NPD GO	THAS_RAT	Thromboxane-A synthase (EC 5.3.99.5) (TXA synthase) (TXS) (Cytochrome P450 5A1)	0.14	-	vac	0	Membrane; multi-pass membrane protein				533
Q5SDL7 UniProt NPD GO	TROPA_IXOSC	Tick receptor for ospA	0.14	-	nuc	0	Cell membrane. Predominantly. May be an integral membrane or secreted. However, no clear transmembra ...				161
P18329 UniProt NPD GO	TX311_DENAN	Toxin C13S1C1 precursor	0.14	-	nuc	1 *	Secreted protein				80
P83476 UniProt NPD GO	TXPR2_THRPR	Toxin ProTx-2 (ProTx-II)	0.14	-	cyt	0	Secreted protein				30
Q8VI73 UniProt NPD GO	TALDO_CRIGR	Transaldolase (EC 2.2.1.2)	0.14	-	mit	0	Cytoplasm (Probable)				337
O77627 UniProt NPD GO	JUN_BOVIN	Transcription factor AP-1 (Activator protein 1) (AP1) (Proto-oncogene c-jun) (V-jun avian sarcoma vi ...	0.14	-	nuc	0	Nucleus				105
O09139 UniProt NPD GO	E2F1_RAT	Transcription factor E2F1 (E2F-1) (Fragment)	0.14	+	cyt	0	Nucleus				38
Q39236 UniProt NPD GO	T2AG_ARATH	Transcription initiation factor IIA gamma chain (TFIIA-gamma)	0.14	-	cyt	0	Nucleus (By similarity)				106
Q95215 UniProt NPD GO	BGH3_RABIT	Transforming growth factor-beta-induced protein ig-h3 precursor (Beta ig-h3) (Kerato-epithelin) (RGD ...	0.14	-	mit	1 *	Secreted protein; extracellular space. May be associated both with microfibrils and with the cell su ...				683
Q43848 UniProt NPD GO	TKTC_SOLTU	Transketolase, chloroplast precursor (EC 2.2.1.1) (TK)	0.14	-	mit	0	Plastid; chloroplast; chloroplast thylakoid membrane (By similarity)	thylakoid membrane (sensu Viridiplantae) [ISS]			741
P41632 UniProt NPD GO	IF1C_PINTH	Translation initiation factor IF-1, chloroplast	0.14	-	nuc	0	Plastid; chloroplast				78
Q4R6T3 UniProt NPD GO	EI2BG_MACFA	Translation initiation factor eIF-2B subunit gamma (eIF-2B GDP-GTP exchange factor subunit gamma)	0.14	-	cyt	0					452
Q5E971 UniProt NPD GO	TMEDA_BOVIN	Transmembrane emp24 domain-containing protein 10 precursor (Transmembrane protein Tmp21) (21 kDa tra ...	0.14	-	end	2 *	Golgi apparatus; Golgi membrane; single-pass type I membrane protein; lumenal side (By similarity)				219
Q28735 UniProt NPD GO	TMEDA_RABIT	Transmembrane emp24 domain-containing protein 10 precursor (Transmembrane protein Tmp21) (21 kDa tra ...	0.14	-	end	2 *	Golgi apparatus; Golgi membrane; single-pass type I membrane protein; lumenal side			1P23	219
Q6AY25 UniProt NPD GO	TMED3_RAT	Transmembrane emp24 domain-containing protein 3 precursor	0.14	-	end	2 *	Endoplasmic reticulum-Golgi intermediate compartment; endoplasmic reticulum-Golgi intermediate compa ...				221
Q2KJ84 UniProt NPD GO	TMED5_BOVIN	Transmembrane emp24 domain-containing protein 5 precursor	0.14	-	end	2 *	Endoplasmic reticulum; endoplasmic reticulum membrane; single-pass type I membrane protein (By simil ...				226
Q7LJR6 UniProt NPD GO	TRI5_FUSAC	Trichodiene synthase (EC 4.2.3.6) (Sesquiterpene cyclase) (TS)	0.14	-	cyt	0					375
Q5RDA5 UniProt NPD GO	TREM1_PONPY	Triggering receptor expressed on myeloid cells 1 precursor (TREM-1)	0.14	-	end	1	Membrane; single-pass type I membrane protein (By similarity)				231
P80322 UniProt NPD GO	TNNC_BRALA	Troponin C	0.14	-	cyt	0					163

You are viewing entries 59101 to 59150 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.