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
Q9NRM0 UniProt NPD GO	GTR9_HUMAN	Solute carrier family 2, facilitated glucose transporter member 9 (Glucose transporter type 9)	0.18	-	end	12	Membrane; multi-pass membrane protein	integral to membrane [NAS]	606142		540
Q9ERB5 UniProt NPD GO	SO1C1_MOUSE	Solute carrier organic anion transporter family member 1C1 (Solute carrier family 21 member 14) (Org ...	0.18	-	end	10	Membrane; multi-pass membrane protein				715
Q92959 UniProt NPD GO	SO2A1_HUMAN	Solute carrier organic anion transporter family member 2A1 (Solute carrier family 21 member 2) (Pros ...	0.18	-	end	11 *	Membrane; multi-pass membrane protein	integral to plasma membrane [TAS] membrane fraction [TAS]	601460		643
P24405 UniProt NPD GO	SOML_ONCKE	Somatolactin precursor (SL)	0.18	-	end	0	Secreted protein				233
P49660 UniProt NPD GO	SSR4_MOUSE	Somatostatin receptor type 4 (SS4R)	0.18	-	end	7 *	Membrane; multi-pass membrane protein				384
P05044 UniProt NPD GO	SORCN_CRIGR	Sorcin (22 kDa protein) (CP-22) (V19)	0.18	-	cyt	0	Cytoplasm			1GJY	198
Q9GU57 UniProt NPD GO	CX9A_CONGL	Spasmodic protein tx9a-like protein precursor (Conotoxin Gm9.1) (Conotoxin gm9a)	0.18	-	exc	1 *	Secreted protein			1IXT	88
P21901 UniProt NPD GO	KAPL_APLCA	Spermatozoon-associated protein kinase (EC 2.7.11.1) (SAK) (C-APL-B)	0.18	-	cyt	0					351
Q9H228 UniProt NPD GO	EDG8_HUMAN	Sphingosine 1-phosphate receptor Edg-8 (Endothelial differentiation sphingolipid G-protein-coupled r ...	0.18	+	end	7 *	Membrane; multi-pass membrane protein		605146		398
Q9BPZ2 UniProt NPD GO	SPIN2_HUMAN	Spindlin-2 (Spindlin-like protein 2) (SPIN-2)	0.18	-	cyt	0			300517		258
Q5RA80 UniProt NPD GO	SPIN2_PONPY	Spindlin-2 (Spindlin-like protein 2) (SPIN-2)	0.18	-	cyt	0					258
Q62203 UniProt NPD GO	SF3A2_MOUSE	Splicing factor 3A subunit 2 (Spliceosome-associated protein 62) (SAP 62) (SF3a66)	0.18	-	nuc	0	Nucleus (By similarity)				475
P13130 UniProt NPD GO	SS100_YEAST	Sporulation-specific wall maturation protein precursor	0.18	-	mit	0					326
P51071 UniProt NPD GO	THS3_VITVI	Stilbene synthase 3 (EC 2.3.1.95) (Resveratrol synthase 3) (Trihydroxystilbene synthase 3) (PSV368) ...	0.18	-	cyt	0	Cytoplasm				389
P24347 UniProt NPD GO	MMP11_HUMAN	Stromelysin-3 precursor (EC 3.4.24.-) (ST3) (SL-3) (Matrix metalloproteinase-11) (MMP-11)	0.18	+	mit	0		extracellular matrix (sensu Metazoa) [TAS]	185261		488
P13708 UniProt NPD GO	SUSY_SOYBN	Sucrose synthase (EC 2.4.1.13) (Sucrose-UDP glucosyltransferase) (Nodulin-100)	0.18	-	mit	0					805
P04712 UniProt NPD GO	SUS1_MAIZE	Sucrose synthase 1 (EC 2.4.1.13) (Sucrose-UDP glucosyltransferase 1) (Shrunken-1)	0.18	-	cyt	0					802
O76156 UniProt NPD GO	SAT_ENTHI	Sulfate adenylyltransferase (EC 2.7.7.4) (Sulfate adenylate transferase) (SAT) (ATP-sulfurylase)	0.18	+	cyt	0					423
P10960 UniProt NPD GO	SAP_RAT	Sulfated glycoprotein 1 precursor (SGP-1) (Prosaposin)	0.18	-	exc	0	Secreted protein; extracellular space				554
Q861R0 UniProt NPD GO	SOCS2_BOVIN	Suppressor of cytokine signaling 2 (SOCS-2)	0.18	-	nuc	0					198
O74559 UniProt NPD GO	SURF4_SCHPO	Surfeit locus protein 4 homolog	0.18	-	end	7	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (By similarity)				302
Q8JFV8 UniProt NPD GO	VAT1_BRARE	Synaptic vesicle membrane protein VAT-1 homolog (EC 1.-.-.-)	0.18	-	nuc	0					484
P15812 UniProt NPD GO	CD1E_HUMAN	T-cell surface glycoprotein CD1e precursor (CD1e antigen) (R2G1)	0.18	-	nuc	1	Membrane; single-pass type I membrane protein	integral to plasma membrane [NAS]	188411		322
P09693 UniProt NPD GO	CD3G_HUMAN	T-cell surface glycoprotein CD3 gamma chain precursor (T-cell receptor T3 gamma chain)	0.18	-	end	2 *	Membrane; single-pass type I membrane protein	integral to plasma membrane [NAS] T cell receptor complex [NAS]	186740	1SY6	182
P41988 UniProt NPD GO	TCPA_CAEEL	T-complex protein 1 subunit alpha (TCP-1-alpha) (CCT-alpha)	0.18	-	nuc	0	Cytoplasm				549
P39076 UniProt NPD GO	TCPB_YEAST	T-complex protein 1 subunit beta (TCP-1-beta) (CCT-beta)	0.18	-	cyt	0	Cytoplasm	chaperonin-containing T-complex [IPI] cytoplasm [IDA] cytoskeleton [TAS]			527
P80317 UniProt NPD GO	TCPZ_MOUSE	T-complex protein 1 subunit zeta (TCP-1-zeta) (CCT-zeta) (CCT-zeta-1)	0.18	-	cyt	0	Cytoplasm	chaperonin-containing T-complex [IDA]			530
P52653 UniProt NPD GO	TBP_ENTHI	TATA-box-binding protein (TATA-box factor) (TATA-binding factor) (TATA sequence-binding protein) (Tr ...	0.18	-	nuc	0	Nucleus				234
Q3SZV6 UniProt NPD GO	TI21L_BOVIN	TIM21-like protein, mitochondrial precursor	0.18	-	nuc	1	Mitochondrion; mitochondrial membrane; single-pass membrane protein (Potential)				244
Q23435 UniProt NPD GO	TWK9_CAEEL	TWiK family of potassium channels protein 9	0.18	+	end	6 *	Membrane; multi-pass membrane protein (Potential)				475
O43914 UniProt NPD GO	TYOBP_HUMAN	TYRO protein tyrosine kinase-binding protein precursor (DNAX-activation protein 12) (Killer-activati ...	0.18	-	end	1 *	Membrane; single-pass type I membrane protein	integral to plasma membrane [TAS]	604142		113
Q646F0 UniProt NPD GO	T2R39_PAPHA	Taste receptor type 2 member 39 (T2R39)	0.18	-	end	7 *	Membrane; multi-pass membrane protein				338
Q646F2 UniProt NPD GO	T2R40_PAPHA	Taste receptor type 2 member 40 (T2R40)	0.18	-	end	6 *	Membrane; multi-pass membrane protein				323
P59532 UniProt NPD GO	T2R41_MOUSE	Taste receptor type 2 member 41 (T2R41) (T2R12) (T2R26)	0.18	-	end	6 *	Membrane; multi-pass membrane protein				308
Q646E5 UniProt NPD GO	TA2R8_PANPA	Taste receptor type 2 member 8 (T2R8)	0.18	-	end	7 *	Membrane; multi-pass membrane protein				309
Q646C5 UniProt NPD GO	TA2R8_PANTR	Taste receptor type 2 member 8 (T2R8)	0.18	-	end	7 *	Membrane; multi-pass membrane protein				309
Q9NYW2 UniProt NPD GO	TA2R8_HUMAN	Taste receptor type 2 member 8 (T2R8) (Taste receptor family B member 5) (TRB5)	0.18	-	end	7 *	Membrane; multi-pass membrane protein	integral to membrane [NAS]	604794		309
Q645T0 UniProt NPD GO	TA2R9_MACMU	Taste receptor type 2 member 9 (T2R9)	0.18	-	end	7 *	Membrane; multi-pass membrane protein				311
P79876 UniProt NPD GO	TEMH_RANTE	Temporin-H precursor	0.18	-	exc	0	Secreted protein				58
Q2QLC3 UniProt NPD GO	TES_CALMO	Testin	0.18	-	nuc	0					421
Q925K9 UniProt NPD GO	TSSK6_MOUSE	Testis-specific serine/threonine-protein kinase 6 (EC 2.7.11.1) (TSSK-6) (Small serine/threonine kin ...	0.18	-	cyt	0					273
P34285 UniProt NPD GO	TSP1_CAEEL	Tetraspanin-1	0.18	-	end	4 *	Membrane; multi-pass membrane protein (Potential)				244
Q86TZ1 UniProt NPD GO	TTC6_HUMAN	Tetratricopeptide repeat protein 6 (TPR repeat protein 6)	0.18	-	cyt	0					520
Q6A555 UniProt NPD GO	TXND8_HUMAN	Thioredoxin domain-containing protein 8 (Spermatid-specific thioredoxin-3) (Sptrx-3) (Thioredoxin-6) ...	0.18	-	cyt	0	Cytoplasm. Golgi apparatus				127
P04801 UniProt NPD GO	SYTC_YEAST	Threonyl-tRNA synthetase, cytoplasmic (EC 6.1.1.3) (Threonine--tRNA ligase) (ThrRS)	0.18	-	cyt	0	Cytoplasm	cytoplasm [IMP] mitochondrion [IDA]			734
Q5W7P8 UniProt NPD GO	TRBM_CANFA	Thrombomodulin precursor (TM) (CD141 antigen)	0.18	-	end	1	Membrane; single-pass type I membrane protein (By similarity)				578
Q1L8P7 UniProt NPD GO	TSP3B_BRARE	Thrombospondin-3b precursor (Thbs3b)	0.18	-	end	0					929
P04216 UniProt NPD GO	THY1_HUMAN	Thy-1 membrane glycoprotein precursor (Thy-1 antigen) (CD90 antigen) (CDw90 antigen)	0.18	-	exc	0	Cell membrane; lipid-anchor; GPI-anchor	cytosol [ISS] external side of plasma membrane [ISS] growth cone [ISS] integral to plasma membrane [TAS] lipid raft [NAS] plasma membrane [ISS]	188230		161
Q60HF8 UniProt NPD GO	FUCO_MACFA	Tissue alpha-L-fucosidase precursor (EC 3.2.1.51) (Alpha-L-fucosidase I) (Alpha-L-fucoside fucohydro ...	0.18	-	exc	1 *	Lysosome (By similarity)				468
O77277 UniProt NPD GO	TORS_DROME	Torsin-like protein precursor	0.18	-	exc	0	Endoplasmic reticulum; endoplasmic reticulum lumen (By similarity)				340

You are viewing entries 53701 to 53750 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.