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
Q12120 UniProt NPD GO	OMTA_ASPPA	Sterigmatocystin 8-O-methyltransferase precursor (EC 2.1.1.110)	0.15	-	cyt	0					418
Q20657 UniProt NPD GO	STO3_CAEEL	Stomatin-3	0.15	-	nuc	1 *					267
Q99470 UniProt NPD GO	SDF2_HUMAN	Stromal cell-derived factor 2 precursor (SDF-2)	0.15	-	exc	0	Secreted protein (Probable)	extracellular space [TAS]	602934		211
Q9UTS0 UniProt NPD GO	PSP3_SCHPO	Subtilase-type proteinase psp3 precursor (EC 3.4.21.-)	0.15	-	end	0					451
P31039 UniProt NPD GO	DHSA_BOVIN	Succinate dehydrogenase [ubiquinone] flavoprotein subunit, mitochondrial precursor (EC 1.3.5.1) (Fp) ...	0.15	-	mit	0	Mitochondrion; mitochondrial inner membrane				665
P52846 UniProt NPD GO	ST1A1_MACFA	Sulfotransferase 1A1 (EC 2.8.2.1) (Aryl sulfotransferase) (Phenol sulfotransferase) (Phenol-sulfatin ...	0.15	-	cyt	0	Cytoplasm (By similarity)				295
Q00637 UniProt NPD GO	SODM_DROME	Superoxide dismutase [Mn], mitochondrial precursor (EC 1.15.1.1)	0.15	-	mit	0	Mitochondrion; mitochondrial matrix				217
Q64232 UniProt NPD GO	GPSN2_RAT	Synaptic glycoprotein SC2	0.15	-	cyt	4	Membrane; multi-pass membrane protein (Potential)				308
P34351 UniProt NPD GO	SNB5_CAEEL	Synaptobrevin-like protein 5	0.15	-	nuc	1					102
P79778 UniProt NPD GO	TBXT_CHICK	T-box-containing protein TBXT	0.15	-	nuc	0	Nucleus (Potential)				397
P01849 UniProt NPD GO	TCA_MOUSE	T-cell receptor alpha chain C region	0.15	-	nuc	0					138
O62848 UniProt NPD GO	CD1D_SHEEP	T-cell surface glycoprotein CD1d precursor (CD1d antigen)	0.15	-	nuc	1	Membrane; single-pass type I membrane protein	integral to plasma membrane [ISS]			335
P18439 UniProt NPD GO	CD3G_SHEEP	T-cell surface glycoprotein CD3 gamma chain (T-cell receptor T3 gamma chain) (Fragment)	0.15	-	nuc	1	Membrane; single-pass type I membrane protein	integral to plasma membrane [ISS] T cell receptor complex [ISS]			147
Q08336 UniProt NPD GO	CD4_CERTO	T-cell surface glycoprotein CD4 (T-cell surface antigen T4/Leu-3) (Fragment)	0.15	-	nuc	1	Membrane; single-pass type I membrane protein	T cell receptor complex [ISS]			397
Q5R637 UniProt NPD GO	TCPD_PONPY	T-complex protein 1 subunit delta (TCP-1-delta) (CCT-delta)	0.15	-	cyt	0	Cytoplasm (By similarity)				538
O77323 UniProt NPD GO	TCPH_PLAF7	T-complex protein 1 subunit eta (TCP-1-eta) (CCT-eta)	0.15	-	cyt	0	Cytoplasm (By similarity)				539
Q9LKI7 UniProt NPD GO	TCPG_THAWE	T-complex protein 1 subunit gamma (TCP-1-gamma) (CCT-gamma)	0.15	-	mit	0	Cytoplasm (By similarity)				558
Q5ZJ54 UniProt NPD GO	TCPZ_CHICK	T-complex protein 1 subunit zeta (TCP-1-zeta) (CCT-zeta)	0.15	-	cyt	0	Cytoplasm (By similarity)				529
O77622 UniProt NPD GO	TCPZ_RABIT	T-complex protein 1 subunit zeta (TCP-1-zeta) (CCT-zeta)	0.15	-	cyt	0	Cytoplasm				530
Q3MHL7 UniProt NPD GO	TCPZ_BOVIN	T-complex protein 1 subunit zeta (TCP-1-zeta) (CCT-zeta) (CCT-zeta-1)	0.15	-	cyt	0	Cytoplasm (By similarity)				530
Q12731 UniProt NPD GO	TBP_EMENI	TATA-box-binding protein (TATA-box factor) (TATA-binding factor) (TATA sequence-binding protein) (TB ...	0.15	-	cyt	0	Nucleus				268
Q5XJS5 UniProt NPD GO	THOC6_BRARE	THO complex subunit 6 homolog (WD repeat protein 58)	0.15	-	cyt	0					323
P69136 UniProt NPD GO	TAC1_CARRO	Tachyplesin-1 (Tachyplesin I)	0.15	-		0	Secreted protein				17
P69135 UniProt NPD GO	TAC1_TACGI	Tachyplesin-1 (Tachyplesin I)	0.15	-		0	Secreted protein				17
Q7RTX0 UniProt NPD GO	TS1R3_HUMAN	Taste receptor type 1 member 3 precursor (Sweet taste receptor T1R3)	0.15	-	end	7	Membrane; multi-pass membrane protein	integral to membrane [IC]	605865		852
Q7TQA7 UniProt NPD GO	TA2R3_MOUSE	Taste receptor type 2 member 3 (T2R3) (T2R137) (T2R37) (mT2r41)	0.15	-	end	7 *	Membrane; multi-pass membrane protein	integral to membrane [NAS]			316
Q646C8 UniProt NPD GO	T2R39_PANPA	Taste receptor type 2 member 39 (T2R39)	0.15	-	end	6 *	Membrane; multi-pass membrane protein				338
Q646A9 UniProt NPD GO	T2R39_PANTR	Taste receptor type 2 member 39 (T2R39)	0.15	-	end	6 *	Membrane; multi-pass membrane protein				338
Q9NYW1 UniProt NPD GO	TA2R9_HUMAN	Taste receptor type 2 member 9 (T2R9) (Taste receptor family B member 6) (TRB6)	0.15	-	end	7 *	Membrane; multi-pass membrane protein	integral to membrane [NAS]	604795		312
Q2QLH9 UniProt NPD GO	TES_OTOGA	Testin	0.15	-	nuc	0					421
P26258 UniProt NPD GO	TETN_CARSP	Tetranectin-like protein	0.15	-	nuc	0					166
Q05998 UniProt NPD GO	THI7_YEAST	Thiamine transporter	0.15	-	end	12 *	Membrane; multi-pass membrane protein	plasma membrane [IMP]			598
Q8LD49 UniProt NPD GO	TRXX_ARATH	Thioredoxin X, chloroplast precursor	0.15	-	mit	0	Plastid; chloroplast (Potential)				182
Q6BIS1 UniProt NPD GO	TRXB_DEBHA	Thioredoxin reductase (EC 1.8.1.9)	0.15	-	cyt	0	Cytoplasm (By similarity)				321
Q9XFI1 UniProt NPD GO	TRXL3_ARATH	Thioredoxin-like 3, chloroplast precursor	0.15	-	nuc	0	Plastid; chloroplast (Potential)				245
Q8VZT6 UniProt NPD GO	TRXL8_ARATH	Thioredoxin-like 8, chloroplast precursor	0.15	-	mit	0	Plastid; chloroplast (Potential)				192
P81946 UniProt NPD GO	THST_DENAN	Thrombostatin (Glycoprotein IIb-IIIa antagonist) (Platelet aggregation inhibitor)	0.15	-	nuc	0	Secreted protein				59
Q8K093 UniProt NPD GO	TRHDE_MOUSE	Thyrotropin-releasing hormone-degrading ectoenzyme (EC 3.4.19.6) (TRH-degrading ectoenzyme) (TRH-DE) ...	0.15	-	mit	1 *	Membrane; single-pass type II membrane protein (By similarity)				1025
Q10836 UniProt NPD GO	TRHDE_RAT	Thyrotropin-releasing hormone-degrading ectoenzyme (EC 3.4.19.6) (TRH-degrading ectoenzyme) (TRH-DE) ...	0.15	-	mit	1 *	Membrane; single-pass type II membrane protein				1025
P61939 UniProt NPD GO	THBG_MOUSE	Thyroxine-binding globulin precursor (T4-binding globulin) (Serpin A7)	0.15	-	end	0	Secreted protein (By similarity)				418
Q99LJ1 UniProt NPD GO	FUCO_MOUSE	Tissue alpha-L-fucosidase precursor (EC 3.2.1.51) (Alpha-L-fucosidase I) (Alpha-L-fucoside fucohydro ...	0.15	-	exc	0	Lysosome (By similarity)				452
Q5NCF2 UniProt NPD GO	TPPC1_MOUSE	Trafficking protein particle complex subunit 1	0.15	-	cyt	0	Golgi apparatus; cis-Golgi network (By similarity)				145
Q9Y5R8 UniProt NPD GO	TPPC1_HUMAN	Trafficking protein particle complex subunit 1 (BET5 homolog) (Multiple myeloma protein 2) (MUM-2)	0.15	-	cyt	0	Golgi apparatus; cis-Golgi network (By similarity)				145
P37837 UniProt NPD GO	TALDO_HUMAN	Transaldolase (EC 2.2.1.2)	0.15	-	mit	0	Cytoplasm (Probable)	cytoplasm [TAS]	602063	1F05	337
Q9EQS0 UniProt NPD GO	TALDO_RAT	Transaldolase (EC 2.2.1.2)	0.15	-	mit	0	Cytoplasm (Probable)				337
Q8SRP3 UniProt NPD GO	TF2B_ENCCU	Transcription initiation factor IIB (General transcription factor TFIIB)	0.15	-	nuc	0	Nucleus (By similarity)				312
Q00899 UniProt NPD GO	TYY1_MOUSE	Transcriptional repressor protein YY1 (Yin and yang 1) (YY-1) (Delta transcription factor) (NF-E1) ( ...	0.15	+	cyt	0	Nucleus; nucleoplasm; nuclear matrix. Associated with the nuclear matrix	transcription factor complex [IDA]			414
Q26643 UniProt NPD GO	TRF_SARPE	Transferrin precursor	0.15	-	exc	0					629
P97891 UniProt NPD GO	TSN_CRIGR	Translin	0.15	-	cyt	0	Nucleus				228
Q8R1V4 UniProt NPD GO	TMED4_MOUSE	Transmembrane emp24 domain-containing protein 4 precursor (p26)	0.15	-	end	2 *	Endoplasmic reticulum; endoplasmic reticulum membrane; single-pass type I membrane protein (By simil ...				227

You are viewing entries 57701 to 57750 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.