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
Q9GLX8 UniProt NPD GO	BKRB2_PIG	B2 bradykinin receptor (BK-2 receptor) (B2R)	0.08	-	end	7 *	Membrane; multi-pass membrane protein				367
Q9BX70 UniProt NPD GO	BTBD2_HUMAN	BTB/POZ domain-containing protein 2	0.08	-	cyt	0	Cytoplasm. Cytoplasmic bodies		608531		525
Q8I009 UniProt NPD GO	BIRC5_CANFA	Baculoviral IAP repeat-containing protein 5 (Apoptosis inhibitor survivin)	0.08	-	nuc	0	Cytoplasm. Nucleus. Localizes on chromosome arms and inner centromeres from prophase through metapha ...				142
Q07469 UniProt NPD GO	BSPA_POPDE	Bark storage protein A precursor	0.08	-	cyt	0					312
Q05537 UniProt NPD GO	CHID_LYCES	Basic endochitinase (EC 3.2.1.14) (Fragment)	0.08	-	cyt	0	Secreted protein; extracellular space (Probable)				246
Q9JJV0 UniProt NPD GO	CRBA4_MOUSE	Beta crystallin A4 (Beta-A4-crystallin)	0.08	-	cyt	0					195
Q9WVJ5 UniProt NPD GO	CRBB1_MOUSE	Beta crystallin B1 [Contains: Beta crystallin B1B]	0.08	-	cyt	0					249
Q9JJS6 UniProt NPD GO	BCDO1_MOUSE	Beta,beta-carotene 15,15'-monooxygenase (EC 1.14.99.36) (Beta-carotene dioxygenase 1)	0.08	-	cyt	0					566
Q5RAL7 UniProt NPD GO	B3GT3_PONPY	Beta-1,3-galactosyltransferase 3 (EC 2.4.1.79) (Beta-1,3-GalTase 3) (Beta3Gal-T3) (b3Gal-T3) (Galact ...	0.08	-	nuc	1 *	Golgi apparatus; Golgi membrane; single-pass type II membrane protein (By similarity)				331
Q8NHY0 UniProt NPD GO	B4GN2_HUMAN	Beta-1,4 N-acetylgalactosaminyltransferase 2 (EC 2.4.1.-) (Sd(a) beta-1,4-GalNAc transferase) (UDP-G ...	0.08	+	mit	1	Golgi apparatus; Golgi membrane; single-pass type II membrane protein (Potential)				566
Q9TST5 UniProt NPD GO	ADRB2_FELCA	Beta-2 adrenergic receptor (Beta-2 adrenoceptor) (Beta-2 adrenoreceptor)	0.08	-	end	7 *	Membrane; multi-pass membrane protein				418
Q28997 UniProt NPD GO	ADRB2_PIG	Beta-2 adrenergic receptor (Beta-2 adrenoceptor) (Beta-2 adrenoreceptor)	0.08	-	end	7 *	Membrane; multi-pass membrane protein				418
Q8BWG8 UniProt NPD GO	ARRB1_MOUSE	Beta-arrestin-1 (Arrestin, beta 1)	0.08	-	mit	0		intracellular [IDA]			418
P29066 UniProt NPD GO	ARRB1_RAT	Beta-arrestin-1 (Arrestin, beta 1)	0.08	-	mit	0		membrane fraction [ISS] plasma membrane [TAS] postsynaptic membrane [IDA]			418
Q39982 UniProt NPD GO	CRTW_HAEPL	Beta-carotene ketolase (EC 1.13.-.-) (Beta-carotene oxygenase)	0.08	-	end	5					320
Q95J24 UniProt NPD GO	BD01_CERAE	Beta-defensin 1 precursor (BD-1) (Defensin, beta 1)	0.08	-	exc	0	Secreted protein				68
Q95M67 UniProt NPD GO	BD01_CERER	Beta-defensin 1 precursor (BD-1) (Defensin, beta 1)	0.08	-	exc	0	Secreted protein				68
Q7JGL8 UniProt NPD GO	BD01_CERPR	Beta-defensin 1 precursor (BD-1) (Defensin, beta 1)	0.08	-	exc	0	Secreted protein				68
Q7JGM0 UniProt NPD GO	BD01_PRECR	Beta-defensin 1 precursor (BD-1) (Defensin, beta 1)	0.08	-	exc	0	Secreted protein				68
Q95J18 UniProt NPD GO	BD01_PREME	Beta-defensin 1 precursor (BD-1) (Defensin, beta 1)	0.08	-	exc	0	Secreted protein				68
Q7JGL9 UniProt NPD GO	BD01_PREOB	Beta-defensin 1 precursor (BD-1) (Defensin, beta 1)	0.08	-	exc	0	Secreted protein				68
P46169 UniProt NPD GO	BD11_BOVIN	Beta-defensin 11 precursor (BNDB-11) (BNBD-11) (Neutrophil beta-defensin 11)	0.08	-	exc	1 *	Secreted protein				60
Q30KK9 UniProt NPD GO	DB118_PANTR	Beta-defensin 118 precursor (Defensin, beta 118)	0.08	-	nuc	0	Secreted protein (Potential)				123
P46170 UniProt NPD GO	BD12_BOVIN	Beta-defensin 12 (BNDB-12) (BNBD-12)	0.08	-	mit	0	Secreted protein			1BNB	38
P46171 UniProt NPD GO	BD13_BOVIN	Beta-defensin 13 (BNDB-13) (BNBD-13)	0.08	-	nuc	0	Secreted protein				42
Q7TNV7 UniProt NPD GO	BD38_MOUSE	Beta-defensin 38 precursor (Defensin, beta 38) (BD-38) (mBD-38)	0.08	-	vac	0	Secreted protein				63
P46162 UniProt NPD GO	BD04_BOVIN	Beta-defensin 4 precursor (BNDB-4) (BNBD-4)	0.08	-	mit	1 *	Secreted protein				63
P45582 UniProt NPD GO	BGAL_ASPOF	Beta-galactosidase precursor (EC 3.2.1.23) (Lactase)	0.08	-	exc	0					832
P23780 UniProt NPD GO	BGAL_MOUSE	Beta-galactosidase precursor (EC 3.2.1.23) (Lactase) (Acid beta-galactosidase)	0.08	-	exc	0	Lysosome				647
P04119 UniProt NPD GO	LACB_PIG	Beta-lactoglobulin-1A/1C precursor (Beta-lactoglobulin IA/IC) (Beta-LG)	0.08	-	exc	0				1EXS	178
Q60538 UniProt NPD GO	SGCB_MESAU	Beta-sarcoglycan (Beta-SG) (43 kDa dystrophin-associated glycoprotein) (43DAG)	0.08	-	mit	1	Sarcolemma; sarcolemmal membrane; single-pass type II membrane protein (By similarity)				320
P56818 UniProt NPD GO	BACE1_MOUSE	Beta-secretase 1 precursor (EC 3.4.23.46) (Beta-site APP cleaving enzyme 1) (Beta-site amyloid precu ...	0.08	-	cyt	1	Membrane; single-pass type I membrane protein	axon [IDA] cytoplasmic vesicle [IDA] endosome [ISS] Golgi apparatus [ISS] integral to membrane [ISS]			501
Q40024 UniProt NPD GO	BADH_HORVU	Betaine-aldehyde dehydrogenase (EC 1.2.1.8) (BADH)	0.08	-	pox	0	Peroxisome (Potential)				505
Q05762 UniProt NPD GO	DRTS1_ARATH	Bifunctional dihydrofolate reductase-thymidylate synthase 1 (DHFR-TS 1) [Includes: Dihydrofolate red ...	0.08	-	cyt	0					519
P49789 UniProt NPD GO	FHIT_HUMAN	Bis(5'-adenosyl)-triphosphatase (EC 3.6.1.29) (Diadenosine 5',5'''-P1,P3-triphosphate hydrolase) (Di ...	0.08	-	cyt	0	Cytoplasm	cytoplasm [IDA]	144700	6FIT	146
P87362 UniProt NPD GO	BLMH_CHICK	Bleomycin hydrolase (EC 3.4.22.40) (BLM hydrolase) (BMH) (BH) (Aminopeptidase H)	0.08	-	cyt	0	Cytoplasm (By similarity)				455
P26726 UniProt NPD GO	BXA3_BOMMO	Bombyxin A-3 precursor (BBX-A3) (4K-prothoracicotropic hormone) (4K-PTTH) [Contains: Bombyxin A-3 B ...	0.08	-	exc	0	Secreted protein				92
P26728 UniProt NPD GO	BXA5_BOMMO	Bombyxin A-5 precursor (BBX-A5) (4K-prothoracicotropic hormone) (4K-PTTH) [Contains: Bombyxin A-5 B ...	0.08	-	exc	0	Secreted protein				92
P81661 UniProt NPD GO	VSPA_BOTJA	Bothrombin (EC 3.4.21.74) (Reptilase)	0.08	-	cyt	0	Secreted protein			1CXM	232
P28664 UniProt NPD GO	BI54_MOUSE	Brain protein I54	0.08	-	mit	0		mitochondrion [IDA]			130
Q66Q82 UniProt NPD GO	BURS_ANOGA	Bursicon precursor (Bursicon subunit alpha) (Cuticle-tanning hormone)	0.08	-	nuc	0	Secreted protein (By similarity)				163
P32246 UniProt NPD GO	CCR1_HUMAN	C-C chemokine receptor type 1 (C-C CKR-1) (CC-CKR-1) (CCR-1) (CCR1) (Macrophage inflammatory protein ...	0.08	-	end	7 *	Membrane; multi-pass membrane protein	integral to plasma membrane [TAS] plasma membrane [IDA]	601159		355
O18793 UniProt NPD GO	CCR2_MACMU	C-C chemokine receptor type 2 (C-C CKR-2) (CC-CKR-2) (CCR-2) (CCR2) (Monocyte chemoattractant protei ...	0.08	-	end	6 *	Membrane; multi-pass membrane protein				360
Q95NC9 UniProt NPD GO	CCR5_ALOSE	C-C chemokine receptor type 5 (C-C CKR-5) (CC-CKR-5) (CCR-5) (CCR5) (CD195 antigen)	0.08	-	end	6 *	Membrane; multi-pass membrane protein				352
Q95NC4 UniProt NPD GO	CCR5_ATEGE	C-C chemokine receptor type 5 (C-C CKR-5) (CC-CKR-5) (CCR-5) (CCR5) (CD195 antigen)	0.08	-	end	6 *	Membrane; multi-pass membrane protein				352
Q95NC2 UniProt NPD GO	CCR5_CALMO	C-C chemokine receptor type 5 (C-C CKR-5) (CC-CKR-5) (CCR-5) (CCR5) (CD195 antigen)	0.08	-	end	6 *	Membrane; multi-pass membrane protein				352
Q63515 UniProt NPD GO	C4BB_RAT	C4b-binding protein beta chain precursor	0.08	-	exc	0					258
O70129 UniProt NPD GO	C5AR_CAVPO	C5a anaphylatoxin chemotactic receptor (C5a-R) (C5aR) (CD88 antigen)	0.08	-	end	7 *	Membrane; multi-pass membrane protein				345
P97520 UniProt NPD GO	C5AR_RAT	C5a anaphylatoxin chemotactic receptor (C5a-R) (C5aR) (CD88 antigen)	0.08	-	end	7 *	Membrane; multi-pass membrane protein	cell surface [IDA]			352
Q80W54 UniProt NPD GO	FACE1_MOUSE	CAAX prenyl protease 1 homolog (EC 3.4.24.84) (Prenyl protein-specific endoprotease 1) (Farnesylated ...	0.08	-	end	7 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (By similarity). ...	membrane fraction [IDA]			475

You are viewing entries 67651 to 67700 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.