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
Q9NZM6 UniProt NPD GO	PK2L2_HUMAN	Polycystic kidney disease 2-like 2 protein (Polycystin-L2)	0.27	-	end	6 *	Membrane; multi-pass membrane protein (Potential)	integral to membrane [TAS]	604669		624
Q9JLG4 UniProt NPD GO	PK2L2_MOUSE	Polycystic kidney disease 2-like 2 protein (Polycystin-L2)	0.27	-	end	7 *	Membrane; multi-pass membrane protein (Potential)				621
P81265 UniProt NPD GO	PIGR_BOVIN	Polymeric-immunoglobulin receptor precursor (Poly-Ig receptor) (PIGR) [Contains: Secretory component ...	0.27	-	end	1	Cell membrane; single-pass type I membrane protein. Processed form: Secreted protein				757
Q9HCQ5 UniProt NPD GO	GALT9_HUMAN	Polypeptide N-acetylgalactosaminyltransferase 9 (EC 2.4.1.41) (Protein-UDP acetylgalactosaminyltrans ...	0.27	-	end	1 *	Golgi apparatus; Golgi membrane; single-pass type II membrane protein (By similarity)	membrane [NAS]	606251		603
Q75DY0 UniProt NPD GO	HEM3_ASHGO	Porphobilinogen deaminase (EC 2.5.1.61) (PBG) (Hydroxymethylbilane synthase) (HMBS) (Pre-uroporphyri ...	0.27	-	cyt	0					326
P50996 UniProt NPD GO	ATP4A_CANFA	Potassium-transporting ATPase alpha chain 1 (EC 3.6.3.10) (Proton pump) (Gastric H+/K+ ATPase subuni ...	0.27	-	end	8	Membrane; multi-pass membrane protein				1033
P18598 UniProt NPD GO	ATP4B_RAT	Potassium-transporting ATPase subunit beta (Proton pump beta chain) (Gastric H(+)/K(+) ATPase beta s ...	0.27	-	mit	1 *	Membrane; single-pass type II membrane protein				294
Q6FQ33 UniProt NPD GO	CWC23_CANGA	Pre-mRNA-splicing factor CWC23	0.27	-	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity)				296
Q5KDR4 UniProt NPD GO	PRP46_CRYNE	Pre-mRNA-splicing factor PRP46 (Pre-mRNA-processing protein 46)	0.27	-	cyt	0	Cytoplasm (By similarity). Nucleus (By similarity)				473
P11464 UniProt NPD GO	PSG1_HUMAN	Pregnancy-specific beta-1-glycoprotein 1 precursor (PSBG-1) (Pregnancy-specific beta-1 glycoprotein ...	0.27	-	nuc	0	Secreted protein (Potential)		176390		419
Q5F495 UniProt NPD GO	MOB3_CHICK	Preimplantation protein 3 (Mps one binder kinase activator-like 3) (Mob1 homolog 3) (Mob3)	0.27	-	nuc	0	Cytoplasm. Membrane; peripheral membrane protein. Golgi apparatus; Golgi stack; Golgi stack membrane ...				223
O63066 UniProt NPD GO	SECY_MAIZE	Preprotein translocase secY subunit, chloroplast precursor (CpSecY)	0.27	-	end	8	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein				553
Q27539 UniProt NPD GO	CLPP_CAEEL	Probable ClpP-like protease (EC 3.4.21.92) (Endopeptidase Clp)	0.27	-	mit	0					206
Q14439 UniProt NPD GO	GP176_HUMAN	Probable G-protein coupled receptor 176 (HB-954)	0.27	-	end	7 *	Membrane; multi-pass membrane protein	integral to plasma membrane [TAS]			515
O94617 UniProt NPD GO	UAP1_SCHPO	Probable UDP-N-acetylglucosamine pyrophosphorylase (EC 2.7.7.23)	0.27	-	nuc	0	Cytoplasm (By similarity)				475
Q651V6 UniProt NPD GO	PIN2_ORYSA	Probable auxin efflux carrier component 2 (OsPIN2)	0.27	-	end	9 *	Membrane; multi-pass membrane protein (Potential)				630
Q2QY12 UniProt NPD GO	ACA4_ORYSA	Probable calcium-transporting ATPase 4, plasma membrane-type (EC 3.6.3.8) (Ca(2+)-ATPase isoform 4)	0.27	-	end	10	Membrane; multi-pass membrane protein (By similarity)				1039
P54678 UniProt NPD GO	ATC1_DICDI	Probable calcium-transporting ATPase PAT1 (EC 3.6.3.-)	0.27	-	end	10	Vacuole; vacuolar membrane; multi-pass membrane protein. Contractile vacuole complex				1115
P87140 UniProt NPD GO	COPG_SCHPO	Probable coatomer subunit gamma (Gamma-coat protein) (Gamma-COP)	0.27	-	cyt	0	Cytoplasm (By similarity). Golgi apparatus; Golgi membrane; peripheral membrane protein; cytoplasmic ...				905
Q9P373 UniProt NPD GO	ATG4_SCHPO	Probable cysteine protease atg4 (EC 3.4.22.-) (Autophagy-related protein 4)	0.27	-	cyt	0	Cytoplasm (By similarity)				320
Q9VCW1 UniProt NPD GO	CP6D4_DROME	Probable cytochrome P450 6d4 (EC 1.14.-.-) (CYPVID4)	0.27	-	end	2 *	Endoplasmic reticulum; endoplasmic reticulum membrane; peripheral membrane protein (Potential)				515
P90771 UniProt NPD GO	C36A1_CAEEL	Probable cytochrome P450 CYP36A1 (EC 1.14.-.-)	0.27	-	end	1 *	Membrane; multi-pass membrane protein (Potential)				493
Q20502 UniProt NPD GO	HUTH_CAEEL	Probable histidine ammonia-lyase (EC 4.3.1.3) (Histidase)	0.27	-	cyt	0					677
O42227 UniProt NPD GO	HDA1B_XENLA	Probable histone deacetylase 1-B (HD1) (RPD3 homolog)	0.27	-	cyt	0	Cytoplasm. Nucleus				480
Q53P49 UniProt NPD GO	GH312_ORYSA	Probable indole-3-acetic acid-amido synthetase GH3.12 (EC 6.3.2.-) (Auxin-responsive GH3-like protei ...	0.27	-	nuc	0					613
Q15031 UniProt NPD GO	SYLM_HUMAN	Probable leucyl-tRNA synthetase, mitochondrial precursor (EC 6.1.1.4) (Leucine--tRNA ligase) (LeuRS) ...	0.27	-	cyt	0	Mitochondrion; mitochondrial matrix (By similarity)		604544		903
Q9V6Y3 UniProt NPD GO	RT16_DROME	Probable mitochondrial 28S ribosomal protein S16 (MRP-S16)	0.27	-	nuc	0	Mitochondrion (By similarity)				129
Q93WF1 UniProt NPD GO	PEL20_ARATH	Probable pectate lyase 20 precursor (EC 4.2.2.2)	0.27	-	exc	0					417
O64510 UniProt NPD GO	PEL6_ARATH	Probable pectate lyase 6 precursor (EC 4.2.2.2)	0.27	-	exc	1 *					455
Q9Y2Q0 UniProt NPD GO	AT8A1_HUMAN	Probable phospholipid-transporting ATPase IA (EC 3.6.3.1) (Chromaffin granule ATPase II) (ATPase cla ...	0.27	-	end	8	Integral membrane protein. Chromaffin granules (By similarity)	integral to membrane [NAS]	609542		1164
P92982 UniProt NPD GO	JP630_ARATH	Probable polygalacturonase non-catalytic subunit JP630 precursor (Aromatic-rich glycoprotein JP630)	0.27	-	mit	0	Secreted protein; extracellular space; apoplast (By similarity). Cell wall (By similarity). Associat ...				622
Q84MS3 UniProt NPD GO	HAK16_ORYSA	Probable potassium transporter 16 (OsHAK16)	0.27	-	end	11	Membrane; multi-pass membrane protein (By similarity)				811
Q7L3T8 UniProt NPD GO	SYPM_HUMAN	Probable prolyl-tRNA synthetase, mitochondrial precursor (EC 6.1.1.15) (Proline--tRNA ligase) (ProRS ...	0.27	-	mit	0	Mitochondrion; mitochondrial matrix (Potential)				475
Q9VQE5 UniProt NPD GO	PSB2_DROME	Probable proteasome subunit beta type 2 (EC 3.4.25.1)	0.27	-	cyt	0	Cytoplasm (By similarity). Nucleus (By similarity)				210
Q9H237 UniProt NPD GO	PORCN_HUMAN	Probable protein-cysteine N-palmitoyltransferase porcupine (EC 2.3.1.-) (Protein MG61)	0.27	-	end	7 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (By similarity)				461
Q9SJ05 UniProt NPD GO	AROK_ARATH	Probable shikimate kinase, chloroplast precursor (EC 2.7.1.71)	0.27	-	cyt	0	Plastid; chloroplast (By similarity)				292
Q9VU02 UniProt NPD GO	SMD1_DROME	Probable small nuclear ribonucleoprotein Sm D1 (snRNP core protein D1) (Sm-D1)	0.27	-	nuc	0	Nucleus (By similarity)	small nuclear ribonucleoprotein complex [ISS]			124
Q9URY8 UniProt NPD GO	SULI_SCHPO	Probable sulfate permease C869.05c	0.27	-	end	11	Membrane; multi-pass membrane protein (Potential)				840
Q8BYL4 UniProt NPD GO	SYYM_MOUSE	Probable tyrosyl-tRNA synthetase, mitochondrial precursor (EC 6.1.1.1) (Tyrosine--tRNA ligase) (TyrR ...	0.27	-	mit	0	Mitochondrion (Potential)	mitochondrion [ISS]			472
Q8VC12 UniProt NPD GO	HUTU_MOUSE	Probable urocanate hydratase (EC 4.2.1.49) (Urocanase) (Imidazolonepropionate hydrolase)	0.27	-	cyt	0					676
Q9M2V6 UniProt NPD GO	WBC17_ARATH	Probable white-brown complex homolog protein 17	0.27	-	end	6	Membrane; multi-pass membrane protein (By similarity)				662
O73811 UniProt NPD GO	GON2_MORSA	Progonadoliberin-2 precursor (Progonadoliberin II) [Contains: Gonadoliberin-2 (Gonadoliberin II) (Lu ...	0.27	-	end	0	Secreted protein				85
Q6PHH3 UniProt NPD GO	PDC10_BRARE	Programmed cell death protein 10	0.27	-	cyt	0					205
Q5ZIV5 UniProt NPD GO	PDC10_CHICK	Programmed cell death protein 10	0.27	-	cyt	0					212
Q8AVR4 UniProt NPD GO	PDC10_XENLA	Programmed cell death protein 10	0.27	-	cyt	0					212
Q8VE70 UniProt NPD GO	PDC10_MOUSE	Programmed cell death protein 10 (TF-1 cell apoptosis-related protein 15)	0.27	-	cyt	0					212
Q9BUL8 UniProt NPD GO	PDC10_HUMAN	Programmed cell death protein 10 (TF-1 cell apoptosis-related protein 15) (Cerebral cavernous malfor ...	0.27	-	cyt	0			609118		212
P01239 UniProt NPD GO	PRL_BOVIN	Prolactin precursor (PRL)	0.27	-	nuc	0	Secreted protein				229
Q08501 UniProt NPD GO	PRLR_MOUSE	Prolactin receptor precursor (PRL-R)	0.27	-	exc	1	Membrane; single-pass type I membrane protein	cell surface [ISS]			608
P14787 UniProt NPD GO	PRLR_RABIT	Prolactin receptor precursor (PRL-R)	0.27	-	exc	2 *	Membrane; single-pass type I membrane protein	cell surface [ISS]		1AN3	616

You are viewing entries 43501 to 43550 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.