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
P29874 UniProt NPD GO	COX2_GALME	Cytochrome c oxidase subunit 2 (EC 1.9.3.1) (Cytochrome c oxidase polypeptide II)	0.09	-	end	2 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				228
O47674 UniProt NPD GO	COX2_LYCPI	Cytochrome c oxidase subunit 2 (EC 1.9.3.1) (Cytochrome c oxidase polypeptide II)	0.09	-	end	2 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				227
Q7IKU8 UniProt NPD GO	COX2_MICTV	Cytochrome c oxidase subunit 2 (EC 1.9.3.1) (Cytochrome c oxidase polypeptide II)	0.09	-	end	2 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				227
P98039 UniProt NPD GO	COX2_NYCCO	Cytochrome c oxidase subunit 2 (EC 1.9.3.1) (Cytochrome c oxidase polypeptide II)	0.09	-	end	2 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				227
O79673 UniProt NPD GO	COX2_PELSU	Cytochrome c oxidase subunit 2 (EC 1.9.3.1) (Cytochrome c oxidase polypeptide II)	0.09	-	end	2 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				229
P50667 UniProt NPD GO	COX2_PIG	Cytochrome c oxidase subunit 2 (EC 1.9.3.1) (Cytochrome c oxidase polypeptide II)	0.09	-	end	2 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				228
Q37685 UniProt NPD GO	COX2_TRAIM	Cytochrome c oxidase subunit 2 (EC 1.9.3.1) (Cytochrome c oxidase polypeptide II)	0.09	-	end	2 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				227
O46589 UniProt NPD GO	COX41_CEBAP	Cytochrome c oxidase subunit 4 isoform 1 (EC 1.9.3.1) (Cytochrome c oxidase subunit IV isoform 1) (C ...	0.09	-	nuc	0	Mitochondrion; mitochondrial inner membrane				55
O46585 UniProt NPD GO	COX41_PITPI	Cytochrome c oxidase subunit 4 isoform 1 (EC 1.9.3.1) (Cytochrome c oxidase subunit IV isoform 1) (C ...	0.09	-	nuc	1	Mitochondrion; mitochondrial inner membrane				144
Q9TTT8 UniProt NPD GO	COX41_RABIT	Cytochrome c oxidase subunit 4 isoform 1, mitochondrial precursor (EC 1.9.3.1) (Cytochrome c oxidase ...	0.09	-	nuc	1	Mitochondrion; mitochondrial inner membrane				169
Q95283 UniProt NPD GO	COX41_PIG	Cytochrome c oxidase subunit 4 isoform 1, mitochondrial precursor (EC 1.9.3.1) (Cytochrome c oxidase ...	0.09	-	mit	0	Mitochondrion; mitochondrial inner membrane				97
P58691 UniProt NPD GO	ACTPA_RADMA	Cytolysin RTX-A	0.09	-	mit	0	Secreted protein. Found in nematocyst				175
Q9H0P0 UniProt NPD GO	5NT3_HUMAN	Cytosolic 5'-nucleotidase III (EC 3.1.3.5) (cN-III) (Pyrimidine 5'-nucleotidase 1) (P5'N-1) (P5N-1) ...	0.09	-	cyt	0	Cytoplasm (Potential). Isoform 2: Endoplasmic reticulum	cytoplasm [IDA] endoplasmic reticulum [IDA]	266120	2CN1	297
P16410 UniProt NPD GO	CTLA4_HUMAN	Cytotoxic T-lymphocyte protein 4 precursor (Cytotoxic T-lymphocyte-associated antigen 4) (CTLA-4) (C ...	0.09	-	mit	2 *	Membrane; single-pass type I membrane protein	integral to plasma membrane [TAS]	123890	1I8L	223
Q9YGH0 UniProt NPD GO	CXL_BUNMU	Cytotoxin-like protein TA-BMBGT3 precursor	0.09	-	nuc	0	Secreted protein (By similarity)				103
P47800 UniProt NPD GO	DRD1L_OREMO	D(1)-like dopamine receptor	0.09	-	end	7 *	Membrane; multi-pass membrane protein				386
P21918 UniProt NPD GO	DRD5_HUMAN	D(1B) dopamine receptor (D(5) dopamine receptor) (D1beta dopamine receptor)	0.09	-	end	6 *	Membrane; multi-pass membrane protein	integral to plasma membrane [TAS]	606798		477
P53454 UniProt NPD GO	DRD5L_FUGRU	D(5)-like dopamine receptor	0.09	-	end	7 *	Membrane; multi-pass membrane protein				463
P40510 UniProt NPD GO	SER33_YEAST	D-3-phosphoglycerate dehydrogenase 2 (EC 1.1.1.95) (3-PGDH 2)	0.09	-	cyt	0		cytoplasm [IDA]			469
Q9Z302 UniProt NPD GO	OXDA_CRIGR	D-amino-acid oxidase (EC 1.4.3.3) (DAMOX) (DAO) (DAAO)	0.09	-	mit	0	Peroxisome (By similarity)				346
P22942 UniProt NPD GO	OXDA_RABIT	D-amino-acid oxidase (EC 1.4.3.3) (DAMOX) (DAO) (DAAO)	0.09	-	mit	0	Peroxisome				347
P54783 UniProt NPD GO	ALO_YEAST	D-arabinono-1,4-lactone oxidase (EC 1.1.3.37) (ALO) (L-galactono-gamma-lactone oxidase)	0.09	-	nuc	0	Mitochondrion; mitochondrial membrane. Membrane-embedded	integral to mitochondrial outer membrane [IDA] mitochondrial outer membrane [IDA] mitochondrion [IDA]			526
Q5ZJZ5 UniProt NPD GO	BDH_CHICK	D-beta-hydroxybutyrate dehydrogenase, mitochondrial precursor (EC 1.1.1.30) (BDH) (3-hydroxybutyrate ...	0.09	-	mit	0	Mitochondrion; mitochondrial matrix (By similarity)				339
Q9EPS3 UniProt NPD GO	GLCE_MOUSE	D-glucuronyl C5-epimerase (EC 5.1.3.-) (Heparin/heparan sulfate:glucuronic acid C5 epimerase)	0.09	-	cyt	1 *	Golgi apparatus; Golgi membrane; single-pass type II membrane protein	Golgi apparatus [IDA]			618
Q59VC6 UniProt NPD GO	DAD3_CANAL	DASH complex subunit DAD2 (Outer kinetochore protein DAD2)	0.09	-	nuc	0	Nucleus (By similarity). Associates with the mitotic spindle and the kinetochore (By similarity)				138
P34471 UniProt NPD GO	PRI1_CAEEL	DNA primase small subunit (EC 2.7.7.-)	0.09	-	cyt	0					410
P46669 UniProt NPD GO	RPA4_YEAST	DNA-dependent RNA polymerase 36 kDa polypeptide (EC 2.7.7.6) (A43)	0.09	-	nuc	0	Nucleus	DNA-directed RNA polymerase I complex [TAS]			326
Q5XK67 UniProt NPD GO	RPO1D_XENLA	DNA-directed RNA polymerase I subunit D (EC 2.7.7.6)	0.09	-	cyt	0	Nucleus (By similarity)				114
O08740 UniProt NPD GO	RPO2J_MOUSE	DNA-directed RNA polymerase II subunit J (EC 2.7.7.6) (DNA-directed RNA polymerase II 13.3 kDa polyp ...	0.09	-	cyt	0	Nucleus	DNA-directed RNA polymerase III complex [TAS] nucleus [IDA]			117
O21260 UniProt NPD GO	RPOA_RECAM	DNA-directed RNA polymerase alpha chain (EC 2.7.7.6) (Transcriptase alpha chain) (RNA polymerase sub ...	0.09	-	cyt	0					222
Q24320 UniProt NPD GO	RPB6_DROME	DNA-directed RNA polymerases I, II, and III 14.4 kDa polypeptide (EC 2.7.7.6) (RPB6)	0.09	-	cyt	0	Nucleus				131
Q9VGY6 UniProt NPD GO	DOMON_DROME	DOMON domain-containing protein CG14681 precursor	0.09	-	vac	1 *					784
P39546 UniProt NPD GO	YAJ3_YEAST	DUP240 protein YAR023C	0.09	-	end	1	Membrane; multi-pass membrane protein (Potential)				240
P25354 UniProt NPD GO	YCP7_YEAST	DUP240 protein YCR007C	0.09	-	end	2	Membrane; multi-pass membrane protein (Potential)				239
Q9XSD9 UniProt NPD GO	PGS2_PIG	Decorin precursor (Bone proteoglycan II) (PG-S2)	0.09	-	exc	0	Secreted protein; extracellular space; extracellular matrix				360
Q22851 UniProt NPD GO	DEGW_CAEEL	Degenerin-like protein T28F4.2 in chromosome I	0.09	-	end	1 *	Membrane; multi-pass membrane protein				545
Q8VID1 UniProt NPD GO	DHRS4_RAT	Dehydrogenase/reductase SDR family member 4 (EC 1.1.1.184) (NADPH-dependent carbonyl reductase/NADP- ...	0.09	-	mit	0	Peroxisome (By similarity)	mitochondrion [ISS] peroxisome [IMP]			260
Q8N5I4 UniProt NPD GO	DHRSX_HUMAN	Dehydrogenase/reductase SDR family member on chromosome X precursor (EC 1.1.-.-) (DHRSXY)	0.09	-	mit	0					330
P54888 UniProt NPD GO	P5CS2_ARATH	Delta 1-pyrroline-5-carboxylate synthetase B (P5CS B) [Includes: Glutamate 5-kinase (EC 2.7.2.11) (G ...	0.09	-	nuc	0					726
Q42836 UniProt NPD GO	HEM2_HORVU	Delta-aminolevulinic acid dehydratase, chloroplast precursor (EC 4.2.1.24) (Porphobilinogen synthase ...	0.09	-	mit	0	Plastid; chloroplast				428
P81885 UniProt NPD GO	TDT1B_HADVE	Delta-atracotoxin-Hv1b (Delta-AcTx-Hv1b)	0.09	-	nuc	0	Secreted protein				42
Q6BJH5 UniProt NPD GO	DHYS_DEBHA	Deoxyhypusine synthase (EC 2.5.1.46) (DHS)	0.09	-	cyt	0					378
P19427 UniProt NPD GO	DERM_BOVIN	Dermatopontin precursor (Tyrosine-rich acidic matrix protein) (TRAMP) (22 kDa extracellular matrix p ...	0.09	-	mit	0	Secreted protein; extracellular space; extracellular matrix				201
P81605 UniProt NPD GO	DCD_HUMAN	Dermcidin precursor (Preproteolysin) [Contains: Survival-promoting peptide; DCD-1]	0.09	-	exc	0	Secreted protein	extracellular region [IDA]	606634		110
Q91611 UniProt NPD GO	DHH2_XENLA	Desert hedgehog protein 2 precursor (DHH-2) (Hedgehog protein 4) (X-HH4) [Contains: Desert hedgehog ...	0.09	-	mit	0	The C-terminal peptide diffuses from the cell, while the N-terminal peptide remains associated with ...				398
P15262 UniProt NPD GO	LVN1_LYTVA	Development-specific protein LVN1.2	0.09	-	cyt	0		cytoplasm [IDA]			189
Q01460 UniProt NPD GO	DIAC_RAT	Di-N-acetylchitobiase precursor (EC 3.2.1.-)	0.09	-	mit	0	Lysosome				367
P19262 UniProt NPD GO	ODO2_YEAST	Dihydrolipoyllysine-residue succinyltransferase component of 2-oxoglutarate dehydrogenase complex, m ...	0.09	-	mit	0	Mitochondrion	mitochondrial nucleoid [IDA] oxoglutarate dehydrogenase complex (sensu E... [IDA]			463
Q18677 UniProt NPD GO	DHP2_CAEEL	Dihydropyrimidinase 2 (EC 3.5.2.2) (CeCRMP/DHP-2) (UlipA)	0.09	-	cyt	0		cytoplasm [IDA]			520
P36366 UniProt NPD GO	FMO2_CAVPO	Dimethylaniline monooxygenase [N-oxide-forming] 2 (EC 1.14.13.8) (Pulmonary flavin-containing monoox ...	0.09	-	end	1	Microsome				534

You are viewing entries 66001 to 66050 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.