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
P04371 UniProt NPD GO	COX1_TRYBB	Cytochrome c oxidase subunit 1 (EC 1.9.3.1) (Cytochrome c oxidase polypeptide I)	0.12	-	end	15 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				549
P68553 UniProt NPD GO	COX2_BOSIN	Cytochrome c oxidase subunit 2 (EC 1.9.3.1) (Cytochrome c oxidase polypeptide II)	0.12	-	end	2 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				227
P68554 UniProt NPD GO	COX2_BOSMU	Cytochrome c oxidase subunit 2 (EC 1.9.3.1) (Cytochrome c oxidase polypeptide II)	0.12	-	end	2 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				227
P68530 UniProt NPD GO	COX2_BOVIN	Cytochrome c oxidase subunit 2 (EC 1.9.3.1) (Cytochrome c oxidase polypeptide II)	0.12	-	end	2 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein			2OCC	227
Q37440 UniProt NPD GO	COX2_CERUN	Cytochrome c oxidase subunit 2 (EC 1.9.3.1) (Cytochrome c oxidase polypeptide II)	0.12	-	end	2 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				227
P50679 UniProt NPD GO	COX2_DAMPP	Cytochrome c oxidase subunit 2 (EC 1.9.3.1) (Cytochrome c oxidase polypeptide II)	0.12	-	end	2 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				227
Q8W9N3 UniProt NPD GO	COX2_DUGDU	Cytochrome c oxidase subunit 2 (EC 1.9.3.1) (Cytochrome c oxidase polypeptide II)	0.12	-	end	2 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				227
P38596 UniProt NPD GO	COX2_HALGR	Cytochrome c oxidase subunit 2 (EC 1.9.3.1) (Cytochrome c oxidase polypeptide II)	0.12	-	end	2 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				227
Q96190 UniProt NPD GO	COX2_RHIUN	Cytochrome c oxidase subunit 2 (EC 1.9.3.1) (Cytochrome c oxidase polypeptide II)	0.12	-	end	2 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				227
P50675 UniProt NPD GO	COX2_SYNCA	Cytochrome c oxidase subunit 2 (EC 1.9.3.1) (Cytochrome c oxidase polypeptide II)	0.12	-	end	2 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				227
O46590 UniProt NPD GO	COX41_SAIUS	Cytochrome c oxidase subunit 4 isoform 1 (EC 1.9.3.1) (Cytochrome c oxidase subunit IV isoform 1) (C ...	0.12	-	nuc	0	Mitochondrion; mitochondrial inner membrane				55
Q61387 UniProt NPD GO	COX7R_MOUSE	Cytochrome c oxidase subunit VIIa-related protein, mitochondrial precursor (Silica-induced gene 81 p ...	0.12	-	nuc	1	Mitochondrion				111
Q4WPF8 UniProt NPD GO	CCPR_ASPFU	Cytochrome c peroxidase, mitochondrial precursor (EC 1.11.1.5) (CCP)	0.12	-	mit	0	Mitochondrion; mitochondrial matrix (By similarity)				366
Q6FMG7 UniProt NPD GO	CCPR_CANGA	Cytochrome c peroxidase, mitochondrial precursor (EC 1.11.1.5) (CCP)	0.12	-	mit	1 *	Mitochondrion; mitochondrial matrix (By similarity)				357
P28838 UniProt NPD GO	AMPL_HUMAN	Cytosol aminopeptidase (EC 3.4.11.1) (Leucine aminopeptidase) (LAP) (Leucyl aminopeptidase) (Proline ...	0.12	-	nuc	0	Cytoplasm	cytoplasm [NAS]	170250		487
Q5RF65 UniProt NPD GO	GBA3_PONPY	Cytosolic beta-glucosidase (EC 3.2.1.21)	0.12	-	cyt	0	Cytoplasm; cytosol (By similarity)				469
P35406 UniProt NPD GO	DRD1_CARAU	D(1) dopamine receptor	0.12	-	end	7 *	Membrane; multi-pass membrane protein				363
Q6CDG5 UniProt NPD GO	DAD4_YARLI	DASH complex subunit DAD4 (Outer kinetochore protein DAD4)	0.12	-	nuc	0	Nucleus (By similarity). Associates with the mitotic spindle and the kinetochore (By similarity)				76
Q9UTG8 UniProt NPD GO	DAD2_SCHPO	DASH complex subunit dad2 (Outer kinetochore protein dad2) (High osmolarity sensitivity protein 2)	0.12	-	nuc	0	Nucleus. Associates with the mitotic spindle and the kinetochore. Kinetochore association occurs onl ...	DASH complex [IDA] spindle pole body [IDA]			94
Q9LQT8 UniProt NPD GO	GAI_ARATH	DELLA protein GAI (Gibberellic acid-insensitive mutant protein) (Restoration of growth on ammonia pr ...	0.12	-	cyt	0	Nucleus	nucleus [TAS]			533
O49552 UniProt NPD GO	DDB1B_ARATH	DNA damage-binding protein 1b (UV-damaged DNA-binding protein 1b) (DDB1b)	0.12	-	end	0	Nucleus (By similarity)				1088
O55230 UniProt NPD GO	RA51D_MOUSE	DNA repair protein RAD51 homolog 4	0.12	-	nuc	0	Nucleus (By similarity)				329
P37382 UniProt NPD GO	RPB3_SCHPO	DNA-directed RNA polymerase II 33 kDa polypeptide (EC 2.7.7.6) (RNA polymerase II subunit 3)	0.12	-	nuc	0	Nucleus	DNA-directed RNA polymerase II, core complex [IDA]			297
Q9BBN0 UniProt NPD GO	RPOA_MARQU	DNA-directed RNA polymerase alpha chain (EC 2.7.7.6) (PEP) (Plastid-encoded RNA polymerase subunit a ...	0.12	-	cyt	0	Plastid; chloroplast				347
P35018 UniProt NPD GO	RPOC2_GALSU	DNA-directed RNA polymerase beta'' chain (EC 2.7.7.6) (PEP) (Plastid-encoded RNA polymerase beta'' s ...	0.12	-	cyt	0	Plastid; chloroplast				85
P61217 UniProt NPD GO	RPB6_CRIGR	DNA-directed RNA polymerases I, II, and III 14.4 kDa polypeptide (EC 2.7.7.6) (RPB6) (RPABC14.4) (RP ...	0.12	-	cyt	0	Nucleus				127
P61219 UniProt NPD GO	RPB6_MOUSE	DNA-directed RNA polymerases I, II, and III 14.4 kDa polypeptide (EC 2.7.7.6) (RPB6) (RPABC14.4) (RP ...	0.12	-	cyt	0	Nucleus (By similarity)				127
Q5R592 UniProt NPD GO	RPB6_PONPY	DNA-directed RNA polymerases I, II, and III 14.4 kDa polypeptide (EC 2.7.7.6) (RPB6) (RPABC14.4) (RP ...	0.12	-	cyt	0	Nucleus (By similarity)				127
O88828 UniProt NPD GO	RPB6_RAT	DNA-directed RNA polymerases I, II, and III 14.4 kDa polypeptide (EC 2.7.7.6) (RPB6) (RPABC14.4) (RP ...	0.12	-	cyt	0	Nucleus	DNA-directed RNA polymerase I complex [TAS] DNA-directed RNA polymerase II, core complex [TAS] DNA-directed RNA polymerase III complex [TAS]			127
P61218 UniProt NPD GO	RPB6_HUMAN	DNA-directed RNA polymerases I, II, and III 14.4 kDa polypeptide (EC 2.7.7.6) (RPB6) (RPABC14.4) (RP ...	0.12	-	cyt	0	Nucleus		604414	1QKL	127
Q75BV8 UniProt NPD GO	RPB10_ASHGO	DNA-directed RNA polymerases I/II/III subunit 10 (EC 2.7.7.6)	0.12	-	cyt	0	Nucleus (By similarity)				70
O13877 UniProt NPD GO	RPB10_SCHPO	DNA-directed RNA polymerases I/II/III subunit 10 (EC 2.7.7.6) (DNA-directed RNA polymerases I, II, a ...	0.12	-	mit	0	Nucleus	DNA-directed RNA polymerase I complex [TAS] DNA-directed RNA polymerase II, holoenzyme [TAS] DNA-directed RNA polymerase III complex [TAS]			71
P39549 UniProt NPD GO	YAJ9_YEAST	DUP240 protein YAR029W	0.12	-	cyt	0	Cytoplasm. Membrane; peripheral membrane protein. Punctate pattern	cytoplasm [IDA]			74
Q29393 UniProt NPD GO	PGS2_CANFA	Decorin precursor (Bone proteoglycan II) (PG-S2)	0.12	-	exc	0	Secreted protein; extracellular space; extracellular matrix (By similarity)				360
P28675 UniProt NPD GO	PGS2_CHICK	Decorin precursor (Bone proteoglycan II) (PG-S2)	0.12	-	exc	0	Secreted protein; extracellular space; extracellular matrix (By similarity)				357
P82140 UniProt NPD GO	DLP2_ORNAN	Defensin-like peptide 2/4 (DLP-2/DLP-4)	0.12	-	nuc	0	Secreted protein	extracellular region [IDA]		1ZUF	42
P28639 UniProt NPD GO	DHN1_PEA	Dehydrin DHN1	0.12	-	cyt	0					197
Q3T046 UniProt NPD GO	DHRS6_BOVIN	Dehydrogenase/reductase SDR family member 6 precursor (EC 1.1.-.-)	0.12	-	cyt	0	Secreted protein (Potential)				245
Q9BUT1 UniProt NPD GO	DHRS6_HUMAN	Dehydrogenase/reductase SDR family member 6 precursor (EC 1.1.-.-) (Oxidoreductase UCPA)	0.12	-	cyt	0	Secreted protein (Potential)	cytoplasm [IDA]		2AG5	245
O65361 UniProt NPD GO	P5CS_MESCR	Delta 1-pyrroline-5-carboxylate synthetase (P5CS) [Includes: Glutamate 5-kinase (EC 2.7.2.11) (Gamma ...	0.12	-	end	0					719
P07275 UniProt NPD GO	PUT2_YEAST	Delta-1-pyrroline-5-carboxylate dehydrogenase, mitochondrial precursor (EC 1.5.1.12) (P5C dehydrogen ...	0.12	-	mit	0	Mitochondrion; mitochondrial inner membrane	mitochondrion [IDA]			575
Q2QDE9 UniProt NPD GO	DNSL1_BOVIN	Deoxyribonuclease I-like 1 precursor (EC 3.1.21.-) (DNase I-like 1) (DNase X)	0.12	-	exc	0	Endoplasmic reticulum (By similarity)				316
P11937 UniProt NPD GO	DNAS1_SHEEP	Deoxyribonuclease-1 (EC 3.1.21.1) (Deoxyribonuclease I) (DNase I)	0.12	-	mit	0	Secretory protein, stored in zymogen granules and found in the nuclear envelope				260
Q9YGI5 UniProt NPD GO	DNAS1_CHICK	Deoxyribonuclease-1 precursor (EC 3.1.21.1) (Deoxyribonuclease I) (DNase I)	0.12	-	end	0	Secretory protein, stored in zymogen granules and found in the nuclear envelope (By similarity)				282
P21704 UniProt NPD GO	DNAS1_RAT	Deoxyribonuclease-1 precursor (EC 3.1.21.1) (Deoxyribonuclease I) (DNase I)	0.12	-	end	1 *	Secretory protein, stored in zymogen granules and found in the nuclear envelope				284
P56541 UniProt NPD GO	DNS2A_BOVIN	Deoxyribonuclease-2-alpha (EC 3.1.22.1) (Deoxyribonuclease II alpha) (DNase II alpha) (Acid DNase) ( ...	0.12	-	cyt	0	Lysosome (By similarity)				276
P36591 UniProt NPD GO	DYR_SCHPO	Dihydrofolate reductase (EC 1.5.1.3)	0.12	-	mit	0					461
P98192 UniProt NPD GO	GNPAT_MOUSE	Dihydroxyacetone phosphate acyltransferase (EC 2.3.1.42) (DHAP-AT) (DAP-AT) (Glycerone-phosphate O-a ...	0.12	-	mit	0	Peroxisome; peroxisomal membrane; matrix side (By similarity). Exclusively localized to the lumenal ...	peroxisomal matrix [TAS]			678
Q75C90 UniProt NPD GO	DIM1_ASHGO	Dimethyladenosine transferase (EC 2.1.1.-) (S-adenosylmethionine-6-N', N'-adenosyl(rRNA) dimethyltra ...	0.12	-	cyt	0					319
Q9USU2 UniProt NPD GO	DIM1_SCHPO	Dimethyladenosine transferase (EC 2.1.1.-) (S-adenosylmethionine-6-N', N'-adenosyl(rRNA) dimethyltra ...	0.12	-	cyt	0					307

You are viewing entries 61051 to 61100 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.