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
Q9FH28 UniProt NPD GO	DNJ49_ARATH	Chaperone protein dnaJ 49 (AtJ49) (AtDjC49)	0.80	+	nuc	1	Membrane; single-pass membrane protein (Potential)				354
P08527 UniProt NPD GO	RR14_MAIZE	Chloroplast 30S ribosomal protein S14	0.80	+	nuc	0	Plastid; chloroplast				103
Q32RK4 UniProt NPD GO	RR15_ZYGCR	Chloroplast 30S ribosomal protein S15	0.80	-	nuc	0	Plastid; chloroplast				87
Q8W8V0 UniProt NPD GO	RR7_PSINU	Chloroplast 30S ribosomal protein S7	0.80	-	nuc	0	Plastid; chloroplast				155
P56794 UniProt NPD GO	RK20_ARATH	Chloroplast 50S ribosomal protein L20	0.80	-	mit	0	Plastid; chloroplast				117
Q7FNS5 UniProt NPD GO	RK20_ATRBE	Chloroplast 50S ribosomal protein L20	0.80	-	mit	0	Plastid; chloroplast				128
Q7YJV3 UniProt NPD GO	RK20_CALFE	Chloroplast 50S ribosomal protein L20	0.80	-	mit	0	Plastid; chloroplast				117
P06386 UniProt NPD GO	RK20_TOBAC	Chloroplast 50S ribosomal protein L20	0.80	-	mit	0	Plastid; chloroplast				127
Q9Y259 UniProt NPD GO	CHKB_HUMAN	Choline/ethanolamine kinase [Includes: Choline kinase beta (EC 2.7.1.32) (CK); Ethanolamine kinase ( ...	0.80	-	mit	0					394
O57472 UniProt NPD GO	CHRD_BRARE	Chordin precursor (Protein chordino)	0.80	-	end	0	Secreted protein (By similarity)				940
O16102 UniProt NPD GO	CHD3_DROME	Chromodomain helicase-DNA-binding protein 3 (EC 3.6.1.-) (ATP-dependent helicase Chd3)	0.80	-	nuc	0	Nucleus (By similarity)	nucleus [ISS]			892
Q5XI29 UniProt NPD GO	CPSF7_RAT	Cleavage and polyadenylation specificity factor 7	0.80	-	nuc	0	Nucleus (By similarity)				462
Q4R6Y7 UniProt NPD GO	CLUA1_MACFA	Clusterin-associated protein 1	0.80	-	nuc	0	Nucleus (By similarity)				414
P00451 UniProt NPD GO	FA8_HUMAN	Coagulation factor VIII precursor (Procoagulant component) (Antihemophilic factor) (AHF) [Contains: ...	0.80	-	nuc	0	Secreted protein; extracellular space	extracellular region [NAS]	134500	1IQD	2351
Q6P0I6 UniProt NPD GO	CCD16_BRARE	Coiled-coil domain-containing protein 16	0.80	-	nuc	0	Nucleus (By similarity). Excluded from nucleolus (By similarity)				326
Q8R4B8 UniProt NPD GO	CIAS1_MOUSE	Cold autoinflammatory syndrome 1 protein homolog (PYRIN-containing APAF1-like protein 1) (Mast cell ...	0.80	-	nuc	0	Cytoplasm	cytoplasm [ISS]			1033
Q811M5 UniProt NPD GO	CO6_RAT	Complement component C6 precursor	0.80	-	exc	0	Secreted protein				934
O43186 UniProt NPD GO	CRX_HUMAN	Cone-rod homeobox protein	0.80	-	nuc	0	Nucleus (By similarity)		602225		299
O54751 UniProt NPD GO	CRX_MOUSE	Cone-rod homeobox protein	0.80	-	nuc	0	Nucleus (By similarity)	nucleus [IDA] transcription factor complex [IDA]			299
Q75QI0 UniProt NPD GO	CFDP1_CHICK	Craniofacial development protein 1 (Bucentaur)	0.80	+	nuc	0					290
Q09760 UniProt NPD GO	CUL3_SCHPO	Cullin-3 (Cul-3)	0.80	-	mit	0					785
P29596 UniProt NPD GO	ATF3_RAT	Cyclic AMP-dependent transcription factor ATF-3 (Activating transcription factor 3) (Liver regenerat ...	0.80	+	nuc	0	Nucleus (By similarity)				181
P34424 UniProt NPD GO	CCNT2_CAEEL	Cyclin-T1.2	0.80	-	nuc	0					555
P21268 UniProt NPD GO	FAR1_YEAST	Cyclin-dependent kinase inhibitor FAR1 (CKI FAR1) (Factor arrest protein)	0.80	-	nuc	0		cytoplasm [IDA] mating projection tip [IDA] membrane [IDA] nucleus [IDA]			830
Q7JII8 UniProt NPD GO	CFTR_MACFA	Cystic fibrosis transmembrane conductance regulator (CFTR) (cAMP-dependent chloride channel) (ATP-bi ...	0.80	-	end	11	Membrane; multi-pass membrane protein				1481
Q7JII7 UniProt NPD GO	CFTR_MACFU	Cystic fibrosis transmembrane conductance regulator (CFTR) (cAMP-dependent chloride channel) (ATP-bi ...	0.80	-	end	11	Membrane; multi-pass membrane protein				1481
Q00553 UniProt NPD GO	CFTR_MACMU	Cystic fibrosis transmembrane conductance regulator (CFTR) (cAMP-dependent chloride channel) (ATP-bi ...	0.80	-	end	11	Membrane; multi-pass membrane protein				1481
Q9TUQ2 UniProt NPD GO	CFTR_MACNE	Cystic fibrosis transmembrane conductance regulator (CFTR) (cAMP-dependent chloride channel) (ATP-bi ...	0.80	-	end	11	Membrane; multi-pass membrane protein				1481
Q9TSP5 UniProt NPD GO	CFTR_PAPAN	Cystic fibrosis transmembrane conductance regulator (CFTR) (cAMP-dependent chloride channel) (ATP-bi ...	0.80	-	end	11	Membrane; multi-pass membrane protein				1481
Q08996 UniProt NPD GO	CBP2_SACDO	Cytochrome B pre-mRNA-processing protein 2	0.80	-	mit	0	Mitochondrion (By similarity)				630
Q96P26 UniProt NPD GO	5NT1B_HUMAN	Cytosolic 5'-nucleotidase 1B (EC 3.1.3.5) (Cytosolic 5'-nucleotidase IB) (cN1B) (cN-IB) (Autoimmune ...	0.80	-	nuc	0	Cytoplasm (By similarity)				610
Q6CVK1 UniProt NPD GO	DAM1_KLULA	DASH complex subunit DAM1 (Outer kinetochore protein DAM1)	0.80	-	nuc	0	Nucleus (By similarity). Associates with the mitotic spindle and the kinetochore (By similarity)				313
Q9JK91 UniProt NPD GO	MLH1_MOUSE	DNA mismatch repair protein Mlh1 (MutL protein homolog 1)	0.80	-	nuc	0	Nucleus (By similarity)	condensed chromosome [IDA] synaptonemal complex [IDA]			760
O60094 UniProt NPD GO	DPO5_SCHPO	DNA polymerase V (EC 2.7.7.7) (POL V)	0.80	-	nuc	0					959
P28519 UniProt NPD GO	RAD14_YEAST	DNA repair protein RAD14	0.80	-	nuc	0	Nucleus	nucleotide-excision repair factor 1 complex [IPI] nucleus [IDA]			371
Q8R4E9 UniProt NPD GO	CDT1_MOUSE	DNA replication factor Cdt1 (Double parked homolog) (DUP) (Retroviral insertion site 2 protein)	0.80	-	mit	0	Nucleus	nucleus [IDA] replication fork [IPI]		1WLQ	557
O24308 UniProt NPD GO	TOP2_PEA	DNA topoisomerase 2 (EC 5.99.1.3) (DNA topoisomerase II) (PsTopII)	0.80	+	nuc	0					1462
P41515 UniProt NPD GO	TOP2A_CRIGR	DNA topoisomerase 2-alpha (EC 5.99.1.3) (DNA topoisomerase II, alpha isozyme)	0.80	+	nuc	0	Nucleus				1526
Q10135 UniProt NPD GO	YAR2_SCHPO	DNA-binding protein C23E2.02 in chromosome I	0.80	-	nuc	0	Nucleus	nucleus [IDA]			1273
Q7ZUX1 UniProt NPD GO	RPC62_BRARE	DNA-directed RNA polymerase III 62 kDa polypeptide (EC 2.7.7.6) (RNA polymerase C subunit 3) (RPC3)	0.80	-	nuc	0	Nucleus (Potential)				539
P60289 UniProt NPD GO	RPOC2_AMBTC	DNA-directed RNA polymerase beta'' chain (EC 2.7.7.6) (PEP) (Plastid-encoded RNA polymerase beta'' s ...	0.80	-	nuc	0	Plastid; chloroplast				1373
Q60596 UniProt NPD GO	XRCC1_MOUSE	DNA-repair protein XRCC1 (X-ray repair cross-complementing protein 1)	0.80	-	nuc	0	Nucleus (Probable)				631
Q80YE7 UniProt NPD GO	DAPK1_MOUSE	Death-associated protein kinase 1 (EC 2.7.11.1) (DAP kinase 1)	0.80	+	mit	0		cytoplasm [IDA]			1442
Q9UIK4 UniProt NPD GO	DAPK2_HUMAN	Death-associated protein kinase 2 (EC 2.7.11.1) (DAP kinase 2) (DAP-kinase-related protein 1) (DRP-1 ...	0.80	-	nuc	0	Cytoplasm	cytoplasm [IEP]		1WRZ	370
O43293 UniProt NPD GO	DAPK3_HUMAN	Death-associated protein kinase 3 (EC 2.7.11.1) (DAP kinase 3) (DAP-like kinase) (Dlk) (ZIP-kinase)	0.80	-	cyt	0	Nucleus (By similarity). Cytoplasm (By similarity). Relocates to the cytoplasm on binding PAWR where ...	nucleus [ISS]	603289	1YRP	454
Q96HP0 UniProt NPD GO	DOCK6_HUMAN	Dedicator of cytokinesis protein 6	0.80	-	nuc	0					2047
Q09274 UniProt NPD GO	DEGX_CAEEL	Degenerin-like protein C41C4.5 in chromosome II	0.80	-	mit	2	Membrane; multi-pass membrane protein				849
P25686 UniProt NPD GO	DNJB2_HUMAN	DnaJ homolog subfamily B member 2 (Heat shock 40 kDa protein 3) (DnaJ protein homolog 1) (HSJ-1)	0.80	-	nuc	0			604139		351
O13601 UniProt NPD GO	RSP1_SCHPO	DnaJ-related protein rsp1	0.80	-	nuc	0	Cytoplasm. Nucleus. Associates with the microtubule bundles				494
Q68SB1 UniProt NPD GO	STAU2_RAT	Double-stranded RNA-binding protein Staufen homolog 2 (r-staufen protein)	0.80	-	nuc	0	Nucleus; nucleolus. Nucleus. Cytoplasm. Shuttles between the nucleolus, nucleus and the cytoplasm. N ...				571

You are viewing entries 8801 to 8850 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.