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
Q9W678 UniProt NPD GO	P53_BARBU	Cellular tumor antigen p53 (Tumor suppressor p53)	0.66	+	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity)				369
P41046 UniProt NPD GO	CORTO_DROME	Centrosomal and chromosomal factor (CCF) (Chromocentrosomin)	0.66	-	mit	0	Nucleus. Centrosome	ESC/E(Z) complex [IPI] polytene chromosome [IDA] PRC1 complex [IPI]			550
Q94AW8 UniProt NPD GO	DNAJ3_ARATH	Chaperone protein dnaJ 3 (AtJ3) (AtDjA3)	0.66	-	nuc	0	Membrane; lipid-anchor (Potential)				420
Q5R861 UniProt NPD GO	CHMP6_PONPY	Charged multivesicular body protein 6 (Chromatin-modifying protein 6)	0.66	-	nuc	0	Intracytoplasmic membrane (By similarity). Endosome; endosomal membrane; lipid-anchor (By similarity ...				200
Q96FZ7 UniProt NPD GO	CHMP6_HUMAN	Charged multivesicular body protein 6 (Chromatin-modifying protein 6) (Vacuolar protein sorting 20) ...	0.66	-	nuc	0	Intracytoplasmic membrane. Endosome; endosomal membrane; lipid-anchor. Localizes to endosomal membra ...				200
P69659 UniProt NPD GO	RR18_ATRBE	Chloroplast 30S ribosomal protein S18	0.66	-	nuc	0	Plastid; chloroplast				101
P69660 UniProt NPD GO	RR18_TOBAC	Chloroplast 30S ribosomal protein S18	0.66	-	nuc	0	Plastid; chloroplast				101
Q6L3A4 UniProt NPD GO	RR2_SACHY	Chloroplast 30S ribosomal protein S2	0.66	-	mit	0	Plastid; chloroplast				236
Q6ENX0 UniProt NPD GO	RR2_SACOF	Chloroplast 30S ribosomal protein S2	0.66	-	mit	0	Plastid; chloroplast				236
P59063 UniProt NPD GO	RR7_CHAGL	Chloroplast 30S ribosomal protein S7	0.66	-	nuc	0	Plastid; chloroplast				155
P12139 UniProt NPD GO	RK20_ORYSA	Chloroplast 50S ribosomal protein L20	0.66	-	mit	0	Plastid; chloroplast				118
P49586 UniProt NPD GO	PCY1A_MOUSE	Choline-phosphate cytidylyltransferase A (EC 2.7.7.15) (Phosphorylcholine transferase A) (CTP:phosph ...	0.66	+	nuc	0	Cytoplasm; cytosol (By similarity). Membrane; peripheral membrane protein (By similarity). It can in ...	endoplasmic reticulum membrane [IDA] glycogen granule [IDA]			367
Q9NYC9 UniProt NPD GO	DYH9_HUMAN	Ciliary dynein heavy chain 9 (Axonemal beta dynein heavy chain 9)	0.66	-	nuc	0		axonemal dynein complex [NAS] cilium axoneme [IDA] cytoskeleton [TAS]	603330		4486
O43040 UniProt NPD GO	CTF1_SCHPO	Cleavage and termination factor 1 (Transcription termination factor ctf1)	0.66	-	nuc	0	Nucleus (Potential)				363
Q8WUD4 UniProt NPD GO	CCD12_HUMAN	Coiled-coil domain-containing protein 12	0.66	-	nuc	0					166
Q9BRQ6 UniProt NPD GO	CHCH6_HUMAN	Coiled-coil-helix-coiled-coil-helix domain-containing protein 6	0.66	-	nuc	0					235
P06298 UniProt NPD GO	COLI1_XENLA	Corticotropin-lipotropin A precursor (Pro-opiomelanocortin A) (POMC-A) [Contains: NPP; Melanotropin ...	0.66	-	mit	0					259
P06299 UniProt NPD GO	COLI2_XENLA	Corticotropin-lipotropin B precursor (Pro-opiomelanocortin B) (POMC-B) [Contains: NPP; Melanotropin ...	0.66	-	mit	0					260
Q29425 UniProt NPD GO	CUL5_RABIT	Cullin-5 (CUL-5) (Vasopressin-activated calcium-mobilizing receptor) (VACM-1)	0.66	-	nuc	0					780
Q9JJ31 UniProt NPD GO	CUL5_RAT	Cullin-5 (CUL-5) (Vasopressin-activated calcium-mobilizing receptor) (VACM-1)	0.66	-	nuc	0		Cul5-RING ubiquitin ligase complex [TAS]			780
P48133 UniProt NPD GO	RR4_CYAPA	Cyanelle 30S ribosomal protein S4	0.66	+	nuc	0	Plastid; cyanelle				201
Q3TZA2 UniProt NPD GO	CDKL4_MOUSE	Cyclin-dependent kinase-like 4 (EC 2.7.11.22)	0.66	-	cyt	0	Cytoplasm (Probable)				342
Q99418 UniProt NPD GO	CYH2_HUMAN	Cytohesin-2 (ARF nucleotide-binding site opener) (ARNO protein) (ARF exchange factor)	0.66	-	cyt	0		membrane fraction [TAS] plasma membrane [TAS]	602488	1S9D	400
Q13409 UniProt NPD GO	DC1I2_HUMAN	Cytoplasmic dynein 1 intermediate chain 2 (Dynein intermediate chain 2, cytosolic) (DH IC-2) (Cytopl ...	0.66	+	nuc	0		cytoplasm [NAS]	603331		638
O95712 UniProt NPD GO	PA24B_HUMAN	Cytosolic phospholipase A2 beta (EC 3.1.1.4) (cPLA2-beta) (Phospholipase A2 group IVB)	0.66	+	cyt	0	Cytoplasm; cytosol. Translocates to membrane vesicles in a calcium-dependent fashion. Isoform 3: mit ...	cytosol [TAS] extracellular region [TAS]	606088		1012
Q39189 UniProt NPD GO	RH7_ARATH	DEAD-box ATP-dependent RNA helicase 7 (EC 3.6.1.-)	0.66	+	nuc	0	Nucleus (By similarity)				671
Q8TEH3 UniProt NPD GO	DEN1A_HUMAN	DENN domain-containing protein 1A	0.66	-	nuc	0					1009
Q9Y6K1 UniProt NPD GO	DNM3A_HUMAN	DNA (cytosine-5)-methyltransferase 3A (EC 2.1.1.37) (Dnmt3a) (DNA methyltransferase HsaIIIA) (DNA MT ...	0.66	-	mit	0	Nucleus (Probable)	cytoplasm [ISS] euchromatin [ISS] nuclear matrix [ISS] nucleus [ISS]	602769		909
P06526 UniProt NPD GO	TDT_BOVIN	DNA nucleotidylexotransferase (EC 2.7.7.31) (Terminal addition enzyme) (Terminal deoxynucleotidyltra ...	0.66	-	cyt	0	Nucleus				520
Q9JIW4 UniProt NPD GO	DPOLM_MOUSE	DNA polymerase mu (EC 2.7.7.7) (Pol Mu)	0.66	+	mit	0					496
P54099 UniProt NPD GO	DPOG1_MOUSE	DNA polymerase subunit gamma 1 (EC 2.7.7.7) (Mitochondrial DNA polymerase catalytic subunit) (PolG-a ...	0.66	-	mit	0	Mitochondrion	mitochondrial inner membrane [IDA]			1239
Q9QYV8 UniProt NPD GO	DPOG1_RAT	DNA polymerase subunit gamma 1 (EC 2.7.7.7) (Mitochondrial DNA polymerase catalytic subunit) (PolG-a ...	0.66	-	mit	0	Mitochondrion	gamma DNA polymerase complex [IDA] mitochondrion [IDA]			1216
Q6NX31 UniProt NPD GO	MCM7_XENTR	DNA replication licensing factor mcm7 (Minichromosome maintenance protein 7) (CDC47 homolog)	0.66	-	nuc	0	Nucleus. Associated with chromatin before the formation of nuclei and detaches from it as DNA replic ...	chromatin [ISS] MCM complex [ISS]			720
P28365 UniProt NPD GO	RPA2_EUPOC	DNA-directed RNA polymerase I second largest subunit (EC 2.7.7.6) (RNA polymerase I subunit 2)	0.66	-	nuc	0	Nucleus				1166
P48119 UniProt NPD GO	RPOB_CYAPA	DNA-directed RNA polymerase beta chain (EC 2.7.7.6) (PEP) (Plastid-encoded RNA polymerase subunit be ...	0.66	+	cyt	0	Plastid; cyanelle				1103
Q32RW5 UniProt NPD GO	RPOB_STAPU	DNA-directed RNA polymerase beta chain (EC 2.7.7.6) (PEP) (Plastid-encoded RNA polymerase subunit be ...	0.66	-	mit	0	Plastid; chloroplast				1068
Q86SQ9 UniProt NPD GO	DHDDS_HUMAN	Dehydrodolichyl diphosphate synthase (EC 2.5.1.-) (Dedol-PP synthase)	0.66	-	cyt	0			608172		333
Q9QZL9 UniProt NPD GO	DKKL1_MOUSE	Dickkopf-like protein 1 precursor (Soggy-1 protein) (SGY-1)	0.66	-	exc	0	Secreted protein				230
Q3MI00 UniProt NPD GO	DNJB1_BOVIN	DnaJ homolog subfamily B member 1	0.66	-	nuc	0	Cytoplasm (By similarity). Translocates rapidly from the cytoplasm to the nuclei, and especially to ...				339
Q9QYJ3 UniProt NPD GO	DNJB1_MOUSE	DnaJ homolog subfamily B member 1 (Heat shock 40 kDa protein 1) (Heat shock protein 40) (HSP40)	0.66	-	nuc	0	Cytoplasm (By similarity). Translocates rapidly from the cytoplasm to the nuclei, and especially to ...				339
Q13217 UniProt NPD GO	DNJC3_HUMAN	DnaJ homolog subfamily C member 3 (Interferon-induced, double-stranded RNA-activated protein kinase ...	0.66	-	cyt	0	Cytoplasm (By similarity). Endoplasmic reticulum (By similarity). Associated with the endoplasmic re ...	cytoplasm [TAS]	601184		504
Q9R0T3 UniProt NPD GO	DNJC3_RAT	DnaJ homolog subfamily C member 3 (Interferon-induced, double-stranded RNA-activated protein kinase ...	0.66	-	nuc	0	Cytoplasm (By similarity). Endoplasmic reticulum (By similarity). Associated with the endoplasmic re ...				504
Q9QYI3 UniProt NPD GO	DNJC7_MOUSE	DnaJ homolog subfamily C member 7 (Tetratricopeptide repeat protein 2) (TPR repeat protein 2) (MDj11 ...	0.66	-	cyt	0					494
Q9M161 UniProt NPD GO	DOF41_ARATH	Dof zinc finger protein DOF4.1 (AtDOF4.1)	0.66	-	nuc	0	Nucleus (Probable)				294
Q9LSL6 UniProt NPD GO	DOF57_ARATH	Dof zinc finger protein DOF5.7 (AtDOF5.7)	0.66	-	nuc	0	Nucleus (Probable)				316
Q61216 UniProt NPD GO	MRE11_MOUSE	Double-strand break repair protein MRE11A (MRE11 homolog 1) (MRE11 meiotic recombination 11 homolog ...	0.66	-	nuc	0	Nucleus (By similarity). Localizes to discrete nuclear foci after treatment with genotoxic agents (B ...	nucleus [IDA]			706
Q9C291 UniProt NPD GO	MRE11_NEUCR	Double-strand break repair protein mus-23 (Recombinational repair protein mus-23)	0.66	-	nuc	0	Nucleus (By similarity)				760
P42697 UniProt NPD GO	DRP1A_ARATH	Dynamin-related protein 1A (Dynamin-like protein A) (Dynamin-like protein 1)	0.66	-	nuc	0	Cytoplasm. Microtubule-associated				610
P45443 UniProt NPD GO	DYHC_NEUCR	Dynein heavy chain, cytosolic (DYHC)	0.66	-	nuc	0	Cytoplasm				4367
Q9UTG2 UniProt NPD GO	PUB2_SCHPO	E3 ubiquitin--protein ligase pub2 (EC 6.3.2.-)	0.66	-	cyt	0	Membrane; peripheral membrane protein. Cytoplasm. Predominantly found at the cell surface of the pol ...	cell cortex of cell tip [IDA] cytoplasm [IDA] nucleus [IDA]			671

You are viewing entries 15701 to 15750 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.