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
O62954 UniProt NPD GO	RK2_PICAB	Chloroplast 50S ribosomal protein L2	0.62	-	nuc	0	Plastid; chloroplast				275
O62940 UniProt NPD GO	RK2_PINTH	Chloroplast 50S ribosomal protein L2	0.62	-	nuc	0	Plastid; chloroplast				276
Q6L3E2 UniProt NPD GO	RK32_SACHY	Chloroplast 50S ribosomal protein L32	0.62	-	mit	0	Plastid; chloroplast				59
Q6ENP9 UniProt NPD GO	RK32_SACOF	Chloroplast 50S ribosomal protein L32	0.62	-	mit	0	Plastid; chloroplast				59
Q8WHY9 UniProt NPD GO	RK36_PSINU	Chloroplast 50S ribosomal protein L36	0.62	-	nuc	0	Plastid; chloroplast				37
P49547 UniProt NPD GO	RK5_ODOSI	Chloroplast 50S ribosomal protein L5	0.62	-	cyt	0	Plastid; chloroplast				238
P70348 UniProt NPD GO	GCM1_MOUSE	Chorion-specific transcription factor GCMa (Glial cells missing homolog 1) (GCM motif protein 1) (mG ...	0.62	-	nuc	0	Nucleus (Potential)			1ODH	436
Q5BK07 UniProt NPD GO	CCD43_RAT	Coiled-coil domain-containing protein 43	0.62	+	cyt	0					222
Q96M83 UniProt NPD GO	CCDC7_HUMAN	Coiled-coil domain-containing protein 7	0.62	-	nuc	0					486
P57678 UniProt NPD GO	GEMI4_HUMAN	Component of gems 4 (Gemin-4) (p97)	0.62	-	cyt	0	Cytoplasm. Nucleus. Nucleus; nucleolus. Localized in subnuclear structures next to coiled bodies, ca ...	cytoplasm [TAS] nucleolus [TAS] small nuclear ribonucleoprotein complex [TAS]	606969		1058
P45815 UniProt NPD GO	CRF1_YARLI	Copper resistance protein CRF1	0.62	-	nuc	0	Nucleus (Potential)				411
P01194 UniProt NPD GO	COLI_RAT	Corticotropin-lipotropin precursor (Pro-opiomelanocortin) (POMC) [Contains: NPP; Melanotropin gamma ...	0.62	-	exc	0					235
Q9R1A0 UniProt NPD GO	CCNH_RAT	Cyclin-H	0.62	+	nuc	0	Nucleus				323
P26361 UniProt NPD GO	CFTR_MOUSE	Cystic fibrosis transmembrane conductance regulator (CFTR) (cAMP-dependent chloride channel) (ATP-bi ...	0.62	-	end	11	Membrane; multi-pass membrane protein			1XFA	1476
P79761 UniProt NPD GO	CP1A5_CHICK	Cytochrome P450 1A5 (EC 1.14.14.1) (CYPIA5) (P450 TCDDAA)	0.62	-	nuc	1 *	Endoplasmic reticulum; endoplasmic reticulum membrane; peripheral membrane protein				528
Q6EIG3 UniProt NPD GO	CP26B_BRARE	Cytochrome P450 26B1 (EC 1.14.-.-) (Cyp26B1) (Retinoic acid-metabolizing cytochrome)	0.62	-	nuc	0	Endoplasmic reticulum; endoplasmic reticulum membrane; peripheral membrane protein (By similarity)	endoplasmic reticulum [ISS] microsome [ISS]			511
Q86XP0 UniProt NPD GO	PA24D_HUMAN	Cytosolic phospholipase A2 delta (EC 3.1.1.4) (cPLA2-delta) (Phospholipase A2 group IVD)	0.62	-	cyt	0	Cytoplasm; cytosol. Translocates to membrane vesicles in a calcium-dependent fashion. Translocates t ...				818
P59103 UniProt NPD GO	DAOA_HUMAN	D-amino acid oxidase activator (Protein G72)	0.62	-	nuc	0	Golgi apparatus		607408		153
Q9H816 UniProt NPD GO	DCR1B_HUMAN	DNA cross-link repair 1B protein (hSNM1B)	0.62	+	nuc	0	Nucleus. Localizes to discrete foci		609683		532
Q27474 UniProt NPD GO	DNLI_CAEEL	DNA ligase (EC 6.5.1.1) (Polydeoxyribonucleotide synthase [ATP])	0.62	-	nuc	0	Nucleus (By similarity)				773
Q8VI24 UniProt NPD GO	SATB2_MOUSE	DNA-binding protein SATB2 (Special AT-rich sequence-binding protein 2)	0.62	-	nuc	0	Nucleus (By similarity)				733
Q85CL6 UniProt NPD GO	RPOC1_ANTFO	DNA-directed RNA polymerase beta' chain (EC 2.7.7.6) (PEP) (Plastid-encoded RNA polymerase beta' sub ...	0.62	-	cyt	0	Plastid; chloroplast				681
P16024 UniProt NPD GO	RPOC1_MAIZE	DNA-directed RNA polymerase beta' chain (EC 2.7.7.6) (PEP) (Plastid-encoded RNA polymerase beta' sub ...	0.62	-	cyt	0	Plastid; chloroplast				683
Q8S2T1 UniProt NPD GO	DDPS6_ARATH	Dehydrodolichyl diphosphate synthase 6 (EC 2.5.1.-) (Dedol-PP synthase 6)	0.62	-	mit	0					295
Q7L190 UniProt NPD GO	DPPA4_HUMAN	Developmental pluripotency-associated protein 4	0.62	-	nuc	0	Nucleus (By similarity)				304
P42659 UniProt NPD GO	DPP6_BOVIN	Dipeptidyl aminopeptidase-like protein 6 (Dipeptidylpeptidase VI) (Dipeptidylpeptidase 6) (Dipeptidy ...	0.62	-	mit	1	Membrane; single-pass type II membrane protein (Probable)				863
P46101 UniProt NPD GO	DPP6_RAT	Dipeptidyl aminopeptidase-like protein 6 (Dipeptidylpeptidase VI) (Dipeptidylpeptidase 6) (Dipeptidy ...	0.62	-	mit	1	Membrane; single-pass type II membrane protein (Probable)				859
Q7SEK8 UniProt NPD GO	DPH4_NEUCR	Diphthamide biosynthesis protein 4	0.62	-	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity)				219
Q91XM9 UniProt NPD GO	DLG2_MOUSE	Discs large homolog 2 (Postsynaptic density protein PSD-93) (Channel-associated protein of synapse-1 ...	0.62	-	nuc	0	Membrane; lipid-anchor (By similarity). Concentrated in soma and postsynaptic density of a subset of ...	postsynaptic membrane [IDA]			852
Q811D0 UniProt NPD GO	DLG1_MOUSE	Disks large homolog 1 (Synapse-associated protein 97) (SAP-97) (Embryo-dlg/synapse-associated protei ...	0.62	-	nuc	0	Membrane; peripheral membrane protein (By similarity). Colocalizes with EPB41 at regions of intercel ...	basolateral plasma membrane [ISS] cell-cell adherens junction [TAS] plasma membrane [ISS]			905
Q91YW3 UniProt NPD GO	DNJC3_MOUSE	DnaJ homolog subfamily C member 3 (Interferon-induced, double-stranded RNA-activated protein kinase ...	0.62	-	mit	0	Cytoplasm. Endoplasmic reticulum. Associated with the endoplasmic reticulum (ER)	cytoplasm [IDA]			504
Q08877 UniProt NPD GO	DYN3_RAT	Dynamin-3 (EC 3.6.5.5) (Dynamin, testicular) (T-dynamin)	0.62	-	nuc	0	Cytoplasm. Microtubule-associated				848
P22681 UniProt NPD GO	CBL_HUMAN	E3 ubiquitin-protein ligase CBL (EC 6.3.2.-) (Signal transduction protein CBL) (Proto-oncogene c-CBL ...	0.62	-	nuc	0	Cytoplasm	plasma membrane [IDA]	165360	2CBL	906
P70459 UniProt NPD GO	ERF_MOUSE	ETS domain-containing transcription factor ERF	0.62	+	nuc	0	Nucleus				551
O08579 UniProt NPD GO	EMD_MOUSE	Emerin	0.62	-	nuc	1	Nucleus; nuclear inner membrane; single-pass membrane protein; nucleoplasmic side (By similarity)	nuclear inner membrane [TAS] nuclear lamina [TAS]			259
Q9SAK2 UniProt NPD GO	KSB_ARATH	Ent-kaurene synthase B, chloroplast precursor (EC 4.2.3.19) (KSB) (AtKS)	0.62	-	nuc	0	Plastid; chloroplast				785
O54839 UniProt NPD GO	EOMES_MOUSE	Eomesodermin homolog	0.62	-	nuc	0	Nucleus (Potential)	nucleus [IDA]			688
P49290 UniProt NPD GO	PERE_MOUSE	Eosinophil peroxidase precursor (EC 1.11.1.7) (EPO) [Contains: Eosinophil peroxidase light chain; Eo ...	0.62	-	exc	0	Cytoplasmic granule. Cytoplasmic granules of eosinophils				716
Q03764 UniProt NPD GO	EKI1_YEAST	Ethanolamine kinase (EC 2.7.1.82) (EK)	0.62	-	nuc	0		cytoplasm [IDA]			534
Q9SXS8 UniProt NPD GO	ERF3_TOBAC	Ethylene-responsive transcription factor 3 (Ethylene-responsive element-binding factor 3 homolog) (E ...	0.62	-	nuc	0	Nucleus (Probable)				225
Q9Z1Z1 UniProt NPD GO	E2AK3_RAT	Eukaryotic translation initiation factor 2-alpha kinase 3 precursor (EC 2.7.11.1) (PRKR-like endopla ...	0.62	-	exc	1 *	Endoplasmic reticulum; endoplasmic reticulum membrane; single-pass type I membrane protein				1108
P97878 UniProt NPD GO	EXOC5_RAT	Exocyst complex component 5 (Exocyst complex component Sec10) (71 kDa component of rsec6/8 secretory ...	0.62	-	cyt	0	Cytoplasm (By similarity)	cytosol [IDA]			708
Q754H0 UniProt NPD GO	EXO70_ASHGO	Exocyst complex protein EXO70	0.62	-	nuc	0	Bud (By similarity). Bud neck (By similarity)				614
Q8BJL1 UniProt NPD GO	FBX30_MOUSE	F-box only protein 30	0.62	-	nuc	0					746
Q5XUX0 UniProt NPD GO	FBX31_HUMAN	F-box only protein 31	0.62	-	nuc	0			609102		539
Q6NS60 UniProt NPD GO	FBX41_MOUSE	F-box only protein 41	0.62	-	nuc	0					872
Q05153 UniProt NPD GO	SSRP1_ARATH	FACT complex subunit SSRP1 (Facilitates chromatin transcription complex subunit SSRP1) (Recombinatio ...	0.62	+	nuc	0	Nucleus. Colocalizes with RNA polymerase II on chromatin. Recruited to actively transcribed loci				646
Q04691 UniProt NPD GO	FBP1_DROME	Fat-body protein 1 precursor (P1 protein)	0.62	-	exc	0					1029
O43103 UniProt NPD GO	SID2_USTMA	Ferrichrome siderophore peptide synthetase (EC 6.-.-.-)	0.62	-	cyt	0					3947
Q40504 UniProt NPD GO	FL1_TOBAC	Floricaula/leafy homolog 1 (NFL1)	0.62	-	cyt	0	Nucleus (Probable)				413

You are viewing entries 17851 to 17900 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.