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
Q69ZX8 UniProt NPD GO	ABLM3_MOUSE	Actin-binding LIM protein 3 (Actin-binding LIM protein family member 3) (abLIM-3)	0.62	-	nuc	0	Cytoplasm (Probable)				682
Q05123 UniProt NPD GO	ARP9_YEAST	Actin-like protein ARP9 (Chromatin structure remodeling complex protein ARP9) (SWI/SNF complex compo ...	0.62	-	cyt	0	Nucleus. Localizes to centromeric and flanking chromatin. Association with these loci is dependent o ...	nucleus [IDA] RSC complex [IDA] SWI/SNF complex [IDA]			467
Q8N9N2 UniProt NPD GO	ASCC1_HUMAN	Activating signal cointegrator 1 complex subunit 1 (ASC-1 complex subunit p50) (Trip4 complex subuni ...	0.62	-	nuc	0	Cytoplasm				400
O35298 UniProt NPD GO	AOAH_MOUSE	Acyloxyacyl hydrolase precursor (EC 3.1.1.77) [Contains: Acyloxyacyl hydrolase small subunit; Acylox ...	0.62	-	exc	0					574
P41765 UniProt NPD GO	AFLR_ASPFL	Aflatoxin biosynthesis regulatory protein	0.62	-	nuc	0	Nucleus				437
O22328 UniProt NPD GO	AGL8_SOLCO	Agamous-like MADS-box protein AGL8 homolog	0.62	-	nuc	0	Nucleus (By similarity)				250
Q42429 UniProt NPD GO	AGL8_SOLTU	Agamous-like MADS-box protein AGL8 homolog (POTM1-1)	0.62	-	nuc	0	Nucleus (By similarity)				250
Q42464 UniProt NPD GO	AGL9_LYCES	Agamous-like MADS-box protein AGL9 homolog (TM5)	0.62	-	nuc	1	Nucleus (By similarity)				224
Q96Q83 UniProt NPD GO	ALKB3_HUMAN	Alkylated repair protein alkB homolog 3 (Prostate cancer antigen 1) (DEPC-1)	0.62	-	nuc	0					286
Q708S3 UniProt NPD GO	ACC4B_BRARE	Amiloride-sensitive cation channel 4-B (Acid-sensing ion channel 4.2) (ZASIC4.2)	0.62	-	nuc	1	Cell membrane; multi-pass membrane protein (Probable)				558
O13263 UniProt NPD GO	SCNNH_XENLA	Amiloride-sensitive sodium channel gamma-2-subunit (Epithelial Na(+) channel gamma-2 subunit) (Gamma ...	0.62	-	mit	1	Cell membrane; apical cell membrane; multi-pass membrane protein (By similarity). Apical membrane of ...				663
P51171 UniProt NPD GO	SCNNG_XENLA	Amiloride-sensitive sodium channel gamma-subunit (Epithelial Na+ channel subunit gamma) (Gamma ENaC) ...	0.62	-	mit	1	Cell membrane; apical cell membrane; multi-pass membrane protein (By similarity). Apical membrane of ...				660
P10505 UniProt NPD GO	APC3_SCHPO	Anaphase-promoting complex subunit 3 (20S cyclosome/APC complex protein apc3) (Nuclear alteration pr ...	0.62	-	nuc	0	Nucleus	anaphase-promoting complex [IDA] nucleus [IDA]			665
Q5EA66 UniProt NPD GO	ANGL7_BOVIN	Angiopoietin-related protein 7 precursor (Angiopoietin-like 7)	0.62	-	cyt	1 *	Secreted protein (Probable)				344
P40603 UniProt NPD GO	APG_BRANA	Anter-specific proline-rich protein APG (Protein CEX) (Fragment)	0.62	-	nuc	0					449
Q5RCR8 UniProt NPD GO	ARMC1_PONPY	Armadillo repeat-containing protein 1	0.62	-	nuc	0					282
Q7TQH0 UniProt NPD GO	ATX2L_MOUSE	Ataxin-2-like protein	0.62	-	nuc	0	Membrane; peripheral membrane protein (By similarity)				1049
Q5IS79 UniProt NPD GO	ATOH1_PANTR	Atonal protein homolog 1	0.62	-	nuc	0	Nucleus (Probable)				356
Q92858 UniProt NPD GO	ATOH1_HUMAN	Atonal protein homolog 1 (Helix-loop-helix protein hATH-1)	0.62	-	nuc	0	Nucleus (Probable)		601461		354
Q63042 UniProt NPD GO	ALR_RAT	Augmenter of liver regeneration	0.62	-	nuc	0	Cytoplasm			1OQC	125
Q6FPD4 UniProt NPD GO	ATG17_CANGA	Autophagy-related protein 17	0.62	-	cyt	0	Cytoplasm (By similarity). Membrane; peripheral membrane protein (By similarity). Cytoplasmic and pu ...				409
Q9SKN5 UniProt NPD GO	ARFJ_ARATH	Auxin response factor 10	0.62	-	cyt	0	Nucleus				693
P93022 UniProt NPD GO	ARFG_ARATH	Auxin response factor 7 (Non-phototropic hypocotyl 4) (Protein BIPOSTO) (Auxin-responsive protein IA ...	0.62	-	nuc	0	Nucleus				1164
Q9Y2T1 UniProt NPD GO	AXN2_HUMAN	Axin-2 (Axis inhibition protein 2) (Conductin) (Axin-like protein) (Axil)	0.62	-	nuc	0	Cytoplasm	nucleus [IDA]	608615		843
Q5XFY4 UniProt NPD GO	BCL7A_BRARE	B-cell CLL/lymphoma 7 protein family member A	0.62	-	nuc	0					201
O22476 UniProt NPD GO	BRI1_ARATH	BRASSINOSTEROID INSENSITIVE 1 precursor (EC 2.7.11.1) (AtBRI1) (Brassinosteroid LRR receptor kinase) ...	0.62	+	end	2 *	Cell membrane; single-pass type I membrane protein. Endosome; endosomal membrane; single-pass type I ...				1196
P35626 UniProt NPD GO	ARBK2_HUMAN	Beta-adrenergic receptor kinase 2 (EC 2.7.11.15) (Beta-ARK-2) (G-protein-coupled receptor kinase 3)	0.62	-	cyt	0			109636		688
Q25386 UniProt NPD GO	SCRB_LIMPO	Beta-scruin	0.62	-	mit	0					916
Q9DBJ3 UniProt NPD GO	BI2L1_MOUSE	Brain-specific angiogenesis inhibitor 1-associated protein 2-like protein 1 (BAI1-associated protein ...	0.62	-	nuc	0				1SPK	514
P01125 UniProt NPD GO	REL_MELGA	C-Rel proto-oncogene protein (C-Rel protein) (p68) (Fragment)	0.62	+	nuc	0	Nucleus				538
P55285 UniProt NPD GO	CADH6_HUMAN	Cadherin-6 precursor (Kidney-cadherin) (K-cadherin)	0.62	-	nuc	1	Membrane; single-pass type I membrane protein		603007		790
P62345 UniProt NPD GO	CDPK4_PLABA	Calcium-dependent protein kinase 4 (EC 2.7.11.1) (PbCDPK4)	0.62	-	cyt	0					527
O04153 UniProt NPD GO	CALR3_ARATH	Calreticulin-3 precursor	0.62	+	end	1 *	Endoplasmic reticulum; endoplasmic reticulum lumen (By similarity)				424
Q9VCW0 UniProt NPD GO	CCAP_DROME	Cardioactive peptide precursor (CCAP) (Crustacean cardioactive peptide) (Cardioacceleratory peptide ...	0.62	-	exc	0	Secreted protein (By similarity)			1Y49	151
Q9P4R5 UniProt NPD GO	CREC_EMENI	Catabolite repression protein creC	0.62	-	exc	1 *		nucleus [NAS]			630
Q9TUB2 UniProt NPD GO	P53_PIG	Cellular tumor antigen p53 (Tumor suppressor p53)	0.62	-	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity)	cytoplasm [ISS] mitochondrion [ISS] nucleolus [ISS] nucleus [ISS]			386
P79892 UniProt NPD GO	P53_HORSE	Cellular tumor antigen p53 (Tumor suppressor p53) (Fragment)	0.62	+	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity)				280
P47167 UniProt NPD GO	MCM22_YEAST	Central kinetochore subunit MCM22 (Minichromosome maintenance protein 22)	0.62	-	nuc	0	Nucleus. Associated with kinetochores	condensed nuclear chromosome kinetochore [IDA]			239
Q5WA50 UniProt NPD GO	CTR2_OCTVU	Cephalotocin receptor 2	0.62	-	end	7 *	Membrane; multi-pass membrane protein (Potential)	integral to membrane [IC]			426
Q49MI3 UniProt NPD GO	CERKL_HUMAN	Ceramide kinase-like protein	0.62	-	mit	0	Cytoplasm. Nucleus; nucleolus. Enriched in nucleoli. May shuttle between nucleus and cytoplasm. Isof ...		608381		558
Q9D8B3 UniProt NPD GO	CHM4B_MOUSE	Charged multivesicular body protein 4b (Chromatin-modifying protein 4b) (CHMP4b)	0.62	-	nuc	0	Cytoplasm (By similarity)				224
Q85UY0 UniProt NPD GO	RR18_PSEMZ	Chloroplast 30S ribosomal protein S18	0.62	-	mit	0	Plastid; chloroplast				86
P17933 UniProt NPD GO	RR2_WHEAT	Chloroplast 30S ribosomal protein S2	0.62	-	mit	0	Plastid; chloroplast				236
Q6H9L1 UniProt NPD GO	RR4_EQUHY	Chloroplast 30S ribosomal protein S4	0.62	-	nuc	0	Plastid; chloroplast				207
P51288 UniProt NPD GO	RR7_PORPU	Chloroplast 30S ribosomal protein S7	0.62	-	mit	0	Plastid; chloroplast				156
Q71L19 UniProt NPD GO	RR7_STAER	Chloroplast 30S ribosomal protein S7	0.62	-	nuc	0	Plastid; chloroplast				156
Q2MIF2 UniProt NPD GO	RR8_SOLBU	Chloroplast 30S ribosomal protein S8	0.62	-	nuc	0	Plastid; chloroplast				134
Q49KT4 UniProt NPD GO	RK2_EUCGG	Chloroplast 50S ribosomal protein L2	0.62	+	nuc	0	Plastid; chloroplast				274
P41096 UniProt NPD GO	RK2_HORVU	Chloroplast 50S ribosomal protein L2	0.62	+	nuc	0	Plastid; chloroplast				273
Q9MDU0 UniProt NPD GO	RK2_OENHO	Chloroplast 50S ribosomal protein L2	0.62	+	nuc	0	Plastid; chloroplast				274

You are viewing entries 17801 to 17850 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.