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
O13058 UniProt NPD GO	VSP3_TRIFL	Venom serine proteinase 3 precursor (EC 3.4.21.-)	0.12	-	exc	0	Secreted protein				257
P38190 UniProt NPD GO	YBF3_YEAST	Very hypothetical protein YBL053W	0.12	-	mit	1 *					124
P53828 UniProt NPD GO	YN36_YEAST	Very hypothetical protein YNL296W	0.12	-	nuc	0					104
P20931 UniProt NPD GO	YYY3_HUMAN	Very very hypothetical B-cell growth factor (BCGF-12 kDa)	0.12	-	cyt	0			109540		124
Q9GZP7 UniProt NPD GO	VN1R1_HUMAN	Vomeronasal type-1 receptor 1 (V1r-like receptor 1) (Vomeronasal olfactory receptor chromosome 19 su ...	0.12	-	cyt	4	Membrane; multi-pass membrane protein	membrane [NAS]	605234		353
Q9BXE9 UniProt NPD GO	VN1R3_HUMAN	Vomeronasal type-1 receptor 3 (V1r-like receptor 3)	0.12	-	end	4 *	Membrane; multi-pass membrane protein				311
P40337 UniProt NPD GO	VHL_HUMAN	Von Hippel-Lindau disease tumor suppressor (pVHL) (G7 protein)	0.12	-	nuc	0	Isoform 1, isoform 3: Cytoplasm. Isoform 1: Membrane; peripheral membrane protein. Isoform 1, isofor ...	cytosol [TAS] endoplasmic reticulum [NAS] mitochondrion [NAS] nucleus [TAS]	193300	1VCB	213
Q68F45 UniProt NPD GO	WIPI3_XENLA	WD repeat domain phosphoinositide-interacting protein 3 (WIPI-3) (WD repeat protein 45-like) (WDR45- ...	0.12	-	cyt	0					344
Q5ZK69 UniProt NPD GO	WDR71_CHICK	WD repeat protein 71	0.12	-	nuc	0					392
P41318 UniProt NPD GO	YNA6_YEAST	WD repeat protein YNL006W	0.12	-	cyt	0		endosome membrane [IDA] extrinsic to internal side of plasma membrane [IDA] Golgi membrane [IDA] peripheral to membrane of membrane fraction [IDA] TORC 1 complex [IPI] TORC 2 complex [IPI]			303
P01402 UniProt NPD GO	TXW1B_HEMHA	Weak toxin CM-1b	0.12	-	nuc	0	Secreted protein				57
Q96I51 UniProt NPD GO	WBS16_HUMAN	Williams-Beuren syndrome chromosome region 16 protein	0.12	-	mit	0			194050		464
Q5R8S4 UniProt NPD GO	XTP3B_PONPY	XTP3-transactivated gene B protein homolog precursor	0.12	-	mit	0	Secreted protein (Potential)				483
Q9SMJ3 UniProt NPD GO	ZDS_CAPAN	Zeta-carotene desaturase, chloroplast precursor (EC 1.14.99.30) (Carotene 7,8-desaturase)	0.12	-	cyt	0	Plastid; chloroplast. Plastid; chromoplast				588
Q9ZTP4 UniProt NPD GO	ZDS_MAIZE	Zeta-carotene desaturase, chloroplast precursor (EC 1.14.99.30) (Carotene 7,8-desaturase)	0.12	-	mit	0	Plastid; chloroplast. Plastid; chromoplast				570
P17021 UniProt NPD GO	ZNF17_HUMAN	Zinc finger protein 17 (Zinc finger protein KOX10) (HPF3) (Fragment)	0.12	-	nuc	0	Nucleus (Potential)				56
Q805F6 UniProt NPD GO	DISB_AGKCO	Zinc metalloproteinase acostatin-beta precursor (EC 3.4.24.-) [Contains: Disintegrin acostatin-beta] ...	0.12	-	nuc	0	Secreted protein				483
Q9IAB0 UniProt NPD GO	DISI_AGKCO	Zinc metalloproteinase contortrostatin precursor (EC 3.4.24.-) [Contains: Disintegrin contortrostati ...	0.12	-	nuc	0	Secreted protein				483
P08947 UniProt NPD GO	LITP_PHYSA	[Phe8]-phyllolitorin precursor	0.12	-	exc	0	Secreted protein				90
Q3SX13 UniProt NPD GO	IPKA_BOVIN	cAMP-dependent protein kinase inhibitor alpha (PKI-alpha)	0.12	-	nuc	0					75
P05383 UniProt NPD GO	KAPCB_PIG	cAMP-dependent protein kinase, beta-catalytic subunit (EC 2.7.11.11) (PKA C-beta)	0.12	-	cyt	0	Inactive holoenzyme, monomeric catalytic subunit: Cytoplasm (By similarity). Monomeric catalytic sub ...	cAMP-dependent protein kinase complex [ISS]			350
P87020 UniProt NPD GO	PRA1_CANAL	pH-regulated antigen PRA1 precursor (58 kDa fibrinogen-binding mannoprotein)	0.12	-	exc	0	Secreted protein. Cell-associated				299
Q58FK4 UniProt NPD GO	ARD2_ORYSA	1,2-dihydroxy-3-keto-5-methylthiopentene dioxygenase 2 (EC 1.13.-.-) (Aci-reductone dioxygenase 2) ( ...	0.11	-	cyt	0					198
P21937 UniProt NPD GO	EXSE_TRICO	11 kDa excretory-secretory protein (TCADES4)	0.11	-	nuc	0					92
P93214 UniProt NPD GO	14339_LYCES	14-3-3 protein 9	0.11	-	cyt	0					261
Q96453 UniProt NPD GO	1433D_SOYBN	14-3-3-like protein D (SGF14D)	0.11	-	cyt	0					261
P05477 UniProt NPD GO	HSP21_SOYBN	17.9 kDa class II heat shock protein	0.11	-	cyt	0	Cytoplasm				159
Q01417 UniProt NPD GO	PM1_SOYBN	18 kDa seed maturation protein	0.11	-	nuc	0					173
Q8R519 UniProt NPD GO	ACMSD_MOUSE	2-amino-3-carboxymuconate-6-semialdehyde decarboxylase (EC 4.1.1.45) (Fragment)	0.11	-	nuc	0					194
P35738 UniProt NPD GO	ODBB_RAT	2-oxoisovalerate dehydrogenase subunit beta, mitochondrial precursor (EC 1.2.4.4) (Branched-chain al ...	0.11	-	mit	0	Mitochondrion; mitochondrial matrix	alpha-ketoglutarate dehydrogenase complex (... [ISS] mitochondrion [ISS]			369
P30187 UniProt NPD GO	CBP2_ARATH	22 kDa calmodulin-like calcium-binding protein (CABP-22)	0.11	-	mit	0					191
P20473 UniProt NPD GO	CB23_TETTH	23 kDa calcium-binding protein (TCBP-23) [Contains: 12 kDa calcium-binding protein (TCBP-12)]	0.11	-	cyt	0					207
Q5E964 UniProt NPD GO	PSD13_BOVIN	26S proteasome non-ATPase regulatory subunit 13 (26S proteasome regulatory subunit S11) (26S proteas ...	0.11	-	cyt	0					376
P84169 UniProt NPD GO	PSD13_CHICK	26S proteasome non-ATPase regulatory subunit 13 (26S proteasome regulatory subunit S11) (26S proteas ...	0.11	-	cyt	0					376
Q9WVJ2 UniProt NPD GO	PSD13_MOUSE	26S proteasome non-ATPase regulatory subunit 13 (26S proteasome regulatory subunit S11) (26S proteas ...	0.11	-	cyt	0		proteasome regulatory particle (sensu Eukar... [IDA]			376
Q26616 UniProt NPD GO	PM27_STRPU	27 kDa primary mesenchyme-specific spicule protein precursor	0.11	-	exc	0	Secreted protein. Secreted to the skeletal compartment and accumulates predominantly at the advancin ...				267
P22072 UniProt NPD GO	3BHS2_RAT	3 beta-hydroxysteroid dehydrogenase/delta 5-->4-isomerase type II (3Beta-HSD II) [Includes: 3-beta-h ...	0.11	-	cyt	0	Endoplasmic reticulum; endoplasmic reticulum membrane; single-pass membrane protein. Mitochondrion; ...				372
Q01559 UniProt NPD GO	HMDH_NICSY	3-hydroxy-3-methylglutaryl-coenzyme A reductase (EC 1.1.1.34) (HMG-CoA reductase)	0.11	-	end	2 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein				604
P20715 UniProt NPD GO	HMDH_XENLA	3-hydroxy-3-methylglutaryl-coenzyme A reductase (EC 1.1.1.34) (HMG-CoA reductase)	0.11	-	end	5 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein				883
P43256 UniProt NPD GO	HMDH2_ARATH	3-hydroxy-3-methylglutaryl-coenzyme A reductase 2 (EC 1.1.1.34) (HMG-CoA reductase 2) (HMGR2)	0.11	-	mit	2 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein				562
Q75CP6 UniProt NPD GO	3HAO_ASHGO	3-hydroxyanthranilate 3,4-dioxygenase (EC 1.13.11.6) (3-HAO) (3-hydroxyanthranilic acid dioxygenase) ...	0.11	-	cyt	0					180
Q6FQ42 UniProt NPD GO	TSC10_CANGA	3-ketodihydrosphingosine reductase TSC10 (EC 1.1.1.102) (3-dehydrosphinganine reductase) (KDS reduct ...	0.11	-	cyt	1	Endoplasmic reticulum (By similarity)				363
P33207 UniProt NPD GO	FABG_ARATH	3-oxoacyl-[acyl-carrier-protein] reductase, chloroplast precursor (EC 1.1.1.100) (3-ketoacyl-acyl ca ...	0.11	-	cyt	0	Plastid; chloroplast. Plastid. And non-photosynthetic plastids				319
P28643 UniProt NPD GO	FABG_CUPLA	3-oxoacyl-[acyl-carrier-protein] reductase, chloroplast precursor (EC 1.1.1.100) (3-ketoacyl-acyl ca ...	0.11	-	mit	0	Plastid; chloroplast. Plastid. And non-photosynthetic plastids				320
Q9C1T1 UniProt NPD GO	PHYA_ASPOR	3-phytase A precursor (EC 3.1.3.8) (Myo-inositol-hexaphosphate 3-phosphohydrolase A) (3 phytase A) ( ...	0.11	-	exc	0	Secreted protein				466
Q750C2 UniProt NPD GO	RT10_ASHGO	30S ribosomal protein S10, mitochondrial precursor (Mitochondrial ribosomal small subunit protein 10 ...	0.11	-	mit	0	Mitochondrion (By similarity)				207
P36573 UniProt NPD GO	LEC1_CAEEL	32 kDa beta-galactoside-binding lectin (32 kDa GBP)	0.11	-	cyt	0					279
Q9NX20 UniProt NPD GO	RM16_HUMAN	39S ribosomal protein L16, mitochondrial precursor (L16mt) (MRP-L16)	0.11	-	mit	0	Mitochondrion				251
Q5R7L3 UniProt NPD GO	RM16_PONPY	39S ribosomal protein L16, mitochondrial precursor (L16mt) (MRP-L16)	0.11	-	mit	0	Mitochondrion (By similarity)				251
Q9BYD2 UniProt NPD GO	RM09_HUMAN	39S ribosomal protein L9, mitochondrial precursor (L9mt) (MRP-L9)	0.11	-	cyt	0	Mitochondrion	mitochondrial ribosome [NAS]			267

You are viewing entries 62151 to 62200 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.