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
P33313 UniProt NPD GO	CNS1_YEAST	Cyclophilin seven suppressor 1 (STI1 stress-inducible protein homolog)	0.27	-	nuc	0		cytoplasm [IPI]			385
O97862 UniProt NPD GO	CYTC_RABIT	Cystatin C precursor	0.27	-	exc	1 *					148
P22282 UniProt NPD GO	22P1_RAT	Cystatin-related protein 1 precursor (CRP-1) (Prostatic 22 kDa glycoprotein P22K16/P22K20) (Androgen ...	0.27	-	vac	1 *					176
P87185 UniProt NPD GO	NFS1_CANAL	Cysteine desulfurase, mitochondrial precursor (EC 2.8.1.7) (tRNA-splicing protein SPL1)	0.27	+	mit	0	Mitochondrion (By similarity)				488
P54107 UniProt NPD GO	CRIS1_HUMAN	Cysteine-rich secretory protein 1 precursor (CRISP-1) (Acidic epididymal glycoprotein homolog) (AEG- ...	0.27	-	nuc	0	Located in the lumen and epithelium of distal ductus efferentes and epididymal ducts, and on the pos ...	extracellular space [TAS]	601193		249
Q9EPT4 UniProt NPD GO	CP11A_MESAU	Cytochrome P450 11A1, mitochondrial precursor (EC 1.14.15.6) (CYPXIA1) (P450(scc)) (Cholesterol side ...	0.27	-	mit	0	Mitochondrion				520
Q29605 UniProt NPD GO	CP19A_RABIT	Cytochrome P450 19A1 (EC 1.14.14.1) (Aromatase) (CYPXIX) (Estrogen synthetase) (P-450AROM)	0.27	+	mit	2 *	Membrane; peripheral membrane protein				503
Q05555 UniProt NPD GO	CP2AA_RABIT	Cytochrome P450 2A10 (EC 1.14.14.1) (CYPIIA10) (P450-IIA10)	0.27	-	mit	1 *	Endoplasmic reticulum; endoplasmic reticulum membrane; peripheral membrane protein				494
P00176 UniProt NPD GO	CP2B1_RAT	Cytochrome P450 2B1 (EC 1.14.14.1) (CYPIIB1) (P450-B) (P450b) (P450-PB1 and P450-PB2) (P450-LM2)	0.27	-	end	1 *	Endoplasmic reticulum; endoplasmic reticulum membrane; peripheral membrane protein				491
P33262 UniProt NPD GO	CP2CK_MACFA	Cytochrome P450 2C20 (EC 1.14.14.1) (CYPIIC20) (P450-MKMP13) (P450-MK1)	0.27	-	vac	1 *	Endoplasmic reticulum; endoplasmic reticulum membrane; peripheral membrane protein				490
O46054 UniProt NPD GO	C4AE1_DROME	Cytochrome P450 4ae1 (EC 1.14.-.-) (CYPIVAE1)	0.27	-	vac	0	Endoplasmic reticulum; endoplasmic reticulum membrane; peripheral membrane protein (Potential)				496
Q95036 UniProt NPD GO	CP6B5_PAPGL	Cytochrome P450 6B5 (EC 1.14.14.1) (CYPVIB5) (CYP6B5V1) (Fragment)	0.27	-	mit	1 *	Endoplasmic reticulum; endoplasmic reticulum membrane; peripheral membrane protein				476
Q9LTM7 UniProt NPD GO	C71BG_ARATH	Cytochrome P450 71B16 (EC 1.14.-.-)	0.27	-	end	2 *					502
Q9SCN2 UniProt NPD GO	C71BU_ARATH	Cytochrome P450 71B31 (EC 1.14.-.-)	0.27	-	nuc	0					498
Q9LIP3 UniProt NPD GO	C71BY_ARATH	Cytochrome P450 71B37 (EC 1.14.-.-)	0.27	-	mit	2 *					500
Q43255 UniProt NPD GO	C71C2_MAIZE	Cytochrome P450 71C2 (EC 1.14.-.-) (Benzoxazineless 3)	0.27	-	nuc	2 *					536
Q42798 UniProt NPD GO	C93A1_SOYBN	Cytochrome P450 93A1 (EC 1.14.-.-)	0.27	-	mit	1 *					509
Q9V4I1 UniProt NPD GO	CP9B2_DROME	Cytochrome P450 9b2 (EC 1.14.-.-) (CYPIXB2)	0.27	-	nuc	0	Endoplasmic reticulum; endoplasmic reticulum membrane; peripheral membrane protein (Potential)				505
Q7YRK1 UniProt NPD GO	COX6C_TRACR	Cytochrome c oxidase polypeptide VIc precursor (EC 1.9.3.1)	0.27	-	mit	1 *	Mitochondrion; mitochondrial inner membrane				75
P11947 UniProt NPD GO	COX1_TETPY	Cytochrome c oxidase subunit 1 (EC 1.9.3.1) (Cytochrome c oxidase polypeptide I)	0.27	-	end	12	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				698
O43639 UniProt NPD GO	NCK2_HUMAN	Cytoplasmic protein NCK2 (NCK adaptor protein 2) (SH2/SH3 adaptor protein NCK-beta) (Nck-2)	0.27	-	cyt	0	Cytoplasm	cytoplasm [NAS]	604930	2FRY	380
Q6FTI5 UniProt NPD GO	DAD2_CANGA	DASH complex subunit DAD2 (Outer kinetochore protein DAD2)	0.27	-	nuc	0	Nucleus (By similarity). Associates with the mitotic spindle and the kinetochore (By similarity)				127
Q96EP5 UniProt NPD GO	DAZP1_HUMAN	DAZ-associated protein 1 (Deleted in azoospermia-associated protein 1)	0.27	-	nuc	0	Cytoplasm (By similarity). Predominantly. Nucleus (By similarity). Nuclear at some stages of spermat ...		607430		407
Q98SJ2 UniProt NPD GO	DAZP1_XENLA	DAZ-associated protein 1 (Deleted in azoospermia-associated protein 1) (Proline-rich Vg1 mRNA-bindin ...	0.27	-	nuc	0	Cytoplasm. Concentrated in the vegetal cortex of stage III/IV oocytes				360
O49139 UniProt NPD GO	CMT1_ARATH	DNA (cytosine-5)-methyltransferase CMT1 (EC 2.1.1.37) (Chromomethylase 1) (Protein CHROMOMETHYLASE1) ...	0.27	-	cyt	0	Nucleus (By similarity)				791
P42657 UniProt NPD GO	RAD25_SCHPO	DNA damage checkpoint protein rad25	0.27	-	nuc	0					270
O54956 UniProt NPD GO	DPOE2_MOUSE	DNA polymerase epsilon subunit 2 (EC 2.7.7.7) (DNA polymerase II subunit 2) (DNA polymerase epsilon ...	0.27	-	mit	0	Nucleus				527
Q9CQ36 UniProt NPD GO	DPOE4_MOUSE	DNA polymerase epsilon subunit 4 (EC 2.7.7.7) (DNA polymerase II subunit 4) (DNA polymerase epsilon ...	0.27	-	cyt	0	Nucleus (Potential)				118
O35654 UniProt NPD GO	DPOD2_MOUSE	DNA polymerase subunit delta 2 (EC 2.7.7.7) (DNA polymerase subunit delta p50)	0.27	-	mit	0	Nucleus				469
Q9W6G7 UniProt NPD GO	DPOG2_XENLA	DNA polymerase subunit gamma 2, mitochondrial precursor (EC 2.7.7.7) (Mitochondrial DNA polymerase a ...	0.27	-	mit	0	Mitochondrion				463
O35719 UniProt NPD GO	RA51B_MOUSE	DNA repair protein RAD51 homolog 2 (R51H2) (RAD51-like protein 1)	0.27	-	cyt	0	Nucleus (Probable)				350
Q9D600 UniProt NPD GO	PSF2_MOUSE	DNA replication complex GINS protein PSF2	0.27	-	nuc	0	Nucleus (By similarity)				185
Q24849 UniProt NPD GO	MCM3_ENTHI	DNA replication licensing factor MCM3	0.27	-	nuc	0	Nucleus (Probable)				597
Q7XLX6 UniProt NPD GO	S1FA2_ORYSA	DNA-binding protein S1FA2	0.27	-	nuc	1 *	Nucleus (Probable)				80
Q85A01 UniProt NPD GO	RPOA_ANTFO	DNA-directed RNA polymerase alpha chain (EC 2.7.7.6) (PEP) (Plastid-encoded RNA polymerase subunit a ...	0.27	-	cyt	0	Plastid; chloroplast				340
Q8SKY1 UniProt NPD GO	RPOA_CUSRE	DNA-directed RNA polymerase alpha chain (EC 2.7.7.6) (PEP) (Plastid-encoded RNA polymerase subunit a ...	0.27	-	mit	0	Plastid				335
P12950 UniProt NPD GO	DHN1_MAIZE	Dehydrin DHN1 (M3) (RAB-17 protein)	0.27	-	nuc	0					168
Q9NQZ3 UniProt NPD GO	DAZ1_HUMAN	Deleted in azoospermia protein 1	0.27	-	nuc	0	Cytoplasm. Predominantly. Nucleus. Nuclear at some stages of spermatozoide development. Localizes bo ...		415000		744
Q9BGN8 UniProt NPD GO	DAZL_CALJA	Deleted in azoospermia-like (DAZ-like autosomal) (Deleted in azoospermia-like 1)	0.27	-	nuc	0	Cytoplasm. Predominantly. Nucleus. Nuclear in spermatogonia until near the end of the meiotic propha ...				296
P54886 UniProt NPD GO	P5CS_HUMAN	Delta 1-pyrroline-5-carboxylate synthetase (P5CS) (Aldehyde dehydrogenase 18 family member A1) [Incl ...	0.27	-	mit	0	Mitochondrion; mitochondrial inner membrane		138250	2H5G	795
Q9FPD5 UniProt NPD GO	ADSL3_ARATH	Delta-9 desaturase-like 3 protein (EC 1.14.19.-)	0.27	-	cyt	3 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (By similarity)				299
O00548 UniProt NPD GO	DLL1_HUMAN	Delta-like protein 1 precursor (Drosophila Delta homolog 1) (Delta1) (H-Delta-1)	0.27	-	exc	1	Membrane; single-pass type I membrane protein	extracellular region [NAS] integral to plasma membrane [NAS]	606582		723
O88671 UniProt NPD GO	DLL3_RAT	Delta-like protein 3 precursor (Drosophila Delta homolog 3)	0.27	-	exc	1	Membrane; single-pass type I membrane protein (By similarity)				589
Q5ZJ39 UniProt NPD GO	DENR_CHICK	Density-regulated protein (DRP)	0.27	-	cyt	0					198
Q5RFP5 UniProt NPD GO	DENR_PONPY	Density-regulated protein (DRP)	0.27	-	cyt	0					198
P05421 UniProt NPD GO	DEM2_PHYSA	Dermorphin-2 precursor [Contains: Dermorphin] (Fragment)	0.27	+	exc	0	Secreted protein	extracellular region [IDA]			198
Q9GKQ8 UniProt NPD GO	DSG1_CANFA	Desmoglein-1 precursor (Desmosomal glycoprotein 1) (DG1) (DGI)	0.27	-	end	0	Membrane; single-pass type I membrane protein (By similarity)				1054
Q7M0E3 UniProt NPD GO	DEST_RAT	Destrin (Actin-depolymerizing factor) (ADF)	0.27	+	cyt	0					164
Q9R0P5 UniProt NPD GO	DEST_MOUSE	Destrin (Actin-depolymerizing factor) (ADF) (Sid 23)	0.27	+	cyt	0		cortical actin cytoskeleton [IDA] cytoplasm [IDA]			164
Q10169 UniProt NPD GO	DSK2_SCHPO	Deubiquitination-protection protein dph1	0.27	-	nuc	0					354

You are viewing entries 43101 to 43150 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.