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
P12791 UniProt NPD GO	CP2BA_MOUSE	Cytochrome P450 2B10 (EC 1.14.14.1) (CYPIIB10) (Testosterone 16-alpha hydroxylase) (P450-16-alpha) ( ...	0.31	-	end	1 *	Endoplasmic reticulum; endoplasmic reticulum membrane; peripheral membrane protein				500
P04167 UniProt NPD GO	CP2B2_RAT	Cytochrome P450 2B2 (EC 1.14.14.1) (CYPIIB2) (P450E) (P450 PB4)	0.31	-	end	1 *	Endoplasmic reticulum; endoplasmic reticulum membrane; peripheral membrane protein				491
O18992 UniProt NPD GO	CP2DJ_CALJA	Cytochrome P450 2D19 (EC 1.14.14.1) (CYPIID19) (P450 CM2D-1)	0.31	-	end	2 *	Endoplasmic reticulum; endoplasmic reticulum membrane; peripheral membrane protein				497
P79401 UniProt NPD GO	CP3AT_PIG	Cytochrome P450 3A29 (EC 1.14.14.1) (CYPIIIA29)	0.31	-	end	2 *	Endoplasmic reticulum; endoplasmic reticulum membrane; peripheral membrane protein	membrane fraction [ISS]			503
Q12585 UniProt NPD GO	CP52T_CANMA	Cytochrome P450 52D1 (EC 1.14.14.-) (CYPLIID1) (Alkane-inducible P450-ALK4)	0.31	-	nuc	1 *					505
Q9T0K2 UniProt NPD GO	C71AK_ARATH	Cytochrome P450 71A20 (EC 1.14.-.-)	0.31	-	nuc	0					495
Q43257 UniProt NPD GO	C71C4_MAIZE	Cytochrome P450 71C4 (EC 1.14.-.-) (Benzoxazineless 2)	0.31	-	nuc	1 *					538
O48923 UniProt NPD GO	C71DA_SOYBN	Cytochrome P450 71D10 (EC 1.14.-.-)	0.31	-	nuc	1 *					510
P48420 UniProt NPD GO	C78A1_MAIZE	Cytochrome P450 78A1 (EC 1.14.-.-) (CYPLXXVIII)	0.31	-	mit	1 *					547
O75881 UniProt NPD GO	CP7B1_HUMAN	Cytochrome P450 7B1 (EC 1.14.13.100) (25-hydroxycholesterol 7-alpha-hydroxylase) (Oxysterol 7-alpha- ...	0.31	-	nuc	2 *	Endoplasmic reticulum; endoplasmic reticulum membrane; peripheral membrane protein		603711		506
Q43078 UniProt NPD GO	C97B1_PEA	Cytochrome P450 97B1 (EC 1.14.-.-) (P450 97A2)	0.31	-	mit	0					552
Q6YFP9 UniProt NPD GO	CX6B2_BOVIN	Cytochrome c oxidase subunit VIb isoform 2 (EC 1.9.3.1) (COX VIb-2) (Cytochrome c oxidase subunit VI ...	0.31	-	nuc	0	Mitochondrion; mitochondrial intermembrane space (By similarity)				88
Q80ZN9 UniProt NPD GO	CX6B2_MOUSE	Cytochrome c oxidase subunit VIb isoform 2 (EC 1.9.3.1) (COX VIb-2) (Cytochrome c oxidase subunit VI ...	0.31	-	nuc	0					88
Q9NRR1 UniProt NPD GO	CYTL1_HUMAN	Cytokine-like protein 1 precursor (Protein C17)	0.31	-	mit	0	Secreted protein	extracellular space [TAS] soluble fraction [TAS]	607930		136
P69850 UniProt NPD GO	DAD3_YEAST	DASH complex subunit DAD3 (Outer kinetochore protein DAD3) (DUO1 and DAM1-interacting protein 3)	0.31	-	nuc	0	Nucleus. Associates with the mitotic spindle and the kinetochore	DASH complex [IDA] kinetochore [IDA] spindle [IDA]			94
Q6EI06 UniProt NPD GO	GAIP_CUCMA	DELLA protein GAIP (Gibberellic acid-insensitive phloem protein) (GAIP) (CmGAIP)	0.31	-	cyt	0	Nucleus (By similarity)				579
P42656 UniProt NPD GO	RAD24_SCHPO	DNA damage checkpoint protein rad24	0.31	-	nuc	0		cytoplasm [IDA]			270
P43248 UniProt NPD GO	MSH2_DROME	DNA mismatch repair protein spellchecker 1	0.31	-	cyt	0		nucleus [NAS]			917
Q5ZKQ6 UniProt NPD GO	DPOE2_CHICK	DNA polymerase epsilon subunit 2 (EC 2.7.7.7) (DNA polymerase II subunit 2) (DNA polymerase epsilon ...	0.31	-	cyt	0	Nucleus (By similarity)				527
P56282 UniProt NPD GO	DPOE2_HUMAN	DNA polymerase epsilon subunit 2 (EC 2.7.7.7) (DNA polymerase II subunit 2) (DNA polymerase epsilon ...	0.31	-	mit	0	Nucleus		602670		527
Q43704 UniProt NPD GO	MCM3_MAIZE	DNA replication licensing factor MCM3 homolog (Replication origin activator) (ROA protein) (Fragment ...	0.31	-	cyt	0	Nucleus (Probable)				600
P20028 UniProt NPD GO	RPA2_DROME	DNA-directed RNA polymerase I 135 kDa polypeptide (EC 2.7.7.6) (RNA polymerase I subunit 2)	0.31	-	cyt	0	Nucleus				1129
O74635 UniProt NPD GO	RPB9_SCHPO	DNA-directed RNA polymerase II subunit 9 (EC 2.7.7.6) (DNA-directed RNA polymerase II 13.2 kDa polyp ...	0.31	-	nuc	0	Nucleus	DNA-directed RNA polymerase II, holoenzyme [TAS]			113
Q9NW08 UniProt NPD GO	RPC2_HUMAN	DNA-directed RNA polymerase III subunit 127.6 kDa polypeptide (EC 2.7.7.6) (RNA polymerase III subun ...	0.31	-	cyt	0	Nucleus				1133
P59470 UniProt NPD GO	RPC2_MOUSE	DNA-directed RNA polymerase III subunit 127.6 kDa polypeptide (EC 2.7.7.6) (RNA polymerase III subun ...	0.31	-	cyt	0	Nucleus (By similarity)				1133
Q85FU3 UniProt NPD GO	RPOA_CYAME	DNA-directed RNA polymerase alpha chain (EC 2.7.7.6) (PEP) (Plastid-encoded RNA polymerase subunit a ...	0.31	-	mit	0	Plastid; chloroplast				316
Q8SL90 UniProt NPD GO	RPOA_EUGMY	DNA-directed RNA polymerase alpha chain (EC 2.7.7.6) (PEP) (Plastid-encoded RNA polymerase subunit a ...	0.31	-	nuc	0	Plastid; chloroplast				207
Q33C00 UniProt NPD GO	RPOA_NICTO	DNA-directed RNA polymerase alpha chain (EC 2.7.7.6) (PEP) (Plastid-encoded RNA polymerase subunit a ...	0.31	-	mit	0	Plastid; chloroplast				337
Q5KHV1 UniProt NPD GO	DCN1_CRYNE	Defective in cullin neddylation protein 1	0.31	-	cyt	0					279
P17533 UniProt NPD GO	DFRC_MOUSE	Defensin-related sequence cryptdin peptide precursor (Cryptdin-related protein 1C) (CRS1C)	0.31	-	exc	0	Secreted protein				116
Q00742 UniProt NPD GO	DHR15_WHEAT	Dehydrin Rab15	0.31	-	nuc	0					149
Q9SID2 UniProt NPD GO	ADS2_ARATH	Delta-9 acyl-lipid desaturase 2 (EC 1.14.19.-)	0.31	+	cyt	4 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (By similarity)				307
P97677 UniProt NPD GO	DLL1_RAT	Delta-like protein 1 precursor (Drosophila Delta homolog 1) (Delta1)	0.31	-	end	1 *	Membrane; single-pass type I membrane protein	extracellular region [ISS] integral to plasma membrane [ISS]			714
Q9NYJ7 UniProt NPD GO	DLL3_HUMAN	Delta-like protein 3 precursor (Drosophila Delta homolog 3)	0.31	-	exc	1	Membrane; single-pass type I membrane protein (Probable)	integral to membrane [NAS]	602768		618
Q6DH65 UniProt NPD GO	DENR_BRARE	Density-regulated protein (DRP)	0.31	+	cyt	0					208
Q75BY0 UniProt NPD GO	DGA1_ASHGO	Diacylglycerol O-acyltransferase 1 (EC 2.3.1.20)	0.31	-	nuc	1	Endoplasmic reticulum; endoplasmic reticulum membrane; single-pass membrane protein (By similarity). ...				461
Q8MK44 UniProt NPD GO	DGAT1_BOVIN	Diacylglycerol O-acyltransferase 1 (EC 2.3.1.20) (Diglyceride acyltransferase)	0.31	-	end	8	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein				489
Q9Z2A7 UniProt NPD GO	DGAT1_MOUSE	Diacylglycerol O-acyltransferase 1 (EC 2.3.1.20) (Diglyceride acyltransferase)	0.31	-	end	8	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein	membrane fraction [IDA]			498
P54290 UniProt NPD GO	CAC2D_RAT	Dihydropyridine-sensitive L-type calcium channel subunits alpha-2/delta precursor [Contains: L-type ...	0.31	-	cyt	0	Membrane; multi-pass membrane protein	voltage-gated calcium channel complex [IMP]			1091
Q91ZV3 UniProt NPD GO	DCBD2_MOUSE	Discoidin, CUB and LCCL domain-containing protein 2 precursor (Endothelial and smooth muscle cell-de ...	0.31	-	nuc	1	Membrane; single-pass type I membrane protein (By similarity)	cell surface [ISS] integral to plasma membrane [ISS]			769
Q969H9 UniProt NPD GO	DIRC1_HUMAN	Disrupted in renal cancer protein	0.31	-	nuc	0			606423		104
P35191 UniProt NPD GO	MDJ1_YEAST	DnaJ homolog 1, mitochondrial precursor	0.31	-	mit	0	Mitochondrion	mitochondrial inner membrane [IDA]			511
Q3TDQ1 UniProt NPD GO	STT3B_MOUSE	Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit STT3B (EC 2.4.1.119) (Oligosa ...	0.31	+	end	10	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein	oligosaccharyl transferase complex [ISS]			823
Q9DBB1 UniProt NPD GO	DUS6_MOUSE	Dual specificity protein phosphatase 6 (EC 3.1.3.48) (EC 3.1.3.16) (Mitogen-activated protein kinase ...	0.31	-	nuc	0	Cytoplasm (By similarity)				381
Q08274 UniProt NPD GO	DMWD_MOUSE	Dystrophia myotonica WD repeat-containing protein (Dystrophia myotonica-containing WD repeat motif p ...	0.31	-	nuc	0					650
P27113 UniProt NPD GO	LYAM2_RABIT	E-selectin precursor (Endothelial leukocyte adhesion molecule 1) (ELAM-1) (Leukocyte-endothelial cel ...	0.31	-	exc	1	Membrane; single-pass type I membrane protein				551
Q4PIR3 UniProt NPD GO	NSE2_SCHPO	E3 SUMO--protein ligase nse2 (EC 6.-.-.-) (Non-structural maintenance of chromosome element 2) (Non- ...	0.31	-	nuc	0	Nucleus	nucleus [IDA] Smc5-Smc6 complex [IDA]			250
Q6Q0C0 UniProt NPD GO	TRAF7_HUMAN	E3 ubiquitin protein ligase TRAF7 (EC 6.3.2.-) (TNF receptor-associated factor 7) (RING finger and W ...	0.31	-	nuc	0	Cytoplasmic vesicle. Colocalizes with MAP3K3 to vesicle-like structures throughout the cytoplasm	ubiquitin ligase complex [IDA]	606692		670
Q9WVJ9 UniProt NPD GO	FBLN4_MOUSE	EGF-containing fibulin-like extracellular matrix protein 2 precursor (Fibulin-4) (FIBL-4) (Mutant p5 ...	0.31	-	exc	0	Secreted protein	extracellular matrix (sensu Metazoa) [TAS]			443
Q9QXT5 UniProt NPD GO	EGFL7_MOUSE	EGF-like domain-containing protein 7 precursor (Multiple EGF-like domain protein 7) (Multiple epider ...	0.31	-	nuc	0	Secreted protein	extracellular region [IDA] extracellular space [IDA]			275

You are viewing entries 39351 to 39400 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.