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
P58806 UniProt NPD GO	CXKR_CONRA	Conantokin-R precursor (Con-R)	0.18	-	nuc	1 *	Secreted protein				107
P49347 UniProt NPD GO	CONB_CANEN	Concanavalin B precursor (Con B)	0.18	-	end	1 *				1CNV	324
P10713 UniProt NPD GO	CON10_NEUCR	Conidiation-specific protein 10	0.18	-	nuc	0					86
P16925 UniProt NPD GO	CNJC_TETTH	Conjugation stage-specific protein	0.18	-	cyt	0	Nucleus				310
P0C1N8 UniProt NPD GO	CXM3B_CONTE	Conotoxin tx3b precursor (Conotoxin Tx3.3)	0.18	-	exc	0	Secreted protein				68
Q02246 UniProt NPD GO	CNTN2_HUMAN	Contactin-2 precursor (Axonin-1) (Axonal glycoprotein TAG-1) (Transient axonal glycoprotein 1) (TAX- ...	0.18	-	exc	0	Cell membrane; lipid-anchor; GPI-anchor. Attached to the neuronal membrane by a GPI-anchor and is al ...	integral to plasma membrane [TAS] plasma membrane [TAS]	190197		1040
Q90W79 UniProt NPD GO	CNTN5_CHICK	Contactin-5 precursor (F11 axonin-1-related protein 2) (FAR-2)	0.18	-	end	0	Cell membrane; lipid-anchor; GPI-anchor (By similarity)				1027
P78357 UniProt NPD GO	CNTP1_HUMAN	Contactin-associated protein 1 precursor (Caspr) (Caspr1) (Neurexin 4) (Neurexin IV) (p190)	0.18	-	end	1	Membrane; single-pass type I membrane protein (Potential)	integral to plasma membrane [TAS]	602346		1384
Q04656 UniProt NPD GO	ATP7A_HUMAN	Copper-transporting ATPase 1 (EC 3.6.3.4) (Copper pump 1) (Menkes disease-associated protein)	0.18	-	end	7	Golgi apparatus; trans-Golgi network; trans-Golgi network membrane; multi-pass membrane protein Cell ...	Golgi apparatus [TAS] integral to plasma membrane [TAS] trans-Golgi network transport vesicle [IMP]	300011	2AW0	1500
Q42840 UniProt NPD GO	HEM6_HORVU	Coproporphyrinogen III oxidase, chloroplast precursor (EC 1.3.3.3) (Coproporphyrinogenase) (Coprogen ...	0.18	-	mit	0	Plastid; chloroplast (Probable)				391
P31146 UniProt NPD GO	COR1A_HUMAN	Coronin-1A (Coronin-like protein p57) (Coronin-like protein A) (CLIPINA) (Tryptophan aspartate-conta ...	0.18	-	nuc	0	In non-infected macrophages, associated with the cortical microtubule network; in mycobacteria-infec ...	actin cytoskeleton [TAS] lysosomal membrane [TAS]	605000		460
Q9ULV4 UniProt NPD GO	COR1C_HUMAN	Coronin-1C (Coronin-3) (hCRNN4)	0.18	-	nuc	0		actin cytoskeleton [TAS]	605269		474
O77667 UniProt NPD GO	DHI2_BOVIN	Corticosteroid 11-beta-dehydrogenase isozyme 2 (EC 1.1.1.-) (11-DH2) (11-beta-hydroxysteroid dehydro ...	0.18	-	nuc	0	Microsome				404
P51976 UniProt NPD GO	DHI2_RABIT	Corticosteroid 11-beta-dehydrogenase isozyme 2 (EC 1.1.1.-) (11-DH2) (11-beta-hydroxysteroid dehydro ...	0.18	-	mit	0	Microsome				406
P35347 UniProt NPD GO	CRFR1_MOUSE	Corticotropin-releasing factor receptor 1 precursor (CRF-R) (CRF1) (Corticotropin-releasing hormone ...	0.18	-	end	7	Membrane; multi-pass membrane protein				415
P24388 UniProt NPD GO	CRHBP_RAT	Corticotropin-releasing factor-binding protein precursor (CRF-binding protein) (CRF-BP) (Corticotrop ...	0.18	-	mit	0		extracellular space [IDA]			322
O13547 UniProt NPD GO	CCW14_YEAST	Covalently-linked cell wall protein 14 precursor (Inner cell wall protein)	0.18	-	exc	0	Cell membrane; lipid-anchor; GPI-anchor	cell wall (sensu Fungi) [IDA] mitochondrion [IDA]			238
O77814 UniProt NPD GO	KCRS_RABIT	Creatine kinase, sarcomeric mitochondrial precursor (EC 2.7.3.2) (S-MtCK) (Mib-CK) (Basic-type mitoc ...	0.18	-	mit	0	Mitochondrion; mitochondrial inner membrane; intermembrane side (By similarity)				419
P83908 UniProt NPD GO	CRU1_SINAL	Cruciferin (11S globulin) (12S storage protein) (Allergen Sin a 2) [Contains: Cruciferin alpha chain ...	0.18	-	nuc	0					56
P16252 UniProt NPD GO	CUC2C_HAECO	Cuticle collagen 2C (Fragment)	0.18	-	nuc	0					210
P78396 UniProt NPD GO	CCNA1_HUMAN	Cyclin-A1	0.18	-	cyt	0		cytosol [TAS]	604036		465
Q8VIH7 UniProt NPD GO	CYYR1_MOUSE	Cysteine and tyrosine-rich protein 1 precursor (Proline-rich domain-containing protein)	0.18	-	nuc	1	Membrane; single-pass type I membrane protein (Potential)	integral to membrane [NAS]			165
Q6DG88 UniProt NPD GO	ATG4B_BRARE	Cysteine protease ATG4B (EC 3.4.22.-) (Autophagy-related protein 4 homolog B)	0.18	-	cyt	0	Cytoplasm (Probable)				394
Q40143 UniProt NPD GO	CYSP3_LYCES	Cysteine proteinase 3 precursor (EC 3.4.22.-)	0.18	-	exc	1 *	Vacuole (Probable)				356
Q43725 UniProt NPD GO	CYSKM_ARATH	Cysteine synthase, mitochondrial precursor (EC 2.5.1.47) (O-acetylserine sulfhydrylase) (O-acetylser ...	0.18	-	mit	0	Mitochondrion				430
Q95M61 UniProt NPD GO	CP19A_CALJA	Cytochrome P450 19A1 (EC 1.14.14.1) (Aromatase) (CYPXIX) (Estrogen synthetase) (P-450AROM)	0.18	+	mit	0	Membrane; peripheral membrane protein				503
P28649 UniProt NPD GO	CP19A_MOUSE	Cytochrome P450 19A1 (EC 1.14.14.1) (Aromatase) (CYPXIX) (Estrogen synthetase) (P-450AROM)	0.18	-	cyt	0	Membrane; peripheral membrane protein				503
P05176 UniProt NPD GO	CP1A1_RABIT	Cytochrome P450 1A1 (EC 1.14.14.1) (CYPIA1) (P450 isozyme 6) (P-450 PHPAH1) (P450 LM6)	0.18	-	nuc	1 *	Endoplasmic reticulum; endoplasmic reticulum membrane; peripheral membrane protein				518
Q64583 UniProt NPD GO	CP2BF_RAT	Cytochrome P450 2B15 (EC 1.14.14.1) (CYPIIB15)	0.18	-	nuc	0	Endoplasmic reticulum; endoplasmic reticulum membrane; peripheral membrane protein (By similarity)				495
P08683 UniProt NPD GO	CP2CB_RAT	Cytochrome P450 2C11 (EC 1.14.14.1) (CYPIIC11) (P-450(M-1)) (P450H) (P450-UT-A) (UT-2)	0.18	-	end	0	Endoplasmic reticulum; endoplasmic reticulum membrane; peripheral membrane protein				500
P17666 UniProt NPD GO	CP2CE_RABIT	Cytochrome P450 2C14 (EC 1.14.14.1) (CYPIIC14) (PHP3)	0.18	-	end	0	Endoplasmic reticulum; endoplasmic reticulum membrane; peripheral membrane protein				490
P10635 UniProt NPD GO	CP2D6_HUMAN	Cytochrome P450 2D6 (EC 1.14.14.1) (CYPIID6) (P450-DB1) (Debrisoquine 4-hydroxylase)	0.18	-	nuc	1 *	Endoplasmic reticulum; endoplasmic reticulum membrane; peripheral membrane protein		124030	2F9Q	497
P08682 UniProt NPD GO	CP2E1_RABIT	Cytochrome P450 2E1 (EC 1.14.14.1) (CYPIIE1) (Isozyme 3A) (P450-ALC)	0.18	-	nuc	1 *	Endoplasmic reticulum; endoplasmic reticulum membrane; peripheral membrane protein				493
P24461 UniProt NPD GO	CP2G1_RABIT	Cytochrome P450 2G1 (EC 1.14.14.1) (CYPIIG1) (P450-NMB) (Olfactive)	0.18	-	nuc	1 *	Endoplasmic reticulum; endoplasmic reticulum membrane; peripheral membrane protein				494
P10610 UniProt NPD GO	CP2G1_RAT	Cytochrome P450 2G1 (EC 1.14.14.1) (CYPIIG1) (P450-OLF1) (Olfactive)	0.18	-	mit	1 *	Endoplasmic reticulum; endoplasmic reticulum membrane; peripheral membrane protein				494
Q96SQ9 UniProt NPD GO	CP2S1_HUMAN	Cytochrome P450 2S1 (EC 1.14.14.1) (CYPIIS1)	0.18	-	nuc	2 *	Endoplasmic reticulum; endoplasmic reticulum membrane; peripheral membrane protein	endoplasmic reticulum [NAS]			504
Q9V3S0 UniProt NPD GO	CP4G1_DROME	Cytochrome P450 4g1 (EC 1.14.-.-) (CYPIVG1)	0.18	-	cyt	1 *	Endoplasmic reticulum; endoplasmic reticulum membrane; peripheral membrane protein (Potential)				556
Q9V769 UniProt NPD GO	C6A22_DROME	Cytochrome P450 6a22 (EC 1.14.-.-) (CYPVIA22)	0.18	-	nuc	0	Endoplasmic reticulum; endoplasmic reticulum membrane; peripheral membrane protein (Potential)				499
Q9STL2 UniProt NPD GO	C71AL_ARATH	Cytochrome P450 71A21 (EC 1.14.-.-)	0.18	-	vac	2 *					490
O65786 UniProt NPD GO	C71B4_ARATH	Cytochrome P450 71B4 (EC 1.14.-.-)	0.18	-	end	2 *					504
Q05047 UniProt NPD GO	C72A1_CATRO	Cytochrome P450 72A1 (EC 1.3.3.9) (CYPLXXII) (Secologanin synthase) (SLS)	0.18	-	nuc	1 *	Vacuole; vacuolar membrane (Probable). Tonoplast (Probable)				524
P37124 UniProt NPD GO	C77A2_SOLME	Cytochrome P450 77A2 (EC 1.14.-.-) (CYPLXXVIIA2) (P-450EG5)	0.18	-	end	2 *					511
Q43246 UniProt NPD GO	C88A1_MAIZE	Cytochrome P450 88A1 (EC 1.14.-.-) (Dwarf3 protein)	0.18	-	end	1 *					519
Q4JQH5 UniProt NPD GO	CYB_TETNG	Cytochrome b	0.18	-	end	8 *					380
Q61462 UniProt NPD GO	CY24A_MOUSE	Cytochrome b-245 light chain (p22 phagocyte B-cytochrome) (Neutrophil cytochrome b 22 kDa polypeptid ...	0.18	-	end	3 *		cytoplasm [IDA]			191
P19967 UniProt NPD GO	CYB5R_DROME	Cytochrome b5-related protein (Protein TU-36B)	0.18	-	end	4		mitochondrion [IDA]			436
Q9BBP4 UniProt NPD GO	CCSA_LOTJA	Cytochrome c biogenesis protein ccsA	0.18	-	end	8 *	Plastid; chloroplast				323
P46659 UniProt NPD GO	CCSA_MAIZE	Cytochrome c biogenesis protein ccsA	0.18	-	end	6 *	Plastid; chloroplast				321
Q6L3E1 UniProt NPD GO	CCSA_SACHY	Cytochrome c biogenesis protein ccsA	0.18	-	end	6 *	Plastid; chloroplast				321
Q6ENP8 UniProt NPD GO	CCSA_SACOF	Cytochrome c biogenesis protein ccsA	0.18	-	end	6 *	Plastid; chloroplast				321

You are viewing entries 52901 to 52950 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.