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
P53068 UniProt NPD GO	APC10_YEAST	Anaphase-promoting complex subunit DOC1 (Destruction of cyclin B protein 1)	0.15	-	cyt	0	Cytoplasm. Nucleus	anaphase-promoting complex [TAS] mitochondrion [IDA]		1GQP	250
P10152 UniProt NPD GO	ANG1_BOVIN	Angiogenin-1 precursor (EC 3.1.27.-)	0.15	-	exc	1 *	Secreted protein	basal lamina [ISS] extracellular space [IDA] nucleolus [ISS] nucleus [ISS]		1GIO	148
P11859 UniProt NPD GO	ANGT_MOUSE	Angiotensinogen precursor [Contains: Angiotensin-1 (Angiotensin I) (Ang I); Angiotensin-2 (Angiotens ...	0.15	-	exc	0	Secreted protein	extracellular space [IDA]			477
Q27701 UniProt NPD GO	NANL_MACDE	Anhydrosialidase precursor (EC 4.2.2.15) (Sialidase L) (Anhydroneuraminidase)	0.15	-	mit	0	Secreted protein; extracellular space			4SLI	762
Q505D1 UniProt NPD GO	ANR28_MOUSE	Ankyrin repeat domain-containing protein 28	0.15	-	cyt	0					1053
Q7Z3H0 UniProt NPD GO	ANR33_HUMAN	Ankyrin repeat domain-containing protein 33	0.15	-	cyt	0					272
P83300 UniProt NPD GO	ACAL_ANSAN	Ansocalcin	0.15	-	cyt	0	Eggshell matrix. May be present in the shell glands on the walls of oviduct and incorporated into th ...				132
Q40285 UniProt NPD GO	UFOG2_MANES	Anthocyanidin 3-O-glucosyltransferase (EC 2.4.1.115) (Flavonol 3-O-glucosyltransferase 2) (UDP-gluco ...	0.15	-	cyt	1 *					346
Q40288 UniProt NPD GO	UFOG6_MANES	Anthocyanidin 3-O-glucosyltransferase (EC 2.4.1.115) (Flavonol 3-O-glucosyltransferase 6) (UDP-gluco ...	0.15	-	cyt	1					394
O24645 UniProt NPD GO	HCBT1_DIACA	Anthranilate N-benzoyltransferase protein 1 (EC 2.3.1.144) (Anthranilate N-hydroxycinnamoyl/benzoylt ...	0.15	-	cyt	0					445
Q02166 UniProt NPD GO	TRPD_ARATH	Anthranilate phosphoribosyltransferase, chloroplast precursor (EC 2.4.2.18)	0.15	-	cyt	0	Plastid; chloroplast (Probable)				444
P20409 UniProt NPD GO	TRPG_PHYBL	Anthranilate synthase component 2 (EC 4.1.3.27) (Anthranilate synthase component II) [Includes: Glut ...	0.15	-	nuc	0					765
P81464 UniProt NPD GO	APID_BOMPA	Apidaecin	0.15	-		0	Secreted protein				17
P48123 UniProt NPD GO	CYF_CYAPA	Apocytochrome f precursor	0.15	-	end	2 *	Plastid; cyanelle; cyanelle thylakoid membrane; single-pass membrane protein (By similarity)				321
Q6B8T0 UniProt NPD GO	CYF_GRATL	Apocytochrome f precursor	0.15	-	mit	2 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				310
Q68RZ3 UniProt NPD GO	CYF_PANGI	Apocytochrome f precursor	0.15	-	cyt	1	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				320
P00155 UniProt NPD GO	CYF_PEA	Apocytochrome f precursor	0.15	-	cyt	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				320
P06449 UniProt NPD GO	CYF_TOBAC	Apocytochrome f precursor	0.15	-	cyt	1	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				320
P12279 UniProt NPD GO	APOC3_CANFA	Apolipoprotein C-III precursor (Apo-CIII) (ApoC-III)	0.15	-	exc	0	Secreted protein				100
Q9HD36 UniProt NPD GO	B2L10_HUMAN	Apoptosis regulator Bcl-B (Bcl-2-like 10 protein) (Bcl2-L-10) (Anti-apoptotic protein NrH)	0.15	-	cyt	1	Mitochondrion. Nucleus; nuclear membrane	membrane fraction [TAS]	606910		194
Q4VK78 UniProt NPD GO	ARGI2_RABIT	Arginase-2, mitochondrial precursor (EC 3.5.3.1) (Arginase II)	0.15	-	mit	0	Mitochondrion				354
O88533 UniProt NPD GO	DDC_MOUSE	Aromatic-L-amino-acid decarboxylase (EC 4.1.1.28) (AADC) (DOPA decarboxylase) (DDC)	0.15	-	cyt	0					480
Q9D668 UniProt NPD GO	ARRD2_MOUSE	Arrestin domain-containing protein 2	0.15	-	mit	0					407
Q924K1 UniProt NPD GO	AIPL1_MOUSE	Aryl-hydrocarbon-interacting protein-like 1	0.15	-	cyt	0	Cytoplasm (By similarity). Nucleus (By similarity)	photoreceptor inner segment [IDA]			328
P50297 UniProt NPD GO	ARY1_RAT	Arylamine N-acetyltransferase 1 (EC 2.3.1.5) (Arylamide acetylase 1) (N-acetyltransferase type 1) (N ...	0.15	-	cyt	0	Cytoplasm				290
Q01802 UniProt NPD GO	AATM_YEAST	Aspartate aminotransferase, mitochondrial precursor (EC 2.6.1.1) (Transaminase A)	0.15	-	mit	0	Mitochondrion; mitochondrial matrix	mitochondrion [IDA]			451
P15287 UniProt NPD GO	AGSA_APLCA	Atrial gland-specific antigen precursor (AGSA) (Mollusk-derived growth factor) (MDGF)	0.15	-	exc	1 *	Dense core vesicles (DCV)				525
Q5K9X6 UniProt NPD GO	ATG3_CRYNE	Autophagy-related protein 3 (Autophagy-related E2-like conjugation enzyme ATG3)	0.15	-	nuc	0	Cytoplasm (By similarity)				385
O43035 UniProt NPD GO	ATG3_SCHPO	Autophagy-related protein 3 (Autophagy-related E2-like conjugation enzyme atg3)	0.15	-	cyt	0	Cytoplasm (By similarity)				275
Q6BGV9 UniProt NPD GO	ATG7_DEBHA	Autophagy-related protein 7 (Autophagy-related E1-like-activating enzyme ATG7)	0.15	-	cyt	0	Cytoplasm (By similarity)				652
Q05349 UniProt NPD GO	12KD_FRAAN	Auxin-repressed 12.5 kDa protein	0.15	-	nuc	0					111
Q95KQ6 UniProt NPD GO	BCL9_PIG	B-cell lymphoma 9 protein (Bcl-9) (Fragment)	0.15	-	nuc	0	Nucleus (By similarity)				130
Q8N3I7 UniProt NPD GO	BBS5_HUMAN	Bardet-Biedl syndrome 5 protein	0.15	-	cyt	0	Localizes to basal bodies (By similarity)		603650		341
Q9TT96 UniProt NPD GO	ADRB1_BOVIN	Beta-1 adrenergic receptor (Beta-1 adrenoceptor) (Beta-1 adrenoreceptor)	0.15	-	end	7	Cell membrane; multi-pass membrane protein (By similarity). Localized at the plasma membrane. Found ...				467
Q28998 UniProt NPD GO	ADRB1_PIG	Beta-1 adrenergic receptor (Beta-1 adrenoceptor) (Beta-1 adrenoreceptor)	0.15	-	end	7	Cell membrane; multi-pass membrane protein (By similarity). Localized at the plasma membrane. Found ...				468
O96024 UniProt NPD GO	B3GT4_HUMAN	Beta-1,3-galactosyltransferase 4 (EC 2.4.1.62) (Beta-1,3-GalTase 4) (Beta3Gal-T4) (b3Gal-T4) (Gangli ...	0.15	-	exc	1 *	Golgi apparatus; Golgi membrane; single-pass type II membrane protein		603095		378
Q9N491 UniProt NPD GO	SQV2_CAEEL	Beta-1,3-galactosyltransferase sqv-2 (EC 2.4.1.134) (Squashed vulva protein 2)	0.15	-	mit	1 *	Golgi apparatus; Golgi membrane; single-pass type II membrane protein (By similarity)				330
O88419 UniProt NPD GO	B4GT6_RAT	Beta-1,4-galactosyltransferase 6 (EC 2.4.1.-) (Beta-1,4-GalTase 6) (Beta4Gal-T6) (b4Gal-T6) (UDP-gal ...	0.15	-	mit	1 *	Golgi apparatus; Golgi stack; Golgi stack membrane; single-pass type II membrane protein (By similar ...				382
P56386 UniProt NPD GO	BD01_MOUSE	Beta-defensin 1 precursor (Defensin, beta 1) (BD-1) (mBD-1)	0.15	-	exc	1 *	Secreted protein (By similarity)				69
Q8NET1 UniProt NPD GO	D108B_HUMAN	Beta-defensin 108B precursor (Defensin, beta 108B) (Defensin, beta 108) (Beta-defensin 8) (DEFB-8) ( ...	0.15	-	mit	0	Secreted protein				73
Q30KL6 UniProt NPD GO	DB111_PANTR	Beta-defensin 111 precursor (Defensin, beta 111)	0.15	-	mit	0	Secreted protein (By similarity)				67
P35699 UniProt NPD GO	ELIB_PHYME	Beta-elicitin MGM-beta	0.15	-	nuc	0	Secreted protein				98
P15569 UniProt NPD GO	ELIB_PHYCI	Beta-elicitin cinnamomin	0.15	-	nuc	0	Secreted protein			2AIB	98
Q641X3 UniProt NPD GO	HEXA_RAT	Beta-hexosaminidase alpha chain precursor (EC 3.2.1.52) (N-acetyl-beta-glucosaminidase) (Beta-N-acet ...	0.15	-	vac	1 *	Lysosome (By similarity)				528
P29127 UniProt NPD GO	XYNA_NEOPA	Bifunctional endo-1,4-beta-xylanase A precursor (EC 3.2.1.8) (XYLA)	0.15	-	vac	0					607
P21810 UniProt NPD GO	PGS1_HUMAN	Biglycan precursor (Bone/cartilage proteoglycan I) (PG-S1)	0.15	-	exc	0	Secreted protein; extracellular space; extracellular matrix (By similarity)	extracellular matrix (sensu Metazoa) [NAS]	301870		368
P52842 UniProt NPD GO	ST2A1_MACFA	Bile salt sulfotransferase (EC 2.8.2.14) (Hydroxysteroid sulfotransferase) (HST)	0.15	-	cyt	0	Cytoplasm (By similarity)				284
P50747 UniProt NPD GO	BPL1_HUMAN	Biotin--protein ligase (EC 6.3.4.-) (Biotin apo-protein ligase) [Includes: Biotin--[methylmalonyl-Co ...	0.15	-	nuc	0	Cytoplasm. Mitochondrion		609018		726
P30424 UniProt NPD GO	BPP4_BOTIN	Bradykinin-potentiating peptide S4,1,2 (Angiotensin-converting enzyme inhibitor)	0.15	-		0					11
P56552 UniProt NPD GO	BRAZ_PENBA	Brazzein	0.15	-	nuc	0	Secreted protein			2BRZ	54

You are viewing entries 56651 to 56700 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.