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
Q41114 UniProt NPD GO	LEA2_PHAVU	Alpha-amylase inhibitor 2 precursor (Alpha-AI-2) (Alpha-AI2) (Lectin) [Contains: Alpha-amylase inhib ...	0.13	-	exc	0					240
O76265 UniProt NPD GO	AMYR_DROER	Alpha-amylase-related protein precursor (EC 3.2.1.1)	0.13	-	cyt	0	Secreted protein (Probable)				493
O77014 UniProt NPD GO	AMYR_DROMA	Alpha-amylase-related protein precursor (EC 3.2.1.1)	0.13	-	nuc	0	Secreted protein (Probable)				493
Q91642 UniProt NPD GO	PEPE_XENLA	Alpha-aspartyl dipeptidase (EC 3.4.13.21) (Asp-specific dipeptidase) (Dipeptidase E)	0.13	-	cyt	0	Cytoplasm (By similarity)				242
P50983 UniProt NPD GO	CXA1_CONIM	Alpha-conotoxin ImI precursor (Alpha-CTx ImI) (Fragment)	0.13	-		0	Secreted protein			2C9T	17
P14749 UniProt NPD GO	AGAL_CYATE	Alpha-galactosidase precursor (EC 3.2.1.22) (Melibiase) (Alpha-D-galactoside galactohydrolase)	0.13	-	end	1 *					411
Q9CY02 UniProt NPD GO	AHSP_MOUSE	Alpha-hemoglobin-stabilizing protein (Erythroid-associated factor) (Erythroid differentiation-relate ...	0.13	-	cyt	0	Cytoplasm	cytoplasm [IDA] hemoglobin complex [ISS]			102
Q16586 UniProt NPD GO	SGCA_HUMAN	Alpha-sarcoglycan precursor (Alpha-SG) (Adhalin) (50 kDa dystrophin-associated glycoprotein) (50DAG) ...	0.13	-	nuc	1	Sarcolemma; sarcolemmal membrane; single-pass type I membrane protein (By similarity)	dystrophin-associated glycoprotein complex [TAS]	608099		387
P04046 UniProt NPD GO	PUR1_YEAST	Amidophosphoribosyltransferase (EC 2.4.2.14) (Glutamine phosphoribosylpyrophosphate amidotransferase ...	0.13	-	cyt	0		cytoplasm [IDA]			510
O18851 UniProt NPD GO	AOFA_SHEEP	Amine oxidase [flavin-containing] A (EC 1.4.3.4) (Monoamine oxidase type A) (MAO-A) (Fragment)	0.13	-	nuc	0	Mitochondrion; mitochondrial outer membrane				46
O09175 UniProt NPD GO	AMPB_RAT	Aminopeptidase B (EC 3.4.11.6) (Ap-B) (Arginyl aminopeptidase) (Arginine aminopeptidase) (Cytosol am ...	0.13	-	cyt	0	Secreted protein	extracellular region [IDA] Golgi apparatus [NAS] plasma membrane [IDA]			650
P47797 UniProt NPD GO	VSP2_AGKRH	Ancrod precursor (EC 3.4.21.74) (Venombin A) (Protein C activator) (ACC-C)	0.13	-	exc	0	Secreted protein				258
Q3TPE9 UniProt NPD GO	ANKY2_MOUSE	Ankyrin repeat and MYND domain-containing protein 2	0.13	-	nuc	0					440
Q9WV74 UniProt NPD GO	ASB1_MOUSE	Ankyrin repeat and SOCS box protein 1 (ASB-1)	0.13	-	cyt	0					336
O88312 UniProt NPD GO	AGR2_MOUSE	Anterior gradient protein 2 homolog precursor (Secreted cement gland protein XAG-2 homolog) (AG-2 pr ...	0.13	-	exc	0	Secreted protein (Probable)				175
Q40287 UniProt NPD GO	UFOG5_MANES	Anthocyanidin 3-O-glucosyltransferase (EC 2.4.1.115) (Flavonol 3-O-glucosyltransferase 5) (UDP-gluco ...	0.13	-	cyt	0					487
P27710 UniProt NPD GO	TRPG_CRYNV	Anthranilate synthase component 2 (EC 4.1.3.27) (Anthranilate synthase component II) [Includes: Glut ...	0.13	-	mit	0					752
P22298 UniProt NPD GO	ALK1_PIG	Antileukoproteinase	0.13	-	nuc	0					115
P41361 UniProt NPD GO	ANT3_BOVIN	Antithrombin-III precursor (ATIII)	0.13	-	exc	0	Secreted protein; extracellular space			1ATT	465
P04658 UniProt NPD GO	CYF_OENHO	Apocytochrome f precursor	0.13	-	nuc	1	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				318
P41619 UniProt NPD GO	CYF_PINTH	Apocytochrome f precursor	0.13	-	cyt	2 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				319
Q8GZR2 UniProt NPD GO	CYF_EUGGR	Apocytochrome f, chloroplast precursor	0.13	-	mit	2 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein	chloroplast [IDA]			496
P81471 UniProt NPD GO	APL3_DIAGR	Apolipophorin-3 (Apolipophorin-III) (ApoLp-III) (Fragment)	0.13	-	nuc	0	Secreted protein (By similarity)				32
P81644 UniProt NPD GO	APOA2_BOVIN	Apolipoprotein A-II precursor (Apo-AII) (ApoA-II) (Antimicrobial peptide BAMP-1) [Contains: Apolipop ...	0.13	-	vac	0	Secreted protein				100
P19035 UniProt NPD GO	APOC3_BOVIN	Apolipoprotein C-III precursor (Apo-CIII) (ApoC-III)	0.13	-	exc	0	Secreted protein				96
O15304 UniProt NPD GO	SIVA_HUMAN	Apoptosis regulatory protein Siva (CD27-binding protein) (CD27BP)	0.13	-	cyt	0	Cytoplasm	integral to plasma membrane [NAS]	605567		175
Q8HXK9 UniProt NPD GO	ASC_BOVIN	Apoptosis-associated speck-like protein containing a CARD (PYD and CARD domain-containing protein)	0.13	-	cyt	0	Cytoplasm (By similarity). Upstream of caspase activation, a redistribution from the cytoplasm to th ...				195
O62735 UniProt NPD GO	AQP2_SHEEP	Aquaporin-2 (AQP-2) (Aquaporin-CD) (AQP-CD) (Water channel protein for renal collecting duct) (ADH w ...	0.13	-	end	6 *	Cell membrane; apical cell membrane; multi-pass membrane protein (By similarity). Cytoplasmic vesicl ...				271
P51545 UniProt NPD GO	KARG_PENJP	Arginine kinase (EC 2.7.3.3) (AK)	0.13	-	cyt	0					355
P91798 UniProt NPD GO	KARG_SCHAM	Arginine kinase (EC 2.7.3.3) (AK)	0.13	-	nuc	0					356
P36577 UniProt NPD GO	ARRD_RAT	Arrestin-D (Fragment)	0.13	-	nuc	0					71
P84748 UniProt NPD GO	PEP16_ARGAU	Astacin-like peptidase p16 (EC 3.4.24.-) (Fragments)	0.13	-	cyt	0					103
Q95NH6 UniProt NPD GO	ATTC_DROME	Attacin-C precursor [Contains: Immune-induced peptide 16 (DIM-16) (MPAC)]	0.13	-	exc	1 *	Secreted protein	extracellular region [IDA]			241
Q5R7W1 UniProt NPD GO	ATG12_PONPY	Autophagy-related protein 12 (APG12-like)	0.13	-	cyt	0	Cytoplasm (By similarity)	cytoplasm [ISS]			140
P13089 UniProt NPD GO	AUX28_SOYBN	Auxin-induced protein AUX28	0.13	-	nuc	0	Nucleus (By similarity)				243
P11912 UniProt NPD GO	CD79A_HUMAN	B-cell antigen receptor complex-associated protein alpha-chain precursor (Ig-alpha) (MB-1 membrane g ...	0.13	-	end	2 *	Membrane; single-pass type I membrane protein		112205		226
P27198 UniProt NPD GO	PHEB_RHOS2	B-phycoerythrin beta chain	0.13	-	nuc	0	Plastid; chloroplast; chloroplast thylakoid lumen			1XG0	177
Q14681 UniProt NPD GO	KCTD2_HUMAN	BTB/POZ domain-containing protein KCTD2	0.13	-	cyt	0					263
Q9NXV2 UniProt NPD GO	KCTD5_HUMAN	BTB/POZ domain-containing protein KCTD5	0.13	-	cyt	0					234
Q8VC57 UniProt NPD GO	KCTD5_MOUSE	BTB/POZ domain-containing protein KCTD5	0.13	-	cyt	0					234
Q7ZWB7 UniProt NPD GO	BBS5_BRARE	Bardet-Biedl syndrome 5 protein homolog	0.13	-	cyt	0					342
Q9FRV0 UniProt NPD GO	CHIC_SECCE	Basic endochitinase C precursor (EC 3.2.1.14) (Rye seed chitinase-c) (RSC-c)	0.13	-	mit	1 *		extracellular region [IC]			266
O08734 UniProt NPD GO	BAK_MOUSE	Bcl-2 homologous antagonist/killer (Apoptosis regulator BAK)	0.13	-	cyt	3	Membrane; single-pass membrane protein (Potential)				208
P47195 UniProt NPD GO	C80A1_BERST	Berbamunine synthase (EC 1.14.21.3) (Cytochrome P450 80) (CYPLXXX) ((S)-N-methylcoclaurine oxidase [ ...	0.13	-	end	1 *	Endoplasmic reticulum; endoplasmic reticulum membrane; peripheral membrane protein				487
O01346 UniProt NPD GO	EGH_DROME	Beta 1,4-mannosyltransferase egh (EC 2.4.1.-) (Protein egghead) (Protein zeste-white-4)	0.13	-	end	5 *	Membrane; multi-pass membrane protein (Potential)	integral to membrane [NAS]			457
P53672 UniProt NPD GO	CRBA2_HUMAN	Beta crystallin A2 (Beta-A2-crystallin)	0.13	-	cyt	0			600836		196
P06504 UniProt NPD GO	CRBS_BOVIN	Beta crystallin S (Gamma crystallin S)	0.13	-	nuc	0				1A7H	177
P79949 UniProt NPD GO	RFNG_XENLA	Beta-1,3-N-acetylglucosaminyltransferase radical fringe (EC 2.4.1.222) (O-fucosylpeptide 3-beta-N-ac ...	0.13	-	exc	1 *	Golgi apparatus; Golgi membrane; single-pass type II membrane protein (Potential)				340
Q5TJE8 UniProt NPD GO	B3GT4_CANFA	Beta-1,3-galactosyltransferase 4 (EC 2.4.1.62) (Beta-1,3-GalTase 4) (Beta3Gal-T4) (b3Gal-T4) (Gangli ...	0.13	-	exc	1 *	Golgi apparatus; Golgi membrane; single-pass type II membrane protein (By similarity)				383
Q09323 UniProt NPD GO	BAGT_LYMST	Beta-N-acetyl-D-glucosaminide beta-1,4-N-acetylglucosaminyl-transferase (EC 2.4.1.-) (UDP-GlcNAc:Glc ...	0.13	-	gol	1 *	Golgi apparatus; Golgi membrane; single-pass type II membrane protein				490

You are viewing entries 59401 to 59450 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.