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
Q01753 UniProt NPD GO	STAD_SIMCH	Acyl-[acyl-carrier-protein] desaturase, chloroplast precursor (EC 1.14.19.2) (Stearoyl-ACP desaturas ...	0.10	-	mit	0	Plastid; chloroplast. In green tissue, found in chloroplasts. Plastid. In non-photosynthetic tissue, ...				398
Q9QYR7 UniProt NPD GO	ACOT3_MOUSE	Acyl-coenzyme A thioesterase 3 (EC 3.1.2.2) (Acyl-CoA thioesterase 3) (Peroxisomal acyl-coenzyme A t ...	0.10	-	pox	0	Peroxisome	peroxisome [TAS]			432
Q8N9L9 UniProt NPD GO	ACOT4_HUMAN	Acyl-coenzyme A thioesterase 4 (EC 3.1.2.2) (Acyl-CoA thioesterase 4) (Peroxisomal acyl coenzyme A t ...	0.10	-	cyt	0	Peroxisome (Potential)				421
Q56JW4 UniProt NPD GO	APT_BOVIN	Adenine phosphoribosyltransferase (EC 2.4.2.7) (APRT)	0.10	-	cyt	0	Cytoplasm (By similarity)				180
P36972 UniProt NPD GO	APT_RAT	Adenine phosphoribosyltransferase (EC 2.4.2.7) (APRT)	0.10	-	cyt	0	Cytoplasm				180
P50246 UniProt NPD GO	SAHH_MEDSA	Adenosylhomocysteinase (EC 3.3.1.1) (S-adenosyl-L-homocysteine hydrolase) (AdoHcyase)	0.10	-	cyt	0					485
P39069 UniProt NPD GO	KAD1_RAT	Adenylate kinase isoenzyme 1 (EC 2.7.4.3) (ATP-AMP transphosphorylase) (AK1) (Myokinase)	0.10	-	cyt	0	Cytoplasm				194
Q9WUR9 UniProt NPD GO	KAD4_MOUSE	Adenylate kinase isoenzyme 4, mitochondrial (EC 2.7.4.3) (Adenylate kinase 3-like 1) (ATP-AMP transp ...	0.10	-	cyt	0	Mitochondrion; mitochondrial matrix (Potential)	mitochondrion [IDA]			223
P54654 UniProt NPD GO	CAP_DICDI	Adenylyl cyclase-associated protein (CAP)	0.10	-	nuc	0	Cell membrane			1TJF	464
P15465 UniProt NPD GO	ALB1_PSOTE	Albumin-1 (WBA-1)	0.10	-	nuc	0				1WBA	175
P17516 UniProt NPD GO	AK1C4_HUMAN	Aldo-keto reductase family 1 member C4 (EC 1.1.1.-) (Chlordecone reductase) (EC 1.1.1.225) (CDR) (3- ...	0.10	-	cyt	0	Cytoplasm	cytoplasm [TAS]	600451	2FVL	323
P25335 UniProt NPD GO	ALLC_YEAST	Allantoicase (EC 3.5.3.4) (Allantoate amidinohydrolase)	0.10	-	cyt	0				1SG3	343
P40757 UniProt NPD GO	ALN_RANCA	Allantoinase, mitochondrial precursor (EC 3.5.2.5)	0.10	-	mit	0	Mitochondrion				484
P83563 UniProt NPD GO	ALL6_APIME	Allergen Api m 6	0.10	-	nuc	0	Secreted protein; extracellular space				71
Q9TLS7 UniProt NPD GO	PHAA_CYACA	Allophycocyanin alpha chain	0.10	-	cyt	0	Plastid; chloroplast				161
P07361 UniProt NPD GO	A1AG2_MOUSE	Alpha-1-acid glycoprotein 2 precursor (AGP 2) (Orosomucoid-2) (OMD 2)	0.10	-	exc	0	Secreted protein				207
Q00896 UniProt NPD GO	A1AT3_MOUSE	Alpha-1-antitrypsin 1-3 precursor (Serine protease inhibitor 1-3) (Alpha-1 protease inhibitor 3)	0.10	-	end	0	Secreted protein				413
O70159 UniProt NPD GO	FETUA_CAVPO	Alpha-2-HS-glycoprotein precursor (Fetuin-A)	0.10	-	exc	0	Secreted protein (By similarity)	extracellular space [ISS]			358
P55963 UniProt NPD GO	CXA4_CONPU	Alpha-A conotoxin PIVA	0.10	-	nuc	0	Secreted protein			1P1P	25
Q9QWR8 UniProt NPD GO	NAGAB_MOUSE	Alpha-N-acetylgalactosaminidase precursor (EC 3.2.1.49) (Alpha-galactosidase B)	0.10	-	cyt	0	Lysosome (By similarity)				415
P17859 UniProt NPD GO	AMYA_VIGMU	Alpha-amylase precursor (EC 3.2.1.1) (1,4-alpha-D-glucan glucanohydrolase)	0.10	-	exc	1 *					421
P01087 UniProt NPD GO	IAAT_ELECO	Alpha-amylase/trypsin inhibitor (RBI) (RATI)	0.10	-	cyt	0	Secreted protein			1TMQ	122
P56638 UniProt NPD GO	CXA1_CONEP	Alpha-conotoxin EpI	0.10	-		0	Secreted protein			1A0M	16
Q9LDJ3 UniProt NPD GO	EXP12_ARATH	Alpha-expansin 12 precursor (AtEXPA12) (At-EXP12) (AtEx12) (Expansin S2) (Ath-ExpAlpha-1.24)	0.10	-	mit	1 *	Cell wall; peripheral membrane protein				252
Q9M2S9 UniProt NPD GO	EXP16_ARATH	Alpha-expansin 16 precursor (AtEXPA16) (At-EXP16) (AtEx16) (Ath-ExpAlpha-1.7)	0.10	-	exc	0	Cell wall; peripheral membrane protein				260
Q28686 UniProt NPD GO	SGCA_RABIT	Alpha-sarcoglycan precursor (Alpha-SG) (Adhalin) (50 kDa dystrophin-associated glycoprotein) (50DAG) ...	0.10	-	end	1	Sarcolemma; sarcolemmal membrane; single-pass type I membrane protein (By similarity)				387
Q40294 UniProt NPD GO	AOX1_MANIN	Alternative oxidase, mitochondrial precursor (EC 1.-.-.-)	0.10	-	mit	0	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein (Probable). Mitochondrial, ...				318
P22952 UniProt NPD GO	AMC2_PIG	Alveolar macrophage chemotactic factor 2 precursor (Alveolar macrophage chemotactic factor II) (AMCF ...	0.10	-	mit	0	Secreted protein				117
Q06203 UniProt NPD GO	PUR1_HUMAN	Amidophosphoribosyltransferase precursor (EC 2.4.2.14) (Glutamine phosphoribosylpyrophosphate amidot ...	0.10	-	cyt	0			172450		517
P27043 UniProt NPD GO	ANGI_CHICK	Angiogenin precursor (EC 3.1.27.-) (Ribonuclease A)	0.10	-	exc	1 *	Secreted protein				139
O35462 UniProt NPD GO	ANGP2_RAT	Angiopoietin-2 (ANG-2) (Fragment)	0.10	-	nuc	0	Secreted protein				137
Q9GLP6 UniProt NPD GO	ANGT_GORGO	Angiotensinogen precursor [Contains: Angiotensin-1 (Angiotensin I) (Ang I); Angiotensin-2 (Angiotens ...	0.10	-	mit	0	Secreted protein (By similarity)				485
Q9Y575 UniProt NPD GO	ASB3_HUMAN	Ankyrin repeat and SOCS box protein 3 (ASB-3)	0.10	-	cyt	0			605760		518
Q9Y574 UniProt NPD GO	ASB4_HUMAN	Ankyrin repeat and SOCS box protein 4 (ASB-4)	0.10	-	mit	0			605761		426
Q92527 UniProt NPD GO	ANKR7_HUMAN	Ankyrin repeat domain-containing protein 7 (Testis-specific protein TSA806)	0.10	-	cyt	0					201
O35640 UniProt NPD GO	ANXA8_MOUSE	Annexin A8 (Annexin VIII)	0.10	-	cyt	0					327
P05328 UniProt NPD GO	TRPG_ASPNG	Anthranilate synthase component 2 (EC 4.1.3.27) (Anthranilate synthase component II) [Includes: Glut ...	0.10	-	nuc	0					770
P00937 UniProt NPD GO	TRPG_YEAST	Anthranilate synthase component 2 (EC 4.1.3.27) (Anthranilate synthase component II) [Includes: Glut ...	0.10	-	cyt	0		anthranilate synthase complex [IPI] cytoplasm [IDA]			484
P20301 UniProt NPD GO	APRN_ENTHI	Antigenic protein NP1 (Non-pathogenic protein 1) (Fragment)	0.10	-	cyt	0					640
P80392 UniProt NPD GO	AMP2_MELGA	Antimicrobial peptide THP2 precursor (Turkey heterophil peptide 2)	0.10	-	vac	0	Secreted protein				64
P80930 UniProt NPD GO	ENA1_HORSE	Antimicrobial peptide eNAP-1 (Fragment)	0.10	-	nuc	0	Secreted protein				46
Q5SD39 UniProt NPD GO	CYF_HUPLU	Apocytochrome f precursor	0.10	-	mit	2 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				320
Q9MUN6 UniProt NPD GO	CYF_MESVI	Apocytochrome f precursor	0.10	-	mit	2 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				313
Q6EW40 UniProt NPD GO	CYF_NYMAL	Apocytochrome f precursor	0.10	-	cyt	1	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				322
Q6ENG0 UniProt NPD GO	CYF_ORYNI	Apocytochrome f precursor	0.10	-	cyt	1	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				320
P07888 UniProt NPD GO	CYF_ORYSA	Apocytochrome f precursor	0.10	-	cyt	1	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				320
Q6YXL3 UniProt NPD GO	CYF_PHYPA	Apocytochrome f precursor	0.10	-	end	2 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				319
Q8WI07 UniProt NPD GO	CYF_PSINU	Apocytochrome f precursor	0.10	-	end	2 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				321
Q24307 UniProt NPD GO	IAP2_DROME	Apoptosis 2 inhibitor (Inhibitor of apoptosis 2) (dIAP2) (DIAP) (IAP homolog A) (IAP-like protein) ( ...	0.10	-	cyt	0					498
P79886 UniProt NPD GO	APOV1_COTJA	Apovitellenin-1 precursor (Apovitellenin I) (Very low density lipoprotein II) (Apo-VLDL-II) (Apo-II) ...	0.10	-	end	0					105

You are viewing entries 63951 to 64000 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.