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
O17502 UniProt NPD GO	ACTM_BRALA	Actin, muscle	0.07	-	cyt	0	Cytoplasm				380
Q98972 UniProt NPD GO	ACT1_ORYLA	Actin, muscle-type (OlMA1)	0.07	-	cyt	0	Cytoplasm				377
P02576 UniProt NPD GO	ACTA_PHYPO	Actin, plasmodial isoform	0.07	-	cyt	0	Cytoplasm				375
P92182 UniProt NPD GO	ACT1_LUMTE	Actin-1	0.07	-	cyt	0	Cytoplasm				376
P53470 UniProt NPD GO	ACT1_SCHMA	Actin-1	0.07	-	cyt	0	Cytoplasm				376
P43239 UniProt NPD GO	ACT1_PNECA	Actin-1 (Actin I)	0.07	-	cyt	0	Cytoplasm				375
P10990 UniProt NPD GO	ACT1_STRFN	Actin-15A	0.07	-	cyt	0	Cytoplasm				376
P69004 UniProt NPD GO	ACT2_STRFN	Actin-15B	0.07	-	cyt	0	Cytoplasm. Cytoskeleton				376
P10984 UniProt NPD GO	ACT2_CAEEL	Actin-2	0.07	-	cyt	0	Cytoplasm				376
Q03341 UniProt NPD GO	ACT2_ECHGR	Actin-2	0.07	-	cyt	0	Cytoplasm				376
P30163 UniProt NPD GO	ACT2_ONCVO	Actin-2	0.07	-	cyt	0	Cytoplasm				376
P41113 UniProt NPD GO	ACT3_PODCA	Actin-3	0.07	-	cyt	0	Cytoplasm				376
P45886 UniProt NPD GO	ACT3_BACDO	Actin-3, muscle-specific	0.07	-	cyt	0	Cytoplasm				376
P53501 UniProt NPD GO	ACT3_DROME	Actin-57B	0.07	-	cyt	0	Cytoplasm				376
P10981 UniProt NPD GO	ACT5_DROME	Actin-87E	0.07	-	cyt	0	Cytoplasm				376
P42528 UniProt NPD GO	ARP3_DICDI	Actin-like protein 3 (Actin-related protein 3)	0.07	-	cyt	0	Mitochondrion				418
P61158 UniProt NPD GO	ARP3_HUMAN	Actin-like protein 3 (Actin-related protein 3)	0.07	-	cyt	0		Arp2/3 protein complex [TAS]	604222		417
Q99JY9 UniProt NPD GO	ARP3_MOUSE	Actin-like protein 3 (Actin-related protein 3)	0.07	-	cyt	0		lamellipodium [IDA]			417
Q5R8R1 UniProt NPD GO	ARP3_PONPY	Actin-like protein 3 (Actin-related protein 3)	0.07	-	cyt	0					417
P61157 UniProt NPD GO	ARP3_BOVIN	Actin-like protein 3 (Actin-related protein 3) (Actin-2)	0.07	-	cyt	0				1U2V	417
Q9Y615 UniProt NPD GO	ACL7A_HUMAN	Actin-like protein 7A (Actin-like-7-alpha)	0.07	-	cyt	0		cytoskeleton [TAS]	604303		435
P45889 UniProt NPD GO	ACTZ_DROME	Actin-like protein 87C	0.07	-	cyt	0					376
Q9NZ32 UniProt NPD GO	ARP10_HUMAN	Actin-related protein 10 (hARP11)	0.07	-	cyt	0					417
Q5I4B8 UniProt NPD GO	ACTPA_OULOR	Actinoporin Or-A (Fragment)	0.07	-	cyt	0	Secreted protein. Found in nematocyst				165
Q13705 UniProt NPD GO	AVR2B_HUMAN	Activin receptor type 2B precursor (EC 2.7.11.30) (Activin receptor type IIB) (ACTR-IIB)	0.07	-	end	1	Membrane; single-pass type I membrane protein	cell surface [IEP] integral to plasma membrane [TAS]	602730		512
Q66T47 UniProt NPD GO	AVR2B_PIG	Activin receptor type 2B precursor (EC 2.7.11.30) (Activin receptor type IIB) (ACTR-IIB)	0.07	-	end	1	Membrane; single-pass type I membrane protein (By similarity)				512
P38445 UniProt NPD GO	AVR2B_RAT	Activin receptor type 2B precursor (EC 2.7.11.30) (Activin receptor type IIB) (ACTR-IIB)	0.07	-	end	1	Membrane; single-pass type I membrane protein			1NYU	513
P27060 UniProt NPD GO	ACP_CYLSN	Acyl carrier protein (ACP)	0.07	-	nuc	0	Plastid; chloroplast				80
O44390 UniProt NPD GO	ACO11_TRINI	Acyl-CoA delta-11 desaturase (EC 1.14.19.-) (Delta(11)-desaturase)	0.07	-	mit	4 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (By similarity)				349
P49753 UniProt NPD GO	ACOT2_HUMAN	Acyl-coenzyme A thioesterase 2 (EC 3.1.2.2) (Acyl-CoA thioesterase 2) (Peroxisomal acyl-coenzyme A t ...	0.07	-	mit	0	Peroxisome	peroxisome [NAS]			483
Q502J0 UniProt NPD GO	AYTL1_BRARE	Acyltransferase-like 1 (EC 2.3.1.-)	0.07	-	nuc	1 *	Membrane; single-pass type II membrane protein (Potential)				529
Q8MXJ9 UniProt NPD GO	S35B2_CAEEL	Adenosine 3'-phospho 5'-phosphosulfate transporter 1 (PAPS transporter 1)	0.07	-	end	9 *	Golgi apparatus; Golgi membrane; multi-pass membrane protein (By similarity)				425
Q5R9A1 UniProt NPD GO	S35B2_PONPY	Adenosine 3'-phospho 5'-phosphosulfate transporter 1 (PAPS transporter 1) (Solute carrier family 35 ...	0.07	-	end	8 *	Golgi apparatus; Golgi membrane; multi-pass membrane protein (By similarity)				432
Q8TB61 UniProt NPD GO	S35B2_HUMAN	Adenosine 3'-phospho 5'-phosphosulfate transporter 1 (PAPS transporter 1) (Solute carrier family 35 ...	0.07	-	end	8 *	Golgi apparatus; Golgi membrane; multi-pass membrane protein	Golgi apparatus [IDA] integral to membrane [NAS] membrane [IDA]			432
Q6DG22 UniProt NPD GO	ADA_BRARE	Adenosine deaminase (EC 3.5.4.4) (Adenosine aminohydrolase)	0.07	-	cyt	0					359
P93253 UniProt NPD GO	SAHH_MESCR	Adenosylhomocysteinase (EC 3.3.1.1) (S-adenosyl-L-homocysteine hydrolase) (AdoHcyase)	0.07	-	nuc	0					485
P05081 UniProt NPD GO	KAD1_CHICK	Adenylate kinase isoenzyme 1 (EC 2.7.4.3) (ATP-AMP transphosphorylase) (AK1) (Myokinase)	0.07	-	cyt	0	Cytoplasm				194
P27144 UniProt NPD GO	KAD4_HUMAN	Adenylate kinase isoenzyme 4, mitochondrial (EC 2.7.4.3) (Adenylate kinase 3-like 1) (ATP-AMP transp ...	0.07	-	mit	0	Mitochondrion; mitochondrial matrix		103030	2BBW	223
Q5R421 UniProt NPD GO	KAD4_PONPY	Adenylate kinase isoenzyme 4, mitochondrial (EC 2.7.4.3) (Adenylate kinase 3-like 1) (ATP-AMP transp ...	0.07	-	mit	0	Mitochondrion; mitochondrial matrix (By similarity)				223
Q8HSW1 UniProt NPD GO	KADC_SOLTU	Adenylate kinase, chloroplast precursor (EC 2.7.4.3) (ATP-AMP transphosphorylase)	0.07	-	mit	0	Plastid; chloroplast				288
P40125 UniProt NPD GO	CAP1_PIG	Adenylyl cyclase-associated protein 1 (CAP 1) (ASP-56 protein) (Fragments)	0.07	-	nuc	0					233
Q43295 UniProt NPD GO	KAP1_ARATH	Adenylyl-sulfate kinase 1, chloroplast precursor (EC 2.7.1.25) (APS kinase) (Adenosine-5'phosphosulf ...	0.07	-	nuc	0	Plastid; chloroplast				276
Q91WW7 UniProt NPD GO	ADPN_MOUSE	Adiponutrin (iPLA2-epsilon) (Calcium-independent phospholipase A2-epsilon) (Patatin-like phospholipa ...	0.07	-	nuc	2 *	Membrane; single-pass membrane protein	membrane [IDA]			413
P26968 UniProt NPD GO	CU22_TENMO	Adult-specific cuticular protein ACP-22 precursor	0.07	-	end	0					199
P31328 UniProt NPD GO	TXAG_AGEOP	Agelenin	0.07	-	nuc	0	Secreted protein				35
O74657 UniProt NPD GO	ALS2_CANAL	Agglutinin-like protein 2 precursor (Fragment)	0.07	-	exc	0					468
O74660 UniProt NPD GO	ALS4_CANAL	Agglutinin-like protein 4 precursor (Fragment)	0.07	-	exc	0					469
P36428 UniProt NPD GO	SYA_ARATH	Alanyl-tRNA synthetase, mitochondrial precursor (EC 6.1.1.7) (Alanine--tRNA ligase) (AlaRS)	0.07	-	mit	0	Mitochondrion. Cytoplasm				1003
P62927 UniProt NPD GO	ALB1B_PEA	Albumin-1 B precursor (PA1 B) [Contains: Albumin-1 B chain b (PA1b B) (Leginsulin B); Albumin-1 B ch ...	0.07	-	nuc	0				1P8B	130
P62931 UniProt NPD GO	ALB1F_PEA	Albumin-1 F precursor (PA1 F) (PsaA1b005/PsaA1b011) [Contains: Albumin-1 F chain b (PA1b F) (Leginsu ...	0.07	-	mit	0				1P8B	130

You are viewing entries 69451 to 69500 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.