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
P00827 UniProt NPD GO	ATPB_MAIZE	ATP synthase subunit beta (EC 3.6.3.14) (ATPase subunit beta) (ATP synthase F1 sector subunit beta)	0.02	-	mit	0	Plastid; chloroplast; chloroplast thylakoid membrane; peripheral membrane protein (By similarity)				498
Q9MUT5 UniProt NPD GO	ATPB_MESVI	ATP synthase subunit beta (EC 3.6.3.14) (ATPase subunit beta) (ATP synthase F1 sector subunit beta)	0.02	-	cyt	0	Plastid; chloroplast; chloroplast thylakoid membrane; peripheral membrane protein (By similarity)				481
P26531 UniProt NPD GO	ATPB_NICSP	ATP synthase subunit beta (EC 3.6.3.14) (ATPase subunit beta) (ATP synthase F1 sector subunit beta)	0.02	-	cyt	0	Plastid; chloroplast; chloroplast thylakoid membrane; peripheral membrane protein (By similarity)				498
Q9MTP7 UniProt NPD GO	ATPB_OENHO	ATP synthase subunit beta (EC 3.6.3.14) (ATPase subunit beta) (ATP synthase F1 sector subunit beta)	0.02	-	cyt	0	Plastid; chloroplast; chloroplast thylakoid membrane; peripheral membrane protein (By similarity)				498
P51259 UniProt NPD GO	ATPB_PORPU	ATP synthase subunit beta (EC 3.6.3.14) (ATPase subunit beta) (ATP synthase F1 sector subunit beta)	0.02	-	cyt	0	Plastid; chloroplast; chloroplast thylakoid membrane; peripheral membrane protein (By similarity)				475
O03079 UniProt NPD GO	ATPB_PTEAQ	ATP synthase subunit beta (EC 3.6.3.14) (ATPase subunit beta) (ATP synthase F1 sector subunit beta)	0.02	-	nuc	0	Plastid; chloroplast; chloroplast thylakoid membrane; peripheral membrane protein (By similarity)				495
Q9MTG8 UniProt NPD GO	ATPB_RAPSA	ATP synthase subunit beta (EC 3.6.3.14) (ATPase subunit beta) (ATP synthase F1 sector subunit beta)	0.02	-	mit	0	Plastid; chloroplast; chloroplast thylakoid membrane; peripheral membrane protein (By similarity)				498
Q9MTX9 UniProt NPD GO	ATPB_SCHSP	ATP synthase subunit beta (EC 3.6.3.14) (ATPase subunit beta) (ATP synthase F1 sector subunit beta)	0.02	-	mit	0	Plastid; chloroplast; chloroplast thylakoid membrane; peripheral membrane protein (By similarity)				498
O03075 UniProt NPD GO	ATPB_MICSZ	ATP synthase subunit beta (EC 3.6.3.14) (ATPase subunit beta) (ATP synthase F1 sector subunit beta) ...	0.02	-	cyt	0	Plastid; chloroplast; chloroplast thylakoid membrane; peripheral membrane protein (By similarity)				473
P00829 UniProt NPD GO	ATPB_BOVIN	ATP synthase subunit beta, mitochondrial precursor (EC 3.6.3.14)	0.02	-	mit	0	Mitochondrion			2CK3	528
P49376 UniProt NPD GO	ATPB_KLULA	ATP synthase subunit beta, mitochondrial precursor (EC 3.6.3.14)	0.02	-	mit	0	Mitochondrion				505
P10719 UniProt NPD GO	ATPB_RAT	ATP synthase subunit beta, mitochondrial precursor (EC 3.6.3.14)	0.02	-	mit	0	Mitochondrion	mitochondrial inner membrane [IDA]		2F43	529
Q9MUV8 UniProt NPD GO	CLPP_MESVI	ATP-dependent Clp protease proteolytic subunit (EC 3.4.21.92) (Endopeptidase Clp)	0.02	-	nuc	0	Plastid; chloroplast				229
P37219 UniProt NPD GO	ASR2_LYCES	Abscisic stress ripening protein 2	0.02	-	cyt	0					114
P08158 UniProt NPD GO	AMDS_EMENI	Acetamidase (EC 3.5.1.4)	0.02	+	cyt	0					548
P10551 UniProt NPD GO	THIL_SACBA	Acetyl-CoA acetyltransferase (EC 2.3.1.9) (Acetoacetyl-CoA thiolase)	0.02	-	mit	0	Cytoplasm				398
P41338 UniProt NPD GO	THIL_YEAST	Acetyl-CoA acetyltransferase (EC 2.3.1.9) (Acetoacetyl-CoA thiolase) (Ergosterol biosynthesis protei ...	0.02	-	mit	0	Cytoplasm				397
Q8S4Y1 UniProt NPD GO	THIC1_ARATH	Acetyl-CoA acetyltransferase, cytosolic 1 (EC 2.3.1.9) (Cytosolic acetoacetyl-CoA thiolase 1) (Thiol ...	0.02	-	cyt	0	Cytoplasm (Potential)				403
Q8HXY6 UniProt NPD GO	THIL_MACFA	Acetyl-CoA acetyltransferase, mitochondrial precursor (EC 2.3.1.9) (Acetoacetyl-CoA thiolase)	0.02	-	mit	0	Mitochondrion (By similarity)				427
Q8QZT1 UniProt NPD GO	THIL_MOUSE	Acetyl-CoA acetyltransferase, mitochondrial precursor (EC 2.3.1.9) (Acetoacetyl-CoA thiolase)	0.02	-	cyt	0	Mitochondrion (By similarity)	mitochondrial inner membrane [IDA] mitochondrion [IDA]			424
P17764 UniProt NPD GO	THIL_RAT	Acetyl-CoA acetyltransferase, mitochondrial precursor (EC 2.3.1.9) (Acetoacetyl-CoA thiolase)	0.02	-	mit	0	Mitochondrion	mitochondrion [TAS]			424
P24752 UniProt NPD GO	THIL_HUMAN	Acetyl-CoA acetyltransferase, mitochondrial precursor (EC 2.3.1.9) (Acetoacetyl-CoA thiolase) (T2)	0.02	-	mit	0	Mitochondrion	mitochondrion [TAS]	203750	2F2S	427
Q6CNR2 UniProt NPD GO	ACH1_KLULA	Acetyl-CoA hydrolase (EC 3.1.2.1) (Acetyl-CoA deacylase) (Acetyl-CoA acylase)	0.02	-	cyt	0	Cytoplasm (By similarity)				523
Q9Y7B5 UniProt NPD GO	ACS2_KLULA	Acetyl-coenzyme A synthetase 2 (EC 6.2.1.1) (Acetate--CoA ligase 2) (Acyl-activating enzyme 2)	0.02	-	nuc	1					684
Q85FW5 UniProt NPD GO	ARGB_CYAME	Acetylglutamate kinase (EC 2.7.2.8) (NAG kinase) (AGK) (N-acetyl-L-glutamate 5-phosphotransferase)	0.02	-	nuc	0	Plastid; chloroplast				290
P23605 UniProt NPD GO	ACH2_LONAC	Achelase-2 (EC 3.4.21.-) (Achelase II)	0.02	-	cyt	0	Secreted protein; extracellular space				214
P70158 UniProt NPD GO	ASM3A_MOUSE	Acid sphingomyelinase-like phosphodiesterase 3a precursor (EC 3.1.4.-) (ASM-like phosphodiesterase 3 ...	0.02	-	mit	0	Secreted protein (By similarity)				445
P22583 UniProt NPD GO	LECA3_PSOSC	Acidic lectin A3 (Fragment)	0.02	-		0					15
Q42669 UniProt NPD GO	ACOC_CUCMC	Aconitase (EC 4.2.1.3) (Aconitate hydratase) (Citrate hydro-lyase) (Fragment)	0.02	-	cyt	0	Cytoplasm				764
Q42560 UniProt NPD GO	ACOC_ARATH	Aconitate hydratase, cytoplasmic (EC 4.2.1.3) (Citrate hydro-lyase) (Aconitase)	0.02	-	cyt	0	Cytoplasm				898
P49609 UniProt NPD GO	ACON_GRAVE	Aconitate hydratase, mitochondrial precursor (EC 4.2.1.3) (Citrate hydro-lyase) (Aconitase)	0.02	-	mit	0	Mitochondrion				779
P53499 UniProt NPD GO	ACT_CHOCR	Actin	0.02	-	cyt	0	Cytoplasm				373
O65315 UniProt NPD GO	ACT_COLSC	Actin	0.02	-	cyt	0	Cytoplasm				377
O65316 UniProt NPD GO	ACT_MESVI	Actin	0.02	-	cyt	0	Cytoplasm				377
P53491 UniProt NPD GO	ACT_ACECL	Actin (Fragment)	0.02	-	cyt	0	Cytoplasm				353
P27131 UniProt NPD GO	ACT1_NAEFO	Actin-1 (Actin I)	0.02	-	cyt	0	Cytoplasm				375
P30172 UniProt NPD GO	ACT12_SOLTU	Actin-100 (Fragment)	0.02	-	cyt	0	Cytoplasm				357
P53496 UniProt NPD GO	ACT11_ARATH	Actin-11	0.02	-	cyt	0	Cytoplasm				377
P46258 UniProt NPD GO	ACT3_PEA	Actin-3	0.02	-	cyt	0	Cytoplasm				377
P02580 UniProt NPD GO	ACT3_SOYBN	Actin-3	0.02	-	cyt	0	Cytoplasm				376
Q03342 UniProt NPD GO	ACT3_ECHGR	Actin-3 (Fragment)	0.02	-	cyt	0	Cytoplasm				309
P93374 UniProt NPD GO	ACT2_TOBAC	Actin-53 (Fragment)	0.02	-	cyt	0	Cytoplasm				336
P30168 UniProt NPD GO	ACT6_SOLTU	Actin-71	0.02	-	cyt	0	Cytoplasm				377
P30169 UniProt NPD GO	ACT7_SOLTU	Actin-75	0.02	-	cyt	0	Cytoplasm				377
P93584 UniProt NPD GO	ACT9_SOLTU	Actin-82 (Fragment)	0.02	-	cyt	0	Cytoplasm				336
Q11176 UniProt NPD GO	WDR1_CAEEL	Actin-interacting protein 1 (AIP1) (Uncoordinated protein 78)	0.02	-	cyt	0		actomyosin, actin part [IDA] sarcoplasm [IDA]		1PEV	611
Q58CQ2 UniProt NPD GO	ARC1B_BOVIN	Actin-related protein 2/3 complex subunit 1B (ARP2/3 complex 41 kDa subunit) (p41-ARC)	0.02	-	cyt	0					371
Q3MHR7 UniProt NPD GO	ARPC2_BOVIN	Actin-related protein 2/3 complex subunit 2 (ARP2/3 complex 34 kDa subunit) (p34-ARC)	0.02	-	cyt	0					300
O15144 UniProt NPD GO	ARPC2_HUMAN	Actin-related protein 2/3 complex subunit 2 (ARP2/3 complex 34 kDa subunit) (p34-ARC)	0.02	-	cyt	0		Arp2/3 protein complex [TAS]	604224		300
Q5R5Z5 UniProt NPD GO	ARPC2_PONPY	Actin-related protein 2/3 complex subunit 2 (ARP2/3 complex 34 kDa subunit) (p34-ARC)	0.02	-	cyt	0					300

You are viewing entries 82301 to 82350 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.