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
P69444 UniProt NPD GO	ATPE_HORVU	ATP synthase epsilon chain (EC 3.6.3.14) (ATP synthase F1 sector epsilon subunit)	0.07	-	nuc	0	Plastid; chloroplast; chloroplast thylakoid membrane; peripheral membrane protein (By similarity)				137
P00835 UniProt NPD GO	ATPE_MAIZE	ATP synthase epsilon chain (EC 3.6.3.14) (ATP synthase F1 sector epsilon subunit)	0.07	-	nuc	0	Plastid; chloroplast; chloroplast thylakoid membrane; peripheral membrane protein (By similarity)				137
Q9TL33 UniProt NPD GO	ATPE_NEPOL	ATP synthase epsilon chain (EC 3.6.3.14) (ATP synthase F1 sector epsilon subunit)	0.07	-	cyt	0	Plastid; chloroplast; chloroplast thylakoid membrane; peripheral membrane protein (By similarity)				133
Q6L393 UniProt NPD GO	ATPE_SACHY	ATP synthase epsilon chain (EC 3.6.3.14) (ATP synthase F1 sector epsilon subunit)	0.07	-	nuc	0	Plastid; chloroplast; chloroplast thylakoid membrane; peripheral membrane protein (By similarity)				137
Q6ENV7 UniProt NPD GO	ATPE_SACOF	ATP synthase epsilon chain (EC 3.6.3.14) (ATP synthase F1 sector epsilon subunit)	0.07	-	nuc	0	Plastid; chloroplast; chloroplast thylakoid membrane; peripheral membrane protein (By similarity)				137
P69443 UniProt NPD GO	ATPE_WHEAT	ATP synthase epsilon chain (EC 3.6.3.14) (ATP synthase F1 sector epsilon subunit)	0.07	-	nuc	0	Plastid; chloroplast; chloroplast thylakoid membrane; peripheral membrane protein (By similarity)				137
P17605 UniProt NPD GO	AT5G1_SHEEP	ATP synthase lipid-binding protein, mitochondrial precursor (EC 3.6.3.14) (ATP synthase proteolipid ...	0.07	-	nuc	2	Mitochondrion; mitochondrial membrane; multi-pass membrane protein				136
Q75G40 UniProt NPD GO	ATP8_ASHGO	ATP synthase protein 8 (EC 3.6.3.14) (ATPase subunit 8)	0.07	-	mit	1 *	Mitochondrion; mitochondrial membrane; single-pass membrane protein				48
O47871 UniProt NPD GO	ATP8_ALLMI	ATP synthase protein 8 (EC 3.6.3.14) (ATPase subunit 8) (A6L)	0.07	-	nuc	1 *	Mitochondrion; mitochondrial membrane; single-pass membrane protein				53
Q33822 UniProt NPD GO	ATP8_ASTPE	ATP synthase protein 8 (EC 3.6.3.14) (ATPase subunit 8) (A6L)	0.07	-	mit	1 *	Mitochondrion; mitochondrial membrane; single-pass membrane protein				54
Q9MQK2 UniProt NPD GO	ATP8_CAPII	ATP synthase protein 8 (EC 3.6.3.14) (ATPase subunit 8) (A6L)	0.07	-	nuc	1 *	Mitochondrion; mitochondrial membrane; single-pass membrane protein				65
P14093 UniProt NPD GO	ATP8_CHICK	ATP synthase protein 8 (EC 3.6.3.14) (ATPase subunit 8) (A6L)	0.07	-	mit	1 *	Mitochondrion; mitochondrial membrane; single-pass membrane protein				54
P03933 UniProt NPD GO	ATP8_DROYA	ATP synthase protein 8 (EC 3.6.3.14) (ATPase subunit 8) (A6L)	0.07	-	mit	1 *	Mitochondrion; mitochondrial membrane; single-pass membrane protein				53
Q34942 UniProt NPD GO	ATP8_LUMTE	ATP synthase protein 8 (EC 3.6.3.14) (ATPase subunit 8) (A6L)	0.07	-	mit	1 *	Mitochondrion; mitochondrial membrane; single-pass membrane protein				53
O79396 UniProt NPD GO	ATP8_RHEAM	ATP synthase protein 8 (EC 3.6.3.14) (ATPase subunit 8) (A6L)	0.07	-	nuc	1 *	Mitochondrion; mitochondrial membrane; single-pass membrane protein				55
P03931 UniProt NPD GO	ATP8_XENLA	ATP synthase protein 8 (EC 3.6.3.14) (ATPase subunit 8) (A6L)	0.07	-	cyt	1 *	Mitochondrion; mitochondrial membrane; single-pass membrane protein				55
Q4G397 UniProt NPD GO	ATPA_EMIHU	ATP synthase subunit alpha (EC 3.6.3.14) (ATPase subunit alpha) (ATP synthase F1 sector subunit alph ...	0.07	-	cyt	0	Plastid; chloroplast; chloroplast thylakoid membrane; peripheral membrane protein (By similarity)				499
Q00820 UniProt NPD GO	ATPA_ODOSI	ATP synthase subunit alpha (EC 3.6.3.14) (ATPase subunit alpha) (ATP synthase F1 sector subunit alph ...	0.07	-	cyt	0	Plastid; chloroplast; chloroplast thylakoid membrane; peripheral membrane protein (By similarity)				503
Q40611 UniProt NPD GO	ATPA_OCHNE	ATP synthase subunit alpha (EC 3.6.3.14) (ATPase subunit alpha) (ATP synthase F1 sector subunit alph ...	0.07	-	cyt	0	Plastid; chloroplast; chloroplast thylakoid membrane; peripheral membrane protein (By similarity)				438
O03063 UniProt NPD GO	ATPB_ASPND	ATP synthase subunit beta (EC 3.6.3.14) (ATPase subunit beta) (ATP synthase F1 sector subunit beta) ...	0.07	-	cyt	0	Plastid; chloroplast; chloroplast thylakoid membrane; peripheral membrane protein (By similarity)				284
P99504 UniProt NPD GO	ATPB_CANFA	ATP synthase subunit beta, mitochondrial (EC 3.6.3.14) (Fragment)	0.07	-		0	Mitochondrion				19
Q9CRA7 UniProt NPD GO	ATP5S_MOUSE	ATP synthase subunit s, mitochondrial precursor (ATP synthase coupling factor B) (Mitochondrial ATP ...	0.07	-	cyt	0	Mitochondrion (By similarity)				200
Q61102 UniProt NPD GO	ABCB7_MOUSE	ATP-binding cassette sub-family B member 7, mitochondrial (ATP-binding cassette transporter 7) (ABC ...	0.07	-	end	5	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein (Potential)	mitochondrial inner membrane [IDA]			694
Q9QYJ4 UniProt NPD GO	ABCB9_RAT	ATP-binding cassette sub-family B member 9 precursor (ATP-binding cassette transporter 9) (ABC trans ...	0.07	-	end	7 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (Probable). Lysos ...	ATP-binding cassette (ABC) transporter complex [TAS]			762
Q9JJ59 UniProt NPD GO	ABCB9_MOUSE	ATP-binding cassette sub-family B member 9 precursor (ATP-binding cassette transporter 9) (ABC trans ...	0.07	-	end	7 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (Probable). Lysos ...				762
Q9H9Y4 UniProt NPD GO	ATPBB_HUMAN	ATP-binding domain 1 family member B	0.07	-	cyt	0					310
Q66KF6 UniProt NPD GO	ATPBB_XENLA	ATP-binding domain 1 family member B	0.07	-	cyt	0					318
Q5BJ53 UniProt NPD GO	ATPBB_XENTR	ATP-binding domain 1 family member B	0.07	-	cyt	0					303
Q5R816 UniProt NPD GO	AB14B_PONPY	Abhydrolase domain-containing protein 14B (CCG1-interacting factor B)	0.07	-	mit	0	Cytoplasm (By similarity). Nucleus (By similarity)				210
P81592 UniProt NPD GO	ACA1_ACALU	Acaloleptin-A1	0.07	-	nuc	0	Secreted protein				71
Q01576 UniProt NPD GO	ACSA_PHYBL	Acetyl-coenzyme A synthetase (EC 6.2.1.1) (Acetate--CoA ligase) (Acyl-activating enzyme)	0.07	-	nuc	0					672
Q13510 UniProt NPD GO	ASAH1_HUMAN	Acid ceramidase precursor (EC 3.5.1.23) (Acylsphingosine deacylase) (N-acylsphingosine amidohydrolas ...	0.07	-	end	0	Lysosome		228000		395
P36908 UniProt NPD GO	CHIA_CICAR	Acidic endochitinase precursor (EC 3.2.1.14)	0.07	-	end	0	Secreted protein; extracellular space				293
Q9FSC0 UniProt NPD GO	ACS2_RUTGR	Acridone synthase 2 (EC 2.3.1.159) (Acridone synthase II)	0.07	-	cyt	0					391
P90689 UniProt NPD GO	ACT_BRUMA	Actin	0.07	-	cyt	0	Cytoplasm				376
P53689 UniProt NPD GO	ACT_PHARH	Actin	0.07	-	cyt	0	Cytoplasm				375
P91754 UniProt NPD GO	ACT_LUMRU	Actin (Fragment)	0.07	-	cyt	0	Cytoplasm				372
P07827 UniProt NPD GO	ACT2_DICDI	Actin A12	0.07	-	cyt	0	Cytoplasm				375
P53480 UniProt NPD GO	ACTC_FUGRU	Actin, alpha cardiac	0.07	-	cyt	0	Cytoplasm				377
P53479 UniProt NPD GO	ACTS_CYPCA	Actin, alpha skeletal muscle (Alpha-actin-1)	0.07	-	cyt	0	Cytoplasm				377
P68264 UniProt NPD GO	ACTS_OREMO	Actin, alpha skeletal muscle (Alpha-actin-1)	0.07	-	cyt	0	Cytoplasm				377
P68140 UniProt NPD GO	ACTS_FUGRU	Actin, alpha skeletal muscle 1	0.07	-	cyt	0	Cytoplasm				377
P18603 UniProt NPD GO	ACT4_ARTSX	Actin, clone 403	0.07	-	cyt	0	Cytoplasm				376
Q964D9 UniProt NPD GO	ACTC_HELTI	Actin, cytoplasmic	0.07	-	cyt	0	Cytoplasm				376
Q93129 UniProt NPD GO	ACTC_BRABE	Actin, cytoplasmic (BbCA1)	0.07	-	cyt	0	Cytoplasm				375
P53486 UniProt NPD GO	ACT3_FUGRU	Actin, cytoplasmic 3 (Beta-actin-3)	0.07	-	cyt	0	Cytoplasm				375
P04829 UniProt NPD GO	ACT3_BOMMO	Actin, cytoplasmic A3	0.07	-	cyt	0	Cytoplasm				376
P53472 UniProt NPD GO	ACTA_STRPU	Actin, cytoskeletal IA	0.07	-	cyt	0	Cytoplasm. Cytoskeleton				376
P69005 UniProt NPD GO	ACTD_STRPU	Actin, cytoskeletal IIB	0.07	-	cyt	0	Cytoplasm. Cytoskeleton				376
P53474 UniProt NPD GO	ACTE_STRPU	Actin, cytoskeletal IIIA	0.07	-	cyt	0	Cytoplasm. Cytoskeleton				376

You are viewing entries 69401 to 69450 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.