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
Q5R6E7 UniProt NPD GO	ARL8B_PONPY	ADP-ribosylation factor-like protein 8B	0.19	-	cyt	0	Endosome; late endosome (By similarity). Lysosome (By similarity). Alternatively, may localize with ...				186
Q920A7 UniProt NPD GO	AFG31_MOUSE	AFG3-like protein 1 (EC 3.4.24.-)	0.19	+	end	2 *	Mitochondrion; mitochondrial membrane; multi-pass membrane protein (Potential)	mitochondrion [IDA]			663
P40518 UniProt NPD GO	ARPC5_YEAST	ARP2/3 complex 16 kDa subunit (p16-ARC)	0.19	-	cyt	0		Arp2/3 protein complex [IDA] mitochondrial envelope [TAS]			154
Q8W4Y5 UniProt NPD GO	ASCL_LYCES	ASC1-like protein (Alternaria stem canker resistance-like protein)	0.19	+	end	5 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (By similarity)				303
Q8HTL5 UniProt NPD GO	ATPF_CHLRE	ATP synthase B chain (EC 3.6.3.14) (ATPase subunit I)	0.19	-	nuc	1 *	Plastid; chloroplast; chloroplast thylakoid membrane				175
P06453 UniProt NPD GO	ATPF_SPIOL	ATP synthase B chain (EC 3.6.3.14) (ATPase subunit I)	0.19	-	nuc	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein				184
Q94516 UniProt NPD GO	AT5F1_DROME	ATP synthase B chain, mitochondrial precursor (EC 3.6.3.14) (FO-ATP synthase subunit B)	0.19	-	nuc	0	Mitochondrion				243
O78478 UniProt NPD GO	ATPX_GUITH	ATP synthase B' chain (EC 3.6.3.14) (Subunit II)	0.19	-	nuc	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein				163
Q12349 UniProt NPD GO	ATP14_YEAST	ATP synthase H chain, mitochondrial precursor (EC 3.6.3.14)	0.19	-	mit	0		proton-transporting ATP synthase complex, c... [IMP]			124
Q9B6H6 UniProt NPD GO	ATP6_RHOPD	ATP synthase a chain (EC 3.6.3.14) (ATPase protein 6)	0.19	-	vac	6 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				217
P05039 UniProt NPD GO	ATPE_PEA	ATP synthase epsilon chain (EC 3.6.3.14) (ATP synthase F1 sector epsilon subunit)	0.19	-	cyt	0	Plastid; chloroplast; chloroplast thylakoid membrane; peripheral membrane protein (By similarity)				137
O03199 UniProt NPD GO	ATP8_CERSI	ATP synthase protein 8 (EC 3.6.3.14) (ATPase subunit 8) (A6L)	0.19	-	nuc	1 *	Mitochondrion; mitochondrial membrane; single-pass membrane protein				68
Q9TBI6 UniProt NPD GO	ATP8_CORCN	ATP synthase protein 8 (EC 3.6.3.14) (ATPase subunit 8) (A6L)	0.19	-	mit	1 *	Mitochondrion; mitochondrial membrane; single-pass membrane protein				55
Q9TBI8 UniProt NPD GO	ATP8_MUSVO	ATP synthase protein 8 (EC 3.6.3.14) (ATPase subunit 8) (A6L)	0.19	-	nuc	1 *	Mitochondrion; mitochondrial membrane; single-pass membrane protein				55
Q96063 UniProt NPD GO	ATP8_RHIUN	ATP synthase protein 8 (EC 3.6.3.14) (ATPase subunit 8) (A6L)	0.19	-	nuc	1 *	Mitochondrion; mitochondrial membrane; single-pass membrane protein				67
P00842 UniProt NPD GO	ATP9_NEUCR	ATP synthase protein 9, mitochondrial precursor (EC 3.6.3.14) (Lipid-binding protein)	0.19	-	end	2	Mitochondrion; mitochondrial membrane; multi-pass membrane protein (Potential)				147
Q5SCX6 UniProt NPD GO	ATPA_HUPLU	ATP synthase subunit alpha (EC 3.6.3.14) (ATPase subunit alpha) (ATP synthase F1 sector subunit alph ...	0.19	-	cyt	0	Plastid; chloroplast; chloroplast thylakoid membrane; peripheral membrane protein (By similarity)				507
P92549 UniProt NPD GO	ATPAM_ARATH	ATP synthase subunit alpha, mitochondrial (EC 3.6.3.14)	0.19	-	cyt	0	Mitochondrion				507
P07251 UniProt NPD GO	ATPA_YEAST	ATP synthase subunit alpha, mitochondrial precursor (EC 3.6.3.14)	0.19	-	mit	0	Mitochondrion; mitochondrial inner membrane	mitochondrial nucleoid [IDA] proton-transporting ATP synthase, catalytic... [IMP]			545
P61222 UniProt NPD GO	ABCE1_MOUSE	ATP-binding cassette sub-family E member 1 (RNase L inhibitor) (Ribonuclease 4 inhibitor) (RNS4I)	0.19	-	nuc	0	Cytoplasm (By similarity). Mitochondrion (By similarity). Localized to clusters of virus formation a ...	cytoplasm [ISS] mitochondrion [ISS]			599
P61221 UniProt NPD GO	ABCE1_HUMAN	ATP-binding cassette sub-family E member 1 (RNase L inhibitor) (Ribonuclease 4 inhibitor) (RNS4I) (2 ...	0.19	-	nuc	0	Cytoplasm. Mitochondrion. Localized to clusters of virus formation at the plasma membrane	cytoplasm [IDA] mitochondrion [IDA]	601213		599
Q99PE7 UniProt NPD GO	ABCG5_RAT	ATP-binding cassette sub-family G member 5 (Sterolin-1)	0.19	-	end	6	Membrane; multi-pass membrane protein (Probable)	ATP-binding cassette (ABC) transporter complex [TAS]			652
Q6CB69 UniProt NPD GO	DED1_YARLI	ATP-dependent RNA helicase DED1 (EC 3.6.1.-)	0.19	-	cyt	0	Cytoplasm (By similarity)				618
Q6FL17 UniProt NPD GO	SUB2_CANGA	ATP-dependent RNA helicase SUB2 (EC 3.6.1.-)	0.19	-	cyt	0	Nucleus (By similarity)				439
Q7SBC6 UniProt NPD GO	DBP2_NEUCR	ATP-dependent RNA helicase dbp-2 (EC 3.6.1.-)	0.19	+	cyt	0	Cytoplasm (By similarity). Nucleus (By similarity)				562
Q4WCW2 UniProt NPD GO	SUB2_ASPFU	ATP-dependent RNA helicase sub2 (EC 3.6.1.-)	0.19	-	cyt	0	Nucleus (By similarity)				448
P20431 UniProt NPD GO	PMA3_ARATH	ATPase 3, plasma membrane-type (EC 3.6.3.6) (Proton pump 3)	0.19	-	end	8	Cell membrane; multi-pass membrane protein (Probable)				948
Q9SU58 UniProt NPD GO	PMA4_ARATH	ATPase 4, plasma membrane-type (EC 3.6.3.6) (Proton pump 4)	0.19	-	end	8	Cell membrane; multi-pass membrane protein (Probable)				960
Q42556 UniProt NPD GO	PMA9_ARATH	ATPase 9, plasma membrane-type (EC 3.6.3.6) (Proton pump 9)	0.19	-	end	8	Membrane; multi-pass membrane protein				954
P28252 UniProt NPD GO	ACCD_ANGLY	Acetyl-coenzyme A carboxylase carboxyl transferase subunit beta (EC 6.4.1.2) (ACCase beta chain)	0.19	-	cyt	0	Plastid; chloroplast				314
P48180 UniProt NPD GO	ACH1_CAEEL	Acetylcholine receptor protein subunit alpha-type acr-16 precursor	0.19	-	end	5	Membrane; multi-pass membrane protein				498
P04755 UniProt NPD GO	ACH3_DROME	Acetylcholine receptor protein subunit beta-like 1 precursor	0.19	-	end	5 *	Membrane; multi-pass membrane protein				521
O43427 UniProt NPD GO	FIBP_HUMAN	Acidic fibroblast growth factor intracellular-binding protein (aFGF intracellular-binding protein) ( ...	0.19	-	cyt	0	Nucleus. Intracellular membrane; peripheral membrane protein. Also associated with cytoplasmic membr ...	membrane fraction [TAS] mitochondrion [TAS] nucleus [TAS]	608296		364
P29293 UniProt NPD GO	ACRO_RAT	Acrosin precursor (EC 3.4.21.10) [Contains: Acrosin light chain; Acrosin heavy chain]	0.19	-	nuc	0		acrosomal matrix [TAS]			437
P26197 UniProt NPD GO	ACT2_ABSGL	Actin-2	0.19	-	cyt	0	Cytoplasm				377
Q39250 UniProt NPD GO	ADF1_ARATH	Actin-depolymerizing factor 1 (ADF-1) (AtADF1)	0.19	-	cyt	0				1F7S	139
Q9DEE9 UniProt NPD GO	ARP6_CHICK	Actin-related protein 6 (gArp6) (gARPX)	0.19	+	cyt	0					396
P60244 UniProt NPD GO	ACL3_AGKAC	Acutolysin-C (EC 3.4.24.-) (Hemorrhagin III)	0.19	-	nuc	0	Secreted protein			1QUA	197
P11829 UniProt NPD GO	ACP1_ARATH	Acyl carrier protein 1, chloroplast precursor (ACP)	0.19	-	mit	0	Plastid; chloroplast				137
Q5R7P6 UniProt NPD GO	ACBD4_PONPY	Acyl-CoA-binding domain-containing protein 4	0.19	-	nuc	0					269
P13798 UniProt NPD GO	ACPH_HUMAN	Acylamino-acid-releasing enzyme (EC 3.4.19.1) (AARE) (Acyl-peptide hydrolase) (APH) (Acylaminoacyl-p ...	0.19	-	nuc	0	Cytoplasm		102645		732
Q4V8A1 UniProt NPD GO	AYT1B_RAT	Acyltransferase-like 1-B (EC 2.3.1.-)	0.19	-	end	3	Membrane; multi-pass membrane protein (Potential)				517
Q02787 UniProt NPD GO	PURA_SCHPO	Adenylosuccinate synthetase (EC 6.3.4.4) (IMP--aspartate ligase) (AdSS) (AMPSase)	0.19	-	cyt	0					434
P46664 UniProt NPD GO	PURA2_MOUSE	Adenylosuccinate synthetase isozyme 2 (EC 6.3.4.4) (Adenylosuccinate synthetase, non-muscle isozyme) ...	0.19	-	cyt	0	Cytoplasm				456
Q9CYT6 UniProt NPD GO	CAP2_MOUSE	Adenylyl cyclase-associated protein 2 (CAP 2)	0.19	-	nuc	0	Cell membrane (By similarity)				476
Q9HGF8 UniProt NPD GO	KAPS_SACBA	Adenylyl-sulfate kinase (EC 2.7.1.25) (APS kinase) (Adenosine-5'phosphosulfate kinase) (ATP adenosin ...	0.19	-	cyt	0					202
Q9C2Y6 UniProt NPD GO	KAPS_SACPS	Adenylyl-sulfate kinase (EC 2.7.1.25) (APS kinase) (Adenosine-5'phosphosulfate kinase) (ATP adenosin ...	0.19	-	cyt	0					202
Q9Y6U3 UniProt NPD GO	ADSV_HUMAN	Adseverin (Scinderin)	0.19	-	cyt	0		cell cortex [ISS] cytoplasm [ISS]			715
Q12437 UniProt NPD GO	ORD2_ASPPA	Aflatoxin biosynthesis protein ord2 (Fragment)	0.19	-	mit	0					286
Q8BGT5 UniProt NPD GO	ALAT2_MOUSE	Alanine aminotransferase 2 (EC 2.6.1.2) (ALT2) (Glutamic--pyruvic transaminase 2) (GPT 2) (Glutamic- ...	0.19	-	mit	0					522

You are viewing entries 51501 to 51550 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.