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
Q5RD23 UniProt NPD GO	ATPO_PONPY	ATP synthase O subunit, mitochondrial precursor (EC 3.6.3.14) (Oligomycin sensitivity conferral prot ...	0.16	-	mit	0	Mitochondrion; mitochondrial matrix				213
P41313 UniProt NPD GO	ATP6_DIDMA	ATP synthase a chain (EC 3.6.3.14) (ATPase protein 6)	0.16	-	end	6 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				226
P97450 UniProt NPD GO	ATP5J_MOUSE	ATP synthase coupling factor 6, mitochondrial precursor (EC 3.6.3.14) (ATPase subunit F6)	0.16	-	mit	0		mitochondrial inner membrane [IDA] mitochondrion [IDA]			108
Q5RBY3 UniProt NPD GO	ATP5J_PONPY	ATP synthase coupling factor 6, mitochondrial precursor (EC 3.6.3.14) (ATPase subunit F6)	0.16	-	mit	0					107
P35010 UniProt NPD GO	ATPD_GALSU	ATP synthase delta chain, chloroplast (EC 3.6.3.14)	0.16	-	cyt	0	Plastid; chloroplast; chloroplast thylakoid membrane				177
Q07300 UniProt NPD GO	ATPD_SORBI	ATP synthase delta chain, chloroplast precursor (EC 3.6.3.14)	0.16	-	mit	0	Plastid; chloroplast; chloroplast thylakoid membrane				247
P09468 UniProt NPD GO	ATPE_ARATH	ATP synthase epsilon chain (EC 3.6.3.14) (ATP synthase F1 sector epsilon subunit)	0.16	-	cyt	0	Plastid; chloroplast; chloroplast thylakoid membrane; peripheral membrane protein (By similarity)				132
P21306 UniProt NPD GO	ATP5E_YEAST	ATP synthase epsilon chain, mitochondrial (EC 3.6.3.14)	0.16	-	nuc	0	Mitochondrion	proton-transporting ATP synthase, central s... [IMP]			61
P29790 UniProt NPD GO	ATPG_TOBAC	ATP synthase gamma chain, chloroplast precursor (EC 3.6.3.14)	0.16	-	mit	0	Plastid; chloroplast; chloroplast thylakoid membrane				377
Q91VR2 UniProt NPD GO	ATPG_MOUSE	ATP synthase gamma chain, mitochondrial precursor (EC 3.6.3.14)	0.16	-	mit	0	Mitochondrion				298
Q9ZZY7 UniProt NPD GO	ATP8_HIPAM	ATP synthase protein 8 (EC 3.6.3.14) (ATPase subunit 8) (A6L)	0.16	-	nuc	1 *	Mitochondrion; mitochondrial membrane; single-pass membrane protein				68
P03928 UniProt NPD GO	ATP8_HUMAN	ATP synthase protein 8 (EC 3.6.3.14) (ATPase subunit 8) (A6L)	0.16	-	nuc	1 *	Mitochondrion; mitochondrial membrane; single-pass membrane protein	proton-transporting ATP synthase complex, c... [NAS]	516070		68
P92663 UniProt NPD GO	ATP8_MACRO	ATP synthase protein 8 (EC 3.6.3.14) (ATPase subunit 8) (A6L)	0.16	-	nuc	1 *	Mitochondrion; mitochondrial membrane; single-pass membrane protein				69
Q35647 UniProt NPD GO	ATP8_PANTR	ATP synthase protein 8 (EC 3.6.3.14) (ATPase subunit 8) (A6L)	0.16	-	nuc	1 *	Mitochondrion; mitochondrial membrane; single-pass membrane protein				68
Q9MET2 UniProt NPD GO	ATP8_PHYCA	ATP synthase protein 8 (EC 3.6.3.14) (ATPase subunit 8) (A6L)	0.16	-	nuc	1 *	Mitochondrion; mitochondrial membrane; single-pass membrane protein				63
O13349 UniProt NPD GO	ATPF_KLULA	ATP synthase subunit 4, mitochondrial precursor (EC 3.6.3.14)	0.16	-	nuc	0	Mitochondrion				237
Q8MA05 UniProt NPD GO	ATPA_CHAGL	ATP synthase subunit alpha (EC 3.6.3.14) (ATPase subunit alpha) (ATP synthase F1 sector subunit alph ...	0.16	-	cyt	0	Plastid; chloroplast; chloroplast thylakoid membrane; peripheral membrane protein (By similarity)				512
Q6YXK3 UniProt NPD GO	ATPA_PHYPA	ATP synthase subunit alpha (EC 3.6.3.14) (ATPase subunit alpha) (ATP synthase F1 sector subunit alph ...	0.16	-	cyt	0	Plastid; chloroplast; chloroplast thylakoid membrane; peripheral membrane protein (By similarity)				507
P41602 UniProt NPD GO	ATPA_PINTH	ATP synthase subunit alpha (EC 3.6.3.14) (ATPase subunit alpha) (ATP synthase F1 sector subunit alph ...	0.16	-	cyt	0	Plastid; chloroplast; chloroplast thylakoid membrane; peripheral membrane protein (By similarity)				494
Q32RL1 UniProt NPD GO	ATPA_ZYGCR	ATP synthase subunit alpha (EC 3.6.3.14) (ATPase subunit alpha) (ATP synthase F1 sector subunit alph ...	0.16	-	cyt	0	Plastid; chloroplast; chloroplast thylakoid membrane; peripheral membrane protein (By similarity)				505
Q9NRK6 UniProt NPD GO	ABCBA_HUMAN	ATP-binding cassette sub-family B member 10, mitochondrial precursor (ATP-binding cassette transport ...	0.16	-	end	5	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein	ATP-binding cassette (ABC) transporter complex [NAS]	605454		738
Q9UBJ2 UniProt NPD GO	ABCD2_HUMAN	ATP-binding cassette sub-family D member 2 (Adrenoleukodystrophy-related protein) (hALDR) (Adrenoleu ...	0.16	-	end	0	Peroxisome; peroxisomal membrane; multi-pass membrane protein	ATP-binding cassette (ABC) transporter complex [TAS] integral to plasma membrane [TAS] peroxisome [TAS]	601081		740
O14678 UniProt NPD GO	ABCD4_HUMAN	ATP-binding cassette sub-family D member 4 (Peroxisomal membrane protein 69) (PMP69) (Peroxisomal me ...	0.16	-	end	4 *	Peroxisome; peroxisomal membrane; multi-pass membrane protein	ATP-binding cassette (ABC) transporter complex [TAS] integral to membrane [TAS]	603214		606
O93988 UniProt NPD GO	ACL1_SORMA	ATP-citrate synthase subunit 1 (EC 2.3.3.8) (ATP-citrate (pro-S-)-lyase 1) (Citrate cleavage enzyme ...	0.16	-	cyt	0	Cytoplasm				674
Q6C3X7 UniProt NPD GO	DBP5_YARLI	ATP-dependent RNA helicase DBP5 (EC 3.6.1.-)	0.16	-	nuc	0	Cytoplasm. Nucleus; nuclear envelope; nuclear pore complex; cytoplasmic side. Nuclear pore complex c ...				488
P48048 UniProt NPD GO	IRK1_HUMAN	ATP-sensitive inward rectifier potassium channel 1 (Potassium channel, inwardly rectifying subfamily ...	0.16	+	mit	2	Membrane; multi-pass membrane protein	voltage-gated potassium channel complex [TAS]	600359		391
Q14654 UniProt NPD GO	IRK11_HUMAN	ATP-sensitive inward rectifier potassium channel 11 (Potassium channel, inwardly rectifying subfamil ...	0.16	-	end	2	Membrane; multi-pass membrane protein	integral to plasma membrane [TAS]	606176		390
Q9LV11 UniProt NPD GO	PMA11_ARATH	ATPase 11, plasma membrane-type (EC 3.6.3.6) (Proton pump 11)	0.16	-	end	9	Membrane; multi-pass membrane protein				956
Q29307 UniProt NPD GO	ATIF1_PIG	ATPase inhibitor, mitochondrial precursor	0.16	-	nuc	0	Mitochondrion				108
Q8WTS1 UniProt NPD GO	ABHD5_HUMAN	Abhydrolase domain-containing protein 5	0.16	-	cyt	0	Cytoplasm (By similarity). Colocalizated with PLIN and ADRP on the surface of lipid droplets. The lo ...		604780		349
Q8JI40 UniProt NPD GO	CRVP_AGKHA	Ablomin precursor	0.16	-	exc	0	Secreted protein				240
P33739 UniProt NPD GO	MS2B_DROSE	Accessory gland-specific peptide 26Ab precursor (Male accessory gland secretory protein 355B)	0.16	-	exc	0	Secreted protein; extracellular space				90
Q07001 UniProt NPD GO	ACHD_HUMAN	Acetylcholine receptor protein subunit delta precursor	0.16	-	end	4 *	Membrane; multi-pass membrane protein	nicotinic acetylcholine-gated receptor-chan... [TAS]	608930		517
P02716 UniProt NPD GO	ACHD_MOUSE	Acetylcholine receptor protein subunit delta precursor	0.16	+	end	4 *	Membrane; multi-pass membrane protein	Golgi apparatus [IDA] plasma membrane [IDA]			520
P21836 UniProt NPD GO	ACES_MOUSE	Acetylcholinesterase precursor (EC 3.1.1.7) (AChE)	0.16	-	exc	0		synapse [IDA]		2C0Q	614
P37136 UniProt NPD GO	ACES_RAT	Acetylcholinesterase precursor (EC 3.1.1.7) (AChE)	0.16	-	exc	0					614
P17514 UniProt NPD GO	CHIQ_TOBAC	Acidic endochitinase Q precursor (EC 3.2.1.14) (Pathogenesis-related protein Q) (PR-Q)	0.16	-	mit	1 *	Secreted protein. Extracellular fluid from leaves				253
P07829 UniProt NPD GO	ACT3_DICDI	Actin-3-sub 1	0.16	-	cyt	0	Cytoplasm				375
P07828 UniProt NPD GO	ACT4_DICDI	Actin-3-sub 2	0.16	-	cyt	0	Cytoplasm				379
Q9FVI2 UniProt NPD GO	ADF1_PETHY	Actin-depolymerizing factor 1 (ADF 1)	0.16	-	cyt	0					139
O94241 UniProt NPD GO	ARP6_SCHPO	Actin-like protein arp6	0.16	-	cyt	0	Cytoplasm (By similarity). Nucleus (By similarity)	nuclear chromosome, telomeric region [IDA]			401
P70539 UniProt NPD GO	ACV1C_RAT	Activin receptor type 1C precursor (EC 2.7.11.30) (ACTR-IC) (Activin receptor-like kinase 7) (ALK-7) ...	0.16	-	end	2 *	Membrane; single-pass type I membrane protein	activin receptor complex [IDA]			493
Q9PWJ0 UniProt NPD GO	ACL2_AGKAC	Acutolysin-2 precursor (EC 3.4.24.-)	0.16	-	nuc	0	Secreted protein (By similarity)				479
O62849 UniProt NPD GO	ACOD_SHEEP	Acyl-CoA desaturase (EC 1.14.19.1) (Stearoyl-CoA desaturase) (Fatty acid desaturase) (Delta(9)-desat ...	0.16	-	end	4	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (Probable)				359
Q4V869 UniProt NPD GO	ACBD6_XENLA	Acyl-CoA-binding domain-containing protein 6	0.16	-	nuc	0					286
Q9R0X4 UniProt NPD GO	ACOT9_MOUSE	Acyl-coenzyme A thioesterase 9, mitochondrial precursor (EC 3.1.2.-) (Acyl-CoA thioesterase 9) (Acyl ...	0.16	-	mit	0	Mitochondrion				439
Q4I8Q4 UniProt NPD GO	APTH1_GIBZE	Acyl-protein thioesterase 1 (EC 3.1.2.-)	0.16	-	cyt	0	Cytoplasm (By similarity)				235
P19205 UniProt NPD GO	ACPH_PIG	Acylamino-acid-releasing enzyme (EC 3.4.19.1) (AARE) (Acyl-peptide hydrolase) (APH) (Acylaminoacyl-p ...	0.16	-	nuc	0	Cytoplasm				732
P69682 UniProt NPD GO	NECP1_RAT	Adaptin ear-binding coat-associated protein 1 (NECAP-1)	0.16	-	nuc	0	Membrane-associated; with clathrin-coated vesicles. Colocalizes with AP-2 at the plasma membrane				277
P55264 UniProt NPD GO	ADK_MOUSE	Adenosine kinase (EC 2.7.1.20) (AK) (Adenosine 5'-phosphotransferase)	0.16	-	cyt	0		nucleus [IDA]			361

You are viewing entries 55251 to 55300 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.