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
O03168 UniProt NPD GO	ATP8_LATCH	ATP synthase protein 8 (EC 3.6.3.14) (ATPase subunit 8) (A6L)	0.13	-	nuc	1 *	Mitochondrion; mitochondrial membrane; single-pass membrane protein				55
Q8LX28 UniProt NPD GO	ATP8_LEMCA	ATP synthase protein 8 (EC 3.6.3.14) (ATPase subunit 8) (A6L)	0.13	-	nuc	1 *	Mitochondrion; mitochondrial membrane; single-pass membrane protein				68
Q9TA25 UniProt NPD GO	ATP8_LOXAF	ATP synthase protein 8 (EC 3.6.3.14) (ATPase subunit 8) (A6L)	0.13	-	nuc	1 *	Mitochondrion; mitochondrial membrane; single-pass membrane protein				66
Q00522 UniProt NPD GO	ATP8_PHOVI	ATP synthase protein 8 (EC 3.6.3.14) (ATPase subunit 8) (A6L)	0.13	-	nuc	1 *	Mitochondrion; mitochondrial membrane; single-pass membrane protein				67
Q9MEV6 UniProt NPD GO	ATP8_SCIVU	ATP synthase protein 8 (EC 3.6.3.14) (ATPase subunit 8) (A6L)	0.13	-	nuc	1 *	Mitochondrion; mitochondrial membrane; single-pass membrane protein				67
Q9ME31 UniProt NPD GO	ATP8_VIRAL	ATP synthase protein 8 (EC 3.6.3.14) (ATPase subunit 8) (A6L)	0.13	-	nuc	1 *	Mitochondrion; mitochondrial membrane; single-pass membrane protein				55
Q758L2 UniProt NPD GO	ATPF_ASHGO	ATP synthase subunit 4, mitochondrial precursor (EC 3.6.3.14)	0.13	-	nuc	0	Mitochondrion (By similarity)				210
O94373 UniProt NPD GO	ATPF_SCHPO	ATP synthase subunit 4, mitochondrial precursor (EC 3.6.3.14)	0.13	-	nuc	0	Mitochondrion (By similarity)				244
Q02848 UniProt NPD GO	ATPA_ANTSP	ATP synthase subunit alpha (EC 3.6.3.14) (ATPase subunit alpha) (ATP synthase F1 sector subunit alph ...	0.13	-	cyt	0	Plastid; chloroplast; chloroplast thylakoid membrane; peripheral membrane protein (By similarity)				505
Q5R9E6 UniProt NPD GO	ATP5S_PONPY	ATP synthase subunit s, mitochondrial precursor (ATP synthase coupling factor B) (Mitochondrial ATP ...	0.13	-	cyt	0	Mitochondrion (By similarity)				200
Q9H222 UniProt NPD GO	ABCG5_HUMAN	ATP-binding cassette sub-family G member 5 (Sterolin-1)	0.13	-	end	5	Membrane; multi-pass membrane protein (Probable)		605459		651
Q6CH89 UniProt NPD GO	SUB2_YARLI	ATP-dependent RNA helicase SUB2 (EC 3.6.1.-)	0.13	-	cyt	0	Nucleus (By similarity)				441
P70673 UniProt NPD GO	IRK11_RAT	ATP-sensitive inward rectifier potassium channel 11 (Potassium channel, inwardly rectifying subfamil ...	0.13	-	end	2	Membrane; multi-pass membrane protein				390
Q5EE05 UniProt NPD GO	ABHD5_PIG	Abhydrolase domain-containing protein 5	0.13	-	cyt	0	Cytoplasm (By similarity). Colocalizated with PLIN and ADRP on the surface of lipid droplets. The lo ...				349
P51371 UniProt NPD GO	ACCA_PORPU	Acetyl-coenzyme A carboxylase carboxyl transferase subunit alpha (EC 6.4.1.2) (Acetyl-CoA carboxylas ...	0.13	-	cyt	0	Plastid; chloroplast				324
P13536 UniProt NPD GO	ACHG_BOVIN	Acetylcholine receptor protein subunit gamma precursor	0.13	-	end	4	Membrane; multi-pass membrane protein				519
P34271 UniProt NPD GO	CUP4_CAEEL	Acetylcholine receptor-like protein cup-4 precursor (Coelomocyte uptake defective protein 4)	0.13	-	end	4	Membrane; multi-pass membrane protein	integral to membrane [NAS]			433
P10626 UniProt NPD GO	ACRO_CAPHI	Acrosin (EC 3.4.21.10) [Contains: Acrosin light chain; Acrosin heavy chain] (Fragment)	0.13	-	cyt	0					60
O17503 UniProt NPD GO	ACTC_BRALA	Actin, cytoplasmic	0.13	-	cyt	0	Cytoplasm				375
P53503 UniProt NPD GO	ACT1_OXYFA	Actin, macronuclear	0.13	-	cyt	0	Cytoplasm				357
Q8ILW9 UniProt NPD GO	ACT2_PLAF7	Actin-2 (Actin II)	0.13	-	cyt	0	Cytoplasm				376
P14883 UniProt NPD GO	ACT2_PLAFA	Actin-2 (Actin II)	0.13	-	cyt	0	Cytoplasm				376
P78712 UniProt NPD GO	ARP3_NEUCR	Actin-like protein 3 (Actin-related protein 3)	0.13	-	nuc	0					439
Q9R0Q6 UniProt NPD GO	ARC1A_MOUSE	Actin-related protein 2/3 complex subunit 1A (SOP2-like protein) (Sid 329)	0.13	-	cyt	0		Arp2/3 protein complex [TAS]			370
Q9W6M5 UniProt NPD GO	ACLE_AGKAC	Acutolysin-E precursor (EC 3.4.24.-)	0.13	-	nuc	0	Secreted protein (By similarity)				609
P48078 UniProt NPD GO	ACP_CYAPA	Acyl carrier protein (ACP)	0.13	-	cyt	0	Plastid; cyanelle				103
P08971 UniProt NPD GO	ACP5_BRANA	Acyl carrier protein, chloroplast precursor (ACP) (Clones 28F10, 10H11/11D11, 34F12 and 04F05/05E01) ...	0.13	-	mit	0	Plastid; chloroplast				134
P31824 UniProt NPD GO	ACBP_MANSE	Acyl-CoA-binding protein homolog (ACBP) (Diazepam-binding inhibitor homolog) (DBI)	0.13	-	nuc	0					90
O15254 UniProt NPD GO	ACOX3_HUMAN	Acyl-coenzyme A oxidase 3, peroxisomal (EC 1.3.3.6) (Pristanoyl-CoA oxidase) (Branched-chain acyl-Co ...	0.13	-	pox	0	Peroxisome (Potential)	peroxisome [TAS]	603402		700
P15802 UniProt NPD GO	AAAA_PENCH	Acyl-coenzyme A:6-aminopenicillanic-acid-acyltransferase 40 kDa form (EC 2.3.1.164) (Isopenicillin-N ...	0.13	-	cyt	0					357
Q94BT6 UniProt NPD GO	ADO1_ARATH	Adagio protein 1 (Protein ZEITLUPE) (LOV kelch protein 1) (Flavin-binding kelch repeat F-box protein ...	0.13	-	cyt	0	Nucleus. Cytoplasm. Nuclear after 9 hours of illumination (afternoon of long days). Cytoplasmic when ...				609
P47957 UniProt NPD GO	APT_MUSSI	Adenine phosphoribosyltransferase (EC 2.4.2.7) (APRT)	0.13	-	nuc	0	Cytoplasm				180
P25824 UniProt NPD GO	KAD_SCHMA	Adenylate kinase (EC 2.7.4.3) (ATP-AMP transphosphorylase) (AK)	0.13	-	cyt	0					197
Q9Y6K8 UniProt NPD GO	KAD5_HUMAN	Adenylate kinase isoenzyme 5 (EC 2.7.4.3) (ATP-AMP transphosphorylase)	0.13	-	cyt	0	Cytoplasm	cytosol [TAS]	608009	2BWJ	198
Q9HDC9 UniProt NPD GO	APMAP_HUMAN	Adipocyte plasma membrane-associated protein (BSCv protein)	0.13	-	mit	1 *	Membrane; single-pass type II membrane protein (Potential)				416
O75366 UniProt NPD GO	AVIL_HUMAN	Advillin (p92)	0.13	-	cyt	0		actin cytoskeleton [TAS]		1UND	819
O95154 UniProt NPD GO	ARK73_HUMAN	Aflatoxin B1 aldehyde reductase member 3 (EC 1.-.-.-) (AFB1-AR 2)	0.13	-	mit	0	Cytoplasm	cytosol [TAS]		2CLP	331
Q00278 UniProt NPD GO	NOR1_ASPPA	Aflatoxin biosynthesis ketoreductase nor-1 (EC 1.1.1.-)	0.13	-	cyt	0					271
P11883 UniProt NPD GO	AL3A1_RAT	Aldehyde dehydrogenase, dimeric NADP-preferring (EC 1.2.1.5) (ALDH class 3) (Tumor-associated aldehy ...	0.13	-	cyt	0	Cytoplasm	cytosol [IDA]		1AD3	452
Q5REQ0 UniProt NPD GO	AK1C1_PONPY	Aldo-keto reductase family 1 member C1 homolog (EC 1.-.-.-) (20-alpha-hydroxysteroid dehydrogenase) ...	0.13	-	cyt	0	Cytoplasm (By similarity)				323
Q95JH5 UniProt NPD GO	AK1C4_MACFA	Aldo-keto reductase family 1 member C4 (EC 1.1.1.-) (Chlordecone reductase) (EC 1.1.1.225) (CDR) (3- ...	0.13	-	cyt	0	Cytoplasm (By similarity)				323
Q95JH4 UniProt NPD GO	AK1C4_MACFU	Aldo-keto reductase family 1 member C4 (EC 1.1.1.-) (Chlordecone reductase) (EC 1.1.1.225) (CDR) (3- ...	0.13	-	cyt	0	Cytoplasm (By similarity)				323
Q6NUM9 UniProt NPD GO	RETST_HUMAN	All-trans-retinol 13,14-reductase precursor (EC 1.3.99.23) (All-trans-13,14-dihydroretinol saturase) ...	0.13	-	end	1 *	Endoplasmic reticulum; endoplasmic reticulum membrane; peripheral membrane protein (By similarity)	endoplasmic reticulum membrane [ISS] nuclear outer membrane [ISS]			610
O42799 UniProt NPD GO	ALL7_ASPFU	Allergen Asp f 7 precursor	0.13	-	exc	0					270
P83088 UniProt NPD GO	FUCTC_DROME	Alpha-(1,3)-fucosyltransferase C (EC 2.4.1.-) (Galactoside 3-L-fucosyltransferase)	0.13	-	mit	1 *	Golgi apparatus; Golgi stack; Golgi stack membrane; single-pass type II membrane protein (By similar ...				425
Q59YV2 UniProt NPD GO	ALG10_CANAL	Alpha-1,2 glucosyltransferase ALG10 (EC 2.4.1.-) (Alpha-2-glucosyltransferase ALG10) (Dolichyl-phosp ...	0.13	-	end	9 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein				450
Q4HZE0 UniProt NPD GO	ALG10_GIBZE	Alpha-1,2 glucosyltransferase ALG10 (EC 2.4.1.-) (Alpha-2-glucosyltransferase ALG10) (Dolichyl-phosp ...	0.13	-	end	10 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein				722
Q4P2W6 UniProt NPD GO	ALG10_USTMA	Alpha-1,2 glucosyltransferase ALG10 (EC 2.4.1.-) (Alpha-2-glucosyltransferase ALG10) (Dolichyl-phosp ...	0.13	-	end	9 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein				633
O02824 UniProt NPD GO	ADA1A_RABIT	Alpha-1A adrenergic receptor (Alpha 1A-adrenoceptor) (Alpha 1A-adrenoreceptor) (Alpha-1C adrenergic ...	0.13	-	end	7 *	Membrane; multi-pass membrane protein				466
P02873 UniProt NPD GO	LEA1_PHAVU	Alpha-amylase inhibitor 1 precursor (Alpha-AI-1) (Alpha-AI1) (Lectin) [Contains: Alpha-amylase inhib ...	0.13	-	exc	0				1VIW	246

You are viewing entries 59351 to 59400 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.