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
O74727 UniProt NPD GO	SUV3_SACDO	ATP-dependent RNA helicase SUV3, mitochondrial precursor (EC 3.6.1.-)	0.47	-	mit	0	Mitochondrion (By similarity)				737
Q9P735 UniProt NPD GO	FAL1_NEUCR	ATP-dependent RNA helicase fal-1 (EC 3.6.1.-)	0.47	-	cyt	0	Nucleus; nucleolus (By similarity)				400
Q06077 UniProt NPD GO	ABRB_ABRPR	Abrin-b precursor [Contains: Abrin-b A chain (EC 3.2.2.22) (rRNA N-glycosidase); Linker peptide; Abr ...	0.47	-	nuc	0					527
Q9BBS1 UniProt NPD GO	ACCD_LOTJA	Acetyl-coenzyme A carboxylase carboxyl transferase subunit beta (EC 6.4.1.2) (ACCase beta chain)	0.47	-	nuc	0	Plastid; chloroplast				501
Q9EST5 UniProt NPD GO	AN32B_MOUSE	Acidic leucine-rich nuclear phosphoprotein 32 family member B (Proliferation-related acidic leucine- ...	0.47	-	nuc	0	Nucleus. Accumulates in the nuclei at the S phase (By similarity)	nucleus [IDA]			272
P04474 UniProt NPD GO	PRP3_RAT	Acidic proline-rich protein PRP33 precursor (Proline-rich proteoglycan 1)	0.47	-	exc	0	Secreted protein (Potential)				206
Q9D8Z1 UniProt NPD GO	ASCC1_MOUSE	Activating signal cointegrator 1 complex subunit 1 (ASC-1 complex subunit p50) (Trip4 complex subuni ...	0.47	-	cyt	0	Cytoplasm (By similarity)				356
P40145 UniProt NPD GO	ADCY8_HUMAN	Adenylate cyclase type 8 (EC 4.6.1.1) (Adenylate cyclase type VIII) (ATP pyrophosphate-lyase 8) (Ca( ...	0.47	-	end	9	Membrane; multi-pass membrane protein	membrane fraction [TAS] plasma membrane [TAS]	103070		1251
Q03101 UniProt NPD GO	CYAG_DICDI	Adenylate cyclase, germination specific (EC 4.6.1.1) (ATP pyrophosphate-lyase) (Adenylyl cyclase)	0.47	-	nuc	2 *	Membrane; single-pass type II membrane protein			1AWM	858
P30566 UniProt NPD GO	PUR8_HUMAN	Adenylosuccinate lyase (EC 4.3.2.2) (Adenylosuccinase) (ASL) (ASASE)	0.47	-	mit	0			608222		484
Q12053 UniProt NPD GO	PKSL1_ASPPA	Aflatoxin biosynthesis polyketide synthase (PKS)	0.47	-	end	0					2109
P80207 UniProt NPD GO	ALL1_BRAJU	Allergen Bra j 1-E (Bra j I) [Contains: Allergen Bra j 1-E small chain; Allergen Bra j 1-E large cha ...	0.47	-	nuc	0					129
Q6CLD6 UniProt NPD GO	ALG11_KLULA	Alpha-1,2-mannosyltransferase ALG11 (EC 2.4.1.-) (Asparagine-linked glycosylation protein 11)	0.47	-	mit	1 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (By similarity)				570
P18841 UniProt NPD GO	ADA1B_MESAU	Alpha-1B adrenergic receptor (Alpha 1B-adrenoceptor) (Alpha 1B-adrenoreceptor)	0.47	+	end	7 *	Membrane; multi-pass membrane protein				515
Q06481 UniProt NPD GO	APLP2_HUMAN	Amyloid-like protein 2 precursor (Amyloid protein homolog) (APPH) (CDEI box-binding protein) (CDEBP) ...	0.47	-	end	2 *	Cell membrane; single-pass type I membrane protein (Potential). Nucleus (Potential)	integral to membrane [NAS] nucleus [IDA]	104776		763
P53995 UniProt NPD GO	ANC1_MOUSE	Anaphase-promoting complex subunit 1 (APC1) (Cyclosome subunit 1) (Protein Tsg24) (Mitotic checkpoin ...	0.47	-	end	0		nucleus [IDA]			1944
Q9UM13 UniProt NPD GO	APC10_HUMAN	Anaphase-promoting complex subunit 10 (APC10) (Cyclosome subunit 10)	0.47	-	nuc	0		anaphase-promoting complex [NAS]		1JHJ	185
Q6PD24 UniProt NPD GO	AN13D_MOUSE	Ankyrin repeat domain-containing protein 13D	0.47	-	nuc	0					518
Q28FJ2 UniProt NPD GO	ANR37_XENTR	Ankyrin repeat domain-containing protein 37	0.47	-	nuc	0					163
P02649 UniProt NPD GO	APOE_HUMAN	Apolipoprotein E precursor (Apo-E)	0.47	-	exc	0	Secreted protein	cytoplasm [TAS] extracellular region [TAS]	104310	1OR3	317
Q9GLM6 UniProt NPD GO	APOE_HYLLA	Apolipoprotein E precursor (Apo-E)	0.47	-	exc	0	Secreted protein	cytoplasm [ISS] extracellular region [ISS]			317
Q9GJU3 UniProt NPD GO	APOE_PANTR	Apolipoprotein E precursor (Apo-E)	0.47	-	exc	0	Secreted protein	cytoplasm [ISS] extracellular region [ISS]			317
P53367 UniProt NPD GO	ARFP1_HUMAN	Arfaptin-1 (ADP-ribosylation factor-interacting protein 1)	0.47	-	nuc	0		cytosol [IDA] Golgi membrane [IDA]	605928		373
P18908 UniProt NPD GO	ANF_CHICK	Atrial natriuretic factor precursor (ANF) (Atrial natriuretic peptide) (ANP) (Prepronatriodilatin)	0.47	-	exc	0	Secreted protein				140
Q3T0A6 UniProt NPD GO	BCL7B_BOVIN	B-cell CLL/lymphoma 7 protein family member B	0.47	-	nuc	0					202
Q9Z2F6 UniProt NPD GO	BCL3_MOUSE	B-cell lymphoma 3-encoded protein homolog (Protein Bcl-3)	0.47	-	nuc	0	Nucleus (By similarity)				440
O95817 UniProt NPD GO	BAG3_HUMAN	BAG family molecular chaperone regulator 3 (BCL-2-binding athanogene-3) (BAG-3) (Bcl-2-binding prote ...	0.47	-	nuc	0		cytosol [IDA]	603883		575
Q12982 UniProt NPD GO	BNIP2_HUMAN	BCL2/adenovirus E1B 19 kDa protein-interacting protein 2	0.47	-	cyt	0	Cytoplasm. Cytoplasm; perinuclear region. Localizes to the nuclear envelope region and to other cyto ...	cytoplasm [IDA] intracellular membrane-bound organelle [IDA] nuclear envelope [IDA]	603292		314
P46737 UniProt NPD GO	BRCC3_MOUSE	BRCA1/BRCA2-containing complex subunit 3	0.47	+	nuc	0					291
Q95J53 UniProt NPD GO	BTBDG_MACFA	BTB/POZ domain-containing protein 16	0.47	-	mit	0					504
P50415 UniProt NPD GO	BCTN7_SHEEP	Bactenecin-7 precursor (Bac7) (Cathelicidin-3) (PR-59)	0.47	+	nuc	0	Secreted protein				190
O08863 UniProt NPD GO	BIRC3_MOUSE	Baculoviral IAP repeat-containing protein 3 (Inhibitor of apoptosis protein 1) (MIAP1) (MIAP-1)	0.47	-	nuc	0	Cytoplasm (Potential)				600
P09619 UniProt NPD GO	PGFRB_HUMAN	Beta platelet-derived growth factor receptor precursor (EC 2.7.10.1) (PDGF-R-beta) (CD140b antigen)	0.47	-	end	1	Membrane; single-pass type I membrane protein		173410	1LWP	1106
Q8WTQ1 UniProt NPD GO	D104A_HUMAN	Beta-defensin 104A precursor (Beta-defensin 4) (DEFB-4) (BD-4) (hBD-4)	0.47	-	exc	0	Secreted protein				72
P19093 UniProt NPD GO	NGF_CAVPO	Beta-nerve growth factor precursor (Beta-NGF)	0.47	-	exc	0	Secreted protein				241
P52849 UniProt NPD GO	NDST2_HUMAN	Bifunctional heparan sulfate N-deacetylase/N-sulfotransferase 2 (EC 2.8.2.8) (Glucosaminyl N-deacety ...	0.47	-	mit	1 *	Golgi apparatus; Golgi membrane; single-pass type II membrane protein (By similarity)	integral to membrane [TAS]	603268		883
P46844 UniProt NPD GO	BIEA_RAT	Biliverdin reductase A precursor (EC 1.3.1.24) (Biliverdin-IX alpha-reductase) (BVR A)	0.47	-	cyt	0	Cytoplasm			1LC3	295
P32451 UniProt NPD GO	BIOB_YEAST	Biotin synthase, mitochondrial precursor (EC 2.8.1.6) (Biotin synthetase)	0.47	-	mit	0	Mitochondrion	mitochondrion [IDA]			375
P33152 UniProt NPD GO	CADHB_XENLA	Blastomere-cadherin precursor (B-cadherin) (XBcad)	0.47	-	end	1	Membrane; single-pass type I membrane protein				884
Q05438 UniProt NPD GO	BMR1B_CHICK	Bone morphogenetic protein receptor type IB precursor (EC 2.7.11.30) (Serine/threonine-protein kinas ...	0.47	-	nuc	1	Membrane; single-pass type I membrane protein				502
O75363 UniProt NPD GO	BCAS1_HUMAN	Breast carcinoma amplified sequence 1 (Novel amplified in breast cancer 1) (Amplified and overexpres ...	0.47	-	nuc	0	Cytoplasm		602968		584
Q09146 UniProt NPD GO	HBA1_SCHPO	Brefeldin A resistance protein (Caffeine resistance protein 1)	0.47	-	nuc	0	Nucleus	nucleoplasm [IDA] nucleus [IDA]			399
P20481 UniProt NPD GO	BUCC_APLCA	Buccalin precursor [Contains: Buccalin-D; Buccalin-E; Buccalin-F; Buccalin-G; Buccalin-H; Buccalin-A ...	0.47	-	exc	0	Secreted protein				505
Q25479 UniProt NPD GO	NKCL_MANSE	Bumetanide-sensitive sodium-(potassium)-chloride cotransporter (Na-K-CL symporter)	0.47	+	end	11	Membrane; multi-pass membrane protein				1060
Q805D4 UniProt NPD GO	ANFC3_FUGRU	C-type natriuretic peptide 3 precursor	0.47	+	exc	0	Secreted protein				158
Q800I8 UniProt NPD GO	ANFC3_ORYLA	C-type natriuretic peptide 3 precursor	0.47	-	exc	0	Secreted protein				112
O02755 UniProt NPD GO	CEBPB_BOVIN	CCAAT/enhancer-binding protein beta (C/EBP beta)	0.47	+	nuc	0	Nucleus				348
Q05826 UniProt NPD GO	CEBPB_CHICK	CCAAT/enhancer-binding protein beta (C/EBP beta) (Transcription factor NF-M) (CCR protein)	0.47	+	nuc	0	Nucleus				328
Q9NNX6 UniProt NPD GO	CD209_HUMAN	CD209 antigen (Dendritic cell-specific ICAM-3-grabbing nonintegrin 1) (DC-SIGN1) (DC-SIGN) (C-type l ...	0.47	-	nuc	0	Isoform 1, isoform 2, isoform 3, isoform 4, isoform 5: Cell membrane; single-pass type II membrane p ...	membrane [TAS]	604672	2B6B	404
Q9BT78 UniProt NPD GO	CSN4_HUMAN	COP9 signalosome complex subunit 4 (Signalosome subunit 4) (SGN4) (JAB1-containing signalosome subun ...	0.47	-	cyt	0	Cytoplasm. Nucleus				406

You are viewing entries 26751 to 26800 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.