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
O78751 UniProt NPD GO	ATP8_SHEEP	ATP synthase protein 8 (EC 3.6.3.14) (ATPase subunit 8) (A6L)	0.10	-	nuc	1 *	Mitochondrion; mitochondrial membrane; single-pass membrane protein				66
O78475 UniProt NPD GO	ATPA_GUITH	ATP synthase subunit alpha (EC 3.6.3.14) (ATPase subunit alpha) (ATP synthase F1 sector subunit alph ...	0.10	-	cyt	0	Plastid; chloroplast; chloroplast thylakoid membrane; peripheral membrane protein (By similarity)				502
Q9TL16 UniProt NPD GO	ATPA_NEPOL	ATP synthase subunit alpha (EC 3.6.3.14) (ATPase subunit alpha) (ATP synthase F1 sector subunit alph ...	0.10	-	cyt	0	Plastid; chloroplast; chloroplast thylakoid membrane; peripheral membrane protein (By similarity)				501
Q32RS8 UniProt NPD GO	ATPA_STAPU	ATP synthase subunit alpha (EC 3.6.3.14) (ATPase subunit alpha) (ATP synthase F1 sector subunit alph ...	0.10	-	cyt	0	Plastid; chloroplast; chloroplast thylakoid membrane; peripheral membrane protein (By similarity)				512
P84582 UniProt NPD GO	ATPA_POPEU	ATP synthase subunit alpha (EC 3.6.3.14) (ATPase subunit alpha) (ATP synthase F1 sector subunit alph ...	0.10	-	cyt	0	Plastid; chloroplast; chloroplast thylakoid membrane; peripheral membrane protein (By similarity)				55
Q9QY44 UniProt NPD GO	ABCD2_RAT	ATP-binding cassette sub-family D member 2 (Adrenoleukodystrophy-related protein)	0.10	-	mit	0	Peroxisome; peroxisomal membrane; multi-pass membrane protein (By similarity)				741
P07712 UniProt NPD GO	AGN5_APLCA	Abdominal ganglion neuropeptides L5-67 precursor [Contains: Luqin; Luqin-B; Luqin-C; Proline-rich ma ...	0.10	-	mit	1 *	Secreted protein				112
Q02066 UniProt NPD GO	AAIP_WHEAT	Abscisic acid-inducible protein kinase (EC 2.7.11.1) (Fragment)	0.10	-	nuc	0					332
P67806 UniProt NPD GO	A70A_DROMA	Accessory gland-specific peptide 70A precursor (Paragonial peptide B)	0.10	-	vac	0	Secreted protein				55
O18417 UniProt NPD GO	A70A_DROSE	Accessory gland-specific peptide 70A precursor (Paragonial peptide B)	0.10	-	vac	0	Secreted protein				55
P67807 UniProt NPD GO	A70A_DROSI	Accessory gland-specific peptide 70A precursor (Paragonial peptide B)	0.10	-	vac	0	Secreted protein				55
P09690 UniProt NPD GO	ACHB_MOUSE	Acetylcholine receptor protein subunit beta precursor	0.10	-	end	4	Membrane; multi-pass membrane protein	Golgi apparatus [IDA] plasma membrane [IDA]			501
P02717 UniProt NPD GO	ACHD_CHICK	Acetylcholine receptor protein subunit delta precursor	0.10	-	end	4	Membrane; multi-pass membrane protein				513
P56161 UniProt NPD GO	ACES_ANOST	Acetylcholinesterase precursor (EC 3.1.1.7) (AChE)	0.10	-	end	2 *	Cell membrane; lipid-anchor; GPI-anchor. Attached to the membrane of the neuronal cholinergic synaps ...				664
O62763 UniProt NPD GO	ACES_FELCA	Acetylcholinesterase precursor (EC 3.1.1.7) (AChE)	0.10	-	exc	1 *					611
P04058 UniProt NPD GO	ACES_TORCA	Acetylcholinesterase precursor (EC 3.1.1.7) (AChE)	0.10	-	exc	0	Isoform H: Cell membrane; lipid-anchor; GPI-anchor. Isoform T: Cell membrane; peripheral membrane pr ...			4ACE	586
O04866 UniProt NPD GO	ARGD_ALNGL	Acetylornithine aminotransferase, mitochondrial precursor (EC 2.6.1.11) (ACOAT) (Acetylornithine tra ...	0.10	-	mit	0	Mitochondrion				451
P29000 UniProt NPD GO	INVA_LYCES	Acid beta-fructofuranosidase precursor (EC 3.2.1.26) (Acid sucrose hydrolase) (Acid invertase) (AI) ...	0.10	-	mit	1 *	Vacuole				636
O24509 UniProt NPD GO	INVA_PHAVU	Acid beta-fructofuranosidase precursor (EC 3.2.1.26) (Acid sucrose hydrolase) (Acid invertase) (AI) ...	0.10	-	cyt	0	Vacuole (Potential)				651
Q9ER34 UniProt NPD GO	ACON_RAT	Aconitate hydratase, mitochondrial precursor (EC 4.2.1.3) (Citrate hydro-lyase) (Aconitase)	0.10	-	mit	0	Mitochondrion (By similarity)				780
Q3C257 UniProt NPD GO	ACR1A_ACTEQ	Acrorhagin-1a precursor (Acrorhagin Ia)	0.10	-	nuc	0	Secreted protein. Found in nematocyst				72
P48465 UniProt NPD GO	ACT_CRYNV	Actin	0.10	-	cyt	0	Cytoplasm				375
P53483 UniProt NPD GO	ACTX_FUGRU	Actin, alpha anomalous	0.10	-	cyt	0	Cytoplasm				376
P62739 UniProt NPD GO	ACTA_BOVIN	Actin, aortic smooth muscle (Alpha-actin-2)	0.10	-	cyt	0	Cytoplasm	actin filament [ISS] cytosol [ISS] soluble fraction [ISS] stress fiber [ISS] striated muscle thin filament [ISS]			377
P62736 UniProt NPD GO	ACTA_HUMAN	Actin, aortic smooth muscle (Alpha-actin-2)	0.10	-	cyt	0	Cytoplasm		102620		377
P62737 UniProt NPD GO	ACTA_MOUSE	Actin, aortic smooth muscle (Alpha-actin-2)	0.10	-	cyt	0	Cytoplasm				377
P62740 UniProt NPD GO	ACTA_RABIT	Actin, aortic smooth muscle (Alpha-actin-2)	0.10	-	cyt	0	Cytoplasm				377
P62738 UniProt NPD GO	ACTA_RAT	Actin, aortic smooth muscle (Alpha-actin-2)	0.10	-	cyt	0	Cytoplasm				377
Q93131 UniProt NPD GO	ACTC_BRAFL	Actin, cytoplasmic (BfCA1)	0.10	-	cyt	0	Cytoplasm				375
P79818 UniProt NPD GO	ACTB_ORYLA	Actin, cytoplasmic 1 (Beta-actin) (OlCA1)	0.10	-	cyt	0	Cytoplasm				375
P53465 UniProt NPD GO	ACT1_LYTPI	Actin, cytoskeletal 1 (LPC1)	0.10	-	cyt	0	Cytoplasm. Cytoskeleton				376
P83969 UniProt NPD GO	ACT1_BACDO	Actin, indirect flight muscle	0.10	-	cyt	0	Cytoplasm				376
P83967 UniProt NPD GO	ACT6_DROME	Actin, indirect flight muscle (Actin-88F)	0.10	-	cyt	0	Cytoplasm				376
P83968 UniProt NPD GO	ACT6_DROSI	Actin, indirect flight muscle (Actin-88F)	0.10	-	cyt	0	Cytoplasm				376
P53467 UniProt NPD GO	ACTM_MOLOC	Actin, larval muscle-type (A1)	0.10	-	cyt	0	Cytoplasm				378
O15998 UniProt NPD GO	ACTM_CIOSA	Actin, muscle	0.10	-	cyt	0	Cytoplasm				378
P26198 UniProt NPD GO	ACTM_STYCL	Actin, muscle	0.10	-	cyt	0	Cytoplasm				378
P53475 UniProt NPD GO	ACTN_STYCL	Actin, muscle	0.10	-	cyt	0	Cytoplasm				378
P27130 UniProt NPD GO	ACT2_HALRO	Actin, muscle 2/4/4A	0.10	-	cyt	0	Cytoplasm				378
P07837 UniProt NPD GO	ACT2_BOMMO	Actin, muscle A2	0.10	-	cyt	0	Cytoplasm				376
P17126 UniProt NPD GO	ACT_HYDAT	Actin, non-muscle 6.2	0.10	-	cyt	0	Cytoplasm				376
O18499 UniProt NPD GO	ACT1_SACKO	Actin-1	0.10	-	cyt	0	Cytoplasm				376
Q7RPB4 UniProt NPD GO	ACT2_PLAYO	Actin-2 (Actin II)	0.10	-	cyt	0	Cytoplasm				376
P42023 UniProt NPD GO	ACTZ_PNECA	Actin-2 (Actin II) (Centractin-like protein)	0.10	-	cyt	0					385
Q07749 UniProt NPD GO	ADF2_CAEEL	Actin-depolymerizing factor 2 (Uncoordinated protein 60)	0.10	-	cyt	0		cytoplasm [IDA]			152
P53487 UniProt NPD GO	ARP2_ACACA	Actin-like protein 2 (Actin-related protein 2)	0.10	-	cyt	0					388
P53488 UniProt NPD GO	ARP2_CHICK	Actin-like protein 2 (Actin-related protein 2) (Actin-like protein ACTL)	0.10	-	cyt	0					394
O73723 UniProt NPD GO	ARP3_FUGRU	Actin-like protein 3 (Actin-related protein 3)	0.10	-	cyt	0					418
O14561 UniProt NPD GO	ACPM_HUMAN	Acyl carrier protein, mitochondrial precursor (ACP) (NADH-ubiquinone oxidoreductase 9.6 kDa subunit) ...	0.10	-	mit	0	Mitochondrion		603836		156
O02858 UniProt NPD GO	ACOD_PIG	Acyl-CoA desaturase (EC 1.14.19.1) (Stearoyl-CoA desaturase) (Fatty acid desaturase) (Delta(9)-desat ...	0.10	-	end	4	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (Probable)				334

You are viewing entries 63901 to 63950 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.