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
P82279 UniProt NPD GO	CRUM1_HUMAN	Crumbs homolog 1 precursor	0.29	-	end	2 *	Isoform 1: Cell membrane; apical cell membrane; single-pass type I membrane protein. Distributed at ...		604210		1406
P14944 UniProt NPD GO	CHH_CARMA	Crustacean hyperglycemic hormones precursor [Contains: CHH precursor-related peptide (CPRP); Crustac ...	0.29	-	nuc	1 *	Secreted protein				142
Q9GZR3 UniProt NPD GO	CFC1_HUMAN	Cryptic protein precursor	0.29	-	exc	0			608808		223
P20630 UniProt NPD GO	COL12_CAEEL	Cuticle collagen 12 precursor	0.29	-	nuc	1 *					316
P91285 UniProt NPD GO	DPY5_CAEEL	Cuticle collagen dpy-5 (Protein dumpy-5)	0.29	+	exc	1 *					284
P20784 UniProt NPD GO	ROL6_CAEEL	Cuticle collagen rol-6 (Protein roller-6)	0.29	-	exc	1 *					348
P25009 UniProt NPD GO	PUC1_SCHPO	Cyclin puc1	0.29	-	nuc	0					359
Q15828 UniProt NPD GO	CYTM_HUMAN	Cystatin M precursor (Cystatin E)	0.29	-	exc	0	Secreted protein		601891		149
P01036 UniProt NPD GO	CYTS_HUMAN	Cystatin S precursor (Salivary acidic protein 1) (Cystatin SA-III)	0.29	-	exc	0			123857		141
P84807 UniProt NPD GO	CR25A_NAJHH	Cysteine-rich venom protein 25-A (CRVP-25h-A) (Fragment)	0.29	-	nuc	0	Secreted protein	extracellular region [IDA]			29
O97598 UniProt NPD GO	CMAH_PANTR	Cytidine monophosphate-N-acetylneuraminic acid hydroxylase (EC 1.14.18.2) (CMP-N-acetylneuraminate m ...	0.29	-	cyt	0	Cytoplasm (By similarity)				590
Q9QZ82 UniProt NPD GO	CP11A_MOUSE	Cytochrome P450 11A1, mitochondrial precursor (EC 1.14.15.6) (CYPXIA1) (P450(scc)) (Cholesterol side ...	0.29	-	mit	0	Mitochondrion	mitochondrion [IDA]			526
Q92111 UniProt NPD GO	CP19A_ICTPU	Cytochrome P450 19A1 (EC 1.14.14.1) (Aromatase) (CYPXIX) (Estrogen synthetase) (P-450AROM)	0.29	-	end	0	Membrane; peripheral membrane protein				524
Q64429 UniProt NPD GO	CP1B1_MOUSE	Cytochrome P450 1B1 (EC 1.14.14.1) (CYPIB1) (P450CMEF) (P450EF)	0.29	-	end	0	Endoplasmic reticulum; endoplasmic reticulum membrane; peripheral membrane protein				543
P00191 UniProt NPD GO	CP21A_BOVIN	Cytochrome P450 21 (EC 1.14.99.10) (Cytochrome P450 XXI) (Steroid 21-hydroxylase) (21-OHase) (P450-C ...	0.29	-	end	1 *	Endoplasmic reticulum; endoplasmic reticulum membrane; peripheral membrane protein				496
P15540 UniProt NPD GO	CP21A_PIG	Cytochrome P450 21 (EC 1.14.99.10) (Cytochrome P450 XXI) (Steroid 21-hydroxylase) (21-OHase) (P450-C ...	0.29	+	end	1 *	Endoplasmic reticulum; endoplasmic reticulum membrane; peripheral membrane protein				492
Q9DBG1 UniProt NPD GO	CP27A_MOUSE	Cytochrome P450 27, mitochondrial precursor (EC 1.14.13.15) (Cytochrome P-450C27/25) (Sterol 26-hydr ...	0.29	-	cyt	0	Mitochondrion (By similarity)	mitochondrial inner membrane [IDA] mitochondrion [IDA]			533
Q16696 UniProt NPD GO	CP2AD_HUMAN	Cytochrome P450 2A13 (EC 1.14.14.1) (CYPIIA13)	0.29	-	mit	1 *	Endoplasmic reticulum; endoplasmic reticulum membrane; peripheral membrane protein		608055		494
O55071 UniProt NPD GO	CP2BJ_MOUSE	Cytochrome P450 2B19 (EC 1.14.14.1) (CYPIIB19)	0.29	-	end	0	Endoplasmic reticulum; endoplasmic reticulum membrane; peripheral membrane protein				492
P19225 UniProt NPD GO	CP270_RAT	Cytochrome P450 2C70 (EC 1.14.14.1) (CYPIIC70) (P-450Md) (P450 P49)	0.29	-	end	1 *	Endoplasmic reticulum; endoplasmic reticulum membrane; peripheral membrane protein	microsome [NAS]			489
P37118 UniProt NPD GO	C71A2_SOLME	Cytochrome P450 71A2 (EC 1.14.-.-) (CYPLXXIA2) (P-450EG4)	0.29	-	nuc	1 *					505
Q9LTM4 UniProt NPD GO	C71BJ_ARATH	Cytochrome P450 71B19 (EC 1.14.-.-)	0.29	-	nuc	1 *					502
Q6FVQ3 UniProt NPD GO	COX19_CANGA	Cytochrome c oxidase assembly protein COX19	0.29	-	nuc	0	Cytoplasm (By similarity). Mitochondrion; mitochondrial intermembrane space (By similarity)				86
Q7Z4L0 UniProt NPD GO	COX83_HUMAN	Cytochrome c oxidase polypeptide 8 isoform 3, mitochondrial precursor (EC 1.9.3.1) (Cytochrome c oxi ...	0.29	-	nuc	1 *	Mitochondrion; mitochondrial inner membrane				72
P08574 UniProt NPD GO	CY1_HUMAN	Cytochrome c1, heme protein, mitochondrial precursor (Cytochrome c-1)	0.29	-	nuc	0	Mitochondrion; mitochondrial intermembrane space	mitochondrion [TAS]	123980		325
O70512 UniProt NPD GO	CISH_RAT	Cytokine-inducible SH2-containing protein (CIS) (CIS-1) (Suppressor of cytokine signaling) (SOCS) (F ...	0.29	-	nuc	0					256
Q91V12 UniProt NPD GO	BACH_MOUSE	Cytosolic acyl coenzyme A thioester hydrolase (EC 3.1.2.2) (Long chain acyl-CoA thioester hydrolase) ...	0.29	-	cyt	0	Isoform A, isoform D: Cytoplasm	cytosol [IDA]			381
P58821 UniProt NPD GO	D1IP_RAT	D1 dopamine receptor-interacting protein calcyon	0.29	-	nuc	1	Membrane; single-pass type III membrane protein (Potential)				226
Q6CGR3 UniProt NPD GO	DAD2_YARLI	DASH complex subunit DAD2 (Outer kinetochore protein DAD2)	0.29	-	mit	0	Nucleus (By similarity). Associates with the mitotic spindle and the kinetochore (By similarity)				114
Q6BLH9 UniProt NPD GO	DAD3_DEBHA	DASH complex subunit DAD3 (Outer kinetochore protein DAD3)	0.29	-	nuc	0	Nucleus (By similarity). Associates with the mitotic spindle and the kinetochore (By similarity)				143
Q8S4W7 UniProt NPD GO	GAI1_VITVI	DELLA protein GAI1 (Gibberellic acid-insensitive mutant protein 1) (VvGAI1)	0.29	-	cyt	0	Nucleus (By similarity)				590
Q7YR23 UniProt NPD GO	ABC3G_MACMU	DNA dC->dU-editing enzyme APOBEC-3G (EC 3.5.4.-) (Fragment)	0.29	-	cyt	0	Cytoplasm (By similarity). Mainly. Nucleus (By similarity). Small amount are found in the nucleus (B ...				370
P56347 UniProt NPD GO	DNE1_CHLVU	DNA endonuclease I-CvuI (EC 3.1.-.-) (23S rRNA intron protein)	0.29	-	cyt	0	Plastid; chloroplast				161
P07992 UniProt NPD GO	ERCC1_HUMAN	DNA excision repair protein ERCC-1	0.29	-	cyt	0	Nucleus	nucleotide-excision repair complex [IDA]	126380	2A1J	297
O15318 UniProt NPD GO	RPO3G_HUMAN	DNA-directed RNA polymerase III subunit G (EC 2.7.7.6) (DNA-directed RNA polymerase III 32 kDa polyp ...	0.29	-	nuc	0	Nucleus (Potential)	DNA-directed RNA polymerase III complex [TAS]			233
Q9MTJ3 UniProt NPD GO	RPOA_OENHO	DNA-directed RNA polymerase alpha chain (EC 2.7.7.6) (PEP) (Plastid-encoded RNA polymerase subunit a ...	0.29	-	mit	0	Plastid; chloroplast				367
Q2MIF6 UniProt NPD GO	RPOA_SOLBU	DNA-directed RNA polymerase alpha chain (EC 2.7.7.6) (PEP) (Plastid-encoded RNA polymerase subunit a ...	0.29	-	mit	0	Plastid; chloroplast				337
Q2VEE8 UniProt NPD GO	RPOA_SOLTU	DNA-directed RNA polymerase alpha chain (EC 2.7.7.6) (PEP) (Plastid-encoded RNA polymerase subunit a ...	0.29	-	mit	0	Plastid; chloroplast				337
Q8HUH0 UniProt NPD GO	RPC2B_CHLRE	DNA-directed RNA polymerase beta' chain C-terminal subunit (EC 2.7.7.6) (PEP) (Plastid-encoded RNA p ...	0.29	-	cyt	0	Plastid; chloroplast				489
Q5EAE6 UniProt NPD GO	DAP1_BOVIN	Death-associated protein 1 (DAP-1)	0.29	-	nuc	0					101
P82106 UniProt NPD GO	DEF5_RAT	Defensin 5 precursor (RD-5) (Enteric defensin)	0.29	-	exc	0	Secreted protein				93
P46524 UniProt NPD GO	CO410_WHEAT	Dehydrin COR410 (Cold-induced COR410 protein)	0.29	-	nuc	0					262
Q64368 UniProt NPD GO	DAZL_MOUSE	Deleted in azoospermia-like (DAZ-like autosomal) (Deleted in azoospermia-like 1)	0.29	-	nuc	0	Cytoplasm	cytoplasm [IDA]			298
P02521 UniProt NPD GO	ARLY1_CHICK	Delta-1 crystallin (Delta crystallin I)	0.29	-	nuc	0					465
P80370 UniProt NPD GO	DLK_HUMAN	Delta-like protein precursor (DLK) (pG2) [Contains: Fetal antigen 1 (FA1)]	0.29	-	exc	1	Membrane; single-pass type I membrane protein	extracellular space [TAS] integral to membrane [TAS] soluble fraction [TAS]	176290		383
P00981 UniProt NPD GO	IVBKI_DENPO	Dendrotoxin-K precursor (DTX-K) (Venom basic protease inhibitor K) (Fragment)	0.29	-	vac	0	Secreted protein			1DTK	79
Q6GLZ1 UniProt NPD GO	DENR_XENLA	Density-regulated protein (DRP)	0.29	-	cyt	0					198
O43583 UniProt NPD GO	DENR_HUMAN	Density-regulated protein (DRP) (Protein DRP1) (Smooth muscle cell-associated protein 3) (SMAP-3)	0.29	-	cyt	0			604550		198
Q9NAH4 UniProt NPD GO	DENR_CAEEL	Density-regulated protein homolog	0.29	+	cyt	0					192
P20192 UniProt NPD GO	DGKA_PIG	Diacylglycerol kinase alpha (EC 2.7.1.107) (Diglyceride kinase alpha) (DGK-alpha) (DAG kinase alpha) ...	0.29	-	cyt	0					734

You are viewing entries 41151 to 41200 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.