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
P50661 UniProt NPD GO	COX2_CALGO	Cytochrome c oxidase subunit 2 (EC 1.9.3.1) (Cytochrome c oxidase polypeptide II) (Fragment)	0.03	-	end	2 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				216
O03892 UniProt NPD GO	COX2_NOTPE	Cytochrome c oxidase subunit 2 (EC 1.9.3.1) (Cytochrome c oxidase polypeptide II) (Fragment)	0.03	-	end	1 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				198
Q35242 UniProt NPD GO	COX3_OCTDO	Cytochrome c oxidase subunit 3 (EC 1.9.3.1) (Cytochrome c oxidase polypeptide III) (Fragment)	0.03	-	end	5 *					204
O46588 UniProt NPD GO	COX41_PRECR	Cytochrome c oxidase subunit 4 isoform 1 (EC 1.9.3.1) (Cytochrome c oxidase subunit IV isoform 1) (C ...	0.03	-	nuc	1	Mitochondrion; mitochondrial inner membrane				99
P10174 UniProt NPD GO	COX7_YEAST	Cytochrome c oxidase subunit 7 (EC 1.9.3.1) (Cytochrome c oxidase polypeptide VII)	0.03	-	nuc	1 *	Mitochondrion; mitochondrial inner membrane	respiratory chain complex IV (sensu Eukaryota) [IPI]			59
Q757F0 UniProt NPD GO	COX9_ASHGO	Cytochrome c oxidase subunit 7A precursor (EC 1.9.3.1) (Cytochrome c oxidase polypeptide VIIA)	0.03	-	cyt	1 *	Mitochondrion; mitochondrial inner membrane (By similarity)				59
O14548 UniProt NPD GO	COX7R_HUMAN	Cytochrome c oxidase subunit VIIa-related protein, mitochondrial precursor (COX7a-related protein) ( ...	0.03	-	mit	1	Mitochondrion (By similarity)		605771		114
P56391 UniProt NPD GO	CX6B1_MOUSE	Cytochrome c oxidase subunit VIb isoform 1 (EC 1.9.3.1) (COX VIb-1)	0.03	-	cyt	0	Mitochondrion; mitochondrial intermembrane space (By similarity)	mitochondrial inner membrane [IDA] mitochondrion [IDA]			85
Q6C0Z6 UniProt NPD GO	CCPR_YARLI	Cytochrome c peroxidase, mitochondrial precursor (EC 1.11.1.5) (CCP)	0.03	-	mit	1 *	Mitochondrion; mitochondrial matrix (By similarity)				340
P04657 UniProt NPD GO	CYC1_DROME	Cytochrome c-1 (Cytochrome c-distal)	0.03	-	cyt	0	Mitochondrion; mitochondrial matrix	mitochondrion [IDA]			104
P84030 UniProt NPD GO	CYC2_CERCA	Cytochrome c-2	0.03	-	cyt	0	Mitochondrion; mitochondrial matrix	mitochondrion [ISS]			107
P84029 UniProt NPD GO	CYC2_DROME	Cytochrome c-2 (Cytochrome c-proximal)	0.03	-	cyt	0	Mitochondrion; mitochondrial matrix	mitochondrion [IDA]			107
P48263 UniProt NPD GO	CY550_CYAPA	Cytochrome c-550 precursor (Cytochrome c550)	0.03	-	cyt	1 *	Plastid; cyanelle				162
O78454 UniProt NPD GO	CY550_GUITH	Cytochrome c-550 precursor (Cytochrome c550)	0.03	-	exc	1 *	Plastid; chloroplast				162
P49510 UniProt NPD GO	CY550_ODOSI	Cytochrome c-550 precursor (Cytochrome c550)	0.03	-	mit	1 *	Plastid; chloroplast				163
Q8WKJ8 UniProt NPD GO	CYC6_PORYE	Cytochrome c6 precursor (Soluble cytochrome f) (Cytochrome c553) (Cytochrome c-553)	0.03	-	exc	1 *	Plastid; chloroplast; chloroplast thylakoid lumen (By similarity)			1GDV	110
Q8CII9 UniProt NPD GO	CRLF2_MOUSE	Cytokine receptor-like factor 2 precursor (Type I cytokine receptor delta 1) (Cytokine receptor-like ...	0.03	-	end	0	Isoform 1, isoform 3: Cell membrane; single-pass type I membrane protein. Isoform 2: Secreted protei ...				359
Q86FQ0 UniProt NPD GO	ACTP1_SAGRO	Cytolysin Src-1 precursor (Src I)	0.03	-	mit	0	Secreted protein. Found in nematocyst				216
P78594 UniProt NPD GO	FCA1_CANAL	Cytosine deaminase (EC 3.5.4.1) (Cytosine aminohydrolase)	0.03	-	cyt	0					150
Q12178 UniProt NPD GO	FCY1_YEAST	Cytosine deaminase (EC 3.5.4.1) (Cytosine aminohydrolase)	0.03	-	nuc	0		cytoplasm [IDA] nucleus [IDA]		1YSD	158
P25517 UniProt NPD GO	CX5_NAJMO	Cytotoxin 5 (CTX V)	0.03	-	nuc	0	Secreted protein				60
P18901 UniProt NPD GO	DRD1_RAT	D(1A) dopamine receptor	0.03	-	end	6 *	Cell membrane; multi-pass membrane protein. Endoplasmic reticulum; endoplasmic reticulum membrane; m ...	integral to membrane [IDA]			446
O02664 UniProt NPD GO	DRD1_RABIT	D(1A) dopamine receptor (Fragment)	0.03	-	end	4 *	Cell membrane; multi-pass membrane protein. Endoplasmic reticulum; endoplasmic reticulum membrane; m ...				180
P25115 UniProt NPD GO	DRD5_RAT	D(1B) dopamine receptor (D(5) dopamine receptor)	0.03	-	end	7 *	Membrane; multi-pass membrane protein				475
P42291 UniProt NPD GO	DRD1C_XENLA	D(1C) dopamine receptor	0.03	-	end	7 *	Membrane; multi-pass membrane protein				465
O04130 UniProt NPD GO	SERA_ARATH	D-3-phosphoglycerate dehydrogenase, chloroplast precursor (EC 1.1.1.95) (3-PGDH)	0.03	-	mit	0	Plastid; chloroplast				624
P38115 UniProt NPD GO	ARA1_YEAST	D-arabinose dehydrogenase [NAD(P)+] heavy chain (EC 1.1.1.117)	0.03	-	cyt	0	Cytoplasm	cytosol [IDA]			344
Q02338 UniProt NPD GO	BDH_HUMAN	D-beta-hydroxybutyrate dehydrogenase, mitochondrial precursor (EC 1.1.1.30) (BDH) (3-hydroxybutyrate ...	0.03	-	mit	0	Mitochondrion; mitochondrial matrix	mitochondrial matrix [NAS]	603063		343
P39976 UniProt NPD GO	DLD3_YEAST	D-lactate dehydrogenase [cytochrome] 3 (EC 1.1.2.4) (D-lactate ferricytochrome C oxidoreductase) (D- ...	0.03	-	cyt	0	Cytoplasm	cytoplasm [IDA] soluble fraction [IDA]			496
P18470 UniProt NPD GO	HB2D_CANFA	DLA class II histocompatibility antigen, DR-1 beta chain precursor	0.03	-	end	2 *	Membrane; single-pass type I membrane protein (Potential)				266
Q5E9B8 UniProt NPD GO	RPB7_BOVIN	DNA-directed RNA polymerase II 19 kDa polypeptide (EC 2.7.7.6) (RPB7)	0.03	-	cyt	0	Nucleus (By similarity)				172
Q7ZW41 UniProt NPD GO	RPB7_BRARE	DNA-directed RNA polymerase II 19 kDa polypeptide (EC 2.7.7.6) (RPB7)	0.03	-	cyt	0	Nucleus (By similarity)				172
P62487 UniProt NPD GO	RPB7_HUMAN	DNA-directed RNA polymerase II 19 kDa polypeptide (EC 2.7.7.6) (RPB7)	0.03	-	cyt	0	Nucleus		602013	2C35	172
P62488 UniProt NPD GO	RPB7_MOUSE	DNA-directed RNA polymerase II 19 kDa polypeptide (EC 2.7.7.6) (RPB7)	0.03	-	cyt	0	Nucleus (By similarity)				172
P62489 UniProt NPD GO	RPB7_RAT	DNA-directed RNA polymerase II 19 kDa polypeptide (EC 2.7.7.6) (RPB7)	0.03	-	cyt	0	Nucleus (By similarity)				172
Q39211 UniProt NPD GO	RPB3A_ARATH	DNA-directed RNA polymerase II 36 kDa polypeptide A (EC 2.7.7.6) (RNA polymerase II subunit 3)	0.03	-	nuc	0	Nucleus				319
Q7PVQ9 UniProt NPD GO	RPO2J_ANOGA	DNA-directed RNA polymerase II subunit J (EC 2.7.7.6)	0.03	-	cyt	0	Nucleus (By similarity)				117
Q9VJE4 UniProt NPD GO	RPO2J_DROME	DNA-directed RNA polymerase II subunit J (EC 2.7.7.6) (DNA-directed RNA polymerase II 13.3 kDa polyp ...	0.03	-	cyt	0	Nucleus (By similarity)				117
Q09177 UniProt NPD GO	RPC19_SCHPO	DNA-directed RNA polymerases I and III 14 kDa polypeptide (EC 2.7.7.6)	0.03	-	cyt	0	Nucleus	DNA-directed RNA polymerase I complex [IGI] DNA-directed RNA polymerase III complex [IGI]			125
Q8NJQ3 UniProt NPD GO	DEC1_COCHE	Decarboxylase DEC1 (EC 4.1.1.-)	0.03	-	cyt	0					253
Q9TTE2 UniProt NPD GO	PGS2_SHEEP	Decorin precursor (Bone proteoglycan II) (PG-S2) (PG40)	0.03	-	nuc	0	Secreted protein; extracellular space; extracellular matrix (By similarity)				360
Q52DM9 UniProt NPD GO	DCN1_MAGGR	Defective in cullin neddylation protein 1	0.03	-	cyt	0					281
Q10745 UniProt NPD GO	DEFI_ALLDI	Defensin	0.03	-	cyt	0	Secreted protein				43
Q17027 UniProt NPD GO	DEFI_ANOGA	Defensin precursor	0.03	-	exc	0	Secreted protein				102
P36192 UniProt NPD GO	DEFI_DROME	Defensin precursor	0.03	-	exc	0	Secreted protein				92
P83404 UniProt NPD GO	DEFI_PHLDU	Defensin precursor	0.03	-	mit	0	Secreted protein	extracellular region [IDA]			98
Q6GU94 UniProt NPD GO	DEFL1_CENLL	Defensin-1 precursor (Cll-dlp)	0.03	-	exc	1 *	Secreted protein	extracellular region [NAS]			56
P81602 UniProt NPD GO	DEFB_AEDAE	Defensin-B	0.03	-	nuc	0	Secreted protein				40
P42758 UniProt NPD GO	XERO2_ARATH	Dehydrin Xero 2 (Low-temperature-induced protein LTI30)	0.03	-	nuc	0					193
Q96LJ7 UniProt NPD GO	DHRS1_HUMAN	Dehydrogenase/reductase SDR family member 1 (EC 1.1.-.-)	0.03	-	pox	0					313

You are viewing entries 79701 to 79750 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.