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
Q36118 UniProt NPD GO	CYB_TOMRA	Cytochrome b (Fragment)	0.02	-	end	3 *					176
P92857 UniProt NPD GO	CYB_TRIST	Cytochrome b (Fragment)	0.02	-	end	5 *					214
Q61093 UniProt NPD GO	CY24B_MOUSE	Cytochrome b-245 heavy chain (p22 phagocyte B-cytochrome) (Neutrophil cytochrome b 91 kDa polypeptid ...	0.02	-	end	4 *	Membrane; multi-pass membrane protein	cytoplasm [IDA] plasma membrane [IDA]			570
Q9Y706 UniProt NPD GO	CYB5_MORAP	Cytochrome b5	0.02	-	cyt	0					130
P00172 UniProt NPD GO	CYB5_PIG	Cytochrome b5	0.02	-	nuc	1	Isoform 1: Microsome; microsomal membrane; peripheral membrane protein. Bound to the cytoplasmic sid ...				133
Q9HFV1 UniProt NPD GO	CYB5_RHIST	Cytochrome b5	0.02	-	nuc	0					131
Q9V4N3 UniProt NPD GO	CYB5_DROME	Cytochrome b5 (CYTB5)	0.02	-	cyt	1	Endoplasmic reticulum; endoplasmic reticulum membrane; peripheral membrane protein; cytoplasmic side ...				134
Q9CQX2 UniProt NPD GO	CYB5B_MOUSE	Cytochrome b5 type B precursor (Cytochrome b5 outer mitochondrial membrane isoform)	0.02	-	cyt	1	Mitochondrion; mitochondrial outer membrane (By similarity)	mitochondrial inner membrane [IDA]			146
Q5RDJ5 UniProt NPD GO	CYB5B_PONPY	Cytochrome b5 type B precursor (Cytochrome b5 outer mitochondrial membrane isoform)	0.02	-	cyt	1	Mitochondrion; mitochondrial outer membrane (By similarity)				146
P56779 UniProt NPD GO	PSBE_ARATH	Cytochrome b559 alpha subunit (PSII reaction center subunit V)	0.02	-	mit	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				82
Q85FQ2 UniProt NPD GO	PSBE_CYAME	Cytochrome b559 alpha subunit (PSII reaction center subunit V)	0.02	-	mit	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				81
Q49KY2 UniProt NPD GO	PSBE_EUCGG	Cytochrome b559 alpha subunit (PSII reaction center subunit V)	0.02	-	mit	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				83
Q9THZ3 UniProt NPD GO	PSBE_GINBI	Cytochrome b559 alpha subunit (PSII reaction center subunit V)	0.02	-	mit	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				82
Q6B8K4 UniProt NPD GO	PSBE_GRATL	Cytochrome b559 alpha subunit (PSII reaction center subunit V)	0.02	-	mit	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				83
Q5SD43 UniProt NPD GO	PSBE_HUPLU	Cytochrome b559 alpha subunit (PSII reaction center subunit V)	0.02	-	mit	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				83
Q332W1 UniProt NPD GO	PSBE_LACSA	Cytochrome b559 alpha subunit (PSII reaction center subunit V)	0.02	-	mit	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				83
Q2MI83 UniProt NPD GO	PSBE_LYCES	Cytochrome b559 alpha subunit (PSII reaction center subunit V)	0.02	-	mit	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				83
Q3C1L3 UniProt NPD GO	PSBE_NICSY	Cytochrome b559 alpha subunit (PSII reaction center subunit V)	0.02	-	mit	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				83
Q76IC3 UniProt NPD GO	PSBE_NICTO	Cytochrome b559 alpha subunit (PSII reaction center subunit V)	0.02	-	mit	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				82
Q68RY9 UniProt NPD GO	PSBE_PANGI	Cytochrome b559 alpha subunit (PSII reaction center subunit V)	0.02	-	mit	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				82
Q6YXL9 UniProt NPD GO	PSBE_PHYPA	Cytochrome b559 alpha subunit (PSII reaction center subunit V)	0.02	-	mit	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				83
P69385 UniProt NPD GO	PSBE_POPDE	Cytochrome b559 alpha subunit (PSII reaction center subunit V)	0.02	-	mit	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				82
P51391 UniProt NPD GO	PSBE_PORPU	Cytochrome b559 alpha subunit (PSII reaction center subunit V)	0.02	-	cyt	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				83
Q3ZJ22 UniProt NPD GO	PSBE_PSEAK	Cytochrome b559 alpha subunit (PSII reaction center subunit V)	0.02	-	mit	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				83
Q8WI04 UniProt NPD GO	PSBE_PSINU	Cytochrome b559 alpha subunit (PSII reaction center subunit V)	0.02	-	mit	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				82
Q2MIH0 UniProt NPD GO	PSBE_SOLBU	Cytochrome b559 alpha subunit (PSII reaction center subunit V)	0.02	-	mit	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				83
Q2VEG1 UniProt NPD GO	PSBE_SOLTU	Cytochrome b559 alpha subunit (PSII reaction center subunit V)	0.02	-	mit	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				83
P69384 UniProt NPD GO	PSBE_TOBAC	Cytochrome b559 alpha subunit (PSII reaction center subunit V)	0.02	-	mit	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				82
Q32RJ5 UniProt NPD GO	PSBE_ZYGCR	Cytochrome b559 alpha subunit (PSII reaction center subunit V)	0.02	-	mit	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				83
Q71L79 UniProt NPD GO	PSBF_CEDDE	Cytochrome b559 beta subunit (PSII reaction center subunit VI)	0.02	-	mit	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				39
Q08363 UniProt NPD GO	PSBF_CHLRE	Cytochrome b559 beta subunit (PSII reaction center subunit VI)	0.02	-	mit	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				44
P56310 UniProt NPD GO	PSBF_CHLVU	Cytochrome b559 beta subunit (PSII reaction center subunit VI)	0.02	-	mit	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				41
Q85FQ3 UniProt NPD GO	PSBF_CYAME	Cytochrome b559 beta subunit (PSII reaction center subunit VI)	0.02	-	mit	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				40
P19153 UniProt NPD GO	PSBF_CYAPA	Cytochrome b559 beta subunit (PSII reaction center subunit VI)	0.02	-	mit	1 *	Plastid; cyanelle; cyanelle thylakoid membrane; single-pass membrane protein (By similarity)				42
P49474 UniProt NPD GO	PSBF_ODOSI	Cytochrome b559 beta subunit (PSII reaction center subunit VI)	0.02	-	mit	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				43
P51390 UniProt NPD GO	PSBF_PORPU	Cytochrome b559 beta subunit (PSII reaction center subunit VI)	0.02	-	mit	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				44
Q9XQU7 UniProt NPD GO	CYB6_HETTR	Cytochrome b6	0.02	-	end	4 *	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein (By similarity)				219
Q5SD34 UniProt NPD GO	PETG_HUPLU	Cytochrome b6-f complex subunit 5 (Cytochrome b6-f complex subunit V) (Cytochrome b6-f complex subun ...	0.02	-	nuc	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				38
P41614 UniProt NPD GO	PETG_PINTH	Cytochrome b6-f complex subunit 5 (Cytochrome b6-f complex subunit V) (Cytochrome b6-f complex subun ...	0.02	-	mit	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				37
P51318 UniProt NPD GO	PETG_PORPU	Cytochrome b6-f complex subunit 5 (Cytochrome b6-f complex subunit V) (Cytochrome b6-f complex subun ...	0.02	-	nuc	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				37
Q8WI02 UniProt NPD GO	PETG_PSINU	Cytochrome b6-f complex subunit 5 (Cytochrome b6-f complex subunit V) (Cytochrome b6-f complex subun ...	0.02	-	cyt	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				37
Q7YJV7 UniProt NPD GO	PETL_CALFE	Cytochrome b6-f complex subunit 6 (Cytochrome b6-f complex subunit VI) (Cytochrome b6-f complex subu ...	0.02	-	nuc	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				31
Q2L924 UniProt NPD GO	PETL_GOSHI	Cytochrome b6-f complex subunit 6 (Cytochrome b6-f complex subunit VI) (Cytochrome b6-f complex subu ...	0.02	-	nuc	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				31
P19445 UniProt NPD GO	PETL_MAIZE	Cytochrome b6-f complex subunit 6 (Cytochrome b6-f complex subunit VI) (Cytochrome b6-f complex subu ...	0.02	-	nuc	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				31
P00065 UniProt NPD GO	CYC_ARUMA	Cytochrome c	0.02	-	nuc	0	Mitochondrion; mitochondrial matrix				111
P00066 UniProt NPD GO	CYC_NIGDA	Cytochrome c	0.02	-	cyt	0	Mitochondrion; mitochondrial matrix				111
P51369 UniProt NPD GO	CCSA_PORPU	Cytochrome c biogenesis protein ccsA	0.02	-	end	8 *	Plastid; chloroplast				319
P29505 UniProt NPD GO	COX5_DICDI	Cytochrome c oxidase polypeptide 5 (EC 1.9.3.1) (Cytochrome c oxidase polypeptide V)	0.02	-	cyt	0	Mitochondrion; mitochondrial inner membrane				119
P10175 UniProt NPD GO	COX81_BOVIN	Cytochrome c oxidase polypeptide VIII-heart, mitochondrial precursor (EC 1.9.3.1) (Cytochrome c oxid ...	0.02	-	mit	1 *	Mitochondrion; mitochondrial inner membrane			2OCC	70
P80981 UniProt NPD GO	COXM_THUOB	Cytochrome c oxidase polypeptide VIIb-liver (EC 1.9.3.1) (Fragment)	0.02	-		0					20

You are viewing entries 83101 to 83150 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.