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
P05108 UniProt NPD GO	CP11A_HUMAN	Cytochrome P450 11A1, mitochondrial precursor (EC 1.14.15.6) (CYPXIA1) (P450(scc)) (Cholesterol side ...	0.10	-	cyt	0	Mitochondrion		201710		521
Q92113 UniProt NPD GO	CP17A_SQUAC	Cytochrome P450 17A1 (EC 1.14.99.9) (CYPXVII) (P450-C17) (P450c17) (Steroid 17-alpha-hydroxylase/17, ...	0.10	-	mit	1 *					509
P46194 UniProt NPD GO	CP19A_BOVIN	Cytochrome P450 19A1 (EC 1.14.14.1) (Aromatase) (CYPXIX) (Estrogen synthetase) (P-450AROM)	0.10	-	cyt	2 *	Membrane; peripheral membrane protein				503
P79699 UniProt NPD GO	CP19A_COTJA	Cytochrome P450 19A1 (EC 1.14.14.1) (Aromatase) (CYPXIX) (Estrogen synthetase) (P-450AROM) (Fragment ...	0.10	-	end	1 *	Membrane; peripheral membrane protein				327
P15123 UniProt NPD GO	CP2CG_RABIT	Cytochrome P450 2C16 (EC 1.14.14.1) (CYPIIC16)	0.10	-	end	0	Endoplasmic reticulum; endoplasmic reticulum membrane; peripheral membrane protein				487
P24457 UniProt NPD GO	CP2DB_MOUSE	Cytochrome P450 2D11 (EC 1.14.14.1) (CYPIID11) (P450-16-alpha) (CC) (Testosterone 16-alpha hydroxyla ...	0.10	-	nuc	2 *	Endoplasmic reticulum; endoplasmic reticulum membrane; peripheral membrane protein				505
Q64403 UniProt NPD GO	CP2DG_CAVPO	Cytochrome P450 2D16 (EC 1.14.14.1) (CYPIID16)	0.10	-	end	2 *	Endoplasmic reticulum; endoplasmic reticulum membrane; peripheral membrane protein				500
O93299 UniProt NPD GO	CP2K3_ONCMY	Cytochrome P450 2K3 (EC 1.14.14.1) (CYPIIK3) (P450 LMC2)	0.10	-	cyt	0	Endoplasmic reticulum; endoplasmic reticulum membrane; peripheral membrane protein (By similarity)				491
Q64459 UniProt NPD GO	CP3AB_MOUSE	Cytochrome P450 3A11 (EC 1.14.14.1) (CYPIIIA11) (P-450IIIAM1) (P-450UT)	0.10	-	nuc	2 *	Endoplasmic reticulum; endoplasmic reticulum membrane; peripheral membrane protein	microsome [IDA]			504
O18993 UniProt NPD GO	CP3AL_CALJA	Cytochrome P450 3A21 (EC 1.14.14.1) (CYPIIIA21) (P450 CM3A-10)	0.10	-	nuc	3 *	Endoplasmic reticulum; endoplasmic reticulum membrane; peripheral membrane protein	membrane fraction [ISS]			503
Q29496 UniProt NPD GO	CP3AO_SHEEP	Cytochrome P450 3A24 (EC 1.14.14.1) (CYPIIIA24)	0.10	-	end	3 *	Endoplasmic reticulum; endoplasmic reticulum membrane; peripheral membrane protein	membrane fraction [ISS]			503
P33268 UniProt NPD GO	CP3A8_MACFA	Cytochrome P450 3A8 (EC 1.14.14.1) (CYPIIIA8) (P450-MKNF2) (P-450-MK2)	0.10	-	end	2 *	Endoplasmic reticulum; endoplasmic reticulum membrane; peripheral membrane protein	membrane fraction [ISS]			503
Q95031 UniProt NPD GO	CP6B6_HELAM	Cytochrome P450 6B6 (EC 1.14.14.1) (CYPVIB6)	0.10	-	mit	1 *	Endoplasmic reticulum; endoplasmic reticulum membrane; peripheral membrane protein (Potential)				504
O22203 UniProt NPD GO	C98A3_ARATH	Cytochrome P450 98A3 (EC 1.14.-.-)	0.10	-	end	0					508
P00003 UniProt NPD GO	CYC_ATESP	Cytochrome c	0.10	-	cyt	0	Mitochondrion; mitochondrial matrix	cytosol [ISS] mitochondrial intermembrane space [ISS]			104
P38091 UniProt NPD GO	CYC_EMENI	Cytochrome c	0.10	-	nuc	0	Mitochondrion; mitochondrial matrix				113
P68097 UniProt NPD GO	CYC_EQUAS	Cytochrome c	0.10	-	cyt	0	Mitochondrion; mitochondrial matrix				104
P68096 UniProt NPD GO	CYC_EQUBU	Cytochrome c	0.10	-	cyt	0	Mitochondrion; mitochondrial matrix				104
P00007 UniProt NPD GO	CYC_HIPAM	Cytochrome c	0.10	-	cyt	0	Mitochondrion; mitochondrial matrix	cytosol [ISS] mitochondrial intermembrane space [ISS]			104
Q85A51 UniProt NPD GO	CCSA_ANTFO	Cytochrome c biogenesis protein ccsA	0.10	-	end	7 *	Plastid; chloroplast				339
Q6J3Q7 UniProt NPD GO	COX17_CANFA	Cytochrome c oxidase copper chaperone	0.10	-	nuc	0	Mitochondrion; mitochondrial intermembrane space (By similarity)				62
P06810 UniProt NPD GO	COX5_NEUCR	Cytochrome c oxidase polypeptide V, mitochondrial precursor (EC 1.9.3.1)	0.10	-	mit	1	Mitochondrion; mitochondrial inner membrane				171
Q863G0 UniProt NPD GO	COX81_ATEBE	Cytochrome c oxidase polypeptide VIII-heart, mitochondrial precursor (EC 1.9.3.1) (Cytochrome c oxid ...	0.10	-	mit	1 *	Mitochondrion; mitochondrial inner membrane				70
P16221 UniProt NPD GO	COX81_RAT	Cytochrome c oxidase polypeptide VIII-heart, mitochondrial precursor (EC 1.9.3.1) (Cytochrome c oxid ...	0.10	-	nuc	1 *	Mitochondrion; mitochondrial inner membrane				70
Q863G4 UniProt NPD GO	COX82_TARSY	Cytochrome c oxidase polypeptide VIII-liver, mitochondrial precursor (EC 1.9.3.1) (Cytochrome c oxid ...	0.10	-	nuc	1 *	Mitochondrion; mitochondrial inner membrane				69
P56392 UniProt NPD GO	CX7A1_MOUSE	Cytochrome c oxidase polypeptide VIIa-heart, mitochondrial precursor (EC 1.9.3.1) (Cytochrome c oxid ...	0.10	-	mit	1	Mitochondrion; mitochondrial inner membrane	mitochondrion [IDA] respiratory chain complex IV (sensu Eukaryota) [ISS]			80
O94581 UniProt NPD GO	COX12_SCHPO	Cytochrome c oxidase polypeptide VIb (EC 1.9.3.1)	0.10	-	mit	0					83
O61694 UniProt NPD GO	COX5A_MANSE	Cytochrome c oxidase polypeptide Va, mitochondrial precursor (EC 1.9.3.1) (Fragment)	0.10	-	mit	0	Mitochondrion; mitochondrial inner membrane				63
Q5REG2 UniProt NPD GO	COX5B_PONPY	Cytochrome c oxidase polypeptide Vb, mitochondrial precursor (EC 1.9.3.1)	0.10	-	mit	0	Mitochondrion; mitochondrial inner membrane (By similarity)				129
Q42841 UniProt NPD GO	COX5C_HORVU	Cytochrome c oxidase polypeptide Vc (EC 1.9.3.1) (Cytochrome c oxidase subunit 5c)	0.10	-	cyt	1 *	Mitochondrion; mitochondrial inner membrane (By similarity)				62
Q9SXX7 UniProt NPD GO	COX5C_ORYSA	Cytochrome c oxidase polypeptide Vc (EC 1.9.3.1) (Cytochrome c oxidase subunit 5c)	0.10	-	cyt	0	Mitochondrion; mitochondrial inner membrane (By similarity)				62
O79672 UniProt NPD GO	COX1_PELSU	Cytochrome c oxidase subunit 1 (EC 1.9.3.1) (Cytochrome c oxidase polypeptide I)	0.10	-	end	12 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				514
P50692 UniProt NPD GO	COX2_AEDAE	Cytochrome c oxidase subunit 2 (EC 1.9.3.1) (Cytochrome c oxidase polypeptide II)	0.10	-	end	2 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				228
P50686 UniProt NPD GO	COX2_CYNVA	Cytochrome c oxidase subunit 2 (EC 1.9.3.1) (Cytochrome c oxidase polypeptide II)	0.10	-	end	2 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				227
P27168 UniProt NPD GO	COX2_DAUCA	Cytochrome c oxidase subunit 2 (EC 1.9.3.1) (Cytochrome c oxidase polypeptide II)	0.10	-	end	2 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				261
P50680 UniProt NPD GO	COX2_GAZSP	Cytochrome c oxidase subunit 2 (EC 1.9.3.1) (Cytochrome c oxidase polypeptide II)	0.10	-	end	2 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				227
P98047 UniProt NPD GO	COX2_LEMVA	Cytochrome c oxidase subunit 2 (EC 1.9.3.1) (Cytochrome c oxidase polypeptide II)	0.10	-	end	2 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				227
Q37595 UniProt NPD GO	COX2_PERFA	Cytochrome c oxidase subunit 2 (EC 1.9.3.1) (Cytochrome c oxidase polypeptide II)	0.10	-	end	2 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				226
P98043 UniProt NPD GO	COX2_TARBA	Cytochrome c oxidase subunit 2 (EC 1.9.3.1) (Cytochrome c oxidase polypeptide II)	0.10	-	end	2 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				227
Q6BPV1 UniProt NPD GO	COX9_DEBHA	Cytochrome c oxidase subunit 7A precursor (EC 1.9.3.1) (Cytochrome c oxidase polypeptide VIIA)	0.10	-	cyt	1 *	Mitochondrion; mitochondrial inner membrane (By similarity)				60
Q6CWK9 UniProt NPD GO	COX9_KLULA	Cytochrome c oxidase subunit 7A precursor (EC 1.9.3.1) (Cytochrome c oxidase polypeptide VIIA)	0.10	-	cyt	1 *	Mitochondrion; mitochondrial inner membrane (By similarity)				59
P20610 UniProt NPD GO	COXS_DICDI	Cytochrome c oxidase subunit 7s (EC 1.9.3.1) (Cytochrome c oxidase polypeptide VIIs)	0.10	-	mit	1 *	Mitochondrion; mitochondrial inner membrane				54
Q3T061 UniProt NPD GO	COX7R_BOVIN	Cytochrome c oxidase subunit VIIa-related protein, mitochondrial precursor	0.10	-	mit	1	Mitochondrion (By similarity)				114
P00431 UniProt NPD GO	CCPR_YEAST	Cytochrome c peroxidase, mitochondrial precursor (EC 1.11.1.5) (CCP)	0.10	-	mit	1 *	Mitochondrion; mitochondrial matrix	mitochondrial intermembrane space [IDA] mitochondrion [IDA]		7CCP	361
P25076 UniProt NPD GO	CY11_SOLTU	Cytochrome c1, heme protein, mitochondrial precursor (Clone PC13III)	0.10	-	mit	0	Mitochondrion; mitochondrial intermembrane space				320
Q93VA3 UniProt NPD GO	CYC6_ARATH	Cytochrome c6, chloroplast precursor (Soluble cytochrome f) (Cytochrome c553) (Cytochrome c-553) (Cy ...	0.10	-	mit	0	Plastid; chloroplast; chloroplast thylakoid lumen (By similarity)				175
Q9LTS3 UniProt NPD GO	CKX3_ARATH	Cytokinin dehydrogenase 3 precursor (EC 1.5.99.12) (Cytokinin oxidase 3) (CKO 3) (AtCKX3)	0.10	-	mit	1 *	Endoplasmic reticulum. Vacuole				523
P81007 UniProt NPD GO	ENT_ENTCO	Cytolytic protein enterolobin	0.10	-	cyt	0					485
P62394 UniProt NPD GO	CX11_NAJHH	Cytotoxin 11 (Cytotoxin CM-12)	0.10	-	nuc	0	Secreted protein				62
P62390 UniProt NPD GO	CX13A_NAJHA	Cytotoxin 11 (Cytotoxin CM-13a)	0.10	-	nuc	0	Secreted protein				62

You are viewing entries 64201 to 64250 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.