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
P38605 UniProt NPD GO	CAS1_ARATH	Cycloartenol synthase (EC 5.4.99.8) (2,3-epoxysqualene--cycloartenol cyclase)	0.09	-	nuc	0					759
P32071 UniProt NPD GO	CYHR_CANMA	Cycloheximide resistance protein	0.09	-	end	12	Membrane; multi-pass membrane protein				552
P53101 UniProt NPD GO	STR3_YEAST	Cystathionine beta-lyase (EC 4.4.1.8) (CBL) (Beta-cystathionase) (Cysteine lyase)	0.09	-	pox	0	Cytoplasm. Nucleus				465
O49543 UniProt NPD GO	NFS1_ARATH	Cysteine desulfurase, mitochondrial precursor (EC 2.8.1.7)	0.09	+	mit	0	Mitochondrion				453
Q7XR52 UniProt NPD GO	CYSP1_ORYSA	Cysteine protease 1 precursor (EC 3.4.22.-) (OsCP1)	0.09	-	exc	1 *					490
P84808 UniProt NPD GO	CRV23_NAJKA	Cysteine-rich venom protein 23 (CRVP-23k) (Fragment)	0.09	-		0	Secreted protein	extracellular region [IDA]			13
Q5EA46 UniProt NPD GO	CREL1_BOVIN	Cysteine-rich with EGF-like domain protein 1 precursor	0.09	-	end	3 *	Membrane; multi-pass membrane protein (Potential)				420
Q8AVF5 UniProt NPD GO	CMAH_XENLA	Cytidine monophosphate-N-acetylneuraminic acid hydroxylase (EC 1.14.18.2) (CMP-N-acetylneuraminate m ...	0.09	-	nuc	0	Cytoplasm (By similarity)				591
P20425 UniProt NPD GO	KCY_DICDI	Cytidylate kinase (EC 2.7.4.14) (Deoxycytidylate kinase) (UMP-CMP kinase)	0.09	-	cyt	0				5UKD	194
P12394 UniProt NPD GO	CP17A_CHICK	Cytochrome P450 17A1 (EC 1.14.99.9) (CYPXVII) (P450-C17) (P450c17) (Steroid 17-alpha-hydroxylase/17, ...	0.09	-	mit	0					508
P79430 UniProt NPD GO	CP192_PIG	Cytochrome P450 19 type II (EC 1.14.14.1) (Aromatase) (CYPXIXA2) (Estrogen synthetase) (P-450AROM)	0.09	-	end	2 *	Membrane; peripheral membrane protein				503
P13107 UniProt NPD GO	CP2B3_RAT	Cytochrome P450 2B3 (EC 1.14.14.1) (CYPIIB3)	0.09	-	nuc	1 *	Endoplasmic reticulum; endoplasmic reticulum membrane; peripheral membrane protein				491
P00179 UniProt NPD GO	CP2C5_RABIT	Cytochrome P450 2C5 (EC 1.14.14.1) (CYPIIC5) (P450 1) (Progesterone 21-hydroxylase) (P450IIC5)	0.09	-	end	0				1NR6	487
P05182 UniProt NPD GO	CP2E1_RAT	Cytochrome P450 2E1 (EC 1.14.14.1) (CYPIIE1) (P450-J) (P450RLM6)	0.09	-	cyt	1 *	Endoplasmic reticulum; endoplasmic reticulum membrane; peripheral membrane protein	microsome [IDA]			492
Q6VVX0 UniProt NPD GO	CP2R1_HUMAN	Cytochrome P450 2R1 (EC 1.14.14.-) (Vitamin D 25-hydroxylase)	0.09	-	end	1 *	Endoplasmic reticulum; endoplasmic reticulum membrane; peripheral membrane protein		608713		501
Q64481 UniProt NPD GO	CP3AG_MOUSE	Cytochrome P450 3A16 (EC 1.14.14.1) (CYPIIIA16)	0.09	-	nuc	1 *	Endoplasmic reticulum; endoplasmic reticulum membrane; peripheral membrane protein				504
P79102 UniProt NPD GO	CP3AS_BOVIN	Cytochrome P450 3A28 (EC 1.14.14.1) (CYPIIIA28)	0.09	-	cyt	2 *	Endoplasmic reticulum; endoplasmic reticulum membrane; peripheral membrane protein				507
P30608 UniProt NPD GO	CP52F_CANTR	Cytochrome P450 52A6 (EC 1.14.14.-) (CYPLIIA6) (Alkane-inducible P450-ALK3)	0.09	+	end	1 *					524
P54781 UniProt NPD GO	ERG5_YEAST	Cytochrome P450 61 (EC 1.14.14.-) (C-22 sterol desaturase)	0.09	-	mit	0					538
Q27594 UniProt NPD GO	CP6A9_DROME	Cytochrome P450 6a9 (EC 1.14.-.-) (CYPVIA9)	0.09	-	mit	1 *	Endoplasmic reticulum; endoplasmic reticulum membrane; peripheral membrane protein (Potential)				504
Q9STK9 UniProt NPD GO	C71AO_ARATH	Cytochrome P450 71A24 (EC 1.14.-.-)	0.09	-	end	2 *					486
P37119 UniProt NPD GO	C71A3_SOLME	Cytochrome P450 71A3 (EC 1.14.-.-) (CYPLXXIA3) (P-450EG3) (Fragment)	0.09	-	nuc	0					365
Q9LIP6 UniProt NPD GO	C71BV_ARATH	Cytochrome P450 71B34 (EC 1.14.-.-)	0.09	-	mit	2 *					500
O64637 UniProt NPD GO	C76C2_ARATH	Cytochrome P450 76C2 (EC 1.14.-.-)	0.09	-	nuc	1 *					512
P48421 UniProt NPD GO	C83A1_ARATH	Cytochrome P450 83A1 (EC 1.14.-.-) (CYPLXXXIII)	0.09	+	mit	2 *	Endoplasmic reticulum (Potential)				502
O88962 UniProt NPD GO	CP8B1_MOUSE	Cytochrome P450 8B1 (EC 1.14.13.95) (CYPVIIIB1) (7-alpha-hydroxycholest-4-en-3-one 12-alpha-hydroxyl ...	0.09	-	mit	1 *	Endoplasmic reticulum; endoplasmic reticulum membrane; single-pass membrane protein				500
Q94WQ8 UniProt NPD GO	CYB_BUTBU	Cytochrome b	0.09	-	end	9 *					380
Q9T9Y3 UniProt NPD GO	CYB_GORGO	Cytochrome b	0.09	-	end	9 *					380
Q91577 UniProt NPD GO	CY561_XENLA	Cytochrome b561 (Cytochrome b-561)	0.09	-	end	6 *	Secretory vesicle; secretory vesicle membrane; multi-pass membrane protein (By similarity). Secretor ...				247
Q8N8Q1 UniProt NPD GO	C56D1_HUMAN	Cytochrome b561 domain-containing protein 1	0.09	-	end	6 *	Membrane; multi-pass membrane protein (Probable)				229
Q9SBN3 UniProt NPD GO	UCRIA_VOLCA	Cytochrome b6-f complex iron-sulfur subunit, chloroplast precursor (EC 1.10.99.1) (Rieske iron-sulfu ...	0.09	-	mit	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein. The transmembran ...				206
Q9SBM8 UniProt NPD GO	PETN_VOLCA	Cytochrome b6-f complex subunit 8, chloroplast precursor (Cytochrome b6-f complex subunit VIII) (Cyt ...	0.09	-	mit	2 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				98
P00032 UniProt NPD GO	CYC_HELAS	Cytochrome c	0.09	-	cyt	0	Mitochondrion; mitochondrial matrix				104
P00041 UniProt NPD GO	CYC_ISSOR	Cytochrome c	0.09	-	nuc	0	Mitochondrion; mitochondrial matrix				109
P00047 UniProt NPD GO	CYC_THELA	Cytochrome c	0.09	-	nuc	0	Mitochondrion; mitochondrial matrix				111
P61905 UniProt NPD GO	COX82_CANFA	Cytochrome c oxidase polypeptide VIII-liver (EC 1.9.3.1) (Cytochrome c oxidase subunit 8-2) (Fragmen ...	0.09	-		0	Mitochondrion; mitochondrial inner membrane				10
Q64445 UniProt NPD GO	COX82_MOUSE	Cytochrome c oxidase polypeptide VIII-liver, mitochondrial precursor (EC 1.9.3.1) (Cytochrome c oxid ...	0.09	-	nuc	1 *	Mitochondrion; mitochondrial inner membrane				69
O13082 UniProt NPD GO	CX6A1_CYPCA	Cytochrome c oxidase polypeptide VIa, mitochondrial precursor (EC 1.9.3.1)	0.09	-	mit	0	Mitochondrion; mitochondrial inner membrane				102
Q02221 UniProt NPD GO	CX6A2_HUMAN	Cytochrome c oxidase polypeptide VIa-heart, mitochondrial precursor (EC 1.9.3.1) (COXVIAH)	0.09	-	mit	0	Mitochondrion; mitochondrial inner membrane		602009		97
Q7YRJ9 UniProt NPD GO	COX6C_SAISC	Cytochrome c oxidase polypeptide VIc precursor (EC 1.9.3.1)	0.09	-	mit	1 *	Mitochondrion; mitochondrial inner membrane				75
P00395 UniProt NPD GO	COX1_HUMAN	Cytochrome c oxidase subunit 1 (EC 1.9.3.1) (Cytochrome c oxidase polypeptide I)	0.09	-	end	12 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein		535000		513
Q9T9X0 UniProt NPD GO	COX1_PANPA	Cytochrome c oxidase subunit 1 (EC 1.9.3.1) (Cytochrome c oxidase polypeptide I)	0.09	-	end	12 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein (By similarity)				513
Q9T9W1 UniProt NPD GO	COX1_PANTR	Cytochrome c oxidase subunit 1 (EC 1.9.3.1) (Cytochrome c oxidase polypeptide I)	0.09	-	end	12 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein (By similarity)				513
Q37369 UniProt NPD GO	COX2_ANTAM	Cytochrome c oxidase subunit 2 (EC 1.9.3.1) (Cytochrome c oxidase polypeptide II)	0.09	-	end	2 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				227
Q37416 UniProt NPD GO	COX2_BISBI	Cytochrome c oxidase subunit 2 (EC 1.9.3.1) (Cytochrome c oxidase polypeptide II)	0.09	-	end	2 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				227
P98031 UniProt NPD GO	COX2_CANSI	Cytochrome c oxidase subunit 2 (EC 1.9.3.1) (Cytochrome c oxidase polypeptide II)	0.09	-	end	2 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				227
O03851 UniProt NPD GO	COX2_CERSI	Cytochrome c oxidase subunit 2 (EC 1.9.3.1) (Cytochrome c oxidase polypeptide II)	0.09	-	end	2 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				227
P98030 UniProt NPD GO	COX2_CHORO	Cytochrome c oxidase subunit 2 (EC 1.9.3.1) (Cytochrome c oxidase polypeptide II)	0.09	-	end	2 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				227
P98033 UniProt NPD GO	COX2_EULMA	Cytochrome c oxidase subunit 2 (EC 1.9.3.1) (Cytochrome c oxidase polypeptide II)	0.09	-	end	2 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				227
P48890 UniProt NPD GO	COX2_FELCA	Cytochrome c oxidase subunit 2 (EC 1.9.3.1) (Cytochrome c oxidase polypeptide II)	0.09	-	end	2 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				227

You are viewing entries 65951 to 66000 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.