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
P07031 UniProt NPD GO	ACYP2_CHICK	Acylphosphatase-2 (EC 3.6.1.7) (Acylphosphate phosphohydrolase 2) (Acylphosphatase, muscle type isoz ...	0.00	-	cyt	0					102
P00821 UniProt NPD GO	ACYP2_MELGA	Acylphosphatase-2 (EC 3.6.1.7) (Acylphosphate phosphohydrolase 2) (Acylphosphatase, muscle type isoz ...	0.00	-	cyt	0					102
P91455 UniProt NPD GO	APT_CAEEL	Adenine phosphoribosyltransferase (EC 2.4.2.7) (APRT)	0.00	-	cyt	0	Cytoplasm (By similarity)				185
Q6BZF9 UniProt NPD GO	APT_DEBHA	Adenine phosphoribosyltransferase (EC 2.4.2.7) (APRT)	0.00	-	cyt	0	Cytoplasm (By similarity). Nucleus (By similarity)				186
Q43199 UniProt NPD GO	APT1_WHEAT	Adenine phosphoribosyltransferase 1 (EC 2.4.2.7) (APRT 1)	0.00	-	cyt	0	Cytoplasm				181
Q42563 UniProt NPD GO	APT2_ARATH	Adenine phosphoribosyltransferase 2 (EC 2.4.2.7) (APRT 2)	0.00	-	cyt	0	Cytoplasm (Potential)				192
P11616 UniProt NPD GO	AA1R_CANFA	Adenosine A1 receptor	0.00	-	end	7 *	Membrane; multi-pass membrane protein				326
P47745 UniProt NPD GO	AA1R_CAVPO	Adenosine A1 receptor	0.00	-	end	7 *	Membrane; multi-pass membrane protein				326
Q60612 UniProt NPD GO	AA1R_MOUSE	Adenosine A1 receptor	0.00	-	end	7 *	Membrane; multi-pass membrane protein				326
P25099 UniProt NPD GO	AA1R_RAT	Adenosine A1 receptor	0.00	-	end	7 *	Membrane; multi-pass membrane protein	plasma membrane [IDA]			326
Q6W3F4 UniProt NPD GO	AA2BR_CANFA	Adenosine A2b receptor	0.00	-	end	7 *	Membrane; multi-pass membrane protein				332
P29276 UniProt NPD GO	AA2BR_RAT	Adenosine A2b receptor	0.00	-	end	7 *	Membrane; multi-pass membrane protein				332
Q28309 UniProt NPD GO	AA3R_CANFA	Adenosine A3 receptor	0.00	-	end	7 *	Membrane; multi-pass membrane protein				314
P47143 UniProt NPD GO	ADK_YEAST	Adenosine kinase (EC 2.7.1.20)	0.00	-	cyt	0		cytoplasm [IDA] nucleus [IDA]			340
Q9TVW2 UniProt NPD GO	ADK_TOXGO	Adenosine kinase (EC 2.7.1.20) (AK) (Adenosine 5'-phosphotransferase)	0.00	-	cyt	0				2ABS	363
P23526 UniProt NPD GO	SAHH_HUMAN	Adenosylhomocysteinase (EC 3.3.1.1) (S-adenosyl-L-homocysteine hydrolase) (AdoHcyase)	0.00	-	cyt	0	Cytoplasm	cytoplasm [NAS]	180960	1LI4	431
P36889 UniProt NPD GO	SAHH_LEIDO	Adenosylhomocysteinase (EC 3.3.1.1) (S-adenosyl-L-homocysteine hydrolase) (AdoHcyase)	0.00	-	cyt	0	Cytoplasm				437
Q710C4 UniProt NPD GO	SAHH_PIG	Adenosylhomocysteinase (EC 3.3.1.1) (S-adenosyl-L-homocysteine hydrolase) (AdoHcyase)	0.00	-	cyt	0	Cytoplasm				431
Q4XZZ5 UniProt NPD GO	SAHH_PLACH	Adenosylhomocysteinase (EC 3.3.1.1) (S-adenosyl-L-homocysteine hydrolase) (AdoHcyase)	0.00	-	nuc	0					479
P10760 UniProt NPD GO	SAHH_RAT	Adenosylhomocysteinase (EC 3.3.1.1) (S-adenosyl-L-homocysteine hydrolase) (AdoHcyase)	0.00	-	cyt	0	Cytoplasm			1XWF	431
P51540 UniProt NPD GO	SAHH_TRIVA	Adenosylhomocysteinase (EC 3.3.1.1) (S-adenosyl-L-homocysteine hydrolase) (AdoHcyase)	0.00	-	cyt	0					486
P39954 UniProt NPD GO	SAHH_YEAST	Adenosylhomocysteinase (EC 3.3.1.1) (S-adenosyl-L-homocysteine hydrolase) (AdoHcyase)	0.00	-	cyt	0		cytoplasm [IDA]			449
P50247 UniProt NPD GO	SAHH_MOUSE	Adenosylhomocysteinase (EC 3.3.1.1) (S-adenosyl-L-homocysteine hydrolase) (AdoHcyase) (Liver copper- ...	0.00	-	cyt	0	Cytoplasm				431
P84533 UniProt NPD GO	SAHH1_POPEU	Adenosylhomocysteinase 1 (EC 3.3.1.1) (S-adenosyl-L-homocysteine hydrolase) (AdoHcyase) (Fragment)	0.00	-		0					13
P84532 UniProt NPD GO	SAHH2_POPEU	Adenosylhomocysteinase 2 (EC 3.3.1.1) (S-adenosyl-L-homocysteine hydrolase) (AdoHcyase) (Fragment)	0.00	-		0					13
O96907 UniProt NPD GO	KAD_ENTHI	Adenylate kinase (EC 2.7.4.3) (ATP-AMP transphosphorylase) (AK)	0.00	-	cyt	0					193
P84241 UniProt NPD GO	AKH_GEOST	Adipokinetic hormone (AKH)	0.00	-		0	Secreted protein				8
P25418 UniProt NPD GO	AKH_LIBAU	Adipokinetic hormone (AKH)	0.00	-		0	Secreted protein				8
P84240 UniProt NPD GO	AKH_MELML	Adipokinetic hormone (AKH)	0.00	-		0	Secreted protein				8
P84242 UniProt NPD GO	AKH_PACMA	Adipokinetic hormone (AKH)	0.00	-		0	Secreted protein				8
P14595 UniProt NPD GO	AKH_TABAT	Adipokinetic hormone (AKH) (Dipteran corpora cardiaca factor I) (DCC I)	0.00	-		0	Secreted protein				8
P61856 UniProt NPD GO	AKH_PROTE	Adipokinetic hormone (AKH) (Hypertrehalosaemic hormone) (HRTH)	0.00	-		0	Secreted protein				8
P67786 UniProt NPD GO	AKH_ROMMI	Adipokinetic hormone (AKH) (RO II)	0.00	-		0	Secreted protein				8
P67787 UniProt NPD GO	AKH_HELZE	Adipokinetic hormone (Hez-AKH)	0.00	-		0	Secreted protein				9
P67785 UniProt NPD GO	AKHG_GRYBI	Adipokinetic hormone G (AKH-G)	0.00	-		0	Secreted protein				8
P08379 UniProt NPD GO	AKH2_LOCMI	Adipokinetic prohormone type 2 precursor [Contains: Adipokinetic hormone 2 (Adipokinetic hormone II) ...	0.00	-	exc	1 *	Secreted protein				61
Q8BQS5 UniProt NPD GO	ADR2_MOUSE	Adiponectin receptor protein 2	0.00	-	end	7	Membrane; multi-pass membrane protein (By similarity). Localized to the cell membrane and intracellu ...	integral to membrane [ISS]			386
Q28928 UniProt NPD GO	ACTHR_PAPHA	Adrenocorticotropic hormone receptor (ACTH receptor) (ACTH-R) (Melanocortin receptor 2) (MC2-R) (Adr ...	0.00	-	end	3 *	Membrane; multi-pass membrane protein				126
P29330 UniProt NPD GO	ADX_SHEEP	Adrenodoxin (Adrenal ferredoxin) (Ferredoxin-1)	0.00	-	cyt	0	Mitochondrion; mitochondrial matrix				128
P83465 UniProt NPD GO	AEGL_AGRAE	Aegerolysin (Fragment)	0.00	-		0					10
P69436 UniProt NPD GO	MAST_AGEPP	Agelaia-mastoparan (Agelaia-MP)	0.00	-		0	Secreted protein				14
P82859 UniProt NPD GO	LECA_CASCR	Agglutinin (CCA)	0.00	-	cyt	0					309
P18670 UniProt NPD GO	LECA_ARTIN	Agglutinin alpha chain (Jacalin alpha chain)	0.00	-	cyt	0				1UH1	133
P84762 UniProt NPD GO	LECA_ARTTO	Agglutinin alpha chain (Jacalin alpha chain) (Fragment)	0.00	-	cyt	0					27
P18674 UniProt NPD GO	LECA_MACPO	Agglutinin alpha chain (MPA)	0.00	-	cyt	0				1JOT	133
P18671 UniProt NPD GO	LECB1_ARTIN	Agglutinin beta-1 chain (Jacalin beta-1 chain)	0.00	-		0				1KUJ	20
P18672 UniProt NPD GO	LECB2_ARTIN	Agglutinin beta-2 chain (Jacalin beta-2 chain)	0.00	-	cyt	0					21
Q9S8T0 UniProt NPD GO	LECB4_ARTIN	Agglutinin beta-4 chain (Jacalin beta-4 chain) (Fragment)	0.00	-		0					20
P84816 UniProt NPD GO	AGSP1_LEPFX	Aggression-stimulating peptide (LASP)	0.00	-	cyt	0	Secreted protein	extracellular region [IDA]			25
P13191 UniProt NPD GO	ALAT1_PIG	Alanine aminotransferase 1 (EC 2.6.1.2) (ALT1) (Glutamic--pyruvic transaminase 1) (GPT 1) (Glutamic- ...	0.00	-		0	Cytoplasm				20

You are viewing entries 92501 to 92550 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.