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
P14392 UniProt NPD GO	HBB_PTEPO	Hemoglobin subunit beta (Hemoglobin beta chain) (Beta-globin)	0.03	-	cyt	0					146
P02058 UniProt NPD GO	HBB_ROUAE	Hemoglobin subunit beta (Hemoglobin beta chain) (Beta-globin)	0.03	-	cyt	0					146
P02039 UniProt NPD GO	HBB_SAGFU	Hemoglobin subunit beta (Hemoglobin beta chain) (Beta-globin)	0.03	-	cyt	0					146
P02038 UniProt NPD GO	HBB_SAGMY	Hemoglobin subunit beta (Hemoglobin beta chain) (Beta-globin)	0.03	-	cyt	0					146
P68054 UniProt NPD GO	HBB_SAGNI	Hemoglobin subunit beta (Hemoglobin beta chain) (Beta-globin)	0.03	-	cyt	0					146
P68055 UniProt NPD GO	HBB_SAGOE	Hemoglobin subunit beta (Hemoglobin beta chain) (Beta-globin)	0.03	-	cyt	0					146
P02032 UniProt NPD GO	HBB_SEMEN	Hemoglobin subunit beta (Hemoglobin beta chain) (Beta-globin)	0.03	-	cyt	0					146
P02060 UniProt NPD GO	HBB_SUNMU	Hemoglobin subunit beta (Hemoglobin beta chain) (Beta-globin)	0.03	-	cyt	0					146
P11756 UniProt NPD GO	HBB_TADBR	Hemoglobin subunit beta (Hemoglobin beta chain) (Beta-globin)	0.03	-	cyt	0					146
P02029 UniProt NPD GO	HBB_THEGE	Hemoglobin subunit beta (Hemoglobin beta chain) (Beta-globin)	0.03	-	cyt	0					146
P20246 UniProt NPD GO	HBB1_TORMA	Hemoglobin subunit beta-1 (Hemoglobin beta-1 chain) (Beta-1-globin)	0.03	-	cyt	0					142
P02050 UniProt NPD GO	HBB_GALCR	Hemoglobin subunit beta-1/2 (Hemoglobin beta-1/2 chain) (Beta-1/2-globin)	0.03	-	cyt	0					146
Q7LZC1 UniProt NPD GO	HBB3_MURHE	Hemoglobin subunit beta-3 (Hemoglobin beta-3 chain) (Beta-3-globin) (Hemoglobin beta-III chain)	0.03	-	cyt	0					147
P02074 UniProt NPD GO	HBB_ODOVI	Hemoglobin subunit beta-3 (Hemoglobin beta-3 chain) (Beta-3-globin) (Hemoglobin beta-III chain)	0.03	-	cyt	0				1HDS	145
P02077 UniProt NPD GO	HBBA_CAPHI	Hemoglobin subunit beta-A (Hemoglobin beta-A chain) (Beta-A-globin) (Alanine beta-globin)	0.03	-	cyt	0					145
P02046 UniProt NPD GO	HBD_AOTTR	Hemoglobin subunit delta (Hemoglobin delta chain) (Delta-globin)	0.03	-	cyt	0					146
Q45XI7 UniProt NPD GO	HBD_DUGDU	Hemoglobin subunit delta (Hemoglobin delta chain) (Delta-globin)	0.03	-	cyt	0					146
Q03902 UniProt NPD GO	HBD_GALCR	Hemoglobin subunit delta (Hemoglobin delta chain) (Delta-globin)	0.03	-	cyt	0					146
P68014 UniProt NPD GO	HBD_SAGMY	Hemoglobin subunit delta (Hemoglobin delta chain) (Delta-globin)	0.03	-	cyt	0					146
P68015 UniProt NPD GO	HBD_SAGNI	Hemoglobin subunit delta (Hemoglobin delta chain) (Delta-globin)	0.03	-	cyt	0					146
P02047 UniProt NPD GO	HBD_SAISC	Hemoglobin subunit delta (Hemoglobin delta chain) (Delta-globin)	0.03	-	cyt	0					146
P06714 UniProt NPD GO	HBAT_HORSE	Hemoglobin subunit theta-1 (Hemoglobin theta-1 chain) (Theta-1-globin)	0.03	-	cyt	0					141
P13786 UniProt NPD GO	HBAZ_CAPHI	Hemoglobin subunit zeta (Hemoglobin zeta chain) (Zeta-globin)	0.03	-	mit	0					141
P58425 UniProt NPD GO	TXHP1_HETVE	Heteropodatoxin-1 (HpTX1) (Toxin AU3/KJ5)	0.03	-	cyt	0	Secreted protein				33
P58427 UniProt NPD GO	TXHP3_HETVE	Heteropodatoxin-3 (HpTX3) (Toxin AU5C/KJ7)	0.03	-	cyt	0	Secreted protein				31
Q8BMS4 UniProt NPD GO	COQ3_MOUSE	Hexaprenyldihydroxybenzoate methyltransferase, mitochondrial precursor (EC 2.1.1.114) (Dihydroxyhexa ...	0.03	-	mit	0	Mitochondrion; mitochondrial matrix (Probable)				370
O97571 UniProt NPD GO	CXCR2_CANFA	High affinity interleukin-8 receptor B (IL-8R B) (CXCR-2) (GRO/MGSA receptor) (CD182 antigen)	0.03	-	end	6 *	Membrane; multi-pass membrane protein				356
P35407 UniProt NPD GO	CXCR2_RAT	High affinity interleukin-8 receptor B (IL-8R B) (CXCR-2) (GRO/MGSA receptor) (CD182 antigen)	0.03	-	end	6 *	Membrane; multi-pass membrane protein				359
O74969 UniProt NPD GO	GHT2_SCHPO	High-affinity glucose transporter ght2 (Hexose transporter 2)	0.03	-	end	12 *	Membrane; multi-pass membrane protein	integral to plasma membrane [TAS]			531
P29105 UniProt NPD GO	HPCL1_BOVIN	Hippocalcin-like protein 1 (Neurocalcin gamma) (Fragments)	0.03	-	cyt	0					74
P28509 UniProt NPD GO	ITHI_HIRME	Hirudin III	0.03	-	nuc	0	Secreted protein				65
P47747 UniProt NPD GO	HRH2_CAVPO	Histamine H2 receptor (H2R) (Gastric receptor I)	0.03	-	end	7 *	Membrane; multi-pass membrane protein				359
P25102 UniProt NPD GO	HRH2_RAT	Histamine H2 receptor (H2R) (Gastric receptor I)	0.03	-	end	7 *	Membrane; multi-pass membrane protein				358
Q5R7C3 UniProt NPD GO	HNMT_PONPY	Histamine N-methyltransferase (EC 2.1.1.8) (HMT)	0.03	-	cyt	0	Cytoplasm (By similarity)				292
P49773 UniProt NPD GO	HINT1_HUMAN	Histidine triad nucleotide-binding protein 1 (Adenosine 5'-monophosphoramidase) (Protein kinase C in ...	0.03	-	cyt	0	Cytoplasm. Nucleus. Interaction with CDK7 leads to a more nuclear localization	cytoskeleton [TAS] nucleus [TAS]	601314	1KPF	125
Q949X3 UniProt NPD GO	HIS8_ARATH	Histidinol-phosphate aminotransferase, chloroplast precursor (EC 2.6.1.9) (Imidazole acetol-phosphat ...	0.03	-	cyt	0	Plastid; chloroplast (Potential)				417
P27203 UniProt NPD GO	H1L5_ENSMI	Histone H1-like protein EM5 (Fragment)	0.03	-	nuc	0	Nucleus				36
P82897 UniProt NPD GO	H2A_OLILU	Histone H2A (Fragment)	0.03	-	nuc	1 *	Nucleus				67
O74515 UniProt NPD GO	CIA1_SCHPO	Histone chaperone cia1	0.03	-	cyt	0					262
Q25055 UniProt NPD GO	HOL3_HOLDI	Holotricin-3 precursor	0.03	+	vac	0	Secreted protein				104
Q6FM51 UniProt NPD GO	LYS4_CANGA	Homoaconitase, mitochondrial precursor (EC 4.2.1.36) (Homoaconitate hydratase)	0.03	-	mit	0					689
P49367 UniProt NPD GO	LYS4_YEAST	Homoaconitase, mitochondrial precursor (EC 4.2.1.36) (Homoaconitate hydratase)	0.03	-	mit	0	Mitochondrion	mitochondrion [IDA]			693
P48570 UniProt NPD GO	HOSC_YEAST	Homocitrate synthase, cytosolic isozyme (EC 2.3.3.14)	0.03	-	cyt	0	Cytoplasm	mitochondrion [IDA] nucleus [IDA]			428
Q9FUM9 UniProt NPD GO	HMT2_MAIZE	Homocysteine S-methyltransferase 2 (EC 2.1.1.10) (S-methylmethionine:homocysteine methyltransferase ...	0.03	-	cyt	0					339
Q9VKJ0 UniProt NPD GO	HGD_DROME	Homogentisate 1,2-dioxygenase (EC 1.13.11.5) (Homogentisicase) (Homogentisate oxygenase) (Homogentis ...	0.03	-	cyt	0					439
P31116 UniProt NPD GO	DHOM_YEAST	Homoserine dehydrogenase (EC 1.1.1.3) (HDH)	0.03	-	cyt	1 *		cytoplasm [IDA] nucleus [IDA]		1TVE	359
Q9M4B0 UniProt NPD GO	HSS1_SENVU	Homospermidine synthase (EC 2.5.1.45)	0.03	-	cyt	0					370
P60038 UniProt NPD GO	HSS2_SENVE	Homospermidine synthase 2 (EC 2.5.1.45) (HSS2)	0.03	-	cyt	0					370
P59850 UniProt NPD GO	KAX2Y_CENLM	Hongotoxin-4 (HgTX4) (Fragment)	0.03	-	nuc	0	Secreted protein				23
P83370 UniProt NPD GO	FA10V_HOPST	Hopsarin-D (EC 3.4.21.6) [Contains: Hopsarin-D light chain; Hopsarin-D heavy chain] (Fragments)	0.03	-	cyt	0	Secreted protein	extracellular region [NAS]			376

You are viewing entries 80201 to 80250 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.