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
P06643 UniProt NPD GO	HBE4_BOVIN	Hemoglobin subunit epsilon-4 (Hemoglobin epsilon-4 chain) (Epsilon-4-globin)	0.01	-	cyt	0					146
P11025 UniProt NPD GO	HBE_DIDMA	Hemoglobin subunit epsilon-M (Hemoglobin epsilon-M chain) (Epsilon-M-globin)	0.01	-	cyt	0					146
P02104 UniProt NPD GO	HBE_MOUSE	Hemoglobin subunit epsilon-Y2 (Hemoglobin epsilon-Y2 chain) (Epsilon-Y2-globin)	0.01	-	cyt	0					146
P68030 UniProt NPD GO	HBG_ALOBE	Hemoglobin subunit gamma (Hemoglobin gamma chain) (Gamma-globin)	0.01	-	cyt	0					146
P68031 UniProt NPD GO	HBG_ALOCA	Hemoglobin subunit gamma (Hemoglobin gamma chain) (Gamma-globin)	0.01	-	cyt	0					146
P56285 UniProt NPD GO	HBG_ALOSE	Hemoglobin subunit gamma (Hemoglobin gamma chain) (Gamma-globin)	0.01	-	cyt	0					146
Q27940 UniProt NPD GO	HBG_AOTAZ	Hemoglobin subunit gamma (Hemoglobin gamma chain) (Gamma-globin)	0.01	-	cyt	0					146
P68068 UniProt NPD GO	HBG_ATEGE	Hemoglobin subunit gamma (Hemoglobin gamma chain) (Gamma-globin)	0.01	-	cyt	0					146
P68069 UniProt NPD GO	HBG_ATEPA	Hemoglobin subunit gamma (Hemoglobin gamma chain) (Gamma-globin)	0.01	-	cyt	0					146
P68071 UniProt NPD GO	HBG_BRAAR	Hemoglobin subunit gamma (Hemoglobin gamma chain) (Gamma-globin)	0.01	-	cyt	0					146
Q9GJS7 UniProt NPD GO	HBG_CALJA	Hemoglobin subunit gamma (Hemoglobin gamma chain) (Gamma-globin)	0.01	-	cyt	0					146
P08224 UniProt NPD GO	HBG_CHEME	Hemoglobin subunit gamma (Hemoglobin gamma chain) (Gamma-globin)	0.01	-	cyt	0					146
Q45XH5 UniProt NPD GO	HBG_DUGDU	Hemoglobin subunit gamma (Hemoglobin gamma chain) (Gamma-globin)	0.01	-	cyt	0					146
Q45XH7 UniProt NPD GO	HBG_ELEMA	Hemoglobin subunit gamma (Hemoglobin gamma chain) (Gamma-globin)	0.01	-	cyt	0					146
P08225 UniProt NPD GO	HBG_EULFU	Hemoglobin subunit gamma (Hemoglobin gamma chain) (Gamma-globin)	0.01	-	cyt	0					146
P19760 UniProt NPD GO	HBG_GALCR	Hemoglobin subunit gamma (Hemoglobin gamma chain) (Gamma-globin)	0.01	-	cyt	0					146
P68070 UniProt NPD GO	HBG_LAGLA	Hemoglobin subunit gamma (Hemoglobin gamma chain) (Gamma-globin)	0.01	-	cyt	0					146
P68078 UniProt NPD GO	HBG_MACFU	Hemoglobin subunit gamma (Hemoglobin gamma chain) (Gamma-globin)	0.01	-	cyt	0					146
P68077 UniProt NPD GO	HBG_MACMU	Hemoglobin subunit gamma (Hemoglobin gamma chain) (Gamma-globin)	0.01	-	cyt	0					146
P02097 UniProt NPD GO	HBG_MACNE	Hemoglobin subunit gamma (Hemoglobin gamma chain) (Gamma-globin)	0.01	-	cyt	0					146
P68079 UniProt NPD GO	HBG_PAPCY	Hemoglobin subunit gamma (Hemoglobin gamma chain) (Gamma-globin)	0.01	-	cyt	0					146
O77655 UniProt NPD GO	HBG_TARBA	Hemoglobin subunit gamma (Hemoglobin gamma chain) (Gamma-globin)	0.01	-	cyt	0					146
P18436 UniProt NPD GO	HBG_TARSY	Hemoglobin subunit gamma (Hemoglobin gamma chain) (Gamma-globin)	0.01	-	cyt	0					147
Q45XH6 UniProt NPD GO	HBG_TRIMA	Hemoglobin subunit gamma (Hemoglobin gamma chain) (Gamma-globin)	0.01	-	cyt	0					146
P02099 UniProt NPD GO	HBG_RABIT	Hemoglobin subunit gamma (Hemoglobin gamma chain) (Gamma-globin) (Hemoglobin beta-3)	0.01	-	cyt	0					146
Q9GLX4 UniProt NPD GO	HBG1_CALMO	Hemoglobin subunit gamma-1 (Hemoglobin gamma-1 chain) (Gamma-1-globin)	0.01	-	cyt	0					146
Q28221 UniProt NPD GO	HBG1_CEBAL	Hemoglobin subunit gamma-1 (Hemoglobin gamma-1 chain) (Gamma-1-globin)	0.01	-	cyt	0					146
P68256 UniProt NPD GO	HBG1_CEBAP	Hemoglobin subunit gamma-1 (Hemoglobin gamma-1 chain) (Gamma-1-globin)	0.01	-	cyt	0					146
P18995 UniProt NPD GO	HBG1_PONPY	Hemoglobin subunit gamma-1 (Hemoglobin gamma-1 chain) (Gamma-1-globin)	0.01	-	cyt	0					146
P62741 UniProt NPD GO	HBG1_GORGO	Hemoglobin subunit gamma-1 (Hemoglobin gamma-1 chain) (Gamma-1-globin) (Hemoglobin gamma-A chain)	0.01	-	cyt	0					146
P61947 UniProt NPD GO	HBG1_HYLLA	Hemoglobin subunit gamma-1 (Hemoglobin gamma-1 chain) (Gamma-1-globin) (Hemoglobin gamma-A chain)	0.01	-	cyt	0					146
Q28779 UniProt NPD GO	HBG1_PANPA	Hemoglobin subunit gamma-1 (Hemoglobin gamma-1 chain) (Gamma-1-globin) (Hemoglobin gamma-A chain)	0.01	-	cyt	0					146
P61920 UniProt NPD GO	HBG1_PANTR	Hemoglobin subunit gamma-1 (Hemoglobin gamma-1 chain) (Gamma-1-globin) (Hemoglobin gamma-A chain)	0.01	-	cyt	0					146
P69891 UniProt NPD GO	HBG1_HUMAN	Hemoglobin subunit gamma-1 (Hemoglobin gamma-1 chain) (Gamma-1-globin) (Hemoglobin gamma-A chain) (H ...	0.01	-	cyt	0			142200	1I3E	146
P68258 UniProt NPD GO	HBG2_CEBAL	Hemoglobin subunit gamma-2 (Hemoglobin gamma-2 chain) (Gamma-2-globin)	0.01	-	cyt	0					146
P68257 UniProt NPD GO	HBG2_CEBAP	Hemoglobin subunit gamma-2 (Hemoglobin gamma-2 chain) (Gamma-2-globin)	0.01	-	cyt	0					146
P18996 UniProt NPD GO	HBG2_PONPY	Hemoglobin subunit gamma-2 (Hemoglobin gamma-2 chain) (Gamma-2-globin)	0.01	-	cyt	0					146
P62742 UniProt NPD GO	HBG2_GORGO	Hemoglobin subunit gamma-2 (Hemoglobin gamma-2 chain) (Gamma-2-globin) (Hemoglobin gamma-G chain)	0.01	-	cyt	0					146
P61948 UniProt NPD GO	HBG2_HYLLA	Hemoglobin subunit gamma-2 (Hemoglobin gamma-2 chain) (Gamma-2-globin) (Hemoglobin gamma-G chain)	0.01	-	cyt	0					146
P61921 UniProt NPD GO	HBG2_PANTR	Hemoglobin subunit gamma-2 (Hemoglobin gamma-2 chain) (Gamma-2-globin) (Hemoglobin gamma-G chain)	0.01	-	cyt	0					146
P69892 UniProt NPD GO	HBG2_HUMAN	Hemoglobin subunit gamma-2 (Hemoglobin gamma-2 chain) (Gamma-2-globin) (Hemoglobin gamma-G chain) (H ...	0.01	-	cyt	0			142250	1FDH	146
P81041 UniProt NPD GO	HBO_MACEU	Hemoglobin subunit omega (Hemoglobin omega chain) (Omega-globin) (Fragment)	0.01	-	cyt	0					54
P04243 UniProt NPD GO	HBPI_CAIMO	Hemoglobin subunit pi (Hemoglobin pi chain) (Pi-globin) (Hemoglobin pi' chain)	0.01	-	cyt	0					141
P02007 UniProt NPD GO	HBPI_CHICK	Hemoglobin subunit pi (Hemoglobin pi chain) (Pi-globin) (Hemoglobin pi' chain)	0.01	-	cyt	0					141
P02127 UniProt NPD GO	HBRH_CHICK	Hemoglobin subunit rho (Hemoglobin rho chain) (Rho-globin)	0.01	-	cyt	0					146
P04246 UniProt NPD GO	HBT_PIG	Hemoglobin subunit theta (Hemoglobin theta chain) (Theta-globin)	0.01	-	cyt	0					146
P13787 UniProt NPD GO	HBAZ_HORSE	Hemoglobin subunit zeta (Hemoglobin zeta chain) (Zeta-globin)	0.01	-	cyt	0					141
P02009 UniProt NPD GO	HBAZ_PIG	Hemoglobin subunit zeta (Hemoglobin zeta chain) (Zeta-globin)	0.01	-	cyt	0					141
P80530 UniProt NPD GO	HGLB2_FASHE	Hemoglobinase-like protein 2 (EC 3.4.22.34) (Newly excysted juvenile protein 6) (Fragment)	0.01	-	cyt	0					22
P80742 UniProt NPD GO	LE01_BIOGL	Hemolymph 65 kDa lectin BG01 (Fragment)	0.01	-	cyt	0	Secreted protein				25

You are viewing entries 88951 to 89000 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.