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
P69081 UniProt NPD GO	LDHA_CHIRA	L-lactate dehydrogenase A chain (EC 1.1.1.27) (LDH-A)	0.01	-	cyt	0	Cytoplasm (By similarity)				330
Q9PW07 UniProt NPD GO	LDHA_COLLI	L-lactate dehydrogenase A chain (EC 1.1.1.27) (LDH-A)	0.01	-	cyt	0	Cytoplasm (By similarity)				331
O93401 UniProt NPD GO	LDHA_CORNI	L-lactate dehydrogenase A chain (EC 1.1.1.27) (LDH-A)	0.01	-	cyt	0	Cytoplasm (By similarity)				331
Q9W7K5 UniProt NPD GO	LDHA_CYPCA	L-lactate dehydrogenase A chain (EC 1.1.1.27) (LDH-A)	0.01	-	cyt	0	Cytoplasm (By similarity)			1V6A	332
Q9PW61 UniProt NPD GO	LDHA_DISEL	L-lactate dehydrogenase A chain (EC 1.1.1.27) (LDH-A)	0.01	-	cyt	0	Cytoplasm (By similarity)				330
O93544 UniProt NPD GO	LDHA_DISMA	L-lactate dehydrogenase A chain (EC 1.1.1.27) (LDH-A)	0.01	-	cyt	0	Cytoplasm (By similarity)				330
O93542 UniProt NPD GO	LDHA_ELEMC	L-lactate dehydrogenase A chain (EC 1.1.1.27) (LDH-A)	0.01	-	cyt	0	Cytoplasm (By similarity)				331
P69083 UniProt NPD GO	LDHA_GILMI	L-lactate dehydrogenase A chain (EC 1.1.1.27) (LDH-A)	0.01	-	cyt	0	Cytoplasm (By similarity)				331
P69084 UniProt NPD GO	LDHA_GILSE	L-lactate dehydrogenase A chain (EC 1.1.1.27) (LDH-A)	0.01	-	cyt	0	Cytoplasm (By similarity)				331
O93540 UniProt NPD GO	LDHA_GOBGI	L-lactate dehydrogenase A chain (EC 1.1.1.27) (LDH-A)	0.01	-	cyt	0	Cytoplasm (By similarity)				330
O93537 UniProt NPD GO	LDHA_HARAN	L-lactate dehydrogenase A chain (EC 1.1.1.27) (LDH-A)	0.01	-	cyt	1 *	Cytoplasm (By similarity)				330
O93545 UniProt NPD GO	LDHA_LEPNU	L-lactate dehydrogenase A chain (EC 1.1.1.27) (LDH-A)	0.01	-	cyt	0	Cytoplasm (By similarity)				330
P69085 UniProt NPD GO	LDHA_NOTAN	L-lactate dehydrogenase A chain (EC 1.1.1.27) (LDH-A)	0.01	-	cyt	0	Cytoplasm (By similarity)				330
O93539 UniProt NPD GO	LDHA_NOTCO	L-lactate dehydrogenase A chain (EC 1.1.1.27) (LDH-A)	0.01	-	cyt	0	Cytoplasm (By similarity)				330
P69082 UniProt NPD GO	LDHA_PAGBE	L-lactate dehydrogenase A chain (EC 1.1.1.27) (LDH-A)	0.01	-	cyt	0	Cytoplasm (By similarity)				330
P69086 UniProt NPD GO	LDHA_PAGBO	L-lactate dehydrogenase A chain (EC 1.1.1.27) (LDH-A)	0.01	-	cyt	0	Cytoplasm (By similarity)				330
O93538 UniProt NPD GO	LDHA_PARCR	L-lactate dehydrogenase A chain (EC 1.1.1.27) (LDH-A)	0.01	-	cyt	0	Cytoplasm (By similarity)				330
O93543 UniProt NPD GO	LDHA_PARMG	L-lactate dehydrogenase A chain (EC 1.1.1.27) (LDH-A)	0.01	-	cyt	0	Cytoplasm (By similarity)				330
O93546 UniProt NPD GO	LDHA_PATTE	L-lactate dehydrogenase A chain (EC 1.1.1.27) (LDH-A)	0.01	-	cyt	0	Cytoplasm (By similarity)				330
Q9PW58 UniProt NPD GO	LDHA_RHIDE	L-lactate dehydrogenase A chain (EC 1.1.1.27) (LDH-A)	0.01	-	cyt	0	Cytoplasm (By similarity)				331
O13277 UniProt NPD GO	LDHA_SPHID	L-lactate dehydrogenase A chain (EC 1.1.1.27) (LDH-A)	0.01	-	cyt	0	Cytoplasm (By similarity)				331
O13278 UniProt NPD GO	LDHA_SPHLU	L-lactate dehydrogenase A chain (EC 1.1.1.27) (LDH-A)	0.01	-	cyt	0	Cytoplasm (By similarity)				331
P42120 UniProt NPD GO	LDHA_XENLA	L-lactate dehydrogenase A chain (EC 1.1.1.27) (LDH-A)	0.01	-	mit	0	Cytoplasm (By similarity)				333
P19858 UniProt NPD GO	LDHA_BOVIN	L-lactate dehydrogenase A chain (EC 1.1.1.27) (LDH-A) (LDH muscle subunit) (LDH-M)	0.01	-	mit	0	Cytoplasm				331
P13491 UniProt NPD GO	LDHA_RABIT	L-lactate dehydrogenase A chain (EC 1.1.1.27) (LDH-A) (LDH muscle subunit) (LDH-M)	0.01	-	cyt	0	Cytoplasm				331
P00338 UniProt NPD GO	LDHA_HUMAN	L-lactate dehydrogenase A chain (EC 1.1.1.27) (LDH-A) (LDH muscle subunit) (LDH-M) (Proliferation-in ...	0.01	-	mit	0	Cytoplasm	cytosol [TAS]	150000	1I10	331
Q92055 UniProt NPD GO	LDHA_FUNHE	L-lactate dehydrogenase A chain (EC 1.1.1.27) (LDH-A) (LDH-M)	0.01	-	cyt	0	Cytoplasm (By similarity)				331
P00341 UniProt NPD GO	LDHA_SQUAC	L-lactate dehydrogenase A chain (EC 1.1.1.27) (LDH-A) (LDH-M)	0.01	-	mit	0	Cytoplasm			8LDH	332
Q3T056 UniProt NPD GO	LDH6B_BOVIN	L-lactate dehydrogenase A-like 6B (EC 1.1.1.27)	0.01	-	mit	0					381
Q9P4B5 UniProt NPD GO	LDHB_RHIOR	L-lactate dehydrogenase B (EC 1.1.1.27) (L-LDH B)	0.01	-	cyt	1 *	Cytoplasm (By similarity)				302
Q9PW05 UniProt NPD GO	LDHB_ALLMI	L-lactate dehydrogenase B chain (EC 1.1.1.27) (LDH-B)	0.01	-	mit	0	Cytoplasm (By similarity)				332
Q9YGL2 UniProt NPD GO	LDHB_ANGRO	L-lactate dehydrogenase B chain (EC 1.1.1.27) (LDH-B)	0.01	-	mit	0	Cytoplasm (By similarity)				332
Q5E9B1 UniProt NPD GO	LDHB_BOVIN	L-lactate dehydrogenase B chain (EC 1.1.1.27) (LDH-B)	0.01	-	cyt	0	Cytoplasm (By similarity)				333
Q9PVK4 UniProt NPD GO	LDHB_BRARE	L-lactate dehydrogenase B chain (EC 1.1.1.27) (LDH-B)	0.01	-	mit	0	Cytoplasm (By similarity)				333
Q98SL1 UniProt NPD GO	LDHB_CAICA	L-lactate dehydrogenase B chain (EC 1.1.1.27) (LDH-B)	0.01	-	cyt	0	Cytoplasm (By similarity)				332
P00337 UniProt NPD GO	LDHB_CHICK	L-lactate dehydrogenase B chain (EC 1.1.1.27) (LDH-B)	0.01	-	mit	0	Cytoplasm (By similarity)				332
P20373 UniProt NPD GO	LDHB_FUNHE	L-lactate dehydrogenase B chain (EC 1.1.1.27) (LDH-B)	0.01	-	mit	0	Cytoplasm (By similarity)				334
Q98SK9 UniProt NPD GO	LDHB_PELSJ	L-lactate dehydrogenase B chain (EC 1.1.1.27) (LDH-B)	0.01	-	mit	0	Cytoplasm (By similarity)				332
P79913 UniProt NPD GO	LDHB_SCEWO	L-lactate dehydrogenase B chain (EC 1.1.1.27) (LDH-B)	0.01	-	end	0	Cytoplasm (By similarity)				332
Q9YI05 UniProt NPD GO	LDHB_SQUAC	L-lactate dehydrogenase B chain (EC 1.1.1.27) (LDH-B)	0.01	-	mit	0	Cytoplasm (By similarity)				334
Q9PT42 UniProt NPD GO	LDHB_TRASC	L-lactate dehydrogenase B chain (EC 1.1.1.27) (LDH-B)	0.01	-	mit	0	Cytoplasm (By similarity)				332
P42119 UniProt NPD GO	LDHB_XENLA	L-lactate dehydrogenase B chain (EC 1.1.1.27) (LDH-B)	0.01	-	mit	0	Cytoplasm (By similarity)				333
P13743 UniProt NPD GO	LDHB_ANAPL	L-lactate dehydrogenase B chain (EC 1.1.1.27) (LDH-B) (Epsilon crystallin)	0.01	-	mit	0	Cytoplasm (By similarity)				332
P42122 UniProt NPD GO	LDHB_FUNPA	L-lactate dehydrogenase B chain (EC 1.1.1.27) (LDH-B) (Fragment)	0.01	-	mit	0	Cytoplasm (By similarity)				322
Q9XT86 UniProt NPD GO	LDHB_MONDO	L-lactate dehydrogenase B chain (EC 1.1.1.27) (LDH-B) (LDH heart subunit) (LDH-H)	0.01	-	cyt	0	Cytoplasm (By similarity)				333
P16125 UniProt NPD GO	LDHB_MOUSE	L-lactate dehydrogenase B chain (EC 1.1.1.27) (LDH-B) (LDH heart subunit) (LDH-H)	0.01	-	cyt	0	Cytoplasm				333
P00336 UniProt NPD GO	LDHB_PIG	L-lactate dehydrogenase B chain (EC 1.1.1.27) (LDH-B) (LDH heart subunit) (LDH-H)	0.01	-	mit	0	Cytoplasm			5LDH	333
P42123 UniProt NPD GO	LDHB_RAT	L-lactate dehydrogenase B chain (EC 1.1.1.27) (LDH-B) (LDH heart subunit) (LDH-H)	0.01	-	cyt	0	Cytoplasm				333
P07195 UniProt NPD GO	LDHB_HUMAN	L-lactate dehydrogenase B chain (EC 1.1.1.27) (LDH-B) (LDH heart subunit) (LDH-H) (NY-REN-46 antigen ...	0.01	-	cyt	0	Cytoplasm	cytoplasm [TAS]	150100	1T2F	333
P07864 UniProt NPD GO	LDHC_HUMAN	L-lactate dehydrogenase C chain (EC 1.1.1.27) (LDH-C) (LDH testis subunit) (LDH-X)	0.01	-	mit	0	Cytoplasm		150150		331

You are viewing entries 89301 to 89350 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.