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
P10777 UniProt NPD GO	HBA1_NOTCO	Hemoglobin subunit alpha-1 (Hemoglobin alpha-1 chain) (Alpha-1-globin)	0.01	-	cyt	0					142
P02019 UniProt NPD GO	HBA1_ONCMY	Hemoglobin subunit alpha-1 (Hemoglobin alpha-1 chain) (Alpha-1-globin)	0.01	-	cyt	0				1OUU	144
P20244 UniProt NPD GO	HBA1_TORMA	Hemoglobin subunit alpha-1 (Hemoglobin alpha-1 chain) (Alpha-1-globin)	0.01	-	cyt	0					141
P41329 UniProt NPD GO	HBA1_ARCGA	Hemoglobin subunit alpha-1 (Hemoglobin alpha-1 chain) (Alpha-1-globin) (Hemoglobin alpha-I chain)	0.01	-	cyt	0					141
P20018 UniProt NPD GO	HBA1_LEMVA	Hemoglobin subunit alpha-1 (Hemoglobin alpha-1 chain) (Alpha-1-globin) (Hemoglobin alpha-I chain)	0.01	-	cyt	0					141
P10783 UniProt NPD GO	HBA1_TRICR	Hemoglobin subunit alpha-1 (Hemoglobin alpha-1 chain) (Alpha-1-globin) (Hemoglobin alpha-major chain ...	0.01	-	cyt	0					142
P07430 UniProt NPD GO	HBA1_XENBO	Hemoglobin subunit alpha-1 (Hemoglobin alpha-1 chain) (Alpha-1-globin) (Hemoglobin alpha-major chain ...	0.01	-	cyt	0					141
P02012 UniProt NPD GO	HBA1_XENLA	Hemoglobin subunit alpha-1 (Hemoglobin alpha-1 chain) (Alpha-1-globin) (Hemoglobin alpha-major chain ...	0.01	-	cyt	0					141
P15163 UniProt NPD GO	HBA_LEPWE	Hemoglobin subunit alpha-1/2 (Hemoglobin alpha-1/2 chain) (Alpha-1/2-globin) (Hemoglobin alpha-I/II ...	0.01	-	cyt	0					141
P83271 UniProt NPD GO	HBA2_ANAMI	Hemoglobin subunit alpha-2 (Hemoglobin alpha-2 chain) (Alpha-2-globin)	0.01	-	mit	0					142
Q1AGS8 UniProt NPD GO	HBA2_BORSA	Hemoglobin subunit alpha-2 (Hemoglobin alpha-2 chain) (Alpha-2-globin)	0.01	-	mit	1					142
P20245 UniProt NPD GO	HBA2_TORMA	Hemoglobin subunit alpha-2 (Hemoglobin alpha-2 chain) (Alpha-2-globin)	0.01	-	cyt	0					141
P18980 UniProt NPD GO	HBA2_UROHA	Hemoglobin subunit alpha-2 (Hemoglobin alpha-2 chain) (Alpha-2-globin) (Fragment)	0.01	-	cyt	0					40
P82112 UniProt NPD GO	HBA2_CATMA	Hemoglobin subunit alpha-2 (Hemoglobin alpha-2 chain) (Alpha-2-globin) (Hb 2)	0.01	-	cyt	0					141
P20019 UniProt NPD GO	HBA2_LEMVA	Hemoglobin subunit alpha-2 (Hemoglobin alpha-2 chain) (Alpha-2-globin) (Hemoglobin alpha-II chain)	0.01	-	cyt	0					141
P06640 UniProt NPD GO	HBA2_PLEWA	Hemoglobin subunit alpha-2 (Hemoglobin alpha-2 chain) (Alpha-2-globin) (Hemoglobin alpha-minor chain ...	0.01	-	cyt	0					133
P08422 UniProt NPD GO	HBA3_XENTR	Hemoglobin subunit alpha-3 (Hemoglobin alpha-3 chain) (Alpha-3-globin) (Larval alpha globin) (Alpha ...	0.01	-	cyt	0					141
P14527 UniProt NPD GO	HBA4_ONCMY	Hemoglobin subunit alpha-4 (Hemoglobin alpha-4 chain) (Alpha-4-globin)	0.01	-	cyt	0					142
P06638 UniProt NPD GO	HBA5_XENLA	Hemoglobin subunit alpha-5 (Hemoglobin alpha-5 chain) (Alpha-5-globin) (Alpha-T5)	0.01	-	cyt	0					141
P83135 UniProt NPD GO	HBAA_GEONI	Hemoglobin subunit alpha-A (Hemoglobin alpha-A chain) (Alpha-A-globin)	0.01	-	cyt	0					141
Q9PVM4 UniProt NPD GO	HBAA_SERQU	Hemoglobin subunit alpha-A (Hemoglobin alpha-A chain) (Alpha-A-globin)	0.01	-	cyt	0					142
P08849 UniProt NPD GO	HBAD_ACCGE	Hemoglobin subunit alpha-D (Hemoglobin alpha-D chain) (Alpha-D-globin)	0.01	-	cyt	0					141
P68059 UniProt NPD GO	HBAD_AEGMO	Hemoglobin subunit alpha-D (Hemoglobin alpha-D chain) (Alpha-D-globin)	0.01	-	cyt	0					141
P04238 UniProt NPD GO	HBAD_ANSAN	Hemoglobin subunit alpha-D (Hemoglobin alpha-D chain) (Alpha-D-globin)	0.01	-	cyt	0					141
P04239 UniProt NPD GO	HBAD_ANSIN	Hemoglobin subunit alpha-D (Hemoglobin alpha-D chain) (Alpha-D-globin)	0.01	-	cyt	0					141
P02001 UniProt NPD GO	HBAD_CHICK	Hemoglobin subunit alpha-D (Hemoglobin alpha-D chain) (Alpha-D-globin)	0.01	-	cyt	0				1HBR	141
O12985 UniProt NPD GO	HBAD_COLLI	Hemoglobin subunit alpha-D (Hemoglobin alpha-D chain) (Alpha-D-globin)	0.01	-	cyt	0					140
P83124 UniProt NPD GO	HBAD_GEONI	Hemoglobin subunit alpha-D (Hemoglobin alpha-D chain) (Alpha-D-globin)	0.01	-	cyt	0					141
P81024 UniProt NPD GO	HBAD_MELGA	Hemoglobin subunit alpha-D (Hemoglobin alpha-D chain) (Alpha-D-globin)	0.01	-	cyt	0					141
P10781 UniProt NPD GO	HBAD_PHACA	Hemoglobin subunit alpha-D (Hemoglobin alpha-D chain) (Alpha-D-globin)	0.01	-	cyt	0					141
P02002 UniProt NPD GO	HBAD_PHACO	Hemoglobin subunit alpha-D (Hemoglobin alpha-D chain) (Alpha-D-globin)	0.01	-	cyt	0					141
P02004 UniProt NPD GO	HBAD_STUVU	Hemoglobin subunit alpha-D (Hemoglobin alpha-D chain) (Alpha-D-globin)	0.01	-	cyt	0					141
P68060 UniProt NPD GO	HBAD_TRIOC	Hemoglobin subunit alpha-D (Hemoglobin alpha-D chain) (Alpha-D-globin)	0.01	-	cyt	0					141
P14523 UniProt NPD GO	HBAD_TURME	Hemoglobin subunit alpha-D (Hemoglobin alpha-D chain) (Alpha-D-globin)	0.01	-	cyt	0					141
P08257 UniProt NPD GO	HBAD_GYPRU	Hemoglobin subunit alpha-D/D' (Hemoglobin alpha-D/D' chain) (Alpha-D/D'-globin)	0.01	-	cyt	0					141
O93349 UniProt NPD GO	HBB2_TRENE	Hemoglobin subunit beta (Hemoglobin beta chain) (Beta-globin)	0.01	-	cyt	0					146
P08851 UniProt NPD GO	HBB_ACCGE	Hemoglobin subunit beta (Hemoglobin beta chain) (Beta-globin)	0.01	-	mit	0					146
P68061 UniProt NPD GO	HBB_AEGMO	Hemoglobin subunit beta (Hemoglobin beta chain) (Beta-globin)	0.01	-	cyt	0					146
P02114 UniProt NPD GO	HBB_ANAPL	Hemoglobin subunit beta (Hemoglobin beta chain) (Beta-globin)	0.01	-	cyt	0					146
P02115 UniProt NPD GO	HBB_ANAPP	Hemoglobin subunit beta (Hemoglobin beta chain) (Beta-globin)	0.01	-	cyt	0					146
P02117 UniProt NPD GO	HBB_ANSAN	Hemoglobin subunit beta (Hemoglobin beta chain) (Beta-globin)	0.01	-	nuc	0				1FAW	146
P02118 UniProt NPD GO	HBB_ANSIN	Hemoglobin subunit beta (Hemoglobin beta chain) (Beta-globin)	0.01	-	nuc	0				1HV4	146
P14388 UniProt NPD GO	HBB_ANTPA	Hemoglobin subunit beta (Hemoglobin beta chain) (Beta-globin)	0.01	-	cyt	0					146
P80216 UniProt NPD GO	HBB_APTFO	Hemoglobin subunit beta (Hemoglobin beta chain) (Beta-globin)	0.01	-	mit	0					146
P15165 UniProt NPD GO	HBB_APUAP	Hemoglobin subunit beta (Hemoglobin beta chain) (Beta-globin)	0.01	-	mit	0					146
P02122 UniProt NPD GO	HBB_AQUCH	Hemoglobin subunit beta (Hemoglobin beta chain) (Beta-globin)	0.01	-	cyt	0					146
P02116 UniProt NPD GO	HBB_ARAAR	Hemoglobin subunit beta (Hemoglobin beta chain) (Beta-globin)	0.01	-	cyt	0					146
P84792 UniProt NPD GO	HBB_AYTFU	Hemoglobin subunit beta (Hemoglobin beta chain) (Beta-globin)	0.01	-	cyt	0		hemoglobin complex [IDA]			146
P18984 UniProt NPD GO	HBB_BALAC	Hemoglobin subunit beta (Hemoglobin beta chain) (Beta-globin)	0.01	-	cyt	0					146
P84217 UniProt NPD GO	HBB_BATEA	Hemoglobin subunit beta (Hemoglobin beta chain) (Beta-globin)	0.01	-	cyt	0					141

You are viewing entries 88701 to 88750 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.