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
P68051 UniProt NPD GO	HBB1_PANPS	Hemoglobin subunit beta-1 (Hemoglobin beta-1 chain) (Beta-1-globin)	0.01	-	cyt	0					146
P68048 UniProt NPD GO	HBB1_PANTS	Hemoglobin subunit beta-1 (Hemoglobin beta-1 chain) (Beta-1-globin)	0.01	-	cyt	0					146
P83624 UniProt NPD GO	HBB1_PSEUR	Hemoglobin subunit beta-1 (Hemoglobin beta-1 chain) (Beta-1-globin)	0.01	-	cyt	0		hemoglobin complex [IDA]			146
P10060 UniProt NPD GO	HBB1_SPHPU	Hemoglobin subunit beta-1 (Hemoglobin beta-1 chain) (Beta-1-globin)	0.01	-	cyt	0					146
Q90486 UniProt NPD GO	HBB1_BRARE	Hemoglobin subunit beta-1 (Hemoglobin beta-1 chain) (Beta-1-globin) (Beta-A1-globin)	0.01	-	cyt	0		hemoglobin complex [ISS] mitochondrion [ISS]			147
Q1AGS3 UniProt NPD GO	HBB1_ARCGL	Hemoglobin subunit beta-1 (Hemoglobin beta-1 chain) (Beta-1-globin) (Fragment)	0.01	-	cyt	0					132
O93348 UniProt NPD GO	HBB1_PAGBO	Hemoglobin subunit beta-1 (Hemoglobin beta-1 chain) (Beta-1-globin) (Hb 1)	0.01	-	cyt	0					146
Q7LZC2 UniProt NPD GO	HBB1_MURHE	Hemoglobin subunit beta-1 (Hemoglobin beta-1 chain) (Beta-1-globin) (Hemoglobin beta-I chain)	0.01	-	cyt	0					146
P02142 UniProt NPD GO	HBB1_ONCMY	Hemoglobin subunit beta-1 (Hemoglobin beta-1 chain) (Beta-1-globin) (Hemoglobin beta-I chain)	0.01	-	cyt	0				1OUU	146
P18993 UniProt NPD GO	HBB1_VAREX	Hemoglobin subunit beta-1 (Hemoglobin beta-1 chain) (Beta-1-globin) (Hemoglobin beta-I chain)	0.01	-	cyt	0					146
P07432 UniProt NPD GO	HBB1_XENBO	Hemoglobin subunit beta-1 (Hemoglobin beta-1 chain) (Beta-1-globin) (Hemoglobin beta-major chain)	0.01	-	cyt	0					145
P02132 UniProt NPD GO	HBB1_XENLA	Hemoglobin subunit beta-1 (Hemoglobin beta-1 chain) (Beta-1-globin) (Hemoglobin beta-major chain)	0.01	-	cyt	0					145
P0C0U8 UniProt NPD GO	HBB1_DRYCE	Hemoglobin subunit beta-1 (Hemoglobin beta-1 chain) (Hemoglobin beta-I chain) (Beta-1-globin)	0.01	-	cyt	0					146
P45720 UniProt NPD GO	HBB_TRENE	Hemoglobin subunit beta-1/2 (Hemoglobin beta-1/2 chain) (Beta-1/2-globin)	0.01	-	cyt	0				1T1N	146
P09905 UniProt NPD GO	HBB_PHYCA	Hemoglobin subunit beta-1/2 (Hemoglobin beta-1/2 chain) (Beta-1/2-globin) (Hemoglobin beta-I/II chai ...	0.01	-	cyt	0					146
P83273 UniProt NPD GO	HBB2_ANAMI	Hemoglobin subunit beta-2 (Hemoglobin beta-2 chain) (Beta-2-globin)	0.01	-	cyt	0					146
P23018 UniProt NPD GO	HBB2_CYGMA	Hemoglobin subunit beta-2 (Hemoglobin beta-2 chain) (Beta-2-globin)	0.01	-	cyt	0					146
P83614 UniProt NPD GO	HBB2_GOBGI	Hemoglobin subunit beta-2 (Hemoglobin beta-2 chain) (Beta-2-globin)	0.01	-	cyt	0		hemoglobin complex [NAS]			146
P68064 UniProt NPD GO	HBB2_PANON	Hemoglobin subunit beta-2 (Hemoglobin beta-2 chain) (Beta-2-globin)	0.01	-	cyt	0					146
P68065 UniProt NPD GO	HBB2_PANPS	Hemoglobin subunit beta-2 (Hemoglobin beta-2 chain) (Beta-2-globin)	0.01	-	cyt	0					146
P68194 UniProt NPD GO	HBB2_PANTS	Hemoglobin subunit beta-2 (Hemoglobin beta-2 chain) (Beta-2-globin)	0.01	-	cyt	0					146
P83625 UniProt NPD GO	HBB2_PSEUR	Hemoglobin subunit beta-2 (Hemoglobin beta-2 chain) (Beta-2-globin)	0.01	-	cyt	0		hemoglobin complex [IDA]			146
P10061 UniProt NPD GO	HBB2_SPHPU	Hemoglobin subunit beta-2 (Hemoglobin beta-2 chain) (Beta-2-globin)	0.01	-	cyt	0					146
P83114 UniProt NPD GO	HBB2_TELPE	Hemoglobin subunit beta-2 (Hemoglobin beta-2 chain) (Beta-2-globin)	0.01	-	cyt	0					145
Q90485 UniProt NPD GO	HBB2_BRARE	Hemoglobin subunit beta-2 (Hemoglobin beta-2 chain) (Beta-2-globin) (Beta-A2-globin)	0.01	-	cyt	0		hemoglobin complex [ISS] mitochondrion [ISS]			147
P18992 UniProt NPD GO	HBB2_UROHA	Hemoglobin subunit beta-2 (Hemoglobin beta-2 chain) (Beta-2-globin) (Fragment)	0.01	-		0					19
P11517 UniProt NPD GO	HBB2_RAT	Hemoglobin subunit beta-2 (Hemoglobin beta-2 chain) (Beta-2-globin) (Hemoglobin beta chain, minor-fo ...	0.01	-	cyt	0					146
P22743 UniProt NPD GO	HBB2_NAJNA	Hemoglobin subunit beta-2 (Hemoglobin beta-2 chain) (Beta-2-globin) (Hemoglobin beta-II chain)	0.01	-	cyt	0					146
P10786 UniProt NPD GO	HBB2_TRICR	Hemoglobin subunit beta-2 (Hemoglobin beta-2 chain) (Beta-2-globin) (Hemoglobin beta-minor chain)	0.01	-	nuc	0					145
P07433 UniProt NPD GO	HBB2_XENBO	Hemoglobin subunit beta-2 (Hemoglobin beta-2 chain) (Beta-2-globin) (Hemoglobin beta-minor chain)	0.01	-	cyt	0					145
P02133 UniProt NPD GO	HBB2_XENLA	Hemoglobin subunit beta-2 (Hemoglobin beta-2 chain) (Beta-2-globin) (Hemoglobin beta-minor chain) (L ...	0.01	-	nuc	0					146
P08423 UniProt NPD GO	HBB2_XENTR	Hemoglobin subunit beta-2 (Hemoglobin beta-2 chain) (Beta-2-globin) (Larval beta-globin)	0.01	-	nuc	0					146
P02136 UniProt NPD GO	HBB3_RANCA	Hemoglobin subunit beta-3 (Hemoglobin beta-3 chain) (Beta-3-globin) (Hemoglobin beta-III chain, larv ...	0.01	-	cyt	0					146
P02141 UniProt NPD GO	HBB4_ONCMY	Hemoglobin subunit beta-4 (Hemoglobin beta-4 chain) (Beta-4-globin) (Hemoglobin beta-IV chain)	0.01	-	cyt	0					147
P07412 UniProt NPD GO	HBB_FELCA	Hemoglobin subunit beta-A/B (Hemoglobin beta-A/B chain) (Beta-A/B-globin)	0.01	-	cyt	0					146
P02139 UniProt NPD GO	HBB_CYPCA	Hemoglobin subunit beta-A/B (Hemoglobin subunit beta-1/2) (Hemoglobin beta-A/B chain)	0.01	-	cyt	0					147
Q9PVM1 UniProt NPD GO	HBBB_SERQU	Hemoglobin subunit beta-B (Hemoglobin beta-B chain) (Beta-B-globin)	0.01	-	cyt	0					147
P68058 UniProt NPD GO	HBBC_AMMLE	Hemoglobin subunit beta-C (Hemoglobin beta-C chain) (Beta-C-globin)	0.01	-	cyt	0					141
P68057 UniProt NPD GO	HBBC_OVIMU	Hemoglobin subunit beta-C (Hemoglobin beta-C chain) (Beta-C-globin)	0.01	-	cyt	0					141
P45722 UniProt NPD GO	HBBC_PAGBE	Hemoglobin subunit beta-C (Hemoglobin beta-C chain) (Beta-C-globin)	0.01	-	cyt	0					146
P68056 UniProt NPD GO	HBBC_SHEEP	Hemoglobin subunit beta-C (Hemoglobin beta-C chain) (Beta-C-globin)	0.01	-	cyt	0					141
P45721 UniProt NPD GO	HBBC_TRENE	Hemoglobin subunit beta-C (Hemoglobin beta-C chain) (Beta-C-globin)	0.01	-	cyt	0				2AA1	146
P02078 UniProt NPD GO	HBBC_CAPHI	Hemoglobin subunit beta-C (Hemoglobin beta-C chain) (Beta-C-globin) (Cysteine beta-globin)	0.01	-	cyt	0					141
P04443 UniProt NPD GO	HBB0_MOUSE	Hemoglobin subunit beta-H0 (Hemoglobin beta-H0 chain) (Beta-H0-globin)	0.01	-	cyt	0					146
P04444 UniProt NPD GO	HBBZ_MOUSE	Hemoglobin subunit beta-H1 (Hemoglobin beta-H1 chain) (Beta-H1-globin) (Protein Z)	0.01	-	cyt	0					146
P02109 UniProt NPD GO	HBB_DIDMA	Hemoglobin subunit beta-M (Hemoglobin beta-M chain) (Beta-M-globin)	0.01	-	cyt	0					146
P07410 UniProt NPD GO	HBB_SPETO	Hemoglobin subunit beta-S/F (Hemoglobin beta-S/F chain) (Beta-S/F-globin)	0.01	-	cyt	0					146
P29626 UniProt NPD GO	HBBY_MESAU	Hemoglobin subunit beta-Y (Hemoglobin beta-Y chain) (Beta-Y-globin)	0.01	-	cyt	0					146
P08261 UniProt NPD GO	HBB_LARRI	Hemoglobin subunit beta/beta' (Hemoglobin beta/beta' chain) (Beta/beta'-globin)	0.01	-	nuc	0					146
Q45XI9 UniProt NPD GO	HBD_ELEMA	Hemoglobin subunit delta (Hemoglobin delta chain) (Delta-globin)	0.01	-	cyt	0					146

You are viewing entries 88851 to 88900 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.