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
P30947 UniProt NPD GO	HS90B_RABIT	Heat shock protein HSP 90-beta (HSP 84) (Fragment)	0.00	-	cyt	0	Cytoplasm				24
P34328 UniProt NPD GO	HSP10_CAEEL	Heat shock protein Hsp-12.2	0.00	-	cyt	0					110
Q9Y5N5 UniProt NPD GO	HEMK2_HUMAN	HemK methyltransferase family member 2 (EC 2.1.1.-) (M.HsaHemK2P)	0.00	-	mit	0					214
Q96NT5 UniProt NPD GO	HCP1_HUMAN	Heme carrier protein 1	0.00	-	end	11	Cell membrane; apical cell membrane; multi-pass membrane protein. Membrane; multi-pass membrane prot ...				459
Q6PEM8 UniProt NPD GO	HCP1_MOUSE	Heme carrier protein 1	0.00	-	end	10 *	Cell membrane; apical cell membrane; multi-pass membrane protein. Intracytoplasmic membrane; multi-p ...				459
Q5EBA8 UniProt NPD GO	HCP1_RAT	Heme carrier protein 1	0.00	-	end	10 *	Cell membrane; apical cell membrane; multi-pass membrane protein (By similarity). Intracytoplasmic m ...				459
Q5ISC6 UniProt NPD GO	HEBP1_PIG	Heme-binding protein 1	0.00	-	cyt	0	Cytoplasm (By similarity)				189
Q9R257 UniProt NPD GO	HEBP1_MOUSE	Heme-binding protein 1 (p22HBP)	0.00	-	cyt	0	Cytoplasm	cytoplasm [IDA] cytosol [IDA] mitochondrion [IDA]		2HC6	190
P22766 UniProt NPD GO	HEMT_SIPCU	Hemerythrin	0.00	-	mit	0					113
P83173 UniProt NPD GO	HCYA_CHEDE	Hemocyanin A chain (Fragment)	0.00	-	cyt	0	Secreted protein; extracellular space				35
P83172 UniProt NPD GO	HCYC_CHEDE	Hemocyanin C chain (Fragment)	0.00	-	nuc	0	Secreted protein; extracellular space				32
P83176 UniProt NPD GO	HCY1_CARMA	Hemocyanin subunit 1 (Fragment)	0.00	-		0	Secreted protein; extracellular space	extracellular region [NAS]			12
P84846 UniProt NPD GO	HCY1_NECPU	Hemocyanin subunit 1 (Fragment)	0.00	-		0	Secreted protein; extracellular space				12
P84462 UniProt NPD GO	HCY2_LIODE	Hemocyanin subunit 2 (Fragment)	0.00	-		0	Secreted protein; extracellular space				12
P82304 UniProt NPD GO	HCY3_MAISQ	Hemocyanin subunit 3 (Fragment)	0.00	-	nuc	0	Secreted protein; extracellular space				25
P82309 UniProt NPD GO	HCY4_CARMA	Hemocyanin subunit 4 (Fragment)	0.00	-	cyt	0	Secreted protein; extracellular space				23
P82306 UniProt NPD GO	HCY4E_MAISQ	Hemocyanin subunit 4e (Fragment)	0.00	-	cyt	0	Secreted protein; extracellular space				24
P82307 UniProt NPD GO	HCY5_MAISQ	Hemocyanin subunit 5 (Fragment)	0.00	-	cyt	0	Secreted protein; extracellular space				26
P83178 UniProt NPD GO	HCYB_CARMA	Hemocyanin subunit B (Fragment)	0.00	-	nuc	0	Secreted protein; extracellular space				26
P83131 UniProt NPD GO	HBA1_ALDEL	Hemoglobin A subunit alpha-1 (Hemoglobin A alpha-1 chain)	0.00	-	cyt	0					141
P83132 UniProt NPD GO	HBA2_ALDEL	Hemoglobin A subunit alpha-2 (Hemoglobin A alpha-2 chain)	0.00	-	cyt	0					141
P06148 UniProt NPD GO	HBF1_URECA	Hemoglobin F-I	0.00	-	cyt	0				1ITH	141
P80726 UniProt NPD GO	HBAC_ANGAN	Hemoglobin cathodic subunit alpha (Hemoglobin cathodic alpha chain)	0.00	-	cyt	0					142
P83479 UniProt NPD GO	HBAC_CONCO	Hemoglobin cathodic subunit alpha (Hemoglobin cathodic alpha chain)	0.00	-	cyt	0					142
P82315 UniProt NPD GO	HBAC_HOPLI	Hemoglobin cathodic subunit alpha (Hemoglobin cathodic alpha chain) (Hb(Ca) alpha chain)	0.00	-	cyt	0					142
Q9PVU6 UniProt NPD GO	HBAE_ORYLA	Hemoglobin embryonic subunit alpha (Hemoglobin alpha-chain, embryonic) (Alpha-globin, embryonic)	0.00	-	cyt	0					143
Q90487 UniProt NPD GO	HBA_BRARE	Hemoglobin subunit alpha (Hemoglobin alpha chain) (Alpha-globin aa1)	0.00	-	cyt	0		hemoglobin complex [NAS] mitochondrion [ISS]			142
P02015 UniProt NPD GO	HBA_AMBME	Hemoglobin subunit alpha (Hemoglobin alpha chain) (Alpha-globin)	0.00	-	cyt	0					142
P01980 UniProt NPD GO	HBA_APTFO	Hemoglobin subunit alpha (Hemoglobin alpha chain) (Alpha-globin)	0.00	-	cyt	0					141
P18971 UniProt NPD GO	HBA_BALAC	Hemoglobin subunit alpha (Hemoglobin alpha chain) (Alpha-globin)	0.00	-	cyt	0					141
P14525 UniProt NPD GO	HBA_BRATR	Hemoglobin subunit alpha (Hemoglobin alpha chain) (Alpha-globin)	0.00	-	cyt	0					141
P02000 UniProt NPD GO	HBA_CAICR	Hemoglobin subunit alpha (Hemoglobin alpha chain) (Alpha-globin)	0.00	-	cyt	0					141
P02018 UniProt NPD GO	HBA_CARAU	Hemoglobin subunit alpha (Hemoglobin alpha chain) (Alpha-globin)	0.00	-	mit	0					142
P01947 UniProt NPD GO	HBA_CAVPO	Hemoglobin subunit alpha (Hemoglobin alpha chain) (Alpha-globin)	0.00	-	cyt	0					141
P19014 UniProt NPD GO	HBA_CRIGA	Hemoglobin subunit alpha (Hemoglobin alpha chain) (Alpha-globin)	0.00	-	cyt	0					141
P18973 UniProt NPD GO	HBA_CROCR	Hemoglobin subunit alpha (Hemoglobin alpha chain) (Alpha-globin)	0.00	-	cyt	0					141
P20854 UniProt NPD GO	HBA_CTEGU	Hemoglobin subunit alpha (Hemoglobin alpha chain) (Alpha-globin)	0.00	-	cyt	0					141
P07419 UniProt NPD GO	HBA_DASVI	Hemoglobin subunit alpha (Hemoglobin alpha chain) (Alpha-globin)	0.00	-	cyt	0					141
P01976 UniProt NPD GO	HBA_DIDMA	Hemoglobin subunit alpha (Hemoglobin alpha chain) (Alpha-globin)	0.00	-	cyt	0					141
P24291 UniProt NPD GO	HBA_ECHTE	Hemoglobin subunit alpha (Hemoglobin alpha chain) (Alpha-globin)	0.00	-	cyt	0					141
P14520 UniProt NPD GO	HBA_ELEEL	Hemoglobin subunit alpha (Hemoglobin alpha chain) (Alpha-globin)	0.00	-	mit	0					142
P10057 UniProt NPD GO	HBA_EUDCR	Hemoglobin subunit alpha (Hemoglobin alpha chain) (Alpha-globin)	0.00	-	cyt	0					141
P07405 UniProt NPD GO	HBA_FELCA	Hemoglobin subunit alpha (Hemoglobin alpha chain) (Alpha-globin)	0.00	-	cyt	0					141
P29623 UniProt NPD GO	HBA_GYMAC	Hemoglobin subunit alpha (Hemoglobin alpha chain) (Alpha-globin)	0.00	-	cyt	0					142
P23740 UniProt NPD GO	HBA_LATCH	Hemoglobin subunit alpha (Hemoglobin alpha chain) (Alpha-globin)	0.00	-	nuc	0					142
P02020 UniProt NPD GO	HBA_LEPPA	Hemoglobin subunit alpha (Hemoglobin alpha chain) (Alpha-globin)	0.00	-	cyt	0					143
P10892 UniProt NPD GO	HBA_LUTLU	Hemoglobin subunit alpha (Hemoglobin alpha chain) (Alpha-globin)	0.00	-	cyt	0					141
P41327 UniProt NPD GO	HBA_LYNLY	Hemoglobin subunit alpha (Hemoglobin alpha chain) (Alpha-globin)	0.00	-	cyt	0					141
P09839 UniProt NPD GO	HBA_MACCA	Hemoglobin subunit alpha (Hemoglobin alpha chain) (Alpha-globin)	0.00	-	cyt	0					141
P81043 UniProt NPD GO	HBA_MACEU	Hemoglobin subunit alpha (Hemoglobin alpha chain) (Alpha-globin)	0.00	-	cyt	0					141

You are viewing entries 94951 to 95000 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.