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
P43060 UniProt NPD GO	PUR7_CANAL	Phosphoribosylaminoimidazole-succinocarboxamide synthase (EC 6.3.2.6) (SAICAR synthetase)	0.01	-	cyt	0					291
P27602 UniProt NPD GO	PUR7_CANMA	Phosphoribosylaminoimidazole-succinocarboxamide synthase (EC 6.3.2.6) (SAICAR synthetase)	0.01	-	cyt	0					291
Q96VP6 UniProt NPD GO	PUR7_PICAN	Phosphoribosylaminoimidazole-succinocarboxamide synthase (EC 6.3.2.6) (SAICAR synthetase)	0.01	-	cyt	0					303
P50124 UniProt NPD GO	PUR7_PICJA	Phosphoribosylaminoimidazole-succinocarboxamide synthase (EC 6.3.2.6) (SAICAR synthetase)	0.01	-	cyt	0					301
Q5M819 UniProt NPD GO	SERB_RAT	Phosphoserine phosphatase (EC 3.1.3.3) (PSP) (O-phosphoserine phosphohydrolase) (PSPase)	0.01	-	cyt	0					225
P42941 UniProt NPD GO	SERB_YEAST	Phosphoserine phosphatase (EC 3.1.3.3) (PSP) (O-phosphoserine phosphohydrolase) (PSPase)	0.01	-	cyt	0		cytoplasm [IDA] nucleus [IDA]			309
Q2KHU0 UniProt NPD GO	SERB_BOVIN	Phosphoserine phosphatase (EC 3.1.3.3) (PSP) (O-phosphoserine phosphohydrolase) (PSPase) (L-3-phosph ...	0.01	-	cyt	0					225
Q9VHF2 UniProt NPD GO	PTER_DROME	Phosphotriesterase-related protein (Parathion hydrolase-related protein)	0.01	-	cyt	0					350
P58309 UniProt NPD GO	PSAA_AMPCA	Photosystem I P700 chlorophyll a apoprotein A1 (PsaA) (PSI-A)	0.01	-	end	11	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein (By similarity)				678
P56766 UniProt NPD GO	PSAA_ARATH	Photosystem I P700 chlorophyll a apoprotein A1 (PsaA) (PSI-A)	0.01	-	end	9	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein (By similarity)				750
Q5SD06 UniProt NPD GO	PSAA_HUPLU	Photosystem I P700 chlorophyll a apoprotein A1 (PsaA) (PSI-A)	0.01	-	end	9	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein (By similarity)				750
P58310 UniProt NPD GO	PSAA_LOTJA	Photosystem I P700 chlorophyll a apoprotein A1 (PsaA) (PSI-A)	0.01	-	end	9	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein (By similarity)				750
P06406 UniProt NPD GO	PSAA_MARPO	Photosystem I P700 chlorophyll a apoprotein A1 (PsaA) (PSI-A)	0.01	-	end	9	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein (By similarity)				750
Q9MUR8 UniProt NPD GO	PSAA_MESVI	Photosystem I P700 chlorophyll a apoprotein A1 (PsaA) (PSI-A)	0.01	-	end	9	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein (By similarity)				750
Q9TKW2 UniProt NPD GO	PSAA_NEPOL	Photosystem I P700 chlorophyll a apoprotein A1 (PsaA) (PSI-A)	0.01	-	end	9	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein (By similarity)				751
Q6EW48 UniProt NPD GO	PSAA_NYMAL	Photosystem I P700 chlorophyll a apoprotein A1 (PsaA) (PSI-A)	0.01	-	end	9	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein (By similarity)				750
P06405 UniProt NPD GO	PSAA_TOBAC	Photosystem I P700 chlorophyll a apoprotein A1 (PsaA) (PSI-A)	0.01	-	end	9	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein (By similarity)				750
P58311 UniProt NPD GO	PSAA_WHEAT	Photosystem I P700 chlorophyll a apoprotein A1 (PsaA) (PSI-A)	0.01	-	end	9	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein (By similarity)				750
Q9MTQ4 UniProt NPD GO	PSAA_AMPOP	Photosystem I P700 chlorophyll a apoprotein A1 (PsaA) (PSI-A) (Fragment)	0.01	-	end	11	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein (By similarity)				671
Q9MUK4 UniProt NPD GO	PSAA_ENCLE	Photosystem I P700 chlorophyll a apoprotein A1 (PsaA) (PSI-A) (Fragment)	0.01	-	end	8	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein (By similarity)				719
Q9MUJ8 UniProt NPD GO	PSAA_EPHTW	Photosystem I P700 chlorophyll a apoprotein A1 (PsaA) (PSI-A) (Fragment)	0.01	-	end	8	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein (By similarity)				720
Q9MUK3 UniProt NPD GO	PSAA_SEQSE	Photosystem I P700 chlorophyll a apoprotein A1 (PsaA) (PSI-A) (Fragment)	0.01	-	end	8	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein (By similarity)				720
Q9MUJ0 UniProt NPD GO	PSAA_TORCL	Photosystem I P700 chlorophyll a apoprotein A1 (PsaA) (PSI-A) (Fragment)	0.01	-	end	8	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein (By similarity)				719
P58765 UniProt NPD GO	PSAB_PSINU	Photosystem I P700 chlorophyll a apoprotein A2 (PsaB) (PSI-B)	0.01	-	end	9	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein (By similarity)				734
P51279 UniProt NPD GO	PSAD_PORPU	Photosystem I reaction center subunit II (Photosystem I 16 kDa polypeptide) (PSI-D)	0.01	-	cyt	0	Plastid; chloroplast				141
O78457 UniProt NPD GO	PSAF_GUITH	Photosystem I reaction center subunit III (PSI-F)	0.01	-	end	3 *	Plastid; chloroplast; chloroplast thylakoid lumen				183
P12356 UniProt NPD GO	PSAF_CHLRE	Photosystem I reaction center subunit III, chloroplast precursor (Light-harvesting complex I 17 kDa ...	0.01	-	mit	0	Plastid; chloroplast; chloroplast thylakoid lumen				227
O19924 UniProt NPD GO	PSAE_CYACA	Photosystem I reaction center subunit IV (PSI-E)	0.01	-	cyt	0	Plastid; chloroplast; chloroplast thylakoid membrane; peripheral membrane protein (By similarity)				69
O78515 UniProt NPD GO	PSAE_GUITH	Photosystem I reaction center subunit IV (PSI-E)	0.01	-	cyt	0	Plastid; chloroplast; chloroplast thylakoid membrane; peripheral membrane protein (By similarity)				64
P69403 UniProt NPD GO	PSAE_PORPU	Photosystem I reaction center subunit IV (PSI-E)	0.01	-	cyt	0	Plastid; chloroplast; chloroplast thylakoid membrane; peripheral membrane protein (By similarity)				62
P69404 UniProt NPD GO	PSAE_PORUM	Photosystem I reaction center subunit IV (PSI-E)	0.01	-	cyt	0	Plastid; chloroplast; chloroplast thylakoid membrane; peripheral membrane protein (By similarity)				62
Q859W0 UniProt NPD GO	PSAJ_ANTFO	Photosystem I reaction center subunit IX (PSI-J)	0.01	-	cyt	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				42
P56769 UniProt NPD GO	PSAJ_ARATH	Photosystem I reaction center subunit IX (PSI-J)	0.01	-	mit	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				44
Q7YJV6 UniProt NPD GO	PSAJ_CALFE	Photosystem I reaction center subunit IX (PSI-J)	0.01	-	mit	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				44
P56340 UniProt NPD GO	PSAJ_CHLVU	Photosystem I reaction center subunit IX (PSI-J)	0.01	-	cyt	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				41
P30394 UniProt NPD GO	PSAJ_EUGGR	Photosystem I reaction center subunit IX (PSI-J)	0.01	-	mit	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				37
Q9BBR3 UniProt NPD GO	PSAJ_LOTJA	Photosystem I reaction center subunit IX (PSI-J)	0.01	-	mit	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				44
P62596 UniProt NPD GO	PSAJ_MAIZE	Photosystem I reaction center subunit IX (PSI-J)	0.01	-	end	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				42
Q6ENF3 UniProt NPD GO	PSAJ_ORYNI	Photosystem I reaction center subunit IX (PSI-J)	0.01	-	end	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				44
Q85X34 UniProt NPD GO	PSAJ_PINKO	Photosystem I reaction center subunit IX (PSI-J)	0.01	-	cyt	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				50
Q6L381 UniProt NPD GO	PSAJ_SACHY	Photosystem I reaction center subunit IX (PSI-J)	0.01	-	end	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				42
Q6ENU4 UniProt NPD GO	PSAJ_SACOF	Photosystem I reaction center subunit IX (PSI-J)	0.01	-	end	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				42
P62595 UniProt NPD GO	PSAJ_WHEAT	Photosystem I reaction center subunit IX (PSI-J)	0.01	-	end	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				42
P17229 UniProt NPD GO	PSAJ_PEA	Photosystem I reaction center subunit IX (PSI-J) (Fragment)	0.01	-		0	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				13
P42049 UniProt NPD GO	PSAG_CUCSA	Photosystem I reaction center subunit V (PSI-G) (Photosystem I 6.8 kDa protein) (PS I subunit 10) (F ...	0.01	-		0	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein. Associated with t ...				14
P20120 UniProt NPD GO	PSAG_PEA	Photosystem I reaction center subunit V (PSI-G) (Photosystem I 9 kDa protein) (Fragment)	0.01	-	cyt	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein (Probable)				39
P14224 UniProt NPD GO	PSAG_CHLRE	Photosystem I reaction center subunit V, chloroplast precursor (PSI-G) (Light-harvesting complex I 1 ...	0.01	-	mit	0	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein (Probable)				126
P20121 UniProt NPD GO	PSAH_PEA	Photosystem I reaction center subunit VI (PSI-H) (Light-harvesting complex I 11 kDa protein) (Fragme ...	0.01	-	cyt	0	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein				36
Q5QA78 UniProt NPD GO	PSAI_ACOGR	Photosystem I reaction center subunit VIII (PSI-I)	0.01	-	nuc	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				36
Q70XZ3 UniProt NPD GO	PSAI_AMBTC	Photosystem I reaction center subunit VIII (PSI-I)	0.01	-	mit	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				36

You are viewing entries 90351 to 90400 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.