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
P82896 UniProt NPD GO	PA25_TRIST	Phospholipase A2, acid 5 (EC 3.1.1.4) (PA2-V) (PLA2-V) (Phosphatidylcholine 2-acylhydrolase)	0.02	-	nuc	0	Secreted protein				122
P22640 UniProt NPD GO	PA2B_TRIMU	Phospholipase A2, basic (EC 3.1.1.4) (Phosphatidylcholine 2-acylhydrolase) (TMV-K49)	0.02	-	nuc	0	Secreted protein				122
Q1ZY03 UniProt NPD GO	PA2B_AGKAC	Phospholipase A2, basic precursor (EC 3.1.1.4) (Phosphatidylcholine 2-acylhydrolase)	0.02	-	cyt	1 *	Secreted protein				138
P84475 UniProt NPD GO	PA21A_BUNCA	Phospholipase A2, neurotoxin T1-1 A chain (EC 3.1.1.4) (Phosphatidylcholine 2-acylhydrolase T1-1 A) ...	0.02	-		0	Secreted protein				14
P84472 UniProt NPD GO	PA22A_BUNCA	Phospholipase A2, neurotoxin T1-2 A chain (EC 3.1.1.4) (Phosphatidylcholine 2-acylhydrolase T1-2 A) ...	0.02	-		0	Secreted protein				14
P21264 UniProt NPD GO	PUR6_YEAST	Phosphoribosylaminoimidazole carboxylase (EC 4.1.1.21) (AIR carboxylase) (AIRC)	0.02	-	cyt	0		cytoplasm [IDA]			571
P27616 UniProt NPD GO	PUR7_YEAST	Phosphoribosylaminoimidazole-succinocarboxamide synthase (EC 6.3.2.6) (SAICAR synthetase)	0.02	-	cyt	0		cytoplasm [IDA] nucleus [IDA]		2CNV	306
P04161 UniProt NPD GO	PUR3_YEAST	Phosphoribosylglycinamide formyltransferase (EC 2.1.2.2) (GART) (GAR transformylase) (5'-phosphoribo ...	0.02	-	nuc	0		cytoplasm [IDA] nucleus [IDA]			214
P33330 UniProt NPD GO	SERC_YEAST	Phosphoserine aminotransferase (EC 2.6.1.52) (PSAT)	0.02	-	cyt	0		cytoplasm [IDA]			395
Q96255 UniProt NPD GO	SERC_ARATH	Phosphoserine aminotransferase, chloroplast precursor (EC 2.6.1.52) (PSAT)	0.02	-	mit	0	Plastid; chloroplast				430
O82796 UniProt NPD GO	SERB_ARATH	Phosphoserine phosphatase, chloroplast precursor (EC 3.1.3.3) (PSP) (O-phosphoserine phosphohydrolas ...	0.02	-	cyt	0	Plastid; chloroplast				295
Q9MUJ3 UniProt NPD GO	PSAA_ADICA	Photosystem I P700 chlorophyll a apoprotein A1 (PsaA) (PSI-A)	0.02	-	end	9	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein (By similarity)				750
Q70Y03 UniProt NPD GO	PSAA_AMBTC	Photosystem I P700 chlorophyll a apoprotein A1 (PsaA) (PSI-A)	0.02	-	end	9	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein (By similarity)				750
Q8S8X4 UniProt NPD GO	PSAA_ATRBE	Photosystem I P700 chlorophyll a apoprotein A1 (PsaA) (PSI-A)	0.02	-	end	9	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein (By similarity)				750
Q7YJX2 UniProt NPD GO	PSAA_CALFE	Photosystem I P700 chlorophyll a apoprotein A1 (PsaA) (PSI-A)	0.02	-	end	9	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein (By similarity)				750
P12154 UniProt NPD GO	PSAA_CHLRE	Photosystem I P700 chlorophyll a apoprotein A1 (PsaA) (PSI-A)	0.02	-	end	9	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein				751
P56341 UniProt NPD GO	PSAA_CHLVU	Photosystem I P700 chlorophyll a apoprotein A1 (PsaA) (PSI-A)	0.02	-	end	9	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein (By similarity)				751
Q85FY7 UniProt NPD GO	PSAA_CYAME	Photosystem I P700 chlorophyll a apoprotein A1 (PsaA) (PSI-A)	0.02	-	end	9	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein				748
P48112 UniProt NPD GO	PSAA_CYAPA	Photosystem I P700 chlorophyll a apoprotein A1 (PsaA) (PSI-A)	0.02	-	end	9	Plastid; cyanelle; cyanelle thylakoid membrane; multi-pass membrane protein (By similarity)				752
Q9MTN8 UniProt NPD GO	PSAA_OENHO	Photosystem I P700 chlorophyll a apoprotein A1 (PsaA) (PSI-A)	0.02	-	end	9	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein (By similarity)				751
Q68S06 UniProt NPD GO	PSAA_PANGI	Photosystem I P700 chlorophyll a apoprotein A1 (PsaA) (PSI-A)	0.02	-	end	9	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein (By similarity)				750
Q9MUJ2 UniProt NPD GO	PSAA_PSINU	Photosystem I P700 chlorophyll a apoprotein A1 (PsaA) (PSI-A)	0.02	-	end	9	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein (By similarity)				750
Q9MUJ5 UniProt NPD GO	PSAA_ANGEV	Photosystem I P700 chlorophyll a apoprotein A1 (PsaA) (PSI-A) (Fragment)	0.02	-	end	8	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein (By similarity)				721
Q9MUJ4 UniProt NPD GO	PSAA_ASPND	Photosystem I P700 chlorophyll a apoprotein A1 (PsaA) (PSI-A) (Fragment)	0.02	-	end	8	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein (By similarity)				719
Q9MUC0 UniProt NPD GO	PSAA_GINBI	Photosystem I P700 chlorophyll a apoprotein A1 (PsaA) (PSI-A) (Fragment)	0.02	-	end	8	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein (By similarity)				721
Q9MUJ1 UniProt NPD GO	PSAA_HUPSQ	Photosystem I P700 chlorophyll a apoprotein A1 (PsaA) (PSI-A) (Fragment)	0.02	-	end	8	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein (By similarity)				715
Q9MUK1 UniProt NPD GO	PSAA_MARBO	Photosystem I P700 chlorophyll a apoprotein A1 (PsaA) (PSI-A) (Fragment)	0.02	-	end	8	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein (By similarity)				720
P48113 UniProt NPD GO	PSAB_CYAPA	Photosystem I P700 chlorophyll a apoprotein A2 (PsaB)	0.02	-	end	9	Plastid; cyanelle; cyanelle thylakoid membrane; multi-pass membrane protein (By similarity)				737
P58383 UniProt NPD GO	PSAB_AMPCA	Photosystem I P700 chlorophyll a apoprotein A2 (PsaB) (PSI-B)	0.02	-	end	12	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein (By similarity)				644
O78507 UniProt NPD GO	PSAB_GUITH	Photosystem I P700 chlorophyll a apoprotein A2 (PsaB) (PSI-B)	0.02	-	end	10 *	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein (By similarity)				734
P06408 UniProt NPD GO	PSAB_MARPO	Photosystem I P700 chlorophyll a apoprotein A2 (PsaB) (PSI-B)	0.02	-	end	9 *	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein (By similarity)				734
P49480 UniProt NPD GO	PSAB_ODOSI	Photosystem I P700 chlorophyll a apoprotein A2 (PsaB) (PSI-B)	0.02	-	end	10 *	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein (By similarity)				733
Q9TM19 UniProt NPD GO	YCF4_CYACA	Photosystem I assembly protein ycf4	0.02	-	end	2 *	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein (By similarity)				183
P51220 UniProt NPD GO	YCF4_PORPU	Photosystem I assembly protein ycf4	0.02	-	mit	2 *	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein (By similarity)				186
P84563 UniProt NPD GO	PSAD_POPEU	Photosystem I reaction center subunit II (Photosystem I 20 kDa subunit) (PSI-D) (Fragment)	0.02	-	nuc	0	Plastid; chloroplast; chloroplast thylakoid membrane; peripheral membrane protein. Stromal side (By ...				29
P20118 UniProt NPD GO	PSAE_PEA	Photosystem I reaction center subunit IV (PSI-E) (Photosystem I 13 kDa protein) (Fragment)	0.02	-		0	Plastid; chloroplast; chloroplast thylakoid membrane; peripheral membrane protein				13
P13194 UniProt NPD GO	PSAE_HORVU	Photosystem I reaction center subunit IV, chloroplast precursor (PSI-E) (Photosystem I 10.8 kDa poly ...	0.02	-	mit	0	Plastid; chloroplast; chloroplast thylakoid membrane; peripheral membrane protein (By similarity)				147
P59777 UniProt NPD GO	PSAJ_CHLRE	Photosystem I reaction center subunit IX (PSI-J)	0.02	-	mit	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				41
Q6EW33 UniProt NPD GO	PSAJ_NYMAL	Photosystem I reaction center subunit IX (PSI-J)	0.02	-	mit	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				44
P12192 UniProt NPD GO	PSAJ_ORYSA	Photosystem I reaction center subunit IX (PSI-J)	0.02	-	cyt	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				44
Q00327 UniProt NPD GO	PSAG_HORVU	Photosystem I reaction center subunit V, chloroplast precursor (PSI-G) (Photosystem I 9 kDa protein) ...	0.02	-	mit	2 *	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein (Probable)				143
O47040 UniProt NPD GO	PSAI_PICAB	Photosystem I reaction center subunit VIII (PSI-I)	0.02	-	nuc	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				36
P52768 UniProt NPD GO	PSAI_PINTH	Photosystem I reaction center subunit VIII (PSI-I)	0.02	-	nuc	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				52
Q9TM17 UniProt NPD GO	PSAL_CYACA	Photosystem I reaction center subunit XI (PSI-L) (PSI subunit V)	0.02	-	mit	3 *	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein (Probable)				152
O19902 UniProt NPD GO	PSAK_CYACA	Photosystem I reaction center subunit psaK (Photosystem I subunit X) (PSI-K)	0.02	-	nuc	2 *	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein (Probable)				84
P14627 UniProt NPD GO	PSAK_SPIOL	Photosystem I reaction center subunit psaK, chloroplast (Photosystem I subunit X) (PSI-K) (Light-har ...	0.02	-	mit	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein (Probable)				29
Q40519 UniProt NPD GO	PSBR_TOBAC	Photosystem II 10 kDa polypeptide, chloroplast precursor (PII10)	0.02	-	cyt	1	Plastid; chloroplast; chloroplast thylakoid membrane. Associated with the photosystem II complex				136
Q9ZQS5 UniProt NPD GO	PSBU_CYACA	Photosystem II 12 kDa extrinsic protein, chloroplast precursor (PS II complex 12 kDa extrinsic prote ...	0.02	-	mit	0	Plastid; chloroplast; chloroplast thylakoid membrane; peripheral membrane protein. Lumenal side. Loo ...				154
Q85FM3 UniProt NPD GO	PSBC_ADICA	Photosystem II 44 kDa reaction center protein (P6 protein) (CP43)	0.02	-	end	6 *	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein				473
P11095 UniProt NPD GO	PSBC_HORVU	Photosystem II 44 kDa reaction center protein (P6 protein) (CP43)	0.02	-	end	5 *	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein				473

You are viewing entries 85001 to 85050 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.