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
Q60559 UniProt NPD GO	AMBP_MESAU	AMBP protein precursor [Contains: Alpha-1-microglobulin; Inter-alpha-trypsin inhibitor light chain ( ...	0.08	-	vac	0	Secreted protein	extracellular region [ISS] plasma membrane [ISS]			349
P59780 UniProt NPD GO	AP3S2_HUMAN	AP-3 complex subunit sigma-2 (Adapter-related protein complex 3 sigma-2 subunit) (Sigma-adaptin 3b) ...	0.08	-	cyt	0	Component of the coat surrounding the cytoplasmic face of coated vesicles located at the Golgi compl ...		602416		193
Q8BSZ2 UniProt NPD GO	AP3S2_MOUSE	AP-3 complex subunit sigma-2 (Adapter-related protein complex 3 sigma-2 subunit) (Sigma-adaptin 3b) ...	0.08	-	cyt	0	Component of the coat surrounding the cytoplasmic face of coated vesicles located at the Golgi compl ...	Golgi trans face [TAS]			193
Q5RDP9 UniProt NPD GO	AP3S2_PONPY	AP-3 complex subunit sigma-2 (Adapter-related protein complex 3 sigma-2 subunit) (Sigma-adaptin 3b) ...	0.08	-	cyt	0	Component of the coat surrounding the cytoplasmic face of coated vesicles located at the Golgi compl ...				193
Q6YWS8 UniProt NPD GO	ASCL2_ORYSA	ASC1-like protein 2 (Alternaria stem canker resistance-like protein 2)	0.08	-	end	5 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (By similarity)				303
O75947 UniProt NPD GO	ATP5H_HUMAN	ATP synthase D chain, mitochondrial (EC 3.6.3.14)	0.08	-	cyt	0					160
P48893 UniProt NPD GO	ATP6_ALBCO	ATP synthase a chain (EC 3.6.3.14) (ATPase protein 6)	0.08	-	end	6 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				214
Q9T9Y7 UniProt NPD GO	ATP6_GORGO	ATP synthase a chain (EC 3.6.3.14) (ATPase protein 6)	0.08	-	end	6 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				226
Q35915 UniProt NPD GO	ATP6_PIG	ATP synthase a chain (EC 3.6.3.14) (ATPase protein 6)	0.08	-	end	6 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				226
Q95913 UniProt NPD GO	ATP6_POLOR	ATP synthase a chain (EC 3.6.3.14) (ATPase protein 6)	0.08	-	end	6 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				227
P05499 UniProt NPD GO	ATP6_TOBAC	ATP synthase a chain (EC 3.6.3.14) (ATPase protein 6)	0.08	-	end	5	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				395
Q42687 UniProt NPD GO	ATPD_CHLRE	ATP synthase delta chain, chloroplast precursor (EC 3.6.3.14)	0.08	-	mit	0	Plastid; chloroplast; chloroplast thylakoid membrane				219
Q5SD05 UniProt NPD GO	ATPE_HUPLU	ATP synthase epsilon chain (EC 3.6.3.14) (ATP synthase F1 sector epsilon subunit)	0.08	-	mit	0	Plastid; chloroplast; chloroplast thylakoid membrane; peripheral membrane protein (By similarity)				138
Q06055 UniProt NPD GO	AT5G2_HUMAN	ATP synthase lipid-binding protein, mitochondrial precursor (EC 3.6.3.14) (ATP synthase proteolipid ...	0.08	-	exc	2	Mitochondrion; mitochondrial membrane; multi-pass membrane protein	proton-transporting ATP synthase complex (s... [TAS]	603193		141
P50655 UniProt NPD GO	ATP8_ANAPL	ATP synthase protein 8 (EC 3.6.3.14) (ATPase subunit 8) (A6L)	0.08	-	nuc	1 *	Mitochondrion; mitochondrial membrane; single-pass membrane protein				55
Q9MIY6 UniProt NPD GO	ATP8_BRARE	ATP synthase protein 8 (EC 3.6.3.14) (ATPase subunit 8) (A6L)	0.08	-	mit	1 *	Mitochondrion; mitochondrial membrane; single-pass membrane protein				54
P05040 UniProt NPD GO	ATP8_CANGA	ATP synthase protein 8 (EC 3.6.3.14) (ATPase subunit 8) (A6L)	0.08	-	pox	1 *	Mitochondrion; mitochondrial membrane; single-pass membrane protein				48
Q9MFP7 UniProt NPD GO	ATP8_COLHO	ATP synthase protein 8 (EC 3.6.3.14) (ATPase subunit 8) (A6L)	0.08	-	vac	1 *	Mitochondrion; mitochondrial membrane; single-pass membrane protein				54
Q9TBI7 UniProt NPD GO	ATP8_CORCR	ATP synthase protein 8 (EC 3.6.3.14) (ATPase subunit 8) (A6L)	0.08	-	nuc	1 *	Mitochondrion; mitochondrial membrane; single-pass membrane protein				55
Q9MDJ1 UniProt NPD GO	ATP8_LOXNO	ATP synthase protein 8 (EC 3.6.3.14) (ATPase subunit 8) (A6L)	0.08	-	nuc	1 *	Mitochondrion; mitochondrial membrane; single-pass membrane protein				55
Q35416 UniProt NPD GO	ATP8_PRODO	ATP synthase protein 8 (EC 3.6.3.14) (ATPase subunit 8) (A6L)	0.08	-	vac	1 *	Mitochondrion; mitochondrial membrane; single-pass membrane protein				55
P00856 UniProt NPD GO	ATP8_YEAST	ATP synthase protein 8 (EC 3.6.3.14) (ATPase subunit 8) (A6L) (ATP-associated protein 1)	0.08	-	pox	1 *	Mitochondrion; mitochondrial membrane; single-pass membrane protein	proton-transporting ATP synthase complex, c... [TAS]			48
O79431 UniProt NPD GO	ATP8_RABIT	ATP synthase protein 8 (EC 3.6.3.14) (ATPase subunit 8) (A6L) (Chargerin II)	0.08	-	nuc	1 *	Mitochondrion; mitochondrial membrane; single-pass membrane protein				67
P26526 UniProt NPD GO	ATPA_CHLRE	ATP synthase subunit alpha (EC 3.6.3.14) (ATPase subunit alpha) (ATP synthase F1 sector subunit alph ...	0.08	-	cyt	0	Plastid; chloroplast; chloroplast thylakoid membrane; peripheral membrane protein (By similarity)				507
Q9MUT2 UniProt NPD GO	ATPA_MESVI	ATP synthase subunit alpha (EC 3.6.3.14) (ATPase subunit alpha) (ATP synthase F1 sector subunit alph ...	0.08	-	cyt	0	Plastid; chloroplast; chloroplast thylakoid membrane; peripheral membrane protein (By similarity)				505
P29685 UniProt NPD GO	ATPBM_HEVBR	ATP synthase subunit beta, mitochondrial precursor (EC 3.6.3.14)	0.08	-	mit	0	Mitochondrion				562
Q25117 UniProt NPD GO	ATPB_HEMPU	ATP synthase subunit beta, mitochondrial precursor (EC 3.6.3.14)	0.08	-	mit	0	Mitochondrion				523
P83484 UniProt NPD GO	ATPBN_ARATH	ATP synthase subunit beta-2, mitochondrial precursor (EC 3.6.3.14)	0.08	-	mit	0	Mitochondrion				556
Q704E8 UniProt NPD GO	ABCB7_RAT	ATP-binding cassette sub-family B member 7, mitochondrial precursor (ATP-binding cassette transporte ...	0.08	-	end	5	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein (Potential)				752
P53396 UniProt NPD GO	ACLY_HUMAN	ATP-citrate synthase (EC 2.3.3.8) (ATP-citrate (pro-S-)-lyase) (Citrate cleavage enzyme)	0.08	-	nuc	0	Cytoplasm	citrate lyase complex [TAS]	108728		1101
Q91V92 UniProt NPD GO	ACLY_MOUSE	ATP-citrate synthase (EC 2.3.3.8) (ATP-citrate (pro-S-)-lyase) (Citrate cleavage enzyme)	0.08	-	nuc	0	Cytoplasm (By similarity)	intracellular [TAS]			1091
P16638 UniProt NPD GO	ACLY_RAT	ATP-citrate synthase (EC 2.3.3.8) (ATP-citrate (pro-S-)-lyase) (Citrate cleavage enzyme)	0.08	-	nuc	0	Cytoplasm				1100
Q9TL09 UniProt NPD GO	CLPP_NEPOL	ATP-dependent Clp protease proteolytic subunit (EC 3.4.21.92) (Endopeptidase Clp)	0.08	-	nuc	0	Plastid; chloroplast				208
P01364 UniProt NPD GO	AGN3_APLCA	Abdominal ganglion neuropeptide R3-14 precursor [Contains: Histidine-rich basic peptide (HRBP); Pept ...	0.08	-	exc	0	Secreted protein				108
Q9MS98 UniProt NPD GO	ILVH_GALSU	Acetolactate synthase small subunit (EC 2.2.1.6) (AHAS) (Acetohydroxy-acid synthase small subunit) ( ...	0.08	-	cyt	0	Plastid; chloroplast				181
P46316 UniProt NPD GO	ACCA_ANTSP	Acetyl-coenzyme A carboxylase carboxyl transferase subunit alpha (EC 6.4.1.2) (Acetyl-CoA carboxylas ...	0.08	-	mit	0	Plastid; chloroplast				322
O94049 UniProt NPD GO	ACS1_CANAL	Acetyl-coenzyme A synthetase 1 (EC 6.2.1.1) (Acetate--CoA ligase 1) (Acyl-activating enzyme 1)	0.08	-	nuc	0					675
P22456 UniProt NPD GO	ACHAA_XENLA	Acetylcholine receptor protein subunit alpha-1-A precursor	0.08	-	end	4	Membrane; multi-pass membrane protein				457
Q92081 UniProt NPD GO	ACES_MYXGL	Acetylcholinesterase (EC 3.1.1.7) (AChE) (Fragment)	0.08	-	cyt	0					338
Q869C3 UniProt NPD GO	ACES_ANOGA	Acetylcholinesterase precursor (EC 3.1.1.7) (AChE)	0.08	-	end	1 *					737
P36196 UniProt NPD GO	ACES_CHICK	Acetylcholinesterase precursor (EC 3.1.1.7) (AChE)	0.08	-	exc	0					767
Q43857 UniProt NPD GO	INVA_VICFA	Acid beta-fructofuranosidase precursor (EC 3.2.1.26) (Acid sucrose hydrolase) (Acid invertase) (AI) ...	0.08	-	mit	1 *	Vacuole (Potential)				642
Q9GL10 UniProt NPD GO	ACRO_SHEEP	Acrosin precursor (EC 3.4.21.10) [Contains: Acrosin light chain; Acrosin heavy chain] (Fragment)	0.08	-	mit	0				1FIW	329
P53455 UniProt NPD GO	ACT_AJECA	Actin	0.08	-	cyt	0	Cytoplasm				375
P14235 UniProt NPD GO	ACT_CANAL	Actin	0.08	-	cyt	0	Cytoplasm				376
P45521 UniProt NPD GO	ACT_PROCL	Actin (Fragment)	0.08	-	cyt	0	Cytoplasm				322
P69002 UniProt NPD GO	ACT1_HELER	Actin CyI, cytoplasmic	0.08	-	cyt	0	Cytoplasm				376
P69003 UniProt NPD GO	ACT1_HELTB	Actin CyI, cytoplasmic	0.08	-	cyt	0	Cytoplasm				376
P68034 UniProt NPD GO	ACTC_CHICK	Actin, alpha cardiac (Alpha-cardiac actin)	0.08	-	cyt	0	Cytoplasm				377
P68032 UniProt NPD GO	ACTC_HUMAN	Actin, alpha cardiac (Alpha-cardiac actin)	0.08	-	cyt	0	Cytoplasm		192600		377

You are viewing entries 67451 to 67500 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.