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
Q35929 UniProt NPD GO	NU3M_SALSA	NADH-ubiquinone oxidoreductase chain 3 (EC 1.6.5.3) (NADH dehydrogenase subunit 3)	0.04	-	end	3 *					116
P03913 UniProt NPD GO	NU4M_ASPAM	NADH-ubiquinone oxidoreductase chain 4 (EC 1.6.5.3) (NADH dehydrogenase subunit 4)	0.04	-	end	14 *					488
P11631 UniProt NPD GO	NU4M_ONCMY	NADH-ubiquinone oxidoreductase chain 4 (EC 1.6.5.3) (NADH dehydrogenase subunit 4)	0.04	-	end	13 *					460
O99825 UniProt NPD GO	NU4M_RHISA	NADH-ubiquinone oxidoreductase chain 4 (EC 1.6.5.3) (NADH dehydrogenase subunit 4)	0.04	-	end	13 *					433
O79410 UniProt NPD GO	NU4M_SCYCA	NADH-ubiquinone oxidoreductase chain 4 (EC 1.6.5.3) (NADH dehydrogenase subunit 4)	0.04	-	end	13 *					460
P15551 UniProt NPD GO	NU4M_STRPU	NADH-ubiquinone oxidoreductase chain 4 (EC 1.6.5.3) (NADH dehydrogenase subunit 4)	0.04	-	end	13 *					463
P34858 UniProt NPD GO	NU4LM_ANOGA	NADH-ubiquinone oxidoreductase chain 4L (EC 1.6.5.3) (NADH dehydrogenase subunit 4L)	0.04	-	end	3 *					99
P33512 UniProt NPD GO	NU4LM_ANOQU	NADH-ubiquinone oxidoreductase chain 4L (EC 1.6.5.3) (NADH dehydrogenase subunit 4L)	0.04	-	end	3 *					99
Q33821 UniProt NPD GO	NU4LM_ASTPE	NADH-ubiquinone oxidoreductase chain 4L (EC 1.6.5.3) (NADH dehydrogenase subunit 4L)	0.04	-	exc	3 *					98
P67783 UniProt NPD GO	NU4LM_CARAU	NADH-ubiquinone oxidoreductase chain 4L (EC 1.6.5.3) (NADH dehydrogenase subunit 4L)	0.04	-	exc	3 *					98
P67784 UniProt NPD GO	NU4LM_CYPCA	NADH-ubiquinone oxidoreductase chain 4L (EC 1.6.5.3) (NADH dehydrogenase subunit 4L)	0.04	-	exc	3 *					98
O03172 UniProt NPD GO	NU4LM_LATCH	NADH-ubiquinone oxidoreductase chain 4L (EC 1.6.5.3) (NADH dehydrogenase subunit 4L)	0.04	-	nuc	2 *					98
O21405 UniProt NPD GO	NU4LM_STRCA	NADH-ubiquinone oxidoreductase chain 4L (EC 1.6.5.3) (NADH dehydrogenase subunit 4L)	0.04	-	exc	3 *					98
P03904 UniProt NPD GO	NU4LM_XENLA	NADH-ubiquinone oxidoreductase chain 4L (EC 1.6.5.3) (NADH dehydrogenase subunit 4L)	0.04	-	cyt	2 *					98
P34854 UniProt NPD GO	NU5M_ANOGA	NADH-ubiquinone oxidoreductase chain 5 (EC 1.6.5.3) (NADH dehydrogenase subunit 5)	0.04	-	end	16 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein (Probable)				580
P24884 UniProt NPD GO	NU5M_ASCSU	NADH-ubiquinone oxidoreductase chain 5 (EC 1.6.5.3) (NADH dehydrogenase subunit 5)	0.04	-	end	15 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein (Probable)				547
P24896 UniProt NPD GO	NU5M_CAEEL	NADH-ubiquinone oxidoreductase chain 5 (EC 1.6.5.3) (NADH dehydrogenase subunit 5)	0.04	-	end	13 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein (Probable)				527
P24979 UniProt NPD GO	NU5M_CYPCA	NADH-ubiquinone oxidoreductase chain 5 (EC 1.6.5.3) (NADH dehydrogenase subunit 5)	0.04	-	end	15 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein (Probable)				607
P18932 UniProt NPD GO	NU5M_DROME	NADH-ubiquinone oxidoreductase chain 5 (EC 1.6.5.3) (NADH dehydrogenase subunit 5)	0.04	-	end	16 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein (Probable)				572
P07706 UniProt NPD GO	NU5M_DROYA	NADH-ubiquinone oxidoreductase chain 5 (EC 1.6.5.3) (NADH dehydrogenase subunit 5)	0.04	-	end	16 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein (Probable)				573
P05510 UniProt NPD GO	NU5M_NEUCR	NADH-ubiquinone oxidoreductase chain 5 (EC 1.6.5.3) (NADH dehydrogenase subunit 5)	0.04	-	end	16 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein (Probable)				715
Q9B6D3 UniProt NPD GO	NU5M_YARLI	NADH-ubiquinone oxidoreductase chain 5 (EC 1.6.5.3) (NADH dehydrogenase subunit 5)	0.04	-	end	16 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein (Probable)				655
Q34052 UniProt NPD GO	NU5M_CERCA	NADH-ubiquinone oxidoreductase chain 5 (EC 1.6.5.3) (NADH dehydrogenase subunit 5) (Fragment)	0.04	-	end	2 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein (Probable)				80
P48925 UniProt NPD GO	NU6M_CYACA	NADH-ubiquinone oxidoreductase chain 6 (EC 1.6.5.3) (NADH dehydrogenase subunit 6)	0.04	-	end	5 *					201
Q37626 UniProt NPD GO	NU6M_PROWI	NADH-ubiquinone oxidoreductase chain 6 (EC 1.6.5.3) (NADH dehydrogenase subunit 6)	0.04	-	end	5 *					207
Q8HEC0 UniProt NPD GO	NU6M_CAEBR	NADH-ubiquinone oxidoreductase chain 6 (EC 1.6.5.3) (NADH dehydrogenase subunit 6) (Fragment)	0.04	-	end	4 *					127
Q37383 UniProt NPD GO	NUGM_ACACA	NADH-ubiquinone oxidoreductase subunit 9 (EC 1.6.5.3) (EC 1.6.99.3)	0.04	-	cyt	0	Mitochondrion; mitochondrial inner membrane				195
P81406 UniProt NPD GO	GAPN_PEA	NADP-dependent glyceraldehyde-3-phosphate dehydrogenase (EC 1.2.1.9) (Non-phosphorylating glyceralde ...	0.04	-	cyt	0	Cytoplasm				496
P84539 UniProt NPD GO	MAOX_POPEU	NADP-dependent malic enzyme (EC 1.1.1.40) (NADP-ME) (Fragments)	0.04	-	cyt	0					23
Q16798 UniProt NPD GO	MAON_HUMAN	NADP-dependent malic enzyme, mitochondrial precursor (EC 1.1.1.40) (NADP-ME) (Malic enzyme 3)	0.04	-	cyt	0	Mitochondrion; mitochondrial matrix	mitochondrion [TAS]	604626		604
P40952 UniProt NPD GO	KYE1_KLULA	NADPH dehydrogenase 1 (EC 1.6.99.1) (Old yellow enzyme 1)	0.04	-	cyt	0					398
Q02899 UniProt NPD GO	OYE1_SACPS	NADPH dehydrogenase 1 (EC 1.6.99.1) (Old yellow enzyme 1)	0.04	-	cyt	0				1OYC	399
P16603 UniProt NPD GO	NCPR_YEAST	NADPH--cytochrome P450 reductase (EC 1.6.2.4) (CPR) (P450R)	0.04	-	mit	0	Endoplasmic reticulum; endoplasmic reticulum membrane; single-pass membrane protein	microsome [IDA] mitochondrial outer membrane [IDA] mitochondrion [IDA]		2BN4	690
Q8RUC6 UniProt NPD GO	RUB2_ARATH	NEDD8-like protein RUB2 precursor (Ubiquitin-related protein 2) (AtRUB2)	0.04	-	cyt	0					78
O65381 UniProt NPD GO	RUB3_ARATH	NEDD8-like protein RUB3 precursor (Ubiquitin-related protein 3) (AtRUB3)	0.04	-	cyt	0					78
Q19143 UniProt NPD GO	KBRAS_CAEEL	NF-kappa-B inhibitor-interacting Ras-like protein (Kappa B-Ras) (KappaB-Ras)	0.04	-	cyt	0					199
Q5ZJW6 UniProt NPD GO	KBRS2_CHICK	NF-kappa-B inhibitor-interacting Ras-like protein 2 (I-kappa-B-interacting Ras-like protein 2) (Kapp ...	0.04	-	cyt	0	Cytoplasm (By similarity)				191
Q21568 UniProt NPD GO	NHPX_CAEEL	NHP2/L7aE family protein YEL026W homolog	0.04	-	cyt	0	Nucleus (Potential)				128
P41251 UniProt NPD GO	NRAM1_MOUSE	Natural resistance-associated macrophage protein 1 (NRAMP 1)	0.04	-	end	10	Membrane; multi-pass membrane protein (Probable)				548
P70553 UniProt NPD GO	NRAM1_RAT	Natural resistance-associated macrophage protein 1 (NRAMP 1)	0.04	-	end	10 *	Membrane; multi-pass membrane protein (Probable)				507
P83349 UniProt NPD GO	FLRF1_SARBU	Neb-FIRFamide-1	0.04	-		0	Secreted protein				12
Q9SPV5 UniProt NPD GO	NEC1_NICPL	Nectarin-1 precursor (EC 1.15.1.1) (Superoxide dismutase [Mn])	0.04	-	mit	0	Secreted protein (By similarity). Secreted in the nectar (By similarity)				229
Q90YJ2 UniProt NPD GO	NGB_BRARE	Neuroglobin	0.04	-	cyt	0					159
P09480 UniProt NPD GO	ACHA2_CHICK	Neuronal acetylcholine receptor protein subunit alpha-2 precursor	0.04	-	end	4	Membrane; multi-pass membrane protein				528
P12389 UniProt NPD GO	ACHA2_RAT	Neuronal acetylcholine receptor protein subunit alpha-2 precursor	0.04	-	end	4	Membrane; multi-pass membrane protein				511
P41967 UniProt NPD GO	NPF_MONEX	Neuropeptide F (NPF)	0.04	-	cyt	0	Secreted protein			1K8V	39
P0C0P8 UniProt NPD GO	NPS_MOUSE	Neuropeptide S precursor	0.04	-	nuc	1 *	Secreted protein (Potential)				89
P0C0P7 UniProt NPD GO	NPS_RAT	Neuropeptide S precursor	0.04	-	exc	1 *	Secreted protein (Potential)				89
O44665 UniProt NPD GO	NLP28_CAEEL	Neuropeptide-like protein 28 precursor [Contains: QWGYGGY-amide; GYGGYGGY-amide; GMYGGY-amide; GMYGG ...	0.04	-	vac	1 *	Secreted protein (Potential)				65
O44664 UniProt NPD GO	NLP29_CAEEL	Neuropeptide-like protein 29 precursor [Contains: QWGYGGY-amide; GYGGYGGY-amide; GMYGGY-amide; GMYGG ...	0.04	-	vac	1 *	Secreted protein (Potential)				73

You are viewing entries 77651 to 77700 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.