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
P68033 UniProt NPD GO	ACTC_MOUSE	Actin, alpha cardiac (Alpha-cardiac actin)	0.08	-	cyt	0	Cytoplasm				377
P68035 UniProt NPD GO	ACTC_RAT	Actin, alpha cardiac (Alpha-cardiac actin)	0.08	-	cyt	0	Cytoplasm				377
P04751 UniProt NPD GO	ACT1_XENLA	Actin, alpha cardiac muscle (Actin alpha 1)	0.08	-	cyt	0	Cytoplasm				377
P10995 UniProt NPD GO	ACT2_XENLA	Actin, alpha sarcomeric/cardiac (Actin alpha 2)	0.08	-	cyt	0	Cytoplasm				377
P20399 UniProt NPD GO	ACT2_XENTR	Actin, alpha sarcomeric/cardiac (Actin alpha 2)	0.08	-	cyt	0	Cytoplasm				377
P04752 UniProt NPD GO	ACT3_XENLA	Actin, alpha sarcomeric/skeletal (Actin alpha 3)	0.08	-	cyt	0	Cytoplasm				377
Q90X97 UniProt NPD GO	ACTS_ATRMM	Actin, alpha skeletal muscle (Alpha-actin-1)	0.08	-	cyt	0	Cytoplasm				377
P68138 UniProt NPD GO	ACTS_BOVIN	Actin, alpha skeletal muscle (Alpha-actin-1)	0.08	-	cyt	0	Cytoplasm	actin filament [ISS] stress fiber [ISS] striated muscle thin filament [ISS]			377
P68139 UniProt NPD GO	ACTS_CHICK	Actin, alpha skeletal muscle (Alpha-actin-1)	0.08	-	cyt	0	Cytoplasm	actin filament [ISS] stress fiber [ISS] striated muscle thin filament [ISS]		1MDU	377
P68133 UniProt NPD GO	ACTS_HUMAN	Actin, alpha skeletal muscle (Alpha-actin-1)	0.08	-	cyt	0	Cytoplasm	actin filament [IDA] stress fiber [IDA] striated muscle thin filament [IDA]	256030		377
P68134 UniProt NPD GO	ACTS_MOUSE	Actin, alpha skeletal muscle (Alpha-actin-1)	0.08	-	cyt	0	Cytoplasm	actin filament [ISS] stress fiber [ISS] striated muscle thin filament [TAS]			377
P68137 UniProt NPD GO	ACTS_PIG	Actin, alpha skeletal muscle (Alpha-actin-1)	0.08	-	cyt	0	Cytoplasm	actin filament [ISS] stress fiber [ISS] striated muscle thin filament [ISS]			377
P68135 UniProt NPD GO	ACTS_RABIT	Actin, alpha skeletal muscle (Alpha-actin-1)	0.08	-	cyt	0	Cytoplasm	actin filament [ISS] stress fiber [ISS] striated muscle thin filament [ISS]		2FXU	377
P68136 UniProt NPD GO	ACTS_RAT	Actin, alpha skeletal muscle (Alpha-actin-1)	0.08	-	cyt	0	Cytoplasm	actin filament [ISS] stress fiber [ISS] striated muscle thin filament [ISS]			377
P53482 UniProt NPD GO	ACTT_FUGRU	Actin, alpha skeletal muscle 2	0.08	-	cyt	0	Cytoplasm				377
P18600 UniProt NPD GO	ACT1_ARTSX	Actin, clone 205	0.08	-	cyt	0	Cytoplasm				376
Q964E3 UniProt NPD GO	ACTC_BIOAL	Actin, cytoplasmic	0.08	-	cyt	0	Cytoplasm				376
P92179 UniProt NPD GO	ACTC_BIOGL	Actin, cytoplasmic	0.08	-	cyt	0	Cytoplasm				376
Q964E1 UniProt NPD GO	ACTC_BIOOB	Actin, cytoplasmic	0.08	-	cyt	0	Cytoplasm				376
Q964E0 UniProt NPD GO	ACTC_BIOTE	Actin, cytoplasmic	0.08	-	cyt	0	Cytoplasm				376
P10993 UniProt NPD GO	ACT2_TETPY	Actin, cytoplasmic (Actin, micronuclear)	0.08	-	cyt	0	Cytoplasm				376
P48975 UniProt NPD GO	ACTB_CRIGR	Actin, cytoplasmic 1 (Beta-actin)	0.08	-	cyt	0	Cytoplasm				375
P53464 UniProt NPD GO	ACTM_HELTB	Actin, cytoskeletal (M)	0.08	-	cyt	0	Cytoplasm. Cytoskeleton				376
P53473 UniProt NPD GO	ACTB_STRPU	Actin, cytoskeletal IB	0.08	-	cyt	0	Cytoplasm. Cytoskeleton				376
Q5E9B5 UniProt NPD GO	ACTH_BOVIN	Actin, gamma-enteric smooth muscle (Smooth muscle gamma actin) (Gamma-2-actin)	0.08	-	cyt	0	Cytoplasm (By similarity)				376
P63270 UniProt NPD GO	ACTH_CHICK	Actin, gamma-enteric smooth muscle (Smooth muscle gamma actin) (Gamma-2-actin) (Alpha-actin-3)	0.08	-	cyt	0	Cytoplasm				376
P63267 UniProt NPD GO	ACTH_HUMAN	Actin, gamma-enteric smooth muscle (Smooth muscle gamma actin) (Gamma-2-actin) (Alpha-actin-3)	0.08	-	cyt	0	Cytoplasm		102545		376
P63268 UniProt NPD GO	ACTH_MOUSE	Actin, gamma-enteric smooth muscle (Smooth muscle gamma actin) (Gamma-2-actin) (Alpha-actin-3)	0.08	-	cyt	0	Cytoplasm				376
P63269 UniProt NPD GO	ACTH_RAT	Actin, gamma-enteric smooth muscle (Smooth muscle gamma actin) (Gamma-2-actin) (Alpha-actin-3)	0.08	-	cyt	0	Cytoplasm				376
P02574 UniProt NPD GO	ACT4_DROME	Actin, larval muscle (Actin-79B)	0.08	-	cyt	0	Cytoplasm				376
P17304 UniProt NPD GO	ACTM_APLCA	Actin, muscle	0.08	-	cyt	0	Cytoplasm				376
Q93132 UniProt NPD GO	ACTM_BRAFL	Actin, muscle	0.08	-	cyt	0	Cytoplasm				378
Q93130 UniProt NPD GO	ACTM_BRABE	Actin, muscle (BbMA1)	0.08	-	cyt	0	Cytoplasm				379
P07836 UniProt NPD GO	ACT1_BOMMO	Actin, muscle A1	0.08	-	cyt	0	Cytoplasm				376
P02582 UniProt NPD GO	ACT1_MAIZE	Actin-1	0.08	-	cyt	0	Cytoplasm				375
P41112 UniProt NPD GO	ACT1_PODCA	Actin-1/2	0.08	-	cyt	0	Cytoplasm				376
Q4YU79 UniProt NPD GO	ACT2_PLABA	Actin-2 (Actin II)	0.08	-	cyt	0	Cytoplasm				376
P45887 UniProt NPD GO	ACT5_BACDO	Actin-5, muscle-specific	0.08	-	cyt	0	Cytoplasm				376
Q9ZNT3 UniProt NPD GO	ADF5_ARATH	Actin-depolymerizing factor 5 (ADF-5) (AtADF5)	0.08	-	cyt	0					143
P45891 UniProt NPD GO	ACTY_DROME	Actin-like protein 53D	0.08	-	cyt	0					376
Q9I8X2 UniProt NPD GO	VSP1_AGKAC	Acutobin precursor (EC 3.4.21.-) (Acuthrombin) (Acutase)	0.08	-	exc	0	Secreted protein				260
P02902 UniProt NPD GO	ACP1_HORVU	Acyl carrier protein 1, chloroplast precursor (Acyl carrier protein I) (ACP I)	0.08	-	mit	0	Plastid; chloroplast				149
Q750X7 UniProt NPD GO	APTH1_ASHGO	Acyl-protein thioesterase 1 (EC 3.1.2.-)	0.08	-	mit	0	Cytoplasm (By similarity)				235
P56544 UniProt NPD GO	ACYP1_DROME	Acylphosphatase-1 (EC 3.6.1.7) (Acylphosphate phosphohydrolase 1) (AcPDro)	0.08	-	nuc	0	Cytoplasm (Potential)				119
Q8NC96 UniProt NPD GO	NECP1_HUMAN	Adaptin ear-binding coat-associated protein 1 (NECAP-1)	0.08	-	nuc	0	Membrane-associated; with clathrin-coated vesicles. Colocalizes with AP-2 at the plasma membrane (By ...				275
P07741 UniProt NPD GO	APT_HUMAN	Adenine phosphoribosyltransferase (EC 2.4.2.7) (APRT)	0.08	-	cyt	0	Cytoplasm	cytoplasm [TAS]	102600	1ZN9	179
Q5ZKP6 UniProt NPD GO	ADA_CHICK	Adenosine deaminase (EC 3.5.4.4) (Adenosine aminohydrolase)	0.08	-	cyt	0					357
Q27580 UniProt NPD GO	SAHH_DROME	Adenosylhomocysteinase (EC 3.3.1.1) (S-adenosyl-L-homocysteine hydrolase) (AdoHcyase)	0.08	-	cyt	0					432
Q9SP37 UniProt NPD GO	SAHH_LUPLU	Adenosylhomocysteinase (EC 3.3.1.1) (S-adenosyl-L-homocysteine hydrolase) (AdoHcyase)	0.08	-	cyt	0					485
O24578 UniProt NPD GO	PURA_MAIZE	Adenylosuccinate synthetase, chloroplast precursor (EC 6.3.4.4) (IMP--aspartate ligase) (AdSS) (AMPS ...	0.08	-	mit	0	Plastid; chloroplast				484

You are viewing entries 67501 to 67550 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.