SBC logo 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):


( 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:

Only show proteins where the PSORT II predicted location
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)    
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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
P62285
UniProt
NPD  GO
ASPM_BOVIN Abnormal spindle-like microcephaly-associated protein homolog (Fragment) 0.92 - nuc 0 Cytoplasm (By similarity). Nucleus (By similarity). The nuclear-cytoplasmic distribution could be re ... 3371
Q01631
UniProt
NPD  GO
CYAA_NEUCR Adenylate cyclase (EC 4.6.1.1) (ATP pyrophosphate-lyase) (Adenylyl cyclase) 0.92 - nuc 0 2300
P49606
UniProt
NPD  GO
CYAA_USTMA Adenylate cyclase (EC 4.6.1.1) (ATP pyrophosphate-lyase) (Adenylyl cyclase) 0.92 - nuc 0 2493
Q4P6G5
UniProt
NPD  GO
SPB1_USTMA AdoMet-dependent rRNA methyltransferase SPB1 (EC 2.1.1.-) (2'-O-ribose RNA methyltransferase) (S-ade ... 0.92 - nuc 0 Nucleus; nucleolus (By similarity) 921
Q4WVH3
UniProt
NPD  GO
SPB1_ASPFU AdoMet-dependent rRNA methyltransferase spb1 (EC 2.1.1.-) (2'-O-ribose RNA methyltransferase) (S-ade ... 0.92 + nuc 0 Nucleus; nucleolus (By similarity) 795
Q61329
UniProt
NPD  GO
ATBF1_MOUSE Alpha-fetoprotein enhancer-binding protein (AT motif-binding factor) (AT-binding transcription facto ... 0.92 - nuc 0 Nucleus mitochondrion [IDA]
nucleus [NAS]
3726
Q8N6M6
UniProt
NPD  GO
AMPO_HUMAN Aminopeptidase O (EC 3.4.11.-) (AP-O) 0.92 + cyt 0 Cytoplasm (Potential) 819
Q811D2
UniProt
NPD  GO
ANR26_MOUSE Ankyrin repeat domain-containing protein 26 0.92 - nuc 0 1581
P79832
UniProt
NPD  GO
ARNT_ONCMY Aryl hydrocarbon receptor nuclear translocator (rtARNT) 0.92 + nuc 0 Nucleus 723
P54254
UniProt
NPD  GO
ATX1_MOUSE Ataxin-1 (Spinocerebellar ataxia type 1 protein homolog) 0.92 + nuc 0 Cytoplasm. Nucleus nuclear inclusion body [IDA] 792
Q51UJ9
UniProt
NPD  GO
ATG11_MAGGR Autophagy-related protein 11 0.92 - nuc 0 Vacuole; vacuolar membrane; peripheral membrane protein (By similarity). Vacuolar and perivacuolar p ... 1407
P12957
UniProt
NPD  GO
CALD1_CHICK Caldesmon (CDM) 0.92 + nuc 0 On thin filaments in smooth muscle and on stress fibers in fibroblasts (nonmuscle) (By similarity) 771
O94983
UniProt
NPD  GO
CMTA2_HUMAN Calmodulin-binding transcription activator 2 0.92 + nuc 0 Nucleus (Probable) 1202
Q80Y50
UniProt
NPD  GO
CMTA2_MOUSE Calmodulin-binding transcription activator 2 0.92 + nuc 0 Nucleus (Probable) 1208
P56369
UniProt
NPD  GO
FTSH_CHLVU Cell division protein ftsH homolog 0.92 - nuc 0 Plastid; chloroplast; chloroplast membrane; multi-pass membrane protein (Potential) 1720
P49454
UniProt
NPD  GO
CENPF_HUMAN Centromere protein F (Kinetochore protein CENP-F) (Mitosin) (AH antigen) 0.92 + nuc 0 Nucleus; nucleoplasm; nuclear matrix. But not in the nucleolus, reorganization to the kinetochore/ce ... cytoplasm [IDA]
kinetochore [IDA]
nuclear envelope [IDA]
nuclear matrix [IDA]
nucleus [IDA]
outer kinetochore of condensed chromosome [IDA]
spindle pole [IDA]
600236 3210
Q9BV73
UniProt
NPD  GO
CP250_HUMAN Centrosome-associated protein CEP250 (Centrosomal protein 2) (Centrosomal Nek2-associated protein 1) ... 0.92 - nuc 0 Cytoplasm; perinuclear region. Centrosome. Component of the core centrosome. In interphase cells, it ... centrosome [IDA] 609689 2442
Q9DB85
UniProt
NPD  GO
HUCE1_MOUSE Cerebral protein 1 homolog 0.92 + nuc 0 Nucleus; nucleolus (By similarity) 457
P32641
UniProt
NPD  GO
RAD24_YEAST Checkpoint protein RAD24 0.92 - mit 0 Nucleus (Potential) DNA replication factor C complex [TAS]
nucleus [IPI]
659
P50531
UniProt
NPD  GO
RAD17_SCHPO Checkpoint protein rad17 0.92 + nuc 0 Nucleus Rad17 RFC-like complex [TAS] 606
O00409
UniProt
NPD  GO
FOXN3_HUMAN Checkpoint suppressor 1 (Forkhead box protein N3) 0.92 + nuc 0 Nucleus (Probable) nucleus [IC] 602628 490
Q499D0
UniProt
NPD  GO
FOXN3_MOUSE Checkpoint suppressor 1 (Forkhead box protein N3) 0.92 + nuc 0 Nucleus (Probable) nucleus [RCA] 457
Q4P209
UniProt
NPD  GO
VID21_USTMA Chromatin modification-related protein VID21 0.92 - nuc 0 Nucleus (Probable) 1654
Q757W2
UniProt
NPD  GO
YNG2_ASHGO Chromatin modification-related protein YNG2 (ING1 homolog 2) 0.92 - nuc 0 Nucleus (By similarity) 285
Q8TDI0
UniProt
NPD  GO
CHD5_HUMAN Chromodomain helicase-DNA-binding protein 5 (EC 3.6.1.-) (ATP-dependent helicase CHD5) (CHD-5) 0.92 + nuc 0 Nucleus (By similarity) 1954
O61735
UniProt
NPD  GO
CLOCK_DROME Circadian locomoter output cycles protein kaput (dCLOCK) (dPAS1) 0.92 + nuc 0 Nucleus (Potential) nucleus [NAS] 1027
O18806
UniProt
NPD  GO
FA8_CANFA Coagulation factor VIII precursor (Procoagulant component) 0.92 - nuc 0 Secreted protein; extracellular space (By similarity) 2343
Q9D3E6
UniProt
NPD  GO
STAG1_MOUSE Cohesin subunit SA-1 (Stromal antigen 1) (SCC3 homolog 1) 0.92 - nuc 0 Nucleus (By similarity). Associates with chromatin. Before prophase it is scattered along chromosome ... 1258
O35638
UniProt
NPD  GO
STAG2_MOUSE Cohesin subunit SA-2 (Stromal antigen 2) (SCC3 homolog 2) 0.92 - nuc 0 Nucleus. Associates with chromatin. Before prophase it is scattered along chromosome arms. During pr ... 1231
Q5PR68
UniProt
NPD  GO
CCD46_MOUSE Coiled coil domain-containing protein 46 0.92 - nuc 0 954
Q8K2I2
UniProt
NPD  GO
CCHCR_MOUSE Coiled-coil alpha-helical rod protein 1 (Alpha helical coiled-coil rod protein) 0.92 - nuc 0 Cytoplasm (By similarity). Nucleus (By similarity) cytoplasm [IDA] 770
Q8CDN8
UniProt
NPD  GO
CCD38_MOUSE Coiled-coil domain-containing protein 38 0.92 - nuc 0 563
Q9UFE4
UniProt
NPD  GO
CCD39_HUMAN Coiled-coil domain-containing protein 39 0.92 - nuc 0 755
Q9Y592
UniProt
NPD  GO
CCD41_HUMAN Coiled-coil domain-containing protein 41 (NY-REN-58 antigen) 0.92 - nuc 0 693
Q568R1
UniProt
NPD  GO
CCD55_BRARE Coiled-coil domain-containing protein 55 0.92 - nuc 0 516
Q04149
UniProt
NPD  GO
MUS81_YEAST Crossover junction endonuclease MUS81 (EC 3.1.22.-) (MMS and UV sensitive protein 81) 0.92 - nuc 0 Nucleus nucleus [IMP] 632
O43889
UniProt
NPD  GO
CREB3_HUMAN Cyclic AMP-responsive element-binding protein 3 (Luman protein) (Transcription factor LZIP-alpha) 0.92 + nuc 0 Endoplasmic reticulum; endoplasmic reticulum membrane; single-pass type II membrane protein. Process ... 606443 395
Q6GN15
UniProt
NPD  GO
CCNL1_XENLA Cyclin-L1 0.92 + nuc 0 Nucleus (By similarity) 496
P35662
UniProt
NPD  GO
CYLC1_BOVIN Cylicin-1 (Cylicin I) (Multiple-band polypeptide I) 0.92 + nuc 0 Calyx. Sperm head cytoskeletal structure 667
Q6E3D4
UniProt
NPD  GO
CPB3_CAERE Cytoplasmic polyadenylation element-binding protein 3 0.92 - nuc 0 766
O75140
UniProt
NPD  GO
DEPD5_HUMAN DEP domain-containing protein 5 0.92 - nuc 0 1572
P61460
UniProt
NPD  GO
DEPD5_MOUSE DEP domain-containing protein 5 0.92 - nuc 0 1527
O74502
UniProt
NPD  GO
MSH6_SCHPO DNA mismatch repair protein msh6 0.92 - nuc 0 Nucleus (Probable) 1254
O00874
UniProt
NPD  GO
DPOLA_LEIDO DNA polymerase alpha catalytic subunit (EC 2.7.7.7) 0.92 + mit 0 Nucleus 1339
Q27152
UniProt
NPD  GO
DPOLA_OXYTR DNA polymerase alpha catalytic subunit (EC 2.7.7.7) 0.92 + nuc 0 Nucleus 1513
Q6FNY7
UniProt
NPD  GO
DPOE_CANGA DNA polymerase epsilon, catalytic subunit A (EC 2.7.7.7) (DNA polymerase II subunit A) 0.92 - nuc 0 Nucleus (By similarity) 2217
Q6CUS7
UniProt
NPD  GO
DPOE_KLULA DNA polymerase epsilon, catalytic subunit A (EC 2.7.7.7) (DNA polymerase II subunit A) 0.92 + nuc 0 Nucleus (By similarity) 2185
Q9UBT6
UniProt
NPD  GO
POLK_HUMAN DNA polymerase kappa (EC 2.7.7.7) (DINB protein) (DINP) 0.92 - nuc 0 Nucleus. Detected throughout the nucleus and at replication foci 605650 1T94 870
P38121
UniProt
NPD  GO
DPOA2_YEAST DNA polymerase subunit alpha B (DNA polymerase I subunit B) (DNA polymerase alpha:primase complex p8 ... 0.92 + nuc 0 Nucleus alpha DNA polymerase:primase complex [TAS]
nuclear envelope [IDA]
nucleus [IDA]
705
Q4IJ84
UniProt
NPD  GO
RAD5_GIBZE DNA repair protein RAD5 (EC 3.6.1.-) 0.92 - nuc 0 Cytoplasm (By similarity). Nucleus (By similarity) 1154

You are viewing entries 3151 to 3200 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.