SBC logo Authors: Bob MacCallum, Andrea Krings, Markus Brameier and Amine Heddad, Stockholm Bioinformatics Center, Stockholm University, Sweden.

NucPred - multiple sequences

Fetching Q9UIE9 from www.uniprot.org...
Fetching Q9CT49 from www.uniprot.org...
Fetching Q9V3Y5 from www.uniprot.org...
Fetching Q8I4F3 from www.uniprot.org...
Got 4 sequences with 3178 residues
Calculating NucPred scores 0.96 0.95 1.00 0.99
Running ClustalW (please be patient)

NucPred coloured multiple alignment (warning - the alignment may be inaccurate in places because we have aligned full-length sequences which may have different domain organisation)

sp|P49756|RBM25_HUMAN  0.96 MSFPPHLNRPPMGIPALPPGIPPPQFPGFPPPVPPGTPMIPVPMSIMAPAPTVLVPTVSM 
sp|B2RY56|RBM25_MOUSE  0.95 MSFPPHLNRPPMGIPALPPGIPPPQFPGFPPPVPPGTPMIPVPMSIMAPAPTVLVPTVSM 
tr|Q9V3Y5|Q9V3Y5_DROME 1.00 MSYPPRAPMPPFMNTAIPP---------------------PHIMQNMAKPPRSFRNSATI 
tr|Q8I4F3|Q8I4F3_CAEEL 0.99 ------------------------------------------------------------ 
                       cons msfpphlnrppmgipalpp                     pvpmsimapaptvlvptvsm 

sp|P49756|RBM25_HUMAN  0.96 VG-KHLGARKDHPGLKAKENDENCGPTTTVFVGNISEKASDMLIRQLLAKCGLVLSWKRV 
sp|B2RY56|RBM25_MOUSE  0.95 VG-KHLGARKDHPGLKLKENDENCGPTTTVFVGNISEKASDMLIRQLLAKCGLVLSWKRV 
tr|Q9V3Y5|Q9V3Y5_DROME 1.00 SSQPTVYQRPPEPQPQFR------GPIITVFVGNISERVPEALLKRILNACGVVINWKRV 
tr|Q8I4F3|Q8I4F3_CAEEL 0.99 ------------------------------------------------------------ 
                       cons vg khlgarkdhpglk k      gptttvfvgnisekasdmlirqllakcglvlswkrv 

sp|P49756|RBM25_HUMAN  0.96 QGASGKLQAFGFCEYKEPESTLRALRLLHDLQIGEKKLLVKVDAKTKAQLDEWKAKKKAS 
sp|B2RY56|RBM25_MOUSE  0.95 QGASGKLQAFGFCEYKEPESTLRALRLLHDLQIGEKKLLVKVDAKTKAQLDEWKAKKKAN 
tr|Q9V3Y5|Q9V3Y5_DROME 1.00 S-------TFGFCEFDGPIAAMRAVRLLSEMEIDGKKLVAKVDAKNKVLIEDYKEQECKN 
tr|Q8I4F3|Q8I4F3_CAEEL 0.99 ------------------------------------------------------------ 
                       cons q       afgfceykepestlralrllhdlqigekkllvkvdaktkaqldewkakkkan 

sp|P49756|RBM25_HUMAN  0.96 NGNARPETVTNDDEEALD------EETKRRDQMIKGAIEVLIREYSSELNAPSQESDSHP 
sp|B2RY56|RBM25_MOUSE  0.95 -GNARPETVTNDDEEALD------EETKRRDQMIKGAIEVLIREYSSELNAPSQESDSHP 
tr|Q9V3Y5|Q9V3Y5_DROME 1.00 GDRSNPVDEKTEDEFAIAQMHEFLEEHKHEFEGFDSSSRADLYGSANRNKKTRREEDIKM 
tr|Q8I4F3|Q8I4F3_CAEEL 0.99 ------------------------------------------------------------ 
                       cons  gnarpetvtnddeeald      eetkrrdqmikgaievlireysselnapsqesdshp 

sp|P49756|RBM25_HUMAN  0.96 RKKKKEKKEDIFRRFPVAPLIPYPLITKEDINAIEMEEDK-RDLISREISKFRDTHKKLE 
sp|B2RY56|RBM25_MOUSE  0.95 RKKKKEKKEDIFRRFPVAPLIPYPLITKEDINAIEMEEDK-RDLISREISKFRDTHKKLE 
tr|Q9V3Y5|Q9V3Y5_DROME 1.00 KVLSENTLEEEKRNLISSEIGKFRMRAEEDEHRKELEKEKEKEKLAASKEKERKKQREME 
tr|Q8I4F3|Q8I4F3_CAEEL 0.99 ------------------------------------------------------------ 
                       cons rkkkkekkedifrrfpvaplipyplitkedinaiemeedk rdlisreiskfrdthkkle 

sp|P49756|RBM25_HUMAN  0.96 -----EEKGKKEKERQEIE----------------KERRERERERERERERRERERERER 
sp|B2RY56|RBM25_MOUSE  0.95 -----EEKGKKEKERQEIE----------------KERRERERERERERERRERERERER 
tr|Q9V3Y5|Q9V3Y5_DROME 1.00 RMSSTSKSGSSSTAAASSSSATATSSTPAADGADMSDKTDKESVAVVIKETVKESKESAS 
tr|Q8I4F3|Q8I4F3_CAEEL 0.99 ----------------------------------------------MYNQPRIGTRYDEH 
                       cons      eekgkkekerqeie                kerrererererererrerererer 

sp|P49756|RBM25_HUMAN  0.96 EREREKEKERERERERDRDRDRTKERDRDRDRERDRDRDRERSSDRNKDRSRSREKSRDR 
sp|B2RY56|RBM25_MOUSE  0.95 EREREKEKERERERERDRDRDRTKERDRDR--ERDRDRDRERSSDRNKDRSRSREKSRDR 
tr|Q9V3Y5|Q9V3Y5_DROME 1.00 STGRKESSSAAIEITQKERRSDSKETRRRRSKSRSKDRERERERELRELRDKERERERDR 
tr|Q8I4F3|Q8I4F3_CAEEL 0.99 KRNR----N---------RRSRSRTRSRERTSRRSRSKESPRSKRSRRSRSSSNSSSESD 
                       cons ereRekekererererdr R r kerdRdR  eR rdr reRssdr kdRsrsreksrdr 

sp|P49756|RBM25_HUMAN  0.96 ERERERERERERERERERERERERERERERERER-----EKDKKRDREEDEEDAYERRKL 
sp|B2RY56|RBM25_MOUSE  0.95 ERERERERERERERERERERERERERERERERE-------KDKKRDREEDEEDAYERRKL 
tr|Q9V3Y5|Q9V3Y5_DROME 1.00 ERERERERNEMRERERNEMREREREREREREREEKLLKPVRDTWREKE-MEDELRDRKKA 
tr|Q8I4F3|Q8I4F3_CAEEL 0.99 SSSSRSSSYSSRSRSRTPQRSRTSKRRRSNSHAS--------------EDSDDAREKRAF 
                       cons ererererereReReRereReRereReRerere       kdkkrdreede da errkl 

sp|P49756|RBM25_HUMAN  0.96 ERKLREKEAAYQERLKNWEIRERKKTREYEKEAEREEERRREMAKEAKRLKEFLEDYDDD 
sp|B2RY56|RBM25_MOUSE  0.95 ERKLREKEAAYQERLKNWEIRERKKTREYEKEAEREEERRREMAKEAKRLKEFLEDYDDD 
tr|Q9V3Y5|Q9V3Y5_DROME 1.00 EKKAREKEIAYQTRLTDWEVREKRKAKENEKYRLKELLRQEERETDAKRLKEFVEDYDDE 
tr|Q8I4F3|Q8I4F3_CAEEL 0.99 KQMMLDKKQAYLARLKRWESRERQMSKRYEREERKEKDRKKTLQKEGKRLKLFLEDYDDE 
                       cons erklreKeaAYqeRLknWEiRErkkt eyEkeae EeeRrremakeaKRLKeFlEDYDD  

sp|P49756|RBM25_HUMAN  0.96 RDDPKYYRGSALQKRLRDREKEMEADERDRKREKEELEEIRQRLLAEGHPDPDAELQRME 
sp|B2RY56|RBM25_MOUSE  0.95 RDDPKYYRGSALQKRLRDREKEMEADERDRKREKEELEEIRQRLLAEGHPDPDAELQRME 
tr|Q9V3Y5|Q9V3Y5_DROME 1.00 RDDSLYYRGRELQQRLAERVREADADSKDREKEAEELAELKSKFFSGEYENPSLEFEKAR 
tr|Q8I4F3|Q8I4F3_CAEEL 0.99 KDDPKYYTSSQFFQRKRDYEREREADQKDRMQEQQEIEELKRQIMEEAANDESINIEEEA 
                       cons rDDpkYYrgsalq Rlrdre EmeADe DRkrEkeEleE  qrllaeghpdp ael rme 

sp|P49756|RBM25_HUMAN  0.96 QEAERRRQP----QIKQEPESEEEEEEKQEKEEK-----REEPMEEEEEPEQKPCLKPTL 
sp|B2RY56|RBM25_MOUSE  0.95 QEAERRRQP----QIKQEPESEEEEEEKQEKEEK-----REEPVEEEEEPEQKPCLKPTL 
tr|Q9V3Y5|Q9V3Y5_DROME 1.00 LEIEKLYEPRILINVNQEPPAAATSSVHQRKQAASAPGEDDEGQKQRQKSQQLDSYDPDM 
tr|Q8I4F3|Q8I4F3_CAEEL 0.99 RKRHKLKEEE---AMRKMRADSGSPNPHQPLGQSAN---GEKSSSEEESDSEKTDVKKEI 
                       cons qeae  r p    qikqepeseeeeee Qekeek     reep eeeeepeqkpclkptl 

sp|P49756|RBM25_HUMAN  0.96 R------PISS------APSVSSASGNATPNTPGDESPCGIIIPHENSPDQQQPEEHRPK 
sp|B2RY56|RBM25_MOUSE  0.95 R------PISS------APSVSSASGNATPNTPGDESPCGIIIPHENSPDQQQPEEHRPK 
tr|Q9V3Y5|Q9V3Y5_DROME 1.00 AGTNDDDSISNDDRASMADTASNASGVYAKNNNNDQSLSNSLSRHNSESRDSLAQIHTPT 
tr|Q8I4F3|Q8I4F3_CAEEL 0.99 K-----DEIKE------EPIDVDISEHVDPNTGSSGTNGNFGWKAIGDDSSLNTKINRPI 
                       cons r      pIss      apsvssaSgnatpNtpgdespc iiiphenspdqqqpe hrPk 

sp|P49756|RBM25_HUMAN  0.96 IGLSLK---------LGASNSPGQP--------NSVKRKKLPVDSVFNKFEDEDSDDVPR 
sp|B2RY56|RBM25_MOUSE  0.95 IGLSLK---------LGASNSPGQP--------NSVKRKKLPVDSVFNKFEDEDSDDVPR 
tr|Q9V3Y5|Q9V3Y5_DROME 1.00 QSAILNDQESGHDAILPSATPPMTMPLISLTLGNNLKKKKIEATGVFVNDDDNDENINPK 
tr|Q8I4F3|Q8I4F3_CAEEL 0.99 ANGNQN---------QPQIKKEASP-----------IPIAQRLSGVFGN--DDDEDDVHS 
                       cons iglsl          l asnspgqp        nsvkrkklpvd VFn feDeD ddvpr 

sp|P49756|RBM25_HUMAN  0.96 KRKLVPLDYGE------------------------------------------------- 
sp|B2RY56|RBM25_MOUSE  0.95 KRKLVPLDYGE------------------------------------------------- 
tr|Q9V3Y5|Q9V3Y5_DROME 1.00 KRKLVPLDYDDNISNTTPSNHAASSGSGAANNSSSSNNNNSSSADRQSSAVSAATAAAAA 
tr|Q8I4F3|Q8I4F3_CAEEL 0.99 KKKLKPFEITR------------------------------------------------- 
                       cons KrKLvPldyge                                                  

sp|P49756|RBM25_HUMAN  0.96 ---------------------DDKNATKGTVN---------------------------- 
sp|B2RY56|RBM25_MOUSE  0.95 ---------------------DDKNATKGTVN---------------------------- 
tr|Q9V3Y5|Q9V3Y5_DROME 1.00 VSQKIAQAFGGGSSGSGSGSGSGSNASGGKNNGGGSSSSSNNKHNSNSKHGKNEAAASAG 
tr|Q8I4F3|Q8I4F3_CAEEL 0.99 -----------------------E-ERMQVMS---------------------------- 
                       cons                      ddknatkgtvn                             

sp|P49756|RBM25_HUMAN  0.96 -------------------TEEKRKHIKSLIEKIPTAKPELFAYPLDWSIVDSILMERRI 
sp|B2RY56|RBM25_MOUSE  0.95 -------------------TEEKRKHIKSLIEKIPTAKPELFAYPLDWSIVDSILMERRI 
tr|Q9V3Y5|Q9V3Y5_DROME 1.00 SSADAAAANIKKDENGAKVYDEKRRHIKSIIDRIPTQKEELFNYKLDRNEIDSGLMERKI 
tr|Q8I4F3|Q8I4F3_CAEEL 0.99 -------------------AEEKRELTKQIIKTIPATKDELFVHRIEWDQLDGKWMNDRI 
                       cons                    teEKRkhiKs IekIPtaKpELFaypldwsivDsilMerrI 

sp|P49756|RBM25_HUMAN  0.96 RPWINKKIIEYIGEEEATLVDFVCSKVMAHSSPQSILDDVAMVLDEEAEVFIVKMWRLLI 
sp|B2RY56|RBM25_MOUSE  0.95 RPWINKKIIEYIGEEEATLVDFVCSKVMAHSSPQSILDDVAMVLDEEAEVFIVKMWRLLI 
tr|Q9V3Y5|Q9V3Y5_DROME 1.00 RPWINKKIIEYIGEPEPTLVDFICSKVLAGSPPQSILDDVQMVLDEEAEVFVVKMWRLLI 
tr|Q8I4F3|Q8I4F3_CAEEL 0.99 RPWVAKKVTQFLGEEDKSFCDFICDQIEKQATPQEILKDVAVIIDEDAEQFVIKMWRLLI 
                       cons RPWinKKiieyiGEeeatlvDF CskvmahssPQsILdDVamvlDEeAEvF vKMWRLLI 

sp|P49756|RBM25_HUMAN  0.96 YETEAKKIGLVK- 
sp|B2RY56|RBM25_MOUSE  0.95 YETEAKKIGLVK- 
tr|Q9V3Y5|Q9V3Y5_DROME 1.00 YELDAKKSGLAGK 
tr|Q8I4F3|Q8I4F3_CAEEL 0.99 YEGQARRLGIT-- 
                       cons YEteAkkiGlvk  

The consensus ('cons') is calculated as follows: the most frequent character in each column is shown in lowercase (unless it is a gap character); uppercase letters represent a column containing just one amino acid and no gaps.

The tags HS, MM, DM... correspond to species names Homo sapiens, Mus musculus, Dropophila melanogaster...

Positively and negatively influencing subsequences are coloured according to the following scale:

(non-nuclear) negative ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| positive (nuclear)



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.