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SLiMSuite SLiMProb Server

# Output for SLiMProb V2.2.5: Tue Dec  8 22:35:32 2015
# 0 warnings; 0 errors.
# JobID: 15120800031

Your SLiMProb job has finished running and outputs have been parsed. Click on tabs to see server output. (Mouseover for description.)

The outfmt tab contains more information on the outputs. Click here for SLiMProb help/documentation.

Content for individual tabs can be returned using &rest=X, where X is the tab name (e.g. &rest=log). Full output can be returned as text using &rest=full and parsed using SLiMParser.

JobID 15120800031 (slimprob) Finished.
IP:129.94.133.155
No queue.
slimprob&uniprotid=E1A_ADE02&motifs=LxCxE,PxDLS
Run Started: 2015-12-08 22:35:32; PID=38726
Run finished: 2015-12-08 22:36:36

Run with &rest=help for general options. Run with &rest=full to get full server output.
Individual outputs can be identified/parsed:
###~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~###
# OUTFMT:
...

Outputs available:
main = main results file ([extras=-1]{cmd:extras})
motifs = Input motifs for searching ([extras=-1]{cmd:extras})
seqin = Input file ([extras=-1]{cmd:extras})
occ = occurrence file ([extras=0]{cmd:extras})
upc = UPC file ([extras=0]{cmd:extras})
slimdb = Fasta file used for UPC generation etc. ([extras=0]{cmd:extras})
masked = masked.fas ([extras=1]{cmd:extras})
mapping = mapping.fas file ([extras=2]{cmd:extras})
motifaln = motif alignments ([extras=2]{cmd:extras})
maskaln = masked motif alignments ([extras=2]{cmd:extras})
dismatrix = *.dis.tdt file ([extras=3]{cmd:extras})

&rest=OUTFMT can then be used to retrieve individual parts of the output in future.
Dataset RunID Masking RunTime SeqNum UPNum AANum Motif Pattern IC N_Occ E_Occ p_Occ pUnd_Occ N_Seq E_Seq p_Seq pUnd_Seq N_UPC E_UPC p_UPC pUnd_UPC
slimprob 15120800031 FreqNoMask 00:00:00 1 1 289 LxCxE L.C.E 3.0 1 0.11 0.10 0.99 1 0.10 0.10 1.00 1 0.10 0.10 1.00
slimprob 15120800031 FreqNoMask 00:00:00 1 1 289 PxDLS P.DLS 4.0 1 0.017 0.017 1.00 1 0.017 0.017 1.00 1 0.017 0.017 1.00
Dataset RunID Masking Motif Seq Start_Pos End_Pos Prot_Len Pattern Match Variant MisMatch Desc UPC
slimprob 15120800031 FreqNoMask LxCxE E1A_ADE02__P03254 122 126 289 L.C.E LTCHE L.C.E 0 RecName: Full=Early E1A protein {ECO:0000305}; AltName: Full=Early E1A 32 kDa protein; 1
slimprob 15120800031 FreqNoMask PxDLS E1A_ADE02__P03254 279 283 289 P.DLS PLDLS P.DLS 0 RecName: Full=Early E1A protein {ECO:0000305}; AltName: Full=Early E1A 32 kDa protein; 1
#slimprob# 1 Seq; 1 UPC; 1.000 MST; Single sequence
UP	N	MST	Seqs
1	1	1.000	E1A_ADE02__P03254
LxCxE
PxDLS

ID   E1A_ADE02               Reviewed;         289 AA.
AC   P03254; P24934; Q67788;
DT   21-JUL-1986, integrated into UniProtKB/Swiss-Prot.
DT   21-JUL-1986, sequence version 1.
DT   11-NOV-2015, entry version 96.
DE   RecName: Full=Early E1A protein {ECO:0000305};
DE   AltName: Full=Early E1A 32 kDa protein;
OS   Human adenovirus C serotype 2 (HAdV-2) (Human adenovirus 2).
OC   Viruses; dsDNA viruses, no RNA stage; Adenoviridae; Mastadenovirus.
OX   NCBI_TaxID=10515;
OH   NCBI_TaxID=9606; Homo sapiens (Human).
RN   [1]
RP   NUCLEOTIDE SEQUENCE [GENOMIC DNA] (ISOFORMS EARLY E1A 32 KDA PROTEIN
RP   AND EARLY E1A 26 KDA PROTEIN).
RX   PubMed=551290; DOI=10.1038/281694a0;
RA   Perricaudet M., Akusjaervi G., Virtanen A., Pettersson U.;
RT   "Structure of two spliced mRNAs from the transforming region of human
RT   subgroup C adenoviruses.";
RL   Nature 281:694-696(1979).
RN   [2]
RP   NUCLEOTIDE SEQUENCE [GENOMIC DNA] (ISOFORMS EARLY E1A 32 KDA PROTEIN;
RP   EARLY E1A 26 KDA PROTEIN AND EARLY E1A 6 KDA PROTEIN).
RX   PubMed=7142161;
RA   Gingeras T.R., Sciaky D., Gelinas R.E., Bing-Dong J., Yen C.E.,
RA   Kelly M.M., Bullock P.A., Parsons B.L., O'Neill K.E., Roberts R.J.;
RT   "Nucleotide sequences from the adenovirus-2 genome.";
RL   J. Biol. Chem. 257:13475-13491(1982).
RN   [3]
RP   INTERACTION WITH HOST ATF7, AND MUTAGENESIS OF CYS-157; THR-178 AND
RP   SER-185.
RX   PubMed=8417352;
RA   Chatton B., Bocco J.L., Gaire M., Hauss C., Reimund B., Goetz J.,
RA   Kedinger C.;
RT   "Transcriptional activation by the adenovirus larger E1a product is
RT   mediated by members of the cellular transcription factor ATF family
RT   which can directly associate with E1a.";
RL   Mol. Cell. Biol. 13:561-570(1993).
CC   -!- FUNCTION: Plays a role in viral genome replication by driving
CC       entry of quiescent cells into the cell cycle. Stimulation of
CC       progression from G1 to S phase allows the virus to efficiently use
CC       the cellular DNA replicating machinery to achieve viral genome
CC       replication. E1A protein has both transforming and trans-
CC       activating activities. Induces the disassembly of the E2F1
CC       transcription factor from RB1 by direct competition for the same
CC       binding site on RB1, with subsequent transcriptional activation of
CC       E2F1-regulated S-phase genes and of the E2 region of the
CC       adenoviral genome. Release of E2F1 leads to the ARF-mediated
CC       inhibition of MDM2 and causes TP53/p53 to accumulate because it is
CC       not targeted for degradation by MDM2-mediated ubiquitination
CC       anymore. This increase in TP53, in turn, would arrest the cell
CC       proliferation and direct its death but this effect is counteracted
CC       by the viral protein E1B-55K. Inactivation of the ability of RB1
CC       to arrest the cell cycle is critical for cellular transformation,
CC       uncontrolled cellular growth and proliferation induced by viral
CC       infection. Interaction with RBX1 and CUL1 inhibits ubiquitination
CC       of the proteins targeted by SCF(FBXW7) ubiquitin ligase complex,
CC       and may be linked to unregulated host cell proliferation. The
CC       tumorigenesis-restraining activity of E1A may be related to the
CC       disruption of the host CtBP-CtIP complex through the CtBP binding
CC       motif. Interacts with host TBP protein; this interaction probably
CC       disrupts the TBP-TATA complex. {ECO:0000250|UniProtKB:P03255}.
CC   -!- SUBUNIT: Interacts with host UBE2I; this interaction interferes
CC       with polySUMOylation. Interacts with host RB1; this interaction
CC       induces the aberrant dissociation of RB1-E2F1 complex thereby
CC       disrupting the activity of RB1 and activating E2F1-regulated
CC       genes. Interacts with host ATF7; the interaction enhances ATF7-
CC       mediated viral transactivation activity which requires the zinc
CC       binding domains of both proteins. Isoform early E1A 32 kDa protein
CC       and isoform early E1A 26 kDa protein interact (via N-terminus)
CC       with CUL1 and E3 ubiquitin ligase RBX1; these interactions inhibit
CC       RBX1-CUL1-dependent elongation reaction of ubiquitin chains and
CC       attenuate ubiquitination of SCF(FBXW7) target proteins. Interacts
CC       (via PXLXP motif) with host ZMYND11/BS69 (via MYND-type zinc
CC       finger); this interaction inhibits E1A mediated transactivation.
CC       Interacts with host EP300; this interaction stimulates the
CC       acetylation of RB1 by recruiting EP300 and RB1 into a multimeric-
CC       protein complex. Interacts with host CTBP1 and CTBP2; this
CC       interaction seems to potentiate viral replication. Interacts with
CC       host DCAF7. Interacts with host DYRK1A. Interacts with host KPNA4;
CC       this interaction allows E1A import into the host nucleus.
CC       Interacts with host EP400; this interaction stabilizes MYC.
CC       {ECO:0000250|UniProtKB:P03255}.
CC   -!- SUBCELLULAR LOCATION: Host nucleus {ECO:0000250|UniProtKB:P03255}.
CC   -!- ALTERNATIVE PRODUCTS:
CC       Event=Alternative splicing; Named isoforms=3;
CC         Comment=Isoforms are derived from the E1 region of the genome.;
CC       Name=early E1A 32 kDa protein; Synonyms=289R, L-E1A;
CC         IsoId=P03254-1; Sequence=Displayed;
CC       Name=early E1A 26 kDa protein; Synonyms=243R, S-E1A;
CC         IsoId=P03254-2; Sequence=VSP_000197;
CC       Name=early E1A 6 kDa protein;
CC         IsoId=P03254-3; Sequence=VSP_028916, VSP_028917;
CC   -!- SIMILARITY: Belongs to the adenoviridae E1A protein family.
CC       {ECO:0000305}.
CC   -----------------------------------------------------------------------
CC   Copyrighted by the UniProt Consortium, see http://www.uniprot.org/terms
CC   Distributed under the Creative Commons Attribution-NoDerivs License
CC   -----------------------------------------------------------------------
DR   EMBL; J01917; AAA92197.1; -; Genomic_DNA.
DR   EMBL; J01917; AAA92198.1; -; Genomic_DNA.
DR   EMBL; J01917; AAA92199.1; -; Genomic_DNA.
DR   PIR; A03824; Q2AD2.
DR   RefSeq; AP_000161.1; AC_000007.1.
DR   DIP; DIP-570N; -.
DR   IntAct; P03254; 1.
DR   MINT; MINT-198575; -.
DR   Proteomes; UP000008167; Genome.
DR   GO; GO:0042025; C:host cell nucleus; IEA:UniProtKB-SubCell.
DR   GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR   GO; GO:0039695; P:DNA-templated viral transcription; IDA:UniProtKB.
DR   GO; GO:0039645; P:modulation by virus of host G1/S transition checkpoint; IEA:UniProtKB-KW.
DR   GO; GO:0039649; P:modulation by virus of host ubiquitin-protein ligase activity; IEA:UniProtKB-KW.
DR   GO; GO:0006355; P:regulation of transcription, DNA-templated; IEA:UniProtKB-KW.
DR   GO; GO:0039657; P:suppression by virus of host gene expression; IEA:UniProtKB-KW.
DR   GO; GO:0039563; P:suppression by virus of host STAT1 activity; IEA:UniProtKB-KW.
DR   GO; GO:0039502; P:suppression by virus of host type I interferon-mediated signaling pathway; IEA:UniProtKB-KW.
DR   InterPro; IPR014410; Aden_E1A.
DR   Pfam; PF02703; Adeno_E1A; 1.
PE   1: Evidence at protein level;
KW   Activator; Alternative splicing; Complete proteome; Early protein;
KW   Eukaryotic host gene expression shutoff by virus;
KW   Eukaryotic host transcription shutoff by virus;
KW   G1/S host cell cycle checkpoint dysregulation by virus;
KW   Host gene expression shutoff by virus; Host nucleus;
KW   Host-virus interaction;
KW   Inhibition of eukaryotic host transcription initiation by virus;
KW   Inhibition of host innate immune response by virus;
KW   Inhibition of host interferon signaling pathway by virus;
KW   Inhibition of host STAT1 by virus; Metal-binding;
KW   Modulation of host cell cycle by virus;
KW   Modulation of host E3 ubiquitin ligases by virus;
KW   Modulation of host ubiquitin pathway by virus; Oncogene;
KW   Phosphoprotein; Reference proteome; Transcription;
KW   Transcription regulation; Viral immunoevasion; Zinc; Zinc-finger.
FT   CHAIN         1    289       Early E1A protein.
FT                                /FTId=PRO_0000221692.
FT   ZN_FING     154    174       {ECO:0000250|UniProtKB:P03255}.
FT   REGION       41     49       Interaction with RB1 in competition with
FT                                E2F1. {ECO:0000250}.
FT   REGION       76    140       Interaction with UBE2I. {ECO:0000250}.
FT   MOTIF       113    117       PXLXP motif, interaction with host
FT                                ZMYND11. {ECO:0000250}.
FT   MOTIF       122    126       LXCXE motif, interaction with host RB1.
FT                                {ECO:0000255}.
FT   MOTIF       258    289       Bipartite nuclear localization signal.
FT                                {ECO:0000250|UniProtKB:P03255,
FT                                ECO:0000255}.
FT   MOTIF       279    283       PXDLS motif, CTBP-binding.
FT                                {ECO:0000250|UniProtKB:P03255}.
FT   MOD_RES      89     89       Phosphoserine; by host. {ECO:0000250}.
FT   MOD_RES     219    219       Phosphoserine; by host. {ECO:0000250}.
FT   MOD_RES     231    231       Phosphoserine; by host. {ECO:0000250}.
FT   VAR_SEQ      29     55       ADNLPPPSHFEPPTLHELYDLDVTAPE -> CLNLSLSPSQ
FT                                NRSLQDLPGVLNWCLLS (in isoform early E1A 6
FT                                kDa protein). {ECO:0000305}.
FT                                /FTId=VSP_028916.
FT   VAR_SEQ      56    289       Missing (in isoform early E1A 6 kDa
FT                                protein). {ECO:0000305}.
FT                                /FTId=VSP_028917.
FT   VAR_SEQ     140    185       Missing (in isoform early E1A 26 kDa
FT                                protein). {ECO:0000305}.
FT                                /FTId=VSP_000197.
FT   MUTAGEN     157    157       C->S: Abolishes ATF7-mediated
FT                                transcriptional activation.
FT                                {ECO:0000269|PubMed:8417352}.
FT   MUTAGEN     178    178       T->P: No effect on ATF7-mediated
FT                                transcriptional activation.
FT                                {ECO:0000269|PubMed:8417352}.
FT   MUTAGEN     185    185       S->R: Abolishes ATF7-mediated
FT                                transcriptional activation.
FT                                {ECO:0000269|PubMed:8417352}.
FT   CONFLICT     68     68       D -> E (in Ref. 2; AAA92197/AAA92199).
FT                                {ECO:0000305}.
FT   CONFLICT     81     81       L -> F (in Ref. 2; AAA92197/AAA92199).
FT                                {ECO:0000305}.
SQ   SEQUENCE   289 AA;  31851 MW;  4264747DAD74FFC5 CRC64;
     MRHIICHGGV ITEEMAASLL DQLIEEVLAD NLPPPSHFEP PTLHELYDLD VTAPEDPNEE
     AVSQIFPDSV MLAVQEGIDL LTFPPAPGSP EPPHLSRQPE QPEQRALGPV SMPNLVPEVI
     DLTCHEAGFP PSDDEDEEGE EFVLDYVEHP GHGCRSCHYH RRNTGDPDIM CSLCYMRTCG
     MFVYSPVSEP EPEPEPEPEP ARPTRRPKLV PAILRRPTSP VSRECNSSTD SCDSGPSNTP
     PEIHPVVPLC PIKPVAVRVG GRRQAVECIE DLLNESGQPL DLSCKRPRP
//
#~~# #~+~~+~# #~~#
#LOG 00:00:00 Activity Log for SLiMSuite V1.5.2: Tue Dec 8 22:35:32 2015
#DIR 00:00:00 Run from directory: /srv/slimsuite/logs/prod
#ARG 00:00:00 Commandline arguments: run ip=129.94.133.155 slimprob&uniprotid=E1A_ADE02&motifs=LxCxE,PxDLS&jobid=15120800031
#VIO 00:00:00 Verbosity: -1; Interactivity: -1.
#PROG 00:00:00 SLiMProb V2.2.5: Short Linear Motif Probability tool
#CMD 00:00:00 Full SLiMProb CmdList: proglog=F iucut=0.2 usegopher=T protscores=T megablam=F orthdb=qfo_ref.2015-04.Eukaryota.fas sourcedate=2015-04-15 walltime=0 runid=15120800031 rest=format uniprotid=E1A_ADE02 motifs=LxCxE,PxDLS jobid=15120800031 resfile=slimprob.csv savespace=0 targz=F megaslim=seqin basefile=slimprob
#DB 00:00:00 /srv/slimsuite/data/orthdb/qfo_ref.2015-04/qfo_ref.2015-04.Eukaryota.fas already formatted. (Force = False).
#DB 00:00:00 /srv/slimsuite/data/orthdb/qfo_ref.2015-04/qfo_ref.2015-04.Eukaryota.fas already formatted. (Force = False).
#MOT 00:00:00 2 motifs read from LxCxE,PxDLS (2 lines): 2 retained.
#ALPH 00:00:00 Alphabet: A C D E F G H I K L M N P Q R S T V W Y
#URL 00:01:04 Extracting 1 AccNum from http://www.uniprot.org/uniprot/: 1 read, 1 extracted; 0 failed; 0 duplicates.
#DAT 00:01:04 Extracting entries from slimprob.dat: 1 read, 1 extracted.
#SEQ 00:01:04 1 sequences loaded from /srv/slimsuite/scratch/prod/slimprob/15120800031/slimprob.dat (Format: uniprot).
#FAS 00:01:04 1 Sequences output to /srv/slimsuite/scratch/prod/slimprob/15120800031/slimprob.fas.
#UPC 00:01:04 No UPC file found.
#UP 00:01:04 slimprob: 1 Seq; 1 UPC; 1.000 MST; Single sequence
#FTMASK 00:01:04 FTMask: None
#SEARCH 00:01:04 1 sequences searched for 2 motifs: 2 occ.
#SAVE 00:01:04 SLiMProb Intermediate saved as /srv/slimsuite/scratch/prod/slimprob/15120800031/slimprob.Commandline.FreqNoMask.pickle (Python pickle).
#GZIP 00:01:04 /srv/slimsuite/scratch/prod/slimprob/15120800031/slimprob.Commandline.FreqNoMask.pickle zipped.
#OCC 00:01:04 Processing 2 occurrences complete.
#PROB 00:01:04 Calculating SLiM Probabilities complete.
#COMB 00:01:04 Combined Occurrence Attributes complete.
#OUT 00:01:04 Summary data for slimprob saved to /srv/slimsuite/scratch/prod/slimprob/15120800031/slimprob.csv
#RES 00:01:04 SLiMProb results output to /srv/slimsuite/scratch/prod/slimprob/15120800031/slimprob.(occ.)csv and /srv/slimsuite/scratch/prod/slimprob/15120800031/slimprob.*
#LOG 00:01:04 SLiMProb V2.2.5 End: Tue Dec 8 22:36:36 2015
#JOBID 00:01:04 15120800031
#REST 00:01:04 URL for future retrieval: http://rest.slimsuite.unsw.edu.au/retrieve&jobid=15120800031&rest=format&password=None
0 warning messages.

© 2015 RJ Edwards. Contact: richard.edwards@unsw.edu.au.