ProDom 2012.1 WWW Server Information

(2012)


If you find bugs, wish to make comments or suggestions about this WWW ProDom Server
or about the ProDom MailServer please send message to Jerome.Gouzy[@]toulouse.inra.fr

Graphic Output

Remark: for the moment only 14160 different domain motifs are available.


Multiple Alignment

ProDom Release 2012.1

Domain PD010000

Graphic representation of all proteins containing this domain.
ClickHere Summarized alignments and trees
MSF Alignment in MSF format
Build an ESPript view
Run Strap server with this domain
Go to 3D Structures

Number of sequences in family8
Most frequent protein names
Commentary (automatic)LECTIN PRECURSOR PROTEIN SIGNAL ER-GOLGI INTERMEDIATE COMPARTMENT TRANSPORT TRANSMEMBRANE GOLGI
Consistency Indicator DIAMETER: 234 PAM
RADIUS OF GYRATION: 68 PAM
SEQUENCE CLOSEST TO CONSENSUS: O94401_SCHPO 8-308 (distance:39 PAM)

                                      10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       
                         wt   ---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|----
  ER53_HUMAN    32   300 0.50 .......GVGGDPAVALPHRRFEYKYSFKGPHLVQSDGTVPFWAHAGNAIPS-SDQIRVAPSLKSQRGSVWTKTK-AAFENWEVEVTFRVTGRGR--IGADGLAIWYAENQGLEGPVFGSADLWNGVGIFFDTFDNDG---KKNNPAIVIIGNNGQIHYDHQNDGASQALAS----CQRDFRNKPYPVRAKITYYQNTLTVMINNGFTPDKNDYEFCAKVENMIIPAQGHFGISAATGGLADDHDVLSFLTFQLTEPGKEPPT--------PDKEISEKEKEKYQEEFEHFQQEL.....................................
Q12895_HUMAN    32   300 0.50 .......GVGGDPAVALPHRRFEYKYSFKGPHLVQSDGTVPFWAHAGNAIPS-SDQIRVAPSLKSQRGSVWTKTK-AAFENWEVEVTFRVTGRGR--IGADGLAIWYAENQGLEGPVFGSADLWNGVGIFFDSFDNDG---KKNNPAIVIIGNNGQIHYDHQNDGASQALAS----CQRDFRNKPYPVRAKITYYQNTLTVMINNGFTPDKNDYEFCAKVENMIIPAQGHFGISAATGGLADDHDVLSFLTFQLTEPGKEPPT--------PDKEISEKEKEKYQEEFEHFQQEL.....................................
  Q62902_RAT    43   308 0.50 ..........AGTQAELPHRRFEYKYSFKGPHLVQSDGTVPFWAHAGNAIPS-ADQIRIAPSLKSQRGSVWTKTK-AAFENWEVEVTFRVTGRGR--IGADGLAIWYTENQGLDGPVFGSADMWNGVGIFFDSFDNDG---KKNNPAIVVVGNNGQINYDHQNDGATQALAS----CQRDFRNKPYPVRAKITYYQKTLTVMINNGFTPDKNDYEFCAKVENMVIPTQGHFGISAATGGLADDHDVLSFLTFQLTEPGKEPPT--------PEKDISEKEKEKYQEEFEHFQQEL.....................................
P90913_CAEEL    28   276 1.45 .....................FEYKHSFRAPNLAQRDGSIPFWIVSGDAIAS-GEQLRLAPSMRSRKGIAWNKRAFLESENFQVDIALKIGGQGR--VGADGLGIWYTSQLGALGPVFGGNDFWTGMGLFLDSFDNDG---QKNNPQVSLMLNDGTRSYDHHTDGSQQILSS----CQRDFRNKPYPVRIRIEYLKNVLTVHIDDGMQPTPR-YELCMRAENIFLPRNGYFGVSAATGGLADDHDVLDFSVFSLFNEQQKPVP--------VAEQIPQQEKQKYDEEFE...........................................
O94401_SCHPO     8   308 1.75 VFLLGIFGFVLGALAE--TSHLERL-SLEAPYINHGMRNL-WWEYGGSTVIDRKNGIFLTQDVQNQQGWISTRLP-TPSSSFEVLFQFRINSEST-SLFGDGLAFFLAAERAKPGPVFGFTDKFNGYGIFIDTYNNHRPG--TLFPRVIVMKGDGHTPYDYENDGKANEIAS----CSALNVRGNDYNLGKLKYDKNAKKLRFEIAYQ-GSSSFIKCFDLNEVELPLTTFMSFSAHTGDLSESHEIAS--ILSRTITDIDDEGT-------PEIPAEELKGTTYGQKKGSFKK------RLIILLLSL---IVIFSIFALRSYQVQQEKNRR
Q12907_HUMAN    33   354 0.83 LFLLLLLGSVTADITDGNSEHLKREHSLIKPYQGVGSSSMPLWDFQGSTMLT-SQYVRLTPDERSKEGSIWNHQP-CFLKDWEMHVHFKVHGTGKKNLHGDGIALWYTRDRLVPGPVFGSKDNFHGLAIFLDTYPNDETT-ERVFPYISVMVNNGSLSYDHSKDGRWTELAG----CTADFRNRDHDTFLAVRYSRGRLTVMTDL--E-DKNEWKNCIDITGVRLPTGYYFGASAGTGDLSDNHDIISMKLFQLMVEHTPDEESIDWTKIEPSVNFLKSPKDNVDDPTGNFRSGPLTGWRVFLLLLCALLGIVVCAVVGAVVFQKRQERNKR
  VP36_CANFA    33   354 0.83 LFLLLLLGPVVADITDGNSEHLKREHSLIKPYQGVGSSSMPLWDFQGSTILT-SQYVRLTPDERSKEGSIWNHQP-CFLKDWEMHVHFKVHGTGKKNLHGDGIALWYTRDRLVPGPVFGSKDNFHGLAIFLDTYPNDETT-ERVFPYISVMVNNGSLSYDHSKDGRWTELAG----CTADFRNRDHDTFLAVRYSRGRLTVMTDL--E-DKNEWKNCIDITGVRLPTGYYFGASAGTGDLSDNHDIISMKLFQLMVEHTPDEENIDWTKIEPSVNFLKSPKDNVDDPTGNFRSGPLTGWRVFLLLLCALLGIIVCAVVGAVVFQKRQERNKR
Q22170_CAEEL    46   265 1.65 ......................KREHSLIKPYTGSGAD-IPNWNIIGSTFVS-SNQIRLTADEQSKAGALWNTQP-VWSRDWELQVSFKVTGS-TGDLFGDGMAIWYTSEPNILGPVFGGKDYFRGLAVFLDTYSNHNGPHQHGHPFISAMVSDGSLHYDHDKDGTHTQLGGENTGCTAKFRNKDHDTQVLIRYVGDTLSIFSDI--E-NKGIWNLCMSVNNVQLPTGYYIGVSAATGDLSDAHDVVSL...................................................................................
consensus                     VFLLGIFGFVLGDLAEGPTEHFERKHSLKKPYLGQGDGSIPFWDYAGSTIVSRSNQIRLTPDERSKQGSIWNKQPFCWSEDWEVEVSFKVNGQGRGNLFGDGLAIWYTSERGVPGPVFGGKDYWNGLGIFLDTYDNDGPPHQKNHPYISVMVNDGSLHYDHENDGKHTELAGENTGCTADFRNKDHPTRVKIRYYKNTLTVMIDIGYEPDKNDWELCMDVNNVQLPTGYYFGVSAATGDLSDDHDVISFKIFQLTVEHTEDEPTIDWTKIEPEVQIEEKEKEKYDEEFGNFKKGPLTGWRLFILLLCLLLGIVICSIFGLRSYQKQQEKNRR

The motif used to represent the domain family is shown on the top of the page. It is linked to the domain accession number.
Also note that multiple aligments and consensus sequences are calculated using different weights (wt) for each sequence.

  • Distances are counted in PAM (percent accepted mutations = number of accepted points mutations per hundred residues). For example 20 PAM correspond to 82% identity.

    Consistency indicators:
  • DIAMETER is the largest distance between 2 members of the domain family.
  • RADIUS OF GYRATION is the square mean distance between the concensus and any member of the domain family

    Smaller are these two values, more homogeneous is the family.


    PROSITE Links

    Links between PROSITE and ProDom 2001.1 were computed using the
    LASSAP program.
    We scanned ProDom consensus sequences with PROSITE patterns, excluding the following frequent patterns:
    ASN_GLYCOSYLATION 
    GLYCOSAMINOGLYCAN 
    CAMP_PHOSPHO_SITE 
    PKC_PHOSPHO_SITE 
    CK2_PHOSPHO_SITE 
    TYR_PHOSPHO_SITE 
    MYRISTYL 
    AMIDATION 
    MICROBODIES_CTER 
    NUCLEAR 
    RGD 
    LEUCINE_ZIPPER
    TONB_DEPENDENT_REC_1
    PROKAR_LIPOPROTEIN
    ATP_GTP_A
    PRENYLATION
    

    PDB Links

    Links between PDB and ProDom 2001.1 were computed using the LASSAP program.
    We scanned ExPDB (from Manuel Claude Peitsch) with each ProDom domain sequence.


    Pfam-A Links

    Links between Pfam-A and ProDom 2001.1 were computed using the MatchDom program (search for overlaps between Pfam-A and ProDom domains).
    We scanned all Pfam-A domains with each ProDom family.


    InterPro Links

    Links between InterPro and ProDom 2001.1 were computed using the MatchDom program (search for overlaps between InterPro and ProDom domains).
    We scanned all InterPro domain families (release 1.2) with each ProDom family.


    Known BUGS

    
    

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