Example response page for submited sequence 'Query':

All comments not found on actual response page are in green.

The first table contains the name of the best matched profile and the zscore of your match.
The best match to your query sequence: PRF_b2053 With a Zscore of: 153.1824
Your query sequence: 
>Query
MSKSKVVLLTGITGQDGSYLSELLLEKGYQVHGIIRRTSTFNTDRIDHLYVDPHDLEAKLRLHYGDLTDGTTLRRILED
VKPTEIYNLGAQSHVRVSFDSPEYTVDSVAMGTLRLLEAIRDYQHRTGIQVRFYQAGSSEMFGKVQEIPQKETTPFYPR
SPYACAKVYGHWQTVNYRESYDLFACNGILFNHESPRRGETFVTRKITRAIARIVAGTQKKLYLGNIDSKRDWGYAKDY
VRAMWAMLQQEQPDDYVVATGETHEVKEFLEIAFGYVNLNWQNYVAFDERYLRPAEVDLLIGDPAKTKAQLGWEPSVTF
TELVHLMVEADLAVLGLTSPNQSGRIKELMAQDMAFIRSQNGHAVD

This section then lists any other profiles your query matched with a zscore above our cutoff.
List of profiles with z scores above our cutoff
PRF_b2053153.1824

This section gives details on the profile and it's defining set. The hyperlinked ID's display our Cross Genome Analysis of that sequence.
Profile Description for PRF_b2053
Information Content = 50.5153 Information Density = 0.158355 Taxonomic spread = Full: 1 Euk., 2 GN, 1 Arc., 1 GP
Profile regular expression representation:

This is a 'human readable' representation of the 3-d score matrix. See the Amino Acid Classes page for the symbol legend.
KXALITGasGQDGhYLArfLLXKGYrVeGfXRRXhsXXXXRarXaXXggXggaXXgDfXkXXXaXsXasXXpXsEaYrL
hAXSeVXXSFkXPXXThrXshfhXXsfLkAaqXXXXsXnggFYQASiSEfdGXXgXXXXsEXiPFXPsSPYhfAKfdhe
WfXXXYREhYXfdAfsGILFNHESPXRGXsFVTRKIiXXfArIXXXXosXaXfGNfshXRDWGeAXkYVrXXeXffQsX
sPkDdVaAThXXeiVRoFfrXhfXXfGXrfXXXXsXXrrXXggRPXkVpXLfGlXXKAXrXLGWrXsXsXXEffsXMfX
XDf
Defining Set: b2053 - E. coli    F56H6_5_CE_NEW - C. elegans    Rv1511 - M. tuberculosis    MTH333 - M. thermoautotrophicum    aq_1082 - A. aeolicus   
ID:Definition:Z-score:Start:Stop:Full Length:
b2053yefA GDP-d-mannose dehydratase f373; 100 pct identical to fragment YEFA_ECOLI SW:P32054 but has 49 additional N-terminal residues; orf0.0of L11721 157.81513352374
F56H6_5_CE_NEWInherited from wormpep16.tbl from F56H6_5_CE_NEW with score: 1973 exp: 2.8e-205. defs:CE16133 (CAMBRIDGE) 163.551234374383
Rv1511gmdA GDP-mannose 4,6 dehydratase 177.08452321341
MTH333GDP-D-mannose dehydratase 178.04662317349
aq_1082rfbD GDP-D-mannose dehydratase 168.73524336346


The final table displays the multi-alignment graph of the defining set against your query sequence (blinking below).

prq-30621 Profile Alignment
1100200300400500
b2053
F56H6_5_CE_NEW
Rv1511
MTH333
aq_1082
Query


The button below (dead in this example) would display a detailed alignment of the query sequence and defining set on a new page, but is included at the bottom of this example.
detailed alignment

And the last part of the response page alows you to save the detailed alignment (below), and the score matrix for the best matched profile.
Please check which type of report you want to save:
The alignment detail file in text format.
The profile score matrix for the best match.





PRF_b2053 - Alignment Used to Generate Trees


        PATTERN  KXALITGasG QDGhYLArfL LXKGYrVeGf XRRXhsXXXX RarXaXXg--
          b2053  KVALITGVTG QDGSYLAEFL LEKGYEVHGI KRRASSFNTE RVDHIYQDPH
 F56H6_5_CE_NEW  KVALITGITG QDGSYLAELL LSKGYKVHGI IRRSSSFNTA RIEHLYGNPV
         Rv1511  KRALITGITG QDGSYLAELL LAKGYEVHGL IRRASTFNTS RIDHLYVDPH
         MTH333  KSALITGITG QDGAYLAKFL LEKGYEVYGI YRRLSTPNFW RLQYLEIF--
        aq_1082  KRALITGIRG QDGAYLAKLL LEKGYEVYGA DRRSGEFASW RLKELGIEN-
          Query  KVVLLTGITG QDGSYLSELL LEKGYQVHGI IRRTSTFNTD RIDHLYVDPH

        PATTERN  -gXg----ga XXgDfXkXXX aXsXasXXpX sEaYrLhAXS eVXXSFkXPX
          b2053  TCNPKF--HL HYGDLSDTSN LTRILREVQP DEVYNLGAMS HVAVSFESPE
 F56H6_5_CE_NEW  THNGSASFSL HYGDMTDSSC LIKLISTIEP TEIYHLAAQS HVKVSFDLPE
         Rv1511  QPGARL--FL HYGDLIDGTR LVTLLSTIEP DEVYNLAAQS HVRVSFDEPV
         MTH333  -DRI----NL VPADLTDEFS LLESLKISDA DEVYHLAAQS FVGTSFEQPT
        aq_1082  -DVK----II HM-DLLEFSN IIRTIEKVQP DEVYNLAAQS FVGVSFEQPI
          Query  -DLEAKL-RL HYGDLTDGTT LRRILEDVKP TEIYNLGAQS HVRVSFDSPE

        PATTERN  XThrXshfhX XsfLkAaqXX XXsXng--gF YQASiSEfdG XXgXXXXsEX
          b2053  YTADVDAMGT LRLLEAIRFL GLEKKT--RF YQASTSELYG LVQEIPQKET
 F56H6_5_CE_NEW  YTAEVDAVGT LRLLDAIHAC RLTEKV--RF YQASTSELYG KVQEIPQSEL
         Rv1511  HTGDTTGMGS MRLLEAVRLS RVHCR----F YQASSSEMFG AS-PPPQNEL
         MTH333  STAHVTGVAV TSMLEAIRHY NPHIR----F YQASSSEIYG DGHTTILNEN
        aq_1082  LTAEVDAIGV LRILEALRTV KPDTK----F YQASTSEMFG KVQEIPQTEK
          Query  YTVDSVAMGT LRLLEAIRDY QHRTGIQVRF YQAGSSEMFG KVQEIPQKET

        PATTERN  iPFXPsSPYh fAKfdheWfX XXYREhYXfd AfsGILFNHE SPXRGXsFVT
          b2053  TPFYPRSPYA VAKLYAYWIT VNYRESYGMY ACNGILFNHE SPRRGETFVT
 F56H6_5_CE_NEW  TPFYPRSPYA VAKMYGYWIV VNYREAYKMF ACNGILFNHE SPRRGETFVT
         Rv1511  TPFYPRSPYG AAKVYSYWAT RNYREAYGLF AVNGILFNHE SPRRGETFVT
         MTH333  SPFKPSSPYA AAKLYGYWMT RIYREGYDIF ACNGILFNHE SPLRGLEFVT
        aq_1082  TPFYPRSPYA VAKLFGHWIT VNYREAYNMF ACSGILFNHE SPLRGIEFVT
          Query  TPFYPRSPYA CAKVYGHWQT VNYRESYDLF ACNGILFNHE SPRRGETFVT

        PATTERN  RKIiXXfArI XXXXosXaXf GNfshXRDWG eAXkYVrXXe XffQsXsPkD
          b2053  RKITRAIANI AQGLESCLYL GNMDSLRDWG HAKDYVKMQW MMLQQEQPED
 F56H6_5_CE_NEW  RKITRSVAKI SLRQQEHIEL GNLSALRDWG HAKEYVEAMW RILQQDTPDD
         Rv1511  RKITRAVARI KAGIQSEVYM GNLDAVRDWG YAPEYVEGMW RMLQTDEPDD
         MTH333  RKISNTAAKI ALGLEDELLL GNLDAKRDWG YAPDYVEAMH MMLQHKEPDD
        aq_1082  RKITYSLARI KYGLQDKLVL GNLNAKRDWG YAPEYVEAMW LMMQQPEPDD
          Query  RKITRAIARI VAGTQKKLYL GNIDSKRDWG YAKDYVRAMW AMLQQEQPDD

        PATTERN  dVaAThXXei VRoFfrXhfX XfGXrfXXXX sXXrrXXg-- ----------
          b2053  FVIATGVQYS VRQFVEMAAA QLGIKLRFEG TGVEEKGIVV SVTGHDAPGV
 F56H6_5_CE_NEW  FVIATGKQFS VREFCNLAFA EIGEQLVWEG EGVDEVGKNQ DGVVRVKVSP
         Rv1511  FVLATGRGFT VREFARAAFE HAGLDWQQYV KFDQRYL--- ----------
         MTH333  FVIATAETHT VREFCEKSFE ELGLDWQDYV KVDKRFF--- ----------
        aq_1082  YVIATGETHT VREFVEKAAK IAGFDIEWVG EGINEKGIDR NTGKVIVEVS
          Query  YVVATGETHE VKEFLEIAFG YVNLNWQNYV AFDERYL--- ----------

        PATTERN  ---------- ---gRPXkVp XLfGlXXKAX rXLGWrXsXs XXEffsXMfX
          b2053  KPGDVIIAVD PRYFRPAEVE TLLGDPTKAH EKLGWKPEIT LREMVSEMVA
 F56H6_5_CE_NEW  KY-------- ---YRPTEVE TLLGNPAKAR KTLGWEPKIT VPELVKEMVA
         Rv1511  ---------- ----RPTEVD SLIGDATKAA ELLGWRASVH TDELARIMVD
         MTH333  ---------- ----RPLDVN YLCGDYSKAR ENLGWQPKTK FEELVKIMVR
        aq_1082  EEF------- ---FRPAEVD ILVGNPEKAM KKLGWKPRTT FDELVEIMME
          Query  ---------- ----RPAEVD LLIGDPAKTK AQLGWEPSVT FTELVHLMVE

        PATTERN  XDf
          b2053  NDL
 F56H6_5_CE_NEW  SDI
         Rv1511  ADM
         MTH333  EDL
        aq_1082  ADL
          Query  ADL
Amino Acid Classes

All Identities are in bolded RED, click Amino Acid Classes for all other assignments.

Members of the defining set are in bold.

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Sëan Quinlan <wwwadmin@darwin.bu.edu>
last modified: Thu Jun 24 14:06:34 EDT 1999