(c) 1992-2000 Regents of the University of California, Santa Cruz
Sequence Alignment and Modeling Software System
http://www.cse.ucsc.edu/research/compbio/sam.html

Citations (SAM, SAM-T99, HMMs)

Sequence numbers correspond to the following labels:

    • 5csmA chorismate mutase (chorismate pyruvate mutase) Mutant b
    • 1ecmAB (1ecmA plus extra helix in active site from 1ecmB)
    • gi|2914553|pdb|3CSM|A_1:256 Chain A, Structure Of Yeast Chorismate Mutase With Bound Trp And An Endooxabicyclic Inhibitor ()
    • gi|2914555|pdb|3CSM|B Chain B, Structure Of Yeast Chorismate Mutase With Bound Trp And An Endooxabicyclic Inhibitor ()
    • gi|2914565|pdb|5CSM|A_1:256 Chain A, Yeast Chorismate Mutase, T226s Mutant, Complex With Trp ()
    • gi|1127167|pdb|1CSM|A_1:256 Chain A, Mol_id: 1; Molecule: Chorismate Mutase; Chain: A, B; Ec: 4.1.3.27; Mutation: Allele Mutant, Thr 226 Ile; Heterogen: Tryptophan; Chain: L, M (Saccharomyces cerevisiae)
    • gi|1127168|pdb|1CSM|B Chain B, Mol_id: 1; Molecule: Chorismate Mutase; Chain: A, B; Ec: 4.1.3.27; Mutation: Allele Mutant, Thr 226 Ile; Heterogen: Tryptophan; Chain: L, M (Saccharomyces cerevisiae)
    • gi|1800001|dbj|BAA16482.1|_3:97 (D90887) chorismate mutase (EC 5.4.99.5) P / prephenate dehydratase (EC 4.2.1.51) [Escherichia coli] (Escherichia coli)
    • gi|1311033|pdb|1ECM|A_3:97 Chain A, P-Protein, Chorismate Mutase Domain Mol_id: 1; Molecule: Endo-Oxabicyclic Transition State Analogue; Chain: A, B; Domain: Chorismate Mutase Domain, Residues 1 - 109; Engineered: Yes (Escherichia coli)
    • gi|1311034|pdb|1ECM|B Chain B, P-Protein, Chorismate Mutase Domain Mol_id: 1; Molecule: Endo-Oxabicyclic Transition State Analogue; Chain: A, B; Domain: Chorismate Mutase Domain, Residues 1 - 109; Engineered: Yes (Escherichia coli) 
               10        20        30        40        50         60   
               |         |         |         |         |          |   
   1 .MDFTKPETVLNLQNIRDELVRMEDSIIFKFIERSHFATCPSVYEANHPGL.EIPNFKGSFLDWA
   2 n----------PLLALREKISALDEKLLALLAERRELA-------------.-------------
   3 .MDFTKPETVLNLQNIRDELVRMEDSIIFKFIERSHFATCPSVYEANHPGL.EIPNFKGSFLDWA
   4 .MDFTKPETVLNLQNIRDELVRMEDSIIFKFIERSHFATCPSVYEANHPGL.EIPNFKGSFLDWA
   5 .MDFTKPETVLNLQNIRDELVRMEDSIIFKFIERSHFATCPSVYEANHPGL.EIPNFKGSFLDWA
   6 .MDFTKPETVLNLQNIRDELVRMEDSIIFKFIERSHFATCPSVYEANHPGL.EIPNFKGSFLDWA
   7 .-LRVDESEYLKLESIRHSLIRQEDSIIFNLLERAQYRYNADTYDED--AF.TMEGFQGSLVEFM
   8 .KKRVDESESLTLEGIRNSLIRQEDSIIFGLLERAKYCYNADTYDPT--AF.DMDGFNGSLVEYM
   9 .KKRVDESESLTLEGIRNSLIRQEDSIIFGLLERAKYCYNADTYDPT--AF.DMDGFNGSLVEYM
  10 .-LRVDESEYLKLESIRHSLIRQEDSIIFNLLERAQYRYNADTYDED--AF.TMEGFQGSLVEFM
  11 .--GSGCSNVLSLDLIRESLIRQEDTIVFSLIERAKFPLNSPAFEES--RC.LDSGSFSSLTEFF
  12 .----GDADKLCLDSIRKSLIRQEDTIIFNLIERIKFPINPTLYKQQ--LP.PSSNFSGSLFQYL
  13 .-DLSDASKALDLANIRFQLIRLEDTITFHLIERVQFPLNKTIYIPG--GV.KIPNEQISLMDYL
  14 .------NEKLKLENIRSALIRQEDTIIFNFLERAQFPRNEKVYKSGKEGClNLENYDGSFLNYL
  15 .--------------------------------------------------.-------------
  16 .--------------------------------------------------.-------------
  17 .--------------------------------------------------.-------------
  18 .--------------------------------------------------.-------------
  19 .--------------------------------------------------.-------------
  20 .--------------------------------------------------.-------------
  21 .--------------------------------------------------.-------------
  22 .--------------------------------------------------.-------------
  23 .--------------------------------------------------.-------------
  24 .--------------------------------------------------.-------------
  25 .--------------------------------------------------.-------------
  26 .--------------------------------------------------.-------------
  27 .--------------------------------------------------.-------------
  28 .--------------------------------------------------.-------------
  29 .--------------------------------------------------.-------------
  30 .--------------------------------------------------.-------------
  31 .--------------------------------------------------.-------------
  32 .--------------------------------------------------.-------------
  33 .--------------------------------------------------.-------------
  34 .--------------------------------------------------.-------------
  35 .--------------------------------------------------.-------------
  36 .--------------------------------------------------.-------------
  37 .--------------------------------------------------.-------------
  38 .--------------------------------------------------.-------------
  39 .--------------------------------------------------.-------------
  40 .--------------------------------------------------.-------------
  41 .--------------------------------------------------.-------------


           70        80        90       100       110       120       1
           |         |         |         |         |         |        
   1 LSNLEIAHSRIRRFESPDETPFFPDKIQKSFLPSINYPQILAPYAPEVNYNDKIKKVYIEKIIPL
   2 -----------------------------------------------------------------
   3 LSNLEIAHSRIRRFESPDETPFFPDKIQKSFLPSINYPQILAPYAPEVNYNDKIKKVYIEKIIPL
   4 LSNLEIAHSRIRRFESPDETPFFPDKIQKSFLPSINYPQILAPYAPEVNYNDKIKKVYIEKIIPL
   5 LSNLEIAHSRIRRFESPDETPFFPDKIQKSFLPSINYPQILAPYAPEVNYNDKIKKVYIEKIIPL
   6 LSNLEIAHSRIRRFESPDETPFFPDKIQKSFLPSINYPQILAPYAPEVNYNDKIKKVYIEKIIPL
   7 VRETEKLHAKVDRYKSPDEHPFFPQCLPEPILPPIQYPQVLHRCAESININKKVWNMYFKHLLPR
   8 VKGTEKLHAKVGRFKSPDEHPFFPDDLPEPMLPPLQYPKVLHFAADSININKKIWNMYFRDLVPR
   9 VKGTEKLHAKVGRFKSPDEHPFFPDDLPEPMLPPLQYPKVLHFAADSININKKIWNMYFRDLVPR
  10 VRETEKLHAKVDRYKSPDEHPFFPQCLPEPILPPIQYPQVLHRCAESININKKVWNMYFKHLLPR
  11 VRETEIIQAKVGRYEYPEENPFFLENIPHSVFPTHKYPSALHPKALSVNINKQIWDIYFKELLPL
  12 FQETESLQSKVGRYLAPEENPFFPDNLSDSIIPLTKCTPVLHPAAESVNVNEKILDIYINQMLPL
  13 LRETERLQSRVRRYQSPDEYPFFPSALEKPILQPLDYPKILHD--NDVNVNETIKTRYVQDILPA
  14 LHEEEKVYALVRRYASPEEYPF-TDNLPEPILPKFSGKFPLHP--NNVNVNSEILEYYINEIVPK
  15 -------HGQVGRYSSPDEHPFFPHVPPEPVLPPLHYPQVLHPIANSININHKVWEMYFRDILPR
  16 -----------------------------------------------------------------
  17 -----------------------------------------------------------------
  18 -----------------------------------------------------------------
  19 -----------------------------------------------------------------
  20 -----------------------------------------------------------------
  21 -----------------------------------------------------------------
  22 -----------------------------------------------------------------
  23 -----------------------------------------------------------------
  24 ---------------------FDPDNLPSSLLPQYNHPQILHPTAAAININETIWDAYVNQLLPL
  25 -----------------------------------------------------------------
  26 -----------------------------------------------------------------
  27 -----------------------------------------------------------------
  28 -----------------------------------------------------------------
  29 -----------------------PEHLPEPISPPLQYPQVLHPVTESININSKIWDMYFRNLVPR
  30 -----------------------PEHLPEPISPPLQYPQVLHPVTESININSKIWDMYFRNLVPR
  31 -----------------------------------------------------------------
  32 ----------------------------------------------------------FPTLLPM
  33 -----------------------------------------------------------------
  34 -----------------------------------------------------------------
  35 -----------------------------------------------------------------
  36 -----------------------------------------------------------------
  37 -----------------------------------------------------------------
  38 -----------------------------------------------------------------
  39 -----------------------------------------------------------------
  40 -----------------------------------------------------------------
  41 -----------------------------------------------------------------


      30            140       150       160       170        180       
      |              |         |         |         |          |       
   1 IS.....KRDGDDKNNFGSVATRDIECLQSLSRRIHFGKFVAEAKFQSD.IPLYTKLIKSKDVEG
   2 --.....----PLLALREKISALDEKLLALLAERRELAVEVGKAKLLSHr---------------
   3 IS.....KRDGDDKNNFGSVATRDIECLQSLSRRIHFGKFVAEAKFQSD.IPLYTKLIKSKDVEG
   4 IS.....KRDGDDKNNFGSVATRDIECLQSLSRRIHFGKFVAEAKFQSD.IPLYTKLIKSKDVEG
   5 IS.....KRDGDDKNNFGSVATRDIECLQSLSRRIHFGKFVAEAKFQSD.IPLYTKLIKSKDVEG
   6 IS.....KRDGDDKNNFGSVATRDIECLQSLSRRIHFGKFVAEAKFQSD.IPLYTKLIKSKDVEG
   7 LV.....KPGDD--GNCGSAALCDTMCLQILSKRIHFGKFVAEAKFREN.PAAYETAIKEQDRTQ
   8 LV.....KKGDD--GNYGSTAVCDAICLQCLSKRIHYGKFVAEAKFQAS.PEAYESAIKAQDKDR
   9 LV.....KKGDD--GNYXSTAVCDAICLQCLSKRIHYGKFVAEAKFQAS.PEAYESAIKAQDKDA
  10 LV.....KPGDD--GNCGSAALCDTMCLQILSKRIHLRKFVADAKFREN.PAAYETAIKEQDRTQ
  11 FV.....KPGDD--GNYPSTAASDLACLQALSRRIHYGKFVAEVKFRDA.PQDYEPAIRAQDREA
  12 FC.....TEVNDD-ANFATTAACDIQLLQALSRRIHYGKFVAEVKFRDS.IDEYKPFILAQDRDA
  13 ICpq6grEDRGETQENYGSAATCDVSCLQALSRRIHFGKFVAESKFQKE.TEKFVALIKAGDRKE
  14 IS.....SPGDDF-DNYGSTVVCDIRCLQSLSRRIHYGKFVAEAKYLAN.PEKYKKLILARDIKG
  15 LV.....KEGDD--GNFGSTAVCDTMCLQALSKRIHYGKFVGECKFRSN.PKSYEAAIIEQNREK
  16 --.....-SENPLLALREKISALDEKLLALLAERRELAVEVGKAKLLSH.RP-------------
  17 --.....-SENPLLALREKISALDEKLLALLAERRELAVEVGKAKLLSH.RP-------------
  18 --.....NPDNPLLALRDKISAVDKKLLTLLAERRLLAVEVAQAKLATH.RP-------------
  19 --.....NPDNPLLALRDKISAVDKKLLTLLAERRLLAVEVAQAKLATH.RP-------------
  20 --.....-SENPLLALREKISALDEKLLALLAERRELAVEVGKAKLLSH.RP-------------
  21 --.....SEADQLKALRVRIDSLDERILDLISERARCAQEVARVKTASW.PKAEEAV--------
  22 --.....SEADQLKALRVRIDSLDERILDLISERARCAQEVARVKTASW.PKAEEAV--------
  23 --.....----ELSDIRQQITQIDRSLLKLLSERHRLAFDVVRSKEISQ.KS-------------
  24 FT.....TEGDD--GNYVPTATSDLQCLQAISRRIHYGKFVAEAK----.---------------
  25 --.....-----LAEIRKKIDEIDNKILKLIAERNSLAKDVAEIKNQLG.IP-------------
  26 --.....----ELKELRKEIDRIDEEILRLLNERAKLAKRIGEIKSKAN.LP-------------
  27 --.....-----LENLRAEIDALDNELSDLLDKRLGIALKIALIKQESP.QE-------------
  28 --.....-----LRRSRQKIDGIDRDILDLITSRIALAREIAEAKEVLG.ME-------------
  29 LV.....KEGED--GNYGATAVCDTICLQALSKR---------------.---------------
  30 LV.....KEGED--GNYGATAVCDTICLQALSKR---------------.---------------
  31 --.....-----LENLRAEIDALDNELSDLLDKRLEIALKIALIKQESP.---------------
  32 TQ.....QRSID--DLRAEVDQINRDLLALISRRGEVVAQIGHAKSAEG.RP-------------
  33 --.....-ATDPLDALRARLDAADAALLDAVRTRLDICLRIGEYKRLHQ.VP-------------
  34 --.....----VLADVRAKIDEIDRGIQALIAERANFAHQVGKAKGKLA.AA-------------
  35 --.....-----LEEFRNKIDAVDDKILDLLNERMTYVKSIGELKQSSG.GS-------------
  36 --.....-----LKDLRSEIDSLDRELIQLFAKRLELVSQVGKVKHQHG.LP-------------
  37 --.....---TELELLRQKADELNLQILKLINERGNVVKEIGKAKEAQG.VN-------------
  38 --.....--REELARLRDSIDNIDAAVVHMLAERFKCTQQVGHLKARHQ.LP-------------
  39 --.....----ELTALRDQIDSVDKALLDLLAKRLELVAEVGEVKSRYG.LP-------------
  40 --.....----ELTALRDQIDEVDKALLNLLAKRLELVAEVGEVKSRFG.LP-------------
  41 -S.....QPVPEIDTLREEIDRLDAEILALVKRRAEVSKAIGKARMASG.GT-------------


      190       200       210             220       230          240   
       |         |         |               |         |            |   
   1 IMKNITNSAVEEKILERLTKKAE.VYGVDP.....TRISPEYLVKIYKEI...VIPITKEVEVEY
   2 ---PVRDIDRERDLLERLITLGK.AH----.....-HLDAHYITRLFQ-L...IIEDSVLTQQAL
   3 IMKNITNSAVEEKILERLTKKAE.VYGVDPte6ieRRITPEYLVKIYKEI...VIPITKEVEVEY
   4 IMKNITNSAVEEKILERLTKKAE.VYGVDPte6ieRRISPEYLVKIYKEI...VIPITKEVEVEY
   5 IMKNITNSAVEEKILERLTKKAE.VYGVDPtn6geRRITPEYLVKIYKEI...VIPITKEVEVEY
   6 IMKNITNSAVEEKILERLTKKAE.VYGVDPtn6geRRIIPEYLVKIYKEI...VIPITKEVEVEY
   7 LMQLLTYETVEEVVKKRVEIKAR.IFGQDIt12psYKIQPSLVAKLYGER...IMPLTKEVQIEY
   8 LMDMLTFPTVEDAIKKRVEMKTR.TYGQEVk19hvYKISPILVGDLYGDW...IMPLTKEVQVEY
   9 LMDMLTFPTVEDAIKKRVEMKTR.TYGQEVk19hvYKISPILVGDLYGDW...IMPLTKEVQVEY
  10 LMQLLTYETVEEVVKKRVEIKAR.IFGQDIt12psYKIQPSLVAKLYGER...IMPLTKEVQIEY
  11 LMKLLTFEKVEEMVKKRVQKKAE.TFGQEVk13kkYKVDPLLASRIYGEW...LIPLTKLVEVEY
  12 LMKLLTFEAVEEMVKKRVAKKAK.VFGQEVs10vkGKIDPLLVSRLYDEW...VMPLTKLVEVEY
  13 IDEAITDAKVEQKVLERLALKAK.TYGTDPgf7sgPKIDVQAVQDMYKEY...VIPLTKVVEVEY
  14 IENEIVDAAQEERVLKRLHYKAL.NYGRDAad7psDRINADCVASIYKDY...VIPMTKKVEVDY
  15 VMGLLTYP---------------.------.....---------------...------------
  16 ----VRDIDRERDLLERLITLGK.AHH---.....--LDAHYITRLFQ-L...IIEDSVLTQQAL
  17 ----VRDIDRERDLLERLITLGK.AHH---.....--LDAHYITRLFQ-L...IIEDSVLTQQAL
  18 ----IRDVERERALLENLIVLGK.AHN---.....--LDAHYITRLFQ-L...VIEDSVLTQQAL
  19 ----IRDVERERALLENLIVLGK.AHN---.....--LDAHYITRLFQ-L...VIEDSVLTQQAL
  20 ----VRDIDRERDLLERLITLGK.AHH---.....--LDAHYITRLFQ-L...IIEDSVLTQQAL
  21 ----FYRPEREAWVLKHIMELNK.------.....GPLDNEEMARLFREImssCLALEQPLRVAY
  22 ----FYRPEREAWVLKHIMELNK.------.....GPLDNEEMARLFREImssCLALEQPLRVAY
  23 ----LRDVEREQQLLQELVQFAE.NEN---.....YQLEAQYITSIFQ-K...IIEDSVLTQQVY
  24 -----------------------.------.....---------------...------------
  25 ----INDPEREKYIYDRIRKLCK.EHN---.....--VDENIGIKIFQ-I...LIEHNKALQKQY
  26 ----IHVPEREREIFEKILRLNKeVYG---.....GVFPQEALVHIYREIisaCLSLEKKIKVAY
  27 --NPIYCPKREQEILKRLSQRGF.------.....KHLNGEILASFYA-E...VFKISRNFQENA
  28 ----ILDPERELQIIERTRKIAR.ENG---.....--IDENKLTELMK-I...LMDLSKTEQKEM
  29 -----------------------.------.....---------------...------------
  30 -----------------------.------.....---------------...------------
  31 ----IYCPKREQEILKRLSQRDF.------.....KHLNGEILTGFYT-E...VFKISRKFQENA
  32 ---NHYDPAREEQQLKELEKINP.------.....GPFPTATVKGIFKEI...------------
  33 ----MMQPHRIAQVHANAARYAA.DHG---.....--IDPAFLRTLYD-T...IITETCRLEDEW
  34 --VDYYRPEREAQVLRMVVDRNE.------.....GPLSDEVLVHVFREImsaCLAQQEPLKIGY
  35 ----IYRPERERAIINRLKNANL.------.....GLLDQNAIEAIYQ-E...IFA---------
  36 ----IYAPEREIAMLQARRLEAE.KAG---.....--ISADLIEDV----...------------
  37 ----RFDPVRERTMLNNIIENND.------.....GPFENSTIQHIFK-E...IFK---------
  38 ----PADPAREAQQIARLRTLAE.SAK---.....--LDPAFAEKFL---...------------
  39 ----IYVPEREASMLASRRKEAE.ALGVPP.....D-----LIED-----...------------
  40 ----IYVPEREASMLASRRAEAE.ALGVPP.....DLIE-----D-----...------------
  41 ----RLVHSREMKVIERYSELG-.------.....---------------...------------


          250
           |
   1 LLRRLEE
   2 LQQH---
   3 LLRRLEE
   4 LLRRLEE
   5 LLRRLEE
   6 LLRRLEE
   7 LLRRL--
   8 LLRRL--
   9 LLRRL--
  10 LLRRL--
  11 LLRRL--
  12 LLRRL--
  13 LMQRL--
  14 LLARL--
  15 -------
  16 LQQHLN-
  17 LQQHLN-
  18 LQKNLN-
  19 LQKNLN-
  20 LQQHLN-
  21 L------
  22 L------
  23 LQNKLNE
  24 -------
  25 L------
  26 L------
  27 L------
  28 LR-----
  29 -------
  30 -------
  31 L------
  32 -------
  33 I------
  34 L------
  35 -------
  36 -------
  37 -------
  38 -------
  39 -------
  40 -------
  41 -------