GapMind for Amino acid biosynthesis

 

Alignments for a candidate for metH in Pseudomonas simiae WCS417

Align methionine synthase; EC 2.1.1.13 (characterized)
to candidate GFF2414 PS417_12310 methionine synthase

Query= CharProtDB::CH_090726
         (1227 letters)



>FitnessBrowser__WCS417:GFF2414
          Length = 1236

 Score = 1617 bits (4187), Expect = 0.0
 Identities = 823/1235 (66%), Positives = 976/1235 (79%), Gaps = 15/1235 (1%)

Query: 2    SSKVEQLRAQLNERILVLDGGMGTMIQSYRLNEADFRGERFADWPCDLKGNNDLLVLSKP 61
            S +++ L   L ERIL+LDGGMGTMIQSY+L E D+RG+RFADWP D+KGNNDLLV+++P
Sbjct: 5    SVRLQALHQALKERILILDGGMGTMIQSYKLEENDYRGKRFADWPSDVKGNNDLLVITRP 64

Query: 62   EVIAAIHNAYFEAGADIIETNTFNSTTIAMADYQMESLSAEINFAAAKLARACADEWTAR 121
            +VI  I  AY +AGADI+ETNTFN+T I+MADY ME+L+ E+N   A+LAR  AD  TA 
Sbjct: 65   DVIGGIEKAYLDAGADILETNTFNATRISMADYGMEALAFELNVEGARLARKIADAKTAE 124

Query: 122  TPEKPRYVAGVLGPTNRTASISPDVNDPAFRNITFDGLVAAYRESTKALVEGGADLILIE 181
            TP+KPR+VAGVLGPT+RT S+SPDVN+P +RN+TFD LV  Y E+TK L+EGGADLILIE
Sbjct: 125  TPDKPRFVAGVLGPTSRTCSLSPDVNNPGYRNVTFDELVENYTEATKGLIEGGADLILIE 184

Query: 182  TVFDTLNAKAAVFAVKTEFEALGVELPIMISGTITDASGRTLSGQTTEAFYNSLRHAEAL 241
            T+FDTLNAKAA+FAV+  FE L +ELPIMISGTITDASGRTLSGQTTEAF+NS+ HA+ +
Sbjct: 185  TIFDTLNAKAAIFAVQGVFEELNIELPIMISGTITDASGRTLSGQTTEAFWNSVAHAKPI 244

Query: 242  TFGLNCALGPDELRQYVQELSRIAECYVTAHPNAGLPNAFGEYDLDADTMAKQIREWAQA 301
            + GLNCALG  ELR Y++ELS  A  +V+AHPNAGLPN FGEYD      AK I E+AQ+
Sbjct: 245  SVGLNCALGASELRPYLEELSNKANTHVSAHPNAGLPNEFGEYDELPSQTAKVIEEFAQS 304

Query: 302  GFLNIVGGCCGTTPQHIAAMSRAVEGLAPRKLPEIPVACRLSGLEPLNIGEDSLFVNVGE 361
            GFLNIVGGCCGTTP HI A+++AV G APR++P+IP ACRLSGLEP  I   SLFVNVGE
Sbjct: 305  GFLNIVGGCCGTTPGHIEAIAKAVAGYAPRQIPDIPKACRLSGLEPFTIDRSSLFVNVGE 364

Query: 362  RTNVTGSAKFKRLIKEEKYSEALDVARQQVENGAQIIDINMDEGMLDAEAAMVRFLNLIA 421
            RTN+TGSAKF RLI+E+ Y+EAL+VA QQVE GAQ+IDINMDEGMLD++ AMV FLNLIA
Sbjct: 365  RTNITGSAKFARLIREDNYTEALEVALQQVEAGAQVIDINMDEGMLDSKKAMVTFLNLIA 424

Query: 422  GEPDIARVPIMIDSSKWDVIEKGLKCIQGKGIVNSISMKEGVDAFIHHAKLLRRYGAAVV 481
            GEPDI+RVPIMIDSSKWDVIE GLKCIQGKGIVNSISMKEGV+ FIHHAKL +RYGAAVV
Sbjct: 425  GEPDISRVPIMIDSSKWDVIEAGLKCIQGKGIVNSISMKEGVEQFIHHAKLCKRYGAAVV 484

Query: 482  VMAFDEQGQADTRARKIEICRRAYKILTEEVGFPPEDIIFDPNIFAVATGIEEHNNYAQD 541
            VMAFDE GQADT ARK EIC+R+Y IL  EVGFPPEDIIFDPNIFAVATGIEEHNNYA D
Sbjct: 485  VMAFDEAGQADTEARKKEICKRSYDILVNEVGFPPEDIIFDPNIFAVATGIEEHNNYAVD 544

Query: 542  FIGACEDIKRELPHALISGGVSNVSFSFRGNDPVREAIHAVFLYYAIRNGMDMGIVNAGQ 601
            FI AC  I+ ELP+AL SGGVSNVSFSFRGN+PVREAIH+VFL YAIRNG+ MGIVNAGQ
Sbjct: 545  FINACAYIRDELPYALTSGGVSNVSFSFRGNNPVREAIHSVFLLYAIRNGLTMGIVNAGQ 604

Query: 602  LAIYDDLPAELRDAVEDVILNRRDDGTERLLELAEKYRGSKTDDTANAQQAEWRSWEVNK 661
            L IYD +PAELRDAVEDV+LNR  DGT+ LL +A+KY+G        A+  EWR W+VNK
Sbjct: 605  LEIYDQIPAELRDAVEDVVLNRTPDGTDALLAIADKYKGD--GSVKEAETEEWRGWDVNK 662

Query: 662  RLEYSLVKGITEFIEQDTEEARQQATRPIEVIEGPLMDGMNVVGDLFGEGKMFLPQVVKS 721
            RLE++LVKGIT  I +DTEE+R    RPIEVIEGPLM GMN+VGDLFG GKMFLPQVVKS
Sbjct: 663  RLEHALVKGITTHIVEDTEESRLSFARPIEVIEGPLMSGMNIVGDLFGAGKMFLPQVVKS 722

Query: 722  ARVMKQAVAYLEPFIEASK-EQGKTNGKMVIATVKGDVHDIGKNIVGVVLQCNNYEIVDL 780
            ARVMKQAVA+L PFIE  K ++ +  GK+++ATVKGDVHDIGKNIVGVVL CN Y+IVDL
Sbjct: 723  ARVMKQAVAHLIPFIELEKGDKPEAKGKILMATVKGDVHDIGKNIVGVVLGCNGYDIVDL 782

Query: 781  GVMVPAEKILRTAKEVNADLIGLSGLITPSLDEMVNVAKEMERQGFTIPLLIGGATTSKA 840
            GVMVPAEKIL+ AKE   D+IGLSGLITPSLDEMV+VA+EM+RQ F +PL+IGGATTSKA
Sbjct: 783  GVMVPAEKILQVAKEQKCDIIGLSGLITPSLDEMVHVAREMQRQDFHLPLMIGGATTSKA 842

Query: 841  HTAVKIEQNYSG-PTVYVQNASRTVGVVAALLSDTQRDDFVARTRKEYETVRIQHGRKKP 899
            HTAVKIE  YS    VYV +ASR VGV   LLS   +  FV RTR+EY  VR +   +  
Sbjct: 843  HTAVKIEPKYSNDAVVYVTDASRAVGVATQLLSKELKAGFVERTREEYVEVRERTSNRSA 902

Query: 900  RTPPVTLEAARDNDFAFDWQAYTPPVAHRLGVQEVE-ASIETLRNYIDWTPFFMTWSLAG 958
            RT  ++  AA      FDW  Y+P V    G + ++   ++ L  YIDWTPFF++W LAG
Sbjct: 903  RTERLSYPAAIAKKPQFDWSTYSPVVPTFTGAKVLDNIDLKVLAEYIDWTPFFISWDLAG 962

Query: 959  KYPRILEDEVVGVEAQRLFKDANDMLDKLSAEKTLNPRGVVGLFPANRV-GDDIEIYRDE 1017
            K+PRIL DEVVG  A  L+ DA +ML KL  EK ++ R V G +P N+V  DD+E+Y D+
Sbjct: 963  KFPRILTDEVVGEAATALYADAQEMLKKLIDEKLISARAVFGFWPTNQVQDDDLEVYGDD 1022

Query: 1018 TRTHVINVSHHLRQQTEKT-GFANYCLADFVAPKLSGKADYIGAFAVTGGLEEDALADAF 1076
             +   I   HHLRQQ  KT G  N+ LADFVAPK SG  DYIG F  T G+  + +A A+
Sbjct: 1023 GQP--IAKLHHLRQQIIKTDGKPNFSLADFVAPKDSGVTDYIGGFITTAGIGAEEVAKAY 1080

Query: 1077 EAQHDDYNKIMVKALADRLAEAFAEYLHERVRKVYWGYAPNENLSNEELIRENYQGIRPA 1136
            +   DDYN IMVKALADRLAEA AE+LH++VRK +WGYA +E L NE LI+E Y GIRPA
Sbjct: 1081 QDAGDDYNSIMVKALADRLAEACAEWLHQQVRKEHWGYAKDEQLDNEALIKEQYSGIRPA 1140

Query: 1137 PGYPACPEHTEKATIWELLEVEK------HTGMKLTESFAMWPGASVSGWYFSHPDSKYY 1190
            PGYPACP+HTEKA +++LL+ E        +G+ LTE +AM+P A+VSGWYF+HP ++Y+
Sbjct: 1141 PGYPACPDHTEKAQLFQLLDPEAREMHAGRSGVFLTEHYAMFPAAAVSGWYFAHPQAQYF 1200

Query: 1191 AVAQIQRDQVEDYARRKGMSVTEVERWLAPNLGYD 1225
            AV ++ +DQV  Y  RKG  ++  ERWLAPNLGYD
Sbjct: 1201 AVGKVDKDQVASYTARKGQDLSVTERWLAPNLGYD 1235


Lambda     K      H
   0.318    0.134    0.391 

Gapped
Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 1
Number of Hits to DB: 3790
Number of extensions: 163
Number of successful extensions: 8
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 1
Number of HSP's successfully gapped: 1
Length of query: 1227
Length of database: 1236
Length adjustment: 47
Effective length of query: 1180
Effective length of database: 1189
Effective search space:  1403020
Effective search space used:  1403020
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 59 (27.3 bits)

Align candidate GFF2414 PS417_12310 (methionine synthase)
to HMM TIGR02082 (metH: methionine synthase (EC 2.1.1.13))

Software error:

../bin/blast/fastacmd -i /tmp/list.11587.in -d ../tmp/orgsDef_201/orgs.faa -p T > /tmp/gapView.11587.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

For help, please send mail to the webmaster (help@microbesonline.org), giving this error message and the time and date of the error.