GapMind for Amino acid biosynthesis

 

Alignments for a candidate for metH in Sphingomonas koreensis DSMZ 15582

Align methionine synthase (EC 2.1.1.13) (characterized)
to candidate Ga0059261_0990 Ga0059261_0990 methionine synthase (B12-dependent) (EC 2.1.1.13)

Query= BRENDA::P13009
         (1227 letters)



>FitnessBrowser__Korea:Ga0059261_0990
          Length = 865

 Score = 1043 bits (2696), Expect = 0.0
 Identities = 545/870 (62%), Positives = 653/870 (75%), Gaps = 16/870 (1%)

Query: 356  FVNVGERTNVTGSAKFKRLIKEEKYSEALDVARQQVENGAQIIDINMDEGMLDAEAAMVR 415
            FVN+GERTNVTGSA+FK+LI    Y+ A++VA QQVE+GAQ++D+NMDEG+LDA  AM  
Sbjct: 8    FVNIGERTNVTGSARFKKLIMAGDYTAAIEVALQQVESGAQVLDVNMDEGLLDAHEAMTT 67

Query: 416  FLNLIAGEPDIARVPIMIDSSKWDVIEKGLKCIQGKGIVNSISMKEGVDAFIHHAKLLRR 475
            FL LI  EPDIAR+P+M+DSSKWDVIE GLKC+ GK IVNSISMKEGVD F+ HA+    
Sbjct: 68   FLKLIQAEPDIARIPVMVDSSKWDVIEAGLKCVSGKPIVNSISMKEGVDQFLEHARKCMA 127

Query: 476  YGAAVVVMAFDEQGQADTRARKIEICRRAYKILTEEVGFPPEDIIFDPNIFAVATGIEEH 535
            YGAAVVVMAFDE GQADT+ RK+EIC RAYK+L   +GFPPEDIIFDPN+FAVATGIEEH
Sbjct: 128  YGAAVVVMAFDEVGQADTKDRKVEICERAYKLLV-GIGFPPEDIIFDPNVFAVATGIEEH 186

Query: 536  NNYAQDFIGACEDIKRELPHALISGGVSNVSFSFRGNDPVREAIHAVFLYYAIRNGMDMG 595
            NNY  DFI AC +IK   PH  ISGG+SN+SFSFRGN+PVR+A+H+VFLY+AI  GMDM 
Sbjct: 187  NNYGVDFIEACREIKARCPHVHISGGLSNLSFSFRGNEPVRKAMHSVFLYHAIPAGMDMA 246

Query: 596  IVNAGQLAIYDDLPAELRDAVEDVILNRRDDGTERLLELAEKYRGSKTDDTANAQQAEWR 655
            IVNAGQL +YD +  ELR A EDVILNR  +  ERL+ LAEK+RG  TD  A  Q AEWR
Sbjct: 247  IVNAGQLDVYDQIEPELRTACEDVILNRDPEAGERLVALAEKFRG--TDAVAEKQAAEWR 304

Query: 656  SWEVNKRLEYSLVKGITEFIEQDTEEARQQATRPIEVIEGPLMDGMNVVGDLFGEGKMFL 715
             W V KRLE++LVKGI +++ +DTEE RQ+A RPIEVIEGPLMDGMNVVGDLFG GKMFL
Sbjct: 305  GWAVEKRLEHALVKGIDQYVVEDTEECRQKADRPIEVIEGPLMDGMNVVGDLFGSGKMFL 364

Query: 716  PQVVKSARVMKQAVAYLEPFIEASKEQG-KTNGKMVIATVKGDVHDIGKNIVGVVLQCNN 774
            PQVVKSARVMK+AVA+L P+IEA+KE G K  GK+V+ATVKGDVHDIGKNIVGVVLQCN 
Sbjct: 365  PQVVKSARVMKKAVAHLLPYIEAAKEPGAKGKGKVVMATVKGDVHDIGKNIVGVVLQCNG 424

Query: 775  YEIVDLGVMVPAEKILRTAKEVNADLIGLSGLITPSLDEMVNVAKEMERQGFTIPLLIGG 834
            +E+VDLGVMVP  KIL  A E +AD+IGLSGLITPSLDEMV VA+EM+R   T+PLLIGG
Sbjct: 425  FEVVDLGVMVPWSKILEAANENDADMIGLSGLITPSLDEMVTVAEEMKRARMTMPLLIGG 484

Query: 835  ATTSKAHTAVKIEQNYSGPTVYVQNASRTVGVVAALLSDTQRDDFVARTRKEYETVRIQH 894
            ATTSK HTA+KI   Y GP V+V +ASR VGV   L+SDT RDD+VA+   EYE VRI  
Sbjct: 485  ATTSKVHTALKIAPAYDGPVVHVLDASRAVGVATTLVSDTIRDDYVAKVAGEYEAVRIAR 544

Query: 895  GRKKPRTPPVTLEAARDNDFAFDWQAYTPPVAHRLGVQEV-EASIETLRNYIDWTPFFMT 953
               K ++  V +  ARDN F  D  +  P      GV    +  +  LR YIDWTPFF  
Sbjct: 545  A-NKGQSELVPIAVARDNAFEAD-MSLKPGKPRMPGVHSFPDWDLADLRQYIDWTPFFRA 602

Query: 954  WSLAGKYPRILEDEVVGVEAQRLFKDANDMLDKLSAEKTLNPRGVVGLFPANRVGDDIEI 1013
            W LAG YP IL D+VVG  A  LF DA  MLDK+  EK L  RGV GL+P  R GDDI +
Sbjct: 603  WELAGNYPAILTDKVVGESATSLFADAQKMLDKIVEEKWLTARGVAGLWPCRREGDDIIV 662

Query: 1014 YRDETRTHVINVSHHLRQQTEK-TGFANYCLADFVAPKLSGKADYIGAFAVTGGLEEDAL 1072
            + ++ +   + +   LRQQ +K  G AN CLADF+      + D+IG FAV     E  L
Sbjct: 663  HVEDEKHVTLPM---LRQQIQKREGRANMCLADFI----DRQGDWIGGFAVGIHGIEPHL 715

Query: 1073 ADAFEAQHDDYNKIMVKALADRLAEAFAEYLHERVRKVYWGYAPNENLSNEELIRENYQG 1132
            A  F+   DDY+ I++KALADRLAEAFAE LH  VR   WGYA  E L+NE LI+E Y+G
Sbjct: 716  A-RFKNAIDDYSDILLKALADRLAEAFAERLHHYVRTALWGYAEGEQLTNEALIKEEYRG 774

Query: 1133 IRPAPGYPACPEHTEKATIWELLEVEKHTGMKLTESFAMWPGASVSGWYFSHPDSKYYAV 1192
            IRPAPGYPACPEH+ K  ++++L+  K TG+ LTESFAM P A+VSG+YF HP ++Y+ V
Sbjct: 775  IRPAPGYPACPEHSLKPILFDMLDAHKRTGISLTESFAMLPTAAVSGFYFGHPQAEYFGV 834

Query: 1193 AQIQRDQVEDYARRKGMSVTEVERWLAPNL 1222
            A++ RDQ+E+YA R+G+S+ + ERWL PNL
Sbjct: 835  ARVGRDQLEEYATRRGVSIEQAERWLRPNL 864


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: 2622
Number of extensions: 115
Number of successful extensions: 7
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: 865
Length adjustment: 45
Effective length of query: 1182
Effective length of database: 820
Effective search space:   969240
Effective search space used:   969240
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: 57 (26.6 bits)

Align methionine synthase (EC 2.1.1.13) (characterized)
to candidate Ga0059261_0991 Ga0059261_0991 Methionine synthase I (cobalamin-dependent), methyltransferase domain

Query= BRENDA::P13009
         (1227 letters)



>FitnessBrowser__Korea:Ga0059261_0991
          Length = 348

 Score =  362 bits (928), Expect = e-104
 Identities = 185/345 (53%), Positives = 243/345 (70%), Gaps = 3/345 (0%)

Query: 6   EQLRAQLNERILVLDGGMGTMIQSYRLNEADFRGERFADWPCDLKGNNDLLVLSKPEVIA 65
           E+L A+  +RIL+ DG  GT IQ+++L+EA + G+       D KGNND+L L+KPEV A
Sbjct: 5   EKLMAEAAKRILITDGAFGTEIQNWKLDEAAYAGDLGLSH--DQKGNNDILALTKPEVPA 62

Query: 66  AIHNAYFEAGADIIETNTFNSTTIAMADYQMESLSAEINFAAAKLARACADEWTARTPEK 125
           +IH AYFEAGADI ETNTF++  I+ ADY  E L   IN  +AK+ARA ADE+ A+   +
Sbjct: 63  SIHRAYFEAGADIAETNTFSANRISQADYGAEHLVHAINCESAKMARAIADEFEAKDG-R 121

Query: 126 PRYVAGVLGPTNRTASISPDVNDPAFRNITFDGLVAAYRESTKALVEGGADLILIETVFD 185
           PR+VAG LGPTN+T S+SPDVNDP +R I FD L   YRE   ALVEGG D +LIETVFD
Sbjct: 122 PRFVAGALGPTNKTLSLSPDVNDPGYREIDFDHLKDVYREQIDALVEGGIDFVLIETVFD 181

Query: 186 TLNAKAAVFAVKTEFEALGVELPIMISGTITDASGRTLSGQTTEAFYNSLRHAEALTFGL 245
           TLNAKA + A     +ALG +LPIM+S T+TD SGR LSG T EAF++++RHA+ +T GL
Sbjct: 182 TLNAKAGIMAAIEAGQALGRDLPIMLSMTLTDLSGRNLSGHTVEAFWHAVRHAKPVTIGL 241

Query: 246 NCALGPDELRQYVQELSRIAECYVTAHPNAGLPNAFGEYDLDADTMAKQIREWAQAGFLN 305
           NC+ G ++LR +V+ LS + +  +  +PNAGLPN  G YD   +T A  + EWA+   +N
Sbjct: 242 NCSFGAEQLRPHVKTLSGLCDTLIMVYPNAGLPNELGAYDEAPETTAGLVGEWAEQAQVN 301

Query: 306 IVGGCCGTTPQHIAAMSRAVEGLAPRKLPEIPVACRLSGLEPLNI 350
           ++GGCCG+TP HI A++ AV GL PR +P   V  RL+GLEP  +
Sbjct: 302 VLGGCCGSTPAHIKAIADAVAGLPPRAIPVPEVRTRLAGLEPFTM 346


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: 1042
Number of extensions: 45
Number of successful extensions: 3
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: 348
Length adjustment: 38
Effective length of query: 1189
Effective length of database: 310
Effective search space:   368590
Effective search space used:   368590
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: 54 (25.4 bits)

Align candidate Ga0059261_0990 Ga0059261_0990 (methionine synthase (B12-dependent) (EC 2.1.1.13))
to HMM TIGR02082 (metH: methionine synthase (EC 2.1.1.13))

Software error:

../bin/blast/fastacmd -i /tmp/list.602.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.602.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.