GapMind for Amino acid biosynthesis

 

Alignments for a candidate for metH in Burkholderia phytofirmans PsJN

Align methionine synthase (EC 2.1.1.13) (characterized)
to candidate BPHYT_RS02305 BPHYT_RS02305 methionine synthase

Query= BRENDA::P13009
         (1227 letters)



>FitnessBrowser__BFirm:BPHYT_RS02305
          Length = 902

 Score = 1060 bits (2741), Expect = 0.0
 Identities = 559/904 (61%), Positives = 664/904 (73%), Gaps = 27/904 (2%)

Query: 341  RLSGLEPLNIGEDSLFVNVGERTNVTGSAKFKRLIKEEKYSEALDVARQQVENGAQIIDI 400
            RLSGLEP N+   +LF+NVGERTNVTGS  F R+I  +++ EA+ VARQQVENGAQ+ID+
Sbjct: 4    RLSGLEPFNVTSGTLFINVGERTNVTGSKAFARMILNDQFDEAVAVARQQVENGAQVIDV 63

Query: 401  NMDEGMLDAEAAMVRFLNLIAGEPDIARVPIMIDSSKWDVIEKGLKCIQGKGIVNSISMK 460
            NMDE MLD++AAMVRF+NLIA EPDIARVPIMIDSSKW+VIE GLKC+QGK IVNSIS+K
Sbjct: 64   NMDEAMLDSKAAMVRFMNLIASEPDIARVPIMIDSSKWEVIEAGLKCVQGKAIVNSISLK 123

Query: 461  EGVDAFIHHAKLLRRYGAAVVVMAFDEQGQADTRARKIEICRRAYKILTEEVGFPPEDII 520
            EG +AF HHA L+RRYGAA VVMAFDEQGQADT  RK +IC+R+Y  L  EVGFPPEDII
Sbjct: 124  EGEEAFRHHANLIRRYGAAAVVMAFDEQGQADTFERKTQICKRSYDFLVNEVGFPPEDII 183

Query: 521  FDPNIFAVATGIEEHNNYAQDFIGACEDIKRELPHALISGGVSNVSFSFRGNDPVREAIH 580
            FDPNIFA+ATGIEEHNNYA DFI A   IK  LP+A +SGGVSNVSFSFRGNDPVREAIH
Sbjct: 184  FDPNIFAIATGIEEHNNYAVDFINATRWIKENLPYAKVSGGVSNVSFSFRGNDPVREAIH 243

Query: 581  AVFLYYAIRNGMDMGIVNAGQLAIYDDLPAELRDAVEDVILNRRDDGTERLLELAEKYRG 640
             VFLY+AI+ GMDMGIVNAGQL +Y DL  ELR+ VEDV+LNRR+DGT+RLLE+A+K+  
Sbjct: 244  TVFLYHAIQAGMDMGIVNAGQLGVYADLDPELRERVEDVVLNRREDGTDRLLEIADKF-- 301

Query: 641  SKTDDTANAQQAEWRSWEVNKRLEYSLVKGITEFIEQDTEEAR----QQATRPIEVIEGP 696
             KT      +  EWR+  V KRL ++LV GIT FI +DTEE R     +  RPI VIEGP
Sbjct: 302  -KTGAAKKEENLEWRNQPVEKRLSHALVHGITNFIVEDTEEVRAKIAAEGGRPINVIEGP 360

Query: 697  LMDGMNVVGDLFGEGKMFLPQVVKSARVMKQAVAYLEPFIEASK----EQG---KTNGKM 749
            LMDGMN+VGDLFG+GKMFLPQVVKSARVMKQAVA+L P+IE  K    E G   +  GK+
Sbjct: 361  LMDGMNIVGDLFGQGKMFLPQVVKSARVMKQAVAHLIPYIEEEKKLLAEAGADVRAKGKI 420

Query: 750  VIATVKGDVHDIGKNIVGVVLQCNNYEIVDLGVMVPAEKILRTAKEVNADLIGLSGLITP 809
            VIATVKGDVHDIGKNIV VVLQCNN+E+V++GVMV    IL  AK   AD+IGLSGLITP
Sbjct: 421  VIATVKGDVHDIGKNIVSVVLQCNNFEVVNMGVMVSCNDILAKAKVEGADIIGLSGLITP 480

Query: 810  SLDEMVNVAKEMERQGF----TIPLLIGGATTSKAHTAVKIEQNYSGPTVYVQNASRTVG 865
            SL+EM  VA EM+R  +     IPLLIGGATTS+ HTAVKI  +Y GP VYV +ASR+V 
Sbjct: 481  SLEEMAYVASEMQRDDYFRVKKIPLLIGGATTSRVHTAVKIAPHYEGPVVYVPDASRSVS 540

Query: 866  VVAALLSDTQRDDFVARTRKEYETVRIQHGRKKPRTPPVTLEAARDNDFAFDWQAYTPPV 925
            V ++LLSD     ++   + +YE +R+QH  KK   P VTL  AR N    DW +Y P  
Sbjct: 541  VASSLLSDEGAAKYLDELKSDYERIRVQHANKK-ALPMVTLAEARANKTKVDWASYQPVK 599

Query: 926  AHRLGVQEVE-ASIETLRNYIDWTPFFMTWSLAGKYPRILEDEVVGVEAQRLFKDANDML 984
               +G +  +   +  L NYIDW PFF TW LAG YP IL DE+VG  A+R+F D   ML
Sbjct: 600  PKFIGRRVFKNFDLSELANYIDWGPFFQTWDLAGPYPAILNDEIVGESARRVFSDGKSML 659

Query: 985  DKLSAEKTLNPRGVVGLFPANRVG-DDIEIYRDETRTHVINVSHHLRQQTEKTGF----- 1038
             +L   + L   GV+ L PAN V  DDIEIY DE+R+ V     +LRQQ+ +        
Sbjct: 660  ARLIQGRWLQANGVIALLPANTVNDDDIEIYTDESRSEVALTWRNLRQQSVRPVVDGVMR 719

Query: 1039 ANYCLADFVAPKLSGKADYIGAFAVTGGLEEDALADAFEAQHDDYNKIMVKALADRLAEA 1098
             N  LADF+APK SG ADYIG FAVT GL  D     FE  HDDY+ IM+KALADR AEA
Sbjct: 720  PNRSLADFIAPKDSGVADYIGMFAVTAGLGVDVKEKQFEKDHDDYSAIMLKALADRFAEA 779

Query: 1099 FAEYLHERVRKVYWGYAPNENLSNEELIRENYQGIRPAPGYPACPEHTEKATIWELLEVE 1158
            FAE LH RVR+  WGYA  E LSN++LI E Y GIRPAPGYPACP+H  K  ++++L   
Sbjct: 780  FAEALHARVRRDLWGYANAETLSNDDLIAEKYHGIRPAPGYPACPDHLVKRDMFDVLHAT 839

Query: 1159 KHTGMKLTESFAMWPGASVSGWYFSHPDSKYYAVAQIQRDQVEDYARRKGMSVTEVERWL 1218
            +  GM +TES AM P ASVSG+Y +HPDS Y++V +I +DQ+EDYA+R  +S T+ ER L
Sbjct: 840  E-IGMSVTESLAMLPAASVSGFYLAHPDSTYFSVGKIGQDQLEDYAKRMSLSKTDAERAL 898

Query: 1219 APNL 1222
            AP L
Sbjct: 899  APLL 902


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: 2609
Number of extensions: 113
Number of successful extensions: 10
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: 902
Length adjustment: 45
Effective length of query: 1182
Effective length of database: 857
Effective search space:  1012974
Effective search space used:  1012974
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: 58 (26.9 bits)

Align methionine synthase (EC 2.1.1.13) (characterized)
to candidate BPHYT_RS02310 BPHYT_RS02310 5-methyltetrahydrofolate--homocysteine methyltransferase

Query= BRENDA::P13009
         (1227 letters)



>FitnessBrowser__BFirm:BPHYT_RS02310
          Length = 356

 Score =  402 bits (1032), Expect = e-116
 Identities = 202/330 (61%), Positives = 257/330 (77%), Gaps = 6/330 (1%)

Query: 8   LRAQLNERILVLDGGMGTMIQSYRLNEADFRGERFADWPCDLKGNNDLLVLSKPEVIAAI 67
           L A L  RIL+LDG MGTMIQ Y+L+EA +RGERF D+  D+KGNN+LL +++P++I  I
Sbjct: 23  LPALLKSRILILDGAMGTMIQRYKLDEARYRGERFKDYGRDIKGNNELLSITQPQIIREI 82

Query: 68  HNAYFEAGADIIETNTFNSTTIAMADYQMESLSAEINFAAAKLARACADEWTARTPEKPR 127
           H  Y  AGADIIETNTF +TT+A ADY ME L+ E+N  +AKLARA  D+++  TP+KPR
Sbjct: 83  HEQYLAAGADIIETNTFGATTVAQADYGMEGLAIEMNLESAKLARAACDKYS--TPDKPR 140

Query: 128 YVAGVLGPTNRTASISPDVNDPAFRNITFDGLVAAYRESTKALVEGGADLILIETVFDTL 187
           +VAG +GPT +TASISPDVNDP  RN+TFD L AAY E  KAL++GGADL L+ET+FDTL
Sbjct: 141 FVAGAIGPTPKTASISPDVNDPGARNVTFDELRAAYYEQAKALLDGGADLFLVETIFDTL 200

Query: 188 NAKAAVFAVKTEFEALGVELPIMISGTITDASGRTLSGQTTEAFYNSLRHAEALTFGLNC 247
           NAKAA+FA+   FE  G  LPIMISGT+TDASGR LSGQT EAF+NSLRHA+ LTFGLNC
Sbjct: 201 NAKAALFALDELFEDTGERLPIMISGTVTDASGRILSGQTVEAFWNSLRHAKPLTFGLNC 260

Query: 248 ALGPDELRQYVQELSRIAECYVTAHPNAGLPNAF---GEYDLDADTMAKQIREWAQAGFL 304
           ALG   +R Y+ EL+++ + YV+ +PNAGLPN     G  +L ADT +  ++E+AQAG +
Sbjct: 261 ALGAALMRPYIAELAKLCDTYVSCYPNAGLPNPMSDTGFDELPADT-SGLLKEFAQAGLV 319

Query: 305 NIVGGCCGTTPQHIAAMSRAVEGLAPRKLP 334
           NI GGCCGTTP+HIAA+++A+  + PR+ P
Sbjct: 320 NIAGGCCGTTPEHIAAIAQALAEVKPRQWP 349


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: 1028
Number of extensions: 29
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: 356
Length adjustment: 38
Effective length of query: 1189
Effective length of database: 318
Effective search space:   378102
Effective search space used:   378102
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 BPHYT_RS02305 BPHYT_RS02305 (methionine synthase)
to HMM TIGR02082 (metH: methionine synthase (EC 2.1.1.13))

Software error:

../bin/blast/fastacmd -i /tmp/list.16452.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.16452.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.