GapMind for Amino acid biosynthesis

 

Alignments for a candidate for metH in Acidovorax sp. GW101-3H11

Align methionine synthase (EC 2.1.1.13) (characterized)
to candidate Ac3H11_3274 5-methyltetrahydrofolate--homocysteine methyltransferase (EC 2.1.1.13)

Query= BRENDA::P13009
         (1227 letters)



>FitnessBrowser__acidovorax_3H11:Ac3H11_3274
          Length = 903

 Score = 1052 bits (2721), Expect = 0.0
 Identities = 566/908 (62%), Positives = 666/908 (73%), Gaps = 32/908 (3%)

Query: 341  RLSGLEPLNIGEDSLFVNVGERTNVTGSAKFKRLIKEEKYSEALDVARQQVENGAQIIDI 400
            +LSGLEP++IGE +LFVN+GERTNVTGS  F R+I   +Y EAL VARQQVENGAQ+IDI
Sbjct: 2    KLSGLEPVSIGEGTLFVNIGERTNVTGSKAFARMILNGQYEEALAVARQQVENGAQVIDI 61

Query: 401  NMDEGMLDAEAAMVRFLNLIAGEPDIARVPIMIDSSKWDVIEKGLKCIQGKGIVNSISMK 460
            NMDE MLD++AAMVRFL LIA EPDIARVPIM+DSSKWDVIE GL+CIQGKGIVNSISMK
Sbjct: 62   NMDEAMLDSKAAMVRFLQLIASEPDIARVPIMVDSSKWDVIEAGLRCIQGKGIVNSISMK 121

Query: 461  EGVDAFIHHAKLLRRYGAAVVVMAFDEQGQADTRARKIEICRRAYKILTEEVGFPPEDII 520
            EGV+ F H A+L+RRYGAA VVMAFDE GQADT ARKIEIC RAY++L +EVGFPPEDII
Sbjct: 122  EGVEKFKHEARLVRRYGAAAVVMAFDEVGQADTYARKIEICERAYRVLVDEVGFPPEDII 181

Query: 521  FDPNIFAVATGIEEHNNYAQDFIGACEDIKRELPHALISGGVSNVSFSFRGNDPVREAIH 580
            FDPNIFAVATGIEEHNNYA DFI A   IK+ LP A +SGGVSNVSFSFRGNDPVREAIH
Sbjct: 182  FDPNIFAVATGIEEHNNYAVDFIEATRWIKQNLPGAKVSGGVSNVSFSFRGNDPVREAIH 241

Query: 581  AVFLYYAIRNGMDMGIVNAGQLAIYDDLPAELRDAVEDVILNRRDDGTERLLELAEKYRG 640
             VFLY+AI+ GMDMGIVNAG + +YDDL   LR+ VEDV+LNRR D  ERL+E+AE  + 
Sbjct: 242  TVFLYHAIQAGMDMGIVNAGMVGVYDDLEPVLRERVEDVVLNRRADAGERLVEIAETAKS 301

Query: 641  SKTDDTANAQQAEWRSW-----EVNKRLEYSLVKGITEFIEQDTEEARQ----QATRPIE 691
               D+   +++ EWR        V +RL ++LV GIT+FI +DTEEA Q    +  RP+ 
Sbjct: 302  GAKDE---SKKLEWRGTPEHPKTVGERLSHALVHGITDFIVEDTEEAYQAIVAKGGRPLH 358

Query: 692  VIEGPLMDGMNVVGDLFGEGKMFLPQVVKSARVMKQAVAYLEPFIEASKEQG-------K 744
            VIEGPLMDGMNVVGDLFG GKMFLPQVVKSARVMK AVA+L P+IE  K Q        +
Sbjct: 359  VIEGPLMDGMNVVGDLFGAGKMFLPQVVKSARVMKSAVAHLIPYIEEEKRQDELAGRDVR 418

Query: 745  TNGKMVIATVKGDVHDIGKNIVGVVLQCNNYEIVDLGVMVPAEKILRTAKEVNADLIGLS 804
            + GK++IATVKGDVHDIGKNIV VVLQCNN+E+V++GVMVP  +IL  AK   AD++GLS
Sbjct: 419  SKGKIIIATVKGDVHDIGKNIVTVVLQCNNFEVVNMGVMVPCHEILARAKVEGADIVGLS 478

Query: 805  GLITPSLDEMVNVAKEMERQGF----TIPLLIGGATTSKAHTAVKIEQNYSGPTVYVQNA 860
            GLITPSL+EM  VA EM++        IPLLIGGATTS+ HTAVKI  +Y GP VYV +A
Sbjct: 479  GLITPSLEEMQYVAGEMQKDDHFRIKKIPLLIGGATTSRVHTAVKIAPHYEGPVVYVPDA 538

Query: 861  SRTVGVVAALLSDTQRDDFVARTRKEYETVRIQHGRKKPRTPPVTLEAARDNDFAFDWQA 920
            SR+V V  +LL D  + ++V     +YE VR QH  KK +TP  +LE AR N    ++  
Sbjct: 539  SRSVSVAQSLLGDGVQ-NYVQELNADYEKVRTQHANKK-QTPMWSLEKARANRTPVNFST 596

Query: 921  YTPPVAHRLGVQEVE-ASIETLRNYIDWTPFFMTWSLAGKYPRILEDEVVGVEAQRLFKD 979
            Y PP    LG +  +   +  L  YIDW PFF TW LAG YP IL DEVVGVEA R+F D
Sbjct: 597  YVPPTPRLLGRRVFKNFDLAELAKYIDWGPFFQTWDLAGPYPAILTDEVVGVEATRVFAD 656

Query: 980  ANDMLDKLSAEKTLNPRGVVGLFPANRVGDDIEIYRDETRTHVINVSHHLRQQTEKTGF- 1038
               ML KL   + L+  GV+ L+PAN VGDDIE Y DETRT V    + +RQQTEK    
Sbjct: 657  GQAMLKKLIEGRWLSASGVMALYPANSVGDDIEFYTDETRTQVAMTWYGMRQQTEKQMID 716

Query: 1039 ----ANYCLADFVAPKLSGKADYIGAFAVTGGLEEDALADAFEAQHDDYNKIMVKALADR 1094
                 + CLADFVAPK SG ADY G FAVT GL  +    AF    DDY+ IM+K+LADR
Sbjct: 717  GVMRPSRCLADFVAPKDSGIADYAGLFAVTAGLGVEKKEQAFVDALDDYSAIMLKSLADR 776

Query: 1095 LAEAFAEYLHERVRKVYWGYAPNENLSNEELIRENYQGIRPAPGYPACPEHTEKATIWEL 1154
            LAEAFAE LH+RVR   WGYA  E LSN+E+I E Y GIRPAPGYPACP+H+ K  ++ +
Sbjct: 777  LAEAFAECLHQRVRTDLWGYAAGEQLSNDEMIAEKYAGIRPAPGYPACPDHSAKQELFRV 836

Query: 1155 LEVEKHTGMKLTESFAMWPGASVSGWYFSHPDSKYYAVAQIQRDQVEDYARRKGMSVTEV 1214
            L+ E+  GM LTES AM P ASVSG+Y  HPDS Y+ V +I  DQ+ D A R+GM    +
Sbjct: 837  LQCEE-IGMGLTESLAMTPAASVSGFYIGHPDSVYFNVGKIGEDQLHDMAERRGMDEKVL 895

Query: 1215 ERWLAPNL 1222
            ER LAPNL
Sbjct: 896  ERLLAPNL 903


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: 2674
Number of extensions: 118
Number of successful extensions: 11
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 1
Length of query: 1227
Length of database: 903
Length adjustment: 45
Effective length of query: 1182
Effective length of database: 858
Effective search space:  1014156
Effective search space used:  1014156
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 Ac3H11_3297 5-methyltetrahydrofolate--homocysteine methyltransferase (EC 2.1.1.13)

Query= BRENDA::P13009
         (1227 letters)



>FitnessBrowser__acidovorax_3H11:Ac3H11_3297
          Length = 354

 Score =  371 bits (953), Expect = e-107
 Identities = 186/344 (54%), Positives = 253/344 (73%), Gaps = 15/344 (4%)

Query: 3   SKVEQLRAQLNERILVLDGGMGTMIQSYRLNEADFRGE----------RFADWPCDLKGN 52
           ++  QL   L +RI++LDG MGTMIQ ++L EA +RGE          RF D+  D+KGN
Sbjct: 7   TRAAQLPDILAQRIVILDGAMGTMIQRFKLGEAQYRGEGYTGPGKAGDRFKDFAYDVKGN 66

Query: 53  NDLLVLSKPEVIAAIHNAYFEAGADIIETNTFNSTTIAMADYQMESLSAEINFAAAKLAR 112
           N+LL L++P+VI+ IH  Y  AGAD+IETNTF +TTIA  DY M +L+ E+N  +A+LAR
Sbjct: 67  NELLSLTRPDVISDIHERYLAAGADLIETNTFGATTIAQEDYHMANLAREMNLRSAELAR 126

Query: 113 ACADEWTARTPEKPRYVAGVLGPTNRTASISPDVNDPAFRNITFDGLVAAYRESTKALVE 172
           A  D+++  TP+KPR+VAG LGPT +TASISPDVNDP  RN+ F+ L AAY E T+ALVE
Sbjct: 127 AACDKYS--TPDKPRFVAGALGPTPKTASISPDVNDPGARNVDFEALRAAYYEQTEALVE 184

Query: 173 GGADLILIETVFDTLNAKAAVFAVKTEFEALGVELPIMISGTITDASGRTLSGQTTEAFY 232
           GG+D++L+ET+FDTLNAKAA+FA+   FE  G  LP++ISGT+TDASGR LSGQT  AF+
Sbjct: 185 GGSDVLLVETIFDTLNAKAALFAIDEYFENSGQRLPLIISGTVTDASGRILSGQTVTAFW 244

Query: 233 NSLRHAEALTFGLNCALGPDELRQYVQELSRIAE-CYVTAHPNAGLPNAFGE--YDLDAD 289
           +S+RH+  L  GLNCALG   +R Y+QEL+R+AE  +++ +PNAGLPN   +  +D   +
Sbjct: 245 HSVRHSRPLAIGLNCALGATLMRPYIQELNRVAEDTFISCYPNAGLPNPMSDTGFDETPE 304

Query: 290 TMAKQIREWAQAGFLNIVGGCCGTTPQHIAAMSRAVEGLAPRKL 333
             ++ + E+A  G +NI+GGCCGTTP HI A+++AVE +  RK+
Sbjct: 305 ITSRLVHEFAAEGLVNILGGCCGTTPDHIGAIAKAVESVPTRKM 348


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: 1007
Number of extensions: 32
Number of successful extensions: 5
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: 354
Length adjustment: 38
Effective length of query: 1189
Effective length of database: 316
Effective search space:   375724
Effective search space used:   375724
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 Ac3H11_3274 (5-methyltetrahydrofolate--homocysteine methyltransferase (EC 2.1.1.13))
to HMM TIGR02082 (metH: methionine synthase (EC 2.1.1.13))

Software error:

../bin/blast/fastacmd -i /tmp/list.26171.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.26171.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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