GapMind for Amino acid biosynthesis

 

Alignments for a candidate for metH in Pedobacter sp. GW460-11-11-14-LB5

Align methionine synthase (EC 2.1.1.13) (characterized)
to candidate CA265_RS23440 CA265_RS23440 methionine synthase

Query= BRENDA::P13009
         (1227 letters)



>FitnessBrowser__Pedo557:CA265_RS23440
          Length = 1233

 Score = 1476 bits (3822), Expect = 0.0
 Identities = 741/1235 (60%), Positives = 927/1235 (75%), Gaps = 22/1235 (1%)

Query: 8    LRAQLNERILVLDGGMGTMIQSYRLNEADFRGERFADWPCDLKGNNDLLVLSKPEVIAAI 67
            +R +L +RILV+DG MGTMIQ Y L E DFRGERF + PCD+KGNNDLL +++P++I  I
Sbjct: 3    IREELEKRILVIDGAMGTMIQRYTLTEEDFRGERFKNHPCDVKGNNDLLNITRPDIIKTI 62

Query: 68   HNAYFEAGADIIETNTFNSTTIAMADYQMESLSAEINFAAAKLARACADEWTARTPEKPR 127
            H  Y  +GADIIETNTF++  I+MADYQME LS E++F  A++A+   +E+ A  P++  
Sbjct: 63   HLEYLASGADIIETNTFSTQRISMADYQMEDLSYEMSFEGARVAKEAVNEFMAANPDRKC 122

Query: 128  YVAGVLGPTNRTASISPDVNDPAFRNITFDGLVAAYRESTKALVEGGADLILIETVFDTL 187
            +VAG +GPTNRT S+SP+VNDP FR + FD L AAY E  + LV+GG+D++LIET+FDTL
Sbjct: 123  FVAGAIGPTNRTLSMSPNVNDPGFRAVYFDELEAAYYEQVRGLVDGGSDVLLIETIFDTL 182

Query: 188  NAKAAVFAVKTEFEALGVELPIMISGTITDASGRTLSGQTTEAFYNSLRHAEALTFGLNC 247
            NAK A+ A+K   E +G +L IMISGTITDASGRTLSGQT EAF NS+ HA+ L+ G NC
Sbjct: 183  NAKVAIVAIKKYEEVIGRKLEIMISGTITDASGRTLSGQTAEAFLNSVMHAKPLSIGFNC 242

Query: 248  ALGPDELRQYVQELSRIAECYVTAHPNAGLPNAFGEYDLDADTMAKQIREWAQAGFLNIV 307
            ALG  E+R +++EL+  A CYV+A+PNAGLPN FG YD      A  + ++  +GF+NIV
Sbjct: 243  ALGAKEMRPHIEELAAKAGCYVSAYPNAGLPNEFGAYDEQPHETAHLVDDFIASGFVNIV 302

Query: 308  GGCCGTTPQHIAAMSRAVEGLAPRKLPEIPVACRLSGLEPLNIGEDSLFVNVGERTNVTG 367
            GGCCGTTP+HI  +++      PRK+P +    RLSGLEP+ I  +S+FVN+GERTN+TG
Sbjct: 303  GGCCGTTPEHIGCIAKNARKAEPRKIPVLEPYMRLSGLEPVTITPESIFVNIGERTNITG 362

Query: 368  SAKFKRLIKEEKYSEALDVARQQVENGAQIIDINMDEGMLDAEAAMVRFLNLIAGEPDIA 427
            S KF +LI    Y  AL VA QQVE GAQ+ID+NMDEGMLD+EAAM +FLNLIA EPDIA
Sbjct: 363  SPKFSKLILGGDYEAALAVALQQVEGGAQVIDVNMDEGMLDSEAAMTKFLNLIASEPDIA 422

Query: 428  RVPIMIDSSKWDVIEKGLKCIQGKGIVNSISMKEGVDAFIHHAKLLRRYGAAVVVMAFDE 487
            ++PIM+DSSKW VIE GLKC+QGKGIVNSIS+KEG D F   A+ + +YGAAVVVMAFDE
Sbjct: 423  KLPIMVDSSKWSVIENGLKCLQGKGIVNSISLKEGEDKFRESARKIMQYGAAVVVMAFDE 482

Query: 488  QGQADTRARKIEICRRAYKILTEEVGFPPEDIIFDPNIFAVATGIEEHNNYAQDFIGACE 547
            QGQAD   R+ EIC+R+Y IL  E+GFP EDIIFDPNI  VATG+EEHNNYA DFI A  
Sbjct: 483  QGQADNYERRKEICKRSYDILVNEIGFPAEDIIFDPNILTVATGLEEHNNYAVDFINATR 542

Query: 548  DIKRELPHALISGGVSNVSFSFRGNDPVREAIHAVFLYYAIRNGMDMGIVNAGQLAIYDD 607
             IK  LPHA +SGGVSN+SFSFRGN+ VREA+H+ FLY+AI+ G+DMGIVNAG L +Y +
Sbjct: 543  WIKENLPHAKVSGGVSNISFSFRGNNTVREAMHSAFLYHAIQAGLDMGIVNAGMLEVYQE 602

Query: 608  LPAELRDAVEDVILNRRDDGTERLLELAEKYRGSKTDDTANAQQAEWRSWEVNKRLEYSL 667
            +P EL + VEDV+LNRRDD TERL+E A+     K+      +  EWR   V +RL +SL
Sbjct: 603  IPPELLERVEDVLLNRRDDATERLVEYADTV---KSKGKEVVKDEEWRKGSVEERLSHSL 659

Query: 668  VKGITEFIEQDTEEARQQATRPIEVIEGPLMDGMNVVGDLFGEGKMFLPQVVKSARVMKQ 727
            VKGI E+++ D EEARQ+  RPI+VIEGPLMDGMN+VGDLFG GKMFLPQVVKSARVMK+
Sbjct: 660  VKGIVEYLDDDVEEARQKYARPIQVIEGPLMDGMNIVGDLFGAGKMFLPQVVKSARVMKK 719

Query: 728  AVAYLEPFIEASK------EQGKTNGKMVIATVKGDVHDIGKNIVGVVLQCNNYEIVDLG 781
            AVAYL PFIE  K      +Q  + G++++ATVKGDVHDIGKNIVGVVL CNN+EIVD+G
Sbjct: 720  AVAYLLPFIEQEKLDNPDQDQNSSAGRVLMATVKGDVHDIGKNIVGVVLACNNFEIVDMG 779

Query: 782  VMVPAEKILRTAKEVNADLIGLSGLITPSLDEMVNVAKEMERQGFTIPLLIGGATTSKAH 841
            VMVPA++I++ AKE+NAD+IGLSGLITPSLDEMV+ AKEMER+GFTIPL+IGGATTS+ H
Sbjct: 780  VMVPAQEIIKKAKEINADIIGLSGLITPSLDEMVHFAKEMEREGFTIPLIIGGATTSRIH 839

Query: 842  TAVKIEQNYSGPTVYVQNASRTVGVVAALLSDTQRDDFVARTRKEYETVRIQHGRKKPRT 901
             AVK+  NYSGP ++V +ASR+V V + L++   +D++VA  R EY+  R  H  K+   
Sbjct: 840  AAVKVAPNYSGPAIHVLDASRSVTVCSTLMNPETKDEYVAGIRAEYDKAREAHLNKRSDK 899

Query: 902  PPVTLEAARDNDFAFDWQAYTPPVAHRLGVQEVE-ASIETLRNYIDWTPFFMTWSLAGKY 960
               TLE AR+N F  D+Q    PV    G +  +   +E L  YIDWTPFF TW L G Y
Sbjct: 900  RFKTLEEARENRFKIDFQP-NLPVPEFTGTRVFDNYPLEELVPYIDWTPFFHTWELRGSY 958

Query: 961  PRILEDEVVGVEAQRLFKDANDMLDKLSAEKTLNPRGVVGLFPANRVGDDIEIYRD---- 1016
            P+I +D+ VG EA++LF DA  +L ++  EK L  R V+G +PAN VGDDI++  D    
Sbjct: 959  PKIFDDKNVGDEAKKLFDDAQTLLKRILDEKLLTARAVIGFWPANTVGDDIQLTVDSSQL 1018

Query: 1017 ------ETRTHVINVSHHLRQQTEKT-GFANYCLADFVAPKLSGKADYIGAFAVTGGLEE 1069
                  +T    +   H LRQQ EK  G   Y L+DF+APK SG  DY G FAVT G+  
Sbjct: 1019 SNDSKLKTENSQLVTIHTLRQQAEKVDGQPYYALSDFIAPKESGIQDYFGGFAVTAGIGI 1078

Query: 1070 DALADAFEAQHDDYNKIMVKALADRLAEAFAEYLHERVRKVYWGYAPNENLSNEELIREN 1129
            D L + FE+ +DDYN IM KALADRLAEAFAE +HERVRK YWGYA +ENLSN+ELI+E 
Sbjct: 1079 DELVNEFESNYDDYNSIMAKALADRLAEAFAERMHERVRKEYWGYAQDENLSNQELIKEE 1138

Query: 1130 YQGIRPAPGYPACPEHTEKATIWELLEVEKHTGMKLTESFAMWPGASVSGWYFSHPDSKY 1189
            Y GIRPAPGYPACPEHTEK T+++LL+ E   G+ LTES+AM+P A+VSG+YF+HPDS+Y
Sbjct: 1139 YAGIRPAPGYPACPEHTEKGTLFQLLDAENKIGLHLTESYAMYPTAAVSGFYFAHPDSRY 1198

Query: 1190 YAVAQIQRDQVEDYARRKGMSVTEVERWLAPNLGY 1224
            + + +I +DQ+EDYA RK M V EVERWL+PNL Y
Sbjct: 1199 FGLGKITKDQIEDYAIRKNMPVEEVERWLSPNLAY 1233


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: 3661
Number of extensions: 153
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: 1233
Length adjustment: 47
Effective length of query: 1180
Effective length of database: 1186
Effective search space:  1399480
Effective search space used:  1399480
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 CA265_RS23440 CA265_RS23440 (methionine synthase)
to HMM TIGR02082 (metH: methionine synthase (EC 2.1.1.13))

Software error:

../bin/blast/fastacmd -i /tmp/list.17694.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.17694.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.