GapMind for catabolism of small carbon sources

 

Alignments for a candidate for mmsA in Burkholderia phytofirmans PsJN

Align malonate-semialdehyde dehydrogenase (EC 1.2.1.15); malonate-semialdehyde dehydrogenase (acetylating) (EC 1.2.1.18); methylmalonate-semialdehyde dehydrogenase (CoA-acylating) (EC 1.2.1.27) (characterized)
to candidate BPHYT_RS28825 BPHYT_RS28825 methylmalonate-semialdehyde dehydrogenase

Query= BRENDA::A0A081YAY7
         (498 letters)



>FitnessBrowser__BFirm:BPHYT_RS28825
          Length = 507

 Score =  609 bits (1570), Expect = e-179
 Identities = 306/491 (62%), Positives = 374/491 (76%), Gaps = 4/491 (0%)

Query: 6   HLIGGELIADT-GRTADVFNPSTGEAVRKVPLADRETMQQAIDAAKAAFPAWRNTPPAKR 64
           H IGG   A T GR  DVFNP+TG+    V LA  E +  A+ AA+AAFPAW  T P KR
Sbjct: 17  HYIGGAPAAPTSGRFKDVFNPATGKVTGSVALASVEEVDAAVQAARAAFPAWSETAPLKR 76

Query: 65  AQVLFRFKQLLEANEERIVKLISEEHGKTIEDAAGELKRGIENVEYATAAPEILKGEYSR 124
           A++LFRFK+LL  + + +  LI+ EHGK   DA GE+ RGIE VE+A   P +LK +++ 
Sbjct: 77  ARILFRFKELLNQHHDELAMLITREHGKVFTDAQGEVVRGIEVVEFACGIPNLLKTDFTD 136

Query: 125 NVGPNIDAWSDFQPIGVVAGITPFNFPAMVPLWMYPLAIACGNTFILKPSERDPSSTLLI 184
            +G  ID W+  Q +GVVAGITPFNFP MVP+WM+P+A+ACGNTF+LKPSERDPS++L +
Sbjct: 137 QIGGGIDNWNLRQALGVVAGITPFNFPVMVPMWMFPVALACGNTFVLKPSERDPSASLRL 196

Query: 185 AELFHEAGLPKGVLNVVHGDKGAVDALIEAPEVKALSFVGSTPIAEYIYSEGTKRGKRVQ 244
           AEL  EAGLP GV NVV+GDK AVDALI+ P+V ALSFVGSTPIAEYI++E +KRGKRVQ
Sbjct: 197 AELLKEAGLPDGVFNVVNGDKVAVDALIDHPDVAALSFVGSTPIAEYIHTEASKRGKRVQ 256

Query: 245 ALGGAKNHAVLMPDADLDNAVSALMGAAYGSCGERCMAISVAVCVGDQIADALVQKLVPQ 304
           ALGGAKNH V+MPDADLD AV AL+GAAYGS GERCMAISVAV VG+ +AD L++KLVP+
Sbjct: 257 ALGGAKNHLVVMPDADLDQAVDALIGAAYGSAGERCMAISVAVAVGN-VADKLIEKLVPR 315

Query: 305 IKGLKIGAGTSCGLDMGPLVTGAARDKVTGYIDTGVAQGAELVVDGRGYKVAGHENGFFL 364
           +K L I  G     +MGPLVT   + KVTGYI +G A+GA+L+VDGR + V  +E GFF+
Sbjct: 316 VKSLVIKNGEHLDAEMGPLVTAEHKAKVTGYIASGEAEGAKLIVDGRAHPVT-NEEGFFV 374

Query: 365 GGTLFDRVTPEMTIYKEEIFGPVLCIVRVNSLEEAMQLINDHEYGNGTCIFTRDGEAARL 424
           GGTLFD V  EM IYKEEIFGPVL +VRV     A+ LIN HE+GNG  +FT DG  AR 
Sbjct: 375 GGTLFDHVGTEMKIYKEEIFGPVLAVVRVPDFASAVDLINAHEFGNGVSLFTSDGGVARA 434

Query: 425 FCDEIEVGMVGVNVPLPVPVAYHSFGGWKRSLFGDLHAYGPDGVRFYTKRKAITQRWPQR 484
           F  +I+VGMVG+NVP+PVP+A+HSFGGWKRSLFGD HAYG +GVRFYT+ K+I QRWP  
Sbjct: 435 FGRQIQVGMVGINVPIPVPMAWHSFGGWKRSLFGDHHAYGEEGVRFYTRYKSIMQRWPDS 494

Query: 485 KSHEAAQFAFP 495
            + + A+F  P
Sbjct: 495 IA-KGAEFTMP 504


Lambda     K      H
   0.319    0.137    0.411 

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: 783
Number of extensions: 26
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: 498
Length of database: 507
Length adjustment: 34
Effective length of query: 464
Effective length of database: 473
Effective search space:   219472
Effective search space used:   219472
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 52 (24.6 bits)

Align candidate BPHYT_RS28825 BPHYT_RS28825 (methylmalonate-semialdehyde dehydrogenase)
to HMM TIGR01722 (mmsA: methylmalonate-semialdehyde dehydrogenase (acylating) (EC 1.2.1.27))

Software error:

../bin/blast/fastacmd -i /tmp/list.8477.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.8477.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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