GapMind for catabolism of small carbon sources

 

Alignments for a candidate for aacS in Burkholderia phytofirmans PsJN

Align acetoacetate-CoA ligase (EC 6.2.1.16) (characterized)
to candidate BPHYT_RS23420 BPHYT_RS23420 acetoacetyl-CoA synthase

Query= BRENDA::Q9Z3R3
         (650 letters)



>FitnessBrowser__BFirm:BPHYT_RS23420
          Length = 1021

 Score =  415 bits (1067), Expect = e-120
 Identities = 258/650 (39%), Positives = 338/650 (52%), Gaps = 18/650 (2%)

Query: 1   MQAERPLWVPDREIVERSPMAEFIDWCGERFGRSFADYDAFHDWSVSERGAFWTAV--WE 58
           M A  P++    E V  S M+ F        G  FADY   H +S  E   FW     W 
Sbjct: 13  MYAREPVFQNLPERVAGSRMSRFTAALENFTGERFADYPELHAYSTREFRRFWQCFLQWT 72

Query: 59  HCKVIGESGEKALVDGDRMLDARFFPEARLNFAENLLRKTGSGD---ALIFRGEDKVSYR 115
                G   E A V GD    A FFP   LN+A+++L    + D   AL  R  D     
Sbjct: 73  EGMEWGGKAEPACV-GDECETASFFPNVELNYAQSVLGSKIAPDESPALTARYADGRRET 131

Query: 116 LTWDELRALVSRLQQALRAQGIGAGDRVAAMMPNMPETIALMLATASVGAIWSSCSPDFG 175
           +T  ELR  V+RL  +L   G+  GDR  A+M N    I   LA  ++GA  S+ +P+ G
Sbjct: 132 MTRGELRERVARLACSLNELGLCPGDRAVAIMRNDAHAIIAALAVTALGATLSTAAPETG 191

Query: 176 EQGVLDRFGQIAPKLFIVCDGYWYNGKRQDVDSKVRAVAKSLGAPTVIVPYAGDSAALAP 235
            Q +LDRF  + P++               + S V AVA +L  PT+      D   L  
Sbjct: 192 VQAILDRFEPLEPRILFAHTTQRSFDTAGSIASHVAAVAAAL--PTLTHVVCLDETPLPS 249

Query: 236 TV-EGGVTLADFIAGFQAGPLVFERLPFGHPLYILFSSGTTGVPKCIVHSAGGTLLQHLK 294
           TV +   +L D I    A    + R PF HPL+I+FSSGTTG PKCIVH AGGTLL+HLK
Sbjct: 250 TVSQPQHSLRDLIVQGDAARFAWRRFPFNHPLFIMFSSGTTGKPKCIVHGAGGTLLEHLK 309

Query: 295 EHRFHCGLRDGERLFYFTTCGWMMWNWLASGLAVGATLCLYDGSPFCPDGNVLFDYAAAE 354
           EH+ H  L  G++L++ T+C WMMWNW  S LA G  +  YDG     + + L+   A E
Sbjct: 310 EHQLHSDLGPGDKLYFHTSCSWMMWNWQLSALASGVEIVTYDGP--VSEVDTLWRMVADE 367

Query: 355 RFAVFGTSAKYIDAVRKGGFTPARTHDLSSLRLMTSTGSPLSPEGFSFVYEGIKPDVQLA 414
           R  VFGTS  Y+      G  P     L +LR M STG+ L    F +V   +KP +QL 
Sbjct: 368 RVTVFGTSPAYLKMCEDAGLKPGEQFGLHALRAMMSTGAVLYDSQFEWVRAYVKP-LQLQ 426

Query: 415 SISGGTDIVSCFVLGNPLKPVWRGEIQGPGLGLAVDVWNDEGKPVRGEKGELVCTRAFPS 474
           SISGGTDI+ CFVLGNP  PV+ GE Q   LGL V  WN EG P     GELVC   FPS
Sbjct: 427 SISGGTDIIGCFVLGNPNLPVYAGEAQCRSLGLDVQAWN-EGAPT-SMTGELVCVNPFPS 484

Query: 475 MPVMFWNDPDGAKYRAAYFDRFDNVWCHGDFAEWTPHGGIVIHGRSDATLNPGGVRIGTA 534
            P+ F+ D DG+++ AAYF     VW HGD  E++  G   +HGRSD  LN  G+ +   
Sbjct: 485 RPLGFFGDADGSRFHAAYFKANPGVWTHGDIIEFSAQGSARLHGRSDGVLNVRGINVSPG 544

Query: 535 EIYNQVEQMDEVAEALCIGQDWED----DVRVVLFVRLARGVELTEALTREIKNRIRSGA 590
           EIY  V  + E+ +++ + Q   D      RVVL + L RG +++ AL   ++  +    
Sbjct: 545 EIYRIVSGIGEINQSMVVAQTTHDASGSGQRVVLLLVLRRGAKMSAALASRVRRELMLQG 604

Query: 591 SPRHVPAKIIAVADIPRTKSGKIVELAVRDVVHGRPVKNKEALANPEALD 640
           S   VP  I  V  +P T +GK  E A RD V+G PV+N  +LANP  ++
Sbjct: 605 SAALVPDVIAEVEALPVTHNGKASEAAARDAVNGLPVRNLSSLANPGCVE 654


Lambda     K      H
   0.322    0.139    0.441 

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: 1744
Number of extensions: 100
Number of successful extensions: 8
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: 650
Length of database: 1021
Length adjustment: 41
Effective length of query: 609
Effective length of database: 980
Effective search space:   596820
Effective search space used:   596820
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 (21.9 bits)
S2: 56 (26.2 bits)

Align candidate BPHYT_RS23420 BPHYT_RS23420 (acetoacetyl-CoA synthase)
to HMM TIGR01217 (acetoacetate-CoA ligase (EC 6.2.1.16))

Software error:

../bin/blast/fastacmd -i /tmp/list.24585.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.24585.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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