GapMind for catabolism of small carbon sources

 

Alignments for a candidate for aacS in Cupriavidus basilensis 4G11

Align acetoacetate-CoA ligase (EC 6.2.1.16) (characterized)
to candidate RR42_RS10085 RR42_RS10085 acetoacetyl-CoA synthase

Query= BRENDA::Q9Z3R3
         (650 letters)



>FitnessBrowser__Cup4G11:RR42_RS10085
          Length = 1020

 Score =  441 bits (1134), Expect = e-128
 Identities = 267/652 (40%), Positives = 346/652 (53%), Gaps = 25/652 (3%)

Query: 6   PLWVPDREIVERSPMAEFIDWCGERFGRSFADYDAFHDWSVSERGAFWTAV--WEHCKVI 63
           P++    E    S M  F        G+ F DYD  HD+SV E   FW     W H    
Sbjct: 10  PIYGSTSERAAASQMTAFTTALQAYTGQVFGDYDTLHDFSVREYRTFWQCFVQWSHGLAW 69

Query: 64  GESGEKALVDGDRMLDARFFPEARLNFAENLLRKTGSGD---ALIFRGEDKVSYRLTWDE 120
             S E   V GD    ARFFP+ +LN+A+NLL +  +     AL     D    RLT  E
Sbjct: 70  SGSTEPVCV-GDECEHARFFPQVQLNYADNLLGQAVAAPDTPALTACHADGRRVRLTRGE 128

Query: 121 LRALVSRLQQALRAQGIGAGDRVAAMMPNMPETIALMLATASVGAIWSSCSPDFGEQGVL 180
           LR  V+RL  AL   G+  GDRV  +M N  + +   LA  ++GA  S+ + +   + +L
Sbjct: 129 LRNRVARLAHALSELGLRDGDRVVGVMRNDADAVVAALAVTALGATLSTAAAEMSVETIL 188

Query: 181 DRFGQIAPKLFIVCDGYWYNGKRQDVDSKVRAVAKSLGAPTVIVPYAGDSAALAPTVEGG 240
           DRF  +AP+L               +   V  +A +L +   +V    D   L  TV+  
Sbjct: 189 DRFAPLAPRLLFAHVAEREFDTGMSLADNVADLAAALPSLQGVVRL--DDGTLPGTVKQR 246

Query: 241 V-TLADFIAGFQAGPLVFERLPFGHPLYILFSSGTTGVPKCIVHSAGGTLLQHLKEHRFH 299
           + +L + I    AG  V+ R PF HPL+I+FSSGTTG PKCIVH AGG+LL+HLKEHR H
Sbjct: 247 IYSLGELIDSGDAGSFVWRRFPFNHPLFIMFSSGTTGKPKCIVHGAGGSLLEHLKEHRLH 306

Query: 300 CGLRDGERLFYFTTCGWMMWNWLASGLAVGATLCLYDGSPFCPDGNVLFDYAAAERFAVF 359
           C LR G+RL++ TTC WMMWNW  S LA GA +  YDG     D   L+   A ER  VF
Sbjct: 307 CDLRPGDRLYFHTTCAWMMWNWQLSALASGAEIVTYDGPISTVD--ALWRLVADERVTVF 364

Query: 360 GTSAKYIDAVRKGGFTPARTHDLSSLRLMTSTGSPLSPEGFSFVYEGIKPDVQLASISGG 419
           GTS  Y+      G  P +  DL +LR M STG+ L    F +V + +KP + L SISGG
Sbjct: 365 GTSPAYLKMCEDAGLVPGQQFDLGALRAMMSTGAVLFDAQFEWVRDHVKP-LPLQSISGG 423

Query: 420 TDIVSCFVLGNPLKPVWRGEIQGPGLGLAVDVWNDEGKPVRGEKGELVCTRAFPSMPVMF 479
           TDI+ CFVLGNP  P++ GE Q   L L V  W       R   GELVC   FPS P+ F
Sbjct: 424 TDILGCFVLGNPNLPIYAGEAQCKSLALDVQAWEQGAHTSR--IGELVCANPFPSRPLGF 481

Query: 480 WNDPDGAKYRAAYFDRFDNVWCHGDFAEWTPHGGIVIHGRSDATLNPGGVRIGTAEIYNQ 539
           + D DG  + AAYF R   VW HGD  E++P G   +HGRSD  LN  G+ +G  EIY  
Sbjct: 482 FGDMDGKGFHAAYFTRNPGVWTHGDRIEFSPEGTARLHGRSDGILNVRGINVGPGEIYRV 541

Query: 540 VEQMDEVAEALCIGQ-----------DWEDDVRVVLFVRLARGVELTEALTREIKNRIRS 588
           +  + ++ EAL + Q               D R+VL + L  GV LT AL   ++  +  
Sbjct: 542 LSDIRDIREALVVEQRSCAAPPDRTHAERYDQRIVLLLVLQDGVALTGALATRVRRDLAR 601

Query: 589 GASPRHVPAKIIAVADIPRTKSGKIVELAVRDVVHGRPVKNKEALANPEALD 640
            ASP HVP  IIAV ++P T +GK+ E A R+ ++G PV N  AL NP  LD
Sbjct: 602 RASPAHVPDLIIAVDELPVTHNGKLSEAAARNAINGLPVGNAAALRNPGCLD 653


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: 1868
Number of extensions: 106
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: 1020
Length adjustment: 41
Effective length of query: 609
Effective length of database: 979
Effective search space:   596211
Effective search space used:   596211
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 RR42_RS10085 RR42_RS10085 (acetoacetyl-CoA synthase)
to HMM TIGR01217 (acetoacetate-CoA ligase (EC 6.2.1.16))

Software error:

../bin/blast/fastacmd -i /tmp/list.4283.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.4283.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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