GapMind for catabolism of small carbon sources

 

Alignments for a candidate for aacS in Pseudomonas putida KT2440

Align acetoacetate-CoA ligase (EC 6.2.1.16) (characterized)
to candidate PP_3071 PP_3071 acetoacetyl-coenzyme A synthetase

Query= BRENDA::Q9Z3R3
         (650 letters)



>FitnessBrowser__Putida:PP_3071
          Length = 650

 Score =  694 bits (1791), Expect = 0.0
 Identities = 366/648 (56%), Positives = 440/648 (67%), Gaps = 6/648 (0%)

Query: 7   LWVPDREIVERSPMAEFIDWCGERFGRSFADYDAFHDWSVSERGAFWTAVWEHCKVIGES 66
           LW P    +E S M  F      R+     DY A H WS+ +R AFW  + E+ +V   +
Sbjct: 5   LWRPSTTQIEASRMDAFRRRVNLRYNLQLNDYQALHGWSIEQRPAFWQTLAEYFQVHWHT 64

Query: 67  G-EKALVDGDRMLDARFFPEARLNFAENLLRKTGSGDALIFRGEDKVSYRLTWDELRALV 125
              + L +G +M DA++F  A LNFAE+LLR+     A++   ED      T  EL A V
Sbjct: 65  PPSQVLSEGPQMPDAQWFANATLNFAEHLLRRRDDRPAVVAVREDGQREVFTHAELAAQV 124

Query: 126 SRLQQALRAQGIGAGDRVAAMMPNMPETIALMLATASVGAIWSSCSPDFGEQGVLDRFGQ 185
           + LQ A +A GI  GDRVAA+MPN  +T+  MLA  S+GA+WS+ SP+FG  G++DRFGQ
Sbjct: 125 AGLQTAFKAVGIVPGDRVAAIMPNTWQTLVAMLACTSLGAVWSTSSPEFGVHGIIDRFGQ 184

Query: 186 IAPKLFIVCDGYWYNGKRQDVDSKVRAVAKSLGA--PTVIVPYAGDSAALAPTVEGGVTL 243
           I PKL IVC GY Y GK  D  +KV  V   L      ++VP+              V+L
Sbjct: 185 IEPKLLIVCAGYQYAGKAIDQVTKVNQVCAQLPGLEHLIVVPHTRKGTRADEFQAANVSL 244

Query: 244 -ADFIAGFQAGPLVFERLPFGHPLYILFSSGTTGVPKCIVHSAGGTLLQHLKEHRFHCGL 302
             DF      G   F  LPF HPLYIL+SSGTTGVPKCIVH AGG LLQHLKEH  H  L
Sbjct: 245 WNDFFQ--PGGEPRFTPLPFDHPLYILYSSGTTGVPKCIVHRAGGVLLQHLKEHGLHNDL 302

Query: 303 RDGERLFYFTTCGWMMWNWLASGLAVGATLCLYDGSPFCPDGNVLFDYAAAERFAVFGTS 362
           +  + LFY+TTCGWMMWNWLASGLAVGATL LYDGSPF P    L D   AE    FGTS
Sbjct: 303 KADDVLFYYTTCGWMMWNWLASGLAVGATLVLYDGSPFHPGPERLLDLIEAEGIHAFGTS 362

Query: 363 AKYIDAVRKGGFTPARTHDLSSLRLMTSTGSPLSPEGFSFVYEGIKPDVQLASISGGTDI 422
           AKY+ A+ + G  PA +H L+SLRL+ STGSPLSP  + +VY+ IK D+ L S+SGGTDI
Sbjct: 363 AKYLAALEQAGLEPANSHCLTSLRLLLSTGSPLSPHSYDYVYDKIKADLWLVSMSGGTDI 422

Query: 423 VSCFVLGNPLKPVWRGEIQGPGLGLAVDVWNDEGKPVRGEKGELVCTRAFPSMPVMFWND 482
           VSCFVLGNP  PV RGEIQ  GLG+AV+VWN++G+PV  EKGELVCTR FPSMP+ FWND
Sbjct: 423 VSCFVLGNPTLPVRRGEIQCKGLGMAVEVWNEQGQPVVDEKGELVCTRNFPSMPLGFWND 482

Query: 483 PDGAKYRAAYFDRFDNVWCHGDFAEWTPHGGIVIHGRSDATLNPGGVRIGTAEIYNQVEQ 542
           PDG +Y  AYF +F  VW  GD+AE    GG+VIHGRSDA LNPGGVRIGTAEIY QVE+
Sbjct: 483 PDGRRYHDAYFSQFPGVWAQGDYAEQRASGGMVIHGRSDAVLNPGGVRIGTAEIYRQVEK 542

Query: 543 MDEVAEALCIGQDWEDDVRVVLFVRLARGVELTEALTREIKNRIRSGASPRHVPAKIIAV 602
           +++V E++ IGQDW  DVRVVLFVRL  G++L EAL + I+  IR   +PRHVPA I  V
Sbjct: 543 VEQVVESVAIGQDWNGDVRVVLFVRLQDGLQLDEALRQHIRQVIRQYTTPRHVPAVIAQV 602

Query: 603 ADIPRTKSGKIVELAVRDVVHGRPVKNKEALANPEALDLFAGLEELKS 650
           +DIPRT SGK+VELA+RDVVHGRPVKN +ALANPEAL+ F    ELKS
Sbjct: 603 SDIPRTISGKLVELAIRDVVHGRPVKNTDALANPEALEQFRDRAELKS 650


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: 1340
Number of extensions: 60
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: 650
Length of database: 650
Length adjustment: 38
Effective length of query: 612
Effective length of database: 612
Effective search space:   374544
Effective search space used:   374544
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: 54 (25.4 bits)

Align candidate PP_3071 PP_3071 (acetoacetyl-coenzyme A synthetase)
to HMM TIGR01217 (acetoacetate-CoA ligase (EC 6.2.1.16))

Software error:

../bin/blast/fastacmd -i /tmp/list.5272.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.5272.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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