GapMind for catabolism of small carbon sources

 

Alignments for a candidate for aacS in Pseudomonas simiae WCS417

Align acetoacetate-CoA ligase (EC 6.2.1.16) (characterized)
to candidate GFF2382 PS417_12145 acetoacetyl-CoA synthetase

Query= BRENDA::Q9Z3R3
         (650 letters)



>FitnessBrowser__WCS417:GFF2382
          Length = 652

 Score =  682 bits (1760), Expect = 0.0
 Identities = 352/647 (54%), Positives = 442/647 (68%), Gaps = 7/647 (1%)

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

Query: 67  GEKA-LVDGDRMLDARFFPEARLNFAENLLRKTGSGDALIFRGEDKVSYRLTWDELRALV 125
              A L++   M  A++FP A LNFAE+LLR+     A++   ED    +LT+ EL A V
Sbjct: 65  PPTAVLIEDAEMPSAQWFPGATLNFAEHLLRRRDGHPAVVALSEDGQREQLTYAELAAHV 124

Query: 126 SRLQQALRAQGIGAGDRVAAMMPNMPETIALMLATASVGAIWSSCSPDFGEQGVLDRFGQ 185
           + LQ +LRA G+  GDRVAA MPN  +T+  MLAT S+GAIWS  SPDFG QGV+DRFGQ
Sbjct: 125 AGLQHSLRAAGVVQGDRVAACMPNTWQTLVGMLATTSLGAIWSCSSPDFGTQGVIDRFGQ 184

Query: 186 IAPKLFIVCDGYWYNGKRQDVDSKVRAVAKSLGA--PTVIVPYAGDSAALAP-TVEGGVT 242
           I PK+ I C GY Y GK  D  +K+  + + L +    +IVPYA   A ++      GV 
Sbjct: 185 IEPKVLITCAGYRYAGKDIDQSAKLNEILERLPSLEQLIIVPYARPQAQVSDYQTHAGVA 244

Query: 243 L-ADFIAGFQAGPLVFERLPFGHPLYILFSSGTTGVPKCIVHSAGGTLLQHLKEHRFHCG 301
           L  DF      G   F  +PF HPLYIL+SSGTTGVPKCI+H  GG LL HLKEH  H  
Sbjct: 245 LWQDFYQ--PGGEPQFVAVPFDHPLYILYSSGTTGVPKCIIHGTGGVLLTHLKEHGLHAD 302

Query: 302 LRDGERLFYFTTCGWMMWNWLASGLAVGATLCLYDGSPFCPDGNVLFDYAAAERFAVFGT 361
           L   + LFY+TTCGWMMWNWL S LA+GAT  LYDGSPF P    L D   AE+ +VFGT
Sbjct: 303 LSRDDCLFYYTTCGWMMWNWLVSVLAIGATAVLYDGSPFHPGPERLIDLIDAEKISVFGT 362

Query: 362 SAKYIDAVRKGGFTPARTHDLSSLRLMTSTGSPLSPEGFSFVYEGIKPDVQLASISGGTD 421
           S K++  + K G  P  +HDL SL+ + STGSPLSP+ + +VY  IK  + L+S+SGGTD
Sbjct: 363 SPKFLATLEKAGLQPRLSHDLGSLKGLISTGSPLSPQSYDYVYREIKAQLCLSSMSGGTD 422

Query: 422 IVSCFVLGNPLKPVWRGEIQGPGLGLAVDVWNDEGKPVRGEKGELVCTRAFPSMPVMFWN 481
           IVSCFV+GNP+ PV RGE+Q   L +A++VW+D+G+P+ GEKGELVCTR FP+MP+  WN
Sbjct: 423 IVSCFVIGNPVLPVRRGEMQCKSLAMAIEVWDDQGRPLIGEKGELVCTRHFPAMPIGLWN 482

Query: 482 DPDGAKYRAAYFDRFDNVWCHGDFAEWTPHGGIVIHGRSDATLNPGGVRIGTAEIYNQVE 541
           DP+  K RA+YF +F  VW  GD+AE  P+G ++IHGRSDA LNPGGVRIGTAEIY QVE
Sbjct: 483 DPECKKLRASYFSQFPGVWAQGDYAEQRPNGSLLIHGRSDAVLNPGGVRIGTAEIYRQVE 542

Query: 542 QMDEVAEALCIGQDWEDDVRVVLFVRLARGVELTEALTREIKNRIRSGASPRHVPAKIIA 601
           ++ +V E+L IGQ W++DVRVVLFVRL  GVEL E L ++I+  IR+  +PRHVPAKI+A
Sbjct: 543 KIPQVQESLAIGQRWQEDVRVVLFVRLNEGVELDETLEQQIRQVIRANTTPRHVPAKILA 602

Query: 602 VADIPRTKSGKIVELAVRDVVHGRPVKNKEALANPEALDLFAGLEEL 648
           V DIPRT SGKIVELAVR+VVHG PVKN +ALANP+AL+ F    EL
Sbjct: 603 VTDIPRTISGKIVELAVRNVVHGEPVKNTDALANPQALEQFRDRPEL 649


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: 1336
Number of extensions: 62
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: 652
Length adjustment: 38
Effective length of query: 612
Effective length of database: 614
Effective search space:   375768
Effective search space used:   375768
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 GFF2382 PS417_12145 (acetoacetyl-CoA synthetase)
to HMM TIGR01217 (acetoacetate-CoA ligase (EC 6.2.1.16))

Software error:

../bin/blast/fastacmd -i /tmp/list.9515.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.9515.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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