GapMind for catabolism of small carbon sources

 

Alignments for a candidate for aacS in Pseudomonas fluorescens FW300-N2E3

Align acetoacetate-CoA ligase (EC 6.2.1.16) (characterized)
to candidate AO353_21765 AO353_21765 acetoacetyl-CoA synthetase

Query= BRENDA::Q9Z3R3
         (650 letters)



>FitnessBrowser__pseudo3_N2E3:AO353_21765
          Length = 651

 Score =  681 bits (1756), Expect = 0.0
 Identities = 348/648 (53%), Positives = 446/648 (68%), Gaps = 9/648 (1%)

Query: 7   LWVPDREIVERSPMAEFIDWCGERFGRSFADYDAFHDWSVSERGAFWTAVWEHCKV-IGE 65
           LW P  E + ++ M  F  +  +R+  + ADY A H WS+ +R  FW A+ +  ++   +
Sbjct: 5   LWQPSAERIGKTRMDAFRRFSNQRYNLTLADYPALHQWSIDQREDFWQAIVDFFEIKFHQ 64

Query: 66  SGEKALVDGDRMLDARFFPEARLNFAENLLRKTGSGDALIFRGEDKVSYRLTWDELRALV 125
                L +G +M +A +FP A LNFAE+LLR+  +  A+I   E+     L++ EL   V
Sbjct: 65  PASTVLREGPQMPNAEWFPGATLNFAEHLLRRRDNAIAVIAIAENGQRESLSYRELAEHV 124

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

Query: 186 IAPKLFIVCDGYWYNGKRQDVDSKVRAVAKSLGA--PTVIVPYAGDSAALAP-TVEGGVT 242
           I PK+ I C GY Y GK+ D  +KV  + + L +    +IVPYA   A +     +  V 
Sbjct: 185 IEPKVLITCAGYRYAGKKIDQTTKVNEILERLPSLQQLIIVPYARPQARVDDYKTQANVA 244

Query: 243 LAD--FIAGFQAGPLVFERLPFGHPLYILFSSGTTGVPKCIVHSAGGTLLQHLKEHRFHC 300
           L D  +  G + G   F  +PF HPLYIL+SSGTTGVPKCI+HS GG LLQH+KEH  H 
Sbjct: 245 LWDSFYRPGGEPG---FVAVPFAHPLYILYSSGTTGVPKCIIHSVGGVLLQHVKEHGLHV 301

Query: 301 GLRDGERLFYFTTCGWMMWNWLASGLAVGATLCLYDGSPFCPDGNVLFDYAAAERFAVFG 360
            L   +RLFY+TTCGWMMWNWL S LAVG+++ LYDGSPF P    L D   +E  +VFG
Sbjct: 302 DLGPDDRLFYYTTCGWMMWNWLVSALAVGSSVVLYDGSPFHPGPQRLIDLIDSEAISVFG 361

Query: 361 TSAKYIDAVRKGGFTPARTHDLSSLRLMTSTGSPLSPEGFSFVYEGIKPDVQLASISGGT 420
           TS KY+  +      P  +HDL SL+ + STGS LSP+ + +VY  IK D+ L+S+SGGT
Sbjct: 362 TSPKYLATLESNEIQPRLSHDLGSLKALLSTGSALSPQSYDYVYREIKSDLCLSSMSGGT 421

Query: 421 DIVSCFVLGNPLKPVWRGEIQGPGLGLAVDVWNDEGKPVRGEKGELVCTRAFPSMPVMFW 480
           DI+SCF+ GNP+ PV RGE+Q  GLG+AV+VWN+ G+PV GEKGELVCTR FP+MP+  W
Sbjct: 422 DIISCFLAGNPVLPVRRGEMQCKGLGMAVEVWNEAGQPVIGEKGELVCTRHFPAMPIGLW 481

Query: 481 NDPDGAKYRAAYFDRFDNVWCHGDFAEWTPHGGIVIHGRSDATLNPGGVRIGTAEIYNQV 540
           NDP   K RA+YF +F  VW  GD+AE  P+G  +IHGRSDA LNPGGVRIGTAEIY QV
Sbjct: 482 NDPQQEKLRASYFSQFPGVWAQGDYAEQRPNGSWLIHGRSDAVLNPGGVRIGTAEIYRQV 541

Query: 541 EQMDEVAEALCIGQDWEDDVRVVLFVRLARGVELTEALTREIKNRIRSGASPRHVPAKII 600
           E++ +V +++ IGQ W+DDVRVVLFVRL  GV L E L +EI+  IR+  +PRHVPAKI+
Sbjct: 542 EKIHQVLDSVAIGQQWQDDVRVVLFVRLRDGVTLDEKLEQEIRQVIRANTTPRHVPAKIV 601

Query: 601 AVADIPRTKSGKIVELAVRDVVHGRPVKNKEALANPEALDLFAGLEEL 648
           AV DIPRT SGK+VELAVR+VVHG+PVKN +ALANPEAL+ F    EL
Sbjct: 602 AVTDIPRTISGKVVELAVRNVVHGQPVKNTDALANPEALEQFRDRPEL 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: 1324
Number of extensions: 59
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: 651
Length adjustment: 38
Effective length of query: 612
Effective length of database: 613
Effective search space:   375156
Effective search space used:   375156
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 AO353_21765 AO353_21765 (acetoacetyl-CoA synthetase)
to HMM TIGR01217 (acetoacetate-CoA ligase (EC 6.2.1.16))

Software error:

../bin/blast/fastacmd -i /tmp/list.4733.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.4733.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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