GapMind for catabolism of small carbon sources

 

Alignments for a candidate for aacS in Pseudomonas fluorescens FW300-N2E2

Align acetoacetate-CoA ligase (EC 6.2.1.16) (characterized)
to candidate Pf6N2E2_2042 Acetoacetyl-CoA synthetase (EC 6.2.1.16)

Query= BRENDA::Q9Z3R3
         (650 letters)



>FitnessBrowser__pseudo6_N2E2:Pf6N2E2_2042
          Length = 651

 Score =  687 bits (1774), Expect = 0.0
 Identities = 355/647 (54%), Positives = 439/647 (67%), Gaps = 7/647 (1%)

Query: 7   LWVPDREIVERSPMAEFIDWCGERFGRSFADYDAFHDWSVSERGAFWTAVWEHCKV-IGE 65
           LW P  E + +S M  F  +   R      DY A H WS+ +R AFW A+ +  ++   +
Sbjct: 5   LWQPSPERIAQSRMNAFRQFVNARHHLQLHDYPALHAWSIDQREAFWQAIVDFFEIHFHQ 64

Query: 66  SGEKALVDGDRMLDARFFPEARLNFAENLLRKTGSGDALIFRGEDKVSYRLTWDELRALV 125
           + +  LV+G +M  A++FP A LNFAE+LLR+     A++   E+    +LTW EL A V
Sbjct: 65  APDAVLVEGAQMPSAQWFPGATLNFAEHLLRRRDDAVAVVALDENGSQEQLTWAELAAHV 124

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

Query: 186 IAPKLFIVCDGYWYNGKRQDVDSKVRAVAKSLGA--PTVIVPYAGDSAALAP--TVEGGV 241
           I PK+ I C GY Y GK  D  +KV  + + L +    +++PYA   A +    T     
Sbjct: 185 IEPKVLITCAGYRYAGKVIDQRTKVNEILERLPSLQQLIVLPYAQPDACVEDFKTPAAVA 244

Query: 242 TLADFIAGFQAGPLVFERLPFGHPLYILFSSGTTGVPKCIVHSAGGTLLQHLKEHRFHCG 301
              DF      G   F  +PF HPLYIL+SSGTTGVPKCIVH  GG LLQH+KEH  H  
Sbjct: 245 LWNDFYQS--GGEPAFVSVPFDHPLYILYSSGTTGVPKCIVHGTGGVLLQHVKEHGLHVD 302

Query: 302 LRDGERLFYFTTCGWMMWNWLASGLAVGATLCLYDGSPFCPDGNVLFDYAAAERFAVFGT 361
           L   +RLFY+TTCGWMMWNWL S LAVG+T+ LYDGSPF P    L D    +R +VFGT
Sbjct: 303 LGPEDRLFYYTTCGWMMWNWLVSALAVGSTVVLYDGSPFHPGPERLLDLIDQQRISVFGT 362

Query: 362 SAKYIDAVRKGGFTPARTHDLSSLRLMTSTGSPLSPEGFSFVYEGIKPDVQLASISGGTD 421
           S K++ A+   G  P +TH L SLR + STGS L+P  + +VY  IK DV LAS+SGGTD
Sbjct: 363 SPKFLAALESEGLKPRQTHRLDSLRALLSTGSALAPHSYDYVYRDIKADVCLASMSGGTD 422

Query: 422 IVSCFVLGNPLKPVWRGEIQGPGLGLAVDVWNDEGKPVRGEKGELVCTRAFPSMPVMFWN 481
           IVSCFV GNPL PV RGE+QG  LG+AV VWN+ G PV GEKGELVCTR FP+MP+  WN
Sbjct: 423 IVSCFVNGNPLSPVSRGEMQGKSLGMAVQVWNEAGNPVIGEKGELVCTRHFPAMPIGLWN 482

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

Query: 542 QMDEVAEALCIGQDWEDDVRVVLFVRLARGVELTEALTREIKNRIRSGASPRHVPAKIIA 601
           ++++V + + IGQ W+ DVRVVLFVRL  GV L EAL ++I+  IR+  +PRHVPAKI+A
Sbjct: 543 KVEQVLDCVAIGQRWQGDVRVVLFVRLRDGVTLNEALAQQIRQVIRANTTPRHVPAKILA 602

Query: 602 VADIPRTKSGKIVELAVRDVVHGRPVKNKEALANPEALDLFAGLEEL 648
           V+DIPRT SGK+VELAVR+VVHG  VKN +ALANPEAL+ F    EL
Sbjct: 603 VSDIPRTISGKVVELAVRNVVHGEAVKNTDALANPEALEQFRDRPEL 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: 1361
Number of extensions: 70
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 Pf6N2E2_2042 (Acetoacetyl-CoA synthetase (EC 6.2.1.16))
to HMM TIGR01217 (acetoacetate-CoA ligase (EC 6.2.1.16))

Software error:

../bin/blast/fastacmd -i /tmp/list.16588.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.16588.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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