GapMind for catabolism of small carbon sources

 

Alignments for a candidate for aacS in Pseudomonas fluorescens FW300-N1B4

Align acetoacetate-CoA ligase (EC 6.2.1.16) (characterized)
to candidate Pf1N1B4_5634 Acetoacetyl-CoA synthetase (EC 6.2.1.16)

Query= BRENDA::Q9Z3R3
         (650 letters)



>FitnessBrowser__pseudo1_N1B4:Pf1N1B4_5634
          Length = 651

 Score =  702 bits (1812), Expect = 0.0
 Identities = 357/646 (55%), Positives = 443/646 (68%), Gaps = 5/646 (0%)

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

Query: 66  SGEKALVDGDRMLDARFFPEARLNFAENLLRKTGSGDALIFRGEDKVSYRLTWDELRALV 125
             +  L++G +M  A++FP A LNFAE+LLR+     A++  GE+    +LTW EL + V
Sbjct: 65  QPDAVLIEGAQMPSAQWFPGATLNFAEHLLRRRDDAVAVVAIGENGQREQLTWAELASHV 124

Query: 126 SRLQQALRAQGIGAGDRVAAMMPNMPETIALMLATASVGAIWSSCSPDFGEQGVLDRFGQ 185
           +  Q  L+A G+G GDRVAA MPN  +T+  MLAT S+GAIWS  SPDFG  GV+DRFGQ
Sbjct: 125 AGFQNGLKAAGVGLGDRVAACMPNTWQTLVAMLATTSLGAIWSCSSPDFGTHGVIDRFGQ 184

Query: 186 IAPKLFIVCDGYWYNGKRQDVDSKVRAVAKSLGA--PTVIVPYAGDSAALAP-TVEGGVT 242
           I PK+ I C GY Y GK  D  +KV  +   L +    ++VPYA   A +     +  VT
Sbjct: 185 IEPKVLITCAGYRYAGKEIDQTAKVNEILGQLPSLQQLIVVPYARPQARIEDFRSQANVT 244

Query: 243 LADFIAGFQAGPLVFERLPFGHPLYILFSSGTTGVPKCIVHSAGGTLLQHLKEHRFHCGL 302
           L D       G   F  +PF HPLYIL+SSGTTGVPKCIVHS GG LLQH+KEH  H  L
Sbjct: 245 LWDDFYD-PGGEPQFIPVPFAHPLYILYSSGTTGVPKCIVHSTGGVLLQHVKEHGLHTDL 303

Query: 303 RDGERLFYFTTCGWMMWNWLASGLAVGATLCLYDGSPFCPDGNVLFDYAAAERFAVFGTS 362
             G+RLFY+TTCGWMMWNWL S LAV + + LYDGSPF P    L D    ER  VFGTS
Sbjct: 304 GPGDRLFYYTTCGWMMWNWLVSALAVDSAVVLYDGSPFHPGPERLIDLIDDERINVFGTS 363

Query: 363 AKYIDAVRKGGFTPARTHDLSSLRLMTSTGSPLSPEGFSFVYEGIKPDVQLASISGGTDI 422
            K++ A+   G  P  +HDLSSL+ + STGS LSP+ F +VY   K D+ L+S+SGGTDI
Sbjct: 364 PKFLTALESNGLKPCDSHDLSSLKTVLSTGSALSPQSFDYVYRAFKSDLCLSSMSGGTDI 423

Query: 423 VSCFVLGNPLKPVWRGEIQGPGLGLAVDVWNDEGKPVRGEKGELVCTRAFPSMPVMFWND 482
           VSCFV+GNP+ PV RGE+Q  GLG+AV+VWND G PV GEKGELVCTR FP+MP+  W+D
Sbjct: 424 VSCFVIGNPVLPVRRGEMQCKGLGMAVEVWNDAGTPVIGEKGELVCTRHFPAMPIGLWHD 483

Query: 483 PDGAKYRAAYFDRFDNVWCHGDFAEWTPHGGIVIHGRSDATLNPGGVRIGTAEIYNQVEQ 542
           PDG K R +YF  F  VW  GD+AE  PHGG++IHGRSDA LNPGGVRIGTAEIY QVE+
Sbjct: 484 PDGEKLRKSYFSLFPGVWAQGDYAEQLPHGGLLIHGRSDAVLNPGGVRIGTAEIYRQVEK 543

Query: 543 MDEVAEALCIGQDWEDDVRVVLFVRLARGVELTEALTREIKNRIRSGASPRHVPAKIIAV 602
           + +V +++ IGQ W+DDVRVVLFV+L  GVEL EAL ++I+  IR+  +PRHVPAKI+AV
Sbjct: 544 IPQVLDSVAIGQQWQDDVRVVLFVKLRDGVELDEALQQQIRQVIRANTTPRHVPAKIVAV 603

Query: 603 ADIPRTKSGKIVELAVRDVVHGRPVKNKEALANPEALDLFAGLEEL 648
            DIPRT SGK+VELAVR+VVHG+ VKN +ALANPEAL+ F    EL
Sbjct: 604 TDIPRTISGKVVELAVRNVVHGQKVKNTDALANPEALEQFRDRPEL 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: 1363
Number of extensions: 63
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 Pf1N1B4_5634 (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.25259.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.25259.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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