GapMind for catabolism of small carbon sources

 

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

Align Acetyl-coenzyme A synthetase (EC 6.2.1.1) (characterized)
to candidate AO353_14365 AO353_14365 acetyl-CoA synthetase

Query= reanno::pseudo5_N2C3_1:AO356_18695
         (651 letters)



>FitnessBrowser__pseudo3_N2E3:AO353_14365
          Length = 645

 Score =  822 bits (2123), Expect = 0.0
 Identities = 399/640 (62%), Positives = 482/640 (75%), Gaps = 5/640 (0%)

Query: 5   SLYPVRPEVAASTLTDEATYKAMYQQSVVNPDGFWREQAKR-LDWIKPFTTVKQTSFDDH 63
           S +P    V  +    +  Y+ +Y+QS+  PD FW EQAKR LDW  P+ +V+ T+    
Sbjct: 5   STFPKADAVRQAAQLSQDDYQRLYRQSIEQPDVFWAEQAKRFLDWSTPWQSVQHTNIKTG 64

Query: 64  HVDIKWFADGTLNVSYNCLDRHLAERGDQIAIIWEGDDPSESRNITYRELHEEVCKFANA 123
               +WFA   LNVSYNC+DRHLA+RG+Q AIIWEGDDP+ES +ITY++LH  VC+ AN 
Sbjct: 65  AA--QWFAGAQLNVSYNCIDRHLAQRGEQTAIIWEGDDPAESLHITYQKLHHCVCRLANV 122

Query: 124 LRGQDVHRGDVVTIYMPMIPEAVVAMLACTRIGAIHSVVFGGFSPEALAGRIIDCKSKVV 183
           L+ + V +GD V IYMPMIPEA  AMLAC RIGA+HSVVFGGFSP++L  RI+D   + V
Sbjct: 123 LKSRGVKKGDRVCIYMPMIPEAAYAMLACARIGAVHSVVFGGFSPDSLRDRILDADCRTV 182

Query: 184 ITADEGVRAGKKIPLKANVDDALTNPETSSIQKVIVCKRTAGNIKWNQHRDIWYEDLMKV 243
           ITADEGVR GK +PLK NVD AL +    ++  V+V + T   + W + RD+WY   ++ 
Sbjct: 183 ITADEGVRGGKYVPLKQNVDKALLS--CPAVSTVVVVEHTQIEVNWVEGRDLWYHQALRD 240

Query: 244 AGTVCAPKEMGAEEALFILYTSGSTGKPKGVQHTTAGYLLYAALTHERVFDYKPGEVYWC 303
               C P+ M AE+ LFILYTSGSTGKPKGV HTT GYLL AA+T + VFDY+ GEV+WC
Sbjct: 241 VSDDCPPEPMDAEDPLFILYTSGSTGKPKGVLHTTGGYLLQAAMTFKYVFDYRDGEVFWC 300

Query: 304 TADVGWVTGHSYIVYGPLANGATTLLFEGVPNYPDITRVAKVIDKHKVSILYTAPTAIRA 363
           TADVGWVTGHSYIVYGPLANGATTL+FEGVP+YP+ +R  +VIDKH+V+I YTAPTA+RA
Sbjct: 301 TADVGWVTGHSYIVYGPLANGATTLIFEGVPSYPNSSRFWQVIDKHQVNIFYTAPTALRA 360

Query: 364 MMASGTAAVEGADGSSLRLLGSVGEPINPEAWDWYYKNVGKERCPIVDTWWQTETGGVLI 423
           +M  G   ++ +  +SLRLLGSVGEPINPEAWDWY+  VG++RCPIVDTWWQTETGG+++
Sbjct: 361 LMREGLEPLKDSSRASLRLLGSVGEPINPEAWDWYFNAVGEQRCPIVDTWWQTETGGIML 420

Query: 424 SPLPGATALKPGSATRPFFGVVPALVDNLGNLIEGAAEGNLVILDSWPGQARTLYGDHDR 483
           SPL  A  +KPG ATRP FGV P L+D  G  I GA  G L I  SWPGQ R++YGD  R
Sbjct: 421 SPLVSAQRIKPGCATRPMFGVQPVLLDEHGKEISGAGSGVLAIKSSWPGQIRSVYGDPQR 480

Query: 484 FVDTYFKTFSGMYFTGDGARRDEDGYYWITGRVDDVLNVSGHRMGTAEIESAMVAHPKVA 543
            +DTYFK + G YFTGDGARRDEDG YWITGR+DDV+NVSGHR+GTAE+ESA+V H  +A
Sbjct: 481 MIDTYFKPYPGYYFTGDGARRDEDGDYWITGRIDDVINVSGHRIGTAEVESALVLHDSIA 540

Query: 544 EAAVVGVPHDIKGQGIYVYVTLNAGEETSEALRLELKNWVRKEIGPIASPDVIQWAPGLP 603
           EAAVVG PHD+KGQGIY +VT   G E S+AL+ EL   V +EIG  A PD+IQWAP LP
Sbjct: 541 EAAVVGYPHDLKGQGIYAFVTPMNGIEPSDALKKELLAHVSQEIGSFAKPDLIQWAPALP 600

Query: 604 KTRSGKIMRRILRKIATAEYDGLGDISTLADPGVVAHLIE 643
           KTRSGKIMRRILRKIA  E D LGD STLADP VVA LI+
Sbjct: 601 KTRSGKIMRRILRKIACNELDSLGDTSTLADPSVVAGLID 640


Lambda     K      H
   0.318    0.135    0.418 

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: 69
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: 651
Length of database: 645
Length adjustment: 38
Effective length of query: 613
Effective length of database: 607
Effective search space:   372091
Effective search space used:   372091
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 54 (25.4 bits)

Align candidate AO353_14365 AO353_14365 (acetyl-CoA synthetase)
to HMM TIGR02188 (acs: acetate--CoA ligase (EC 6.2.1.1))

Software error:

../bin/blast/fastacmd -i /tmp/list.10946.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.10946.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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