GapMind for catabolism of small carbon sources

 

Alignments for a candidate for acs in Shewanella loihica PV-4

Align Acetyl-coenzyme A synthetase (EC 6.2.1.1) (characterized)
to candidate 5209055 Shew_1533 acetyl-CoA synthetase (RefSeq)

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



>FitnessBrowser__PV4:5209055
          Length = 650

 Score =  984 bits (2544), Expect = 0.0
 Identities = 461/644 (71%), Positives = 537/644 (83%)

Query: 1   MSAASLYPVRPEVAASTLTDEATYKAMYQQSVVNPDGFWREQAKRLDWIKPFTTVKQTSF 60
           MS  SLY V  E+AA+   ++  YK MYQ+SVVNP+GFWRE  +R+DW+KPFT VK+TSF
Sbjct: 1   MSTQSLYKVPSEIAANAHINDEKYKKMYQESVVNPEGFWREHGQRIDWMKPFTKVKKTSF 60

Query: 61  DDHHVDIKWFADGTLNVSYNCLDRHLAERGDQIAIIWEGDDPSESRNITYRELHEEVCKF 120
           DDH++ I WF DGTLN S NCLDRHLA+  D++AIIWEGDD ++ R +TY ELH EVCKF
Sbjct: 61  DDHNLSINWFYDGTLNASVNCLDRHLADNADKLAIIWEGDDAADQRTLTYGELHTEVCKF 120

Query: 121 ANALRGQDVHRGDVVTIYMPMIPEAVVAMLACTRIGAIHSVVFGGFSPEALAGRIIDCKS 180
           ANALR Q V RGDVVT+YMPM+PEA V MLAC RIGAIHSVVFGGFSP+++A R+ID KS
Sbjct: 121 ANALRSQGVRRGDVVTVYMPMVPEAAVVMLACARIGAIHSVVFGGFSPDSIASRVIDGKS 180

Query: 181 KVVITADEGVRAGKKIPLKANVDDALTNPETSSIQKVIVCKRTAGNIKWNQHRDIWYEDL 240
           KVVITADEGVR G+ IPLKAN+D+AL++P+ + ++KVIV +RT   + W + RDI +  L
Sbjct: 181 KVVITADEGVRGGRTIPLKANIDEALSHPDVTCVEKVIVLERTGNPVNWVEGRDIKWASL 240

Query: 241 MKVAGTVCAPKEMGAEEALFILYTSGSTGKPKGVQHTTAGYLLYAALTHERVFDYKPGEV 300
           M+ A   C  +EMGAE+ LF+LYTSGSTG PKGV HTT GYL+YA++THE VFDYK GE+
Sbjct: 241 METASEHCVAEEMGAEDPLFLLYTSGSTGNPKGVLHTTGGYLVYASMTHEYVFDYKEGEI 300

Query: 301 YWCTADVGWVTGHSYIVYGPLANGATTLLFEGVPNYPDITRVAKVIDKHKVSILYTAPTA 360
           YWCTADVGW+TGHSY+VYGPLANGAT L+ EG+PNYP   R+ ++ID+HKV+ILYTAPT 
Sbjct: 301 YWCTADVGWITGHSYMVYGPLANGATILIHEGIPNYPTPARLGEMIDRHKVNILYTAPTL 360

Query: 361 IRAMMASGTAAVEGADGSSLRLLGSVGEPINPEAWDWYYKNVGKERCPIVDTWWQTETGG 420
           IRA+MA G    +G DGSSLR++GSVGEPINPEAW WY++ +G E CPIVDTWWQTETGG
Sbjct: 361 IRALMAEGKEQFDGFDGSSLRIMGSVGEPINPEAWRWYHEVIGHENCPIVDTWWQTETGG 420

Query: 421 VLISPLPGATALKPGSATRPFFGVVPALVDNLGNLIEGAAEGNLVILDSWPGQARTLYGD 480
           +LISPLPGAT  KPGSATRPFFGV PALVDN+GN+I+GAAEGNLVILDSWPGQ RT+YGD
Sbjct: 421 ILISPLPGATDTKPGSATRPFFGVQPALVDNMGNIIDGAAEGNLVILDSWPGQMRTVYGD 480

Query: 481 HDRFVDTYFKTFSGMYFTGDGARRDEDGYYWITGRVDDVLNVSGHRMGTAEIESAMVAHP 540
           HDRF  TYFKTF GMYFTGDGARRDEDGYYWITGRVDDV+NVSGHR+GTAE+ESA+VAH 
Sbjct: 481 HDRFALTYFKTFRGMYFTGDGARRDEDGYYWITGRVDDVINVSGHRLGTAEVESALVAHE 540

Query: 541 KVAEAAVVGVPHDIKGQGIYVYVTLNAGEETSEALRLELKNWVRKEIGPIASPDVIQWAP 600
            VAEAAVVG PHDIKGQGIY YVTL  G + SE LR EL+ WVRKEIG +A+PD+IQWA 
Sbjct: 541 HVAEAAVVGYPHDIKGQGIYAYVTLTKGTQESEELRQELRQWVRKEIGALATPDLIQWAG 600

Query: 601 GLPKTRSGKIMRRILRKIATAEYDGLGDISTLADPGVVAHLIET 644
           GLPKTRSGKIMRR LRKIA  E   LGD STLADP V+  LIET
Sbjct: 601 GLPKTRSGKIMRRFLRKIAANEVTNLGDASTLADPAVIDTLIET 644


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: 1474
Number of extensions: 50
Number of successful extensions: 1
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: 650
Length adjustment: 38
Effective length of query: 613
Effective length of database: 612
Effective search space:   375156
Effective search space used:   375156
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 5209055 Shew_1533 (acetyl-CoA synthetase (RefSeq))
to HMM TIGR02188 (acs: acetate--CoA ligase (EC 6.2.1.1))

Software error:

../bin/blast/fastacmd -i /tmp/list.27442.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.27442.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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