GapMind for catabolism of small carbon sources

 

Alignments for a candidate for acs in Phaeobacter inhibens BS107

Align Acetyl-coenzyme A synthetase (EC 6.2.1.1) (characterized)
to candidate GFF1279 PGA1_c12950 acetyl-coenzyme A synthetase Acs

Query= reanno::pseudo3_N2E3:AO353_03060
         (651 letters)



>FitnessBrowser__Phaeo:GFF1279
          Length = 695

 Score =  833 bits (2153), Expect = 0.0
 Identities = 411/644 (63%), Positives = 477/644 (74%), Gaps = 5/644 (0%)

Query: 2   SAASLYPVRPEVAANTLTDEATYKAMYQQSVVNPDGFWREQAKRLDWIKPFTTVKQTSFD 61
           S +  Y    E  A    + A Y  MY  S+ +P+GFWR+QA+R+DWIKPFT VK   F 
Sbjct: 47  SDSKAYAPSEETVARAHVNAAQYDEMYAASMQDPEGFWRQQAERIDWIKPFTQVKDVDFT 106

Query: 62  DHHVDIKWFADGTLNVSYNCLDRHLAERGDQIAIIWEGDDPAES-RNITYRELHEQVCKF 120
             +V I W+ADGTLNV+ NC+DRHL  RGDQ AIIWE D P E+ ++I+Y++LH +VC+ 
Sbjct: 107 LGNVSINWYADGTLNVAANCIDRHLDTRGDQTAIIWEPDSPDEAAQHISYKQLHTRVCRM 166

Query: 121 ANALRGQDVHRGDVVTIYMPMIPEAVVAMLACTRIGAIHSVVFGGFSPEALAGRIIDCKS 180
           AN L    V +GD V IY+PMIPEA  AMLAC RIGAIHS+VF GFSP+ALA R+  C +
Sbjct: 167 ANVLETMGVRKGDRVVIYLPMIPEAAYAMLACARIGAIHSIVFAGFSPDALAARVNGCDA 226

Query: 181 KVVITADEGLRAGKKISLKANVDDALTNPETSSIQKVIVCKRTGGNIKWNQHRDIWYEDL 240
           KV+ITADE  R G+K  LK+N D AL +  T    K +V KRTGG   W   RD  Y ++
Sbjct: 227 KVLITADEAPRGGRKTPLKSNADAALLH--TKDTVKCLVVKRTGGQTTWIDGRDYDYNEM 284

Query: 241 MKVAGTVCAPKEMGAEEALFILYTSGSTGKPKGVQHTTGGYLLYAALTHERVFDYRPGEI 300
              A     P EM AE+ LFILYTSGSTG+PKGV HTTGGYL YAA+THE  FDY  G+I
Sbjct: 285 ALEADDYSKPAEMNAEDPLFILYTSGSTGQPKGVVHTTGGYLTYAAMTHEITFDYHDGDI 344

Query: 301 YWCTADVGWVTGHTYIVYGPLANGATTLLFEGVPNYPDITRVAKIIDKHKVNILYTAPTA 360
           YWCTADVGWVTGH+YIVYGPLANGATTL+FEGVP YPD +R  ++ DKHKV   YTAPTA
Sbjct: 345 YWCTADVGWVTGHSYIVYGPLANGATTLMFEGVPTYPDASRFWQVCDKHKVTQFYTAPTA 404

Query: 361 IRAMMAQGTAAVEGADGSSLRLLGSVGEPINPEAWEWYYKNVGQSRCPIVDTWWQTETGA 420
           +RA+M QG   VE  D SSLR LG+VGEPINPEAW WY   VG+ +CPIVDTWWQTETG 
Sbjct: 405 LRALMGQGNEWVEKCDLSSLRTLGTVGEPINPEAWNWYNDIVGKGKCPIVDTWWQTETGG 464

Query: 421 TLMSPLPGAHGLKPGSAARPFFGVVPALVD-NLGNIIEG-VAEGNLVILDSWPGQARTLY 478
            LM+PLPGAH  KPG+A +PFFGV P ++D   G  I G   EG L I DSWPGQ RT++
Sbjct: 465 HLMTPLPGAHATKPGAAMKPFFGVAPVVLDPQSGEEITGNGVEGVLCIKDSWPGQMRTVW 524

Query: 479 GDHDRFVDTYFKTFRGMYFTGDGARRDADGYWWITGRVDDVLNVSGHRMGTAEIESAMVA 538
           GDH+RF  TYF  ++G YFTGDG RRD DG +WITGRVDDV+NVSGHRMGTAE+ESA+VA
Sbjct: 525 GDHERFEKTYFSDYKGYYFTGDGCRRDEDGDYWITGRVDDVINVSGHRMGTAEVESALVA 584

Query: 539 HPKVAEAAVVGVPHDIKGQGIYVYVTLNGGEEPSEALRLELKNWVRKEIGPIASPDVIQW 598
           H  VAEAAVVG PH+IKGQGIY YVTL    EPS+ L  EL+ WVR EIGPIASPDVIQW
Sbjct: 585 HAAVAEAAVVGYPHEIKGQGIYCYVTLMNDREPSDELVKELRTWVRTEIGPIASPDVIQW 644

Query: 599 APGLPKTRSGKIMRRILRKIATGEYDGLGDISTLADPGVVQHLI 642
           APGLPKTRSGKIMRRILRKIA  ++  LGD STLADP VV  LI
Sbjct: 645 APGLPKTRSGKIMRRILRKIAENDFGSLGDTSTLADPSVVDDLI 688


Lambda     K      H
   0.319    0.136    0.425 

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: 1580
Number of extensions: 86
Number of successful extensions: 4
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: 695
Length adjustment: 39
Effective length of query: 612
Effective length of database: 656
Effective search space:   401472
Effective search space used:   401472
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 (21.7 bits)
S2: 54 (25.4 bits)

Align candidate GFF1279 PGA1_c12950 (acetyl-coenzyme A synthetase Acs)
to HMM TIGR02188 (acs: acetate--CoA ligase (EC 6.2.1.1))

Software error:

../bin/blast/fastacmd -i /tmp/list.3243.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.3243.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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