GapMind for catabolism of small carbon sources

 

Alignments for a candidate for acs in Sinorhizobium meliloti 1021

Align Acetyl-coenzyme A synthetase (EC 6.2.1.1) (characterized)
to candidate SMc04093 SMc04093 acetyl-CoA synthetase

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



>FitnessBrowser__Smeli:SMc04093
          Length = 649

 Score =  885 bits (2286), Expect = 0.0
 Identities = 423/638 (66%), Positives = 500/638 (78%), Gaps = 3/638 (0%)

Query: 7   YPVRPEVAASTLTDEATYKAMYQQSVVNPDGFWREQAKRLDWIKPFTTVKQTSFDDHHVD 66
           YPV       TL D ATY   Y++SV +P+ FW E  KR++W +P+T VK TSF+   V 
Sbjct: 6   YPVLEAAKNRTLLDNATYLEWYRESVADPEKFWGEHGKRIEWFEPYTKVKNTSFEGD-VS 64

Query: 67  IKWFADGTLNVSYNCLDRHLAERGDQIAIIWEGDDPSESRNITYRELHEEVCKFANALRG 126
           IKWF DG  NVSYNC+DRHL   G++ AIIWEGD+P   + ITY EL+++VC+ AN L+ 
Sbjct: 65  IKWFEDGLTNVSYNCIDRHLKTHGEKTAIIWEGDNPYLDKKITYNELYDKVCRLANVLKE 124

Query: 127 QDVHRGDVVTIYMPMIPEAVVAMLACTRIGAIHSVVFGGFSPEALAGRIIDCKSKVVITA 186
           Q V +GD VTIYMPMIPEA  AMLAC RIGAIHSVVFGGFSPEALAGRI+DC+S  VIT 
Sbjct: 125 QGVKKGDRVTIYMPMIPEAAYAMLACARIGAIHSVVFGGFSPEALAGRIVDCESTFVITC 184

Query: 187 DEGVRAGKKIPLKANVDDAL--TNPETSSIQKVIVCKRTAGNIKWNQHRDIWYEDLMKVA 244
           DEGVR GK + LK N D A+     +  ++ KV+V +RT G + W   RD+WY      A
Sbjct: 185 DEGVRGGKPVALKENTDTAIDIAARQHVTVSKVLVVRRTGGKVGWAPGRDLWYHQETAAA 244

Query: 245 GTVCAPKEMGAEEALFILYTSGSTGKPKGVQHTTAGYLLYAALTHERVFDYKPGEVYWCT 304
              C P++M AE+ LFILYTSGSTGKPKGV HTT GYL+YA++TH+ VFDY+ G++YWCT
Sbjct: 245 EPHCPPEKMNAEDPLFILYTSGSTGKPKGVLHTTGGYLVYASMTHQYVFDYQDGDIYWCT 304

Query: 305 ADVGWVTGHSYIVYGPLANGATTLLFEGVPNYPDITRVAKVIDKHKVSILYTAPTAIRAM 364
           ADVGWVTGHSYIVYGPLAN ATTL+FEGVPN+PD  R  +V+DKHKV+I YTAPTAIR++
Sbjct: 305 ADVGWVTGHSYIVYGPLANAATTLMFEGVPNFPDAGRFWEVVDKHKVNIFYTAPTAIRSL 364

Query: 365 MASGTAAVEGADGSSLRLLGSVGEPINPEAWDWYYKNVGKERCPIVDTWWQTETGGVLIS 424
           M +G   V+ +  SSLRLLG+VGEPINPEAW+WYY  VG ERCP+VDTWWQTETGG+LI+
Sbjct: 365 MGAGDDFVKRSSRSSLRLLGTVGEPINPEAWEWYYHVVGDERCPVVDTWWQTETGGILIT 424

Query: 425 PLPGATALKPGSATRPFFGVVPALVDNLGNLIEGAAEGNLVILDSWPGQARTLYGDHDRF 484
           PLPGAT LKPGSATRPFFGV P +VD+ G +++GAA+GNL I DSWPGQ RT+YGDH+RF
Sbjct: 425 PLPGATDLKPGSATRPFFGVQPQIVDSDGKVVDGAADGNLCITDSWPGQMRTVYGDHERF 484

Query: 485 VDTYFKTFSGMYFTGDGARRDEDGYYWITGRVDDVLNVSGHRMGTAEIESAMVAHPKVAE 544
           + TYF T+ G YFTGDG RRDEDGYYWITGRVDDVLNVSGHR+GTAE+ESA+V+H  V+E
Sbjct: 485 IQTYFSTYKGKYFTGDGCRRDEDGYYWITGRVDDVLNVSGHRLGTAEVESALVSHNLVSE 544

Query: 545 AAVVGVPHDIKGQGIYVYVTLNAGEETSEALRLELKNWVRKEIGPIASPDVIQWAPGLPK 604
           AAVVG PH IKGQGIY YV+L AGE   + LR  L   VR EIGPIA+PD IQ+APGLPK
Sbjct: 545 AAVVGYPHPIKGQGIYCYVSLMAGEVGDDELRQALVKHVRSEIGPIATPDKIQFAPGLPK 604

Query: 605 TRSGKIMRRILRKIATAEYDGLGDISTLADPGVVAHLI 642
           TRSGKIMRRILRKIA  ++  LGD STLADPGVV  LI
Sbjct: 605 TRSGKIMRRILRKIAEDDFGSLGDTSTLADPGVVDDLI 642


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: 1468
Number of extensions: 72
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: 649
Length adjustment: 38
Effective length of query: 613
Effective length of database: 611
Effective search space:   374543
Effective search space used:   374543
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 SMc04093 SMc04093 (acetyl-CoA synthetase)
to HMM TIGR02188 (acs: acetate--CoA ligase (EC 6.2.1.1))

Software error:

../bin/blast/fastacmd -i /tmp/list.6944.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.6944.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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