GapMind for catabolism of small carbon sources

 

Alignments for a candidate for acs in Sphingomonas koreensis DSMZ 15582

Align Acetyl-coenzyme A synthetase (EC 6.2.1.1) (characterized)
to candidate Ga0059261_1313 Ga0059261_1313 acetyl-coenzyme A synthetase (EC 6.2.1.1)

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



>FitnessBrowser__Korea:Ga0059261_1313
          Length = 645

 Score =  882 bits (2279), Expect = 0.0
 Identities = 422/638 (66%), Positives = 500/638 (78%), Gaps = 3/638 (0%)

Query: 6   LYPVRPEVAASTLTDEATYKAMYQQSVVNPDGFWREQAKRLDWIKPFTTVKQTSFDDHHV 65
           ++PV  E A     D A Y+ +Y +S+ +P  FW +QAKRLDW+K        SFD+   
Sbjct: 5   IHPVPAEWAREARYDAAGYEQLYGRSIADPGSFWLDQAKRLDWVKRPELAGDWSFDESDF 64

Query: 66  DIKWFADGTLNVSYNCLDRHLAERGDQIAIIWEGDDPSE-SRNITYRELHEEVCKFANAL 124
            I+WFADG LNV+ NC+DRHLA RGD++AIIWE DDP+E SR  TYRELHEEVC+FAN L
Sbjct: 65  RIEWFADGKLNVAANCIDRHLASRGDEVAIIWEPDDPAEASRQFTYRELHEEVCRFANVL 124

Query: 125 RGQDVHRGDVVTIYMPMIPEAVVAMLACTRIGAIHSVVFGGFSPEALAGRIIDCKSKVVI 184
           +GQ V +GD VTIYMPMIPEA  A+LAC R+GAIHSVVFGGFSPEALAGRI DC S VVI
Sbjct: 125 KGQGVKKGDRVTIYMPMIPEAAFAILACARLGAIHSVVFGGFSPEALAGRITDCDSSVVI 184

Query: 185 TADEGVRAGKKIPLKANVDDALTNPETSSIQKVIVCKRTAGNIKWNQHRDIWYEDLMKVA 244
           TADEG R GK+I LKANVD A       +++KVIV K T G++     RD+WY +     
Sbjct: 185 TADEGRRGGKRIALKANVDAAAER--APALEKVIVVKATGGHVTMTPGRDVWYHEAAAGV 242

Query: 245 GTVCAPKEMGAEEALFILYTSGSTGKPKGVQHTTAGYLLYAALTHERVFDYKPGEVYWCT 304
           GT C  + M AE+ LFILYTSGSTGKPKGV HT+AGYLL+A+LTHE  FDY+PG V+WC 
Sbjct: 243 GTDCPAETMNAEDPLFILYTSGSTGKPKGVLHTSAGYLLWASLTHELAFDYRPGNVWWCA 302

Query: 305 ADVGWVTGHSYIVYGPLANGATTLLFEGVPNYPDITRVAKVIDKHKVSILYTAPTAIRAM 364
           AD+GWVTGHSYI+YGPLANGATTL++EG+PN+PD +R+ +V+D+H V  ++TAPTA+RA+
Sbjct: 303 ADIGWVTGHSYILYGPLANGATTLMYEGLPNWPDASRIWQVVDRHNVHTIFTAPTALRAL 362

Query: 365 MASGTAAVEGADGSSLRLLGSVGEPINPEAWDWYYKNVGKERCPIVDTWWQTETGGVLIS 424
           M  G   V     +SLRLLG+VGEPINPEAW WY++ VG+ RCPI+DTWWQTETGG +I+
Sbjct: 363 MKDGDDFVTKTSRTSLRLLGTVGEPINPEAWRWYHEVVGESRCPIIDTWWQTETGGAMIA 422

Query: 425 PLPGATALKPGSATRPFFGVVPALVDNLGNLIEGAAEGNLVILDSWPGQARTLYGDHDRF 484
           P+PGAT LKPGSATRP  GV P LVD+ G ++ GA EGNLVI  SWPGQ RT++GDH+RF
Sbjct: 423 PMPGATDLKPGSATRPLPGVDPQLVDSEGAVLHGATEGNLVIARSWPGQMRTVWGDHERF 482

Query: 485 VDTYFKTFSGMYFTGDGARRDEDGYYWITGRVDDVLNVSGHRMGTAEIESAMVAHPKVAE 544
             TYF T+ G YFTGDG RRDEDGYYWITGRVDDV+NVSGHRMGTAE+ESA+V HPKVAE
Sbjct: 483 FQTYFTTYPGKYFTGDGCRRDEDGYYWITGRVDDVINVSGHRMGTAEVESALVLHPKVAE 542

Query: 545 AAVVGVPHDIKGQGIYVYVTLNAGEETSEALRLELKNWVRKEIGPIASPDVIQWAPGLPK 604
           AAVVG+PHD+KGQGIY YVTLNAG    +ALR EL  WVR EIGPIA+PD +Q+APGLPK
Sbjct: 543 AAVVGMPHDVKGQGIYAYVTLNAGCAADDALRAELVKWVRTEIGPIATPDALQFAPGLPK 602

Query: 605 TRSGKIMRRILRKIATAEYDGLGDISTLADPGVVAHLI 642
           TRSGKIMRRILRKIA  +   LGD STLADP VV  L+
Sbjct: 603 TRSGKIMRRILRKIAEGDVSSLGDTSTLADPSVVDDLV 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: 1489
Number of extensions: 68
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 Ga0059261_1313 Ga0059261_1313 (acetyl-coenzyme A synthetase (EC 6.2.1.1))
to HMM TIGR02188 (acs: acetate--CoA ligase (EC 6.2.1.1))

Software error:

../bin/blast/fastacmd -i /tmp/list.21749.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.21749.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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