GapMind for catabolism of small carbon sources

 

Alignments for a candidate for acs in Pseudomonas simiae WCS417

Align Acetyl-coenzyme A synthetase (EC 6.2.1.1) (characterized)
to candidate GFF4246 PS417_21750 acetyl-CoA synthetase

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



>FitnessBrowser__WCS417:GFF4246
          Length = 651

 Score = 1298 bits (3359), Expect = 0.0
 Identities = 626/651 (96%), Positives = 637/651 (97%)

Query: 1   MSAASLYPVRPEVAANTLTDEATYKAMYQQSVVNPDGFWREQAKRLDWIKPFTTVKQTSF 60
           MSAASLYPVRPEVAANTLTDEATYKAMYQQSVVNPDGFWREQAKRLDWIKPFTTVKQTSF
Sbjct: 1   MSAASLYPVRPEVAANTLTDEATYKAMYQQSVVNPDGFWREQAKRLDWIKPFTTVKQTSF 60

Query: 61  DDHHVDIKWFADGTLNVSYNCLDRHLAERGDQIAIIWEGDDPAESRNITYRELHEQVCKF 120
           DDHHVDIKWFADGTLNVSYNCLDRHLAERGDQ AIIWEGDDP+ESR ITYRELHE+VCKF
Sbjct: 61  DDHHVDIKWFADGTLNVSYNCLDRHLAERGDQAAIIWEGDDPSESRTITYRELHEEVCKF 120

Query: 121 ANALRGQDVHRGDVVTIYMPMIPEAVVAMLACTRIGAIHSVVFGGFSPEALAGRIIDCKS 180
           ANALRGQDVHRGDVVTIYMPMIPEAVVAMLACTRIGAIHSVVFGGFSPEALAGRIIDCKS
Sbjct: 121 ANALRGQDVHRGDVVTIYMPMIPEAVVAMLACTRIGAIHSVVFGGFSPEALAGRIIDCKS 180

Query: 181 KVVITADEGLRAGKKISLKANVDDALTNPETSSIQKVIVCKRTGGNIKWNQHRDIWYEDL 240
           KVVITADEG+RAGKKI LKANVDDALTNPETSSIQKVIVCKRT GNIKWNQHRDIWYEDL
Sbjct: 181 KVVITADEGIRAGKKIPLKANVDDALTNPETSSIQKVIVCKRTNGNIKWNQHRDIWYEDL 240

Query: 241 MKVAGTVCAPKEMGAEEALFILYTSGSTGKPKGVQHTTGGYLLYAALTHERVFDYRPGEI 300
           MKVAGTVCAPKEMGAEEALFILYTSGSTGKPKGVQHTTGGYLLYAALTHERVFDYRPGEI
Sbjct: 241 MKVAGTVCAPKEMGAEEALFILYTSGSTGKPKGVQHTTGGYLLYAALTHERVFDYRPGEI 300

Query: 301 YWCTADVGWVTGHTYIVYGPLANGATTLLFEGVPNYPDITRVAKIIDKHKVNILYTAPTA 360
           YWCTADVGWVTGHTYIVYGPLANGATTLLFEGVPNYPDITRVAKI+DKHKVNILYTAPTA
Sbjct: 301 YWCTADVGWVTGHTYIVYGPLANGATTLLFEGVPNYPDITRVAKIVDKHKVNILYTAPTA 360

Query: 361 IRAMMAQGTAAVEGADGSSLRLLGSVGEPINPEAWEWYYKNVGQSRCPIVDTWWQTETGA 420
           IRAMMA GTAA EGADGSSLRLLGSVGEPINPEAW+WYYKNVGQSRCPIVDTWWQTETG 
Sbjct: 361 IRAMMASGTAACEGADGSSLRLLGSVGEPINPEAWDWYYKNVGQSRCPIVDTWWQTETGG 420

Query: 421 TLMSPLPGAHGLKPGSAARPFFGVVPALVDNLGNIIEGVAEGNLVILDSWPGQARTLYGD 480
            +MSPLPGAH LKPGSAARPFFGVVPALVDNLGN+IEG AEGNLVILDSWPGQARTL+GD
Sbjct: 421 NMMSPLPGAHALKPGSAARPFFGVVPALVDNLGNLIEGAAEGNLVILDSWPGQARTLFGD 480

Query: 481 HDRFVDTYFKTFRGMYFTGDGARRDADGYWWITGRVDDVLNVSGHRMGTAEIESAMVAHP 540
           HDRFVDTYFKTFRGMYFTGDGARRD DGY+WITGRVDDVLNVSGHRMGTAEIESAMVAHP
Sbjct: 481 HDRFVDTYFKTFRGMYFTGDGARRDEDGYYWITGRVDDVLNVSGHRMGTAEIESAMVAHP 540

Query: 541 KVAEAAVVGVPHDIKGQGIYVYVTLNGGEEPSEALRLELKNWVRKEIGPIASPDVIQWAP 600
           KVAEAAVVGVPHDIKGQGIYVYVTL  GEEP+EALRLELKNWVRKEIGPIASPDVIQWAP
Sbjct: 541 KVAEAAVVGVPHDIKGQGIYVYVTLKNGEEPNEALRLELKNWVRKEIGPIASPDVIQWAP 600

Query: 601 GLPKTRSGKIMRRILRKIATGEYDGLGDISTLADPGVVQHLIDTHKTMNVA 651
           GLPKTRSGKIMRRILRKIATGEYDGLGDISTLADPGVV HLI+THKTMNVA
Sbjct: 601 GLPKTRSGKIMRRILRKIATGEYDGLGDISTLADPGVVAHLIETHKTMNVA 651


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: 1751
Number of extensions: 56
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: 651
Length adjustment: 38
Effective length of query: 613
Effective length of database: 613
Effective search space:   375769
Effective search space used:   375769
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 GFF4246 PS417_21750 (acetyl-CoA synthetase)
to HMM TIGR02188 (acs: acetate--CoA ligase (EC 6.2.1.1))

Software error:

../bin/blast/fastacmd -i /tmp/list.792.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.792.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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