GapMind for catabolism of small carbon sources

 

Alignments for a candidate for acs in Pseudomonas fluorescens GW456-L13

Align Acetyl-coenzyme A synthetase (EC 6.2.1.1) (characterized)
to candidate PfGW456L13_1963 Acetyl-coenzyme A synthetase (EC 6.2.1.1)

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



>FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1963
          Length = 651

 Score = 1295 bits (3352), Expect = 0.0
 Identities = 623/651 (95%), Positives = 639/651 (98%)

Query: 1   MSAASLYPVRPEVAANTLTDEATYKAMYQQSVVNPDGFWREQAKRLDWIKPFTTVKQTSF 60
           MSAASLYPVRPEV ANTLTDEATYKAMYQQSVVNPDGFWREQAKRLDWIKPFTTVKQTSF
Sbjct: 1   MSAASLYPVRPEVLANTLTDEATYKAMYQQSVVNPDGFWREQAKRLDWIKPFTTVKQTSF 60

Query: 61  DDHHVDIKWFADGTLNVSYNCLDRHLAERGDQIAIIWEGDDPAESRNITYRELHEQVCKF 120
           DDHHVDIKWFADGTLNVSYNCLDRHLAERGDQ+AIIWEGDDPAESRNITYRELHEQVCKF
Sbjct: 61  DDHHVDIKWFADGTLNVSYNCLDRHLAERGDQVAIIWEGDDPAESRNITYRELHEQVCKF 120

Query: 121 ANALRGQDVHRGDVVTIYMPMIPEAVVAMLACTRIGAIHSVVFGGFSPEALAGRIIDCKS 180
           ANALRGQDVHRGDVVTIYMPMIPEAVVAMLACTRIGAIHSVVFGGFSPEALAGRIIDC+S
Sbjct: 121 ANALRGQDVHRGDVVTIYMPMIPEAVVAMLACTRIGAIHSVVFGGFSPEALAGRIIDCRS 180

Query: 181 KVVITADEGLRAGKKISLKANVDDALTNPETSSIQKVIVCKRTGGNIKWNQHRDIWYEDL 240
           KVVITADEG+RAGKKI LKANVDDALTNPETSSIQKVIVCKRTGG+IKWNQHRDIW+EDL
Sbjct: 181 KVVITADEGIRAGKKIPLKANVDDALTNPETSSIQKVIVCKRTGGDIKWNQHRDIWFEDL 240

Query: 241 MKVAGTVCAPKEMGAEEALFILYTSGSTGKPKGVQHTTGGYLLYAALTHERVFDYRPGEI 300
           MKVAGTVCAPKEMGAEEALFILYTSGSTGKPKGVQHTTGGYLLYAA+THERVFDYRPGEI
Sbjct: 241 MKVAGTVCAPKEMGAEEALFILYTSGSTGKPKGVQHTTGGYLLYAAMTHERVFDYRPGEI 300

Query: 301 YWCTADVGWVTGHTYIVYGPLANGATTLLFEGVPNYPDITRVAKIIDKHKVNILYTAPTA 360
           YWCTADVGWVTGH+YIVYGPLANGATTLLFEGVPNYPDITRVAKI+DKHKVNILYTAPTA
Sbjct: 301 YWCTADVGWVTGHSYIVYGPLANGATTLLFEGVPNYPDITRVAKIVDKHKVNILYTAPTA 360

Query: 361 IRAMMAQGTAAVEGADGSSLRLLGSVGEPINPEAWEWYYKNVGQSRCPIVDTWWQTETGA 420
           IRAMMA GTAAVEGADGSSLRLLGSVGEPINPEAW+WYYKNVG+SRCPIVDTWWQTETG 
Sbjct: 361 IRAMMASGTAAVEGADGSSLRLLGSVGEPINPEAWDWYYKNVGKSRCPIVDTWWQTETGG 420

Query: 421 TLMSPLPGAHGLKPGSAARPFFGVVPALVDNLGNIIEGVAEGNLVILDSWPGQARTLYGD 480
            +MSPLPGAH LKPGSAARPFFGVVPALVDNLGNI+EG AEGNLVILDSWPGQARTL+GD
Sbjct: 421 NMMSPLPGAHALKPGSAARPFFGVVPALVDNLGNIVEGEAEGNLVILDSWPGQARTLFGD 480

Query: 481 HDRFVDTYFKTFRGMYFTGDGARRDADGYWWITGRVDDVLNVSGHRMGTAEIESAMVAHP 540
           HDRFVDTYFKTFRGMYFTGDGARRDADGY+WITGRVDDVLNVSGHRMGTAEIESAMVAHP
Sbjct: 481 HDRFVDTYFKTFRGMYFTGDGARRDADGYYWITGRVDDVLNVSGHRMGTAEIESAMVAHP 540

Query: 541 KVAEAAVVGVPHDIKGQGIYVYVTLNGGEEPSEALRLELKNWVRKEIGPIASPDVIQWAP 600
           KVAEAAVVGVPHDIKGQGIYVYVTL  GEEP+E LRLELKNWVRKEIGPIASPDVIQWAP
Sbjct: 541 KVAEAAVVGVPHDIKGQGIYVYVTLKNGEEPNEQLRLELKNWVRKEIGPIASPDVIQWAP 600

Query: 601 GLPKTRSGKIMRRILRKIATGEYDGLGDISTLADPGVVQHLIDTHKTMNVA 651
           GLPKTRSGKIMRRILRKIAT EY+GLGDISTLADP VVQHLIDTHKTMNVA
Sbjct: 601 GLPKTRSGKIMRRILRKIATAEYEGLGDISTLADPSVVQHLIDTHKTMNVA 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: 1747
Number of extensions: 55
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 PfGW456L13_1963 (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.32392.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.32392.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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