GapMind for catabolism of small carbon sources

 

Alignments for a candidate for acs in Pseudomonas putida KT2440

Align Acetyl-coenzyme A synthetase (EC 6.2.1.1) (characterized)
to candidate PP_4487 PP_4487 acetyl-CoA synthetase

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



>FitnessBrowser__Putida:PP_4487
          Length = 696

 Score = 1243 bits (3216), Expect = 0.0
 Identities = 597/651 (91%), Positives = 623/651 (95%)

Query: 1   MSAASLYPVRPEVAASTLTDEATYKAMYQQSVVNPDGFWREQAKRLDWIKPFTTVKQTSF 60
           MSAA LYPVRPEVAA+TLTDEATYKAMYQQSV+NPDGFWREQA+R+DWIKPFT VKQTSF
Sbjct: 44  MSAAPLYPVRPEVAATTLTDEATYKAMYQQSVINPDGFWREQAQRIDWIKPFTKVKQTSF 103

Query: 61  DDHHVDIKWFADGTLNVSYNCLDRHLAERGDQIAIIWEGDDPSESRNITYRELHEEVCKF 120
           DDHHVDIKWFADGTLNVS NCLDRHL ERGDQ+AIIWEGDDPSE RNITYRELHE+VCKF
Sbjct: 104 DDHHVDIKWFADGTLNVSSNCLDRHLEERGDQLAIIWEGDDPSEHRNITYRELHEQVCKF 163

Query: 121 ANALRGQDVHRGDVVTIYMPMIPEAVVAMLACTRIGAIHSVVFGGFSPEALAGRIIDCKS 180
           ANALRGQDVHRGDVVTIYMPMIPEAVVAMLAC RIGAIHSVVFGGFSPEALAGRIIDCKS
Sbjct: 164 ANALRGQDVHRGDVVTIYMPMIPEAVVAMLACARIGAIHSVVFGGFSPEALAGRIIDCKS 223

Query: 181 KVVITADEGVRAGKKIPLKANVDDALTNPETSSIQKVIVCKRTAGNIKWNQHRDIWYEDL 240
           KVVITADEGVR G++ PLKANVD ALTNPETSS+QK+IVCKRT G+I W+QHRDIWYEDL
Sbjct: 224 KVVITADEGVRGGRRTPLKANVDLALTNPETSSVQKIIVCKRTGGDIAWHQHRDIWYEDL 283

Query: 241 MKVAGTVCAPKEMGAEEALFILYTSGSTGKPKGVQHTTAGYLLYAALTHERVFDYKPGEV 300
           MKVA + CAPKEMGAEEALFILYTSGSTGKPKGV HTT GYL+YAALTHERVFDY+PGEV
Sbjct: 284 MKVASSHCAPKEMGAEEALFILYTSGSTGKPKGVLHTTGGYLVYAALTHERVFDYRPGEV 343

Query: 301 YWCTADVGWVTGHSYIVYGPLANGATTLLFEGVPNYPDITRVAKVIDKHKVSILYTAPTA 360
           YWCTADVGWVTGHSYIVYGPLANGATTLLFEGVPNYPDITRV+K++DKHKV+ILYTAPTA
Sbjct: 344 YWCTADVGWVTGHSYIVYGPLANGATTLLFEGVPNYPDITRVSKIVDKHKVNILYTAPTA 403

Query: 361 IRAMMASGTAAVEGADGSSLRLLGSVGEPINPEAWDWYYKNVGKERCPIVDTWWQTETGG 420
           IRAMMA G AAVEGADGSSLRLLGSVGEPINPEAW+WYYK VGKERCPIVDTWWQTETGG
Sbjct: 404 IRAMMAEGQAAVEGADGSSLRLLGSVGEPINPEAWNWYYKTVGKERCPIVDTWWQTETGG 463

Query: 421 VLISPLPGATALKPGSATRPFFGVVPALVDNLGNLIEGAAEGNLVILDSWPGQARTLYGD 480
           +LISPLPGAT LKPGSATRPFFGVVPALVDNLGNLI+GAAEGNLVILDSWPGQ+R+LYGD
Sbjct: 464 ILISPLPGATGLKPGSATRPFFGVVPALVDNLGNLIDGAAEGNLVILDSWPGQSRSLYGD 523

Query: 481 HDRFVDTYFKTFSGMYFTGDGARRDEDGYYWITGRVDDVLNVSGHRMGTAEIESAMVAHP 540
           HDRFVDTYFKTF GMYFTGDGARRDEDGYYWITGRVDDVLNVSGHRMGTAEIESAMVAH 
Sbjct: 524 HDRFVDTYFKTFRGMYFTGDGARRDEDGYYWITGRVDDVLNVSGHRMGTAEIESAMVAHS 583

Query: 541 KVAEAAVVGVPHDIKGQGIYVYVTLNAGEETSEALRLELKNWVRKEIGPIASPDVIQWAP 600
           KVAEAAVVGVPHDIKGQGIYVYVTLNAG E SE LRLELKNWVRKEIGPIASPDVIQWAP
Sbjct: 584 KVAEAAVVGVPHDIKGQGIYVYVTLNAGIEASEQLRLELKNWVRKEIGPIASPDVIQWAP 643

Query: 601 GLPKTRSGKIMRRILRKIATAEYDGLGDISTLADPGVVAHLIETHKTMNVA 651
           GLPKTRSGKIMRRILRKIAT EYD LGDISTLADPGVV HLI+THK MN+A
Sbjct: 644 GLPKTRSGKIMRRILRKIATGEYDALGDISTLADPGVVQHLIDTHKAMNLA 694


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: 1751
Number of extensions: 57
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: 696
Length adjustment: 39
Effective length of query: 612
Effective length of database: 657
Effective search space:   402084
Effective search space used:   402084
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 PP_4487 PP_4487 (acetyl-CoA synthetase)
to HMM TIGR02188 (acs: acetate--CoA ligase (EC 6.2.1.1))

Software error:

../bin/blast/fastacmd -i /tmp/list.11777.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.11777.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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