GapMind for catabolism of small carbon sources

 

Alignments for a candidate for boxC in Magnetospirillum magneticum AMB-1

Align Benzoyl-CoA-dihydrodiol lyase; EC 4.1.2.44 (characterized)
to candidate WP_011382621.1 AMB_RS00885 2,3-epoxybenzoyl-CoA dihydrolase

Query= SwissProt::Q84HH6
         (555 letters)



>NCBI__GCF_000009985.1:WP_011382621.1
          Length = 550

 Score =  613 bits (1582), Expect = e-180
 Identities = 303/550 (55%), Positives = 388/550 (70%), Gaps = 6/550 (1%)

Query: 12  LVDYRTEPSKYRHWSLATDGEIATLTLNIDEDGGIRPGYKLKLNSYDLGVDIELHDALQR 71
           +++++T P  YRHW LA DG +ATLT+++D    + PGY+LK+NSYDLGVDIEL+DA+QR
Sbjct: 1   MINFQTSPESYRHWKLAFDGPVATLTMDVDPASTLAPGYELKMNSYDLGVDIELYDAVQR 60

Query: 72  VRFEHPEVRTVVVTSGKPKIFCSGANIYMLGLSTHAWKVNFCKFTNETRNGIEDSSQYSG 131
           +RFEHPEVR VV+ S  PKIFC+GANI MLG+S+H  KVNFCKFTNETRN IED+S+ S 
Sbjct: 61  LRFEHPEVRAVVMASANPKIFCAGANIKMLGVSSHGHKVNFCKFTNETRNSIEDASENSR 120

Query: 132 LKFLAACNGTTAGGGYELALACDEIVLVDDRNSSVSLPEVPLLGVLPGTGGLTRVTDKRR 191
             +L A  GT AGGGYELALA D I++VDD N++VSLPEVPLL VLPGTGGLTRV DKR+
Sbjct: 121 QTYLCAVTGTAAGGGYELALATDYIMMVDDGNTAVSLPEVPLLAVLPGTGGLTRVVDKRK 180

Query: 192 VRRDHADIFCTISEGVRGQRAKDWRLVDDVVKQQQFAEHIQARAKALAQTSDRPAGAKGV 251
           VRRD ADIFC+I EGV+G+RA +WRLVD+V+    F   +  +A  LA  SDRP   KGV
Sbjct: 181 VRRDLADIFCSIEEGVKGKRAVEWRLVDEVIPSSAFKAAVAKKAAELAARSDRPTAEKGV 240

Query: 252 KLTTLERTVDEKGYHYEFVDATIDADGRTVTLTVRAPAAVTAKTAAEIEAQGIKWWPLQM 311
            L+ + R +      Y  +D   D   R   +T++ P A      A I+AQG+ ++PL +
Sbjct: 241 VLSQVSRVIGTDSVTYPHIDIAFDRATRAANITIKGPKAACPADLAGIKAQGVDFYPLAL 300

Query: 312 ARELDDAILNLRTNHLDVGLWQLRTEGDAQVVLDIDATIDA-NRDNWFVRETIGMLRRTL 370
           ARELDDAIL+LR N   +  W  RT+GDA +V+  DA +      +W VRE +   +RT+
Sbjct: 301 ARELDDAILHLRANETTIATWVFRTQGDADLVMGYDAALQTFGASDWLVREILLYWKRTM 360

Query: 371 ARIDVSSRSLYALIEPGSCFAGTLLEIALAADRSYMLDAAEAKN-----VVGLSAMNFGT 425
            R+DV+SR+L+AL+EPGSCFAG + EI  A DRS+MLD     N      + LSA+NF  
Sbjct: 361 KRLDVTSRTLFALVEPGSCFAGFVAEILFAVDRSFMLDGTFEDNPAPAAAIRLSALNFDG 420

Query: 426 FPMVNGLSRIDARFYQEEAPVAAVKAKQGSLLSPAEAMELGLVTAIPDDLDWAEEVRIAI 485
            PM NG+SR+  RF  E   V   +   G  L  A   +LGLVT  PDD+DW +E+R+ I
Sbjct: 421 LPMGNGISRLATRFLGEPDSVGKARDTIGKDLDAAACAKLGLVTGTPDDIDWEDEIRLMI 480

Query: 486 EERAALSPDALTGLEANLRFGPVETMNTRIFGRLSAWQNWIFNRPNAVGENGALKLFGSG 545
           EERA+ SPD+LTG+EANLRF   ETM T+IFGRL+AWQNWIF RPNAVG+ GALKL+G+G
Sbjct: 481 EERASFSPDSLTGMEANLRFAGPETMETKIFGRLTAWQNWIFQRPNAVGDQGALKLYGTG 540

Query: 546 KKAQFDWNRV 555
           K+A ++  RV
Sbjct: 541 KRAAYNQERV 550


Lambda     K      H
   0.318    0.134    0.397 

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: 778
Number of extensions: 32
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: 555
Length of database: 550
Length adjustment: 36
Effective length of query: 519
Effective length of database: 514
Effective search space:   266766
Effective search space used:   266766
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: 53 (25.0 bits)

Align candidate WP_011382621.1 AMB_RS00885 (2,3-epoxybenzoyl-CoA dihydrolase)
to HMM TIGR03222 (boxC: benzoyl-CoA-dihydrodiol lyase (EC 4.1.2.44))

Software error:

../bin/blast/fastacmd -i /tmp/list.2750.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.2750.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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