GapMind for catabolism of small carbon sources

 

Alignments for a candidate for paaK in Dechlorosoma suillum PS

Align Phenylacetate-coenzyme A ligase; Phenylacetyl-CoA ligase; PA-CoA ligase; EC 6.2.1.30 (characterized)
to candidate Dsui_1443 Dsui_1443 phenylacetate-CoA ligase

Query= SwissProt::Q9L9C1
         (440 letters)



>FitnessBrowser__PS:Dsui_1443
          Length = 438

 Score =  594 bits (1531), Expect = e-174
 Identities = 285/429 (66%), Positives = 350/429 (81%), Gaps = 3/429 (0%)

Query: 12  EPIEKASQDELRALQLERLKWSVRHAYENVPHYRKAFDAKGVHPDDLKSLADLAKFPFTA 71
           E I +AS+DE+ ALQL+RL+ S+RHAYE VPH R  FDA GVHPDDLK+LADLA+FPFT 
Sbjct: 12  ERIARASRDEIAALQLKRLQQSLRHAYEKVPHTRAKFDAHGVHPDDLKTLADLARFPFTG 71

Query: 72  KGDLRDNYPFGMFAVPREKVARVHASSGTTGKPTVVGYTLKDIDTWATVVARSIRASGGR 131
           K DLRDNYP+G+FAVP   + RVHASSGTTGKPTVVGYT  DID WA ++AR++RA+G  
Sbjct: 72  KQDLRDNYPYGLFAVPMRDIVRVHASSGTTGKPTVVGYTAGDIDRWADIMARALRAAGAG 131

Query: 132 AGDMVHIAYGYGLFTGGLGAHYGAEKLGCTVVPMSGGQTEKQIQLIQDFKPDIIMVTPSY 191
             D+VH+A+GYGLFTGGLG HYG E+LG T VP+SGGQTE+Q+QLI DFKP +++VTPSY
Sbjct: 132 PEDIVHVAHGYGLFTGGLGVHYGVERLGATAVPVSGGQTERQVQLIADFKPTVLVVTPSY 191

Query: 192 MLTVLDEMERMGIDPHQTSLKVGIFGAEPWTQAMRAAMEARAGIDAVDIYGLSEVMGPGV 251
            L + DE E  G D   +SL++G+FGAEPW ++MRA +E R GI A+D+YGLSEVMGPGV
Sbjct: 192 ALNLADECEHQGFDLAGSSLRIGLFGAEPWGESMRAEIERRFGIAAMDLYGLSEVMGPGV 251

Query: 252 ANECIEAKDGPVIWEDHFYPEIIDPHTGEVLPDGSEGELVFTTLTKEAMPVIRYRTRDLT 311
           A+ECIE++DGP IWEDHFYPEIIDP+TGEVLPDG+ GELVFT+LTKE MPV+RYRTRDLT
Sbjct: 252 ASECIESRDGPTIWEDHFYPEIIDPNTGEVLPDGAHGELVFTSLTKEGMPVVRYRTRDLT 311

Query: 312 RLLPPTARSMRRMAKITGRSDDMLIIRGVNLFPTQVEELICKNPKLAPQYLLEVDKDGHM 371
            LLPPTARS RR+ KITGRSDDMLIIRGVN+FP+Q+EE + K  +L+P Y LEV ++GH+
Sbjct: 312 TLLPPTARSFRRIGKITGRSDDMLIIRGVNVFPSQIEEFVLKQAELSPHYQLEVWREGHL 371

Query: 372 DTLTVKVEINPE-ANVGRHPEQKEALAKELQHDIKTFIGVSAKVHVCEPFAIERVTIGKA 430
           D L ++VE+ PE AN G H    E  A+ELQH IK++IG+S +V V    +IER   GKA
Sbjct: 372 DKLDIRVELKPEFANAGTH--VSEQAARELQHHIKSYIGISTRVRVEAVGSIERAVGGKA 429

Query: 431 KRVVDRRPK 439
           +RVVD+RP+
Sbjct: 430 RRVVDKRPQ 438


Lambda     K      H
   0.318    0.137    0.406 

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: 709
Number of extensions: 21
Number of successful extensions: 2
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: 440
Length of database: 438
Length adjustment: 32
Effective length of query: 408
Effective length of database: 406
Effective search space:   165648
Effective search space used:   165648
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: 51 (24.3 bits)

Align candidate Dsui_1443 Dsui_1443 (phenylacetate-CoA ligase)
to HMM TIGR02155 (paaF: phenylacetate-CoA ligase (EC 6.2.1.30))

Software error:

../bin/blast/fastacmd -i /tmp/list.7416.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.7416.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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