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_1441 Dsui_1441 phenylacetate-CoA ligase

Query= SwissProt::Q9L9C1
         (440 letters)



>FitnessBrowser__PS:Dsui_1441
          Length = 434

 Score =  641 bits (1654), Expect = 0.0
 Identities = 308/429 (71%), Positives = 364/429 (84%), Gaps = 2/429 (0%)

Query: 11  LEPIEKASQDELRALQLERLKWSVRHAYENVPHYRKAFDAKGVHPDDLKSLADLAKFPFT 70
           L+ IE AS+DE+ ALQ+ERL+W+++HAY+NVPHYR  FDA+GVHPDD  SL DL KFPFT
Sbjct: 8   LDAIENASRDEITALQVERLRWTLKHAYDNVPHYRAKFDAQGVHPDDFHSLDDLRKFPFT 67

Query: 71  AKGDLRDNYPFGMFAVPREKVARVHASSGTTGKPTVVGYTLKDIDTWATVVARSIRASGG 130
            K DLRDNYPF MFA PRE+V RVHASSGTTGKPTVVGYT KDIDTWA ++ARSI A+GG
Sbjct: 68  TKQDLRDNYPFKMFATPREEVVRVHASSGTTGKPTVVGYTQKDIDTWAHLMARSIYAAGG 127

Query: 131 RAGDMVHIAYGYGLFTGGLGAHYGAEKLGCTVVPMSGGQTEKQIQLIQDFKPDIIMVTPS 190
           R GD++H+AYGYGLFTGGLGAHYGAE LGCTV+PMSGGQTEKQ+QLI DF P IIM TPS
Sbjct: 128 RRGDIIHVAYGYGLFTGGLGAHYGAEALGCTVIPMSGGQTEKQVQLIADFAPRIIMCTPS 187

Query: 191 YMLTVLDEMERMGIDPHQTSLKVGIFGAEPWTQAMRAAMEARAGIDAVDIYGLSEVMGPG 250
           YML + DE +R G+DP  TSL++GI GAEPWT  MR  +E   GIDAVDIYGLSEVMGPG
Sbjct: 188 YMLNIADEFKRQGMDPRGTSLRIGIHGAEPWTDGMRQEIENLLGIDAVDIYGLSEVMGPG 247

Query: 251 VANECIEAKDGPVIWEDHFYPEIIDPHTGEVLPDGSEGELVFTTLTKEAMPVIRYRTRDL 310
           VANECIE+KDGPVIWEDHFYPEIIDP+TGEVLP+GS+GELVFT+L+KEA+PV+RYRTRDL
Sbjct: 248 VANECIESKDGPVIWEDHFYPEIIDPNTGEVLPEGSQGELVFTSLSKEALPVVRYRTRDL 307

Query: 311 TRLLPPTARSMRRMAKITGRSDDMLIIRGVNLFPTQVEELICKNPKLAPQYLLEVDKDGH 370
           TRLL PT+RS RR+ KITGRSDDMLIIRGVN+FP+Q+EELI K  KL+  YLLEV +DGH
Sbjct: 308 TRLLTPTSRSFRRIGKITGRSDDMLIIRGVNVFPSQIEELILKQAKLSGHYLLEVARDGH 367

Query: 371 MDTLTVKVEINPEANVGRHPEQKEALAKELQHDIKTFIGVSAKVHVCEPFAIERVTIGKA 430
           +D++TV VE+ PE  +    E KE +A ELQH IK++IG+S +V + E   IER ++GKA
Sbjct: 368 LDSITVNVEMKPEFGIATAAE-KEYVAHELQHHIKSYIGISTQVRIVEVGGIER-SVGKA 425

Query: 431 KRVVDRRPK 439
           KRV+D+RP+
Sbjct: 426 KRVIDKRPR 434


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: 696
Number of extensions: 18
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: 440
Length of database: 434
Length adjustment: 32
Effective length of query: 408
Effective length of database: 402
Effective search space:   164016
Effective search space used:   164016
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_1441 Dsui_1441 (phenylacetate-CoA ligase)
to HMM TIGR02155 (paaF: phenylacetate-CoA ligase (EC 6.2.1.30))

Software error:

../bin/blast/fastacmd -i /tmp/list.11399.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.11399.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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