GapMind for catabolism of small carbon sources

 

Alignments for a candidate for paaK in Marinobacter adhaerens HP15

Align Phenylacetate-coenzyme A ligase; Phenylacetyl-CoA ligase; PA-CoA ligase; EC 6.2.1.30 (characterized)
to candidate GFF2752 HP15_2696 phenylacetate-CoA ligase

Query= SwissProt::O33469
         (439 letters)



>FitnessBrowser__Marino:GFF2752
          Length = 436

 Score =  642 bits (1657), Expect = 0.0
 Identities = 316/425 (74%), Positives = 357/425 (84%), Gaps = 1/425 (0%)

Query: 12  LDPMETASVDALRQHQLERLRWSLKHAYDNVPLYRQRFAECGAHPDDLTCLEDLAKFPFT 71
           LD METAS+D LR  QL+RLRWS+ HAY NVP YR+ F + G  P D+  LEDLAK PFT
Sbjct: 11  LDRMETASIDELRHEQLQRLRWSVVHAYTNVPFYRKAFDDQGLKPMDINSLEDLAKVPFT 70

Query: 72  GKNDLRDNYPYGMFAVPQEEVVRLHASSGTTGKPTVVGYTQNDINTWANVVARSIRAAGG 131
            K DLRDNYP+GMFA P  +VVR+HASSGTTGKPTVVGYTQ+DINTWA++VARSIRA GG
Sbjct: 71  TKADLRDNYPFGMFATPMSDVVRVHASSGTTGKPTVVGYTQSDINTWADIVARSIRAGGG 130

Query: 132 RKGDKVHVSYGYGLFTGGLGAHYGAERLGCTVIPMSGGQTEKQVQLIRDFQPDIIMVTPS 191
            +GDKVHV+YGYGLFTGGLGAHYGAERLGCTVIPMSGGQTEKQVQLI+DF+PDIIMVTPS
Sbjct: 131 SRGDKVHVAYGYGLFTGGLGAHYGAERLGCTVIPMSGGQTEKQVQLIKDFEPDIIMVTPS 190

Query: 192 YMLNLADEIERQGIDPHDLKLRLGIFGAEPWTDELRRSIEQRLGINALDIYGLSEIMGPG 251
           YMLN+ADE+ERQGIDPH L LRLGIFGAEPWT+ +R  IE+RLGI ALDIYGLSE+MGPG
Sbjct: 191 YMLNIADEMERQGIDPHKLPLRLGIFGAEPWTNAMRSEIEERLGIEALDIYGLSEVMGPG 250

Query: 252 VAMECIETKDGPTIWEDHFYPEIIDPVTGEVLPDGQLGELVFTSLSKEALPMVRYRTRDL 311
           V MECIETKDGPTIWEDHFYPEII+P TGEVLPDG+ GELVFTSL+K ALP++RYRTRDL
Sbjct: 251 VGMECIETKDGPTIWEDHFYPEIINPETGEVLPDGEYGELVFTSLTKVALPILRYRTRDL 310

Query: 312 TRLLPGTARPMRRIGKITGRSDDMLIIRGVNVFPTQIEEQVLKIKQLSEMYEIHLYRNGN 371
           TRLLPGTARPMRRI KITGRSDDMLIIRGVNVFP+QIEEQVLK + L+  YEI +Y+ GN
Sbjct: 311 TRLLPGTARPMRRIDKITGRSDDMLIIRGVNVFPSQIEEQVLKCEALAPHYEIEVYKEGN 370

Query: 372 LDSVEVHVELRAECQHLDEGQRKLVIGELSKQIKTYIGISTQVHLQACGTLKRSEGKACH 431
           LD V++  EL+       E  R     EL+  IK+YIGIST+V +     L RSEGKA  
Sbjct: 371 LDCVDIRTELKPGVTDTPE-SRAAAAKELAHHIKSYIGISTRVEVVETNRLARSEGKAKR 429

Query: 432 VYDKR 436
           V+D+R
Sbjct: 430 VFDRR 434


Lambda     K      H
   0.320    0.138    0.415 

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: 723
Number of extensions: 24
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: 439
Length of database: 436
Length adjustment: 32
Effective length of query: 407
Effective length of database: 404
Effective search space:   164428
Effective search space used:   164428
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 (21.8 bits)
S2: 51 (24.3 bits)

Align candidate GFF2752 HP15_2696 (phenylacetate-CoA ligase)
to HMM TIGR02155 (paaF: phenylacetate-CoA ligase (EC 6.2.1.30))

Software error:

../bin/blast/fastacmd -i /tmp/list.19051.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.19051.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

For help, please send mail to the webmaster (help@microbesonline.org), giving this error message and the time and date of the error.