GapMind for catabolism of small carbon sources

 

Alignments for a candidate for paaK in Dinoroseobacter shibae DFL-12

Align phenylacetate-CoA ligase (EC 6.2.1.30) (characterized)
to candidate 3610443 Dshi_3824 phenylacetate-CoA ligase (RefSeq)

Query= BRENDA::B4E7B5
         (432 letters)



>FitnessBrowser__Dino:3610443
          Length = 436

 Score =  573 bits (1476), Expect = e-168
 Identities = 280/425 (65%), Positives = 336/425 (79%), Gaps = 1/425 (0%)

Query: 7   LEPIETASRDELTALQLERLKWSLRHAYDHSPVYRRKFDEAGVHPDDLKTLADLSRFPFT 66
           L+PIE ASRDE+ ALQL+R+KWSLRHAYD+ P+YR +FD AGVHPDDL+ L DL++FPFT
Sbjct: 11  LDPIEIASRDEIAALQLDRMKWSLRHAYDNVPMYRARFDAAGVHPDDLRDLKDLAKFPFT 70

Query: 67  TKGDLRDSYPFGMFAVPQDRISRIHASSGTTGKPTVVGYTAADIDTWANLVARSIRAAGA 126
            K DLRD YPFGM AVP+DR+ R+HASSGTTGKPTVV YT  DI+ WA+ +ARS+RA+G 
Sbjct: 71  HKSDLRDHYPFGMSAVPRDRLVRVHASSGTTGKPTVVVYTRHDIEVWADTLARSLRASGL 130

Query: 127 RRGDKVHVSYGYGLFTGGLGAHYGAERAGLTVIPFGGGQTEKQVQLIQDFRPDIIMVTPS 186
           R GD +H +YGYGLFTGGLGAHYG E+ G TVIP GGGQTEKQV LI DFRP  IMVTPS
Sbjct: 131 RAGDMIHNAYGYGLFTGGLGAHYGIEKLGATVIPMGGGQTEKQVSLIHDFRPTAIMVTPS 190

Query: 187 YMLSIADEIERQGLDPVQSSLRIGIFGAEPWTNDMRVAIEQRMGIDAVDIYGLSEVMGPG 246
           YML+I +   + GLDP QSSL++G+FGAEPWTN MR  +E+   + AVDIYGLSEVMGPG
Sbjct: 191 YMLNILEGFHKAGLDPRQSSLQVGVFGAEPWTNAMRQEVEEAFDMHAVDIYGLSEVMGPG 250

Query: 247 VASECVETKDGPTIWEDHFYPEIIDPETGEVLPDGELGELVFTSLTKEALPIIRYRTRDL 306
           VA+ECVETKDG  +WEDH+YPEIIDP+TGEVL DG  GELVFT+LTKE +P+IRYRTRDL
Sbjct: 251 VANECVETKDGLHVWEDHYYPEIIDPQTGEVLKDGAEGELVFTTLTKEGMPMIRYRTRDL 310

Query: 307 TRLLPGTARTMRRMEKITGRSDDMMIVRGVNVFPTQIEEQLLKQRALAPHYQIVLTKEGP 366
           TRLLPGTAR+MRR+EKITGRSDDMMI+RGVNVFPTQIEEQ++    L P++QI L   G 
Sbjct: 311 TRLLPGTARSMRRIEKITGRSDDMMILRGVNVFPTQIEEQVMATGGLGPYFQIELYTSGR 370

Query: 367 LDVLTLNVEPCPETAPDTAAIQVAKQALAYDIKSLIGVTAVINVLPVNGIERSVGKARRV 426
           LD + + VE  P  A D  +   A + L   ++ ++GV+  + V     + RS GKA RV
Sbjct: 371 LDAMRVFVEATP-AAADELSRTAAARVLTKHVRDMVGVSIEVVVGDPGSVARSQGKAVRV 429

Query: 427 VDKRK 431
           +D RK
Sbjct: 430 IDNRK 434


Lambda     K      H
   0.319    0.137    0.404 

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: 630
Number of extensions: 10
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: 432
Length of database: 436
Length adjustment: 32
Effective length of query: 400
Effective length of database: 404
Effective search space:   161600
Effective search space used:   161600
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 3610443 Dshi_3824 (phenylacetate-CoA ligase (RefSeq))
to HMM TIGR02155 (paaF: phenylacetate-CoA ligase (EC 6.2.1.30))

Software error:

../bin/blast/fastacmd -i /tmp/list.6587.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.6587.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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