GapMind for catabolism of small carbon sources

 

Alignments for a candidate for paaJ2 in Klebsiella michiganensis M5al

Align 3-oxoadipyl-CoA thiolase; EC 2.3.1.174 (characterized, see rationale)
to candidate BWI76_RS16135 BWI76_RS16135 acetyl-CoA acetyltransferase

Query= uniprot:D8ITH5
         (401 letters)



>FitnessBrowser__Koxy:BWI76_RS16135
          Length = 400

 Score =  617 bits (1590), Expect = 0.0
 Identities = 310/399 (77%), Positives = 352/399 (88%), Gaps = 1/399 (0%)

Query: 2   EALICDAIRTPFGRYGGALGAVRADDLAAAPIRSLMERNPGVDWSRVEDILYGCANQAGE 61
           +A ICDA+RTPFGR+GG L  +RADDLAA P+++L+ERNPG+D +R++D++YGCANQAGE
Sbjct: 3   QAFICDAVRTPFGRFGGTLATLRADDLAALPLKALLERNPGLDPARIDDVIYGCANQAGE 62

Query: 62  DNRNVARMAGLLAGLPIAVPGSTVNRLCGSSLDAVGMAARAIKSGEVQLMIAGGVESMTR 121
           DNRNVARMA LLAGLP +VPGSTVNRLCGSSLDA+G+AARAIKSGE QLMIAGGVESM+R
Sbjct: 63  DNRNVARMALLLAGLPESVPGSTVNRLCGSSLDAIGIAARAIKSGETQLMIAGGVESMSR 122

Query: 122 APFVMGKAESAFARSAAIFDTTIGWRFVNPLMKAQYGIDSMPETAENVATDFQINRADQD 181
           APFVMGKAESAF+R+  + DTTIGWRF+NP MKA YG+DSMPETAENVA DF I+RADQD
Sbjct: 123 APFVMGKAESAFSRTMRMEDTTIGWRFINPQMKALYGVDSMPETAENVADDFAISRADQD 182

Query: 182 AFALRSQQRWAAAQAAGFFAGEIAPLTIPQKKGDPLVVTTDEHPRPDTTLATLAKLKGVV 241
           AFALRSQ R AAAQ AG FA E+  +++PQ+KG+PL+ + DEHPR  TT   LA+L+GVV
Sbjct: 183 AFALRSQLRTAAAQEAGRFADELIAVSVPQRKGEPLLFSRDEHPR-TTTAEALARLRGVV 241

Query: 242 RPDGTVTAGNASGVNDGACALLLASPKAADLYRLKPRARVLGMATAGVAPRIMGFGPAPA 301
           RPDGTVTAGNASGVNDGACALLLAS +A     L+P ARV+G+ATAGVAPRIMGFGPAPA
Sbjct: 242 RPDGTVTAGNASGVNDGACALLLASEQALAANDLQPLARVVGVATAGVAPRIMGFGPAPA 301

Query: 302 VRKVLAQVGLTLAQMDVIELNEAFAAQGLAVMRDLGLPDDAAHVNPNGGAIAIGHPLGAS 361
           VRKVLAQ GLTL QMDVIELNEAFAAQ LAV RDLGLPDDAA+VNPNGGAIA+GHPLGAS
Sbjct: 302 VRKVLAQTGLTLGQMDVIELNEAFAAQALAVTRDLGLPDDAAYVNPNGGAIALGHPLGAS 361

Query: 362 GARLVTTAINQLERSGGRYALCTMCIGVGQGIALVIERV 400
           G RL  TA  QL R+GGRYALCTMCIGVGQGIAL+IERV
Sbjct: 362 GGRLAMTAAYQLRRTGGRYALCTMCIGVGQGIALIIERV 400


Lambda     K      H
   0.320    0.135    0.394 

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: 594
Number of extensions: 16
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: 401
Length of database: 400
Length adjustment: 31
Effective length of query: 370
Effective length of database: 369
Effective search space:   136530
Effective search space used:   136530
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: 50 (23.9 bits)

Align candidate BWI76_RS16135 BWI76_RS16135 (acetyl-CoA acetyltransferase)
to HMM TIGR02430 (pcaF: 3-oxoadipyl-CoA thiolase (EC 2.3.1.174))

Software error:

../bin/blast/fastacmd -i /tmp/list.22689.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.22689.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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