GapMind for catabolism of small carbon sources

 

Alignments for a candidate for fadA in Pseudomonas putida KT2440

Align acetyl-CoA C-acetyltransferase (EC 2.3.1.16) (characterized)
to candidate PP_4636 PP_4636 acetyl-CoA acetyltransferase

Query= metacyc::MONOMER-20831
         (393 letters)



>FitnessBrowser__Putida:PP_4636
          Length = 392

 Score =  660 bits (1704), Expect = 0.0
 Identities = 332/392 (84%), Positives = 366/392 (93%)

Query: 1   MQDVVIVAATRTAVGSFQGSLASIPAPELGAAVIRRLLEQTGLDPAQVDEVILGQVLTAG 60
           M DVVIVAATRTA+GSFQG+LA++PA +LGAAVI++LL+QTGLDPAQVDEVILGQVLTAG
Sbjct: 1   MNDVVIVAATRTAIGSFQGALATVPAVDLGAAVIKQLLKQTGLDPAQVDEVILGQVLTAG 60

Query: 61  SGQNPARQASILAGLPHAVPSLTLNKVCGSGLKALHLGAQAIRCGDAEVIIAGGMENMSL 120
           +GQNPARQA+I AGLP +VP+LTLNKVCGSGLKALHL AQAIRCGDAEV+IAGG ENMSL
Sbjct: 61  AGQNPARQAAIKAGLPFSVPALTLNKVCGSGLKALHLAAQAIRCGDAEVVIAGGQENMSL 120

Query: 121 APYVLPAARTGLRMGHAKMIDSMITDGLWDAFNDYHMGITAENLVDKYGISREAQDAFAA 180
           APYV+P+ARTG RMGH ++IDSMITDGLWDAFNDYHMGITAENLVDKYG+SRE QDAFAA
Sbjct: 121 APYVMPSARTGQRMGHGQLIDSMITDGLWDAFNDYHMGITAENLVDKYGLSREQQDAFAA 180

Query: 181 ASQQKATAAIEAGRFVDEITPILIPQRKGDPVAFAVDEQPRAGTTAESLAKLKPAFKKDG 240
            SQ+KA AAIEAGRF  EITPI++PQ+KG+P  FA DEQPR  TTAESLAKL+PAFKKDG
Sbjct: 181 ESQRKAVAAIEAGRFDAEITPIVLPQKKGEPKVFARDEQPRPDTTAESLAKLRPAFKKDG 240

Query: 241 SVTAGNASSLNDGAAAVLLMSADKAKALGLPVLARIASYANAGVDPAIMGIGPVSATRRC 300
           SVTAGNASSLNDGAAAVLLMSA KA+ALGLPVLA+IA+YA+AGVDPAIMGIGPVSAT+RC
Sbjct: 241 SVTAGNASSLNDGAAAVLLMSAAKAEALGLPVLAKIAAYASAGVDPAIMGIGPVSATQRC 300

Query: 301 LDKAGWSLGDLDLIEANEAFAAQSLAVGKELEWDAEKVNVNGGAIAIGHPIGASGCRVLV 360
           LDKAGW L +LDLIEANEAFAAQ+LAVG  L WDA +VNVNGGAIA+GHPIGASGCRVLV
Sbjct: 301 LDKAGWQLAELDLIEANEAFAAQALAVGNALAWDAARVNVNGGAIALGHPIGASGCRVLV 360

Query: 361 TLLHEMIKRDAKKGLATLCIGGGQGVALALER 392
           TLLHEMIKRD KKGLATLCIGGGQGVALA+ER
Sbjct: 361 TLLHEMIKRDVKKGLATLCIGGGQGVALAIER 392


Lambda     K      H
   0.317    0.133    0.378 

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: 556
Number of extensions: 12
Number of successful extensions: 1
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: 393
Length of database: 392
Length adjustment: 31
Effective length of query: 362
Effective length of database: 361
Effective search space:   130682
Effective search space used:   130682
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 50 (23.9 bits)

Align candidate PP_4636 PP_4636 (acetyl-CoA acetyltransferase)
to HMM TIGR01930 (acetyl-CoA C-acyltransferase (EC 2.3.1.16))

Software error:

../bin/blast/fastacmd -i /tmp/list.2653.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.2653.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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