GapMind for catabolism of small carbon sources

 

Alignments for a candidate for fadA in Pseudomonas stutzeri RCH2

Align acetyl-CoA C-acetyltransferase (EC 2.3.1.16) (characterized)
to candidate GFF1043 Psest_1076 acetyl-CoA acetyltransferases

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



>FitnessBrowser__psRCH2:GFF1043
          Length = 393

 Score =  656 bits (1693), Expect = 0.0
 Identities = 327/392 (83%), Positives = 363/392 (92%)

Query: 1   MQDVVIVAATRTAVGSFQGSLASIPAPELGAAVIRRLLEQTGLDPAQVDEVILGQVLTAG 60
           MQDVVIVAATRTA+GSFQGSLA++PA ELGA VIR LLE+TG++PAQVDEVILG VLTAG
Sbjct: 1   MQDVVIVAATRTAIGSFQGSLANVPAVELGATVIRALLEKTGIEPAQVDEVILGHVLTAG 60

Query: 61  SGQNPARQASILAGLPHAVPSLTLNKVCGSGLKALHLGAQAIRCGDAEVIIAGGMENMSL 120
           +GQN ARQASI AGLPHAVPS+TLNKVCGSGLKA+HL  QAIRCGDA+VIIAGGMENMSL
Sbjct: 61  AGQNTARQASIKAGLPHAVPSMTLNKVCGSGLKAVHLAVQAIRCGDADVIIAGGMENMSL 120

Query: 121 APYVLPAARTGLRMGHAKMIDSMITDGLWDAFNDYHMGITAENLVDKYGISREAQDAFAA 180
           APYVLP ARTGLRMGHA+++D+MITDGLWDAFNDYHMGITAENL +KYGI R  QDAFAA
Sbjct: 121 APYVLPGARTGLRMGHAQIVDTMITDGLWDAFNDYHMGITAENLAEKYGIDRAQQDAFAA 180

Query: 181 ASQQKATAAIEAGRFVDEITPILIPQRKGDPVAFAVDEQPRAGTTAESLAKLKPAFKKDG 240
            SQQ+A AAIE+GRF  EITP++IPQRKGDP+AFA DEQPRAGTTAESL  L+ AFKKDG
Sbjct: 181 QSQQRAAAAIESGRFDAEITPVMIPQRKGDPLAFARDEQPRAGTTAESLGGLRAAFKKDG 240

Query: 241 SVTAGNASSLNDGAAAVLLMSADKAKALGLPVLARIASYANAGVDPAIMGIGPVSATRRC 300
            VTAGNAS+LNDGAAAV+LMSA KA+ALGLPVLA+IA YANAGVDPAIMGIGPV+ATRRC
Sbjct: 241 CVTAGNASTLNDGAAAVVLMSASKAEALGLPVLAKIAGYANAGVDPAIMGIGPVTATRRC 300

Query: 301 LDKAGWSLGDLDLIEANEAFAAQSLAVGKELEWDAEKVNVNGGAIAIGHPIGASGCRVLV 360
           LDKAGW+L +LDLIEANEAFA Q+L+VGKEL WDA+KVNVNGGAIA+GHPIGASGCR+LV
Sbjct: 301 LDKAGWTLAELDLIEANEAFAVQALSVGKELGWDADKVNVNGGAIALGHPIGASGCRILV 360

Query: 361 TLLHEMIKRDAKKGLATLCIGGGQGVALALER 392
           TLLHEM +RD +KGLATLCIGGGQGVALA+ER
Sbjct: 361 TLLHEMQRRDVRKGLATLCIGGGQGVALAVER 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: 537
Number of extensions: 13
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: 393
Length adjustment: 31
Effective length of query: 362
Effective length of database: 362
Effective search space:   131044
Effective search space used:   131044
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 GFF1043 Psest_1076 (acetyl-CoA acetyltransferases)
to HMM TIGR01930 (acetyl-CoA C-acyltransferase (EC 2.3.1.16))

Software error:

../bin/blast/fastacmd -i /tmp/list.8644.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.8644.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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