GapMind for catabolism of small carbon sources

 

Alignments for a candidate for fadA in Burkholderia phytofirmans PsJN

Align Acetyl-CoA acetyltransferase; Acetoacetyl-CoA thiolase; Beta-ketothiolase; EC 2.3.1.9 (characterized)
to candidate BPHYT_RS09150 BPHYT_RS09150 acetyl-CoA acetyltransferase

Query= SwissProt::P14611
         (393 letters)



>FitnessBrowser__BFirm:BPHYT_RS09150
          Length = 393

 Score =  664 bits (1714), Expect = 0.0
 Identities = 335/392 (85%), Positives = 362/392 (92%)

Query: 1   MTDVVIVSAARTAVGKFGGSLAKIPAPELGAVVIKAALERAGVKPEQVSEVIMGQVLTAG 60
           MTDVVIVSAARTAVGKFGGSLAKI APELGA VI+A LERAG+KPEQVSEVI+GQVLTAG
Sbjct: 1   MTDVVIVSAARTAVGKFGGSLAKIAAPELGATVIRAVLERAGLKPEQVSEVILGQVLTAG 60

Query: 61  SGQNPARQAAIKAGLPAMVPAMTINKVCGSGLKAVMLAANAIMAGDAEIVVAGGQENMSA 120
           SGQNPARQA IKAGLP  VP MTIN VCGSGLKAVMLAANAI+AGDA+IVVAGGQENMSA
Sbjct: 61  SGQNPARQAVIKAGLPTAVPGMTINVVCGSGLKAVMLAANAIIAGDADIVVAGGQENMSA 120

Query: 121 APHVLPGSRDGFRMGDAKLVDTMIVDGLWDVYNQYHMGITAENVAKEYGITREAQDEFAV 180
           APHVLPGSRDGFRMGDAKL+D+MIVDGLWDVYNQYHMG+TAENVAKEYGITRE QD FA 
Sbjct: 121 APHVLPGSRDGFRMGDAKLIDSMIVDGLWDVYNQYHMGVTAENVAKEYGITREQQDAFAA 180

Query: 181 GSQNKAEAAQKAGKFDEEIVPVLIPQRKGDPVAFKTDEFVRQGATLDSMSGLKPAFDKAG 240
            SQNKAEAAQKAG+FD+EIVPV IPQRKG+P+ F TDEFVR G T +S++GLKPAF K G
Sbjct: 181 LSQNKAEAAQKAGRFDDEIVPVEIPQRKGEPLRFATDEFVRHGVTAESLAGLKPAFSKEG 240

Query: 241 TVTAANASGLNDGAAAVVVMSAAKAKELGLTPLATIKSYANAGVDPKVMGMGPVPASKRA 300
           +VTAANASGLNDGAAAV+VMSA KA+ LGL PLA IK+YA +G+DPKVMGMGPVPAS+R 
Sbjct: 241 SVTAANASGLNDGAAAVLVMSAKKAEALGLKPLARIKAYATSGLDPKVMGMGPVPASRRC 300

Query: 301 LSRAEWTPQDLDLMEINEAFAAQALAVHQQMGWDTSKVNVNGGAIAIGHPIGASGCRILV 360
           L RA WTP DLDLMEINEAFAAQA AV+QQMGWDTSK+NVNGGAIAIGHPIGASGCRILV
Sbjct: 301 LERAGWTPADLDLMEINEAFAAQACAVNQQMGWDTSKINVNGGAIAIGHPIGASGCRILV 360

Query: 361 TLLHEMKRRDAKKGLASLCIGGGMGVALAVER 392
           TLLHEM++RDAKKGLASLCIGGGMGVALA+ER
Sbjct: 361 TLLHEMQKRDAKKGLASLCIGGGMGVALALER 392


Lambda     K      H
   0.315    0.131    0.369 

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: 18
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 (21.6 bits)
S2: 50 (23.9 bits)

Align candidate BPHYT_RS09150 BPHYT_RS09150 (acetyl-CoA acetyltransferase)
to HMM TIGR01930 (acetyl-CoA C-acyltransferase (EC 2.3.1.16))

Software error:

../bin/blast/fastacmd -i /tmp/list.23086.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.23086.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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