GapMind for catabolism of small carbon sources

 

Alignments for a candidate for astD in Escherichia coli BW25113

Align aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) (characterized)
to candidate 15864 b1746 succinylglutamic semialdehyde dehydrogenase (NCBI)

Query= BRENDA::P76217
         (492 letters)



>FitnessBrowser__Keio:15864
          Length = 492

 Score =  991 bits (2563), Expect = 0.0
 Identities = 492/492 (100%), Positives = 492/492 (100%)

Query: 1   MTLWINGDWITGQGASRVKRNPVSGEVLWQGNDADAAQVEQACRAARAAFPRWARLSFAE 60
           MTLWINGDWITGQGASRVKRNPVSGEVLWQGNDADAAQVEQACRAARAAFPRWARLSFAE
Sbjct: 1   MTLWINGDWITGQGASRVKRNPVSGEVLWQGNDADAAQVEQACRAARAAFPRWARLSFAE 60

Query: 61  RHAVVERFAALLESNKAELTAIIARETGKPRWEAATEVTAMINKIAISIKAYHVRTGEQR 120
           RHAVVERFAALLESNKAELTAIIARETGKPRWEAATEVTAMINKIAISIKAYHVRTGEQR
Sbjct: 61  RHAVVERFAALLESNKAELTAIIARETGKPRWEAATEVTAMINKIAISIKAYHVRTGEQR 120

Query: 121 SEMPDGAASLRHRPHGVLAVFGPYNFPGHLPNGHIVPALLAGNTIIFKPSELTPWSGEAV 180
           SEMPDGAASLRHRPHGVLAVFGPYNFPGHLPNGHIVPALLAGNTIIFKPSELTPWSGEAV
Sbjct: 121 SEMPDGAASLRHRPHGVLAVFGPYNFPGHLPNGHIVPALLAGNTIIFKPSELTPWSGEAV 180

Query: 181 MRLWQQAGLPPGVLNLVQGGRETGQALSALEDLDGLLFTGSANTGYQLHRQLSGQPEKIL 240
           MRLWQQAGLPPGVLNLVQGGRETGQALSALEDLDGLLFTGSANTGYQLHRQLSGQPEKIL
Sbjct: 181 MRLWQQAGLPPGVLNLVQGGRETGQALSALEDLDGLLFTGSANTGYQLHRQLSGQPEKIL 240

Query: 241 ALEMGGNNPLIIDEVADIDAAVHLTIQSAFVTAGQRCTCARRLLLKSGAQGDAFLARLVA 300
           ALEMGGNNPLIIDEVADIDAAVHLTIQSAFVTAGQRCTCARRLLLKSGAQGDAFLARLVA
Sbjct: 241 ALEMGGNNPLIIDEVADIDAAVHLTIQSAFVTAGQRCTCARRLLLKSGAQGDAFLARLVA 300

Query: 301 VSQRLTPGNWDDEPQPFIGGLISEQAAQQVVTAWQQLEAMGGRPLLAPRLLQAGTSLLTP 360
           VSQRLTPGNWDDEPQPFIGGLISEQAAQQVVTAWQQLEAMGGRPLLAPRLLQAGTSLLTP
Sbjct: 301 VSQRLTPGNWDDEPQPFIGGLISEQAAQQVVTAWQQLEAMGGRPLLAPRLLQAGTSLLTP 360

Query: 361 GIIEMTGVAGVPDEEVFGPLLRVWRYDTFDEAIRMANNTRFGLSCGLVSPEREKFDQLLL 420
           GIIEMTGVAGVPDEEVFGPLLRVWRYDTFDEAIRMANNTRFGLSCGLVSPEREKFDQLLL
Sbjct: 361 GIIEMTGVAGVPDEEVFGPLLRVWRYDTFDEAIRMANNTRFGLSCGLVSPEREKFDQLLL 420

Query: 421 EARAGIVNWNKPLTGAASTAPFGGIGASGNHRPSAWYAADYCAWPMASLESDSLTLPATL 480
           EARAGIVNWNKPLTGAASTAPFGGIGASGNHRPSAWYAADYCAWPMASLESDSLTLPATL
Sbjct: 421 EARAGIVNWNKPLTGAASTAPFGGIGASGNHRPSAWYAADYCAWPMASLESDSLTLPATL 480

Query: 481 NPGLDFSDEVVR 492
           NPGLDFSDEVVR
Sbjct: 481 NPGLDFSDEVVR 492


Lambda     K      H
   0.318    0.134    0.412 

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: 1050
Number of extensions: 36
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: 492
Length of database: 492
Length adjustment: 34
Effective length of query: 458
Effective length of database: 458
Effective search space:   209764
Effective search space used:   209764
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: 52 (24.6 bits)

Align candidate 15864 b1746 (succinylglutamic semialdehyde dehydrogenase (NCBI))
to HMM TIGR03240 (astD: succinylglutamate-semialdehyde dehydrogenase (EC 1.2.1.71))

Software error:

../bin/blast/fastacmd -i /tmp/list.7621.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.7621.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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