GapMind for catabolism of small carbon sources

 

Alignments for a candidate for astD in Shewanella amazonensis SB2B

Align Succinylglutamic semialdehyde dehydrogenase (EC 1.2.1.71) (characterized)
to candidate 6938906 Sama_3009 succinylglutamic semialdehyde dehydrogenase (RefSeq)

Query= reanno::SB2B:6938906
         (486 letters)



>FitnessBrowser__SB2B:6938906
          Length = 486

 Score =  968 bits (2502), Expect = 0.0
 Identities = 486/486 (100%), Positives = 486/486 (100%)

Query: 1   MTQFINGQWLAGEGKEMQSKNPANGEVIWQGKAAVPAQVQAAVMAARDAQFEWFMLGFEG 60
           MTQFINGQWLAGEGKEMQSKNPANGEVIWQGKAAVPAQVQAAVMAARDAQFEWFMLGFEG
Sbjct: 1   MTQFINGQWLAGEGKEMQSKNPANGEVIWQGKAAVPAQVQAAVMAARDAQFEWFMLGFEG 60

Query: 61  RQAIVEAYRNELEANKAELAEVIAQETGKPRWETATEAAAMIGKIGLSVSAYHKRTGTEV 120
           RQAIVEAYRNELEANKAELAEVIAQETGKPRWETATEAAAMIGKIGLSVSAYHKRTGTEV
Sbjct: 61  RQAIVEAYRNELEANKAELAEVIAQETGKPRWETATEAAAMIGKIGLSVSAYHKRTGTEV 120

Query: 121 NEGAAGRAVLRHKPHGVVAVFGPYNFPGHLPNGHIVPALLAGNTVVFKPSELTPKVAELM 180
           NEGAAGRAVLRHKPHGVVAVFGPYNFPGHLPNGHIVPALLAGNTVVFKPSELTPKVAELM
Sbjct: 121 NEGAAGRAVLRHKPHGVVAVFGPYNFPGHLPNGHIVPALLAGNTVVFKPSELTPKVAELM 180

Query: 181 LKLWEKAGLPAGVINLVQGEVETGKALASHPQLDGLFFTGSSRTGHLLHQQYAGHPGKIL 240
           LKLWEKAGLPAGVINLVQGEVETGKALASHPQLDGLFFTGSSRTGHLLHQQYAGHPGKIL
Sbjct: 181 LKLWEKAGLPAGVINLVQGEVETGKALASHPQLDGLFFTGSSRTGHLLHQQYAGHPGKIL 240

Query: 241 ALEMGGNNPLIVKGVSDTRAAIHDIIQSAFISSGQRCTCARRLYVEKGAEGDKLLAGLVE 300
           ALEMGGNNPLIVKGVSDTRAAIHDIIQSAFISSGQRCTCARRLYVEKGAEGDKLLAGLVE
Sbjct: 241 ALEMGGNNPLIVKGVSDTRAAIHDIIQSAFISSGQRCTCARRLYVEKGAEGDKLLAGLVE 300

Query: 301 AVKAIKVGPWNADPQPFMGSMISETAAKGMLDAQRNLLNLGAKSLVEMTHLQAGTGLVSP 360
           AVKAIKVGPWNADPQPFMGSMISETAAKGMLDAQRNLLNLGAKSLVEMTHLQAGTGLVSP
Sbjct: 301 AVKAIKVGPWNADPQPFMGSMISETAAKGMLDAQRNLLNLGAKSLVEMTHLQAGTGLVSP 360

Query: 361 GLIDVTEVIELPDEEYFGPLLQVVRYTSFDEAIRLANDTRYGLSAGILADDKADYEYFLA 420
           GLIDVTEVIELPDEEYFGPLLQVVRYTSFDEAIRLANDTRYGLSAGILADDKADYEYFLA
Sbjct: 361 GLIDVTEVIELPDEEYFGPLLQVVRYTSFDEAIRLANDTRYGLSAGILADDKADYEYFLA 420

Query: 421 RIRAGIVNWNKQITGASGAAPFGGVGASGNHRASAFYAADYCAYPVASMEADSVTLPASL 480
           RIRAGIVNWNKQITGASGAAPFGGVGASGNHRASAFYAADYCAYPVASMEADSVTLPASL
Sbjct: 421 RIRAGIVNWNKQITGASGAAPFGGVGASGNHRASAFYAADYCAYPVASMEADSVTLPASL 480

Query: 481 SPGLTL 486
           SPGLTL
Sbjct: 481 SPGLTL 486


Lambda     K      H
   0.317    0.133    0.393 

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: 969
Number of extensions: 21
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: 486
Length of database: 486
Length adjustment: 34
Effective length of query: 452
Effective length of database: 452
Effective search space:   204304
Effective search space used:   204304
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: 52 (24.6 bits)

Align candidate 6938906 Sama_3009 (succinylglutamic semialdehyde dehydrogenase (RefSeq))
to HMM TIGR03240 (astD: succinylglutamate-semialdehyde dehydrogenase (EC 1.2.1.71))

Software error:

../bin/blast/fastacmd -i /tmp/list.25303.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.25303.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

For help, please send mail to the webmaster (help@microbesonline.org), giving this error message and the time and date of the error.