GapMind for Amino acid biosynthesis

 

Alignments for a candidate for asd in Cupriavidus basilensis 4G11

Align Aspartate-semialdehyde dehydrogenase; ASA dehydrogenase; ASADH; Aspartate-beta-semialdehyde dehydrogenase; EC 1.2.1.11 (characterized)
to candidate RR42_RS14380 RR42_RS14380 aspartate-semialdehyde dehydrogenase

Query= SwissProt::Q51344
         (370 letters)



>FitnessBrowser__Cup4G11:RR42_RS14380
          Length = 378

 Score =  511 bits (1316), Expect = e-149
 Identities = 254/375 (67%), Positives = 299/375 (79%), Gaps = 9/375 (2%)

Query: 4   VGLIGWRGMVGSVLMQRMLEERDFDLIEPVFFTTSNVGGQGPEVGKDIAPLKDAYSIDEL 63
           VGL+GWRGMVGSVLMQRM EERDFD IEPVFF+TSN GGQ P + K+   LKDA  I+ L
Sbjct: 3   VGLVGWRGMVGSVLMQRMQEERDFDHIEPVFFSTSNAGGQAPAMAKNETKLKDANDIEAL 62

Query: 64  KTLDVILTCQGGDYTSEVFPKLREAGWQGYWIDAASSLRMEDDAVIVLDPVNRKVIDQAL 123
           K  DV+LT QGGDYT+E+FP+LR AGW+GYWIDAASSLRM+DDA+IVLDPVN  VI  AL
Sbjct: 63  KKCDVVLTAQGGDYTNEIFPQLRAAGWKGYWIDAASSLRMKDDAIIVLDPVNLGVIKDAL 122

Query: 124 DAGTRNYIGGNCTVSLMLMALGGLFDAGLVEWMSAMTYQAASGAGAQNMRELLKQMGAAH 183
             G +N+IGGNCTVS M+M LGGLF   L++WM++MTYQAASG GAQ+MRELL Q G  +
Sbjct: 123 AKGVKNFIGGNCTVSCMMMGLGGLFQHDLIDWMTSMTYQAASGGGAQHMRELLTQFGTLN 182

Query: 184 ASVADDLANPASAILDIDRKVAETLRS-EAFPTEHFGAPLGGSLIPWIDKELPNGQSREE 242
           ASV   L NPASAIL+IDR +  T     A  T+ FG PL G+LIPWIDK+L NG S+EE
Sbjct: 183 ASVKSLLDNPASAILEIDRTILATQHGLSADETKQFGVPLAGNLIPWIDKDLGNGVSKEE 242

Query: 243 WKAQAETNKILARFKN--------PIPVDGICVRVGAMRCHSQALTIKLNKDVPLTDIEG 294
           WKA AETNKIL R +         PI VDG+CVR+GAMRCHSQALTIKL +DVPL +IE 
Sbjct: 243 WKAGAETNKILGRGEGFLGATGAAPIAVDGLCVRIGAMRCHSQALTIKLRRDVPLDEIEA 302

Query: 295 LISQHNPWVKLVPNHREVSVRELTPAAVTGTLSVPVGRLRKLNMGSQYLGAFTVGDQLLW 354
           +++++N W K+VPN RE S+ +LTPAAVTGTL++PVGRLRK+ MG +YL AFTVGDQLLW
Sbjct: 303 MLAENNQWAKVVPNTREASMTDLTPAAVTGTLTIPVGRLRKMQMGGEYLSAFTVGDQLLW 362

Query: 355 GAAEPLRRMLRILLE 369
           GAAEPLRRMLRIL+E
Sbjct: 363 GAAEPLRRMLRILIE 377


Lambda     K      H
   0.319    0.136    0.409 

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: 518
Number of extensions: 14
Number of successful extensions: 3
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: 370
Length of database: 378
Length adjustment: 30
Effective length of query: 340
Effective length of database: 348
Effective search space:   118320
Effective search space used:   118320
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 (21.8 bits)
S2: 50 (23.9 bits)

Align candidate RR42_RS14380 RR42_RS14380 (aspartate-semialdehyde dehydrogenase)
to HMM TIGR01745 (asd: aspartate-semialdehyde dehydrogenase (EC 1.2.1.11))

Software error:

../bin/blast/fastacmd -i /tmp/list.9497.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.9497.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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