GapMind for Amino acid biosynthesis

 

Alignments for a candidate for asd in Herbaspirillum seropedicae SmR1

Align Aspartate-semialdehyde dehydrogenase; ASA dehydrogenase; ASADH; Aspartate-beta-semialdehyde dehydrogenase; EC 1.2.1.11 (characterized)
to candidate HSERO_RS16495 HSERO_RS16495 aspartate-semialdehyde dehydrogenase

Query= SwissProt::Q51344
         (370 letters)



>FitnessBrowser__HerbieS:HSERO_RS16495
          Length = 370

 Score =  521 bits (1343), Expect = e-153
 Identities = 257/368 (69%), Positives = 299/368 (81%), Gaps = 2/368 (0%)

Query: 1   MKRVGLIGWRGMVGSVLMQRMLEERDFDLIEPVFFTTSNVGGQGPEVGKDIAPLKDAYSI 60
           MK VGL+GWRGMVGSVLMQRM +E DFD IEPVFF+TSN GG+ P   K    LKDA SI
Sbjct: 1   MKLVGLVGWRGMVGSVLMQRMQDEGDFDHIEPVFFSTSNAGGKAPSFAKKETTLKDANSI 60

Query: 61  DELKTLDVILTCQGGDYTSEVFPKLREAGWQGYWIDAASSLRMEDDAVIVLDPVNRKVID 120
           DELK  D+I+T QGGDYT+E+FPKLR AGW GYWIDAASSLRM+DDAVIVLDPVN  VI 
Sbjct: 61  DELKKCDIIITAQGGDYTNEIFPKLRAAGWDGYWIDAASSLRMKDDAVIVLDPVNNNVIK 120

Query: 121 QALDAGTRNYIGGNCTVSLMLMALGGLFDAGLVEWMSAMTYQAASGAGAQNMRELLKQMG 180
            AL  G +NYIGGNCT S++LM +GGLF  GLVEW+S+MTYQAASG GA +MRELLK MG
Sbjct: 121 DALAKGVKNYIGGNCTNSILLMGVGGLFKEGLVEWVSSMTYQAASGGGANHMRELLKGMG 180

Query: 181 AAHASVADDLANPASAILDIDRKVAETLRSEAFPTEHFGAPLGGSLIPWIDKELPNGQSR 240
             +A+VAD+LA P+SAILDIDRKVA+T+R E  PTE FGAPL G LIPWID +L NGQS+
Sbjct: 181 VINAAVADELATPSSAILDIDRKVAKTIR-EDVPTEFFGAPLAGGLIPWIDAQLENGQSK 239

Query: 241 EEWKAQAETNKILARFKNPIPVDGICVRVGAMRCHSQALTIKLNKDVPLTDIEGLISQHN 300
           EEWK QAE NKIL   +  IPVDG+CVR+GAMRCHS ALTIKL +D+PL +IE +I   N
Sbjct: 240 EEWKGQAEVNKILGN-EQIIPVDGLCVRIGAMRCHSLALTIKLKRDLPLAEIESIIRAGN 298

Query: 301 PWVKLVPNHREVSVRELTPAAVTGTLSVPVGRLRKLNMGSQYLGAFTVGDQLLWGAAEPL 360
            WVK VPN R ++V+ELTPA++TG L + VGR+RKLN G +Y+ AF +GDQLLWGAAEPL
Sbjct: 299 QWVKWVPNDRAITVKELTPASITGGLEIGVGRVRKLNQGPEYISAFVIGDQLLWGAAEPL 358

Query: 361 RRMLRILL 368
           RRMLRI+L
Sbjct: 359 RRMLRIIL 366


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: 513
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: 370
Length adjustment: 30
Effective length of query: 340
Effective length of database: 340
Effective search space:   115600
Effective search space used:   115600
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: 49 (23.5 bits)

Align candidate HSERO_RS16495 HSERO_RS16495 (aspartate-semialdehyde dehydrogenase)
to HMM TIGR01745 (asd: aspartate-semialdehyde dehydrogenase (EC 1.2.1.11))

Software error:

../bin/blast/fastacmd -i /tmp/list.17451.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.17451.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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