GapMind for Amino acid biosynthesis

 

Alignments for a candidate for asd in Caulobacter crescentus NA1000

Align Aspartate-semialdehyde dehydrogenase 2; ASA dehydrogenase 2; ASADH 2; Aspartate-beta-semialdehyde dehydrogenase 2; EC 1.2.1.11 (characterized)
to candidate CCNA_00253 CCNA_00253 aspartate-semialdehyde dehydrogenase

Query= SwissProt::P23247
         (337 letters)



>FitnessBrowser__Caulo:CCNA_00253
          Length = 342

 Score =  310 bits (793), Expect = 4e-89
 Identities = 161/330 (48%), Positives = 226/330 (68%), Gaps = 4/330 (1%)

Query: 5   FNVAIFGATGAVGETMLEVLQEREFPVDELFLLASERSEGKTYRFNGKTVRVQNVEEFDW 64
           + VA+ GATG VG  M  +L+E +FPVD++  +AS +S G    F  + ++ +++E+FD+
Sbjct: 3   YRVAVVGATGNVGREMFNILEEVKFPVDKMHAIASRKSIGVEVSFGNEILKCEDLEQFDF 62

Query: 65  SQVHIALFSAGGELSAKWAPIAAEAGVVVIDNTSHFRYDYDIPLVVPEVNPEAIAEFRNR 124
           S+V + L SAGG +S  W      AG +VIDN+SHFR D D+PLVVPEVNPEA+     +
Sbjct: 63  SKVDLVLMSAGGSISKAWGEKIGAAGPIVIDNSSHFRMDPDVPLVVPEVNPEAVNSI-PK 121

Query: 125 NIIANPNCSTIQMLVALKPIYDAVGIERINVTTYQSVSGAGKAGIDELAGQTAKLLNGYP 184
           NIIANPNCST Q++VALKP++D   I+R+ V+TYQSVSGAGK G+DEL  QT  +     
Sbjct: 122 NIIANPNCSTAQLVVALKPLHDEAKIKRVVVSTYQSVSGAGKEGMDELWDQTKGVYVLGA 181

Query: 185 AETNTFSQQIAFNCIPQIDQFMDNGYTKEEMKMVWETQKIFNDPSIMVNPTCVRVPVFYG 244
                F++QIAFN IP ID FMD+G+TKEE KM  ETQKI  DP+I +  TCVRVPV  G
Sbjct: 182 PPPKKFTKQIAFNVIPHIDVFMDDGFTKEEWKMAVETQKIL-DPAIKLTATCVRVPVMVG 240

Query: 245 HAEAVHVETRAPIDAEQVMDMLEQTDGIELFRGADFPTQV--RDAGGKDHVLVGRVRNDI 302
           H+E+V+VE  +P+D ++  ++L + DGI +    +    +  +++ G+  V + R+R D 
Sbjct: 241 HSESVNVEFESPLDEDEAREILREADGIVVVDKREDGGYITPKESQGEFPVYISRIRKDP 300

Query: 303 SHHSGINLWVVADNVRKGAATNAVQIAELL 332
           +  +G+  W V+DN+RKGAA NAVQIA+LL
Sbjct: 301 TVENGLAFWCVSDNLRKGAALNAVQIAQLL 330


Lambda     K      H
   0.319    0.135    0.395 

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: 316
Number of extensions: 10
Number of successful extensions: 5
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: 337
Length of database: 342
Length adjustment: 28
Effective length of query: 309
Effective length of database: 314
Effective search space:    97026
Effective search space used:    97026
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 CCNA_00253 CCNA_00253 (aspartate-semialdehyde dehydrogenase)
to HMM TIGR01296 (asd: aspartate-semialdehyde dehydrogenase (EC 1.2.1.11))

Software error:

../bin/blast/fastacmd -i /tmp/list.5849.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.5849.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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