GapMind for Amino acid biosynthesis

 

Alignments for a candidate for asd in Desulfovibrio vulgaris Miyazaki F

Align Aspartate-semialdehyde dehydrogenase 2; ASA dehydrogenase 2; ASADH 2; Aspartate-beta-semialdehyde dehydrogenase 2; EC 1.2.1.11 (characterized)
to candidate 8501664 DvMF_2382 aspartate-semialdehyde dehydrogenase (RefSeq)

Query= SwissProt::P23247
         (337 letters)



>FitnessBrowser__Miya:8501664
          Length = 349

 Score =  328 bits (841), Expect = 1e-94
 Identities = 175/332 (52%), Positives = 224/332 (67%), Gaps = 10/332 (3%)

Query: 7   VAIFGATGAVGETMLEVLQEREFPVDELFLLASERSEGKTYRFNGKTVRVQNVEEFDWSQ 66
           VA+ GATGAVG  ML  L++REFP  E+   AS RS G    F G  + V+ + E  +  
Sbjct: 8   VAVCGATGAVGREMLNTLEQREFPAAEVIPFASARSAGNKVPFMGGELTVRELTEESFRG 67

Query: 67  VHIALFSAGGELSAKWAPIAAEAGVVVIDNTSHFRYDYDIPLVVPEVNPEAIAEFRNRNI 126
           V IALFSAGG  S K+AP A +AG VV+DN+S +R D   PLVVPEVN  A+A   +  I
Sbjct: 68  VDIALFSAGGSTSEKFAPHAVQAGCVVVDNSSAWRMDERCPLVVPEVNAHALAA--HNGI 125

Query: 127 IANPNCSTIQMLVALKPIYDAVGIERINVTTYQSVSGAGKAGIDELAGQTAKLLNGYPAE 186
           IANPNCSTIQM+VALKP++DA  I R+ V+TYQ+VSG G+  IDEL  Q  ++ N    +
Sbjct: 126 IANPNCSTIQMVVALKPLHDAARITRVVVSTYQAVSGTGQKAIDELEKQVRQMFNMQEPD 185

Query: 187 TNTFSQQIAFNCIPQIDQFMDNGYTKEEMKMVWETQKIFNDPSIMVNPTCVRVPVFYGHA 246
              +  +IAFNC+PQID FMDN YTKEEMKMV ET KI  DPS+ V  TCVRVPVFYGH+
Sbjct: 186 VAVYPHRIAFNCLPQIDVFMDNDYTKEEMKMVLETVKIMEDPSVKVTATCVRVPVFYGHS 245

Query: 247 EAVHVETRAPIDAEQVMDMLEQTDGIELFRGADFPTQVR-----DAGGKDHVLVGRVRND 301
           E+V++ET   + A++   +L Q  G+ ++   D P Q       DA G+D   VGR+R D
Sbjct: 246 ESVNIETERKLSAKEARAILAQAPGVRVY---DNPAQKMYPMPIDAAGEDDTFVGRIRED 302

Query: 302 ISHHSGINLWVVADNVRKGAATNAVQIAELLV 333
            +  +G+N+W+V+DN+RKGAA NAVQIAE LV
Sbjct: 303 ETIANGLNMWIVSDNIRKGAALNAVQIAEALV 334


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: 334
Number of extensions: 10
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: 337
Length of database: 349
Length adjustment: 29
Effective length of query: 308
Effective length of database: 320
Effective search space:    98560
Effective search space used:    98560
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 8501664 DvMF_2382 (aspartate-semialdehyde dehydrogenase (RefSeq))
to HMM TIGR01296 (asd: aspartate-semialdehyde dehydrogenase (EC 1.2.1.11))

Software error:

../bin/blast/fastacmd -i /tmp/list.16314.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.16314.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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