GapMind for Amino acid biosynthesis

 

Alignments for a candidate for asd in Sphingomonas koreensis DSMZ 15582

Align Aspartate-semialdehyde dehydrogenase 2; ASA dehydrogenase 2; ASADH 2; Aspartate-beta-semialdehyde dehydrogenase 2; EC 1.2.1.11 (characterized)
to candidate Ga0059261_4003 Ga0059261_4003 aspartate-semialdehyde dehydrogenase (peptidoglycan organisms)

Query= SwissProt::P23247
         (337 letters)



>FitnessBrowser__Korea:Ga0059261_4003
          Length = 341

 Score =  326 bits (836), Expect = 5e-94
 Identities = 178/335 (53%), Positives = 225/335 (67%), Gaps = 7/335 (2%)

Query: 5   FNVAIFGATGAVGETMLEVLQEREFPVDELFLLASERSEGKTYRFN--GKTVRVQNVEEF 62
           + V + GATG VG  ML +L EREFP+DEL +LAS RS G    F   GK  ++QN+E F
Sbjct: 3   YRVVVAGATGNVGREMLNILAEREFPIDELAVLASSRSTGDMVDFGETGKQYKIQNIEHF 62

Query: 63  DWSQVHIALFSAGGELSAKWAPIAAEAGVVVIDNTSHFRYDYDIPLVVPEVNPEAIAEFR 122
           D +   +ALF+ G E +   AP  A AG  VIDN+S +R D D+PL+VPEVNPEAI  ++
Sbjct: 63  DPTGWDMALFAIGSEATKVHAPRFAAAGCTVIDNSSLYRMDPDVPLIVPEVNPEAIDGYK 122

Query: 123 NRNIIANPNCSTIQMLVALKPIYDAVGIERINVTTYQSVSGAGKAGIDELAGQTAKLLNG 182
            +NIIANPNCST QM+VALKP++DA G++R+ V TYQSVSGAGK G+DEL  Q+  +  G
Sbjct: 123 AKNIIANPNCSTAQMVVALKPLHDAAGVKRVVVATYQSVSGAGKEGMDELFEQSRNIFVG 182

Query: 183 YPAETNTFSQQIAFNCIPQIDQFMDNGYTKEEMKMVWETQKIFNDPSIMVNPTCVRVPVF 242
             AE   F++QIAFN IP ID F+D+GYTKEE KMV ET+KI  DP + V  TCVRVPVF
Sbjct: 183 DQAEPKKFTKQIAFNVIPHIDSFLDDGYTKEEWKMVVETKKIL-DPKVKVTATCVRVPVF 241

Query: 243 YGHAEAVHVETRAPIDAEQVMDMLEQTDGIELF---RGADFPTQVRDAGGKDHVLVGRVR 299
            GH+EAV+VE    + AE    +L +  GI L        + T V +  G     V RVR
Sbjct: 242 VGHSEAVNVELERELSAEDAQKILREAPGIMLVDKREDGGYVTPV-ECVGDYATFVSRVR 300

Query: 300 NDISHHSGINLWVVADNVRKGAATNAVQIAELLVR 334
            D++  +G+  W V+DN+RKGAA NAVQIAELL R
Sbjct: 301 EDVTVENGLAFWCVSDNLRKGAALNAVQIAELLGR 335


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: 335
Number of extensions: 15
Number of successful extensions: 4
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: 341
Length adjustment: 28
Effective length of query: 309
Effective length of database: 313
Effective search space:    96717
Effective search space used:    96717
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 Ga0059261_4003 Ga0059261_4003 (aspartate-semialdehyde dehydrogenase (peptidoglycan organisms))
to HMM TIGR01296 (asd: aspartate-semialdehyde dehydrogenase (EC 1.2.1.11))

Software error:

../bin/blast/fastacmd -i /tmp/list.14856.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.14856.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.