GapMind for catabolism of small carbon sources

 

Alignments for a candidate for astD in Sphingomonas koreensis DSMZ 15582

Align N-succinylglutamate 5-semialdehyde dehydrogenase; Succinylglutamic semialdehyde dehydrogenase; SGSD; EC 1.2.1.71 (characterized)
to candidate Ga0059261_1495 Ga0059261_1495 succinylglutamic semialdehyde dehydrogenase (EC 1.2.1.71)

Query= SwissProt::O50174
         (487 letters)



>FitnessBrowser__Korea:Ga0059261_1495
          Length = 480

 Score =  454 bits (1168), Expect = e-132
 Identities = 241/460 (52%), Positives = 305/460 (66%), Gaps = 7/460 (1%)

Query: 15  GETLESLDPVGQGVVWSGRGADATQVDAAVCAAREAFPAWARRPLEQRIELLERFAATLK 74
           G  + S +P    V+W     D   VDA V AAR ++  WA RPL  RIE L RFA  ++
Sbjct: 12  GSEIISTEPATGAVLWRRPIGD---VDAEVAAARASWADWAARPLTYRIEALRRFANVVR 68

Query: 75  SRADELARVIGEETGKPLWESATEVTSMVNKVAISVQAFRERTGEK--SGPLADATAVLR 132
            +++    +I  ETGKPLWE+ TEV +++ KV ISV AF ERTG++    P+    A LR
Sbjct: 69  QKSEAFTDLIARETGKPLWEARTEVETVIAKVDISVTAFSERTGQRRIEAPMNTRLA-LR 127

Query: 133 HKPHGVVAVFGPYNFPGHLPNGHIVPALLAGNCVVFKPSELTPKVAELTLKAWIQAGLPA 192
           HKPHGV+AV GPYNFP HLPNGHIVPALLAGN VVFKPSE TP      ++ +  AG+P 
Sbjct: 128 HKPHGVLAVLGPYNFPAHLPNGHIVPALLAGNAVVFKPSEKTPATGAFLVECYHAAGIPE 187

Query: 193 GVLNLVQGGRETGVALAAHRGLDGLFFTGSSRTGNLLHSQFGGQPQKILALEMGGNNPLV 252
           G + L+ GG + G ALA H G+DGL FTGS+RTG  L+  F  +P+KILALEMGGNNP++
Sbjct: 188 GCIRLLIGGPDEGKALAGHDGIDGLLFTGSARTGIALNRAFAAKPEKILALEMGGNNPIL 247

Query: 253 VEEVADLDAAVYTIIQSAFISAGQRCTCARRLLVPQGAWGDALLARLVAVSATLRVGRFD 312
           V    D+ +A   +IQSAF SAGQRCT ARRL+V +  + D LL  +  +   L VG   
Sbjct: 248 VWSTPDIYSAAVLVIQSAFTSAGQRCTAARRLIVDEKLY-DPLLEEVNKLIGRLIVGEPH 306

Query: 313 EQPAPFMGAVISLSAAEHLLKAQEHLIGKGAQPLLAMTQPIDGAALLTPGILDVSAVAER 372
             PAPFMG VI    A+ L ++   L   G +PL  M +P+DG   LTP ++D++   E+
Sbjct: 307 ADPAPFMGPVIDNDTADLLTESFLELSFMGGRPLRHMERPVDGRPFLTPAMIDMTDAKEK 366

Query: 373 PDEEFFGPLLQVIRYSDFAAAIREANATQYGLAAGLLSDSRERFEQFLVESRAGIVNWNK 432
           PD E FGP+LQVIR   F  AI EAN T+YGL+A L+S   + ++QF    RAGIVNWN+
Sbjct: 367 PDVELFGPILQVIRARTFEEAIAEANNTRYGLSASLVSQDPKLYDQFWANIRAGIVNWNR 426

Query: 433 QLTGAASSAPFGGIGASGNHRPSAYYAADYCAYPVASLES 472
              GA+S+APFGGIG SGNHRPSA+YAADYCAYPV S E+
Sbjct: 427 PTNGASSAAPFGGIGWSGNHRPSAFYAADYCAYPVVSSEA 466


Lambda     K      H
   0.318    0.134    0.396 

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: 695
Number of extensions: 32
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: 487
Length of database: 480
Length adjustment: 34
Effective length of query: 453
Effective length of database: 446
Effective search space:   202038
Effective search space used:   202038
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 52 (24.6 bits)

Align candidate Ga0059261_1495 Ga0059261_1495 (succinylglutamic semialdehyde dehydrogenase (EC 1.2.1.71))
to HMM TIGR03240 (astD: succinylglutamate-semialdehyde dehydrogenase (EC 1.2.1.71))

Software error:

../bin/blast/fastacmd -i /tmp/list.17756.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.17756.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.