GapMind for catabolism of small carbon sources

 

Alignments for a candidate for astD in Pseudomonas fluorescens FW300-N1B4

Align Succinylglutamic semialdehyde dehydrogenase (EC 1.2.1.71) (characterized)
to candidate Pf1N1B4_3444 Succinylglutamic semialdehyde dehydrogenase (EC 1.2.1.71)

Query= reanno::pseudo13_GW456_L13:PfGW456L13_1974
         (488 letters)



>FitnessBrowser__pseudo1_N1B4:Pf1N1B4_3444
          Length = 488

 Score =  926 bits (2393), Expect = 0.0
 Identities = 465/487 (95%), Positives = 477/487 (97%)

Query: 1   MKSLYIAGEWLAGGGEAFESLNPVTQQVLWSGVGATAGQVESAVQAARQAFPDWARRTLE 60
           M SLYIAGEWLAG GE+F+S+NPVTQQVLW+G GAT GQVESAVQAARQAFP WARRTLE
Sbjct: 1   MNSLYIAGEWLAGQGESFQSVNPVTQQVLWAGEGATTGQVESAVQAARQAFPGWARRTLE 60

Query: 61  ERISVLEAFAAALKNHADELAHTIGEETGKPLWEAATEVTSMVNKIAISVQSYRERTGEK 120
           ERI VLEAFAAALKNHADELA TIGEETGKPLWEAATEVTSMVNKIAISVQSYRERTGEK
Sbjct: 61  ERIGVLEAFAAALKNHADELARTIGEETGKPLWEAATEVTSMVNKIAISVQSYRERTGEK 120

Query: 121 SGPLGDATAVLRHKPHGVVAVFGPYNFPGHLPNGHIVPALLAGNSVLFKPSELTPKVAEL 180
           SGPLGDATAVLRHKPHGVVAVFGPYNFPGHLPNGHIVPALLAGNSVLFKPSELTPKVAEL
Sbjct: 121 SGPLGDATAVLRHKPHGVVAVFGPYNFPGHLPNGHIVPALLAGNSVLFKPSELTPKVAEL 180

Query: 181 TVKCWIEAGLPAGVLNLLQGARETGIALAANPGIDGLFFTGSSRTGNHLHQQFAGRPDKI 240
           TVKCWIEAGLPAGVLNLLQGARETGIALAANPGIDGLFFTGSSRTGNHLH+QF+GRPDKI
Sbjct: 181 TVKCWIEAGLPAGVLNLLQGARETGIALAANPGIDGLFFTGSSRTGNHLHKQFSGRPDKI 240

Query: 241 LALEMGGNNPLVVDQVADLDAAVYTIIQSAFISAGQRCTCARRLLVPQGAWGDSLLARLV 300
           LALEMGGNNPLVVDQVADLDAAVYTIIQSAFISAGQRCTCARRLLVPQGAWGD+LLARLV
Sbjct: 241 LALEMGGNNPLVVDQVADLDAAVYTIIQSAFISAGQRCTCARRLLVPQGAWGDTLLARLV 300

Query: 301 AVSSTLSVGAFDQQPAPFMGSVVSLGAAKALMDAQEHLLANGAVALLEMTQPQAQSALLT 360
           AVSST+ VGAFDQQPAPFMGSV+SLGAAKALMDAQEHLLANGAVALLEMTQPQAQ+ALLT
Sbjct: 301 AVSSTIEVGAFDQQPAPFMGSVISLGAAKALMDAQEHLLANGAVALLEMTQPQAQAALLT 360

Query: 361 PGILDVSAVADRPDEELFGPLLQVIRYADFEAAIAEANDTAYGLAAGLLSDSEARYQQFW 420
           PGILDV+AVADRPDEELFGPLLQVIRYADFEAAIAEANDT YGLAAGLLSDSEARYQQFW
Sbjct: 361 PGILDVTAVADRPDEELFGPLLQVIRYADFEAAIAEANDTDYGLAAGLLSDSEARYQQFW 420

Query: 421 LESRAGIVNWNKQLTGAASSAPFGGVGASGNHRASAYYAADYCAYPVASLETPSLVLPSA 480
           LESRAGIVNWNKQLTGAASSAPFGGVGASGNHRASAYYAADYCAYPVASLETPSLVLP+ 
Sbjct: 421 LESRAGIVNWNKQLTGAASSAPFGGVGASGNHRASAYYAADYCAYPVASLETPSLVLPAT 480

Query: 481 LTPGVKM 487
           LTPGVKM
Sbjct: 481 LTPGVKM 487


Lambda     K      H
   0.316    0.132    0.388 

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: 934
Number of extensions: 23
Number of successful extensions: 1
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: 488
Length of database: 488
Length adjustment: 34
Effective length of query: 454
Effective length of database: 454
Effective search space:   206116
Effective search space used:   206116
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 (21.6 bits)
S2: 52 (24.6 bits)

Align candidate Pf1N1B4_3444 (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.23200.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.23200.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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