GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gnd in Pedobacter sp. GW460-11-11-14-LB5

Align phosphogluconate dehydrogenase (NADP+-dependent, decarboxylating) (EC 1.1.1.44) (characterized)
to candidate CA265_RS09805 CA265_RS09805 phosphogluconate dehydrogenase (NADP(+)-dependent, decarboxylating)

Query= BRENDA::P80859
         (469 letters)



>FitnessBrowser__Pedo557:CA265_RS09805
          Length = 471

 Score =  447 bits (1149), Expect = e-130
 Identities = 221/467 (47%), Positives = 314/467 (67%), Gaps = 5/467 (1%)

Query: 3   KQQIGVIGLAVMGKNLALNIESRGFSVSVYNRSSSKTEEFLQEAKGKNVVGTYSIEEFVQ 62
           K ++G+IGL  MG+NL LN+  +GFSV+ Y++      +  +E K  N+ G   IE F+ 
Sbjct: 8   KYKLGMIGLGTMGRNLLLNMADKGFSVTGYDKDRKMISKLEEEGKKHNLEGFDDIESFIS 67

Query: 63  SLETPRKILLMVKAGTATDATIQSLLPHLEKDDILIDGGNTYYKDTQRRNKELAESGIHF 122
           SL+T R ++L+V AG   D+ I  L P L K DI+ID GN+++ DT RR  EL + G+HF
Sbjct: 68  SLQTSRTLILLVPAGPIVDSVIAELKPLLSKGDIIIDSGNSHFTDTNRRVDELEKDGLHF 127

Query: 123 IGTGVSGGEEGALKGPSIMPGGQKEAHELVKPILEAISAKVDGEPCTTYIGPDGAGHYVK 182
            G G+SGGEEGA  GPS+MPGG K+A+ +VK + +A++AKV  +PC TYIGP  +GH+VK
Sbjct: 128 FGMGISGGEEGARFGPSMMPGGDKQAYNVVKDVFDAVAAKVGTDPCVTYIGPGASGHFVK 187

Query: 183 MVHNGIEYGDMQLISESYFILKQVLGLSADELHEVFAEWNKGELDSYLIEITADIFTKKD 242
           MVHNGIEY  M+LI+E Y ILK  LG S +E+++VF +WN+G L S+L+EITA+IF  KD
Sbjct: 188 MVHNGIEYAIMELIAEVYGILKNGLGYSNNEIYQVFKKWNEGRLQSFLLEITAEIFLFKD 247

Query: 243 EETGKPLVDVILDKAGQKGTGKWTSQSALDLGVPLPIITESVFARFISAMKEERVKASGL 302
            ET   L+D I D+A  KGTGKWTS+ +++L +P+P I E+V  R +S  K+ RV     
Sbjct: 248 TETQNDLLDQIKDEARSKGTGKWTSEVSMELQLPVPTINEAVSNRDLSKFKKLRVSLEEA 307

Query: 303 LSGPEVKPVTENKEELIEAVRKALFMSKICSYAQGFAQMKAASEEYNWDLKYGEIAMIFR 362
               + K         ++ +  A + S I +YAQG   +  AS+EY +DL+  EIA I+R
Sbjct: 308 FGKKDTKIAV-----TVDELEDAFYFSMISAYAQGMHLLVQASKEYQYDLQLQEIAKIWR 362

Query: 363 GGCIIRAAFLQKIKEAYDREPELDNLLLDSYFKNIVESYQGALRQVISLAVAQGVPVPSF 422
           GGCIIRA FL+ I +AYD+   L++L  D+  +NI++      R+ IS  +  G+ +P+F
Sbjct: 363 GGCIIRAKFLEDIYQAYDKNNALEHLFGDAGIQNIIKGTLPGTRKTISACINSGLGIPAF 422

Query: 423 SSALAYYDSYRTAVLPANLIQAQRDYFGAHTYERTDKEGIFHTEWMK 469
           +S L Y+D+  TA +P+NLIQAQRD+FGAHT+ER DK+G+FH +W K
Sbjct: 423 ASTLTYFDTITTARMPSNLIQAQRDFFGAHTFERIDKDGVFHADWNK 469


Lambda     K      H
   0.315    0.134    0.379 

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: 577
Number of extensions: 29
Number of successful extensions: 2
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: 469
Length of database: 471
Length adjustment: 33
Effective length of query: 436
Effective length of database: 438
Effective search space:   190968
Effective search space used:   190968
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 (21.5 bits)
S2: 51 (24.3 bits)

Align candidate CA265_RS09805 CA265_RS09805 (phosphogluconate dehydrogenase (NADP(+)-dependent, decarboxylating))
to HMM TIGR00873 (gnd: 6-phosphogluconate dehydrogenase (decarboxylating) (EC 1.1.1.44))

Software error:

../bin/blast/fastacmd -i /tmp/list.10131.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.10131.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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