GapMind for catabolism of small carbon sources

 

Alignments for a candidate for amaB in Phaeobacter inhibens BS107

Align aldehyde dehydrogenase (NAD+) (EC 1.2.1.3); L-aminoadipate-semialdehyde dehydrogenase (EC 1.2.1.31) (characterized)
to candidate GFF3775 PGA1_262p01790 aldehyde dehydrogenase

Query= BRENDA::P49419
         (539 letters)



>FitnessBrowser__Phaeo:GFF3775
          Length = 483

 Score =  227 bits (578), Expect = 9e-64
 Identities = 149/461 (32%), Positives = 229/461 (49%), Gaps = 11/461 (2%)

Query: 57  GSWGGRGEVITTYCPAN-NEPIARVRQASVADYEETVKKAREAWKIWADIPAPKRGEIVR 115
           G W      I    P++ N+ I    QAS    + T+++A+ A   WA     ++  ++ 
Sbjct: 11  GDWVAGATEIENRNPSDLNDLIGMFAQASPDQLDATLEQAQRAQVEWAGYGIERKYNVLM 70

Query: 116 QIGDALREKIQVLGSLVSLEMGKILVEGVGEVQEYVDICDYAVGLSRMIGGPILPSERSG 175
            IG  +  + + LG+L++ E GK L EG GEV        Y    +    G    S R G
Sbjct: 71  AIGTEMMTRAEELGTLLAREEGKPLAEGKGEVYRAGQFFTYYAAETLRQMGDTADSVRDG 130

Query: 176 HALIEQWNPVGLVGIITAFNFPVAVYGWNNAIAMICGNVCLWKGAPTTSLISVAVTKIIA 235
             +  +  PVG+V +I+ +NFP A   W  A A+  GN  +WK A  T   +VA+ +IIA
Sbjct: 131 IEIDVRREPVGVVVVISPWNFPTATASWKIAPALCYGNAVVWKPANVTPASAVALVEIIA 190

Query: 236 KVLEDNKLPGAICSLTCG-GADIGTAMAKDERVNLLSFTGSTQVGKQVGLMVQERFGRSL 294
           +      +P  + SL  G G+ IG  + +  +VN +SFTGS  VGK +     +   R  
Sbjct: 191 R----QDIPKGLVSLVMGAGSSIGQRLVESPKVNAISFTGSVPVGKGIAACAIQNLTRVQ 246

Query: 295 LELGGNNAIIAFEDADLSLVVPSALFAAVGTAGQRCTTARRLFIHESIHDEVVNRLKKAY 354
           +E+G  NA+   +DAD+ L V  AL  A G +GQ+CT + RL +H+SIHD+ V +L    
Sbjct: 247 MEMGSKNALAVMDDADIDLAVSLALGGAFGGSGQKCTASSRLVVHQSIHDQFVEKLVMGA 306

Query: 355 AQIRVGNPWDPNVLYGPLHTKQAVSMFLGAVEEAKKEGGTVVYGGK--VMDRPGNYVEPT 412
             ++VG+  +     GP+ ++Q ++  L  V+ A  EG  ++ GG+   M   G YV P 
Sbjct: 307 KAMKVGHALEAGTQMGPVVSEQQLNENLAYVDLAASEGAELLCGGQRLEMATDGYYVSPG 366

Query: 413 IVTGLGHDASIAHTETFAPILYVFKFKNEEEVFAWNNEVKQGLSSSIFTKDLGRIFRWLG 472
           I  G  +D  I   E FAP+  V    + +E     N+   GL++ I T +L R   +  
Sbjct: 367 IFVGTNNDMRINREEMFAPLACVIPVASYDEALHVVNDTNFGLTAGIVTTNLARATHF-- 424

Query: 473 PKGSDCGIVNVNIPTSGAEIGGAFGGEKHTG-GGRESGSDA 512
            + +  G V VN+PT+G +    FGG   +  G RE G  A
Sbjct: 425 RRNAQSGCVMVNLPTAGTDYHVPFGGRGDSSYGPREQGQTA 465


Lambda     K      H
   0.318    0.136    0.417 

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: 631
Number of extensions: 40
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: 539
Length of database: 483
Length adjustment: 34
Effective length of query: 505
Effective length of database: 449
Effective search space:   226745
Effective search space used:   226745
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)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

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About GapMind

Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.

A candidate for a step is "high confidence" if either:

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

Otherwise, a candidate is "medium confidence" if either:

Other blast hits with at least 50% coverage are "low confidence."

Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:

GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).

For more information, see:

If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know

by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory