GapMind for catabolism of small carbon sources

 

Alignments for a candidate for amaB in Marinobacter adhaerens HP15

Align aldehyde dehydrogenase (NAD+) (EC 1.2.1.3); L-aminoadipate-semialdehyde dehydrogenase (EC 1.2.1.31) (characterized)
to candidate GFF2064 HP15_2020 succinate-semialdehyde dehydrogenase I

Query= BRENDA::P49419
         (539 letters)



>FitnessBrowser__Marino:GFF2064
          Length = 489

 Score =  215 bits (548), Expect = 3e-60
 Identities = 143/477 (29%), Positives = 227/477 (47%), Gaps = 15/477 (3%)

Query: 47  LREENEGVYNGSW--GGRGEVITTYCPANNEPIARVRQASVADYEETVKKAREAWKIWAD 104
           LRE+     NG W     G+      PAN E +A V      D    ++ A  AW  W  
Sbjct: 11  LREQ--AYINGQWITAKSGKTFAVNDPANGEQLATVPDMDDTDARAAIEAASAAWPAWRS 68

Query: 105 IPAPKRGEIVRQIGDALREKIQVLGSLVSLEMGKILVEGVGEVQEYVDICDYAVGLSRMI 164
            PA +R  I+R+  + L    + L  L++ E GK L E  GEV       ++    ++  
Sbjct: 69  TPAKERANILRKWFNLLMANQEDLARLMTAEQGKPLAESRGEVGYGASFIEWFAEEAKRA 128

Query: 165 GGPILPSERSGHALIEQWNPVGLVGIITAFNFPVAVYGWNNAIAMICGNVCLWKGAPTTS 224
            G ++P       ++    PVG+V  IT +NFP+A+     A A+  G   + K A  T 
Sbjct: 129 YGDVIPGHGKDKRIVVIKQPVGVVAAITPWNFPIAMITRKVAPALAAGCPVVVKPAEDTP 188

Query: 225 LISVAVTKIIAKVLEDNKLP-GAICSLTCG---GADIGTAMAKDERVNLLSFTGSTQVGK 280
           L ++A+T +     E+  +P G I  +TC       +G+ +  +  V  +SFTGST VGK
Sbjct: 189 LSALAITALA----EEAGVPAGLINIITCSKPNAVSVGSELTGNPIVRKVSFTGSTPVGK 244

Query: 281 QVGLMVQERFGRSLLELGGNNAIIAFEDADLSLVVPSALFAAVGTAGQRCTTARRLFIHE 340
            +     +   +  LELGGN   I F+DADL   V   + +     GQ C  A R+++  
Sbjct: 245 LLMRQASDTVKKVSLELGGNAPFIVFDDADLDAAVAGLMASKYRNTGQTCVCANRVYVQA 304

Query: 341 SIHDEVVNRLKKAYAQIRVGNPWDPNVLYGPLHTKQAVSMFLGAVEEAKKEGGTVVYGGK 400
            ++D    +LK A +++ VG   +     GPL    A++     +E+A  +G  V  GG+
Sbjct: 305 GVYDAFAEKLKAAVSKMVVGPGLEGETQQGPLINDAALAKVKRHIEDATSKGAKVALGGR 364

Query: 401 VMDRPGNYVEPTIVTGLGHDASIAHTETFAPILYVFKFKNEEEVFAWNNEVKQGLSSSIF 460
                G + EPTI+T    +  IA  ETF P+  +FKF+ ++E  A  N+ + GLS+  +
Sbjct: 365 AHSLGGTFFEPTILTHATQEMLIAREETFGPVAPLFKFETDDEAIAMANDSEFGLSAYFY 424

Query: 461 TKDLGRIFRWLGPKGSDCGIVNVNIPTSGAEIGGAFGGEKHTGGGRESGSDAWKQYM 517
           ++++ R+  W   +  + G++ VN      E+   FGG K +G GRE       +YM
Sbjct: 425 SRNIHRV--WRVAEELESGMIGVNEGIISTEV-APFGGVKESGLGREGSHYGLDEYM 478


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: 688
Number of extensions: 28
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: 539
Length of database: 489
Length adjustment: 35
Effective length of query: 504
Effective length of database: 454
Effective search space:   228816
Effective search space used:   228816
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