GapMind for catabolism of small carbon sources

 

Aligments for a candidate for kbl in Paraburkholderia bryophila 376MFSha3.1

Align 8-amino-7-oxononanoate synthase/2-amino-3-ketobutyrate coenzyme A ligase; AONS/AKB ligase; 7-keto-8-amino-pelargonic acid synthase; 7-KAP synthase; KAPA synthase; 8-amino-7-ketopelargonate synthase; Alpha-oxoamine synthase; Glycine acetyltransferase; EC 2.3.1.29; EC 2.3.1.47 (characterized)
to candidate H281DRAFT_02095 H281DRAFT_02095 8-amino-7-oxononanoate synthase

Query= SwissProt::Q5SHZ8
         (395 letters)



>FitnessBrowser__Burk376:H281DRAFT_02095
          Length = 394

 Score =  229 bits (585), Expect = 8e-65
 Identities = 139/395 (35%), Positives = 215/395 (54%), Gaps = 14/395 (3%)

Query: 3   LDLRARVREELERLKREGLYISPKVLEAPQEPVTRVEGREVVNLASNNYLGFANHPYLKE 62
           + L  R+ E L+ +   GL    +  + P      V+GRE++  ASN+YLG A HP L  
Sbjct: 1   MHLLDRLSEGLKEIDERGLRRRRRTADTPCAAHMTVDGREIIGFASNDYLGLAAHPQLIA 60

Query: 63  KARQYLEKWGAGSGAVRTIAGTFTYHVELEEALARFKG----TESALVLQSGFTANQGVL 118
              +  +++GAGSG    + G    H +LE+ LA F G    T  AL   +G+ AN   L
Sbjct: 61  AIAEGAQRYGAGSGGSHLLGGHSRAHAQLEDDLAEFVGGFVDTPRALYFSTGYMANLATL 120

Query: 119 GALLKEGDVVFSDELNHASIIDGLRLTKATRLVFRHADVAHLEELLKAHDTDGLKLIVTD 178
            AL   G  +FSD LNHAS+IDG RL++A   ++ H D+  L  +L A D D +K IV+D
Sbjct: 121 TALAGRGTTLFSDALNHASLIDGARLSRADVQIYPHCDMEALSAMLDASDAD-VKAIVSD 179

Query: 179 GVFSMDGDIAPLDKIVPLAKKYKAVVYVDDAHGSGVLGEKGKGTVHHFGFHQDPDVVQVA 238
            VFSMDGDIAPL +++ LA+++ A + VDDAHG GVLG +G+G V      + P+++ + 
Sbjct: 180 TVFSMDGDIAPLPRLLELAEQHGAWLIVDDAHGFGVLGPQGRGAVADAAL-RSPNLISIG 238

Query: 239 TLSKAWAGIGGYAAGARELKDLLINKARPFLFSTSHPPAVVGALLGALELI-----EKEP 293
           TL KA    G + A    + + L+ +ARP++F+T+  PA   A+  +L +I     ++  
Sbjct: 239 TLGKAAGVSGAFVAAHETVIEWLVQRARPYIFTTASVPAAAHAVSASLRIIGGNEGDERR 298

Query: 294 ERVERLWENTRYFKRELARLGYDTLGSQTPITPVLFGEAPLAFEASRLLLEEGVFAVGIG 353
             + +L E TR   +    +  D   S T + P++ G      + +  L   G++   I 
Sbjct: 299 AHLRQLIERTRAMLKSTPWIPVD---SHTAVQPLVIGANEATLDIAASLDRAGLWVPAIR 355

Query: 354 FPTVPRGKARIRNIVTAAHTKEMLDKALEAYEKVG 388
            PTVP G +R+R  ++AAH+   LD+     ++ G
Sbjct: 356 PPTVPTGTSRLRISLSAAHSHADLDRLEAGLQQAG 390


Lambda     K      H
   0.319    0.137    0.394 

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: 360
Number of extensions: 17
Number of successful extensions: 5
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: 395
Length of database: 394
Length adjustment: 31
Effective length of query: 364
Effective length of database: 363
Effective search space:   132132
Effective search space used:   132132
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 50 (23.9 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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code.

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