GapMind for catabolism of small carbon sources

 

Aligments for a candidate for amaB in Burkholderia phytofirmans PsJN

Align Alpha-aminoadipic semialdehyde dehydrogenase; Alpha-AASA dehydrogenase; Aldehyde dehydrogenase family 7 member A1; Antiquitin-1; Betaine aldehyde dehydrogenase; Delta1-piperideine-6-carboxylate dehydrogenase; P6c dehydrogenase; EC 1.2.1.31; EC 1.2.1.3; EC 1.2.1.8 (characterized)
to candidate BPHYT_RS34305 BPHYT_RS34305 succinate-semialdehyde dehydrogenase

Query= SwissProt::Q64057
         (539 letters)



>lcl|FitnessBrowser__BFirm:BPHYT_RS34305 BPHYT_RS34305
           succinate-semialdehyde dehydrogenase
          Length = 479

 Score =  221 bits (562), Expect = 6e-62
 Identities = 140/460 (30%), Positives = 218/460 (47%), Gaps = 6/460 (1%)

Query: 57  GSWGGRGEVITTYCPANNEPIARVRQASMKDYEETIGKAKKAWNIWADIPAPKRGEIVRK 116
           G W    +      PA  E +A V +    +  + I  A++A+  W  + A +R   V++
Sbjct: 13  GEWYEGADTYAVLNPATGEVVAHVAKGGAAETAQAIAAAERAFPAWRALTAKERSARVKR 72

Query: 117 IGDALREKIQLLGRLVSLEMGKILVEGIGEVQEYVDVCDYAAGLSRMIGGPTLPSERPGH 176
            G+ + E    L  L++LE GK L E  GEV       ++ A  ++   G  +PS  P  
Sbjct: 73  WGELMLENRDALAELLTLEQGKPLAEARGEVGYAASFFEWFAEEAKRAYGDVIPSPNPNA 132

Query: 177 ALMEQWNPLGLVGIITAFNFPVAVFGWNNAIALITGNVCLWKGAPTTSLVSIAVTKIIAK 236
            ++    P+G+V  IT +NFP+A+       AL  G   + K +  T L + A+  + AK
Sbjct: 133 KIIVTREPVGVVAAITPWNFPLAMITRKAGPALAAGCTMVLKPSEETPLSAFALAVLAAK 192

Query: 237 VLEDNLLPGAICSLTCGGADMGTAMARDERVNLLSFTGSTQVGKQVALMVQERFGKSLLE 296
                + PG    ++     +G A+   + V  LSFTGST+VGK +A    +   K  LE
Sbjct: 193 A---GIPPGVFNIVSGDAVAIGGALTESDVVRKLSFTGSTRVGKLLAKQSADTLKKLSLE 249

Query: 297 LGGNNAIIAFEDADLSLVLPSALFAAVGTAGQRCTTVRRLFLHESIHDEVVDRLKNAYSQ 356
           LGGN   I F+DADL   +  A+ +     GQ C  V R ++ + I+D     L  A  +
Sbjct: 250 LGGNAPFIVFDDADLDAAVQGAMASKFRNTGQTCVCVNRFYVQDGIYDAFTSALTQAVRK 309

Query: 357 IRVGNPWDPNILYGPLHTKQAVSMFVQAVEEAKKEGGTVVYGGKVMDHPGNYVEPTIVTG 416
           +RVGN     +  GPL  + A+      V +A ++G  ++ GGK     G + EPT++  
Sbjct: 310 MRVGNALQGEVEQGPLINQAALKKVETHVADALQKGAKILTGGKPHTLGGTFYEPTVLAD 369

Query: 417 LVHDAPIVHKETFAPILYVFKFKNEEEVFEWNNEVKQGLSSSIFTKDLGRIFRWLGPKGS 476
             +   I  +ETF P+   F+FK E E  E  N+   GLS+  +T+DL R   W   +  
Sbjct: 370 ADNSMLIAGEETFGPVAACFRFKTEAEAIEAANDTPFGLSAYFYTRDLAR--AWRVGEAL 427

Query: 477 DCGIVNVNIPTSGAEIGGAFGGEKHTGGGRESGSDAWKQY 516
           + G+V +N      E+   FGG K +G GRE       +Y
Sbjct: 428 ESGMVGINEGIVSTEV-APFGGVKQSGLGREGSKYGLDEY 466


Lambda     K      H
   0.319    0.137    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: 657
Number of extensions: 43
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: 479
Length adjustment: 34
Effective length of query: 505
Effective length of database: 445
Effective search space:   224725
Effective search space used:   224725
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: 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 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