GapMind for catabolism of small carbon sources

 

Aligments for a candidate for amaB in Herbaspirillum seropedicae SmR1

Align L-piperidine-6-carboxylate dehydrogenase; EC 1.2.1.21 (characterized, see rationale)
to candidate HSERO_RS05645 HSERO_RS05645 succinate-semialdehyde dehdyrogenase

Query= uniprot:Q88CC3
         (496 letters)



>lcl|FitnessBrowser__HerbieS:HSERO_RS05645 HSERO_RS05645
           succinate-semialdehyde dehdyrogenase
          Length = 493

 Score =  211 bits (538), Expect = 4e-59
 Identities = 149/462 (32%), Positives = 226/462 (48%), Gaps = 21/462 (4%)

Query: 23  VHTPIDGSQIASVKLLGKAETIARIDQAQSAFEAWRSVPAPRRGELVRLFGEVLREHKAD 82
           V  P  G   ASV   G A+  A ++ A +AF AWR+ PA +R  +++ + ++L  H+ D
Sbjct: 33  VSDPATGQVFASVPDGGAADARAAVEAAVAAFAAWRATPAKQRAGIIKRWNDLLLAHQDD 92

Query: 83  LGELVSIEAGKITQEGLGEVQEMIDICDFAVGLSRQLYGLTIASERPGHHMRETWHPLGV 142
           LG L+S E GK   E  GEV       ++    + +  G  I +   G  M     P+GV
Sbjct: 93  LGRLISREQGKPLAEAKGEVAYAASYVEWFGEEATRANGDIIPAPVTGRRMMALKEPVGV 152

Query: 143 VGVISAFNFPVAVWAWNTALALVAGNSVVWKPSEKTPLTALACQALFEKALKAFGDAPAG 202
           V  I+ +NFP A+ A   A AL AG +VV KP+E TPLT+LA   L ++A       P G
Sbjct: 153 VAAITPWNFPAAMIARKIAPALAAGCTVVCKPAEDTPLTSLALVRLAQEA-----GVPVG 207

Query: 203 LAQLVIGGREAGEAMVD----DPRVPLVSATGSTRMGREVGPRVAARFGRSILELGGNNA 258
           +  +V   RE    +VD    D RV  +S TGST +G+ +    A    +  LELGGN  
Sbjct: 208 VINIVTASRERTPEVVDVWLADGRVRKISFTGSTAVGKHLARHSADTLKKLSLELGGNAP 267

Query: 259 MILAPSADLDLAVRGILFSAVGTAGQRCTTLRRLIVHRSIKDEVVARVKAAYGKVRIGDP 318
            I+   AD+D A+ G++ +     GQ C +  R+ V   + D  V ++ A    +++G P
Sbjct: 268 FIVFDDADVDAAIDGVMAAKFRNGGQTCVSPNRIYVQEKVYDAFVDKLGARVAALKVG-P 326

Query: 319 RKD--NLVGPLIDKQSFDAMQGALAKARDEGGQVFGGERQLADQYP----NAYYVSPAIA 372
             D  + +GP+I+ ++   +   +  A   G +V  G ++L  Q P    + YY    +A
Sbjct: 327 ATDPASQIGPMINARAIAKIDQHVRDAIARGARVITGGKRL--QGPGFGSDNYYAPTVLA 384

Query: 373 EMPAQSDVVRHETFAPILYVLAYDDFEEALRLNNEVPQGLSSCIFTTDIREAERFQSASG 432
           ++         ETF P+  +  +   +E +   N  P GL++  ++TD+R   R   A  
Sbjct: 385 DVTGAMQCSCEETFGPVAPITRFATEDEVIAAANATPFGLAAYFYSTDVRRIHRVTDALE 444

Query: 433 SDCGIANVNIGTSGAEIGGAFGGEKETGGGRESGSDAWKGYM 474
           S  GI  VN G   AE    FGG KE+G GRE        Y+
Sbjct: 445 S--GIVGVNEGALAAE-AAPFGGVKESGYGREGSVHGLDDYL 483


Lambda     K      H
   0.318    0.135    0.396 

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: 616
Number of extensions: 34
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: 496
Length of database: 493
Length adjustment: 34
Effective length of query: 462
Effective length of database: 459
Effective search space:   212058
Effective search space used:   212058
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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint 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