GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__HerbieS:HSERO_RS05645
          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:

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