GapMind for catabolism of small carbon sources

 

Alignments for a candidate for liuA in Hydrogenophaga taeniospiralis CCUG 15921 NBRC 102512

Align Isovaleryl-CoA dehydrogenase (EC 1.3.8.4) (characterized)
to candidate WP_068170917.1 HTA01S_RS11035 isovaleryl-CoA dehydrogenase

Query= reanno::acidovorax_3H11:Ac3H11_2991
         (396 letters)



>NCBI__GCF_001592305.1:WP_068170917.1
          Length = 393

 Score =  751 bits (1938), Expect = 0.0
 Identities = 372/391 (95%), Positives = 384/391 (98%)

Query: 6   NLPGLNFQLGEDIDALRDAVRDFAQAEIAPRAADIDKSDQFPMDLWRKMGDLGVLGITVP 65
           NLPGLNFQLGEDIDALRDAVR+FAQAEIAPRAA+IDKSDQFPMD WRKMG+LGVLGITVP
Sbjct: 3   NLPGLNFQLGEDIDALRDAVREFAQAEIAPRAAEIDKSDQFPMDCWRKMGELGVLGITVP 62

Query: 66  EQYGGAAMGYLAHMVAMEEISRASASVGLSYGAHSNLCVNQINRNGNEAQKAKYLSKLIS 125
           EQYGGA MGYLAHMVAMEEISRASASVGLSYGAHSNLCVNQINRNGN+AQKAKYL KLIS
Sbjct: 63  EQYGGANMGYLAHMVAMEEISRASASVGLSYGAHSNLCVNQINRNGNDAQKAKYLPKLIS 122

Query: 126 GEHVGALAMSEPGAGSDVISMKLKAEDKGGYYLLNGSKMWITNGPDADTLVVYAKTEPEL 185
           GEHVGALAMSEPGAGSDVISMKLKAEDKGGYYLLNG+KMWITNGPDADTLVVYAK+EPE+
Sbjct: 123 GEHVGALAMSEPGAGSDVISMKLKAEDKGGYYLLNGNKMWITNGPDADTLVVYAKSEPEM 182

Query: 186 GARGVTAFLIEKGMKGFSIAQKLDKLGMRGSHTGELVFQDVEVPAENVLGGLNQGAKVLM 245
           GARGVTAFLIEKGM GFSIAQKLDKLGMRGSHTGELVFQ+VEVPA+N+LGGLN GAKVLM
Sbjct: 183 GARGVTAFLIEKGMPGFSIAQKLDKLGMRGSHTGELVFQNVEVPAQNILGGLNMGAKVLM 242

Query: 246 SGLDYERAVLTGGPLGIMQSVMDNVIPYIHDRKQFGQSIGEFQLIQGKVADMYTVLQAGR 305
           SGLDYERAVLTGGPLGIMQSVMDNVIPYIHDRKQFGQSIGEFQLIQGKVADMYTVLQA R
Sbjct: 243 SGLDYERAVLTGGPLGIMQSVMDNVIPYIHDRKQFGQSIGEFQLIQGKVADMYTVLQAAR 302

Query: 306 SFAYTVAKNLDMLGTDHVRQVRKDCASVILWCAEKATWMAGEGVQIYGGNGYINEYPLGR 365
           SFAYTVAKNLD+LGT+HVRQVRKDCASVILW AEKATWMAGEGVQIYGGNGYINEYPLGR
Sbjct: 303 SFAYTVAKNLDLLGTEHVRQVRKDCASVILWTAEKATWMAGEGVQIYGGNGYINEYPLGR 362

Query: 366 LWRDAKLYEIGAGTSEIRRMLIGRELFAETC 396
           LWRDAKLYEIGAGTSEIRRMLIGRELFAETC
Sbjct: 363 LWRDAKLYEIGAGTSEIRRMLIGRELFAETC 393


Lambda     K      H
   0.318    0.136    0.400 

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: 689
Number of extensions: 17
Number of successful extensions: 1
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: 396
Length of database: 393
Length adjustment: 31
Effective length of query: 365
Effective length of database: 362
Effective search space:   132130
Effective search space used:   132130
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: 50 (23.9 bits)

This GapMind analysis is from Apr 09 2024. 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