GapMind for catabolism of small carbon sources

 

Alignments for a candidate for liuA in Leeuwenhoekiella blandensis MED217

Align Isovaleryl-CoA dehydrogenase (EC 1.3.8.4) (characterized)
to candidate WP_009778630.1 MED217_RS01145 acyl-CoA dehydrogenase

Query= reanno::ANA3:7024494
         (389 letters)



>NCBI__GCF_000152985.1:WP_009778630.1
          Length = 392

 Score =  231 bits (589), Expect = 3e-65
 Identities = 135/380 (35%), Positives = 214/380 (56%), Gaps = 5/380 (1%)

Query: 5   YTSLNFGLGEEVDMLRDAVQDFAKHEIAPIAAKVDHDNAFPNEIWPVLGGMGLLGVTVPE 64
           Y +L+  L EE  ++R A +D+ K +++PI  +      FP EI   L  +G  G  +PE
Sbjct: 11  YYNLDDLLTEEHKLVRSAARDWVKRDVSPIIEEAAQKAEFPKEIIKGLAEIGAFGPYIPE 70

Query: 65  EYGGANMGYLAHVVAMEEISRASASIGLSYGAHSNLCVNQINRNGNAEQKAKYLPKLVSG 124
           EYGGA +  +++ + M+EI R  + +  +    S+L +  I + G   Q+ KYLPKL SG
Sbjct: 71  EYGGAGLDQISYGLIMQEIERGDSGVRSTASVQSSLVMYPIFKFGTEVQRKKYLPKLASG 130

Query: 125 EHIGALAMSEPNAGSDVVSMKLHARKEGDRYILNGNKMWITNGPDANTYVIYAKTDLTKG 184
           E +G   ++EP+ GS+   M  + + +GD Y+LNG KMWI+N P A+  V++AK D +  
Sbjct: 131 EFMGCFGLTEPDHGSNPGGMVTNFKDKGDHYLLNGAKMWISNAPFADIAVVWAK-DESGR 189

Query: 185 AHGITAFIVERGFKGFSQAQKLDKLGMRGSNTCELVFEDVEVPEENILGGLNNGVKVLMS 244
            HG+   IVERG +GFS     +K  +R S T EL+F++V++P+EN+L    +G+   + 
Sbjct: 190 IHGL---IVERGMEGFSTPTTHNKWSLRASATGELIFDNVKIPKENLLPN-KSGLGAPLM 245

Query: 245 GLDYERVVLSGGPLGIMNACMDIVVPYIHEREQFGKSIGEFQLVQGKLADMYTGMNAAKA 304
            LD  R  ++ G +G    C D  + Y  EREQFGK IG FQL Q KLA+M T +  A+ 
Sbjct: 246 CLDSARFGIAWGAIGAAMDCYDTALRYAKEREQFGKPIGSFQLQQKKLAEMITEITKAQL 305

Query: 305 YVYSVAKSCDRGETTRKDAAGAILYSAELATKMALDAIQLLGGNGYVNEYATGRLLRDAK 364
             + +    +  + T    + A   + E+A K+A +A Q+LGG G   EY+  R + + +
Sbjct: 306 LAWRLGALRNEDKATSAQISMAKRNNVEMALKIAREARQILGGMGITGEYSIMRHMMNLE 365

Query: 365 LYEIGAGTSEIRRMLIGREL 384
                 GT +I  ++ G ++
Sbjct: 366 SVVTYEGTHDIHLLITGMDI 385


Lambda     K      H
   0.316    0.135    0.388 

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: 352
Number of extensions: 13
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: 389
Length of database: 392
Length adjustment: 31
Effective length of query: 358
Effective length of database: 361
Effective search space:   129238
Effective search space used:   129238
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 (21.6 bits)
S2: 50 (23.9 bits)

This GapMind analysis is from Sep 24 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