GapMind for catabolism of small carbon sources

 

Alignments for a candidate for liuA in Jannaschia aquimarina GSW-M26

Align Isovaleryl-CoA dehydrogenase (EC 1.3.8.4) (characterized)
to candidate WP_043918838.1 jaqu_RS10025 acyl-CoA dehydrogenase family protein

Query= reanno::psRCH2:GFF1051
         (387 letters)



>NCBI__GCF_000877395.1:WP_043918838.1
          Length = 379

 Score =  226 bits (575), Expect = 1e-63
 Identities = 133/379 (35%), Positives = 211/379 (55%), Gaps = 5/379 (1%)

Query: 6   LNFALGETIDMLREQVQAFVAAEIAPRAEAIDQENLFPADMWRKFGEMGLLGVTVSEEYG 65
           ++FAL E    +    +    AEIAP A A +     P D+W K  E+GL G+ VSEE G
Sbjct: 1   MDFALSEESRAIFNMARDVGQAEIAPHARAWEAAGDIPRDLWPKLAELGLAGLYVSEEAG 60

Query: 66  GAGLGYLAHVVAMEEISRGSASVALSYGAHSNLCVNQINRNGNPEQKARYLPKLISGEHV 125
           G GL  L   +  E +S    SVA     H N+C   I+  G+ E K R LPK ++ E  
Sbjct: 61  GTGLTRLDATLVFEALSMACPSVASFLSIH-NMCARMIDAYGSDELKDRMLPKALTCETW 119

Query: 126 GALAMSEPNAGSDVVSMKLRAEKRGDRYVLNGSKTWITNGPDANTYVIYAKTDLDKGAHG 185
            +  ++EP +GSD  ++K RAE+  + + L G+K +I+ G  ++ Y++ A++  + G  G
Sbjct: 120 LSYCLTEPGSGSDAAALKTRAERTNEGWRLTGTKAFISGGGYSDAYIVMARSG-EAGPRG 178

Query: 186 ITAFIVERDWKGFSRGNKFDKLGMRGSNTCELFFDDVEVPQENVLGAENGGVKVLMSGLD 245
           I+AF+VE    G S G   DK+G R   T ++  DD  VP  N+LG E  G +  M+GLD
Sbjct: 179 ISAFVVEDGTDGLSFGGLEDKMGWRSQPTRQVQLDDAPVPASNLLGEEGHGFRYAMAGLD 238

Query: 246 YERVVLAGGPTGIMQSCLDVVVPYIHDRKQFGQSIGEFQFIQGKVADMYTQLNASRAYLY 305
             R+ +A    G  Q  LD+ + Y+ +RK FGQS+ +FQ  Q ++A+M  +L ++R +L 
Sbjct: 239 GGRLNIAACSLGAAQQALDLTLAYVRERKAFGQSLADFQNTQFRLAEMEIELQSARTFLR 298

Query: 306 AVAQACDRG--ETTRKDAAGVILYTAENATQMALQAIQILGGNGYINEFPTGRLLRDAKL 363
             A   D+G  E T+  A    + T E  +++    +Q+ GG GY+ ++   +L RD ++
Sbjct: 299 QAAWHLDQGTPEATKFCAMAKKMVT-EAGSRVVDGCLQLHGGYGYLADYGIEKLSRDLRV 357

Query: 364 YEIGAGTSEIRRMLIGREL 382
           ++I  GT+EI R+++ R +
Sbjct: 358 HQILEGTNEIMRLIVARNM 376


Lambda     K      H
   0.318    0.135    0.391 

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: 346
Number of extensions: 18
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: 387
Length of database: 379
Length adjustment: 30
Effective length of query: 357
Effective length of database: 349
Effective search space:   124593
Effective search space used:   124593
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 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