GapMind for catabolism of small carbon sources

 

Aligments for a candidate for acdH in Dechlorosoma suillum PS

Align isobutyryl-CoA dehydrogenase (EC 1.3.8.1) (characterized)
to candidate Dsui_3369 Dsui_3369 acyl-CoA dehydrogenase

Query= reanno::psRCH2:GFF2392
         (383 letters)



>lcl|FitnessBrowser__PS:Dsui_3369 Dsui_3369 acyl-CoA dehydrogenase
          Length = 394

 Score =  198 bits (504), Expect = 2e-55
 Identities = 120/374 (32%), Positives = 196/374 (52%), Gaps = 2/374 (0%)

Query: 3   DLELSEDQRMIRDMARDFARREIAPHAQAWEKAGWIDDTLVAQMGELGLLGMVVPEEWGG 62
           D +LS ++R +RD AR +++  + P      +    D  +  ++GELGLLG  + + +G 
Sbjct: 13  DDQLSAEERQVRDTARQYSQDRLLPRIVQAFRHEQTDPAIFRELGELGLLGATL-DGYGC 71

Query: 63  SYIDYVAYALAVEEISAGDGATGALMSIHNSVGCGPVLNYGSQAQKDEWLTELASGRAIG 122
           +   YV+Y L   EI   D    +++S+ +S+   P+  +GS+A K+  L ++A+G  IG
Sbjct: 72  AGASYVSYGLLAREIERVDSGYRSMVSVQSSLAMYPIHAFGSEALKERLLPKMATGELIG 131

Query: 123 CFALTEPQAGSEAHNLRTRAELVDGHWVLNGSKQFCSNAKRSKLAIVFAVTDPELGKKGL 182
           CF LTEP  GS+  ++ +RAE V G W L G+K + +N+  + + +V+A    +     +
Sbjct: 132 CFGLTEPNHGSDPGSMESRAEAVPGGWELTGAKMWITNSPIADVFVVWAKDGQDEDGGEI 191

Query: 183 SAFLVPTDTPGFAVERSEHKMGIRASDTCGVSLSDCRIPEANLLGERGKGLAIALSNLEG 242
             F++     G +    + KMG+RAS T  + +    +PE NLL  + KGL    + L  
Sbjct: 192 RGFVLEKGMKGLSAPVIQGKMGLRASVTGEIVMDKVFVPEENLL-PKVKGLKGPFACLNQ 250

Query: 243 GRIGIGAQALGIARAAFEAALLYARERVQFGKPIAEHQSIANMLADMQTQLNAARLLILH 302
            R GI   ALG A A + AA  Y  +R QFG+P+A +Q +   LADMQT++       L 
Sbjct: 251 ARYGIAWGALGAAEACWHAARQYTLDRPQFGRPLAANQLVQKKLADMQTEIALGLQGCLR 310

Query: 303 AARLKSAGLPCLSEASQAKLFASEMAEKVCSQAVQIHGGYGYLEDYPVERYYRDARITQI 362
             RLK  G       S  K  +   A ++   A  +HGG G  +++ V R+  +  +   
Sbjct: 311 LGRLKDEGKDAPEMTSLLKRNSCGKALEIARTARDMHGGNGISDEFHVVRHMLNLEVVNT 370

Query: 363 YEGSSEIQRLLIAR 376
           YEG+ +I  L++ R
Sbjct: 371 YEGTHDIHALILGR 384


Lambda     K      H
   0.318    0.133    0.390 

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: 345
Number of extensions: 18
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: 383
Length of database: 394
Length adjustment: 30
Effective length of query: 353
Effective length of database: 364
Effective search space:   128492
Effective search space used:   128492
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 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