GapMind for catabolism of small carbon sources

 

Alignments for a candidate for acdH in Sphingomonas koreensis DSMZ 15582

Align short-chain acyl-CoA dehydrogenase monomer (EC 1.3.8.1) (characterized)
to candidate Ga0059261_2164 Ga0059261_2164 Acyl-CoA dehydrogenases

Query= metacyc::MONOMER-17424
         (375 letters)



>FitnessBrowser__Korea:Ga0059261_2164
          Length = 394

 Score =  228 bits (580), Expect = 3e-64
 Identities = 137/371 (36%), Positives = 198/371 (53%), Gaps = 3/371 (0%)

Query: 3   VNDEQQQIADAVRAFAQERLKPFAEQWDKDHRFPKEAIDEMAELGLFGMLVPEQWGGSDT 62
           + DE++ + DA RA+AQERL P   +   D  F +E + EM +LGL G  +PE +GG+  
Sbjct: 19  LTDEERMVRDAARAYAQERLLPRVTRAFLDENFDREIMSEMGQLGLLGPTIPETYGGAGL 78

Query: 63  GYVAYAMALEEIAAGDGACSTIMSVHNSVGCVPILRFGNEQQKEQFLTPLATGAMLGAFA 122
           GYVAY +   E+ A D    + MSV +S+   PI  +G E+QK ++L  L +G  +G F 
Sbjct: 79  GYVAYGLVAREVEAVDSGYRSAMSVQSSLVMHPINAYGTEEQKRKYLPKLLSGEWVGCFG 138

Query: 123 LTEPQAGSDASSLKTRARLEGDHYVLNGSKQFITSGQNAGVVIVFAVTDPEAGKRGISAF 182
           LTEP AGSD  S++TRA      Y + GSK +IT+   A V +V+A +D   G  GI  F
Sbjct: 139 LTEPDAGSDPGSMRTRAEKIDGGYRITGSKMWITNSPIADVFVVWAKSDAHGG--GIKGF 196

Query: 183 IVPTDSPGYQVARVEDKLGQHASDTCQIVFDNVQVPVANRLGAEGEGYKIALANLEGGRI 242
           ++     G    ++E KL   AS T +IV D V+V   + L  E +G K     L   R 
Sbjct: 197 VLEKGMKGLSAPKIEGKLSLRASITGEIVMDGVEVS-EDALLPEVQGLKGPFGCLNRARY 255

Query: 243 GIASQAVGMARAAFEVARDYANERQSFGKPLIEHQAVAFRLADMATKISVARQMVLHAAA 302
           GIA  ++G A A F  AR Y  +RQ FG+PL   Q V  +LA+M T+I++  Q  L A  
Sbjct: 256 GIAWGSMGAAEACFHAARQYTLDRQQFGRPLAATQLVQLKLANMETEIALGLQAALRAGR 315

Query: 303 LRDAGRPALVEASMAKLFASEMAEKVCSDALQTLGGYGYLSDFPLERIYRDVRVCQIYEG 362
           + D G  A    S+ K      A ++   A    GG G  ++F + R   ++     YEG
Sbjct: 316 MFDQGELAPEAISIIKRNNCGKALEIARVARDMHGGNGISAEFHVMRHAINLETVNTYEG 375

Query: 363 TSDIQRMVIAR 373
           T D+  +++ R
Sbjct: 376 THDVHGLILGR 386


Lambda     K      H
   0.319    0.134    0.382 

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: 348
Number of extensions: 15
Number of successful extensions: 2
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: 375
Length of database: 394
Length adjustment: 30
Effective length of query: 345
Effective length of database: 364
Effective search space:   125580
Effective search space used:   125580
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 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:

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