GapMind for catabolism of small carbon sources

 

Alignments for a candidate for acdH in Sphingomonas koreensis DSMZ 15582

Align 2-methylbutanoyl-CoA dehydrogenase / butanoyl-CoA dehydrogenase / isobutyryl-CoA dehydrogenase (EC 1.3.8.1; EC 1.3.8.5) (characterized)
to candidate Ga0059261_2164 Ga0059261_2164 Acyl-CoA dehydrogenases

Query= reanno::pseudo3_N2E3:AO353_25680
         (375 letters)



>FitnessBrowser__Korea:Ga0059261_2164
          Length = 394

 Score =  219 bits (558), Expect = 1e-61
 Identities = 132/370 (35%), Positives = 194/370 (52%), Gaps = 3/370 (0%)

Query: 4   TDEQLQISDAARQFAQERLKPFAAEWDREHRFPKEAIGEMAELGFFGMLVPEQWGGCDTG 63
           TDE+  + DAAR +AQERL P       +  F +E + EM +LG  G  +PE +GG   G
Sbjct: 20  TDEERMVRDAARAYAQERLLPRVTRAFLDENFDREIMSEMGQLGLLGPTIPETYGGAGLG 79

Query: 64  YLAYAMALEEIAAGDGACSTIMSVHNSVGCVPILKFGNDDQKERFLKPLASGAMLGAFAL 123
           Y+AY +   E+ A D    + MSV +S+   PI  +G ++QK ++L  L SG  +G F L
Sbjct: 80  YVAYGLVAREVEAVDSGYRSAMSVQSSLVMHPINAYGTEEQKRKYLPKLLSGEWVGCFGL 139

Query: 124 TEPQAGSDASSLKTRARLNGDHYVLNGCKQFITSGQNAGVVIVFAVTDPSAGKRGISAFI 183
           TEP AGSD  S++TRA      Y + G K +IT+   A V +V+A +D   G  GI  F+
Sbjct: 140 TEPDAGSDPGSMRTRAEKIDGGYRITGSKMWITNSPIADVFVVWAKSDAHGG--GIKGFV 197

Query: 184 VPTDSPGYKVARVEDKLGQHASDTCQILFEDVQVPVANRLGEEGEGYKIALANLEGGRVG 243
           +     G    ++E KL   AS T +I+ + V+V   + L  E +G K     L   R G
Sbjct: 198 LEKGMKGLSAPKIEGKLSLRASITGEIVMDGVEVS-EDALLPEVQGLKGPFGCLNRARYG 256

Query: 244 IASQSVGMARAAFEAARDYARERESFGKPIIEHQAVAFRLADMATQIAVARQMVHYAAAL 303
           IA  S+G A A F AAR Y  +R+ FG+P+   Q V  +LA+M T+IA+  Q    A  +
Sbjct: 257 IAWGSMGAAEACFHAARQYTLDRQQFGRPLAATQLVQLKLANMETEIALGLQAALRAGRM 316

Query: 304 RDSGKPALVEASMAKLFASEMAEKVCSTALQTLGGYGYLSDFPLERIYRDVRVCQIYEGT 363
            D G+ A    S+ K      A ++   A    GG G  ++F + R   ++     YEGT
Sbjct: 317 FDQGELAPEAISIIKRNNCGKALEIARVARDMHGGNGISAEFHVMRHAINLETVNTYEGT 376

Query: 364 SDIQRMVISR 373
            D+  +++ R
Sbjct: 377 HDVHGLILGR 386


Lambda     K      H
   0.319    0.134    0.389 

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: 342
Number of extensions: 12
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