GapMind for catabolism of small carbon sources

 

Alignments for a candidate for acdH in Magnetospirillum magneticum AMB-1

Align 2-methylbutanoyl-CoA dehydrogenase / butanoyl-CoA dehydrogenase / isobutyryl-CoA dehydrogenase (EC 1.3.8.1; EC 1.3.8.5) (characterized)
to candidate WP_043745120.1 AMB_RS18150 acyl-CoA dehydrogenase

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



>NCBI__GCF_000009985.1:WP_043745120.1
          Length = 378

 Score =  303 bits (775), Expect = 7e-87
 Identities = 164/373 (43%), Positives = 229/373 (61%), Gaps = 3/373 (0%)

Query: 4   TDEQLQISDAARQFAQERLKPFAAEWDREHRFPKEAIGEMAELGFFGMLVPEQWGGCDTG 63
           T +Q     AA  FA   + P AA WD E  FP++ + + AELGF G+ V E  GG    
Sbjct: 6   TPDQEAFRQAAHDFAVGEMAPHAAHWDEEGIFPEDTLRKAAELGFAGIYVGEDVGGSALS 65

Query: 64  YLAYAMALEEIAAGDGACSTIMSVHNSVGCVPILKFGNDDQKERFLKPLASGAMLGAFAL 123
            L  A+  EE+AA   + +  +S+HN    + I  FG+ +Q+ RFL  L S     ++ L
Sbjct: 66  RLDAALIFEELAAACPSTAAYISIHNMAAWM-IDSFGDQEQRRRFLPDLCSMRKFASYCL 124

Query: 124 TEPQAGSDASSLKTRARLNGDHYVLNGCKQFITSGQNAGVVIVFAVTDPSAGKRGISAFI 183
           TEP AGSDA+SL+T+A  +GDHYVLNG K FI+ G  + V +V   T  + G +GIS  +
Sbjct: 125 TEPNAGSDAASLRTKAERDGDHYVLNGTKAFISGGGRSDVYVVMVRTG-APGPKGISCLV 183

Query: 184 VPTDSPGYKVARVEDKLGQHASDTCQILFEDVQVPVANRLGEEGEGYKIALANLEGGRVG 243
           V   +PG    + E KLG     T  ++FED +VPVANR+G EG+G+KIA+  L+GGR+ 
Sbjct: 184 VEAGTPGLSFGKQEKKLGWKTQPTASVIFEDCRVPVANRIGAEGDGFKIAMKGLDGGRIN 243

Query: 244 IASQSVGMARAAFEAARDYARERESFGKPIIEHQAVAFRLADMATQIAVARQMVHYAAAL 303
           I + S+G ARA  E A +Y  +R+ FG+ I   QA  F+LADMAT++  AR M+H AA  
Sbjct: 244 IGACSLGGARACLEHAIEYTGQRQQFGQAISAFQATQFKLADMATELEAARLMIHRAAHS 303

Query: 304 RDSGKP-ALVEASMAKLFASEMAEKVCSTALQTLGGYGYLSDFPLERIYRDVRVCQIYEG 362
            DS  P A V  +MAK  A+++   V   ALQ  GGYGY+ ++P+ER +RD+RV QI EG
Sbjct: 304 LDSKSPQATVHCAMAKRMATDVGFAVTDAALQLHGGYGYIKEYPIERYFRDLRVHQILEG 363

Query: 363 TSDIQRMVISRNL 375
           +++I R++I R L
Sbjct: 364 SNEIMRVIIGRAL 376


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: 375
Number of extensions: 14
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: 375
Length of database: 378
Length adjustment: 30
Effective length of query: 345
Effective length of database: 348
Effective search space:   120060
Effective search space used:   120060
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