GapMind for catabolism of small carbon sources

 

Alignments for a candidate for acdH in Xanthobacter autotrophicus Py2

Align 2-methylbutanoyl-CoA dehydrogenase (EC 1.3.8.5) (characterized)
to candidate WP_012116241.1 XAUT_RS21625 isovaleryl-CoA dehydrogenase

Query= reanno::pseudo6_N2E2:Pf6N2E2_1146
         (375 letters)



>NCBI__GCF_000017645.1:WP_012116241.1
          Length = 390

 Score =  274 bits (700), Expect = 3e-78
 Identities = 144/371 (38%), Positives = 220/371 (59%)

Query: 5   EEQTQIRDMARQFAEERLKPFAAEWDREHRFPREAIDEMAELGFFGMLVPEQWGGCDTGY 64
           E    +RD  R F++  + P AAE DR ++FPR+   ++  LG  G+   E++GG   GY
Sbjct: 15  ETADMLRDTVRSFSDAEIAPRAAEIDRTNQFPRDLWPKLGALGLLGVTAEEEYGGSGLGY 74

Query: 65  LAYAMTLEEIAAGDGACSTIMSVHNSVGCVPILKFGNDEQKAKFLTPLASGAMLGAFALT 124
           L + + +EEI+    +       H+++    I + G  EQKAK+L  L SG  +GA A++
Sbjct: 75  LEHVIAMEEISRASASVGLSYGAHSNLCINQISRNGTAEQKAKYLPKLISGEHVGALAMS 134

Query: 125 EPQAGSDASSLKTRARLEGDHYVLNGCKQFITSGQNAGVVIVFAVTDPSAGKRGISAFIV 184
           EP AGSD  S++TRA  +GD Y+LNG K +IT+G  A  ++V+A TDP+AG +G++AF+V
Sbjct: 135 EPGAGSDVVSMRTRADKKGDRYILNGSKMWITNGPIAETLVVYAKTDPAAGPKGMTAFLV 194

Query: 185 PTDSPGYSVARVEDKLGQHASDTCQILFEDLKVPVGNRLGEEGEGYKIALANLEGGRVGI 244
             D PG+S A+  DKLG   SDT +++F+D +VP  N LG  G G  + ++ L+  R  +
Sbjct: 195 ERDFPGFSTAQKLDKLGMRGSDTGELVFQDCEVPEENVLGAVGRGVNVLMSGLDYERAVL 254

Query: 245 AAQAVGMARAAFEAARDYARERSSFGKPIIEHQAVAFRLADMATQIAVARQMVHYAAALR 304
           A    G+ +A  +    Y  ER  FG+PI   Q +  ++ADM   +   +  V+  A   
Sbjct: 255 AGGPTGIMQACMDIVLPYVHERKQFGQPIGTFQLMQGKIADMYVTMNATKAYVYAVAKAC 314

Query: 305 DSGQPALVEASMAKLFASEMAEKVCSMALQTLGGYGYLNDFPLERIYRDVRVCQIYEGTS 364
           D G     +A+ A L+A+E A  +   A+QTLGG GY+ND+P  R+ RD ++ +I  GTS
Sbjct: 315 DRGATTREDAAGAILYAAEKATWMALEAIQTLGGNGYINDYPTGRLLRDAKLYEIGAGTS 374

Query: 365 DIQRMVISRNL 375
           +I+RM+I R L
Sbjct: 375 EIRRMLIGRQL 385


Lambda     K      H
   0.320    0.134    0.388 

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: 319
Number of extensions: 12
Number of successful extensions: 1
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: 390
Length adjustment: 30
Effective length of query: 345
Effective length of database: 360
Effective search space:   124200
Effective search space used:   124200
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 Apr 09 2024. 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