GapMind for catabolism of small carbon sources

 

Aligments for a candidate for acdH in Azospirillum brasilense Sp245

Align 2-methylbutanoyl-CoA dehydrogenase / butanoyl-CoA dehydrogenase / isobutyryl-CoA dehydrogenase (EC 1.3.8.1; EC 1.3.8.5) (characterized)
to candidate AZOBR_RS22310 AZOBR_RS22310 isovaleryl-CoA dehydrogenase

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



>lcl|FitnessBrowser__azobra:AZOBR_RS22310 AZOBR_RS22310
           isovaleryl-CoA dehydrogenase
          Length = 390

 Score =  271 bits (694), Expect = 2e-77
 Identities = 145/366 (39%), Positives = 219/366 (59%)

Query: 10  ISDAARQFAQERLKPFAAEWDREHRFPKEAIGEMAELGFFGMLVPEQWGGCDTGYLAYAM 69
           + D  R FA + + P AAE DR + FP E   +  +LG  G+   E++GG   GYL + +
Sbjct: 20  LRDTVRSFAADEIAPRAAEIDRTNEFPNELWRKFGDLGVLGITAEEEYGGAGMGYLEHVV 79

Query: 70  ALEEIAAGDGACSTIMSVHNSVGCVPILKFGNDDQKERFLKPLASGAMLGAFALTEPQAG 129
           A+EEI+    +       H+++    I K G  +QK R+L  L SG  +GA A++EP AG
Sbjct: 80  AMEEISRASASVGLSYGAHSNLCVNQIRKNGTAEQKTRYLPKLISGEHIGALAMSEPNAG 139

Query: 130 SDASSLKTRARLNGDHYVLNGCKQFITSGQNAGVVIVFAVTDPSAGKRGISAFIVPTDSP 189
           SD  S+K RA   GD YVLNG K +IT+G +A  ++V+A TD +AG RGI+AF++     
Sbjct: 140 SDVVSMKLRAEKQGDRYVLNGTKMWITNGPDADTLVVYAKTDVNAGPRGITAFLIEKSFK 199

Query: 190 GYKVARVEDKLGQHASDTCQILFEDVQVPVANRLGEEGEGYKIALANLEGGRVGIASQSV 249
           G+ VA+  DKLG   S+T +++FED +VP  N LG  G G  + ++ L+  R  +A   +
Sbjct: 200 GFSVAQKLDKLGMRGSNTGELVFEDCEVPEENILGGVGRGVNVLMSGLDYERAVLAGGPL 259

Query: 250 GMARAAFEAARDYARERESFGKPIIEHQAVAFRLADMATQIAVARQMVHYAAALRDSGKP 309
           G+ +A  +    Y  +R+ FG+PI E Q +  +LADM T +  A+  V+  A   D G+ 
Sbjct: 260 GIMQACMDVVVPYLHDRKQFGQPIGEFQLMQGKLADMYTIMNAAKAYVYAVAKACDRGET 319

Query: 310 ALVEASMAKLFASEMAEKVCSTALQTLGGYGYLSDFPLERIYRDVRVCQIYEGTSDIQRM 369
           A  +A+ A LFA+E A  +   A+QTLGG GY++++P  R+ RD ++ +I  GTS+I+RM
Sbjct: 320 ARKDAAGAILFAAEKATWMALEAIQTLGGNGYINEYPTGRLLRDAKLYEIGAGTSEIRRM 379

Query: 370 VISRNL 375
           +I R L
Sbjct: 380 LIGREL 385


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: 325
Number of extensions: 15
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 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 paper from 2022 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