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_RS22365 AZOBR_RS22365 acyl-CoA dehydrogenase

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



>lcl|FitnessBrowser__azobra:AZOBR_RS22365 AZOBR_RS22365 acyl-CoA
           dehydrogenase
          Length = 379

 Score =  318 bits (816), Expect = 1e-91
 Identities = 171/373 (45%), Positives = 240/373 (64%), Gaps = 3/373 (0%)

Query: 4   TDEQLQISDAARQFAQERLKPFAAEWDREHRFPKEAIGEMAELGFFGMLVPEQWGGCDTG 63
           ++EQ    D AR FAQ+ + P AA WD    FP + + + A LGF G+ V E++GG   G
Sbjct: 6   SEEQQAFRDTARDFAQQEMAPNAAHWDENSVFPVDTLRQAAALGFAGIYVGEEFGGSGLG 65

Query: 64  YLAYAMALEEIAAGDGACSTIMSVHNSVGCVPILKFGNDDQKERFLKPLASGAMLGAFAL 123
            L  A+  EE++A   + +  +S+HN    + I +FGN +Q+ERFL  L +     ++ L
Sbjct: 66  RLDAALIFEELSAACPSTAAYISIHNMASWM-IDRFGNAEQRERFLPKLTTMEHFASYCL 124

Query: 124 TEPQAGSDASSLKTRARLNGDHYVLNGCKQFITSGQNAGVVIVFAVTDPSAGKRGISAFI 183
           TEP AGSDA+SL+TRA   GDHYVLNG K FI+ G  + V +    T    G +GIS   
Sbjct: 125 TEPGAGSDAASLRTRAERVGDHYVLNGSKAFISGGGTSDVYVCMVRTG-EPGPKGISCIA 183

Query: 184 VPTDSPGYKVARVEDKLGQHASDTCQILFEDVQVPVANRLGEEGEGYKIALANLEGGRVG 243
           V   +PG    + E KLG  +  T  ++FE+ +VPVANR+GEEGEG++IA+  L+GGR+ 
Sbjct: 184 VEKGTPGLSFGKQEHKLGWKSQPTSAVIFENCRVPVANRIGEEGEGFRIAMKGLDGGRLN 243

Query: 244 IASQSVGMARAAFEAARDYARERESFGKPIIEHQAVAFRLADMATQIAVARQMVHYAAAL 303
           IA+ SVG AR   E A  Y  ER+ FGKP+   QA+ F+LADMAT++  AR M+H AAA 
Sbjct: 244 IAACSVGGARFCLEQAVAYTTERKQFGKPLNAFQALQFKLADMATELDAARLMLHRAAAS 303

Query: 304 RDSGKP-ALVEASMAKLFASEMAEKVCSTALQTLGGYGYLSDFPLERIYRDVRVCQIYEG 362
            D+G P A    +MAK FA++   +V + ALQ  GGYGY+ ++P+ERI+RD+RV QI EG
Sbjct: 304 LDAGSPEATAHCAMAKRFATDAGFQVVNEALQLHGGYGYIKEYPIERIFRDLRVHQILEG 363

Query: 363 TSDIQRMVISRNL 375
           T++I R++I+R+L
Sbjct: 364 TNEIMRVIIARHL 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: 12
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: 379
Length adjustment: 30
Effective length of query: 345
Effective length of database: 349
Effective search space:   120405
Effective search space used:   120405
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.

Links

Downloads

Related tools

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