GapMind for catabolism of small carbon sources

 

Aligments for a candidate for acdH in Shewanella sp. ANA-3

Align 2-methylbutanoyl-CoA dehydrogenase / butanoyl-CoA dehydrogenase / isobutyryl-CoA dehydrogenase (EC 1.3.8.1; EC 1.3.8.5) (characterized)
to candidate 7024494 Shewana3_1672 isovaleryl-CoA dehydrogenase (RefSeq)

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



>lcl|FitnessBrowser__ANA3:7024494 Shewana3_1672 isovaleryl-CoA
           dehydrogenase (RefSeq)
          Length = 389

 Score =  270 bits (690), Expect = 5e-77
 Identities = 143/371 (38%), Positives = 222/371 (59%)

Query: 5   DEQLQISDAARQFAQERLKPFAAEWDREHRFPKEAIGEMAELGFFGMLVPEQWGGCDTGY 64
           +E   + DA + FA+  + P AA+ D ++ FP E    +  +G  G+ VPE++GG + GY
Sbjct: 14  EEVDMLRDAVQDFAKHEIAPIAAKVDHDNAFPNEIWPVLGGMGLLGVTVPEEYGGANMGY 73

Query: 65  LAYAMALEEIAAGDGACSTIMSVHNSVGCVPILKFGNDDQKERFLKPLASGAMLGAFALT 124
           LA+ +A+EEI+    +       H+++    I + GN +QK ++L  L SG  +GA A++
Sbjct: 74  LAHVVAMEEISRASASIGLSYGAHSNLCVNQINRNGNAEQKAKYLPKLVSGEHIGALAMS 133

Query: 125 EPQAGSDASSLKTRARLNGDHYVLNGCKQFITSGQNAGVVIVFAVTDPSAGKRGISAFIV 184
           EP AGSD  S+K  AR  GD Y+LNG K +IT+G +A   +++A TD + G  GI+AFIV
Sbjct: 134 EPNAGSDVVSMKLHARKEGDRYILNGNKMWITNGPDANTYVIYAKTDLTKGAHGITAFIV 193

Query: 185 PTDSPGYKVARVEDKLGQHASDTCQILFEDVQVPVANRLGEEGEGYKIALANLEGGRVGI 244
                G+  A+  DKLG   S+TC+++FEDV+VP  N LG    G K+ ++ L+  RV +
Sbjct: 194 ERGFKGFSQAQKLDKLGMRGSNTCELVFEDVEVPEENILGGLNNGVKVLMSGLDYERVVL 253

Query: 245 ASQSVGMARAAFEAARDYARERESFGKPIIEHQAVAFRLADMATQIAVARQMVHYAAALR 304
           +   +G+  A  +    Y  ERE FGK I E Q V  +LADM T +  A+  V+  A   
Sbjct: 254 SGGPLGIMNACMDIVVPYIHEREQFGKSIGEFQLVQGKLADMYTGMNAAKAYVYSVAKSC 313

Query: 305 DSGKPALVEASMAKLFASEMAEKVCSTALQTLGGYGYLSDFPLERIYRDVRVCQIYEGTS 364
           D G+    +A+ A L+++E+A K+   A+Q LGG GY++++   R+ RD ++ +I  GTS
Sbjct: 314 DRGETTRKDAAGAILYSAELATKMALDAIQLLGGNGYVNEYATGRLLRDAKLYEIGAGTS 373

Query: 365 DIQRMVISRNL 375
           +I+RM+I R L
Sbjct: 374 EIRRMLIGREL 384


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: 314
Number of extensions: 11
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: 389
Length adjustment: 30
Effective length of query: 345
Effective length of database: 359
Effective search space:   123855
Effective search space used:   123855
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