GapMind for catabolism of small carbon sources

 

Alignments for a candidate for acdH in Hydrogenophaga taeniospiralis CCUG 15921 NBRC 102512

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_068170917.1 HTA01S_RS11035 isovaleryl-CoA dehydrogenase

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



>NCBI__GCF_001592305.1:WP_068170917.1
          Length = 393

 Score =  251 bits (640), Expect = 3e-71
 Identities = 132/371 (35%), Positives = 218/371 (58%), Gaps = 5/371 (1%)

Query: 10  ISDAARQFAQERLKPFAAEWDREHRFPKEAIGEMAELGFFGMLVPEQWGGCDTGYLAYAM 69
           + DA R+FAQ  + P AAE D+  +FP +   +M ELG  G+ VPEQ+GG + GYLA+ +
Sbjct: 18  LRDAVREFAQAEIAPRAAEIDKSDQFPMDCWRKMGELGVLGITVPEQYGGANMGYLAHMV 77

Query: 70  ALEEIAAGDGACSTIMSVHNSVGCVPILKFGNDDQKERFLKPLASGAMLGAFALTEPQAG 129
           A+EEI+    +       H+++    I + GND QK ++L  L SG  +GA A++EP AG
Sbjct: 78  AMEEISRASASVGLSYGAHSNLCVNQINRNGNDAQKAKYLPKLISGEHVGALAMSEPGAG 137

Query: 130 SDASSLKTRARLNGDHYVLNGCKQFITSGQNAGVVIVFAVTDPSAGKRGISAFIVPTDSP 189
           SD  S+K +A   G +Y+LNG K +IT+G +A  ++V+A ++P  G RG++AF++    P
Sbjct: 138 SDVISMKLKAEDKGGYYLLNGNKMWITNGPDADTLVVYAKSEPEMGARGVTAFLIEKGMP 197

Query: 190 GYKVARVEDKLGQHASDTCQILFEDVQVPVANRLGEEGEGYKIALANLEGGRVGIASQSV 249
           G+ +A+  DKLG   S T +++F++V+VP  N LG    G K+ ++ L+  R  +    +
Sbjct: 198 GFSIAQKLDKLGMRGSHTGELVFQNVEVPAQNILGGLNMGAKVLMSGLDYERAVLTGGPL 257

Query: 250 GMARAAFEAARDYARERESFGKPIIEHQAVAFRLADMATQIAVARQMVHYAAALRD---- 305
           G+ ++  +    Y  +R+ FG+ I E Q +  ++ADM T +  AR   +  A   D    
Sbjct: 258 GIMQSVMDNVIPYIHDRKQFGQSIGEFQLIQGKVADMYTVLQAARSFAYTVAKNLDLLGT 317

Query: 306 -SGKPALVEASMAKLFASEMAEKVCSTALQTLGGYGYLSDFPLERIYRDVRVCQIYEGTS 364
              +    + +   L+ +E A  +    +Q  GG GY++++PL R++RD ++ +I  GTS
Sbjct: 318 EHVRQVRKDCASVILWTAEKATWMAGEGVQIYGGNGYINEYPLGRLWRDAKLYEIGAGTS 377

Query: 365 DIQRMVISRNL 375
           +I+RM+I R L
Sbjct: 378 EIRRMLIGREL 388


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: 319
Number of extensions: 14
Number of successful extensions: 2
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: 393
Length adjustment: 30
Effective length of query: 345
Effective length of database: 363
Effective search space:   125235
Effective search space used:   125235
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