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 (EC 1.3.8.5) (characterized)
to candidate WP_068170917.1 HTA01S_RS11035 isovaleryl-CoA dehydrogenase

Query= reanno::pseudo5_N2C3_1:AO356_26355
         (375 letters)



>NCBI__GCF_001592305.1:WP_068170917.1
          Length = 393

 Score =  256 bits (653), Expect = 1e-72
 Identities = 136/376 (36%), Positives = 220/376 (58%), Gaps = 5/376 (1%)

Query: 5   EEQTQIRDMARQFAQERLKPFAAEWDREHRFPREAIAEMAELGFFGMLVPEQWGGCDTGY 64
           E+   +RD  R+FAQ  + P AAE D+  +FP +   +M ELG  G+ VPEQ+GG + GY
Sbjct: 13  EDIDALRDAVREFAQAEIAPRAAEIDKSDQFPMDCWRKMGELGVLGITVPEQYGGANMGY 72

Query: 65  LAYAMTLEEIAAGDGACSTIMSVHNSVGCVPILKFGNDEQKAKFLTPLASGAMLGAFALT 124
           LA+ + +EEI+    +       H+++    I + GND QKAK+L  L SG  +GA A++
Sbjct: 73  LAHMVAMEEISRASASVGLSYGAHSNLCVNQINRNGNDAQKAKYLPKLISGEHVGALAMS 132

Query: 125 EPQAGSDASSLKTRARLEGDHYVLNGCKQFITSGQNAGVVIVFAVTDPSAGKRGISAFIV 184
           EP AGSD  S+K +A  +G +Y+LNG K +IT+G +A  ++V+A ++P  G RG++AF++
Sbjct: 133 EPGAGSDVISMKLKAEDKGGYYLLNGNKMWITNGPDADTLVVYAKSEPEMGARGVTAFLI 192

Query: 185 PTDSPGYSVARVEDKLGQHASDTCQILFEEVKVPVGNRLGEEGEGYKIALANLEGGRVGI 244
               PG+S+A+  DKLG   S T +++F+ V+VP  N LG    G K+ ++ L+  R  +
Sbjct: 193 EKGMPGFSIAQKLDKLGMRGSHTGELVFQNVEVPAQNILGGLNMGAKVLMSGLDYERAVL 252

Query: 245 AAQAVGMARAAFEAARDYARERSSFGKPIIEHQAVAFRLADMATQIAVARQMVHYAAALR 304
               +G+ ++  +    Y  +R  FG+ I E Q +  ++ADM T +  AR   +  A   
Sbjct: 253 TGGPLGIMQSVMDNVIPYIHDRKQFGQSIGEFQLIQGKVADMYTVLQAARSFAYTVAKNL 312

Query: 305 D-----SGQPALVEASMAKLFASEMAEKVCSMALQTLGGYGYLNDFPLERIYRDVRVCQI 359
           D       +    + +   L+ +E A  +    +Q  GG GY+N++PL R++RD ++ +I
Sbjct: 313 DLLGTEHVRQVRKDCASVILWTAEKATWMAGEGVQIYGGNGYINEYPLGRLWRDAKLYEI 372

Query: 360 YEGTSDIQRMVISRNL 375
             GTS+I+RM+I R L
Sbjct: 373 GAGTSEIRRMLIGREL 388


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: 313
Number of extensions: 12
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