GapMind for catabolism of small carbon sources

 

Alignments for a candidate for liuA in Acidovorax caeni R-24608

Align acyl-CoA dehydrogenase subunit (EC 1.3.8.4; EC 1.3.8.5) (characterized)
to candidate WP_054255950.1 BN2503_RS07075 acyl-CoA dehydrogenase

Query= metacyc::MONOMER-11693
         (386 letters)



>NCBI__GCF_001298675.1:WP_054255950.1
          Length = 376

 Score =  263 bits (672), Expect = 6e-75
 Identities = 148/382 (38%), Positives = 231/382 (60%), Gaps = 13/382 (3%)

Query: 5   LTPELEELRRTVEEFAHDVVAPKIGDFYERHEFPYEIVREMGRMGLFGLPFPEEYGGMGG 64
           LT +   +R  V +F  + + P    + + H FP ++ + + ++G +G+  PE+YGG G 
Sbjct: 3   LTQDQTMVRDAVRDFVREQITPHAARWDKEHHFPRDVHQGLAQLGAYGICVPEQYGGAGL 62

Query: 65  DYLALGIALEELARVDSSVAITLEAGVSLGAMPIHL----FGTDAQKAEWLPRLCSGEIL 120
           DY+ L + LEE+A  D   +      +S+   P++     +G++AQK +WL  L  GE+L
Sbjct: 63  DYVTLALVLEEIAAGDGGTS----TAISVTNCPVNAILMRYGSEAQKQQWLAPLARGEML 118

Query: 121 GAFGLTEPDGGSDAGATRTTARLDESTNEWVINGTKCFITNSGTDITGLVTVTAVTGRKP 180
           GAF LTEP  GSDA A RTTA  +   +++VING K FIT+      G V +      K 
Sbjct: 119 GAFCLTEPHVGSDASALRTTATREG--DDYVINGVKQFITSGKN---GHVAIVIAVTDKA 173

Query: 181 DGKPLISSIIVPSGTPGFTVAAPYSKVGWNASDTRELSFADVRVPAANLLGEQGRGYAQF 240
            GK  +S+ +VP+  PG+ VA    K+G ++SDT +++F + R+PAANL+G +G GY   
Sbjct: 174 AGKKGMSAFLVPTSNPGYQVARLEEKLGQHSSDTAQINFDNCRIPAANLIGAEGEGYKIA 233

Query: 241 LRILDEGRIAISALATGLAQGCVDESVKYAGERHAFGRNIGAYQAIQFKIADMEMKAHMA 300
           L  L+ GRI I+A + G+A+   + +++Y+ ER +FG+ I  +QA+ F++AD   +   A
Sbjct: 234 LSALEGGRIGIAAQSVGMARAAFECALQYSKERESFGQPIFNHQAVGFRLADCATQLEAA 293

Query: 301 RVGWRDAASRLVAGEPFKKEAAIAKLYSSTVAVDNAREATQIHGGYGFMNEYPVARMWRD 360
           R     AAS   AG+P  KEAA+AKL++S +A      A Q  GGYG +N++PV R +RD
Sbjct: 294 RQLIWHAASLRDAGQPCLKEAAMAKLFASEMAERVCSAAIQTLGGYGVVNDFPVERFYRD 353

Query: 361 SKILEIGEGTSEVQRMLIAREL 382
            ++ +I EGTS+VQ+++I R L
Sbjct: 354 VRVCQIYEGTSDVQKIIIQRAL 375


Lambda     K      H
   0.318    0.136    0.402 

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: 402
Number of extensions: 17
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: 386
Length of database: 376
Length adjustment: 30
Effective length of query: 356
Effective length of database: 346
Effective search space:   123176
Effective search space used:   123176
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 50 (23.9 bits)

This GapMind analysis is from Sep 24 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:

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