GapMind for catabolism of small carbon sources

 

Alignments for a candidate for liuA in Rhodococcus qingshengii djl-6-2

Align acyl-CoA dehydrogenase subunit (EC 1.3.8.4; EC 1.3.8.5) (characterized)
to candidate WP_050655857.1 C1M55_RS09530 acyl-CoA dehydrogenase

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



>NCBI__GCF_002893965.1:WP_050655857.1
          Length = 380

 Score =  246 bits (629), Expect = 6e-70
 Identities = 138/382 (36%), Positives = 215/382 (56%), Gaps = 11/382 (2%)

Query: 4   RLTP--ELEELRRTVEEFAHDVVAPKIGDFYERHEFPYEIVREMGRMGLFGLPFPEEYGG 61
           RL P  E  +L     + A  V+APK+ ++ +  ++P  +   +G+ GL  LP+PEE+GG
Sbjct: 5   RLMPSQEARDLIELTRDVADKVLAPKVNEYEKAEKYPDGVFPALGQAGLLSLPYPEEFGG 64

Query: 62  MGGDYLALGIALEELARVDSSVAITLEAGVSLGAMPIHLFGTDAQKAEWLPRLCSGEILG 121
               Y      LEE+A   ++VA+ +    SL   P+  FGTD QK  WLP +  G  +G
Sbjct: 65  GDQPYEVYLQVLEEIASRWAAVAVAVSVH-SLSCFPLFTFGTDEQKNRWLPDMLGGNTIG 123

Query: 122 AFGLTEPDGGSDAGATRTTARLDESTNEWVINGTKCFITNSG-TDITGLVTVTAVTGRKP 180
           A+ L+E   GSDA A   + +   +   + +NG+K +ITN G  D   L   T+      
Sbjct: 124 AYSLSEAQAGSDAAAL--SCKATPTDGGYRVNGSKAWITNGGKADFYNLFARTS-----D 176

Query: 181 DGKPLISSIIVPSGTPGFTVAAPYSKVGWNASDTRELSFADVRVPAANLLGEQGRGYAQF 240
           DG   +S ++V     G +   P  K+G  A  T   ++ D  +P   L+G++G+G    
Sbjct: 177 DGSRGVSCLLVDKDAEGLSFGKPEEKMGLRAVPTASANYDDAFIPEERLIGQRGQGLPIA 236

Query: 241 LRILDEGRIAISALATGLAQGCVDESVKYAGERHAFGRNIGAYQAIQFKIADMEMKAHMA 300
              LD GR+ I+A+A G+AQG +D++V YA ER AFG+ I  +Q + F +ADM      A
Sbjct: 237 FSALDSGRLGIAAVAVGIAQGALDDAVAYAKERKAFGKRIIDHQGLGFVLADMAAAVDSA 296

Query: 301 RVGWRDAASRLVAGEPFKKEAAIAKLYSSTVAVDNAREATQIHGGYGFMNEYPVARMWRD 360
           R  + DAA R  AG P+ + A++AKL ++  A+    +A Q+ GGYG+  ++PV R  R+
Sbjct: 297 RATYLDAARRRDAGVPYSRNASVAKLVATDAAMKVTTDAVQVFGGYGYTQDFPVERYMRE 356

Query: 361 SKILEIGEGTSEVQRMLIAREL 382
           +KI +I EGT+++QR++IAR+L
Sbjct: 357 AKITQIFEGTNQIQRLVIARQL 378


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: 446
Number of extensions: 27
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: 380
Length adjustment: 30
Effective length of query: 356
Effective length of database: 350
Effective search space:   124600
Effective search space used:   124600
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