GapMind for catabolism of small carbon sources

 

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

Align butanoyl-CoA dehydrogenase (NAD+, ferredoxin) (subunit 1/3) (EC 1.3.1.109); short-chain acyl-CoA dehydrogenase (subunit 1/2) (EC 1.3.8.1) (characterized)
to candidate WP_050655857.1 C1M55_RS09530 acyl-CoA dehydrogenase

Query= BRENDA::D2RL84
         (383 letters)



>NCBI__GCF_002893965.1:WP_050655857.1
          Length = 380

 Score =  307 bits (786), Expect = 4e-88
 Identities = 161/372 (43%), Positives = 236/372 (63%), Gaps = 2/372 (0%)

Query: 6   TEDQQMIKDMAAEFAEKFLAPTVEERDKAHIWDRKLIDKMGEAGFCGICFPEEYGGMGLD 65
           +++ + + ++  + A+K LAP V E +KA  +   +   +G+AG   + +PEE+GG    
Sbjct: 9   SQEARDLIELTRDVADKVLAPKVNEYEKAEKYPDGVFPALGQAGLLSLPYPEEFGGGDQP 68

Query: 66  VLSYILAVEELSKVDDGTGITLSANVSLCATPIYMFGTEEQKQKYLAPIAEGTHVGAFGL 125
              Y+  +EE++       + +S + SL   P++ FGT+EQK ++L  +  G  +GA+ L
Sbjct: 69  YEVYLQVLEEIASRWAAVAVAVSVH-SLSCFPLFTFGTDEQKNRWLPDMLGGNTIGAYSL 127

Query: 126 TEPSAGTDASAQQTTAVLKGDKYILNGSKIFITNGKEADTYVVFAMTDKSQGVHGISAFI 185
           +E  AG+DA+A    A      Y +NGSK +ITNG +AD Y +FA T    G  G+S  +
Sbjct: 128 SEAQAGSDAAALSCKATPTDGGYRVNGSKAWITNGGKADFYNLFARTS-DDGSRGVSCLL 186

Query: 186 LEKGMPGFRFGKIEDKMGGHTSITAELIFEDCEVPKENLLGKEGEGFKIAMETLDGGRIG 245
           ++K   G  FGK E+KMG     TA   ++D  +P+E L+G+ G+G  IA   LD GR+G
Sbjct: 187 VDKDAEGLSFGKPEEKMGLRAVPTASANYDDAFIPEERLIGQRGQGLPIAFSALDSGRLG 246

Query: 246 VAAQALGIAEGALAAAVKYSKEREQFGRSISKFQALQFMMADMATKIEAARYLVYHAAML 305
           +AA A+GIA+GAL  AV Y+KER+ FG+ I   Q L F++ADMA  +++AR     AA  
Sbjct: 247 IAAVAVGIAQGALDDAVAYAKERKAFGKRIIDHQGLGFVLADMAAAVDSARATYLDAARR 306

Query: 306 KNEGKPYSEAAAMAKCFASDVAMEVTTDAVQIFGGYGYTVDYPAERYMRNAKITQIYEGT 365
           ++ G PYS  A++AK  A+D AM+VTTDAVQ+FGGYGYT D+P ERYMR AKITQI+EGT
Sbjct: 307 RDAGVPYSRNASVAKLVATDAAMKVTTDAVQVFGGYGYTQDFPVERYMREAKITQIFEGT 366

Query: 366 NQVMRIVTSRAL 377
           NQ+ R+V +R L
Sbjct: 367 NQIQRLVIARQL 378


Lambda     K      H
   0.318    0.134    0.379 

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: 387
Number of extensions: 14
Number of successful extensions: 3
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: 383
Length of database: 380
Length adjustment: 30
Effective length of query: 353
Effective length of database: 350
Effective search space:   123550
Effective search space used:   123550
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