GapMind for catabolism of small carbon sources

 

Alignments for a candidate for bcd in Echinicola vietnamensis KMM 6221, DSM 17526

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 Echvi_1473 Echvi_1473 Acyl-CoA dehydrogenases

Query= BRENDA::D2RL84
         (383 letters)



>FitnessBrowser__Cola:Echvi_1473
          Length = 380

 Score =  381 bits (978), Expect = e-110
 Identities = 191/379 (50%), Positives = 265/379 (69%)

Query: 1   MDFNLTEDQQMIKDMAAEFAEKFLAPTVEERDKAHIWDRKLIDKMGEAGFCGICFPEEYG 60
           M+F LTE+Q MI  M  +F  K + P  +E D    +   L  K+GE G  G+  P EYG
Sbjct: 2   MNFQLTENQSMIAQMIRDFGAKEITPFRKEWDDHQTFPLPLFKKLGELGLMGVLIPSEYG 61

Query: 61  GMGLDVLSYILAVEELSKVDDGTGITLSANVSLCATPIYMFGTEEQKQKYLAPIAEGTHV 120
           G G   L Y+ A+ EL+K+D G G++++A+ SLC+  I +FG+EEQKQKYL  +A    +
Sbjct: 62  GSGFGYLEYVTAILELAKLDPGIGLSMAAHNSLCSGHIMLFGSEEQKQKYLPKLASCEFL 121

Query: 121 GAFGLTEPSAGTDASAQQTTAVLKGDKYILNGSKIFITNGKEADTYVVFAMTDKSQGVHG 180
           GA+GLTEP+ G+DA+  +TTA  +GD ++LNG+K FIT+G   D  VV A T +    HG
Sbjct: 122 GAWGLTEPNTGSDAANMKTTATAEGDYFVLNGAKNFITHGVSGDVAVVIARTGEVGDKHG 181

Query: 181 ISAFILEKGMPGFRFGKIEDKMGGHTSITAELIFEDCEVPKENLLGKEGEGFKIAMETLD 240
           ++AF++EKG  GFR G+ EDK+G  TS TAELIFEDC V K  +LG+ GEGF  +M+ LD
Sbjct: 182 MTAFVVEKGTEGFRGGRKEDKLGMRTSETAELIFEDCRVHKSQILGEVGEGFIQSMKVLD 241

Query: 241 GGRIGVAAQALGIAEGALAAAVKYSKEREQFGRSISKFQALQFMMADMATKIEAARYLVY 300
           GGRI +AA +LGIAEGA  AA+ YSKER+QF + IS +Q + F +ADMATK+EAA+ L +
Sbjct: 242 GGRISIAALSLGIAEGAFEAALSYSKERQQFQKPISAYQGISFKLADMATKLEAAKLLTF 301

Query: 301 HAAMLKNEGKPYSEAAAMAKCFASDVAMEVTTDAVQIFGGYGYTVDYPAERYMRNAKITQ 360
            AA LKN G+  + A+A AK +AS++A+E+  +AVQ++GGYG+T DYP E+Y R+ K+  
Sbjct: 302 KAADLKNRGEYVTLASAQAKYYASEIAVELANEAVQVYGGYGFTKDYPVEKYYRDVKLCT 361

Query: 361 IYEGTNQVMRIVTSRALLR 379
           I EGT+++ +IV SR LL+
Sbjct: 362 IGEGTSEIQKIVISRELLK 380


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: 393
Number of extensions: 13
Number of successful extensions: 1
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 17 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