GapMind for catabolism of small carbon sources

 

Alignments for a candidate for bcd in Sedimenticola selenatireducens DSM 17993

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_029134232.1 A3GO_RS0115815 acyl-CoA dehydrogenase

Query= BRENDA::D2RL84
         (383 letters)



>NCBI__GCF_000428045.1:WP_029134232.1
          Length = 397

 Score =  221 bits (564), Expect = 2e-62
 Identities = 135/376 (35%), Positives = 208/376 (55%), Gaps = 6/376 (1%)

Query: 1   MDFNLTEDQQMIKDMAAEFAEKFLAPTVEERDKAHIWDRKLIDKMGEAGFCGICFPEEYG 60
           +D  LTE+++M++D A ++ ++ L P V E ++   +DR+++++MGE G  G+   + Y 
Sbjct: 19  LDQQLTEEERMVRDTAQKYCQEQLMPRVLEANRHEHFDREIMNEMGELGLLGVTI-DGYD 77

Query: 61  GMGLDVLSYILAVEELSKVDDGTGITLSANVSLCATPIYMFGTEEQKQKYLAPIAEGTHV 120
             GL+ +SY L   E+ +VD G    +S   SL   PIY +GTEEQ++KYL  +A G  V
Sbjct: 78  CAGLNYVSYGLIAREVERVDSGYRSAMSVQSSLVMHPIYAYGTEEQREKYLPKLATGELV 137

Query: 121 GAFGLTEPSAGTDASAQQTTAVLKGDKYILNGSKIFITNGKEADTYVVFAMTDKSQGVHG 180
           G FGLTEP  G+D +  +T A      Y L+GSK++ITN   AD ++V+A  D  +GV  
Sbjct: 138 GCFGLTEPDHGSDPAGMKTRARTVDGGYSLSGSKMWITNSPIADVFIVWAKDD--EGV-- 193

Query: 181 ISAFILEKGMPGFRFGKIEDKMGGHTSITAELIFEDCEVPKENLLGKEGEGFKIAMETLD 240
           I  FILEKGM G    KIE K     SIT E++ ++  VP ENLL    +G       L+
Sbjct: 194 IRGFILEKGMKGLSAPKIEGKFSLRASITGEIVMDEVFVPAENLL-PNVKGLAGPFGCLN 252

Query: 241 GGRIGVAAQALGIAEGALAAAVKYSKEREQFGRSISKFQALQFMMADMATKIEAARYLVY 300
             R G+A   LG AE     A+ Y+ +R+QFGR ++  Q +Q  +A+M T+I        
Sbjct: 253 RARYGIAWGVLGAAEDCWHRALTYTLDRKQFGRPLAANQLIQLKLANMQTEITLGLQGCL 312

Query: 301 HAAMLKNEGKPYSEAAAMAKCFASDVAMEVTTDAVQIFGGYGYTVDYPAERYMRNAKITQ 360
               L + G+   EA ++ K   +  A+++   A  + GG G + ++   R+  N +   
Sbjct: 313 QLGRLFDAGQAAPEAISLMKRNNAGKALDIARIARDMHGGNGISDEFHVIRHAMNLEAVN 372

Query: 361 IYEGTNQVMRIVTSRA 376
            YEGT+ V  ++  RA
Sbjct: 373 TYEGTHDVHALILGRA 388


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: 340
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: 383
Length of database: 397
Length adjustment: 30
Effective length of query: 353
Effective length of database: 367
Effective search space:   129551
Effective search space used:   129551
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 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