GapMind for catabolism of small carbon sources

 

Alignments for a candidate for fadA in Desulfoscipio geothermicus DSM 3669

Align acetyl-CoA C-acetyltransferase (EC 2.3.1.9) (characterized)
to candidate WP_092484149.1 BM299_RS11340 acetyl-CoA C-acetyltransferase

Query= BRENDA::P45359
         (392 letters)



>NCBI__GCF_900115975.1:WP_092484149.1
          Length = 393

 Score =  389 bits (999), Expect = e-113
 Identities = 204/390 (52%), Positives = 268/390 (68%), Gaps = 1/390 (0%)

Query: 1   MKEVVIASAVRTAIGSYGKSLKDVPAVDLGATAIKEAVKKAGIKPEDVNEVILGNVLQAG 60
           M++ VI SA RT  G  G +LK++ A  LG  AI EAV++AGI    V+ VI G VLQ G
Sbjct: 1   MRQSVIVSAARTPFGKLGGALKNLKATQLGGIAIAEAVRRAGIDGATVDNVIFGQVLQGG 60

Query: 61  LGQNPARQASFKAGLPVEIPAMTINKVCGSGLRTVSLAAQIIKAGDADVIIAGGMENMSR 120
            GQ P+RQA+ +AGLP E P+ TINKVC SGLR V++  QII+AGDADVI+AGGME+MS 
Sbjct: 61  CGQIPSRQAAREAGLPWETPSETINKVCASGLRAVTMGDQIIRAGDADVIVAGGMESMSN 120

Query: 121 APYLANNARWGYRMGNAKFVDEMITDGLWDAFNDYHMGITAENIAERWNISREEQDEFAL 180
           APY    ARWG RM N +F D M+ DGLW +F D HM I    +A  +NISREEQDE+AL
Sbjct: 121 APYFVPGARWGLRMFNTQFTDLMVHDGLWCSFYDRHMAIHGGEVAVEYNISREEQDEWAL 180

Query: 181 ASQKKAEEAIKSGQFKDEIVPVVIKGRKGE-TVVDTDEHPRFGSTIEGLAKLKPAFKKDG 239
            S + A  AI  G+ K+EI+PV I  +KG+  VVDTDE PR  +++E L KL P F  + 
Sbjct: 181 RSHQLAISAIDGGRLKEEIIPVTIPRKKGDPVVVDTDEGPRRETSMEALRKLPPVFDPNN 240

Query: 240 TVTAGNASGLNDCAAVLVIMSAEKAKELGVKPLAKIVSYGSAGVDPAIMGYGPFYATKAA 299
           TVTAGNA G+ND A  LVIMS EKA ELG+KP+A ++ + S   +   +   P  +    
Sbjct: 241 TVTAGNAPGVNDGAGALVIMSNEKAGELGIKPMATVLGHASVSQEAKYIATVPGLSINKL 300

Query: 300 IEKAGWTVDELDLIESNEAFAAQSLAVAKDLKFDMNKVNVNGGAIALGHPIGASGARILV 359
           +++ G T+D++DL+E NEAFAA +L   K   ++ +KVNVNGGAIA GHPIGASGARIL+
Sbjct: 301 LKQKGMTIDQVDLLEVNEAFAAVALVSGKIAGWNPDKVNVNGGAIAFGHPIGASGARILM 360

Query: 360 TLVHAMQKRDAKKGLATLCIGGGQGTAILL 389
           TL++ +++R    G+A +C G  QG A+++
Sbjct: 361 TLIYELRRRGGGIGVAAICSGAAQGDAVMV 390


Lambda     K      H
   0.315    0.132    0.375 

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: 455
Number of extensions: 16
Number of successful extensions: 2
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: 392
Length of database: 393
Length adjustment: 31
Effective length of query: 361
Effective length of database: 362
Effective search space:   130682
Effective search space used:   130682
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 (21.6 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