GapMind for catabolism of small carbon sources

 

Alignments for a candidate for paaJ2 in Desulfoscipio geothermicus DSM 3669

Align 3-oxoadipyl-CoA thiolase; EC 2.3.1.174 (characterized, see rationale)
to candidate WP_092484149.1 BM299_RS11340 acetyl-CoA C-acetyltransferase

Query= uniprot:B2SYZ2
         (400 letters)



>NCBI__GCF_900115975.1:WP_092484149.1
          Length = 393

 Score =  279 bits (713), Expect = 1e-79
 Identities = 164/398 (41%), Positives = 240/398 (60%), Gaps = 9/398 (2%)

Query: 1   MNDAFICDAIRTPIGRYGGALKDVRADDLGAVPIKALIERNPGVDWRTVDDVIYGCANQA 60
           M  + I  A RTP G+ GGALK+++A  LG + I   + R  G+D  TVD+VI+G   Q 
Sbjct: 1   MRQSVIVSAARTPFGKLGGALKNLKATQLGGIAIAEAVRR-AGIDGATVDNVIFGQVLQG 59

Query: 61  GEDNRNVARMSALLAGLPVEAPGSTINRLCGSGMDAVGTAARAIKAGEARLMIAGGVESM 120
           G   +  +R +A  AGLP E P  TIN++C SG+ AV    + I+AG+A +++AGG+ESM
Sbjct: 60  G-CGQIPSRQAAREAGLPWETPSETINKVCASGLRAVTMGDQIIRAGDADVIVAGGMESM 118

Query: 121 TRAPFVMGKATSAFARQADIYDTTIGWRFINPLMKRQYGVDSMPETAENVAAEFSVSRAD 180
           + AP+ +  A         +++T      ++  +   +    M      VA E+++SR +
Sbjct: 119 SNAPYFVPGARWGLR----MFNTQFTDLMVHDGLWCSFYDRHMAIHGGEVAVEYNISREE 174

Query: 181 QDAFALASQQKAARAQQDGTLAQEIVGVEIAQKKGDPVRALLDEHPR-ETSLESLGKLKG 239
           QD +AL S Q A  A   G L +EI+ V I +KKGDPV    DE PR ETS+E+L KL  
Sbjct: 175 QDEWALRSHQLAISAIDGGRLKEEIIPVTIPRKKGDPVVVDTDEGPRRETSMEALRKLPP 234

Query: 240 VVRPDGSVTAGNASGVNDGACALLLANQQAADQYGLRRRARVVGMATAGVEPRIMGIGPA 299
           V  P+ +VTAGNA GVNDGA AL++ + + A + G++  A V+G A+   E + +   P 
Sbjct: 235 VFDPNNTVTAGNAPGVNDGAGALVIMSNEKAGELGIKPMATVLGHASVSQEAKYIATVPG 294

Query: 300 PATQKLLKQLGMTLEQLDVIELNEAFASQGLAVLRTLGLRDDDPRVNPNGGAIALGHPLG 359
            +  KLLKQ GMT++Q+D++E+NEAFA+  L   +  G   D  +VN NGGAIA GHP+G
Sbjct: 295 LSINKLLKQKGMTIDQVDLLEVNEAFAAVALVSGKIAGWNPD--KVNVNGGAIAFGHPIG 352

Query: 360 ASGARLITTALYQLERTNGRFALCTMCIGVGQGIALVI 397
           ASGAR++ T +Y+L R  G   +  +C G  QG A+++
Sbjct: 353 ASGARILMTLIYELRRRGGGIGVAAICSGAAQGDAVMV 390


Lambda     K      H
   0.318    0.135    0.386 

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: 410
Number of extensions: 20
Number of successful extensions: 6
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: 400
Length of database: 393
Length adjustment: 31
Effective length of query: 369
Effective length of database: 362
Effective search space:   133578
Effective search space used:   133578
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.

Links

Downloads

Related tools

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