GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pcaF in Halomonas xinjiangensis TRM 0175

Align β-ketoadipyl-CoA thiolase (EC 2.3.1.174; EC 2.3.1.223) (characterized)
to candidate WP_043530869.1 JH15_RS12340 acetyl-CoA C-acetyltransferase

Query= metacyc::MONOMER-15952
         (401 letters)



>NCBI__GCF_000759345.1:WP_043530869.1
          Length = 393

 Score =  331 bits (849), Expect = 2e-95
 Identities = 187/406 (46%), Positives = 259/406 (63%), Gaps = 20/406 (4%)

Query: 1   MNEALIIDAVRTPIGRYAGALASVRADDLGAIPLKALIARHPQLDWSAVDDVIYGCANQA 60
           M + +I+ A RT IG + G+LA + A DLGA+ +K L+AR   +    VD+V+ G    A
Sbjct: 1   MQDVVIVAARRTAIGTFGGSLAGIPASDLGALVIKDLLAR-TGVSGDQVDEVLLGQVLTA 59

Query: 61  GEDNRNVARMAALLAGLPVSVPGTTLNRLCGSGLDAVGSAARALRCGEAGLMLAGGVESM 120
           G   +N AR AA+ AGLP +VP  T+N++CGSGL A+  A +A+RCG+A L++AGG E+M
Sbjct: 60  GV-GQNPARQAAIKAGLPDAVPAMTINKVCGSGLKALHLATQAIRCGDADLIIAGGQENM 118

Query: 121 SRAPFVMGKSE--QAFGRSAEIFDTTIGWRFVNKLMQQG----FGIDSMPETAENVAAQF 174
           S +P V+  S   Q  G           W+ ++ ++  G    F    M  TAEN+A ++
Sbjct: 119 SMSPHVLPNSRNGQRMG----------DWKAIDTMVHDGLWDAFNNYHMGITAENLAEKY 168

Query: 175 NISRADQDAFALRSQHKAAAAIANGRLAKEIVAVEIAQRKGPAKIVEHDEHPRGDTTLEQ 234
            I+R + D F+  SQ KAAAAI +GR   ++V VEI QRKG   + + DE PR   T E+
Sbjct: 169 GITRDEMDEFSAASQQKAAAAIDSGRFDSQVVPVEIPQRKGDPIVFDKDEGPRAGVTAEK 228

Query: 235 LAKLGTPFRQGGSVTAGNASGVNDGACALLLASSEAAQRHGLKARARVVGMATAGVEPRI 294
           L  +   F++ G++TAGNAS +NDGA A+++ S+E A+  GL+  A +   A AGV+P I
Sbjct: 229 LGGMKPAFKKDGTITAGNASSINDGAAAVMICSAEKAKALGLEPLAYIKAYANAGVDPSI 288

Query: 295 MGIGPVPATRKVLELTGLALADMDVIELNEAFAAQGLAVLRELGLADDDERVNPNGGAIA 354
           MGIGP PATR+ LE  G +L ++D++E NEAFAAQ LAV +ELG   D  ++N NGGAIA
Sbjct: 289 MGIGPAPATRRCLEKAGWSLDELDLVEANEAFAAQALAVNKELGW--DTSKINVNGGAIA 346

Query: 355 LGHPLGMSGARLVTTALHELEERQGRYALCTMCIGVGQGIALIIER 400
           LGHP+G SG R+  T LHE+  R     L T+CIG GQG+AL IER
Sbjct: 347 LGHPIGASGCRVFVTLLHEMIARDVHKGLATLCIGGGQGVALAIER 392


Lambda     K      H
   0.319    0.134    0.384 

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: 429
Number of extensions: 20
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: 401
Length of database: 393
Length adjustment: 31
Effective length of query: 370
Effective length of database: 362
Effective search space:   133940
Effective search space used:   133940
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 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