GapMind for catabolism of small carbon sources

 

Aligments for a candidate for atoB in Burkholderia phytofirmans PsJN

Align acetyl-CoA C-acetyltransferase (EC 2.3.1.9) (characterized)
to candidate BPHYT_RS21955 BPHYT_RS21955 acetyl-CoA acetyltransferase

Query= BRENDA::P45359
         (392 letters)



>lcl|FitnessBrowser__BFirm:BPHYT_RS21955 BPHYT_RS21955 acetyl-CoA
           acetyltransferase
          Length = 395

 Score =  382 bits (982), Expect = e-111
 Identities = 192/389 (49%), Positives = 266/389 (68%)

Query: 2   KEVVIASAVRTAIGSYGKSLKDVPAVDLGATAIKEAVKKAGIKPEDVNEVILGNVLQAGL 61
           +EVVI + VRT IG++G +LK+VPA  LGA A++E ++++ +   ++  V++GNV+QAG 
Sbjct: 5   REVVICNPVRTPIGAFGGALKEVPATTLGAVAVRETLRRSRLDAAELASVVMGNVIQAGN 64

Query: 62  GQNPARQASFKAGLPVEIPAMTINKVCGSGLRTVSLAAQIIKAGDADVIIAGGMENMSRA 121
             N ARQAS   G+PV +PA+T+N+VCGSG + ++ AAQ I  G  D  +AGGMENM RA
Sbjct: 65  KMNAARQASIGGGVPVAVPALTVNRVCGSGAQAIASAAQEILLGLGDAAVAGGMENMDRA 124

Query: 122 PYLANNARWGYRMGNAKFVDEMITDGLWDAFNDYHMGITAENIAERWNISREEQDEFALA 181
           PYL +  RWGYRMGNA+  D ++ DGL DAF+  H G   E++  +++I+RE QD +A  
Sbjct: 125 PYLLDGGRWGYRMGNAQIHDSLLRDGLNDAFSGEHSGWHTEDLVAQFDITRETQDRWAAR 184

Query: 182 SQKKAEEAIKSGQFKDEIVPVVIKGRKGETVVDTDEHPRFGSTIEGLAKLKPAFKKDGTV 241
           SQ++  EA   G F  E+V V I GRKG      DE PR  +T+E LAKL+PAF+ DGT+
Sbjct: 185 SQQRFSEAQARGDFDAELVGVEIAGRKGPQHFTRDEQPRPDTTVETLAKLRPAFRPDGTI 244

Query: 242 TAGNASGLNDCAAVLVIMSAEKAKELGVKPLAKIVSYGSAGVDPAIMGYGPFYATKAAIE 301
           TAGNA GLN  AA +++     A+  G+ PLA++VSYG A V+P + G GP  A + A+ 
Sbjct: 245 TAGNAPGLNSGAAAMLVAERGFAEARGIAPLARLVSYGVAAVEPGMFGLGPVPAVQMALA 304

Query: 302 KAGWTVDELDLIESNEAFAAQSLAVAKDLKFDMNKVNVNGGAIALGHPIGASGARILVTL 361
           +AGW + +++  E NEAFAA  +AVA+ L      +NV GGAIA GHPIGA+GA +   L
Sbjct: 305 RAGWQLHDVERFEINEAFAAVPIAVARKLGIADELINVRGGAIAHGHPIGATGAVLTTRL 364

Query: 362 VHAMQKRDAKKGLATLCIGGGQGTAILLE 390
           +H+MQ+   K+G+ TLCIGGGQG A+ LE
Sbjct: 365 LHSMQRDGIKRGIVTLCIGGGQGIALALE 393


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: 459
Number of extensions: 11
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: 392
Length of database: 395
Length adjustment: 31
Effective length of query: 361
Effective length of database: 364
Effective search space:   131404
Effective search space used:   131404
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 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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.

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