GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__BFirm:BPHYT_RS21955
          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:

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