GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pccA2 in Azospirillum thiophilum BV-S

Align acyl CoA carboxylase biotin carboxyl carrier protein subunit (EC 2.1.3.15; EC 6.4.1.3; EC 6.3.4.14) (characterized)
to candidate WP_045585974.1 AL072_RS28295 acetyl/propionyl/methylcrotonyl-CoA carboxylase subunit alpha

Query= metacyc::MONOMER-13596
         (167 letters)



>NCBI__GCF_001305595.1:WP_045585974.1
          Length = 667

 Score = 55.8 bits (133), Expect = 1e-12
 Identities = 35/101 (34%), Positives = 53/101 (52%), Gaps = 7/101 (6%)

Query: 66  ILLDNASVFRLERLTELPSKEGESIEEMIKGKEGEVISPLQGRIVTIRVNEGDAVNKGQP 125
           +L+D A    + RLT L      + E+  +G  G + +P+ G +V + V  G +V  G P
Sbjct: 569 VLIDGA----VSRLT-LDDPSARAAEQ--EGGSGRLTAPMPGTVVRVLVEPGQSVEAGTP 621

Query: 126 LLSVEAMKSETIISAPIAGIVEKIIVKPGQGVKKGDTLLII 166
           L+ +EAMK E  I AP AG V  +    G  V +G  LL++
Sbjct: 622 LMLLEAMKMEHTIKAPAAGTVSAVNFSAGDQVSEGVDLLVL 662



 Score = 31.6 bits (70), Expect = 3e-05
 Identities = 11/30 (36%), Positives = 23/30 (76%)

Query: 138 ISAPIAGIVEKIIVKPGQGVKKGDTLLIIK 167
           ++AP+ G V +++V+PGQ V+ G  L++++
Sbjct: 597 LTAPMPGTVVRVLVEPGQSVEAGTPLMLLE 626


Lambda     K      H
   0.313    0.136    0.368 

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: 267
Number of extensions: 12
Number of successful extensions: 2
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 167
Length of database: 667
Length adjustment: 28
Effective length of query: 139
Effective length of database: 639
Effective search space:    88821
Effective search space used:    88821
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.9 bits)
S2: 48 (23.1 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