GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pccA2 in Marinobacter adhaerens HP15

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 GFF3995 HP15_3935 pyruvate carboxylase subunit B

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



>FitnessBrowser__Marino:GFF3995
          Length = 599

 Score = 57.8 bits (138), Expect = 3e-13
 Identities = 30/70 (42%), Positives = 40/70 (57%)

Query: 97  KEGEVISPLQGRIVTIRVNEGDAVNKGQPLLSVEAMKSETIISAPIAGIVEKIIVKPGQG 156
           KEG V + + G IV + V EGD V  G P+L +EAMK ET + A  AG V  + +  G  
Sbjct: 529 KEGHVTTSMPGNIVDVLVKEGDEVQAGDPVLIIEAMKMETEVKATTAGKVSGVFIAKGDR 588

Query: 157 VKKGDTLLII 166
           V  G+ L+ I
Sbjct: 589 VVPGEVLVEI 598



 Score = 24.6 bits (52), Expect = 0.003
 Identities = 10/30 (33%), Positives = 19/30 (63%)

Query: 138 ISAPIAGIVEKIIVKPGQGVKKGDTLLIIK 167
           ++  + G +  ++VK G  V+ GD +LII+
Sbjct: 533 VTTSMPGNIVDVLVKEGDEVQAGDPVLIIE 562


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: 213
Number of extensions: 10
Number of successful extensions: 3
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 3
Number of HSP's successfully gapped: 2
Length of query: 167
Length of database: 599
Length adjustment: 27
Effective length of query: 140
Effective length of database: 572
Effective search space:    80080
Effective search space used:    80080
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 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