GapMind for catabolism of small carbon sources

 

Alignments for a candidate for paaG in Magnetospirillum magneticum AMB-1

Align 2-(1,2-epoxy-1,2-dihydrophenyl)acetyl-CoA isomerase (EC 5.3.3.18) (characterized)
to candidate WP_011386482.1 AMB_RS20905 enoyl-CoA hydratase/carnithine racemase

Query= BRENDA::Q5SLK3
         (254 letters)



>NCBI__GCF_000009985.1:WP_011386482.1
          Length = 254

 Score =  147 bits (370), Expect = 3e-40
 Identities = 94/252 (37%), Positives = 140/252 (55%), Gaps = 6/252 (2%)

Query: 1   MVLKERQDGVLVLTLNRPEKLNAITGELLDALYAALKEGEEDREVRALLLTGAGRAFSAG 60
           +VL   + GV V+ +NRP+K NA+ GE+  AL  A  +GE D +V   L+ G+   FSAG
Sbjct: 4   LVLSHVEGGVQVVRMNRPDKKNALIGEMYAALAEAFAKGEADDDVNVFLILGSQTDFSAG 63

Query: 61  QDLTEFGDRKPDYEAHLRRY-NRVVEALSGLEKPLVVAVNGVAAGAGMSLALWGDLRLAA 119
            DL +F      +EA      +R + A++G  KP+V AV G A G G +L    DL  AA
Sbjct: 64  NDLPDF----LTWEALSGSVADRFIRAVAGARKPVVAAVRGAAIGIGSTLLPHCDLVYAA 119

Query: 120 VGASFTTAFVRIGLVPDSGLSFLLPRLVGLAKAQELLLLSPRLSAEEALALGLVHRVVPA 179
            G  F   F+ +G+VP++G S  +P L G  +A E+L+L      + A A+GL++ VVP 
Sbjct: 120 PGTRFHMPFINLGIVPEAGSSQTMPALAGHRRAAEMLMLGEPFGVDTAEAVGLINGVVPG 179

Query: 180 EKLMEEALSLAKELAQGPTRAYALTKKLLLETYRLSLTEALALEAVLQGQAGQTQDHEEG 239
           E L E A++ A++LA  P R+  +  K L++T    + + L  EA +     + +   E 
Sbjct: 180 EDLEETAMAAARKLAAKP-RSILVQIKALMKTPAEPIMDRLTREAAVFDTCLKGEALNEA 238

Query: 240 VRAFREKRPPRF 251
           V AF+EKR P F
Sbjct: 239 VSAFKEKRAPDF 250


Lambda     K      H
   0.318    0.135    0.371 

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: 145
Number of extensions: 5
Number of successful extensions: 3
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: 254
Length of database: 254
Length adjustment: 24
Effective length of query: 230
Effective length of database: 230
Effective search space:    52900
Effective search space used:    52900
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 (21.7 bits)
S2: 47 (22.7 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