GapMind for catabolism of small carbon sources

 

Alignments for a candidate for xacB in Dinoroseobacter shibae DFL-12

Align L-arabinose 1-dehydrogenase (EC 1.1.1.46) (characterized)
to candidate 3608790 Dshi_2182 3-oxoacyl-(acyl-carrier-protein) reductase (RefSeq)

Query= reanno::pseudo5_N2C3_1:AO356_20240
         (272 letters)



>FitnessBrowser__Dino:3608790
          Length = 245

 Score =  138 bits (347), Expect = 1e-37
 Identities = 82/251 (32%), Positives = 140/251 (55%), Gaps = 9/251 (3%)

Query: 19  LKDKVVLLTGAAQGIGEAIVAAFASQQARLVISDIQAQKVEAVAAHWRERGADVHALQAD 78
           L  K  L+TGA+ GIG AI  A  +Q A + +S  +   +EA+AA   ER    H L  +
Sbjct: 4   LTGKTALVTGASGGIGGAIATALHAQGATVGLSGTRVDPLEALAAELGERA---HVLPCN 60

Query: 79  VSKQQDLQAMARRAVELHGRIDVLVNCAGVNVFRDPLEMTEEDWRRCFAIDLDGAWYGCK 138
           +S    ++A+ ++AV   G +D+LVN AG+      + M++E+W     ++L      C+
Sbjct: 61  LSDADAVEALPKQAVAAMGSVDILVNNAGITRDNLFMRMSDEEWASVLDVNLTSTMRLCR 120

Query: 139 AVLPQMIEQGVGSIINIASVHSSHIIPGCFPYPVAKHGLLGLTRALGIEYAPKGVRVNAI 198
            VL  M++   G I+NI+SV  +   PG   Y  +K G++G++++L  E A +G+ VNA+
Sbjct: 121 GVLRGMMKARWGRIVNISSVVGATGNPGQGNYAASKAGMVGMSKSLAYEVASRGITVNAV 180

Query: 199 APGYIETQLNVDYWNGFADPHAERQRALDLHPPRRVGQPIEVAMTAVFLASDEAPFINAS 258
           APG+I T +     +       ++ + L   P  R+G+P E+A   V+LAS EA ++  S
Sbjct: 181 APGFISTAMTDKLTDD------QKDKLLVQVPSGRMGEPGEIAAAVVYLASPEAGYVTGS 234

Query: 259 CITIDGGRSVM 269
            + ++GG +++
Sbjct: 235 VLHVNGGLAMI 245


Lambda     K      H
   0.321    0.137    0.419 

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: 151
Number of extensions: 11
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: 272
Length of database: 245
Length adjustment: 24
Effective length of query: 248
Effective length of database: 221
Effective search space:    54808
Effective search space used:    54808
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 47 (22.7 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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