GapMind for catabolism of small carbon sources

 

Alignments for a candidate for xacB in Burkholderia phytofirmans PsJN

Align L-arabinose 1-dehydrogenase / D-galactose 1-dehydrogenase (EC 1.1.1.46; EC 1.1.1.48) (characterized)
to candidate BPHYT_RS05365 BPHYT_RS05365 3-ketoacyl-ACP reductase

Query= reanno::pseudo1_N1B4:Pf1N1B4_412
         (272 letters)



>FitnessBrowser__BFirm:BPHYT_RS05365
          Length = 252

 Score =  147 bits (371), Expect = 2e-40
 Identities = 84/252 (33%), Positives = 134/252 (53%), Gaps = 2/252 (0%)

Query: 18  RLKNKVVLLTGAAQGIGEAIVATFASQQARLVISDIQGEKVEKVAAHWREQGADVVAIKA 77
           RL  K  ++TG   G GE I  T+A + A +V++D+ G   E+VA+     G   +A+  
Sbjct: 2   RLTGKTAIVTGGGSGFGEGIAKTYAREGANVVVNDLNGPAAERVASEIALAGGKAIAVTG 61

Query: 78  DVSRQQDLHAMARLAIELHGRIDVLVNCAGVNVFRDP-LQMTEEDWHRCFAIDLDGAWYG 136
           +V++++D   +   A+E  G + ++VN AG      P + +TE ++ R +A+++   ++ 
Sbjct: 62  NVAQREDWQTLREAALEDFGSVQIVVNNAGTTHRNKPVMDVTEAEFDRVYAVNVKSIYWS 121

Query: 137 CKAVLPQMIEQGIGSIINIASTHSTHIIPGCFPYPVAKHGLLGLTRALGIEYAPKGIRVN 196
            +  +P   EQG G  INIAST      PG   Y  +K  ++  +++L +E  P  IRVN
Sbjct: 122 VQEFVPYFREQGGGCFINIASTAGVRPRPGLVWYNGSKGAVIIASKSLAVELGPDRIRVN 181

Query: 197 AIAPGYIETQLNVDYWNGFADPHAERQRAFDLHPPRRIGQPIEVAMTAVFLASDEAPFIN 256
            + P   ET L  ++  G  D    RQR     P  R   P ++A  A++LASDEA FI 
Sbjct: 182 CVNPVIGETALLAEFM-GVEDTPENRQRFLAGIPLGRFSTPQDIANAALYLASDEAEFIT 240

Query: 257 ASCITIDGGRSV 268
             C+ +DGGR V
Sbjct: 241 GVCLEVDGGRCV 252


Lambda     K      H
   0.321    0.138    0.424 

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: 152
Number of extensions: 6
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: 252
Length adjustment: 25
Effective length of query: 247
Effective length of database: 227
Effective search space:    56069
Effective search space used:    56069
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