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_RS16940 BPHYT_RS16940 short-chain dehydrogenase

Query= reanno::pseudo6_N2E2:Pf6N2E2_5967
         (272 letters)



>FitnessBrowser__BFirm:BPHYT_RS16940
          Length = 258

 Score =  328 bits (841), Expect = 7e-95
 Identities = 161/257 (62%), Positives = 194/257 (75%), Gaps = 1/257 (0%)

Query: 17  ERLKNKVVLLTGAAQGIGEAIVAAFASQQARLVISDIQAEKVETVAAHWR-ERGADVHAL 75
           +RL  KV L+TGA +GIG AI  AFA + A +V++++  E     A H + + GA V A+
Sbjct: 2   KRLAGKVALVTGAGRGIGSAIAHAFAREGAAVVLAELDIETARQTAEHIKAQTGARVLAV 61

Query: 76  KADVSNQQDLHAMARHAVERHGRIDVLVNCAGVNVFRDPLEMTEEDWRRCFAIDLDGAWY 135
             DV+    +      A    G +DVLVN AG+NVF DPL MT++DWRRCFA+DLDG W 
Sbjct: 62  HTDVTQSASVQHAVSEAERAFGALDVLVNNAGINVFCDPLTMTDDDWRRCFAVDLDGVWN 121

Query: 136 GCKAVLPQMIEQGVGSIINIASTHSSHIIPGCFPYPVAKHGLLGLTRALGIEYAPKGVRV 195
           GC+A LP M+E+G GSI+NIASTHS  IIPGCFPYPVAKHG++GLTRALGIEYAP+ VRV
Sbjct: 122 GCRAALPGMVERGAGSIVNIASTHSFKIIPGCFPYPVAKHGVIGLTRALGIEYAPRNVRV 181

Query: 196 NAIAPGYIETQLNVDYWNGFADPYAERQRALDLHPPRRIGQPIEVAMTAVFLASDEAPFI 255
           NAIAPGYIETQL  D+WN  ADP A +Q  LDL P +RIG+P EVAMTAVFLASDEAPFI
Sbjct: 182 NAIAPGYIETQLTHDWWNEQADPAAAQQATLDLQPMKRIGRPEEVAMTAVFLASDEAPFI 241

Query: 256 NASCITIDGGRSVMYHD 272
           NA+CIT+DGGRS +YHD
Sbjct: 242 NATCITVDGGRSALYHD 258


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: 256
Number of extensions: 6
Number of successful extensions: 2
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: 258
Length adjustment: 25
Effective length of query: 247
Effective length of database: 233
Effective search space:    57551
Effective search space used:    57551
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 (21.8 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