GapMind for catabolism of small carbon sources

 

Alignments for a candidate for galdh in Paraburkholderia bryophila 376MFSha3.1

Align L-arabinose 1-dehydrogenase / D-galactose 1-dehydrogenase (EC 1.1.1.46; EC 1.1.1.48) (characterized)
to candidate H281DRAFT_03713 H281DRAFT_03713 NAD(P)-dependent dehydrogenase, short-chain alcohol dehydrogenase family

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



>FitnessBrowser__Burk376:H281DRAFT_03713
          Length = 254

 Score =  154 bits (388), Expect = 2e-42
 Identities = 89/254 (35%), Positives = 141/254 (55%), Gaps = 6/254 (2%)

Query: 17  ERLKNKVVLLTGAAQGIGEAIVAAFASQQARLVISDIQAEKVETVAAHWRERGADVHALK 76
           +RL  KV ++TGA+ GIG A    FA + A++VI+  +A ++E +AA     G +   L 
Sbjct: 2   QRLIGKVAIVTGASAGIGRATAKLFAKEGAKVVIAARRAAELEALAAEIASEGGEAAYLA 61

Query: 77  ADVSNQQDLHAMARHAVERHGRIDVLVNCAGVNVFRDP-LEMTEEDWRRCFAIDLDGAWY 135
            DV ++    A+   AV R GR+D+  N AG      P   ++E  W    A +L  A+ 
Sbjct: 62  GDVQSEDFAKALVELAVGRFGRLDIAYNNAGTLGEMGPSTGISEAGWNAALATNLTSAFL 121

Query: 136 GCKAVLPQMIEQGVGSIINIAS-THSSHIIPGCFPYPVAKHGLLGLTRALGIEYAPKGVR 194
           G K  +P+M++ G GSII  ++    S   PG   Y  +K GL+GLT+AL  EY  +GVR
Sbjct: 122 GAKHQIPEMLKHGGGSIIFTSTFVGYSFAFPGTAAYAASKAGLIGLTQALAAEYGAQGVR 181

Query: 195 VNAIAPGYIETQLNVDYWNGFADPYAERQRALDLHPPRRIGQPIEVAMTAVFLASDEAPF 254
           VNA+ PG ++T++    + G  D    +     LH  +R+ +P E+A + ++LASD++ F
Sbjct: 182 VNAVLPGAVDTEM----YRGMNDSDESQAFVTGLHALKRVAKPEELARSVLYLASDDSSF 237

Query: 255 INASCITIDGGRSV 268
           +  +   +DGG S+
Sbjct: 238 VTGTASLVDGGASI 251


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: 135
Number of extensions: 7
Number of successful extensions: 4
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: 254
Length adjustment: 25
Effective length of query: 247
Effective length of database: 229
Effective search space:    56563
Effective search space used:    56563
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