GapMind for catabolism of small carbon sources

 

Alignments for a candidate for xacB in Marinobacter adhaerens HP15

Align L-arabinose 1-dehydrogenase / D-galactose 1-dehydrogenase (EC 1.1.1.46; EC 1.1.1.48) (characterized)
to candidate GFF3984 HP15_3924 short-chain dehydrogenase/reductase SDR

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



>FitnessBrowser__Marino:GFF3984
          Length = 255

 Score =  146 bits (368), Expect = 5e-40
 Identities = 88/251 (35%), Positives = 136/251 (54%), Gaps = 5/251 (1%)

Query: 19  LKNKVVLLTGAAQGIGEAIVATFASQQARLVISDIQGEKVEKVAAHWREQGADVVAIKAD 78
           +  KV ++TG+ +GIG AI    A   A++VIS  + E  E++A   + QG + +AI   
Sbjct: 8   MTGKVAVITGSTKGIGRAIAGEMAVCGAKVVISSRKAEACEQMAEELKAQGFEAMAIPCH 67

Query: 79  VSRQQDLHAMARLAIELHGRIDVLVNCAGVN-VFRDPLQMTEEDWHRCFAIDLDGAWYGC 137
           V R++DL  + +   E  G IDVLV  A  N V+    +MT++ W +    ++   ++  
Sbjct: 68  VGRKEDLQNLVKKTNEAWGSIDVLVCNAATNPVYGPTAEMTDDAWDKIMDTNVKSTFWLT 127

Query: 138 KAVLPQMIEQGIGSIINIASTHSTHIIPGCFPYPVAKHGLLGLTRALGIEYAPKGIRVNA 197
             VLPQM E+G G+++ ++S            Y V+K     L R L +E+ PKGIR+N+
Sbjct: 128 NMVLPQMAEKGEGAVVLLSSIAGLRGNTVIGTYGVSKAAEAALARNLAVEWGPKGIRINS 187

Query: 198 IAPGYIETQLNVDYWNGFADPHAERQRAFDLHPPRRIGQPIEVAMTAVFLASDEAPFINA 257
           IAPG I+T      W    DP   +Q A D  P RRIG P+++A  AVFL++  + +I  
Sbjct: 188 IAPGLIKTDFARALWE---DPERAKQ-AEDRTPLRRIGDPVDIAGLAVFLSTKASAYITG 243

Query: 258 SCITIDGGRSV 268
             I  DGG ++
Sbjct: 244 QVIVADGGETI 254


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: 150
Number of extensions: 12
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: 255
Length adjustment: 25
Effective length of query: 247
Effective length of database: 230
Effective search space:    56810
Effective search space used:    56810
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.

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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