GapMind for catabolism of small carbon sources

 

Alignments for a candidate for xylGsa in Flavobacterium ummariense DS-12

Align Xylose/arabinose import ATP-binding protein XylG; EC 7.5.2.13 (characterized, see rationale)
to candidate WP_091521216.1 BM253_RS06735 LPS export ABC transporter ATP-binding protein

Query= uniprot:P0DTT6
         (251 letters)



>NCBI__GCF_900115115.1:WP_091521216.1
          Length = 246

 Score =  113 bits (283), Expect = 3e-30
 Identities = 70/217 (32%), Positives = 118/217 (54%), Gaps = 6/217 (2%)

Query: 5   LEIRDVHKSFGAVKALDGVSMEINKGEVVALLGDNGAGKSTLIKIISGYHKPDRGDLVFE 64
           L   ++ K++   K + GVS+E+N+GE+V LLG NGAGK+T   +I G  KP+ G++  +
Sbjct: 3   LRAENLIKTYKGRKVVKGVSVEVNQGEIVGLLGPNGAGKTTSFYMIVGLVKPNSGNIFLD 62

Query: 65  GKKVIFNSPNDARSL-GIETIYQDLALIPDLPIYYNIFLAREVTNKIFLNKKKMMEESKK 123
              +  N P   R+  GI  + Q+ ++   L I  NI    ++T    L KK+   + + 
Sbjct: 63  NLNIT-NYPMYKRAQNGIGYLAQEASVFRKLSIEDNILSVLQLTT---LTKKEQEAKMES 118

Query: 124 LLDSLQIRIPDINMKVENLSGGQRQAVAVARAVYFSAKMILMDEPTAALSVVEARKVLEL 183
           L+D   ++    N + + LSGG+R+   +ARA+    K IL+DEP A +  V    +  +
Sbjct: 119 LIDEFSLQHIRTN-RGDLLSGGERRRTEIARALATDPKFILLDEPFAGVDPVAVEDIQRI 177

Query: 184 ARNLKKKGLGVLIITHNIIQGYEVADRIYVLDRGKII 220
              LK K +G+LI  HN+ +   + D+ Y++  G I+
Sbjct: 178 VAQLKNKNIGILITDHNVQETLAITDKTYLMFEGGIL 214


Lambda     K      H
   0.318    0.137    0.371 

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: 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: 251
Length of database: 246
Length adjustment: 24
Effective length of query: 227
Effective length of database: 222
Effective search space:    50394
Effective search space used:    50394
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 46 (22.3 bits)

This GapMind analysis is from Sep 24 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