GapMind for catabolism of small carbon sources

 

Alignments for a candidate for PS417_12055 in Rhizobium freirei PRF 81

Align Putative xylitol transport system substrate-binding protein; SubName: Full=Sugar ABC transporter substrate-binding protein (characterized, see rationale)
to candidate WP_037155072.1 RHSP_RS28510 sugar ABC transporter substrate-binding protein

Query= uniprot:A0A1N7UEK0
         (335 letters)



>NCBI__GCF_000359745.1:WP_037155072.1
          Length = 309

 Score =  127 bits (319), Expect = 4e-34
 Identities = 87/280 (31%), Positives = 144/280 (51%), Gaps = 12/280 (4%)

Query: 14  SLLACSIAMAADGKTYKVGAAVYGLKGQFMQNWVRELKEHPAVKDGTVQLTVFDGNYDAL 73
           S +A  ++ AA  +T  V  A++     F+      ++++     G V L V D   D  
Sbjct: 8   SAMALLLSTAAHAQTIGVSMALFD--DNFLTVLRNGMQDYAKGMSG-VTLQVEDAQNDVA 64

Query: 74  TQNNQIENMVTQRYDAILFVPIDTKAGVGTVKAAMSNDVVVIASNTKVADA-SVP----Y 128
            Q +QI+N +  + DAI+  P+DT A     K A    + ++  N + A+  S+P    +
Sbjct: 65  KQQSQIQNFIASKVDAIIVNPVDTDATAAISKLAADAKIPLVYVNREPANVDSLPDKQAF 124

Query: 129 VGNDDVEGGRLQAQAMVDKLNGKGNVVIIQGPIGQSAQIDREKGELEVLGKH--PDIKII 186
           V +++ E G L+ + +   L GKG  V++ G +   A   R K   +VL       IKI+
Sbjct: 125 VASNEQESGTLETKEVCRILGGKGKAVVMMGELSNQAARMRTKDVHDVLATDGCKGIKIV 184

Query: 187 EKKTANWDRAQALALTEDWLNAHPKGINGVIAQNDDMALGAVQALKSHGLTSKDVPVTSI 246
           +++TANW R Q   L  +WL++  +  + VI+ ND+MA+GA+QALK+ G     + V  +
Sbjct: 185 QEQTANWQRTQGADLMTNWLSSGLE-FDAVISNNDEMAIGAIQALKAAGKPMDKIVVAGV 243

Query: 247 DGMPDAIQAAKKDEV-TTFLQDAQAQSQGALDVALRALAG 285
           D   DA+ A +  ++  T  QDA  Q +GA+D AL+   G
Sbjct: 244 DATQDALAAMQAGDLKVTVFQDAAGQGKGAVDAALKLAKG 283


Lambda     K      H
   0.314    0.130    0.373 

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: 268
Number of extensions: 15
Number of successful extensions: 5
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: 335
Length of database: 309
Length adjustment: 28
Effective length of query: 307
Effective length of database: 281
Effective search space:    86267
Effective search space used:    86267
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.9 bits)
S2: 48 (23.1 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