GapMind for catabolism of small carbon sources

 

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

Align Sugar ABC transporter, periplasmic sugar-binding protein (characterized, see rationale)
to candidate H281DRAFT_02713 H281DRAFT_02713 monosaccharide ABC transporter substrate-binding protein, CUT2 family

Query= uniprot:Q9WXW9
         (335 letters)



>FitnessBrowser__Burk376:H281DRAFT_02713
          Length = 313

 Score =  187 bits (474), Expect = 4e-52
 Identities = 121/297 (40%), Positives = 171/297 (57%), Gaps = 18/297 (6%)

Query: 32  LTIGVIGKSVHPYWSQVEQGVKAAGKALGVDTKFFVPQKEDINAQLQMLESFIAEGVNGI 91
           +++ VI K   P++    +G K A    GV  ++ VPQ    + Q+Q++E  I+  V+GI
Sbjct: 31  ISVAVIPKVAVPFFDDCNKGAKTAAGKAGVKYQWVVPQNTQGSTQVQIIEDLISRHVDGI 90

Query: 92  AIAPSDPTAVIPTIKKALEMGIPVVTLDTDSPDSGRYVYIGTDNYQAGYTAGLIMKELLG 151
           AI+ ++P +V   +K+A + GI V+T D+DSP SGR +YIGT+N QAG T    M + L 
Sbjct: 91  AISVNEPKSVESVMKRAEQSGIKVLTYDSDSPRSGRSMYIGTNNEQAGATMAETMGKALN 150

Query: 152 GKGKVVIGTGSLTAMNSLQRIQGFKDAI-KDSEIEIVDILNDEEDGARAVSLAEAALNAH 210
           G+G+V I TG L A+N  +RI G K  + K   I+IV+    ++D AR VS+ E  L AH
Sbjct: 151 GQGEVAIITGQLGAVNLNERIAGIKKGLAKYPGIKIVETQGTDDDLARGVSVVETTLRAH 210

Query: 211 PDLDAFFGVYAYNGPAQALVV--KNAGKV-GKVKIVCFDTTPDILQYVKEGVIQATMGQR 267
           P L   FGV    GPA A V+  K  G + GK++++ FD  PD L+ +KEG IQ  M QR
Sbjct: 211 PQLKGIFGVSQVGGPAVAKVLNTKEFGTMKGKLEVLAFDDLPDTLKGLKEGYIQGIMVQR 270

Query: 268 PYMMGYLSVTVLYLMNKIGVQNTLMMLPKVKVDGKVDYVIDTGVDVVTPENLDEYLK 324
           P  MG  S+ V +L+ +I  Q      PK          IDTGV VVT +N+  Y K
Sbjct: 271 PVTMG--SLAVEHLVAQIQGQEA---QPK---------DIDTGVTVVTKDNMTSYTK 313


Lambda     K      H
   0.318    0.137    0.388 

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: 252
Number of extensions: 20
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: 335
Length of database: 313
Length adjustment: 28
Effective length of query: 307
Effective length of database: 285
Effective search space:    87495
Effective search space used:    87495
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: 48 (23.1 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