GapMind for catabolism of small carbon sources

 

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

Align Sugar ABC transporter permease (characterized, see rationale)
to candidate H281DRAFT_03745 H281DRAFT_03745 carbohydrate ABC transporter membrane protein 2, CUT1 family

Query= uniprot:A0A161ZE72
         (280 letters)



>FitnessBrowser__Burk376:H281DRAFT_03745
          Length = 283

 Score =  162 bits (410), Expect = 8e-45
 Identities = 97/284 (34%), Positives = 156/284 (54%), Gaps = 8/284 (2%)

Query: 3   LRLLKKALLRLGFWCLIGVLLLYAVFPFYYAIVTSLKPSSALFEV-SYWIE-NPDFSNYA 60
           + L  KA   L  W  +  L++  +FPF   + T+LKP+S +F   + W+  +  +SN+ 
Sbjct: 1   MTLSAKAKRSLWCWLALSPLVVVVLFPFAVMLFTALKPASEIFVYPARWLPVHWQWSNFV 60

Query: 61  AVLNQASFLRAIGNSLVVALCVVTLALFLSLTAAYALGRVKFRGRGTVLMMVLGVSMFPQ 120
            +   A+F  A+ NS V++L    LAL +SL AAYAL R  FRGRGT    +L   M   
Sbjct: 61  DMWQAANFGVALRNSTVISLLSTLLALAVSLPAAYALARFPFRGRGTYRQFLLVTQMLSP 120

Query: 121 VAVLSGLFEVIRAL-----GLYNTSWALILSYTIFTLPFTVWVLTTFMGQLPHELEEAAI 175
           + ++ GLF +   +      L ++   +I+SY  F + F VW+L+++   +P +LEE+A 
Sbjct: 121 ILLVVGLFRLAAMIPYGDGNLVDSKIGVIVSYAAFNIAFAVWMLSSYFQTVPRDLEESAW 180

Query: 176 MDGASPWVTLTRVLLPLLWPALVTTGLLAFIAAWNEFLFALTFTLTDTQRTVPVAIALIS 235
           ++G      + +V LPL  PA+V T +  FI AWNEF    T   +   +T+ V +  + 
Sbjct: 181 LEGCGRTKAVFKVFLPLAVPAIVVTAIFTFINAWNEFAVVYTLIRSPENKTLTVQVTDMV 240

Query: 236 GGSPHELPWGLLMAASVVVTVPLVILVLIFQRRIVSGLTAGALK 279
            G  + + W L+MAA++  T+P+ I+    QR +V GL  GA+K
Sbjct: 241 AGK-YVVEWHLVMAATLCATLPVSIVFAWLQRYLVKGLALGAVK 283


Lambda     K      H
   0.329    0.141    0.433 

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: 207
Number of extensions: 15
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: 280
Length of database: 283
Length adjustment: 26
Effective length of query: 254
Effective length of database: 257
Effective search space:    65278
Effective search space used:    65278
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (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