GapMind for catabolism of small carbon sources

 

Alignments for a candidate for LRA1 in Bacteroides thetaiotaomicron VPI-5482

Align NAD(P)+-dependent L-rhamnose 1-dehydrogenase (EC 1.1.1.378; EC 1.1.1.173) (characterized)
to candidate 351439 BT1911 7-alpha-hydroxysteroid dehydrogenase (NCBI ptt file)

Query= metacyc::MONOMER-16230
         (256 letters)



>FitnessBrowser__Btheta:351439
          Length = 259

 Score =  134 bits (338), Expect = 1e-36
 Identities = 89/253 (35%), Positives = 137/253 (54%), Gaps = 9/253 (3%)

Query: 5   DKTVIVTGASRGIGRAAARECARQGARVVIGHSGSDEGRAGALSLAEEIAAFGGTAIAVG 64
           +K V++TGA+ GIG A  R    +G +VVI    +D  +  A  LA E+   G     + 
Sbjct: 6   NKVVVITGAAGGIGEATTRRIVSEGGKVVI----ADLSQERADKLAAELTQAGADVRPIY 61

Query: 65  ADAADLDSGEKLVAAAVEAFGSVDVLVNNAGICPFHSFLDMPR---ELYLKTVGTNLNGA 121
             A +L S ++LV  A++ +G +DVL+NN G       L++ +   + + +    NL   
Sbjct: 62  FSATELQSCKELVDFAMKEYGQIDVLINNVGGTDPKRDLNIEKLDIDYFDEVFHLNLCCT 121

Query: 122 YFTVQAAARRMKEQGRGGAIIAVSSISALVGGAMQTHYTPTKAGLLSLMQSCAIALGPYG 181
            +  Q     M   G GG I+ V+SIS L   A  T Y  +KAG+++L +  A  +G   
Sbjct: 122 MYLSQQVIPIMTTHG-GGNIVNVASISGLTADANGTLYGASKAGVINLTKYIATQMGKKN 180

Query: 182 IRCNAVLPGTIATDINKEDLSDLEKRERMTSRVPLGRLGEPDDLAGPIVFLASDMARYVT 241
           IRCNAV PG + T    ++L++ E R     +     LGEP+D+A  I FLAS+ ARY+T
Sbjct: 181 IRCNAVAPGLVLTPAALDNLNE-EVRNIFLGQCATPYLGEPEDVAATIAFLASNDARYIT 239

Query: 242 GASLLVDGGLFVN 254
           G +++VDGGL ++
Sbjct: 240 GQTIVVDGGLTIH 252


Lambda     K      H
   0.319    0.136    0.383 

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: 177
Number of extensions: 11
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: 256
Length of database: 259
Length adjustment: 24
Effective length of query: 232
Effective length of database: 235
Effective search space:    54520
Effective search space used:    54520
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 (21.8 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