GapMind for catabolism of small carbon sources

 

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

Align L-arabinose 1-dehydrogenase; D-galactose 1-dehydrogenase (EC 1.1.1.46; EC 1.1.1.48) (characterized)
to candidate 350543 BT1015 putative oxidoreductase (NCBI ptt file)

Query= reanno::BFirm:BPHYT_RS16920
         (266 letters)



>FitnessBrowser__Btheta:350543
          Length = 295

 Score =  133 bits (334), Expect = 5e-36
 Identities = 84/268 (31%), Positives = 138/268 (51%), Gaps = 18/268 (6%)

Query: 2   SSPANANVRLADSAFARYPSLVDRTVLITGGATGIGASFVEHFAAQGARVAFFDIDASAG 61
           ++ +     +A    ++  SL  R + +TGGA GIG + VE F   G +VAF DI+A +G
Sbjct: 32  TTSSQVKTEVAGEIVSKSDSLKKR-IFVTGGAEGIGRAIVEAFCKDGHQVAFCDINAVSG 90

Query: 62  EALADELGDSKHKPLFLSCDLTDIDALQKAIADVKAALGPIQVLVNNAANDKRHTIGEVT 121
           +  A + G      +F   D++D +AL+  +  +      I +++NN    K  +I E +
Sbjct: 91  QQTARDTG-----AIFHPVDVSDKEALESCMQQILDEWKDIDIVINNVGISKFSSITETS 145

Query: 122 RESFDAGIAVNIRHQFFAAQAVMEDMKAANS----GSIINLGSISWMLKNGGYPVYVMSK 177
            E FD  ++VN+R  F  ++ +    KA +     G IIN+ S  +++   G   Y  SK
Sbjct: 146 VEDFDKILSVNLRPVFITSRLLAIHRKAQSDSNPYGRIINICSTRYLMSEPGSEGYAASK 205

Query: 178 SAVQGLTRGLARDLGHFNIRVNTLVPGWVMTEKQKRLWLDDAGRR-SIKEGQCIDAELEP 236
             +  LT  LA  L  +NI VN++ PGW+ T+   +L  +D  +  S + G       +P
Sbjct: 206 GGIYSLTHALALSLSEWNITVNSIAPGWIQTQNYDQLRPEDHSQHPSRRVG-------KP 258

Query: 237 ADLARMALFLAADDSRMITAQDIVVDGG 264
            D+ARM LFL  D++  I  ++I +DGG
Sbjct: 259 EDIARMCLFLCRDENDFINGENITIDGG 286


Lambda     K      H
   0.320    0.134    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: 148
Number of extensions: 6
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: 266
Length of database: 295
Length adjustment: 26
Effective length of query: 240
Effective length of database: 269
Effective search space:    64560
Effective search space used:    64560
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