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 351439 BT1911 7-alpha-hydroxysteroid dehydrogenase (NCBI ptt file)

Query= reanno::pseudo6_N2E2:Pf6N2E2_5967
         (272 letters)



>FitnessBrowser__Btheta:351439
          Length = 259

 Score =  126 bits (316), Expect = 5e-34
 Identities = 80/255 (31%), Positives = 131/255 (51%), Gaps = 8/255 (3%)

Query: 17  ERLKNKVVLLTGAAQGIGEAIVAAFASQQARLVISDIQAEKVETVAAHWRERGADVHALK 76
           +R +NKVV++TGAA GIGEA      S+  ++VI+D+  E+ + +AA   + GADV  + 
Sbjct: 2   KRFENKVVVITGAAGGIGEATTRRIVSEGGKVVIADLSQERADKLAAELTQAGADVRPIY 61

Query: 77  ADVSNQQDLHAMARHAVERHGRIDVLVNCAGVNVFRDPLEMTEED---WRRCFAIDLDGA 133
              +  Q    +   A++ +G+IDVL+N  G    +  L + + D   +   F ++L   
Sbjct: 62  FSATELQSCKELVDFAMKEYGQIDVLINNVGGTDPKRDLNIEKLDIDYFDEVFHLNLCCT 121

Query: 134 WYGCKAVLPQMIEQGVGSIINIASTHSSHIIPGCFPYPVAKHGLLGLTRALGIEYAPKGV 193
            Y  + V+P M   G G+I+N+AS            Y  +K G++ LT+ +  +   K +
Sbjct: 122 MYLSQQVIPIMTTHGGGNIVNVASISGLTADANGTLYGASKAGVINLTKYIATQMGKKNI 181

Query: 194 RVNAIAPGYIETQLNVDYWNGFADPYAERQRALDLHPPRRIGQPIEVAMTAVFLASDEAP 253
           R NA+APG + T   +D  N        R   L       +G+P +VA T  FLAS++A 
Sbjct: 182 RCNAVAPGLVLTPAALDNLN-----EEVRNIFLGQCATPYLGEPEDVAATIAFLASNDAR 236

Query: 254 FINASCITIDGGRSV 268
           +I    I +DGG ++
Sbjct: 237 YITGQTIVVDGGLTI 251


Lambda     K      H
   0.321    0.137    0.419 

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: 149
Number of extensions: 16
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: 272
Length of database: 259
Length adjustment: 25
Effective length of query: 247
Effective length of database: 234
Effective search space:    57798
Effective search space used:    57798
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