GapMind for catabolism of small carbon sources

 

Alignments for a candidate for xdh in Escherichia coli BW25113

Align D-xylose 1-dehydrogenase (EC 1.1.1.175) (characterized)
to candidate 15740 b1619 7-alpha-hydroxysteroid dehydrogenase (NCBI)

Query= BRENDA::B8H1Z0
         (248 letters)



>FitnessBrowser__Keio:15740
          Length = 255

 Score =  105 bits (261), Expect = 1e-27
 Identities = 72/242 (29%), Positives = 120/242 (49%), Gaps = 5/242 (2%)

Query: 9   LKGKRVVITGGGSGIGAGLTAGFARQGAEVIFLDIADEDSRALEAELAGSPIPPVYKRCD 68
           L GK  +ITG G+GIG  +   FA  GA V+  DI  + +  +  E+          RCD
Sbjct: 9   LDGKCAIITGAGAGIGKEIAITFATAGASVVVSDINADAANHVVDEIQQLGGQAFACRCD 68

Query: 69  LMNLEAIKAV----FAEIGDVDVLVNNAGNDDRHKLADVTGAYWDERINVNLRHMLFCTQ 124
           + + + + A+     +++G VD+LVNNAG     K  D+  A +     +N+      +Q
Sbjct: 69  ITSEQELSALADFAISKLGKVDILVNNAGGGGP-KPFDMPMADFRRAYELNVFSFFHLSQ 127

Query: 125 AVAPGMKKRGGGAVINFGSISWHLGLEDLVLYETAKAGIEGMTRALARELGPDDIRVTCV 184
            VAP M+K GGG ++   S++      ++  Y ++KA    + R +A +LG  +IRV  +
Sbjct: 128 LVAPEMEKNGGGVILTITSMAAENKNINMTSYASSKAAASHLVRNMAFDLGEKNIRVNGI 187

Query: 185 VPGNVKTKRQEKWYTPEGEAQIVAAQCLKGRIVPENVAALVLFLASDDASLCTGHEYWID 244
            PG + T   +   TPE E +++    ++    P+++A   LFL S  AS  +G    + 
Sbjct: 188 APGAILTDALKSVITPEIEQKMLQHTPIRRLGQPQDIANAALFLCSPAASWVSGQILTVS 247

Query: 245 AG 246
            G
Sbjct: 248 GG 249


Lambda     K      H
   0.319    0.137    0.416 

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: 125
Number of extensions: 5
Number of successful extensions: 2
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: 248
Length of database: 255
Length adjustment: 24
Effective length of query: 224
Effective length of database: 231
Effective search space:    51744
Effective search space used:    51744
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 (21.7 bits)
S2: 46 (22.3 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