GapMind for catabolism of small carbon sources

 

Alignments for a candidate for xdh in Leeuwenhoekiella blandensis MED217

Align D-xylose 1-dehydrogenase (EC 1.1.1.175) (characterized)
to candidate WP_009780934.1 MED217_RS12720 SDR family oxidoreductase

Query= reanno::Korea:Ga0059261_1894
         (259 letters)



>NCBI__GCF_000152985.1:WP_009780934.1
          Length = 246

 Score =  127 bits (320), Expect = 2e-34
 Identities = 79/238 (33%), Positives = 127/238 (53%), Gaps = 5/238 (2%)

Query: 22  LVTGGGSGIGAGIVEGFARQGADVTFFDIAGAESQLLVERLSADGHKACFERVDLTDVAS 81
           +VTGG SG+G  I   F   G  V    I G   +   +     G        DL ++ +
Sbjct: 7   VVTGGNSGLGYAIARKFCDAGYKVY---IIGRNEEKTRQAADNLGELVVPIVFDLNNLEA 63

Query: 82  LQAVIARLIKGAGGFDILVNNAANDDRHAIDEITEAYWDERLSVNLKHIFFCAQAVVPAM 141
           +  +I  L++  G  D+LVNNA  + +    E+T+A +D  L  N+K +F  ++ VV +M
Sbjct: 64  IPKLIDELLQATGKIDVLVNNAGINMKKDFAEVTDAEFDRILHTNVKSVFAISREVVKSM 123

Query: 142 RARGGGAIVNLGSISWHLGLSDLVLYQTCKAAIEGLTRSLARDLGRDGIRATCVIPGNVR 201
           +   GG+IVN+ S++   G+  ++ Y   K AIEG+TR++A DL +  IR  CV PG ++
Sbjct: 124 KGNYGGSIVNISSMAAQYGIPQVIAYTASKTAIEGMTRAMAVDLAQYNIRVNCVAPGFIK 183

Query: 202 TPRQLK-WYSPEGEAEIVAAQCLDGRL-APEDVAAMVLFLASDDARLVTGHSYFVDAG 257
           TP   K   S +   + V ++   G++ APED+A  V +LA  +++ +TG    VD G
Sbjct: 184 TPMTAKALNSDKQRKDRVFSRTPMGKMGAPEDIADAVFYLAGKESKFITGTVLCVDGG 241


Lambda     K      H
   0.321    0.137    0.409 

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: 136
Number of extensions: 6
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: 259
Length of database: 246
Length adjustment: 24
Effective length of query: 235
Effective length of database: 222
Effective search space:    52170
Effective search space used:    52170
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 (21.9 bits)
S2: 46 (22.3 bits)

This GapMind analysis is from Sep 24 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