GapMind for catabolism of small carbon sources

 

Alignments for a candidate for xdh in Dinoroseobacter shibae DFL-12

Align D-xylose 1-dehydrogenase (EC 1.1.1.175) (characterized)
to candidate 3609507 Dshi_2891 short-chain dehydrogenase/reductase SDR (RefSeq)

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



>FitnessBrowser__Dino:3609507
          Length = 242

 Score =  125 bits (313), Expect = 1e-33
 Identities = 88/246 (35%), Positives = 126/246 (51%), Gaps = 13/246 (5%)

Query: 16  LKGKRVLVTGGGSGIGAGIVEGFARQGADVTFFDIAGAESQLLVERLSADGHKACFERVD 75
           L+GK  +VTGGGSG GAGIV  FA +GA V   DI    ++ + E            +VD
Sbjct: 3   LEGKTAIVTGGGSGFGAGIVRKFAAEGAQVIVADINKGAAEAVAEEYGGTA-----AQVD 57

Query: 76  LTDVASLQAVIARLIKGAGGFDILVNNAANDDR-HAIDEITEAYWDERLSVNLKHIFFCA 134
           ++D  S+ A    L +  G  DILVNNA        ++E+TE  +D  L+VN K ++  A
Sbjct: 58  VSDADSMAA----LAEAHGAPDILVNNAGITHLPKPMEEVTEEEFDRVLAVNAKSVYLSA 113

Query: 135 QAVVPAMRARGGGAIVNLGSISWHLGLSDLVLYQTCKAAIEGLTRSLARDLGRDGIRATC 194
           +  VPAM+ARG GAI+N+ S +       L  Y   K  +   T+++A +L   GIR   
Sbjct: 114 RVFVPAMKARGSGAILNIASTAGVSPRPKLNWYNASKGWMITATKAMAVELAPFGIRVNA 173

Query: 195 VIPGNVRTPRQLKWY---SPEGEAEIVAAQCLDGRLAPEDVAAMVLFLASDDARLVTGHS 251
           + P    TP    +    +PE  A+ +A   L     PED+     FL SD+A ++TG +
Sbjct: 174 LNPVAGETPLLASFMGEDTPEMRAKFLATIPLGRFSQPEDLGNAAAFLCSDEASMITGVA 233

Query: 252 YFVDAG 257
             VD G
Sbjct: 234 MEVDGG 239


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: 135
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: 259
Length of database: 242
Length adjustment: 24
Effective length of query: 235
Effective length of database: 218
Effective search space:    51230
Effective search space used:    51230
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 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