GapMind for catabolism of small carbon sources

 

Alignments for a candidate for xdhA in Snodgrassella alvi wkB2

Align L-iditol 2-dehydrogenase; EC 1.1.1.14 (characterized)
to candidate WP_025330258.1 SALWKB2_RS03265 zinc-dependent alcohol dehydrogenase family protein

Query= CharProtDB::CH_000596
         (353 letters)



>NCBI__GCF_000600005.1:WP_025330258.1
          Length = 347

 Score =  143 bits (360), Expect = 8e-39
 Identities = 101/310 (32%), Positives = 147/310 (47%), Gaps = 21/310 (6%)

Query: 9   MKAAVMHNTREIKIETLPVPDINHD-EVLIKVMAVGICGSDLHYYTNGRIGNYVVEKPFI 67
           MK AV    R++ I  +  P I    + +I+++   +CGSDL +Y     G    E   I
Sbjct: 1   MKVAVFVEPRKVAIREMEKPVIQKSTDAIIRIVRACVCGSDLWWYR----GISTCEPERI 56

Query: 68  LGHECAGEIAAVGSSVDQFKVGDRVAVEPGVTCGRCEACKEGRYNLCPDVQ--------- 118
           +GHE  G + A GS+V   + GD V V     CG C ACK G    C + +         
Sbjct: 57  VGHEAIGVVEATGSAVTHVRNGDFVIVPFTHGCGHCAACKAGFDGNCQNKEDERNGGYQG 116

Query: 119 -FLATPPVDGAFVQYIKMRQDFVFLIPDSLSYEEAALIEPFSVGIHAAARTKLQPGSTIA 177
            +L     D A V+     QD+   + +SL      L +  + G HAAA  +++PG T+ 
Sbjct: 117 EYLRFTNADWALVKIPGQPQDYSDAVLNSL----LTLADVMATGYHAAASAEVKPGDTVV 172

Query: 178 IMGMGPVGLMAVAAAKAFGAGTIIVTDLEPLRLEAAKKMGATHIINIREQDALEEIKTIT 237
           +MG G VGL AV AAK  GA  II     P R + A++ GAT I+  R  +A+E++ ++T
Sbjct: 173 VMGDGAVGLCAVIAAKLRGAERIIAMSRHPDRAKLAEEFGATDIVPERGDEAVEKVLSLT 232

Query: 238 NDRGVDVAWETAGNPAALQSALASVRRGGKLAIVGLPSQNEIPLNVPFIADNEIDIYGIF 297
              G D   E  G   +LQ+A+A  R G  +  VG+    EI  +  F     I + G  
Sbjct: 233 RQAGADAVLECVGTQQSLQTAVAVARPGAIVGCVGIQHDTEIKTSDVFW--RNIGLRGGI 290

Query: 298 RYANTYPKGI 307
               TY K +
Sbjct: 291 ASVTTYDKNL 300


Lambda     K      H
   0.320    0.137    0.401 

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: 284
Number of extensions: 13
Number of successful extensions: 3
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: 353
Length of database: 347
Length adjustment: 29
Effective length of query: 324
Effective length of database: 318
Effective search space:   103032
Effective search space used:   103032
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: 49 (23.5 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