GapMind for catabolism of small carbon sources

 

Alignments for a candidate for xdhA in Klebsiella michiganensis M5al

Align Sorbitol dehydrogenase; SDH; EC 1.1.1.-; Glucitol dehydrogenase; L-iditol 2-dehydrogenase; EC 1.1.1.14; Polyol dehydrogenase; Xylitol dehydrogenase; EC 1.1.1.9 (uncharacterized)
to candidate BWI76_RS11535 BWI76_RS11535 putative oxidoreductase, Zn-dependent and NAD(P)-binding protein

Query= curated2:Q9Z9U1
         (343 letters)



>FitnessBrowser__Koxy:BWI76_RS11535
          Length = 358

 Score =  181 bits (459), Expect = 3e-50
 Identities = 113/358 (31%), Positives = 180/358 (50%), Gaps = 23/358 (6%)

Query: 1   MKALVKTQHGTGHFAVQEKPEPTPGKHQVKIKVKYTGVCGSDIHTYEGHYPVAAPVTL-- 58
           MKAL +     G + + + PEP  G   V I++K   +CG+D+     HY V +      
Sbjct: 1   MKALARFGKAFGGYKMIDVPEPVCGPDDVVIEIKAAAICGADMK----HYNVDSGSDQFN 56

Query: 59  ---GHEFSGEIVELGEGVTGFNVGDRVTSETTYSICGKCSYCTSGDYNLCSHRKGLG--- 112
              GHEF+G IV +G+ V  + VG RV S+ +  +CG C  C  GD+  C+ +  LG   
Sbjct: 57  SIRGHEFAGAIVRVGDKVKDWKVGQRVVSDNSGHVCGVCPACEQGDFLCCAEKVNLGLDN 116

Query: 113 NQQDGSFAKYVIA-------RQESLHHLPAGVDDRSAAMTEPLACTHHAIAKTS-INKGD 164
           N   G F+KY +         + +L  +P GVD   AA+ +P+   + ++A+ S    G 
Sbjct: 117 NTWGGGFSKYCLVPGEILKIHRHALWEIPPGVDYEDAAVLDPICNAYKSLAQQSKFLPGQ 176

Query: 165 LVVVTGPGPIGLLAAQVAKSHGG-TVIITGLSND-QVRLKKAKEVGIDYAIDTQEVDIKE 222
            VVV G GP+GL + Q+A+  G   +++ GL  D  VR   AK +G    ++    D+  
Sbjct: 177 DVVVFGTGPLGLFSVQMARIMGAVNIVMVGLEEDVAVRFPIAKALGATAVVNASTEDVVA 236

Query: 223 LVSELTDGYGADVVLECSGAVPAAKQGIDLLRKKGQYAQVGLFAQPEIQFNFEKIIQKEI 282
               +       +V+ECSGA  A KQ I++LR  G+  +VG+  QP + F+   I     
Sbjct: 237 RCQAICGKDNLGLVIECSGANIALKQSIEMLRPNGEVVRVGMGFQP-LDFSINDITTWNK 295

Query: 283 SVVGSRSQKPADWEPALSLLNEKKVNAKTLVTHEYTISEWDKAYHAIKSGEAIKVLLT 340
           S++G  +     W  A+ LL    +  K ++TH   +S+W + + A+    AIKV++T
Sbjct: 296 SIIGHMAYDSTSWRNAIRLLASGAIKVKPMITHRIGLSQWREGFDAMVDKTAIKVIMT 353


Lambda     K      H
   0.315    0.133    0.388 

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: 343
Number of extensions: 23
Number of successful extensions: 6
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: 343
Length of database: 358
Length adjustment: 29
Effective length of query: 314
Effective length of database: 329
Effective search space:   103306
Effective search space used:   103306
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (22.0 bits)
S2: 49 (23.5 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