GapMind for catabolism of small carbon sources

 

Alignments for a candidate for xdhA in Echinicola vietnamensis KMM 6221, DSM 17526

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 Echvi_0507 Echvi_0507 Threonine dehydrogenase and related Zn-dependent dehydrogenases

Query= curated2:Q9Z9U1
         (343 letters)



>FitnessBrowser__Cola:Echvi_0507
          Length = 337

 Score =  179 bits (454), Expect = 9e-50
 Identities = 109/322 (33%), Positives = 173/322 (53%), Gaps = 9/322 (2%)

Query: 1   MKALVKTQHGTGHFAVQEKPEPTPGKHQVKIKVKYTGVCGSDIHTYEGHYPVAA-PVTLG 59
           MK L  T+ G   ++  EKP  +PG+    IK+K  G+CG+D+H YEG  P    P  LG
Sbjct: 1   MKILTCTEPGNFEYSEGEKPTLSPGR--AIIKIKRIGICGTDLHAYEGTQPFFNYPRVLG 58

Query: 60  HEFSGEIVELGEGVTGFNVGDRVTSETTYSICGKCSYCTSGDYNLCSHRKGLGNQQDGSF 119
           HE SGE+VE+ +G  GF  GD VT    Y  CG+C  C +G  N C+     G  +DG  
Sbjct: 59  HELSGELVEV-DGAEGFVPGDLVTI-IPYFNCGECVACKAGKPNCCATISVFGVHEDGGM 116

Query: 120 AKYVIARQESLHHLPAGVDDRSAAMTEPLACTHHAIAKTSINKGDLVVVTGPGPIGLLAA 179
            +++     SL     G+     A+ EPLA   H + +  +  G+ VVV G GPIGL   
Sbjct: 117 KEFISVPSSSLVK-QEGLSLEQLALAEPLAIGAHGVRRAGVQPGEFVVVMGAGPIGLGVM 175

Query: 180 QVAKSHGGTVIITGLSNDQVRLKKAKEVGIDYAIDTQEVDIKELVSELTDGYGADVVLEC 239
           + A+  GG VI   ++ D++   + + +G++Y ++ +  D K  ++++T G  A+ V++ 
Sbjct: 176 EFARIAGGKVIAMDINEDRLAFCR-ETLGVEYTVNAKG-DFKAAIADITGGSFAESVIDA 233

Query: 240 SGAVPAAKQGIDLLRKKGQYAQVGLFAQPEIQFNFEKIIQKEISVVGSRSQKPADWEPAL 299
           +G+  A   G  L+   G+Y  VGL   P I+FN  +  ++E +++ SR+    D++  L
Sbjct: 234 TGSSVAIHHGFGLMAHGGRYVLVGLQKGP-IEFNHPEFHKRESTLMSSRNATREDFDTVL 292

Query: 300 SLLNEKKVNAKTLVTHEYTISE 321
             L E+KV A + +THE    +
Sbjct: 293 KALKEQKVKAASYITHEVAFDQ 314


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: 351
Number of extensions: 21
Number of successful extensions: 7
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: 337
Length adjustment: 28
Effective length of query: 315
Effective length of database: 309
Effective search space:    97335
Effective search space used:    97335
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