GapMind for catabolism of small carbon sources

 

Alignments for a candidate for xdhA in Acidovorax sp. GW101-3H11

Align D-xylulose reductase (EC 1.1.1.9) (characterized)
to candidate Ac3H11_3163 S-(hydroxymethyl)glutathione dehydrogenase (EC 1.1.1.284)

Query= BRENDA::P22144
         (363 letters)



>FitnessBrowser__acidovorax_3H11:Ac3H11_3163
          Length = 371

 Score = 80.1 bits (196), Expect = 9e-20
 Identities = 99/346 (28%), Positives = 147/346 (42%), Gaps = 36/346 (10%)

Query: 30  DVLVQVKKTGICGSDIHFYAHGRIGNFVLTKPMVLGHESAGTVVQVGKGVTSLKVGDNVA 89
           +VL+++  TG+C +D  F   G     +   P+VLGHE AG VV+VG+GVTS+K GD+V 
Sbjct: 29  EVLIRITDTGVCHTDA-FTLSGDDPEGLF--PVVLGHEGAGIVVEVGEGVTSVKPGDHV- 84

Query: 90  IEPGIPSRFSD-----EYKSGHYNLCPH---------MAFAATPNSKEGEP----NPPGT 131
               IP   ++       KSG  NLC           M    T  S  G+P        T
Sbjct: 85  ----IPLYTAECGECLFCKSGKTNLCVSVRATQGKGVMPDGTTRFSYNGQPIYHYMGCST 140

Query: 132 LCKYFKSPEDFLVKLPDHVSLELGALVE-PLSVGVHASK-LGSVAFGDYVAVFGAGPVGL 189
             +Y    E  L K+    + E   L+   ++ G+ A K    V  GD VAVFG G +GL
Sbjct: 141 FSEYTVVAEVSLAKVNPQANPEQVCLLGCGVTTGLGAVKNTAKVQEGDTVAVFGLGGIGL 200

Query: 190 LAAAVAKTFGAKGVIVVDIFDNKLKMAKDIGAATHTFNSKTGGS--EELIKAFGGNVPNV 247
                AK   A  +I VD   +K  +A+  G AT   N K      +++I        + 
Sbjct: 201 AVIQGAKLAKAGRIIAVDTNPSKFDLARTFG-ATDCINPKDFDKPIQQVIVEMTTWGVDH 259

Query: 248 VLECTGAEPCIKLGVDAIAPG-GRFVQVGNAAGPVSFPITVFAMKELTLFGSFRYGFNDY 306
             EC G    ++  ++    G G+ V +G A          F +     +    +G    
Sbjct: 260 SFECIGNVNVMRAALECAHRGWGQSVIIGVAGAGQEISTRPFQLVTGRKWLGTAFGGVKG 319

Query: 307 KTAVGIFDTNYQNGRENAPIDFEQLITHRYKFKDAIEAYDLVRAGK 352
           ++ +     +   G+    I  E  +TH    KD  EA+DL+  GK
Sbjct: 320 RSELPGMVEDAMAGK----IQLEPFVTHTMGLKDINEAFDLMHEGK 361


Lambda     K      H
   0.318    0.138    0.411 

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: 354
Number of extensions: 16
Number of successful extensions: 3
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 363
Length of database: 371
Length adjustment: 30
Effective length of query: 333
Effective length of database: 341
Effective search space:   113553
Effective search space used:   113553
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: 41 (21.7 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