GapMind for catabolism of small carbon sources

 

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

Align 2-ketogluconate 6-phosphate reductase (EC 1.1.1.43) (characterized)
to candidate Ac3H11_2599 Glyoxylate reductase (EC 1.1.1.79) / Glyoxylate reductase (EC 1.1.1.26) / Hydroxypyruvate reductase (EC 1.1.1.81); 2-ketoaldonate reductase, broad specificity (EC 1.1.1.215) (EC 1.1.1.-)

Query= reanno::BFirm:BPHYT_RS11290
         (321 letters)



>FitnessBrowser__acidovorax_3H11:Ac3H11_2599
          Length = 329

 Score =  226 bits (577), Expect = 4e-64
 Identities = 144/324 (44%), Positives = 191/324 (58%), Gaps = 12/324 (3%)

Query: 3   KIVAWKSLPEDVLAYLQQHAQVVQVDATQHDAF------VAALKDADGGIGS-SVKITPA 55
           +I+  +++  D++  L++H     V+A   D         A L D DG + + S +I  A
Sbjct: 5   RILVARAIFPDIVDRLREH---FDVEANPDDVIWTPQELAARLADKDGVLTTGSQRIDAA 61

Query: 56  MLEGATRLKALSTISVGFDQFDVADLTRRGIVLANTPDVLTESTADTVFSLILASARRVV 115
           +L  A RLK  + ++VG++ FDV  +T  G+   NTPDVLTE+TAD  F+L++A+ARR+ 
Sbjct: 62  LLAAAPRLKICANMAVGYNNFDVDAMTAAGVQGTNTPDVLTETTADFGFALLMATARRMT 121

Query: 116 ELAEWVKAGHWQHSIGPALFGVDVQGKTLGIVGLGRIGGAVARRAALGFNMKVLYTNRS- 174
           E   +++AG W         G D+ G TLGI+G+GRIG  +A+R A GF MKV+Y NRS 
Sbjct: 122 ESEHYLRAGQWTKWSYDMFAGSDIHGSTLGIIGMGRIGQGIAKRGAHGFGMKVIYHNRSR 181

Query: 175 ANPQAEEAYGARRVELAELLATADFVCLQVPLTPETKHLIGAAELKSMKKSAILINASRG 234
            + + E    A  V   ELL TAD V L VP T  + H IGAAEL  MK +A LIN +RG
Sbjct: 182 LSAELEAECKASYVGKDELLRTADHVMLVVPYTAASHHTIGAAELALMKPTATLINIARG 241

Query: 235 ATVDEKALIEALQNGTIHGAGLDVFETEPLPSDSPLLKLANVVALPHIGSATHETRHAMA 294
             VD+ AL  AL+ G I  AGLDVFE EP      LL + NVV  PHI SAT  TR AMA
Sbjct: 242 GIVDDAALAVALREGRIAAAGLDVFEGEP-SVHPDLLTVPNVVLTPHIASATVPTRRAMA 300

Query: 295 RNAAENLVAALDGTLTSNIVNREV 318
             AA+NL+A L G      VN+ V
Sbjct: 301 NLAADNLIAFLGGRGPLTPVNQPV 324


Lambda     K      H
   0.317    0.131    0.366 

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: 232
Number of extensions: 7
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: 321
Length of database: 329
Length adjustment: 28
Effective length of query: 293
Effective length of database: 301
Effective search space:    88193
Effective search space used:    88193
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: 48 (23.1 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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