GapMind for catabolism of small carbon sources

 

Alignments for a candidate for kguD in Shewanella oneidensis MR-1

Align 2-ketogluconate 6-phosphate reductase (EC 1.1.1.43) (characterized)
to candidate 202189 SO3071 erythronate-4-phosphate dehydrogenase (NCBI ptt file)

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



>FitnessBrowser__MR1:202189
          Length = 376

 Score = 97.8 bits (242), Expect = 4e-25
 Identities = 86/257 (33%), Positives = 118/257 (45%), Gaps = 36/257 (14%)

Query: 39  LKDADGGIGSSV-KITPAMLEGATRLKALSTISVGFDQFDVADLTRRGIVLANTPDVLTE 97
           ++DAD  +  SV ++  A+LE   +LK + + ++G D  D+A L  RGIV +N P     
Sbjct: 35  VQDADVLLVRSVTRVNAALLEANQKLKFVGSATIGTDHVDLAYLATRGIVFSNAPGCNAT 94

Query: 98  STADTVFSLILASARRVVELAEWVKAGHWQHSIGPALFGVDVQGKTLGIVGLGRIGGAVA 157
           +  +  F  +L  A R                     F   ++GK +GIVG G  G A A
Sbjct: 95  AVGEFAFIAMLELAAR---------------------FNSPLRGKVVGIVGAGNTGSATA 133

Query: 158 RRAALGFNMKVLYTNRSANPQAEEAYGARR--VELAELLATADFVCLQVPLTP----ETK 211
           +     F +KVL      N   +EA G  R  V L  LL  AD + L VP+T     +T 
Sbjct: 134 K-CLEAFGIKVLL-----NDPIKEAEGDPRDFVSLETLLQEADIISLHVPITRTGEHKTL 187

Query: 212 HLIGAAELKSMKKSAILINASRGATVDEKALIEALQNGTIHGAGLDVFETEPLPSDSPLL 271
           HL   A L S+K +  LIN  RG  +D +ALI+  Q        LDV+E EP P   P L
Sbjct: 188 HLFDEARLMSLKANIWLINCCRGDVIDNQALIKVKQQRDDLKLVLDVWEGEPNP--MPEL 245

Query: 272 KLANVVALPHIGSATHE 288
                 A PHI   + E
Sbjct: 246 VPFAEFATPHIAGYSLE 262


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: 253
Number of extensions: 7
Number of successful extensions: 2
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: 376
Length adjustment: 29
Effective length of query: 292
Effective length of database: 347
Effective search space:   101324
Effective search space used:   101324
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