GapMind for catabolism of small carbon sources

 

Alignments for a candidate for kguD in Shewanella sp. ANA-3

Align 2-ketogluconate 6-phosphate reductase (EC 1.1.1.43) (characterized)
to candidate 7024284 Shewana3_1476 D-isomer specific 2-hydroxyacid dehydrogenase, catalytic region (RefSeq)

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



>FitnessBrowser__ANA3:7024284
          Length = 376

 Score = 88.6 bits (218), Expect = 2e-22
 Identities = 77/255 (30%), Positives = 116/255 (45%), Gaps = 32/255 (12%)

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

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

Query: 158 RRAALGFNMKVLYTNRSANPQAEEAYGARRVELAELLATADFVCLQVPLTP----ETKHL 213
           +     + +KVL  +     +A E      V L  LL  AD + L VP+T     +T HL
Sbjct: 134 K-CLEAYGIKVLLNDPI---KAAEGDPRHFVSLETLLHEADIISLHVPITRTGEHKTLHL 189

Query: 214 IGAAELKSMKKSAILINASRGATVDEKALIEALQNGTIHGAGLDVFETEPLPSDSPLLKL 273
              A + S+K +  L+N  RG  +D +ALI+  +        LDV+E EP P   P L  
Sbjct: 190 FDEARMMSLKPNTWLLNCCRGDVIDNQALIKVKEQRDDLKLVLDVWEGEPNP--MPELVP 247

Query: 274 ANVVALPHIGSATHE 288
               A PHI   + E
Sbjct: 248 FAEFATPHIAGYSLE 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: 249
Number of extensions: 8
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