GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gadh3 in Herbaspirillum seropedicae SmR1

Align Gluconate 2-dehydrogenase small subunit (characterized, see rationale)
to candidate HSERO_RS22800 HSERO_RS22800 hypothetical protein

Query= uniprot:A4PIA9
         (242 letters)



>FitnessBrowser__HerbieS:HSERO_RS22800
          Length = 237

 Score =  172 bits (436), Expect = 5e-48
 Identities = 92/228 (40%), Positives = 144/228 (63%), Gaps = 13/228 (5%)

Query: 15  RRAMLQGTALGLVVAA---LFHFPSEGVSEAADREYAYRPVFFSDDEWQTLNSFVDRLIP 71
           RRA+L  TA  + + +   L    ++G+ E  + ++ Y+PVFF+  +W  + +  DRLIP
Sbjct: 9   RRAVLAATAAAVPLVSIPLLKEAQADGL-EGIELQH-YKPVFFNPAQWLFILAACDRLIP 66

Query: 72  ADVEGPGALEAHVPEFIDRQMNTPYGHGSEWYLRPPLMKTS-AALGYQFLFTPRDIYKQG 130
           A+  GPGALE +VP FID+Q++   G GS+ Y + P    + A LG+Q  + P+D+Y+ G
Sbjct: 67  AEGRGPGALETNVPVFIDQQLHA--GLGSDIYQQGPHQPDAPATLGFQIPYAPQDVYRIG 124

Query: 131 LPALHSAIMQRYGKPFHQLDAGERDRIIGQMEKGSLTLSPVPSKLL-----FGQILKNCK 185
           +        Q++GKPF QLDA ++D ++  ++K  +  + +  K +     FGQ+L + K
Sbjct: 125 ITLTQQISQQQHGKPFEQLDAKDKDALLTALQKNGVDFAALGEKSMRPSQFFGQLLGDTK 184

Query: 186 EGYFADPIHGGNYEMGAWKMIGFPGARADFTDWVDRYGARYPLSPVSV 233
            GY ADP++GGN +M AW  IGFPGARA +T+WVD++  +YPL PVS+
Sbjct: 185 NGYLADPMYGGNKDMKAWVAIGFPGARAAYTEWVDQHNVKYPLGPVSL 232


Lambda     K      H
   0.321    0.140    0.441 

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: 185
Number of extensions: 8
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: 242
Length of database: 237
Length adjustment: 23
Effective length of query: 219
Effective length of database: 214
Effective search space:    46866
Effective search space used:    46866
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 46 (22.3 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