GapMind for catabolism of small carbon sources

 

Alignments for a candidate for galdh in Herbaspirillum seropedicae SmR1

Align L-arabinose 1-dehydrogenase / D-galactose 1-dehydrogenase (EC 1.1.1.46; EC 1.1.1.48) (characterized)
to candidate HSERO_RS12375 HSERO_RS12375 3-oxoacyl-ACP reductase

Query= reanno::pseudo6_N2E2:Pf6N2E2_5967
         (272 letters)



>FitnessBrowser__HerbieS:HSERO_RS12375
          Length = 261

 Score =  139 bits (349), Expect = 8e-38
 Identities = 88/256 (34%), Positives = 138/256 (53%), Gaps = 13/256 (5%)

Query: 13  PPKGERLKNKVVLLTGAAQGIGEAIVAAFASQQARLVISDIQAEKVETVAAHWR-ERGAD 71
           P + +R + KVV++TGAA GIGEA    F+ + AR++++D  A  +  V      ER A 
Sbjct: 6   PSRLQRFEGKVVIVTGAASGIGEATARRFSDEGARVLLADRDAAALGKVFDSLPPERTA- 64

Query: 72  VHALKADVSNQQDLHAMARHAVERHGRIDVLVNCAGVNVFRDPLEMTEEDWRRCFAIDLD 131
             A + DVS+ + +  +   A+ER G++DVLV+ AGV    +  E++ EDW R  A +++
Sbjct: 65  --ARETDVSHHEQVRQLVDFAIERFGQLDVLVSDAGVFAEGNVTEVSPEDWHRVQATNVN 122

Query: 132 GAWYGCKAVLPQMIEQGVGSIINIASTHSSHIIPGCFPYPVAKHGLLGLTRALGIEYAPK 191
           G +YG +  LP  +E+  G I+N+AS            Y  +K  +  LTRA+ +++  K
Sbjct: 123 GVFYGAREALPH-LEKTRGCIVNVASVSGLAADWNLSAYNASKGAVCNLTRAMALDFGRK 181

Query: 192 GVRVNAIAPGYIETQLNVDYWNG--FADPYAERQRALDLHPPRRIGQPIEVAMTAVFLAS 249
           GVR+NA+ P    T +  D  +     D +AER          R   P+E+A    FLAS
Sbjct: 182 GVRINAVCPSLTHTAMTADMADDPPLLDKFAERIAL------GRGADPLEIAAVITFLAS 235

Query: 250 DEAPFINASCITIDGG 265
            +A F+N   + +DGG
Sbjct: 236 PDASFVNGVNLPVDGG 251


Lambda     K      H
   0.321    0.137    0.419 

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: 160
Number of extensions: 8
Number of successful extensions: 4
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: 272
Length of database: 261
Length adjustment: 25
Effective length of query: 247
Effective length of database: 236
Effective search space:    58292
Effective search space used:    58292
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 (21.8 bits)
S2: 47 (22.7 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