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_RS05210 HSERO_RS05210 3-oxoacyl-ACP reductase

Query= reanno::acidovorax_3H11:Ac3H11_614
         (280 letters)



>FitnessBrowser__HerbieS:HSERO_RS05210
          Length = 261

 Score =  335 bits (860), Expect = 5e-97
 Identities = 165/253 (65%), Positives = 201/253 (79%), Gaps = 1/253 (0%)

Query: 28  LAKFPSLQGRAVFVTGGGSGIGAAIVAAFAEQGARVAFVDVAREASEALAQHIADAGLPR 87
           LA FPSL+G+ VF+TGGG+GIGAAIV AFA+QGA VAFVD+A EASEAL   +A AG P+
Sbjct: 10  LASFPSLKGKRVFITGGGTGIGAAIVEAFAQQGAHVAFVDIATEASEALCNEVAAAGHPK 69

Query: 88  PWWRVCDVRDVQALQACMADAAAELGSDFAVLVNNVASDDRHTLESVTPEYYDERMAINE 147
           P +R CD+RD+ A QA +A+  A+LG DF VLVNN A+D RH LE VT EY+++R+AIN+
Sbjct: 70  PLFRHCDLRDIPAFQATIAELQAQLG-DFDVLVNNAANDQRHKLEEVTLEYWNDRIAINQ 128

Query: 148 RPAFFAIQAVVPGMRRLGAGSVINLGSTGWQGKGTGYPCYAIAKSSVNGLTRGLAKTLGQ 207
           RP+FFA+Q+VV GM+R G GS+IN  S  W   G G+P Y  AK+S  GLTRGLA+ LG 
Sbjct: 129 RPSFFAVQSVVEGMKRRGGGSIINFSSISWHQSGGGFPVYTTAKASTLGLTRGLARDLGP 188

Query: 208 DRIRINTVSPGWVMTERQIKLWLDAEGEKELARNQCLPDKLRPHDIARMVLFLASDDAAM 267
            +IR+NTV+PGWVMTERQIKLWLD EG+K +ARNQCL   L P  +ARMVLFLA+DD+AM
Sbjct: 189 HKIRVNTVTPGWVMTERQIKLWLDEEGKKAIARNQCLQGDLLPWHLARMVLFLAADDSAM 248

Query: 268 CTAQEFKVDAGWV 280
           CTAQEF VDAGWV
Sbjct: 249 CTAQEFIVDAGWV 261


Lambda     K      H
   0.320    0.133    0.405 

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: 216
Number of extensions: 2
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: 280
Length of database: 261
Length adjustment: 25
Effective length of query: 255
Effective length of database: 236
Effective search space:    60180
Effective search space used:    60180
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