GapMind for catabolism of small carbon sources

 

Alignments for a candidate for xacB in Erythrobacter marinus HWDM-33

Align L-arabinose 1-dehydrogenase (EC 1.1.1.46) (characterized)
to candidate WP_047094222.1 AAV99_RS11820 SDR family oxidoreductase

Query= reanno::HerbieS:HSERO_RS05210
         (261 letters)



>NCBI__GCF_001013305.1:WP_047094222.1
          Length = 261

 Score =  249 bits (637), Expect = 3e-71
 Identities = 126/250 (50%), Positives = 163/250 (65%), Gaps = 2/250 (0%)

Query: 11  ASFPSLKGKRVFITGGGTGIGAAIVEAFAQQGAHVAFVDIATEASEALCNEVAAAGHPKP 70
           A +PSL  KRV I+GGG+GIGA IVE F +QGA VAFVD+   ASEALC  +A A H +P
Sbjct: 13  AVYPSLLDKRVIISGGGSGIGAGIVEGFVRQGARVAFVDVQDAASEALCARLADAAH-QP 71

Query: 71  LFRHCDLRDIPAFQATIAELQAQLGDFDVLVNNAANDQRHKLEEVTLEYWNDRIAINQRP 130
           ++RHCD+ D   +   I+ L  +LG  DV++NNA ND RH + +VT EYW+ R+A+N + 
Sbjct: 72  VYRHCDITDTDGYSRCISSLVDRLGGCDVIINNAGNDDRHAIADVTSEYWDQRMAVNLKH 131

Query: 131 SFFAVQSVVEGMKRRGGGSIINFSSISWHQSGGGFPVYTTAKASTLGLTRGLARDLGPHK 190
            FFA ++V   M+  GGG+IIN  SISWH       VY TAKA+  GLTR LAR+LGP  
Sbjct: 132 HFFAAKTVAPAMRNAGGGAIINLGSISWHLGLENLTVYQTAKAAIEGLTRSLARELGPDN 191

Query: 191 IRVNTVTPGWVMTERQIKLWLDEEGKKAIARNQCLQGDLLPWHLARMVLFLAADDSAMCT 250
           IRVN + PG V T RQ + W   E +  I   QCL G + P  +A M +FLA+DD+  C+
Sbjct: 192 IRVNAILPGNVQTPRQ-QEWYTPEQEDEIVEAQCLPGRIQPADIAAMAMFLASDDARFCS 250

Query: 251 AQEFIVDAGW 260
              + VDAGW
Sbjct: 251 GHNYWVDAGW 260


Lambda     K      H
   0.321    0.134    0.411 

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: 172
Number of extensions: 6
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: 261
Length of database: 261
Length adjustment: 25
Effective length of query: 236
Effective length of database: 236
Effective search space:    55696
Effective search space used:    55696
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: 47 (22.7 bits)

This GapMind analysis is from Sep 24 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