GapMind for catabolism of small carbon sources

 

Alignments for a candidate for xacB in Klebsiella michiganensis M5al

Align L-arabinose 1-dehydrogenase (EC 1.1.1.46) (characterized)
to candidate BWI76_RS16625 BWI76_RS16625 putative oxidoreductase

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



>FitnessBrowser__Koxy:BWI76_RS16625
          Length = 294

 Score = 97.8 bits (242), Expect = 2e-25
 Identities = 76/247 (30%), Positives = 118/247 (47%), Gaps = 6/247 (2%)

Query: 16  LKGKRVFITGGGTGIGAAIVEAFAQQGAHVAFVDIATEASEA--LCNEVAAAGHPKPLFR 73
           L GKR  ITGG +GIG A+  AFA++GA VA   +  E S+A  +   + A G  + +  
Sbjct: 47  LAGKRALITGGDSGIGRAVAIAFAREGADVAINYLPEEESDAQTVIALIEAEGR-QAVAI 105

Query: 74  HCDLRDIPAFQATIAELQAQLGDFDVLVNNAANDQR-HKLEEVTLEYWNDRIAINQRPSF 132
             D+RD    +  + +  ++LG  D+LVNNA   Q    LEE+T   ++     N   +F
Sbjct: 106 PGDVRDESFCETLVEQAASELGGLDILVNNAGRQQYCESLEELTTADFDATFKTNVYAAF 165

Query: 133 FAVQSVVEGMKRRGGGSIINFSSISWHQSGGGFPVYTTAKASTLGLTRGLARDLGPHKIR 192
           +  ++ +  +K     +IIN SS+   +       Y   KA  +  T+ LA+ LGP  IR
Sbjct: 166 WITKAALRHLKEH--SAIINTSSVQAFKPSPILLDYAQTKACLVAFTKSLAKQLGPKGIR 223

Query: 193 VNTVTPGWVMTERQIKLWLDEEGKKAIARNQCLQGDLLPWHLARMVLFLAADDSAMCTAQ 252
           VN V PG   T  Q      +E  +    +  L     P  +A + + LA+D  +  + Q
Sbjct: 224 VNAVAPGPYWTVLQSSGGQPDEKVRQFGADTPLGRPGQPVEIAPLYVTLASDACSFTSGQ 283

Query: 253 EFIVDAG 259
            +  D G
Sbjct: 284 VWCSDGG 290


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: 159
Number of extensions: 7
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: 294
Length adjustment: 25
Effective length of query: 236
Effective length of database: 269
Effective search space:    63484
Effective search space used:    63484
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 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