GapMind for catabolism of small carbon sources

 

Alignments for a candidate for xacB in Flavobacterium glycines Gm-149

Align L-arabinose 1-dehydrogenase (EC 1.1.1.46) (characterized)
to candidate WP_066329803.1 BLR17_RS09120 SDR family oxidoreductase

Query= reanno::ANA3:7024897
         (256 letters)



>NCBI__GCF_900100165.1:WP_066329803.1
          Length = 254

 Score =  108 bits (270), Expect = 1e-28
 Identities = 74/259 (28%), Positives = 129/259 (49%), Gaps = 22/259 (8%)

Query: 9   SLQGKTIFISGGATGIGACLVNAFLEQGAKVAFVDILVEESTQLVADLKQTQPEASVTFY 68
           SL+ K   I+GG +GIG  +   F +QGA+V  +++  E +   V ++     E    F 
Sbjct: 3   SLKDKKAIITGGGSGIGKAISVLFAKQGAEVHIIELTAESAQSTVDEITA---EGGKVFA 59

Query: 69  HCDLVDIAALKRVIAQVEDDLGPISVLINNAACDQRHSIDEVTPEYWDQCLNTNLRHYFF 128
           H    ++A    V+A  E  +G I +L+NNA       +D      +D+ ++ N++  + 
Sbjct: 60  HA--CNVAKHDEVVATFEK-IGNIHILVNNAGIAHVGKVDTTPEADFDRIMDVNVKGVYN 116

Query: 129 AVQAVRPQMQRLGGGSVINLGSMSWHNRQAGMAGYTASKAGAMGLTRGLAADLGKDKIRI 188
            + A  PQ ++ GGGS++N+ S++     +    Y+ +K   M +T  +A D   + IR 
Sbjct: 117 CLFASIPQFRKSGGGSIVNMASIASWVGISDRFAYSTAKGAVMSMTLSVARDYINENIRC 176

Query: 189 NTLTPGWVMTKRQLTHWVDKDTAKHIENN-----------QCIKEYVMPEDIAAMALFLA 237
           N+++P      R  T +VD   AK+   N           Q I     PE+IA +ALFLA
Sbjct: 177 NSISPA-----RVHTPFVDGFIAKNYPGNEAEIFDKLSKSQPIGRMGKPEEIATLALFLA 231

Query: 238 ADDSKLCTAQNFIVDGGWI 256
           ++++   T  ++ +DGG+I
Sbjct: 232 SEEAGFITGSDYPIDGGFI 250


Lambda     K      H
   0.320    0.134    0.406 

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: 163
Number of extensions: 10
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: 256
Length of database: 254
Length adjustment: 24
Effective length of query: 232
Effective length of database: 230
Effective search space:    53360
Effective search space used:    53360
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 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