GapMind for catabolism of small carbon sources

 

Alignments for a candidate for xacB in Methylocapsa aurea KYG

Align L-arabinose 1-dehydrogenase (EC 1.1.1.46) (characterized)
to candidate WP_036258924.1 DL86_RS05195 acetoacetyl-CoA reductase

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



>NCBI__GCF_000746085.1:WP_036258924.1
          Length = 241

 Score =  117 bits (292), Expect = 3e-31
 Identities = 76/239 (31%), Positives = 118/239 (49%), Gaps = 9/239 (3%)

Query: 17  ISGGATGIGACLVNAFLEQGAKVAFVDILVEESTQLVADLKQTQPEASVTFYHCDLVDIA 76
           +SGG+ GIGA +       G KVA      +E+    A+ K    E  +  Y  D+ +  
Sbjct: 7   VSGGSRGIGAAISKGLHAAGYKVAATYAGNDEAA---ANFKA---ETGIPVYKWDVSNYK 60

Query: 77  ALKRVIAQVEDDLGPISVLINNAACDQRHSIDEVTPEYWDQCLNTNLRHYFFAVQAVRPQ 136
                + +V DDLGPI +LINNA   +     ++TPE W   +NTNL   F   + V   
Sbjct: 61  ECAEGLKKVGDDLGPIEILINNAGITRDTMFHKMTPEQWFDVINTNLNSLFNMTRPVIEG 120

Query: 137 MQRLGGGSVINLGSMSWHNRQAGMAGYTASKAGAMGLTRGLAADLGKDKIRINTLTPGWV 196
           M+  G G ++N+ S++    Q G   YTASKAG +G T+ LA +     I +N + PG++
Sbjct: 121 MRERGFGRIVNISSINGQKGQMGQTNYTASKAGDIGFTKSLAQENAGKGITVNAVCPGYI 180

Query: 197 MTKRQLTHWVDKDT-AKHIENNQCIKEYVMPEDIAAMALFLAADDSKLCTAQNFIVDGG 254
            T   +   V K+   K +     ++    PE++A + +FL A++S   T     V+GG
Sbjct: 181 AT--DMVKAVPKEVLEKSVLPLIPLRRLGEPEEVARVVVFLVAEESGFITGSTLSVNGG 237


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: 147
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: 256
Length of database: 241
Length adjustment: 24
Effective length of query: 232
Effective length of database: 217
Effective search space:    50344
Effective search space used:    50344
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: 46 (22.3 bits)

This GapMind analysis is from Apr 09 2024. 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