GapMind for Amino acid biosynthesis

 

Alignments for a candidate for metX in Clostridium kluyveri DSM 555

Align Homoserine O-acetyltransferase; HAT; Homoserine transacetylase; HTA; EC 2.3.1.31 (characterized)
to candidate WP_012102004.1 CKL_RS07910 homoserine O-succinyltransferase

Query= SwissProt::A5N8M0
         (309 letters)



>NCBI__GCF_000016505.1:WP_012102004.1
          Length = 309

 Score =  638 bits (1645), Expect = 0.0
 Identities = 309/309 (100%), Positives = 309/309 (100%)

Query: 1   MPIKIKDDLPAAEILNSENIFIMPENVAFHQDIRPLKIAILNLMPIKITTEVQLLRLIGN 60
           MPIKIKDDLPAAEILNSENIFIMPENVAFHQDIRPLKIAILNLMPIKITTEVQLLRLIGN
Sbjct: 1   MPIKIKDDLPAAEILNSENIFIMPENVAFHQDIRPLKIAILNLMPIKITTEVQLLRLIGN 60

Query: 61  TALQIEIELLHLKTHVCKNTSEEYLTNFYRTFDEIKNEKFDGLIITGAPIEQLEFSRVNY 120
           TALQIEIELLHLKTHVCKNTSEEYLTNFYRTFDEIKNEKFDGLIITGAPIEQLEFSRVNY
Sbjct: 61  TALQIEIELLHLKTHVCKNTSEEYLTNFYRTFDEIKNEKFDGLIITGAPIEQLEFSRVNY 120

Query: 121 WEELKDIMEWSKCHVYSTLHICWGAQAGLYYHYGIPKYILKEKLFGVFKHEVTEEKEKLV 180
           WEELKDIMEWSKCHVYSTLHICWGAQAGLYYHYGIPKYILKEKLFGVFKHEVTEEKEKLV
Sbjct: 121 WEELKDIMEWSKCHVYSTLHICWGAQAGLYYHYGIPKYILKEKLFGVFKHEVTEEKEKLV 180

Query: 181 RGFDDEFYVPHSRYTEVKREDVEKVKELTILAQSKKAGVYLILDNKGRRIFVTGHSEYDP 240
           RGFDDEFYVPHSRYTEVKREDVEKVKELTILAQSKKAGVYLILDNKGRRIFVTGHSEYDP
Sbjct: 181 RGFDDEFYVPHSRYTEVKREDVEKVKELTILAQSKKAGVYLILDNKGRRIFVTGHSEYDP 240

Query: 241 LTLKDEYMRDISKGEDIKMPENYFPDDNPDRKPVVKWRSHADLLFSNWLNYYVYQETPYD 300
           LTLKDEYMRDISKGEDIKMPENYFPDDNPDRKPVVKWRSHADLLFSNWLNYYVYQETPYD
Sbjct: 241 LTLKDEYMRDISKGEDIKMPENYFPDDNPDRKPVVKWRSHADLLFSNWLNYYVYQETPYD 300

Query: 301 LSEMPPSFL 309
           LSEMPPSFL
Sbjct: 301 LSEMPPSFL 309


Lambda     K      H
   0.320    0.139    0.420 

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: 530
Number of extensions: 8
Number of successful extensions: 1
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: 309
Length of database: 309
Length adjustment: 27
Effective length of query: 282
Effective length of database: 282
Effective search space:    79524
Effective search space used:    79524
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: 48 (23.1 bits)

This GapMind analysis is from Jul 25 2024. The underlying query database was built on Jul 25 2024.

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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