GapMind for Amino acid biosynthesis

 

Alignments for a candidate for metX in Thermophagus xiamenensis HS1

Align Homoserine O-acetyltransferase; HAT; Homoserine transacetylase; HTA; EC 2.3.1.31 (characterized)
to candidate WP_010526168.1 GQW_RS0100790 homoserine O-succinyltransferase

Query= SwissProt::Q5LHS7
         (305 letters)



>NCBI__GCF_000220155.1:WP_010526168.1
          Length = 302

 Score =  401 bits (1030), Expect = e-116
 Identities = 182/300 (60%), Positives = 234/300 (78%)

Query: 1   MPLNLPDKLPAIELLKEENIFVIDNSRATQQDIRPLRIVILNLMPLKITTETDLVRLLSN 60
           MP+N+PD LPA  LL+ EN+FV+  SRA  QDIRPLRI+ILNLMPLKI TET L+R+LSN
Sbjct: 1   MPVNIPDLLPAKSLLEAENVFVMGESRAVTQDIRPLRILILNLMPLKIKTETHLLRVLSN 60

Query: 61  TPLQVEISFMKIKSHTSKNTPIEHMKTFYTDFDKMREDRYDGMIITGAPVEQMEFEEVNY 120
           TPLQVE+  +   +HT KNTP +H+ +FY  FD+++   YDG IITGAPVE ++FE+V Y
Sbjct: 61  TPLQVEVELLITSTHTPKNTPSQHLISFYKTFDEIKGKNYDGFIITGAPVELLDFEKVTY 120

Query: 121 WDEITEIFDWARTHVTSTLYICWAAQAGLYHHYGIPKYALDKKMFGIFKHRTLLPLHPIF 180
           W+E+ +I DW++THVTSTL+ICW AQAGLYHHYGIPK+ L  K+FG+F+H    P  P+ 
Sbjct: 121 WNELQKIMDWSKTHVTSTLHICWGAQAGLYHHYGIPKHELPAKLFGVFEHFVYDPTEPLV 180

Query: 181 RGFDDEFYVPHSRHTEVRKEDILKVPELTLLSESDDSGVYMVVARGGREFFVTGHSEYSP 240
           RGFDD F+ PHSR+TEVRKEDI KV  L LL++S+++G Y+++++   + F+TGH EY  
Sbjct: 181 RGFDDLFWAPHSRYTEVRKEDIEKVDNLILLADSEEAGPYIILSKDRSQVFITGHPEYDK 240

Query: 241 LTLDTEYRRDVSKGLPIEIPRNYYVNDDPDKGPLVRWRGHANLLFSNWLNYFVYQETPYN 300
           LTL  EY+RD  KGL   IP+NYY+NDDP K  +VRWR HA LL+SNWLNY+VYQ TPY+
Sbjct: 241 LTLGEEYQRDQKKGLSTAIPKNYYLNDDPSKEAVVRWRSHAQLLYSNWLNYYVYQSTPYD 300


Lambda     K      H
   0.321    0.140    0.428 

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: 408
Number of extensions: 17
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: 305
Length of database: 302
Length adjustment: 27
Effective length of query: 278
Effective length of database: 275
Effective search space:    76450
Effective search space used:    76450
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: 48 (23.1 bits)

This GapMind analysis is from Jul 26 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