GapMind for Amino acid biosynthesis

 

Alignments for a candidate for lysJ in Thermocrinis albus DSM 14484

Align Putative [LysW]-aminoadipate semialdehyde/glutamate semialdehyde transaminase; EC 2.6.1.118; EC 2.6.1.124 (uncharacterized)
to candidate WP_012991510.1 THAL_RS02335 glutamate-1-semialdehyde 2,1-aminomutase

Query= curated2:Q5JFW3
         (362 letters)



>NCBI__GCF_000025605.1:WP_012991510.1
          Length = 424

 Score =  126 bits (316), Expect = 1e-33
 Identities = 97/297 (32%), Positives = 143/297 (48%), Gaps = 25/297 (8%)

Query: 14  EGVYVWDEKGRRYLDLIAGIGVNVLGHAHPEWVLDMSRQLEKIVVAG-PMFEHDEREEML 72
           +G  +WD +G+ Y+D +   G  +LGHAHP  V ++ RQL + +  G   +E     E++
Sbjct: 39  KGCRLWDVEGKEYIDFLMSWGPLILGHAHPYVVSEVERQLSRGMSYGLTCYEEIRLAELV 98

Query: 73  EELSHWVDYEYVYMGNSGTEAVEAAIKFARLATGRSEIVAMTNAFHGRTLGSLSATWKKK 132
             +S     E V   +SGTEA  +AI+ AR  TGR  +V     +HG   G L +     
Sbjct: 99  --VSSVPSVEMVRFVSSGTEATMSAIRLARGYTGRKFVVKFEGCYHGHYDGLLVSAGSGV 156

Query: 133 YREGFGPLVPGFKH--------IPFNNVEAAK---EAITKETAAVIFEPIQGEGGIVPAD 181
              G  P  PG           +P+N+ +A     E   ++ A VI EP+ G  G+V   
Sbjct: 157 ATLGI-PGTPGVPEEIAGLTLVLPYNDTDAVLSTFERYGEDIACVIVEPVAGNMGVVLPS 215

Query: 182 EEFVKTLRDLTEDVGALLIADEVQSGLRTGKFLAIEHYGVRPDIVTMGKGIGNGFPVSLT 241
           E F++ LR++T   GA+LI DEV +  R     A E+Y + PDI  MGK +G G P+   
Sbjct: 216 EGFLEVLREVTRKYGAVLIFDEVITNFRLSVGGAQEYYAIDPDITCMGKILGGGMPLGAY 275

Query: 242 LTDLEI-----PRGK--HGSTFGGNPLAC---RAVATTLRILRRDRLVEKAGEKFME 288
               EI     P GK     T  GNP++    RA    L  L+  +L+E+   +  E
Sbjct: 276 GGKKEIMSHVAPEGKVYQAGTLSGNPVSVVCGRATLEELLRLKPYQLLEERTRRLAE 332


Lambda     K      H
   0.320    0.140    0.410 

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: 347
Number of extensions: 21
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: 362
Length of database: 424
Length adjustment: 31
Effective length of query: 331
Effective length of database: 393
Effective search space:   130083
Effective search space used:   130083
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: 50 (23.9 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