Align Ornithine aminotransferase; Orn-AT; Lysine aminotransferase; Lys-AT; EC 2.6.1.13; EC 2.6.1.36 (characterized)
to candidate WP_043764857.1 U743_RS01125 glutamate-1-semialdehyde 2,1-aminomutase
Query= SwissProt::Q5JEW1 (445 letters) >NCBI__GCF_000733765.1:WP_043764857.1 Length = 426 Score = 122 bits (307), Expect = 2e-32 Identities = 93/308 (30%), Positives = 141/308 (45%), Gaps = 27/308 (8%) Query: 37 PIVIERGEGIRVYDVDGNVFYDFASGVGVINVGHSHPRVVEAIKKQAEKFTHYSLTDFFY 96 P IE EG + DVDGN + D+ G + +GH HP VV+A++ QA + + Sbjct: 33 PRFIETAEGAWMTDVDGNRYIDYIGSWGPMLLGHGHPDVVQAVQAQAGRGISFGAPT--- 89 Query: 97 ENAIILAEKLIELAPGDIERKVVYGNSGAEANEAAMKLVKYGTGRKQFLAFYHAFHGRTQ 156 E + +AE + E P K+ +SG EA +A++L + +GR L F +HG + Sbjct: 90 EAEVEMAELIRERVPS--MEKLRLNSSGTEATMSAVRLARAASGRDGVLKFEGCYHGHSD 147 Query: 157 AVLSLTASKWVQQDGFFPTMPGVTHIPYPNPYRNTWGIDGYEEPDELTNRVLDFIEEYVF 216 ++L S + P+ PG+ D + T LD + E Sbjct: 148 SLLVKAGSGALTFGE--PSSPGIP-------------ADIAKHTRTATYNDLDSVREAFA 192 Query: 217 RHVPPHEIGAIFFEPIQGEGGYVVPPKGFFKALKKFADEYGILLADDEVQMGIGRTGKFW 276 ++ P IG + EP+ G V P GF + L+ DE G LL DEV G R Sbjct: 193 QN--PGAIGCVIVEPVAGNMNMVPPAPGFLEGLRSICDEQGALLIFDEVMTGF-RVHPGG 249 Query: 277 AIEHFGVEPDLIQFGKAIGGGLPLAGVIHRADI----TFDKPGRHATTFGGNPVAIAAGI 332 A +GV PDL GK +GGG+P+ RA + + + P A T G+P+A AAG+ Sbjct: 250 AQALYGVTPDLTALGKIVGGGMPVGAFGGRAAVMDMLSPEGPVYQAGTLSGSPLATAAGL 309 Query: 333 EVVEIVKE 340 + + + Sbjct: 310 ATLRAIDD 317 Lambda K H 0.320 0.141 0.418 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: 421 Number of extensions: 24 Number of successful extensions: 5 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: 445 Length of database: 426 Length adjustment: 32 Effective length of query: 413 Effective length of database: 394 Effective search space: 162722 Effective search space used: 162722 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 (21.7 bits) S2: 51 (24.3 bits)
This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.
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:
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