Align Ornithine aminotransferase; Orn-AT; Lysine aminotransferase; Lys-AT; EC 2.6.1.13; EC 2.6.1.36 (characterized)
to candidate WP_012991510.1 THAL_RS02335 glutamate-1-semialdehyde-2,1-aminomutase
Query= SwissProt::Q5JEW1 (445 letters) >NCBI__GCF_000025605.1:WP_012991510.1 Length = 424 Score = 127 bits (320), Expect = 5e-34 Identities = 94/312 (30%), Positives = 149/312 (47%), Gaps = 27/312 (8%) Query: 37 PIVIERGEGIRVYDVDGNVFYDFASGVGVINVGHSHPRVVEAIKKQAEKFTHYSLTDFFY 96 PIV+ +G R++DV+G + DF G + +GH+HP VV +++Q + Y LT + Sbjct: 32 PIVVREAKGCRLWDVEGKEYIDFLMSWGPLILGHAHPYVVSEVERQLSRGMSYGLTCY-- 89 Query: 97 ENAIILAEKLIELAPGDIERKVVYGNSGAEANEAAMKLVKYGTGRKQFLAFYHAFHGRTQ 156 I LAE ++ P V + +SG EA +A++L + TGRK + F +HG Sbjct: 90 -EEIRLAELVVSSVPS--VEMVRFVSSGTEATMSAIRLARGYTGRKFVVKFEGCYHGHYD 146 Query: 157 AVLSLTASKWVQQDGFFPTMPGVTHIPYPNPYRNTWGIDGYEEPDELTNRVLDFIEEYVF 216 +L ++A V G P PGV P + Y + T+ VL E Y Sbjct: 147 GLL-VSAGSGVATLG-IPGTPGV-----PEEIAGLTLVLPYND----TDAVLSTFERY-- 193 Query: 217 RHVPPHEIGAIFFEPIQGEGGYVVPPKGFFKALKKFADEYGILLADDEVQMGIGRTGKFW 276 +I + EP+ G G V+P +GF + L++ +YG +L DEV R Sbjct: 194 ----GEDIACVIVEPVAGNMGVVLPSEGFLEVLREVTRKYGAVLIFDEVITNF-RLSVGG 248 Query: 277 AIEHFGVEPDLIQFGKAIGGGLPLAGVIHRADITF----DKPGRHATTFGGNPVAIAAGI 332 A E++ ++PD+ GK +GGG+PL + +I + A T GNPV++ G Sbjct: 249 AQEYYAIDPDITCMGKILGGGMPLGAYGGKKEIMSHVAPEGKVYQAGTLSGNPVSVVCGR 308 Query: 333 EVVEIVKELLPH 344 +E + L P+ Sbjct: 309 ATLEELLRLKPY 320 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: 499 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: 424 Length adjustment: 32 Effective length of query: 413 Effective length of database: 392 Effective search space: 161896 Effective search space used: 161896 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 Apr 10 2024. The underlying query database was built on Apr 09 2024.
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