Align Ornithine aminotransferase; Orn-AT; Ornithine delta-aminotransferase; EC 2.6.1.13 (characterized)
to candidate WP_035239836.1 Q366_RS13500 4-aminobutyrate--2-oxoglutarate transaminase
Query= SwissProt::O50131 (454 letters) >NCBI__GCF_000745975.1:WP_035239836.1 Length = 415 Score = 228 bits (582), Expect = 2e-64 Identities = 141/409 (34%), Positives = 214/409 (52%), Gaps = 32/409 (7%) Query: 40 IERAEGVYWIDVDGNVLLDFSSGIGVMNVGLRNPKVIEAIKKQLDLVLHAAGTDYYNPYQ 99 ++ A+G DV G +DF+ GI VMNVG +PKV+ AIK Q + H NPY Sbjct: 27 VDSAKGAIITDVQGKQYIDFAGGIAVMNVGHSHPKVVAAIKAQAEKFTHTCFM--VNPYD 84 Query: 100 V--ELAKKLVEIAPGDIERKVFLSNSGTEANEAALKIAKWSTNRKMFIAFIGAFHGRTHG 157 V LA +L +I PG ++K NSG EA E A+KIA++ T R+ + F G++HGRT+ Sbjct: 85 VAVRLADRLCKITPGTFDKKALFVNSGAEAVENAVKIARYYTQRQGVVTFDGSYHGRTYL 144 Query: 158 TMSLTASKPVQRSRMFPTMPGVVHVPYPNPYRNPWGIDGYENPDELINRVIDYIEEYLFE 217 TM++T + P P V P+ N D+ F Sbjct: 145 TMAMTTKVKPYKCGFGPLAPEVYRAPFGN-----------------FKAFTDF-----FI 182 Query: 218 HYVPAEEVAGIFFEPIQGEGGYVVPPKNFFKELKKLADKHGILLIDDEVQMGMGRTGRMW 277 + E A + EPIQGEGG++ PP +F ++ + +GI+ I DE+Q GMGR+G+M+ Sbjct: 183 TGINPENTAAVVIEPIQGEGGFIAPPADFLPQVAQFCKDNGIVFIADEIQSGMGRSGKMF 242 Query: 278 AIEHFDIVPDIVTVAKALGGGIPIGATIFRAD-LDFGVSGVHSNTFGGNTVAAAAALAVI 336 AIE+F + PD++TVAK++ G+P+ A + R + +D G T+G N VA AAA AV+ Sbjct: 243 AIENFGVEPDLMTVAKSIAAGMPLSAVVGRKEIMDSVHPGGLGGTYGANPVACAAAHAVL 302 Query: 337 EEL-QNGLIENAQKLEPLFRERLEEMKEKYEIIGDVRGLGLAWGVEFVKDRKTKEYATKE 395 + + L+E AQ + +K++ +G+VRG+G G V T A + Sbjct: 303 DIFEEENLLEKAQAIGEKLGATFGAWTQKFDHVGEVRGIGAMRGYTIVNADGTP--APDK 360 Query: 396 RGEIVVEALKRGLALLGCG--KSAIRLIPPLIISEEEAKMGLDIFEEAI 442 + GL L CG + IR++ PL+I +++ + GLDI E + Sbjct: 361 AKTLSAYCFDNGLITLVCGIEGNVIRVLMPLVIEDDQLQKGLDIMEAGL 409 Lambda K H 0.319 0.139 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: 481 Number of extensions: 27 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: 454 Length of database: 415 Length adjustment: 32 Effective length of query: 422 Effective length of database: 383 Effective search space: 161626 Effective search space used: 161626 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