Align ornithine aminotransferase (EC 2.6.1.13) (characterized)
to candidate YP_425268.1 Rru_A0176 acetylornithine aminotransferase
Query= BRENDA::P31893 (426 letters) >NCBI__GCF_000013085.1:YP_425268.1 Length = 313 Score = 127 bits (318), Expect = 6e-34 Identities = 83/245 (33%), Positives = 123/245 (50%), Gaps = 4/245 (1%) Query: 74 GKRYFDFLSAYSAVNQGHCHPKIVNTMVEQAQRLTLTSRAFYTDVLGEYEEFLTKLFNYD 133 G+RY DF + + G+ HP +V + Q ++L S + E LT D Sbjct: 29 GERYLDFGAGIAVNALGYSHPHLVGALERQGRKLWHLSNVYRISEAERLAERLTAACFAD 88 Query: 134 KVLPMNTGVEGGETACKIARCWAYMKKKVPENQAKIIFAENNFWGRTLSAISASTDPMSY 193 N+G E E A KIAR + + PE +II + F GRTL+ ++A + Sbjct: 89 VAFFANSGAEANECAIKIARRHHHAHGR-PERW-RIITFDGAFHGRTLATMAAGGNRKYL 146 Query: 194 DELRPYMPGFEIVKYNDTAALEKAFQDPNVCAYMVEPIQGEAGVVALDAGYLTEVRELCT 253 D P + GF+ D A+ +A P A M+EPIQGE+G+ + G+L ++RELC Sbjct: 147 DGFGPPVDGFDQCPLEDIEAV-RARVGPRTAALMIEPIQGESGIRPVSHGFLRQLRELCD 205 Query: 254 KYNVLFIADEVQTGLARTGRMLAVDHEDVKPDLLILGKALSGGLYPVSAVLRDDHIMDCI 313 + +L I DE+Q G+ARTG + A V PD++ L K L GG +P+ A L + Sbjct: 206 ERGLLLIFDEIQCGMARTGHLFAHQEAGVVPDIMSLAKGLGGG-FPIGACLATRGAAFGM 264 Query: 314 QPGLH 318 +PG H Sbjct: 265 RPGAH 269 Lambda K H 0.322 0.137 0.424 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: 313 Number of extensions: 12 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: 426 Length of database: 313 Length adjustment: 30 Effective length of query: 396 Effective length of database: 283 Effective search space: 112068 Effective search space used: 112068 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: 49 (23.5 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