Align Ornithine aminotransferase; Orn-AT; Ornithine delta-aminotransferase; EC 2.6.1.13 (characterized)
to candidate WP_013420667.1 RVAN_RS15555 aspartate aminotransferase family protein
Query= SwissProt::O50131 (454 letters) >NCBI__GCF_000166055.1:WP_013420667.1 Length = 449 Score = 180 bits (457), Expect = 7e-50 Identities = 132/426 (30%), Positives = 221/426 (51%), Gaps = 32/426 (7%) Query: 39 VIERAEGVYWIDVDGNVLLDFSSGIGVMNVGLRNPKVIEAIKKQLDLVLHAAGTDYYNPY 98 V+ A+G+++ +DG +LD +G+ +N G ++ EA+++QL + +A +P Sbjct: 38 VLVEAQGMHYTAMDGRKVLDGVAGLWCVNAGHGRREIAEAVERQLLTMDYATAFQIGHPG 97 Query: 99 QVELAKKLVEIAPGDIERKVFLSNSGTEANEAALKIA------KWSTNRKMFIAFIGAFH 152 ELA ++ IAP ++R VF +NSG+EA E+ALKIA + R F+ +H Sbjct: 98 AFELAARIARIAPEGLDR-VFFANSGSEAVESALKIALAYHHARGQAQRTRFVGREKGYH 156 Query: 153 GRTHGTMSLTASKPVQRSRMFPTM-PGVVHVPYP-NPYRNPWGIDGYENPDELINRVIDY 210 G G MS+ V R F + P V ++P+ + RN + E+ EL D Sbjct: 157 GCNFGGMSVGGL--VNNRRAFGALLPYVDYLPHTLDIKRNAFTKGQPEHGAELA----DA 210 Query: 211 IEEYLFEHYVPAEEVAGIFFEPIQGEGGYVVPPKNFFKELKKLADKHGILLIDDEVQMGM 270 +E + H A+ +AG+ EP+ G G ++PPK + + L+ + D+HG+LLI DEV G Sbjct: 211 LEGIIALH--GADTIAGVIVEPMSGSAGVILPPKGYLERLRAICDRHGLLLIFDEVITGF 268 Query: 271 GRTGRMWAIEHFDIVPDIVTVAKAL-GGGIPIGATIFRADL--------DFGVSGVHSNT 321 GR G +A + + PDI TVAK + G IP+GA I + ++ + + H T Sbjct: 269 GRMGAAFASQALGVTPDIFTVAKGITNGAIPMGAAIAKREIHDAIMQGPEHVIELFHGYT 328 Query: 322 FGGNTVAAAAALAVIEELQN-GLIENAQKLEPLFRERLEEMKEKYEIIGDVRGLGLAWGV 380 + G+ VA AA LA ++ ++ GL E A L P++ E + +K + ++ D+R G+ G+ Sbjct: 329 YSGHPVACAAGLATLDIYESEGLFERAAALAPVWEEAVHSLKGEPHVV-DIRNTGIVAGM 387 Query: 381 EFVKDRKTKEYATKERGEIVVEALKRGLALLGCGKSAIRLIPPLIISEEEAKMGLDIFEE 440 E + A K ++ + G+ L+ G I L PPLI++E + +D Sbjct: 388 EL---EPRADGAGKRAFDVYQDCFANGV-LVRQGGEIIALSPPLIVTESQVGEIVDALRN 443 Query: 441 AIKVVS 446 A++ V+ Sbjct: 444 ALRRVA 449 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: 517 Number of extensions: 29 Number of successful extensions: 4 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: 449 Length adjustment: 33 Effective length of query: 421 Effective length of database: 416 Effective search space: 175136 Effective search space used: 175136 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