Align Ornithine aminotransferase; Orn-AT; Lysine aminotransferase; Lys-AT; EC 2.6.1.13; EC 2.6.1.36 (characterized)
to candidate WP_034995196.1 DL88_RS09505 aspartate aminotransferase family protein
Query= SwissProt::Q5JEW1 (445 letters) >NCBI__GCF_000745425.1:WP_034995196.1 Length = 449 Score = 149 bits (376), Expect = 2e-40 Identities = 131/429 (30%), Positives = 202/429 (47%), Gaps = 42/429 (9%) Query: 37 PIVIERGEGIRVYDVDGNVFYDFASGVGVINVGHSHPRVVEAIKKQAEKFTHYSLTDFFY 96 P ++ + + Y DG D +G+ N GHS ++V+AI+ QA + F + Sbjct: 35 PRIVASAKDMHYYTTDGRPILDGTAGLWCSNAGHSRDKIVQAIQAQAAELDFAPPFQFGH 94 Query: 97 ENAIILAEKLIELAPGDIERKVVYGNSGAEANEAAMKLVK-----YGTG-RKQFLAFYHA 150 LA ++ LAPGD++ V + NSG+EA + A+K+ G G R + + A Sbjct: 95 PKVFALAARVAALAPGDLDH-VFFTNSGSEAVDTALKIALAYHNIQGQGSRVRLIGRERA 153 Query: 151 FHG---RTQAVLSLTASKWVQQDGFFPTMPGVTHIPYPNPYRNTWGIDGYEEPDELTNRV 207 +HG AV + ++ F + GV H+P Y EP E + Sbjct: 154 YHGVGFGGGAVGGVPGNR----KAFGALLAGVDHLP--TTYNRAEQAFTKGEP-EWGAHL 206 Query: 208 LDFIEEYVFRHVPPHEIGAIFFEPIQGEGGYVVPPKGFFKALKKFADEYGILLADDEVQM 267 D +E+ V H I A+ EP+ G G + PPKG+ + L+ D+YGILL DEV Sbjct: 207 ADDLEKLVALH-DASTIAAVIVEPMAGSTGVLPPPKGYLQKLRAICDKYGILLIFDEVIC 265 Query: 268 GIGRTGKFWAIEHFGVEPDLIQFGKAI-GGGLPLAGVIHR----------ADITFDKPGR 316 G GR G +A E +GV PD+I F K I G +P+ GV+ R D+ + P Sbjct: 266 GYGRLGYAFAAERYGVLPDMITFAKGITSGTVPMGGVLIRKPIFDAFMKGPDLAVELP-- 323 Query: 317 HATTFGGNPVAIAAGIEVVEIVKE--LLPHVQEVGDYLHKYLEEFKEKYEVIGDARGLGL 374 H T+ G+P+A AAG+ +++ KE L V+++ + K ++ D R +GL Sbjct: 324 HGYTYSGHPLACAAGLATLDLYKEEGLFERVRKLEPLWADTVHGLKGLPNIL-DIRTVGL 382 Query: 375 AQAVEIVKSKETKEKYPELRDRIVKESAKRGLVLL-GCGDNSIRFIPPLIVTKEEIDVAM 433 A+++ + P R V + A L LL +SI PPLIV++ +I Sbjct: 383 TAAIDLAPIPDA----PGKRAFGVMDKAFHELDLLTRIAGDSIILTPPLIVSESQI---A 435 Query: 434 EIFEEALKA 442 EI E+ KA Sbjct: 436 EIVEKTGKA 444 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: 541 Number of extensions: 27 Number of successful extensions: 5 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 445 Length of database: 449 Length adjustment: 33 Effective length of query: 412 Effective length of database: 416 Effective search space: 171392 Effective search space used: 171392 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