Align Ornithine aminotransferase; Orn-AT; Lysine aminotransferase; Lys-AT; EC 2.6.1.13; EC 2.6.1.36 (characterized)
to candidate WP_025272511.1 HALAL_RS0102620 aspartate aminotransferase family protein
Query= SwissProt::Q5JEW1 (445 letters) >NCBI__GCF_000527155.1:WP_025272511.1 Length = 417 Score = 270 bits (690), Expect = 6e-77 Identities = 156/416 (37%), Positives = 224/416 (53%), Gaps = 18/416 (4%) Query: 37 PIVIERGEGIRVYDVDGNVFYDFASGVGVINVGHSHPRVVEAIKKQAEKFTHYSLTDFFY 96 P+V + GEG+ +YD DG + DF +G+GV + GH HP VV+A ++Q K H T + Sbjct: 13 PVVADHGEGVYLYDADGRRYLDFTAGIGVTSTGHCHPHVVQAAQEQVGKLIHGQYTTVMH 72 Query: 97 ENAIILAEKLIELAPGDIERKVVYGNSGAEANEAAMKLVKYGTGRKQFLAFYHAFHGRTQ 156 + + L +L ++ P ++ + + NSG+EA EAA++L + TGR + F FHGRT Sbjct: 73 QPLLELTRRLGDVLPAGLD-SLFFSNSGSEAVEAALRLSRQATGRPNIVVFQGGFHGRTV 131 Query: 157 AVLSLTASKWVQQDGFFPTMPGVTHIPYPNPYRNTWGIDGYEEPDELTNRVLDFIEEYVF 216 A +LT S G P M GV P+P YR W E R LD++ V Sbjct: 132 ATATLTTSGTRFSAGISPLMSGVHMAPFPYAYRYGWD---ESTATEFALRELDYLFATV- 187 Query: 217 RHVPPHEIGAIFFEPIQGEGGYVVPPKGFFKALKKFADEYGILLADDEVQMGIGRTGKFW 276 P E A F EP+ GEGGYV F L++ ADE+GILL DE+Q G GRTGKFW Sbjct: 188 --TSPAETAAFFIEPVLGEGGYVPANPEFLAGLRQRADEHGILLVLDEIQTGFGRTGKFW 245 Query: 277 AIEHFGVEPDLIQFGKAIGGGLPLAGVIHRADITFDK-PGRHATTFGGNPVAIAAGIEVV 335 +HFGV PD++ K + G PL+G+ ++ PG T+GGN VA AA + + Sbjct: 246 GHDHFGVHPDVVLIAKGLASGFPLSGMATSEELMSQAWPGSQGGTYGGNAVACAAAVATL 305 Query: 336 EIVKE--LLPHVQEVGDYLHKYLEEFKEKYEVIGDARGLGLAQAVEIVKSKETKEKYPE- 392 ++++ L+ + + G L + EK +IGD RGLGL E T + P+ Sbjct: 306 DVIQREGLVDNAADRGRQLLEGARHIGEKTPLIGDVRGLGLMVGSEFT----TPDGQPDT 361 Query: 393 -LRDRIVKESAKRGLVLLGCGD--NSIRFIPPLIVTKEEIDVAMEIFEEALKAALK 445 KE+A RGL+LL CG N +R IPPL+V ++D A++I+ E + + K Sbjct: 362 ATAQAAQKEAAARGLMLLTCGAHMNVVRMIPPLVVDAAQVDEALDIWSEVVSSVAK 417 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: 446 Number of extensions: 16 Number of successful extensions: 7 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: 417 Length adjustment: 32 Effective length of query: 413 Effective length of database: 385 Effective search space: 159005 Effective search space used: 159005 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