Align Ornithine aminotransferase; Orn-AT; Lysine aminotransferase; Lys-AT; EC 2.6.1.13; EC 2.6.1.36 (characterized)
to candidate WP_050461046.1 AKL27_RS02370 4-aminobutyrate--2-oxoglutarate transaminase
Query= SwissProt::Q5JEW1 (445 letters) >NCBI__GCF_001189915.1:WP_050461046.1 Length = 422 Score = 258 bits (659), Expect = 3e-73 Identities = 152/407 (37%), Positives = 221/407 (54%), Gaps = 17/407 (4%) Query: 42 RGEGIRVYDVDGNVFYDFASGVGVINVGHSHPRVVEAIKKQAEKFTHYSLTDFFYENAII 101 R E ++DV+G + DFA+G+ V+N GH HP++V AIK+Q + FTH + Y + + Sbjct: 28 RAENSELWDVEGRRYIDFAAGIAVLNTGHRHPKLVAAIKQQLDHFTHTAYQIVPYASYVE 87 Query: 102 LAEKLIELAPGDIERKVVYGNSGAEANEAAMKLVKYGTGRKQFLAFYHAFHGRTQAVLSL 161 LAE++ LAPG +K ++GAEA E A+K+ + TGR +AF FHGRT ++L Sbjct: 88 LAERINTLAPGAFPKKTALFSTGAEAVENAIKIARAATGRAAVIAFSGGFHGRTMMGMAL 147 Query: 162 TASKWVQQDGFFPTMPGVTHIPYPNPYRNTWGIDGYEEPDELTNRVLDFIEEYVFRHVPP 221 T + GF P V H+P+P+ D T L I+ V Sbjct: 148 TGKVVPYKVGFGPFPGDVYHVPFPSALH-----------DISTEDSLSAIQALFKSDVEA 196 Query: 222 HEIGAIFFEPIQGEGGYVVPPKGFFKALKKFADEYGILLADDEVQMGIGRTGKFWAIEHF 281 + AI EP+QGEGG+ P L++ DE+GILL DEVQ G RTGK +A+EH+ Sbjct: 197 KRVAAIIIEPVQGEGGFQAAPPELMHGLRRICDEHGILLIADEVQTGFARTGKLFAMEHY 256 Query: 282 GVEPDLIQFGKAIGGGLPLAGVIHRADI-TFDKPGRHATTFGGNPVAIAAGIEVVEIVKE 340 V DLI K++ GG+PL+ V R +I PG T+ GNP+A+A+ + V++++KE Sbjct: 257 DVAADLITMAKSLAGGMPLSAVCGRTEIMDAPAPGGLGGTYAGNPLAVASALAVLDVIKE 316 Query: 341 --LLPHVQEVGDYLHKYLEEFKEKYEVIGDARGLGLAQAVEIVKSKETKEKYPELRDRIV 398 L+ +GD L L E + IG+ RG G AVE VK T E + R+ Sbjct: 317 EQLVERGARLGDQLKATLNELRGSVPAIGEIRGPGAMVAVEFVKPGST-EPDADFTKRVQ 375 Query: 399 KESAKRGLVLLGCG--DNSIRFIPPLIVTKEEIDVAMEIFEEALKAA 443 + ++GL+LL CG N IRF+ PL + +D A+ I + L+AA Sbjct: 376 TLALQQGLLLLSCGTYGNVIRFLFPLTIQDAVMDEALAILRQVLRAA 422 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: 491 Number of extensions: 24 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: 445 Length of database: 422 Length adjustment: 32 Effective length of query: 413 Effective length of database: 390 Effective search space: 161070 Effective search space used: 161070 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 Jul 25 2024. The underlying query database was built on Jul 25 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